Parkin: an Extremely Versatile E3 Ubiquitin Ligase / 中国生物化学与分子生物学报

Parkin, also known as PARK2, has been closely related to Parkinson's disease (PD) since its discovery. It is considered to be a neuroprotective gene. With the in-depth understanding for its structure, Parkin has been unveiled as an E3 ubiquitin ligase. Parkin is involved in the regulation of cell cycle, mitochondrial homeostasis, energy metabolism and other cellular processes, and is closely related to many diseases. It even plays completely opposite roles in the same pathway, namely cell proliferation and apoptosis, indicating that this must be a gene with an extremely broad and important role. This article summarizes the discovery and structure of Parkin and its self-inhibiting characteristics, focusing on the ubiquitination process that it participates in as E3 ubiquitin ligase and the resulting autophagy, protein degradation, changes in protein subcellular localization and protein interaction. These may all serve as the basis for Parkin to prevent PD and suppress tumors. On this basis, two reasons for Parkin abnormalities leading to PD are summarized: abnormal protein quality control and mitochondrial dysfunction, and extended to cardiovascular and kidney diseases caused by the abnormality of Parkin due to mitochondrial dysfunction. The internal connection between Parkin and cancer is also introduced from the aspects of Parkin as a tumor suppressor, regulating cell cycle, apoptosis and metastasis, oxidative stress and energy metabolism. By maintaining the active state of Parkin or enhancing its expression, it may be possible to improve the condition of PD patients. But the mechanism of Parkin's inhibition of tumor growth remains to be deciphered, and the potential role of Parkin in mediating the relationship between PD and cancer risk should be strengthened. These follow-up in-depth studies and their role in the diagnosis and treatment of related diseases and application of target molecules laid the foundation.

Detection and analysis of virulence genes for autosomal dominant polycystic kidney disease in 129 Chinese families / 第二军医大学学报

Objective To investigate the mutation types of polycystic kidney disease 1 gene (PKD1) and polycystic kidney disease 2 gene (PKD2) in Chinese patients with autosomal dominant polycystic kidney disease (ADPKD). Methods The mutations of PKD1 and PKD2 in 129 inherited ADPKD families were analyzed by long PCR and high-throughput sequencing. The positive mutation was verified by Sanger sequencing method. Results A total of 118 mutation sites of PKD1 or PKD2 in 116 inherited ADPKD families were detected from 129 families, with the detection rate being 89.9% (116/129). The mutation rates of PKD1 and PKD2 were 92.2% (107/116) and 8.6% (10/116), respectively. Of the 118 mutation sites, 80 (67.8%) were new mutations and 38 (32.2%) were known mutations; and 109 mutation sites were located in PKD1 (33 known mutations and 76 new mutations) and 9 in PKD2 (5 known mutations and 4 new mutations). Conclusion The newly discovered PKD1 and PKD2 mutations may contribute to early diagnosis and prognosis prediction of ADPKD patients, and may provide basic genetic information for clinical intervention.

Application of whole exome sequencing technique for the pathogenic gene screening of rare osteopetrosis / 国际检验医学杂志

Objective To screen the pathogenic gene of osteopetrosis to provide reference for its genetic di-agnosis and prognosis .Methods The clinical data and peripheral blood samples were collected from the pa-tients with osteopetrosis ,DNA was extracted ,the whole exome sequencing library was built ,then the high throughput detection was performed and the pathogenic gene was screened by combining with the bioinformat-ics technology .Results The whole exomes in 2 cases of osteopetrosis were analyzed ,the average sequencing depth of the two samples were 169 .38X and 231 .06X respectively ,in which the case 1 carried rare mutation TCIRG1(c .1305+2T>C) ,TCIRG1(c .2008C> T ) and CLCN7(c .1116C> T );the case 2 carried a rare muta-tion CLCN7(c .857G>A ) .T he bioinformatics analysis indicated that the rare mutations carried by these cases all had different degrees of influence on the structure and function of gene products .Conclusion The whole exome sequencing can once screen the know n pathogenic mutations of osteopetrosis ,is an effective tool for pathogenic mutation screening of osteopetrosis ,the clinical disease in 2 cases of osteopetrosis may be closely related with the patient′s carrying TCIRG1 and CLCN7 mutation .

