tbuckley/cabot-search huggingface dataset:
A high omega-3, low omega-6 diet with fish oil for men with prostate cancer on active surveillance: The CAPFISH-3 randomized clinical trial.
Authors: William Aronson, Tristan Grogan, Pei Liang, Patricia Jardack, Amana Liddell, Claudia Perez, Mikayla Lerman, David Elashoff, Jonathan W. Said, Pinchas Cohen, Leonard S. Marks, Susanne M Henning
Journal: Journal of Clinical Oncology (2025)

312 Background: Men on active surveillance for prostate cancer are extremely interested in dietary changes or supplements to prevent progression of their disease. There are presently no prospective trials supporting such changes. We sought to determine if a high omega-3, low omega-6 fatty acid diet with fish oil capsules (D+FO) decreases proliferation (Ki-67) in prostate biopsies in men with prostate cancer on active surveillance over a 1-year time period. Methods: In this Phase II, prospective randomized trial, men (N=100) with grade group 1 or 2 prostate cancer that elected active surveillance were randomized to the D+FO or a control group. Same site prostate biopsies were obtained at baseline and 1-year tracked using an image-fusion device. The primary endpoint was the change in Ki-67 index from baseline to 1-year from same site biopsies compared between the groups. Ki-67 index was determined using multiplex immunofluorescence analysis. Secondary outcomes included compliance, grade group, maximum tumor length, the Decipher 22 gene score, serum PSA, lipid levels, and adverse events. Results: The Ki-67 index decreased in the D+FO group by approximately 15% from baseline to 1-year (1.34% at baseline, 1.14% at 1-year) and increased in the control group by approximately 24% from baseline to 1-year (1.23% at baseline, 1.52% at 1-year) resulting in a statistically significant difference in the change of Ki-67 index between the groups (95% CI 2%, 52%, p=0.043). There was no significant difference in the secondary outcomes grade group, tumor length, decipher genomic score or PSA between the two groups. There was a significant decrease in serum triglyceride (p=0.016) and serum colony stimulating factor-1 (p=0.017) in the D+FO group compared to control. Four patients in the D+FO group were withdrawn from the trial due to adverse events related to the FO. Conclusions: A high omega-3, low omega-6 diet with FO for 1-year resulted in a significant reduction in Ki-67 index (compared to the control group), a biomarker for prostate cancer progression, metastasis and death. These findings support future Phase III trials incorporating this intervention in men on active surveillance. Clinical trial information: NCT02176902 .
Assessment of pathologic responses from unstructured pathology reports using large language models.
Authors: Swati Popli, Muhammad Umair Anjum, Syed Arsalan Ahmed Naqvi, Prateek Jain, Parminder Singh, Yousef Zakharia, Irbaz Bin Riaz
Journal: Journal of Clinical Oncology (2025)

866 Background: Emerging data suggests that Language Models (LLMs) provide an unprecedented opportunity to extract critical data from the unstructured pathology reports. However, the performance of state of art (SOTA) models on clinically meaningful tasks such as assessment of pathologic responses in patients receiving neoadjuvant chemotherapy (NAC) in muscle invasive bladder cancer(MIBC) is not well known. Methods: This retrospective cohort included patients with pathologically confirmed Muscle-Invasive Bladder Cancer from the year 2018 to 2024. Selected patients included those who underwent Neoadjuvant chemotherapy followed by definitive cystectomy at Mayo Clinic. Gold standard labels were manually curated by trained clinicians. The state of the art (SOTA) LLM – GPT4 – was utilized using a structured zero-shot prompt to extract relevant phenotypic variables such as tumor site, tumor histology and additional histological variants if any, presence of in-situ / invasive carcinoma, presence of lamina propria / muscularis propria / lympho-vascular / perineural invasion, and T-stage from unstructured pathology reports. Structured prompts were iteratively developed for each data variable and validated using ~5% of the total dataset. The extracted variables were manually compared and labelled as True positive / True negative / False positive / False negative. Final performance was assessed against a held-out expert annotated test dataset using evaluation metric (accuracy). Results: A total of 200 reports from 99 patients were extracted by the LLM. Of the 200 reports, 41 duplicate / other pathology reports (e.g. – autopsy, cholecystectomy, etc.) were removed during final assessment. Significant characteristics such as tumor site, histology, and additional histology variant had an accuracy of 89%, 87%, and 91% respectively. Notably, accuracy of detection of in-situ versus invasive carcinoma was 70% versus 91%. Specific variables such as lamina propria / muscularis propria invasion / T-stage / lympho-vascular invasion / perineural invasion were answered with the accuracy of 75%, 75%, 67%, 90%, and 94% respectively. Conclusions: LLMs have the potential to extract critical data from unstructured pathology reports and automate assessment of pathologic responses in MIBC patients receiving NAC. Iterative improvements in performance can be achieved by improving prompt design using expert clinical input. This process can be potentially scaled to automate cancer registries.
