Knockdown the expression of ku70 and lig4 in HEK293T cells by CRISPR/Cas13 system / 生物工程学报

Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) system is a hotspot of gene editing and gene expression research, in which CRISPR/Cas13 system provides a new direction for RNA interference and editing. In this study, we designed and synthesized the corresponding gRNAs of CRISPR/Cas13a and CRISPR/Cas13b systems in non-homologous end joining (NHEJ) pathway, such as Ku70 and Lig4, and then detected the expression of ku70 and lig4 in HEK293T cells. The CRISPR/Cas13a system could efficiently knockdown the mRNA expression of ku70 and lig4 more than 50%, and CRISPR/Cas13b system also suppressed ku70 and lig4 about 92% and 76%, respectively. Also, CRISPR/Cas13a, b systems could down-regulate Ku70 and Lig4 proteins level to 68% and 53%, respectively. The study demonstrates that the CRISPR/Cas13 system could effectively knockdown the expression of RNA and protein in HEK293T cells, providing a new strategy for gene function and regulation research.

Estudo dos mecanismos moleculares do reparo de quebra de duplas fitas no DNA mitocondrial / Study of the molecular mechanisms of double-strand break repair in mitochondrial DNA

O DNA está constantemente exposto a danos causados tanto por agentes endógenos quanto exógenos. Estes podem causar diferentes tipos de lesões incluindo modificações de bases e do açúcar, além de quebras de fitas simples ou duplas. As quebras de duplas fitas, quando comparadas às demais, constituem as mais citotóxicas e podem resultar em deleções no DNA e instabilidade genética. Deleções no DNA mitocondrial (mtDNA) causam diversas doenças e estão envolvidas no processo de envelhecimento. No núcleo, as quebras de duplas fitas no DNA podem ser reparadas por recombinação homóloga (HR), ligação de pontas não homólogas (NHEJ) e anelamento de fita simples (SSA). No entanto, em mitocôndrias de células de mamíferos, o reparo de quebras de duplas fitas ainda não foi completamente caracterizado. Experimentos in vitro usando extratos mitocondriais de células de roedores mostraram que estes são capazes de reparar essas quebras, no entanto pouco é sabido sobre quais proteínas são responsáveis por cada etapa de reparo, bem como sua implicação na manutenção da integridade do genoma mitocondrial. Sendo assim, nesse trabalho investigamos a localização e função mitocondrial das proteínas ATM, Rad51, Rad52, Ku70/86 e DNA-PKCs, que são sabidamente envolvidas em reparo de quebras de duplas fitas no núcleo. Para identificar essas proteínas em mitocôndrias de células de mamíferos, mitocôndrias foram isoladas a partir de células da linhagem HEK293T, usando centrifugação diferencial seguida por gradiente de Percoll. Para as proteínas de recombinação homóloga, ATM e Rad51, imunodetectamos isoformas semelhantes em todos os compartimentos celulares. Já para a proteína Rad52 o mesmo anticorpo imunodetectou duas bandas distintas na mitocôndria ao passo que no núcleo foram quatro. Além disso, verificamos que baixos níveis de proteína Rad52, induzidos pela expressão de shRNA (short hairping RNA) específico, resultam em diminuição do número de cópias de mtDNA bem como acúmulo de deleções no genoma mitocondrial. Para as proteínas de NHEJ, DNA-PKCs e a subunidade Ku70, identificamos isoformas semelhantes em todos os compartimentos celulares. Já para a subunidade 86 do heterodímero Ku70/86 o anticorpo detectou, somente em mitocôndrias, uma banda menor de 50 kDa, a qual difere na região N-terminal da subunidade detectada no núcleo (86 KDa). Experimentos de co-imunprecitação de proteínas mostraram que essa isoforma menor compõe o heterodímero mitocondrial juntamente com a subunidade 70 (mtKu70/50) e que esse interage com DNA ligase III mitocondrial. Nossos resultados também mostraram que a estabilidade proteica de mtKu70/50 é regulada por ATM. Tratamento das células com peróxido de hidrogênio, que induz quebras de duplas fitas, aumentou a associação do heterodímero mtKu70/50 com o mtDNA, de forma independente de aumento da concentração proteica intra-mitocondrial. Já a diminuição dos níveis proteicos de Ku, induzida através de shRNA, resultou em diminuição do número de cópias de mtDNA e acumulo de danos nesse genoma. Extratos mitocondriais de células knockdown para Ku apresentaram menor atividade de reparo NHEJ em um ensaio in vitro, sugerindo que o acúmulo de danos nestas células é provavelmente devido a deficiências na via de NHEJ. Em conjunto, nossos dados sugerem que tanto HR quanto NHEJ operam em mitocôndrias. Além disso, a via de NHEJ mitocondrial utiliza o heterodímero mitocondrial Ku70/50 o qual está envolvido na manutenção do mtDNA. Ademais, nossos resultados mostram uma grande conservação molecular e funcional entre as vias de reparo de NHEJ e HR no núcleo e na mitocôndria, o que reforça sua importância para a manutenção da estabilidade genômica mitocondrial e, provavelmente a função mitocondrial

