Application of Artificially Induced Double-strand Breaks (DSB) and Triplex-forming Oligonucleotides (TFO) in the Improvement of Gene Targeting Efficiency

Gene targeting technology is an important means to investigate gene functions, but its efficiency of gene targeting is very low, especially for somatic cell targeting. Artificially induced double-strand breaks （DSB） and triplex forming oligonucleotide （TFO） are currently developed methods to improve the targeting efficiency. This paper summarized the basic principles, design ideas and application in gene targeting efficiency improvement of these two methods, analyzed and com- pared their characteristics, and finally proposed prospects for their future development.

DNA Double-Strand Breaks,Potential Targets for HBV Integration

Hepatitis B virus(HBV)-induced hepatocellular carcinoma(HCC) is one of the most fre-quently 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 integra-tion occurred between part of HBV x gene and the I-SceI induced breaks.The results suggested that DSBs,as the DNA damages,may serve as potential targets for hepadnaviral DNA insertion and the integrants would lead to widespread host genome changes necessarily.It provided a new site to investi-gate the integration.

Double-stranded DNA breaks and gene functions in recombination and meiosis

Meiotic prophase I is a long and complex phase. Homologous recombination is an important process that occurs between homologous chromosomes during meiotic prophase I. Formation of chiasmata, which hold homologous chromosomes together until the metaphase I to anaphase I transition, is critical for proper chromosome segregation. Recent studies have suggested that the SPO 11 proteins have conserved functions in a number of organisms in generating sites of double-stranded DNA breaks （DSBs） that are thought to be the starting points of homologous recombination. Processing of these sites of DSBs requires the function of RecA homologs, such as RAD5 1, DMC 1, and others, as suggested by mutant studies; thus the failure to repair these meiotic DSBs results in abnormal chromosomal alternations, leading to disrupted meiosis. Recent discoveries on the functions of these RecA homologs have improved the understanding of the mechanisms underlying meiotic homologous recombination.

Exposure to Long Magnetic Resonance Imaging Thermometry Does Not Cause Significant DNA Double-Strand Breaks on CF-1 Mice

The purpose of the study was to investigate if the high gradient strength and slew rate used for long MRI-thermometry monitoring could cause DNA double-stranded breaks (DSBs). To this end, an enzyme-linked immunosorbent assay (ELISA) was used to quantify γH2AX, a molecular marker for DSBs, in the blood of mice after a 6-hour exposure to magnetic resonance imaging (MRI). Fourteen CF-1 female mice were separated into 4 experimental groups: Untreated negative control, MRI-treated, MRI-Control, and exposed to ionizing radiation positive control. Untreated negative control was used as a baseline for ELISA to quantify γH2AX. MRI-treated consisted of a 6-hour continuous magnetic resonance imaging (MRI) echo planar imaging (EPI) sequence with a slew rate of 192 mT/m/s constituting a significantly longer imaging time than routine clinical imaging. MRI-control mice were maintained under the same conditions outside the MRI scanner for 6-hours. Mice in the irradiation group served as a positive control of DSBs and were exposed to either 2 Gy, 5 Gy or 10 Gy of ionizing radiation. DSBs in the blood lymphocytes from the treatment groups were analyzed using the γH2AX ELISA and compared. Total protein concentration in lysates was determined for each blood sample and averaged 1 ± 0.35 mg/mL. Irradiated positive controls were used to test radiation dose-dependency of the γH2AX ELISA assay where a linear dependency on radiation exposure was observed (r2 = 0.93) between untreated and irradiated samples. Mean and standard error mean of γH2AX formation were calculated and compared between each treatment group. Repeated measures 1-way ANOVA showed statistically significant differences between the means of irradiated controls and both the MRI-control and MRI-treated groups. There was no statistically significant difference between the MRI-treated samples and the MRI-control groups. Our results show that long MRI exposure at a high slew rate did not cause increased levels of γH2AX when compared to control mice, suggesting that no increase in DSBs was caused by the long MR thermometry imaging session. The novelty of this work contradicts other studies that have suggested MRI may cause DSBs;this work suggests an alternative cause of DNA damage.

