Comparison of multiple gene expression platforms for measuring a bladder cancer hypoxia signature (2022)

Type of publication:
Journal article

Smith TAD; Lane B; More E; Valentine H; Lunj S; Abdelkarem OA; Irlam-Jones J; Shabbir R; Vora S; *Denley H; Reeves KJ; Hoskin PJ; Choudhury A; West CML

Molecular Medicine Reports, 2022 Aug; Vol. 26 (2)

Tumour hypoxia status provides prognostic information and predicts response to hypoxia modifying treatments. A previous study by our group derived a 24 gene signature to assess hypoxia in bladder cancer. The objectives of the present study were to compare platforms for generating signature scores, identify cut off values for prospective studies, assess intra tumour heterogeneity and confirm hypoxia relevance. Briefly, RNA was extracted from prospectively collected diagnostic biopsies of muscle invasive bladder cancer (51 patients), and gene expression was measured using customised Taqman Low Density Array (TLDA) cards, NanoString and Clariom S arrays. Cross platform transferability of the gene signature was assessed using regression and concordance analysis. The cut off values were the cohort median expression values. Intra and inter tumour variability were determined in a retrospective patient cohort (n=51) with multiple blocks (2 18) from the same tumour. To demonstrate relevance, bladder cancer cell lines were exposed to hypoxia (0.1% oxygen, 24 h), and extracted RNA was run on custom TLDA cards. Hypoxia scores (HS) values showed good agreement between platforms: Clariom S vs. TLDA (r=0.72, P<0.0001; concordance 73%); Clariom S vs. NanoString (r=0.84, P<0.0001; 78%); TLDA vs. NanoString (r=0.80, P<0.0001; 78%). Cut off values were 0.047 (TLDA), 7.328 (NanoString) and 6.667 (Clariom S). Intra tumour heterogeneity in gene expression and HS (coefficient of variation 3.9%) was less than inter tumour (7.9%) variability. HS values were higher in bladder cancer cells exposed to hypoxia compared with normoxia (P<0.02). In conclusion, the present study revealed that application of the 24 gene bladder cancer hypoxia signature was platform agnostic, cut off values determined prospectively can be used in a clinical trial, intra tumour heterogeneity was low and the signature was sensitive to changes in oxygen levels in vitro.