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Volobaev VP, Kunizheva SS, Uralsky LI, Kupriyanova DA, Rogaev EI. Quantifying human genome parameters in aging. Vavilovskii Zhurnal Genet Selektsii 2023; 27:495-501. [PMID: 37808212 PMCID: PMC10551942 DOI: 10.18699/vjgb-23-60] [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: 11/28/2022] [Revised: 02/07/2023] [Accepted: 02/07/2023] [Indexed: 10/10/2023] Open
Abstract
Healthy human longevity is a global goal of the world health system. Determining the causes and processes influencing human longevity is the primary fundamental goal facing the scientific community. Currently, the main efforts of the scientific community are aimed at identifying the qualitative characteristics of the genome that determine the trait. At the same time, when evaluating qualitative characteristics, there are many challenges that make it difficult to establish associations. Quantitative traits are burdened with such problems to a lesser extent, but they are largely overlooked in current genomic studies of aging and longevity. Although there is a wide repertoire of quantitative trait analyses based on genomic data, most opportunities are ignored by authors, which, along with the inaccessibility of published data, leads to the loss of this important information. This review focuses on describing quantitative traits important for understanding aging and necessary for analysis in further genomic studies, and recommends the inclusion of the described traits in the analysis. The review considers the relationship between quantitative characteristics of the mitochondrial genome and aging, longevity, and age-related neurodegenerative diseases, such as the frequency of extensive mitochondrial DNA (mtDNA) deletions, mtDNA half-life, the frequency of A>G replacements in the mtDNA heavy chain, the number of mtDNA copies; special attention is paid to the mtDNA methylation sign. A separate section of this review is devoted to the correlation of telomere length parameters with age, as well as the association of telomere length with the amount of mitochondrial DNA. In addition, we consider such a quantitative feature as the rate of accumulation of somatic mutations with aging in relation to the lifespan of living organisms. In general, it may be noted that there are quite serious reasons to suppose that various quantitative characteristics of the genome may be directly or indirectly associated with certain aspects of aging and longevity. At the same time, the available data are clearly insufficient for definitive conclusions and the determination of causal relationships.
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Affiliation(s)
- V P Volobaev
- Sirius University of Science and Technology, Scientific Center for Genetics and Life Sciences, Sochi, Russia
| | - S S Kunizheva
- Sirius University of Science and Technology, Scientific Center for Genetics and Life Sciences, Sochi, Russia Vavilov Institute of General Genetics, Russian Academy of Sciences, Department of Genomics and Human Genetics, Moscow, Russia Lomonosov Moscow State University, Center for Genetics and Genetic Technologies, Faculty of Biology, Moscow, Russia
| | - L I Uralsky
- Sirius University of Science and Technology, Scientific Center for Genetics and Life Sciences, Sochi, Russia Vavilov Institute of General Genetics, Russian Academy of Sciences, Department of Genomics and Human Genetics, Moscow, Russia
| | - D A Kupriyanova
- Sirius University of Science and Technology, Scientific Center for Genetics and Life Sciences, Sochi, Russia
| | - E I Rogaev
- Sirius University of Science and Technology, Scientific Center for Genetics and Life Sciences, Sochi, Russia Vavilov Institute of General Genetics, Russian Academy of Sciences, Department of Genomics and Human Genetics, Moscow, Russia Lomonosov Moscow State University, Center for Genetics and Genetic Technologies, Faculty of Biology, Moscow, Russia University of Massachusetts Chan Medical School, Department of Psychiatry, Shrewsbury, USA
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Kuznetsova IL, Uralsky LI, Tyazhelova TV, Andreeva TV, Rogaev EI. Mosaic loss of the Y chromosome in human neurodegenerative and oncological diseases. Vavilovskii Zhurnal Genet Selektsii 2023; 27:502-511. [PMID: 37808213 PMCID: PMC10551935 DOI: 10.18699/vjgb-23-61] [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: 12/13/2022] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 10/10/2023] Open
Abstract
The development of new biomarkers for prediction and early detection of human diseases, as well as for monitoring the response to therapy is one of the most relevant areas of modern human genetics and genomics. Until recently, it was believed that the function of human Y chromosome genes was limited to determining sex and controlling spermatogenesis. Thanks to occurance of large databases of the genome-wide association study (GWAS), there has been a transition to the use of large samples for analyzing genetic changes in both normal and pathological conditions. This has made it possible to assess the association of mosaic aneuploidy of the Y chromosome in somatic cells with a shorter lifespan in men compared to women. Based on data from the UK Biobank, an association was found between mosaic loss of the Y chromosome (mLOY) in peripheral blood leukocytes and the age of men over 70, as well as a number of oncological, cardiac, metabolic, neurodegenerative, and psychiatric diseases. As a result, mLOY in peripheral blood cells has been considered a potential marker of biological age in men and as a marker of certain age-related diseases. Currently, numerous associations have been identified between mLOY and genes based on GWAS and transcriptomes in affected tissues. However, the exact cause of mLOY and the impact and consequences of this phenomenon at the whole organism level have not been established. In particular, it is unclear whether aneuploidy of the Y chromosome in blood cells may affect the development of pathologies that manifest in other organs, such as the brain in Alzheimer's disease, or whether it is a neutral biomarker of general genomic instability. This review examines the main pathologies and genetic factors associated with mLOY, as well as the hypotheses regarding their interplay. Special attention is given to recent studies on mLOY in brain cells in Alzheimer's disease.
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Affiliation(s)
- I L Kuznetsova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Department of Genomics and Human Genetics, Moscow, Russia Sirius University of Science and Technology, Scientific Center for Genetics and Life Sciences, Sochi, Russia
| | - L I Uralsky
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Department of Genomics and Human Genetics, Moscow, Russia Sirius University of Science and Technology, Scientific Center for Genetics and Life Sciences, Sochi, Russia
| | - T V Tyazhelova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Department of Genomics and Human Genetics, Moscow, Russia
| | - T V Andreeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Department of Genomics and Human Genetics, Moscow, Russia Sirius University of Science and Technology, Scientific Center for Genetics and Life Sciences, Sochi, Russia Lomonosov Moscow State University, Center for Genetics and Genetic Technologies, Faculty of Biology, Moscow, Russia
| | - E I Rogaev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Department of Genomics and Human Genetics, Moscow, Russia Sirius University of Science and Technology, Scientific Center for Genetics and Life Sciences, Sochi, Russia Lomonosov Moscow State University, Center for Genetics and Genetic Technologies, Faculty of Biology, Moscow, Russia
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Ponomareva NV, Andreeva TV, Protasova MS, Kunizheva SS, Kuznetsova IL, Kolesnikova EP, Malina DD, Mitrofanov AA, Fokin VF, Illarioshkin SN, Rogaev EI. Neuronal Hyperactivation in EEG Data during Cognitive Tasks Is Related to the Apolipoprotein J/Clusterin Genotype in Nondemented Adults. Int J Mol Sci 2023; 24:6790. [PMID: 37047762 PMCID: PMC10095572 DOI: 10.3390/ijms24076790] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 03/24/2023] [Accepted: 03/30/2023] [Indexed: 04/08/2023] Open
Abstract
The clusterin (CLU) rs11136000 CC genotype is a probable risk factor for Alzheimer's disease (AD). CLU, also known as the apolipoprotein J gene, shares certain properties with the apolipoprotein E (APOE) gene with a well-established relationship with AD. This study aimed to determine whether the electrophysiological patterns of brain activation during the letter fluency task (LFT) depend on CLU genotypes in adults without dementia. Previous studies have shown that LFT performance involves activation of the frontal cortex. We examined EEG alpha1 and alpha2 band desynchronization in the frontal regions during the LFT in 94 nondemented individuals stratified by CLU (rs11136000) genotype. Starting at 30 years of age, CLU CC carriers exhibited more pronounced task-related alpha2 desynchronization than CLU CT&TT carriers in the absence of any differences in LFT performance. In CLU CC carriers, alpha2 desynchronization was significantly correlated with age. Increased task-related activation in individuals at genetic risk for AD may reflect greater "effort" to perform the task and/or neuronal hyperexcitability. The results show that the CLU genotype is associated with neuronal hyperactivation in the frontal cortex during cognitive tasks performances in nondemented individuals, suggesting systematic vulnerability of LFT related cognitive networks in people carrying unfavorable CLU alleles.
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Affiliation(s)
- Natalya V. Ponomareva
- Research Center of Neurology, 125367 Moscow, Russia
- Center for Genetics and Life Science, Sirius University of Science and Technology, 354349 Sochi, Russia
| | - Tatiana V. Andreeva
- Center for Genetics and Life Science, Sirius University of Science and Technology, 354349 Sochi, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
- Centre for Genetics and Genetic Technologies, Faculty of Biology, Lomonosov Moscow State University, 119192 Moscow, Russia
| | - Maria S. Protasova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Svetlana S. Kunizheva
- Center for Genetics and Life Science, Sirius University of Science and Technology, 354349 Sochi, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Irina L. Kuznetsova
- Center for Genetics and Life Science, Sirius University of Science and Technology, 354349 Sochi, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
| | | | | | | | | | | | - Evgeny I. Rogaev
- Center for Genetics and Life Science, Sirius University of Science and Technology, 354349 Sochi, Russia
- Department of Psychiatry, Umass Chan Medical School, Shrewsbury, MA 01545, USA
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Protasova MS, Andreeva TV, Klyushnikov SA, Illarioshkin SN, Rogaev EI. Genetic Variant in GRM1 Underlies Congenital Cerebellar Ataxia with No Obvious Intellectual Disability. Int J Mol Sci 2023; 24:ijms24021551. [PMID: 36675067 PMCID: PMC9865416 DOI: 10.3390/ijms24021551] [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] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/29/2022] [Accepted: 01/03/2023] [Indexed: 01/15/2023] Open
Abstract
Metabotropic glutamate receptor 1 (mGluR1) plays a crucial role in slow excitatory postsynaptic conductance, synapse formation, synaptic plasticity, and motor control. The GRM1 gene is expressed mainly in the brain, with the highest expression in the cerebellum. Mutations in the GRM1 gene have previously been known to cause autosomal recessive and autosomal dominant spinocerebellar ataxias. In this study, whole-exome sequencing of a patient from a family of Azerbaijani origin with a diagnosis of congenital cerebellar ataxia was performed, and a new homozygous missense mutation in the GRM1 gene was identified. The mutation leads to the homozygous amino acid substitution of p.Thr824Arg in an evolutionarily highly conserved region encoding the transmembrane domain 7, which is critical for ligand binding and modulating of receptor activity. This is the first report in which a mutation has been identified in the last transmembrane domain of the mGluR1, causing a congenital autosomal recessive form of cerebellar ataxia with no obvious intellectual disability. Additionally, we summarized all known presumable pathogenic genetic variants in the GRM1 gene to date. We demonstrated that multiple rare variants in the GRM1 underlie a broad diversity of clinical neurological and behavioral phenotypes depending on the nature and protein topology of the mutation.
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Affiliation(s)
- Maria S. Protasova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Tatiana V. Andreeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
- Center for Genetics and Life Science, Department of Genetics, Sirius University of Science and Technology, 354340 Sochi, Russia
- Centre for Genetics and Genetic Technologies, Department of Genetics, Faculty of Biology, Lomonosov Moscow State University, 119192 Moscow, Russia
- Correspondence: (T.V.A.); (E.I.R.)
| | | | | | - Evgeny I. Rogaev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
- Center for Genetics and Life Science, Department of Genetics, Sirius University of Science and Technology, 354340 Sochi, Russia
- Department of Psychiatry, UMass Chan Medical School, Shrewsbury, MA 01545, USA
- Correspondence: (T.V.A.); (E.I.R.)
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Ponomareva NV, Andreeva TV, Protasova M, Konovalov RN, Krotenkova MV, Kolesnikova EP, Malina DD, Kanavets EV, Mitrofanov AA, Fokin VF, Illarioshkin SN, Rogaev EI. Genetic association of apolipoprotein E genotype with EEG alpha rhythm slowing and functional brain network alterations during normal aging. Front Neurosci 2022; 16:931173. [PMID: 35979332 PMCID: PMC9376365 DOI: 10.3389/fnins.2022.931173] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/27/2022] [Indexed: 12/02/2022] Open
Abstract
The ε4 allele of the apolipoprotein E (APOE4+) genotype is a major genetic risk factor for Alzheimer’s disease (AD), but the mechanisms underlying its influence remain incompletely understood. The study aimed to investigate the possible effect of the APOE genotype on spontaneous electroencephalogram (EEG) alpha characteristics, resting-state functional MRI (fMRI) connectivity (rsFC) in large brain networks and the interrelation of alpha rhythm and rsFC characteristics in non-demented adults during aging. We examined the EEG alpha subband’s relative power, individual alpha peak frequency (IAPF), and fMRI rsFC in non-demented volunteers (age range 26–79 years) stratified by the APOE genotype. The presence of the APOE4+ genotype was associated with lower IAPF and lower relative power of the 11–13 Hz alpha subbands. The age related decrease in EEG IAPF was more pronounced in the APOE4+ carriers than in the APOE4+ non-carriers (APOE4-). The APOE4+ carriers had a stronger fMRI positive rsFC of the interhemispheric regions of the frontoparietal, lateral visual and salience networks than the APOE4– individuals. In contrast, the negative rsFC in the network between the left hippocampus and the right posterior parietal cortex was reduced in the APOE4+ carriers compared to the non-carriers. Alpha rhythm slowing was associated with the dysfunction of hippocampal networks. Our results show that in adults without dementia APOE4+ genotype is associated with alpha rhythm slowing and that this slowing is age-dependent. Our data suggest predominant alterations of inhibitory processes in large-scale brain network of non-demented APOE4+ carriers. Moreover, dysfunction of large-scale hippocampal network can influence APOE-related alpha rhythm vulnerability.
