Citations

Abstract Irritable bowel syndrome (IBS) is a chronic disorder of gut-brain interaction that impacts a significant portion of the population and is associated with substantial morbidity, reduced quality of life, and economic impact globally. The pathophysiology of IBS is complex and incompletely understood, and the heterogeneity of IBS is reflected in the variety of pharmaceutical and non-pharmaceutical therapies utilized for the management of IBS. Given limitations with pharmaceutical treatments, many patients with IBS seek non-pharmaceutical options. Several non-pharmaceutical treatments such as the low FODMAP diet and brain-gut behavior interventions such as gut directed hypnosis and cognitive behavioral therapy are now considered standard of care and are part of all major guidelines for the treatment of IBS. However, challenges with access to and optimal implementation of these therapies remain. This review focuses on the current evidence for common non-pharmaceutical treatments for IBS, including the latest advances in dietary and brain-gut behavioral care, in addition other complementary and integrative health practices and emerging therapies.

Abstract The interactions between transcription factors (TFs) and the target genes could provide a basis for constructing gene regulatory networks (GRNs) for mechanistic understanding of various biological complex processes. From gene expression data, particularly single-cell transcriptomic data containing rich cell-to-cell variations, it is highly desirable to infer TF–gene interactions (TGIs) using deep learning technologies. Numerous models or software including deep learning–based algorithms have been designed to identify transcriptional regulatory relationships between TFs and the downstream genes. However, these methods do not significantly improve predictions of TGIs due to some limitations regarding constructing underlying interactive structures linking regulatory components. In this study, we introduce a deep learning framework, DeepTGI, that encodes gene expression profiles from single-cell and/or bulk transcriptomic data and predicts TGIs with high accuracy. Our approach could fuse the features extracted from Auto-encoder with self-attention mechanism and other networks and could transform multihead attention modules to define representative features. By comparing it with other models or methods, DeepTGI exhibits its superiority to identify more potential TGIs and to reconstruct the GRNs and, therefore, could provide broader perspectives for discovery of more biological meaningful TGIs and for understanding transcriptional gene regulatory mechanisms.

Trauma-induced coagulopathy (TIC) is common after injury and reliable quantification of its severity is lacking. The objective of this study was to evaluate whether thrombin generation would be significantly altered if whole blood samples from trauma patients were collected without (citrate-only) and with corn trypsin inhibitor (CTI+). In a prospective cohort study, 36 trauma pts presenting to a Level I Trauma Center within 12 hours of injury, had whole blood collected simultaneously in citrate-only (3.2%) and citrated plus CTI (CTI+ [final 25 ug/mL]), and processed to platelet free plasma by double centrifugation (3000g, 15 minutes). Samples were stored at -80C with no thawing until analysis. Thrombin generation profiles were measured using the ST Genesia assay (Diagnostica STAGO SAS) and parameters included endogenous thrombin potential (ETP), lag time (LT), peak height, start of tail, velocity index, and time to peak (ttPeak) were analyzed for trauma pts. Data presented as median [IQR] or n (%), with paired t-test and Spearman's correlation analysis were performed between citrated non-CTI and citrated CTI spiked blood samples, with p-value <0.05 statistically significant. Pts presented with significant injury ISS 13 [5, 21], age 45 [29, 59] years, 80.6% male, BMI 26.9 [25.4, 28.3], 94.4% blunt trauma, 22.3% had surgery by day 1 of admission. Significant differences were found between the citrated-only and CTI +tubes in several thrombin generation parameters: ETP (1339 Nm*min [1172.5,1417], 1124.5 [925.4,1285], p<0.001), peak height (222.3 Nm [186.0, 275.6], 160.6 [132.7,208.3], p<0.001), ttPeak (5.64 min [4.86,6.63], 6.19 [5.36, 7.34], p<0.001), start of tail (19.4 min [17.6,21.3], 21.6 [18.9, 23.6], p=0.014), and velocity index (117.6 Nm/min [77.9, 163.1], 71.9 [54.9,106.0], p<0.001). However, LT (3.14 min [2.74, 3.90], 3.08 [2.84, 3.96], p=0.665) did not show a statistically significant difference. Spearman's correlation analysis showed high correlation between citrate-only and CTI+ citrated plasma samples, with Spearman's rank correlation coefficients for LT (0.941), peak height (0.760), ttPeak (0.928), ETP (0.770), start of tail (0.869), and velocity index (0.766) respectively. The results suggest that use of CTI+ decrease thrombin generation kinetics from blood samples obtained from trauma patients. These findings underscore the need for careful consideration of sample collection and processing for use of thrombin generation assays in clinical setting. However, there is very strong correlation of the thrombin parameters obtained from citrated-only plasma to CTI+ plasma samples, suggesting they capture similar information. CTI-spiked citrated tubes appear to reduce contact activation with respect to thrombin generation profiles compared to standard citrated only tubes. This should be a consideration for platform-based lab processing of thrombin generation assays for assessment of coagulopathy after injury; however, given the cost of CTI, citrated-only tubes can be an option for characterization of thrombin generation profile in clinical samples.

