Journal for ImmunoTherapy of Cancer
● BMJ
Preprints posted in the last 7 days, ranked by how well they match Journal for ImmunoTherapy of Cancer's content profile, based on 75 papers previously published here. The average preprint has a 0.10% match score for this journal, so anything above that is already an above-average fit.
Wang, L. D.; Oill, A. M. T.; Lindner, S. E.; Stiller, T.; Egelston, C.; Blanchard, M. S.; Mudunuri, R.; Hibbard, J. C.; Wu, M.; Sepulveda, S. M.; Peter, L.; Kilpatrick, J. L.; Stratman, J.; Mee, E. D.; Chen, D. G.; Oliveira, G.; Munoz, M.; Burmayan, A.; Wagner, J.; Dolatabadi, A. M.; Nisis, M.; Shepphird, J. K.; Sanchez, G.; Natri, H. M.; Oliver-Cervantes, C.; Feldman, L.; Aftabizadeh, M.; Arvanitis, L.; Campbell, K. M.; Cotter, J. A.; Read, J. A.; Read, J. A.; Shahani, S.; Forman, S. J.; Adam, T.; de la Nava Martin, D.; Richman, S. A.; Paul, J.; Wadden, J.; Badie, B.; Tamrazi, B.; Koschmann,
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Outcomes for high-grade pediatric brain tumor patients remain poor, but there is optimism that chimeric antigen receptor (CAR) T cell therapy can improve prognosis. We present the results from a phase I clinical trial of IL13BBz-CAR T cells infused weekly into the cerebral ventricles in pediatric and young adult patients with recurrent or refractory brain tumors. The trial met its primary objectives of feasibility, safety, and tolerability, with one dose-limiting toxicity. 8 of 16 patients evaluable for response experienced radiographic size decreases consistent with biologic activity and with an anti-tumor response. Two patients met protocol criteria for response. Median survival for patients receiving lymphodepletion was 20.5 months from diagnosis and 6.9 months from treatment for patients with midline glioma, and 187 months from diagnosis and 7.5 months from treatment for patients with ependymoma. Importantly, patients who did not receive lymphodepletion developed anti-CAR humoral and cellular immune responses detectable in the CSF and peripheral blood, whereas patients receiving lymphodepletion had no evidence of CSF anti-CAR immunity. Taken together, these findings demonstrate the safety, tolerability, and biological activity of locoregionally-delivered IL13BBz-CAR T cells for children and young adults with CNS tumors. Moreover, we show that anti-CAR immune responses arise in patients not receiving lymphodepletion, but not in the CSF of patients receiving systemic lymphodepletion. Further investigation of adoptive cellular therapies combined with immunosuppression is warranted in this patient population. ClinicalTrials.gov registration: NCT04510051.
Mukherjee, E. M.; Asiaee, A.; Park, D.; Krantz, M. S.; Stone, C. A.; Martin-Pozo, M.; Phillips, E. J.
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Importance: Immune checkpoint inhibitors (ICIs) produce diverse immune toxicities, but whether checkpoint blockade also modifies associations between other drugs and adverse events is poorly understood. Objective: To define ICI-associated toxicity organization and determine whether drug-associated adverse events and onset vary with ICI exposure and checkpoint pathway. Design and Setting: Cross-sectional analysis of deduplicated FAERS reports from 2016 through 2025; analyses performed in 2026. Participants: Among 13,701,106 deduplicated reports, 2,365,269 were cancer associated and 256,940 contained an ICI. Median age among cancer reports with observed age was 66 years (IQR, 56-75 years); 1,031,999 (43.6%) were female and 1,003,154 (42.4%) were male. Exposures: ICI exposure in any reported drug role, individual primary-suspect drugs, and checkpoint-pathway exposure. Main Outcomes and Measures: Reporting odds ratios (ORs), cross-organ adverse-event communities, adjusted primary-suspect drug x ICI interaction ORs for Stevens-Johnson syndrome/toxic epidermal necrolysis (SJS/TEN), drug reaction with eosinophilia and systemic symptoms (DRESS), acute generalized exanthematous pustulosis (AGEP), interstitial nephritis, drug-induced liver injury (DILI), and vomiting (VOM), and accelerated failure-time model time ratios for documented onset. Results: Of 3001 eligible Preferred Terms in cancer-associated reports, 2091 differed at a false discovery rate (FDR) less than .05. Four cross-organ toxicity communities were identified. Of 138 eligible drug-phenotype pairs, 65 had FDR-significant interactions, including moxifloxacin-SJS/TEN amplification (interaction OR, 101.72; 95% CI, 39.11-264.55), enfortumab vedotin-SJS/TEN attenuation (interaction OR, 0.17; 95% CI, 0.13-0.23), and omeprazole-interstitial nephritis amplification (interaction OR, 10.35; 95% CI, 7.62-14.05). Among 60,324 reports contributing to temporal analyses, ICI exposure was associated with longer adjusted documented time to onset for 5 of 6 phenotypes (time ratios, 1.37-1.59) but not AGEP (time ratio, 0.99; 95% CI, 0.67-1.46). Temporal associations also differed across checkpoint pathways. Conclusions and Relevance: ICIs were associated with a structured cross-organ toxicity landscape, phenotype-specific modification of drug-associated adverse events, and distinct temporal patterns across checkpoint pathways. These findings support checkpoint blockade as a modifier of drug-associated toxicity and motivate longitudinal and mechanistic validation.
