A novel start-loss mutation of the SLC29A3 gene in a consanguineous family with H syndrome: clinical characteristics, in silico analysis and literature review.

BACKGROUND: The SLC29A3 gene, which encodes a nucleoside transporter protein, is primarily located in intracellular membranes. The mutations in this gene can give rise to various clinical manifestations, including H syndrome, dysosteosclerosis, Faisalabad histiocytosis, and pigmented hypertrichosis with insulin-dependent diabetes. The aim of this study is to present two Iranian patients with H syndrome and to describe a novel start-loss mutation in SLC29A3 gene. METHODS: In this study, we employed whole-exome sequencing (WES) as a method to identify genetic variations that contribute to the development of H syndrome in a 16-year-old girl and her 8-year-old brother. These siblings were part of an Iranian family with consanguineous parents. To confirmed the pathogenicity of the identified variant, we utilized in-silico tools and cross-referenced various databases to confirm its novelty. Additionally, we conducted a co-segregation study and verified the presence of the variant in the parents of the affected patients through Sanger sequencing. RESULTS: In our study, we identified a novel start-loss mutation (c.2T > A, p.Met1Lys) in the SLC29A3 gene, which was found in both of two patients. Co-segregation analysis using Sanger sequencing confirmed that this variant was inherited from the parents. To evaluate the potential pathogenicity and novelty of this mutation, we consulted various databases. Additionally, we employed bioinformatics tools to predict the three-dimensional structure of the mutant SLC29A3 protein. These analyses were conducted with the aim of providing valuable insights into the functional implications of the identified mutation on the structure and function of the SLC29A3 protein. CONCLUSION: Our study contributes to the expanding body of evidence supporting the association between mutations in the SLC29A3 gene and H syndrome. The molecular analysis of diseases related to SLC29A3 is crucial in understanding the range of variability and raising awareness of H syndrome, with the ultimate goal of facilitating early diagnosis and appropriate treatment. The discovery of this novel biallelic variant in the probands further underscores the significance of utilizing genetic testing approaches, such as WES, as dependable diagnostic tools for individuals with this particular condition.

Identification of novel and known genetic variants associated with hereditary hearing loss in iranian families using whole exome sequencing.

BACKGROUND: Hearing loss (HL) is a common sensory impairment worldwide, with genetic and environmental factors contributing to its occurrence. Next Generation Sequencing (NGS) plays a crucial role in identifying the genetic factors involved in this heterogeneous disorder. METHODS AND RESULTS: In this study, a total of 9 unrelated Iranian families, each having at least one affected individual who tested negative for mutations in GJB2, underwent screening using whole exome sequencing (WES). The pathogenicity and novelty of the identified variant was checked using various databases. Co-segregation study was also performed to confirm the presence of the candidate variants in parents. Plus, The pathogenicity of the detected variant was assessed through in silico analysis using a number of mutation prediction software tools. Among the 9 investigated families, hearing loss-causing genes were identified in 6 families. the mutations were observed in USH2A, CLRN1, BSND, SLC26A4, and MITF, with two of the identified mutations being novel. CONCLUSION: Discovering additional variants and broadening the range of mutations associated with hearing impairment has the potential to enhance the diagnostic effectiveness of molecular testing in patient screening, and can also lead to improved counseling aimed at reducing the risk of affected offspring for high-risk couples.

A case report of Ring chromosome 18 with systemic Lupus Erythematosus and Crohn's disease.

BACKGROUND: Ring Chromosome 18 is a rare chromosomal disorder caused by missing pieces of one or both ends of chromosome 18. The clinical phenotype of the Ring 18 syndrome depended on the rate and the locality of genetic material lost. Here, we report a 27 years old girl with symptoms including microcephaly, mental and motor retardation, hypotonia, and autoimmune diseases consist of Rheumatoid arthritis, Systemic Lupus Erythematosus, and Crohn's disease. This research contributes to a better understanding of disease and can lead to improvement in diagnosis and treatment. METHOD AND RESULT: The Chromosomal analysis was performed based on the GTG banding technique on peripheral blood lymphocytes. Karyotype analysis indicated the existence of a Ring chromosome 18 with deletions at 18p11.32 and18q22-2. Following that, the parental karyotype of the affected girl confirmed that Ring 18 was caused by a de novo mistake very early in embryonic development. CONCLUSION: Ring chromosome 18 is a rare chromosomal disorder that is generally caused by de novo errors very early in the development of the embryo. Previously studies have reported a relationship between autoimmune diseases and Ring 18. Our patient has disclosed specific types of autoimmune diseases, including Systemic Lupus Erythematosus, and Crohn's disease.

