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

  • Authors:
    • Tim A.D. Smith
    • Brian Lane
    • Elisabet More
    • Helen Valentine
    • Sapna Lunj
    • Omneya A. Abdelkarem
    • J. Irlam‑Jones
    • Rekaya Shabbir
    • Shrushti Vora
    • Helen Denley
    • Kimberley J. Reeves
    • Peter J. Hoskin
    • Ananya Choudhury
    • Catharine M.L. West

  • View Affiliations

  • Published online on: June 20, 2022     https://doi.org/10.3892/mmr.2022.12777
  • Article Number: 261
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Abstract

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.
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August-2022
Volume 26 Issue 2

Print ISSN: 1791-2997
Online ISSN:1791-3004

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  • Journal Metrics
  • Impact Factor: 3.4
  • Ranked Medicine Research and Experimental
    (total number of cites)
  • CiteScore: 7.6
  • CiteScore Rank: Q1: #82/347 Biochemistry, Genetics and Molecular Biology
  • Source Normalized Impact per Paper (SNIP): 0.647
  • SCImago Journal Rank (SJR): 0.781
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Spandidos Publications style
Smith TA, Lane B, More E, Valentine H, Lunj S, Abdelkarem OA, Irlam‑Jones J, Shabbir R, Vora S, Denley H, Denley H, et al: Comparison of multiple gene expression platforms for measuring a bladder cancer hypoxia signature. Mol Med Rep 26: 261, 2022.
APA
Smith, T.A., Lane, B., More, E., Valentine, H., Lunj, S., Abdelkarem, O.A. ... West, C.M. (2022). Comparison of multiple gene expression platforms for measuring a bladder cancer hypoxia signature. Molecular Medicine Reports, 26, 261. https://doi.org/10.3892/mmr.2022.12777
MLA
Smith, T. A., Lane, B., More, E., Valentine, H., Lunj, S., Abdelkarem, O. A., Irlam‑Jones, J., Shabbir, R., Vora, S., Denley, H., Reeves, K. J., Hoskin, P. J., Choudhury, A., West, C. M."Comparison of multiple gene expression platforms for measuring a bladder cancer hypoxia signature". Molecular Medicine Reports 26.2 (2022): 261.
Chicago
Smith, T. A., Lane, B., More, E., Valentine, H., Lunj, S., Abdelkarem, O. A., Irlam‑Jones, J., Shabbir, R., Vora, S., Denley, H., Reeves, K. J., Hoskin, P. J., Choudhury, A., West, C. M."Comparison of multiple gene expression platforms for measuring a bladder cancer hypoxia signature". Molecular Medicine Reports 26, no. 2 (2022): 261. https://doi.org/10.3892/mmr.2022.12777