PhD Scientific Days 2025

Poster Session I. - D: Pathological and Oncological Sciences

Genome-Wide DNA Methylation Changes in Breast Cancer Analyzed Using 2677 Tissue Samples

Előadó neve

Müller Dalma, MSc

Neptun code

ZHUJHN

Előadó munkahelye

Semmelweis University

Előadó telefonszáma

+36702132172

Előadó e-mail címe

dalma.muller2@gmail.com

Az előadás címe

Genome-Wide DNA Methylation Changes in Breast Cancer Analyzed Using 2677 Tissue Samples

Szerző(k) neve és munkahelye

Dalma Müller MSc¹, Prof. Dr. Balázs Győrffy¹

1: Semmelweis University

Bemutatás módja

Poszter

Szekció

Poster Session I. - D: Pathological and Oncological Sciences

Language of the presentation

English

Preferred session

Pathological and Oncological Sciences

Összefoglaló szövege

Introduction: Epigenetic changes contribute to regulatory dysregulation in breast cancer cells. DNA methylation studies have advanced the understanding of cancer progression and the identification of novel biomarkers.
Aims: To assemble an integrated database of Illumina HumanMethylation450K data from breast cancer and normal tissues to analyze methylation differences between normal tissues and breast cancer subtypes.
Methods: We integrated methylation data (Illumina HumanMethylation450K array) from publicly available studies in the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas Breast Invasive Carcinoma (TCGA-BRCA) project. Raw data processing, quality control, and normalization were performed using R packages minfi and wateRmelon. Methylation patterns of normal tissues, primary tumor samples (stratified by estrogen receptor (ER) status, where available), and lymph node metastasis samples were compared using the Kruskal-Wallis test with Bonferroni correction.
Results: The database comprises 2,677 samples (221 normal, 2,412 primary tumors, and 44 lymph node metastases) from 14 GEO datasets and TCGA-BRCA. Analysis of 25,120 CpG islands (CGIs) revealed 605 hypermethylated CGIs in tumors compared to normal tissues (p < 0.001, Δβ ≥ 0.2). Subtype-specific comparisons identified 1,313 hypermethylated CGIs in ER-positive tumors and 775 in ER-negative tumors, with 559 shared between both subtypes. The most hypermethylated CGI across all tumors was chr1:169396621-169396869 (C1orf114; Δβ = 0.44). ER-positive tumors exhibited specific hypermethylation at chr19:50030981-50031300 (RCN3; Δβ = 0.4) and chr9:94183407-94183994 (NFIL3; Δβ = 0.4). ER-negative tumors showed unique hypermethylation at chr19:49646092-49646308 (PPFIA3; Δβ = 0.34) and chr11:3181574-3182120 (OSBPL5; Δβ = 0.32).
Conclusion: This large-scale analysis reveals distinct DNA methylation profiles in breast cancer subtypes, underscoring the role of epigenetic dysregulation in tumor heterogeneity. These findings provide a foundation for future functional studies to explore the clinical utility of methylation markers.

University

Semmelweis University

Supervisor

Prof. Dr. Balázs Győrffy

Publication of my abstract

I do not give consent to the publication of my abstract on the website of the congress.

phd.section.field

in doctoral studies after complex exam (PhD)

Kind

Szabad

Status

elfogadva

Accepted presentation method

poszter

Előadás fájl jóváhagyás

nem rendelkezett róla

Előadó

6817

Start

17:36

End

17:42