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Mercer EM, Ramay HR, Moossavi S, Laforest-Lapointe I, Reyna ME, Becker AB, Simons E, Mandhane PJ, Turvey SE, Moraes TJ, Sears MR, Subbarao P, Azad MB, Arrieta MC. Divergent maturational patterns of the infant bacterial and fungal gut microbiome in the first year of life are associated with inter-kingdom community dynamics and infant nutrition. MICROBIOME 2024; 12:22. [PMID: 38326891 PMCID: PMC10848358 DOI: 10.1186/s40168-023-01735-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 12/01/2023] [Indexed: 02/09/2024]
Abstract
BACKGROUND The gut microbiome undergoes primary ecological succession over the course of early life before achieving ecosystem stability around 3 years of age. These maturational patterns have been well-characterized for bacteria, but limited descriptions exist for other microbiota members, such as fungi. Further, our current understanding of the prevalence of different patterns of bacterial and fungal microbiome maturation and how inter-kingdom dynamics influence early-life microbiome establishment is limited. RESULTS We examined individual shifts in bacterial and fungal alpha diversity from 3 to 12 months of age in 100 infants from the CHILD Cohort Study. We identified divergent patterns of gut bacterial or fungal microbiome maturation in over 40% of infants, which were characterized by differences in community composition, inter-kingdom dynamics, and microbe-derived metabolites in urine, suggestive of alterations in the timing of ecosystem transitions. Known microbiome-modifying factors, such as formula feeding and delivery by C-section, were associated with atypical bacterial, but not fungal, microbiome maturation patterns. Instead, fungal microbiome maturation was influenced by prenatal exposure to artificially sweetened beverages and the bacterial microbiome, emphasizing the importance of inter-kingdom dynamics in early-life colonization patterns. CONCLUSIONS These findings highlight the ecological and environmental factors underlying atypical patterns of microbiome maturation in infants, and the need to incorporate multi-kingdom and individual-level perspectives in microbiome research to improve our understandings of gut microbiome maturation patterns in early life and how they relate to host health. Video Abstract.
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Affiliation(s)
- Emily M Mercer
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB, Canada
- Department of Pediatrics, University of Calgary, Calgary, AB, Canada
- International Microbiome Center, University of Calgary, Calgary, AB, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute (ACHRI), Calgary, AB, Canada
| | - Hena R Ramay
- International Microbiome Center, University of Calgary, Calgary, AB, Canada
| | - Shirin Moossavi
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Louvain, Belgium
- VIB Center for Microbiology, VIB, Louvain, Belgium
| | | | - Myrtha E Reyna
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- Department of Translational Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Allan B Becker
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada
- Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
| | - Elinor Simons
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada
- Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
| | - Piush J Mandhane
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
| | - Stuart E Turvey
- Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Theo J Moraes
- Department of Translational Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Malcolm R Sears
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Padmaja Subbarao
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- Department of Translational Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Meghan B Azad
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada
- Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
- Manitoba Interdisciplinary Lactation Centre (MILC), Winnipeg, MB, Canada
| | - Marie-Claire Arrieta
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB, Canada.
- Department of Pediatrics, University of Calgary, Calgary, AB, Canada.
- International Microbiome Center, University of Calgary, Calgary, AB, Canada.
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada.
- Alberta Children's Hospital Research Institute (ACHRI), Calgary, AB, Canada.
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2
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Størdal K, Tapia G, Lund-Blix NA, Stene LC. Genotypes predisposing for celiac disease and autoimmune diabetes and risk of infections in early childhood. J Pediatr Gastroenterol Nutr 2024; 78:295-303. [PMID: 38374560 DOI: 10.1002/jpn3.12078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/28/2023] [Accepted: 11/28/2023] [Indexed: 02/21/2024]
Abstract
OBJECTIVES Infections in early childhood have been associated with risk of celiac disease (CD) and type 1 diabetes (T1D). We investigated whether this is driven by susceptibility genes for autoimmune disease by comparing infection frequency by genetic susceptibility variants for CD or T1D. METHODS We genotyped 373 controls and 384 children who developed CD or T1D in the population-based Norwegian Mother, Father and Child Cohort study (MoBa) study for human leukocyte antigen (HLA)-DQ, FUT2, SH2B3, and PTPN22, and calculated a weighted non-HLA genetic risk score (GRS) for CD and T1D based on over 40 SNPs. Parents reported infections in questionnaires when children were 6 and 18 months old. We used negative binomial regression to estimate incidence rate ratio (IRR) for infections by genotype. RESULTS HLA genotypes for CD and T1D or non-HLA GRS for T1D were not associated with infections. The non-HLA GRS for CD was associated with a nonsignificantly lower frequency of infections (aIRR: 0.95, 95% CI: 0.87-1.03 per weighted allele score), and significantly so when restricting to healthy controls (aIRR: 0.89, 0.81-0.99). Participants homozygous for rs601338(A;A) at FUT2, often referred to as nonsecretors, had a nonsignificantly lower risk of infections (aIRR: 0.91, 95% CI: 0.83-1.01). SH2B3 and PTPN22 genotypes were not associated with infections. The association between infections and risk of CD (OR: 1.15 per five infections) was strengthened after adjustment for HLA genotype and non-HLA GRS (OR: 1.24). CONCLUSIONS HLA variants and non-HLA GRS conferring susceptibility for CD were not associated with increased risk of infections in early childhood and is unlikely to drive the observed association between infections and risk of CD or T1D in many studies.
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Affiliation(s)
- Ketil Størdal
- Department of Pediatric Research, Faculty of Medicine, University of Oslo, Oslo, Norway
- Division of Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - German Tapia
- Norwegian Institute of Public Health, Oslo, Norway
| | | | - Lars C Stene
- Norwegian Institute of Public Health, Oslo, Norway
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Xie X, Kong S, Cao W. Targeting protein glycosylation to regulate inflammation in the respiratory tract: novel diagnostic and therapeutic candidates for chronic respiratory diseases. Front Immunol 2023; 14:1168023. [PMID: 37256139 PMCID: PMC10225578 DOI: 10.3389/fimmu.2023.1168023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/02/2023] [Indexed: 06/01/2023] Open
Abstract
Protein glycosylation is a widespread posttranslational modification that can impact the function of proteins. Dysregulated protein glycosylation has been linked to several diseases, including chronic respiratory diseases (CRDs). CRDs pose a significant public health threat globally, affecting the airways and other lung structures. Emerging researches suggest that glycosylation plays a significant role in regulating inflammation associated with CRDs. This review offers an overview of the abnormal glycoenzyme activity and corresponding glycosylation changes involved in various CRDs, including chronic obstructive pulmonary disease, asthma, cystic fibrosis, idiopathic pulmonary fibrosis, pulmonary arterial hypertension, non-cystic fibrosis bronchiectasis, and lung cancer. Additionally, this review summarizes recent advances in glycomics and glycoproteomics-based protein glycosylation analysis of CRDs. The potential of glycoenzymes and glycoproteins for clinical use in the diagnosis and treatment of CRDs is also discussed.
