mohammad amin tabatabaiefar

Approximately 3% of the human genome is rich in GCs. These regions are often found in the promoter of genes, especially housekeeping genes and tumor suppressor genes. Amplification of these GC-rich regions can be challenging. Because the stability of GC-rich DNA sequences is higher, secondary structures are easily formed in these regions. Type 4 non-medullary thyroid carcinoma has been linked to the FOXE1 gene as a risk factor. FOXE1 belongs to a large family of transcription factors principal for the development of the thyroid gland's morphology.

With a high proportion of GC, a portion of the FOXE1 gene sequence cannot be amplified using the usual polymerase chain reaction. This work is an experimental study that deals with this issue.

The results of the present study showed that the Touchdown polymerase chain reaction, in combination with CO-amplification materials such as betaine and Dimethyl Sulfoxide (DMSO), is effective in amplifying the sequence of this region of the FOXE1 gene by destruction of the secondary structures formed in the sequence and increasing the reaction product.

Using this method, GC-rich regions in additional genes with a similar degree of GC as the FOXE1 gene can be amplified.

Lynch syndrome (LS) predisposes individuals to early-onset colorectal and other Lynch-associated cancer. This disorder is an autosomal dominant genetic disturbance caused by germline mutations in one of the mismatch repair genes. Different clinical and molecular criteria are used to diagnose LS. Microsatellite instability testing and immunohistochemistry are two widely used methods for the molecular screening of LS-associated cancers. According to the immunohistochemistry and Microsatellite instability testing, we introduce three Persian families with Lynch-like syndrome (LLS) who met clinical Amsterdam-II criteria and their probands were mismatch repair deficient. In the case of immunohistochemistry-MLH1 absent, BRAF-V600E mutation was evaluated to rule out the sporadic colorectal cancer cases. No pathogenic germline variants were found by next generation sequencing method. Multiplex ligation-dependant probe amplification technique was done to find large in/dels within MLH1/MSH2 genes of the probands. A two-exon deletion within MLH1 gene was eventually identified in one of the patients. Finally, we have represented a molecular pipeline to diagnose LLS based on literature review and the introduced cases.

Microsatellite instability (MSI) in colorectal cancer (CRC) patients is considered as a diagnostic and prognostic marker. MSI is a consequence of mismatch repair deficiency which is evaluated using the different microsatellite markers on the whole genome. In this pilot study, the diagnostic value of a novel triplex panel including three mononucleotide markers has been evaluated in comparison to the standard Promega kit for MSI testing in CRC patients with Amsterdam II criteria.

DNA extracted from tumors and normal Formalin‑Fixed Paraffin‑Embedded (FFPE) tissues of index cases from 37 HNPCC (Hereditary non‑polyposis colorectal cancer) families were evaluated for MSI state. Primer design for three markers, including BAT25, ACVR2, and TGFBR2, was performed using 19 nucleotides of the M‑13 phage. The instability of each marker was assessed through fragment analysis in comparison with Promega kit markers for all patients. The sensitivity and specificity of each marker have been calculated.

The comparative evaluation of MSI in both tumors and normal adjacent FFPE tissues demonstrated a separate sensitivity as 100%, 83.3%, and 76.9% for BAT25, ACVR2, and TGFBR2, respectively, and 100% sensitivity in the form of a triplex. Moreover, the specificity for each of these three markers in MSI testing was estimated as 100%, separately and in the form of the triplex in comparison with the Promega pentaplex standard Kit.

A high sensitivity and specificity for the novel triplex panel in MSI‑testing were estimated among Iranian patients. More studies are recommended to confirm this panel as a diagnostic kit for MSI testing.

Breast cancer is a type of cancer that starts in the breast tissue and affects about 10% of women at different stages of their lives. In this study, we applied a new method to predict recurrence in biological networks made from gene expression data.

The method includes the steps such as data collection, clustering, determining differentiating genes, and classification. The eight techniques consist of random forest, support vector machine and neural network, randomforest + k‑means, hidden markov model, joint mutual information, neural network + k‑means and suportvector machine + k‑menas were implemented on 12172 genes and 200 samples.

Thirty genes were considered as differentiating genes which used for the classification. The results showed that random forest + k‑means get better performance than other techniques. The two techniques including neural network + k‑means and random forest + k‑means performed better than other techniques in identifying high risk cases.

