Systematic analysis of DNA polymerases as therapeutic targets in pan-cancers

Introduction:DNA polymerases are crucial for maintaining genome stability and influencing tumorigenesis.However,the clinical implications of DNA polymerases in tumorigenesis and their potential as anti-cancer therapy targets are not well understood.Methods:We conducted a systematic analysis using TCGA Pan-Cancer Atlas data and Gene Set Cancer Analysis results to examine the expression profiles of 15 DNA polymerases(POLYs)and their clinical correlations.We also evaluated the prognostic value of POLYs by analyzing their expression levels in relation to overall survival time(OS)using Kaplan-Meier survival curves.Additionally,we investigated the correlations between POLY expression and immune cells,DNA damage repair(DDR)pathways,and ubiquitination.Drug sensitivity analysis was performed to assess the relationship between POLY expression and drug response.Results:Our analysis revealed that 14 out of 15 POLYs exhibited significantly distinct expression patterns between tumor and normal samples across most cancer types,except for DNA nucleotidylexotransferase(DNTT).Specifically,POLD1 and POLE showed elevated expression in almost all cancers,while POLQ exhibited high expression levels in all cancer types.Some POLYs showed heightened expression in specific cancer subtypes,while others exhibited low expression.Kaplan-Meier survival curves demonstrated significant prognostic value of POLYs in multiple cancers,including PAAD,KIRC,and ACC.Cox analysis further validated these findings.Alteration patterns of POLYs varied significantly among different cancer types and were associated with poorer survival outcomes.Significant correlations were observed between the expression of POLY members and immune cells,DDR pathways,and ubiquitination.Drug sensitivity analysis indicated an inverse relationship between POLY expression and drug response.Conclusion:Our comprehensive study highlights the significant role of POLYs in cancer development and identifies them as promising prognostic and immunological biomarkers for various cancer types.Additionally,targeting POLYs therapeutically holds promise for tumor immunotherapy.

Possible Role of DNA Polymerase beta in Protecting Human Bronchial Epithelial Cells Against Cytotoxicity of Hydroquinone

Objective To explore the toxicological mechanism of hydroquinone in human bronchial epithelial cells and to investigate whether DNA polymerase beta is involved in protecting cells from damage caused by hydroquinone. Methods DNA polymerase beta knock-down cell line was established via RNA interference as an experimental group. Normal human bronchial epithelial cells and cells transfected with the empty vector of pEGFP-C1 were used as controls. Cells were treated with different concentrations of hydroquinone （ranged from 10 μmol/L to 120 μmol/L） for 4 hours. MTT assay and Comet assay [single-cell gel electrophoresis （SCGE）] were performed respectively to detect the toxicity of hydroquinone. Results assay showed that DNA polymerase beta knock-down cells treated with different concentrations of hydroquinone had a lower absorbance value at 490 nm than the control cells in a dose-dependant manner. Comet assay revealed that different concentrations of hydroquinone caused more severe DNA damage in DNA polymerase beta knock-down cell line than in control cells and there was no significant difference in the two control groups. Conclusions Hydroquinone has significant toxicity to human bronchial epithelial cells and causes DNA damage. DNA polymerase beta knock-down cell line appears more sensitive to hydroquinone than the control cells. The results suggest that DNA polymerase beta is involved in protecting cells from damage caused by hydroquinone.

THE INHIBITORY EFFECT OF EXTRACT OF CAMELLIA SINENSIS AND EXTRACT OF CAMELLIA PTILOPHYLLA CHANG ON DNA POLYMERASE OF EHRLICH ASCITES CARCINOMA CELLS

