Citations

Abstract Chimeric antigen receptor (CAR) T-cell (CAR-T) treatment for B-cell acute lymphoblastic leukemia (ALL) induces high initial response rates, but most patients relapse. Low disease burden (often defined as <5% blasts in the bone marrow) is associated with better outcomes. CAR HEMATOTOX (HT) is a score using prelymphodepletion hematologic and inflammatory parameters to predict outcomes in lymphoma. Here, we assess its prognostic utility in a large multicenter adult B-cell ALL cohort. Patients who received brexucabtagene autoleucel across 33 centers in North America were included as part of the Real-World Outcomes Collaborative of CAR-T in Adult ALL (ROCCA) consortium. An independent cohort of 61 patients with ALL treated with an investigational CD19 CAR-T therapy at 1 center was also described. Among 199 ROCCA consortium patients, 43 (22%) patients with HTlow scores had lower rates of delayed neutrophil recovery than those with HThigh scores (26% vs 52%, P = .002) and fewer severe infections (2.5% vs 18.8%, P = .011). They also had higher response rates, overall survival (OS), and event-free survival (EFS), as well as lower nonrelapse mortality and cumulative incidence of relapse. The survival differences remained significant after multivariable adjustment for disease burden and other covariates. In the investigational cohort of 61 patients, patients with HTlow scores had improved OS and EFS, as well as higher peak CAR-T expansion. In summary, CAR HT score is a prognostic factor independent of disease burden in adult ALL. HTlow score is associated with superior outcomes after CD19 CAR-Ts and higher CAR-T expansion in a single-center cohort. These trials were registered at www.clinicaltrials.gov as #NCT01044069 and #NCT01860937.

Background: Cirrhosis and cirrhosis-related deaths have risen in the United States in recent years. Ascites is a common complication, often requiring large-volume paracentesis (LVP). The American Association for the Study of Liver Diseases (AASLD) recommends the administration of albumin in conjunction with LVP to prevent further complications of cirrhosis. Emerging research in cirrhosis care reveals significant variations in outcomes among different demographics. Therefore, we assessed the use of guideline-adherent albumin and outcomes in U.S. patients undergoing LVPs, particularly at the intersection of race, ethnicity, socioeconomic disparities, and cirrhosis. Methods: This retrospective study utilized Cerner Real World Data to identify adults with cirrhosis and ascites undergoing LVP between January 2016 and June 2022. We assessed albumin utilization patterns across racial and ethnic groups and payor types, and their overall impact on acute kidney injury (AKI)-related hospitalization using an adjusted generalized linear model (aGLM). Results: We identified 736 patients: 301 in the LVP + albumin group and 435 in the LVP-only group. Despite clinical recommendations, only 41% undergoing LVPs received albumin. White patients and commercially insured patients received albumin at higher rates (p=0.042 and p=0.009, respectively). The overall rate of AKI-related admissions within the 30-day post-procedure period was 26%. However, patients who received albumin during LVP had a 36% lower risk of short-term AKI-related hospitalization (OR: 0.64; p=0.03). Conclusions: These findings indicate a potential for broader albumin utilization in U.S. patients with refractory ascites undergoing repeated LVPs to reduce AKI-related admissions.

Background: It is crucial to evaluate liver fibrosis in metabolic dysfunction-associated steatotic liver disease (MASLD). Digital pathology, an automated method for quantitative fibrosis measurement, provides valuable support to pathologists by providing refined continuous metrics and addressing inter-observer variability. Although non-invasive tests (NITs) have been validated as consistent with manual pathology, the relationship between digital pathology and NITs remains unexplored. Methods: This study included 99 biopsy-proven MASLD patients. Quantitative-fibrosis (Q-Fibrosis) used second-harmonic generation/two-photon excitation fluorescence microscopy (SHG/TPEF) to quantify fibrosis parameters (q-FPs). Correlations between eight NITs and q-FPs were analyzed. Results: Using manual pathology as standard, Q-Fibrosis exhibited excellent diagnostic performance in fibrosis stages assessment with area under the receiver operating characteristic curves (AUCs) ranging from 0.924 to 0.967. In addition, magnetic resonance elastography (MRE) achieved the highest diagnostic accuracy (AUC: 0.781–0.977) among the eight NITs. Furthermore, MRE-assessed liver stiffness measurement (MRE-LSM) showed the strongest correlation with q-FPs, particularly adjusted by string length, string width, and the number of short and thick strings within the portal region. Conclusions: Both MRE and digital pathology demonstrated excellent diagnostic accuracy. MRE-LSM was primarily determined by collagen extent, location and pattern, which provide a new perspective for understanding the relationship between the change in MRE and histological fibrosis reverse.

