1
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Farias TD, Brugiapaglia S, Croci S, Magistroni P, Curcio C, Zguro K, Fallerini C, Fava F, Pettini F, Kichula KM, Pollock NR, Font-Porterias N, Palmer WH, Marin WM, Baldassarri M, Bruttini M, Hollenbach JA, Hendricks AE, Meloni I, Novelli F, Renieri A, Furini S, Norman PJ, Amoroso A. HLA-DPB1*13:01 associates with enhanced, and KIR2DS4*001 with diminished protection from developing severe COVID-19. HLA 2024; 103:e15251. [PMID: 37850268 PMCID: PMC10873037 DOI: 10.1111/tan.15251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 08/22/2023] [Accepted: 09/26/2023] [Indexed: 10/19/2023]
Abstract
Extreme polymorphism of HLA and killer-cell immunoglobulin-like receptors (KIR) differentiates immune responses across individuals. Additional to T cell receptor interactions, subsets of HLA class I act as ligands for inhibitory and activating KIR, allowing natural killer (NK) cells to detect and kill infected cells. We investigated the impact of HLA and KIR polymorphism on the severity of COVID-19. High resolution HLA class I and II and KIR genotypes were determined from 403 non-hospitalized and 1575 hospitalized SARS-CoV-2 infected patients from Italy collected in 2020. We observed that possession of the activating KIR2DS4*001 allotype is associated with severe disease, requiring hospitalization (OR = 1.48, 95% CI 1.20-1.85, pc = 0.017), and this effect is greater in individuals homozygous for KIR2DS4*001 (OR = 3.74, 95% CI 1.75-9.29, pc = 0.003). We also observed the HLA class II allotype, HLA-DPB1*13:01 protects SARS-CoV-2 infected patients from severe disease (OR = 0.49, 95% CI 0.33-0.74, pc = 0.019). These association analyses were replicated using logistic regression with sex and age as covariates. Autoantibodies against IFN-α associated with COVID-19 severity were detected in 26% of 156 hospitalized patients tested. HLA-C*08:02 was more frequent in patients with IFN-α autoantibodies than those without, and KIR3DL1*01502 was only present in patients lacking IFN-α antibodies. These findings suggest that KIR and HLA polymorphism is integral in determining the clinical outcome following SARS-CoV-2 infection, by influencing the course both of innate and adaptive immunity.
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Affiliation(s)
- Ticiana D.J. Farias
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
| | - Silvia Brugiapaglia
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, 10126, Italy
- Laboratory of Tumor Immunology Center for Experimental Research and Medical Studies, Città della Salute e della Scienza di Torino, Turin, 10126, Italy
| | - Susanna Croci
- Medical Genetics, University of Siena, Siena, 53100, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy
| | - Paola Magistroni
- Immunogenetics and Transplant Biology, Azienda Ospedaliera Universitaria, Città della Salute e della Scienza di Torino, Turin, 10126, Italy
| | - Claudia Curcio
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, 10126, Italy
- Laboratory of Tumor Immunology Center for Experimental Research and Medical Studies, Città della Salute e della Scienza di Torino, Turin, 10126, Italy
| | - Kristina Zguro
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy
| | - Chiara Fallerini
- Medical Genetics, University of Siena, Siena, 53100, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy
| | - Francesca Fava
- Medical Genetics, University of Siena, Siena, 53100, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, 53100, Italy
| | - Francesco Pettini
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, 53100, Italy
| | - Katherine M. Kichula
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
| | - Nicholas R. Pollock
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
| | - Neus Font-Porterias
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
| | - William H. Palmer
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
| | - Wesley M. Marin
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Margherita Baldassarri
- Medical Genetics, University of Siena, Siena, 53100, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy
| | - Mirella Bruttini
- Medical Genetics, University of Siena, Siena, 53100, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, 53100, Italy
| | - Jill A. Hollenbach
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Audrey E. Hendricks
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
- Department of Mathematical and Statistical Sciences, and Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
| | - Ilaria Meloni
- Medical Genetics, University of Siena, Siena, 53100, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy
| | - Francesco Novelli
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, 10126, Italy
- Laboratory of Tumor Immunology Center for Experimental Research and Medical Studies, Città della Salute e della Scienza di Torino, Turin, 10126, Italy
- Molecular Biotechnology Center, University of Turin, Turin, 10126, Italy
| | | | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, 53100, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, 53100, Italy
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, 53100, Italy
| | - Simone Furini
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy
| | - Paul J. Norman
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
| | - Antonio Amoroso
- Immunogenetics and Transplant Biology, Azienda Ospedaliera Universitaria, Città della Salute e della Scienza di Torino, Turin, 10126, Italy
- Department of Medical Sciences, University of Turin, Turin, 10126, Italy
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2
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Arora K, Gaudioso G, Solovyev P, Tuohy K, Di Cagno R, Gobbetti M, Fava F. In vitro faecal fermentation of Tritordeum breads and its effect on the human gut health. Curr Res Microb Sci 2023; 6:100214. [PMID: 38116184 PMCID: PMC10727946 DOI: 10.1016/j.crmicr.2023.100214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023] Open
Abstract
Spontaneous fermentation of Tritordeum flour enhances the nutritional potential of this hybrid cereal. However, the effect of consumption of Tritordeum sourdough bread (SDB) on gut health remains to be elucidated. This study investigated the effect of in vitro digestion and faecal fermentation of SDB compared to that of traditional baker's yeast (BYB) Tritordeum bread. After 24-h anaerobic faecal fermentation, both SDB and BYB (1% w/v) induced an increase in the relative abundances of Bifidobacterium, Megasphaera, Mitsuokella, and Phascolarctobacterium genera compared to baseline, while concentrations of acetate and butyrate were significantly higher at 24 h for SDB compared to those for BYB. Integrity of intestinal epithelium, as assessed through in vitro trans-epithelial electrical resistance (TEER) assay, was slightly increased after incubation with SDB fermentation supernatants, but not after incubation with BYB fermentation supernatants. The SDB stimulated in vitro mucosal immune response by inducing early secretion of inflammatory cytokines, IL-6 and TNF-α, followed by downregulation of the inflammatory trigger through induction of anti-inflammatory IL-10 expression. Overall, our findings suggest that Tritordeum sourdough can modulate gut microbiota fermentation activity and positively impact the gut health.
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Affiliation(s)
- Kashika Arora
- Faculty of Agricultural, Environmental and Food Sciences, Libera Università di Bolzano, Piazza Università, 5, Bolzano 39100, Italy
| | - Giulia Gaudioso
- Nutrition and Nutrigenomics Unit, Fondazione Edmund Mach di San Michele all'Adige Via E. Mach, 1 38098 S. Michele all'Adige, Italy
| | - Pavel Solovyev
- Traceability Unit, Fondazione Edmund Mach di San Michele all'Adige Via E. Mach, 1 38098 S. Michele all'Adige, Italy
| | - Kieran Tuohy
- Nutrition and Nutrigenomics Unit, Fondazione Edmund Mach di San Michele all'Adige Via E. Mach, 1 38098 S. Michele all'Adige, Italy
- School of Food Science & Nutrition, University of Leeds, Leeds LS2 9JT, UK
| | - Raffaella Di Cagno
- Faculty of Agricultural, Environmental and Food Sciences, Libera Università di Bolzano, Piazza Università, 5, Bolzano 39100, Italy
| | - Marco Gobbetti
- Faculty of Agricultural, Environmental and Food Sciences, Libera Università di Bolzano, Piazza Università, 5, Bolzano 39100, Italy
| | - Francesca Fava
- Nutrition and Nutrigenomics Unit, Fondazione Edmund Mach di San Michele all'Adige Via E. Mach, 1 38098 S. Michele all'Adige, Italy
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3
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Kamer O, Rinott E, Tsaban G, Kaplan A, Yaskolka Meir A, Zelicha H, Knights D, Tuohy K, Fava F, Uwe Scholz M, Ziv O, Rubin E, Blüher M, Stumvoll M, Ceglarek U, Clément K, Koren O, Hu FB, Stampfer MJ, Wang DD, Youngster I, Shai I. Successful weight regain attenuation by autologous fecal microbiota transplantation is associated with non-core gut microbiota changes during weight loss; randomized controlled trial. Gut Microbes 2023; 15:2264457. [PMID: 37796016 PMCID: PMC10557561 DOI: 10.1080/19490976.2023.2264457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 09/25/2023] [Indexed: 10/06/2023] Open
Abstract
We previously reported that autologous-fecal-microbiota-transplantation (aFMT), following 6 m of lifestyle intervention, attenuated subsequent weight regain and insulin rebound for participants consuming a high-polyphenol green-Mediterranean diet. Here, we explored whether specific changes in the core (abundant) vs. non-core (low-abundance) gut microbiome taxa fractions during the weight-loss phase (0-6 m) were differentially associated with weight maintenance following aFMT. Eighty-two abdominally obese/dyslipidemic participants (age = 52 years; 6 m weightloss = -8.3 kg) who provided fecal samples (0 m, 6 m) were included. Frozen 6 m's fecal samples were processed into 1 g, opaque and odorless aFMT capsules. Participants were randomly assigned to receive 100 capsules containing their own fecal microbiota or placebo over 8 m-14 m in ten administrations (adherence rate > 90%). Gut microbiome composition was evaluated using shotgun metagenomic sequencing. Non-core taxa were defined as ≤ 66% prevalence across participants. Overall, 450 species were analyzed. At baseline, 13.3% were classified as core, and Firmicutes presented the highest core proportion by phylum. During 6 m weight-loss phase, abundance of non-core species changed more than core species (P < .0001). Subject-specific changes in core and non-core taxa fractions were strongly correlated (Jaccard Index; r = 0.54; P < .001). Following aFMT treatment, only participants with a low 6 m change in core taxa, and a high change in non-core taxa, avoided 8-14 m weight regain (aFMT = -0.58 ± 2.4 kg, corresponding placebo group = 3.18 ± 3.5 kg; P = .02). In a linear regression model, low core/high non-core 6 m change was the only combination that was significantly associated with attenuated 8-14 m weight regain (P = .038; P = .002 for taxa patterns/treatment intervention interaction). High change in non-core, low-abundance taxa during weight-loss might mediate aFMT treatment success for weight loss maintenance.ClinicalTrials.gov: NCT03020186.
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Affiliation(s)
- Omer Kamer
- Faculty of Health Sciences, Ben-Gurion University of the Negev, The International Center of Health, Innovation & Nutrition On the memory of Manya Igel, Beer-Sheva, Israel
| | - Ehud Rinott
- Department of Medicine, Hebrew University and Hadassah Medical Center, Jerusalem, Israel
| | - Gal Tsaban
- Faculty of Health Sciences, Ben-Gurion University of the Negev, The International Center of Health, Innovation & Nutrition On the memory of Manya Igel, Beer-Sheva, Israel
| | - Alon Kaplan
- Faculty of Health Sciences, Ben-Gurion University of the Negev, The International Center of Health, Innovation & Nutrition On the memory of Manya Igel, Beer-Sheva, Israel
| | - Anat Yaskolka Meir
- Faculty of Health Sciences, Ben-Gurion University of the Negev, The International Center of Health, Innovation & Nutrition On the memory of Manya Igel, Beer-Sheva, Israel
| | - Hila Zelicha
- Faculty of Health Sciences, Ben-Gurion University of the Negev, The International Center of Health, Innovation & Nutrition On the memory of Manya Igel, Beer-Sheva, Israel
| | - Dan Knights
- BioTechnology Institute, University of Minnesota, St Paul, USA
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, USA
| | - Kieran Tuohy
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
- School of Food Science & Nutrition, University of Leeds, Leeds, UK
| | - Francesca Fava
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
| | - Matthias Uwe Scholz
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
| | - Oren Ziv
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Elad Rubin
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Matthias Blüher
- Department of Medicine, University of Leipzig, Leipzig, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - Michael Stumvoll
- Department of Medicine, University of Leipzig, Leipzig, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - Uta Ceglarek
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Karine Clément
- Inserm, Nutrition and obesities: systemic approaches, nutriOmicsn Research Unit, Nutrition Department, Pitié-Salpêtrière Hospital, Assistance-Publique Hopitaux de Paris, Sorbonne University, Paris, France
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Frank B. Hu
- Harvard T.H. Chan School of Public Health, Boston, USA
- Department of Medicine, Channing Division of Network Medicine, Department of Medicine, Harvard Medical School and Brigham and Women’s Hospital, Boston, USA
| | - Meir J. Stampfer
- Harvard T.H. Chan School of Public Health, Boston, USA
- Department of Medicine, Channing Division of Network Medicine, Department of Medicine, Harvard Medical School and Brigham and Women’s Hospital, Boston, USA
| | - Dong D. Wang
- Harvard T.H. Chan School of Public Health, Boston, USA
| | - Ilan Youngster
- Pediatric Division and Center for Microbiome Research, Shamir Medical Center, Be’er Ya’akov, Israel
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Iris Shai
- Faculty of Health Sciences, Ben-Gurion University of the Negev, The International Center of Health, Innovation & Nutrition On the memory of Manya Igel, Beer-Sheva, Israel
- Harvard T.H. Chan School of Public Health, Boston, USA
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Menghi L, Cliceri D, Fava F, Pindo M, Gaudioso G, Giacalone D, Gasperi F. Salivary microbial profiles associate with responsiveness to warning oral sensations and dietary intakes. Food Res Int 2023; 171:113072. [PMID: 37330830 DOI: 10.1016/j.foodres.2023.113072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/28/2023] [Accepted: 05/29/2023] [Indexed: 06/19/2023]
Abstract
Oral microbiota-host interactions are gaining recognition as potential factors contributing to interindividual variations in taste perception. However, whether such possible links imply specific bacterial co-occurrence networks remains unknown. To address this issue, we used 16 s rRNA gene sequencing to profile the salivary microbiota of 100 healthy individuals (52 % women; 18-30 y/o), who provided hedonic and psychophysical responses to 5 liquid and 5 solid commercially-available foods, each chosen to elicit a target sensation (sweet, sour, bitter, salty, pungent). The same cohort also completed several psychometric measures and a 4-day food diary. Unsupervised data-driven clustering of genus-level Aitchison distances supported the existence of two salivary microbial profiles (CL-1, CL-2). While CL-1 (n = 57; 49.1 % women) exhibited higher α-diversity metrics and was enriched in microbial genera assigned to the class Clostridia (e.g., Lachnospiraceae_[G-3]), CL-2 (n = 43; 55.8 % women) harbored greater amounts of taxa with potential cariogenic effects (e.g., genus Lactobacillus) and significantly lower abundances of inferred MetaCyc pathways related to the metabolic fate of acetate. Intriguingly, CL-2 showed enhanced responsiveness to warning oral sensations (bitter, sour, astringent) and a higher propensity to crave sweet foods or engage in prosocial behaviors. Further, the same cluster reported habitually consuming more simple carbohydrates and fewer beneficial nutrients (vegetable proteins, monounsaturated fatty acids). In summary, while the mediating role of participants' baseline diet on findings can not be definitively excluded, this work provides evidence suggesting that microbe-microbe and microbe-taste interactions may exert an influence on dietary habits and motivates further research to uncover a potential "core" taste-related salivary microbiota.
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Affiliation(s)
- Leonardo Menghi
- Center Agriculture Food Environment, University of Trento, Via Mach 1, San Michele all'Adige, 38098, Italy; Department of Technology and Innovation, University of Southern Denmark, Campusvej 55, Odense 5230, Denmark; Research and Innovation Centre, Fondazione Edmund Mach, Via Mach 1, San Michele all'Adige, 38098, Italy
| | - Danny Cliceri
- Center Agriculture Food Environment, University of Trento, Via Mach 1, San Michele all'Adige, 38098, Italy
| | - Francesca Fava
- Research and Innovation Centre, Fondazione Edmund Mach, Via Mach 1, San Michele all'Adige, 38098, Italy
| | - Massimo Pindo
- Research and Innovation Centre, Fondazione Edmund Mach, Via Mach 1, San Michele all'Adige, 38098, Italy
| | - Giulia Gaudioso
- Research and Innovation Centre, Fondazione Edmund Mach, Via Mach 1, San Michele all'Adige, 38098, Italy
| | - Davide Giacalone
- Department of Technology and Innovation, University of Southern Denmark, Campusvej 55, Odense 5230, Denmark.
| | - Flavia Gasperi
- Center Agriculture Food Environment, University of Trento, Via Mach 1, San Michele all'Adige, 38098, Italy; Research and Innovation Centre, Fondazione Edmund Mach, Via Mach 1, San Michele all'Adige, 38098, Italy.
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5
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Pushpass RAG, Alzoufairi S, Mancini A, Quilter K, Fava F, Delaiti S, Vrhovsek U, Christensen C, Joyce SA, Tuohy KM, Jackson KG, Lovegrove JA. Chronic consumption of probiotics, oats, and apples has differential effects on postprandial bile acid profile and cardiometabolic disease risk markers compared with an isocaloric control (cornflakes): a randomized trial. Am J Clin Nutr 2023; 117:252-265. [PMID: 36811563 DOI: 10.1016/j.ajcnut.2022.10.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 10/11/2022] [Accepted: 10/28/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Dietary components that impact the gut microbiota may beneficially affect cardiometabolic health, possibly by altered bile acid metabolism. However, impacts of these foods on postprandial bile acids, gut microbiota, and cardiometabolic risk markers are unclear. OBJECTIVES The aim of this study was to determine the chronic effects of probiotics, oats, and apples on postprandial bile acids, gut microbiota, and cardiometabolic health biomarkers. METHODS Using an acute within chronic parallel design, 61 volunteers (mean ± SD: age 52 ± 12 y; BMI 24.8 ± 3.4 kg/m2) were randomly assigned to consume 40 g cornflakes (control), 40 g oats or 2 Renetta Canada apples each with 2 placebo capsules per day or 40 g cornflakes with 2 Lactobacillus reuteri capsules (>5 × 109 CFU) per day, for 8 wk. Fasting and postprandial serum/plasma bile acids and cardiometabolic health biomarkers, fecal bile acids, and gut microbiota composition were determined. RESULTS At week 0, oats and apples significantly decreased postprandial serum insulin [area under the curve (AUC): 25.6 (17.4, 33.8) and 23.4 (15.4, 31.4) vs. 42.0 (33.7, 50.2) pmol/L × min and incremental AUC (iAUC): 17.8 (11.6, 24.0) and 13.7 (7.7, 19.8) vs. 29.6 (23.3, 35.8) pmol/L × min] and C-peptide responses [AUC: 599 (514, 684) and 550 (467, 632) vs. 750 (665, 835) ng/mL × min], whereas non-esterified fatty acids were increased [AUC 135 (117, 153) vs. 86.3 (67.9, 105) and iAUC 96.2 (78.8, 114) vs. 60 (42.1, 77.9) mmol/L × min] after the apples vs. control (P ≤ 0.05). Postprandial unconjugated [AUC: predicted means (95% CI) 1469 (1101, 1837) vs. 363 (-28, 754) μmol/L × min and iAUC: 923 (682, 1165) vs. 22.0 (-235, 279) μmol/L × min)] and hydrophobic [iAUC: 1210 (911, 1510) vs. 487 (168, 806) μmol/L × min] bile acid responses were increased after 8 wk probiotic intervention vs. control (P ≤ 0.049). None of the interventions modulated the gut microbiota. CONCLUSIONS These results support beneficial effects of apples and oats on postprandial glycemia and the ability of the probiotic Lactobacillus reuteri to modulate postprandial plasma bile acid profiles compared with control (cornflakes), with no relationship evident between circulating bile acids and cardiometabolic health biomarkers.
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Affiliation(s)
- Rose-Anna Grace Pushpass
- Hugh Sinclair Unit of Human Nutrition, Department of Food and Nutritional Sciences, Institute for Food, Nutrition and Health, and Institute for Cardiovascular and Metabolic Research, University of Reading, Harry Nursten Building, Reading, UK
| | - Shouq Alzoufairi
- Hugh Sinclair Unit of Human Nutrition, Department of Food and Nutritional Sciences, Institute for Food, Nutrition and Health, and Institute for Cardiovascular and Metabolic Research, University of Reading, Harry Nursten Building, Reading, UK
| | - Andrea Mancini
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Karena Quilter
- School of Biochemistry and Cell Biology, Biosciences Institute, University College Cork, Ireland; APC Microbiome Ireland, University College Cork, Ireland
| | - Francesca Fava
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Simone Delaiti
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Urska Vrhovsek
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Camilla Christensen
- Hugh Sinclair Unit of Human Nutrition, Department of Food and Nutritional Sciences, Institute for Food, Nutrition and Health, and Institute for Cardiovascular and Metabolic Research, University of Reading, Harry Nursten Building, Reading, UK
| | - Susan A Joyce
- School of Biochemistry and Cell Biology, Biosciences Institute, University College Cork, Ireland; APC Microbiome Ireland, University College Cork, Ireland
| | - Kieran M Tuohy
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Kim G Jackson
- Hugh Sinclair Unit of Human Nutrition, Department of Food and Nutritional Sciences, Institute for Food, Nutrition and Health, and Institute for Cardiovascular and Metabolic Research, University of Reading, Harry Nursten Building, Reading, UK
| | - Julie A Lovegrove
- Hugh Sinclair Unit of Human Nutrition, Department of Food and Nutritional Sciences, Institute for Food, Nutrition and Health, and Institute for Cardiovascular and Metabolic Research, University of Reading, Harry Nursten Building, Reading, UK.
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6
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Baldassarri M, Zguro K, Tomati V, Pastorino C, Fava F, Croci S, Bruttini M, Picchiotti N, Furini S, Pedemonte N, Gabbi C, Renieri A, Fallerini C. Gain- and Loss-of-Function CFTR Alleles Are Associated with COVID-19 Clinical Outcomes. Cells 2022; 11:cells11244096. [PMID: 36552859 PMCID: PMC9776607 DOI: 10.3390/cells11244096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/25/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Carriers of single pathogenic variants of the CFTR (cystic fibrosis transmembrane conductance regulator) gene have a higher risk of severe COVID-19 and 14-day death. The machine learning post-Mendelian model pinpointed CFTR as a bidirectional modulator of COVID-19 outcomes. Here, we demonstrate that the rare complex allele [G576V;R668C] is associated with a milder disease via a gain-of-function mechanism. Conversely, CFTR ultra-rare alleles with reduced function are associated with disease severity either alone (dominant disorder) or with another hypomorphic allele in the second chromosome (recessive disorder) with a global residual CFTR activity between 50 to 91%. Furthermore, we characterized novel CFTR complex alleles, including [A238V;F508del], [R74W;D1270N;V201M], [I1027T;F508del], [I506V;D1168G], and simple alleles, including R347C, F1052V, Y625N, I328V, K68E, A309D, A252T, G542*, V562I, R1066H, I506V, I807M, which lead to a reduced CFTR function and thus, to more severe COVID-19. In conclusion, CFTR genetic analysis is an important tool in identifying patients at risk of severe COVID-19.
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Affiliation(s)
- Margherita Baldassarri
- Medical Genetics, University of Siena, 53100 Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Kristina Zguro
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Valeria Tomati
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, 16148 Genova, Italy
| | - Cristina Pastorino
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, 16148 Genova, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16126 Genoa, Italy
| | - Francesca Fava
- Medical Genetics, University of Siena, 53100 Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, 53100 Siena, Italy
| | - Susanna Croci
- Medical Genetics, University of Siena, 53100 Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Mirella Bruttini
- Medical Genetics, University of Siena, 53100 Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, 53100 Siena, Italy
| | - Nicola Picchiotti
- Department of Mathematics, University of Pavia, 27100 Pavia, Italy
- University of Siena, DIISM-SAILAB, 53100 Siena, Italy
| | - Simone Furini
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | | | - Nicoletta Pedemonte
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, 16148 Genova, Italy
- Correspondence: (N.P.); (A.R.); Tel.: +39-010-5636-3178 (N.P.); +39-0577-233303 (A.R.); Fax: +39-0577-233325 (A.R.)
| | - Chiara Gabbi
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Alessandra Renieri
- Medical Genetics, University of Siena, 53100 Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, 53100 Siena, Italy
- Correspondence: (N.P.); (A.R.); Tel.: +39-010-5636-3178 (N.P.); +39-0577-233303 (A.R.); Fax: +39-0577-233325 (A.R.)
| | - Chiara Fallerini
- Medical Genetics, University of Siena, 53100 Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
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7
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Butler-Laporte G, Povysil G, Kosmicki JA, Cirulli ET, Drivas T, Furini S, Saad C, Schmidt A, Olszewski P, Korotko U, Quinodoz M, Çelik E, Kundu K, Walter K, Jung J, Stockwell AD, Sloofman LG, Jordan DM, Thompson RC, Del Valle D, Simons N, Cheng E, Sebra R, Schadt EE, Kim-Schulze S, Gnjatic S, Merad M, Buxbaum JD, Beckmann ND, Charney AW, Przychodzen B, Chang T, Pottinger TD, Shang N, Brand F, Fava F, Mari F, Chwialkowska K, Niemira M, Pula S, Baillie JK, Stuckey A, Salas A, Bello X, Pardo-Seco J, Gómez-Carballa A, Rivero-Calle I, Martinón-Torres F, Ganna A, Karczewski KJ, Veerapen K, Bourgey M, Bourque G, Eveleigh RJM, Forgetta V, Morrison D, Langlais D, Lathrop M, Mooser V, Nakanishi T, Frithiof R, Hultström M, Lipcsey M, Marincevic-Zuniga Y, Nordlund J, Schiabor Barrett KM, Lee W, Bolze A, White S, Riffle S, Tanudjaja F, Sandoval E, Neveux I, Dabe S, Casadei N, Motameny S, Alaamery M, Massadeh S, Aljawini N, Almutairi MS, Arabi YM, Alqahtani SA, Al Harthi FS, Almutairi A, Alqubaishi F, Alotaibi S, Binowayn A, Alsolm EA, El Bardisy H, Fawzy M, Cai F, Soranzo N, Butterworth A, Geschwind DH, Arteaga S, Stephens A, Butte MJ, Boutros PC, Yamaguchi TN, Tao S, Eng S, Sanders T, Tung PJ, Broudy ME, Pan Y, Gonzalez A, Chavan N, Johnson R, Pasaniuc B, Yaspan B, Smieszek S, Rivolta C, Bibert S, Bochud PY, Dabrowski M, Zawadzki P, Sypniewski M, Kaja E, Chariyavilaskul P, Nilaratanakul V, Hirankarn N, Shotelersuk V, Pongpanich M, Phokaew C, Chetruengchai W, Tokunaga K, Sugiyama M, Kawai Y, Hasegawa T, Naito T, Namkoong H, Edahiro R, Kimura A, Ogawa S, Kanai T, Fukunaga K, Okada Y, Imoto S, Miyano S, Mangul S, Abedalthagafi MS, Zeberg H, Grzymski JJ, Washington NL, Ossowski S, Ludwig KU, Schulte EC, Riess O, Moniuszko M, Kwasniewski M, Mbarek H, Ismail SI, Verma A, Goldstein DB, Kiryluk K, Renieri A, Ferreira MAR, Richards JB. Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative. PLoS Genet 2022; 18:e1010367. [PMID: 36327219 PMCID: PMC9632827 DOI: 10.1371/journal.pgen.1010367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/29/2022] [Indexed: 11/05/2022] Open
Abstract
Host genetics is a key determinant of COVID-19 outcomes. Previously, the COVID-19 Host Genetics Initiative genome-wide association study used common variants to identify multiple loci associated with COVID-19 outcomes. However, variants with the largest impact on COVID-19 outcomes are expected to be rare in the population. Hence, studying rare variants may provide additional insights into disease susceptibility and pathogenesis, thereby informing therapeutics development. Here, we combined whole-exome and whole-genome sequencing from 21 cohorts across 12 countries and performed rare variant exome-wide burden analyses for COVID-19 outcomes. In an analysis of 5,085 severe disease cases and 571,737 controls, we observed that carrying a rare deleterious variant in the SARS-CoV-2 sensor toll-like receptor TLR7 (on chromosome X) was associated with a 5.3-fold increase in severe disease (95% CI: 2.75-10.05, p = 5.41x10-7). This association was consistent across sexes. These results further support TLR7 as a genetic determinant of severe disease and suggest that larger studies on rare variants influencing COVID-19 outcomes could provide additional insights.
