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Browsing by Author "Khomtchouk, Bohdan B."
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Item CETP and SGLT2 inhibitor combination therapy improves glycemic control(medRxiv, 2023-06-16) Khomtchouk, Bohdan B.; Sun, Patrick; Ditmarsch, Marc; Kastelein, John J. P.; Davidson, Michael H.; BioHealth Informatics, School of Informatics and ComputingImportance: Cholesteryl ester transfer protein (CETP) inhibition has been associated with decreased risk of new-onset diabetes in past clinical trials exploring their efficacy in cardiovascular disease and can potentially be repurposed to treat metabolic disease. Notably, as an oral drug it can potentially be used to supplement existing oral drugs such as sodium-glucose cotransporter 2 (SGLT2) inhibitors before patients are required to take injectable drugs such as insulin. Objective: To identify whether CETP inhibitors could be used as an oral add-on to SGLT2 inhibition to improve glycemic control. Design setting and participants: 2×2 factorial Mendelian Randomization (MR) is performed on the general population of UK Biobank participants with European ancestry. Exposures: Previously constructed genetic scores for CETP and SGLT2 function are combined in a 2×2 factorial framework to characterize the associations between joint CETP and SGLT2 inhibition compared to either alone. Main outcomes and measures: Glycated hemoglobin and type-2 diabetes incidence. Results: Data on 233,765 UK Biobank participants suggests that individuals with genetic inhibition of both CETP and SGLT2 have significantly lower glycated hemoglobin levels (mmol/mol) than control (Effect size: -0.136; 95% CI: -0.190 to -0.081; p-value: 1.09E-06), SGLT2 inhibition alone (Effect size: -0.082; 95% CI: -0.140 to -0.024; p-value: 0.00558), and CETP inhibition alone (Effect size: -0.08479; 95% CI: -0.136 to -0.033; p-value: 0.00118). Furthermore, joint CETP and SGLT2 inhibition is associated with decreased incidence of diabetes (log-odds ratio) compared to control (Effect size: -0.068; 95% CI: -0.115 to -0.021; p-value: 4.44E-03) and SGLT2 inhibition alone (Effect size: -0.062; 95% CI: -0.112 to -0.012; p-value: 0.0149). Conclusions and relevance: Our results suggest that CETP and SGLT2 inhibitor therapy may improve glycemic control over SGLT2 inhibitors alone. Future clinical trials can explore whether CETP inhibitors can be repurposed to treat metabolic disease and provide an oral therapeutic option to benefit high-risk patients before escalation to injectable drugs such as insulin or glucagon-like peptide 1 (GLP1) receptor agonists.Item Computational integration and meta-analysis of abandoned cardio-(vascular/renal/metabolic) therapeutics discontinued during clinical trials from 2011 to 2022(Frontiers, 2023-02) Zeng, Carisa; Lee, Yoon Seo; Szatrowski, Austin; Mero, Deniel; Khomtchouk, Bohdan B.; Biohealth Informatics, School of Informatics and ComputingCardiovascular/renal/metabolic (CVRM) diseases collectively comprise the leading cause of death worldwide and disproportionally affect older demographics and historically underrepresented minority populations. Despite these critical unmet needs, pharmaceutical research and development (R&D) efforts have historically struggled with high drug failure rates, low approval rates, and other challenges. Drug repurposing is one approach to recovering R&D costs and meeting unmet demands in therapeutic markets. While there are multiple approaches to conducting drug repurposing, we recognize the importance of bringing together and consolidating discontinued drug information to help identify prospective repurposing candidates. In this study, we have harmonized and integrated information on all relevant CVRM drug assets from U.S. Securities and Exchange Commission (SEC) filings, clinical trial records, PharmGKB, Open Targets, and other platforms. A list of existing therapeutics discontinued or shelved by pharmaceutical/biotechnology companies in 2011-2022 were manually curated and interpreted for insights using information on each drug's genetic target, mechanism of action (MOA), clinical indication, and R&D information including highest phase of clinical development, year of discontinuation, previous repurposing attempts (if any), and other actionable metadata. This study also summarizes the profiles of CVRM drugs discontinued within the past decade and identifies the limitations of publicly available information on discontinued drug assets. The constructed database could serve as a tool for identifying candidates for drug repurposing and developing query methods for collecting R&D information.Item Machine learning classifiers predict key genomic and evolutionary traits across the kingdoms of life(Nature, 2023-02-06) Hallee, Logan; Khomtchouk, Bohdan B.; Biohealth Informatics, School of Informatics and ComputingIn this study, we investigate how an organism's codon usage bias can serve as a predictor and classifier of various genomic and evolutionary traits across the domains of life. We perform secondary analysis of existing genetic datasets to build several AI/machine learning models. When trained on codon usage patterns of nearly 13,000 organisms, our models accurately predict the organelle of origin and taxonomic identity of nucleotide samples. We extend our analysis to identify the most influential codons for phylogenetic prediction with a custom feature ranking ensemble. Our results suggest that the genetic code can be utilized to train accurate classifiers of taxonomic and phylogenetic features. We then apply this classification framework to open reading frame (ORF) detection. Our statistical model assesses all possible ORFs in a nucleotide sample and rejects or deems them plausible based on the codon usage distribution. Our dataset and analyses are made publicly available on GitHub and the UCI ML Repository to facilitate open-source reproducibility and community engagement.Item Targeting long non-coding RNA NUDT6 enhances smooth muscle cell survival and limits vascular disease progression(Cold Spring Harbor Laboratory, 2023-06-07) Winter, Hanna; Winski, Greg; Busch, Albert; Chernogubova, Ekaterina; Fasolo, Francesca; Wu, Zhiyuan; Bäcklund, Alexandra; Khomtchouk, Bohdan B.; Van Booven, Derek J.; Sachs, Nadja; Eckstein, Hans-Henning; Wittig, Ilka; Boon, Reinier A.; Jin, Hong; Maegdefessel, Lars; Biohealth Informatics, School of Informatics and ComputingLong non-coding RNAs (lncRNAs) orchestrate various biological processes and regulate the development of cardiovascular diseases. Their potential therapeutic benefit to tackle disease progression has recently been extensively explored. Our study investigates the role of lncRNA Nudix Hydrolase 6 (NUDT6) and its antisense target fibroblast growth factor 2 (FGF2) in two vascular pathologies: abdominal aortic aneurysms (AAA) and carotid artery disease. Using tissue samples from both diseases, we detected a substantial increase of NUDT6, whereas FGF2 was downregulated. Targeting Nudt6 in vivo with antisense oligonucleotides in three murine and one porcine animal model of carotid artery disease and AAA limited disease progression. Restoration of FGF2 upon Nudt6 knockdown improved vessel wall morphology and fibrous cap stability. Overexpression of NUDT6 in vitro impaired smooth muscle cell (SMC) migration, while limiting their proliferation and augmenting apoptosis. By employing RNA pulldown followed by mass spectrometry as well as RNA immunoprecipitation, we identified Cysteine and Glycine Rich Protein 1 (CSRP1) as another direct NUDT6 interaction partner, regulating cell motility and SMC differentiation. Overall, the present study identifies NUDT6 as a well-conserved antisense transcript of FGF2. NUDT6 silencing triggers SMC survival and migration and could serve as a novel RNA-based therapeutic strategy in vascular diseases.