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Sun L, Sun J, Li C, Wu K, Gu Z, Guo L, Zhou Y, Han B, Chang J. STAT3-specific nanocarrier for shRNA/drug dual delivery and tumor synergistic therapy. Bioact Mater 2024; 41:137-157. [PMID: 39131627 PMCID: PMC11314445 DOI: 10.1016/j.bioactmat.2024.07.010] [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: 04/03/2024] [Revised: 06/28/2024] [Accepted: 07/05/2024] [Indexed: 08/13/2024] Open
Abstract
Non-small cell lung cancer (NSCLC) is a major disease with high incidence, low survival rate and prone to develop drug resistance to chemotherapy. The mechanism of secondary drug resistance in NSCLC chemotherapy is very complex, and studies have shown that the abnormal activation of STAT3 (Signal Transducer and Activator of Transcription 3) plays an important role in it. In this study, the pGPU6/GFP/Neo STAT3-shRNA recombinant plasmid was constructed with STAT3 as the precise target. By modifying hydrophilic and hydrophobic blocks onto chitosan, a multifunctional vitamin E succinate-chitosan-polyethylene glycol monomethyl ether histidine (VES-CTS-mPEG-His) micelles were synthesized. The micelles could encapsulate hydrophobic drug doxorubicin through self-assembly, and load the recombinant pGPU6/GFP/Neo STAT3-shRNA (pDNA) through positive and negative charges to form dual-loaded nanoparticles DOX/VCPH/pDNA. The co-delivery and synergistic effect of DOX and pDNA could up-regulate the expression of PTEN (Phosphatase and Tensin Homolog), down-regulate the expression of CD31, and induce apoptosis of tumor cells. The results of precision targeted therapy showed that DOX/VCPH/pDNA could significantly down-regulate the expression level of STAT3 protein, further enhancing the efficacy of chemotherapy. Through this study, precision personalized treatment of NSCLC could be effectively achieved, reversing its resistance to chemotherapy drugs, and providing new strategies for the treatment of drug-resistant NSCLC.
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Affiliation(s)
- Le Sun
- College of Marine Life Science, Ocean University of China, Qingdao, 266003, PR China
| | - Jishang Sun
- College of Marine Life Science, Ocean University of China, Qingdao, 266003, PR China
| | - Cuiyao Li
- College of Marine Life Science, Ocean University of China, Qingdao, 266003, PR China
| | - Keying Wu
- College of Marine Life Science, Ocean University of China, Qingdao, 266003, PR China
| | - Zhiyang Gu
- College of Marine Life Science, Ocean University of China, Qingdao, 266003, PR China
| | - Lan Guo
- College of Marine Life Science, Ocean University of China, Qingdao, 266003, PR China
| | - Yi Zhou
- College of Marine Life Science, Ocean University of China, Qingdao, 266003, PR China
| | - Baoqin Han
- College of Marine Life Science, Ocean University of China, Qingdao, 266003, PR China
- Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, Qingdao, 266237, PR China
| | - Jing Chang
- College of Marine Life Science, Ocean University of China, Qingdao, 266003, PR China
- Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, Qingdao, 266237, PR China
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2
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He P, Liu X, Yu G, Wang Y, Wang S, Liu J, An Y. METTL3 facilitates prostate cancer progression via inducing HOXC6 m6A modification and stabilizing its expression through IGF2BP2-dependent mechanisms. Mol Cell Biochem 2024; 479:1707-1720. [PMID: 38822192 DOI: 10.1007/s11010-024-05023-y] [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: 01/05/2024] [Accepted: 04/26/2024] [Indexed: 06/02/2024]
Abstract
HOXC6 (Homeobox C6) and methyltransferase-like 3 (METTL3) have been shown to be involved in the progression of prostate cancer (PCa). However, whether HOXC6 performs oncogenic effects in PCa via METTL3-mediated N6-methyladenosine (m6A) modification is not yet reported. The Cell Counting Kit-8 (CCK-8), 5-ethynyl-2'-deoxyuridine (EdU), flow cytometry, transwell, scratch, sphere formation assays were applied for cell growth, invasion, migration and stemness analyses. Glycolysis was evaluated by measuring glucose consumption, lactate generation and ATP/ADP ratio. The N6-methyladenine (m6A) modification profile was determined by RNA immunoprecipitation (Me-RIP) assay. The proteins that interact with PGK1 (phosphoglycerate kinase 1) were confirmed by Co-immunoprecipitation assay. Tumor formation experiments in mice were conducted for in vivo assay. PCa tissues and cells showed highly expressed HOXC6 and METTL3. Functionally, the silencing of HOXC6 or METTL3 suppresses PCa cell proliferation, invasion, migration, stemness, and glycolysis. Moreover, METTL3-induced HOXC6 m6A modification to stabilize its expression. In addition, the m6A reader IGF2BP2 directly recognized and bound to HOXC6 mRNA, and maintained its stability, and was involved in the regulation of HOXC6 expression by METTL3. Furthermore, IGF2BP2 knockdown impaired PCa cell proliferation, invasion, migration, stemness, and glycolysis by regulating HOXC6. Besides that HOXC6 interacted with the glycoytic enzyme PGK1 in PCa cells. In vivo assays further showed that METTL3 silencing reduced the expression of HOXC6 and PGK1, and impeded PCa growth. METTL3 promoted PCa progression by maintaining HOXC6 expression in an m6A-IGF2BP2-dependent mechanism.
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Affiliation(s)
- Peng He
- Department of Urology, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, No. 32, West Section 2, 1st Ring Road, Qingyang District, Chengdu, 610072, Sichuan Province, China
| | - Xuehui Liu
- Department of Geratology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, China
| | - Gui Yu
- Department of Urology, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, No. 32, West Section 2, 1st Ring Road, Qingyang District, Chengdu, 610072, Sichuan Province, China
| | - Yu Wang
- Department of Urology, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, No. 32, West Section 2, 1st Ring Road, Qingyang District, Chengdu, 610072, Sichuan Province, China
| | - Shize Wang
- Department of Urology, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, No. 32, West Section 2, 1st Ring Road, Qingyang District, Chengdu, 610072, Sichuan Province, China
| | - Jing Liu
- Department of Urology, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, No. 32, West Section 2, 1st Ring Road, Qingyang District, Chengdu, 610072, Sichuan Province, China
| | - Yu An
- Department of Urology, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, No. 32, West Section 2, 1st Ring Road, Qingyang District, Chengdu, 610072, Sichuan Province, China.
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3
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Ahmed T. Lipid nanoparticle mediated small interfering RNA delivery as a potential therapy for Alzheimer's disease. Eur J Neurosci 2024; 59:2915-2954. [PMID: 38622050 DOI: 10.1111/ejn.16336] [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: 09/18/2023] [Revised: 02/21/2024] [Accepted: 03/14/2024] [Indexed: 04/17/2024]
Abstract
Alzheimer's disease (AD) is a neurodegenerative condition that exhibits a gradual decline in cognitive function and is prevalent among a significant number of individuals globally. The use of small interfering RNA (siRNA) molecules in RNA interference (RNAi) presents a promising therapeutic strategy for AD. Lipid nanoparticles (LNPs) have been developed as a delivery vehicle for siRNA, which can selectively suppress target genes, by enhancing cellular uptake and safeguarding siRNA from degradation. Numerous research studies have exhibited the effectiveness of LNP-mediated siRNA delivery in reducing amyloid beta (Aβ) levels and enhancing cognitive function in animal models of AD. The feasibility of employing LNP-mediated siRNA delivery as a therapeutic approach for AD is emphasized by the encouraging outcomes reported in clinical studies for other medical conditions. The use of LNP-mediated siRNA delivery has emerged as a promising strategy to slow down or even reverse the progression of AD by targeting the synthesis of tau phosphorylation and other genes linked to the condition. Improvement of the delivery mechanism and determination of the most suitable siRNA targets are crucial for the efficacious management of AD. This review focuses on the delivery of siRNA through LNPs as a promising therapeutic strategy for AD, based on the available literature.
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Affiliation(s)
- Tanvir Ahmed
- Department of Pharmaceutical Sciences, North South University, Dhaka, Bangladesh
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4
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Cao Y, Xu Y, Zhang R, Qi J, Su Q, Chen Z. Circ_0000115 Protects Against Cerebral Ischemia Injury by Suppressing Neuronal Apoptosis, Oxidative Stress and Inflammation by miR-1224-5p/Nos3 Axis In Vitro. Mol Biotechnol 2024; 66:1082-1094. [PMID: 38151617 DOI: 10.1007/s12033-023-01005-5] [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: 05/08/2023] [Accepted: 11/27/2023] [Indexed: 12/29/2023]
Abstract
Cerebral ischemia is a severe neurological disability related to neuronal apoptosis and cellular stress response. Circular RNAs (circRNAs) are emerging regulators of cerebral ischemia. Herein, this study proposed to probe the action of circ_0000115 in cerebral ischemia injury. The mouse neuroblastoma cells N2a and HT22 underwent oxygen-glucose deprivation (OGD) were used as a model of in vitro cerebral ischemia. Levels of genes and proteins were detected by qRT-PCR and western blotting. Cell proliferation and apoptosis were determined by EdU assay and flow cytometry. Western blotting was used to detect the protein level of pro-inflammatory factors. The oxidative stress injury was evaluated by detecting reactive oxygen species (ROS), malondialdehyde (MDA) and superoxide dismutase (SOD) generation. Dual-luciferase reporter and RIP assays were used to confirm the target relationship between miR-1224-5p and circ_0000115 or nitric oxide synthase 3 (NOS3). OGD exposure decreased circ_0000115 and NOS3 expression, and increased miR-1224-5p in N2a and HT22 cells in a time-dependent manner. Circ_0000115 silencing attenuated OGD-induced apoptosis, oxidative stress and inflammation in N2a and HT22 cells. Mechanistically, circ_0000115 directly sponged miR-1224-5p, which targeted NOS3. Furthermore, rescue experiments showed that miR-1224-5p overexpression abolished the neuroprotective effect of circ_0000115 in N2a and HT22 cells under OGD treatment. Besides that, silencing of miR-1224-5p protected N2a and HT22 cells against OGD-evoked injury, which was counteracted by NOS3 knockdown. Circ_0000115 protects N2a and HT22 cells against OGD-evoked neuronal apoptosis, inflammation, and oxidative stress via the miR-1224-5p/NOS3 axis, providing an exciting view of the pathogenesis of cerebral ischemia.
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Affiliation(s)
- Ying Cao
- Department of Critical Care Medicine, The First Affiliated Hospital of Army Medical University, Chongqing, 400038, People's Republic of China
| | - Yanbing Xu
- Department of Critical Care Medicine, The First Affiliated Hospital of Army Medical University, Chongqing, 400038, People's Republic of China
| | - Rui Zhang
- Department of Critical Care Medicine, The First Affiliated Hospital of Army Medical University, Chongqing, 400038, People's Republic of China
| | - Junsheng Qi
- Department of Critical Care Medicine, The First Affiliated Hospital of Army Medical University, Chongqing, 400038, People's Republic of China
| | - Qiuyu Su
- Department of Neurosurgery, The Fifth Clinical College of Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Zhiqiang Chen
- Department of Pediatrics, The First Affiliated Hospital of Army Medical University, No.30, Gaotanyan Street, Chongqing, 400038, People's Republic of China.
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5
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Broc B, Varini K, Sonnette R, Pecqueux B, Benoist F, Masse M, Mechioukhi Y, Ferracci G, Temsamani J, Khrestchatisky M, Jacquot G, Lécorché P. LDLR-Mediated Targeting and Productive Uptake of siRNA-Peptide Ligand Conjugates In Vitro and In Vivo. Pharmaceutics 2024; 16:548. [PMID: 38675209 PMCID: PMC11054735 DOI: 10.3390/pharmaceutics16040548] [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: 02/13/2024] [Revised: 03/29/2024] [Accepted: 04/02/2024] [Indexed: 04/28/2024] Open
Abstract
Small RNA molecules such as microRNA and small interfering RNA (siRNA) have become promising therapeutic agents because of their specificity and their potential to modulate gene expression. Any gene of interest can be potentially up- or down-regulated, making RNA-based technology the healthcare breakthrough of our era. However, the functional and specific delivery of siRNAs into tissues of interest and into the cytosol of target cells remains highly challenging, mainly due to the lack of efficient and selective delivery systems. Among the variety of carriers for siRNA delivery, peptides have become essential candidates because of their high selectivity, stability, and conjugation versatility. Here, we describe the development of molecules encompassing siRNAs against SOD1, conjugated to peptides that target the low-density lipoprotein receptor (LDLR), and their biological evaluation both in vitro and in vivo.
