Bioinformatics Approach for Pattern of Myelin-Specific Proteins and Related Human Disorders

Background: Recent neuroinformatic studies, on the structure-function interaction of proteins, causative agents basis of human disease have implied that dysfunction or defect of different protein classes could be associated with several related diseases. Objectives: The aim of this study was the use of bioinformatics approaches for understanding the structure, function and relationship of myelin protein 2 (PMP2), a myelin-basic protein in the basis of neuronal disorders. Methods: A collection of databases for exploiting classification information systematically, including, protein structure, protein family and classification of human disease, based on a new approach was used. Knowledge discovery was carried out based on collections criteria and in silico integrative in vitro studies. Results: The results of the evaluation of bioinformatics comorbid proteomics studies revealed that PMP2, an intracellular andmembrane myelin protein, is specific for a neuritis disease and collaborative to other diseases. Leprosy, another neuronal disease that could be related to neuritis, consists of interferon gamma (IFNG), a secreted protein included various protein classes from what is neuritis. Conclusions: The growth rate of information in bioinformatics databases could facilitate studies of live organisms prior to observation studies. Two different protein classes could be causative agents of one disease. However, two related diseases from one disease group could consist of different protein classes. Future research in the field of proteomics could allow modern insight to reshuffling of proteins in different diseases, and lead to the discovery of the etiology of such diseases

Mutation analysis of connexin 26 gene and del (GJB6-D13S1830) in patients with hereditary deafness from two provinces in Iran

Mutations in the connexin 26 (Cx26) gene at the DFNB1 locus on chromosome 13q12 are associated with autosomal recessive non-syndromic hearing loss (ARNSHL). There are many known mutations in this gene that cause hearing loss. A single frameshift, at position 35 (35delG) accounts for 50% of mutations in the Caucasian population with carrier frequencies of 1.5-2.5%. In this study we investigated the prevalence of Cx26 gene mutations by directly sequencing the coding exon of this gene belonging to ARNSHL individuals from 53 families in Qom and Markazi provinces of Iran. Seven different Cx26 variants were identified. Five Cx26 mutations including 35delG, 233delC, 176del16, W24X, L90P were found in 10 of 53 families (18.87%). One olymorphism V153I was also found. One variant A171T with unknown effects was also detected. Six of the 53 families were observed to have GJB2 mutations in both alleles (11.32%). The most common mutation was 35delG. Three out of 10 families (30%) with GJB2 variants contained 35delG mutation in both alleles and the frequency of 35delG allele was 0.50 among 10 out of 53 families. Also screening for the 342-kb GJB6 deletion mutant did not reveal any large deletion among families studied. Thus, in the two provinces, contribution of GJB2 (Gap Junction Protein Beta 2) mutations to familial deafness appears to be less significant. This necessitates further assessment of the other known genes regions as well as a search for new genetic factors in hereditary deafness in the Iranian population

Genetic study of the NOTCH3 gene in CADASIL patients

Background: Cerebral autosomal-dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a monogenic, hereditary, neurological syndrome characterized by small vessel disease (SVD), stroke, vascular cognitive impairment and dementia. It is caused by mutations in the NOTCH3  gene, affecting the number of cysteines in the extracellular domain of the receptor, causing protein misfolding and receptor aggregation. The pathogenic role of cysteine-sparing NOTCH3 missense mutations in patients with typical clinical CADASIL syndrome is unknown. No therapies are available for this condition.Objective: Genetic study of the NOTCH3 gene in CADASIL patients who were referred to the Fazeli-Sanati Genetics Laboratory.Subjects and methods: Peripheral blood samples were collected from 10 CADASIL patients to extract genomic DNA. DNA sequences of exons 2–8, 11–12 and 18–19, where NOTCH3 mutations are typically located; were amplified by using PCR and analyzed by direct sequencing.Results: 11 NOTCH3 exons were analyzed. Homozygous IVS7 + 15A>G mutation were found in five patients, Homozygous IVS7 + 16A>G mutation in one patient, Heterozygous for the Pro109Thr and Pro203His mutations in one patient, which were not reported previously. Heterozygous C395R and R153C mutations were found in two patients. One of the patients has no mutation in 11 analyzed NOTCH3 exons.Conclusion: We found four novel mutations (P109T, P203H, IVS7 + 15A>G and IVS7 + 16A>G) and 2 reported NOTCH3 mutations. Exon 4 and Intron 7 are hotspots in the patients we examined with the NOTCH3 mutations. These findings broaden the mutational spectrum of CADASIL.Keywords:  CADASIL, NOTCH3, Mutation, Exo

