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ORIGINAL RESEARCH article

Front. Genet.
Sec. Computational Genomics
Volume 15 - 2024 | doi: 10.3389/fgene.2024.1505011
This article is part of the Research Topic Computational Approaches Integrate Multi-Omics Data for Disease Diagnosis and Treatment View all 4 articles

The analysis of gene co-expression network and immune infiltration revealed biomarkers between triple-negative and non-triple negative breast cancer

Provisionally accepted
Yifeng Zhang Yifeng Zhang Lianhua Xie Lianhua Xie *Shuxian Lu Shuxian Lu *Yao Yi Yao Yi *
  • Jiangxi University of Traditional Chinese Medicine, Nanchang, China

The final, formatted version of the article will be published soon.

    Background: Triple-negative breast cancer (TNBC) is a heterogeneous disease with a worse prognosis. Despite ongoing efforts, existing therapeutic approaches show limited success in improving early recurrence and survival outcomes for TNBC patients. Therefore, there is an urgent need to discover novel and targeted therapeutic strategies, particularly those focusing on the immune infiltrate in TNBC, to enhance diagnosis and prognosis for affected individuals. Results: The gene co-expression network and gene ontology analyses revealed 19 modules identified using the dataset GSE76275. Of these, modules 5, 11, and 12 showed significant differences between in breast cancer tissue between TNBC and non-TNBC. Notably, module 11 showed significant enrichment in the WNT signaling pathway, while module 12 demonstrated enrichment in lipid/fatty acid metabolism pathways. Subsequently, we identified SHC4/KCNK5 and ABCC11/ABCA12 as key genes in module 11 and module 12, respectively. These key genes proved to be crucial in accurately distinguishing between TNBC and non-TNBC, as evidenced by the promising average AUC value of 0.963 obtained from the logistic regression model based on their combinations. Furthermore, we found compelling evidence indicating the prognostic significance of three key genes, KCNK5, ABCC11, and ABCA12, in TNBC. Finally, we also identified the immune cell compositions in breast cancer tissue between TNBC and non-TNBC. Our findings revealed a notable increase in M0 and M1 macrophages in TNBC compared to non-TNBC, while M2 macrophages exhibited a significant reduction in TNBC. Particularly intriguing discovery emerged with respect to the transcription factor FOXM1, which demonstrated a significant regulatory role in genes positively correlated with the proportions of M0 and M1 macrophages, while displaying a negative correlation with the proportion of M2 macrophages in breast cancer tissue. Conclusions: Our research provides new insight into the biomarkers and immune infiltration of TNBC, which could be useful for clinical diagnosis of TNBC.

    Keywords: Gene Co-expression Network, Immune infiltration, biomarkers, Macrophages, Triple negative breast cancer

    Received: 01 Oct 2024; Accepted: 09 Dec 2024.

    Copyright: © 2024 Zhang, Xie, Lu and Yi. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence:
    Lianhua Xie, Jiangxi University of Traditional Chinese Medicine, Nanchang, China
    Shuxian Lu, Jiangxi University of Traditional Chinese Medicine, Nanchang, China
    Yao Yi, Jiangxi University of Traditional Chinese Medicine, Nanchang, China

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.