Citations

INTRODUCTION: Long-term data are needed for offspring exposed in utero to medications for inflammatory bowel disease (IBD). METHODS: We used a prospective cohort of pregnant women with IBD and their offspring (Pregnancy in IBD and Neonatal Outcomes) to compare rates of serious infection, congenital malformations, and developmental delay by medication exposures. RESULTS: We included 438 offspring with at least 4 years of follow-up. No differences in adverse outcomes were observed by medication. Preterm birth, but not specific drug exposure, was associated with infection risk. Breastfeeding was not associated with serious infection differences. DISCUSSION: These findings support the use of effective IBD therapies throughout pregnancy.

This slide presentation uses real-world examples from diverse modern systems to categorize digital radiographic artifacts by likely cause and outlines investigation and mitigation strategies to improve troubleshooting, artifact prevention, and patient care.

Abstract Background Cardiomegaly is a clinically significant incidental finding on chest computed tomography (CT) associated with heart failure, arrhythmias, and sudden cardiac death. Qualitative radiologist assessment is variable, and automated AI tools may enable objective opportunistic cardiac volumetry. Purpose To evaluate whether AI-enabled total cardiac volume (TCVAI) derived from non-ECG-gated, non-contrast chest CT can identify cardiomegaly as defined by echocardiography. Materials and Methods This retrospective study included 307 consecutive patients (median age, 67 years; 56% male) who underwent non-contrast chest CT at a single center on 7 scanner types (4 vendors) and clinically indicated echocardiography within 31 days. A commercially available AI tool (AI-Rad Companion, Siemens Healthineers) automatically quantified TCVAI, indexed to body surface area (TCVAI/BSA). Echocardiography reports were reviewed for chamber dilation and left ventricular hypertrophy (LVH), collectively defined as cardiomegaly. Associations between TCVAI/BSA and echocardiographic findings were assessed using correlation, ordinal regression, and receiver operating characteristic (ROC). Interscan repeatability was evaluated in 248 patients with 544 repeat CT examinations. Prespecified sex-specific thresholds were tested in a temporally independent validation cohort of 50 patients. Results Median TCVAI was higher in patients with cardiomegaly than those without (1061.9 vs 798.4 mL; P < .001). TCVAI/BSA was associated with chamber dilation and LVH severity on univariate analysis and remained associated in multivariable ordinal models, except for right ventricular dilation. Discriminatory performance was fair to good, with area under the curve (AUC) 0.81 (95% CI, 0.75-0.87) in men and 0.77 (95% CI, 0.69-0.85) in women. Interscan repeatability was excellent (intraclass correlation coefficient [ICC]: 0.93). In independent validation, performance ranged from sensitivity 89.3%/specificity 27.3% at a high-sensitivity threshold to sensitivity 28.6%/specificity 100% at a high-specificity threshold. Conclusion AI-derived cardiac volume from routine chest CT shows fair to good performance for identifying echocardiography-defined cardiomegaly with high measurement repeatability, supporting a potential role for automated cardiac volumetry as an objective, opportunistic biomarker.

Background: Transanal total mesorectal excision (taTME) facilitates sphincter preservation in low rectal cancer. Preliminary results and functional outcomes from the North American multicenter phase II taTME trial (NCT03144765) have been published. Three-year outcomes are reported. Methods: Patients with stage I to III rectal adenocarcinoma were enrolled across 11 centers (2017–2022). Endpoints included TME grade, 3-year overall survival, disease-free survival, cancer-specific survival, recurrence, late (beyond 90 d) complications, and stoma-free survival. Surveillance followed National Comprehensive Cancer Network guidelines, with pelvic magnetic resonance imaging (MRI) at 3 years to assess for pelvic sidewall recurrence when possible. Kaplan–Meier analysis assessed oncologic outcomes. Results: One hundred patients underwent taTME for tumors at a median of 5.8 cm from the anal verge, with intersphincteric resection in 36% and handsewn anastomosis in 54%. Median follow-up was 50.9 months. Late complications occurred in 32 patients, including 21 severe (Clavien-Dindo ≥3). Late anastomotic complications occurred in 5 patients; one required surgical revision. Estimated 3-year overall survival, cancer-specific survival, and disease-free survival were 93.7%, 96.6%, and 84.6%, respectively. Distant recurrence occurred in 15 patients (median: 17.6 months), most commonly in the lung and liver. Locoregional recurrence occurred in 2 patients. Preoperative N stage, lymph node yield, tumor deposits, and perineural invasion were associated with recurrence. Among 100 patients diverted at taTME, 97% were stoma-free at 3 years; 4 patients later underwent secondary diversion. Conclusions: Three-year outcomes of this multicenter trial support the safety and efficacy of taTME in resectable mid and low rectal tumors, with outcomes comparable to contemporary studies. Longer-term oncologic and functional outcomes are needed.

