A Roadmap for the Human Gut Cell Atlas

Abstract

The number of studies investigating the human gastrointestinal tract using various single-cell profiling methods has increased substantially in the past few years. Although this increase provides a unique opportunity for the generation of the first comprehensive Human Gut Cell Atlas (HGCA), there remains a range of major challenges ahead. Above all, the ultimate success will largely depend on a structured and coordinated approach that aligns global efforts undertaken by a large number of research groups. In this Roadmap, we discuss a comprehensive forward-thinking direction for the generation of the HGCA on behalf of the Gut Biological Network of the Human Cell Atlas. Based on the consensus opinion of experts from across the globe, we outline the main requirements for the first complete HGCA by summarizing existing data sets and highlighting anatomical regions and/or tissues with limited coverage. We provide recommendations for future studies and discuss key methodologies and the importance of integrating the healthy gut atlas with related diseases and gut organoids. Importantly, we critically overview the computational tools available and provide recommendations to overcome key challenges.

Fig. 1 ∣. Profiling the human gastrointestinal tract.

a, A complete map of the human gastrointestinal tract requires the inclusion of the entire intestinal tube and associated organs. b, Profiling must also consider the effect of the developmental stage, gut microbiome and potential effects of environmental factors such as diet, toxins and medication. In addition to transcriptional profiling, capturing the underlying genome sequence and the epigenetic programme will yield critical information.

Fig. 2 ∣. Summary of main tissue types and sampling strategies available.

The main advantages and limitations of the tissue types and sampling strategies are illustrated.

Fig. 3 ∣. Template metadata for gut-related single-cell studies.

Template table for the collection of basic information required to enable future studies to be included in the HGCA. ATAC-seq, single-cell assay for transposase-accessible chromatin sequencing; CCF, common coordinate framework; H&E, haematoxylin and eosin; RNA-seq, RNA sequencing; scRNA-seq, single-cell RNA-seq. ^aIf available, provide distance (in mm/cm) from the nearest anatomical landmark: gastroduodenal junction, ileocaecal valve, hepatic flexure, splenic flexure or anus.

Fig. 4 ∣. Data integration, processing and analysing strategies.

a, Generation of the Human Gut Cell Atlas (HGCA) requires successful integration of various data sets, data types, and associated patient and donor metadata. b,c, Successful integration will allow a range of queries to be performed and outputs generated. Simultaneous profiling of epigenetic mechanisms on a single-cell level will allow the identification of regulatory cellular networks and help to define cellular identities. G&T-seq, genome and transcriptome sequencing; RNA-seq, RNA sequencing; scATAC-seq, single-cell assay for transposase-accessible chromatin; scChiP-seq, single-cell chromatin immunoprecipitation sequencing; scRRBS-seq, single-cell reduced representation bisulfite sequencing; VDJ-seq, variability, diversity and joining sequencing.

Fig. 5 ∣. Current applications for the Human Gut Cell Atlas Common Coordinate Framework.

a, Human BioMolecular Atlas Program (HuBMAP) Registration User Interface (CCF-RUI) showing the gut visibility controls in the left panel, interactive block registration interface in the centre panel and block specification controls in the right panel. b, Gut Atlas CCF browser interface shows the one-dimensional conceptual model for the full large and small intestines with a zoom panel and ontology listings at the top, with two-dimensional and three-dimensional interactive displays for all of the available models. The position of the current region of interest is displayed in each common coordinate framework (CCF) view and is fully interoperable in the sense that position selection in any view will be updated immediately in all the other views. c, European Bioinformatics Institute (EBI) Single-Cell Expression Atlas (SCEA) anatomogram for the large and small intestines enables the selection of any structure identified in the anatomical structures, cell types and biomarker (ASCT) tables. d, Expanded view of the anal canal to show relevant cell types and tissue organization of that region.

Fig. 6 ∣. HGCA in health and disease.

Integration of data sets generated from intestinal tissues obtained from healthy individuals and patients with related diseases, including inflammatory bowel disease (IBD) and colorectal cancer, will enhance the future value of the Human Gut Cell Atlas (HGCA). Single-cell profiling of intestinal organoids, followed by their integration into the HGCA, will provide unique opportunities for translational research, including regenerative medicine, drug testing and development.