Association between interleukin-10 gene polymorphisms and severe chronic periodontitis.

OBJECTIVE: Periodontitis is an inflammatory disease that is a result of the interaction between pathogenic bacteria and host immune response. Genetic alterations in interleukin-10 (IL-10) gene may be associated with the increased risk of periodontitis. We investigated the association between genotype and haplotype frequencies of IL-10 gene polymorphisms and susceptibility to periodontitis in an Iranian population. METHODS: In this case-control study, a total of 64 patients with periodontitis and 128 healthy subjects were recruited. The PCR-RFLP technique was used to detect IL-10 promoter genotypes at the positions of -1082 (G/A), -819 (C/T), and -592 (C/A) in association with the susceptibility to severe chronic periodontitis. RESULTS: Regarding IL-10 -592 (C/A) and IL-10 -819 (C/T) alleles and genotypes, no significant association was observed between the risk of periodontitis and genotype frequencies. However, the frequency of GG genotype in IL-10 -1082 (G/A) polymorphic region was higher in normal subjects and was associated with the decreased risk of periodontitis under recessive model [OR = 2.89, 95% CI (0.99-8.43), p = 0.039]. Haplotype analysis revealed a significantly higher presence of H7 (AGC; -592/-1082/-819) [OR = 97.74, 95% CI (95.52-99.96), p < 0.0001]. CONCLUSION: IL-10 -1082(G/A) polymorphism and AGC (-592/-1082/-819) haplotype could be associated with the susceptibility to chronic periodontitis.

The X-ray Repair Cross-Complementing Group 1 Arg399Gln Genetic Polymorphism and Risk of Hepatocellular Carcinoma in an Iranian Population.

BACKGROUND The association between X-ray repair cross-complementing group 1 (XRCC1) Arg399Gln gene polymorphism and hepatocellular carcinoma (HCC) has been investigated in several populations. However, the findings are controversial. The aim of this study was to address the association between XRCC1 Arg399Gln polymorphism and HCC in an Iranian population. METHODS We have evaluated the association between XRCC1 Arg399Gln gene polymorphism and HCC in 151 Iranian individuals (50 patients with HCC and 101 healthy matched controls) using polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLP) method. RESULTS Significant association was found for the XRCC1 A allele and HCC [OR = 1.93, 95% CI (1.16 - 3.25), P = 0.0099]. Also, genotype analysis by SNPStats online software showed a significant association between XRCC1 gene polymorphisms and HCC under co-dominant, dominant, and recessive genetic models. CONCLUSION Our study provides evidence that the XRCC1 Arg399Gln polymorphism may be associated with the risk of HCC development in Iranian population.

Association of the epidermal growth factor gene +61A>G polymorphism with hepatocellular carcinoma in an Iranian population.

AIM: The aim of this study was to address the association of the EGF gene +61A/G polymorphisms and HCC susceptibility in an Iranian population. BACKGROUND: The association of epidermal growth factor (EGF) gene +61A/G polymorphism (rs4444903) and hepatocellular carcinoma (HCC) has been investigated in several populations. However, the findings are controversial. METHODS: A total of 40 unrelated HCC patients and 106 healthy individuals were enrolled in this study. Genomic DNA of HCC patients was extracted from formalin-fixed, paraffin-embedded samples using CinnaPure DNA kit according to manufacturer's instructions. Genomic DNA of healthy individuals, also, was extracted from peripheral blood cells using the boiling method. The rs4444903 (A/G) polymorphism was genotyped using the polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) method. RESULTS: Significant association was found for the EGF +61A allele and HCC risk [OR = 1.72, 95% CI (1.02 - 2.90), P value = 0.04]. Also, significant association was observed for the EGF +61A/G genotypes and HCC risk under codominant and dominant models by SNPStats software analysis. CONCLUSION: Our findings suggest that the EGF gene +61A/G polymorphism (rs4444903) might be a risk factor for susceptibility to HCC in Iranian population. However, further studies using more samples are needed.

