Citations

566 Background: FGFR inhibitors (FGFRi) have an established role in treating FGFR2-altered (alt) cholangiocarcinoma (CCA). Tinengotinib, a novel FGFRi, has shown promising activity overcoming acquired resistance to prior FGFRi. We present biomarker analyses evaluating tinengotinib’s ability to overcome prior FGFRi resistance and to elucidate mechanism of resistance to tinengotinib. Methods: Eligible patients (pts) with advanced/metastatic CCA who had received ≥ 1 prior systemic chemotherapy were treated with tinengotinib 10 mg daily across 4 Cohorts: A1: FGFR2 fusion (fus) with primary progressive disease (PD) on prior FGFRi; A2: FGFR2 fus with PD after prior response to FGFRi; B: FGFR alt without FGFR2 fus; C: FGFR wild-type. Efficacy was assessed by RECIST v1.1. All pts underwent liquid biopsy for circulating tumor DNA (ctDNA) at baseline; additional timepoints include cycle 3 day 1 (C3D1), time of PD, and end of treatment (EOT). Samples were analyzed using FoundationOne Liquid panel. Results: 27 out of 55 enrolled pts had biomarker samples collected at baseline and C3D1. Among them, pts in A1 (n=10, 107 mutations (mut)), B (n=8, 90 mut) and C (n=5, 74 mut) showed a significant decrease in short variant allele frequencies (VAF) from baseline to C3D1 by a median relative VAF reduction of 100% (p<0.0001) for each of the three cohorts. Although a median relative VAF reduction of 33.3% was seen in A2 (n=4, 15 mut), this was not significant (p=0.6093) likely due to low baseline mutation burden. A ≥50% reduction in ctDNA was associated with improved progression free survival (p<0.0014). Additionally, 100% of median relative reductions in FGFR2 kinase domain (KD) mut were seen in A1 and B (p<0.0001, 95% CI 100-100% and p=0.0156, 95% CI 83.6-100%, respectively), with 92% and 57% clearance of initial FGFR2 KD mut by C3D1. In a subgroup of 10 pts with biomarker sampling at baseline and EOT, 3 pts in A1 with acquired resistance showed emergence of novel FGFR2 mut, loss of FGFR-sensitive mut and new mut in alternate pathways (e.g., AKT, EGFR, RAS/MAPK) while retaining the original FGFR2 fus. 1 pt from B developed resistance due to new FGFR2 rearrangements and FGFR2 mut. 4 FGFR wild-type pts from C developed resistance involving mut in TP53, KRAS, and other oncogenic drivers. Conclusions: These findings provide genomic evidence that tinengotinib may overcome resistance to prior FGFRi treatment in FGFR2 fus-positive CCA, as reflected by significantly reductions in ctDNA VAFs and frequent clearance of FGFR2 KD mutations. The emergence of resistance alterations including de novo FGFR2 mutations and bypass pathways activations indicates acquired resistance that may limit long-term benefit. These results support further investigation with expanded biomarker sampling to better characterize resistance evolution and guide therapy optimization in an ongoing Phase 3 trial. Clinical trial information: NCT04919642 .

Abstract Background The rare APOE3 ‐Christchurch ( APOE3Ch ) variant is associated with remarkable protective effects, delaying the age at onset of PSEN1 ‐E280A driven autosomal dominant Alzheimer's disease (AD). While much of the research on APOE3C h has focused on its role in AD, little is known about how this variant impacts APOE biology under non‐disease conditions. Using cortical organoids as a model system, we aim to investigate the fundamental mechanisms by which APOE3Ch alters APOE biology, including its effects on metabolism and cellular interactions, to better understand its unique properties and potential implications for broader applications. Method Cortical organoids were derived from the isogenic neurodegeneration iPSC line series, with either the APOE3 or APOE3Ch genotype. Single‐cell RNA sequencing (scRNA‐seq) was performed on three independent batches of 6‐month‐old cerebral organoids to identify pathways differentially regulated by APOE3Ch. To further investigate APOE lipidation and its effects on lipid metabolism, lipidomics analysis was conducted on 8‐month‐old cerebral organoids, offering additional insights into APOE3Ch ‐specific biological mechanisms. Validation was also carried out using iPSC‐derived astrocytes and neurons to confirm key findings. Result ScRNA‐seq revealed differences in cell populations and astrocyte subtypes between APOE3 and APOE3Ch organoids, with mitochondrial‐related pathways differentially regulated in APOE3Ch cerebral organoids. These findings were validated in iPSC‐derived astrocytes. APOE3Ch iPSC‐derived astrocytes exhibited increased APOE secretion compared to APOE3 . They also demonstrated enhanced mitochondrial function, as evidenced by increased spare respiratory capacity measured by Seahorse stress assays. Furthermore, APOE3Ch astrocytes showed reduced lipid droplet formation following oleic acid treatment. Lipidomics analysis of APOE3Ch cerebral organoids revealed decreased cholesterol ester levels, suggesting alterations in lipid metabolism. Conclusion Our findings provide novel insights into how the APOE3Ch variant alters APOE biology, revealing differences in mitochondrial function and lipid metabolism. The differential regulation of mitochondrial pathways in APOE3Ch cerebral organoids, along with the enhanced mitochondrial capacity and altered lipid metabolism observed in APOE3Ch astrocytes, highlights the unique properties of this variant. These results offer valuable mechanistic understanding that may inform future therapeutic strategies targeting APOE biology, particularly in the context of AD.

