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Sarkar S, Moitra P, Bera S, Bhattacharya S. Antisense Oligonucleotide Embedded Context Responsive Nanoparticles Derived from Synthetic Ionizable Lipids for lncRNA Targeted Therapy of Breast Cancer. ACS APPLIED MATERIALS & INTERFACES 2024; 16:45871-45887. [PMID: 39163516 DOI: 10.1021/acsami.4c04893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/22/2024]
Abstract
The long noncoding RNAs (lncRNA) are primarily associated with several essential gene regulations but are also connected to cancer metabolism and progression. HOTAIR and MALAT1 are two such lncRNAs that are detected in malignancies of various origins and are responsible for the poor prognosis of cancer patients. Due to these factors, the lncRNAs have emerged as prime targets for the development of anticancer therapeutics. However, nonviral delivery of lncRNA-targeted antisense oligonucleotides (ASOs) still remains a critical challenge while maintaining their structural and functional integrity. Herein, we have designed and synthesized a new series of ionizable lipids with variations in their head groups to prepare lipid nanoparticle (LNP) formulation along with cholesterol-based twin cationic lipid and amphiphilic zwitterionic lipid. The context responsiveness of these formulations in delivering the ASOs has been thoroughly investigated by various bioanalytical techniques, and an optimum formulation has been identified. The LNPs are utilized to deliver the ASOs targeting HOTAIR lncRNA in human cancer cell lines and MALAT1 lncRNA in mouse models. This study thus standardizes an advanced nanomaterial system for nonviral gene delivery that has been validated by a considerable reduction in the target lncRNA level under in vitro and a significant reduction in tumor volume under in vivo settings.
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Affiliation(s)
- Sourav Sarkar
- School of Applied & Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Parikshit Moitra
- Department of Chemical Sciences, Indian Institute of Science Education and Research Berhampur (IISER Berhampur), Berhampur, Odisha 760003, India
| | - Sayan Bera
- School of Applied & Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Santanu Bhattacharya
- School of Applied & Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
- Technical Research Centre, Indian Association for the Cultivation of Science, Kolkata 700032, India
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India
- Department of Chemistry, Indian Institute of Science Education and Research Tirupati (IISER Tirupati), Srinivasapuram, Yerpedu Mandal, Tirupati District, Andhra Pradesh 517619, India
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2
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Zhang K, Shi Y, Jin Z, He J. Advances in tumor vascular growth inhibition. Clin Transl Oncol 2024; 26:2084-2096. [PMID: 38504070 DOI: 10.1007/s12094-024-03432-5] [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: 01/04/2024] [Accepted: 03/01/2024] [Indexed: 03/21/2024]
Abstract
Tumor growth and metastasis require neovascularization, which is dependent on a complex array of factors, such as the production of various pro-angiogenic factors by tumor cells, intercellular signaling, and stromal remodeling. The hypoxic, acidic tumor microenvironment is not only conducive to tumor cell proliferation, but also disrupts the equilibrium of angiogenic factors, leading to vascular heterogeneity, which further promotes tumor development and metastasis. Anti-angiogenic strategies to inhibit tumor angiogenesis has, therefore, become an important focus for anti-tumor therapy. The traditional approach involves the use of anti-angiogenic drugs to inhibit tumor neovascularization by targeting upstream and downstream angiogenesis-related pathways or pro-angiogenic factors, thereby inhibiting tumor growth and metastasis. This review explores the mechanisms involved in tumor angiogenesis and summarizes currently used anti-angiogenic drugs, including monoclonal antibody, and small-molecule inhibitors, as well as the progress and challenges associated with their use in anti-tumor therapy. It also outlines the opportunities and challenges of treating tumors using more advanced anti-angiogenic strategies, such as immunotherapy and nanomaterials.
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Affiliation(s)
- Keyong Zhang
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Yuanyuan Shi
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Ze Jin
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Jian He
- State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-Targeting Theranostics, Guangxi Key Laboratory of Bio-Targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, 530021, Guangxi, China.
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LIU ZIYONG, MA TAO, LI JINFANG, REN WEI, ZHANG ZHIXIN. IL13RA2 promotes progression of infantile haemangioma by activating glycolysis and the Wnt/β-catenin signaling pathway. Oncol Res 2024; 32:1453-1465. [PMID: 39220137 PMCID: PMC11361910 DOI: 10.32604/or.2024.048315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/01/2024] [Indexed: 09/04/2024] Open
Abstract
Background Interleukin 13 receptor subunit alpha 2 (IL13RA2) plays an essential role in the progression of many cancers. However, the role of IL13RA2 in infantile haemangioma (IH) is still unknown. Materials and Methods IL13RA2 expression in IH tissues was analyzed using western blot, qRT-PCR, and immunofluorescence. The role of IL13RA2 in haemangioma-derived endothelial cells (HemECs) was determined following knockdown or overexpression of IL13RA2 using CCK-8, colony formation, apoptosis, wound healing, tubule formation, Transwell, and western blot. Results IL13RA2 expression was upregulated in IH tissues. IL13RA2 overexpression promoted proliferation, migration, and invasion of HemECs and induced glycolysis, which was confirmed with a glycolysis inhibitor. Specifically, IL13RA2 interacted with β-catenin and activated the Wnt/β-catenin pathway in HemECs, which were involved in the above-mentioned effects of IL13RA2. Conclusions These findings revealed that targeting IL13RA2 is a potential therapeutic approach for IH.
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Affiliation(s)
- ZIYONG LIU
- Department of Cardiothoracic Surgery, 970th Hospital of the People’s Liberation Army, Weihai, 264209, China
| | - TAO MA
- Department of Cardiothoracic Surgery, 970th Hospital of the People’s Liberation Army, Weihai, 264209, China
| | - JINFANG LI
- Department of Cardiac Ultrasound, Weihai Municipal Hospital, Weihai, 264200, China
| | - WEI REN
- Department of Cardiothoracic Surgery, 970th Hospital of the People’s Liberation Army, Weihai, 264209, China
| | - ZHIXIN ZHANG
- Department of Cardiothoracic Surgery, 970th Hospital of the People’s Liberation Army, Weihai, 264209, China
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4
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Khampang S, Lorthongpanich C, Laowtammathron C, Klaihmon P, Meesa S, Suksomboon W, Jiamvoraphong N, Kheolamai P, Luanpitpong S, Easley CA, Mahyari E, Issaragrisil S. The dynamic expression of YAP is essential for the development of male germ cells derived from human embryonic stem cells. Sci Rep 2024; 14:15732. [PMID: 38977826 PMCID: PMC11231333 DOI: 10.1038/s41598-024-66852-x] [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: 01/11/2024] [Accepted: 07/04/2024] [Indexed: 07/10/2024] Open
Abstract
YAP plays a vital role in controlling growth and differentiation in various cell lineages. Although the expression of YAP in mice testicular and spermatogenic cells suggests its role in mammalian spermatogenesis, the role of YAP in the development of human male germ cells has not yet been determined. Using an in vitro model and a gene editing approach, we generated human spermatogonia stem cell-like cells (hSSLCs) from human embryonic stem cells (hESCs) and investigated the role of YAP in human spermatogenesis. The results showed that reducing YAP expression during the early stage of spermatogenic differentiation increased the number of PLZF+ hSSLCs and haploid spermatid-like cells. We also demonstrated that the up-regulation of YAP is essential for maintaining spermatogenic cell survival during the later stages of spermatogenic differentiation. The expression of YAP that deviates from this pattern results in a lower number of hSSLCs and an increased level of spermatogenic cell death. Taken together, our result demonstrates that the dynamic expression pattern of YAP is essential for human spermatogenesis. Modulating the level of YAP during human spermatogenesis could improve the production yield of male germ cells derived from hESCs, which could provide the optimization method for in vitro gametogenesis and gain insight into the application in the treatment of male infertility.
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Affiliation(s)
- Sujittra Khampang
- Siriraj Center of Excellence for Stem Cell Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Chanchao Lorthongpanich
- Siriraj Center of Excellence for Stem Cell Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
| | - Chuti Laowtammathron
- Siriraj Center of Excellence for Stem Cell Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Phatchanat Klaihmon
- Siriraj Center of Excellence for Stem Cell Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Sukanya Meesa
- Division of Medical Genetics, Department of Obstetrics and Gynaecology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Wichuda Suksomboon
- Division of Medical Genetics, Department of Obstetrics and Gynaecology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Nittaya Jiamvoraphong
- Siriraj Center of Excellence for Stem Cell Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Pakpoom Kheolamai
- Center of Excellence in Stem Cell Research and Innovation, Faculty of Medicine, Thammasat University, Pathum Thani, 12121, Thailand
| | - Sudjit Luanpitpong
- Siriraj Center of Excellence for Stem Cell Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Charles A Easley
- Division of Neuropharmacology and Neurologic Diseases, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- Department of Environmental Health Sciences, College of Public Health, University of Georgia, Athens, GA, 30602, USA
- Regenerative Bioscience Center, University of Georgia, Athens, GA, 30602, USA
| | - Eisa Mahyari
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Portland, OR, 97006, USA
| | - Surapol Issaragrisil
- Siriraj Center of Excellence for Stem Cell Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Division of Hematology, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Bangkok Hematology Center, Wattanosoth Hospital, BDMS Center of Excellence for Cancer, Bangkok, 10310, Thailand
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Xu K, Yang Y, Ding J, Wang J, Fang Y, Tian H. Spatially Precise Genetic Engineering at the Electrode-Tissue Interface. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2401327. [PMID: 38692704 DOI: 10.1002/adma.202401327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/17/2024] [Indexed: 05/03/2024]
Abstract
The interface between electrodes and neural tissues plays a pivotal role in determining the efficacy and fidelity of neural activity recording and modulation. While considerable efforts have been made to improve the electrode-tissue interface, the majority of studies have primarily concentrated on the development of biocompatible neural electrodes through abiotic materials and structural engineering. In this study, an approach is presented that seamlessly integrates abiotic and biotic engineering principles into the electrode-tissue interface. Specifically, ultraflexible neural electrodes with short hairpin RNAs (shRNAs) designed to silence the expression of endogenous genes within neural tissues are combined. The system facilitates shRNA-mediated knockdown of phosphatase and tensin homolog deleted on chromosome 10 (PTEN) and polypyrimidine tract-binding protein 1 (PTBP1), two essential genes associated in neural survival/growth and neurogenesis, within specific cell populations located at the electrode-tissue interface. Additionally, it is demonstrated that the downregulation of PTEN in neurons can result in an enlargement of neuronal cell bodies at the electrode-tissue interface. Furthermore, the system enables long-term monitoring of neuronal activities following PTEN knockdown in a mouse model of Parkinson's disease and traumatic brain injury. The system provides a versatile approach for genetically engineering the electrode-tissue interface with unparalleled precision, paving the way for the development of regenerative electronics and next-generation brain-machine interfaces.
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Affiliation(s)
- Ke Xu
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
- CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
- School of Nanoscience and Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yinan Yang
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
- CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
- School of Nanoscience and Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianfei Ding
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Jinfen Wang
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
- Chinese Institute for Brain Research, Beijing, 102206, China
| | - Ying Fang
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
- CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
- School of Nanoscience and Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
- Chinese Institute for Brain Research, Beijing, 102206, China
| | - Huihui Tian
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
- Chinese Institute for Brain Research, Beijing, 102206, China
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Weidle UH, Nopora A. CircRNAs in Pancreatic Cancer: New Tools for Target Identification and Therapeutic Intervention. Cancer Genomics Proteomics 2024; 21:327-349. [PMID: 38944427 PMCID: PMC11215428 DOI: 10.21873/cgp.20451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 07/01/2024] Open
Abstract
We have reviewed the literature for circular RNAs (circRNAs) with efficacy in preclinical pancreatic-cancer related in vivo models. The identified circRNAs target chemoresistance mechanisms (n=5), secreted proteins and transmembrane receptors (n=15), transcription factors (n=9), components of the signaling- (n=11), ubiquitination- (n=2), autophagy-system (n=2), and others (n=9). In addition to identifying targets for therapeutic intervention, circRNAs are potential new entities for treatment of pancreatic cancer. Up-regulated circRNAs can be inhibited by antisense oligonucleotides (ASO), small interfering RNAs (siRNAs), short hairpin RNAs (shRNAs) or clustered regularly interspaced short-palindromic repeats-CRISPR associated protein (CRISPR-CAS)-based intervention. The function of down-regulated circRNAs can be reconstituted by replacement therapy using plasmids or virus-based vector systems. Target validation experiments and the development of improved delivery systems for corresponding agents were examined.
