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Faraci M, Bonaretti C, Dell'Orso G, Pierri F, Giardino S, Angiero F, Blasi S, Farronato G, Di Marco E, Trevisiol A, Olcese E, Rufino L, Squillario M, Biassoni R. Association between oral and fecal microbiome dysbiosis and treatment complications in pediatric patients undergoing allogeneic hematopoietic stem cell transplantation. Sci Rep 2024; 14:6708. [PMID: 38509104 PMCID: PMC10954761 DOI: 10.1038/s41598-024-55690-6] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 02/26/2024] [Indexed: 03/22/2024] Open
Abstract
The oral and gastrointestinal mucosae represent the main targets of the toxic effect of chemo and/or radiotherapy administered during the conditioning regimen before hematopoietic stem cell transplant (HSCT). These harmful consequences and the immunological complications that may occur after the transplant (such as Graft versus Host Disease, GvHD) are responsible for the clinical symptoms associated with mucositis during the aplasia phase, like pain, nausea, vomiting, and diarrhea. These toxicities could play a critical role in the oral and gastrointestinal microbiomes during the post-transplant phase, and the degree of microbial dysbiosis and dysregulation among different bacterial species could also be crucial in intestinal mucosa homeostasis, altering the host's innate and adaptive immune responses and favoring abnormal immune responses responsible for the occurrence of GvHD. This prospective pediatric study aims to analyze longitudinally oral and gut microbiomes in 17 pediatric patients who received allogeneic HSCT for malignant and non-malignant diseases. The oral mucositis was mainly associated with an increased relative abundance of Fusobacteria, and Prevotella species, while Streptococcus descendants showed a negative correlation. The fecal microbiome of subjects affected by cutaneous acute GvHD (aGvHD) correlated with Proteobacteria. Oral mucosal microbiota undergoes changes after HSCT, Fusobacteria, and Prevotella represent bacterial species associated with mucositis and they could be the target for future therapeutic approaches, while fecal microbiome in patients with acute GvHD (aGvHD) revealed an increase of different class of Proteobacteria (Alphaproteobacteria and Deltaproteobacteria) and a negative correlation with the class of Gammaproteobacteria.
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Affiliation(s)
- M Faraci
- Hematopoietic Stem Cell Transplant Unit, Department of Hemato-Oncology, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - C Bonaretti
- Molecular Diagnostic Laboratory, IRCCS Istituto Giannina. Gaslini, Genova, Italy
| | - G Dell'Orso
- Hematopoietic Stem Cell Transplant Unit, Department of Hemato-Oncology, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - F Pierri
- Hematopoietic Stem Cell Transplant Unit, Department of Hemato-Oncology, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - S Giardino
- Hematopoietic Stem Cell Transplant Unit, Department of Hemato-Oncology, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - F Angiero
- Department of Surgical and Diagnostic Sciences, University of Genova, Genova, Italy
| | - S Blasi
- Department of Surgical and Diagnostic Sciences, University of Genova, Genova, Italy
| | - G Farronato
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milano, Italy
| | - E Di Marco
- Laboratory of Clinical Analysis, IRCCS Istituto G. Gaslini, Genova, Italy
| | - A Trevisiol
- Department of Surgical and Diagnostic Sciences, University of Genova, Genova, Italy
| | - E Olcese
- Hematopoietic Stem Cell Transplant Unit, Department of Hemato-Oncology, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - L Rufino
- Department of Surgical and Diagnostic Sciences, University of Genova, Genova, Italy
| | - M Squillario
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - R Biassoni
- Molecular Diagnostic Laboratory, IRCCS Istituto Giannina. Gaslini, Genova, Italy.
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2
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Erculiani M, Poluzzi F, Mottadelli G, Felici E, Ml N, Caraccia M, Grandi A, Casella S, Giacometti L, Montobbio G, Ceccherini I, Di Marco E, Bonaretti C, Biassoni R, Squillario M, Pietrantoni A, Villanacci V, Pini Prato A. A unicentric cross-sectional observational study on chronic intestinal inflammation in total colonic aganglionosis: beware of an underestimated condition. Orphanet J Rare Dis 2023; 18:339. [PMID: 37891621 PMCID: PMC10612252 DOI: 10.1186/s13023-023-02958-1] [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: 06/20/2023] [Accepted: 10/23/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Inflammatory Bowel Diseases (IBD) are known to occur in association with Hirschsprung disease (HSCR). Most of cases are represented by Crohn Disease (CD) occurring in patients with Total Colonic Aganglionosis (TCSA) with an estimated prevalence of around 2%. Based on these considerations and on a number of provisional data belonging to our Center for Digestive Diseases, we developed a unicentric cross-sectional observational study aimed at describing phenotype, genotype, pathology and metagenomics of all patients with TCSA and Crohn-like lesions. RESULTS Out of a series of 62 eligible TCSA patients, 48 fulfilled inclusion criteria and were enrolled in the study. Ten patients did not complete the study due to non-compliance or withdrawal of consent and were subsequently dropped out. A total of 38 patients completed the study. All patients were tested for chronic intestinal inflammation by a combination of fecal calprotectine (FC) or occult fecal blood (OFB) and underwent fecal metagenomics. Nineteen (50%) tested positive for FC, OFB, or both and subsequently underwent retrograde ileoscopy. Fourteen patients (36.8%) presented Crohn-like lesions, occurring after a median of 11.5 years after surgery (range 8 months - 21.5 years). No statistically significant differences regarding demographic, phenotype and genotype were observed comparing patients with and without lesions, except for need for blood transfusion that was more frequent in those with lesions. Faecal microbiome of patients with lesions (not that of caregivers) was less biodiverse and characterized by a reduction of Bacteroidetes, and an overabundance of Proteobacteria. FC tested negative in 3/14 patients with lesions (21%). CONCLUSIONS Our study demonstrated an impressive 10-folds higher incidence of chronic inflammation in TCSA. Up to 50% of patients may develop IBD-like lesions postoperatively. Nonetheless, we failed in identifying specific risk factors to be used to implement prevention strategies. Based on the results of our study, we suggest screening all TCSA patients with retrograde ileoscopy regardless of FC/OFB values. The frequency of endoscopic assessments and the role of FC/OFB screening in prompting endoscopy is yet to be determined.
