Clinical Cancer Research

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.

Purpose: Response-adapted bladder preservation has emerged as a potential alternative to immediate radical cystectomy for selected patients with muscle-invasive bladder cancer (MIBC), but biomarkers to guide treatment de-escalation are lacking. We report the clinical outcomes of the phase II RETAIN2 trial together with a retrospective circulating tumor DNA (ctDNA) analysis of the RETAIN1 and RETAIN2 studies. Patients and Methods: RETAIN2 prospectively evaluated neoadjuvant accelerated methotrexate, vinblastine, doxorubicin, and cisplatin (AMVAC) plus nivolumab followed by response-adapted management based on clinical restaging. A retrospective tumor-informed ctDNA analysis evaluated longitudinal ctDNA dynamics and associations with clinical outcomes. Results: Seventy one evaluable patients were enrolled in RETAIN2. The trial met its primary endpoint, with a 2 year metastasis free rate of 77.5% after a median follow-up of 34.7 months. Among 22 patients managed with active surveillance, 15 (68.2%) remained metastasis free with an intact, non irradiated bladder and 3 (13.6%) developed metastatic disease. In a sensitivity analysis using time to metastasis, the Kaplan Meier estimated 2 year metastasis free probability was 83.7% overall and 85.5% with active surveillance. Retrospective ctDNA analyses were performed in 111 patients from RETAIN1 and RETAIN2. Baseline and post-treatment ctDNA positivity were associated with metastatic progression and inferior overall survival. Among patients managed with active surveillance who were ctDNA-negative after treatment, the 2 year Kaplan Meier estimated metastasis free probability and overall survival were 91% and 97%, respectively. Plasma ctDNA predicted metastatic progression but not intravesical recurrence. Conclusion: Response adapted bladder preservation after neoadjuvant AMVAC plus nivolumab achieved encouraging long term outcomes in selected patients with MIBC. Retrospective ctDNA analyses suggest that plasma ctDNA reflects occult systemic disease rather than bladder confined recurrence and may refine patient selection for bladder preservation. These findings support prospective evaluation of ctDNA guided strategies while emphasizing the continued need for bladder directed surveillance and complementary urinary biomarkers.

Amygdala metabolic activity (AmygAc) measured by [18F]FDG PET has been associated with chronic psychological stress and adverse clinical outcomes, but its relationship with antitumor immunity and treatment response remains incompletely understood. We investigated AmygAc as a host-derived imaging biomarker in non-small cell lung cancer (NSCLC) and examined its association with survival, response to immune checkpoint inhibition (ICI), and the tumor immune microenvironment. Methods: In this multicenter retrospective study, baseline [18F]FDG PET scans from 256 treatment-naive patients with NSCLC were analyzed to quantify AmygAc. Overall survival was assessed in the full cohort, and treatment response was evaluated in 79 patients who subsequently received neoadjuvant ICI therapy. AmygAc was integrated with clinical and tumor-derived imaging parameters. To investigate its biological correlates, tumor tissue from a selected subcohort was analyzed using multiplex immunofluorescence and spatial transcriptomics.

Importance: Recurrence rates in head and neck squamous cell carcinoma (HNSCC) remain high, yet current post-treatment surveillance relies primarily on clinical examination and imaging with known limitations. Circulating tumor DNA (ctDNA) has shown promise for recurrence detection in HPV-positive HNSCC, but less is known about its role in non-virally associated disease. Objective: To evaluate the diagnostic performance of a methylation-based ctDNA assay for detecting recurrence during post-treatment surveillance of non-virally associated HNSCC and to assess its prognostic association with survival outcomes. Design, Setting, and Participants: This retrospective single-institution cohort study included patients with non-metastatic non-virally associated HNSCC who underwent definitive therapy and had at least one Guardant360 ctDNA test during post-treatment surveillance between January 2024 and October 2025. Guardant360 identifies tumor-specific DNA methylation patterns via next-generation sequencing of plasma cell-free DNA. A positive result was defined by a methylation signal of 0.05% or greater. Main Outcomes and Measures: Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and area under the receiver operating characteristic curve (AUC). Progression-free survival (PFS) and overall survival (OS) were estimated using the Kaplan-Meier method. Results: Fifty patients were included; most had larynx (38%) or oral cavity (36%) primaries, AJCC stage IVA-IVB disease (72%), T3-T4 tumors (69%), and N2-N3 nodal classification (48%). Treatment was chemoradiation (54%) or surgery (46%). At a median follow-up of 18.0 months, 13 patients recurred, and 12 had positive ctDNA results. Sensitivity, specificity, PPV, and NPV were 76.9%, 94.6%, 83.3%, and 92.1%, respectively (AUC, .858; 95% CI, .733-.982). Positive ctDNA was associated with worse PFS (1-year: 25.0% vs 96.4%; P < .001) and OS (1-year: 75.0% vs 100%; P < .001). Among 10 patients with recurrence and positive ctDNA, ctDNA preceded clinical detection in 6 (60%) by a median of 131 days. An exploratory analysis identified TP53, SETD2, and ROBO2 mutations as associated with recurrence. Conclusions and Relevance: A methylation-based ctDNA assay demonstrated high sensitivity and specificity for detecting disease recurrence in non-virally associated HNSCC. Positive post-treatment ctDNA was associated with inferior survival and preceded clinical detection in most cases, supporting ctDNA integration into surveillance strategies, though prospective validation is warranted.