Abstract With the rapid advancements in large language model technology and the emergence of bioinformatics‐specific language models (BioLMs), there is a growing need for a comprehensive analysis of the current landscape, computational characteristics, and diverse applications. This survey aims to address this need by providing a thorough review of BioLMs, focusing on their evolution, classification, and distinguishing features, alongside a detailed examination of training methodologies, datasets, and evaluation frameworks. We explore the wide‐ranging applications of BioLMs in critical areas such as disease diagnosis, drug discovery, and vaccine development, highlighting their impact and transformative potential in bioinformatics. We identify key challenges and limitations inherent in BioLMs, including data privacy and security concerns, interpretability issues, biases in training data and model outputs, and domain adaptation complexities. Finally, we highlight emerging trends and future directions, offering valuable insights to guide researchers and clinicians toward advancing BioLMs for increasingly sophisticated biological and clinical applications.

Abstract BACKGROUND Intraductal papillary mucinous neoplasm (IPMN) is one of the two most common precursor lesions leading to the development of pancreatic ductal adenocarcinoma (PDA). IPMNs comprise a heterogeneous group of tumors with a wide range of grades and histotypes, and the emergence of single-cell RNA sequencing (RNA-seq) and multiplex digital spatial profiling have characterized unique cell populations, including dysplastic epithelial and immune cells, within the heterogeneous tumor microenvironment that carry signature gene expressions, which could be used as markers for disease progression. However, it is not clear on the heterogeneity of the epithelial and immune response of the evolution during progression of IPMN to PDA. OBJECTIVE Combining nuclear GSK-3β with oncogenic KRas mice (referred to as KNGC – KRas, nuclear GSK-3β, Cre) resulted in the development of IPMN. We have found that 4-week-old KNGC mice show progressive desmoplasia and ductal lesion development with increased M2-like macrophage infiltration. Interestingly, CX3CL1 (fractalkine), a chemokine involved in the recruitment of CX3CR1-expressing monocytes and M2-like macrophage conversion in various disease models is expressed by IPMN progenitor ductal cells. We aim to investigate expression and contribution of CX3CL1-CX3CL1 axis in the development and progression of IPMN. METHODS We utilized a newly generated CX3CL1-mCherry and well-established CX3CR1-GFP knockin/knockout mouse for crossbreeding with KNGC and KGC (KRas, GNas, Cre) for lineage tracing and function analysis by immunofluorescent staining, flow cytometry and CyTOF. RESULTS Both KNGC- and KGC-3LmCherry/+ mice harbor a large population of CX3CL1-mCherry/EPCAM+ epithelial cells as compared to 3LmCherry/+ and wildtype (WT) control mice. In KNGC and KGC mice, we show that there was a unique population of macrophages (CD45+ CD11b+ Ly6G- F4/80+ Ly6c- ) with significantly higher expression of CX3CR1 (CX3CR1Hi) that was not seen in WT mice. Significantly, Knockout of CX3CR1 in KNGC-3RGFP/GFP animals had a paucity of M2-like macrophages, reduced T regulatory cells (Tregs), substantially reduced desmoplasia and impaired development of IPMN. CONCLUSIONS The study provides important knowledge regarding the role of CX3CL1-CX3CR1 axis in recruitment and generation of M2-like macrophages, and their impact on the initiation of the immune/stroma microenvironment facilitating IPMN development. Further investigations using these models have the potential to identify new biomarkers for risk stratification and therapeutic intervention. Citation Format: Li Ding, Kaely Roeck, Easton Maeder, Cheng Zhang, Taylor Weiskittel, Esther Rodman, Mark Maynes, Bibo Zhu, Aaron Johnson, Jie Sun, Li Hu, Daniel Billadeau. Uncoupling CX3CL1-CX3CR1 Axis in IPMN Development Through Transgenic Mouse Models [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research—Emerging Science Driving Transformative Solutions; Boston, MA; 2025 Sep 28-Oct 1; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2025;85(18_Suppl_3):Abstract nr A064.

