Genome, Environment, Microbiome & Metabolome in Autism: an integrated multi-omic systems biology approach to identify biomarkers for personalized treatment and primary prevention of Autism Spectr

Informations projet

GEMMA

N° de convention de subvention: 825033

DOI

10.3030/825033

Date de signature de la CE 22 Novembre 2018

Date de début 1 Janvier 2019

Date de fin 31 Decembre 2025

Financé au titre de

• SOCIETAL CHALLENGES - Health, demographic change and well-being

Coût total

€ 14 225 757,50

Contribution de l’UE

€ 14 225 757,50

Coordonné par

FONDAZIONE EBRIS
Italy

CORDIS fournit des liens vers les livrables publics et les publications des projets HORIZON.

Les liens vers les livrables et les publications des projets du 7e PC, ainsi que les liens vers certains types de résultats spécifiques tels que les jeux de données et les logiciels, sont récupérés dynamiquement sur OpenAIRE .

Livrables

Documents, reports (12)

Report on the participation to the IHMC congress in Barcelona 2020

Report on the outcomes of the participation of GEMMA at the 8th International Human Microbiome Congress in 2020 (Barcelona)

Final clinical protocols

Study protocols to submit for the approbation to the ethical committee

Pre-clinical study 2 report

A report providing the results of the trial 2 to investigate if the ASD phenotype is dependent on microbiome-induced systemic immune activation, via adoptive splenocyte transfer studies

Theoretical qualitative models of ASD pathogenesis mechanisms

A model specifically detail the mechanisms whereby alterations in gut microbiome may lead to persistent, low-grade feverless systemic inflammation and how this could then affect CNS metabolism and neuronal arborescence preferentially in male developing infants

Pre-clinical study 3/2 report

A second report providing the results of trial 3 to establish whether correction of dysbiosis by pre/pro/symbiotic intervention prevents and/or treats increased the impaired gut permeability, changes in metabolic profile, modification of the immune response, and, ultimately, the onset of ASD behavioural symptoms in humanized murine models of ASD (mice transplanted with faecal bacterial content of ASD patient donor sample

Pre-clinical study ethical approval report

A study protocol to submit for the approbation to the ethical committee

Pre-clinical study 1 report

A report providing the results of the the trial 1 focus on exploring if the behavioural phenotype of ASD patients is transferrable to mice via faecal transplantation

Genome, epigenome and immune function interplay summary of hypothesis

An hypothesis regarding how the genome/metagenome interplay is responsible for the switch from immune tolerance to immune response to environmental stimuli (antigens) including dietary and microbial factors leading to neuroinflammation responsible of behavioural changes that characterize ASD and gut inflammation causing its GI co-morbidities

Pre-clinical study 3/3 report

A third report providing the results of trial 3 to establish whether correction of dysbiosis by pre/pro/symbiotic intervention prevents and/or treats increased the impaired gut permeability, changes in metabolic profile, modification of the immune response, and, ultimately, the onset of ASD behavioural symptoms in humanized murine models of ASD (mice transplanted with faecal bacterial content of ASD patient donor sample

Updated state of the art report

Report providing a brief relation about the state of the art in the ASD biomarker and therapy

Microbiome, metabolome and immune function interplay summary of hypothesis

An hypothesis regarding how the gut bacterial dysbiosis leads to epigenetic modifications, changes in metabolic profiles, increased gut permeability, increased antigen trafficking and, ultimately to altered immune responses to promote disease in a subset of individuals at-risk of ASD

Pre-clinical study 3/1 report

A first report providing the results of trial 3 to establish whether correction of dysbiosis by pre/pro/symbiotic intervention prevents and/or treats increased the impaired gut permeability, changes in metabolic profile, modification of the immune response, and, ultimately, the onset of ASD behavioural symptoms in humanized murine models of ASD (mice transplanted with faecal bacterial content of ASD patient donor sample

Demonstrators, pilots, prototypes (3)

First release of the multi-omics platform (pre-clinical trials)

An algorithms able to associate various biomarker levels observed in infants with ASD and GI symptoms. This alghorithm will use advanced statistical analysis methods such as sparse canonical correlation (a linear correlation method) combined with random forests (a non-linear correlation method) to detect these associations between the omics data.

Second release of the multi-omics platform (observational trials)

An analysis of the fitting between the correlations put forward by the multi-omics analyses and the biological outcome of the interventional part of the observational study

OmnomicsNGS v2 release

A new relase of the software OmnomicsNGS including a tool for dynamic variant analysis and interpretation

Open Research Data Pilot (1)

Open data management plan

GEMMA participation on H2020 open data pilot

Websites, patent fillings, videos etc. (1)

External project website

Project website: project description, public deliverables, scientific news, other

Publications

Peer reviewed articles (31)

An integrative network analysis framework for identifying molecular functions in complex disorders examining major depressive disorder as a test case.

