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Da Broi MG, Plaça JR, Silva WAD, Ferriani RA, Navarro PA. Screening of Variants in the Transcript Profile of Eutopic Endometrium from Infertile Women with Endometriosis during the Implantation Window. REVISTA BRASILEIRA DE GINECOLOGIA E OBSTETRÍCIA 2021; 43:457-466. [PMID: 34318471 PMCID: PMC10411168 DOI: 10.1055/s-0041-1730287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 02/12/2021] [Indexed: 10/20/2022] Open
Abstract
OBJECTIVE Abnormalities in the eutopic endometrium of women with endometriosis may be related to disease-associated infertility. Although previous RNA-sequencing analysis did not show differential expression in endometrial transcripts of endometriosis patients, other molecular alterations could impact protein synthesis and endometrial receptivity. Our aim was to screen for functional mutations in the transcripts of eutopic endometria of infertile women with endometriosis and controls during the implantation window. METHODS Data from RNA-Sequencing of endometrial biopsies collected during the implantation window from 17 patients (6 infertile women with endometriosis, 6 infertile controls, 5 fertile controls) were analyzed for variant discovery and identification of functional mutations. A targeted study of the alterations found was performed to understand the data into disease's context. RESULTS None of the variants identified was common to other samples within the same group, and no mutation was repeated among patients with endometriosis, infertile and fertile controls. In the endometriosis group, nine predicted deleterious mutations were identified, but only one was previously associated to a clinical condition with no endometrial impact. When crossing the mutated genes with the descriptors endometriosis and/or endometrium, the gene CMKLR1 was associated either with inflammatory response in endometriosis or with endometrial processes for pregnancy establishment. CONCLUSION Despite no pattern of mutation having been found, we ponder the small sample size and the analysis on RNA-sequencing data. Considering the purpose of the study of screening and the importance of the CMKLR1 gene on endometrial modulation, it could be a candidate gene for powered further studies evaluating mutations in eutopic endometria from endometriosis patients.
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Affiliation(s)
- Michele Gomes Da Broi
- Department of Gynecology and Obstetrics, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Jessica Rodrigues Plaça
- Department of Gynecology and Obstetrics, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Wilson Araújo da Silva
- Department of Gynecology and Obstetrics, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Rui Alberto Ferriani
- Department of Gynecology and Obstetrics, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Paula Andrea Navarro
- Department of Gynecology and Obstetrics, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
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Gorlov IP, Xia X, Tsavachidis S, Gorlova OY, Amos CI. Tumor somatic mutations also existing as germline polymorphisms may help to identify functional SNPs from genome-wide association studies. Carcinogenesis 2020; 41:1353-1362. [PMID: 32681635 DOI: 10.1093/carcin/bgaa077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/06/2020] [Accepted: 07/15/2020] [Indexed: 11/12/2022] Open
Abstract
We hypothesized that a joint analysis of cancer risk-associated single-nucleotide polymorphism (SNP) and somatic mutations in tumor samples can predict functional and potentially causal SNPs from GWASs. We used mutations reported in the Catalog of Somatic Mutations in Cancer (COSMIC). Confirmed somatic mutations were subdivided into two groups: (1) mutations reported as SNPs, which we call mutational/SNPs and (2) somatic mutations that are not reported as SNPs, which we call mutational/noSNPs. It is generally accepted that the number of times a somatic mutation is reported in COSMIC correlates with its selective advantage to tumors, with more frequently reported mutations being more functional and providing a stronger selective advantage to the tumor cell. We found that mutations reported ≥10 times in COSMIC-frequent mutational/SNPs (fmSNPs) are likely to be functional. We identified 12 cancer risk-associated SNPs reported in the Catalog of published GWASs at least 10 times as confirmed somatic mutations and therefore deemed to be functional. Additionally, we have identified 42 SNPs that are tightly linked (R2 ≥ 0.8) to SNPs reported in the Catalog of published GWASs as cancer risk associated and that are also reported as fmSNPs. As a result, 54 candidate functional/potentially causal cancer risk associated SNPs were identified. We found that fmSNPs are more likely to be located in evolutionarily conserved regions compared with cancer risk associated SNPs that are not fmSNPs. We also found that fmSNPs also underwent positive selection, which can explain why they exist as population polymorphisms.
