Back to Authors

Karnes, R. Jeffrey

https://orcid.org/0000-0003-2339-5925

Mayo Clinic

Mayo Clinic

Citations 233

Beyond Binary PTEN Loss: Integrating Genomics, Long-Term Outcomes, and AI-Assisted Digital Pathology to Define Actionable PTEN Deficiency in Prostate Cancer.
Zarka, Jabra, Pessoa, Rodrigo Rodrigues , Gupta, Sounak , Chen, Eric, Greipp, Patricia, Orme, Jacob J., Karnes, R. Jeffrey, Cheville, John C. , Heath, Elisabeth, Zarka, Jabra , Greipp, Patricia T. , Childs, Daniel S. , Orme, Jacob J. , Karnes, R. Jeffrey

International Journal of Cancer Care and Delivery | September 10, 2026 | Volume: No volume available | Issue: No issue available | Pages: No page available

10.53876/001a.129758 Get It

Intermediate clinical endpoints as surrogates for overall survival after salvage prostatectomy
Roessler, Navid , Nowicka, Zuzanna , Miszczyk, Marcin , Calleris, Giorgio , Dematteis, Alessandro , Vetterlein, Malte W. , Albisinni, Simone , Poel, H J van der, Cathcart, Paul, Cacciamani, Giovanni , Persad, Raj , Joniau, Steven , Sanchez‐Salas, Rafael , Smith, Joseph A. , Karnes, R. Jeffrey , Ahmed, Mohamed E., Rajwa, Paweł , Shariat, S, Party, the Young Academic Urologists Prostate Cancer Working, Cacciamani, Giovanni E , Gill, Inderbir S , Persad, Raj A , Joniau, Steven , Sanchez-Salas, Rafael , Smith, Joseph A , Karnes, Jeffrey , Rajwa, Pawel , Tilki, Derya , Gontero, Paolo , Marra, Giancarlo , Miszczyk, Marcin , Cathcart, P. , Gill, Inderbir S. , Tilki, Derya , Shariat, Shahrokh F. , Gontero, Paolo , Marra, Giancarlo

BJU International | June 16, 2026 | Volume: 138 | Issue: 3 | Pages: 430-437

10.1111/bju.70352 Get It

Objectives To evaluate biochemical recurrence‐free survival (BRFS) and metastasis‐free survival (MFS) as potential intermediate clinical endpoints (ICEs) for overall survival (OS) in patients undergoing salvage radical prostatectomy (sRP). Patients and Methods Evaluable patients were selected from a retrospective dataset, resulting in a cohort of 879 patients with recurrent, non‐metastatic, hormone‐sensitive prostate cancer treated with sRP at 13 centres. ICE surrogacy was evaluated using a two‐stage approach: (i) at the individual‐patient level by fitting Clayton copula models and estimating Kendall's ( >0.7 indicating a strong association) and (ii) at the centre level, by fitting weighted linear regression of 5‐year OS on 3‐year BRFS and MFS. Results The two‐step analysis included 759 patients for BRFS (366 events) and 476 for MFS (137 events), with median follow‐up of 37 months (95% confidence interval [CI] 36–42 months) and 34 months (95% CI 31–37 months), respectively. At the individual‐patient level, MFS showed a strong association with OS (Kendall's 0.85, 95% CI 0.82–0.88), which was not observed for BRFS (Kendall's 0.63, 95% CI 0.56–0.69). At the centre level, neither 3‐year BRFS ( R 2 = 0.15; slope = 0.34, P = 0.2) nor 3‐year MFS ( R 2 = 0.21; slope = 0.26, P = 0.14) predicted 5‐year OS with sufficient explanatory power. Limitations include the fact that centre‐level analysis was based on single‐arm associations rather than on treatment‐effect surrogacy across arms, and retrospective data collection. Conclusions The BRFS should not be used as a surrogate endpoint in the sRP setting. MFS requires further validation in future prospective studies to confirm its association with OS. Patient‐reported outcomes, such as quality‐of‐life and treatment‐related toxicity, should be considered in parallel with OS.
FAP+FN1+CAV1+ cancer-associated fibroblast subtype and its association with aggressive behavior in localized prostate cancer.
Shahait, Mohammed, Alshalalfa, Mohammed , Jiang, Ruochen, Davicioni, Elai, Spratt, Daniel Eidelberg, Karnes, R. Jeffrey, Shahait, Mohammed , Davicioni, Elai , Karnes, R. Jeffrey , Lee, David I.