TPS276 Background: Metastatic castration-resistant prostate cancer (mCRPC) can evolve into a neuroendocrine-like subtype with aggressive behavior and poor outcomes (1). Nuclear Receptor-Binding SET Domain Protein 2 (NSD2) is overexpressed in prostate cancer and is a driver of both androgen-receptor (AR)-dependent signaling and of neuroendocrine differentiation, where cancer cells lose AR dependence and response to AR pathway inhibitors (ARPIs) (2,3,4). In studies of patient-derived neuroendocrine prostate cancer (NEPC) models, genetic depletion of NSD2 led to restoration of AR expression, reversal of adeno-to-neuroendocrine differentiation, and re-sensitization to ARPI (4). We hypothesize that NSD2 inhibition can reverse resistance to ARPIs in patients with progressive mCRPC, including with neuroendocrine differentiation. KTX-2001 is an oral, potent and selective small molecule inhibitor of NSD2. It is the sponsor’s second NSD2 inhibitor to enter the clinic. The sponsor’s first in class NSD2 inhibitor, KTX-1001, was shown to be tolerable and have preliminary efficacy in patients with relapsed/refractory multiple myeloma (5). Methods: STRIKE-001 (NCT07103018) is a multicenter, open-label phase 1 dose escalation trial of KTX-2001 monotherapy (Part A) and KTX-2001 + darolutamide (Part B). Key inclusion criteria are males age ≥18 years with mCRPC, progression after receiving ARPI, Eastern Cooperative Oncology Group performance score of 0-1, willingness to undergo biopsy if safe and feasible, and life expectancy of ≥6 months. Participants take KTX-2001 by mouth once daily alone (Part A) or with darolutamide 600 mg twice daily (Part B). Dose escalation of KTX-2001 in Parts A and B will follow a 3+3 design and occur in parallel at multiple planned dose levels. Primary objectives are to assess the safety and tolerability, determine MTD, and determine RP2D(s) for further study of KTX-2001 alone and in combination with darolutamide. Secondary objectives include characterization of efficacy and PK parameters for both KTX-2001 monotherapy and in combination with darolutamide. Exploratory objectives include study of pharmacodynamic effects, circulating tumor cells, and cell-free DNA. 1. Conteduca V, Eur J Cancer 2019. 2. Parolia A, Nat Genet 2024. 3. Aytes A, Nat Commun 2018 4. Li J, bioRxiv 2023.07.18.549585 5. Bories P, Blood Vol 144, Suppl 1,2024. Clinical trial information: NCT07103018 .

