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Surgical Pathology Clinics

Molecular Genetics of Prostate Cancer and Role of Genomic Testing

Open AccessPublished:October 12, 2022DOI:https://doi.org/10.1016/j.path.2022.08.002

      Keywords

      Key points
      • PCa molecular landscape is profoundly heterogeneous and a classification into 7 molecular subgroups has been proposed based on molecular profiling of localized PCa (TCGA cohort).
      • For localized PCa, several genomic classifiers are available to predict risk of distant metastasis, or/and PCa-related mortality. These assays can support clinical decision making regarding active surveillance or indication of adjuvant therapy following radical prostatectomy.
      • In metastatic disease, main therapeutically actionable alterations are HRD, MSI-H, and CDK12 deficiency. Alterations in DNA damage response genes are present in 19% of localized and up to 31% of metastatic PCas. Genomic instability assays assessing HRD may predict sensitivity to PARP inhibitors.
      • MSI-H (1–5%) sensitizes to immune checkpoint inhibitors (ICIs) and can be identified by immunohistochemistry (IHC), microsatellite PCR, or NGS, as well as sequencing of mismatch repair (MMR) genes. CDK12-deficient PCas (1%–5%) present variable degrees of sensitivities to ICIs.
      • Germline testing is recommended in patients with personal history of high or very-high-risk localized PCa, regional or metastatic PCa, as well as family history of PCa.

      Overview

      Comprehensive molecular profiling of large cohorts of primary prostate cancer (PCa) and metastatic PCa (mPCa), using genome-wide next-generation sequencing (NGS) approaches, has significantly contributed to the characterization of the profoundly heterogeneous molecular landscape of PCa.
      The molecular taxonomy of primary prostate cancer.
      • Robinson D.
      • Van Allen E.M.
      • Wu Y.M.
      • et al.
      Integrative clinical genomics of advanced prostate cancer.
      • Abida W.
      • Cyrta J.
      • Heller G.
      • et al.
      Genomic correlates of clinical outcome in advanced prostate cancer.
      • van Dessel L.F.
      • van Riet J.
      • Smits M.
      • et al.
      The genomic landscape of metastatic castration-resistant prostate cancers reveals multiple distinct genotypes with potential clinical impact.
      • Chung J.H.
      • Dewal N.
      • Sokol E.
      • et al.
      Prospective comprehensive genomic profiling of primary and metastatic prostate tumors.
      These studies have identified main therapeutically actionable molecular subtypes of PCa, such as homologous recombination-deficient (HRD), defined as harboring alterations in the homologous recombination repair pathway (HRR)
      • Li X.
      • Heyer W.-D.
      Homologous recombination in DNA repair and DNA damage tolerance.
      and more strictly an HRD mutational signature
      • Gulhan D.C.
      • Lee J.J.-K.
      • Melloni G.E.M.
      • et al.
      Detecting the mutational signature of homologous recombination deficiency in clinical samples.
      ,
      • Rosenthal R.
      • McGranahan N.
      • Herrero J.
      • et al.
      deconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution.
      ; microsatellite instability-high (MSI-H); or CDK12-deficient tumors.
      The molecular taxonomy of primary prostate cancer.
      • Robinson D.
      • Van Allen E.M.
      • Wu Y.M.
      • et al.
      Integrative clinical genomics of advanced prostate cancer.
      • Abida W.
      • Cyrta J.
      • Heller G.
      • et al.
      Genomic correlates of clinical outcome in advanced prostate cancer.
      • van Dessel L.F.
      • van Riet J.
      • Smits M.
      • et al.
      The genomic landscape of metastatic castration-resistant prostate cancers reveals multiple distinct genotypes with potential clinical impact.
      • Chung J.H.
      • Dewal N.
      • Sokol E.
      • et al.
      Prospective comprehensive genomic profiling of primary and metastatic prostate tumors.
      In localized disease, multiple studies have shown that gene expression assays performed on PCa biopsies or prostatectomy samples can predict risk of metastatic progression and PCa-specific mortality,
      • Feng F.Y.
      • Huang H.C.
      • Spratt D.E.
      • et al.
      Validation of a 22-gene genomic classifier in patients with recurrent prostate cancer: an ancillary study of the NRG/RTOG 9601 randomized clinical trial.
      • Spratt D.E.
      • Yousefi K.
      • Deheshi S.
      • et al.
      Individual Patient-level meta-analysis of the performance of the decipher genomic classifier in high-risk men after prostatectomy to predict development of metastatic disease.
      • Cullen J.
      • Rosner I.L.
      • Brand T.C.
      • et al.
      A biopsy-based 17-gene genomic prostate score predicts recurrence after radical prostatectomy and adverse surgical pathology in a racially diverse population of men with clinically low- and intermediate-risk prostate cancer.
      • Cooperberg M.R.
      • Simko J.P.
      • Cowan J.E.
      • et al.
      Validation of a Cell-cycle progression gene panel to improve risk stratification in a contemporary prostatectomy cohort.
      • Cuzick J.
      • Stone S.
      • Fisher G.
      • et al.
      Validation of an RNA cell cycle progression score for predicting death from prostate cancer in a conservatively managed needle biopsy cohort.
      and current clinical guidelines integrate these assays as a useful tool to support clinical decision making regarding active surveillance and indication of intensification of therapy following radical prostatectomy (RP).
      • Schaeffer E.
      • Srinivas S.
      • Antonarakis E.S.
      • et al.
      NCCN guidelines insights: prostate cancer, version 1.2021.
      In the metastatic disease scenario, recent clinical studies have demonstrated efficacy of targeted treatment of specific molecular subtypes of PCa, such as poly(ADP-ribose)polymerase (PARP) inhibitors for HRD PCas,
      • de Bono J.
      • Mateo J.
      • Fizazi K.
      • et al.
      Olaparib for metastatic castration-resistant prostate cancer.
      • Mateo J.
      • Porta N.
      • Bianchini D.
      • et al.
      Olaparib in patients with metastatic castration-resistant prostate cancer with DNA repair gene aberrations (TOPARP-B): a multicentre, open-label, randomised, phase 2 trial.
      • Carreira S.
      • Porta N.
      • Arce-Gallego S.
      • et al.
      Biomarkers associating with PARP inhibitor benefit in prostate cancer in the TOPARP-B trial.
      • Chi K.N.
      • Rathkopf D.E.
      • Smith M.R.
      • et al.
      Phase 3 MAGNITUDE study: First results of niraparib (NIRA) with abiraterone acetate and prednisone (AAP) as first-line therapy in patients (pts) with metastatic castration-resistant prostate cancer (mCRPC) with and without homologous recombination repair (HRR) gene alterations.
      • Saad F.
      • Armstrong A.J.
      • Thiery-Vuillemin A.
      • et al.
      PROpel: Phase III trial of olaparib (ola) and abiraterone (abi) versus placebo (pbo) and abi as first-line (1L) therapy for patients (pts) with metastatic castration-resistant prostate cancer (mCRPC).
      and immune checkpoint inhibitors (ICIs) for MSI-H
      • Le D.T.
      • Uram J.N.
      • Wang H.
      • et al.
      PD-1 blockade in tumors with mismatch-repair deficiency.
      ,
      • Le D.T.
      • Durham J.N.
      • Smith K.N.
      • et al.
      Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade.
      and a subset of CDK12-deficient
      • Antonarakis E.S.
      • Velho P.I.
      • Fu W.
      • et al.
      CDK12-altered prostate cancer: clinical features and therapeutic outcomes to standard systemic therapies, poly (ADP-Ribose) polymerase inhibitors, and PD-1 inhibitors.
      PCas. These advances in PCa precision oncology treatment have motivated an increasing demand on genomic testing for patients with mPCa, starting from early treatment lines.
      • Merseburger A.S.
      • Waldron N.
      • Ribal M.J.
      • et al.
      Genomic testing in patients with metastatic castration-resistant prostate cancer: a pragmatic guide for clinicians.
      In this article, the molecular alterations reported in localized and advanced PCa are summarized, and main molecular diagnostic assays are reviewed, with focus on gene expression assays for localized PCa and genomic instability and MSI assays for advanced disease.

