Citations

Abstract Spatial transcriptomics analyses often require coordinating specialized Python and R methods. When analytical intent is translated through ad hoc scripts or unconstrained LLM generated code, workflows can be difficult to inspect, rerun, or compare. We present ChatSpatial, a schema enforced orchestration framework in which an LLM selects versioned tools and parameters rather than executable code. Built on the Model Context Protocol, ChatSpatial integrates 65 methods across 15 analytical categories into 20 typed tools with curated defaults. In two cancer case studies, ChatSpatial coordinated cross ecosystem workflows that recovered the analytical structure and central conclusions of published ovarian cancer and oral squamous cell carcinoma analyses. Across three LLMs, schema enforcement raised parameter validity from 20% to 98% and stabilized method selection. In end to end benchmarks against two code generation alternatives, it yielded higher execution success and output concordance.

Dominant-inactivating mutations in the colony stimulating factor-1 receptor ( CSF1R ) cause CSF-1R–related leukoencephalopathy (CRL), an adult-onset neurodegenerative disease that is modeled in the Csf1r +/– mouse. CRL is caused by microglial dysfunction. However, the primary microglial deficit is unknown. To address this question, we employed single-nucleus RNA sequencing of brains from young Csf1r +/– mice without pathological or behavioral alterations. Reduction of CSF-1R signaling caused metal ion accumulation in brain macrophages, with concomitant activation of cell death and stress response pathways in oligodendrocytes and neuronal subpopulations. Reduction of metallothionein 1 ( Mt1 ) and 3 ( Mt3 ) gene expression was a common feature in glial and neuronal cells of Csf1r +/– mice. Overexpression of Mt1 restored metal ion homeostasis, normalized ROS production in microglia, and prevented the development of behavioral deficits, while Mt3 deletion had disease-enhancing effects. These findings demonstrate CSF-1R regulation of metal ion homeostasis via metallothioneins in the brain.

PURPOSE The continuous development of new imaging approaches, molecular phenotyping, genetic subtypes, prognosis assessments, and effective therapies across a range of disease states has created a need to redefine terminology and best practices for clinical trial conduct in patients with advanced prostate cancer. Methods We convened an international expert committee of diverse working groups, the Prostate Cancer Working Group 4 (PCWG4), between 2016 and 2025. Our objective was to formulate updated criteria based on emerging evidence and clinical trial data in a biomarker context to provide guidance for clinical trial design, eligibility, and end point assessments for patients with advanced prostate cancer. RESULTS PCWG4 redefines terminology around the disease state and previous therapies in a patient-centric context and terminology focused on androgen pathway modulation. We consider imaging, with a particular focus on positron emission tomography (PET)–defined disease. New recommendations are provided for disease state terminology, defining eligibility criteria, response and delay/prevent end points, intervals for reassessments including imaging, and patient-reported outcome determination. We provide recommendations in a biomarker-based context of use for the intended indication, reflective of patient benefit for specific interventions. We emphasize the need for development of validated PET imaging and molecular and phenotypic criteria as well as trial designs to appropriately risk stratify patients, predict and assess benefit, and measure post-treatment outcomes reliably in a trial framework. CONCLUSION PCWG4 updates recommendations on patient and tumor characterization, therapy development, and imaging criteria and extends guidance into earlier androgen pathway modulator–naïve/sensitive disease states to reflect an evolving, heterogeneous, and diverse patient population to optimize treatment benefits for all patients.

Background Bileaflet aortic valve prevalence in transcatheter aortic valve replacement (TAVR) patients is poorly defined. We evaluated a TAVR cohort to determine the bileaflet aortic valve prevalence and understand features which may improve detection. In addition, we related valvar morphology to the occurrence of permanent pacemaker implantation (PPI) following TAVR. Methods Aortic valvar morphology diagnosis was recorded from the pre-procedural cardiac CTA reports prior to TAVR. Commissural angles, comparison of commissural heights, and dynamic visual inspection of the aortic valve were subsequently evaluated on pre-procedural cardiac CTA by an expert cardiac anatomist and imager, methods previously validated in a surgical cohort, to determine aortic valvar morphology and compared to the historical diagnosis. Relationships between valvar morphological characteristics with the need for PPM within 30-days post-TAVR were determined. Results Four-hundred and thirty-three (mean age 81.3 ± 6.6 years, 53.8% female) underwent TAVR [corrected diagnosis: 393 (90.8%) trileaflet vs. 40 (9.2%) bileaflet valves]. Bileaflet valves were historically misdiagnosed in 80% of pre-procedural cardiac CTA reports. Thirty-four (85.0%) had intercoronary leaflet fusion [mean commissural angle = 148.1 (18.3) degrees]. A commissural angle threshold of 141.1 degrees had a sensitivity of 0.73 and specificity of 0.86 for identifying a bileaflet valve. PPI post-TAVR occurred in 38% bileaflet vs. 19% trileaflet patients ( p = 0.0114 ) [unadjusted OR for bileaflet valve requiring PPI = 2.54, 95% CI (1.25–5.01)]. Conclusions Bileaflet aortic valves are commonly misdiagnosed. Assessment of the commissural angle and comparison of commissural heights may improve CTA-based diagnostic accuracy prior to TAVR. Improved detection may guide improved outcomes in this higher risk population.