Journal of Clinical Oncology | March 2, 2026 | Volume: 44 | Issue: 7_suppl | Pages: 392-392

10.1200/jco.2026.44.7_suppl.392 Get It

392 Background: Cancer-associated fibroblasts (CAFs) are a major component of the tumor microenvironment, exerting both tumor-promoting and tumor-restrictive effects, and in some cases, dual roles. CAFs are heterogeneous and have been implicated in tumor progression, metastasis, and therapeutic resistance. Recent translational evidence suggests the existence of at least two CAF subtypes: CAV1+ CAFs and FAP+FN1+ CAFs. The clinical utility of subclassifying CAFs in prostate cancer remains undefined. In this study, we aimed to examine the correlation of CAF subtypes in localized prostate cancer with Decipher genomic classifier (GC) scores, Grade Group (GG), and the presence of adverse pathological features (APF). Methods: We retrieved de-identified transcriptomic and pathological data from 55,329 radical prostatectomy (RP) samples tested with the Decipher prostate genomic classifier (Veracyte, San Diego, CA) between 2016 and 2024, available through the GRID registry (NCT02609269). A subset of 855 patients (META855 cohort) treated with RP was utilized for outcomes analyses. CAF subtypes were defined based on the expression of key biomarkers (FN1, FAP, and CAV1), normalized to total CAF estimates. Correlation analyses and multivariable Cox regression models were performed to evaluate the association of CAF subtypes with GC scores, GG, APF. Metastasis-free survival (MFS) estimates were generated using Kaplan–Meier methodology. Results: FAP and FN1 normalized expressions were highly correlated (r=0.61) and weakly correlated with CAV1 suggesting that they represent two distinct subtypes of CAF. Samples with high expression (top 25%) of FN1 (FN1+) and FAP (FAP+) were enriched with very high Decipher (> 0.85, VHD) and GG4-5. As such, 37% and 32% of FAP+ were VHD and GG4-5 respectively compared to ~18% for low FAP(low 25%). While for FN+ 33.9% were VHD, and 31.5% GG4-5. Patients with FAP+FN1+, 42.5% and 37.1% were VHD, and had GG4-5. Samples with high CAV1 (CAV1+) were associated with lower rate of VHD (15.5%) or GG4-5 (20.8%) compared to low CAV1 (35.4% for VHD and 24.5% for GG4-5). When evaluating VHD in FAP+FN1+CAV1- subgroup, 58% were VHD compared to 6.4% in FAP-FN1-CAV1+. The 5-year MFS was 78% in FAP+FN1+CAV- compared to 96% in FAP-FN1-CAV1+ (p<0.01). When evaluating the biological implications of FAP+FN1+, we found that FAP and FN1 expression is highly correlated to angiogenesis and EMT pathways, radiation sensitivity signature (PORTOS). Conclusions: FAP+FN1+CAV- is a unique subset of CAFs that is associated with aggressive prostate cancer behavior. Our findings may lay the foundation for future efforts to modulate CAFs in localized prostate cancer with existing therapeutics targeting FAP or FN1.
Comprehensive analysis of androgen production, uptake, and conversion (APUC) genes to highlight SRD5 family diversity in a large localized prostate cancer cohort.
Shi, Xiaolei, Alshalalfa, Mohammed , Boytim, Ella, Karnes, R. Jeffrey, Spratt, Daniel Eidelberg, Lacuna, Kristine Peregrino , Halabi, Susan, Sharifi, Nima , Tang, Chad, Ross, Ashley, Davicioni, Elai, Antonarakis, Emmanuel S., Ryan, Charles J. , Tran, Phuoc T., Hwang, Justin, Halabi, Susan , Lacuna, Kristine P. , Halabi, Susan , Karnes, R. Jeffrey , Shetty, Amol Carl , Bergom, Hannah E. , Patel, Krishnan R. , Tang, Chad , Davicioni, Elai , Antonarakis, Emmanuel S.

