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Imirowicz I, Saifee A, Henry L, Tunkle L, Popescu A, Huang P, Jakpor J, Barbano A, Goru R, Gunawan A, Sicilia M, Ono M, Bao X, Lee I. Unique tRNA Fragment Upregulation with SARS-CoV-2 but Not with SARS-CoV Infection. Int J Mol Sci 2023; 25:399. [PMID: 38203569 PMCID: PMC10779308 DOI: 10.3390/ijms25010399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/18/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Unlike other coronaviruses, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly infected the global population, with some suffering long-term effects. Thanks to extensive data on SARS-CoV-2 made available through global, multi-level collaborative research, investigators are getting closer to understanding the mechanisms of SARS-CoV-2 infection. Here, using publicly available total and small RNAseq data of Calu3 cell lines, we conducted a comparative analysis of the changes in tRNA fragments (tRFs; regulatory small noncoding RNAs) in the context of severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 infections. We found extensive upregulation of multiple tRFs in SARS-CoV-2 infection that was not present in SARS-CoV or other virus infections our group has studied. By comparing the total RNA changes in matching samples, we identified significant downregulation of TRDMT1 (tRNA methyltransferase), only in SARS-CoV-2 infection, a potential upstream event. We further found enriched neural functions among downregulated genes with SARS-CoV-2 infection. Interestingly, theoretically predicted targets of the upregulated tRFs without considering mRNA expression data are also enriched in neural functions such as axon guidance. Based on a combination of expression data and theoretical calculations, we propose potential targets for tRFs. For example, among the mRNAs downregulated with SARS-CoV-2 infection (but not with SARS-CoV infection), SEMA3C is a theoretically calculated target of multiple upregulated tRFs and a ligand of NRP1, a SARS-CoV-2 receptor. Our analysis suggests that tRFs contribute to distinct neurological features seen in SARS-CoV-2.
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Affiliation(s)
| | - Azeem Saifee
- Outreach Division, miRcore, Ann Arbor, MI 48104, USA
| | - Leanne Henry
- Outreach Division, miRcore, Ann Arbor, MI 48104, USA
| | - Leo Tunkle
- Outreach Division, miRcore, Ann Arbor, MI 48104, USA
| | | | - Philip Huang
- Outreach Division, miRcore, Ann Arbor, MI 48104, USA
| | - Jibiana Jakpor
- Outreach Division, miRcore, Ann Arbor, MI 48104, USA
- miRcore Volunteer Program, miRcore, Ann Arbor, MI 40104, USA
| | - Ava Barbano
- Outreach Division, miRcore, Ann Arbor, MI 48104, USA
- miRcore Volunteer Program, miRcore, Ann Arbor, MI 40104, USA
| | - Rohit Goru
- Outreach Division, miRcore, Ann Arbor, MI 48104, USA
| | | | - Maria Sicilia
- miRcore Volunteer Program, miRcore, Ann Arbor, MI 40104, USA
| | - Mori Ono
- Outreach Division, miRcore, Ann Arbor, MI 48104, USA
| | - Xiaoyong Bao
- Department of Pediatrics, The University of Texas Medical Branch, Galveston, TX 77555, USA;
| | - Inhan Lee
- Outreach Division, miRcore, Ann Arbor, MI 48104, USA
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Wu W, Choi EJ, Wang B, Zhang K, Adam A, Huang G, Tunkle L, Huang P, Goru R, Imirowicz I, Henry L, Lee I, Dong J, Wang T, Bao X. Changes of Small Non-coding RNAs by Severe Acute Respiratory Syndrome Coronavirus 2 Infection. Front Mol Biosci 2022; 9:821137. [PMID: 35281271 PMCID: PMC8905365 DOI: 10.3389/fmolb.2022.821137] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/19/2022] [Indexed: 01/11/2023] Open
Abstract
The ongoing pandemic of coronavirus disease 2019 (COVID-19), which results from the rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a significant global public health threat, with molecular mechanisms underlying its pathogenesis largely unknown. In the context of viral infections, small non-coding RNAs (sncRNAs) are known to play important roles in regulating the host responses, viral replication, and host-virus interaction. Compared with other subfamilies of sncRNAs, including microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs), tRNA-derived RNA fragments (tRFs) are relatively new and emerge as a significant regulator of host-virus interactions. Using T4 PNK‐RNA‐seq, a modified next-generation sequencing (NGS), we found that sncRNA profiles in human nasopharyngeal swabs (NPS) samples are significantly impacted by SARS-CoV-2. Among impacted sncRNAs, tRFs are the most significantly affected and most of them are derived from the 5′-end of tRNAs (tRF5). Such a change was also observed in SARS-CoV-2-infected airway epithelial cells. In addition to host-derived ncRNAs, we also identified several small virus-derived ncRNAs (svRNAs), among which a svRNA derived from CoV2 genomic site 346 to 382 (sv-CoV2-346) has the highest expression. The induction of both tRFs and sv-CoV2-346 has not been reported previously, as the lack of the 3′-OH ends of these sncRNAs prevents them to be detected by routine NGS. In summary, our studies demonstrated the involvement of tRFs in COVID-19 and revealed new CoV2 svRNAs.