DETECTION OF STRAND BREAKS OF DNA IN HUMAN EARLY CHORIONIC VILLUS CELLS INDUCED BY DIAGNOSTIC ULTRASOUND USING ^(32)P-LABELED ALU HYBRIDIZATION

Objective To explore if strand breaks of DNA in human early chorionic villus cells in uterus were induced by diagnostic ultrasound and to evaluate the method used for detection of single-stranded breaks and double-stranded breaks in human DNA. Methods 60 normal pregnant women aged 20-30, who underwent artificial abortion during 6-8 weeks of gestation, were randomly divided into 2 experimental groups: All 30 cases were exposed to diagnostic ultrasound in uterus for 10 minutes, and 24 hours later chorionic villi were extracted; the other 30 cases were taken as the control group. Single-stranded DNA and double-stranded DNA in villus cells in all cases were isolated by the alkaline unwinding combined with hydroxylapatite chromatography, and were quantitatively detected using 32 P-labeled Alu probe for dot-blotting hybridization. Results There was no significant difference in quantity and percentage in single-stranded DNA and double-stranded DNA between 2 groups (P>0.05). 32 P-Alu probe could only hybridize with human DNA, and could detect DNA isolated from as few as 2.5×10 3 chorionic villus cells and 0.45ng DNA in human leukocytes. Conclusion The results suggested that there were no DNA strand damages in human chorionic villus cells when the uterus was exposed to diagnostic ultrasound for 10 minutes. The method,^(32)P-Alu probe for dot-blotting hybridization, was even more specific, sensitive and accurate than conventional approaches.

Maternal gene Ooep may participate in homologous recombination-mediated DNA double-strand break repair in mouse oocytes

DNA damage in oocytes can cause infertility and birth defects. DNA double-strand breaks （DSBs） are highly deleterious and can substantially impair genome integrity. Homologous recombination （HR）-mediated DNA DSB repair plays dominant roles in safeguarding oocyte quantity and quality. However, little is known regarding the key players of the HR repair pathway in oocytes. Here, we identified oocyte-specific gene Ooep as a novel key component of the HR repair pathway in mouse oocytes. OOEP was required for efficient ataxia telangiectasia mutated （ATM） kinase activation and Rad51 recombinase （RAD51） focal accumulation at DNA DSBs. Ooep null oocytes were defective in DNA DSB repair and prone to apoptosis upon exogenous DNA damage insults. Moreover, Ooep null oocytes exhibited delayed meiotic maturation. Therefore, OOEP played roles in preserving oocyte quantity and quality by maintaining genome stability. Ooep expression decreased with the advance of maternal age, suggesting its involvement in maternal aging.

Telomeric DNA breaks in human induced pluripotent stem cells trigger ATR-mediated arrest and telomerase-independent telomere damage repair

Although mechanisms of telomere protection are well-defined in differentiated cells,how stem cells sense and respond to telomere dysfunction,in particular telomeric double-strand breaks(DSBs),is poorly characterized.Here,we report the DNA damage signaling,cell cycle,and transcriptome changes in human induced pluripotent stem cells(iPSCs)in response to telomere-internal DSBs.We engineer human iPSCs with an inducible TRF1-FokI fusion protein to acutely induce DSBs at telomeres.Using this model,we demonstrate that TRF1-FokI DSBs activate an ATR-dependent DNA damage response,which leads to p53-independent cell cycle arrest in G2.Using CRISPR–Cas9 to cripple the catalytic domain of telomerase reverse transcriptase,we show that telomerase is largely dispensable for survival and lengthening of TRF1-FokI-cleaved telomeres,which instead are effectively repaired by robust homologous recombination(HR).In contrast to HR-based telomere maintenance in mouse embryonic stem cells,where HR causes ZSCAN4-dependent extension of telomeres beyond their initial lengths,HR-based repair of telomeric breaks is sufficient to maintain iPSC telomeres at a normal length,which is compatible with sustained survival of the cells over several days of TRF1-FokI induction.Our findings suggest a previously unappreciated role for HR in telomere maintenance in telomerase-positive iPSCs and reveal distinct iPSC-specific responses to targeted telomeric DNA damage.

