AbstractThere is considerable evidence implicating maternal immune activation (MIA) and cytokine dysregulation in the pathophysiology of Autism. However, cytokines, due to their lack of specificity are unlikely to translate clinically as prognostic biomarkers. Our aim was to explore the perinatal molecular pathways dysregulated in umbilical cord blood, which precede a diagnosis of childhood Autism, and ascertain whether these putative biomarkers persisted into pre-pubertal childhood. In a cohort of 2137 mother-infant dyads, we conducted a nested case-control study in the BASELINE Birth Cohort. Proteomic and metabolomic analysis was performed on cord blood plasma from 22 children diagnosed with Autism before age 5, and 44 neurotypical controls. In a clinical diagnostic follow-up between 7–10 years in the PiRAMiD Cohort, 24 children with Autism and 48 controls provided blood samples for molecular profiling. In cord blood, proteomics revealed altered glycolysis, selenium metabolism, oxygen transport, and complement signalling. Alterations in these protein pathways persisted into childhood, and dysregulation of GAPDH, SELENBP1, and BLVRB proteins were evident in both cord blood and in serum from pre-pubertal children with Autism. In cord blood, metabolomics analysis indicated Autism outcome was associated with reduced levels of circulating steroids and increased sulfate. We confirmed androstenedione was reduced in cord blood, in Autism cases in comparison to controls, however changes in androstenedione levels were not evident in serum from pre-pubertal children with Autism. Our findings were further corroborated using machine learning approaches, with an AUROC ranging from 0.82 to 0.85 for proteomic and metabolomic cord blood prediction models, respectively. Collectively, these findings confirm a cord blood molecular signature precedes the onset of Autism and has the potential to lead to prognostic biomarkers. Our integrative multi-omics analysis reveals materno-feto-placental molecular processes which potentially underpin Autism aetiology.This is a preview of subscription content, access via your institutionAccess optionsSubscribe to this journalReceive 12 print issues and online access269,00 € per yearonly 22,42 € per issueLearn moreBuy this articlePurchase on SpringerLinkInstant access to full article PDFBuy nowPrices may be subject to local taxes which are calculated during checkoutFig. 1: Study design and graphical abstract.Fig. 2: Results from cord blood proteomics analysis.Fig. 3: Results from childhood serum proteomic analysis.Fig. 4: Results from cord blood metabolomics analysis.Fig. 5: Targeted MRM analysis of steroid metabolites in cord blood and serum from children with autism and neurotypical controls.Data availabilityThe clinical data is not publicly available because it contains sensitive patient information. Requests for access can be made directly to INFANT centre at infant@ucc.ie. The proteomics data has been uploaded to the Mass Spectrometry Interactive Virtual Environment at MassIVE repository. The proteomics data for this study can be accessed using accession MSV000097274 at the following URL ftp://massive.ucsd.edu/v09/MSV000097274/. The metabolomics data (Project ID: PR002383) is available at the NIH Common Fund’s National Metabolomics Data Repository (NMDR; [87]), at Metabolomics Workbench whereby the positive mode data (Study ID ST003810; https://doi.org/10.21228/M8M820) and the negative mode data (Study ID ST003809; https://doi.org/10.21228/M8M820) is available for download.ReferencesBoilson AM, Staines A, Ramirez A, Posada M, Sweeney MR. Operationalisation of the European Protocol for Autism Prevalence (EPAP) for Autism spectrum disorder prevalence measurement in Ireland. J Autism Dev Disord. 2016;46:3054–67.CAS PubMed Google Scholar Buescher AVS, Cidav Z, Knapp M, Mandell DS. 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Autism. 2016;20:442–62.PubMed Google Scholar Download referencesAcknowledgementsWe are extremely grateful to all the families who took part in the BASELINE and PiRAMiD studies, the midwives and clinical workers who helped recruiting participants, and the whole INFANT team, (interviewers, computer and laboratory technicians, clerical workers, research scientists, volunteers, managers, receptionists, and nurses). This publication is the work of the authors, who will serve as guarantors for the contents of this paper. We also thank Prof Gerard Cagney and the Mass Spectrometry Core Facility, Conway Institute, UCD, for access to services and support in our proteomic workflows. Additionally, we would like to thank Ms Tara Foley, Department of Anatomy and Neuroscience, for technical support. This manuscript written in accordance with guidelines published by the Aims2trial (https://www.aims-2-trials.eu/language/), to ensure our research communication and language is respectful and acceptable to autistic people and the Autism community [88].FundingThis research was specifically funded by the Irish Health Research