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Affiliation(s)
- Ulrich H Weidle
- Roche Pharma Research and Early Development, Roche Innovation Center Munich, Penzberg, Germany
| | - Adam Nopora
- Roche Pharma Research and Early Development, Roche Innovation Center Munich, Penzberg, Germany
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Traber GM, Yu AM. The Growing Class of Novel RNAi Therapeutics. Mol Pharmacol 2024; 106:13-20. [PMID: 38719476 PMCID: PMC11187687 DOI: 10.1124/molpharm.124.000895] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 04/15/2024] [Indexed: 06/20/2024] Open
Abstract
The clinical use of RNA interference (RNAi) molecular mechanisms has introduced a novel, growing class of RNA therapeutics capable of treating diseases by controlling target gene expression at the posttranscriptional level. With the newly approved nedosiran (Rivfloza), there are now six RNAi-based therapeutics approved by the United States Food and Drug Administration (FDA). Interestingly, five of the six FDA-approved small interfering RNA (siRNA) therapeutics [patisiran (Onpattro), lumasiran (Oxlumo), inclisiran (Leqvio), vutrisiran (Amvuttra), and nedosiran] were revealed to act on the 3'-untranslated regions of target mRNAs, instead of coding sequences, thereby following the common mechanistic action of genome-derived microRNAs (miRNA). Furthermore, three of the FDA-approved siRNA therapeutics [patisiran, givosiran (Givlaari), and nedosiran] induce target mRNA degradation or cleavage via near-complete rather than complete base-pair complementarity. These features along with previous findings confound the currently held characteristics to distinguish siRNAs and miRNAs or biosimilars, of which all converge in the RNAi regulatory pathway action. Herein, we discuss the RNAi mechanism of action and current criteria for distinguishing between miRNAs and siRNAs while summarizing the common and unique chemistry and molecular pharmacology of the six FDA-approved siRNA therapeutics. The term "RNAi" therapeutics, as used previously, provides a coherently unified nomenclature for broader RNAi forms as well as the growing number of therapeutic siRNAs and miRNAs or biosimilars that best aligns with current pharmacological nomenclature by mechanism of action. SIGNIFICANCE STATEMENT: The common and unique chemistry and molecular pharmacology of six FDA-approved siRNA therapeutics are summarized, in which nedosiran is newly approved. We point out rather a surprisingly mechanistic action as miRNAs for five siRNA therapeutics and discuss the differences and similarities between siRNAs and miRNAs that supports using a general and unified term "RNAi" therapeutics to align with current drug nomenclature criteria in pharmacology based on mechanism of action and embraces broader forms and growing number of novel RNAi therapeutics.
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Affiliation(s)
- Gavin M Traber
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California - Davis, Sacramento, California
| | - Ai-Ming Yu
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California - Davis, Sacramento, California
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Lamptey RNL, Sun C, Singh J. Blood pressure reduction through brain delivery of nanoparticles loaded with plasmid DNA encoding angiotensin receptor shRNA. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102210. [PMID: 38827383 PMCID: PMC11141442 DOI: 10.1016/j.omtn.2024.102210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/03/2024] [Indexed: 06/04/2024]
Abstract
Elevated brain angiotensin II activity plays a key role in the development of neurogenic hypertension. While blood pressure (BP) control in neurogenic hypertension has been successfully demonstrated by regulating central angiotensin II activity, current techniques involving cerebrovascular injections of potential therapeutic agents are not suitable for clinical translation. To address this gap, we present the synthesis of dual-functionalized liposomes functionalized with targeting ligand and cell-penetrating peptide. Functionalized liposomes were synthesized using the thin film hydration technique and loaded with plasmid DNA encoding short hairpin RNA targeted toward angiotensin II receptors (PEAS), via the post-insertion method. The synthesized liposomes had a cationic surface charge, an average size of 150 nm, and effectively entrapped more than 89% of loaded PEAS. These liposomes loaded with PEAS demonstrated biocompatibility and efficient delivery to brain-derived cell lines, resulting in a remarkable reduction of more than 70% in receptor expression within 7 days. To assess the therapeutic potential, spontaneously hypertensive rats were administered intravenous injections of functionalized liposomes loaded with PEAS, and the changes in mean arterial pressure were monitored for 45 days. Remarkably, this treatment led to a significant (p < 0.001) decrease in BP of more than 30 mm Hg compared with saline-treated rats.
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Affiliation(s)
| | - Chengwen Sun
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Jagdish Singh
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND 58102, USA
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9
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Wang Y, Yang J, Wu C, Guo Y, Ding Y, Zou X. LncRNA SNHG14 silencing attenuates the progression of diabetic nephropathy via the miR-30e-5p/SOX4 axis. J Diabetes 2024; 16:e13565. [PMID: 38751373 PMCID: PMC11096814 DOI: 10.1111/1753-0407.13565] [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: 08/31/2023] [Revised: 02/05/2024] [Accepted: 03/19/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Diabetic nephropathy (DN) is a diabetic complication. LncRNAs are reported to participate in the pathophysiology of DN. Here, the function and mechanism of lncRNA small nucleolar RNA host gene 14 (SNHG14) in DN were explored. METHODS Streptozotocin (STZ)-induced DN mouse models and high glucose (HG)-treated human mesangial cells (MCs) were used to detect SNHG14 expression. SNHG14 silencing plasmids were applied to examine the function of SNHG14 on proliferation and fibrosis in HG-treated MCs. Potential targets of SNHG14 were predicted using bioinformatics tools and verified by luciferase reporter, RNA pulldown, and northern blotting assays. The functional role of SNHG14 in DN in vivo was detected by injection with adenoviral vector carrying sh-SNHG14 into DN mice. Serum creatinine, blood urea nitrogen, blood glucose, 24-h proteinuria, relative kidney weight, and renal pathological changes were examined in DN mice. RESULTS SNHG14 expression was elevated in the kidneys of DN mice and HG-treated MCs. SNHG14 silencing inhibited proliferation and fibrosis of HG-stimulated MCs. SNHG14 bound to miR-30e-5p to upregulate SOX4 expression. In rescue assays, SOX4 elevation diminished the effects of SNHG14 silencing in HG-treated MCs, and SOX4 silencing reversed the effects of SNHG14 overexpression. In in vivo studies, SNHG14 downregulation significantly ameliorated renal injuries and renal interstitial fibrosis in DN mice. CONCLUSIONS SNHG14 silencing attenuates kidney injury in DN mice and reduces proliferation and fibrotic phenotype of HG-stimulated MCs via the miR-30e-5p/SOX4 axis.
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Affiliation(s)
- YunXia Wang
- Department of Renal MedicineHuai'an Rehabilitation Hospital (Jinhu People's Hospital)Huai'anChina
| | - JiaJia Yang
- Department of Renal MedicineHuai'an Rehabilitation Hospital (Jinhu People's Hospital)Huai'anChina
| | - Chun Wu
- Department of Renal MedicineHuai'an Rehabilitation Hospital (Jinhu People's Hospital)Huai'anChina
| | - Yuqin Guo
- Department of Renal MedicineHuai'an Rehabilitation Hospital (Jinhu People's Hospital)Huai'anChina
| | - Yuan Ding
- Department of Renal MedicineHuai'an Rehabilitation Hospital (Jinhu People's Hospital)Huai'anChina
| | - Xiujuan Zou
- Department of Renal MedicineHuai'an Rehabilitation Hospital (Jinhu People's Hospital)Huai'anChina
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Sarangi P, Senthilkumar MB, Amit S, Kumar N, Jayandharan GR. AAV mediated repression of Neat1 lncRNA combined with F8 gene augmentation mitigates pathological mediators of joint disease in haemophilia. J Cell Mol Med 2024; 28:e18460. [PMID: 38864710 PMCID: PMC11167708 DOI: 10.1111/jcmm.18460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 04/24/2024] [Accepted: 05/16/2024] [Indexed: 06/13/2024] Open
Abstract
Haemophilic arthropathy (HA), a common comorbidity in haemophilic patients leads to joint pain, deformity and reduced quality of life. We have recently demonstrated that a long non-coding RNA, Neat1 as a primary regulator of matrix metalloproteinase (MMP) 3 and MMP13 activity, and its induction in the target joint has a deteriorating effect on articular cartilage. In the present study, we administered an Adeno-associated virus (AAV) 5 vector carrying an short hairpin (sh)RNA to Neat1 via intra-articular injection alone or in conjunction with systemic administration of a capsid-modified AAV8 (K31Q) vector carrying F8 gene (F8-BDD-V3) to study its impact on HA. AAV8K31Q-F8 vector administration at low dose, led to an increase in FVIII activity (16%-28%) in treated mice. We further observed a significant knockdown of Neat1 (~40 fold vs. untreated injured joint, p = 0.005) in joint tissue of treated mice and a downregulation of chondrodegenerative enzymes, MMP3, MMP13 and the inflammatory mediator- cPLA2, in mice receiving combination therapy. These data demonstrate that AAV mediated Neat1 knockdown in combination with F8 gene augmentation can potentially impact mediators of haemophilic joint disease.
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Affiliation(s)
- Pratiksha Sarangi
- Laurus Center for Gene Therapy, Department of Biological Sciences and Bioengineering and Mehta Family Centre for Engineering in Medicine and Gangwal School of Medical Sciences and TechnologyIndian Institute of Technology KanpurKanpurUttar PradeshIndia
| | - Mohankumar B. Senthilkumar
- Laurus Center for Gene Therapy, Department of Biological Sciences and Bioengineering and Mehta Family Centre for Engineering in Medicine and Gangwal School of Medical Sciences and TechnologyIndian Institute of Technology KanpurKanpurUttar PradeshIndia
| | - Sonal Amit
- Department of PathologyAutonomous State Medical CollegeKanpurUttar PradeshIndia
| | - Narendra Kumar
- Laurus Center for Gene Therapy, Department of Biological Sciences and Bioengineering and Mehta Family Centre for Engineering in Medicine and Gangwal School of Medical Sciences and TechnologyIndian Institute of Technology KanpurKanpurUttar PradeshIndia
| | - Giridhara R. Jayandharan
- Laurus Center for Gene Therapy, Department of Biological Sciences and Bioengineering and Mehta Family Centre for Engineering in Medicine and Gangwal School of Medical Sciences and TechnologyIndian Institute of Technology KanpurKanpurUttar PradeshIndia
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Cottrell KA, Ryu S, Donelick H, Mai H, Pierce JR, Bass BL, Weber JD. Activation of PKR by a short-hairpin RNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.592371. [PMID: 38766230 PMCID: PMC11100704 DOI: 10.1101/2024.05.08.592371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Recognition of viral infection often relies on the detection of double-stranded RNA (dsRNA), a process that is conserved in many different organisms. In mammals, proteins such as MDA5, RIG-I, OAS, and PKR detect viral dsRNA, but struggle to differentiate between viral and endogenous dsRNA. This study investigates an shRNA targeting DDX54's potential to activate PKR, a key player in the immune response to dsRNA. Knockdown of DDX54 by a specific shRNA induced robust PKR activation in human cells, even when DDX54 is overexpressed, suggesting an off-target mechanism. Activation of PKR by the shRNA was enhanced by knockdown of ADAR1, a dsRNA binding protein that suppresses PKR activation, indicating a dsRNA-mediated mechanism. In vitro assays confirmed direct PKR activation by the shRNA. These findings emphasize the need for rigorous controls and alternative methods to validate gene function and minimize unintended immune pathway activation.
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Affiliation(s)
- Kyle A. Cottrell
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, Saint Louis, Missouri, USA
- ICCE Institute, Washington University School of Medicine, Saint Louis, Missouri, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Sua Ryu
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, Saint Louis, Missouri, USA
- ICCE Institute, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Helen Donelick
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Hung Mai
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, Saint Louis, Missouri, USA
- ICCE Institute, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Jackson R. Pierce
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Brenda L. Bass
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Jason D. Weber
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, Saint Louis, Missouri, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, Missouri, USA
- Department of Biology, Siteman Cancer Center, Washington University School of Medicine, Saint Louis, Missouri, USA
- ICCE Institute, Washington University School of Medicine, Saint Louis, Missouri, USA
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12
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Uriu K, Hernandez-Sanchez JP, Kojima S. Impacts of the feedback loop between sense-antisense RNAs in regulating circadian rhythms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.28.591560. [PMID: 38746188 PMCID: PMC11092440 DOI: 10.1101/2024.04.28.591560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Antisense transcripts are a unique group of non-coding RNAs that are transcribed from the opposite strand of a sense coding gene in an antisense orientation. Even though they do not encode a protein, these transcripts play a regulatory role in a variety of biological processes, including circadian rhythms. We and others found an antisense transcript, Per2AS , that is transcribed from the strand opposite the sense transcript Period2 ( Per2 ) and exhibits a rhythmic and antiphasic expression pattern compared to Per2 in mouse. By assuming that Per2AS and Per2 mutually repress each other, our previous mathematical model predicted that Per2AS regulates the robustness and the amplitude of circadian rhythms. In this study, we revised our previous model and developed a new mathematical model that mechanistically described the mutually repressive relationship between Per2 and Per2AS via transcriptional interference. We found that the simulation results are largely consistent with experimental observations including the counterintuitive ones that could not be fully explained by our previous model. These results indicate that our revised model serves as a foundation to build more detailed models in the future to better understand the impact of Per2AS-Per2 interaction in the mammalian circadian clock. Our mechanistic description of Per2AS-Per2 interaction can also be extended to other mathematical models that involve sense-antisense RNA pairs that mutually repress each other.