Thirty of 12,172 genes are considered for classification that the use of clustering has improved the classification techniques performance.

Trinucleotide repeat (TNR) expansion is a kind of mutation with instability in the number of microsatellite repeats. This nature of mutation leads to the different kinds of neurological and neuromuscular disorders; among them, fragile‑X syndrome is the main cause of intellectual disability in which the increasing number of CGG TNR in 5’ untranslated region is the main reason for epigenetic silencing of Fragile X mental retardation 1 gene. The aim of this study is to decrease the CG content of the candidate region to facilitate amplification by conventional polymerase chain reaction (PCR). Bisulfite treatment of the genomic DNA results in conversion of unmethylated cytosine to uridine and may overcome the diagnostic pitfalls.

The whole blood DNA was extracted and bisulfite treated. Then any simplification in PCR process of desire sequence were assayed through following conventional PCR using specifically designed primers for converted sequence. Bisulfite‑treated PCR product of a nearby sequence confirmed our results as a conversion control.

Both the control and the candidate sequences undergoing bisulfite treatment were successfully amplified by PCR.

Decreasing the GC content of the sequence by bisulfite treating could be a new approach to overcome difficulties in amplifying GC‑rich sequences.

Prostate cancer (PC) is the second most prevalent cancer in men. Prostate-specific antigen (PSA) is the main biomarker for screening PC. An increase in PSA could lead to false-positive results. Thus, more appropriate markers should be investigated. In the present study, JPX and LINC00641 expression levels were measured in tumoral prostate tissue compared with the non-tumor tissue.

Experimental approach:

43 pairs of prostate tumoral and non-tumor tissue were prepared. The expression levels of JPX and LINC00641 were investigated by RT-qPCR.

Significant upregulation of LINC00641 (2.47 ± 0.5 vs</em> 1.41 ± 0.2) and downregulation of JPX (1.42 ± 0.6 vs</em> 2.83 ± 1.0) were observed in PC tissues compared with the normal tissues (their adjacent non-tumoral tissues).

Conclusion and implications:

Dysregulation of JPX and LINC00641 in PC patients could be used in the future as a prognostic biomarker in PC.

 BRAF-V600E is a known prognostic/predictive marker in colorectal cancer (CRC), detected in 4 - 12% of all patients with this cancer. Familial-CRC-type-X (FCCX) is a subtype of mismatch-repair (MMR) proficient CRC with an unknown genetic cause.

 Given the lack of enough information on the molecular aspects of FCCX among Iranians, this study was conducted to evaluate the BRAF-V600E hot-spot mutation in tumor DNA in FCCX probands in Central Iran.

 This was a cross-sectional study in which 48 FCCX probands were recruited according to Amsterdam-II criteria, and MMR proficiency was confirmed by MSI testing and IHC-MMRs. Tumors’ DNA samples were assessed for the BRAF-V600E mutation by Sanger-sequencing.

 None of the 48 assessed FCCX probands presented the BRAF-V600E mutation.

 It can be suggested that FCCX tumors have a good prognosis compared to other CRCs.

The precision and time required for analysis of data in next-generation sequencing (NGS) depends on many factors including the tools utilized for alignment, variant calling, annotation and filtering of variants, personnel expertise in data analysis and interpretation, and computational capacity of the lab and its optimization is a challenging task. 

An application software was designed and implemented in C# for optimizing the third step of NGS data analysis. In this study, annotation, filtering, and interpretation of NGS data were specifically optimized for non-syndromic autosomal recessive hearing loss disease.

Whole-exome sequencing data of a patient with a pathogenic mutation confirmed by familial genetic analysis, which contained a total number of 671829 variants after primary analysis, were evaluated by the implemented software. After filtering the variants based on a predefined BED file, 508 variants remained. According to the patient’s pedigree, in the next step of analysis, homozygote variants were selected and only 187 variants remained. After applying the population frequency threshold of 0.6% on gnomeAD and ExAC databases, the number of variants reached 110 and 3, respectively. The identified pathogen was approved by the results of Sanger sequencing done for family co-segregation. This analysis took about 15 minutes on a moderate PC.

The designed software is a fully graphical one that has the capability of comparing, viewing, filtering, and merging input files without any coding. Moreover, it can construct a local database from the analyzed files and apply region constraints and user-defined thresholds on various fields of the database.

