Citations

Abstract Motivation Intratumor heterogeneity arises from ongoing somatic evolution and complicates cancer diagnosis, prognosis, and treatment. Reconstructing evolutionary dynamics typically requires spatiotemporal samples, which are often unavailable in clinical settings. Computational approaches that can infer tumor evolutionary history from single-timepoint bulk sequencing data remain limited. Results We present estimating evolutionary events through single-timepoint sequencing (TEATIME), a novel computational framework that models tumors as mixtures of two competing cell populations: an ancestral clone with baseline fitness and a derived subclone with elevated fitness. Using cross-sectional bulk sequencing data, TEATIME estimates mutation rates, timing of subclone emergence, relative fitness, and number of generations of growth. To quantify intratumor fitness asymmetries, we introduce a novel metric—fitness diversity—which captures the imbalance between competing cell populations and serves as a measure of functional intratumor heterogeneity. Applying TEATIME to 33 tumor types from The Cancer Genome Atlas, we revealed divergent as well as convergent evolutionary patterns. Notably, we found that immune-hot microenvironments constraint subclonal expansion and limit fitness diversity. Moreover, we detected temporal dependencies in mutation acquisition, where early driver mutations in ancestral clones epistatically shape the fitness landscape, predisposing specific subclones to selective advantages. These findings underscore the importance of intratumor competition and tumor-microenvironment interactions in shaping evolutionary trajectories, driving intratumor heterogeneity. Lastly, we demonstrate that TEATIME-derived evolutionary parameters and fitness diversity offer novel prognostic insights across multiple cancer types. Availability and implementation R implementation of TEATIME is available on GitHub (https://github.com/liliulab/TEATIME) and Zenodo (https://zenodo.org/records/17422174).

Objective: This post hoc analysis of the CHAMPION-NMOSD trial evaluated the safety and efficacy of ravulizumab in patients with aquaporin-4 antibody-positive (AQP4-Ab+) neuromyelitis optica spectrum disorder (NMOSD) previously exposed or naïve to rituximab (RTX). Methods: Patients received weight-based intravenous ravulizumab with a loading dose followed by maintenance dosing every 8 weeks. Patients were stratified by prior RTX exposure: no RTX exposure (RTX-naïve) vs RTX exposure > 3 months before initiating ravulizumab (RTX-exposed). Key outcomes included treatment-emergent adverse events (TEAEs), serious TEAEs (TESAEs), relapse rates, and vaccination timing from the last RTX dose. Results: Of the 58 patients enrolled, 89.7% were female, with a mean age of 47.4 years, and 21/58 (36.2%) were RTX-exposed. Relapses occurred in 12/21 (57.1%) RTX-exposed patients between their first RTX dose and study entry. The safety profile of ravulizumab was generally similar between RTX-exposed and RTX-naïve groups. Common TEAEs included COVID-19, headache, urinary tract infection, and upper respiratory tract infection. UTIs were more frequent in RTX-exposed individuals. One patient in each group experienced a meningococcal infection. No adjudicated on-trial relapses were reported while on ravulizumab. Conclusions: Following initiation of ravulizumab, RTX-exposed and RTX-naïve patients with AQP4-Ab+ NMOSD achieved sustained disease control and demonstrated a manageable safety profile. Clinical Trial Information: The CHAMPION-NMOSD Trial; ClinicalTrials.gov identifier: NCT04201262 (registered October 06, 2020).

Abstract INTRODUCTION The tau positron emission tomography (PET) overlap index (OI) has shown promise in maximizing signal‐to‐noise for longitudinal tau PET imaging, particularly for early tau pathology, but requires validation against neuropathology. METHODS Fifty‐seven participants who underwent serial tau PET imaging (flortaucipir) and subsequent autopsy were included. Tau PET OI and standardized uptake value ratios (SUVRs) were compared across neuropathological diagnoses. RESULTS Tau PET OI showed greater concordance with neurofibrillary tangle (NFT) severity in the entorhinal cortex (a key region for Alzheimer's disease [AD] tauopathy) than SUVR, particularly in early Braak tangle stages (positivity: 52.2% for OI vs. 13.0% for SUVR). OI detected overlapping tau voxels that exhibited spatial correspondence with immunohistochemical and autoradiography measures of tau deposition across both AD and non‐AD tauopathies. DISCUSSION These findings demonstrate the enhanced capacity of OI in serial tau PET to robustly detect early and spatially localized tau pathology, supporting its application as a sensitive imaging metric in AD and select non‐AD tauopathies.