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Affiliation(s)
- Xiaofeng Xie
- Shanghai Fifth People’s Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Siyuan Kong
- Shanghai Fifth People’s Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Weiqian Cao
- Shanghai Fifth People’s Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China
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4
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Singhal P, Veturi Y, Dudek SM, Lucas A, Frase A, van Steen K, Schrodi SJ, Fasel D, Weng C, Pendergrass R, Schaid DJ, Kullo IJ, Dikilitas O, Sleiman PMA, Hakonarson H, Moore JH, Williams SM, Ritchie MD, Verma SS. Evidence of epistasis in regions of long-range linkage disequilibrium across five complex diseases in the UK Biobank and eMERGE datasets. Am J Hum Genet 2023; 110:575-591. [PMID: 37028392 PMCID: PMC10119154 DOI: 10.1016/j.ajhg.2023.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/07/2023] [Indexed: 04/09/2023] Open
Abstract
Leveraging linkage disequilibrium (LD) patterns as representative of population substructure enables the discovery of additive association signals in genome-wide association studies (GWASs). Standard GWASs are well-powered to interrogate additive models; however, new approaches are required for invesigating other modes of inheritance such as dominance and epistasis. Epistasis, or non-additive interaction between genes, exists across the genome but often goes undetected because of a lack of statistical power. Furthermore, the adoption of LD pruning as customary in standard GWASs excludes detection of sites that are in LD but might underlie the genetic architecture of complex traits. We hypothesize that uncovering long-range interactions between loci with strong LD due to epistatic selection can elucidate genetic mechanisms underlying common diseases. To investigate this hypothesis, we tested for associations between 23 common diseases and 5,625,845 epistatic SNP-SNP pairs (determined by Ohta's D statistics) in long-range LD (>0.25 cM). Across five disease phenotypes, we identified one significant and four near-significant associations that replicated in two large genotype-phenotype datasets (UK Biobank and eMERGE). The genes that were most likely involved in the replicated associations were (1) members of highly conserved gene families with complex roles in multiple pathways, (2) essential genes, and/or (3) genes that were associated in the literature with complex traits that display variable expressivity. These results support the highly pleiotropic and conserved nature of variants in long-range LD under epistatic selection. Our work supports the hypothesis that epistatic interactions regulate diverse clinical mechanisms and might especially be driving factors in conditions with a wide range of phenotypic outcomes.
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Affiliation(s)
- Pankhuri Singhal
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yogasudha Veturi
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Scott M Dudek
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anastasia Lucas
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alex Frase
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kristel van Steen
- Department of Human Genetics, Katholieke Universiteit Leuven, ON4 Herestraat 49, 3000 Leuven, Belgium
| | - Steven J Schrodi
- Laboratory of Genetics, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA
| | - David Fasel
- Columbia University, New York, NY 10027, USA
| | | | | | | | | | | | | | - Hakon Hakonarson
- Children's Hospital of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jason H Moore
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Scott M Williams
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Marylyn D Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Shefali S Verma
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Zheng J, Zhu T. Polymorphism of fucosyltransferase 3 gene is associated with inflammatory bowel disease: a systematic review. ASIAN BIOMED 2023; 17:45-54. [PMID: 37719320 PMCID: PMC10505062 DOI: 10.2478/abm-2023-0044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Background Inflammatory bowel disease (IBD) is a condition with an unclear genetic basis. Fucosyltransferase 3 (FUT3) could potentially be linked to IBD susceptibility. Objective To investigate the association between FUT3 gene polymorphisms and IBD. Methods Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 checklist and Population, Intervention, Comparison, Outcomes, and Study (PICOS) guidelines, case-control studies published until April 30, 2020 was searched. Two independent reviewers conducted screening, data extraction, and quality assessment using the Newcastle-Ottawa Scale. Meta-analysis, sensitivity analysis, and Egger tests were performed using RevMan and Stata12.0. Results The review included 5 articles and 12 case-control studies involving 1712 IBD patients and 1903 controls. The meta-analysis revealed the following combined odds ratios [95% confidence intervals]: rs3745635 genotype (GA+AA vs GG) 0.84 (0.72-0.97), (GG+GA vs AA) 1.93 (1.23-3.05), (GG vs AA) 2.38 (1.52-3.74), (A vs G) 0.84 (0.73-0.96); rs3894326 genotype (TA+AA vs TT) 1.03 (0.87-1.23), (TT+TA vs AA) 1.19 (0.56-2.51), (TT vs AA) 1.19 (0.56-2.51), (A vs T) 1.02 (0.86-1.20); rs28362459 genotype (TG+GG vs TT) 0.98 (0.85-1.12), (TT+TG vs GG) 1.20 (0.90-1.61), (TT vs GG) 1.21 (0.90-1.62), (G vs T) 0.96 (0.86-1.07). Sensitivity analysis indicated the stability of the results, and Egger analysis showed no significant publication bias. Conclusions The rs3745635 gene polymorphism may be associated with IBD susceptibility, whereas the rs3894326 and rs28362459 gene polymorphisms may not be associated with IBD.
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Affiliation(s)
- Jiansheng Zheng
- Department of Public Health, School of Basic Medical Science, Putian University, Putian, Fujian351100, China
| | - Tang Zhu
- Key Laboratory of Translational Tumor Medicine in Fujian Province, School of Basic Medical Science, Putian University, Putian, Fujian351100, China
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Baumgartel K, Stevens M, Vijayakumar N, Saint Fleur A, Prescott S, Groer M. The Human Milk Metabolome: A Scoping Literature Review. J Hum Lact 2023; 39:255-277. [PMID: 36924445 DOI: 10.1177/08903344231156449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
BACKGROUND Human milk is a complex source of nutrition and other bioactives that protects infants from disease, holding a lifetime of beneficial effects. The field of metabolomics provides a robust platform through which we can better understand human milk at a level rarely examined. RESEARCH AIM To Identify, describe, synthesize, and critically analyze the literature within the past 5 years related to the human milk metabolome. METHODS We conducted a scoping literature review and quality analysis of the recent science reflecting untargeted metabolomic approaches to examining human milk. We searched six databases using the terms "breast milk," "metabolome," "metabolite," and "human milk," Out of more than 1,069 abstracts, we screened and identified 22 articles that met our inclusion criteria. RESULTS We extracted data related to the study author, geographic location, research design, analyses, platform used, and results. We also extracted data related to human milk research activities, including collection protocol, infant/maternal considerations, and time. Selected studies focused on a variety of phenotypes, including maternal and infant disease. Investigators used varying approaches to evaluate the metabolome, and differing milk collection protocols were observed. CONCLUSION The human milk metabolome is informed by many factors-which may contribute to infant health outcomes-that have resulted in disparate milk metabolomic profiles. Standardized milk collection and storage procedures should be implemented to minimize degradation. Investigators may use our findings to develop research questions that test a targeted metabolomic approach.