      Molecular landscape of localized and metastatic prostate cancer

      Most frequent genomic alterations in localized PCa and mPCa are fusions implicating members of the E26 transformation-specific (ETS) transcription factors family. Concretely, the TMPRSS2-ERG fusion is the overall most frequent molecular alteration, found in 40% to 50% of PCas.
      The molecular taxonomy of primary prostate cancer.
      ,
      • Robinson D.
      • Van Allen E.M.
      • Wu Y.M.
      • et al.
      Integrative clinical genomics of advanced prostate cancer.
      ,
      • van Dessel L.F.
      • van Riet J.
      • Smits M.
      • et al.
      The genomic landscape of metastatic castration-resistant prostate cancers reveals multiple distinct genotypes with potential clinical impact.
      ,
      • Tomlins S.A.
      • Rhodes D.R.
      • Perner S.
      • et al.
      Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer.
      ,
      • Tomlins S.A.
      • Bjartell A.
      • Chinnaiyan A.M.
      • et al.
      ETS gene fusions in prostate cancer: from discovery to daily clinical practice.
      Following the ETS fusions, most frequent genomic alterations in localized PCa are found in PTEN (17%), most frequently homozygous deletions; SPOP (11%); TP53 (8%); and FOXA1 (4%).1 Based on whole exome sequencing (WES) data from 333 primary PCas, The Cancer Genome Atlas (TCGA) Research Network proposed PCa classification into the following 7 molecular subtypes: PCas with ERG (46%), ETV1 (8%), ETV4 (4%), and FLI1 (1%) fusions and SPOP- (11%), FOXA1- (3%), and IDH1-mutated (1%) PCas.
      The molecular taxonomy of primary prostate cancer.
      SPOP mutations are the most frequent mutations in localized PCa and are mutually exclusive with the ETS fusions.
      The molecular taxonomy of primary prostate cancer.
      This molecular classification could cluster 74% of the analyzed tumors. The remaining “not-clusterable” group of PCa tumors (26%) was enriched in mutations in TP53, KDM6A, and KMT2D; deletions in chromosomes 6 and 16; as well as MYC and CCND1 amplifications (Fig. 1).
      Figure thumbnail gr1
      Fig. 1Molecular landscape of localized and metastatic prostate cancer. Genomic alterations reported from the analysis of the TCGA, CRPC500-SU2C, and CPCT-02 cohorts are illustrated. amp., amplification; ARSI, androgen receptor signaling inhibitors; chr., chromosome; del., deletions; dMMR/MSI-H, mismatch repair deficient, microsatellite instable-high; FA, Fanconi anemia pathway; mut., mutations; OS, overall survival. aActionable alterations; bAlterations in RB1, AR, and TP53 associated with shorter response to ARSI and RB1 additionally with shorter OS.
      In addition, molecular profiling data from several cohorts of mPCa are available. Whole genome sequencing (WGS) of the CPCT-02 cohort, consisting of 197 metastatic castration-resistant PCas (mCRPC), revealed that 68% of the cases could be clustered into the 7 subtypes proposed by the TCGA classification, and that the therapeutically actionable subtypes HRD, MSI-H, and CDK12−/− (tandem duplication genotype) did not show correlation with the TCGA subgroups.
      • van Dessel L.F.
      • van Riet J.
      • Smits M.
      • et al.
      The genomic landscape of metastatic castration-resistant prostate cancers reveals multiple distinct genotypes with potential clinical impact.
      Other studies have shown that CDK12 alterations are relatively mutually exclusive with SPOP, ETS fusions, TP53, and PTEN/PIK3CA alterations.
      • Antonarakis E.S.
      • Velho P.I.
      • Fu W.
      • et al.
      CDK12-altered prostate cancer: clinical features and therapeutic outcomes to standard systemic therapies, poly (ADP-Ribose) polymerase inhibitors, and PD-1 inhibitors.
      ,
      • Wu Y.M.
      • Cieślik M.
      • Lonigro R.J.
      • et al.
      Inactivation of CDK12 delineates a distinct immunogenic class of advanced prostate cancer.
      In the CPCT-02 cohort, mutations in AR, TP53, ZMYM3, APC, RB1, CDK12, ERF, and ZFP36L2 were significantly enriched in mCRPC when compared with the TCGA cohort.
      • van Dessel L.F.
      • van Riet J.
      • Smits M.
      • et al.
      The genomic landscape of metastatic castration-resistant prostate cancers reveals multiple distinct genotypes with potential clinical impact.
      WES and transcriptomics profiling of the SU2C-PCF cohort including 150 patients with mCRPC showed that most frequently altered genes in mCRPC are AR (62.7%), most frequently amplifications; ETS-family members (56.7%); TP53 (53.3%); and PTEN (40.7%). Also in this cohort, AR and TP53 alterations were enriched in mCRPC when compared with primary PCas, with AR and GNAS mutations being uniquely found in mCRPC.
      • Robinson D.
      • Van Allen E.M.
      • Wu Y.M.
      • et al.
      Integrative clinical genomics of advanced prostate cancer.
      In addition to the ETS fusions, other fusions uncovered involved BRAF, RAF1, PIK3CA/B, and RSPO2.
      • Robinson D.
      • Van Allen E.M.
      • Wu Y.M.
      • et al.
      Integrative clinical genomics of advanced prostate cancer.
      From a therapeutical point of view, whereas SPOP mutations are associated with longer response to androgen receptor signaling inhibitors (ARSI), shorter responses have been associated with alterations in RB1, TP53, and AR. Moreover, alterations in RB1 have been correlated with shorter overall survival (OS)
      • Abida W.
      • Cyrta J.
      • Heller G.
      • et al.
      Genomic correlates of clinical outcome in advanced prostate cancer.
      (see Fig. 1).

