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

• Published in: The Prostate Vol. 84; no. 10; pp. 977 - 990
• Main Authors: Charlton, Philip Vincent, O'Reilly, Dawn, Philippou, Yiannis, Rao, Srinivasa Rao, Lamb, Alastair David Gordon, Mills, Ian Geoffrey, Higgins, Geoff Stuart, Hamdy, Freddie Charles, Verrill, Clare, Buffa, Francesca Meteora, Bryant, Richard John
• Format: Journal Article
• Language: English
• Published: United States Wiley Subscription Services, Inc 01-07-2024; John Wiley and Sons Inc
• Subjects: Aged; Biopsy; Cohort Studies; diagnostic biopsies; Disease Progression; DNA probes; Genomics; Humans; Male; Malignancy; Metastases; Metastasis; Middle Aged; molecular analysis; Neoplasm Metastasis; Original; Patients; Principal components analysis; Prostate - pathology; Prostate cancer; Prostatic Neoplasms - genetics; Prostatic Neoplasms - pathology; Prostatic Neoplasms - radiotherapy; Radiation therapy; radiotherapy; Sequence analysis; radiotherapy; prostate cancer; metastasis; molecular analysis; diagnostic biopsies
• ISSN: 0270-4137; 1097-0045; 1097-0045
• DOI: 10.1002/pros.24715

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.