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Lehrich BM, Delgado ER. Lipid Nanovesicle Platforms for Hepatocellular Carcinoma Precision Medicine Therapeutics: Progress and Perspectives. Organogenesis 2024; 20:2313696. [PMID: 38357804 PMCID: PMC10878025 DOI: 10.1080/15476278.2024.2313696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 01/30/2024] [Indexed: 02/16/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related mortality globally. HCC is highly heterogenous with diverse etiologies leading to different driver mutations potentiating unique tumor immune microenvironments. Current therapeutic options, including immune checkpoint inhibitors and combinations, have achieved limited objective response rates for the majority of patients. Thus, a precision medicine approach is needed to tailor specific treatment options for molecular subsets of HCC patients. Lipid nanovesicle platforms, either liposome- (synthetic) or extracellular vesicle (natural)-derived present are improved drug delivery vehicles which may be modified to contain specific cargos for targeting specific tumor sites, with a natural affinity for liver with limited toxicity. This mini-review provides updates on the applications of novel lipid nanovesicle-based therapeutics for HCC precision medicine and the challenges associated with translating this therapeutic subclass from preclinical models to the clinic.
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Affiliation(s)
- Brandon M. Lehrich
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Medical Scientist Training Program, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Evan R. Delgado
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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2
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Li B, Li X, Jiang Z, Zhou D, Feng Y, Chen G, Li N. LncRNA XIST modulates miR-328-3p ectopic expression in lung injury induced by tobacco-specific lung carcinogen NNK both in vitro and in vivo. Br J Pharmacol 2024; 181:2509-2527. [PMID: 38589338 DOI: 10.1111/bph.16373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 04/10/2024] Open
Abstract
BACKGROUND AND PURPOSE It is well acknowledged that tobacco-derived lung carcinogens can induce lung injury and even lung cancer through a complex mechanism. MicroRNAs (MiRNAs) are differentially expressed in tobacco-derived carcinogen nicotine-derived nitrosamine ketone (NNK)-treated A/J mice. EXPERIMENTAL APPROACH RNA sequencing was used to detect the level of long non-coding RNAs (lncRNAs). Murine and human lung normal and cancer cells were used to evaluate the function of lncRNA XIST and miR-328-3p in vitro, and NNK-treated A/J mice were used to test their function in vivo. In vivo levels of miR-328-3p and lncRNA XIST were analysed, using in situ hybridization. miR-328-3p agomir and lncRNA XIST-specific siRNA were used to manipulate in vivo levels of miR-328-3p and lncRNA XIST in A/J mice. KEY RESULTS LncRNA XIST was up-regulated in NNK-induced lung injury and dominated the NNK-induced ectopic miRNA expression in NNK-induced lung injury both in vitro and in vivo. Either lncRNA XIST silencing or miR-328-3p overexpression exerted opposing effects in lung normal and cancer cells regarding cell migration. LncRNA XIST down-regulated miR-328-3p levels as a miRNA sponge, and miR-328-3p targeted the 3'-UTR of FZD7 mRNA, which is ectopically overexpressed in lung cancer patients. Both in vivo lncRNA XIST silencing and miR-328 overexpression could rescue NNK-induced lung injury and aberrant overexpression of the lung cancer biomarker CK19 in NNK-treated A/J mice. CONCLUSIONS AND IMPLICATIONS Our results highlight the promotive effect of lncRNA XIST in NNK-induced lung injury and elucidate its post-transcriptional mechanisms, indicating that targeting lncRNA XIST/miR-328-3p could be a potential therapeutic strategy to prevent tobacco carcinogen-induced lung injury in vivo.
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Affiliation(s)
- Bingxin Li
- School of Traditional Chinese Materia Medica, Key Laboratory of Innovative Traditional Chinese Medicine for Major Chronic Diseases of Liaoning Province, Key Laboratory for TCM Material Basis Study and Innovative Drug Development of Shenyang City, Shenyang Pharmaceutical University, Shenyang, China
| | - Xuezheng Li
- Department of PIVAS, Yanbian University Hospital, Yanji, China
| | - Zhe Jiang
- Department of PIVAS, Yanbian University Hospital, Yanji, China
| | - Di Zhou
- School of Traditional Chinese Materia Medica, Key Laboratory of Innovative Traditional Chinese Medicine for Major Chronic Diseases of Liaoning Province, Key Laboratory for TCM Material Basis Study and Innovative Drug Development of Shenyang City, Shenyang Pharmaceutical University, Shenyang, China
| | - Yuan Feng
- School of Traditional Chinese Materia Medica, Key Laboratory of Innovative Traditional Chinese Medicine for Major Chronic Diseases of Liaoning Province, Key Laboratory for TCM Material Basis Study and Innovative Drug Development of Shenyang City, Shenyang Pharmaceutical University, Shenyang, China
| | - Gang Chen
- School of Traditional Chinese Materia Medica, Key Laboratory of Innovative Traditional Chinese Medicine for Major Chronic Diseases of Liaoning Province, Key Laboratory for TCM Material Basis Study and Innovative Drug Development of Shenyang City, Shenyang Pharmaceutical University, Shenyang, China
| | - Ning Li
- School of Traditional Chinese Materia Medica, Key Laboratory of Innovative Traditional Chinese Medicine for Major Chronic Diseases of Liaoning Province, Key Laboratory for TCM Material Basis Study and Innovative Drug Development of Shenyang City, Shenyang Pharmaceutical University, Shenyang, China
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Lebenzon JE, Toxopeus J. Knock down to level up: Reframing RNAi for invertebrate ecophysiology. Comp Biochem Physiol A Mol Integr Physiol 2024; 297:111703. [PMID: 39029617 DOI: 10.1016/j.cbpa.2024.111703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 07/16/2024] [Accepted: 07/16/2024] [Indexed: 07/21/2024]
Abstract
Comparative ecophysiologists strive to understand physiological problems in non-model organisms, but molecular tools such as RNA interference (RNAi) are under-used in our field. Here, we provide a framework for invertebrate ecophysiologists to use RNAi to answer questions focused on physiological processes, rather than as a tool to investigate gene function. We specifically focus on non-model invertebrates, in which the use of other genetic tools (e.g., genetic knockout lines) is less likely. We argue that because RNAi elicits a temporary manipulation of gene expression, and resources to carry out RNAi are technically and financially accessible, it is an effective tool for invertebrate ecophysiologists. We cover the terminology and basic mechanisms of RNA interference as an accessible introduction for "non-molecular" physiologists, include a suggested workflow for identifying RNAi gene targets and validating biologically relevant gene knockdowns, and present a hypothesis-testing framework for using RNAi to answer common questions in the realm of invertebrate ecophysiology. This review encourages invertebrate ecophysiologists to use these tools and workflows to explore physiological processes and bridge genotypes to phenotypes in their animal(s) of interest.
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Affiliation(s)
- Jacqueline E Lebenzon
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4.
| | - Jantina Toxopeus
- Department of Biology, St. Francis Xavier University, 2321 Notre Dame Ave, Antigonish, NS, Canada B2G 2W5
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Ogasawara T, Ito S, Ogashira S, Hoshino T, Sotomaru Y, Yoshiko Y, Tanimoto K. The expression of MIR125B transcripts and bone phenotypes in Mir125b2-deficient mice. PLoS One 2024; 19:e0304074. [PMID: 38976685 PMCID: PMC11230526 DOI: 10.1371/journal.pone.0304074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/06/2024] [Indexed: 07/10/2024] Open
Abstract
MIR125B, particularly its 5p strand, is apparently involved in multiple cellular processes, including osteoblastogenesis and osteoclastogenesis. Given that MIR125B is transcribed from the loci Mir125b1 and Mir125b2, three mature transcripts (MIR125B-5p, MIR125B1-3p, and MIR125B2-3p) are generated (MIR125B-5p is common to both); however, their expression profiles and roles in the bones remain poorly understood. Both primary and mature MIR125B transcripts were differentially expressed in various organs, tissues, and cells, and their expression patterns did not necessarily correlate in wild-type (WT) mice. We generated Mir125b2 knockout (KO) mice to examine the contribution of Mir125b2 to MIR125B expression profiles and bone phenotypes. Mir125b2 KO mice were born and grew normally without any changes in bone parameters. Interestingly, in WT and Mir125b2 KO, MIR125B-5p was abundant in the calvaria and bone marrow stromal cells. These results indicate that the genetic ablation of Mir125b2 does not impinge on the bones of mice, attracting greater attention to MIR125B-5p derived from Mir125b1. Future studies should investigate the conditional deletion of Mir125b1 and both Mir125b1 and Mir125b2 in mice.
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Affiliation(s)
- Tomohiro Ogasawara
- Department of Orthodontics, Division of Oral Health and Development, Hiroshima University Hospital, Hiroshima, Japan
| | - Shota Ito
- Department of Orthodontics, Division of Oral Health and Development, Hiroshima University Hospital, Hiroshima, Japan
| | - Shintaro Ogashira
- Department of Orthodontics, Division of Oral Health and Development, Hiroshima University Hospital, Hiroshima, Japan
| | - Tomonori Hoshino
- Neuroprotection Research Laboratories, Department of Neurology and Radiology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, United States of America
| | - Yusuke Sotomaru
- Natural Science Center for Basic Research and Development, Hiroshima University, Hiroshima, Japan
| | | | - Kotaro Tanimoto
- Department of Orthodontics and Craniofacial Developmental Biology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
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Taeb S, Rostamzadeh D, Amini SM, Rahmati M, Eftekhari M, Safari A, Najafi M. MicroRNAs targeted mTOR as therapeutic agents to improve radiotherapy outcome. Cancer Cell Int 2024; 24:233. [PMID: 38965615 PMCID: PMC11229485 DOI: 10.1186/s12935-024-03420-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 06/22/2024] [Indexed: 07/06/2024] Open
Abstract
MicroRNAs (miRNAs) are small RNA molecules that regulate genes and are involved in various biological processes, including cancer development. Researchers have been exploring the potential of miRNAs as therapeutic agents in cancer treatment. Specifically, targeting the mammalian target of the rapamycin (mTOR) pathway with miRNAs has shown promise in improving the effectiveness of radiotherapy (RT), a common cancer treatment. This review provides an overview of the current understanding of miRNAs targeting mTOR as therapeutic agents to enhance RT outcomes in cancer patients. It emphasizes the importance of understanding the specific miRNAs that target mTOR and their impact on radiosensitivity for personalized cancer treatment approaches. The review also discusses the role of mTOR in cell homeostasis, cell proliferation, and immune response, as well as its association with oncogenesis. It highlights the different ways in which miRNAs can potentially affect the mTOR pathway and their implications in immune-related diseases. Preclinical findings suggest that combining mTOR modulators with RT can inhibit tumor growth through anti-angiogenic and anti-vascular effects, but further research and clinical trials are needed to validate the efficacy and safety of using miRNAs targeting mTOR as therapeutic agents in combination with RT. Overall, this review provides a comprehensive understanding of the potential of miRNAs targeting mTOR to enhance RT efficacy in cancer treatment and emphasizes the need for further research to translate these findings into improved clinical outcomes.
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Affiliation(s)
- Shahram Taeb
- Department of Radiology, School of Paramedical Sciences, Guilan University of Medical Sciences, Rasht, Iran
| | - Davoud Rostamzadeh
- Department of Immunology, University of Connecticut Health Center, Farmington, CT, USA
| | - Seyed Mohammad Amini
- Radiation Biology Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Rahmati
- Department of Medical Biotechnology, Faculty of Paramedicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Mohammad Eftekhari
- Department of Medical Biotechnology, Faculty of Paramedicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Arash Safari
- Department of Radiology, Ionizing and Non-Ionizing Radiation Protection Research Center (INIRPRC), School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, 71439-14693, Iran
| | - Masoud Najafi
- Radiology and Nuclear Medicine Department, School of Paramedical Sciences, Kermanshah University of Medical Sciences, Kermanshah, Iran.
- Medical Biology Research Center, Institute of Health Technology, Kermanshah University of Medical Sciences, Kermanshah, Iran.
- Medical Technology Research Center, Institute of Health Technology, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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Aute R, Waghela N, Deshmukh MV. Key arginine residues in R2D2 dsRBD1 and dsRBD2 lead the siRNA recognition in Drosophila melanogaster RNAi pathway. Biophys Chem 2024; 310:107247. [PMID: 38663122 DOI: 10.1016/j.bpc.2024.107247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/04/2024] [Accepted: 04/16/2024] [Indexed: 05/23/2024]
Abstract
In Drosophila melanogaster, Dcr-2:R2D2 heterodimer binds to the 21 nucleotide siRNA duplex to form the R2D2/Dcr-2 Initiator (RDI) complex, which is critical for the initiation of siRNA-induced silencing complex (RISC) assembly. During RDI complex formation, R2D2, a protein that contains three dsRNA binding domains (dsRBD), senses two aspects of the siRNA: thermodynamically more stable end (asymmetry sensing) and the 5'-phosphate (5'-P) recognition. Despite several detailed studies to date, the molecular determinants arising from R2D2 for performing these two tasks remain elusive. In this study, we have performed structural, biophysical, and biochemical characterization of R2D2 dsRBDs. We found that the solution NMR-derived structure of R2D2 dsRBD1 yielded a canonical α1-β1-β2-β3-α2 fold, wherein two arginine salt bridges provide additional stability to the R2D2 dsRBD1. Furthermore, we show that R2D2 dsRBD1 interacts with thermodynamically asymmetric siRNA duplex independent of its 5'-phosphorylation state, whereas R2D2 dsRBD2 prefers to interact with 5'-P siRNA duplex. The mutation of key arginine residues, R53 and R101, in concatenated dsRBDs of R2D2 results in a significant loss of siRNA duplex recognition. Our study deciphers the active roles of R2D2 dsRBDs by showing that dsRBD1 initiates siRNA recognition, whereas dsRBD2 senses 5'-phosphate as an authentic mark on functional siRNA.
