Hike funding

Pitt researchers part of team that received renewed funding to run ‘Google maps’ of cells

Getting from point A to point B has never been easier thanks to digital maps on our smartphones. With the swipe of a finger, we can plan a route to the grocery store, hike a hiking trail, or choose a perfect vacation destination. Soon, biomedical researchers will have a similar tool to easily navigate the vast network of cells in the human body.

The Human Biomolecular Atlas Program, or HuBMAP, is an international consortium of researchers whose common goal is to develop a global atlas of healthy cells in the human body. Once completed, the resource will be made freely available to drug developers and clinical researchers who could use it to shape the development of specialized medical treatments.

Dr Jonathan Silverstein

The idea behind HuBMAP is akin to the National Institutes of Health’s Human Genome Project, which sequenced every gene in the human body. Completed nearly 20 years ago, this massive undertaking kick-started a renaissance in clinical research and laid the foundation for innovative approaches to gene therapies. But instead of collecting genetic information at the whole-organism level, HuBMAP goes further with the aim of mapping gene expression, proteins, metabolites and other information in different cell types across various organs. and fabrics.

The next step of transforming this vast wealth of data into a user-friendly tool is managed by bioinformaticians from University of Pittsburghthe Pittsburgh Supercomputing Center (PSC), Carnegie Mellon University (CMU) and Stanford University. The teams recently received $20 million in renewed funding from the NIH to continue these efforts.

“Creating an ecosystem that can connect all the different data into one big knowledge resource is a tough task, but that’s where this team has particular expertise. We’re good at integrating all kinds of software and making them function.” said Pittsburgh HuBMAP infrastructure and engagement component co-lead, Dr. Jonathan Silverstein, a professor at theDepartment of Biomedical Informaticsto Pitt.

The team, led by Silverstein, who is also director of research computing at Pitt and UPMCInstitute of Precision Medicine, and SPC Scientific Director Dr. Phil Blood will embark on a long journey of annotating vast amounts of data at the molecular level from thousands of tissue samples collected from more than 60 institutions across the country. A locally maintained and developed hybrid cloud infrastructure for data integration and software development is used to shape the resulting library of healthy cell genetic and protein signatures into a comprehensive map.

The HuBMAP Computational Tools Component, led by Dr. Matthew Ruffalo of CMU’s Department of Computational Biology, has developed computational pipelines for processing these molecular datasets, enabling efficient data integration across data types, fabrics and more.

The team is also involved in projects aimed at creating a atlas of aging and senescent cells (SenNet) and the construction of a framework for the study of molecular markers of breast cancer.

“In addition to research, the HuBMAP and SenNet consortia are really helping to shape the ecosystem and culture around the projects that this work will impact,” said Kay Metis, SenNet program manager at Pitt. “This project has the potential to impact research on Alzheimer’s disease and aging and make a big difference in the future direction of medical research. I love being part of the effort to contribute to the social impact of what a project of this magnitude can accomplish. »