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Research Article
Identification of biomarkers and enrichment analysis in pancreatic adenocarcinoma through transcriptome analysis
1 Faculty, Department of Emergency Medical Services, Prince Sultan Bin Abdulaziz College for EMS, King Saud University, Riyadh, Saudi Arabia
2 Researcher, Department of Emergency Medical Services, Prince Sultan Bin Abdulaziz College for EMS, King Saud University, Riyadh, Saudi Arabia
3 Researcher, College of Nursing, King Saud University, Riyadh, Saudi Arabia
4 Faculty, Department of Family Medicine, King Fahad Medical City, Riyadh, Saudi Arabia
Address correspondence to:
Ehtesham Ahmed Shariff
Faculty, Department of Emergency Medical Services, Prince Sultan Bin Abdulaziz College for EMS, King Saud University, Riyadh,
Saudi Arabia
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Article ID: 100106Z04ES2025
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Shariff EA, Khan A, Hasan Z, Azharuddin A, Tabassum R, Al-Enazi KM. Identification of biomarkers and enrichment analysis in pancreatic adenocarcinoma through transcriptome analysis. Int J Hepatobiliary Pancreat Dis 2025;15(1):1–16.ABSTRACT
Aims: Pancreatic cancer is a major disease to fatalities worldwide. To understand its molecular mechanisms is crucial for improving diagnosis and treatment. We aim to identify key biomarkers and biological pathways associated with pancreatic adenocarcinoma using RNA sequencing data from The Cancer Genome Atlas (TCGA). To analyze differentially expressed genes in pancreatic cancer, performed enrichment analysis to uncover crucial biological processes and cellular components, evaluated the impact of identified genes on patient survival and prognosis.
Methods: We examined RNA sequencing data from TCGA to identify differentially expressed genes (DEGs), crucial biological processes, and cellular components associated with pancreatic cancer. Enrichment analysis was conducted to pinpoint significant genes involved in various pathways, and survival analysis was performed to assess the impact of these genes on patient outcomes.
Results: Our analysis identified several significant genes linked to pancreatic cancer, including EDN1, KDM1A, KDM5D, KDM6A, NLGN4Y, RASGRP, SQLE, TMSB4Y, TNF, USP9Y, 1UTY, and ZRSR2. Notably, Ras guanyl nucleotide-releasing protein (RASGRP), tumor necrosis factor (TNF), and ZRSR2 showed lower expression levels than normal tissues, while KDM1A and KDM3A were significantly overexpressed, correlating with poor prognostic outcomes. Survival analysis indicated that EDN1, KDM1A, RASGRP, and squalene epoxidase (SQLE) are associated with mortality risk or disease recurrence.
Conclusion: Our findings highlight key biomarkers and pathways involved in pancreatic cancer, emphasizing the potential of KDM1A and KDM3A as therapeutic targets. By identifying these biomarkers, we aim to contribute to developing targeted therapies that could enhance patient prognoses and improve treatment strategies for pancreatic cancer.
Keywords: Biomarkers, Enrichment analysis, Pancreatic cancer, RNA-Seq, Survival analysis, Transcriptome
SUPPORTING INFORMATION
Author Contributions
Ehtesham Ahmed Shariff - Substantial contributions to conception and design, Acquisition of data, Revising it critically for important intellectual content, Final approval of the version to be published
Amjad Khan - Substantial contributions to conception and design, Acquisition of data, Revising it critically for important intellectual content, Final approval of the version to be published
Zafrul Hasan - Substantial contributions to conception and design, Acquisition of data, Revising it critically for important intellectual content, Final approval of the version to be published
Ahmed Azharuddin - Substantial contributions to conception and design, Acquisition of data, Revising it critically for important intellectual content, Final approval of the version to be published
Rabeena Tabassum - Substantial contributions to conception and design, Acquisition of data, Revising it critically for important intellectual content, Final approval of the version to be published
Khalaf Mahdi Al-Enazi - Substantial contributions to conception and design, Acquisition of data, Revising it critically for important intellectual content, Final approval of the version to be published
Guarantor of SubmissionThe corresponding author is the guarantor of submission.
Source of SupportNone
Consent StatementWritten informed consent was obtained from the patient for publication of this article.
Data AvailabilityAll relevant data are within the paper and its Supporting Information files.
Conflict of InterestAuthors declare no conflict of interest.
Copyright© 2025 Ehtesham Ahmed Shariff et al. This article is distributed under the terms of Creative Commons Attribution License which permits unrestricted use, distribution and reproduction in any medium provided the original author(s) and original publisher are properly credited. Please see the copyright policy on the journal website for more information.
