scholarly journals Target-specific precision of CRISPR-mediated genome editing

2018 ◽  
Author(s):  
Anob M. Chakrabarti ◽  
Tristan Henser-Brownhill ◽  
Josep Monserrat ◽  
Anna R. Poetsch ◽  
Nicholas M. Luscombe ◽  
...  
Keyword(s):  
Dna Repair ◽  
Human Cells ◽  
End Joining ◽  
Single Nucleotide ◽  
Dna Repair Mechanisms ◽  
Wide Range ◽  
Repair Mechanisms ◽  
Dna Editing ◽  
Nucleotide Insertions ◽  
Eukaryotic Genomes

ABSTRACTThe CRISPR-Cas9 system has successfully been adapted to edit the genome of various organisms. However, our ability to predict editing accuracy, efficacy and outcome at specific sites is limited by an incomplete understanding of how the bacterial system interacts with eukaryotic genomes and DNA repair machineries. Here, we performed the largest comparison of indel profiles to date, examining over one thousand sites in the genome of human cells, and uncovered general principles guiding CRISPR-mediated DNA editing. We find that precision of DNA editing varies considerably among sites, with some targets showing one highly-preferred indel and others displaying a wide range of infrequent indels. Editing precision correlates with editing efficiency, homology-associated end-joining for both insertions and deletions, and a preference for single-nucleotide insertions. Precise targets and the identity of their preferred indel can be predicted based on simple rules that mainly depend on the fourth nucleotide upstream of the PAM sequence. Regardless of precision, site-specific indel profiles are highly robust and depend on both DNA sequence and chromatin features. Our findings have important implications for clinical applications of CRISPR technology and reveal general patterns of broken end-joining that can inform us on DNA repair mechanisms in human cells.

scholarly journals Downregulation of both mismatch repair and non-homologous end-joining pathways in hypoxic brain tumour cell lines

2020 ◽  
Author(s):  
Sophie Cowman ◽  
Barry Pizer ◽  
Violaine Sée
Keyword(s):  
Gene Expression ◽  
Dna Repair ◽  
Mismatch Repair ◽  
Cell Lines ◽  
End Joining ◽  
Repair Gene ◽  
Dna Repair Mechanisms ◽  
Dna Repair Gene ◽  
Repair Mechanisms ◽  
Non Homologous End Joining

AbstractGlioblastoma, a grade IV astrocytoma, has a poor survival rate in part due to ineffective treatment options available. These tumours are heterogeneous with areas of low oxygen levels, termed hypoxic regions. Many intra-cellular signalling pathways, including DNA repair, can be altered by hypoxia. Since DNA damage induction and subsequent activation of DNA repair mechanisms is the cornerstone of glioblastoma treatment, alterations to DNA repair mechanisms could have a direct influence on treatment success. Our aim was to elucidate the impact of chronic hypoxia on DNA repair gene expression in a range of glioblastoma cell lines. We adopted a NanoString transcriptomic approach to examine the expression of 180 DNA repair related genes in four classical glioblastoma cell lines (U87-MG, U251-MG, D566-MG, T98G) exposed to 5 days of normoxia (21% O2), moderate (1% O2) or severe (0.1% O2) hypoxia. We observed altered gene expression in several DNA repair pathways including homologous recombination repair, non-homologous end-joining and mismatch repair, with hypoxia primarily resulting in downregulation of gene expression. The extend of gene expression changes was function of the hypoxic severity. Some, but not all, of these downregulations were directly under the control of HIF activity. For example, the downregulation of LIG4, a key component of non-homologous end-joining, was reversed upon inhibition of the hypoxia inducible factor (HIF). In contrast, the downregulation of the mismatch repair gene, PMS2, was not affected by HIF inhibition. This suggests that numerous molecular mechanisms lead to hypoxia-induced reprogramming of the transcriptional landscape of DNA repair. Whilst the global impact of hypoxia on DNA repair gene expression is likely to lead to genomic instability, tumorigenesis and reduced sensitivity to anti-cancer treatment, treatment re-sensitizing might require additional approaches to a simple HIF inhibition.

scholarly journals Downregulation of both mismatch repair and non-homologous end-joining pathways in hypoxic brain tumour cell lines

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11275
Author(s):  
Sophie Cowman ◽  
Barry Pizer ◽  
Violaine Sée
Keyword(s):  
Gene Expression ◽  
Dna Repair ◽  
Mismatch Repair ◽  
Cell Lines ◽  
End Joining ◽  
Repair Gene ◽  
Dna Repair Mechanisms ◽  
Dna Repair Gene ◽  
Repair Mechanisms ◽  
Non Homologous End Joining