Journal of Clinical Oncology | March 2, 2026 | Volume: 44 | Issue: 7_suppl | Pages: 382-382

10.1200/jco.2026.44.7_suppl.382 Get It

382 Background: Androgen receptor signaling drives prostate cancer (PC) progression, and genes involved in androgen production, uptake, and conversion (APUC) are key therapeutic targets. We previously defined a 6-APUC gene set ( HSD3B1, HSD3B2, CYP3A43, CYP11A1, CYP11B1, and CYP17A1 ), that identified metastatic PC with favorable prognosis and predict docetaxel benefit. However, the expression landscape and clinical relevance of APUC genes have not been interrogated in localized PC. Methods: We analyzed the expression of 21 APUC genes in 55,329 radical prostatectomy tumor samples that underwent Decipher prostate genomic classifier (GC) testing (Veracyte Inc) between 2016-2024. Baseline clinical/pathologic factors were retrieved from Decipher GRID database (NCT02609269). Associations between gene expression quartiles with PathoGenomic Risk Factors (PGRF) including Very High Decipher score >0.85 (VHD), Grade Group (GG) 4-5, LNI and SVI were examined. Associations with distant metastatic (DM) outcomes and metastasis free survival (MFS) were evaluated using logistic regression in Mayo545 and Cox regression in Meta855 RP cohorts, respectively. Results: High expression of SRD5A2 was associated with favorable PGRF (lower odds ratio (OR), p<0.0001), lower rate of development of DM (OR 0.36, p<0.05), and longer MFS (Hazard ratio (HR) 0.51, p<0.05). HSD17B6 showed similar results for PGRF (lower OR, p<0.0001), DM (OR 0.58, p<0.05) and longer MFS (HR 0.39, p<0.05) despite being associated with GG4-5 and SVI+ in samples with VHD. In contrast, high expression of SRD5A3 and HSD17B10 had high OR for PGRFs (p<0.0001). High expression of SLCO2B1 , an androgen uptake gene, had the strongest association with GG4-5 and SVI/LNI (p<0.001 for both). We noted that SRD5A2 lacked correlation with SRD5A1 and SRD5A3 , which instead correlated with each other. Compared to all APUC genes, SRD5A2 had limited correlations with almost all APUC genes, including ones that exhibited robust cross correlation with each other . Similar to our prior finding, most APUC genes demonstrated negative correlation with AR expression and AR activity signatures. Key outcomes were validated based on transcriptomic data from 492 samples from TCGA database. Conclusions: Comprehensive analysis of 21 APUC genes in over 55,000 PC identified distinct, context-dependent associations with metastatic outcomes and clinical and molecular risk factors. Notably, high SRD5A2 expression was associated with lower odds of high-risk features and metastatic outcomes, whereas SRD5A1 and SRD5A3 linked to adverse outcomes, suggesting critical yet divergent roles among 5-alpha-reductase family members. These findings underscoring androgen-metabolic heterogeneity and highlighting SRD5A2 as a potential biomarker of indolent biology in localized prostate cancer.
CAST-AI: Cystectomy after systemic therapy with ADC and immunotherapy.
Zarka, Jabra , Bering, Elisabeth, Flickinger, Lynn M. , Gregory, Susanna, Roberson, Daniel S. , Sharma, Vidit, Chaudhuri, Aadel A. , Khanna, Abhinav, Karnes, R. Jeffrey, Boorjian, S., Sartor, Alton Oliver, Cheville, John C. , Domingo-Doménech, Josep, Shah, Paras H., Orme, Jacob J. , Zarka, Jabra G , Bobek, Olivia , Roberson, Daniel S. , Sharma, Vidit, Pritchett, Joshua C. , Jang, Albert , Karnes, R. Jeffrey , Lucien, Fabrice , Ballman, Karla V. , Domingo‐Domenech, Josep

Journal of Clinical Oncology | March 2, 2026 | Volume: 44 | Issue: 7_suppl | Pages: No page available