Homologous recombination (HR) deficiency underlies a range of cancers, and PARP inhibitors (PARPi) targeting this vulnerability have demonstrated clinical efficacy in BRCA1/2-mutant tumors. However, resistance mechanisms and tolerability issues limit their long-term clinical effectiveness. Here, we characterize RP-3467, a novel, selective small-molecule inhibitor targeting the ATPase domain of DNA polymerase theta (Pol{theta}), the key mediator of the error-prone microhomology-mediated end joining (MMEJ) pathway. We demonstrate that RP-3467 potently suppresses Pol{theta} enzymatic activity, abrogates MMEJ, and disrupts mitotic DNA repair in HR-deficient (HRD) models, inducing synthetic lethality. In preclinical studies, we show that RP-3467 synergizes strongly with PARPi (olaparib and rucaparib), achieving sustained tumor regression across multiple xenograft and patient-derived xenograft (PDX) models without added systemic toxicity. Mechanistically, we find that RP-3467 increases mitotic DNA damage in vivo, as evidenced by elevated micronuclei and CIP2A foci. RP-3467 was evaluated in a phase 1 clinical trial (NCT06560632) and has shown preliminary signs of clinical activity. A heavily pretreated germline BRCA1-mutant ovarian cancer patient achieved a confirmed partial response to RP-3467 plus olaparib (RECIST v1.1), with retrospective profiling revealing a TP53BP1 loss-of-function mutation previously linked to both PARPi resistance and POLQ dependency. Although broader clinical validation is needed, these early findings suggest that Pol{theta} inhibition has the potential to address PARPi resistance and offer therapeutic benefit in HRD cancers.

Purpose To assess whether follow-up MRI, biopsy status, and timing of cribriform disease detection predict active surveillance (AS) failure in a contemporary transatlantic cohort. Materials and Methods. Retrospective MRI-driven AS cohort of 619 men at two academic centers (UK/USA), 2012-2024. Primary outcome: AS failure (disease-specific mortality, metastasis, grade group [GG] [&ge;]4 progression, or post-treatment biochemical recurrence). Key exposures: final MRI and biopsy status, timing of cribriform [&ge;]GG2 detection. Cumulative incidence was derived; independent predictors used multivariable Fine-Gray models. Results. Over median follow-up of 6.4 years, 39/619 men (6%) experienced AS failure. Cribriform [&ge;]GG2 was detected in 82/619 (13%) on follow-up biopsy versus 24/619 (4%) at baseline, comparably in baseline GG1 (10%) and non-cribriform GG2 (9%), and only in MRI-visible tumors. Three-year AS failure after final biopsy was 31% in men with cribriform [&ge;]GG2 versus 0-2% with stable or non-cribriform disease; 44% of failures had stable MRI. On Fine-Gray analysis, cribriform [&ge;]GG2 was the only independent predictor of AS failure in re-biopsied men (SHR 30; 95% CI 5.2-167; P<0.001); no type of MRI progression category was independently predictive. Among 595 men cribriform-negative at baseline, 6-year AS failure after a second biopsy was 34% if cribriform [&ge;]GG2 was detected versus 7% if still cribriform-negative. Conclusions. Cribriform status at follow-up biopsy independently predicts AS failure, whereas MRI progression does not. The three-fold higher cribriform prevalence at follow-up likely reflects baseline sampling error. Because newly detected cribriform tumours were exclusively MRI-visible, early repeat biopsy of patients with MRI-visible disease may considerably improve risk stratification.

