In silico prediction discontinuous B cell epitope peptide vaccine against leishmaniasis

Introduction: The kinetoplastid protozoan parasites of the genus Leishmania cause diseases for which treatment is difficult and there is still no vaccine for use in humans. Leishmanolysin is the major enzymatic protein component of the promastigote surface. Because of its role as a ligand involved in the interaction of the parasite with defensive systems of the host, including components of the complement system and the macrophage surface is an attractive candidate for designing peptide vaccines.  Methods and Results: In the current study, PEPOP was used to predict peptides from Leishmanolysin in the form of discontinuous B-cell epitopes. PEPOP identified segments comprised of accessible and sequence continuous amino acids. These segments were clustered according to their spatial distances using method of extensions: Optimized Nearest Neighbor (ONN), Optimized Flanking Nearest Neighbor (OFN), Optimized Patched segments Path (OPP), Traveling Salesman Problem (TSP), and Shortest Path (SHP). Each peptide sequence has been generally comprised of several segments. From 3D structure of Leishmanolysin, PEPOP identified 100 segments gathered in three clusters according to their spatial distances. In this study, we wanted to predict peptides from a specific region of the protein, the residue 264-345 on the active site of Leishmanolysin. It corresponds to the segments S34 to S48. The predicted peptides, which did not relate to this region (264-345) were removed and at last 29 peptides were selected. Conclusions: These results using bioinformatics analyses could be conducted in vaccine design against Leishmania infections

Identification of B and T cell epitope peptide vaccines from IGF-1 Receptor in breast cancer

Introduction: The insulin-like growth factor-1 receptor (IGF-1R) plays a key role in proliferation, growth, differentiation, and development of several human malignancies including breast and pancreatic adenocarcinoma. IGF-1R targeted immunotherapeutic approaches are particularly attractive, as they may potentially elicit even stronger antitumor responses than traditional targeted approaches. Cancer peptide vaccines can produce immunologic responses against cancer cells by triggering helper T cell (Th) or cytotoxic T cells (CTL) in association with Major Histocompatibility Complex (MHC) class I or II molecules on the cell surface of antigen presenting cells.  Methods and Results: In our previous study, we set a technique based on molecular docking in order to find the best MHC class I and II binder peptides using GOLD. In the present work, molecular docking analyses on a library consisting of 30 peptides mimicking discontinuous epitopes from IGF-1R extracellular domain identified peptides 249 and 86, as the best MHC binder peptides to both MHC class I and II molecules. The receptors most often targeted by peptide 249 are HLA-DR4, HLA-DR3 and HLA-DR2 and those most often targeted by peptide 86 are HLA-DR4, HLA-DP2 , and HLA-DR3. Conclusions: These findings, based on bioinformatics analyses, can be conducted in further experimental analyses in cancer therapy and vaccine design

Clinical feature and Genetics in Rett syndrome; A report on Iranian patients

Background: Rett Syndrome is characterized by normal development for the first 6–18 months of life followed by the loss of fine and gross motor skills and the ability to engage in social interaction. Mutations methyl CpG-binding protein 2 gene (MECP2) have been found in the majority of patients. This study was performed to investigate the relation of Rett clinical diagnosis and its relation with mutations in MECP2. Materials and Methods: children suspected to Rett syndrome were invited to take part in this study. Those who had met classic Rett syndrome diagnostic criteria were enrolled. Severity of symptoms was assessed for all patients. Of peripheral blood samples collected in EDTA tubes, the genomic DNA was extracted by standard salting out method. MEPC2 gene mutation was studied by DNA sequencing method. Results and conclusion: 23 patients accepted to participate in the study. 11(47.8%) patients had MECP2 gene mutation meanwhile 12 ones (52.2%) had no mutation. change in genetics was in association with phenotypical manifestations. The most prevalent mutation was p.v288 which is mostly in association with partially or uncontrolled seizures. This was the first time that Rett syndrome patients were studied in both clinical manifestations and genetic changes in Iran

Report a Novel Mutation in Human Prostacyclin Receptor Gene in patient affected with Migraine

Objective: The human prostacyclin receptor gene (PTGIR) encodes the human prostacyclin (PGI2) receptor. PTGIR is a part of vasodilator system during the migraine attacks and probably has an important role in the mechanism of this disease. Materials and Methods: We used direct PCR and sequencing to determine the any variants in PTGIR gene. A blood sample was collected from the patients and genomic DNA was extracted. Polymerase chain reaction was carried out on extracted DNA. The PCR products were then sequenced using a cycle sequencing kit, on an automated DNA sequencing machine. Results: In reviewing of familial and clinopathological of these two patients, both patients have migraines with visual aura and their mothers also are suffering from migraines. Their parents had been married strangers. Direct sequencing analysis of exon 2 of the PTGIR gene showing the presence of two mutations in two patients. These mutations were heterozygote that made the following changes; g.1626T>A, c.754T>A, cDNA.867T>A, and p.S252T for the first mutation and c.753C>T, cDNA866C>T, g.1625C>T, p.C251C for the second mutation. The first mutation alters the amino acid and is a novel mutation. The second change is a conservative mutation that have already been reported. Conclusion: The prediction results predicted the variant would negatively affect the protein’s function and seems to be disease causing. Although functional analysis is required to confirm the association between the variant and the disease

