Yerkes genomics research will help predict COVID-19 disease severity, inform treatment decisions

Woodruff Health Sciences Center | Aug. 20, 2020

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Lisa Newbern
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As part of Emory University’s participation in the multi-center Immunophenotyping Assessment in a COVID-19 Cohort (IMPACC), the Yerkes National Primate Research Center has received a one-year, $4.1 million grant supplement from the National Institute of Allergy and Infectious Diseases (NIAID) to track gene expression from 1,000 COVID-19 patients. This information will help IMPACC’s efforts to develop COVID-19 biomarkers, which are necessary for predicting disease severity and informing treatment decisions. Patient recruitment for this study is under way, and the researchers expect to have initial biomarkers results by October. 

Lead researcher Steve Bosinger, PhD, and his research team will produce RNA sequencing data from COVID-19 patients’ blood, which healthcare professionals will collect at several time points after infection. Emory University’s Nadine Rouphael, MD, is one of the healthcare professionals as are providers at more than 15 other academic health centers across the country. Bosinger is assistant professor, Department of Pathology & Laboratory Medicine, Emory School of Medicine (SOM) and Emory Vaccine Center (EVC); director, Yerkes Nonhuman Primate (NHP) Genomics Core; and a researcher in Yerkes’ Division of Microbiology and Immunology. Rouphael is associate professor of medicine, Emory SOM, and IMPACC’s chair, and she is funded by NIAID’s Division of Allergy, Immunology and Transplantation. 

The Emory researchers will combine their sequencing data with data from the University of California, San Francisco, which is Emory’s partner site in this component of the IMPACC study. “The goal of combining the patient data, which hospital systems will begin collecting at 48 hours after admission through one year after hospital discharge, is to develop actionable biomarkers healthcare professionals can use to inform their treatment and management decisions,” says Bosinger.

To develop the biomarkers, IMPACC researchers and healthcare professionals will initially search for molecular patterns that can predict disease and recovery. Later analyses will focus on protecting patients from potential reinfection and monitoring the impact of new treatments against the virus.  

“The lack of detailed molecular and immunological information severely impairs accurate decision-making, such as not being able to prioritize patients who will progress to severe COVID-19 disease,” Bosinger adds. “By combining our immunogenomics experience and dedicated infrastructure for next-generation sequencing with the expertise of our clinical partners, we can empower healthcare providers and systems with the information they need to make faster, data-driven clinical decisions, increase definitive communication with patients and, ultimately, better serve those seeking healthcare at this critical time.”

“Given the importance this study holds for informing treatment decisions and better helping patients, we are taking extra steps to ensure synchronicity across Emory and UCSF,” says Rafi Ahmed, PhD, EVC director and GRA eminent scholar. “For example, we are benchmarking with a common set of reference samples and employing balanced experimental design between the sites so we can generate the data faster and accommodate more patient information, which will facilitate better patient care,” he continues.

This study is a supplement to grant U19 A1090023 from the Human Immunology Project Consortium (HIPC), which Bali Pulendran, PhD, leads. Pulendran, who is the Violetta L. Horton professor of microbiology and immunology at Stanford University, says, “We are confident our experience using genomics and systems biological approaches to predict the effectiveness of vaccines will translate directly into predicting disease severity at an early stage of infection in people who have COVID-19.”

Others working with Bosinger, Rouphael, Ahmed and Pulendran include: Kathryn Pellegrini, PhD, technical director, and Adam Ericsen, PhD, assistant director, Yerkes NHP Genomics Core; Mehul Suthar, PhD, assistant professor of pediatrics, Emory SOM, and EVC researcher; Jonathan Sevransky, MD, professor of medicine, and Erin Scherer, PhD, assistant professor of medicine, Emory SOM; David Erle, MD, principal investigator, UCSF IMPACC program, professor and associate chair for biomedical research, Department of Medicine, and director, UCSF CoLabs; Walter Eckalbar, PhD, co-investigator, UCSF IMPACC program, assistant professor of medicine, and director, UCSF Genomics CoLab; and Prescott Woodruff, MD, MPH, co-investigator, UCSF IMPACC program and professor of medicine.

In addition to the U19 supplemental funding covering the genomics research reported in this release, NIAID is also supporting UCSF with grant 3U19 AI077439-13S2; only a portion of that U19 grant will be spent on the genomics research reported in this release (the funds also support IMPACC clinical research and two national cores). The Yerkes National Primate Research Center base grant, P51 OD011132, from the NIH Office of the Director, Office of Research Infrastructure Programs (OD/ORIP), is helping support infrastructure needs of this research. NIH OD/ORIP also provided an equipment grant S10 OD026799 to the Yerkes Genomics Core for the purchase of a single piece of equipment that will be used in this genomics study as well as others.

Grant amounts (direct + indirect):
U19 AI090023-11S1  $4,164,318
3U19 AI077439-13S2  $8,630,785/2 years
P51 OD011132  $10,540,602/yr
S10 OD026799  $985,030 

About Yerkes National Primate Research Center

For more information about Yerkes COVID-19 research, read: Yerkes Awarded NIAID Grant to Develop COVID-19 Vaccine (5/18/20). A news release with the initial study results in a mouse model is forthcoming and will be posted at yerkes.emory.edu.

Dedicated to discovering causes, preventions, treatments and cures of disease, the Yerkes National Primate Research Center (NPRC), part of Emory University’s Robert W. Woodruff Health Sciences Center, is fighting diseases and improving human health and lives worldwide. The center, one of only seven NPRCs the National Institutes of Health (NIH) funds, is supported by more than $74 million in research funding (all sources, fiscal year 2018). Yerkes researchers are making landmark discoveries in microbiology and immunology; neurologic diseases; neuropharmacology; behavioral, cognitive, and developmental neuroscience; and psychiatric disorders. Since 1984, the center has been fully accredited by the AAALAC International, regarded as the gold seal of approval for laboratory animal care. For more information about Yerkes and the seven NPRCs, visit NPRC.org and follow us at @NPRCnews.