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Updated: Jun 14, 2025

Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers MADM
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Human brain ancestral barcodes.

Darryl Shibata1

  • 1Department of Pathology, University of Southern California, Keck School of Medicine, Los Angeles, United States.

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|June 10, 2025
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Summary
This summary is machine-generated.

Dynamic CpG methylation patterns, or "barcodes," from single human brain cells reveal cell age and ancestry. These epigenetic markers, found on X-chromosome sites, distinguish thousands of cells and map their developmental relationships.

Keywords:
developmenthumanlineage-tracingneuronneuroscience

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Area of Science:

  • Epigenetics
  • Neuroscience
  • Genomics

Background:

  • Dynamic CpG methylation patterns, termed 'barcodes,' are crucial for understanding cellular heterogeneity.
  • Analyzing these barcodes in single human brain cells presents challenges due to sparse sequencing data.

Purpose of the Study:

  • To develop and apply a method for reading dynamic CpG methylation barcodes from thousands of single human brain cells.
  • To investigate the potential of these barcodes to record cellular age, ancestry, and migration patterns.

Main Methods:

  • Sequencing of ~31,000 rapidly fluctuating X-chromosome CpG sites (fCpGs) across 15,000-21,000 single cells from human male brains.
  • Utilizing a minimum of 500 covered sites per cell and 30 common sites between cell pairs to establish methylation barcodes.
  • Analyzing pairwise differences (PWDs) to assess cell relatedness and reconstruct phylogenetic trees.

Main Results:

  • CpG methylation barcodes appear to initiate as methylated and record mitotic age, with later-developing cells (excitatory neurons, glial cells) showing lower methylation.
  • Average pairwise differences (PWDs) between cells were ~0.5, with highly related cell pairs exhibiting PWDs <0.05.
  • Reconstructed cell trees indicated phenotypic similarity among related cells, with inhibitory neurons showing evidence of tangential migration across cortical regions.

Conclusions:

  • fCpG methylation barcodes are polymorphic during development and can effectively distinguish between thousands of human cells.
  • These epigenetic barcodes provide a novel means to infer cellular age, ancestry, and migration patterns within the human brain.
  • The findings open new avenues for studying cellular development and heterogeneity using epigenetic information.