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Grants
- U24 CA224319 NCI NIH HHS
- RG/13/13/30194 British Heart Foundation
- U01 DK124165 NIDDK NIH HHS
- C18281/A29019 Cancer Research UK
- MC_PC_20004 Medical Research Council
- UL1 TR001873 NCATS NIH HHS
- RG/18/13/33946 British Heart Foundation
- CH/12/2/29428 British Heart Foundation
- CanCOGeN HostSeq
- Fonds de Recherche Québec Santé (FRQS)
- Génome Québec
- Public Health Agency of Canada
- Canadian Institutes of Health Research (CIHR)
- Lady Davis Institute of the Jewish General Hospital
- Canadian Foundation for Innovation
- NIH Foundation
- McGill Interdisciplinary Initiative in Infection and Immunity (MI4)
- Jewish General Hospital Foundation
- McGill University
- Calcul Québec and Compute Canada
- Compute Canada
- Vagelos College of Physicians & Surgeons Office for Research
- Biomedical Informatics Resource of the Columbia University Irving Institute for Clinical and Translational Research (CTSA)
- National Center for Advancing Translational Sciences, National Institutes of Health
- German Research Foundation
- NGS Competence Center Tübingen
- West German Genome Center
- Stiftung Universitätsmedizin Essen
- Technical University of Munich
- BONFOR program of the Medical Faculty, University of Bonn
- Emmy-Noether programm of the German Research Foundation
- State of Saarland
- Dr. Rolf M. Schwiete Foundation
- Munich Clinician Scientist Programm
- Netzwerk-Universitaetsmedizin-COVIM
- Federal Ministry of Education and Research
- Swiss National Science Foundation
- Leenaards Foundation
- Santos-Suarez Foundation
- Carigest
- MIUR project “Dipartimenti di Eccellenza 2018-2020”
- Bando Ricerca COVID-19 Toscana
- charity fund 2020 from Intesa San Paolo
- Italian Ministry of University and Research
- Istituto Buddista Italiano Soka Gakkai
- Instituto de Salud Carlos III
- GePEM
- DIAVIR
- Resvi-Omics
- ReSVinext
- Enterogen
- Agencia Gallega para la Gestión del Conocimiento en Salud
- BI-BACVIR
- CovidPhy
- Agencia Gallega de Innovación (GAIN):
- GEN-COVID
- Framework Partnership Agreement between the Consellería de Sanidad de la XUNTA de Galicia
- GENVIP-IDIS
- consorcio Centro de Investigación Biomédica en Red de Enfermedades Respiratorias
- F. Hoffmann-La Roche Ltd
- U.S. Department of Health and Human Services, Office of the Assistant Secretary for Preparedness and Response, and Biomedical Advanced Research and Development Authority
- Nevada Governor's Office of Economic Development
- Renown Health and the Renown Health Foundation
- Ratchadapiseksompotch Fund, Faculty of Medicine, Chulalongkorn University
- Healthcare-associated Infection Research Group STAR (Special Task Force for Activating Research)
- Grant for Development of New Faculty Staff, Ratchadaphiseksomphot Endowment Fund
- e-ASIA Joint Research Program (National Science and Technology Development Agency)
- Health Systems Research Institute, TSRI Fund
- Thailand Research Fund
- Ratchadapiseksompotch Fund
- Ratchadapiseksompotch Fund, Faculty of Medicine,Chulalongkorn University, Bangkok, Thailand
- Health Systems Research Institute
- Ratchadapisek Sompoch Endowment Fund, Chulalongkorn University
- NHS Blood and Transplant
- National Institute for Health Research
- UK Medical Research Council
- Japan Agency for Medical Research and Development
- Japan Science and Technology Agency
- National Center for Global Health and Medicine
- Agency for Medical Research and Development
- Polish National Science Centre
- Medical Research Agency
- Perelman School of Medicine at University of Pennsylvania
- Smilow family
- National Center for Advancing Translational Sciences of the National Institutes of Health
- Polish Medical Research Agency
- Qatar Foundation for Education, Science and Community Development
- Saudi Ministry of Health
- King Abdulaziz City for Science and Technology
- European Union’s Horizon 2020 research and innovation program
- Science for Life Laboratory
- Swedish Research Council
- Knut and Alice Wallenberg Foundation
- OCRC
- Microsoft COVID Compute Funding
- Illumina
- UCLA David Geffen School of Medicine - Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research Award Program
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Affiliation(s)
- Guillaume Butler-Laporte
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Gundula Povysil
- Institute for Genomic Medicine, Columbia University, New York city, New York, United States of America
| | - Jack A. Kosmicki
- Regeneron Genetics Center, Tarrytown, New York, United States of America
| | | | - Theodore Drivas
- Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Simone Furini
- Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
| | - Chadi Saad
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Axel Schmidt
- Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany
| | | | - Urszula Korotko
- IMAGENE.ME SA, Bialystok, Poland
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
| | - Elifnaz Çelik
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
| | - Kousik Kundu
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Klaudia Walter
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Junghyun Jung
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, California, United States of America
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Amy D. Stockwell
- Genentech Inc, South San Francisco, California, United States of America
| | - Laura G. Sloofman
- Seaver Autism Center for Research and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Daniel M. Jordan
- Mount Sinai Clnical Intelligence Center, Charles Bronfman Institute for Personalized Medicine, Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Ryan C. Thompson
- Icahn Institute of Data Science and Genomics Technology, New York city, New York, United States of America
| | - Diane Del Valle
- Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Nicole Simons
- Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Esther Cheng
- Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York city,New York, United States of America
| | - Eric E. Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York city,New York, United States of America
| | - Seunghee Kim-Schulze
- Department of Oncological Science, Human Immune Monitoring Center, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Sacha Gnjatic
- Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Miriam Merad
- Precision Immunology Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Joseph D. Buxbaum
- Seaver Autism Center for Research and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Noam D. Beckmann
- Precision Immunology Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Alexander W. Charney
- Mount Sinai Clinical Intelligence Center; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | | | - Timothy Chang
- Department of Neurology, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Tess D. Pottinger
- Institute for Genomic Medicine, Columbia University, New York city, New York, United States of America
| | - Ning Shang
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York city, New York, United States of America
| | - Fabian Brand
- Institute of Genomic Statistics and Bioinformatics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Francesca Fava
- Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
- Medical Genetics, University of Siena, Siena, Italy
| | - Francesca Mari
- Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
- Medical Genetics, University of Siena, Siena, Italy
| | - Karolina Chwialkowska
- IMAGENE.ME SA, Bialystok, Poland
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Magdalena Niemira
- Centre for Clinical Research, Medical University of Bialystok, Bialystok, Poland
| | | | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
- Centre for Inflammation Research, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | | | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias, Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Galicia, Spain
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Xabier Bello
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias, Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Galicia, Spain
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Jacobo Pardo-Seco
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias, Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Galicia, Spain
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Alberto Gómez-Carballa
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias, Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Galicia, Spain
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Irene Rivero-Calle
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Federico Martinón-Torres
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachussets, United States of America
| | - Konrad J. Karczewski
- Stanley Center for Psychiatric Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Kumar Veerapen
- Stanley Center for Psychiatric Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Mathieu Bourgey
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
- McGill Genome Center, McGill University, Montréal, Québec, Canada
| | - Guillaume Bourque
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
- McGill Genome Center, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Robert JM Eveleigh
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
- McGill Genome Center, McGill University, Montréal, Québec, Canada
| | - Vincenzo Forgetta
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - David Morrison
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - David Langlais
- McGill Genome Center, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Mark Lathrop
- McGill Genome Center, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Vincent Mooser
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Tomoko Nakanishi
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Research Fellow, Japan Society for the Promotion of Science, Tokyo, Japan
| | - Robert Frithiof
- Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Michael Hultström
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
- Integrative Physiology, Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Miklos Lipcsey
- Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
- Hedenstierna Laboratory, CIRRUS, Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Yanara Marincevic-Zuniga
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - William Lee
- Helix, San Mateo, California, United States of America
| | | | - Simon White
- Helix, San Mateo, California, United States of America
| | | | | | | | - Iva Neveux
- Center for Genomic Medicine, Desert Research Institute, Reno, Nevada United States of America
| | - Shaun Dabe
- Renown Health, Reno, Nevada, United States of America
| | - Nicolas Casadei
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
- NGS Competence Center Tuebingen, Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Susanne Motameny
- West German Genome Center, site Cologne, University of Cologne, Cologne, Germany
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Manal Alaamery
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Saudi Human Genome Project at King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Salam Massadeh
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Saudi Human Genome Project at King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Nora Aljawini
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Saudi Human Genome Project at King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Mansour S. Almutairi
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Saudi Human Genome Project at King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Yaseen M. Arabi
- Ministry of the National Guard Health Affairs, King Abdullah International Medical Research Center and King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Saleh A. Alqahtani
- Liver Transplant Unit, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
- Division of Gastroenterology and Hepatology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Fawz S. Al Harthi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Amal Almutairi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Fatima Alqubaishi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Sarah Alotaibi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Albandari Binowayn
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Ebtehal A. Alsolm
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Hadeel El Bardisy
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Mohammad Fawzy
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Fang Cai
- Genentech Inc, South San Francisco, California, United States of America
| | - Nicole Soranzo
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Adam Butterworth
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
| | | | | | | | | | | | | | | | | | - Daniel H. Geschwind
- Department of Neurology, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Stephanie Arteaga
- Department of Neurology, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Alexis Stephens
- Department of Pediatrics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Manish J. Butte
- Department of Pediatrics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
- Department of Microbiology, Immunology, and Molecular Genetics (MIMG), David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Paul C. Boutros
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Takafumi N. Yamaguchi
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Shu Tao
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Stefan Eng
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Timothy Sanders
- Office of Health Informatics and Analytics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Paul J. Tung
- Office of Health Informatics and Analytics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Michael E. Broudy
- Office of Health Informatics and Analytics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Yu Pan
- Office of Health Informatics and Analytics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Alfredo Gonzalez
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Nikhil Chavan
- Office of Health Informatics and Analytics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Ruth Johnson
- Department of Computer Science, McGill University, Montréal, Québec, Canada
| | - Bogdan Pasaniuc
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
- Department of Computational Medicine, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
- Department of Pathology, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Brian Yaspan
- Genentech Inc, South San Francisco, California, United States of America
| | - Sandra Smieszek
- Vanda Pharmaceuticals, Washington, District of Columbia, United States of America
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
| | - Stephanie Bibert
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Pierre-Yves Bochud
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Maciej Dabrowski
- MNM Bioscience Inc., Cambridge, Massachusetts, United States of America
| | - Pawel Zawadzki
- MNM Bioscience Inc., Cambridge, Massachusetts, United States of America
- Faculty of Physics, Adam Mickiewicz University, Poznan, Poland
| | | | - Elżbieta Kaja
- MNM Bioscience Inc., Cambridge, Massachusetts, United States of America
- Department of Medical Chemistry and Laboratory Medicine, Poznań University of Medical Sciences, Poznań, Poland
| | - Pajaree Chariyavilaskul
- Clinical Pharmacokinetics and Pharmacogenomics Research Unit, Department of Pharmacology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Voraphoj Nilaratanakul
- Healthcare-associated Infection Research Group STAR (Special Task Force for Activating Research) and Division of Infectious Diseases, Department of Medicine,Chulalongkorn University, Bangkok, Thailand
| | - Nattiya Hirankarn
- Center of Excellence in Immunology and Immune-mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, and Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Monnat Pongpanich
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Chureerat Phokaew
- Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Wanna Chetruengchai
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Katsushi Tokunaga
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Masaya Sugiyama
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Yosuke Kawai
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Takanori Hasegawa
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tatsuhiko Naito
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Ho Namkoong
- Department of Infectious Diseases, Keio University School of Medicine, Tokyo, Japan
| | - Ryuya Edahiro
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Akinori Kimura
- Institute of Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Takanori Kanai
- Division of Gastroenterology and Hepatology, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Koichi Fukunaga
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Japan
| | - Seiya Imoto
- Division of Health Medical Intelligence, Human Genome Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Satoru Miyano
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Serghei Mangul
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, California, United States of America
| | - Malak S. Abedalthagafi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Hugo Zeberg
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Joseph J. Grzymski
- Center for Genomic Medicine, Desert Research Institute, Reno, Nevada United States of America
| | | | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
- NGS Competence Center Tuebingen, Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Kerstin U. Ludwig
- Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany
- West German Genome Center, site Bonn, University of Bonn, Bonn, Germany
| | - Eva C. Schulte
- Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany
- Institute of Virology, Technical University Munich/Helmholtz Zentrum München, Munich, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
- NGS Competence Center Tuebingen, Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Marcin Moniuszko
- Department of Regenerative Medicine and Immune Regulation, Medical University of Bialystok, Bialystok, Poland
- Department of Allergology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
| | - Miroslaw Kwasniewski
- IMAGENE.ME SA, Bialystok, Poland
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Hamdi Mbarek
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Said I. Ismail
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Anurag Verma
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Corporal Michael Crescenz VA Medical Center, Philadelphia, Pennsylvania, United States of America
| | - David B. Goldstein
- Institute for Genomic Medicine, Columbia University, New York city, New York, United States of America
- Department of Genetics & Development, Columbia University, New York city, New York, United States of America
| | - Krzysztof Kiryluk
- Institute for Genomic Medicine, Columbia University, New York city, New York, United States of America
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York city, New York, United States of America
| | - Alessandra Renieri
- Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
- Medical Genetics, University of Siena, Siena, Italy
| | | | - J Brent Richards
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
- Department of Twin Research, King’s College London, London, United Kingdom
- 5 Prime Sciences Inc, Montreal, Quebec, Canada
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8
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Gaudioso G, Weil T, Marzorati G, Solovyev P, Bontempo L, Franciosi E, Bertoldi L, Pedrolli C, Tuohy KM, Fava F. Microbial and metabolic characterization of organic artisanal sauerkraut fermentation and study of gut health-promoting properties of sauerkraut brine. Front Microbiol 2022; 13:929738. [PMID: 36312966 PMCID: PMC9606823 DOI: 10.3389/fmicb.2022.929738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 09/09/2022] [Indexed: 12/03/2022] Open
Abstract
Sauerkraut is a traditionally fermented cabbage, and recent evidence suggests that it has beneficial properties for human health. In this work, a multi-disciplinary approach was employed to characterize the fermentation process and gut health-promoting properties of locally produced, organic sauerkraut from two distinct producers, SK1 and SK2. 16S rRNA metataxonomics showed that bacterial diversity gradually decreased as fermentation progressed. Differences in sauerkraut microbiota composition were observed between the two producers, especially at the start of fermentation. Lactic acid bacteria (LAB) dominated the microbiota after 35 days, with Lactiplantibacillus being the dominant genus in both sauerkraut products, together with Leuconostoc and Paucilactobacillus in SK1, and with Pediococcus, Levilactibacillus, and Leuconostoc in SK2. LAB reached between 7 and 8 Log CFU/mL brine at the end of fermentation (35 days), while pH lowering happened within the first week of fermentation. A total of 220 LAB strains, corresponding to 133 RAPD-PCR biotypes, were successfully isolated. Lactiplantibacillus plantarum and Lactiplantibacillus pentosus accounted for 67% of all SK1 isolates, and Lactiplantibacillus plantarum/paraplantarum and Leuconostoc mesenteroides represented 72% of all the isolates from SK2. 1H-NMR analysis revealed significant changes in microbial metabolite profiles during the fermentation process, with lactic and acetic acids, as well as amino acids, amines, and uracil, being the dominant metabolites quantified. Sauerkraut brine did not affect trans-epithelial electrical resistance through a Caco-2 cell monolayer as a measure of gut barrier function. However, significant modulation of inflammatory response after LPS stimulation was observed in PBMCs-Caco-2 co-culture. Sauerkraut brine supported a robust inflammatory response to endotoxin, by increasing TNF-α and IL-6 production while also stimulating the anti-inflammatory IL-10, therefore suggesting positive resolution of inflammation after 24 h and supporting the potential of sauerkraut brine to regulate intestinal immune function.
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Affiliation(s)
- Giulia Gaudioso
- Nutrition and Nutrigenomics Unit, Research and Innovation Center, Fondazione Edmund Mach, San Michele all'Adige, Italy
- Centre for Integrative Biology (CIBIO) – Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Tobias Weil
- Nutrition and Nutrigenomics Unit, Research and Innovation Center, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Giulia Marzorati
- Nutrition and Nutrigenomics Unit, Research and Innovation Center, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Pavel Solovyev
- Traceability Unit, Research and Innovation Center, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Luana Bontempo
- Traceability Unit, Research and Innovation Center, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Elena Franciosi
- Nutrition and Nutrigenomics Unit, Research and Innovation Center, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Luigi Bertoldi
- Organic Agriculture Unit, Environmental Department, Technology Transfer Center, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Carlo Pedrolli
- Dietetics and Clinical Nutrition, Nutrition Department, S. Chiara Hospital, Azienda Provinciale per I Servizi Sanitari, Trento, Italy
| | - Kieran Michael Tuohy
- Nutrition and Nutrigenomics Unit, Research and Innovation Center, Fondazione Edmund Mach, San Michele all'Adige, Italy
- School of Food Science and Nutrition, University of Leeds, Leeds, United Kingdom
| | - Francesca Fava
- Nutrition and Nutrigenomics Unit, Research and Innovation Center, Fondazione Edmund Mach, San Michele all'Adige, Italy
- *Correspondence: Francesca Fava
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9
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Fava F, Pereira CO, Siqueira JVB, Veroneze B, Guerrero N, Farias JSH, Kozonoe MI, Ioshii SO, Beltrame MP. APRESENTAÇÃO ATÍPICA DE MIELOMA MÚLTIPLO E A IMPORTÂNCIA DA CITOMETRIA DE FLUXO NA DECISÃO TERAPÊUTICA. Hematol Transfus Cell Ther 2022. [DOI: 10.1016/j.htct.2022.09.967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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10
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Quadros GMS, Becker LF, Costa GL, Veroneze B, Munhoz EC, Beltrame MP, Fava F, Pereira CO, Siqueira JVB. NEOPLASIA DE CÉLULAS T IMATURAS EM ADULTO DIAGNOSTICADA A PARTIR DE DERRAME PERICÁRDICO - RELATO DE CASO. Hematol Transfus Cell Ther 2022. [DOI: 10.1016/j.htct.2022.09.273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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11
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Pereira CO, Fava F, Siqueira JVB, Assis KLB, Quadros GMS, Veroneze B, Farias JSH, Kozonoe MI, Ioshii SO, Beltrame MP. A CITOMETRIA DE FLUXO COMO FERRAMENTA DIAGNÓSTICA EM TUMOR SÓLIDO - OSTEOSSARCOMA. Hematol Transfus Cell Ther 2022. [DOI: 10.1016/j.htct.2022.09.966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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12
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Zhang S, Cooper-Knock J, Weimer AK, Shi M, Kozhaya L, Unutmaz D, Harvey C, Julian TH, Furini S, Frullanti E, Fava F, Renieri A, Gao P, Shen X, Timpanaro IS, Kenna KP, Baillie JK, Davis MM, Tsao PS, Snyder MP. Multiomic analysis reveals cell-type-specific molecular determinants of COVID-19 severity. Cell Syst 2022; 13:598-614.e6. [PMID: 35690068 PMCID: PMC9163145 DOI: 10.1016/j.cels.2022.05.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 04/02/2022] [Accepted: 05/18/2022] [Indexed: 01/26/2023]
Abstract
The determinants of severe COVID-19 in healthy adults are poorly understood, which limits the opportunity for early intervention. We present a multiomic analysis using machine learning to characterize the genomic basis of COVID-19 severity. We use single-cell multiome profiling of human lungs to link genetic signals to cell-type-specific functions. We discover >1,000 risk genes across 19 cell types, which account for 77% of the SNP-based heritability for severe disease. Genetic risk is particularly focused within natural killer (NK) cells and T cells, placing the dysfunction of these cells upstream of severe disease. Mendelian randomization and single-cell profiling of human NK cells support the role of NK cells and further localize genetic risk to CD56bright NK cells, which are key cytokine producers during the innate immune response. Rare variant analysis confirms the enrichment of severe-disease-associated genetic variation within NK-cell risk genes. Our study provides insights into the pathogenesis of severe COVID-19 with potential therapeutic targets.
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Affiliation(s)
- Sai Zhang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; VA Palo Alto Epidemiology Research and Information Center for Genomics, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA; Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Johnathan Cooper-Knock
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK
| | - Annika K Weimer
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Minyi Shi
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lina Kozhaya
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Derya Unutmaz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Calum Harvey
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK
| | - Thomas H Julian
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK
| | - Simone Furini
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Elisa Frullanti
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; Medical Genetics, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Francesca Fava
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; Medical Genetics, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; Genetica Medica, Azienda Ospedaliero-Universitaria Senese, 53100 Siena, Italy
| | - Alessandra Renieri
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; Medical Genetics, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; Genetica Medica, Azienda Ospedaliero-Universitaria Senese, 53100 Siena, Italy
| | - Peng Gao
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Xiaotao Shen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ilia Sarah Timpanaro
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Kevin P Kenna
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK; Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Mark M Davis
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Philip S Tsao
- VA Palo Alto Epidemiology Research and Information Center for Genomics, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA; Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Pathak GA, Karjalainen J, Stevens C, Neale BM, Daly M, Ganna A, Andrews SJ, Kanai M, Cordioli M, Polimanti R, Harerimana N, Pirinen M, Liao RG, Chwialkowska K, Trankiem A, Balaconis MK, Nguyen H, Solomonson M, Veerapen K, Wolford B, Roberts G, Park D, Ball CA, Coignet M, McCurdy S, Knight S, Partha R, Rhead B, Zhang M, Berkowitz N, Gaddis M, Noto K, Ruiz L, Pavlovic M, Hong EL, Rand K, Girshick A, Guturu H, Baltzell AH, Niemi MEK, Rahmouni S, Guntz J, Beguin Y, Cordioli M, Pigazzini S, Nkambule L, Georges M, Moutschen M, Misset B, Darcis G, Guiot J, Azarzar S, Gofflot S, Claassen S, Malaise O, Huynen P, Meuris C, Thys M, Jacques J, Léonard P, Frippiat F, Giot JB, Sauvage AS, Frenckell CV, Belhaj Y, Lambermont B, Nakanishi T, Morrison DR, Mooser V, Richards JB, Butler-Laporte G, Forgetta V, Li R, Ghosh B, Laurent L, Belisle A, Henry D, Abdullah T, Adeleye O, Mamlouk N, Kimchi N, Afrasiabi Z, Rezk N, Vulesevic B, Bouab M, Guzman C, Petitjean L, Tselios C, Xue X, Afilalo J, Afilalo M, Oliveira M, Brenner B, Brassard N, Durand M, Schurr E, Lepage P, Ragoussis J, Auld D, Chassé M, Kaufmann DE, Lathrop GM, Adra D, Hayward C, Glessner JT, Shaw DM, Campbell A, Morris M, Hakonarson H, Porteous DJ, Below J, Richmond A, Chang X, Polikowski H, Lauren PE, Chen HH, Wanying Z, Fawns-Ritchie C, North K, McCormick JB, Chang X, Glessner JR, Hakonarson H, Gignoux CR, Wicks SJ, Crooks K, Barnes KC, Daya M, Shortt J, Rafaels N, Chavan S, Timmers PRHJ, Wilson JF, Tenesa A, Kerr SM, D’Mellow K, Shahin D, El-Sherbiny YM, von Hohenstaufen KA, Sobh A, Eltoukhy MM, Nkambul L, Elhadidy TA, Abd Elghafar MS, El-Jawhari JJ, Mohamed AAS, Elnagdy MH, Samir A, Abdel-Aziz M, Khafaga WT, El-Lawaty WM, Torky MS, El-shanshory MR, Yassen AM, Hegazy MAF, Okasha K, Eid MA, Moahmed HS, Medina-Gomez C, Ikram MA, Uitterlinden AG, Mägi R, Milani L, Metspalu A, Laisk T, Läll K, Lepamets M, Esko T, Reimann E, Naaber P, Laane E, Pesukova J, Peterson P, Kisand K, Tabri J, Allos R, Hensen K, Starkopf J, Ringmets I, Tamm A, Kallaste A, Alavere H, Metsalu K, Puusepp M, Batini C, Tobin MD, Venn LD, Lee PH, Shrine N, Williams AT, Guyatt AL, John C, Packer RJ, Ali A, Free RC, Wang X, Wain LV, Hollox EJ, Bee CE, Adams EL, Palotie A, Ripatti S, Ruotsalainen S, Kristiansson K, Koskelainen S, Perola M, Donner K, Kivinen K, Palotie A, Kaunisto M, Rivolta C, Bochud PY, Bibert S, Boillat N, Nussle SG, Albrich W, Quinodoz M, Kamdar D, Suh N, Neofytos D, Erard V, Voide C, Bochud PY, Rivolta C, Bibert S, Quinodoz M, Kamdar D, Neofytos D, Erard V, Voide C, Friolet R, Vollenweider P, Pagani JL, Oddo M, zu Bentrup FM, Conen A, Clerc O, Marchetti O, Guillet A, Guyat-Jacques C, Foucras S, Rime M, Chassot J, Jaquet M, Viollet RM, Lannepoudenx Y, Portopena L, Bochud PY, Vollenweider P, Pagani JL, Desgranges F, Filippidis P, Guéry B, Haefliger D, Kampouri EE, Manuel O, Munting A, Papadimitriou-Olivgeris M, Regina J, Rochat-Stettler L, Suttels V, Tadini E, Tschopp J, Van Singer M, Viala B, Boillat-Blanco N, Brahier T, Hügli O, Meuwly JY, Pantet O, Gonseth Nussle S, Bochud M, D’Acremont V, Estoppey Younes S, Albrich WC, Suh N, Cerny A, O’Mahony L, von Mering C, Bochud PY, Frischknecht M, Kleger GR, Filipovic M, Kahlert CR, Wozniak H, Negro TR, Pugin J, Bouras K, Knapp C, Egger T, Perret A, Montillier P, di Bartolomeo C, Barda B, de Cid R, Carreras A, Moreno V, Kogevinas M, Galván-Femenía I, Blay N, Farré X, Sumoy L, Cortés B, Mercader JM, Guindo-Martinez M, Torrents D, Garcia-Aymerich J, Castaño-Vinyals G, Dobaño C, Gori M, Renieri A, Mari F, Mondelli MU, Castelli F, Vaghi M, Rusconi S, Montagnani F, Bargagli E, Franchi F, Mazzei MA, Cantarini L, Tacconi D, Feri M, Scala R, Spargi G, Nencioni C, Bandini M, Caldarelli GP, Canaccini A, Ognibene A, D’Arminio Monforte A, Girardis M, Antinori A, Francisci D, Schiaroli E, Scotton PG, Panese S, Scaggiante R, Monica MD, Capasso M, Fiorentino G, Castori M, Aucella F, Biagio AD, Masucci L, Valente S, Mandalà M, Zucchi P, Giannattasio F, Coviello DA, Mussini C, Tavecchia L, Crotti L, Rizzi M, Rovere MTL, Sarzi-Braga S, Bussotti M, Ravaglia S, Artuso R, Perrella A, Romani D, Bergomi P, Catena E, Vincenti A, Ferri C, Grassi D, Pessina G, Tumbarello M, Pietro MD, Sabrina R, Luchi S, Furini S, Dei S, Benetti E, Picchiotti N, Sanarico M, Ceri S, Pinoli P, Raimondi F, Biscarini F, Stella A, Zguro K, Capitani K, Nkambule L, Tanfoni M, Fallerini C, Daga S, Baldassarri M, Fava F, Frullanti E, Valentino F, Doddato G, Giliberti A, Tita R, Amitrano S, Bruttini M, Croci S, Meloni I, Mencarelli MA, Rizzo CL, Pinto AM, Beligni G, Tommasi A, Sarno LD, Palmieri M, Carriero ML, Alaverdian D, Busani S, Bruno R, Vecchia M, Belli MA, Mantovani S, Ludovisi S, Quiros-Roldan E, Antoni MD, Zanella I, Siano M, Emiliozzi A, Fabbiani M, Rossetti B, Bergantini L, D’Alessandro M, Cameli P, Bennett D, Anedda F, Marcantonio S, Scolletta S, Guerrini S, Conticini E, Frediani B, Spertilli C, Donati A, Guidelli L, Corridi M, Croci L, Piacentini P, Desanctis E, Cappelli S, Verzuri A, Anemoli V, Pancrazzi A, Lorubbio M, Miraglia FG, Venturelli S, Cossarizza A, Vergori A, Gabrieli A, Riva A, Paciosi F, Andretta F, Gatti F, Parisi SG, Baratti S, Piscopo C, Russo R, Andolfo I, Iolascon A, Carella M, Merla G, Squeo GM, Raggi P, Marciano C, Perna R, Bassetti M, Sanguinetti M, Giorli A, Salerni L, Parravicini P, Menatti E, Trotta T, Coiro G, Lena F, Martinelli E, Mancarella S, Gabbi C, Maggiolo F, Ripamonti D, Bachetti T, Suardi C, Parati G, Bottà G, Domenico PD, Rancan I, Bianchi F, Colombo R, Barbieri C, Acquilini D, Andreucci E, Segala FV, Tiseo G, Falcone M, Lista M, Poscente M, Vivo OD, Petrocelli P, Guarnaccia A, Baroni S, Hayward C, Porteous DJ, Fawns-Ritchie C, Richmond A, Campbell A, van Heel DA, Hunt KA, Trembath RC, Huang QQ, Martin HC, Mason D, Trivedi B, Wright J, Finer S, Akhtar S, Anwar M, Arciero E, Ashraf S, Breen G, Chung R, Curtis CJ, Chowdhury M, Colligan G, Deloukas P, Durham C, Finer S, Griffiths C, Huang QQ, Hurles M, Hunt KA, Hussain S, Islam K, Khan A, Khan A, Lavery C, Lee SH, Lerner R, MacArthur D, MacLaughlin B, Martin H, Mason D, Miah S, Newman B, Safa N, Tahmasebi F, Trembath RC, Trivedi B, van Heel DA, Wright J, Griffiths CJ, Smith AV, Boughton AP, Li KW, LeFaive J, Annis A, Niavarani A, Aliannejad R, Sharififard B, Amirsavadkouhi A, Naderpour Z, Tadi HA, Aleagha AE, Ahmadi S, Moghaddam SBM, Adamsara A, Saeedi M, Abdollahi H, Hosseini A, Chariyavilaskul P, Jantarabenjakul W, Hirankarn N, Chamnanphon M, Suttichet TB, Shotelersuk V, Pongpanich M, Phokaew C, Chetruengchai W, Putchareon O, Torvorapanit P, Puthanakit T, Suchartlikitwong P, Nilaratanakul V, Sodsai P, Brumpton BM, Hveem K, Willer C, Wolford B, Zhou W, Rogne T, Solligard E, Åsvold BO, Franke L, Boezen M, Deelen P, Claringbould A, Lopera E, Warmerdam R, Vonk JM, van Blokland I, Lanting P, Ori APS, Feng YCA, Mercader J, Weiss ST, Karlson EW, Smoller JW, Murphy SN, Meigs JB, Woolley AE, Green RC, Perez EF, Wolford B, Zöllner S, Wang J, Beck A, Sloofman LG, Ascolillo S, Sebra RP, Collins BL, Levy T, Buxbaum JD, Sealfon SC, Jordan DM, Thompson RC, Gettler K, Chaudhary K, Belbin GM, Preuss M, Hoggart C, Choi S, Underwood SJ, Salib I, Britvan B, Keller K, Tang L, Peruggia M, Hiester LL, Niblo K, Aksentijevich A, Labkowsky A, Karp A, Zlatopolsky M, Zyndorf M, Charney AW, Beckmann ND, Schadt EE, Abul-Husn NS, Cho JH, Itan Y, Kenny EE, Loos RJF, Nadkarni GN, Do R, O’Reilly P, Huckins LM, Ferreira MAR, Abecasis GR, Leader JB, Cantor MN, Justice AE, Carey DJ, Chittoor G, Josyula NS, Kosmicki JA, Horowitz JE, Baras A, Gass MC, Yadav A, Mirshahi T, Hottenga JJ, Bartels M, de geus EEJC, Nivard MMG, Verma A, Ritchie MD, Rader D, Li B, Verma SS, Lucas A, Bradford Y, Abedalthagafi M, Alaamery M, Alshareef A, Sawaji M, Massadeh S, AlMalik A, Alqahtani S, Baraka D, Harthi FA, Alsolm E, Safieh LA, Alowayn AM, Alqubaishi F, Mutairi AA, Mangul S, Almutairi M, Aljawini N, Albesher N, Arabi YM, Mahmoud ES, Khattab AK, Halawani RT, Alahmadey ZZ, Albakri JK, Felemban WA, Suliman BA, Hasanato R, Al-Awdah L, Alghamdi J, AlZahrani D, AlJohani S, Al-Afghani H, AlDhawi N, AlBardis H, Alkwai S, Alswailm M, Almalki F, Albeladi M, Almohammed I, Barhoush E, Albader A, Alotaibi S, Alghamdi B, Jung J, fawzy MS, Alrashed M, Zeberg H, Nkambul L, Frithiof R, Hultström M, Lipcsey M, Tardif N, Rooyackers O, Grip J, Maricic T, Helgeland Ø, Magnus P, Trogstad LIS, Lee Y, Harris JR, Mangino M, Spector TD, Emma D, Moutsianas L, Caulfield MJ, Scott RH, Kousathanas A, Pasko D, Walker S, Stuckey A, Odhams CA, Rhodes D, Fowler T, Rendon A, Chan G, Arumugam P, Karczewski KJ, Martin AR, Wilson DJ, Spencer CCA, Crook DW, Wyllie DH, O’Connell AM, Atkinson EG, Kanai M, Tsuo K, Baya N, Turley P, Gupta R, Walters RK, Palmer DS, Sarma G, Solomonson M, Cheng N, Lu W, Churchhouse C, Goldstein JI, King D, Zhou W, Seed C, Daly MJ, Neale BM, Finucane H, Bryant S, Satterstrom FK, Band G, Earle SG, Lin SK, Arning N, Koelling N, Armstrong J, Rudkin JK, Callier S, Bryant S, Cusick C, Soranzo N, Zhao JH, Danesh J, Angelantonio ED, Butterworth AS, Sun YV, Huffman JE, Cho K, O’Donnell CJ, Tsao P, Gaziano JM, Peloso G, Ho YL, Smieszek SP, Polymeropoulos C, Polymeropoulos V, Polymeropoulos MH, Przychodzen BP, Fernandez-Cadenas I, Planas AM, Perez-Tur J, Llucià-Carol L, Cullell N, Muiño E, Cárcel-Márquez J, DeDiego ML, Iglesias LL, Soriano A, Rico V, Agüero D, Bedini JL, Lozano F, Domingo C, Robles V, Ruiz-Jaén F, Márquez L, Gomez J, Coto E, Albaiceta GM, García-Clemente M, Dalmau D, Arranz MJ, Dietl B, Serra-Llovich A, Soler P, Colobrán R, Martín-Nalda A, Martínez AP, Bernardo D, Rojo S, Fiz-López A, Arribas E, de la Cal-Sabater P, Segura T, González-Villa E, Serrano-Heras G, Martí-Fàbregas J, Jiménez-Xarrié E, de Felipe Mimbrera A, Masjuan J, García-Madrona S, Domínguez-Mayoral A, Villalonga JM, Menéndez-Valladares P, Chasman DI, Sesso HD, Manson JE, Buring JE, Ridker PM, Franco G, Davis L, Lee S, Priest J, Sankaran VG, van Heel D, Biesecker L, Kerchberger VE, Baillie JK. A first update on mapping the human genetic architecture of COVID-19. Nature 2022; 608:E1-E10. [PMID: 35922517 PMCID: PMC9352569 DOI: 10.1038/s41586-022-04826-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 04/29/2022] [Indexed: 01/04/2023]
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Buchanan CJ, Gaunt B, Harrison PJ, Yang Y, Liu J, Khan A, Giltrap AM, Le Bas A, Ward PN, Gupta K, Dumoux M, Tan TK, Schimaski L, Daga S, Picchiotti N, Baldassarri M, Benetti E, Fallerini C, Fava F, Giliberti A, Koukos PI, Davy MJ, Lakshminarayanan A, Xue X, Papadakis G, Deimel LP, Casablancas-Antràs V, Claridge TDW, Bonvin AMJJ, Sattentau QJ, Furini S, Gori M, Huo J, Owens RJ, Schaffitzel C, Berger I, Renieri A, Naismith JH, Baldwin AJ, Davis BG. Pathogen-sugar interactions revealed by universal saturation transfer analysis. Science 2022; 377:eabm3125. [PMID: 35737812 DOI: 10.1126/science.abm3125] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Many pathogens exploit host cell-surface glycans. However, precise analyses of glycan ligands binding with heavily modified pathogen proteins can be confounded by overlapping sugar signals and/or compounded with known experimental constraints. Universal saturation transfer analysis (uSTA) builds on existing nuclear magnetic resonance spectroscopy to provide an automated workflow for quantitating protein-ligand interactions. uSTA reveals that early-pandemic, B-origin-lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike trimer binds sialoside sugars in an "end-on" manner. uSTA-guided modeling and a high-resolution cryo-electron microscopy structure implicate the spike N-terminal domain (NTD) and confirm end-on binding. This finding rationalizes the effect of NTD mutations that abolish sugar binding in SARS-CoV-2 variants of concern. Together with genetic variance analyses in early pandemic patient cohorts, this binding implicates a sialylated polylactosamine motif found on tetraantennary N-linked glycoproteins deep in the human lung as potentially relevant to virulence and/or zoonosis.
