Understanding Spondyloarthritis Pathogenesis: The Promise of Single-Cell Profiling

Ermann J. Pathogenesis of axial spondyloarthritis - sources and current state of knowledge. Rheum Dis Clin North Am. 2020;46(2):193–206. https://doi.org/10.1016/j.rdc.2020.01.016.

Article  PubMed  Google Scholar 

Futamura K, Sekino M, Hata A, Ikebuchi R, Nakanishi Y, Egawa G, et al. Novel full-spectral flow cytometry with multiple spectrally-adjacent fluorescent proteins and fluorochromes and visualization of in vivo cellular movement. Cytometry A. 2015;87(9):830–42. https://doi.org/10.1002/cyto.a.22725.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Niewold P, Ashhurst TM, Smith AL, King NJC. Evaluating spectral cytometry for immune profiling in viral disease. Cytometry A. 2020;97(11):1165–79. https://doi.org/10.1002/cyto.a.24211.

Article  CAS  PubMed  Google Scholar 

Park LM, Lannigan J, Jaimes MC. OMIP-069: forty-color full spectrum flow cytometry panel for deep immunophenotyping of major cell subsets in human peripheral blood. Cytometry A. 2020;97(10):1044–51. https://doi.org/10.1002/cyto.a.24213. Description of a 40-color staining panel for human immune cells documenting the power of spectral flow cytometry.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sahir F, Mateo JM, Steinhoff M, Siveen KS. Development of a 43 color panel for the characterization of conventional and unconventional T-cell subsets, B cells, NK cells, monocytes, dendritic cells, and innate lymphoid cells using spectral flow cytometry. Cytometry A. 2020; https://doi.org/10.1002/cyto.a.24288. Description of a 43-color staining panel for human immune cells documenting the power of spectral flow cytometry.

Zuba-Surma EK, Ratajczak MZ. Analytical capabilities of the ImageStream cytometer. Methods Cell Biol. 2011;102:207–30. https://doi.org/10.1016/b978-0-12-374912-3.00008-0.

Article  PubMed  Google Scholar 

Schraivogel D, Kuhn TM, Rauscher B, Rodriguez-Martinez M, Paulsen M, Owsley K, et al. High-speed fluorescence image-enabled cell sorting. Science. 2022;375(6578):315–20. https://doi.org/10.1126/science.abj3013.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bandura DR, Baranov VI, Ornatsky OI, Antonov A, Kinach R, Lou X, et al. Mass cytometry: technique for real time single cell multitarget immunoassay based on inductively coupled plasma time-of-flight mass spectrometry. Anal Chem. 2009;81(16):6813–22. https://doi.org/10.1021/ac901049w.

Article  CAS  PubMed  Google Scholar 

Tsai AG, Glass DR, Juntilla M, Hartmann FJ, Oak JS, Fernandez-Pol S, et al. Multiplexed single-cell morphometry for hematopathology diagnostics. Nat Med. 2020;26(3):408–17. https://doi.org/10.1038/s41591-020-0783-x.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bendall SC, Nolan GP, Roederer M, Chattopadhyay PK. A deep profiler’s guide to cytometry. Trends Immunol. 2012;33(7):323–32. https://doi.org/10.1016/j.it.2012.02.010.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, Xu N, et al. mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods. 2009;6(5):377–82. https://doi.org/10.1038/nmeth.1315.

Article  CAS  PubMed  Google Scholar 

Macosko EZ, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M, et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell. 2015;161(5):1202–14. https://doi.org/10.1016/j.cell.2015.05.002.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Stoeckius M, Zheng S, Houck-Loomis B, Hao S, Yeung BZ, Mauck WM 3rd, et al. Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics. Genome Biol. 2018;19(1):224. https://doi.org/10.1186/s13059-018-1603-1.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wolock SL, Lopez R, Klein AM. Scrublet: computational identification of cell doublets in single-cell transcriptomic data. Cell Syst. 2019;8(4):281–91 e9. https://doi.org/10.1016/j.cels.2018.11.005.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kang HM, Subramaniam M, Targ S, Nguyen M, Maliskova L, McCarthy E, et al. Multiplexed droplet single-cell RNA-sequencing using natural genetic variation. Nat Biotechnol. 2018;36(1):89–94. https://doi.org/10.1038/nbt.4042.

Article  CAS  PubMed  Google Scholar 

Young MD, Behjati S. SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data. Gigascience. 2020;9(12) https://doi.org/10.1093/gigascience/giaa151.

Stoeckius M, Hafemeister C, Stephenson W, Houck-Loomis B, Chattopadhyay PK, Swerdlow H, et al. Simultaneous epitope and transcriptome measurement in single cells. Nat Methods. 2017;14(9):865–8. https://doi.org/10.1038/nmeth.4380.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Peterson VM, Zhang KX, Kumar N, Wong J, Li L, Wilson DC, et al. Multiplexed quantification of proteins and transcripts in single cells. Nat Biotechnol. 2017;35(10):936–9. https://doi.org/10.1038/nbt.3973.

