CRISPR/Cas9-mediated genome editing: from basic research to gene therapy

CRISPR/Cas9 mediated genome editing is one of the most significant molecular tools discovered to edit the desired genes. It has ushered in a new era of novel possibilities of gene therapy. CRISPR/Cas9 system was originally observed as a part of the adaptive immune system in bacteria. It later on was adapted to carry precise and targeted alterations to the DNA in human cells to be used for gene therapy to correct genetic disorders and treat various severe diseases associated with the genetic changes. Besides this, the CRISPR/Cas9 system has been employed in pharmacogenomics to develop new drugs based on the patient’s genes, in modifying the organisms for research and even for diagnostic purposes in developing CRISPR based COVID-9 test. The recent approval of a CRISPR/Cas9 cellular gene therapy by FDA named “Casgevy” to treat sickle cell anemia is a testimonial to the potentials of CRISPR/Cas9 system in developing innovative gene therapies. This review details the mechanisms of CRISPR/Cas9 gene editing and its utilization in the ongoing clinical trials in the treatment of not only the monogenic disorders like sickle cell disease, thalassemia, and genetic blindness but also in treating multi-factorial diseases like cancers, cardiac diseases, diabetes, autoimmune diseases, viral infections such as human immunodeficiency virus (HIV) etc. An attempt has also been made to discuss the various limitations, challenges and ethical frameworks encompassing CRISPR/Cas9 based gene therapy in clinical settings.

ZNF451 promotes DNA damage repair by recruiting 53BP1/MDC1 in A549 and HeLa cells / 中华放射医学与防护杂志

Objective:To investigate the role of SUMO E3 ligase ZNF451 in DNA damage repair and explore the underlying mechanism in non-small cell lung cancer A549 cells and cervical cancer HeLa cells.Methods:A549 cells and HeLa cells were irradiated with γ-ray irradiation or treated with etoposide. Cell proliferation viability was detected by the cell counting kit-8 assay. Protein expression was detected by Western blot assay. DNA damage repair level was detected by DR-GFP plasmid system, and the spatial positioning was detected by immunofluorescence.Results:Etoposide decreased the expression level of ZNF451 in a dose- and time- dependent manner. After treatment with 30, 50, 80 μmol/L etoposide, the cell viability were reduced after the knockdown of ZNF451 in A549 and HeLa cells(A549: t = 27.62, 25.61, 5.32, P<0.01; HeLa: t = 30.77, 21.28, 4.18, P<0.01). Furthermore, ZNF451 was recruited at DNA damage sites. A co-localization and endogenous interaction were found between ZNF451 and γ-H2AX after the treatment of irradiation or etoposide. Moreover, the expression level of γ-H2AX was significantly increased after treatment with 30, 50, 80 μmol/L etoposide(A549: t = 6.12, 10.67, 4.68, P<0.01; HeLa: t = 7.94, 9.81, 15.12, P<0.01)and the repair efficiency of NHEJ was reduced in ZNF451 knockdown cells( t = 18.60, P<0.05). Finally, the immunofluorescence assay showed that ZNF451 was co-localizated with 53BP1 and MDC1 after irradiation or etoposide treatment. Conclusions:Knockdown of ZNF451 inhibits cell proliferation and increases the level of DNA damage in A549 and HeLa cells. ZNF451 was recruited to DNA damage sites after DSBs and participated in NHEJ repair by co-localizing with DNA damage repair factor 53BP1/MDC1.

