Epigenetic silencing of miR-342-3p in B cell lymphoma and its impact on autophagy

Clin Epigenetics. 2020 Oct 19;12(1):150. doi: 10.1186/s13148-020-00926-1.


Background: miR-342-3p, localized to 14q32, is a tumor suppressor miRNA implicated in carcinogenesis. Given the presence of a promotor-associated CpG island for its host gene, EVL, we hypothesized that intronic miR-342-3p is a tumor suppressor co-regulated with host gene by promoter DNA methylation in B cell lymphoma.

Results: By bisulfite pyrosequencing-verified methylation-specific PCR (MSP), EVL/MIR342 methylation was detected in five (50%) lymphoma cell lines but not normal peripheral blood and tonsils. EVL/MIR342 methylation correlated with repression of both miR-342-3p and EVL in cell lines. In completely methylated SU-DHL-16 cells, 5-AzadC treatment resulted in promoter demethylation and re-expression of miR-342-3p and EVL. In 132 primary lymphoma samples, EVL/MIR342 was preferentially methylated in B cell lymphomas (N = 68; 68.7%) than T cell lymphoma (N = 8; 24.2%) by MSP (P < 0.0001). Moreover, EVL/MIR342 methylation was associated with lower miR-342-3p expression in 79 primary NHL (P = 0.0443). In SU-DHL-16 cells, the tumor suppressor function of miR-342-3p was demonstrated by the inhibition of cellular proliferation and increase of cell death upon over-expression of miR-342-3p. Mechanistically, overexpression of miR-342-3p resulted in a decrease of LC3-II, a biomarker of autophagy, which was pro-survival for SU-DHL-16. Pre-treatment with 3-methyladenine, an autophagy inhibitor, abrogated tumor suppression associated with miR-342-3p overexpression. By luciferase assay, MAP1LC3B, a precursor of LC3-II, was confirmed as a direct target of miR-342-3p. Finally, in SU-DHL-16 cells, overexpression of miR-342-3p downregulated the known target DNMT1, with promoter demethylation and re-expression of tumor suppressor E-cadherin.

Conclusions: Intronic miR-342-3p is co-regulated with its host gene EVL by tumor-specific promoter DNA methylation in B cell lymphoma. The tumor suppressor function of miR-342-3p was mediated via inhibition of pro-survival autophagy by targeting MAP1LC3B and downregulation of DNMT1 with demethylation and re-expression of tumor suppressor genes.

Keywords: Autophagy; B cell lymphoma; DNA methylation; Tumor suppressor miRNA; miR-342-3p.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Autophagy / drug effects
  • Autophagy / genetics
  • Cell Line, Tumor / drug effects
  • Cell Proliferation / drug effects
  • CpG Islands / genetics
  • DNA (Cytosine-5-)-Methyltransferase 1 / drug effects
  • DNA (Cytosine-5-)-Methyltransferase 1 / genetics
  • DNA Methylation / genetics*
  • Decitabine / pharmacology
  • Down-Regulation
  • Enzyme Inhibitors / pharmacology
  • Epigenesis, Genetic / genetics*
  • Female
  • Gene Silencing
  • Genes, Tumor Suppressor / drug effects
  • Humans
  • Lymphoma, B-Cell / drug therapy
  • Lymphoma, B-Cell / genetics*
  • Male
  • MicroRNAs / genetics*
  • Microtubule-Associated Proteins
  • Promoter Regions, Genetic / drug effects


  • Enzyme Inhibitors
  • MAP1LC3B protein, human
  • MIRN342 microRNA, human
  • MicroRNAs
  • Microtubule-Associated Proteins
  • Decitabine
  • DNA (Cytosine-5-)-Methyltransferase 1
  • DNMT1 protein, human