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Affiliation(s)
- Charles J Buchanan
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK.,Kavli Institute of Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Ben Gaunt
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK
| | - Peter J Harrison
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK.,Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire, UK
| | - Yun Yang
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
| | - Jiwei Liu
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK
| | - Aziz Khan
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Andrew M Giltrap
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Audrey Le Bas
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
| | - Philip N Ward
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
| | - Kapil Gupta
- Max Planck Bristol Centre for Minimal Biology, University of Bristol, Bristol, UK
| | - Maud Dumoux
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK
| | - Tiong Kit Tan
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Lisa Schimaski
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Sergio Daga
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Nicola Picchiotti
- Department of Information Engineering and Mathematics, University of Siena, Siena, Italy.,Department of Mathematics, University of Pavia, Pavia, Italy
| | - Margherita Baldassarri
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Elisa Benetti
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Chiara Fallerini
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Francesca Fava
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Annarita Giliberti
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Panagiotis I Koukos
- Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Matthew J Davy
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK
| | - Abirami Lakshminarayanan
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Xiaochao Xue
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK.,Sir William Dunn School of Pathology, Oxford, UK
| | | | | | - Virgínia Casablancas-Antràs
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK.,Kavli Institute of Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | | | - Alexandre M J J Bonvin
- Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | | | - Simone Furini
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Marco Gori
- Department of Information Engineering and Mathematics, University of Siena, Siena, Italy.,Maasai, I3S CNRS, Université Côte d'Azur, Nice, France
| | - Jiandong Huo
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
| | - Raymond J Owens
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
| | - Christiane Schaffitzel
- Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Imre Berger
- Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | | | - James H Naismith
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
| | - Andrew J Baldwin
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK.,Kavli Institute of Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Benjamin G Davis
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Oxford OX11 0FA, UK.,Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK.,Department of Pharmacology, University of Oxford, Oxford OX1 3QT, UK
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15
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Loberti L, Bruno LP, Granata S, Doddato G, Resciniti S, Fava F, Carullo M, Rahikkala E, Jouret G, Menke LA, Lederer D, Vrielynck P, Ryba L, Brunetti-Pierri N, Lasa-Aranzasti A, Cueto-González AM, Trujillano L, Valenzuela I, Tizzano EF, Spinelli AM, Bruno I, Currò A, Stanzial F, Benedicenti F, Lopergolo D, Santorelli FM, Aristidou C, Tanteles GA, Maystadt I, Tkemaladze T, Reimand T, Lokke H, Õunap K, Haanpää MK, Holubová A, Zoubková V, Schwarz M, Žordania R, Muru K, Roht L, Tihveräinen A, Teek R, Thomson U, Atallah I, Superti-Furga A, Buoni S, Canitano R, Scandurra V, Rossetti A, Grosso S, Battini R, Baldassarri M, Mencarelli MA, Rizzo CL, Bruttini M, Mari F, Ariani F, Renieri A, Pinto AM. Natural history of KBG syndrome in a large European cohort. Hum Mol Genet 2022; 31:4131-4142. [PMID: 35861666 PMCID: PMC9759332 DOI: 10.1093/hmg/ddac167] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/22/2022] [Accepted: 07/07/2022] [Indexed: 01/21/2023] Open
Abstract
KBG syndrome (KBGS) is characterized by distinctive facial gestalt, short stature and variable clinical findings. With ageing, some features become more recognizable, allowing a differential diagnosis. We aimed to better characterize natural history of KBGS. In the context of a European collaborative study, we collected the largest cohort of KBGS patients (49). A combined array- based Comparative Genomic Hybridization and next generation sequencing (NGS) approach investigated both genomic Copy Number Variants and SNVs. Intellectual disability (ID) (82%) ranged from mild to moderate with severe ID identified in two patients. Epilepsy was present in 26.5%. Short stature was consistent over time, while occipitofrontal circumference (median value: -0.88 SD at birth) normalized over years. Cerebral anomalies, were identified in 56% of patients and thus represented the second most relevant clinical feature reinforcing clinical suspicion in the paediatric age when short stature and vertebral/dental anomalies are vague. Macrodontia, oligodontia and dental agenesis (53%) were almost as frequent as skeletal anomalies, such as brachydactyly, short fifth finger, fifth finger clinodactyly, pectus excavatum/carinatum, delayed bone age. In 28.5% of individuals, prenatal ultrasound anomalies were reported. Except for three splicing variants, leading to a premature termination, variants were almost all frameshift. Our results, broadening the spectrum of KBGS phenotype progression, provide useful tools to facilitate differential diagnosis and improve clinical management. We suggest to consider a wider range of dental anomalies before excluding diagnosis and to perform a careful odontoiatric/ear-nose-throat (ENT) evaluation in order to look for even submucosal palate cleft given the high percentage of palate abnormalities. NGS approaches, following evidence of antenatal ultrasound anomalies, should include ANKRD11.
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Affiliation(s)
| | | | - Stefania Granata
- Medical Genetics, University of Siena, Siena 53100, Italy,Med Biotech Hub and Competence Centre, Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena 53100, Italy
| | - Gabriella Doddato
- Medical Genetics, University of Siena, Siena 53100, Italy,Med Biotech Hub and Competence Centre, Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy
| | - Sara Resciniti
- Medical Genetics, University of Siena, Siena 53100, Italy,Med Biotech Hub and Competence Centre, Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy
| | - Francesca Fava
- Medical Genetics, University of Siena, Siena 53100, Italy,Med Biotech Hub and Competence Centre, Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena 53100, Italy
| | - Michele Carullo
- Medical Genetics, University of Siena, Siena 53100, Italy,Med Biotech Hub and Competence Centre, Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy
| | - Elisa Rahikkala
- Department of Clinical Genetics, PEDEGO Research Unit, and Medical Research Center Oulu, University of Oulu and Oulu University Hospital, Oulu 90014, Finland
| | - Guillaume Jouret
- National Center of Genetics (NCG), Laboratoire national de santé (LNS), L-3555 Dudelange, Luxembourg
| | - Leonie A Menke
- Amsterdam UMC location University of Amsterdam, Department of Pediatrics, Amsterdam 1100, The Netherlands
| | - Damien Lederer
- Institut de Pathologie et de Génétique; Centre de Génétique Humaine, Gosselies 6041, Belgium
| | - Pascal Vrielynck
- William Lennox Neurological Hospital, Reference Center for Refractory Epilepsy UCLouvain, Ottignies 1340, Belgium
| | - Lukáš Ryba
- Department of Biology and Medical Genetics, Charles University – 2 Faculty of Medicine and University Hospital Motol, Prague 150 00, Czech Republic
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, University of Naples "Federico II", Naples 80125, Italy
| | - Amaia Lasa-Aranzasti
- Area of Clinical and Molecular Genetics, Vall d’Hebron University Hospital, Barcellona 08035, Spain
| | | | - Laura Trujillano
- Area of Clinical and Molecular Genetics, Vall d’Hebron University Hospital, Barcellona 08035, Spain
| | - Irene Valenzuela
- Area of Clinical and Molecular Genetics, Vall d’Hebron University Hospital, Barcellona 08035, Spain
| | - Eduardo F Tizzano
- Area of Clinical and Molecular Genetics, Vall d’Hebron University Hospital, Barcellona 08035, Spain
| | | | - Irene Bruno
- Institute for Maternal and Child Health, Trieste 34100, Italy
| | - Aurora Currò
- Genetic Counseling Service, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano 39100, Italy
| | - Franco Stanzial
- Genetic Counseling Service, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano 39100, Italy
| | - Francesco Benedicenti
- Genetic Counseling Service, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano 39100, Italy
| | - Diego Lopergolo
- IRCCS Stella Maris Foundation, Molecular Medicine for Neurodegenerative and Neuromuscular Disease Unit, Pisa 98125, Italy
| | - Filippo Maria Santorelli
- IRCCS Stella Maris Foundation, Molecular Medicine for Neurodegenerative and Neuromuscular Disease Unit, Pisa 98125, Italy
| | - Constantia Aristidou
- Department of Clinical Genetics and Genomics, The Cyprus Institute of Neurology & Genetics, Nicosia 1683, Cyprus
| | - George A Tanteles
- Department of Clinical Genetics and Genomics, The Cyprus Institute of Neurology & Genetics, Nicosia 1683, Cyprus
| | - Isabelle Maystadt
- Institut de Pathologie et de Génétique; Centre de Génétique Humaine, Gosselies 6041, Belgium
| | - Tinatin Tkemaladze
- Department of Molecular and Medical Genetics, Tbilisi State Medical University, Tbilisi 0162, Georgia
| | - Tiia Reimand
- Department of Clinical Genetics, Genetic and Personalized Medicine Clinic, Tartu University Hospital, Tartu 50406, Estonia,Institute of Clinical Medicine, University of Tartu, Tartu 50406, Estonia
| | - Helen Lokke
- Department of Clinical Genetics, Genetic and Personalized Medicine Clinic, Tartu University Hospital, Tartu 50406, Estonia,Institute of Clinical Medicine, University of Tartu, Tartu 50406, Estonia
| | - Katrin Õunap
- Department of Clinical Genetics, Genetic and Personalized Medicine Clinic, Tartu University Hospital, Tartu 50406, Estonia,Institute of Clinical Medicine, University of Tartu, Tartu 50406, Estonia
| | - Maria K Haanpää
- Department of Genomics and Clinical Genetics, Turku University Hospital, Turku 20500, Finland
| | - Andrea Holubová
- Department of Biology and Medical Genetics, Charles University – 2 Faculty of Medicine and University Hospital Motol, Prague 150 00, Czech Republic
| | - Veronika Zoubková
- Department of Biology and Medical Genetics, Charles University – 2 Faculty of Medicine and University Hospital Motol, Prague 150 00, Czech Republic
| | - Martin Schwarz
- Department of Biology and Medical Genetics, Charles University – 2 Faculty of Medicine and University Hospital Motol, Prague 150 00, Czech Republic
| | - Riina Žordania
- Department of Clinical Genetics, Genetic and Personalized Medicine Clinic, Tartu University Hospital, Tartu 50406, Estonia
| | - Kai Muru
- Department of Clinical Genetics, Genetic and Personalized Medicine Clinic, Tartu University Hospital, Tartu 50406, Estonia,Institute of Clinical Medicine, University of Tartu, Tartu 50406, Estonia
| | - Laura Roht
- Department of Clinical Genetics, Genetic and Personalized Medicine Clinic, Tartu University Hospital, Tartu 50406, Estonia,Institute of Clinical Medicine, University of Tartu, Tartu 50406, Estonia
| | - Annika Tihveräinen
- Department of Child Neurology, Turku University Hospital, Turku 20500, Finland
| | - Rita Teek
- Department of Clinical Genetics, Genetic and Personalized Medicine Clinic, Tartu University Hospital, Tartu 50406, Estonia
| | - Ulvi Thomson
- Centre for Neurological Diseases, West-Tallinn Central Hospital, Tallinn 10617, Estonia
| | - Isis Atallah
- Division of Genetic Medicine, Lausanne University Hospital (CHUV) and University of Lausanne, 1011 Lausanne, Switzerland
| | - Andrea Superti-Furga
- Division of Genetic Medicine, Lausanne University Hospital (CHUV) and University of Lausanne, 1011 Lausanne, Switzerland
| | - Sabrina Buoni
- Division of Child and Adolescent Neuropsychiatry, University of Siena, Siena 53100, Italy
| | - Roberto Canitano
- Division of Child and Adolescent Neuropsychiatry, University of Siena, Siena 53100, Italy
| | - Valeria Scandurra
- Division of Child and Adolescent Neuropsychiatry, University of Siena, Siena 53100, Italy
| | - Annalisa Rossetti
- Clinical Paediatrics, Department of Molecular Medicine and Development, University of Siena, Siena 53100, Italy
| | - Salvatore Grosso
- Clinical Paediatrics, Department of Molecular Medicine and Development, University of Siena, Siena 53100, Italy
| | - Roberta Battini
- IRCCS Stella Maris Foundation, Department of Developmental Neuroscience, Pisa 98125, Italy,Department of Clinical and Experimental Medicine, University of Pisa, Pisa 56122, Italy
| | - Margherita Baldassarri
- Medical Genetics, University of Siena, Siena 53100, Italy,Med Biotech Hub and Competence Centre, Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy
| | | | - Caterina Lo Rizzo
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena 53100, Italy
| | - Mirella Bruttini
- Medical Genetics, University of Siena, Siena 53100, Italy,Med Biotech Hub and Competence Centre, Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena 53100, Italy
| | - Francesca Mari
- Medical Genetics, University of Siena, Siena 53100, Italy,Med Biotech Hub and Competence Centre, Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena 53100, Italy
| | - Francesca Ariani
- Medical Genetics, University of Siena, Siena 53100, Italy,Med Biotech Hub and Competence Centre, Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena 53100, Italy
| | - Alessandra Renieri
- To whom correspondence should be addressed at: Medical Genetics Unit, University of Siena, Policlinico Santa Maria alle Scotte, Viale Bracci, 2, 53100 Siena, Italy. Tel: 39 0577 233303; Fax: 39 0577 233325;
| | - Anna Maria Pinto
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena 53100, Italy
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16
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Cruz R, Almeida SDD, Heredia ML, Quintela I, Ceballos FC, Pita G, Lorenzo-Salazar JM, González-Montelongo R, Gago-Domínguez M, Porras MS, Castaño JAT, Nevado J, Aguado JM, Aguilar C, Aguilera-Albesa S, Almadana V, Almoguera B, Alvarez N, Andreu-Bernabeu Á, Arana-Arri E, Arango C, Arranz MJ, Artiga MJ, Baptista-Rosas RC, Barreda-Sánchez M, Belhassen-Garcia M, Bezerra JF, Bezerra MAC, Boix-Palop L, Brion M, Brugada R, Bustos M, Calderón EJ, Carbonell C, Castano L, Castelao JE, Conde-Vicente R, Cordero-Lorenzana ML, Cortes-Sanchez JL, Corton M, Darnaude MT, De Martino-Rodríguez A, Campo-Pérez V, Bustamante AD, Domínguez-Garrido E, Luchessi AD, Eirós R, Sanabria GME, Fariñas MC, Fernández-Robelo U, Fernández-Rodríguez A, Fernández-Villa T, Gil-Fournier B, Gómez-Arrue J, Álvarez BG, Quirós FGB, González-Peñas J, Gutiérrez-Bautista JF, Herrero MJ, Herrero-Gonzalez A, Jimenez-Sousa MA, Lattig MC, Borja AL, Lopez-Rodriguez R, Mancebo E, Martín-López C, Martín V, Martinez-Nieto O, Martinez-Lopez I, Martinez-Resendez MF, Martinez-Perez Á, Mazzeu JA, Macías EM, Minguez P, Cuerda VM, Silbiger VN, Oliveira SF, Ortega-Paino E, Parellada M, Paz-Artal E, Santos NPC, Pérez-Matute P, Perez P, Pérez-Tomás ME, Perucho T, Pinsach-Abuin ML, Pompa-Mera EN, Porras-Hurtado GL, Pujol A, León SR, Resino S, Fernandes MR, Rodríguez-Ruiz E, Rodriguez-Artalejo F, Rodriguez-Garcia JA, Ruiz-Cabello F, Ruiz-Hornillos J, Ryan P, Soria JM, Souto JC, Tamayo E, Tamayo-Velasco A, Taracido-Fernandez JC, Teper A, Torres-Tobar L, Urioste M, Valencia-Ramos J, Yáñez Z, Zarate R, Nakanishi T, Pigazzini S, Degenhardt F, Butler-Laporte G, Maya-Miles D, Bujanda L, Bouysran Y, Palom A, Ellinghaus D, Martínez-Bueno M, Rolker S, Amitrano S, Roade L, Fava F, Spinner CD, Prati D, Bernardo D, Garcia F, Darcis G, Fernández-Cadenas I, Holter JC, Banales JM, Frithiof R, Duga S, Asselta R, Pereira AC, Romero-Gómez M, Nafría-Jiménez B, Hov JR, Migeotte I, Renieri A, Planas AM, Ludwig KU, Buti M, Rahmouni S, Alarcón-Riquelme ME, Schulte EC, Franke A, Karlsen TH, Valenti L, Zeberg H, Richards B, Ganna A, Boada M, Rojas I, Ruiz A, Sánchez P, Real LM, Guillen-Navarro E, Ayuso C, González-Neira A, Riancho JA, Rojas-Martinez A, Flores C, Lapunzina P, Carracedo Á. Novel genes and sex differences in COVID-19 severity. Hum Mol Genet 2022; 31:3789-3806. [PMID: 35708486 DOI: 10.1093/hmg/ddac132] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/16/2022] [Accepted: 06/01/2022] [Indexed: 01/08/2023] Open
Abstract
Here we describe the results of a genome-wide study conducted in 11 939 COVID-19 positive cases with an extensive clinical information that were recruited from 34 hospitals across Spain (SCOURGE consortium). In sex-disaggregated genome-wide association studies for COVID-19 hospitalization, genome-wide significance (p < 5x10-8) was crossed for variants in 3p21.31 and 21q22.11 loci only among males (p = 1.3x10-22 and p = 8.1x10-12, respectively), and for variants in 9q21.32 near TLE1 only among females (p = 4.4x10-8). In a second phase, results were combined with an independent Spanish cohort (1598 COVID-19 cases and 1068 population controls), revealing in the overall analysis two novel risk loci in 9p13.3 and 19q13.12, with fine-mapping prioritized variants functionally associated with AQP3 (p = 2.7x10-8) and ARHGAP33 (p = 1.3x10-8), respectively. The meta-analysis of both phases with four European studies stratified by sex from the Host Genetics Initiative confirmed the association of the 3p21.31 and 21q22.11 loci predominantly in males and replicated a recently reported variant in 11p13 (ELF5, p = 4.1x10-8). Six of the COVID-19 HGI discovered loci were replicated and an HGI-based genetic risk score predicted the severity strata in SCOURGE. We also found more SNP-heritability and larger heritability differences by age (<60 or ≥ 60 years) among males than among females. Parallel genome-wide screening of inbreeding depression in SCOURGE also showed an effect of homozygosity in COVID-19 hospitalization and severity and this effect was stronger among older males. In summary, new candidate genes for COVID-19 severity and evidence supporting genetic disparities among sexes are provided.
