Researchers Develop AI Model to Better Predict Which Drugs May Cause Birth Defects
Data harnessed to identify previously unknown associations between genes, congenital disabilities, and drugs
Data scientists at the Icahn School of Medicine at Mount Sinai in New York and colleagues have created an artificial intelligence model that may more accurately predict which existing medicines, not currently classified as harmful, may in fact lead to congenital disabilities.
The model, or “knowledge graph,” described in the July 17 issue of the Nature journal Communications Medicine [DOI: 10.1038/s43856-023-00329-2],also has the potential to predict the involvement of pre-clinical compounds that may harm the developing fetus. The study is the first known of its kind to use knowledge graphs to integrate various data types to investigate the causes of congenital disabilities.
Birth defects are abnormalities that affect about 1 in 33 births in the United States. They can be functional or structural and are believed to result from various factors, including genetics. However, the causes of most of these disabilities remain unknown. Certain substances found in medicines, cosmetics, food, and environmental pollutants can potentially lead to birth defects if exposed during pregnancy.
“We wanted to improve our understanding of reproductive health and fetal development, and importantly, warn about the potential of new drugs to cause birth defects before these drugs are widely marketed and distributed,” says Avi Ma’ayan, PhD, Professor, Pharmacological Sciences, and Director of the Mount Sinai Center for Bioinformatics at Icahn Mount Sinai, and senior author of the paper. “Although identifying the underlying causes is a complicated task, we offer hope that through complex data analysis like this that integrates evidence from multiple sources, we will be able, in some cases, to better predict, regulate, and protect against the significant harm that congenital disabilities could cause.”
The researchers gathered knowledge across several datasets on birth-defect associations noted in published work, including those produced by NIH Common Fund programs, to demonstrate how integrating data from these resources can lead to synergistic discoveries. Particularly, the combined data is from the known genetics of reproductive health, classification of medicines based on their risk during pregnancy, and how drugs and pre-clinical compounds affect the biological mechanisms inside human cells.
Specifically, the data included studies on genetic associations, drug- and preclinical-compound-induced gene expression changes in cell lines, known drug targets, genetic burden scores for human genes, and placental crossing scores for small molecule drugs.
Importantly, using ReproTox-KG, with semi-supervised learning (SSL), the research team prioritized 30,000 preclinical small molecule drugs for their potential to cross the placenta and induce birth defects. SSL is a branch of machine learning that uses a small amount of labeled data to guide predictions for much larger unlabeled data. In addition, by analyzing the topology of the ReproTox-KG more than 500 birth-defect/gene/drug cliques were identified that could explain molecular mechanisms that underlie drug-induced birth defects. In graph theory terms, cliques are subsets of a graph where all the nodes in the clique are directly connected to all other nodes in the clique.
The investigators caution that the study's findings are preliminary and that further experiments are needed for validation.
Next, the investigators plan to use a similar graph-based approach for other projects focusing on the relationship between genes, drugs, and diseases. They also aim to use the processed dataset as training materials for courses and workshops on bioinformatics analysis. In addition, they plan to extend the study to consider more complex data, such as gene expression from specific tissues and cell types collected at multiple stages of development.
“We hope that our collaborative work will lead to a new global framework to assess potential toxicity for new drugs and explain the biological mechanisms by which some drugs, known to cause birth defects, may operate. It’s possible that at some point in the future, regulatory agencies such as the U.S. Food and Drug Administration and the U.S. Environmental Protection Agency may use this approach to evaluate the risk of new drugs or other chemical applications,” says Dr. Ma’ayan.
The paper is titled “Toxicology Knowledge Graph for Structural Birth Defects.”
Additional co-authors are John Erol Evangelista (Icahn Mount Sinai), Daniel J. B. Clarke (Icahn Mount Sinai), Zhuorui Xie (Icahn Mount Sinai), Giacomo B. Marino, (Icahn Mount Sinai), Vivian Utti (Icahn Mount Sinai), Sherry L. Jenkins (Icahn Mount Sinai), Taha Mohseni Ahooyi (Children’s Hospital of Philadelphia), Cristian G. Bologa (University of New Mexico), Jeremy J. Yang (University of New Mexico), Jessica L. Binder (University of New Mexico), Praveen Kumar (University of New Mexico), Christophe G. Lambert (University of New Mexico), Jeffrey S. Grethe (University of California San Diego), Eric Wenger (Children’s Hospital of Philadelphia), Deanne Taylor, (Children’s Hospital of Philadelphia), Tudor I. Oprea (Children’s Hospital of Philadelphia), and Bernard de Bono (University of Auckland, New Zealand).
