Predictive Molecular Biomarkers for Human Health Risk

Molecular biomarkers play vital roles in disease risk assessment, personalized treatment selection and therapy response monitoring. This thesis explores the use of diverse molecular biomarkers for the assessment of human health risks, primarily in cancers. MiRNAs and their isoforms (isomiR) are promising biomarker candidates due to their comprehensive regulation of gene expression and involvement in physiology and pathological processes. The first study demonstrates that genetic variations in miRNA precursor regions influence the biogenesis of isomiRs in 95 SNP-isomiR pairs. Notably, we identified a SNP (rs6505162) impacting hsa-miR-423 isomiRs, potentially linked to breast cancer pathogenesis, suggesting their potential as biomarkers in disease assessment. The findings also highlight the mechanism of genetic regulation of isomiR generation and advance our understanding of miRNA mediated post-transcriptional regulation. Secondly, we explored the predictive capacity of aberrant intron-retention neoantigen burden (INB) in predicting the response to immune checkpoint inhibitors (ICI) in metastatic cancers. Both INB and tumor mutation burden (TMB) were strong predictors of ICI therapy duration (p = 0.019 and 0.038, respectively), with patients exhibiting elevated levels demonstrating exceptional treatment duration. Patients with high INB or TMB had improved overall survival (OS) (p = 1.1×10-4). Importantly, INB and TMB were uncorrelated, indicating that they capture distinct aspects of tumor neoantigen. Together, the combined assessment of INB and TMB offers improved accuracy in predicting clinical response to ICI therapies. Finally, we extend the application of molecular biomarkers to the assessment of minimal residual disease for risk stratification in triple negative breast cancer (TNBC) with residual disease after neoadjuvant chemotherapy. Detection of circulating tumor DNA (ctDNA) was a significant predictor of inferior distant disease-free survival (DDFS) (p = 0.006), disease-free survival (DFS) (p = 0.009) and OS (p = 0.002). The combination of circulating tumor cell (CTC) and ctDNA markers provided superior sensitivity and prognostic value. In conclusion, the studies provide compelling evidence for the utility of diverse molecular biomarkers – including miRNA isoforms, abnormal splicing-based neoantigen metrics and circulating tumor DNA in disease prediction and treatment efficacy assessment. By elucidating the roles of diverse biomarkers in predicting cancer pathogenesis and therapeutic response, we pave the way towards more personalized and effective approaches to managing human health risks

Artificial intelligence in gastrointestinal endoscopy: a comprehensive review

Integrating artificial intelligence (AI) into gastrointestinal (GI) endoscopy heralds a significant leap forward in managing GI disorders. AI-enabled applications, such as computer-aided detection and computer-aided diagnosis, have significantly advanced GI endoscopy, improving early detection, diagnosis and personalized treatment planning. AI algorithms have shown promise in the analysis of endoscopic data, critical in conditions with traditionally low diagnostic sensitivity, such as indeterminate biliary strictures and pancreatic cancer. Convolutional neural networks can markedly improve the diagnostic process when integrated with cholangioscopy or endoscopic ultrasound, especially in the detection of malignant biliary strictures and cholangiocarcinoma. AI's capacity to analyze complex image data and offer real-time feedback can streamline endoscopic procedures, reduce the need for invasive biopsies, and decrease associated adverse events. However, the clinical implementation of AI faces challenges, including data quality issues and the risk of overfitting, underscoring the need for further research and validation. As the technology matures, AI is poised to become an indispensable tool in the gastroenterologist's arsenal, necessitating the integration of robust, validated AI applications into routine clinical practice. Despite remarkable advances, challenges such as operator-dependent accuracy and the need for intricate examinations persist. This review delves into the transformative role of AI in enhancing endoscopic diagnostic accuracy, particularly highlighting its utility in the early detection and personalized treatment of GI diseases

Licensed Clinical Addiction Counselor Pathways: Playbook Project

This document provides the pathway from education to practice for a Licensed Clinical Addiction Counselor in Indiana

Expanding Access to Comprehensive Geriatric Evaluation via Telehealth: Development of Hybrid-Virtual Home Visits

Background: In response to the aging population, the Department of Veterans Affairs (VA) seeks to expand access to evidence-based practices which support community-dwelling older persons such as the Geriatric Resources for Assessment and Care of Elders (GRACE) program. GRACE is a multidisciplinary care model which provides home-based geriatric evaluation and management for older Veterans residing within a 20-mile drive radius from the hospital. We sought to expand the geographic reach of VA-GRACE by developing a hybrid-virtual home visit (TeleGRACE). Objectives: The objectives were to: (1) describe challenges encountered and solutions implemented during the iterative, pre-implementation program development process; and (2) illustrate potential successes of the program with two case examples. Design: Quality improvement project with longitudinal qualitative data collection. Program description: The hybrid-virtual home visit involved a telehealth technician travelling to patients' homes and connecting virtually to VA-GRACE team members who participated remotely. Approach & participants: We collected multiple data streams throughout program development: TeleGRACE staff periodic reflections, fieldnotes, and team meeting notes; and VA-GRACE team member interviews. Key results: The five program domains that required attention and problem-solving were: telehealth connectivity and equipment, virtual physical examination, protocols and procedures, staff training, and team integration. For each domain, we describe several challenges and solutions. An example from the virtual physical examination domain: several iterations were required to identify the combination of telehealth stethoscope with dedicated headphones that allowed remote nurse practitioners to hear heart and lung sounds. The two cases illustrate how this hybrid-virtual home visit model provided care for patients who would not otherwise have received timely healthcare services. Conclusions: These results provide a blueprint to translate an in-person home-based geriatrics program into a hybrid-virtual model and support the feasibility of using hybrid-virtual home visits to expand access to comprehensive geriatric evaluation and ongoing care for high-risk, community-dwelling older persons who reside geographically distant from the primary VA facility