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Affiliation(s)
- Natalya V. Ponomareva
- Research Center of Neurology, Moscow, Russia
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia
- *Correspondence: Natalya V. Ponomareva,
| | - Tatiana V. Andreeva
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences (RAS), Moscow, Russia
| | - Maria Protasova
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences (RAS), Moscow, Russia
| | | | | | | | | | | | | | | | | | - Evgeny I. Rogaev
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences (RAS), Moscow, Russia
- Brudnick Neuropsychiatric Research Institute (BNRI), University of Massachusetts Medical School, Worcester, MA, United States
- Evgeny I. Rogaev,
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Andreeva TV, Manakhov AD, Gusev FE, Patrikeev AD, Golovanova LV, Doronichev VB, Shirobokov IG, Rogaev EI. Genomic analysis of a novel Neanderthal from Mezmaiskaya Cave provides insights into the genetic relationships of Middle Palaeolithic populations. Sci Rep 2022; 12:13016. [PMID: 35906446 PMCID: PMC9338269 DOI: 10.1038/s41598-022-16164-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/05/2022] [Indexed: 11/09/2022] Open
Abstract
The Mezmaiskaya cave is located on the North Caucasus near the border that divides Europe and Asia. Previously, fossil remains for two Neanderthals were reported from Mezmaiskaya Cave. A tooth from the third archaic hominin specimen (Mezmaiskaya 3) was retrieved from layer 3 in Mezmaiskaya Cave. We performed genome sequencing of Mezmaiskaya 3. Analysis of partial nuclear genome sequence revealed that it belongs to a Homo sapiens neanderthalensis female. Based on a high-coverage mitochondrial genome sequence, we demonstrated that the relationships of Mezmaiskaya 3 to Mezmaiskaya 1 and Stajnia S5000 individuals were closer than those to other Neanderthals. Our data demonstrate the close genetic connections between the early Middle Palaeolithic Neanderthals that were replaced by genetically distant later group in the same geographic areas. Based on mitochondrial DNA (mtDNA) data, we suggest that Mezmaiskaya 3 was the latest Neanderthal individual from the early Neanderthal’s branches. We proposed a hierarchical nomenclature for the mtDNA haplogroups of Neanderthals. In addition, we retrieved ancestral mtDNA mutations in presumably functional sites fixed in the Neanderthal clades, and also provided the first data showing mtDNA heteroplasmy in Neanderthal specimen.
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Affiliation(s)
- Tatiana V Andreeva
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia, 354340. .,Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia, 119333. .,Faculty of Biology, Centre for Genetics and Genetic Technologies, Lomonosov Moscow State University, Moscow, Russia, 119192.
| | - Andrey D Manakhov
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia, 354340.,Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia, 119333.,Faculty of Biology, Centre for Genetics and Genetic Technologies, Lomonosov Moscow State University, Moscow, Russia, 119192
| | - Fedor E Gusev
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia, 354340.,Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia, 119333.,Faculty of Biology, Centre for Genetics and Genetic Technologies, Lomonosov Moscow State University, Moscow, Russia, 119192
| | - Anton D Patrikeev
- Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia, 119333
| | | | | | - Ivan G Shirobokov
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, St. Petersburg, Russia, 199034
| | - Evgeny I Rogaev
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia, 354340. .,Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia, 119333. .,Faculty of Biology, Centre for Genetics and Genetic Technologies, Lomonosov Moscow State University, Moscow, Russia, 119192. .,Department of Psychiatry, University of Massachusetts Medical School, Worcester, MA, 01604, USA.
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Manakhov AD, Mintseva MY, Uralsky LI, Andreeva TV, Trapezov OV, Rogaev EI. Identification of mutant gene for Black crystal coat and non-allelic gene interactions in Neogale vison. Sci Rep 2022; 12:10483. [PMID: 35729186 PMCID: PMC9213499 DOI: 10.1038/s41598-022-14079-z] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 06/01/2022] [Indexed: 12/30/2022] Open
Abstract
Sable (Martes zibellina) and American mink (Neogale vison) are valuable species characterized by a variety of coat colour produced on fur farms. Black crystal fur phenotype is Mendelian codominant trait: heterozygous animals (Cr/ +) have white guard hairs scattered predominantly on the spine and the head, while homozygous (Cr/Cr) minks have coats resembling the Himalayan (ch/ch) or white Hedlund (h/h) types. It is one of the most recent of more than 35 currently known phenotypic traits of fur colour in American mink. Black crystal fur phenotype was first described in 1984 in the Russian population of mink, which had undergone selection for domestic defensive response to humans. Here, we performed whole-genome sequencing of American mink with Cr/Cr phenotype. We identified a missense mutation in the gene encoding the α-COP subunit of the COPI complex (COPA). The COPI complex mediates retrograde trafficking from the Golgi system to the endoplasmic reticulum and sorting of transmembrane proteins. We observed an interaction between a newly identified mutation in the COPA gene and a mutation in the microphthalmia-associated transcription factor (MITF), the latter mutation led to the formation of the white Hedlund (h/h) phenotype. Double heterozygotes for these mutations have an entirely white coat and a black-eyed phenotype similar to the phenotype of Cr/Cr or h/h minks. Our data could be useful for tracking economically valuable fur traits in mink breeding programs to contribute to global fur production.
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Affiliation(s)
- Andrey D. Manakhov
- grid.510477.0Department of Genetics, Centre for Genetics and Life Science, Sirius University of Science and Technology, 354340 Sochi, Russia ,grid.4886.20000 0001 2192 9124Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia ,grid.14476.300000 0001 2342 9668Centre for Genetics and Genetic Technologies, Faculty of Biology, Lomonosov Moscow State University, 119192 Moscow, Russia
| | - Maria Yu. Mintseva
- grid.4886.20000 0001 2192 9124Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
| | - Lev I. Uralsky
- grid.510477.0Department of Genetics, Centre for Genetics and Life Science, Sirius University of Science and Technology, 354340 Sochi, Russia ,grid.4886.20000 0001 2192 9124Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
| | - Tatiana V. Andreeva
- grid.4886.20000 0001 2192 9124Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia ,grid.14476.300000 0001 2342 9668Centre for Genetics and Genetic Technologies, Faculty of Biology, Lomonosov Moscow State University, 119192 Moscow, Russia
| | - Oleg V. Trapezov
- grid.415877.80000 0001 2254 1834Department of Animals and Human Genetics, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia ,grid.4605.70000000121896553Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Evgeny I. Rogaev
- grid.510477.0Department of Genetics, Centre for Genetics and Life Science, Sirius University of Science and Technology, 354340 Sochi, Russia ,grid.4886.20000 0001 2192 9124Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia ,grid.14476.300000 0001 2342 9668Centre for Genetics and Genetic Technologies, Faculty of Biology, Lomonosov Moscow State University, 119192 Moscow, Russia ,Department of Psychiatry, UMass Chan Medical School, Worcester, MA 01604 USA
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Protasova MS, Gusev FE, Andreeva TV, Klyushnikov SA, Illarioshkin SN, Rogaev EI. Novel genes bearing mutations in rare cases of early-onset ataxia with cerebellar hypoplasia. Eur J Hum Genet 2022; 30:703-711. [PMID: 35351988 DOI: 10.1038/s41431-022-01088-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 02/09/2022] [Accepted: 03/10/2022] [Indexed: 12/13/2022] Open
Abstract
We propose an approach for the identification of mutant genes for rare diseases in single cases of unknown etiology. All genes with rare biologically significant variants sorted from individual exome data are tested further for profiling of their spatial-temporal and cell/tissue specific expression compared to that of their paralogs. We developed a simple bioinformatics tool ("Essential Paralogue by Expression" (EPbE)) for such analysis. Here, we present rare clinical forms of early ataxia with cerebellar hypoplasia. Using whole-exome sequencing and the EPbE tool, we identified two novel mutant genes previously not associated with congenital human diseases. In Family I, the unique missense mutation (p.Lys258Glu) was found in the LRCH2 gene inherited in an X-linked manner. p.Lys258Glu occurs in the evolutionarily invariant site of the leucine-rich repeat domain of LRCH2. In Family II and Family III, the identical genetic variant was found in the CSMD1 gene inherited as an autosomal-recessive trait. The variant leads to amino acid substitution p.Gly2979Ser in a highly conserved region of the complement-interacting domain of CSMD1. The LRCH2 gene for Family I patients (in which congenital cerebellar hypoplasia was associated with demyelinating polyneuropathy) is expressed in Schwann and precursor Schwann cells and predominantly over its paralogous genes in the developing cerebellar cortex. The CSMD1 gene is predominantly expressed over its paralogous genes in the cerebellum, specifically in the period of late childhood. Thus, the comparative spatial-temporal expression of the selected genes corresponds to the neurological manifestations of the disease.
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Affiliation(s)
- Maria S Protasova
- Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics Russian Academy of Sciences, 119333, Moscow, Russia
| | - Fedor E Gusev
- Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics Russian Academy of Sciences, 119333, Moscow, Russia
| | - Tatiana V Andreeva
- Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics Russian Academy of Sciences, 119333, Moscow, Russia.,Faculty of Biology, Lomonosov Moscow State University, 119234, Moscow, Russia
| | - Sergey A Klyushnikov
- Department of Neurogenetics, Research Center of Neurology, 123367, Moscow, Russia
| | | | - Evgeny I Rogaev
- Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics Russian Academy of Sciences, 119333, Moscow, Russia. .,Center for Genetics and Life Science, Sirius University of Science and Technology, 354340, Sochi, Russia. .,Department of Psychiatry, UMass Chan Medical School, Shrewsbury, MA, 01545, USA.
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9
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Manakhov AD, Mintseva MY, Andreeva TV, Trapezov OV, Rogaev EI. Shadow coat colour in American mink associated with a missense mutation in the KIT gene. Anim Genet 2022; 53:522-525. [PMID: 35481560 DOI: 10.1111/age.13202] [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: 11/01/2021] [Revised: 03/21/2022] [Accepted: 04/04/2022] [Indexed: 11/26/2022]
Abstract
The classical genetic analysis describes more 35 mutations that are involved in the formation of the American mink (Neovison vison) fur colour phenotype. To date, only eight of these mutations have been linked to specific genes. Shadow is a member of the commercially valuable Black cross colour family. Here, we performed whole-genome sequencing of the American mink with a Shadow Silverblue (Sh /+ p/p) phenotype. We identified a missense mutation (c.2374 G>T) in the gene encoding the KIT proto-oncogene, receptor tyrosine kinase gene (KIT), which plays a critical role in melanogenesis as well as in the survival, growth and development of other cell types. The reported mutation results in amino acid substitution p.Asp792Tyr in a highly conserved catalytic loop of the KIT protein.
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Affiliation(s)
- Andrey D Manakhov
- Centre for Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia.,Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.,Centre for Genetics and Genetic Technologies, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Maria Yu Mintseva
- Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana V Andreeva
- Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.,Centre for Genetics and Genetic Technologies, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Oleg V Trapezov
- Department of Animals and Human Genetics, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Evgeny I Rogaev
- Centre for Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia.,Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.,Centre for Genetics and Genetic Technologies, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,Department of Psychiatry, UMass Chan Medical School, Worcester, Massachusetts, USA
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10
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Altemose N, Glennis A, Bzikadze AV, Sidhwani P, Langley SA, Caldas GV, Hoyt SJ, Uralsky L, Ryabov FD, Shew CJ, Sauria MEG, Borchers M, Gershman A, Mikheenko A, Shepelev VA, Dvorkina T, Kunyavskaya O, Vollger MR, Rhie A, McCartney AM, Asri M, Lorig-Roach R, Shafin K, Aganezov S, Olson D, de Lima LG, Potapova T, Hartley GA, Haukness M, Kerpedjiev P, Gusev F, Tigyi K, Brooks S, Young A, Nurk S, Koren S, Salama SR, Paten B, Rogaev EI, Streets A, Karpen GH, Dernburg AF, Sullivan BA, Straight AF, Wheeler TJ, Gerton JL, Eichler EE, Phillippy AM, Timp W, Dennis MY, O'Neill RJ, Zook JM, Schatz MC, Pevzner PA, Diekhans M, Langley CH, Alexandrov IA, Miga KH. Complete genomic and epigenetic maps of human centromeres. Science 2022; 376:eabl4178. [PMID: 35357911 PMCID: PMC9233505 DOI: 10.1126/science.abl4178] [Citation(s) in RCA: 157] [Impact Index Per Article: 78.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Existing human genome assemblies have almost entirely excluded repetitive sequences within and near centromeres, limiting our understanding of their organization, evolution, and functions, which include facilitating proper chromosome segregation. Now, a complete, telomere-to-telomere human genome assembly (T2T-CHM13) has enabled us to comprehensively characterize pericentromeric and centromeric repeats, which constitute 6.2% of the genome (189.9 megabases). Detailed maps of these regions revealed multimegabase structural rearrangements, including in active centromeric repeat arrays. Analysis of centromere-associated sequences uncovered a strong relationship between the position of the centromere and the evolution of the surrounding DNA through layered repeat expansions. Furthermore, comparisons of chromosome X centromeres across a diverse panel of individuals illuminated high degrees of structural, epigenetic, and sequence variation in these complex and rapidly evolving regions.