      Alterations in DNA Repair

      Alterations in Homologous Recombination, Fanconi Anemia Pathway, and CDK12

      Alterations in DNA damage response (DDR) genes have been reported in 19% of the 333 primary PCa tumors from the TCGA cohort, including alteration in the distinct genes involved in the HRR
      • Li X.
      • Heyer W.-D.
      Homologous recombination in DNA repair and DNA damage tolerance.
      • Gulhan D.C.
      • Lee J.J.-K.
      • Melloni G.E.M.
      • et al.
      Detecting the mutational signature of homologous recombination deficiency in clinical samples.
      • Rosenthal R.
      • McGranahan N.
      • Herrero J.
      • et al.
      deconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution.
      and Fanconi anemia (FA) pathways, as well as CDK12.
      The molecular taxonomy of primary prostate cancer.
      ,
      • Lozano R.
      • Castro E.
      • Aragón I.M.
      • et al.
      Genetic aberrations in DNA repair pathways: a cornerstone of precision oncology in prostate cancer.
      Similarly, the SU2C-PCF cohort reported alterations in DDR genes in 23% of the cases.
      • Robinson D.
      • Van Allen E.M.
      • Wu Y.M.
      • et al.
      Integrative clinical genomics of advanced prostate cancer.
      ,
      • Abida W.
      • Cyrta J.
      • Heller G.
      • et al.
      Genomic correlates of clinical outcome in advanced prostate cancer.
      A cohort of 3476 PCas (1660 samples from localized stage and 1816 mPCa samples) has been molecularly profiled using the FoundationOneCDx assay.
      • Chung J.H.
      • Dewal N.
      • Sokol E.
      • et al.
      Prospective comprehensive genomic profiling of primary and metastatic prostate tumors.
      Alterations in the HRR and FA pathways have been uncovered in 24.4% of the cases, with most frequent alterations found in BRCA2 (9.8%) and ATM (5.2%).
      • Chung J.H.
      • Dewal N.
      • Sokol E.
      • et al.
      Prospective comprehensive genomic profiling of primary and metastatic prostate tumors.
      In addition, 5.6% of the cases had alterations in CDK12.
      • Chung J.H.
      • Dewal N.
      • Sokol E.
      • et al.
      Prospective comprehensive genomic profiling of primary and metastatic prostate tumors.
      In the TCGA cohort of localized PCas, the most frequent alterations were found in FANCD2 (7%), ATM (4%), BRCA2 (3%), and RAD51 C (3%),
      The molecular taxonomy of primary prostate cancer.
      and, in the mCRPC SU2C-PCF cohort, in BRCA2 (13%) and ATM (7.3%).
      • Robinson D.
      • Van Allen E.M.
      • Wu Y.M.
      • et al.
      Integrative clinical genomics of advanced prostate cancer.
      ,
      • Lozano R.
      • Castro E.
      • Aragón I.M.
      • et al.
      Genetic aberrations in DNA repair pathways: a cornerstone of precision oncology in prostate cancer.

      Alterations in Mismatch Repair Genes

      MSI-H or mismatch repair deficiency (dMMR) has been reported in 1% to 5% of PCas.
      The molecular taxonomy of primary prostate cancer.
      ,
      • Robinson D.
      • Van Allen E.M.
      • Wu Y.M.
      • et al.
      Integrative clinical genomics of advanced prostate cancer.
      ,
      • Ritch E.
      • Fu S.Y.F.
      • Herberts C.
      • et al.
      Identification of hypermutation and defective mismatch repair in ctDNA from metastatic prostate cancer.
      ,
      • Abida W.
      • Cheng M.L.
      • Armenia J.
      • et al.
      Analysis of the prevalence of microsatellite instability in prostate cancer and response to immune checkpoint blockade.
      In the SU2C-PCF, 3 cases of MSH2 (2%) and 1 case of MLH1 (0.7%) mutations have been reported, corresponding to hypermutated tumors with high tumor mutational burden (TMB).
      • Robinson D.
      • Van Allen E.M.
      • Wu Y.M.
      • et al.
      Integrative clinical genomics of advanced prostate cancer.
      In the PCa cohort analyzed by FoundationOneCDx assay, 4% of the cases harbored alterations in MMR genes (most frequently in MSH2 and MSH6, followed by MLH1 und PMS2) and 0.1% in POLE (V411 E).
      • Chung J.H.
      • Dewal N.
      • Sokol E.
      • et al.
      Prospective comprehensive genomic profiling of primary and metastatic prostate tumors.
      In a cohort of 433 patients with mPCa, who underwent liquid biopsy with targeted cell-free DNA (cfDNA) sequencing, pathogenic mutations in MSH2 or MSH6 were uncovered in 2.3% of the cases.
      • Ritch E.
      • Fu S.Y.F.
      • Herberts C.
      • et al.
      Identification of hypermutation and defective mismatch repair in ctDNA from metastatic prostate cancer.

      Germline Alterations

      Main germline alterations reported in PCa involve DDR and MMR genes. In the SU2C-PCF cohort, germline alterations in DDR genes were found in 8% of the patients, most frequently BRCA2 mutations (5.3%), followed by ATM (1.3%) and BRCA1 (0.7%).
      • Robinson D.
      • Van Allen E.M.
      • Wu Y.M.
      • et al.
      Integrative clinical genomics of advanced prostate cancer.
      In a study including 3607 men diagnosed with PCa and who received germline testing, germline variants associated with PCa were identified in 17.2% of patients,
      • Nicolosi P.
      • Ledet E.
      • Yang S.
      • et al.
      Prevalence of germline variants in prostate cancer and implications for current genetic testing guidelines.
      with most frequent alterations found in BRCA2 (4.7%), CHEK2 (2.9%), MUTYH (2.4%), and ATM (2.0%). In this study distinct assays had been used, covering between 2 and 80 genes. Alterations in HOXB13 were reported in 1.1%, and in MMR genes (MLH1, MSH2, MSH6 and PMS2), in 1.7% of the patients. Screening for germline alterations across 20 DDR genes in a cohort of 692 unselected patients with mPCa uncovered pathogenic mutations involving 16 genes in 11.8% of the studied cohort, with most frequent alterations in BRCA2 (5.3%), ATM (1.6%), CHEK2 (1.9%), and BRCA1 (0.9%).
      • Pritchard C.C.
      • Mateo J.
      • Walsh M.F.
      • et al.
      Inherited DNA-repair gene mutations in men with metastatic prostate cancer.
      When compared with metastatic cohorts, the frequency of germline alterations in localized PCa (TCGA) was 4.6%.
      The molecular taxonomy of primary prostate cancer.

