1
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Abbasi SF, Mahjabeen I, Parveen N, Qamar I, Haq MFU, Shafique R, Saeed N, Ashraf NS, Kayani MA. Exploring homologous recombination repair and base excision repair pathway genes for possible diagnostic markers in hematologic malignancies. Mol Genet Genomics 2023; 298:1527-1543. [PMID: 37861816 DOI: 10.1007/s00438-023-02078-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 10/04/2023] [Indexed: 10/21/2023]
Abstract
Hematologic malignancies (HMs) are a collection of malignant transformations, originating from the cells in the bone marrow and lymphoid organs. HMs comprise three main types; leukemia, lymphoma, and multiple myeloma. Globally, HMS accounts for approximately 10% of newly diagnosed cancer. DNA repair pathways defend the cells from recurrent DNA damage. Defective DNA repair mechanisms such as homologous recombination repair (HRR), nucleotide excision repair (NER), and base excision repair (BER) pathways may lead to genomic instability, which initiates HM progression and carcinogenesis. Expression deregulation of HRR, NER, and BER has been investigated in various malignancies. However, no studies have been reported to assess the differential expression of selected DNA repair genes combinedly in HMs. The present study was designed to assess the differential expression of HRR and BER pathway genes including RAD51, XRCC2, XRCC3, APEX1, FEN1, PARP1, and XRCC1 in blood cancer patients to highlight their significance as diagnostic/ prognostic marker in hematological malignancies. The study cohort comprised of 210 blood cancer patients along with an equal number of controls. For expression analysis, q-RT PCR was performed. DNA damage was measured in blood cancer patients and controls using the comet assay and LORD Q-assay. Data analysis showed significant downregulation of selected genes in blood cancer patients compared to healthy controls. To check the diagnostic value of selected genes, the Area under curve (AUC) was calculated and 0.879 AUC was observed for RAD51 (p < 0.0001) and 0.830 (p < 0.0001) for APEX1. Kaplan-Meier analysis showed that downregulation of RAD51 (p < 0.0001), XRCC3 (p < 0.02), and APEX1 (p < 0.0001) was found to be associated with a significant decrease in survival of blood cancer patients. Cox regression analysis showed that deregulation of RAD51 (p < 0.0001), XRCC2 (p < 0.02), XRCC3 (p < 0.003), and APEX1 (p < 0.00001) was found to be associated with the poor prognosis of blood cancer patients. Comet assay showed an increased number of comets in blood cancer patients compared to controls. These results are confirmed by performing the LORD q-assay and an increased frequency of lesions/Kb was observed in selected genes in cancer patients compared to controls. Our results showed significant downregulation of RAD51, XRCC2, XRCC3, APEX1, FEN1, PARP1, and XRCC1 genes with increased DNA damage in blood cancer patients. The findings of the current research suggested that deregulated expression of HRR and BER pathway genes can act as a diagnostic/prognostic marker in hematologic malignancies.
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Affiliation(s)
- Sumaira Fida Abbasi
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan
| | - Ishrat Mahjabeen
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan.
