Molecular characterization of the tumor microenvironment in chromophobe renal cell carcinoma (ChRCC) and related oncocytic neoplasms.

Authors

Chris Labaki

Chris Labaki

Dana Farber Cancer Institute, Boston, MA

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

Organizations

Dana Farber Cancer Institute, Boston, MA, Brigham and Women's Hospital, Boston, MA, Dana-Farber Cancer Institute, Boston, MA, Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, Dana-Farber Cancer Institute/Harvard Medical School, Boston, MA, Brigham and Women's Hosp, Brookline, MA, Yale School of Medicine, New Haven, CT, Brigham and Women’s Hospital, Dana-Farber Cancer Institute, and Harvard Medical School, Boston, MA, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, Brigham & Women`s Hospital, Boston, MA

Research Funding

Other Government Agency

Background: ChRCC represents about 5% of all kidney cancer and has a dismal prognosis in the metastatic setting, with limited response to immune checkpoint inhibitors (ICI) and targeted therapy. We evaluated the molecular properties of ChRCC and related oncocytic neoplasms to define the tumor immune microenvironment and identify potential therapeutic strategies. Methods: ChRCC, renal oncocytoma (RO) and low-grade oncocytic tumor (LOT) samples with matched normal kidney specimens were evaluated using single-cell RNA sequencing (scRNA-seq) and single-cell T-cell receptor sequencing (scTCR-seq). T-cell antigenic specificities from scTCR-seq were inferred using a comprehensive database of annotated T-cell receptor sequences (VDJdb). The infiltration of CD45+ immune cells in renal oncocytic tumors and ccRCC samples was quantified using immunohistochemistry (IHC). Bulk RNA-sequencing (RNA-seq) data of clear cell RCC (ccRCC) and ChRCC were further analyzed using The Cancer Genome Atlas (TCGA) KIRC and KICH cohorts, respectively, with immune cell fractions calculated using CIBERSORTx. Results: After quality-control, 46,817 cells from 5 tumor (ChRCC: n = 3, RO: n = 1 and LOT: n = 1) and 4 normal samples were isolated for scRNA-seq analysis. Renal oncocytic tumors (ChRCC, RO, and LOT) had a low density of CD45+ cells (mean: 739 ± 114 cells/mm2; n = 5) compared to ccRCC (mean: 3,420 ± 1,979 cells/mm2; n = 5) (p < 0.05). Across all tumors, CD8+ T-cell clusters displayed a low expression of immune exhaustion markers (i.e. PDCD1 [PD-1], CTLA4, LAG3, HAVCR2 [TIM-3], and TIGIT). Analysis of TCGA bulk RNA-seq data after adjustment for CD8 T-cell fraction showed no difference in the expression of most immune exhaustion markers (i.e. PDCD1, CTLA4, LAG3) in ChRCC compared to normal samples (p > 0.05), contrasting with a substantially higher expression in ccRCC versus normal kidney (p < 0.05). Analysis of the T-cell repertoire (scTCR-seq) of ChRCC, RO and LOT samples did not identify a pattern of clonal expansion, and a considerable proportion of clonotypes were inferred to have specificity for viral antigens (range: 1.3 to 34.4% among all samples; 11.3 to 34.4% after filtering out two samples with a low ( < 300) number of T-cells). Conclusions: Renal oncocytic tumors, including ChRCC, exhibit a low infiltration of immune cells, a non-exhausted immune phenotype and, a lack of clonally expanded tumor-specific T-cells. These findings may partially explain the molecular basis for the lack of response to ICIs in advanced ChRCC and outline the unique exhaustion phenotype of renal oncocytic tumors.

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Abstract Details

Meeting

2022 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 40, 2022 (suppl 16; abstr 4549)

DOI

10.1200/JCO.2022.40.16_suppl.4549

Abstract #

4549

Poster Bd #

40

Abstract Disclosures