The Human Cell Atlas bone marrow single-cell interactive web portal

Abstract

The Human Cell Atlas (HCA) is expected to facilitate the creation of reference cell profiles, marker genes, and gene regulatory networks that will provide a deeper understanding of healthy and disease cell types from clinical biospecimens. The hematopoietic system includes dozens of distinct, transcriptionally coherent cell types, including intermediate transitional populations that have not been previously described at a molecular level. Using the first data release from the HCA bone marrow tissue project, we resolved common, rare, and potentially transitional cell populations from over 100,000 hematopoietic cells spanning 35 transcriptionally coherent groups across eight healthy donors using emerging new computational approaches. These data highlight novel mixed-lineage progenitor populations and putative trajectories governing granulocytic, monocytic, lymphoid, erythroid, megakaryocytic, and eosinophil specification. Our analyses suggest significant variation in cell-type composition and gene expression among donors, including biological processes affected by donor age. To enable broad exploration of these findings, we provide an interactive website to probe intra-cell and extra-cell population differences within and between donors and reference markers for cellular classification and cellular trajectories through associated progenitor states.

Figure 1.

Integrated analysis of bone marrow hematopoietic cells from healthy donors. (A) Applied computational workflow to bone marrow cells processed by the HCA project. The three principle approaches applied are ICGS (unsupervised population analysis), cellHarmony (population alignment between donors), and SPRING (lineage trajectory analysis). An interactive web interface provides in-depth exploration of these data. (B) Integrated results heatmap for ~100,000 cells from all eight donors classified along 27 ICGS populations. Columns are cells and rows are genes. The top MarkerFinder gene for each population gene cluster is shown (left). Cells for each donor are shown below the heatmap. (C) Populations differing according to the average number of genes expressed. Error bars indicate standard deviation. (D) Statistical enrichment of gene sets from the Molecular Signature Database (Broad Institute) in the software GO-Elite corresponding to two frequently enriched progenitor categories as either upregulated or downregulated genes.

Figure 2.

Identification of rare transitional progenitor populations. (A) ICGS analysis of ~12,000 combined donor CD34⁺ populations selected from Figure 1B. The top two MarkerFinder genes for each population gene cluster are shown (left). (B) SPRING analysis of all associated cells using ICGS population-associated genes. ICGS populations are notated by distinct colors and are labeled according to frequency. (C) Visualization of predicted transitional population (CLP, LMPP, Multi-Lin*, MEP, MDP)-associated marker genes in the SPRING graph according to normalized gene values (red=high expression bin, grey=no expression). (D) Bar plot of genes with evidence of multilineage priming in multiple ICGS populations, corresponding to transitional cell populations.

Figure 3.

Cell populations and genes covary among donors. (A) SPRING analysis of all combined populations (top 1,500 cellHarmony-ranked cells per population). Dual lineage-associated cell populations (e.g., stromal) are predicted to be grouped with other lineages. (B,C) SPRING analysis of individual donors with varying cell population frequencies (immature neutrophils and erythroblasts). Population colors match panel (A). (D) Relative differences in population frequencies between donors organized according to annotated lineages (y-axis). (E) HSC cell frequency anticorrelation with age. (F) Visualization of correlated (red) and anticorrelated (blue) genes in HSC with donor age (rho > 0.6 or rho < −0.6) upon the Electron Transport Chain WikiPathway (WP111). (G) Variation in the expression of the prior proposed human HSC marker gene EMCN in our HCA web viewer.

Figure 4.

Interactive web portal for the HCA bone marrow data. Visualization options within the HCA bone marrow browser. (A) Global view for interactive visualization of the CD34⁺ cell SPRING analysis. Genes can be directly queried in the interface or identified from the list of cell- population-specific markers (sortable table). Each dot represents a single cell and specific cell populations can be hidden or exposed. (B) Combined donor view displaying the boxplot of the mean expression of each gene for each donor for each specific cell population. The donor information associated with each data point can be determined by mouse-over. (C,D) Individual donor expression variation viewed as data points for each individual cell as a (C) boxplot or (D) a bar chart to evaluate the frequency and amplitude of gene expression in all eight donors. New genes can be selected through the interface on the left. Source files can be downloaded through the interface (downloads tab).