Citations

Abstract With the increasing volume of biomedical experimental data, standardizing, sharing, and integrating heterogeneous experimental data across domains has become a major challenge. To address this challenge, we have developed an ontology-supported Study-Experiment-Assay (SEA) common data model (CDM), which includes 10 core and 3 auxiliary classes based on object-oriented modeling. SEA CDM uses interoperable ontologies for data standardization and knowledge inference. Building on the SEA CDM, we developed the Ontology-based SEA Network (OSEAN) relational database and knowledge graph, along with a set of ETL (Extract, Transform, Load) and query tools, and further applied them to represent 1,278 immune studies with over two million samples from three resources: VIGET, ImmPort, and CELLxGENE. Using simple, robust queries and analyses, our research identified multiple scientific insights into sex-specific immune responses, such as neutrophil degranulation and TNF binding to physiological receptors, following live attenuated and trivalent inactivated influenza vaccination. The novel SEA CDM system lays a foundation for establishing an integrative biodata ecosystem across biological and biomedical domains.

Increasing evidence strongly links neuroinflammation to Alzheimer’s disease (AD) pathogenesis. Peripheral monocytes are crucial components of the human immune system, but their contribution to AD pathogenesis is still largely understudied partially due to limited human models. Here, we introduce human cortical organoid microphysiological systems (hCO-MPSs) to study AD monocyte-mediated neuroinflammation. By culturing doughnut-shape organoids on 3D-printed devices within standard 96-well plates, we generate hCO-MPSs with reduced necrosis, minimized hypoxia, and improved viability. Using these models, we found that monocytes from AD patients exhibit increased infiltration ability, decreased amyloid-β clearance capacity, and stronger inflammatory response than monocytes from age-matched control donors. Moreover, we observed that AD monocytes induce pro-inflammatory effects such as elevated astrocyte activation and neuronal apoptosis. Furthermore, the marked increase in IL1B and CCL3 expression underscores their pivotal role in AD monocyte-mediated neuroinflammation. Our findings provide insight into understanding monocytes’ role in AD pathogenesis, and our lab-compatible MPS models may offer a promising way for studying various neuroinflammatory diseases.

Background: Lung cancer ranks as the leading cause of cancer-related mortality worldwide. The complexity of tumor delineation, crucial for radiation therapy, requires expertise often unavailable in resource-limited settings. Artificial Intelligence (AI), particularly with advancements in deep learning (DL) and natural language processing (NLP), offers potential solutions yet is challenged by high false positive rates. Purpose: The Oncology Contouring Copilot (OCC) system is developed to leverage oncologist expertise for precise tumor contouring using textual descriptions, aiming to increase the efficiency of oncological workflows by combining the strengths of AI with human oversight. Methods: Our OCC system initially identifies nodule candidates from CT scans. Employing Language Vision Models (LVMs) like GPT-4V, OCC then effectively reduces false positives with clinical descriptive texts, merging textual and visual data to automate tumor delineation, designed to elevate the quality of oncology care by incorporating knowledge from experienced domain experts. Results: The deployment of the OCC system resulted in a 35.0% reduction in the false discovery rate, a 72.4% decrease in false positives per scan, and an F1-score of 0.652 across our dataset for unbiased evaluation. Conclusions: OCC represents a significant advance in oncology care, particularly through the use of the latest LVMs, improving contouring results by (1) streamlining oncology treatment workflows by optimizing tumor delineation and reducing manual processes; (2) offering a scalable and intuitive framework to reduce false positives in radiotherapy planning using LVMs; (3) introducing novel medical language vision prompt techniques to minimize LVM hallucinations with ablation study; and (4) conducting a comparative analysis of LVMs, highlighting their potential in addressing medical language vision challenges.

