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Establishment and validation of an individualized macrophage-related gene signature to predict overall survival in patients with triple negative breast cancer

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Title: Establishment and validation of an individualized macrophage-related gene signature to predict overall survival in patients with triple negative breast cancer
Authors: Peng Su, Ziqi Peng, Boyang Xu, Bowen Yang, Feng Jin
Source: PeerJ, Vol 9, p e12383 (2021)
Publisher Information: PeerJ Inc., 2021.
Publication Year: 2021
Collection: LCC:Medicine
LCC:Biology (General)
Subject Terms: Triple negative breast Cancer, Macrophages, Nomogram, Tumor microenvironment, Vinorelbine, Medicine, Biology (General), QH301-705.5
More Details: Background Recently, researchers have classified highly heterogeneous triple negative breast cancer (TNBC) into different subtypes from different perspectives and investigated the characteristics of different subtypes to pursue individualized treatment. With the increase of immunotherapy and its preliminary application in TNBC treatment, the value of immune-related strategies in the treatment of TNBC has been initially reflected. Based thereon, this study plans to classify and further explore TNBC from the perspective of immune cell infiltration. Method The fractions of immune cells of TNBC patients were assessed by six immune component analysis methods in The Cancer Genome Atlas (TCGA) database. Hub genes significantly related to poor prognosis were verified by weighted gene co-expression network analysis (WGCNA) analysis, Lasso analysis, and univariate KM analysis. Two cohorts of TNBC patients with complete prognosis information were collected for validation analysis. Finally, the Genomics of Drug Sensitivity in Cancer (GDSC) database was adopted to ascertain the sensitivity differences of different populations based on hub-gene grouping to different chemotherapy drugs. Results Five hub genes (CD79A, CXCL13, IGLL5, LHFPL2, and PLEKHF1) of the key co-expression gene module could divide TNBC patients into two groups (Cluster A and Cluster B) based on consistency cluster analysis. The patients with Cluster A were responsible for significantly worse prognosis than the patients with Cluster B (P = 0.023). In addition, another classification method, PCoA, and two other datasets (GSE103091 and GSE76124), were used to obtain consistent results with previous findings, which verified the stability of the classification method and dataset in this study. The grouping criteria based on the previous results were developed and the accuracy of the cut-off values was validated. A prognosis model of TNBC patients was then constructed based on the grouping results of five hub genes and N staging as prognostic factors. The results of ROC and decision curve analyses showed that this model had high prediction accuracy and patients could benefit therefrom. Finally, GDSC database analysis proved that patients in Cluster A were more sensitive to Vinorelbine. Separate analysis of the sensitivity of patients in Cluster A to Gemcitabine and Vinorelbine showed that the patients in Cluster A exhibited higher sensitivity to Vinorelbine. We hypothesized that these five genes were related to gemcitabine resistance and they could serve as biomarkers for clinical drug decision-making after anthracene resistance and taxane resistance in patients with advanced TNBC. Conclusion This study found five hub prognostic genes associated with macrophages, and a prognostic model was established to predict the survival of TNBC patients. Finally, these five genes were related to gemcitabine resistance in TNBC patients.
Document Type: article
File Description: electronic resource
Language: English
ISSN: 2167-8359
Relation: https://peerj.com/articles/12383.pdf; https://peerj.com/articles/12383/; https://doaj.org/toc/2167-8359
DOI: 10.7717/peerj.12383
Access URL: https://doaj.org/article/b0fc2fc110e84301b96bd81c5a68a4ca
Accession Number: edsdoj.b0fc2fc110e84301b96bd81c5a68a4ca
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  Data: Establishment and validation of an individualized macrophage-related gene signature to predict overall survival in patients with triple negative breast cancer
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  Data: <searchLink fieldCode="DE" term="%22Triple+negative+breast+Cancer%22">Triple negative breast Cancer</searchLink><br /><searchLink fieldCode="DE" term="%22Macrophages%22">Macrophages</searchLink><br /><searchLink fieldCode="DE" term="%22Nomogram%22">Nomogram</searchLink><br /><searchLink fieldCode="DE" term="%22Tumor+microenvironment%22">Tumor microenvironment</searchLink><br /><searchLink fieldCode="DE" term="%22Vinorelbine%22">Vinorelbine</searchLink><br /><searchLink fieldCode="DE" term="%22Medicine%22">Medicine</searchLink><br /><searchLink fieldCode="DE" term="%22Biology+%28General%29%22">Biology (General)</searchLink><br /><searchLink fieldCode="DE" term="%22QH301-705%2E5%22">QH301-705.5</searchLink>
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  Data: Background Recently, researchers have classified highly heterogeneous triple negative breast cancer (TNBC) into different subtypes from different perspectives and investigated the characteristics of different subtypes to pursue individualized treatment. With the increase of immunotherapy and its preliminary application in TNBC treatment, the value of immune-related strategies in the treatment of TNBC has been initially reflected. Based thereon, this study plans to classify and further explore TNBC from the perspective of immune cell infiltration. Method The fractions of immune cells of TNBC patients were assessed by six immune component analysis methods in The Cancer Genome Atlas (TCGA) database. Hub genes significantly related to poor prognosis were verified by weighted gene co-expression network analysis (WGCNA) analysis, Lasso analysis, and univariate KM analysis. Two cohorts of TNBC patients with complete prognosis information were collected for validation analysis. Finally, the Genomics of Drug Sensitivity in Cancer (GDSC) database was adopted to ascertain the sensitivity differences of different populations based on hub-gene grouping to different chemotherapy drugs. Results Five hub genes (CD79A, CXCL13, IGLL5, LHFPL2, and PLEKHF1) of the key co-expression gene module could divide TNBC patients into two groups (Cluster A and Cluster B) based on consistency cluster analysis. The patients with Cluster A were responsible for significantly worse prognosis than the patients with Cluster B (P = 0.023). In addition, another classification method, PCoA, and two other datasets (GSE103091 and GSE76124), were used to obtain consistent results with previous findings, which verified the stability of the classification method and dataset in this study. The grouping criteria based on the previous results were developed and the accuracy of the cut-off values was validated. A prognosis model of TNBC patients was then constructed based on the grouping results of five hub genes and N staging as prognostic factors. The results of ROC and decision curve analyses showed that this model had high prediction accuracy and patients could benefit therefrom. Finally, GDSC database analysis proved that patients in Cluster A were more sensitive to Vinorelbine. Separate analysis of the sensitivity of patients in Cluster A to Gemcitabine and Vinorelbine showed that the patients in Cluster A exhibited higher sensitivity to Vinorelbine. We hypothesized that these five genes were related to gemcitabine resistance and they could serve as biomarkers for clinical drug decision-making after anthracene resistance and taxane resistance in patients with advanced TNBC. Conclusion This study found five hub prognostic genes associated with macrophages, and a prognostic model was established to predict the survival of TNBC patients. Finally, these five genes were related to gemcitabine resistance in TNBC patients.
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        Value: 10.7717/peerj.12383
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      – Text: English
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      Pagination:
        StartPage: e12383
    Subjects:
      – SubjectFull: Triple negative breast Cancer
        Type: general
      – SubjectFull: Macrophages
        Type: general
      – SubjectFull: Nomogram
        Type: general
      – SubjectFull: Tumor microenvironment
        Type: general
      – SubjectFull: Vinorelbine
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      – TitleFull: Establishment and validation of an individualized macrophage-related gene signature to predict overall survival in patients with triple negative breast cancer
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