PTMD: A Database of Human Disease-associated Post-translational Modifications / 基因组蛋白质组与生物信息学报·英文版

Various posttranslational modifications (PTMs) participate in nearly all aspects of biological processes by regulating protein functions, and aberrant states of PTMs are frequently implicated in human diseases. Therefore, an integral resource of PTM-disease associations (PDAs) would be a great help for both academic research and clinical use. In this work, we reported PTMD, a well-curated database containing PTMs that are associated with human diseases. We manually collected 1950 known PDAs in 749 proteins for 23 types of PTMs and 275 types of diseases from the literature. Database analyses show that phosphorylation has the largest number of disease associations, whereas neurologic diseases have the largest number of PTM associations. We classified all known PDAs into six classes according to the PTM status in diseases and demonstrated that the upregulation and presence of PTM events account for a predominant proportion of disease-associated PTM events. By reconstructing a disease-gene network, we observed that breast cancers have the largest number of associated PTMs and AKT1 has the largest number of PTMs connected to diseases. Finally, the PTMD database was developed with detailed annotations and can be a useful resource for further analyzing the relations between PTMs and human diseases. PTMD is freely accessible at http://ptmd.biocuckoo.org.

GAAD: A Gene and Autoimmiune Disease Association Database / 基因组蛋白质组与生物信息学报·英文版

Autoimmune diseases (ADs) arise from an abnormal immune response of the body against substances and tissues normally present in the body. More than a hundred of ADs have been described in the literature so far. Although their etiology remains largely unclear, various types of ADs tend to share more associated genes with other types of ADs than with non-AD types. Here we present GAAD, a gene and AD association database. In GAAD, we collected 44,762 associations between 49 ADs and 4249 genes from public databases and MEDLINE documents. We manually verified the associations to ensure the quality and credibility. We reconstructed and recapitulated the relationships among ADs using their shared genes, which further validated the quality of our data. We also provided a list of significantly co-occurring gene pairs among ADs; with embedded tools, users can query gene co-occurrences and construct customized co-occurrence network with genes of interest. To make GAAD more straightforward to experimental biologists and medical scientists, we extracted additional information describing the associations through text mining, including the putative diagnostic value of the associations, type and position of gene polymorphisms, expression changes of implicated genes, as well as the phenotypical consequences, and grouped the associations accordingly. GAAD is freely available at http://gaad.medgenius.info.

A Primer for Disease Gene Prioritization Using Next-Generation Sequencing Data

High-throughput next-generation sequencing (NGS) technology produces a tremendous amount of raw sequence data. The challenges for researchers are to process the raw data, to map the sequences to genome, to discover variants that are different from the reference genome, and to prioritize/rank the variants for the question of interest. The recent development of many computational algorithms and programs has vastly improved the ability to translate sequence data into valuable information for disease gene identification. However, the NGS data analysis is complex and could be overwhelming for researchers who are not familiar with the process. Here, we outline the analysis pipeline and describe some of the most commonly used principles and tools for analyzing NGS data for disease gene identification.

Review of Biological Network Data and Its Applications

Studying biological networks, such as protein-protein interactions, is key to understanding complex biological activities. Various types of large-scale biological datasets have been collected and analyzed with high-throughput technologies, including DNA microarray, next-generation sequencing, and the two-hybrid screening system, for this purpose. In this review, we focus on network-based approaches that help in understanding biological systems and identifying biological functions. Accordingly, this paper covers two major topics in network biology: reconstruction of gene regulatory networks and network-based applications, including protein function prediction, disease gene prioritization, and network-based genome-wide association study.