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Affiliation(s)
- M Erculiani
- Umberto Bosio Center for Digestive Diseases, AO SS Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - F Poluzzi
- Umberto Bosio Center for Digestive Diseases, AO SS Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - G Mottadelli
- Umberto Bosio Center for Digestive Diseases, AO SS Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - E Felici
- Umberto Bosio Center for Digestive Diseases, AO SS Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - Novi Ml
- Umberto Bosio Center for Digestive Diseases, AO SS Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - M Caraccia
- Umberto Bosio Center for Digestive Diseases, AO SS Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - A Grandi
- Umberto Bosio Center for Digestive Diseases, AO SS Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - S Casella
- Umberto Bosio Center for Digestive Diseases, AO SS Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - L Giacometti
- Umberto Bosio Center for Digestive Diseases, AO SS Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
- Division of Pathology, Department of Health Sciences, University of Eastern Piedmont, Novara, Italy
| | - G Montobbio
- Umberto Bosio Center for Digestive Diseases, AO SS Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - I Ceccherini
- UOSD Laboratory of Genetics and Genomics of Rare Diseases, IRCCS Istituto Giannina Gaslini, University of Genoa, Genoa, Italy
| | - E Di Marco
- Central Laboratory, Giannina Gaslini Institute, Genoa, Italy
| | - C Bonaretti
- Molecular Diagnostic, Giannina Gaslini Institute, Genoa, Italy
| | - R Biassoni
- Molecular Diagnostic, Giannina Gaslini Institute, Genoa, Italy
| | - M Squillario
- IRCCS Ospedale Policlinico San Martino Genoa, Genoa, Italy
| | - A Pietrantoni
- Institute of Pathology, ASST-Spedali Civili, University of Brescia, Brescia, Italy
| | - V Villanacci
- Institute of Pathology, ASST-Spedali Civili, University of Brescia, Brescia, Italy
| | - A Pini Prato
- Umberto Bosio Center for Digestive Diseases, AO SS Antonio e Biagio e Cesare Arrigo, Alessandria, Italy.
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Squillario M, Bonaretti C, La Valle A, Di Marco E, Piccolo G, Minuto N, Patti G, Napoli F, Bassi M, Maghnie M, d'Annunzio G, Biassoni R. Gut-microbiota in children and adolescents with obesity: inferred functional analysis and machine-learning algorithms to classify microorganisms. Sci Rep 2023; 13:11294. [PMID: 37438382 DOI: 10.1038/s41598-023-36533-2] [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] [Received: 11/30/2022] [Accepted: 06/05/2023] [Indexed: 07/14/2023] Open
Abstract
The fecal microbiome of 55 obese children and adolescents (BMI-SDS 3.2 ± 0.7) and of 25 normal-weight subjects, matched both for age and sex (BMI-SDS - 0.3 ± 1.1) was analysed. Streptococcus, Acidaminococcus, Sutterella, Prevotella, Sutterella wadsworthensis, Streptococcus thermophilus, and Prevotella copri positively correlated with obesity. The inferred pathways strongly associated with obesity concern the biosynthesis pathways of tyrosine, phenylalanine, tryptophan and methionine pathways. Furthermore, polyamine biosynthesis virulence factors and pro-inflammatory lipopolysaccharide biosynthesis pathway showed higher abundances in obese samples, while the butanediol biosynthesis showed low abundance in obese subjects. Different taxa strongly linked with obesity have been related to an increased risk of multiple diseases involving metabolic pathways related to inflammation (polyamine and lipopolysaccharide biosynthesis). Cholesterol, LDL, and CRP positively correlated with specific clusters of microbial in obese patients. The Firmicutes/Bacteroidetes-ratio was lower in obese samples than in controls and differently from the literature we state that this ratio could not be a biomarker for obesity.
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Affiliation(s)
| | - Carola Bonaretti
- Molecular Diagnostics, Analysis Laboratory, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Alberto La Valle
- Pediatric Clinic, Regional Center for Pediatric Diabetes, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Eddi Di Marco
- Molecular Diagnostics, Analysis Laboratory, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Gianluca Piccolo
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, (DINOGMI), Università degli Studi di Genova, Genoa, Italy
- Neuro-Oncology Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Nicola Minuto
- Pediatric Clinic, Regional Center for Pediatric Diabetes, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Giuseppa Patti
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, (DINOGMI), Università degli Studi di Genova, Genoa, Italy
- Department of Pediatrics, Pediatric Clinic, Regional Center for Pediatric Diabetes, IRCCS Istituto Giannina Gaslini, Via Gaslini 5, 16147, Genoa, Italy
| | - Flavia Napoli
- Department of Pediatrics, Pediatric Clinic, Regional Center for Pediatric Diabetes, IRCCS Istituto Giannina Gaslini, Via Gaslini 5, 16147, Genoa, Italy
| | - Marta Bassi
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, (DINOGMI), Università degli Studi di Genova, Genoa, Italy
- Department of Pediatrics, Pediatric Clinic, Regional Center for Pediatric Diabetes, IRCCS Istituto Giannina Gaslini, Via Gaslini 5, 16147, Genoa, Italy
| | - Mohamad Maghnie
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, (DINOGMI), Università degli Studi di Genova, Genoa, Italy
- Department of Pediatrics, Pediatric Clinic, Regional Center for Pediatric Diabetes, IRCCS Istituto Giannina Gaslini, Via Gaslini 5, 16147, Genoa, Italy
| | - Giuseppe d'Annunzio
- Department of Pediatrics, Pediatric Clinic, Regional Center for Pediatric Diabetes, IRCCS Istituto Giannina Gaslini, Via Gaslini 5, 16147, Genoa, Italy.
| | - Roberto Biassoni
- Molecular Diagnostics, Analysis Laboratory, IRCCS Istituto Giannina Gaslini, Genoa, Italy
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Turrisi R, Squillario M, Abate G, Uberti D, Barla A. An overview of data integration in neuroscience with focus on Alzheimer's Disease. IEEE J Biomed Health Inform 2023; PP:1-12. [PMID: 37079415 DOI: 10.1109/jbhi.2023.3268729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
This work represents the first attempt to provide an overview of how to face data integration as the result of a dialogue between neuroscientists and computer scientists. Indeed, data integration is fundamental for studying complex multifactorial diseases, such as the neurodegenerative diseases. This work aims at warning the readers of common pitfalls and critical issues in both medical and data science fields. In this context, we define a road map for data scientists when they first approach the issue of data integration in the biomedical domain, highlighting the challenges that inevitably emerge when dealing with heterogeneous, large-scale and noisy data and proposing possible solutions. Here, we discuss data collection and statistical analysis usually seen as parallel and independent processes, as cross-disciplinary activities. Finally, we provide an exemplary application of data integration to address Alzheimer's Disease (AD), which is the most common multifactorial form of dementia worldwide. We critically discuss the largest and most widely used datasets in AD, and demonstrate how the emergence of machine learning and deep learning methods has had a significant impact on disease's knowledge particularly in the perspective of an early AD diagnosis.