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Affiliation(s)
- Nicolas Altemose
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - A. Glennis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Andrey V. Bzikadze
- Graduate Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla, CA, USA
| | - Pragya Sidhwani
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Sasha A. Langley
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Gina V. Caldas
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Savannah J. Hoyt
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Lev Uralsky
- Sirius University of Science and Technology, Sochi, Russia
- Vavilov Institute of General Genetics, Moscow, Russia
| | | | - Colin J. Shew
- Genome Center, MIND Institute, and Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, USA
| | | | | | - Ariel Gershman
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD, USA
| | - Alla Mikheenko
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
| | | | - Tatiana Dvorkina
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
| | - Olga Kunyavskaya
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
| | - Mitchell R. Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ann M. McCartney
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mobin Asri
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Ryan Lorig-Roach
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Kishwar Shafin
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Sergey Aganezov
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Daniel Olson
- Department of Computer Science, University of Montana, Missoula, MT. USA
| | | | - Tamara Potapova
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Gabrielle A. Hartley
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Marina Haukness
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | | | - Fedor Gusev
- Vavilov Institute of General Genetics, Moscow, Russia
| | - Kristof Tigyi
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Shelise Brooks
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alice Young
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sergey Nurk
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sofie R. Salama
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, CA, USA
| | - Evgeny I. Rogaev
- Sirius University of Science and Technology, Sochi, Russia
- Vavilov Institute of General Genetics, Moscow, Russia
- Department of Psychiatry, University of Massachusetts Medical School, Worcester, MA, USA
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Aaron Streets
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Gary H. Karpen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- BioEngineering and BioMedical Sciences Department, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Abby F. Dernburg
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
| | - Beth A. Sullivan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | | | - Travis J. Wheeler
- Department of Computer Science, University of Montana, Missoula, MT. USA
| | - Jennifer L. Gerton
- Stowers Institute for Medical Research, Kansas City, MO, USA
- University of Kansas Medical School, Department of Biochemistry and Molecular Biology and Cancer Center, University of Kansas, Kansas City, KS, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Adam M. Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Winston Timp
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Megan Y. Dennis
- Genome Center, MIND Institute, and Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, USA
| | - Rachel J. O'Neill
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Justin M. Zook
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Michael C. Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Pavel A. Pevzner
- Department of Computer Science and Engineering, University of California at San Diego, San Diego, CA, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Charles H. Langley
- Department of Evolution and Ecology, University of California Davis, Davis, CA, USA
| | - Ivan A. Alexandrov
- Vavilov Institute of General Genetics, Moscow, Russia
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Karen H. Miga
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, CA, USA
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11
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Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A, Aganezov S, Hoyt SJ, Diekhans M, Logsdon GA, Alonge M, Antonarakis SE, Borchers M, Bouffard GG, Brooks SY, Caldas GV, Chen NC, Cheng H, Chin CS, Chow W, de Lima LG, Dishuck PC, Durbin R, Dvorkina T, Fiddes IT, Formenti G, Fulton RS, Fungtammasan A, Garrison E, Grady PG, Graves-Lindsay TA, Hall IM, Hansen NF, Hartley GA, Haukness M, Howe K, Hunkapiller MW, Jain C, Jain M, Jarvis ED, Kerpedjiev P, Kirsche M, Kolmogorov M, Korlach J, Kremitzki M, Li H, Maduro VV, Marschall T, McCartney AM, McDaniel J, Miller DE, Mullikin JC, Myers EW, Olson ND, Paten B, Peluso P, Pevzner PA, Porubsky D, Potapova T, Rogaev EI, Rosenfeld JA, Salzberg SL, Schneider VA, Sedlazeck FJ, Shafin K, Shew CJ, Shumate A, Sims Y, Smit AFA, Soto DC, Sović I, Storer JM, Streets A, Sullivan BA, Thibaud-Nissen F, Torrance J, Wagner J, Walenz BP, Wenger A, Wood JMD, Xiao C, Yan SM, Young AC, Zarate S, Surti U, McCoy RC, Dennis MY, Alexandrov IA, Gerton JL, O’Neill RJ, Timp W, Zook JM, Schatz MC, Eichler EE, Miga KH, Phillippy AM. The complete sequence of a human genome. Science 2022; 376:44-53. [PMID: 35357919 PMCID: PMC9186530 DOI: 10.1126/science.abj6987] [Citation(s) in RCA: 894] [Impact Index Per Article: 447.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Since its initial release in 2000, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing the remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium presents a complete 3.055 billion-base pair sequence of a human genome, T2T-CHM13, that includes gapless assemblies for all chromosomes except Y, corrects errors in the prior references, and introduces nearly 200 million base pairs of sequence containing 1956 gene predictions, 99 of which are predicted to be protein coding. The completed regions include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies.
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Affiliation(s)
- Sergey Nurk
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
| | - Mikko Rautiainen
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
| | - Andrey V. Bzikadze
- Graduate Program in Bioinformatics and Systems Biology, University of California, San Diego; La Jolla, CA, USA
| | - Alla Mikheenko
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University; Saint Petersburg, Russia
| | - Mitchell R. Vollger
- Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA
| | - Nicolas Altemose
- Department of Bioengineering, University of California, Berkeley; Berkeley, CA, USA
| | - Lev Uralsky
- Sirius University of Science and Technology; Sochi, Russia
- Vavilov Institute of General Genetics; Moscow, Russia
| | - Ariel Gershman
- Department of Molecular Biology and Genetics, Johns Hopkins University; Baltimore, MD, USA
| | - Sergey Aganezov
- Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
| | - Savannah J. Hoyt
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut; Storrs, CT, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
| | - Glennis A. Logsdon
- Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA
| | - Michael Alonge
- Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
| | | | | | - Gerard G. Bouffard
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
| | - Shelise Y. Brooks
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
| | - Gina V. Caldas
- Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA, USA
| | - Nae-Chyun Chen
- Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
| | - Haoyu Cheng
- Department of Data Sciences, Dana-Farber Cancer Institute; Boston, MA
- Department of Biomedical Informatics, Harvard Medical School; Boston, MA
| | | | | | | | - Philip C. Dishuck
- Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA
| | - Richard Durbin
- Wellcome Sanger Institute; Cambridge, UK
- Department of Genetics, University of Cambridge; Cambridge, UK
| | - Tatiana Dvorkina
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University; Saint Petersburg, Russia
| | | | - Giulio Formenti
- Laboratory of Neurogenetics of Language and The Vertebrate Genome Lab, The Rockefeller University; New York, NY, USA
- Howard Hughes Medical Institute; Chevy Chase, MD, USA
| | - Robert S. Fulton
- Department of Genetics, Washington University School of Medicine; St. Louis, MO, USA
| | | | - Erik Garrison
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
- University of Tennessee Health Science Center; Memphis, TN, USA
| | - Patrick G.S. Grady
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut; Storrs, CT, USA
| | | | - Ira M. Hall
- Department of Genetics, Yale University School of Medicine; New Haven, CT, USA
| | - Nancy F. Hansen
- Comparative Genomics Analysis Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
| | - Gabrielle A. Hartley
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut; Storrs, CT, USA
| | - Marina Haukness
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
| | | | | | - Chirag Jain
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
- Department of Computational and Data Sciences, Indian Institute of Science; Bangalore KA, India
| | - Miten Jain
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
| | - Erich D. Jarvis
- Laboratory of Neurogenetics of Language and The Vertebrate Genome Lab, The Rockefeller University; New York, NY, USA
- Howard Hughes Medical Institute; Chevy Chase, MD, USA
| | | | - Melanie Kirsche
- Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
| | - Mikhail Kolmogorov
- Department of Computer Science and Engineering, University of California, San Diego; San Diego, CA, USA
| | | | - Milinn Kremitzki
- McDonnell Genome Institute, Washington University in St. Louis; St. Louis, MO, USA
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute; Boston, MA
- Department of Biomedical Informatics, Harvard Medical School; Boston, MA
| | - Valerie V. Maduro
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
| | - Tobias Marschall
- Heinrich Heine University Düsseldorf, Medical Faculty, Institute for Medical Biometry and Bioinformatics; Düsseldorf, Germany
| | - Ann M. McCartney
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
| | - Jennifer McDaniel
- Biosystems and Biomaterials Division, National Institute of Standards and Technology; Gaithersburg, MD, USA
| | - Danny E. Miller
- Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children’s Hospital; Seattle, WA, USA
| | - James C. Mullikin
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
- Comparative Genomics Analysis Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
| | - Eugene W. Myers
- Max-Planck Institute of Molecular Cell Biology and Genetics; Dresden, Germany
| | - Nathan D. Olson
- Biosystems and Biomaterials Division, National Institute of Standards and Technology; Gaithersburg, MD, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
| | | | - Pavel A. Pevzner
- Department of Computer Science and Engineering, University of California, San Diego; San Diego, CA, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA
| | - Tamara Potapova
- Stowers Institute for Medical Research; Kansas City, MO, USA
| | - Evgeny I. Rogaev
- Sirius University of Science and Technology; Sochi, Russia
- Vavilov Institute of General Genetics; Moscow, Russia
- Department of Psychiatry, University of Massachusetts Medical School; Worcester, MA, USA
- Faculty of Biology, Lomonosov Moscow State University; Moscow, Russia
| | | | - Steven L. Salzberg
- Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University; Baltimore, MD, USA
| | - Valerie A. Schneider
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health; Bethesda, MD, USA
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine; Houston TX, USA
| | - Kishwar Shafin
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
| | - Colin J. Shew
- Genome Center, MIND Institute, Department of Biochemistry and Molecular Medicine, University of California, Davis; CA, USA
| | - Alaina Shumate
- Department of Biomedical Engineering, Johns Hopkins University; Baltimore, MD, USA
| | - Ying Sims
- Wellcome Sanger Institute; Cambridge, UK
| | | | - Daniela C. Soto
- Genome Center, MIND Institute, Department of Biochemistry and Molecular Medicine, University of California, Davis; CA, USA
| | - Ivan Sović
- Pacific Biosciences; Menlo Park, CA, USA
- Digital BioLogic d.o.o.; Ivanić-Grad, Croatia
| | | | - Aaron Streets
- Department of Bioengineering, University of California, Berkeley; Berkeley, CA, USA
- Chan Zuckerberg Biohub; San Francisco, CA, USA
| | - Beth A. Sullivan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine; Durham, NC, USA
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health; Bethesda, MD, USA
| | | | - Justin Wagner
- Biosystems and Biomaterials Division, National Institute of Standards and Technology; Gaithersburg, MD, USA
| | - Brian P. Walenz
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
| | | | | | - Chunlin Xiao
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health; Bethesda, MD, USA
| | - Stephanie M. Yan
- Department of Biology, Johns Hopkins University; Baltimore, MD, USA
| | - Alice C. Young
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
| | - Samantha Zarate
- Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
| | - Urvashi Surti
- Department of Pathology, University of Pittsburgh; Pittsburgh, PA, USA
| | - Rajiv C. McCoy
- Department of Biology, Johns Hopkins University; Baltimore, MD, USA
| | - Megan Y. Dennis
- Genome Center, MIND Institute, Department of Biochemistry and Molecular Medicine, University of California, Davis; CA, USA
| | - Ivan A. Alexandrov
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University; Saint Petersburg, Russia
- Vavilov Institute of General Genetics; Moscow, Russia
- Research Center of Biotechnology of the Russian Academy of Sciences; Moscow, Russia
| | - Jennifer L. Gerton
- Stowers Institute for Medical Research; Kansas City, MO, USA
- Department of Biochemistry and Molecular Biology, University of Kansas Medical School; Kansas City, MO, USA
| | - Rachel J. O’Neill
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut; Storrs, CT, USA
| | - Winston Timp
- Department of Molecular Biology and Genetics, Johns Hopkins University; Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University; Baltimore, MD, USA
| | - Justin M. Zook
- Biosystems and Biomaterials Division, National Institute of Standards and Technology; Gaithersburg, MD, USA
| | - Michael C. Schatz
- Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
- Department of Biology, Johns Hopkins University; Baltimore, MD, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA
- Howard Hughes Medical Institute; Chevy Chase, MD, USA
| | - Karen H. Miga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, CA, USA
| | - Adam M. Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
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12
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Erofeeva TV, Grigorenko AP, Gusev FE, Kosevich IA, Rogaev EI. Studying of Molecular Regulation of Developmental Processes of Lower Metazoans Exemplified by Cnidaria Using High-Throughput Sequencing. Biochemistry (Mosc) 2022; 87:269-293. [PMID: 35526848 DOI: 10.1134/s0006297922030075] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/13/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
A unique set of features and characteristics of species of the Cnidaria phylum is the one reason that makes them a model for a various studies. The plasticity of a life cycle and the processes of cell differentiation and development of an integral multicellular organism associated with it are of a specific scientific interest. A new stage of development of molecular genetic methods, including methods for high-throughput genome, transcriptome, and epigenome sequencing, both at the level of the whole organism and at the level of individual cells, makes it possible to obtain a detailed picture of the development of these animals. This review examines some modern approaches and advances in the reconstruction of the processes of ontogenesis of cnidarians by studying the regulatory signal transduction pathways and their interactions.