Han, F.; Wang, J.; Shi, S.; Jin, M.; Ren, C.
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IMPORTANCE: A recent meta-analysis showed that chemoimmunotherapy was associated with improved overall survival (OS) compared with immune checkpoint inhibitor (ICI) monotherapy for programmed death-ligand 1 (PD-L1) tumor proportion score (TPS) [≥] 50% advanced non-small-cell lung cancer (NSCLC). However, whether this benefit reflects chemotherapy effect or ICI heterogeneity remains unclear. OBJECTIVE: To reassess the survival benefit of adding chemotherapy to ICI monotherapy using agent-stratified comparisons anchored to chemotherapy. DATA SOURCES: The 24 phase 3 randomized clinical trials included in the original meta-analysis (search date, August 3, 2025). DATA EXTRACTION AND SYNTHESIS: Hazard ratios (HRs) for OS and progression-free survival (PFS) were extracted from each trial in the original meta-analysis. Two analytic frameworks were used: within-agent comparisons (same ICI in both chemoimmunotherapy and monotherapy) and across-agent comparisons (ICI in one treatment strategy only). For within-agent comparisons, a two-stage random-effects meta-analysis was conducted. In stage 1, ICI-specific HRs for chemoimmunotherapy and ICI monotherapy versus chemotherapy were pooled and their ratio was calculated (RHR = HRchemoimmuno/HRmono; RHR < 1 favors chemoimmunotherapy). The RHRs were pooled in stage 2. For across-agent comparisons, RHR was derived from pooled HRs by treatment strategy. MAIN OUTCOMES AND MEASURES: Endpoints were OS and PFS. RESULTS: In within-agent comparisons (4 ICIs; 13 trials; N = 3252), pooled RHR was 0.94 (95% CI, 0.78-1.13; P = .48; I2 = 0.0%) for OS and 0.85 (95% CI, 0.68-1.06; P = .14; I2 = 0.0%) for PFS. In across-agent comparisons (7 ICIs; 11 trials; N = 2231), RHR favored chemoimmunotherapy for OS (0.68; 95% CI, 0.50-0.92; P = .01) and PFS (0.46; 95% CI, 0.37-0.58; P < .001). In a sensitivity analysis restricted to trials of NCCN-recommended regimens, pooled RHR was 1.02 (95% CI, 0.81-1.28; P = .87) for OS. CONCLUSIONS AND RELEVANCE: In the within-agent comparisons, adding chemotherapy to ICI monotherapy did not improve OS or PFS in patients with PD-L1 TPS [≥] 50% advanced NSCLC. The benefit in the original meta-analysis appears driven by across-ICI heterogeneity. These findings are consistent with ICI monotherapy as a standard first-line option and underscore the need for agent-level stratification in across-trial comparisons.
Wang, B.; Mukherjee, S.; Baj, A.; Trostel, S. Y.; Lis, R. T.; Whitlock, N. C.; Ku, A. T.; Heyward, K. E.; Kartal, S.; Wang, K.; Voznesensky, O. S.; Calagua, C.; Siddiqui, J.; Martin, R. S.; Kollath, L. A.; Custer, J.; Michael, P. D.; Kunju, L. P.; Lake, R.; Harris, C. C.; Aldape, K. D.; True, L. D.; Tatsuoka, C.; Fertig, E. J.; Chinnaiyan, A.; Gurram, S.; Pinto, P. A.; Weiner, A. B.; Morrissey, C.; Salami, S. S.; Einstein, D. J.; Balk, S. P.; Sowalsky, A. G.; Ruppin, E.
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Background: Biochemical recurrence (BCR) occurs in 20-40% of men after radical prostatectomy. Existing postoperative recurrence risk tools based on PSA and pathology are clinically useful but show only moderate and variable discrimination, highlighting the need for biomarkers that improve risk stratification and consequent treatment decisions. We hypothesized that the prostate microenvironment, including both the tumor and non-cancerous adjacent tissue, may contain prognostic features associated with adverse postoperative PSA outcomes. Methods: We assembled a cohort of matched tumor-adjacent benign and tumor prostate tissue from 243 men across three institutions to establish a discovery cohort (n=123; 43 postoperative PSA events, 35%) and validation cohort (n=120; 46 events, 38%). For primary binary analyses, a postoperative PSA event included BCR, defined as two consecutive postoperative PSA values >=0.2 ng/mL, or PSA persistence. We performed RNA sequencing of matched tumor-adjacent benign and tumor tissues, quantified immune signatures, and developed an integrated model combining the adjacent-tissue B-cell signature, preoperative PSA, and radical prostatectomy Gleason score (BRIGADE). CAPRA-S-adjusted Cox analyses excluding recurrence-time-0 cases evaluated time to BCR, and CD19 multiplex immunofluorescence provided tissue-level confirmation (n=10). Results: In prostatectomy specimens, tumors from patients without a postoperative PSA event were enriched for B-cell transcriptional programs, whereas tumors from event-positive patients showed elevated proliferation signatures. B-cell-related transcriptional programs were correlated between tumor and adjacent tissue. Tumor-adjacent benign B-cell scores were higher in no-event cases and discriminated postoperative PSA-event status in PCBN discovery (AUC 0.63) and BM validation (AUC 0.81) cohorts, outperforming numerous other immune-related signatures. In CAPRA-S-adjusted Cox sensitivity analyses excluding recurrence-time-0 cases, higher adjacent-tissue B-cell activity was associated with reduced recurrence risk in PCBN (HR 0.42, 95% CI 0.19-0.94; BH-adjusted p=0.035) and BM (HR 0.54, 95% CI 0.30-0.95; BH-adjusted p=0.034). Tissue-based validation showed that CD19+ B-cell density in adjacent benign tissue was higher in no-event than event-positive patients (median 0.1145 vs 0.0471; p=0.008). BRIGADE achieved an AUC of 0.68 in cross-validation and 0.83 in independent validation, compared to AUCs of 0.54-0.63 and 0.44-0.78 for the tested clinical predictors, respectively. At the fixed classification threshold, the validation-cohort odds ratio for BRIGADE was 2.75. The adjacent B-cell score remained associated with lower odds of a postoperative PSA event after adjustment for PSA and Gleason score. Conclusions: B-cell infiltration in tumor-adjacent benign prostate tissue may complement existing clinicopathologic models for stratifying adverse postoperative PSA outcomes and subsequent BCR after radical prostatectomy. The transcriptomic signal was recapitulated by CD19-based tissue staining, supporting further development of a pathology-based assay.
