Poster Presentation 45th Lorne Genome Conference 2024

Deciphering the molecular roles of the developmental epigenetic priming factors DPPA2/4 in cancer (#205)

Janith A Seneviratne 1 2 , Benjamin L Parker 3 , Aled J Parry 4 , Melanie Stammers 4 , Melanie A Eckersley-Maslin 1 3
  1. Peter MacCallum Cancer Centre, Melbourne, Australia
  2. Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
  3. Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Australia
  4. Babraham Institute, Cambridge, United Kingdom

The epigenetic plasticity of a cell determines how malleable its chromatin landscape is. Developmental Pluripotency Associated 2 and 4 (DPPA2/4) are heterodimerising DNA-binding proteins that are restricted to the early embryo where they facilitate epigenetic plasticity1,2. Through analyses of several cancer datasets, we found that DPPA2/4 are re-expressed in a subset of cancers, in particular non-small cell lung cancer (NSCLC) where co-expression of DPPA2/4 signifies poorer outcomes. We hypothesised that re-expression of these developmental regulators may be promoting heightened embryonic-like plasticity in these cancers.

To understand the functional roles of DPPA2/4 in cancer, we depleted DPPA2 and/or DPPA4 by RNAi or CRISPR-KO in the NCI-H661 NSCLC cell line and performed molecular and phenotypic characterisations. Endogenous DPPA2/4 protein immunoprecipitation and mass spectrometry were used to identify bound cofactors. Through this we confirmed DPPA2/4 forms heterodimers, with stoichiometry revealing strong heterodimeric preferences for DPPA2 that we found to be necessary for protein stability. The DPPA2 interactors also included the H3K36me2 histone demethylase, KDM2A3. ChIP-seq revealed both DPPA2 and KDM2A were co-enriched at CpG rich genic regions. RNA-seq revealed that DPPA2/4 depletion had minimal effects on gene transcription which posits a model where DPPA2/4 prime the epigenome for future gene expression changes following selective pressure. Supporting this, initial ATAC-seq nucleosome position analysis showed that DPPA2 binds both open and closed chromatin, suggesting pioneer activity. Consistently, depletion of DPPA2/4 led to a loss of chromatin accessibility at gene promoters associated with chromatin organisation and DNA damage/repair. Supporting an epigenetic priming model, phenotypic assays demonstrated increased chemosensitivity and reduced cell viability, colony formation and cell migration upon DPPA2/4 depletion indicating their importance in driving cancer cell adaptation. Collectively we show that DPPA2/4 contribute to malignant phenotypes in NSCLC through their molecular functions as epigenetic priming factors.

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