ABSTRACT J‐wave syndromes (JWS)—comprising Brugada syndrome (BrS) and early repolarization syndrome (ERS)—are important causes of malignant ventricular arrhythmias and sudden cardiac death in patients whose hearts appear structurally normal. Since the 2016 consensus, advances in genetics, pathophysiology, and therapy have redefined both understanding and management. BrS, once viewed as a purely electrical disorder, is now recognized along a microstructural–electrical continuum, with sodium‐channel dysfunction and subtle epicardial fibrosis of the right ventricular outflow tract as key contributors. Likewise, ERS—historically considered benign—carries significant risk when inferolateral J‐waves coexist with arrhythmic events. Genetically, SCN5A remains the sole gene with definitive disease association, while polygenic susceptibility materially modulates risk, underscoring complex inheritance. Risk stratification remains challenging: patients with prior cardiac arrest or arrhythmic syncope are highest risk, whereas asymptomatic individuals warrant multiparametric assessment integrating clinical features, ECG markers, electrophysiologic studies, and genetics. For decades, treatment centered on implantable cardioverter‐defibrillators and quinidine, both limited by availability, tolerance, and device complications. More recently, epicardial substrate ablation has emerged as a transformative therapy, with large registries and randomized trials demonstrating durable suppression of ventricular fibrillation and acceptable safety. This APHRS‐organized international consensus updates and extends the 2016 Expert Consensus and the 2022 ESC Guidelines, providing contemporary diagnostic frameworks, pragmatic risk‐stratification tools, and treatment algorithms for BrS and ERS. It emphasizes JWS as a microstructural–electrical disease spectrum and elevates substrate ablation as a major therapeutic advance, while outlining priorities for genetics, risk‐stratification and treatment algorithms.

Abstract Adoptive T-cell therapies using tumour-specific T-cell receptors (TCRs) are limited by competition with endogenous receptors, which impairs efficacy and poses risks of off-target autoreactivity. Here we present a CRISPR-based platform that completely and selectively eliminates both endogenous TCR-α and -β chains without affecting introduced transgenic TCRs, irrespective of codon optimization. This approach achieves >90% deletion efficiency in Jurkat and primary human T cells, markedly enhancing the expression, pairing fidelity, and functional potency of transgenic receptors. Using a clinically relevant HLA-A*02:01-restricted DMF5 TCR, we show that dual TCR ablation boosts antigen-specific activation and cytotoxicity in vitro and significantly enhances tumor clearance in vivo in human immune system (HIS) mice, while preventing graft-versus-host disease (GVHD). Targeted locus amplification revealed that CRISPR-induced double-strand breaks did not alter lentiviral integration profiles, confirming genomic safety. Extending this approach to four insulin-reactive TCRs demonstrated that removal of endogenous receptors increased transduction efficiency and functional activity, with one (1E6) showing selective activation and infiltration of stem cell–derived islet grafts (SC-islets) in vivo . This study establishes a universal, safe, and scalable genome-editing platform for generating functionally precise human T cells. By integrating cancer immunotherapy and autoimmune disease modelling within a single framework, it provides a strong preclinical rationale for dual endogenous TCR removal as a route to improved specificity, safety, and therapeutic efficacy in TCR-based cell therapies.

