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Lu J, Liu J, Guo Y, Zhang Y, Xu Y, Wang X. CRISPR-Cas9: A method for establishing rat models of drug metabolism and pharmacokinetics. Acta Pharm Sin B 2021; 11:2973-2982. [PMID: 34745851 PMCID: PMC8551406 DOI: 10.1016/j.apsb.2021.01.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/25/2020] [Accepted: 11/16/2020] [Indexed: 02/07/2023] Open
Abstract
The 2020 Nobel Prize in Chemistry recognized CRISPR-Cas9, a super-selective and precise gene editing tool. CRISPR-Cas9 has an obvious advantage in editing multiple genes in the same cell, and presents great potential in disease treatment and animal model construction. In recent years, CRISPR-Cas9 has been used to establish a series of rat models of drug metabolism and pharmacokinetics (DMPK), such as Cyp, Abcb1, Oatp1b2 gene knockout rats. These new rat models are not only widely used in the study of drug metabolism, chemical toxicity, and carcinogenicity, but also promote the study of DMPK related mechanism, and further strengthen the relationship between drug metabolism and pharmacology/toxicology. This review systematically introduces the advantages and disadvantages of CRISPR-Cas9, summarizes the methods of establishing DMPK rat models, discusses the main challenges in this field, and proposes strategies to overcome these problems.
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Key Words
- AAV, adeno-associated virus
- ADMET, absorption, distribution, metabolism, excretion and toxicity
- Animal model
- BSEP, bile salt export pump
- CRISPR-Cas, clustered regularly interspaced short palindromic repeats-CRISPR-associated
- CRISPR-Cas9
- DDI, drug–drug interaction
- DMPK, drug metabolism and pharmacokinetics
- DSB, double-strand break
- Drug metabolism
- Gene editing
- HBV, hepatitis B virus
- HDR, homology directed repair
- HIV, human immunodeficiency virus
- HPV, human papillomaviruses
- KO, knockout
- NCBI, National Center for Biotechnology Information
- NHEJ, non-homologous end joining
- OATP1B, organic anion transporting polypeptides 1B
- OTS, off-target site
- PAM, protospacer-associated motif
- Pharmacokinetics
- RNP, ribonucleoprotein
- SD, Sprague–Dawley
- SREBP-2, sterol regulatory element-binding protein 2
- T7E I, T7 endonuclease I
- TALE, transcriptional activator-like effector
- TALEN, transcriptional activators like effector nucleases
- WT, wild-type
- ZFN, zinc finger nucleases
- crRNAs, CRISPR RNAs
- pre-crRNA, pre-CRISPR RNA
- sgRNA, single guide RNA
- tracRNA, trans-activating crRNA
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Maestro S, Weber ND, Zabaleta N, Aldabe R, Gonzalez-Aseguinolaza G. Novel vectors and approaches for gene therapy in liver diseases. JHEP Rep 2021; 3:100300. [PMID: 34159305 PMCID: PMC8203845 DOI: 10.1016/j.jhepr.2021.100300] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/23/2021] [Accepted: 04/18/2021] [Indexed: 12/13/2022] Open
Abstract
Gene therapy is becoming an increasingly valuable tool to treat many genetic diseases with no or limited treatment options. This is the case for hundreds of monogenic metabolic disorders of hepatic origin, for which liver transplantation remains the only cure. Furthermore, the liver contains 10-15% of the body's total blood volume, making it ideal for use as a factory to secrete proteins into the circulation. In recent decades, an expanding toolbox has become available for liver-directed gene delivery. Although viral vectors have long been the preferred approach to target hepatocytes, an increasing number of non-viral vectors are emerging as highly efficient vehicles for the delivery of genetic material. Herein, we review advances in gene delivery vectors targeting the liver and more specifically hepatocytes, covering strategies based on gene addition and gene editing, as well as the exciting results obtained with the use of RNA as a therapeutic molecule. Moreover, we will briefly summarise some of the limitations of current liver-directed gene therapy approaches and potential ways of overcoming them.
