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Sadeq S, Chitcharoen S, Al-Hashimi S, Rattanaburi S, Casement J, Werner A. Significant Variations in Double-Stranded RNA Levels in Cultured Skin Cells. Cells 2024; 13:226. [PMID: 38334619 PMCID: PMC10854852 DOI: 10.3390/cells13030226] [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: 11/27/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
Endogenous double-stranded RNA has emerged as a potent stimulator of innate immunity. Under physiological conditions, endogenous dsRNA is maintained in the cell nucleus or the mitochondria; however, if protective mechanisms are breached, it leaches into the cytoplasm and triggers immune signaling pathways. Ectopic activation of innate immune pathways is associated with various diseases and senescence and can trigger apoptosis. Hereby, the level of cytoplasmic dsRNA is crucial. We have enriched dsRNA from two melanoma cell lines and primary dermal fibroblasts, including a competing probe, and analyzed the dsRNA transcriptome using RNA sequencing. There was a striking difference in read counts between the cell lines and the primary cells, and the effect was confirmed by northern blotting and immunocytochemistry. Both mitochondria (10-20%) and nuclear transcription (80-90%) contributed significantly to the dsRNA transcriptome. The mitochondrial contribution was lower in the cancer cells compared to fibroblasts. The expression of different transposable element families was comparable, suggesting a general up-regulation of transposable element expression rather than stimulation of a specific sub-family. Sequencing of the input control revealed minor differences in dsRNA processing pathways with an upregulation of oligoadenylate synthase and RNP125 that negatively regulates the dsRNA sensors RIG1 and MDA5. Moreover, RT-qPCR, Western blotting, and immunocytochemistry confirmed the relatively minor adaptations to the hugely different dsRNA levels. As a consequence, these transformed cell lines are potentially less tolerant to interventions that increase the formation of endogenous dsRNA.
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Affiliation(s)
- Shaymaa Sadeq
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (S.S.); (S.A.-H.)
- Fallujah College of Medicine, University of Fallujah, Al-Fallujah 31002, Iraq
| | - Suwalak Chitcharoen
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand;
- Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Surar Al-Hashimi
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (S.S.); (S.A.-H.)
- College of Medicine, University of Misan, Al-Sader Teaching Hospital, Amarah 62001, Iraq
| | - Somruthai Rattanaburi
- Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand;
| | - John Casement
- Bioinformatics Support Unit, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK;
| | - Andreas Werner
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (S.S.); (S.A.-H.)
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Sadeq S, Lovat P, Nelson G, Mcdonald D, Filby A, Werner A. 463 Implications of the ds-RNA stress response in melanoma cell lines and patient samples. J Invest Dermatol 2022. [DOI: 10.1016/j.jid.2022.09.477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Werner A, Clark JE, Samaranayake C, Casement J, Zinad HS, Sadeq S, Al-Hashimi S, Smith M, Kotaja N, Mattick JS. Widespread formation of double-stranded RNAs in testis. Genome Res 2021; 31:1174-1186. [PMID: 34158368 PMCID: PMC8256860 DOI: 10.1101/gr.265603.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 05/05/2020] [Accepted: 06/02/2021] [Indexed: 12/27/2022]
Abstract
The testis transcriptome is highly complex and includes RNAs that potentially hybridize to form double-stranded RNA (dsRNA). We isolated dsRNA using the monoclonal J2 antibody and deep-sequenced the enriched samples from testes of juvenile Dicer1 knockout mice, age-matched controls, and adult animals. Comparison of our data set with recently published data from mouse liver revealed that the dsRNA transcriptome in testis is markedly different from liver: In testis, dsRNA-forming transcripts derive from mRNAs including promoters and immediate downstream regions, whereas in somatic cells they originate more often from introns and intergenic transcription. The genes that generate dsRNA are significantly expressed in isolated male germ cells with particular enrichment in pachytene spermatocytes. dsRNA formation is lower on the sex (X and Y) chromosomes. The dsRNA transcriptome is significantly less complex in juvenile mice as compared to adult controls and, possibly as a consequence, the knockout of Dicer1 has only a minor effect on the total number of transcript peaks associated with dsRNA. The comparison between dsRNA-associated genes in testis and liver with a reported set of genes that produce endogenous siRNAs reveals a significant overlap in testis but not in liver. Testis dsRNAs also significantly associate with natural antisense genes-again, this feature is not observed in liver. These findings point to a testis-specific mechanism involving natural antisense transcripts and the formation of dsRNAs that feed into the RNA interference pathway, possibly to mitigate the mutagenic impacts of recombination and transposon mobilization.
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Affiliation(s)
- Andreas Werner
- Biosciences Institute, Medical School, Newcastle University, Newcastle, NE2 4HH, United Kingdom
| | - James E Clark
- Biosciences Institute, Medical School, Newcastle University, Newcastle, NE2 4HH, United Kingdom
| | - Calum Samaranayake
- Biosciences Institute, Medical School, Newcastle University, Newcastle, NE2 4HH, United Kingdom
| | - John Casement
- Bioinformatics Support Unit, Medical School, Newcastle University, Newcastle, NE2 4HH, United Kingdom
| | - Hany S Zinad
- Biosciences Institute, Medical School, Newcastle University, Newcastle, NE2 4HH, United Kingdom
| | - Shaymaa Sadeq
- Biosciences Institute, Medical School, Newcastle University, Newcastle, NE2 4HH, United Kingdom
- Fallujah College of Medicine, Al-Fallujah University, Al-Fallujah, 9Q4V+H3, Iraq
| | - Surar Al-Hashimi
- Biosciences Institute, Medical School, Newcastle University, Newcastle, NE2 4HH, United Kingdom
| | - Martin Smith
- CHU Sainte-Justine Research Centre, Montreal, QC H3T 1C5, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Noora Kotaja
- Institute of Biomedicine, University of Turku, Turku, FIN-20520, Finland
| | - John S Mattick
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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Abstract
The birth of long non-coding RNAs (lncRNAs) is closely associated with the presence and activation of repetitive elements in the genome. The transcription of endogenous retroviruses as well as long and short interspersed elements is not only essential for evolving lncRNAs but is also a significant source of double-stranded RNA (dsRNA). From an lncRNA-centric point of view, the latter is a minor source of bother in the context of the entire cell; however, dsRNA is an essential threat. A viral infection is associated with cytoplasmic dsRNA, and endogenous RNA hybrids only differ from viral dsRNA by the 5' cap structure. Hence, a multi-layered defense network is in place to protect cells from viral infections but tolerates endogenous dsRNA structures. A first line of defense is established with compartmentalization; whereas endogenous dsRNA is found predominantly confined to the nucleus and the mitochondria, exogenous dsRNA reaches the cytoplasm. Here, various sensor proteins recognize features of dsRNA including the 5' phosphate group of viral RNAs or hybrids with a particular length but not specific nucleotide sequences. The sensors trigger cellular stress pathways and innate immunity via interferon signaling but also induce apoptosis via caspase activation. Because of its central role in viral recognition and immune activation, dsRNA sensing is implicated in autoimmune diseases and used to treat cancer.
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Affiliation(s)
| | | | | | - Andreas Werner
- Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (S.S.); (S.A.-H.); (C.M.C.)
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