1
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Chan N, Huang J, Ma G, Zeng H, Donahue K, Wang Y, Li L, Xu W. The transcriptional elongation factor CTR9 demarcates PRC2-mediated H3K27me3 domains by altering PRC2 subtype equilibrium. Nucleic Acids Res 2022; 50:1969-1992. [PMID: 35137163 PMCID: PMC8887485 DOI: 10.1093/nar/gkac047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 01/07/2022] [Accepted: 01/14/2022] [Indexed: 01/27/2023] Open
Abstract
CTR9 is the scaffold subunit in polymerase-associated factor complex (PAFc), a multifunctional complex employed in multiple steps of RNA Polymerase II (RNAPII)-mediated transcription. CTR9/PAFc is well known as an evolutionarily conserved elongation factor that regulates gene activation via coupling with histone modifications enzymes. However, little is known about its function to restrain repressive histone markers. Using inducible and stable CTR9 knockdown breast cancer cell lines, we discovered that the H3K27me3 levels are strictly controlled by CTR9. Quantitative profiling of histone modifications revealed a striking increase of H3K27me3 levels upon loss of CTR9. Moreover, loss of CTR9 leads to genome-wide expansion of H3K27me3, as well as increased recruitment of PRC2 on chromatin, which can be reversed by CTR9 restoration. Further, CTR9 depletion triggers a PRC2 subtype switch from the less active PRC2.2, to the more active PRC2.1 with higher methyltransferase activity. As a consequence, CTR9 depletion generates vulnerability that renders breast cancer cells hypersensitive to PRC2 inhibitors. Our findings that CTR9 demarcates PRC2-mediated H3K27me3 levels and genomic distribution provide a unique mechanism that explains the transition from transcriptionally active chromatin states to repressive chromatin states and sheds light on the biological functions of CTR9 in development and cancer.
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Affiliation(s)
- Ngai Ting Chan
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Junfeng Huang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Gui Ma
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Hao Zeng
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kristine Donahue
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yidan Wang
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA,Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Wei Xu
- To whom correspondence should be addressed. Tel: +1 608 265 5540; Fax: +1 608 262 2824; Email :
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2
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Savarin M, Kamensek U, Znidar K, Todorovic V, Sersa G, Cemazar M. Evaluation of a Novel Plasmid for Simultaneous Gene Electrotransfer-Mediated Silencing of CD105 and CD146 in Combination with Irradiation. Int J Mol Sci 2021; 22:ijms22063069. [PMID: 33802812 PMCID: PMC8002395 DOI: 10.3390/ijms22063069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/12/2021] [Accepted: 03/13/2021] [Indexed: 12/12/2022] Open
Abstract
Targeting tumor vasculature through specific endothelial cell markers represents a promising approach for cancer treatment. Here our aim was to construct an antibiotic resistance gene-free plasmid encoding shRNAs to simultaneously target two endothelial cell markers, CD105 and CD146, and to test its functionality and therapeutic potential in vitro when delivered by gene electrotransfer (GET) and combined with irradiation (IR). Functionality of the plasmid was evaluated by determining the silencing of the targeted genes using qRT-PCR. Antiproliferative and antiangiogenic effects were determined by the cytotoxicity assay tube formation assay and wound healing assay in murine endothelial cells 2H-11. The functionality of the plasmid construct was also evaluated in malignant melanoma tumor cell line B16F10. Additionally, potential activation of immune response was measured by induction of DNA sensor STING and proinflammatory cytokines by qRT-PCR in endothelial cells 2H-11. We demonstrated that the plasmid construction was successful and can efficiently silence the expression of the two targeted genes. As a consequence of silencing, reduced migration rate and angiogenic potential was confirmed in 2H-11 endothelial cells. Furthermore, induction of DNA sensor STING and proinflammatory cytokines were determined, which could add to the therapeutic effectiveness when used in vivo. To conclude, we successfully constructed a novel plasmid DNA with two shRNAs, which holds a great promise for further in vivo testing.
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Affiliation(s)
- Monika Savarin
- Department of Experimental Oncology, Institute of Oncology Ljubljana, 1000 Ljubljana, Slovenia; (U.K.); (K.Z.); (V.T.); (G.S.)