Camacho, L.; Cacho-Navas, C.; Agüero, J.; Batmunkh, B.; Gracia, J. M.; O Sullivan, K.; Rementeria, M.; Miles, J.; Gumuzio, J.; Aguirre, F.; Martin Algarra, S.; de Andrea, C. E.; Parker, P. J.; Calleja, V.
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Immune checkpoint inhibitors targeting the PD-1/PD-L1 axis have shown great promise in treating bladder cancer and are now part of the standard treatment for advanced disease. However, many patients still fail to respond to treatment and at present many biomarkers are assessed but have yet shown only limited results. Therefore, with the advent of combination treatments and the increase of immune related adverse event, the search for reliable predictive biomarkers is paramount. Using a multiplexed enhanced FRET-FLIM based technique (QF-Pro) we quantified the interaction of PD-1/PD-L1, CTLA-4/CD80 and TIGIT/CD155 immune checkpoints in a pre-treatment TMA of 46 patients treated with atezolizumab. The association between higher PD-1/PD-L1 ICP interaction state and treatment efficacy was demonstrated in the male sample cohort, where it identified patients with better PFS. Conversely, patients exhibiting higher CTLA-4/CD80 engagement had a worse response to atezolizumab. Remarkably, the dual assessment of patients with high PD-1/PD-L1 and low CTLA-4/CD80 allowed to identify the best responders. These results indicate that the monitoring of patients immune profile in urothelial carcinoma might be critical in identifying patients who may benefit from combination therapy.
Lebmeier, A.; Lindner, T.; Karl, C.; Schöler, T.; Rank, A.
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Background: Immunochemotherapy (ICT) is considered standard in regards to care for small-cell lung cancer (SCLC) in extensive stages, yet reliable biomarkers for treatment response remain elusive. While previous univariate analyses suggest specific peripheral lymphocyte subsets correlate with survival, the systemic immune response involves complex, multivariate interactions that require advanced analytical approaches. Methods: This paper analysed high-dimensional flow cytometry data from 32 patients with stage IV SCLC treated with carboplatin, etoposide, and atezolizumab. Peripheral blood was analysed at baseline (V0) and longitudinally during treatment. To identify potential early predictive biomarkers and mitigate sample attrition in later cycles, we focused on baseline and measurements after two cycles of ICT (V1). We employed a rigorous machine learning framework utilising nested cross-validation, bootstrapping, and permutation-based statistical testing to evaluate eleven different regression and survival models. Results: Under model-appropriate metrics, regressors did not generalise (R2 <0); conversely, censoring-aware Random Survival Forests (RSF) successfully extracted robust prognostic signatures. Baseline immune profiles (V0) achieved a concordance index (C-index) of 0.66 (p= 0.015), while dynamic changes from V0 to V1 ({triangleup}V) achieved a C-index of 0.65 (p= 0.022). Crucially, absolute values measured after two cycles of ICT (V1) yielded no significant signal (p= 0.445). Feature importance analysis confirmed the prognostic value of Th17 normalisation and identified Naive Regulatory T cells and Memory B cells as candidate components. Conclusion: Machine learning validation confirms a predictive signal in the peripheral immune profile of SCLC patients. Early dynamic shifts in the balance between regulatory and effector immune arms are associated with prognosis, contrasting with the lack of signal in absolute counts after two cycles of ICT. These findings establish a proof of concept for multivariate liquid biopsy immune profiling, warranting confirmation in larger cohorts and highlighting the necessity of integrating systemic and tumour-intrinsic data.
Majumder, B. P.; Linak, J. A.; Adamson, R.; Aguilera, R. L.; Agarwal, D.; Reitz, Z.; Loiselle, S.; Devarakonda, S.; Clark, P.; Paulson, K. G.; Stanton, S.
