Publications by authors named "Javad Mohammadi-Asl"

51 Publications

The antioxidant and anti-inflammatory effects of astaxanthin supplementation on the expression of miR-146a and miR-126 in patients with type 2 diabetes mellitus: A randomised, double-blind, placebo-controlled clinical trial.

Int J Clin Pract 2021 Jan 14:e14022. Epub 2021 Jan 14.

Nutrition and Metabolic Diseases Research Center and Department of Nutrition, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.

Background: The pathogenesis of type 2 diabetes mellitus (T2DM) is associated with chronic oxidative stress and inflammation. It is well known that the expression of some miRNAs such as miRNA-146a is upregulated in diabetic and hyperglycaemic patients, whereas circulating miRNA-126 is reduced. Therefore, we aimed to determine the effects of astaxanthin (AST) supplementation on the circulating malondialdehyde (MDA) and interleukin 6 (IL-6) levels, and the expression of miR-146a and miR-126 in patients with T2DM.

Methods: This randomised, double-blind, placebo-controlled clinical trial was conducted in 44 patients with T2DM randomly receiving 8 mg/d of oral AST (n = 22) or placebo (n = 22) for 8 weeks.

Results: We observed that AST supplementation could decrease plasma levels of MDA and IL-6 (P < .05) and decrease the expression level of miR-146a over time (fold change: -1/388) (P < .05).

Conclusion: AST supplementation might be beneficial for improving circulating MDA and IL-6 and the down-regulation of miR-146a. However, future investigations are suggested to confirm these results.
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http://dx.doi.org/10.1111/ijcp.14022DOI Listing
January 2021

Effect of weight-loss diet combined with taurine supplementation on body composition and some biochemical markers in obese women: a randomized clinical trial.

Amino Acids 2020 Aug 21;52(8):1115-1124. Epub 2020 Jul 21.

Faculty of Public Health, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.

Taurine (Tau), an endogenous non-protein and sulfuric-amino acid, is involved in various biological pathways including anti-inflammatory, anti-oxidation, insulin resistance inhibition, and lipid profile improvement. According to some experimental and clinical studies, insulin resistance and excess body weight are associated with reduced serum level of Tau. Therefore, this study was aimed to evaluate Tau supplementation and a diet-induced weight-loss intervention on body composition and some biochemical indices of obese women. Participants were divided randomly into the intervention (standard weight-loss group + cap Tau 3 g/day for 8 weeks, n = 20) and control (standard weight-loss group + cap placebo for 8 weeks, n = 18) groups. To achieve weight loss, all participants received an individualized diet that included a 30% reduction in their total energy intake. Chi-square test was applied to compare categorical variables between two groups at baseline. Paired t test and independent-sample t test were also used to analyze the parametric continuous data within and between the two groups, respectively. Analysis of covariance was run for controlling the confounding variables. At the post-intervention, the mean changes of total cholesterol (p = 0.03), low-density lipoprotein cholesterol (p = 0.03), leptin (p = 0. 006), total adiponectin (p = 0.04), and high sensitivity C-reactive protein (p = 0.03) decreased significantly in Tau group compared with the control group. No significant results were found in the mean changes of high-density lipoprotein cholesterol, anthropometric measurements, glycemic indices, and liver enzymes between the two groups (p > 0.05). The findings showed that Tau supplementation along with a weight-loss diet may be more effective in improving the lipid profile and metabolic risk factors compared with a weight-loss diet alone.
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http://dx.doi.org/10.1007/s00726-020-02876-7DOI Listing
August 2020

Ginger in patients with active ulcerative colitis: a study protocol for a randomized controlled trial.

Trials 2020 Mar 18;21(1):278. Epub 2020 Mar 18.

Faculty of Public Health, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.

Background: As a lifetime disorder, ulcerative colitis (UC) is an inflammatory bowel disease (IBD) that affects quality of life and also demands long-term interventions. In spite of considerable side effects and sometimes restricted uses, efficient medications are available for UC treatment. Some in vitro and in vivo examinations have correspondingly introduced ginger and its active components with antioxidant, anti-inflammatory, and anti-ulcerative properties. Therefore, this trial aims to evaluate the effect of ginger supplementation on patients with active UC.

Methods: This study will be a 12-week, double-blind, parallel-group, randomized, controlled trial (RCT) in which 44 patients will be allocated to ginger and placebo groups receiving basic routine treatments plus ginger or placebo capsules, respectively. The primary outcomes are inflammatory markers (TNF-α and hs-CRP) and total antioxidant capacity.

Discussion: The findings of this trial will provide evidence on the effect of ginger on patients with active UC.

Trial Registration: Iranian Registry of Clinical Trials, IRCT20190129042552N1. Registered on 21 June 2019.
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http://dx.doi.org/10.1186/s13063-020-4193-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7079449PMC
March 2020

Effect of lipoic acid supplementation on gene expression and activity of glutathione S-transferase enzyme in infertile men.

Hum Fertil (Camb) 2019 Jul 11:1-8. Epub 2019 Jul 11.

a Nutrition and Metabolic Diseases Research Center , Ahvaz Jundishapur, University of Medical Sciences , Ahvaz , Iran.

Oxidative stress has become the focus of interest as a potential cause of male infertility. We evaluate effects of lipoic acid (LA) supplementation on glutathione S-transferase (GST) expression. This randomized, triple-blind, placebo-controlled clinical trial was conducted on 44 infertile males with idiopathic asthenozoospermia. Men were randomized to receive 600 mg LA or placebo once daily for 12 weeks and semen samples and venous blood samples were obtained. GST expression, reactive oxygen species (ROS) levels, GST activity and reproductive hormone profiles were also measured. GST expression in the intervention group were significantly higher than the control group. Also, at the end of the study, GST activity increased, and ROS levels decreased significantly compared to the baseline. Additionally, the intervention group showed an increase in testosterone and decrease in serum follicle-stimulating hormone (FSH), luteinizing hormone (LH) and prolactin after 12 weeks, but this difference was not significant. We conclude a 12-week treatment with LA leads to improvements in reproductive hormones in serum, and significantly reduces the generation of ROS and increases the gene expression and activity of GST in seminal fluid.
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http://dx.doi.org/10.1080/14647273.2019.1639221DOI Listing
July 2019

Whole exome sequencing revealed a novel dystrophin-related protein-2 () deletion in an Iranian family with symptoms of polyneuropathy.