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Key Words
- AAT, α1-antitrypsin
- AAV, adeno-associated virus
- AHP, acute hepatic porphyrias
- AIP, acute intermittent porphyria
- ALAS1, aminolevulic synthase 1
- APCs, antigen-presenting cells
- ASGCT, American Society of Gene and Cell Therapy
- ASGPR, asialoglycoprotein receptor
- ASOs, antisense oligonucleotides
- Ad, adenovirus
- CBS, cystathionine β-synthase
- CN, Crigel-Najjar
- CRISPR, clustered regularly interspaced short palindromic repeats
- CRISPR/Cas9, CRISPR associated protein 9
- DSBs, double-strand breaks
- ERT, enzyme replacement therapy
- FH, familial hypercholesterolemia
- FSP27, fat-specific protein 27
- GO, glycolate oxidase
- GSD1a, glycogen storage disorder 1a
- GT, gene therapy
- GUSB, β-glucuronidase
- GalNAc, N-acetyl-D-galactosamine
- HDAd, helper-dependent adenovirus
- HDR, homology-directed repair
- HT, hereditary tyrosinemia
- HemA/B, haemophilia A/B
- IDS, iduronate 2-sulfatase
- IDUA, α-L-iduronidase
- IMLD, inherited metabolic liver diseases
- ITR, inverted terminal repetition
- LDH, lactate dehydrogenase
- LDLR, low-density lipoprotein receptor
- LNP, Lipid nanoparticles
- LTR, long terminal repeat
- LV, lentivirus
- MMA, methylmalonic acidemia
- MPR, metabolic pathway reprograming
- MPS type I, MPSI
- MPS type VII, MPSVII
- MPS, mucopolysaccharidosis
- NASH, non-alcoholic steatohepatitis
- NHEJ, non-homologous end joining
- NHPs, non-human primates
- Non-viral vectors
- OLT, orthotopic liver transplantation
- OTC, ornithine transcarbamylase
- PA, propionic acidemia
- PB, piggyBac
- PCSK9, proprotein convertase subtilisin/kexin type 9
- PEG, polyethylene glycol
- PEI, polyethyleneimine
- PFIC3, progressive familial cholestasis type 3
- PH1, Primary hyperoxaluria type 1
- PKU, phenylketonuria
- RV, retrovirus
- S/MAR, scaffold matrix attachment regions
- SB, Sleeping Beauty
- SRT, substrate reduction therapy
- STK25, serine/threonine protein kinase 25
- TALEN, transcription activator-like effector nucleases
- TTR, transthyretin
- UCD, urea cycle disorders
- VLDLR, very-low-density lipoprotein receptor
- WD, Wilson’s disease
- ZFN, zinc finger nucleases
- apoB/E, apolipoprotein B/E
- dCas9, dead Cas9
- efficacy
- gene addition
- gene editing
- gene silencing
- hepatocytes
- immune response
- lncRNA, long non-coding RNA
- miRNAs, microRNAs
- siRNA, small-interfering RNA
- toxicity
- viral vectors
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Affiliation(s)
- Sheila Maestro
- Gene Therapy Area, Foundation for Applied Medical Research, University of Navarra, IdisNA, Pamplona, Spain
| | | | - Nerea Zabaleta
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA
| | - Rafael Aldabe
- Gene Therapy Area, Foundation for Applied Medical Research, University of Navarra, IdisNA, Pamplona, Spain
- Corresponding authors. Address: CIMA, Universidad de Navarra. Av. Pio XII 55 31008 Pamplona. Spain
| | - Gloria Gonzalez-Aseguinolaza
- Gene Therapy Area, Foundation for Applied Medical Research, University of Navarra, IdisNA, Pamplona, Spain
- Vivet Therapeutics, Pamplona, Spain
- Corresponding authors. Address: CIMA, Universidad de Navarra. Av. Pio XII 55 31008 Pamplona. Spain
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Ginn SL, Amaya AK, Liao SHY, Zhu E, Cunningham SC, Lee M, Hallwirth CV, Logan GJ, Tay SS, Cesare AJ, Pickett HA, Grompe M, Dilworth K, Lisowski L, Alexander IE. Efficient in vivo editing of OTC-deficient patient-derived primary human hepatocytes. JHEP Rep 2020; 2:100065. [PMID: 32039406 PMCID: PMC7005564 DOI: 10.1016/j.jhepr.2019.100065] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/12/2019] [Accepted: 12/15/2019] [Indexed: 12/19/2022] Open
Abstract
Background & Aims Genome editing technology has immense therapeutic potential and is likely to rapidly supplant contemporary gene addition approaches. Key advantages include the capacity to directly repair mutant loci with resultant recovery of physiological gene expression and maintenance of durable therapeutic effects in replicating cells. In this study, we aimed to repair a disease-causing point mutation in the ornithine transcarbamylase (OTC) locus in patient-derived primary human hepatocytes in vivo at therapeutically relevant levels. Methods Editing reagents for precise CRISPR/SaCas9-mediated cleavage and homology-directed repair (HDR) of the human OTC locus were first evaluated against an OTC minigene cassette transposed into the mouse liver. The editing efficacy of these reagents was then tested on the native OTC locus in patient-derived primary human hepatocytes xenografted into the FRG (Fah-/-Rag2-/-Il2rg-/-) mouse liver. A highly human hepatotropic capsid (NP59) was used for adeno-associated virus (AAV)-mediated gene transfer. Editing events were characterised using next-generation sequencing and restoration of OTC expression was evaluated using immunofluorescence. Results Following AAV-mediated delivery of editing reagents to patient-derived primary human hepatocytes in vivo, OTC locus-specific cleavage was achieved at efficiencies of up to 72%. Importantly, successful editing was observed in up to 29% of OTC alleles at clinically relevant vector doses. No off-target editing events were observed at the top 10 in silico-predicted sites in the genome. Conclusions We report efficient single-nucleotide correction of a disease-causing mutation in the OTC locus in patient-derived primary human hepatocytes in vivo at levels that, if recapitulated in the clinic, would provide benefit for even the most therapeutically challenging liver disorders. Key challenges for clinical translation include the cell cycle dependence of classical HDR and mitigation of unintended on- and off-target editing events. Lay summary The ability to efficiently and safely correct disease-causing mutations remains the holy grail of gene therapy. Herein, we demonstrate, for the first time, efficient in vivo correction of a patient-specific disease-causing mutation in the OTC gene in primary human hepatocytes, using therapeutically relevant vector doses. We also highlight the challenges that need to be overcome for this technology to be translated into clinical practice. Therapeutically relevant levels of single-nucleotide repair of the human OTC locus were achieved in vivo. Single-nucleotide editing of primary human hepatocytes was facilitated by a highly hepatotropic bioengineered AAV capsid. A novel human minigene platform proved highly effective for evaluation of human liver-specific genome editing reagents.