Importance Neoadjuvant therapy (NT) is an increasingly used treatment strategy for patients with localized pancreatic ductal adenocarcinoma (PDAC). Little research has been conducted on cancer care delivery during NT, and the standards for optimal delivery of NT have not been defined. Objective To develop consensus best practices for delivering NT to patients with localized PDAC. Design, Setting, and Participants This study used a modified Delphi approach consisting of 2 rounds of voting, and a series of virtual conferences (from October to December 2023) to reach expert consensus on candidate best practice statements generated from a systematic review of the literature and expert opinion. An interdisciplinary panel was formed including 47 North American experts from surgical, medical, and radiation oncology, radiology, pathology, gastroenterology, integrative oncology, anesthesia, pharmacy, nursing, cancer care delivery research, and nutrition as well as patient and caregiver stakeholders. Main Outcome and Measures Statements that reached 75% agreement or greater were included in final consensus statements. Results Of the 47 participating panel members, 27 (57.64%) were male, and the mean (SD) age was 47.6 (8.2) years. Physicians reported completing training a mean (SD) 14.6 (8.6) years prior and seeing a mean (SD) 110.6 (38.4) patients with PDAC annually; 35 (77.7%) were in academic practice. Final consensus was reached on 82 best practices for delivering NT. Of these, 38 statements focused on pre-NT practices, including diagnosis and staging (n = 15), evaluation and optimization (n = 20), and decision-making (n = 3); 29 statements defined best practices during NT, including initiation (n = 3), delivery of therapy (n = 8), restaging practices (n = 12), and management of complications during NT (n = 6); and 15 best practices were identified to guide treatment post-NT, focusing on surgery (n = 7), pathology (n = 4), and follow-up (n = 3). Conclusions Using a modified Delphi consensus technique, best practice guidelines were developed focusing on the optimal standards for delivering NT to patients with localized PDAC. Given the prognostic importance of completing multimodality therapy, efforts to standardize and optimize the delivery of NT represent an immediate opportunity to decrease care variation and improve outcomes for patients with PDAC. Future research should focus on validating and implementing best practice standards into clinical practice.

Importance Vaginal fibroblast function is altered in people with pelvic organ prolapse. Thus, it is important to study vaginal fibroblasts to better understand the pathophysiology of prolapse. Objective This study aimed to compare 3 culturing methods of primary vaginal fibroblasts. Study Design This was an in vitro study. Patients who were undergoing surgery for vaginal prolapse were recruited. Excess vaginal epithelial tissue that would have otherwise been discarded was collected. The vaginal fibroblasts from each participant were cultured via (1) 3-hour digest, (2) coverslip, and (3) gelatin-coat methods. Differences in the efficiency of cell isolation, expression of known fibroblast-associated genes, and cellular function were compared between the 3 methods using one-way analysis of variance and Tukey test for post hoc pairwise comparisons ( P < 0.05). Results Five patients with pelvic organ prolapse were recruited. Fibroblasts cultured via the 3-hour digest method became confluent within 3–5 days in a 100-mm dish compared to 2–3 weeks in a 6-well dish for the coverslip and gelatin-coat methods. Cells from all culture methods expressed similar amounts of vimentin and α smooth muscle actin. There were no significant differences in morphology; gene expression levels of MMP1 , MMP2 , ACTA2 , COL1A1 , COL3A1 , and LOXL1 on qPCR; cell viability; proliferation; and migration between the 3 culturing methods. Conclusion Culturing primary vaginal fibroblasts via the 3-hour digest, coverslip, and gelatin-coat methods similarly resulted in reliable primary vaginal fibroblast growth and function.

PURPOSE BRAF and MEK inhibitors are standard treatments in histiocytic disorders, such as Erdheim-Chester disease (ECD). Some patients lack MAPK-pathway alterations, making these treatments less effective. METHODS We describe three patients with histiocytic disorders who have novel non-MAPK pathway alterations. These alterations were studied through genomic and in silico analyses when applicable, then treated with off-label medications rationally selected on the basis of genomic alterations. RESULTS Patient 1 had rapidly progressive ECD involving the CNS. A CSF1R in-frame deletion (p.S560_P566del) was identified, and in silico modeling predicted a gain-of-function mutation. This alteration was targeted with pexidartinib, which led to a clinical complete response (CR) within 2 months, and a partial response (PR) on imaging after 3 months. After 15 months, the disease became resistant to pexidartinib and transformed to histiocytic sarcoma. Patient 2 has skin-only involvement of a xanthogranuloma disorder. A KIF5B-FGFR1 fusion was identified on RNA sequencing and targeted with pemigatinib. At 24 months of follow-up, she remains in a clinical PR. Patient 3 has ECD involving the bone marrow, gastrointestinal tract, and subcutaneous tissues. A MEF2C-FLT3 fusion was identified and targeted with sorafenib. He achieved a clinical CR and radiographic PR within 3 months, which has continued for 30 months. CONCLUSION We report three patients with histiocytic disorders harboring novel alterations who had sustained responses to off-label kinase inhibitors specific to their histiocytic disorder. Pathogenic variants outside of the MAPK pathway, including variants of unknown significant, may be targeted with readily available small molecules.

