In Silico Analysis of Missense Mutations as a First Step in Functional Studies: Examples from Two Sphingolipidoses

Case report: A single novel calpain 3 gene variant associated with mild myopathy

Recessively inherited limb-girdle muscular dystrophy type 1, caused by mutations in the calpain 3 gene, is the most common limb-girdle muscular dystrophy worldwide. Recently, cases of autosomal dominant calpainopathy have been described. A man was referred to our neurological outpatient clinic at the age of 54 for persistent hyperCKemia (>1000 U/l) associated with muscle fatigue and myalgia. Clinical examination revealed mild proximal weakness in the lower limbs. His brother exhibited a moderate increase in serum creatine kinase levels (up to 2000 U/l) without other signs of myopathy. Their father experienced slowly progressive lower limb weakness after the age of 50. The calpain 3 variant c.1478G>A (p.Arg493Gln) in the heterozygous state was identified in both brothers. In silico modeling studies predict that this substitution may disrupt protein folding. This represents the first description of the heterozygous p.Arg493Gln calpain 3 variant as a potential cause of mild calpainopathy.

Evaluation of Pathogenicity and Structural Alterations for the Mutations Identified in the Conserved Region of the C-Terminal Kinase Domain of Human-Ribosomal S6 Kinase 1

Human-ribosomal s6 kinase 1 (h-RSK1) is an effector kinase of the Ras/MAPK signaling pathway, which is involved in the regulation of the cell cycle, proliferation, and survival. RSKs comprise two functionally distinct kinase domains at the N-terminal (NTKD) and C-terminal (CTKD) separated by a linker region. The mutations in RSK1 may have the potential to provide an extra benefit to the cancer cell to proliferate, migrate, and survive. The present study focuses on evaluating the structural basis for the missense mutations identified at the C-terminal kinase domain of human-RSK1. A total of 139 mutations reported on RSK1 were retrieved from cBioPortal, where 62 were located at the CTKD region. Furthermore, 10 missense mutations Arg434Pro, Thr701Met, Ala704Thr, Arg725Trp, Arg726Gln, His533Asn, Pro613Leu, Ser720Cys, Arg725Gln, and Ser732Phe were predicted to be deleterious using in silico tools. To our observation, these mutations are located in the evolutionarily conserved region of RSK1 and shown to alter the inter- and intramolecular interactions and also the conformational stability of RSK1-CTKD. The molecular dynamics (MD) simulation study further revealed that the five mutations Arg434Pro, Thr701Met, Ala704Thr, Arg725Trp, and Arg726Gln showed maximum structural alterations in RSK1-CTKD. Thus, based on the in silico and MD simulation analysis, it can be concluded that the reported mutations may serve as potential candidates for further functional studies.

Metabolite Profiling of the Environmental-Controlled Growth of Marsilea crenata Presl. and Its In Vitro and In Silico Antineuroinflammatory Properties

This study was aimed to evaluate the metabolite contents and antineuroinflammatory potential of Marsilea crenata Presl. grown under a controlled environmental condition. The antineuroinflammatory test has been carried out in vitro using ethanolic extract of M. crenata leaves on HMC3 microglia cells. An in silico approach was applied to predict the active compounds of the extract. The HMC3 microglia cells were induced with IFNγ to create prolonged inflammatory conditions and then treated with 96% ethanolic extract of the M. crenata leaves of 62.5, 125, and 250 μg/mL. The expression of MHC II was analyzed using the ICC method with the CLSM instrument. Metabolites of the extract were profiled using UPLC-QToF-MS/MS instrument and MassLynx 4.1 software. In silico evaluation was conducted with molecular docking on 3OLS protein using PyRx 0.8 software, and physicochemical properties of the compounds were analyzed using SwissADME webtool. The ethanolic extract of M. crenata leaves could reduce the MHC II expression in HMC3 microglia cells in all concentrations with the values 97.458, 139.574, and 82.128 AU. The result of metabolite profiling found 79 compounds in the extract. In silico evaluation showed that 19 compounds gave agonist interaction toward 3OLS, and three met all parameters of physicochemical analysis. The ethanolic extract of the environmental-controlled growth of M. crenata leaves antineuroinflammatory activity on HMC3 microglia cells. The extract was predicted to contain some phytoestrogen compounds which act as 3OLS agonists.

