Retrospective Analysis of Transcriptomic Differences between Triple-Negative Breast Cancer (TNBC) and non-TNBC
2024
Çağlar Berkel
Objective: Triple-negative breast cancer (TNBC), which has no expression of estrogen receptor, progesterone receptor and HER2, is an aggressive subgroup. Molecular differences between TNBC and non-TNBC should be better understood to develop tailored treatment strategies. Materials and Methods: The expression of the most frequently mutated genes, and of genes for which copy number variation events are observed in the highest percentage of breast cancer patients, was compared between TNBC and non-TNBC samples, in R programming environment, using TCGA-BRCA transcriptomics dataset. Results: 70% of the most frequently mutated genes in breast cancer (CDH1, GATA3, MLL3 (KMT2C), MAP3K1, PTEN, NCOR1, FAT3, MAP2K4, NF1, ARID1A, LRP1B, RUNX1, MLL2 (KMT2D) and TBX3) was found to have decreased expression in TNBC compared to non-TNBC. The expression of 40% of the genes with the highest frequency of copy number gain events in breast cancer (SLC45A3, PTPRC, ELF3, FCGR2B, AKT3, FH, TPM3 and SETDB1) was increased in TNBC compared with non-TNBC. The half of the genes with the highest percentage of copy number loss events in breast cancer (CBFA2T3, CDH1, ZFHX3, CDH11, MAP2K4, GAS7, PER1, RABEP1, NCOR1 and PCM1) was observed to have decreased expression in TNBC compared to non-TNBC. Lastly, the expression of BRCA2, but not of BRCA1, was found to be higher in TNBC than in non-TNBC. Conclusion: This study provides further evidence in support of previous research, which show the presence of a large number of molecular differences between TNBC and non-TNBC, pointing to the need for more tailored treatment strategies for patients with TNBC.
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