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Key Words
- 7 NGS, next-generation sequencing
- AAV, adeno-associated virus
- BrdU, bromodeoxyuridine
- CRISPR-Cas9
- FRG, Fah-/-Rag2-/-Il2rg-/-
- HDR, homology-directed repair
- ITR, inverted terminal repeats
- InDels, insertions and deletions
- LSP1, liver-specific promoter
- NHEJ, non-homologous end joining
- NP59 capsid
- OTC deficiency
- PAM, protospacer adjacent motif
- PRE, mutant form of the Woodchuck hepatitis virus posttranscriptional regulatory element
- RTA, Real Time Analysis
- SV40 pA, SV40 polyadenylation signal sequence
- SaCas9, Staphylococcus aureus Cas9 nuclease
- TBG, human thyroxine binding globulin promoter
- U6, RNA polymerase III promoter for human U6 snRNA
- WT, wild-type
- genome editing
- homology-directed repair
- humanised FRG mice
- pA, bovine growth hormone polyadenylation signal sequence
- primary human hepatocytes
- rAAV, recombinant adeno-associated virus
- recombinant AAV
- sgRNA, single guide RNA
- synthetic capsid
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Affiliation(s)
- Samantha L Ginn
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, Australia
| | - Anais K Amaya
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, Australia
| | - Sophia H Y Liao
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, Australia
| | - Erhua Zhu
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, Australia
| | - Sharon C Cunningham
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, Australia
| | - Michael Lee
- Telomere Length Regulation Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Claus V Hallwirth
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, Australia
| | - Grant J Logan
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, Australia
| | - Szun S Tay
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, Australia
| | - Anthony J Cesare
- Genome Integrity Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Hilda A Pickett
- Telomere Length Regulation Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Markus Grompe
- School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Kimberley Dilworth
- Translational Vectorology Group and Vector & Genome Engineering Facility, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Leszek Lisowski
- Translational Vectorology Group and Vector & Genome Engineering Facility, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia.,Military Institute of Hygiene and Epidemiology, Pulway, Poland
| | - Ian E Alexander
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, Australia.,Discipline of Child and Adolescent Health, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
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Venkatachalam S, Mettler E, Fottner C, Miederer M, Kaina B, Weber MM. The impact of the IGF-1 system of cancer cells on radiation response - An in vitro study. Clin Transl Radiat Oncol 2017; 7:1-8. [PMID: 29594222 PMCID: PMC5862664 DOI: 10.1016/j.ctro.2017.09.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 08/29/2017] [Accepted: 09/18/2017] [Indexed: 12/22/2022] Open
Abstract
Background Overexpression of the insulin-like growth factor-1 receptor (IGF-1R) is associated with increased cell proliferation, differentiation, transformation, and tumorigenicity. Additionally, signaling involved in the resistance of cancer cells to radiotherapy originates from IGF-1R. The purpose of this study was to investigate the role of the IGF-1 system in the radiation response and further evaluate its effect on the expression of DNA repair pathway genes. Methods To inhibit the IGF-1 system, we stably transfected the Caco-2 cell line to express a kinase-deficient IGF-1R mutant. We then studied the effects of this mutation on cell growth, the response to radiation, and clonogenic survival, as well as using a cell viability assay to examine DNA damage and repair. Finally, we performed immunofluorescence for γ-H2AX to examine double-strand DNA breaks and evaluated the expression of 84 key genes involved in DNA repair with a real-time PCR array. Results Mutant IGF-1R cells exhibited significantly blunted cell growth and viability, compared to wild-type cells, as well as reduced clonogenic survival after γ-irradiation. However, mutant IGF-1R cells did not show any significant delays in the repair of radiation-induced DNA double-strand breaks. Furthermore, expression of mutant IGF-1R significantly down-regulated the mRNA levels of BRCA2, a major protein involved in homologous recombination DNA repair. Conclusion These results indicate that blocking the IGF-1R-mediated signaling cascade, through the expression of a kinase-deficient IGF-1R mutant, reduces cell growth and sensitizes cancer cells to ionizing radiation. Therefore, the IGF-1R system could be a potential target to enhance radio-sensitivity and the efficacy of cancer treatments.
