Effects Of Nonsynonymous Mutations Research Articles

DNA ligase I variants fail in the ligation of mutagenic repair intermediates with mismatches and oxidative DNA damage.

DNA ligase I (LIG1) joins DNA strand breaks during DNA replication and repair transactions and contributes to genome integrity. The mutations (P529L, E566K, R641L and R771W) in LIG1 gene are described in patients with LIG1-deficiency syndrome that exhibit immunodeficiency. LIG1 senses 3'-DNA ends with a mismatch or oxidative DNA base inserted by a repair DNA polymerase. However, the ligation efficiency of the LIG1 variants for DNA polymerase-promoted mutagenesis products with 3'-DNA mismatches or 8-oxo-2'-deoxyguanosine (8-oxodG) remains undefined. Here, we report that R641L and R771W fail in the ligation of nicked DNA with 3'-8-oxodG, leading to an accumulation of 5'-AMP-DNA intermediates in vitro. Moreover, we found that the presence of all possible 12 non-canonical base pairs variously impacts the ligation efficiency by P529L and R771W depending on the architecture at the DNA end, whereas E566K exhibits no activity against all substrates tested. Our results contribute to the understanding of the substrate specificity and mismatch discrimination of LIG1 for mutagenic repair intermediates and the effect of non-synonymous mutations on ligase fidelity.

The pathogenicity, structural and functional exploration of human HMGB1 single nucleotide polymorphisms using in silico study

The human HMGB1 gene mutations have a major impact on several immune-related diseases and cancer. The detrimental effect of non-synonymous mutations of HMGB1 has not been investigated yet, hence the present study aims to examine single nucleotide polymorphisms and their implications on the structure-function of human HMGB1. The multifaceted HMGB1 protein acts as pleiotropic cytokine and regulates essential genes for coordinated cellular functions. The mutational effect on HMGB1 was analyzed by sequence-based homology methods, supervised learning methods, and structure-based methods. The study identified 58 non-synonymous mutations in human HMGB1, out of which only 2 mutations; R10T (rs61742222) and F103C (rs61733675) were classified as the SNPs with highest deleterious and disease-causing mutants. The effect of these mutations in structure of HMGB1 was scrutinized and the R10T mutant found to have a distinct structural behaviour in the B-box domain. In addition, R10T mutant predicted that it affects the MoRF function of HMGB1 and it could disrupt the DNA binding or/and protein partner interaction activity by HMGB1. F103C mutation takes place at the TLR binding and cytokine inducing region of HMGB1, hence it could affect the protein binding activity which involves in many cellular signaling. The study identified potent mutations R10T (a cancer-causing somatic mutation) and F103C (a novel mutation) and these mutations either directly or indirectly hinder DNA binding activity and TLR and cytokine binding of HMGB1. These findings will help in understanding the molecular basis of these promising mutations and functional role of human HMGB1 in cancer and immunological diseases.AbbreviationsAGERAdvanced glycosylation end product-specific receptorCXCLChemokine (C-X-C motif) liganddbSNPThe single nucleotide polymorphism databaseHMGB1High mobility group box 1LINCSLINear Constraint SolverMDSMolecular dynamics simulationMoRFMolecular recognition featuresNPTNumber of particle, Pressure and TemperatureNVTNumber of particle, Volume and TemperaturensSNPNon-synonymous SNPPBCPartial boundary conditionPCAPrincipal component analysisPMEPartial mesh EwaldRMSDRoot mean square deviationRMSFRoot mean square fluctuationSNPSingle nucleotide polymorphismSPCSingle-point chargeTLRToll-like receptorUTRUn-translated RegionCommunicated by Ramaswamy H. Sarma

Assessment of epigenetic alterations and in silico analysis of mutation affecting PTEN expression among Indian cervical cancer patients.