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13
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Wang W, Chen X, Chen J, Xu M, Liu Y, Yang S, Zhao W, Tan S. Engineering lentivirus envelope VSV-G for liver targeted delivery of IDOL-shRNA to ameliorate hypercholesterolemia and atherosclerosis. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102115. [PMID: 38314097 PMCID: PMC10835450 DOI: 10.1016/j.omtn.2024.102115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 01/05/2024] [Indexed: 02/06/2024]
Abstract
Lentiviral vectors (LVs) have been widely used as a tool for gene therapies. However, tissue-selective transduction after systemic delivery remains a challenge. Inducible degrader of low-density lipoprotein receptor is an attractive target for treating hypercholesterolemia. Here, a liver-targeted LV, CS8-LV-shIDOL, is developed by incorporating a hepatocyte-targeted peptide derived from circumsporozoite protein (CSP) into the lentivirus envelope for liver-targeted delivery of IDOL-shRNA (short hairpin RNA) to alleviate hypercholesterolemia. Tail-vein injection of CS8-LV-shIDOL results in extremely high accumulation in liver and nearly undetectable levels in other organs in mice. In addition, it shows superior therapeutic efficacy in lowering serum low-density lipoprotein cholesterol (LDL-C) and reducing atherosclerotic lesions over unmodified LV-shIDOL in hyperlipidemic mice. Mechanically, the envelope-engineered CS8-LV-shIDOL can enter liver cells via low-density lipoprotein receptor-related protein (LRP). Thus, this study provides a novel approach for liver-targeted delivery of IDOL-shRNA to treat hypercholesterolemia by using an envelope-engineered LV, and this delivery system has great potential for liver-targeted transgene therapy.
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Affiliation(s)
- Wei Wang
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, China
| | - Xuemei Chen
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, China
| | - Jiali Chen
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, China
| | - Menglong Xu
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, China
| | - Ying Liu
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, China
| | - Shijie Yang
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, China
| | - Wenfeng Zhao
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, China
| | - Shuhua Tan
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, China
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14
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Jamal A, Usman S, Teh MT, Waseem A. Preparation and Use of shRNA for Knocking Down Specific Genes. Methods Mol Biol 2024; 2849:55-72. [PMID: 38411888 DOI: 10.1007/7651_2024_515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Short hairpin RNA (shRNA) is a technique used to silence gene expression stably in various cells. There are however several reported problems. First, the cloning of oligos can lead to ligation of multiple copies; second, premature termination of sequencing reaction during confirmation of hairpin template; third, microdeletions/substitutions in hairpin during cloning; and fourth, off target effects. In this chapter, we have described a retrovirus transduction-based protocol that can be used on cells in culture without encountering any of the reported issues. We have used this protocol to clone shRNA templates for at least 10 different genes and confirmed them by dideoxy sequencing. The knockdown of 75-90% for two mRNA expressing genes, CDH5 and keratin KRT80, and a long non-coding RNA, XIST, is presented here.
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Affiliation(s)
- Ahmad Jamal
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Saima Usman
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Muy-Teck Teh
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Ahmad Waseem
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
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15
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Hinton SD. Understanding Pseudophosphatase Function Through Biochemical Interactions. Methods Mol Biol 2024; 2743:21-41. [PMID: 38147206 DOI: 10.1007/978-1-0716-3569-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Pseudophosphatases have been solidified as important signaling molecules that regulate signal transduction cascades. However, their mechanisms of action remain enigmatic. Reflecting this mystery, the prototypical pseudophosphatase STYX (phospho-serine-threonine/tyrosine-binding protein) was named with allusion to the river of the dead in Greek mythology to emphasize that these molecules are "dead" phosphatases. Although proteins with STYX domains do not catalyze dephosphorylation, this does not preclude their having other functions, including as integral elements of signaling networks. Thus, understanding their roles may mark them as potential novel drug targets. This chapter outlines common strategies used to characterize the functions of pseudophosphatases, using as an example MK-STYX [MAPK (mitogen-activated protein kinase) phospho-serine-threonine/tyrosine-binding], which has been linked to tumorigenesis, hepatocellular carcinoma, glioblastoma, apoptosis, and neuronal differentiation. We start with the importance of "restoring" (when possible) phosphatase activity in a pseudophosphatase, so the active mutant may be used as a comparison control throughout immunoprecipitation and mass spectrometry analyses. To this end, we provide protocols for site-directed mutagenesis, mammalian cell transfection, co-immunoprecipitation, phosphatase activity assays, and immunoblotting that we have used to investigate MK-STYX and the active mutant MK-STYXactive. We also highlight the importance of utilizing RNA interference (RNAi) "knockdown" technology to determine a cellular phenotype in various cell lines. Therefore, we outline our protocols for introducing short hairpin RNA (shRNA) expression plasmids into mammalian cells and quantifying knockdown of gene expression with real-time quantitative PCR (qPCR). We also provide a bioinformatic approach to investigating MK-STYX and MK-STYX(active mutant). These bioinformatic approaches can stand alone experimentally but also complement and enhance "wet" bench approaches such as binding assays and/or activity assays. A combination of cellular, molecular, biochemical, proteomic, and bioinformatic techniques has been a powerful tool in identifying novel functions of MK-STYX. Likewise, the information provided here should be a helpful guide to elucidating the functions of other pseudophosphatases.
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Affiliation(s)
- Shantá D Hinton
- Department of Biology, College of William and Mary, Williamsburg, VA, USA.
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16
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Lu Y, Huang R, Zhang Y, Xiang W, Zhang X, Chen F, An L, Yuan H, Wen F, Xu Y. Porphyromonas gingivalis induced UCHL3 to promote colon cancer progression. Am J Cancer Res 2023; 13:5981-5995. [PMID: 38187053 PMCID: PMC10767335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/01/2023] [Indexed: 01/09/2024] Open
Abstract
Porphyromonas gingivalis (P. gingivalis), a Gram-negative oral anaerobe, was demonstrated to facilitate colonization and progression in colonic tumor, while the underlying mechanism still remains to be clarified. Here, we identified the proteome profile changed by P. gingivalis infection in HCT116 cells through label-free quantitative proteomics, and found that deubiquitinase UCHL3 was a key protein that response for P. gingivalis infection. By CCK8, colony formation, wound healing assays, and in vivo subcutaneous tumor mouse moudle, we proved that P. gingivalis could promote the proliferation and migration of colon cancer, while the process was inhibited by UCHL3 knock down. Through IP-MS, we identified GNG12 as the UCHL3 interacting protein. The protein level of GNG12 was significantly reduced when knock out UCHL3. Thus we propose that GNG12 is a substrate protein of UCHL3. Furthermore, we demonstrated that overexpression of GNG12 could restore the tumor inhibition effect caused by UCHL3 knock down, and UCHL3-GNG12 axis promote colon cancer progression via the NF-κB signal pathway. Collectively, this study unveiled that P. gingivalis infection up-regulated UCHL3 and stabilized its substrate protein GNG12 to activate the NF-κB signal pathway to promote colon cancer progression. Our study indicate that UCHL3 is a potential biomarker and therapeutic target for colon cancer which infected with P. gingivalis.
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Affiliation(s)
- Yang Lu
- Department of Stomatology, Shanghai Tenth People’s Hospital, Tongji University School of MedicineShanghai, China
| | - Renhuan Huang
- Department of Stomatology, Shanghai Tenth People’s Hospital, Tongji University School of MedicineShanghai, China
| | - Yiming Zhang
- Department of Stomatology, Shanghai Tenth People’s Hospital, Tongji University School of MedicineShanghai, China
| | - Wei Xiang
- Department of Stomatology, Shanghai Tenth People’s Hospital, Tongji University School of MedicineShanghai, China
| | - Xu Zhang
- Department of Stomatology, Shanghai Tenth People’s Hospital, Tongji University School of MedicineShanghai, China
| | - Fubo Chen
- Department of Stomatology, Shanghai Tenth People’s Hospital, Tongji University School of MedicineShanghai, China
| | - Liwei An
- Department of Stomatology, Shanghai Tenth People’s Hospital, Tongji University School of MedicineShanghai, China
- Department of Medical Stomatology, Shanghai Tenth People’s Hospital, Tongji University Cancer Center, Tongji University School of MedicineShanghai, China
| | - Hang Yuan
- Department of Stomatology, Shanghai Tenth People’s Hospital, Tongji University School of MedicineShanghai, China
| | - Fuping Wen
- Department of Stomatology, Shanghai Tenth People’s Hospital, Tongji University School of MedicineShanghai, China
| | - Yuanzhi Xu
- Department of Stomatology, Shanghai Tenth People’s Hospital, Tongji University School of MedicineShanghai, China
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17
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Viktorsson K, Rieckmann T, Fleischmann M, Diefenhardt M, Hehlgans S, Rödel F. Advances in molecular targeted therapies to increase efficacy of (chemo)radiation therapy. Strahlenther Onkol 2023; 199:1091-1109. [PMID: 37041372 PMCID: PMC10673805 DOI: 10.1007/s00066-023-02064-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 02/19/2023] [Indexed: 04/13/2023]
Abstract
Recent advances in understanding the tumor's biology in line with a constantly growing number of innovative technologies have prompted characterization of patients' individual malignancies and may display a prerequisite to treat cancer at its patient individual tumor vulnerability. In recent decades, radiation- induced signaling and tumor promoting local events for radiation sensitization were explored in detail, resulting the development of novel molecular targets. A multitude of pharmacological, genetic, and immunological principles, including small molecule- and antibody-based targeted strategies, have been developed that are suitable for combined concepts with radiation (RT) or chemoradiation therapy (CRT). Despite a plethora of promising experimental and preclinical findings, however, so far, only a very limited number of clinical trials have demonstrated a better outcome and/or patient benefit when RT or CRT are combined with targeted agents. The current review aims to summarize recent progress in molecular therapies targeting oncogenic drivers, DNA damage and cell cycle response, apoptosis signaling pathways, cell adhesion molecules, hypoxia, and the tumor microenvironment to impact therapy refractoriness and to boost radiation response. In addition, we will discuss recent advances in nanotechnology, e.g., RNA technologies and protein-degrading proteolysis-targeting chimeras (PROTACs) that may open new and innovative ways to benefit from molecular-targeted therapy approaches with improved efficacy.
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Affiliation(s)
- Kristina Viktorsson
- Department of Oncology/Pathology, Karolinska Institutet, Visionsgatan 4, 17164, Solna, Sweden
| | - Thorsten Rieckmann
- Department of Radiation Oncology, University Medical Center Hamburg Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
- Department of Otolaryngology, University Medical Center Hamburg Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Maximilian Fleischmann
- Department of Radiotherapy and Oncology, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
- Frankfurt Cancer Institute (FCI), University of Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Markus Diefenhardt
- Department of Radiotherapy and Oncology, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
- Frankfurt Cancer Institute (FCI), University of Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Stephanie Hehlgans
- Department of Radiotherapy and Oncology, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Franz Rödel
- Department of Radiotherapy and Oncology, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany.
- Frankfurt Cancer Institute (FCI), University of Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany.
- German Cancer Consortium (DKTK) partner site: Frankfurt, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
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18
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Molenda S, Sikorska A, Florczak A, Lorenc P, Dams-Kozlowska H. Oligonucleotide-Based Therapeutics for STAT3 Targeting in Cancer-Drug Carriers Matter. Cancers (Basel) 2023; 15:5647. [PMID: 38067351 PMCID: PMC10705165 DOI: 10.3390/cancers15235647] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 09/08/2024] Open
Abstract
High expression and phosphorylation of signal transducer and transcription activator 3 (STAT3) are correlated with progression and poor prognosis in various types of cancer. The constitutive activation of STAT3 in cancer affects processes such as cell proliferation, apoptosis, metastasis, angiogenesis, and drug resistance. The importance of STAT3 in cancer makes it a potential therapeutic target. Various methods of directly and indirectly blocking STAT3 activity at different steps of the STAT3 pathway have been investigated. However, the outcome has been limited, mainly by the number of upstream proteins that can reactivate STAT3 or the relatively low specificity of the inhibitors. A new branch of molecules with significant therapeutic potential has emerged thanks to recent developments in the regulatory function of non-coding nucleic acids. Oligonucleotide-based therapeutics can silence target transcripts or edit genes, leading to the modification of gene expression profiles, causing cell death or restoring cell function. Moreover, they can reach untreatable targets, such as transcription factors. This review briefly describes oligonucleotide-based therapeutics that found application to target STAT3 activity in cancer. Additionally, this review comprehensively summarizes how the inhibition of STAT3 activity by nucleic acid-based therapeutics such as siRNA, shRNA, ASO, and ODN-decoy affected the therapy of different types of cancer in preclinical and clinical studies. Moreover, due to some limitations of oligonucleotide-based therapeutics, the importance of carriers that can deliver nucleic acid molecules to affect the STAT3 in cancer cells and cells of the tumor microenvironment (TME) was pointed out. Combining a high specificity of oligonucleotide-based therapeutics toward their targets and functionalized nanoparticles toward cell type can generate very efficient formulations.
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Affiliation(s)
- Sara Molenda
- Department of Cancer Immunology, Poznan University of Medical Sciences, 15 Garbary St., 61-866 Poznan, Poland; (S.M.); (A.S.); (A.F.); (P.L.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 15 Garbary St., 61-866 Poznan, Poland
| | - Agata Sikorska
- Department of Cancer Immunology, Poznan University of Medical Sciences, 15 Garbary St., 61-866 Poznan, Poland; (S.M.); (A.S.); (A.F.); (P.L.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 15 Garbary St., 61-866 Poznan, Poland
| | - Anna Florczak
- Department of Cancer Immunology, Poznan University of Medical Sciences, 15 Garbary St., 61-866 Poznan, Poland; (S.M.); (A.S.); (A.F.); (P.L.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 15 Garbary St., 61-866 Poznan, Poland
| | - Patryk Lorenc
- Department of Cancer Immunology, Poznan University of Medical Sciences, 15 Garbary St., 61-866 Poznan, Poland; (S.M.); (A.S.); (A.F.); (P.L.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 15 Garbary St., 61-866 Poznan, Poland
| | - Hanna Dams-Kozlowska
- Department of Cancer Immunology, Poznan University of Medical Sciences, 15 Garbary St., 61-866 Poznan, Poland; (S.M.); (A.S.); (A.F.); (P.L.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 15 Garbary St., 61-866 Poznan, Poland
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19
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Banerjee S, Smith IM, Hengen AC, Stroka KM. Methods for studying mammalian aquaporin biology. Biol Methods Protoc 2023; 8:bpad031. [PMID: 38046463 PMCID: PMC10689382 DOI: 10.1093/biomethods/bpad031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/29/2023] [Accepted: 11/09/2023] [Indexed: 12/05/2023] Open
Abstract
Aquaporins (AQPs), transmembrane water-conducting channels, have earned a great deal of scrutiny for their critical physiological roles in healthy and disease cell states, especially in the biomedical field. Numerous methods have been implemented to elucidate the involvement of AQP-mediated water transport and downstream signaling activation in eliciting whole cell, tissue, and organ functional responses. To modulate these responses, other methods have been employed to investigate AQP druggability. This review discusses standard in vitro, in vivo, and in silico methods for studying AQPs, especially for biomedical and mammalian cell biology applications. We also propose some new techniques and approaches for future AQP research to address current gaps in methodology.