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Affiliation(s)
- Ramdas Aute
- CSIR - Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Nilam Waghela
- CSIR - Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mandar V Deshmukh
- CSIR - Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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7
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Hu W, Kumar A, Ahmed SF, Qi S, Ma DKG, Chen H, Singh GJ, Casan JML, Haber M, Voskoboinik I, McKay MR, Trapani JA, Ekert PG, Fareh M. Single-base tiled screen unveils design principles of PspCas13b for potent and off-target-free RNA silencing. Nat Struct Mol Biol 2024:10.1038/s41594-024-01336-0. [PMID: 38951623 DOI: 10.1038/s41594-024-01336-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 05/15/2024] [Indexed: 07/03/2024]
Abstract
The development of precise RNA-editing tools is essential for the advancement of RNA therapeutics. CRISPR (clustered regularly interspaced short palindromic repeats) PspCas13b is a programmable RNA nuclease predicted to offer superior specificity because of its 30-nucleotide spacer sequence. However, its design principles and its on-target, off-target and collateral activities remain poorly characterized. Here, we present single-base tiled screening and computational analyses that identify key design principles for potent and highly selective RNA recognition and cleavage in human cells. We show that the de novo design of spacers containing guanosine bases at precise positions can greatly enhance the catalytic activity of inefficient CRISPR RNAs (crRNAs). These validated design principles (integrated into an online tool, https://cas13target.azurewebsites.net/ ) can predict highly effective crRNAs with ~90% accuracy. Furthermore, the comprehensive spacer-target mutagenesis revealed that PspCas13b can tolerate only up to four mismatches and requires ~26-nucleotide base pairing with the target to activate its nuclease domains, highlighting its superior specificity compared to other RNA or DNA interference tools. On the basis of this targeting resolution, we predict an extremely low probability of PspCas13b having off-target effects on other cellular transcripts. Proteomic analysis validated this prediction and showed that, unlike other Cas13 orthologs, PspCas13b exhibits potent on-target activity and lacks collateral effects.
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Affiliation(s)
- Wenxin Hu
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Amit Kumar
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
- Diagnostic Genomics, Monash Health Pathology, Monash Medical Centre, Clayton, Victoria, Australia
| | - Syed Faraz Ahmed
- Department of Electrical and Electronic Engineering, The University of Melbourne, Parkville, Victoria, Australia
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Shijiao Qi
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - David K G Ma
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Honglin Chen
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Gurjeet J Singh
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Joshua M L Casan
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Michelle Haber
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, New South Wales, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Ilia Voskoboinik
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Matthew R McKay
- Department of Electrical and Electronic Engineering, The University of Melbourne, Parkville, Victoria, Australia
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Joseph A Trapani
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Paul G Ekert
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, New South Wales, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Mohamed Fareh
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia.
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Dong Y, Zhang Q, Mao Y, Wu M, Wang Z, Chang L, Zhang J. Control of two insect pests by expression of a mismatch corrected double-stranded RNA in plants. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:2010-2019. [PMID: 38426894 PMCID: PMC11182576 DOI: 10.1111/pbi.14321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 02/01/2024] [Accepted: 02/18/2024] [Indexed: 03/02/2024]
Abstract
RNA interference (RNAi) has emerged as an efficient technology for pest control by silencing the essential genes of targeted insects. Owing to its nucleotide sequence-guided working mechanism, RNAi has a high degree of species-specificity without impacts on non-target organisms. However, as plants are inevitably under threat by two or more insect pests in nature, the species-specific mode of RNAi-based technology restricts its wide application for pest control. In this study, we artificially designed an intermediate dsRNA (iACT) targeting two β-Actin (ACT) genes of sap-sucking pests Bemisia tabaci and Myzus persicae by mutual correction of their mismatches. When expressing hairpin iACT (hpiACT) from tobacco nuclear genome, transgenic plants are well protected from both B. tabaci and M. persicae, either individually or simultaneously, as evidenced by reduced fecundity and suppressed ACT gene expression, whereas expression of hpRNA targeting BtACT or MpACT in transgenic tobacco plants could only confer specific resistance to either B. tabaci or M. persicae, respectively. In sum, our data provide a novel proof-of-concept that two different insect species could be simultaneously controlled by artificial synthesis of dsRNA with sequence optimization, which expands the range of transgenic RNAi methods for crop protection.
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Affiliation(s)
- Yi Dong
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life SciencesHubei UniversityWuhanChina
| | - Qi Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life SciencesHubei UniversityWuhanChina
| | - Yarou Mao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life SciencesHubei UniversityWuhanChina
| | - Mengting Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life SciencesHubei UniversityWuhanChina
| | - Zican Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life SciencesHubei UniversityWuhanChina
| | - Ling Chang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life SciencesHubei UniversityWuhanChina
| | - Jiang Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life SciencesHubei UniversityWuhanChina
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
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Kang G, Lee SH, Cho M, Kim JH, Cho H, Kang H. Evaluation of RNA Secondary Stem-Loop Structures in the UTRs of Mouse Hepatitis Virus as New Therapeutic Targets. Pathogens 2024; 13:518. [PMID: 38921815 PMCID: PMC11206603 DOI: 10.3390/pathogens13060518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/17/2024] [Accepted: 06/17/2024] [Indexed: 06/27/2024] Open
Abstract
MHV-A59 is a beta-coronavirus that causes demyelinating encephalitis and hepatitis in mice. Recently, the mouse infection model of MHV-A59 has been used as an alternative animal infection model for SARS-CoV and SARS-CoV-2, aiding the development of new antiviral drugs. In this study, the MHV-A59 model was employed to investigate the potential of SARS-CoV-2 UTRs as new targets for antiviral drugs. Optimal targets within the MHV-A59 UTRs were identified using a shRNA and siRNA design tool, focusing on RNA secondary stem-loop (SL) structures in the UTRs. We then examined whether the designed RNAi constructs could inhibit MHV-A59 replication. In the 5'UTR, the stem-loop 1 (SL1) was identified as the most effective target, while in the 3'UTR, the minimal element for the initiation of negative-strand RNA synthesis (MIN) proved to be the most effective. Importantly, siRNAs targeting SL1 and MIN structures significantly reduced total RNA synthesis, negative-strand genomic RNA synthesis, subgenomic (sg) RNA synthesis, viral titer, and the plaque size of MHV-A59 compared to the control. Although not statistically significant, the combination of siSL1 and siMIN had a stronger effect on inhibiting MHV-A59 replication than either siRNA monotherapy. Interestingly, while the SL1 structure is present in both MHV and SARS-CoV-2, the MIN structure is unique to MHV. Thus, the SL1 of SARS-CoV-2 may represent a novel and promising target for RNAi-based antiviral drugs.
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Affiliation(s)
- Gyuhyun Kang
- Vessel-Organ Interaction Research Center, Research Institute of Pharmaceutical Science, College of Pharmacy, Kyungpook National University, Daegu 41566, Republic of Korea; (G.K.); (S.H.L.); (M.C.); (J.-h.K.)
| | - Sun Hee Lee
- Vessel-Organ Interaction Research Center, Research Institute of Pharmaceutical Science, College of Pharmacy, Kyungpook National University, Daegu 41566, Republic of Korea; (G.K.); (S.H.L.); (M.C.); (J.-h.K.)
| | - Miyeon Cho
- Vessel-Organ Interaction Research Center, Research Institute of Pharmaceutical Science, College of Pharmacy, Kyungpook National University, Daegu 41566, Republic of Korea; (G.K.); (S.H.L.); (M.C.); (J.-h.K.)
| | - Ji-hyeon Kim
- Vessel-Organ Interaction Research Center, Research Institute of Pharmaceutical Science, College of Pharmacy, Kyungpook National University, Daegu 41566, Republic of Korea; (G.K.); (S.H.L.); (M.C.); (J.-h.K.)
| | - Hyosun Cho
- Duksung Innovative Drug Center, College of Pharmacy, Duksung Women’s University, Seoul 01369, Republic of Korea
| | - Hyojeung Kang
- Vessel-Organ Interaction Research Center, Research Institute of Pharmaceutical Science, College of Pharmacy, Kyungpook National University, Daegu 41566, Republic of Korea; (G.K.); (S.H.L.); (M.C.); (J.-h.K.)
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10
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Shibamoto A, Kitsu Y, Shibata K, Kaneko Y, Moriizumi H, Takahashi T. microRNA-guided immunity against respiratory virus infection in human and mouse lung cells. Biol Open 2024; 13:bio060172. [PMID: 38875000 PMCID: PMC11212637 DOI: 10.1242/bio.060172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 05/16/2024] [Indexed: 06/15/2024] Open
Abstract
Viral infectivity depends on multiple factors. Recent studies showed that the interaction between viral RNAs and endogenous microRNAs (miRNAs) regulates viral infectivity; viral RNAs function as a sponge of endogenous miRNAs and result in upregulation of its original target genes, while endogenous miRNAs target viral RNAs directly and result in repression of viral gene expression. In this study, we analyzed the possible interaction between parainfluenza virus RNA and endogenous miRNAs in human and mouse lungs. We showed that the parainfluenza virus can form base pairs with human miRNAs abundantly than mouse miRNAs. Furthermore, we analyzed that the sponge effect of endogenous miRNAs on viral RNAs may induce the upregulation of transcription regulatory factors. Then, we performed RNA-sequence analysis and observed the upregulation of transcription regulatory factors in the early stages of parainfluenza virus infection. Our studies showed how the differential expression of endogenous miRNAs in lungs could contribute to respiratory virus infection and species- or tissue-specific mechanisms and common mechanisms could be conserved in humans and mice and regulated by miRNAs during viral infection.
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Affiliation(s)
- Ayaka Shibamoto
- Department of Biochemistry and Molecular Biology, Faculty of Science, Saitama University, Saitama 338-8570, Japan
| | - Yoshiaki Kitsu
- Department of Biochemistry and Molecular Biology, Faculty of Science, Saitama University, Saitama 338-8570, Japan
| | - Keiko Shibata
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Yuka Kaneko
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Harune Moriizumi
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Tomoko Takahashi
- Department of Biochemistry and Molecular Biology, Faculty of Science, Saitama University, Saitama 338-8570, Japan
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
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11
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Opdensteinen P, Charudattan R, Hong JC, Rosskopf EN, Steinmetz NF. Biochemical and nanotechnological approaches to combat phytoparasitic nematodes. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38831638 DOI: 10.1111/pbi.14359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 03/09/2024] [Accepted: 04/05/2024] [Indexed: 06/05/2024]
Abstract
The foundation of most food production systems underpinning global food security is the careful management of soil resources. Embedded in the concept of soil health is the impact of diverse soil-borne pests and pathogens, and phytoparasitic nematodes represent a particular challenge. Root-knot nematodes and cyst nematodes are severe threats to agriculture, accounting for annual yield losses of US$157 billion. The control of soil-borne phytoparasitic nematodes conventionally relies on the use of chemical nematicides, which can have adverse effects on the environment and human health due to their persistence in soil, plants, and water. Nematode-resistant plants offer a promising alternative, but genetic resistance is species-dependent, limited to a few crops, and breeding and deploying resistant cultivars often takes years. Novel approaches for the control of phytoparasitic nematodes are therefore required, those that specifically target these parasites in the ground whilst minimizing the impact on the environment, agricultural ecosystems, and human health. In addition to the development of next-generation, environmentally safer nematicides, promising biochemical strategies include the combination of RNA interference (RNAi) with nanomaterials that ensure the targeted delivery and controlled release of double-stranded RNA. Genome sequencing has identified more than 75 genes in root knot and cyst nematodes that have been targeted with RNAi so far. But despite encouraging results, the delivery of dsRNA to nematodes in the soil remains inefficient. In this review article, we describe the state-of-the-art RNAi approaches targeting phytoparasitic nematodes and consider the potential benefits of nanotechnology to improve dsRNA delivery.
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Affiliation(s)
- Patrick Opdensteinen
- Department of NanoEngineering, University of California, San Diego, La Jolla, California, USA
- Center for Nano-ImmunoEngineering, University of California, San Diego, La Jolla, California, USA
- Shu and K.C. Chien and Peter Farrell Collaboratory, University of California, San Diego, La Jolla, California, USA
| | | | - Jason C Hong
- USDA-ARS-U.S. Horticultural Research Laboratory, Fort Pierce, Florida, USA
| | - Erin N Rosskopf
- USDA-ARS-U.S. Horticultural Research Laboratory, Fort Pierce, Florida, USA
| | - Nicole F Steinmetz
- Department of NanoEngineering, University of California, San Diego, La Jolla, California, USA
- Center for Nano-ImmunoEngineering, University of California, San Diego, La Jolla, California, USA
- Shu and K.C. Chien and Peter Farrell Collaboratory, University of California, San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
- Department of Radiology, University of California, San Diego, La Jolla, California, USA
- Institute for Materials Discovery and Design, University of California, San Diego, La Jolla, California, USA
- Moores Cancer Center, University of California, San Diego, La Jolla, California, USA
- Center for Engineering in Cancer, Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California, USA
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12
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Mukherjee S, Beligala G, Feng C, Marzano SY. Double-Stranded RNA Targeting White Mold Sclerotinia sclerotiorum Argonaute 2 for Disease Control via Spray-Induced Gene Silencing. PHYTOPATHOLOGY 2024; 114:1253-1262. [PMID: 38170667 DOI: 10.1094/phyto-11-23-0431-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Sclerotinia sclerotiorum, the causal agent of white mold infection, is a cosmopolitan fungal pathogen that causes major yield losses in many economically important crops. Spray-induced gene silencing has recently been shown to be a promising alternative method for controlling plant diseases. Based on our prior research, we focused on developing a spray-induced gene silencing approach to control white mold by silencing S. sclerotiorum argonaute 2 (SsAgo2), a crucial part of the fungal small RNA pathway. We compared the lesion size as a result of targeting each ∼500-bp segment of SsAgo2 from the 5' to the 3' end and found that targeting the PIWI/RNaseH domain of SsAgo2 is most effective. External application of double-stranded RNA (dsRNA)-suppressed white mold infection using either in vitro or in vivo transcripts was determined at the rate of 800 ng/0.2 cm2 area with a downregulation of SsAgo2 from infected leaf tissue confirmed by RT-qPCR. Furthermore, magnesium/iron-layered double hydroxide nanosheets loaded with in vitro- and in vivo-transcribed dsRNA segments significantly reduced the rate of S. sclerotiorum lesion expansion. In vivo-produced dsRNA targeting the PIWI/RNaseH domain of the SsAgo2 transcript showed increased efficacy in reducing the white mold symptoms of S. sclerotiorum when combined with layered double hydroxide nanosheets. This approach is promising to produce a large scale of dsRNA that can be deployed as an environmentally friendly fungicide to manage white mold infections in the field.