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Biassoni R, Di Marco E, Squillario M, Ugolotti E, Mosconi M, Faticato MG, Mattioli G, Avanzini S, Pini Prato A. Pathways and microbiome modifications related to surgery and enterocolitis in Hirschsprung disease. Pediatr Surg Int 2022; 38:83-98. [PMID: 34677676 DOI: 10.1007/s00383-021-05012-y] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/11/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Hirschsprung disease (HSCR) is a congenital anomaly of the enteric nervous system. Abnormal microbiome composition was reported in HSCR patients. In this study, we addressed and analyzed microbiome modifications with relation tosurgery and HSCR associated enterocolitis (HAEC). METHODS The faecal microbiome of 31 HSCR patients (overall 64 samples) was analyzed. HAEC was diagnosed and classified according to a combination of Pastor's and Elhalabi's criteria. Stool samples were analyzed by 16S sequencing (7 out of 9 polymorphic regions). Compositional and relative abundance profiles, as well as the functional potentials of the microbial community, were analyzed with the marker gene sequencing profiles using PICRUSt. RESULTS The relative abundance of Bacteroidetes showed a severe decrease with slow recovery after surgery. Conversely, Proteobacteria transiently increased their abundance. Noteworthy, a strong linkage has been found between Proteobacteria descendants and HAEC occurrences. The inferred functional analysis indicated that virulence factors and fimbriae or pili might be associated with HAEC. CONCLUSIONS Our study, addressing microbiome dynamics, demonstrated relevant changes after surgical manipulation. Alpha-diversity analyses indicated that surgery deeply affects microbiome composition. Proteobacteria and Enterobacteriaceae seem to play a pivotal role in HAEC occurrences. Several virulence factors, such as fimbriae or pili, might explain the HAEC-predisposing potential of selected microbiomes. These results suggest some innovative therapeutic approaches that deserve to be tested in appropriate clinical trials.
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Affiliation(s)
- Roberto Biassoni
- IRCCS Istituto Giannina Gaslini, Genova, Italy. .,Dipartimento Ricerca Traslazionale, Medicina Di Laboratorio, Diagnostica E Servizi, U.O.C. Laboratorio Analisi- U.O.S. Diagnostica Molecolare, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147, Genova, Italy.
| | | | | | | | | | - Maria Grazia Faticato
- Umberto Bosio Center for Digestive Diseases, The Children Hospital, Azienda Ospedaliera SS Antonio E Biagio E Cesare Arrigo, Alessandria, Italy
| | - Girolamo Mattioli
- Umberto Bosio Center for Digestive Diseases, The Children Hospital, Azienda Ospedaliera SS Antonio E Biagio E Cesare Arrigo, Alessandria, Italy
| | | | - Alessio Pini Prato
- Umberto Bosio Center for Digestive Diseases, The Children Hospital, Azienda Ospedaliera SS Antonio E Biagio E Cesare Arrigo, Alessandria, Italy
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Cerminara M, Spirito G, Pisciotta L, Squillario M, Servetti M, Divizia MT, Lerone M, Berloco B, Boeri S, Nobili L, Vozzi D, Sanges R, Gustincich S, Puliti A. Case Report: Whole Exome Sequencing Revealed Disease-Causing Variants in Two Genes in a Patient With Autism Spectrum Disorder, Intellectual Disability, Hyperactivity, Sleep and Gastrointestinal Disturbances. Front Genet 2021; 12:625564. [PMID: 33679889 PMCID: PMC7930735 DOI: 10.3389/fgene.2021.625564] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/19/2021] [Indexed: 12/26/2022] Open
Abstract
Autism Spectrum Disorder (ASD) refers to a broad range of conditions characterized by difficulties in communication, social interaction and behavior, and may be accompanied by other medical or psychiatric conditions. Patients with ASD and comorbidities are often difficult to diagnose because of the tendency to consider the multiple symptoms as the presentation of a complicated syndromic form. This view influences variant filtering which might ignore causative variants for specific clinical features shown by the patient. Here we report on a male child diagnosed with ASD, showing cognitive and motor impairments, stereotypies, hyperactivity, sleep, and gastrointestinal disturbances. The analysis of whole exome sequencing (WES) data with bioinformatic tools for oligogenic diseases helped us to identify two major previously unreported pathogenetic variants: a maternally inherited missense variant (p.R4122H) in HUWE1, an ubiquitin protein ligase associated to X-linked intellectual disability and ASD; and a de novo stop variant (p.Q259X) in TPH2, encoding the tryptophan hydroxylase 2 enzyme involved in serotonin synthesis and associated with susceptibility to attention deficit-hyperactivity disorder (ADHD). TPH2, expressed in central and peripheral nervous tissues, modulates various physiological functions, including gut motility and sleep. To the best of our knowledge, this is the first case presenting with ASD, cognitive impairment, sleep, and gastrointestinal disturbances linked to both HUWE1 and TPH2 genes. Our findings could contribute to the existing knowledge on clinical and genetic diagnosis of patients with ASD presentation with comorbidities.
