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Yildiz SN, Entezari M, Paskeh MDA, Mirzaei S, Kalbasi A, Zabolian A, Hashemi F, Hushmandi K, Hashemi M, Raei M, Goharrizi MASB, Aref AR, Zarrabi A, Ren J, Orive G, Rabiee N, Ertas YN. Nanoliposomes as nonviral vectors in cancer gene therapy. MedComm (Beijing) 2024; 5:e583. [PMID: 38919334 PMCID: PMC11199024 DOI: 10.1002/mco2.583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 04/19/2024] [Accepted: 04/26/2024] [Indexed: 06/27/2024] Open
Abstract
Nonviral vectors, such as liposomes, offer potential for targeted gene delivery in cancer therapy. Liposomes, composed of phospholipid vesicles, have demonstrated efficacy as nanocarriers for genetic tools, addressing the limitations of off-targeting and degradation commonly associated with traditional gene therapy approaches. Due to their biocompatibility, stability, and tunable physicochemical properties, they offer potential in overcoming the challenges associated with gene therapy, such as low transfection efficiency and poor stability in biological fluids. Despite these advancements, there remains a gap in understanding the optimal utilization of nanoliposomes for enhanced gene delivery in cancer treatment. This review delves into the present state of nanoliposomes as carriers for genetic tools in cancer therapy, sheds light on their potential to safeguard genetic payloads and facilitate cell internalization alongside the evolution of smart nanocarriers for targeted delivery. The challenges linked to their biocompatibility and the factors that restrict their effectiveness in gene delivery are also discussed along with exploring the potential of nanoliposomes in cancer gene therapy strategies by analyzing recent advancements and offering future directions.
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Affiliation(s)
| | - Maliheh Entezari
- Department of GeneticsFaculty of Advanced Science and TechnologyTehran Medical SciencesIslamic Azad UniversityTehranIran
- Department of Medical Convergence SciencesFarhikhtegan Hospital Tehran Medical SciencesIslamic Azad UniversityTehranIran
| | - Mahshid Deldar Abad Paskeh
- Department of GeneticsFaculty of Advanced Science and TechnologyTehran Medical SciencesIslamic Azad UniversityTehranIran
- Department of Medical Convergence SciencesFarhikhtegan Hospital Tehran Medical SciencesIslamic Azad UniversityTehranIran
| | - Sepideh Mirzaei
- Department of BiologyFaculty of ScienceIslamic Azad UniversityScience and Research BranchTehranIran
| | - Alireza Kalbasi
- Department of PharmacyBrigham and Women's HospitalHarvard Medical SchoolBostonMassachusettsUSA
| | - Amirhossein Zabolian
- Department of OrthopedicsShahid Beheshti University of Medical SciencesTehranIran
| | - Farid Hashemi
- Department of Comparative BiosciencesFaculty of Veterinary MedicineUniversity of TehranTehranIran
| | - Kiavash Hushmandi
- Department of Clinical Sciences InstituteNephrology and Urology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | - Mehrdad Hashemi
- Department of GeneticsFaculty of Advanced Science and TechnologyTehran Medical SciencesIslamic Azad UniversityTehranIran
- Department of Medical Convergence SciencesFarhikhtegan Hospital Tehran Medical SciencesIslamic Azad UniversityTehranIran
| | - Mehdi Raei
- Department of Epidemiology and BiostatisticsSchool of HealthBaqiyatallah University of Medical SciencesTehranIran
| | | | - Amir Reza Aref
- Belfer Center for Applied Cancer ScienceDana‐Farber Cancer InstituteHarvard Medical SchoolBostonMassachusettsUSA
- Department of Translational SciencesXsphera Biosciences Inc.BostonMassachusettsUSA
| | - Ali Zarrabi
- Department of Biomedical EngineeringFaculty of Engineering and Natural SciencesIstinye UniversityIstanbulTurkey
| | - Jun Ren
- Shanghai Institute of Cardiovascular DiseasesDepartment of CardiologyZhongshan HospitalFudan UniversityShanghaiChina
| | - Gorka Orive
- NanoBioCel Research GroupSchool of PharmacyUniversity of the Basque Country (UPV/EHU)Vitoria‐GasteizSpain
- University Institute for Regenerative Medicine and Oral Implantology ‐ UIRMI (UPV/EHU‐Fundación Eduardo Anitua)Vitoria‐GasteizSpain
- Bioaraba, NanoBioCel Research GroupVitoria‐GasteizSpain
- The AcademiaSingapore Eye Research InstituteSingaporeSingapore
| | - Navid Rabiee
- Centre for Molecular Medicine and Innovative TherapeuticsMurdoch UniversityPerthWestern AustraliaAustralia
| | - Yavuz Nuri Ertas
- Department of Biomedical EngineeringErciyes UniversityKayseriTurkey
- ERNAM—Nanotechnology Research and Application CenterErciyes UniversityKayseriTurkey
- UNAM−National Nanotechnology Research CenterBilkent UniversityAnkaraTurkey
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2
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Di Meo D, Kundu T, Ravindran P, Shah B, Püschel AW. Pip5k1γ regulates axon formation by limiting Rap1 activity. Life Sci Alliance 2024; 7:e202302383. [PMID: 38438249 PMCID: PMC10912816 DOI: 10.26508/lsa.202302383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 03/06/2024] Open
Abstract
During their differentiation, neurons establish a highly polarized morphology by forming axons and dendrites. Cortical and hippocampal neurons initially extend several short neurites that all have the potential to become an axon. One of these neurites is then selected as the axon by a combination of positive and negative feedback signals that promote axon formation and prevent the remaining neurites from developing into axons. Here, we show that Pip5k1γ is required for the formation of a single axon as a negative feedback signal that regulates C3G and Rap1 through the generation of phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2). Impairing the function of Pip5k1γ results in a hyper-activation of the Fyn/C3G/Rap1 pathway, which induces the formation of supernumerary axons. Application of a hyper-osmotic shock to modulate membrane tension has a similar effect, increasing Rap1 activity and inducing the formation of supernumerary axons. In both cases, the induction of supernumerary axons can be reverted by expressing constitutively active Pip5k. Our results show that PI(4,5)P2-dependent membrane properties limit the activity of C3G and Rap1 to ensure the extension of a single axon.
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Affiliation(s)
- Danila Di Meo
- https://ror.org/00pd74e08 Institut für Integrative Zellbiologie und Physiologie, Universität Münster, Münster, Germany
- https://ror.org/00pd74e08 Cells-in-Motion Interfaculty Center, University of Münster, Münster, Germany
| | - Trisha Kundu
- https://ror.org/00pd74e08 Institut für Integrative Zellbiologie und Physiologie, Universität Münster, Münster, Germany
- https://ror.org/00pd74e08 Cells-in-Motion Interfaculty Center, University of Münster, Münster, Germany
| | - Priyadarshini Ravindran
- https://ror.org/00pd74e08 Institut für Integrative Zellbiologie und Physiologie, Universität Münster, Münster, Germany
| | - Bhavin Shah
- https://ror.org/00pd74e08 Institut für Integrative Zellbiologie und Physiologie, Universität Münster, Münster, Germany
| | - Andreas W Püschel
- https://ror.org/00pd74e08 Institut für Integrative Zellbiologie und Physiologie, Universität Münster, Münster, Germany
- https://ror.org/00pd74e08 Cells-in-Motion Interfaculty Center, University of Münster, Münster, Germany
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3
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Abstract
Mouse models of colorectal cancer (CRC) have been crucial in the identification of the role of genes responsible for the full range of pathology of the human disease and have proved to be dependable for testing anti-cancer drugs. Recent research points toward the relevance of tumor, angiogenic, and immune microenvironments in CRC progression to late-stage disease, as well as the treatment of it. This study examines important mouse models in CRC, discussing inherent strengths and weaknesses disclosed during their construction. It endeavors to provide both a synopsis of previous work covering how investigators have defined various models and to evaluate critically how researchers are most likely to use them in the future. Accumulated evidence regarding the metastatic process and the hope of using checkpoint inhibitors and immunological inhibitor therapies points to the need for a genetically engineered mouse model that is both immunocompetent and autochthonous.
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Affiliation(s)
- Melanie Haas Kucherlapati
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Boston, MA, USA
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4
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Semple SL, Au SKW, Jacob RA, Mossman KL, DeWitte-Orr SJ. Discovery and Use of Long dsRNA Mediated RNA Interference to Stimulate Antiviral Protection in Interferon Competent Mammalian Cells. Front Immunol 2022; 13:859749. [PMID: 35603190 PMCID: PMC9120774 DOI: 10.3389/fimmu.2022.859749] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/04/2022] [Indexed: 12/20/2022] Open
Abstract
In invertebrate cells, RNA interference (RNAi) acts as a powerful immune defense that stimulates viral gene knockdown thereby preventing infection. With this pathway, virally produced long dsRNA (dsRNA) is cleaved into short interfering RNA (siRNA) by Dicer and loaded into the RNA-induced silencing complex (RISC) which can then destroy/disrupt complementary viral mRNA sequences. Comparatively, in mammalian cells it is believed that the type I interferon (IFN) pathway is the cornerstone of the innate antiviral response. In these cells, dsRNA acts as a potent inducer of the IFN system, which is dependent on dsRNA length, but not sequence, to stimulate an antiviral state. Although the cellular machinery for RNAi is intact and functioning in mammalian cells, its role to trigger an antiviral response using long dsRNA (dsRNAi) remains controversial. Here we show that dsRNAi is not only functional but has a significant antiviral effect in IFN competent mammalian cells. We found that pre-soaking mammalian cells with concentrations of sequence specific dsRNA too low to induce IFN production could significantly inhibit vesicular stomatitis virus expressing green fluorescent protein (VSV-GFP), and the human coronaviruses (CoV) HCoV-229E and SARS-CoV-2 replication. This phenomenon was shown to be dependent on dsRNA length, was comparable in effect to transfected siRNAs, and could knockdown multiple sequences at once. Additionally, knockout cell lines revealed that functional Dicer was required for viral inhibition, revealing that the RNAi pathway was indeed responsible. These results provide the first evidence that soaking with gene-specific long dsRNA can generate viral knockdown in mammalian cells. We believe that this novel discovery provides an explanation as to why the mammalian lineage retained its RNAi machinery and why vertebrate viruses have evolved methods to suppress RNAi. Furthermore, demonstrating RNAi below the threshold of IFN induction has uses as a novel therapeutic platform, both antiviral and gene targeting in nature.
