OBJECTIVE: To analyze the clinical phenotype and genetic characteristics of a child with Perlman syndrome. METHODS: Genomic DNA was extracted from peripheral blood samples from the patient and her parents. Whole exome sequencing (WES) was carried out to detect potential variant in the proband. Candidate variant was verified by Sanger sequencing. The pathogenicity of candidate variants was evaluated according to the guidelines of the American College of Medical Genetics and Genomics (ACMG). RESULTS: The results of WES showed that the proband has harbored compound heterozygous variants of the DIS3L2 gene, namely c.2109delC and c.1829.c.1830insC, which were respectively inherited from her mother and father. The results were confirmed by Sanger sequencing. Based on the ACMG guidelines, the two novel variants were both predicted to be pathogenic (PVS1+PS2+PM2). CONCLUSION The compound heterozygous variants of the DIS3L2 gene probably underlay the Perlman syndrome in this patient. Above finding has enriched the spectrum of DIS3L2 gene mutations.
Exoribonucleases ; Female ; Fetal Macrosomia ; Genetic Testing ; Genomics ; Humans ; Mutation ; Whole Exome Sequencing ; Wilms Tumor

Exonuclease Ⅷ (Exo Ⅷ), an ATP-independent dsDNA 5'-3' exonuclease, is a candidate protein with great application value for in vitro DNA recombination. However, the application of Exo Ⅷ in DNA recombination in vitro has not been reported. In this study, the recombinant expression vector of the truncated Exo Ⅷ (tExo Ⅷ) with the full exonuclease activity was built and used to achieve the overexpression of tExo Ⅷ in Escherichia coli. Based on the purified tExo Ⅷ protein with high-purity, the feasibility of tExo Ⅷ applied in vitro DNA recombination and effects of the reaction temperatures, reaction duration, and homology arm lengths were examined. The results showed that tExo Ⅷ was highly expressed in soluble form in E. coli. One liter of bacterial culture yielded 92.40 mg of purified tExo Ⅷ with the specific activity of 1.21×10⁵ U/mg. In a 10 μL recombination system containing 2.5 U tExo Ⅷ, the highest cloning efficiency was achieved in a reaction at 25 °C for 12.5 min and followed by incubation at 50 °C for 50 min. With addition of Pfu DNA polymerase, the homology arm extension strategy can effectively improve the recombination efficiency. Using competent E. coli Mach1 T1 with 2.2×10⁶ cfu/μg transformation efficiency as recipient cell, the recombination of a 1 kb fragment with a 21 bp homology arm and a 5.8 kb linearized vector can form about 1.1×10⁴ recombinant clones per μg vector, and the positive rates was over 80%. The recombination efficiency was increased with the increasing length of homology arm ranged from 8 to 21 bp. Under the optimal reaction condition, only 8 bp homology arm can still achieve valid DNA recombination. This novel in vitro DNA recombination system mediated by tExo Ⅷ was particularly characterized by its easy preparation, no limitation on restriction sites and high recombination cloning efficiency. All results revealed that the new efficient gene cloning system has potential application in the field of molecular biology.
Cloning, Molecular ; Escherichia coli ; genetics ; Exonucleases ; genetics ; Recombinant Proteins ; metabolism ; Recombination, Genetic

OBJECTIVE: To investigate the differentially expressed genes between gastric cancer and normal gastric mucosa by bioinformatics analysis, identify the important gene participating in the occurrence and progression of gastric cancer, and predict the functions of these genes. METHODS: The gene expression microarray data GSE100935 (including 18 gastric cancer samples and normal gastric mucosal tissues) downloaded from the GEO expression profile database were analyzed using Morpheus to obtain the differentially expressed genes in gastric cancer, and a cluster analysis heat map was constructed. The online database UALCAN was used to obtain the expression levels of these differentially expressed genes in gastric cancer and normal gastric mucosa. The prognostic value of the differentially expressed genes in gastric cancer was evaluated with Kaplan-Meier survival analysis. GO functional enrichment analysis was performed using Fun-Rich software, and the STRING database was exploited to establish a PPI network for the differentially expressed genes. RESULTS: A total of 45119 differentially expressed genes were identified from GSE100935 microarray data. Analysis with UALCAN showed an obvious high expression of EXD3 gene in gastric cancer, and survival analysis suggested that a high expression level of EXD3 was associated with a poorer prognosis of the patients with gastric cancer. GO functional enrichment analysis found that the differentially expressed genes in gastric cancer were involved mainly in the regulation of nucleotide metabolism and the activity of transcription factors in the cancer cells. CONCLUSIONS EXD3 may be a potential oncogene in gastric cancer possibly in relation to DNA damage repair. The up-regulation of EXD3 plays an important role in the development and prognosis of gastric cancer, and may serve as an important indicator for prognostic evaluation of the patients.
Computational Biology ; Databases, Genetic ; Exonucleases ; genetics ; Gastric Mucosa ; chemistry ; enzymology ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Humans ; Neoplasm Proteins ; genetics ; Prognosis ; Stomach Neoplasms ; enzymology ; genetics ; mortality