Evaluating the miR-302b and miR-145 expression in formalin-fixed paraffin-embedded samples of esophageal squamous cell carcinoma.

BACKGROUND: MicroRNAs are involved in key cellular processes regulating, and their misregulation is linked to cancer. The miR-302-367 cluster is exclusively expressed in embryonic stem and carcinoma cells. This cluster also promotes cell reprogramming and stemness process. In contrast, miR-145 is mostly regarded as a tumor suppressor, where it regulates cellular functions such as cell division, differentiation, and apoptosis. By suppressing the main pluripotency factors (OCT4, SOX2, MYC and KLF4), miR-145 silences the self-renewal program in ESCs. Therefore, the main aim of this study is to find a potential link between the expression level of hsa-miR-302b and hsa-miR-145 with tumor vs. non-tumor as well as high-grade vs. low-grade states of the esophageal tissue samples. METHODS: A total number of 40 formalin-fixed, paraffin-embedded (FFPE) samples of esophageal squamous-cell carcinoma (ESCC) were obtained, and the tumor and marginal non-tumor areas delineated and punched off by an expert pathologist. Total RNA was extracted with Trizol, and cDNA synthesized using the miRCURY LNA™ Universal RT microRNA PCR Kit. Real-time reverse transcription polymerase chain reaction (RT-PCR) assays were performed using specific LNA-primers and SYBR Green master mix. RESULTS: The expression level of miR-302b failed to show any significant difference, neither between tumor and their non-tumor counterparts, nor among tumors with different grades of malignancies (p > 0.05). In contrast, miR-145 was significantly down regulated in all grades of tumor samples (p < 0.001). However, its expression level could not discriminate between different grades of malignancy (p > 0.05). CONCLUSION: Our data revealed a significant down-regulation of miR-145 in ESCC tissue samples. Based on our ROC curve analysis data (AUC = 0.74, p < 0.001) miR-145 could be regarded as a potential tumor marker for diagnosis of esophageal cancer.

Use of integrase-minus lentiviral vector for transient expression.

OBJECTIVE: Lentivirus-derived vectors are among the most promising viral vectors for gene therapy which is currently available, but their use in clinical practice is limited due to associated risk of insertional mutagenesis. Gene targeting is an ideal method for gene therapy, but it has low efficiency in comparison to viral vector methods. In this study, we are going to design and construct an integrase-minus lentiviral vector. This vector is suitable for transient expression of gene and gene targeting with viral vector. MATERIALS AND METHODS: In this experimental study, three missense mutations were induced in the catalytic domain of Integrase gene in the pLP1 plasmid and resulted D64V, D116A and E152G changes in the amino acid sequence through site directed mutagenesis. The pLenti6.2-GW/EmGFP transfer vector, associated with native and mutated packaging mix, was transfected into 293T cell line. In order to titer the lentivirus stock, the viruses were harvested. Finally, the viruses transduced into COS-7 cell line to assess green fluorescent protein (GFP) gene expression by a fluorescence microscopy. RESULTS: Recombinant and wild lentiviruses titer was about 5~8×10(6) transducing units/ml in COS-7 cell line. The number of GFP-positive cells transduced with native viruses was decreased slightly during two weeks after viral transduction. In contrast, in the case of integrase-minus viruses, a dramatic decrease in the number of GFP positive cells was observed. CONCLUSION: This study was conducted to overcome the integration of lentiviral genome into a host genome. Nonintegrating lentiviral vectors can be used for transient gene expression and gene targeting if a Target gene cassette is placed in the lentivirus gene structure. This combination method decreases disadvantages of both processes, such as random integration of lentiviruses and low efficiency of gene targeting.