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Affiliation(s)
- Baptiste Broc
- Vect-Horus S.A.S, Faculté des Sciences Médicales et Paramédicales Secteur Timone, 13385 Marseille, France
- Aix-Marseille Univ, CNRS, INP, Inst Neurophysiopathol, 13005 Marseille, France
| | - Karine Varini
- Vect-Horus S.A.S, Faculté des Sciences Médicales et Paramédicales Secteur Timone, 13385 Marseille, France
| | - Rose Sonnette
- Vect-Horus S.A.S, Faculté des Sciences Médicales et Paramédicales Secteur Timone, 13385 Marseille, France
| | - Belinda Pecqueux
- Vect-Horus S.A.S, Faculté des Sciences Médicales et Paramédicales Secteur Timone, 13385 Marseille, France
| | - Florian Benoist
- Vect-Horus S.A.S, Faculté des Sciences Médicales et Paramédicales Secteur Timone, 13385 Marseille, France
| | - Maxime Masse
- Vect-Horus S.A.S, Faculté des Sciences Médicales et Paramédicales Secteur Timone, 13385 Marseille, France
| | - Yasmine Mechioukhi
- Vect-Horus S.A.S, Faculté des Sciences Médicales et Paramédicales Secteur Timone, 13385 Marseille, France
| | - Géraldine Ferracci
- Aix-Marseille Univ, CNRS, INP, Inst Neurophysiopathol, 13005 Marseille, France
| | - Jamal Temsamani
- Vect-Horus S.A.S, Faculté des Sciences Médicales et Paramédicales Secteur Timone, 13385 Marseille, France
| | | | - Guillaume Jacquot
- Vect-Horus S.A.S, Faculté des Sciences Médicales et Paramédicales Secteur Timone, 13385 Marseille, France
| | - Pascaline Lécorché
- Vect-Horus S.A.S, Faculté des Sciences Médicales et Paramédicales Secteur Timone, 13385 Marseille, France
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6
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Li D, Du F, Jiao H, Zhang F, Wang X, Zhang S. CircHSPB6 Promotes Tumor-Associated Macrophages M2 Polarization and Infiltration to Accelerate Cell Malignant Properties in Lung Adenocarcinoma by CCL2. Biochem Genet 2024; 62:1379-1395. [PMID: 37610692 DOI: 10.1007/s10528-023-10482-x] [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: 06/27/2023] [Accepted: 08/02/2023] [Indexed: 08/24/2023]
Abstract
Circular RNAs (circRNAs) are reported to be involved in the tumorigenesis of lung adenocarcinoma (LUAD). Here, this study focused on studying the function and mechanism of circHSPB6 in LUAD progression. Levels of genes and proteins were tested using qRT-PCR and western blotting analyses. The 5-ethynyl-2'-deoxyuridine (EdU), colony formation, flow cytometry, and transwell assays were adopted for in vitro assays. In vivo assay was conducted using mouse xenograft models. The binding between let-7a-2-3p and circHSPB6 or CCL2 was validated using RIP and dual-luciferase reporter assays. The M2 polarization of tumor-associated macrophages (TAMs) was analyzed by flow cytometry. LUAD tissues and cells showed high circHSPB6 expression, knockdown of circHSPB6-suppressed LUAD cell proliferation, migration, invasion, and induced cell apoptosis in vitro, as well as hindered tumor growth in vivo. Mechanistically, circHSPB6/let-7a-2-3p/CCL2 forms a feedback loop. CircHSPB6 could regulate CCL2 expression via sponging let-7a-2-3p. Further rescue assays showed that the effects of circHSPB6 silencing on LUAD cells were reversed by let-7a-2-3p inhibition or CCL2 overexpression. Moreover, circHSPB6 promoted the M2 polarization and infiltration of TAMs by CCL2. Functionally, circHSPB6 knockdown in A549 and H1299 cells inhibited TAM M2 polarization and then suppressed cell proliferation, migration, invasion, and emergency medical technicians (EMT) progression, while these effects were reversed by CCL2 up-regulation CircHSPB6 induced TAM M2 polarization to promote LUAD cell proliferation, migration, invasion, and EMT progression through let-7a-2-3p/CCL2 axis.
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Affiliation(s)
- Danqing Li
- Department of Radiotherapy, Xingtai People`S Hospital, Xingtai, China
| | - Fan Du
- Department of Thoracic Surgery, Xingtai People`S Hospital, No. 16 Hongxing Street, Xiangdu District, Xingtai City, Hebei Province, China
| | - Huiru Jiao
- Department of Radiotherapy, Xingtai People`S Hospital, Xingtai, China
| | - Fen Zhang
- Department of Radiotherapy, Xingtai People`S Hospital, Xingtai, China
| | - Xiaozhen Wang
- Department of Radiotherapy, Xingtai People`S Hospital, Xingtai, China
| | - Shaofeng Zhang
- Department of Radiotherapy, Xingtai People`S Hospital, Xingtai, China.
- Department of Thoracic Surgery, Xingtai People`S Hospital, No. 16 Hongxing Street, Xiangdu District, Xingtai City, Hebei Province, China.
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7
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Guo M, Su F, Chen Y, Su B. Methyltransferase METTL3-mediated maturation of miR-4654 facilitates high glucose-induced apoptosis and oxidative stress in lens epithelial cells via decreasing SOD2. Chem Biol Drug Des 2024; 103:e14491. [PMID: 38404215 DOI: 10.1111/cbdd.14491] [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: 10/07/2023] [Revised: 01/23/2024] [Accepted: 02/12/2024] [Indexed: 02/27/2024]
Abstract
N6-methyladenosine (m6 A) modification has been reported to have roles in modulating the development of diabetic cataract (DC). Methyltransferase-like 3 (METTL3) is a critical m6 A methyltransferase involving in m6 A modification activation. Here, we aimed to explore the action and mechanism of METTL3-mediated maturation of miR-4654 in DC progression. Human lens epithelial cells (HLECs) were exposed to high glucose (HG) to imitate DC condition in vitro. Levels of genes and proteins were tested via qRT-PCR and western blotting assays. The proliferation and apoptosis of HLECs were evaluated by cell counting kit-8, 5-ethynyl-2'-deoxyuridine (EdU), and flow cytometry assays, respectively. Oxidative stress was analyzed by detecting the contents of reactive oxygen species (ROS), superoxide dismutase (SOD) and malondialdehyde (MDA). The binding of miR-4654 and SOD2 was confirmed by dual-luciferase reporter assay. The m6 A-RNA immunoprecipitation (MeRIP) assay detected the m6 A modification profile. Thereafter, we found that miR-4654 expression was elevated in DC samples and HG-induced HLECs. MiR-4654 knockdown reversed HG-mediated apoptosis and oxidative stress in HLECs. Mechanistically, miR-4654 directly targeted SOD2, silencing of SOD2 abolished the protective effects of miR-4654 knockdown on HLECs under HG condition. In addition, METTL3 induced miR-4654 maturation through promoting pri-miR-4654 m6 A modification, thereby increasing miR-4654 content in HLECs. METTL3 was highly expressed in DC samples and HG-induced HLECs, METTL3 deficiency protected HLECs against HG-mediated apoptotic and oxidative injury via down-regulating miR-4654. In all, METTL3 induced miR-4654 maturation in a m6 A-dependent manner, which was then reduced SOD2 expression, thus promoting apoptosis and oxidative stress in HLECs, suggesting a novel path for DC therapy.
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Affiliation(s)
- Ming Guo
- Department of Ophthalmology, Jingzhou Hospital, Yangtze University, (Jingzhou Central Hospital), Jingzhou, Hubei, China
| | - Fanfan Su
- Department of Ophthalmology, Jingzhou Hospital, Yangtze University, (Jingzhou Central Hospital), Jingzhou, Hubei, China
| | - Yao Chen
- Department of Ophthalmology, Jingzhou Hospital, Yangtze University, (Jingzhou Central Hospital), Jingzhou, Hubei, China
| | - Bo Su
- Department of Pathology, School of Medicine, Yangtze University, Jingzhou, Hubei, China
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8
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Yang D, Wei H, Sheng Y, Peng T, Zhao Q, Xie L, Yang J. Circ_0006640 transferred by bone marrow-mesenchymal stem cell-exosomes suppresses lipopolysaccharide-induced apoptotic, inflammatory and oxidative injury in spinal cord injury. J Orthop Surg Res 2024; 19:50. [PMID: 38195468 PMCID: PMC10777583 DOI: 10.1186/s13018-023-04523-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 12/30/2023] [Indexed: 01/11/2024] Open
Abstract
BACKGROUND Emerging proofs have shown that differentially expressed circular RNAs (circRNAs) are closely associated with the pathophysiological process of spinal cord injury (SCI). Mesenchymal stem cell (MSC)-exosomes have been demonstrated to possess favorable therapeutic effects in diseases. Herein, this work aimed to investigate the action of circ_0006640 transferred by MSC-exosomes functional recovery after SCI. METHODS SCI animal models were established by spinal cord contusion surgery in mice and lipopolysaccharide (LPS)-stimulated mouse microglial cell line BV2. Levels of genes and proteins were detected by qRT-PCR and Western blot. Properties of BV2 cells were characterized using CCK-8 assay, flow cytometry and ELISA analysis. The oxidative stress was evaluated. Dual-luciferase reporter assay was used for verifying the binding between miR-382-5p and circ_0006640 or IGF-1 (Insulin-like Growth Factor 1). Exosome separation was conducted by using the commercial kit. RESULTS Circ_0006640 expression was lower in SCI mice and LPS-induced microglial cells. Circ_0006640 overexpression protected microglial cells from LPS-induced apoptotic, inflammatory and oxidative injury. Mechanistically, circ_0006640 directly sponged miR-382-5p, which targeted IGF-1. MiR-382-5p was increased, while IGF-1 was decreased in SCI mice and LPS-induced microglial cells. Knockdown of miR-382-5p suppressed apoptosis, inflammation and oxidative stress in LPS-induced microglial cells, which were reversed by IGF-1 deficiency. Moreover, miR-382-5p up-regulation abolished the protective functions of circ_0006640 in LPS-induced microglial cells. Additionally, circ_0006640 was packaged into MSC-exosomes and could be transferred by exosomes. Exosomal circ_0006640 also had protective effects on microglial cells via miR-382-5p/IGF-1 axis. CONCLUSION Circ_0006640 transferred by BMSC-exosomes suppressed LPS-induced apoptotic, inflammatory and oxidative injury via miR-382-5p/IGF-1 axis, indicating a new insight into the clinical application of exosomal circRNA-based therapeutic in the function recovery after SCI.
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Affiliation(s)
- Dan Yang
- Department of Rehabilitation Medicine, Hankou Hospital of Wuhan, No. 2273 Jiefang Dadao, Wuhan City, 430014, Hubei, China
| | - Haitang Wei
- Department of Rehabilitation Medicine, Hankou Hospital of Wuhan, No. 2273 Jiefang Dadao, Wuhan City, 430014, Hubei, China
| | - Yang Sheng
- Department of Rehabilitation Medicine, Hankou Hospital of Wuhan, No. 2273 Jiefang Dadao, Wuhan City, 430014, Hubei, China
| | - Tao Peng
- Department of Rehabilitation Medicine, Hankou Hospital of Wuhan, No. 2273 Jiefang Dadao, Wuhan City, 430014, Hubei, China
| | - Qiang Zhao
- Department of Rehabilitation Medicine, Hankou Hospital of Wuhan, No. 2273 Jiefang Dadao, Wuhan City, 430014, Hubei, China
| | - Liang Xie
- Department of Rehabilitation Medicine, Hankou Hospital of Wuhan, No. 2273 Jiefang Dadao, Wuhan City, 430014, Hubei, China
| | - Jun Yang
- Department of Rehabilitation Medicine, Hankou Hospital of Wuhan, No. 2273 Jiefang Dadao, Wuhan City, 430014, Hubei, China.
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9
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Ma M, Ciren D, Feng M, Zhen L, Jin G. Gentiana macrophylla flavonoids from Tibetan medicine decreases circ_0059665 to alleviate the progression of non-small cell lung cancer under hypoxia. Thorac Cancer 2024; 15:77-88. [PMID: 37993113 PMCID: PMC10761625 DOI: 10.1111/1759-7714.15165] [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: 08/18/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND Gentiana macrophylla Pall. is a traditional Tibetan medicinal herb possessing antinociceptive and anti-inflammatory activities. Circular RNAs (circRNAs) have been identified to be involved in the tumorigenesis of non-small cell lung cancer (NSCLC). Here, this study focused on investigating the function and mechanism of Gentiana macrophylla flavonoids (GF) and circ_0059665 in NSCLC progression. METHODS The contents of mRNA and protein were detected using qRT-PCR and western blotting analysis. Cell proliferative and invasive abilities were evaluated by cell counting kit-8, EdU, colony formation and transwell assays, respectively. M2 macrophage polarization was analyzed by flow cytometry. RESULTS GF treatment suppressed NSCLC cell proliferation, invasion and M2 macrophage polarization under hypoxic conditions. Circ_0059665 was highly expressed in NSCLC tissues and cells. Its expression was increased under hypoxic conditions but was reduced following GF treatment. Furthermore, circ_0059665 overexpression reversed the anticancer effects of GF on NSCLC cells under hypoxic conditions. Mechanistically, circ_0059665 acted as a sponge for miR-512-5p to regulate NOVA2 expression. Hypoxia decreased miR-512-5p levels, and increased NOVA2 levels in NSCLC cells, while these tendencies were abolished after GF treatment. Circ_0059665 silencing inhibited NSCLC cell proliferation, invasion and M2 macrophage polarization in hypoxic environments, which were counteracted by NOVA2 overexpression. Moreover, NOVA2 upregulation reversed the suppressive effects of GF on NSCLC cells with hypoxia treatment. In addition, GF impeded NSCLC tumor growth in vivo via suppressing circ_0059665. CONCLUSION GF treatment in hypoxic environments suppressed NSCLC cell proliferation, invasion and M2 macrophage polarization via the circ_0059665/miR-512-5p/NOVA2 axis.
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Affiliation(s)
- Mi Ma
- University of Tibetan MedicineLhasaChina
| | | | | | - Luo Zhen
- University of Tibetan MedicineLhasaChina
| | - Guilin Jin
- University of Tibetan MedicineLhasaChina
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10
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Xie J, Zhuang Z, Gou S, Zhang Q, Wang X, Lan T, Lian M, Li N, Liang Y, Ouyang Z, Ye Y, Wu H, Lai L, Wang K. Precise genome editing of the Kozak sequence enables bidirectional and quantitative modulation of protein translation to anticipated levels without affecting transcription. Nucleic Acids Res 2023; 51:10075-10093. [PMID: 37650635 PMCID: PMC10570039 DOI: 10.1093/nar/gkad687] [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: 10/25/2022] [Revised: 07/31/2023] [Accepted: 08/10/2023] [Indexed: 09/01/2023] Open
Abstract
None of the existing approaches for regulating gene expression can bidirectionally and quantitatively fine-tune gene expression to desired levels. Here, on the basis of precise manipulations of the Kozak sequence, which has a remarkable influence on translation initiation, we proposed and validated a novel strategy to directly modify the upstream nucleotides of the translation initiation codon of a given gene to flexibly alter the gene translation level by using base editors and prime editors. When the three nucleotides upstream of the translation initiation codon (named KZ3, part of the Kozak sequence), which exhibits the most significant base preference of the Kozak sequence, were selected as the editing region to alter the translation levels of proteins, we confirmed that each of the 64 KZ3 variants had a different translation efficiency, but all had similar transcription levels. Using the ranked KZ3 variants with different translation efficiencies as predictors, base editor- and prime editor-mediated mutations of KZ3 in the local genome could bidirectionally and quantitatively fine-tune gene translation to the anticipated levels without affecting transcription in vitro and in vivo. Notably, this strategy can be extended to the whole Kozak sequence and applied to all protein-coding genes in all eukaryotes.
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Affiliation(s)
- Jingke Xie
- China–New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China
- Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, Wuyi University, Jiangmen 529020, China
| | - Zhenpeng Zhuang
- China–New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shixue Gou
- China–New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China
| | - Quanjun Zhang
- China–New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou 510530, China
| | - Xia Wang
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Ting Lan
- China–New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meng Lian
- China–New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou 510530, China
| | - Nan Li
- China–New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China
- Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, Wuyi University, Jiangmen 529020, China
| | - Yanhui Liang
- China–New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China
| | - Zhen Ouyang
- China–New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China
- Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, Wuyi University, Jiangmen 529020, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou 510530, China
| | - Yinghua Ye
- China–New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou 510530, China
| | - Han Wu
- China–New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou 510530, China
| | - Liangxue Lai
- China–New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China
- Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, Wuyi University, Jiangmen 529020, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou 510530, China
| | - Kepin Wang
- China–New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya 572000, China
- Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, Wuyi University, Jiangmen 529020, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou 510530, China
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Tan Y, Yu Z, Li P, Liu Y, You T, Kuang F, Luo W. Circ_0001714 knockdown alleviates lipopolysaccharide-induced apoptosis and inflammation in renal tubular epithelial cells via miR-129-5p/TRAF6 axis in septic acute kidney injury. J Bioenerg Biomembr 2023; 55:289-300. [PMID: 37526815 DOI: 10.1007/s10863-023-09975-6] [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: 12/30/2022] [Accepted: 06/28/2023] [Indexed: 08/02/2023]
Abstract
BACKGROUND Circular RNAs (circRNAs) have been shown to play roles in regulating sepsis. Sepsis is a major cause of acute kidney injury (AKI). Herein, we aimed to investigate the role and mechanism of circ_0001714 in the progression of sepsis-induced AKI. METHODS Human HK-2 cells were exposed to lipopolysaccharide (LPS) for functional experiments. Quantitative real-time polymerase chain reaction and western blotting were used for expression analysis. Functional experiments were performed by using MTT assay, 5-ethynyl-2'-deoxyuridine assay, flow cytometry, and enzyme-linked immunosorbent assay (ELISA). The binding between miR-129-5p and circ_0001714 or TRAF6 (TNF receptor associated factor 6) was validated using dual-luciferase reporter assay. RESULTS Circ_0001714 expression was higher in sepsis-AKI patients. HK-2 cells were exposed to LPS to imitate the injury of renal tubular epithelial cells during sepsis-AKI. LPS dose-dependently up-regulated circ_0001714, moreover, circ_0001714 silencing reversed LPS-evoked apoptosis and inflammation in HK-2 cells. Mechanistically, circ_0001714 sequestered miR-129-5p to up-regulate TRAF6 expression, implying the circ_0001714/miR-129-5p/TRAF6 feedback loop. MiR-129-5p was decreased, while TRAF6 was increased in sepsis-AKI patients and LPS-stimulated HK-2 cells. MiR-129-5p re-expression or TRAF6 silencing protected against LPS-induced HK-2 cell apoptosis and inflammation. Additionally, a series of rescue experiments showed that miR-129-5p inhibition reversed the inhibitory action of circ_0001714 knockdown on LPS-induced HK-2 cell injury. Furthermore, TRAF6 overexpression also attenuated the protective effects of miR-129-5p on HK-2 cells under LPS treatment. CONCLUSION Circ_0001714 silencing might alleviate LPS-induced apoptosis and inflammation via targeting miR-129-5p/TRAF6 axis in HK-2 cells.
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Affiliation(s)
- Yiqing Tan
- The First Affiliated Hospital, Department of Critical Care Medicine, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Ziying Yu
- The First Affiliated Hospital, Department of Emergency, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Pei Li
- The First Affiliated Hospital, Department of Clinical Laboratory, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Yu Liu
- The First Affiliated Hospital, Department of Emergency, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Ting You
- The First Affiliated Hospital, Department of Emergency, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Feng Kuang
- The First Affiliated Hospital, Department of Emergency, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Wei Luo
- The First Affiliated Hospital, Department of Cardiovasology, Hengyang Medical School, University of South China, Hengyang, Hunan, China.
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Alagia A, Tereňová J, Ketley RF, Di Fazio A, Chelysheva I, Gullerova M. Small vault RNA1-2 modulates expression of cell membrane proteins through nascent RNA silencing. Life Sci Alliance 2023; 6:e202302054. [PMID: 37037596 PMCID: PMC10087102 DOI: 10.26508/lsa.202302054] [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: 03/23/2023] [Revised: 03/24/2023] [Accepted: 03/28/2023] [Indexed: 04/12/2023] Open
Abstract
Gene expression can be regulated by transcriptional or post-transcriptional gene silencing. Recently, we described nuclear nascent RNA silencing that is mediated by Dicer-dependent tRNA-derived small RNA molecules. In addition to tRNA, RNA polymerase III also transcribes vault RNA, a component of the ribonucleoprotein complex vault. Here, we show that Dicer-dependent small vault RNA1-2 (svtRNA1-2) associates with Argonaute 2 (Ago2). Although endogenous vtRNA1-2 is present mostly in the cytoplasm, svtRNA1-2 localises predominantly in the nucleus. Furthermore, in Ago2 and Dicer knockdown cells, a subset of genes that are up-regulated at the nascent level were predicted to be targeted by svtRNA1-2 in the intronic region. Genomic deletion of vtRNA1-2 results in impaired cellular proliferation and the up-regulation of genes associated with cell membrane physiology and cell adhesion. Silencing activity of svtRNA1-2 molecules is dependent on seed-plus-complementary-paired hybridisation features and the presence of a 5-nucleotide loop protrusion on target RNAs. Our data reveal a role of Dicer-dependent svtRNA1-2, possessing unique molecular features, in modulation of the expression of membrane-associated proteins at the nascent RNA level.
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Affiliation(s)
- Adele Alagia
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Jana Tereňová
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Ruth F Ketley
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Arianna Di Fazio
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Irina Chelysheva
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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Liu L, Liu Y, Zhao Y. Circular RNA circ_0008896 contributes to oxidized low-density lipoprotein-induced aortic endothelial cell injury via targeting miR-188-3p/NOD2 axis. Cell Stress Chaperones 2023; 28:275-287. [PMID: 36940068 PMCID: PMC10167080 DOI: 10.1007/s12192-023-01336-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 02/07/2023] [Accepted: 03/07/2023] [Indexed: 03/21/2023] Open
Abstract
We aimed to investigate the role and mechanism of circ_0008896 in Atherosclerosis (AS) by using oxidized low-density lipoprotein (ox-LDL)-induced human aortic endothelial cell (HAECs). Levels of genes and proteins were measured by quantitative real-time PCR and Western blot. Functional experiments, including enzyme-linked immunosorbent assay analysis, cell counting kit-8, 5-ethynyl-2'-deoxyuridine (EdU), flow cytometry, tube formation assays and the detection of reactive oxygen species (ROS), malondialdehyde (MDA) and superoxide dismutase (SOD) generation, were performed to investigate the role of circ_0008896 on ox-LDL-induced HAEC damage. Circ_0008896 was increased in AS patients and ox-LDL-stimulated HAECs. Functionally, circ_0008896 knockdown reversed ox-LDL-induced inflammatory response, oxidative stress, apoptosis as well as arrest of proliferation and angiogenesis in HAECs in vitro. Mechanistically, circ_0008896 functioned as a sponge for miR-188-3p to relieve the repression of miR-188-3p on its target NOD2. A series of rescue experiments showed that miR-188-3p inhibition attenuated the protective effects of circ_0008896 knockdown on ox-LDL-stimulated HAECs, and NOD2 overexpression abolished the beneficial action of miR-188-3p in the suppression of inflammatory response and oxidative stress, and the promotion of cell growth and angiogenesis in HAECs under ox-LDL treatment. Circ_0008896 silencing attenuates ox-LDL-induced inflammatory response, oxidative stress, and growth arrest in HAECs in vitro, adding further understanding for the pathogenesis of AS.
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Affiliation(s)
- Liping Liu
- Heart Function Examination Room, the Second Hospital of Dalian Medical University, Dalian, China
| | - Yan Liu
- Department of Cardiology, the Second Hospital of Dalian Medical University, Dalian, China
| | - Yueyan Zhao
- Department of Cardiology, the Second Hospital of Dalian Medical University, Dalian, China.
- , Dalian City, China.
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Chen Y, Zhang Y. CircDLG1 promotes malignant development of non-small cell lung cancer through regulation of the miR-630/CENPF axis. Strahlenther Onkol 2023; 199:169-181. [PMID: 35748916 DOI: 10.1007/s00066-022-01965-8] [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: 01/18/2022] [Accepted: 05/22/2022] [Indexed: 01/28/2023]
Abstract
BACKGROUND Circular RNAs (circRNAs) have been reported to be crucial modulatory molecules in the etiology of non-small cell lung cancer (NSCLC). This study aimed to probe the precise role and mechanism of circRNA discs large MAGUK scaffold protein 1 (circDLG1) in the malignant progression of NSCLC. METHODS The abundances of circDLG1, miR-630, and centromere protein F (CENPF) mRNAs were gauged by quantitative real-time polymerase chain reaction (qRT-PCR). Cell proliferation was tested in 3‑(4, 5‑dimethylthiazol-2-yl)-2, 5‑diphenyltetrazolium bromide (MTT) assay and 5‑ethynyl-2'-deoxyuridine (EdU)-incorporation assay. Cell apoptosis was analyzed by flow cytometry. Cell migration and invasion were assessed by transwell assay. Western blot was exploited to examine the levels of all proteins. The interaction between miR-630 and circDLG1 or CENPF was verified by dual-luciferase reporter, RNA pull-down, and/or RNA immunoprecipitation assays. Tumor xenograft assay and immunohistochemistry (IHC) were executed for the role of circDLG1 in tumor growth in vivo. RESULTS CircDLG1 and CENPF were highly expressed in NSCLC, while miR-630 was downregulated. CircDLG1 silencing repressed proliferation, migration, and invasion, and expedited apoptosis of NSCLC cells in vitro. Mechanistically, circDLG1 deficiency modulated NSCLC cell malignant development through interacting with miR-630. Furthermore, CENPF was targeted by miR-630, and circDLG1 could positively control CENPF expression through acting as an miR-630 sponge. Furthermore, CENPF overexpression reversed the repressive impacts of circDLG1 inhibition in the malignant behaviors of NSCLC cells. Besides, circDLG1 interference hindered tumor growth in vivo. CONCLUSION CircDLG1 knockdown could impede NSCLC advancement through modulating the miR-630/CENPF axis, manifesting as a promising molecular target for NSCLC treatment.
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Affiliation(s)
- Yingying Chen
- Department of Pulmonary and Critical Care Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Ying Zhang
- Department of Clinical Oncology, Shengjing Hospital of China Medical University, No. 39 Huaxiang Road, 110022, Tiexi District, Shenyang, Liaoning Province, China.
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Stabilized Double-Stranded RNA Strategy Improves Cotton Resistance to CBW ( Anthonomus grandis). Int J Mol Sci 2022; 23:ijms232213713. [PMID: 36430188 PMCID: PMC9691246 DOI: 10.3390/ijms232213713] [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: 06/30/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 11/11/2022] Open
Abstract
Cotton is the most important crop for fiber production worldwide. However, the cotton boll weevil (CBW) is an insect pest that causes significant economic losses in infested areas. Current control methods are costly, inefficient, and environmentally hazardous. Herein, we generated transgenic cotton lines expressing double-stranded RNA (dsRNA) molecules to trigger RNA interference-mediated gene silencing in CBW. Thus, we targeted three essential genes coding for chitin synthase 2, vitellogenin, and ecdysis-triggering hormone receptor. The stability of expressed dsRNAs was improved by designing a structured RNA based on a viroid genome architecture. We transformed cotton embryos by inserting a promoter-driven expression cassette that overexpressed the dsRNA into flower buds. The transgenic cotton plants were characterized, and positive PCR transformed events were detected with an average heritability of 80%. Expression of dsRNAs was confirmed in floral buds by RT-qPCR, and the T1 cotton plant generation was challenged with fertilized CBW females. After 30 days, data showed high mortality (around 70%) in oviposited yolks. In adult insects fed on transgenic lines, chitin synthase II and vitellogenin showed reduced expression in larvae and adults, respectively. Developmental delays and abnormalities were also observed in these individuals. Our data remark on the potential of transgenic cotton based on a viroid-structured dsRNA to control CBW.
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Controllable DNA hybridization by host-guest complexation-mediated ligand invasion. Nat Commun 2022; 13:5936. [PMID: 36209265 PMCID: PMC9547909 DOI: 10.1038/s41467-022-33738-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/30/2022] [Indexed: 11/09/2022] Open
Abstract
Dynamic regulation of nucleic acid hybridization is fundamental for switchable nanostructures and controllable functionalities of nucleic acids in both material developments and biological regulations. In this work, we report a ligand-invasion pathway to regulate DNA hybridization based on host-guest interactions. We propose a concept of recognition handle as the ligand binding site to disrupt Watson-Crick base pairs and induce the direct dissociation of DNA duplex structures. Taking cucurbit[7]uril as the invading ligand and its guest molecules that are integrated into the nucleobase as recognition handles, we successfully achieve orthogonal and reversible manipulation of DNA duplex dissociation and recovery. Moreover, we further apply this approach of ligand-controlled nucleic acid hybridization for functional regulations of both the RNA-cleaving DNAzyme in test tubes and the antisense oligonucleotide in living cells. This ligand-invasion strategy establishes a general pathway toward dynamic control of nucleic acid structures and functionalities by supramolecular interactions.
