Abstract
Since the advent of single-cell RNA sequencing (scRNA-seq) methodology, single-cell analysis has become a powerful tool for exploration of cellular networks and dysregulated immune responses in disease pathogenesis. Advanced bioinformatics tools have enabled the combined analysis of scRNA-seq data and information on various cell properties, such as cell surface molecular profiles, chromatin accessibility and spatial information, leading to a deeper understanding of pathology. This Review provides an overview of the achievements in single-cell analysis applied to clinical samples of rheumatic and allergic diseases, including rheumatoid arthritis, systemic lupus erythematosus, systemic sclerosis, allergic airway diseases and atopic dermatitis, with an expanded scope beyond peripheral blood cells to include local diseased tissues. Despite the valuable insights that single-cell analysis has provided into disease pathogenesis, challenges remain in translating single-cell findings into clinical practice and developing personalized treatment strategies. Beyond understanding the atlas of cellular diversity, we discuss the application of data obtained in each study to clinical practice, with a focus on identifying biomarkers and therapeutic targets.
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Acknowledgements
The authors thank N. Nakajima for advice on the historical overview of single-cell analysis. They also thank R. Edahiro, K. Nishimura, S. Metsugi, H. Matsushita and M. Narazaki for their excellent technical advice. They also thank K. Mogi for contributions to figure illustrations. They are deeply grateful to all the pioneers who have contributed to the development of this area and apologize to the researchers whose work was not cited in this Review owing to space limitations. This work was financially supported by research grants from the Japan Society for the Promotion of Science (JSPS) KAKENHI (JP22K16361 to M.N. and JP18H05282 to A.K.), UBE foundation (to M.N.), Takeda Science Foundation (to M.N.), Japan Agency for Medical Research and Development (AMED) (223fa627002h0001 to A.K.), JSPS Core-to-Core Program (JP223fa627002 to A.K.) and Japan Agency for Medical Research and Development — Core Research for Evolutional Science and Technology (AMED–CREST) (22gm1810003h0001 to A.K.). This research was conducted as part of the All-Osaka U Research in ‘The Nippon Foundation — Osaka University Project for Infectious Disease Prevention’.
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M.N. and A.K. designed the concept of this article. M.N. and H.S. wrote the manuscript. A.K. supervised the structure of this work. All authors contributed to the discussion of the content and approved the final version of the manuscript.
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Nishide, M., Shimagami, H. & Kumanogoh, A. Single-cell analysis in rheumatic and allergic diseases: insights for clinical practice. Nat Rev Immunol (2024). https://doi.org/10.1038/s41577-024-01043-3
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DOI: https://doi.org/10.1038/s41577-024-01043-3
