Transcriptomic profiling as proof of concept for investigation of collecting duct carcinoma (CDC).

Abstract

714 Background: Collecting duct carcinoma is a rare, highly aggressive and molecularly uncharacterized kidney disease with poor outcome. To date, no standard therapies are available and treatment choice is based on retrospective data. Identifying molecular features of this tumor could provide a biologic rationale for novel targeted systemic therapies. Methods: Total RNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissues of 6 CDCs, 5 clear cell renal carcinomas (ccRCCs) and 4 adjacent normal tissues. Samples were profiled by GeneChip Human Transcriptome Array 2.0 (Affymetrix) and constituted the Istituto Nazionale dei Tumori (INT) dataset. Data were pre-processed using the robust multi-array average method and differentially expressed genes were identified according to the limma pipeline. Genes with a false discovery rate < 0.25 were selected. Pathway analysis was performed by gene set enrichment analysis (GSEA), single sample (ss) GSEA, DAVID Bioinformatics Resources 6.8 and Pathfinder Bioconductor package. Moreover, a list of genes representing angiogenesis and immune biology, previously used in the IMmotion150 study, was chosen to explore further functional subcategories of CDC. Available RNA-Seq data of 7 CDCs and 5 matched normal tissue from GSE89122 dataset were used for validation. Results: Comparison of transcriptome profiles of CDCs and ccRCCs versus normal tissue led to the identification of a core of 14 genes specifically up-regulated in CDC, 5 of which (SFN, S100A11, CKAP5, CDH1 and CD44) were significantly involved in extracellular matrix organization. Other deregulated genes were related to immune system, cell cycle progression, glucose and pentose phosphate metabolism and EGFR-signaling. In addition, ssGSEA permitted to identify two major distinct biological subgroups in CDC of both INT and GSE89122 datasets, based on relative expression levels of angiogenesis and immune genes. Conclusions: Our study reveals novel insights into the biology and heterogeneity of CDCs. Although further validation using larger samples is needed, the current findings suggest that this heterogeneity could have clinical implications for the treatment of patients with this rare kidney cancer.