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What Single Cell RNA Sequencing Has Taught Us about Chronic Obstructive Pulmonary Disease

  • Don D. Sin (Centre for Heart Lung Innovation, St. Paul's Hospital and Division of Respiratory Medicine, University of British Columbia)
  • Received : 2024.01.03
  • Accepted : 2024.02.17
  • Published : 2024.07.31

Abstract

Chronic obstructive pulmonary disease (COPD) affects close to 400 million people worldwide and is the 3rd leading cause of mortality. It is a heterogeneous disorder with multiple endophenotypes, each driven by specific molecular networks and processes. Therapeutic discovery in COPD has lagged behind other disease areas owing to a lack of understanding of its pathobiology and scarcity of biomarkers to guide therapies. Single cell RNA sequencing (scRNA-seq) is a powerful new tool to identify important cellular and molecular networks that play a crucial role in disease pathogenesis. This paper provides an overview of the scRNA-seq technology and its application in COPD and the lessons learned to date from scRNA-seq experiments in COPD.

Keywords

References

  1. Alexander MJ, Budinger GR, Reyfman PA. Breathing fresh air into respiratory research with single-cell RNA sequencing. Eur Respir Rev 2020;29:200060.
  2. Jovic D, Liang X, Zeng H, Lin L, Xu F, Luo Y. Single-cell RNA sequencing technologies and applications: a brief overview. Clin Transl Med 2022;12:e694.
  3. Method of the year 2013. Nat Methods 2014;11:1.
  4. Zappia L, Theis FJ. Over 1000 tools reveal trends in the single-cell RNA-seq analysis landscape. Genome Biol 2021;22:301.
  5. Lim B, Lin Y, Navin N. Advancing cancer research and medicine with single-cell genomics. Cancer Cell 2020;37:456-70. https://doi.org/10.1016/j.ccell.2020.03.008
  6. See P, Lum J, Chen J, Ginhoux F. A single-cell sequencing guide for immunologists. Front Immunol 2018;9:2425.
  7. Franks TJ, Colby TV, Travis WD, Tuder RM, Reynolds HY, Brody AR, et al. Resident cellular components of the human lung: current knowledge and goals for research on cell phenotyping and function. Proc Am Thorac Soc 2008;5:763-6. https://doi.org/10.1513/pats.200803-025HR
  8. McKinnon KM. Flow cytometry: an overview. Curr Protoc Immunol 2018;120:5.1.1-11. https://doi.org/10.1002/cpim.40
  9. Montoro DT, Haber AL, Biton M, Vinarsky V, Lin B, Birket SE, et al. A revised airway epithelial hierarchy includes CFTR-expressing ionocytes. Nature 2018;560:319-24. https://doi.org/10.1038/s41586-018-0393-7
  10. Plasschaert LW, Zilionis R, Choo-Wing R, Savova V, Knehr J, Roma G, et al. A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte. Nature 2018;560:377-81. https://doi.org/10.1038/s41586-018-0394-6
  11. Crystal RG, Randell SH, Engelhardt JF, Voynow J, Sunday ME. Airway epithelial cells: current concepts and challenges. Proc Am Thorac Soc 2008;5:772-7. https://doi.org/10.1513/pats.200805-041HR
  12. Sikkema L, Ramirez-Suastegui C, Strobl DC, Gillett TE, Zappia L, Madissoon E, et al. An integrated cell atlas of the lung in health and disease. Nat Med 2023;29:1563-77. https://doi.org/10.1038/s41591-023-02327-2
  13. Deprez M, Zaragosi LE, Truchi M, Becavin C, Ruiz Garcia S, Arguel MJ, et al. A single-cell atlas of the human healthy airways. Am J Respir Crit Care Med 2020;202:1636-45. https://doi.org/10.1164/rccm.201911-2199OC
  14. Ye Q, Bankova LG. Brush cells fine-tune neurogenic inflammation in the airways. J Clin Invest 2022;132:e161439.
  15. Weiler P, Van den Berge K, Street K, Tiberi S. A guide to trajectory inference and RNA velocity. Methods Mol Biol 2023;2584:269-92. https://doi.org/10.1007/978-1-0716-2756-3_14
  16. Van de Sande B, Lee JS, Mutasa-Gottgens E, Naughton B, Bacon W, Manning J, et al. Applications of single-cell RNA sequencing in drug discovery and development. Nat Rev Drug Discov 2023;22:496-520. https://doi.org/10.1038/s41573-023-00688-4
  17. Ziegenhain C, Vieth B, Parekh S, Reinius B, Guillaumet-Adkins A, Smets M, et al. Comparative analysis of single-cell RNA sequencing methods. Mol Cell 2017;65:631-43. https://doi.org/10.1016/j.molcel.2017.01.023
  18. Chen G, Ning B, Shi T. Single-cell RNA-seq technologies and related computational data analysis. Front Genet 2019;10:317.