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Affiliation(s)
- Maria Cerminara
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DiNOGMI), University of Genoa, Genoa, Italy
| | - Giovanni Spirito
- Neuroscience Area, International School for Advanced Studies (SISSA), Trieste, Italy
| | - Livia Pisciotta
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DiNOGMI), University of Genoa, Genoa, Italy.,Child Neuropsychiatry Unit, Azienda Socio Sanitaria Territoriale Fatebenefratelli Sacco (ASST Fbf Sacco), Milan, Italy
| | - Margherita Squillario
- Medical Genetics Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Giannina Gaslini, Genoa, Italy
| | - Martina Servetti
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DiNOGMI), University of Genoa, Genoa, Italy.,Medical Genetics Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Giannina Gaslini, Genoa, Italy
| | - Maria Teresa Divizia
- Medical Genetics Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Giannina Gaslini, Genoa, Italy
| | - Margherita Lerone
- Medical Genetics Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Giannina Gaslini, Genoa, Italy
| | - Bianca Berloco
- Child Neuropsychiatry Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Giannina Gaslini, Genoa, Italy
| | - Silvia Boeri
- Child Neuropsychiatry Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Giannina Gaslini, Genoa, Italy
| | - Lino Nobili
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DiNOGMI), University of Genoa, Genoa, Italy.,Child Neuropsychiatry Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Giannina Gaslini, Genoa, Italy
| | - Diego Vozzi
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Remo Sanges
- Neuroscience Area, International School for Advanced Studies (SISSA), Trieste, Italy.,Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Stefano Gustincich
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Aldamaria Puliti
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DiNOGMI), University of Genoa, Genoa, Italy.,Medical Genetics Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Giannina Gaslini, Genoa, Italy
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Biassoni R, Di Marco E, Squillario M, Barla A, Piccolo G, Ugolotti E, Gatti C, Minuto N, Patti G, Maghnie M, d'Annunzio G. Gut Microbiota in T1DM-Onset Pediatric Patients: Machine-Learning Algorithms to Classify Microorganisms as Disease Linked. J Clin Endocrinol Metab 2020; 105:5871462. [PMID: 32692360 DOI: 10.1210/clinem/dgaa407] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 07/01/2020] [Indexed: 12/14/2022]
Abstract
AIMS The purpose of this work is to find the gut microbial fingerprinting of pediatric patients with type 1 diabetes. METHODS The microbiome of 31 children with type 1 diabetes at onset and of 25 healthy children was determined using multiple polymorphic regions of the 16S ribosomal RNA. We performed machine-learning analyses and metagenome functional analysis to identify significant taxa and their metabolic pathways content. RESULTS Compared with healthy controls, patients showed a significantly higher relative abundance of the following most important taxa: Bacteroides stercoris, Bacteroides fragilis, Bacteroides intestinalis, Bifidobacterium bifidum, Gammaproteobacteria and its descendants, Holdemania, and Synergistetes and its descendants. On the contrary, the relative abundance of Bacteroides vulgatus, Deltaproteobacteria and its descendants, Parasutterella and the Lactobacillus, Turicibacter genera were significantly lower in patients with respect to healthy controls. The predicted metabolic pathway more associated with type 1 diabetes patients concerns "carbon metabolism," sugar and iron metabolisms in particular. Among the clinical variables considered, standardized body mass index, anti-insulin autoantibodies, glycemia, hemoglobin A1c, Tanner stage, and age at onset emerged as most significant positively or negatively correlated with specific clusters of taxa. CONCLUSIONS The relative abundance and supervised analyses confirmed the importance of B stercoris in type 1 diabetes patients at onset and showed a relevant role of Synergistetes and its descendants in patients with respect to healthy controls. In general the robustness and coherence of the showed results underline the relevance of studying the microbioma using multiple polymorphic regions, different types of analysis, and different approaches within each analysis.
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Affiliation(s)
- Roberto Biassoni
- Molecular Diagnostics, Analysis Laboratory, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Eddi Di Marco
- Molecular Diagnostics, Analysis Laboratory, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | | | | | - Gianluca Piccolo
- Pediatric Clinic Regional Center for Pediatric Diabetes, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Elisabetta Ugolotti
- Molecular Diagnostics, Analysis Laboratory, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Cinzia Gatti
- Molecular Diagnostics, Analysis Laboratory, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Nicola Minuto
- Pediatric Clinic Regional Center for Pediatric Diabetes, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Giuseppa Patti
- Department of Pediatrics, IRCCS Istituto Giannina Gaslini, University of Genoa, Genoa, Italy
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University Of Genoa, Genoa, Italy
| | - Mohamad Maghnie
- Pediatric Clinic Regional Center for Pediatric Diabetes, IRCCS Istituto Giannina Gaslini, Genoa, Italy
- Department of Pediatrics, IRCCS Istituto Giannina Gaslini, University of Genoa, Genoa, Italy
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University Of Genoa, Genoa, Italy
| | - Giuseppe d'Annunzio
- Pediatric Clinic Regional Center for Pediatric Diabetes, IRCCS Istituto Giannina Gaslini, Genoa, Italy
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Squillario M, Abate G, Tomasi F, Tozzo V, Barla A, Uberti D. A telescope GWAS analysis strategy, based on SNPs-genes-pathways ensamble and on multivariate algorithms, to characterize late onset Alzheimer's disease. Sci Rep 2020; 10:12063. [PMID: 32694537 PMCID: PMC7374579 DOI: 10.1038/s41598-020-67699-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 10/04/2019] [Accepted: 06/10/2020] [Indexed: 12/18/2022] Open
Abstract
Genome–wide association studies (GWAS) have revealed a plethora of putative susceptibility genes for Alzheimer’s disease (AD), with the sole exception of APOE gene unequivocally validated in independent study. Considering that the etiology of complex diseases like AD could depend on functional multiple genes interaction network, here we proposed an alternative GWAS analysis strategy based on (i) multivariate methods and on a (ii) telescope approach, in order to guarantee the identification of correlated variables, and reveal their connections at three biological connected levels. Specifically as multivariate methods, we employed two machine learning algorithms and a genetic association test and we considered SNPs, Genes and Pathways features in the analysis of two public GWAS dataset (ADNI-1 and ADNI-2). For each dataset and for each feature we addressed two binary classifications tasks: cases vs. controls and the low vs. high risk of developing AD considering the allelic status of APOEe4. This complex strategy allowed the identification of SNPs, genes and pathways lists statistically robust and meaningful from the biological viewpoint. Among the results, we confirm the involvement of TOMM40 gene in AD and we propose GRM7 as a novel gene significantly associated with AD.