Low testing rates and high BRCA prevalence: Poly (ADP-ribose) polymerase inhibitor use in Middle East BRCA/homologous recombination deficiency-positive cancer patients

BACKGROUND Poly(ADP-ribose)polymerase inhibitors(PARPis)are approved as first-line therapies for breast cancer gene(BRCA)-positive,human epidermal growth factor receptor 2-negative locally advanced or metastatic breast cancer.They are also effective for new and recurrent ovarian cancers that are BRCA-or homologous recombination deficiency(HRD)-positive.However,data on these mutations and PARPi use in the Middle East are limited.AIM To assess BRCA/HRD prevalence and PARPi use in patients in the Middle East with breast/ovarian cancer.METHODS This was a single-center retrospective study of 57 of 472 breast cancer patients tested for BRCA mutations,and 25 of 65 ovarian cancer patients tested for HRD.These adult patients participated in at least four visits to the oncology service at our center between August 2021 and May 2023.Data were summarized using descriptive statistics and compared using counts and percentages.Response to treatment was assessed using Response Evaluation Criteria in Solid Tumors criteria.RESULTS Among the 472 breast cancer patients,12.1%underwent BRCA testing,and 38.5%of 65 ovarian cancer patients received HRD testing.Pathogenic mutations were found in 25.6%of the tested patients:26.3%breast cancers had germline BRCA(gBRCA)mutations and 24.0%ovarian cancers showed HRD.Notably,40.0%of gBRCA-positive breast cancers and 66.0%of HRD-positive ovarian cancers were Middle Eastern and Asian patients,respectively.PARPi treatment was used in 5(33.3%)gBRCA-positive breast cancer patients as first-line therapy(n=1;7-months progression-free),for maintenance(n=2;>15-months progression-free),or at later stages due to compliance issues(n=2).Four patients(66.6%)with HRD-positive ovarian cancer received PARPi and all remained progression-free.CONCLUSION Lower testing rates but higher BRCA mutations in breast cancer were found.Ethnicity reflected United Arab Emirates demographics,with breast cancer in Middle Eastern and ovarian cancer in Asian patients.

与真核生物DSBs修复有关的NHEJ途径研究进展

DNA双链断裂是真核生物最严重的DNA损伤形式。如果断裂的DNA双链无法及时修复,将可能导致细胞死亡。非同源末端连接途径在真核生物DSBs修复中起重要作用。综述了真核生物NHEJ途径中核心蛋白质Ku、DNA-PKcs、DNA连接酶IV、XRCC4、ARTEMIS和XIF等因子的结构和功能,并简要介绍了NHEJ修复途径的分子机制,其中涉及到DSBs位点蛋白复合体组装的两种模型。

BRCA1与DSB修复路径取向

乳腺癌易感基因1(BRCA1)是一个肿瘤抑制基因.BRCA1参与DNA末端切除、细胞周期调控以及染色体修饰等来维护基因组的稳定性.有研究表明,它能够促进正确的DNA双链断裂(DSBs)修复,如同源重组修复(HDR)和经典的非同源末端连接(C-NHEJ);而抑制错误性的DSB修复,如单链退火修复(SSA)和非经典的末端连接(A-EJ);其机制是通过与某些DNA修复相关蛋白质的相互作用来引导DSB修复.目前,BRCA1在DSB修复通路中的作用机制尚未完全明确,仍有待进一步的研究.本文主要阐述BRCA1在DSB各修复通路中是如何发挥其引导作用的.

The molecular control of meiotic double-strand break (DSB) formation and its significance in human infertility

Meiosis is an essential step in gametogenesis which is the key process in sexually reproducing organisms as meiotic aberrations may result in infertility. In meiosis, programmed DNA double-strand break (DSB) formation is one of the fundamental processes that are essential for maintaining homolog interactions and correcting segregation of chromosomes. Although the number and distribution of meiotic DSBs are tightly regulated, still abnormalities in DSB formation are known to cause meiotic arrest and infertility. This review is a detailed account of molecular bases of meiotic DSB formation, its evolutionary conservation, and variations in different species. We further reviewed the mutations of DSB formation genes in association with human infertility and also proposed the future directions and strategies about the study of meiotic DSB formation.