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Affiliation(s)
| | - Monica Stevens
- College of Medicine, University of South Florida, Tampa, FL, USA
| | - Nisha Vijayakumar
- School of Public Health, University of South Florida, Tampa, FL, USA
| | | | | | - Maureen Groer
- College of Nursing, University of Tennessee, Knoxville, TN, USA
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7
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Jajosky RP, Wu SC, Zheng L, Jajosky AN, Jajosky PG, Josephson CD, Hollenhorst MA, Sackstein R, Cummings RD, Arthur CM, Stowell SR. ABO blood group antigens and differential glycan expression: Perspective on the evolution of common human enzyme deficiencies. iScience 2023; 26:105798. [PMID: 36691627 PMCID: PMC9860303 DOI: 10.1016/j.isci.2022.105798] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Enzymes catalyze biochemical reactions and play critical roles in human health and disease. Enzyme variants and deficiencies can lead to variable expression of glycans, which can affect physiology, influence predilection for disease, and/or directly contribute to disease pathogenesis. Although certain well-characterized enzyme deficiencies result in overt disease, some of the most common enzyme deficiencies in humans form the basis of blood groups. These carbohydrate blood groups impact fundamental areas of clinical medicine, including the risk of infection and severity of infectious disease, bleeding risk, transfusion medicine, and tissue/organ transplantation. In this review, we examine the enzymes responsible for carbohydrate-based blood group antigen biosynthesis and their expression within the human population. We also consider the evolutionary selective pressures, e.g. malaria, that may account for the variation in carbohydrate structures and the implications of this biology for human disease.
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Affiliation(s)
- Ryan Philip Jajosky
- Joint Program in Transfusion Medicine, Brigham and Women’s Hospital, Harvard Medical School, 630E New Research Building, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
- Biconcavity Inc, Lilburn, GA, USA
| | - Shang-Chuen Wu
- Joint Program in Transfusion Medicine, Brigham and Women’s Hospital, Harvard Medical School, 630E New Research Building, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Leon Zheng
- Joint Program in Transfusion Medicine, Brigham and Women’s Hospital, Harvard Medical School, 630E New Research Building, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Audrey N. Jajosky
- University of Rochester Medical Center, Department of Pathology and Laboratory Medicine, West Henrietta, NY, USA
| | | | - Cassandra D. Josephson
- Cancer and Blood Disorders Institute and Blood Bank/Transfusion Medicine Division, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, USA
- Departments of Oncology and Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marie A. Hollenhorst
- Department of Pathology and Department of Medicine, Stanford University, Stanford, CA, USA
| | - Robert Sackstein
- Translational Glycobiology Institute, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Richard D. Cummings
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Connie M. Arthur
- Joint Program in Transfusion Medicine, Brigham and Women’s Hospital, Harvard Medical School, 630E New Research Building, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Sean R. Stowell
- Joint Program in Transfusion Medicine, Brigham and Women’s Hospital, Harvard Medical School, 630E New Research Building, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
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The contribution of common and rare genetic variants to variation in metabolic traits in 288,137 East Asians. Nat Commun 2022; 13:6642. [PMID: 36333282 PMCID: PMC9636136 DOI: 10.1038/s41467-022-34163-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
Metabolic traits are heritable phenotypes widely-used in assessing the risk of various diseases. We conduct a genome-wide association analysis (GWAS) of nine metabolic traits (including glycemic, lipid, liver enzyme levels) in 125,872 Korean subjects genotyped with the Korea Biobank Array. Following meta-analysis with GWAS from Biobank Japan identify 144 novel signals (MAF ≥ 1%), of which 57.0% are replicated in UK Biobank. Additionally, we discover 66 rare (MAF < 1%) variants, 94.4% of them co-incident to common loci, adding to allelic series. Although rare variants have limited contribution to overall trait variance, these lead, in carriers, substantial loss of predictive accuracy from polygenic predictions of disease risk from common variant alone. We capture groups with up to 16-fold variation in type 2 diabetes (T2D) prevalence by integration of genetic risk scores of fasting plasma glucose and T2D and the I349F rare protective variant. This study highlights the need to consider the joint contribution of both common and rare variants on inherited risk of metabolic traits and related diseases.
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Elling CL, Scholes MA, Streubel SO, Larson ED, Wine TM, Bootpetch TC, Yoon PJ, Kofonow JM, Gubbels SP, Cass SP, Robertson CE, Jenkins HA, Prager JD, Frank DN, Chan KH, Friedman NR, Ryan AF, Santos-Cortez RLP. The FUT2 Variant c.461G>A (p.Trp154*) Is Associated With Differentially Expressed Genes and Nasopharyngeal Microbiota Shifts in Patients With Otitis Media. Front Cell Infect Microbiol 2022; 11:798246. [PMID: 35096646 PMCID: PMC8798324 DOI: 10.3389/fcimb.2021.798246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/20/2021] [Indexed: 12/30/2022] Open
Abstract
Otitis media (OM) is a leading cause of childhood hearing loss. Variants in FUT2, which encodes alpha-(1,2)-fucosyltransferase, were identified to increase susceptibility to OM, potentially through shifts in the middle ear (ME) or nasopharyngeal (NP) microbiotas as mediated by transcriptional changes. Greater knowledge of differences in relative abundance of otopathogens in carriers of pathogenic variants can help determine risk for OM in patients. In order to determine the downstream effects of FUT2 variation, we examined gene expression in relation to carriage of a common pathogenic FUT2 c.461G>A (p.Trp154*) variant using RNA-sequence data from saliva samples from 28 patients with OM. Differential gene expression was also examined in bulk mRNA and single-cell RNA-sequence data from wildtype mouse ME mucosa after inoculation with non-typeable Haemophilus influenzae (NTHi). In addition, microbiotas were profiled from ME and NP samples of 65 OM patients using 16S rRNA gene sequencing. In human carriers of the FUT2 variant, FN1, KMT2D, MUC16 and NBPF20 were downregulated while MTAP was upregulated. Post-infectious expression in the mouse ME recapitulated these transcriptional differences, with the exception of Fn1 upregulation after NTHi-inoculation. In the NP, Candidate Division TM7 was associated with wildtype genotype (FDR-adj-p=0.009). Overall, the FUT2 c.461G>A variant was associated with transcriptional changes in processes related to response to infection and with increased load of potential otopathogens in the ME and decreased commensals in the NP. These findings provide increased understanding of how FUT2 variants influence gene transcription and the mucosal microbiota, and thus contribute to the pathology of OM.
