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Cardioinformatics Research Program

Image of heart in a high tech environment to illustrate cardioinformatics, an interdisciplinary field that applies bioinformatics and computational biology approaches to cardiovascular disease data storage, computing and analysis. Cardioinformatics is an interdisciplinary field that applies bioinformatics and computational biology approaches to cardio-(vascular/renal/metabolic) disease data storage, computing and analysis. Similar to other areas of research that integrate informatics techniques with clinical domain expertise, the application of computational methods to heart research and its associated renal and metabolic systems, poses a unique set of challenges and opportunities for biomedical innovation. With the rise of large-scale databases and other advanced computing infrastructure to support healthcare and biotechnology initiatives that accelerate drug target discovery and development in these therapeutic areas, we anticipate that cardioinformatics advancements will continue to inform clinical practice and transform public health. Formally defined as the nexus of bioinformatics and precision cardiology, cardioinformatics focuses on heart and vascular system research and provides a constellation of data that can inform researchers on both a broad and granular level on intersecting subspecialties related to the cardiovascular system, including endocrinology, nephrology and metabolism.

Bohdan Khomtchouk, PhD, a primary investigator at the Krannert Cardiovascular Research Center at Indiana University School of Medicine, is a human geneticist and pioneer in the interdisciplinary field of cardioinformatics. Dr. Khomtchouk brings a critical skill set to cardiovascular research, as his team works toward integrating computational biology and AI/machine learning-based approaches to decipher cardiovascular genomics and facilitate novel drug target discovery and repurposing strategies to treat heart disease, including its associated renal and metabolic co-morbidities, with a focus on addressing genomic health disparities and building biobanks for historically underrepresented populations.

As an assistant professor of Bioinformatics and Data Science at the Luddy School of Informatics, Computing, and Engineering at Indiana University Indianapolis, Dr. Khomtchouk’s research focuses on integrating biological database technologies and high-performance computing resources to offer data-driven insights into complex biomedical datasets that could someday inform new approaches to clinical care and the development of novel computationally-derived therapeutics.

Current Challenges

Diverse seniors sitting in rows of seats in multi-purpose room.According to the National Institute on Aging, the population for people over 65-years-old, is expected to double by 2050, and triple for individuals over 80 years of age, which will create a future demand for health care innovation to address cardiovascular disease.

 Given that cardiovascular risk factors develop over several years and possibly decades, cardiovascular pathologies present very differently from patient to patient due to genetic heterogeneity, morphing from lesions in the walls of the arteries, called arteriosclerosis — to greater disease progression found in ischemic heart disease —to overt clinical episodes such as myocardial infarctions and strokes.  Longitudinal studies such as the UK Biobank and NIH Framingham Heart Study or All of Us Research Program, are key resources to analyze these growing genetic and associated clinical datasets. 

To meet tomorrow’s challenges, Dr. Khomtchouk notes that cardiovascular investigators should look beyond traditional research methodologies and include a hybrid of data modalities in bulk tissue and single cell types that encompass protein expression profiles, DNA-methylation profiles, RNA expressional profiles, metabolic and microbiome profiles, and others, as they design their studies.   

Databases and Biobanks

Heart BioPortal LogoIn addition to teaching the Luddy School of Informatics’ B556 course, Biological Database Management, Dr. Khomtchouk also serves as the principal investigator of the HeartBioPortal project, the world’s largest human cardiovascular and cerebrovascular disease genetics database. This online platform provides intuitive visualization analysis and downloads large-scale publicly available cardiovascular disease datasets focused on gene expression, genetic association and ancestry information. It is a resource that the greater cardiovascular research community can utilize and query for associations of genetic variants to heart disease, which can be customized upon request. As of May 2024, the HeartBioPortal featured nearly 45,000 human genic and intergenic regions and more than 6.9 million variants across 37 cardiovascular disease phenotypes and 56 cardiometabolic quantitative traits.