Careful design in the primary steps of a next‑generation sequencing study is critical for obtaining successful results in downstream analysis.

In this study, a framework is proposed to evaluate and improve the sequence mapping in targeted regions of the reference genome. In this regard, simulated short reads were produced from the coding regions of the human genome and mapped to a Customized Target‑Based Reference (CTBR) by the alignment tools that have been introduced recently. The short reads produced by different sequencing technologies aligned to the standard genome and also CTBR with and without well‑defined mutation types where the amount of unmapped and misaligned reads and runtime was measured for comparison.

The results showed that the mapping accuracy of the reads generated from Illumina Hiseq2500 using Stampy as the alignment tool whenever the CTBR was used as reference was significantly better than other evaluated pipelines. Using CTBR for alignment significantly decreased the mapping error in comparison to other expanded or more limited references. While intentional mutations were imported in the reads, Stampy showed the minimum error of 1.67% using CTBR. However, the lowest error obtained by stampy too using whole genome and one chromosome as references was 3.78% and 20%, respectively. Maximum and minimum misalignment errors were observed on chromosome Y and 20, respectively.

Therefore using the proposed framework in a clinical targeted sequencing study may lead to predict the error and improve the performance of variant calling regarding the genomic regions targeted in a clinical study.

Hereditary diffuse gastric cancer (HDGC) is a hereditable form of diffuse gastric cancer with very aggressive tumors, poor prognosis, and delayed clinical signs.

We assessed 17 probands identified with HDGC upon gastrectomy according to the histopathological criteria confirmed by a pathologist and familial history. We extracted DNA from peripheral blood and formalin fixed paraffin-embedded tissues. DNA sequencing was done following PCR amplification of 16 exons and exon/intron boundaries of the CDH1 gene and exon 2 of CTNNA1 gene. The Multiplex Ligation-dependent Probe Amplification technique was performed on patients with no pathogenic variants in sequencing.

Totally, 17 probands comprising seven males and 10 females were assessed. In three patients, we recognized the tumors in the early TNM stage (I, II), while in 14 cases, tumors were observed in the late stages (III, IV). Overall, DNA sequencing of the CDH1 gene identified 16 variants (seven exonic including five new variants and nine intronic containing six new variants). Moreover, Multiplex Ligation-dependent Probe Amplification detected one deletion in exon 1 of two patients.

Our results showed that E-cadherin deficiency in HDGC was related to CDH1 gene point mutations and large deletion with high heterogeneity, which should be considered in the diagnosis and treatment of HDGC patients.

Diabetes mellitus (DM) is a group of metabolic disorders in the body, accompanied with increasing blood sugar levels. Diabetes is classified into three groups: Type 1 DM (T1DM), Type 2 DM (T2DM), and monogenic diabetes. Maturity-onset diabetes of the young (MODY) is a monogenic diabetes that is frequently mistaken for T1D or T2D. The aim of this study was to diagnose MODY and its subtype frequency in a diabetic population in Iran.

In this study among ten diabetic families that were highly suspected to MODY by nongenetic biomarkers and without any pathogenic mutation in GCK and HNF1A genes, two patients from two unrelated families were examined via whole-exome sequencing (WES) in order to detect the causative gene of diabetes. Co-segregation analysis of the identified variant was performed using Sanger sequencing.

In this study, no pathogenic variant was found in GCK and HNF1A genes (MODY2 and MODY3), while these two types of MODY were introduced as the most frequent in other studies. By using WES, a pathogenic variant (p.I488T) was found in one of the patients in CEL gene causing MODY8 that its frequency is very rare in other studied populations. A high-risk variant associated with diabetes was found in another patient.

WES was applied in this study to reveal the cause of MODY in 1 family. This pathogenic mutation was previously reported as a disease causing mutation.

Granular and lattice corneal dystrophies (GCDs & LCDs) are autosomal dominant inherited disorders of the cornea. Due to genetic heterogeneity and large genes, unraveling the mutation is challenging.

Patients underwent comprehensive clinical examination, and targeted next-generation sequencing (NGS) was used for mutation detection. Co-segregation and in silico analysis was accomplished.

Patients suffered from GCD. NGS disclosed a known pathogenic variant, c.371G>A (p.R124H), in exon 4 of TGFBI. The variant co-segregated with the phenotype in the family. Homozygous patients manifested with more severe phenotypes. Variable expressivity was observed among heterozygous patients.