Auteurs: Oommen AM, Cunningham S, O'Súilleabháin PS, Hughes BM, Joshi L
Publié dans: Scientific Reports, Numéro (2021) 11:9645, 2021, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-021-89040-7

Neurotensin-Binding Immunoglobulin G in Patients with Parkinson’s Disease

Auteurs: Muruzheva ZM, Egorov DS, Absalyamova MT, Traktirov DS, Karpenko MN, and Fetissov SO
Publié dans: Neuroimmunomodulation, Numéro 30(1), 2023, Page(s) 15-27, ISSN 1021-7401
Éditeur: S. Karger AG
DOI: 10.1159/000527872

Mechanisms of Glucose Absorption in the Small Intestine in Health and Metabolic Diseases and Their Role in Appetite Regulation

Auteurs: Lyudmila V. Gromova, Serguei O. Fetissov, Andrey A. Gruzdkov
Publié dans: Nutrients, Numéro 13/7, 2021, Page(s) 2474, ISSN 2072-6643
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/nu13072474

Prebiotic diet normalizes aberrant immune and behavioral phenotypes in a mouse model of autism spectrum disorder

Auteurs: Naika Prince, Lucia N Peralta Marzal, Anastasia Markidi, Sabbir Ahmed, Youri Adolfs, R Jeroen Pasterkamp, Himanshu Kumar, Guus Roeselers, Johan Garssen, Aletta D Kraneveld, Paula Perez-Pardo
Publié dans: Acta Pharmacologica Sinica, Numéro 45, 2024, Page(s) 1591-1603, ISSN 1671-4083
Éditeur: Shanghai Institute of Materia Medica
DOI: 10.1038/s41401-024-01268-x

Network Diffusion Promotes the Integrative Analysis of Multiple Omics

Auteurs: Noemi Di Nanni, Matteo Bersanelli, Luciano Milanesi, Ettore Mosca
Publié dans: Frontiers in Genetics, Numéro 11, 2020, ISSN 1664-8021
Éditeur: Frontiers Media
DOI: 10.3389/fgene.2020.00106

Analysis of Faecal Microbiota and Small ncRNAs in Autism: Detection of miRNAs and piRNAs with Possible Implications in Host-Gut Microbiota Cross-Talk

Auteurs: Chiappori F., Cupaioli F.A., Consiglio A., Di Nanni N., Mosca E., Licciulli V.F., Mezzelani A.
Publié dans: Nutrients, Numéro 14(7):1340, 2022 Mar 23, 2022, Page(s) 1-23, ISSN 2072-6643
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/nu14071340

Microbiota influence on behavior: Integrative analysis of serotonin metabolism and behavioral profile in germ‐free mice

Auteurs: Léa Roussin, Elisa Gry, Mira Macaron, Sandy Ribes, Magali Monnoye, Véronique Douard, Laurent Naudon, Sylvie Rabot
Publié dans: The FASEB Journal, Numéro 38, 2024, ISSN 0892-6638
Éditeur: Federation of American Societies for Experimental Biology
DOI: 10.1096/fj.202400334r

The interaction between intestinal bacterial metabolites and phosphatase and tensin homolog in autism spectrum disorder

Auteurs: Zheng Y, Prince N, van Hattem C, Garssen J, Pardo PP, Kraneveld AD
Publié dans: Molecular and Celullar Neuroscience, Numéro Dec 30;124:103805, 2023, Page(s) 1-11, ISSN 1044-7431
Éditeur: Academic Press
DOI: 10.1016/j.mcn.2022.103805

The role of bacterial-derived aromatic amino acids metabolites relevant in autism spectrum disorders: A comprehensive review

Auteurs: Yuanpeng Zheng, Marie K Bek, Naika Z Prince, Lucia N Peralta Marzal, Johan Garssen, Paula Perez Pardo, Aletta D Kraneveld
Publié dans: Frontiers in Neuroscience, Numéro October, 2021, Page(s) 1401, ISSN 1662-453X
Éditeur: Frontiers
DOI: 10.3389/fnins.2021.738220

Autonomic Nervous System Neuroanatomical Alterations Could Provoke and Maintain Gastrointestinal Dysbiosis in Autism Spectrum Disorder (ASD): A Novel Microbiome–Host Interaction Mechanistic Hypothesis

