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Changes in DNA methylation of tandem DNA repeats are different from interspersed repeats in cancer

Si Ho Choi1, Scott Worswick, Hyang-Min Byun

  • 1Jane Anne Nohl Division of Hematology, Center for Blood Diseases, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.

International Journal of Cancer
|May 14, 2009
PubMed

Insights

DNA repetitive elements show unique methylation changes in cancer. Hypomethylation of interspersed repeats and some tandem repeats occurred in bladder cancer, while D4Z4 methylation increased.

Area of Science:

  • Epigenetics
  • Cancer Biology
  • Genomics

Background:

  • Hypomethylation of DNA repetitive elements is a hallmark of cancer.
  • Limited understanding exists regarding methylation changes in specific interspersed (LINE1, Alu Yb8) and tandem (Sat-alpha, NBL-2, D4Z4) DNA repeats.
  • Epigenetic alterations in repetitive elements may serve as cancer biomarkers.

Purpose of the Study:

  • To quantitatively assess DNA methylation levels of five distinct repetitive elements in normal and cancerous tissues.
  • To investigate tissue- and cancer-type specific DNA methylation patterns of interspersed and tandem repeats.
  • To explore the potential of repetitive element DNA methylation as a global biomarker for cancer.

Main Methods:

  • Bisulfite-PCR Pyrosequencing was employed for quantitative DNA methylation analysis.
  • Analysis included normal autopsy tissues, paired bladder cancer tissues, chronic myelogenous leukemia, and acute promyelocytic leukemia samples.
  • Five specific DNA repetitive elements (LINE1, Alu Yb8, Sat-alpha, NBL-2, D4Z4) were targeted.

Main Results:

  • Interspersed repeats (LINE1, Alu Yb8) showed consistent methylation across tissues and individuals.
  • Tandem repeats exhibited greater variability in normal tissues.
  • Bladder cancer displayed hypomethylation of LINE1, Alu Yb8, Sat-alpha, and NBL-2, with hypermethylation of D4Z4.
  • Leukemia samples showed no significant LINE1/Alu Yb8 methylation changes but hypermethylation of NBL-2 and D4Z4.

Conclusions:

  • DNA methylation changes in individual repetitive elements are unique and specific to the element.
  • These distinct epigenetic patterns suggest varying regulatory mechanisms for different repetitive elements.
  • The unique methylation profiles highlight the potential and limitations of using repetitive element DNA methylation as global cancer biomarkers.

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