Evaluation of the impact on overall survival curves of patients with metastatic castration-sensitive prostate cancer staged with PET-PSMA and classified according to current prognostic criteria by volume and risk.
Authors: Isadora Martins de Sousa, Luciana de Moura Leite, André Marcondes Braga Ribeiro, Eduardo Nobrega Pereira Lima, José Augusto Rinck
Journal: Journal of Clinical Oncology (2025)

36 Background: The treatment of metastatic castration-sensitive prostate cancer (mCSPC) has evolved over the years. These therapies are guided by current volume (CHAARTED) and risk (LATITUDE) criteria, instituted based on conventional exams. The emergence of new imaging exams like PSMA PET, with its greater accuracy and early detection of metastatic disease, raises questions about the applicability of these criteria in this context. Methods: We conducted a retrospective, single-center study comparing patients staged with PSMA PET between August 2017 and February 2022 and classified as metastatic, after curative therapy or de novo metastatic. Patients with stage IVA, i.e., N1, were also included. Patients were stratified into high and low volume and risk, with the aim of comparing these prognostic factors with outcome of OS. Results: 48 patients with a median age of 66 years at diagnosis were selected: 81.3% had Gleason scores between 8 to 10, 57% had T classification greater than or equal to T3 and 32% were N1 by conventional exams. According to PSMA PET, 40% were de novo metastatic, with disease sites being bones (M1b - 52%), non-pelvic lymph nodes (M1a - 21%), pelvic lymph nodes (N1 - 17%), and viscera (M1c - 10%). 71% of them were low volume and 75% were low risk. With a median follow-up of 37.5 months and 7 deaths, at 36 months we had 64.6% of the high-volume population alive versus 96.6% of low-volume patients (p=0.054), 77.8% of high-risk patients alive compared to 89.9% of low-risk ones (p=0.739). There was a 67% increase in distant metastasis detection. When correlated with bone scintigraphy (BS), there was a 78.9% discordance between the number and/or location of bone lesions, and in 53.3% of cases, PSMA PET was positive for bone disease with negative BS at the same time. Conclusions: PSMA PET appears to be prognostic when applied to volume curves, despite p=0.054, which does not happen for risk, in addition to increasing the detection of metastatic disease compared to conventional exams and being more accurate in the detection of bone disease when compared to BS.
DNA damage repair alterations as predictive biomarker for platinum-based chemotherapy in metastatic urothelial cancer.
Authors: Michal Sternschuss, Alexander Paynter, Wenxin Xu, Chelsea Nichols, Jennifer Hoppe, Nancy B Davis, Di Maria Jiang, Neil J. Shah
Journal: Journal of Clinical Oncology (2025)

853 Background: DNA damage repair gene alterations (DDRa), especially ERCC2 mutations, have been associated with improved clinical outcomes in patients with urothelial cancer (UC) treated with cisplatin-based neoadjuvant chemotherapy. The predictive value of DDR alterations for platinum-based chemotherapy in metastatic disease is not well-defined. Methods: We analyzed the American Association of Cancer Research (AACR) Genomics Evidence Neoplasia Information Exchange (GENIE) Biopharma Collaborative consortium (BPC), including patients with UC treated at 4 academic centers in North America between 2013 and 2018, with Next Generation Sequencing (NGS) data available. We assessed overall survival among patients treated with first line platinum-based chemotherapy for metastatic UC, and compared the outcomes based on DDRa status using Cox models adjusted with risk-set adjustment for delayed entry. DDRa were defined as any mutation defined as “likely oncogenic” or “oncogenic” in OncoKB for the genes ERCC2, ERCC5, BRCA1, BRCA2, RECQL4, ATM, ATR, RAD51C and FANCC . Results: Of 716 patients with UC, 103 (14%) had any DDRa, and 32 (4.5%) had an ERCC2 mutation. Among 566 patients (79%) who developed metastatic disease at any time during follow up, median age was 66 years, 22% were female and 25% had upper tract