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Affiliation(s)
- Raquel Cruz
- Centro Nacional de Genotipado (CEGEN), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain.,Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Silvia Diz-de Almeida
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Miguel López Heredia
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Inés Quintela
- Centro Nacional de Genotipado (CEGEN), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Francisco C Ceballos
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Guillermo Pita
- Human Genotyping-CEGEN Unit, Spanish National Cancer Research Centre, Madrid, Spain
| | - José M Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
| | | | - Manuela Gago-Domínguez
- Fundación Pública Galega de Medicina Xenómica, Sistema Galego de Saúde (SERGAS), Santiago de Compostela, Spain.,Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
| | - Marta Sevilla Porras
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz-IDIPAZ, Madrid, Spain
| | - Jair Antonio Tenorio Castaño
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz-IDIPAZ, Madrid, Spain.,ERN-ITHACA-European Reference Network
| | - Julian Nevado
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz-IDIPAZ, Madrid, Spain.,ERN-ITHACA-European Reference Network
| | - Jose María Aguado
- Unit of Infectious Diseases, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI RD16/0016/0002), Instituto de Salud Carlos III, Madrid, Spain.,School of Medicine, Universidad Complutense, Madrid, Spain.,Centre for Biomedical Network Research on Infectious Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Sergio Aguilera-Albesa
- Pediatric Neurology Unit, Department of Pediatrics, Navarra Health Service Hospital, Pamplona, Spain.,Navarra Health Service, Navarra BioMed Research Group, Pamplona, Spain
| | | | - Berta Almoguera
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital - Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Nuria Alvarez
- Human Genotyping-CEGEN Unit, Spanish National Cancer Research Centre, Madrid, Spain
| | - Álvaro Andreu-Bernabeu
- Spanish Network for Research in Infectious Diseases (REIPI RD16/0016/0002), Instituto de Salud Carlos III, Madrid, Spain.,Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón (IiSGM), Madrid, Spain
| | - Eunate Arana-Arri
- Biocruces Bizkai HRI, Bizkaia, Spain.,Cruces University Hospital, Osakidetza, Bizkaia, Spain
| | - Celso Arango
- School of Medicine, Universidad Complutense, Madrid, Spain.,Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón (IiSGM), Madrid, Spain.,Centre for Biomedical Network Research on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
| | - María J Arranz
- Fundació Docència I Recerca Mutua Terrassa, Barcelona, Spain
| | | | - Raúl C Baptista-Rosas
- Hospital General de Occidente, Zapopan Jalisco, Mexico.,Centro Universitario de Tonalá, Universidad de Guadalajara, Tonalá Jalisco, Mexico.,Centro de Investigación Multidisciplinario en Salud, Universidad de Guadalajara, Tonalá Jalisco, Mexico
| | - María Barreda-Sánchez
- Instituto Murciano de Investigación Biosanitaria (IMIB-Arrixaca), Murcia, Spain.,Universidad Católica San Antonio de Murcia (UCAM), Murcia, Spain
| | - Moncef Belhassen-Garcia
- Servicio de Medicina Interna-Unidad de Enfermedades Infecciosas, Hospital Universitario de Salamanca-IBSAL, Salamanca, Spain.,Universidad de Salamanca, Salamanca, Spain
| | - Joao F Bezerra
- Escola Tecnica de Saúde, Laboratorio de Vigilancia Molecular Aplicada, Brazil
| | - Marcos A C Bezerra
- Genetics Postgraduate Program, Federal University of Pernambuco, Recife, PE, Brazil
| | | | - María Brion
- Xenética Cardiovascular, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain.,Centre for Biomedical Network Research on Cardiovascular Diseases (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain
| | - Ramón Brugada
- Centre for Biomedical Network Research on Cardiovascular Diseases (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain.,Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona (IDIBGI), Girona, Spain.,Medical Science Department, School of Medicine, University of Girona, Girona, Spain.,Cardiology Service, Hospital Josep Trueta, Girona, Spain
| | - Matilde Bustos
- Institute of Biomedicine of Seville (IBiS), Consejo Superior de Investigaciones Científicas (CSIC)- University of Seville- Virgen del Rocio University Hospital, Seville, Spain
| | - Enrique J Calderón
- Departemento de Medicina, Hospital Universitario Virgen del Rocío, Universidad de Sevilla, Seville, Spain.,Centre for Biomedical Network Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Biomedicina de Sevilla, Seville, Spain
| | - Cristina Carbonell
- Universidad de Salamanca, Salamanca, Spain.,Servicio de Medicina Interna, Hospital Universitario de Salamanca-IBSAL, Salamanca, Spain
| | - Luis Castano
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Biocruces Bizkai HRI, Bizkaia, Spain.,Osakidetza, Cruces University Hospital, Bizkaia, Spain.,Centre for Biomedical Network Research on Diabetes and Metabolic Associated Diseases (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain.,University of Pais Vasco, UPV/EHU, Bizkaia, Spain
| | - Jose E Castelao
- Oncology and Genetics Unit, Instituto de Investigacion Sanitaria Galicia Sur, Xerencia de Xestion Integrada de Vigo-Servizo Galego de Saúde, Vigo, Spain
| | | | - M Lourdes Cordero-Lorenzana
- Servicio de Medicina intensiva, Complejo Hospitalario Universitario de A Coruña (CHUAC), Sistema Galego de Saúde (SERGAS), A Coruña, Spain
| | - Jose L Cortes-Sanchez
- Tecnológico de Monterrey, Monterrey, Mexico.,Departament of Microgravity and Translational Regenerative Medicine, Otto von Guericke University, Magdeburg, Germany
| | - Marta Corton
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital - Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | | | - Alba De Martino-Rodríguez
- Instituto Aragonés de Ciencias de la Salud (IACS), Zaragoza, Spain.,Instituto Investigación Sanitaria Aragón (IIS-Aragon), Zaragoza, Spain
| | - Victor Campo-Pérez
- Preventive Medicine Department, Instituto de Investigacion Sanitaria Galicia Sur, Xerencia de Xestion Integrada de Vigo-Servizo Galego de Saúde, Vigo, Spain
| | | | | | - Andre D Luchessi
- Departamento de Analises Clinicas e Toxicologicas, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Rocío Eirós
- Servicio de Cardiología, Hospital Universitario de Salamanca-IBSAL, Salamanca, Spain
| | | | - María Carmen Fariñas
- IDIVAL, Cantabria, Spain.,Universidad de Cantabria, Cantabria, Spain.,Hospital U M Valdecilla, Cantabria, Spain
| | - Uxía Fernández-Robelo
- Urgencias Hospitalarias, Complejo Hospitalario Universitario de A Coruña (CHUAC), Sistema Galego de Saúde (SERGAS), A Coruña, Spain
| | - Amanda Fernández-Rodríguez
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Tania Fernández-Villa
- Grupo de Investigación en Interacciones Gen-Ambiente y Salud (GIIGAS) - Instituto de Biomedicina (IBIOMED), Universidad de León, León, Spain
| | | | - Javier Gómez-Arrue
- Instituto Aragonés de Ciencias de la Salud (IACS), Zaragoza, Spain.,Instituto Investigación Sanitaria Aragón (IIS-Aragon), Zaragoza, Spain
| | - Beatriz González Álvarez
- Instituto Aragonés de Ciencias de la Salud (IACS), Zaragoza, Spain.,Instituto Investigación Sanitaria Aragón (IIS-Aragon), Zaragoza, Spain
| | | | - Javier González-Peñas
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón (IiSGM), Madrid, Spain.,School of Medicine, Universidad Complutense, Madrid, Spain.,Centre for Biomedical Network Research on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
| | - Juan F Gutiérrez-Bautista
- Servicio de Análisis Clínicos e Inmunología, Hospital Universitario Virgen de las Nieves, Granada, Spain
| | - María José Herrero
- Plataforma de Farmacogenética, IIS La Fe, Valencia, Spain.,Departamento de Farmacología, Universidad de Valencia, Valencia, Spain
| | - Antonio Herrero-Gonzalez
- Data Analysis Department, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital - Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - María A Jimenez-Sousa
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - María Claudia Lattig
- Facultad de Ciencias, Universidad de los Andes, Bogotá, Colombia.,SIGEN Alianza Universidad de los Andes - Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | | | - Rosario Lopez-Rodriguez
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital - Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Esther Mancebo
- Department of Immunology, Hospital Universitario 12 de Octubre, Madrid, Spain.,Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Transplant Immunology and Immunodeficiencies Group, Madrid, Spain
| | | | - Vicente Martín
- Centre for Biomedical Network Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Biomedicina (IBIOMED), Universidad de León, León, Spain
| | - Oscar Martinez-Nieto
- SIGEN Alianza Universidad de los Andes - Fundación Santa Fe de Bogotá, Bogotá, Colombia.,Departamento Patologia y Laboratorios, Fundación Santa Fe de Bogota, Bogotá, Colombia
| | - Iciar Martinez-Lopez
- Unidad de Genética y Genómica Islas Baleares, Islas Baleares, Spain.,Unidad de Diagnóstico Molecular y Genética Clínica, Hospital Universitario Son Espases, Islas Baleares, Spain
| | | | - Ángel Martinez-Perez
- Genomics of Complex Diseases Unit, Research Institute of Hospital de la Santa Creu i Sant Pau, IIB Sant Pau, Barcelona, Spain
| | - Juliana A Mazzeu
- Faculdade de Medicina, Universidade de Brasília, Brazil.,Programa de Pós-Graduação em Ciências Médicas (UnB), Brazil.,Programa de Pós-Graduação em Ciencias da Saude (UnB), Brazil
| | | | - Pablo Minguez
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital - Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Victor Moreno Cuerda
- Medicina Interna, Hospital Universitario Mostoles, Madrid, Spain.,Universidad Francisco de Vitoria, Madrid, Spain
| | - Vivian N Silbiger
- Departamento de Analises Clinicas e Toxicologicas, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Silviene F Oliveira
- Programa de Pós-Graduação em Ciencias da Saude (UnB), Brazil.,Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brazil.,Programa de Pós-Graduação em Biologia Animal (UnB), Brazil.,Programa de Pós-Graduação Profissional em Ensino de Biologia (UnB), Brazil
| | - Eva Ortega-Paino
- Spanish National Cancer Research Center, CNIO Biobank, Madrid, Spain
| | - Mara Parellada
- School of Medicine, Universidad Complutense, Madrid, Spain.,Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón (IiSGM), Madrid, Spain.,Centre for Biomedical Network Research on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
| | - Estela Paz-Artal
- Department of Immunology, Hospital Universitario 12 de Octubre, Madrid, Spain.,Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Transplant Immunology and Immunodeficiencies Group, Madrid, Spain.,Department of Immunology, Ophthalmology and ENT, Universidad Complutense de Madrid, Madrid, Spain
| | - Ney P C Santos
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Patricia Pérez-Matute
- Infectious Diseases, Microbiota and Metabolism Unit, Center for Biomedical Research of La Rioja (CIBIR), Logroño, Spain
| | | | - M Elena Pérez-Tomás
- Instituto Murciano de Investigación Biosanitaria (IMIB-Arrixaca), Murcia, Spain
| | | | - Mel Lina Pinsach-Abuin
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica Girona (IDIBGI), Girona, Spain.,Centre for Biomedical Network Research on Cardiovascular Diseases (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain
| | - Ericka N Pompa-Mera
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Instituto Mexicano del Seguro Social (IMSS), Centro Médico Nacional Siglo XXI, Mexico City, Mexico
| | | | - Aurora Pujol
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Bellvitge Biomedical Research Institute (IDIBELL), Neurometabolic Diseases Laboratory, L'Hospitalet de Llobregat, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
| | | | - Salvador Resino
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Marianne R Fernandes
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, Pará, Brazil.,Departamento de Ensino e Pesquisa, Hospital Ophir Loyola, Belém, Pará, Brazil
| | - Emilio Rodríguez-Ruiz
- Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain.,Unidad de Cuidados Intensivos, Hospital Clínico Universitario de Santiago (CHUS), Sistema Galego de Saúde (SERGAS), Santiago de Compostela, Spain
| | - Fernando Rodriguez-Artalejo
- Centre for Biomedical Network Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,Department of Preventive Medicine and Public Health, School of Medicine, Universidad Autónoma de Madrid, Madrid, Spain.,IdiPaz (Instituto de Investigación Sanitaria Hospital Universitario La Paz), Madrid, Spain.,IMDEA-Food Institute, CEI UAM+CSIC, Madrid, Spain
| | | | - Francisco Ruiz-Cabello
- Servicio de Análisis Clínicos e Inmunología, Hospital Universitario Virgen de las Nieves, Granada, Spain.,Instituto de Investigación Biosanitaria de Granada (ibs GRANADA), Granada, Spain.,Departamento Bioquímica, Biología Molecular e Inmunología III, Universidad de Granada, Granada, Spain
| | - Javier Ruiz-Hornillos
- Allergy Unit, Valdemoro, Hospital Infanta Elena, Madrid, Spain.,Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital - Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Faculty of Medicine, Universidad Francisco de Vitoria, Madrid, Spain
| | - Pablo Ryan
- Hospital Universitario Infanta Leonor, Madrid, Spain.,Complutense University of Madrid, Madrid, Spain.,Gregorio Marañón Health Research Institute (IiSGM), Madrid, Spain
| | - José Manuel Soria
- Genomics of Complex Diseases Unit, Research Institute of Hospital de la Santa Creu i Sant Pau, IIB Sant Pau, Barcelona, Spain
| | - Juan Carlos Souto
- Haemostasis and Thrombosis Unit, Hospital de la Santa Creu i Sant Pau, IIB Sant Pau, Barcelona, Spain
| | - Eduardo Tamayo
- Servicio de Anestesiologia y Reanimación, Hospital Clinico Universitario de Valladolid, Valladolid, Spain.,Departamento de Cirugía, Universidad de Valladolid, Valladolid, Spain
| | - Alvaro Tamayo-Velasco
- Servicio de Hematologia y Hemoterapia, Hospital Clinico Universitario de Valladolid, Valladolid, Spain
| | - Juan Carlos Taracido-Fernandez
- Data Analysis Department, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital - Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Alejandro Teper
- Hospital de Niños Ricardo Gutierrez, Buenos Aires, Argentina
| | | | - Miguel Urioste
- Familial Cancer Clinical Unit, Spanish National Cancer Research Centre, Madrid, Spain
| | | | - Zuleima Yáñez
- Facultad de Ciencias de la Salud, Universidad Simón Bolívar, Barranquilla, Colombia
| | - Ruth Zarate
- Centro para el Desarrollo de la Investigación Científica, Paraguay
| | - Tomoko Nakanishi
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Finland.,Department of Human Genetics, McGill University, Montréal, Québec, Canada.,Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada.,Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Research Fellow, Japan Society for the Promotion of Science, Japan
| | - Sara Pigazzini
- University of Milano-Bicocca, Milano, Italy.,Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Frauke Degenhardt
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany.,University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Guillaume Butler-Laporte
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada.,Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
| | - Douglas Maya-Miles
- Digestive Diseases Unit, Virgen del Rocio University Hospital, Institute of Biomedicine of Seville, University of Seville, Seville, Spain.,Centre for Biomedical Network Research on Hepatic and Digestive Diseases (CIBEREHD), Instituto de Salud Carlos III, Madrid, Spain
| | - Luis Bujanda
- Centre for Biomedical Network Research on Hepatic and Digestive Diseases (CIBEREHD), Instituto de Salud Carlos III, Madrid, Spain.,Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute - Donostia University Hospital, University of the Basque Country (UPV/EHU), San Sebastian, Spain
| | - Youssef Bouysran
- Centre de Génétique Humaine, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Adriana Palom
- Liver Unit, Department of Internal Medicine, Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.,Departament de Medicina, Universitat Autònoma de Barcelona, Bellatera, Barcelona, Spain.,Liver Diseases, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany.,Novo Nordisk Foundation Center for Protein Research, Disease Systems Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Manuel Martínez-Bueno
- GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain
| | - Selina Rolker
- Institute of Human Genetics, University Hospital Bonn, Medical Faculty University of Bonn, Bonn, Germany
| | - Sara Amitrano
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Italy
| | - Luisa Roade
- Centre for Biomedical Network Research on Hepatic and Digestive Diseases (CIBEREHD), Instituto de Salud Carlos III, Madrid, Spain.,Liver Unit, Department of Internal Medicine, Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.,Universitat Autònoma de Barcelona, Departament de Medicina, Bellatera, Barcelona, Spain
| | - Francesca Fava
- Medical Genetics, University of Siena, Italy.,Azienda Ospedaliero-Universitaria Senese, Genetica Medica, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy
| | - Christoph D Spinner
- Technical University of Munich, School of Medicine, University Hospital rechts der Isar, Department of Internal Medicine II, Munich, Germany
| | - Daniele Prati
- Department of Transfusion Medicine and Hematology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milano, Italy
| | - David Bernardo
- Centre for Biomedical Network Research on Hepatic and Digestive Diseases (CIBEREHD), Instituto de Salud Carlos III, Madrid, Spain.,Mucosal Immunology Lab, Unidad de Excelencia del Instituto de Biomedicina y Genética Molecular (IBGM, Universidad de Valladolid-CSIC), Valladolid, Spain
| | - Federico Garcia
- Hospital Universitario Clinico San Cecilio, Granada, Spain.,Instituto de Investigación Ibs.Granada, Granada, Spain
| | - Gilles Darcis
- University of Liege. GIGA-Insitute, Liege, Belgium.,Liege University Hospital (CHU of Liege), Liege, Belgium
| | - Israel Fernández-Cadenas
- Biomedical Research Institute Sant Pau (IIB Sant Pau), Stroke Pharmacogenomics and Genetics Group, Barcelona, Spain
| | - Jan Cato Holter
- Department of Microbiology, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Jesus M Banales
- Centre for Biomedical Network Research on Hepatic and Digestive Diseases (CIBEREHD), Instituto de Salud Carlos III, Madrid, Spain.,Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute - Donostia University Hospital, University of the Basque Country (UPV/EHU), Ikerbasque, San Sebastian, Spain
| | - Robert Frithiof
- Department of Surgical Sciences, Anaesthesiology and Intensive Care Medicine, Uppsala University, Uppsala, Sweden
| | - Stefano Duga
- Department of Biomedical Sciences, Humanitas University, Milan, Italy.,IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Milan, Italy.,IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | | | - Manuel Romero-Gómez
- Digestive Diseases Unit, Virgen del Rocio University Hospital, Institute of Biomedicine of Seville, University of Seville, Seville, Spain.,Centre for Biomedical Network Research on Hepatic and Digestive Diseases (CIBEREHD), Instituto de Salud Carlos III, Madrid, Spain
| | - Beatriz Nafría-Jiménez
- Osakidetza Basque Health Service, Donostialdea Integrated Health Organisation, Clinical Biochemistry Department, San Sebastian, Spain
| | - Johannes R Hov
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Norwegian PSC Research Center and Section of Gastroenterology, Dept Transplantation Medicine, Oslo University Hospital, Oslo, Norway.,Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway
| | - Isabelle Migeotte
- Centre de Génétique Humaine, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium.,Fonds de la Recherche Scientifique (FNRS)
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Italy.,Azienda Ospedaliero-Universitaria Senese, Genetica Medica, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy
| | - Anna M Planas
- Institute for Biomedical Researhc of Barcelona (IIBB), National Spanish Research Council (CSIC), Barcelona, Spain.,Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Kerstin U Ludwig
- Institute of Human Genetics, University Hospital Bonn, Medical Faculty University of Bonn, Bonn, Germany
| | - Maria Buti
- Centre for Biomedical Network Research on Hepatic and Digestive Diseases (CIBEREHD), Instituto de Salud Carlos III, Madrid, Spain.,Liver Unit, Department of Internal Medicine, Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.,Universitat Autònoma de Barcelona, Departament de Medicina, Bellatera, Barcelona, Spain
| | | | - Marta E Alarcón-Riquelme
- GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain.,Institute for Environmental Medicine, Karolinska Institutet, Solna, Sweden
| | - Eva C Schulte
- Institute of Virology, Technical University Munich/Helmholtz Zentrum München, Munich, Germany.,Institute of Psychiatric Phenomics and Genomics, University Hospital, LMU Munich University, Munich, Germany.,Department of Psychiatry, University Hospital, LMU Munich University, Munich, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany.,University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Tom H Karlsen
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Norwegian PSC Research Center and Section of Gastroenterology, Dept Transplantation Medicine, Oslo University Hospital, Oslo, Norway.,Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway
| | - Luca Valenti
- Department of Pathopgysiology and Transplantation, Università degli Studi di Milano, Milano, Italy.,Department of Transfusion Medicine and Hematology, Precision Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Hugo Zeberg
- Department of Neuroscience, Karolinska Institutet, Sweden.,Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Brent Richards
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada.,Department of Human Genetics, Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada.,King's College London, Department of Twin Research, London, United Kingdom
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland.,Massachusetts General Hospital, Harvard Medical School, Boston, USA
| | - Mercè Boada
- Research Center and Memory clinic, ACE Alzheimer Center Barcelona, Universitat Internacional de Catalunya, Spain.,Centre for Biomedical Network Research on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Itziar Rojas
- Research Center and Memory clinic, ACE Alzheimer Center Barcelona, Universitat Internacional de Catalunya, Spain.,Centre for Biomedical Network Research on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Agustín Ruiz
- Research Center and Memory clinic, ACE Alzheimer Center Barcelona, Universitat Internacional de Catalunya, Spain.,Centre for Biomedical Network Research on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Pascual Sánchez
- CIEN Foundation/Queen Sofia Foundation Alzheimer Center, Madrid, Spain
| | - Luis Miguel Real
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario de Valme, Sevilla, Spain
| | | | | | | | - Encarna Guillen-Navarro
- Instituto Murciano de Investigación Biosanitaria (IMIB-Arrixaca), Murcia, Spain.,Sección Genética Médica - Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, Servicio Murciano de Salud, Murcia, Spain.,Departamento Cirugía, Pediatría, Obstetricia y Ginecología, Facultad de Medicina, Universidad de Murcia (UMU), Murcia, Spain.,Grupo Clínico Vinculado, Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Ayuso
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital - Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Anna González-Neira
- Human Genotyping-CEGEN Unit, Spanish National Cancer Research Centre, Madrid, Spain
| | - José A Riancho
- IDIVAL, Cantabria, Spain.,Universidad de Cantabria, Cantabria, Spain.,Hospital U M Valdecilla, Cantabria, Spain
| | | | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain.,Research Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain.,Centre for Biomedical Network Research on Respiratory Diseases (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Pablo Lapunzina
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz-IDIPAZ, Madrid, Spain.,ERN-ITHACA-European Reference Network
| | - Ángel Carracedo
- Centro Nacional de Genotipado (CEGEN), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Fundación Pública Galega de Medicina Xenómica, Sistema Galego de Saúde (SERGAS), Santiago de Compostela, Spain.,Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain.,Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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17
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Zguro K, Baldassarri M, Fava F, Beligni G, Daga S, Leoncini R, Galasso L, Cirianni M, Rusconi S, Siano M, Francisci D, Schiaroli E, Luchi S, Morelli G, Martinelli E, Girardis M, Busani S, Parisi SG, Panese S, Piscopo C, Capasso M, Tacconi D, Spertilli Raffaelli C, Giliberti A, Gori G, Katsikis PD, Lorubbio M, Calzoni P, Ognibene A, Bocchia M, Tozzi M, Bucalossi A, Marotta G, Furini S, Renieri A, Fallerini C. Carriers of ADAMTS13 Rare Variants Are at High Risk of Life-Threatening COVID-19. Viruses 2022; 14:v14061185. [PMID: 35746657 PMCID: PMC9227269 DOI: 10.3390/v14061185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/25/2022] [Accepted: 05/25/2022] [Indexed: 01/08/2023] Open
Abstract
Thrombosis of small and large vessels is reported as a key player in COVID-19 severity. However, host genetic determinants of this susceptibility are still unclear. Congenital Thrombotic Thrombocytopenic Purpura is a severe autosomal recessive disorder characterized by uncleaved ultra-large vWF and thrombotic microangiopathy, frequently triggered by infections. Carriers are reported to be asymptomatic. Exome analysis of about 3000 SARS-CoV-2 infected subjects of different severities, belonging to the GEN-COVID cohort, revealed the specific role of vWF cleaving enzyme ADAMTS13 (A disintegrin-like and metalloprotease with thrombospondin type 1 motif, 13). We report here that ultra-rare variants in a heterozygous state lead to a rare form of COVID-19 characterized by hyper-inflammation signs, which segregates in families as an autosomal dominant disorder conditioned by SARS-CoV-2 infection, sex, and age. This has clinical relevance due to the availability of drugs such as Caplacizumab, which inhibits vWF–platelet interaction, and Crizanlizumab, which, by inhibiting P-selectin binding to its ligands, prevents leukocyte recruitment and platelet aggregation at the site of vascular damage.
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Affiliation(s)
- Kristina Zguro
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (K.Z.); (M.B.); (F.F.); (G.B.); (S.D.); (S.F.); (C.F.)
| | - Margherita Baldassarri
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (K.Z.); (M.B.); (F.F.); (G.B.); (S.D.); (S.F.); (C.F.)
- Medical Genetics, University of Siena, 53100 Siena, Italy
| | - Francesca Fava
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (K.Z.); (M.B.); (F.F.); (G.B.); (S.D.); (S.F.); (C.F.)
- Medical Genetics, University of Siena, 53100 Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, 53100 Siena, Italy
| | - Giada Beligni
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (K.Z.); (M.B.); (F.F.); (G.B.); (S.D.); (S.F.); (C.F.)
- Medical Genetics, University of Siena, 53100 Siena, Italy
| | - Sergio Daga
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (K.Z.); (M.B.); (F.F.); (G.B.); (S.D.); (S.F.); (C.F.)
- Medical Genetics, University of Siena, 53100 Siena, Italy
| | - Roberto Leoncini
- Laboratorio Patologia Clinica, Azienda Ospedaliero-Universitaria Senese, 53100 Siena, Italy; (R.L.); (L.G.); (M.C.); (P.C.)
| | - Lucrezia Galasso
- Laboratorio Patologia Clinica, Azienda Ospedaliero-Universitaria Senese, 53100 Siena, Italy; (R.L.); (L.G.); (M.C.); (P.C.)
| | - Michele Cirianni
- Laboratorio Patologia Clinica, Azienda Ospedaliero-Universitaria Senese, 53100 Siena, Italy; (R.L.); (L.G.); (M.C.); (P.C.)
| | - Stefano Rusconi
- Infectious Diseases Unit, ASST Ovest Milanese, 20025 Legnano, Italy;
- Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, 20157 Milan, Italy;
| | - Matteo Siano
- Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, 20157 Milan, Italy;
| | - Daniela Francisci
- Infectious Diseases Clinic, “Santa Maria della Misericordia” Hospital, University of Perugia, 06124 Perugia, Italy; (D.F.); (E.S.)
| | - Elisabetta Schiaroli
- Infectious Diseases Clinic, “Santa Maria della Misericordia” Hospital, University of Perugia, 06124 Perugia, Italy; (D.F.); (E.S.)
| | - Sauro Luchi
- Infectious Disease Unit, Hospital of Lucca, 55100 Lucca, Italy; (S.L.); (G.M.)
| | - Giovanna Morelli
- Infectious Disease Unit, Hospital of Lucca, 55100 Lucca, Italy; (S.L.); (G.M.)
| | - Enrico Martinelli
- Department of Respiratory Diseases, Azienda Ospedaliera di Cremona, 26100 Cremona, Italy;
| | - Massimo Girardis
- Department of Anesthesia and Intensive Care, University of Modena and Reggio Emilia, 41124 Modena, Italy; (M.G.); (S.B.)
| | - Stefano Busani
- Department of Anesthesia and Intensive Care, University of Modena and Reggio Emilia, 41124 Modena, Italy; (M.G.); (S.B.)
| | | | - Sandro Panese
- Clinical Infectious Diseases, Mestre Hospital, 30171 Venezia, Italy;
| | - Carmelo Piscopo
- Medical Genetics and Laboratory Genetics Unit, “Antonio Cardarelli” hospital, 80131 Naples, Italy;
| | - Mario Capasso
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80138 Naples, Italy;
- CEINGE Biotecnologie Avanzate, 80145 Naples, Italy
| | - Danilo Tacconi
- Department of Specialized and Internal Medicine, Infectious Diseases Unit, San Donato Hospital Arezzo, 52100 Arezzo, Italy; (D.T.); (C.S.R.)
| | - Chiara Spertilli Raffaelli
- Department of Specialized and Internal Medicine, Infectious Diseases Unit, San Donato Hospital Arezzo, 52100 Arezzo, Italy; (D.T.); (C.S.R.)
| | - Annarita Giliberti
- Medical Genetics Unit, Meyer Children’s University Hospital, 50134 Florence, Italy; (A.G.); (G.G.)
| | - Giulia Gori
- Medical Genetics Unit, Meyer Children’s University Hospital, 50134 Florence, Italy; (A.G.); (G.G.)
| | - Peter D. Katsikis
- Department of Immunology, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands;
| | - Maria Lorubbio
- UOC Laboratorio Analisi Chimico Cliniche, 52100 Arezzo, Italy; (M.L.); (A.O.)
| | - Paola Calzoni
- Laboratorio Patologia Clinica, Azienda Ospedaliero-Universitaria Senese, 53100 Siena, Italy; (R.L.); (L.G.); (M.C.); (P.C.)
| | - Agostino Ognibene
- UOC Laboratorio Analisi Chimico Cliniche, 52100 Arezzo, Italy; (M.L.); (A.O.)
| | - Monica Bocchia
- Hematology Unit, Department of Medical Science, Surgery and Neuroscience, University of Siena, 53100 Siena, Italy;
| | - Monica Tozzi
- Stem Cell Transplant and Cellular Therapy Unit, University Hospital of Siena, 53100 Siena, Italy; (M.T.); (A.B.); (G.M.)
| | - Alessandro Bucalossi
- Stem Cell Transplant and Cellular Therapy Unit, University Hospital of Siena, 53100 Siena, Italy; (M.T.); (A.B.); (G.M.)
| | - Giuseppe Marotta
- Stem Cell Transplant and Cellular Therapy Unit, University Hospital of Siena, 53100 Siena, Italy; (M.T.); (A.B.); (G.M.)
| | - Simone Furini
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (K.Z.); (M.B.); (F.F.); (G.B.); (S.D.); (S.F.); (C.F.)
| | | | - Alessandra Renieri
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (K.Z.); (M.B.); (F.F.); (G.B.); (S.D.); (S.F.); (C.F.)
- Medical Genetics, University of Siena, 53100 Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, 53100 Siena, Italy
- Correspondence:
| | - Chiara Fallerini
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (K.Z.); (M.B.); (F.F.); (G.B.); (S.D.); (S.F.); (C.F.)
- Medical Genetics, University of Siena, 53100 Siena, Italy
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18
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Fallerini C, Picchiotti N, Baldassarri M, Zguro K, Daga S, Fava F, Benetti E, Amitrano S, Bruttini M, Palmieri M, Croci S, Lista M, Beligni G, Valentino F, Meloni I, Tanfoni M, Minnai F, Colombo F, Cabri E, Fratelli M, Gabbi C, Mantovani S, Frullanti E, Gori M, Crawley FP, Butler-Laporte G, Richards B, Zeberg H, Lipcsey M, Hultström M, Ludwig KU, Schulte EC, Pairo-Castineira E, Baillie JK, Schmidt A, Frithiof R, Mari F, Renieri A, Furini S. Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severity. Hum Genet 2022; 141:147-173. [PMID: 34889978 PMCID: PMC8661833 DOI: 10.1007/s00439-021-02397-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/26/2021] [Indexed: 12/13/2022]
Abstract
The combined impact of common and rare exonic variants in COVID-19 host genetics is currently insufficiently understood. Here, common and rare variants from whole-exome sequencing data of about 4000 SARS-CoV-2-positive individuals were used to define an interpretable machine-learning model for predicting COVID-19 severity. First, variants were converted into separate sets of Boolean features, depending on the absence or the presence of variants in each gene. An ensemble of LASSO logistic regression models was used to identify the most informative Boolean features with respect to the genetic bases of severity. The Boolean features selected by these logistic models were combined into an Integrated PolyGenic Score that offers a synthetic and interpretable index for describing the contribution of host genetics in COVID-19 severity, as demonstrated through testing in several independent cohorts. Selected features belong to ultra-rare, rare, low-frequency, and common variants, including those in linkage disequilibrium with known GWAS loci. Noteworthily, around one quarter of the selected genes are sex-specific. Pathway analysis of the selected genes associated with COVID-19 severity reflected the multi-organ nature of the disease. The proposed model might provide useful information for developing diagnostics and therapeutics, while also being able to guide bedside disease management.