| | - Neelam Parveen
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan
| | - Imama Qamar
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan
| | - Maria Fazal Ul Haq
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan
| | - Rabia Shafique
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan
| | - Nadia Saeed
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan
| | - Nida Sarosh Ashraf
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan
| | - Mahmood Akhtar Kayani
- Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan
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2
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Hillen AEJ, Hruzova M, Rothgangl T, Breur M, Bugiani M, van der Knaap MS, Schwank G, Heine VM. In vivo targeting of a variant causing vanishing white matter using CRISPR/Cas9. Mol Ther Methods Clin Dev 2022; 25:17-25. [PMID: 35317047 PMCID: PMC8917273 DOI: 10.1016/j.omtm.2022.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 02/19/2022] [Indexed: 11/17/2022]
Abstract
Vanishing white matter (VWM) is a leukodystrophy caused by recessive variants in subunits of eIF2B. At present, no curative treatment is available and patients often die at young age. Due to its monogenic nature, VWM is a promising candidate for the development of CRISPR/Cas9-mediated gene therapy. Here we tested a dual-AAV approach in VWM mice encoding CRISPR/Cas9 and a DNA donor template to correct a pathogenic variant in Eif2b5. We performed sequencing analysis to assess gene correction rates and examined effects on the VWM phenotype, including motor behavior. Sequence analysis demonstrated that over 90% of CRISPR/Cas9-induced edits at the targeted locus are insertion or deletion (indel) mutations, rather than precise corrections from the DNA donor template by homology-directed repair. Around half of the CRISPR/Cas9-treated animals died prematurely. VWM mice showed no improvement in motor skills, weight, or neurological scores at 7 months of age, and CRISPR/Cas9-treated controls displayed an induced VWM phenotype. In conclusion, CRISPR/Cas9-induced DNA double-strand breaks (DSBs) at the Eif2b5 locus did not lead to sufficient correction of the VWM variant. Moreover, indel formation in Eif2b5 induced an exacerbated VWM phenotype. Therefore, DSB-independent strategies like base- or prime editing might better suited for VWM correction.
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Affiliation(s)
- Anne E J Hillen
- Department of Pediatrics and Child Neurology, Emma Children's Hospital, Amsterdam Neuroscience, Amsterdam UMC, De Boelelaan 1117, 1081 Amsterdam, the Netherlands
| | - Martina Hruzova
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, 8093 Zurich, Switzerland.,Institute of Pharmacology and Toxicology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Tanja Rothgangl
- Institute of Pharmacology and Toxicology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Marjolein Breur
- Department of Pediatrics and Child Neurology, Emma Children's Hospital, Amsterdam Neuroscience, Amsterdam UMC, De Boelelaan 1117, 1081 Amsterdam, the Netherlands
| | - Marianna Bugiani
- Department of Pediatrics and Child Neurology, Emma Children's Hospital, Amsterdam Neuroscience, Amsterdam UMC, De Boelelaan 1117, 1081 Amsterdam, the Netherlands
| | - Marjo S van der Knaap
- Department of Pediatrics and Child Neurology, Emma Children's Hospital, Amsterdam Neuroscience, Amsterdam UMC, De Boelelaan 1117, 1081 Amsterdam, the Netherlands.,Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University, De Boelelaan 1085, 1081 Amsterdam, the Netherlands
| | - Gerald Schwank
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, 8093 Zurich, Switzerland.,Institute of Pharmacology and Toxicology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Vivi M Heine
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University, De Boelelaan 1085, 1081 Amsterdam, the Netherlands.,Department of Child and Adolescence Psychiatry, Emma Children's Hospital, Amsterdam Neuroscience, Amsterdam UMC, De Boelelaan 1085, 1081 Amsterdam, the Netherlands
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3
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Modulation of DNA double-strand break repair as a strategy to improve precise genome editing. Oncogene 2020; 39:6393-6405. [PMID: 32884115 DOI: 10.1038/s41388-020-01445-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 08/07/2020] [Accepted: 08/21/2020] [Indexed: 12/11/2022]
Abstract
In the present day, it is possible to incorporate targeted mutations or replace a gene using genome editing techniques such as customisable CRISPR/Cas9 system. Although induction of DNA double-strand breaks (DSBs) by genome editing tools can be repaired by both non-homologous end joining (NHEJ) and homologous recombination (HR), the skewness of the former pathway in human and other mammals normally result in imprecise repair. Scientists working at the crossroads of DNA repair and genome editing have devised new strategies for using a specific pathway to their advantage. Refinement in the efficiency of precise gene editing was witnessed upon downregulation of NHEJ by knockdown or using small molecule inhibitors on one hand, and upregulation of HR proteins and addition of HR stimulators, other hand. The exploitation of cell cycle phase differences together with appropriate donor DNA length/sequence and small molecules has provided further improvement in precise genome editing. The present article reviews the mechanisms of improving the efficiency of precise genome editing in several model organisms and in clinics.