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Affiliation(s)
- Shawna L. Semple
- Department of Health Sciences, Wilfrid Laurier University, Waterloo, ON, Canada
| | - Sarah K. W. Au
- Department of Health Sciences, Wilfrid Laurier University, Waterloo, ON, Canada
| | - Rajesh A. Jacob
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
| | - Karen L. Mossman
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
| | - Stephanie J. DeWitte-Orr
- Department of Health Sciences, Wilfrid Laurier University, Waterloo, ON, Canada
- *Correspondence: Stephanie J. DeWitte-Orr,
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Use of PepFect14 and siRNA for Targeted Gene Silencing in Human Embryonic Stem Cells. Methods Mol Biol 2021. [PMID: 34766315 DOI: 10.1007/978-1-0716-1752-6_37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The unique properties of human embryonic stem (hES) cells render them invaluable for many scientific and clinical endeavors. Wider application of hES cells requires a comprehensive understanding of their biology that can be dissected using RNA interference-based gene silencing. However, commonly used transfection methods to deliver nucleic acids into a cell often lead to differentiation of hES cells. For that reason, effective transfection technique with minimal side effects is essential for studying and employing hES cells. Here, we describe a CPP-based method for targeted gene silencing in hES cells using siRNA complexed with PepFect 14 (PF14). This approach results in effective downregulation of mRNA and protein levels of a target gene without adverse effects on cell viability and pluripotency.
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6
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Khelghati N, Soleimanpour Mokhtarvand J, Mir M, Alemi F, Asemi Z, Sadeghpour A, Maleki M, Samadi Kafil H, Jadidi-Niaragh F, Majidinia M, Yousefi B. The importance of co-delivery of nanoparticle-siRNA and anticancer agents in cancer therapy. Chem Biol Drug Des 2021; 97:997-1015. [PMID: 33458952 DOI: 10.1111/cbdd.13824] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/10/2021] [Indexed: 01/12/2023]
Abstract
According to global statistics, cancer is the second leading cause of death worldwide. Because of the heterogeneity of cancer, single-drug therapy has many limitations due to low efficacy. Therefore, combination therapy with two or more therapeutic agents is being arisen. One of the most important approaches in cancer therapy is the shot down of key genes involved in apoptotic processes and cell cycle. In this regard, siRNA is a good candidate, a highly attractive method to suppressing tumor growth and invasion. Combination therapy with siRNAs and chemotherapeutic agents can overcome the multidrug resistance and increase apoptosis. The efficient delivery of siRNA to the target cell/tissue/organ has been a challenge. To overcome these challenges, the presence of suitable delivery systems by using nanoparticles is interesting. In this review, we discuss the current challenges for successful RNA interference. Also, we suggested proper a strategy for delivering siRNA that can be useful in targeting therapy. Finally, the combination of a variety of anticancer drugs and siRNA through acceptable delivery systems and their effects on cell cycle and apoptosis will be evaluated.
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Affiliation(s)
- Nafiseh Khelghati
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Mostafa Mir
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Forough Alemi
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Science, Tabriz, Iran
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran
| | - Alireza Sadeghpour
- Department of Orthopedic Surgery, School of Medicine and Shohada Educational Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Masomeh Maleki
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Science, Tabriz, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Maryam Majidinia
- Solid Tumor Research Center, Urmia University of Medical Sciences, Urmia, Iran
| | - Bahman Yousefi
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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Bagheri HS, Karimipour M, Heidarzadeh M, Rajabi H, Sokullu E, Rahbarghazi R. Does the Global Outbreak of COVID-19 or Other Viral Diseases Threaten the Stem Cell Reservoir Inside the Body? Stem Cell Rev Rep 2021; 17:214-230. [PMID: 33403490 PMCID: PMC7785129 DOI: 10.1007/s12015-020-10108-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2020] [Indexed: 12/20/2022]
Abstract
The COVID-19 pandemic has profoundly influenced public health and contributed to global economic divergences of unprecedented dimensions. Due to the high prevalence and mortality rates, it is then expected that the consequence and public health challenges will last for long periods. The rapid global spread of COVID-19 and lack of enough data regarding the virus pathogenicity multiplies the complexity and forced governments to react quickly against this pandemic. Stem cells represent a small fraction of cells located in different tissues. These cells play a critical role in the regeneration and restoration of injured sites. Because of their specific niche and a limited number of stem cells, the key question is whether there are different anti-viral mechanisms against viral infection notably COVID-19. Here, we aimed to highlight the intrinsic antiviral resistance in different stem cells against viral infection. These data could help us to understand the possible viral infections in different stem cells and the activation of specific molecular mechanisms upon viral entrance.
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Affiliation(s)
| | - Mohammad Karimipour
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Morteza Heidarzadeh
- Koç University Translational Medicine Research Center (KUTTAM) Rumeli Feneri, Sarıyer, Istanbul, Turkey
| | - Hadi Rajabi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Emel Sokullu
- Koç University Translational Medicine Research Center (KUTTAM) Rumeli Feneri, Sarıyer, Istanbul, Turkey. .,School of Medicine, Biophysics Department, Koç University, Rumeli Fener, Sarıyer, Istanbul, Turkey.
| | - Reza Rahbarghazi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran. .,Department of Applied Cell Sciences, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.
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8
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Zabel MD, Mollnow L, Bender H. siRNA Therapeutics for Protein Misfolding Diseases of the Central Nervous System. Methods Mol Biol 2021; 2282:377-394. [PMID: 33928585 DOI: 10.1007/978-1-0716-1298-9_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Nanoparticles have been used to deliver siRNA to tissues and cells to silence specific genes in diverse organisms. Research and clinical application of nanoparticles like liposomes for drug delivery requires targeting them to specific anatomic regions or cell types, while avoiding off-target effects or clearance by the liver, kidney, or the immune system. Delivery to the central nervous system (CNS) presents additional challenges to cross the blood-brain barrier (BBB) to specific cell types like neurons, astrocytes, or glia. Here, we describe the generation of three different liposomal siRNA delivery vehicles to the CNS using the thin film hydration method. Utilizing cationic or anionic liposomes protects the siRNA from serum nucleases and proteases en route. To deliver the siRNA specifically to the CNS, the liposomes are complexed to a peptide that acts as a neuronal address by binding to nicotinic acetylcholine receptors (nAchRs). When injected intravenously or instilled intranasally, these liposome-siRNA-peptide complexes (LSPCs) or peptide addressed liposome-encapsulated therapeutic siRNA (PALETS) resist serum degradation, effectively cross the BBB, and deliver siRNA to AchR-expressing cells to suppress protein expression in the CNS.
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Affiliation(s)
- Mark D Zabel
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.
| | - Luke Mollnow
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Heather Bender
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
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Sundara Rajan S, Ludwig KR, Hall KL, Jones TL, Caplen NJ. Cancer biology functional genomics: From small RNAs to big dreams. Mol Carcinog 2020; 59:1343-1361. [PMID: 33043516 PMCID: PMC7702050 DOI: 10.1002/mc.23260] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 09/23/2020] [Indexed: 12/14/2022]
Abstract
The year 2021 marks the 20th anniversary of the first publications reporting the discovery of the gene silencing mechanism, RNA interference (RNAi) in mammalian cells. Along with the many studies that delineated the proteins and substrates that form the RNAi pathway, this finding changed our understanding of the posttranscriptional regulation of mammalian gene expression. Furthermore, the development of methods that exploited the RNAi pathway began the technological revolution that eventually enabled the interrogation of mammalian gene function-from a single gene to the whole genome-in only a few days. The needs of the cancer research community have driven much of this progress. In this perspective, we highlight milestones in the development and application of RNAi-based methods to study carcinogenesis. We discuss how RNAi-based functional genetic analysis of exemplar tumor suppressors and oncogenes furthered our understanding of cancer initiation and progression and explore how such studies formed the basis of genome-wide scale efforts to identify cancer or cancer-type specific vulnerabilities, including studies conducted in vivo. Furthermore, we examine how RNAi technologies have revealed new cancer-relevant molecular targets and the implications for cancer of the first RNAi-based drugs. Finally, we discuss the future of functional genetic analysis, highlighting the increasing availability of complementary approaches to analyze cancer gene function.
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Affiliation(s)
- Soumya Sundara Rajan
- Functional Genetics Section, Genetics BranchCenter for Cancer Research, National Cancer Institute, NIHBethesdaMarylandUSA
| | - Katelyn R. Ludwig
- Functional Genetics Section, Genetics BranchCenter for Cancer Research, National Cancer Institute, NIHBethesdaMarylandUSA
| | - Katherine L. Hall
- Functional Genetics Section, Genetics BranchCenter for Cancer Research, National Cancer Institute, NIHBethesdaMarylandUSA
| | - Tamara L. Jones
- Functional Genetics Section, Genetics BranchCenter for Cancer Research, National Cancer Institute, NIHBethesdaMarylandUSA
| | - Natasha J. Caplen
- Functional Genetics Section, Genetics BranchCenter for Cancer Research, National Cancer Institute, NIHBethesdaMarylandUSA
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10
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Han Q, Chen G, Wang J, Jee D, Li WX, Lai EC, Ding SW. Mechanism and Function of Antiviral RNA Interference in Mice. mBio 2020; 11:e03278-19. [PMID: 32753500 PMCID: PMC7407090 DOI: 10.1128/mbio.03278-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 07/02/2020] [Indexed: 12/18/2022] Open
Abstract
Distinct mammalian RNA viruses trigger Dicer-mediated production of virus-derived small-interfering RNAs (vsiRNA) and encode unrelated proteins to suppress vsiRNA biogenesis. However, the mechanism and function of the mammalian RNA interference (RNAi) response are poorly understood. Here, we characterized antiviral RNAi in a mouse model of infection with Nodamura virus (NoV), a mosquito-transmissible positive-strand RNA virus encoding a known double-stranded RNA (dsRNA)-binding viral suppressor of RNAi (VSR), the B2 protein. We show that inhibition of NoV RNA replication by antiviral RNAi in mouse embryonic fibroblasts (MEFs) requires Dicer-dependent vsiRNA biogenesis and Argonaute-2 slicer activity. We found that VSR-B2 of NoV enhances viral RNA replication in wild-type but not RNAi-defective MEFs such as Argonaute-2 catalytic-dead MEFs and Dicer or Argonaute-2 knockout MEFs, indicating that VSR-B2 acts mainly by suppressing antiviral RNAi in the differentiated murine cells. Consistently, VSR-B2 expression in MEFs has no detectable effect on the induction of interferon-stimulated genes or the activation of global RNA cleavages by RNase L. Moreover, we demonstrate that NoV infection of adult mice induces production of abundant vsiRNA active to guide RNA slicing by Argonaute-2. Notably, VSR-B2 suppresses the biogenesis of both vsiRNA and the slicing-competent vsiRNA-Argonaute-2 complex without detectable inhibition of Argonaute-2 slicing guided by endogenous microRNA, which dramatically enhances viral load and promotes lethal NoV infection in adult mice either intact or defective in the signaling by type I, II, and III interferons. Together, our findings suggest that the mouse RNAi response confers essential protective antiviral immunity in both the presence and absence of the interferon response.IMPORTANCE Innate immune sensing of viral nucleic acids in mammals triggers potent antiviral responses regulated by interferons known to antagonize the induction of RNA interference (RNAi) by synthetic long double-stranded RNA (dsRNA). Here, we show that Nodamura virus (NoV) infection in adult mice activates processing of the viral dsRNA replicative intermediates into small interfering RNAs (siRNAs) active to guide RNA slicing by Argonaute-2. Genetic studies demonstrate that NoV RNA replication in mouse embryonic fibroblasts is inhibited by the RNAi pathway and enhanced by the B2 viral RNAi suppressor only in RNAi-competent cells. When B2 is rendered nonexpressing or nonfunctional, the resulting mutant viruses become nonpathogenic and are cleared in adult mice either intact or defective in the signaling by type I, II, and III interferons. Our findings suggest that mouse antiviral RNAi is active and necessary for the in vivo defense against viral infection in both the presence and absence of the interferon response.
