Citations

Abstract Breast cancer is the leading cause of cancer death among women worldwide. Most cases occur in those without identifiable modifiable risk factors, highlighting critical gaps in our understanding of breast cancer biology including the influence of the gut microbiome. Here we studied the gut microbiome with shallow shotgun metagenomic sequencing from preoperative stool samples in a well-characterized clinical cohort of 131 women, median age 59 years, undergoing breast-conserving surgery for benign (n=23), high-risk (n=47), or malignant (n=61) breast disease. Taxonomic profiling was performed with Sourmasth 4.2.4 with GTDBv202 as reference database; functional profiling of metagenomic data employed HUMAnN 3.6 with identified gene families mapped to MetaCyc pathways. Differences in alpha diversity in terms of species richness were observed across diagnosis groups (benign, high-risk, malignant) and was lowest for high-risk lesions (p=0.031). Decreased alpha diversity was also associated with higher body mass index (BMI) (Shannon p=0.12, Inverse Simpson p=0.025). Significant beta diversity differences across diagnosis groups also were seen (Bray-Curtis p=0.044, Jaccard p=0.013) as were differences in association with BMI (Bray-Curtis, Jaccard, both p=0.002). No significant diversity differences associated with age, mammographic breast density or menopausal status were observed. Functional pathway profiling stratified by BMI showed a correlation between increasing BMI and greater relative abundance of genes in nicotinamide adenine dinucleotide (NAD) biosynthesis, folate metabolism, and aromatic amino acid metabolism pathways (p=0.0279, 0.0667 and 0.0860, respectively) - pathways implicated in breast cancer detection, survival and prognosis. Cross-referencing our significantly (FDR <5%) differentially abundant taxonomic findings with these functional pathway data identified enrichment of several Blautia species, linked to NAD biosynthesis via tryptophan metabolism, in patients with higher BMI. We also noted enrichment of Dorea formicigenerans, a species associated with increased breast cancer risk in obese women due to its pro-inflammatory effects, in individuals with a higher BMI. Here we report significant differences in gut microbiome diversity, taxonomy and functional pathway signals in association with BMI in women with breast disease. Differentially abundant species seen with rising BMI may contribute to functional pathways that drive increased breast cancer risk and may provide an actionable target for risk reduction independent of conventional risk reduction strategies. Citation Format: Jack W. Sample, Matteo Redaelli, Stephen Johnson, Tanya L. Hoskin, Marina R. Walther-Antonio, Jun Chen, Tina J. Hieken. Obesity alters cancer-related microbial pathways in women with benign and malignant breast disease [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2213.

Abstract Introduction: Src Family Kinases (SFKs) have a crucial role in tumor proliferation, survival, and metastasis. NXP900 is a highly selective SFK inhibitor a novel mechanism of action that locks SFKs in a closed, inhibited conformation, preventing interaction with substrate proteins, unlike other SFK inhibitors like dasatinib. A phase 1 study of NXP900 in patients with advanced solid tumors was recently initiated. Our preclinical studies showed therapeutic efficacy of NXP900 in cholangiocarcinoma (CCA) through decreased YAP, RAF-MAP and PI3K-AKT signaling. Here, we examined mechanisms of sensitivity and resistance to SFK inhibition. Methods: Secondary resistance was explored by generating a NXP900-resistant human cell line (HuCCT1-R) via prolonged exposure to NXP900, followed by multiomic profiling. Primary resistance was studied in vivo using nine heterogeneous patient-derived xenograft (PDX) tumors implanted in the flanks of NOD/SCID mice. Tumor-bearing mice were treated with vehicle or 40 mg/kg NXP900 daily for up to 4 weeks. To identify factors associated with response, a multiomic approach was used, integrating RNA-Seq, global proteomics, and phosphoproteomics. A hierarchical-all-against-all algorithm (HallA) assessed associations between multiomic features and drug response in tumor growth. Kinase enrichment analysis (KEA3) identified features linked to sensitivity or resistance. Results: HuCCT1-R cells showed increased pTyr abundancy of TNK2, a protein known to increase PIP3 levels leading to AKT activation, and of DYRK3 and LAMTOR1, both of which can sustain AKT phosphorylation via mTORC, indicating acquired resistance through bypassing inhibited PI3K-AKT signaling to rescue AKT. NXP900 reduced tumor growth rates in 5 of 9 PDX models. Kinases associated with sensitivity in the PDX models included SFKs (SRC, LYN, and FYN), and AKT, PTK2, PRKCZ, EGFR, SYK, and GSK3B, suggesting involvement of the PI3K-AKT pathway in responsiveness to NXP900. Based on tumor inhibition responses in the tested models, we estimated NXP900 response for our additional PDX models, predicting 39% (11/28) of patient tumors may respond. Conclusion: This study identified molecular markers linked to response to SFK inhibition, which could be utilized for patient selection for NXP900 treatment. Further studies are validating these findings and exploring combination therapies to address resistance mechanisms. Citation Format: Hendrien Kuipers, Danielle M. Carlson, Jack W. Sample, Erik Jessen, Dong-Gi Mun, Aushinie M. Abeynayake, Jennifer L. Tomlinson, Amro M. Abdelrahman, Nathan W. Werneburg, Binbin Li, Mitesh J. Borad, Mark J. Truty, Sumera I. Ilyas, Gregory J. Gores, Rory L. Smoot. Multiomic profiling identified biomarkers of response to selective Src family kinase inhibition in preclinical models of cholangiocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 5595.