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Affiliation(s)
| | - Giulia Abate
- Department of Molecular and Translational Medicine, University of Brescia, 25123, Brescia, Italy
| | | | | | | | - Daniela Uberti
- Department of Molecular and Translational Medicine, University of Brescia, 25123, Brescia, Italy
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Colombo M, Bagnara D, Reverberi D, Matis S, Cardillo M, Massara R, Mastracci L, Ravetti JL, Agnelli L, Neri A, Mazzocco M, Squillario M, Mazzarello AN, Cutrona G, Agathangelidis A, Stamatopoulos K, Ferrarini M, Fais F. Tracing CLL-biased stereotyped immunoglobulin gene rearrangements in normal B cell subsets using a high-throughput immunogenetic approach. Mol Med 2020; 26:25. [PMID: 32156260 PMCID: PMC7063734 DOI: 10.1186/s10020-020-00151-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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: 07/01/2019] [Accepted: 02/21/2020] [Indexed: 01/10/2023] Open
Abstract
Background B cell receptor Immunoglobulin (BcR IG) repertoire of Chronic Lymphocytic Leukemia (CLL) is characterized by the expression of quasi-identical BcR IG. These are observed in approximately 30% of patients, defined as stereotyped receptors and subdivided into subsets based on specific VH CDR3 aa motifs and phylogenetically related IGHV genes. Although relevant to CLL ontogeny, the distribution of CLL-biased stereotyped immunoglobulin rearrangements (CBS-IG) in normal B cells has not been so far specifically addressed using modern sequencing technologies. Here, we have investigated the presence of CBS-IG in splenic B cell subpopulations (s-BCS) and in CD5+ and CD5− B cells from the spleen and peripheral blood (PB). Methods Fractionation of splenic B cells into 9 different B cell subsets and that of spleen and PB into CD5+ and CD5− cells were carried out by FACS sorting. cDNA sequences of BcR IG gene rearrangements were obtained by NGS. Identification of amino acidic motifs typical of CLL stereotyped subsets was carried out on IGHV1-carrying gene sequences and statistical evaluation has been subsequently performed to assess stereotypes distribution. Results CBS-IG represented the 0.26% average of IGHV1 genes expressing sequences, were detected in all of the BCS investigated. CBS-IG were more abundant in splenic and circulating CD5+ B (0.57%) cells compared to CD5− B cells (0.17%). In all instances, most CBS IG did not exhibit somatic hypermutation similar to CLL stereotyped receptors. However, compared to CLL, they exhibited a different CLL subset distribution and a broader utilization of the genes of the IGHV1 family. Conclusions CBS-IG receptors appear to represent a part of the “public” BcR repertoire in normal B cells. This repertoire is observed in all BCS excluding the hypothesis that CLL stereotyped BcR accumulate in a specific B cell subset, potentially capable of originating a leukemic clone. The different relative representation of CBS-IG in normal B cell subgroups suggests the requirement for additional selective processes before a full transformation into CLL is achieved.
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Affiliation(s)
- Monica Colombo
- U.O. Molecular Pathology, IRCCS Ospedale Policlinico San Martino, Genoa, Italy.
| | - Davide Bagnara
- Department of Experimental Medicine, University of Genoa, Genoa, Italy
| | - Daniele Reverberi
- U.O. Molecular Pathology, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Serena Matis
- U.O. Molecular Pathology, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Martina Cardillo
- U.O. Molecular Pathology, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Rosanna Massara
- U.O. Molecular Pathology, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Luca Mastracci
- U.O. Pathology, IRCCS Ospedale Policlinico San Martino, Genoa, Italy.,Department of Surgical Sciences and Integrated Diagnostics, University of Genoa, Genoa, Italy
| | | | - Luca Agnelli
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - Antonino Neri
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - Michela Mazzocco
- U.O. Laboratorio di Istocompatibilità, E.O. Ospedali Galliera, Genoa, Italy
| | - Margherita Squillario
- Department of Informatic Bioengeneering, Robotic and System Engeneering, University of Genoa, Genoa, Italy
| | | | - Giovanna Cutrona
- U.O. Molecular Pathology, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Andreas Agathangelidis
- Institute of Applied Biosciences, Center for Research and Technology Hellas CERTH, Thessaloniki, Greece
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Center for Research and Technology Hellas CERTH, Thessaloniki, Greece
| | - Manlio Ferrarini
- Department of Experimental Medicine, University of Genoa, Genoa, Italy
| | - Franco Fais
- U.O. Molecular Pathology, IRCCS Ospedale Policlinico San Martino, Genoa, Italy.,Department of Experimental Medicine, University of Genoa, Genoa, Italy
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10
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Pesce S, Belgrano V, Greppi M, Carlomagno S, Squillario M, Barla A, Della Chiesa M, Di Domenico S, Mavilio D, Moretta L, Candiani S, Sivori S, De Cian F, Marcenaro E. Different Features of Tumor-Associated NK Cells in Patients With Low-Grade or High-Grade Peritoneal Carcinomatosis. Front Immunol 2019; 10:1963. [PMID: 31497016 PMCID: PMC6712073 DOI: 10.3389/fimmu.2019.01963] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 05/13/2019] [Accepted: 08/05/2019] [Indexed: 12/16/2022] Open
Abstract
Peritoneal carcinomatosis (PC) is a rare disease defined as diffused implantation of neoplastic cells in the peritoneal cavity. This clinical picture occurs during the evolution of peritoneal tumors, and it is the main cause of morbidity and mortality of patients affected by these pathologies, though cytoreductive surgery with heated intra-peritoneal chemotherapy (CRS/HIPEC) is yielding promising results. In the present study, we evaluated whether the tumor microenvironment of low-grade and high-grade PC could affect the phenotypic and functional features and thus the anti-tumor potential of NK cells. We show that while in the peritoneal fluid (PF) of low-grade PC most CD56dim NK cells show a relatively immature phenotype (NKG2A+KIR-CD57-CD16dim), in the PF of high-grade PC NK cells are, in large majority, mature (CD56dimKIR+CD57+CD16bright). Furthermore, in low-grade PC, PF-NK cells are characterized by a sharp down-regulation of some activating receptors, primarily NKp30 and DNAM-1, while, in high-grade PC, PF-NK cells display a higher expression of the PD-1 inhibitory checkpoint. The compromised phenotype observed in low-grade PC patients corresponds to a functional impairment. On the other hand, in the high-grade PC patients PF-NK cells show much more important defects that only partially reflect the compromised phenotype detected. These data suggest that the PC microenvironment may contribute to tumor escape from immune surveillance by inducing different NK cell impaired features leading to altered anti-tumor activity. Notably, after CRS/HIPEC treatment, the altered NK cell phenotype of a patient with a low-grade disease and favorable prognosis was reverted to a normal one. Our present data offer a clue for the development of new immunotherapeutic strategies capable of restoring the NK-mediated anti-tumor responses in association with the CRS/HIPEC treatment to increase the effectiveness of the current therapy.