Auteurs: Athanasios Beopoulos, Manuel Gea, Alessio Fasano, François Iris
Publié dans: Nutrients, 2021, ISSN 2072-6643
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/nu14010065

Assessment of haptoglobin alleles in autism spectrum disorders

Auteurs: Cupaioli FA, Mosca E, Magri C, Gennarelli M, Moscatelli M, Raggi ME, Landini M, Galluccio N, Villa L, Bonfanti A, Renieri A, Fallerini C, Minelli A, Marabotti A, Milanesi L, Fasano A, Mezzelani A
Publié dans: Scientific Reports, Numéro 10(1):7758, 2020 May 8, 2020, Page(s) 1-11, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-020-64679-w

Lactobacillus salivarius and Lactobacillus gasseri supplementation reduces stress-induced sugar craving in mice

Auteurs: Nicol M., Lahaye E., El Mehdi M., do Rego J.-L., do Rego J.-C., Fetissov S.O.
Publié dans: European Eating Disorders Review, 2023, ISSN 1099-0968
Éditeur: Wiley
DOI: 10.1002/erv.3004

The Impact of Gut Microbiota-Derived Metabolites in Autism Spectrum Disorders

Auteurs: Lucía N. Peralta-Marzal, Naika Prince, Djordje Bajic, Léa Roussin, Laurent Naudon, Sylvie Rabot, Johan Garssen, Aletta D. Kraneveld and Paula Perez-Pardo
Publié dans: International Journal of Molecular Sciences, Numéro Volume 22, Numéro 18, 2021, semimonthly, 2021, ISSN 1422-0067
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms221810052

The Gut-Brain Axis in Autism Spectrum Disorder: A Focus on the Metalloproteases ADAM10 and ADAM17

Auteurs: Yuanpeng Zheng, Tessa A. Verhoeff, Paula Perez Pardo, Johan Garssen and Aletta D. Kraneveld
Publié dans: International Journal of Molecular Sciences, Numéro volume 22, issue 1, 2021, semimonthly, 2021, ISSN 1422-0067
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms22010118

The Autism Spectrum Disorder-Associated Bacterial Metabolite p-Cresol Derails the Neuroimmune Response of Microglial Cells Partially via Reduction of ADAM17 and ADAM10

Auteurs: Zheng, Y.; Prince, N.Z.; Peralta Marzal, L.N.; Ahmed, S.; Garssen, J.; Perez Pardo, P.; Kraneveld, A.D.
Publié dans: Int J Mol Sci, Numéro Sep 20;23(19):11013, 2022, Page(s) 1-17, ISSN 1422-0067
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms231911013

Autism Spectrum Disorders: Analysis of Mobile Elements at 7q11.23 Williams–Beuren Region by Comparative Genomics

Auteurs: Francesca Anna Cupaioli, Chiara Fallerini, Maria Antonietta Mencarelli, Valentina Perticaroli, Virginia Filippini, Francesca Mari, Alessandra Renieri, Alessandra Mezzelani
Publié dans: Genes, Numéro 12/10, 2021, Page(s) 1605, ISSN 2073-4425
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/genes12101605

Characterization and comparison of gene-centered human interactomes

Auteurs: Ettore Mosca, Matteo Bersanelli, Tommaso Matteuzzi, Noemi Di Nanni, Gastone Castellani, Luciano Milanesi, Daniel Remondini
Publié dans: Briefings in Bioinformatics, 2021, ISSN 1467-5463
Éditeur: Oxford University Press
DOI: 10.1093/bib/bbab153

A robust microbiome signature for autism spectrum disorder across different studies using machine learning

Auteurs: Lucia N. Peralta-Marzal, David Rojas-Velazquez, Douwe Rigters, Naika Prince, Johan Garssen, Aletta D. Kraneveld, Paula Perez-Pardo, Alejandro Lopez-Rincon
Publié dans: Scientific Reports, Numéro 14, 2024, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-023-50601-7

Protein extract of a probiotic strain Hafnia alvei and bacterial ClpB protein improve glucose tolerance in mice

Auteurs: Zolotarev V.A., Murovets V.O., Sepp A.L., Sozontov E.A., Lukina E.A., Khropycheva R.P., Pestereva N.S., Ivleva I.S., El Mehdi M., Lahaye E., Chartrel N., Fetissov S.O.
Publié dans: International Journal of Molecular Sciences, Numéro 24(13), 10590, 2023, ISSN 1422-0067
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms241310590

Genome, Environment, Microbiome and Metabolome in Autism (GEMMA) Study Design: Biomarkers Identification for Precision Treatment and Primary Prevention of Autism Spectrum Disorders by an Integrated Multi-Omics Systems Biology Approach