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Affiliation(s)
- Chiara Fallerini
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy
| | - Nicola Picchiotti
- grid.9024.f0000 0004 1757 4641University of Siena, DIISM-SAILAB, Siena, Italy ,grid.8982.b0000 0004 1762 5736Department of Mathematics, University of Pavia, Pavia, Italy
| | - Margherita Baldassarri
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy
| | - Kristina Zguro
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
| | - Sergio Daga
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy
| | - Francesca Fava
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy ,grid.411477.00000 0004 1759 0844Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Elisa Benetti
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
| | - Sara Amitrano
- grid.411477.00000 0004 1759 0844Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Mirella Bruttini
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy ,grid.411477.00000 0004 1759 0844Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Maria Palmieri
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy
| | - Susanna Croci
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy
| | - Mirjam Lista
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy
| | - Giada Beligni
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy
| | - Floriana Valentino
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy
| | - Ilaria Meloni
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy
| | - Marco Tanfoni
- grid.9024.f0000 0004 1757 4641University of Siena, DIISM-SAILAB, Siena, Italy
| | - Francesca Minnai
- grid.429135.80000 0004 1756 2536Istituto di Tecnologie Biomediche-Consiglio Nazionale delle Ricerche, Segrate, MI Italy
| | - Francesca Colombo
- grid.429135.80000 0004 1756 2536Istituto di Tecnologie Biomediche-Consiglio Nazionale delle Ricerche, Segrate, MI Italy
| | - Enrico Cabri
- grid.4527.40000000106678902Pharmacogenomics Unit, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Maddalena Fratelli
- grid.4527.40000000106678902Pharmacogenomics Unit, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Chiara Gabbi
- grid.4714.60000 0004 1937 0626Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Stefania Mantovani
- grid.419425.f0000 0004 1760 3027Department of Medicine, Clinical Immunology and Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Elisa Frullanti
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy
| | - Marco Gori
- grid.9024.f0000 0004 1757 4641University of Siena, DIISM-SAILAB, Siena, Italy ,grid.503321.60000 0001 0561 3840Models and Algorithms for Artificial Intelligence (MAASAI) Research Group, Université Côte d’Azur, Inria, CNRS, I3S, Biot, France
| | - Francis P. Crawley
- Good Clinical Practice Alliance-Europe (GCPA) and Strategic Initiative for Developing Capacity in Ethical Review (SIDCER), Leuven, Belgium
| | - Guillaume Butler-Laporte
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC Canada ,grid.14709.3b0000 0004 1936 8649Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC Canada
| | - Brent Richards
- grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC Canada ,grid.14709.3b0000 0004 1936 8649Department of Human Genetics, McGill University, Montreal, QC Canada ,grid.13097.3c0000 0001 2322 6764Department of Twin Research, King’s College London, London, UK
| | - Hugo Zeberg
- grid.4714.60000 0004 1937 0626Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Miklos Lipcsey
- grid.8993.b0000 0004 1936 9457Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden ,grid.8993.b0000 0004 1936 9457Hedenstierna Laboratory, CIRRUS, Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Michael Hultström
- grid.8993.b0000 0004 1936 9457Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden ,grid.8993.b0000 0004 1936 9457Integrative Physiology, Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Kerstin U. Ludwig
- grid.10388.320000 0001 2240 3300Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Eva C. Schulte
- grid.411095.80000 0004 0477 2585Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, 80336 Munich, Germany ,grid.5252.00000 0004 1936 973XDepartment of Psychiatry and Psychotherapy, University Hospital, LMU Munich, 80336 Munich, Germany ,grid.6936.a0000000123222966Institute of Virology, Technical University Munich/Helmholtz Zentrum München, Munich, Germany
| | - Erola Pairo-Castineira
- grid.4305.20000 0004 1936 7988MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU UK ,grid.4305.20000 0004 1936 7988Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG UK
| | - John Kenneth Baillie
- grid.4305.20000 0004 1936 7988MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU UK ,grid.4305.20000 0004 1936 7988Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG UK ,grid.418716.d0000 0001 0709 1919Intensive Care Unit, Royal Infirmary of Edinburgh, 54 Little France Drive, Edinburgh, H16 5SA UK
| | - Axel Schmidt
- grid.10388.320000 0001 2240 3300Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Robert Frithiof
- grid.8993.b0000 0004 1936 9457Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | | | | | | | - Francesca Mari
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy ,grid.9024.f0000 0004 1757 4641Medical Genetics, University of Siena, Siena, Italy ,grid.411477.00000 0004 1759 0844Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Alessandra Renieri
- Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy. .,Medical Genetics, University of Siena, Siena, Italy. .,Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy. .,Medical Genetics Unit, University of Siena, Policlinico Le Scotte, Viale Bracci, 2, 53100, Siena, Italy.
| | - Simone Furini
- grid.9024.f0000 0004 1757 4641Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
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19
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Croci S, Venneri MA, Mantovani S, Fallerini C, Benetti E, Picchiotti N, Campolo F, Imperatore F, Palmieri M, Daga S, Gabbi C, Montagnani F, Beligni G, Farias TDJ, Carriero ML, Di Sarno L, Alaverdian D, Aslaksen S, Cubellis MV, Spiga O, Baldassarri M, Fava F, Norman PJ, Frullanti E, Isidori AM, Amoroso A, Mari F, Furini S, Mondelli MU, Gen-Covid Multicenter Study, Chiariello M, Renieri A, Meloni I. The polymorphism L412F in TLR3 inhibits autophagy and is a marker of severe COVID-19 in males. Autophagy 2021; 18:1662-1672. [PMID: 34964709 PMCID: PMC9298458 DOI: 10.1080/15548627.2021.1995152] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The polymorphism L412F in TLR3 has been associated with several infectious diseases. However, the mechanism underlying this association is still unexplored. Here, we show that the L412F polymorphism in TLR3 is a marker of severity in COVID-19. This association increases in the sub-cohort of males. Impaired macroautophagy/autophagy and reduced TNF/TNFα production was demonstrated in HEK293 cells transfected with TLR3L412F-encoding plasmid and stimulated with specific agonist poly(I:C). A statistically significant reduced survival at 28 days was shown in L412F COVID-19 patients treated with the autophagy-inhibitor hydroxychloroquine (p = 0.038). An increased frequency of autoimmune disorders such as co-morbidity was found in L412F COVID-19 males with specific class II HLA haplotypes prone to autoantigen presentation. Our analyses indicate that L412F polymorphism makes males at risk of severe COVID-19 and provides a rationale for reinterpreting clinical trials considering autophagy pathways. Abbreviations: AP: autophagosome; AUC: area under the curve; BafA1: bafilomycin A1; COVID-19: coronavirus disease-2019; HCQ: hydroxychloroquine; RAP: rapamycin; ROC: receiver operating characteristic; SARS-CoV-2: severe acute respiratory syndrome coronavirus 2; TLR: toll like receptor; TNF/TNF-α: tumor necrosis factor
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Affiliation(s)
- Susanna Croci
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Mary Anna Venneri
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Stefania Mantovani
- Division of Clinical Immunology and Infectious Diseases, Department of Medicine, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Chiara Fallerini
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Elisa Benetti
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Nicola Picchiotti
- DIISM-SAILAB, University of Siena, Siena, Italy.,Department of Mathematics, University of Pavia, Pavia, Italy
| | - Federica Campolo
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Francesco Imperatore
- Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Core Research Laboratory, Via Fiorentina, Siena, Italy.,Consiglio Nazionale delle Ricerche, Istituto DI Fisiologia Clinica, Siena, Italy
| | - Maria Palmieri
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Sergio Daga
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Chiara Gabbi
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Francesca Montagnani
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy.,Department of Medical Sciences, Infectious and Tropical Diseases Unit, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Giada Beligni
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Ticiana D J Farias
- Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Miriam Lucia Carriero
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Laura Di Sarno
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Diana Alaverdian
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Sigrid Aslaksen
- Department of Clinical Science, Universty of Bergen and K.G. Jebsen Center for Autoimmune Diseases, University of Bergen, Bergen, Norway
| | | | - Ottavia Spiga
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Margherita Baldassarri
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Francesca Fava
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Paul J Norman
- Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Elisa Frullanti
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Andrea M Isidori
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Antonio Amoroso
- Department of Medical Sciences, University of Turin, Turin, Italy.,Immunogenetics and Transplant Biology, Azienda Ospedaliera Universitaria Città della Salute e della Scienza di Torino, Italy
| | - Francesca Mari
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Italy
| | - Simone Furini
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Mario U Mondelli
- Division of Clinical Immunology and Infectious Diseases, Department of Medicine, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.,Department of Internal Medicine and Therapeutics, University of Pavia, Pavia, Italy
| | | | - Mario Chiariello
- Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Core Research Laboratory, Via Fiorentina, Siena, Italy.,Consiglio Nazionale delle Ricerche, Istituto DI Fisiologia Clinica, Siena, Italy
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Italy
| | - Ilaria Meloni
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
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20
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Bruno LP, Doddato G, Valentino F, Baldassarri M, Tita R, Fallerini C, Bruttini M, Lo Rizzo C, Mencarelli MA, Mari F, Pinto AM, Fava F, Fabbiani A, Lamacchia V, Carrer A, Caputo V, Granata S, Benetti E, Zguro K, Furini S, Renieri A, Ariani F. New Candidates for Autism/Intellectual Disability Identified by Whole-Exome Sequencing. Int J Mol Sci 2021; 22:ijms222413439. [PMID: 34948243 PMCID: PMC8707363 DOI: 10.3390/ijms222413439] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/07/2021] [Accepted: 12/10/2021] [Indexed: 12/27/2022] Open
Abstract
Intellectual disability (ID) is characterized by impairments in the cognitive processes and in the tasks of daily life. It encompasses a clinically and genetically heterogeneous group of neurodevelopmental disorders often associated with autism spectrum disorder (ASD). Social and communication abilities are strongly compromised in ASD. The prevalence of ID/ASD is 1–3%, and approximately 30% of the patients remain without a molecular diagnosis. Considering the extreme genetic locus heterogeneity, next-generation sequencing approaches have provided powerful tools for candidate gene identification. Molecular diagnosis is crucial to improve outcome, prevent complications, and hopefully start a therapeutic approach. Here, we performed parent–offspring trio whole-exome sequencing (WES) in a cohort of 60 mostly syndromic ID/ASD patients and we detected 8 pathogenic variants in genes already known to be associated with ID/ASD (SYNGAP1, SMAD6, PACS1, SHANK3, KMT2A, KCNQ2, ACTB, and POGZ). We found four de novo disruptive variants of four novel candidate ASD/ID genes: MBP, PCDHA1, PCDH15, PDPR. We additionally selected via bioinformatic tools many variants in unknown genes that alone or in combination can contribute to the phenotype. In conclusion, our data confirm the efficacy of WES in detecting pathogenic variants of known and novel ID/ASD genes.
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Affiliation(s)
- Lucia Pia Bruno
- Medical Genetics, University of Siena, 53100 Siena, Italy; (L.P.B.); (G.D.); (F.V.); (M.B.); (C.F.); (M.B.); (F.M.); (F.F.); (A.F.); (V.L.); (A.C.); (V.C.); (S.G.); (A.R.)
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (K.Z.); (S.F.)
| | - Gabriella Doddato
- Medical Genetics, University of Siena, 53100 Siena, Italy; (L.P.B.); (G.D.); (F.V.); (M.B.); (C.F.); (M.B.); (F.M.); (F.F.); (A.F.); (V.L.); (A.C.); (V.C.); (S.G.); (A.R.)
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (K.Z.); (S.F.)
| | - Floriana Valentino
- Medical Genetics, University of Siena, 53100 Siena, Italy; (L.P.B.); (G.D.); (F.V.); (M.B.); (C.F.); (M.B.); (F.M.); (F.F.); (A.F.); (V.L.); (A.C.); (V.C.); (S.G.); (A.R.)
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (K.Z.); (S.F.)
| | - Margherita Baldassarri
- Medical Genetics, University of Siena, 53100 Siena, Italy; (L.P.B.); (G.D.); (F.V.); (M.B.); (C.F.); (M.B.); (F.M.); (F.F.); (A.F.); (V.L.); (A.C.); (V.C.); (S.G.); (A.R.)
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (K.Z.); (S.F.)
| | - Rossella Tita
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy; (R.T.); (C.L.R.); (M.A.M.); (A.M.P.)
| | - Chiara Fallerini
- Medical Genetics, University of Siena, 53100 Siena, Italy; (L.P.B.); (G.D.); (F.V.); (M.B.); (C.F.); (M.B.); (F.M.); (F.F.); (A.F.); (V.L.); (A.C.); (V.C.); (S.G.); (A.R.)
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (K.Z.); (S.F.)
| | - Mirella Bruttini
- Medical Genetics, University of Siena, 53100 Siena, Italy; (L.P.B.); (G.D.); (F.V.); (M.B.); (C.F.); (M.B.); (F.M.); (F.F.); (A.F.); (V.L.); (A.C.); (V.C.); (S.G.); (A.R.)
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy; (R.T.); (C.L.R.); (M.A.M.); (A.M.P.)
| | - Caterina Lo Rizzo
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy; (R.T.); (C.L.R.); (M.A.M.); (A.M.P.)
| | - Maria Antonietta Mencarelli
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy; (R.T.); (C.L.R.); (M.A.M.); (A.M.P.)
| | - Francesca Mari
- Medical Genetics, University of Siena, 53100 Siena, Italy; (L.P.B.); (G.D.); (F.V.); (M.B.); (C.F.); (M.B.); (F.M.); (F.F.); (A.F.); (V.L.); (A.C.); (V.C.); (S.G.); (A.R.)
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (K.Z.); (S.F.)
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy; (R.T.); (C.L.R.); (M.A.M.); (A.M.P.)
| | - Anna Maria Pinto
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy; (R.T.); (C.L.R.); (M.A.M.); (A.M.P.)
| | - Francesca Fava
- Medical Genetics, University of Siena, 53100 Siena, Italy; (L.P.B.); (G.D.); (F.V.); (M.B.); (C.F.); (M.B.); (F.M.); (F.F.); (A.F.); (V.L.); (A.C.); (V.C.); (S.G.); (A.R.)
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (K.Z.); (S.F.)
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy; (R.T.); (C.L.R.); (M.A.M.); (A.M.P.)
| | - Alessandra Fabbiani
- Medical Genetics, University of Siena, 53100 Siena, Italy; (L.P.B.); (G.D.); (F.V.); (M.B.); (C.F.); (M.B.); (F.M.); (F.F.); (A.F.); (V.L.); (A.C.); (V.C.); (S.G.); (A.R.)
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (K.Z.); (S.F.)
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy; (R.T.); (C.L.R.); (M.A.M.); (A.M.P.)
| | - Vittoria Lamacchia
- Medical Genetics, University of Siena, 53100 Siena, Italy; (L.P.B.); (G.D.); (F.V.); (M.B.); (C.F.); (M.B.); (F.M.); (F.F.); (A.F.); (V.L.); (A.C.); (V.C.); (S.G.); (A.R.)
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (K.Z.); (S.F.)
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy; (R.T.); (C.L.R.); (M.A.M.); (A.M.P.)
| | - Anna Carrer
- Medical Genetics, University of Siena, 53100 Siena, Italy; (L.P.B.); (G.D.); (F.V.); (M.B.); (C.F.); (M.B.); (F.M.); (F.F.); (A.F.); (V.L.); (A.C.); (V.C.); (S.G.); (A.R.)
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (K.Z.); (S.F.)
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy; (R.T.); (C.L.R.); (M.A.M.); (A.M.P.)
| | - Valentina Caputo
- Medical Genetics, University of Siena, 53100 Siena, Italy; (L.P.B.); (G.D.); (F.V.); (M.B.); (C.F.); (M.B.); (F.M.); (F.F.); (A.F.); (V.L.); (A.C.); (V.C.); (S.G.); (A.R.)
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (K.Z.); (S.F.)
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy; (R.T.); (C.L.R.); (M.A.M.); (A.M.P.)
| | - Stefania Granata
- Medical Genetics, University of Siena, 53100 Siena, Italy; (L.P.B.); (G.D.); (F.V.); (M.B.); (C.F.); (M.B.); (F.M.); (F.F.); (A.F.); (V.L.); (A.C.); (V.C.); (S.G.); (A.R.)
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (K.Z.); (S.F.)
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy; (R.T.); (C.L.R.); (M.A.M.); (A.M.P.)
| | - Elisa Benetti
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (K.Z.); (S.F.)
| | - Kristina Zguro
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (K.Z.); (S.F.)
| | - Simone Furini
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (K.Z.); (S.F.)
| | - Alessandra Renieri
- Medical Genetics, University of Siena, 53100 Siena, Italy; (L.P.B.); (G.D.); (F.V.); (M.B.); (C.F.); (M.B.); (F.M.); (F.F.); (A.F.); (V.L.); (A.C.); (V.C.); (S.G.); (A.R.)
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (K.Z.); (S.F.)
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy; (R.T.); (C.L.R.); (M.A.M.); (A.M.P.)
| | - Francesca Ariani
- Medical Genetics, University of Siena, 53100 Siena, Italy; (L.P.B.); (G.D.); (F.V.); (M.B.); (C.F.); (M.B.); (F.M.); (F.F.); (A.F.); (V.L.); (A.C.); (V.C.); (S.G.); (A.R.)
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (K.Z.); (S.F.)
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy; (R.T.); (C.L.R.); (M.A.M.); (A.M.P.)
- Correspondence: ; Tel.: +39-0577-233303
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21
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Diotallevi C, Fontana M, Latimer C, Ternan NG, Pourshahidi LK, Lawther R, O'Connor G, Conterno L, Gasperotti M, Angeli A, Lotti C, Bianchi M, Vrhovsek U, Fava F, Gobbetti M, Gill CIR, Tuohy KM. Ex Vivo Fecal Fermentation of Human Ileal Fluid Collected After Wild Strawberry Consumption Modulates Human Microbiome Community Structure and Metabolic Output and Protects Against DNA Damage in Colonic Epithelial Cells. Mol Nutr Food Res 2021; 66:e2100405. [PMID: 34821456 DOI: 10.1002/mnfr.202100405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 09/09/2021] [Indexed: 11/06/2022]
Abstract
SCOPE Wild strawberries (Fragaria vesca) are richer in (poly)phenols than common commercial strawberry varieties, e.g., Fragaria × ananassa. (Poly)phenols and their microbiota-derived metabolites are hypothesized to exert bioactivity within the human gut mucosa. To address this, the effects of wild strawberries are investigated with respect to their bioactivity and microbiota-modulating capacity using both in vitro and ex vivo approaches. METHODS AND RESULTS Ileal fluids collected pre- (0h) and post-consumption (8h) of 225 g wild strawberries by ileostomates (n = 5) and also in vitro digested strawberry varieties (Fragaria vesca and Fragaria × ananassa Duchesne) supernatants are collected. Subsequent fermentation of these supernatants using an in vitro batch culture proximal colon model reveals significant treatment-specific changes in microbiome community structure in terms of alpha but not beta diversity at 24 h. Nutri-kinetic analysis reveals a significant increase in the concentration of gut microbiota catabolites, including 3-(4hydroxyphenyl)propionic acid, 3-(3-hydroxyphenyl)propanoic acid, and benzoic acid. Furthermore, post-berry ileal fermentates (24 h) significantly (p < 0.01) decrease DNA damage (% Tail DNA, COMET assay) in both HT29 cells (∼45%) and CCD 841 CoN cells (∼25%) compared to untreated controls. CONCLUSIONS Post berry consumption fermentates exhibit increased overall levels of (poly)phenolic metabolites, which retains their bioactivity, reducing DNA damage in colonocytes.
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Affiliation(s)
- Camilla Diotallevi
- Department of Food Quality and Nutrition, Fondazione Edmund Mach, San Michele all'Adige (TN), Italy.,Freie Universität Bozen-Libera Università di Bolzano, Faculty of Science and Technology, Bolzano (BZ), Italy
| | - Massimiliano Fontana
- Department of Food Quality and Nutrition, Fondazione Edmund Mach, San Michele all'Adige (TN), Italy.,Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine, Northern Ireland, UK
| | - Cheryl Latimer
- Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine, Northern Ireland, UK
| | - Nigel G Ternan
- Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine, Northern Ireland, UK
| | - L Kirsty Pourshahidi
- Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine, Northern Ireland, UK
| | - Roger Lawther
- Altnagelvin Area Hospital, Western Health and Social Care Trust, Londonderry, UK
| | - Gloria O'Connor
- Altnagelvin Area Hospital, Western Health and Social Care Trust, Londonderry, UK
| | - Lorenza Conterno
- Fermentation and Distillation Group, Laimburg Research Centre, Vadena (BZ), Italy
| | - Mattia Gasperotti
- Department of Food Quality and Nutrition, Fondazione Edmund Mach, San Michele all'Adige (TN), Italy
| | - Andrea Angeli
- Department of Food Quality and Nutrition, Fondazione Edmund Mach, San Michele all'Adige (TN), Italy
| | - Cesare Lotti
- Department of Food Quality and Nutrition, Fondazione Edmund Mach, San Michele all'Adige (TN), Italy
| | - Martina Bianchi
- Department of Food Quality and Nutrition, Fondazione Edmund Mach, San Michele all'Adige (TN), Italy
| | - Urska Vrhovsek
- Department of Food Quality and Nutrition, Fondazione Edmund Mach, San Michele all'Adige (TN), Italy
| | - Francesca Fava
- Department of Food Quality and Nutrition, Fondazione Edmund Mach, San Michele all'Adige (TN), Italy
| | - Marco Gobbetti
- Freie Universität Bozen-Libera Università di Bolzano, Faculty of Science and Technology, Bolzano (BZ), Italy
| | - Chris I R Gill
- Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine, Northern Ireland, UK
| | - Kieran M Tuohy
- Department of Food Quality and Nutrition, Fondazione Edmund Mach, San Michele all'Adige (TN), Italy
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22
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Bruno LP, Fava F, Baldassarri M, Salvati VM, Scandurra V, Canitano R, Valentino F, Doddato G, Tita R, Giliberti A, Renieri A, Ariani F. Identification of a Novel Pathogenic Variant in the NAGLU Gene in a Child with Neurodevelopmental Delay. J Autism Dev Disord 2021; 52:4605-4607. [PMID: 34709531 DOI: 10.1007/s10803-021-05332-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2021] [Indexed: 11/27/2022]
Affiliation(s)
- Lucia Pia Bruno
- Medical Genetics Unit, University of Siena, Policlinico Le Scotte, Viale Bracci, 2, 53100, Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Francesca Fava
- Medical Genetics Unit, University of Siena, Policlinico Le Scotte, Viale Bracci, 2, 53100, Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Margherita Baldassarri
- Medical Genetics Unit, University of Siena, Policlinico Le Scotte, Viale Bracci, 2, 53100, Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Virginia M Salvati
- UOSD Pediatria Cava de' Tirreni- AOU S. Giovanni di Dio e Ruggi d'Aragona, Salerno, Italy
| | - Valeria Scandurra
- Division of Child and Adolescent Neuropsychiatry, University Hospital of Siena, Siena, Italy
| | - Roberto Canitano
- Division of Child and Adolescent Neuropsychiatry, University Hospital of Siena, Siena, Italy
| | - Floriana Valentino
- Medical Genetics Unit, University of Siena, Policlinico Le Scotte, Viale Bracci, 2, 53100, Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Gabriella Doddato
- Medical Genetics Unit, University of Siena, Policlinico Le Scotte, Viale Bracci, 2, 53100, Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Rossella Tita
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Annarita Giliberti
- Medical Genetics Unit, University of Siena, Policlinico Le Scotte, Viale Bracci, 2, 53100, Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Alessandra Renieri
- Medical Genetics Unit, University of Siena, Policlinico Le Scotte, Viale Bracci, 2, 53100, Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Francesca Ariani
- Medical Genetics Unit, University of Siena, Policlinico Le Scotte, Viale Bracci, 2, 53100, Siena, Italy.
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy.
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy.
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23
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Nakanishi T, Pigazzini S, Degenhardt F, Cordioli M, Butler-Laporte G, Maya-Miles D, Bujanda L, Bouysran Y, Niemi ME, Palom A, Ellinghaus D, Khan A, Martínez-Bueno M, Rolker S, Amitrano S, Roade Tato L, Fava F, Spinner CD, Prati D, Bernardo D, Garcia F, Darcis G, Fernandez-Cadenas I, Holter JC, Banales JM, Frithiof R, Kiryluk K, Duga S, Asselta R, Pereira AC, Romero-Gómez M, Nafría-Jiménez B, Hov JR, Migeotte I, Renieri A, Planas AM, Ludwig KU, Buti M, Rahmouni S, Alarcón-Riquelme ME, Schulte EC, Franke A, Karlsen TH, Valenti L, Zeberg H, Richards JB, Ganna A. Age-dependent impact of the major common genetic risk factor for COVID-19 on severity and mortality. J Clin Invest 2021; 131:152386. [PMID: 34597274 DOI: 10.1172/jci152386] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/28/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND There is considerable variability in COVID-19 outcomes amongst younger adults-and some of this variation may be due to genetic predisposition. METHODS We combined individual level data from 13,888 COVID-19 patients (N=7,185 hospitalized) from 17 cohorts in nine countries to assess the association of the major common COVID-19 genetic risk factor (chromosome 3 locus tagged by rs10490770) with mortality, COVID-19-related complications and laboratory values. We next performed meta-analyses using FinnGen and the Columbia University COVID-19 Biobank. RESULTS We found that rs10490770 risk allele carriers experienced an increased risk of all-cause mortality (HR 1.4, 95%CI 1.2-1.7). Risk allele carriers had increased odds of several COVID-19 complications: severe respiratory failure (OR 2.1, 95%CI 1.6-2.6), venous thromboembolism (OR 1.7, 95%CI 1.2-2.4), and hepatic injury (OR 1.5, 95%CI 1.2-2.0). Risk allele carriers ≤60 years had higher odds of death or severe respiratory failure (OR 2.7, 95%CI 1.8-3.9) compared to those >60 years (OR 1.5, 95%CI 1.2-1.8, interaction-p=0.038). Amongst individuals ≤60 years who died or experienced severe respiratory failure, 32.3% were risk variant carriers, compared to 13.9% of those not experiencing these outcomes. The genetic risk improved the prediction of death or severe respiratory failure similarly to, or better than, most established clinical risk factors. CONCLUSIONS The major common COVID-19 genetic risk factor is associated with increased risks of morbidity and mortality, which are more pronounced amongst individuals ≤60 years. The effect was similar in magnitude and more common than most established clinical risk factors, suggesting potential implications for future clinical risk management.
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Affiliation(s)
- Tomoko Nakanishi
- Department of Human Genetics, McGill University, Montreal, Canada
| | - Sara Pigazzini
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Frauke Degenhardt
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Mattia Cordioli
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Guillaume Butler-Laporte
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Canada
| | | | - Luis Bujanda
- Department of Liver and Gastrointestinal Diseases, Donostia University Hospital, University of Basque Country, San Sebastian, Spain
| | - Youssef Bouysran
- Centre de Génétique Humaine, Hôpital Erasme-Université Libre de Bruxelles, Brussels, Belgium
| | - Mari Ek Niemi
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Adriana Palom
- Department of Internal Medicine, Vall d'Hebron Barcelona Hospital, Barcelona, Spain
| | - David Ellinghaus
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Atlas Khan
- Department of Medicine, Columbia University, New York, United States of America
| | | | - Selina Rolker
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Sara Amitrano
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Luisa Roade Tato
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digest, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Christoph D Spinner
- Department of Internal Medicine II, University Hospital rechts der Isar, Munich, Germany
| | - Daniele Prati
- Department of Transfusion Medicine and Hematology, Università degli Studi di Milano, Milano, Italy
| | - David Bernardo
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digest, Instituto de Salud Carlos III, Madrid, Spain
| | - Federico Garcia
- Department of Pathology, Hospital Virgen del Camino, Pamplona, Spain
| | - Gilles Darcis
- Infectious Diseases Department, Liège University Hospital, Liège, Belgium
| | - Israel Fernandez-Cadenas
- Stroke Pharmacogenomics and Genetics Group, Biomedical Research Institute Sant Pau, Barcelona, Spain
| | - Jan Cato Holter
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Jesus M Banales
- Department of Biochemistry and Genetics, University of Navarra, Pamplona, Spain
| | - Robert Frithiof
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Krzysztof Kiryluk
- Department of Medicine, Columbia University, New York, United States of America
| | - Stefano Duga
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, Milan, Italy
| | - Rosanna Asselta
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, Milan, Italy
| | - Alexandre C Pereira
- Laboratory of Genetics and Molecular Cardiology, University of São Paulo Medical School, São Paulo, Brazil
| | | | | | - Johannes R Hov
- Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
| | - Isabelle Migeotte
- Centre de Génétique Humaine, Hôpital Erasme-Université Libre de Bruxelles, Brussels, Belgium
| | - Alessandra Renieri
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Anna M Planas
- Department of Brain Ischemia and Neurodegeneration, Institute for Biomedical Research of Barcelona, Barcelona, Spain
| | | | - Maria Buti
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digest, Instituto de Salud Carlos III, Madrid, Spain
| | - Souad Rahmouni
- GIGA-R, Laboratory of Immunology and Infectious Diseases, University of Liège, Liège, Belgium
| | | | - Eva C Schulte
- Institute of Virology, Technical University Munich/Helmholtz Zentrum, Munich, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Tom H Karlsen
- Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
| | - Luca Valenti
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Hugo Zeberg
- Department of Neuroscience, Karolinska Institutet, Solna, Sweden
| | | | - Andrea Ganna
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
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24
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Doddato G, Valentino F, Giliberti A, Papa FT, Tita R, Bruno LP, Resciniti S, Fallerini C, Benetti E, Palmieri M, Mencarelli MA, Fabbiani A, Bruttini M, Orrico A, Baldassarri M, Fava F, Lopergolo D, Rizzo CL, Lamacchia V, Mannucci S, Pinto AM, Currò A, Mancini V, Mari F, Renieri A, Ariani F. Corrigendum: Exome Sequencing in BRCA1-2 Candidate Familias: The Contribution of Other Cancer Susceptibility Genes. Front Oncol 2021; 11:740860. [PMID: 34485163 PMCID: PMC8416239 DOI: 10.3389/fonc.2021.740860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 07/27/2021] [Indexed: 11/23/2022] Open
Affiliation(s)
- Gabriella Doddato
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena Italy, Siena, Italy
| | - Floriana Valentino
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena Italy, Siena, Italy
| | - Annarita Giliberti
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena Italy, Siena, Italy
| | - Filomena Tiziana Papa
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena Italy, Siena, Italy
| | - Rossella Tita
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Lucia Pia Bruno
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena Italy, Siena, Italy
| | - Sara Resciniti
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena Italy, Siena, Italy
| | - Chiara Fallerini
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena Italy, Siena, Italy
| | - Elisa Benetti
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena Italy, Siena, Italy
| | - Maria Palmieri
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena Italy, Siena, Italy
| | | | - Alessandra Fabbiani
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena Italy, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Mirella Bruttini
- Medical Genetics, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Alfredo Orrico
- Molecular Diagnosis and Characterization of Pathogenic Mechanisms of Rare Genetic Diseases, Azienda Ospedaliera Universitaria Senese and Clinical Genetics, ASL Toscana SudEst. Ospedale della Misericordia, Grosseto, Italy
| | - Margherita Baldassarri
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena Italy, Siena, Italy
| | - Francesca Fava
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena Italy, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Diego Lopergolo
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena Italy, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Caterina Lo Rizzo
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Vittoria Lamacchia
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena Italy, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Sara Mannucci
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena Italy, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Anna Maria Pinto
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Aurora Currò
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena Italy, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Virginia Mancini
- Unit of Pathology, Department of Medical Biotechnology, University of Siena, Siena, Italy
| | | | | | | | | | - Francesca Mari
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena Italy, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena Italy, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Francesca Ariani
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena Italy, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
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25
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Diotallevi C, Gaudioso G, Fava F, Angeli A, Lotti C, Vrhovsek U, Rinott E, Shai I, Gobbetti M, Tuohy K. Measuring the effect of Mankai® (Wolffia globosa) on the gut microbiota and its metabolic output using an in vitro colon model. J Funct Foods 2021. [DOI: 10.1016/j.jff.2021.104597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
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26
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Zhang S, Cooper-Knock J, Weimer AK, Harvey C, Julian TH, Wang C, Li J, Furini S, Frullanti E, Fava F, Renieri A, Pan C, Song J, Billing-Ross P, Gao P, Shen X, Timpanaro IS, Kenna KP, Davis MM, Tsao PS, Snyder MP. Common and rare variant analyses combined with single-cell multiomics reveal cell-type-specific molecular mechanisms of COVID-19 severity. medRxiv 2021:2021.06.15.21258703. [PMID: 34189540 PMCID: PMC8240695 DOI: 10.1101/2021.06.15.21258703] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The determinants of severe COVID-19 in non-elderly adults are poorly understood, which limits opportunities for early intervention and treatment. Here we present novel machine learning frameworks for identifying common and rare disease-associated genetic variation, which outperform conventional approaches. By integrating single-cell multiomics profiling of human lungs to link genetic signals to cell-type-specific functions, we have discovered and validated over 1,000 risk genes underlying severe COVID-19 across 19 cell types. Identified risk genes are overexpressed in healthy lungs but relatively downregulated in severely diseased lungs. Genetic risk for severe COVID-19, within both common and rare variants, is particularly enriched in natural killer (NK) cells, which places these immune cells upstream in the pathogenesis of severe disease. Mendelian randomization indicates that failed NKG2D-mediated activation of NK cells leads to critical illness. Network analysis further links multiple pathways associated with NK cell activation, including type-I-interferon-mediated signalling, to severe COVID-19. Our rare variant model, PULSE, enables sensitive prediction of severe disease in non-elderly patients based on whole-exome sequencing; individualized predictions are accurate independent of age and sex, and are consistent across multiple populations and cohorts. Risk stratification based on exome sequencing has the potential to facilitate post-exposure prophylaxis in at-risk individuals, potentially based around augmentation of NK cell function. Overall, our study characterizes a comprehensive genetic landscape of COVID-19 severity and provides novel insights into the molecular mechanisms of severe disease, leading to new therapeutic targets and sensitive detection of at-risk individuals.