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Affiliation(s)
- Ivan P Gorlov
- Department of Medicine, Baylor College of Medicine, One Baylor Plaza, Mailstop BCM451, Houston, TX, USA
| | - Xiangjun Xia
- Department of Medicine, Baylor College of Medicine, One Baylor Plaza, Mailstop BCM451, Houston, TX, USA
| | - Spiridon Tsavachidis
- Department of Medicine, Baylor College of Medicine, One Baylor Plaza, Mailstop BCM451, Houston, TX, USA
| | - Olga Y Gorlova
- Department of Medicine, Baylor College of Medicine, One Baylor Plaza, Mailstop BCM451, Houston, TX, USA
| | - Christopher I Amos
- Department of Medicine, Baylor College of Medicine, One Baylor Plaza, Mailstop BCM451, Houston, TX, USA
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Muniz JR, Szeto NWS, Frise R, Lee WH, Wang XS, Thöny B, Himmelreich N, Blau N, Hsiao KJ, Liu TT, Gileadi O, Oppermann U, Von Delft F, Yue WW, Tang NLS. Role of protein structure in variant annotation: structural insight of mutations causing 6-pyruvoyl-tetrahydropterin synthase deficiency. Pathology 2019; 51:274-280. [DOI: 10.1016/j.pathol.2018.11.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/13/2018] [Accepted: 11/19/2018] [Indexed: 10/27/2022]
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4
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Solomon O, Kunik V, Simon A, Kol N, Barel O, Lev A, Amariglio N, Somech R, Rechavi G, Eyal E. G23D: Online tool for mapping and visualization of genomic variants on 3D protein structures. BMC Genomics 2016; 17:681. [PMID: 27565432 PMCID: PMC5002099 DOI: 10.1186/s12864-016-3028-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 08/19/2016] [Indexed: 11/10/2022] Open
Abstract
Background Evaluation of the possible implications of genomic variants is an increasingly important task in the current high throughput sequencing era. Structural information however is still not routinely exploited during this evaluation process. The main reasons can be attributed to the partial structural coverage of the human proteome and the lack of tools which conveniently convert genomic positions, which are the frequent output of genomic pipelines, to proteins and structure coordinates. Results We present G23D, a tool for conversion of human genomic coordinates to protein coordinates and protein structures. G23D allows mapping of genomic positions/variants on evolutionary related (and not only identical) protein three dimensional (3D) structures as well as on theoretical models. By doing so it significantly extends the space of variants for which structural insight is feasible. To facilitate interpretation of the variant consequence, pathogenic variants, functional sites and polymorphism sites are displayed on protein sequence and structure diagrams alongside the input variants. G23D also provides modeling of the mutant structure, analysis of intra-protein contacts and instant access to functional predictions and predictions of thermo-stability changes. G23D is available at http://www.sheba-cancer.org.il/G23D. Conclusions G23D extends the fraction of variants for which structural analysis is applicable and provides better and faster accessibility for structural data to biologists and geneticists who routinely work with genomic information.
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Affiliation(s)
- Oz Solomon
- Cancer Research Center, Sheba Medical Center, Ramat-Gan, Israel.,The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Vered Kunik
- Cancer Research Center, Sheba Medical Center, Ramat-Gan, Israel
| | - Amos Simon
- Pediatric Immunology Service, Jeffrey Modell Foundation, Sheba Medical Center, Ramat-Gan, Israel
| | - Nitzan Kol
- Cancer Research Center, Sheba Medical Center, Ramat-Gan, Israel
| | - Ortal Barel
- Cancer Research Center, Sheba Medical Center, Ramat-Gan, Israel
| | - Atar Lev
- Pediatric Immunology Service, Jeffrey Modell Foundation, Sheba Medical Center, Ramat-Gan, Israel
| | - Ninette Amariglio
- Cancer Research Center, Sheba Medical Center, Ramat-Gan, Israel.,The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Raz Somech
- Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat-Gan, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Gidi Rechavi
- Cancer Research Center, Sheba Medical Center, Ramat-Gan, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eran Eyal
- Cancer Research Center, Sheba Medical Center, Ramat-Gan, Israel.
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Yamada KD, Nishi H, Nakata J, Kinoshita K. Structural characterization of single nucleotide variants at ligand binding sites and enzyme active sites of human proteins. Biophys Physicobiol 2016; 13:157-163. [PMID: 27924270 PMCID: PMC5042176 DOI: 10.2142/biophysico.13.0_157] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 04/10/2016] [Indexed: 12/15/2022] Open
Abstract
Functional sites on proteins play an important role in various molecular interactions and reactions between proteins and other molecules. Thus, mutations in functional sites can severely affect the overall phenotype. Progress of genome sequencing projects has yielded a wealth of information on single nucleotide variants (SNVs), especially those with less than 1% minor allele frequency (rare variants). To understand the functional influence of genetic variants at a protein level, we investigated the relationship between SNVs and protein functional sites in terms of minor allele frequency and the structural position of variants. As a result, we observed that SNVs were less abundant at ligand binding sites, which is consistent with a previous study on SNVs and protein interaction sites. Additionally, we found that non-rare variants tended to be located slightly apart from enzyme active sites. Examination of non-rare variants revealed that most of the mutations resulted in moderate changes of the physico-chemical properties of amino acids, suggesting the existence of functional constraints. In conclusion, this study shows that the mapping of genetic variants on protein structures could be a powerful approach to evaluate the functional impact of rare genetic variations.