“The vision of our HeartBioPortal has always been to bridge these gaps by heralding in a data-driven future for cardiovascular clinical patient care, effectively building the computational supply needed to address future demand at the population levels projected in 2050 and beyond,” Dr. Khomtchouk said.

Rohan Dharmakumar, executive director of Krannert Cardiovascular Research Center and the Charles Fisch Professor of Cardiology, said he is grateful to have Dr. Khomtchouk’s expertise in cardioinformatics at Indiana University and available to investigators at the Krannert Cardiovascular Research Center. “As we expand our research facilities and introduce our Cardiovascular Imaging Research Core, we are poised to incorporate data-driven research into our future cardiovascular research studies,” Dr. Dharmakumar said.

Active Funding

Project: 5R01DK132090: Molecular Genetics of Hereditary Endoplasmic Reticulum Diabetes

PIs/Project Leaders: Bohdan Khomtchouk, PhD, Assistant Professor, Bioinformatics, Data Science, Luddy School of Informatics, Computing and Engineering, Indiana University Indianapolis; Fumihiko Urano, MD, PhD, Professor of Medicine and Pathology and Immunology, Washington University"

Funding Source: National Institute of Diabetes and Digestive and Kidney Diseases

Time Frame: 2022–2026

Scope of Work: Dr. Khomtchouk’s group at Indiana University seeks to adapt the HeartBioPortal data capture to further understand the pathogenicity of gene variants associated with hereditary endoplasmic reticulum diabetes. Their major goal for this project is to add more information on genes associated with hereditary endoplasmic reticulum diabetes to the HeartBioPortal and incorporate additional data sets, indel and drug discovery information to complement the current Genome-Wide Association Studies (GWAS), gene expression, ancestry and splicing data already captured in HeartBioPortal.

Dr. Khomtchouk’s group will harmonize and integrate existing monogenic diabetes data captured by his lab from large-scale biological databases/registries as well as computationally analyze new data generated and shared by Dr. Urano’s group. They will also work toward answering the research question of how to use cardioinformatics and genetic validation approaches to rank and shortlist putative pathogenic variants contributing to ER diabetes in known genes (WFS1, CISD2, INS, EIAF2AK3, IER3IP1) as well as identify new prospective candidate ER diabetes genes that can facilitate precision medicine approaches (e.g., druggable targets) in ER diabetes.

“Our strategy for overcoming this challenge is to focus on monogenic forms of diabetes in which mutations in single genes are involved in ER dysfunction and disease manifestations,” Khomtchouk said.  “We will carry out molecular genetic studies of five types of ER diabetes to characterize variants using functional assays and bioinformatics and then develop novel treatments targeting the common molecular pathways altered in hereditary ER diabetes.”

 

 

Featured Publication

The Molecular-Social-Genetic Determinants of Cardiovascular Health in Pacific Islanders
Yoon Seo Lee BS, George Lord BS, Austin Szatrowski BS, Zane A. Maggio BS, Andrew Kekūpa ‘a Knutson PhD, Jerris R. Hedges PhD, Bohdan B. Khomtchouk PhD, JACC: Asia, 2024 June 18, https://doi.org/10.1016/j.jacasi.2024.04.012Access made possible through Creative Commons

 

This graphic of a principal component analysis illustrates the need to distinguish between Native Hawaiian and Other Pacific Islanders (NHOPIs) and Asian populations. This research was conducted by cardioinformatics researchers at Indiana University.

Distinguishing Pacific and Asian Populations

Picture of Native Hawaiian Woman with flower below one shoulder.According to Khomtchouk, Native Hawaiian and Other Pacific Islanders (NHOPIs) are often underrepresented or could have been aggregated with population data from Asia in most large cardiovascular biology databases. 

The Khomtchouk Lab analyzed the National Institutes of Health All of Us Research Program biobank data and discovered that NHOPIs share a common genetic ancestry which should be recognized when seeking to address inherited metabolic responses to diet, activities, medications, behavioral stress and the environment.