Integrin-linked kinase-frizzled 7 interaction maintains cancer stem cells to drive platinum resistance in ovarian cancer

Background: Platinum-based chemotherapy regimens are a mainstay in the management of ovarian cancer (OC), but emergence of chemoresistance poses a significant clinical challenge. The persistence of ovarian cancer stem cells (OCSCs) at the end of primary treatment contributes to disease recurrence. Here, we hypothesized that the extracellular matrix protects CSCs during chemotherapy and supports their tumorigenic functions by activating integrin-linked kinase (ILK), a key enzyme in drug resistance. Methods: TCGA datasets and OC models were investigated using an integrated proteomic and gene expression analysis and examined ILK for correlations with chemoresistance pathways and clinical outcomes. Canonical Wnt pathway components, pro-survival signaling, and stemness were examined using OC models. To investigate the role of ILK in the OCSC-phenotype, a novel pharmacological inhibitor of ILK in combination with carboplatin was utilized in vitro and in vivo OC models. Results: In response to increased fibronectin (FN) secretion and integrin β1 clustering, aberrant ILK activation supported the OCSC phenotype, contributing to OC spheroid proliferation and reduced response to platinum treatment. Complexes formed by ILK with the Wnt receptor frizzled 7 (Fzd7) were detected in tumors and showed a strong correlation with metastatic progression. Moreover, TCGA datasets confirmed that combined expression of ILK and Fzd7 in high grade serous ovarian tumors is correlated with reduced response to chemotherapy and poor patient outcomes. Mechanistically, interaction of ILK with Fzd7 increased the response to Wnt ligands, thereby amplifying the stemness-associated Wnt/β-catenin signaling. Notably, preclinical studies showed that the novel ILK inhibitor compound 22 (cpd-22) alone disrupted ILK interaction with Fzd7 and CSC proliferation as spheroids. Furthermore, when combined with carboplatin, this disruption led to sustained AKT inhibition, apoptotic damage in OCSCs and reduced tumorigenicity in mice. Conclusions: This "outside-in" signaling mechanism is potentially actionable, and combined targeting of ILK-Fzd7 may represent a new therapeutic strategy to eradicate OCSCs and improve patient outcomes

Higher education and philanthropy in sub-Saharan Africa: The enabling environment webinar synopsis

Building on the IU Lilly Family School of Philanthropy’s ongoing Higher Education Philanthropy Initiative, this webinar seeks to amplify the voices of a range of thought leaders from within the philanthropy ecosystem for higher education in Africa to explore the opportunities and challenges that the enabling legal and regulatory environment for philanthropy brings to donors, academic advancement officers, and both public and private universities

Cervical cancer prevention and care in HIV clinics across sub-Saharan Africa: results of a facility-based survey

Introduction: To eliminate cervical cancer (CC), access to and quality of prevention and care services must be monitored, particularly for women living with HIV (WLHIV). We assessed implementation practices in HIV clinics across sub-Saharan Africa (SSA) to identify gaps in the care cascade and used aggregated patient data to populate cascades for WLHIV attending HIV clinics. Methods: Our facility-based survey was administered between November 2020 and July 2021 in 30 HIV clinics across SSA that participate in the International epidemiology Databases to Evaluate AIDS (IeDEA) consortium. We performed a qualitative site-level assessment of CC prevention and care services and analysed data from routine care of WLHIV in SSA. Results: Human papillomavirus (HPV) vaccination was offered in 33% of sites. Referral for CC diagnosis (42%) and treatment (70%) was common, but not free at about 50% of sites. Most sites had electronic health information systems (90%), but data to inform indicators to monitor global targets for CC elimination in WLHIV were not routinely collected in these sites. Data were collected routinely in only 36% of sites that offered HPV vaccination, 33% of sites that offered cervical screening and 20% of sites that offered pre-cancer and CC treatment. Conclusions: Though CC prevention and care services have long been available in some HIV clinics across SSA, patient and programme monitoring need to be improved. Countries should consider leveraging their existing health information systems and use monitoring tools provided by the World Health Organization to improve CC prevention programmes and access, and to track their progress towards the goal of eliminating CC

A long-read draft assembly of the Chinese mantis (Mantodea: Mantidae: Tenodera sinensis) genome reveals patterns of ion channel gain and loss across Arthropoda