The results, in accordance with previous studies, indicate that the c.371G>A in TGFBI is associated with GCD. Some phenotypic variations are related to factors such as modifier genes, reduced penetrance and environmental effects.

Short Tandem Repeats (STRs), which are located out of pseudo-autosomal parts of the human Y chromosome and passed-down from fathers to the male offspring in a non-recombinant form, are regarded as appropriate markers for forensic purposes and evolutionary investigations. Few studies concerned the genotyping of Y chromosome short tandem repeats (Y-STRs) among the ethnic groups of the north of Iran, especially the province of Golestan which is a multiethnic region of Iran. Thus, in this work we investigated the frequency of Y-STR haplotypes among the male population from Golestan province, to elucidate their identity and kinship patterns. A total number of 106 unrelated male individuals participated in this study. Genomic DNA was extracted from blood samples and the multiplex polymerase chain reaction was employed to amplify DNA fragments. Genotyping was performed using capillary electrophoresis and, finally, allele polymorphisms, haplotype diversity (HD) and haplotype discrimination capacity (DC) were determined using GenAlEXv6.5 and Arlequin v5.3.2 software and compared to other regions of Iran. A total number of 87 unique haplotypes were determined. The highest and least allelic polymorphism was observed for the DYS385b and DYS391 loci, respectively. HD and DC were 0.9962 and 0.8207, respectively. In the case of locus with the least allelic variation, we didn’t observe any difference between the Gilan and Golestan but there was a difference between the Golestan and Mazandaran provinces. Our results indicated the efficiency of Y-STRs to be used as genetic markers for forensic medicine, and also the evolutionary comparison of different ethnic groups of Golestan, Iran. Also, a low genetic distance between the population of Golestan with other northern provinces was noticed.

Diabetes mellitus is a group of metabolic disorders resulting in increased level of blood sugar. Type 1 Diabetes (T1D), Type 2 Diabetes (T2D) and monogenic diabetes are there major groups of diabetes. Maturity-onset diabetes of the young (MODY) is a monogenic diabetes that is frequently mistaken for T1D or T2D and it has 14 different subgroups. The aim of this study was to diagnose MODY and determine the frequency of its 2 major subgroups in Isfahan diabetic population.

In this descriptive-experimental study with the aim of determining type and the frequency of mutations in GCK and HNF1A genes in 26 families with MODY from Isfahan using genetic linkage analysis method and select of 4 markers for each gene. Linkage results was confirmed by fragment analysis and then all the exons of genes were sequenced in any linked families.

In this study from 26 families, 4 families were linked to markers of GCK gene and 3 families were linked to HNF1A gene. After sequencing of all exons of these 2 genes in the related families, variants were analyzed and their effects on diabetes were surveyed. There was no pathogenic mutation but some polymorphisms with increasing effects on susceptibility to diabetes were found.

in this study despite of the fact that some families were linked to markers of these 2 gene, and the results of other studies that mutations in these 2 genes are the frequent reasons of MODY, there were any pathogenic variant in any of the patients. So it seems that the genetic profile of this population is different from other studied populations.

Carriers of structural chromosomal rearrangements such as Robertsonian or reciprocal translocations have an increased risk of spontaneous abortion and producing offspring with genetic abnormalities. Robertsonian translocations are present in 0.1% of the general population and 1% of the infertile population. Two types of Robertsonian translocations occur more frequently than all others, being 45,XX,rob(13;14)(q10;q10) and 45,XX,rob(14;21)(q10;q10) respectively. The history of repeated abortions could be the outcome of unbalanced gametes (either monosomy or trisomy) resulting during the meiotic segregation of the balanced heterozygote female carrier. In the present report, uncommon Robertsonian translocation in a couple with spontaneous repeated abortions is reported. Cytogenetic analysis of a couple revealed the presence of 45, XY, t (15; 15) (10q; 10q) chromosomal constitution in the male partner. The cytogenetic analysis of couples with repeated abortions is obligatory to identify any probable chromosomal aberrations. As far as we know this is the first instance reported in Iran.