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Poletto E, Baldo G, Gomez-Ospina N. Genome Editing for Mucopolysaccharidoses. Int J Mol Sci 2020; 21:E500. [PMID: 31941077 PMCID: PMC7014411 DOI: 10.3390/ijms21020500] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 02/07/2023] Open
Abstract
Genome editing holds the promise of one-off and potentially curative therapies for many patients with genetic diseases. This is especially true for patients affected by mucopolysaccharidoses as the disease pathophysiology is amenable to correction using multiple approaches. Ex vivo and in vivo genome editing platforms have been tested primarily on MSPI and MPSII, with in vivo approaches having reached clinical testing in both diseases. Though we still await proof of efficacy in humans, the therapeutic tools established for these two diseases should pave the way for other mucopolysaccharidoses. Herein, we review the current preclinical and clinical development studies, using genome editing as a therapeutic approach for these diseases. The development of new genome editing platforms and the variety of genetic modifications possible with each tool provide potential applications of genome editing for mucopolysaccharidoses, which vastly exceed the potential of current approaches. We expect that in a not-so-distant future, more genome editing-based strategies will be established, and individual diseases will be treated through multiple approaches.
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Affiliation(s)
- Edina Poletto
- Gene Therapy Center, Hospital de Clinicas de Porto Alegre, Porto Alegre 90035-007, Brazil; (E.P.); (G.B.)
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil
| | - Guilherme Baldo
- Gene Therapy Center, Hospital de Clinicas de Porto Alegre, Porto Alegre 90035-007, Brazil; (E.P.); (G.B.)
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil
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5
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Gomez-Ospina N, Scharenberg SG, Mostrel N, Bak RO, Mantri S, Quadros RM, Gurumurthy CB, Lee C, Bao G, Suarez CJ, Khan S, Sawamoto K, Tomatsu S, Raj N, Attardi LD, Aurelian L, Porteus MH. Human genome-edited hematopoietic stem cells phenotypically correct Mucopolysaccharidosis type I. Nat Commun 2019; 10:4045. [PMID: 31492863 PMCID: PMC6731271 DOI: 10.1038/s41467-019-11962-8] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 08/09/2019] [Indexed: 12/26/2022] Open
Abstract
Lysosomal enzyme deficiencies comprise a large group of genetic disorders that generally lack effective treatments. A potential treatment approach is to engineer the patient’s own hematopoietic system to express high levels of the deficient enzyme, thereby correcting the biochemical defect and halting disease progression. Here, we present an efficient ex vivo genome editing approach using CRISPR-Cas9 that targets the lysosomal enzyme iduronidase to the CCR5 safe harbor locus in human CD34+ hematopoietic stem and progenitor cells. The modified cells secrete supra-endogenous enzyme levels, maintain long-term repopulation and multi-lineage differentiation potential, and can improve biochemical and phenotypic abnormalities in an immunocompromised mouse model of Mucopolysaccharidosis type I. These studies provide support for the development of genome-edited CD34+ hematopoietic stem and progenitor cells as a potential treatment for Mucopolysaccharidosis type I. The safe harbor approach constitutes a flexible platform for the expression of lysosomal enzymes making it applicable to other lysosomal storage disorders. Mucopolysaccharidosis type I (MPSI) is a lysosomal storage disease caused by insufficient iduronidase (IDUA) activity. Here, the authors use an ex vivo genome editing approach to overexpress IDUA in human hematopoietic stem and progenitor cells and show it can phenotypically correct MSPI in mouse model.