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Affiliation(s)
- Christina L. Elling
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Melissa A. Scholes
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Pediatric Otolaryngology, Children’s Hospital Colorado, Aurora, CO, United States
| | - Sven-Olrik Streubel
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Pediatric Otolaryngology, Children’s Hospital Colorado, Aurora, CO, United States
| | - Eric D. Larson
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Todd M. Wine
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Pediatric Otolaryngology, Children’s Hospital Colorado, Aurora, CO, United States
| | - Tori C. Bootpetch
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Patricia J. Yoon
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Pediatric Otolaryngology, Children’s Hospital Colorado, Aurora, CO, United States
| | - Jennifer M. Kofonow
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Samuel P. Gubbels
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Stephen P. Cass
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Charles E. Robertson
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Herman A. Jenkins
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Jeremy D. Prager
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Pediatric Otolaryngology, Children’s Hospital Colorado, Aurora, CO, United States
| | - Daniel N. Frank
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Kenny H. Chan
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Pediatric Otolaryngology, Children’s Hospital Colorado, Aurora, CO, United States
| | - Norman R. Friedman
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Pediatric Otolaryngology, Children’s Hospital Colorado, Aurora, CO, United States
| | - Allen F. Ryan
- Division of Otolaryngology, Department of Surgery, San Diego School of Medicine and Veterans Affairs Medical Center, University of California, La Jolla, CA, United States
| | - Regie Lyn P. Santos-Cortez
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Center for Children’s Surgery, Children’s Hospital Colorado, Aurora, CO, United States
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10
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LeMay-Nedjelski L, Yonemitsu C, Asbury MR, Butcher J, Ley SH, Hanley AJ, Kiss A, Unger S, Copeland JK, Wang PW, Stintzi A, Bode L, O'Connor DL. Oligosaccharides and Microbiota in Human Milk Are Interrelated at 3 Months Postpartum in a Cohort of Women with a High Prevalence of Gestational Impaired Glucose Tolerance. J Nutr 2021; 151:3431-3441. [PMID: 34510198 PMCID: PMC8562078 DOI: 10.1093/jn/nxab270] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/07/2021] [Accepted: 07/22/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Human milk is a rich source of human milk oligosaccharides (HMOs) and bacteria. It is unclear how these components interact within the breast microenvironment. OBJECTIVES The objectives were first, to investigate the association between maternal characteristics and HMOs, and second, to assess the association between HMOs and microbial community composition and predicted function in milk from women with high rates of gestational glucose intolerance. METHODS This was an exploratory analysis of a previously completed prospective cohort study (NCT01405547) where milk samples (n = 107) were collected at 3 mo postpartum. Milk microbiota composition was analyzed by V4-16S ribosomal RNA gene sequencing and HMOs by rapid high-throughput HPLC. Data were stratified and analyzed by maternal secretor status phenotype and associations between HMOs and microbiota were determined using linear regression models (ɑ-diversity), Adonis (B-diversity), Poisson regression models (differential abundance), and general linear models (predicted microbial function). RESULTS Prepregnancy BMI, race, and frequency of direct breastfeeding, but not gestational glucose intolerance, were found to be significantly associated with a number of HMOs among secretors and non-secretors. Fucosyllacto-N-hexaose was negatively associated with microbial richness (Chao1) among secretors [B-estimate (SE): -9.3 × 102 (3.4 × 102); P = 0.0082] and difucosyllacto-N-hexaose was negatively associated with microbiota diversity (Shannon index) [-1.7 (0.78); P = 0.029] among secretors. Lacto-N-neotetraose (LNnT) was associated with both microbial B-diversity (weighted UniFrac R2 = 0.040, P = 0.036) and KEGG ortholog B-diversity (Bray-Curtis R2 = 0.039, P = 0.043) in secretors. Additionally, difucosyllactose in secretors and disialyllacto-N-hexaose and LNnT in non-secretors were associated with enrichment of predicted microbial genes encoding for metabolism- and infection-related pathways (P-false discovery rate < 0.1). CONCLUSIONS HMOs are associated with the microbial composition and predicted microbial functions in human milk at 3 mo postpartum. Further research is needed to investigate the role these relations play in maternal and infant health.
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Affiliation(s)
- Lauren LeMay-Nedjelski
- Department of Nutritional Sciences, University of Toronto, Toronto, Ontario, Canada
- Translational Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Chloe Yonemitsu
- Department of Pediatrics and Mother-Milk-Infant Center of Research Excellence (MOMI CORE), University of California, San Diego, La Jolla, CA, USA
| | - Michelle R Asbury
- Department of Nutritional Sciences, University of Toronto, Toronto, Ontario, Canada
- Translational Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - James Butcher
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Sylvia H Ley
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Anthony J Hanley
- Department of Nutritional Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Alex Kiss
- Department of Research Design and Biostatistics, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Sharon Unger
- Department of Nutritional Sciences, University of Toronto, Toronto, Ontario, Canada
- Translational Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
- Department of Pediatrics, Sinai Health, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Julia K Copeland
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Ontario, Canada
| | - Pauline W Wang
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Ontario, Canada
| | - Alain Stintzi
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Lars Bode
- Department of Pediatrics and Mother-Milk-Infant Center of Research Excellence (MOMI CORE), University of California, San Diego, La Jolla, CA, USA
| | - Deborah L O'Connor
- Department of Nutritional Sciences, University of Toronto, Toronto, Ontario, Canada
- Translational Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada
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11
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Noori M, Shokri P, Nejadghaderi SA, Golmohammadi S, Carson-Chahhoud K, Bragazzi NL, Ansarin K, Kolahi AA, Arshi S, Safiri S. ABO blood groups and risk of human immunodeficiency virus infection: A systematic review and meta-analysis. Rev Med Virol 2021; 32:e2298. [PMID: 34590759 DOI: 10.1002/rmv.2298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/10/2021] [Accepted: 09/12/2021] [Indexed: 11/09/2022]
Abstract
The last few decades have seen a pandemic of human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS), which continues to cause substantial morbidity and mortality. ABO blood groups are anthropological and genetic characteristics of a population whose associations with HIV infection are still controversial. This systematic review with meta-analysis was undertaken to investigate whether certain blood groups may have associations with HIV infection. PubMed, Scopus and Web of Science databases were systematically searched as of 6 September 2021. Grey literature was identified through screening Google Scholar, and reference lists of relevant studies. All observational studies providing data on ABO blood group distribution among HIV-infected and uninfected participants were included. Using a random effect model, risk ratios (RR) and 95% confidence intervals (CIs) were pooled to quantify this relationship. Fifty eligible studies with a total of 3,068,244 participants and 6508 HIV-infected cases were included. The overall analysis found that blood group AB increased the risk of HIV infection by 19% as compared with non-AB blood groups (RR = 1.19, 95% CI: 1.03-1.39, p = 0.02). Pooled estimates for other blood groups failed to reach statistical significance. Subgroup analyses identified a positive relationship between AB blood group and HIV infection within Asia, patient populations (as opposed to blood donors and general populations), studies with lower sample sizes, high-income countries and studies with a moderate quality score. The sequential omission and re-analysis of studies within sensitivity analyses produced no change in the overall pooled effect. In conclusion, this study identified that blood group AB carriers were more susceptible to HIV infection. Future investigations should be directed toward clarification of the exact role of ABO blood groups in HIV infection and the possible underlying mechanisms.