Objective: To detect the effect of extract of Camellia Sinensis (ECS) and extract of Camellia Ptilophylla Chang (ECPC) on DNA polymerase (Pol) of Ehrlich ascites tumor cells Methods: Referring to the method of K Ono, Pol was extracted from Ehrlich ascites tumor cells in mice Pol α, β, and γ were separated by phosphocellulose column chromatography and were identified The effect of ECPC and ECS on Pol was studied Results: ECPC and ECS were shown to inhibit the activity of Pol α, β, and γ IC 50 values of ECS on Pol α , β, and γ were 10 2μg/ml, 9 9μg/ml and 28 9μg/ml respectively IC 50 values of ECPC on Pol α, Pol β and Pol γ were 5 6μg/ml, 15μg/ml and 14 7μg/ml respectively The modes of inhibition of ECPC on Pol α, Pol β and Pol γ were noncompetitive with respect to template DNA The Ki values of ECPC on Pol α , β, and γ were 2 68±0 12μg/ml, 2 24±0 12μg/ml , 2 56±0 18μg/ml Conclusion: ECPC and ECS were shown to have inhibitory effect on DNA polymerase of tumor cells The mode of inhibition of ECPC on Pol α, Pol β and Pol γ were noncompetitive with respect to template DNA

Characterization of DNA polymerase δ from deep-sea hydrothermal vent shrimp Rimicaris exoculata

DNA polymerase δ(Polδ)plays a crucial and versatile role in DNA replication and DNA repair processes.Vent shrimp Rimicaris exoculata is the primary megafaunal community living in hydrothermal vents.In this study,the Polδfrom shrimp Rimicaris exoculata was cloned,expressed and characterized.The results showed that the Polδcatalytic subunit(POLD1),852 amino acids in length,shared high homology with crayfish Procambarus clarkii and shrimp Oratosquilla oratoria.The recombinant POLD1 expressed in Escherichia coli showed that the enzyme was active in a range of 20℃ to 40℃ with an optimum temperature at 25℃ and in a wide range of p H with an optimum at pH 6.0.The activities of POLD1 were significantly enhanced in the presence of Triton-X 100,Tween 20 and Mn^(2+).The K_(m)(dNTP)value of POLD1 was 4.7μmol/L.The present study would be helpful to reveal the characterization of Polδof deep-sea vent animals.

THE RADIOBIOLOGIC CHARACTERISTICS OF DNA POLYMERASE β IN HEPATOMAS

To investigate the effects of γ rays on DNA polymerase β properties and its DNA repair functions before or after γ rays exposure, DNA polymerase βactivity, gene expression and mRNA levels in SMMC-LTNM hepatomas horn on nude mice or the samples of the liver cancer tissues from 15 patients were measured with 3H-TTP incorporation test, immunocytochemistry and cytoplasmic dot hybridization analysis, respectively.Irradiation was carried out with 60Co-γ rays at ice bath. It was found that DNA polymerase β activity, gene expression and the amount of mRNA were much higher in hepatoma cells than those in normal hepatocytes (P<0.01). In vitro studies, the enzyme activity both in hepatoma and normal liver cells appeared unchanged within 40 Gy γ-ray exposure. Following whole-body exposure of the nude mice bearing SMMC-LTNM with 2 Gy or 4 Gy of γ rays, DNA polymerase β activity in hepatoma increased temorarily at 48 hours postirradiation, and its gene expression seemed more active.The euzyme mRNA increased to 1.76-fold of the control group. 72 hours after exposure, all of these changes returned to normal levels. DNA polymerase βparticipated in DNA repair synthesis and this effect was different between hepatoma and hepatocytes because there were some biologic differences of the enzyme between hepatoma cells and normal liver cells. These data suggested that DNA polymeraseβactivity, its gene expression and mRNA level in hepatomas could increased temporarily after γ rays exposure, which may facilitate the cells to repair DNA damages from radiation.

