mutation

Presently, the development of effective vaccines against SARS-CoV-2 is absolutely necessary, especially regarding the emergence of new variants that cause increasing morbidity and fatalities.

In the present study we designed a mosaic vaccine targeting the mutational spike protein of COVID-19 using a bioinformatics approach. Various immunoinformatics tools were utilized to provide the highest potential for a mosaic vaccine that could activate immune responses against COVID-19.

The evaluation of the constructed vaccine revealed that it is antigenic and immunogenic as well as nonallergenic. The physicochemical properties also show promising characteristics, including being highly stable and hydrophilic. As expected, the vaccine shows strong interactions with several important receptors including angiotensin-converting enzyme 2 (ACE2), Toll-like receptor 3 (TLR3) and TLR8 by the lowest energy level, docking score and binding free energy. The vaccine binds to receptors via certain amino acids using various types of binding including salt bridges, hydrogen bonds, and other means. As shown in computationally derived models, the interactions promote activation of the immune response by eliciting the release of various cytokines, antibodies, memory B and T cells, as well as increasing of natural killer cell and dendrite cell counts.

Therefore, the novel designed mosaic vaccine could be considered as a potential vaccine candidate for immediate production to stem the continuing and tragic effects of the COVID-19 pandemic. However, several advanced experimental studies should be conducted to ensure and verify the effectivity and safety against SARS‑CoV‑2 in vivo.

Familial Mediterranean fever (FMF) is caused by mutations in the MEFV (Mediterranean fever) gene and is characterized by recurrent, self-limiting attacks of fever with polyserositis. This study aimed to identify MEFV gene variants in suspected FMF patients in the southwest of Iran.

We obtained whole blood samples from 40 unrelated pediatric patients suspected to have FMF between 2020 and 2024. The entire coding and flanking regions of the MEFV gene were sequenced using genomic DNA. We employed in-silico tools to detect the pathogenicity predictions of the rare mutation. Further, the clinical symptoms experienced by the patients were recorded and evaluated.

We identified eight different mutations, including six common mutations (p.E148Q, p.M694I, p.M694V, p.A744S, p.M680I (c.2082G>A), p.V726A), one uncommon mutation (p. R202Q), and one rare mutation located in exon 3 (p.S339F). The most frequently reported mutant allele was p.E148Q (50%), followed by p.R202Q (43.75%). We reported the rare mutation p.S339F for the first time in Iranian FMF patients. Bioinformatics prediction tools confirmed the pathogenicity of this mutation, and for the first time, we used the I-mutant website for this mutation. Fever and abdominal pain were the most prevalent clinical symptoms.

These findings can be used to develop the genetic database of MEFV gene mutations and help in detection of hotspot regions in the Iranian population, especially in the southwest. Our results can be helpful in early diagnosis and pharmacotherapy for patients suspected of having FMF.

Ataxia Telangiectasia (A-T) is a rare autosomal recessive neurodegenerative disease caused by mutations in the ataxia telengiectasia mutated (ATM) gene. The gene is on chromosome 11q22-23 and codes for the protein kinase ATM, which plays an essential role in DNA damage repair. In this study, we review the clinical characteristics of 13 A-T patients, 2 of whom displayed novel mutations. Thirteen patients with ataxia-telangiectasia from 10 unrelated families were referred to  Immunology, Asthma and Allergy Research Institute, Tehran, Iran. After clinical confirmation, blood samples were collected from the patients and their parents. Genetic analysis for 8 patients was conducted using whole-exome sequencing; in the other 3 patients, polymerase chain reaction was used, followed by sequencing. We identified 11 different mutations in the ATM gene. Two patients had mutations as compound heterozygous, while 9 other patients were homozygous for the mutations. Among these, 2 likely pathogenic mutations (ie, c.2639-1G>A and c.7940_7970del​TTCCAGCAGA​CCAGCCAATT​ACTAAACTTAA) have not been reported. Our study highlights the significance of next-generation sequencing techniques in identifying novel ATM mutations in A-T patients. Although all reported A-T mutations reside in 1 gene, the absence of a mutation hotspot for this gene necessitates the use of next-generation sequencing techniques. Specifically, we identified 2 mutations that have not been reported previously, emphasizing the importance of continued research in this area. This study provides new insights into the genetic underpinnings of A-T and underscores the potential clinical implications of identifying novel mutations.

