Exploring Differentially Expressed Genes and Immune Modulation in Diffuse Large B-Cell Lymphoma through RNA Sequencing Analysis - Original Article

Q: What was the goal of the study in DLBCL patients?

The study examined differentially expressed genes at the transcriptome level and molecular pathways associated with diffuse large B-cell lymphoma.

Q: How were differentially expressed genes identified?

RNA sequencing was analyzed using the DESeq2 R package with a negative binomial model, and genes were considered significant with false discovery rate <0.05 and log2 fold change (FC) thresholds.

Q: Which immune-related pathways were found to be downregulated?

Reactome pathway analysis associated downregulation with antimicrobial humoral response, neutrophil degranulation, chemokine/chemokine receptor binding, defensins, and angiotensinogen metabolism.

Sep 21, 2026

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Background: Diffuse large B-cell lymphoma (DLBCL) is the most prevalent and aggressive non-Hodgkin lymphoma subtype worldwide, with conventional therapies that may lead to resistance or relapse over time. Methods: RNA sequencing compared transcriptomes from five DLBCL patients and two healthy volunteers, identifying differentially expressed genes using DESeq2 with adjusted false discovery rate <0.05. Results: 73 genes differed, including 70 downregulated and three upregulated, with Reactome pathways linked to reduced antimicrobial humoral response, neutrophil degranulation, chemokine signaling, defensins, and angiotensinogen metabolism. Conclusion: These pathways may drive cancer progression and weaken immune response, offering targets and mechanistic insight.

LanguageEnglish

CategoryResearch & Report

FormatPDF

Pages9

Reading Time23 min

AccessFree to download

Abstract

Background

Methods

Results

Conclusion

Introduction

Lymphoma overview and DLBCL characteristics

Differentially expressed genes in diffuse large B-cell lymphoma

IJMS Vol 49, No 10, October 2024 Original Article Exploring Differentially Expressed Genes and Immune Modulation in Diffuse Large B-Cell Lymphoma through RNA Sequencing Analysis Nor Adzimah Johdi1, PhD; Amanda Seng2 , PhD; Wei-Kang Lee2 , PhD; Hanif Zulkhairi Mohamad Said1, Dip MLT; Wan Fariza Wan Jamaluddin3 , MD 1UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur, Malaysia; 2Codon Genomics Sdn Bhd, Seri Kembangan Selangor Darul Ehsan, Malaysia; 3Cell Therapy Center, Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur, Malaysia Correspondence: NorAdzimah Johdi, PhD; UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Cheras, Postal code: 56000,Kuala Lumpur, Malaysia Tel: +60 3 91719065 Email: [adzimah@ppukm.ukm.edu.my](adzimah@ppukm.ukm.edu.my), [adzimahjohdi@gmail.com](adzimahjohdi@gmail.com)[ ](adzimahjohdi@gmail.com)[Received: 17 September 2023](Received: 17 September 2023) [Revised: 29 October 2023](Revised: 29 October 2023) [Accepted: 19 November 2023](Accepted: 19 November 2023) |
What’s Known
• The immune landscape in lymphoma comprises a diverse milieu of immune cells such as T cells, B cells, and macrophages, interacting with malignant lymphocytes. Immune checkpoints, cytokines, and genetic alterations influence responses.
• Immunotherapies, targeting these dynamics, show promise in enhancing anti-lymphoma immunity and improving treatment outcomes.

What’s New | | --- | | • There were 73 differentially expressed genes between diffuse large B-cell lymphoma patients and healthy controls, with 70 downregulated and three upregulated genes.
• Antimicrobial humoral response, neutrophil degranulation and activation, chemokine response, and defensins pathways were significantly downregulated. | Abstract Background: Diffuse large B-cell lymphoma (DLBCL) is globally recognized as the most prevalent and aggressive subtype of non-Hodgkin lymphoma. While conventional treatments are effective initially, the disease can become resistant or relapse over time. This study aimed to examine the differentially expressed genes at the transcriptome level and molecular pathways in DLBCL patients. Methods: This investigation utilized RNA sequencing analysis to compare differentially expressed gene samples from five diffuse large B-cell lymphoma patients with two healthy volunteers. These participants were admitted to UKM Medical Center, Kuala Lumpur between 2019 and 2020. The differentially expressed genes were identified using the DESeq2 R package (version 1.10.1) using a negative binomial distribution model. The obtained P values were corrected with the Benjamin and Hochberg method and identified using a False Discovery Rate threshold of <0.05, with log2 fold change (FC) of ≥2 or ≤-2 . Results:Resultsshowed73differentiallyexpressedgenesbetween the two groups, among which 70 genes were downregulated, and three genes were upregulated. The differentially expressed genes analyzed with the Reactome pathway were significantly associated with the downregulation of antimicrobial humoral response (P<0.001), neutrophil degranulation (P<0.001), chemokine receptors bind chemokines (P=0.028), defensins (P=0.028) and metabolism of angiotensinogen (P=0.040). Conclusion: These findings suggest that the identified pathways may contribute to cancer progression and weaken the immune response in diffuse large B-cell lymphoma patients. This study offers fresh insights into previously undiscovered downstream targets and pathways modulated by diffuse large B-cell lymphoma. Please cite this article as: Johdi NA, Seng A, Lee WK, Mohamad Said HZ, Wan Jamaluddin WF. Exploring Differentially Expressed Genes and Immune Modulation in Diffuse Large B-Cell Lymphoma through RNASequencingAnalysis. Iran J Med Sci. 2024;49(10):652-660 . doi: 10.30476/IJMS.2023.100149.3234. Keywords ● Diffuse large B-cell lymphoma ● RNA sequencing ● Gene ontology ● Trans

FAQs

What was the goal of the study in DLBCL patients?

The study examined differentially expressed genes at the transcriptome level and molecular pathways associated with diffuse large B-cell lymphoma.

How were differentially expressed genes identified?

RNA sequencing was analyzed using the DESeq2 R package with a negative binomial model, and genes were considered significant with false discovery rate <0.05 and log2 fold change (FC) thresholds.

Which immune-related pathways were found to be downregulated?

Reactome pathway analysis associated downregulation with antimicrobial humoral response, neutrophil degranulation, chemokine/chemokine receptor binding, defensins, and angiotensinogen metabolism.

Sep 21, 2026

Uploaded by Sage