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Affiliation(s)
- Kazunori D Yamada
- Graduate School of Information Sciences, Tohoku University, Miyagi 980-8597, Japan
| | - Hafumi Nishi
- Graduate School of Information Sciences, Tohoku University, Miyagi 980-8597, Japan
| | - Junichi Nakata
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi 980-8573, Japan
| | - Kengo Kinoshita
- Graduate School of Information Sciences, Tohoku University, Miyagi 980-8597, Japan; Tohoku Medical Megabank Organization, Tohoku University, Miyagi 980-8573, Japan; Institute of Development, Aging, and Cancer, Tohoku University, Miyagi 980-8575, Japan
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Mueller SC, Backes C, Gress A, Baumgarten N, Kalinina OV, Moll A, Kohlbacher O, Meese E, Keller A. BALL-SNPgp-from genetic variants toward computational diagnostics. Bioinformatics 2016; 32:1888-90. [PMID: 27153685 DOI: 10.1093/bioinformatics/btw084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 02/07/2016] [Indexed: 11/14/2022] Open
Abstract
UNLABELLED In medical research, it is crucial to understand the functional consequences of genetic alterations, for example, non-synonymous single nucleotide variants (nsSNVs). NsSNVs are known to be causative for several human diseases. However, the genetic basis of complex disorders such as diabetes or cancer comprises multiple factors. Methods to analyze putative synergetic effects of multiple such factors, however, are limited. Here, we concentrate on nsSNVs and present BALL-SNPgp, a tool for structural and functional characterization of nsSNVs, which is aimed to improve pathogenicity assessment in computational diagnostics. Based on annotated SNV data, BALL-SNPgp creates a three-dimensional visualization of the encoded protein, collects available information from different resources concerning disease relevance and other functional annotations, performs cluster analysis, predicts putative binding pockets and provides data on known interaction sites. AVAILABILITY AND IMPLEMENTATION BALL-SNPgp is based on the comprehensive C ++ framework Biochemical Algorithms Library (BALL) and its visualization front-end BALLView. Our tool is available at www.ccb.uni-saarland.de/BALL-SNPgp CONTACT ballsnp@milaman.cs.uni-saarland.de.
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Affiliation(s)
- Sabine C Mueller
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken 66123, Germany Department of Human Genetics, Saarland University, Homburg 66421, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken 66123, Germany
| | - Alexander Gress
- Max Planck Institute for Informatics, Saarland University, Saarbrücken 66123, Germany
| | - Nina Baumgarten
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken 66123, Germany
| | - Olga V Kalinina
- Max Planck Institute for Informatics, Saarland University, Saarbrücken 66123, Germany
| | - Andreas Moll
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken 66123, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center Department of Computer Science, University of Tuebingen, Tübingen 72076, Germany, Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, Homburg 66421, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken 66123, Germany
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Gress A, Ramensky V, Büch J, Keller A, Kalinina OV. StructMAn: annotation of single-nucleotide polymorphisms in the structural context. Nucleic Acids Res 2016; 44:W463-8. [PMID: 27150811 PMCID: PMC4987916 DOI: 10.1093/nar/gkw364] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 04/22/2016] [Indexed: 01/08/2023] Open
Abstract
The next generation sequencing technologies produce unprecedented amounts of data on the genetic sequence of individual organisms. These sequences carry a substantial amount of variation that may or may be not related to a phenotype. Phenotypically important part of this variation often comes in form of protein-sequence altering (non-synonymous) single nucleotide variants (nsSNVs). Here we present StructMAn, a Web-based tool for annotation of human and non-human nsSNVs in the structural context. StructMAn analyzes the spatial location of the amino acid residue corresponding to nsSNVs in the three-dimensional (3D) protein structure relative to other proteins, nucleic acids and low molecular-weight ligands. We make use of all experimentally available 3D structures of query proteins, and also, unlike other tools in the field, of structures of proteins with detectable sequence identity to them. This allows us to provide a structural context for around 20% of all nsSNVs in a typical human sequencing sample, for up to 60% of nsSNVs in genes related to human diseases and for around 35% of nsSNVs in a typical bacterial sample. Each nsSNV can be visualized and inspected by the user in the corresponding 3D structure of a protein or protein complex. The StructMAn server is available at http://structman.mpi-inf.mpg.de.