Natural selection, a cornerstone of evolutionary biology, shapes the adaptations organisms develop to survive environmental pressures. This paper explores how natural selection drives biological adaptations to radiation exposure. We examine the genetic mechanisms at play, exemplified by the enhanced DNA repair capabilities observed in bacteria like Escherichia coli (E. coli) following exposure to radiation. We then investigate adaptations in humans residing in high-background radiation areas, highlighting potential genetic variations for radiation resistance. Finally, the contemporary relevance of natural selection is discussed, emphasizing its role in the emergence of antibiotic-resistant bacteria and the need for sustainable medical practices. By studying these adaptations, we gain a deeper understanding of evolution and its implications for medicine, conservation, and our overall understanding of life.

Cancer is a polygenic complex disorder involving a network of genes. The phosphatidylinositol 3-kinase (PIK3CA) has been reported as an oncogene that plays a role in many cancer types. The present study aims to demonstrate the association between the genetic alterations observed in the PIK3CA gene network and its role in establishing breast cancer. In the present observational study, we used multiple tools (STRING, cBioportal, PANTHER, and UALCAN) to demonstrate the genetic alterations in the Breast Cancer Dataset (TCGA, Firehose Legacy). The PIK3CA gene interaction network was deduced, followed by the identification of genetic alterations, gene ontology, gene expression and survival analysis. The PIK3CA gene was found to harbor 36% of genetic alterations in the form of gene amplification and mutations. The gene expression profile indicated the significant downregulation of PIK3CA gene transcripts. Interestingly, the Kaplan Meier survival analysis demonstrated that low/medium expression of PIK3CA presented with a good prognosis when compared with the high expression group. These results support the fact that PIK3CA is oncogenic. The PIK3CA gene has been considered as one of the potential druggable targets for breast cancer. The genetic alterations reported in the gene might influence its function. Therefore, further experimental validation is required to provide more insight into the functional association of mutations. Also, the effect of tumor suppressors and epigenetic factors targeting PIK3CA has to be assessed to gain more insight into the increased expression of PIK3CA in breast cancer patients.

Tanshinone IIA is effective in the treatment of various cardiovascular diseases. Currently, tanshinone IIA is primarily derived from the roots and rhizomes of Salvia miltiorrhiza Bunge. However, resources of S. miltiorrhiza are already facing scarcity.

The aim of this study was to obtain an alternative and high-yield mutagenic strain of tanshinone IIA, thus establishing a cost-effective and non-plant-derived substitute for tanshinone IIA.

The mutants with enhanced tanshinone IIA production were selected through protoplast mutation induced by ultraviolet radiation (UV) and sodium nitrite (NaNO 2 ). The yield of tanshinone IIA (YT) was determined using a TU-1810 ultraviolet-visible (UV/Vis) Spectrophotometer and LC-2010A high-performance liquid chromatography (HPLC). The selected mutant strains with the highest yield were subjected to continuous cultivation, and the dry weight of mycelium (DW) and the YT in the first generation were used as controls to assess passage stability. Fungal genomic DNA from the wild-type and mutant strains was extracted from axenic cultures using the modified cetyltrimethyl ammonium bromide (CTAB) method.

The colony morphological characteristics exhibited significant differences between the wild-type TR21 and the mutant NU204. The NU204 demonstrated a significantly higher tanshinone IIA yield at 165 ± 2.52 μg/g, which was 4.67-fold greater than that of TR21 (P < 0.01), indicating a substantial enhancement in NU204 production compared to TR21. The NU204 underwent continuous cultivation for five generations, and there were no significant differences in the DW and YT among the different generations (P > 0.05). The observed genetic changes between TR21 and NU204 were induced by the protoplast mutation.

The mutant NU204 is emerging as a promising novel alternative source for tanshinone IIA, offering potential practical applications in production.

The occurrence of specific mutations within the Hepatitis B virus (HBV) genome is associated with the progression of chronic hepatitis B infection towards more severe outcomes.

This study aimed to investigate mutational patterns in the X -gene and their influence on the outcome of chronic HBV infection (CHB) across three generations in a family.

Ninety CHB patients, meeting the inclusion criteria, were recruited from cases referred to the Center of Hepatology at Golestan University of Medical Sciences between September 2020 and January 2021. The HBx gene was amplified using semi-nested PCR from serum samples and then subjected to sequencing.

A comparison of the sequences from CHB patients indicated that children and mothers in the two-generation group exhibited the highest similarity (79.3%) in the X -gene, with the lowest mutation rate (20.7%). The N-terminal region of the X -gene showed the highest mutation frequency in the three-generation group, including C1491G (25%), G1613T (23.9%), C1500T (43.4%), and G1658T (33.4%). The mutation rate was notably higher in HBeAg -negative patients across the three groups compared to HBe- Ag-positive CHB patients, with a statistically significant difference (P = 0.03). A1762T/G1764A mutations were observed in 15.6% of patients, and their presence showed a significant difference (P = 0.03). Additionally, in the three-generation group, a silent mutation (A1727G, 10%) and a missense mutation (A1727T, 30%) were detected.