DNA polymerase delta interacting protein 3 facilitates the activation and maintenance of DNA damage checkpoint in response to replication stress

Background:Replication stress response is crucial for the maintenance of a stable ge-nome.POLDIP3(DNA polymerase delta interacting protein 3)was initially identified as one of the DNA polymeraseδ(Polδ)interacting proteins almost 20 years ago.Using a variety of in vitro biochemical assays,we previously established that POLDIP3 is a key regulator of the enzymatic activity of Polδ.However,the in vivo function of POLDIP3 in DNA replication and DNA damage response has been elusive.Methods:We first generated POLDIP3 knockout(KO)cells using the CRISPR/Cas9 technology.We then investigated its biological functions in vivo using a variety of biochemical and cell biology assays.Results:We showed that although the POLDIP3-KO cells manifest no pronounced defect in global DNA synthesis under nonstress conditions,they are sensitive to a va-riety of replication fork blockers.Intriguingly,we found that POLDIP3 plays a crucial role in the activation and maintenance of the DNA damage checkpoint in response to exogenous as well as endogenous replication stress.Conclusion:Our results indicate that when the DNA replication fork is blocked,POLDIP3 can be recruited to the stalled replication fork and functions to bridge the early DNA damage checkpoint response and the later replication fork repair/restart.

Biochemical Characterization of Translesion Synthesis by Sulfolobus acidocaldarius DNA Polymerases

To study the DNA synthesis mechanism of Sulfolobus acidocaldarius, a thermophilic species from Crenarehaeota, two DNA polymerases of B family（polB1 and polB3）, and one DNA polymerase of Y family（polIV） were recombinantly expressed, purified and biochemically characterized. Both DNA polymerases polBl（Saci_1537） and polB3（Saci_0074） possessed DNA polymerase and 3＇ to 5＇ exonuclease activities; however, both the activities of B3 were very inefficient in vitro. The polIV（Saci_0554） was a polymerase, not an exonuclease. The activities of all the three DNA polymerases were dependent on divalent metal ions Mn1＋ and Mg2＋. They showed the highest activity at pH values ranging from 8.0 to 9.5. Their activities were inhibited by KC1 with high concentration. The optimal reaction temperatures for the three DNA polymerases were between 60 and 70 ℃. Deaminated bases dU and dI on DNA template strongly hindered primer extension by the two DNA polymerases of B family, not by the DNA polymerase of Y family. DNA polymerase of Y Family bypassed the two AP site analogues dSpacer and propane on template more easily than DNA polymerases of B family. Our results suggest that the three DNA polymerases coordinate to fulfill various DNA synthesis in Sulfolobus acidocaldarius cell.

A simplified method for reconstituting active E.coli DNA polymerase Ⅲ

Genome duplication in E.coli is carried out by DNA polymeraseⅢ,an enzyme complex consisting of ten subunits.Investigations of the biochemical and structural properties of DNA polymeraseⅢrequire the expression and purification of subunits includingα,ε,θ,γ,δ′,δ,andβseparately followed by in vitro reconstitution of the polⅢcore and clamp loader.Here we propose a new method for expressing and purifying DNA polymeraseⅢcomponents by utilizing a protein coexpression strategy.Our results show that the subunits of the polⅢcore and those of the clamp loader can be coexpressed and purified based on inherent interactions between the subunits.The resulting polⅢcore,clamp loader and sliding clamp can be reconstituted effectively to perform DNA polymerization.Our strategy considerably simplifies the expression and purification of DNA polymeraseⅢand provides a feasible and convenient method for exploring other multi-subunit systems.

Comparative Analysis of Eubacterial DNA Polymerase III Alpha Subunits

DNA polymerase Ⅲ is one of the five eubacterial DNA polymerases that is responsible for the replication of DNA duplex. Among the ten subunits of the DNA polymerase Ⅲ core enzyme, the alpha subunit catalyzes the reaction for polymerizing both DNA strands. In this study, we extracted genomic sequences of the alpha subunit from 159 sequenced eubacterial genomes, and carried out sequence- based phylogenetic and structural analyses. We found that all eubacterial genomes have one or more alpha subunits, which form either homodimers or heterodimers. Phylogenetic and domain structural analyses as well as copy number variations of the alpha subunit in each bacterium indicate the classification of alpha subunit into four basic groups: polC, dnaE1, dnaE2, and dnaE3. This classification is of essence in genome composition analysis. We also consolidated the naming convention to avoid further confusion in gene annotations.

