Tissue Mapping Center

Stanford Tissue Mapping Center



The small bowel and colon are critical organs for maintaining homeostasis of the human body by mediating nutritional absorption upon the ingestion of food. Though both organs are extensive in length, there are known differences in function and cellular heterogeneity within different portions of each. A cross section of the bowel reveals a complex layering of components involved in absorption and secretion, motility of gut contents, circulation, and immunity. In this submission, we propose to continue our efforts in the Stanford Tissue Mapping Center (TMC) to produce multi-modal, 3D, single-cell resolution maps of the small bowel and colonic wall structure. This will serve as a community resource to further study intestinal function and disease. We will collect tissues from deceased organ donors with explicit consent for distribution among the HuBMAP consortium and broad access genome data sharing (GDS). Three sets of technologies will then be employed. Tissue samples will be subjected to single-nuclei ATAC-seq and RNA-seq. These open chromatin and transcriptomic profiles will be spatially mapped to tissue sections using the CODEX (CO-Detection by indEXing) multiplexed spatial immunoassay. We will also employ the Molecular Cartography multiplexed fluorescence in situ hybridization (FISH) assay to enable more accurate integration of CODEX and single-nuclei data. The resulting 3D maps will span all layers of the bowel wall and include the epithelial, enteroendocrine, vascular, lymphatic, nervous, immune, and muscular cell populations that contribute to normal bowel function.

Public health relevance statement

In the first phase of HuBMAP, we established the Stanford Tissue Mapping Center to map the complexity of cellular architecture and biomolecular profiles of the small bowel and colon – organs that play wide-ranging roles in maintaining normal physiologies of metabolism, immunity, and even neural function. We applied the deep expertise of our team to obtain high-quality biospecimens, characterize tissues using cutting-edge omics and multiparametric imaging techniques, and perform integrative analyses to understand the biomolecular profiles in the context of spatial tissue structure. We have scaled these data-generation and analysis pipelines for production-scale interrogation of the intestinal wall. We will continue these efforts to build 3D multi-modal (snRNA, snATAC, CODEX, multiplex FISH) spatial maps that will give the greater scientific community insights into the molecular underpinnings of normal bowel function.

Fast Facts
Project title: Stanford Tissue Mapping Center
Organ specialty: Small bowel and colon
PIs: Michael Snyder and Garry Nolan, Stanford University
Co-Investigators: Yiing Lin, Washington University in St. Louis; William Greenleaf, Anshul Kundaje, Laren Becker, and Yvonne Maldonado, Stanford University; Shin Lin, University of Washington; Joseph Yracheta, Navite BioData Consortium
Project Manager: Emma Monte
Assay Types: simultaneous snATAC-seq and snRNA-seq (multiome), CODEX, multiplex FISH
Grant number: 1U54HG012723-01
Learn More: Visit this lab's website, and follow them on Twitter.