Supplementary Table 1 from An Empirical Approach Leveraging Tumorgrafts to Dissect the Tumor Microenvironment in Renal Cell Carcinoma Identifies Missing Link to Prognostic Inflammatory Factors

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posted on 2023-04-03, 21:44 authored by Tao Wang, Rong Lu, Payal Kapur, Bijay S. Jaiswal, Raquibul Hannan, Ze Zhang, Ivan Pedrosa, Jason J. Luke, He Zhang, Leonard D. Goldstein, Qurratulain Yousuf, Yi-Feng Gu, Tiffani McKenzie, Allison Joyce, Min S. Kim, Xinlei Wang, Danni Luo, Oreoluwa Onabolu, Christina Stevens, Zhiqun Xie, Mingyi Chen, Alexander Filatenkov, Jose Torrealba, Xin Luo, Wenbin Guo, Jingxuan He, Eric Stawiski, Zora Modrusan, Steffen Durinck, Somasekar Seshagiri, James Brugarolas

List of UTSW KCP patients with RNA-Seq and exome-seq. Sheet 1 contains information of 35 patients whose matched trio RNA-Seq data were used in the primary DisHet analyses. Sheet 2 contains information of patients whose bulk tumors were analyzed by RNA-Seq and whose follow up data are available. There are overlap between patients from these two sheets. Sheet 3 contains the information of tumorgraft data used in Fig. 5bc.

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NIH

Center for Translational Medicine of UT Southwestern

Cancer Prevention and Research Institute of Texas

American Cancer Society

KCP Patient Council

Kidney Cancer Coalition

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ARTICLE ABSTRACT

By leveraging tumorgraft (patient-derived xenograft) RNA-sequencing data, we developed an empirical approach, DisHet, to dissect the tumor microenvironment (eTME). We found that 65% of previously defined immune signature genes are not abundantly expressed in renal cell carcinoma (RCC) and identified 610 novel immune/stromal transcripts. Using eTME, genomics, pathology, and medical record data involving >1,000 patients, we established an inflamed pan-RCC subtype (IS) enriched for regulatory T cells, natural killer cells, TH1 cells, neutrophils, macrophages, B cells, and CD8+ T cells. IS is enriched for aggressive RCCs, including BAP1-deficient clear-cell and type 2 papillary tumors. The IS subtype correlated with systemic manifestations of inflammation such as thrombocytosis and anemia, which are enigmatic predictors of poor prognosis. Furthermore, IS was a strong predictor of poor survival. Our analyses suggest that tumor cells drive the stromal immune response. These data provide a missing link between tumor cells, the TME, and systemic factors.Significance: We undertook a novel empirical approach to dissect the renal cell carcinoma TME by leveraging tumorgrafts. The dissection and downstream analyses uncovered missing links between tumor cells, the TME, systemic manifestations of inflammation, and poor prognosis. Cancer Discov; 8(9); 1142–55. ©2018 AACR.This article is highlighted in the In This Issue feature, p. 1047

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Keywords

Computational Methods Gene expression profiling Genitourinary Cancers Immunology Immune responses to cancer

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