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Affiliation(s)
- Silvia Pesce
- Department of Experimental Medicine, University of Genoa, Genoa, Italy
| | - Valerio Belgrano
- Department of Surgical Sciences and Integrated Diagnostics, IRCCS Policlinico San Martino, University General Hospital, University of Genoa, Genoa, Italy.,Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy at the University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Marco Greppi
- Department of Experimental Medicine, University of Genoa, Genoa, Italy.,Centre of Excellence for Biomedical Research, University of Genoa, Genoa, Italy
| | - Simona Carlomagno
- Department of Experimental Medicine, University of Genoa, Genoa, Italy
| | - Margherita Squillario
- Department of Informatic Bioengineering, Robotic and System Engineering, University of Genoa, Genoa, Italy
| | - Annalisa Barla
- Department of Informatic Bioengineering, Robotic and System Engineering, University of Genoa, Genoa, Italy
| | - Mariella Della Chiesa
- Department of Experimental Medicine, University of Genoa, Genoa, Italy.,Centre of Excellence for Biomedical Research, University of Genoa, Genoa, Italy
| | - Stefano Di Domenico
- Department of Surgical Sciences and Integrated Diagnostics, IRCCS Policlinico San Martino, University General Hospital, University of Genoa, Genoa, Italy
| | - Domenico Mavilio
- Unit of Clinical and Experimental Immunology, Humanitas Clinical and Research Center, Rozzano, Milan, Italy.,Department of Medical Biotechnologies and Translational Medicine, University of Milan, Milan, Italy
| | - Lorenzo Moretta
- Department of Immunology, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Simona Candiani
- Department of Earth Science, Environment and Life, University of Genoa, Genoa, Italy
| | - Simona Sivori
- Department of Experimental Medicine, University of Genoa, Genoa, Italy.,Centre of Excellence for Biomedical Research, University of Genoa, Genoa, Italy
| | - Franco De Cian
- Department of Surgical Sciences and Integrated Diagnostics, IRCCS Policlinico San Martino, University General Hospital, University of Genoa, Genoa, Italy
| | - Emanuela Marcenaro
- Department of Experimental Medicine, University of Genoa, Genoa, Italy.,Centre of Excellence for Biomedical Research, University of Genoa, Genoa, Italy
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11
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Pesce S, Squillario M, Greppi M, Loiacono F, Moretta L, Moretta A, Sivori S, Castagnola P, Barla A, Candiani S, Marcenaro E. New miRNA Signature Heralds Human NK Cell Subsets at Different Maturation Steps: Involvement of miR-146a-5p in the Regulation of KIR Expression. Front Immunol 2018; 9:2360. [PMID: 30374356 PMCID: PMC6196268 DOI: 10.3389/fimmu.2018.02360] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [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: 07/31/2018] [Accepted: 09/24/2018] [Indexed: 12/21/2022] Open
Abstract
Natural killer cells are cytotoxic innate lymphoid cells that play an important role for early host defenses against infectious pathogens and surveillance against tumor. In humans, NK cells may be divided in various subsets on the basis of the relative CD56 expression and of the low-affinity FcγRIIIA CD16. In particular, the two main NK cell subsets are represented by the CD56bright/CD16−/dim and the CD56dim/CD16bright NK cells. Experimental evidences indicate that CD56bright and CD56dim NK cells represent different maturative stages of the NK cell developmental pathway. We identified multiple miRNAs differentially expressed in CD56bright/CD16− and CD56dim/CD16bright NK cells using both univariate and multivariate analyses. Among these, we found a few miRNAs with a consistent differential expression in the two NK cell subsets, and with an intermediate expression in the CD56bright/CD16dim NK cell subset, representing a transitional step of maturation of NK cells. These analyses allowed us to establish the existence of a miRNA signature able to efficiently discriminate the two main NK cell subsets regardless of their surface phenotype. In addition, by analyzing the putative targets of representative miRNAs we show that hsa-miR-146a-5p, may be involved in the regulation of killer Ig-like receptor (KIR) expression. These results contribute to a better understanding of the physiologic significance of miRNAs in the regulation of the development/function of human NK cells. Moreover, our results suggest that hsa-miR-146a-5p targeting, resulting in KIR down-regulation, may be exploited to generate/increment the effect of NK KIR-mismatching against HLA-class I+ tumor cells and thus improve the NK-mediated anti-tumor activity.
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Affiliation(s)
- Silvia Pesce
- Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy
| | - Margherita Squillario
- Department of Informatic Bioengeneering, Robotic and System Engeneering, University of Genoa, Genoa, Italy
| | - Marco Greppi
- Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy.,Centre of Excellence for Biomedical Research (CEBR), University of Genoa, Genoa, Italy
| | - Fabrizio Loiacono
- Immunology Operative Unit, IRCCS San Martino Polyclinical Hospital, Genoa, Italy
| | - Lorenzo Moretta
- Department of Immunology, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Alessandro Moretta
- Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy.,Centre of Excellence for Biomedical Research (CEBR), University of Genoa, Genoa, Italy
| | - Simona Sivori
- Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy.,Centre of Excellence for Biomedical Research (CEBR), University of Genoa, Genoa, Italy
| | - Patrizio Castagnola
- Department of Integrated Oncological Therapies, IRCCS San Martino Polyclinical Hospital, Genoa, Italy
| | - Annalisa Barla
- Department of Informatic Bioengeneering, Robotic and System Engeneering, University of Genoa, Genoa, Italy
| | - Simona Candiani
- Department of Earth Science, Environment and Life (DISTAV), University of Genoa, Genoa, Italy
| | - Emanuela Marcenaro
- Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy.,Centre of Excellence for Biomedical Research (CEBR), University of Genoa, Genoa, Italy
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12
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Squillario M, Barbieri M, Verri A, Barla A. Enhancing Interpretability of Gene Signatures with Prior Biological Knowledge. Microarrays (Basel) 2016; 5:microarrays5020015. [PMID: 27600081 PMCID: PMC5003491 DOI: 10.3390/microarrays5020015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 05/25/2016] [Accepted: 05/31/2016] [Indexed: 11/27/2022]
Abstract
Biological interpretability is a key requirement for the output of microarray data analysis pipelines. The most used pipeline first identifies a gene signature from the acquired measurements and then uses gene enrichment analysis as a tool for functionally characterizing the obtained results. Recently Knowledge Driven Variable Selection (KDVS), an alternative approach which performs both steps at the same time, has been proposed. In this paper, we assess the effectiveness of KDVS against standard approaches on a Parkinson’s Disease (PD) dataset. The presented quantitative analysis is made possible by the construction of a reference list of genes and gene groups associated to PD. Our work shows that KDVS is much more effective than the standard approach in enhancing the interpretability of the obtained results.