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Affiliation(s)
- Qingxia Han
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Gang Chen
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Jinyan Wang
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - David Jee
- Department of Developmental Biology, Sloan Kettering Institute, New York, New York, USA
| | - Wan-Xiang Li
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Eric C Lai
- Department of Developmental Biology, Sloan Kettering Institute, New York, New York, USA
| | - Shou-Wei Ding
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
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11
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Xiao J, Wei Z, Chen X, Chen W, Zhang H, Yang C, Shang Y, Liu J. Experimental abdominal aortic aneurysm growth is inhibited by blocking the JAK2/STAT3 pathway. Int J Cardiol 2020; 312:100-106. [PMID: 32334849 DOI: 10.1016/j.ijcard.2020.03.072] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 01/05/2020] [Accepted: 03/27/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND The JAK/STAT pathway is a vital transcription signaling pathway that regulates gene expression and cellular activity. Our recently published study highlighted the role of IL-17A in abdominal aortic aneurysm (AAA) formation and rupture. IL-17A has been proven to upregulate vascular endothelial growth factor (VEGF) expression in some diseases. However, no study has demonstrated the relationships among JAK2/STAT3, IL-17A and VEGF. Therefore, we hypothesized that IL-17A may up-regulate VEGF expression via the JAK2/STAT3 signaling pathway to amplify the inflammatory response, exacerbate neovascularization, and accelerate AAA progression. METHODS To fully verify our hypothesis, two separate studies were performed: i) a study investigating the influence of JAK2/STAT3 on AAA formation and progression. ii) a study evaluating the relationship among IL-17A, JAK2/STAT3 and VEGF. Human tissues were collected from 7 AAA patients who underwent open surgery and 7 liver transplantation donors. All human aortic tissues were examined by histological and immunohistochemical staining, and Western blotting. Furthermore, mouse aortic tissues were also examined by histological and immunohistochemical staining and Western blotting, and the mouse aortic diameters were assessed by high-resolution Vevo 2100 microimaging system. RESULTS Among human aortic tissues, JAK2/STAT3, IL-17A and VEGF expression levels were higher in AAA tissues than in control tissues. Group treated with WP1066 (a selective JAK2/STAT3 pathway inhibitor), IL-17A, and VEGF groups had AAA incidences of 25%, 40%, and 65%, respectively, while the control group had an incidence of 75%. Histopathological analysis revealed that the IL-17A- and VEGF-related inflammatory responses were attenuated by WP1066. Thus, blocking the JAK2/STAT3 pathway with WP1066 attenuated experimental AAA progression. In addition, in study ii, we found that IL-17A siRNA seemed to attenuate the expression of IL-17A and VEGF in vivo study; treatment with VEGF siRNA decreased the expression of VEGF, while IL-17A expression remained high. In an in vitro study, rhIL-17A treatment increased JAK2/STAT3 and VEGF expression in macrophages in a dose-dependent manner. CONCLUSION Blocking the JAK2/STAT3 pathway with WP1066 (a JAK2/STAT3 specific inhibitor) attenuates experimental AAA progression. During AAA progression, IL-17A may influence the expression of VEGF via the JAK2/STAT3 signaling pathway. This potential mechanism may suggest a novel strategy for nonsurgical AAA treatment.
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Affiliation(s)
- Jie Xiao
- Department of Cardiovascular Surgery, Central Hospital of Wuhan, Tongji Medical college, Huazhong University of Science and Technology, Wuhan, 430014, Hubei, China
| | - Zhanjie Wei
- Department of Thyroid and Breast Surgery, Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, Hubei, China
| | - Xing Chen
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical college, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, China
| | - Weiqiang Chen
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical college, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, China
| | - Hua Zhang
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical college, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, China
| | - Chuanlei Yang
- Department of Cardiovascular Surgery, Central Hospital of Wuhan, Tongji Medical college, Huazhong University of Science and Technology, Wuhan, 430014, Hubei, China
| | - Yuqiang Shang
- Department of Cardiovascular Surgery, Central Hospital of Wuhan, Tongji Medical college, Huazhong University of Science and Technology, Wuhan, 430014, Hubei, China
| | - Jinping Liu
- Department of Cardiovascular Surgery, Zhongnan Hospital, Wuhan University, Wuhan, 430071, Hubei, China.
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12
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Systemic delivery of Eg5 shRNA-expressing plasmids using PEGylated DC-Chol/DOPE cationic liposome: Long-term silencing and anticancer effects in vivo. Biochem Pharmacol 2019; 166:192-202. [DOI: 10.1016/j.bcp.2019.05.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 05/21/2019] [Indexed: 12/23/2022]
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13
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Abstract
RNA interference is a relatively new tool used to silence specific genes in diverse biological systems. The development of this promising new technique for research and therapeutic use in studying and treating neurological diseases has been hampered by the lack of an efficient way to deliver siRNA transvascularly across the blood-brain barrier (BBB) to the central nervous system (CNS). Here we describe the generation of three different liposomal siRNA delivery vehicles to the CNS using the thin film hydration method. Utilizing cationic or anionic liposomes protects the siRNA from serum nucleases and proteases en route. To deliver the siRNA specifically to the CNS, the liposomes are complexed to a peptide that acts as a neuronal address by binding to nicotinic acetylcholine receptors (nAchRs). When injected intravenously, these liposome-siRNA-peptide complexes (LSPCs) or peptide addressed liposome encapsulated therapeutic siRNA (PALETS) resist serum degradation, effectively cross the BBB and deliver siRNA to AchR-expressing cells to suppress protein expression in the CNS.
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14
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Antiviral RNAi in Insects and Mammals: Parallels and Differences. Viruses 2019; 11:v11050448. [PMID: 31100912 PMCID: PMC6563508 DOI: 10.3390/v11050448] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/14/2019] [Accepted: 05/15/2019] [Indexed: 12/26/2022] Open
Abstract
The RNA interference (RNAi) pathway is a potent antiviral defense mechanism in plants and invertebrates, in response to which viruses evolved suppressors of RNAi. In mammals, the first line of defense is mediated by the type I interferon system (IFN); however, the degree to which RNAi contributes to antiviral defense is still not completely understood. Recent work suggests that antiviral RNAi is active in undifferentiated stem cells and that antiviral RNAi can be uncovered in differentiated cells in which the IFN system is inactive or in infections with viruses lacking putative viral suppressors of RNAi. In this review, we describe the mechanism of RNAi and its antiviral functions in insects and mammals. We draw parallels and highlight differences between (antiviral) RNAi in these classes of animals and discuss open questions for future research.
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15
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Maillard PV, van der Veen AG, Poirier EZ, Reis e Sousa C. Slicing and dicing viruses: antiviral RNA interference in mammals. EMBO J 2019; 38:e100941. [PMID: 30872283 PMCID: PMC6463209 DOI: 10.15252/embj.2018100941] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 01/17/2019] [Accepted: 01/25/2019] [Indexed: 12/15/2022] Open
Abstract
To protect against the harmful consequences of viral infections, organisms are equipped with sophisticated antiviral mechanisms, including cell-intrinsic means to restrict viral replication and propagation. Plant and invertebrate cells utilise mostly RNA interference (RNAi), an RNA-based mechanism, for cell-intrinsic immunity to viruses while vertebrates rely on the protein-based interferon (IFN)-driven innate immune system for the same purpose. The RNAi machinery is conserved in vertebrate cells, yet whether antiviral RNAi is still active in mammals and functionally relevant to mammalian antiviral defence is intensely debated. Here, we discuss cellular and viral factors that impact on antiviral RNAi and the contexts in which this system might be at play in mammalian resistance to viral infection.
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Affiliation(s)
- Pierre V Maillard
- Division of Infection and Immunity, University College London, London, UK
| | | | - Enzo Z Poirier
- Immunobiology Laboratory, The Francis Crick Institute, London, UK
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16
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Watson SF, Knol LI, Witteveldt J, Macias S. Crosstalk Between Mammalian Antiviral Pathways. Noncoding RNA 2019; 5:E29. [PMID: 30909383 PMCID: PMC6468734 DOI: 10.3390/ncrna5010029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 03/19/2019] [Accepted: 03/20/2019] [Indexed: 12/15/2022] Open
Abstract
As part of their innate immune response against viral infections, mammals activate the expression of type I interferons to prevent viral replication and dissemination. An antiviral RNAi-based response can be also activated in mammals, suggesting that several mechanisms can co-occur in the same cell and that these pathways must interact to enable the best antiviral response. Here, we will review how the classical type I interferon response and the recently described antiviral RNAi pathways interact in mammalian cells. Specifically, we will uncover how the small RNA biogenesis pathway, composed by the nucleases Drosha and Dicer can act as direct antiviral factors, and how the type-I interferon response regulates the function of these. We will also describe how the factors involved in small RNA biogenesis and specific small RNAs impact the activation of the type I interferon response and antiviral activity. With this, we aim to expose the complex and intricate network of interactions between the different antiviral pathways in mammals.
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Affiliation(s)
- Samir F Watson
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK.
| | - Lisanne I Knol
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK.
| | - Jeroen Witteveldt
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK.
| | - Sara Macias
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK.
