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Skorodumova LO, Davydenko KA, Filatova AY, Skoblov MY, Kulemin NA, Khadzhieva MB, Zakharova ES, Gordeeva VD, Smetanina NS, Fedyushkina IV, Anastasevich LA, Larin SS. Splice-site variant in the RPS7 5'-UTR leads to a decrease in the mRNA level and development of Diamond-Blackfan anemia. Clin Genet 2023; 103:93-96. [PMID: 36057918 DOI: 10.1111/cge.14221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/11/2022] [Accepted: 08/23/2022] [Indexed: 12/13/2022]
Abstract
Diamond-Blackfan anemia (DBA) is an inherited bone marrow failure syndrome characterized by erythroid aplasia. Pathogenic variants in ribosomal protein (RP) genes, GATA1, TSR2, and EPO, are considered to be the etiology of DBA. Variants in 5'-untranslated regions (UTRs) of these genes are poorly studied and can complicate the variant interpretation. We investigated the functional consequences NM_001011.4:c.-19 + 1G > T variant in the donor splice-site of the RPS7 5'-UTR. This variant was found in a family where two sons with DBA were carriers. Father, who also had this variant, developed myelodysplastic syndrome, which caused his death. Search for candidate causal variants and copy number variations in DBA-associated genes left RPS7 variant as the best candidate. Trio whole exome sequencing analysis revealed no pathogenic variants in other genes. Functional analysis using luciferase expression system revealed that this variant leads to disruption of splicing. Also, a decrease in the levels of mRNA and protein expression was detected. In conclusion, the established consequences of 5'-UTR splice-site variant c.-19 + 1G > T in the RPS7 gene provide evidence that it is likely pathogenic.
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Affiliation(s)
- Liubov O Skorodumova
- Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation.,Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russian Federation
| | | | | | | | - Nikolay A Kulemin
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russian Federation
| | - Maryam B Khadzhieva
- Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation.,Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russian Federation
| | - Elena S Zakharova
- Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Veronika D Gordeeva
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russian Federation
| | - Nataliya S Smetanina
- Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Irina V Fedyushkina
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russian Federation
| | - Lyudmila A Anastasevich
- Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Sergey S Larin
- Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
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Marakhonov AV, Přechová M, Konovalov FA, Filatova AY, Zamkova MA, Kanivets IV, Solonichenko VG, Semenova NA, Zinchenko RA, Treisman R, Skoblov MY. Mutation in PHACTR1 associated with multifocal epilepsy with infantile spasms and hypsarrhythmia. Clin Genet 2021; 99:673-683. [PMID: 33463715 PMCID: PMC8629116 DOI: 10.1111/cge.13926] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/07/2021] [Accepted: 01/13/2021] [Indexed: 11/28/2022]
Abstract
A young boy with multifocal epilepsy with infantile spasms and hypsarrhythmia with minimal organic lesions of brain structures underwent DNA diagnosis using whole‐exome sequencing. A heterozygous amino‐acid substitution p.L519R in a PHACTR1 gene was identified. PHACTR1 belongs to a protein family of G‐actin binding protein phosphatase 1 (PP1) cofactors and was not previously associated with a human disease. The missense single nucleotide variant in the proband was shown to occur de novo in the paternal allele. The mutation was shown in vitro to reduce the affinity of PHACTR1 for G‐actin, and to increase its propensity to form complexes with the catalytic subunit of PP1. These properties are associated with altered subcellular localization of PHACTR1 and increased ability to induce cytoskeletal rearrangements. Although the molecular role of the PHACTR1 in neuronal excitability and differentiation remains to be defined, PHACTR1 has been previously shown to be involved in Slack channelopathy pathogenesis, consistent with our findings. We conclude that this activating mutation in PHACTR1 causes a severe type of sporadic multifocal epilepsy in the patient.