Variants in Human Prostacyclin Receptor Gene in Patients with Migraine Headache

Objective: Prostaglandin I2 receptor plays a major physiologic role in the relaxation of arterial smooth muscle and vasodilation and possibly during migraine attacks. Therefore, in this study, the coding and noncoding exons and exon-intron boundaries of Prostaglandin I2 receptor  gene were examined in patients with migraine headache and healthy controls and the potential effects of identified single nucleotide variations were evaluated using direct PCR-sequencing and in silico analysis. Method: In this study, the peripheral blood samples of 50 patients and 50 controls were examined to find any mutation in coding and noncoding exons and exon-intron boundaries of PTGIR gene. DNA was extracted and all the samples were amplified by polymerase chain reaction (PCR) and sequenced. Results: In this study, the patients had a mean age of 35.235 ± 10.99 years (range, 9–60 yrs.), and female to male ratio was 4:1 in this group. The controls had a mean age of 35.058 ± 11.116 years (range, 8–59 yrs.), and female to male ratio was 3.7:1.3 in this group. Two patients had mutations in exon 2. The first mutation was located in exon 2 (at amino acid position 251) of PTGIR gene at nucleotide position c.866A > T, a synonymous variant described previously in the database. The second mutation was located in exon 2 c.867G > A, which is a missense variant. Sequence analysis revealed high occurrence of previously reported intronic variants mostly in a homozygous statue. Conclusion: The data supported the hypothesis that mutations in PTGIR gene, particularly the mutation we described, should be considered even in cases of migraine. The presence of this mutation in patients with family history raises important issues regarding genetic counselling.

Report of SLC3A1/rBAT gene mutations in Iranian cystinuria patients: A direct sequencing study

Background: Considering a few studies on the genetic basis of the cystinuria in the Middle East and the population-specific distribution of mutations in the SLC3A1, we tried to find genetic variants in three exons (1, 3, and 8) of SLC3A1. Materials and Methods: In this study, exons 1, 3, and 8 of SLC3A1 gene of 25 unrelated cystinuria patients searched for genetic variations by polymerase chain reaction and sequencing. Results: There were five different variations in our studied population. We found one mutation in the SLC3A1 gene including missense variant M467K and identified three polymorphisms: nonsynonymous variant G38G, c. 610 + 169C>T and c. 610 + 147C>G within the SLC3A1 gene, and one new variant. Conclusion: Our results confirm that cystinuria is a heterogeneous disorder at the molecular level and more studies are needed to identify the distribution and frequency of mutations causing cystinuria in the Iranian population

In silico analysis of A novel pathogenic variant in an Iranian Mucopolysaccharidosis IIIB patient identified by targeted next-generation sequencing

Mucopolysaccharidosis IIIB (MPS IIIB) (Sanfilippo Syndrome Type B; OMIM 252920) is an autosomal recessive metabolic disorder caused by mutations in the NAGLU gene which encode for lysosomal enzyme N-acetyl-glucosaminidase, involved in degradation of complex polysaccharide, heparan sulfate. The disease characterized by progressive cognitive decline and behavioral difficulties and motor function retardation. In this study, using targeted exome sequencing, we identified a novel heterozygote deletion variant (c.1294-1304 del CTCTTCCCCAA, p.432LeufsX25) in the NAGLU gene in consanguineous parent of a child who was dying in her 14 years old where the diagnosis of death was Mucopolysaccharidosis. Sanger sequencing was used to confirm the candidate pathogenic variants in extended family members and segregation analysis. Computational docking using the Molegro Virtual Docker (MVD) 6.0.1 software confirmed different affinity binding of truncated protein for its ligand-Acetyl-D-Glucosamine. Moreover, with I-TASSER software functional alterations between wild and mutant proteins evaluated. The variant was classified as pathogenic based on the American College of Medical Genetics and Genomics guideline. This study expands the spectrum of NAGLU pathogenic variants and confirms the utility of targeted NGS sequencing in genetic diagnosis and also the utility and power of additional family information

Effect of teicoplanin on the expression of c-myc and c-fos proto-oncogenes in MCF-7 breast cancer cell line

Background: Teicoplanin is a member of vancomycin-ristocetin family of glycopeptide antibiotics. It mediated wound healing by increasing neovascularization possibly through activation of MAP kinase signaling pathway. The aim of this study is an evaluation of c-myc and c-fos genes expression after treatment of cells by teicoplanin and determines whether this glycopeptide antibiotic exerts its proliferation effects by influencing the expression of these genes. Hence, this study was designed to elucidate one possible mechanism underlying teicoplanin effects on cell proliferation using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay. Materials and Methods: Breast cancer cell line, MCF-7, was cultured, and three different concentrations of teicoplanin were added to the plates. We measured the cell proliferation rate by MTT assay. After cell harvesting, total RNA was extracted to synthesize single-stranded cDNA. Real-time polymerase chain reaction was performed, and the data were analyzed. Results: It was observed that the level of c-fos and c-myc genes' expressions was decreased at all three different concentrations of teicoplanin. Conclusion: it could be concluded that although teicoplanin is considered as an enhancing cell growth and proliferation, but probably its effect is not through MAP kinase signaling pathway or perhaps even has inhibitory effect on the expression of some genes such as c-myc and c-fos in this pathway. Hence, the mechanism of action of teicoplanin for increasing cell propagation, through cell signaling pathways or chromosomal abnormalities, remains unclear, and further studies should be conducted

Brain tumors: Special characters for research and banking

A brain tumor is an intracranial neoplasm within the brain or in the central spinal canal. Primary malignant brain tumors affect about 200,000 people worldwide every year. Brain cells have special characters. Due to the specific properties of brain tumors, including epidemiology, growth, and division, investigation of brain tumors and the interpretation of results is not simple. Research to identify the genetic alterations of human tumors improves our knowledge of tumor biology, genetic interactions, progression, and preclinical therapeutic assessment. Obtaining data for prevention, diagnosis, and therapy requires sufficient samples, and brain tumors have a wide range. As a result, establishing the bank of brain tumors is very important and essential