Board through an Emerging Investigator Award to Dr Jane English (EIA-2017-023). The Science Foundation Ireland (SFI) Postgraduate Scheme funded Dr Daragh O’Boyle (17/RC-PhD/3482). Dr Michael Carter was funded by the NCRC (National Children’s Research Centre, Crumlin, Dublin 12, Ireland; Grant Code D/19/1). The BASELINE birth cohort was funded by the NCRC in 2008 and a grant received from the UK Food Standards Agency in 2009.Author informationAuthors and AffiliationsDepartment of Anatomy and Neuroscience, University College Cork, Cork, IrelandAisling Noone, Kirsten Dowling, Daragh O’Boyle, Anna V. Golubeva & Jane A. EnglishINFANT Research Centre, University College Cork, Cork, IrelandAisling Noone, Kirsten Dowling, Daragh O’Boyle, Michael Carter, Ali S. Khashan, Deirdre M. Murray & Jane A. EnglishDepartment of Paediatrics and Child Health, University College Cork, Cork, IrelandMichael Carter & Deirdre M. MurrayNational Children’s Research Centre (NCRC), Crumlin, Dublin, IrelandMichael CarterConway Institute of Bio-molecular and Biomedical Research, University College Dublin, Dublin, IrelandCaitriona ScaifeDepartment of Public Health, Aarhus University, Aarhus, DenmarkBodil H. BechDepartment of Clinical Medicine, Aarhus University, Aarhus, DenmarkTine B. HenriksenDepartment of Paediatrics and Adolescent Medicine, Aarhus University Hospital, Aarhus, DenmarkTine B. HenriksenHospital for Sick Children, Toronto, ON, CanadaLouise GallagherCentre for Addiction and Mental Health, Toronto, ON, CanadaLouise GallagherDepartment of Psychiatry, University of Toronto, Toronto, ON, CanadaLouise GallagherSchool of Medicine, Trinity College Dublin, Dublin, IrelandLouise GallagherFutureNeuro Research Ireland Centre, School of Computer Science, University College Dublin, Dublin, IrelandCatherine MooneySchool of Public Health, University College Cork, Cork, IrelandAli S. KhashanAuthorsAisling NooneView author publicationsSearch author on:PubMed Google ScholarKirsten DowlingView author publicationsSearch author on:PubMed Google ScholarDaragh O’BoyleView author publicationsSearch author on:PubMed Google ScholarMichael CarterView author publicationsSearch author on:PubMed Google ScholarAnna V. GolubevaView author publicationsSearch author on:PubMed Google ScholarCaitriona ScaifeView author publicationsSearch author on:PubMed Google ScholarBodil H. BechView author publicationsSearch author on:PubMed Google ScholarTine B. HenriksenView author publicationsSearch author on:PubMed Google ScholarLouise GallagherView author publicationsSearch author on:PubMed Google ScholarCatherine MooneyView author publicationsSearch author on:PubMed Google ScholarAli S. KhashanView author publicationsSearch author on:PubMed Google ScholarDeirdre M. MurrayView author publicationsSearch author on:PubMed Google ScholarJane A. EnglishView author publicationsSearch author on:PubMed Google ScholarContributionsA.N. performed HPLC immunodepletions and all associated proteomic sample preparation for LC-MS/MS analysis. A.N. also co-wrote the manuscript, prepared associated tables and figures, and undertook manuscript revisions, K.D. performed discovery metabolomics and targeted MRM steroids analysis. K.D. also co-wrote the manuscript, prepared associated tables and figures, and undertook manuscript revisions. D.O.B. undertook statistical analysis of metabolomic and proteomic datasets, performed ML analysis, and prepared associated figures. M.C. undertook the clinical follow-up of children in the PiRAMiD cohort and contributed to the manuscript by preparing participant tables and interpretating results. A.N. and A.V.G. performed the ELISA work, associated statistical analysis and figures, alongside manuscript revisions. C.S. oversaw the proteomic LC-MS/MS analysis and bioinformatics for proteomics. B.H.B., was involved in study design and interpretation of results. T.B.H., was involved in interpretation of results and providing expertise in the field of paediatrics. L.G., was involved in interpretation of results and providing expertise in the field of Autism. C.M. was involved in study design, interpretation of results, and student supervision. A.K. was involved in study design and interpretation of results. D.M. is the PI of BASELINE and PiRAMiD and was involved in the ethical approval, data management, study design, and student supervision. J.E conceived the study, was involved in study design, data management and analysis, interpretation of results, student supervision, and co-wrote the manuscript. All authors critically reviewed the manuscript and approved the final version for submission.Corresponding authorCorrespondence to Jane A. English.Ethics declarationsCompeting interestsThe authors declare no competing interests.Additional informationPublisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.Supplementary informationSupplementary informationSupplementary figures 1-5Rights and permissionsSpringer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.Reprints and permissionsAbout this article