  19. Gerayeli FV, Milne S, Yang CX, Li X, Guinto E, Yang JS, et al. Single-cell RNA sequencing of bronchoscopy specimens: development of a rapid minimal handling protocol. Biotechniques 2023;75:157-67. https://doi.org/10.2144/btn-2023-0017
  20. Tran HT, Ang KS, Chevrier M, Zhang X, Lee NY, Goh M, et al. A benchmark of batch-effect correction methods for single-cell RNA sequencing data. Genome Biol 2020;21:12.
  21. Neuschulz A, Bakina O, Badillo-Lisakowski V, Olivares-Chauvet P, Conrad T, Gotthardt M, et al. A single-cell RNA labeling strategy for measuring stress response upon tissue dissociation. Mol Syst Biol 2023;19:e11147.
  22. Stark R, Grzelak M, Hadfield J. RNA sequencing: the teenage years. Nat Rev Genet 2019;20:631-56. https://doi.org/10.1038/s41576-019-0150-2
  23. Gerayeli FV, Park HY, Milne S, Li X, Yang CX, Tuong J, et al. Single cell sequencing reveals cellular landscape alterations in the airway mucosa of patients with pulmonary long COVID. medRxiv [Preprint] 2024 Feb 28. https://doi.org/10.1101/2024.02.26.24302674.
  24. Sun S, Zhu J, Ma Y, Zhou X. Accuracy, robustness and scalability of dimensionality reduction methods for single-cell RNA-seq analysis. Genome Biol 2019;20:269.
  25. Duo A, Robinson MD, Soneson C. A systematic performance evaluation of clustering methods for single-cell RNA-seq data. F1000Res 2018;7:1141.
  26. Clarke ZA, Andrews TS, Atif J, Pouyabahar D, Innes BT, MacParland SA, et al. Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods. Nat Protoc 2021;16:2749-64. https://doi.org/10.1038/s41596-021-00534-0
  27. Hanzelmann S, Castelo R, Guinney J. GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinformatics 2013;14:7.
  28. Qiu X, Mao Q, Tang Y, Wang L, Chawla R, Pliner HA, et al. Reversed graph embedding resolves complex single-cell trajectories. Nat Methods 2017;14:979-82. https://doi.org/10.1038/nmeth.4402
  29. Gorin G, Fang M, Chari T, Pachter L. RNA velocity unraveled. PLoS Comput Biol 2022;18:e1010492.
  30. Agusti A, Celli BR, Criner GJ, Halpin D, Anzueto A, Barnes P, et al. Global initiative for chronic obstructive lung disease 2023 report: GOLD executive summary. Eur Respir J 2023;61:2300239.
  31. Lee H, Sin DD. GETting to know the many causes and faces of COPD. Lancet Respir Med 2022;10:426-8. https://doi.org/10.1016/S2213-2600(22)00049-2
  32. Blackburn JB, Li NF, Bartlett NW, Richmond BW. An update in club cell biology and its potential relevance to chronic obstructive pulmonary disease. Am J Physiol Lung Cell Mol Physiol 2023;324:L652-65. https://doi.org/10.1152/ajplung.00192.2022
  33. Rustam S, Hu Y, Mahjour SB, Rendeiro AF, Ravichandran H, Urso A, et al. A unique cellular organization of human distal airways and its disarray in chronic obstructive pulmonary disease. Am J Respir Crit Care Med 2023;207:1171-82. https://doi.org/10.1164/rccm.202207-1384OC
  34. Zuo WL, Rostami MR, Shenoy SA, LeBlanc MG, Salit J, Strulovici-Barel Y, et al. Cell-specific expression of lung disease risk-related genes in the human small airway epithelium. Respir Res 2020;21:200.
  35. Hu Y, Shao X, Xing L, Li X, Nonis GM, Koelwyn GJ, et al. Single-cell sequencing of lung macrophages and monocytes reveals novel therapeutic targets in COPD. Cells 2023;12:2771.
  36. Lee Y, Song J, Jeong Y, Choi E, Ahn C, Jang W. Meta-analysis of single-cell RNA-sequencing data for depicting the transcriptomic landscape of chronic obstructive pulmonary disease. Comput Biol Med 2023;167:107685.
  37. Li Y, Yang Y, Guo T, Weng C, Yang Y, Wang Z, et al. Heme oxygenase-1 determines the cell fate of ferroptotic death of alveolar macrophages in COPD. Front Immunol 2023;14:1162087.
  38. Sauler M, McDonough JE, Adams TS, Kothapalli N, Barnthaler T, Werder RB, et al. Characterization of the COPD alveolar niche using single-cell RNA sequencing. Nat Commun 2022;13:494.
  39. Slyper M, Porter CB, Ashenberg O, Waldman J, Drokhlyansky E, Wakiro I, et al. A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors. Nat Med 2020;26:792-802.
  40. Grandi FC, Modi H, Kampman L, Corces MR. Chromatin accessibility profiling by ATAC-seq. Nat Protoc 2022;17:1518-52. https://doi.org/10.1038/s41596-022-00692-9