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17
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Demeter T, Vaskovicova M, Malik R, Horvat F, Pasulka J, Svobodova E, Flemr M, Svoboda P. Main constraints for RNAi induced by expressed long dsRNA in mouse cells. Life Sci Alliance 2019; 2:2/1/e201800289. [PMID: 30808654 PMCID: PMC6391682 DOI: 10.26508/lsa.201800289] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 02/09/2019] [Accepted: 02/11/2019] [Indexed: 12/13/2022] Open
Abstract
A systematic survey of dsRNA expression in mouse fibroblasts and embryonic stem cells shows main constraints for RNAi. RNAi activity depends on the initial Dicer cleavage of dsRNA, having implications for the evolution of mammalian RNAi functions. RNAi is the sequence-specific mRNA degradation guided by siRNAs produced from long dsRNA by RNase Dicer. Proteins executing RNAi are present in mammalian cells but rather sustain the microRNA pathway. Aiming for a systematic analysis of mammalian RNAi, we report here that the main bottleneck for RNAi efficiency is the production of functional siRNAs, which integrates Dicer activity, dsRNA structure, and siRNA targeting efficiency. Unexpectedly, increased expression of Dicer cofactors TARBP2 or PACT reduces RNAi but not microRNA function. Elimination of protein kinase R, a key dsRNA sensor in the interferon response, had minimal positive effects on RNAi activity in fibroblasts. Without high Dicer activity, RNAi can still occur when the initial Dicer cleavage of the substrate yields an efficient siRNA. Efficient mammalian RNAi may use substrates with some features of microRNA precursors, merging both pathways even more than previously suggested. Although optimized endogenous Dicer substrates mimicking miRNA features could evolve for endogenous regulations, the same principles would make antiviral RNAi inefficient as viruses would adapt to avoid efficacy.
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Affiliation(s)
- Tomas Demeter
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Michaela Vaskovicova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Radek Malik
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Filip Horvat
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic.,Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Josef Pasulka
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Eliska Svobodova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Matyas Flemr
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Petr Svoboda
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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18
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Logrip ML. Molecular tools to elucidate factors regulating alcohol use. Alcohol 2019; 74:3-9. [PMID: 30033149 DOI: 10.1016/j.alcohol.2018.03.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/15/2018] [Accepted: 03/15/2018] [Indexed: 12/20/2022]
Abstract
Alcohol use disorder (AUD) is a pervasive societal problem, marked by high levels of alcohol intake and recidivism. Despite these common disease traits, individuals diagnosed with AUD display a range of disordered drinking and alcohol-related behaviors. The diversity in disease presentation, as well as the established polygenic nature of the disorder and complex neurocircuitry, speaks to the variety of neurochemical changes resulting from alcohol intake that may differentially regulate alcohol-related behaviors. Investigations into the molecular adaptations responsible for maladaptive alcohol-related behavioral outcomes require an ever-evolving set of molecular tools to elucidate with increasing precision how alcohol alters behavior through neurochemical changes. This review highlights recent advances in molecular methodology, addressing how incorporation of these cutting-edge techniques not only may enhance current knowledge of the molecular bases of AUD, but also may facilitate identification of improved treatment targets that may be therapeutic in specific subpopulations of AUD individuals.
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19
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Wu X, Kwong AC, Rice CM. Antiviral resistance of stem cells. Curr Opin Immunol 2019; 56:50-59. [PMID: 30352329 PMCID: PMC6462420 DOI: 10.1016/j.coi.2018.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 09/27/2018] [Accepted: 10/02/2018] [Indexed: 01/07/2023]
Abstract
Stem cells are important for growth and regeneration given their ability to self-renew and differentiate into mature cells. Resistance to certain viral infections has been established as a phenotype of stem cells, a protection in line with their important physiological function. Antiviral resistance is critical to all cells, but it is differentially regulated between stem cells and differentiated cells. Stem cells utilize antiviral RNA interference, interferon-independent repression of endogenous retroviruses and intrinsic expression of antiviral interferon-stimulated genes. Differentiated cells often rely on the interferon-associated protein-based response to induce a local antiviral state. This review outlines the antiviral resistance mechanisms of stem cells and discusses some ideas as to why stem cells and differentiated cells may have evolved to utilize distinct mechanisms.
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Affiliation(s)
- Xianfang Wu
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, United States
| | - Andrew C Kwong
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, United States; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, United States.
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20
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Abstract
Like humans, insects face the threat of viral infection. Despite having repercussions on human health and disease, knowledge gaps exist for how insects cope with viral pathogens. Drosophila melanogaster serves as an ideal insect model due to its genetic tractability. When encountering a pathogen, two major approaches to fight disease are resistance strategies and tolerance strategies. Disease resistance strategies promote the health of the infected host by reducing pathogen load. Multiple disease resistance mechanisms have been identified in Drosophila: RNA interference, Jak/STAT signaling, Toll signaling, IMD signaling, and autophagy. Disease tolerance mechanisms, in contrast, do not reduce pathogen load directly, but rather mitigate the stress and damage incurred by infection. The main benefit of tolerance mechanisms may therefore be to provide the host with time to engage antiviral resistance mechanisms that eliminate the threat. In this review, antiviral resistance mechanisms used by Drosophila will be described and compared to mammalian antiviral mechanisms. Disease tolerance will then be explained in a broader context as this is a burgeoning field of study.
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Affiliation(s)
- Jonathan Chow
- Division of Gastroenterology, Harvard Medical School, Boston Children's Hospital, Boston, MA, United States
| | - Jonathan C Kagan
- Division of Gastroenterology, Harvard Medical School, Boston Children's Hospital, Boston, MA, United States.
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21
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Artigas F, Celada P, Bortolozzi A. Can we increase the speed and efficacy of antidepressant treatments? Part II. Glutamatergic and RNA interference strategies. Eur Neuropsychopharmacol 2018. [PMID: 29525411 DOI: 10.1016/j.euroneuro.2018.01.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In the second part we focus on two treatment strategies that may overcome the main limitations of current antidepressant drugs. First, we review the experimental and clinical evidence supporting the use of glutamatergic drugs as fast-acting antidepressants. Secondly, we review the involvement of microRNAs (miRNAs) in the pathophysiology of major depressive disorder (MDD) and the use of small RNAs (e.g.., small interfering RNAs or siRNAs) to knockdown genes in monoaminergic and non-monoaminergic neurons and induce antidepressant-like responses in experimental animals. The development of glutamatergic agents is a promising venue for antidepressant drug development, given the antidepressant properties of the non-competitive NMDA receptor antagonist ketamine. Its unique properties appear to result from the activation of AMPA receptors by a metabolite [(2S,6S;2R,6R)-hydroxynorketamine (HNK)] and mTOR signaling. These effects increase synaptogenesis in prefrontal cortical pyramidal neurons and enhance serotonergic neurotransmission via descending inputs to the raphe nuclei. This view is supported by the cancellation of ketamine's antidepressant-like effects by inhibition of serotonin synthesis. We also review existing evidence supporting the involvement of miRNAs in MDD and the preclinical use of RNA interference (RNAi) strategies to target genes involved in antidepressant response. Many miRNAs have been associated to MDD, some of which e.g., miR-135 targets genes involved in antidepressant actions. Likewise, SSRI-conjugated siRNA evokes faster and/or more effective antidepressant-like responses. Intranasal application of sertraline-conjugated siRNAs directed to 5-HT1A receptors and SERT evoked much faster changes of pre- and postsynaptic antidepressant markers than those produced by fluoxetine.
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Affiliation(s)
- F Artigas
- Department of Neurochemistry and Neuropharmacology, Institut d'Investigacions Biomèdiques de Barcelona, Consejo Superior de Investigaciones Científicas (CSIC), Spain; CIBERSAM (Centro de Investigació Biomédica en Red de Salud Mental), Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Spain.
| | - P Celada
- Department of Neurochemistry and Neuropharmacology, Institut d'Investigacions Biomèdiques de Barcelona, Consejo Superior de Investigaciones Científicas (CSIC), Spain; CIBERSAM (Centro de Investigació Biomédica en Red de Salud Mental), Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Spain
| | - A Bortolozzi
- Department of Neurochemistry and Neuropharmacology, Institut d'Investigacions Biomèdiques de Barcelona, Consejo Superior de Investigaciones Científicas (CSIC), Spain; CIBERSAM (Centro de Investigació Biomédica en Red de Salud Mental), Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Spain
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22
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Zhou Q, Wang Y, Xiang J, Piao Y, Zhou Z, Tang J, Liu X, Shen Y. Stabilized calcium phosphate hybrid nanocomposite using a benzoxaborole-containing polymer for pH-responsive siRNA delivery. Biomater Sci 2018; 6:3178-3188. [DOI: 10.1039/c8bm00575c] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Herein, we developed a PEG-PBO/siRNA/CaP hybrid nanocomposite with excellent stability and high siRNA loading content for effective pH-responsive siRNA delivery.
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Affiliation(s)
- Quan Zhou
- Center for Bionanoengineering and Key Laboratory of Biomass Chemical Engineering of Ministry of Education
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou 310027
- China
| | - Yue Wang
- Center for Bionanoengineering and Key Laboratory of Biomass Chemical Engineering of Ministry of Education
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou 310027
- China
| | - Jiajia Xiang
- Center for Bionanoengineering and Key Laboratory of Biomass Chemical Engineering of Ministry of Education
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou 310027
- China
| | - Ying Piao
- Center for Bionanoengineering and Key Laboratory of Biomass Chemical Engineering of Ministry of Education
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou 310027
- China
| | - Zhuxian Zhou
- Center for Bionanoengineering and Key Laboratory of Biomass Chemical Engineering of Ministry of Education
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou 310027
- China
| | - Jianbin Tang
- Center for Bionanoengineering and Key Laboratory of Biomass Chemical Engineering of Ministry of Education
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou 310027
- China
| | - Xiangrui Liu
- Center for Bionanoengineering and Key Laboratory of Biomass Chemical Engineering of Ministry of Education
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou 310027
- China
| | - Youqing Shen
- Center for Bionanoengineering and Key Laboratory of Biomass Chemical Engineering of Ministry of Education
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou 310027
- China
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23
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Construction and Application of Random dsRNA Interference Library for Functional Genetic Screens in Embryonic Stem Cells. Methods Mol Biol 2017. [PMID: 28674802 DOI: 10.1007/978-1-4939-7108-4_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
RNA interference (RNAi) libraries have been proven to be a powerful tool for large-scale functional genetic screens. To facilitate high-throughput functional genetic screens in embryonic stem cells, a system for construction of random dsRNA-expressing RNAi libraries was developed. Previous studies have demonstrated that sequence-specific gene silencing could be induced by long dsRNA in mouse embryos, mouse oocytes, embryonic stem cells, and some other mammalian cells. Our study demonstrated that the dsRNA interference library can be used for functional genetic screens of genes involved in self-renewal of embryonic stem cells (ES cells). The random RNAi library is easy to construct and provides a useful tool for investigation of molecular mechanisms of cellular development and differentiation.
