Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Single-cell genomic approaches for developing the next generation of immunotherapies


Recent progress in single-cell genomics urges its application in drug development, particularly of cancer immunotherapies. Current immunotherapy pipelines are focused on functional outcome and simple cellular and molecular readouts. A thorough mechanistic understanding of the cells and pathways targeted by immunotherapy agents is lacking, which limits the success rate of clinical trials. A large leap forward can be made if the immunotherapy target cells and pathways are characterized at high resolution before and after treatment, in clinical cohorts and model systems. This will enable rapid development of effective immunotherapies and data-driven design of synergistic drug combinations. In this Perspective, we discuss how emerging single-cell genomic technologies can serve as an engine for target identification and drug development.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1: Challenges in understanding the cellular effects of immunotherapies.
Fig. 2: Single-cell analysis as an engine for driving drug development.
Fig. 3: Incorporation of single-cell genomics in clinical trials.


  1. 1.

    Keener, A. B. Single-cell sequencing edges into clinical trials. Nat. Med. 25, 1322–1326 (2019).

    Article  Google Scholar 

  2. 2.

    Regev, A. et al. The Human Cell Atlas. eLife 6, e27041 (2017).

    Article  Google Scholar 

  3. 3.

    Giladi, A. & Amit, I. Single-cell genomics: a stepping stone for future immunology discoveries. Cell 172, 14–21 (2018).

    CAS  Article  Google Scholar 

  4. 4.

    Ziegenhain, C. et al. Comparative analysis of single-cell RNA sequencing methods. Mol. Cell 65, 631–643.e4 (2017).

    CAS  Article  Google Scholar 

  5. 5.

    Zheng, C. et al. Landscape of infiltrating T cells in liver cancer revealed by single-cell sequencing. Cell 169, 1342–1356.e16 (2017).

    CAS  Article  Google Scholar 

  6. 6.

    Azizi, E. et al. Single-cell map of diverse immune phenotypes in the breast tumor microenvironment. Cell 174, 1293–1308.e36 (2018).

    CAS  Article  Google Scholar 

  7. 7.

    Li, H. et al. Dysfunctional CD8 T cells form a proliferative, dynamically regulated compartment within human melanoma. Cell 176, 775–789.e18 (2019).

    CAS  Article  Google Scholar 

  8. 8.

    Gubin, M. M. et al. High-dimensional analysis delineates myeloid and lymphoid compartment remodeling during successful immune-checkpoint cancer therapy. Cell 175, 1014–1030.e19 (2018).

    CAS  Article  Google Scholar 

  9. 9.

    Yost, K. E. et al. Clonal replacement of tumor-specific T cells following PD-1 blockade. Nat. Med. 25, 1251–1259 (2019).

    CAS  Article  Google Scholar 

  10. 10.

    Savage, P. et al. A Targetable EGFR-dependent tumor-initiating program in breast cancer. Cell Rep. 21, 1140–1149 (2017).

    CAS  Article  Google Scholar 

  11. 11.

    Zitvogel, L., Pitt, J. M., Daillère, R., Smyth, M. J. & Kroemer, G. Mouse models in oncoimmunology. Nat. Rev. Cancer 16, 759–773 (2016).

    CAS  Article  Google Scholar 

  12. 12.

    Lavin, Y. et al. Innate immune landscape in early lung adenocarcinoma by paired single-cell analyses. Cell 169, 750–765.e17 (2017).

    CAS  Article  Google Scholar 

  13. 13.

    Zilionis, R. et al. Single-cell transcriptomics of human and mouse lung cancers reveals conserved myeloid populations across individuals and species. Immunity 50, 1317–1334.e10 (2019).

    CAS  Article  Google Scholar 

  14. 14.

    Stoeckius, M. et al. Simultaneous epitope and transcriptome measurement in single cells. Nat. Methods 14, 865–868 (2017).

    CAS  Article  Google Scholar 

  15. 15.

    Wolchok, J. D. et al. Overall survival with combined nivolumab and ipilimumab in advanced melanoma. N. Engl. J. Med. 377, 1345–1356 (2017).

    CAS  Article  Google Scholar 

  16. 16.

    Mariathasan, S. et al. TGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells. Nature 554, 544–548 (2018).

    CAS  Article  Google Scholar 

  17. 17.

    Christmas, B. J. et al. Entinostat converts immune-resistant breast and pancreatic cancers into checkpoint-responsive tumors by reprogramming tumor-infiltrating MDSCs. Cancer Immunol. Res. 6, 1561–1577 (2018).

    Article  Google Scholar 

  18. 18.

    Bibeau, F. et al. Impact of FcγRIIa-FcγRIIIa polymorphisms and KRAS mutations on the clinical outcome of patients with metastatic colorectal cancer treated with cetuximab plus irinotecan. J. Clin. Oncol. 27, 1122–1129 (2009).

    CAS  Article  Google Scholar 

  19. 19.

    Selby, M. J. et al. Anti-CTLA-4 antibodies of IgG2a isotype enhance antitumor activity through reduction of intratumoral regulatory T cells. Cancer Immunol. Res. 1, 32–42 (2013).

    CAS  Article  Google Scholar 

  20. 20.

    Arce Vargas, F. et al. Fc effector function contributes to the activity of human anti-CTLA-4 antibodies. Cancer Cell 33, 649–663.e4 (2018).

    CAS  Article  Google Scholar 

  21. 21.

    Dahan, R. et al. FcγRs Modulate the anti-tumor activity of antibodies targeting the PD-1/PD-L1 axis. Cancer Cell 28, 285–295 (2015).

    CAS  Article  Google Scholar 

  22. 22.