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Affiliation(s)
- Natalia Gomez-Ospina
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
| | | | - Nathalie Mostrel
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, DK-8000, Aarhus C., Denmark.,Aarhus Institute of Advanced Studies (AIAS), Aarhus University, DK-8000, Aarhus C., Denmark
| | - Sruthi Mantri
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Rolen M Quadros
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE, USA
| | - Channabasavaiah B Gurumurthy
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE, USA.,Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Ciaran Lee
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Carlos J Suarez
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Shaukat Khan
- Nemours/ Alfred I. duPont Hospital for Children, Wilmington, DE, 19803, USA
| | - Kazuki Sawamoto
- Nemours/ Alfred I. duPont Hospital for Children, Wilmington, DE, 19803, USA
| | - Shunji Tomatsu
- Nemours/ Alfred I. duPont Hospital for Children, Wilmington, DE, 19803, USA
| | - Nitin Raj
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Laura D Attardi
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Laure Aurelian
- Stanford University School of Medicine, Stanford, CA, 94305, USA.,University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
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6
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Liu M, Rehman S, Tang X, Gu K, Fan Q, Chen D, Ma W. Methodologies for Improving HDR Efficiency. Front Genet 2019; 9:691. [PMID: 30687381 PMCID: PMC6338032 DOI: 10.3389/fgene.2018.00691] [Citation(s) in RCA: 186] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 12/11/2018] [Indexed: 12/26/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9) is a precise genome manipulating technology that can be programmed to induce double-strand break (DSB) in the genome wherever needed. After nuclease cleavage, DSBs can be repaired by non-homologous end joining (NHEJ) or homology-directed repair (HDR) pathway. For producing targeted gene knock-in or other specific mutations, DSBs should be repaired by the HDR pathway. While NHEJ can cause various length insertions/deletion mutations (indels), which can lead the targeted gene to lose its function by shifting the open reading frame (ORF). Furthermore, HDR has low efficiency compared with the NHEJ pathway. In order to modify the gene precisely, numerous methods arose by inhibiting NHEJ or enhancing HDR, such as chemical modulation, synchronized expression, and overlapping homology arm. Here we focus on the efficiency and other considerations of these methodologies.
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Affiliation(s)
- Mingjie Liu
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Saad Rehman
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Xidian Tang
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Kui Gu
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Qinlei Fan
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Dekun Chen
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Wentao Ma
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
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7
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Devkota S. The road less traveled: strategies to enhance the frequency of homology-directed repair (HDR) for increased efficiency of CRISPR/Cas-mediated transgenesis. BMB Rep 2018. [PMID: 30103848 PMCID: PMC6177507 DOI: 10.5483/bmbrep.2018.51.9.187] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Non-homologous end joining (NHEJ), and to a lesser extent, the error-free pathway known as homology-directed repair (HDR) are cellular mechanisms for recovery from double-strand DNA breaks (DSB) induced by RNA-guided programmable nuclease CRISPR/Cas. Since NHEJ is equivalent to using a duck tape to stick two pieces of metals together, the outcome of this repair mechanism is prone to error. Any out-of-frame mutations or premature stop codons resulting from NHEJ repair mechanism are extremely handy for loss-of-function studies. Substitution of a mutation on the genome with the correct exogenous repair DNA requires coordination via an error-free HDR, for targeted transgenesis. However, several practical limitations exist in harnessing the potential of HDR to replace a faulty mutation for therapeutic purposes in all cell types and more so in somatic cells. In germ cells after the DSB, copying occurs from the homologous chromosome, which increases the chances of incorporation of exogenous DNA with some degree of homology into the genome compared with somatic cells where copying from the identical sister chromatid is always preferred. This review summarizes several strategies that have been implemented to increase the frequency of HDR with a focus on somatic cells. It also highlights the limitations of this technology in gene therapy and suggests specific solutions to circumvent those barriers.