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24
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Adams FF, Heckl D, Hoffmann T, Talbot SR, Kloos A, Thol F, Heuser M, Zuber J, Schambach A, Schwarzer A. An optimized lentiviral vector system for conditional RNAi and efficient cloning of microRNA embedded short hairpin RNA libraries. Biomaterials 2017; 139:102-115. [PMID: 28599149 DOI: 10.1016/j.biomaterials.2017.05.032] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 05/17/2017] [Accepted: 05/19/2017] [Indexed: 02/06/2023]
Abstract
RNA interference (RNAi) and CRISPR-Cas9-based screening systems have emerged as powerful and complementary tools to unravel genetic dependencies through systematic gain- and loss-of-function studies. In recent years, a series of technical advances helped to enhance the performance of virally delivered RNAi. For instance, the incorporation of short hairpin RNAs (shRNAs) into endogenous microRNA contexts (shRNAmiRs) allows the use of Tet-regulated promoters for synchronous onset of gene knockdown and precise interrogation of gene dosage effects. However, remaining challenges include lack of efficient cloning strategies, inconsistent knockdown potencies and leaky expression. Here, we present a simple, one-step cloning approach for rapid and efficient cloning of miR-30 shRNAmiR libraries. We combined a human miR-30 backbone retaining native flanking sequences with an optimized all-in-one lentiviral vector system for conditional RNAi to generate a versatile toolbox characterized by higher doxycycline sensitivity, reduced leakiness and enhanced titer. Furthermore, refinement of existing shRNA design rules resulted in substantially improved prediction of powerful shRNAs. Our approach was validated by accurate quantification of the knockdown potency of over 250 single shRNAmiRs. To facilitate access and use by the scientific community, an online tool was developed for the automated design of refined shRNA-coding oligonucleotides ready for cloning into our system.
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Affiliation(s)
- Felix F Adams
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Dirk Heckl
- Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Thomas Hoffmann
- Research Institute of Molecular Pathology (IMP), 1030 Vienna, Austria
| | - Steven R Talbot
- Institute of Physiological Chemistry, Hannover Medical School, 30625 Hannover, Germany
| | - Arnold Kloos
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, 30625 Hannover, Germany
| | - Felicitas Thol
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, 30625 Hannover, Germany
| | - Michael Heuser
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, 30625 Hannover, Germany
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), 1030 Vienna, Austria
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, USA
| | - Adrian Schwarzer
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, 30625 Hannover, Germany.
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25
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Affiliation(s)
- Benjamin R tenOever
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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26
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Mohammadzadeh R, Saeid Harouyan M, Ale Taha SM. Silencing of bach1 gene by small interfering RNA–mediation regulates invasive and expression level of miR-203, miR-145, matrix metalloproteinase-9, and CXCR4 receptor in MDA-MB-468 breast cancer cells. Tumour Biol 2017; 39:1010428317695925. [DOI: 10.1177/1010428317695925] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: Recently experimental validation of the networks revealed bach1, a basic leucine zipper transcription factor, as the common regulator of several functional invasive genes. The expression of bach1 and its target genes was linked to the higher risk of breast cancer recurrence in patients. The aim of this study was to investigate the effect of specific bach1 small interfering RNAs, on the invasive and expression level of miR-203, miR-145, matrix metalloproteinase-9, and CXCR4 receptor which play a role in cancer metastasis, in MDA-MB-468 cell lines. Methods: Small interfering RNA transfection was performed with transfection regent. The survival effects of small interfering RNA were determined using trypan blue assay cells. The expression level of messenger RNA and matrix metalloproteinase-9 to assess cell invasion and the expression level of miR-203, miR-145, and CXCR4 receptor were measured by quantitative real-time polymerase chain reaction analysis on the MDA-MB-468 cell lines. Results: Transfection with small interfering RNA significantly suppressed the expression of bach1 gene in dose-dependent manner after 48 h ( p < 0.0001). A significant reduction in cell invasion and CXCR4 receptor, matrix metalloproteinase-9 expression were observed ( p < 0.0001). It was also a dramatic increase in the expression level of miR-203 and miR-145 ( p < 0.0001). Conclusions: Our results suggest that the bach1-specific small interfering RNA effectively decrease CXCR4 receptor, matrix metalloproteinase-9 expression and breast adenocarcinoma cells invasive, also increased the expression of tumor-suppressive microRNA-203 and miR-145. Thus, these microRNAs may play a role in invasive/metastasis of carcinogenic breast cancer cells. Therefore, bach1 knockdown can be considered as a potent adjuvant in breast cancer therapy.
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Affiliation(s)
- Reza Mohammadzadeh
- Department of Cell and Molecular Biology, Faculty of Basic Science, University of Maragheh, Maragheh, Iran
| | - Mojgan Saeid Harouyan
- Department of Biotechnology, Faculty of Basic Science, Islamic Azad University, Urmia, Iran
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27
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Chen X, Luo Y, Jia G, Liu G, Zhao H, Huang Z. FTO Promotes Adipogenesis through Inhibition of the Wnt/β-catenin Signaling Pathway in Porcine Intramuscular Preadipocytes. Anim Biotechnol 2017; 28:268-274. [PMID: 28267420 DOI: 10.1080/10495398.2016.1273835] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Numerous studies have demonstrated that FTO plays an important role in adipogenesis. Herein, we designed a small interfering RNA targeting FTO to knock down its endogenous expression and investigated its effects on the proliferation and differentiation of porcine intramuscular preadipocytes. Its possible mechanism was also investigated. We showed that FTO silencing significantly decreased the level of phospho-Histone H3 protein and inhibited the proliferation of porcine intramuscular preadipocytes. In addition, the expressions of peroxisome proliferators-activated receptor γ (PPARγ) and CAAT/enhancer binding protein (C/EBPα) were down-regulated, but the expression of β-catenin was up-regulated, by FTO silencing. Of specific interest here was that LiCl, a Wnt/β-catenin signaling specific activator, attenuated the FTO-induced upregulation of PPARγ and downregulation of β-catenin. Collectively, our data demonstrated that FTO silence decreased the proliferation and differentiation of porcine intramuscular preadipocytes, and FTO affects the porcine intramuscular preadipocytes differentiation might be via Wnt/β-catenin signaling pathway.
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Affiliation(s)
- Xiaoling Chen
- a Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education , Institute of Animal Nutrition, Sichuan Agricultural University , Chengdu , Sichuan , P. R. China
| | - Yanliu Luo
- a Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education , Institute of Animal Nutrition, Sichuan Agricultural University , Chengdu , Sichuan , P. R. China
| | - Gang Jia
- a Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education , Institute of Animal Nutrition, Sichuan Agricultural University , Chengdu , Sichuan , P. R. China
| | - Guangmang Liu
- a Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education , Institute of Animal Nutrition, Sichuan Agricultural University , Chengdu , Sichuan , P. R. China
| | - Hua Zhao
- a Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education , Institute of Animal Nutrition, Sichuan Agricultural University , Chengdu , Sichuan , P. R. China
| | - Zhiqing Huang
- a Key Laboratory for Animal Disease-Resistance Nutrition of China Ministry of Education , Institute of Animal Nutrition, Sichuan Agricultural University , Chengdu , Sichuan , P. R. China
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28
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Branchini BR, Southworth TL. A Highly Sensitive Biosensor for ATP Using a Chimeric Firefly Luciferase. Methods Enzymol 2017; 589:351-364. [PMID: 28336069 DOI: 10.1016/bs.mie.2017.01.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Firefly luciferases, which emit visible light in a highly specific ATP-dependent process, have been adapted for a variety of applications based on the detection of the enzymes or using the proteins to measure ATP levels. Based on studies of chimeric luciferases, we engineered a novel luciferase called PLG2 that has enhanced specific activity, and thermal and pH stability compared to the commonly used Photinus pyralis luciferase. We present here protocols for preparing a single assay mixture containing PLG2 that can be used to readily detect femtomole levels of ATP. Our methodology can be used with a variety of samples, including human and bacterial cells, where measurements of ATP can be used as a biosensor for the detection of viable cells.
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Mathupala SP, Guthikonda M, Sloan AE. RNAi Based Approaches to the Treatment of Malignant Glioma. Technol Cancer Res Treat 2016; 5:261-9. [PMID: 16700622 DOI: 10.1177/153303460600500313] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
RNA interference (RNAi) is a recently discovered, powerful molecular mechanism that can be harnessed to engineer gene-specific silencing in mammalian tissues. A mechanism, where short double-stranded RNA (dsRNA) molecules, when introduced into cells elicit specific “knock-down” of gene expression via degradation of targeted messenger RNA, has lately become the technique of choice for analysis of gene function in oncology research. Thus, RNAi is currently being extensively evaluated as a potential therapeutic strategy against malignant gliomas, since surgical, radiological, and chemotherapeutic interventions during the past few decades have done little to improve the poor prognosis rate for patients with these dreaded tumors. This review summarizes the pre-clinical studies that are currently underway to test the validity of RNAi as a potential therapeutic strategy against malignant gliomas, and discusses the potential technical Hurdles that remain to be overcome before the technique can become a promising clinical therapy to combat this frequently lethal disease.
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Affiliation(s)
- Saroj P Mathupala
- Department of Neurological Surgery, Karmanos Cancer Institute, Wayne State University School of Medicine, 808 HWCRC, 4100 John R. Road, Detroit, MI 48201, USA.
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Selli C, Erac Y, Tosun M. Effects of cell seeding density on real-time monitoring of anti-proliferative effects of transient gene silencing. ACTA ACUST UNITED AC 2016; 23:20. [PMID: 27981039 PMCID: PMC5133759 DOI: 10.1186/s40709-016-0057-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 11/25/2016] [Indexed: 01/15/2023]
Abstract
Background Real-time cellular analysis systems enable impedance-based label-free and dynamic monitoring of various cellular events such as proliferation. In this study, we describe the effects of initial cell seeding density on the anti-proliferative effects of transient gene silencing monitored via real-time cellular analysis. We monitored the real-time changes in proliferation of Huh7 hepatocellular carcinoma and A7r5 vascular smooth muscle cells with different initial seeding densities following transient receptor potential canonical 1 (TRPC1) silencing using xCELLigence system. Huh7 and A7r5 cells were seeded on E-plate 96 at 10,000, 5000, 1250 and 5000, 2500 cells well−1, respectively, following silencing vector transfection. The inhibitory effects of transient silencing on cell proliferation monitored every 30 min for 72 h. Results TRPC1 silencing did not inhibit the proliferation rates of Huh7 cells at 10,000 cells well−1 seeding density. However, a significant anti-proliferative effect was observed at 1250 cells well−1 density at each time point throughout 72 h. Furthermore, significant inhibitory effects on A7r5 proliferation were observed at both 5000 and 2500 cells well−1 for 72 h. Conclusions Data suggest that the effects of transient silencing on cell proliferation differ depending on the initial cell seeding density. While high seeding densities mask the significant changes in proliferation, the inhibitory effects of silencing become apparent at lower seeding densities as the entry into log phase is delayed. Using the optimal initial seeding density is crucial when studying the effects of transient gene silencing. In addition, the results suggest that TRPC1 may contribute to proliferation and phenotypic switching of vascular smooth muscle cells.