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Drozd VS, Eldeeb AA, Kolpashchikov DM, Nedorezova DD. Binary Antisense Oligonucleotide Agent for Cancer Marker-Dependent Degradation of Targeted RNA. Nucleic Acid Ther 2022; 32:412-420. [DOI: 10.1089/nat.2021.0108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Valeriia S. Drozd
- Laboratory of Molecular Robotics and Biosensor Materials, SCAMT Institute, ITMO University, St. Petersburg, Russian Federation
| | - Ahmed A. Eldeeb
- Laboratory of Molecular Robotics and Biosensor Materials, SCAMT Institute, ITMO University, St. Petersburg, Russian Federation
| | - Dmitry M. Kolpashchikov
- Laboratory of Molecular Robotics and Biosensor Materials, SCAMT Institute, ITMO University, St. Petersburg, Russian Federation
- Chemistry Department, University of Central Florida, Orlando, Florida, USA
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, USA
| | - Daria D. Nedorezova
- Laboratory of Molecular Robotics and Biosensor Materials, SCAMT Institute, ITMO University, St. Petersburg, Russian Federation
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Cabrera-Becerra SE, Vera-Juárez G, García-Rubio VG, Ocampo-Ortega SA, Blancas-Napoles CM, Aguilera-Mendez A, Romero-Nava R, Huang F, Hong E, Villafaña S. siRNA knockdown of Angiopoietin 2 significantly reduces neovascularization in diabetic rats. J Drug Target 2022; 30:673-686. [PMID: 35289235 DOI: 10.1080/1061186x.2022.2052888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Diabetes is a disease that leads to proliferative diabetic retinopathy (PDR), which is associated with an increase of new vessels formation due to an overexpression of angiogenic factors, such as angiopoietin 2 (ANGPT2). The aim of this work was to design a siRNA targeting ANGPT2 to decrease the retinal neovascularization associated with PDR. Adult male Wistar rats weighing 325-375 g were used. Diabetes was induced by a single dose of streptozotocin (STZ, 60 mg/kg i.p.). The siRNAs were designed, synthesized and administered intravitreally at the beginning of diabetes induction (t0), and after 4 weeks of diabetes evolution (t4), subsequently evaluated the retinal neovascularization (junctions and lacunarity) and ANGPT2 expression in the retina by RT-PCR, after 4 weeks of the siRNAs administration. The results showed that the administration of STZ produced significantly increases in blood glucose levels, retinal neovascularization (augmented junctions and lower lacunarity) and ANGPT2 expression, while the administration the ANGPT2-siRNAs at different groups (t0 and t4) reduces the junctions and increases the lacunarity in diabetic rats. Therefore, we conclude that the administration of siRNAs targeting ANGPT2 could be an option to decrease the retinal neovascularization associated with PDR and halt the progression of blindness caused by diabetes.
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Affiliation(s)
- Sandra Edith Cabrera-Becerra
- Laboratorio de Señalización Intracelular, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México, México
| | - Gerardo Vera-Juárez
- Laboratorio de neurofarmacología, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México, México
| | - Vanessa Giselle García-Rubio
- Laboratorio de Señalización Intracelular, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México, México
| | - Sergio Adrián Ocampo-Ortega
- Laboratorio de Señalización Intracelular, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México, México
| | - Citlali Margarita Blancas-Napoles
- Laboratorio de Señalización Intracelular, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México, México
| | - Asdrubal Aguilera-Mendez
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás Hidalgo, Morelia, México
| | - Rodrigo Romero-Nava
- Laboratorio de Señalización Intracelular, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México, México
| | - Fengyang Huang
- Departamento de Farmacología y Toxicología, Hospital Infantil de México "Federico Gómez", Ciudad de México, México
| | - Enrique Hong
- Departamento de Neurofarmacología, Centro de Investigación y de Estudios Avanzados, Ciudad de México, México
| | - Santiago Villafaña
- Laboratorio de Señalización Intracelular, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México, México
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Fàbrega C, Aviñó A, Eritja R. Chemical Modifications in Nucleic Acids for Therapeutic and Diagnostic Applications. CHEM REC 2021; 22:e202100270. [DOI: 10.1002/tcr.202100270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/26/2021] [Accepted: 11/26/2021] [Indexed: 11/08/2022]
Affiliation(s)
- Carme Fàbrega
- Department of Surfactants and Nanobiotechnology Institute for Advanced Chemistry of Catalonia (IQAC) Spanish National Research Council (CSIC) Jordi Girona 18–26 E-08034 Barcelona Spain
- Networking Center on Bioengineering Biomaterials and Nanomedicine (CIBER-BBN) E-08034 Barcelona Spain
| | - Anna Aviñó
- Department of Surfactants and Nanobiotechnology Institute for Advanced Chemistry of Catalonia (IQAC) Spanish National Research Council (CSIC) Jordi Girona 18–26 E-08034 Barcelona Spain
- Networking Center on Bioengineering Biomaterials and Nanomedicine (CIBER-BBN) E-08034 Barcelona Spain
| | - Ramon Eritja
- Department of Surfactants and Nanobiotechnology Institute for Advanced Chemistry of Catalonia (IQAC) Spanish National Research Council (CSIC) Jordi Girona 18–26 E-08034 Barcelona Spain
- Networking Center on Bioengineering Biomaterials and Nanomedicine (CIBER-BBN) E-08034 Barcelona Spain
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Klabenkova K, Fokina A, Stetsenko D. Chemistry of Peptide-Oligonucleotide Conjugates: A Review. Molecules 2021; 26:5420. [PMID: 34500849 PMCID: PMC8434111 DOI: 10.3390/molecules26175420] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 12/25/2022] Open
Abstract
Peptide-oligonucleotide conjugates (POCs) represent one of the increasingly successful albeit costly approaches to increasing the cellular uptake, tissue delivery, bioavailability, and, thus, overall efficiency of therapeutic nucleic acids, such as, antisense oligonucleotides and small interfering RNAs. This review puts the subject of chemical synthesis of POCs into the wider context of therapeutic oligonucleotides and the problem of nucleic acid drug delivery, cell-penetrating peptide structural types, the mechanisms of their intracellular transport, and the ways of application, which include the formation of non-covalent complexes with oligonucleotides (peptide additives) or covalent conjugation. The main strategies for the synthesis of POCs are viewed in detail, which are conceptually divided into (a) the stepwise solid-phase synthesis approach and (b) post-synthetic conjugation either in solution or on the solid phase, especially by means of various click chemistries. The relative advantages and disadvantages of both strategies are discussed and compared.
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Affiliation(s)
- Kristina Klabenkova
- Faculty of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia; (K.K.); (D.S.)
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
| | - Alesya Fokina
- Faculty of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia; (K.K.); (D.S.)
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
| | - Dmitry Stetsenko
- Faculty of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia; (K.K.); (D.S.)
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
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21
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Guagliardo R, Herman L, Penders J, Zamborlin A, De Keersmaecker H, Van de Vyver T, Verstraeten S, Merckx P, Mingeot-Leclercq MP, Echaide M, Pérez-Gil J, Stevens MM, De Smedt SC, Raemdonck K. Surfactant Protein B Promotes Cytosolic SiRNA Delivery by Adopting a Virus-like Mechanism of Action. ACS NANO 2021; 15:8095-8109. [PMID: 33724778 DOI: 10.1021/acsnano.0c04489] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
RNA therapeutics are poised to revolutionize medicine. To unlock the full potential of RNA drugs, safe and efficient (nano)formulations to deliver them inside target cells are required. Endosomal sequestration of nanocarriers represents a major bottleneck in nucleic acid delivery. Gaining more detailed information on the intracellular behavior of RNA nanocarriers is crucial to rationally develop delivery systems with improved therapeutic efficiency. Surfactant protein B (SP-B) is a key component of pulmonary surfactant (PS), essential for mammalian breathing. In contrast to the general belief that PS should be regarded as a barrier for inhaled nanomedicines, we recently discovered the ability of SP-B to promote gene silencing by siRNA-loaded and lipid-coated nanogels. However, the mechanisms governing this process are poorly understood. The major objective of this work was to obtain mechanistic insights into the SP-B-mediated cellular delivery of siRNA. To this end, we combined siRNA knockdown experiments, confocal microscopy, and focused ion beam scanning electron microscopy imaging in an in vitro non-small-cell lung carcinoma model with lipid mixing assays on vesicles that mimic the composition of (intra)cellular membranes. Our work highlights a strong correlation between SP-B-mediated fusion with anionic endosomal membranes and cytosolic siRNA delivery, a mode of action resembling that of certain viruses and virus-derived cell-penetrating peptides. Building on these gained insights, we optimized the SP-B proteolipid composition, which dramatically improved delivery efficiency. Altogether, our work provides a mechanistic understanding of SP-B-induced perturbation of intracellular membranes, offering opportunities to fuel the rational design of SP-B-inspired RNA nanoformulations for inhalation therapy.
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Affiliation(s)
- Roberta Guagliardo
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Lore Herman
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Jelle Penders
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, U.K
| | - Agata Zamborlin
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Herlinde De Keersmaecker
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
- Centre for Advanced Light Microscopy, Ghent University, 9000 Ghent, Belgium
| | - Thijs Van de Vyver
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Sandrine Verstraeten
- Université Catholique de Louvain, Louvain Drug Research Institute, Pharmacologie Cellulaire et Moléculaire, Avenue E. Mounier 73, UCL B1.73.05, 1200 Brussels, Belgium
| | - Pieterjan Merckx
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Marie-Paule Mingeot-Leclercq
- Université Catholique de Louvain, Louvain Drug Research Institute, Pharmacologie Cellulaire et Moléculaire, Avenue E. Mounier 73, UCL B1.73.05, 1200 Brussels, Belgium
| | - Mercedes Echaide
- Departamento de Bioquímica y Biología Molecular, Facultad de Biologia, and Research Institute Hospital 12 de Octubre, Universidad Complutense, José Antonio Novais 12, 28040 Madrid, Spain
| | - Jesús Pérez-Gil
- Departamento de Bioquímica y Biología Molecular, Facultad de Biologia, and Research Institute Hospital 12 de Octubre, Universidad Complutense, José Antonio Novais 12, 28040 Madrid, Spain
| | - Molly M Stevens
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, U.K
| | - Stefaan C De Smedt
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Koen Raemdonck
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
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22
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A small interfering RNA (siRNA) database for SARS-CoV-2. Sci Rep 2021; 11:8849. [PMID: 33893357 PMCID: PMC8065152 DOI: 10.1038/s41598-021-88310-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 04/09/2021] [Indexed: 12/13/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) rapidly transformed into a global pandemic, for which a demand for developing antivirals capable of targeting the SARS-CoV-2 RNA genome and blocking the activity of its genes has emerged. In this work, we presented a database of SARS-CoV-2 targets for small interference RNA (siRNA) based approaches, aiming to speed the design process by providing a broad set of possible targets and siRNA sequences. The siRNAs sequences are characterized and evaluated by more than 170 features, including thermodynamic information, base context, target genes and alignment information of sequences against the human genome, and diverse SARS-CoV-2 strains, to assess possible bindings to off-target sequences. This dataset is available as a set of four tables, available in a spreadsheet and CSV (Comma-Separated Values) formats, each one corresponding to sequences of 18, 19, 20, and 21 nucleotides length, aiming to meet the diversity of technology and expertise among laboratories around the world. A metadata table (Supplementary Table S1), which describes each feature, is also provided in the aforementioned formats. We hope that this database helps to speed up the development of new target antivirals for SARS-CoV-2, contributing to a possible strategy for a faster and effective response to the COVID-19 pandemic.
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23
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Xu M, Zhang K, Song J. Targeted Therapy in Cardiovascular Disease: A Precision Therapy Era. Front Pharmacol 2021; 12:623674. [PMID: 33935716 PMCID: PMC8085499 DOI: 10.3389/fphar.2021.623674] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/22/2021] [Indexed: 12/12/2022] Open
Abstract
Targeted therapy refers to exploiting the specific therapeutic drugs against the pathogenic molecules (a protein or a gene) or cells. The drug specifically binds to disease-causing molecules or cells without affecting normal tissue, thus enabling personalized and precision treatment. Initially, therapeutic drugs included antibodies and small molecules, (e.g. nucleic acid drugs). With the advancement of the biology technology and immunotherapy, the gene editing and cell editing techniques are utilized for the disease treatment. Currently, targeted therapies applied to treat cardiovascular diseases (CVDs) mainly include protein drugs, gene editing technologies, nucleic acid drugs and cell therapy. Although targeted therapy has demonstrated excellent efficacy in pre-clinical and clinical trials, several limitations need to be recognized and overcome in clinical application, (e.g. off-target events, gene mutations, etc.). This review introduces the mechanisms of different targeted therapies, and mainly describes the targeted therapy applied in the CVDs. Furthermore, we made comparative analysis to clarify the advantages and disadvantages of different targeted therapies. This overview is expected to provide a new concept to the treatment of the CVDs.