Iran J Basic Med Sci 2019 May;22(5):576-580

Aboozar Children's Hospital, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.

Objectives: Charcot-Marie Tooth disease (CMT) is one of the main inherited causes of motor and sensory neuropathies with variable expressivity and age-of onset. Although more than 70 genes have been identified for CMT, more studies are needed to discover other genes involved in CMT. Introduction of whole exome sequencing (WES) to capture all the exons may help to find these genes.

Materials And Methods: Here, we tried to find the genetic cause of the neuropathy in two Iranian brothers using WES. Blood sample was collected from probands and their family members to extract the genomic DNA. The extracted DNA from one of the affected case was subjected for WES. The variant calls were filtered to reveal the pathogenic variant. Presence of the candidate mutation was confirmed using Sanger sequencing. The pathogenic potential of the variant was examined using in silico software. Using ClustalW multiple alignment, the presence of variant in conserved domain of protein was investigated. The parent and another affected boy were also checked for presence of the variant using PCR-sequencing.

Results: The obtained data presented a novel TTC del mutation in CDS 738 of dystrophin related protein 2 () gene, which was validated by sequencing. The variant was located in a conserved domain of DRP2 protein and predicted as pathogenic. Two affected boys were hemizygous for the mutation and received the mutation from mother.

Conclusion: Here, we provided the evidence for the contribution of in CMT. Also, the symptoms shed light on molecular aspect of this genetically heterogeneous disease.
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http://dx.doi.org/10.22038/ijbms.2019.30754.7414DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6556509PMC
May 2019

A pathogenic variant in is associated with Pendred syndrome in a consanguineous Iranian family.

Int J Audiol 2019 10 12;58(10):628-634. Epub 2019 Jun 12.

Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences , Shahrekord , Iran.

Hearing loss (HL) is a common sensory deficit with high phenotypic and genotypic heterogeneity. A large Iranian family with HL was genetically assessed in this study. A proband from a consanguineous multiplex HL family from Iran was examined via Targeted Next-Generation Sequencing (TNGS). Sanger sequencing allowed the segregation analysis of the variant of interest and the investigation of its presence in a cohort of 50 ethnicity-matched healthy control individuals. The gene was previously associated with HL. Therefore, to determine whether the variant was specifically associated with Pendred Syndrome (PDS) or DFNB4, biochemical analyses, PTA, thyroid scans by Tc99m, perchlorate discharge test and high-resolution CT scan of the temporal bone were carried out on the affected family members. Ten members of a large multiplex Iranian family with HL were recruited in this study. In addition, 50 unrelated healthy controls of the same ethnic group were randomly selected to genotype the variant. A homozygous missense variant (NM_000441.1: c.1211C > T/p.Thr404Ile) in exon 10 was found segregating in the family. Based on the ACMG's guidelines, the variant was classified as pathogenic. This study expands the spectrum of pathogenic variants in hearing loss.
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http://dx.doi.org/10.1080/14992027.2019.1619945DOI Listing
October 2019

Exome sequencing revealed a p.G299R mutation in the COMP gene in an Iranian family suffering from pseudoachondroplasia.

J Gene Med 2019 08 11;21(8):e3103. Epub 2019 Jul 11.

Noor Pathobiology and Genetic Laboratory, Tehran, Iran.

Background: Short-stature (SS) is multifactorial pathologic condition that originates from either genetic or environmental factors. The diagnosis is based on family history, clinical findings, radiological examination and genetic analysis. A variety of genes have been reported for SS, among which FGFR-3 was the main gene in achondroplasia and hypochondroplasia. In other forms of SS, the gene involved varies from one patient to another. Whole exome sequencing (WES) and comparative genomic hybridization (CGH) have recently introduced a growing body of genes annually. The present study performed a WES analysis on an Iranian family suffering from an inherited form of SS aiming to diagnose the causative gene. The father and all of his four sons were diagnosed as SS.

Methods: The blood samples were collected from the proband and his available family members. Genomic DNA was extracted using salting-out method. The DNA of the proband was analyzed using WES and confirmed through polymerase chain reaction (PCR)-sequencing. The WES-extracted variant was evaluated in silico using software aiming to determine whether this nucleotide change is pathogenic. The presence of the variant was traced in other affected family members using PCR-sequencing.

Results: Following segregation analysis, variant c.896 G>A of the COMP gene was found in all of the affected individuals in a heterozygous form. This variant resulted in substitution of glycine 299 with arginine and was previously predicted as pathogenic in the Human Gene Mutation Database dataset, although it represents the first report in Iran.

Conclusions: The findings of the present study suggest consideration of the c.896 G>A variant of the COMP gene with respect to the genetic counseling of inherited skeletal dysplasia in Iran.
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http://dx.doi.org/10.1002/jgm.3103DOI Listing
August 2019

Evaluation of the effect of oral taurine supplementation on fasting levels of fibroblast growth factors, β-Klotho co-receptor, some biochemical indices and body composition in obese women on a weight-loss diet: a study protocol for a double-blind, randomized controlled trial.

Trials 2019 May 31;20(1):315. Epub 2019 May 31.

Faculty of Public Health, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.