10.1200/jco.2026.44.7_suppl.tps892 Get It

TPS892 Background: Enfortumab Vedotin (EV) plus pembrolizumab (Pembro) is now first-line therapy for advanced urothelial carcinoma (UC), yielding ~30% complete response (CR) rates; nevertheless, most patients (pts) progress within 1 year and median overall survival (OS) remains < 3 years. In muscle invasive bladder cancer, local consolidation after systemic therapy improves outcomes, suggesting that residual, treatment-refractory intravesical disease drives relapse. We hypothesize that cytoreductive cystectomy/nephroureterectomy (CC/U)—with metastasis-directed therapy (MDT) as needed—can consolidate responses to EV/Pembro and extend benefit in regionally advanced or metastatic UC. CAST-AI prospectively evaluates this multimodal strategy and integrates correlative studies of exosomal Nectin-4 and circulating tumor DNA (ctDNA) from blood and urine as predictive/MRD biomarkers. Methods: CAST-AI is a phase II, decentralized single-arm trial enrolling pts with histologically confirmed UC of the bladder or upper urinary tract with ≥N1 and/or M1 disease and ECOG PS 0–2 who are potential surgical candidates (planned n = 75). Treatment: EV 1.25 mg/kg IV D1 & D8 + Pembro 200 mg IV D1 q21d, ≥4 cycles; MDT permitted any time pre-surgery. Response assessments occur q9 weeks (±4) to 18 months, then q12 weeks (±4). Surgical eligibility requires: (A) fitness for surgery; (B) complete or partial response (CR/PR) or, for select low-burden/unmeasurable disease, urologist-adjudicated candidacy; (C) all distant sites addressed; and (D) procedure in pt’s best interest. Post-CC/U maintenance EV/Pembro is encouraged per clinical discretion and guided by definitive surgical pathology results, which provide true pathologic staging often unattainable through imaging after systemic therapy. Primary endpoint: 12-month progression-free survival (PFS). Secondary endpoints: Objective response rate (ORR), CR rate, down-staging at CC/U, PFS, OS, and safety (using CTCAE). Exploratory endpoints: longitudinal exosomal Nectin-4 and ctDNA dynamics as MRD and early relapse indicators; tissue–blood–urine Nectin-4 concordance; pt-reported tolerability (using CIPN20). Key exclusions: > 20% variant histology or disallowed subtypes (e.g., micropapillary, plasmacytoid, sarcomatoid, neuroendocrine); prior chemotherapy for UC; contraindications to surgery/EV/ICI; or active uncontrolled comorbidities/infections. Status: Enrollment is open and ongoing, with 25 of 75 pts enrolled as of September 2025. The trial uses a decentralized model, allowing pts to receive EV/Pembro at their local facility, with central coordination, biospecimen shipping, and surgical evaluation at Mayo Clinic or affiliated sites. ClinicalTrials.gov: NCT06764095. Clinical trial information: NCT06764095 .
Recent Advances in Immunotherapy for Non-Muscle-Invasive Bladder Cancer
Grier, Abby , Zhong, Mr Jeffrey, Basourakos, Spyridon P. , Singh, Parminder, Zakharia, Yousef , Lucien, Fabrice , Karnes, R. Jeffrey, Sharma, Vidit, Shah, Paras, Costello, Brian A. , Pagliaro, Lance C. , Orme, Jacob J. , Brown, Jason R., Jang, Albert , Brown, Jason R. , Singh, Parminder , Grier, Abby L , Basourakos, Spyridon , Singh, Parminder , Zakharia, Yousef , Lucien, Fabrice , Orme, Jacob J , Brown, Jason R , Jang, Albert , Calaway, Adam , Karnes, R. Jeffrey , Sharma, Vidit, Shah, Paras

