Molecular dynamic simulation and functional analysis of pathogenic PTEN mutations in glioblastoma

PTEN, a dual-phosphatase and scaffold protein, is one of the most commonly mutated tumour suppressor gene across various cancer types in human. The aim of this study therefore was to investigate the stability, structural and functional effects, and pathogenicity of 12 missense PTEN mutations (R15S, E18G, G36R, N49I, Y68H, I101T, C105F, D109N, V133I, C136Y, R173C and N276S) found by next generation sequencing of the PTEN gene in tissue samples obtained from glioblastoma patients. Computational tools and molecular dynamic simulation programs were used to identify the deleterious effects of these mutations. Furthermore, PTEN mRNA and protein expression levels were evaluated by qRT-PCR, Western Blot, and immunohistochemistry staining methods. Various computational tools predicted strong deleterious effects for the G36R, C105F, C136Y and N276S mutations. Molecular dynamic simulation revealed a significant decrease in protein stability for the Y68H and N276S mutations when compared with the wild type protein; whereas, C105F, D109N, V133I and R173C showed partial stability reduction. Significant residual fluctuations were observed in the R15S, N49I and C136Y mutations and radius of gyration graphs revealed the most compact structure for D109N and least for C136Y. In summary, our study is the first one to show the presence of PTEN E18G, N49I, D109N and N276S mutations in glioblastoma patients; where, D109N is neutral and N276S is a damaging and disease-associated mutation.Communicated by Ramaswamy H. Sarma.

[1]  S. Montazersaheb,et al.  Evaluation of exosomal non-coding RNAs in cancer using high-throughput sequencing , 2022, Journal of Translational Medicine.

[2]  B. Dehury,et al.  Molecular characterization and structural dynamics of Aquaporin1 from walking catfish in lipid bilayers. , 2021, International journal of biological macromolecules.

[3]  Yinglong Hou,et al.  MicroRNAs sequencing of plasma exosomes derived from patients with atrial fibrillation: miR-124-3p promotes cardiac fibroblast activation and proliferation by regulating AXIN1 , 2021, Journal of Physiology and Biochemistry.

[4]  Takeshi Takayasu,et al.  PTEN mutations predict benefit from tumor treating fields (TTFields) therapy in patients with recurrent glioblastoma , 2021, Journal of Neuro-Oncology.

[5]  R. Nussinov,et al.  The mechanism of full activation of tumor suppressor PTEN at the phosphoinositide-enriched membrane , 2021, bioRxiv.

[6]  Thomas M. Keane,et al.  Twelve years of SAMtools and BCFtools , 2020, GigaScience.

[7]  D. Nam,et al.  Mutation-specific non-canonical pathway of PTEN as a distinct therapeutic target for glioblastoma , 2020, Cell Death & Disease.

[8]  R. Verhaak,et al.  A validated integrated clinical and molecular glioblastoma long-term survival-predictive nomogram , 2020, Neuro-oncology advances.

[9]  Rohit Karn,et al.  Molecular dynamic study on PTEN frameshift mutations in breast cancer provide c2 domain as a potential biomarker , 2020, Journal of biomolecular structure & dynamics.

[10]  N. Batada,et al.  Is there a causal link between PTEN deficient tumors and immunosuppressive tumor microenvironment? , 2020, Journal of Translational Medicine.

[11]  Barry P. Young,et al.  Multi-model functionalization of disease-associated PTEN missense mutations identifies multiple molecular mechanisms underlying protein dysfunction , 2019, Nature Communications.

[12]  Kenneth A. Matreyek,et al.  The Impact of Genetic Variants on PTEN Molecular Functions and Cellular Phenotypes. , 2019, Cold Spring Harbor perspectives in medicine.

[13]  F. Cheng,et al.  Conformational Dynamics and Allosteric Regulation Landscapes of Germline PTEN Mutations Associated with Autism Compared to Those Associated with Cancer. , 2019, American journal of human genetics.

[14]  C. Eng,et al.  Dynamics and structural stability effects of germline PTEN mutations associated with cancer versus autism phenotypes , 2019, Journal of biomolecular structure & dynamics.

[15]  R. Rabadán,et al.  Immune and genomic correlates of response to anti-PD-1 immunotherapy in glioblastoma , 2019, Nature Medicine.

[16]  Elahe Naderali,et al.  Regulation and modulation of PTEN activity , 2018, Molecular Biology Reports.

[17]  P. Pandolfi,et al.  The functions and regulation of the PTEN tumour suppressor: new modes and prospects , 2018, Nature Reviews Molecular Cell Biology.

[18]  K. Choy,et al.  Identification of a PTEN mutation with reduced protein stability, phosphatase activity, and nuclear localization in Hong Kong patients with autistic features, neurodevelopmental delays, and macrocephaly , 2018, Autism research : official journal of the International Society for Autism Research.