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Affiliation(s)
- Cigdem Selli
- Applied Bioinformatics of Cancer, Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XR UK ; Department of Pharmacology, Faculty of Pharmacy, Ege University, 35040 Izmir, Turkey
| | - Yasemin Erac
- Department of Pharmacology, Faculty of Pharmacy, Ege University, 35040 Izmir, Turkey
| | - Metiner Tosun
- Department of Pharmacology, Faculty of Pharmacy, Ege University, 35040 Izmir, Turkey ; Faculty of Medicine, Izmir University of Economics, 35330 Izmir, Turkey
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31
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Maillard PV, Van der Veen AG, Deddouche-Grass S, Rogers NC, Merits A, Reis e Sousa C. Inactivation of the type I interferon pathway reveals long double-stranded RNA-mediated RNA interference in mammalian cells. EMBO J 2016; 35:2505-2518. [PMID: 27815315 PMCID: PMC5167344 DOI: 10.15252/embj.201695086] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 09/02/2016] [Accepted: 09/12/2016] [Indexed: 12/22/2022] Open
Abstract
RNA interference (RNAi) elicited by long double-stranded (ds) or base-paired viral RNA constitutes the major mechanism of antiviral defence in plants and invertebrates. In contrast, it is controversial whether it acts in chordates. Rather, in vertebrates, viral RNAs induce a distinct defence system known as the interferon (IFN) response. Here, we tested the possibility that the IFN response masks or inhibits antiviral RNAi in mammalian cells. Consistent with that notion, we find that sequence-specific gene silencing can be triggered by long dsRNAs in differentiated mouse cells rendered deficient in components of the IFN pathway. This unveiled response is dependent on the canonical RNAi machinery and is lost upon treatment of IFN-responsive cells with type I IFN Notably, transfection with long dsRNA specifically vaccinates IFN-deficient cells against infection with viruses bearing a homologous sequence. Thus, our data reveal that RNAi constitutes an ancient antiviral strategy conserved from plants to mammals that precedes but has not been superseded by vertebrate evolution of the IFN system.
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Affiliation(s)
| | | | | | - Neil C Rogers
- Immunobiology Laboratory, The Francis Crick Institute, London, UK
| | - Andres Merits
- Institute of Technology, University of Tartu, Tartu, Estonia
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32
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Cheng L, Li L. Systematic Quality Control Analysis of LINCS Data. CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2016; 5:588-598. [PMID: 27796074 PMCID: PMC5192966 DOI: 10.1002/psp4.12107] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 07/27/2016] [Indexed: 12/18/2022]
Abstract
The Library of Integrated Cellular Signatures (LINCS) project provides comprehensive transcriptome profiling of human cell lines before and after chemical and genetic perturbations. Its L1000 platform utilizes 978 landmark genes to infer the transcript levels of 14,292 genes computationally. Here we conducted the L1000 data quality control analysis by using MCF7, PC3, and A375 cell lines as representative examples. Before perturbations, a promising 80% correlation in transcriptome was observed between L1000- and Affymetrix HU133A-platforms. After library-based shRNA perturbations, a moderate 30% of differentially expressed genes overlapped between any two selected controls viral vectors using the L1000 platform. The mitogen-activated protein kinase, vascular endothelial growth factor, and T-cell receptor pathways were identified as the most significantly shared pathways between chemical and genetic perturbations in cancer cells. In conclusion, L1000 platform is reliable in assessing transcriptome before perturbation. Its response to perturbagens needs to be interpreted with caution. A quality control analysis pipeline of L1000 is recommended before addressing biological questions.
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Affiliation(s)
- L Cheng
- Centers for Computational Biology and Bioinformatics, School of Medicine, Indiana University, Indianapolis, Indiana, USA.,Department of Medical and Molecular Genetics, School of Medicine, Indiana University, Indianapolis, Indiana, USA
| | - L Li
- Centers for Computational Biology and Bioinformatics, School of Medicine, Indiana University, Indianapolis, Indiana, USA.,Department of Medical and Molecular Genetics, School of Medicine, Indiana University, Indianapolis, Indiana, USA
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33
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Abstract
Self-replicating genetic material presumably provided the architecture necessary for generating the last universal ancestor of all nucleic-acid-based life. As biological complexity increased in the billions of years that followed, the same genetic material also morphed into a wide spectrum of viruses and other parasitic genetic elements. The resulting struggle for existence drove the evolution of host defenses, giving rise to a perpetual arms race. This Perspective summarizes the antiviral mechanisms evident across the tree of life, discussing each in their evolutionary context to postulate how the coevolution of host and pathogen shaped the cellular antiviral defenses we know today.
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34
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Watanabe C, Cuellar TL, Haley B. Quantitative evaluation of first, second, and third generation hairpin systems reveals the limit of mammalian vector-based RNAi. RNA Biol 2016; 13:25-33. [PMID: 26786363 PMCID: PMC4829305 DOI: 10.1080/15476286.2015.1128062] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Incorporating miRNA-like features into vector-based hairpin scaffolds has been shown to augment small RNA processing and RNAi efficiency. Therefore, defining an optimal, native hairpin context may obviate a need for hairpin-specific targeting design schemes, which confound the movement of functional siRNAs into shRNA/artificial miRNA backbones, or large-scale screens to identify efficacious sequences. Thus, we used quantitative cell-based assays to compare separate third generation artificial miRNA systems, miR-E (based on miR-30a) and miR-3G (based on miR-16-2 and first described in this study) to widely-adopted, first and second generation formats in both Pol-II and Pol-III expression vector contexts. Despite their unique structures and strandedness, and in contrast to first and second-generation RNAi triggers, the third generation formats operated with remarkable similarity to one another, and strong silencing was observed with a significant fraction of the evaluated target sequences within either promoter context. By pairing an established siRNA design algorithm with the third generation vectors we could readily identify targeting sequences that matched or exceeded the potency of those discovered through large-scale sensor-based assays. We find that third generation hairpin systems enable the maximal level of siRNA function, likely through enhanced processing and accumulation of precisely-defined guide RNAs. Therefore, we predict future gains in RNAi potency will come from improved hairpin expression and identification of optimal siRNA-intrinsic silencing properties rather than further modification of these scaffolds. Consequently, third generation systems should be the primary format for vector-based RNAi studies; miR-3G is advantageous due to its small expression cassette and simplified, cost-efficient cloning scheme.
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Affiliation(s)
- Colin Watanabe
- a Departments of Bioinformatics and Computational Biology , South San Francisco , CA 94080.,c Genentech, Inc . South San Francisco , CA 94080 , USA
| | - Trinna L Cuellar
- b Molecular Biology South San Francisco , CA 94080.,c Genentech, Inc . South San Francisco , CA 94080 , USA
| | - Benjamin Haley
- b Molecular Biology South San Francisco , CA 94080.,c Genentech, Inc . South San Francisco , CA 94080 , USA
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35
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Abstract
Short interfering RNAs (siRNAs) are as effective at targeting and silencing genes by RNA interference (RNAi) as long double-stranded RNAs (dsRNAs). siRNAs are widely used for assessing gene function in cultured mammalian cells or early developing vertebrate embryos. siRNAs are also promising reagents for developing gene-specific therapeutics. Specifically, the inhibition of HIV-1 replication is particularly well-suited to RNAi, as several stages of the viral life cycle and many viral and cellular genes can be targeted. The future success of this approach will depend on recent advances in siRNA-based silencing technologies.
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Affiliation(s)
- Hiroshi Takaku
- Department of Life & Environmental Sciences and High Technology Research Center, Chiba Institute of Technology, Chiba, Japan.
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36
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Herbert KM, Nag A. A Tale of Two RNAs during Viral Infection: How Viruses Antagonize mRNAs and Small Non-Coding RNAs in The Host Cell. Viruses 2016; 8:E154. [PMID: 27271653 PMCID: PMC4926174 DOI: 10.3390/v8060154] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 05/12/2016] [Accepted: 05/20/2016] [Indexed: 02/06/2023] Open
Abstract
Viral infection initiates an array of changes in host gene expression. Many viruses dampen host protein expression and attempt to evade the host anti-viral defense machinery. Host gene expression is suppressed at several stages of host messenger RNA (mRNA) formation including selective degradation of translationally competent messenger RNAs. Besides mRNAs, host cells also express a variety of noncoding RNAs, including small RNAs, that may also be subject to inhibition upon viral infection. In this review we focused on different ways viruses antagonize coding and noncoding RNAs in the host cell to its advantage.
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Affiliation(s)
- Kristina M Herbert
- Department of Experimental Microbiology, Center for Scientific Research and Higher Education of Ensenada (CICESE), Ensenada, Baja California 22860, Mexico.
| | - Anita Nag
- Department of Chemistry, Florida A&M University, Tallahassee, FL 32307, USA.
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37
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Unsoy G, Gunduz U. Targeted silencing of Survivin in cancer cells by siRNA loaded chitosan magnetic nanoparticles. Expert Rev Anticancer Ther 2016; 16:789-97. [PMID: 27130312 DOI: 10.1080/14737140.2016.1184981] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
BACKGROUND The aim of this study was to silence Survivin expression, related with drug-resistance, via siRNA-loaded CS-MNPs. METHODS AND RESULTS The highest siRNA-loading efficiency was achieved at siRNA:CS-MNP ratio of 1:2. Nanoparticles had spherical morphology and homogenous size distribution in TEM. After siRNA loading, core sizes (3-5 nm) of CS-MNPs didn't change significantly, however hydrodynamic diameters increased ~10 nm, indicating swelling of chitosan coat due to efficient siRNA loading. 73% of siRNA was pH-dependently released at 24hours, after 30% burst release at first 3.5hours. Stability was high enough to keep siRNAs in CS-MNPs at pH7.2. Cellular-internalization of Survivin-siRNA-CS-MNPs was high and localized in cytoplasm of cells. CONCLUSION Although, mock-siRNA loaded/unloaded CS-MNPs weren't cytotoxic, cell-death of breast cancer cells was significantly increased, after the treatment of Survivin-siRNA-loaded CS-MNPs. This reveals, successful loading of Survivin-siRNA on CS-MNPs and significant silencing of Survivin expression by triggering cell-death. Consequently, CS-MNPs are highly efficient delivery systems for intact siRNAs.
