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Published on: February 22, 2020
Oncogenic Network and Hub Genes for Natural Killer/T-Cell Lymphoma Utilizing WGCNA
Huijiao Liu1,2, Mei Liu3, Hua You2
1Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing, China.
Abstract:
Natural killer (NK)/T-cell lymphoma (NKTCL) is a subtype of non-Hodgkin lymphoma with aggressive progression and poor prognosis. The molecular mechanisms of NKTCL have not been well-studied. Herein, we revealed the lymphoma-associated dysregulated genes and signaling pathways or biological processes in NKTCL. We characterized that the extracellular matrix (ECM) receptor interaction pathway and T-cell receptor signaling pathway were the main dysregulated pathways in NKTCL by Gene Ontology (GO) analysis and pathway enrichment analysis. By using weighted gene co-expression network analysis (WGCNA), the gene co-expression network of NKTCL (SRP049695) was constructed, and hub genes (LMO3, GRB14) were identified. In addition, another Gene Expression Omnibus (GEO) dataset (GSE69406) was used to validate these hub genes. Furthermore, these hub genes were identified and validated by survival analysis (GSE90597). These results provided novel insights into the pathogenesis of NKTCL. Of particular interest, LMO3 and GRB14 might be potential oncoproteins and biomarkers for the diagnosis and treatment of NKTCL.
Insights
This study identifies key molecular pathways and genes involved in Natural Killer (NK)/T-cell lymphoma (NKTCL). LMO3 and GRB14 are highlighted as potential diagnostic and therapeutic targets for this aggressive lymphoma.
Area of Science:
- Oncology
- Molecular Biology
- Genetics
Background:
- Natural Killer (NK)/T-cell lymphoma (NKTCL) is an aggressive non-Hodgkin lymphoma with poorly understood molecular mechanisms.
- Identifying dysregulated genes and pathways is crucial for understanding NKTCL pathogenesis.
Purpose of the Study:
- To elucidate the molecular mechanisms underlying NKTCL by identifying dysregulated genes and signaling pathways.
- To discover potential oncoproteins and biomarkers for NKTCL diagnosis and treatment.
Main Methods:
- Gene Ontology (GO) analysis and pathway enrichment analysis were performed to identify dysregulated pathways.
- Weighted Gene Co-expression Network Analysis (WGCNA) was used to construct the NKTCL gene co-expression network and identify hub genes.
- Validation of hub genes was conducted using independent Gene Expression Omnibus (GEO) datasets and survival analysis.
Main Results:
- The extracellular matrix (ECM) receptor interaction and T-cell receptor signaling pathways were identified as significantly dysregulated in NKTCL.
- Hub genes LMO3 and GRB14 were identified through WGCNA and validated across multiple datasets.
- Survival analysis confirmed the significance of LMO3 and GRB14 in NKTCL patient outcomes.
Conclusions:
- This research provides novel insights into the pathogenesis of NKTCL.
- LMO3 and GRB14 represent promising oncoproteins and potential biomarkers for the diagnosis and targeted therapy of NKTCL.
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