Predicting the Most Deleterious Missense Nonsynonymous Single-Nucleotide Polymorphisms of Hennekam Syndrome-Causing CCBE1 Gene, in Silico Analysis

Hennekam lymphangiectasia-lymphedema syndrome has been linked to single-nucleotide polymorphisms in the CCBE1 (collagen and calcium-binding EGF domains 1) gene. Several bioinformatics methods were used to find the most dangerous nsSNPs that could affect CCBE1 structure and function. Using state-of-the-art in silico tools, this study examined the most pathogenic nonsynonymous single-nucleotide polymorphisms (nsSNPs) that disrupt the CCBE1 protein and extracellular matrix remodeling and migration. Our results indicate that seven nsSNPs, rs115982879, rs149792489, rs374941368, rs121908254, rs149531418, rs121908251, and rs372499913, are deleterious in the CCBE1 gene, four (G330E, C102S, C174R, and G107D) of which are the highly deleterious, two of them (G330E and G107D) have never been seen reported in the context of Hennekam syndrome. Twelve missense SNPs, rs199902030, rs267605221, rs37517418, rs80008675, rs116596858, rs116675104, rs121908252, rs147974432, rs147681552, rs192224843, rs139059968, and rs148498685, are found to revert into stop codons. Structural homology-based methods and sequence homology-based tools revealed that 8.8% of the nsSNPs are pathogenic. SIFT, PolyPhen2, M-CAP, CADD, FATHMM-MKL, DANN, PANTHER, Mutation Taster, LRT, and SNAP2 had a significant score for identifying deleterious nsSNPs. The importance of rs374941368 and rs200149541 in the prediction of post-translation changes was highlighted because it impacts a possible phosphorylation site. Gene-gene interactions revealed CCBE1's association with other genes, showing its role in a number of pathways and coexpressions. The top 16 deleterious nsSNPs found in this research should be investigated further in the future while researching diseases caused CCBE1 gene specifically HS. The FT web server predicted amino acid residues involved in the ligand-binding site of the CCBE1 protein, and two of the substitutions (R167W and T153N) were found to be involved. These highly deleterious nsSNPs can be used as marker pathogenic variants in the mutational diagnosis of the HS syndrome, and this research also offers potential insights that will aid in the development of precision medicines. CCBE1 proteins from Hennekam syndrome patients should be tested in animal models for this purpose. © 2021 Khyber Shinwari et al.The work was carried out within the framework of state research at the Institute of Immunology and Physiology of the Ural Branch of the Russian Academy of Sciences, project number AAAA-A21-121012090091-6

Novel Disease-Associated Missense Single-Nucleotide Polymorphisms Variants Predication by Algorithms Tools and Molecular Dynamics Simulation of Human TCIRG1 Gene Causing Congenital Neutropenia and Osteopetrosis

T Cell Immune Regulator 1, ATPase H + Transporting V0 Subunit A3 (TCIRG1 gene provides instructions for making one part, the a3 subunit, of a large protein complex known as a vacuolar H + -ATPase (V-ATPase). V-ATPases are a group of similar complexes that act as pumps to move positively charged hydrogen atoms (protons) across membranes. Single amino acid changes in highly conserved areas of the TCIRG1 protein have been linked to autosomal recessive osteopetrosis and severe congenital neutropenia. We used multiple computational approaches to classify disease-prone single nucleotide polymorphisms (SNPs) in TCIRG1. We used molecular dynamics analysis to identify the deleterious nsSNPs, build mutant protein structures, and assess the impact of mutation. Our results show that fifteen nsSNPs (rs199902030, rs200149541, rs372499913, rs267605221, rs374941368, rs375717418, rs80008675, rs149792489, rs116675104, rs121908250, rs121908251, rs121908251, rs149792489 and rs116675104) variants are likely to be highly deleterious mutations as by incorporating them into wild protein they destabilize the wild protein structure and function. They are also located in the V-ATPase I domain, which may destabilize the structure and impair TCIRG1 protein activation, as well as reduce its ATPase effectiveness. These mutants have not yet been identified in patients suffering from CN and osteopetrosis while (G405R, R444L, and D517N) reported in our study are already associated with osteopetrosis. Mutation V52L reported in our study was identified in a patient suspected for CN. Finally, these mutants can help to further understand the broad pool of illness susceptibilities associated with TCIRG1 catalytic kinase domain activation and aid in the development of an effective treatment for associated diseases. Copyright © 2022 Shinwari, Rehman, Liu, Bolkov, Tuzankina and Chereshnev.Ural Branch, Russian Academy of Sciences, UB RAS: AAAA-A21-121012090091-6The work was carried out within the framework of research at the Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Sciences, project number AAAA-A21-121012090091-6

Defining muscle-invasive bladder cancer immunotypes by introducing tumor mutation burden, CD8+ T cells, and molecular subtypes

