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

Nature Communications

Volumn 9, Issue 1, 2018, Pages

  Stephenson, William ^a   Donlin, Laura T ^b,c   Butler, Andrew ^a,d   Rozo, Cristina ^b   Bracken, Bernadette ^a,d   Rashidfarrokhi, Ali ^a,e   Goodman, Susan M ^b,c   Ivashkiv, Lionel B ^b,c   Bykerk, Vivian P ^b,c   Orange, Dana E ^b,f   Darnell, Robert B ^a,f   Swerdlow, Harold P ^a   Satija, Rahul ^a,c,d  

^a NEW YORK GENOME CENTER   (United States)

^b HOSPITAL FOR SPECIAL SURGERY   (United States)

^c WEILL CORNELL MEDICAL COLLEGE   (United States)

^d NEW YORK UNIVERSITY   (United States)

^e NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

^f ROCKEFELLER UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CD16 ANTIGEN; CD56 ANTIGEN; CXCL13 CHEMOKINE; DECAY ACCELERATING FACTOR; GELATINASE A; IMMUNOGLOBULIN A; PROGRAMMED DEATH 1 LIGAND 1; PROTEIN; PROTEIN CLU; PROTEIN COL1A2; PROTEIN COL3A1; STROMELYSIN; THY 1 MEMBRANE GLYCOPROTEIN; TRANSCRIPTION FACTOR MAF; TRANSCRIPTOME; UNCLASSIFIED DRUG; RNA;

ATLAS; BIOLOGY; CELL; DETECTION METHOD; DISEASE; INSTRUMENTATION; QUATERNARY; TECHNOLOGY ADOPTION; THREE-DIMENSIONAL MODELING;

ARTICLE; CD4+ T LYMPHOCYTE; CD8+ T LYMPHOCYTE; CLINICAL ARTICLE; CONTROLLED STUDY; CYTOKINE PRODUCTION; FIBROBLAST; FLUID FLOW; GENE EXPRESSION; HUMAN; HUMAN CELL; HUMAN TISSUE; LYMPHOCYTE SUBPOPULATION; MICROFLUIDICS; RHEUMATOID ARTHRITIS; RNA SEQUENCE; SYNOVIUM; THREE DIMENSIONAL PRINTING; CYTOLOGY; DEVICES; ECONOMICS; EVALUATION STUDY; GENE EXPRESSION PROFILING; GENETICS; METABOLISM; PROCEDURES; SINGLE CELL ANALYSIS;

ARTHRITIS, RHEUMATOID; FIBROBLASTS; GENE EXPRESSION PROFILING; HUMANS; MICROFLUIDICS; RNA; SINGLE-CELL ANALYSIS; SYNOVIAL MEMBRANE;

EID: 85042524658     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/s41467-017-02659-x     Document Type: Article

References (49)

