HuBMAP Consortium Charts out Goals for Navigable 3D Map in Article in Nature

Oct. 9, 2019

A national collaboration of scientists has taken the first steps to creating a 3D map of the human body, down to the level of single cells and smaller. In an article in the prestigious journal Nature, the Human Biomolecular Atlas Program (HuBMAP) Consortium charts out its goals for creating an interactive map that scientists can use to navigate through the human body to answer questions about its functions in health and disease. HuBMAP will continue over the next four years with an anticipated total of $54 million in grants, pending availability of resources, from the NIH Common Fund over the lifespan of the program.

The Pittsburgh Supercomputing Center (PSC), Carnegie Mellon University (CMU), and the University of Pittsburgh are playing leading roles in the consortium.

“This project will transform our understanding of the human body and how it works,” said Michael Snyder, PhD, principal author of the article and Principal Investigator/Project Leader for the Stanford Tissue Mapping Center of HuBMAP. “It is a major step forward toward understanding how our ten trillion cells are organized and work together to make a complicated human being. By mapping these cells in a normal person, we will better understand what is happening during human disease.”

Understanding important high-resolution features of cells in tissues remains a challenge. Recently developed technologies, including many supported through NIH programs, allow researchers to explore the organization of large numbers of cells at the individual cell level. These advances opened the possibility to study and map the organization of all cells within tissues or organs across the human body. While HuBMAP is not anticipated to map the entire body, it will get the work started, providing a framework for more complete mapping and making data available to the research community for further study.

HuBMAP’s tissue-mapping centers will collect and analyze tissues from mostly healthy men and women of different ethnicities and ages. Organs to be sampled include discrete organs such as the kidney, ureter, bladder, lung, breast, small intestine and colon; the blood vessels; and immune-system organs such as the lymphatic tissues, spleen, thymus and lymph nodes. The scientists will obtain consent from participants over and above standard regulations when possible in order to make the data available for “open access.” The goal is to help the open biomedical research community make maximum use of HuBMAP’s data.

HuBMAP is funded by the NIH Common Fund. It is managed by a trans-NIH working group and led by staff from the Common Fund; National Heart, Lung, and Blood Institute; National Institute of Biomedical Imaging and Bioengineering; and the National Institute of Diabetes and Digestive and Kidney Diseases.

“NIH Common Fund programs are intended to have far-reaching influences across many areas of biomedical science,” said James M. Anderson, MD, PhD, Director of the Division of Program Coordination, Planning, and Strategic Initiatives, which oversees the Common Fund. “HuBMAP plans to provide a framework for researchers, scientists, and clinicians to understand the organization and function of the human body at the biomolecular level. The new technologies and high-resolution data created by HuBMAP will change our view of the human body.”

In order to make optimal use of the diversity of data that the HuBMAP scientists expect to collect, the collaborators will develop new tools to visualize and analyze microscopic images. In addition to working with its own data, software and computational resources, HuBMAP will cooperate with scientists in the international community as part of a global effort to build high-resolution maps of the human body. HuBMAP scientists expect that their initial maps will represent the “tip of the iceberg;” while they hope to contribute to the understanding of human health and disease, they also see their efforts serving as a foundation for future applications of anatomical data to diagnose, study and treat disease.

Several research institutions in Pittsburgh are playing key roles in HuBMAP.

Scientists at the Pittsburgh Supercomputing Center (PSC)—a joint center of CMU and Pitt—and Pitt’s Department of Biomedical Informatics (DBMI) lead the central Infrastructure and Engagement Component (IEC) of HuBMAP. Initially, the CMU/Pitt collaboration had been named to the infrastructure component, but has taken on the additional role of engagement and outreach.

The IEC is developing and implementing data and computational infrastructure to unify the HuBMAP Consortium to enable the first public HuBMAP data release, targeted for June 2020. Working across the Consortium and more broadly, the IEC will ensure that the initial data release has substantial scientific value and leads to a subsequent quarterly cadence of data releases together with maps and tools of increasing investigative power.

“HuBMAP will greatly advance our understanding of the human body by providing not only data at unprecedented resolution, but also analytic tools and computational resources to unlock the value of that very large data,” said Nick Nystrom, PhD, Principal Investigator for the IEC and PSC Chief Scientist. “Providing ways for people to participate without having to be computer experts and enabling scientific reproducibility will democratize access to our unique HuBMAP dataset.”

PSC and DBMI bring great depth in the development of flexible, user-friendly, scalable infrastructure together with extensive experience in genomics, imaging, and medical data. Through a subcontract to Knowinnovation Inc., the IEC brings in additional talent for maximizing the effectiveness of key meetings and broadening engagement. The IEC has received over $2.8 million in funding from NIH to date.

“We are pleased to lead, with our colleagues across Pittsburgh, in this exciting effort across dozens of institutions to collect, organize, and provide vast and deep human biological and medical data,” said Jonathan Silverstein, MD, Principal Investigator for the IEC and Chief Research Informatics Officer for Pitt’s Health Sciences and Institute for Precision Medicine.
The HuBMAP Computational Tools Center, led by the CMU School of Computer Science (SCS), will focus on the computational methods necessary for processing massive amounts of raw data, constructing the high-resolution tissue maps and building an atlas of tissue maps. The Computational Tools Center will receive $2 million in NIH funding, supporting work by SCS scientists and their colleagues at the University of California Santa Cruz and the Wellcome Sanger Institute in the U.K.

Read the Nature article here.