Abstract SWI/SNF chromatin remodeling complexes are frequently mutated across human cancers, including cholangiocarcinoma (CCA). Dysregulation of this complex due to loss of function mutations in AT-rich interaction domain-1A (ARID1A) and polybromo-1 (PBRM1) occur in up to 18% and 10% of cases respectively. SWI/SNF subunit mutations frequently co-occur alongside PI3K/AKT pathway activation. Preexisting literature suggests altered gene expression and protein synthesis contribute to CCA oncogenesis, but our understanding of these mechanisms remains immature. Genetically accurate preclinical models are needed to define the roles of ARID1A and PBRM1 in CCA and identify therapeutic targets. We developed novel murine models of CCA with either ARID1A, PBRM1 or dual ARID1A/PBRM1 (APAC) knockout in the context of AKT activation, utilizing a surgical biliary transfection method for somatic gene editing with CRISPR/Cas9. Within 8 months, mice formed numerous liver tumors, predominantly CCA and mixed CCA/HCC. Knockout of ARID1A and PBRM1 was confirmed through genomic PCR, qRT-PCR, and immunoblot assays. Histologically, murine APAC tumors displayed phenotypic similarities to human CCA, including dense cancer-associated fibroblast infiltration and variable CD45+ immune cell infiltration. A novel, syngeneic CCA cell line was isolated from a dual ARID1A/PBRM1 knockout tumor (APAC-2). RNA-sequencing of primary tumors and the APAC-2 cell line versus a non-invasive cholangiocyte cell line with AKT activation only (AC), was performed to identify differentially expressed genes (DEGs) of interest in ARID1A and PBRM1-deficient CCA. Periostin (Postn) was among the top upregulated genes in the APAC-2 cell line. POSTN is a secreted glycoprotein that is upregulated in human CCA and may be therapeutically targetable. Knockdown of periostin inhibited the in vitro growth of APAC-2 cells and a human CCA cell line with ARID1A mutation and periostin overexpression (HuH-28). These studies serve to characterize and validate a genetically relevant murine model of epigenetic dysregulation in ARID1A and PBRM1-deficient CCA. This model can be used for identification and validation of potential drug targets. Ongoing work focuses on studying multiple dysregulated pathways and testing dependence on genes of interest, including periostin, as potential treatment strategies for CCA. Citation Format: Jayla Millender, Jennifer Tomlinson, Ryan Watkins, Danielle Carlson, Jack Sample, Nathan Werneburg, Rory Smoot, Keith Robertson, Gregory Gores, Caitlin Conboy. Novel murine models of epigenetic dysregulation in SWI/SNF-mutated cholangiocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2741.