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In large data sets discovery is often limited to pre-conceived hypotheses and data fishing. Here we tested whether systematic exploration of AI generated hypotheses could uncover clinically meaningful signals in extensively studied data. We deployed AutoDiscovery, a newly launched large language model (LLM) framework designed to search for hypotheses based on surprisal and systematically interrogate complex datasets, on The Cancer Genome Atlas breast cancer cohort. The system did not identify clinically meaningful novel findings without human input. However, a seeded warm-start run with minimal text input from an oncologist revealed multiple interesting and surprising hypotheses. Among these was that a robust immune signature was present across all subtypes of invasive lobular carcinoma (ILC) that exceeded invasive ductal carcinoma (IDC). This observation was independently validated in independent cohorts and confirmed by high-sensitivity multi-immunofluorescence tumor tissue analyses. These results suggest immunotherapy approaches should be tested in ILC including early stage ER+HER2- ILC; these patients are currently excluded from large neoadjuvant immunotherapy trials. They further demonstrate that surprisal-based hypothesis generation frameworks can extract previously unappreciated patterns from deeply interrogated cancer datasets and imply that disease domain experts working with LLMs can derive more meaningful insights from complex data than either could achieve alone.
Gill, P. A.; Bradbury, L. R.; Wang, A.; Hogg, J.; Demase, K.; McKenzie, J.; Fryer, H. A.; Geers, D.; Zaeck, L. M.; Boo, I.; Hogarth, M. P.; Drummer, H. E.; de Vries, R. D.; O'Hehir, R. E.; Sparrow, M. P.; van Zelm, M. C.
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Background: Patients receiving anti-TNF treatment for chronic inflammatory disease display impaired antibody responses, but it remains unclear how immune memory formation is affected. We evaluated antibody responses and memory B cells (Bmem) after COVID-19 booster vaccination in inflammatory bowel disease (IBD) patients receiving anti-TNF treatment. Methodology: Blood was sampled at baseline, 1, and 6 months after WH1/BA.5 bivalent or XBB.1.5 monovalent vaccination from 27 IBD patients receiving intravenous anti-TNF and 44 controls. Neutralizing antibodies were measured using an infectious virus assay. SARS-CoV-2 spike receptor binding domain (RBD)-specific serum IgG was quantified by ELISA, and RBD-specific Bmem were immunophenotyped by flow cytometry using recombinant proteins from ancestral, Omicron BA.1, BA.5, XBB.1.5, and JN.1 variants. Results: Serum IgG to vaccine RBD and neutralizing antibodies in patients increased pre to 1 month post-vaccination, but were lower than controls. Ancestral-, BA.5- and XBB.1.5-specific Bmem increased after vaccination but were significantly lower in patients than controls. Within RBD-specific Bmem, frequencies of recently activated CD21lo cells were increased after vaccination, and were higher in patients than controls. Fewer antigen-specific Bmem in patients expressed IgG4, and more expressed IgG3 or IgD following vaccination. Following vaccination, more RBD-specific Bmem recognized multiple viral variants. However, patients had fewer Bmem that could bind to subvariants than controls. Conclusion: Antibody and Bmem responses to COVID-19 booster vaccination in anti-TNF-treated IBD patients displayed reduced capacity, durability and cross-reactivity, suggesting impaired immune memory for protection against breakthrough infection. This supports the recommendation for annual booster vaccination to prevent severe disease and viral spread.
Yang, Y.; Vasudevaraja, V.; Serrano, J.; Mohamed, H.; Kelly, S.; Jour, G.; Gindin, T.; Park, K.; Jones, D.; Feng, X.; Pinnell, J.; Mclennan, S.; Tin, M. Y.; Tsirigos, A.; Snuderl, M.; Wrzeszczynski, K. O.
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Next-generation sequencing (NGS) for the detection of somatic variants has become the method of choice in a variety of molecular oncology fields and in the clinic. Its use ranges from sequencing entire tumor genomes and transcriptomes to targeted clinical diagnostic gene panels. The NYU Langone Genome PACT (Profiling of Actionable Cancer Targets, LG-PACT) assay is a qualitative in vitro diagnostic test that uses targeted next generation sequencing (NGS) of formalin-fixed paraffin-embedded (FFPE) tumor tissue matched with normal specimens from patients to detect gene alterations in a targeted panel covering 606 genes and the TERT promoter. Indications for testing are cancer (solid tumors and hematological malignancies) where a mutational profile from multiple genes would be informative for disease stratification, prognosis, or treatment options including targeted therapies and eligibility for clinical trials. The test is intended to provide information on somatic mutations including point mutations, small insertions/deletions (indels), and copy number aberrations for diagnostic and treatment decisions. LG-PACT is a United States Food and Drug Administration (FDA) cleared diagnostic test (510K: K202304). The clinical interpretation of sequencing data of molecular tumor markers from NGS encompasses automated variant calling tools with human interpretation. This final mostly manual review of data step is intensive, involving highly trained scientists, encompassing literature review, interpretation and clinical tier classification by pathologists, who then provide a complete molecular diagnostic report to the treating oncologists. We provide analysis of 1339 clinical genomic profiles from 31 different cancers and their subtypes, comprising of central nervous system (CNS) 792 (59%) cases (incl. meningioma, glioma and glioblastoma), with 267 (20%) cases predominantly of lung, pancreatic and colorectal and 280 of others (21%). Here, we present the technical challenges of validating an NGS oncological diagnostic targeted assay for clinical grade accuracy and sensitivity for patient care. We show how copy number alterations provide a more comprehensive description of the tumors genomic profile. We then outline the utility of targeted panel sequencing based on certified pathologist selection of reportable variants for our current patient cohort. Where analysis of variant detection has led to 49.4% (661/1339) of our clinical tumor samples containing mutations in known therapy targeted genes, 35.6% (477/1339) with mutation detected in other genes, and 15% (201/1339) cases being negative.