Background: Taurine (Tau) is involved in many biochemical functions such as regulation of glucose and lipid metabolism, enhancement of energy expenditure, anti-inflammatory effects and appetite control. The most important effect of Tau in obesity is its direct effect on adipose tissue. Some evidence has shown an impaired FGF (fibroblast growth factor) 19 and 21 biosyntheses in obesity. Besides the effects of eicosapentaenoic acid on serum FGF concentrations, the effect of other nutrients on FGFs is not clear. Since obesity as an important health problem is rising around the world and on the other side, Tau biosynthesis is reduced by adipose-tissue-derived factors in obesity, the effects of Tau and a weight-loss diet on obesity need to be investigated further.

Methods: We will conduct an 8-week. double-blind, parallel-group, randomized controlled clinical trial to investigate the effect of Tau supplementation on fasting serum levels of FGFs, β-Klotho co-receptor, some biochemical indices and body composition in 50 obese women aged between 18 and 49 years on a weight-loss diet.

Discussion: We will determine the other advantages of a weight-loss diet on new metabolic risk factors. Since Tau may regulate adipose-tissue-derived factors and a weight-loss diet can promote the useful effects of Tau supplementation; for the first time, the effects of a weight-loss diet along with Tau supplementation on these variables will be assessed.

Trial Registration: Iran Clinical Trials Registry, ID: IRCT20131125015542N2 . Registered on 24 November 2018.
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http://dx.doi.org/10.1186/s13063-019-3421-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6544910PMC
May 2019

Exome sequencing found a novel homozygous deletion in ADCK3 gene involved in autosomal recessive spinocerebellar ataxia.

Gene 2019 Aug 10;708:10-13. Epub 2019 May 10.

Department of Biotechnology, Ahvaz Branch, Islamic Azad University, Ahvaz, Iran.

Autosomal recessive cerebellar ataxia is heterogeneous inherited neurodegenerative disorders with more than 70 involved genes. The development of next generation sequencing opens a new window in rapid diagnosis of such heterogeneous condition in medical genetics laboratories. Here, we present ADCK3; del.CD (229-230) mutation in an Iranian consanguineous family with three cerebellar ataxic boys using whole exome sequencing. The mutation was predicted pathogenic and all the affected individuals were homozygous for the variant. Although, the ADCK3 was previously reported as one of the master genes of ARSC, our mutation was novel as has been not previously reported in dbSNP or literature.
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http://dx.doi.org/10.1016/j.gene.2019.05.016DOI Listing
August 2019

Identification and Clinical Implications of a Novel MYO15A Variant in a Consanguineous Iranian Family by Targeted Exome Sequencing.

Audiol Neurootol 2019 3;24(1):25-31. Epub 2019 Apr 3.

Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran,

Background And Objectives: Hereditary hearing loss (HL) is known by a very high genetic heterogeneity, which makes a molecular diagnosis problematic. Next-generation sequencing (NGS) is a new strategy that can overcome this problem.

Method: A comprehensive family history was obtained, and clinical evaluations and pedigree analysis were performed in the family with 3 affected members. After excluding mutations in the GJB2 and 7 other most common autosomal recessive nonsyndromic HL genes via Sanger sequencing and genetic linkage analysis in the family, we applied the Otogenetics deafness NGS panel in the proband of this family.

Results: NGS results showed a novel rare variant (c.7720C>T) in the MYO15A gene. This nonsense variant in the exon 40 of the MYO15A gene fulfills the criteria of being categorized as pathogenic according to the American College of Medical Genetics and Genomics guideline.

Conclusions: New DNA sequencing technologies could lead to identification of the disease causing variants in highly heterogeneous disorders such as HL.
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http://dx.doi.org/10.1159/000498843DOI Listing
February 2020

A novel infram deletion in MSH6 gene in glioma: Conversation on MSH6 mutations in brain tumors.

J Cell Physiol 2019 07 27;234(7):11092-11102. Epub 2018 Nov 27.

Department of Genetics, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran.

Objective And Background: Histological and molecular information and biopsy help in the diagnosis of the type and grade of tumors and increase the value of estimation of the biological behavior of tumors. In this study, we focused on a consanguineous Iranian Family with high prevalence of brain tumors in their pedigree and reviewed the literature on MSH6 mutations in brain tumors and the treatment responses focused on Gliomas.

Method: We chose a family with a high prevalence of brain tumor in their pedigree. We studied the proband's neuroimaging and brain proton magnetic resonance spectroscopy (MRS), magnetic resonance imaging (MRI), biopsy result, and whole-genome sequencing.

Result: The neuroimaging and brain proton MRS reported a lesion in the right frontoparietal. The MRI revealed a large enhancible heterogenous mass in the right temporo-fronto-parieto-occipital lobes with involvement of corpus callosum which was suggestive of glioma. The patient revealed a homozygous pattern for a novel 9 base-pare deletion at the 912-914 codon on exon 4 of the MSH6 gene.

Discussion: We discuss several studies on MSH6 mutations in brain tumors and we discuss treatment responses in MSH6 mutations and the studies conducted to sensitize chemotherapy and radiotherapy resistance brain tumors to face this subject efficiently.

Conclusion: Patients should be evaluated for MMR mutation before chemo and radiotherapy, and it is valuable to follow-up these mutations during the treatment too. In temozolomide (TMZ)-resitance cases, it is suggested to use complementary strategies such as using HDACis and a combination of a STAT3 Inhibitor and an mTOR inhibitor, BER inhibition mechanism, and PARP-1 inhibitor.
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http://dx.doi.org/10.1002/jcp.27759DOI Listing
July 2019

Long Noncoding RNAs in Colorectal Adenocarcinoma; an in silico Analysis.

Pathol Oncol Res 2019 Oct 13;25(4):1387-1394. Epub 2018 Jun 13.

Department of Medical Genetics, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.

