Logo Medical Science Monitor

Call: +1.631.470.9640
Mon - Fri 10:00 am - 02:00 pm EST

Contact Us

Logo Medical Science Monitor Logo Medical Science Monitor Logo Medical Science Monitor

06 April 2020 : Database Analysis  

Identification of Genes with Prognostic Value in the Breast Cancer Microenvironment Using Bioinformatics Analysis

Haoyu Ren1BCDE, Daixing Hu2DEF, Yu Mao3CDE, Xinliang Su1AG*

DOI: 10.12659/MSM.920212

Med Sci Monit 2020; 26:e920212

Abstract

BACKGROUND: Stromal and immune cells play essential roles in the development of breast cancer (BC). This study was conducted to identify prognosis-related genes from the tumor microenvironment.

MATERIAL AND METHODS: The gene expression profiles of 622 BC samples were downloaded from TCGA (The Cancer Genome Atlas) database. Stromal and immune scores were calculated by using the ESTIMATE (Estimation of STromal and Immune cells in MAlignant Tumours using Expression data) algorithm. Then, differentially expressed genes (DEGs) between the high score group and the low score group were screened. The intersecting DEGs were selected through Venn diagrams, and survival analysis was conducted. Functional and pathway enrichment analyses were performed using the DAVID (Database for Annotation, Visualization and Integrated Discovery), and a protein–protein interaction (PPI) network was constructed with the STRING database and Cytoscape. These genes were validated for prognostic value by use of the KM (Kaplan-Meier) plotter tool.

RESULTS: The low immune score group was associated with a poor prognosis. However, there was no difference in the prognosis between the high and low stromal score groups. A total of 248 intersecting DEGs were found in BC, and 61 genes were significantly associated with the prognosis of BC patients in the TCGA database. These genes were enriched in the immune response, components of the plasma membrane, and receptor activity. Furthermore, in the validation group, 31 of 61 genes were significantly associated with prognosis.

CONCLUSIONS: Our bioinformatics analysis identified 31 tumor microenvironment-related genes as potential prognostic predictors for breast cancer patients. Some of these genes that have not been widely investigated previously, such as CXCL9, GPR18, S1PR4, SASH3, and PYH1N1, might be additional predictive factors for BC patients.

Keywords: Breast Neoplasms, Prognosis, tumor microenvironment, Biomarkers, Tumor, Breast, Computational Biology, Databases, Genetic, Gene Expression Regulation, Neoplastic, Kaplan-Meier Estimate, Protein Interaction Maps, Survival Analysis, transcriptome

0 Comments

Editorial

04 June 2022 : Editorial  

Editorial: Acute Hepatitis of Unknown Origin in Children. Is Autoimmunity at Play?

Nahum Mendez-Sanchez, Shreya C. Pal
Faculty of Medicine, National Autonomous University of Mexico, Mexico City, Mexico

DOI: 10.12659/MSM.937371

Med Sci Monit 2022; 28:e937371

SARS-CoV-2/COVID-19

30 June 2022 : Editorial  

Editorial: World Health Organization (WHO) Variants of Concern Lineages Under Monitoring (VOC-LUM) in Respo...

Med Sci Monit In Press; DOI: 10.12659/MSM.937676  

27 June 2022 : Clinical Research  

Shoulder Injury Related to Vaccine Administration (SIRVA) in 16 Patients Following COVID-19 Vaccination Who...

Med Sci Monit In Press; DOI: 10.12659/MSM.937430  

In Press

30 Jun 2022 : Laboratory Research  

Bcl-2 19-kDa Interacting Protein 3 (BNIP3)-Mediated Mitophagy Attenuates Intermittent Hypoxia-Induced Human...

Med Sci Monit In Press; DOI: 10.12659/MSM.936760  

30 Jun 2022 : Editorial  

Editorial: World Health Organization (WHO) Variants of Concern Lineages Under Monitoring (VOC-LUM) in Respo...

Med Sci Monit In Press; DOI: 10.12659/MSM.937676  

30 Jun 2022 : Clinical Research  

Antioxidant System and Ions Concentrations After Femoral Neck and Resurfacing Hip Arthroplasty

Med Sci Monit In Press; DOI: 10.12659/MSM.936335  

28 Jun 2022 : Meta-Analysis  

Urodynamics in Early Diagnosis of Diabetic Bladder Dysfunction in Women: A Systematic Review and Meta-Analysis

Med Sci Monit In Press; DOI: 10.12659/MSM.937166  

Most Viewed Current Articles

30 Dec 2021 : Clinical Research  

Retrospective Study of Outcomes and Hospitalization Rates of Patients in Italy with a Confirmed Diagnosis o...

DOI :10.12659/MSM.935379

Med Sci Monit 2021; 27:e935379

08 Mar 2022 : Review article  

A Review of the Potential Roles of Antioxidant and Anti-Inflammatory Pharmacological Approaches for the Man...

DOI :10.12659/MSM.936292

Med Sci Monit 2022; 28:e936292

01 Nov 2020 : Review article  

Long-Term Respiratory and Neurological Sequelae of COVID-19

DOI :10.12659/MSM.928996

Med Sci Monit 2020; 26:e928996

01 Jan 2022 : Editorial  

Editorial: Current Status of Oral Antiviral Drug Treatments for SARS-CoV-2 Infection in Non-Hospitalized Pa...

DOI :10.12659/MSM.935952

Med Sci Monit 2022; 28:e935952

Your Privacy

We use cookies to ensure the functionality of our website, to personalize content and advertising, to provide social media features, and to analyze our traffic. If you allow us to do so, we also inform our social media, advertising and analysis partners about your use of our website, You can decise for yourself which categories you you want to deny or allow. Please note that based on your settings not all functionalities of the site are available. View our privacy policy.

Medical Science Monitor eISSN: 1643-3750
Medical Science Monitor eISSN: 1643-3750