Integrated bulk and single-cell RNA-sequencing identified disease-relevant monocytes and a gene network module underlying systemic sclerosis

J Autoimmun. 2021 Jan:116:102547. doi: 10.1016/j.jaut.2020.102547. Epub 2020 Oct 8.


Objective: Immunological disturbances have been reported in systemic sclerosis (SSc). This study assessed the transcriptome disturbances in immune cell subsets in SSc and characterized a disease-related gene network module and immune cell cluster at single cell resolution.

Methods: Twenty-one Japanese SSc patients were enrolled and compared with 13 age- and sex-matched healthy controls (HC). Nineteen peripheral blood immune cell subsets were sorted by flow cytometry and bulk RNA-seq analysis was performed for each. Differential expression and pathway analyses were conducted. Iterative weighted gene correlation network analysis (iWGCNA) of each subset revealed clustered co-expressed gene network modules. Random forest analysis prioritized a disease-related gene module. Single cell RNA-seq analysis of 878 monocytes was integrated with bulk RNA-seq analysis and with a public database for single cell RNA-seq analysis of SSc patients.

Results: Inflammatory pathway genes were differentially expressed in widespread immune cell subsets of SSc. An inflammatory gene module from CD16+ monocytes, which included KLF10, PLAUR, JUNB and JUND, showed the greatest discrimination between SSc and HC. One of the clusters of SSc monocytes identified by single-cell RNA-seq analysis characteristically expressed these inflammatory co-expressed genes and was similar to lung infiltrating FCN1hi monocytes expressing IL1B.

Conclusions: Our integrated analysis of bulk and single cell RNA-seq analysis identified an inflammatory gene module and a cluster of monocytes that are relevant to SSc pathophysiology. They could serve as candidate novel therapeutic targets in SSc.

Keywords: Bulk RNA-seq; Immune cells; Monocytes; Single cell RNA-seq; Systemic sclerosis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Aged
  • Aged, 80 and over
  • Cells, Cultured
  • Cluster Analysis
  • Female
  • Gene Expression Profiling / methods*
  • Gene Regulatory Networks*
  • Humans
  • Male
  • Middle Aged
  • Monocytes / classification
  • Monocytes / cytology
  • Monocytes / metabolism*
  • RNA-Seq / methods*
  • Receptors, IgG / genetics
  • Receptors, IgG / metabolism
  • Scleroderma, Systemic / genetics*
  • Scleroderma, Systemic / therapy
  • Single-Cell Analysis / methods*


  • Receptors, IgG