Single-nucleus cross-tissue molecular reference maps to decipher disease gene function

Abstract

Understanding the function of genes and their regulation in tissue homeostasis and disease requires knowing the cellular context in which genes are expressed in tissues across the body. Single cell genomics allows the generation of detailed cellular atlases in human tissues, but most efforts are focused on single tissue types. Here, we establish a framework for profiling multiple tissues across the human body at single-cell resolution using single nucleus RNA-Seq (snRNA-seq), and apply it to 8 diverse, archived, frozen tissue types (three donors per tissue). We apply four snRNA-seq methods to each of 25 samples from 16 donors, generating a cross-tissue atlas of 209,126 nuclei profiles, and benchmark them vs. scRNA-seq of comparable fresh tissues. We use a conditional variational autoencoder (cVAE) to integrate an atlas across tissues, donors, and laboratory methods. We highlight shared and tissue-specific features of tissue-resident immune cells, identifying tissue-restricted and non-restricted resident myeloid populations. These include a cross-tissue conserved dichotomy between LYVE1- and HLA class II-expressing macrophages, and the broad presence of LAM-like macrophages across healthy tissues that is also observed in disease. For rare, monogenic muscle diseases, we identify cell types that likely underlie the neuromuscular, metabolic, and immune components of these diseases, and biological processes involved in their pathology. For common complex diseases and traits analyzed by GWAS, we identify the cell types and gene modules that potentially underlie disease mechanisms. The experimental and analytical frameworks we describe will enable the generation of large-scale studies of how cellular and molecular processes vary across individuals and populations.

The Power of Single-Cell RNA Sequencing in eQTL Discovery

“…However, in situations where nuclear genome expression is under study, nuclei isolated from purified cells can be used. This was shown in a framework for colocalizing human eQTL with 21 complex traits by Eraslan et al [ 5 ]. Similar methods could prove powerful in cis- eQTL analysis and understanding patterns of human disease and development.…”

“…eQTL analysis using scRNA-seq is a relatively new approach and only a dozen studies are available [ 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 ]. These studies show diverse applications of scRNA-seq in identification of the quantitative effects of genetic variants or loci using purified cell types [ 4 , 5 ], induced pluripotent stem cells (iPSCs) [ 6 , 9 , 11 , 13 ] or whole organisms [ 10 ] and to study population ancestry and cell type specific response to an environmental stimulus such as viral infection [ 12 ]. In the following sections, we review the published sc-studies for of cis- eQTL analysis, and compare the results to bulk RNA-Seq based analysis ( Figure 1 ; Table 1 ).…”

The Tabula Sapiens: a multiple organ single cell transcriptomic atlas of humans

“…As another example, one can compare gene expression in fetal human cell types (48) to those determined here in adults to glean insight into the effects of aging and the loss of plasticity from early development to maturity. Many of these datasets were created with different technical approaches and having data from cell types shared across many organs may facilitate the development of normalization methods to compare such diverse data -and also may enable better understanding of technical artifacts introduced by the various approaches (8,9,49,50). The Tabula Sapiens has enabled several discoveries relating to shared behavior or subtle organ specific differences across a number of cell types.…”

“…Similarly, comparing fetal human cell types ( 33 ) to those determined here in adults may give insight into the loss of plasticity from early development to maturity. Having multi-organ data from individual donors may facilitate development of methods to compare diverse datasets and yield understanding of technical artifacts from various approaches ( 8, 9, 34, 35 ). The Tabula Sapiens has enabled discoveries relating to shared behavior and organ specific differences across cell types.…”

A decade of molecular cell atlases

“…In 2021, the Tabula Sapiens released its preprint and data set across 15 donors, 59 samples, and 20 tissues [40]. Related preprints based on separate work from the Broad [41] and Sanger [42] institutes were released concurrently, and the Swedish consortium published an important contribution at the same time [43]. Collectively, these molecular atlases are truly companion resources to the genome of an organism.…”