Auteurs: Jacopo Troisi, Reija Autio, Thanos Beopoulos, Carmela Bravaccio, Federica Carraturo, Giulio Corrivetti, Stephen Cunningham, Samantha Devane, Daniele Fallin, Serguei Fetissov, Manuel Gea, Antonio Giorgi, François Iris, Lokesh Joshi, Sarah Kadzielski, Aletta Kraneveld, Himanshu Kumar, Christine Ladd-Acosta, Geraldine Leader, Arlene Mannion, Elise Maximin, Alessandra Mezzelani, Luciano Milanesi, Lau
Publié dans: Brain Sciences, Numéro 10/10, 2020, Page(s) 743, ISSN 2076-3425
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/brainsci10100743

Gut Reactions: How Far Are We from Understanding and Manipulating the Microbiota Complexity and the Interaction with Its Host? Lessons from Autism Spectrum Disorder Studies

Auteurs: Martina Lombardi, Jacopo Troisi
Publié dans: Nutrients, Numéro 13/10, 2021, Page(s) 3492, ISSN 2072-6643
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/nu13103492

Change of Communication Strategy to Increase Engagement during the SARS-Cov-2Pandemic: The Experience of the European GEMMA Project in Italy

Auteurs: Cupaioli Francesca Anna, Corrivetti Giulio, Tamburro Ilaria, Fasano Alessio, Mezzelani Alessandra
Publié dans: International Journal of Humanities, Social Sciences and Education, Numéro 7/9, 2020, ISSN 2349-0381
Éditeur: ARC Publications Pvt Ltd
DOI: 10.20431/2349-0381.0709013

Network-Based Integrative Analysis of Genomics, Epigenomics and Transcriptomics in Autism Spectrum Disorders

Auteurs: Noemi Di Nanni, Matteo Bersanelli, Francesca Anna Cupaioli, Luciano Milanesi, Alessandra Mezzelani, Ettore Mosca
Publié dans: International Journal of Molecular Sciences, Numéro 20/13, 2019, Page(s) 3363, ISSN 1422-0067
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms20133363

Role of the Gut Microbiota in the Pathophysiology of Autism Spectrum Disorder: Clinical and Preclinical Evidence

Auteurs: Léa Roussin, Naika Prince, Paula Perez-Pardo, Aletta D. Kraneveld, Sylvie Rabot, Laurent Naudon
Publié dans: Microorganisms, Numéro 8/9, 2020, Page(s) 1369, ISSN 2076-2607
Éditeur: MDPI
DOI: 10.3390/microorganisms8091369

Blood levels of neuropeptide 26RFa in relation to anxiety and aggressive behavior in humans - an exploratory study

Auteurs: Værøy H., Takhlidjt S., Cherifi Y., Lahaye E., Chartrel N., Fetissov S.O.
Publié dans: Brain Sciences, Numéro 13(2), 237, 2023, ISSN 2076-3425
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/brainsci13020237

Immunoglobulin G is a natural oxytocin carrier which modulates oxytocin receptor signaling - relevance to aggressive behavior in humans

Auteurs: Værøy H., Lahaye E., Dubessy C., Benard M., Nicol M., Cherifi Y., Takhlidjt S., do Rego J.-L., do Rego J.-C., Chartrel N., Fetissov S.O.
Publié dans: Discover Mental Health, Numéro Oct 19;3(1):21, 2023, Page(s) Volume 3, article number 21, ISSN 2731-4383
Éditeur: Springer
DOI: 10.1007/s44192-023-00048-z

Autism spectrum disorders pathogenesis: Toward a comprehensive model based on neuroanatomic and neurodevelopment considerations

Auteurs: Beopoulos A, Géa M, Fasano A, Iris F
Publié dans: Frontiers in neuroscience, Numéro Nov 03 3;16:988735, 2022, Page(s) 1-24, ISSN 1662-453X
Éditeur: Frontiers
DOI: 10.3389/fnins.2022.988735

Mouse strain-specific responses along the gut-brain axis upon fecal microbiota transplantation from children with autism

Auteurs: Naika Prince, Lucia N. Peralta Marzal, Léa Roussin, Magali Monnoye, Catherine Philippe, Elise Maximin, Sabbir Ahmed, Karoliina Salenius, Jake Lin, Reija Autio, Youri Adolfs, R. Jeroen Pasterkamp, Johan Garssen, Laurent Naudon, Sylvie Rabot, Aletta D. Kraneveld, Paula Perez-Pardo
Publié dans: Gut Microbes, Numéro 17, 2025, ISSN 1949-0976
Éditeur: Landes Bioscience
DOI: 10.1080/19490976.2024.2447822