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Affiliation(s)
- Maryam Noori
- Student Research Committee, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Pourya Shokri
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed Aria Nejadghaderi
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Saeid Golmohammadi
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kristin Carson-Chahhoud
- Australian Centre for Precision Health, University of South Australia, Adelaide, South Australia, Australia.,School of Medicine, University of Adelaide, Adelaide, South Australia, Australia
| | | | - Khalil Ansarin
- Rahat Breath and Sleep Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali-Asghar Kolahi
- Social Determinants of Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shahnam Arshi
- Social Determinants of Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Saeid Safiri
- Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Community Medicine, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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12
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Hill DR, Chow JM, Buck RH. Multifunctional Benefits of Prevalent HMOs: Implications for Infant Health. Nutrients 2021; 13:3364. [PMID: 34684364 PMCID: PMC8539508 DOI: 10.3390/nu13103364] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 12/13/2022] Open
Abstract
Breastfeeding is the best source of nutrition during infancy and is associated with a broad range of health benefits. However, there remains a significant and persistent need for innovations in infant formula that will allow infants to access a wider spectrum of benefits available to breastfed infants. The addition of human milk oligosaccharides (HMOs) to infant formulas represents the most significant innovation in infant nutrition in recent years. Although not a direct source of calories in milk, HMOs serve as potent prebiotics, versatile anti-infective agents, and key support for neurocognitive development. Continuing improvements in food science will facilitate production of a wide range of HMO structures in the years to come. In this review, we evaluate the relationship between HMO structure and functional benefits. We propose that infant formula fortification strategies should aim to recapitulate a broad range of benefits to support digestive health, immunity, and cognitive development associated with HMOs in breastmilk. We conclude that acetylated, fucosylated, and sialylated HMOs likely confer important health benefits through multiple complementary mechanisms of action.
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Affiliation(s)
| | | | - Rachael H. Buck
- Abbott Nutrition, 3300 Stelzer Road, Columbus, OH 43219, USA; (D.R.H.); (J.M.C.)
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13
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Hodel F, Chong AY, Scepanovic P, Xu ZM, Naret O, Thorball CW, Rüeger S, Marques-Vidal P, Vollenweider P, Begemann M, Ehrenreich H, Brenner N, Bender N, Waterboer T, Mentzer AJ, Hill AVS, Hammer C, Fellay J. Human genomics of the humoral immune response against polyomaviruses. Virus Evol 2021; 7:veab058. [PMID: 34532061 PMCID: PMC8438875 DOI: 10.1093/ve/veab058] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/30/2021] [Accepted: 06/09/2021] [Indexed: 12/21/2022] Open
Abstract
Human polyomaviruses are widespread in humans and can cause severe disease in immunocompromised individuals. To identify human genetic determinants of the humoral immune response against polyomaviruses, we performed genome-wide association studies and meta-analyses of qualitative and quantitative immunoglobulin G responses against BK polyomavirus (BKPyV), JC polyomavirus (JCPyV), Merkel cellpolyomavirus (MCPyV), WU polyomavirus (WUPyV), and human polyomavirus 6 (HPyV6) in 15,660 individuals of European ancestry from three independent studies. We observed significant associations for all tested viruses: JCPyV, HPyV6, and MCPyV associated with human leukocyte antigen class II variation, BKPyV and JCPyV with variants in FUT2, responsible for secretor status, MCPyV with variants in STING1, involved in interferon induction, and WUPyV with a functional variant in MUC1, previously associated with risk for gastric cancer. These results provide insights into the genetic control of a family of very prevalent human viruses, highlighting genes and pathways that play a modulating role in human humoral immunity.
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Affiliation(s)
| | - A Y Chong
- The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - P Scepanovic
- Roche Pharmaceutical Research and Early Development, F. Hoffmann-La Roche Ltd, Headquarters Grenzacherstrasse 124, CH-4070 Basel, Switzerland
| | - Z M Xu
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland,Swiss Institute of Bioinformatics, Quartier UNIL-Sorge, CH-1015 Lausanne, Switzerland
| | - O Naret
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland,Swiss Institute of Bioinformatics, Quartier UNIL-Sorge, CH-1015 Lausanne, Switzerland
| | - C W Thorball
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland,Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Rue du Bugnon 46, CH-1011 Lausanne, Switzerland
| | - S Rüeger
- Institute for Molecular Medicine Finland, Institute of Life Science HiLIFE, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland
| | - P Marques-Vidal
- Department of Medicine, Internal Medicine, Lausanne University Hospital and University of Lausanne, Rue du Bugnon 46, CH-1011 Lausanne, Switzerland
| | | | - M Begemann
- Clinical Neuroscience, Max Planck Institute of Experimental Medicine, DFG Research Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Hermann-Rein-Straße 3, 37075 Göttingen, Germany
| | - H Ehrenreich
- Clinical Neuroscience, Max Planck Institute of Experimental Medicine, DFG Research Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Hermann-Rein-Straße 3, 37075 Göttingen, Germany
| | - N Brenner
- Infections and Cancer Epidemiology, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - N Bender
- Infections and Cancer Epidemiology, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - T Waterboer
- Infections and Cancer Epidemiology, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | | | - A V S Hill
- The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom,The Jenner Institute, University of Oxford, Old Road Campus Research Build, Roosevelt Dr, Oxford OX1 2JD, United Kingdom
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14
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Shapiro MR, Thirawatananond P, Peters L, Sharp RC, Ogundare S, Posgai AL, Perry DJ, Brusko TM. De-coding genetic risk variants in type 1 diabetes. Immunol Cell Biol 2021; 99:496-508. [PMID: 33483996 PMCID: PMC8119379 DOI: 10.1111/imcb.12438] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/08/2021] [Accepted: 01/20/2021] [Indexed: 12/13/2022]
Abstract
The conceptual basis for a genetic predisposition underlying the risk for developing type 1 diabetes (T1D) predates modern human molecular genetics. Over half of the genetic risk has been attributed to the human leukocyte antigen (HLA) class II gene region and to the insulin (INS) gene locus - both thought to confer direction of autoreactivity and tissue specificity. Notwithstanding, questions still remain regarding the functional contributions of a vast array of minor polygenic risk variants scattered throughout the genome that likely influence disease heterogeneity and clinical outcomes. Herein, we summarize the available literature related to the T1D-associated coding variants defined at the time of this review, for the genes PTPN22, IFIH1, SH2B3, CD226, TYK2, FUT2, SIRPG, CTLA4, CTSH and UBASH3A. Data from genotype-selected human cohorts are summarized, and studies from the non-obese diabetic (NOD) mouse are presented to describe the functional impact of these variants in relation to innate and adaptive immunity as well as to β-cell fragility, with expression profiles in tissues and peripheral blood highlighted. The contribution of each variant to progression through T1D staging, including environmental interactions, are discussed with consideration of how their respective protein products may serve as attractive targets for precision medicine-based therapeutics to prevent or suspend the development of T1D.