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Key Words
- BAX, BCL-2-associated X
- BCL-2, B-cell lymphoma 2
- BRCA2
- Caco-2-KR4, IGF-1R/KR clone number 4
- Colorectal carcinmoma
- Dominant negative mutant
- HRR, homologous recombination repair
- IGF-1R, insulin-like growth factor 1 receptor
- IGF-1R/KR, kinase-deficient IGF-1R
- IRS-1, insulin receptor substrate 1
- Insulin-like growth factor-1 receptor
- MVP, major vault protein
- NHEJ, non-homologous end joining
- PTEN, phosphatase and tensin homolog
- RAD 51
- Radiosensitivity
- SF, surviving fractions
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Affiliation(s)
| | - Esther Mettler
- Department of Endocrinology and Metabolic Diseases, University Medical Center, Mainz, Germany
- Corresponding author.
| | - Christian Fottner
- Department of Endocrinology and Metabolic Diseases, University Medical Center, Mainz, Germany
| | - Matthias Miederer
- Department of Nuclear Medicine, University Medical Center, Mainz, Germany
| | - Bernd Kaina
- Institute of Toxicology, University Medical Center, Mainz, Germany
| | - Matthias M. Weber
- Department of Endocrinology and Metabolic Diseases, University Medical Center, Mainz, Germany
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5
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Abstract
In the past few years, new technologies have arisen that enable higher efficiency of gene editing. With the increase ease of using gene editing technologies, it is important to consider the best method for transferring new genetic material to livestock animals. Microinjection is a technique that has proven to be effective in mice but is less efficient in large livestock animals. Over the years, a variety of methods have been used for cloning as well as gene transfer including; nuclear transfer, sperm mediated gene transfer (SMGT), and liposome-mediated DNA transfer. This review looks at the different success rate of these methods and how they have evolved to become more efficient. As well as gene editing technologies, including Zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and the most recent clustered regulatory interspaced short palindromic repeats (CRISPRs). Through the advancements in gene-editing technologies, generating transgenic animals is now more accessible and affordable. The goals of producing transgenic animals are to 1) increase our understanding of biology and biomedical science; 2) increase our ability to produce more efficient animals; and 3) produce disease resistant animals. ZFNs, TALENs, and CRISPRs combined with gene transfer methods increase the possibility of achieving these goals.
