Machine learning algorithms reveal unique gene expression profiles in muscle biopsies from patients with different types of myositis

• Published in: Annals of the rheumatic diseases Vol. 79; no. 9; pp. 1234 - 1242
• Main Authors: Pinal-Fernandez, Iago, Casal-Dominguez, Maria, Derfoul, Assia, Pak, Katherine, Miller, Frederick W, Milisenda, Jose César, Grau-Junyent, Josep Maria, Selva-O'Callaghan, Albert, Carrion-Ribas, Carme, Paik, Julie J, Albayda, Jemima, Christopher-Stine, Lisa, Lloyd, Thomas E, Corse, Andrea M, Mammen, Andrew L
• Format: Journal Article
• Language: English
• Published: London BMJ Publishing Group LTD 01.09.2020
• Subjects: Accuracy; Algorithms; Autoantibodies; Biopsy; Ca2+/calmodulin-dependent protein kinase; Calcium-binding protein; Calmodulin; Cell adhesion & migration; Cell adhesion molecules; Computer applications; Dermatomyositis; EGR-4 protein; Gene expression; Hydroxymethylglutaryl-CoA reductase; Immunoglobulins; Inflammatory diseases; Interleukin 8; Learning algorithms; Machine learning; Mucosa; Musculoskeletal diseases; Musculoskeletal system; Myopathy; Myositis; Patients; Polymyositis; Ribonucleic acid; RNA; Transcriptomics
• ISSN: 0003-4967; 1468-2060
• DOI: 10.1136/annrheumdis-2019-216599

ObjectivesMyositis is a heterogeneous family of diseases that includes dermatomyositis (DM), antisynthetase syndrome (AS), immune-mediated necrotising myopathy (IMNM), inclusion body myositis (IBM), polymyositis and overlap myositis. Additional subtypes of myositis can be defined by the presence of myositis-specific autoantibodies (MSAs). The purpose of this study was to define unique gene expression profiles in muscle biopsies from patients with MSA-positive DM, AS and IMNM as well as IBM.MethodsRNA-seq was performed on muscle biopsies from 119 myositis patients with IBM or defined MSAs and 20 controls. Machine learning algorithms were trained on transcriptomic data and recursive feature elimination was used to determine which genes were most useful for classifying muscle biopsies into each type and MSA-defined subtype of myositis.ResultsThe support vector machine learning algorithm classified the muscle biopsies with >90% accuracy. Recursive feature elimination identified genes that are most useful to the machine learning algorithm and that are only overexpressed in one type of myositis. For example, CAMK1G (calcium/calmodulin-dependent protein kinase IG), EGR4 (early growth response protein 4) and CXCL8 (interleukin 8) are highly expressed in AS but not in DM or other types of myositis. Using the same computational approach, we also identified genes that are uniquely overexpressed in different MSA-defined subtypes. These included apolipoprotein A4 (APOA4), which is only expressed in anti-3-hydroxy-3-methylglutaryl-CoA reductase (HMGCR) myopathy, and MADCAM1 (mucosal vascular addressin cell adhesion molecule 1), which is only expressed in anti-Mi2-positive DM.ConclusionsUnique gene expression profiles in muscle biopsies from patients with MSA-defined subtypes of myositis and IBM suggest that different pathological mechanisms underly muscle damage in each of these diseases.