Abstract Medulloblastoma (MB) is one of the most prevalent malignant brain tumors in children, with tremendous cognitive and neuroendocrine disability among survivors. Group 3 (G3) MBs have poor overall survival at &lt;50%, higher frequency of metastasis, and no targeted therapies. Amplification of MYC and activation of TGFβ signaling are frequent in G3MB. Remarkably, some tumors have no reported mutations, suggesting roles for chromatin-driven mechanisms in this disease. We have generated novel humanized models for G3MB by transducing neuroepithelial stem cells (NESC) derived from human induced pluripotent stem cells with TGFβ effectors alone and/or in combination with MYC, prioritizing combinations observed in patients. We determined that both MYC and TGFβ effectors drove tumor formation in vivo with the combination driving more aggressive tumors and higher frequency of metastasis. Importantly, NESC-derived tumors clustered with human G3MB, indicating our models recapitulated human disease. To decipher mechanisms of resistance, we integrated CUT&RUN for MYC genomic localization and histone PTMs with RNA-sequencing and discovered MYC-bound neural developmental genes repressed in MYC and TGFβR1-driven lines. These gene signatures were associated with the Polycomb Repressive Complex (PRC) and demarcated with H3K27me3; the histone mark directly regulated by PRC. Further interrogation identified JARID1B, a MYC binding partner and H3K4me3 demethylase, as a regulator of these repressed neural genes. This is further reinforced by the observation of higher H3K27me3 levels concurrent with increased JARID1B expression in human G3MB patient samples, compared to other subtypes. We postulate that deregulation of MYC and context-specific targeting to the chromatin template culminates in transcriptional alterations that promote aggressive G3MB. These studies support a critical role of MYC in repressing target genes to drive tumor formation and JARID1B as a new target for therapy. Collectively, we present a critical framework for understanding mechanisms of resistance and the chromatin landscape of MYC- and TGFβ-driven G3MB.

Background: MARVEL-HCM is a US multicenter study assessing the safety and effectiveness of mavacamten in real-world academic and community practices. Mavacamten is a first-in-class cardiac myosin inhibitor (CMI) and the only CMI currently approved in over 50 countries for use in patients with symptomatic obstructive hypertrophic cardiomyopathy (oHCM). Modest evidence exists describing the effectiveness and safety of mavacamten monotherapy. Aims: To describe the real-world outcomes of patients using mavacamten as monotherapy for oHCM. Methods: Patient-level data from medical records at 5 sites were analyzed to describe mavacamten monotherapy, defined as monotherapy at baseline or after background HCM therapy (beta-blockers [BB], calcium channel blockers [CCB], disopyramide) discontinuation within 12 weeks(wks) of mavacamten initiation and without reinitiation, up to 60 wks. A minimum of 12 wks follow-up was required for inclusion. Patient characteristics, echocardiographic data, and safety are reported at baseline and follow-up visits. Results: The monotherapy cohort comprised 13.4% (32/239) of patients: 24 were on mavacamten monotherapy at initiation, and 8 discontinued background therapy. Baseline characteristics included: NYHA Class II (46.9%) and III (53.1%), female (66%), hypertension (50%), and atrial fibrillation (AF) (18%) (Table 1). Median follow-up and duration of mavacamten monotherapy were 48 wks (range 12-60 wks) and 57 wks (range 14-60 wks), respectively. Resting left ventricular outflow tract gradient (LVOTg) was ≤ 30 mmHg in 93%, 91% and 100% of patients at Wk 24, 36, and 60. Valsalva LVOTg was ≤ 30 mmHg in 61%, 77% and 86% of patients at Wk 24, 36, and 60 (Fig 1). No patients were in NYHA Class III at wk 60, and ~50% of patients were NYHA Class I by wk 48 (Fig 2). Mean reduction in LVEF was 4.8% over 60 wks. One patient had LVEF < 50% at Wk 20, resulting in a dose reduction (10 to 7.5 mg). Safety events included 3 hospitalizations due to AF ablation (n=1), viral gastrointestinal illness (n=1) and heart failure (n=1). Demographic, clinical characteristics, and outcomes were similar across the mavacamten monotherapy cohort, mavacamten in combination with background HCM therapy (n=207), and the overall cohort of MARVEL-HCM (N=239). Conclusions: Mavacamten monotherapy was effective, safe, and consistent with the overall MARVEL cohort, as well as previously reported monotherapy cohorts from pivotal, long-term, and real-world evidence.

