Pitt researchers are leading the way toward a Google Maps of cells
Pitt researchers led to Google Maps of cells.
Getting from point A to point B has never been easier thanks to the digital maps on our smartphones. With the swipe of a finger, we can plan a route to the grocery store, head out on a hiking trail or choose the perfect vacation destination. Biomedical researchers will soon have a tool like this to help them explore the huge network of cells in the human body.
The Human Biomolecular Map Program, or HuBMAP, is an international consortium of researchers working together to create a worldwide atlas of healthy cells in the human body.
Once complete, the resource will be made freely available to drug developers and medical researchers who can use it to develop specialized medical treatments.
Pitt researchers led to Google Maps of cells.
The idea behind HuBMAP is similar to that of the National Institutes of Health’s Human Genome Project, which has sequenced every single gene in the human body.
Completed nearly 20 years ago, the massive work sparked a renaissance in medical research and laid the foundation for modern approaches to gene-based therapy.
But instead of collecting genetic information at the level of an entire organism, HuBMAP goes deeper with the goal of mapping gene expression, proteins, metabolites, and other information in numerous cell kinds in diverse organs and tissues.
The next step in turning this vast wealth of data into a user-friendly tool is being led by bioinformatics experts from the University of Pittsburgh, Pittsburgh Supercomputing Center (PSC), Carnegie Mellon University, and Stanford University. The NIH has renewed $20 million in funding for the teams to continue their studies.
“Creating an ecosystem that can connect all of the diverse pieces of data into a single large knowledge resource is a difficult endeavor, but one in which this team excels.”
We’re able to connect all kinds of different pieces of software and are good at running them,” said Pittsburgh HuBMAP Infrastructure and Engagement Component Co-Chair Jonathan Silverstein, a professor in Pitt’s Department of Biomedical Informatics.
The team, led by Silverstein, who is also a chief research informatics officer at Pitt and UPMC’s Institute for Precision Medicine, and Phil Blood, PSC’s scientific director, set out to interpret vast amounts of molecular-level data from thousands of tissues. I will start a long journey.
Samples were collected at more than 60 institutions across the country. A locally maintained and developed hybrid cloud infrastructure for data integration and software development is being used to map a library of genetic and protein signatures of healthy cells into a comprehensive map.
The HuBMAP Computational Tools component, led by Matthew Ruffalo of Carnegie Mellon’s Department of Computational Biology, has developed computational pipelines to process these molecular datasets, allowing data to be analyzed across species, tissues, and more. Effective integration may be allowed.
The team is also involved in projects aimed at creating an atlas of senescent and senescent cells (SenNet) and a framework for studying molecular markers of breast cancer.
“In addition to research, the HuBMAP and SenNet consortiums are contributing to defining the ecosystem and culture around the projects that will be influenced by this work,” said Kay Metis, director of the HuBMAP and SenNet consortia.
SenNet program manager at Pitt. This project has the potential to impact Alzheimer’s and aging research and make a big difference in the direction of medical research moving forward. I’m excited to contribute to the societal impact of what a project of this scale can achieve. I’d love to be a part of the effort.
Expertise in molecular biology and clinical data, experience in managing research consortia, and deep knowledge of software integration, along with the computing resources provided by PSC, make Pittsburgh uniquely qualified to tackle a complex task like HuBMAP.
“I came to Pitt because it has a diverse set of interests and scientific capabilities, and people here are willing to collaborate not only in Pittsburgh but globally.” We’ve built a team that’s not only clinical and on the biological data side but also the technology side,” Silverstein said.
The Human Biomolecular Atlas Program
The Human Biomolecular Atlas Program (HuBMAP) aims to develop an open and global platform for mapping healthy cells in the human body. In humans, the proper functioning of organs and tissues depends on the interaction, spatial organization, and specialization of all our cells. Scientists estimate that there are 37 trillion cells in an adult human body, so determining the function and relationship between these cells is an important task.
Using the latest molecular and cellular biology technologies, HuBMAP researchers are studying the connections that cells make with each other throughout the body.
HuBMAP will develop the tools, resources, and framework necessary to build cell models to determine how the relationships between cells can affect an individual’s health.