1. Macosko, E. Z., et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell 161, 1202-1214 (2015).
2. Klein, A. M., et al. Droplet barcoding for single-cell transcriptomics applied to embryonic stem sells. Cell 161, 1187-1201 (2015).
3. Vitak, S. A., et al. Sequencing thousands of single-cell genomes with combinatorial indexing. Nat. Methods 14, 302-8 (2017).
4. Zheng, G. X. Y., et al. Massively parallel digital transcriptional profiling of single cells. Nat. Commun. 8, 1-12 (2017).
5. Shekhar, K., et al. Comprehensive classification of retinal bipolar neurons by single-cell transcriptomics. Cell 166, 1308-1323.e30 (2016).
6. Baron, M., et al. A single-cell transcriptomic map of the human and mouse pancreas reveals Inter-and intra-cell population structure. Cell Syst. 3, 346-360 (2016).
7. Shembekar, N., Chaipan, C., Utharala, R. & Merten, C. A. Droplet-based microfluidics in drug discovery, transcriptomics and high-throughput molecular genetics. Lab. Chip. 16, 1314-31 (2016).
8. Kaminski, T. S., Scheler, O. & Garstecki, P. Droplet microfluidics for microbiology: Techniques, applications and challenges. Lab. Chip. 16, 2168-2187 (2016).
9. Alles, J., et al. Cell fixation and preservation for droplet-based single-cell transcriptomics. Bmc. Biol. 15, 44 (2017).
10. Gierahn, T. M., et al. Seq-Well: Portable, low-cost RNA sequencing of single cells at high throughput. Nat. Methods https://doi.org/10.1038/nmeth.4179, 1-8 (2017).
11. Yuan, J. & Sims, P. A. An automated microwell platform for large-scale single cell RNA-seq. Sci. Rep. 6, 33883 (2016).
12. Bose, S., et al. Scalable microfluidics for single-cell RNA printing and sequencing. Genome Biol. 16, 120 (2015).
13. Briggs, A. W., et al. Tumor-infiltrating immune repertoires captured by single-cell barcoding in emulsion. BioRxiv http://biorxiv.org/content/early/2017/05/05/134841.abstract, 1-34 (2017).
14. Stoeckius, M., et al. Simultaneous epitope and transcriptome measurement in single cells. Nat. Methods 14, 865-868 (2017).
15. Zhang, Y. & Jiang, H. R. A review on continuous-flow microfluidic PCR in droplets: Advances, challenges and future. Anal. Chim. Acta 914, 7-16 (2016).
16. Sidore, A. M., Lan, F., Lim, S. W. & Abate, A. R. Enhanced sequencing coverage with digital droplet multiple displacement amplification. Nucleic Acids Res. https://doi.org/10.1093/nar/gkv1493, gkv1493 (2015).
17. Kamperman, T., Henke, S., Visser, C. W., Karperien, M. & Leijten, J. Centering Single Cells in Microgels via Delayed Crosslinking Supports Long-Term 3D Culture by Preventing Cell Escape. Small https://doi.org/10.1002/smll.201603711, 1603711 (2017).
18. Siltanen, C., et al. One step fabrication of hydrogel microcapsules with hollow core for assembly and cultivation of hepatocyte spheroids. Acta Biomater. 50, 428-436 (2017).
19. Lee, K., et al. Generalized serial dilution module for monotonic and arbitrary microfluidic gradient generators. Lab. Chip. 9, 709-17 (2009).
20. Ozkumur, E., et al. Inertial focusing for tumor antigen-dependent and-independent sorting of rare circulating tumor cells. Sci. Transl. Med 5, 179ra47 (2013).
21. Martel, J. M., et al. Continuous flow microfluidic bioparticle concentrator. Sci. Rep. 5, 11300 (2015).
22. Di Carlo, D., Irimia, D., Tompkins, R. G. & Toner, M. Continuous inertial focusing, ordering, and separation of particles in microchannels. Proc. Natl. Acad. Sci. U.S.A. 104, 18892-18897 (2007).
23. Scott, D. L., Wolfe, F. & Huizinga, T. W. J. Rheumatoid arthritis. Lancet 376, 1094-1108 (2010).
24. McInnes, I. B. & Schett, G. The pathogenesis of rheumatoid arthritis. N. Engl. J. Med. 365, 2205-19 (2011).
25. Aletaha, D., et al. Rheumatoid arthritis classification criteria: An American College of Rheumatology/European League Against Rheumatism collaborative initiative. Arthritis Rheum. 62, 2569-2581 (2010).