Abstract Introduction: Accurate detection and prioritization of tumor-specific somatic variants is foundational to the development of personalized immunotherapies. Traditional pipelines for neoepitope identification rely heavily on short-read next-generation sequencing (NGS) and DNA-based variant calling, followed by RNA expression filtering and HLA-binding prediction. However, this approach is limited by time-intensive workflows, potential false positives from DNA-only calls, and poor capture of complex isoforms or RNA-level editing. Moreover, the accuracy of neoepitope prediction is constrained by conventional sequence-based HLA binding algorithms that do not account for structural and biophysical features of peptide-MHC interactions, particularly across underrepresented HLA alleles. Methods: To overcome these limitations, we developed a streamlined, sequencing-to-vaccine framework that leverages long-read RNA sequencing for direct detection of expressed somatic variants, including fusions, indels, and single nucleotide variants. Using Oxford Nanopore Technologies’ cDNA-PCR approach, we enable comprehensive, full-length transcript characterization from both fresh and frozen breast tumor samples. Our bioinformatic pipeline, NeoTarget, integrates alignment, variant calling, and neoepitope inference from tumor RNA in a single, modular workflow. A core innovation of this pipeline is HLA-Inception, a deep convolutional neural network trained to predict peptide-MHC class I binding using features derived from molecular dynamics-based modeling of electrostatic potential at the peptide-HLA interface, enhancing generalizability across diverse HLA subtypes. Results: Expanding on previous results, the current NeoTarget pipeline identifies, evaluates, and prioritizes single nucleotide variants, indels, and fusions. To validate this system, we used a set of 9 human breast cancer tumors benchmarked with short read sequencing. Identified neoantigens included most variants shown by clinical short read sequencing and also novel structural variants (i.e., fusions) only revealed with long read sequencing with high confidence. Conclusion: Here, we describe the design and performance of the NeoTarget pipeline, and show proof-of-concept feasibility of applying this fast and cost-effective workflow for HLA-restricted epitope discovery in breast tumors using long-read RNA sequencing. Overall, these methods can be applied to rapidly identify and prioritize neoantigens for personalized neoantigen-based immune therapies. Citation Format: F. Batalini, S. Henry, Y. Zhang, R. Foster, J. M. Gayton, A. Hostal, E. A. Wilson, A. Singharoy, M. Gustafson, B. Pockaj, J. Park, K. S. Anderson. Somatic variant detection using long read RNA sequencing reveals HLA-restricted targets for immunotherapy [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 PS3-06-08.

Abstract Background: Invasive lobular carcinoma (ILC) accounts for up to 15% of breast cancer (BC) cases and has distinct clinical and biological features compared to invasive carcinoma of no special type (IBC-NST). Prior studies, including PENELOPE-B, suggested greater benefit from adjuvant palbociclib (palbo) in ILC. We assessed the prognostic and predictive value of histology in patients (pts) treated with endocrine therapy (ET) ± palbo. Methods: PALLAS is a global, phase III trial in which pts with stage II-III, HR+/HER2− BC were randomized to 2 years (y) of adjuvant palbo + ET or ET alone. Pts with IBC-NST or pure ILC per local pathology assessment were included. Endpoints included invasive disease-free (IDFS; primary), distant recurrence-free (DRFS), locoregional recurrence-free (LRRFS), and overall survival (OS). Prognostic value was assessed using univariable and multivariate Cox models adjusted for age, T and N stage, grade, and progesterone receptor. Predictive value was assessed using histology-by-treatment interactions. Results: Among 5,748 pts in the ITT population, 4,982 (87%) were included (3,838 IBC-NST [67%], 1,144 ILC [20%]); median follow-up 6.9y. Compared with IBC-NST, ILC was associated with older age (median 54 vs 51 y), higher T stage (T3/T4: 41.7% vs 20.4%), fewer grade 3 tumors (12.7% vs 33.5%), higher mastectomy rates (74.5% vs 58.4%), less (neo)adjuvant chemotherapy (72.2% vs 86.2%), and less tamoxifen as initial ET (28.8% vs 34.5%) (all p<0.001). ILC prevalence varied by country: lower in Asia (Japan 10.5%, Korea 0%, Taiwan 2.8%) and higher in Europe (23.1%) and North America (24.0%). When evaluating the predictive value, palbo appeared to confer greater benefit in ILC for all endpoints (HRs ranging from 0.41 to 0.86) and not in IBC-NST (HRs ranging from 0.97 to 1.01), although the histology-by-treatment interaction was significant only for LRRFS (Table). In the overall population, 7-year IDFS was 79.3% for IBC-NST and 75.8% for ILC. While the difference was significant in univariable analysis (HR 1.17, 95% CI 1.01-1.35), it was not in multivariable analysis (HR 1.06, 0.91-1.24). Notably, the proportional hazards assumption was violated, and time-dependent modeling demonstrated that worse outcomes for ILC on IDFS, DRFS, and other endpoints emerged predominantly beyond 3 years. Conclusions: In this large, randomized dataset of pts with early HR+/HER2− breast cancer with long-term follow-up, ILC demonstrated distinct clinicopathologic features and geographic distribution. While ILC was not an independent prognostic factor over the entire follow-up, time-dependent modeling revealed worse long-term outcomes which only emerged after 3 years. Palbo appeared to be associated with more favorable outcomes in ILC than in IBC-NST across endpoints. These findings suggest a potential benefit of palbo in ILC that warrants further investigation in other adjuvant trials evaluating CDK4/6 inhibitors. Citation Format: G. Nader-Marta, C. Desmedt, D. Hlauschek, A. DeMichele, G. Zoppoli, E. Blondeaux, E. de Azambuja, M. Bellet-Ezquerra, O. Metzger-Filho, J. M. Suga, G. Pfeiler, M. P. Goetz, M. Ruiz-Borrego, S. Loibl, J. Meisel, A. Ring, K. Van Baelen, E. P. Mamounas, N. Zdenkowski, E. Agostinetto, M. Lambertini, E. Gauthier, L. Soelkner, A. C. Dueck, M. Gnant, E. L. Mayer. Long-term prognostic and predictive value of lobular histology in the PALLAS trial [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 PS3-11-06.