DNA is constantly exposed to damaging agents from both endogenous and exogenous sources. These can cause different types of DNA lesions that include base and sugar modifications and single and double strand breaks. DNA doublestrand breaks (DSBs) are among the most cytotoxic DNA lesions, which can result in deletions and genetic instability. Deletions in the mitochondrial DNA (mtDNA) cause numerous human diseases and drive normal aging. DSBs in the nuclear DNA are repaired by non-homologous DNA end joining (NHEJ), homologous recombination (HR) or Single Strand Annealing (SSA). Yet, repair of DSBs in mammalian mitochondria has not been fully characterized. Mitochondrial extracts from rodent cells are proficient in ligating DNA ends in vitro, but little is known about which proteins are responsible for each enzymatic step and its implication in mitochondrial genome maintenance. Thus, we investigated mitochondrial localization and function of DSBR (double strand break repair) proteins ATM, Rad51, Rad52, the Ku70/86 heterodimer and DNA-PKCs.To identify DSBR proteins in mammalian mitochondria, highly purified mitochondria from HEK293T cells were isolated using differential centrifugation followed by Percoll gradient. For HR proteins, we detected similar isoforms for ATM and Rad51 proteins in all cellular compartments. Two mitochondriaspecific isoforms of Rad52 were detected, while the same antibody detected four isoforms in the nucleus. In addition, lower Rad52 protein levels, induced by specific shRNA expression, result in decreased mtDNA copy number and accumulation of deleted mitochondrial genomes. For NHEJ proteins, similar isoforms of DNA-PKcs and the Ku70 subunit were detected in all cellular compartments. On the other hand, antibodies against the Ku86 subunit detected a smaller band in mitochondrial extracts (50 KDa), lacking the N-terminal region of the canonical isoform detected in the nucleus (86 KDa). The mitochondrial Ku70/50 heterodimer interacts with mitochondrial DNA ligase III, suggesting a role in DSBR. Moreover, stability of the mtKu heterodimer is regulated by ATM. Hydrogen peroxide treatment, which induces DSBs, increases mtKu70/50 association with the mtDNA and cells with reduced Ku levels, also induced by shRNA transfection, have lower mtDNA copy number and accumulate mtDNA damage. Moreover, mitochondrial extracts from Ku knockdown cells show lower NHEJ repair activity in an in vitro assay, suggesting that damage accumulation in these cells is likely due to deficiencies in NHEJ. Together, our data suggest that both HR and NHEJ operate in mitochondria. Also, mtNHEJ requires the Ku heterodimer and is involved in mtDNA maintenance. Moreover, our results indicate that there is a significant molecular and functional conservation between NHEJ and HR repair pathways in the nucleus and in mitochondria, which reinforces their importance for maintenance of mitochondrial genomic stability and, likely mitochondrial function