Glioblastoma, a grade IV astrocytoma, has a poor survival rate in part due to ineffective treatment options available. These tumours are heterogeneous with areas of low oxygen levels, termed hypoxic regions. Many intra-cellular signalling pathways, including DNA repair, can be altered by hypoxia. Since DNA damage induction and subsequent activation of DNA repair mechanisms is the cornerstone of glioblastoma treatment, alterations to DNA repair mechanisms could have a direct influence on treatment success. Our aim was to elucidate the impact of chronic hypoxia on DNA repair gene expression in a range of glioblastoma cell lines. We adopted a NanoString transcriptomic approach to examine the expression of 180 DNA repair-related genes in four classical glioblastoma cell lines (U87-MG, U251-MG, D566-MG, T98G) exposed to 5 days of normoxia (21% O2), moderate (1% O2) or severe (0.1% O2) hypoxia. We observed altered gene expression in several DNA repair pathways including homologous recombination repair, non-homologous end-joining and mismatch repair, with hypoxia primarily resulting in downregulation of gene expression. The extent of gene expression changes was dependent on hypoxic severity. Some, but not all, of these downregulations were directly under the control of HIF activity. For example, the downregulation of LIG4, a key component of non-homologous end-joining, was reversed upon inhibition of the hypoxia-inducible factor (HIF). In contrast, the downregulation of the mismatch repair gene, PMS2, was not affected by HIF inhibition. This suggests that numerous molecular mechanisms lead to hypoxia-induced reprogramming of the transcriptional landscape of DNA repair. Whilst the global impact of hypoxia on DNA repair gene expression is likely to lead to genomic instability, tumorigenesis and reduced sensitivity to anti-cancer treatment, treatment re-sensitising might require additional approaches to a simple HIF inhibition.

scholarly journals Global and Local Manipulation of DNA Repair Mechanisms to Alter Site-Specific Gene Editing Outcomes in Hematopoietic Stem Cells

2020 ◽  
Vol 2 ◽  
Author(s):  
Elizabeth K. Benitez ◽  
Anastasia Lomova Kaufman ◽  
Lilibeth Cervantes ◽  
Danielle N. Clark ◽  
Paul G. Ayoub ◽  
...  
Keyword(s):  
Dna Repair ◽  
Gene Editing ◽  
Ex Vivo ◽  
Specific Gene ◽  
Gene Correction ◽  
End Joining ◽  
Therapeutic Success ◽  
Hematopoietic Stem ◽  
Dna Repair Mechanisms ◽  
Repair Mechanisms

Monogenic disorders of the blood system have the potential to be treated by autologous stem cell transplantation of ex vivo genetically modified hematopoietic stem and progenitor cells (HSPCs). The sgRNA/Cas9 system allows for precise modification of the genome at single nucleotide resolution. However, the system is reliant on endogenous cellular DNA repair mechanisms to mend a Cas9-induced double stranded break (DSB), either by the non-homologous end joining (NHEJ) pathway or by the cell-cycle regulated homology-directed repair (HDR) pathway. Here, we describe a panel of ectopically expressed DNA repair factors and Cas9 variants assessed for their ability to promote gene correction by HDR or inhibit gene disruption by NHEJ at the HBB locus. Although transient global overexpression of DNA repair factors did not improve the frequency of gene correction in primary HSPCs, localization of factors to the DSB by fusion to the Cas9 protein did alter repair outcomes toward microhomology-mediated end joining (MMEJ) repair, an HDR event. This strategy may be useful when predictable gene editing outcomes are imperative for therapeutic success.

scholarly journals Inherited Genetic Mutations and Polymorphisms in Malignant Mesothelioma: A Comprehensive Review

2020 ◽  
Vol 21 (12) ◽  
pp. 4327 ◽  
Author(s):  
Vasiliki Panou ◽  
Oluf Dimitri Røe
Keyword(s):  
Dna Repair ◽  
Malignant Mesothelioma ◽  
Gene Interaction ◽  
Genetic Alterations ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Dna Repair Mechanisms ◽  
Repair Mechanisms ◽  
Recombination Pathway ◽  
Inherited Mutations