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Affiliation(s)
- Taisia V Erofeeva
- Department Research Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Krasnodar Region, 354349, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Anastasia P Grigorenko
- Department Research Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Krasnodar Region, 354349, Russia.
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Fedor E Gusev
- Department Research Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Krasnodar Region, 354349, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Igor A Kosevich
- Department Research Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Krasnodar Region, 354349, Russia
- Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Evgeny I Rogaev
- Department Research Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Krasnodar Region, 354349, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
- Lomonosov Moscow State University, Moscow, 119234, Russia
- Department of Psychiatry, UMass Chan Medical School, Shrewsbury, MA 01545, USA
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13
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Malyarchuk AB, Andreeva TV, Kuznetsova IL, Kunizheva SS, Protasova MS, Uralsky LI, Tyazhelova TV, Gusev FE, Manakhov AD, Rogaev EI. Genomics of Ancient Pathogens: First Advances and Prospects. Biochemistry Moscow 2022; 87:242-258. [PMID: 35526849 PMCID: PMC8916790 DOI: 10.1134/s0006297922030051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Paleogenomics is one of the urgent and promising areas of interdisciplinary research in the today’s world science. New genomic methods of ancient DNA (aDNA) analysis, such as next generation sequencing (NGS) technologies, make it possible not only to obtain detailed genetic information about historical and prehistoric human populations, but also to study individual microbial and viral pathogens and microbiomes from different ancient and historical objects. Studies of aDNA of pathogens by reconstructing their genomes have so far yielded complete sequences of the ancient pathogens that played significant role in the history of the world: Yersiniapestis (plague), Variola virus (smallpox), Vibriocholerae (cholera), HBV (hepatitis B virus), as well as the equally important endemic human infectious agents: Mycobacteriumtuberculosis (tuberculosis), Mycobacteriumleprae (leprosy), and Treponemapallidum (syphilis). Genomic data from these pathogens complemented the information previously obtained by paleopathologists and allowed not only to identify pathogens from the past pandemics, but also to recognize the pathogen lineages that are now extinct, to refine chronology of the pathogen appearance in human populations, and to reconstruct evolutionary history of the pathogens that are still relevant to public health today. In this review, we describe state-of-the-art genomic research of the origins and evolution of many ancient pathogens and viruses and examine mechanisms of the emergence and spread of the ancient infections in the mankind history.
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Affiliation(s)
- Alexandra B Malyarchuk
- Center for Genetics and Genetic Technologies, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
| | - Tatiana V Andreeva
- Center for Genetics and Genetic Technologies, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
| | - Irina L Kuznetsova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, 354340, Russia
| | - Svetlana S Kunizheva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, 354340, Russia
| | - Maria S Protasova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
| | - Lev I Uralsky
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, 354340, Russia
| | - Tatiana V Tyazhelova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
| | - Fedor E Gusev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
| | - Andrey D Manakhov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, 354340, Russia
| | - Evgeny I Rogaev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia.
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, 354340, Russia
- Department of Psychiatry, UMass Chan Medical School, Shrewsbury, MA 01545, USA
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14
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Grigorenko AP, Protasova MS, Lisenkova AA, Reshetov DA, Andreeva TV, Garcias GDL, Martino Roth MDG, Papassotiropoulos A, Rogaev EI. Neurodevelopmental Syndrome with Intellectual Disability, Speech Impairment, and Quadrupedia Is Associated with Glutamate Receptor Delta 2 Gene Defect. Cells 2022; 11:400. [PMID: 35159210 PMCID: PMC8834146 DOI: 10.3390/cells11030400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/16/2022] [Accepted: 01/19/2022] [Indexed: 02/05/2023] Open
Abstract
Bipedalism, speech, and intellect are the most prominent traits that emerged in the evolution of Homo sapiens. Here, we describe a novel genetic cause of an "involution" phenotype in four patients, who are characterized by quadrupedal locomotion, intellectual impairment, the absence of speech, small stature, and hirsutism, observed in a consanguineous Brazilian family. Using whole-genome sequencing analysis and homozygous genetic mapping, we identified genes bearing homozygous genetic variants and found a homozygous 36.2 kb deletion in the gene of glutamate receptor delta 2 (GRID2) in the patients, resulting in the lack of a coding region from the fifth to the seventh exons. The GRID2 gene is highly expressed in the cerebellum cortex from prenatal development to adulthood, specifically in Purkinje neurons. Deletion in this gene leads to the loss of the alpha chain in the extracellular amino-terminal protein domain (ATD), essential in protein folding and transport from the endoplasmic reticulum (ER) to the cell surface. Then, we studied the evolutionary trajectories of the GRID2 gene. There was no sign of strong selection of the highly conservative GRID2 gene in ancient hominids (Neanderthals and Denisovans) or modern humans; however, according to in silico tests using the Mfold tool, the GRID2 gene possibly gained human-specific mutations that increased the stability of GRID2 mRNA.
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Affiliation(s)
- Anastasia P. Grigorenko
- Center for Genetics and Life Science, Sirius University of Science and Technology, 354340 Sochi, Russia; (A.P.G.); (T.V.A.)
- Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia; (M.S.P.); (A.A.L.); (D.A.R.)
- Department of Psychiatry, UMass Chan Medical School, Shrewsbury, MA 01545, USA
| | - Maria S. Protasova
- Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia; (M.S.P.); (A.A.L.); (D.A.R.)
| | - Alexandra A. Lisenkova
- Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia; (M.S.P.); (A.A.L.); (D.A.R.)
| | - Denis A. Reshetov
- Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia; (M.S.P.); (A.A.L.); (D.A.R.)
| | - Tatiana V. Andreeva
- Center for Genetics and Life Science, Sirius University of Science and Technology, 354340 Sochi, Russia; (A.P.G.); (T.V.A.)
- Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia; (M.S.P.); (A.A.L.); (D.A.R.)
- Center for Genetics and Genetic Technologies, Department of Genetics, Faculty of Biology, Lomonosov Moscow State University, 119192 Moscow, Russia
| | - Gilberto De Lima Garcias
- Catholic University of Pelotas, Pelotas 96015-560, RS, Brazil; (G.D.L.G.); (M.D.G.M.R.)
- Federal University of Pelotas, Pelotas 96010-610, RS, Brazil
| | | | - Andreas Papassotiropoulos
- Transfaculty Research Platform, University of Basel, CH-4055 Basel, Switzerland;
- Psychiatric University Clinics, University of Basel, CH-4055 Basel, Switzerland
| | - Evgeny I. Rogaev
- Center for Genetics and Life Science, Sirius University of Science and Technology, 354340 Sochi, Russia; (A.P.G.); (T.V.A.)
- Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia; (M.S.P.); (A.A.L.); (D.A.R.)
- Department of Psychiatry, UMass Chan Medical School, Shrewsbury, MA 01545, USA
- Center for Genetics and Genetic Technologies, Department of Genetics, Faculty of Biology, Lomonosov Moscow State University, 119192 Moscow, Russia
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15
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Ponomareva NV, Andreeva T, Protasova M, Kolesnikova EV, Malina D, Fokin V, Illarioshkin S, Rogaev EI. Genetic association of APOE epsilon2 genotype with neurophysiological characteristics in healthy adults. Alzheimers Dement 2021. [DOI: 10.1002/alz.056413] [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: 11/05/2022]
Affiliation(s)
| | - Tatiana Andreeva
- Vavilov Institute of General Genetics of Russian Academy of Science Moscow Russian Federation
| | - Maria Protasova
- Department of Human Genetics and Genomics Vavilov Institute of General Genetics of Russian Academy of Science Moscow Russia
| | | | - Daria Malina
- Research Center of Neurology Moscow Russian Federation
| | - Vitaly Fokin
- Research Center of Neurology Moscow Russian Federation
| | | | - Evgeny I Rogaev
- Vavilov Institute of General Genetics of Russian Academy of Science Moscow Russian Federation
- University of Massachusetts Medical School Worcester MA USA
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16
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Aliseychik MP, Patrikeev A, Gusev F, Grigorenko A, Andreeva T, Biragyn A, Rogaev EI. Properties of TCR gamma clonotypes in AD brain and peripheral blood. Alzheimers Dement 2020. [DOI: 10.1002/alz.042028] [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: 11/09/2022]
Affiliation(s)
- Maria P. Aliseychik
- University of Massachusetts Medical School Worcester MA USA
- Vavilov Institute of General Genetics of Russian Academy of Science Moscow Russia
- Center for Genetics and Genetic Technologies Faculty of Biology Lomonosov Moscow State University Moscow Russia
| | - Anton Patrikeev
- Vavilov Institute of General Genetics of Russian Academy of Science Moscow Russia
| | - Fedor Gusev
- Vavilov Institute of General Genetics of Russian Academy of Science Moscow Russia
| | - Anastasia Grigorenko
- University of Massachusetts Medical School Worcester MA USA
- Vavilov Institute of General Genetics of Russian Academy of Science Moscow Russia
| | - Tatiana Andreeva
- Vavilov Institute of General Genetics of Russian Academy of Science Moscow Russia
- Center for Genetics and Genetic Technologies Faculty of Biology Lomonosov Moscow State University Moscow Russia
| | - Arya Biragyn
- Immunoregulation Section National Institute on Aging Baltimore MD USA
| | - Evgeny I. Rogaev
- University of Massachusetts Medical School Worcester MA USA
- Vavilov Institute of General Genetics of Russian Academy of Science Moscow Russia
- Center for Genetics and Genetic Technologies Faculty of Biology Lomonosov Moscow State University Moscow Russia
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17
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Manakhov AD, Andreeva TV, Rogaev EI. The curly coat phenotype of the Ural Rex feline breed is associated with a mutation in the lipase H gene. Anim Genet 2020; 51:584-589. [PMID: 32463158 DOI: 10.1111/age.12958] [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] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2020] [Indexed: 01/03/2023]
Abstract
Mutations in lipase H (LIPH) and lysophosphatidic acid receptor 6 (LPAR6), which are essential for the lysophosphatidic acid (LPA) signalling pathway, are associated with hypotrichosis and wooly hair in humans. Mutations in LPAR6 and keratin 71 (KRT71), result in unusual fur growth and hair structure in several cat breeds (Cornish Rex, Devon Rex and Selkirk Rex). Here, we performed target sequencing of the LIPH, LPAR6 and KRT71 genes in six cat breeds with specific hair-growth phenotypes. A LIPH genetic variant (LIPH:c.478_483del; LIPH:p.Ser160_Gly161del) was found in Ural Rex cats with curly coats from Russia, but was absent in all other cat breeds tested. In silico three-dimensional analysis of the LIPH mutant protein revealed a contraction of the α3-helix structure in the enzyme phospholipid binding site that may affect its activity.