Purpose: Mifamurtide (liposomal muramyl tripeptide phosphatidylethanolamine [L-MTP-PE] is approved in many countries for osteosarcoma but remains unavailable for routine use in the United States (US). We describe the feasibility and outcomes of patients with osteosarcoma treated with mifamurtide at Memorial Sloan Kettering Cancer Center (MSK) through expanded access (EAP) and compassionate use (SPU) pathways. Methods: Medical records were retrospectively reviewed for patients with completely resected, high-grade osteosarcoma treated with mifamurtide at MSK from 2016-2026 through EAP or SPU protocols. Mifamurtide 2 mg per meter squared was administered intravenously twice weekly for 12 weeks, followed by weekly administration for 24 weeks. Outcomes were evaluated by treatment setting and, for upfront therapy, metastatic status and histologic necrosis. Results: Fifty-seven patients received mifamurtide (median age, 14 years; range, 2-60); 72% had localized and 28% metastatic disease at diagnosis. No serious adverse events were considered possibly or probably related to mifamurtide, and no new grade 3-4 safety signals emerged. Five patients with localized disease and [&ge;]90% necrosis at resection had no events, with 100% progression-free survival (PFS) and overall survival (OS) at median follow-up of 29 months. Among 22 patients with localized disease and <90% necrosis treated upfront, PFS was 82%, 66%, and 59% at 12, 24, and 48 months, respectively; OS was 95% at 12, 24, and 60 months. Among 8 patients with metastatic disease treated upfront, PFS was 73%, 58%, and 39% at 12, 24, and 36 months, respectively; OS was 100%, 86%, and 86%. Among 22 patients treated after relapse, PFS was 34%, 23%, and 17% at 12, 24, and 36 months, respectively; OS was 91%, 70%, and 35% at 12, 24, and 60 months. Conclusions: In this real-world US cohort, mifamurtide was feasible and safe to administer. Despite limitations of the EAP/SPU setting, single-institution administration, and patient heterogeneity, overall survival outcomes were encouraging.

Background: Prostate-specific membrane antigen (PSMA) positron emission tomography (PET) is increasingly used to characterize newly diagnosed prostate cancer on the assumption that uptake highlights aggressive disease. However, maximum standardized uptake value (SUVmax) varies widely across localized tumors. Recent genomic assessments have suggested SUVmax reflects tumor biology even when accounting for other tumor indices. Here, we examined highly annotated pathologic, imaging and clinical correlates of intraprostatic SUVmax at the level of individual tumor foci in a prospective multimodal cohort. Methods: Exploratory lesion-level analysis of the radical prostatectomy arm of a single-center prospective diagnostic-accuracy trial (NCT04461509). Patients underwent simultaneous 18F-DCFPyL PSMA PET, multiparametric magnetic resonance imaging (MRI) and high-resolution MRI before prostatectomy, with central blinded pathology and imaging review. Grade Group (GG) [&ge;]2 foci measuring [&ge;]10 mm were eligible. The primary outcome was focus-level SUVmax. Correlates spanning histology, tumor microenvironment, MRI and clinical indices were examined by Spearman correlation and rank-based group comparison, followed by separate linear regressions of log(1+SUVmax) each adjusted for GG and tumor size. A digital-pathology sensitivity analysis quantified immune, stromal and tumor pixel-area fractions on hematoxylin and eosin (H&E) sections from a subset of foci using a trained QuPath classifier. Results: Twenty-seven patients contributed 34 tumor foci, of which 21 (61.8%) were GG2. Median SUVmax was 5.7 (interquartile range [IQR] 3.9 - 12.1; range 0.0 - 57.9). SUVmax rose across the cribriform/intraductal carcinoma (Crib/IDC) gradient (median 3.9, 4.8 and 10.2 for absent, focal and extensive; p = 0.010), correlated with % Gleason pattern 4 ({rho} = +0.47, p = 0.005) and correlated inversely with stromal content ({rho} = - 0.40, p = 0.020). Grade Group (p = 0.115), Prostate Imaging Reporting and Data System (PI-RADS) 4 versus 5 (p = 0.705), standard apparent diffusion coefficient (ADC) ({rho} = - 0.27, p = 0.130), baseline prostate-specific antigen (PSA) ({rho} = +0.04, p = 0.816) and PSA density ({rho} = - 0.02, p = 0.918) were not associated with SUVmax. In separate models of log(1+SUVmax) adjusted for Grade Group and tumor size, % Gleason pattern 4 remained associated with uptake (standardized {beta} = +0.76, 95% CI +0.11 to +1.41), Crib/IDC ({beta} = +0.36, - 0.03 to +0.74), and stromal content ({beta} = - 0.30, - 0.62 to +0.02). On 18 slides re-quantified by pixel classifier, no pixel-based compartment fraction correlated with SUVmax (immune {rho} = - 0.06, stroma {rho} = +0.02, tumor {rho} = - 0.04; all p > 0.5). Conclusions: In this prospective lesion-level cohort, intraprostatic PSMA SUVmax was associated with increased Gleason pattern 4 and cribriform/intraductal burden but not with other common risk indices. SUVmax therefore appears to carry information additive to conventional risk factors. Further investigations examining the tumor biology that reflects SUVmax are warranted.