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Affiliation(s)
- Andrey V Marakhonov
- Laboratory of Genetic Epidemiology, Laboratory of Functional Genomics, Department of Genetic Counseling, Research Centre for Medical Genetics, Moscow, Russia
| | - Magdalena Přechová
- Laboratory of Integrative Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.,Signalling and Transcription Laboratory, Francis Crick Institute, London, UK
| | | | - Alexandra Yu Filatova
- Laboratory of Genetic Epidemiology, Laboratory of Functional Genomics, Department of Genetic Counseling, Research Centre for Medical Genetics, Moscow, Russia
| | - Maria A Zamkova
- Laboratory of Regulatory Mechanisms in Immunity, Institute of Carcinogenesis, N.N. Blokhin Russian Cancer Research Center, Moscow, Russia
| | - Ilya V Kanivets
- Laboratory of Molecular Pathology, Genomed Ltd., Moscow, Russia.,Medical Genetic Centre, Filatov Moscow Pediatric Clinical Hospital, Moscow, Russia
| | | | - Natalia A Semenova
- Laboratory of Genetic Epidemiology, Laboratory of Functional Genomics, Department of Genetic Counseling, Research Centre for Medical Genetics, Moscow, Russia
| | - Rena A Zinchenko
- Laboratory of Genetic Epidemiology, Laboratory of Functional Genomics, Department of Genetic Counseling, Research Centre for Medical Genetics, Moscow, Russia.,N.A. Semashko National Research Institute of Public Health, Moscow, Russia
| | - Richard Treisman
- Signalling and Transcription Laboratory, Francis Crick Institute, London, UK
| | - Mikhail Yu Skoblov
- Laboratory of Genetic Epidemiology, Laboratory of Functional Genomics, Department of Genetic Counseling, Research Centre for Medical Genetics, Moscow, Russia
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3
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Krivosheeva IA, Filatova AY, Moshkovskii SA, Baranova AV, Skoblov MY. Analysis of candidate genes expected to be essential for melanoma surviving. Cancer Cell Int 2020; 20:488. [PMID: 33041669 PMCID: PMC7541296 DOI: 10.1186/s12935-020-01584-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/28/2020] [Indexed: 11/10/2022] Open
Abstract
Introduction Cancers may be treated by selective targeting of the genes vital for their survival. A number of attempts have led to discovery of several genes essential for surviving of tumor cells of different types. In this work, we tried to analyze genes that were previously predicted to be essential for melanoma surviving. Here we present the results of transient siRNA-mediated knockdown of the four of such genes, namely, UNC45A, STK11IP, RHPN2 and ZNFX1, in melanoma cell line A375, then assayed the cells for their viability, proliferation and ability to migrate in vitro. In our study, the knockdown of the genes predicted as essential for melanoma survival does not lead to statistically significant changes in cell viability. On the other hand, for each of the studied genes, mobility assays showed that the knockdown of each of the target genes accelerates the speed of cells migrating. Possible explanation for such counterintuitive results may include insufficiency of the predicting computational models or the necessity of a multiplex knockdown of the genes. Aims To examine the hypothesis of essentiality of hypomutated genes for melanoma surviving we have performed knockdown of several genes in melanoma cell line and analyzed cell viability and their ability to migrate. Methods Knockdown was performed by siRNAs transfected by Metafectene PRO. The levels of mRNAs before and after knockdown were evaluated by RT-qPCR analysis. Cell viability and proliferation were assessed by MTT assay. Cell migration was assessed by wound healing assay. Results The knockdown of the genes predicted as essential for melanoma survival does not lead to statistically significant changes in cell viability. On the other hand, for each of the studied genes, mobility assays showed that the knockdown of each of the target genes accelerates the speed of cells migrating. Conclusion Our results do not confirm initial hypothesis that the genes predicted essential for melanoma survival as a matter of fact support the survival of melanoma cells.
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Affiliation(s)
- Irina A Krivosheeva
- Laboratory of Functional Genomics, Research Centre of Medical Genetics, Erevanskaya Street, 10 building 2, Floor 44, Moscow, 115304 Russia
| | - Alexandra Yu Filatova
- Laboratory of Functional Genomics, Research Centre of Medical Genetics, Erevanskaya Street, 10 building 2, Floor 44, Moscow, 115304 Russia
| | - Sergei A Moshkovskii
- Laboratory of Medical Proteomics, Institute of Biomedical Chemistry, Moscow, Russia
| | - Ancha V Baranova
- School of Systems Biology, George Mason University, Fairfax, VA USA.,Laboratory of Functional Genomics, Research Centre of Medical Genetics, Erevanskaya Street, 10 building 2, Floor 44, Moscow, 115304 Russia
| | - Mikhail Yu Skoblov
- Laboratory of Functional Genomics, Research Centre of Medical Genetics, Erevanskaya Street, 10 building 2, Floor 44, Moscow, 115304 Russia
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Lavrov AV, Varenikov GG, Skoblov MY. Genome scale analysis of pathogenic variants targetable for single base editing. BMC Med Genomics 2020; 13:80. [PMID: 32948190 PMCID: PMC7499999 DOI: 10.1186/s12920-020-00735-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 06/01/2020] [Indexed: 11/12/2022] Open
Abstract
Background Single nucleotide variants account for approximately 90% of all known pathogenic variants responsible for human diseases. Recently discovered CRISPR/Cas9 base editors can correct individual nucleotides without cutting DNA and inducing double-stranded breaks. We aimed to find all possible pathogenic variants which can be efficiently targeted by any of the currently described base editors and to present them for further selection and development of targeted therapies. Methods ClinVar database (GRCh37_clinvar_20171203) was used to search and select mutations available for current single-base editing systems. We included only pathogenic and likely pathogenic variants for further analysis. For every potentially editable mutation we checked the presence of PAM. If a PAM was found, we analyzed the sequence to find possibility to edit only one nucleotide without changing neighboring nucleotides. The code of the script to search Clinvar database and to analyze the sequences was written in R and is available in the appendix. Results We analyzed 21 editing system currently reported in 9 publications. Every system has different working characteristics such as the editing window and PAM sequence. C > T base editors can precisely target 3196 mutations (46% of all pathogenic T > C variants), and A > G editors – 6900 mutations (34% of all pathogenic G > A variants). Conclusions Protein engineering helps to develop new enzymes with a narrower window of base editors as well as using new Cas9 enzymes with different PAM sequences. But, even now the list of mutations which can be targeted with currently available systems is huge enough to choose and develop new targeted therapies.
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Affiliation(s)
| | | | - Mikhail Yu Skoblov
- Research Center for Medical Genetics, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia
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5
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Milovidova TB, Schagina OA, Freire MV, Demina NA, Filatova AY, Skoblov MY, Stepanova AA, Chuhrova AL, Polyakov AV. X-linked hypohidrotic ectodermal dysplasia: clinical and molecular genetic analysis of a large Russian family with a synonymous p.Ser267= (c.801A>G) splice site mutation. J Eur Acad Dermatol Venereol 2019; 33:e468-e470. [PMID: 31306530 DOI: 10.1111/jdv.15798] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- T B Milovidova
- Federal State Budgetary Scientific Institution "Research Centre for Medical Genetics", Moscow, Russia
| | - O A Schagina
- Federal State Budgetary Scientific Institution "Research Centre for Medical Genetics", Moscow, Russia
| | - M V Freire
- Federal State Budgetary Scientific Institution "Research Centre for Medical Genetics", Moscow, Russia
| | - N A Demina
- Federal State Budgetary Scientific Institution "Research Centre for Medical Genetics", Moscow, Russia
| | - A Y Filatova
- Federal State Budgetary Scientific Institution "Research Centre for Medical Genetics", Moscow, Russia