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Affiliation(s)
- Sushil Devkota
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
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8
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Devkota S. The road less traveled: strategies to enhance the frequency of homology-directed repair (HDR) for increased efficiency of CRISPR/Cas-mediated transgenesis. BMB Rep 2018; 51:437-443. [PMID: 30103848 PMCID: PMC6177507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Indexed: 09/29/2023] Open
Abstract
Non-homologous end joining (NHEJ), and to a lesser extent, the error-free pathway known as homology-directed repair (HDR) are cellular mechanisms for recovery from double-strand DNA breaks (DSB) induced by RNA-guided programmable nuclease CRISPR/Cas. Since NHEJ is equivalent to using a duck tape to stick two pieces of metals together, the outcome of this repair mechanism is prone to error. Any out-of-frame mutations or premature stop codons resulting from NHEJ repair mechanism are extremely handy for loss-of-function studies. Substitution of a mutation on the genome with the correct exogenous repair DNA requires coordination via an error-free HDR, for targeted transgenesis. However, several practical limitations exist in harnessing the potential of HDR to replace a faulty mutation for therapeutic purposes in all cell types and more so in somatic cells. In germ cells after the DSB, copying occurs from the homologous chromosome, which increases the chances of incorporation of exogenous DNA with some degree of homology into the genome compared with somatic cells where copying from the identical sister chromatid is always preferred. This review summarizes several strategies that have been implemented to increase the frequency of HDR with a focus on somatic cells. It also highlights the limitations of this technology in gene therapy and suggests specific solutions to circumvent those barriers. [BMB Reports 2018; 51(9): 437-443].
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Affiliation(s)
- Sushil Devkota
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093,
USA
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9
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Sarwar R, Sheikh AK, Mahjabeen I, Bashir K, Saeed S, Kayani MA. Upregulation of RAD51 expression is associated with progression of thyroid carcinoma. Exp Mol Pathol 2017; 102:446-454. [PMID: 28502582 DOI: 10.1016/j.yexmp.2017.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 04/21/2017] [Accepted: 05/08/2017] [Indexed: 01/21/2023]
Abstract
AIMS RAD51 participates in homologous recombination repair (HRR) of double-stranded DNA breaks (DSBs) which may cause genomic instability and cancer. The aim of this study was to investigate RAD51 gene expression at transcriptional and translational levels to measure mRNA and protein level and to correlate its relationship with proliferation marker, Ki67 in thyroid cancer patients. This study also explored correlation of these genes with different clinicopathological parameters of the study cohort by Spearman's rank correlation coefficient. METHODS Quantitative real time polymerase chain reaction (qRT-PCR) and immunohistochemistry were used to detect mRNA transcript levels and protein expression of RAD51 and Ki67 in 102 cases of thyroid cancer tissues and equal number of uninvolved healthy thyroid tissue controls. RESULTS Data showed that expression for both RAD51 and Ki67 was significantly increased in thyroid cancer (p<0.001). High RAD51 and Ki67 expression was associated with later stages, poor tissue differentiation, large tumor size, positive lymph node metastasis and distant metastasis. The correlation analysis demonstrated a strong positive correlation (r=0.461) between RAD51 and Ki67 on mRNA level and on protein level (r=0.866). Strong correlation was observed between clinicopathological characteristics and selected molecules. CONCLUSION The present study concluded that upregulation of RAD51 and overexpression of Ki67 may be associated with the progression of thyroid cancer.
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Affiliation(s)
- R Sarwar
- Cancer Genetics and Epigenetics Lab, Department of Biosciences, COMSATS Institute of Information Technology Islamabad, Pakistan
| | - A K Sheikh
- Pathology Department, Pakistan Institute of Medical Sciences Islamabad (PIMS), Pakistan
| | - I Mahjabeen
- Cancer Genetics and Epigenetics Lab, Department of Biosciences, COMSATS Institute of Information Technology Islamabad, Pakistan
| | - K Bashir
- Cancer Genetics and Epigenetics Lab, Department of Biosciences, COMSATS Institute of Information Technology Islamabad, Pakistan
| | - S Saeed
- Cancer Genetics and Epigenetics Lab, Department of Biosciences, COMSATS Institute of Information Technology Islamabad, Pakistan
| | - M A Kayani
- Cancer Genetics and Epigenetics Lab, Department of Biosciences, COMSATS Institute of Information Technology Islamabad, Pakistan.