Abstract Background and Aims The long-term efficacy and safety of upadacitinib in patients with moderate to severe Crohn’s disease (CD) were evaluated in the U-ENDURE Long-Term Extension (LTE) study. Here we report the results after 2 years of total maintenance treatment. Methods U-ENDURE is an ongoing 240-week LTE study conducted at 243 sites across 43 countries (first patient enrolled in LTE 21 March 2019). Patients who completed the 52-week maintenance study continued their previously assigned treatment, once-daily upadacitinib 15 mg or upadacitinib 30 mg. Efficacy was analyzed at week 48 of the LTE; safety was analyzed in the cumulative study population (combined 52 week maintenance and 48 week LTE) and the LTE study population only (cutoff date: 19 December 2023). Results From LTE week 0 to week 48, as-observed efficacy rates for clinical remission (per stool frequency/abdominal pain score, upadacitinib 15 mg: 78.3% to 82.9%; upadacitinib 30 mg: 84.7% to 76.6%; per CD Activity Index, upadacitinib 15 mg: 81.3% to 83.1%; upadacitinib 30 mg: 86.1% to 86.8%), endoscopic response (upadacitinib 15 mg: 59.6% to 67.1%; upadacitinib 30 mg: 71.2% to 69.6%), inflammatory biomarkers, and quality-of-life outcomes remained stable. The safety profile of the cumulative maintenance population observed through LTE week 48 was consistent with previous trials in the upadacitinib CD program. Treatment-emergent adverse event rates for the cumulative maintenance population were 283.1 and 273.4 events/100 patient-years for upadacitinib 15 mg and upadacitinib 30 mg, respectively. Event rates of serious treatment-­emergent adverse events were 16.0 events/100 patient-years for upadacitinib 15 mg and 14.6 events/100 patient-years for upadacitinib 30 mg. The most common adverse events of special interest (≥ 5.0 events/100 patient-years) were hepatic disorder, lymphopenia, creatine phosphokinase elevation, herpes zoster, and anemia. There was 1 treatment-emergent adverse event of suicide leading to death. Conclusion Sustained clinical, endoscopic, quality-of-life, and biomarker outcomes were observed in patients who were initial responders to upadacitinib and completed 2 years of maintenance therapy, with no new safety signals identified. Clinical trial identifier U-ENDURE; ClinicalTrials.gov number, NCT03345823.

ABSTRACTBackgroundPercutaneous transluminal angioplasty and stenting (PTAS) in patients with carotid stenosis may have potential effects on brain parenchyma. However, current studies on parenchymal changes are scarce due to the need for advanced imaging modalities. Consequently, the alterations in brain parenchyma following PTAS remain an unsolved issue.PurposeTo investigate changes to the brain parenchyma using magnetic resonance elastography (MRE).Study TypeProspective.Population13 patients (6 women and 7 men; 39 MRI imaging sessions) with severe unilateral carotid stenosis patients indicated for PTAS were recruited between 2021 and 2024.Field Strength/SequenceNoncontrast MRI sequences including MRE (spin echo) were acquired using 3 T scanners.AssessmentAll patients underwent MRE before (preprocedural), within 24 h (early postprocedural) and 3 months after (delayed postprocedural) PTAS. Preprocedural and delayed postprocedural ultrasonographic peak systolic velocity (PSV) was recorded. MRE stiffness and damping ratio were evaluated via neural network inversion of the whole brain, in 14 gray matter (GM) and 12 white matter (WM) regions.Statistical TestsStiffness and damping ratio differences between each pair of MR sessions for each subject were identified by paired sample t tests. The correlations of stiffness and damping ratio with stenosis grade and ultrasonographic PSV dynamics were evaluated by Pearson correlation coefficients. The statistical significance was defined as p < 0.05.ResultsThe stiffness of lesion side insula, deep GM, and deep WM increased significantly from preprocedural to delayed postprocedural MRE. Increasing deep GM stiffness on the lesion side was positively correlated with the DSA stenosis grade significantly (r = 0.609). The lesion side insula stiffness increments were positively correlated with PSV decrements significantly (r = 0.664).Data ConclusionRegional brain stiffness increased 3 months after PTAS. Lesion side stiffness was positively correlated with stenosis grades in deep GM and PSV decrements in the insula.Evidence Level2.Technical EfficacyStage 2.

ABSTRACTBackgroundWe aim to evaluate whether increased lymph node yield at prostatectomy (RP) is associated with improved outcomes in NRG/RTOG 9601, a randomized clinical trial of men who underwent either radiation (RT) alone or RT + bicalutamide for PSA elevation following RP for pT2/T3 prostate cancer.MethodsWe reviewed available pathology reports for patients in NRG/RTOG 9601 to determine the nodal count at RP. Cox proportional hazards models were used to assess effect of lymph nodes yield, arm (RT alone or RT + bicalutamide), Gleason score, positive margins, and seminal vesicle invasion on the following endpoints: times to local and distant failure and overall and disease‐specific survival.ResultsOf 760 patients, 552 (73%, 276 in each arm) had complete data available. Median node count in the entire cohort was 6 (range: 0–33, IQR: 3–9). There were no significant differences between arms in terms of patient demographic or clinical characteristics, including total lymph nodes removed in either arm. There was no significant association between total lymph nodes and overall or disease‐specific survival with both arms combined and when adjusting for arm. Notably, interaction analysis revealed that in seminal vesicle invasion, there was a significant association between lymph node yield and OS and DSS (HR = 0.91, 95% CI: 0.83–0.99, p = 0.034; HR = 0.87, 95% CI: 0.77–0.99, p = 0.029, respectively).ConclusionsAlthough lymph node yield in NRG/RTOG 9601 did not show association with adverse outcomes in the entire cohort or either arm alone, there was significant association between lymph node yield and adverse outcomes when seminal vesicle invasion was present. The therapeutic benefit of extensive lymph node dissection remains uncertain but could be more relevant in higher risk patients.

