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Whole exome sequencing and transcriptome-wide profiling identify potentially subtype-relevant genes of nasopharyngeal
Ji Liu1, Xu Li2, Shanshan Yang3
1Department of Oncology, the Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, China.
Background:
To date, no targeted therapy has been approved for nasopharyngeal carcinoma (NPC), suggesting that comprehensive understanding of genomic changes turns out to be an urgent need to break through the calm of currently known therapies of NPC.
Methods:
Whole exome sequencing (WES) was performed for 14 NPC patients, including 6 NPC-IIA cases, 8 NPC-IIB cases. The cancer chip expression data named GSE12452 was downloaded from the Gene Expression Omnibus (GEO) database, and differentially expressed genes (DEGs) of each subtype were obtained using the Lima R package. Then gene ontology (GO) function enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed. Protein-protein interaction (PPI) network and Gene Set Enrichment Analysis (GSEA) were performed. Finally 7 potentially subtype relevant genes (PSRGs)1 were obtained.
Results:
In total, 37 clinically relevant mutations (CRMs)2 were obtained from WES. The 2 NPC subtypes exhibited different mutational landscapes, indicating that different NPC subtypes harbor different CRMs. Notably, we discovered that mutations of CCND1 and FGF family appeared simultaneously in 3 NPC-IIB cases, but 0 in NPC-IIA. In addition, 1395 DEGs were identified from GSE12452. PI3K-Akt signaling pathway showed significant enrichment in both the pathway distribution of CRMs and KEGG analysis of DEGs, suggesting that it is a key pathway in the development of NPC. Through PPI analysis of genes involved in the PI3K-Akt pathways and expression significance analysis of DEGs co-expressed by the 2 subtypes, 54 genes finally were screened for expression significance analysis. The GSEA analysis between patients with high and low expression of 11 candidate genes were performed. As a result, 7 PSRGs were selected, including COL4A1, ASB9, RDH10, TNFRSF21, BACE2, EVA1C and LHX2.
Conclusions:
These results indicate that different NPC subtypes have different genetic changes, suggesting that they may be potential targets for the diagnosis and treatment of NPC, and ultimately point to new strategies for intelligence.
Insights
Genomic analysis revealed distinct genetic alterations in nasopharyngeal carcinoma (NPC) subtypes. These findings identify potential therapeutic targets and diagnostic strategies for NPC, advancing treatment options.
Area of Science:
- Oncology
- Genomics
- Molecular Biology
Background:
- Nasopharyngeal carcinoma (NPC) lacks targeted therapies, necessitating a deeper understanding of its genomic landscape.
- Identifying subtype-specific genomic alterations is crucial for developing novel treatment strategies.
Purpose of the Study:
- To investigate the genomic differences between NPC subtypes (IIA and IIB).
- To identify potential subtype-specific genes and pathways for NPC diagnosis and treatment.
Main Methods:
- Whole exome sequencing (WES) of 14 NPC patients.
- Analysis of Gene Expression Omnibus (GEO) data (GSE12452) to identify differentially expressed genes (DEGs).
- Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, Protein-Protein Interaction (PPI) network, and Gene Set Enrichment Analysis (GSEA).
Main Results:
- Identified 37 clinically relevant mutations (CRMs), with distinct mutational landscapes between NPC subtypes.
- CCND1 and FGF family mutations co-occurred in NPC-IIB but not NPC-IIA cases.
- The PI3K-Akt signaling pathway was significantly enriched in both CRMs and DEGs.
- Seven potentially subtype-relevant genes (PSRGs) were identified: COL4A1, ASB9, RDH10, TNFRSF21, BACE2, EVA1C, and LHX2.
Conclusions:
- Different NPC subtypes exhibit unique genetic alterations.
- These subtype-specific genetic changes represent potential targets for NPC diagnosis and therapy.
- The findings offer new avenues for developing targeted strategies against NPC.
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