An efficient marker-free genome editing method for Aspergillus niger / 生物工程学报

Aspergillus niger is an important industrial strain which has been widely used for production of enzymes and organic acids. Genome modification of A. niger is required to further improve its potential for industrial production. CRISPR/Cas9 is a widely used genome editing technique for A. niger, but its application in industrial strains modification is hampered by the need for integration of a selection marker into the genome or low gene editing efficiency. Here we report a highly efficient marker-free genome editing method for A. niger based on CRISPR/Cas9 technique. Firstly, we constructed a co-expression plasmid of sgRNA and Cas9 with a replication initiation region fragment AMA1 (autonomously maintained in Aspergillus) by using 5S rRNA promoter which improved sgRNA expression. Meanwhile, a strain deficient in non-homologous end-joining (NHEJ) was developed by knocking out the kusA gene. Finally, we took advantage of the instability of plasmid containing AMA1 fragment to cure the co-expression plasmid containing sgRNA and Cas9 through passaging on non-selective plate. With this method, the efficiency of gene editing reached 100% when using maker-free donor DNA with a short homologous arm of 20 bp. This method may facilitate investigation of gene functions and construction of cell factories for A. niger.

cGAS guards against chromosome end-to-end fusions during mitosis and facilitates replicative senescence

As a sensor of cytosolic DNA, the role of cyclic GMP-AMP synthase (cGAS) in innate immune response is well established, yet how its functions in different biological conditions remain to be elucidated. Here, we identify cGAS as an essential regulator in inhibiting mitotic DNA double-strand break (DSB) repair and protecting short telomeres from end-to-end fusion independent of the canonical cGAS-STING pathway. cGAS associates with telomeric/subtelomeric DNA during mitosis when TRF1/TRF2/POT1 are deficient on telomeres. Depletion of cGAS leads to mitotic chromosome end-to-end fusions predominantly occurring between short telomeres. Mechanistically, cGAS interacts with CDK1 and positions them to chromosome ends. Thus, CDK1 inhibits mitotic non-homologous end joining (NHEJ) by blocking the recruitment of RNF8. cGAS-deficient human primary cells are defective in entering replicative senescence and display chromosome end-to-end fusions, genome instability and prolonged growth arrest. Altogether, cGAS safeguards genome stability by controlling mitotic DSB repair to inhibit mitotic chromosome end-to-end fusions, thus facilitating replicative senescence.

Research progress on HPV-positive oropharyngeal carcinoma sensitive to radiation therapy / 口腔疾病防治

@#Oropharyngeal carcinoma is a highly heterogeneous disease that is mainly caused by tobacco and alcohol abuse or high-risk human papillomavirus (HPV) infection. HPV-positive oropharyngeal carcinoma and HPV-negative oropharyngeal carcinoma have obvious differences in etiology, epidemiology and prognosis; therefore, different methods should be adopted for treatment. It is known that the TP53 gene is not mutated in HPV-positive oropharyngeal carcinoma, and radiation therapy can activate it and induce cell apoptosis via DNA damage. There are common repair pathways to DNA damage, such as nonhomologous end joining, and this pathway is more sensitive to radiotherapy under the inhibition of HPV oncoprotein. In addition, the further activation of the immune response under the effect of radiation also participates in the elimination of tumors. In this paper, we reviewed the research on the sensitivity of HPV-positive oropharyngeal cancer to radiotherapy to provide a scientific basis for targeted treatment for various pathogenic factors and clinical stages of oropharyngeal cancer in the future.

MRN complex is an essential effector of DNA damage repair / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

Genome stability can be threatened by both endogenous and exogenous agents. Organisms have evolved numerous mechanisms to repair DNA damage, including homologous recombination (HR) and non-homologous end joining (NHEJ). Among the factors associated with DNA repair, the MRE11-RAD50-NBS1 (MRN) complex (MRE11-RAD50-XRS2 in

Regulation of DNA double-strand break repair pathway choice: a new focus on 53BP1 / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

Maintenance of cellular homeostasis and genome integrity is a critical responsibility of DNA double-strand break (DSB) signaling. P53-binding protein 1 (53BP1) plays a critical role in coordinating the DSB repair pathway choice and promotes the non-homologous end-joining (NHEJ)-mediated DSB repair pathway that rejoins DSB ends. New insights have been gained into a basic molecular mechanism that is involved in 53BP1 recruitment to the DNA lesion and how 53BP1 then recruits the DNA break-responsive effectors that promote NHEJ-mediated DSB repair while inhibiting homologous recombination (HR) signaling. This review focuses on the up- and downstream pathways of 53BP1 and how 53BP1 promotes NHEJ-mediated DSB repair, which in turn promotes the sensitivity of poly(ADP-ribose) polymerase inhibitor (PARPi) in BRCA1-deficient cancers and consequently provides an avenue for improving cancer therapy strategies.

