Background Methyl Methanesulfonate-Sensitivity Protein 22-Like (MMS22L) plays a key role in homology-directed DNA repair, and experimental models have shown that its loss confers sensitivity to Poly (ADP-ribose) polymerase inhibitors (PARPi). A rare germline loss-of-function founder mutation in MMS22L, F722fs (c.2164_2168del), was recently identified as a prostate cancer risk factor among individuals of Ashkenazi Jewish ancestry. The impact of this mutation on the disease course following prostate cancer diagnosis remains unclear. Here, we report the longitudinal outcomes of seven MMS22L F722fs carriers diagnosed with different stages of prostate cancer identified at the Brady Urological Institute at Johns Hopkins University.Methods We investigated the longitudinal outcomes of seven MMS22L F722fs carriers diagnosed with different stages of prostate cancer identified at the Brady Urological Institute.Results With a follow-up time ranging from 5 to 27 years, five of the seven patients who were initially treated with radical prostatectomy remain alive and disease-free, including two patients who had adjuvant and salvage therapies, and one patient who was cured after developing metastatic disease post-surgery. For the remaining two patients with metastatic prostate cancer at diagnosis, one patient responded to ADT for 11 years, and the other died of unknown causes 5 years after diagnosis. None of these patients received PARPi.Conclusions Although limited by its retrospective design and small cohort size, this series suggests the potential for exceptional outcomes in F722fs mutation carriers diagnosed with prostate cancer, despite the aggressive disease features and lack of treatment with PARPi. The findings also suggest that prostate cancer patients with this mutation may respond well to standard systemic treatments.

The NCCN Biomarkers Resource Committee (BRC) was established to provide molecular expertise and guidance related to key aspects of biomarker testing in NCCN publications. A key aim is to reduce inconsistencies and standardize biomarker testing terms and definitions for suggested use across all NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines). The key areas found to need terminology clarification and harmonization included those describing types of genomic events and testing approaches. For these areas, current professional society guidelines regarding terminology, utilization within current guidelines, and common parlance in practice were explored. Synonyms were also identified. Each area was discussed to nominate preferred (and, when applicable, nonpreferred) terminology with a rationale. The aims of this document are to define commonly used terms for clinical care providers and provide recommendations for the standardized use of this biomarker terminology within NCCN Guidelines and publications.

Prostate cancer with isocitrate dehydrogenase 1 (IDH1) or isocitrate dehydrogenase 2 (IDH2) mutation appears to be a unique molecular subclass, but its associated clinical features have not been previously described. Here, we performed a retrospective analysis of clinical and molecular features of prostate cancer with IDH1 p.R132 or IDH2 p.R172 mutations. A series of 99 IDH1-mutated and 12 IDH2-mutated cases was identified using genomics databases at multiple institutions. An IDH1/2 wild-type control cohort was generated with matched clinical features at diagnosis. IDH-mutated cases frequently presented with localized disease (91%), but exhibited high tumor stage (42% T3) and grade (54% grade group 5). Compared with matched controls, patients with IDH1 mutations exhibited longer overall survival (hazard ratio [HR], 0.16; 95% confidence interval [CI], 0.04-0.68; p = 0.01), metastasis-free survival (HR, 0.22; 95% CI, 0.09-0.58; p = 0.002), and progression-free survival on hormonal therapy (HR, 0.35; 95% CI, 0.16-0.76; p = 0.036). IDH1-mutant cases were enriched for concurrent activating mutations of FOXA1 and CTNNB1 and tended to lack TMPRSS2-ERG fusions, SPOP mutations, and RB1 alterations. IDH1 mutations were associated with global transcriptional repression and evidence of metabolic and epigenetic reprogramming. These results depict IDH-mutant prostate cancer as a subtype that can present with high tumor stage and grade, but is associated with favorable outcomes.

Supplementary Table S8. Difference in Median HLA Average H-score in Combined Cohorts by Race.