    Pincetic, A. et al. Type I and type II Fc receptors regulate innate and adaptive immunity. Nat. Immunol. 15, 707–716 (2014).

    CAS  Article  Google Scholar 

  23. 23.

    Smith, P., DiLillo, D. J., Bournazos, S., Li, F. & Ravetch, J. V. Mouse model recapitulating human Fcγ receptor structural and functional diversity. Proc. Natl Acad. Sci. USA 109, 6181–6186 (2012).

    CAS  Article  Google Scholar 

  24. 24.

    Lux, A. & Nimmerjahn, F. Of mice and men: the need for humanized mouse models to study human IgG activity in vivo. J. Clin. Immunol. 33(Suppl 1), S4–S8 (2013).

    Article  Google Scholar 

  25. 25.

    Soerensen, M. M. et al. Safety, PK/PD, and anti-tumor activity of RO6874281, an engineered variant of interleukin-2 (IL-2v) targeted to tumor-associated fibroblasts via binding to fibroblast activation protein (FAP). J. Clin. Oncol. 36, e15155 (2018).

    Article  Google Scholar 

  26. 26.

    Peterson, V. M. et al. Multiplexed quantification of proteins and transcripts in single cells. Nat. Biotechnol. 35, 936–939 (2017).

    CAS  Article  Google Scholar 

  27. 27.

    Lareau, C. A. et al. Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility. Nat. Biotechnol. 37, 916–924 (2019).

    CAS  Article  Google Scholar 

  28. 28.

    Satpathy, A. T. et al. Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion. Nat. Biotechnol. 37, 925–936 (2019).

    CAS  Article  Google Scholar 

  29. 29.

    Keren, L. et al. A structured tumor-immune microenvironment in triple negative breast cancer revealed by multiplexed ion beam imaging. Cell 174, 1373–1387.e19 (2018).

    CAS  Article  Google Scholar 

  30. 30.

    Ståhl, P. L. et al. Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science 353, 78–82 (2016).

    Article  Google Scholar 

  31. 31.

    Pauken, K. E. et al. Epigenetic stability of exhausted T cells limits durability of reinvigoration by PD-1 blockade. Science 354, 1160–1165 (2016).

    CAS  Article  Google Scholar 

  32. 32.

    Scott, A. C. et al. TOX is a critical regulator of tumour-specific T cell differentiation. Nature 571, 270–274 (2019).

    CAS  Article  Google Scholar 

  33. 33.

    Simpson, T. R. et al. Fc-dependent depletion of tumor-infiltrating regulatory T cells co-defines the efficacy of anti-CTLA-4 therapy against melanoma. J. Exp. Med. 210, 1695–1710 (2013).

    CAS  Article  Google Scholar 

  34. 34.

    Sharma, A. et al. Anti-CTLA-4 immunotherapy does not deplete FOXP3+ regulatory T cells (Tregs) in human cancers. Clin. Cancer Res. 25, 1233–1238 (2019).

    Article  Google Scholar 

  35. 35.

    Siddiqui, I. et al. Intratumoral Tcf1+PD-1+CD8+ T cells with stem-like properties promote tumor control in response to vaccination and checkpoint blockade immunotherapy. Immunity 50, 195–211.e10 (2018).

    Article  Google Scholar 

Download references


We thank J.-P. Halle (Merck KGaA, Darmstadt) for critical discussions, input and feedback on this manuscript, and G. Brodsky from the Scientific Illustration unit of the Weizmann Institute for artwork. I.Y. is a Cancer Research Institute Irvington Fellow supported by the Cancer Research Institute. I.A. is supported by the Chan Zuckerberg Initiative; an HHMI International Scholar award; a Merck KGaA, Darmstadt, Germany, research grant; European Research Council Consolidator Grant (ERC-COG) 724471-HemTree2.0; the Thompson Family Foundation; an MRA Established Investigator Award (509044); an Eden and Steven Romick Professorial Chair and Eden and Steven Romick Post-Doctoral Fellowship Fund; the Israel Science Foundation (703/15); the Ernest and Bonnie Beutler Research Program for Excellence in Genomic Medicine; the Helen and Martin Kimmel award for innovative investigation; the NeuroMac DFG/Transregional Collaborative Research Center Grant; an International Progressive MS Alliance/NMSS PA-1604-08459; and an Adelis Foundation grant. I.A. is the incumbent of the Alan and Laraine Fischer Career Development Chair. R.D. is supported by a Teva Pharmaceutical Industries research grant, the Rising Tide Translation Cancer Research Fund, a Melanoma Research Alliance (MRA) Young Investigator Award, an Israel Cancer Research Fund (ICRF) Research Career Development Award, an Israel Cancer Association Research Grant, the Mizutani Foundation for Glycoscience, the Emerson Collective Cancer Research Fund, an Israel Science Foundation (ISF) Individual Research Grant, the Moross Integrated Cancer Center, a Harry J. Lloyd Trust Career Development Award, Flight Attendant Medical Research Institute (FAMRI) Research Grants, the Ira and Diana Riklis Fund for CAR-T Therapy, the Enoch Foundation, the Pearl Welinsky Merlo Foundation and the Benoziyo Fund for the Advancement of Science, and by a grant from Gerty Schwarz Schaier. R. D. is the incumbent of the Rina Gudinski Career Development Chair.

Author information



Corresponding author

Correspondence to Ido Amit.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Peer review information Hannah Stower was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Yofe, I., Dahan, R. & Amit, I. Single-cell genomic approaches for developing the next generation of immunotherapies. Nat Med 26, 171–177 (2020).

Download citation

Further reading


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing