Association between polymorphism at codon 469 of the ICAM-1 gene and Henoch-Schönlein purpura in an Iranian cohort

Henoch-Schönlein purpura (HSP) is a common form of IgA1-mediated blood vessel inflammation affecting mainly children. Intercellular adhesion molecule-1 (ICAM-1) gene polymorphisms have been shown to be associated with HSP in different populations; in this study, we investigated its potential association and influence on the development of severe complications in Iranian HSP patients. Twenty-three patients diagnosed with IgAV/HSP according to the criteria of the American College of Rheumatology (ACR) with 53 age- and sex-matched control subjects were referred to us. Cases and controls were genotyped using Sanger sequencing. Based on our research data, we found an association between codon 469 K/E of the ICAM1 gene and risk of HSP. Our results revealed that KK genotype and allele K are more common in control than in the HSP group, therefore the subjects with KK genotype are protected against HSP. Our data also suggested that the genotype EE is associated with higher risk of HSP progression compared to KK genotype.

Genetic analysis of nephrogenic diabetes insipidus patients: A study on the Iranian population

INTRODUCTION

Nephrogenic diabetes insipidus (NDI) is a rare genetic disease that causes water imbalance. The kidneys play a crucial role in regulating body fluids by controlling water balance through urine excretion. This highlights their essential function in managing the body's water levels, but individuals with NDI may have excess urine production (polyuria), that leads to excessive thirst (polydipsia). Untreated affected individuals may exhibit poor feeding and failure to thrive. This disease is caused by mutations in the AVPR2 and the AQP2 genes which have the X-linked and autosomal recessive/dominant inheritance, respectively. Both of these genes are expressed in the kidney.

METHODS

Twelve Iranian patients from 10 consanguineous families were studied in this project. DNA was extracted from the whole blood samples of the patients and their parents. All coding exons and exon-intron boundaries of the AVPR2 and AQP2 genes were sequenced in the affected individuals, and the identified variants were investigated in the parents. All variants were analyzed according to the ACMG (American College of Medical Genetics and Genomics) guidelines.

RESULTS

In this study, 6 different mutations were identified in the patients, including 5 in the AQP2 gene (c.439G>A, c.538G>A, c.140C>T, c.450T>A, and the novel c.668T>C) and 1 in the AVPR2 gene (c.337C>T) in the present study.

DISCUSSION

As expected, all the detected mutations in this study were missense. According to the ACMG guideline, the identified mutations were categorized as pathogenic or likely pathogenic. Unlike previous studies which showed more than 90% of mutations were in the AVPR2 gene, and only less than 10% of the mutations were in the AQP2 gene, it was found that more than 90% of our identified mutations located in the AQP2 gene, and only one mutation was observed in the AVPR2 gene, which seems it may be a result of the high rate of consanguineous marriages in the Iranian population. We observed genotype-phenotype correlation in some of our affected individuals, and some of the mutations were observed in unrelated families from same ethnicity which could be suggestive of a founder mutation.

DNA repair-related heritable photosensitivity syndromes: Mutation landscape in a multiethnic cohort of 17 multigenerational families with high degree of consanguinity

Inherited photosensitivity syndromes are a heterogeneous group of genetic skin disorders with tremendous phenotypic variability, characterized by photosensitivity and defective DNA repair, especially nucleotide excision repair. A cohort of 17 Iranian families with heritable photosensitivity syndromes was evaluated to identify their genetic defect. The patients' DNA was analyzed with either whole-exome sequencing or RNA sequencing (RNA-Seq). The interpretations of the genomic results were guided by genome-wide homozygosity mapping. Haplotype analysis was performed for cases with recurrent mutations. RNA-Seq, in addition to mutation detection, was also utilized to confirm the pathogenicity. Thirteen sequence variants, including six previously unreported pathogenic variants, were disclosed in 17 Iranian families, with XPC as the most common mutated gene in 10 families (59%). In one patient, RNA-Seq, as a first-tier diagnostic approach, revealed a non-canonical homozygous germline variant: XPC:c.413-9 T > A. The Sashimi plot showed skipping of exon 4 with dramatic XPC down-expression. Haplotype analysis of XPC:c.2251-1 G>C and XPC:1243 C>T in four families showed common haplotypes of 1.7 Mb and 2.6 Mb, respectively, denoting a founder effect. Lastly, two extremely rare cases were presented in this report: a homozygous UVSSA:c .1990 C>T was disclosed, and ERCC2-related cerebro-oculo-facio-skeletal (COFS) syndrome with an early childhood death. A direct comparison of our data with the results of previously reported cohorts demonstrates the international mutation landscape of DNA repair-related photosensitivity disorders, although population-specific differences were observed.