Expression of Human Cytomegalovirus DNA Polymerase in Insect Cells Using Baculovirus Expression System：Purification and Biochemical Characterizations

Human Cytomegalovirus (HCMV) DNA polymerase gene was overexpressed in insect cells using the baculovirus transfer system. A6. 2 kb HCMV Rsr Ⅱ-EcoRI DNA fragment with intact HCMV pci gene coding sequence was engineered into NheI site of vector pBlueBac under the control of polyhedrin promoter of Autographa californica nuclear polyhedrosis virus (AcNPV). Recombinant AcNPV carried HCMV pci gene was generated by cotransfection of Spodoptera frugiperta cell (SF21) with AcNPV DNA and baculovirus transfer vector with HCMV pci gene. In fection of SF21 cell with recombinant virus lead to the expression of 140 kD peptide of HCMV specific DNA polymerase at the level approximately 2 mg per 108 cells. The polypeptide was purified from the infected SF21 cells by a series of column chromatography to homogeneity. The purified enzyme had a molecular weight of 140 kD and reacted with antiserum specific for HCMV DNA polymerase. It exhibited both 3'-5'and 5'-3' exonuclease activities.This enzyme is also sensitive to phosphono acetate.

Biochemical Characterization of Uracil-DNA Glycosylase from Pyrococcus furiosus

We report the characterization of a uracil-DNA glycosylase（UDG） from the hyperthermophilic archaea Pyrococcus furiosus（P, furiosus）. P. furiosus UDG（PfUDG） has high sequence similarity to the families IV and V UDGs（thermostable UDG family and PaUDG-b family）. PfUDG excises uracil from various DNA substrates with the following order： U/T=U/C〉U/G=U/AP=U/-〉U/U=U/I=U/A. The optimal temperature and pH value for uracil exci- sion by PfUDG are 70 ℃ and 9.0, respectively. The removal of U is inhibited by the divalent ions of Fe, Ca, Zn, Cu, Co, Ni and Mn, as well as a high concentration of NaC1. The phosphorothioates near uracil strongly inhibit the exci- sion of uracil by PfUDG. Interestingly, pfuDNA（Pyrococcusfuriosus DNA） polymerase, which tightly binds the ura- cil-carrying oligonucleotide, does not inhibit the excision by Pfl.IDG, suggesting PfUDG in vivo functions as the re- pair enzyme to excise uracil damage in genome.

POLE2 Regulates Apoptosis of Oral Squamous Cell Carcinoma Cells through the PI3K/AKT Signaling Pathway

Objective Oral squamous cell carcinoma(OSCC)is the most common malignant tumor of the head and neck,but its occurrence and progression mechanisms remain unclear.In addition-there is a lack of effective targeting drugs.The second major subunit of DNA polymerase(POLE2)catalyzes the prolongation of new strand replication and modifies exonuclease domain activity.Our previous study found that POLE2 was associated with OSCC progression,but the mechanism remains unclear.Methods The expression of POLE2 in OSCC tissues was detected using immunological assays.Mann-Whitney U analysis was used to investigate the relationship between POLE2 gene expression and tumor classification and prognosis of OSCC.POLE2 expression was inhibited in OSCC cells,and the effects of gene and protein expression were detected using RT-PCR and Western blotting.The POLE2 knockout model was constructed by transfecting a lentiviral vector.Cell proliferation,apoptosis,and migration were detected using various assays including colony formation,MTT,flow cytometry,wound healing assay,Transwell assay,and the Human Apoptosis Antibody Array.The animal model of OSCC was established by subcutaneous injection of transfected HN6 into 4-week-old female nude mice.After 30 days,tumors were removed under anesthesia and tumor weight and dimension were recorded.Tumor cell proliferation was analyzed using Ki67 staining.Results POLE2 gene levels were significantly higher in the OSCC tissues than in the normal tissues.In addition,POLE2 gene levels were statistically correlated with tumor classification and prognosis.Silencing POLE2 inhibited the proliferation of oral cancer cells and promoted apoptosis in vitro.Animal experiments also supported a positive correlation between POLE2 and OSCC tumor formation.We further demonstrated that POLE2 could upregulate the expression of apoptosis-related proteins such as caspase-3,CD40,CD40L,DR6,Fas,IGFBP-6,p21,and SMAC.In addition,POLE2 regulated OSCC development by inhibiting the PI3K/AKT signaling pathway.Conclusion POLE2 is closely related to the progression of OSCC.Thus,POLE2 may be a potential target for OSCC treatment.

