Multi-OMICS analyses unveil STAT1 as a potential modifier gene in mevalonate kinase deficiency

• Published in: Annals of the rheumatic diseases Vol. 77; no. 11; pp. 1675 - 1687
• Main Authors: Carapito, Raphael, Carapito, Christine, Morlon, Aurore, Paul, Nicodème, Vaca Jacome, Alvaro Sebastian, Alsaleh, Ghada, Rolli, Véronique, Tahar, Ouria, Aouadi, Ismail, Rompais, Magali, Delalande, François, Pichot, Angélique, Georgel, Philippe, Messer, Laurent, Sibilia, Jean, Cianferani, Sarah, Van Dorsselaer, Alain, Bahram, Seiamak
• Format: Journal Article
• Language: English
• Published: England Elsevier Limited 01.11.2018; BMJ Publishing Group
• Subjects: Adult; Basic and Translational Research; Chemical Sciences; Disease; Exome; Female; Fever; Gene expression; Gene Expression Profiling - methods; Genes; Genes, Modifier; Genomes; Genomics; Humans; Hypotheses; Hypothesis testing; Immunoglobulin D; Inflammatory diseases; Janus kinase; Kinases; Mevalonate kinase; Mevalonate Kinase Deficiency - genetics; Mevalonic acid; Middle Aged; Mutation; Mutation, Missense; Penicillin; Phenotype; Phenotypes; Polymorphism, Single Nucleotide; Proteomes; Proteomics; Proteomics - methods; Rheumatoid arthritis; Siblings; Signal transduction; Software; Stat1 protein; STAT1 Transcription Factor - genetics; Transcription; California; France; United States > US; Massachusetts; inflammation; gene polymorphism; familial mediterranean fever
• ISSN: 0003-4967; 1468-2060; 1468-2060
• DOI: 10.1136/annrheumdis-2018-213524

ObjectivesThe objective of the present study was to explain why two siblings carrying both the same homozygous pathogenic mutation for the autoinflammatory disease hyper IgD syndrome, show opposite phenotypes, that is, the first being asymptomatic, the second presenting all classical characteristics of the disease.MethodsWhere single omics (mainly exome) analysis fails to identify culprit genes/mutations in human complex diseases, multiomics analyses may provide solutions, although this has been seldom used in a clinical setting. Here we combine exome, transcriptome and proteome analyses to decipher at a molecular level, the phenotypic differences between the two siblings.ResultsThis multiomics approach led to the identification of a single gene—STAT1—which harboured a rare missense variant and showed a significant overexpression of both mRNA and protein in the symptomatic versus the asymptomatic sister. This variant was shown to be of gain of function nature, involved in an increased activation of the Janus kinase/signal transducer and activator of transcription signalling (JAK/STAT) pathway, known to play a critical role in inflammatory diseases and for which specific biotherapies presently exist. Pathway analyses based on information from differentially expressed transcripts and proteins confirmed the central role of STAT1 in the proposed regulatory network leading to an increased inflammatory phenotype in the symptomatic sibling.ConclusionsThis study demonstrates the power of a multiomics approach to uncover potential clinically actionable targets for a personalised therapy. In more general terms, we provide a proteogenomics analysis pipeline that takes advantage of subject-specific genomic and transcriptomic information to improve protein identification and hence advance individualised medicine.