Pregnancy-related hypertension – 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 ACCESS resources 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.
“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 ACCESS allocations on Expanse provided the power they needed to conduct their study. Specifically, she said that Tatineni and Kandes helped the team install necessary software, improve their data analysis scripts and resolve errors to ensure accurate results in their study.
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 rare disorder in which a pregnant woman’s heart becomes weakened and enlarged) while the Asian and European ancestry preeclampsia patients with the highest placental IL3RA for their ancestries developed unexplained tachycardia (heart rate over 100 beats a minute).
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.
–Mariko Horii, professor of pathology, UC San Diego
”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 now begun work – using additional ACCESS allocations – to examine other immune-associated genes. Their goal is to better understand the genetic causes of severe preeclampsia complications.
According to the Centers for Disease Control and Prevention (CDC), preeclampsia occurs in roughly one in 25 pregnancies in the United States. For more information about the preeclampsia study conducted by the UC San Diego School of Medicine team utilizing Expanse, read their publication in the Placenta journal.
Project Details
Resource Provider Institution(s): San Diego Supercomputer Center (SDSC)
Affiliations: UC San Diego School of Medicine
Funding Agency: NSF
Grant or Allocation Number(s): MED220016
The science story featured here was enabled by the U.S. National Science Foundation’s ACCESS program, which is supported by National Science Foundation grants #2138259, #2138286, #2138307, #2137603, and #2138296.