Serum anti-Ku86: a potential biomarker for early detection of hepatocellular carcinoma / 中华肿瘤杂志

<p><b>OBJECTIVE</b>To investigate the clinical value of serum anti-Ku86 in early detection of hepatocellular carcinoma (HCC).</p><p><b>METHODS</b>Expression levels of Ku86 protein in HCC and adjacent normal liver tissues were detected by Western blotting. Serum anti-Ku86 level in 83 patients with early HCC and 124 patients with liver cirrhosis were detected by enzyme-linked immunosorbent assay (ELISA). Chemiluminescence was used to measure the serum level of α-fetoprotein (AFP).</p><p><b>RESULTS</b>Expression of Ku86 protein in HCC was increased when compared with the adjacent normal liver tissues (0.21 ± 0.05 vs. 0.08 ± 0.02, P < 0.01). Serum anti-Ku86 level was significantly elevated in HCC patients compared with that in liver cirrhosis patients (0.47 ± 0.22 vs. 0.22 ± 0.06 Abs at 450 nm, P < 0.01), but there was no significant difference between HBV infection and HCV infection in HCC patients (0.51 ± 0.19 vs. 0.47 ± 0.24, P = 0.267). Of note, serum anti-Ku86 level was significantly decreased after surgical resection of the tumors in the 30 HCC cases tested (P < 0.01). The results of ROC analysis indicated a better performance of anti-Ku86 (0.857) than AFP (0.739) for early detection of HCC. In 83 HCC patients, the positive rate of anti-Ku86 was 61.4% (51/83), significantly higher than that of the AFP positive rate (27.7%, 23/83). The anti-Ku86 level was positive in 37 of 60 HCC cases with negative AFP. Combination assay of AFP and anti-Ku86 could detect 60 of 83 HCC cases (72.3%, 60/83). There was no significant correlation of anti-Ku86 and AFP (r = 0.156, P = 0.161).</p><p><b>CONCLUSIONS</b>Serum anti-Ku86 level is significantly elevated and is not related to HBV and HCV infection in HCC patients. Serum anti-Ku86 antibody may be a potential biomarker for early detection of HCC, and can be used in combination with AFP in clinics.</p>

Nampt is involved in DNA double-strand break repair / 癌症

DNA double-strand break (DSB) is the most severe form of DNA damage, which is repaired mainly through high-fidelity homologous recombination (HR) or error-prone non-homologous end joining (NHEJ). Defects in the DNA damage response lead to genomic instability and ultimately predispose organs to cancer. Nicotinamide phosphoribosyltransferase (Nampt), which is involved in nicotinamide adenine dinucleotide metabolism, is overexpressed in a variety of tumors. In this report, we found that Nampt physically associated with CtIP and DNA-PKcs/Ku80, which are key factors in HR and NHEJ, respectively. Depletion of Nampt by small interfering RNA (siRNA) led to defective NHEJ-mediated DSB repair and enhanced HR-mediated repair. Furthermore, the inhibition of Nampt expression promoted proliferation of cancer cells and normal human fibroblasts and decreased β-galactosidase staining, indicating a delay in the onset of cellular senescence in normal human fibroblasts. Taken together, our results suggest that Nampt is a suppressor of HR-mediated DSB repair and an enhancer of NHEJ-mediated DSB repair, contributing to the acceleration of cellular senescence.

