HCMV miR-UL70-3p downregulates the rapamycin-induced autophagy by targeting the autophagy-related protein 9A (ATG9A)

Abstract

Human cytomegalovirus (HCMV) is a representative β-herpesvirus that establishes persistent infections in humans, and exhibits high seropositivity rates in adults. It has co-evolved with its human host and employs various strategies to evade antiviral mechanisms by utilizing a significant portion of its genome. HCMV-encoded proteins and miRNAs have been implicated in regulating these mechanisms, enabling viral survival within the human body. During viral infections, autophagy, a conserved catabolic process essential for cellular homeostasis, acts as an antiviral defense mechanism. Multiple studies have reported that HCMV can modulate autophagy through its proteins and miRNAs, thereby influencing its survival within the host. In this study, we showed the potential involvement of HCMV miRNAs in cellular autophagy. We employed various bioinformatic tools to predict putative HCMV miRNAs that target autophagy-related genes and their corresponding cellular autophagy genes. Our results show that the 3'UTR of autophagy-related genes, including ATG9A, ATG9B, ATG16L2, SQSTM1, and EIF2AK2, harbors potential binding sites for hcmv-miR-UL70-3p. Experimental manipulation involving ectopic expression of hcmv-miR-UL70-3p demonstrated a significant reduction in rapamycin-induced autophagy, with ATG9A as its functional target. These findings establish that hcmv-miR-UL70-3p acts as an autophagy inhibitor by suppressing the expression of ATG9A.

Graphical Abstract

Keywords:

• Autophagy
• autophagy-related protein 9A (ATG9A)
• hcmv-miR-UL70-3p
• human cytomegalovirus (HCMV)

Acknowledgements

Babasaheb Bhimrao Ambedkar University, Lucknow for Confocal Microscopy facility; All India Institute of Medical Sciences, New Delhi, for Transmission Electron Microscopy and Centre for BioMedical Research, Lucknow for DNA/RNA quantifications. The funder had no role in the study design, data collection and analysis, publication decision, or manuscript preparation.

Author contributions

Raj Kumar Khalko: Investigation, collection of data, analysis and interpretation of data, methodology, Writing Original Draft of manuscript. Abhishek Pandeya: Investigation, data collection, analysis and interpretation of data, Validation, drafting the manuscript and critical revision of the manuscript. Sangeeta Saxena: Supervision, revision of the manuscript. Sunil Babu Gosipatala: Visualization, Conception and design of the study, Funding acquisition, Project administration, Resources, Supervision, reviewing & editing the manuscript.

Declaration of Interest

The authors report no conflicts of interest.

Data availability

Supporting data is included as supplementary material.

Additional information

Funding

The authors would like to thank DST-SERB for financial support (Project No: EEQ/2017/000438); NFST to Raj Kumar Khalko (Ref. No: 201819-NFST-JHA-02141).