1. Molecular Characterization of Clear Cell Renal Cell Carcinoma Reveals Prognostic Significance of Epithelial-mesenchymal Transition Gene Expression Signature
- Author
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Alexander Zaslavsky, Andi K. Cani, Chia Jen Liu, Simpa S. Salami, Judith Stangl-Kremser, Randy Vince, Rohit Mehra, Razeen Karim, Ganesh S. Palapattu, Todd M. Morgan, Trinh Pham, Christopher M. Russell, Srinivas Nallandhighal, Aaron M. Udager, Kevin Hu, Marcin Cieslik, and Skylar Groves
- Subjects
Male ,Oncology ,medicine.medical_specialty ,Epithelial-Mesenchymal Transition ,Urology ,medicine.medical_treatment ,Inferior vena cava ,Internal medicine ,Biomarkers, Tumor ,medicine ,Humans ,Radiology, Nuclear Medicine and imaging ,Epithelial–mesenchymal transition ,Carcinoma, Renal Cell ,Survival analysis ,Retrospective Studies ,business.industry ,Cell cycle ,Prognosis ,medicine.disease ,Primary tumor ,Kidney Neoplasms ,Nephrectomy ,Clear cell renal cell carcinoma ,medicine.vein ,Female ,Surgery ,Transcriptome ,business ,Kidney cancer - Abstract
Background There is an ongoing need to develop prognostic biomarkers to improve the management of clear cell renal cell carcinoma (ccRCC). Objective To leverage enriched pathways in ccRCC to improve risk-stratification. Design, setting, and participants We retrospectively identified two complementary discovery cohorts of patients with ccRCC who underwent (1) radical nephrectomy (RNx) with inferior vena cava tumor thrombectomy (patients = 5, samples = 24) and (2) RNx for localized disease and developed recurrence versus no recurrence (n = 36). Patients with localized ccRCC (M0) in The Cancer Genome Atlas (TCGA, n = 386) were used for validation. Outcome measurements and statistical analysis A differential expression gene (DEG) analysis was performed on targeted RNA next-generation sequencing data from both discovery cohorts. Using TCGA for validation, Kaplan-Meier survival analysis and multivariable Cox proportional hazard testing were utilized to investigate the prognostic impact of DEGs, cell cycle proliferation (CCP), and a novel epithelial-mesenchymal transition (EMT) score on progression-free (PFS) and disease-specific (DSS) survival. Results and limitations In the discovery cohorts, we observed overexpression of WT1 and CCP genes in the tumor thrombus versus the primary tumor, as well as in patients with recurrence versus those without recurrence. A hallmark pathway analysis demonstrated enrichment of the EMT- and CCP-related pathways in patients with high WT1 expression in the TCGA (validation) ccRCC cohort. CCP and EMT scores were derived in the validation cohort, which was stratified into four risk groups using Youden Index cut points: CCPlow/EMTlow, CCPlow/EMThigh, CCPhigh/EMTlow, and CCPhigh/EMThigh. The CCPhigh/EMThigh risk group was associated with the worst PFS and DSS (both p Conclusions We demonstrate the synergistic prognostic impact of EMT in tumors with a high CCP score. Our novel EMT score has the potential to improve risk stratification and provide potential novel therapeutic targets. Patient summary Genes involved in epithelial-mesenchymal transition provides important prognostic information for patients with clear cell renal cell carcinoma.
- Published
- 2022