Objective Closed-source large language models (LLMs) like generative pre-trained transformer 4o (GPT-4o) have shown promise for clinical information extraction but are potentially limited by cost, data security concerns and inflexibility. Open-source models are an attractive alternative with various adaptation strategies with no consensus on best practices. This study aims to rigorously identify optimal adaptation strategies for open-source models and evaluate their performance relative to closed-source alternatives. Methods and Analysis We studied three LLM adaptation strategies: chain-of-thought prompting, few-shot prompting and fine-tuning. Our target for information extraction was the Mayo Endoscopic Subscore (MES). We applied those strategies in all combinations to six open-source models (8–70 billion parameters) using an annotated set of colonoscopy procedure reports from the University of California, San Francisco (N=608) and San Francisco General Hospital (N=217). We analysed the relationship of these strategies to several performance metrics with a mixed-effects model, accounting for the variability between centres and LLMs. GPT-4o served as a closed-source oracle and provided in-depth commentary on the cost-effectiveness of these options. Results Quantised low-rank adaptation (QLoRA) statistically improves ( p §amp;lt; 0.001 ) ) the performance of open-source LLMs by 9.1–15.7 percentage points across accuracy, precision recall and annotation eligibility accuracy. However, GPT-4o with prompt engineering outperforms the best open-source model by 4.9%–11.2%. A simple cost-effectiveness analysis suggests that GPT-4o is more affordable compared with open-source alternatives. Conclusion GPT-4o is currently the most efficient LLM for MES extraction. If unavailable, QLoRA-optimised open-source models are a competitive alternative. However, results also suggest that current instruction-following LLMs including GPT-4o do not fully follow user-provided instructions, leaving room for improvement. More work is needed to achieve consistent, near-perfect performance in clinical information extraction by LLMs.

EndMT has been reported to contribute to the pathogenesis of PAH. In this study, we aimed to determine the role of Ca 2+ signaling in the development of EndMT in human lung vascular endothelial cells. Our data suggest that TGF-β 1 requires store-operated Ca 2+ entry through STIM1/Orai channels to induce SNAI-mediated EndMT. For the first time, we demonstrated that TGF-β 1 -induced EndMT is a Ca 2+ -dependent event, whereas inhibition of STIM1/Orai interaction attenuated EndMT in response to TGF-β 1 .

Background: Cognitive change is an important factor in understanding dementia. Estimating effects of exposures on cognitive change requires choosing an analytical timescale, typically time on study or current age. There is limited consensus regarding timescale choice in epidemiologic cognitive aging research. Methods: Using a coordinated analytic approach in 10 cohorts of older adults, we evaluated whether estimated effects of two exposures on memory change differed depending on timescale (time on study or current age). We modeled effects of apolipoprotein-E (APOE) ε4 genotype (a time-invariant exposure) and diabetes (a potentially time-varying/acquired exposure evaluated at baseline) using mixed-effects models with linear and nonlinear time specifications for both timescales. Results: Among APOE ε4 carriers, model-estimated memory scores at baseline (time on study timescale) or at each cohort’s median baseline age (current age timescale) were lower, and the average rate of decline was faster than among APOE ε4 noncarriers. Model-estimated memory scores at baseline or at median baseline age were generally similar across baseline diabetes status, with variability across cohorts in the diabetes-memory change association. In some cohorts, trends in diabetes-memory change associations differed in direction across timescales. Conclusions: Timescale was largely inconsequential for estimated effects of APOE genotype, but yielded differences in estimated diabetes effects, raising questions about the appropriate scale. The current age scale may be problematic because diabetes was measured heterogeneously in age across individuals, a common issue in aging cohorts. Our work demonstrates approaches to evaluate alternative timescales, including in multicohort analyses, and highlights potential implications for estimated exposure effects on cognitive change.