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Affiliation(s)
- Soumya Mukherjee
- Department of Environmental Sciences, University of Toledo, Toledo, OH
| | | | - Chenchen Feng
- Department of Environmental Sciences, University of Toledo, Toledo, OH
| | - Shin-Yi Marzano
- U.S. Department of Agriculture-Agricultural Research Services, Application Technology Research Unit, Toledo, OH
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13
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Kou J, Li Y, Zhao Z, Qiao J, Zhang Q, Han X, Cheng X, Man S, Ma L. Simultaneous Dual-Gene Test of Methicillin-Resistant Staphylococcus Aureus using an Argonaute-Centered Portable and Visual Biosensor. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2311764. [PMID: 38506607 DOI: 10.1002/smll.202311764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Indexed: 03/21/2024]
Abstract
The development of novel method for drug-resistant bacteria detection is imperative. A simultaneous dual-gene Test of methicillin-resistant Staphylococcus aureus (MRSA) is developed using an Argonaute-centered portable biosensor (STAR). This is the first report concerning Argonaute-based pathogenic bacteria detection. Simply, the species-specific mecA and nuc gene are isothermally amplified using loop-mediated isothermal amplification (LAMP) technique, followed by Argonaute-based detection enabled by its programmable, guided, sequence-specific recognition and cleavage. With the strategy, the targeted nucleic acid signals gene are dexterously converted into fluorescent signals. STAR is capable of detecting the nuc gene and mecA gene simultaneously in a single reaction. The limit of detection is 10 CFU/mL with a dynamic range from 10 to 107 CFU/mL. The sample-to-result time is <65 min. This method is successfully adapted to detect clinical samples, contaminated foods, and MRSA-infected animals. This work broadens the reach of Argonaute-based biosensing and presents a novel bacterial point-of-need (PON) detection platform.
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Affiliation(s)
- Jun Kou
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Yaru Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Zhiying Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Jiali Qiao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Qiang Zhang
- Branch of Tianjin Third Central Hospital, Tianjin, 300250, China
| | - Xiao Han
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Xinkuan Cheng
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Shuli Man
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Long Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
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14
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Di Martino P, Marcozzi V, Bibbò S, Ghinassi B, Di Baldassarre A, Gaggi G, Di Credico A. Unraveling the Epigenetic Landscape: Insights into Parkinson's Disease, Amyotrophic Lateral Sclerosis, and Multiple Sclerosis. Brain Sci 2024; 14:553. [PMID: 38928553 PMCID: PMC11202179 DOI: 10.3390/brainsci14060553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/23/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024] Open
Abstract
Parkinson's disease (PD), multiple sclerosis (MS), and amyotrophic lateral sclerosis (ALS) are examples of neurodegenerative movement disorders (NMDs), which are defined by a gradual loss of motor function that is frequently accompanied by cognitive decline. Although genetic abnormalities have long been acknowledged as significant factors, new research indicates that epigenetic alterations are crucial for the initiation and development of disease. This review delves into the complex interactions that exist between the pathophysiology of NMDs and epigenetic mechanisms such DNA methylation, histone modifications, and non-coding RNAs. Here, we examine how these epigenetic changes could affect protein aggregation, neuroinflammation, and gene expression patterns, thereby influencing the viability and functionality of neurons. Through the clarification of the epigenetic terrain underpinning neurodegenerative movement disorders, this review seeks to enhance comprehension of the underlying mechanisms of the illness and augment the creation of innovative therapeutic strategies.
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Affiliation(s)
- Pierpaolo Di Martino
- Department of Medicine and Aging Sciences, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (P.D.M.); (V.M.); (S.B.); (B.G.); (A.D.B.); (A.D.C.)
| | - Valentina Marcozzi
- Department of Medicine and Aging Sciences, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (P.D.M.); (V.M.); (S.B.); (B.G.); (A.D.B.); (A.D.C.)
| | - Sandra Bibbò
- Department of Medicine and Aging Sciences, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (P.D.M.); (V.M.); (S.B.); (B.G.); (A.D.B.); (A.D.C.)
- Cell Reprogramming and Differentiation Lab, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
| | - Barbara Ghinassi
- Department of Medicine and Aging Sciences, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (P.D.M.); (V.M.); (S.B.); (B.G.); (A.D.B.); (A.D.C.)
- Cell Reprogramming and Differentiation Lab, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
- UdA-Tech Lab, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
| | - Angela Di Baldassarre
- Department of Medicine and Aging Sciences, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (P.D.M.); (V.M.); (S.B.); (B.G.); (A.D.B.); (A.D.C.)
- Cell Reprogramming and Differentiation Lab, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
- UdA-Tech Lab, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
| | - Giulia Gaggi
- Department of Medicine and Aging Sciences, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (P.D.M.); (V.M.); (S.B.); (B.G.); (A.D.B.); (A.D.C.)
- Cell Reprogramming and Differentiation Lab, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
- UdA-Tech Lab, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
| | - Andrea Di Credico
- Department of Medicine and Aging Sciences, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (P.D.M.); (V.M.); (S.B.); (B.G.); (A.D.B.); (A.D.C.)
- Cell Reprogramming and Differentiation Lab, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
- UdA-Tech Lab, G. D’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
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15
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Consalvo CD, Aderounmu AM, Donelick HM, Aruscavage PJ, Eckert DM, Shen PS, Bass BL. Caenorhabditis elegans Dicer acts with the RIG-I-like helicase DRH-1 and RDE-4 to cleave dsRNA. eLife 2024; 13:RP93979. [PMID: 38747717 PMCID: PMC11095941 DOI: 10.7554/elife.93979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024] Open
Abstract
Invertebrates use the endoribonuclease Dicer to cleave viral dsRNA during antiviral defense, while vertebrates use RIG-I-like Receptors (RLRs), which bind viral dsRNA to trigger an interferon response. While some invertebrate Dicers act alone during antiviral defense, Caenorhabditis elegans Dicer acts in a complex with a dsRNA binding protein called RDE-4, and an RLR ortholog called DRH-1. We used biochemical and structural techniques to provide mechanistic insight into how these proteins function together. We found RDE-4 is important for ATP-independent and ATP-dependent cleavage reactions, while helicase domains of both DCR-1 and DRH-1 contribute to ATP-dependent cleavage. DRH-1 plays the dominant role in ATP hydrolysis, and like mammalian RLRs, has an N-terminal domain that functions in autoinhibition. A cryo-EM structure indicates DRH-1 interacts with DCR-1's helicase domain, suggesting this interaction relieves autoinhibition. Our study unravels the mechanistic basis of the collaboration between two helicases from typically distinct innate immune defense pathways.
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Affiliation(s)
- Claudia D Consalvo
- Department of Biochemistry, University of UtahSalt Lake CityUnited States
| | | | - Helen M Donelick
- Department of Biochemistry, University of UtahSalt Lake CityUnited States
| | | | - Debra M Eckert
- Department of Biochemistry, University of UtahSalt Lake CityUnited States
| | - Peter S Shen
- Department of Biochemistry, University of UtahSalt Lake CityUnited States
| | - Brenda L Bass
- Department of Biochemistry, University of UtahSalt Lake CityUnited States
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16
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Chen L, Bosmajian C, Woo S. A highly sensitive stem-loop RT-qPCR method to study siRNA intracellular pharmacokinetics and pharmacodynamics. Biol Methods Protoc 2024; 9:bpae029. [PMID: 38783988 PMCID: PMC11112049 DOI: 10.1093/biomethods/bpae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/25/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024] Open
Abstract
Small interfering RNA (siRNA) is a powerful tool for sequence-specific silencing of disease-related genes. In this study, we established and validated a stem-loop reverse transcription-quantitative polymerase chain reaction (RT-qPCR) method applicable for both chemically unmodified and modified siRNA, aiming to elucidate mechanistic intracellular pharmacokinetic and pharmacodynamic (PK/PD) properties of siRNA. We conducted a comprehensive evaluation of factors affecting intracellular siRNA quantification. Our study revealed that immobilization-based siRNA extraction introduced high variation, making it unsuitable for absolute quantification. Conversely, direct cell lysis followed by stem-loop RT-qPCR demonstrated excellent reproducibility, with a quantification range from 0.0002 to 20 femtomole (fmole) for unmodified siRNA and 0.02 to 20 fmole for modified siRNA. The design of a 6-bp overlapping RT primer facilitated the distinction of full-length antisense from its 3'-metabolites, and pre-annealing of antisense to RT primer enhanced sensitivity and reproducibility. Differences in siRNA loss during storage and sample processing were noted among microcentrifuge tubes from various manufacturers. Endogenous miR-16 served as a reference for normalizing cytoplasmic siRNA, while protein concentration post-immunoprecipitation lysis was used to normalize RNA-induced silencing complex (RISC)-loaded siRNA levels. This method successfully enabled a detailed characterization of the time profiles of cytoplasmic and RISC-loaded siRNA, advancing the in vitro-in vivo translation of siRNA therapeutics.
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Affiliation(s)
- Lin Chen
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14214, United States
| | - Caroline Bosmajian
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14214, United States
| | - Sukyung Woo
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14214, United States
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17
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Iracane E, Arias-Sardá C, Maufrais C, Ene IV, d’Enfert C, Buscaino A. Identification of an active RNAi pathway in Candida albicans. Proc Natl Acad Sci U S A 2024; 121:e2315926121. [PMID: 38625945 PMCID: PMC11047096 DOI: 10.1073/pnas.2315926121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 03/08/2024] [Indexed: 04/18/2024] Open
Abstract
RNA interference (RNAi) is a fundamental regulatory pathway with a wide range of functions, including regulation of gene expression and maintenance of genome stability. Although RNAi is widespread in the fungal kingdom, well-known species, such as the model yeast Saccharomyces cerevisiae, have lost the RNAi pathway. Until now evidence has been lacking for a fully functional RNAi pathway in Candida albicans, a human fungal pathogen considered critically important by the World Health Organization. Here, we demonstrated that the widely used C. albicans reference strain (SC5314) contains an inactivating missense mutation in the gene encoding for the central RNAi component Argonaute. In contrast, most other C. albicans isolates contain a canonical Argonaute protein predicted to be functional and RNAi-active. Indeed, using high-throughput small and long RNA sequencing combined with seamless CRISPR/Cas9-based gene editing, we demonstrate that an active C. albicans RNAi machinery represses expression of subtelomeric gene families. Thus, an intact and functional RNAi pathway exists in C. albicans, highlighting the importance of using multiple reference strains when studying this dangerous pathogen.
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Affiliation(s)
- Elise Iracane
- Kent Fungal Group, School of Biosciences, Division of Natural Sciences, University of Kent, CanterburyCT2 7NZ, United Kingdom
| | - Cristina Arias-Sardá
- Kent Fungal Group, School of Biosciences, Division of Natural Sciences, University of Kent, CanterburyCT2 7NZ, United Kingdom
| | - Corinne Maufrais
- Institut Pasteur, Université Paris Cité, Bioinformatic Hub, ParisF-75015, France
| | - Iuliana V. Ene
- Institut Pasteur, Université Paris Cité, Fungal Heterogeneity Group, ParisF-75015, France
| | - Christophe d’Enfert
- Institut Pasteur, Université Paris Cité, Institut national de recherche pour l’agriculture, l’alimentation et l’environnement USC2019, Fungal Biology and Pathogenicity Unit, ParisF-75015, France
| | - Alessia Buscaino
- Kent Fungal Group, School of Biosciences, Division of Natural Sciences, University of Kent, CanterburyCT2 7NZ, United Kingdom
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18
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Lin S, Jing H, Du X, Yang X, Wang J. Optimization of lipid assisted polymeric nanoparticles for siRNA delivery and cancer immunotherapy. Biomater Sci 2024; 12:2057-2066. [PMID: 38469870 DOI: 10.1039/d3bm02071a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
To date, five siRNA-based medications have received clinical approval and have demonstrated remarkable therapeutic efficacy in treating various diseases. However, their application has been predominantly limited to liver-specific diseases due to constraints in siRNA delivery capabilities. In this study, we have developed a siRNA delivery system utilizing clinically approved mPEG-b-PLGA, a cationic lipid, and an ionizable lipid. We optimized this system by carefully adjusting their mass ratios, resulting in highly efficient gene silencing. Furthermore, the optimized nanoparticle formulation, which encapsulates siRNA targeting CD47, induces a robust immune response. This response effectively suppresses the progression of melanoma tumors by blocking this critical immune checkpoint.
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Affiliation(s)
- Song Lin
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, Guangdong 511442, P. R. China.
| | - Houjin Jing
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, Guangdong 511442, P. R. China.
| | - Xiaojiao Du
- School of Medicine, South China University of Technology, Guangzhou 510006, PR China.
| | - Xianzhu Yang
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, Guangdong 511442, P. R. China.
| | - Jun Wang
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, Guangdong 511442, P. R. China.
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19
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Dabin A, Stirnemann G. Atomistic simulations of RNA duplex thermal denaturation: Sequence- and forcefield-dependence. Biophys Chem 2024; 307:107167. [PMID: 38262278 DOI: 10.1016/j.bpc.2023.107167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/26/2023] [Accepted: 12/28/2023] [Indexed: 01/25/2024]
Abstract
Double-stranded RNA is the end-product of template-based replication, and is also the functional state of some biological RNAs. Similarly to proteins and DNA, they can be denatured by temperature, with important physiological and technological implications. Here, we use an in silico strategy to probe the thermal denaturation of RNA duplexes. Following previous results that were obtained on a few different duplexes, and which nuanced the canonical 2-state picture of nucleic acid denaturation, we here specifically address three different aspects that greatly improve our description of the temperature-induced dsRNA separation. First, we investigate the effect of the spatial distribution of weak and strong base-pairs among the duplex sequence. We show that the deviations from the two-state dehybridization mechanism are more pronounced when a strong core is flanked with weak extremities, while duplexes with a weak core but strong extremities exhibit a two-state behavior, which can be explained by the key role played by base fraying. This was later verified by generating artificial hairpin or circular states containing one or two locked duplex extremities, which results in an important reinforcement of the entire HB structure of the duplex and higher melting temperatures. Finally, we demonstrate that our results are little sensitive to the employed combination of RNA and water forcefields. The trends in thermal stability among the different sequences as well as the observed unfolding mechanisms (and the deviations from a two-state scenario) remain the same regardless of the employed atomistic models. However, our study points to possible limitations of recent reparametrizations of the Amber RNA forcefield, which sometimes results in duplexes that readily denature under ambient conditions, in contradiction with available experimental results.
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Affiliation(s)
- Aimeric Dabin
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Université de Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Guillaume Stirnemann
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
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20
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Klementieva NV, Lunev EA, Shmidt AA, Loseva EM, Savchenko IM, Svetlova EA, Galkin II, Polikarpova AV, Usachev EV, Vassilieva SG, Marina VI, Dzhenkova MA, Romanova AD, Agutin AV, Timakova AA, Reshetov DA, Egorova TV, Bardina MV. RNA Interference Effectors Selectively Silence the Pathogenic Variant GNAO1 c.607 G > A In Vitro. Nucleic Acid Ther 2024; 34:90-99. [PMID: 38215303 DOI: 10.1089/nat.2023.0043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2024] Open
Abstract
RNA interference (RNAi)-based therapeutics hold the potential for dominant genetic disorders, enabling sequence-specific inhibition of pathogenic gene products. We aimed to direct RNAi for the selective suppression of the heterozygous GNAO1 c.607 G > A variant causing GNAO1 encephalopathy. By screening short interfering RNA (siRNA), we showed that GNAO1 c.607G>A is a druggable target for RNAi. The si1488 candidate achieved at least twofold allelic discrimination and downregulated mutant protein to 35%. We created vectorized RNAi by incorporating the si1488 sequence into the short hairpin RNA (shRNA) in the adeno-associated virus (AAV) vector. The shRNA stem and loop were modified to improve the transcription, processing, and guide strand selection. All tested shRNA constructs demonstrated selectivity toward mutant GNAO1, while tweaking hairpin structure only marginally affected the silencing efficiency. The selectivity of shRNA-mediated silencing was confirmed in the context of AAV vector transduction. To conclude, RNAi effectors ranging from siRNA to AAV-RNAi achieve suppression of the pathogenic GNAO1 c.607G>A and discriminate alleles by the single-nucleotide substitution. For gene therapy development, it is crucial to demonstrate the benefit of these RNAi effectors in patient-specific neurons and animal models of the GNAO1 encephalopathy.
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Affiliation(s)
- Natalia V Klementieva
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
| | - Evgenii A Lunev
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna A Shmidt
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Irina M Savchenko
- Marlin Biotech LLC, Sochi, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina A Svetlova
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
| | - Ivan I Galkin
- Marlin Biotech LLC, Sochi, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna V Polikarpova
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
| | - Evgeny V Usachev
- Laboratory of Translational Biomedicine, Gamaleya National Research Center for Epidemiology, Moscow, Russia
| | - Svetlana G Vassilieva
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
| | | | - Marina A Dzhenkova
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
| | - Anna D Romanova
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
| | - Anton V Agutin
- State Budgetary Healthcare Institution of Moscow Region "Balashikha Hospital," Balashikha, Russia
| | - Anna A Timakova
- Institute for Regenerative Medicine, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | | | - Tatiana V Egorova
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
| | - Maryana V Bardina
- Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Marlin Biotech LLC, Sochi, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
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21
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Silvestrini AVP, Morais MF, Debiasi BW, Praça FG, Bentley MVLB. Nanotechnology strategies to address challenges in topical and cellular delivery of siRNAs in skin disease therapy. Adv Drug Deliv Rev 2024; 207:115198. [PMID: 38341146 DOI: 10.1016/j.addr.2024.115198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/14/2023] [Accepted: 02/02/2024] [Indexed: 02/12/2024]
Abstract
Gene therapy is one of the most advanced therapies in current medicine. In particular, interference RNA-based therapy by small interfering RNA (siRNA) has gained attention in recent years as it is a highly versatile, selective and specific therapy. In dermatological conditions, topical delivery of siRNA offers numerous therapeutic advantages, mainly by inhibiting the expression of target transcripts directly in the skin. However, crossing the stratum corneum and overcoming intracellular barriers is an inherent challenge. Substantial efforts by scientists have moved towards the use of multimodal and multifunctional nanoparticles to overcome these barriers and achieve greater bioavailability in their site of action, the cytoplasm. In this review the most innovative strategies based on nanoparticle and physical methods are presented, as well as the design principles and the main factors that contribute to the performance of these systems. This review also highlights the synergistic contributions of medicine, nanotechnology, and molecular biology to advancing translational research into siRNA-based therapeutics for skin diseases.
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Affiliation(s)
- Ana Vitoria Pupo Silvestrini
- School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Av. do Café, s/n, 14040-903 Ribeirão Preto, SP, Brazil
| | - Milena Finazzi Morais
- School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Av. do Café, s/n, 14040-903 Ribeirão Preto, SP, Brazil
| | - Bryan Wender Debiasi
- School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Av. do Café, s/n, 14040-903 Ribeirão Preto, SP, Brazil
| | - Fabíola Garcia Praça
- School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Av. do Café, s/n, 14040-903 Ribeirão Preto, SP, Brazil
| | - Maria Vitória Lopes Badra Bentley
- School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Av. do Café, s/n, 14040-903 Ribeirão Preto, SP, Brazil.
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22
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Shatskikh AS, Fefelova EA, Klenov MS. Functions of RNAi Pathways in Ribosomal RNA Regulation. Noncoding RNA 2024; 10:19. [PMID: 38668377 PMCID: PMC11054153 DOI: 10.3390/ncrna10020019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/19/2024] [Accepted: 03/27/2024] [Indexed: 04/29/2024] Open
Abstract
Argonaute proteins, guided by small RNAs, play crucial roles in gene regulation and genome protection through RNA interference (RNAi)-related mechanisms. Ribosomal RNAs (rRNAs), encoded by repeated rDNA units, constitute the core of the ribosome being the most abundant cellular transcripts. rDNA clusters also serve as sources of small RNAs, which are loaded into Argonaute proteins and are able to regulate rDNA itself or affect other gene targets. In this review, we consider the impact of small RNA pathways, specifically siRNAs and piRNAs, on rRNA gene regulation. Data from diverse eukaryotic organisms suggest the potential involvement of small RNAs in various molecular processes related to the rDNA transcription and rRNA fate. Endogenous siRNAs are integral to the chromatin-based silencing of rDNA loci in plants and have been shown to repress rDNA transcription in animals. Small RNAs also play a role in maintaining the integrity of rDNA clusters and may function in the cellular response to rDNA damage. Studies on the impact of RNAi and small RNAs on rRNA provide vast opportunities for future exploration.
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Affiliation(s)
- Aleksei S. Shatskikh
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilov Street, 119334 Moscow, Russia;
| | - Elena A. Fefelova
- Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., 123182 Moscow, Russia
| | - Mikhail S. Klenov
- Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., 123182 Moscow, Russia
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA
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23
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Soares S, Aires F, Monteiro A, Pinto G, Faria I, Sales G, Correa-Duarte MA, Guerreiro S, Fernandes R. Radiotherapy Metastatic Prostate Cancer Cell Lines Treated with Gold Nanorods Modulate miRNA Signatures. Int J Mol Sci 2024; 25:2754. [PMID: 38474003 DOI: 10.3390/ijms25052754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 02/21/2024] [Accepted: 02/24/2024] [Indexed: 03/14/2024] Open
Abstract
MicroRNA (miRNA) modulation has been identified as a promising strategy for improving the response of human prostate cancer (PCa) to radiotherapy (RT). Studies have shown that mimics or inhibitors of miRNAs could modulate the sensitivity of PCa cells to RT. In addition, pegylated gold nanoparticles have been studied as a therapeutic approach to treat PCa cells and/or vehicles for carrying miRNAs to the inside of cells. Therefore, we evaluated the capacity of hypofractionated RT and pegylated gold nanorods (AuNPr-PEG) to modulate the miRNA signature on PCa cells. Thus, RT-qPCR was used to analyze miRNA-95, miRNA-106-5p, miRNA-145-5p, and miRNA-541-3p on three human metastatic prostate cell lines (PC3, DU145, and LNCaP) and one human prostate epithelial cell line (HprEpiC, a non-tumor cell line) with and without treatment. Our results showed that miRNA expression levels depend on cell type and the treatment combination applied using RT and AuNPr-PEG. In addition, cells pre-treated with AuNPr-PEG and submitted to 2.5 Gy per day for 3 days decreased the expression levels of miRNA-95, miRNA-106, miRNA-145, and miRNA-541-3p. In conclusion, PCa patients submitted to hypofractionated RT could receive personalized treatment based on their metastatic cellular miRNA signature, and AuNPr-PEG could be used to increase metastatic cell radiosensitivity.
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Affiliation(s)
- Sílvia Soares
- (i3S), Instituto de Investigação e Inovação em Saúde, 4200-135 Porto, Portugal
- FP-I3ID, Instituto de Investigação, Inovação e Desenvolvimento, FP-BHS, Biomedical and Health Sciences, Universidade Fernando Pessoa (UFP), 4249-004 Porto, Portugal
- CECLIN, Centro de Estudos Clínicos, Hospital Escola Fernando Pessoa, 4420-096 Gondomar, Portugal
- Faculty of Chemistry, University of Vigo, 36310 Vigo, Spain
- CEB, Centre of Biological Engineering, Minho University, 4710-057 Braga, Portugal
- Biomark@UC/CEB-Centre of Biological Engineering of Minho University, Department of Chemical Engineering, Faculty of Sciences and Technology, Coimbra University, 3030-790 Coimbra, Portugal
- Radiotherapy Service, São João Hospital Center, 4200-319 Porto, Portugal
| | - Fátima Aires
- Radiotherapy Service, São João Hospital Center, 4200-319 Porto, Portugal
| | - Armanda Monteiro
- Radiotherapy Service, São João Hospital Center, 4200-319 Porto, Portugal
| | - Gabriela Pinto
- Radiotherapy Service, São João Hospital Center, 4200-319 Porto, Portugal
| | - Isabel Faria
- FP-I3ID, Instituto de Investigação, Inovação e Desenvolvimento, FP-BHS, Biomedical and Health Sciences, Universidade Fernando Pessoa (UFP), 4249-004 Porto, Portugal
- CECLIN, Centro de Estudos Clínicos, Hospital Escola Fernando Pessoa, 4420-096 Gondomar, Portugal
| | - Goreti Sales
- CEB, Centre of Biological Engineering, Minho University, 4710-057 Braga, Portugal
- Biomark@UC/CEB-Centre of Biological Engineering of Minho University, Department of Chemical Engineering, Faculty of Sciences and Technology, Coimbra University, 3030-790 Coimbra, Portugal
| | - Miguel A Correa-Duarte
- CINBIO, University of Vigo, 36310 Vigo, Spain
- Southern Galicia Institute of Health Research (IISGS), Biomedical Research Networking Center for Mental Health (CIBERSAM), 36310 Madrid, Spain
| | - Susana Guerreiro
- (i3S), Instituto de Investigação e Inovação em Saúde, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto-IPATIMUP, 4200-465 Porto, Portugal
- Department of Biomedicine, Biochemistry Unit, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
- Faculty of Nutrition and Food Sciences, University of Porto, 4150-180 Porto, Portugal
| | - Rúben Fernandes
- (i3S), Instituto de Investigação e Inovação em Saúde, 4200-135 Porto, Portugal
- FP-I3ID, Instituto de Investigação, Inovação e Desenvolvimento, FP-BHS, Biomedical and Health Sciences, Universidade Fernando Pessoa (UFP), 4249-004 Porto, Portugal
- CECLIN, Centro de Estudos Clínicos, Hospital Escola Fernando Pessoa, 4420-096 Gondomar, Portugal
- UFP@RISE, Rede de Investigação em Saúde, Universidade Fernando Pessoa, 4249-004 Porto, Portugal
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24
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Kiselev KV, Suprun AR, Aleynova OA, Ogneva ZV, Dubrovina AS. Simultaneous Application of Several Exogenous dsRNAs for the Regulation of Anthocyanin Biosynthesis in Arabidopsis thaliana. PLANTS (BASEL, SWITZERLAND) 2024; 13:541. [PMID: 38498529 PMCID: PMC10893326 DOI: 10.3390/plants13040541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/10/2024] [Accepted: 02/14/2024] [Indexed: 03/20/2024]
Abstract
Plant surface treatment with double-stranded RNAs (dsRNAs) has gained recognition as a promising method for inducing gene silencing and combating plant pathogens. However, the regulation of endogenous plant genes by external dsRNAs has not been sufficiently investigated. Also, the effect of the simultaneous application of multiple gene-specific dsRNAs has not been analyzed. The aim of this study was to exogenously target five genes in Arabidopsis thaliana, namely, three transcription factor genes (AtCPC, AtMybL2, AtANAC032), a calmodulin-binding protein gene (AtCBP60g), and an anthocyanidin reductase gene (AtBAN), which are known as negative regulators of anthocyanin accumulation. Exogenous dsRNAs encoding these genes were applied to the leaf surface of A. thaliana either individually or in mixtures. The mRNA levels of the five targets were analyzed using qRT-PCR, and anthocyanin content was evaluated through HPLC-MS. The results demonstrated significant downregulation of all five target genes by the exogenous dsRNAs, resulting in enhanced expression of chalcone synthase (AtCHS) gene and increased anthocyanin content. The simultaneous foliar application of the five dsRNAs proved to be more efficient in activating anthocyanin accumulation compared to the application of individual dsRNAs. These findings hold considerable importance in plant biotechnology and gene function studies.
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Affiliation(s)
- Konstantin V Kiselev
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia
| | - Andrey R Suprun
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia
| | - Olga A Aleynova
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia
| | - Zlata V Ogneva
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia
| | - Alexandra S Dubrovina
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia
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25
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Montagud‐Martínez R, Márquez‐Costa R, Heras‐Hernández M, Dolcemascolo R, Rodrigo G. On the ever-growing functional versatility of the CRISPR-Cas13 system. Microb Biotechnol 2024; 17:e14418. [PMID: 38381083 PMCID: PMC10880580 DOI: 10.1111/1751-7915.14418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 02/22/2024] Open
Abstract
CRISPR-Cas systems evolved in prokaryotes to implement a powerful antiviral immune response as a result of sequence-specific targeting by ribonucleoproteins. One of such systems consists of an RNA-guided RNA endonuclease, known as CRISPR-Cas13. In very recent years, this system is being repurposed in different ways in order to decipher and engineer gene expression programmes. Here, we discuss the functional versatility of the CRISPR-Cas13 system, which includes the ability for RNA silencing, RNA editing, RNA tracking, nucleic acid detection and translation regulation. This functional palette makes the CRISPR-Cas13 system a relevant tool in the broad field of systems and synthetic biology.
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Affiliation(s)
- Roser Montagud‐Martínez
- Institute for Integrative Systems Biology (I2SysBio)CSIC – University of ValenciaPaternaSpain
| | - Rosa Márquez‐Costa
- Institute for Integrative Systems Biology (I2SysBio)CSIC – University of ValenciaPaternaSpain
| | - María Heras‐Hernández
- Institute for Integrative Systems Biology (I2SysBio)CSIC – University of ValenciaPaternaSpain
| | - Roswitha Dolcemascolo
- Institute for Integrative Systems Biology (I2SysBio)CSIC – University of ValenciaPaternaSpain
| | - Guillermo Rodrigo
- Institute for Integrative Systems Biology (I2SysBio)CSIC – University of ValenciaPaternaSpain
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26
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Lu P, Simas TAM, Delpapa E, ZhuGe R. Bitter taste receptors in the reproductive system: Function and therapeutic implications. J Cell Physiol 2024; 239:e31179. [PMID: 38219077 PMCID: PMC10922893 DOI: 10.1002/jcp.31179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/21/2023] [Accepted: 12/11/2023] [Indexed: 01/15/2024]
Abstract
Type 2 taste receptors (TAS2Rs), traditionally known for their role in bitter taste perception, are present in diverse reproductive tissues of both sexes. This review explores our current understanding of TAS2R functions with a particular focus on reproductive health. In males, TAS2Rs are believed to play potential roles in processes such as sperm chemotaxis and male fertility. Genetic insights from mouse models and human polymorphism studies provide some evidence for their contribution to male infertility. In female reproduction, it is speculated that TAS2Rs influence the ovarian milieu, shaping the functions of granulosa and cumulus cells and their interactions with oocytes. In the uterus, TAS2Rs contribute to uterine relaxation and hold potential as therapeutic targets for preventing preterm birth. In the placenta, they are proposed to function as vigilant sentinels, responding to infection and potentially modulating mechanisms of fetal protection. In the cervix and vagina, their analogous functions to those in other extraoral tissues suggest a potential role in infection defense. In addition, TAS2Rs exhibit altered expression patterns that profoundly affect cancer cell proliferation and apoptosis in reproductive cancers. Notably, TAS2R agonists show promise in inducing apoptosis and overcoming chemoresistance in these malignancies. Despite these advances, challenges remain, including a lack of genetic and functional studies. The application of techniques such as single-cell RNA sequencing and clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated endonuclease 9 gene editing could provide deeper insights into TAS2Rs in reproduction, paving the way for novel therapeutic strategies for reproductive disorders.
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Affiliation(s)
- Ping Lu
- Department of Microbiology and Physiological System, UMass Chan Medical School, 363 Plantation St., Worcester, MA, USA
| | - Tiffany A. Moore Simas
- Department of Obstetrics and Gynecology, UMass Chan Medical School/UMass Memorial Health, Memorial Campus 119 Belmont St., Worcester, MA, USA
| | - Ellen Delpapa
- Department of Obstetrics and Gynecology, UMass Chan Medical School/UMass Memorial Health, Memorial Campus 119 Belmont St., Worcester, MA, USA
| | - Ronghua ZhuGe
- Department of Microbiology and Physiological System, UMass Chan Medical School, 363 Plantation St., Worcester, MA, USA
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27
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Bahl E, Jyoti A, Singh A, Siddqui A, Upadhyay SK, Jain D, Shah MP, Saxena J. Nanomaterials for intelligent CRISPR-Cas tools: improving environment sustainability. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024:10.1007/s11356-024-32101-x. [PMID: 38291210 DOI: 10.1007/s11356-024-32101-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 01/17/2024] [Indexed: 02/01/2024]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) is a desirable gene modification tool covering a wide area in various sectors of medicine, agriculture, and microbial biotechnology. The role of this incredible genetic engineering technology has been extensively investigated; however, it remains formidable with cargo choices, nonspecific delivery, and insertional mutagenesis. Various nanomaterials including lipid, polymeric, and inorganic are being used to deliver the CRISPR-Cas system. Progress in nanomaterials could potentially address these challenges by accelerating precision targeting, cost-effectiveness, and one-step delivery. In this review, we highlighted the advances in nanotechnology and nanomaterials as smart delivery systems for CRISPR-Cas so as to ameliorate applications for environmental remediation including biomedical research and healthcare, strategies for mitigating antimicrobial resistance, and to be used as nanofertilizers for enhancing crop growth, and reducing the environmental impact of traditional fertilizers. The timely co-evolution of nanotechnology and CRISPR technologies has contributed to smart novel nanostructure hybrids for improving the onerous tasks of environmental remediation and biological sustainability.
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Affiliation(s)
- Ekansh Bahl
- Department of Biotechnology, University Institute of Biotechnology, Chandigarh University, S.A.S Nagar, 140413, Punjab, India
| | - Anupam Jyoti
- Department of Life Science, Parul Institute of Applied Science, Parul University, Vadodara, Gujarat, India
| | - Abhijeet Singh
- Department of Biosciences, Manipal University Jaipur, Rajasthan, 303007, India
| | - Arif Siddqui
- Department of Biology, College of Science, University of Ha'il, P.O. Box 2440, Ha'il, Saudi Arabia
| | - Sudhir K Upadhyay
- Department of Environmental Science, V.B.S. Purvanchal University, Jaunpur, 222003, India
| | - Devendra Jain
- Department of Molecular Biology and Biotechnology, Rajasthan College of Agriculture, Maharana Pratap University of Agriculture and Technology, Udaipur, 313001, India
| | - Maulin P Shah
- Industrial Wastewater Research Lab, Ankleshwar, India
| | - Juhi Saxena
- Department of Biotechnology, University Institute of Biotechnology, Chandigarh University, S.A.S Nagar, 140413, Punjab, India.
- Department of Biotechnology, Parul Institute of Technology, Parul University, Vadodara, Gujarat, India.
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28
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Mueller F, Witteveldt J, Macias S. Antiviral Defence Mechanisms during Early Mammalian Development. Viruses 2024; 16:173. [PMID: 38399949 PMCID: PMC10891733 DOI: 10.3390/v16020173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/11/2024] [Accepted: 01/20/2024] [Indexed: 02/25/2024] Open
Abstract
The type-I interferon (IFN) response constitutes the major innate immune pathway against viruses in mammals. Despite its critical importance for antiviral defence, this pathway is inactive during early embryonic development. There seems to be an incompatibility between the IFN response and pluripotency, the ability of embryonic cells to develop into any cell type of an adult organism. Instead, pluripotent cells employ alternative ways to defend against viruses that are typically associated with safeguard mechanisms against transposable elements. The absence of an inducible IFN response in pluripotent cells and the constitutive activation of the alternative antiviral pathways have led to the hypothesis that embryonic cells are highly resistant to viruses. However, some findings challenge this interpretation. We have performed a meta-analysis that suggests that the susceptibility of pluripotent cells to viruses is directly correlated with the presence of receptors or co-receptors for viral adhesion and entry. These results challenge the current view of pluripotent cells as intrinsically resistant to infections and raise the fundamental question of why these cells have sacrificed the major antiviral defence pathway if this renders them susceptible to viruses.
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Affiliation(s)
- Felix Mueller
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, King’s Buildings, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK; (F.M.); (J.W.)
- Centre for Virus Research, MRC-University of Glasgow, Garscube Campus, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Jeroen Witteveldt
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, King’s Buildings, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK; (F.M.); (J.W.)
| | - Sara Macias
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, King’s Buildings, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK; (F.M.); (J.W.)
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29
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Nguyen Thi YV, Ngo AD, Chu DT, Lin SC, Wu CC. RNA therapeutics for regenerative medicine. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 204:163-176. [PMID: 38458737 DOI: 10.1016/bs.pmbts.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/10/2024]
Abstract
It is estimated that millions of people around the world experience various types of tissue injuries every year. Regenerative medicine was born and developed for understanding and application with the aim of replacing affected organs or some cells. The research, manufacture, production, and distribution of RNA in cells have acted as a basic foundation for the development and testing of therapies and treatments that are widely applied in different fields of medicine. Vaccines against COVID-19 are considered one of the brilliant and outstanding successes of RNA therapeutics research. With the characteristics of bio-derived RNA therapeutics, the mechanism of rapid implementation, safe production, and flexibility to create proteins depending on actual requirements. Based on the advantages above in this review, we discuss RNA therapeutics for regenerative medicine, and the types of RNA therapies currently being used for regenerative medicine. The relationship between disease and regenerative medicine is currently being studied or tested in RNA therapeutics. We have also covered the mechanisms of action of RNA therapy for regenerative medicine and some of the limitations in our current understanding of the effects of RNA therapy in this area. Additionally, we have also covered developing RNA therapeutics for regenerative medicine, focusing on RNA therapeutics for regenerative medicine. As a final point, we discuss potential applications for therapeutics for regenerative medicine in the future, as well as their mechanisms.
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Affiliation(s)
- Yen Vy Nguyen Thi
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam
| | - Anh Dao Ngo
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Dinh-Toi Chu
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam; Department of Cell Biology and Anatomy, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
| | - Sheng-Che Lin
- Department of Cell Biology and Anatomy, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Division of Plastic and Reconstructive Surgery, Tainan Municipal An-Nan Hospital-China Medical University, Tainan, Taiwan.
| | - Chia-Ching Wu
- Department of Cell Biology and Anatomy, College of Medicine, National Cheng Kung University, Tainan, Taiwan; International Center for Wound Repair and Regeneration, National Cheng Kung University, Tainan, Taiwan; Department of Biomedical Engineering, National Cheng Kung University, Tainan, Taiwan.
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30
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Consalvo CD, Aderounmu AM, Donelick HM, Aruscavage PJ, Eckert DM, Shen PS, Bass BL. C. elegans Dicer acts with the RIG-I-like helicase DRH-1 and RDE-4 to cleave dsRNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.21.558868. [PMID: 37790392 PMCID: PMC10542151 DOI: 10.1101/2023.09.21.558868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Invertebrates use the endoribonuclease Dicer to cleave viral dsRNA during antiviral defense, while vertebrates use RIG-I-like Receptors (RLRs), which bind viral dsRNA to trigger an interferon response. While some invertebrate Dicers act alone during antiviral defense, C. elegans Dicer acts in a complex with a dsRNA binding protein called RDE-4, and an RLR ortholog called DRH-1. We used biochemical and structural techniques to provide mechanistic insight into how these proteins function together. We found RDE-4 is important for ATP-independent and ATP-dependent cleavage reactions, while helicase domains of both DCR-1 and DRH-1 contribute to ATP-dependent cleavage. DRH-1 plays the dominant role in ATP hydrolysis, and like mammalian RLRs, has an N-terminal domain that functions in autoinhibition. A cryo-EM structure indicates DRH-1 interacts with DCR-1's helicase domain, suggesting this interaction relieves autoinhibition. Our study unravels the mechanistic basis of the collaboration between two helicases from typically distinct innate immune defense pathways.
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Affiliation(s)
| | - Adedeji M. Aderounmu
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112
- These authors contributed equally
| | - Helen M. Donelick
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112
- These authors contributed equally
| | - P. Joe Aruscavage
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112
| | - Debra M. Eckert
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112
| | - Peter S. Shen
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112
| | - Brenda L. Bass
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112
- Lead Contact
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31
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Martinsen E, Jinnurine T, Subramani S, Rogne M. Advances in RNA therapeutics for modulation of 'undruggable' targets. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 204:249-294. [PMID: 38458740 DOI: 10.1016/bs.pmbts.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/10/2024]
Abstract
Over the past decades, drug discovery utilizing small pharmacological compounds, fragment-based therapeutics, and antibody therapy have significantly advanced treatment options for many human diseases. However, a major bottleneck has been that>70% of human proteins/genomic regions are 'undruggable' by the above-mentioned approaches. Many of these proteins constitute essential drug targets against complex multifactorial diseases like cancer, immunological disorders, and neurological diseases. Therefore, alternative approaches are required to target these proteins or genomic regions in human cells. RNA therapeutics is a promising approach for many of the traditionally 'undruggable' targets by utilizing methods such as antisense oligonucleotides, RNA interference, CRISPR/Cas-based genome editing, aptamers, and the development of mRNA therapeutics. In the following chapter, we will put emphasis on recent advancements utilizing these approaches against challenging drug targets, such as intranuclear proteins, intrinsically disordered proteins, untranslated genomic regions, and targets expressed in inaccessible tissues.
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Affiliation(s)
| | | | - Saranya Subramani
- Pioneer Research AS, Oslo Science Park, Oslo, Norway; Department of Pharmacy, Section for Pharmacology and Pharmaceutical Biosciences, University of Oslo, Oslo, Norway
| | - Marie Rogne
- Pioneer Research AS, Oslo Science Park, Oslo, Norway; Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway.
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32
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Shehzada S, Noto T, Saksouk J, Mochizuki K. A SUMO E3 ligase promotes long non-coding RNA transcription to regulate small RNA-directed DNA elimination. eLife 2024; 13:e95337. [PMID: 38197489 PMCID: PMC10830130 DOI: 10.7554/elife.95337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 01/03/2024] [Indexed: 01/11/2024] Open
Abstract
Small RNAs target their complementary chromatin regions for gene silencing through nascent long non-coding RNAs (lncRNAs). In the ciliated protozoan Tetrahymena, the interaction between Piwi-associated small RNAs (scnRNAs) and the nascent lncRNA transcripts from the somatic genome has been proposed to induce target-directed small RNA degradation (TDSD), and scnRNAs not targeted for TDSD later target the germline-limited sequences for programmed DNA elimination. In this study, we show that the SUMO E3 ligase Ema2 is required for the accumulation of lncRNAs from the somatic genome and thus for TDSD and completing DNA elimination to make viable sexual progeny. Ema2 interacts with the SUMO E2 conjugating enzyme Ubc9 and enhances SUMOylation of the transcription regulator Spt6. We further show that Ema2 promotes the association of Spt6 and RNA polymerase II with chromatin. These results suggest that Ema2-directed SUMOylation actively promotes lncRNA transcription, which is a prerequisite for communication between the genome and small RNAs.
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Affiliation(s)
- Salman Shehzada
- Institute of Human Genetics (IGH), CNRS, University of MontpellierMontpellierFrance
| | - Tomoko Noto
- Institute of Human Genetics (IGH), CNRS, University of MontpellierMontpellierFrance
| | - Julie Saksouk
- Institute of Human Genetics (IGH), CNRS, University of MontpellierMontpellierFrance
| | - Kazufumi Mochizuki
- Institute of Human Genetics (IGH), CNRS, University of MontpellierMontpellierFrance
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Chou HT, Valencia F, Alexander JC, Bell AD, Deb D, Pollard DA, Paaby AB. Diversification of small RNA pathways underlies germline RNA interference incompetence in wild Caenorhabditis elegans strains. Genetics 2024; 226:iyad191. [PMID: 37865119 PMCID: PMC10763538 DOI: 10.1093/genetics/iyad191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 07/09/2023] [Accepted: 08/12/2023] [Indexed: 10/23/2023] Open
Abstract
The discovery that experimental delivery of dsRNA can induce gene silencing at target genes revolutionized genetics research, by both uncovering essential biological processes and creating new tools for developmental geneticists. However, the efficacy of exogenous RNA interference (RNAi) varies dramatically within the Caenorhabditis elegans natural population, raising questions about our understanding of RNAi in the lab relative to its activity and significance in nature. Here, we investigate why some wild strains fail to mount a robust RNAi response to germline targets. We observe diversity in mechanism: in some strains, the response is stochastic, either on or off among individuals, while in others, the response is consistent but delayed. Increased activity of the Argonaute PPW-1, which is required for germline RNAi in the laboratory strain N2, rescues the response in some strains but dampens it further in others. Among wild strains, genes known to mediate RNAi exhibited very high expression variation relative to other genes in the genome as well as allelic divergence and strain-specific instances of pseudogenization at the sequence level. Our results demonstrate functional diversification in the small RNA pathways in C. elegans and suggest that RNAi processes are evolving rapidly and dynamically in nature.
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Affiliation(s)
- Han Ting Chou
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Francisco Valencia
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Jacqueline C Alexander
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA
| | - Avery Davis Bell
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Diptodip Deb
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Janelia Research Campus, Ashburn, VA 20147, USA
| | - Daniel A Pollard
- Department of Biology, Western Washington University, Bellingham, WA 98225, USA
| | - Annalise B Paaby
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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Ping N, Hara-Kuge S, Yagi Y, Kazama T, Nakamura T. Translational enhancement of target endogenous mRNA in mammalian cells using programmable RNA-binding pentatricopeptide repeat proteins. Sci Rep 2024; 14:251. [PMID: 38167853 PMCID: PMC10762265 DOI: 10.1038/s41598-023-50776-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 12/25/2023] [Indexed: 01/05/2024] Open
Abstract
Programmable protein scaffolds are invaluable in the development of genome engineering tools. The pentatricopeptide repeat (PPR) protein is an attractive platform for RNA manipulation because of its programmable RNA-binding selectivity, which is determined by the combination of amino acid species at three specific sites in the PPR motif. Translation is a key RNA regulatory step that determines the final gene expression level and is involved in various human diseases. In this study, designer PPR protein was used to develop a translational enhancement technique by fusion with the translation initiation factor eIF4G. The results showed that the PPR-eIF4G fusion protein could activate the translation of endogenous c-Myc and p53 mRNAs and control cell fate, indicating that PPR-based translational enhancement is a versatile technique applicable to various endogenous mRNAs in mammalian cells. In addition, the translational enhancement was dependent on both the target position and presence of eIF4G, suggesting the presence of an unknown translation activation mechanism.
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Affiliation(s)
- Ning Ping
- Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581, Japan
| | - Sayuri Hara-Kuge
- Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581, Japan
| | | | - Tomohiko Kazama
- Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581, Japan
| | - Takahiro Nakamura
- Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581, Japan.
- EditForce, Inc., Fukuoka, 819-0395, Japan.
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Khajeei A, Masoomzadeh S, Gholikhani T, Javadzadeh Y. The Effect of PEGylation on Drugs' Pharmacokinetic Parameters; from Absorption to Excretion. Curr Drug Deliv 2024; 21:978-992. [PMID: 37345248 DOI: 10.2174/1567201820666230621124953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/06/2023] [Accepted: 04/06/2023] [Indexed: 06/23/2023]
Abstract
Until the drugs enter humans life, they may face problems in transportation, drug delivery, and metabolism. These problems can cause reducing drug's therapeutic effect and even increase its side effects. Together, these cases can reduce the patient's compliance with the treatment and complicate the treatment process. Much work has been done to solve or at least reduce these problems. For example, using different forms of a single drug molecule (like Citalopram and Escitalopram); slight changes in the drug's molecule like Meperidine and α-Prodine, and using carriers (like Tigerase®). PEGylation is a recently presented method that can use for many targets. Poly Ethylene Glycol or PEG is a polymer that can attach to drugs by using different methods and resulting sustained release, controlled metabolism, targeted delivery, and other cases. Although they will not necessarily lead to an increase in the effect of the drug, they will lead to the improvement of the treatment process in certain ways. In this article, the team of authors has tried to collect and carefully review the best cases based on the PEGylation of drugs that can help the readers of this article.
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Affiliation(s)
- Ali Khajeei
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
- Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Salar Masoomzadeh
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
- Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Tooba Gholikhani
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
- Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yousef Javadzadeh
- Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
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Werner A. RNA Double-Helix Hybridization Measured by Fluorescence Correlation Spectroscopy. Methods Mol Biol 2024; 2741:175-181. [PMID: 38217653 DOI: 10.1007/978-1-0716-3565-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2024]
Abstract
RNA double-strand hybridization is a key player in gene expression regulation. Single-stranded RNA of up to 300 nucleotides forms Watson-Crick base pairs with complementary messenger RNA. Fluorescence-based single-molecule methods allow to study RNA-RNA interaction under physiological conditions. Here is described, how the dissociation constant of RNA double strands can be determined by applying fluorescence correlation spectroscopy.
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Affiliation(s)
- Arne Werner
- Institute for Biochemistry and Molecular Biology, Department of Chemistry, Faculty of Mathematics, Computer Science and Natural Science, Hamburg University, Hamburg, Germany.
- Institute for Microbiology, Faculty for Mathematics and Natural Science, University Kiel, Kiel, Germany.
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Harisa GI, Faris TM, Sherif AY, Alzhrani RF, Alanazi SA, Kohaf NA, Alanazi FK. Gene-editing technology, from macromolecule therapeutics to organ transplantation: Applications, limitations, and prospective uses. Int J Biol Macromol 2023; 253:127055. [PMID: 37758106 DOI: 10.1016/j.ijbiomac.2023.127055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 09/04/2023] [Accepted: 09/15/2023] [Indexed: 10/03/2023]
Abstract
Gene editing technologies (GETs) could induce gene knockdown or gene knockout for biomedical applications. The clinical success of gene silence by RNAi therapies pays attention to other GETs as therapeutic approaches. This review aims to highlight GETs, categories, mechanisms, challenges, current use, and prospective applications. The different academic search engines, electronic databases, and bibliographies of selected articles were used in the preparation of this review with a focus on the fundamental considerations. The present results revealed that, among GETs, CRISPR/Cas9 has higher editing efficiency and targeting specificity compared to other GETs to insert, delete, modify, or replace the gene at a specific location in the host genome. Therefore, CRISPR/Cas9 is talented in the production of molecular, tissue, cell, and organ therapies. Consequently, GETs could be used in the discovery of innovative therapeutics for genetic diseases, pandemics, cancer, hopeless diseases, and organ failure. Specifically, GETs have been used to produce gene-modified animals to spare human organ failure. Genetically modified pigs are used in clinical trials as a source of heart, liver, kidneys, and lungs for xenotransplantation (XT) in humans. Viral, non-viral, and hybrid vectors have been utilized for the delivery of GETs with some limitations. Therefore, extracellular vesicles (EVs) are proposed as intelligent and future cargoes for GETs delivery in clinical applications. This study concluded that GETs are promising for the production of molecular, cellular, and organ therapies. The use of GETs as XT is still in the early stage as well and they have ethical and biosafety issues.
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Affiliation(s)
- Gamaleldin I Harisa
- Kayyali Chair for Pharmaceutical Industry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia; Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia; Department of Biochemistry and Molecular Biology, College of Pharmacy, Al-Azhar University, Nasr City, Cairo, Egypt.
| | - Tarek M Faris
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, Saudi Arabia
| | - Abdelrahman Y Sherif
- Kayyali Chair for Pharmaceutical Industry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia; Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Riyad F Alzhrani
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia; Nanobiotechnology Research Unit, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Saleh A Alanazi
- Pharmaceutical Care Services, King Abdulaziz Medical City, King Saud bin Abdulaziz University for Health Science Collage of Pharmacy, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Neveen A Kohaf
- Department of Clinical Pharmacy, Faculty of Pharmacy, Al-Azhar University, Cairo 11651, Egypt
| | - Fars K Alanazi
- Kayyali Chair for Pharmaceutical Industry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia; Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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38
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Guidi R, Wedeles C, Xu D, Kolmus K, Headland SE, Teng G, Guillory J, Zeng YJ, Cheung TK, Chaudhuri S, Modrusan Z, Liang Y, Horswell S, Haley B, Rutz S, Rose C, Franke Y, Kirkpatrick DS, Hackney JA, Wilson MS. Argonaute3-SF3B3 complex controls pre-mRNA splicing to restrain type 2 immunity. Cell Rep 2023; 42:113515. [PMID: 38096048 DOI: 10.1016/j.celrep.2023.113515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 08/28/2023] [Accepted: 11/15/2023] [Indexed: 12/30/2023] Open
Abstract
Argonaute (AGO) proteins execute microRNA (miRNA)-mediated gene silencing. However, it is unclear whether all 4 mammalian AGO proteins (AGO1, AGO2, AGO3, and AGO4) are required for miRNA activity. We generate Ago1, Ago3, and Ago4-deficient mice (Ago134Δ) and find AGO1/3/4 to be redundant for miRNA biogenesis, homeostasis, or function, a role that is carried out by AGO2. Instead, AGO1/3/4 regulate the expansion of type 2 immunity via precursor mRNA splicing in CD4+ T helper (Th) lymphocytes. Gain- and loss-of-function experiments demonstrate that nuclear AGO3 interacts directly with SF3B3, a component of the U2 spliceosome complex, to aid global mRNA splicing, and in particular the isoforms of the gene Nisch, resulting in a dysregulated Nisch isoform ratio. This work uncouples AGO1, AGO3, and AGO4 from miRNA-mediated RNA interference, identifies an AGO3:SF3B3 complex in the nucleus, and reveals a mechanism by which AGO proteins regulate inflammatory diseases.