Epithelioid sarcoma (EpS) is an ultra-rare, aggressive soft tissue sarcoma (STS) driven by INI1 loss and consequent hyperactivation of the chromatin-modifying enzyme EZH2. Although the EZH2 inhibitor tazemetostat has shown clinical activity, responses remain limited, highlighting the need for improved treatment strategies. Here, using two in-house generated patient-derived xenograft models and matched cell lines derived from INI-1 deficient EpS, we investigated EZH2 inhibition in combination with doxorubicin, the first-line standard for advanced STSs, identifying distinct patterns of response and resistance. Integrated transcriptomic and functional analyses revealed that response to EZH2 inhibition-based therapy was associated with chromatin remodeling, characterized by increased H3K27 acetylation and downregulation of histone deacetylase (HDAC)-related transcriptional programs. Conversely, the intrinsically resistant model failed to undergo this epigenetic transition despite EZH2 inhibition. Pharmacological HDAC inhibition restored H3K27 acetylation, promoted apoptosis, and enhanced the activity of EZH2 inhibition-based therapy. These findings identify failure to accumulate H3K27 acetylation as a hallmark of resistance to EZH2 inhibition-based treatment, and show that pharmacological HDAC inhibition can restore this chromatin transition and re-sensitize resistant tumors, providing a rationale for combined epigenetic targeting strategies in INI1-deficient malignancies. Translational relevanceProspective trials are challenging in rare tumors such as epithelioid sarcoma (EpS), limiting the level of evidence for existing therapies and the development of new agents. This is particularly relevant for EpS, where drug regimens are those used for all soft tissue sarcomas (STSs), and the specific mechanisms of drug response remain poorly understood. This preclinical study of tazemetostat in combination with doxorubicin shows differential outcomes in two INI1-deficient proximal-type EpS models, providing evidence of the heterogeneity that exists even within the same tumor subtype and fostering the need to better understand the molecular mechanisms driving drug sensitivity/resistance in this disease. In addition, we demonstrated the potential to treat EpS models through modulation of epigenetic mechanisms, showing that HDAC inhibition may restore sensitivity to EZH2-targeted therapy. These findings support the rationale for developing combination strategies incorporating epigenetic modulators and provide a preclinical framework for overcoming resistance to current therapies in EpS.

Background: 177Lu-PSMA-617 radioligand treatment represents a major advancement in the management of metastatic castration-resistant prostate cancer (mCRPC), but key questions remain about tumor-cell dynamics and evolution in patients who have received this drug. Here, we used a circulating tumor cell (CTC) capture assay to assess the prognostic capacity of CTC subset dynamics following 177Lu-PSMA-617 treatment in a cohort of mCRPC patients. Methods: Using an AI-empowered holographic imaging platform combined with in-flow protein marker analysis, we prospectively analyzed serial CTC samples from patients receiving 177Lu-PSMA-617 therapy at pre-treatment and on-treatment time points (n=39 of 100 enrolled patients). PSMA and EpCAM proteins in CTCs were determined by immunofluorescence staining. Proportions and absolute counts of CTC subsets delineated by PSMA and EpCAM proteins were assessed in PSA50 responders (n=19) and non-responders (n=20). Within-patient changes in CTC subsets were compared using Wilcoxon signed-rank tests with Benjamini-Hochberg correction. Associations of CTC subset abundance and dynamics with overall survival were assessed using Kaplan-Meier estimates with log-rank tests and univariable Cox proportional hazards models. Results: PSMA and EpCAM stratified CTCs into subsets, some of which were associated with survival outcomes following 177Lu-PSMA-617. We observed an increase in the proportion of PSMA-/EpCAM+ CTCs following 177Lu-PSMA-617, with a larger increase occurring in PSA50 responders (6.2% to 18.7%; p=0.041) than non-responders (7.9% to 15.4%; p=0.023). This corresponded to a decrease in the proportion of PSMA+/EpCAM- CTCs, whereas the proportion of PSMA+/EpCAM+ CTCs did not decline. On-treatment counts of >5 CTCs, relative to [&le;]5 CTCs, were associated with shorter overall survival in the PSMA+/EpCAM+ (HR 3.56, 95%CI 1.32-9.60, p=0.012) and PSMA+/EpCAM- (HR 7.50, 95%CI 0.96-52.99, p=0.054) subsets. Finally, on-treatment declines in PSMA+/EpCAM+ (HR 0.74, p=0.49) and PSMA+/EpCAM- (HR 0.61, p=0.215) CTC subsets were not significantly associated with overall survival relative to sustained high levels of these cells. Conclusions: In mCRPC patients receiving 177Lu-PSMA-617, dynamic changes in CTC subsets delineated by PSMA and EpCAM expression may have prognostic value, justifying additional evaluation.