Abstract Background Acupuncture, a key modality in traditional Chinese medicine, is gaining global recognition as a complementary therapy and a subject of increasing scientific interest. However, fragmented and unstructured acupuncture knowledge spread across diverse sources poses challenges for semantic retrieval, reasoning, and in-depth analysis. To address this gap, we developed AcuKG, a comprehensive knowledge graph that systematically organizes acupuncture-related knowledge to support sharing, discovery, and artificial intelligence–driven innovation in the field. Methods AcuKG integrates data from multiple sources, including online resources, guidelines, PubMed literature, ClinicalTrials.gov, and multiple ontologies (SNOMED CT, UBERON, and MeSH). We employed entity recognition, relation extraction, and ontology mapping to establish AcuKG, with human-in-the-loop to ensure data quality. Two cases evaluated AcuKG’s usability: (1) how AcuKG advances acupuncture research for obesity and (2) how AcuKG enhances large language model (LLM) application on acupuncture question-answering. Results AcuKG comprises 1839 entities and 11 527 relations, mapped to 1836 standard concepts in 3 ontologies. Two use cases demonstrated AcuKG’s effectiveness and potential in advancing acupuncture research and supporting LLM applications. In the obesity use case, AcuKG identified highly relevant acupoints (eg, ST25, ST36) and uncovered novel research insights based on evidence from clinical trials and literature. When applied to LLMs in answering acupuncture-related questions, integrating AcuKG with GPT-4o and LLaMA 3 significantly improved accuracy (GPT-4o: 46% → 54%, P = .03; LLaMA 3: 17% → 28%, P = .01). Conclusion AcuKG is an open dataset that provides a structured and computational framework for acupuncture applications, bridging traditional practices with acupuncture research and cutting-edge LLM technologies.

Normothermic machine perfusion (NMP) enables preservation and functional assessment of liver allografts, improving outcomes, particularly in marginal organs. However, the TransMedics Organ Care System (OCS) permits only single hepatic artery (HA) cannulation, limiting its use in grafts with variant arterial anatomy. Arterial reconstruction before NMP may overcome this limitation and expand the pool of grafts eligible for perfusion. We conducted a retrospective single-center cohort study of adult liver transplants utilizing OCS from January 2022 to September 2024. Allografts with variant hepatic artery anatomy requiring arterial reconstruction before NMP initiation were identified. Postoperative outcomes, including vascular and biliary complications, were compared between reconstructed and non-reconstructed grafts. Among 541 OCS-preserved grafts, 74 (13.7%) underwent arterial reconstruction. Compared with non-reconstructed grafts, reconstructed grafts had longer cross-clamp to cannulation time (2.8 vs. 2.4 h, p <0.001), but similar rates of early allograft dysfunction (23.0% vs. 20.8%, p =0.65), ischemic cholangiopathy (4.1% vs. 4.1%, p =1.00), and primary nonfunction (0.0% vs. 0.4%, p =1.00). Early (2.7% vs. 0.2%, p =0.05) and late hepatic artery thrombosis (HAT) (4.1% vs. 2.1%, p =0.40) were infrequent and not significantly different between non-reconstructed and reconstructed groups, respectively. Hepatic artery stenosis occurred more often in reconstructed grafts (12.2% vs. 4.1%, p =0.008), though most cases were managed with interventional radiology or surgical revision. Only one reconstructed graft required retransplantation due to vascular complications. Arterial reconstruction before NMP is safe and feasible, enabling successful perfusion and transplantation of liver allografts with variant HA anatomy. These findings support the broader application of NMP in anatomically complex donor livers.