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Affiliation(s)
- Riccardo Guidi
- Immunology Discovery, Genentech, South San Francisco, CA 94080, USA
| | | | - Daqi Xu
- Immunology Discovery, Genentech, South San Francisco, CA 94080, USA
| | - Krzysztof Kolmus
- OMNI Bioinformatics, Genentech, South San Francisco, CA 94080, USA
| | - Sarah E Headland
- Immunology Discovery, Genentech, South San Francisco, CA 94080, USA
| | - Grace Teng
- Immunology Discovery, Genentech, South San Francisco, CA 94080, USA
| | - Joseph Guillory
- Next Generation Sequencing (NGS), Genentech, South San Francisco, CA 94080, USA
| | - Yi Jimmy Zeng
- Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA 94080, USA
| | - Tommy K Cheung
- Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA 94080, USA
| | - Subhra Chaudhuri
- Next Generation Sequencing (NGS), Genentech, South San Francisco, CA 94080, USA
| | - Zora Modrusan
- Next Generation Sequencing (NGS), Genentech, South San Francisco, CA 94080, USA
| | - Yuxin Liang
- Next Generation Sequencing (NGS), Genentech, South San Francisco, CA 94080, USA
| | - Stuart Horswell
- Bioinformatic and Biostatistics, The Francis Crick Institute, London, UK
| | - Benjamin Haley
- Molecular Biology, Genentech, South San Francisco, CA 94080, USA
| | - Sascha Rutz
- Cancer Immunology, Genentech, South San Francisco, CA 94080, USA
| | - Christopher Rose
- Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA 94080, USA
| | - Yvonne Franke
- Protein Sciences, Genentech, South San Francisco, CA 94080, USA
| | - Donald S Kirkpatrick
- Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA 94080, USA
| | - Jason A Hackney
- OMNI Bioinformatics, Genentech, South San Francisco, CA 94080, USA
| | - Mark S Wilson
- Immunology Discovery, Genentech, South San Francisco, CA 94080, USA.
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Mohanty P, Panda P, Acharya RK, Pande B, Bhaskar LVKS, Verma HK. Emerging perspectives on RNA virus-mediated infections: from pathogenesis to therapeutic interventions. World J Virol 2023; 12:242-255. [PMID: 38187500 PMCID: PMC10768389 DOI: 10.5501/wjv.v12.i5.242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/07/2023] [Accepted: 11/29/2023] [Indexed: 12/25/2023] Open
Abstract
RNA viruses continue to pose significant threats to global public health, necessitating a profound understanding of their pathogenic mechanisms and the development of effective therapeutic interventions. This manuscript provides a comprehensive overview of emerging perspectives on RNA virus-mediated infections, spanning from the intricate intricacies of viral pathogenesis to the forefront of innovative therapeutic strategies. A critical exploration of antiviral drugs sets the stage, highlighting the diverse classes of compounds that target various stages of the viral life cycle, underscoring the ongoing efforts to combat viral infections. Central to this discussion is the exploration of RNA-based therapeutics, with a spotlight on messenger RNA (mRNA)-based approaches that have revolutionized the landscape of antiviral interventions. Furthermore, the manuscript delves into the intricate world of delivery systems, exploring inno-vative technologies designed to enhance the efficiency and safety of mRNA vaccines. By analyzing the challenges and advancements in delivery mechanisms, this review offers a roadmap for future research and development in this critical area. Beyond conventional infectious diseases, the document explores the expanding applications of mRNA vaccines, including their promising roles in cancer immunotherapy and personalized medicine approaches. This manuscript serves as a valuable resource for researchers, clinicians, and policymakers alike, offering a nuanced perspective on RNA virus pathogenesis and the cutting-edge therapeutic interventions. By synthesizing the latest advancements and challenges, this review contributes significantly to the ongoing discourse in the field, driving the development of novel strategies to combat RNA virus-mediated infections effectively.
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Affiliation(s)
- Pratik Mohanty
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Guwahati 781039, Assam, India
| | - Poojarani Panda
- Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Rakesh Kumar Acharya
- Department of Zoology, Guru Ghasidas Vishwavidyalaya, Bilaspur, Bilaspur 495009, Chhattisgarh, India
| | - Babita Pande
- Department of Physiology, All India Institute of Medical Science, Raipur 492001, chhattisgarh, India
| | - LVKS Bhaskar
- Department of Zoology, Guru Ghasidas Vishwavidyalaya, Bilaspur, Bilaspur 495009, Chhattisgarh, India
| | - Henu Kumar Verma
- Lung Health and Immunity, Helmholtz Zentrum Munich, Munich 85764, Bayren, Germany
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40
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Chen Y, Lin T, Tang L, He L, He Y. MiRNA signatures in nasopharyngeal carcinoma: molecular mechanisms and therapeutic perspectives. Am J Cancer Res 2023; 13:5805-5824. [PMID: 38187072 PMCID: PMC10767356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 10/10/2023] [Indexed: 01/09/2024] Open
Abstract
Nasopharyngeal carcinoma (NPC) is a prevalent cancerous tumor that affects the head and neck region. Recent studies have provided compelling evidence indicating the significant involvement of microRNAs (miRNAs) in the development and progression of NPC. This review aims to present a comprehensive summary of the current knowledge regarding miRNA signatures in NPC, encompassing their expression patterns, molecular mechanisms, and potential therapeutic implications. Initially, the article outlines the aberrant expression of miRNAs in NPC and elucidates their roles in tumor initiation, invasion, and metastasis. Subsequently, the underlying molecular mechanisms of miRNA-mediated regulation of NPC-associated signaling pathways are discussed. Additionally, the review highlights the potential clinical applications of miRNAs as diagnostic and prognostic biomarkers, as well as their therapeutic potential in NPC treatment. In conclusion, this review underscores the critical involvement of miRNAs in NPC pathogenesis and underscores their promise as novel therapeutic targets for combating this devastating disease.
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Affiliation(s)
- Yan Chen
- School of Medicine, Hunan University of Chinese MedicineChangsha, Hunan, China
| | - Ting Lin
- Hunan Provincial Engineering and Technological Research Center for Prevention and Treatment of Ophthalmology and Otolaryngology Diseases with Chinese Medicine and Protecting Visual Function, Hunan University of Chinese MedicineChangsha 410208, China
- Hunan Provincial Key Lab for The Prevention and Treatment of Ophthalmology and Otolaryngology Diseases with Traditional Chinese Medicine, Hunan University of Chinese MedicineChangsha 410208, China
| | - Le Tang
- School of Medicine, Hunan University of Chinese MedicineChangsha, Hunan, China
- Hunan Provincial Engineering and Technological Research Center for Prevention and Treatment of Ophthalmology and Otolaryngology Diseases with Chinese Medicine and Protecting Visual Function, Hunan University of Chinese MedicineChangsha 410208, China
| | - Lan He
- Hunan Provincial Engineering and Technological Research Center for Prevention and Treatment of Ophthalmology and Otolaryngology Diseases with Chinese Medicine and Protecting Visual Function, Hunan University of Chinese MedicineChangsha 410208, China
- The First Affiliated Hospital of Hunan University of Chinese MedicineChangsha, Hunan, China
| | - Yingchun He
- School of Medicine, Hunan University of Chinese MedicineChangsha, Hunan, China
- Hunan Provincial Engineering and Technological Research Center for Prevention and Treatment of Ophthalmology and Otolaryngology Diseases with Chinese Medicine and Protecting Visual Function, Hunan University of Chinese MedicineChangsha 410208, China
- Hunan Provincial Key Lab for The Prevention and Treatment of Ophthalmology and Otolaryngology Diseases with Traditional Chinese Medicine, Hunan University of Chinese MedicineChangsha 410208, China
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41
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Ebrahimi N, Manavi MS, Nazari A, Momayezi A, Faghihkhorasani F, Rasool Riyadh Abdulwahid AH, Rezaei-Tazangi F, Kavei M, Rezaei R, Mobarak H, Aref AR, Fang W. Nano-scale delivery systems for siRNA delivery in cancer therapy: New era of gene therapy empowered by nanotechnology. ENVIRONMENTAL RESEARCH 2023; 239:117263. [PMID: 37797672 DOI: 10.1016/j.envres.2023.117263] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 09/17/2023] [Accepted: 09/27/2023] [Indexed: 10/07/2023]
Abstract
RNA interference (RNAi) is a unique treatment approach used to decrease a disease's excessive gene expression, including cancer. SiRNAs may find and destroy homologous mRNA sequences within the cell thanks to RNAi processes. However, difficulties such poor cellular uptake, off-target effects, and susceptibility to destruction by serum nucleases in the bloodstream restrict the therapeutic potential of siRNAs. Since some years ago, siRNA-based therapies have been in the process of being translated into the clinic. Therefore, the primary emphasis of this work is on sophisticated nanocarriers that aid in the transport of siRNA payloads, their administration in combination with anticancer medications, and their use in the treatment of cancer. The research looks into molecular manifestations, difficulties with siRNA transport, the design and development of siRNA-based delivery methods, and the benefits and drawbacks of various nanocarriers. The trapping of siRNA in endosomes is a challenge for the majority of delivery methods, which affects the therapeutic effectiveness. Numerous techniques for siRNA release, including as pH-responsive release, membrane fusion, the proton sponge effect, and photochemical disruption, have been studied to overcome this problem. The present state of siRNA treatments in clinical trials is also looked at in order to give a thorough and systematic evaluation of siRNA-based medicines for efficient cancer therapy.
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Affiliation(s)
- Nasim Ebrahimi
- Genetics Division, Department of Cell and Molecular Biology and Microbiology, Faculty of Science and Technology, University of Isfahan, Iran
| | | | - Ahmad Nazari
- Tehran University of Medical Science, Tehran, Iran
| | - Amirali Momayezi
- School of Chemical Engineering, Iran University of Science, and Technology, Tehran, Iran
| | | | | | - Fatemeh Rezaei-Tazangi
- Department of Anatomy, School of Medicine, Fasa University of Medical Science, Fasa, Iran
| | - Mohammed Kavei
- Department of Biology, Faculty of Science, Arak University, Arak, Iran
| | - Roya Rezaei
- Department of Microbiology, College of Science, Agriculture and Modern Technology, Shiraz Branch, Islamic Azad University, Shiraz, Iran
| | - Halimeh Mobarak
- Clinical Pathologist, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Amir Reza Aref
- Xsphera Biosciences, Translational Medicine Group, 6 Tide Street, Boston, MA, 02210, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA.
| | - Wei Fang
- Department of Laser and Aesthetic Medicine, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China.
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42
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Gouda MNR, Jeevan H, Shashank HG. CRISPR/Cas9: a cutting-edge solution for combatting the fall armyworm, Spodoptera frugiperda. Mol Biol Rep 2023; 51:13. [PMID: 38085335 DOI: 10.1007/s11033-023-08986-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/13/2023] [Indexed: 12/18/2023]
Abstract
The utilization of CRISPR/Cas9 in Spodoptera frugiperda, commonly known as fall armyworm, presents a groundbreaking avenue for pest management. With its ability to precisely modify the insect's genome, CRISPR/Cas9 offers innovative strategies to combat this destructive pest. The application of CRISPR/Cas9 in S. frugiperda holds immense potential. It enables the identification and functional analysis of key genes associated with its behavior, development, and insecticide resistance. This knowledge can unveil novel target sites for more effective and specific insecticides. Additionally, CRISPR/Cas9 can facilitate the development of population control methods by disrupting vital genes essential for survival. However, challenges such as off-target effects and the efficient delivery of CRISPR/Cas9 components remain. Addressing these obstacles is vital to ensure accurate and reliable results. Furthermore, ethical considerations, biosafety protocols, and regulatory frameworks must be integral to the adoption of this technology. Looking forward, CRISPR/Cas9-based gene drive systems hold the potential to promulgate desirable genetic traits within S. frugiperda populations, offering a sustainable and eco-friendly approach. This could curtail their reproductive capabilities or make them more susceptible to certain interventions. In conclusion, CRISPR/Cas9 presents a transformative platform for precise and targeted pest management in S. frugiperda. By deciphering the insect's genetic makeup and developing innovative strategies, we can mitigate the devastating impact of fall armyworm on agriculture while ensuring environmental sustainability.