Influence of epidermal growth factor receptor monoclony antibody MAb225 on DNA repair of tongue carcinoma cell after radiation / 华西口腔医学杂志

<p><b>OBJECTIVE</b>The objective of this study is to investigate the effect of epidermal growth factor receptor (EGFR) monoclonal antibody MAb225 on repair of DNA double strand break (DNA-DSB) after radiation in tongue squamous cell carcinoma cell.</p><p><b>METHODS</b>The single cell gel electrophoresis (SCGE) was performed to estimate the repair of DNA-DSB induced by radiation in human tongue carcinoma cells Tca8113 treated with or without MAb225. Expression of Ku70 and Ku80 were detected by semiquantitative reverse transcription polymerase chain reaction and Western bolt.</p><p><b>RESULTS</b>Comet tail moment of MAb225 treated cell was significantly higher than untreated cell (P < 0.05). The expression of Ku70 and Ku80 were inhibited by MAb225.</p><p><b>CONCLUSION</b>MAb225 can inhibit repair of DNA-DSB induced by down-regulated expression of Ku70 and Ku80.</p>

The roles of Ku80/p53 pathway in silica-induced cell cycle changes in human embryo lung fibroblasts / 中华劳动卫生职业病杂志

<p><b>OBJECTIVE</b>To study the roles of Ku80/p53 pathway in silica-induced cell cycle changes in human embryo lung fibroblasts (HELF).</p><p><b>METHODS</b>Ku80 siRNA expression vectors were transfected into HELF by lipofectamine. Flow cytometry was used to detect the distributions of cell cycle and western blot assay was used to determine the expression level of Ku80, p53 and p21 proteins or the phosphorylation levels of p53-ser15 after cells were exposed to silica.</p><p><b>RESULTS</b>The expression levels of Ku80 protein increased in concentration-dependent and time-dependent manners after cells were exposed to silica. The proportion of G1 phases in H-NC cells (controls) decreased from 89.28% +/- 2.19% to 68.93% +/- 3.79% after exposure to silica, and the proportion of G1 phases in HELF cells (H-Ku80) decreased from 85.16% +/- 3.73% to 59.92% +/- 3.31% after exposure to silica (P<0.05). The expression levels of Ku80, p53 proteins or p21 proteins or phosphorylation level of p53-ser15 were obviously suppressed in H-Ku80, as compared with H-NC.</p><p><b>CONCLUSION</b>Ku80/p53 pathway plays a role in the cell cycle charges induced by silica in human embryo lung fibroblasts.</p>

Roles of phosphatidylinositol 3 kinase in silica-induced DNA double strand breaks damage repair in human embryo lung fibroblasts / 中华劳动卫生职业病杂志

<p><b>OBJECTIVE</b>To study the role of Phosphatidylinositol 3 kinase (PI3K) in silica-induced DNA double strand break repair in human embryo lung fibroblasts (HELF).</p><p><b>METHODS</b>Control HELF cells and DN-Deltap85 (HELF transfected with Dominant negative mutant of PI3K) were treated with 200 microg/ml silica for different times. The expression levels of phosphor-H2AX (H2AX), Ku70, Ku80 and DNA-PKcs were determined by Western blot. Furthermore, DNA double strand breaks were measured by neutral comet assay after cells were treated with 200 microg/ml silica for 0, 12 and 24 h.</p><p><b>RESULTS</b>After treatment with 200 microg/ml silica for different times, the levels of H2AX were increased in a time-dependent manner and the expression levels of H2AX were obviously suppressed in DN-Deltap85 compared with control cells. The levels of Ku70 and Ku80 were also significantly suppressed in DN-Deltap85 (0.37 +/- 0.14, 0.55 +/- 0.17) compared with control cells (0.58 +/- 0.09, 0.95 +/- 0.21) after treatment with 200 microg/ml silica for 12 h (P < 0.05). Both the percentage of tail DNA in HELF and DN-Deltap85 increased significantly at 12 h (9.78 +/- 1.15, 11.79 +/- 4.90) compared with groups without treatment with silica (2.40 +/- 0.69, 3.31 +/- 1.35) and then decreased at 24 h (4.19 +/- 0.47, 7.58 +/- 4.32), but only the decrease of HELF at 24 h was significant compared with HELF at 12 h (P < 0.05). DNA repair competence of HELF was 75.74% and that of DN-Deltap85 declined to 49.64%.</p><p><b>CONCLUSION</b>Silica dust can induce DNA double strand breaks in human embryo lung fibroblasts. PI3K might play a role in silica-induced DNA double strand break repair by regulating the expression levels of Ku70 and Ku80.</p>