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Affiliation(s)
- A D Manakhov
- Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina str., 3, Moscow, 119333, Russia.,Centre for Genetics and Genetic Technologies, Faculty of Biology, Lomonosov Moscow State University, Lomonosovsky prospekt, 27-1, Moscow, 119192, Russia
| | - T V Andreeva
- Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina str., 3, Moscow, 119333, Russia.,Centre for Genetics and Genetic Technologies, Faculty of Biology, Lomonosov Moscow State University, Lomonosovsky prospekt, 27-1, Moscow, 119192, Russia
| | - E I Rogaev
- Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina str., 3, Moscow, 119333, Russia.,Centre for Genetics and Genetic Technologies, Faculty of Biology, Lomonosov Moscow State University, Lomonosovsky prospekt, 27-1, Moscow, 119192, Russia.,Department of Psychiatry, University of Massachusetts Medical School, Maple Avenue, 222, Shrewsbury, MA, 01545, USA
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18
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Gusev FE, Reshetov DA, Mitchell AC, Andreeva TV, Dincer A, Grigorenko AP, Fedonin G, Halene T, Aliseychik M, Goltsov AY, Solovyev V, Brizgalov L, Filippova E, Weng Z, Akbarian S, Rogaev EI. Epigenetic-genetic chromatin footprinting identifies novel and subject-specific genes active in prefrontal cortex neurons. FASEB J 2019; 33:8161-8173. [PMID: 30970224 DOI: 10.1096/fj.201802646r] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Human prefrontal cortex (PFC) is associated with broad individual variabilities in functions linked to personality, social behaviors, and cognitive functions. The phenotype variabilities associated with brain functions can be caused by genetic or epigenetic factors. The interactions between these factors in human subjects is, as of yet, poorly understood. The heterogeneity of cerebral tissue, consisting of neuronal and nonneuronal cells, complicates the comparative analysis of gene activities in brain specimens. To approach the underlying neurogenomic determinants, we performed a deep analysis of open chromatin-associated histone methylation in PFC neurons sorted from multiple human individuals in conjunction with whole-genome and transcriptome sequencing. Integrative analyses produced novel unannotated neuronal genes and revealed individual-specific chromatin "blueprints" of neurons that, in part, relate to genetic background. Surprisingly, we observed gender-dependent epigenetic signals, implying that gender may contribute to the chromatin variabilities in neurons. Finally, we found epigenetic, allele-specific activation of the testis-specific gene nucleoporin 210 like (NUP210L) in brain in some individuals, which we link to a genetic variant occurring in <3% of the human population. Recently, the NUP210L locus has been associated with intelligence and mathematics ability. Our findings highlight the significance of epigenetic-genetic footprinting for exploring neurologic function in a subject-specific manner.-Gusev, F. E., Reshetov, D. A., Mitchell, A. C., Andreeva, T. V., Dincer, A., Grigorenko, A. P., Fedonin, G., Halene, T., Aliseychik, M., Goltsov, A. Y., Solovyev, V., Brizgalov, L., Filippova, E., Weng, Z., Akbarian, S., Rogaev, E. I. Epigenetic-genetic chromatin footprinting identifies novel and subject-specific genes active in prefrontal cortex neurons.
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Affiliation(s)
- Fedor E Gusev
- Department of Psychiatry, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Department of Human Genetics and Genomics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics of Russian Academy of Science, Moscow, Russia.,Center of Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Denis A Reshetov
- Department of Human Genetics and Genomics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics of Russian Academy of Science, Moscow, Russia.,Center of Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Amanda C Mitchell
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Tatiana V Andreeva
- Department of Human Genetics and Genomics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics of Russian Academy of Science, Moscow, Russia.,Center of Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Aslihan Dincer
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Anastasia P Grigorenko
- Department of Psychiatry, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Department of Human Genetics and Genomics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics of Russian Academy of Science, Moscow, Russia.,Center of Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Gennady Fedonin
- Department of Human Genetics and Genomics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics of Russian Academy of Science, Moscow, Russia
| | - Tobias Halene
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Maria Aliseychik
- Department of Human Genetics and Genomics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics of Russian Academy of Science, Moscow, Russia.,Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Andrey Y Goltsov
- Department of Human Genetics and Genomics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics of Russian Academy of Science, Moscow, Russia
| | - Victor Solovyev
- Department of Cell Biology, Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
| | - Leonid Brizgalov
- Center of Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Elena Filippova
- Department of Psychiatry, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Zhiping Weng
- Department of Cell Biology, Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
| | - Schahram Akbarian
- Department of Psychiatry, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Evgeny I Rogaev
- Department of Psychiatry, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Department of Human Genetics and Genomics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics of Russian Academy of Science, Moscow, Russia.,Center for Genetics and Genetic Technologies, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
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19
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Bryzgalov DV, Kuznetsova IL, Rogaev EI. Enhancement of Declarative Memory: From Genetic Regulation to Non-invasive Stimulation. Biochemistry (Mosc) 2018; 83:1124-1138. [PMID: 30472951 DOI: 10.1134/s0006297918090146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The problem of memory enhancement is extremely important in intellectual activity areas and therapy of different types of dementia, including Alzheimer's disease (AD). The attempts to solve this problem have come from different research fields. In the first part of our review, we describe the results of targeting certain genes involved in memory-associated molecular pathways. The second part of the review is focused on the deep stimulation of brain structures that can slow down memory loss in AD. The third part describes the results of the use of non-invasive brain stimulation techniques for memory modulation, consolidation, and retrieval in healthy people and animal models. Integration of data from different research fields is essential for the development of efficient strategies for memory enhancement.
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Affiliation(s)
- D V Bryzgalov
- Memory, Oscillations, Brain States (MOBS) Team, Brain Plasticity Unit, CNRS UMR 8249, ESPCI Paris, Paris, France.
| | - I L Kuznetsova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - E I Rogaev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia. .,Department of Psychiatry, University of Massachusetts Medical School, Worcester, MA 01605, USA.,Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia.,Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119234, Russia
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20
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Abstract
The current issue is dedicated to the studies of neurodegenerative diseases and memory. Molecular mechanisms and mutant genes have already been revealed for many neurodegenerative diseases. However, in many cases the cause of selective death of neurons in different brain regions remains unclear. Genetic predisposition and aging are well established risk factors in many neurodegenerative diseases. A large body of evidence has been obtained that shows an important role of immune factors in the modulation of neurodegenerative processes. The progress in the treatment of neurodegenerative diseases requires new cell models for identification of non-canonical pharmacological targets and development of approaches for memory regulation. Gene therapy technologies based on genome editing and RNA interference methods are among promising approaches for repairing primary molecular defects underlying neurodegenerative pathologies.
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Affiliation(s)
- E I Rogaev
- Department of Psychiatry, University of Massachusetts Medical School, Worcester, MA 01605, USA. .,Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia.,Lomonosov Moscow State University, Center of Genetics and Genetic Technologies, Moscow, 119991, Russia
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21
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Ponomareva NV, Andreeva TV, Protasova MA, Filippova YV, Kolesnikova EP, Fokin VF, Illarioshkin SN, Rogaev EI. Genetic Association between Alzheimer's Disease Risk Variant of the PICALM Gene and Auditory Event-Related Potentials in Aging. Biochemistry (Mosc) 2018; 83:1075-1082. [PMID: 30472946 DOI: 10.1134/s0006297918090092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Aging and genetic predisposition are major risk factors in age-related neurodegenerative disorders. The most common neurodegenerative disorder is Alzheimer's disease (AD). Genome-wide association studies (GWAS) have identified statistically significant association of the PICALM rs3851179 polymorphism with AD. The PICALM G allele increases the risk of AD, while the A allele has a protective effect. We examined the association of the PICALM rs3851179 polymorphism with parameters of the P3 component of auditory event-related potentials (ERPs) in 87 non-demented volunteers (age, 19-77 years) subdivided into two cohorts younger and older than 50 years of age. We found statistically significant association between the AD risk variant PICALM GG and increase in the P3 latency in subjects over 50 years old. The age-dependent increase in the P3 latency was more pronounced in the PICALM GG carriers than in the carriers of the PICALM AA and PICALM AG genotypes. The observed PICALM-associated changes in the neurophysiological processes indicate a decline in the information processing speed with aging due, probably, to neuronal dysfunction and subclinical neurodegeneration of the neuronal networks in the hippocampus and the frontal and parietal cortical areas. Such changes were less pronounced in the carriers of the PICALM gene A allele, which might explain the protective effect of this allele in the cognitive decline and AD development.
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Affiliation(s)
- N V Ponomareva
- Research Center for Neurology, Moscow, 125367, Russia. .,Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - T V Andreeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia.,Lomonosov Moscow State University, Department of Biology, Center of Genetics and Genetic Technologies, Moscow, 119991, Russia
| | - M A Protasova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | | | | | - V F Fokin
- Research Center for Neurology, Moscow, 125367, Russia
| | | | - E I Rogaev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia. .,Lomonosov Moscow State University, Department of Biology, Center of Genetics and Genetic Technologies, Moscow, 119991, Russia.,Brudnick Neuropsychiatric Research Institute, Department of Psychiatry, University of Massachusetts Medical School, Worcester, USA
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22
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Abstract
Background APOE ε4 allele is most common genetic risk factor for Alzheimer’s disease (AD) and cognitive decline. However, it remains poorly understood why only some carriers of APOE ε4 develop AD and how ethnic variabilities in APOE locus contribute to AD risk. Here, to address the role of APOE haplotypes, we reassessed the diversity of APOE locus in major ethnic groups and in Alzheimer’s Disease Neuroimaging Initiative (ADNI) dataset on patients with AD, and subjects with mild cognitive impairment (MCI), and control non-demented individuals. Results We performed APOE gene haplotype analysis for a short block of five SNPs across the gene using the ADNI whole genome sequencing dataset. The compilation of ADNI data with 1000 Genomes identified the APOE ε4 linked haplotypes, which appeared to be distant for the Asian, African and European populations. The common European ε4-bearing haplotype is associated with AD but not with MCI, and the Africans lack this haplotype. Haplotypic inference revealed alleles that may confer protection against AD. By assessing the DNA methylation profile of the APOE haplotypes, we found that the AD-associated haplotype features elevated APOE CpG content, implying that this locus can also be regulated by genetic-epigenetic interactions. Conclusions We showed that SNP frequency profiles within APOE locus are highly skewed to population-specific haplotypes, suggesting that the ancestral background within different sites at APOE gene may shape the disease phenotype. We propose that our results can be utilized for more specific risk assessment based on population descent of the individuals and on higher specificity of five site haplotypes associated with AD. Electronic supplementary material The online version of this article (10.1186/s12868-018-0413-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vladimir N Babenko
- The Federal Research Center Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Center of Neurobiology and Neurogenetics, Lavrentieva str. 10, Novosibirsk, Russia, 630090. .,Novosibirsk State University, Pirogova Str, 2, Novosibirsk, Russia, 630090.
| | - Dmitry A Afonnikov
- The Federal Research Center Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Center of Neurobiology and Neurogenetics, Lavrentieva str. 10, Novosibirsk, Russia, 630090.,Novosibirsk State University, Pirogova Str, 2, Novosibirsk, Russia, 630090
| | - Elena V Ignatieva
- The Federal Research Center Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Center of Neurobiology and Neurogenetics, Lavrentieva str. 10, Novosibirsk, Russia, 630090.,Novosibirsk State University, Pirogova Str, 2, Novosibirsk, Russia, 630090
| | - Anton V Klimov
- The Federal Research Center Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Center of Neurobiology and Neurogenetics, Lavrentieva str. 10, Novosibirsk, Russia, 630090.,Novosibirsk State University, Pirogova Str, 2, Novosibirsk, Russia, 630090
| | - Fedor E Gusev
- Vavilov Institute of General Genetics RAS, Gubkina str. 3, Moscow, Russia, 119991
| | - Evgeny I Rogaev
- The Federal Research Center Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Center of Neurobiology and Neurogenetics, Lavrentieva str. 10, Novosibirsk, Russia, 630090.,Vavilov Institute of General Genetics RAS, Gubkina str. 3, Moscow, Russia, 119991.,Department of Psychiatry, University of Massachusetts Medical School, BNRI, Worcester, MA, 15604, USA.,Faculty of Biology, Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia, 119234
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Saik OV, Demenkov PS, Ivanisenko TV, Bragina EY, Freidin MB, Goncharova IA, Dosenko VE, Zolotareva OI, Hofestaedt R, Lavrik IN, Rogaev EI, Ivanisenko VA. Novel candidate genes important for asthma and hypertension comorbidity revealed from associative gene networks. BMC Med Genomics 2018; 11:15. [PMID: 29504915 PMCID: PMC6389037 DOI: 10.1186/s12920-018-0331-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Hypertension and bronchial asthma are a major issue for people's health. As of 2014, approximately one billion adults, or ~ 22% of the world population, have had hypertension. As of 2011, 235-330 million people globally have been affected by asthma and approximately 250,000-345,000 people have died each year from the disease. The development of the effective treatment therapies against these diseases is complicated by their comorbidity features. This is often a major problem in diagnosis and their treatment. Hence, in this study the bioinformatical methodology for the analysis of the comorbidity of these two diseases have been developed. As such, the search for candidate genes related to the comorbid conditions of asthma and hypertension can help in elucidating the molecular mechanisms underlying the comorbid condition of these two diseases, and can also be useful for genotyping and identifying new drug targets. RESULTS Using ANDSystem, the reconstruction and analysis of gene networks associated with asthma and hypertension was carried out. The gene network of asthma included 755 genes/proteins and 62,603 interactions, while the gene network of hypertension - 713 genes/proteins and 45,479 interactions. Two hundred and five genes/proteins and 9638 interactions were shared between asthma and hypertension. An approach for ranking genes implicated in the comorbid condition of two diseases was proposed. The approach is based on nine criteria for ranking genes by their importance, including standard methods of gene prioritization (Endeavor, ToppGene) as well as original criteria that take into account the characteristics of an associative gene network and the presence of known polymorphisms in the analysed genes. According to the proposed approach, the genes IL10, TLR4, and CAT had the highest priority in the development of comorbidity of these two diseases. Additionally, it was revealed that the list of top genes is enriched with apoptotic genes and genes involved in biological processes related to the functioning of central nervous system. CONCLUSIONS The application of methods of reconstruction and analysis of gene networks is a productive tool for studying the molecular mechanisms of comorbid conditions. The method put forth to rank genes by their importance to the comorbid condition of asthma and hypertension was employed that resulted in prediction of 10 genes, playing the key role in the development of the comorbid condition. The results can be utilised to plan experiments for identification of novel candidate genes along with searching for novel pharmacological targets.