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Affiliation(s)
- Melanie R Shapiro
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, Diabetes Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Puchong Thirawatananond
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, Diabetes Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Leeana Peters
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, Diabetes Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Robert C Sharp
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, Diabetes Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Similoluwa Ogundare
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, Diabetes Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Amanda L Posgai
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, Diabetes Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Daniel J Perry
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, Diabetes Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Todd M Brusko
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, Diabetes Institute, University of Florida, Gainesville, FL, 32610, USA
- Department of Pediatrics, College of Medicine, Diabetes Institute, University of Florida, Gainesville, FL, 32610, USA
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15
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Mankelow TJ, Singleton BK, Moura PL, Stevens-Hernandez CJ, Cogan NM, Gyorffy G, Kupzig S, Nichols L, Asby C, Pooley J, Ruffino G, Hosseini F, Moghaddas F, Attwood M, Noel A, Cooper A, Arnold DT, Hamilton F, Hyams C, Finn A, Toye AM, Anstee DJ. Blood group type A secretors are associated with a higher risk of COVID-19 cardiovascular disease complications. ACTA ACUST UNITED AC 2021; 2:175-187. [PMID: 34124710 PMCID: PMC8176350 DOI: 10.1002/jha2.180] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/24/2021] [Accepted: 02/25/2021] [Indexed: 01/01/2023]
Abstract
The SARS-CoV-2 virus causes COVID-19, an infection capable of causing severe disease and death but which can also be asymptomatic or oligosymptomatic. We investigated whether ABO blood group or secretor status was associated with COVID-19 severity. We investigated secretor status because expression of ABO glycans on secreted proteins and non-erythroid cells are controlled by a fucosyltransferase (FUT2), and inactivating FUT2 mutations result in a non-secretor phenotype which protects against some viral infections. Data combined from healthcare records and our own laboratory tests (n = 275) of hospitalized SARS-CoV-2 polymerase chain reaction positive patients confirmed higher than expected numbers of blood group A individuals compared to O (RR = 1.24, CI 95% [1.05, 1.47], p = 0.0111). There was also a significant association between group A and COVID-19-related cardiovascular complications (RR = 2.56, CI 95% [1.43, 4.55], p = 0.0011) which is independent of gender. Molecular analysis revealed that group A non-secretors are significantly less likely to be hospitalized than secretors. Testing of convalescent plasma donors, among whom the majority displayed COVID-19 symptoms and only a small minority required hospitalization, group A non-secretors were slightly over-represented. Our findings showed that group A non-secretors are not resistant to infection by SARS-CoV-2, but are more likely to experience a less severe form of associated disease.
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Affiliation(s)
- Tosti J Mankelow
- Bristol Institute for Transfusion Sciences (BITS) NHSBT, Filton Bristol UK.,NIHR Blood and Transplant Research Unit in Red Cell Products Bristol UK
| | - Belinda K Singleton
- Bristol Institute for Transfusion Sciences (BITS) NHSBT, Filton Bristol UK.,NIHR Blood and Transplant Research Unit in Red Cell Products Bristol UK
| | - Pedro L Moura
- Center for Hematology and Regenerative Medicine Department of Medicine (MedH) Karolinska Institutet Stockholm Sweden
| | - Christian J Stevens-Hernandez
- Bristol Institute for Transfusion Sciences (BITS) NHSBT, Filton Bristol UK.,NIHR Blood and Transplant Research Unit in Red Cell Products Bristol UK.,School of Biochemistry Biomedical Sciences Building University of Bristol Bristol UK
| | - Nicola M Cogan
- Bristol Institute for Transfusion Sciences (BITS) NHSBT, Filton Bristol UK.,NIHR Blood and Transplant Research Unit in Red Cell Products Bristol UK
| | - Gyongyver Gyorffy
- Bristol Institute for Transfusion Sciences (BITS) NHSBT, Filton Bristol UK.,NIHR Blood and Transplant Research Unit in Red Cell Products Bristol UK.,School of Biochemistry Biomedical Sciences Building University of Bristol Bristol UK
| | - Sabine Kupzig
- Bristol Institute for Transfusion Sciences (BITS) NHSBT, Filton Bristol UK.,NIHR Blood and Transplant Research Unit in Red Cell Products Bristol UK
| | - Luned Nichols
- Acute Medical Unit, Southmead Hospital North Bristol NHS Trust Bristol UK
| | - Claire Asby
- Acute Medical Unit, Southmead Hospital North Bristol NHS Trust Bristol UK
| | - Jennifer Pooley
- Acute Medical Unit, Southmead Hospital North Bristol NHS Trust Bristol UK
| | - Gabriella Ruffino
- Acute Medical Unit, Southmead Hospital North Bristol NHS Trust Bristol UK
| | - Faroakh Hosseini
- Acute Medical Unit, Southmead Hospital North Bristol NHS Trust Bristol UK
| | - Fiona Moghaddas
- Acute Medical Unit, Southmead Hospital North Bristol NHS Trust Bristol UK
| | - Marie Attwood
- Infection Sciences, Southmead Hospital North Bristol NHS Trust Bristol UK
| | - Alan Noel
- Infection Sciences, Southmead Hospital North Bristol NHS Trust Bristol UK
| | - Alex Cooper
- Infection Sciences, Southmead Hospital North Bristol NHS Trust Bristol UK
| | - David T Arnold
- Infection Sciences, Southmead Hospital North Bristol NHS Trust Bristol UK
| | - Fergus Hamilton
- Infection Sciences, Southmead Hospital North Bristol NHS Trust Bristol UK.,Population Health Sciences University of Bristol Bristol UK
| | - Catherine Hyams
- Acute Medical Unit, Southmead Hospital North Bristol NHS Trust Bristol UK.,Academic Respiratory Unit Southmead Hospital North Bristol NHS Trust Bristol UK.,Population Health Sciences University of Bristol Bristol UK
| | - Adam Finn
- Cellular and Molecular Medicine Biomedical Sciences Building, University of Bristol Bristol UK.,Population Health Sciences University of Bristol Bristol UK.,Bristol Vaccine Centre University of Bristol Bristol UK
| | - Ashley M Toye
- Bristol Institute for Transfusion Sciences (BITS) NHSBT, Filton Bristol UK.,NIHR Blood and Transplant Research Unit in Red Cell Products Bristol UK.,School of Biochemistry Biomedical Sciences Building University of Bristol Bristol UK
