Differential expression and methylation profile of Heat Shock Proteins genes in breast cancer molecular subtypes

GUERRERO GIMENEZ, MARTIN EDUARDO; ZOPPINO, FELIPE CARLOS MARTIN; CIOCCA, DANIEL RAMON

Bogota

Conferencia; Second Latin America Conference of the Cell Stress Society International; 2016

Cell Stress Society International

Aim: to evaluate the differential expression levels of the Heat Shock Proteins (HSPs) genes and their methylation status in the different breast cancer (BC) molecular subtypes to identify HSPs coding genomic regions associated with the disease. Methods: Software exclusively supported in R were used to carry out the various analyzes. The data were extracted from the publicly available TCGA data set of mammary adenocarcinoma downloaded on May 01, 2015 (https://tcga-data.nci.nih.gov/tcga/). The ?TCGA assambler" v.1.0.3 package was used to programmatically download level 3's standardized and non-standardized gene expression levels from 1097 tumor samples and 114 normal breast tissue data available in the RNASeqV2 platform. The level 3 methylation profile for each sample available in the JHU_USC__HumanMethylation4 50k platform was downloaded manually from the TCGA website on October 10, 2014 (81 normal tissue samples and 726 tumor samples). Given the expression levels of 50 different specific genes PAM50 classification was performed to classify the samples (LumA, LumB, Basal Like, Her2, Normal Like). To assess the differential gene expression (DGE) between normal tissue and tumor samples we implemented DESeq2 and EdgeR. DGE analysis, in both cases log2 Fold change values were obtained associated with exact p-values and False Discovery Rate values (FDR). Methylation levels of each tumor subtype relative to normal breast tissue were compared. For this task the algorithm "bumphunter" was performed using the R "MINFI" package. Bumphunter provides a robust method for detecting differentially methylated loci by performing a probe-level regression and smoothing the coefficient of interest within clusters to identify bumps along the genome. A Pearson correlation of the methylation values of each CpG site opposed to the gene expression was performed to assess the overall impact of the CpG site methylation in gene expression. Results: We found important HSPs differential gene expression levels in BC, the magnitude of these variations were related with the BC molecular subtypes. Importantly we identify that almost all of the Chaperonines and the HSPCs were up regulated in BC and that this deregulation was not associated with changes in the methylation profiles of the genes. Another important finding of our study is that there was a small cluster of small heat shock proteins (HSPBs) that appeared strongly down regulated in BC and this could be due to gene methylation. Finally we could identify CRYAB, HSPB2 and HSPB6 among the most both methylated and down regulated HSPs genes in breast cancer.