Maturity‑onset diabetes of the young (MODY) is a clinically and genetically heterogeneous group of diabetes characterized by noninsulin‑dependent, autosomal‑dominant disorder with strong familial history, early age of onset, and pancreatic beta‑cell dysfunction. Mutations in at least 14 different genes are responsible for various MODY subtypes. Heterozygous mutations in the hepatocyte nuclear factor 1 alpha (HNF1A) gene are responsible for the MODY3 subtype, which is a common subtype of MODY in different studied populations. To date, more than 450 different variants of this gene have been reported as disease causing for MODY3. This study was carried out to evaluate HNF1A mutations in Iranian diabetic families fulfilling MODY criteria.

Polymerase chain reaction and Sanger sequencing were performed. All the ten exons of the HNF1A gene were sequenced in ten families, followed by cosegregation analysis and in silico evaluation. Computational protein modeling was accomplished for the identified mutation.

MODY3 was confirmed in two large families by detecting a mutation (p.G253E) in coding regions of HNF1A. Compound heterozygous state for two common variants in HNF1A (p.I27 L and p.S487N) was detected in affected members of 5 families, and in one family, a rare benign variant in the coding sequence for Kozak sequence was detected. Two new nonpathogenic variants were found in noncoding regions of HNF1A.

It seems that HNF1A mutations are a common cause of MODY in Iranian diabetic patients. Identified common variants in heterozygous state can cause diabetes Type II in earlier ages. The role of rare variant rs3455720 is unknown, and more investigation is needed to uncover the function of this variant.

Hearing loss (HL) is the most common sensorineural disorder affecting 1 in 1000 newborns. Autosomal recessive non-syndromic hearing loss (ARNSHL), which is the most common cause of severe HL, is caused by mutations in more than 80 loci. The OTOA gene located on DFNB22 is a rare cause of the disease and the gene studied less in Iranian ARNSHL families. Hence, limited information is available on the frequency and type of OTOA mutations in different populations. In this study, we investigated the role of DFNB22 locus in ARNSHL patients in Khuzestan province, Iran.

In this descriptive-experimental study, 23 large families with pre-lingual ARNSHL from Khuzestan province were enrolled. Mutations in GJB2 were excluded by DNA sequencing followed by linkage analysis. Homozygosity mapping of DFNB22 was conducted using 6 short tandem repeat polymorphic markers via touch-down PCR and polyacrylamide gel electrophoresis. Homozygosityby-descent was identified by calculating two-point and multi-point LOD score and haplotype reconstruction.

Families were negative for GJB2 mutations. Genotyping the STRP markers, haplotype reconstruction, and two-point and multiplepoint LOD scores did not show homozygosity-by-descent in any of the pedigrees.

Our findings suggest that OTOA mutations might not contribute significantly to the molecular pathophysiology of ARNSHL in Khuzestan province. However, extending the sample size can illuminate the role of this gene in Khuzestan province.

Green fluorescent protein (GFP) has played an important role in biochemistry and cell biology as a reporter gene. It has been used to assess the potency of promoters for recombinant protein production.This investigation reveals evidences suggesting that the gfp GFP gene (EGFP) could be expressed without the promoter. In a study, a pLenti-F/GFP vector was constructed with the purpose to allow GFP expression in transduced cells but not in packaging cells; however, after transfecting the HEK293T cell line, GFP gene  was expressed, compared to pLOX/CWgfp-transfected cells showed expression lag, lower levels and reduced percentage of GFP expression in the cells. This unexpected result could be due to auto transduction in packaging cell, possible retrotransposon activity in the cell line, possible contamination of pLenti-F/GFP with the pLOX/CWgfp and possible presence of a promoter within backbone of the vector.   All the possibilities were ruled out. To exclude the possibility that a sequence within the region might act as a promoter, the fragment to be transfected was minimized to a region containing “from the start of  the GFP gene to 5’LTR R”. The GFP gene was again expressed. Therefore, our findings suggest the EGFP does not need promoter for expression. This should appeal to the researchers designing GFP based assays  to evaluate the potency of promoters, since possible aberrant expression may have a potential to influenceon the results of a planned experiment.

Autosomal recessive non-syndromic hearing loss (ARNSHL), one of the global public health concerns, is marked by a high degree of genetic heterogeneity. The role of GJB2, as the most common cause of ARNSHL, is only <20% in the Iranian population. Here, we aimed to determine the relative contribution of several apparently most common loci in a cohort of ARNSHL Iranian families that were negative for the GJB2 mutations.