Long noncoding RNAs (lncRNAs) are lengthy noncoding transcripts which are involved in critical signaling pathways including cell cycle and apoptosis so it is not surprising to see their altered expression in human tumors. Colorectal adenocarcinoma is one the most frequent malignancies worldwide. The role of lncRNAs in colorectal adenocarcinoma is not well understood. To study the significance of lncRNAs in colorectal adenocarcinoma, we retrieved 189 approved lncRNAs from HGNC. The genes were imported into the cBioPortal database for transcriptomic analyses. We queried all the samples from TCGA provisional colorectal adenocarcinoma with RNA-seq v2 data in our study and considered RNA dysregulation with Z-score: ±2. The lncRNA which was altered in most of the patients were considered as "significant lncRNA" for further analyses. We considered the association of candidate lncRNAs with clinicopathologic parameters of samples including tumor disease anatomic site, neoplasm histologic types, tumor stage and survival. We also compute the specificity of the significant lncRNAs expression in colorectal adenocarcinoma comparing with other human cancers in cancer portal. Our analysis showed that lncRNAs SNHG6, PVT1 and ZFAS1 allocated the maximum alteration among the colorectal cases. The expression of SNHG6 and ZFAS1 was more in rectal adenocarcinoma than the colon carcinoma while the PVT1 showed the same expression levels in both tissues. However, we found that upregulation of PVT1 has been reduced the overall survival in patients. Altogether these data showed SNHG6, PVT1 and ZFAS1, are promising candidates for experimental research on colorectal adenocarcinoma to discover novel biomarker for this prevalent cancer.
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http://dx.doi.org/10.1007/s12253-018-0428-2DOI Listing
October 2019

Mutational spectrum of the CYP1B1 gene in Iranain primary congenital glaucoma family.

Can J Ophthalmol 2018 06 26;53(3):e87-e89. Epub 2017 Oct 26.

Shahid Beheshti University of Medical Science, Tehran, Iran.

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http://dx.doi.org/10.1016/j.jcjo.2017.08.019DOI Listing
June 2018

A novel pathogenic variant in the MARVELD2 gene causes autosomal recessive non-syndromic hearing loss in an Iranian family.

Genomics 2019 07 9;111(4):840-848. Epub 2018 May 9.

Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran. Electronic address:

Background And Aims: Hearing loss (HL) is the most common sensorineural disorder and one of the most common human defects. HL can be classified according to main criteria, including: the site (conductive, sensorineural and mixed), onset (pre-lingual and post-lingual), accompanying signs and symptoms (syndromic and non-syndromic), severity (mild, moderate, severe and profound) and mode of inheritance (Autosomal recessive, autosomal dominant, X-linked and mitochondrial). Autosomal recessive non-syndromic HL (ARNSHL) forms constitute a major share of the HL cases. In the present study, next-generation sequencing (NGS) was applied to investigate the underlying etiology of HL in a multiplex ARNSHL family from Khuzestan province, southwest Iran.

Methods: In this descriptive study, 20 multiplex ARNSHL families from Khuzestan province, southwest of Iran were recruited. After DNA extraction, genetic linkage analysis (GLA) was applied to screen for a panel of more prevalent loci. One family, which was not linked to these loci, was subjected to Otogenetics deafness Next Generation Sequencing (NGS) panel.

Results: NGS results showed a novel deletion-insertion variant (c.1555delinsAA) in the MARVELD2 gene. The variant which is a frameshift in the seventh exon of the MARVELD2 gene fulfills the criteria of being categorized as pathogenic according to the American College of Medical Genetics and Genomics (ACMG) guideline.

Conclusion: NGS is very promising to identify the molecular etiology of highly heterogeneous diseases such as HL. MARVELD2 might be important in the etiology of HL in this region of Iran.
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http://dx.doi.org/10.1016/j.ygeno.2018.05.008DOI Listing
July 2019

Identification of A Novel Missense Mutation in The Norrie Disease Gene: The First Molecular Genetic Analysis and Prenatal Diagnosis of Norrie Disease in An Iranian Family.

Cell J 2018 Jul 18;20(2):290-292. Epub 2018 Mar 18.

Department of Social Science, Islamic Azad University of Shoushtar, Shoushtar, Iran.

Norrie disease (ND) is a rare X-linked recessive disorder, which is characterized by congenital blindness and, in several cases, accompanied with mental retardation and deafness. ND is caused by mutations in NDP, located on the proximal short arm of the X chromosome (Xp11.3). The disease has been observed in many ethnic groups worldwide, however, no such case has been reported from Iran. In this study, we present the molecular analysis of two patients with ND and the subsequent prenatal diagnosis. Screening of NDP identified a hemizygous missense mutation (p.Ser133Cys) in the affected male siblings of the family. The mother was the carrier for the mutation (p.Ser133Cys). In a subsequent chorionic amniotic pregnancy, we carried out prenatal diagnosis by sequencing NDP in the chorionic villi sample at 11 weeks of gestation. The fetus was carrying the mutation and thus unaffected. This is the first mutation report and prenatal diagnosis of an Iranian family with ND, and highlights the importance of prenatal diagnostic screening of this congenital disorder and relevant genetic counseling.
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http://dx.doi.org/10.22074/cellj.2018.5090DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5893302PMC
July 2018

A novel missense mutation in GIPC3 causes sensorineural hearing loss in an Iranian family revealed by targeted next-generation sequencing.

Int J Pediatr Otorhinolaryngol 2018 May 31;108:8-11. Epub 2018 Jan 31.

Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran. Electronic address:

Background: Recent studies have confirmed the utility of targeted next-generation sequencing (NGS), providing a remarkable opportunity to find variants in known disease genes, especially in genetically heterogeneous disorders such as hearing loss (HL).