The lead author of the study, Yoonseo Lee, who is now pursing her PhD in bioengineering at Harvard University, served as an undergraduate research assistant in the Khomtchouk Lab from 2020 to 2023. Collaborators included researchers from University of Chicago, University of Hawaii at Manoa and the dean emeritus from the University of Hawaii John A. Burns School of Medicine, some of whom were Native Hawaiian investigators. This study was supported by National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) R01 funding, as part of the grant, Molecular Genetics of Hereditary Endoplasmic Reticulum Diabetes.


Highlighted Publications

CETP and SGLT2 inhibitor combination therapy improves glycemic control: a 2x2 factorial Mendelian Randomization analysis
Bohdan B. Khomtchouk, PhD, Patrick Sun, BS, Zane A. Maggio, BS, Marc Ditmarsch, MD, John J.P. Kastelein, MD, PhD, and Michael H. Davidson, MD. Frontiers in Endocrinology, 2024 May, Vol. 15, doi: 10.3389/fendo.2024.1359780


The Molecular-Social-Genetic Determinants of Cardiovascular Health in Pacific Islanders
Yoon Seo Lee, George Lord, Austin Szatrowski, Zane A. Maggio, Andrew Kekūpaʻa Knutson, Jerris R. Hedges, Bohdan B. Khomtchouk, JACC Asia, 2024 (7)) 559-565, doi:10.1016/j.jaci.2024.04.012


Computational Integration and Meta-Analysis of Abandoned Cardio- (vascular/renal/metabolic) therapeutics discontinued during clinical trials from 2011 to 2022
Carisa Zeng, Yoon Seo Lee, Austin Szatrowski, Deniel Mero, Bohdan B. Khomtchouk, Frontiers in Cardiovascular Medicine, Feb. 6, 2023, Volume 10, 2023


Cardioinformatics Advancements in Healthcare and Biotechnology
Bohdan B. Khomtchouk, Circulation: Genomic and Precision Medicine, June 14, 2023; 16: 283-285


Epidermal growth factor receptor inhibition prevents vascular calcifying extracellular vesicle biogenesis
Amirala Bakhshian Nik, Hooi Hooi Ng, Sophie K. Ashbrook, Patrick Sun, Francesco Iacoviello, Paul R. Shearing, Sergio Bertazzo, Deniel Mero, Bohdan B. Khomtchouk and Joshua D. Hutcheson. Am J of Physiol Heart Circ Physiol, 23 March 2023, https://doi.org/10.1152.ajpheart.00280.2022


Enhanced single-cell transcriptomics workflow reveals coronary artery disease cellular cross-talk and candidate drug targets
Wei Feng Ma, Chani Hodonsky, Adam Turner, Y Song, JV Mosquera, AV Ligay, L Slenders, C Gancayco, H Pan, NB Barrientos, D Mai, GF Alencar, K Owsiany, G Owens, MP Reilly, M Li, G Pasterkamp, M Mokry, SW van der Laan, Bohdan B. Khomtchouk, CL Miller. Atherosclerosis, Volume 340, P12-22, January 2022


Cardioinformatics: the nexus of bioinformatics and precision cardiology
Bohdan B. Khomtchouk, Diem-Trang Tran, Kasra A Vand, Matthew Might, Or Gozani, Themistocles L. Assimes, Briefings in Bioinformatics, Volume 21, Issue 6, November 2020, Pages 2031-2051


HeartBioPortal2.0: new developments and updates for genetic ancestry and cardiometabolic quantitative traits in diverse human populations
Bohdan B. Khomtchouk, Christopher S. Nelson, Kasra A. Vand, Salvator Palmisano and Robert L. Grossman, Database (Oxford), Dec. 31, 2020


Principal Investigator
Professional headshot of Bohdan Khomtchouk, assistant professor, Bioinformatics, Data Science, IU Luddy School of Informatics

Bohdan Khomtchouk, PhD

Assistant Professor, Bioinformatics, Data Science
Luddy School of Informatics, Computing and Engineering

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