| | - M Y Skoblov
- Federal State Budgetary Scientific Institution "Research Centre for Medical Genetics", Moscow, Russia
| | - A A Stepanova
- Federal State Budgetary Scientific Institution "Research Centre for Medical Genetics", Moscow, Russia
| | - A L Chuhrova
- Federal State Budgetary Scientific Institution "Research Centre for Medical Genetics", Moscow, Russia
| | - A V Polyakov
- Federal State Budgetary Scientific Institution "Research Centre for Medical Genetics", Moscow, Russia
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Marakhonov AV, Brodehl A, Myasnikov RP, Sparber PA, Kiseleva AV, Kulikova OV, Meshkov AN, Zharikova AA, Koretsky SN, Kharlap MS, Stanasiuk C, Mershina EA, Sinitsyn VE, Shevchenko AO, Mozheyko NP, Drapkina OM, Boytsov SA, Milting H, Skoblov MY. Back Cover, Volume 40, Issue 6. Hum Mutat 2019. [DOI: 10.1002/humu.23796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Andrey V. Marakhonov
- Laboratory of Genetic EpidemiologyResearch Centre for Medical Genetics (RCMG)Moscow Russia
- School of BiomedicineFar Eastern Federal UniversityVladivostok Russia
| | - Andreas Brodehl
- Erich and Hanna Klessmann Institute, Heart and Diabetes Centre NRWUniversity Hospital of the Ruhr‐University BochumBad Oeynhausen Germany
| | - Roman P. Myasnikov
- Department of Clinical Cardiology and Molecular GeneticsFederal State Institution National Center for Preventive MedicineMoscow Russia
| | - Peter A. Sparber
- School of BiomedicineFar Eastern Federal UniversityVladivostok Russia
| | - Anna V. Kiseleva
- Laboratory of Molecular GeneticsFederal State Institution National Center for Preventive MedicineMoscow Russia
| | - Olga V. Kulikova
- Department of Clinical Cardiology and Molecular GeneticsFederal State Institution National Center for Preventive MedicineMoscow Russia
| | - Alexey N. Meshkov
- Department of Molecular and Cellular GeneticsPirogov Russian National Research Medical UniversityMoscow Russia
- Laboratory of Molecular GeneticsFederal State Institution National Center for Preventive MedicineMoscow Russia
| | - Anastasia A. Zharikova
- M.V. Lomonosov Moscow State UniversityMoscow Russia
- Laboratory of Molecular GeneticsFederal State Institution National Center for Preventive MedicineMoscow Russia
| | - Serguey N. Koretsky
- Department of Fundamental and Applied Aspects of ObesityFederal State Institution National Center for Preventive MedicineMoscow Russia
| | - Maria S. Kharlap
- Cardiac Arrhythmias DepartmentFederal State Institution National Center for Preventive MedicineMoscow Russia
| | - Caroline Stanasiuk
- Erich and Hanna Klessmann Institute, Heart and Diabetes Centre NRWUniversity Hospital of the Ruhr‐University BochumBad Oeynhausen Germany
| | - Elena A. Mershina
- M.V. Lomonosov Moscow State UniversityMoscow Russia
- Radiology DepartmentLomonosov Moscow State University Medical Research and Educational CenterMoscow Russia
| | - Valentin E. Sinitsyn
- M.V. Lomonosov Moscow State UniversityMoscow Russia
- Radiology DepartmentLomonosov Moscow State University Medical Research and Educational CenterMoscow Russia
| | - Alexey O. Shevchenko
- Department of Critical Care Translational MedicineV.I. Shumakov National Medical Research Center of Transplantology and Artificial OrgansMoscow Russia
| | - Natalia P. Mozheyko
- Pathology DepartmentV.I. Shumakov National Medical Research Center of Transplantology and Artificial OrgansMoscow Russia
| | - Oksana M. Drapkina
- Department of Fundamental and Applied Aspects of ObesityFederal State Institution National Center for Preventive MedicineMoscow Russia
| | | | - Hendrik Milting
- Erich and Hanna Klessmann Institute, Heart and Diabetes Centre NRWUniversity Hospital of the Ruhr‐University BochumBad Oeynhausen Germany
| | - Mikhail Yu. Skoblov
- Laboratory of Functional GenomicsResearch Centre for Medical Genetics (RCMG)Moscow Russia Russia
- School of BiomedicineFar Eastern Federal UniversityVladivostok Russia
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7
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Abstract