Abstract Increased innate immune activity promotes neurodegeneration and contributes to progression in multiple sclerosis. This prospective case-control study aims to investigate thalamic microglia density on 18kDa translocator protein PET in patients with multiple sclerosis using a third-generation radioligand, 11C-ER176, and investigate the associations of 11C-ER176 PET uptake with imaging and clinical measures of progression in multiple sclerosis. Patients with multiple sclerosis (n = 50) and controls (n = 55) were prospectively enrolled and they underwent 11C-ER176 PET and MRI including diffusion MRI with neurite orientation dispersion and density imaging. Disease characteristics, expanded disability status scale and multiple sclerosis functional composite scores were obtained in patients with multiple sclerosis. Age at imaging (mean ± standard deviation: patients = 49.6 ± 12.9 years, controls = 48.2 ± 15.4 years, P = 0.63) and sex (female ratio; patients = 72%, controls = 65%, P = 0.47) were not different between the groups. Thalamus 11C-ER176 PET uptake was highest in patients with progressive multiple sclerosis (1.272 ± 0.072 standardized uptake value ratio), followed by patients with relapsing multiple sclerosis (1.209 ± 0.074 standardized uptake value ratio) and lowest in controls (1.162 ± 0.067 standardized uptake value ratio, P < 0.001). Patients with thalamic lesions had higher thalamus 11C-ER176 PET uptake than those without thalamic lesions in both relapsing multiple sclerosis and progressive multiple sclerosis (P < 0.001). In patients with multiple sclerosis, higher thalamus 11C-ER176 PET uptake correlated with lower thalamic volume (r = −0.45, P = 0.001), higher mean diffusivity (r = 0.56, P < 0.001), lower neurite density index (r = −0.43, P = 0.002), lower orientation dispersion index (r = −0.40, P = 0.005) and higher free water fraction (r = 0.42, P = 0.003) in the thalamus. In patients with multiple sclerosis, higher thalamus 11C-ER176 PET uptake also correlated with higher mean diffusivity (r = 0.47, P < 0.001) and lower neurite density index (r = −0.36, P = 0.012) in the corpus callosum. In patients with multiple sclerosis, higher thalamus 11C-ER176 PET uptake correlated with worse expanded disability status scale scores (r = 0.33, P = 0.02), paced auditory serial addition test scores (r = −0.43, P = 0.003) and multiple sclerosis functional composite z-scores (r = −0.46, P = 0.001). Microglia density in the thalamus is highest in patients with progressive multiple sclerosis and is associated with imaging biomarkers of neurodegeneration and clinical disease severity. As a signature imaging biomarker of progression in multiple sclerosis, effectively reflecting the global disease burden, 11C-ER176 PET may aid development and efficacy evaluation of therapeutics targeting microglia.

Abstract INTRODUCTION Biomarkers play a crucial role in understanding Alzheimer's disease (AD) pathogenesis and treatment effects. However, comparing biomarker measures without standardization and appreciating their magnitude relative to the disease can be challenging. METHODS To address this issue, we propose the CentiMarker approach, similar to Centiloid, which provides a standardized scale between normal (0) and nearly maximum abnormal AD (100) ranges. We applied this scale to cerebrospinal fluid (CSF) biomarkers in dominantly inherited AD and sporadic AD cohorts. RESULTS CentiMarkers facilitated the interpretation of disease abnormality, demonstrating comparable changes and distributions of AD biomarkers across disease stages. CentiMarkers make the treatment effect more comparable than their original scales across various biomarkers. DISCUSSION The versatility of CentiMarkers makes it a valuable tool for standardized biomarker comparison in AD research, enabling informed cross‐study comparisons and contributing to accelerated therapeutic development. Adoption of the CentiMarker scale could enhance biomarker reporting and advance our understanding of AD. Highlights Comparing fluid biomarkers without appreciating their magnitude relative to the disease can be challenging. We propose a CentiMarker metric to standardize biomarker measures from normal (0) and nearly maximum abnormal AD (100) ranges. CentiMarkers make the treatment effect more comparable across various biomarkers than when using the original scales.

Background: Medicaid reimbursement to physicians is often perceived to be lower than Medicare, but little is known about orthopaedic foot and ankle reimbursement. This study sought to compare Medicare and Medicaid reimbursement for the 20 most common foot and ankle procedures. Methods: Medicare reimbursement rates for common foot and ankle codes were obtained from the online Centers for Medicare & Medicaid fee schedule, while Medicaid rates were found from individual state fee schedule websites. Medicaid rates were compared by state and pooled to obtain national differences. The Medicare Wage Index was used to adjust Medicaid rates by state wages to ensure a more accurate comparison. Variability between states was measured using state percentages of Medicare and coefficient of variation values. Results: Medicaid reimbursed physicians higher than Medicare in 31 states overall, with average reimbursement ranging from 37% to 324% of Medicare. Nationally, Medicaid reimbursed 8.8% higher than Medicare, but Medicare reimbursed 3.7% higher when adjusted for the Medicare Wage Index. The Current Procedural Terminology ( CPT ) codes with the highest ratio of Medicaid to Medicare reimbursement were CPT 28002 for incision and drainage of the foot (176.6%) and CPT 28820 for toe amputation (167.6%). Five codes had lower relative Medicaid reimbursement on average: CPT 27687 for repair procedures on the leg and ankle joint, CPT 28810 for amputation procedures on the foot and toes, CPT 28010 for toe tenotomy, CPT 28005 for incision procedures on the foot and toes, and CPT 28470 for closed treatment of a metatarsal fracture. The coefficient of variation values ranged from 0.34 to 0.84 in the Medicaid group and 0.40 to 0.78 in the adjusted group, indicating high variability between states and between procedures. Conclusion: Medicaid reimbursement is highly inconsistent between states, ranging from 37% to 324% of Medicare. Medicaid reimbursed more than Medicare overall, which is in contrast with most published findings that tend to show higher reimbursement for Medicare when compared to Medicaid. When adjusting for wage differences between states, Medicare reimbursed slightly higher than Medicaid. Level of Evidence: Level IV, economic analysis.