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Affiliation(s)
- Olga V. Saik
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Pavel S. Demenkov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Timofey V. Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Elena Yu Bragina
- Research Institute of Medical Genetics, Tomsk NRMC, Tomsk, Russia
| | - Maxim B. Freidin
- Research Institute of Medical Genetics, Tomsk NRMC, Tomsk, Russia
| | | | | | - Olga I. Zolotareva
- Bielefeld University, International Research Training Group “Computational Methods for the Analysis of the Diversity and Dynamics of Genomes”, Bielefeld, Germany
| | - Ralf Hofestaedt
- Bielefeld University, Technical Faculty, AG Bioinformatics and Medical Informatics, Bielefeld, Germany
| | - Inna N. Lavrik
- Department of Translational Inflammation, Institute of Experimental Internal Medicine, Otto von Guericke University, Magdeburg, Germany
| | - Evgeny I. Rogaev
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
- University of Massachusetts Medical School, Worcester, MA USA
- Department of Genomics and Human Genetics, Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Center for Genetics and Genetic Technologies, Faculty of Biology, Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Vladimir A. Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
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24
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Protasova MS, Gusev FE, Grigorenko AP, Kuznetsova IL, Rogaev EI, Andreeva TV. Quantitative Analysis of L1-Retrotransposons in Alzheimer's Disease and Aging. Biochemistry (Mosc) 2017; 82:962-971. [PMID: 28941465 DOI: 10.1134/s0006297917080120] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
LINE1 retrotransposons are members of a class of mobile genetic elements capable of retrotransposition in the genome via a process of reverse transcription. LINE1 repeats, integrating into different chromosomal loci, affect the activity of genes and cause different genomic mutations. Somatic variability of the human genome is linked to the activity of some subfamilies of LINE1, in particular, a high level of LINE1 retrotranspositions has been observed in brain tissues. However, the contribution of LINE1 to genomic variability during normal aging and in age-related neurodegenerative diseases is poorly understood. We conducted quantitative real-time PCR analysis of active subfamilies of LINE1 repeats (aL1) using genomic DNA extracted from brain specimens of Alzheimer's disease (AD) patients and individuals without neuropsychiatric pathologies, as well as DNA extracted from blood specimens of individuals of different ages (healthy and AD subjects). Inter-individual quantitative variations of active families of aL1 repeats in the genome were observed. No significant age-dependent differences were identified. Likewise, no difference of aL1 copy number in brain and blood were indicated between AD patients and the aged-matched control group without dementia. These data imply that aging and the AD-associated neurodegenerative process are not the major factors contributing to the retrotransposition processes of active LINE1 repeats.
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Affiliation(s)
- M S Protasova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia.
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25
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Grigorenko AP, Moliaka YK, Plotnikova OV, Smirnov A, Nikishina VA, Goltsov AY, Gusev F, Andreeva TV, Nelson O, Bezprozvanny I, Rogaev EI. Mutational re-modeling of di-aspartyl intramembrane proteases: uncoupling physiologically-relevant activities from those associated with Alzheimer's disease. Oncotarget 2017; 8:82006-82026. [PMID: 29137240 PMCID: PMC5669866 DOI: 10.18632/oncotarget.18299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 10/04/2016] [Accepted: 04/28/2017] [Indexed: 12/18/2022] Open
Abstract
The intramembrane proteolytic activities of presenilins (PSEN1/PS1 and PSEN2/PS2) underlie production of β-amyloid, the key process in Alzheimer’s disease (AD). Dysregulation of presenilin-mediated signaling is linked to cancers. Inhibition of the γ-cleavage activities of PSENs that produce Aβ, but not the ε-like cleavage activity that release physiologically essential transcription activators, is a potential approach for the development of rational therapies for AD. In order to identify whether different activities of PSEN1 can be dissociated, we designed multiple mutations in the evolutionary conserved sites of PSEN1. We tested them in vitro and in vivo assays and compared their activities with mutant isoforms of presenilin-related intramembrane di-aspartyl protease (IMPAS1 (IMP1)/signal peptide peptidase (SPP)). PSEN1 auto-cleavage was more resistant to the mutation remodeling than the ε-like proteolysis. PSEN1 with a G382A or a P433A mutation in evolutionary invariant sites retains functionally important APP ε- and Notch S3- cleavage activities, but G382A inhibits APP γ-cleavage and Aβ production and a P433A elevates Aβ. The G382A variant cannot restore the normal cellular ER Ca2+ leak in PSEN1/PSEN2 double knockout cells, but efficiently rescues the loss-of-function (Egl) phenotype of presenilin in C. elegans. We found that, unlike in PSEN1 knockout cells, endoplasmic reticulum (ER) Ca2+ leak is not changed in the absence of IMP1/SPP. IMP1/SPP with the analogous mutations retained efficiency in cleavage of transmembrane substrates and rescued the lethality of Ce-imp-2 knockouts. In summary, our data show that mutations near the active catalytic sites of intramembrane di-aspartyl proteases have different consequences on proteolytic and signaling functions.
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Affiliation(s)
- Anastasia P Grigorenko
- Department of Psychiatry, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA.,Department of Genomics and Human Genetics, Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991 Russia.,Center for Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Youri K Moliaka
- Department of Psychiatry, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Olga V Plotnikova
- Department of Psychiatry, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Alexander Smirnov
- Department of Psychiatry, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Vera A Nikishina
- Department of Psychiatry, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Andrey Y Goltsov
- Department of Genomics and Human Genetics, Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991 Russia.,Center for Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Fedor Gusev
- Department of Genomics and Human Genetics, Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991 Russia.,Center for Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Tatiana V Andreeva
- Department of Genomics and Human Genetics, Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991 Russia.,Center for Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Omar Nelson
- Department of Physiology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9040, USA
| | - Ilya Bezprozvanny
- Department of Physiology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9040, USA
| | - Evgeny I Rogaev
- Department of Psychiatry, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA.,Department of Genomics and Human Genetics, Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991 Russia.,Center for Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.,Center for Genetics and Genetic Technologies, Faculty of Biology, Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
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26
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Abstract
Alzheimer’s disease (AD) is a terminal, age-related neurological syndrome exhibiting progressive cognitive and memory decline, however AD patients in addition exhibit ancillary neuropsychiatric symptoms (NPSs) and these include aggression. In this communication we provide recent evidence for the mis-regulation of a small family of genes expressed in the human hippocampus that appear to be significantly involved in expression patterns common to both AD and aggression. DNA array- and mRNA transcriptome-based gene expression analysis and candidate gene association and/or genome-wide association studies (CGAS, GWAS) of aggressive attributes in humans have revealed a surprisingly small subset of six brain genes that are also strongly associated with altered gene expression patterns in AD. These genes encoded on five different chromosomes (chr) include the androgen receptor (AR; chrXq12), brain-derived neurotrophic factor (BDNF; chr11p14.1), catechol-O-methyl transferase (COMT; chr22q11.21), neuronal specific nitric oxide synthase (NOS1; chr12q24.22), dopamine beta-hydroxylase (DBH chr9q34.2) and tryptophan hydroxylase (TPH1, chr11p15.1 and TPH2, chr12q21.1). Interestingly, (i) the expression of three of these six genes (COMT, DBH, NOS1) are highly variable; (ii) three of these six genes (COMT, DBH, TPH1) are involved in DA or serotonin metabolism, biosynthesis and/or neurotransmission; and (iii) five of these six genes (AR, BDNF, COMT, DBH, NOS1) have been implicated in the development, onset and/or propagation of schizophrenia. The magnitude of the expression of genes implicated in aggressive behavior appears to be more pronounced in the later stages of AD when compared to MCI. These recent genetic data further indicate that the extent of cognitive impairment may have some bearing on the degree of aggression which accompanies the AD phenotype.
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Affiliation(s)
- Walter J Lukiw
- Louisiana State University (LSU) Neuroscience Center, Louisiana State University Health Science CenterNew Orleans, LA, USA.,Department of Ophthalmology, Louisiana State University Health Science CenterNew Orleans, LA, USA.,Department of Neurology, Louisiana State University Health Science CenterNew Orleans, LA, USA.,Bollinger Professor of Alzheimer's disease (AD), Louisiana State University Health Sciences CenterNew Orleans, LA, USA
| | - Evgeny I Rogaev
- Vavilov Institute of General Genetics, Russian Academy of SciencesMoscow, Russia.,Center for Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of SciencesNovosibirsk, Russia.,Department of Psychiatry, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical SchoolWorcester, MA, USA.,School of Bioengineering and Bioinformatics, Lomonosov Moscow State UniversityMoscow, Russia
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27
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Abstract
Certain cellular proteins normally soluble in the living organism under certain conditions form aggregates with a specific cross-β sheet structure called amyloid. These intra- or extracellular insoluble aggregates (fibers or plaques) are hallmarks of many neurodegenerative pathologies including Alzheimer's disease (AD), Huntington's disease, Parkinson's disease, prion disease, and other progressive neurological diseases that develop in the aging human central nervous system. Amyloid diseases (amyloidoses) are widespread in the elderly human population, a rapidly expanding demographic in many global populations. Increasing age is the most significant risk factor for neurodegenerative diseases associated with amyloid plaques. To date, nearly three dozen different misfolded proteins targeting brain and other organs have been identified in amyloid diseases and AD, the most prevalent neurodegenerative amyloid disease affecting over 15 million people worldwide. Here we (i) highlight the latest data on mechanisms of amyloid formation and further discuss a hypothesis on the amyloid cascade as a primary mechanism of AD pathogenesis and (ii) review the evolutionary aspects of amyloidosis, which allow new insight on human-specific mechanisms of dementia development.
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Affiliation(s)
- T V Andreeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia.