Background: Acoramidis is a novel, potent, investigational, transthyretin (TTR) stabilizer under development for the treatment of TTR amyloidosis that results in near-complete (≥90%) TTR stabilization. In a phase 3 study, ATTRibute-CM, acoramidis demonstrated improved clinical outcomes in participants with transthyretin amyloid cardiomyopathy (ATTR-CM), including a 50% reduction in the risk of CVH compared to placebo over 30 months. The study also demonstrated that cardiovascular hospitalization (CVH) during the study predicted a higher subsequent mortality in participants with ATTR-CM. Hypothesis: CVH portends a higher risk of mortality in participants with ATTR-CM. Since acoramidis reduces CVH, it can improve the prognosis of participants with ATTR-CM. Aim: To evaluate the relationship between CVH and survival in the acoramidis group within ATTRibute-CM. Methods: In this post-hoc analysis, the relationship between those with or without CVH and survival was analyzed within the acoramidis treatment group using the Kaplan-Meier (KM) estimator method. Results: Demographics and baseline disease characteristics were mostly comparable between acoramidis-treated participants with and without CVH, although participants with CVH had a higher baseline NT-proBNP and lower eGFR. At Month 30, in acoramidis-treated participants, those without any CVH (n=300) had a higher survival [86.8% (95% CI = 82.2, 90.3)] versus 62.4% (95% CI = 52.6, 70.7) in those who had any CVH (n=109); p<0.0001 from log-rank test (Figure). Conclusion: In the ATTRibute-CM study, pts without any CVH receiving acoramidis have a higher survival rate. CVHs remain a powerful predictor of mortality. This reinforces the importance of an effective therapy that reduces CVH and in turn may improve survival in patients with ATTR-CM.

SUMMARY Goal While studies have examined quality and health outcomes related to the Centers for Medicare & Medicaid Services’ (CMS’s) Hospital Value-Based Purchasing (HVBP) Program, a significant gap exists in the literature regarding the relationship between pay-for-performance initiatives and hospital financial performance in the program’s Efficiency and Cost Reduction domain. This study examined the association between hospitals’ cost inefficiency and participation in the HVBP Program by estimating the probability and magnitude of improvement or achievement in the program’s Efficiency and Cost Reduction domain. Methods The 2014–2019 Efficiency and Cost Reduction domain data were obtained from CMS and merged with the American Hospital Association’s Annual Survey Database. We conducted a zero-inflated negative binomial regression to account for the excessive number of zeros in the data. Principal Findings The negative binomial component of the model assessed the magnitude of the impact on the Efficiency and Cost Reduction improvement from each covariate, while the zero-inflated component assessed the odds of being in the “certain-zero” group, meaning no chance to improve or achieve. Hospital ownership, location, size, safety-net status, percentage of Medicare patients, and the number of registered nurses per bed were statistically significant. Additionally, the Herfindahl-Hirschman Index and teaching status significantly influenced efficiency performance. Practical Applications Changes in hospital performance in this domain exist and have evolved. Hospitals might be at a disadvantage with this performance measure because of their inherent organizational structure. The HVBP Program may not provide clear enough direction or actionable incentive to address the needs of stakeholders influenced primarily by measures of Medicare spending per beneficiary. This study’s findings hold practical value for policymakers, healthcare administrators, and researchers. Policymakers can use this information to tailor future pay-for-performance programs and effectively allocate resources. Healthcare administrators can identify areas for improvement and benchmark their performance against similar institutions. Researchers can explore the program’s long-term sustainability and investigate cost drivers within different hospital groups. By understanding the link between hospital characteristics and cost reduction, all stakeholders can contribute to a more efficient healthcare system.

