Molecular analysis of archival diagnostic prostate cancer biopsies identifies genomic similarities in cases with progression post-radiotherapy, and those with de novo metastatic disease

Philip Vincent Charlton; Dawn O'Reilly; Yiannis Philippou; Srinivasa Rao Rao; Alastair David Gordon Lamb; Ian Geoffrey Mills; Geoff Stuart Higgins; Freddie Charles Hamdy; Clare Verrill; Francesca Meteora Buffa; Richard John Bryant

doi:10.1002/pros.24715

Molecular analysis of archival diagnostic prostate cancer biopsies identifies genomic similarities in cases with progression post-radiotherapy, and those with de novo metastatic disease

Prostate. 2024 Apr 23. doi: 10.1002/pros.24715. Online ahead of print.

Authors

Philip Vincent Charlton^{1

2}, Dawn O'Reilly¹, Yiannis Philippou³, Srinivasa Rao Rao⁴, Alastair David Gordon Lamb^{3

4}, Ian Geoffrey Mills⁴, Geoff Stuart Higgins^{1

2}, Freddie Charles Hamdy^{3

4}, Clare Verrill^{4

5}, Francesca Meteora Buffa¹, Richard John Bryant^{3

4}

Affiliations

¹ Department of Oncology, University of Oxford, Oxford, UK.
² Department of Oncology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
³ Department of Urology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
⁴ Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK.
⁵ Department of Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.

PMID: 38654435
DOI: 10.1002/pros.24715

Abstract

Background: It is important to identify molecular features that improve prostate cancer (PCa) risk stratification before radical treatment with curative intent. Molecular analysis of historical diagnostic formalin-fixed paraffin-embedded (FFPE) prostate biopsies from cohorts with post-radiotherapy (RT) long-term clinical follow-up has been limited. Utilizing parallel sequencing modalities, we performed a proof-of-principle sequencing analysis of historical diagnostic FFPE prostate biopsies. We compared patients with (i) stable PCa (sPCa) postprimary or salvage RT, (ii) progressing PCa (pPCa) post-RT, and (iii) de novo metastatic PCa (mPCa).

Methods: A cohort of 19 patients with diagnostic prostate biopsies (n = 6 sPCa, n = 5 pPCa, n = 8 mPCa) and mean 4 years 10 months follow-up (diagnosed 2009-2016) underwent nucleic acid extraction from demarcated malignancy. Samples underwent 3'RNA sequencing (3'RNAseq) (n = 19), nanoString analysis (n = 12), and Illumina 850k methylation (n = 8) sequencing. Bioinformatic analysis was performed to coherently identify differentially expressed genes and methylated genomic regions (MGRs).

Results: Eighteen of 19 samples provided useable 3'RNAseq data. Principal component analysis (PCA) demonstrated similar expression profiles between pPCa and mPCa cases, versus sPCa. Coherently differentially methylated probes between these groups identified ~600 differentially MGRs. The top 50 genes with increased expression in pPCa patients were associated with reduced progression-free survival post-RT (p < 0.0001) in an external cohort.

Conclusions: 3'RNAseq, nanoString and 850k-methylation analyses are each achievable from historical FFPE diagnostic pretreatment prostate biopsies, unlocking the potential to utilize large cohorts of historic clinical samples. Profiling similarities between individuals with pPCa and mPCa suggests biological similarities and historical radiological staging limitations, which warrant further investigation.

Keywords: diagnostic biopsies; metastasis; molecular analysis; prostate cancer; radiotherapy.

Abstract

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