Primary cilia are increasingly recognized as regulators of cellular signaling and plasticity. Here, we examined their distribution and potential relevance in neuroendocrine (NE) prostate cancer. While typically absent in localized hormone-sensitive prostate tumor cells, we detected primary cilia in neuroendocrine-like cells both in vitro and in castration-resistant prostate cancer (CRPC) samples. In vivo, cilia were consistently observed in CRPC tumor cells exhibiting FDG-PET positivity and NE features, supporting an association between ciliogenesis, metabolic reprogramming, and disease progression. These aggressive tumors also displayed reduced mitochondrial activity, consistent with a shift away from oxidative metabolism. Building on our work in ccRCC, we identified a GLI1⁺/IFT20⁺ or GLI1⁺/IFT80⁺ signature enriched in ciliated, NE-prone subpopulations. In vitro, YAP1 inhibition alone did not induce ciliogenesis, whereas cytoskeletal remodeling with jasplakinolide restored cilium assembly and enabled partial NE transdifferentiation. Single-cell RNA-seq analyses further showed enrichment of ciliogenesis-related genes within NE clusters in CRPC. Together, these observations support a model in which primary cilia are closely associated with NE identity and metabolic adaptation, rather than serving solely as passive markers, and suggest a structural-metabolic axis that may represent a source of biomarkers and therapeutic vulnerabilities.

Supplementary Information 1. Post-workshop survey questions.

Background Renal cell neoplasms with FLCN mutations, classically seen in Birt-Hogg-Dubé (BHD) syndrome typically include oncocytoma, chromophobe RCC, and hybrid oncocytic/chromophobe tumors (HOCT). Recent studies have highlighted FLCN-mutated renal cell carcinomas (RCCs) with unclassified morphologies, raising diagnostic challenges. Methods We retrospectively identified renal tumors with FLCN mutations by targeted next-generation sequencing at our institution (2015-2024). Clinical records, tumor morphology, immunohistochemistry, and genomic profiles were reviewed. Results Seven patients were identified. Four exhibited unclassified morphologies with features overlapping with translocation RCC, as well as papillary RCC and eosinophilic solid and cystic (ESC) RCC. One clear cell RCC harbored a secondary probable germline FLCN mutation and TFEB locus amplification, while two were consistent with conventional oncocytic morphology. Germline FLCN mutation was confirmed in two patients with BHD syndrome. Recurrent copy number changes in these tumors included loss of 1p, 15q, 17p and 14q, and gain of 17q. CD117 and CK7 were negative to focal in majority of the cases, TFE3 showed diffuse to focal positivity, while GPNMB was diffusely positive in all 5 cases with material available. Clinical outcomes ranged from indolent disease to metastasis and late recurrence. Conclusions FLCN-mutated RCCs comprise a morphologically heterogeneous yet molecularly defined group. Conventional oncoytic morphology was associated with germline alterations while unclassified morphologies could be associated with somatic alterations and possibly germline mutations. FLCN mutations may also be incidental germline mutations in other RCC subtypes. Tumors with unclassified morphologies evoked morphological and immunohistochemical diagnostic consideration of other oncocytic and papillary RCCs and could be associated with adverse outcomes. Recognition may be aided by diffuse GPNMB expression, but definitive classification, especially in cases without conventional morphology, requires molecular testing. These findings broaden the spectrum of FLCN-driven tumors and support their distinction as a unique molecular entity.

Supplementary Table S7. Spearman Correlation Coefficients of Tumor HLA-I Average H-score with Tumor Immune Cell Densities.

Background Identification and characterization of prostate tumor markers differentially expressed in European American (EA) men vs African American (AA) men has been one of the focus areas positioned to understand and address prostate cancer disparity in the US. Whereas some genes are differentially expressed, validation studies are limited, and the impact of these expression differences on recurrence risk remains unclear.Methods This study focused on phospholipase A2 group 7 (PLA2G7) in prostate cancer surgical specimens from EA and AA patients. A nested case-control study was conducted to evaluate the prognostic value of the PLA2G7 protein while controlling for age, stage, and Gleason, followed by re-analysis of a published dataset of 556 EA and 596 AA prostate cancer patients. Expression signatures correlated with PLA2G7 were investigated in both patient populations.Results PLA2G7 was more frequently overexpressed in EA tumors than AA tumors, and higher tumor-specific PLA2G7 expression was associated with divergent outcomes: lower biochemical recurrence risk in EA men but elevated risk in AA men. Expression in noncancer tissues showed no prognostic value. Whereas androgen response signatures were consistently enriched in high-PLA2G7 tumors across both groups, immune and inflammatory response gene sets showed opposite enrichment trends between AA and EA men.Conclusion This study represents the first identification and validation of a tumor-specific marker that is both differentially expressed between prostate cancers in AA and EA men and demonstrates opposite prognostic effects based on self-reported race/ethnicity. The findings emphasize the importance of evaluating prostate tumor markers across diverse geographic ancestries.