Background It was shown that the major part of human genome is transcribed and produces a large number of long noncoding RNAs (lncRNAs). Today there are many evidences that lncRNAs play important role in the regulation of gene expression during different cellular processes. Moreover, lncRNAs are involved in the development of various human diseases. However, the function of the major part of annotated transcripts is currently unknown, whereas different lncRNAs annotations tend to have low overlap. Recent studies revealed that some lncRNAs have small open reading frames (smORFs), that produce the functional microproteins. However, the question whether the function of such genes is determined by microprotein or RNA itself or both remains open. Thus, the study of new lncRNA genes is important to understanding the functional role of such a heterogeneous class of genes. Results In the present study, we used reverse transcription PCR and rapid amplification of cDNA ends (RACE) analysis to determine the structure of the LINC01420 transcript. We revealed that LINC01420 has two isoforms that differ in length of the last exon and are localized predominantly in the cytoplasm. We showed that expression of the short isoform is much higher than the long. Besides, MTT and wound-healing assays revealed that LINC01420 inhibited cell migration in human melanoma cell line A375, but does not influence on cell viability. Conclusion During our work, D’Lima et al. found smORF in the first exon of the LINC01420 gene. This smORF produces functional microprotein named non-annotated P-body dissociating polypeptide (NoBody). However, our results provide new facts about LINC01420 transcript and its function.
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Affiliation(s)
- Daria O Konina
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology (State University), Dolgoprudny, 141701, Russian Federation
| | | | - Mikhail Yu Skoblov
- Research Centre for Medical Genetics, Moscow, Russian Federation, 115522.,Far Eastern Federal University, Vladivostok, 690090, Russian Federation
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Affiliation(s)
- Ancha V. Baranova
- School of Systems Biology, George Mason University, Fairfax, VA USA
- Research Centre for Medical Genetics, 115478 Moscow, Russia
| | | | - Elena N. Voropaeva
- Research Institute of Internal and Preventive Medicine - Branch of the Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | | | - Yuriy L. Orlov
- Research Institute of Internal and Preventive Medicine - Branch of the Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
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9
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Marakhonov AV, Brodehl A, Myasnikov RP, Sparber PA, Kiseleva AV, Kulikova OV, Meshkov AN, Zharikova AA, Koretsky SN, Kharlap MS, Stanasiuk C, Mershina EA, Sinitsyn VE, Shevchenko AO, Mozheyko NP, Drapkina OM, Boytsov SA, Milting H, Skoblov MY. Noncompaction cardiomyopathy is caused by a novel in-frame desmin (DES) deletion mutation within the 1A coiled-coil rod segment leading to a severe filament assembly defect. Hum Mutat 2019; 40:734-741. [PMID: 30908796 DOI: 10.1002/humu.23747] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 03/03/2019] [Accepted: 03/06/2019] [Indexed: 11/07/2022]
Abstract
Mutations in DES, encoding desmin protein, are associated with different kinds of skeletal and/or cardiac myopathies. However, it is unknown, whether DES mutations are associated with left ventricular hypertrabeculation (LVHT). Here, we performed a clinical examination and subsequent genetic analysis in a family, with two individuals presenting LVHT with conduction disease and skeletal myopathy. The genetic analysis revealed a novel small in-frame deletion within the DES gene, p.Q113_L115del, affecting the α-helical rod domain. Immunohistochemistry analysis of explanted myocardial tissue from the index patient revealed an abnormal cytoplasmic accumulation of desmin and a degraded sarcomeric structure. Cell transfection experiments with wild-type and mutant desmin verified the cytoplasmic aggregation and accumulation of mutant desmin. Cotransfection experiments were performed to model the heterozygous state of the patients and revealed a dominant negative effect of the mutant desmin on filament assembly. DES:p.Q113_L115del is classified as a pathogenic mutation associated with dilated cardiomyopathy with prominent LVHT.