Comparative Analysis of 198 SARS-CoV-2 Genomes from Iran and West Asia, February 2020 to December 2021

Background & Objective

Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), resulting in a worldwide pandemic. The first case of COVID-19 was reported from Wuhan in the Hubei Province of China in December 2019; however, the disease's origin is still mysterious. Whole-genome sequence analysis is essential for monitoring the spread of infectious diseases as well as studying the pathogenesis and evolution of viruses. In this study, analysis of 198 fully sequenced genomes from Iran and West Asia was carried out to study mutations, phylogeny, amino acid changes, clades, and lineages of these genomes as well as comparison of these sequences with those of reference Wuhan genome of NC_045512.2.

Methods

In total, 198 completely sequenced genome data from Iran and West Asia were collected from GenBank. Mutation detection was carried out using a trial version of CLC Genomics Workbench v.21.0 (QIAGEN, Germany). Online tools such as GISAID Mutations App and Pangolin were used for further analysis of the results.

Results

In this study, several unique mutation sites were identified in the Iranian genomes (n = 8); positions 1397 G>A and 29742 G>T were the most frequent changes in more than 85% of the Iranian genomes. Mutation rate, mutation per sequence, and transition versus transversion for the Iranian genomes included 4.73, 14.14, and 1.6, respectively. Generally, C>T alteration was the most common substitution in all the sequences.

Conclusion

The ORF1ab, N, and S were the genes with the most changes. The current data can help researchers predict future epidemics and establish better strategies to control viral pandemics.

A Study on the CLCN5 Gene in Iranian Patients: A Report of Novel and Recurrent Mutations

INTRODUCTION

Dent's disease is an X-linked inherited renal tubular disorder characterized by proteinuria, hypercalciuria, nephrocalcinosis, nephrolithiasis, rickets, and end-stage renal disease. Almost 60% of patients have causative mutations in the CLCN5 gene (Dent 1), and 15% of affected individuals have mutations in the OCRL1 gene (Dent 2). The aims of this study are to identify CLCN5 mutations in Iranian families with Dent's disease and to characterize the associated clinical syndromes.

METHODS

We studied 14 patients from 13 unrelated Iranian families with a clinical diagnosis of Dent's disease. Proteinuria was detected in all patients. Nephrolithiasis was found in 5 patient, and hematuria in 2 patients. Most of the affected individuals had nephrocalcinosis. PCR-sequencing for the CLCN5 gene was performed in all 14 patients. Next-generation sequencing (NGS) has also been performed in one patient who we did not find causative mutation.

RESULTS

We identified four different CLCN5 mutations including one missense mutation (c.731C>T), one nonsense mutation (c.100C>T), and two novel mutations, consisting of one frameshift mutation (c.1241_1242dupAA) and one splicing mutation (c.805-2A>G). We also identified one OCRL1 mutation, one splicing mutation (c.1466 + 1G>A), using NGS.

CONCLUSION

This is the first report to characterize mutations in the CLCN5 gene in Iranian patients with Dent's disease and expands the spectrum of CLCN5 mutations by reporting two novel mutations, c.1241_1242dupAA and c.805-2A>G.