| | - David J Anstee
- Bristol Institute for Transfusion Sciences (BITS) NHSBT, Filton Bristol UK.,NIHR Blood and Transplant Research Unit in Red Cell Products Bristol UK.,School of Biochemistry Biomedical Sciences Building University of Bristol Bristol UK
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16
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Muthumuni D, Miliku K, Wade KH, Timpson NJ, Azad MB. Enhanced Protection Against Diarrhea Among Breastfed Infants of Nonsecretor Mothers. Pediatr Infect Dis J 2021; 40:260-263. [PMID: 33315747 DOI: 10.1097/inf.0000000000003014] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Diarrhea is a major cause of infant mortality. Being a "nonsecretor" (having an inactive fucosyltransferase-2 gene) protects against diarrhea by inhibiting enteric infections. Breastfeeding also protects against diarrhea; however, the impact of maternal secretor status is unknown. In the ALSPAC cohort (N = 4971), we found that breastfeeding by nonsecretor mothers was especially protective against diarrhea, which could inform new prevention strategies.
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Affiliation(s)
- Dhasni Muthumuni
- From the Department of Pediatrics and Child Health, University of Manitoba and Manitoba Interdisciplinary Lactation Centre (MILC), Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Kozeta Miliku
- From the Department of Pediatrics and Child Health, University of Manitoba and Manitoba Interdisciplinary Lactation Centre (MILC), Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Kaitlin H Wade
- Population Health Sciences, Bristol Medical School, Faculty of Health Sciences, University of Bristol, Bristol, United Kingdom
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - Nicholas J Timpson
- Population Health Sciences, Bristol Medical School, Faculty of Health Sciences, University of Bristol, Bristol, United Kingdom
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- Avon Longitudinal Study of Parents and Children, University of Bristol, Bristol, United Kingdom
| | - Meghan B Azad
- From the Department of Pediatrics and Child Health, University of Manitoba and Manitoba Interdisciplinary Lactation Centre (MILC), Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
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17
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Wu Y, Murray GK, Byrne EM, Sidorenko J, Visscher PM, Wray NR. GWAS of peptic ulcer disease implicates Helicobacter pylori infection, other gastrointestinal disorders and depression. Nat Commun 2021; 12:1146. [PMID: 33608531 PMCID: PMC7895976 DOI: 10.1038/s41467-021-21280-7] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 01/06/2021] [Indexed: 01/31/2023] Open
Abstract
Genetic factors are recognized to contribute to peptic ulcer disease (PUD) and other gastrointestinal diseases, such as gastro-oesophageal reflux disease (GORD), irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD). Here, genome-wide association study (GWAS) analyses based on 456,327 UK Biobank (UKB) individuals identify 8 independent and significant loci for PUD at, or near, genes MUC1, MUC6, FUT2, PSCA, ABO, CDX2, GAST and CCKBR. There are previously established roles in susceptibility to Helicobacter pylori infection, response to counteract infection-related damage, gastric acid secretion or gastrointestinal motility for these genes. Only two associations have been previously reported for duodenal ulcer, here replicated trans-ancestrally. The results highlight the role of host genetic susceptibility to infection. Post-GWAS analyses for PUD, GORD, IBS and IBD add insights into relationships between these gastrointestinal diseases and their relationships with depression, a commonly comorbid disorder.
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Affiliation(s)
- Yeda Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia.
| | - Graham K Murray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
- Department of Psychiatry, University of Cambridge, Cambridge, UK
- Behavioural and Clinical Neuroscience Institute, University of Cambridge, Cambridge, UK
- Cambridgeshire and Peterborough NHS Foundation Trust, Cambridge, UK
| | - Enda M Byrne
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Julia Sidorenko
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia.
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia.
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18
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Giampaoli O, Conta G, Calvani R, Miccheli A. Can the FUT2 Non-secretor Phenotype Associated With Gut Microbiota Increase the Children Susceptibility for Type 1 Diabetes? A Mini Review. Front Nutr 2020; 7:606171. [PMID: 33425974 PMCID: PMC7785815 DOI: 10.3389/fnut.2020.606171] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/07/2020] [Indexed: 12/12/2022] Open
Abstract
The global toll of type 1 diabetes (T1D) has steadily increased over the last decades. It is now widely acknowledged that T1D pathophysiology is more complex than expected. Indeed, a multifaceted interplay between genetic, metabolic, inflammatory and environmental factors exists that leads to heterogeneous clinical manifestations across individuals. Children with non-secretor phenotype and those affected by T1D share low abundance of bifidobacteria, low content of short-chain fatty acids, intestinal phosphatase alkaline and a high incidence of inflammatory bowel diseases. In this context, host-gut microbiota dyad may represent a relevant contributor to T1D development and progression due to its crucial role in shaping host immunity and susceptibility to autoimmune conditions. The FUT2 gene is responsible for the composition and functional properties of glycans in mucosal tissues and bodily secretions, including human milk. FUT2 polymorphisms may profoundly influence gut microbiota composition and host susceptibility to viral infections and chronic inflammatory disease. In this minireview, the possible interplay between mothers' phenotype, host FUT2 genetic background and gut microbiota composition will be discussed in perspective of the T1D onset. The study of FUT2-gut microbiota interaction may add a new piece on the puzzling T1D etiology and unveil novel targets of intervention to contrast T1D development and progression. Dietary interventions, including the intake of α-(1, 2)-fucosyl oligosaccharides in formula milk and the use of specific prebiotics and probiotics, could be hypothesized.