Crystallography, X-Ray ; DNA Repair ; Exodeoxyribonucleases ; chemistry ; Humans ; Protein Conformation

Gene cloning is one of the most important and widely used technologies in molecular biology research. Generally, DNA fragment is cut with restriction enzyme, and then the product is ligated to a linearized vector with complementary sticky end or blunt end by DNA-ligase. This traditional DNA cloning method requires compatible enzyme recognition sites existing in both PCR fragment and targeted vector. Several ligase-free methods have been established to avoid the using of restriction enzyme. However, those methods are time-consuming, labor-intensive and expensive. To overcome these shortcomings, we developed an Exonuclease III based DNA cloning method that takes only 30 minutes with high cloning efficiency and significant economic advantage. Therefore, this method is suitable for large-scale gene cloning.
Cloning, Molecular ; methods ; DNA ; chemistry ; DNA Restriction Enzymes ; Exodeoxyribonucleases ; chemistry ; Genetic Vectors ; Polymerase Chain Reaction

OBJECTIVEAicardi-Goutières syndrome (AGS) is a rare early-onset genetic encephalopathy. The aim of this study was to explore the clinical, imaging and genetic features of a family with AGS, which may contribute to definite diagnosis, genetic counseling and prenatal diagnosis of this rare disease in China. We summarized the characteristics of AGS through reviewing related references.

METHODInformation of the proband and other family members as well as their DNA samples were collected. All the exons and exon-intron boundaries of pathogenic genes were amplified with PCR and were directly sequenced for genomic DNA. And we reviewed the reports of 252 cases.

RESULT(1) The proband was a 6 years plus 7 months old boy. He presented with severe developmental delay and abnormal posture mainly as torsion of limbs. By physical examination he was found to have some chilblain-like skin lesions at the end of limbs and microcephaly. The CT scan of his head displayed multiple calcification, especially in the basal ganglia. The MRI of his head displayed a hypointense signal in T1-weighted (T1W) images and a hyperintense signal in T2-weighted (T2W) in cerebral white matter and cystic lesions in temporal white matter. The younger sister of the proband presented with chilblain-like skin lesions on her face and the end of limbs had no developmental delay. The CT of her head showed multiple calcification, especially in the basal ganglia. (2) Two mutations were identified in TREX1, one was a novel nonsense mutation (c.294_295insA), and the other was a known pathogenic mutation (c.868_885del). (3) The common performances of AGS included mental retardation [92% (231/252) ], dystonia [75% (189/252)], microcephaly [63% (159/252) ], chilblain [42% (106/252) ], basal ganglia calcification [100% (252/252)], brain atrophy[88% (222/252)] and cerebral white matter lesions [86% (217/252)]. TREX1 [38% (96/252) ] and RNASEH2B [23% (58/252)]are the most common pathogenic genes.

CONCLUSIONWe determined pathogenic gene of these patients which is the basis of genetic counseling for this family. c.294_295insA mutation is a novel mutation not reported around the world yet.

Atrophy ; Autoimmune Diseases of the Nervous System ; diagnosis ; genetics ; Calcinosis ; Child ; China ; Exodeoxyribonucleases ; genetics ; Exons ; genetics ; Genetic Testing ; Humans ; Magnetic Resonance Imaging ; Male ; Mutation ; Nervous System Malformations ; diagnosis ; genetics ; Pedigree ; Phosphoproteins ; genetics

OBJECTIVETo analysis the molecular interaction network of 14-3-3 sigma in non small cell lung cancer (NSCLC) cells.

METHODSEstablished stable over-expressed 14-3-3 sigma protein PG cells, MTT assay was used to assess the growth rate of PG cells. Though stable isotope labeling by amino acids in cell culture (SILAC) and Mass spectrometry (MS) technology, to identify difference expressed proteins caused by over expressed 14-3-3 sigma. The protein expressed >2 or <0.5 times was termed as the differential protein. By searching Human protein reference database (HPRD) and Kyoto encyclopedia of genes and genomes (KEGG), established the molecular interaction network of tumor suppressor gene 14-3-3 sigma.

RESULTSThe growth rate of over-expressed 14-3-3 sigma PG cell was obviously slower down compared to vector PG cells. A database including 147 differential protein was established. And a molecular interaction network of 14-3-3 sigma containing 26 protein was constructed.In this network, the expression of CSNK2A1 (casein kinase II subunit alpha), involved in numerous cellular processes, such as cell cycle progression, apoptosis and transcription, was the most significantly increased. A DNA repair protein, MEN1 (Menin) which functions as a transcriptional regulator was the most significantly decreased.