An evaluation of gastric adenocarcinoma-associated CircRNAs based on microarray meta-analysis and ceRNA networks

Gastric cancer is the fourth leading cause of cancer-related mortality and one of the most commonly diagnosed malignancies worldwide. Gastric adenocarcinoma (GAC) accounts for the majority of gastric cancer cases. Circular RNAs (circRNAs) have been shown to be associated with carcinogenesis and cancer progression. This research aims to investigate GAC-associated circRNAs and the underlying mechanisms of circRNA-miRNA-mRNA networks in the development and progression of GAC. Differentially expressed miRNAs and mRNAs (DEMs and DEGs) were identified in Gene Expression Omnibus (GEO) microarray datasets using the R package Limma. A microarray meta-analysis was performed to identify potential GAC-associated circRNAs with high statistical power, resulting in 13 up-regulated and 19 down-regulated circRNAs. CircRNA-miRNA-mRNA networks were constructed by combining predicted and experimentally validated databases and considering differentially expressed miRNAs and mRNAs. The constructed ceRNA networks revealed the potential regulatory effect of hsa_circ_0002019 and hsa_circ_0074736 on key survival-related genes. The expression levels of these two circRNAs were measured in plasma samples from GAC patients and healthy controls using SYBR Green-based real-time PCR. Axon guidance, cellular senescence, AGE-RAGE signaling pathway in diabetic complications, and AMPK signaling pathway were among the major significant (P-value <0.05) enriched pathways of "main mRNAs" in the constructed ceRNA networks. In conclusion, we identified strongly correlated circRNAs and their likely mechanisms of action in GAC, which may improve the knowledge of regulatory networks underlying GAC formation and contribute to developing better strategies for early diagnosis, prognosis, and treatment.

Genetic diagnosis of Bartter syndrome in Iranian patients and detection of a novel homozygous CLCNKB mutation

An Iranian girl with clinical symptoms of Bartter syndrome like hypokalemia, polyuria, polydipsia, hyponatremia, and hypochloremic alkalosis was referred to us in whom the CLCNKB gene was genetically evaluated using Sanger sequencing. A homozygous pathogenic variant of c.1332_1335delCTCT was detected in this patient.

A decade of molecular preimplantation genetic diagnosis of 350 blastomeres for beta-thalassemia combined with HLA typing, aneuploidy screening and sex selection in Iran

Background

Preimplantation genetic diagnosis (PGD) has been developed to detect genetic disorders before pregnancy which is usually done on blastomeres biopsied from 8-cell stage embryos obtained from in vitro fertilization method (IVF).

Here we report molecular PGD results for diagnosing of beta thalassemia (beta-thal) which are usually accompanied with evaluating chromosomal aneuploidies, HLA typing and sex selection.

Methods

In this study, haplotype analysis was performed using short tandem repeats (STRs) in a multiplex nested PCR and the causative mutation was detected by Sanger sequencing.

Results

We have performed PGDs on 350 blastomeres from 55 carrier couples; 142 blastomeres for beta-thal only, 75 for beta-thal and HLA typing, 76 for beta-thal in combination with sex selection, and 57 for beta-thal and aneuploidy screening. 150 blastomeres were transferable, 15 pregnancies were happened, and 11 babies born.

We used 6 markers for beta-thal, 36 for aneuploidy screening, 32 for sex selection, and 35 for HLA typing. To our knowledge combining all these markers together and the number of STR markers are much more than any other studies which have ever done.

Conclusions

PGD is a powerful diagnostic tool for carrier couples who desire to have a healthy child and wish to avoid medical abortion.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12884-022-04660-9.

Genetic study of a patient with congenital central hypoventilation syndrome in Iran: a case report

BACKGROUND

Congenital central hypoventilation syndrome (CCHS) is an extremely rare genetic disorder characterized by Autonomic nervous system dysregulation caused by mutations in the PHOX2B gene. Here we introduce the first genetic analysis of a one-month-old CCHS baby girl in Iran.

METHODS AND RESULTS

Genetic analysis of the PHOX2B gene was performed by Sanger sequencing and interpreted using the American College of Medical Genetics and Genomics (ACMG) guideline. The results showed a heterozygous duplication in exon 3, causing a polyalanine repeat expansion mutation to 27 repeats in thePHOX2B gene (20/27 genotype).The patient's parents did not demonstrate this mutation on genetic studies.