A retrospective review of multidisciplinary velopharyngeal insufficiency (VPI) Clinic records from 2010 to 2024 was completed. Inclusion criteria for the review were diagnosis of childhood apraxia of speech (CAS) and documented evaluation for velopharyngeal dysfunction (VPD). Adequacy of velopharyngeal closure and perceptual judgment of resonance were identified as primary outcome measures. Surgical interventions and speech outcomes were also described. This review identified 74 children who were diagnosed with CAS and evaluated for VPD in the VPI Clinic. For the subset (n = 50) of children who had surgical intervention, speech therapy, and long-term follow-up, all had improved velopharyngeal closure and resonance.

Abstract Recent advances in long-read transcriptome sequencing enable high-throughput profiling of full-length RNA isoforms in bulk, single-cell, and single-nucleus samples. However, long-read datasets typically contain a mixture of complete and partial transcripts, leading to pervasive ambiguity in read-to-isoform assignment and complicating accurate isoform identification and quantification, particularly in the absence of reliable reference annotations. These challenges are further amplified in single-cell and single-nucleus samples, where coverage is sparse and transcriptional heterogeneity is high. Here, we present the Long Read Alignment Assembler (LRAA), a unified and versatile computational framework for isoform identification and quantification from long-read RNA sequencing data across bulk, single-cell, and single-nucleus transcriptomic samples. LRAA combines splice-graph based structural modeling with expectation maximization based optimization to probabilistically resolve ambiguous read assignments and improve isoform abundance estimation. The framework supports quantification-only, reference-guided, and fully reference-free (de novo) modes of analysis within a single methodological paradigm. We benchmarked LRAA using both simulated and genuine long-read datasets spanning sequencing standards and whole transcriptomes. Central to this evaluation is a novel benchmarking strategy based on Multiplexed Overexpression of Regulatory Factors (MORFs), which provides biologically expressed, barcoded isoforms with unambiguous read-level ground truth. Across all benchmarks, including MORFs, synthetic spike-ins, and whole-transcriptome datasets, LRAA consistently outperformed state-of-the-art methods in isoform identification accuracy, sensitivity, and expression quantification. Finally, we demonstrate the biological utility of LRAA by resolving cell-type-specific isoform usage across peripheral blood immune cell populations and by detecting a pathogenic cryptic isoform of STMN2 with associated transcriptional changes in single-nucleus RNA-seq data from frontal cortex tissue of an individual with frontotemporal dementia (FTD). Together, these results establish LRAA as a robust and general solution for resolving transcript diversity in complex biological systems, from development to disease.