Abstract Background. Extracellular vesicles (EV) are emerging as new biomarkers for cancer diagnostics and therapeutic monitoring1. For example, in patients that receive PD1/PD-L1 immune checkpoint inhibitors (a key pillar of cancer immunotherapy), circulating EV-derived PD-L1 is gaining attention as a non-invasive biomarker for therapeutic efficacy. Standard methodologies to measure EV-derived PD-L1 requires ultracentrifugation to first separate EVs and then quantify those that express PD-L1 using nano flow cytometry. These are tedious processes that require trained technologists in centralized facilities, which is a key barrier to frequently monitoring EV-based biomarkers. Yet, frequent monitoring is crucial to quickly identify and stop an ineffective therapy while more fruitful options are still available. Method. To bridge the gap, we develop a proof-of-concept digital microfluidic (DMF) device that can separate EVs directly from biofluids and quantify PD-L1+ EVs automatedly. Briefly, DMF device supports automatedly droplet handling, including droplet transport, splitting and mixing, based on electrowetting principles2. Immunomagnetic beads were used to capture EVs from biofluids, and EVs were then detected by electrochemical sensors inserted into the device. These tips of the electrochemical sensors were modified with gold nanoparticle self-assembled layers to enhance target binding, and CD9 antibodies were immobilized on the tips to bind to EVs. We then used anti-PD-L1 as secondary antibodies for target detection. Differential Pulse Voltammetry (DPV)3 were performed to obtain the results. Results. We used the DMF device to extract 109- 1011 #/mL EVs secreted by a human breast cancer cell line (MDA-MB-231). Briefly, 10 mL of cell culture media was loaded into the DMF device, and the sample was mixed and incubated with a 10 mL droplet of immunomagnetic beads to capture EVs. After 5 min, EVs were eluted in 20 mL of elution buffer, and the beads were discarded. We estimated the number of EVs using Nanoparticle Tracking Analysis; the number of EVs extracted on-chip was comparable with those that were extracted using standard in-tube method. We also verified the purity of the EVs extracted on-chip using Western Blot. Our results showed that the electrochemical sensors can detect as low as 104 #/mL PD-L1+ EVs, with a linear range of 104 – 107 #/mL (R2=0.9701). The entire process can be completed within 1 hour. Conclusion. We integrated automated EV extraction and their surface marker detection in a single DMF device. Our next step is to extract and detect EV-based biomarkers from plasma samples. This platform holds promise for the regular monitoring of EV-based biomarkers that are indicators of therapeutic responses in patients that receive cancer immunotherapies. References1. F. Lucien, D. Gustafson, M. Lenassi et al, Journal of extracellular vesicles 12 (12), 12385 (2023). 2. Y. Zhang and Y. Liu, Sensors & Diagnostics (2022). 3. Y. Zhang, J. Liu, T.-W. Lo et al, Biosensors and Bioelectronics: X, 100490 (2024). Citation Format: Ting-Wen Lo, Yuqian Zhang, Jing Liu, Yohan Kim, Haidong Dong, Fabrice Lucien, Yuguang Liu. Rapid extraction and detection of extracellular vesicle-derived PD-L1 in a microfluidic platform [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr A030.

Abstract BACKGROUND Standard of care treatment for recurrent malignant glioma after prior radiotherapy (RT) is not well established. Proton therapy (PT) is increasingly used for reirradiation (ReRT) at the time of recurrence; however, treatment outcomes, toxicity, and prognostic factors for patients treated with PT-ReRT remain poorly defined. METHODS The prospective, multi-institutional Proton Collaborative Group (PCG) registry was queried for patients with malignant glioma who previously received RT and underwent PT-ReRT between 7/2011-12/2023. Overall survival (OS) and progression-free survival (PFS) were assessed using the Kaplan-Meier method, and Cox proportional hazards regression was used for uni- and multivariate analysis (UVA and MVA). Dose was calculated using equivalent dose in 2-Gy fractions (EQD2). RESULTS 143 consecutive patients were identified. Median follow-up was 11.2 months and median time interval (TI) from prior RT (median 58.5 Gy) to PT-ReRT (median 44.6 Gy) was 42.4 months. Primary histology was glioblastoma (n=74), astrocytoma (n=35), and oligodendroglioma (n=34). Median PFS and OS were 8.1 and 11.2 months, respectively. On UVA, improved OS was associated with oligodendroglioma (HR 0.37) and astrocytoma histology (HR 0.53) compared to glioblastoma, TI &gt;60 months (HR 0.2), CNS WHO Grade 2 compared to 4 (HR 0.42), and ECOG performance status 0 (HR 0.47). On MVA, improved OS remained associated only with oligodendroglioma (HR 0.42) and TI &gt;60 months (HR 0.49). Acute and Late Grade 3 toxicity occurred in 7% and 4% of patients. Acute Grade 3 toxicity was associated with poor performance status (HR 16.15). CONCLUSIONS In the largest series of glioma PT-ReRT reported to date, retreatment appears well tolerated with variable outcomes based on clinical prognostic factors. Toxicity rates were acceptable compared to historical photon-based literature despite a high median prescription dose.