Abstract Diffuse large B-cell lymphoma (DLBCL) poses a challenge in hematology given its varied symptoms, and the complex interplay between disease and treatment effects on health-related quality of life (HRQoL). The phase 3 POLARIX study demonstrated superior progression-free survival and a similar safety profile with polatuzumab vedotin plus rituximab, cyclophosphamide, doxorubicin, and prednisone (Pola-R-CHP) vs R-CHOP (rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone) in patients with previously untreated DLBCL. Here, we evaluate HRQoL through patient-reported outcome (PRO) instruments to fully characterize the patient experience in the POLARIX study. Changes from baseline in HRQoL, lymphoma symptoms, and gastrointestinal (GI) symptoms were assessed, as well as incidence and severity of common symptoms by PROs vs clinician-reported adverse events (AEs). Baseline characteristics of PRO-evaluable patients (N = 874) were consistent. Comparison between PROs and clinician-reported AEs revealed a notable discordance; patients generally reported a higher incidence of symptoms than clinicians, emphasizing the need for patient-centric tools to accurately capture the patient experience. Both treatments exhibited rapid and sustained improvements in HRQoL and lymphoma symptoms, with the most substantial improvements seen in global health status/QoL, lymphoma symptoms, fatigue, role, emotional, and social functioning. GI symptoms (diarrhea, constipation, nausea, and vomiting) were generally similar between treatment arms and returned to baseline levels after treatment completion. These HRQoL data underscore the complementarity of PROs, as an adjunct to clinician-reported AEs, in evaluating the efficacy and tolerability of new treatments, including Pola-R-CHP, which may represent a new benchmark for patient-reported HRQoL in previously untreated DLBCL. This trial was registered at www.clinicaltrials.gov as NCT03274492.

PURPOSE Ziftomenib—a potent, highly selective, oral menin inhibitor—was well tolerated and demonstrated encouraging clinical activity as monotherapy for relapsed/refractory NPM1 -mutated ( NPM1 -m) and KMT2A -rearranged AML in the KOMET-001 phase I trial. METHODS In the registration-enabling phase II part of KOMET-001, patients with relapsed/refractory NPM1 -m AML received ziftomenib 600 mg once daily. The primary end point was the rate of complete remission with full hematologic recovery (CR)/CR with partial hematologic recovery (CRh). RESULTS From January 26, 2023, to May 13, 2024, 92 patients (median age, 69 years [range, 33-84]) were treated. The primary end point was met, with a CR/CRh rate of 22% (95% CI, 14 to 32; P = .0058); 61% were negative for measurable residual disease. Overall response rate was 33% (95% CI, 23 to 43), with a median duration of 4.6 months (95% CI, 2.8 to 7.4). Prespecified subgroup analyses showed comparable CR/CRh regardless of previous therapy, including venetoclax, or type of comutations. Median overall survival was 6.6 months (95% CI, 3.6 to 8.6). Common grade ≥3 treatment-emergent adverse events were febrile neutropenia (26%), anemia (20%), and thrombocytopenia (20%). Differentiation syndrome occurred in 25% of patients (15% grade 3; no grade 4-5) and was manageable with protocol-defined mitigation. Three patients (3%) discontinued treatment because of ziftomenib-related adverse events. CONCLUSION Ziftomenib demonstrated significant clinical benefit and deep responses in patients with heavily pretreated, relapsed/refractory NPM1 -m AML. Ziftomenib was well tolerated with a safety profile consistent with previous studies, including manageable differentiation syndrome, lack of clinically significant QTc prolongation, and low rates of myelosuppression.