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Affiliation(s)
- Shohini Banerjee
- Fischell Department of Bioengineering, University of Maryland, MD 20742, United States
| | - Ian M Smith
- Fischell Department of Bioengineering, University of Maryland, MD 20742, United States
| | - Autumn C Hengen
- Fischell Department of Bioengineering, University of Maryland, MD 20742, United States
| | - Kimberly M Stroka
- Fischell Department of Bioengineering, University of Maryland, MD 20742, United States
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore MD 21201, United States
- Biophysics Program, University of Maryland, MD 20742, United States
- Center for Stem Cell Biology and Regenerative Medicine, University of Maryland, Baltimore MD 21201, United States
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20
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Wong B, Birtch R, Rezaei R, Jamieson T, Crupi MJF, Diallo JS, Ilkow CS. Optimal delivery of RNA interference by viral vectors for cancer therapy. Mol Ther 2023; 31:3127-3145. [PMID: 37735876 PMCID: PMC10638062 DOI: 10.1016/j.ymthe.2023.09.012] [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: 05/31/2023] [Revised: 08/28/2023] [Accepted: 09/14/2023] [Indexed: 09/23/2023] Open
Abstract
In recent years, there has been a surge in the innovative modification and application of the viral vector-based gene therapy field. Significant and consistent improvements in the engineering, delivery, and safety of viral vectors have set the stage for their application as RNA interference (RNAi) delivery tools. Viral vector-based delivery of RNAi has made remarkable breakthroughs in the treatment of several debilitating diseases and disorders (e.g., neurological diseases); however, their novelty has yet to be fully applied and utilized for the treatment of cancer. This review highlights the most promising and emerging viral vector delivery tools for RNAi therapeutics while discussing the variables limiting their success and suitability for cancer therapy. Specifically, we outline different integrating and non-integrating viral platforms used for gene delivery, currently employed RNAi targets for anti-cancer effect, and various strategies used to optimize the safety and efficacy of these RNAi therapeutics. Most importantly, we provide great insight into what challenges exist in their application as cancer therapeutics and how these challenges can be effectively navigated to advance the field.
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Affiliation(s)
- Boaz Wong
- Centre for Innovative Cancer Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Rayanna Birtch
- Centre for Innovative Cancer Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Reza Rezaei
- Centre for Innovative Cancer Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Taylor Jamieson
- Centre for Innovative Cancer Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Mathieu J F Crupi
- Centre for Innovative Cancer Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Jean-Simon Diallo
- Centre for Innovative Cancer Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Carolina S Ilkow
- Centre for Innovative Cancer Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada.
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21
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Velazquez Sanchez AK, Klopprogge B, Zimmermann KH, Ignatova Z. Tailored Synthetic sRNAs Dynamically Tune Multilayer Genetic Circuits. ACS Synth Biol 2023; 12:2524-2535. [PMID: 37595156 DOI: 10.1021/acssynbio.2c00614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2023]
Abstract
Predictable and controllable tuning of genetic circuits to regulate gene expression, including modulation of existing circuits or constructs without the need for redesign or rebuilding, is a persistent challenge in synthetic biology. Here, we propose rationally designed new small RNAs (sRNAs) that dynamically modulate gene expression of genetic circuits with a broad range (high, medium, and low) of repression. We designed multiple multilayer genetic circuits in which the variable effector element is a transcription factor (TF) controlling downstream the production of a reporter protein. The sRNAs target TFs instead of a reporter gene, and harnessing the intrinsic RNA-interference pathway in E. coli allowed for a wide range of expression modulation of the reporter protein, including the most difficult to achieve dynamic switch to an OFF state. The synthetic sRNAs are expressed independently of the circuit(s), thus allowing for repression without modifying the circuit itself. Our work provides a frame for achieving independent modulation of gene expression and dynamic and modular control of the multilayer genetic circuits by only including an independent control circuit expressing synthetic sRNAs, without altering the structure of existing genetic circuits.
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Affiliation(s)
- Ana K Velazquez Sanchez
- Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | - Bjarne Klopprogge
- Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | - Karl-Heinz Zimmermann
- Algebraic Engineering, Institute of Embedded Systems, Hamburg University of Technology, 21073 Hamburg, Germany
| | - Zoya Ignatova
- Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
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22
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Huang H, Liao D, Zhou G, He B, Pu R, Cui Y. MicroRNA-194-3p impacts autophagy and represses rotavirus replication via targeting silent information regulator 1. Virol J 2023; 20:210. [PMID: 37697309 PMCID: PMC10496334 DOI: 10.1186/s12985-023-02175-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 08/31/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND Rotavirus (RV) is the main cause of serious diarrhea in infants and young children worldwide. Numerous studies have demonstrated that RV use host cell mechanisms to motivate their own stabilization and multiplication by degrading, enhancing, or hijacking microRNAs (miRNAs). Therefore, exploring the molecular mechanisms by which miRNAs motivate or restrain RV replication by controlling different biological processes, including autophagy, will help to better understand the pathogenesis of RV development. This study mainly explored the effect of miR-194-3p on autophagy after RV infection and its underlying mechanism of the regulation of RV replication. METHODS Caco-2 cells were infected with RV and used to measure the expression levels of miR-194-3p and silent information regulator 1 (SIRT1). After transfection with plasmids and RV infection, viral structural proteins, RV titer, cell viability, and autophagy-linked proteins were tested. The degree of acetylation of p53 was further investigated. A RV-infected neonatal mouse model was constructed in vivo and was evaluated for diarrhea symptoms and lipid droplet formation. RESULTS The results showed that miR-194-3p was reduced but SIRT1 was elevated after RV infection. Elevation of miR-194-3p or repression of SIRT1 inhibited RV replication through the regulation of autophagy. The overexpression of SIRT1 reversed the effects of miR-194-3p on RV replication. The upregulation of miR-194-3p or the downregulation of SIRT1 repressed RV replication in vivo. MiR-194-3p targeted SIRT1 to decrease p53 acetylation. CONCLUSION These results were used to determine the mechanism of miR-194-3p in RV replication, and identified a novel therapeutic small RNA molecule that can be used against RV.
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Affiliation(s)
- Haohai Huang
- Department of Clinical Pharmacy, SSL Central Hospital of Dongguan, Dongguan Third People's Hospital, Affiliated Dongguan Shilong People's Hospital of Southern Medical University, Dongguan, Guangdong, China.
- Medical and Pharmacy Research Laboratory, SSL Central Hospital of Dongguan, Dongguan Third People's Hospital, Affiliated Dongguan Shilong People's Hospital of Southern Medical University, No.1, Huangzhou Xianglong Road of Shilong Town, 523326, Dongguan, Guangdong, China.
| | - Dan Liao
- Department of Gynaecology, SSL Central Hospital of Dongguan, Dongguan Third People's Hospital, Affiliated Dongguan Shilong People's Hospital of Southern Medical University, Dongguan, Guangdong, China
| | - Guanghui Zhou
- Department of Rehabilitation medicine, SSL Central Hospital of Dongguan, Dongguan Third People's Hospital, Affiliated Dongguan Shilong People's Hospital of Southern Medical University, Dongguan, Guangdong, China
| | - Bin He
- Medical and Pharmacy Research Laboratory, SSL Central Hospital of Dongguan, Dongguan Third People's Hospital, Affiliated Dongguan Shilong People's Hospital of Southern Medical University, No.1, Huangzhou Xianglong Road of Shilong Town, 523326, Dongguan, Guangdong, China
| | - Rong Pu
- Department of Clinical Laboratory, SSL Central Hospital of Dongguan, Dongguan Third People's Hospital, Affiliated Dongguan Shilong People's Hospital of Southern Medical University, Dongguan, Guangdong, China
| | - Yejia Cui
- Department of Clinical Laboratory, SSL Central Hospital of Dongguan, Dongguan Third People's Hospital, Affiliated Dongguan Shilong People's Hospital of Southern Medical University, Dongguan, Guangdong, China
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Daich Varela M, Georgiadis A, Michaelides M. Genetic treatment for autosomal dominant inherited retinal dystrophies: approaches, challenges and targeted genotypes. Br J Ophthalmol 2023; 107:1223-1230. [PMID: 36038193 DOI: 10.1136/bjo-2022-321903] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/01/2022] [Indexed: 11/04/2022]
Abstract
Inherited retinal diseases (IRDs) have been in the front line of gene therapy development for the last decade, providing a useful platform to test novel therapeutic approaches. More than 40 clinical trials have been completed or are ongoing, tackling autosomal recessive and X-linked conditions, mostly through adeno-associated viral vector delivery of a normal copy of the disease-causing gene. However, only recently has autosomal dominant (ad) disease been targeted, with the commencement of a trial for rhodopsin (RHO)-associated retinitis pigmentosa (RP), implementing antisense oligonucleotide (AON) therapy, with promising preliminary results (NCT04123626).Autosomal dominant RP represents 15%-25% of all RP, with RHO accounting for 20%-30% of these cases. Autosomal dominant macular and cone-rod dystrophies (MD/CORD) correspond to approximately 7.5% of all IRDs, and approximately 35% of all MD/CORD cases, with the main causative gene being BEST1 Autosomal dominant IRDs are not only less frequent than recessive, but also tend to be less severe and have later onset; for example, an individual with RHO-adRP would typically become severely visually impaired at an age 2-3 times older than in X-linked RPGR-RP.Gain-of-function and dominant negative aetiologies are frequently seen in the prevalent adRP genes RHO, RP1 and PRPF31 among others, which would not be effectively addressed by gene supplementation alone and need creative, novel approaches. Zinc fingers, RNA interference, AON, translational read-through therapy, and gene editing by clustered regularly interspaced short palindromic repeats/Cas are some of the strategies that are currently under investigation and will be discussed here.
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Affiliation(s)
- Malena Daich Varela
- Moorfields Eye Hospital, London, UK
- UCL Institute of Ophthalmology, University College London, London, UK
| | | | - Michel Michaelides
- Moorfields Eye Hospital, London, UK
- UCL Institute of Ophthalmology, University College London, London, UK
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24
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Mokhtari-Esbuie F, Gheshlaghi S, Abraham JM, Harmon JW. Adenoviral delivery of DNA plasmid for RNA silencing: pros and cons. ANNALS OF TRANSLATIONAL MEDICINE 2023; 11:334. [PMID: 37675310 PMCID: PMC10477637 DOI: 10.21037/atm-23-1646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/19/2023] [Indexed: 09/08/2023]
Affiliation(s)
| | | | - John M. Abraham
- Bayview Surgical Research Laboratory, Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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25
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Uppaluri KR, Challa HJ, Gaur A, Jain R, Krishna Vardhani K, Geddam A, Natya K, Aswini K, Palasamudram K, K SM. Unlocking the potential of non-coding RNAs in cancer research and therapy. Transl Oncol 2023; 35:101730. [PMID: 37406550 PMCID: PMC10366642 DOI: 10.1016/j.tranon.2023.101730] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/30/2023] [Accepted: 06/21/2023] [Indexed: 07/07/2023] Open
Abstract
Non-coding RNAs (ncRNAs) have emerged as key regulators of gene expression, with growing evidence implicating their involvement in cancer development and progression. The potential of ncRNAs as diagnostic and prognostic biomarkers for cancer is promising, with emphasis on their use in liquid biopsy and tissue-based diagnostics. In a nutshell, the review comprehensively summarizes the diverse classes of ncRNAs implicated in cancer, including microRNAs, long non-coding RNAs, and circular RNAs, and their functions and mechanisms of action. Furthermore, we describe the potential therapeutic applications of ncRNAs, including anti-miRNA oligonucleotides, siRNAs, and other RNA-based therapeutics in cancer treatment. However, significant challenges remain in developing effective ncRNA-based diagnostics and therapeutics, including the lack of specificity, limited understanding of mechanisms, and delivery challenges. This review also covers the current state-of-the-art non-coding RNA research technologies and bioinformatic analysis tools. Lastly, we outline future research directions in non-coding RNA research in cancer, including developing novel biomarkers, therapeutic targets, and modalities. In summary, this review provides a comprehensive understanding of non-coding RNAs in cancer and their potential clinical applications, highlighting both the opportunities and challenges in this rapidly evolving field.
