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

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    Authors
    Smith, Tim A D
    Lane, Brian
    More, Elisabet
    Valentine, Helen R
    Lunj, Sapna
    Abdelkarem, O. A.
    Irlam-Jones, Joely J
    Shabbir, Rekaya
    Vora, Shrushti
    Denley, H.
    Reeves, Kimberley J
    Hoskin, Peter J
    Choudhury, Ananya
    West, Catharine M L
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    Affiliation
    Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester M20 4GJ, UK
    Issue Date
    2022
    
    Metadata
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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.
    Citation
    Smith TAD, Lane B, More E, Valentine H, Lunj S, Abdelkarem OA, et al. Comparison of multiple gene expression platforms for measuring a bladder cancer hypoxia signature. Molecular Medicine Reports. 2022 Aug;26(2). PubMed PMID: WOS:000822697700001.
    Journal
    Molecular Medicine Reports
    URI
    http://hdl.handle.net/10541/625523
    DOI
    10.3892/mmr.2022.12777.
    PubMed ID
    35730624
    Additional Links
    https://dx.doi.org/10.3892/mmr.2022.12777.
    Type
    Meetings and Proceedings
    ae974a485f413a2113503eed53cd6c53
    10.3892/mmr.2022.12777.
    Scopus Count
    Collections
    All Paterson Institute for Cancer Research

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