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Affiliation(s)
| | - Matteo Barbieri
- DIBRIS, University of Genoa, Via Dodecaneso 35, I-16146 Genova, Italy.
| | - Alessandro Verri
- DIBRIS, University of Genoa, Via Dodecaneso 35, I-16146 Genova, Italy.
| | - Annalisa Barla
- DIBRIS, University of Genoa, Via Dodecaneso 35, I-16146 Genova, Italy.
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13
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Bagnara D, Squillario M, Kipling D, Mora T, Walczak AM, Da Silva L, Weller S, Dunn-Walters DK, Weill JC, Reynaud CA. A Reassessment of IgM Memory Subsets in Humans. J Immunol 2015; 195:3716-24. [PMID: 26355154 DOI: 10.4049/jimmunol.1500753] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 08/06/2015] [Indexed: 12/22/2022]
Abstract
From paired blood and spleen samples from three adult donors, we performed high-throughput VH sequencing of human B cell subsets defined by IgD and CD27 expression: IgD(+)CD27(+) ("marginal zone [MZ]"), IgD(-)CD27(+) ("memory," including IgM ["IgM-only"], IgG and IgA) and IgD(-)CD27(-) cells ("double-negative," including IgM, IgG, and IgA). A total of 91,294 unique sequences clustered in 42,670 clones, revealing major clonal expansions in each of these subsets. Among these clones, we further analyzed those shared sequences from different subsets or tissues for VH gene mutation, H-CDR3-length, and VH/JH usage, comparing these different characteristics with all sequences from their subset of origin for which these parameters constitute a distinct signature. The IgM-only repertoire profile differed notably from that of MZ B cells by a higher mutation frequency and lower VH4 and higher JH6 gene usage. Strikingly, IgM sequences from clones shared between the MZ and the memory IgG/IgA compartments showed a mutation and repertoire profile of IgM-only and not of MZ B cells. Similarly, all IgM clonal relationships (among MZ, IgM-only, and double-negative compartments) involved sequences with the characteristics of IgM-only B cells. Finally, clonal relationships between tissues suggested distinct recirculation characteristics between MZ and switched B cells. The "IgM-only" subset (including cells with its repertoire signature but higher IgD or lower CD27 expression levels) thus appear as the only subset showing precursor-product relationships with CD27(+) switched memory B cells, indicating that they represent germinal center-derived IgM memory B cells and that IgM memory and MZ B cells constitute two distinct entities.
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Affiliation(s)
- Davide Bagnara
- Institut Necker-Enfants Malades, INSERM U1151-Centre National de la Recherche Scientifique Unité Mixte de Recherche 8253, Université Paris Descartes, Faculté de Médecine-Site Broussais, 75993 Paris Cedex 14, France
| | - Margherita Squillario
- Dipartimento di Informatica, Bioingegneria, Robotica e Ingegneria dei Sistemi, Università degli Studi di Genova, 16146 Genoa, Italy
| | - David Kipling
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Thierry Mora
- Laboratoire de Physique Statistique, Centre National de la Recherche Scientifique Unité Mixte de Recherche 8550, Université Pierre et Marie Curie and Ecole Normale Supérieure, 75005 Paris, France
| | - Aleksandra M Walczak
- Laboratoire de Physique Théorique, Unité Mixte de Recherche 8549, Centre National de la Recherche Scientifique and Ecole Normale Supérieure, 75005 Paris, France; and
| | - Lucie Da Silva
- Institut Necker-Enfants Malades, INSERM U1151-Centre National de la Recherche Scientifique Unité Mixte de Recherche 8253, Université Paris Descartes, Faculté de Médecine-Site Broussais, 75993 Paris Cedex 14, France
| | - Sandra Weller
- Institut Necker-Enfants Malades, INSERM U1151-Centre National de la Recherche Scientifique Unité Mixte de Recherche 8253, Université Paris Descartes, Faculté de Médecine-Site Broussais, 75993 Paris Cedex 14, France
| | - Deborah K Dunn-Walters
- Department of Immunobiology, Faculty of Life Sciences and Medicine, King's College London, London SE1 9RT, United Kingdom
| | - Jean-Claude Weill
- Institut Necker-Enfants Malades, INSERM U1151-Centre National de la Recherche Scientifique Unité Mixte de Recherche 8253, Université Paris Descartes, Faculté de Médecine-Site Broussais, 75993 Paris Cedex 14, France;
| | - Claude-Agnès Reynaud
- Institut Necker-Enfants Malades, INSERM U1151-Centre National de la Recherche Scientifique Unité Mixte de Recherche 8253, Université Paris Descartes, Faculté de Médecine-Site Broussais, 75993 Paris Cedex 14, France;
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14
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Scala M, Lenarduzzi S, Spagnolo F, Trapasso M, Ottonello C, Muraglia A, Barla A, Squillario M, Strada P. Regenerative medicine for the treatment of Teno-desmic injuries of the equine. A series of 150 horses treated with platelet-derived growth factors. In Vivo 2014; 28:1119-1123. [PMID: 25398809] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
BACKGROUND/AIM The aim of the present study was to evaluate the safety and the clinical outcome of platelet-rich plasma for the treatment of teno-desmic injures in competition horses. PATIENTS AND METHODS From January 2009 to December 2011, 150 sport horses suffering from teno-desmic injuries were treated with no-gelled platelet-concentrate. RESULTS No horse showed any major adverse reaction as a result of the procedure. Full healing was obtained for 81% of the horses. Twelve percent had clinical improvement and only 7% a failure. Eight percent of cases of relapse were observed. No statistically significant correlation existed between clinical outcome and the area of the lesion. A statistically significant correlation existed between the clinical outcome and the age of the horse. CONCLUSION Treatment with platelet-derived growth factors leads to the formation of a tendon with normal morphology and functionality, which translate in the resumption of the agonistic activity for the horses we treated.