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Affiliation(s)
- Kalyan Ram Uppaluri
- GenepoweRx, Uppaluri K&H Personalized Medicine Clinic, Suit #2B, Plot No. 240, Nirvana, Road No. 36, Jawahar Colony, Jubilee Hills, Hyderabad, Telangana 500033, India.
| | - Hima J Challa
- GenepoweRx, Uppaluri K&H Personalized Medicine Clinic, Suit #2B, Plot No. 240, Nirvana, Road No. 36, Jawahar Colony, Jubilee Hills, Hyderabad, Telangana 500033, India
| | - Ashish Gaur
- Department of Biotechnology, GLA University, Mathura, India
| | - Rajul Jain
- Dayalbagh Educational Institute, Agra, India
| | - K Krishna Vardhani
- GenepoweRx, Uppaluri K&H Personalized Medicine Clinic, Suit #2B, Plot No. 240, Nirvana, Road No. 36, Jawahar Colony, Jubilee Hills, Hyderabad, Telangana 500033, India
| | - Anusha Geddam
- GenepoweRx, Uppaluri K&H Personalized Medicine Clinic, Suit #2B, Plot No. 240, Nirvana, Road No. 36, Jawahar Colony, Jubilee Hills, Hyderabad, Telangana 500033, India
| | - K Natya
- GenepoweRx, Uppaluri K&H Personalized Medicine Clinic, Suit #2B, Plot No. 240, Nirvana, Road No. 36, Jawahar Colony, Jubilee Hills, Hyderabad, Telangana 500033, India
| | - K Aswini
- GenepoweRx, Uppaluri K&H Personalized Medicine Clinic, Suit #2B, Plot No. 240, Nirvana, Road No. 36, Jawahar Colony, Jubilee Hills, Hyderabad, Telangana 500033, India
| | - Kalyani Palasamudram
- GenepoweRx, Uppaluri K&H Personalized Medicine Clinic, Suit #2B, Plot No. 240, Nirvana, Road No. 36, Jawahar Colony, Jubilee Hills, Hyderabad, Telangana 500033, India
| | - Sri Manjari K
- GenepoweRx, Uppaluri K&H Personalized Medicine Clinic, Suit #2B, Plot No. 240, Nirvana, Road No. 36, Jawahar Colony, Jubilee Hills, Hyderabad, Telangana 500033, India.
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Huang LA, Lin C, Yang L. Plumbing mysterious RNAs in "dark genome" for the conquest of human diseases. Mol Ther 2023; 31:1577-1595. [PMID: 37165619 PMCID: PMC10278048 DOI: 10.1016/j.ymthe.2023.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/11/2023] [Accepted: 05/05/2023] [Indexed: 05/12/2023] Open
Abstract
Next-generation sequencing has revealed that less than 2% of transcribed genes are translated into proteins, with a large portion transcribed into noncoding RNAs (ncRNAs). Among these, long noncoding RNAs (lncRNAs) represent the largest group and are pervasively transcribed throughout the genome. Dysfunctions in lncRNAs have been found in various diseases, highlighting their potential as therapeutic, diagnostic, and prognostic targets. However, challenges, such as unknown molecular mechanisms and nonspecific immune responses, and issues of drug specificity and delivery present obstacles in translating lncRNAs into clinical applications. In this review, we summarize recent publications that have explored lncRNA functions in human diseases. We also discuss challenges and future directions for developing lncRNA treatments, aiming to bridge the gap between functional studies and clinical potential and inspire further exploration in the field.
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Affiliation(s)
- Lisa A Huang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chunru Lin
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Liuqing Yang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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27
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Liu L, Zhang Y, Fu J, Ai X, Long D, Leng X, Zhang Y, Huang B, Li C, Zhou Y, Feng C. Gli1 depletion induces oxidative stress and apoptosis of nucleus pulposus cells via Fos in intervertebral disc degeneration. J Orthop Translat 2023; 40:116-131. [PMID: 37457313 PMCID: PMC10338909 DOI: 10.1016/j.jot.2023.05.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 04/01/2023] [Accepted: 05/19/2023] [Indexed: 07/18/2023] Open
Abstract
Background Intervertebral disc degeneration (IDD) is the most common chronic disease. Oxidative stress and apoptosis of nucleus pulposus (NP) cells disrupt intervertebral disc (IVD) homeostasis, which is the main cause of IDD. Glioma-associated oncogene 1 (Gli1) is an important transcription factor in the Hedgehog (Hh) pathway. Depletion of Gli1 accelerates the occurrence and development of degenerative diseases. This study aimed to explore the role of aging related Gli1 depletion in the progression of IDD. Methods The relationship between aging related Gli1 depletion and IDD was studied in the NP tissues of human and rats of different ages, and the levels of oxidative stress and NP cell apoptosis during IDD were explored. Gli1 depletion of NP cells were established by targeting inhibitor GANT61 or lentivirus-coated Gli1 sh-RNA (sh-Gli1) to explore the role of Gli1 in NP cells and underlying mechanism. Exogenous Gli1 depletion induced IDD of rats was established by intraperitoneal injection of GANT61. Also, the roles of Fos in the Gli1 depletion induced NP cell oxidative stress, apoptosis and IDD were investigated. Results Gli1 was down-regulated in the tissues of degenerative NP, and the level of Gli1 was negatively correlated with the severity of aging related IDD in human and rats. Furthermore, we found enhanced oxidative stress and apoptosis in degenerative NP tissues. Gli1 depletion promoted oxidative stress and apoptosis of NP cells and resulted in the degradation of extracellular matrix (ECM) and decreased ECM synthesis. Transcriptome sequencing showed that Gli1 depletion caused Fos activation in NP cells. the effect of Gli1 depletion on the oxidative stress and apoptosis of NP cells were retarded by Fos inhibitor. In vivo, Fos inhibition alleviated the IDD induced by exogenous Gli1 depletion. Conclusions This study revealed for the first time that Gli1 is gradually depleted in NP with IDD progression. Exogenous Gli1 depletion causes oxidative stress and apoptosis of NP cells both in vivo and in vitro. Fos suppression effectively retards the destructive effects of Gli1 depletion on IVD homoeostasis.The translational potential of this article: This study may provide new potential targets for preventing and reversing IDD. Maintaining Gli1 expression in NP and suppressing Fos activation may be an effective treatment strategy for IDD.
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Jogdeo CM, Panja S, Kanvinde S, Kapoor E, Siddhanta K, Oupický D. Advances in Lipid-Based Codelivery Systems for Cancer and Inflammatory Diseases. Adv Healthc Mater 2023; 12:e2202400. [PMID: 36453542 PMCID: PMC10023350 DOI: 10.1002/adhm.202202400] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/13/2022] [Indexed: 12/03/2022]
Abstract
Combination therapy targeting multiple therapeutic targets is a favorable strategy to achieve better therapeutic outcomes in cancer and inflammatory diseases. Codelivery is a subfield of drug delivery that aims to achieve combined delivery of diverse therapeutic cargoes within the same delivery system, thereby ensuring delivery to the same site and providing an opportunity to tailor the release kinetics as desired. Among the wide range of materials being investigated in the design of codelivery systems, lipids have stood out on account of their low toxicity, biocompatibility, and ease of formulation scale-up. This review highlights the advances of the last decade in lipid-based codelivery systems focusing on the codelivery of drug-drug, drug-nucleic acid, nucleic acid-nucleic acid, and protein therapeutic-based combinations for targeted therapy in cancer and inflammatory diseases.
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Affiliation(s)
- Chinmay M. Jogdeo
- Center for Drug Delivery and Nanomedicine, Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Sudipta Panja
- Center for Drug Delivery and Nanomedicine, Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Shrey Kanvinde
- Center for Drug Delivery and Nanomedicine, Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Ekta Kapoor
- Center for Drug Delivery and Nanomedicine, Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Kasturi Siddhanta
- Center for Drug Delivery and Nanomedicine, Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - David Oupický
- Center for Drug Delivery and Nanomedicine, Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
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29
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Dreismann AK, Hallam TM, Tam LC, Nguyen CV, Hughes JP, Ellis S, Harris CL. Gene targeting as a therapeutic avenue in diseases mediated by the complement alternative pathway. Immunol Rev 2023; 313:402-419. [PMID: 36369963 PMCID: PMC10099504 DOI: 10.1111/imr.13149] [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: 11/15/2022]
Abstract
The complement alternative pathway (AP) is implicated in numerous diseases affecting many organs, ranging from the rare hematological disease paroxysmal nocturnal hemoglobinuria (PNH), to the common blinding disease age-related macular degeneration (AMD). Critically, the AP amplifies any activating trigger driving a downstream inflammatory response; thus, components of the pathway have become targets for drugs of varying modality. Recent validation from clinical trials using drug modalities such as inhibitory antibodies has paved the path for gene targeting of the AP or downstream effectors. Gene targeting in the complement field currently focuses on supplementation or suppression of complement regulators in AMD and PNH, largely because the eye and liver are highly amenable to drug delivery through local (eye) or systemic (liver) routes. Targeting the liver could facilitate treatment of numerous diseases as this organ generates most of the systemic complement pool. This review explains key concepts of RNA and DNA targeting and discusses assets in clinical development for the treatment of diseases driven by the alternative pathway, including the RNA-targeting therapeutics ALN-CC5, ARO-C3, and IONIS-FB-LRX, and the gene therapies GT005 and HMR59. These therapies are but the spearhead of potential drug candidates that might revolutionize the field in coming years.
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30
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Tu MJ, Yu AM. Recent Advances in Novel Recombinant RNAs for Studying Post-transcriptional Gene Regulation in Drug Metabolism and Disposition. Curr Drug Metab 2023; 24:175-189. [PMID: 37170982 PMCID: PMC10825985 DOI: 10.2174/1389200224666230425232433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 03/02/2023] [Accepted: 03/08/2023] [Indexed: 05/13/2023]
Abstract
Drug-metabolizing enzymes and transporters are major determinants of the absorption, disposition, metabolism, and excretion (ADME) of drugs, and changes in ADME gene expression or function may alter the pharmacokinetics/ pharmacodynamics (PK/PD) and further influence drug safety and therapeutic outcomes. ADME gene functions are controlled by diverse factors, such as genetic polymorphism, transcriptional regulation, and coadministered medications. MicroRNAs (miRNAs) are a superfamily of regulatory small noncoding RNAs that are transcribed from the genome to regulate target gene expression at the post-transcriptional level. The roles of miRNAs in controlling ADME gene expression have been demonstrated, and such miRNAs may consequently influence cellular drug metabolism and disposition capacity. Several types of miRNA mimics and small interfering RNA (siRNA) reagents have been developed and widely used for ADME research. In this review article, we first provide a brief introduction to the mechanistic actions of miRNAs in post-transcriptional gene regulation of drug-metabolizing enzymes, transporters, and transcription factors. After summarizing conventional small RNA production methods, we highlight the latest advances in novel recombinant RNA technologies and applications of the resultant bioengineered RNA (BioRNA) agents to ADME studies. BioRNAs produced in living cells are not only powerful tools for general biological and biomedical research but also potential therapeutic agents amenable to clinical investigations.
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Affiliation(s)
- Mei-Juan Tu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA
| | - Ai-Ming Yu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA
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Zhang Z, Zhang D, Wang F, Liu J, Sun Y, Anuchapreeda S, Tima S, Xiao Z, Duangmano S. Sema4D silencing increases the sensitivity of nivolumab to B16-F10 resistant melanoma via inhibiting the PI3K/AKT signaling pathway. PeerJ 2023; 11:e15172. [PMID: 37096066 PMCID: PMC10122458 DOI: 10.7717/peerj.15172] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 03/13/2023] [Indexed: 04/26/2023] Open
Abstract
Melanoma is a common skin tumor that causes a high rate of mortality, especially in Europe, North America and Oceania. Immunosuppressants such as anti-PD-1 have been used in the treatment of malignant melanoma, however, nearly 60% of patients do not respond to these treatments. Sema4D, also called CD100, is expressed in T cells and tumor tissues. Sema4D and its receptor, Plexin-B1, play crucial roles in the process of immune regulation, angiogenesis, and tumor progression. The role of Sema4D in melanoma with anti-PD-1 resistance is poorly understood. Through a combination of molecular biology techniques and in silico analysis, the role of Sema4D in improving anti-PD-L1 sensitivity in melanoma was explored. The results showed that the expression of Sema4D, Plexin-B1 and PD-L1 was significantly increased in B16-F10R cells. Sema4D knockdown synergizes with anti-PD-1 treatment, cell viability, cell invasion and migration were significantly decreased, while the apoptosis was increased, the growth of tumors on the mice was also inhibited. Mechanistically, bioinformatics analysis revealed that Sema4D is involved in the PI3K/AKT signaling pathway; the downregulation of p-PI3K/PI3K and p-AKT/AKT expression were observed in Sema4D knockdown, therefore, nivolumab resistance is related to Sema4D and Sema4D silencing can improve sensitivity to nivolumab via inhibition of the PI3K/AKT signaling pathway.
