Multi-omics analysis reveals genomic, clinical and immunological features of SARS-CoV-2 virus target genes in pan-cancer

Yong Liao; Jiaojiao Wang; Jiami Zou; Yong Liu; Zhiping Liu; Zunnan Huang

doi:10.3389/fimmu.2023.1112704

Multi-omics analysis reveals genomic, clinical and immunological features of SARS-CoV-2 virus target genes in pan-cancer

Front Immunol. 2023 Feb 17:14:1112704. doi: 10.3389/fimmu.2023.1112704. eCollection 2023.

Authors

Yong Liao^{1

2

3}, Jiaojiao Wang^{4

5}, Jiami Zou⁵, Yong Liu^{1

3}, Zhiping Liu⁵, Zunnan Huang^{1

3}

Affiliations

¹ Key Laboratory of Computer-Aided Drug Design of Dongguan City, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, China.
² Department of Pharmacy, Maoming People's Hospital, Maoming, China.
³ Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China.
⁴ Center of Scientific Research, Department of Cardiology, Maoming People's Hospital, Maoming, China.
⁵ Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou, China.

Abstract

The SARS-CoV-2 virus, also known as the severe acute respiratory syndrome coronavirus 2, has raised great threats to humans. The connection between the SARS-CoV-2 virus and cancer is currently unclear. In this study, we thus evaluated the multi-omics data from the Cancer Genome Atlas (TCGA) database utilizing genomic and transcriptomic techniques to fully identify the SARS-CoV-2 target genes (STGs) in tumor samples from 33 types of cancers. The expression of STGs was substantially linked with the immune infiltration and may be used to predict survival in cancer patients. STGs were also substantially associated with immunological infiltration, immune cells, and associated immune pathways. At the molecular level, the genomic changes of STGs were frequently related with carcinogenesis and patient survival. In addition, pathway analysis revealed that STGs were involved in the control of signaling pathways associated with cancer. The prognostic features and nomogram of clinical factors of STGs in cancers have been developed. Lastly, by mining the cancer drug sensitivity genomics database, a list of potential STG-targeting medicines was compiled. Collectively, this work demonstrated comprehensively the genomic alterations and clinical characteristics of STGs, which may offer new clues to explore the mechanisms on a molecular level between SARS-CoV-2 virus and cancers as well as provide new clinical guidance for cancer patients who are threatened by the COVID-19 epidemic.

Keywords: SARS-CoV-2; immunological features; multi-omics; pan-cancer; target genes.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

COVID-19*
Genomics
Humans
Multiomics
Neoplasms*
SARS-CoV-2

Grants and funding

Thanks to the Key Discipline Construction Project of Guangdong Medical University (4SG22004G), the National Natural Science Foundation of China (No. 82203304, 82270500), High-level Hospital Construction Research Project of Maoming People’s Hospital (Yueweihan(2018)413), the Science and Technology Plan Project of Maoming (NO.210416154552665), the Excellent Young Talent Program of Maoming People’s Hospital (NO.SY2022006), the Start-up fund of postdoctoral fellows to Jiaojiao Wang (BS2021011).