StrokeBase: A Database of Cerebrovascular Disease-related Candidate Genes

Complex diseases such as stroke and cancer have two or more genetic loci and are affected by environmental factors that contribute to the diseases. Due to the complex characteristics of these diseases, identifying candidate genes requires a system-level analysis of the following: gene ontology, pathway, and interactions. A database and user interface, termed StrokeBase, was developed; StrokeBase provides queries that search for pathways, candidate genes, candidate SNPs, and gene networks. The database was developed by using in silico data mining of HGNC, ENSEMBL, STRING, RefSeq, UCSC, GO, HPRD, KEGG, GAD, and OMIM. Forty candidate genes that are associated with cerebrovascular disease were selected by human experts and public databases. The networked cerebrovascular disease gene maps also were developed; these maps describe genegene interactions and biological pathways. We identified 1127 genes, related indirectly to cerebrovascular disease but directly to the etiology of cerebrovascular disease. We found that a protein-protein interaction (PPI) network that was associated with cerebrovascular disease follows the power-law degree distribution that is evident in other biological networks. Not only was in silico data mining utilized, but also 250K Affymetrix SNP chips were utilized in the 320 control/disease association study to generate associated markers that were pertinent to the cerebrovascular disease as a genome- wide search. The associated genes and the genes that were retrieved from the in silico data mining system were compared and analyzed. We developed a well-curated cerebrovascular disease-associated gene network and provided bioinformatic resources to cerebrovascular disease researchers. This cerebrovascular disease network can be used as a frame of systematic genomic research, applicable to other complex diseases. Therefore, the ongoing database efficiently supports medical and genetic research in order to overcome cerebrovascular disease.

Therapeutic Benefit of TH,AADC,and GCH-I Genes for Parkinson's Disease in Rat Model / 中国生物工程杂志

Parkinson's disease(PD) is a common neurodegenerative disorder with no effective protective treatment,characterized by a massive degeneration of dopaminergic neurons in the substantia nigra(SNpc) and the subsequent loss of their projecting nerve fibers in the striatum.The major neurochemical manifestation of this disorder is the loss of the neurotransmitter dopamine(DA) in the striatum as a result of the progressive degeneration of the dopaminergic neurons in the substantia nigra.There have been significant progresses in recent years reporting on the use of mesenchymal stem cells(MSCs)in gene therapy,with specific application towards PD.MSCs,a kind of multipotent adult progenitor cells,are considered as a useful vehicle for cell and gene therapy because of their multiple differentiation potentiality and self-transplantation.The present study was focused on treating rat model of PD using human tyrosine hydroxylase gene(hTH),human aromatic L-amino acid decarboxylase gene(hAADC) and human GT Pcyclohydrolase I gene(hGCH-I) engineered MSCs,in order to provide a better understanding about the application of these cells in the therapeutic benifit of PD.The gene of hTH,hAADC and hGCH-I were introduced via recombinant adeno-associated virus(rAAV) infection into the MSCs in vitro.The genetically modified MSCs expressing hTH,hAADC and hGCH-I were transplanted into the striatum of PD rat models.The behavior,the nigra-striatal level of DA and its metabolite were detected.The results of present study were shown as follows:hTH,hAADC,hGCH-I and LacZ gene were transfected into MSCs with adeno-associated virus vectors.The HEK293 packaging cells(ATCC) were transfected with the plasmids of pAAV-hTH,pAAV-hAADC,pAAV-hGCH-I,pAAV-LacZ,pAAV-RC,pHelper by using calcium phosphate precipitation.Titer was detected using HT1080 cells.Viral particles were collected and used to infect MSCs.The purified modified MSCs expressing the three kinds of genes were selected separately and were grafted in the striatum of the PD model rats in the lesion side.The MSCs genetically modified suvived well 12 weeks after transplantation.The improvements of the behavior were observed every week after transplantation.Compared with the control group,the rounds of asymmetric rotation after apomorphine administration decreased in the groups double or triple genes engineered MSCs grafted(p

