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Updated: Jan 31, 2026
Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization
Published on: October 3, 2025
Transcriptome analysis of differentially expressed genes and pathways associated with mitoxantrone treatment prostate
Sanqiang Li1,2, Ruifang Li3, Yu Ma1
1Key laboratory of Infection and Immunization, Department of Immunology, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China.
Abstract:
The global physiological function of specifically expressed genes of mitoxantrone (MTX)-resistant prostate cancer (PCa) is unclear. In this study, gene expression pattern from microarray data was investigated for identifying differentially expressed genes (DEGs) in MTX-resistant PCa xenografts. Human PCa cell lines DU145 and PC3 were cultured in vitro and xenografted into severe combined immunodeficiency (SCID) mice, treated with MTX intragastrically, three times a week until all mice relapsed. Gene expression profiles of the xenografts from castrated mice were performed with Affymetrix human whole genomic oligonucleotide microarray. The Cytoscape software was used to investigate the relationship between proteins and the signalling transduction network. A total of 355 overlapping genes were differentially expressed in MTX-resistant DU145R and PC3R xenografts. Of these, 16 genes were selected to be validated by quantitative real-time PCR (qRT-PCR) in these xenografts, and further tested in a set of formalin-fixed, paraffin-embedded and optimal cutting temperature (OCT) clinical tumour samples. Functional and pathway enrichment analyses revealed that these DEGs were closely related to cellular activity, androgen synthesis, DNA damage and repair, also involved in the ERK/MAPK, PI3K/serine-threonine protein kinase, also known as protein kinase B, PKB (AKT) and apoptosis signalling pathways. This exploratory analysis provides information about potential candidate genes and may bring new insights into the molecular cascade involvement in MTX-resistant PCa.
Insights
Researchers identified 355 differentially expressed genes in mitoxantrone (MTX)-resistant prostate cancer (PCa) xenografts. These genes are linked to cellular activity, DNA repair, and key signaling pathways, offering potential therapeutic targets for resistant PCa.
Area of Science:
- Oncology
- Genomics
- Molecular Biology
Background:
- The precise physiological role of genes driving mitoxantrone (MTX) resistance in prostate cancer (PCa) remains largely unknown.
- Understanding these genetic alterations is crucial for developing effective treatment strategies against resistant PCa.
Purpose of the Study:
- To identify and characterize differentially expressed genes (DEGs) associated with MTX resistance in prostate cancer.
- To explore the functional and pathway involvement of these DEGs in the context of resistant PCa.
Main Methods:
- Gene expression profiling using Affymetrix microarrays on MTX-resistant PCa xenografts (DU145R and PC3R) in SCID mice.
- Bioinformatic analysis with Cytoscape to map protein-protein interactions and signaling networks.
- Validation of selected DEGs using quantitative real-time PCR (qRT-PCR) in xenografts and clinical samples.
Main Results:
- Identified 355 overlapping DEGs between MTX-resistant DU145R and PC3R xenografts.
- Functional enrichment analysis linked these DEGs to cellular activity, androgen synthesis, DNA damage/repair.
- DEGs are implicated in critical signaling pathways including ERK/MAPK, PI3K/AKT, and apoptosis.
Conclusions:
- This study reveals key genes and pathways involved in MTX resistance in prostate cancer.
- The identified DEGs represent potential biomarkers and therapeutic targets for overcoming treatment resistance.
- Further investigation into these molecular mechanisms may provide novel insights for managing resistant PCa.
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