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Affiliation(s)
- Ottavia Giampaoli
- Department of Chemistry, Sapienza University of Rome, Rome, Italy.,NMR-Based Metabolomics Laboratory (NMLab), Sapienza University of Rome, Rome, Italy
| | - Giorgia Conta
- Department of Chemistry, Sapienza University of Rome, Rome, Italy.,NMR-Based Metabolomics Laboratory (NMLab), Sapienza University of Rome, Rome, Italy
| | - Riccardo Calvani
- Fondazione Policlinico Universitario 'Agostino Gemelli' IRCCS, Rome, Italy
| | - Alfredo Miccheli
- NMR-Based Metabolomics Laboratory (NMLab), Sapienza University of Rome, Rome, Italy.,Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
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19
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Butler-Laporte G, Kreuzer D, Nakanishi T, Harroud A, Forgetta V, Richards JB. Genetic Determinants of Antibody-Mediated Immune Responses to Infectious Diseases Agents: A Genome-Wide and HLA Association Study. Open Forum Infect Dis 2020; 7:ofaa450. [PMID: 33204752 PMCID: PMC7641500 DOI: 10.1093/ofid/ofaa450] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 09/22/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Infectious diseases are causally related to a large array of noncommunicable diseases (NCDs). Identifying genetic determinants of infections and antibody-mediated immune responses may shed light on this relationship and provide therapeutic targets for drug and vaccine development. METHODS We used the UK biobank cohort of up to 10 000 serological measurements of infectious diseases and genome-wide genotyping. We used data on 13 pathogens to define 46 phenotypes: 15 seropositivity case-control phenotypes and 31 quantitative antibody measurement phenotypes. For each of these, we performed genome-wide association studies (GWAS) using the fastGWA linear mixed model package and human leukocyte antigen (HLA) classical allele and amino acid residue associations analyses using Lasso regression for variable selection. RESULTS We included a total of 8735 individuals for case-control phenotypes, and an average (range) of 4286 (276-8555) samples per quantitative analysis. Fourteen of the GWAS yielded a genome-wide significant (P < 5 ×10-8) locus at the major histocompatibility complex (MHC) on chromosome 6. Outside the MHC, we found a total of 60 loci, multiple associated with Epstein-Barr virus (EBV)-related NCDs (eg, RASA3, MED12L, and IRF4). FUT2 was also identified as an important gene for polyomaviridae. HLA analysis highlighted the importance of DRB1*09:01, DQB1*02:01, DQA1*01:02, and DQA1*03:01 in EBV serologies and of DRB1*15:01 in polyomaviridae. CONCLUSIONS We have identified multiple genetic variants associated with antibody immune response to 13 infections, many of which are biologically plausible therapeutic or vaccine targets. This may help prioritize future research and drug development.
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Affiliation(s)
- 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
| | - Devin Kreuzer
- Lady Davis Institute, Jewish General Hospital, 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
| | - Adil Harroud
- Department of Neurology, University of California San Francisco, San Francisco, California, USA
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, California, USA
| | - Vincenzo Forgetta
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - J Brent Richards
- 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 Human Genetics, McGill University, Montréal, Québec, Canada
- Department of Twin Research, King’s College London, London, UK
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20
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Komorniak N, Martynova-Van Kley A, Nalian A, Wardziukiewicz W, Skonieczna-Żydecka K, Styburski D, Palma J, Kowalewski B, Kaseja K, Stachowska E. Can the FUT 2 Gene Variant Have an Effect on the Body Weight of Patients Undergoing Bariatric Surgery?-Preliminary, Exploratory Study. Nutrients 2020; 12:E2621. [PMID: 32872099 PMCID: PMC7551162 DOI: 10.3390/nu12092621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/24/2020] [Accepted: 08/26/2020] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The FUT2 gene (Se gene) encoding the enzyme α-1,2-L-fucosyltransferase 2 seems to have a significant effect on the number and type of bacteria colonizing the intestines. METHODS In a group of 19 patients after bariatric surgery, the polymorphism (rs601338) of FUT2 gene was analyzed in combination with body mass reduction, intestinal microbiome (16S RNA sequencing), and short chain fatty acids (SCFA) measurements in stools. RESULTS Among the secretors (Se/Se polymorphism of the FUT2 gene rs601338, carriers of GG variant), correlations between waist-hip ratio (WHR) and propionate content and an increase in Prevotella, Escherichia, Shigella, and Bacteroides were observed. On the other hand-in non-secretors (carriers of GA and AA variants)-higher abundance of Enterobacteriaceae, Ruminococcaceae, Enterobacteriaceae, Clostridiales was recorded. CONCLUSIONS The increased concentrations of propionate observed among the GG variants of FUT 2 may be used as an additional source of energy for the patient and may have a higher risk of increasing the WHR than carriers of the other variants (GA and AA).
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Affiliation(s)
- Natalia Komorniak
- Department of Human Nutrition and Metabolomics, Pomeranian Medical University in Szczecin, 71-460 Szczecin, Poland; (N.K.); (W.W.); (K.S.-Ż.); (D.S.); (J.P.)
| | | | - Armen Nalian
- Department of Biology, Stephen F. Austin State University, Nacogdoches, TX 75962, USA; (A.M.-V.K.); (A.N.)
| | - Wiktoria Wardziukiewicz
- Department of Human Nutrition and Metabolomics, Pomeranian Medical University in Szczecin, 71-460 Szczecin, Poland; (N.K.); (W.W.); (K.S.-Ż.); (D.S.); (J.P.)
| | - Karolina Skonieczna-Żydecka
- Department of Human Nutrition and Metabolomics, Pomeranian Medical University in Szczecin, 71-460 Szczecin, Poland; (N.K.); (W.W.); (K.S.-Ż.); (D.S.); (J.P.)
| | - Daniel Styburski
- Department of Human Nutrition and Metabolomics, Pomeranian Medical University in Szczecin, 71-460 Szczecin, Poland; (N.K.); (W.W.); (K.S.-Ż.); (D.S.); (J.P.)
| | - Joanna Palma
- Department of Human Nutrition and Metabolomics, Pomeranian Medical University in Szczecin, 71-460 Szczecin, Poland; (N.K.); (W.W.); (K.S.-Ż.); (D.S.); (J.P.)
| | - Bartosz Kowalewski
- Independent Provincial Public Hospital Complex in Szczecin—Zdunowo, 70-891 Szczecin, Poland;
| | - Krzysztof Kaseja
- Department of General Surgery and Transplantation, Independent Public Clinical Hospital No.2, 70-111 Szczecin, Poland;
| | - Ewa Stachowska
- Department of Human Nutrition and Metabolomics, Pomeranian Medical University in Szczecin, 71-460 Szczecin, Poland; (N.K.); (W.W.); (K.S.-Ż.); (D.S.); (J.P.)
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