Expanse Supercomputer Enables Discovery of Biomarkers that Can Indicate Preeclampsia Complications

Published May 1, 2024

By Kimberly Mann Bruch, SDSC Communications

According to the Centers for Disease Control and Prevention (CDC), pregnancy-related hypertension, or preeclampsia, occurs in roughly one in 25 pregnancies in the United States.  Preeclampsia can lead to adverse perinatal outcomes, such as preterm delivery and cardiovascular complications.

Researchers from the UC San Diego School of Medicine have been using Expanse at the San Diego Supercomputer Center (SDSC) at UC San Diego to better understand why this condition is more prevalent in women of African ancestry than those of European and Asian ancestries, as well as how certain placental biomarkers can be indicative of severe cardiovascular issues in preeclampsia patients. Their study has been published in the Placenta journal.

“This condition is one of five leading causes of maternal mortality worldwide, but genomic data analysis is compute-intensive; however, our access to SDSC’s Expanse enabled us to perform RNA sequencing data processing in order to discover differentially expressed genes between normal and preeclamptic placental tissue,” said UC San Diego Assistant Professor of Pathology Mariko Horii, the study’s senior author. “Without access to Expanse and the technical support of Mahidhar Tatineni and Marty Kandes, we would not have been able to perform our data analysis to make this discovery regarding these important biomarkers during pregnancy.”

Horii said that Tatineni and Kandes helped the researchers install necessary software, improve their data analysis scripts and resolve errors to ensure accurate results in their study. “We have been working on software installs and process optimizations on SDSC machines (Comet, Expanse) with Prof. Horii's research team for almost a decade,” Kandes said. “This particular study required the computational power and large memory per node provided by Expanse and the filesystem options to handle these large datasets efficiently.”

Credit: UC San Diego

During the team’s data analysis of placental tissue RNA of 123 patients, they identified specific genes – such as IL3RA – that appear to be associated with preeclampsia complications that affect the heart. The African ancestry patient with the highest placental IL3RA developed peripartum cardiomyopathy — a heart muscle affliction that makes it harder for the heart to pump blood to the rest of the body — while the Asian and European ancestry preeclampsia patients with the highest placental IL3RA for their ancestries developed unexplained tachycardia — a heart rate above 100 beats per minute.

”Patients of African ancestry tend to be more negatively impacted by preeclampsia than those of Asian and European descent, our data suggests that this is because those of African descent have a high upregulation of both genes typically associated with preeclampsia (canonical preeclampsia genes) as well as genes that activate the immune response in contrast to Asian and European ancestry patients who tend to upregulate only canonical preeclampsia genes,” said UC San Diego Assistant Professor of Pathology Omonigho Aisagbonhi, the study’s first author.

To better understand these variations, the research team has begun work using Expanse to examine other immune associated genes, including the genetic causes of severe preeclampsia complications.

Computational work was funded by the U.S. National Science Foundation ACCESS program (allocation no. MED220016).