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Abstract
With the introduction of precision genome editing using CRISPR-Cas9 technology, we have entered a new era of genetic engineering and gene therapy. With RNA-guided endonucleases, such as Cas9, it is possible to engineer DNA double strand breaks (DSB) at specific genomic loci. DSB repair by the error-prone non-homologous end-joining (NHEJ) pathway can disrupt a target gene by generating insertions and deletions. Alternatively, Cas9-mediated DSBs can be repaired by homology-directed repair (HDR) using an homologous DNA repair template, thus allowing precise gene editing by incorporating genetic changes into the repair template. HDR can introduce gene sequences for protein epitope tags, delete genes, make point mutations, or alter enhancer and promoter activities. In anticipation of adapting this technology for gene therapy in human somatic cells, much focus has been placed on increasing the fidelity of CRISPR-Cas9 and increasing HDR efficiency to improve precision genome editing. In this review, we will discuss applications of CRISPR technology for gene inactivation and genome editing with a focus on approaches to enhancing CRISPR-Cas9-mediated HDR for the generation of cell and animal models, and conclude with a discussion of recent advances and challenges towards the application of this technology for gene therapy in humans.
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Affiliation(s)
- Jayme Salsman
- a Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Graham Dellaire
- a Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada
- b Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
- c Beatrice Hunter Cancer Research Institute, Halifax, NS B3H 4R2, Canada
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11
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Tosato V, Sidari S, Bruschi CV. Bridge-induced chromosome translocation in yeast relies upon a Rad54/Rdh54-dependent, Pol32-independent pathway. PLoS One 2013; 8:e60926. [PMID: 23613757 PMCID: PMC3629078 DOI: 10.1371/journal.pone.0060926] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 03/04/2013] [Indexed: 11/18/2022] Open
Abstract
While in mammalian cells the genetic determinism of chromosomal translocation remains unclear, the yeast Saccharomyces cerevisiae has become an ideal model system to generate ad hoc translocations and analyze their cellular and molecular outcome. A linear DNA cassette carrying a selectable marker flanked by perfect homologies to two chromosomes triggers a bridge-induced translocation (BIT) in budding yeast, with variable efficiency. A postulated two-step process to produce BIT translocants is based on the cooperation between the Homologous Recombination System (HRS) and Break-Induced Replication (BIR); however, a clear indication of the molecular factors underlying the genetic mechanism is still missing. In this work we provide evidence that BIT translocation is elicited by the Rad54 helicase and completed by a Pol32-independent replication pathway. Our results demonstrate also that Rdh54 is involved in the stability of the translocants, suggesting a mitotic role in chromosome pairing and segregation. Moreover, when RAD54 is over-expressed, an ensemble of secondary rearrangements between repeated DNA tracts arise after the initial translocation event, leading to severe aneuploidy with loss of genetic material, which prompts the identification of fragile sites within the yeast genome.
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Affiliation(s)
- Valentina Tosato
- Yeast Molecular Genetics Laboratory, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy.
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12
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Smith KR, Chan S, Harris J. Human germline genetic modification: scientific and bioethical perspectives. Arch Med Res 2012; 43:491-513. [PMID: 23072719 DOI: 10.1016/j.arcmed.2012.09.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 09/06/2012] [Indexed: 11/29/2022]
Abstract
The latest mammalian genetic modification technology offers efficient and reliable targeting of genomic sequences, in the guise of designer genetic recombination tools. These and other improvements in genetic engineering technology suggest that human germline genetic modification (HGGM) will become a safe and effective prospect in the relatively near future. Several substantive ethical objections have been raised against HGGM including claims of unacceptably high levels of risk, damage to the status of future persons, and violations of justice and autonomy. This paper critically reviews the latest GM science and discusses the key ethical objections to HGGM. We conclude that major benefits are likely to accrue through the use of safe and effective HGGM and that it would thus be unethical to take a precautionary stance against HGGM.
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Affiliation(s)
- Kevin R Smith
- School of Contemporary Sciences, Abertay University, Dundee, United Kingdom.
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