Gene relevance based on multiple evidences in complex networks

Auteurs: Noemi Di Nanni, Matteo Gnocchi, Marco Moscatelli, Luciano Milanesi, Ettore Mosca
Publié dans: Bioinformatics, 2019, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btz652

Transcriptomic Analysis of Respiratory Tissue and Cell Line Models to Examine Glycosylation Machinery during SARS-CoV-2 Infection

Auteurs: Oommen A, Cunningham S, Joshi L.
Publié dans: Viruses, Numéro Jan 8;13(1):82, 2021, Page(s) 1-15, ISSN 1999-4915
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v13010082

Food, nutrition, and autism: from soil to fork

Auteurs: Melissa Maitin-Shepard, Perrie O’Tierney-Ginn, Aletta D Kraneveld, Kristen Lyall, Daniele Fallin, Manish Arora, Alessio Fasano, Noel T Mueller, Xiaobin Wang, Laura E Caulfield, Aisha S Dickerson, Rochellys Diaz Heijtz, Tomo Tarui, Jeffrey B Blumberg, Calliope Holingue, Rebecca J Schmidt, Johan Garssen, Katherine Almendinger, Pi-I Debby Lin, Dariush Mozaffarian
Publié dans: The American Journal of Clinical Nutrition, Numéro 120, 2025, Page(s) 240-256, ISSN 0002-9165
Éditeur: American Society for Clinical Nutrition, Inc.
DOI: 10.1016/j.ajcnut.2024.04.020

Conference proceedings (1)

Genome, Environment, Microbiome and Metabolome in Autism (GEMMA) Study: Beyond biomarker identification for the precision treatment and early detection of autism spectrum disorders

Auteurs: J. Troisi, M. Lombardi, SJK Symes, G. Scala, M. Delli Carri, SM Richards & GEMMA Consortium
Publié dans: Bioinformatics and Computational Biology Conference, 2022
Éditeur: F1000 Research
DOI: 10.7490/f1000research.1119307.1

Other (5)

Progress in the Puzzle Resolution: The Molecular Genetics Underpinning Autism Spectrum Disorders

Auteurs: Mezzelani A, Cupaioli F.A.
Publié dans: Brain Science, Numéro 2023 Dec 7;13(12):1688, 2023, ISSN 2076-3425
Éditeur: MDPI
DOI: 10.3390/brainsci13121688

Plasma and Fecal Metabolite Profiles in Autism Spectrum Disorder

Auteurs: Brittany D. Needham, Mark D. Adame, Gloria Serena, Destanie R. Rose, Gregory M. Preston, Mary C. Conrad, A. Stewart Campbell, David H. Donabedian, Alessio Fasano, Paul Ashwood, Sarkis K. Mazmanian
Publié dans: Journal Biological Psychiatry, Numéro Volume 89, Numéro 5, 2021, Page(s) 451-462, ISSN 0006-3223
Éditeur: Elsevier
DOI: 10.1016/j.biopsych.2020.09.025

Gut Microbiota-Brain Axis in Regulation of Feeding Behavior

Auteurs: Fetissov SO
Publié dans: Microorganisms, Numéro 11(3), 749, 2023, ISSN 2076-2607
Éditeur: MDPI
DOI: 10.3390/microorganisms11030749

Zonulin-Dependent Intestinal Permeability in Children Diagnosed with Mental Disorders: A Systematic Review and Meta-Analysis

Auteurs: Asbjornsdottir, B.; Snorradottir, H.; Andresdottir, E.; Fasano, A.; Lauth, B.; Gudmundsson, L.S.; Gottfredsson, M.; Halldorsson, T.I.; Birgisdottir, B.E.
Publié dans: Nutrients, Numéro Jul 3;12(7):1982, 2020, Page(s) 1-27, ISSN 2072-6643
Éditeur: MDPI
DOI: 10.3390/nu12071982

Optimization of Peripheral Blood Mononuclear Cell Extraction from Small Volume of Blood Samples: Potential Implications for Children-Related Diseases

Auteurs: Patrone, D.; Alessio, N.; Antonucci, N.; Brigida, A.L.; Peluso, G.; Galderisi, U.; Siniscalco, D.
Publié dans: Journal Methods Protoc, Numéro Feb 24;5(2):20, 2022, Page(s) 1-6, ISSN 2409-9279
Éditeur: MDPI
DOI: 10.3390/mps5020020