Abstract Background: Survivor plots permit adjustment by baseline demographics and clinical characteristics; log-normal survival analysis may be more robust than a Cox model under departures from model assumptions. We depicted distant disease-free survival (DDFS) for statistically standardized quantitated ER, PgR, and HER2. Methods: We utilized CCTG MA.27 (NCT00066573), an adjuvant phase III trial of exemestane versus anastrozole in postmenopausal women with ER+ and/or PgR+ tumours. IHC ER, PgR, and HER2 HSCORE were centrally assessed by machine image quantitation, and statistically standardized to mean of 0, standard deviation (SD) of 1 following Box-Cox variance stabilization transformations of square for ER, natural logarithm (ln) and square root for PgR, and ln for HER2. For the ln transformation, 0.1 was added to 0 HSCOREs for a stable transformation. The primary endpoint was DDFS at the longest trial follow-up of 4.1 years. For log-normal survival analysis, ln(time) is a linear function of covariates and had a normal distribution; the Cox models were log-linear for covariates. Survival was depicted with log-normal and Cox survivor plots adjusted at the means of age, T and N stage, grade, lymphovascular invasion, treatment, and baseline patient demographics. We examined ER and PgR ASCO/CAP cut-points at (0; >0), HER2 cut-points at (IHC 0, 0 stain; IHC 0, (0,10%] stain; IHC 1+; IHC 2+; IHC 3+), and ER/PgR/HER2 standardized cut-points at standard deviations about mean of 0 (<-1; (-1,0]; (0,1]; >1). P was based on the likelihood ratio criterion (∼Χ2 (1)) for the addition of ER/PgR/HER2 to the model of baseline covariates, and had nominal significance if P<0.05. Log-normal and Cox multivariable regressions with unstandardized and standardized categorical, and continuous, ER, PgR, and HER2 were adjusted by baseline covariates; 2-sided Wald tests had nominal significance if P<0.05. Results: Of 7576 MA.27 patients, 2325 patients had quantitated image analysis assessments for ER, PgR, and HER2; 113 of 2325 (4.9%) patients experienced a DDFS event during follow-up. Multivariable log-normal survival analysis indicated DDFS was significantly longer for patients with T1 (p=0.01), N0 (p=.002), and grade 1/2 tumors (p=0.01); similar significance levels were found with a Cox model. Log-normal survivor plots were smooth, while Cox survivor plots were step-wise discontinuous at events. Adjusted log-normal survivor plots indicated similar 5-year DDFS for patients by standardized ER categories (p=0.43): 95.4% for those with ER <-1.0 (n=401); 95.8%, for (-1.0,0.0] (n=737); 96.1%, for (0.0,1.0] (n=737); and 96.4%, for >1.0 (n=450). The log-normal standardized PgR survivor plots indicated patients had significantly different 5-year DDFS (p<.001) by categories, with both ln and square root transformations of HSCORE: with a ln transformation, 93.7% for <-1.0 (n=607); 95.4%, for (-1.0,0.0] (n=390); 96.8%, for (0.0,1.0] (n=826); and 97.8%, for >1.0 (n=502). Patients had similar 5-year DDFS by standardized HER2 categories (p=0.71): 96.2% for <-1.0 (n=83); 96.0%, for (-1.0,0.0] (n=1201); 95.9%, for (0.0,1.0] (n=527); and 95.7%, for >1.0 (n=514). In full fit multivariable log-normal survival analyses, DDFS was not significantly different for ER (p=0.51-0.89) and HER2 (p=0.12-0.98); higher PgR was associated with significantly better DDFS (p=0.01 to <.001). Adjusted Cox survival analyses had similar results. Conclusions: Survivor plots adjusted for baseline demographic and clinical characteristics provided similar indications of significance for standardized ER, PgR, and HER2 as those seen in multivariable models with both log-normal and Cox survival analyses. Higher PgR was associated with significantly better DDFS. Citation Format: J. W. Chapman, J. Bayani, S. SenGupta, J. M. S. Bartlett, T. Piper, M. A. Quintayo, S. Virk, P. E. Goss, J. N. Ingle, M. J. Ellis, G. W. Sledge, G. T. Budd, M. Rabaglio, R. H. Ansari, R. Tozer, D. P. D'Souza, H. Chalchal, S. Spadafora, V. Stearns, E. A. Perez, K. A. Gelmon, T. J. Whelan, C. Elliott, L. E. Shepherd, B. E. Chen, K. J. Taylor. Survivor plots for quantitated adjunctive statistically standardized ER, PgR, and HER2 in adjuvant postmenopausal breast cancer: Canadian Cancer Trials Group MA.27 trial of exemestane versus anastrozole [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(4 Suppl):Abstract nr PS3-07-23.