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Affiliation(s)
- Mengda Xu
- Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kailun Zhang
- Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China,*Correspondence: Kailun Zhang, ; Jiangping Song,
| | - Jiangping Song
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China,*Correspondence: Kailun Zhang, ; Jiangping Song,
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24
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Portet A, Galinier R, Lassalle D, Faille A, Gourbal B, Duval D. Hemocyte siRNA uptake is increased by 5' cholesterol-TEG addition in Biomphalaria glabrata, snail vector of schistosome. PeerJ 2021; 9:e10895. [PMID: 33665030 PMCID: PMC7908872 DOI: 10.7717/peerj.10895] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 01/13/2021] [Indexed: 12/24/2022] Open
Abstract
Biomphalaria glabrata is one of the snail intermediate hosts of Schistosoma mansoni, the causative agent of intestinal schistosomiasis disease. Numerous molecular studies using comparative approaches between susceptible and resistant snails to S. mansoni infection have helped identify numerous snail key candidates supporting such susceptible/resistant status. The functional approach using RNA interference (RNAi) remains crucial to validate the function of such candidates. CRISPR-Cas systems are still under development in many laboratories, and RNA interference remains the best tool to study B. glabrata snail genetics. Herein, we describe the use of modified small interfering RNA (siRNA) molecules to enhance cell delivery, especially into hemocytes, the snail immune cells. Modification of siRNA with 5′ Cholesteryl TriEthylene Glycol (Chol-TEG) promotes cellular uptake by hemocytes, nearly eightfold over that of unmodified siRNA. FACS analysis reveals that more than 50% of hemocytes have internalized Chol-TEG siRNA conjugated to Cy3 fluorophores, 2 hours only after in vivo injection into snails. Chol-TEG siRNA targeting BgTEP1 (ThioEster-containing Protein), a parasite binding protein, reduced BgTEP1 transcript expression by 70–80% compared to control. The level of BgTEP1 protein secreted in the hemolymph was also decreased. However, despite the BgTEP1 knock-down at both RNA and protein levels, snail compatibility with its sympatric parasite is not affected suggesting functional redundancy among the BgTEP genes family in snail-schistosoma interaction.
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Affiliation(s)
- Anaïs Portet
- IHPE UMR 5244, CNRS, IFREMER, University of Montpellier, University of Perpignan, Perpignan, France.,Department of Medicine, Molecular Immunity Unit, University of Cambridge, Cambridge, United Kingdom
| | - Richard Galinier
- IHPE UMR 5244, CNRS, IFREMER, University of Montpellier, University of Perpignan, Perpignan, France
| | - Damien Lassalle
- IHPE UMR 5244, CNRS, IFREMER, University of Montpellier, University of Perpignan, Perpignan, France
| | - Alexandre Faille
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom.,Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.,Cambridge Institute for Medical Research, Cambridge, United Kingdom
| | - Benjamin Gourbal
- IHPE UMR 5244, CNRS, IFREMER, University of Montpellier, University of Perpignan, Perpignan, France
| | - David Duval
- IHPE UMR 5244, CNRS, IFREMER, University of Montpellier, University of Perpignan, Perpignan, France
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25
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Varley AJ, Desaulniers JP. Chemical strategies for strand selection in short-interfering RNAs. RSC Adv 2021; 11:2415-2426. [PMID: 35424193 PMCID: PMC8693850 DOI: 10.1039/d0ra07747j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/24/2020] [Indexed: 12/13/2022] Open
Abstract
Therapeutic small interfering RNAs (siRNAs) are double stranded RNAs capable of potent and specific gene silencing through activation of the RNA interference (RNAi) pathway. The potential of siRNA drugs has recently been highlighted by the approval of multiple siRNA therapeutics. These successes relied heavily on chemically modified nucleic acids and their impact on stability, delivery, potency, and off-target effects. Despite remarkable progress, clinical trials still face failure due to off-target effects such as off-target gene dysregulation. Each siRNA strand can downregulate numerous gene targets while also contributing towards saturation of the RNAi machinery, leading to the upregulation of miRNA-repressed genes. Eliminating sense strand uptake effectively reduces off-target gene silencing and helps limit the disruption to endogenous regulatory mechanisms. Therefore, our understanding of strand selection has a direct impact on the success of future siRNA therapeutics. In this review, the approaches used to improve strand uptake are discussed and effective methods are summarized.
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Affiliation(s)
- Andrew J Varley
- Faculty of Science, University of Ontario Institute of Technology Oshawa Ontario L1G 0C5 Canada +1 905 721 3304 +1 905 721 8668 (ext. 3621)
| | - Jean-Paul Desaulniers
- Faculty of Science, University of Ontario Institute of Technology Oshawa Ontario L1G 0C5 Canada +1 905 721 3304 +1 905 721 8668 (ext. 3621)
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26
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Mukushkina D, Aisina D, Pyrkova A, Ryskulova A, Labeit S, Ivashchenko A. In silico Prediction of miRNA Interactions With Candidate Atherosclerosis Gene mRNAs. Front Genet 2020; 11:605054. [PMID: 33329752 PMCID: PMC7672156 DOI: 10.3389/fgene.2020.605054] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 10/15/2020] [Indexed: 12/14/2022] Open
Abstract
The involvement of genes and miRNAs in the development of atherosclerosis is a challenging problem discussed in recent publications. It is necessary to establish which miRNAs affect the expression of candidate genes. We used known candidate atherosclerosis genes to predict associations. The quantitative characteristics of interactions of miRNAs with mRNA candidate genes were determined using the program, which identifies the localization of miRNA binding sites in mRNA, the free energy interaction of miRNA with mRNA. In mRNAs of GAS6 and NFE2L2 candidate genes, binding sites of 21 miRNAs and of 15 miRNAs, respectively, were identified. In IRS2 mRNA binding sites of 25 miRNAs were located in a cluster of 41 nt. In ADRB3, CD36, FASLG, FLT1, PLA2G7, and PPARGC1A mRNAs, clusters of miR-466, ID00436.3p-miR, and ID01030.3p-miR BS were identified. The organization of overlapping miRNA binding sites in clusters led to their compaction and caused competition among the miRNAs. The binding of 53 miRNAs to the mRNAs of 14 candidate genes with free energy interactions greater than -130 kJ/mole was determined. The miR-619-5p was fully complementary to ADAM17 and CD36 mRNAs, ID01593.5p-miR to ANGPTL4 mRNA, ID01935.5p-miR to NFE2L2, and miR-5096 to IL18 mRNA. Associations of miRNAs and candidate atherosclerosis genes are proposed for the early diagnosis of this disease.
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Affiliation(s)
- Dina Mukushkina
- Department of Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Dana Aisina
- Department of Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Anna Pyrkova
- Department of Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Alma Ryskulova
- Department of microbiology, Kazakh Medical University of Continuing Education, Almaty, Kazakhstan
| | - Siegfried Labeit
- Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Anatoliy Ivashchenko
- Department of Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
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27
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Naik S, Shreya AB, Raychaudhuri R, Pandey A, Lewis SA, Hazarika M, Bhandary SV, Rao BSS, Mutalik S. Small interfering RNAs (siRNAs) based gene silencing strategies for the treatment of glaucoma: Recent advancements and future perspectives. Life Sci 2020; 264:118712. [PMID: 33159955 DOI: 10.1016/j.lfs.2020.118712] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/28/2020] [Accepted: 10/31/2020] [Indexed: 01/22/2023]
Abstract
RNA-interference-based mechanisms, especially the use of small interfering RNAs (siRNAs), have been under investigation for the treatment of several ailments and have shown promising results for ocular diseases including glaucoma. The eye, being a confined compartment, serves as a good target for the delivery of siRNAs. This review focuses on siRNA-based strategies for gene silencing to treat glaucoma. We have discussed the ocular structures and barriers to gene therapy (tear film, corneal, conjunctival, vitreous, and blood ocular barriers), methods of administration for ocular gene delivery (topical instillation, periocular, intracameral, intravitreal, subretinal, and suprachoroidal routes) and various viral and non-viral vectors in siRNA-based therapy for glaucoma. The components and mechanism of siRNA-based gene silencing have been mentioned briefly followed by the basic strategies and challenges faced during siRNA therapeutics development. We have emphasized different therapeutic targets for glaucoma which have been under research by scientists and the current siRNA-based drugs used in glaucoma treatment. We also mention briefly strategies for siRNA-based treatment after glaucoma surgery.
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Affiliation(s)
- Santoshi Naik
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka State, India
| | - Ajjappla Basavaraj Shreya
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka State, India
| | - Ruchira Raychaudhuri
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka State, India
| | - Abhijeet Pandey
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka State, India
| | - Shaila A Lewis
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka State, India
| | - Manali Hazarika
- Department of Ophthalmology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal 576104, Karnataka State, India
| | - Sulatha V Bhandary
- Department of Ophthalmology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal 576104, Karnataka State, India
| | - Bola Sadashiva Satish Rao
- Director - Research, Directorte of Research, Manipal Academy of Higher Education, Manipal and School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka State, India
| | - Srinivas Mutalik
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka State, India.
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28
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Kotikam V, Rozners E. Amide-Modified RNA: Using Protein Backbone to Modulate Function of Short Interfering RNAs. Acc Chem Res 2020; 53:1782-1790. [PMID: 32658452 DOI: 10.1021/acs.accounts.0c00249] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
RNA-based technologies to control gene expression, such as RNA interference (RNAi) and CRISPR-Cas9, have become powerful tools in molecular biology and genomics. The exciting potential that RNAi and CRISPR-Cas9 may also become new therapeutic approaches has reinvigorated interest in chemically modifying RNA to improve its properties for in vivo applications. Chemical modifications can improve enzymatic stability, in vivo delivery, cellular uptake, and sequence specificity as well as minimize off-target activity of short interfering RNAs (siRNAs) and CRISPR associated RNAs. While numerous good solutions for improving stability toward enzymatic degradation have emerged, optimization of the latter functional properties remains challenging. In this Account, we discuss synthesis, structure, and biological activity of novel nonionic analogues of RNA that have the phosphodiester backbone replaced by amide linkages (AM1). Our long-term goal is to use the amide backbone to improve the stability and specificity of siRNAs and other functional RNAs. Our work in this area was motivated by early discoveries that nonionic backbone modifications, including AM1, did not disturb the overall structure or thermal stability of RNA duplexes. We hypothesized that the reduced negative charge and hydrophobic nature of the AM1 backbone modification might be useful in optimizing functional applications through enhanced cellular uptake, and might suppress unwanted off-target effects of siRNAs. NMR and X-ray crystallography studies showed that AM1 was an excellent mimic of phosphodiester linkages in RNA. The local conformational changes caused by the amide linkages were easily accommodated by small adjustments in RNA's conformation. Further, the amide carbonyl group assumed an orientation that is similar to one of the nonbridging P-O bonds, which may enable amide/phosphate mimicry by conserving hydrogen bonding interactions. The crystal structure of a short amide-modified DNA-RNA hybrid in complex with RNase H indicated that the amide N-H could also act as an H-bond donor to stabilize RNA-protein interactions, which is an interaction mode not available to phosphate groups. Functional assays established that amides were well tolerated at internal positions in both strands of siRNAs. Surprisingly, amide modifications in the middle of the guide strand and at the 5'-end of the passenger strand increased RNAi activity compared to unmodified siRNA. Most importantly, an amide linkage between the first and second nucleosides of the passenger strand completely abolished its undesired off-target activity while enhancing the desired RNAi activity. These results suggest that RNAi may tolerate more substantial modifications of siRNAs than the chemistries tried so far. The findings are also important and timely because they demonstrate that amide modifications may reduce off-target activity of siRNAs, which remains an important roadblock for clinical use of RNAi. Taken together, our work suggests that amide linkages have underappreciated potential to optimize the biological and pharmacological properties of RNA. Expanded use of amide linkages in RNA to enhance CRISPR and other technologies requiring chemically stable, functional mimics of noncoding RNAs is expected.
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Affiliation(s)
- Venubabu Kotikam
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
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29
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Khan AH, Lin A, Wang RT, Bloom JS, Lange K, Smith DJ. Pooled analysis of radiation hybrids identifies loci for growth and drug action in mammalian cells. Genome Res 2020; 30:1458-1467. [PMID: 32878976 PMCID: PMC7605260 DOI: 10.1101/gr.262204.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 08/26/2020] [Indexed: 12/16/2022]
Abstract
Genetic screens in mammalian cells commonly focus on loss-of-function approaches. To evaluate the phenotypic consequences of extra gene copies, we used bulk segregant analysis (BSA) of radiation hybrid (RH) cells. We constructed six pools of RH cells, each consisting of ∼2500 independent clones, and placed the pools under selection in media with or without paclitaxel. Low pass sequencing identified 859 growth loci, 38 paclitaxel loci, 62 interaction loci, and three loci for mitochondrial abundance at genome-wide significance. Resolution was measured as ∼30 kb, close to single-gene. Divergent properties were displayed by the RH-BSA growth genes compared to those from loss-of-function screens, refuting the balance hypothesis. In addition, enhanced retention of human centromeres in the RH pools suggests a new approach to functional dissection of these chromosomal elements. Pooled analysis of RH cells showed high power and resolution and should be a useful addition to the mammalian genetic toolkit.