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Affiliation(s)
- Marco Scala
- Department of Plastic and Reconstructive Surgery, IRCCS Azienda Ospedaliera Universitaria San Martino, Istituto Nazionale Per La Ricerca Sul Cancro, Genova, Italy
| | - Silvia Lenarduzzi
- Department of Medical and Veterinary Sciences, University of Parma, Parma, Italy
| | - Francesco Spagnolo
- Department of Plastic and Reconstructive Surgery, IRCCS Azienda Ospedaliera Universitaria San Martino, Istituto Nazionale Per La Ricerca Sul Cancro, Genova, Italy
| | - Maria Trapasso
- Department of Plastic and Reconstructive Surgery, IRCCS Azienda Ospedaliera Universitaria San Martino, Istituto Nazionale Per La Ricerca Sul Cancro, Genova, Italy
| | - Chiara Ottonello
- Department of Experimental Medicine, University of Genova, Genova, Italy
| | - Anita Muraglia
- Department of Experimental Medicine, University of Genova, Genova, Italy
| | - Annalisa Barla
- Department of Computer and Information Science (DISI), University of Genova, Genova, Italy
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15
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Zycinski G, Barla A, Squillario M, Sanavia T, Camillo BD, Verri A. Knowledge Driven Variable Selection (KDVS) - a new approach to enrichment analysis of gene signatures obtained from high-throughput data. Source Code Biol Med 2013; 8:2. [PMID: 23302187 PMCID: PMC3605163 DOI: 10.1186/1751-0473-8-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 12/13/2012] [Indexed: 11/10/2022]
Abstract
Background High–throughput (HT) technologies provide huge amount of gene expression data that can be used to identify biomarkers useful in the clinical practice. The most frequently used approaches first select a set of genes (i.e. gene signature) able to characterize differences between two or more phenotypical conditions, and then provide a functional assessment of the selected genes with an a posteriori enrichment analysis, based on biological knowledge. However, this approach comes with some drawbacks. First, gene selection procedure often requires tunable parameters that affect the outcome, typically producing many false hits. Second, a posteriori enrichment analysis is based on mapping between biological concepts and gene expression measurements, which is hard to compute because of constant changes in biological knowledge and genome analysis. Third, such mapping is typically used in the assessment of the coverage of gene signature by biological concepts, that is either score–based or requires tunable parameters as well, limiting its power. Results We present Knowledge Driven Variable Selection (KDVS), a framework that uses a priori biological knowledge in HT data analysis. The expression data matrix is transformed, according to prior knowledge, into smaller matrices, easier to analyze and to interpret from both computational and biological viewpoints. Therefore KDVS, unlike most approaches, does not exclude a priori any function or process potentially relevant for the biological question under investigation. Differently from the standard approach where gene selection and functional assessment are applied independently, KDVS embeds these two steps into a unified statistical framework, decreasing the variability derived from the threshold–dependent selection, the mapping to the biological concepts, and the signature coverage. We present three case studies to assess the usefulness of the method. Conclusions We showed that KDVS not only enables the selection of known biological functionalities with accuracy, but also identification of new ones. An efficient implementation of KDVS was devised to obtain results in a fast and robust way. Computing time is drastically reduced by the effective use of distributed resources. Finally, integrated visualization techniques immediately increase the interpretability of results. Overall, KDVS approach can be considered as a viable alternative to enrichment–based approaches.
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Affiliation(s)
- Grzegorz Zycinski
- DIBRIS, University of Genoa, via Dodecaneso 35, I-16146 Genova, Italy.
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16
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Di Camillo B, Sanavia T, Martini M, Jurman G, Sambo F, Barla A, Squillario M, Furlanello C, Toffolo G, Cobelli C. Effect of size and heterogeneity of samples on biomarker discovery: synthetic and real data assessment. PLoS One 2012; 7:e32200. [PMID: 22403633 PMCID: PMC3293892 DOI: 10.1371/journal.pone.0032200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [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: 06/30/2011] [Accepted: 01/24/2012] [Indexed: 01/04/2023] Open
Abstract
MOTIVATION The identification of robust lists of molecular biomarkers related to a disease is a fundamental step for early diagnosis and treatment. However, methodologies for the discovery of biomarkers using microarray data often provide results with limited overlap. These differences are imputable to 1) dataset size (few subjects with respect to the number of features); 2) heterogeneity of the disease; 3) heterogeneity of experimental protocols and computational pipelines employed in the analysis. In this paper, we focus on the first two issues and assess, both on simulated (through an in silico regulation network model) and real clinical datasets, the consistency of candidate biomarkers provided by a number of different methods. METHODS We extensively simulated the effect of heterogeneity characteristic of complex diseases on different sets of microarray data. Heterogeneity was reproduced by simulating both intrinsic variability of the population and the alteration of regulatory mechanisms. Population variability was simulated by modeling evolution of a pool of subjects; then, a subset of them underwent alterations in regulatory mechanisms so as to mimic the disease state. RESULTS The simulated data allowed us to outline advantages and drawbacks of different methods across multiple studies and varying number of samples and to evaluate precision of feature selection on a benchmark with known biomarkers. Although comparable classification accuracy was reached by different methods, the use of external cross-validation loops is helpful in finding features with a higher degree of precision and stability. Application to real data confirmed these results.
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Affiliation(s)
| | - Tiziana Sanavia
- Information Engineering Department, University of Padova, Padova, Italy
| | - Matteo Martini
- Information Engineering Department, University of Padova, Padova, Italy
| | | | - Francesco Sambo
- Information Engineering Department, University of Padova, Padova, Italy
| | - Annalisa Barla
- Department of Computer and Information Science, University of Genova, Genova, Italy
| | | | | | - Gianna Toffolo
- Information Engineering Department, University of Padova, Padova, Italy
| | - Claudio Cobelli
- Information Engineering Department, University of Padova, Padova, Italy
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17
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Squillario M, Barla A. A computational procedure for functional characterization of potential marker genes from molecular data: Alzheimer's as a case study. BMC Med Genomics 2011; 4:55. [PMID: 21726470 PMCID: PMC3149568 DOI: 10.1186/1755-8794-4-55] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [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: 10/15/2010] [Accepted: 07/05/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A molecular characterization of Alzheimer's Disease (AD) is the key to the identification of altered gene sets that lead to AD progression. We rely on the assumption that candidate marker genes for a given disease belong to specific pathogenic pathways, and we aim at unveiling those pathways stable across tissues, treatments and measurement systems. In this context, we analyzed three heterogeneous datasets, two microarray gene expression sets and one protein abundance set, applying a recently proposed feature selection method based on regularization. RESULTS For each dataset we identified a signature that was successively evaluated both from the computational and functional characterization viewpoints, estimating the classification error and retrieving the most relevant biological knowledge from different repositories. Each signature includes genes already known to be related to AD and genes that are likely to be involved in the pathogenesis or in the disease progression. The integrated analysis revealed a meaningful overlap at the functional level. CONCLUSIONS The identification of three gene signatures showing a relevant overlap of pathways and ontologies, increases the likelihood of finding potential marker genes for AD.
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Affiliation(s)
- Margherita Squillario
- Department of Computer and Information Science (DISI), Università degli Studi di Genova, Via Dodecaneso 35, Genova, I-16146, Italy.
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