Cancers | February 16, 2026 | Volume: 18 | Issue: 4 | Pages: 623

10.3390/cancers18040623 Get It

Non-muscle-invasive bladder cancer (NMIBC) comprises approximately 75% of new bladder cancer cases and generally carries a favorable prognosis, yet high rates of recurrence and progression necessitate close surveillance with frequent cystoscopies and repeated transurethral resections. Upfront treatment for high-risk disease is typically Bacillus Calmette-Guérin (BCG), although combinations with immune checkpoint inhibitors have reported results. Patients with BCG-unresponsive, intolerant, or refractory disease represent a subset of patients with high risk of progression, with early radical cystectomy being the standard approach for this setting. Global BCG shortages and the substantial impact of cystectomy on quality of life underscore the need for therapeutic alternatives. Over the past decade, investigational trials in immunotherapy have expanded treatment options for BCG-unresponsive NMIBC with CIS, leading to FDA approval of intravesical nadofaragene firadenovec, nogapendekin alfa-inbakicept, and systemic pembrolizumab. This narrative review summarizes developments in intravesical and systemic immunotherapies for NMIBC, highlights ongoing trials, and addresses controversies in trial design, treatment sequencing, comparative efficacy, and safety.
Salvage Focal Therapy vs Radical Prostatectomy for Localized Radiorecurrent Prostate Cancer
Light, Alexander, Peters, Max, Arya, Manit, Tanaka, Mariana Bertoncelli , Dudderidge, Tim , Emberton, Mark, Grey, Alistair , Hindley, Richard, Laniado, Marc, McCraken, Stuart, Moore, Caroline M., Nigam, Raj , Noureldin, Mohamed , Reddy, Deepika, Virdi, Jaspal, Ahmed, Mohamed, Albisinni, Simone, Cathcart, P. , Joniau, S., Karnes, Robert Jeffrey, Persad, Raj , Rajwa, Paweł, Sanchez-Salas, Rafael, Shariat, Shahrokh F., Smith, Joseph A., Tilki, Derya, Poel, H. G. van der, Calleris, Giorgio , Gontero, P., Marra, Giancarlo, Ahmed, Hashim U., Joniau, Steven , Emberton, Mark , Rajwa, Paweł , Moore, Caroline M. , Joniau, Steven , Rajwa, Pawel , Light, Alexander J. W., Peters, Max , Emara, Amr M. , Moore, Caroline , Orczyk, Clément , Reddy, Deepika , Albisinni, Simone , Karnes, R. Jeffrey , Shariat, Shahrokh F. , Tilki, Derya , Poel, HG van der, Marra, Giancarlo , Ahmed, Hashim U. , Shah, Taimur Tariq

JAMA Oncology | February 12, 2026 | Volume: 12 | Issue: 4 | Pages: 364

10.1001/jamaoncol.2025.6448 Get It

Importance Patients with recurrent prostate cancer after previous radiotherapy typically have poor survival. Those with recurrences prostate confined might be suitable for salvage focal therapy (sFT) or salvage radical prostatectomy (sRP). sFT may offer good cancer control with comparatively less toxic effects, but outcomes beyond 5 years have not been reported, and no study has compared sFT to sRP. Objective To compare cancer control and perioperative complications among patients after sFT vs sRP. Design, Setting, and Participants In this international, multicenter cohort study of matched comparison data, patients undergoing sFT were derived from the prospective UK HIFU (high-intensity focused ultrasound) Evaluation and Treatment and International Cryotherapy Evaluation registries (9 centers; 2006-2024) and the prospective UK Focal Recurrent Assessment and Salvage Treatment cohort study (6 centers; 2014-2018). Patients undergoing sRP were derived from an international retrospective registry (12 centers in 8 countries; 2000-2021). Patients with biopsy-confirmed, localized recurrent prostate cancer postradiotherapy, either external beam radiotherapy, brachytherapy, or both, were included. Data were analyzed from March to July 2025. Exposures sFT using HIFU or cryotherapy vs sRP. Main Outcomes and Measures The primary outcome was cancer-specific survival up to 10 years. Secondary outcomes were overall survival, any perioperative complications (Clavien-Dindo grades 1-5), and major perioperative complications (Clavien-Dindo grades 3-5). Comparisons were made on matched patients following 1:1 cardinality matching within individual multiply-imputed datasets. Matching variables used were radiotherapeutic treatment, years between primary and salvage treatments, European Association of Urology recurrence risk group, and presalvage age, prostate-specific antigen, prostate volume, grade group, T stage, and androgen-deprivation therapy use. Results A total of 923 patients were eligible for matching (419 undergoing sFT and 504 undergoing sRP). Of the patients undergoing sFT, 325 (77.6%) underwent HIFU and the remainder cryotherapy, with 241 (57.5%) treated with quadrant ablation. Of patients treated with sRP, 376 (74.6%) underwent open surgery and the remainder robot-assisted surgery. For sFT vs sRP, 10-year cancer-specific survival was 92% (95% CI, 86%-98%) vs 99% (95% CI, 97%-100%), with no statistically significant difference (restricted mean time lost, −0.09 years; 95% CI, −0.22 to 0.03 years; P = .15; subdistribution hazard ratio, 0.45; 95% CI, 0.05-4.00; P = .47). There was no statistically significant difference in 10-year overall survival (restricted mean survival time, −0.13 years; 95% CI, −0.86 to 0.60 years; P = .72). Undergoing sRP was associated with statistically significant higher odds of any complication (adjusted odds ratio, 24.20; 95% CI, 12.94-45.27; P &amp;lt; .001) and major complication (adjusted odds ratio, 9.31; 95% CI, 3.42-25.36; P &amp;lt; .001). Conclusions and Relevance In this cohort study, sFT and sRP were effective for treating localized radiorecurrent prostate cancer, while sFT was associated with fewer perioperative complications. sFT may provide a favorable therapeutic ratio for many patients with localized radiorecurrent prostate cancer.
Adoption and Regional Variation of Prostate-Specific Membrane Antigen Positron Emission Tomography in the United States
Leapman, Michael S., Long, Jessica B., Westvold, Sarah , Rabil, Maximilian , Sprenkle, Preston C. , Kim, Isaac Y., Spilberg, Gabriela , Saperstein, Lawrence, Fallah, Jaleh , Suzman, Daniel L. , Lerro, Catherine, Xu, Jianjin , Rivera, Donna R. , Karnes, R. Jeffrey, Dinan, Michaela, Mitchell, Aaron Philip , Wang, S, Gross, Cary P. , Leapman, Michael , Westvold, Sarah J. , Leapman, Michael S , Dinan, Michaela A , Mitchell, Aaron P , Wang, Shi-Yi , Ma, Xiaomei , Rivera, Donna R. , Kluetz, Paul Gustav , Karnes, R. Jeffrey , Dinan, Michaela A. , Kunst, Natalia , Ma, Xiaomei