Praying mantids (Mantodea: Mantidae) are iconic insects that have captivated biologists for decades, especially the species with cannibalistic copulatory behavior. This behavior has been cited as evidence that insects lack nociceptive capacities and cannot feel pain; however, this behaviorally driven hypothesis has never been rigorously tested at the genetic or functional level. To enable future studies of nociceptive capabilities in mantids, we sequenced and assembled a draft genome of the Chinese praying mantis (Tenodera sinensis) and identified multiple classes of nociceptive ion channels by comparison to orthologous gene families in Arthropoda. Our assembly—produced using PacBio HiFi reads—is fragmented (total size = 3.03 Gb; N50 = 1.8 Mb; 4,966 contigs), but is highly complete with respect to gene content (BUSCO complete = 98.7% [odb10_insecta]). The size of our assembly is substantially larger than that of most other insects, but is consistent with the size of other mantid genomes. We found that most families of nociceptive ion channels are present in the T. sinensis genome; that they are most closely related to those found in the damp-wood termite (Zootermopsis nevadensis); and that some families have expanded in T. sinensis while others have contracted relative to nearby lineages. Our findings suggest that mantids are likely to possess nociceptive capabilities and provide a foundation for future experimentation regarding ion channel functions and their consequences for insect behavior

Studying the Effect of TBX4 Loss-of-Function on Postnatal Lung Development and How it Predisposes to Pulmonary Hypertension

The term pulmonary hypertension (PH) describes a heterogeneous group of pulmonary and cardiovascular disorders and is estimated to affect 1% of the global population. The World Symposium on Pulmonary Hypertension divides patients into a five-tier classification system based on etiology and clinical findings with the aim of improving the clinical approach to patients. Group 1 PH, also known as pulmonary arterial hypertension, is a rare form of the disease with a prevalence of 15-50 cases per one million individuals. Deleterious variants within the bone morphogenetic protein receptor type 2 (BMPR2) gene are found in approximately 70-80% of the cases. However, at least twelve additional genes are known to have a definitive gene-disease relationship with PAH, including T-box 4 (TBX4). Genetic predisposition may also contribute to group 3 PH, also known as PH due to chronic lung disease or hypoxia. Heterozygous pathogenic variants within TBX4 have been reported in cases from both PH groups. Therefore, the diagnosis and classification of PH in patients with TBX4 mutations may be more challenging due to its contributions to the pathogenesis of both groups. For a decade, deleterious variants or large mutations involving TBX4 have been reported throughout the literature, but more progress has yet to be made toward understanding the mechanisms underlying the pathogenesis of PH in those patients. Therefore, in this project, using mouse genetics, we sought to disrupt Tbx4 expression and investigate if there is consistency with the diseases observed in humans. We found that Tbx4 mutant lungs have increasing alveolar simplification as confirmed by mean linear intercept (MLI) at P14 (25%), P36 (31.7%), and P180 (49.5%). The lungs also have reduced vascularization as indicated by a 39.4% reduction in the number of vWF-positive vessels. Consistent with PH, mutant mice have higher RVSP (19.4%), vascular remodeling, and mild right ventricular hypertrophy (RVH). RNA sequence analyses revealed enrichment of pathways (canonical WNT, VEGF, and BMP signaling) and genes (Lgr5, Tnc, Wnt3a, Areg, Gdf2, and Bmper) relevant to lung alveologenesis, angiogenesis, and PH. This study contributes significant knowledge that clinicians can use to diagnose, classify, and treat patients with TBX4 mutations

Dietary Phosphorus Levels Influence Protein-Derived Uremic Toxin Production in Nephrectomized Male Rats

Gut microbiota-derived uremic toxins (UT) accumulate in patients with chronic kidney disease (CKD). Dietary phosphorus and protein restriction are common in CKD treatment, but the relationship between dietary phosphorus, a key nutrient for the gut microbiota, and protein-derived UT is poorly studied. Thus, we explored the relationship between dietary phosphorus and serum UT in CKD rats. For this exploratory study, we used serum samples from a larger study on the effects of dietary phosphorus on intestinal phosphorus absorption in nephrectomized (Nx, n = 22) or sham-operated (sham, n = 18) male Sprague Dawley rats. Rats were randomized to diet treatment groups of low or high phosphorus (0.1% or 1.2% w/w, respectively) for 1 week, with serum trimethylamine oxide (TMAO), indoxyl sulfate (IS), and p-cresol sulfate (pCS) analyzed by LC-MS. Nx rats had significantly higher levels of serum TMAO, IS, and pCS compared to sham rats (all p < 0.0001). IS showed a significant interaction between diet and CKD status, where serum IS was higher with the high-phosphorus diet in both Nx and sham rats, but to a greater extent in the Nx rats. Serum TMAO (p = 0.24) and pCS (p = 0.34) were not affected by dietary phosphorus levels. High dietary phosphorus intake for 1 week results in higher serum IS in both Nx and sham rats. The results of this exploratory study indicate that reducing dietary phosphorus intake in CKD may have beneficial effects on UT accumulation