Ataxia-telangiectasia mutated plays an important role in cerebellar integrity and functionality

Accumulating evidence indicates that ataxia-telangiectasia mutated kinase is critical for maintaining cellular homeostasis and that it has both nuclear and cytoplasmic functions.However,the functions of ataxia-telangiectasia mutated that when lost lead to cerebellar degeneration are still unknown.In this review,we first describe the role of ataxia-telangiectasia mutated in cerebellar pathology.In addition to its canonical nuclear functions in DNA damage response circuits,ataxia-telangiectasia mutated functions in various cytoplasmic and mitochondrial processes that are critically important for cellular homeostasis.We discuss these functions with a focus on the role of ataxia-telangiectasia mutated in maintaining the homeostatic redox state.Finally,we describe the unique functions of ataxia-telangiectasia mutated in various types of neuronal and glial cells including cerebellar granule neurons,astrocytes,and microglial cells.

Hot spots of DNA double-strand breaks and genomic contacts of human rDNA units are involved in epigenetic regulation

DNA double-strand breaks(DSBs)are involved in many cellular mechanisms,including replication,transcription,and genome rearrangements.The recent observation that hot spots of DSBs in human chromosomes delimit DNA domains that possess coordinately expressed genes suggests a strong relationship between the organization of transcription patterns and hot spots of DSBs.In this study,we performed mapping of hot spots of DSBs in a human 43-kb ribosomal DNA(rDNA)repeated unit.We observed that rDNA units corresponded to the most fragile sites in human chromosomes and that these units possessed at least nine specific regions containing clusters of extremely frequently occurring DSBs,which were located exclusively in non-coding intergenic spacer(IGS)regions.The hot spots of DSBs corresponded to only a specific subset of DNase-hypersensitive sites,and coincided with CTCF,PARP1,and HNRNPA2B1 binding sites,and H3K4me3 marks.Our rDNA-4C data indicate that the regions of IGS containing the hot spots of DSBs often form contacts with specific regions in different chromosomes,including the pericentromeric regions,as well as regions that are characterized by H3K27ac and H3K4me3 marks,CTCF binding sites,ChIA-PET and RIP signals,and high levels of DSBs.The data suggest a strong link between chromosome breakage and several different mechanisms of epigenetic regulation of gene expression.

基于机器学习方法对人类基因组DNA双链断裂位点进行识别

DNA双链断裂(double-strand break,DSB)是细胞中一种严重的DNA损伤形式,与包括癌症、重组异常、神经元发育异常在内的多种基因组不稳定性疾病密切相关。由于成本和技术门槛的限制,高通量测序技术绘制的高分辨率DSB图谱十分有限,这阻碍了我们对不同物种基因组中DSB情况的认知。据此,我们建立了以随机森林(RF)、支持向量机(SVM)和逻辑回归(LR)三种分类器为基础算法的分类预测模型,对人类上皮细胞基因组DSB位点进行预测。除了之前预测研究中常用到的表观特征和DNA形状特征外,我们发现DNA序列特征(k-mer频数、GC含量、GC-偏移和互信息)也能表征DSB位点。同时,在考虑DNA物理性质、化学位移和自相关信息后,预测结果得到有效提高。将上述所有特征合并后进行预测,得到了较好的分类预测结果,其中逻辑回归(LR)的分类预测性能是最佳(AUC=0.97),与以往的预测结果相当(AUC=0.964)。另外,通过特征递增搜索方法,得到由294个特征组成的最优特征集,对应的AUC值达到0.974。