JCO Oncology Practice | February 3, 2026 | Volume: No volume available | Issue: No issue available | Pages: No page available

10.1200/op-25-00617 Get It

PURPOSE Despite evidence of diagnostic accuracy but unclear long-term clinical benefit, national utilization patterns of prostate-specific membrane antigen positron emission tomography (PSMA-PET) are undefined. METHODS We conducted a serial cross-sectional study to evaluate the use of PET imaging among commercial insurance beneficiaries with prostate cancer using administrative claims from deidentified Blue Cross Blue Shield Axis database. Eligible patients included prevalent and incident prostate cancer cases. We calculated the proportions undergoing PET imaging in semiannual periods from January 1, 2016, through December 31, 2024. We examined the association between regional-level contextual sociodemographic and health care characteristics, and regional use of PSMA-PET imaging in 2024. RESULTS A total of 514,750 male beneficiaries age 40-89 years with prostate cancer were identified between 2016 and 2024. The proportion of individuals with prostate cancer undergoing PET imaging increased from 4.5 [95% CI, 4.1 to 4.9] per 1,000 in the first half of 2016 to 77.6 (95% CI, 76.2 to 79.1) per 1,000 in the second half of 2024, P < .001. Increases in PET were driven by uptake of PSMA-PET following approval in 2021, which increased from 0.8 (95% CI, 0.6 to 0.9) per 1,000 in the second half of 2021 to 77.0 (95% CI, 75.5 to 78.5) per 1,000 in the second half of 2024, P < .001. PSMA-PET use in 2024 was higher in regions with greater education (99.3 v 114.6 per 1,000 in lowest [Q1] v highest [Q4] educated) and income (95.4 v 112.3 per 1,000 in Q1 v Q4 income) measures, P < .001. CONCLUSION PSMA-PET was rapidly incorporated into clinical practice among commercial insurance beneficiaries with prostate cancer with higher adoption in geographic regions with higher income and education.
Abstract B079: Persist: a molecular signature for prostate cancer patients with preexisting treatment-persistent cells associated with aggressive disease
Ballesio, Francesco , Taavitsainen, Sinja , Alshalalfa, Mohammed , Kiviaho, Antti , Ismail, Mazlina , Nätkin, Reetta , Giesen, Alexander, Munro, Thomas, Proudfoot, James A., Davicioni, Elai, Cooperberg, Matthew, Karnes, R. Jeffrey., Jiang, Ruochen, Joniau, Steven, Attard, Gerhardt, Nykter, Matti , Joniau, Steven , Joniau, Steven , Proudfoot, James A. , Ryu, Hyunnam Monica , Davicioni, Elai , Cooperberg, Matthew R , Karnes, R. Jeffrey , Jiang, Ruochen, Attard, Gerhardt , Claessens, Frank , Urbanucci, Alfonso