Totally, 80 Iranian ARNSHL families with 3 or more affected individuals from Isfahan and Hamedan provinces, Iran were enrolled in 2017. After excluding mutations in the GJB2 gene via Sanger sequencing, 60 negative samples (30 families from each province) were analyzed using homozygosity mapping for 10 ARNSHL loci.

Fourteen families were found to be linked to five different known loci, including DFNB4 (5 families), DFNB2 (3 families), DFNB7/11 (1 family), DFNB9 (2 families) and DFNB3 (3 families).

Despite the high heterogeneity of ARNSHL, the genetic causes were determined in 23.5% of the studied families using homozygosity mapping. This data gives an overview of the ARNSHL etiology in the center and west of Iran, used to establish a diagnostic gene panel including most common loci for hearing loss diagnostics.

Translocations are the most common structural abnormality in the human genome. Carriers of balanced chromosome rearrangements exhibit increased risk of abortion or a chromosomally-unbalanced child. The present study was carried out in 2017 at the Iranian Blood Transfusion Research Center. This study reported a rare chromosomal disorder with 4p duplication and 10q distal deletion syndrome which is associated with various complications at birth. Defects included the following characteristics: dysmorphic facial characteristic, hand or foot anomalies, growth retardation, developmental delay, strabismus, heart defects and renal anomalies. Cytogenetic analysis and array CGH were performed and, for the first time, we reported a patient with trisomy 4p16.3p12 and monosomy 10q26.3. The patient was found to have: arr 4p16.3p12 (37,152–45,490,207) x3, 10q26.3 (134,872,562–135,434,149) x1 genomic imbalances.

Hearing loss (HL) is a highly prevalent heterogeneous deficiency of sensory‑neural system with involvement of several dozen genes. Whole‑exome sequencing (WES) is capable of discovering known and novel genes involved with HL.

Two pedigrees with HL background from Khuzestan province of Iran were selected. Polymerase chain reaction‑sequencing of GJB2 and homozygosity mapping of 16 DFNB loci were performed. One patient of the first and two affected individuals from the second pedigree were subjected to WES. The result files were analyzed using tools on Ubuntu 16.04. Short reads were mapped to reference genome (hg19, NCBI Build 37). Sorting and duplication removals were done. Variants were obtained and annotated by an online software tool. Variant filtration was performed. In the first family, ENDEAVOUR was applied to prioritize candidate genes. In the second family, a combination of shared variants, homozygosity mapping, and gene expression were implemented to launch the disease‑causing gene.

GJB2 sequencing and linkage analysis established no homozygosity‑by‑descent at any DFNB loci. Utilizing ENDEAVOUR, BBX: C.C857G (P.A286G), and MYH15: C.C5557T (P.R1853C) were put forward, but none of the variants co‑segregated with the phenotype. Two genes, UNC13B and TRAK1, were prioritized in the homozygous regions detected by HomozygosityMapper.

WES is regarded a powerful approach to discover molecular etiology of Mendelian inherited disorders, but as it fails to enrich GC‑rich regions, incapability of capturing noncoding regulatory regions and limited specificity and accuracy of copy number variations detection tools from exome data, it is assumed an insufficient procedure.

Waardenburg syndrome (WS) is a neurocristopathy with an autosomal dominant mode of inheritance, and considerable clinical and genetic heterogeneity. WS type II is the most common type of WS in many populations presenting with sensorineural hearing impairment, heterochromia iridis, hypoplastic blue eye, and pigmentary abnormalities of the hair and skin. To date, mutations of MITF, SOX10, and SNAI2 have been implicated in the pathogenesis of WS2. Although different pathogenic mutations have been reported in many ethnic groups, the data on Iranian WS2 patients is insufficient. 31 WS2 patients, including 22 men and 9 women from 14 families were included. Waardenburg consortium guidelines were employed for WS2 diagnosis. WS2 patients underwent screening for MITF, SOX10, and SNAI2 mutations using direct sequencing and MLPA analysis. Clinical evaluation revealed prominent phenotypic variability in Iranian WS2 patients. Sensorineural hearing impairment and heterochromia iridis were the most common features (67% and 45%, respectively), whereas anosmia was the least frequent phenotype. Molecular analysis revealed a de novo heterozygous c.640C>T (p.R214X) in MITF and a de novo heterozygous SOX10 gross deletion in the study population. Our data help illuminate the phenotypic and genotypic spectrum of WS2 in an Iranian series of patients, and could have implications for the genetic counseling of WS in Iran.