IGF-1 Accelerates Cell Aging by Inhibiting POLD1 Expression

Objective The individual cascades of the insulin-like growth factor-1(IGF-1)signaling pathway and the molecular mechanism of aging have not been fully clarified.In the current study,we explored the effect of DNA polymerase delta 1(POLD1)on the IGF-1 signaling pathway in cell aging.Methods First,we analyzed the relationship between IGF-1 and POLD1 expression in aging.To investigate the effect of IGF-1 on POLD1 expression and aging,the 2BS cells were incubated with youngage or old-age human serum,IGF-1 protein,or linsitinib.Next,the effect of IGF-1 on aging was examined in the 2BS cells with increased or decreased POLD1 expression to clarify the molecular mechanism.Results In this study,we found that IGF-1 expression increased and POLD1 expression decreased with aging in human serum and hippocampal tissues of SAMP8 mice,and a negative relationship between IGF-1 and POLD1 expression was observed.Furthermore,the cells cultured with old-age human serum or IGF-1 showed lower POLD1 expression and more pronounced senescence characteristics,and the effect could be reversed by treatment with linsitinib or overexpression of POLD1,while the effect of linsitinib on cell aging could be reversed with the knockdown of POLD1.Conclusion Taken collectively,our findings demonstrate that IGF-1 promotes aging by binding to IGF-1R and inhibiting the expression of POLD1.These findings offer a new target for anti-aging strategies.

DETECTION OF HUMAN PAPILLOMAVIRUS TYPES 16, 18 DNA RELATED SEQUENCES IN BRONCHOGENIC CARCINOMA BY POLYMERASE CHAIN REACTION

In studying the relationship between human papillomavirus (HPV) and bronchogenic carcinoma, 'high-risk' HPV 16, 18 DNA sequences were detected in samples from 50 lung cancer patients, 18 patients with benign pulmonary diseases and 4 fetal lung tissues by polymerase chain reaction (PCR) and dot-blot hybridization with biotin-labelled probes. The results showed that HPV 16, 18 DNA related sequences were found in 32% of lung cancer specimens, with 10 cases of HPV 16, 5 cases of HPV 18 and 1 case of both types. 48.15% (13 / 27) of squamous cell carcinomas were shown to be positive for HPV 16, 18 DNA. In addition, two adenocarcinomas and one small cell carcinoma were positive for HPV 16 DNA. No specimens from benign diseases tissues and fetal lung tissues showed positive results. These results suggest that primary bronchogenic carcinoma is related to HPV infection.

Next-generation sequencing-based analysis of the effect of N^(6)-methyldeoxyadenosine modification on DNA replication in human cells

N^(6)-methyldeoxyadenosine(6 mdA) modification is considered as a new epigenetic mark that may play important roles in various biological processes.However,it remains unclear about the effect of 6 mdA on DNA replication in human cells.Herein,we combined next-generation sequencing with shuttle vector technology to explore how 6 mdA affects the efficiency and accuracy of DNA replication in human cells.Our results showed that 6 mdA neither blocked DNA replication nor induced mutations in human cells.Moreover,we found that the depletion of translesion synthesis DNA polymerase(Pol) κ,Pol η,Pol ι or Pol ζ did not significantly change the biological consequences of 6 mdA during replication in human cells.The negligible impact of 6 mdA on DNA replication is consistent with its potential role in epigenetic gene expression.