      The role of genomic testing in localized and advanced prostate cancer

      Gene Expression Assays for Risk Stratification in Localized Prostate Cancer

      For localized PCa, active surveillance is recommended for patients with very-low-risk and most patients with low-risk PCa.
      • Schaeffer E.
      • Srinivas S.
      • Antonarakis E.S.
      • et al.
      NCCN guidelines insights: prostate cancer, version 1.2021.
      Several studies have shown that in addition to clinical and pathologic features, gene expression assays can improve risk stratification for localized PCa.
      • Cullen J.
      • Rosner I.L.
      • Brand T.C.
      • et al.
      A biopsy-based 17-gene genomic prostate score predicts recurrence after radical prostatectomy and adverse surgical pathology in a racially diverse population of men with clinically low- and intermediate-risk prostate cancer.
      • Cooperberg M.R.
      • Simko J.P.
      • Cowan J.E.
      • et al.
      Validation of a Cell-cycle progression gene panel to improve risk stratification in a contemporary prostatectomy cohort.
      • Cuzick J.
      • Stone S.
      • Fisher G.
      • et al.
      Validation of an RNA cell cycle progression score for predicting death from prostate cancer in a conservatively managed needle biopsy cohort.
      ,
      • Kim H.L.
      • Li P.
      • Huang H.-C.
      • et al.
      Validation of the Decipher Test for predicting adverse pathology in candidates for prostate cancer active surveillance.
      ,
      • Klein E.A.
      • Haddad Z.
      • Yousefi K.
      • et al.
      Decipher genomic classifier measured on prostate biopsy predicts metastasis risk.
      Based on this, these assays have been integrated into the routine assessment and therapeutic decision making for localized PCa.
      • Eggener S.E.
      • Rumble R.B.
      • Armstrong A.J.
      • et al.
      Molecular biomarkers in localized prostate cancer: ASCO guideline.
      Five gene expression assays are commercially available: Decipher, Decipher PORTOS, Oncotype Dx Genomic Prostate Score (GPS), Prolaris, and ProMark.
      • Eggener S.E.
      • Rumble R.B.
      • Armstrong A.J.
      • et al.
      Molecular biomarkers in localized prostate cancer: ASCO guideline.
      Decipher is a 22 gene-expression assay suitable for formalin-fixed paraffin-embedded (FFPE), both PCa biopsy and prostatectomy material,
      • Feng F.Y.
      • Huang H.C.
      • Spratt D.E.
      • et al.
      Validation of a 22-gene genomic classifier in patients with recurrent prostate cancer: an ancillary study of the NRG/RTOG 9601 randomized clinical trial.
      which was developed based on an originally whole-transcriptome panel.
      • Erho N.
      • Crisan A.
      • Vergara I.A.
      • et al.
      Discovery and validation of a prostate cancer genomic classifier that predicts early metastasis following radical prostatectomy.
      In a prospective registry of 855 patients receiving PCa biopsy, high-risk scores on the Decipher Biopsy test predicted shorter time to treatment in patients undergoing active surveillance and shorter time to treatment failure in patients receiving local treatment.
      • Vince R.A.
      • Jiang R.
      • Qi J.
      • et al.
      Impact of Decipher Biopsy testing on clinical outcomes in localized prostate cancer in a prospective statewide collaborative.
      In the post-RP setting, the prognostic value of Decipher has been assessed within the NRG/RTOG 9601 trial, which randomized patients with PCa with biochemical recurrence and pT3N0 or pT2N0 disease with positive margins, to receive salvage radiotherapy with placebo versus salvage radiotherapy with antiandrogen therapy (bicalutamide for 2 years).
      • Feng F.Y.
      • Huang H.C.
      • Spratt D.E.
      • et al.
      Validation of a 22-gene genomic classifier in patients with recurrent prostate cancer: an ancillary study of the NRG/RTOG 9601 randomized clinical trial.
      ,
      • WU Shipley
      • Seiferheld W.
      • Lukka H.R.
      • et al.
      Radiation with or without antiandrogen therapy in recurrent prostate cancer.
      The analysis of 352 RP samples from this study using the Decipher classifier showed that the test was independently prognostic for distant metastasis, PCa-specific mortality, and OS, when used as a continuous score (0 to 1.0), or following a risk category classification.
      • Feng F.Y.
      • Huang H.C.
      • Spratt D.E.
      • et al.
      Validation of a 22-gene genomic classifier in patients with recurrent prostate cancer: an ancillary study of the NRG/RTOG 9601 randomized clinical trial.
      In addition, this study suggested that patients with lower Decipher scores derived little or no benefit from the addition of antiandrogen therapy to salvage radiotherapy, whereas those patients with higher Decipher scores obtained much more benefit from the antiandrogen therapy. Moreover, a meta-analysis including 5 retrospective studies and a total of 855 patients evaluated the prognostic role of Decipher post-RP, and confirmed that the test can successfully predict the 10-year metastasis risk.
      • Spratt D.E.
      • Yousefi K.
      • Deheshi S.
      • et al.
      Individual Patient-level meta-analysis of the performance of the decipher genomic classifier in high-risk men after prostatectomy to predict development of metastatic disease.
      As a consequence of these studies, the National Comprehensive Cancer Network (NCCN) guidelines now recommend consideration of Decipher testing to aid decision making in the postoperative setting.
      • Schaeffer E.
      • Srinivas S.
      • Antonarakis E.S.
      • et al.
      NCCN guidelines insights: prostate cancer, version 1.2021.
      Another complementary test, the Decipher PORTOS score, covers 24 genes and was validated in a matched retrospective study, which demonstrated that high PORTOS scores were significantly associated with decreased 10-year metastasis risk in patients who received postoperative radiotherapy compared with those who did not; conversely, low PORTOS scores were not associated with any difference in metastases rates based on treatment with postoperative radiotherapy.
      • Zhao S.G.
      • Chang S.L.
      • Spratt D.E.
      • et al.
      Development and validation of a 24-gene predictor of response to postoperative radiotherapy in prostate cancer: a matched, retrospective analysis.
      Therefore, Decipher PORTOS is the only genomic classifier with predictive value regarding response to adjuvant or salvage radiotherapy.
      • Eggener S.E.
      • Rumble R.B.
      • Armstrong A.J.
      • et al.
      Molecular biomarkers in localized prostate cancer: ASCO guideline.
      Oncotype DX GPS is another gene-expression panel consisting of 12 PCa-related and 5 housekeeping genes (score 0 to 100), suitable for formalin-fixed biopsy material. This assay has been assessed in a cohort of 431 low- to intermediate-risk PCa biopsies, showing correlation with adverse pathologic features (Grade Group ≥ 3 or extraprostatic extension), biochemical recurrence, and risk of metastasis.
      • Cullen J.
      • Rosner I.L.
      • Brand T.C.
      • et al.
      A biopsy-based 17-gene genomic prostate score predicts recurrence after radical prostatectomy and adverse surgical pathology in a racially diverse population of men with clinically low- and intermediate-risk prostate cancer.
      However, a more recent study in a large prospective cohort of 432 patients treated with active surveillance failed to validate the GPS test, and suggested that adding GPS to a model containing Prostate-specific antigen (PSA) kinetics and diagnostic Gleason grading did not significantly improve stratification of risk for adverse pathology over the clinical variables alone.
      • Lin D.W.
      • Zheng Y.
      • McKenney J.K.
      • et al.
      17-gene genomic prostate score test results in the canary prostate active surveillance study (PASS) cohort.
      Prolaris is a broader gene-expression panel including 31 cell cycle-related and 5 housekeeping genes, which can be performed on FFPE material and has shown prognostic value when applied to biopsies and RP samples, being able to predict 10-year metastatic risk after RP and PCa-specific mortality after conservative treatment.
      • Cooperberg M.R.
      • Simko J.P.
      • Cowan J.E.
      • et al.
      Validation of a Cell-cycle progression gene panel to improve risk stratification in a contemporary prostatectomy cohort.
      ,
      • Cuzick J.
      • Stone S.
      • Fisher G.
      • et al.
      Validation of an RNA cell cycle progression score for predicting death from prostate cancer in a conservatively managed needle biopsy cohort.
      ,
      • Eggener S.E.
      • Rumble R.B.
      • Armstrong A.J.
      • et al.
      Molecular biomarkers in localized prostate cancer: ASCO guideline.
      The NCCN guidelines propose the use of Decipher or Prolaris to support risk assessment in patients with unfavorable intermediate- to high-risk localized PCa and a life expectancy of at least 10 years, and allow the use of any of the 3 tests (Decipher, Prolaris, or Oncotype DX Prostate) for patients with low to favorable intermediate risk.
      • Schaeffer E.
      • Srinivas S.
      • Antonarakis E.S.
      • et al.
      NCCN guidelines insights: prostate cancer, version 1.2021.
      ProMark is an 8 protein-based assay, which showed ability to predict adverse pathologic features (Grade Group ≥ 2 or T ≥ 3b) when applied to PCa biopsies.
      • Blume-Jensen P.
      • Berman D.M.
      • Rimm D.L.
      • et al.
      Development and clinical validation of an in situ biopsy-based multimarker assay for risk stratification in prostate cancer.