Role of deubiquitinating enzymes in DNA double-strand break repair / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

DNA is the hereditary material in humans and almost all other organisms. It is essential for maintaining accurate transmission of genetic information. In the life cycle, DNA replication, cell division, or genome damage, including that caused by endogenous and exogenous agents, may cause DNA aberrations. Of all forms of DNA damage, DNA double-strand breaks (DSBs) are the most serious. If the repair function is defective, DNA damage may cause gene mutation, genome instability, and cell chromosome loss, which in turn can even lead to tumorigenesis. DNA damage can be repaired through multiple mechanisms. Homologous recombination (HR) and non-homologous end joining (NHEJ) are the two main repair mechanisms for DNA DSBs. Increasing amounts of evidence reveal that protein modifications play an essential role in DNA damage repair. Protein deubiquitination is a vital post-translational modification which removes ubiquitin molecules or polyubiquitinated chains from substrates in order to reverse the ubiquitination reaction. This review discusses the role of deubiquitinating enzymes (DUBs) in repairing DNA DSBs. Exploring the molecular mechanisms of DUB regulation in DSB repair will provide new insights to combat human diseases and develop novel therapeutic approaches.

Effect and mechanism of down-regulating REV7 expression on the radiosensitivity of human colon cancer cell HCT116 / 中华放射肿瘤学杂志

Objective To evaluate the effect and mechanism of down-regulating the expression of REV7 on the radiosensitivity of human colon cancer cell HCT116.Methods HCT116 cells were cultured and the expression of REV7 was down-regulated by RNA interference technique.HCT116 cells were divided into the blank group,negative control transfected with negative RNA oligo group and REV7 expression down-regulation transfected with REV7 RNA oligo group,respectively.The cell proliferation was determined by colony formation assay.The expression levels of the proteins of relevant genes were detected by Western blot.The level of cell apoptosis and non-homologous end joining was evaluated.Results The colony formation rate was significantly reduced in THE REV7 siRNA group after 6Gy irradiation (P＜0.05).The down-regulating efficiency rate of REV7 gene was ＞ 60％ in the REV7 siRNA group.The expression levels of γ H2AX and Caspase9 were significantly up-regulated,whereas those of KU80 and XRCC4 were remarkably down-regulated in the REV7 siRNA group (all P＜0.05).Conclusions The radiosensitivity of human colon cancer cell HCT116 can be increased by down-regulating the expression of REV7.The underlying mechanism may be related to the lower incidence rate of non-homologous end joining.

Effect and mechanism of down-regulating REV7 expression on the radiosensitivity of human colon cancer cell HCT116 / 中华放射肿瘤学杂志

Objective@#To evaluate the effect and mechanism of down-regulating the expression of REV7 on the radiosensitivity of human colon cancer cell HCT116.@*Methods@#HCT116 cells were cultured and the expression of REV7 was down-regulated by RNA interference technique. HCT116 cells were divided into the blank group, negative control transfected with negative RNA oligo group and REV7 expression down-regulation transfected with REV7 RNA oligo group, respectively. The cell proliferation was determined by colony formation assay. The expression levels of the proteins of relevant genes were detected by Western blot. The level of cell apoptosis and non-homologous end joining was evaluated.@*Results@#The colony formation rate was significantly reduced in THE REV7 siRNA group after 6Gy irradiation (P<0.05). The down-regulating efficiency rate of REV7 gene was>60% in the REV7 siRNA group. The expression levels of γH2AX and Caspase9 were significantly up-regulated, whereas those of KU80 and XRCC4 were remarkably down-regulated in the REV7 siRNA group (all P<0.05).@*Conclusions@#The radiosensitivity of human colon cancer cell HCT116 can be increased by down-regulating the expression of REV7. The underlying mechanism may be related to the lower incidence rate of non-homologous end joining.