Specific mutational patterns in the HBx gene may be valuable in predicting clinical outcomes in CHB patients and could serve as warning indicators for increased susceptibility to hepatocellular carcinoma (HCC).

The envelope (E) protein of globally circulating severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) is highly conserved. This study aimed to find the mutation rate of the E genes in COVID-19 patients, and also to evaluate the conformational characteristics of viral E protein.

In this study, 120 patients with SARS-CoV-2 positive test results were selected according to real-time PCR assay. Specific primers for conventional PCR have been used to amplify E gene; furthermore, to identify the E gene mutations, direct sequencing of the E genes was also done. Bioinformatics techniques were used to investigate the possible effects of antigenic changes and 3D characteristics of amino acid substitutions. Also, the immunogenicity of wild-type and mutant E was analyzed utilizing a ClusPro docking server and the IEDB online platform.

A total of 120 COVID-19 patients were included (57.5% were male and 42.5% female), with an overall mean age of 55.70±10.61 years old. Of 10 nucleotide changes, 8 (80%) were silent. Also, 2 (20%) missense mutations (amino acid altering) were found in the E gene (L73F and S68F).

These mutations insert some new helix structures in the E mutants. Also, the results of molecular docking studies indicated that both S68F and L73F mutations could notably enhance the stability and binding affinity of protein E's C-terminal motif to the Protein Associated with LIN7 1, MAGUK P55 Family Member (PALS1) which may probably increase local viral spread, and infiltration of immune cells into lung alveolar spaces.

In a system biology-based study, we previously reported that IL-6 and IL6R -specific m-RNA levels were elevated in leukocytes of patients with Rheumatoid arthritis (RA). Here, the association of toll-like receptor4 (TLR4) rs 141534085 and cytochrome P450 family 51 subfamily A member 1(CYP51A1) rs6 with tumor necrosis factor-α (TNF- α), rheumatoid factor (RF)- and Anti- cyclic citrullinated peptide (anti-CCP) antibody -positivity was investigated in almost the same subjects. Forty-six patients and 48 normal subjects were recruited in this study. The blood leucocytes TLR4 rs 141534085 and CYP51A1 rs6 -comprising DNA sequences were amplified by using tetra-primer amplification refractory mutation system polymerase chain reaction (T-ARMS-PCR) technique and the PCR products were checked by Sanger DNA sequencing method. ELISA method was used to determine plasma levels of TNF- α, anti-CCP antibody and RF positivity of plasma was evaluated through a latex agglutination test. The TNF- α level was significantly higher in the patient group than control subjects (p= 0.001). Moreover, we were not able to find any correlation between TNF-α levels and RF as well as anti-CCP antibodies when we used the K2/ Fisher's exact test and Pearson test respectively. Our DNA sequencing data revealed the following new mutations in TLR4 rs141534085 comprising regions: A>T in position 1050, T>A in position 1052, and C>A in position 1054; and for CYP51A1 rs6 encompassing region, the new mutations were; G>A in position 21680, the T nucleotide was inserted in position 21762 and the G nucleotide was inserted in position 21763, G>T in position 21764. The data of this study showed that both TLR4 rs141534085 and CYP51A1 rs6 related DNA regions should be considered as hotspot areas in RA pathogenicity. Moreover, these data indicated that, TNF- α did not alter the production of anti-CCP and RF pathogenic antibodies   in patients with long-term RA.

Thalassemia is a widespread disease affecting people across various ethnicities and regions. In comparison to previous studies conducted in different regions of Iran, such as those in Lorestan and Sistan-Baluchestan, this study highlights unique mutation patterns prevalent in the southwestern population, emphasizing the genetic heterogeneity in this region. The identification of common mutations of beta-thalassemia in various ethnic groups within the nation is regarded as a practical solution for thalassemia prevention and prenatal diagnosis.

In this retrospective observational study, the medical records of 545 patients with various types of beta-thalassemia (silent, minor, intermediate, and major), referred to the center at Baqaei 2 hospital over a 14-year period (2008–2022), were examined. The age range of patients spanned from a 2-month-old fetus to a 34-year-old individual. Their mutations and thalassemia types were determined and confirmed using molecular methods, including PCR-ARMS (polymerase chain reaction-amplification refractory mutation system) and sequencing. The results were analyzed using SPSS software.

The study examined 545 patients and identified 81 types of mutations. The most frequent mutations observed were CD36-37(-T)/N, IVSII-1/N, and IVS1-110(G>A). The study also noted population heterogeneity, reflected in the wide range of mutations found in the region. Among the patients, 6 had the silent form of beta-thalassemia, 488 had the minor form (464 patients and 24 fetuses), 9 had the intermediate form (8 patients and 1 fetus), and 42 had the major form (26 fetuses and 16 adults).