Chung, S. A.; Stelzig, L.; Sherman, M. A.; Gao, W.; Tosta, P.; Cooney, L. A.; Adler, S.; Aslam, N.; Ayoub, I.; Bomback, A. S.; Coppock, G.; Derebail, V. K.; Kamal, F.; Rizk, D. V.; Tuttle, K. R.; Waldman, M.; Barry, W. T.; Nachman, P. H.
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Introduction: B cell depletion with rituximab leads to complete or partial remission (CR/PR) in only ~60% of patients with primary membranous nephropathy (PMN). Adding belimumab to rituximab may result in greater depletion of memory B cells, limit the re-emergence of autoreactive B cells, and improve clinical responses. Methods: REBOOT Part A (NCT03949855) is a single arm, open-label, pharmacokinetic study where all participants had proteinuria [≥] 4g/day and detectable serum anti-phospholipase A2 receptor (anti-PLA2R) antibodies. Participants received belimumab 200 mg subcutaneously weekly for 52 weeks and rituximab 1000 mg intravenously at weeks 4 and 6. Assessments included belimumab exposure at week 4 and CR/PR at week 104. Results: Seventeen participants started belimumab. Belimumab exposure was not significantly reduced in those with high (> 9 g/day) proteinuria at week 4. Among all treated participants, 59% (10/17) achieved CR/PR at week 104, while in per protocol analyses, 91% (10/11) achieved CR/PR at week 104. All participants in per protocol analyses had normal serum albumin and undetectable serum anti-PLA2R by week 104. Circulating memory B cells increased before rituximab and were depleted by rituximab. B cell re-constitution occurred after week 52 with primarily naive and transitional B cells. Belimumab with rituximab was well-tolerated, with one participant discontinuing belimumab due to infection. Conclusion: In this study, a high proportion of participants receiving belimumab with rituximab achieved CR/PR. Thus, a multi-targeted approach to B cell depletion may improve immunologic and clinical outcomes in PMN and is being studied in a larger, randomized, placebo-controlled clinical trial.
Sah, B. K.; Li, C.; Li, J.; Zhu, Z.
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Background Conversion surgery for stage IV gastric cancer is supported by a pooled overall survival hazard ratio of 0.36 (95% confidence interval 0.32-0.40) and, in the largest international cohort, median survival of 36.7 versus 12.5-13.8 months on chemotherapy. Survival is measured from diagnosis; the median diagnosis-to-gastrectomy interval is 124 days, which patients must survive to be counted surgical. Methods We simulated cohorts of 3,177 stage IV gastric cancer patients from published parameters: background median survival 14.5 months; median diagnosis-to-surgery interval 124 days (category-specific 92-174 days). Surgery had no effect (true hazard ratio 1.00 by construction). Data were analysed as the literature analyses them (exposure fixed at baseline, follow-up from diagnosis), and by time-varying Cox and landmark analysis. Confounding by indication was added in a second scenario. Results Under immortal time bias alone the naive analysis returned a hazard ratio of 0.794 (95% simulation interval 0.743-0.851), median survival 16.8 versus 12.8 months. Time-varying Cox recovered 1.000 and landmark analysis 1.000-1.004. Bias scaled with the interval: 0.849 at 92 days, 0.715 at 174 days. Adding confounding, the naive estimate fell to 0.601 (0.560-0.644) at strength 0.5 and 0.356 (0.323-0.385) at strength 1.5, overlapping the published estimate; median survival 21.9 versus 8.7 months. Correcting immortal time alone left residual bias (hazard ratio 0.439). Conclusions The reported survival advantage of conversion surgery is reproducible where the operation does nothing; published estimates cannot distinguish benefit from bias. Resolving this requires individual patient data analysed with methods that assign person-time correctly, or completion of JCOG2301.
Oyarzun Silva, R.; Hernandez Hernandez, P.
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Background. Accurate delineation of the gross tumour volume (GTV) - primary tumour (GTVp) and nodal disease (GTVn) - on FDG-PET/CT is a critical step of head and neck radiotherapy planning. Comparisons between lightweight custom networks and the auto-configured nnU-Net v2 are usually reported as end-to-end pipelines, conflating the contribution of the network with that of the inference-time post-processing applied on top of it. We separated the two. Methods. MiniUNet3D (custom 3D U-Net, 18.3 M parameters) and nnU-Net v2 (3d_fullres, 88.2 M parameters) were trained on the same 578 FDG-PET/CT cases (85/15 author-defined split of the HECKTOR 2025 Task 1 set, 8 centres) and evaluated on the same internal cohort. Three arms were compared pairwise: MiniUNet3D raw output at a fixed 0.5 threshold, MiniUNet3D with a locked adaptive post-processing pipeline, and nnU-Net v2. Comparisons used paired Wilcoxon tests with bootstrap confidence intervals, Bonferroni and Benjamini-Hochberg correction, and Cohen's d; catastrophic failure (Dice < 0.01) was compared with an exact McNemar test. Cases with an empty reference for a given target were excluded from that target's analysis (n = 98 GTVp, n = 93 GTVn). Results. With post-processing matched off, nnU-Net v2 was superior: median GTVp Dice 0.799 versus 0.592 (mean difference -0.244, 95 % CI -0.300 to -0.191; d = -0.88) and GTVn 0.774 versus 0.598 (d = -0.82). Post-processing raised MiniUNet3D to 0.800 (GTVp) and 0.738 (GTVn), recovering 79 % of that difference. Post-processed, MiniUNet3D matched nnU-Net v2 on GTVp Dice (p = 0.113) but remained inferior on nodal disease after Bonferroni correction (Dice p = 0.041; surface Dice p = 0.049). Catastrophic GTVp failures were 25/98 raw, 8/98 post-processed and 1/98 for nnU-Net v2 (McNemar p = 0.016). Inference took 34 s versus 78 s per case on the same GPU. Conclusions. Post-processing recovered most, but not all, of the difference between the two models, and it did not confer robustness: an eight-fold higher rate of empty contours on small primaries persisted, which is the more consequential difference for planning safety. Pipeline comparisons reported without a post-processing ablation risk attributing to a network what post-processing supplied.