Background/Objectives: The accurate delineation of primary tumors (GTVp) and metastatic lymph nodes (GTVn) in head and neck (HN) cancers is essential for effective radiation treatment planning, yet remains a challenging and laborious task. This study aims to develop a deep-learning-based auto-segmentation (DLAS) model trained on external datasets with false-positive elimination using clinical diagnosis reports. Methods: The DLAS model was trained on a multi-institutional public dataset with 882 cases. Forty-four institutional cases were randomly selected as the external testing dataset. DLAS-generated GTVp and GTVn were validated against clinical diagnosis reports to identify false-positive and false-negative segmentation errors using two large language models: ChatGPT-4 and Llama-3. False-positive ruling out was conducted by matching the centroids of AI-generated contours with the slice locations or anatomical regions described in the reports. Performance was evaluated using the Dice similarity coefficient (DSC), 95th percentile Hausdorff distance (HD95), and tumor detection precision. Results: ChatGPT-4 outperformed Llama-3 in accurately extracting tumor locations from the diagnostic reports. False-positive contours were identified in 15 out of 44 cases. The DSCmean of the DLAS contours for GTVp and GTVn increased from 0.68 to 0.75 and from 0.69 to 0.75, respectively, after the ruling-out process. Notably, the average HD95 value for GTVn decreased from 18.81 mm to 5.2 mm. Post ruling out, the model achieved 100% precision for GTVp and GTVn when compared with the results of physician-determined contours. Conclusions: The false-positive ruling-out approach based on diagnostic reports effectively enhances the precision of DLAS in the HN region. The model accurately identifies the tumor location and detects all false-negative errors.

TPS5127 Background: Androgen deprivation therapy (ADT) ± androgen receptor pathway inhibitor therapy is a primary treatment for metastatic hormone-sensitive prostate cancer, but is noncurative and has significant toxicities when used long-term. In patients with OMPC for whom delaying ADT is appropriate, metastasis-directed therapy such as stereotactic body radiation therapy (SBRT) has been shown to provide local disease control. However, many patients do not experience a complete prostate-specific antigen (PSA) response and develop poly-metastatic disease. [ 177 Lu]Lu-PSMA-617 ( 177 Lu-PSMA-617) is a prostate-specific membrane antigen (PSMA)-targeted radioligand therapy with demonstrated efficacy and a manageable safety profile in patients with PSMA-positive metastatic castration-resistant prostate cancer in the VISION and PSMAfore trials. PSMA-DC (NCT05939414) is an ongoing, international, randomized phase 3 trial to evaluate the efficacy of 177 Lu-PSMA-617 versus observation after SBRT in delaying castration and disease progression in patients with PSMA-positive OMPC. Methods: Eligible patients have histologically confirmed prostate cancer, biochemical recurrence post-definitive treatment, OMPC with ≤ 5 PSMA-positive metastatic lesions including ≥ 1 distant metastasis on PSMA PET/CT scans (all must be amenable to SBRT), PSA doubling time < 10 months and non-castration testosterone levels (> 100 ng/dL). Exclusion criteria include distant metastasis by conventional imaging (CI; CT/MRI and bone scans) at screening, prior ADT (except adjuvant ADT completed > 12 months before randomization), or other systemic therapy for metastatic prostate cancer. Patients (N = ~450) will be randomized 2:1 to 177 Lu-PSMA-617 or observation and will receive SBRT to all metastatic lesions within 14 days, completed within 3 weeks. Patients will then receive either intravenous 177 Lu-PSMA-617 (7.4 GBq/6 weeks; 4 cycles), starting 7–21 days after SBRT, or undergo observation only. Additional SBRT for new lesions is allowed. ADT is allowed after a metastasis-free survival (MFS) event by CI confirmed by blinded independent review committee (BIRC). Safety follow-up will occur 42 days after the last 177 Lu-PSMA-617 dose and at the week 24 visit for the observational arm. Long-term follow-up for the 177 Lu-PSMA-617 arm will include safety assessments every ~32 weeks. The primary endpoint is MFS by CI as assessed by BIRC using RECIST v1.1, or death. To provide 90% power to detect a hazard ratio of 0.6, 187 MFS events are required. The key secondary endpoint is time to next hormonal therapy. Additional secondary endpoints include time to PSA progression, radiographic progression-free survival, symptomatic progression, patient-reported health-related quality of life, overall survival and safety. Shore et al. PSMA-delay castration (DC): an open-label, multicenter, randomized phase 3 study of [ 177 Lu]Lu-PSMA-617 versus observation in patients with metachronous PSMA-positive oligometastatic prostate cancer (OMPC). J Urol 2025;213 (5S2_suppl):e28. https://www.auajournals.org/doi/10.1097/01.JU.0001110444.53548.eb . Reused with permission; ©American Urological Association, 2025. This abstract previously presented at 2025 AUA Annual Meeting. Clinical trial information: NCT05939414 .