      Genomic Instability Assays to Assess Homologous Recombination Deficiency

      To date a limited number of studies have evaluated the role of HRD scores in PCa as a predictive biomarker of response to PARP inhibitors or platin-based chemotherapy. For ovarian cancer, Myriad Genetics MyChoice CDx is the only US Food and Drug Administration (FDA)-approved test developed to assess HRD. This assay calculates a genomic instability score (GIS) taking into account genomewide loss of heterozygosity (LOH), telomeric allelic imbalance, and large-scale state transitions, with a score greater than or equal to 42 classified as high. In addition, the assay detects variants and large rearrangements in BRCA1 and BRCA2.
      • Patel J.N.
      • Braicu I.
      • Timms K.M.
      • et al.
      Characterisation of homologous recombination deficiency in paired primary and recurrent high-grade serous ovarian cancer.
      GIS analysis has been performed in a cohort of 557 localized PCas, and showed that patients with BRCA2 alterations and higher HRD scores had longer progression-free survival (PFS) on olaparib.
      • Lotan T.L.
      • Kaur H.B.
      • Salles D.C.
      • et al.
      Homologous recombination deficiency (HRD) score in germline BRCA2- versus ATM-altered prostate cancer.
      Interestingly, tumors with alterations in ATM and CHEK2 had lower scores when compared with BRCA2-altered samples.
      • Lotan T.L.
      • Kaur H.B.
      • Salles D.C.
      • et al.
      Homologous recombination deficiency (HRD) score in germline BRCA2- versus ATM-altered prostate cancer.
      TruSight Oncology 500 HRD test is a recently developed assay, combining targeted NGS (Illumina TruSight Oncology 500) with Myriad HRD assay. Illumina TruSight Oncology 500 interrogates for single nucleotide variants, deletions, insertions, and copy number variants in a total of 523 genes, as well as for fusions in 55 genes, providing also information on MSI status and TMB. The combined assay showed high agreement with the results of Myriad MyChoice CDx Plus regarding presence of BRCA mutations and GIS in ovarian cancer.
      • Weichert W.
      • Qiu P.
      • Lunceford J.
      • et al.
      Assessing homologous recombination deficiency (HRD) in ovarian cancer: Optimizing concordance of the regulatory-approved companion diagnostic and a next-generation sequencing (NGS) assay kit.
      FoundationOneCDx assay provides information on genomic LOH (gLOH) score. This score is calculated as percentage of LOH genome, with gLOH of 16 or higher considered as “LOH high.” FoundationOneCDx assay has been used for tumor tissue testing in the PROFound phase 3 trial, which compared the efficacy of treatment with olaparib versus physician’s choice in patients with mCRPC with alterations in HRD-related genes who progressed to a previous treatment with ARSI, showing prolonged PFS and OS for patients with BRCA1, BRCA2, and ATM alterations.
      • de Bono J.
      • Mateo J.
      • Fizazi K.
      • et al.
      Olaparib for metastatic castration-resistant prostate cancer.
      ,
      • Hussain M.
      • Mateo J.
      • Fizazi K.
      • et al.
      Survival with olaparib in metastatic castration-resistant prostate cancer.
      In a cohort of 3476 PCas molecularly characterized using the FoundationOneCDx assay,
      • Chung J.H.
      • Dewal N.
      • Sokol E.
      • et al.
      Prospective comprehensive genomic profiling of primary and metastatic prostate tumors.
      gLOH scores were high in tumors harboring BRCA1, BRCA2, ATR, and FANCA alterations, whereas only a minority of CDK12-altered tumors presented a high score.
      • Chung J.H.
      • Dewal N.
      • Sokol E.
      • et al.
      Prospective comprehensive genomic profiling of primary and metastatic prostate tumors.
      Classifier of Homologous Recombination Deficiency (CHORD) is a genome-wide random forest-based approach, developed to detect tumor chromosomal instability.
      • Nguyen L.
      • Martens J W.M.
      • Van Hoeck A.
      • et al.
      Pan-cancer landscape of homologous recombination deficiency.
      In a cohort of 3504 solid tumors, analyzed by WGS, the CHORD was able to distinguish between “BRCA1-like” (BRCA1 alterations) and “BRCA2-like” (BRCA2, PALB2, and RAD51 C alterations) phenotypes.
      • Nguyen L.
      • Martens J W.M.
      • Van Hoeck A.
      • et al.
      Pan-cancer landscape of homologous recombination deficiency.
      Another supervised learning algorithm, HRDetect, is a lasso logistic regression model developed to identify BRCA1 and BRCA2 mutational signatures in breast cancer tumors.
      • Davies H.
      • Glodzik D.
      • Morganella S.
      • et al.
      HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures.
      ,
      • Sztupinszki Z.
      • Diossy M.
      • Krzystanek M.
      • et al.
      Detection of molecular signatures of homologous recombination deficiency in prostate cancer with or without BRCA1/2 mutations.
      This algorithm, applied to a cohort of 311 PCa samples analyzed by WGS, correctly discriminated samples with biallelic BRCA1/2 mutations, as well as identified further BRCA1/2 nonmutant cases with a high HRDetect scores (>0.7). HRDetect showed lower specificity when applied to WES data from the same cohort.
      • Sztupinszki Z.
      • Diossy M.
      • Krzystanek M.
      • et al.
      Detection of molecular signatures of homologous recombination deficiency in prostate cancer with or without BRCA1/2 mutations.