Supplementary Figure 2. Example case 2.

Supplementary Figure S6: HLA Class I expression in the pN1 Cohort.

Figure S1. Inclusion flowchart, participants of the Health Professionals Follow-up Study (1986 to 2020) and Physicians’ Health Study (1982 to 2014) with prostate cancer and tumor tissue on tissue microarrays (TMAs).

Supplementary Figure S8: DNA methylation in HLA Class I genes and PTEN status.

Supplementary Table 1. Performance metrics for the ERG prediction model in the TCGA testing cohort. The table shows the model’s performance in the TCGA testing cohort consisting of 59 whole slide images using different thresholds derived from the training data. PPV: positive predictive value; NPV: negative predictive value; MCC: Matthews Correlation Coefficient. Supplementary Table 2. Performance metrics for the ERG prediction model in the natural history cohort. The table shows the model’s performance in the natural history cohort consisting of 314 whole slide images using different thresholds derived from the training data. PPV: positive predictive value; NPV: negative predictive value; MCC: Matthews Correlation Coefficient.

Figure S3. Cumulative-average prediagnostic dietary cholesterol.

Abstract Human leukocyte antigen class I (HLA-I) downregulation in prostate cancer may contribute to tumor immune evasion. We digitally quantified HLA-I protein expression in a cohort of racially diverse and molecularly characterized prostatectomy specimens, as well as additional cohorts of metastatic hormone-sensitive prostate cancer (mHSPC) and castration-resistant prostate cancer (mCRPC). We confirm that HLA-I protein expression is negatively associated with intragenic methylation of major HLA-I genes, downregulated in tumor compared with benign glands, but not associated with race, genetic ancestry, or clinicopathologic parameters in primary prostate cancer. Compared with matched primary tumor tissue, HLA-I expression is higher in HSPC pelvic lymph node metastases, and increased primary tumor expression is inversely associated with metastasis among self-identified White patients, but not Black patients. HLA-I expression in primary tumors is positively correlated with infiltrating immune cell densities, consistent with its established role in tumor cell immunogenicity. Surprisingly, primary tumors with PTEN loss show significantly higher HLA-I expression than those with intact PTEN, and this finding is validated in preclinical cell line and animal models, with a similar (nonsignificant) trend in mCRPC. Implications: The novel finding that PTEN loss is associated with higher tumoral HLA-I expression is concordant with observed increased immune cell infiltrates in tumors lacking PTEN and may be relevant for precision medicine therapeutic approaches.

Supplementary Figure 4. Example case 4.

Supplementary Figure 1. Example case 1.

The time dependence in the performance of prognostic factors for cancer survival is typically incompletely understood, including in prostate cancer. We applied a "cumulative/dynamic" time-varying area under the curve (tAUC) for cumulative incidence of lethal prostate cancer (metastases/cancer-specific death). In two prospective prostate cancer patient cohorts followed for lethal outcomes after radical prostatectomy, genitourinary pathologists undertook a histopathologic review of tumor specimens to assign Gleason grade groups 1-5, a known strong short-term prognostic factor. Among 1490 patients, 144 lethal events occurred during 35 years of follow-up (median, 18). The 10-year risk of lethal disease was 2% (95% CI, 1-3) for grade group 2 and 21% (95% CI, 16-28) for grade group 5 cancers. By 25 years, risks were 5% (95% CI, 3-8) and 32% (95% CI, 26-41), respectively. Prediction accuracy was strongest over the first 10 years (tAUC 0.83 [95% CI, 0.79-0.86]) but remained informative for 25 years (tAUC 0.76 [95% CI, 0.70-0.81]), including among long-term metastasis-free survivors. Risk-based AUCs instead of hazard-based "incident/dynamic" AUCs allowed for interpretable characterization of prognostic accuracy over well-defined time periods. Lethal progression of high-grade prostate cancer occurred predominantly early, while that of lower grade tumors accumulated over decades after surgery.