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28
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Ponomareva NV, Andreeva TV, Protasova MS, Shagam LI, Malina DD, Goltsov AY, Fokin VF, Illarioshkin SN, Rogaev EI. Quantitative EEG during normal aging: association with the Alzheimer's disease genetic risk variant in PICALM gene. Neurobiol Aging 2017; 51:177.e1-177.e8. [DOI: 10.1016/j.neurobiolaging.2016.12.010] [Citation(s) in RCA: 9] [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: 03/17/2016] [Revised: 11/14/2016] [Accepted: 12/11/2016] [Indexed: 10/20/2022]
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29
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Ignatieva EV, Afonnikov DA, Saik OV, Rogaev EI, Kolchanov NA. A compendium of human genes regulating feeding behavior and body weight, its functional characterization and identification of GWAS genes involved in brain-specific PPI network. BMC Genet 2016; 17:158. [PMID: 28105929 PMCID: PMC5249002 DOI: 10.1186/s12863-016-0466-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [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] [Indexed: 12/31/2022] Open
Abstract
Background Obesity is heritable. It predisposes to many diseases. The objectives of this study were to create a compendium of genes relevant to feeding behavior (FB) and/or body weight (BW) regulation; to construct and to analyze networks formed by associations between genes/proteins; and to identify the most significant genes, biological processes/pathways, and tissues/organs involved in BW regulation. Results The compendium of genes controlling FB or BW includes 578 human genes. Candidate genes were identified from various sources, including previously published original research and review articles, GWAS meta-analyses, and OMIM (Online Mendelian Inheritance in Man). All genes were ranked according to knowledge about their biological role in body weight regulation and classified according to expression patterns or functional characteristics. Substantial and overrepresented numbers of genes from the compendium encoded cell surface receptors, signaling molecules (hormones, neuropeptides, cytokines), transcription factors, signal transduction proteins, cilium and BBSome components, and lipid binding proteins or were present in the brain-specific list of tissue-enriched genes identified with TSEA tool. We identified 27 pathways from KEGG, REACTOME and BIOCARTA whose genes were overrepresented in the compendium. Networks formed by physical interactions or homological relationships between proteins or interactions between proteins involved in biochemical/signaling pathways were reconstructed and analyzed. Subnetworks and clusters identified by the MCODE tool included genes/proteins associated with cilium morphogenesis, signal transduction proteins (particularly, G protein–coupled receptors, kinases or proteins involved in response to insulin stimulus) and transcription regulation (particularly nuclear receptors). We ranked GWAS genes according to the number of neighbors in three networks and revealed 22 GWAS genes involved in the brain-specific PPI network. On the base of the most reliable PPIs functioning in the brain tissue, new regulatory schemes interpreting relevance to BW regulation are proposed for three GWAS genes (ETV5, LRP1B, and NDUFS3). Conclusions A compendium comprising 578 human genes controlling FB or BW was designed, and the most significant functional groups of genes, biological processes/pathways, and tissues/organs involved in BW regulation were revealed. We ranked genes from the GWAS meta-analysis set according to the number and quality of associations in the networks and then according to their involvement in the brain-specific PPI network and proposed new regulatory schemes involving three GWAS genes (ETV5, LRP1B, and NDUFS3) in BW regulation. The compendium is expected to be useful for pathology risk estimation and for design of new pharmacological approaches in the treatment of human obesity. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0466-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elena V Ignatieva
- Center for Brain Neurobiology and Neurogenetics, The Federal Research Center Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Novosibirsk, 630090, Russia. .,Laboratory of Evolutionary Bioinformatics and Theoretical Genetics, The Federal Research Center Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
| | - Dmitry A Afonnikov
- Center for Brain Neurobiology and Neurogenetics, The Federal Research Center Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia.,Laboratory of Evolutionary Bioinformatics and Theoretical Genetics, The Federal Research Center Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Olga V Saik
- Center for Brain Neurobiology and Neurogenetics, The Federal Research Center Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Evgeny I Rogaev
- Center for Brain Neurobiology and Neurogenetics, The Federal Research Center Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.,BNRI, Department of Psychiatry, University of Massachusetts Medical School, Worcester, MA, 15604, USA
| | - Nikolay A Kolchanov
- Novosibirsk State University, Novosibirsk, 630090, Russia.,Department of Systems Biology, The Federal Research Center Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
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30
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Lisenkova AA, Grigorenko AP, Tyazhelova TV, Andreeva TV, Gusev FE, Manakhov AD, Goltsov AY, Piraino S, Miglietta MP, Rogaev EI. Complete mitochondrial genome and evolutionary analysis of Turritopsis dohrnii, the "immortal" jellyfish with a reversible life-cycle. Mol Phylogenet Evol 2016; 107:232-238. [PMID: 27845203 DOI: 10.1016/j.ympev.2016.11.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 10/10/2016] [Accepted: 11/10/2016] [Indexed: 12/30/2022]
Abstract
Turritopsis dohrnii (Cnidaria, Hydrozoa, Hydroidolina, Anthoathecata) is the only known metazoan that is capable of reversing its life cycle via morph rejuvenation from the adult medusa stage to the juvenile polyp stage. Here, we present a complete mitochondrial (mt) genome sequence of T. dohrnii, which harbors genes for 13 proteins, two transfer RNAs, and two ribosomal RNAs. The T. dohrnii mt genome is characterized by typical features of species in the Hydroidolina subclass, such as a high A+T content (71.5%), reversed transcriptional orientation for the large rRNA subunit gene, and paucity of CGN codons. An incomplete complementary duplicate of the cox1 gene was found at the 5' end of the T. dohrnii mt chromosome, as were variable repeat regions flanking the chromosome. We identified species-specific variations (nad5, nad6, cob, and cox1 genes) and putative selective constraints (atp8, nad1, nad2, and nad5 genes) in the mt genes of T. dohrnii, and predicted alterations in tertiary structures of respiratory chain proteins (NADH4, NADH5, and COX1 proteins) of T. dohrnii. Based on comparative analyses of available hydrozoan mt genomes, we also determined the taxonomic relationships of T. dohrnii, recovering Filifera IV as a paraphyletic taxon, and assessed intraspecific diversity of various Hydrozoa species.
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Affiliation(s)
- A A Lisenkova
- Department of Genomics and Human Genetics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina 3, Moscow 119991, Russia.
| | - A P Grigorenko
- Department of Genomics and Human Genetics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina 3, Moscow 119991, Russia; Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, 303 Belmont Street, Worcester, MA 01604, USA; Center for Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - T V Tyazhelova
- Department of Genomics and Human Genetics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina 3, Moscow 119991, Russia
| | - T V Andreeva
- Department of Genomics and Human Genetics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina 3, Moscow 119991, Russia; Center for Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - F E Gusev
- Department of Genomics and Human Genetics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina 3, Moscow 119991, Russia; Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, 303 Belmont Street, Worcester, MA 01604, USA
| | - A D Manakhov
- Department of Genomics and Human Genetics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina 3, Moscow 119991, Russia; Center of Genetics and Genetic Technologies, Lomonosov Moscow State University, GSP-1, Leninskie Gory, Moscow 119991, Russia
| | - A Yu Goltsov
- Department of Genomics and Human Genetics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina 3, Moscow 119991, Russia
| | - S Piraino
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, I-73100 Lecce, Italy.
| | - M P Miglietta
- Texas A&M University at Galveston, Dept. of Marine Biology, OCSB, Galveston, TX 77553, United States.
| | - E I Rogaev
- Department of Genomics and Human Genetics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina 3, Moscow 119991, Russia; Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, 303 Belmont Street, Worcester, MA 01604, USA; Center for Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; Center of Genetics and Genetic Technologies, Lomonosov Moscow State University, GSP-1, Leninskie Gory, Moscow 119991, Russia.
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31
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Andreeva TV, Tyazhelova TV, Rykalina VN, Gusev FE, Goltsov AY, Zolotareva OI, Aliseichik MP, Borodina TA, Grigorenko AP, Reshetov DA, Ginter EK, Amelina SS, Zinchenko RA, Rogaev EI. Whole exome sequencing links dental tumor to an autosomal-dominant mutation in ANO5 gene associated with gnathodiaphyseal dysplasia and muscle dystrophies. Sci Rep 2016; 6:26440. [PMID: 27216912 PMCID: PMC4877638 DOI: 10.1038/srep26440] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 04/29/2016] [Indexed: 12/19/2022] Open
Abstract
Tumors of the jaws may represent different human disorders and frequently associate with pathologic bone fractures. In this report, we analyzed two affected siblings from a family of Russian origin, with a history of dental tumors of the jaws, in correspondence to original clinical diagnosis of cementoma consistent with gigantiform cementoma (GC, OMIM: 137575). Whole exome sequencing revealed the heterozygous missense mutation c.1067G > A (p.Cys356Tyr) in ANO5 gene in these patients. To date, autosomal-dominant mutations have been described in the ANO5 gene for gnathodiaphyseal dysplasia (GDD, OMIM: 166260), and multiple recessive mutations have been described in the gene for muscle dystrophies (OMIM: 613319, 611307); the same amino acid (Cys) at the position 356 is mutated in GDD. These genetic data and similar clinical phenotypes demonstrate that the GC and GDD likely represent the same type of bone pathology. Our data illustrate the significance of mutations in single amino-acid position for particular bone tissue pathology. Modifying role of genetic variations in another gene on the severity of the monogenic trait pathology is also suggested. Finally, we propose the model explaining the tissue-specific manifestation of clinically distant bone and muscle diseases linked to mutations in one gene.
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Affiliation(s)
- T V Andreeva
- Department of Genomics and Human Genetics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia.,Center for Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - T V Tyazhelova
- Department of Genomics and Human Genetics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia
| | - V N Rykalina
- Max-Planck Institute for Molecular Genetics, Berlin 14195, Germany.,Alacris Theranostics GmbH, Berlin 14195, Germany.,Freie Universitaät Berlin, Berlin 14195, Germany
| | - F E Gusev
- Department of Genomics and Human Genetics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia.,Center for Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - A Yu Goltsov
- Department of Genomics and Human Genetics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia
| | - O I Zolotareva
- Department of Genomics and Human Genetics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia.,Faculty of Bioengineering and Bioinformatics, Center of Genetics and Genetic Technologies, Lomonosov Moscow State University, Moscow 119234, Russia
| | - M P Aliseichik
- Department of Genomics and Human Genetics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia
| | - T A Borodina
- Max-Planck Institute for Molecular Genetics, Berlin 14195, Germany.,Alacris Theranostics GmbH, Berlin 14195, Germany.,Freie Universitaät Berlin, Berlin 14195, Germany
| | - A P Grigorenko
- Department of Genomics and Human Genetics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia.,Center for Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.,Department of Psychiatry, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01604, USA
| | - D A Reshetov
- Department of Genomics and Human Genetics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia
| | - E K Ginter
- Federal State Budgetary Institution «Research Centre for Medical Genetics», Moscow 115478, Russia
| | - S S Amelina
- The Rostov State Medical University, Rostov-on-Don 344022, Russia
| | - R A Zinchenko
- Federal State Budgetary Institution «Research Centre for Medical Genetics», Moscow 115478, Russia.,Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - E I Rogaev
- Department of Genomics and Human Genetics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia.,Center for Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.,Faculty of Bioengineering and Bioinformatics, Center of Genetics and Genetic Technologies, Lomonosov Moscow State University, Moscow 119234, Russia.,Department of Psychiatry, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01604, USA
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Shepelev VA, Uralsky LI, Alexandrov AA, Yurov YB, Rogaev EI, Alexandrov IA. Annotation of suprachromosomal families reveals uncommon types of alpha satellite organization in pericentromeric regions of hg38 human genome assembly. Genom Data 2015; 5:139-146. [PMID: 26167452 PMCID: PMC4496801 DOI: 10.1016/j.gdata.2015.05.035] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- V A Shepelev
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq. 2, Moscow 123182, Russia ; Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia ; Center for Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - L I Uralsky
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq. 2, Moscow 123182, Russia ; Center for Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - A A Alexandrov
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq. 2, Moscow 123182, Russia
| | - Y B Yurov
- Research Center of Mental Health, Russian Academy of Medical Sciences, Zagorodnoe sh. 2, Moscow 113152, Russia
| | - E I Rogaev
- Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia ; Center for Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia ; Department of Psychiatry, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA ; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119234, Russia
| | - I A Alexandrov
- Research Center of Mental Health, Russian Academy of Medical Sciences, Zagorodnoe sh. 2, Moscow 113152, Russia
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Rykalina VN, Shadrin AA, Amstislavskiy VS, Rogaev EI, Lehrach H, Borodina TA. Exome sequencing from nanogram amounts of starting DNA: comparing three approaches. PLoS One 2014; 9:e101154. [PMID: 24992588 PMCID: PMC4081514 DOI: 10.1371/journal.pone.0101154] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 06/03/2014] [Indexed: 01/08/2023] Open
Abstract
Hybridization-based target enrichment protocols require relatively large starting amounts of genomic DNA, which is not always available. Here, we tested three approaches to pre-capture library preparation starting from 10 ng of genomic DNA: (i and ii) whole-genome amplification of DNA samples with REPLI-g (Qiagen) and GenomePlex (Sigma) kits followed by standard library preparation, and (iii) library construction with a low input oriented ThruPLEX kit (Rubicon Genomics). Exome capture with Agilent SureSelectXT2 Human AllExon v4+UTRs capture probes, and HiSeq2000 sequencing were performed for test libraries along with the control library prepared from 1 µg of starting DNA. Tested protocols were characterized in terms of mapping efficiency, enrichment ratio, coverage of the target region, and reliability of SNP genotyping. REPLI-g- and ThruPLEX-FD-based protocols seem to be adequate solutions for exome sequencing of low input samples.
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Affiliation(s)
- Vera N. Rykalina
- Max-Planck Institute for Molecular Genetics, Berlin, Germany
- AlacrisTheranostics GmbH, Berlin, Germany
- Freie Universität Berlin, Berlin, Germany
| | - Alexey A. Shadrin
- Max-Planck Institute for Molecular Genetics, Berlin, Germany
- Freie Universität Berlin, Berlin, Germany
| | | | | | - Hans Lehrach
- Max-Planck Institute for Molecular Genetics, Berlin, Germany
| | - Tatiana A. Borodina
- Max-Planck Institute for Molecular Genetics, Berlin, Germany
- AlacrisTheranostics GmbH, Berlin, Germany
- * E-mail:
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Nizamutdinov II, Andreeva TV, Stepanov VA, Marusin AV, Rogaev EI, Zasedatelev AS, Nasedkina TV. [Biochip for determination of genetic markers of sporadic Alzheimer's disease in the Russian Slavic population]. Mol Biol (Mosk) 2013; 47:949-958. [PMID: 25509857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A biological microchip (biochip) for the genetic predis- position to sporadic form of Alzheimer's disease studying has been developed. The biochip allows determina- tion of ten genetic polymorphisms within APOE, TOMM40, APOJ, EXOC3L2, GAB2, A2M, CR1, BIN1 and PICALM genes. The genotyping assay includes the amplification of loci of interest and further allele-specific hybridization of the fluorescent labeled amplicons with oligonucleotides immobilized on a biochip. Based on the results of genotyping of 166 patients and 128 controls APOE epsilon4 allele was found to be significantly associated with Alzheimer's disease susceptibility (OR = 2.275, 95% CI = 1.045-4.954,p = 0.034). Additionally, protective effects for the APOE epsilon2 allele and CLUT-allele (rs11136000) were observed (OR = 0.215, 95% CI = 0.090-0.516, p = 0.001 and OR = 0.679, 95% CI = 0.47-0.99, p = 0.042, respectively). Gene-gene interaction revealed two genotype combinations associated with Alzheimer's disease: APOE E3/E4 GAB2 G/G (OR = 2.49; CI = 1.43-4.32, p = 0.001) and APOE epsilon4 GAB2 G/G (OR = 3.55, CI = 1.23-10.24,p = 0.015). Based on the results of the combined multivariate analysis the algorithm for identifying of individuals at increased risk of Alzheimer's disease was developed.
