Creating Disease Gene Maps Using Single-Nucleus Cross-Tissue Analysis
Summary
To understand gene function and regulation in homeostasis and sickness, one must understand the cellular and tissue settings in which genes are expressed. Four single-nucleus RNA sequencing methods were used for eight kinds of archived, frozen tissues from 16 donors and 25 samples in this study. The scientists mapped a cross-tissue atlas by merging the 209,126 nucleus profiles across tissues, donors, and lab processes using a conditional variational autoencoder. Using the cross-tissue atlas, they identify cell types that may contribute to the neuromuscular, metabolic, and immune components of monogenic diseases and the biological processes underlying their pathogenesis, as well as cell types and gene modules that may underlie disease mechanisms for complex traits investigated by genome-wide association studies.
Fig.1 Graphical abstract. (Eraslan, 2022)
Research Criteria
The pleiotropy and specificity of disease-associated variants necessitate the investigation of several tissues and individuals in order to comprehensively link variants to cells and molecular processes. For older cell atlases, fresh tissue samples from a single organ or tissue were the primary source of information. Single-nucleus RNA sequencing (snRNA-seq) can be used to identify cell types that do not survive tissue separation in a variety of tissues. Using techniques of deep learning, it is possible to merge data from several individuals and tissues while preserving biological variation and batch effects.
Fig.2 Experimental design. (Eraslan, 2022)
Sample Type
Frozen archived tissues from a human.
Result—A Multitissue, Multi-Individual Single-Nucleus Reference Atlas from Archived, Frozen Human Tissues
They processed the initial single nuclei RNA sequencing profiles in order to retain high-quality nuclei profiles and eliminate the impacts of contaminating transcripts from ambient RNA. Some tissues and methods exhibited greater levels of ambient RNA contamination, which manifested as the presence of highly expressed transcripts from one cell type in the nucleus profiles of other cell types. Regardless of technique, these effects were most pronounced in skeletal muscle and heart, although they also occurred in other tissues.
Fig.3 Ambient RNA contamination level of different tissues. (Eraslan, 2022)
Result—Cross-Tissue Atlas Annotation Recovers Diverse Cell Types, Including Difficult-to-Profile and Rare Cell Subsets
Using a conditional variational autoencoder, they combined data from each sample and methodology (cVAE). The fact that cells cluster first by cell type and then by tissue-specific subclusters indicates that diversity across cell types is greater than variation within a cell type across tissues. Then, they classified cellular compartments shared across tissues, broad cell types, granular cell subsets, and annotated cell types within each tissue. Across extraction procedures, tissues, and donors, the annotations were consistent. Cross-tissue and cross-sample integration improved the capacity to distinguish numerous rare cell subsets. Since these uncommon cells contribute to a variety of diseases, their profiling in human tissues will facilitate investigations of diseases.
Fig.4 Cross-tissue snRNA-seq atlas in eight archived, frozen adult human tissues. (Eraslan, 2022)
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Learn moreCreative Biolabs offers single nuclei RNA sequencing services to researchers and scientists in the biomedical field. Our service allows for the analysis of gene expression at the single nuclei level, providing valuable insights into cellular heterogeneity and function. We use state-of-the-art techniques and equipment to ensure high-quality results and work with a variety of sample types, including complex tissues, rare, and cryopreserved samples. Our team of experts is dedicated to providing timely and efficient services to support your scientific endeavors.
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Reference
- >Eraslan, G.; et al. Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function. Science. 2022, 376(6594): eabl4290.