Use of phage display to isolate specific human monoclonal antibody fragments against a potential target for multiple myeloma

<p><b>INTRODUCTION</b>Multiple myeloma (MM), a malignancy of plasma cells, accounts for 10% of all haematological malignancies and is currently incurable. Although it can be treated, the disease tends to relapse after several years and becomes increasingly resistant to conventional therapy. Investigations into using humoral therapy for MM are now underway with a view that novel therapeutic agents may provide a more targeted therapy for MM.</p><p><b>MATERIALS AND METHODS</b>Here, phage display, a faster and more efficient method compared to classical hybridoma fusion technology, was used as a proof-of-concept to isolate several single-chain Fragment variables (scFv) against Ku86.</p><p><b>RESULTS</b>Anti-Ku86 polyclonal scFvs biopanning was successful where third round scFvs (A(450)~1.1) showed a 1/3 increase in binding as compared to the fi rst round scFvs (A(450)~0.4) with 100 microg/mL of antigen (purified human Ku86). Subsequent selection and verification of monoclonal antibodies using third round biopanning revealed 4 good affinity binding clones ranging from A(450)~0.1 to A450~0.15 on 12.5 microg/mL of antigen as compared to low binders (A(450)~0.07) and these antibodies bind to Ku86 in a specific and dose-dependent manner. Comparative studies were also performed with commercially available murine antibodies and results suggest that 2 of the clones may bind close to the following epitopes aa506-541 and aa1-374.</p><p><b>CONCLUSIONS</b>These studies using phage display provide an alternative and viable method to screen for antibodies quickly and results show that good affinity antibodies against Ku86 have been successfully isolated and they can be used for further studies on MM and form the basis for further development as anti-cancer therapeutic agents.</p>

Expression of recombination-activating genes and T cell receptor gene recombination in the human T cell leukemia cell line / 中华医学杂志(英文版)

<p><b>BACKGROUND</b>Recent studies have suggested that mature T cells can change their specificity through reexpression of recombination-activating genes (RAG) and RAG-mediated V(D)J recombination. This process is named receptor revision and has been observed in mature peripheral T cells from transgenic mice and human donors. However, whether thebreceptor revision in mature T cells is a random or orientated process remains poorly understood. Here we used the Jurkathuman T cell line, which represents a mature stage of T cell development, as a model to investigate the regulation of Tcell receptor (TCR) gene recombination.</p><p><b>METHODS</b>TCR Dbeta-Jbeta signal joint T cell receptor excision DNA circles (sjTRECs) were determined by nested and seminested PCR. Double-strand DNA breaks at recombination signal sequences (RSSs) in the TCRVbeta chain locus were detected by ligation-mediated-PCR. Further analysis of the complementarity-determining region 3 (CDR3) size of the TCRVbeta chain was examined by the TCR GeneScan technique.</p><p><b>RESULTS</b>RAG1, RAG2, and three crucial components of the nonhomologous DNA end-joining (NHEJ) pathway were readily detected in Jurkat. Characteristics of junctional diversity of Dbeta2-Jbeta2 signal joints and ds RSS breaks associated with the Dbeta2 5' and Dbeta 2 3' sites were detected in DNA from Jurkat cells. CDR3 size and the gene sequences of the TCRVbeta chain did not change during cell proliferation.</p><p><b>CONCLUSIONS</b>RAG1 and RAG2 and ongoing TCR gene recombination are coexpressed in Jurkat cells, but the ongoing recombination process may not play a role in modification of the TCR repertoire.However, the results suggest that Jurkat could be used as a model for studying the regulation of RAGs and V(D)J recombination and as a "special" model of the coexistence of TCR gene rearrangements and "negative" receptor revision.</p>