Inactivation of the NHEJ Activity of DNA-PKcs Prevents Fanconi Anemia Pre-Leukemic HSC Expansion

Fanconi anemia (FA) is a genetic disorder characterized by bone marrow failure and high risk of cancer particularly leukemia. Here we show that inactivation of the non-homologous end-joining (NHEJ) activity of DNA-PKcs prevented DNA damage-induced expansion of FA pre-leukemic hematopoietic stem cells (HSCs). Furthermore, we performed serial BM transplantation to demonstrate that the DNA damage-induced expanded FA HSC compartment contained pre-leukemic stem cells that required the NHEJ activity of DNA-PKcs to induce leukemia in the secondary recipients. These results suggest that NHEJ may collaborate with FA deficiency to promote DNA damage-induced expansion of pre-leukemic HSCs.

Research progress of SUMOylation modification in DNA double-strand break repair / 国际生物医学工程杂志

The small ubiquitin-like modified protein (SUMO) is a protein structurally similar to ubiquitin which is involved in post-translational modification of proteins. SUMOylation refers to the process that SUMO molecule covalently binding to the specific lysine site of target proteins through maturation, activation, binding and ligation by ubiquitin-like specific protease 1 (Ulp1), E1 activating enzyme, E2 binding enzyme, and E3 ligase. SUMOylation alters the activity of target proteins, which is involved in the regulation of various cellular functions such as transcriptional regulation, regulation of embryonic development, cellular stress, maintenance of chromatin structure and genomic stability. In recent years, it has been found that SUMOylation modification is also widely involved in DNA damage repair, especially DNA double-strand breaks (DSBs), which are the most serious types of DNA damage. SUMOylation is involved in almost all processes of DSBs repair, so its role in DNA damage repair has become a research hotspot. In this paper, the research progress of the regulation of SUMOylation in DSBs repair was reviewed.

Effect and mechanism of neuroepithelial cell transforming gene 1 on cellular radiosensitivity / 中华放射医学与防护杂志

Objective To study the effect of neuroepithelial cell transforming gene 1 (Net1) on the cellular radiosensitivity and underlying mechanism.Methods Real-time quantitative PCR was used to measure the variations in Net1 expression level upon irradiation.Radiosensitivity was analyzed by colonyforming assay after Net1-siRNAs.Net1-associated proteins were identified by co-immunoprecipitation.Results The Net1 mRNA level in the cells was increased significantly (t =-10.52,P ＜ 0.05) after irradiation.Compared to the control group,siRNA-mediated silencing of Net1 enhanced cell radiosensitivity (t =15.31,11.65,P ＜0.05).Net1 was found to interact with Ku70,Ku80 and DNA-PKcs under either normal conditions or after irradiation.Conclusions Net1 could protect cells from irradiation by interaction with DNA repair proteins in non-homologous end joining pathway.

Non-Homologous End Joining Repair Mechanism-Mediated Deletion of CHD7 Gene in a Patient with Typical CHARGE Syndrome

CHARGE syndrome MIM #214800 is an autosomal dominant syndrome involving multiple congenital malformations. Clinical symptoms include coloboma, heart defects, choanal atresia, retardation of growth or development, genital hypoplasia, and ear anomalies or deafness. Mutations in the chromodomain helicase DNA binding protein 7 (CHD7) gene have been found in 65-70% of CHARGE syndrome patients. Here, we describe a 16-month-old boy with typical CHARGE syndrome, who was referred for CHD7 gene analysis. Sequence analysis and multiplex ligation-dependent probe amplification were performed. A heterozygous 38,304-bp deletion encompassing exon 3 with a 4-bp insertion was identified. There were no Alu sequences adjacent to the breakpoints, and no sequence microhomology was observed at the junction. Therefore, this large deletion may have been mediated by non-homologous end joining. The mechanism of the deletion in the current case differs from the previously suggested mechanisms underlying large deletions or complex genomic rearrangements in the CHD7 gene, and this is the first report of CHD7 deletion by this mechanism worldwide.

