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Emerging clinical applications of single-cell RNA sequencing in oncology

Nature Reviews Clinical Oncology volume 22, pages 315–326 (2025)Cite this article

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Abstract

Single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of complex tissues both in health and in disease. Over the past decade, scRNA-seq has been applied to tumour samples obtained from patients with cancer in hundreds of studies, thereby advancing the view that each tumour is a complex ecosystem and uncovering the diverse states of both cancer cells and the tumour microenvironment. Such studies have primarily investigated and provided insights into the basic biology of cancer, although considerable research interest exists in leveraging these findings towards clinical applications. In this Review, we summarize the available data from scRNA-seq studies investigating samples from patients with cancer with a particular focus on findings that are of potential clinical relevance. We highlight four main research objectives of scRNA-seq studies and describe some of the most relevant findings towards such goals. We also describe the limitations of scRNA-seq, as well as future approaches in this field that are anticipated to further advance clinical applicability.

Key points

  • Single-cell RNA sequencing (scRNA-seq) technologies facilitate a comprehensive understanding of the tumour ecosystem, particularly the intratumour heterogeneity of cancer cells and those of the tumour microenvironment.

  • With the maturation of the field, scRNA-seq is now increasingly being applied to address clinically important questions in a way that might ultimately inform routine patient management.

  • Potential clinical applications of scRNA-seq might be broadly described by four objectives: the refinement of tumour subtyping, the characterization of treatment-induced changes, the identification of expression programmes predictive of treatment response and the discovery of novel therapeutic targets.

  • Barriers to a more streamlined embedding of scRNA-seq into clinical research include difficulties in sample acquisition and the computational challenges inherent in integrating varied datasets.

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Fig. 1: Common clinically relevant objectives of single-cell RNA sequencing cancer studies.
Fig. 2: Discovery of novel therapeutic targets.
Fig. 3: Challenges encountered over the course of a typical scRNA-seq experiment.

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Author notes

  1. These authors contributed equally: Emily Boxer, Nisan Feigin, Roi Tschernichovsky.

Authors and Affiliations

  1. Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel

    Emily Boxer, Nisan Feigin, Roi Tschernichovsky, Noam Galili Darnell, Alissa R. Greenwald, Rouven Hoefflin, Daniel Kovarsky, Dor Simkin, Shira Turgeman, Lingling Zhang & Itay Tirosh

  2. Davidoff Cancer Center, Rabin Medical Center, Petah Tikva, Israel

    Roi Tschernichovsky

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Contributions

E.B., N.F., R.T., N.G.D., A.G., R.H., D.K., D.S., S.T. and L.Z. researched data for the manuscript, E.B., N.F., R.T. and I.T. made a substantial contribution to discussions of content. All authors wrote the manuscript, and E.B., N.F., R.T. and I.T. reviewed and/or edited before submission.

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Correspondence to Itay Tirosh.

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I.T. is a co-founder and adviser of Cellyrix Therapeutics and an adviser of Immunitas Therapeutic. The other authors declare no competing interests.

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Boxer, E., Feigin, N., Tschernichovsky, R. et al. Emerging clinical applications of single-cell RNA sequencing in oncology. Nat Rev Clin Oncol 22, 315–326 (2025). https://doi.org/10.1038/s41571-025-01003-3

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