Background: Circulating tumor DNA (ctDNA) is an emerging biomarker of treatment response and recurrence risk, while residual cancer burden (RCB) after neoadjuvant treatment (NAT) is a well-established risk factor for distant recurrence. Here, we examined the association between high ctDNA concentration at diagnosis and risk of distant recurrence after neoadjuvant treatment (NAT), in the context of RCB. Methods: The study included 712 patients with high-risk breast cancer in the neoadjuvant I-SPY2 trial. Tumor-informed ctDNA test results at diagnosis were used to stratify patients into ctDNA-negative and ctDNA-positive groups. For this analysis, the ctDNA-positive group was divided into tertiles (low, intermediate, high) based on ctDNA concentration reported as mean tumor molecules per mL [MTM/mL] of plasma. Correlations between MTM/mL at diagnosis and ctDNA dynamics during NAT, residual cancer burden (RCB), and distant recurrence-free survival (DRFS) were examined across all subtypes. Results: In all subtypes, high ctDNA concentration at diagnosis was associated with worse DRFS, whereas low ctDNA concentration or ctDNA-negative status was associated with improved DRFS, even with high tumor burden after NAT (RCB-II/RCB-III). We also found that patients with high ctDNA concentration, regardless of subtype, were less likely to experience early ctDNA clearance; however, those who did had a significantly higher likelihood of achieving a favorable response (RCB-0/RCB-I) than those with late or no ctDNA clearance. Furthermore, across all subtypes, patients with early ctDNA clearance, including those with substantial residual cancer (RCB-II/RCB-III) after NAT, had improved DRFS, irrespective of the ctDNA concentration at diagnosis. Conclusions: Across all subtypes, pathologic response and ctDNA clearance reduce the risk of distant recurrence associated with high ctDNA concentration at diagnosis. ctDNA concentration at diagnosis and ctDNA clearance dynamics during NAT may facilitate the prediction of treatment response and further stratify the risk of metastatic recurrence in non-responders.

Background: Liquid biopsy-based monitoring of circulating tumor DNA (ctDNA) holds promises for real-time assessment of tumor burden and treatment response in precision oncology. However, mutation-based approaches alone show limited sensitivity, particularly in low-shedding tumors. We evaluated whether integrating epigenomic biomarkers (specifically LINE-1 retrotransposon (L1PA) hypomethylation and copy number variation (CNV)) with standard mutation-based ctDNA analysis could improve cancer detection and longitudinal monitoring in patients enrolled in the SHIVA02 precision oncology trial. Methods: We performed a retrospective analysis of 32 patients with advanced or metastatic solid tumors who received molecularly matched targeted therapies within the SHIVA02 trial (NCT03084757). Plasma samples were collected at baseline and longitudinally every two months and at progression. Multimodal ctDNA profiling was performed using the DRAGON targeted NGS panel covering SNVs, indels and focal CNVs in 571 genes and the DIAMOND assay profiling L1PA methylation and genome-wide CNV. A three-step classification algorithm integrating maximum variant allele frequency (MaxVAF), L1PA methylation-based cancer probability (MethPCancer), and genome-wide CNV scores was developed to maximize ctDNA detectability. Results: At baseline, mutation-based profiling detected ctDNA in 62.5% of patients. L1PA hypomethylation alone identified ctDNA in 78.1% of patients, including cases with undetectable mutations. The three-step integrative model increased overall detectability to 93.8%. Concordance analyses between tumor tissue and plasma revealed that 80.6% of mutations and 60% of CNVs identified in tumor biopsies were detectable in matched ctDNA. The three modalities showed limited pairwise correlation at baseline, supporting their complementarity. Longitudinal analysis demonstrated that changes in MaxVAF, MethPCancer, and L1PA CNV scores over time were informative on treatment response across tumor types, with ctDNA detected in 94.5% of samples collected at disease progression. In selected patients, ctDNA alterations preceded radiological progression by four months. Conclusions: Multimodal ctDNA profiling integrating mutation analysis, CNV profiling, and LINE-1 hypomethylation substantially improves ctDNA detection at baseline and during treatment in a pan-cancer precision oncology setting. These complementary genomic and epigenomic biomarkers provide a more comprehensive and dynamic assessment of tumor burden than single-modality approaches, supporting prospective validation in larger cohorts for integration into precision oncology workflows.

Background Immune checkpoint inhibitor (ICI) therapies have revolutionized oncology, but identifying patients who benefit remains a challenge, particularly in populations where ICIs are not the standard of care, including microsatellite stable colorectal cancer (MSS CRC) and rare solid cancers. We evaluated real-world performance of the Immune Profile Score (IPS), a validated DNA- and RNA-based molecular signature, in these cohorts. Methods In an exploratory analysis, we analyzed two real-world cohorts: 1) MSS CRC; and 2) MSS, tumor mutational burden-low rare solid cancers treated with off-label ICI. IPS-High and IPS-Low were calculated using a previously validated threshold. Cox proportional hazards models were fit to demonstrate prognostic utility for real-world overall survival (rwOS). In MSS CRC, time-to-next-treatment (TTNT) on prior non-ICI therapy was compared to rwOS on subsequent ICI therapy. Results In MSS CRC (n=46), IPS-High patients (13%) demonstrated clinically meaningful improvement in rwOS versus IPS-Low (Median OS: not reached vs 7.3 months; HR = 0.22, 90% CI 0.04-1.16). While IPS was not associated with TTNT on the preceding non-ICI line (HR = 1.07, 90% CI 0.60-1.91), it was associated with OS in patients receiving later line ICI (HR 0.21, 90% CI 0.04-1.22). In the rare cancers cohort (n=90; 26 unique malignancies), IPS-High (17.8%) was associated with longer OS to ICI therapy (HR = 0.26, 90% CI 0.11-0.61), even when restricted to histologies represented in both IPS groups (HR = 0.18, 90%, CI 0.05-0.62). Conclusions Preliminary evidence suggests that IPS may serve as a generalizable, pan-cancer biomarker capable of stratifying outcomes for ICI treatment in populations traditionally excluded from immunotherapy benefit.