UC. The median overall survival (mOS) from diagnosis of metastatic disease was 15.1 months (95% CI 12.6-18.6). For patients treated with first line platinum-based chemotherapy (n=258), the presence of DDRa was associated with significantly improved mOS compared with absence of DDRa: 22.7 versus 11.2 months, hazard ratio (HR) 0.54 (95% CI 0.34-0.86, p=0.009). Similar trends were seen when analyzing patients treated with cisplatin or carboplatin, separately. Conclusions: DDRa were associated with improved survival in metastatic UC patients treated with platinum-based chemotherapy. Further studies are needed to explore the prognostic and predictive value of DDRa as the role of platinum-based chemotherapy evolves in the enfortumab vedotin and pembrolizumab era. DDRa No DDRa First Line treatment for metastatic UC N Median OS months (95% CI) N Median OS months (95% CI) HR (95% CI) P value Any platinum-based chemotherapy 32 22.7 (14.5, 66.9) 226 11.2 (9.4, 15.1) 0.54 (0.34, 0.86) 0.009 Cisplatin-based chemotherapy 22 25.9 (14.5, NR) 142 13.6 (10.4, 18.8) 0.57 (0.32, 1.01) 0.06 Carboplatin- based chemotherapy 10 17.4 (7.26, NR) 84 9.9 (6.6, 12.7) 0.53 (0.25, 1.17) 0.12 CI= Confidence interval; DDRa= DNA damage repair alteration; HR=Hazard ratio; NR=Not reached; OS= Overall survival; UC= Urothelial Carcinoma.
Effects of integrating palliative care on the uptake of advance care planning among elderly patients with advanced genitourinary cancers.
Authors: Phichai Chansriwong, Tanin Tiyanont, Siriporn Semsarn, Nintita Sripaibookij Thokanit
Journal: Journal of Clinical Oncology (2025)

49 Background: Integrating palliative care (PC) into oncology has been demonstrated to significantly enhance the quality of life for these patients and facilitating patient decision-making, particularly concerning advance care planning (ACP). ACP is a structured process that ensures patients' values and preferences regarding the end-of-life care are respected, and frequently results in the completion of advance directives (AD). This study aims to evaluate the impact of PC on the uptake of ACP among patients with advanced GU cancers. Methods: A retrospective analysis was conducted using a claims database from Ramathibodi Hospital, encompassing elderly cancer patients who had a medical claim for death between Jan1, 2016, and Dec31, 2021 included 1,013 patients, with 532 males, and a mean age of 72.37 years (60.5-99). Among these, 215 patients (21.2%) received integrated palliative care (PC). 102 patients with GU malignancies, including 44 with TCC, 36 with prostate cancer, 22 with RCC. Of these, 22 patients (21.6%) were treated with PC. The primary outcomes measured were the completion rates of ACP and AD. Secondary outcomes included the utilization of treatments in the 6 months preceding death. Comparative analyzes were performed between the PC and UC groups to assess the impact of PC on these outcomes. Results: Regarding ACP, 78.9% of patients in the UC group engaged in ACP, with a median time of 4.5 days (range: 0-324 days) before death. In contrast, 100% of patients in the PC group engaged in ACP, with a median time of 259.7 days (range: 0-2,077 days) before death. 46.5% of patients in the PC group completed AD, whereas no patients in the UC group completed AD. Patients receiving palliative chemotherapy within 30 days before death were significantly lower in the PC group, with an odds ratio of 3.30 (P &lt; 0.001). In the 6 months preceding death, the PC group exhibited significantly lower ER visits (P = 0.011), inpatient admissions (P &lt; 0.001), and total hospital visits (P = 0.002) compared to the UC group. Conclusions: Integrating palliative care into the oncology treatment framework significantly improves the uptake of ACP among patients with advanced GU cancers. This comprehensive approach not only reduces the utilization of aggressive treatments near the end of life, but also enhances the alignment of medical care with patients' values and preferences. Clinical trial information: COA. MURA2023/258 .
Implementation of a digital multimedia tool for prostate cancer patient consultation.