Screening of OTULIN gene mutation with targeted next generation sequencing in Turkish populations and in silico analysis of these mutations

BACKGROUND

OTULIN-related autoinflammatory syndrome (ORAS) is an autosomal recessive disease characterized by systemic inflammation, recurrent fever. Due to limited knowledge about the OTULIN DNA variants that cause ORAS, the diagnosis and treatment of this disease is difficult. In this study, we aim to identify OTULIN DNA variants responsible for the genetic pathology of ORAS and observe the effects of these variants on the OTULIN protein structure and the function with different bioinformatics approaches.

METHODS

The present study included 3230 individuals with the suspicion of an autoinflammatory disease who were referred to Ege University Children's Hospital Molecular Medicine Laboratory. OTULIN variants were detected using a panel consisting of 37 different autoinflammatory diseases (AID) genes via targeted Next-Generation Sequencing.

RESULTS

As a result of the study, DNA variants associated with various AID were detected in 65% of the individuals to whom the panel was applied. Among these variants, only three different OTULIN variants (p.Val82Ile, p.Gln115His and p.Leu131_Arg132insLeuCysThrGlu) were detected. The pathogenic effects of the variants detected in the OTULIN gene were determined by using Polyphen2 as "Probably Pathogenic" for the p.Val82Ile and "benign" for the p.Gln115His. At the same time, the effects of these variants on the structure and function of the OTULIN protein were investigated by in silico approaches. Both variants reduce protein stability and binding affinity.

CONCLUSION

The results of the current study suggest that the evaluation of OTULIN variants with in silico approaches will contribute to the development of personalized treatments by diagnosing the disease specific to the variant.

The Impact of Mutations on the Pathogenic and Antigenic Activity of SARS-CoV-2 during the First Wave of the COVID-19 Pandemic: A Comprehensive Immunoinformatics Analysis

An in-depth analysis of first-wave SARS-CoV-2 genome is required to identify various mutations that significantly affect viral fitness. In the present study, we performed a comprehensive in silico mutational analysis of 3C-like protease (3CLpro), RNA-dependent RNA polymerase (RdRp), and spike (S) proteins with the aim of gaining important insights into first-wave virus mutations and their functional and structural impact on SARS-CoV-2 proteins. Our integrated analysis gathered 6000 SARS-CoV-2 sequences and identified 92 mutations in S, 37 in RdRp, and 11 in 3CLpro regions. The impact of these mutations was also investigated using various in silico approaches. Among these, 32 mutations in S, 15 in RdRp, and 3 in 3CLpro proteins were found to be deleterious in nature and could alter the structural and functional behavior of the encoded proteins. The D614G mutation in spike and the P323Lmutation in RdRp are the globally dominant variants with a high frequency. Most of the identified mutations were also found in the binding moiety of the viral proteins which determine their critical involvement in host-pathogen interactions and may represent drug targets. Furthermore, potential CD4+ and CD8+ T cell epitopes were predicted, and their overlap with genetic variations was explored. This study also highlights several hot spots in which HLA and drug selective pressure overlap. The findings of the current study may allow a better understanding of COVID-19 diagnostics, vaccines, and therapeutics.