[19]  R. Simon,et al.  Loss of PTEN-assisted G2/M checkpoint impedes homologous recombination repair and enhances radio-curability and PARP inhibitor treatment response in prostate cancer , 2018, Scientific Reports.

[20]  Taylor L. Mighell,et al.  A saturation mutagenesis approach to understanding PTEN lipid phosphatase activity and genotype-phenotypes relationships , 2018, bioRxiv.

[21]  Pixu Liu,et al.  PTEN deficiency sensitizes endometrioid endometrial cancer to compound PARP-PI3K inhibition but not PARP inhibition as monotherapy , 2017, Oncogene.

[22]  M. Born,et al.  Thyroid disease in children and adolescents with PTEN hamartoma tumor syndrome (PHTS) , 2018, European Journal of Pediatrics.

[23]  Andrea Gazzo,et al.  PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update , 2017, Nucleic Acids Res..

[24]  J. Briggs,et al.  Structural mutation analysis of PTEN and its genotype‐phenotype correlations in endometriosis and cancer , 2016, Proteins.

[25]  Itay Mayrose,et al.  ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules , 2016, Nucleic Acids Res..

[26]  F. Cunningham,et al.  The Ensembl Variant Effect Predictor , 2016, bioRxiv.

[27]  Helio A. Costa,et al.  Discovery and functional characterization of a neomorphic PTEN mutation , 2015, Proceedings of the National Academy of Sciences.

[28]  Yuxin Yin,et al.  PTEN regulates RPA1 and protects DNA replication forks , 2015, Cell Research.

[29]  Berk Hess,et al.  GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers , 2015 .

[30]  Víctor J. Cid,et al.  A Functional Dissection of PTEN N-Terminus: Implications in PTEN Subcellular Targeting and Tumor Suppressor Activity , 2015, PloS one.

[31]  G. Stock,et al.  Principal component analysis of molecular dynamics: on the use of Cartesian vs. internal coordinates. , 2014, The Journal of chemical physics.

[32]  M. Sansom,et al.  Interactions of Phosphatase and Tensin Homologue (PTEN) Proteins with Phosphatidylinositol Phosphates: Insights from Molecular Dynamics Simulations of PTEN and Voltage Sensitive Phosphatase , 2014, Biochemistry.

[33]  A. Vanderver,et al.  Characteristic brain magnetic resonance imaging pattern in patients with macrocephaly and PTEN mutations , 2014, American journal of medical genetics. Part A.

[34]  P. Devreotes,et al.  Mechanism of Human PTEN Localization Revealed by Heterologous Expression in Dictyostelium , 2013, Oncogene.

[35]  D. Haussler,et al.  The Somatic Genomic Landscape of Glioblastoma , 2013, Cell.

[36]  Jennifer S. Yu,et al.  Nuclear PTEN Controls DNA Repair and Sensitivity to Genotoxic Stress , 2013, Science.

[37]  C. George Priya Doss,et al.  A New Insight into Structural and Functional Impact of Single-Nucleotide Polymorphisms in PTEN Gene , 2013, Cell Biochemistry and Biophysics.

[38]  J. Miller,et al.  Predicting the Functional Effect of Amino Acid Substitutions and Indels , 2012, PloS one.

[39]  A. Ashworth,et al.  Treatment with olaparib in a patient with PTEN-deficient endometrioid endometrial cancer , 2011, Nature Reviews Clinical Oncology.

[40]  P. Bork,et al.  A method and server for predicting damaging missense mutations , 2010, Nature Methods.

[41]  Elena Papaleo,et al.  Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: the myoglobin case. , 2009, Journal of molecular graphics & modelling.

[42]  T. Akalın,et al.  Medulloblastoma: clinicopathologic evaluation of 42 pediatric cases , 2009, Child's Nervous System.

[43]  B. Rost,et al.  SNAP: predict effect of non-synonymous polymorphisms on function , 2007, Nucleic acids research.

[44]  Manfred J. Sippl,et al.  Thirty years of environmental health research--and growing. , 1996, Nucleic Acids Res..

[45]  P. Mischel,et al.  Loss of tumor suppressor PTEN function increases B7-H1 expression and immunoresistance in glioma , 2007, Nature Medicine.

[46]  Piero Fariselli,et al.  I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure , 2005, Nucleic Acids Res..

[47]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[48]  A. Elofsson,et al.  Can correct protein models be identified? , 2003, Protein science : a publication of the Protein Society.

[49]  K. Ichimura,et al.  Mutational profile of the PTEN gene in primary human astrocytic tumors and cultivated xenografts. , 1999, Journal of neuropathology and experimental neurology.

[50]  M. Wigler,et al.  The lipid phosphatase activity of PTEN is critical for its tumor supressor function. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[51]  T. Yeates,et al.  Verification of protein structures: Patterns of nonbonded atomic interactions , 1993, Protein science : a publication of the Protein Society.

[52]  Roland L. Dunbrack,et al.  Backbone-dependent rotamer library for proteins. Application to side-chain prediction. , 1993, Journal of molecular biology.