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27
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Isidori AM, Marcelli M, Castagna MG, Baldassarri M, Fava F, Renieri A. In response to the letter to the editor by Soha Ghanian et al. re our publication "Shorter androgen receptor polyQ alleles protect against life-threatening COVID-19 disease in European males". EBioMedicine 2021; 68:103426. [PMID: 34134089 PMCID: PMC8197779 DOI: 10.1016/j.ebiom.2021.103426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 05/19/2021] [Indexed: 11/18/2022] Open
Affiliation(s)
- Andrea M Isidori
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Marco Marcelli
- Department of Medicine, Baylor College of Medicine, Houston TX, USA
| | - Maria Grazia Castagna
- Department of Medical, Surgical and Neurological Sciences, University of Siena, Italy
| | - Margherita Baldassarri
- Medical Genetics, University of Siena, Italy; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy
| | - Francesca Fava
- Medical Genetics, University of Siena, Italy; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy; Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Italy
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Italy; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy; Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Italy.
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28
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Doddato G, Valentino F, Giliberti A, Papa FT, Tita R, Bruno LP, Resciniti S, Fallerini C, Benetti E, Palmieri M, Mencarelli MA, Fabbiani A, Bruttini M, Orrico A, Baldassarri M, Fava F, Lopergolo D, Lo Rizzo C, Lamacchia V, Mannucci S, Pinto AM, Curr A, Mancini V, Mari F, Renieri A, Ariani F. Whole Exome Sequencing in BRCA1-2 Candidate Families: The Contribution of Other Cancer Susceptibility Genes. Front Oncol 2021; 11:649435. [PMID: 34026625 PMCID: PMC8139251 DOI: 10.3389/fonc.2021.649435] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 04/06/2021] [Indexed: 12/14/2022] Open
Abstract
Hereditary Breast and Ovarian Cancer (HBOC) syndrome is a condition in which the risk of breast and ovarian cancer is higher than in the general population. The prevalent pathogenesis is attributable to inactivating variants of the BRCA1-2 highly penetrant genes, however, other cancer susceptibility genes may also be involved. By Exome Sequencing (ES) we analyzed a series of 200 individuals selected for genetic testing in BRCA1-2 genes according to the updated National Comprehensive Cancer Network (NCCN) guidelines. Analysis by MLPA was performed to detect large BRCA1-2 deletions/duplications. Focusing on BRCA1-2 genes, data analysis identified 11 cases with pathogenic variants (4 in BRCA1 and 7 in BRCA1-2) and 12 with uncertain variants (7 in BRCA1 and 5 in BRCA2). Only one case was found with a large BRCA1 deletion. Exome analysis allowed to characterize pathogenic variants in 21 additional genes: 10 genes more traditionally associated to breast and ovarian cancer (ATM, BRIP1, CDH1, PALB2, PTEN, RAD51C, and TP53) (5% diagnostic yield) and 11 in candidate cancer susceptibility genes (DPYD, ERBB3, ERCC2, MUTYH, NQO2, NTHL1, PARK2, RAD54L, and RNASEL). In conclusion, this study allowed a personalized risk assessment and clinical surveillance in an increased number of HBOC families and to broaden the spectrum of causative variants also to candidate “non-canonical” genes.
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Affiliation(s)
- Gabriella Doddato
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Floriana Valentino
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Annarita Giliberti
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Filomena Tiziana Papa
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Rossella Tita
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Lucia Pia Bruno
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Sara Resciniti
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Chiara Fallerini
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Elisa Benetti
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Maria Palmieri
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | - Alessandra Fabbiani
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Mirella Bruttini
- Medical Genetics, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Alfredo Orrico
- Molecular Diagnosis and Characterization of Pathogenic Mechanisms of Rare Genetic Diseases, Azienda Ospedaliera Universitaria Senese and Clinical Genetics, ASL Toscana SudEst. Ospedale della Misericordia, Grosseto, Italy
| | - Margherita Baldassarri
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Francesca Fava
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Diego Lopergolo
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Caterina Lo Rizzo
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Vittoria Lamacchia
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Sara Mannucci
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Anna Maria Pinto
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Aurora Curr
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Virginia Mancini
- Unit of Pathology, Department of Medical Biotechnology, University of Siena, Siena, Italy
| | | | | | - Francesca Mari
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Francesca Ariani
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
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29
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Daga S, Fallerini C, Baldassarri M, Fava F, Valentino F, Doddato G, Benetti E, Furini S, Giliberti A, Tita R, Amitrano S, Bruttini M, Meloni I, Pinto AM, Raimondi F, Stella A, Biscarini F, Picchiotti N, Gori M, Pinoli P, Ceri S, Sanarico M, Crawley FP, Birolo G, Renieri A, Mari F, Frullanti E. Employing a systematic approach to biobanking and analyzing clinical and genetic data for advancing COVID-19 research. Eur J Hum Genet 2021; 29:745-759. [PMID: 33456056 PMCID: PMC7811682 DOI: 10.1038/s41431-020-00793-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/27/2020] [Accepted: 11/25/2020] [Indexed: 02/07/2023] Open
Abstract
Within the GEN-COVID Multicenter Study, biospecimens from more than 1000 SARS-CoV-2 positive individuals have thus far been collected in the GEN-COVID Biobank (GCB). Sample types include whole blood, plasma, serum, leukocytes, and DNA. The GCB links samples to detailed clinical data available in the GEN-COVID Patient Registry (GCPR). It includes hospitalized patients (74.25%), broken down into intubated, treated by CPAP-biPAP, treated with O2 supplementation, and without respiratory support (9.5%, 18.4%, 31.55% and 14.8, respectively); and non-hospitalized subjects (25.75%), either pauci- or asymptomatic. More than 150 clinical patient-level data fields have been collected and binarized for further statistics according to the organs/systems primarily affected by COVID-19: heart, liver, pancreas, kidney, chemosensors, innate or adaptive immunity, and clotting system. Hierarchical clustering analysis identified five main clinical categories: (1) severe multisystemic failure with either thromboembolic or pancreatic variant; (2) cytokine storm type, either severe with liver involvement or moderate; (3) moderate heart type, either with or without liver damage; (4) moderate multisystemic involvement, either with or without liver damage; (5) mild, either with or without hyposmia. GCB and GCPR are further linked to the GCGDR, which includes data from whole-exome sequencing and high-density SNP genotyping. The data are available for sharing through the Network for Italian Genomes, found within the COVID-19 dedicated section. The study objective is to systematize this comprehensive data collection and begin identifying multi-organ involvement in COVID-19, defining genetic parameters for infection susceptibility within the population, and mapping genetically COVID-19 severity and clinical complexity among patients.
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Affiliation(s)
- Sergio Daga
- Medical Genetics, University of Siena, Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Chiara Fallerini
- Medical Genetics, University of Siena, Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Margherita Baldassarri
- Medical Genetics, University of Siena, Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Francesca Fava
- Medical Genetics, University of Siena, Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Floriana Valentino
- Medical Genetics, University of Siena, Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Gabriella Doddato
- Medical Genetics, University of Siena, Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Elisa Benetti
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Simone Furini
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Annarita Giliberti
- Medical Genetics, University of Siena, Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Rossella Tita
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Sara Amitrano
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Mirella Bruttini
- Medical Genetics, University of Siena, Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Ilaria Meloni
- Medical Genetics, University of Siena, Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Anna Maria Pinto
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | | | - Alessandra Stella
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biologia e Biotecnologia Agraria (IBBA), Milano, Italy
| | - Filippo Biscarini
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biologia e Biotecnologia Agraria (IBBA), Milano, Italy
- ERCEA (European Research Council Executive Agency), Bruxelles, Belgium
| | - Nicola Picchiotti
- University of Siena, DIISM- SAILAB, Siena, Italy
- Department of Mathematics, University of Pavia, Pavia, Italy
| | - Marco Gori
- University of Siena, DIISM- SAILAB, Siena, Italy
- Université Côte d'Azur, Inria, CNRS, I3S, Maasai, Italy
| | - Pietro Pinoli
- Department of Electronics, Information and Bioengineering (DEIB), Politecnico di Milano, Milano, Italy
| | - Stefano Ceri
- Department of Electronics, Information and Bioengineering (DEIB), Politecnico di Milano, Milano, Italy
| | | | - Francis P Crawley
- Good Clinical Practice Alliance-Europe (GCPA) and Strategic Initiative for Developing Capacity in Ethical Review-Europe (SIDCER), Brussels, Belgium
- ERCEA (European Research Council Executive Agency), Bruxelles, Belgium
| | - Giovanni Birolo
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy.
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy.
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy.
| | - Francesca Mari
- Medical Genetics, University of Siena, Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Elisa Frullanti
- Medical Genetics, University of Siena, Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
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30
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Nakanishi T, Pigazzini S, Degenhardt F, Cordioli M, Butler-Laporte G, Maya-Miles D, Nafría-Jiménez B, Bouysran Y, Niemi M, Palom A, Ellinghaus D, Khan A, Martínez-Bueno M, Rolker S, Amitano S, Tato LR, Fava F, Spinner CD, Prati D, Bernardo D, Garcia F, Darcis G, Fernández-Cadenas I, Holter JC, Banales J, Frithiof R, Kiryluk K, Duga S, Asselta R, Pereira AC, Romero-Gómez M, Bujanda L, Hov JR, Migeotte I, Renieri A, Planas AM, Ludwig KU, Buti M, Rahmouni S, Alarcón-Riquelme ME, Schulte EC, Franke A, Karlsen TH, Valenti L, Zeberg H, Richards JB, Ganna A. Age-dependent impact of the major common genetic risk factor for COVID-19 on severity and mortality. medRxiv 2021:2021.03.07.21252875. [PMID: 33758887 PMCID: PMC7987046 DOI: 10.1101/2021.03.07.21252875] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND There is considerable variability in COVID-19 outcomes amongst younger adults-and some of this variation may be due to genetic predisposition. We characterized the clinical implications of the major genetic risk factor for COVID-19 severity, and its age-dependent effect, using individual-level data in a large international multi-centre consortium. METHOD The major common COVID-19 genetic risk factor is a chromosome 3 locus, tagged by the marker rs10490770. We combined individual level data for 13,424 COVID-19 positive patients (N=6,689 hospitalized) from 17 cohorts in nine countries to assess the association of this genetic marker with mortality, COVID-19-related complications and laboratory values. We next examined if the magnitude of these associations varied by age and were independent from known clinical COVID-19 risk factors. FINDINGS We found that rs10490770 risk allele carriers experienced an increased risk of all-cause mortality (hazard ratio [HR] 1·4, 95% confidence interval [CI] 1·2-1·6) and COVID-19 related mortality (HR 1·5, 95%CI 1·3-1·8). Risk allele carriers had increased odds of several COVID-19 complications: severe respiratory failure (odds ratio [OR] 2·0, 95%CI 1·6-2·6), venous thromboembolism (OR 1·7, 95%CI 1·2-2·4), and hepatic injury (OR 1·6, 95%CI 1·2-2·0). Risk allele carriers ≤ 60 years had higher odds of death or severe respiratory failure (OR 2·6, 95%CI 1·8-3·9) compared to those > 60 years OR 1·5 (95%CI 1·3-1·9, interaction p-value=0·04). Amongst individuals ≤ 60 years who died or experienced severe respiratory COVID-19 outcome, we found that 31·8% (95%CI 27·6-36·2) were risk variant carriers, compared to 13·9% (95%CI 12·6-15·2%) of those not experiencing these outcomes. Prediction of death or severe respiratory failure among those ≤ 60 years improved when including the risk allele (AUC 0·82 vs 0·84, p=0·016) and the prediction ability of rs10490770 risk allele was similar to, or better than, most established clinical risk factors. INTERPRETATION The major common COVID-19 risk locus on chromosome 3 is associated with increased risks of morbidity and mortality-and these are more pronounced amongst individuals ≤ 60 years. The effect on COVID-19 severity was similar to, or larger than most established risk factors, suggesting potential implications for clinical risk management. FUNDING Funding was obtained by each of the participating cohorts individually.
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Affiliation(s)
- Tomoko Nakanishi
- Institute for Molecular Medicine Finland, Univerisity of Helsinki, Helsinki, Finland
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Research Fellow, Japan Society for the Promotion of Science, Tokyo, Japan
| | - Sara Pigazzini
- Institute for Molecular Medicine Finland, Univerisity of Helsinki, Helsinki, Finland
- University of Milano-Bicocca, Milano, Italy
| | - Frauke Degenhardt
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
- University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Mattia Cordioli
- Institute for Molecular Medicine Finland, Univerisity of Helsinki, Helsinki, Finland
| | - Guillaume Butler-Laporte
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
| | - Douglas Maya-Miles
- Digestive Diseases Unit, Virgen del Rocio University Hospital, Institute of Biomedicine of Seville, University of Seville, Seville, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Beatriz Nafría-Jiménez
- Osakidetza Basque Health Service, Donostialdea Integrated Health Organisation. Clinical Biochemistry Department, Sebastian, Spain
| | - Youssef Bouysran
- Centre de Génétique Humaine, Hopital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Mari Niemi
- Institute for Molecular Medicine Finland, Univerisity of Helsinki, Helsinki, Finland
| | - Adriana Palom
- Liver Unit, Department of Internal Medicine, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Universitat Autònoma de Barcelona. Departament de Medicina.Bellatera, Barcelona, Spain
- Vall d’Hebron Institut de Recerca (VHIR). Liver Diseases
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
- Novo Nordisk Foundation Center for Protein Research, Disease Systems Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen
| | - Atlas Khan
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY
| | - Manuel Martínez-Bueno
- GENYO. Centre for Genomics and Oncological Research: Pfizer / University of Granada / Andalusian Regional Government, Granada, Spain
| | - Selina Rolker
- Institute of Human Genetics, University Hospital Bonn, Medical Faculty University of Bonn, Bonn, Germany
| | - Sara Amitano
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Italy
| | - Luisa Roade Tato
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Liver Unit, Department of Internal Medicine, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Universitat Autònoma de Barcelona. Departament de Medicina.Bellatera, Barcelona, Spain
| | | | - Francesca Fava
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Italy
- Medical Genetics, University of Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy
| | - Christoph D. Spinner
- Technical University of Munich, School of Medicine, University Hospital rechts der Isar, Department of Internal Medicine II, Munich, Germany
| | - Daniele Prati
- Department of Transfusion Medicine and Hematology, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milano, Italy
| | - David Bernardo
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Mucosal Immunology Lab, Institute of Biomedicine and Molecular Genetics (IBGM), University of Valladolid-CSIC. Valladolid, Spain
| | - Federico Garcia
- Hospital Universitario Clinico San Cecilio, Granada, Spain
- Instituto de Investigación Ibs.Granada. Granada, Spain
| | - Gilles Darcis
- University of Liege, GIGA-Insitute, Liege, Belgium
- Liege University Hospital (CHU of Liege), Liege, Belgium
| | - Israel Fernández-Cadenas
- Stroke Pharmacogenomics and Genetics Group, Biomedical Research Institute Sant Pau (IIB Sant Pau), Barcelona, Spain
| | - Jan Cato Holter
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Jesus Banales
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute - Donostia University Hospital, University of the Basque Country (UPV/EHU), CIBERehd, Ikerbasque, San Sebastian, Spain
| | - Robert Frithiof
- Department of Surgical Sciences, Anaesthesiology and Intensive Care Medicine, Uppsala University, Uppsala, Sweden
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY
| | - Stefano Duga
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
- IRCCS Humanitas Research Hospital, Milan, Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
- IRCCS Humanitas Research Hospital, Milan, Italy
| | | | - Manuel Romero-Gómez
- Digestive Diseases Unit, Virgen del Rocio University Hospital, Institute of Biomedicine of Seville, University of Seville, Seville, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Luis Bujanda
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute - Donostia University Hospital, University of the Basque Country (UPV/EHU), CIBERehd, Ikerbasque, San Sebastian, Spain
| | - Johannes R. Hov
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Norwegian PSC Research Center and Section of Gastroenterology, Dept Transplantation Medicine, Oslo University Hospital, Oslo, Norway
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway
| | - Isabelle Migeotte
- Centre de Génétique Humaine, Hopital Erasme, Université Libre de Bruxelles, Brussels, Belgium
- Fonds de la Recherche Scientifique (FNRS), Brussels, Belgium
| | - Alessandra Renieri
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Italy
- Medical Genetics, University of Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy
| | - Anna M. Planas
- Institute for Biomedical Researhc of Barcelona (IIBB), National Spanish Research Council (CSIC), Barcelona, Spain
- Institut d’Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Kerstin U. Ludwig
- Institute of Human Genetics, University Hospital Bonn, Medical Faculty University of Bonn, Bonn, Germany
| | - Maria Buti
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Liver Unit, Department of Internal Medicine, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Universitat Autònoma de Barcelona. Departament de Medicina.Bellatera, Barcelona, Spain
| | | | - Marta E. Alarcón-Riquelme
- GENYO. Centre for Genomics and Oncological Research: Pfizer / University of Granada / Andalusian Regional Government, Granada, Spain
- Institute for Environmental Medicine, Karolinska Institutet, 17167, Solna, Sweden
| | - Eva C. Schulte
- Institute of Virology, Technical University Munich/Helmholtz Zentrum München, Munich, Germany
- Institute of Psychiatric Phenomics and Genomics, University Hospital, LMU Munich University, Munich, Germany
- Department of Psychiatry, University Hospital, LMU Munich University, Munich, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
- University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Tom H Karlsen
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Norwegian PSC Research Center and Section of Gastroenterology, Dept Transplantation Medicine, Oslo University Hospital, Oslo, Norway
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway
| | - Luca Valenti
- Department of Pathopgysiology and Transplantation, Università degli Studi di Milano, Milano, Italy
- Department of Transfusion Medicine and Hematology, Precision Medicine, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Hugo Zeberg
- Department of Neuroscience, Karolinska Institutet, Sweden
- Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - J. Brent Richards
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
- Department of Twin Research, King’s College London, London, United Kingdom
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, Univerisity of Helsinki, Helsinki, Finland
- Massachusetts General Hospital, Harvard Medical School
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Fallerini C, Daga S, Mantovani S, Benetti E, Picchiotti N, Francisci D, Paciosi F, Schiaroli E, Baldassarri M, Fava F, Palmieri M, Ludovisi S, Castelli F, Quiros-Roldan E, Vaghi M, Rusconi S, Siano M, Bandini M, Spiga O, Capitani K, Furini S, Mari F, Renieri A, Mondelli MU, Frullanti E. Association of Toll-like receptor 7 variants with life-threatening COVID-19 disease in males: findings from a nested case-control study. eLife 2021; 10:67569. [PMID: 33650967 PMCID: PMC7987337 DOI: 10.7554/elife.67569] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 02/24/2021] [Indexed: 12/26/2022] Open
Abstract
Background: Recently, loss-of-function variants in TLR7 were identified in two families in which COVID-19 segregates like an X-linked recessive disorder environmentally conditioned by SARS-CoV-2. We investigated whether the two families represent the tip of the iceberg of a subset of COVID-19 male patients. Methods: This is a nested case-control study in which we compared male participants with extreme phenotype selected from the Italian GEN-COVID cohort of SARS-CoV-2-infected participants (<60 y, 79 severe cases versus 77 control cases). We applied the LASSO Logistic Regression analysis, considering only rare variants on young male subsets with extreme phenotype, picking up TLR7 as the most important susceptibility gene. Results: Overall, we found TLR7 deleterious variants in 2.1% of severely affected males and in none of the asymptomatic participants. The functional gene expression profile analysis demonstrated a reduction in TLR7-related gene expression in patients compared with controls demonstrating an impairment in type I and II IFN responses. Conclusions: Young males with TLR7 loss-of-function variants and severe COVID-19 represent a subset of male patients contributing to disease susceptibility in up to 2% of severe COVID-19. Funding: Funded by private donors for the Host Genetics Research Project, the Intesa San Paolo for 2020 charity fund, and the Host Genetics Initiative. Clinical trial number: NCT04549831.
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Affiliation(s)
- Chiara Fallerini
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Sergio Daga
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Stefania Mantovani
- Division of Infectious Diseases and Immunology, Department of Medical Sciences and Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Elisa Benetti
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Nicola Picchiotti
- Department of Mathematics, University of Pavia, Pavia, Italy.,University of Siena, DIISM-SAILAB, Siena, Italy
| | - Daniela Francisci
- Infectious Diseases Clinic, Department of Medicine 2, Azienda Ospedaliera di Perugia and University of Perugia, Santa Maria Hospital, Perugia, Italy.,Infectious Diseases Clinic, "Santa Maria" Hospital, University of Perugia, Perugia, Italy
| | - Francesco Paciosi
- Infectious Diseases Clinic, Department of Medicine 2, Azienda Ospedaliera di Perugia and University of Perugia, Santa Maria Hospital, Perugia, Italy.,Infectious Diseases Clinic, "Santa Maria" Hospital, University of Perugia, Perugia, Italy
| | - Elisabetta Schiaroli
- Infectious Diseases Clinic, Department of Medicine 2, Azienda Ospedaliera di Perugia and University of Perugia, Santa Maria Hospital, Perugia, Italy
| | - Margherita Baldassarri
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Francesca Fava
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Maria Palmieri
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Serena Ludovisi
- Division of Infectious Diseases and Immunology, Department of Medical Sciences and Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.,Department of Internal Medicine and Therapeutics, University of Pavia, Pavia, Italy
| | - Francesco Castelli
- Department of Infectious and Tropical Diseases, University of Brescia and ASST Spedali Civili Hospital, Brescia, Italy
| | - Eugenia Quiros-Roldan
- Department of Infectious and Tropical Diseases, University of Brescia and ASST Spedali Civili Hospital, Brescia, Italy
| | - Massimo Vaghi
- Chirurgia Vascolare, Ospedale Maggiore di Crema, Crema, Italy
| | - Stefano Rusconi
- Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy.,III Infectious Diseases Unit, ASST-FBF-Sacco, Milan, Italy
| | - Matteo Siano
- Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy
| | - Maria Bandini
- Department of Preventive Medicine, Azienda USL Toscana Sud Est, Siena, Italy
| | - Ottavia Spiga
- University of Siena, DIISM-SAILAB, Siena, Italy.,Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Katia Capitani
- Medical Genetics, University of Siena, Siena, Italy.,Molecular Mechanisms of Oncogenesis, ISPRO Core Research Laboratory (CRL), Firenze, Italy
| | - Simone Furini
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Francesca Mari
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
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- Medical Genetics, University of Siena, Siena, Italy
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Mario U Mondelli
- Division of Infectious Diseases and Immunology, Department of Medical Sciences and Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.,Department of Internal Medicine and Therapeutics, University of Pavia, Pavia, Italy
| | - Elisa Frullanti
- Medical Genetics, University of Siena, Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
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Rinott E, Youngster I, Yaskolka Meir A, Tsaban G, Zelicha H, Kaplan A, Knights D, Tuohy K, Fava F, Scholz MU, Ziv O, Rubin E, Tirosh A, Rudich A, Blüher M, Stumvoll M, Ceglarek U, Clement K, Koren O, Wang DD, Hu FB, Stampfer MJ, Shai I. Effects of Diet-Modulated Autologous Fecal Microbiota Transplantation on Weight Regain. Gastroenterology 2021; 160:158-173.e10. [PMID: 32860791 PMCID: PMC7755729 DOI: 10.1053/j.gastro.2020.08.041] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 08/10/2020] [Accepted: 08/20/2020] [Indexed: 12/30/2022]
Abstract
BACKGROUND & AIMS We evaluated the efficacy and safety of diet-modulated autologous fecal microbiota transplantation (aFMT) for treatment of weight regain after the weight-loss phase. METHODS In the DIRECT PLUS (Dietary Intervention Randomized Controlled Trial Polyphenols-Unprocessed) weight-loss trial (May 2017 through July 2018), abdominally obese or dyslipidemic participants in Israel were randomly assigned to healthy dietary guidelines, Mediterranean diet, and green-Mediterranean diet weight-loss groups. All groups received free gym membership and physical activity guidelines. Both isocaloric Mediterranean groups consumed 28 g/d walnuts (+440 mg/d polyphenols provided). The green-Mediterranean dieters also consumed green tea (3-4 cups/d) and a Wolffia globosa (Mankai strain, 100 g/d) green shake (+800 mg/d polyphenols provided). After 6 months (weight-loss phase), 90 eligible participants (mean age, 52 years; mean weight loss, 8.3 kg) provided a fecal sample that was processed into aFMT by frozen, opaque, and odorless capsules. The participants were then randomly assigned to groups that received 100 capsules containing their own fecal microbiota or placebo until month 14. The primary outcome was regain of the lost weight over the expected weight-regain phase (months 6-14). Secondary outcomes were gastrointestinal symptoms, waist circumference, glycemic status, and changes in the gut microbiome, as measured by metagenomic sequencing and 16s ribosomal RNA. We validated the results in a parallel in vivo study of mice specifically fed with Mankai compared with control chow diet. RESULTS Of the 90 participants in the aFMT trial, 96% ingested at least 80 of 100 oral aFMT or placebo frozen capsules during the transplantation period. No aFMT-related adverse events or symptoms were observed. For the primary outcome, although no significant differences in weight regain were observed among the participants in the different lifestyle interventions during months 6-14 (aFMT, 30.4% vs placebo, 40.6%; P = .28), aFMT significantly attenuated weight regain in the green-Mediterranean group (aFMT, 17.1%, vs placebo, 50%; P = .02), but not in the dietary guidelines (P = .57) or Mediterranean diet (P = .64) groups (P for the interaction = .03). Accordingly, aFMT attenuated waist circumference gain (aFMT, 1.89 cm vs placebo, 5.05 cm; P = .01) and insulin rebound (aFMT, -1.46 ± 3.6 μIU/mL vs placebo, 1.64 ± 4.7 μIU/mL; P = .04) in the green-Mediterranean group but not in the dietary guidelines or Mediterranean diet (P for the interaction = .04 and .03, respectively). The green-Mediterranean diet was the only intervention to induce a significant change in microbiome composition during the weight-loss phase, and to prompt preservation of weight-loss-associated specific bacteria and microbial metabolic pathways (mainly microbial sugar transport) after the aFMT. In mice, Mankai-modulated aFMT in the weight-loss phase compared with control diet aFMT, significantly prevented weight regain and resulted in better glucose tolerance during a high-fat diet-induced regain phase (all, P < .05). CONCLUSIONS Autologous FMT, collected during the weight-loss phase and administrated in the regain phase, might preserve weight loss and glycemic control, and is associated with specific microbiome signatures. A high-polyphenols, green plant-based or Mankai diet better optimizes the microbiome for an aFMT procedure. ClinicalTrials.gov number, NCT03020186.
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Affiliation(s)
- Ehud Rinott
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Ilan Youngster
- Pediatric Division and Center for Microbiome Research, Shamir Medical Center, Be'er Ya'akov, Israel; Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel.
| | - Anat Yaskolka Meir
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Gal Tsaban
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Hila Zelicha
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Alon Kaplan
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Dan Knights
- BioTechnology Institute, University of Minnesota, St Paul, Minnesota; Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota
| | - Kieran Tuohy
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
| | - Francesca Fava
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
| | - Matthias Uwe Scholz
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
| | - Oren Ziv
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Elad Rubin
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Amir Tirosh
- Division of Endocrinology, Diabetes and Metabolism, Sheba Medical Center, Tel-Hashomer, Israel; Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel; Division of Endocrinology, Diabetes, and Hypertension, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Assaf Rudich
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | | | | | - Uta Ceglarek
- Department of Medicine, University of Leipzig, German
| | - Karine Clement
- Sorbonne University/Inserm, NutriOmics Research Unit, Nutrition Department, Pitié-Salpêtrière Hospital, Assistance-Publique Hopitaux de Paris, Paris, France
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Dong D Wang
- Harvard T.H. Chan School of Public Health, Cambridge, Massachusetts
| | - Frank B Hu
- Harvard T.H. Chan School of Public Health, Cambridge, Massachusetts; Channing Division of Network Medicine, Department of Medicine, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts
| | - Meir J Stampfer
- Harvard T.H. Chan School of Public Health, Cambridge, Massachusetts; Channing Division of Network Medicine, Department of Medicine, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts
| | - Iris Shai
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel; Harvard T.H. Chan School of Public Health, Cambridge, Massachusetts.
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33
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Benetti E, Giliberti A, Emiliozzi A, Valentino F, Bergantini L, Fallerini C, Anedda F, Amitrano S, Conticini E, Tita R, d’Alessandro M, Fava F, Marcantonio S, Baldassarri M, Bruttini M, Mazzei MA, Montagnani F, Mandalà M, Bargagli E, Furini S, Renieri A, Mari F. Clinical and molecular characterization of COVID-19 hospitalized patients. PLoS One 2020; 15:e0242534. [PMID: 33206719 PMCID: PMC7673557 DOI: 10.1371/journal.pone.0242534] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/05/2020] [Indexed: 01/08/2023] Open
Abstract
Clinical and molecular characterization by Whole Exome Sequencing (WES) is reported in 35 COVID-19 patients attending the University Hospital in Siena, Italy, from April 7 to May 7, 2020. Eighty percent of patients required respiratory assistance, half of them being on mechanical ventilation. Fiftyone percent had hepatic involvement and hyposmia was ascertained in 3 patients. Searching for common genes by collapsing methods against 150 WES of controls of the Italian population failed to give straightforward statistically significant results with the exception of two genes. This result is not unexpected since we are facing the most challenging common disorder triggered by environmental factors with a strong underlying heritability (50%). The lesson learned from Autism-Spectrum-Disorders prompted us to re-analyse the cohort treating each patient as an independent case, following a Mendelian-like model. We identified for each patient an average of 2.5 pathogenic mutations involved in virus infection susceptibility and pinpointing to one or more rare disorder(s). To our knowledge, this is the first report on WES and COVID-19. Our results suggest a combined model for COVID-19 susceptibility with a number of common susceptibility genes which represent the favorite background in which additional host private mutations may determine disease progression.
