Abstract
BackgroundLarge-scale initiatives like The Cancer Genome Atlas (TCGA) performed genomics studies on predominantly Caucasian kidney cancer. In this study, we aimed to investigate genomics of Chinese clear cell renal cell carcinoma (ccRCC).MethodsWe performed whole-transcriptomic sequencing on 55 tumor tissues and 11 matched normal tissues from Chinese ccRCC patients. We systematically analyzed the data from our cohort and comprehensively compared with the TCGA ccRCC cohort.ResultsIt found that PBRM1 mutates with a frequency of 11% in our cohort, much lower than that in TCGA Caucasians (33%). Besides, 31 gene fusions including 5 recurrent ones, that associated with apoptosis, tumor suppression and metastasis were identified. We classified our cohort into three classes by gene expression. Class 1 shows significantly elevated gene expression in the VEGF pathway, while Class 3 has comparably suppressed expression of this pathway. Class 2 is characterized by increased expression of extracellular matrix organization genes and is associated with high-grade tumors. Applying the classification to TCGA ccRCC patients revealed better distinction of tumor prognosis than reported classifications. Class 2 shows worst survival and Class 3 is a rare subtype ccRCC in the TCGA cohort. Furthermore, computational analysis on the immune microenvironment of ccRCC identified immune-active and tolerant tumors with significant increased macrophages and depleted CD4 positive T-cells, thus some patients may benefit from immunotherapies.ConclusionIn summary, results presented in this study shed light into distinct genomic expression profiles in Chinese population, modified the stratification patterns by new molecular classification, and gave practical guidelines on clinical treatment of ccRCC patients.
Highlights
Large-scale initiatives like The Cancer Genome Atlas (TCGA) performed genomics studies on predominantly Caucasian kidney cancer
Patient clinical information Transcriptome sequencing was performed on 55 tumor tissue samples from CccRCC patients, 11 of which with matched normal tissues
Driver mutations and gene fusions To investigate population-specific genomic features, important driver mutations and recurrent gene fusions were identified in CccRCC tumors (Fig. 1)
Summary
Large-scale initiatives like The Cancer Genome Atlas (TCGA) performed genomics studies on predominantly Caucasian kidney cancer. We aimed to investigate genomics of Chinese clear cell renal cell carcinoma (ccRCC). Renal cell carcinoma (RCC), accounts for about 2–3% of tumor malignancy in adults, and is one of the most lethal urological cancers [1]. Clear cell renal cell carcinoma (ccRCC) is its most common subtype (75–85%). Genomic characterizations of resource datasets on RCCs have been performed in the past few years, including clear cell renal cell carcinoma (ccRCC) [7,8,9], chromophobe renal cell carcinoma [10], papillary renal cell carcinoma [11] and renal medullary carcinoma [12]. One integrative taxonomy research has been performed to assemble three TCGA renal carcinoma subtypes [13]
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