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Key Words
- BLG, β-lactoglobulin
- CRISPR
- CRISPRs, clustered regulatory interspaced short palindromic repeats
- EG, embryonic germ
- ES, Embryonic stem
- ESC, Embryonic stem cell
- HDR, homology directed repair
- ICM, inner cell mass
- ICSI, intracytoplasmic sperm injection
- NHEJ, non-homologous end joining
- NT, nuclear transfers
- OBCT, oocyte bisection technique
- PAM, protospacer adjacent motif
- PCR, polymerase chain reaction
- PGCS, primordial germ cells
- RVDs, repeat variable diresidues
- SMGT
- SMGT, sperm mediated gene transfer
- SV40, simian virus 40
- TALEN
- TALENs, transcription activator-like effector nucleases
- ZFN
- ZFN, Zinc-finger nucleases
- gene editing
- gene transfer
- iPSC, induced pluripotent stem cells
- nuclear transfer
- ssODN, single strand oligo nucleotide
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Affiliation(s)
- Samantha N Lotti
- a Department of Animal Sciences , University of Illinois at Urbana-Champaign , Urbana , Illinois , USA
| | - Kathryn M Polkoff
- a Department of Animal Sciences , University of Illinois at Urbana-Champaign , Urbana , Illinois , USA
| | - Marcello Rubessa
- b Carl R. Woese Institute for Genomic Biology, University of Illinois , Urbana , IL , USA
| | - Matthew B Wheeler
- a Department of Animal Sciences , University of Illinois at Urbana-Champaign , Urbana , Illinois , USA.,b Carl R. Woese Institute for Genomic Biology, University of Illinois , Urbana , IL , USA
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Abstract
DNA repair is an important signaling mechanism that is necessary to maintain genomic stability. Various types of DNA repair proteins are involved in the repair of different types of DNA damage. However, most of the DNA repair proteins are modified post-translation in order to activate their repair function, such as, ubiquitination, phosphorylation, acetylation, etc. Similarly, DNA repair proteins are also regulated by posttranscriptional modifications. Non-coding microRNAs (miRNAs) induced posttranscriptional regulation of mRNAs has gained attention in recent years. MiRNA-induced regulation of DNA repair proteins is of great interest, owing to its potential role in cancer therapy. In this review, we have summarized the role of different miRNAs in the regulation of various types of DNA repair proteins, which are essential for the maintenance of genomic stability.
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Key Words
- ATM, ataxia-telangiectasia mutated
- ATR, ataxia-telangiectasia mutated related
- BER, base excision repair
- DNA damage
- DNA repair
- DSB repair
- DSB, double strand break
- FA, Fanconi anemia
- Genomic instability
- HR, homologous recombination
- MIS, micro-instability syndrome
- NER
- NER, nucleotide excision repair
- NHEJ, non-homologous end joining
- TLS, translesion synthesis
- miRNAs
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Affiliation(s)
- Venkateswaran Natarajan
- Diagnostic Molecular Oncology Centre, Department of Pathology, National University Hospital, Singapore
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Kotula E, Berthault N, Agrario C, Lienafa MC, Simon A, Dingli F, Loew D, Sibut V, Saule S, Dutreix M. DNA-PKcs plays role in cancer metastasis through regulation of secreted proteins involved in migration and invasion. Cell Cycle 2016; 14:1961-72. [PMID: 26017556 DOI: 10.1080/15384101.2015.1026522] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The DNA-dependent protein kinase catalytic subunit (DNA-PKcs) plays a major role in DNA damage signaling and repair and is also frequently overexpressed in tumor metastasis. We used isogenic cell lines expressing different levels of DNA-PKcs to investigate the role of DNA-PKcs in metastatic development. We found that DNA-PKcs participates in melanoma primary tumor and metastasis development by stimulating angiogenesis, migration and invasion. Comparison of conditioned medium content from DNA-PKcs-proficient and deficient cells reveals that DNA-PKcs controls secretion of at least 103 proteins (including 44 metastasis-associated with FBLN1, SERPINA3, MMP-8, HSPG2 and the inhibitors of matrix metalloproteinases, such as α-2M and TIMP-2). High throughput analysis of secretomes, proteomes and transcriptomes, indicate that DNA-PKcs regulates the secretion of 85 proteins without affecting their gene expression. Our data demonstrate that DNA-PKcs has a pro-metastatic activity via the modification of the tumor microenvironment. This study shows for the first time a direct link between DNA damage repair and cancer metastasis and highlights the importance of DNA-PKcs as a potential target for anti-metastatic treatment.
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Key Words
- CM, conditioned media
- DNA damage
- DNA-PK
- DNA-PK, DNA-dependent protein kinase
- DNA-PKcs, DNA-PK catalytic subunit
- DSB, double-strand break
- ECM, extracellular matrix
- MMP inhibition
- MMP, matrix metalloproteinase
- MS, mass spectrometry
- NHEJ, non-homologous end joining
- SILAC, stable isotope labeling by amino acids in cell culture
- TIMP, tissue inhibitor of metalloproteinase.