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Affiliation(s)
- Zhuo Zhang
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
- Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Duoli Zhang
- Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Fang Wang
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
- Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Jiao Liu
- Department of Pharmacy, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Yuhong Sun
- Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Songyot Anuchapreeda
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Singkome Tima
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Zhangang Xiao
- Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Suwit Duangmano
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
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Chen D, Liu X, Lu X, Tian J. Nanoparticle drug delivery systems for synergistic delivery of tumor therapy. Front Pharmacol 2023; 14:1111991. [PMID: 36874010 PMCID: PMC9978018 DOI: 10.3389/fphar.2023.1111991] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/02/2023] [Indexed: 02/18/2023] Open
Abstract
Nanoparticle drug delivery systems have proved anti-tumor effects; however, they are not widely used in tumor therapy due to insufficient ability to target specific sites, multidrug resistance to anti-tumor drugs, and the high toxicity of the drugs. With the development of RNAi technology, nucleic acids have been delivered to target sites to replace or correct defective genes or knock down specific genes. Also, synergistic therapeutic effects can be achieved for combined drug delivery, which is more effective for overcoming multidrug resistance of cancer cells. These combination therapies achieve better therapeutic effects than delivering nucleic acids or chemotherapeutic drugs alone, so the scope of combined drug delivery has also been expanded to three aspects: drug-drug, drug-gene, and gene-gene. This review summarizes the recent advances of nanocarriers to co-delivery agents, including i) the characterization and preparation of nanocarriers, such as lipid-based nanocarriers, polymer nanocarriers, and inorganic delivery carriers; ii) the advantages and disadvantages of synergistic delivery approaches; iii) the effectual delivery cases that are applied in the synergistic delivery systems; and iv) future perspectives in the design of nanoparticle drug delivery systems to co-deliver therapeutic agents.
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Affiliation(s)
- Daoyuan Chen
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China
| | - Xuecun Liu
- Shandong Boan Biotechnology Co., Ltd., Yantai, China
| | - Xiaoyan Lu
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China
| | - Jingwei Tian
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China
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Guzman G, Creek C, Farley S, Tafesse FG. Genetic Tools for Studying the Roles of Sphingolipids in Viral Infections. Methods Mol Biol 2022; 2610:1-16. [PMID: 36534277 DOI: 10.1007/978-1-0716-2895-9_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Sphingolipids are a critical family of membrane lipids with diverse functions in eukaryotic cells, and a growing body of literature supports that these lipids play essential roles during the lifecycles of viruses. While small molecule inhibitors of sphingolipid synthesis and metabolism are widely used, the advent of CRISPR-based genomic editing techniques allows for nuanced exploration into the manners in which sphingolipids influence various stages of viral infections. Here we describe some of these critical considerations needed in designing studies utilizing genomic editing techniques for manipulating the sphingolipid metabolic pathway, as well as the current body of literature regarding how viruses depend on the products of this pathway. Here, we highlight the ways in which sphingolipids affect viruses as these pathogens interact with and influence their host cell and describe some of the many open questions remaining in the field.
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Affiliation(s)
- Gaelen Guzman
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Cameron Creek
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Scotland Farley
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Fikadu G Tafesse
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, USA.
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Yasmin T, Adiba M, Saba AA, Nabi AHMN. In Silico Design of siRNAs for Silencing CLEC5A Receptor as a Potential Therapeutic Approach Against Dengue and Japanese Encephalitis Virus Infection in Human. Bioinform Biol Insights 2022; 16:11779322221142122. [PMID: 36530559 PMCID: PMC9749047 DOI: 10.1177/11779322221142122] [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: 05/09/2022] [Accepted: 11/09/2022] [Indexed: 09/04/2024] Open
Abstract
Dengue and Japanese encephalitis virus (JEV) are mosquito-borne RNA viruses that can cause severe illness leading to death in the tropics and subtropics. Both of these viruses interact directly with the C-type lectin domain family 5, member A receptor (CLEC5A) on human macrophages which stimulates the release of proinflammatory cytokines. Since blockade of this interaction has been shown to suppress the secretion of cytokines, CLEC5A is considered a potential target for the development of new treatments to reduce virus-induced brain damage. Developing a vaccine against dengue is challenging because this virus can cause disease through 4 different serotypes. Therefore, the vaccine must immunize against all 4 serotypes to be effective, while unvaccinated people still contract JEV and suffer from its complications. Small interfering RNAs (siRNAs) play an important role in regulating gene expression by causing the degradation of target mRNAs. In this study, we attempted to rationally design potential siRNA molecules using various software, targeting the CLEC5A gene. In total, 3 siRNAs were found to be potential candidates for CLEC5A silencing. They showed good target accessibility, optimum guanine-cytosine (GC) content, the least chance of off-target effects, positive energy of folding, and strong interaction with Argonaute2 protein as denoted by a negative docking energy score. In addition, molecular dynamics simulation of the siRNA-Ago2-docked complexes showed the stability of the complexes over 1.5 nanoseconds. These predicted siRNAs might effectively downregulate the expression of the CLEC5A receptor and thus prove vital in the treatment of dengue and JEV infections.
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Affiliation(s)
- Tahirah Yasmin
- Laboratory of Population Genetics, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Maisha Adiba
- Laboratory of Population Genetics, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Abdullah Al Saba
- Laboratory of Population Genetics, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - AHM Nurun Nabi
- Laboratory of Population Genetics, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
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Danaeifar M. Recent advances in gene therapy: genetic bullets to the root of the problem. Clin Exp Med 2022:10.1007/s10238-022-00925-x. [PMID: 36284069 DOI: 10.1007/s10238-022-00925-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 10/14/2022] [Indexed: 12/28/2022]
Abstract
Genetics and molecular genetic techniques have changed many perspectives and paradigms in medicine. Using genetic methods, many diseases have been cured or alleviated. Gene therapy, in its simplest definition, is application of genetic materials and related techniques to treat various human diseases. Evaluation of the trends in the field of medicine and therapeutics clarifies that gene therapy has attracted a lot of attention due to its powerful potential to treat a number of diseases. There are various genetic materials that can be used in gene therapy such as DNA, single- and double-stranded RNA, siRNA and shRNA. The main gene editing techniques used for in vitro and in vivo gene modification are ZNF, TALEN and CRISPR-Cas9. The latter has increased hopes for more precise and efficient gene targeting as it requires two separate recognition sites which makes it more specific and can also cause rapid and sufficient cleavage within the target sequence. There must be carriers for delivering genes to the target tissue. The most commonly used carriers for this purpose are viral vectors such as adenoviruses, adeno-associated viruses and lentiviruses. Non-viral vectors consist of bacterial vectors, liposomes, dendrimers and nanoparticles.
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Ding Y, Zhang Y, Liu X. Combinational treatments of RNA interference and extracellular vesicles in the spinocerebellar ataxia. Front Mol Neurosci 2022; 15:1043947. [PMID: 36311034 PMCID: PMC9606576 DOI: 10.3389/fnmol.2022.1043947] [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: 09/14/2022] [Accepted: 09/21/2022] [Indexed: 11/13/2022] Open
Abstract
Spinocerebellar ataxia (SCA) is an autosomal dominant neurodegenerative disease (ND) with a high mortality rate. Symptomatic treatment is the only clinically adopted treatment. However, it has poor effect and serious complications. Traditional diagnostic methods [such as magnetic resonance imaging (MRI)] have drawbacks. Presently, the superiority of RNA interference (RNAi) and extracellular vesicles (EVs) in improving SCA has attracted extensive attention. Both can serve as the potential biomarkers for the diagnosing and monitoring disease progression. Herein, we analyzed the basis and prospect of therapies for SCA. Meanwhile, we elaborated the development and application of miRNAs, siRNAs, shRNAs, and EVs in the diagnosis and treatment of SCA. We propose the combination of RNAi and EVs to avoid the adverse factors of their respective treatment and maximize the benefits of treatment through the technology of EVs loaded with RNA. Obviously, the combinational therapy of RNAi and EVs may more accurately diagnose and cure SCA.
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Affiliation(s)
- Yingying Ding
- Department of Histology and Embryology, Medical College, Shaoxing University, Shaoxing, Zhejiang, China
- Department of Clinical Medicine, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Yong Zhang
- Department of Histology and Embryology, Medical College, Shaoxing University, Shaoxing, Zhejiang, China
| | - Xuehong Liu
- Department of Histology and Embryology, Medical College, Shaoxing University, Shaoxing, Zhejiang, China
- *Correspondence: Xuehong Liu,
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Tingey M, Schnell SJ, Yu W, Saredy J, Junod S, Patel D, Alkurdi AA, Yang W. Technologies Enabling Single-Molecule Super-Resolution Imaging of mRNA. Cells 2022; 11:3079. [PMID: 36231040 PMCID: PMC9564294 DOI: 10.3390/cells11193079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/22/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
The transient nature of RNA has rendered it one of the more difficult biological targets for imaging. This difficulty stems both from the physical properties of RNA as well as the temporal constraints associated therewith. These concerns are further complicated by the difficulty in imaging endogenous RNA within a cell that has been transfected with a target sequence. These concerns, combined with traditional concerns associated with super-resolution light microscopy has made the imaging of this critical target difficult. Recent advances have provided researchers the tools to image endogenous RNA in live cells at both the cellular and single-molecule level. Here, we review techniques used for labeling and imaging RNA with special emphases on various labeling methods and a virtual 3D super-resolution imaging technique.
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Affiliation(s)
| | | | | | | | | | | | | | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
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Goel K, Ploski JE. RISC-y Business: Limitations of Short Hairpin RNA-Mediated Gene Silencing in the Brain and a Discussion of CRISPR/Cas-Based Alternatives. Front Mol Neurosci 2022; 15:914430. [PMID: 35959108 PMCID: PMC9362770 DOI: 10.3389/fnmol.2022.914430] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/16/2022] [Indexed: 11/23/2022] Open
Abstract
Manipulating gene expression within and outside the nervous system is useful for interrogating gene function and developing therapeutic interventions for a variety of diseases. Several approaches exist which enable gene manipulation in preclinical models, and some of these have been approved to treat human diseases. For the last couple of decades, RNA interference (RNAi) has been a leading technique to knockdown (i.e., suppress) specific RNA expression. This has been partly due to the technology's simplicity, which has promoted its adoption throughout biomedical science. However, accumulating evidence indicates that this technology can possess significant shortcomings. This review highlights the overwhelming evidence that RNAi can be prone to off-target effects and is capable of inducing cytotoxicity in some cases. With this in mind, we consider alternative CRISPR/Cas-based approaches, which may be safer and more reliable for gene knockdown. We also discuss the pros and cons of each approach.
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Affiliation(s)
- Kanishk Goel
- School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Jonathan E. Ploski
- Department of Neural and Behavioral Sciences, Penn State College of Medicine, Hershey, PA, United States
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Pena-Leon V, Folgueira C, Barja-Fernández S, Pérez-Lois R, Da Silva Lima N, Martin M, Heras V, Martinez-Martinez S, Valero P, Iglesias C, Duquenne M, Al-Massadi O, Beiroa D, Souto Y, Fidalgo M, Sowmyalakshmi R, Guallar D, Cunarro J, Castelao C, Senra A, González-Saenz P, Vázquez-Cobela R, Leis R, Sabio G, Mueller-Fielitz H, Schwaninger M, López M, Tovar S, Casanueva FF, Valjent E, Diéguez C, Prevot V, Nogueiras R, Seoane LM. Prolonged breastfeeding protects from obesity by hypothalamic action of hepatic FGF21. Nat Metab 2022; 4:901-917. [PMID: 35879461 PMCID: PMC9314260 DOI: 10.1038/s42255-022-00602-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 06/08/2022] [Indexed: 12/25/2022]
Abstract
Early-life determinants are thought to be a major factor in the rapid increase of obesity. However, while maternal nutrition has been extensively studied, the effects of breastfeeding by the infant on the reprogramming of energy balance in childhood and throughout adulthood remain largely unknown. Here we show that delayed weaning in rat pups protects them against diet-induced obesity in adulthood, through enhanced brown adipose tissue thermogenesis and energy expenditure. In-depth metabolic phenotyping in this rat model as well as in transgenic mice reveals that the effects of prolonged suckling are mediated by increased hepatic fibroblast growth factor 21 (FGF21) production and tanycyte-controlled access to the hypothalamus in adulthood. Specifically, FGF21 activates GABA-containing neurons expressing dopamine receptor 2 in the lateral hypothalamic area and zona incerta. Prolonged breastfeeding thus constitutes a protective mechanism against obesity by affecting long-lasting physiological changes in liver-to-hypothalamus communication and hypothalamic metabolic regulation.