- Correspondence: (M.S.); (M.C.)
| | - Urska Kamensek
- Department of Experimental Oncology, Institute of Oncology Ljubljana, 1000 Ljubljana, Slovenia; (U.K.); (K.Z.); (V.T.); (G.S.)
- Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Katarina Znidar
- Department of Experimental Oncology, Institute of Oncology Ljubljana, 1000 Ljubljana, Slovenia; (U.K.); (K.Z.); (V.T.); (G.S.)
| | - Vesna Todorovic
- Department of Experimental Oncology, Institute of Oncology Ljubljana, 1000 Ljubljana, Slovenia; (U.K.); (K.Z.); (V.T.); (G.S.)
| | - Gregor Sersa
- Department of Experimental Oncology, Institute of Oncology Ljubljana, 1000 Ljubljana, Slovenia; (U.K.); (K.Z.); (V.T.); (G.S.)
- Faculty of Health Sciences, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Maja Cemazar
- Department of Experimental Oncology, Institute of Oncology Ljubljana, 1000 Ljubljana, Slovenia; (U.K.); (K.Z.); (V.T.); (G.S.)
- Faculty of Health Sciences, University of Primorska, 6310 Izola, Slovenia
- Correspondence: (M.S.); (M.C.)
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3
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A multi-target dsRNA for simultaneous inhibition of yellow head virus and white spot syndrome virus in shrimp. J Biotechnol 2020; 321:48-56. [PMID: 32615142 DOI: 10.1016/j.jbiotec.2020.06.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 06/26/2020] [Accepted: 06/29/2020] [Indexed: 12/13/2022]
Abstract
Outbreaks of diseases caused by yellow head virus (YHV) and white spot syndrome virus (WSSV) infection in shrimp have resulted in economic losses worldwide. DsRNA-mediated RNAi has been used to control these viruses, and the best target genes for efficient inhibition of YHV and WSSV are the protease and ribonuleotide reductase small subunit (rr2), respectively. However, one dsRNA can suppress only one virus, and therefore the production of multi-target dsRNA to effectively inhibit both YHV and WSSV is needed. In this study, plasmids pETpro-rr2_one stem and pETpro-rr2_two stems were constructed to produce two different forms of multi-target dsRNA in E. coli, which were designed specifically to both YHV protease and WSSV rr2 genes. The potency of each dsRNA in inhibiting YHV and WSSV and reducing shrimp death were investigated in L. vannamei. Shrimp were injected with the dsRNAs into the hemolymph before challenge with YHV or WSSV. The results showed that both dsRNAs could inhibit the viruses, however the one stem construct was more effective than the two stems construct when shrimp were infected with WSSV. This study establishes a potential strategy for dual inhibition of YHV and WSSV for further application in shrimp aquaculture.
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4
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Aznan AN, Abdul Karim N, Wan Ngah WZ, Jubri Z. Critical factors for lentivirus-mediated PRDX4 gene transfer in the HepG2 cell line. Oncol Lett 2018; 16:73-82. [PMID: 29930713 PMCID: PMC6006497 DOI: 10.3892/ol.2018.8650] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 12/04/2017] [Indexed: 12/19/2022] Open
Abstract
Optimization of critical factors affects transduction efficiency and is able to reduce reagent consumption. The present study aimed to determine the optimum transduction conditions of small hairpin (sh)RNA against peroxiredoxin 4 (PRDX4) in the HepG2 cell line. Cell viability assays were conducted based on serum condition, incubation time, polybrene concentration and antibiotic dose selection. Non-targeting control shRNA was transduced into HepG2 cells in a 5-fold serial dilution, and colonies positive for green fluorescent protein were counted using ImageJ software. Reverse transcription-quantitative polymerase chain reaction and western blot analysis were performed to validate PRDX4 expression. The optimum cell density for transduction was 5.0×103 cells/well in 96-well plates to achieve 40 to 50% confluency the following day. The transduction media consisted of 10% fetal bovine serum (FBS) and 12 µg/ml polybrene, and was used to dilute lentiviral particles at a functional titer of 4.9×105 TU/ml for multiplicity of infection (MOI) of 20, 15 and 10, for 24 h of incubation. Selection with 7 µg/ml puromycin was performed in transduced cells. shRNA 3 was revealed to inhibit PRDX4 mRNA and protein expression. In conclusion, PRDX4 was successfully silenced in 5.0×103 HepG2 cells cultured with 10% FBS and 12 µg/ml polybrene, at a 4.9×105 TU/ml functional titer for MOI of 20, 15 and 10.
