UT Health scientist continues study of children’s cancer using new grant to predict drug responses from genomic data

UT Health San Antonio received more than $1 million from the Cancer Prevention Research Institute of Texas in its summer round of funding, announced Aug. 22.

The largest award, $892,157, went to Yidong Chen, Ph.D., a professor of population health sciences in the Joe R. and Teresa Lozano Long School of Medicine. Yogesh Gupta, Ph.D., an assistant professor in the Department of Biochemistry and Structural Biology, and the Greehey Children’s Cancer Research Institute, received a high-impact, high-risk award of $199,996. A UT Health San Antonio-related spinoff company also received a $3 million seed award for product development.

Yidong Chen, Ph.D.

Dr. Chen is director of the computational biology and bioinformatics program in the university’s Greehey Children’s Cancer Research Institute. He also is co-director of the Next-Generation Sequencing Shared Resource.

Computational science uses big data to develop models and algorithms to better understand biological systems and relationships. Dr. Chen’s CPRIT award is “Predicting drug response from genomic data using deep learning methods.”

“The technological breakthrough in deep learning, part of artificial intelligence (AI), has revolutionized industries, automation and biomedical research. Its impact is only beginning to be felt in our daily life. Some examples are AI-enabled consumer products and autonomous driving cars,” he explained.

In May 2016, Dr. Chen received $3.6 million from CPRIT to update and expand existing infrastructure to establish the Cancer Genome Sequencing Facility and Computational Core for the South Texas community through UT Health San Antonio. In 2012, he received $816,000 from CPRIT for his collaborative work with UT Southwestern Medical Center to study treatable genetic abnormalities in sarcoma patients

Yogesh Gupta, Ph.D.

Dr. Gupta’s laboratory is studying the three-dimensional structures and function of certain enzymes and how they change the architecture of genetic material leading to pediatric cancers. One of the genetic processes he is studying is called chromatin remodeling by BAF complex. The BAF complex consists of more than 15 different proteins.

In malignant cells and especially in pediatric cancers, both the assembly and recruitment of the BAF complex proteins are disrupted by mutations, deletions and overexpression of individual proteins resulting in formation of abnormal or defective BAF complexes.  Ewing’s sarcoma and synovial sarcoma are examples of pediatric cancers where defective BAF complexes play a central role in forming tumors.

His CPRIT award, titled “Mechanism-based targeting of core molecules of the BAF complex in cancer,” will allow Dr. Gupta to use structural and chemical biology approaches to define how BAF complexes operate in pediatric sarcomas. Dr. Gupta anticipates that this work will lead to the development of more effective treatments for children with highly aggressive tumors of bone and soft tissues that are hard to treat with existing therapies.

CPRIT also awarded $3 million to Emtora Biosciences, formerly called Rapamycin Holdings. The award is for a clinical trial investigating a formulation of rapamycin called eRapa to treat familial adenomatous polyposis. This is an inherited disorder in which noncancerous polyps form in the digestive system early in life. If not removed, the polyps can become malignant.

“Rapamycin continues to be studied globally for various medicinal uses. The UT Health San Antonio team led by Randy Strong, Ph.D., and Dave Sharp, Ph.D., is a key player in the rapamycin ecosystem.


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