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Affiliation(s)
- Gozde Unsoy
- a Department of Biotechnology , Middle East Technical University , Ankara , Turkey
| | - Ufuk Gunduz
- a Department of Biotechnology , Middle East Technical University , Ankara , Turkey.,b Department of Biological Sciences , Middle East Technical University , Ankara , Turkey
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38
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Sequential protein expression and selective labeling for in-cell NMR in human cells. Biochim Biophys Acta Gen Subj 2016; 1860:527-33. [DOI: 10.1016/j.bbagen.2015.12.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 12/17/2015] [Accepted: 12/22/2015] [Indexed: 11/23/2022]
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39
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Culibrk L, Croft CA, Tebbutt SJ. Systems Biology Approaches for Host-Fungal Interactions: An Expanding Multi-Omics Frontier. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 20:127-38. [PMID: 26885725 PMCID: PMC4799697 DOI: 10.1089/omi.2015.0185] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Opportunistic fungal infections are an increasing threat for global health, and for immunocompromised patients in particular. These infections are characterized by interaction between fungal pathogen and host cells. The exact mechanisms and the attendant variability in host and fungal pathogen interaction remain to be fully elucidated. The field of systems biology aims to characterize a biological system, and utilize this knowledge to predict the system's response to stimuli such as fungal exposures. A multi-omics approach, for example, combining data from genomics, proteomics, metabolomics, would allow a more comprehensive and pan-optic "two systems" biology of both the host and the fungal pathogen. In this review and literature analysis, we present highly specialized and nascent methods for analysis of multiple -omes of biological systems, in addition to emerging single-molecule visualization techniques that may assist in determining biological relevance of multi-omics data. We provide an overview of computational methods for modeling of gene regulatory networks, including some that have been applied towards the study of an interacting host and pathogen. In sum, comprehensive characterizations of host-fungal pathogen systems are now possible, and utilization of these cutting-edge multi-omics strategies may yield advances in better understanding of both host biology and fungal pathogens at a systems scale.
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Affiliation(s)
- Luka Culibrk
- Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Carys A. Croft
- Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Scott J. Tebbutt
- Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
- Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
- Department of Medicine, Division of Respiratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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40
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Nebane NM, Coric T, McKellip S, Woods L, Sosa M, Rasmussen L, Bjornsti MA, White EL. Acoustic Droplet Ejection Technology and Its Application in High-Throughput RNA Interference Screening. ACTA ACUST UNITED AC 2015; 21:198-203. [PMID: 26663785 DOI: 10.1177/2211068215620346] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Indexed: 12/14/2022]
Abstract
The development of acoustic droplet ejection (ADE) technology has resulted in many positive changes associated with the operations in a high-throughput screening (HTS) laboratory. Originally, this liquid transfer technology was used to simply transfer DMSO solutions of primarily compounds. With the introduction of Labcyte's Echo 555, which has aqueous dispense capability, the application of this technology has been expanded beyond its original use. This includes the transfer of many biological reagents solubilized in aqueous buffers, including siRNAs. The Echo 555 is ideal for siRNA dispensing because it is accurate at low volumes and a step-down dilution is not necessary. The potential for liquid carryover and cross-contamination is eliminated, as no tips are needed. Herein, we describe the siRNA screening platform at Southern Research's HTS Center using the ADE technology. With this technology, an siRNA library can be dispensed weeks or even months in advance of the assay itself. The protocol has been optimized to achieve assay parameters comparable to small-molecule screening parameters, and exceeding the norm reported for genomewide siRNA screens.
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Affiliation(s)
- N Miranda Nebane
- High Throughput Screening Center, Southern Research, Birmingham, AL, USA
| | - Tatjana Coric
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sara McKellip
- High Throughput Screening Center, Southern Research, Birmingham, AL, USA
| | - LaKeisha Woods
- High Throughput Screening Center, Southern Research, Birmingham, AL, USA
| | - Melinda Sosa
- High Throughput Screening Center, Southern Research, Birmingham, AL, USA
| | - Lynn Rasmussen
- High Throughput Screening Center, Southern Research, Birmingham, AL, USA
| | - Mary-Ann Bjornsti
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - E Lucile White
- High Throughput Screening Center, Southern Research, Birmingham, AL, USA
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41
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Production of functional small interfering RNAs by an amino-terminal deletion mutant of human Dicer. Proc Natl Acad Sci U S A 2015; 112:E6945-54. [PMID: 26621737 DOI: 10.1073/pnas.1513421112] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Although RNA interference (RNAi) functions as a potent antiviral innate-immune response in plants and invertebrates, mammalian somatic cells appear incapable of mounting an RNAi response and few, if any, small interfering RNAs (siRNAs) can be detected. To examine why siRNA production is inefficient, we have generated double-knockout human cells lacking both Dicer and protein kinase RNA-activated. Using these cells, which tolerate double-stranded RNA expression, we show that a mutant form of human Dicer lacking the amino-terminal helicase domain can process double-stranded RNAs to produce high levels of siRNAs that are readily detectable by Northern blot, are loaded into RNA-induced silencing complexes, and can effectively and specifically inhibit the expression of cognate mRNAs. Remarkably, overexpression of this mutant Dicer, but not wild-type Dicer, also resulted in a partial inhibition of Influenza A virus-but not poliovirus-replication in human cells.
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42
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Li G, Fu L, Jiang J, Ping Y, Huang Y, Wang Y. siRNA combinations mediate greater suppression of hepatitis B virus replication in mice. Cell Biochem Biophys 2015; 69:641-7. [PMID: 24549857 DOI: 10.1007/s12013-014-9846-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Hepatitis B virus (HBV) infection is a major world-wide health problem. The major obstacles for current anti-HBV therapy are the low efficacy and the occurrence of drug resistant HBV mutations. Recent studies have demonstrated that combination therapy can enhance antiviral efficacy and overcome shortcomings of established drugs. In this study, the inhibitory effect mediated by combination of siRNAs targeting different sites of HBV in transgenic mice was analyzed. HBsAg and HBeAg in the sera of the mice were analyzed by enzyme-linked immunoadsorbent assay, HBV DNA by real-time PCR and HBV mRNA by RT-PCR. Our data demonstrated that all the three siRNAs employed showed marked anti-HBV effects. The expression of HBsAg and the replication of HBV DNA could be specifically inhibited in a dose-dependent manner by siRNAs. Furthermore, combination of siRNAs compared with individual use of each siRNA, exerted a stronger inhibition on antigen expression and viral replication, even though the final concentration of siRNA used for therapy was the same. Secreted HBsAg and HBeAg in the serum of mice treated with siRNA combination were reduced by 96.7 and 96.6 %, respectively. Immunohistochemical detection of liver tissue revealed 91 % reduction of HBsAg-positive cells in the combination therapy group. The combination of siRNAs caused a greater inhibition in the levels of viral mRNA and DNA (90 and 87.7 %) relative to the control group. It was noted that the siRNA3 showed stronger inhibition of cccDNA (78.6 %). Our results revealed that combination of siRNAs mediated a stronger inhibition of viral replication and antigen expression in transgenic mice than single siRNAs.
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Affiliation(s)
- Guiqiu Li
- Department of Clinical Laboratory, the Affiliated First Hospital of Harbin Medical University, Harbin, 150001, China
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43
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Branchini BR, Southworth TL, Fontaine DM, Kohrt D, Talukder M, Michelini E, Cevenini L, Roda A, Grossel MJ. An enhanced chimeric firefly luciferase-inspired enzyme for ATP detection and bioluminescence reporter and imaging applications. Anal Biochem 2015; 484:148-53. [PMID: 26049097 PMCID: PMC4496250 DOI: 10.1016/j.ab.2015.05.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/26/2015] [Accepted: 05/29/2015] [Indexed: 10/23/2022]
Abstract
Firefly luciferases, which emit visible light in a highly specific ATP-dependent process, have been adapted for a variety of applications, including gene reporter assays, whole-cell biosensor measurements, and in vivo imaging. We previously reported the approximately 2-fold enhanced activity and 1.4-fold greater bioluminescence quantum yield properties of a chimeric enzyme that contains the N-domain of Photinus pyralis luciferase joined to the C-domain of Luciola italica luciferase. Subsequently, we identified 5 amino acid changes based on L. italica that are the main determinants of the improved bioluminescence properties. Further engineering to enhance thermal and pH stability produced a novel luciferase called PLG2. We present here a systematic comparison of the spectral and physical properties of the new protein with P. pyralis luciferase and demonstrate the potential of PLG2 for use in assays based on the detection of femtomole levels of ATP. In addition, we compared the performance of a mammalian codon-optimized version of the cDNA for PLG2 with the luc2 gene in HEK293T cells. Using an optimized low-cost assay system, PLG2 activity can be monitored in mammalian cell lysates and living cells with 4.4-fold and approximately 3.0-fold greater sensitivity, respectively. PLG2 could be an improved alternative to Promega's luc2 for reporter and imaging applications.
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Affiliation(s)
- Bruce R Branchini
- Department of Chemistry, Connecticut College, New London, CT 06320, USA.
| | - Tara L Southworth
- Department of Chemistry, Connecticut College, New London, CT 06320, USA
| | | | - Dawn Kohrt
- Department of Biology, Connecticut College, New London, CT 06320, USA
| | - Munya Talukder
- Department of Chemistry, Connecticut College, New London, CT 06320, USA
| | - Elisa Michelini
- Department of Chemistry "G. Ciamician", University of Bologna, 40126 Bologna, Italy
| | - Luca Cevenini
- Department of Chemistry "G. Ciamician", University of Bologna, 40126 Bologna, Italy
| | - Aldo Roda
- Department of Chemistry "G. Ciamician", University of Bologna, 40126 Bologna, Italy
| | - Martha J Grossel
- Department of Biology, Connecticut College, New London, CT 06320, USA
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Abstract
Hepatitis C virus (HCV) is a leading cause of chronic hepatitis and infects approximately three to four million people per year, about 170 million infected people in total, making it one of the major global health problems. In a minority of cases HCV is cleared spontaneously, but in most of the infected individuals infection progresses to a chronic state associated with high risk to develop liver cirrhosis, hepatocellular cancer, or liver failure. The treatment of HCV infection has evolved over the years. Interferon (IFN)-α in combination with ribavirin has been used for decades as standard therapy. More recently, a new standard-of-care treatment has been approved based on a triple combination with either HCV protease inhibitor telaprevir or boceprevir. In addition, various options for all-oral, IFN-free regimens are currently being evaluated. Despite substantial improvement of sustained virological response rates, some intrinsic limitations of these new direct-acting antivirals, including serious side effects, the risk of resistance development and high cost, urge the development of alternative or additional therapeutic strategies. Gene therapy represents a feasible alternative treatment. Small RNA technology, including RNA interference (RNAi) techniques and antisense approaches, is one of the potentially promising ways to investigate viral and host cell factors that are involved in HCV infection and replication. With this, newly developed gene therapy regimens will be provided to treat HCV. In this chapter, a comprehensive overview guides you through the current developments and applications of RNAi and microRNA-based gene therapy strategies in HCV treatment.