- metastasis
- secretion
- α-2M, α-2-macroglobulin
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Affiliation(s)
- Ewa Kotula
- a Centre National de Recherche Scientifique (CNRS) UMR3347; Institut National de la Santé et de Recherche Médicale (INSERM) U1021; Institut Curie ; Orsay , France
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8
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Abstract
Maintenance of genome integrity relies on multiple DNA repair pathways as well as on checkpoint regulation. Activation of the checkpoint kinases Chk1 and Chk2 by DNA damage triggers cell cycle arrest and improved DNA repair, or apoptosis in case of excessive damage. Chk1 and Chk2 have been reported to act in a complementary or redundant fashion, depending on the physiological context. During secondary immunoglobulin (Ig) diversification in B lymphocytes, DNA damage is abundantly introduced by activation-induced cytidine deaminase (AID) and processed to mutations in a locus-specific manner by several error-prone DNA repair pathways. We have previously shown that Chk1 negatively regulates Ig somatic hypermutation by promoting error-free homologous recombination and Ig gene conversion. We now report that Chk2 shows opposite effects to Chk1 in the regulation of these processes. Chk2 inactivation in B cells leads to decreased Ig hypermutation and Ig class switching, and increased Ig gene conversion activity. This is linked to defects in non-homologous end joining and increased Chk1 activation upon interference with Chk2 function. Intriguingly, in the context of physiological introduction of substantial DNA damage into the genome during Ig diversification, the 2 checkpoint kinases thus function in an opposing manner, rather than redundantly or cooperatively.
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Key Words
- AID, activation-induced cytidine deaminase
- APE1, apurinic endonuclease 1
- ATM, ataxia telangiectasia mutated
- ATR, ataxia telangiectasia and rad3 related
- Chk, checkpoint kinase
- DNA repair
- HR, homologous recombination
- Ig, immunoglobulin
- MMR mismatch repair
- MMS, methyl methansulfonate
- NHEJ, non-homologous end joining
- UNG, uracil N-glycosilase
- checkpoint signaling
- germinal center
- immunoglobulin diversification
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Affiliation(s)
- Kathrin Davari
- a Department of Cell Biology; Institute of Biochemistry and Biophysics; Center for Molecular Biomedicine ; Friedrich-Schiller University Jena ; Jena , Germany
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9
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Abstract
DNA is the prime target of anticancer treatments. DNA damage triggers a series of signaling cascades promoting cellular survival, including DNA repair, cell cycle arrest, and autophagy. The elevated basal and/or stressful levels of both DNA repair and autophagy observed in tumor cells, in contrast to normal cells, have been identified as the most important drug-responsive programs that impact the outcome of anticancer therapy. The exact relationship between DNA repair and autophagy in cancer cells remains unclear. On one hand, autophagy has been shown to regulate some of the DNA repair proteins after DNA damage by maintaining the balance between their synthesis, stabilization, and degradation. One the other hand, some evidence has demonstrated that some DNA repair molecular have a crucial role in the initiation of autophagy. In this review, we mainly discuss the interplay between DNA repair and autophagy in anticancer therapy and expect to enlighten some effective strategies for cancer treatment.
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Key Words
- AMPK, adenosine monophosphate-activated protein kinase
- ATG5, autophagy-related gene 5
- ATM, ataxia-telangiectasia mutated
- ATR, ATM and Rad3-related
- BER, base excision repair
- Chk1, check-point kinase 1
- Chk2, check-point kinase 2
- DDR, DNA damage response
- DNA damage
- DNA damage response
- DNA repair
- DNA-PKcs, DNA-dependent protein kinase catalytic subunit
- DSBs, double-strand breaks
- HDAC, histone deacetylases
- HR, homologous recombination
- IR, ionizing radiation
- MGMT, O6 methylguanine –DNA methyltransferase
- MMR, mismatch repair
- MRN, Mre11-Rad50-Nbs1
- NER, nucleotide excision recombination
- NHEJ, non-homologous end joining
- OGG1, 8-oxoguannine DNA glycosidase
- PARP-1, poly (ADP-ribose) polymerase 1
- PI3K, phosphoinositide 3-kinase
- PML, promyelocytic leukemia
- SSBs, single-strand break
- TMZ, temozolomide
- TSC2, tuberous sclerosis complex 2
- anticancer therapy
- apoptosis
- autophagy
- cell cycle arrest
- mTOR, mammalian target of rapamycin
- γ-H2AX, phosphorylated histone
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Affiliation(s)
- Dan Zhang
- a Department of Gastroenterology; Xinqiao Hospital; Third Military Medical University ; Chongqing , China
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10
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Stovicek V, Borodina I, Forster J. CRISPR-Cas system enables fast and simple genome editing of industrial Saccharomyces cerevisiae strains. Metab Eng Commun 2015; 2:13-22. [PMID: 34150504 DOI: 10.1016/j.meteno.2015.03.001] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 01/21/2015] [Accepted: 03/11/2015] [Indexed: 11/24/2022] Open
Abstract
There is a demand to develop 3rd generation biorefineries that integrate energy production with the production of higher value chemicals from renewable feedstocks. Here, robust and stress-tolerant industrial strains of Saccharomyces cerevisiae will be suitable production organisms. However, their genetic manipulation is challenging, as they are usually diploid or polyploid. Therefore, there is a need to develop more efficient genetic engineering tools. We applied a CRISPR–Cas9 system for genome editing of different industrial strains, and show simultaneous disruption of two alleles of a gene in several unrelated strains with the efficiency ranging between 65% and 78%. We also achieved simultaneous disruption and knock-in of a reporter gene, and demonstrate the applicability of the method by designing lactic acid-producing strains in a single transformation event, where insertion of a heterologous gene and disruption of two endogenous genes occurred simultaneously. Our study provides a foundation for efficient engineering of industrial yeast cell factories. We developed CRISPR–Cas9-based system for gene disruptions in industrial yeast. We showed high rate of disruption efficiency in unrelated industrial strains. Gene knock-in may be performed simultaneously with gene disruption. Use of the described Cas9-based system results in marker-free stable genetic modifications. The method was applied for single-step construction of lactic acid-producing strains.