BACKGROUND/ The aim of this study was to investigate the effect of Berberis vulgaris (BV) juice consumption on insulin homeostasis, glycemic profiles of patients with benign breast disease (BBD).
SUBJECTS/ This parallel design, triple-blind, randomized and placebo controlled clinical trial was conducted on 85 eligible women diagnosed with BBD who recruited from Nour-Nejat hospital, Tabriz, Iran. Participants were randomly allocated into either intervention group who received BV juice (480 ml/day, n=44) or BV juice placebo group at the same time (480 ml/day, n=41). After a 7 day run-in period, treatments were administered for the duration of 8 weeks. Participants, care givers and those who assessed laboratory analyses were blinded to the assignments (IRCT registry no: IRCT2012110511335N2).
The relative treatment effects of BV supplementation showed decreased serum levels of insulin for 19%, C-peptide for 8%, homeostasis model assessment of insulin resistance index (HOMA-IR) for 16% and glucose to insulin ratio for 22% but HOMA-B increased 44% relative to placebo group over 8 weeks BV supplementation. Although these changes were not statistical significant, the mean changes for C-peptide and HOMA-B were significant just after adjusting for baseline data and covariates.
Administration of BV juice showed controlling effects on HOMA related indices, consequently might have beneficial effects on insulin signaling-related functions in women with benign breast tumor.

Integrins are adhesion molecules which play crucial roles in cell-cell and cell-extracellular matrix interactions. Very late antigen-4 or α4β1 and lymphocyte Peyer’s patch adhesion molecule-1 or α4β7, are key factors in the invasion of tumor cells and metastasis. Based on the previous reports, integrin α4 (ITGA4) is overexpressed in some immune disorders and cancers. Thus, inhibition of ITGA4 could be a therapeutic strategy. In the present study, miR-30a was selected in order to suppress ITGA4 expression. The ITGA4 3´UTR was amplified, cloned in the Z2827-M67-(ITGA4) plasmid and named as Z2827-M67/3´UTR. HeLa cells were divided into five groups; (1) untreated without any transfection, (2) mock with Z2827-M67/3´UTR transfection and X-tremeGENE reagent, (3) negative control with Z2827-M67/3´UTR transfection alone, (4) test with miR-30a mimic and Z2827-M67/3´UTR transfection and (5) scramble with miR-30a scramble and Z2827-M67/3´UTR transfection. The MTT assay was performed to evaluate cell survival and cytotoxicity in each group. Real-time RT-PCR was applied for the ITGA4 expression analysis. The findings of this study showed that miR-30a downregulated ITGA4 expression and had no effect on the cell survival. Due to the silencing effect of miR-30a on the ITGA4 gene expression, this agent could be considered as a potential tool for cancer and immune disorders therapy.

Hearing loss (HL) is a most common sensory deficit in humans and approximately one in 1,000 newborns has severe-to-profound HL. About 50% of HL cases are inherited and approximately 70 percent of HL cases are Non-syndromic that about 80 percent of this type of HL is inherited in recessive manner (ARNSHL). This is a heterogeneous disease and its prevalence is higher in developing countries. In Iran due to high rate of consanguinity has high frequency, too. The purpose of the present study was to investigate genetic linkage analysis of DFNB39 locus in families with autosomal recessive nonsyndromic HL from Khuzestan province.
In this descriptive laboratory study, to determine type and frequency of HGF mutations 300 individuals of 25 families from Khuzestan province with autosomal recessive nonsyndromic hearing loss were examined. Selected families in this study had consanguinity and had at least 2 patients and also they were negative for GJB2 gene mutations. Linkage analysis was performed by 6 markers STR (Short tandem repeats) which were located in or were tightly linked to DFNB39 locus conventional PCR and PAGE.
After examining different families, it was revealed non of the families did not show linkage to the DFNB39 locus. Lack of HGF gene mutations in mentioned family suggests that the HGF's mutations probably have no role in causing HL in the studied families.
Based on the results of this study, DFNB39 locus may not be important role in causing hearing loss of population studied. However, further studies are necessary to determine more precisely the role of this locus in hearing loss in Iranian population.