Gao, Y.; Yu, S.; Xia, Y.; Chen, S.; Xia, S.; An, R.; Zeng, J.; Zhao, F.; Ma, Y.; Wang, Y.; Xie, X.; Zhang, J.
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Prognostic models in oncology are developed one cancer at a time, from that cancer's own labelled outcomes, and fail where prognostic information is scarcest. Rare cancers account for roughly a fifth of diagnoses and most paediatric malignancies, yet seldom supply enough events for a reliable time-to-event model. We therefore asked whether a representation learned without outcome labels can supply what those cohorts cannot. A Transformer encoder was pretrained by masked field-value modelling on 9425135 tumour records from the SEER 17 registries, diagnosed in 2000 to 2023. Only diagnosis-time fields passing a fail-closed coding-verification gate were admitted, and each record was emitted as an era-specific and a harmonised view, keeping two decades of recoding auditable. The encoder was then frozen and read by a linear Cox head for overall survival. Nine rare cancers were removed from the pretraining corpus entirely, each requiring an independent pretraining run. On a sealed test partition, all nine exceeded an architecture-identical random frozen encoder in Harrell concordance by +0.0034 to +0.0368, every lower confidence limit above zero. At 256 labelled patients, all 67 cancers favoured the pretrained representation over budget-matched Cox regression, median difference +0.0283. The advantage was bounded: given the entire training set, Cox regression was favoured in seven of nine rare cancers. The encoder did not outperform a field-frequency baseline on its own objective, so upstream reconstruction did not predict downstream transfer. Outcome-agnostic registry pretraining carries prognostic signal into cancers it has never seen, and is most useful where labels are fewest, without establishing clinical utility.
Gorobets, O.; Vinh-Hung, V.
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Background: Prostate cancer enzalutamide treatment is approved at a standard dose of 160 mg daily. Concerns for real-world patients -- older and more fragile than those enrolled in clinical trials -- have prompted consideration of initiating treatment with lower doses, but the long-term efficacy of this approach remains unknown. We evaluate the long-term survival and longevity in patients treated with standard versus upfront low-dose enzalutamide. Methods: Retrospective analysis of 151 patients treated with enzalutamide (102 receiving 160 mg; 49 receiving [≤]80 mg) between 2014--2021 at the Centre Hospitalier Universitaire de Martinique, with complete follow-up through end of life (98.7% completeness of follow-up). Primary outcomes were overall survival (OS), progression-free survival (PFS), and longevity (attained age). Results: Doses [≤]80 mg were associated with longer median OS (36.3 vs. 20.7 months), improved restricted mean OS (difference of 0.7 years, p=0.05), and enhanced longevity (median 82.5 vs. 78.3 years, p=0.004). PSA response rate at 12 weeks was higher with lower-dose (71.4% vs. 48.8%, p=0.016). In multivariable models adjusted for prognostic factors, [≤]40 mg compared with 160 mg was non-inferior regarding OS (HR=0.61, 95% CI 0.36--1.06), superior regarding PFS (HR=0.59, 95% CI 0.35--0.99), and superior regarding longevity (HR=0.48, 95% CI 0.28--0.84). Bone metastasis, poor performance status, PSA response, time to PSA nadir, and disease duration were independent predictors of outcomes. A post-hoc analysis revealed a strong association between dose and physician-prescribing profiles, ranging from "endorse-lowest-dose" to "never-deviate-from-full-dose". Conclusions: Lower doses of enzalutamide were non-inferior to full-dose. Dose-adapted strategies warrant further investigation.
Chowdhury, D.; Chatterjee, S.; Chakraborty, S.; Mahata, A.; Vashistha, B.
