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Updated: Jun 3, 2026
Comprehensive DNA Methylation Analysis Using a Methyl-CpG-binding Domain Capture-based Method in Chronic Lymphocytic Leukemia Patients
Published on: June 16, 2017
Systematic Identification of Immune Regulatory Gene Networks in Leukemia Using Integrated Transcriptomic and
Haiyan Chen1, Junyao Liao1, Junxia Liu1
1Department of Hematology, Dongfang Hospital affiliated to Beijing University of Chinese Medicine, Fengtai, Beijing, 100078, China.
Introduction/Background:
Leukemia progression is strongly influenced by the immune microenvironment, yet the regulatory gene networks that coordinate immune activity in leukemia remain incompletely defined. Identifying immune-associated hub genes with diagnostic, prognostic, and functional relevance may improve biological understanding and guide biomarker development.
Methods:
GEO datasets (GSE9476, GSE12417, GSE13159) were analyzed by WGCNA to identify immune-related hub genes. Expression, diagnostic, and prognostic value were validated in independent AML cohorts (GSE37642, GSE6891, TCGA-LAML). Genomic alterations and miRNA regulators were assessed bioinformatically and confirmed by luciferase assays. Functional effects were examined via gene knockdown/overexpression and functional assays.
Results:
WGCNA identified an immune-associated module significantly correlated with leukemia and immune infiltration, from which CXCR4, LCP2, ITGAM, and HLA-DRA emerged as hub genes. All four genes were significantly upregulated in leukemia and demonstrated strong diagnostic performance (AUC 0.78-0.85). The four-gene prognostic model stratified survival consistently across three independent cohorts. Mutational and copy number profiling revealed low but functionally relevant genomic alterations. miR-27a-3p and miR-185-5p were identified and experimentally validated as shared upstream regulators. Knockdown of hub genes reduced proliferation, clonogenicity, and migration in leukemia cells, whereas overexpression enhanced these malignant phenotypes.
Discussion:
In this study, we identified a robust immune-associated gene module in leukemia and demonstrated that CXCR4, LCP2, ITGAM, and HLA-DRA function as central hubs with consistent diagnostic and prognostic value across multiple independent cohorts. Integrated transcriptomic, genomic, and experimental analyses revealed that these genes are coordinately regulated by shared miRNAs and actively promote leukemic proliferation, clonogenicity, and migration. Our findings highlight the importance of immune-tumor interactions in leukemia progression and suggest that this four-gene signature may serve as a promising biomarker set and therapeutic target for immune-informed leukemia management.
Conclusion:
This integrative multi-omic and functional study identifies a four-gene immuneassociated module with diagnostic, prognostic, and biological significance in leukemia. The coordinated regulation of hub genes by shared miRNAs and their functional impact on leukemic behavior highlight potential avenues for biomarker development and therapeutic targeting.