      Microsatellite Instability Testing

      Alterations in MMR genes have been reported in 4% to 5% of mCRPC.
      • Robinson D.
      • Van Allen E.M.
      • Wu Y.M.
      • et al.
      Integrative clinical genomics of advanced prostate cancer.
      ,
      • Abida W.
      • Cyrta J.
      • Heller G.
      • et al.
      Genomic correlates of clinical outcome in advanced prostate cancer.
      ,
      • Chung J.H.
      • Dewal N.
      • Sokol E.
      • et al.
      Prospective comprehensive genomic profiling of primary and metastatic prostate tumors.
      MSI status has been classically assessed by IHC for MLH1, MSH2, MSH6, and PMS2 proteins.
      • Lynch H.T.
      • Snyder C.L.
      • Shaw T.G.
      • et al.
      Milestones of Lynch syndrome: 1895–2015.
      • Hampel H.
      • Frankel W.L.
      • Martin E.
      • et al.
      Screening for the lynch syndrome (hereditary nonpolyposis colorectal cancer).
      • Lindor N.M.
      • Burgart L.J.
      • Leontovich O.
      • et al.
      Immunohistochemistry versus microsatellite instability testing in phenotyping colorectal tumors.
      For IHC scoring, a product of intensity of the staining (0–3) and percentage of positive cells (0–3, 0 [0%], 1 [1%–33%], 2 [34%–66%], and 3 [67%–100%]) is calculated, with a product score of 3 or less classified as “loss of protein expression.”
      • Lee J.H.
      • Cragun D.
      • Thompson Z.
      • et al.
      Association between IHC and MSI testing to identify mismatch repair-deficient patients with ovarian cancer.
      An alternative strategy is to assess MSI status by sequencing of specific microsatellite (or tandem repeats) loci using polymerase chain reaction (PCR). With this approach, panels of 5 (Bethesda,
      • Boland C.R.
      • Thibodeau S.N.
      • Hamilton S.R.
      • et al.
      A National Cancer Institute Workshop on Microsatellite Instability for cancer detection and familial predisposition: development of international criteria for the determination of microsatellite instability in colorectal cancer.
      OncoMate MSI Dx Analysis System
      • Bacher J.W.
      • Flanagan L.A.
      • Smalley R.L.
      • et al.
      Development of a fluorescent multiplex assay for detection of MSI-high tumors.
      ) to 8 (LMR MSI Analysis System
      • Lin J.H.
      • Chen S.
      • Pallavajjala A.
      • et al.
      Validation of long mononucleotide repeat markers for detection of microsatellite instability.
      ) microsatellite loci have been developed. In colorectal cancer (CRC), MSI-H detection by IHC has shown a 91.9% agreement with the detection by PCR, with high negative predictive and low positive predictive values, when compared with PCR.
      • Chen M.L.
      • Chen J.Y.
      • Hu J.
      • et al.
      Comparison of microsatellite status detection methods in colorectal carcinoma.
      Over the past years, NGS approach has enabled parallel assessment of multiple microsatellite loci.
      • Hempelmann J.A.
      • Lockwood C.M.
      • Konnick E.Q.
      • et al.
      Microsatellite instability in prostate cancer by PCR or next-generation sequencing.
      Most of these NGS panels have been optimized for CRC (MSIPlus,
      • Hempelmann J.A.
      • Scroggins S.M.
      • Pritchard C.C.
      • et al.
      MSIplus for integrated colorectal cancer molecular testing by next-generation sequencing.
      ColoSeq
      • Pritchard C.C.
      • Smith C.
      • Salipante S.J.
      • et al.
      ColoSeq provides comprehensive lynch and polyposis syndrome mutational analysis using massively parallel sequencing.
      ). In a cohort of 91 PCas, with MSI status additionally tested by deep targeted sequencing of the MMR genes, 5-marker PCR panel had a sensitivity of 72.4% and a specificity of 100%, and larger NGS panels (>60 markers) showed a sensitivity of 93.1% and a specificity of 98.4%.
      • Hempelmann J.A.
      • Lockwood C.M.
      • Konnick E.Q.
      • et al.
      Microsatellite instability in prostate cancer by PCR or next-generation sequencing.
      MSIsensor is an algorithm developed to detect somatic microsatellite alterations from paired normal-tumor-targeted NGS data.
      • Middha S.
      • Zhang L.
      • Nafa K.
      • et al.
      Reliable pan-cancer microsatellite instability assessment by using targeted next-generation sequencing data.
      ,
      • Niu B.
      • Ye K.
      • Zhang Q.
      • et al.
      MSIsensor: microsatellite instability detection using paired tumor-normal sequence data.
      A cohort of 1033 localized PCas and mPCas with available normal tumor NGS data (MSK-Impact)
      • Abida W.
      • Armenia J.
      • Gopalan A.
      • et al.
      Prospective genomic profiling of prostate cancer across disease states reveals germline and somatic alterations that may affect clinical decision making.
      has been analyzed with this algorithm, uncovering MSI-H or dMMR tumors in 3.1% of the cases, with 29.1% of these samples harboring pathogenic germline alterations in Lynch syndrome-related genes.
      • Abida W.
      • Cheng M.L.
      • Armenia J.
      • et al.
      Analysis of the prevalence of microsatellite instability in prostate cancer and response to immune checkpoint blockade.
      Half of these patients with MSI-H/dMMR showed more than 50% PSA declines under anti-PD1/PD-L1 ICIs.
      • Abida W.
      • Cheng M.L.
      • Armenia J.
      • et al.
      Analysis of the prevalence of microsatellite instability in prostate cancer and response to immune checkpoint blockade.
      MSI status in PCa can be also evaluated by liquid biopsy and cfDNA analysis (Guardant360 CDx,
      • Barata P.
      • Agarwal N.
      • Nussenzveig R.
      • et al.
      Clinical activity of pembrolizumab in metastatic prostate cancer with microsatellite instability high (MSI-H) detected by circulating tumor DNA.
      FoundationOne Liquid CDx
      • Trujillo B.
      • Wu A.
      • Wetterskog D.
      • et al.
      Blood-based liquid biopsies for prostate cancer: clinical opportunities and challenges.
      ) (Table 1).
      Table 1Summary of available homologous recombination deficiency and microsatellite instability tissue-based assays
      MethodAssay/Analysis MethodScore and ThresholdInterpretation
      HRD tumor testing
       Targeted NGSMyriad Genetics MyChoice CDx
      • LOH + LST + TAI (threshold ≥ 42)
      • Variants and large rearrangements in 15 genes (ATM, BARD1, BRCA1, BRCA2, BRIP1, CDK12, CHEK1, CHEK2, FANCL, PALB2, PPP2R2A, RAD51 B, RAD51 C, RAD51D, and RAD54 L).
      • GIS
      • Pathogenicity of variants
      Myriad Genetics MyChoice CDx Plus
      • LOH + LST + TAI (threshold ≥ 42)
      • Variants and large rearrangements in BRCA1 and BRCA2
      • GIS
      • Pathogenicity of variants
      TruSight Oncology 500 HRD
      • SNV, indels, CNV in 523 genes, rearrangements in 55 genes
      • MSI and TMB
      • LOH + LST + TAI (threshold ≥ 42)
      • Genomic alterations
      • MSI and TMB
      • GIS
      FoundationOneCDx
      • SNV, indels, CNV in 324 genes, rearrangements in selected genes
      • MSI and TMB
      • gLOH ≥ 16
      • Genomic alterations
      • MSI and TMB
      • gLOH low/high
       Genome-wide NGS (WGS, WES)CHORD
      • Biallelic loss (deep deletion), presence of LOH, pathogenicity of variants
      • Threshold ≥ 0.5
      • Probability of BRCA1/2 deficiency
      • HRD
      HRDetect
      • Mutational signatures analysis, HRD index score, analysis of variants in BRCA1/2 and other HRR-related genes
      • Threshold > 0.7
      • Probability of BRCA1/2 deficiency
      • HRD
      MSI testing
       IHC of MMR proteinsMLH1, MSH2, MSH6, and PMS2
      • Intensity of staining: 0–3
      • Percentage of positivity: 0–3
      • Product score (threshold ≤ 3)
      • Loss of MMR protein expression (dMMR)
       PCR of microsatellitesBethesda panel
      • 5 microsatellite markers: 2 mononucleotide (Bat25, Bat26) and 3 dinucleotide (D2S123, D5S346, and D17S250)
      • Threshold: ≥ 2 markers positive for shifts in the allelic bands
      • MSS
      • MSI-L (1 marker)
      • MSI-H (≥ 2 markers)
      MSI Analysis System Version 1.2/OncoMate MSI Dx Analysis System
      • 5 SMR markers (BAT-25, BAT-26, NR-21, NR-24, and MONO-27) and 2 pentanucleotide repeat markers (Penta C and Penta D)
      • Threshold: ≥ 2 markers positive for shifts in the allelic bands
      • MSS
      • MSI-L (1 marker)
      • MSI-H (≥ 2 markers)
      LMR MSI Analysis System
      • 4 SMR markers (BAT-25, BAT-26, NR-21, and MONO-27), 4 LMR markers (BAT-52, BAT-56, BAT-59, and BAT-60), and 2 pentanucleotide repeat markers (Penta C and Penta D)
      • Threshold: ≥ 3 markers positive for shifts in the allelic bands
      • MSS
      • MSI-L (1–2 markers)
      • MSI-H (≥ 3 markers)
       NGSMSIPlus
      • Optimized for CRC
      • 16 microsatellite markers and hotspots in KRAS, NRAS, and BRAF
      • MSI-H (following mSINGS score)
      ColoSeq
      • Optimized for CRC
      • SNV, deletions or rearrangements in MMR-related genes (MLH1, MSH2, MSH6, PMS2, EPCAM, APC, MUTYH) and 24 additional genes
      • Variant interpretation
      NGS-targeted panels including MMR genes (eg, MSK-Impact)
      • MSISensor score ≥ 10
      • MSI-H
       Targeted sequencing of MMR genesAny NGS-targeted panel covering MMR genes
      • SNV, indels, CNV in MMR genes
      • Variant interpretation
      Abbreviations: CNV, copy number variations; LMR, long mononucleotide repeats; LST, large-scale transitions; MSI-L, MSI-low; MSS, microsatellite stable; SMR, single mononucleotide repeats; SNV, single nucleotide variants; TAI, telomeric allelic imbalance; TMB, tumor mutational burden.