CONCLUSIONS

According to the ACMG guideline, the mutation is pathogenic, and it was a denovo mutation in the family. The genetic study can help the family for prenatal diagnosis or pre-implantation diagnosis if the parents have gonadal mosaicism.

Hints From the Cellular Functions to the Practical Outlook of Circular RNAs

Although it has been about 30 years since the discovery of circular RNAs (circRNAs) in mammalian cells, these subtypes of RNAs’ capabilities have come into focus in recent years. The unique structure and various functional roles of circRNAs in many cellular processes have aroused researchers’ interest and raised many questions about whether circRNAs can facilitate the diagnosis and treatment of diseases. To answer these questions, we will illustrate the main known functions and regulatory roles of circRNAs in the cell after presenting a brief history of the discovery of circRNAs and the main proposed theories of the biogenesis of circRNAs. Afterward, the practical application of circRNAs as biomarkers of different pathophysiological conditions will be discussed, mentioning some examples and challenges in this area. We also consider one of the main questions that human beings have always been faced, “the origin of life,” and its possible connection to circRNAs. Finally, focusing on the various capabilities of circRNAs, we discuss their potential therapeutic applications considering the immunity response toward exogenous circRNAs. However, there are still disputes about the exact immune system reaction, which we will discuss in detail.

Reporting a rare form of myopathy, myopathy with extrapyramidal signs, in an Iranian family using next generation sequencing: a case report

Background

Myopathy with extrapyramidal signs (MPXPS) is an autosomal recessive mitochondrial disorder which is caused by mutation in mitochondrial calcium uptake 1 (MICU1) gene located on chromosome 10q22.1. Next Generation Sequencing (NGS) technology is the most effective method for identification of pathogenic variants with the ability to overcome some limitations which Sanger sequencing may encountered. There are few reports on this rare disease around the world and here in this study we first revealed genetic identification of two affected individuals in an Iranian family with a novel mutation.

Case presentation

The proband was a 5-year-old girl from consanguenous parents. She was first clinically suspicious of affected with limb-girdle muscular dystrophy (LGMD). Muscle biopsy studies and autozygosity mapping, using four short tandem repeat (STR) markers linked to 6 genes of the most prevalent forms of LGMD, ruled out calpainopathy, dysferlinopathy, and sarcoglycanopathis. DNA sample of the proband was sent for NGS. Whole exome sequencing (WES) revealed a novel mutation c.1295delA in exon 13 of MICU1 gene. This homozygous deletion creates a frameshift and a premature stop codon downstream of canonical EF4 calcium binding motif of MICU1. According to the American College of Medical Genetics and Genomics (ACMG) guidline for sequence interpretation, this variant was a pathogenic one. Sanger sequencing in all family members confirmed the results of the WES.

Conclusions

This study was the first report of MPXPS in Iranian population which also revealed a novel mutation in the MICU1 gene.

Mutational spectrum of autosomal recessive limb-girdle muscular dystrophies in a cohort of 112 Iranian patients and reporting of a possible founder effect

Background

Limb-girdle muscular dystrophies are a group of genetically heterogeneous diseases that are inherited in both autosomal dominant (LGMDD) and autosomal recessive forms (LGMDR), the latter is more common especially in populations with high consanguineous marriages like Iran. In the present study, we aimed to investigate the genetic basis of patients who are suspicious of being affected by LGMDR.

DNA samples of 60 families suspected of LGMD were extracted from their whole blood. Four short tandem repeat (STR) markers for each candidate genes related to LGMD R1 (calpain3 related)- R6 (δ-sarcoglycan-related) were selected, and all these 24 STRs were applied in two sets of multiplex PCR. After autozygosity mapping, Sanger sequencing and variant analysis were done. Predicting identified variants’ effect was performed using in-silico tools, and they were interpreted according to the American College of Medical Genomics and Genetics (ACMG) guideline. MLPA was used for those patients who had large deletions.

Fresh muscle specimens were taken from subjects and were evaluated using the conventional panel of histochemical stains.