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Affiliation(s)
- M N Rudra Gouda
- Division of Entomology, Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - H Jeevan
- Division of Nematology, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - H G Shashank
- Division of Plant Genetic Resources, Indian Agricultural Research Institute, New Delhi, 110012, India
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Jagrosse ML, Baliga UK, Jones CW, Russell JJ, García CI, Najar RA, Rahman A, Dean DA, Nilsson BL. Impact of Peptide Sequence on Functional siRNA Delivery and Gene Knockdown with Cyclic Amphipathic Peptide Delivery Agents. Mol Pharm 2023; 20:6090-6103. [PMID: 37963105 DOI: 10.1021/acs.molpharmaceut.3c00455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Short-interfering RNA (siRNA) oligonucleotide therapeutics that modify gene expression by accessing RNA-interference (RNAi) pathways have great promise for the treatment of a range of disorders; however, their application in clinical settings has been limited by significant challenges in cellular delivery. Herein, we report a structure-function study using a series of modified cyclic amphipathic cell-penetrating peptides (CAPs) to determine the impact of peptide sequence on (1) siRNA-binding efficiency, (2) cellular delivery and knockdown efficiency, and (3) the endocytic uptake mechanism. Nine cyclic peptides of the general sequence Ac-C[XZ]4CG-NH2 in which X residues are hydrophobic/aromatic (Phe, Tyr, Trp, or Leu) and Z residues are charged/hydrophilic (Arg, Lys, Ser, or Glu) are assessed along with one acyclic peptide, Ac-(WR)4G-NH2. Cyclization is enforced by intramolecular disulfide bond formation between the flanking Cys residues. Binding analyses indicate that strong cationic character and the presence of aromatic residues that are competent to participate in CH-π interactions lead to CAP sequences that most effectively interact with siRNA. CAP-siRNA binding increases in the following order as a function of CAP hydrophobic/aromatic content: His < Phe < Tyr < Trp. Both cationic charge and disulfide-constrained cyclization of CAPs improve uptake of siRNA in vitro. Net neutral CAPs and an acyclic peptide demonstrate less-efficient siRNA translocation compared to the cyclic, cationic CAPs tested. All CAPs tested facilitated efficient siRNA target gene knockdown of at least 50% (as effective as a lipofectamine control), with the best CAPs enabling >80% knockdown. Significantly, gene knockdown efficiency does not strongly correlate with CAP-siRNA internalization efficiency but moderately correlates with CAP-siRNA-binding affinity. Finally, utilization of small-molecule inhibitors and targeted knockdown of essential endocytic pathway proteins indicate that most CAP-siRNA nanoparticles facilitate siRNA delivery through clathrin- and caveolin-mediated endocytosis. These results provide insight into the design principles for CAPs to facilitate siRNA delivery and the mechanisms by which these peptides translocate siRNA into cells. These studies also demonstrate the nature of the relationships between peptide-siRNA binding, cellular delivery of siRNA cargo, and functional gene knockdown. Strong correlations between these properties are not always observed, which illustrates the complexity in the design of optimal next-generation materials for oligonucleotide delivery.
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Affiliation(s)
- Melissa L Jagrosse
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
| | - Uday K Baliga
- Department of Pediatrics and Neonatology, University of Rochester Medical Center, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, United States
| | - Christopher W Jones
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
| | - Jade J Russell
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
| | - Claudia I García
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
| | - Rauf Ahmad Najar
- Department of Pediatrics and Neonatology, University of Rochester Medical Center, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, United States
| | - Arshad Rahman
- Department of Pediatrics and Neonatology, University of Rochester Medical Center, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, United States
| | - David A Dean
- Department of Pediatrics and Neonatology, University of Rochester Medical Center, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, United States
| | - Bradley L Nilsson
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
- Materials Science Program, University of Rochester, Rochester, New York 14627, United States
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Cao X, Wang C, Deng Z, Zhong Y, Chen H. Efficient ocular delivery of siRNA via pH-sensitive vehicles for corneal neovascularization inhibition. Int J Pharm X 2023; 5:100183. [PMID: 37234133 PMCID: PMC10206438 DOI: 10.1016/j.ijpx.2023.100183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/05/2023] [Accepted: 04/28/2023] [Indexed: 05/27/2023] Open
Abstract
Corneal neovascularization (CoNV)-induced blindness is an enduring and challenging condition with limited management options. Small interfering RNA (siRNA) is a promising strategy for preventing CoNV. This study reported a new strategy using siVEGFA to silence vascular endothelial growth factor A (VEGFA) for CoNV treatment. To improve the efficacy of siVEGFA delivery, a pH-sensitive polycationic mPEG2k-PAMA30-P(DEA29-D5A29) (TPPA) was fabricated. TPPA/siVEGFA polyplexes enter cells via clathrin-mediated endocytosis, resulting in higher cellular uptake efficiency and comparable silencing efficiency than that of Lipofectamine 2000 in vitro. Hemolytic assays verified that TPPA safe in normal physiological environments (pH 7.4) but can easily destroy membranes in acidic mature endosomes (pH 4.0). Studies on the distribution of TPPA in vivo showed that it could prolong the retention time of siVEGFA and promote its penetration in the cornea. In a mouse model induced by alkali burn, TPPA efficiently delivered siVEGFA to the lesion site and achieved VEGFA silencing efficiency. Importantly, the inhibitory effect of TPPA/siVEGFA on CoNV was comparable to that of the anti-VEGF drug ranibizumab. Delivering siRNA using pH-sensitive polycations to the ocular environment provides a new strategy to efficiently inhibit CoNV.
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Affiliation(s)
- Xiaowen Cao
- School of Ophthalmology and Optometry/School of Biomedical Engineering, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Changrong Wang
- Engineering Research Center of Molecular & Neuroimaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi 710126, China
| | - Zhennv Deng
- School of Ophthalmology and Optometry/School of Biomedical Engineering, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Yiming Zhong
- School of Ophthalmology and Optometry/School of Biomedical Engineering, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Hao Chen
- School of Ophthalmology and Optometry/School of Biomedical Engineering, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
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Aute R, Deshmukh MV. Chemical shift assignments of dsRBD1 and linker region of R2D2, a siRNA binding protein in the Drosophila RNAi pathway. BIOMOLECULAR NMR ASSIGNMENTS 2023; 17:211-215. [PMID: 37405581 DOI: 10.1007/s12104-023-10143-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 06/23/2023] [Indexed: 07/06/2023]
Abstract
In the model organism Drosophila melanogaster, one of the Dicer homologs, Dcr-2, initiates the RNA interference pathway by cleaving long double-stranded RNA into small interfering RNA (siRNA). The Dcr-2:R2D2 heterodimer subsequently binds to the 21-nucleotide siRNA to form the R2D2:Dcr-2 Initiator (RDI) complex, which is critical for initiating the assembly of the RNA-induced silencing complex containing guide siRNA strand. During RDI complex formation, R2D2 senses the stability of the 5' end of the siRNA and a 5'-phosphate group, although the underlying mechanism of siRNA asymmetry sensing and 5'-phosphate recognition by R2D2 is elusive. In this study, we present nearly complete chemical shift assignments of the backbone and the side chain of a construct that comprises the N-terminus dsRBD1 and linker of R2D2 (~ 10.3 kDa; henceforth: R2D2D1L). Our study would further aid in the structural and functional characterization of R2D2.
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Affiliation(s)
- Ramdas Aute
- CSIR-Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad, Telangana, 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Mandar V Deshmukh
- CSIR-Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad, Telangana, 500007, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Paturi S, Deshmukh MV. NMR resonance assignments of 18.5 kDa complex of Arabidopsis thaliana DRB7.2:DRB4 interaction domains. BIOMOLECULAR NMR ASSIGNMENTS 2023; 17:173-178. [PMID: 37256435 DOI: 10.1007/s12104-023-10137-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 05/24/2023] [Indexed: 06/01/2023]
Abstract
In higher eukaryotes, the dsRNA binding proteins (dsRBPs) assist the corresponding Dicer in the cleavage of dsRNA precursors to effect post-transcriptional gene regulation through RNA interference. In contrast, the DRB7.2:DRB4 complex in Arabidopsis thaliana acts as a potent inhibitor of Dicer-like 3 (DCL3) processing by sequestering endogenous inverted-repeat dsRNA precursors. DRB7.2 possesses a single dsRNA Binding Domain (dsRBD) flanked by unstructured N- and C-terminal regions. Whereas, DRB4 has two concatenated N-terminal dsRBDs and a long unstructured C-terminus harboring a small domain of unidentified function, D3. Here, we present near-complete backbone and partial side chain assignments of the interaction domains, DRB7.2M (i.e., DRB7.2 (71-162)) and DRB4D3 (i.e., DRB4 (294-355)) as a complex. Our findings establish the groundwork for future structural, dynamic, and functional research on DRB7.2 and DRB4, and provide clues for the endo-IR pathway in plants.
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Affiliation(s)
- Sneha Paturi
- CSIR - Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad, 500007, Telangana, India
| | - Mandar V Deshmukh
- CSIR - Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad, 500007, Telangana, India.
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Wu Z, Yu X, Zhang S, He Y, Guo W. Novel roles of PIWI proteins and PIWI-interacting RNAs in human health and diseases. Cell Commun Signal 2023; 21:343. [PMID: 38031146 PMCID: PMC10685540 DOI: 10.1186/s12964-023-01368-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
Non-coding RNA has aroused great research interest recently, they play a wide range of biological functions, such as regulating cell cycle, cell proliferation, and intracellular substance metabolism. Piwi-interacting RNAs (piRNAs) are emerging small non-coding RNAs that are 24-31 nucleotides in length. Previous studies on piRNAs were mainly limited to evaluating the binding to the PIWI protein family to play the biological role. However, recent studies have shed more lights on piRNA functions; aberrant piRNAs play unique roles in many human diseases, including diverse lethal cancers. Therefore, understanding the mechanism of piRNAs expression and the specific functional roles of piRNAs in human diseases is crucial for developing its clinical applications. Presently, research on piRNAs mainly focuses on their cancer-specific functions but lacks investigation of their expressions and epigenetic modifications. This review discusses piRNA's biogenesis and functional roles and the recent progress of functions of piRNA/PIWI protein complexes in human diseases. Video Abstract.
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Affiliation(s)
- Zeyu Wu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China
| | - Xiao Yu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China
| | - Shuijun Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China
| | - Yuting He
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China.
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China.
| | - Wenzhi Guo
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China.
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China.
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Smeele ZE, Baty JW, Lester PJ. Effects of Deformed Wing Virus-Targeting dsRNA on Viral Loads in Bees Parasitised and Non-Parasitised by Varroa destructor. Viruses 2023; 15:2259. [PMID: 38005935 PMCID: PMC10674661 DOI: 10.3390/v15112259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
The Varroa destructor mite is a devastating parasite of honey bees; however the negative effects of varroa parasitism are exacerbated by its role as an efficient vector of the honey bee pathogen, Deformed wing virus (DWV). While no direct treatment for DWV infection is available for beekeepers to use on their hives, RNA interference (RNAi) has been widely explored as a possible biopesticide approach for a range of pests and pathogens. This study tested the effectiveness of three DWV-specific dsRNA sequences to lower DWV loads and symptoms in honey bees reared from larvae in laboratory mini-hives containing bees and varroa. The effects of DWV-dsRNA treatment on bees parasitised and non-parasitised by varroa mites during development were investigated. Additionally, the impact of DWV-dsRNA on viral loads and gene expression in brood-parasitising mites was assessed using RNA-sequencing. Bees parasitised during development had significantly higher DWV levels compared to non-parasitised bees. However, DWV-dsRNA did not significantly reduce DWV loads or symptoms in mini-hive reared bees, possibly due to sequence divergence between the DWV variants present in bees and varroa and the specific DWV-dsRNA sequences used. Varroa mites from DWV-dsRNA treated mini-hives did not show evidence of an elevated RNAi response or significant difference in DWV levels. Overall, our findings show that RNAi is not always successful, and multiple factors including pathogen diversity and transmission route may impact its efficiency.
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Affiliation(s)
- Zoe E. Smeele
- School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington 6140, New Zealand; (J.W.B.); (P.J.L.)
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Gotlib J. Introduction to a review series on RNA therapeutics in hematology. Blood 2023; 142:1577-1579. [PMID: 37944179 DOI: 10.1182/blood.2023020910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 09/18/2023] [Indexed: 11/12/2023] Open
Abstract
Small molecule inhibitors and antibody therapies have led the way for targeted therapy of a range of hematologic disorders; however, the number of amenable targets is limited. RNA-directed therapies can be a solution for targets deemed “undruggable,” with modulation of RNA expression through a variety of methods, expanding the therapeutic possibilities. In this Review Series edited by Associate Editor Jason Gotlib, 3 articles highlight areas in which RNA therapeutics are most advanced: acute hepatic porphyria, transthyretin amyloidosis, and hemophilia. This series offers insight into the promise of these new therapies.
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50
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Animasaun DA, Lawrence JA. Antisense RNA (asRNA) technology: the concept and applications in crop improvement and sustainable agriculture. Mol Biol Rep 2023; 50:9545-9557. [PMID: 37755651 DOI: 10.1007/s11033-023-08814-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 09/11/2023] [Indexed: 09/28/2023]
Abstract
Antisense RNA (asRNA) technology is a method used to silence genes and inhibit their expression. Gene function relies on expression, which follows the central dogma of molecular biology. The use of asRNA can regulate gene expression by targeting specific mRNAs, which can result in changes in phenotype, disease resistance, and other traits associated with protein expression profiles. This technology uses short, single-stranded oligonucleotide strands that are complementary to the targeted mRNA. Manipulating and regulating protein expression during its translation can either knock out or knock down the expression of a gene of interest. Therefore, functional genomics can benefit from this technology since it allows for the regulation of protein expression. In this review, we discuss the concept, and applications of asRNA technology which include delaying ripening, prolonging shelf life, biofortification, and increasing biotic and abiotic resistance among others in crop improvement and sustainable agriculture.
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Affiliation(s)
- David Adedayo Animasaun
- Department of Plant Biology, Faculty of Life Sciences, University of Ilorin, P.M.B. 1515, Ilorin, Kwara State, Nigeria.
- Plant Tissue Culture Lab, Central Research Laboratories, University of Ilorin, P.M.B.1515, Ilorin, Kwara State, Nigeria.
| | - Judith Amaka Lawrence
- Department of Plant Biology, Faculty of Life Sciences, University of Ilorin, P.M.B. 1515, Ilorin, Kwara State, Nigeria.
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