Contribution of GJB2 mutations and Four common DFNB loci in autosomal recessive non-syndromic hearing impairment in Markazi and Qom provinces of Iran

This study aimed to investigate the contribution of four common DFNB ("DFN" for deafness and "B" for autosomal resessive locus) loci and GJB2 gene mutations (exon 2) in hearing impairment in individuals living in Markazi and Qom provinces of Iran. Forty consanguineous Iranian families with at least three affected individuals in family or pedigree who suffer from an autosomal recessive non-syndromic congenital hearing impairment were the subjects of this study. Blood samples were taken from both hearing and non-hearing individuals, DNA was extracted and amplified by using specific primers for the coding region of GJB2 gene (exon 2). The PCR product of GJB2 gene was then sequenced. Also short tandem repeat (STR) markers amplified by using specific primers for loci DFNB2, DFNB3, DFNB4 and DFNB21. At least 2 microsatellite markers (STR) for each DFNB locus exceeding to 4-6 markers for the linked families were used. The amplified markers were analyzed by conventional Polyacrylamide Gel Electrophoresis followed by silver staining. Six families were homozygous or compound heterozygous for GJB2 mutations and were excluded from further studies. Linkage analysis was carried out for the remaining 34 families by genotyping the flanked STR markers of DFNB2, DFNB3, DFNB4 and DFNB21 loci. Six families showed linkage; including one family to DFNB2, two families to DFNB3 and three families to DFNB4 locus while no family showed linkage to DFNB21 locus. Undoubtedly, the best understanding of the genetic basis of hearing loss in Iranian population will be achieved by performing similar experiments in other provinces and also by analyzing more loci

Bioinformatics Approach for Pattern of Myelin-Specific Proteins and Related Human Disorders

Background: Recent neuroinformatic studies, on the structure-function interaction of proteins, causative agents basis of human disease have implied that dysfunction or defect of different protein classes could be associated with several related diseases. Objectives: The aim of this study was the use of bioinformatics approaches for understanding the structure, function and relationship of myelin protein 2 (PMP2), a myelin-basic protein in the basis of neuronal disorders. Methods: A collection of databases for exploiting classification information systematically, including, protein structure, protein family and classification of human disease, based on a new approach was used. Knowledge discovery was carried out based on collections criteria and in silico integrative in vitro studies. Results: The results of the evaluation of bioinformatics comorbid proteomics studies revealed that PMP2, an intracellular andmembrane myelin protein, is specific for a neuritis disease and collaborative to other diseases. Leprosy, another neuronal disease that could be related to neuritis, consists of interferon gamma (IFNG), a secreted protein included various protein classes from what is neuritis. Conclusions: The growth rate of information in bioinformatics databases could facilitate studies of live organisms prior to observation studies. Two different protein classes could be causative agents of one disease. However, two related diseases from one disease group could consist of different protein classes. Future research in the field of proteomics could allow modern insight to reshuffling of proteins in different diseases, and lead to the discovery of the etiology of such diseases. Keywords: Bioinformatics Databases, Myelin Protein 2 (PMP2), Protein Classes, Human Disorder

Study of Th1/Th2 balance in peripheral blood mononuclear cells of patients with alopecia areata

Alopecia areata represents an autoimmune pathological process driven primarily by cellular aberrations contained within the immune system, which activates various humoral and cellular elements of the immune response. The aim of this study was to determine the mRNA expression levels of T-bet and GATA-3 as potential inducers of T helper (Th)1 and Th2 differentiation, respectively, as well as Th1(IFN-γ) and Th2(IL-4) cytokine mRNA expression in patients with alopecia areata. Using real-time reverse transcriptase PCR (RT-PCR), the relative amounts of T-bet, GATA-3, IFN-γ, and IL-4 mRNA transcripts were determined in PBMCs from 20 Iranian patients with alopecia areata and compared with those of 20 healthy control subjects. In comparison with the normal group, T-bet and IFN-γ mRNA expression levels were significantly up-regulated in the alopecia areata patients, while GATA-3 and IL-4 mRNA expression levels were down-regulated. Notably, positive correlation (P < 0.05) was found between IFN-γ and T-bet levels in patients and controls. In addition, significant positive correlations existed between GATA-3 and IL-4 (P < 0.05). These results indicate that a Th1/Th2 imbalance exists in alopecia areata, and it may be implicated in the pathogenesis of disease

