Analysis of gene expression to explore the contribution of cancer-associated fibroblasts to breast cancer progression: a computational analysis

Nail Beşli; Nilufer Ercin; Bahar Sarikamis Johnson; Ulkan Celik

doi:10.17944/interdiscip.1828109

Analysis of gene expression to explore the contribution of cancer-associated fibroblasts to breast cancer progression: a computational analysis

Abstract

Objective: Cancer-associated fibroblasts (CAFs) are critical components of the tumor microenvironment that greatly influence breast cancer progression. In this study, we used in silico analysis to determine the potential pathways and genes that could affect breast cancer progression associated with CAFs. Method: Data from breast cancer patients, collected through microarray and next-generation sequencing (NGS), were retrieved using the Gene Expression Omnibus (GEO) platform. The differentially expressed genes (DEGs) were determined and further analyzed through Gene Ontology (GO) and pathway analysis, and potential therapeutic targets were predicted via hub genes. Results: In CAFs, 940 genes were upregulated, and 561 genes were downregulated. These genes were significantly linked to pathways such as MAPK signaling, estrogen signaling, NF-kB signaling, IL-17 signaling, and TGF-ß signaling. These pathways suggest that CAFs are involved in the progression of breast cancer. The hub genes, namely ESR1, MET, IL1B, SMAD3, and FOS, were found to be enriched in key pathways and were associated with certain anti-tumor drugs that are either undergoing clinical trials or have been approved for clinical use. Conclusion: This findings suggest that critical genes such as ESR1, MET, IL1B, SMAD3, and FOS are predicted to contribute to CAF-mediated regulatory networks in breast cancer.

Keywords

Supporting Institution

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Ethical Statement

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Thanks

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Details

Primary Language

English

Subjects

Medical Genetics (Excl. Cancer Genetics)

Journal Section

Research Article

Authors

Nail Beşli ^*
0000-0002-6174-915X
Türkiye

Nilufer Ercin
0000-0003-0137-4963
Türkiye

Bahar Sarikamis Johnson
0000-0003-4407-3829
Türkiye

Ulkan Celik
0000-0002-6895-8560
Türkiye

Publication Date

August 23, 2026

Submission Date

November 25, 2025

Acceptance Date

May 4, 2026

Published in Issue

Year 2026 Volume: 17 Number: 58

DOI

https://doi.org/10.17944/interdiscip.1828109

IZ

https://izlik.org/JA84UX72KE

Cite

RIS / Bibtex

APA

Beşli, N., Ercin, N., Sarikamis Johnson, B., & Celik, U. (2026). Analysis of gene expression to explore the contribution of cancer-associated fibroblasts to breast cancer progression: a computational analysis. Interdisciplinary Medical Journal, 17(58), 115-128. https://doi.org/10.17944/interdiscip.1828109

AMA

1.Beşli N, Ercin N, Sarikamis Johnson B, Celik U. Analysis of gene expression to explore the contribution of cancer-associated fibroblasts to breast cancer progression: a computational analysis. Interdiscip Med J. 2026;17(58):115-128. doi:10.17944/interdiscip.1828109

Chicago

Beşli, Nail, Nilufer Ercin, Bahar Sarikamis Johnson, and Ulkan Celik. 2026. “Analysis of Gene Expression to Explore the Contribution of Cancer-Associated Fibroblasts to Breast Cancer Progression: A Computational Analysis”. Interdisciplinary Medical Journal 17 (58): 115-28. https://doi.org/10.17944/interdiscip.1828109.

EndNote

Beşli N, Ercin N, Sarikamis Johnson B, Celik U (August 1, 2026) Analysis of gene expression to explore the contribution of cancer-associated fibroblasts to breast cancer progression: a computational analysis. Interdisciplinary Medical Journal 17 58 115–128.

IEEE

[1]N. Beşli, N. Ercin, B. Sarikamis Johnson, and U. Celik, “Analysis of gene expression to explore the contribution of cancer-associated fibroblasts to breast cancer progression: a computational analysis”, Interdiscip Med J, vol. 17, no. 58, pp. 115–128, Aug. 2026, doi: 10.17944/interdiscip.1828109.

ISNAD

Beşli, Nail - Ercin, Nilufer - Sarikamis Johnson, Bahar - Celik, Ulkan. “Analysis of Gene Expression to Explore the Contribution of Cancer-Associated Fibroblasts to Breast Cancer Progression: A Computational Analysis”. Interdisciplinary Medical Journal 17/58 (August 1, 2026): 115-128. https://doi.org/10.17944/interdiscip.1828109.

JAMA

1.Beşli N, Ercin N, Sarikamis Johnson B, Celik U. Analysis of gene expression to explore the contribution of cancer-associated fibroblasts to breast cancer progression: a computational analysis. Interdiscip Med J. 2026;17:115–128.

MLA

Beşli, Nail, et al. “Analysis of Gene Expression to Explore the Contribution of Cancer-Associated Fibroblasts to Breast Cancer Progression: A Computational Analysis”. Interdisciplinary Medical Journal, vol. 17, no. 58, Aug. 2026, pp. 115-28, doi:10.17944/interdiscip.1828109.

Vancouver

1.Nail Beşli, Nilufer Ercin, Bahar Sarikamis Johnson, Ulkan Celik. Analysis of gene expression to explore the contribution of cancer-associated fibroblasts to breast cancer progression: a computational analysis. Interdiscip Med J. 2026 Aug. 1;17(58):115-28. doi:10.17944/interdiscip.1828109