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Mammalian RNA virus-derived small RNA: biogenesis and functional activity. Microbes Infect 2015; 17:557-63. [PMID: 25980760 DOI: 10.1016/j.micinf.2015.04.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 04/30/2015] [Indexed: 11/24/2022]
Abstract
The role of virus-derived small RNAs (vsRNAs) has been identified as an antiviral mechanism in plants, arthropods, and nematodes. Although mammalian DNA viruses have been observed to encode functional miRNAs, whether RNA virus infection generates functional vsRNAs remains under discussion. This article reviews the most recent reports regarding pathways for generating vsRNAs and the identified vsRNA activity in mammalian cells infected with RNA viruses. We also discuss several hypotheses regarding the roles of mammalian vsRNAs and comment on the potential directions for this research field.
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46
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Weinheimer I, Jiu Y, Rajamäki ML, Matilainen O, Kallijärvi J, Cuellar WJ, Lu R, Saarma M, Holmberg CI, Jäntti J, Valkonen JPT. Suppression of RNAi by dsRNA-degrading RNaseIII enzymes of viruses in animals and plants. PLoS Pathog 2015; 11:e1004711. [PMID: 25747942 PMCID: PMC4352025 DOI: 10.1371/journal.ppat.1004711] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 01/28/2015] [Indexed: 01/08/2023] Open
Abstract
Certain RNA and DNA viruses that infect plants, insects, fish or poikilothermic animals encode Class 1 RNaseIII endoribonuclease-like proteins. dsRNA-specific endoribonuclease activity of the RNaseIII of rock bream iridovirus infecting fish and Sweet potato chlorotic stunt crinivirus (SPCSV) infecting plants has been shown. Suppression of the host antiviral RNA interference (RNAi) pathway has been documented with the RNaseIII of SPCSV and Heliothis virescens ascovirus infecting insects. Suppression of RNAi by the viral RNaseIIIs in non-host organisms of different kingdoms is not known. Here we expressed PPR3, the RNaseIII of Pike-perch iridovirus, in the non-hosts Nicotiana benthamiana (plant) and Caenorhabditis elegans (nematode) and found that it cleaves double-stranded small interfering RNA (ds-siRNA) molecules that are pivotal in the host RNA interference (RNAi) pathway and thereby suppresses RNAi in non-host tissues. In N. benthamiana, PPR3 enhanced accumulation of Tobacco rattle tobravirus RNA1 replicon lacking the 16K RNAi suppressor. Furthermore, PPR3 suppressed single-stranded RNA (ssRNA)--mediated RNAi and rescued replication of Flock House virus RNA1 replicon lacking the B2 RNAi suppressor in C. elegans. Suppression of RNAi was debilitated with the catalytically compromised mutant PPR3-Ala. However, the RNaseIII (CSR3) produced by SPCSV, which cleaves ds-siRNA and counteracts antiviral RNAi in plants, failed to suppress ssRNA-mediated RNAi in C. elegans. In leaves of N. benthamiana, PPR3 suppressed RNAi induced by ssRNA and dsRNA and reversed silencing; CSR3, however, suppressed only RNAi induced by ssRNA and was unable to reverse silencing. Neither PPR3 nor CSR3 suppressed antisense-mediated RNAi in Drosophila melanogaster. These results show that the RNaseIII enzymes of RNA and DNA viruses suppress RNAi, which requires catalytic activities of RNaseIII. In contrast to other viral silencing suppression proteins, the RNaseIII enzymes are homologous in unrelated RNA and DNA viruses and can be detected in viral genomes using gene modeling and protein structure prediction programs.
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Affiliation(s)
- Isabel Weinheimer
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Yaming Jiu
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | | | - Olli Matilainen
- Research Programs Unit, Translational Cancer Biology, and Institute of Biomedicine, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
| | - Jukka Kallijärvi
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Wilmer J. Cuellar
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Rui Lu
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Mart Saarma
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Carina I. Holmberg
- Research Programs Unit, Translational Cancer Biology, and Institute of Biomedicine, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
| | - Jussi Jäntti
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Jari P. T. Valkonen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
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Shen Y, Wang J, Li Y, Tian Y, Sun H, Ammar O, Tu J, Wang B, Sun C. Co-delivery of siRNA and paclitaxel into cancer cells by hyaluronic acid modified redox-sensitive disulfide-crosslinked PLGA–PEI nanoparticles. RSC Adv 2015. [DOI: 10.1039/c5ra03085d] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Schematic diagram showing the structure of the co-delivery nano-complex and the process of entering tumor cells.
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Affiliation(s)
- Yan Shen
- State Key Laboratory of Natural Medicines
- Department of Pharmaceutics
- School of Pharmacy
- China Pharmaceutical University
- Nanjing
| | - Jue Wang
- National Institute for Food and Drug Control
- Beijing
- China
| | - Yanan Li
- State Key Laboratory of Natural Medicines
- Department of Pharmaceutics
- School of Pharmacy
- China Pharmaceutical University
- Nanjing
| | - Yu Tian
- State Key Laboratory of Natural Medicines
- Department of Pharmaceutics
- School of Pharmacy
- China Pharmaceutical University
- Nanjing
| | - Huimin Sun
- National Institute for Food and Drug Control
- Beijing
- China
| | - Ouahab Ammar
- Department of Pharmacy
- Institute of Medical Sciences
- Batna Elhadj Lakhdar University
- Algeria
| | - Jiasheng Tu
- State Key Laboratory of Natural Medicines
- Department of Pharmaceutics
- School of Pharmacy
- China Pharmaceutical University
- Nanjing
| | - Buhai Wang
- Department of Oncology
- Subei People's Hospital
- Yangzhou
- China
| | - Chunmeng Sun
- State Key Laboratory of Natural Medicines
- Department of Pharmaceutics
- School of Pharmacy
- China Pharmaceutical University
- Nanjing
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48
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Lee H. Genetically engineered mouse models for drug development and preclinical trials. Biomol Ther (Seoul) 2014; 22:267-74. [PMID: 25143803 PMCID: PMC4131519 DOI: 10.4062/biomolther.2014.074] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 07/14/2014] [Accepted: 07/15/2014] [Indexed: 12/21/2022] Open
Abstract
Drug development and preclinical trials are challenging processes and more than 80% to 90% of drug candidates fail to gain approval from the United States Food and Drug Administration. Predictive and efficient tools are required to discover high quality targets and increase the probability of success in the process of new drug development. One such solution to the challenges faced in the development of new drugs and combination therapies is the use of low-cost and experimentally manageable in vivo animal models. Since the 1980's, scientists have been able to genetically modify the mouse genome by removing or replacing a specific gene, which has improved the identification and validation of target genes of interest. Now genetically engineered mouse models (GEMMs) are widely used and have proved to be a powerful tool in drug discovery processes. This review particularly covers recent fascinating technologies for drug discovery and preclinical trials, targeted transgenesis and RNAi mouse, including application and combination of inducible system. Improvements in technologies and the development of new GEMMs are expected to guide future applications of these models to drug discovery and preclinical trials.
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Affiliation(s)
- Ho Lee
- Division of Convergence Technology, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang 410-769, Republic of Korea
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49
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Gou LT, Dai P, Liu MF. Small noncoding RNAs and male infertility. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:733-45. [PMID: 25044449 DOI: 10.1002/wrna.1252] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 05/29/2014] [Accepted: 06/03/2014] [Indexed: 11/07/2022]
Abstract
Small noncoding RNAs (ncRNAs) are a novel class of gene regulators that modulate gene expression at transcriptional, post-transcriptional, and epigenetic levels, and they play crucial roles in almost all cellular processes in eukaryotes. Recent studies have indicated that several types of small noncoding RNAs, including microRNAs (miRNAs), endo-small interference RNAs (endo-siRNAs), and Piwi-interacting RNAs (piRNAs), are expressed in the male germline and are required for spermatogenesis in animals. In this review, we summarize the recent knowledge of these small noncoding RNAs in male germ cells and their biological functions and mechanisms of action in animal spermatogenesis.
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Affiliation(s)
- Lan-Tao Gou
- Center for RNA Research, State Key Laboratory of Molecular Biology-University of Chinese Academy of Sciences, Shanghai, China; Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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50
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Jiwaji M, Sandison ME, Reboud J, Stevenson R, Daly R, Barkess G, Faulds K, Kolch W, Graham D, Girolami MA, Cooper JM, Pitt AR. Quantification of functionalised gold nanoparticle-targeted knockdown of gene expression in HeLa cells. PLoS One 2014; 9:e99458. [PMID: 24926959 PMCID: PMC4057226 DOI: 10.1371/journal.pone.0099458] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 05/13/2014] [Indexed: 12/26/2022] Open
Abstract
INTRODUCTION Gene therapy continues to grow as an important area of research, primarily because of its potential in the treatment of disease. One significant area where there is a need for better understanding is in improving the efficiency of oligonucleotide delivery to the cell and indeed, following delivery, the characterization of the effects on the cell. METHODS In this report, we compare different transfection reagents as delivery vehicles for gold nanoparticles functionalized with DNA oligonucleotides, and quantify their relative transfection efficiencies. The inhibitory properties of small interfering RNA (siRNA), single-stranded RNA (ssRNA) and single-stranded DNA (ssDNA) sequences targeted to human metallothionein hMT-IIa are also quantified in HeLa cells. Techniques used in this study include fluorescence and confocal microscopy, qPCR and Western analysis. FINDINGS We show that the use of transfection reagents does significantly increase nanoparticle transfection efficiencies. Furthermore, siRNA, ssRNA and ssDNA sequences all have comparable inhibitory properties to ssDNA sequences immobilized onto gold nanoparticles. We also show that functionalized gold nanoparticles can co-localize with autophagosomes and illustrate other factors that can affect data collection and interpretation when performing studies with functionalized nanoparticles. CONCLUSIONS The desired outcome for biological knockdown studies is the efficient reduction of a specific target; which we demonstrate by using ssDNA inhibitory sequences targeted to human metallothionein IIa gene transcripts that result in the knockdown of both the mRNA transcript and the target protein.
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Affiliation(s)
- Meesbah Jiwaji
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- School of Life and Health Science, Aston University, Birmingham, United Kingdom
| | - Mairi E. Sandison
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Julien Reboud
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Ross Stevenson
- Centre for Molecular Nanometrology, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Rónán Daly
- School of Computing Science, University of Glasgow, Glasgow, United Kingdom
| | - Gráinne Barkess
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Karen Faulds
- Centre for Molecular Nanometrology, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Walter Kolch
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Systems Biology Ireland and the Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Duncan Graham
- Centre for Molecular Nanometrology, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Mark A. Girolami
- School of Computing Science, University of Glasgow, Glasgow, United Kingdom
- Department of Statistical Science, University College London, London, United Kingdom
| | - Jonathan M. Cooper
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Andrew R. Pitt
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- School of Life and Health Science, Aston University, Birmingham, United Kingdom
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