Mutation Analysis of KRAS and BRAF in Iranian Colorectal Cancer patients: A Novel Variant in Exon 15 of BRAF.

BACKGROUND: Mitogen-Activated Protein Kinase (MAPK) pathway and its downstream signaling pathways, play an important role in intracellular signaling. Mutations in KRAS (activating mutation) and BRAF proto-oncogenes are identified as key finding of colorectal cancer. The aim of this study was to examine mutation analysis of KRAS and BRAF in Iranian Colorectal cancer patients. METHODS: We used fifty archived formalin fixed paraffin-embedded (FFPE) blocks of Iranian colorectal cancer patients. DNA was extracted from FFPE blocks for PCR assay. The quality of PCR products was determined using horizontal electrophoresis. Then, sequencing and analysis of the sequencing results were performed to investigate variation status in the sequences. RESULTS: KRAS exons and BRAF genes exon 15 in 50 CRC patients were analyzed, among the 19 mutant KRAS samples, 18 (36%) patients had a single base substitution (synonymous mutation) in exon 5, p. Arg161Arg (c.483G>A) and 1 (2%) patient in exon 2 (codon 12), p. Gly12Cys (c.34G>T). Also, we observed two mutations p. Val600Glu (c.1799 T>A) and p. Ser616Thr (c.1846T>A) in exon 15 of BRAF gene. CONCLUSIONS: We found a novel variant in BRAF gene. The p. Ser616Thr (c.1846T>A) mutation was not previously reported and we conclude that other new mutations can be identified in KRAS and BRAF which may lead to colorectal cancer.

Evaluation of DNA repair capacity in parents of pediatric patients diagnosed with autism spectrum disorder using the comet assay procedure.

Background: Autism Spectrum Disorder (ASD) is characterized by impairments in social communication, limited repetitive behaviors, impaired language development, and interest or activity patterns, which include a group complex neurodevelopmental syndrome with diverse phenotypes that reveal considerable etiological and clinical heterogeneity and are also considered one of the most heritable disorders (over 90%). Genetic, epigenetic, and environmental factors play a role in the development of ASD. Aim: This study was designed to investigate the extent of DNA damage in parents of autistic children by treating peripheral blood mononuclear cells (PBMCs) with bleomycin and hydrogen peroxide (H2O2). Methods: Peripheral blood mononuclear cells (PBMCs) were isolated by the Ficoll method and treated with a specific concentration of bleomycin and H2O2 for 30 min and 5 min, respectively. Then, the degree of DNA damage was analyzed by the alkaline comet assay or single cell gel electrophoresis (SCGE), an effective way to measure DNA fragmentation in eukaryotic cells. Results: Our findings revealed that there is a significant difference in the increase of DNA damage in parents with affected children compared to the control group, which can indicate the inability of the DNA molecule repair system. Furthermore, our study showed a significant association between fathers' occupational difficulties (exposed to the influence of environmental factors), as well as family marriage, and suffering from ASD in offspring. Conclusion: Our results suggested that the influence of environmental factors on parents of autistic children may affect the development of autistic disorder in their offspring. Subsequently, based on our results, investigating the effect of environmental factors on the amount of DNA damage in parents with affected children requires more studies.

Assessment of Peripheral Blood Lymphocytes in Parents of Autistic Children by Cytokinesis Block Micronucleus Assay.

Autism spectrum disorders are neurodevelopmental complex diseases with causative de-novo and inherited genetic factors. They include a range of cognitive and behavioral conditions such as pervasive developmental disorder, Asperger's syndrome, and autism. Cytokinesis-block micronucleus assay, as a cytogenetic study has been considered as one of the indicators of chromosomal damage in peripheral blood. This study aimed to investigate the frequency of micronucleus (MN) in peripheral blood lymphocytes of parents with autistic children. The study was case-control and the cases were parents of autistic children referring to the psychiatric department of the Ali-Asghar Hospital of Tehran. The total number of samples was 60 cases and 30 controls. The results showed that autistic children's parents had a significant increase in MN frequency in binucleated lymphocytes. Further researches are suggested to analyze the environmental and genetic reasons for MN increase in autistic children parents.

