Distinct oncogenes drive different genome and epigenome alterations in human mammary epithelial cells.

Claire Fonti,Emeline Schmitt,Béatrice Orsetti,Anne Saumet,Amanda Abi‐Khalil,Michael Weber,Charles Theillet,Ambre Bender,Stanislas Du Manoir,Elouan Cleroux,Michael Dumas,Jacques Colinge,William Jacot,Claude Sardet

doi:10.1002/ijc.32413

Abstract

Molecular subtypes of breast cancer are defined on the basis of gene expression and genomic/epigenetic pattern differences. Different subtypes are thought to originate from distinct cell lineages, but the early activation of an oncogene could also play a role. It is difficult to discriminate the respective inputs of oncogene activation or cell type of origin. In this work, we wished to determine whether activation of distinct oncogenic pathways in human mammary epithelial cells (HMEC) could lead to different patterns of genetic and epigenetic changes. To this aim, we transduced shp53 immortalized HMECs in parallel with the CCNE1, WNT1 and RASv12 oncogenes which activate distinct oncogenic pathways and characterized them at sequential stages of transformation for changes in their genetic and epigenetic profiles. We show that initial activation of CCNE1, WNT1 and RASv12, in shp53 HMECs results in different and reproducible changes in mRNA and micro-RNA expression, copy number alterations (CNA) and DNA methylation profiles. Noticeably, HMECs transformed by RAS bore very specific profiles of CNAs and DNA methylation, clearly distinct from those shown by CCNE1 and WNT1 transformed HMECs. Genes impacted by CNAs and CpG methylation in the RAS and the CCNE1/WNT1 clusters showed clear differences, illustrating the activation of distinct pathways. Our data show that early activation of distinct oncogenic pathways leads to active adaptive events resulting in specific sets of CNAs and DNA methylation changes. We, thus, propose that activation of different oncogenes could have a role in reshaping the genetic landscape of breast cancer subtypes.

Highlights

Genetic instability lies at the core of neoplastic development with up to 85% of human cancers showing loss of chromosome integrity at varying levels such as aberrant copy numbers and aneuploidy
Using primary human mammary epithelial cells (HMEC), that classified as luminal progenitors 33 (Supporting Information Fig.10E), we show that cell transformation by way of distinct oncogenes resulted in different patterns of aberrations at both the copy number alterations (CNA) and DNA methylation levels, as well as distinct phenotypes
HMECs transformed by RASv12 presented clearly distinct patterns of genetic and epigenetic modifications compared to their shp53-CCNE1 or shp53-WNT1 counterparts

Summary

Introduction

Genetic instability lies at the core of neoplastic development with up to 85% of human cancers showing loss of chromosome integrity at varying levels such as aberrant copy numbers and aneuploidy. Founding events due to early activation of distinct oncogenic pathways in a single cell type could have an impact on genomic and epigenetic changes and induce the selection of anomalies functionally coherent with the activated pathway 12-15. This is supported by studies showing that expression of RASv12 and of BRAFv600 resulted in the transcriptional repression and hypermethylation of distinct gene sets, involving different cascades of repressors and DNA methylases 16,17. These results support a model in which genetic and epigenetic changes in cancer cells reflect adaptive responses to the oncogenic driver

Methods

Results

Conclusion