Single-cell sequencing links multiregional immune landscapes and tissue-resident T cells in ccRCC to tumor topology and therapy efficacy

Chirag Krishna, Renzo G. DiNatale, Fengshen Kuo, Raghvendra M. Srivastava, Lynda Vuong, Diego Chowell, Sounak Gupta, Chad Vanderbilt, Tanaya A. Purohit, Ming Liu, Emily Kansler, Briana G. Nixon, Ying-Bei Chen, Vladimir Makarov, Kyle A. Blum, Kyrollis Attalla, Stanley Weng, Michael L. Salmans, Mahdi Golkaram, Li Liu, Shile Zhang, Raakhee Vijayaraghavan, Traci Pawlowski, Victor Reuter, Maria I. Carlo, Martin H. Voss, Jonathan Coleman, Paul Russo, Robert J. Motzer, Ming O. Li, Christina S. Leslie, Timothy A. Chan, A. Ari Hakimi

Abstract

Clear cell renal cell carcinomas (ccRCCs) are highly immune infiltrated, but the effect of immune heterogeneity on clinical outcome in ccRCC has not been fully characterized. Here we perform paired single-cell RNA (scRNA) and T cell receptor (TCR) sequencing of 167,283 cells from multiple tumor regions, lymph node, normal kidney, and peripheral blood of two immune checkpoint blockade (ICB)-naïve and four ICB-treated patients to map the ccRCC immune landscape. We detect extensive heterogeneity within and between patients, with enrichment of CD8A+ tissue-resident T cells in a patient responsive to ICB and tumor-associated macrophages (TAMs) in a resistant patient. A TCR trajectory framework suggests distinct T cell differentiation pathways between patients responding and resistant to ICB. Finally, scRNA-derived signatures of tissue-resident T cells and TAMs are associated with response to ICB and targeted therapies across multiple independent cohorts. Our study establishes a multimodal interrogation of the cellular programs underlying therapeutic efficacy in ccRCC.

Datasets

1. Single-cell sequencing links multiregional immune landscapes and tissue-resident T cells in ccRCC to tumor topology and therapy efficacy
Metadata
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Tumor107806 cells
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Single-cell sequencing links multiregional immune landscapes and tissue-resident T cells in ccRCC to tumor topology and therapy efficacy

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Source data

https://cellxgene.cziscience.com/collections/3f50314f-bdc9-40c6-8e4a-b0901ebfbe4c

Alias names

SRZ190804, PRJNA705464, PMID33861994, PMC8268947

Cite this study

Krishna, C., DiNatale, R.G., Kuo, F., Srivastava, R.M., Vuong, L., Chowell, D., Gupta, S., Vanderbilt, C., Purohit, T.A., Liu, M. and Kansler, E., 2021. Single-cell sequencing links multiregional immune landscapes and tissue-resident T cells in ccRCC to tumor topology and therapy efficacy. Cancer cell, 39(5), pp.662-677. https://doi.org/10.1016/j.ccell.2021.03.007