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Affiliation(s)
- Andrey V Marakhonov
- Laboratory of Genetic Epidemiology, Research Centre for Medical Genetics (RCMG), Moscow, Russia.,School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Andreas Brodehl
- Erich and Hanna Klessmann Institute, Heart and Diabetes Centre NRW, University Hospital of the Ruhr-University Bochum, Bad Oeynhausen, Germany
| | - Roman P Myasnikov
- Department of Clinical Cardiology and Molecular Genetics, Federal State Institution National Center for Preventive Medicine, Moscow, Russia
| | - Peter A Sparber
- School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Anna V Kiseleva
- Laboratory of Molecular Genetics, Federal State Institution National Center for Preventive Medicine, Moscow, Russia
| | - Olga V Kulikova
- Department of Clinical Cardiology and Molecular Genetics, Federal State Institution National Center for Preventive Medicine, Moscow, Russia
| | - Alexey N Meshkov
- Department of Molecular and Cellular Genetics, Pirogov Russian National Research Medical University, Moscow, Russia.,Laboratory of Molecular Genetics, Federal State Institution National Center for Preventive Medicine, Moscow, Russia
| | - Anastasia A Zharikova
- M.V. Lomonosov Moscow State University, Moscow, Russia.,Laboratory of Molecular Genetics, Federal State Institution National Center for Preventive Medicine, Moscow, Russia
| | - Serguey N Koretsky
- Department of Fundamental and Applied Aspects of Obesity, Federal State Institution National Center for Preventive Medicine, Moscow, Russia
| | - Maria S Kharlap
- Cardiac Arrhythmias Department, Federal State Institution National Center for Preventive Medicine, Moscow, Russia
| | - Caroline Stanasiuk
- Erich and Hanna Klessmann Institute, Heart and Diabetes Centre NRW, University Hospital of the Ruhr-University Bochum, Bad Oeynhausen, Germany
| | - Elena A Mershina
- M.V. Lomonosov Moscow State University, Moscow, Russia.,Radiology Department, Lomonosov Moscow State University Medical Research and Educational Center, Moscow, Russia
| | - Valentin E Sinitsyn
- M.V. Lomonosov Moscow State University, Moscow, Russia.,Radiology Department, Lomonosov Moscow State University Medical Research and Educational Center, Moscow, Russia
| | - Alexey O Shevchenko
- Department of Critical Care Translational Medicine, V.I. Shumakov National Medical Research Center of Transplantology and Artificial Organs, Moscow, Russia
| | - Natalia P Mozheyko
- Pathology Department, V.I. Shumakov National Medical Research Center of Transplantology and Artificial Organs, Moscow, Russia
| | - Oksana M Drapkina
- Department of Fundamental and Applied Aspects of Obesity, Federal State Institution National Center for Preventive Medicine, Moscow, Russia
| | | | - Hendrik Milting
- Erich and Hanna Klessmann Institute, Heart and Diabetes Centre NRW, University Hospital of the Ruhr-University Bochum, Bad Oeynhausen, Germany
| | - Mikhail Yu Skoblov
- Laboratory of Functional Genomics, Research Centre for Medical Genetics (RCMG), Moscow, Russia, Russia.,School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia
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10
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Abstract
miRNAs play a key role in regulation of gene expression. Nowadays it is known more than 2500 human miRNAs, while a majority of miRNA-mRNA interactions remains unidentified. The recent development of a high-throughput CLASH (crosslinking, ligation and sequencing of hybrids) technique for discerning miRNA-mRNA interactions allowed an experimental analysis of the human miRNA-mRNA interactome. Therefore, it allowed us, for the first time, make an experimental analysis of the human miRNA-mRNA interactome as a whole and an evaluation of the quality of most commonly used miRNA prediction tools (TargetScan, PicTar, PITA, RNA22 and miRanda). To estimate efficiency of the miRNA-mRNA prediction tools, we used next parameters: sensitivity, positive predicted value, predictions in different mRNA regions (3' UTR, CDS, 5' UTR), predictions for different types of interactions (5 classes), predictions of "canonical" and "nocanonical" interactions, similarity with the random generated data. The analysis revealed low efficiency of all prediction programs in comparison with the CLASH data in terms of the all examined parameters.
