The Use of Single-Cell Mitochondrial DNA SNP Combinations for Distinguishing Organ-Specific Cell Types

Area of Science:

• Developmental Biology
• Regenerative Medicine
• Genomics
• Cell Biology

Background:

• Fluorescent labeling advances cell lineage studies but lacks unbiased, non-invasive methods.
• Distinguishing cell types within an individual and tracking their fate remains a challenge.
• Mitochondrial DNA (mtDNA) single-nucleotide polymorphisms (SNPs) offer potential for individual cell identification.

Purpose of the Study:

• To develop and validate unbiased methods for distinguishing cell types and tracing cell lineages using mtDNA SNPs.
• To apply these methods to identify cell types in organs and track cell fate in liver regeneration.
• To establish mtDNA SNPs as a tool for cell lineage relationship studies.

Main Methods:

• Mitochondrial Alteration Enrichment and Sequencing (MAESTER) to detect mtDNA SNPs.
• Mitochondrial single-cell assay for transposase-accessible chromatin with sequencing (mtscATAC-seq) for SNP detection in single cells.
• Application in a partial hepatectomy mouse model with fluorescently labeled cholangiocytes.

Main Results:

• MAESTER successfully defined specific cell types in the liver and spleen using unique mtDNA SNP combinations.
• mtscATAC-seq detected mtDNA SNP panels in pre-hepatectomy cholangiocytes.
• These mtDNA SNP panels faithfully traced cell fate in post-hepatectomy liver samples.

Conclusions:

• mtDNA SNPs can serve as intrinsic, individual-specific markers for cell identification.
• The developed MAESTER and mtscATAC-seq approaches provide unbiased tools for cell lineage tracing.
• This methodology holds promise for advancing research in liver regeneration and developmental biology.