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

Abstract

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.

Identification of Three Rheumatoid Arthritis Disease Subtypes by Machine Learning Integration of Synovial Histologic Features and RNA Sequencing Data

“…Functional annotation clustering of genes with increased expression in the low inflammatory subtype compared to the other subtypes identified enrichment in pathways that included glycoproteins (Figure B) (see also Supplementary Table 8, http://onlinelibrary.wiley.com/doi/10.1002/art.40428/abstract). These genes included markers of lining layer fibroblasts such as CD55 , transforming growth factor β (TGFβ) superfamily genes ( TGFBR1, TGFBR2 , TGFB2 , and BMP6 ), and genes involved in the regulation of extracellular glycoproteins such as GCNT3 (a glycosyltransferase that mediates core O ‐glycan branching, a critical step in mucin synthesis) . Another enriched pathway in the low inflammatory subtype included cell adhesion (Figure B).…”

Candida albicans exhibits distinct cytoprotective responses to anti-fungal drugs that facilitate the evolution of drug resistance

“…In general, DROP-seq devices have been shown to be near equivalent to commercial systems 45 . In particular, here we built a printed circuit board to control microfluidic flow inspired by Stephenson et al 46 , and 3D printed plastic syringe pumps and cheap cameras inspired by Booeshaghi et al 47 ( Figure 1A ). The cost per device is well below $1K USD.…”

Microfluidics‐Based Biomaterials and Biodevices

“…Emerging single‐cell technologies have made significant progress toward revealing the heterogeneity of the single cell. With the capability of miniaturizing fluid control to size scales, microfluidics has been emerging as a leading technology for the single cell capture, preservation, and analysis . Currently, extensive microfluidics‐based techniques have been developed for the single‐cell high‐throughput analysis, including droplet‐based microfluidics, valve‐based microfluidics, and compartment‐based microfluidics.…”