Novel inhibitor of DNA ligase IV with a promising cancer therapeutic potential.

Cancer is a dreaded disease where effective and cheap drugs are wanting. A large body of research is trying to identify anti-cancer molecules from nature, including plants, marine organisms, microorganisms, etc., and to ultimately synthesize promising molecules in the laboratory. Antibodies to tumour antigens/ receptors, microtubule inhibitors and DNA linking agents have been developed and used as drugs. Today the thrust is on identifying druggable molecules within the tumour cell. Small molecule inhibitors, targeted against crucial enzymes such as kinases, has led to the discovery of important anti-cancer drugs such as Glivec and Gefitinib. There is a great deal of interest in the development and use of therapeutics that target DNA repair pathways. Raghavan and his group chose Ligase IV as their target in the DNA repair pathway (Srivastava et al. 2012) Maintenance of genomic integrity is essential for cell homeostasis. Efficient repair of DNA damage ensures genomic stability. However, cancer therapies such as radiation and chemotherapy function by damaging genomic DNA, by specifically targeting rapidly dividing cancer cells, ultimately leading to cell death. Most of the cancer cells are repair-deficient, thereby providing a therapeutic opportunity to target DNA repair machinery. Although radiation and genotoxic drugs are initially effective in arresting tumour growth and reducing tumour burden, resistance and disease progression eventually occur. The resistance is acquired due to constant selection pressure by the therapeutics. Genetic mutations in the DNA repair genes are not only the initiating event in a cancer cell but also its limitation because the mutated gene function is often required by the cancer cell to maintain its own survival. This limitation has been exploited to specifically kill the tumour cells by targeting the mutated DNA repair gene while sparing the normal ones, a concept known as ‘synthetic lethality’ (Kaelin 2005). One of the main DNA damage repair pathways is double strand break (DSB) repair, which includes nonhomologous end joining (NHEJ) and homologous recombination (HR). It is plausible that targeting the molecular machinery driving the DNA damage repair (DDR), particularly NHEJ with small molecule inhibitors, will effectively enhance the efficacy of current cancer treatments that generate DNA damage and exploit synthetic lethal interactions. Radiation therapy and chemotherapy leads to DSB where NHEJ plays a major role in providing resistance to these agents in a cancer cell. The initial inhibitor L189 against Ligase I, III and IV reported in literature was non-specific (Chen et al. 2008). Raghavan and his group overcame this limitation by targeted design using specific docking of Ligase IV and comparing with L189 (Srivastava et al. 2012). The clever strategy led to the discovery of a novel specific inhibitor SCR7 for Ligase IV. Using elegant experiments on cell lines and mouse model the authors convincingly demonstrated that SCR7 was a specific Ligase IV inhibitor. SCR7 inhibits end joining of double strand breaks in diverse cell types resulting in tumour regression by activation of p53 mediated apoptosis (figure 1). Notably SCR7 treatment did not result in any adverse effects in mice and did not inhibit Ligase III. The authors have envisaged and addressed the likely limitations of SCR7 as a potential anti-cancer drug in humans and have proposed that cancer cells, due to their higher replication, high DNA damage rate and defective cell-cycle checkpoints, will be more sensitive to SCR7 compared to surrounding normal tissues (Srivastava et al. 2012). This may also reduce the possibility of resistance to SCR7. The therapeutic efficacy of SCR7 could be enhanced by specific delivery of SCR7 to the tumour tissue and as adjuvant cancer therapy.

