High-Dimensional Analysis Reveals Distinct Endotypes in Patients With Idiopathic Inflammatory Myopathies

Abstract

The idiopathic inflammatory myopathies (IIM) are a rare clinically heterogeneous group of conditions affecting the skin, muscle, joint, and lung in various combinations. While myositis specific autoantibodies are well described, we postulate that broader immune endotypes exist in IIM spanning B cell, T cell, and monocyte compartments. This study aims to identify immune endotypes through detailed immunophenotyping of peripheral blood mononuclear cells (PBMCs) in IIM patients compared to healthy controls. We collected PBMCs from 17 patients with a clinical diagnosis of inflammatory myositis and characterized the B, T, and myeloid cell subsets using mass cytometry by time of flight (CyTOF). Data were analyzed using a combination of the dimensionality reduction algorithm t-distributed stochastic neighbor embedding (t-SNE), cluster identification, characterization, and regression (CITRUS), and marker enrichment modeling (MEM); supervised biaxial gating validated populations identified by these methods to be differentially abundant between groups. Using these approaches, we identified shared immunologic features across all IIM patients, despite different clinical features, as well as two distinct immune endotypes. All IIM patients had decreased surface expression of RP105/CD180 on B cells and a reduction in circulating CD3+CXCR3+ subsets relative to healthy controls. One IIM endotype featured CXCR4 upregulation across all cellular compartments. The second endotype was hallmarked by an increased frequency of CD19+CD21loCD11c+ and CD3+CD4+PD1+ subsets. The experimental and analytical methods we describe here are broadly applicable to studying other immune-mediated diseases (e.g., autoimmunity, immunodeficiency) or protective immune responses (e.g., infection, vaccination).

Type 1 interferon signature in peripheral blood mononuclear cells and monocytes of idiopathic inflammatory myopathy patients with different myositis-specific autoantibodies

“…The plasma levels of monocyte-related proinflammatory cytokines and chemokines increased, and the monocytes in patients had upregulated IFN-related gene expressions. Consistent with a previous research, patients with IIM had increased monocytes ( 44 ). Active IIM patients were found with decreased classical and increased intermediate monocyte subsets, and intermediate monocytes increased in treatment-responsive patients, while it decreased in non-responders ( 45 , 46 ).…”

Identification of distinct immune signatures in inclusion body myositis by peripheral blood immunophenotyping using machine learning models

“…[21][22][23][24][25] Recent studies have shown that unsupervised clustering models can be used to identify discrete groups of IIM patients based on their immune profiles. 21,26,27 In this study, we conducted comprehensive immunophenotyping of peripheral blood leucocytes using multi-parameter flow cytometry. Our analysis encompassed a comparative cross-sectional exploration of IBM patients and healthy controls.…”

“…To date, several studies investigating the phenotypical, genomic, metabolomic and transcriptomic alterations in idiopathic inflammatory myopathies (IIM) have utilised the power of ML models 21–25 . Recent studies have shown that unsupervised clustering models can be used to identify discrete groups of IIM patients based on their immune profiles 21,26,27 …”

“… 21 , 22 , 23 , 24 , 25 Recent studies have shown that unsupervised clustering models can be used to identify discrete groups of IIM patients based on their immune profiles. 21 , 26 , 27 …”

Immune cell profiles of idiopathic inflammatory myopathy patients expressed anti-aminoacyl tRNA synthetase or anti-melanoma differentiation-associated gene 5 autoantibodies

“…The innate and adaptive immune systems are believed to be involved in the development of IIM [ 17 , 18 ]. Recent studies have found that IIM patients had a reduction in the circulating subsets of CXCR3 + T cells and memory B cells [ 19 – 21 ]. Using immunocytochemical analysis, CD4 + and CD8 + T cells are found to mainly infiltrate the endomysial and perivascular regions of muscle tissues from polymyositis patients and the perivascular region of muscle tissues from dermatomyositis patients [ 22 , 23 ].…”