The simultaneous knock-down of Ku70 and Ku80 by a tandem Ku-shRNA-encoding plasmid expression system / 中华肝脏病杂志

<p><b>OBJECTIVE</b>To extend the use of vector-derived siRNA by generating multiple shRNAs in the same plasmid.</p><p><b>METHODS</b>Construct a vector that expresses shRNAs targeting on Ku70 and Ku80 in tandem. The gene silencing efficiency of each shRNA was verified previously. After identification by restriction digestion and DNA sequencing, the reconstructed plasmid, named psiRNAKus, was transfected into the human hepatoma cell line HepG2. The tandem-shRNA-induced silencing of targeted genes was determined by RT-PCR at RNA level and Western blot at protein level.</p><p><b>RESULTS</b>The shRNAs encoded by psiRNAKus down-regulated both the expression of Ku70 and Ku80.</p><p><b>CONCLUSION</b>The vector-derived siRNA delivery system that allows multiple shRNA species to be expressed from the same vector may be of value in experimental and therapeutic applications.</p>

Expression of DNA-PK in hepato- and cholangio-neoplasms and its significance / 中华肝脏病杂志

<p><b>OBJECTIVE</b>To characterize DNA-PKcs and Ku70 expressions in hepato- and cholangio-neoplastic tissues and the association with the degree of malignancy and invasiveness of the tumors.</p><p><b>METHODS</b>The expression of DNA-PKcs and Ku70 was examined in 47 cases of hepato- or cholangio-neoplasm by immunohistochemistry.</p><p><b>RESULTS</b>Ku70 was expressed in all of the neoplastic tissues examined and with a little variation in levels. The highest expression was observed in adenocarcinomas and adenomas. There was no statistically significant association between Ku70 expression level and the degree of their malignancy extent or invasiveness. In contrast to Ku 70, a wide variation in expression levels of DNA-Pkcs was observed among different types of neoplastic tissues. The highest ratio of positive expressing cells was detected in hepatocellular carcinomas (92.1%), which was significantly higher than that in cholangioadeno carcinomas (65.3%) and biliary cystadenocarcinomas (51.9%). Low or no expression level was detected in papillary adenoma cases. DNA-PKcs expression of invasive adenomas and adeno-carcinomas (61.2%) was significantly higher than that of non-invasive adenomas and adeno-carcinomas (30.4%). There was no expression observed in the normal tissues adjacent to the tumors.</p><p><b>CONCLUSION</b>DNA-PKcs is expressed in hepato- and cholangio-neoplasms and its variable level of expression is associated with the types of the tumor and their degree of malignancy and invasiveness. DNA-PKcs could be recognized as a new biomarker for liver neoplasm.</p>

Construction of double-strand break repair protein hKu70 deficient cell strain and its biologic characters / 中华劳动卫生职业病杂志

<p><b>OBJECTIVE</b>To construct DNA double-strand break (DSB) repair protein hKu70 deficient cell strain and to observe its biological characters for studying the functions of hKu70 gene and the effects of occupational harmfulness factors on DSB repair.</p><p><b>METHODS</b>Human lung fibroblasts (HLF) were transfected with the eukaryotic expression plasmids of hKu70 gene antisense RNA (pEGFP-C1-K) to construct hKu70 protein deficient cells (named as "HLFK"). The protein expression levels of hKu70 gene in HLFC and HLFK were detected by the Western blotting to estimate the effects of antisense inhibition. Morphology, growth character and growth status in soft agar of transfected HLFK were observed.</p><p><b>RESULTS</b>pEGFP-C1-K vector was successfully expressed in HLF. The protein expression level of hKu70 gene in HLFK was decreased by 42% as compared with that in HLFC. No obvious changes of the biologic characters were observed in HLFK.</p><p><b>CONCLUSION</b>The hKu70 protein deficient cell strain was successfully constructed. The hKu70 protein deficiency alone didn't induce obvious changes of the biological characters in HLFK.</p>