Up-regulation of DNA-PKcs and Its Mechanism in Human Glioma / 中国肿瘤临床

Objective: To detect the gene expression of Ku70, Ku80, ERCC4, lig4 and DNA-PKcs in non-homologous end joining pathway in human pdmary glioma tissues and normal brain tissues and to explore the underlying mechanism. Methods: The expression levels of Ku70, Ku80, ERCC4, lig4 and DNA-PKcsin in 36 glioma samples and 12 normal brain tissue samples were measured by SYBR Green real-time quantitative PCR. Methylation of DNA-PKcs was detected by methylation-specific PCR (MSP). Results: There was no significant difference in Ku70, Ku80, ERCC4 and lig4 expression between human primary glioma and normal brain tissues (P<0.05), while DNA-PKcs was significantly up-regulated (P= 0.002). The expression of DNA-PKcs was significantly higher in grade Ⅲ and Ⅳ glioma than that in grade Ⅱ glioma and normal brain tissues (P<0.05). Moreover, glioma tissues showed weaker methylation than normal brain tissues. Conclusion: The up-regulation of DNA-PKcs may be associated with pathogenesis of glioma. Demethylation of DNA-PKcs promoter is an important reason for its up-regulated expression in glioma.

DNA Double-Strand Breaks, Potential Targets for HBV Integration / 华中科技大学学报（医学）（英德文版）

Hepatitis B virus (HBV)-induced hepatocellular carcinoma (HCC) is one of the most frequently occurring cancers. Hepadnaviral DNA integrations are considered to be essential agents which can promote the process of the hepatocarcinogenesis. More and more researches were designed to find the relationship of the two. In this study, we investigated whether HBV DNA integration occurred at sites of DNA double-strand breaks (DSBs), one of the most detrimental DNA damage. An 18-bp I-SceI homing endonuclease recognition site was introduced into the DNA of HepG2 cell line by stable DNA transfection, then cells were incubated in patients' serum with high HBV DNA copies and at the same time, DSBs were induced by transient expression of I-SceI after transfection of an I-SceI expression vector. By using nest PCR, the viral DNA was detected at the sites of the break. It appeared that integration occurred between part of HBV x gene and the I-Scel induced breaks. The results suggested that DSBs, as the DNA damages, may serve as potential targets for bepadnaviral DNA insertion and the integrants would lead to widespread host genome changes necessarily. It provided a new site to investigate the integration.

Pathways and genes of DNA double-strand break repair associated with head and neck cancer

DNA double-strand breaks (DSBs) occur commonly in the all living and in cycling cells. They constitute one of the most severe form of DNA damage, because they affect both strand of DNA. DSBs result in cell death or a genetic alterations including deletion, loss of heterozygosity, translocation, and chromosome loss. DSBs arise from endogenous sources like metabolic products and reactive oxygen, and also exogenous factors like ionizing radiation. Defective DNA DSBs can lead to toxicity and large scale sequence rearrangement that can cause cancer and promote premature aging. There are two major pathways for their repair: homologous recombination(HR) and non-homologous end-joining(NHEJ). The HR pathway is a known "error-free" repair mechanism, in which a homologous sister chromatid serves as a template. NHEJ, on the other hand, is a "error-prone" pathway, in which the two termini of the broken DNA molecule are used to form compatible ends that are directly ligated. This review aims to provide a fundamental understanding of how HR and NHEJ pathways operate, cause genome instability, and what kind of genes during the pathways are associated with head and neck cancer.

Pathways and genes of DNA double-strand break repair associated with head and neck cancer

DNA double-strand breaks (DSBs) occur commonly in the all living and in cycling cells. They constitute one of the most severe form of DNA damage, because they affect both strand of DNA. DSBs result in cell death or a genetic alterations including deletion, loss of heterozygosity, translocation, and chromosome loss. DSBs arise from endogenous sources like metabolic products and reactive oxygen, and also exogenous factors like ionizing radiation. Defective DNA DSBs can lead to toxicity and large scale sequence rearrangement that can cause cancer and promote premature aging. There are two major pathways for their repair: homologous recombination(HR) and non-homologous end-joining(NHEJ). The HR pathway is a known "error-free" repair mechanism, in which a homologous sister chromatid serves as a template. NHEJ, on the other hand, is a "error-prone" pathway, in which the two termini of the broken DNA molecule are used to form compatible ends that are directly ligated. This review aims to provide a fundamental understanding of how HR and NHEJ pathways operate, cause genome instability, and what kind of genes during the pathways are associated with head and neck cancer.