Authors: Kristin Walker, Samira Samadi, Joe Chen, Timothy N Showalter, Christopher Luminais
Journal: Journal of Clinical Oncology (2025)

345 Background: MyCareGorithm, is a digital health tool designed to improve the cancer consultation experience for patients, companions, and physicians. This tool provides audiovisual guides for cancer related evaluation and management. This study aims to evaluate the effectiveness of this tool for both the patient and physician. Methods: In a prospective, IRB-approved, pilot study, 31 patients with prostate cancer and 12 companions from a single institution underwent an initial consult using this digital multimedia tool. They completed a survey of 6 “yes” or “no” questions to evaluate their understanding of their disease and treatment options. Two physicians completed a 7-question survey to evaluate their experience with this tool. Descriptive statistics were used to analyze the data. Results: Over 90% of patients reported this tool helped them better understand their cancer diagnosis, treatment options, and felt their understating of their medical situation and the quality of the consult was enhanced. 100% would recommend this to other patients. Their companions agreed and answered “yes” over 90% of the time in all categories. Comments from patients include phrase “very helpful” multiple times. Physicians agreed 97% of the time that this helped communicating difficult information and enhanced the quality of the consult. Physicians agreed that the patient had a greater understanding of their cancer, treatment, and that they would use this tool again 100% of the time. 94% of physicians agreed this tool improved efficiency and provided a more effective consult. Physician comments described the infographics as “helpful” in several instances. Survey questions and results are shown (Table). Conclusions: Implementing the MyCareGorithm digital health tool resulted in high levels patient satisfaction, comprehension, and enhanced the overall consult experience. Physicians also report high patient satisfaction and comprehension, enhancements to the overall consult, and improved clinical efficiency. The recurring comment from both physicians and patients was “helpful.” The positive results show the value of this digital communication tool. Further studies with a larger cohort and other disease sites should be assessed. Patient, companion, and physician survey questions and results. Survey Questions % Patients Agreed % Companions Agreed % Physicians Agreed Helped patient greater understand their prostate cancer 97% 100% 100% Helped patient greater understand treatment 90% 100% 100% Enhanced the quality of the consultation 97% 100% 97% Helped patient greater understand their medical situation 100% 100% - Would recommend this tool to other patients 100% 100% 100% Would review the information after consult 84% 92%* - Improved efficiency of the consultation - - 94% Helped physician provide more effective consult - - 94% Helped ease communication of complex information - - 97%
Innovative diagnostic approaches: Serum protein markers in renal cell carcinoma.
Authors: Laura Elizabeth Davis, Betty Wang, Eran Ndegwa Maina, Rebecca Campbell, Mohit Sindhani, Christopher Eing Wee, Christopher Weight, Phillip Abbosh, Steven Campbell, Robert Abouassaly, Adam C. Calaway, Pedro C. Barata, Laura Bukavina
Journal: Journal of Clinical Oncology (2025)

560 Background: In the era of precision medicine, we pursue less invasive, more powerful methods for screening, response prediction, and recurrence detection. While liquid biopsy has proven useful in other malignancies, similar diagnostic and prognostic tools for renal cell carcinoma (RCC) remain to be elucidated. We therefore aimed to investigate serum protein expression in patients before their RCC diagnosis vs. non-cancer controls to identify protein-cancer associations likely to have a role in cancer development and progression. Methods: Utilizing UK Biobank, we analyzed proteomic data in patients previously diagnosed with RCC (n=2245) vs. patients without RCC at time of serum collection who were later diagnosed (n=1225) vs. a cohort of non-cancer controls (n=44386). We estimated hazard ratios (HRs) and 95% confidence intervals (CI) using Cox proportional regression models. We investigated protein and RCC cancer-risk associations to examine the effects of reverse causality and conducted analyses to generate area under the curve (AUC) values to evaluate diagnostic performance of biomarkers. Results: We identified associations between elevated levels of tafa5, klk11, klk8, csdn, and clmp proteins and undiagnosed RCC. Highly expressed proteins in each cohort showed increased HR for cancer association (95% CI), with tafa5 exhibiting the highest HR in the treated group HR 9.7 (95%CI 6.3-12.0;p&lt;0.00). Receiver operating characteristic curve demonstrated strong predictive capabilities: igfbp4 (AUC 0.9127;SN 0.8056;SP 0.8606), tafa5 (AUC 0.9134;SN 0.7500;SP 0.8996), tgfbr2 (AUC 0.9057;SN 0.6667;SP 0.9083), scarb2 (AUC 0.8968;SN 0.7500;SP 0.9197), nectin4 (AUC 0.9269;SN 0.7222;SP 0.9299) in the treated group. These findings indicate that specific proteomic biomarkers may have a significant association with RCC diagnosis, with high AUC values supporting their potential utility in RCC diagnosis and prognosis. Prospective validation in clinical settings is warranted. Conclusions: Our study highlights distinct protein elevations between patients presenting with RCC vs. those who were later diagnosed. Although further studies are warranted, the favorable HR, AUC, SN, and SP values for several proteins identified here underscore their potential as biomarkers for RCC diagnosis and prognosis.
