Evaluation of homologous recombination repair status in metastatic prostate cancer by next-generation sequencing and functional tissue-based immunofluorescence assays

Arce-Gallego, S.; Morgado, P. C.; Delgado-Serrano, L.; Simonetti, S.; Gonzalez, M.; Marmolejo, D.; Morales-Barrera, R.; Mir, G.; Semidey, M. E.; Lozano, P. R.; Cordoba-Terreros, S.; Mast, R.; de Albert, M.; Planas, J.; Cuadras, M.; Maldonado, X.; Suarez, C.; Casanova-Salas, I.; Nonell, L.; Dienstmann, R.; Nuciforo, P.; Vivancos, A.; Llop-Guevara, A.; Carles, J.; Serra, V.; Mateo, J.

doi:10.1101/2024.01.28.577367

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bioRxiv · 10.1101/2024.01.28.577367

Evaluation of homologous recombination repair status in metastatic prostate cancer by next-generation sequencing and functional tissue-based immunofluorescence assays

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Abstract

PurposeMetastatic prostate cancer (mPC) is enriched for homologous recombination repair (HRR) gene alterations; these biomarkers have prognostic and predictive value. Next-generation sequencing (NGS) allows for patient stratification based on these biomarkers, but widespread clinical implementation is still limited. Moreover, not all mutations in HRR genes result in functional HRR loss in the tumor. We investigated the correlation between genomic and functional loss of HRR, using NGS and an optimized RAD51 immunofluorescence (RAD51-IF) assay in mPC clinical biopsies. Experimental designObservational study including patients with stage IV prostate cancer. Biopsies from either primary tumor or metastatic biopsies underwent NGS (targeted sequencing and/or whole-exome sequencing), and RAD51-IF. Clinical data was extracted from electronic patient records. Results219 biopsies from 187 patients were acquired, including primary (151/219) and metastatic (68/219) tumor biopsies collected either in the metastatic hormone- sensitive (169/219) or castration-resistant (50/219) setting. NGS (181 biopsies from 157 patients) showed frequent genomic alterations in TP53 (40%), AR (15%), PTEN (14%), MYC (10%), BRCA2 (9%), ATM (8%) and BRCA1 (2%). Tissue for RAD51 IF was available for 206 samples; of those, 140/206 (68%) were evaluable for RAD51- IF. Based on a previously defined threshold of 10% RAD51-positive cells, 21% samples had RAD51-low results compatible with HRR deficiency (HRD). Sample matched RAD51-IF and genomics data were obtained for 128 biopsies (117 patients): RAD51-IF had a high sensitivity (68%) and specificity (85%) to identify cases with BRCA1/2 alterations. Additionally, the RAD51-IF assay was able to identify restoration of HRR function in selected cases with BRCA2 reversion mutations or BRCA1 expression. ConclusionsRAD51-IF is feasible in routine clinical samples from mPC patients and associates strongly with clinically relevant HRR gene alterations.

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Arce-Gallego, S., Morgado, P. C., Delgado-Serrano, L., Simonetti, S., Gonzalez, M., Marmolejo, D., Morales-Barrera, R., Mir, G., Semidey, M. E., Lozano, P. R., Cordoba-Terreros, S., Mast, R., de Albert, M., Planas, J., Cuadras, M., Maldonado, X., Suarez, C., Casanova-Salas, I., Nonell, L., Dienstmann, R., Nuciforo, P., Vivancos, A., Llop-Guevara, A., Carles, J., Serra, V., Mateo, J.. 2024-01-31. Evaluation of homologous recombination repair status in metastatic prostate cancer by next-generation sequencing and functional tissue-based immunofluorescence assays. https://doi.org/10.1101/2024.01.28.577367

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