Attempts to activate an anti-tumor immune response in glioblastoma (GBM) have been met with many challenges due to its inherently immunosuppressive tumor microenvironment. The degree and mechanisms by which molecularly and phenotypically diverse tumor-propagating glioma stem cells (GSCs) contribute to this state are poorly defined. In this study, our multifaceted approach combining bioinformatics analyses of clinical and experimental datasets, single-cell sequencing, and the molecular and pharmacologic manipulation of patient-derived cells identified GSCs expressing immunosuppressive effectors mimicking regulatory T cells (Tregs). We showed that this immunosuppressive Treg-like (ITL) GSC state is specific to the mesenchymal GSC subset and is associated with and driven specifically by TGFβ type II receptor (TGFBR2) in contrast to TGFBR1. Transgenic TGFBR2 expression in patient-derived GBM neurospheres promoted a mesenchymal transition and induced a six-gene ITL signature consisting of CD274 (PD-L1), NT5E (CD73), ENTPD1 (CD39), LGALS1 (galectin-1), PDCD1LG2 (PD-L2), and TGFB1. This TGFBR2-driven ITL signature was identified in clinical GBM specimens, patient-derived GSCs, and systemic mesenchymal malignancies. TGFBR2high GSCs inhibited CD4+ and CD8+ T cell viability and their capacity to kill GBM cells, effects reversed by pharmacologic and shRNA-based TGFBR2 inhibition. Collectively, our data identify an immunosuppressive GSC state that is TGFBR2-dependent and susceptible to TGFBR2-targeted therapeutics.

Background: The purpose of this study was to investigate the association between cannabis use and postoperative complications following ankle and hindfoot arthrodesis. Methods: A retrospective cohort study using a large national insurance database from 2010 to 2022 was conducted. All patients who underwent ankle or hindfoot arthrodesis with at least 2 years’ follow-up were included. Patients were divided into 4 groups: cannabis-only users, tobacco-only users, cannabis and tobacco users, and nonuser controls. Groups were matched 1:4 with nonuser controls based on demographic variables and comorbidities. Also, both cannabis and tobacco users were matched 1:4 with tobacco-only users based on demographics and comorbidities. Medical complications within 90 days of surgery and surgery-specific complications within 2 years were compared between groups with multivariable logistic regressions. Results: Compared with nonuser controls, cannabis users only were not at increased risk of 90-day medical complications or 2-year surgical complications. Tobacco use alone was associated with increased risk of postoperative admission (OR 1.32, 95% CI 1.21-1.43) and emergency department (ED) utilization (OR 1.57, 95% CI 1.48-1.66) within 90 days as well as infection (OR 1.24, 95% CI 1.18-1.30), hardware removal (OR 1.12, 95% CI 1.07-1.18), nonunion (OR 1.33, 95% CI 1.27-1.40), and wound dehiscence (OR 1.38, 95% CI 1.27-1.49) within 2 years of surgery compared with nonuser controls. Compared with tobacco-only use, combined cannabis and tobacco use was associated with increased risk of ED visits within 90 days (OR 1.45, 95% CI 1.30-1.62) and nonunion within 2 years of surgery (OR 1.19, 95% CI 1.05-1.35). Conclusion: These findings suggest that although cannabis use alone was not associated with a higher risk of postoperative complications, its concurrent use with tobacco was linked to greater rates of adverse outcomes. Level of Evidence: Level III, retrospective case control study.

Artificial intelligence (AI) has emerged as a promising adjunct in the diagnosis and management of infective endocarditis (IE), a disease characterized by diagnostic complexity and significant morbidity. Machine learning (ML) models such as SABIER and SYSUPMIE have demonstrated strong predictive accuracy for early IE diagnosis, embolic risk stratification, and postoperative mortality, surpassing traditional clinical scoring systems. In imaging, AI-enhanced echocardiography and advanced modalities like FDG-PET/CT offer improved sensitivity, specificity, and reduced inter-observer variability, potentially transforming clinical decision making. Additionally, AI-powered microbiological techniques, including MALDI-TOF mass spectrometry combined with ML and neural network-based metagenomic classifiers, show promise in rapidly identifying pathogens and predicting antimicrobial resistance. Despite encouraging early results, widespread adoption faces barriers, including data limitations, interpretability issues, ethical concerns, and the need for robust validation. Future directions include leveraging generative AI as clinical consultative tools, provided their capabilities and limitations are carefully managed. Ultimately, collaborative efforts addressing these challenges could transform IE care, enhancing diagnostic accuracy, clinical outcomes, and patient safety.