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Affiliation(s)
- Elisa Benetti
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | - Arianna Emiliozzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
- Department of Specialized and Internal Medicine, Tropical and Infectious Diseases Unit, Azienda Ospedaliera Universitaria Senese, Senese, Italy
| | | | - Laura Bergantini
- Unit of Respiratory Diseases and Lung Transplantation, Department of Internal and Specialist Medicine, University of Siena, Siena, Italy
| | | | - Federico Anedda
- Department of Emergency and Urgency, Medicine, Surgery and Neurosciences, Unit of Intensive Care Medicine, Siena University Hospital, Siena, Italy
| | - Sara Amitrano
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Senese, Italy
| | - Edoardo Conticini
- Rheumatology Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, Policlinico Le Scotte, Siena, Italy
| | - Rossella Tita
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Senese, Italy
| | - Miriana d’Alessandro
- Unit of Respiratory Diseases and Lung Transplantation, Department of Internal and Specialist Medicine, University of Siena, Siena, Italy
| | - Francesca Fava
- Medical Genetics, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Senese, Italy
| | - Simona Marcantonio
- Department of Emergency and Urgency, Medicine, Surgery and Neurosciences, Unit of Intensive Care Medicine, Siena University Hospital, Siena, Italy
| | | | - Mirella Bruttini
- Medical Genetics, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Senese, Italy
| | - Maria Antonietta Mazzei
- Department of Medical, Surgical and Neuro Sciences and Radiological Sciences, Unit of Diagnostic Imaging, University of Siena, Azienda Ospedaliera Universitaria Senese, Senese, Italy
| | - Francesca Montagnani
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
- Department of Specialized and Internal Medicine, Tropical and Infectious Diseases Unit, Azienda Ospedaliera Universitaria Senese, Senese, Italy
| | - Marco Mandalà
- Otolaryngology Unit, University of Siena, Siena, Italy
| | - Elena Bargagli
- Unit of Respiratory Diseases and Lung Transplantation, Department of Internal and Specialist Medicine, University of Siena, Siena, Italy
| | - Simone Furini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Senese, Italy
| | - Francesca Mari
- Medical Genetics, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Senese, Italy
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Tognetti L, Baldassarri M, Fava F, Provvidenziale L, Cinotti E, Renieri A, Rubegni P. A novel mutation in LMX1B gene in a newborn with nail-patella syndrome: Clinical and dermoscopic findings. Pediatr Dermatol 2020; 37:1205-1206. [PMID: 32892417 DOI: 10.1111/pde.14337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
We report on a 3-month-old female patient presenting with bilateral anonychia of the thumbnails and hyponychia of the index nails. Clinico-dermoscopic examination revealed triangular lunulae in all fingernails. Sequence analysis of LMX1B gene identified a novel heterozygous de novo mutation within exon 2, pathogenetic for a nail-patella syndrome.
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Affiliation(s)
- Linda Tognetti
- Dermatology Unit, Department of Medical, Surgical and Neurosciences, Siena University Hospital, Italy
| | | | - Francesca Fava
- Medical Genetics, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Luca Provvidenziale
- Dermatology Unit, Department of Medical, Surgical and Neurosciences, Siena University Hospital, Italy
| | - Elisa Cinotti
- Dermatology Unit, Department of Medical, Surgical and Neurosciences, Siena University Hospital, Italy
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Pietro Rubegni
- Dermatology Unit, Department of Medical, Surgical and Neurosciences, Siena University Hospital, Italy
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35
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Diotallevi C, Fava F, Gobbetti M, Tuohy K. Healthy dietary patterns to reduce obesity-related metabolic disease: polyphenol-microbiome interactions unifying health effects across geography. Curr Opin Clin Nutr Metab Care 2020; 23:437-444. [PMID: 32941185 DOI: 10.1097/mco.0000000000000697] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE OF REVIEW The spread of the Western lifestyle across the globe has led to a pandemic in obesity-related metabolic disease. The Mediterranean diet (MedDiet), Okinawa diet (OkD) and Nordic diet, derived from very different regions of the world and culinary traditions, have a large whole plant food component and are associated with reduced disease risk. This review focuses on polyphenol : microbiome interactions as one possible common mechanistic driver linking the protective effects whole plant foods against metabolic disease across healthy dietary patterns irrespective of geography. RECENT FINDINGS Although mechanistic evidence in humans is still scarce, animal studies suggest that polyphenol or polyphenol rich foods induce changes within the gut microbiota and its metabolic output of trimethylamine N-oxide, short-chain fatty acids, bile acids and small phenolic acids. These cross-kingdom signaling molecules regulate mammalian lipid and glucose homeostasis, inflammation and energy storage or thermogenesis, physiological processes determining obesity-related metabolic and cardiovascular disease risk. However, it appears that where in the intestine metabolites are produced, the microbiota communities involved, and interactions between the metabolites themselves, can all influence physiological responses, highlighting the need for a greater understanding of the kinetics and site of production of microbial metabolites within the gut. SUMMARY Interactions between polyphenols and metabolites produced by the gut microbiota are emerging as a possible unifying protective mechanism underpinning diverse healthy dietary patterns signaling across culinary traditions, across geography and across domains of life.
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Affiliation(s)
- Camilla Diotallevi
- Faculty of Science and Technology, Freie Universität Bozen-Libera Università di Bolzano, Bolzano
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy
| | - Francesca Fava
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy
| | - Marco Gobbetti
- Faculty of Science and Technology, Freie Universität Bozen-Libera Università di Bolzano, Bolzano
| | - Kieran Tuohy
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy
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36
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Staudacher HM, Scholz M, Lomer MC, Ralph FS, Irving PM, Lindsay JO, Fava F, Tuohy K, Whelan K. Gut microbiota associations with diet in irritable bowel syndrome and the effect of low FODMAP diet and probiotics. Clin Nutr 2020; 40:1861-1870. [PMID: 33183883 DOI: 10.1016/j.clnu.2020.10.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND AND AIMS Diet is both a modulator of the gastrointestinal microbiota and an important therapy in irritable bowel syndrome (IBS). We aimed to comprehensively (i) identify diet-microbiota associations in adults with IBS consuming habitual diet; (ii) assess the impact of two nutritional interventions on the microbiota; and (iii) determine whether baseline microbiota can predict clinical response to diet or probiotic intervention. METHODS Data were analyzed from 95 individuals with IBS participating in a previously published 4-week 2x2 factorial design randomized controlled trial investigating the impact of the low FODMAP diet (LFD) and co-administration of a probiotic. Diet was assessed at four hierarchical levels and partial 16S rRNA gene sequencing was used to profile the microbiota. RESULTS There were numerous diet-microbiota associations especially at the nutrient level, including a negative association between protein and Bifidobacterium abundance (rs = -0.358, p < 0.001). After correction for multiple testing, the significance for this association (q = 0.237) and all others was lost. Low FODMAP diet led to changes in abundance of major saccharolytic genera compared with sham diet, including higher Bacteroides (LFD 34.1% (15.7%) vs sham 23.3% (15.2%), q = 0.01) and lower Bifidobacterium (0.9% (1.0%) vs 2.1%, (2.5%) q = 0.029). Compared with placebo, probiotic supplementation led to higher Lactobacillus (probiotic 0.08% (0.1%) vs placebo 0.03% (0.2%), q < 0.001), and Streptococcus abundance (2.0% (2.2%) vs 0.6% (1.2%), q = 0.001). The probiotic treatment buffered the impact of the low FODMAP diet on Bifidobacterium. Baseline microbiota did not predict clinical response to either intervention. CONCLUSIONS Although diet modifies the gut microbiota, bivariate correlation analysis may only provide a limited explanation of the complex diet interactions with individual gut bacteria in IBS. Some diet interventions modify the microbiota in IBS. TRIAL REGISTRY ISRCTN (http://www.isrctn.com) Registered under ISRCTN registry identifier no.ISRCTN02275221.
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Affiliation(s)
- Heidi M Staudacher
- King's College London, Department of Nutritional Sciences, London, United Kingdom
| | - Matthias Scholz
- Research and Innovation Centre, Department of Food Quality and Nutrition, Nutrition and Nutrigenomics Group, Fondazione Edmund Mach, Trento, Italy
| | - Miranda Ce Lomer
- King's College London, Department of Nutritional Sciences, London, United Kingdom; Guy's and St Thomas' NHS Foundation Trust, Department of Gastroenterology, London, UK
| | - Frances S Ralph
- King's College London, Department of Nutritional Sciences, London, United Kingdom
| | - Peter M Irving
- King's College London, Department of Nutritional Sciences, London, United Kingdom; Guy's and St Thomas' NHS Foundation Trust, Department of Gastroenterology, London, UK
| | - James O Lindsay
- Barts Health NHS Trust, Department of Gastroenterology, Royal London Hospital, London, UK; Queen Mary University of London, Centre for Immunobiology, London, UK
| | - Francesca Fava
- Research and Innovation Centre, Department of Food Quality and Nutrition, Nutrition and Nutrigenomics Group, Fondazione Edmund Mach, Trento, Italy
| | - Kieran Tuohy
- Research and Innovation Centre, Department of Food Quality and Nutrition, Nutrition and Nutrigenomics Group, Fondazione Edmund Mach, Trento, Italy
| | - Kevin Whelan
- King's College London, Department of Nutritional Sciences, London, United Kingdom.
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Mastrocola R, Collotta D, Gaudioso G, Le Berre M, Cento AS, Ferreira Alves G, Chiazza F, Verta R, Bertocchi I, Manig F, Hellwig M, Fava F, Cifani C, Aragno M, Henle T, Joshi L, Tuohy K, Collino M. Effects of Exogenous Dietary Advanced Glycation End Products on the Cross-Talk Mechanisms Linking Microbiota to Metabolic Inflammation. Nutrients 2020; 12:nu12092497. [PMID: 32824970 PMCID: PMC7551182 DOI: 10.3390/nu12092497] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/15/2020] [Accepted: 08/17/2020] [Indexed: 12/12/2022] Open
Abstract
Heat-processed diets contain high amounts of advanced glycation end products (AGEs). Here we explore the impact of an AGE-enriched diet on markers of metabolic and inflammatory disorders as well as on gut microbiota composition and plasma proteins glycosylation pattern. C57BL/6 mice were allocated into control diet (CD, n = 15) and AGE-enriched diet (AGE-D, n = 15) for 22 weeks. AGE-D was prepared replacing casein by methylglyoxal hydroimidazolone-modified casein. AGE-D evoked increased insulin and a significant reduction of GIP/GLP-1 incretins and ghrelin plasma levels, altered glucose tolerance, and impaired insulin signaling transduction in the skeletal muscle. Moreover, AGE-D modified the systemic glycosylation profile, as analyzed by lectin microarray, and increased Nε-carboxymethyllysine immunoreactivity and AGEs receptor levels in ileum and submandibular glands. These effects were associated to increased systemic levels of cytokines and impaired gut microbial composition and homeostasis. Significant correlations were recorded between changes in bacterial population and in incretins and inflammatory markers levels. Overall, our data indicates that chronic exposure to dietary AGEs lead to a significant unbalance in incretins axis, markers of metabolic inflammation, and a reshape of both the intestinal microbiota and plasma protein glycosylation profile, suggesting intriguing pathological mechanisms underlying AGEs-induced metabolic derangements.
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Affiliation(s)
- Raffaella Mastrocola
- Department of Clinical and Biological Sciences, University of Turin, 10125 Turin, Italy; (A.S.C.); (M.A.)
- Correspondence: (R.M.); (M.C.); Tel.: +39-011-6707758 (R.M.); +39-011-6706861 (M.C.)
| | - Debora Collotta
- Department of Drug Science and Technology, University of Turin, 10125 Turin, Italy; (D.C.); (G.F.A.); (F.C.); (R.V.)
| | - Giulia Gaudioso
- Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy; (G.G.); (F.F.); (K.T.)
| | - Marie Le Berre
- Biomedical Sciences, National University of Ireland, H91 TK33 Galway, Ireland; (M.L.B.); (L.J.)
| | - Alessia Sofia Cento
- Department of Clinical and Biological Sciences, University of Turin, 10125 Turin, Italy; (A.S.C.); (M.A.)
| | - Gustavo Ferreira Alves
- Department of Drug Science and Technology, University of Turin, 10125 Turin, Italy; (D.C.); (G.F.A.); (F.C.); (R.V.)
| | - Fausto Chiazza
- Department of Drug Science and Technology, University of Turin, 10125 Turin, Italy; (D.C.); (G.F.A.); (F.C.); (R.V.)
| | - Roberta Verta
- Department of Drug Science and Technology, University of Turin, 10125 Turin, Italy; (D.C.); (G.F.A.); (F.C.); (R.V.)
| | - Ilaria Bertocchi
- Department of Neuroscience, University of Turin, 10124 Turin, Italy;
| | - Friederike Manig
- Chair of Food Chemistry, Technische Universität Dresden, 01062 Dresden, Germany; (F.M.); (M.H.); (T.H.)
| | - Michael Hellwig
- Chair of Food Chemistry, Technische Universität Dresden, 01062 Dresden, Germany; (F.M.); (M.H.); (T.H.)
| | - Francesca Fava
- Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy; (G.G.); (F.F.); (K.T.)
| | - Carlo Cifani
- Pharmacology Unit, School of Pharmacy, University of Camerino, 62032 Camerino, Italy;
| | - Manuela Aragno
- Department of Clinical and Biological Sciences, University of Turin, 10125 Turin, Italy; (A.S.C.); (M.A.)
| | - Thomas Henle
- Chair of Food Chemistry, Technische Universität Dresden, 01062 Dresden, Germany; (F.M.); (M.H.); (T.H.)
| | - Lokesh Joshi
- Biomedical Sciences, National University of Ireland, H91 TK33 Galway, Ireland; (M.L.B.); (L.J.)
| | - Kieran Tuohy
- Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy; (G.G.); (F.F.); (K.T.)
| | - Massimo Collino
- Department of Drug Science and Technology, University of Turin, 10125 Turin, Italy; (D.C.); (G.F.A.); (F.C.); (R.V.)
- Correspondence: (R.M.); (M.C.); Tel.: +39-011-6707758 (R.M.); +39-011-6706861 (M.C.)
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Koutsos A, Riccadonna S, Ulaszewska MM, Franceschi P, Trošt K, Galvin A, Braune T, Fava F, Perenzoni D, Mattivi F, Tuohy KM, Lovegrove JA. Two apples a day lower serum cholesterol and improve cardiometabolic biomarkers in mildly hypercholesterolemic adults: a randomized, controlled, crossover trial. Am J Clin Nutr 2020; 111:307-318. [PMID: 31840162 PMCID: PMC6997084 DOI: 10.1093/ajcn/nqz282] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 10/21/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Apples are rich in bioactive polyphenols and fiber. Evidence suggests that consumption of apples or their bioactive components is associated with beneficial effects on lipid metabolism and other markers of cardiovascular disease (CVD). However, adequately powered randomized controlled trials are necessary to confirm these data and explore the mechanisms. OBJECTIVE We aimed to determine the effects of apple consumption on circulating lipids, vascular function, and other CVD risk markers. METHODS The trial was a randomized, controlled, crossover, intervention study. Healthy mildly hypercholesterolemic volunteers (23 women, 17 men), with a mean ± SD BMI 25.3 ± 3.7 kg/m2 and age 51 ± 11 y, consumed 2 apples/d [Renetta Canada, rich in proanthocyanidins (PAs)] or a sugar- and energy-matched apple control beverage (CB) for 8 wk each, separated by a 4-wk washout period. Fasted blood was collected before and after each treatment. Serum lipids, glucose, insulin, bile acids, and endothelial and inflammation biomarkers were measured, in addition to microvascular reactivity, using laser Doppler imaging with iontophoresis, and arterial stiffness, using pulse wave analysis. RESULTS Whole apple (WA) consumption decreased serum total (WA: 5.89 mmol/L; CB: 6.11 mmol/L; P = 0.006) and LDL cholesterol (WA: 3.72 mmol/L; CB: 3.86 mmol/L; P = 0.031), triacylglycerol (WA: 1.17 mmol/L; CB: 1.30 mmol/L; P = 0.021), and intercellular cell adhesion molecule-1 (WA: 153.9 ng/mL; CB: 159.4 ng/mL; P = 0.028), and increased serum uric acid (WA: 341.4 μmol/L; CB: 330 μmol/L; P = 0.020) compared with the CB. The response to endothelium-dependent microvascular vasodilation was greater after the apples [WA: 853 perfusion units (PU), CB: 760 PU; P = 0.037] than after the CB. Apples had no effect on blood pressure or other CVD markers. CONCLUSIONS These data support beneficial hypocholesterolemic and vascular effects of the daily consumption of PA-rich apples by mildly hypercholesterolemic individuals.This trial was registered at clinicaltrials.gov as NCT01988389.
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Affiliation(s)
- Athanasios Koutsos
- Hugh Sinclair Unit of Human Nutrition and the Institute for Cardiovascular and Metabolic Research, Department of Food and Nutritional Sciences, University of Reading, Reading, United Kingdom
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Samantha Riccadonna
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Maria M Ulaszewska
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Pietro Franceschi
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Kajetan Trošt
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
- Steno Diabetes Centre Copenhagen, Gentofte, Denmark
| | - Amanda Galvin
- Hugh Sinclair Unit of Human Nutrition and the Institute for Cardiovascular and Metabolic Research, Department of Food and Nutritional Sciences, University of Reading, Reading, United Kingdom
| | - Tanya Braune
- Hugh Sinclair Unit of Human Nutrition and the Institute for Cardiovascular and Metabolic Research, Department of Food and Nutritional Sciences, University of Reading, Reading, United Kingdom
| | - Francesca Fava
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Daniele Perenzoni
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Fulvio Mattivi
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
- Department of Physics, University of Trento, Povo, Italy
| | - Kieran M Tuohy
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Julie A Lovegrove
- Hugh Sinclair Unit of Human Nutrition and the Institute for Cardiovascular and Metabolic Research, Department of Food and Nutritional Sciences, University of Reading, Reading, United Kingdom
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Palmieri M, Baldassarri M, Fava F, Fabbiani A, Gelli E, Tita R, Torre P, Petrioli R, Hadijstilianou T, Galimberti D, Cinotti E, Bengala C, Mandalà M, Piu P, Miano ST, Martellucci I, Vannini A, Pinto AM, Mencarelli MA, Marsili S, Renieri A, Frullanti E. Two-point-NGS analysis of cancer genes in cell-free DNA of metastatic cancer patients. Cancer Med 2020; 9:2052-2061. [PMID: 31991072 PMCID: PMC7064095 DOI: 10.1002/cam4.2782] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 11/18/2019] [Accepted: 12/02/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Although the efficacy of molecularly target agents in vitro, their use in routine setting is limited mainly to the use of anti-HER2 and antiEGFR agents in vivo. Moreover, core biopsy of a single cancer site may not be representative of the whole expanding clones and cancer molecular profile at relapse may differ with respect to the primary tumor. METHODS We assessed the status of a large panel of cancer driver genes by cell-free DNA (cfDNA) analysis in a cohort of 68 patients with 13 different solid tumors at disease progression. Whenever possible, a second cfDNA analysis was performed after a mean of 2.5 months, in order to confirm the identified clone(s) and to check the correlation with clinical evolution. RESULTS The approach was able to identify clones plausibly involved in the disease progression mechanism in about 65% of cases. A mean of 1.4 mutated genes (range 1-3) for each tumor was found. Point mutations in TP53, PIK3CA, and KRAS and copy number variations in FGFR3 were the gene alterations more commonly observed, with a rate of 48%, 20%, 16%, and 20%, respectively. Two-points-Next-Generation Sequencing (NGS) analysis demonstrated statistically significant correlation between allele frequency variation and clinical outcome (P = .026). CONCLUSIONS Irrespective of the primary tumor mutational burden, few mutated genes are present at disease progression. Clinical outcome is consistent with variation of allele frequency of specific clones indicating that cfDNA two-point-NGS analysis of cancer driver genes could be an efficacy tool for precision oncology.
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Affiliation(s)
| | | | - Francesca Fava
- Medical Genetics, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Alessandra Fabbiani
- Medical Genetics, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Elisa Gelli
- Medical Genetics, University of Siena, Siena, Italy
| | - Rossella Tita
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Pamela Torre
- Oncology, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Roberto Petrioli
- Oncology, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Theodora Hadijstilianou
- Department of Ophthalmology, Referral Center for Retinoblastoma, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Daniela Galimberti
- Department of Ophthalmology, Referral Center for Retinoblastoma, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Elisa Cinotti
- Department of Medical, Surgical and Neurosciences, Dermatology Unit, University of Siena, Siena, Italy
| | - Carmelo Bengala
- Medical Oncology, Ospedale Misericordia, Azienda Toscana Sud-Est, Grosseto, Italy
| | - Marco Mandalà
- Department of Otology and Skull Base Surgery, University of Siena, Siena, Italy
| | - Pietro Piu
- VisMederi s.r.l, Strada del Petriccio e Belriguardo, Siena, Italy
| | | | | | - Agnese Vannini
- Oncology, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Anna Maria Pinto
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | | | - Stefania Marsili
- Oncology, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
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40
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Palmieri M, Baldassarri M, Fava F, Fabbiani A, Campennì GM, Mencarelli MA, Tita R, Marsili S, Renieri A, Frullanti E. PIK3CA-CDKN2A clonal evolution in metastatic breast cancer and multiple points cell-free DNA analysis. Cancer Cell Int 2019; 19:274. [PMID: 31673247 PMCID: PMC6819469 DOI: 10.1186/s12935-019-0991-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 10/12/2019] [Indexed: 11/25/2022] Open
Abstract
Background Daily experience tells us that breast cancer can be controlled using standard protocols up to the advent of a relapse. Now new frontiers in precision medicine like liquid biopsy of cell free DNA (cfDNA) give us the possibility to understand cancer evolution and pick up the key mutation on specific cancer driver gene. However, tight schedule of standardized protocol may impair the use of personalized experimental drugs in a timely therapeutic window. Main body Here, using a combination of deep next generation sequencing and cfDNA liquid biopsy, we demonstrated that it is possible to monitor cancer relapse over time. We showed for the first time the exact correspondence from the increasing clonal expansion and clinical worsening of metastatic breast cancer. Conclusion Thanks to liquid biopsy may be possible to introduce new experimental drugs in the correct therapeutic window which would lead in the near future to an effective treatment which otherwise remains challenging.
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Affiliation(s)
- Maria Palmieri
- 1Medical Genetics Unit, Policlinico "Santa Maria alle Scotte", University of Siena, Viale Bracci, 2, 53100 Siena, Italy
| | | | - Francesca Fava
- 1Medical Genetics Unit, Policlinico "Santa Maria alle Scotte", University of Siena, Viale Bracci, 2, 53100 Siena, Italy
| | - Alessandra Fabbiani
- 1Medical Genetics Unit, Policlinico "Santa Maria alle Scotte", University of Siena, Viale Bracci, 2, 53100 Siena, Italy
| | | | | | - Rossella Tita
- 2Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Stefania Marsili
- 4Oncology, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Alessandra Renieri
- 1Medical Genetics Unit, Policlinico "Santa Maria alle Scotte", University of Siena, Viale Bracci, 2, 53100 Siena, Italy.,2Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Elisa Frullanti
- 1Medical Genetics Unit, Policlinico "Santa Maria alle Scotte", University of Siena, Viale Bracci, 2, 53100 Siena, Italy
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41
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Frullanti E, Palmieri M, Baldassarri M, Fava F, Fabbiani A, Gelli E, Tita R, Torre P, Petrioli R, Hadijstilianou T, Galimberti D, Cinotti E, Mencarelli MA, Pinto AM, Francini E, Marsili S, Francini G, Renieri A. Specific clonal expansion at disease progression (PD) in solid cancers pinpointed by cell free DNA analysis. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.e13144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e13144 Background: More than 50% of solid cancers sooner or later escape control of standard treatments. Detection and analysis of cell free circulating DNA (cfDNA) now offer the possibility to detect key mutations of cancer driver genes which may play a major role in the therapy escaping mechanism. We sought to identify clones of solid tumors escaping standard treatments in order to assess personalized treatment at PD. Methods: A cohort of patients with 10 different solid tumors progressing after standard therapy were selected. CfDNA analysis was performed using PAXgene blood ccfDNA tubes (QIAGEN), MagMAX cell-free total nucleic acid isolation kit, and ION PROTON platform (ThermoFisher Scientific). Results: Next generation sequencing analysis of 52 cancer-driver genes of cfDNA samples of 39 patients allowed for picking up clones plausibly involved in the PD mechanism in 60% of cases. A mean of 1.3 mutated genes (range 1-3) for each tumor was found. Point mutations in TP53, PIK3CA, and CNV in FGFR3 were the most commonly observed, with a rate of 41%, 16%, and 13%, respectively. Increased copy number variations of FGF receptors were identified in patients with non-small cell lung, pancreatic, and gastric cancer, and cholangiocarcinoma. Other clones had mutations in ESR1 (breast), CTNNB1 (uterus), KRAS and CCND2 (pancreas), EGFR and BRAF (lung). Interestingly, retinoblastomas resistant to Melphalan showed expanding mutated clones in PTEN or SMAD4. Increased levels of cfDNA were observed in the plasma of all patients. Conclusions: The results presented here show that irrespective of the primary tumor mutational burden and subsequent complex clonal evolution, a simplified mutational load is present at PD. One or few “sniper” clones drive progression and the molecular profile has a weak correlation with the primary tumor. Single driver mutations in TP53 remain the main target of a not yet developed specific therapy in most tumors such as breast, ovarian, uterine, lung, gastric cancers and glioblastoma. Among the actionable mutations, PIK3CA were found, not only in breast cancers, but also in uterine carcinoma, Sezary syndrome and glioblastoma, pinpointing the needs of specific trials in these tumors.
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Affiliation(s)
| | | | | | - Francesca Fava
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | | | - Elisa Gelli
- Medical Genetics, University of Siena, Siena, Italy
| | | | - Pamela Torre
- Medical Genetics, University of Siena, Siena, Italy
| | - Roberto Petrioli
- Medical Oncology, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Theodora Hadijstilianou
- Department of Ophthalmology, Referral Center for Retinoblastoma, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Daniela Galimberti
- Department of Ophthalmology, Referral Center for Retinoblastoma, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Elisa Cinotti
- Department of Medical, Surgical and Neuro-Sciences, Dermatology Unit, University of Siena, Siena, Italy
| | | | - Anna Maria Pinto
- Genetica medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | | | - Stafania Marsili
- Medical Oncology, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Guido Francini
- Medical Genetics, University of Siena, Italy, Siena, Italy
| | - Alessandra Renieri
- Medical Genetics, University of Siena and Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
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42
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Rizzetto L, Fava F, Tuohy KM, Selmi C. Connecting the immune system, systemic chronic inflammation and the gut microbiome: The role of sex. J Autoimmun 2018; 92:12-34. [PMID: 29861127 DOI: 10.1016/j.jaut.2018.05.008] [Citation(s) in RCA: 192] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/18/2018] [Accepted: 05/21/2018] [Indexed: 12/12/2022]
Abstract
Unresolved low grade systemic inflammation represents the underlying pathological mechanism driving immune and metabolic pathways involved in autoimmune diseases (AID). Mechanistic studies in animal models of AID and observational studies in patients have found alterations in gut microbiota communities and their metabolites, suggesting a microbial contribution to the onset or progression of AID. The gut microbiota and its metabolites have been shown to influence immune functions and immune homeostasis both within the gut and systematically. Microbial derived-short chain fatty acid (SCFA) and bio-transformed bile acid (BA) have been shown to influence the immune system acting as ligands specific cell signaling receptors like GPRCs, TGR5 and FXR, or via epigenetic processes. Similarly, intestinal permeability (leaky gut) and bacterial translocation are important contributors to chronic systemic inflammation and, without repair of the intestinal barrier, might represent a continuous inflammatory stimulus capable of triggering autoimmune processes. Recent studies indicate gender-specific differences in immunity, with the gut microbiota shaping and being concomitantly shaped by the hormonal milieu governing differences between the sexes. A bi-directional cross-talk between microbiota and the endocrine system is emerging with bacteria being able to produce hormones (e.g. serotonin, dopamine and somatostatine), respond to host hormones (e.g. estrogens) and regulate host hormones' homeostasis (e.g by inhibiting gene prolactin transcription or converting glucocorticoids to androgens). We review herein how gut microbiota and its metabolites regulate immune function, intestinal permeability and possibly AID pathological processes. Further, we describe the dysbiosis within the gut microbiota observed in different AID and speculate how restoring gut microbiota composition and its regulatory metabolites by dietary intervention including prebiotics and probiotics could help in preventing or ameliorating AID. Finally, we suggest that, given consistent observations of microbiota dysbiosis associated with AID and the ability of SCFA and BA to regulate intestinal permeability and inflammation, further mechanistic studies, examining how dietary microbiota modulation can protect against AID, hold considerable potential to tackle increased incidence of AID at the population level.
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Affiliation(s)
- Lisa Rizzetto
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy.
| | - Francesca Fava
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy
| | - Kieran M Tuohy
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy
| | - Carlo Selmi
- Division of Rheumatology and Clinical Immunology, Humanitas Research Hospital, Rozzano, Italy; BIOMETRA Department, University of Milan, Italy
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Tocci N, Perenzoni D, Iamonico D, Fava F, Weil T, Mattivi F. Extracts From Hypericum hircinum subsp. majus Exert Antifungal Activity Against a Panel of Sensitive and Drug-Resistant Clinical Strains. Front Pharmacol 2018; 9:382. [PMID: 29755350 PMCID: PMC5932341 DOI: 10.3389/fphar.2018.00382] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 04/03/2018] [Indexed: 12/27/2022] Open
Abstract
During the last two decades incidences of fungal infections dramatically increased and the often accompanying failure of available antifungal therapies represents a substantial clinical problem. The urgent need for novel antimycotics called particular attention to the study of natural products. The genus Hypericum includes many species that are used in the traditional medicine to treat pathological states like inflammations and infections caused by fungi. However, despite the diffused use of Hypericum-based products the antifungal potential of the genus is still poorly investigated. In this study five Hypericum species autochthonous of Central and Eastern Europe were evaluated regarding their polyphenolic content, their toxicological safety and their antifungal potential against a broad panel of clinical fungal isolates. LC-MS analysis led to the identification and quantification of 52 compounds, revealing that Hypericum extracts are rich sources of flavonols, benzoates and cinnamates, and of flavan-3-ols. An in-depth screen of the biological activity of crude extracts clearly unveiled H. hircinum subsp. majus as a promising candidate species for the search of novel antifungals. H. hircinum is diffused in the Mediterranean basin from Spain to Turkey where it is traditionally used to prepare a herbal tea indicated for the treatment of respiratory tract disorders, several of which are caused by fungi. Noteworthy, the infusion of H. hircinum subsp. majus excreted broad antifungal activity against Penicillium, Aspergillus and non-albicans Candida isolates comprising strains both sensitive and resistant to fluconazole. Additionally, it showed no cytotoxicity on human cells and the chemical characterization of the H. hircinum subsp. majus infusion revealed high amounts of the metabolite hyperoside. These results scientifically support the traditional use of H. hircinum extracts for the treatment of respiratory tract infections and suggest the presence of exploitable antifungal principles for further investigations aimed at developing novel antifungal therapies.
