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Single-cell DNA replication dynamics in genomically unstable cancers.

Adam C Weiner1,2, Marc J Williams1, Hongyu Shi1,3

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Biorxiv : the Preprint Server for Biology
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We developed a new method to study DNA replication timing in aneuploid cells. This method reveals how replication dynamics influence copy number changes and cell proliferation in cancer.

Keywords:
DNA replicationgenomic instabilitysingle-cell whole genome sequencing

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Area of Science:

  • Genomics
  • Cell Biology
  • Cancer Research

Background:

  • Aneuploidy, an abnormal chromosome number, is linked to DNA replication errors.
  • Understanding DNA replication dynamics in aneuploid cells is crucial but remains understudied.

Purpose of the Study:

  • To develop a method for inferring cell-specific DNA replication states.
  • To investigate clone-specific DNA replication timing (RT) in diverse aneuploid cell populations.
  • To correlate RT profiles with genomic instability and cellular behavior.

Main Methods:

  • Developed a novel method, PERT (probabilistic estimation of replication timing), for single-cell whole genome sequencing analysis.
  • Applied PERT to over 50,000 cells from aneuploid cell lines, xenografts, and primary tumors.
  • Analyzed replication timing heterogeneity and its association with genomic alterations and cell type.

Main Results:

  • Clone RT profiles predicted future copy number changes in cell lines.
  • Cell type was the primary driver of RT heterogeneity.
  • Whole genome doubling and specific mutational processes correlated with late S-phase accumulation.
  • Copy number alterations on chromosome X significantly impacted RT, including X-inactivation dynamics.
  • Cell cycle distributions in xenografts reflected clone proliferation and fitness.

Conclusions:

  • The PERT method enables detailed analysis of replication timing in complex aneuploid populations.
  • Replication timing is a key factor influencing genomic instability and clonal evolution in cancer.
  • Cell type and chromosomal alterations, particularly on chromosome X, critically shape replication dynamics.