Abstract Background: (Z)-endoxifen (ENDX) is an oral SERM that dually targets ERα (> 5 ng/ml) and PKCβ1 (>500 ng/ml). It has been tested in the endocrine resistant setting at doses of 20-360 mg/day; however, the optimal dose in an endocrine naïve population is not defined. We explored 10 mg/day dose of neoadjuvant ENDX in the Endocrine Optimization Pilot (EOP) of I-SPY2. Methods: EOP eligibility included pts with Stage II/III HR+ HER2- breast cancer, MammaPrint (MP) low. Pts with MP High1 scores were eligible if clinically node-negative. Pts received ENDX 10 mg orally once daily for 6 cycles (each cycle = 28 days). Premenopausal pts started ovarian function suppression on cycle 2, day 1. ENDX was continued until the day prior to surgery. The primary study endpoint was feasibility, defined as >75% of pts completing >75% of ENDX. Baseline (T0), 3-wk (T1) biopsies, and the surgical specimen (T3) were assessed centrally for Ki-67. Rates of modified preoperative endocrine prognostic index (mPEPI) 0 were reported, defined as pT1-2 pN0, Ki67< 2.7%, or pathologic complete response. A genomic index for sensitivity to endocrine therapy (SET) index was done at T0. Breast MRI measurement of functional tumor volume (FTV) was performed at T0, T1, 12 weeks (T2), and pre-operatively (T3). Blood was collected for tumor informed ctDNA at T0, T1, T2, T3 and for pharmacokinetic (PK) steady state concentrations (Css) at T1. Safety data using CTCAE V5 is reported. Results: Between March 2023 and May 2024, 20 pts were enrolled in this arm. The median age was 52.5 years (range 32 -73), 13 (65%) were premenopausal, and 55% had clinically positive lymph nodes. Tumors were MPHigh1 in 3 pts (15%) and SET2,3 index high in 16 pts (80%). The primary endpoint was met with 95% of study participants completing ≥75% of therapy. The T0 median Ki-67 was 10.5% (range 2-60%). At T1 (n=19) and T3 (n=18), median Ki-67 was 5% (range 0-35%) and 5% (range 0-45%), respectively. The 3-week rate of Ki-67 ≤10% at T1 was 61.5% in premenopausal and 71.4% in postmenopausal women. The rate of Ki-67 ≤10% at surgery was 81.8% in premenopausal and 57.1% in postmenopausal women. An mPEPI score of 0 was observed in 1 (5%) of participants. The median T0 FTV was 8.9 ccs (range 0.9 to 251.1). The median T3 FTV was 1.3 ccs (range 0 to 11.2) and the median change in FTV from T0 to T3 was -72.0% (range -88.5% to -61.6%). ctDNA analysis was performed in 17 pts longitudinally across 64 blood samples.10 pts had positive ctDNA at T0, with 7 converting to ctDNA undetectable during treatment with ENDX. 1/7 pts who was ctDNA negative at T0 became positive at T1 and then reverted to undetectable ctDNA. The other 6 pts remained ctDNA negative at all timepoints. The median ENDX T1 Css was 79.3 ng/mL (range 73.6 - 906.4 ng /mL). The most common side effects reported were Grade 1 hot flush (70%), nausea (40%), fatigue (40%), and insomnia (35%). Grade 2 side effects included fatigue (15%) and night sweats (5%). No dose reductions or discontinuations due to toxicity occurred. Conclusions: ENDX at 10 mg was well tolerated and demonstrated reductions in Ki-67, MRI FTV, and ctDNA. The ISPY2 EOP is currently enrolling patients to ENDX 40 mg/day (intended to dually target ERα and PKCβ1) in combination with abemaciclib (with and without OFS). Citation Format: K. V. Giridhar, M. P. Goetz, C. Yau, A. M. Wallace, C. Falkson, J. Boughey, M. Arora, E. Stringer-Reasor, C. Nangia, C. Gallagher, A. Elias, A. Zimmer, M. S. Trivedi, C. Omene, L. van 't Veer, L. Brown Swigart, G. L. Hirst, W. Symmans, A. D. Borowsky, N. Onishi, N. Hylton, C. Vakalvas, M. Wei, J. M. Reid, S. Alhafaji, N. Chen, R. M. Mukhtar, L. Huppert, O. Opopade, L. J. Esserman, A. Chein. Low dose (Z)-endoxifen in the I-SPY2 Endocrine Optimization Pilot [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(4 Suppl):Abstract nr PS3-07-10.