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Affiliation(s)
- Noemi Tocci
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Daniele Perenzoni
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Duilio Iamonico
- Laboratory of Phytogeography and Applied Geobotany, Section Environment and Landscape, Department of Planning, Design, and Technology of Architecture, Sapienza University of Rome, Rome, Italy
| | - Francesca Fava
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Tobias Weil
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Fulvio Mattivi
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.,Centre Agriculture Food Environment, University of Trento, Trento, Italy
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44
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D'hoe K, Conterno L, Fava F, Falony G, Vieira-Silva S, Vermeiren J, Tuohy K, Raes J. Prebiotic Wheat Bran Fractions Induce Specific Microbiota Changes. Front Microbiol 2018; 9:31. [PMID: 29416529 PMCID: PMC5787670 DOI: 10.3389/fmicb.2018.00031] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/09/2018] [Indexed: 01/08/2023] Open
Abstract
Wheat bran fibers are considered beneficial to human health through their impact on gut microbiota composition and activity. Here, we assessed the prebiotic potential of selected bran fractions by performing a series of fecal slurry anaerobic fermentation experiments using aleurone as well as total, ultrafine, and soluble wheat bran (swb) as carbon sources. By combining amplicon-based community profiling with a fluorescent in situ hybridization (FISH) approach, we found that incubation conditions favor the growth of Proteobacteria such as Escherichia and Bilophila. These effects were countered in all but one [total wheat bran (twb)] fermentation experiments. Growth of Bifidobacterium species was stimulated after fermentation using ultrafine, soluble, and twb, in the latter two as part of a general increase in bacterial load. Both ultrafine and swb fermentation resulted in a trade-off between Bifidobacterium and Bilophila, as previously observed in human dietary supplementation studies looking at the effect of inulin-type fructans on the human gut microbiota. Aleurone selectively stimulated growth of Dorea and butyrate-producing Roseburia. All fermentation experiments induced enhanced gas production; increased butyrate concentrations were only observed following soluble bran incubation. Our results open perspectives for the development of aleurone as a complementary prebiotic selectively targeting colon butyrate producers.
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Affiliation(s)
- Kevin D'hoe
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.,Jeroen Raes Lab, VIB KU Leuven Center for Microbiology, Leuven, Belgium.,Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Lorenza Conterno
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy.,Fermentation and Distillation, Laimburg Research Centre, Bolzano, Italy
| | - Francesca Fava
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
| | - Gwen Falony
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.,Jeroen Raes Lab, VIB KU Leuven Center for Microbiology, Leuven, Belgium
| | - Sara Vieira-Silva
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.,Jeroen Raes Lab, VIB KU Leuven Center for Microbiology, Leuven, Belgium
| | | | - Kieran Tuohy
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
| | - Jeroen Raes
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.,Jeroen Raes Lab, VIB KU Leuven Center for Microbiology, Leuven, Belgium.,Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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Conterno L, Martinelli F, Tamburini M, Fava F, Mancini A, Sordo M, Pindo M, Martens S, Masuero D, Vrhovsek U, Dal Lago C, Ferrario G, Morandini M, Tuohy K. Measuring the impact of olive pomace enriched biscuits on the gut microbiota and its metabolic activity in mildly hypercholesterolaemic subjects. Eur J Nutr 2017; 58:63-81. [PMID: 29124388 PMCID: PMC6424929 DOI: 10.1007/s00394-017-1572-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 10/24/2017] [Indexed: 12/21/2022]
Abstract
Purpose Olive pomace is a major waste product of olive oil production but remains rich in polyphenols and fibres. We measured the potential of an olive pomace-enriched biscuit formulation delivering 17.1 ± 4.01 mg/100 g of hydroxytyrosol and its derivatives, to modulate the composition and metabolic activity of the human gut microbiota. Methods In a double-blind, controlled parallel dietary intervention 62 otherwise healthy hypercholesterolemic (total plasma cholesterol 180–240 mg/dl) subjects were randomly assigned to eat 90 g of olive pomace-enriched biscuit (olive-enriched product, OEP) or an isoenergetic control (CTRL) for 8 weeks. Fasted blood samples, 24-h urine and faecal samples were collected before and after dietary intervention for measurement of microbiota, metabolites and clinical parameters. Results Consumption of OEP biscuits did not impact on the diversity of the faecal microbiota and there was no statistically significant effect on CVD markers. A trend towards reduced oxidized LDL cholesterol following OEP ingestion was observed. At the genus level lactobacilli and Ruminococcus were reduced in OEP compared to CTRL biscuits. A trend towards increased bifidobacteria abundance was observed after OEP ingestion in 16S rRNA profiles, by fluorescent in situ hybridization and by qPCR. Targeted LC–MS revealed significant increases phenolic acid concentrations in 24-h urine following OEP ingestion and 3,4-dihydroxyphenylacetic acid (DOPAC) and homovanillic acid, derivatives of hydroxytyrosol, were elevated in blood. A sex effect was apparent in urine small phenolic acid concentrations, and this sex effect was mirrored by statistically significant differences in relative abundances of faecal bacteria between men and women. Conclusion Ingestion of OEP biscuits led to a significant increase in the metabolic output of the gut microbiota with an apparent sex effect possibly linked to differences in microbiota makeup. Increased levels of homovanillic acid and DOPAC, thought to be involved in reducing oxidative LDL cholesterol, were observed upon OEP ingestion. However, OEP did not induce statistically significant changes in either ox-LDL or urinary isoprostane in this study.
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Affiliation(s)
- Lorenza Conterno
- OlioCRU s.r.l. Research and Development Group, Via Aldo Moro 1, 38062, Arco, TN, Italy
| | - Francesca Martinelli
- OlioCRU s.r.l. Research and Development Group, Via Aldo Moro 1, 38062, Arco, TN, Italy
| | - Matteo Tamburini
- OlioCRU s.r.l. Research and Development Group, Via Aldo Moro 1, 38062, Arco, TN, Italy
| | - Francesca Fava
- Department of Food Quality and Nutrition, Research and Innovation Centre-Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Andrea Mancini
- Department of Food Quality and Nutrition, Research and Innovation Centre-Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Maddalena Sordo
- Department of Food Quality and Nutrition, Research and Innovation Centre-Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Massimo Pindo
- Genomics and Advanced Biology Unit, Research and Innovation Centre-Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Stefan Martens
- Department of Food Quality and Nutrition, Research and Innovation Centre-Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Domenico Masuero
- Department of Food Quality and Nutrition, Research and Innovation Centre-Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Urska Vrhovsek
- Department of Food Quality and Nutrition, Research and Innovation Centre-Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Claudia Dal Lago
- Casa di Cura Eremo di Arco s.r.l., Via XXI Aprile 1, 38062, Arco, TN, Italy
| | - Gabriele Ferrario
- Casa di Cura Eremo di Arco s.r.l., Via XXI Aprile 1, 38062, Arco, TN, Italy
| | - Mario Morandini
- OlioCRU s.r.l. Research and Development Group, Via Aldo Moro 1, 38062, Arco, TN, Italy
| | - Kieran Tuohy
- Department of Food Quality and Nutrition, Research and Innovation Centre-Fondazione Edmund Mach, San Michele all'Adige, Italy.
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Staudacher HM, Lomer MCE, Farquharson FM, Louis P, Fava F, Franciosi E, Scholz M, Tuohy KM, Lindsay JO, Irving PM, Whelan K. A Diet Low in FODMAPs Reduces Symptoms in Patients With Irritable Bowel Syndrome and A Probiotic Restores Bifidobacterium Species: A Randomized Controlled Trial. Gastroenterology 2017. [PMID: 28625832 DOI: 10.1053/j.gastro.2017.06.010] [Citation(s) in RCA: 255] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
BACKGROUND & AIMS Dietary restriction of fermentable carbohydrates (a low FODMAP diet) has been reported to reduce symptoms in some patients with irritable bowel syndrome (IBS). We performed a randomized, placebo-controlled study to determine its effects on symptoms and the fecal microbiota in patients with IBS. METHODS We performed a 2×2 factorial trial of 104 patients with IBS (18-65 years old), based on the Rome III criteria, at 2 hospitals in the United Kingdom. Patients were randomly assigned (blinded) to groups given counselling to follow a sham diet or diet low in FODMAPs for 4 weeks, along with a placebo or multistrain probiotic formulation, resulting in 4 groups (27 receiving sham diet/placebo, 26 receiving sham diet/probiotic, 24 receiving low FODMAP diet /placebo, and 27 receiving low FODMAP diet/probiotic). The sham diet restricted a similar number of staple and non-staple foods as the low FODMAP diet; the diets had similar degrees of difficulty to follow. Dietary counselling was given to patients in all groups and data on foods eaten and compliance were collected. The incidence and severity of 15 gastrointestinal symptoms and overall symptoms were measured daily for 7 days before the study period; along with stool frequency and consistency. At baseline, global and individual symptoms were measured, along with generic and disease-specific health-related quality of life, using standard scoring systems. All data were collected again at 4 weeks, and patients answered questions about adequate symptom relief. Fecal samples were collected at baseline and after 4 weeks and analyzed by quantitative PCR and 16S rRNA sequencing. The co-primary endpoints were adequate relief of symptoms and stool Bifidobacterium species abundance at 4 weeks. RESULTS There was no significant interaction between the interventions in adequate relief of symptoms (P = .52) or Bifidobacterium species (P = .68). In the intention-to-treat analysis, a higher proportion of patients in the low FODMAP diet had adequate symptom relief (57%) than in the sham diet group (38%), although the difference was not statistically significant (P = .051). In the per-protocol analysis, a significantly higher proportion of patients on the low FODMAP diet had adequate symptom relief (61%) than in the sham diet group (39%) (P = .042). Total mean IBS-Severity Scoring System score was significantly lower for patients on the low FODMAP diet (173 ± 95) than the sham diet (224 ± 89) (P = .001), but not different between those given probiotic (207 ± 98) or placebo (192 ± 93) (P = .721) Abundance of Bifidobacterium species was lower in fecal samples from patients on the low FODMAP diet (8.8 rRNA genes/g) than patients on the sham diet (9.2 rRNA genes/g) (P = .008), but higher in patients given probiotic (9.1 rRNA genes/g) than patients given placebo (8.8 rRNA genes/g) (P = .019). There was no effect of the low FODMAP diet on microbiota diversity in fecal samples. CONCLUSIONS In a placebo-controlled study of patients with IBS, a low FODMAP diet associates with adequate symptom relief and significantly reduced symptom scores compared with placebo. It is not clear whether changes resulted from collective FODMAP restriction or removal of a single component, such as lactose. Co-administration of the multistrain probiotic increased numbers of Bifidobacterium species, compared with placebo, and might be given to restore these bacteria to patients on a low FODMAP diet. Trial registration no: ISRCTN02275221.
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Affiliation(s)
- Heidi Maria Staudacher
- Faculty of Life Sciences and Medicine, Diabetes and Nutritional Sciences Division, King's College London, London, United Kingdom
| | - Miranda C E Lomer
- Faculty of Life Sciences and Medicine, Diabetes and Nutritional Sciences Division, King's College London, London, United Kingdom; Department of Gastroenterology, Guys and St Thomas' NHS Foundation Trust, London, United Kingdom; Department of Nutrition and Dietetics, Guys and St Thomas' NHS Foundation Trust, London, United Kingdom
| | - Freda M Farquharson
- The Rowett Institute, University of Aberdeen, Gut Health Group, Aberdeen, United Kingdom
| | - Petra Louis
- The Rowett Institute, University of Aberdeen, Gut Health Group, Aberdeen, United Kingdom
| | - Francesca Fava
- Research and Innovation Centre, Department of Food Quality and Nutrition, Nutrition and Nutrigenomics Group, Fondazione Edmund Mach, Trento, Italy
| | - Elena Franciosi
- Research and Innovation Centre, Department of Food Quality and Nutrition, Nutrition and Nutrigenomics Group, Fondazione Edmund Mach, Trento, Italy
| | - Matthias Scholz
- Research and Innovation Centre, Department of Food Quality and Nutrition, Nutrition and Nutrigenomics Group, Fondazione Edmund Mach, Trento, Italy
| | - Kieran M Tuohy
- Research and Innovation Centre, Department of Food Quality and Nutrition, Nutrition and Nutrigenomics Group, Fondazione Edmund Mach, Trento, Italy
| | - James O Lindsay
- Blizard Institute, Queen Mary University of London, Centre for Immunobiology, London, United Kingdom; Barts Health NHS Trust, London, United Kingdom
| | - Peter M Irving
- Faculty of Life Sciences and Medicine, Diabetes and Nutritional Sciences Division, King's College London, London, United Kingdom; Department of Gastroenterology, Guys and St Thomas' NHS Foundation Trust, London, United Kingdom
| | - Kevin Whelan
- Faculty of Life Sciences and Medicine, Diabetes and Nutritional Sciences Division, King's College London, London, United Kingdom.
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Ceppa F, Faccenda F, De Filippo C, Albanese D, Pindo M, Martelli R, Marconi P, Lunelli F, Fava F, Parisi G. Influence of essential oils in diet and life-stage on gut microbiota and fillet quality of rainbow trout (Oncorhynchus mykiss). Int J Food Sci Nutr 2017; 69:318-333. [PMID: 28859525 DOI: 10.1080/09637486.2017.1370699] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Developing fish farming to meet the demands of food security and sustainability in the 21st century will require new farming systems and improved feeds. Diet and microbe interactions in the gut is an important variable with the potential to make a significant impact on future fish farming diets and production systems. It was monitored the gut microbiota of farmed rainbow trout using 16S rRNA profiling over 51 weeks during standard rearing conditions and feeding diet with supplementation of an essential oils (MixOil) mixture from plants (at a concentration in diet of 200 mg/kg). Gut microbiota 16S rRNA profiling indicated that the fish gut was dominated by Actinobacteria, Proteobacteria, Bacteroidetes and Firmicutes. Although the dietary supplementation with MixOil had no impact on either the composition or architecture of gut microbiota, significant changes in alpha and beta diversity and relative abundance of groups of gut bacteria were evident during growth stages on test feeds, especially upon prolonged growth on finishing feed. Fish fillet quality to guarantee palatability and safety for human consumption was also evaluated. Significant differences within the gut microbiota of juvenile and adult trout under the same rearing conditions were observed, The addition of essential oil blend affected some physicochemical characteristics of trout fillets, including their resistance to oxidative damage and their weight loss (as liquid loss and water holding capacity) during the first period of storage, that are two important parameters related to product shelf life and susceptibility to spoilage. The results highlighted the need for further studies concern dietary microbiome modulation at different life stages and its influence on animal health, growth performance and final product quality.
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Affiliation(s)
- Florencia Ceppa
- a Department of Food Quality and Nutrition, Nutrition and Nutrigenomics Unit, Research and Innovation Center , Fondazione Edmund Mach , Trento , Italy
| | - Filippo Faccenda
- b Technology Transfer Centre, Experiment and Technological Services Department , Fondazione Edmund Mach , Trento , Italy
| | - Carlotta De Filippo
- c Institute of Biometeorology , National Research Council (IBIMET-CNR) , Firenze , Italy
| | - Davide Albanese
- d Computational Biology Department, Research and Innovation Center , Fondazione Edmund Mach , Trento , Italy
| | - Massimo Pindo
- e Genomics Platform, Genomics and Biology of Fruit Crop Department, Research and Innovation Center , Fondazione Edmund Mach , Trento , Italy
| | - Roberta Martelli
- f Department of Agri-Food Production and Environmental Sciences, Section of Animal Sciences , University of Firenze , Firenze , Italy
| | - Paola Marconi
- g Istituto Zooprofilattico Sperimentale del Lazio e della Toscana M. Aleandri , Firenze , Italy
| | - Fernando Lunelli
- b Technology Transfer Centre, Experiment and Technological Services Department , Fondazione Edmund Mach , Trento , Italy
| | - Francesca Fava
- a Department of Food Quality and Nutrition, Nutrition and Nutrigenomics Unit, Research and Innovation Center , Fondazione Edmund Mach , Trento , Italy
| | - Giuliana Parisi
- f Department of Agri-Food Production and Environmental Sciences, Section of Animal Sciences , University of Firenze , Firenze , Italy
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Lotti C, Rubert J, Fava F, Tuohy K, Mattivi F, Vrhovsek U. Development of a fast and cost-effective gas chromatography–mass spectrometry method for the quantification of short-chain and medium-chain fatty acids in human biofluids. Anal Bioanal Chem 2017; 409:5555-5567. [DOI: 10.1007/s00216-017-0493-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 06/08/2017] [Accepted: 06/23/2017] [Indexed: 01/05/2023]
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Affiliation(s)
- Francesca Fava
- Nutrition and Nutrigenomics Unit, Department of food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, 38010, Italy
| | - Kieran M Tuohy
- Nutrition and Nutrigenomics Unit, Department of food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, 38010, Italy
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Karavana V, Smith I, Kanellis G, Sigala I, Kinsella T, Zakynthinos S, Liu L, Chen J, Zhang X, Liu A, Guo F, Liu S, Yang Y, Qiu H, Grimaldi DG, Kaya E, Acicbe O, Kayaalp I, Asar S, Dogan M, Eren G, Hergunsel O, Pavelescu D, Grintescu I, Mirea L, Guanziroli M, Gotti M, Marino A, Cressoni M, Vergani G, Chiurazzi C, Chiumello D, Gattinoni L, Guanziroli M, Gotti M, Vergani G, Cressoni M, Chiurazzi C, Marino A, Spano S, Chiumello D, Gattinoni L, Guanziroli M, Gotti M, Vergani G, Marino A, Cressoni M, Chiurazzi C, Chiumello D, Gattinoni L, Massaro F, Moustakas A, Johansson S, Larsson A, Perchiazzi G, Zhang XW, Guo FM, Chen JX, Xue M, Yang Y, Qiu HB, Chen JX, Liu L, Yang L, Zhang XW, Guo FM, Yang Y, Qiu HB, Fister M, Knafelj R, Suzer MA, Kavlak ME, Atalan HK, Gucyetmez B, Cakar N, Weller D, Grootendorst AF, Dijkstra A, Kuijper TM, Cleffken BI, Regli A, De Keulenaer B, Van Heerden P, Hadfield D, Hopkins PA, Penhaligon B, Reid F, Hart N, Rafferty GF, Grasselli G, Mauri T, Lazzeri M, Carlesso E, Cambiaghi B, Eronia N, Maffezzini E, Bronco A, Abbruzzese C, Rossi N, Foti G, Bellani G, Pesenti A, Bassi GL, Panigada M, Ranzani O, Kolobow T, Zanella A, Cressoni M, Berra L, Parrini V, Kandil H, Salati G, Livigni S, Livigni S, Amatu A, Girardis M, Barbagallo M, Moise G, Mercurio G, Costa A, Vezzani A, Lindau S, Babel J, Cavana M, Torres A, Panigada M, Bassi GL, Ranzani OT, Kolobow T, Zanella A, Cressoni M, Berra L, Parrini V, Kandil H, Salati G, Livigni S, Amatu A, Girardis M, Barbagallo M, Moise G, Mercurio G, Costa A, Vezzani A, Lindau S, Babel J, Cavana M, Torres A, Umbrello M, Taverna M, Formenti P, Mistraletti G, Vetrone F, Marino A, Vergani G, Baisi A, Chiumello D, Garnero AG, Novotni DN, Arnal JA, Urner M, Fan E, Dres M, Vorona S, Brochard L, Ferguson ND, Goligher EC, Leung C, Joynt G, Wong W, Lee A, Gomersall C, Poels S, Casaer M, Schetz M, Van den Berghe G, Meyfroidt G, Holzgraefe B, Von Kobyletzki LB, Larsson A, Cianchi G, Becherucci F, Batacchi S, Cozzolino M, Franchi F, Di Valvasone S, Ferraro MC, Peris A, Phiphitthanaban H, Wacharasint P, Wongsrichanalai V, Lertamornpong A, Pengpinij O, Wattanathum A, Oer-areemitr N, Boddi M, Cianchi G, Cappellini E, Ciapetti M, Batacchi S, Di Lascio G, Bonizzoli M, Cozzolino M, Peris A, Lazzeri C, Cianchi G, Bonizzoli M, Di Lascio G, Cozzolino M, Peris A, Katsin ML, Hurava MY, Dzyadzko AM, Hermann A, Schellongowski P, Bojic A, Riss K, Robak O, Lamm W, Sperr W, Staudinger T, Buoninsegni LT, Bonizzoli M, Cozzolino M, Parodo J, Ottaviano A, Cecci L, Corsi E, Ricca V, Peris A, de Garibay APR, Ende-Schneider B, Schreiber C, Kreymann B, Turani F, Resta M, Niro D, Castaldi P, Boscolo G, Gonsales G, Martini S, Belli A, Zamidei L, Falco M, Lamas T, Mendes J, Galazzi A, Mauri T, Benco B, Binda F, Masciopinto L, Lazzeri M, Carlesso E, Lissoni A, Grasselli G, Adamini I, Pesenti A, Thamjamrassri T, Watcharotayangul J, Numthavaj P, Kongsareepong S, Higuera J, Cabestrero D, Rey L, Narváez G, Blandino A, Aroca M, Saéz S, De Pablo R, Mohamed A, Sklar M, Munshi L, Mauri T, Lazzeri M, Alban L, Turrini C, Panigada M, Taccone P, Carlesso E, Marenghi C, Spadaro S, Grasselli G, Volta C, Pesenti A, Higuera J, Alonso DC, Blandino A, Narváez G, González LR, Aroca M, Saéz S, De Pablo R, Franci A, Stocchi G, Cappuccini G, Socci F, Cozzolino M, Guetti C, Rastrelli P, Peris A, Nestorowicz A, Glapinski J, Fijalkowska-Nestorowicz A, Wosko J, Fijalkowska-Nestorowicz A, Glapinski J, Wosko J, Duprez F, Bonus T, Cuvelier G, Mashayekhi S, Ollieuz S, Reychler G, Bonus T, Duprez F, Cuvelier G, Mashayekhi S, Ollieuz S, Reychler G, Kuchyn I, Bielka K, Sergienko A, Jones H, Day C, Park SC, Yeom SR, Myatra SN, Gupta S, Rajnala V, Divatia J, Silva JV, Olvera OA, Schulte RC, Bermudez MC, Zorrilla LP, Ferretis HL, García KT, Balciuniene N, Ramsaite J, Kriukelyte O, Krikscionaitiene A, Tamosuitis T, Terragni P, Brazzi L, Falco D, Pistidda L, Magni G, Bartoletti L, Mascia L, Filippini C, Ranieri V, Kyriakoudi A, Rovina N, Koltsida O, Konstantellou E, Kardara M, Kostakou E, Gavriilidis G, Vasileiadis I, Koulouris N, Koutsoukou A, Van Snippenburg W, Kröner A, Flim M, Buise M, Hemler R, Spronk P, Regli A, Noffsinger B, De Keulenaer B, Singh B, Hockings L, Van Heerden P, Spina C, Bronco A, Magni F, Di Giambattista C, Vargiolu A, Bellani G, Foti G, Citerio G, Scaramuzzo G, Spadaro S, Waldmann AD, Böhm SH, Ragazzi R, Volta CA, Heines SJ, Strauch U, Van de Poll MC, Roekaerts PM, Bergmans DC, Sosio S, Gatti S, Maffezzini E, Punzi V, Asta A, Foti G, Bellani G, Glapinski J, Mroczka J, Nestorowicz A, Fijalkowska-Nestorowicz A, Yaroshetskiy AI, Rezepov NA, Mandel IA, Gelfand BR, Ozen E, Karakoc E, Ayyildiz A, Kara S, Ekemen S, Yelken BB, Saasouh W, Freeman J, Turan A, Hajjej Z, Sellami W, Bousselmi M, Samoud W, Gharsallah H, Labbene I, Ferjani M, Vetrugno L, Barbariol F, Forfori F, Regeni I, Della Rocca G, Jansen D, Jonkman A, Doorduin J, Roesthuis L, Van der Hoeven J, Heunks L, Marocco SA, Bottiroli M, Pinciroli R, Galanti V, Calini A, Gagliardone M, Bellani G, Fumagalli R, Gatti S, Abbruzzese C, Ippolito D, Sala VL, Meroni V, Bronco A, Foti G, Bellani G, Elbanna M, Nassar Y, Abdelmohsen A, Yahia M, Mongodi S, Mojoli F, Via G, Tavazzi G, Fava F, Pozzi M, Iotti GA, Bouhemad B, Ruiz-Ferron F, Simón JS, Gordillo-Resina M, Chica-Saez V, Garcia MR, Vela-Colmenero R, Redondo-Orts M, Gontijo-Coutinho C, Ozahata T, Nocera P, Franci D, Santos T, Carvalho-Filho M, Fochi O, Gatti S, Nacoti M, Signori D, Bronco A, Bonacina D, Bellani G, Bonanomi E, Mongodi S, Bonvecchio E, Stella A, Roldi E, Orlando A, Luperto M, Bouhemad B, Iotti GA, Mojoli F, Trunfio D, Licitra G, Martinelli R, Vannini D, Giuliano G, Vetrugno L, Forfori F, Näslund E, Lindberg LG, Lund I, Larsson A, Frithiof R, Nichols A, Freeman J, Pentakota S, Kodali B, Pranskunas A, Kiudulaite I, Simkiene J, Damanskyte D, Pranskuniene Z, Arstikyte J, Vaitkaitis D, Pilvinis V, Brazaitis M, Pool R, Haugaa H, Botero A, Escobar D, Maberry D, Tønnessen T, Zuckerbraun B, Pinsky M, Gomez H, Lyons H, Trimmings A, Domizi R, Scorcella C, Damiani E, Pierantozzi S, Tondi S, Monaldi V, Carletti A, Zuccari S, Adrario E, Pelaia P, Donati A, Kazune S, Grabovskis A, Volceka K, Rubins U, Bol M, Suverein M, Delnoij T, Driessen R, Heines S, Delhaas T, Vd Poll M, Sels J, Jozwiak M, Chambaz M, Sentenac P, Richard C, Monnet X, Teboul JL, Bitar Z, Maadarani O, Al Hamdan R, Huber W, Malbrain M, Chew M, Mallat J, Tagami T, Hundeshagen S, Wolf S, Huber W, Mair S, Schmid R, Aron J, Adlam M, Dua G, Mu L, Chen L, Yoon J, Clermont G, Dubrawski A, Duhailib Z, Al Assas K, Shafquat A, Salahuddin N, Donaghy J, Morgan P, Valeanu L, Stefan M, Provenchere S, Longrois D, Shaw A, Mythen MG, Shook D, Hayashida D, Zhang X, Munson SH, Sawyer A, Mariyaselvam M, Blunt M, Young P, Nakwan N, Khwannimit B, Checharoen P, Berger D, Moller P, Bloechlinger S, Bloch A, Jakob S, Takala J, Van den Brule JM, Stolk R, Vinke E, Van Loon LM, Pickkers P, Van der Hoeven JG, Kox M, Hoedemaekers CW, 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J, Lahmer T, Schmid R, Latham H, Bengtson CD, Satterwhite L, Stites M, Simpson SQ, Latham H, Bengtson CD, Satterwhite L, Stites M, Simpson SQ, Skladzien T, Cicio M, Garlicki J, Serednicki W, Wordliczek J, Vargas P, Salazar A, Mercado P, Espinoza M, Graf J, Kongpolprom N, Sanguanwong N, Jonnada S, Gerrard C, Jones N, Morley T, Thorburn PT, Trimmings A, Musaeva T, Zabolotskikh I, Salazar A, Vargas P, Mercado P, Espinoza M, Graf J, Horst S, Lipcsey M, Kawati R, Pikwer A, Rasmusson J, Castegren M, Shilova A, Yafarova A, Gilyarov M, Shilova A, Yafarova A, Gilyarov M, Stojiljkovic DLL, Ulici A, Reidt S, Lam T, Jancik J, Ragab D, Taema K, Farouk W, Saad M, Liu X, Holmberg MJ, Uber A, Montissol S, Donnino M, Andersen LW, Perlikos F, Lagiou M, Papalois A, Kroupis C, Toumpoulis I, Osawa E, Carter D, Sardo S, Almeida J, Galas F, Rizk S, Franco R, Hajjar L, Landoni G, Kongsayreepong S, Sungsiri R, Wongsripunetit P, Marchio P, Guerra-Ojeda S, Gimeno-Raga M, Mauricio MD, Valles SL, Aldasoro C, Jorda A, Aldasoro M, Vila JM, Borg UB, Neitenbach AM, García M, González PG, Romero MG, Orduña PS, Cano AG, Rhodes A, Grounds RM, Cecconi M, Lee C, Hatib F, Jian Z, Rinehart J, De Los Santos J, Canales C, Cannesson M, García MIM, Hatib F, Jian Z, Scheeren T, Jian Z, Hatib F, Pinsky M, Chantziara V, Vassi A, Michaloudis G, Sanidas E, Golemati S, Bateman RM, Mokhtar A, Omar W, Aziz KA, El Azizy H, Nielsen DLL, Holler JG, Lassen A, Eriksson M, Strandberg G, Lipcsey M, Larsson A, Capoletto C, Almeida J, Ferreira G, Fukushima J, Nakamura R, Risk S, Osawa E, Park C, Oliveira G, Galas F, Franco R, Hajjar L, Dias F, D’Arrigo N, Fortuna F, Redaelli S, Zerman L, Becker L, Serrano T, Cotes L, Ramos F, Fadel L, Coelho F, Mendes C, Real J, Pedron B, Kuroki M, Costa E, Azevedo L. 37th International Symposium on Intensive Care and Emergency Medicine (part 1 of 3). Crit Care 2017. [PMCID: PMC5374603 DOI: 10.1186/s13054-017-1628-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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