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Affiliation(s)
- Wenzhe Wu
- Department of Pediatrics, The University of Texas Medical Branch, Galveston, TX, United States
| | - Eun-Jin Choi
- Department of Pediatrics, The University of Texas Medical Branch, Galveston, TX, United States
| | - Binbin Wang
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, United States
| | - Ke Zhang
- Department of Pediatrics, The University of Texas Medical Branch, Galveston, TX, United States
| | - Awadalkareem Adam
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, United States
| | - Gengming Huang
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, United States
| | - Leo Tunkle
- miRcore, Ann Arbor, MI, United States
- Department of Nuclear Engineering and Radiological Sience, University of Michigan, Ann Arbor, MI, United States
- Department of Computer Science, University of Michigan, Ann Arbor, MI, United States
| | - Philip Huang
- miRcore, Ann Arbor, MI, United States
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Rohit Goru
- miRcore, Ann Arbor, MI, United States
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Isabella Imirowicz
- miRcore, Ann Arbor, MI, United States
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Leanne Henry
- miRcore, Ann Arbor, MI, United States
- Department of Computer Science, University of Michigan, Ann Arbor, MI, United States
| | - Inhan Lee
- miRcore, Ann Arbor, MI, United States
| | - Jianli Dong
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, United States
- The Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, TX, United States
| | - Tian Wang
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, United States
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, United States
- The Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, TX, United States
| | - Xiaoyong Bao
- Department of Pediatrics, The University of Texas Medical Branch, Galveston, TX, United States
- The Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, TX, United States
- The Institute of Translational Sciences, The University of Texas Medical Branch, Galveston, TX, United States
- *Correspondence: Xiaoyong Bao,
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Wu W, Choi EJ, Wang B, Zhang K, Adam A, Huang G, Tunkle L, Huang P, Goru R, Imirowicz I, Henry L, Lee I, Dong J, Wang T, Bao X. Changes of small non-coding RNAs by severe acute respiratory syndrome coronavirus 2 infection. bioRxiv 2021. [PMID: 34981063 DOI: 10.1101/2021.12.16.472982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The ongoing pandemic of coronavirus disease 2019 (COVID-19), which results from the rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a significant global public health threat, with molecular mechanisms underlying its pathogenesis largely unknown. Small non-coding RNAs (sncRNAs) are known to play important roles in almost all biological processes. In the context of viral infections, sncRNAs have been shown to regulate the host responses, viral replication, and host-virus interaction. Compared with other subfamilies of sncRNAs, including microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs), tRNA-derived RNA fragments (tRFs) are relatively new and emerge as a significant regulator of host-virus interactions. Using T4 PNK-RNA-seq, a modified next-generation sequencing (NGS), we recently found that nasopharyngeal swabs (NPS) samples from SARS-CoV-2 positive and negative subjects show a significant difference in sncRNA profiles. There are about 166 SARS-CoV-2-impacted sncRNAs. Among them, tRFs are the most significantly affected and almost all impacted tRFs are derived from the 5'-end of tRNAs (tRF5). Using a modified qRT-PCR, which was recently developed to specifically quantify tRF5s by isolating the tRF signals from its corresponding parent tRNA signals, we validated that tRF5s derived from tRNA GluCTC (tRF5-GluCTC), LysCTT (tRF5-LysCTT), ValCAC (tRF5-ValCAC), CysGCA (tRF5-CysGCA) and GlnCTG (tRF5-GlnCTG) are enhanced in NPS samples of SARS-CoV2 patients and SARS-CoV2-infected airway epithelial cells. In addition to host-derived ncRNAs, we also identified several sncRNAs derived from the virus (svRNAs), among which a svRNA derived from CoV2 genomic site 346 to 382 (sv-CoV2-346) has the highest expression. The induction of both tRFs and sv-CoV2-346 has not been reported previously, as the lack of the 3'-OH ends of these sncRNAs prevents them to be detected by routine NGS. In summary, our studies demonstrated the involvement of tRFs in COVID-19 and revealed new CoV2 svRNAs.
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