CpG-ODN对重离子辐射所致脾脏损伤的救治作用

本次研究主要探讨CpG-ODN对重离子辐射所致脾脏损伤的救治作用。实验中C57BL/6L小鼠受到5 Gy12C6+离子全身照射,在照射后急性期计算小鼠脾脏指数,苏木精-伊红(Hematoxylin-Eosin staining,HE)染色观察脾脏组织结构变化。另外,免疫组化法检测γ-H2AX蛋白含量以判断脾脏细胞DNA发生双链断裂(Double-strand break,DSB)情况,末端脱氧核苷酸转移酶介导的dUTP缺口末端标(Terminal deoxynucleotidyl transferase-mediatedd UTPnickandlabeling,TUNEL)法检测脾脏细胞凋亡水平,荧光标记法检测外周血CD19+B细胞数量。结果显示,经12C6+离子照射后CpG-ODN处理,小鼠脾脏指数提高,脾脏红髓萎缩程度减轻,白髓面积增大,其内淋巴B细胞排列密度提高,发生DSB和凋亡的细胞数量减少,外周血CD19+B细胞数量增加。这些表明CpG-ODN能减轻12C6+离子照射后脾脏损伤,其原因可能与CpG-ODN抑制细胞发生DSB和凋亡有关。

Effect of prolonging interval time between coronary angiography and percutaneous coronary intervention on X-ray-induced DNA double-strand breaks in blood lymphocytes

Background It is desirable to minimize the risk of adverse radiation effects associated with percutaneous coronary intervention.The aim of this study was to determine the impact of prolonging the interval between coronary angiography and percutaneous coronary intervention on X-ray-induced DNA double-strand breaks in blood lymphocytes using γ-H2AX immunofluorescence microscopy.Methods Blood samples of eight patients were taken before the first exposure to ionizing radiation,10 minutes,20 minutes,30 minutes,1 hour,and 24 hours after the last exposure to determine the γ-H2AX foci repair kinetics.Fifty-eight patients undergoing percutaneous coronary intervention were randomized to an intermittent radiation exposure group and a continuous radiation exposure group.Blood samples were taken before coronary angiography and 15 minutes after the last exposure.By enumerating γ-H2AX foci,the impact of prolonging the interval on DNA double-strand breaks was investigated.Student t-test was used to compare the difference in DNA double-strand breaks between the two groups.Results An increase in foci was found in all patients received percutaneous coronary intervention.The maximum number of γ-H2AX foci was found 10-20 minutes after the end of the last exposure.There was no statistically significant difference between the two groups in γ-H2AX foci at baseline.On average there were （0.79±0.15） γ-H2AX foci induced by interventional X-rays per lymphocyte in the continuous radiation exposure group and （0.66±0.21） in the intermittent radiation exposure group after exposure （P〈0.05）.Conclusions A significant number of γ-H2AX foci develop following the percutaneous coronary intervention procedures.The number of X-ray-induced DNA double-strand breaks may be decreased by prolonging the interval time between coronary angiography and percutaneous coronary intervention to 30 minutes.

与细胞周期G_2/M期进程相关的H2AX磷酸化

γH2AX焦点(foci)被普遍当做DNA双链断裂(DSB)损伤的分子标志物.为探讨细胞周期进程相关的H2AX磷酸化规律特征,采用胸腺嘧啶双阻滞结合噻氨酯哒唑(nocodazole)的后续处理,将HeLa细胞同步于有丝分裂的前中期.然后,用流式细胞仪检测细胞周期、Western印迹和免疫荧光法,观察γH2AX表达和γH2AX焦点的形成.结果显示,细胞进入G2/M期和有丝分裂过程中,γH2AX水平显著增加;在无DNA DSB发生的情况下,部分M期细胞中也存在大量的γH2AX焦点.随着细胞完成有丝分裂从M期退出再进入G1期,γH2AX的表达水平逐渐降低.这种γH2AX表达变化特征与G2/M期密切关联的PLK1和Cyclin B1的表达规律相类似.在4 Gy大剂量照射下,HeLa细胞于照后8到12 h出现明显的G2/M期阻滞.γH2AX焦点数在照后1 h达高峰,随后降低,照后8 h又上升,出现了第2个峰值.与之不同的是,在1 Gy低剂量照射下,细胞的G2/M期阻滞微弱,γH2AX焦点数在照后0.5 h最高,随后下降,且无反弹,符合DNA DSB的修复动力学特征.因此,将γH2AX当做DNA DSB分子标志物时,还需要考虑细胞周期变化的影响.γH2AX适合作为1 Gy以下照射的DNA双链断裂损伤的分子标志.