Abstract Rare Mendelian disorders affect 300-400 million people globally. Although genetic testing has become widely adopted, gene-specific evidence for tailored variant interpretation remains scattered across resources. We present Gene Portals, a framework for gene-centered multimodal knowledge bases that co-localize expert-harmonized clinical data, functional assays, population variation, structural annotations and gene-specific ACMG/AMP specifications within a single resource. A modular interface integrates this unified evidence with VCEP-refined ACMG specifications to enable automated gene-specific variant classification, infer molecular mechanisms, and support cross-gene analyses. We demonstrate the framework’s utility across five Gene portals spanning eleven neurodevelopmental disorder-associated genes, integrating data from 4,423 individuals with 2,838 unique variants, 36,149 ClinVar submissions, and 1,044 expert-curated molecular readouts. By organizing evidence that is otherwise dispersed across multiple sources into a unified, queryable framework, the SCN, GRIN, CACNA1A, SATB2 and SLC6A1 Gene Portals became widely used community resources and provide an extensible template for standardized rare-disease variant interpretation and mechanism-aware discovery.

794 Background: HER2 protein, encoded by ERBB2 gene, is the target of emerging therapies for patients (pts) with advanced urothelial carcinoma (aUC). High HER2 IHC expression (IHC 3+) is present in ~15% of pts with aUC, while >50% of pts have HER2 IHC 1+/2+/3+ expression. EVP is the preferred 1 st line regimen for pts with aUC, but the impact of HER2 status on EVP outcomes is unclear. Methods: We identified pts from the UNITE study with tumor samples tested for HER2 by IHC and another cohort with next-generation sequencing (NGS) data available. Outcomes were compared by HER2 IHC status (HER2 IHC 0/1+ vs 2+/3+) and separately based on ERBB2 status (alteration vs wild-type). X 2 test was used to compare observed response rate (ORR) and logistic regression was used to compare disease control rate (DCR). Duration of response (DOR), progression-free survival (PFS) and overall survival (OS) from EVP start were evaluated using log-rank test and Cox proportional hazards models. Multivariate analysis (MVA) included age, sex, race, ECOG PS, neutrophil:lymphocyte ratio, albumin, hemoglobin, primary tumor site, tumor histology, prior lines of treatment, and metastatic sites as covariates. Results: Among 521 pts treated with EVP from 16 sites, 112 had HER2 IHC data and 313 had NGS. Median age was 71, 74% were men, 84% Caucasian, 82% had ECOG PS 0-1, 65% pure urothelial histology, and 73% received frontline EVP. HER2 IHC distribution (n=112) was 27%/21%/37%/15% for 0/1+/2+/3+, respectively. ERBB2 alterations were present in 14% (44/313). Baseline characteristics were similar in HER2 0/1+ and 2+/3+ pts, except more primary bladder tumors in 2+/3+ pts (83% vs 63%, p=0.01). For the overall cohort (n=521), with a median follow up of 7.3 mos from EVP start, ORR was 54%, DCR 81%, median DOR (mDOR) 8.5 mos, median PFS (mPFS) 8.5 mos, and median OS (mOS) 19.8 mos. Pt outcomes by HER2 IHC status are shown (Table). In univariate analysis (UVA), pts with HER2 IHC 0/1+ had longer mOS compared to HER2 IHC 2+/3+, but this was not significant in MVA (HR: 0.5; CI: 0.2–1.3, p=0.17). No significant differences were observed in other outcomes. Evaluating clinical outcomes by ERRB2 status, no significant differences were seen for ERBB2 -altered vs wild-type pts. Conclusions: In this retrospective study, no significant differences were seen in EVP treatment outcomes based on HER2 IHC status or ERBB2 status. These findings are hypothesis-generating and require validation in larger and prospective cohorts. HER2 0/1+ (n=54)* HER2 2+/3+ (n=58) OR (95%CI, p) HR UVA (95%CI, p) HR MVA (95%CI, p) ORR 49% (23/47) 55% (27/49) 1.3 (0.6-2.9, p=0.5) - - DCR 79% (37/47) 88% (43/49) 1.9 (0.7-6.2, p=0.2) - - mDOR 11.7 mos 10.4 mos - 1.3 (0.7-2.4, p=0.4) 1.2 (0.4-3.3, p=0.8) mPFS 5.9 mos 7.1 mos - 0.8 (0.5-1.4, p=0.5) 1.1 (0.5-2.5, p=0.9) mOS 42.4 mos 18.7 mos - 2.3 (1.1-4.5, p=0.02) 2.0 (0.8-5.4, p=0.2) *HER2 0/1+ used as reference.

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

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