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Purpose/Objective There is paucity of data reporting outcomes of breast cancers with initial internal mammary nodal involvement and no visceral metastases, treated with curative hypofractionated radiotherapy . We report the outcomes from a tertiary centre alongside spatial patterns of recurrences in the above group Material/Methods For this retrospective cross-sectional study, consecutive patients contoured as per the ESTRO 2013 guidelines, treated between 2016-2022 were eligible if their diagnostic imaging demonstrated involvement of the internal mammary nodes. Radiotherapy (40 Gy/15#/3 weeks) was delivered to the residual breast / thoracic wall, SCF region corresponding to the ESTRO lymph node level 4 and internal mammary chain nodes. Residual IMN/ level 4 nodes received a boost of 10Gy/5#. Spatial mapping of sites of recurrence at the local site and three nodal sites (axilla, SCF and IMN) was performed using deformable image registration. Sites of recurrence at the local site and three nodal levels were contoured separately. Volumetric intersection of the recurrent gross tumour volume (GTV_recurrence) with treated clinical target volume (CTV) was calculated. Actuarial overall (OS), disease free survival (DFS) & cumulative incidence of local (LR), regional (RR) and loco-regional recurrence(LRR) were calculated using Kaplan Meier method. Univariate comparison of outcomes with or without residual disease was performed using the log rank test. Results The median age of the 61 eligible women was 49 years. 77% received neoadjuvant chemotherapy and the rest adjuvant chemotherapy. 82% patients had a mastectomy. Axillary lymph node dissection was done in 96.7%. Boosts to residual IMN and SCF nodes were delivered to 21(34.4%) and 2 (3.3%) respectively. Median follow up was 3.6 years. Out of the 61 patients, 42 patients were disease free with an estimated 3 year disease free survival of 75% (95% CI 64, 88%). Spatial mapping of locoregional recurrence was possible in all but 1 patient with local (only) recurrence who was lost to follow-up after mammogram only. Among the patients with loco regional recurrence 1 had recurrence in local site + SCF +axilla, 3 had recurrence in the SCF+axilla, 2 in the SCF+IMN and 1 in the axilla+SCF+IMN. Only one patient had isolated axillary recurrence or isolated SCF recurrence. There were no IMN only recurrences. Among the 8 patients with nodal recurrence, a total of 27 individual GTV_recurrence were identified in the axilla(n=11), SCF(n=11) and IMN (n=5). IMN recurrences showed complete or partial overlap with CTV. SCF recurrences were a mix with predominantly in-field recurrences while axillary recurrences occurred outside the treated volume.Four (6.6%) patients had Grade 2 lymphoedema as documented late side effect. Conclusion Aggressive treatment of IMN disease with adjuvant radiation is effective with good locoregional control. Systemic recurrences are common and may benefit from intensification strategies.
Mathew, Z.; Mehta, R.; Kim, S.; Jeyaraj, J.; Asif, T.
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Background: Primary malignant cardiac tumors (PMCTs) are rare and histologically heterogeneous. Objective: To compare demographics, specific ICD-O-3 morphologies, first-course treatment patterns, annual registered case counts, and unadjusted overall survival between soft-tissue and hematologic PMCTs. Methods: We identified 730 PMCT cases diagnosed from 2000 to 2021 in SEER 18 (ICD-O-3 topography C38.0). Histologic lineage was assigned from ICD-O-3 morphology. Comparative analyses included soft-tissue (n=458) and hematologic (n=212) tumors. First-course variables were primary-site surgery, chemotherapy (yes versus no/unknown), and radiotherapy (radiation versus none/unknown). Groups were compared with chi-square tests. Overall survival was estimated with Kaplan-Meier methods; follow-up was truncated at 120 months. Results: Soft-tissue PMCTs occurred predominantly at ages 45-64 years (67.9%), whereas hematologic PMCTs occurred predominantly at age [≥]65 years (63.2%; p<0.001). Men comprised 59.9% of hematologic and 49.3% of soft-tissue cases (p=0.014). The leading soft-tissue morphology was hemangiosarcoma/angiosarcoma (ICD-O-3 9120/3; 201/458, 43.9%); synovial sarcoma accounted for 20/458 cases (4.4%). Diffuse large B-cell lymphoma, NOS, accounted for 131/212 hematologic tumors (61.8%). Any primary-site surgery was recorded in 66.6% of soft-tissue versus 15.6% of hematologic cases (p<0.001). Chemotherapy was recorded in 67.5% versus 51.1% (p<0.001), and radiotherapy in 9.0% versus 20.5% (p<0.001). In exploratory Kaplan-Meier analyses, hematologic patients with recorded chemotherapy had higher unadjusted 120-month overall survival than those without recorded chemotherapy (42.0% versus 12.2%; log-rank p=7.5x10-). Radiation-associated survival differences were not statistically significant in either lineage. Conclusions: Soft-tissue and hematologic PMCTs have distinct age distributions, named histologies, and first-course treatment patterns in SEER. These findings describe registry coding and do not establish treatment effectiveness or population incidence.
Niemiec, I.; Shabanova, A.; Ruuska, E.; Tissarinen, M.; Liang, Z.; Anandagoda, G.; Shah, S.; Kang, Z.; Junquera, A.; Salko, M.; Haltia, U.-M.; Virtanen, A.; Farkkila, A.
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High-grade serous ovarian carcinoma (HGSC) responds poorly to immune checkpoint blockade, partly due to a macrophage-dominated immunosuppressive microenvironment. We integrated single-cell spatial proteomics and spatial transcriptomics across 50 HGSC tumors and applied SPACEstat to resolve higher-order immune communities and their transcriptional programs. We identified six immune community types, with macrophage-dominated Myelonets representing the predominant spatial pattern of immune organisation. In chemotherapy-exposed tumors, Myelonets showed coordinated lipid metabolism-immunosuppression and inflammation-MHC-II macrophage transcriptional programs, with SPP1, C1Q, VEGF, MMPs, and CCL18 linked to immunosuppressive states and fibroblasts emerging as key mediators of macrophage communication. Chemotherapy contracted large Myelonets while increasing CD8+ T-cell organization into Lymphonets. Persistent macrophage dominance within Myelonets was associated with adverse outcomes among patients who achieved a complete response to treatment. Together, we identify Myelonets as clinically relevant, multicellular immunoregulatory niches sustained by spatiotemporally coordinated macrophage programs and stromal crosstalk.