26. Buckley, C. D., Barone, F., Nayar, S., Bénézech, C. & Caamanõ, J. Stromal cells in chronic inflammation and tertiary lymphoid organ formation. Annu. Rev. Immunol. 33, 715-45 (2015).
27. Noss, E. H. & Brenner, M. B. The role and therapeutic implications of fibroblast-like synoviocytes in inflammation and cartilage erosion in rheumatoid arthritis. Immunol. Rev. 223, 252-270 (2008).
28. Naylor, A. J., Filer, A. & Buckley, C. D. The role of stromal cells in the persistence of chronic inflammation. Clin. Exp. Immunol. 171, 30-35 (2013).
29. Bartok, B. & Firestein, G. S. Fibroblast-like synoviocytes: Key effector cells in rheumatoid arthritis. Immunol. Rev. 233, 233-255 (2010).
30. Fassbender, H. G. Histomorphological basis of articular cartilage destruction in rheumatoid arthritis. Coll. Relat. Res. 3, 141-155 (1983).
31. Müller-Ladner, U., et al. Synovial fibroblasts of patients with rheumatoid arthritis attach to and invade normal human cartilage when engrafted into SCID mice. Am. J. Pathol. 149, 1607-15 (1996).
32. Lafyatis, R., et al. Anchorage-independent growth of synoviocytes from arthritic and normal joints. J. Clin. Investig. Inc. 83, 1267-1276 (1989).
33. Müller-ladner, U., Ospelt, C., Gay, S., Distler, O. & Pap, T. Cells of the synovium in rheumatoid arthritis. Synovial fibroblasts. Arthritis Res. Ther. 9, 223 (2007).
34. Pap, T., et al. Activation of synovial fibroblasts in rheumatoid arthritis: Lack of expression of the tumour suppressor PTEN at sites of invasive growth and destruction. Arthritis Res. 2, 59-64 (2000).
35. Pap, T., Müller-Ladner, U., Gay, R. E. & Gay, S. Fibroblast biology. Role of synovial fibroblasts in the pathogenesis of rheumatoid arthritis. Arthritis Res. 2, 361-7 (2000).
36. Gravallese, E. M., Darling, J. M., Ladd, A. L., Katz, J. N. & Glimcher, L. H. In situ hybridization studies of stromelysin and collagenase messenger RNA expression in rheumatoid synovium. Arthritis Rheum. 34, 1076-1084 (1991).
37. Kong, D. S., et al. Open-source, community-driven microfluidics with Metafluidics. Nat. Biotechnol. 35, 523-529 (2017).
38. Villani, A.-C., et al. Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors. Sci. 356, 1-12 (2017).
39. Rao, D. A., et al. Pathologically expanded peripheral T helper cell subset drives B cells in rheumatoid arthritis. Nature 542, 110-114 (2017).
40. Fan, J., et al. Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis. Nat. Methods 13, 241-244 (2016).
41. Blaschke, S., et al. Expression of activation-induced, T cell-derived, and chemokine-related cytokine/lymphotactin and its functional role in rheumatoid arthritis. Arthritis Rheum. 48, 1858-1872 (2003).
42. Poli, A., et al. CD56bright natural killer (NK) cells: An important NK cell subset. Immunology 126, 458-465 (2009).
43. Moradi, B., et al. CD4 regulatory T cells are enriched in rheumatoid arthritis and osteoarthritis joints-analysis of frequency and phenotype in synovial membrane, synovial fluid and peripheral blood. Arthritis Res. Ther. 16, R97 (2014).
44. Jurisic, G., Iolyeva, M., Proulx, S. T., Halin, C. & Detmar, M. Thymus cellantigen1 (Thy1, CD90) is expressed by lymphatic vessels and mediates cell adhesion to lymphatic endothelium. Exp. Cell Res 316, 2982-92 (2010).
45. Scialdone, A., et al. Computational assignment of cell-cycle stage from single-cell transcriptome data. Methods 85, 54-61 (2015).
46. Tirosh, I., et al. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Sci. 352, 189-196 (2016
47. Blondel, V. D., Guillaume, J.-L., Lambiotte, R. & Lefebvre, E. Fast unfolding of communities in large networks. J. Stat. Mech. 10, 10008 (2008).
48. Wright, M. N. & Ziegler, A. ranger: A fast implementation of random forests for high dimensional data in C and R. Journal of Statistical Software, 77, 1 (2017).
49. Mayer, C., et al. Inhibitory neuron diversity originates from cardinal classes shared across germinal zones. Preprint at b ioRxiv https://doi.org/10.1101/105312 (2017).