Cancer Research | January 20, 2026 | Volume: 86 | Issue: 2_Supplement | Pages: B079-B079

10.1158/1538-7445.prostateca26-b079 Get It

Abstract Background Prostate cancer is a heterogeneous disease comprising diverse cell types within the tumor microenvironment that support cancer cell survival. Using single cell and spatial transcriptomics, we previously identified subpopulations of treatment-persistent cancer cells exhibiting regenerative properties and a distinct molecular signature. Herein, we aimed to characterize the locked ‘Persist’ signature (PS) and its association with outcomes in a large cohort of non-metastatic prostate cancer tumors. Methods Patients with non-metastatic prostate cancer that underwent Decipher prostate genomic classifier and whole-transcriptome profiling on biopsy (BX, n=146,941) and radical prostatectomy (RP, n=55,329) specimens between October 2016 and February 2024 were included (Veracyte Inc., San Diego, CA, USA). Baseline clinical and pathological data from deidentified patients as well as signature scores were retrieved from the Decipher Genomic Resource for Intelligent Discovery (GRID) registry (Clinical Trials identifier: NCT02609269). The PS score based on the expression of 17 genes was calculated for all samples. Results PS was significantly associated with adverse clinical and pathological variables. In biopsy sample, PS was higher in cases with worse T3/4 clinical stage, Grade group (GG4-5), and high/very high NCCN risk (p&lt;0.001 for all). In RP sample, PS was significantly higher in patients with GG4-5, extraprostatic extension, seminal vesicle invasion and lymph node involvement (p&lt;0.001 for all). PS was also higher in patients with very high Decipher (&gt;0.85) in both BX and RP (p&lt;0.001 for both). When evaluating the prognosis of PS in multiple retrospective cohorts, PS in biopsy was prognostic of adverse pathology features at RP. PS was also prognostic of distance metastasis (DM) in multiple RP cohorts with long-term follow up (META855). In the ARNEO trial testing apalutamide in addition to ADT as neo-adjuvant treatment prior RP, PS was prognostic of early recurrence. In the Stampede trial, PS was prognostic of progression free survival, PCSM and OS in both non-metastatic and metastatic disease. When associating PS with other GRID signatures, PS was higher in samples with homologous recombination deficiency, TP53 mutations, Luminal B and luminal proliferating subtypes. On the other hand, PS was lower in samples with low androgen receptor-activity, RB-loss and neuroendocrine-like tumors. Finally, PS was positively correlated with radiation sensitivity signatures. Conclusions Persist is a novel molecular signature associated with more aggressive tumor characteristics. Future studies aim to further examine beyond this signature potential to identify patients at risk of aggressive prostate cancer, and understand what the optimal treatments for those with treatment-persistent prostate cancer cells are. Citation Format: Francesco Ballesio, Sinja Taavitsainen, Mohammed Alshalalfa, Antti Kiviaho, Mazlina Ismail, Reetta Nätkin, Alexander Giesen, Thomas Munro, James A. Proudfoot, Hyunnam Ryu, Elai Davicioni, Matthew C. Cooperberg, R. Jeffrey. Karnes, Ruochen Jiang, Steven Joniau, Gerhardt Attard, Frank Claessens, Matti Nykter, Alfonso Urbanucci. Persist: a molecular signature for prostate cancer patients with preexisting treatment-persistent cells associated with aggressive disease [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Innovations in Prostate Cancer Research and Treatment; 2026 Jan 20-22; Philadelphia PA. Philadelphia (PA): AACR; Cancer Res 2026;86(2_Suppl):Abstract nr B079.