      Germline Homologous Recombination Deficiency Testing

      In the PROfound phase 3 study,
      • de Bono J.
      • Mateo J.
      • Fizazi K.
      • et al.
      Olaparib for metastatic castration-resistant prostate cancer.
      BRCAanalysis CDx identified germline BRCA1/2 alterations in blood samples of the 16% of the included patients. This HRD germline population constituted 53.5% of all patients with tumor BRCA1/2 alterations in the study. When considering the 62 evaluable patients with a positive BRCAanalysis CDx test for germline BRCA1/2 alterations, their PFS was 10.12 versus 1.87 months for olaparib versus physician’s choice (hazard ratio, 0.08, P < 0.0001)., For tumor tissue testing, FoundationOneCDx assay was used in the study.
      • de Bono J.
      • Mateo J.
      • Fizazi K.
      • et al.
      Olaparib for metastatic castration-resistant prostate cancer.
      Myriad’s BRACAnalysis CDx is currently FDA approved for patients with ovarian, breast, and pancreatic cancers and PCa who meet criteria for germline testing to identify pathogenic BRCA1 and BRCA2 mutations. For PCa, the NCCN guidelines recommend germline testing for patients with personal history of PCa, diagnosed at any age and starting from high-risk localized stage, as well as for patients with familiar history of PCa (Table 2). It is recommended that germline panels include the Lynch syndrome-related genes MLH1, MSH2, MSH6, and PMS2, and the HRD genes BRCA1, BRCA2, ATM, PALB2, and CHEK2.
      • Schaeffer E.
      • Srinivas S.
      • Antonarakis E.S.
      • et al.
      NCCN guidelines insights: prostate cancer, version 1.2021.
      Other genes, such as HOXB13, should also be considered.
      • Schaeffer E.
      • Srinivas S.
      • Antonarakis E.S.
      • et al.
      NCCN guidelines insights: prostate cancer, version 1.2021.
      ,
      • Giri V.N.
      • Knudsen K.E.
      • Kelly W.K.
      • et al.
      Implementation of germline testing for prostate cancer: philadelphia prostate cancer consensus conference 2019.
      Table 2National Comprehensive Cancer Network guidelines recommendation for germline testing in patients with diagnosis of prostate cancer