Methods: After excluding mutations in the most common autosomal recessive non-syndromic HL (ARNSHL) genes via Sanger sequencing and genetic linkage analysis, we performed NGS in the proband an Iranian family with ARNSHL. The NimbleGen sequence capture array captures codingsequences (CDSs) and 100 bp of the flanking sequence of 129 common deafness genes (cat# Oto-DA3). NGSwas performed on the IlluminaHiSeq2000. BWA, SAMtools, Picard, GATK, Variant Tools, ANNOVAR, and IGV were applied for Bioinformatics analyses. Data filtering with allele frequencies (<5% in the 1000 Genomes Project and 5400 NHLBI exomes) and PolyPhen2/SIFTscores (>0.95) prioritized 1indel (insertions/deletions) and 3 missense variants in this family. Eventually, Sanger sequencing, segregation pattern, the frequency in 50 healthy matched normal controls, and evolutionary conservation of amino acid residues revealed the pathogenic variant.

Results: We identified a novel missenseGIPC3 mutation, c.472G > A (p.Glu158 Lys). The pathogenicity of GIPC3c.472G > A was supported by its absence in the population databases and the healthy-matched controls.Sanger sequencing confirmed co-segregation of the mutation with HL.

Conclusions: This study is the first report of the contribution of theGIPC3 gene to HL in the Iranian population.Targeted NGS allows easier detection of mutations in relatively uncommon deafness genes in families with ARNSHL.
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http://dx.doi.org/10.1016/j.ijporl.2018.01.006DOI Listing
May 2018

A Novel Pathologic Variant in OTOF in an Iranian Family Segregating Hereditary Hearing Loss.

Otolaryngol Head Neck Surg 2018 06 27;158(6):1084-1092. Epub 2018 Feb 27.

6 Department of Medical Genetics, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.

Objective Hearing loss (HL) is the most common sensory-neural defect and the most heterogeneous trait in humans, with the involvement of >100 genes, which make a molecular diagnosis problematic. Next-generation sequencing (NGS) is a new strategy that can overcome this problem. Study Design Descriptive experimental study. Setting Diagnostic laboratory. Subjects and Methods A comprehensive family history was obtained, and clinical evaluations and pedigree analysis were performed in a family with multiple individuals with HL. As the first tier, GJB2 was sequenced, and genetic linkage analysis of DFNB1A/B was performed to rule out the most common cause of the disease. Targeted NGS was used to unravel the molecular etiology of the disease in the HL-associated genes in the proband. Two homozygous variants remained in OTOF after proper filtration. Cosegregation and in silico analysis were done. Preimplantation genetic diagnosis (PGD) was accomplished via linkage analysis and direct sequencing of the pathogenic variant. Results Clinical evaluations suggested autosomal recessive nonsyndromic HL. Two homozygous variants, c.367G>A (p.Gly123Ser) and c.1392+1G>A, were identified in cis status. c.1392+1G>A met the criteria for being pathogenic according to the variant interpretation guideline of the American College of Medical Genetics and Genomics. PGD was successfully performed to prevent the recurrence of the disease in the related family. Conclusion A novel OTOF mutation causing HL was identified. Here, we report the effectiveness of the combined application of targeted NGS and PGD in diagnosis and prevention of hereditary HL.
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http://dx.doi.org/10.1177/0194599818759007DOI Listing
June 2018

Identification of Novel PTPRQ and MYO1A Mutations in An Iranian Pedigree with Autosomal Recessive Hearing Loss.

Cell J 2018 Apr 1;20(1):127-131. Epub 2017 Dec 1.

Department of Nursing, Shoushtar Faculty of Medical Sciences, Shoushtar, Iran.

Autosomal recessive non-syndromic hearing loss (ARNSHL) is defined as a genetically heterogeneous disorder. The aim of the present study was to screen for pathogenic variants in an Iranian pedigree with ARNSHL. Next-generation targeted sequencing of 127 deafness genes in the proband detected two novel variants, a homozygous missense variant in PTPRQ (c.2599 T>C, p.Ser867Pro and a heterozygous missense variant in MYO1A (c.2804 T>C, p.Ile935Thr), both of which were absent in unaffected sibs and two hundred unaffected controls. Our results suggest that the homozygous PTPRQ variant maybe the pathogenic variant for ARNSHL due to the recessive nature of the disorder. Nevertheless, the heterozygous MYO1A may also be involved in this disorder due to the multigenic pattern of ARNSHL. Our data extend the mutation spectrum of PTPRQ and MYO1A, and have important implications for genetic counseling in unaffected sibs of this family. In addition, PTPRQ and MYO1A pathogenic variants have not to date been reported in the Iranian population.
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http://dx.doi.org/10.22074/cellj.2018.4805DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5759675PMC
April 2018

How is the relationship between TWIST-1 and BCR-ABL1 gene expressions in chronic myeloid leukaemia patients?

Biomarkers 2018 Jan 12:1-6. Epub 2018 Jan 12.

a Thalassemia and Hemoglobinopathy Research Center, Research Institute of Health, Ahvaz Jundishapur University of Medical Sciences , Ahvaz , Iran.

Background: The activation and increased expression of BCR-ABL1 lead to malignant chronic myelogenous leukaemia (CML) cells, as well as the resistance to antitumour agents and apoptosis inducers. Moreover, TWIST-1 protein is a prognostic factor of leukemogenesis, and its level is raised in CML patients with cytogenetic resistance to imatinib. So, there is a likely relationship between BCR-ABL1 and TWIST-1 genes.

Objective: The aim of the study was to assess the relationship between TWIST-1 and BCR-ABL1 expressions.

Methods: Peripheral blood samples were obtained from 44 CML patients under treatment and also from ten healthy subjects as normal controls. The expression of TWIST-1 and BCR-ABL1 genes was measured using real-time PCR, and ABL1 was used as the reference gene. The gene expression was evaluated by REST software.

Results: The expression levels of TWIST-1 and BCR-ABL1 genes in CML patients was changed 40.23 ± 177.75-fold and 6 ± 18-fold, respectively.

Discussion: No significant relationship was observed between the expressions of TWIST-1 and BCR-ABL1 genes. All patients with TWIST-1 expression levels ≥100-fold had failure of response to treatment.