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Affiliation(s)
- Afiah Nasuha Aznan
- Department of Biochemistry, National University of Malaysia Medical Centre, Kuala Lumpur 56000, Malaysia
| | - Norwahidah Abdul Karim
- Department of Biochemistry, National University of Malaysia Medical Centre, Kuala Lumpur 56000, Malaysia
| | - Wan Zurinah Wan Ngah
- Department of Biochemistry, National University of Malaysia Medical Centre, Kuala Lumpur 56000, Malaysia
| | - Zakiah Jubri
- Department of Biochemistry, National University of Malaysia Medical Centre, Kuala Lumpur 56000, Malaysia
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5
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Najm FJ, Strand C, Donovan KF, Hegde M, Sanson KR, Vaimberg EW, Sullender ME, Hartenian E, Kalani Z, Fusi N, Listgarten J, Younger ST, Bernstein BE, Root DE, Doench JG. Orthologous CRISPR-Cas9 enzymes for combinatorial genetic screens. Nat Biotechnol 2018; 36:179-189. [PMID: 29251726 PMCID: PMC5800952 DOI: 10.1038/nbt.4048] [Citation(s) in RCA: 175] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 11/04/2017] [Indexed: 12/21/2022]
Abstract
Combinatorial genetic screening using CRISPR-Cas9 is a useful approach to uncover redundant genes and to explore complex gene networks. However, current methods suffer from interference between the single-guide RNAs (sgRNAs) and from limited gene targeting activity. To increase the efficiency of combinatorial screening, we employ orthogonal Cas9 enzymes from Staphylococcus aureus and Streptococcus pyogenes. We used machine learning to establish S. aureus Cas9 sgRNA design rules and paired S. aureus Cas9 with S. pyogenes Cas9 to achieve dual targeting in a high fraction of cells. We also developed a lentiviral vector and cloning strategy to generate high-complexity pooled dual-knockout libraries to identify synthetic lethal and buffering gene pairs across multiple cell types, including MAPK pathway genes and apoptotic genes. Our orthologous approach also enabled a screen combining gene knockouts with transcriptional activation, which revealed genetic interactions with TP53. The "Big Papi" (paired aureus and pyogenes for interactions) approach described here will be widely applicable for the study of combinatorial phenotypes.
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Affiliation(s)
- Fadi J Najm
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Christine Strand
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | | | - Mudra Hegde
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Kendall R Sanson
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Emma W Vaimberg
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | | | - Ella Hartenian
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Zohra Kalani
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Nicolo Fusi
- Microsoft Research New England, Cambridge, Massachusetts, USA
| | | | - Scott T Younger
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Bradley E Bernstein
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - David E Root
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - John G Doench
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
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6
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Shneor D, Folberg R, Pe'er J, Honigman A, Frenkel S. Stable knockdown of CREB, HIF-1 and HIF-2 by replication-competent retroviruses abrogates the responses to hypoxia in hepatocellular carcinoma. Cancer Gene Ther 2016; 24:64-74. [PMID: 27934882 PMCID: PMC5339434 DOI: 10.1038/cgt.2016.68] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 09/05/2016] [Accepted: 09/07/2016] [Indexed: 12/19/2022]
Abstract
The fast proliferation of tumor cells develops faster than the vasculature, resulting, in most malignant tumors, in generation of hypoxic regions. Hypoxia renders solid tumors resistant to radiation and chemotherapeutics while providing opportunities for tumor-selective therapies targeting tumor hypoxia. Here we exploit two properties of tumors: propagation of tumor cells and ongoing generation of hypoxic regions to construct a system that preferentially leads to the death of tumor cells and thus hinders tumor growth. We constructed murine leukemia virus replication-competent (RCR) viruses that infect only propagating cells. These viruses express small hairpin RNAs (shRNAs) targeting cyclic AMP-response-element binding protein (CREB), hypoxia-inducible factors 1 (HIF)-1 or HIF-2 individually or all three together (X3). These viruses efficiently infected in vitro human hepatocellular carcinoma (HepG2 and FLC4) cells and established persistence of the virus and knocked down the expression of the regulators of the hypoxia-responding genes. Knockdown of either HIF-1 or CREB or both in hypoxia reduced the expression of hypoxia-response elements- and CRE-mediated gene expression, diminished cell proliferation and increased caspase-3 activity. We did not detect any significant effect of the efficiently knocked down HIF-2 on any of the functions tested in vitro. Moreover, severe combined immunodeficiency mice implanted subcutaneously with HepG2 stably infected with recombinant RCRs showed reduction of tumor growth and vascular endothelial growth factor expression, and no hypoxia-guided neovascularization. Combined treatment (RCRs+doxorubicin) improved efficacy in the context of in vitro hypoxia and in vivo (with either vACE-CREB or vACE-X3). This synergistic effect may lead to an improved efficacy and safety profile of the treatment that may result in fewer side effects.