Background: Immune checkpoint inhibitors (ICI) are efficacious in many solid tumors, but response in glioma is restricted to a small subgroup. The determinants of response and resistance to ICI remain poorly understood. Methods: Here we exploit a syngeneic hypermutated high-grade glioma model with dichotomous response to combined PD-1 and CTLA-4 inhibition to unravel determinants of tumor-infiltrating T-cells driving response. Tumor-infiltrating T-cells from ICI-responsive and non-responsive tumors were analyzed by single-cell RNA and T-cell receptor sequencing and tumor-reactive T-cell receptor clonotypes were functionally validated to characterize their transcriptional phenotypes. We verify our findings in IDH1 wildtype glioblastoma patients treated with neoadjuvant pembrolizumab. Results: ICI response was associated with intratumoral clonal expansion of tumor-reactive cytotoxic T-cells and increased infiltration of CXCR6+ CD4+ tissue resident memory T-cells (Trm). CD4 stem-like memory T-cells in responding tumors demonstrated elevated interferon responses, following trajectories toward clonally expanded Trm, versus trajectories toward exhaustion in non-responsive tumors. In responsive tumors, CD4+ Trm interacted with infiltrating CXCR3+ tumor-reactive and clonally expanded, yet transcriptionally versatile cytotoxic T-cells. Probing the post neoadjuvant ICI high-grade glioma patient tissue dataset, we confirmed increased CXCR6 expression in CD4+ T cells and the association of CD4+ Trm with prolonged overall survival. Conclusion: These findings identify CD4 tissue-resident memory T-cells as determinants of ICI response in IDH1 wildtype high-grade glioma and warrant their further investigation to improve immunotherapy outcomes.

Background: Relapsed and refractory osteosarcoma (OS) remains a major therapeutic challenge, with fewer than 20% of patients surviving beyond 3 years. Increasing evidence indicates that MYC amplification/overexpression is associated with inferior survival. Small molecule inhibitors and immunotherapies have limited single-agent efficacy in pediatric solid tumors. Using syngeneic cell lines derived from p53-driven and MYC-hyperactivated genetically engineered mouse models (GEMMs) of OS, we tested cabozantinib, a multi-tyrosine kinase inhibitor with immunomodulatory properties, with TIGIT immune checkpoint blockade and investigated mechanisms underlying therapeutic response and resistance. Methods: In vitro cabozantinib sensitivity was established in GEMM-derived cell lines. Mice bearing tibial tumors were randomized to vehicle control, cabozantinib, anti-TIGIT antibody, or combination therapy, and tumor growth and survival assessed after a 3-week treatment period. Temporal RNA sequencing was performed at early (8-15 days) and late (18-24 days) time points to characterize transcriptomic changes associated with efficacy. Results: MYC-hyperactivated cell lines were more resistant to cabozantinib in vitro than p53-driven lines (mean IC50 5.51 vs 0.65 mciroM, p=0.0016). In p53-driven orthotopic models, combination therapy significantly decreased tumor growth and improved survival compared to solvent and cabozantinib alone, while in MYC-hyperactivated models cabozantinib-containing regimens delayed tumor progression relative to control or anti-TIGIT monotherapy, however the addition of anti-TIGIT did not significantly improve survival over cabozantinib alone. Temporal transcriptomics revealed upregulated anti-tumor immune-response pathways and decreased M2 macrophages only with combination treatment in the p53-driven model. In contrast, combination-treated MYC-hyperactivated models demonstrated increased TNF signaling and elevated Cxcl5 and Ccr2 expression, indicative of increased myeloid cell recruitment, and upregulation of extracellular matrix (ECM) remodeling pathways suggest a therapy-induced stress adapted state that propagates treatment resistance over time. Conclusion: New therapies are needed for patients with relapse or refractory OS. By targeting tumor-intrinsic resistance mechanisms and modulating the tumor microenvironment using cabozantinib and anti-TIGIT therapy, improved tumor control and survival was achieved in p53-driven orthotopic OS models. MYC-hyperactivated models were able to overcome therapeutic pressure and employ myeloid recruitment and ECM remodeling programs to achieve treatment resistance. Targeting of these programs should be considered in future studies investigating therapeutic strategies in relapsed and refractory OS.

