Validation of a companion diagnostic biomarker for prospective use in prostate radiotherapy trials
Thiruthaneeswaran, Niluja Bibby, Becky A Pereira, R. More, E. Bristow, Robert G Choudhury, Ananya West, Catharine M L
Thiruthaneeswaran, Niluja
Bibby, Becky A
Pereira, R.
More, E.
Bristow, Robert G
Choudhury, Ananya
West, Catharine M L
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Abstract
Purpose or Objective
A 28-gene hypoxia-associated signature (HS) was derived
for prostate cancer. The signature was validated for
prognostic significance in eight prostatectomy, a definitive
radiotherapy cohort and a salvage radiotherapy cohort.
Biomarker validation using scant or minimal formalin-fixed
paraffin-embedded (FFPE) tissue from diagnostic biopsies
is a challenge due to nucleic acid degradation and low
tissue volume. The aim of this study was to technically
validate the robustness of the signature for
reproducibility, reliability and intratumour heterogeneity.
Material and Methods
Diagnostic FFPE needle core (NC) biopsies from high-risk
prostate cancer patients treated with different
radiotherapy regimens were collected (n=663).
Intratumour heterogeneity was assessed in 40 patient
samples with multiple tumour FFPE NC blocks. Correlation
was assessed in matched needle core to macrodissected
prostatectomy samples in 12 patients. To assess
downstream usability of extracted retrospective RNA three gene expression technologies were assessed (Taqman array
cards, RNA-seq, Affymetrix Clariom S).
Results
The 24 prospective samples (age <12 months) yielded
higher quality RNA than the retrospective samples (p =
0.008). Success rate of gene expression using Clariom S was
achieved in 560 samples (84%). All samples passed QC
metric and all 28 genes of the prostate HS were detected
and measurable. RNA quality (r=0.03) and yield (r=-0.05)
did not correlate with HS. HS did not increase with Gleason
grade group (G3 2.40±0.16, G4 2.31±0.30, G5 2.69±0.22).
Clariom S consistently outperformed the other platforms
studied. There was an inverse correlation between probe
amplicon length and gene expression (n=33, r=-0.67) with
the Taqman array card. Intratumour heterogeneity based
on HS group was demonstrated in 18 samples (45%). No
correlation was seen between histopathological adverse
features and HS.
Conclusion
This is the largest prostate radiotherapy cohort with full
gene expression data available and hence a valuable
resource for research. The Clariom S gene expression
platform was superior to Taqman array cards and RNA-seq
for validation of a prostate hypoxia gene signature in
definitive radiotherapy cohorts using archival FFPE NC.
Description
Date
2020
Publisher
Collections
Keywords
Type
Meetings and Proceedings
Citation
Thiruthaneeswaran N, Bibby BAS, Pereira R, More E, Bristow RG, Choudhury A, et al. OC-0319: Validation of a companion diagnostic biomarker for prospective use in prostate radiotherapy trials. Radiotherapy and Oncology . 2020 Nov;152:S167–8.