The project was supported by National Institutes of Health grants OT2OD030160, OT2OD030546, OT2OD032619, and OT2OD030162.
About the Icahn School of Medicine at Mount Sinai
The Icahn School of Medicine at Mount Sinai is internationally renowned for its outstanding research, educational, and clinical care programs. It is the sole academic partner for the eight- member hospitals* of the Mount Sinai Health System, one of the largest academic health systems in the United States, providing care to a large and diverse patient population.
Ranked 14th nationwide in National Institutes of Health (NIH) funding and among the 99th percentile in research dollars per investigator according to the Association of American Medical Colleges, Icahn Mount Sinai has a talented, productive, and successful faculty. More than 3,000 full-time scientists, educators, and clinicians work within and across 44 academic departments and 36 multidisciplinary institutes, a structure that facilitates tremendous collaboration and synergy. Our emphasis on translational research and therapeutics is evident in such diverse areas as genomics/big data, virology, neuroscience, cardiology, geriatrics, as well as gastrointestinal and liver diseases.
Icahn Mount Sinai offers highly competitive MD, PhD, and Master’s degree programs, with current enrollment of approximately 1,300 students. It has the largest graduate medical education program in the country, with more than 2,000 clinical residents and fellows training throughout the Health System. In addition, more than 550 postdoctoral research fellows are in training within the Health System.
A culture of innovation and discovery permeates every Icahn Mount Sinai program. Mount Sinai’s technology transfer office, one of the largest in the country, partners with faculty and trainees to pursue optimal commercialization of intellectual property to ensure that Mount Sinai discoveries and innovations translate into healthcare products and services that benefit the public.
Icahn Mount Sinai’s commitment to breakthrough science and clinical care is enhanced by academic affiliations that supplement and complement the School’s programs.
Through the Mount Sinai Innovation Partners (MSIP), the Health System facilitates the real-world application and commercialization of medical breakthroughs made at Mount Sinai. Additionally, MSIP develops research partnerships with industry leaders such as Merck & Co., AstraZeneca, Novo Nordisk, and others.
The Icahn School of Medicine at Mount Sinai is located in New York City on the border between the Upper East Side and East Harlem, and classroom teaching takes place on a campus facing Central Park. Icahn Mount Sinai’s location offers many opportunities to interact with and care for diverse communities. Learning extends well beyond the borders of our physical campus, to the eight hospitals of the Mount Sinai Health System, our academic affiliates, and globally.
* Mount Sinai Health System member hospitals: The Mount Sinai Hospital; Mount Sinai Beth Israel; Mount Sinai Brooklyn; Mount Sinai Morningside; Mount Sinai Queens; Mount Sinai South Nassau; Mount Sinai West; and New York Eye and Ear Infirmary of Mount Sinai.
About the Mount Sinai Health System
Mount Sinai Health System is one of the largest academic medical systems in the New York metro area, with more than 43,000 employees working across eight hospitals, over 400 outpatient practices, nearly 300 labs, a school of nursing, and a leading school of medicine and graduate education. Mount Sinai advances health for all people, everywhere, by taking on the most complex health care challenges of our time — discovering and applying new scientific learning and knowledge; developing safer, more effective treatments; educating the next generation of medical leaders and innovators; and supporting local communities by delivering high-quality care to all who need it.
Through the integration of its hospitals, labs, and schools, Mount Sinai offers comprehensive health care solutions from birth through geriatrics, leveraging innovative approaches such as artificial intelligence and informatics while keeping patients’ medical and emotional needs at the center of all treatment. The Health System includes approximately 7,300 primary and specialty care physicians; 13 joint-venture outpatient surgery centers throughout the five boroughs of New York City, Westchester, Long Island, and Florida; and more than 30 affiliated community health centers. We are consistently ranked by U.S. News & World Report's Best Hospitals, receiving high "Honor Roll" status, and are highly ranked: No. 1 in Geriatrics and top 20 in Cardiology/Heart Surgery, Diabetes/Endocrinology, Gastroenterology/GI Surgery, Neurology/Neurosurgery, Orthopedics, Pulmonology/Lung Surgery, Rehabilitation, and Urology. New York Eye and Ear Infirmary of Mount Sinai is ranked No. 12 in Ophthalmology. U.S. News & World Report’s “Best Children’s Hospitals” ranks Mount Sinai Kravis Children's Hospital among the country’s best in several pediatric specialties.