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Affiliation(s)
- Arshad H Khan
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, California 90095-1735, USA
| | - Andy Lin
- Office of Information Technology, UCLA, Los Angeles, California 90095-1557, USA
| | - Richard T Wang
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, California 90095-7088, USA
| | - Joshua S Bloom
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, California 90095-7088, USA.,Howard Hughes Medical Institute, David Geffen School of Medicine, UCLA, Los Angeles, California 90095-7088, USA
| | - Kenneth Lange
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, California 90095-7088, USA
| | - Desmond J Smith
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, California 90095-1735, USA
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30
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In Vitro Screening and Transfection Concentration Optimization of Cynomolgus Monkey I κB α-siRNA. J Ophthalmol 2020; 2020:1848540. [PMID: 32377413 PMCID: PMC7180988 DOI: 10.1155/2020/1848540] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 03/09/2020] [Indexed: 12/04/2022] Open
Abstract
Purpose To seek for a small interfering RNA (siRNA) sequence targeting a cynomolgus monkey inhibitor of nuclear factor kappa B α (IκBα) that can specifically and effectively suppress IκBα gene expression of cynomolgus monkey ciliary muscle (CM) cells and trabecular meshwork (TM) cells in vitro and screen for optimal siRNA transfection concentration. Methods Three IκBα-specific double-stranded siRNAs were designed and synthesized. They were transfected into primarily cultured cynomolgus monkey CM cells and TM cells. The mRNA and protein levels of IκBα were examined by using real-time quantitative polymerase chain reaction (real-time PCR) and western blot to screen a pair of candidate valid sequences with the highest inhibitory rate. Both cells were transfected with Cy5-labeled nonspecific control-siRNA (NC-siRNA) of four different concentrations (10, 20, 50, and 100 nmol/L(nM)), and flow cytometry was used to assess transfection efficiency. Then, cells were transfected with the candidate valid IκBα -siRNA of the same four concentrations, and the cytotoxicity was detected by using Cell Counting Kit-8 (CCK8), and the inhibitory efficiency of IκBα was identified via real-time PCR to find out optimal siRNA transfection concentration. Results The suppression effect of the siRNA targeting the GCACTTAGCCTCTATCCAT of IκBα gene was most obvious by in vitro screening. The inhibitory rate of IκBα was 82% for CM cells and 82% for TM cells on the mRNA level and 98% for CM cells and 93% for TM cells on the protein level, respectively. The results of flow cytometry showed that the transfection efficiency was the highest at 100 nM, which was 89.0% for CM cells and 48.2% for TM cells, respectively. The results of CCK8 showed that there was no statistically significant difference in cell viability after transfection of different concentrations of IκBα-siRNA. The results of real-time PCR indicated that there was no statistical difference in the inhibitory efficiency of IκBα after transfection of different concentrations of IκBα-siRNA. Conclusion It proves that the siRNA targeting the GCACTTAGCCTCTATCCAT of IκBα gene is the valid sequence to suppress cynomolgus monkey IκBα expression of CM cells and TM cells by RNAi. 10 nM is the optimal transfection concentration.
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Epanchintseva AV, Poletaeva JE, Pyshnyi DV, Ryabchikova EI, Pyshnaya IA. Long-term stability and scale-up of noncovalently bound gold nanoparticle-siRNA suspensions. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2019; 10:2568-2578. [PMID: 31921536 PMCID: PMC6941443 DOI: 10.3762/bjnano.10.248] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 11/27/2019] [Indexed: 06/10/2023]
Abstract
Gold nanoparticles (AuNPs) are a platform for the creation of nanoconstructions that can have a variety of functions, including the delivery of therapeutic nucleic acids. We previously designed a AuNP/small interfering RNA (siRNA) nanoconstruction consisting of siRNA noncovalently bound on the AuNP surface and showed that this construction, when coated with a lipid shell, was an efficient vehicle for the delivery of siRNA into cells. The goal of the present work was to study the possibility of scaling up the synthesis of AuNP-siRNA and its long-term storage without loss of physicochemical characteristics and siRNA duplex integrity as well as siRNA surface density. Dynamic light scattering, transmission electron microscopy, UV-vis spectroscopy, and electrophoresis were used to study the effect of scaling up the AuNP-siRNA synthesis and long term storage of its suspension on physicochemical properties of the samples and integrity of the siRNA duplex. It was shown that a ten-fold increase in the volume of the reaction mixture decreased the surface density of siRNA by about 10%, which influenced the corresponding physicochemical characteristics of the AuNP-siRNA suspension. The storage of the AuNP-siRNA suspension at 4 °C for different times resulted in the formation of particle clusters of high colloidal stability as demonstrated by conventional methods. These clusters completely disintegrated when albumin was added, indicating that they are agglomerates (and not aggregates) of AuNP-siRNA. The AuNPs-siRNA nanoconstruction demonstrated integrity of the siRNA duplex and high stability of the siRNA surface density during storage for seven months at 4 °C. Thus, it can be concluded that it is possible to scale-up the synthesis of noncovalent AuNP-siRNA and to obtain a nanoconstruction possessing high stability in terms of physicochemical characteristics and siRNA surface density for a long period.
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Affiliation(s)
- Anna V Epanchintseva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Science, Lavrent’ev av., 8, Novosibirsk, 630090, Russian Federation
| | - Julia E Poletaeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Science, Lavrent’ev av., 8, Novosibirsk, 630090, Russian Federation
| | - Dmitrii V Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Science, Lavrent’ev av., 8, Novosibirsk, 630090, Russian Federation
| | - Elena I Ryabchikova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Science, Lavrent’ev av., 8, Novosibirsk, 630090, Russian Federation
| | - Inna A Pyshnaya
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Science, Lavrent’ev av., 8, Novosibirsk, 630090, Russian Federation
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Zhang Y, Li S, Zhou X, Sun J, Fan X, Guan Z, Zhang L, Yang Z. Construction of a Targeting Nanoparticle of 3',3″-Bis-Peptide-siRNA Conjugate/Mixed Lipid with Postinserted DSPE-PEG2000-cRGD. Mol Pharm 2019; 16:4920-4928. [PMID: 31642677 DOI: 10.1021/acs.molpharmaceut.9b00800] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The cyclic Arg-Gly-Asp (cRGD) peptides are widely used as tumor-targeting ligands due to their specific binding ability to integrin αvβ3, which is overexpressed on the surface of various cancer cells and the endothelial cells of new blood vessels within tumor tissues. In this paper, the postinsertion strategy of DSPE-PEG2000-cRGD has been applied to the nanoparticles of 3',3″-bis-peptide-siRNA (pp-siRNA) encapsulated by gemini-like cationic lipid (CLD) and neutral cytosin-1-yl lipid (DNCA) from our lab. It was confirmed that the nanoparticles of pp-siRNA/CLD/DNCA/DSPE-PEG2000-cRGD (PCNR) were able to specifically target tumor cells with highly expressed integrin αvβ3; moreover, it efficiently downregulated the levels of BRAF mRNA and the BRAF protein and inhibited cell proliferation in A375 cells, in comparison with the nontargeted nanocomplex of pp-siRNA/CLD/DNCA/cRAD (PCNA). The uptake pathways of PCNR are mostly dependent on CvME-mediated endocytosis and macropinocytosis in A375 cells, which could bypass lysosome or quickly lead to the lysosomal escape to reduce siRNA degradation. Finally, the biodistribution study showed that PCNR exhibited a high ability to accumulate in tumor tissues. These results suggest that the nanocomplex of PCNR is promising to be highly effective in the treatment of melanomas including their mutation.
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Affiliation(s)
- Yanfen Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, P. R. China.,School of Pharmaceutical Sciences, HeZe University, Heze, Shandong 274015, P. R. China
| | - Sixiu Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, P. R. China
| | - Xinyang Zhou
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, P. R. China
| | - Jing Sun
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, P. R. China
| | - Xinmeng Fan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, P. R. China
| | - Zhu Guan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, P. R. China
| | - Lihe Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, P. R. China
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, P. R. China
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Greenidge PA, Blommers MJJ, Priestle JP, Hunziker J. How to Computationally Stack the Deck for Hit-to-Lead Generation: In Silico Molecular Interaction Energy Profiling for de Novo siRNA Guide Strand Surrogate Selection. J Chem Inf Model 2019; 59:1897-1908. [PMID: 31021613 DOI: 10.1021/acs.jcim.8b00892] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The Argonaute-2 protein is part of the RNA-induced silencing complex (RISC) and anchors the guide strand of the small interfering RNA (siRNA). The 3'-end of the RNA contains two unpaired nucleotides (3'-overhang) that interact with the PAZ (PIWI/Argonaute/Zwille) domain of the protein. Theoretical and experimental evidence points toward a direct connection between the PAZ/3'-overhang binding affinity and siRNA's potency and specificity. Among the challenges to overcome when deploying siRNA molecules as therapeutics are their ready degradation under physiological conditions and off-target effects. It has been demonstrated that nuclease resistance can be improved via replacement of the dinucleotide overhang by small molecules which retain the interactions of the RNA guide strand with the PAZ domain. Most commonly, nucleotide analogues are used to substitute the siRNA overhang. However, in this study we adopt a de novo approach to its modification. The X-ray structure of human Argonaute-2 PAZ domain served to perform virtual screening and molecular interaction energy profiling (i.e., decomposition of the force field calculated protein-ligand interaction energies) of tailored-to-purpose fragment libraries. The binding of fragments to the PAZ domain was validated experimentally by NMR spectroscopy. The in silico guided protocol led to the efficient discovery of a number of PAZ domain ligands with affinities comparable to that of a reference dinucleotide (UpU, Kd = 33 μM). Originally starting from a generic fragment library, hits progress from 930 μM down to 14 μM within three iterations for the fragments selected via in silico molecular interaction energy profiling from a bespoke library. These dinucleotide siRNA guide strand surrogates represent potential new siRNA-based therapeutics (when attached to siRNA to form bioconjugates) featuring improved efficacy, specificity, stability, and cellular uptake. This project yielded a portfolio of seven patent applications, four of which have been granted to date.
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Affiliation(s)
- Paulette A Greenidge
- Novartis Institutes for BioMedical Research (NIBR), Novartis Pharma AG , Forum 1, Novartis Campus, Fabrikstrasse 2 , CH-4056 Basel , Switzerland.,Sprint Bioscience AB , Hälsovägen 7 , SE-141 57 Huddinge , Sweden
| | - Marcel J J Blommers
- Novartis Institutes for BioMedical Research (NIBR), Novartis Pharma AG , Forum 1, Novartis Campus, Fabrikstrasse 2 , CH-4056 Basel , Switzerland.,Saverna Therapeutics AG , Pumpmattenweg 3 , CH-4105 Biel-Benken , Switzerland
| | - John P Priestle
- Novartis Institutes for BioMedical Research (NIBR), Novartis Pharma AG , Forum 1, Novartis Campus, Fabrikstrasse 2 , CH-4056 Basel , Switzerland
| | - Jürg Hunziker
- Novartis Institutes for BioMedical Research (NIBR), Novartis Pharma AG , Forum 1, Novartis Campus, Fabrikstrasse 2 , CH-4056 Basel , Switzerland
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Mahmoodi Chalbatani G, Dana H, Gharagouzloo E, Grijalvo S, Eritja R, Logsdon CD, Memari F, Miri SR, Rad MR, Marmari V. Small interfering RNAs (siRNAs) in cancer therapy: a nano-based approach. Int J Nanomedicine 2019; 14:3111-3128. [PMID: 31118626 PMCID: PMC6504672 DOI: 10.2147/ijn.s200253] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 03/23/2019] [Indexed: 12/31/2022] Open
Abstract
Cancer is one of the most complex diseases that has resulted in multiple genetic disorders and cellular abnormalities. Globally, cancer is the most common health concern disease that is affecting human beings. Great efforts have been made over the past decades in biology with the aim of searching novel and more efficient tools in therapy. Thus, small interfering RNAs (siRNAs) have been considered one of the most noteworthy developments which are able to regulate gene expression following a process known as RNA interference (RNAi). RNAi is a post-transcriptional mechanism that involves the inhibition of gene expression through promoting cleavage on a specific area of a target messenger RNA (mRNA). This technology has shown promising therapeutic results for a good number of diseases, especially in cancer. However, siRNA therapeutics have to face important drawbacks in therapy including stability and successful siRNA delivery in vivo. In this regard, the development of effective siRNA delivery systems has helped addressing these issues by opening novel therapeutic windows which have allowed to build up important advances in Nanomedicine. In this review, we discuss the progress of siRNA therapy as well as its medical application via nanoparticle-mediated delivery for cancer treatment.
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Affiliation(s)
| | - Hassan Dana
- Cancer Research Center, Cancer Institute of Iran, Tehran University of Medical Science, Tehran, Iran
- Department of Biology, Damghan Branch, Islamic Azad University, Damghan, Iran
| | - Elahe Gharagouzloo
- Cancer Research Center, Cancer Institute of Iran, Tehran University of Medical Science, Tehran, Iran
| | - Santiago Grijalvo
- Institute of Advanced Chemistry of Catalonia (IQAC-CSIC), Barcelona08034, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER BBN), Madrid, Spain
| | - Ramon Eritja
- Institute of Advanced Chemistry of Catalonia (IQAC-CSIC), Barcelona08034, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER BBN), Madrid, Spain
| | - Craig D Logsdon
- Department of Cancer Biology, University of Texas, M.D. Anderson Cancer Center, Houston, TX, USA
- Department of GI Medical Oncology, University of Texas, M.D. Anderson Cancer Center, Houston, TX, USA
| | - Fereidoon Memari
- Cancer Research Center, Cancer Institute of Iran, Tehran University of Medical Science, Tehran, Iran
| | - Seyed Rouhollah Miri
- Cancer Research Center, Cancer Institute of Iran, Tehran University of Medical Science, Tehran, Iran
| | | | - Vahid Marmari
- Department of Biology, Damghan Branch, Islamic Azad University, Damghan, Iran
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Martín-Vicente M, Resino S, Martínez I. siRNA-Mediated Simultaneous Regulation of the Cellular Innate Immune Response and Human Respiratory Syncytial Virus Replication. Biomolecules 2019; 9:biom9050165. [PMID: 31035368 PMCID: PMC6572644 DOI: 10.3390/biom9050165] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 04/22/2019] [Accepted: 04/23/2019] [Indexed: 12/15/2022] Open
Abstract
Human respiratory syncytial virus (HRSV) infection is a common cause of severe lower respiratory tract diseases such as bronchiolitis and pneumonia. Both virus replication and the associated inflammatory immune response are believed to be behind these pathologies. So far, no vaccine or effective treatment is available for this viral infection. With the aim of finding new strategies to counteract HRSV replication and modulate the immune response, specific small interfering RNAs (siRNAs) were generated targeting the mRNA coding for the viral fusion (F) protein or nucleoprotein (N), or for two proteins involved in intracellular immune signaling, which are named tripartite motif-containing protein 25 (TRIM25) and retinoic acid-inducible gene-I (RIG-I). Furthermore, two additional bispecific siRNAs were designed that silenced F and TRIM25 (TRIM25/HRSV-F) or N and RIG-I (RIG-I/HRSV-N) simultaneously. All siRNAs targeting N or F, but not those silencing TRIM25 or RIG-I alone, significantly reduced viral titers. However, while siRNAs targeting F inhibited only the expression of the F mRNA and protein, the siRNAs targeting N led to a general inhibition of viral mRNA and protein expression. The N-targeting siRNAs also induced a drastic decrease in the expression of genes of the innate immune response. These results show that both virus replication and the early innate immune response can be regulated by targeting distinct viral products with siRNAs, which may be related to the different role of each protein in the life cycle of the virus.