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Affiliation(s)
- Veronica Pena-Leon
- Endocrine Physiopathology Group, Instituto de Investigación Sanitaria de Santiago de Compostela, Complejo Hospitalario Universitario de Santiago/SERGAS, Santiago de Compostela, Spain
- CIMUS, University of Santiago de Compostela-Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain
| | - Cintia Folgueira
- Endocrine Physiopathology Group, Instituto de Investigación Sanitaria de Santiago de Compostela, Complejo Hospitalario Universitario de Santiago/SERGAS, Santiago de Compostela, Spain
- CIMUS, University of Santiago de Compostela-Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain
- CIBEROBN Physiopathology of Obesity and Nutrition, ISCIII, Santiago de Compostela, Spain
| | - Silvia Barja-Fernández
- Endocrine Physiopathology Group, Instituto de Investigación Sanitaria de Santiago de Compostela, Complejo Hospitalario Universitario de Santiago/SERGAS, Santiago de Compostela, Spain
| | - Raquel Pérez-Lois
- Endocrine Physiopathology Group, Instituto de Investigación Sanitaria de Santiago de Compostela, Complejo Hospitalario Universitario de Santiago/SERGAS, Santiago de Compostela, Spain
- CIMUS, University of Santiago de Compostela-Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain
| | - Natália Da Silva Lima
- CIMUS, University of Santiago de Compostela-Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain
| | - Marion Martin
- Laboratory of Development and Plasticity of the Neuroendocrine Brain, Inserm, University of Lille, Lille, France
| | - Violeta Heras
- CIMUS, University of Santiago de Compostela-Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain
| | - Sara Martinez-Martinez
- CIMUS, University of Santiago de Compostela-Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain
| | - Paola Valero
- CIMUS, University of Santiago de Compostela-Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain
| | - Cristina Iglesias
- CIMUS, University of Santiago de Compostela-Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain
| | - Mannon Duquenne
- Laboratory of Development and Plasticity of the Neuroendocrine Brain, Inserm, University of Lille, Lille, France
| | - Omar Al-Massadi
- Endocrine Physiopathology Group, Instituto de Investigación Sanitaria de Santiago de Compostela, Complejo Hospitalario Universitario de Santiago/SERGAS, Santiago de Compostela, Spain
- CIBEROBN Physiopathology of Obesity and Nutrition, ISCIII, Santiago de Compostela, Spain
| | - Daniel Beiroa
- CIMUS, University of Santiago de Compostela-Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain
| | - Yara Souto
- CIMUS, University of Santiago de Compostela-Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain
| | - Miguel Fidalgo
- CIMUS, University of Santiago de Compostela-Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain
| | - Rasika Sowmyalakshmi
- Laboratory of Development and Plasticity of the Neuroendocrine Brain, Inserm, University of Lille, Lille, France
| | - Diana Guallar
- CIMUS, University of Santiago de Compostela-Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain
| | - Juan Cunarro
- CIMUS, University of Santiago de Compostela-Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain
| | - Cecilia Castelao
- Endocrine Physiopathology Group, Instituto de Investigación Sanitaria de Santiago de Compostela, Complejo Hospitalario Universitario de Santiago/SERGAS, Santiago de Compostela, Spain
- CIBEROBN Physiopathology of Obesity and Nutrition, ISCIII, Santiago de Compostela, Spain
| | - Ana Senra
- CIMUS, University of Santiago de Compostela-Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain
| | - Patricia González-Saenz
- Endocrine Physiopathology Group, Instituto de Investigación Sanitaria de Santiago de Compostela, Complejo Hospitalario Universitario de Santiago/SERGAS, Santiago de Compostela, Spain
| | - Rocío Vázquez-Cobela
- Pediatrics Department, GI Pediatric Nutrition, Galicia Research Unit for Development, Growth and Human Nutrition, Complejo Hospitalario Universitario de Santiago, Santiago de Compostela, Spain
| | - Rosaura Leis
- Pediatrics Department, GI Pediatric Nutrition, Galicia Research Unit for Development, Growth and Human Nutrition, Complejo Hospitalario Universitario de Santiago, Santiago de Compostela, Spain
| | | | - Helge Mueller-Fielitz
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany
| | - Markus Schwaninger
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany
| | - Miguel López
- CIMUS, University of Santiago de Compostela-Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain
- CIBEROBN Physiopathology of Obesity and Nutrition, ISCIII, Santiago de Compostela, Spain
| | - Sulay Tovar
- CIMUS, University of Santiago de Compostela-Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain
- CIBEROBN Physiopathology of Obesity and Nutrition, ISCIII, Santiago de Compostela, Spain
| | - Felipe F Casanueva
- CIBEROBN Physiopathology of Obesity and Nutrition, ISCIII, Santiago de Compostela, Spain
| | - Emmanuel Valjent
- IGF, University of Montpellier, CNRS, Inserm, Montpellier, France
| | - Carlos Diéguez
- CIMUS, University of Santiago de Compostela-Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain
- CIBEROBN Physiopathology of Obesity and Nutrition, ISCIII, Santiago de Compostela, Spain
| | - Vincent Prevot
- Laboratory of Development and Plasticity of the Neuroendocrine Brain, Inserm, University of Lille, Lille, France
| | - Rubén Nogueiras
- CIMUS, University of Santiago de Compostela-Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain.
- CIBEROBN Physiopathology of Obesity and Nutrition, ISCIII, Santiago de Compostela, Spain.
- Galician Agency of Innovation (GAIN), Xunta de Galicia, Santiago de Compostela, Spain.
| | - Luisa M Seoane
- Endocrine Physiopathology Group, Instituto de Investigación Sanitaria de Santiago de Compostela, Complejo Hospitalario Universitario de Santiago/SERGAS, Santiago de Compostela, Spain.
- CIBEROBN Physiopathology of Obesity and Nutrition, ISCIII, Santiago de Compostela, Spain.
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Casello SM, Flores RJ, Yarur HE, Wang H, Awanyai M, Arenivar MA, Jaime-Lara RB, Bravo-Rivera H, Tejeda HA. Neuropeptide System Regulation of Prefrontal Cortex Circuitry: Implications for Neuropsychiatric Disorders. Front Neural Circuits 2022; 16:796443. [PMID: 35800635 PMCID: PMC9255232 DOI: 10.3389/fncir.2022.796443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 04/27/2022] [Indexed: 01/08/2023] Open
Abstract
Neuropeptides, a diverse class of signaling molecules in the nervous system, modulate various biological effects including membrane excitability, synaptic transmission and synaptogenesis, gene expression, and glial cell architecture and function. To date, most of what is known about neuropeptide action is limited to subcortical brain structures and tissue outside of the central nervous system. Thus, there is a knowledge gap in our understanding of neuropeptide function within cortical circuits. In this review, we provide a comprehensive overview of various families of neuropeptides and their cognate receptors that are expressed in the prefrontal cortex (PFC). Specifically, we highlight dynorphin, enkephalin, corticotropin-releasing factor, cholecystokinin, somatostatin, neuropeptide Y, and vasoactive intestinal peptide. Further, we review the implication of neuropeptide signaling in prefrontal cortical circuit function and use as potential therapeutic targets. Together, this review summarizes established knowledge and highlights unknowns of neuropeptide modulation of neural function underlying various biological effects while offering insights for future research. An increased emphasis in this area of study is necessary to elucidate basic principles of the diverse signaling molecules used in cortical circuits beyond fast excitatory and inhibitory transmitters as well as consider components of neuropeptide action in the PFC as a potential therapeutic target for neurological disorders. Therefore, this review not only sheds light on the importance of cortical neuropeptide studies, but also provides a comprehensive overview of neuropeptide action in the PFC to serve as a roadmap for future studies in this field.
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Affiliation(s)
- Sanne M. Casello
- Unit on Neuromodulation and Synaptic Integration, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, United States
| | - Rodolfo J. Flores
- Unit on Neuromodulation and Synaptic Integration, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, United States
| | - Hector E. Yarur
- Unit on Neuromodulation and Synaptic Integration, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, United States
| | - Huikun Wang
- Unit on Neuromodulation and Synaptic Integration, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, United States
| | - Monique Awanyai
- Unit on Neuromodulation and Synaptic Integration, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, United States
| | - Miguel A. Arenivar
- Unit on Neuromodulation and Synaptic Integration, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, United States
| | - Rosario B. Jaime-Lara
- Unit on Neuromodulation and Synaptic Integration, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, United States
- National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, United States
| | - Hector Bravo-Rivera
- Unit on Neuromodulation and Synaptic Integration, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, United States
| | - Hugo A. Tejeda
- Unit on Neuromodulation and Synaptic Integration, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, United States
- *Correspondence: Hugo A. Tejeda,
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Yuan A, Wu P, Zhong Z, He Z, Li W. Long non-coding RNA Gm37494 alleviates osteoarthritis chondrocyte injury via the microRNA-181a-5p/GABRA1 axis. J Orthop Surg Res 2022; 17:304. [PMID: 35689264 PMCID: PMC9185876 DOI: 10.1186/s13018-022-03202-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/25/2022] [Indexed: 11/10/2022] Open
Abstract
Objective This study was conducted to investigate the effect of long non-coding RNA (lncRNA) Gm37494 on osteoarthritis (OA) and its related molecular mechanism. Methods The cartilage tissues were obtained from OA patients, and an OA mouse model was induced by the destabilization of the medial meniscus, followed by measurement of Gm37494, microRNA (miR)-181a-5p, GABRA1 mRNA, and the encoded GABAARα1 protein expression. Thereafter, a cellular model was induced by interleukin-1β (IL-1β) treatment in chondrocytes, followed by ectopic and silencing experiments. Chondrocyte proliferation was detected by CCK-8 and EdU assays, chondrocyte apoptosis by flow cytometry and western blot, and the levels of inflammatory factors by ELISA. The binding of Gm37494 to miR-181a-5p was evaluated by dual-luciferase reporter gene and RIP assays, and that of GABRA1 to miR-181a-5p by dual-luciferase reporter gene and RNA pull-down assays. Results OA patients and mice had decreased GABRA1 mRNA and GABAARα1 protein levels and elevated miR-181a-5p expression in cartilage tissues. Additionally, Gm37494 was poorly expressed in OA mice. Mechanistically, Gm37494 directly bound to and inversely modulated miR-181a-5p that negatively targeted GABRA1. In IL-1β-induced chondrocytes, Gm37494 overexpression enhanced cell proliferation and suppressed cell apoptosis and inflammation, whereas further miR-181a-5p up-regulation or GABRA1 silencing abolished these trends. Conclusions Conclusively, Gm37494 elevated GABRA1 expression by binding to miR-181a-5p, thus ameliorating OA-induced chondrocyte damage. Supplementary Information The online version contains supplementary material available at 10.1186/s13018-022-03202-5.
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Affiliation(s)
- Aidong Yuan
- Department of Joint and Sports Medicine, The First People's Hospital of Shaoguan City, No.3 Dongdi South Road, Zhenjiang District, Shaoguan, 512000, Guangdong, People's Republic of China.
| | - Penghuan Wu
- Department of Joint and Sports Medicine, The First People's Hospital of Shaoguan City, No.3 Dongdi South Road, Zhenjiang District, Shaoguan, 512000, Guangdong, People's Republic of China
| | - Zhinian Zhong
- Department of Joint and Sports Medicine, The First People's Hospital of Shaoguan City, No.3 Dongdi South Road, Zhenjiang District, Shaoguan, 512000, Guangdong, People's Republic of China
| | - Zhengyan He
- Department of Joint and Sports Medicine, The First People's Hospital of Shaoguan City, No.3 Dongdi South Road, Zhenjiang District, Shaoguan, 512000, Guangdong, People's Republic of China
| | - Wenhu Li
- Department of Joint and Sports Medicine, The First People's Hospital of Shaoguan City, No.3 Dongdi South Road, Zhenjiang District, Shaoguan, 512000, Guangdong, People's Republic of China
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Sun Z, Zhao S, Suo X, Dou Y. Sirt1 protects against hippocampal atrophy and its induced cognitive impairment in middle-aged mice. BMC Neurosci 2022; 23:33. [PMID: 35668361 PMCID: PMC9169381 DOI: 10.1186/s12868-022-00718-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 05/23/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sirtuin 1 (Sirt1) is a recognized longevity gene and has been shown to be associated with aging and its related diseases. Hippocampal volume is considered to be the most sensitive brain imaging phenotype for cognition, but the effect of Sirt1 on hippocampal morphology during aging has not been reported. RESULTS Herein, we investigated the effect of conditional Sirt1 knockdown on hippocampal volume in middle-aged mice, as well as its cognitive function and the underlying molecular mechanisms. Brain structural magnetic resonance imaging (MRI) showed that adeno-associated virus (AAV) mediated hippocampal Sirt1 knockdown caused hippocampal atrophy in 8-month-old mice. Open field test (OFT) and Morris Water Maze (MWM) test revealed that hippocampal Sirt1 knockdown significantly weakened spatial learning and memory of mice without effect on anxiety and exploratory behavior. Western blotting analysis showed that P-tau levels at serine 396 epitope were significantly increased with slightly decreased T-tau levels, while PSD95 and NMDAR2B levels were obviously reduced, indicating that hippocampal Sirt1 knockdown could activate tau hyperphosphorylation and synaptic damage. CONCLUSIONS This work revealed that Sirt1 is an important protective gene against hippocampal atrophy and its induced cognitive impairment during aging, providing potential therapeutic targets for the prevention and intervention of aging-related neuropsychic diseases.
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Affiliation(s)
- Zuhao Sun
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin, 300052, People's Republic of China.,School of Medical Technology, Tianjin Medical University, Tianjin, 300070, People's Republic of China
| | - Shuang Zhao
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin, 300052, People's Republic of China
| | - Xinjun Suo
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin, 300052, People's Republic of China.,School of Medical Technology, Tianjin Medical University, Tianjin, 300070, People's Republic of China
| | - Yan Dou
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin, 300052, People's Republic of China.
