Single-cell Multi-omics in Tissue Development, Degenerative Disease, and Tissue Regeneration

Single-cell sequencing technologies are revolutionizing biomedical research and providing deep biological insights. One of the most popular technologies, single-cell RNA sequencing (scRNA-seq), has been used to measure transcriptomics at single-cell resolution for thousands of cells. Nowadays, parallel single-cell sequencing technologies unlock the possibility of detecting transcriptomes and epigenomes for the same cells. For instance, scRNA-seq data could be simultaneously profiled with single-cell epigenomic sequencing, such as scATAC-seq for single-cell sequencing of chromatin accessibility. Recently, single-cell sequencing technologies have been combined with spatial sequencing technologies to capture gene activities at the spatial resolution of tissues. Single-cell and spatial multi-omics provide unprecedented opportunities to explore the heterogeneity of tissues and to reveal cellular and molecular mechanisms during diverse biological processes, e.g., tissue development, tissue degeneration, and tissue regeneration.

Although single-cell RNA sequencing technology is well established, single-cell epigenomic and spatial sequencing technologies are still under development. The major challenges come from both multi-omics techniques and computational analysis. The single-cell sequencing technologies require a higher resolution and a larger scale of biological multi-omics measurement, as well as efficient spatial sequencing technologies for complementing the homeless of single cells. The computational challenge is to precisely analyze single-cell multi-omics data, e.g., data normalization, batch effect removal, and multi-omics integration. New computational methods are highly required for single-cell and spatial sequencing data analysis to identify key regulatory factors and networks, which may provide valuable biological insights in tissue development, tissue degeneration, tissue regeneration, and so on.

This Research Topic aims to publish and highlight new research for tissue development, degenerative disease, and tissue regeneration by using single-cell multi-omics and spatial sequencing technologies.

This collection publishes Original Research, Brief Reports, Methods, and Reviews related to single-cell and spatial multi-omics in tissue development, degenerative disease, and tissue regeneration. The scope of the Research Topic includes, but is not limited to:

• single-cell and spatial sequencing technologies: The research for developing new or improved single-cell and spatial sequencing technologies.

• methods of multi-omics data analysis: Approaches for analysis of single-cell sequencing data, and the integration of single-cell with spatial sequencing data, especially regulatory network analysis.

• single-cell and spatial multi-omics in development, degenerative disease, and tissue regeneration: Degenerative diseases include neoplastic diseases and nervous system diseases which cause a tissue or organ to deteriorate over time, such as cancer, neurodegenerative disease, and so on. We require studies on cellular and molecular mechanisms of tissue development, degenerative disease, and tissue regeneration through single-cell and spatial multi-omics.