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MESH Headings
- Base Sequence
- Cell Line, Tumor
- Gene Expression Regulation, Viral
- Gene Silencing
- Genome, Viral
- Humans
- Immunity, Innate/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Small Interfering/metabolism
- RNA, Viral/metabolism
- Respiratory Syncytial Virus, Human/genetics
- Respiratory Syncytial Virus, Human/growth & development
- Respiratory Syncytial Virus, Human/immunology
- Respiratory Syncytial Virus, Human/physiology
- Viral Proteins/genetics
- Viral Proteins/metabolism
- Virus Replication/physiology
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Affiliation(s)
- María Martín-Vicente
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain.
| | - Salvador Resino
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain.
| | - Isidoro Martínez
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain.
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Yoshimura H, Shibata SB, Ranum PT, Moteki H, Smith RJH. Targeted Allele Suppression Prevents Progressive Hearing Loss in the Mature Murine Model of Human TMC1 Deafness. Mol Ther 2019; 27:681-690. [PMID: 30686588 DOI: 10.1016/j.ymthe.2018.12.014] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 12/20/2018] [Accepted: 12/27/2018] [Indexed: 12/19/2022] Open
Abstract
Hearing loss is the most common human sensory deficit. Its correction has been the goal of several gene-therapy based studies exploring a variety of interventions. Although these studies report varying degrees of success, all treatments have targeted developing inner ears in neonatal mice, a time point in the structural maturation of the cochlea prior to 26 weeks gestational age in humans. It is unclear whether cochlear gene therapy can salvage hearing in the mature organ of Corti. Herein, we report the first study to test gene therapy in an adult murine model of human deafness. Using a single intracochlear injection of an artificial microRNA carried in an AAV vector, we show that RNAi-mediated gene silencing can slow progression of hearing loss, improve inner hair cell survival, and prevent stereocilia bundle degeneration in the mature Beethoven mouse, a model of human TMC1 deafness. The ability to study gene therapy in mature murine ears constitutes a significant step toward its translation to human subjects.
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Affiliation(s)
- Hidekane Yoshimura
- Molecular Otolaryngology and Renal Research Laboratories, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA; Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan
| | - Seiji B Shibata
- Molecular Otolaryngology and Renal Research Laboratories, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA; Department of Otolaryngology-Head and Neck Surgery, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Paul T Ranum
- Molecular Otolaryngology and Renal Research Laboratories, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Hideaki Moteki
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan
| | - Richard J H Smith
- Molecular Otolaryngology and Renal Research Laboratories, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA; Department of Otolaryngology-Head and Neck Surgery, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
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Kwon YM, Kim KW, Choi TY, Kim SY, Kim JYH. Manipulation of the microalgal chloroplast by genetic engineering for biotechnological utilization as a green biofactory. World J Microbiol Biotechnol 2018; 34:183. [PMID: 30478596 DOI: 10.1007/s11274-018-2567-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 11/23/2018] [Indexed: 12/16/2022]
Abstract
The chloroplast is an essential organelle in microalgae for conducting photosynthesis, thus enabling the photoautotrophic growth of microalgae. In addition to photosynthesis, the chloroplast is capable of various biochemical processes for the synthesis of proteins, lipids, carbohydrates, and terpenoids. Due to these attractive characteristics, there has been increasing interest in the biotechnological utilization of microalgal chloroplast as a sustainable alternative to the conventional production platforms used in industrial biotechnology. Since the first demonstration of microalgal chloroplast transformation, significant development has occurred over recent decades in the manipulation of microalgal chloroplasts through genetic engineering. In the present review, we describe the advantages of the microalgal chloroplast as a production platform for various bioproducts, including recombinant proteins and high-value metabolites, features of chloroplast genetic systems, and the development of transformation methods, which represent important factors for gene expression in the chloroplast. Furthermore, we address the expression of various recombinant proteins in the microalgal chloroplast through genetic engineering, including reporters, biopharmaceutical proteins, and industrial enzymes. Finally, we present many efforts and achievements in the production of high-value metabolites in the microalgal chloroplast through metabolic engineering. Based on these efforts and advances, the microalgal chloroplast represents an economically viable and sustainable platform for biotechnological applications in the near future.
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Affiliation(s)
- Yong Min Kwon
- Department of Applied Research, National Marine Biodiversity Institute of Korea, Jangsan-ro 101-75, Seocheon, Chungcheongnamdo, 33662, Republic of Korea
| | - Kyung Woo Kim
- Department of Applied Research, National Marine Biodiversity Institute of Korea, Jangsan-ro 101-75, Seocheon, Chungcheongnamdo, 33662, Republic of Korea
| | - Tae-Young Choi
- Department of Genetic Resources Research, National Marine Biodiversity Institute of Korea, Jangsan-ro 101-75, Seocheon, Chungcheongnamdo, 33662, Republic of Korea
| | - Sun Young Kim
- Department of Applied Research, National Marine Biodiversity Institute of Korea, Jangsan-ro 101-75, Seocheon, Chungcheongnamdo, 33662, Republic of Korea
| | - Jaoon Young Hwan Kim
- Department of Applied Research, National Marine Biodiversity Institute of Korea, Jangsan-ro 101-75, Seocheon, Chungcheongnamdo, 33662, Republic of Korea.
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Dindo M, Conter C, Oppici E, Ceccarelli V, Marinucci L, Cellini B. Molecular basis of primary hyperoxaluria: clues to innovative treatments. Urolithiasis 2018; 47:67-78. [PMID: 30430197 DOI: 10.1007/s00240-018-1089-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 11/08/2018] [Indexed: 12/21/2022]
Abstract
Primary hyperoxalurias (PHs) are rare inherited disorders of liver glyoxylate metabolism, characterized by the abnormal production of endogenous oxalate, a metabolic end-product that is eliminated by urine. The main symptoms are related to the precipitation of calcium oxalate crystals in the urinary tract with progressive renal damage and, in the most severe form named Primary Hyperoxaluria Type I (PH1), to systemic oxalosis. The therapies currently available for PH are either poorly effective, because they address the symptoms and not the causes of the disease, or highly invasive. In the last years, advances in our understanding of the molecular bases of PH have paved the way for the development of new therapeutic strategies. They include (i) substrate-reduction therapies based on small-molecule inhibitors or the RNA interference technology, (ii) gene therapy, (iii) enzyme administration approaches, (iv) colonization with oxalate-degrading intestinal microorganisms, and, in PH1, (v) design of pharmacological chaperones. This paper reviews the basic principles of these new therapeutic strategies and what is currently known about their application to PH.
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Affiliation(s)
- Mirco Dindo
- Department of Experimental Medicine, University of Perugia, P.le Gambuli 1, 06132, Perugia, Italy
| | - Carolina Conter
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Strada le Grazie 8, 37134, Verona, VR, Italy
| | - Elisa Oppici
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Strada le Grazie 8, 37134, Verona, VR, Italy
| | - Veronica Ceccarelli
- Department of Experimental Medicine, University of Perugia, P.le Gambuli 1, 06132, Perugia, Italy
| | - Lorella Marinucci
- Department of Experimental Medicine, University of Perugia, P.le Gambuli 1, 06132, Perugia, Italy
| | - Barbara Cellini
- Department of Experimental Medicine, University of Perugia, P.le Gambuli 1, 06132, Perugia, Italy.
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Liu D, Yuan R, Yang F, Zhang D. Effects of tanshinones mediated by forkhead box O3a transcription factor on the proliferation and apoptosis of lung cancer cells. Oncol Lett 2018; 17:450-455. [PMID: 30655786 DOI: 10.3892/ol.2018.9530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Accepted: 08/08/2017] [Indexed: 12/20/2022] Open
Abstract
According to global cancer statistics in 2012, lung cancer (LC) was the most frequently diagnosed cancer and the leading cause of cancer-associated mortality among males worldwide. Owing to the limited therapeutic approaches available, novel methods for treating LC are required. Tanshinones (Ts) have previously been proved to be effective in treating cardiovascular disease, inflammatory disease and cancer, and have been reported to regulate cell proliferation and apoptosis of LC. The underlying molecular mechanism of action of Ts remains unclear. Furthermore, forkhead box O3a (FoxO3a) has been reported to be a critical gene in cell apoptosis. Therefore, the A549 lung cancer cell line was transfected with FoxO3a small interfering RNA (siRNA) or scrambled siRNA, and the cells which exhibited the most successful transfection efficacy were selected for further investigation into the underlying molecular mechanism of the influence of Ts on FoxO3a in LC cells. Various concentrations of Ts were assigned to experimental groups I-IV (5, 10, 20 and 30 µmol/l Ts, respectively). An MTT assay revealed that Ts inhibited cell proliferation in a dose- and time-dependent manner compared with the control group (CON; without Ts administration) with a maximal dose of 20 µmol/l at 72 h treatment (P<0.05). Similarly, compared with CON, flow cytometry results revealed that Ts induce LC cell apoptosis in a dose-dependent manner (P<0.05). Consistently, the expression levels of FoxO3a mRNA and protein were restored following treatment with Ts in a dose-dependent manner, alongside caspase-3 activation. On the basis of these results, we hypothesize that Ts regulate LC cell proliferation and apoptosis by triggering an apoptotic cascade through the FoxO3a/caspase-3 signaling pathway.
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Affiliation(s)
- Dongjie Liu
- Oncology Department, Daqing Oil Field General Hospital, Daqing, Heilongjiang 163000, P.R. China
| | - Renbing Yuan
- Oncology Department, Daqing Oil Field General Hospital, Daqing, Heilongjiang 163000, P.R. China
| | - Fang Yang
- Oncology Department, Daqing Oil Field General Hospital, Daqing, Heilongjiang 163000, P.R. China
| | - Dehui Zhang
- Oncology Department, Daqing Oil Field General Hospital, Daqing, Heilongjiang 163000, P.R. China
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Alagia A, Jorge AF, Aviñó A, Cova TFGG, Crehuet R, Grijalvo S, Pais AACC, Eritja R. Exploring PAZ/3'-overhang interaction to improve siRNA specificity. A combined experimental and modeling study. Chem Sci 2018; 9:2074-2086. [PMID: 29719684 PMCID: PMC5896489 DOI: 10.1039/c8sc00010g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 01/15/2018] [Indexed: 12/29/2022] Open
Abstract
The understanding of the dynamical and mechanistic aspects that lie behind siRNA-based gene regulation is a requisite to boost the performance of siRNA therapeutics. A systematic experimental and computational study on the 3'-overhang structural requirements for the design of more specific and potent siRNA molecules was carried out using nucleotide analogues differing in structural parameters, such as sugar constraint, lack of nucleobase, distance between the phosphodiester backbone and nucleobase, enantioselectivity, and steric hindrance. The results established a set of rules governing the siRNA-mediated silencing, indicating that the thermodynamic stability of the 5'-end is a crucial determinant for antisense-mediated silencing but is not sufficient to avoid sense-mediated silencing. Both theoretical and experimental approaches consistently evidence the existence of a direct connection between the PAZ/3'-overhang binding affinity and siRNA's potency and specificity. An overall description of the systems is thus achieved by atomistic simulations and free energy calculations that allow us to propose a robust and self-contained procedure for studying the factors implied in PAZ/3'-overhang siRNA interactions. A higher RNAi activity is associated with a moderate-to-strong PAZ/3'-overhang binding. Contrarily, lower binding energies compromise siRNA potency, increase specificity, and favor siRNA downregulation by Ago2-independent mechanisms. This work provides in-depth details for the design of powerful and safe synthetic nucleotide analogues for substitution at the 3'-overhang, enabling some of the intrinsic siRNA disadvantages to be overcome.
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Affiliation(s)
- Adele Alagia
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) , Jordi Girona 18-26 , E-08034 Barcelona , Spain . ; ; Tel: +34 934006145
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN) , Jordi Girona 18-26 , E-08034 Barcelona , Spain
| | - Andreia F Jorge
- CQC , Department of Chemistry , University of Coimbra , Rua Larga , 3004-535 Coimbra , Portugal .
| | - Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) , Jordi Girona 18-26 , E-08034 Barcelona , Spain . ; ; Tel: +34 934006145
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN) , Jordi Girona 18-26 , E-08034 Barcelona , Spain
| | - Tânia F G G Cova
- CQC , Department of Chemistry , University of Coimbra , Rua Larga , 3004-535 Coimbra , Portugal .
| | - Ramon Crehuet
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) , Jordi Girona 18-26 , E-08034 Barcelona , Spain . ; ; Tel: +34 934006145
| | - Santiago Grijalvo
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) , Jordi Girona 18-26 , E-08034 Barcelona , Spain . ; ; Tel: +34 934006145
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN) , Jordi Girona 18-26 , E-08034 Barcelona , Spain
| | - Alberto A C C Pais
- CQC , Department of Chemistry , University of Coimbra , Rua Larga , 3004-535 Coimbra , Portugal .
