Functional genomics identifies novel genes essential for clear cell renal cell carcinoma tumor cell proliferation and migration

Abstract

Currently there is a lack of targeted therapies that lead to long-term attenuation or regression of disease in patients with advanced clear cell renal cell carcinoma (ccRCC). Our group has implemented a high-throughput genetic analysis coupled with a high-throughput proliferative screen in order to investigate the genetic contributions of a large cohort of overexpressed genes at the functional level in an effort to better understand factors involved in tumor initiation and progression.Patient gene array analysis identified transcripts that are consistently elevated in patient ccRCC as compared to matched normal renal tissues. This was followed by a high-throughput lentivirus screen, independently targeting 195 overexpressed transcripts identified in the gene array in four ccRCC cell lines. This revealed 31 ‘hits’ that contribute to ccRCC cell proliferation.Many of the hits identified are not only presented in the context of ccRCC for the first time, but several have not been previously linked to cancer. We further characterize the function of a group of hits in tumor cell invasion. Taken together these findings reveal pathways that may be critical in ccRCC tumorigenicity, and identifies novel candidate factors that could serve as targets for therapeutic intervention or diagnostic/prognostic biomarkers for patients with advanced ccRCC.

Defining the human kidney N‐glycome in normal and cancer tissues using MALDI imaging mass spectrometry

“…Using previously published proteogenomic studies in a ccRCC cohort of matched tumor and normal tissues from our group, transcriptomic gene array data were assessed for the glycosyltransferase family of fucosyltransferases, FUT1 to FUT11. These enzymes are responsible for the presence or absence of the multifucosylated structures detected in the tubule and tumor regions.…”

“…This FUT8 expression pattern was similar for other FUT genes tested (FUT1, FUT2, FUT4, FUT5, FUT7, FUT9, and FUT10; data not shown) . The FUT11 gene was the only gene increased in tumors, and it is known to be involved in O‐glycosylation addition of fucose residues to glycoproteins. It has been reported previously to be a potential biomarker of ccRCC [26].…”

“…All ccRCC tissue samples were obtained from the Mayo Clinic biorepository as previously described . Briefly, samples were part of an IRB‐approved study begun in 2003 to obtain discarded tissues from any patient with sporadic conventional RCC who underwent nephrectomy and gave informed consent.…”

“…A previously published gene array dataset for paired normal and ccRCC tumors (stages 1‐4) was derived from Affymetrix Human Genome U133 Plus 2.0 Array chip expression analysis …”

“…Previous collaborative genomic and proteomic studies from our groups reported the use of paired ccRCC tissues representing nontumor and tumor stages 1 to 4 . These studies identified multiple transcriptomic and proteomic changes in tumors associated with a fundamental Warburg effect type metabolism of glucose utilization.…”