PurposeSWI/SNF (BAF) chromatin remodeling complex alterations are common in urothelial carcinoma, yet no biomarker-directed therapeutic strategies have been established for this population. We investigated whether BAF alterations delineate a biologically distinct, therapeutically actionable urothelial carcinoma subtype. Experimental DesignWe performed integrative genomic and transcriptomic analyses of 792 urothelial carcinoma tumors from the Oncology Research Information Exchange Network (ORIEN) and validated findings in the TCGA-BLCA cohort. Mechanistic studies incorporated RNA sequencing and ATAC-seq following histone deacetylase (HDAC) inhibition. Functional dependencies were assessed using patient-derived xenograft organoids and cell line models. Clinical relevance was explored in a biomarker-enriched investigator-initiated trial. ResultsApproximately half of urothelial carcinoma tumors exhibited BAF alterations, defining a previously unrecognized chromatin-altered molecular subtype characterized by activation of proliferative programs, loss of lineage identity, and altered metabolic signaling. This subtype was enriched for transcriptomic programs associated with HDAC inhibitor sensitivity and depleted of HDAC inhibitor resistance signatures. Mechanistically, HDAC inhibition induced widespread chromatin remodeling with reduced accessibility at AP-1 and TEAD-associated regions, and downregulation of E2F- and MYC-driven transcriptional networks. Functional studies confirmed enhanced HDAC inhibition sensitivity in ARID1A-mutated cell lines and a patient-derived organoid model. Early clinical observations demonstrated a durable responder treated with HDAC inhibitors and immunotherapy. ConclusionsBAF alterations define a chromatin-dependent tumor state in urothelial carcinoma that is selectively vulnerable to HDAC inhibition. Integrating genomic, epigenomic, functional, and early clinical evidence, these findings provide a rationale for biomarker-enriched clinical trials and HDAC inhibitor-based combination strategies in urothelial carcinoma.

IDH inhibitors promote differentiation and hematological improvement in myeloid malignancies by reversing epigenetic dysregulation. However, molecular predictors of response remain poorly defined. We retrospectively analyzed 79 patients with IDH mutated myeloid malignancies treated with either ivosidenib (IDH1; n=36) or enasidenib (IDH2; n=43). Hematologic benefit was assessed using a composite complete hematologic response (CHR), defined by neutrophil and platelet recovery, and transfusion independence. Targeted sequencing was performed at baseline and at best hematologic response. Associations between co mutations, hematologic response, and treatment duration were evaluated using multivariable models. Overall, 43% of patients achieved CHR, with similar rates between inhibitors. Ivosidenib treated patients achieving CHR demonstrated a significant reduction in IDH1 VAF (p=0.010), which was not observed in enasidenib-treated CHR patients. Within the CHR cohort, ivosidenib patients had a greater reduction in IDH VAF relative to enasidenib patients (mean VAF change -16.74% vs -0.05%, p=0.034). Ivosidenib responders demonstrated a trend toward more durable treatment duration compared with enasidenib responders (p = 0.0908). RUNX1 and BCOR mutations were significantly enriched among patients with incomplete hematologic response and were independently associated with shorter treatment duration after adjustment for clinical factors (RUNX1: HR 2.53, p=0.0024; BCOR: HR 2.31, p=0.0058). IDH1 inhibition was associated with clonal contraction and durable hematologic benefit, a pattern not observed with IDH2 inhibition. Co mutations in RUNX1 and BCOR identified patients unlikely to achieve sustained hematologic improvement, suggesting a secondary block to differentiation. These findings support the integration of mutational and molecular profiling to refine patient selection and guide combinatorial strategies in IDH mutated myeloid malignancies.

The limited efficacy of immune checkpoint inhibitor (ICI) therapy in triple-negative breast cancer (TNBC) highlights the need for combination strategies that enhance antitumor responses. Sorafenib, a multikinase inhibitor with anti-angiogenic and immunomodulatory activity, represents a rational partner for ICI-based combination therapy. However, therapeutic responses to such combinations are biologically complex and cannot be fully characterized by any single biomarker or imaging modality. Here, we evaluated ICI therapy combined with sorafenib in the aggressive and ICI-refractory orthotopic 4T1 TNBC model. Therapeutic responses were assessed using a unique longitudinal multimodal imaging framework integrating [Zr]Zr-DFO-anti-CD8 minibody and [{superscript 1}F]FDG PET, as well as perfluorocarbon (PFC)-based {superscript 1}F MRI and hyperpolarized {superscript 1}3C MRS, together with ex vivo analyses. Only the ICI-sorafenib combination suppressed tumor growth, whereas both monotherapies showed limited antitumor activity. Multimodal imaging, together with complementary ex vivo analyses, uncovered coordinated tumor microenvironment (TME) remodeling, including vascular normalization, elevated CD8 cell presence with modest enrichment in the tumor center, delayed increase in phagocyte-associated {superscript 1}F MRI signal coupled with reduced CD206 cell infiltration, and sustained metabolic activity. These findings support ICI-sorafenib combination therapy as a promising therapeutic strategy for TNBC. Therapeutic efficacy reflected coordinated vascular, immune, and metabolic remodeling. This multimodal imaging framework enables non-invasive longitudinal monitoring of these complementary TME changes, providing a comprehensive strategy for treatment assessment in immunotherapy-based combination therapies. One Sentence SummaryLongitudinal multimodal imaging identified a multidimensional TME response signature of effective ICI-sorafenib therapy in TNBC.