Diversity and relationship between Iranian ethnic groups: Human dopamine transporter gene (DAT1) VNTR genotyping

The 40-bp VNTR polymorphism in the 3′ untranslated region of the human DAT1 (dopamine transporter 1) was analyzed in the Iranian ethnic groups in order to examine the influence of geographical and linguistic affiliation on the genetic affinities among the Iranian population. A total of 449 subjects belonging to nine ethnic groups from the Iranian population were included in the study. The screening of 898 chromosomes showed five alleles (6, 7, 8, 9, 10, and 11), of which allele 10 revealed the highest frequency in most regions. Allele 8 was predominant in one ethnicity and occurred more frequently in the center of Iran. This study shows that the DAT1 distribution in Iran has a different pattern from those in other studies, which can contribute to an understanding of differentiation and diversity of Iranian ethnic groups. This polymorphism could represent the genetic diversity among the various ethnic groups of Iran. © 2007 Wiley-Liss, Inc

Study of the association of DFNB3 locus with autosomal recessive non-syndromic hearing loss in iranian deaf population using genetic linkage analysis

Background: Hearing loss is a common sensory disorder that typically illustrates genetic heterogeneity in human populations. The incidence of congenital hearing loss is estimated at 1 in 500 births of which approximately 70 of cases are attributed to genetic factors. Genetic hearing impairment can be classified as either syndromic or non-syndromic and among non-syndromic hearing loss autosomal recessive (ALNSHL) accounts for approximately 75-80 of cases. This type of hearing loss is extremely heterogeneous and includes over 100 loci. For recessive deafness, most frequent genes are GJB2, SLC26A4, MYO15A, OTOF, and CDH23 in worldwide. This study aimed to determine the role of MYO15A (DFNB3) gene mutations in Iranian deaf population using linkage analysis. Methods: To investigate the frequency of DFNB3 gene mutation, linkage analysis was performed in 30 Iranian families with over three deaf child and negative GJB2. The negative mutations pedigrees for these gene mutations were then tested for the linkage to DFNB3 (MYO15A) locus, using short tandem repeat (STR) markers. Findings: Mutation 35delG was identified in 5 families out of 30 by sequencing the coding region of GJB2 gene. One family showed linkage to DFNB3 locus. Conclusion: Based on the results of this study, DFNB3 locus is the third cause of deafness after DFNB1 (GJB2) and DFNB4 (SLC26A4). © 2014, Isfahan University of Medical Sciences(IUMS). All rights reserved

The Study of SLC26A4 Gene Causing Autosomal Recessive Hearing Loss by Linkage Analysis in a Cohort of Iranian Populations.

Sensorineural non-syndromic hearing loss is the most common disorder which affects 1 in 500 newborns. Hearing loss is an extremely heterogeneous defect with more than 100 loci identified to date. According to the studies, mutations in GJB2 are estimated to be involved in 50- 80% of autosomal recessive non-syndromic hearing loss cases, but contribution of other loci in this disorder is yet ambiguous. With regard to studies, DFNB4 locus (SLC26A4) can be classified as the second cause of hearing loss. So, this study aimed to determine the contribution of this locus in hearing loss as well as the frequency of SLC26A4 gene mutations in a population in the west of Iran. In this descriptive laboratory study, we included 30 families from the west of Iran with no mutation in GJB2 gene. Linkage analysis was performed by DFNB4 (SLC26A4) molecular markers (STR). The families with hearing loss linked to this locus were further analyzed for mutation detection. SLC26A4 gene exons were amplified and analyzed using direct DNA sequencing. In studied families, 2 families displayed linkage to DFNB4 locus. Identified mutations include mutation in exon 5 (c.416 G>T) and in splicing site of exon 7 (IVS-2 A>G or c.919-2 A>G)