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Key Words
- Biorefineries
- CRISPR–Cas9
- CRISPR–Cas9, clustered regularly interspaced short palindromic repeats–CRISPR-associated endonuclease 9
- Chemical production
- DSB, double strand break
- GOI, gene of interest
- Genome editing
- HDR, homology-directed repair
- HR, homologous recombination
- Industrial yeast
- NHEJ, non-homologous end joining
- PAM, protospacer adjacent motif
- PI, propidium iodide
- SNPs, single nucleotide polymorphisms
- TALENs, transcription activator-like effector nucleases
- USER, uracil-specific excision reaction
- ZFNs, zinc finger nucleases
- crRNA, CRISPR RNA
- gRNA, guide RNA
- tracrRNA, trans-activating RNA
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Brandl C, Ortiz O, Röttig B, Wefers B, Wurst W, Kühn R. Creation of targeted genomic deletions using TALEN or CRISPR/Cas nuclease pairs in one-cell mouse embryos. FEBS Open Bio 2014; 5:26-35. [PMID: 25685662 PMCID: PMC4309836 DOI: 10.1016/j.fob.2014.11.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Revised: 11/25/2014] [Accepted: 11/27/2014] [Indexed: 12/26/2022] Open
Abstract
Targeted genomic deletions can be generated directly in one-cell mouse embryos using sequence-specific nucleases. Deletions occur by end ligation repair and are not supported by homologous recombination. TALEN as well as CRISPR/Cas nucleases can be used. Homozygous mutants exhibiting phenotypes can be obtained in a single step.
The use of TALEN and CRISPR/CAS nucleases is becoming increasingly popular as a means to edit single target sites in one-cell mouse embryos. Nevertheless, an area that has received less attention concerns the engineering of structural genome variants and the necessary religation of two distant double-strand breaks. Herein, we applied pairs of TALEN or sgRNAs and Cas9 to create deletions in the Rab38 gene. We found that the deletion of 3.2 or 9.3 kb, but not of 30 kb, occurs at a frequency of 6–37%. This is sufficient for the direct production of mutants by embryo microinjection. Therefore, deletions up to ∼10 kb can be readily achieved for modeling human disease alleles. This work represents an important step towards the establishment of new protocols that support the ligation of remote DSB ends to achieve even larger rearrangements.