Prognostic value of quantitative PSMA-PET parameters during chemotherapy in prostate cancer.
Authors: Stephan Skawran, Andrei Gafita, Theo Lorenzini, Sebastian Hoberück, Francesco Mattana, Andrea Di Giorgio, Matthias Miederer, Channing Judith Paller, Loic Djaileb, Lilja B Solnes, Andrea Farolfi, Francesco Ceci, Matthias Eiber, Andrew F Voter
Journal: Journal of Clinical Oncology (2025)

33 Background: PSMA-PET/CT is increasingly being used to monitor chemotherapy in prostate cancer and shows promise for predicting outcomes and improving response evaluation. This retrospective study aimed to determine the prognostic value of quantitative tumor burden parameters derived from PSMA-PET/CT for overall survival (OS) during taxane-based chemotherapy. Methods: Databases from 6 institutions were screened for patients who underwent[ 68 Ga]Ga-PSMA11-PET and serum PSA measurements at baseline and within three months after last taxane based chemotherapy dose. Tumor segmentation was performed using DeepPSMA software and PSMA-PET whole-body quantitative parameters were obtained: PSMA-positive tumor volume (PSMA-VOL) and maximum/average standardized uptake value (SUV max , SUV mean ). Univariate Cox-regression analyses by hazard ratio (HR) with 95% confidence interval (CI) were used to evaluate association of whole-body quantitative PSMA parameters and PSA levels with OS. Harrell’s concordance index (C-index) was used to determine prognostic accuracy. Optimal cut points were determined by maximizing the log-rank statistic. Results: A total of 128 patients were included, of whom 62/128 (48%) had castration-sensitive prostate cancer and 66/128 (52%) castration-resistant prostate cancer. At baseline, PSMA-VOL numerically reached the highest prognostic value for OS (C-index: 0.88) followed by PSA (C-index: 0.80, p = 0.85), while the percentage change in PSA levels had the highest prognostic value during treatment (C-index: 0.94) significantly higher than percentage change in PSMA-VOL (C-index: 0.85, p = 0.02), (complete data shown in Table 1). Conclusions: Baseline and post-therapeutic PSMA-PET/CT quantitative parameters are prognostic for OS after taxane-based chemotherapy in prostate cancer. Baseline PSMA-VOL had the highest prognostic value for OS, while changes in PSA levels outperformed changes in quantitative PSMA-PET parameters during treatment. Parameter Cut point HR (95% CI) P-value C-index (95% CI) PSMA vol , baseline &gt; 28 ml 5.59 (2.77 – 11.27) &lt; 0.001 0.88 (0.81 – 0.96) SUV mean , baseline &lt; 13.2 2.00 (0.96 – 4.15) 0.06 0.29 (0.13 – 0.45) SUV max , baseline &gt; 71 2.18 (1.23 – 3.86) 0.007 0.69 (0.57 – 0.82) PSA, baseline &gt; 3.9 ng/ml 3.53 (1.75 – 7.13) &lt; 0.001 0.80 (0.69 – 0.92) PSMA vol , relative change &gt; -21 % 4.48 (2.80 – 7.17) &lt; 0.001 0.85 (0.78 – 0.91) SUV max , relative change &gt; -70 % 2.42 (1.50 – 3.82) &lt; 0.001 0.76 (0.67 – 0.86) SUV mean , relative change &gt; -44 % 5.98 (2.57 – 13.88) &lt; 0.001 0.85 (0.73 – 0.98) PSA, relative change &gt; -97 % 7.03 (3.20 – 15.43) &lt; 0.001 0.94 (0.88 – 0.99)