Pitt themes tapped to develop “Google Maps” of cells important in aging
Most cells in the human body can divide and multiply to replace old cells and repair damaged tissue, but cells can lose their ability to proliferate in response to certain stimuli.
Senescent cells are those that have lost this ability. They accumulate with age and can contribute to cancer and age-related disorders such as chronic lung disease, cardiovascular disease, frailty, and dementia by pumping signals that damage neighboring tissues.
The molecular landscape of senescence has been relatively unknown.
To address this knowledge gap, the National Institutes of Health’s Common Fund established the Cellular Senescence Network (SenNet) program to create “Google Maps” of the body’s aging tissues that any scientist can access.
Today, the program announced it will award $125 million to 16 teams to form the new SenNet consortium—and two projects led by researchers at the University of Pittsburgh and UPMC, which will receive a total of $31 million over five years. will
“Aging is in many ways the final frontier of medicine,” said Anantha Shekhar, senior vice chancellor for health sciences, and John and Gertrude Peterson, dean of the School of Medicine.
“These funds demonstrate Pitt’s breadth and depth of knowledge in the field of aging research, as well as our strong inter-institutional relationships with UPMC, the Pittsburgh Supercomputing Center, and other institutions.” and Carnegie Mellon University.”
SenNet’s primary mission is to dive deep into the process of cellular senescence, decoding how it occurs at both the biochemical and cellular levels.
Just as Google Maps provides detailed information about each location it stores, SenNet will provide data and analysis on the senescence process of cells, tissues, and organs at the molecular scale.
Torn Finkel, distinguished professor of cardiology and director of the Aging Institute at Pitt and UPMC, leads the TriState SenNet Tissue Mapping Center, one of two projects led by Pitt.
It will contribute to the atlas by generating maps of senescence in heart and lung cells, which will be combined with maps of different organs created by other teams in the consortium.
Like molecular cartographers, researchers will map gene expression and protein structure in senescent cells from pieces of human tissue and lab-grown miniature organs, or organoids.
They will compare different types of senescent cells across the lifespan to identify markers or biomarkers of senescence. Finkel will collaborate with co-principal investigators Melanie Kongshoff, a visiting professor of medicine at Pitt, Irfan Rahman of the University of Rochester, and Anna Mora of Ohio State University.
“We don’t know if cellular senescence is a single phenomenon or a collection of phenomena,” Finkel added. “Take cancer, for example, lung cancer, pancreatic cancer, and lymphoma are all highly distinct, even though we all call them cancer.” Pitt researchers are leading
senescent cells are found in different strains and different tissues and how they differ. Pitt researchers are leading
A second SenNet project led by Pitt will create an organized and navigable atlas that is accessible to everyone. Jonathan Silverstein, professor in the Department of Biomedical Informatics at Pitt and chief research informatics officer at Pitt and UPMC’s Institute for Precision Medicine; full build of the Pittsburgh Supercomputing Center, a joint research center of CMU and Pitt; and Zev Bar-Joseph of Carnegie Mellon University School of Computer Science will jointly lead SenNet’s Consortium Organization and Data Coordinating Center (CODCC). He will build on previous success in managing the Human Biomolecular Atlas program, a similar program aimed at mapping healthy human tissue at the cellular level.
In addition to managing the SenNet consortium, CODCC will be instrumental in providing the computing software and hardware that will integrate SenNet’s eight tissue mapping centers and seven technology development and application projects.
With a focus on data analysis and integration, the Pittsburgh-led center will set standards for data accuracy and progress, provide reliable and extensive data storage, and enable scientists to disseminate data and analytical tools. This will help to anticipate the tsunami of information.
Finally, the Atlas of Cellular Senescence will be published online in an open-source repository, providing a publicly accessible and searchable database so that other researchers can explore this data to learn more about senescent cells. can be explored and how they contribute to human health. Pitt researchers are leading
Silverstein said that “I think senescent cell science is incredibly fascinating because of the potential influence on a range of disorders.” “There is enormous opportunity to learn more about the role these cells play in the body by undertaking the basic science of gathering all of this information and presenting it through SenNet.” disease and developing pharmaceuticals that target them. “
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