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Affiliation(s)
- Alexander Gress
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1 4, 66123 Saarbrücken, Germany Graduate School of Computer Science, Saarland University, Campus E1 3, 66123 Saarbrücken, Germany
| | - Vasily Ramensky
- Center for Neurobehavioral Genetics, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | - Joachim Büch
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1 4, 66123 Saarbrücken, Germany
| | - Andreas Keller
- Chair for Medical Bioinformatics, Saarland University, Campus E2 2, 66123 Saarbrücken, Germany
| | - Olga V Kalinina
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1 4, 66123 Saarbrücken, Germany
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Mueller SC, Sommer B, Backes C, Haas J, Meder B, Meese E, Keller A. From Single Variants to Protein Cascades: MULTISCALE MODELING OF SINGLE NUCLEOTIDE VARIANT SETS IN GENETIC DISORDERS. J Biol Chem 2016; 291:1582-1590. [PMID: 26601959 DOI: 10.1074/jbc.m115.695247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Indexed: 01/18/2023] Open
Abstract
Understanding the role of genetics in disease has become a central part of medical research. Non-synonymous single nucleotide variants (nsSNVs) in coding regions of human genes frequently lead to pathological phenotypes. Beyond single variations, the individual combination of nsSNVs may add to pathogenic processes. We developed a multiscale pipeline to systematically analyze the existence of quantitative effects of multiple nsSNVs and gene combinations in single individuals on pathogenicity. Based on this pipeline, we detected in a data set of 842 nsSNVs discovered in 76 genes related to cardiomyopathies, associated nsSNV combinations in seven genes present in at least 70% of all 639 patient samples, but not in a control cohort of healthy humans. Structural analyses of these revealed primarily an influence on the protein stability. For amino acid substitutions located at the protein surface, we generally observed a proximity to putative binding pockets. To computationally analyze cumulative effects and their impact, pathogenicity methods are currently being developed. Our approach supports this process, as shown on the example of a cardiac phenotype but can be likewise applied to other diseases such as cancer.
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Affiliation(s)
- Sabine C Mueller
- From the Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany,; Department of Human Genetics, Saarland University, 66421 Homburg, Germany,.
| | - Björn Sommer
- the Bio-/Medical Informatics Department, Faculty of Technology, Bielefeld University, 33501 Bielefeld, Germany,; Clayton School of Information Technology, Faculty of Information Technology, Monash University, Melbourne 3800, Australia
| | - Christina Backes
- From the Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Jan Haas
- the Department of Internal Medicine III, Heidelberg University, 69120 Heidelberg, Germany, and; the DZHK (German Centre for Cardiovascular Research), 69120 Heidelberg, Germany
| | - Benjamin Meder
- the Department of Internal Medicine III, Heidelberg University, 69120 Heidelberg, Germany, and; the DZHK (German Centre for Cardiovascular Research), 69120 Heidelberg, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Andreas Keller
- From the Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
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Sneha P, Doss CGP. Molecular Dynamics: New Frontier in Personalized Medicine. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2015; 102:181-224. [PMID: 26827606 DOI: 10.1016/bs.apcsb.2015.09.004] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The field of drug discovery has witnessed infinite development over the last decade with the demand for discovery of novel efficient lead compounds. Although the development of novel compounds in this field has seen large failure, a breakthrough in this area might be the establishment of personalized medicine. The trend of personalized medicine has shown stupendous growth being a hot topic after the successful completion of Human Genome Project and 1000 genomes pilot project. Genomic variant such as SNPs play a vital role with respect to inter individual's disease susceptibility and drug response. Hence, identification of such genetic variants has to be performed before administration of a drug. This process requires high-end techniques to understand the complexity of the molecules which might bring an insight to understand the compounds at their molecular level. To sustenance this, field of bioinformatics plays a crucial role in revealing the molecular mechanism of the mutation and thereby designing a drug for an individual in fast and affordable manner. High-end computational methods, such as molecular dynamics (MD) simulation has proved to be a constitutive approach to detecting the minor changes associated with an SNP for better understanding of the structural and functional relationship. The parameters used in molecular dynamic simulation elucidate different properties of a macromolecule, such as protein stability and flexibility. MD along with docking analysis can reveal the synergetic effect of an SNP in protein-ligand interaction and provides a foundation for designing a particular drug molecule for an individual. This compelling application of computational power and the advent of other technologies have paved a promising way toward personalized medicine. In this in-depth review, we tried to highlight the different wings of MD toward personalized medicine.
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Affiliation(s)
- P Sneha
- Medical Biotechnology Division, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, India
| | - C George Priya Doss
- Medical Biotechnology Division, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, India.
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