D2GSNP: a web server for the selection of Single Nucleotide Polymorphisms within human disease genes

D2GSNP is a web-based server for the selection of single nucleotide polymorph isms (SNPs) within genes related to human diseases. The D2GSNP is based on a relational database created by downloading and parsing OMIM, GAD, and dbSNP, and merging it with positional information of UCSC Golden Path. Totally our server provides 5,142 and 1,932 non-redundant disease genes from OMIM and GAD, respectively. With the D2GSNP web interface, users can select SNPs within genes responding to certain diseases and get their flanking sequences for further genotyping experiments such as association studies.

Study on polymorphisms and mutations in the promoter region of WD gene / 中国实用内科杂志

Objective To screen polymorphisms and mutations in the promoter region of WD gene.Methods DNA from peripheral blood was obtained from 71 subjects of 36 family (48 WD patients,23 patients first-degree relatives) and 20 healthy people from Feb.2001 to Feb.2004.DNA sequence of the genes was analyzed by PCR amplification and direct genomic sequencing.Results There were three polymorphisms at positions-190,-78,+260(transcription start site as +1) of the promoter region of WD gene.Normal controls,WD patients and patients’ first-degree relatives all showed the polymorphisms;three of 48 WD patients presented C→T base substitution mutations at the same position -183:two were homozygous mutation,while the other was heterozygous.Normal control subjects and patients' relatives didn’t show this kind of mutation.Conclusion It suggests that the mutation of the promoter region is one of WD pathogenesis.

Mutation Analysis of Wilson Disease Gene: Arg778Leu Mutation in Korean Children / 대한소아소화기영양학회지

BACKGROUND: Wilson disease (WD) is an autosomal recessive disorder of copper transport and characterized by degenerative changes in the brain, liver dysfunction, and Kayser-Fleischer rings due to toxic accumulation of copper. Since the identification of Wilson disease gene (ATP7B), more than 80 mutations have been detected among the different ethnic groups. METHODS: Twenty three children with Wilson disease were included in this study. They were all diagnosed by low serum ceruloplasmin and increased 24 hour urinary copper excretion with characteristic clinical findings. We analysed WD gene mutation by assessing the nucleotide sequence of exon 7, 8, 9 and 10 including intron-exon boundaries of ATP7B gene from genomic DNA. RESULTS: Arg778Leu mutation was identified in 16 WD patients; three were homozygous and 13 were heterozygous for this mutation. Of the 46 alleles, 19 alleles had a Arg778Leu mutation (19/46=41%). Homozygote patients had neurologic forms of WD. Arg778Leu mutation was not found among 50 normal healthy persons. CONCLUSION: Arg778Leu mutation is a common mutation in Korean WD gene. Arg778Leu mutation screening might be used as a useful supplementary diagnostic test in some patients to confirm Wilson disease in Korea.

Study on apolipoprotein E gene polymorphism and mtDAN4336 mutation in patients with Alzheimer's disease / 临床神经病学杂志

Objective To study the distribution of Apolipoprotein E(ApoE) gene polymorphism and mtDAN*!4336 mutation in patients with sporadic Alzheimer's disease(AD),and analyse the difference of frequency of ApoE genotype from some other studies.Methods The polymerase chain reaction-restriction fragment length polymorphism(PCR-RFLP) technique was used to analyze the ApoE allele genotype and mtDAN mutation of 127 AD patients and 138 healthy elderly controls.Results In AD group, we found 2.4% of the patients with 2 ApoE4 allele gene, 18.1% of the patients with 1 ApoE4 allele gene, and 79.5% of the patients without ApoE4 allele gene. However, in control group, the frequency was 0.7%, 10.1% and 89.2% respectively. There was a significant difference between the two groups( P