CONCLUSIONAfter stable transfected with 14-3-3 sigma gene, growth rate of PG cells was inhibited, the proteins associated with cell cycle, DNA damage repair mechanisms were significantly changed, and constructed the molecular interaction network.

14-3-3 Proteins ; genetics ; Amino Acids ; Biomarkers, Tumor ; genetics ; Carcinoma, Non-Small-Cell Lung ; genetics ; Cell Cycle ; Cell Line, Tumor ; Cell Proliferation ; Exoribonucleases ; genetics ; Humans ; Isotope Labeling ; methods ; Lung Neoplasms ; genetics ; Mass Spectrometry ; Transfection

OBJECTIVETo explore the relationship between SULF2 and WRN promoter methylation and chemosensitivity to irinotecan, and also the clinicopathological features in patients with gastric cancer.

METHODSThe chemosensitivity to irinotecan was tested by MTT assay. The methylation of SULF2 and WRN promoter in the fresh gastric cancer tissues was detected by methylation specific PCR. The differences of chemosensitivity and clinicopathological features of the methylation group were compared with that of the non-methylation group. The tumor growth in nude mice bearing human gastric cancer xenografts treated with CPT-11was also observed.

RESULTSThe methylation rates of SULF2 and WRN were 28.4% (29/102) and 23.5% (24/102), respectively. There were no significant association between promoter methylation and clinicopathological features of patients including age, gender, histologic type, lymphatic invasion, and TNM Stage. In all the 102 cases, there were 30 cases of irrinotecan-sensitive group, and 72 cases of the irrinotecan-resistant group. The SULF2 methylation rate was 46.7% (14/30)in the sensitive group, and 20.8% (15/72) in the resistant group (P = 0.008),The WRN methylation rate was 33.3% (10/30) in the sensitive group, and 19.4% (14/72) in the resistant group (P = 0.214). Gastric cancer tissues were more sensitive to irrinotecan when both the genes were methylated. The nude mice bearing human gastric cancer xenografts with SULF2 methylation were more sensitive to irrinotecan.

CONCLUSIONSThe detection of SULF2 and WRN promoter methylation may provide evidence for screening and targeting the most sensitive gastric cancer subpopulation suitable for personalized irrinotecan chemotherapy.

Antineoplastic Agents, Phytogenic ; pharmacology ; Camptothecin ; analogs & derivatives ; pharmacology ; DNA Methylation ; Exodeoxyribonucleases ; metabolism ; Humans ; Methylation ; Promoter Regions, Genetic ; RecQ Helicases ; metabolism ; Stomach Neoplasms ; metabolism ; Sulfotransferases ; metabolism ; Werner Syndrome Helicase

Chilblain lupus erythematosus (LE) is a rare, chronic form of cutaneous LE (CLE), which presents mostly in women as erythematous to violaceous plaques on the acral areas and face, precipitated by cold and damp climates. It may be accompanied by discoid LE (DLE) lesions or other forms of CLE. Up to 20% of patients develop systemic LE (SLE). Although two missense mutations in TREX1, encoding the 3'-5' repair exonuclease 1, were described in familial chilblain LE, the pathogenesis of sporadic chilblain LE remains unknown. To our knowledge, there are a few reports of chilblain LE in the Korean dermatologic literature. Herein, we present a rare and interesting case of sporadic chilblain LE in 71-year-old man and review the Korean literatures.
Aged ; Chilblains ; Climate ; Cold Temperature ; Exodeoxyribonucleases ; Female ; Humans ; Lupus Erythematosus, Cutaneous ; Mutation, Missense

A recently identified protein, FAN1 (FANCD2-associated nuclease 1, previously known as KIAA1018), is a novel nuclease associated with monoubiquitinated FANCD2 that is required for cellular resistance against DNA interstrand crosslinking (ICL) agents. The mechanisms of FAN1 regulation have not yet been explored. Here, we provide evidence that FAN1 is degraded during mitotic exit, suggesting that FAN1 may be a mitotic substrate of the anaphase-promoting cyclosome complex (APC/C). Indeed, Cdh1, but not Cdc20, was capable of regulating the protein level of FAN1 through the KEN box and the D-box. Moreover, the up- and down-regulation of FAN1 affected the progression to mitotic exit. Collectively, these data suggest that FAN1 may be a new mitotic substrate of APC/CCdh1 that plays a key role during mitotic exit.
Anaphase-Promoting Complex-Cyclosome ; Bone Neoplasms ; metabolism ; pathology ; Cadherins ; genetics ; metabolism ; Cdc20 Proteins ; Cell Cycle Proteins ; genetics ; metabolism ; Cell Line, Tumor ; Exodeoxyribonucleases ; genetics ; metabolism ; HEK293 Cells ; Humans ; Mitosis ; Osteosarcoma ; metabolism ; pathology ; Ubiquitin-Protein Ligase Complexes ; genetics ; metabolism