Article  CAS  PubMed  Google Scholar 

Buenrostro JD, Wu B, Litzenburger UM, Ruff D, Gonzales ML, Snyder MP, et al. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature. 2015;523(7561):486–90. https://doi.org/10.1038/nature14590.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Swanson E, Lord C, Reading J, Heubeck AT, Genge PC, Thomson Z, et al. Simultaneous trimodal single-cell measurement of transcripts, epitopes, and chromatin accessibility using TEA-seq. Elife. 2021:10. https://doi.org/10.7554/eLife.63632.

Mimitou EP, Lareau CA, Chen KY, Zorzetto-Fernandes AL, Hao Y, Takeshima Y, et al. Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells. Nat Biotechnol. 2021;39(10):1246–58. https://doi.org/10.1038/s41587-021-00927-2.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Baysoy A, Bai Z, Satija R, Fan R. The technological landscape and applications of single-cell multi-omics. Nat Rev Mol Cell Biol. 2023:1–19. https://doi.org/10.1038/s41580-023-00615-w. State-of-the-art review of single-cell multi-omics.

Wang X, Fan D, Yang Y, Gimple RC, Zhou S. Integrative multi-omics approaches to explore immune cell functions: challenges and opportunities. iScience. 2023;26(4):106359. https://doi.org/10.1016/j.isci.2023.106359. State-of-the-art review of single-cell multi-omics

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bodenmiller B. Multiplexed epitope-based tissue imaging for discovery and healthcare applications. Cell Syst. 2016;2(4):225–38. https://doi.org/10.1016/j.cels.2016.03.008.

Article  CAS  PubMed  Google Scholar 

Rao A, Barkley D, Franca GS, Yanai I. Exploring tissue architecture using spatial transcriptomics. Nature. 2021;596(7871):211–20. https://doi.org/10.1038/s41586-021-03634-9. State-of-the-art review of spatial transcriptomics.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hickey JW, Neumann EK, Radtke AJ, Camarillo JM, Beuschel RT, Albanese A, et al. Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging. Nat Methods. 2022;19(3):284–95. https://doi.org/10.1038/s41592-021-01316-y.

Article  CAS  PubMed  Google Scholar 

Moffitt JR, Lundberg E, Heyn H. The emerging landscape of spatial profiling technologies. Nat Rev Genet. 2022;23(12):741–59. https://doi.org/10.1038/s41576-022-00515-3. State-of-the-art review of spatial transcriptomics.

Article  CAS  PubMed  Google Scholar 

Ranjit S, Lanzano L, Libby AE, Gratton E, Levi M. Advances in fluorescence microscopy techniques to study kidney function. Nat Rev Nephrol. 2021;17(2):128–44. https://doi.org/10.1038/s41581-020-00337-8.

Article  CAS  PubMed  Google Scholar 

Gerner MY, Kastenmuller W, Ifrim I, Kabat J, Germain RN. Histo-cytometry: a method for highly multiplex quantitative tissue imaging analysis applied to dendritic cell subset microanatomy in lymph nodes. Immunity. 2012;37(2):364–76. https://doi.org/10.1016/j.immuni.2012.07.011.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Black S, Phillips D, Hickey JW, Kennedy-Darling J, Venkataraaman VG, Samusik N, et al. CODEX multiplexed tissue imaging with DNA-conjugated antibodies. Nat Protoc. 2021;16(8):3802–35. https://doi.org/10.1038/s41596-021-00556-8. Imaging of up to 60 protein markers in tissue sections using DNA-conjugated monoclonal antibodies and fluorescently labelled oligonucleotide probes.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yang B, Treweek JB, Kulkarni RP, Deverman BE, Chen CK, Lubeck E, et al. Single-cell phenotyping within transparent intact tissue through whole-body clearing. Cell. 2014;158(4):945–58. https://doi.org/10.1016/j.cell.2014.07.017.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Weiss KR, Voigt FF, Shepherd DP, Huisken J. Tutorial: practical considerations for tissue clearing and imaging. Nat Protoc. 2021;16(6):2732–48. https://doi.org/10.1038/s41596-021-00502-8.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Giesen C, Wang HA, Schapiro D, Zivanovic N, Jacobs A, Hattendorf B, et al. Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nat Methods. 2014;11(4):417–22. https://doi.org/10.1038/nmeth.2869.

Article  CAS  PubMed  Google Scholar 

Angelo M, Bendall SC, Finck R, Hale MB, Hitzman C, Borowsky AD, et al. Multiplexed ion beam imaging of human breast tumors. Nat Med. 2014;20(4):436–42. https://doi.org/10.1038/nm.3488.

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