Introduction: Tumor mutational burden (TMB) is a biomarker for immune checkpoint inhibitor therapy, traditionally measured in tissue (tTMB). Blood-based TMB (bTMB), derived from circulating tumor DNA, is minimally invasive but shows modest concordance with tTMB. The significance of blood-tissue TMB discordance remains unclear. Methods: We retrospectively analyzed 105 patients with advanced NSCLC who underwent pretreatment blood and tissue next-generation sequencing between October 2020 and September 2024. The blood-to-tissue TMB ratio was defined as ln[(1 + bTMB)/(1 + tTMB)]. Outcomes were overall survival (OS) and progression-free survival (PFS). Survival was assessed using Kaplan-Meier methods and multivariable Cox models. Results: Median follow-up was 10 months. Patients in the lowest ratio tertile had longer OS than those in the upper two tertiles (median, 33 vs 11 months; hazard ratio [HR], 0.55; 95% confidence interval [CI], 0.32-0.97; p = 0.04), whereas PFS did not differ (HR, 0.89; p = 0.62). A higher ratio, analyzed continuously, was independently associated with shorter OS (HR per 1-unit increase, 1.60; 95% CI, 1.10-2.31; p = 0.01), but not PFS. The association persisted after adjustment for metastatic organ count and radiographic tumor burden. The high-bTMB/low-tTMB subgroup had the poorest OS (HR, 3.17 vs low-bTMB/high-tTMB; p = 0.01). Conclusions: A higher blood-to-tissue TMB ratio was independently associated with worse OS in advanced NSCLC. Directional discordance between bTMB and tTMB may reflect tumor heterogeneity and provide prognostic information beyond either measure alone.

Background Chemotherapy (CT) de-escalation strategies based on dual HER2 blockade with trastuzumab and pertuzumab (HP) have shown promising efficacy in HER2-positive (HER2+) early breast cancer (EBC), but biomarkers to guide patient selection are lacking. The Ataraxis Breast platform (ATX) uses artificial intelligence (AI) models integrating hematoxylin-eosin (H&E) whole-slide images and clinical variables to predict pathological complete response (pCR) and long-term outcomes. We evaluated ATX in the phase II PHERGain (NCT03161353) and PHERGain-2 (NCT04733118) trials. Methods The ATX NEO model was assessed for pCR prediction in PHERGain (n=306 evaluable patients) and PHERGain-2 (n=383 evaluable patients). The ATX RISK model was evaluated for prognosis in PHERGain (n=309 evaluable patients). Prespecified cutoffs classified patients into low-, medium-, and high-probability groups for pCR and low- or high-risk groups for recurrence. Associations with pCR were assessed using logistic regression. Prognostic performance was evaluated using Cox proportional hazards models, Kaplan-Meier estimates, and Harrell's C-index. Results Overall pCR rates were 40.2% in PHERGain and 60.3% in PHERGain-2. Continuous NEO scores were significantly associated with pCR in both PHERGain (odds ratio [OR], 1.28; 95% CI, 1.11-1.48; P<0.001) and PHERGain-2 (OR, 1.30; 95% CI, 1.13-1.52; P<0.001). Using prespecified cutoffs, pCR rates increased across low-, medium-, and high-probability groups (19.2%, 41.3%, and 48.3% in PHERGain; 29.5%, 61.6%, and 70.1% in PHERGain-2). In PHERGain, the RISK score was significantly associated with event-free survival (hazard ratio per 1-SD increase, 1.56; 95% CI, 1.17-2.08; P=0.002; C-index, 0.66). Five-year event-free survival was 93.9% in the low-risk group and 83.1% in the high-risk group. Conclusions NEO score was consistently associated with pCR across two independent HER2+ EBC trials, while RISK score provided prognostic information for long-term outcomes in PHERGain. Prespecified score categories identified clinically distinct response and risk groups. These findings support further evaluation of AI-based biomarkers to refine patient selection for CT de-escalation strategies in HER2+ EBC.