Chau, G. N.; Biswas, B. A.; Wagle, B. R.; Maeder, M. E.; Yu, J. B.; Bhattacharya, I.
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Automated lesion segmentation is increasingly central to PSMA PET/CT interpretation, supporting staging, treatment planning, and response assessment at a scale that outpaces available nuclear-medicine expertise. However, automated PSMA-PET/CT whole-body lesion segmentation models are trained on images alone, with no knowledge of where in the body prostate metastases actually tend to occur. Radiologists use clinical domain knowledge of metastatic spread, but its absence in machine learning models produces false positives in anatomically implausible locations and missed lesions in high-risk sites such as the liver. In this work, we explore whether population-level spatial knowledge of metastatic spread can be used to augment deep learning segmentation predictions, and how such a prior should be fused with a network's output, without additional training. We build a data-driven metastasis atlas from 375 expert-annotated whole-body PSMA PET/CT scans and investigate its fusion with a trained segmentation network under a Bayesian framework, in which prediction probabilities from an nnU-Net-based lesion segmentation model serve as the likelihood and the data-driven atlas as the prior. Because metastases occupy only a small fraction of whole-body voxels, the atlas's peak probability is too low, and standard power-scaled or naive Bayesian pooling references lack the tools to deal with this shortcoming. This causes these standard fusion strategies to fail and, in the naive Bayesian case, to sharply degrade performance. We instead derive a calibrated, background-referenced log-odds fusion, one of many possible approaches to combine a population atlas with a deep learning model's predictions, distinct from classical multi-atlas label fusion in that it fuses a single population prior with a trained network's softmax rather than combining several registered atlases. Furthermore, this approach is neutral outside atlas support by construction, reduces exactly to the baseline network when unweighted, and requires no retraining. This atlas fusion significantly improved mean Dice over the baseline nnU-Net on a disjoint internal test set ($+0.011$, Holm-adjusted $p=0.021$) and on an independent external cohort ($+0.0129$, Holm-adjusted $p=3.8\times10^{-16}$), with lesion sensitivity improving from 0.849 to 0.861 internally and Dice improving over baseline in every stratified anatomic region, including the rare, high-risk sites motivating this work, while naive Bayesian pooling degrades performance sharply and power-scaled pooling underperforms it throughout. Our findings suggest that population-level spatial priors can meaningfully augment deep learning predictions in whole-body oncologic segmentation, provided the fusion rule is calibrated to where the prior actually carries signal.
Kristensen, D. T.; Broendum, R. F.; Knudsen, M.; Grubach, L.; Marcher, C.; Preiss, B.; Bibi, M. L.; Hoegdall, E.; Poulsen, T.; Skov, V.; Oerskov, A. D.; Groenbaek, K.; Hansen, J. W.; Schoellkopf, C.; Cowland, J.; Andersen, M. K.; Severinsen, M. T.; Vejgaard, C.; Larsen, O. H.; Vang, S.; Boegsted, M.; Roug, A. S.
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Large genomically annotated acute myeloid leukaemia (AML) datasets exist, but population-based contemporary cohorts remain scarce. Here we report clinicopathological, genomic, and outcome data from Danish AML patients. 2,512 AML patients were identified between 2015-2022, of whom 33.8% had available NGS data (NGS+). In patients [≤]70 years, baseline characteristics and outcomes were comparable between NGS+ and NGS- groups. In patients >70 years, more NGS+ patients received intensive treatment, but survival was similar among intensively treated patients. The distribution of mutations varied significantly by age and sex, with older age and male sex exhibiting higher frequencies of adverse-risk gene mutations. In intensively treated NGS+ patients, ELN2017 stratified 5-year OS: 58.4% (favorable), 43.4% (intermediate), and 28.2% (adverse), with hazard ratios (HRs) of 0.63 (favorable) and 1.45 (adverse) relative to intermediate. ELN2022 yielded corresponding OS rates of 56.9%, 51.8%, and 29.7%, with HRs of 0.78 and 1.86. The two models had comparable predictive performance for OS in a time-dependent model. In conclusion, outcomes of intensively treated AML patients were comparable irrespective of NGS status, underscoring the representativeness of the REFORM-AML database for the Danish AML population. Age and male sex correlated with adverse-risk mutations, and both ELN2017 and ELN2022 robustly predicted survival.
SHI, J.; Gu, Q.; Pan, J.; Yang, A.; Fan, M.
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To evaluate the cost-utility and 5-year budget impact of first-line olaparib plus abiraterone versus abiraterone alone for metastatic castration-resistant prostate cancer (mCRPC) in China after the eleventh round of volume-based procurement (VBP). The intention-to-treat (ITT) population was assigned primary decision-analytic weight; the prespecified BRCA1/2-mutated (BRCAm) subgroup was a supporting analysis.