      Discussion

      Over the past years, tumor molecular characterization has been progressively integrated into the clinical management of patients with localized PCa and mPCa.
      • Schaeffer E.
      • Srinivas S.
      • Antonarakis E.S.
      • et al.
      NCCN guidelines insights: prostate cancer, version 1.2021.
      For localized PCa, multiple pretreatment risk stratification algorithms are available based on clinical and pathologic features (eg, GS, PSA level, clinical T stage).
      • Zelic R.
      • Garmo H.
      • Zugna D.
      • et al.
      Predicting prostate cancer death with different pretreatment risk stratification tools: a head-to-head comparison in a nationwide cohort study.
      For patients with biopsied PCas and NCCN low to favorable intermediate risk, genomic classifiers, independently or in combination with multiparametric MRI,
      • Salmasi A.
      • Said J.
      • Shindel A.W.
      • et al.
      A 17-gene genomic prostate score assay provides independent information on adverse pathology in the setting of combined multiparametric magnetic resonance imaging fusion targeted and systematic prostate biopsy.
      can help identify better candidates for active surveillance, although further validation is needed for some of these classifiers.
      • Schaeffer E.
      • Srinivas S.
      • Antonarakis E.S.
      • et al.
      NCCN guidelines insights: prostate cancer, version 1.2021.
      ,
      • Eggener S.E.
      • Rumble R.B.
      • Armstrong A.J.
      • et al.
      Molecular biomarkers in localized prostate cancer: ASCO guideline.
      For patients who have biochemical recurrence after RP, the NCCN guidelines recommend that physicians consider adding androgen deprivation therapy (ADT) to salvage radiotherapy for patients; the use of genomic classifiers such as Decipher may help identify patients most likely to benefit from the addition of ADT to salvage radiotherapy in this setting. Across the spectrum of localized PCa, several gene expression classifiers are available as prognostic tools to aid in risk stratification for clinical decision making.
      For advanced PCa, recent advances in targeted therapeutic approaches have increased the clinical need to screen mPCa tumors for targetable molecular alterations. Most relevant therapeutic advances have been made for DDR
      • de Bono J.
      • Mateo J.
      • Fizazi K.
      • et al.
      Olaparib for metastatic castration-resistant prostate cancer.
      • Mateo J.
      • Porta N.
      • Bianchini D.
      • et al.
      Olaparib in patients with metastatic castration-resistant prostate cancer with DNA repair gene aberrations (TOPARP-B): a multicentre, open-label, randomised, phase 2 trial.
      • Carreira S.
      • Porta N.
      • Arce-Gallego S.
      • et al.
      Biomarkers associating with PARP inhibitor benefit in prostate cancer in the TOPARP-B trial.
      and MSI-H tumors,
      • Le D.T.
      • Uram J.N.
      • Wang H.
      • et al.
      PD-1 blockade in tumors with mismatch-repair deficiency.
      ,
      • Le D.T.
      • Durham J.N.
      • Smith K.N.
      • et al.
      Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade.
      as well as CDK12-altered PCas.
      • Antonarakis E.S.
      • Velho P.I.
      • Fu W.
      • et al.
      CDK12-altered prostate cancer: clinical features and therapeutic outcomes to standard systemic therapies, poly (ADP-Ribose) polymerase inhibitors, and PD-1 inhibitors.
      However, despite these relevant advances, targeted treatment with PARP inhibitors and immunotherapy is successful only in a subset of DDR,
      • Carreira S.
      • Porta N.
      • Arce-Gallego S.
      • et al.
      Biomarkers associating with PARP inhibitor benefit in prostate cancer in the TOPARP-B trial.
      MSI-H,
      • Abida W.
      • Cheng M.L.
      • Armenia J.
      • et al.
      Analysis of the prevalence of microsatellite instability in prostate cancer and response to immune checkpoint blockade.
      and CDK12-altered PCas,
      • Antonarakis E.S.
      • Velho P.I.
      • Fu W.
      • et al.
      CDK12-altered prostate cancer: clinical features and therapeutic outcomes to standard systemic therapies, poly (ADP-Ribose) polymerase inhibitors, and PD-1 inhibitors.
      ,
      • Rescigno P.
      • Gurel B.
      • Pereira R.
      • et al.
      Characterizing CDK12-mutated prostate cancers.
      and further development and validation of solid predictive biomarkers is needed. For instance, distinct HRD genotypes harbor different degrees of sensitivities to PARP inhibitors.
      • de Bono J.
      • Mateo J.
      • Fizazi K.
      • et al.
      Olaparib for metastatic castration-resistant prostate cancer.
      ,
      • Carreira S.
      • Porta N.
      • Arce-Gallego S.
      • et al.
      Biomarkers associating with PARP inhibitor benefit in prostate cancer in the TOPARP-B trial.
      Beyond germline alterations in BRCA1 and BRCA2, biomarker analysis from the TOPAR-B phase 2 trial showed that PCas with homozygous BRCA2 and PALB2 deficiency, as well as tumors with loss of ATM protein expression, had most benefit from treatment with olaparib.
      • Carreira S.
      • Porta N.
      • Arce-Gallego S.
      • et al.
      Biomarkers associating with PARP inhibitor benefit in prostate cancer in the TOPARP-B trial.
      In ovarian cancer, first-line maintenance treatment with olaparib in combination with bevacizumab is indicated for patients with HRD tumors assessed by Myriad Genetics MyChoice CDx, based on the results of the PAOLA-1 phase 3 trial.
      • Ray-Coquard I.
      • Pautier P.
      • Pignata S.
      • et al.
      Olaparib plus bevacizumab as first-line maintenance in ovarian cancer.
      In PCa, still limited studies are available correlating GIS score with efficacy of PARP inhibitors.
      • de Bono J.
      • Mateo J.
      • Fizazi K.
      • et al.
      Olaparib for metastatic castration-resistant prostate cancer.
      ,
      • Lotan T.L.
      • Kaur H.B.
      • Salles D.C.
      • et al.
      Homologous recombination deficiency (HRD) score in germline BRCA2- versus ATM-altered prostate cancer.
      For MSI-H/dMMR tumors, the KEYNOTE-158 phase 2 study assessed the efficacy of pembrolizumab in distinct MSI-H/dMMR tumor entities, including 6 patients with mPCa, showing an overall response rate of 34.3% and a median OS of 23.5 months (95% confidence interval, 13.5–not reached) for the entire study cohort.
      • Marabelle A.
      • Le D.T.
      • Ascierto P.A.
      • et al.
      Efficacy of pembrolizumab in patients with noncolorectal high microsatellite instability/mismatch repair–deficient cancer: results from the phase II KEYNOTE-158 study.
      MSI status was assessed either by IHC or 5 microsatellite loci PCR panel.
      • Marabelle A.
      • Le D.T.
      • Ascierto P.A.
      • et al.
      Efficacy of pembrolizumab in patients with noncolorectal high microsatellite instability/mismatch repair–deficient cancer: results from the phase II KEYNOTE-158 study.
      Based on this and other studies, pembrolizumab is currently approved for MSI-H/dMMR mPCas, which progressed after at least 1 prior systemic treatment line. Moreover, for patients with uncovered pathogenic or likely pathogenic mutations in Lynch syndrome-associated genes, germline counseling and/or testing is recommended, as well as for patients with personal or familiar history of PCa (see Table 2). Clinical and molecular features of CDK12-altered mPCas have been analyzed in a retrospective study, which included 60 patients, 51.7% of them harboring a biallelic alteration in CDK12.
      • Antonarakis E.S.
      • Velho P.I.
      • Fu W.
      • et al.
      CDK12-altered prostate cancer: clinical features and therapeutic outcomes to standard systemic therapies, poly (ADP-Ribose) polymerase inhibitors, and PD-1 inhibitors.
      The study showed that CDK12-altered tumors had poor responses to ARSI and taxane-based chemotherapy, lack of response to PARP inhibitors, and variable responses to PD-1 inhibitors (pembrolizumab and nivolumab).
      • Antonarakis E.S.
      • Velho P.I.
      • Fu W.
      • et al.
      CDK12-altered prostate cancer: clinical features and therapeutic outcomes to standard systemic therapies, poly (ADP-Ribose) polymerase inhibitors, and PD-1 inhibitors.
      Mechanistically, the lack of response to PARP inhibitors of this molecular subtype of PCa has been correlated with a genomic instability phenotype distinct from HRD, characterized by tandem duplications and gene fusions.
      • Antonarakis E.S.
      • Velho P.I.
      • Fu W.
      • et al.
      CDK12-altered prostate cancer: clinical features and therapeutic outcomes to standard systemic therapies, poly (ADP-Ribose) polymerase inhibitors, and PD-1 inhibitors.
      Finally, recent studies have been assessing the role of liquid biopsy for molecular subtyping and identification of predictive biomarkers in advanced PCa.
      • Barata P.
      • Agarwal N.
      • Nussenzveig R.
      • et al.
      Clinical activity of pembrolizumab in metastatic prostate cancer with microsatellite instability high (MSI-H) detected by circulating tumor DNA.
      ,
      • Trujillo B.
      • Wu A.
      • Wetterskog D.
      • et al.
      Blood-based liquid biopsies for prostate cancer: clinical opportunities and challenges.
      ,
      • Herberts C.
      • Annala M.
      • Sipola J.
      • et al.
      Deep whole-genome ctDNA chronology of treatment-resistant prostate cancer.
      Surgical pathologists play a critical role in triaging tissue for molecular biomarker testing in PCa. It is important for pathologists to understand when biomarker testing may be appropriate, and how these tests are performed. Pathologists should be aware that preanalytic and histopathologic factors may affect these tests. Because these assays are validated only on FFPE specimens containing untreated PCa, specimens that were previously frozen or fixed in nonformalin fixatives should not be used for these tests. In addition, tumors that have been treated with radiation or ADT are not eligible for these assays. When choosing tissue for these tests, pathologists should pick the most representative tissue blocks with the highest Gleason grade and largest tumor volume. Pathologists should also make sure there is sufficient tumor in the tissue submitted for testing.

      Summary

      Molecular tumor profiling has gained relevance in personalized clinical management and precision oncology treatment of localized PCa and mPCa. Use of gene expression assays for genomic risk stratification can support decision algorithm regarding active surveillance or indication of intensification of therapy in localized PCa. For mPCa, tumor molecular characterization by NGS, as well as by assays assessing HRD and MSI status, are essential to predict benefit form molecularly targeted therapies, such as PARP inhibitors and immunotherapy. Moreover, because PCa tumor responses to targeted treatment are still highly heterogeneous, further development and validation of robust predictive biomarkers is required.

      Clinics care points

      • Molecular tumor testing is essential in metastatic PCa, in order to identify patients with targetable alterations, such as HRD and dMMR/MSI-H tumors.
      • Genomic classifiers may help identify patients most likely to benefit from the addition of ADT to radiotherapy in the biochemical recurrence setting.
      • Germline testing should be offered to patients with metastatic or nodal positive PCa, as well as to a subset of patients with high risk localized PCa.

      Acknowledgments

      The authors thank Dr Mariana Ricca at the University of Bern for editorial support. This work has been supported by funding from the following research foundations: SPHN SOCIBP, Krebsliga Schweiz ( Swiss Cancer League ), Nuovo-Soldati Foundation for Cancer Research , ISREC Fondation Recherche Cancer , and Werner and Hedy Berger-Janser Foundation . The figure 1 has been created using images from BioRender.com.

      Disclosure

      D. Akhoundova and. C.C. Pritchard declare no conflicts of interests. F.Y. Feng serves on the Scientific Advisory Board of Artera, BlueStar Genomics, SerImmune, and the Immuno-Oncology Program for Bristol Myers Squibb, and has consulted for Foundation Medicine, Tempus, Janssen, Astellas, Bayer, Myovant, Roivant, and Novartis. M.A. Rubin is a coinventor on patents in the area for diagnosis and therapy in prostate cancer for ETS fusions (University of Michigan and the Brigham and Women’s Hospital), SPOP mutations (Cornell University), and EZH2 (University of Michgian).

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