Characterization of the immunophenotype and tumor specificity of CD8+ T-cells in chromophobe renal cell carcinoma (ChRCC) and renal oncocytic neoplasms.

Authors

Chris Labaki

Chris Labaki

Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA

Chris Labaki , Charbel Hobeika , Yue Hou , Long Zhang , Kevin Bi , Ziad Bakouny , Sabrina Yvonne Camp , Carmen Priolo , Damir Khabibullin , Nicholas R Schindler , Michel Alchoueiry , Thomas Denize , Renee Maria Saliby , Sayed Matar , Sabina Signoretti , Eliezer Mendel Van Allen , Sachet A Shukla , Elizabeth Henske , Toni K. Choueiri , David A. Braun

Organizations

Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, St. Elizabeth's Medical Center, Brighton, MA, Dana-Farber Cancer Institute, Boston, MA, Brigham and Women's Hospital, Boston, MA, Brigham and Women's Hospital, Brookline, MA, Yale School of Medicine, New Haven, CT, Massachusetts general hospital, Boston, MA, Brigham and Women's Hospital, Cambridge, MA, School of Medicine, Yale University, New Haven, CT

Research Funding

Other Government Agency
Department of Defense (DOD)

Background: ChRCC is an uncommon kidney cancer variant that has a poor prognosis in the metastatic setting, with limited response to current standard-of-care immune checkpoint inhibitors (ICIs) used for other RCC histologies. We evaluated the tumor-immune microenvironment of ChRCC and other related oncocytic neoplasms to better understand the immunophenotype of these tumors. Methods: We performed paired single-cell RNA sequencing (scRNA-seq), single-cell T-cell receptor sequencing (scTCR-seq), and CD45 immunohistochemistry (IHC) of ChRCC, renal oncocytoma (RO) and low-grade oncocytic tumor (LOT) tumor and matched normal samples. Bulk RNA-sequencing (RNA-seq) data of clear cell RCC (ccRCC), papillary RCC (pRCC) and ChRCC were additionally analyzed using The Cancer Genome Atlas (TCGA) kidney cancer cohorts. T cell antigenic specificities from scTCR-seq were inferred using a comprehensive database of annotated T-cell receptor sequences (VDJdb). Single-cell transcriptomic signatures were used to infer the tumor specificity (Oliveira G, Nature, 2021 and Lowery FJ, Science, 2022) and viral specificity (Oliveira G, Nature, 2021) of CD8+ T-cells from ChRCC, as compared to those from ccRCC (Braun DA, Cancer Cell, 2021). Results: ChRCC and other oncocytic tumors had a lower infiltration of CD45+ immune cells as compared to ccRCC (p<0.01). Single-cell analysis was performed on 46,817 cells from 5 tumors (ChRCC: n=3, RO: n=1 and LOT: n=1) and 4 normal samples. Across all tumors, CD8+ T cell clusters displayed a lower expression of immune checkpoints (i.e. PDCD1 [PD-1], CTLA4, LAG3, HAVCR2 [TIM-3], and TIGIT) as compared to ccRCC. This was further validated in a bulk RNA-seq analysis using TCGA data, with a significantly lower expression of all immune checkpoints in ChRCC compared to both ccRCC (p<0.01) and papillary RCC (pRCC; p<0.01). Analysis of the T cell receptor repertoire (scTCR-seq) of ChRCC, RO and LOT samples did not show any pattern of clonal expansion, and a higher proportion of T cells in ChRCC were inferred to have a viral specificity, as compared to ccRCC (0.79 vs. 0.1%, respectively). CD8+ T cells from ChRCC (vs. ccRCC) displayed a significantly lower expression of two signatures of tumor specificity (p<0.01), and a higher expression of the viral-specific signature (p<0.01). Conclusions: In ChRCC, there is low infiltration by CD45+ immune cells. Although infiltrating CD8+ T cells have a predominantly non-exhausted immune phenotype, they likely lack anti-tumor specificity (i.e. are “bystander” T cells). These findings may help to understand the molecular basis for the lack of response to immunotherapy recently identified among patients with advanced ChRCC, and support future therapeutic strategies to increase infiltration of tumor-specific T cells into the tumor microenvironment.

Disclaimer

This material on this page is ©2024 American Society of Clinical Oncology, all rights reserved. Licensing available upon request. For more information, please contact licensing@asco.org

Abstract Details

Meeting

2023 ASCO Annual Meeting

Session Type

Poster Session

Session Title

Genitourinary Cancer—Kidney and Bladder

Track

Genitourinary Cancer—Kidney and Bladder

Sub Track

Kidney Cancer

Citation

J Clin Oncol 41, 2023 (suppl 16; abstr 4558)

DOI

10.1200/JCO.2023.41.16_suppl.4558

Abstract #

4558

Poster Bd #

50

Abstract Disclosures

Similar Abstracts

First Author: Bernardo Leon Rapoport

First Author: Chris Labaki

Abstract

2024 ASCO Gastrointestinal Cancers Symposium

PD1 and CD39 expression on tumor infiltrating lymphocytes in patients with gastric cancer.

First Author: Takafumi Okayama