Conclusion: The probability of the relationship between BCR-ABL1 and TWIST-1 is still debatable, and the average of TWIST-1 expression has been higher in patients without response to treatment. Definitive conclusion needs further investigations.
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http://dx.doi.org/10.1080/1354750X.2018.1423705DOI Listing
January 2018

Next-generation sequencing identifies three novel missense variants in ILDR1 and MYO6 genes in an Iranian family with hearing loss with review of the literature.

Int J Pediatr Otorhinolaryngol 2017 Dec 20;103:103-108. Epub 2017 Sep 20.

Department of Midwifery, Shoushtar Faculty of Medical Sciences, Shoushtar, Iran.

Objectives: Hearing impairment is the most common sensorineural disorder and is genetically heterogeneous. Identification of the pathogenic mutations underlying hearing impairment is difficult, since causative mutations in 127 different genes have so far been reported.

Methods: In this study, we performed Next-generation sequencing (NGS) in 2 individuals from a consanguineous family with hearing loss.

Results: Three novel mutations in known deafness genes were identified in the family; MYO6-p.R928C and -p.D1223N in heterozygous state and ILDR1-p.Y143C in homozygous state. Sanger sequencing confirmed co-segregation of the three mutations with deafness in the family. The identified mutation in ILDR1 gene is located in the immunoglobulin-type domain of the ILDR1 protein and the detected mutations in MY06 are located in the tail domain of the MYO6 protein. The mutations are predicted to be pathogenic by SIFT, PolyPhen and Mutation Taster.

Conclusions: Our results suggest that either the homozygous ILDR1-p.Y143C mutation might be the pathogenic variant for ARNSHL or heterozygous MYO6- p.R928C, -p.D1223N might be involved in these patient's disorder due to compound heterozygousity. To our knowledge, this is the first ILDR1 and MYO6 mutations recognized in the southwest Iran. Our data expands the spectrum of mutations in ILDR1 and MYO6 genes.
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http://dx.doi.org/10.1016/j.ijporl.2017.09.018DOI Listing
December 2017

Identification of a novel mutation in ARSA gene in three patients of an Iranian family with metachromatic leukodystrophy disorder.

Genet Mol Biol 2017 Oct-Dec;40(4):759-762. Epub 2017 Nov 6.

Department of Medical Genetics, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Iran.

Metachromatic leukodystrophy disorder (MLD) is an autosomal recessive and lysosomal storage disease. The disease is caused by the deficiency of the enzyme arylsulfatase A (ARSA) which is encoded by the ARSA gene. Different mutations have been reported in different populations. The present study was aimed to detect the mutation type of the ARSA gene in three relative Iranian patients. We found a novel homozygous missense mutation c.1070 G > T (p.Gly357Val) in exon 6 of these patients. The mutation was found to be reported for the first time in MLD patients. The data can update the mutation profile and contribute toward improved clinical management and counseling of MLD patients.
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http://dx.doi.org/10.1590/1678-4685-GMB-2016-0110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5738620PMC
November 2017

Study of the Role of siRNA Mediated Promoter Methylation in DNMT3B Knockdown and Alteration of Promoter Methylation of CDH1, GSTP1 Genes in MDA-MB -453 Cell Line.

Iran J Pharm Res 2017 ;16(2):771-780

Department of Pharmacology and Toxicology, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran.

Promoter methylation is one of the main epigenetic mechanisms that leads to the inactivation of tumor suppressor genes during carcinogenesis. Due to the reversible nature of DNA methylation, many studies have been performed to correct theses epigenetic defects by inhibiting DNA methyltransferases (DNMTs). In this case novel therapeutics especially siRNA oligonucleotides have been used to specifically knock down the DNMTs at mRNA level. Also many studies have focused on transcriptional gene silencing in mammalian cells via siRNA mediated promoter methylation. The present study was designed to assess the role of siRNA mediated promoter methylation in DNMT3B knockdown and alteration of promoter methylation of Cadherin-1 (CDH1), Glutathione S-Transferase Pi 1(GSTP1), and DNMT3B genes in MDA-MB-453 cell line. MDA-MB-453 cells were transfected with siDNMT targeting DNMT3B promoter and harvested at 24 and 48 h post transfection to monitor gene silencing and promoter methylation respectively. DNMT3B expression was monitored by quantitative RT-PCR method. Promoter methylation was quantitatively evaluated using differential high resolution melting analysis. A non-significant 20% reduction in DNMT3B mRNA level was shown only after first transfection with siDNMT, which was not reproducible. Promoter methylation levels of DNMT3B, CDH1, and GSTP1 were detected at about 15%, 70% and 10% respectively, in the MDA-MB-453 cell line, with no significant change after transfection. Our results indicated that siDNMT sequence were not able to affect promoter methylation and silencing of DNMT3B in MDA-MB-453 cells. However, quantitation of methylation confirmed a hypermethylated phenotype at CDH1 and GSTP1 promoters as well as a differential methylation pattern at DNMT3B promoter in breast cancer.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5603887PMC
January 2017

A novel pathogenic variant in an Iranian Ataxia telangiectasia family revealed by next-generation sequencing followed by in silico analysis.

J Neurol Sci 2017 Aug 12;379:212-216. Epub 2017 Jun 12.

