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

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.

A predictable conserved DNA base composition signature defines human core DNA replication origins

“…As aberrant DNA replication is a hallmark of many cancer cells, we next asked whether the origin repertoire was disturbed after cell immortalisation, a key step in cancer development leading to uncontrolled cell proliferation. To this aim, we used three previously described immortalised cell lines obtained by mis-expression of oncogenes 42 of the parental Human Mammary Epithelial Cell (HMEC) cell line: (i) ImM-1 in which p53 levels was reduced by at least 50% (ΔTP53), (ii) ImM-2 in which the oncogene RAS is overexpressed and (iii) ImM-3 in which WNT is overexpressed 42 . We identified more origins in the immortalised cell types than in the untransformed cell types (hESC, HC and HMEC; on average 100,000 vs 70,000 origins).…”

Integration of Epigenetic Mechanisms into Non-Genotoxic Carcinogenicity Hazard Assessment: Focus on DNA Methylation and Histone Modifications

“…Indeed, 7 NGTxC with different modes of action induced different DNAm profiles 10 to 15 days after transformation of the v-Ha-RAS-transfected BALB/c 3T3 Bhas42 cell line [230,231]. Similarly, Fonti et al [232] investigated the chronology of genomic changes after immortalizing primary human mammary epithelial cells (HMEC) with a shRNA inactivating TP53, and adding a second oncogenic vector to activate different oncogenic pathways, either CCNE1 (coding for CYCLIN E1), WNT1, or HRAS v12 . They observed changes in miRNA and mRNA expression, followed by DNAm changes, and later by gene copy number alterations (CNA).…”

“…They observed changes in miRNA and mRNA expression, followed by DNAm changes, and later by gene copy number alterations (CNA). The HMEC transformed by HRAS had clearly distinct patterns of genetic and epigenetic modifications compared to CCNE1 or WNT1 transformed cell lines, whereas the latter two induced similar CNA and DNAm patterns [232]. These findings indicate that oncogenic pathways and epigenetic changes can change depending upon the early activation of pathways in different transformed cell lines, and this complicates the identification of a "standardised" carcinogenic epigenetic signature for NGTxC using different models and with different modes of action.…”

“…Many cell lines undergo genetic drift that may induce interlaboratory variability [642], and reproducibility issues through time. Epigenetics and gene expression profiles differ depending on the gene initially mutated that drives the early carcinogenic process [232], hence these activated pathways may affect cellular responses when testing chemicals. Consequently, data related to effects of chemical exposure using cell lines may reflect anomalies in this cell type and may therefore not be relevant to chemical-induced mechanisms in normal cells.…”

Inhibiting HER3 Hyperphosphorylation in HER2‐Overexpressing Breast Cancer through Multimodal Therapy with Branched Gold Nanoshells

“…The overexpression of the HER1, HER2, and HER3 receptors, and the amplification of their related genes is directly linked to the aggressive and metastatic nature of many human epithelial-based tumors. [1,2] All these receptors embody an extracellular ligand-binding region that includes four domains (i.e., I/L1, II/CR1, III/L2, and IV/CR2), a transmembrane domain, and an intracellular receptor domain with tyrosine-kinase activity (except for HER3). When a ligand binds to the extracellular region, a receptor-receptor interaction is promoted resulting in dimerization and activating a downstream signaling including phosphoinositide-3-kinase-protein kinase B/Akt (PI3K/AKT) and RAS/mitogen activated protein kinase, involved in cell survival and cell proliferation, respectively (see Figure S1 in the Supporting Information).…”