Vitamin D receptor ( <i>VDR</i>) mRNA overexpression is associated with poor prognosis in breast carcinoma

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Abstract

Purpose

The prognostic value of vitamin D receptor gene ( VDR) expression in breast cancer development is unclear. Here, we aimed to investigate whether VDR expression can be used as a prognostic indicator of breast cancer.

Methods

We used various public bioinformatics platforms: Oncomine, GEPIA, UALCAN, Kaplan-Meier plotter, UCSC XENA, bc-GenExMiner, WebGestalt, and STRING database.

Results

We found that VDR was upregulated in breast cancer in comparison to normal tissues. Overexpression of VDR was significantly associated with worse overall survival in breast cancer. The expression of VDR was related to age, TNM stages, estrogen receptor status, progesterone receptor status, human epidermal growth factor receptor 2 status, basal-like (PAM 50) status, triple-negative breast cancer (TNBC) status, and basal-like (PAM 50) & TNBC status (P < 0.05). Increased VDR expression in breast cancer was significantly associated with older age. The 5 hub genes for VDR were NCOA1, EP300, CREBBP, and RXRA.

Conclusion

Our investigation offers hints about the prognostic role of VDR in breast cancer. The findings suggest that VDR expression might be used as a marker to determine a breast cancer patient’s prognosis. Nevertheless, further validation is warranted.

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Most cited references 27

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Cytoscape: a software environment for integrated models of biomolecular interaction networks.

Paul Shannon, Andrew Markiel, Owen Ozier … (2003)

Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.

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GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses

Zefang Tang, Chenwei Li, Boxi Kang … (2017)

Abstract Tremendous amount of RNA sequencing data have been produced by large consortium projects such as TCGA and GTEx, creating new opportunities for data mining and deeper understanding of gene functions. While certain existing web servers are valuable and widely used, many expression analysis functions needed by experimental biologists are still not adequately addressed by these tools. We introduce GEPIA (Gene Expression Profiling Interactive Analysis), a web-based tool to deliver fast and customizable functionalities based on TCGA and GTEx data. GEPIA provides key interactive and customizable functions including differential expression analysis, profiling plotting, correlation analysis, patient survival analysis, similar gene detection and dimensionality reduction analysis. The comprehensive expression analyses with simple clicking through GEPIA greatly facilitate data mining in wide research areas, scientific discussion and the therapeutic discovery process. GEPIA fills in the gap between cancer genomics big data and the delivery of integrated information to end users, thus helping unleash the value of the current data resources. GEPIA is available at http://gepia.cancer-pku.cn/.

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UALCAN: A Portal for Facilitating Tumor Subgroup Gene Expression and Survival Analyses1

Darshan S. Chandrashekar, Bhuwan Bashel, Sai Balasubramanya … (2017)

Genomics data from The Cancer Genome Atlas (TCGA) project has led to the comprehensive molecular characterization of multiple cancer types. The large sample numbers in TCGA offer an excellent opportunity to address questions associated with tumo heterogeneity. Exploration of the data by cancer researchers and clinicians is imperative to unearth novel therapeutic/diagnostic biomarkers. Various computational tools have been developed to aid researchers in carrying out specific TCGA data analyses; however there is need for resources to facilitate the study of gene expression variations and survival associations across tumors. Here, we report UALCAN, an easy to use, interactive web-portal to perform to in-depth analyses of TCGA gene expression data. UALCAN uses TCGA level 3 RNA-seq and clinical data from 31 cancer types. The portal's user-friendly features allow to perform: 1) analyze relative expression of a query gene(s) across tumor and normal samples, as well as in various tumor sub-groups based on individual cancer stages, tumor grade, race, body weight or other clinicopathologic features, 2) estimate the effect of gene expression level and clinicopathologic features on patient survival; and 3) identify the top over- and under-expressed (up and down-regulated) genes in individual cancer types. This resource serves as a platform for in silico validation of target genes and for identifying tumor sub-group specific candidate biomarkers. Thus, UALCAN web-portal could be extremely helpful in accelerating cancer research. UALCAN is publicly available at http://ualcan.path.uab.edu.

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Author and article information

Journal

Journal ID (nlm-ta): Ann Surg Treat Res

Journal ID (iso-abbrev): Ann Surg Treat Res

Journal ID (publisher-id): ASTR

Title: Annals of Surgical Treatment and Research

Publisher: The Korean Surgical Society

ISSN (Print): 2288-6575

ISSN (Electronic): 2288-6796

Publication date (Print): October 2022

Publication date (Electronic): 07 October 2022

Volume: 103

Issue: 4

Pages: 183-194

Affiliations

[1 ]Department of Surgery, Konkuk University School of Medicine, Seoul, Korea.

[2 ]Research Institute of Medical Science, Konkuk University School of Medicine, Seoul, Korea.

[3 ]Department of Surgery, Konkuk University Medical Center, Seoul, Korea.

[4 ]Department of Surgery, Kyung Hee University School of Medicine, Seoul, Korea.

Author notes

Corresponding Author: Kyoung Sik Park. Department of Surgery, Konkuk University Medical Center, Konkuk University School of Medicine, 120-1 Neungdong-ro, Gwangjin-gu, Seoul 05030, Korea. Tel: +82-2-2030-7697, Fax: +82-2-2030-8270, kspark@ 123456kuh.ac.kr

Author information

Sang Eun Nam https://orcid.org/0000-0001-8253-6420

TongYi Jin https://orcid.org/0000-0002-6285-3901

Kyoung Sik Park https://orcid.org/0000-0001-9806-9839

Madhuri Saindane https://orcid.org/0000-0002-3691-9436

Woo Chul Noh https://orcid.org/0000-0003-3770-1612

Young Bum Yoo https://orcid.org/0000-0002-9137-9268

Won Seo Park https://orcid.org/0000-0002-0774-7911

Ik Jin Yun https://orcid.org/0000-0003-4013-6714

Article

DOI: 10.4174/astr.2022.103.4.183

PMC ID: 9582618

PubMed ID: 36304189

SO-VID: 08126e33-cfd6-40ef-8eb8-47bf9adedd14

License:

Annals of Surgical Treatment and Research is an Open Access Journal. All articles are distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/4.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

History

Date received : 11 August 2022

Date revision received : 07 September 2022

Date accepted : 17 September 2022

Funding

Funded by: Konkuk University Medical Center, CrossRef https://doi.org/10.13039/100019704;

Vitamin D receptor ( VDR) mRNA overexpression is associated with poor prognosis in breast carcinoma

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Abstract

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Most cited references 27

Cytoscape: a software environment for integrated models of biomolecular interaction networks.

GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses

UALCAN: A Portal for Facilitating Tumor Subgroup Gene Expression and Survival Analyses1

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