Ahvaz Noor Genetics Laboratory, Ahvaz, Iran; Department of Medical Genetics, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran. Electronic address:

Ataxia telangiectasia (A-T) is a neurodegenerative autosomal recessive disorder with the main characteristics of progressive cerebellar degeneration, sensitivity to ionizing radiation, immunodeficiency, telangiectasia, premature aging, recurrent sinopulmonary infections, and increased risk of malignancy, especially of lymphoid origin. Ataxia Telangiectasia Mutated gene, ATM, as a causative gene for the A-T disorder, encodes the ATM protein, which plays an important role in the activation of cell-cycle checkpoints and initiation of DNA repair in response to DNA damage. Targeted next-generation sequencing (NGS) was performed on an Iranian 5-year-old boy presented with truncal and limb ataxia, telangiectasia of the eye, Hodgkin lymphoma, hyper pigmentation, total alopecia, hepatomegaly, and dysarthria. Sanger sequencing was used to confirm the candidate pathogenic variants. Computational docking was done using the HEX software to examine how this change affects the interactions of ATM with the upstream and downstream proteins. Three different variants were identified comprising two homozygous SNPs and one novel homozygous frameshift variant (c.80468047delTA, p.Thr2682ThrfsX5), which creates a stop codon in exon 57 leaving the protein truncated at its C-terminal portion. Therefore, the activation and phosphorylation of target proteins are lost. Moreover, the HEX software confirmed that the mutated protein lost its interaction with upstream and downstream proteins. The variant was classified as pathogenic based on the American College of Medical Genetics and Genomics guideline. This study expands the spectrum of ATM pathogenic variants in Iran and demonstrates the utility of targeted NGS in genetic diagnostics.
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http://dx.doi.org/10.1016/j.jns.2017.06.012DOI Listing
August 2017

Is There a Relationship Between CXCR4 Gene Expression and Prognosis of Immune Thrombocytopenia in Children?

Indian J Hematol Blood Transfus 2017 Jun 22;33(2):216-221. Epub 2016 Jan 22.

Health Research Institute, Thalassemia and Hemoglobinopathy Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.

Immune thrombocytopenia (ITP) is a common autoimmune disorder characterized by decreased platelet count (thrombocytopenia) and bleeding symptoms due to production of autoantibodies against platelets. Chemokines are molecules inducing chemotaxis and play an important role in megakaryopoiesis, including CXCR4 chemokine receptor. CXCR4 is expressed on cells of megakaryocytic series, especially platelets, and triggers several mechanisms in these cells. The purpose of this study was to evaluate the pattern of CXCR4 gene changes upon diagnosis and after treatment and its comparison with laboratory findings in peripheral blood samples from newly diagnosed ITP patients. 35 newly diagnosed patients with ITP and 35 healthy controls were enrolled in this study. CXCR4 gene expression was investigated before and after treatment using real-time PCR. HPRT gene was used as the reference gene to calculate the expression rate of CXCR4 as CXCR4/HPRT ratio. CXCR4 gene expression upon diagnosis and after treatment in peripheral blood plasma of ITP patients showed a significant decrease in comparison with the control group while its expression did not change before and after treatment. No significant correlation was found between the expression of this gene and laboratory parameters. Due to unpredictable course of ITP in patients and the possibility of its progress to refractory form, accurate choice of a biomarker is essential for evaluating prognosis and detection of resistant forms.
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http://dx.doi.org/10.1007/s12288-016-0648-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5442042PMC
June 2017

A novel pathogenic variant in the FZD6 gene causes recessive nail dysplasia in a large Iranian kindred.

J Dermatol Sci 2017 Oct 13;88(1):134-138. Epub 2017 May 13.

Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran; Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran. Electronic address:

Background: Nail disorder nonsyndromic congenital (NDNC) is a very rare clinically and genetically heterogeneous disease inherited both in recessive or dominant modes. FZD6 is a component of Wnt-FZD signaling pathway in which recessive loss-of-function variants in the corresponding genes could lead to nail anomalies.

Objective: A large multiplex family with NDNC was referred for genetic counselling. Thorough genetic evaluation was performed.

Methods: PCR-Sanger sequencing was carried out for the coding exons and exon-intron boundaries of the FZD6 gene. Co-segregation analysis, in silico evaluation and computational protein modeling was accomplished.

Results: A homozygous 1bp deletion variant, c.1859delC (p.Ser620Cysfs*75), leading to a truncating protein was found in the patient. Parents were heterozygous for the variant. The variant was found to be co-segreagting with the phenotype in the family. Computational analysis and protein modeling revealed its pathogenic consequence by disturbing the cytoplasmic domain structure and signaling through loss of phosphorylation residues. The variant met the criteria of being pathogenic according to the ACMG guideline.

Conclusions: This is the first report of the genetic diagnosis of NDNC in Iran. We also report a novel pathogenic variant. The study of the FZD6 gene is recommended as the first step in the diagnostic routing of the autosomal recessive NDNC patients with enlarged nails.
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http://dx.doi.org/10.1016/j.jdermsci.2017.04.017DOI Listing
October 2017

Identification of a novel missence mutation in FGFR3 gene in an Iranian family with LADD syndrome by Next-Generation Sequencing.

Int J Pediatr Otorhinolaryngol 2017 Jun 12;97:192-196. Epub 2017 Apr 12.

Department of E.N.T, Faculty of Medicine, Guilan University of Medical Sciences, Guilan, Iran.

Lacrimo-auriculo-dento-digital syndrome (LADD) is a multiple congenital anomaly and a genetically heterogeneous disorder. The aim of this study was to identify the pathogenic gene in an Iranian family with LADD syndrome and review the literature on reported mutations that involved in pathogenesis of LADD syndrome. One novel variant, c.1882 G > A, in fibroblast growth factor receptor 3 (FGFR3) was identified by next generation sequencing and Sanger sequencing. The heterozygous FGFR3 c.1882 G > A variant results in substitution of aspartic acid with asparagine at amino acid 628 (p.D628N) and co-segregated with the phenotype in the LADD family. Our findings suggest that the heterozygous FGFR3 c.1882 G > A variant might be the pathogenic mutation, because this amino acid is conserved in several species. Our data extend the mutation spectrum of the FGFR3 gene and have important implications for genetic counseling for the families. This is the second report of FGFR3 involvement in syndromic deafness in humans, and confirms the gene's positive role in inner ear development. In addition, this is the first FGFR3 mutation recognized in the Iranian LADD family.
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http://dx.doi.org/10.1016/j.ijporl.2017.04.016DOI Listing
June 2017

Next-Generation Sequencing Reveals One Novel Missense Mutation in COL1A2 Gene in an Iranian Family with Osteogenesis imperfecta

Iran Biomed J 2017 09 22;21(5):338-41. Epub 2017 Apr 22.

