By Pete DiPrimio
An ambitious set of projects funded by the National Institutes of Health aims to map the 37 trillion cells in an adult human body to produce ground-breaking medical advances. Scientific map making is a core expertise of Dr. Katy Börner’s team at the Luddy School of Informatics, Computing and Engineering’s Cyberinfrastructure for Network Science Center. NIH has awarded CNS more than $11 million in grants over multiple years for two projects that will support constructing a Human Reference Atlas—a comprehensive, high-resolution, three-dimensional atlas of all the cells in a healthy body.
“I’m super proud and excited that these projects were awarded to our team at IU. We look forward to mapping the human body using human and machine intelligence.” said Katy Börner, Victor H. Yngve distinguished professor of engineering and information science, and CNS director.
The evolving Human Reference Atlas provides standard terminologies and data structures for describing anatomical structures, cell types, and biomarkers across the human body. The goal is to develop a Common Coordinate Framework for the healthy human body that makes it possible to construct an “address system” for cells and microanatomical structures. The atlas will support cataloging different types of individual cells, understanding the functions and relationships among those cells, and modeling their individual and collective function.
One of the funded projects is the production phase of the Human BioMolecular Atlas Program, a consortium of 18 diverse collaborative research teams across the United States and Europe.
“It is an honor and pleasure to work in this interdisciplinary team of experts from around the globe which is poised to map the human body at single-cell resolution,” Börner said.
While the human genome is a one-dimensional structure and the DNA of any two people is 99 percent identical, the body is a three-dimensional structure that comes in many shapes and sizes. As a human ages, exercises, or gets sick, the number, type, size, and location of cells changes.
“Creating a Human Reference Atlas,” she said, “is a wonderful opportunity to show the power of data visualization for federating biomolecular data across scales (from the human body to the single-cell level), and to model and communicate the structure and function of human cells across time and other experimental conditions.”
Projects receiving funding include:
The focus is to develop an open and global platform to map healthy cells in the human body.In humans, the proper functioning of organs and tissues is dependent on the interaction, spatial organization, and specialization of all our cells.
Cellular Senescence Network / SenNet Overview video
Established to comprehensively identify and characterize senescent cells across various states of human health and across the lifespan. SenNet will provide publicly accessible atlases of senescent cell types, the differences among them, and the molecules they secrete, using data collected from multiple human and model organism tissues.
During the initial four years of HuBMAP, Börner’s team built first elements of the Human Reference Atlas:
- Her team led the construction of Anatomical Structures, Cell Types, and Biomarkers (ASCT+B) Tables for many organs and implemented a CCF Ontology.
- Collaborated with NIAID at NIH on the design of a 3D Reference Object Library.
- Developed three interactive Common Coordinate Framework (CCF) user interfaces:
- The CCF ASCT+B Reporter supports the authoring and interactive review of ASCT+B Tables.
- The CCF Registration User Interface (RUI) supports uniform tissue data registration across organs and labs.
- The CCF Exploration User Interface (EUI) supports exploration of semantically and spatially explicit data—from the whole body to the single cell level.
- For an introduction to HuBMAP goals, data, and code visit the free Visible Human MOOC (VHMOOC).
The IU team includes Dr. Andreas Bueckle, CNS Research Lead. He said challenges are socio-technical. Technology alone does not suffice to empower experts from different disciplines to “add their experimental data to the evolving human reference atlas and to use the atlas in research and clinical practice.”
“For me, the most exciting task is designing user-friendly interfaces to allow researchers, clinicians, and other stakeholders to explore human tissue data from about thirty organs.”
He has been working on a VR Organ Gallery that can be explored at https://hubmapconsortium.github.io/ccf/pages/ccf-gallery.html.
This work has been funded by grants from the NIH Common Fund: 1OT2 OD033756-01 and 1U24 CA268108-01.