Results

forty out of sixty families showed homozygote haplotypes in CAPN3, DYSF, SGCA, and SGCB genes. The exons and intron-exon boundaries of the relevant genes were sequenced and totally 38 mutations including CAPN3 (n = 15), DYSF (n = 9), SGCB (n = 11), and SGCA (n = 3) were identified. Five out of them were novel. The most prevalent form of LGMDs in our study was calpainopathy followed by sarcoglycanopathy in which beta-sarcoglycanopathy was the most common form amongst them. Exon 2 deletion in the SGCB gene was the most frequent mutation in this study.

We also reported evidence of a possible founder effect in families with mutations in DYSF and SGCB genes. We also detected a large consanguineous family suffered from calpainopathy who showed allelic heterogeneity.

Conclusions

This study can expand our knowledge about the genetic spectrum of LGMD in Iran, and also suggest the probable founder effects in some Iranian subpopulations which confirming it with more sample size can facilitate our genetic diagnosis and genetic counseling.

Genetic variability in Iranian limb-girdle muscular dystrophy type 2B patients: An evidence of a founder effect

Background

Dysferlinopathies are a group of autosomal recessive limb‐girdle muscular dystrophies (LGMDs) caused by mutations in DYSF (#603,009). This gene encodes a transmembrane protein called dysferlin. Since there are few reports on Iranian dysferlinopathy patients, we tried to identify the DYSF mutations in affected individuals of Iran.

Methods

Eight unrelated Iranian families have been selected for this study. Sanger sequencing followed by haplotype analysis was performed to identify individual variations in DYSF sequence. Identified variants were analyzed, and their pathogenicity was interpreted according to the recommendations of the American College of Medical Genetics and Genomics.

Results

We identified two new mutations in DYSF, the first one is a nonsense mutation c.2419C > T (p.Gln807*), which eliminates downstream part of the protein. Another novel mutation is c. (1,053 + 1_1,054‐1)_(1,397 + 1_1,398‐1)del, which causes deletion of the DNA segment from exon 12 to exon 15.

Conclusion

Two of the other six families are from the same ethnicity and share the same mutation and haplotype patterns, suggesting a founder mutation. Genetic analysis of dysferlinopathy can prevent a wrong diagnosis of myositis for these patients.

A rare form of limb girdle muscular dystrophy (type 2E) seen in an Iranian family detected by autozygosity mapping

Sarcoglycanopathies (SGPs) constitute a subgroup of autosomal recessive limb girdle muscular dystrophies (LGMDs) which are caused by mutations in sarcoglycan (SGs) genes. SG proteins form a core complex consisting of α, β, γ and δ sarcoglycans which are encoded by SGCA, SGCB, SGCG and SGCD genes, respectively. Genetic defect, in any of these SG proteins, results in instability of the whole complex. This effect can be helpful in interpreting muscle biopsy results. Autozygosity mapping is a gene mapping approach which can be applied in large consanguineous families for tracking the defective gene in most autosomal recessive disorders. In the present study, we used autozygosity mapping, to find the gene responsible for muscular dystrophy. Proband was a 10-year-old boy referred to our center for ruling out DMD (Duchenne muscular dystrophy). According to the pedigree and clinical reports, we assessed him for SGPs. Haplotyping, using the four short tandem repeat (STR) markers for each of the SG genes, showed that the phenotype may segregate with SGCB gene; and observing two crossing overs which occurred within the gene suggested that the mutation might be in the first two exons of SGCB gene. Mutation analysis showed a 26 bp duplication (10 bp before the initiation codon till 13 bp after the ATG start codon). This will cause a frameshift in protein synthesis.