The identification of prevalent beta-thalassemia mutations facilitates disease control and prevention programs and is crucial for the identification of various beta-thalassemia gene mutations. This should be re-evaluated periodically. Observing a wide range of beta-thalassemia genotypes in the southwestern region of Iran suggests gene flow; thus, identifying these genotypes is instrumental in preventing and controlling the disease.

Veno-occlusive disease with immunodeficiency (VODI) syndrome is a rare genetic disorder characterized by immunesystem irregularities and a significant mortality rate, despite its infrequency. SP110, situated on chromosome 2q37.1,plays a pivotal role in VODI syndrome, and its association with tuberculosis has been extensively studied. Theidentification of SP110 mutations holds promise for accelerating the diagnosis and treatment of VODI syndrome, byproviding a comprehensive panel for diagnosis and potentially leading to targeted therapies. In this case study, weexamined a three-year-old girl born to a consanguineous union who was suspected of having an immunodeficiencydisorder. Whole-exome sequencing (WES) and clinical assessments were conducted to screen for and confirmpotentially pathogenic mutations. The detected mutation was further analyzed using bioinformatics tools to forecastits impact on protein structure. WES analysis revealed a novel deletion-insertion mutation, c.1181-1182delAGinsT,within SP110. Protein analysis indicated substantial structural modifications in the SP110 protein. This study identifieda novel deletion-insertion mutation as a potential contributor to VODI syndrome by affecting the functionality of theSP110 protein. By including various mutations associated with the SP110 gene, this study aimed to expedite diagnosisby creating a comprehensive panel for VODI syndrome.

There are more than 1100 different pathogenic variants in the phenylalanine hydroxylase (PAH) gene that are responsible for phenylketonuria (PKU) diseases, and the spectrum of these mutations varies in different ethnic groups. The aim of the present study was to identify the frequency of pathogenic variants in all 13 exons of the PAH gene among patients with PKU in Mazandaran and Golestan provinces in the north of Iran.

Forty unrelated PKU patients from Mazandaran and Golestan provinces were enrolled in the study. Genomic DNA was extracted from leukocytes using a Qiagen DNA extraction kit and polymerase chain reaction – restriction fragment length polymorphism (PCR‑RFLP), and Sanger sequencing methods were applied to detect the variants. In the case of new variants, the InterVar online tool (PMID: 28132688) was used to classify the variants.

Twenty‑one different pathogenic variants were observed among the 40 investigated patients. The c.106611G>A variant had the highest frequency (27.5%) in the region, and the c.168+5G>C, c.473G>A, and c.782 G>A variants were the other most frequent mutations with allelic frequencies of 7.5, 5, and 5%, respectively. Three novel pathogenic variants including c.773T>G, c.878 T>C, and c. 1245del variants were observed among the investigated patients.

The introduction of pathogenic variants in the PAH gene in each ethnic group provides valuable data regarding the understanding of the pathogenesis of the disease and can be helpful for prenatal diagnosis programs.

Phosphorylation reactions highlight the essential role of protein kinases in sperm motility. TSSK6 protein is thought to play a crucial role in this process. Indeed, sperm obtained from mice with the Tssk6-/- genotype are unable to carry out fertilization and exhibit decreased motility. This leads us to investigate the causes of asthenozoospermia by searching for polymorphisms in the TSSK6 gene. Therefore, the objective of this study is to identify polymorphisms in the TSSK6 gene in men affected by asthenozoospermia.

The methodology involved direct sequencing of spermatozoa DNA. Thirty ejaculates were analyzed, including 20 from asthenozoospermic men and 10 from normozoospermic men. Spermograms were performed according to WHO procedures. DNA extraction was carried out using the phenol/chloroform method followed by conventional PCR. The amplicons were sequenced using the Sanger method, and the sequences were analyzed with BioEdit software. The data were analyzed using Fisher and Mann-Whitney tests.

The results revealed mutations in the TSSK6 gene in both normospermic and asthenozoospermic ejaculates. The synonymous mutations c.690T>C (p.Tyr230Tyr) and c.372C>A (p.Arg124Arg) were the most frequent, occurring at rates of 50% and 33.33%, respectively. Analysis of the mutations using PolyPhen-2 indicated that all mutations observed in normozoospermic samples are benign and would not affect sperm quality. However, only the mutations described in asthenozoospermic samples are predicted to be damaging to the protein.

 In conclusion, mutations in the TSSK6 gene were observed in infertile men. Deleterious mutations in the TSSK6 protein are associated with asthenozoospermia