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Wei Z, Zhou H, Fei W, Nie X, Li M. Effect of SOX2 gene on the biological characteristics of salivary adenoid cystic carcinoma cells. HUA XI KOU QIANG YI XUE ZA ZHI = HUAXI KOUQIANG YIXUE ZAZHI = WEST CHINA JOURNAL OF STOMATOLOGY 2022; 40:341-349. [PMID: 38597017 PMCID: PMC9207786 DOI: 10.7518/hxkq.2022.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 10/14/2021] [Indexed: 01/24/2023]
Abstract
OBJECTIVES This study aimed to investigate the effect of transfecting SOX2-shRNA vector lentivirus to SACC cell lines on the biological behavior of salivary adenoid cystic carcinoma (SACC)-LM and SACC-83. METHODS Three types of SOX2-shRNA lentiviral vectors (817, 818, and 819) were constructed and transfected successfully. The shRNA with the best inhibitory effect was screened out and transfected into SACC cells. Real-time fluorescence quantitative polymerase chain reaction (RT-qPCR) and Western blot were used to detect the expressions of Survivin, E-cadherin, and N-cadherin of SACC-LM and SACC-83. CCK-8 and flow cytometry were used to detect SACC-LM and SACC-83 proliferation and apoptosis. Cell scratch test and Transwell method were used to detect the migration and invasion capabilities of SACC-LM and SACC-83. RESULTS SOX2-shRNA-819 had the best interference effect among the three lentiviruses. After transfecting SOX2-shRNA-819 into SACC-LM and SACC-83, the expressions of SOX2, Survivin, and N-cadherin were significantly reduced, and that of E-cadherin was significantly increased (P<0.05). The cell proliferation ability decreased, and the number of apoptotic cells increased (P<0.05). The cell migration and invasion ability decreased (P<0.05). CONCLUSIONS shRNA interference technology reduced SOX2 expression while downregulating Survivin expression. These two expressions may be related. Low SOX2 expression inhibits the proliferation, migration, and invasion of SACC cells and promotes the apoptosis of SACC cells. SOX2 may be involved in the epithelial⁃mesenchymal transition process. This study provided a relevant theoretical basis for targeting SOX2 gene therapy in SACC.
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Affiliation(s)
- Zhuo Wei
- Dept. of Stomatology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu 610072, China
- School of Stomatology, North Sichuan Medical College, Nanchong 637000, China
| | - Hao Zhou
- Dept. of Stomatology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu 610072, China
| | - Wei Fei
- Dept. of Stomatology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu 610072, China
- School of Stomatology, North Sichuan Medical College, Nanchong 637000, China
| | - Xiong Nie
- School of Stomatology, North Sichuan Medical College, Nanchong 637000, China
| | - Mingfang Li
- School of Stomatology, North Sichuan Medical College, Nanchong 637000, China
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Secondary structure RNA elements control the cleavage activity of DICER. Nat Commun 2022; 13:2138. [PMID: 35440644 PMCID: PMC9018771 DOI: 10.1038/s41467-022-29822-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 03/23/2022] [Indexed: 12/05/2022] Open
Abstract
The accurate and efficient cleavage of shRNAs and pre-miRNAs by DICER is crucial for their gene-silencing activity. Here, we conduct high-throughput DICER cleavage assays for more than ~20,000 different shRNAs and show the comprehensive cleavage activities of DICER on these sequences. We discover a single-nucleotide bulge (22-bulge), which facilitates the cleavage activity of DICER on shRNAs and human pre-miRNAs. As a result, this 22-bulge enhances the gene-silencing activity of shRNAs and the accuracy of miRNA biogenesis. In addition, various single-nucleotide polymorphism-edited 22-bulges are found to govern the cleavage sites of DICER on pre-miRNAs and thereby control their functions. Finally, we identify the single cleavage of DICER and reveal its molecular mechanism. Our findings improve the understanding of the DICER cleavage mechanism, provide a foundation for the design of accurate and efficient shRNAs for gene-silencing, and indicate the function of bulges in regulating miRNA biogenesis. MicroRNA precursors are cleaved by DICER to generate mature microRNAs in the cytoplasm. Here the authors employ high-throughput analysis of DICER cleavage activity and identify RNA secondary elements in precursor miRNAs and shRNAs, including a single nucleotide bulge, which govern its cleavage efficiency and accuracy.
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Targeting non-coding RNAs to overcome cancer therapy resistance. Signal Transduct Target Ther 2022; 7:121. [PMID: 35418578 PMCID: PMC9008121 DOI: 10.1038/s41392-022-00975-3] [Citation(s) in RCA: 143] [Impact Index Per Article: 71.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 03/07/2022] [Accepted: 03/07/2022] [Indexed: 02/07/2023] Open
Abstract
It is now well known that non-coding RNAs (ncRNAs), rather than protein-coding transcripts, are the preponderant RNA transcripts. NcRNAs, particularly microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), are widely appreciated as pervasive regulators of multiple cancer hallmarks such as proliferation, apoptosis, invasion, metastasis, and genomic instability. Despite recent discoveries in cancer therapy, resistance to chemotherapy, radiotherapy, targeted therapy, and immunotherapy continue to be a major setback. Recent studies have shown that ncRNAs also play a major role in resistance to different cancer therapies by rewiring essential signaling pathways. In this review, we present the intricate mechanisms through which dysregulated ncRNAs control resistance to the four major types of cancer therapies. We will focus on the current clinical implications of ncRNAs as biomarkers to predict treatment response (intrinsic resistance) and to detect resistance to therapy after the start of treatment (acquired resistance). Furthermore, we will present the potential of targeting ncRNA to overcome cancer treatment resistance, and we will discuss the challenges of ncRNA-targeted therapy—especially the development of delivery systems.
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Bharathkumar N, Sunil A, Meera P, Aksah S, Kannan M, Saravanan KM, Anand T. CRISPR/Cas-Based Modifications for Therapeutic Applications: A Review. Mol Biotechnol 2022; 64:355-372. [PMID: 34741732 PMCID: PMC8571677 DOI: 10.1007/s12033-021-00422-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/28/2021] [Indexed: 12/11/2022]
Abstract
The CRISPR-Cas genome editing system is an intrinsic property of a bacteria-based immune system. This employs a guide RNA to detect and cleave the PAM-associated target DNA or RNA in subsequent infections, by the invasion of a similar bacteriophage. The discovery of Cas systems has paved the way to overcome the limitations of existing genome editing tools. In this review, we focus on Cas proteins that are available for gene modifications among which Cas9, Cas12a, and Cas13 have been widely used in the areas of medicine, research, and diagnostics. Since CRISPR has been already proven for its potential research applications, the next milestone for CRISPR will be proving its efficacy and safety. In this connection, we systematically review recent advances in exploring multiple variants of Cas proteins and their modifications for therapeutic applications.
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Affiliation(s)
| | - Abraham Sunil
- Department of Animal Behavior and Physiology, Madurai Kamaraj University, Madurai, Tamil Nadu India
| | - Prabhakar Meera
- B Aatral Biosciences Private Limited, Bangalore, Karnataka India
| | - Sam Aksah
- B Aatral Biosciences Private Limited, Bangalore, Karnataka India
| | - Muthu Kannan
- B Aatral Biosciences Private Limited, Bangalore, Karnataka India
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Quinzo MJ, Perteguer MJ, Brindley PJ, Loukas A, Sotillo J. Transgenesis in parasitic helminths: a brief history and prospects for the future. Parasit Vectors 2022; 15:110. [PMID: 35346328 PMCID: PMC8962113 DOI: 10.1186/s13071-022-05211-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/18/2022] [Indexed: 12/15/2022] Open
Abstract
Helminth infections impact the health of hundreds of millions of persons globally and also cause important economic losses in livestock farming. Methodological limitations as well as the low attention given to the study of helminths have impacted biological research and, thus, the procurement of accurate diagnosis and effective treatments. Understanding the biology of helminths using genomic and proteomic approaches could contribute to advances in understanding host-helminth interactions and lead to new vaccines, drugs and diagnostics. Despite the significant advances in genomics in the last decade, the lack of methodological adaptation of current transgenesis techniques has hampered the progression of post-genomic research in helminthology. However, the application of new techniques, such as CRISPR, to the study of trematodes and nematodes has opened new avenues for genome editing-powered functional genomics for these pathogens. This review summarises the historical advances in functional genomics in parasitic helminths and highlights pending limitations that will need to be overcome to deploy transgenesis tools.
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Affiliation(s)
- M J Quinzo
- Parasitology Reference and Research Laboratory, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- Escuela Internacional de Doctorado, Universidad Nacional de Educación a Distancia (UNED), Madrid, Spain
| | - M J Perteguer
- Parasitology Reference and Research Laboratory, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - P J Brindley
- Department of Microbiology, Immunology and Tropical Medicine, and Research Center for Neglected Diseases of Poverty, School of Medicine and Health Sciences, George Washington University, Washington, DC, 20037, USA
| | - A Loukas
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - J Sotillo
- Parasitology Reference and Research Laboratory, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
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Liu W, Zhong W, Chen J, Huang B, Hu M, Li Y. Understanding Regulatory Mechanisms of Brain Function and Disease through 3D Genome Organization. Genes (Basel) 2022; 13:586. [PMID: 35456393 PMCID: PMC9027261 DOI: 10.3390/genes13040586] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/17/2022] [Accepted: 03/23/2022] [Indexed: 02/01/2023] Open
Abstract
The human genome has a complex and dynamic three-dimensional (3D) organization, which plays a critical role for gene regulation and genome function. The importance of 3D genome organization in brain development and function has been well characterized in a region- and cell-type-specific fashion. Recent technological advances in chromosome conformation capture (3C)-based techniques, imaging approaches, and ligation-free methods, along with computational methods to analyze the data generated, have revealed 3D genome features at different scales in the brain that contribute to our understanding of genetic mechanisms underlying neuropsychiatric diseases and other brain-related traits. In this review, we discuss how these advances aid in the genetic dissection of brain-related traits.
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Affiliation(s)
- Weifang Liu
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (W.L.); (J.C.)
| | - Wujuan Zhong
- Biostatistics and Research Decision Sciences, Merck & Co., Inc., Rahway, NJ 07065, USA;
| | - Jiawen Chen
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (W.L.); (J.C.)
| | - Bo Huang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA;
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
| | - Yun Li
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (W.L.); (J.C.)
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Srivastava R, Sarkar K, Bonnerjee D, Bagh S. Synthetic Genetic Reversible Feynman Gate in a Single E. coli Cell and Its Application in Bacterial to Mammalian Cell Information Transfer. ACS Synth Biol 2022; 11:1040-1048. [PMID: 35179369 DOI: 10.1021/acssynbio.1c00392] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Reversible computing is a nonconventional form of computing where the inputs and outputs are mapped in a unique one-to-one fashion. Reversible logic gates in single living cells have not been demonstrated. Here, we constructed a synthetic genetic reversible Feynman gate in single E. coli cells, and the input-output relations were measured in a clonal population. The inputs were extracellular chemicals, isopropyl β-d-1-thiogalactopyranoside (IPTG), and anhydrotetracycline (aTc), and the outputs were two fluorescence proteins. We developed a simple mathematical model and simulation to capture the essential features of the circuit and experimentally demonstrated that the behavior of the circuit was ultrasensitive and predictive. We showed an application by creating an intercellular Feynman gate, where input information from bacteria was computed and transferred to HeLa cells through shRNAs delivery and the output signals were observed as silencing of native AKT1 and CTNNB1 genes. The introduction of reversible logics in synthetic biology is new, and given that one-to-one input-output mapping, such reversible genetic systems might have applications in sensing, diagnostics, cellular computing, and synthetic biology.
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Affiliation(s)
- Rajkamal Srivastava
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute (HBNI), Block A/F, Sector-I, Bidhannagar, Kolkata 700064, India
| | - Kathakali Sarkar
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute (HBNI), Block A/F, Sector-I, Bidhannagar, Kolkata 700064, India
| | - Deepro Bonnerjee
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute (HBNI), Block A/F, Sector-I, Bidhannagar, Kolkata 700064, India
| | - Sangram Bagh
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute (HBNI), Block A/F, Sector-I, Bidhannagar, Kolkata 700064, India
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Wang TN, Hu XG, Chen GX. Uses of knockout, knockdown, and transgenic models in the studies of glucose transporter 4. World J Meta-Anal 2022; 10:1-11. [DOI: 10.13105/wjma.v10.i1.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/10/2021] [Accepted: 02/23/2022] [Indexed: 02/06/2023] Open
Abstract
Currently, glucose transporter 4 (GLUT4) has been considered as the key player for the insulin-stimulated glucose transport in the muscle and adipose tissues. The development of recombinant DNA techniques allows the creations of genetically knockout, knockdown and transgenic animals and cells for the study of GLUT4’s physiological functions. Here, we have used key words to search the PubMed and summarized the methods used in Slc2a4 gene knockout, GLUT4 knockdown and overexpression in the whole body and tissue specific manner. The whole body GLUT4-null mice have growth retardation, but normal glucose tolerance and basal glucose turnover rates. Compared with whole body Slc2a4 knockout mice, adipose and muscle double knockout mice have impaired insulin tolerance and glucose intolerance. The results of GLUT4 knockdown in 3T3-L1 adipocytes have shown that its expression is needed for lipogenesis after, but not during, differentiation. Transgenic mice with the whole body GLUT4 overexpression have normal body weight and lowered blood glucose level. The adipose tissue specific overexpression of GLUT4 leads to increases in mouse body weight and adipose tissue weight. The insulin-stimulated GLUT4 translocation in the skeletal muscle contributes to the regulation of glucose homeostasis. Data from both transgenic overexpression and tissue specific Slc2a4 knockout indicate that GLUT4 probably plays a role in the glucose uptake in the fasting state. More studies are warranted to use advanced molecular biology tools to decipher the roles of GLUT4 in the control of glucose homeostasis.
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Affiliation(s)
- Tian-Nan Wang
- Department of Nutrition, The University of Tennessee, Knoxville, TN 37996, United States
| | - Xin-Ge Hu
- Department of Nutrition, The University of Tennessee, Knoxville, TN 37996, United States
| | - Guo-Xun Chen
- Department of Nutrition, The University of Tennessee, Knoxville, TN 37996, United States
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