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Affiliation(s)
- D Shneor
- Department of Biochemistry and Molecular Biology, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem, Israel.,Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - R Folberg
- Departments of Pathology, Ophthalmology and Biomedical Sciences, Oakland University William Beaumont School of Medicine, Rochester, MI, USA
| | - J Pe'er
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - A Honigman
- Department of Biochemistry and Molecular Biology, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem, Israel.,Department of Biotechnology, Hadassah Academic College, Jerusalem, Israel
| | - S Frenkel
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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7
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Abstract
Genetic screens are invaluable tools for dissection of biological phenomena. Optimization of such screens to enhance discovery of candidate genes and minimize false positives is thus a critical aim. Here, we report several sources of error common to pooled genetic screening techniques used in mammalian cell culture systems, and demonstrate methods to eliminate these errors. We find that reverse transcriptase-mediated recombination during retroviral replication can lead to uncoupling of molecular tags, such as DNA barcodes (BCs), from their associated library elements, leading to chimeric proviral genomes in which BCs are paired to incorrect ORFs, shRNAs, etc This effect depends on the length of homologous sequence between unique elements, and can be minimized with careful vector design. Furthermore, we report that residual plasmid DNA from viral packaging procedures can contaminate transduced cells. These plasmids serve as additional copies of the PCR template during library amplification, resulting in substantial inaccuracies in measurement of initial reference populations for screen normalization. The overabundance of template in some samples causes an imbalance between PCR cycles of contaminated and uncontaminated samples, which results in a systematic artifactual depletion of GC-rich library elements. Elimination of contaminating plasmid DNA using the bacterial endonuclease Benzonase can restore faithful measurements of template abundance and minimize GC bias.
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8
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Hati Boruah JL, Ranjan R, Gogoi H, Pandey SK, Kumar D, Phukan AJ, Bori J, Sarkhel BC. Effect of Co-transfection of Anti-myostatin shRNA Constructs in Caprine Fetal Fibroblast Cells. Anim Biotechnol 2016; 27:44-51. [PMID: 26690650 DOI: 10.1080/10495398.2015.1074915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Knockdown of myostatin gene (MSTN), transforming growth factor-β superfamily, and a negative regulator of the skeletal muscle growth, by RNA interference (RNAi), has been reported to increase muscle mass in mammals. The current study was aimed to cotransfect two anti-MSTN short hairpin RNA (shRNA) constructs in caprine fetal fibroblast cells for transient silencing of MSTN gene. In the present investigation, approximately 89% MSTN silencing was achieved in transiently transfected caprine fetal fibroblast cells by cotransfection of two best out of four anti-MSTN shRNA constructs. Simultaneously, we also monitored the induction of IFN responsive genes (IFN), pro-apoptotic gene (caspase3) and anti-apoptotic gene (MCL-1) due to cotransfection of different anti-MSTN shRNA constructs. We observed induction of 0.66-19.12, 1.04-4.14, 0.50-3.43, and 0.42-1.98 for folds IFN-β, OAS1, caspase3, and MCL-1 genes, respectively (p < 0.05). This RNAi based cotransfection method could provide an alternative strategy of gene knockout and develop stable caprine fetal fibroblast cells. Furthermore, these stable cells can be used as a cell donor for the development of transgenic cloned embryos by somatic cell nuclear transfer (SCNT) technique.
