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CD44 alternative splicing senses intragenic DNA methylation in tumors via direct and indirect mechanisms

Eric Batsché1,2,3, Jia Yi2,3,4, Oriane Mauger2,3,4

  • 1Epigenetics and RNA metabolism in human diseases. CNRS UMR8256 - Biological Adaptation and Ageing. Institut de Biologie Paris-Seine. Sciences Sorbonne Université. 7-9 Quai Saint Bernard, 75005 Paris, France.

Nucleic Acids Research
|June 4, 2021
PubMed

Insights

DNA methylation (meDNA) influences alternative splicing, impacting cancer development. Loss of DNA methylases in colon cancer cells altered splicing, suggesting meDNA

Area of Science:

  • Molecular Biology
  • Epigenetics
  • Cancer Biology

Background:

  • DNA methylation (meDNA) regulates gene expression and is implicated in tumorigenesis.
  • Alternative splicing perturbations are frequent in cancer, yet their link to meDNA is underexplored.

Purpose of the Study:

  • To investigate the impact of DNA methylation on alternative splicing and its role in cancer.
  • To explore meDNA's role in epithelial to mesenchymal transition and cancer progression.

Main Methods:

  • Utilized HCT116 colon carcinoma cells with inactivated DNA methylases (DNMT1/3b).
  • Employed CRISPR-based dCas9/DNMT3b tool to manipulate DNA methylation.
  • Analyzed splicing changes, chromatin factor involvement (MBD1/2/3, HP1γ), and RNA polymerase II phosphorylation.
  • Assessed meDNA levels in MCF10A breast cancer model and B-cell acute lymphoblastic leukemia (B-ALL) patient samples.

Main Results:

  • Inactivation of DNMT1/3b in HCT116 cells induced partial epithelial to mesenchymal transition with increased CD44 variant exon skipping.
  • Exon skipping was directly linked to loss of intragenic meDNA, MBD1/2/3, HP1γ, and altered RNA polymerase II phosphorylation.
  • DNA methylation modulation using dCas9/DNMT3b confirmed its role in alternative splicing.
  • Correlations found between differentially spliced genes (splicing, signal transduction) and local meDNA modulation in breast cancer and B-ALL models.

Conclusions:

  • DNA methylation directly influences alternative splicing patterns, affecting cancer-related processes like EMT.
  • meDNA's impact on splicing may occur through direct mechanisms and indirectly via splicing isoforms of meDNA-binding proteins.
  • Splicing alterations linked to meDNA modulation hold potential as biomarkers for cancer progression.

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