Abstract 6544: Identification of epigenetic regulatory networks associated with the basal-like breast cancer subtype
Authors: Okano Larissa Miyuki , Azevedo Alexandre Luiz , Carvalho Tamyres Mingorance , Berti Fernanda Brandão , Cavalli Luciane Regina 
Published: April 2023

Abstract
Purpose: Basal-like breast cancer (BLBC) is a biologically aggressive and molecular heterogeneous breast cancer subtype that confers to the patient´s poor prognosis. The crosstalk of epigenetic regulators, such as methylation events and microRNA (miRNA) deregulation, drives breast cancer progression and modulates aggressive tumor phenotypes. However, few studies have specifically characterized the epigenetic regulatory networks of genome-wide DNA methylation-based modifications, miRNAs and transcription factors (TF) expression in BLBC. Therefore, the main objective of this study was to identify and correlate the DNA methylation profiles and the transcriptional expression of miRNAs and TFs of the BLBC subtype.
Methods: To achieve our goal, a comprehensive computational pipeline using the R language was used. First, the transcriptional expression profiles and DNA methylation data of BLBC and non-tumor samples were downloaded from The Cancer Genome Atlas (TCGA). Then, the ELMER package was used to determine the differentially methylated distal probes between these two groups, identifying gene-probes pairs that can be regulated by un/methylated regions that affect the function of TFs. The different expressed (DE) miRNAs were identified using the DESeq2 package. To determine the regulatory pairs (gene, miRNA and TF interactions) the multiMiR, miRWalk, ENCODE, and hTFtarget were used and the regulatory networks were identified by the FANMOD algorithm. Finally, pathway enrichment analysis (PEA) was conducted using the Reactome database and microT-CDS (Diana Tools mirPath v.3).
Results: A total of 147 and 199 pairs of gene-probes were identified in hypermethylation and hypomethylation analyses, respectively. Fifty genes and 59 regulatory TFs whose expression was associated with DNA methylation were selected, including members of the E2F (E2Fs) and Krüppel-like factor (KLFs) family. Eleven DE miRNAs, out of the 51 identified, were selected based on their interaction with genes and TFs. These pairs of miRNAs, TF, and genes generated three types of feed-forward loops (FFLs): coherent FFLs, mediated by miRNAs; incoherent FFLs, mediated by TFs; and compost FFLs, mediated by TF and miRNAs. Finally, the PEA analysis showed 51 pathways in which miRNAs, genes, or TFs may interact, including pathways related to DNA repair, cell cycle, pathways in cancer, as well as the defective binding of RB1 mutants to E2F1, and the ErbB signaling pathway.
Conclusion: Our findings demonstrated the epigenetic regulation of methylation patterns and miRNA expression and their impact on the expression of TFs that may exert critical roles in the BLBC. The functional analysis of these regulatory networks in well-established BLBC models, targeting the signaling pathways identified, can determine whether they modulate the BLBC phenotype and can be used as potential clinical targets.
Citation Format: Larissa Miyuki Okano, Alexandre Luiz Azevedo, Tamyres Mingorance Carvalho, Fernanda Brandão Berti, Luciane Regina Cavalli. Identification of epigenetic regulatory networks associated with the basal-like breast cancer subtype. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6544.