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Affiliation(s)
- Jyoti Lakshmi Hati Boruah
- a Animal Biotechnology Center , Nanaji Deshmukh Veterinary Science University , Jabalpur , Madhya Pradesh , India
| | - Rakesh Ranjan
- a Animal Biotechnology Center , Nanaji Deshmukh Veterinary Science University , Jabalpur , Madhya Pradesh , India
| | - Hamen Gogoi
- a Animal Biotechnology Center , Nanaji Deshmukh Veterinary Science University , Jabalpur , Madhya Pradesh , India
| | - Saurabh Kumar Pandey
- a Animal Biotechnology Center , Nanaji Deshmukh Veterinary Science University , Jabalpur , Madhya Pradesh , India
| | - Dharmendra Kumar
- a Animal Biotechnology Center , Nanaji Deshmukh Veterinary Science University , Jabalpur , Madhya Pradesh , India
| | - Amlan Jyoti Phukan
- a Animal Biotechnology Center , Nanaji Deshmukh Veterinary Science University , Jabalpur , Madhya Pradesh , India
| | - Joygeswar Bori
- a Animal Biotechnology Center , Nanaji Deshmukh Veterinary Science University , Jabalpur , Madhya Pradesh , India
| | - Bikash Chandra Sarkhel
- a Animal Biotechnology Center , Nanaji Deshmukh Veterinary Science University , Jabalpur , Madhya Pradesh , India
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9
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Méndez C, Ahlenstiel CL, Kelleher AD. Post-transcriptional gene silencing, transcriptional gene silencing and human immunodeficiency virus. World J Virol 2015; 4:219-244. [PMID: 26279984 PMCID: PMC4534814 DOI: 10.5501/wjv.v4.i3.219] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Revised: 01/24/2015] [Accepted: 04/29/2015] [Indexed: 02/05/2023] Open
Abstract
While human immunodeficiency virus 1 (HIV-1) infection is controlled through continuous, life-long use of a combination of drugs targeting different steps of the virus cycle, HIV-1 is never completely eradicated from the body. Despite decades of research there is still no effective vaccine to prevent HIV-1 infection. Therefore, the possibility of an RNA interference (RNAi)-based cure has become an increasingly explored approach. Endogenous gene expression is controlled at both, transcriptional and post-transcriptional levels by non-coding RNAs, which act through diverse molecular mechanisms including RNAi. RNAi has the potential to control the turning on/off of specific genes through transcriptional gene silencing (TGS), as well as fine-tuning their expression through post-transcriptional gene silencing (PTGS). In this review we will describe in detail the canonical RNAi pathways for PTGS and TGS, the relationship of TGS with other silencing mechanisms and will discuss a variety of approaches developed to suppress HIV-1 via manipulation of RNAi. We will briefly compare RNAi strategies against other approaches developed to target the virus, highlighting their potential to overcome the major obstacle to finding a cure, which is the specific targeting of the HIV-1 reservoir within latently infected cells.
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10
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The expression of HIV-1 Vpu in monocytes causes increased secretion of TGF-β that activates profibrogenic genes in hepatic stellate cells. PLoS One 2014; 9:e88934. [PMID: 24551192 PMCID: PMC3923874 DOI: 10.1371/journal.pone.0088934] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 01/13/2014] [Indexed: 11/19/2022] Open
Abstract
There is faster progression to fibrosis in persons with liver injury who are also infected with HIV. Other reports have suggested that HIV can directly infect and activate stellate cells, and the viral Tat and gp160 proteins also induce profibrogenic factors from peripheral blood mononuclear cells (PBMCs). We tested the role of HIV-1 Vpu accessory protein in promoting profibrogenic activation of hepatic stellate cells. Human stellate LX2 cells were cocultured with human monocytic U937 cells stably expressing the Vpu protein or latently infected U1 cells knocked down for Vpu expression, LX2 cells were also cultured with the supernatants from these cells. The expression of profibrogenic markers was evaluated in LX2 cells usingquantitative reverse transcription polymerase chain reaction (qRT-PCR),western blotting, immunofluorescence,flow cytometry and ELISA were used to confirm and quantitate protein expression. Monocytic cells expressing Vpu increased the expression of profibrogenic markers in LX2 cells. The culture supernatants of these cells contained increased levels of transforming growth factor beta (TGF-β), which correlated with increased activity of the AP-1 transcription factor. Antibodies against TGF-β or a TGF-β receptor inhibitor (SB431452) reversed Vpu-mediated profibrogenic activation of LX2 cells, suggesting that TGF-β mediated these effects. The cytokine macrophage migration inhibitory factor (MIF) attenuated Vpu-mediated TGF-β secretion and profibrogenic effects on LX2 cells. Besides its other roles in pathogenesis, Vpu is likely to contribute to hepatic fibrosis through this hitherto unknown mechanism.