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Affiliation(s)
- Christina Brandl
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany ; Technische Universität München, 85350 Freising-Weihenstephan, Germany
| | - Oskar Ortiz
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Bernhard Röttig
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany ; Technische Universität München, 85350 Freising-Weihenstephan, Germany
| | - Benedikt Wefers
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany ; Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE), 80336 Munich, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany ; Technische Universität München, 85350 Freising-Weihenstephan, Germany ; Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE), 80336 Munich, Germany ; Max-Planck-Institute of Psychiatry, 80804 Munich, Germany ; Munich Cluster for Systems Neurology (SyNergy), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
| | - Ralf Kühn
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany ; Technische Universität München, 85350 Freising-Weihenstephan, Germany ; Max-Delbrück-Centrum für Molekulare Medizin (MDC), 13125 Berlin, Germany
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Anuranjani, Bala M. Concerted action of Nrf2-ARE pathway, MRN complex, HMGB1 and inflammatory cytokines - implication in modification of radiation damage. Redox Biol 2014; 2:832-46. [PMID: 25009785 PMCID: PMC4085347 DOI: 10.1016/j.redox.2014.02.008] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 02/25/2014] [Accepted: 02/25/2014] [Indexed: 12/30/2022] Open
Abstract
Whole body exposure to low linear energy transfer (LET) ionizing radiations (IRs) damages vital intracellular bio-molecules leading to multiple cellular and tissue injuries as well as pathophysiologies such as inflammation, immunosuppression etc. Nearly 70% of damage is caused indirectly by radiolysis of intracellular water leading to formation of reactive oxygen species (ROS) and free radicals and producing a state of oxidative stress. The damage is also caused by direct ionization of biomolecules. The type of radiation injuries is dependent on the absorbed radiation dose. Sub-lethal IR dose produces more of DNA base damages, whereas higher doses produce more DNA single strand break (SSBs), and double strand breaks (DSBs). The Nrf2-ARE pathway is an important oxidative stress regulating pathway. The DNA DSBs repair regulated by MRN complex, immunomodulation and inflammation regulated by HMGB1 and various types of cytokines are some of the key pathways which interact with each other in a complex manner and modify the radiation response. Because the majority of radiation damage is via oxidative stress, it is essential to gain in depth understanding of the mechanisms of Nrf2-ARE pathway and understand its interactions with MRN complex, HMGB1 and cytokines to increase our understanding on the radiation responses. Such information is of tremendous help in development of medical radiation countermeasures, radioprotective drugs and therapeutics. Till date no approved and safe countermeasure is available for human use. This study reviews the Nrf2-ARE pathway and its crosstalk with MRN-complex, HMGB1 and cytokines (TNF-a, IL-6, IFN-? etc.). An attempt is also made to review the modification of some of these pathways in presence of selected antioxidant radioprotective compounds or herbal extracts. Exposure to low linear energy transfer (LET) ionizing radiation (IR) causes intracellular oxidative stress and activate the Nrf2-ARE antioxidant pathway. Irradiation also causes inflammation and DNA damage which affect other pathways related to MRN complex and HMGB1 proteins. The antioxidant Keap1-Nrf2-ARE pathway most importantly regulates intracellular oxidative stress. The interaction of Keap1-Nrf2-ARE pathway with HMGB1 regulated inflammation; MRN complex regulated DNA repair is reviewed.
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Key Words
- .OH, hydroxyl radical
- AP1, activator protein-1
- ARE, antioxidant response element
- ATM, ataxia telangiectasia mutagenesis
- Bcl-2, B cell lymphoma-2 protein
- CBP, CREB-binding protein
- Chk-2, checkpoint kinase-2 protein
- DAMP, death associated molecular pattern
- DDR, DNA damage response
- DGR, double glycine repeats
- DSB, double strands break
- FGF, fibroblast growth factor
- FGF2, fibroblast growth factor-2
- GM-CSF, granulocytes macrophages colony stimulating factor
- GPx, glutathione peroxidase
- GSH, glutathione (reduced)
- GSK-3ß, glycogen synthase kinase 3 beta
- HMGB1
- HMGB1, high mobility group Box 1
- HR, homologous recombination
- IR, ionizing radiation
- Keap1, Kelch like ECH associated protein 1
- LET, linear energy transfer
- MDA, malondialdehyde
- MIP, macrophages inflammatory proteins
- MRN complex
- MRN, Mre11, Rad50 and Nbs1 subunits
- MRP, multidrug resistance protein
- NADPH, nicotinamide adenine dinucleotide phosphate
- NES, nuclear export sequence
- NHEJ, non-homologous end joining
- NLS, nuclear localization sequence
- Nrf2-ARE pathway
- PKC, protein kinase C
- RAGE, receptor for advance glycation end products
- RIF, radiation induced foci
- RNS, reactive nitrogen species
- ROS, reactive oxygen species
- Radio-modification
- SOD, superoxide dismutase
- SSBs, single strand DNA breaks
- TRAIL, TNF related apoptosis inducing ligand
- TWEAK
- TWEAK, tumour necrosis factor weak inducer of apoptosis
- VEGF, vascular endothelial growth factor
- VSMC, vascular smooth muscle cells
- bFGF, basal fibroblast growth factor
- t-BHQ, tert butyl hydroquinone
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Affiliation(s)
- Anuranjani
- Radiation Biology Department, Institute of Nuclear Medicine and Allied Sciences, Brig SK Mazumdar Marg, Delhi -110054, India
| | - Madhu Bala
- Radiation Biology Department, Institute of Nuclear Medicine and Allied Sciences, Brig SK Mazumdar Marg, Delhi -110054, India
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