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) , Jordi Girona 18-26 , E-08034 Barcelona , Spain . ; ; Tel: +34 934006145
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN) , Jordi Girona 18-26 , E-08034 Barcelona , Spain
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41
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Grijalvo S, Alagia A, Jorge AF, Eritja R. Covalent Strategies for Targeting Messenger and Non-Coding RNAs: An Updated Review on siRNA, miRNA and antimiR Conjugates. Genes (Basel) 2018; 9:E74. [PMID: 29415514 PMCID: PMC5852570 DOI: 10.3390/genes9020074] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 01/26/2018] [Accepted: 01/26/2018] [Indexed: 12/11/2022] Open
Abstract
Oligonucleotide-based therapy has become an alternative to classical approaches in the search of novel therapeutics involving gene-related diseases. Several mechanisms have been described in which demonstrate the pivotal role of oligonucleotide for modulating gene expression. Antisense oligonucleotides (ASOs) and more recently siRNAs and miRNAs have made important contributions either in reducing aberrant protein levels by sequence-specific targeting messenger RNAs (mRNAs) or restoring the anomalous levels of non-coding RNAs (ncRNAs) that are involved in a good number of diseases including cancer. In addition to formulation approaches which have contributed to accelerate the presence of ASOs, siRNAs and miRNAs in clinical trials; the covalent linkage between non-viral vectors and nucleic acids has also added value and opened new perspectives to the development of promising nucleic acid-based therapeutics. This review article is mainly focused on the strategies carried out for covalently modifying siRNA and miRNA molecules. Examples involving cell-penetrating peptides (CPPs), carbohydrates, polymers, lipids and aptamers are discussed for the synthesis of siRNA conjugates whereas in the case of miRNA-based drugs, this review article makes special emphasis in using antagomiRs, locked nucleic acids (LNAs), peptide nucleic acids (PNAs) as well as nanoparticles. The biomedical applications of siRNA and miRNA conjugates are also discussed.
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Affiliation(s)
- Santiago Grijalvo
- Institute of Advanced Chemistry of Catalonia (IQAC, CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain.
- Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, 08034 Barcelona, Spain.
| | - Adele Alagia
- Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, 08034 Barcelona, Spain.
| | - Andreia F Jorge
- Coimbra Chemistry Centre, (CQC), Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal.
| | - Ramon Eritja
- Institute of Advanced Chemistry of Catalonia (IQAC, CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain.
- Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, 08034 Barcelona, Spain.
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42
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Mutisya D, Hardcastle T, Cheruiyot SK, Pallan PS, Kennedy SD, Egli M, Kelley ML, Smith AVB, Rozners E. Amide linkages mimic phosphates in RNA interactions with proteins and are well tolerated in the guide strand of short interfering RNAs. Nucleic Acids Res 2017; 45:8142-8155. [PMID: 28854734 PMCID: PMC5737567 DOI: 10.1093/nar/gkx558] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/18/2017] [Indexed: 12/21/2022] Open
Abstract
While the use of RNA interference (RNAi) in molecular biology and functional genomics is a well-established technology, in vivo applications of synthetic short interfering RNAs (siRNAs) require chemical modifications. We recently found that amides as non-ionic replacements for phosphodiesters may be useful modifications for optimization of siRNAs. Herein, we report a comprehensive study of systematic replacement of a single phosphate with an amide linkage throughout the guide strand of siRNAs. The results show that amides are surprisingly well tolerated in the seed and central regions of the guide strand and increase the silencing activity when placed between nucleosides 10 and 12, at the catalytic site of Argonaute. A potential explanation is provided by the first crystal structure of an amide-modified RNA-DNA with Bacillus halodurans RNase H1. The structure reveals how small changes in both RNA and protein conformation allow the amide to establish hydrogen bonding interactions with the protein. Molecular dynamics simulations suggest that these alternative binding modes may compensate for interactions lost due to the absence of a phosphodiester moiety. Our results suggest that an amide can mimic important hydrogen bonding interactions with proteins required for RNAi activity and may be a promising modification for optimization of biological properties of siRNAs.
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Affiliation(s)
- Daniel Mutisya
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, NY 13902, USA
| | | | - Samwel K Cheruiyot
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, NY 13902, USA
| | - Pradeep S Pallan
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - Scott D Kennedy
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | | | | | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, NY 13902, USA
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43
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Québatte M, Dehio C. Systems-level interference strategies to decipher host factors involved in bacterial pathogen interaction: from RNAi to CRISPRi. Curr Opin Microbiol 2017; 39:34-41. [DOI: 10.1016/j.mib.2017.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/02/2017] [Accepted: 08/02/2017] [Indexed: 12/16/2022]
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44
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Molecular chaperone Jiv promotes the RNA replication of classical swine fever virus. Virus Genes 2017; 53:426-433. [PMID: 28341934 DOI: 10.1007/s11262-017-1448-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 03/18/2017] [Indexed: 12/18/2022]
Abstract
The nonstructural protein 2 (NS2) of classical swine fever virus (CSFV) is a self-splicing ribozyme wherein the precursor protein NS2-3 is cleaved, and the cleavage efficiency of NS2-3 is crucial to the replication of viral RNA. However, the proteolytic activity of NS2 autoprotease may be achieved through a cellular chaperone called J-domain protein interacting with viral protein (Jiv) or its fragment Jiv90, as evidence suggests that Jiv is required for the proper functioning of the NS2 protein of bovine viral diarrhea virus. Hence, the expression of Jiv may be correlated with the replication efficiency of CSFV RNA. We investigated the expression levels of Jiv and viral RNA in CSFV-infected cells and tissues using Real-time RT-PCR or Western blot analysis. The obtained results show that Jiv90 possibly plays an important role in the lifecycle of CSFV because the distribution of Jiv90 protein shows a positive correlation with the viral load of CSFV. Furthermore, the overexpression or knockdown of Jiv90 in swine cells can also significantly promote or decrease the viral load, respectively. The detection of Flow cytometry shows that the overexpression of Jiv90 prolongs the G1 phase of cell cycles but has no effect on apoptosis. These findings are likely to be of benefit in clarifying the pathogenesis of the CSFV.
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45
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Affiliation(s)
- Barbara Cellini
- Department of Neuroscience, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Verona (VR), Italy
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46
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Li X, Peng C, Wang X, Wen X. One-cell model for inhibiting Cav3.3 mRNA expression by RNA interference. BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2017.1282838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Xiaohong Li
- Department of Pain Clinic, The First Affiliated Hospital of Jinan University, Guangzhou, PR China
- Department of Anesthesiology, The First People's Hospital of Foshan & Foshan Hospital of Sun Yat-sen University, Foshan, PR China
| | - Changzheng Peng
- Department of Anesthesiology, Dongcheng People's Hospital of Dongwan City, Dongwan, PR China
| | - Xiaoping Wang
- Department of Pain Clinic, The First Affiliated Hospital of Jinan University, Guangzhou, PR China
| | - Xianjie Wen
- Department of Anesthesiology, The First People's Hospital of Foshan & Foshan Hospital of Sun Yat-sen University, Foshan, PR China
- Department of Anesthesiology, The Sixth Affiliated Hospital of Guangzhou Medical University, Qinyuan, PR China
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47
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Crouchet E, Saad R, Affolter-Zbaraszczuk C, Ogier J, Baumert TF, Schuster C, Meyer F. Composite vector formulation for multiple siRNA delivery as a host targeting antiviral in a cell culture model of hepatitis C virus (HCV) infection. J Mater Chem B 2017; 5:858-865. [PMID: 32263854 PMCID: PMC7613424 DOI: 10.1039/c6tb01718e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Hepatitis C virus (HCV) infection is a major cause of chronic liver disease and cancer worldwide. RNA interference (RNAi)-based gene therapies have emerged recently as a promising tool to treat chronic viral infections. Indeed, small interfering RNAs (siRNAs) provide an opportunity to target host factors required for the viral life cycle. In this study, we evaluated a novel nanovector-based approach for siRNA delivery in a model of chronically infected hepatic cells. We designed original composite nanoparticles by coating the calcium phosphate core with siRNAs targeting HCV host-factors and pyridylthiourea-grafted polyethyleneimine (πPEI). Using combinations of different siRNAs, we observed an efficient and prolonged decrease of HCV replication. Moreover, we showed that the layer-by-layer technique of coating applied to our nanoparticles triggers a sequential release of siRNAs acting on different steps of the HCV life cycle. Together, our results demonstrate the efficacy of these nanoparticles for siRNA delivery and open new perspectives for antiviral therapies.
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Affiliation(s)
- E. Crouchet
- Inserm
- U1110
- Institut de Recherche sur les Maladies Virales et Hépatiques
- 67000 Strasbourg
- France
| | - R. Saad
- Inserm
- U1110
- Institut de Recherche sur les Maladies Virales et Hépatiques
- 67000 Strasbourg
- France
| | | | - J. Ogier
- Université de Strasbourg
- 67000 Strasbourg
- France
- Inserm
- U1121
| | - T. F. Baumert
- Inserm
- U1110
- Institut de Recherche sur les Maladies Virales et Hépatiques
- 67000 Strasbourg
- France
| | - C. Schuster
- Inserm
- U1110
- Institut de Recherche sur les Maladies Virales et Hépatiques
- 67000 Strasbourg
- France
| | - F. Meyer
- Université de Strasbourg
- 67000 Strasbourg
- France
- Inserm
- U1121
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48
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Abstract
RNA interference is a convenient and highly effective technique to investigate the biological function of genes. Adequately designed RNA molecules introduced into an oocyte are able to bind specific endogenous mRNAs and trigger their degradation. Subsequent fertilization of these oocytes will result in the generation of embryos in which the expression of the gene of interest is downregulated, and following the degradation of maternal proteins the role of the gene product can be studied. Here, we describe the approach how post-transcriptional gene silencing can be achieved in oocytes and early embryos using siRNA.
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Affiliation(s)
- Lu Zhang
- Department of Animal Sciences, Purdue University, Lilly Hall of Life Sciences, 915 W. State Street, West Lafayette, IN, 47907, USA
| | - Zoltan Machaty
- Department of Animal Sciences, Purdue University, Lilly Hall of Life Sciences, 915 W. State Street, West Lafayette, IN, 47907, USA.
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49
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Fokina AA, Chelobanov BP, Fujii M, Stetsenko DA. Delivery of therapeutic RNA-cleaving oligodeoxyribonucleotides (deoxyribozymes): from cell culture studies to clinical trials. Expert Opin Drug Deliv 2016; 14:1077-1089. [PMID: 27892730 DOI: 10.1080/17425247.2017.1266326] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
INTRODUCTION Development of efficient in vivo delivery systems remains a major challenge en route to clinical application of antisense technology, including RNA-cleaving molecules such as deoxyribozymes (DNAzymes). The mechanisms of oligonucleotide uptake and trafficking are clearly dependent on cell type and the type of oligonucleotide analogue. It appears likely that each particular disease target would pose its own specific requirements for a delivery method. Areas covered. In this review we will discuss the available options for DNAzyme delivery in vitro and in vivo, outline various exogenous and endogenous strategies that have been, or are still being, developed and ascertain their applicability with emphasis on those methods that are currently being used in clinical trials. Expert opinion. The available information suggests that a practical system for in vivo delivery has to be biodegradable, as to minimize concerns over long-term toxicity, it should not accumulate in the organism. Extracellular vesicles may offer the most organic way for drug delivery especially as they can be fused with artificial liposomes to produce hybrid nanoparticles. Chemical modification of DNAzymes holds great potential to apply oligonucleotide analogs that would not only be resistant to nuclease digestion, but also able to penetrate cells without external delivery agents.
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Affiliation(s)
- Alesya A Fokina
- a Institute of Chemical Biology and Fundamental Medicine , Siberian Branch of the Russian Academy of Sciences , Novosibirsk , Russia
| | - Boris P Chelobanov
- a Institute of Chemical Biology and Fundamental Medicine , Siberian Branch of the Russian Academy of Sciences , Novosibirsk , Russia
| | - Masayuki Fujii
- b Department of Biological & Environmental Chemistry , Kindai University , Iizuka, Fukuoka , Japan
| | - Dmitry A Stetsenko
- a Institute of Chemical Biology and Fundamental Medicine , Siberian Branch of the Russian Academy of Sciences , Novosibirsk , Russia
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50
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Pitchers WR, Constantinou SJ, Losilla M, Gallant JR. Electric fish genomics: Progress, prospects, and new tools for neuroethology. ACTA ACUST UNITED AC 2016; 110:259-272. [PMID: 27769923 DOI: 10.1016/j.jphysparis.2016.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/06/2016] [Accepted: 10/16/2016] [Indexed: 01/01/2023]
Abstract
Electric fish have served as a model system in biology since the 18th century, providing deep insight into the nature of bioelectrogenesis, the molecular structure of the synapse, and brain circuitry underlying complex behavior. Neuroethologists have collected extensive phenotypic data that span biological levels of analysis from molecules to ecosystems. This phenotypic data, together with genomic resources obtained over the past decades, have motivated new and exciting hypotheses that position the weakly electric fish model to address fundamental 21st century biological questions. This review article considers the molecular data collected for weakly electric fish over the past three decades, and the insights that data of this nature has motivated. For readers relatively new to molecular genetics techniques, we also provide a table of terminology aimed at clarifying the numerous acronyms and techniques that accompany this field. Next, we pose a research agenda for expanding genomic resources for electric fish research over the next 10years. We conclude by considering some of the exciting research prospects for neuroethology that electric fish genomics may offer over the coming decades, if the electric fish community is successful in these endeavors.
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Affiliation(s)
- William R Pitchers
- Dept. of Integrative Biology, Michigan State University, 288 Farm Lane RM 203, East Lansing, MI 48824, USA.
| | - Savvas J Constantinou
- Dept. of Integrative Biology, Michigan State University, 288 Farm Lane RM 203, East Lansing, MI 48824, USA
| | - Mauricio Losilla
- Dept. of Integrative Biology, Michigan State University, 288 Farm Lane RM 203, East Lansing, MI 48824, USA
| | - Jason R Gallant
- Dept. of Integrative Biology, Michigan State University, 288 Farm Lane RM 203, East Lansing, MI 48824, USA.
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