Linkage Study Revealed Complex Haplotypes in a Multifamily due to Different Mutations in CAPN3 Gene in an Iranian Ethnic Group

Calpainopathy is an autosomal recessive form of limb girdle muscular dystrophies which is caused by mutation in CAPN3 gene. In the present study, co-segregation of this disorder was analyzed with four short tandem repeat markers linked to the CAPN3 gene. Three apparently unrelated Iranian families with same ethnicity were investigated. Haplotype analysis and sequencing of the CAPN3 gene were performed. DNA sample from one of the patients was simultaneously sent for next-generation sequencing. DNA sequencing identified two mutations. It was seen as a homozygous c.2105C>T in exon 19 in one family, a homozygous novel mutation c.380G>A in exon 3 in another family, and a compound heterozygote form of these two mutations in the third family. Next-generation sequencing also confirmed our results. It was expected that, due to the rare nature of limb girdle muscular dystrophies, affected individuals from the same ethnic group share similar mutations. Haplotype analysis showed two different homozygote patterns in two families, yet a compound heterozygote pattern in the third family as seen in the mutation analysis. This study shows that haplotype analysis would help in determining presence of different founders.

A novel mutation in alpha sarcoglycan gene in an Iranian family with limb girdle muscular dystrophy 2D

OBJECTIVE AND IMPORTANCE

The sarcoglycanopathies (SGPs) are a subgroup of autosomal recessive limb girdle muscular dystrophies. They are caused by mutations in gamma, alpha, beta, and delta sarcoglycans (SGs) genes. Alpha-SGPs are the most frequent form of SGPs. Muscle biopsy studies in patients with SGPs have indicated that loss of one SG subunit leads to instability of whole SG complex. Autozygosity mapping is a powerful gene mapping approach for rare recessive inherited disorders in consanguineous families.

CLINICAL PRESENTATION

In the present study, proband was a 9 year old girl from consanguineous parents. She was diagnosed at the age of 5 when she had problems climbing stairs. Her creatine kinase level was 16428 U/L. Proximal weakness and ankle contracture were also observed in the patient.

TECHNIQUES

Autozygosity mapping, using short tandem repeat (STR) markers linked to the SG genes, showed co-segregation of the phenotype with STR markers linked to the SGCA (Alpha-sarcoglycan) gene. Her muscle biopsy also suggested alpha sarcoglycanopathy. Mutation analyses revealed a novel homozygous deletion of 11 base pairs in exon 4 of this gene. This deletion introduces a premature termination codon after the 4th amino acid. This will eliminate the expression of the downstream part of the extracellular domain of the protein. This domain has a critical role by associating with other molecules of dystrophin-glycoprotein complexes.

CONCLUSION

IHC (Immunohistochemistry) studies combined with autozygosity mapping and mutation screening is an efficient diagnostic method in the SGPs.

Sex-specific association of RANTES gene -403 variant in Meniere's disease

Several studies have shown the correlation between RANTES gene and inflammatory disorders; the aim of the present study was to investigate the association between RANTES promoter gene polymorphism and Meniere's disease (MD) in an Iranian population. In this study patients with MD comprising definite MD (N = 56) and probable MD (N = 15) were selected according to diagnostic criteria of AAO-HNS. The control group (N = 101) were healthy normal subjects who did not have a history of ear disease and vertigo. PCR-RFLP for RANTES -403G>A has been performed. We found a protective role for RANTES -403A allele in male group in our population. None of the male patients with MD were carrier of allele A which was significantly different from the presence of allele A in the male control group (AA+GA vs. GG: p = 0.0004, OR 0.05, 95 % CI 0.001-0.39). This difference was not significant in female group. There was no significant association between RANTES gene polymorphism and the level of hearing loss. our results showed a sex-specific association between RANTES gene polymorphism and MD but more studies are necessary to further assess this association.

The expression of peroxisomal protein transcripts increased by retinoic acid during neural differentiation

Peroxisomal matrix protein is mainly expressed in heart, skeletal muscle, and brain tissues. To study the expression of peroxisomal protein (PEP) during neurogenesis, we employed mouse embryonic carcinoma cells (P19) and embryonic stem cells (mESCs) as an in vitro model for neural differentiation by retinoic acid (RA) induction. Expression pattern of PEP was investigated under distinct steps of differentiation by RT-PCR and real-time PCR. The results revealed that expression of PEP transcripts was markedly increased after the RA treatment at embryoid body and neural stages. Therefore, we concluded that PEP might be involved in the early process of neurogenesis, which needs further verification.