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Affiliation(s)
- O M Plotnikova
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow oblast, 141700 Russia.,
| | - M Y Skoblov
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow oblast, 141700 Russia.,Research Centre for Medical Genetics, Moscow, 115478 Russia
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11
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Filatova AY, Vasilyeva TA, Marakhonov AV, Voskresenskaya AA, Zinchenko RA, Skoblov MY. Functional reassessment of PAX6 single nucleotide variants by in vitro splicing assay. Eur J Hum Genet 2018; 27:488-493. [PMID: 30315214 DOI: 10.1038/s41431-018-0288-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 08/14/2018] [Accepted: 09/28/2018] [Indexed: 11/09/2022] Open
Abstract
Nucleotide variants that disrupt normal splicing might be the cause of a large number of diseases. Nevertheless, because of the complexity of splicing regulation, it is not always possible to accurately predict the effect of nucleotide sequence changes on splicing events and mRNA structure. Thereby, a number of newly identified nucleotide variants are falsely classified as VUS (a variant of uncertain significance). In the present study we used the minigene assay to analyze the functional consequences of six intronic (c.142-5T>G, c.142-14C>G, c.142-64A>C, c.141+4A>G, c.1032+ 6T>G, c.682+4delA), one missense (c.140A>G) and one synonymous (c.174C>T) variants in the PAX6 gene found in patients with congenital aniridia. We revealed that all except one (c.142-64A>C) variants lead to the disruption of normal splicing patterns resulting in premature termination codon formation followed by mRNA degradation through the nonsense mediated decay pathway. This produces a null allele of the PAX6 gene. That allowed us to reclassify the analyzed variants as loss-of-function and to establish their functional role.
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Affiliation(s)
| | | | - Andrey V Marakhonov
- Research Centre for Medical Genetics, Moscow, Russian Federation.,Moscow Institute of Physics and Technology (State University), Moscow, Russian Federation
| | - Anna A Voskresenskaya
- Cheboksary branch of S. Fyodorov Eye Microsurgery Federal State Institution, Cheboksary, Russian Federation
| | - Rena A Zinchenko
- Research Centre for Medical Genetics, Moscow, Russian Federation.,Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - Mikhail Yu Skoblov
- Research Centre for Medical Genetics, Moscow, Russian Federation.,Moscow Institute of Physics and Technology (State University), Moscow, Russian Federation
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12
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Marakhonov AV, Tabakov VY, Zernov NV, Dadali EL, Sharkova IV, Skoblov MY. Two novel COL6A3 mutations disrupt extracellular matrix formation and lead to myopathy from Ullrich congenital muscular dystrophy and Bethlem myopathy spectrum. Gene 2018; 672:165-171. [DOI: 10.1016/j.gene.2018.06.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 04/21/2018] [Accepted: 06/08/2018] [Indexed: 01/15/2023]
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13
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Gus’kova AA, Skoblov MY, Korovina AN, Yasko MV, Karpenko IL, Kukhanova MK, Andronova VL, Galegov GA, Skoblov YS. Antiherpetic Properties of Acyclovir 5′-Hydrogenphosphonate and the Mutation Analysis of Herpes Virus Resistant Strains. Chem Biol Drug Des 2009; 74:382-9. [DOI: 10.1111/j.1747-0285.2009.00874.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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