Positional cloning and comprehensive mutation analysis of a Japanese family with lithium-responsive bipolar disorder identifies a novel DOCK5 mutation

Bipolar disorder (BD) is a severe psychiatric disorder characterized by the recurrence of depressive and manic episodes. Its heritability is high, and many linkage and association studies have been performed. Although various linkage regions and candidate genes have been reported, few have shown sufficient reproducibility, and none have identified the pathogenic genes based on the results of the linkage analysis. To find functional variants that are expected to be rare and have strong genetic effects, we recruited ten healthy individuals, two individuals with unknown status, and six patients with BD or recurrent major depressive disorder (MDD) from a Japanese family consisting of 21 members. We performed a genome-wide linkage analysis using a 100K single-nucleotide polymorphism (SNP) array and microsatellite markers to narrow linkage regions within this family. Subsequently, we performed whole-exome sequencing for two patients with BD to identify genetic mutations in the narrowed linkage regions. Then, we performed co-segregation analysis for DNA variants obtained from the results of the exome sequencing. Finally, we identified a rare heterozygous mutation in exon 31 of DOCK5 (c.3170A>G, p.E1057G). Convergent functional genomics analysis revealed that DOCK5 was listed as one of the biomarkers for mood state and suicidality. Although DOCK5 is still a functionally unknown gene, our findings highlight the possibility of a pathological relationship between BD and DOCK5.

Assessing Lysosomal Disorders in the NGS Era: Identification of Novel Rare Variants

Lysosomal storage diseases (LSDs) are a heterogeneous group of genetic disorders with variable degrees of severity and a broad phenotypic spectrum, which may overlap with a number of other conditions. While individually rare, as a group LSDs affect a significant number of patients, placing an important burden on affected individuals and their families but also on national health care systems worldwide. Here, we present our results on the use of an in-house customized next-generation sequencing (NGS) panel of genes related to lysosome function as a first-line molecular test for the diagnosis of LSDs. Ultimately, our goal is to provide a fast and effective tool to screen for virtually all LSDs in a single run, thus contributing to decrease the diagnostic odyssey, accelerating the time to diagnosis. Our study enrolled a group of 23 patients with variable degrees of clinical and/or biochemical suspicion of LSD. Briefly, NGS analysis data workflow, followed by segregation analysis allowed the characterization of approximately 41% of the analyzed patients and the identification of 10 different pathogenic variants, underlying nine LSDs. Importantly, four of those variants were novel, and, when applicable, their effect over protein structure was evaluated through in silico analysis. One of the novel pathogenic variants was identified in the GM2A gene, which is associated with an ultra-rare (or misdiagnosed) LSD, the AB variant of GM2 Gangliosidosis. Overall, this case series highlights not only the major advantages of NGS-based diagnostic approaches but also, to some extent, its limitations ultimately promoting a reflection on the role of targeted panels as a primary tool for the prompt characterization of LSD patients.

Is the alpha-galactosidase A variant p.Asp313Tyr (p.D313Y) pathogenic for Fabry disease? A systematic review

The identification of pathogenic GLA variants plays a central role in the establishment of a definite Fabry disease (FD) diagnosis. We aimed to review and interpret the published data on the p.Asp313Tyr (p.D313Y) variant pathogenicity and clinical relevance. We performed a systematic review of peer-reviewed publications and case-reports on individuals and populations harbouring the p.Asp313Tyr variant. Overall, 35 studies were included in this review. We collected data regarding the clinical manifestations, alpha-galactosidase A enzyme activity, levels of the biomarkers globotriaosylceramide (Gb₃ ) and sphingosine-globotriaosylceramide (lyso-Gb₃ ) and histological findings of p.Asp313Tyr carriers. The prevalence of p.Asp313Tyr in populations at risk for FD (kidney, heart, neurologic disorders, or symptomatic populations) was calculated. We found high residual enzyme activity, low frequency of clinical features specific for FD, non-elevated lysoGb₃ /Gb₃ concentrations and lack of intracellular Gb₃ accumulation in biopsies in the p.Asp313Tyr carriers. The prevalence of the variant in populations at risk for FD was comparable to the reported frequency in the general population. A possible higher frequency was only observed in neurologic disorders. p.Asp313Tyr can be classified as neutral or variant of unknown significance. Further investigations will be helpful to clarify a possible association between the variant and manifestations in the brain vessels.