Study on vertical transmision of Chlamydia trachomatis using PCR and DNA sequencing

Objective To investigate the vertical transmission rate of Chlamy dia trachomatis (CT) in Chongqing, China. Methods Specimens taken from 278 women and from their 79 infants were e xamined b y cell culture, polymerase chain reaction (PCR) and DNA sequence analysis. Chlam ydia trachomatis was isolated in McCoy cell culture. CT DNA was extracted with a modified NaI method. After cloning, recombinant plasmids were used for sequence analysis with the dideoxy chain termination method.Results 10.8% (30/278) of the cervical cultures of pregnant women were positive for Chlamydia trachomatis, while the positive rate tested by PCR was 14.0% (39/2 78). The vertical transmission rate of Chlamydia trachomatis was 55. 0% (11/20). The incidences of conjunctivitis and pneumonia in infants with Chlamydia t rachom atis positive mothers were 27.3% and 18.2%, respectively. DNA sequence s of Chlam ydia trachomatis isolated from the cervix of a mother and the nasopharynx of her baby were identical.Conclusion Chlamydia trachomatis infection is quite common in Cho ngqing , China. Our report is the first report of CT vertical transmission proved by DN A sequence analysis.

DNA extraction from fresh-frozen and formalin-fixed, paraffinembedded human brain tissue

Both fresh-frozen and formalin-fixed,paraffinembedded（FFPE）human brain tissues are invaluable resources for molecular genetic studies of central nervous system diseases,especially neurodegenerative disorders.To identify the optimal method for DNA extraction from human brain tissue,we compared methods on differently-processed tissues.Fragments of LRRK2 and MAPT（257 bp and 483 bp/245 bp）were amplified for evaluation.We found that for FFPE samples,the success rate of DNA extraction was greater when using a commercial kit than a laboratory-based method（successful DNA extraction from 76%versus 33%of samples）.PCR amplicon size and storage period were key factors influencing the success rate of DNA extraction from FFPE samples.In the fresh-frozen samples,the DNA extraction success rate was 100%using either a commercial kit（QIAamp DNA Micro）or a laboratorybased method（sample boiling in 0.1 mol/L NaOH,followed by proteinase K digestion,and then DNA extraction using Chelex-100）regardless of PCR amplicon length or tissue storage time.Although the present results demonstrate that PCR-amplifiable genomic DNA can be extracted from both fresh-frozen and FFPE samples,fresh brain tissue is recommended for DNA extraction in future neuropathological studies.

The History and Advances of Reversible Terminators Used in New Generations of Sequencing Technology

DNA sequencing using reversible terminators, as one sequencing by synthesis strategy, has garnered a great deal of interest due to its popular application in the second-generation high-throughput DNA sequencing technology. In this review, we provided its history of develop- ment, classification, and working mechanism of this technology. We also outlined the screening strategies for DNA polymerases to accommodate the reversible terminators as substrates during polymerization; particularly, we introduced the ＂REAP＂ method developed by us. At the end of this review, we discussed current limitations of this approach and provided potential solutions to extend its application.

A novel marker for the platyfish (Xiphophorus maculatus) W chromosome is derived from a Polinton transposon

A consensus sequence, encoding a putative DNA polymerase type B derived from a Polinton transposon, was assembled from the sex determination region of Xiphophorus maculatus. This predicted protein, which is 1,158 aa in length, contains a DNAA_pol_B_2 domain and a DTDS motif. The DNA polymerase type B gene has about 10 copies in the haploid X. maculatus genome with one Y-specific copy. Interestingly, it has specific copies on the W chromosome in the X. maculatus Usumacinta strain （sex determination with female het- erogamety）, which represent new markers for this type of sex chromosome in platyfish. This marker with W- and Y-specific copies suggests relationship between different types of gonosomes and allows comparing male and female heterogameties in the platyfish. Further molecular analysis of the DNA polymerase type B gene in X. maculatus will shed new light on the evolution of sex chromosomes in platyfish.