中性彗星分析法检测肿瘤细胞的放射敏感性

[目的]研究中性彗星分析法检测肿瘤细胞内在放射敏感性的可靠性和影响因素。[方法]人鼻咽高分化鳞癌细胞株CNE鄄1和人纤维肉瘤细胞株HT1080细胞,用6MVX线以0、100、200、300、400、600、800、1000cGy等不同剂量点照射,克隆形成法制定存活曲线,比较其放射敏感性的差异。然后进行两种细胞于600cGy照射后1、2、4、8h的中性彗星分析,以尾力矩为指标,动态检测不同时间点残留的DNA双链断裂,并与克隆形成分析结果相比较。[结果]克隆形成分析法显示CNE鄄1细胞的放射敏感性低于HT1080细胞,其2Gy照射后存活分数(SF2)和平均致死剂量D0值分别为0.397、0.331和1.898、1.287。两种细胞在照射后1、2、4h的中性彗星尾力矩分别为0.148±0.106、0.100±0.083、0.058±0.043和0.297±0.179、0.157±0.092、0.092±0.060,各时间点之间有显著性差异(P<0.05),但差别逐渐减小;照射后2h和4h的尾力矩比值分别为0.637和0.630,与SF2比值和D0比值的倒数(0.834和0.678)较接近;两种细胞照射后8h的尾力矩比较差异无显著性。[结论]中性彗星分析法与克隆形成分析法的检测结果有确切的相关性,照射后一定时间内的残留DNA双链断裂有可能成为检测肿瘤细胞放射敏感性的指标。

DNA-PKcs在鼻咽癌组织中的表达及其临床意义

背景与目的:DNA双链断裂(DNA double-strand break,DSB)是射线杀灭肿瘤细胞的主要机制,而同源重组(homologous recombination,HR)和非同源性末端连接(DNA nonhomologous end-joining,NHEJ)是DSB的两条重要修复途径。DNA-PK催化亚单位(catalytic subunit of DNA-dependent protein kinase,DNA-PKcs)是NHEJ途径的主要修复蛋白之一,在DSB中发挥着重要作用。本研究旨在通过检测鼻咽癌组织中DNA-PKcs的表达情况,探讨其与鼻咽癌临床病理特征及预后的关系。方法:采用免疫组化SP法检测223例鼻咽癌患者组织中DNA-PKcs的表达,并结合患者的临床及预后资料进行分析。结果:223例鼻咽癌患者中,DNA-PKcs的过表达率为36.8%。卡方检验显示,DNA-PKcs表达强弱与患者的性别、年龄、病理分型及N分期的相关性均无统计学意义(P>0.05),与TNM分期、T分期、M分期均有关(P<0.05)。单因素生存分析显示,DNA-PKcs过表达患者5年总生存率低于低表达患者(54.6%vs.79.4%),差异有统计学意义(P<0.05)。多因素Cox回归模型分析显示T、N、M分期及DNA-PKcs表达水平是影响鼻咽癌患者预后的独立因素(P<0.05)。结论:DNA-PKcs在大部分鼻咽癌组织中均有表达,DNA-PKcs的表达水平与鼻咽癌患者预后相关,对患者的预后判断有一定的指导意义。

恒场电泳检测DNA双链断裂及其应用

应用普通恒场琼脂糖凝胶电泳检测受γ射线照射后小鼠胸腺细胞ＤＮＡ双链断裂（ｄｓｂ）。在一定条件下，该法可以获得与脉冲凝胶电泳相似的结果。用此法观察了离体照射小鼠胸腺细胞ＤＮＡｄｓｂ修复作用，发现该法可以检测到ＤＮＡ“梯状”带，可做为一种研究细胞凋亡的新方法。