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11
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Ang J, Harris E, Hussey BJ, Kil R, McMillen DR. Tuning response curves for synthetic biology. ACS Synth Biol 2013; 2:547-67. [PMID: 23905721 PMCID: PMC3805330 DOI: 10.1021/sb4000564] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Indexed: 01/07/2023]
Abstract
Synthetic biology may be viewed as an effort to establish, formalize, and develop an engineering discipline in the context of biological systems. The ability to tune the properties of individual components is central to the process of system design in all fields of engineering, and synthetic biology is no exception. A large and growing number of approaches have been developed for tuning the responses of cellular systems, and here we address specifically the issue of tuning the rate of response of a system: given a system where an input affects the rate of change of an output, how can the shape of the response curve be altered experimentally? This affects a system's dynamics as well as its steady-state properties, both of which are critical in the design of systems in synthetic biology, particularly those with multiple components. We begin by reviewing a mathematical formulation that captures a broad class of biological response curves and use this to define a standard set of varieties of tuning: vertical shifting, horizontal scaling, and the like. We then survey the experimental literature, classifying the results into our defined categories, and organizing them by regulatory level: transcriptional, post-transcriptional, and post-translational.
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Affiliation(s)
- Jordan Ang
- Department of Chemical and Physical Sciences and Institute
for Optical Sciences, University of Toronto, Mississauga, Ontario, Canada L5L 1C6
| | - Edouard Harris
- Department of Chemical and Physical Sciences and Institute
for Optical Sciences, University of Toronto, Mississauga, Ontario, Canada L5L 1C6
| | - Brendan J. Hussey
- Department of Chemical and Physical Sciences and Institute
for Optical Sciences, University of Toronto, Mississauga, Ontario, Canada L5L 1C6
| | - Richard Kil
- Department of Chemical and Physical Sciences and Institute
for Optical Sciences, University of Toronto, Mississauga, Ontario, Canada L5L 1C6
| | - David R. McMillen
- Department of Chemical and Physical Sciences and Institute
for Optical Sciences, University of Toronto, Mississauga, Ontario, Canada L5L 1C6
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12
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Abstract
Since the first application of RNA interference (RNAi) in mammalian cells, the expression of short hairpin RNAs (shRNAs) for targeted gene silencing has become a benchmark technology. Using plasmid and viral vectoring systems, the transcription of shRNA precursors that are effectively processed by the RNAi pathway can lead to potent gene knockdown. The past decade has seen continual advancement and improvement to the various strategies that can be used for shRNA delivery, and the use of shRNAs for clinical applications is well underway. Driving these developments has been the many benefits afforded by shRNA technologies, including the stable integration of expression constructs for long-term expression, infection of difficult-to-target cell lines and tissues using viral vectors, and the temporal control of shRNA transcription by inducible promoters. The use of different effector molecule formats, promoters, and vector types, has meant that experiments can be tailored to target specific cell types and minimize cellular toxicities. Through the application of combinatorial RNAi (co-RNAi), multiple shRNA delivery strategies can improve gene knockdown, permit multiple transcripts to be targeted simultaneously, and curtail the emergence of viral escape mutants. This chapter reviews the history, cellular processing, and various applications of shRNAs in mammalian systems, including options for effector molecule design, vector and promoter types, and methods for multiple shRNA delivery.
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Affiliation(s)
- Luke S Lambeth
- Murdoch Childrens Research Institute, Royal Childrens Hospital, Melbourne, VIC, Australia.
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13
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Ramirez-Carvajal L, Long CR. Down-regulation of viral replication by lentiviral-mediated expression of short-hairpin RNAs against vesicular stomatitis virus ribonuclear complex genes. Antiviral Res 2012; 95:150-8. [DOI: 10.1016/j.antiviral.2012.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 05/03/2012] [Accepted: 05/17/2012] [Indexed: 10/28/2022]
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