Multi-omics Approach Reveals Influenza-A Virus Target Genes Associated Genomic, Clinical and Immunological Characteristics in Cancers

• Published in: Biomedical and environmental sciences 2024-07, Vol.37 (7), p.698-715
• Main Authors: Wang, Jiaojiao, Liao, Yong, Yang, Pinglian, Ye, Weile, Liu, Yong, Xiao, Chunxia, Liao, Weixiong, Chen, Chunbo, Liu, Zhiping, Huang, Zunnan
• Format: Article
• Language: English
• Subjects: DNA Copy Number Variations; Drug resistance; Experimental validation; Genomic changes; Genomics; Humans; Immune microenvironment; Influenza A virus - genetics; Multiomics; Neoplasms - genetics; Neoplasms - immunology; Neoplasms - virology; Prognosis
• ISSN: 0895-3988; 2214-0190; 2214-0190
• DOI: 10.3967/bes2024.094

To examine the precise function of influenza A virus target genes (IATGs) in malignancy. Using multi-omics data from the TCGA and TCPA datasets, 33 tumor types were evaluated for IATGs. IATG expression in cancer cells was analyzed using transcriptome analysis. Copy number variation (CNV) was assessed using GISTICS 2.0. Spearman’s analysis was used to correlate mRNA expression with methylation levels. GSEA was used for the enrichment analysis. Pearson’s correlation analysis was used to examine the association between IATG mRNA expression and IC50. The ImmuCellAI algorithm was used to calculate the infiltration scores of 24 immune cell types. In 13 solid tumors, IATG mRNA levels were atypically expressed. Except for UCS, UVM, KICH, PCPG, THCA, CHOL, LAMI, and MESO, most cancers contained somatic IATG mutations. The main types of CNVs in IATGs are heterozygous amplifications and deletions. In most tumors, IATG mRNA expression is adversely associated with methylation. RT-PCR demonstrated that EGFR, ANXA5, CACNA1C, CD209, UVRAG were upregulated and CLEC4M was downregulated in KIRC cell lines, consistent with the TCGA and GTEx data. Genomic changes and clinical characteristics of IATGs were identified, which may offer fresh perspectives linking the influenza A virus to cancer.