Department of Midwifery, Shoushtar Faculty of Medical Sciences, Shoushtar, Iran.

Background: Osteogenesis imperfecta (OI) is a clinically and genetically heterogeneous disorder characterized by bone loss and bone fragility. The aim of this study was to investigate the variants of three genes involved in the pathogenesis of OI.

Methods: Molecular genetic analyses were performed for COL1A1, COL1A2, and CRTAP genes in an Iranian family with OI. The DNA samples were analyzed by next-generation sequencing (NGS) gene panel and Sanger sequencing.

Results: Five different variants were identified in COL1A1 and COL1A2, including two variants in COL1A1 and three variants in COL1A2. Among the five causative COL1A1 and COL1A2 variants, one novel variants, c.1081 G>A, was found in COL1A2, which was identified in two siblings.

Conclusion: Our finding extends the variant spectrum of the COL1A2 gene and has important implications for genetic counseling of families. The NGS is a powerful molecular diagnostic strategy for OI, a heterogeneous disorder.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5548966PMC
http://dx.doi.org/10.18869/acadpub.ibj.21.5.338DOI Listing
September 2017

A Novel Splicesite Mutation in the Gene Causes Severe Autosomal Recessive Hypohydrotic (Anhidrotic) Ectodermal Dysplasia in an Iranian Family.

Int J Mol Cell Med 2016 23;5(4):260-263. Epub 2016 Oct 23.

Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.

Hypohidrotic ectodermal dysplasia (HED) is a rare congenital disorder arising from deficient development of ectoderm-derived structures including skin, nails, glands and teeth. The phenotype of HED is associated with mutation in and genes, all of them disruptingNF-κB signaling cascade necessary for initiation, formation and differentiation in the embryo and adult. Here we describe a novel acceptor splice site mutation c.730-2 A>G(IVS 8-2 A>G) in gene in homozygous form in all affected members of a family,and in heterozygous form in carriers. Bioinformatics analysis showed that this mutation can create a new broken splicing site and lead to aberrant splicing.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5353988PMC
October 2016

Gene-Targeted Next Generation Sequencing Identifies PNPLA1 Mutations in Patients with a Phenotypic Spectrum of Autosomal Recessive Congenital Ichthyosis: The Impact of Consanguinity.

J Invest Dermatol 2017 03 21;137(3):678-685. Epub 2016 Nov 21.

Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA; Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, USA. Electronic address:

Autosomal recessive congenital ichthyosis is a heterogeneous group of disorders associated with mutations in at least nine distinct genes. To ascertain the molecular basis of ichthyosis patients in Iran, a country of approximately 80 million people with a high prevalence of customary consanguineous marriages, we have developed a gene-targeted next generation sequencing array consisting of 38 genes reported in association with ichthyosis phenotypes. In a subset of nine extended consanguineous families, we found homozygous missense mutations in the PNPLA1 gene, six of them being distinct and, to our knowledge, previously unpublished. This gene encodes an enzyme with lipid hydrolase activity, important for development and maintenance of the barrier function of the epidermis. These six mutations, as well as four previously published mutations, reside exclusively within the patatin-like subdomain of PNPLA1 containing the catalytic site. The mutations clustered around the active center of the enzyme or resided at the surface of the protein possibly involved in the protein-protein interactions. Clinical features of the patients showed considerable intra- and interfamilial heterogeneity. Knowledge of the specific mutations allows identification of heterozygous carriers, assisting in genetic counseling, prenatal testing, and preimplantation genetic diagnosis in extended families at risk of recurrence of this disorder, the incidence of which is significantly increased in consanguineous marriages.
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http://dx.doi.org/10.1016/j.jid.2016.11.012DOI Listing
March 2017

Quantitation of CDH1 promoter methylation in formalin-fixed paraffin-embedded tissues of breast cancer patients using differential high resolution melting analysis.

Adv Biomed Res 2016 30;5:91. Epub 2016 May 30.

Applied Physiology Research Centre, Isfahan University of Medical Sciences, Isfahan, Iran.

Background: E-cadherin (CDH1) plays an important role in cell-cell adhesion of epithelial tissues. Loss of E-cadherin expression can lead to loss of tissue integrity, metastasis, and cancer progression. Also loss of E-cadherin expression might be related to aberrant promoter methylation of the CDH1 gene. Many studies have been performed on CDH1 promoter methylation, especially in breast cancer. Although most of the studies have used qualitative methods for methylation analysis, this study is designed to quantitatively investigate CDH1 promoter methylation in breast cancer and its correlation with patients' clinicopathological features.

Materials And Methods: Using differential high resolution melting analysis (D-HRMA), the methylation level of the CDH1 gene promoter was quantified in 98 breast cancer formalin-fixed paraffin-embedded (FFPE) tissues and also 10 fresh frozen normal breast tissues.

Results: All samples were detected to be methylated at the CDH1 promoter region. About 74.5% of the breast cancer samples were hypermethylated with an average methylation level of around 60%, while 25.5% of the patients were methylated with the mean methylation level of about 33%, and 90% of the normal samples had a mean methylation level of about 18%. Statistical analyses represented a significant correlation between CDH1 promoter methylation and cancer progression hallmarks, such as, clinical stage, nodal involvement, tumor size, and histological grade.

Conclusion: In summary, quantitation of CDH1 promoter methylation can serve as a diagnostic and prognostic tool in breast cancer. Also D-HRMA can be used as a fast and reliable method for quantitation of promoter methylation.
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http://dx.doi.org/10.4103/2277-9175.183139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4908786PMC
June 2016