MicroRNA-Targeted Signaling Pathways in the Autism Spectrum Disorder: Implications for Early Detection and Targeted Therapy.

BACKGROUND & OBJECTIVE: Autism Spectrum Disorders (ASD) is known as a neurodevelopmental disorder showing communication impairments and unusual patterns of behavior. Presently, it seems that ASD frequency is on the increase. Therefore, diagnostic tools that help detect the disease in the early stages can be very useful in better management of the disease. Recent studies demonstrate that miRNAs as novel biomarkers can be used to find out the process and etiology of ASD by regulating various genes of multiple pathways. However, ASD associated pathway targeted by miRNA is still in infancy. METHODS: In this in silico study taking into consideration the importance of miRNAs, we reviewed bioinformatics databases for finding possible pathways and potential miRNAs related to selected pathways. RESULTS: The results displayed some prominent pathways involved in ASD, as well as some experimental and predicted miRNAs that may regulate targets associated with these pathways such as neuroactive ligand-receptor interaction, serotonergic synapse, calcium signaling pathway, cAMP Signaling Pathway, PI3K-Akt signaling pathway. CONCLUSION: This study showed that the identified miRNAs may be involved in ASD-related pathways and may be considered as a new diagnostic tool and provide potential targets for the treatment of ASD.

Whole exome sequencing revealed a novel homozygous variant in the DGKE catalytic domain: a case report of familial hemolytic uremic syndrome.

BACKGROUND: Atypical hemolytic uremic syndrome (aHUS) is a rare disease characterized by microangiopathic hemolytic anemia caused by small vessel thrombosis, thrombocytopenia, and renal failure. The common cause of aHUS is a dysregulation in the alternative complement pathway. Mutations in none complement genes such as diacylglycerol kinase epsilon (DGKE) can also result in this syndrome. CASE PRESENTATION: Here, we report on a 19-year-old female with the clinical diagnosis of aHUS, who has unaffected consanguineous parents and an older sibling who was deceased from aHUS when she was seven months old. We performed whole exome sequencing (WES) followed by evaluation of detected variants for functional significance, using several online prediction tools. Next, in order to confirm the detected pathogenic variant in proband and segregation analysis in her family, Sanger sequencing was done. The novel variant was analyzed in terms of its impact on the protein 3-dimensional structure by computational structural modeling. The results revealed that the proband carried a novel homozygous missense variant in DGKE located in exon 6 of the gene (NM_003647.3, c.942C > G [p.Asn314Lys]), and in silico analysis anticipated it as damaging. Protein computational study confirmed the influence of potential pathogenic variant on structural stability and protein function. CONCLUSION: We suggest that some variations in the catalytic domain of DGKE like p.Asn314Lys which can cause alterations in secondary and 3-D structure of protein, might lead to aHUS.

Whole Exome Sequencing Reveals a XPNPEP3 Novel Mutation Causing Nephronophthisis in a Pediatric Patient

Background: Nephronophthisis (NPHP) is a progressive tubulointestinal kidney condition that demonstrates an AR inheritance pattern. Up to now, more than 20 various genes have been detected for NPHP, with NPHP1 as the first one detected. X-prolyl aminopeptidase 3 (XPNPEP3) mutation is related to NPHP-like 1 nephropathy and late onset NPHP. Methods: The proband (index patient) had polyuria, polydipsia and chronic kidney disease and was clinically suspected of NPHP. After the collection of blood sample from proband and her parents, whole exome sequencing (WES) was performed to identify the possible variants in the proband from a consanguineous marriage. The functional importance of variants was estimated by bioinformatic analysis. In the affected proband and her parents, Sanger sequencing was conducted for variants' confirmation and segregation analysis. Results: Clinical and paraclinical investigations of the patient was not informative. Using WES, we could detect a novel homozygous frameshift mutation in XPNPEP3 (NM_022098.2: c.719_720insA; p. Q241Tfs*13), and by Sanger sequencing, we demonstrated an insertion in XPNPEP3. Conclusion: The homozygous genotype of the novel p.Q241Tfs*31 variant in XPNPEP3 may cause NPHP in the early childhood age.