Genetic and epigenetic anomalies accountable for genetic dysregulation are the most common aberrations that determine the underlying heterogeneity of the tumor cells. Currently, phosphatase and tensin homolog (PTEN) incongruity has emerged as potent and persuasive malfunctioning in varied human malignancies. In this study, we have analysed the promoter hypermethylation and expression status of PTEN. We identified different mutations in the exonic region of PTEN. Functional consequences of these mutations were explored using in silico techniques. Promoter hypermethylation of PTEN was detected using methylation-specific polymerase chain reaction (MS-PCR), expression analysis was performed with immunohistochemistry (IHC) and mutation by direct sequencing in a total of 168 uterine cervix tumor cases. The findings were statistically correlated with the clinical parameters. In addition, the effect of nonsynonymous mutations was studied with molecular dynamics simulations. PTEN promoter hypermethylation (45.8%) was found to be significantly associated with the of PTEN loss (57.14%, P < 0.0001). Tumor stages, tumor size, lymph node (LN) were found to be significantly correlated with both PTEN promoter hypermethylation and PTEN loss. Histological grade, however, showed a significant association with only PTEN loss. In total, 11.76% of tumors exhibited mutations in exon 5 and 7, out of which E150K of exon 5 showed the highest deviations in the crystal structure of PTEN by in silico analysis. This study provides valuable insights into oncology and paves the path in the development of efficient biomarker and/or imperative therapeutic tool for cervical cancer treatment.

Abstract 1322A: Computational study of the effects of non-synonymous mutations in human UBE3A gene present in virus-associated cancers

Abstract UBE3A gene encodes the ubiquitin ligase E6 associated protein (E6AP), an enzyme that catalyzes the high-risk human papilloma virus (HPV) E6-mediated ubiquitination of p53. Such modification in p53 contributes to the neoplastic progression of cells infected by HPV-16/18 that leads to cervical cancer (CC). The hijacking of E6AP also occurs by Hepatitis C virus (HCV) that targets Rb protein thus conducting to hepatocellular carcinoma (HCC). We hypothesized that certain non-synonymous (missense) mutations of E6AP drives to elevated degradation rates of either p53 or Rb by increasing its enzymatic activity. This study aimed to predict changes in: (i) functional activity in E6AP mutants, and (b) E6AP affinity to viral oncoproteins and p53/Rb. A subset of three virus-associated cancers including cervical carcinoma (CC), hepatocellular carcinoma (HCC) and oral squamous carcinoma (OSC) were analyzed. The Cancer Genome Atlas (TCGA) dataset as well as Biomuta were mined and missense mutations in human UBE3A gene were retrieved. To explore the impairment of protein function and stability across the UBE3A gene mutants, machine learning approaches (i.e. Polyphen, I-Mutant 3.0, Panther and Provean) and NetSurfP were applied. The 3D structures of E6AP variants were modelled and docking simulations with viral oncoproteins and p53/Rb were performed using PyDock. Our results showed 22 mutations in UBE3A gene that were present across CC, HCC and OSC, with most of variants (60%) appearing in HCC. UBE3A variants were different across the three tumor types analyzed. Seven of 22 UBE3A variants were predicted damaging or deleterious substitutions. Five damaging mutations affected the HECT domain responsible for the enzyme activity. Such corresponded to E743K and P850A, existing in CC, as well as M589L, E754K, and Q576*, found in HCC. Two predicted damaging mutations were located within the HCV binding site including G492V (found in CC) as well as F477C (present in OSC). No mutation involved the highly conserved LXXL domain implicated in E6 binding or the E6AP trimerization residues. The predicted E6AP-E6 complexes revealed that LXXLL domain in E6AP participates in E6 binding, both in wild-type and mutants. Interestingly, E6AP E743K mutant showed increased complex stability in comparison with wild-type. In conclusion, most of E6AP mutations (68%) existing in CC, HCC and OSC are likely to be neutral whereas some others (32%) are potentially damaging variants and likely to increase E6AP activity. E6AP-dependent ubiquitylation of p53 represents an important opportunity to discover novel entities that inhibit protein-protein interactions thus avoiding p53 degradation. Citation Format: Claudia Machicado, Maria Pia Soto. Computational study of the effects of non-synonymous mutations in human UBE3A gene present in virus-associated cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1322A.

Statistical Inference of Selection and Divergence from a Time-Dependent Poisson Random Field Model

We apply a recently developed time-dependent Poisson random field model to aligned DNA sequences from two related biological species to estimate selection coefficients and divergence time. We use Markov chain Monte Carlo methods to estimate species divergence time and selection coefficients for each locus. The model assumes that the selective effects of non-synonymous mutations are normally distributed across genetic loci but constant within loci, and synonymous mutations are selectively neutral. In contrast with previous models, we do not assume that the individual species are at population equilibrium after divergence. Using a data set of 91 genes in two Drosophila species, D. melanogaster and D. simulans, we estimate the species divergence time (or 1.68 million years, assuming the haploid effective population size years) and a mean selection coefficient per generation . Although the average selection coefficient is positive, the magnitude of the selection is quite small. Results from numerical simulations are also presented as an accuracy check for the time-dependent model.