Malignant mesothelioma (MM) is mainly caused by air-born asbestos but genetic susceptibility is also suspected to be a risk factor. Recent studies suggest an increasing number of candidate genes that may predispose to MM besides the well-characterized BRCA1-associated protein-1 gene. The aim of this review is to summarize the most important studies on germline mutations for MM. A total of 860 publications were retrieved from Scopus, PubMed and Web of Science, of which 81 met the inclusion criteria and were consider for this review. More than 50% of the genes that are reported to predispose to MM are involved in DNA repair mechanisms, and the majority of them have a role in the homologous recombination pathway. Genetic alterations in tumor suppressor genes involved in chromatin, transcription and hypoxia regulation have also been described. Furthermore, we identified several single nucleotide polymorphisms (SNPs) that may promote MM tumorigenesis as a result of an asbestos–gene interaction, including SNPs in DNA repair, carcinogen detoxification and other genes previously associated with other malignancies. The identification of inherited mutations for MM and an understanding of the underlying pathways may allow early detection and prevention of malignancies in high-risk individuals and pave the way for targeted therapies.

scholarly journals Acetylation regulates DNA repair mechanisms in human cells

Cell Cycle ◽  
2016 ◽  
Vol 15 (11) ◽  
pp. 1506-1517 ◽  
Author(s):  
Dorota Piekna-Przybylska ◽  
Robert A. Bambara ◽  
Lata Balakrishnan
Keyword(s):  
Dna Repair ◽  
Human Cells ◽  
Dna Repair Mechanisms ◽  
Repair Mechanisms

scholarly journals DNA Damage Response in Multiple Myeloma: The Role of the Tumor Microenvironment

Cancers ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 504
Author(s):  
Takayuki Saitoh ◽  
Tsukasa Oda
Keyword(s):  
Multiple Myeloma ◽  
Dna Damage ◽  
Dna Repair ◽  
Tumor Microenvironment ◽  
Dna Damage Response ◽  
Genetic Instability ◽  
Dna Repair Mechanisms ◽  
Damage Response ◽  
Repair Mechanisms

Multiple myeloma (MM) is an incurable plasma cell malignancy characterized by genomic instability. MM cells present various forms of genetic instability, including chromosomal instability, microsatellite instability, and base-pair alterations, as well as changes in chromosome number. The tumor microenvironment and an abnormal DNA repair function affect genetic instability in this disease. In addition, states of the tumor microenvironment itself, such as inflammation and hypoxia, influence the DNA damage response, which includes DNA repair mechanisms, cell cycle checkpoints, and apoptotic pathways. Unrepaired DNA damage in tumor cells has been shown to exacerbate genomic instability and aberrant features that enable MM progression and drug resistance. This review provides an overview of the DNA repair pathways, with a special focus on their function in MM, and discusses the role of the tumor microenvironment in governing DNA repair mechanisms.

scholarly journals Ancient Sturgeons Possess Effective DNA Repair Mechanisms: Influence of Model Genotoxicants on Embryo Development of Sterlet, Acipenser ruthenus

2020 ◽  
Vol 22 (1) ◽  
pp. 6
Author(s):  
Ievgeniia Gazo ◽  
Roman Franěk ◽  
Radek Šindelka ◽  
Ievgen Lebeda ◽  
Sahana Shivaramu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Damage ◽  
Dna Repair ◽  
Embryo Development ◽  
Hatching Rate ◽  
Embryo Survival ◽  
Dna Repair Mechanisms ◽  
Acipenser Ruthenus ◽  
Repair Mechanisms ◽  
Sterlet Acipenser Ruthenus

DNA damage caused by exogenous or endogenous factors is a common challenge for developing fish embryos. DNA damage repair (DDR) pathways help organisms minimize adverse effects of DNA alterations. In terms of DNA repair mechanisms, sturgeons represent a particularly interesting model due to their exceptional genome plasticity. Sterlet (Acipenser ruthenus) is a relatively small species of sturgeon. The goal of this study was to assess the sensitivity of sterlet embryos to model genotoxicants (camptothecin, etoposide, and benzo[a]pyrene), and to assess DDR responses. We assessed the effects of genotoxicants on embryo survival, hatching rate, DNA fragmentation, gene expression, and phosphorylation of H2AX and ATM kinase. Exposure of sterlet embryos to 1 µM benzo[a]pyrene induced low levels of DNA damage accompanied by ATM phosphorylation and xpc gene expression. Conversely, 20 µM etoposide exposure induced DNA damage without activation of known DDR pathways. Effects of 10 nM camptothecin on embryo development were stage-specific, with early stages, before gastrulation, being most sensitive. Overall, this study provides foundational information for future investigation of sterlet DDR pathways.

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