Immunotherapy, especially anti-PD-1, is becoming a pillar of modern muscle-invasive bladder cancer (MIBC) treatment. However, the objective response rates (ORR) are relatively low due to the lack of precise biomarkers to select patients. Herein, the molecular subtype, tumor mutation burden (TMB), and CD8+ T cells were calculated by the gene expression and mutation profiles of MIBC patients. MIBC immunotypes were constructed using clustering analysis based on tumor mutation burden, CD8+ T cells, and molecular subtypes. Mutated genes, enriched functional KEGG pathways and GO terms, and co-expressed network-specific hub genes have been identified. We demonstrated that ORR of immunotype A patients identified by molecular subtype, CD8+ T cells, and TMB is about 36% predictable. PIK3CA, RB1, FGFR3, KMT2C, MACF1, RYR2, and EP300 are differentially mutated among three immunotypes. Pathways such as ECM-receptor interaction, PI3K-Akt signaling pathway, and TGF-beta signaling pathway are top-ranked in enrichment analysis. Low expression of ACTA2 was associated with the MIBC survival benefit. The current study constructs a model that could identify suitable MIBC patients for immunotherapy, and it is an important step forward to the personalized treatment of bladder cancers. © 2021, The Author(s).This study was funded by the Act 211 Government of the Russian Federation (No.02.A03.21.0006) and the IIP UB RAS project (No.AAAA-A18–118020590108-7)

In Silico Analysis Revealed Five Novel High-Risk Single-Nucleotide Polymorphisms (rs200384291, rs201163886, rs193141883, rs201139487, and rs201723157) in ELANE Gene Causing Autosomal Dominant Severe Congenital Neutropenia 1 and Cyclic Hematopoiesis

Single-nucleotide polymorphisms in the ELANE (Elastase, Neutrophil Expressed) gene are associated with severe congenital neutropenia, while the ELANE gene provides instructions for making a protein called neutrophil elastase. We identified disease susceptibility single-nucleotide polymorphisms (SNPs) in the ELANE gene using several computational tools. We used cutting-edge computational techniques to investigate the effects of ELANE mutations on the sequence and structure of the protein. Our study suggested that eight nsSNPs (rs28931611, rs57246956, rs137854448, rs193141883, rs201723157, rs201139487, rs137854451, and rs200384291) are the most deleterious in ELANE gene and disturb protein structure and function. The mutants F218L, R34W, G203S, R193W, and T175M have not yet been identified in patients suffering from SCN and cyclic hematopoiesis, while C71Y, P139R, C151Y, G214R, and G203C reported in our study are already associated with both of the disorders. These mutations are shown to destabilize structure and disrupt ELANE protein activation, splicing, and folding and might diminish trypsin-like serine protease efficiency. Prediction of posttranslation modifications highlighted the significance of deleterious nsSNPs because some of nsSNPs affect potential phosphorylation sites. Gene-gene interactions showed the relation of ELANE with other genes depicting its importance in numerous pathways and coexpressions. We identified the deleterious nsSNPs, constructed mutant protein structures, and evaluated the impact of mutation by employing molecular docking. This research sheds light on how ELANE failure upon mutation results in disease progression, including congenital neutropenia, and validation of these novel predicted nsSNPs is required through the wet lab. © 2022 Khyber Shinwari et al.Ural Branch, Russian Academy of Sciences, UB RAS: AAAAA-A21- 121012090091-6The work was carried out in accordance with the state order of the Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Sciences, AAAAA-A21- 121012090091-6

Transient ischemic attack in childhren and young: risk factors and therapy approaches

The article summarizes the risk factors identified in 70 patients with Transient Ischemic Attack (TIA), aged 0-18 years. Adolescence was showed as the most frequent age debut for TIA. Genetically determined procoagulant status, dyslipidemia, hyperhomocysteinemia and cerebrovascular abnormalities were the most likely etiopathogenetic factor in this age period, but their verification has occurred only after the fact of TIA. The authors found the most probable thrombophylic gene-gene combinations which increase the risk of TIA in two or more times. The proposed strategy of active secondary prevention with aspirin and clopidogrel reduced the risk of recurrent TIA 2-4 times.В статье обобщены сведения о факторах риска, выявленных у 70 пациентов с диагностированной транзиторной ишемической атакой (ТИА) в возрасте 0-18 лет. Показан подростковый возраст как наиболее частый для дебюта ТИА. Генетически детерминированная прокоагулянтная настроенность, дислипидемии, гипергомоцистеинемия, а также аномалии строения цереброваскулярного русла выступили в качестве наиболее вероятного этиопатогенетического фактора в этом возрастном периоде, однако верификация их произошла только после факта ТИА. Авторы показали наиболее вероятные тромбофильные ген-генные сочетания, носительство которых повышало вероятность ТИА в два и более раз. Предложенная тактика активной вторичной профилактики с использованием препаратов аспирина (кардиомагнил) и клопидогреля снижала риск повторного ТИА в 2-4 раза

CYTOKINE REGULATION OF REGENERATIVE PROCESSES IN PANCREATIC GLAND IN ALLOXAN-INDUCED DIABETIC RATS, AND IT CORRECTION BY 1,3,4-THIADIAZINE COMPOSITION AND LIPOIC ACID

A comprehensive comparative evaluation of the ability of L-17 compound (2-morpholino-5- phenyl-1,3,4-thiadiazine) and antioxidant lipoic acid (LA) to correct blood cytokine levels, metabolic disorders and morphological alterations in pancreas in alloxan-induced diabetes was performed for the first time, using an experimental in vivo model. All the tested compounds have been found to correct hyperglycemia and decreased accumulation of glycated blood proteins. The tested L-17 compound belongs to the 1,3,4-thiadiazine series and is able to correct metabolic disorders occurring in alloxan-induced diabetes comparable to activity of LA antioxidant. However, L-17 reduces the cytokine levels to the values of intact animals, that preventing development of systemic inflammatory response which causes damage of target organs in diabetes mellitus