Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low-cost microfluidic instrumentation

Nat Commun. 2018 Feb 23;9(1):791. doi: 10.1038/s41467-017-02659-x.


Droplet-based single-cell RNA-seq has emerged as a powerful technique for massively parallel cellular profiling. While this approach offers the exciting promise to deconvolute cellular heterogeneity in diseased tissues, the lack of cost-effective and user-friendly instrumentation has hindered widespread adoption of droplet microfluidic techniques. To address this, we developed a 3D-printed, low-cost droplet microfluidic control instrument and deploy it in a clinical environment to perform single-cell transcriptome profiling of disaggregated synovial tissue from five rheumatoid arthritis patients. We sequence 20,387 single cells revealing 13 transcriptomically distinct clusters. These encompass an unsupervised draft atlas of the autoimmune infiltrate that contribute to disease biology. Additionally, we identify previously uncharacterized fibroblast subpopulations and discern their spatial location within the synovium. We envision that this instrument will have broad utility in both research and clinical settings, enabling low-cost and routine application of microfluidic techniques.

Publication types

  • Evaluation Study
  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Arthritis, Rheumatoid / genetics*
  • Arthritis, Rheumatoid / metabolism
  • Fibroblasts / metabolism
  • Gene Expression Profiling
  • Humans
  • Microfluidics / economics
  • Microfluidics / instrumentation
  • Microfluidics / methods*
  • RNA / genetics*
  • RNA / metabolism
  • Single-Cell Analysis / economics
  • Single-Cell Analysis / instrumentation
  • Single-Cell Analysis / methods*
  • Synovial Membrane / cytology
  • Synovial Membrane / metabolism


  • RNA