AccScience Publishing / EJMO / Online First / DOI: 10.36922/EJMO025470488
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ORIGINAL RESEARCH ARTICLE

Integrated transcriptomic analysis and RT-qPCR validation using FFPE patient tissues reveal the role of FOXQ1 and MCM10 in ovarian cancer

Dwi A. Suryandari1* ,  Luluk Yunaini1 ,  Khaerunissa Anbar Istiadi2 ,  Alfi Khatib3 ,  Fadilah Fadilah4,5
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1 Department of Medical Biology, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
2 Department of Biology, Faculty of Science, Institut Teknologi Sumatera, Terusan Ryacudu, Lampung, Indonesia
3 Drug Design and Synthesis Research Group, Department of Pharmaceutical Chemistry, Kulliyyah of Pharmacy, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
4 Department of Medical Chemistry, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
5 Bioinformatics Core Facilities, IMERI, Faculty of Medicine, Universitas Indonesia – Dr. Cipto Mangunkusumo Hospital, Jakarta, Indonesia
EJMO, 025470488 https://doi.org/10.36922/EJMO025470488
Received: 19 November 2025 | Revised: 24 January 2026 | Accepted: 27 February 2026 | Published online: 14 August 2026
© 2026 by the Author(s). This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution -Noncommercial 4.0 International License (CC-by the license) ( https://creativecommons.org/licenses/by-nc/4.0/ )
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Abstract

Introduction: Ovarian cancer has a high mortality rate due to late diagnosis and limited availability of reliable molecular biomarkers. Integrated transcriptomic analysis may facilitate the identification of key regulatory genes involved in tumor progression.

Objective: To identify and validate key regulatory genes associated with ovarian cancer progression through integrated transcriptomic analysis and experimental validation.

Methods: Differential gene expression analysis was conducted using the GSE18520 microarray dataset to compare ovarian cancer tissues with normal ovarian epithelium. Genes with log2 fold change ≥ 1, and adjusted p-value < 0.05 were considered significant. Functional enrichment and protein–protein interaction (PPI) network analyses were performed to prioritize hub genes. FOXQ1 and MCM10 were selected for experimental validation using quantitative real-time polymerase chain reaction (RT-qPCR) in formalin-fixed paraffin-embedded (FFPE) ovarian cancer tissues. Relative expression levels were calculated using the 2⁻ΔΔCt method and normalized to GAPDH.

Results: Transcriptomic analysis identified multiple differentially expressed genes associated with cell cycle regulation, DNA replication, and transcriptional control. FOXQ1 (log2 fold change = +5.00) and MCM10 (log2 fold change  = +2.74) were significantly upregulated and occupied central hub positions in the PPI network. RT-qPCR validation confirmed marked overexpression of FOXQ1 (45.3×) and MCM10 (11.3×) in FFPE ovarian cancer tissues.

Conclusion: This integrated transcriptomic and experimental validation study identifies FOXQ1 and MCM10 as key regulators in ovarian cancer, highlighting their potential as biomarkers for disease progression.

Keywords
Ovarian cancer
GSE18520
Differential gene expression
FOXQ1
MCM10
Quantitative reverse transcription polymerase chain reaction
Funding
None.
Conflict of interest
There is no conflict of interest in this research.
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Eurasian Journal of Medicine and Oncology, Electronic ISSN: 2587-196X Print ISSN: 2587-2400, Published by AccScience Publishing
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