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Lukiw WJ, Andreeva TV, Grigorenko AP, Rogaev EI. Studying micro RNA Function and Dysfunction in Alzheimer's Disease. Front Genet 2013; 3:327. [PMID: 23390425 PMCID: PMC3565163 DOI: 10.3389/fgene.2012.00327] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [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: 11/06/2012] [Accepted: 12/28/2012] [Indexed: 01/18/2023] Open
Abstract
Alzheimer’s disease (AD) is a tragic, progressive, age-related neurological dysfunction, representing one of the most prevalent neurodegenerative disorders in industrialized societies. Globally, 5 million new cases of AD are diagnosed annually, with one new AD case being reported every 7 s. Most recently there has been a surge in the study of the regulatory mechanisms of the AD process, and the particular significance of small non-coding ∼22 ribonucleotide RNAs called micro RNAs (miRNAs). Abundant data have profiled miRNA patterns in healthy, aging brain, in mild cognitive impairment (MCI), and in the moderate- and late-stages of AD. The major mode of action of miRNA is to interact, via base-pair complementarity, with ribonucleotides located within the 3′ untranslated region (3′-UTR) of multiple target messenger RNAs (mRNAs), and in doing so decrease the capability of that specific mRNA to be expressed. Many miRNAs are highly cell- and tissue-specific. The human brain appears to use only a highly specific fraction of all known human miRNAs, whose speciation and complexity are defined as a discrete subset of all known small non-coding RNAs (sncRNAs) in the brain. In general, in contrast to normally, aging human brain, in AD a family of pathogenically up-regulated miRNAs appear to be down-regulating the expression certain brain-essential mRNA targets, including key regulatory genes involved interactively in neuroinflammation, synaptogenesis, neurotrophic functions, and amyloidogenesis. These up-regulated, NF-kB-sensitive miRNAs, involved in the innate immune and inflammatory response and synaptic, neurotrophic, and amyloidogenic functions include miRNA-9, miRNA-125b, miRNA-146a, and miRNA-155. Other miRNAs of the miRNA-15/107 family, miRNA-153 and miRNA-190, and others, will be discussed. Overall, this manuscript will review the known contribution of miRNAs to aging brain function and the role they appear to play in the incidence and progression of AD.
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Affiliation(s)
- Walter J Lukiw
- Department of Neurology, LSU Neuroscience Center, Louisiana State University Health Sciences Center New Orleans, LA, USA ; Department of Ophthalmology, LSU Neuroscience Center, Louisiana State University Health Sciences Center New Orleans, LA, USA
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Shulha HP, Crisci JL, Reshetov D, Tushir JS, Cheung I, Bharadwaj R, Chou HJ, Houston IB, Peter CJ, Mitchell AC, Yao WD, Myers RH, Chen JF, Preuss TM, Rogaev EI, Jensen JD, Weng Z, Akbarian S. Human-specific histone methylation signatures at transcription start sites in prefrontal neurons. PLoS Biol 2012; 10:e1001427. [PMID: 23185133 PMCID: PMC3502543 DOI: 10.1371/journal.pbio.1001427] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Accepted: 10/12/2012] [Indexed: 11/18/2022] Open
Abstract
Cognitive abilities and disorders unique to humans are thought to result from adaptively driven changes in brain transcriptomes, but little is known about the role of cis-regulatory changes affecting transcription start sites (TSS). Here, we mapped in human, chimpanzee, and macaque prefrontal cortex the genome-wide distribution of histone H3 trimethylated at lysine 4 (H3K4me3), an epigenetic mark sharply regulated at TSS, and identified 471 sequences with human-specific enrichment or depletion. Among these were 33 loci selectively methylated in neuronal but not non-neuronal chromatin from children and adults, including TSS at DPP10 (2q14.1), CNTN4 and CHL1 (3p26.3), and other neuropsychiatric susceptibility genes. Regulatory sequences at DPP10 and additional loci carried a strong footprint of hominid adaptation, including elevated nucleotide substitution rates and regulatory motifs absent in other primates (including archaic hominins), with evidence for selective pressures during more recent evolution and adaptive fixations in modern populations. Chromosome conformation capture at two neurodevelopmental disease loci, 2q14.1 and 16p11.2, revealed higher order chromatin structures resulting in physical contact of multiple human-specific H3K4me3 peaks spaced 0.5-1 Mb apart, in conjunction with a novel cis-bound antisense RNA linked to Polycomb repressor proteins and downregulated DPP10 expression. Therefore, coordinated epigenetic regulation via newly derived TSS chromatin could play an important role in the emergence of human-specific gene expression networks in brain that contribute to cognitive functions and neurological disease susceptibility in modern day humans.
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Affiliation(s)
- Hennady P. Shulha
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Jessica L. Crisci
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Denis Reshetov
- Department of Human Genetics and Genomics, Vavilov Institute of General Genetics, Moscow, Russian Federation
| | - Jogender S. Tushir
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Iris Cheung
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Rahul Bharadwaj
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Hsin-Jung Chou
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Isaac B. Houston
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Cyril J. Peter
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Amanda C. Mitchell
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Wei-Dong Yao
- New England Primate Center, Southboro, Massachusetts, United States of America
| | - Richard H. Myers
- Department of Neurology, Boston University, Boston, Massachusetts, United States of America
| | - Jiang-fan Chen
- Department of Neurology, Boston University, Boston, Massachusetts, United States of America
| | - Todd M. Preuss
- Yerkes National Primate Research Center/Emory University, Atlanta, Georgia, United States of America
| | - Evgeny I. Rogaev
- Department of Human Genetics and Genomics, Vavilov Institute of General Genetics, Moscow, Russian Federation
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Research Center of Mental Health, Russian Academy of Medical Sciences, Moscow, Russian Federation
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russian Federation
| | - Jeffrey D. Jensen
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Schahram Akbarian
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Departments of Psychiatry and Neuroscience, Friedman Brain Institute, Mount Sinai School of Medicine, New York, New York, United States of America
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Affiliation(s)
- Evgeny I Rogaev
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School Worcester, MA, USA
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38
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Selezneva ND, Roshchina IF, Gavrilova SI, Fedorova IB, Gantman MV, Korovaĭtseva GI, Kunizheva SS, Rogaev EI. [Mental disorders of cognitive and non-cognitive spectrum in the first-degree relatives of patients with Alzheimer's disease]. Zh Nevrol Psikhiatr Im S S Korsakova 2012; 112:8-13. [PMID: 23250590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Mental disorders of cognitive and non-cognitive spectrum in the first-degree relatives of patients with Alzheimer's disease (AD) were studied in 134 relatives, mean age 47.6 years, including 110 children and 24 siblings of probands. Compared to the age-matched controls (22 normals without relatives with AD), the higher frequency of the following mental disorders was found in the relatives: Alzheimer's phobia, irritable weakness, mild cognitive impairment, including difficulties in learning new information and reduced sustained attention due to tiredness (2 times more frequent), difficulties in recollection of remote events (1.4 times more frequent), signs of constitutional cognitive deficit in the anamnesis (2-4 times more frequent), the combinations of two or three types of cognitive deficits (3-4 times more frequent), the combination of communicating hydrocephalus with MRI signs of cerebrovascular pathology (3,4 times more frequent). The data obtained in the study can help develop treatment/ rehabilitation measures to prevent the progression of cognitive deficit.
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Ponomareva NV, Goltsov AY, Kunijeva SS, Scheglova NS, Malina DD, Mitrofanov AA, Boikova TI, Rogaev EI. Age- and genotype-related neurophysiologic reactivity to oxidative stress in healthy adults. Neurobiol Aging 2011; 33:839.e11-21. [PMID: 22206848 DOI: 10.1016/j.neurobiolaging.2011.11.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 07/15/2011] [Accepted: 11/08/2011] [Indexed: 10/14/2022]
Abstract
The epsilon4 allele of the apolipoprotein E gene (ApoE), as well as aging increase the risk of Alzheimer's and vascular diseases. Electroencephalogram (EEG) reactivity to hyperventilation (HV) depends on hypocapnia-induced cerebral vasoconstriction, which may be impaired in subjects with subclinical cerebrovascular disease. Quantitative EEG at rest and under 3-minute HV was examined in 125 healthy subjects divided into younger (age range 28-50) and older (age range 51-82) cohorts and stratified by ApoE genotype. The younger ApoE-epsilon4 carriers had excessive EEG reactivity to HV characterized by the manifestation of high-voltage delta, theta activity and sharp waves, and larger HV-induced changes in EEG relative powers than in the younger ApoE-epsilon4 noncarriers. EEG reactivity to HV decreased with aging, and in the ApoE-epsilon4 carriers the decrease was more pronounced than in the ApoE-epsilon4 noncarriers. The older ApoE-epsilon4 carriers had smaller HV-induced changes in EEG relative powers than the older ApoE-epsilon4 noncarriers. A marked decline of EEG reactivity to HV in the older ApoE-epsilon4 carriers suggests the possible impact of vascular factors on the pathogenesis of ApoE-induced Alzheimer disease.
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Berdichevets IN, Tyazhelova TV, Shimshilashvili KR, Rogaev EI. Lysophosphatidic acid is a lipid mediator with wide range of biological activities. Biosynthetic pathways and mechanism of action. Biochemistry (Mosc) 2011; 75:1088-97. [PMID: 21077828 DOI: 10.1134/s0006297910090026] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Lysophosphatidic acid (LPA) is a lipid mediator required for maintaining homeostasis of numerous physiological functions and also involved in development of some pathological processes through interactions with G protein-coupled receptors. Recently many data have appeared about the role of this phospholipid in humans, but pathways of LPA biosynthesis and mechanisms of its action remain unclear. This review presents modern concepts about biosynthesis, reception, and biological activity of LPA in humans. Natural and synthetic LPA analogs are considered in the view of their possible use in pharmacology as agonists and/or antagonists of G protein-coupled receptors of LPA.
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Affiliation(s)
- I N Berdichevets
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia.
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Underhill PA, Myres NM, Rootsi S, Metspalu M, Zhivotovsky LA, King RJ, Lin AA, Chow CET, Semino O, Battaglia V, Kutuev I, Järve M, Chaubey G, Ayub Q, Mohyuddin A, Mehdi SQ, Sengupta S, Rogaev EI, Khusnutdinova EK, Pshenichnov A, Balanovsky O, Balanovska E, Jeran N, Augustin DH, Baldovic M, Herrera RJ, Thangaraj K, Singh V, Singh L, Majumder P, Rudan P, Primorac D, Villems R, Kivisild T. Erratum: Separating the post-Glacial coancestry of European and Asian Y chromosomes within haplogroup R1a. Eur J Hum Genet 2010. [DOI: 10.1038/ejhg.2010.65] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Golenkina SA, Gol'tsov AI, Kuznetsova IL, Grigorenko AP, Andreeva TV, Reshetov DA, Kunizheva SS, Shagam LI, Morozova II, Goldenkova-Pavlova IV, Shimshilashvili K, Viacheslavova AO, Faskhutdinova G, Gareeva AÉ, Zaĭnullina AG, Khusnutdinova ÉK, Puzyrev VP, Stepanov VA, Kolotvin AV, Samokhodskaia LM, Selezneva ND, Gavrilova SI, Rogaev EI. [Analysis of clusterin gene (CLU/APOJ) polymorphism in Alzheimer's disease patients and in normal cohorts from Russian populations]. Mol Biol (Mosk) 2010; 44:620-626. [PMID: 20873220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Three genes mutations in which cause familial forms of Alzheimer's disease are known to date:PSEN1, PSEN2 and APP; and APOE gene polymorphism is a strong risk factor for Alzheimer's disease. We have evaluated allele and genotype frequency distribution of rs11136000 polymorphism in clusterin (CLU) gene (or apolipoprotein J, APOJ) in populations of three Russian regions and i nAlzheimhner's diseasepatients. Genome-wideassociation studies in samples from several European populations have recently revealed highly significant association o fCLU gene with AD (p = 8.5 x 10(-10)). We found no differences in allele and genotype frequencies of rs11136000 between populations from Moscow, Ural and Siberia regions. The allele frequencies are close to those in European populations. The genetic association analysis in cohort of Alzheimer's disease patients and normal individuals (>500 individuals ineach group) revealed no significant association of the rs11136000 polymorphism in CLU with Alzheimer's disease in Russian populations. Although our resultsdo not confirm the role of CLU gene as a majorgenetic factor forcommon form of Alzheimer's disease, the data do not rule out the possibility of modest effect of CLU and interaction between CLU and APOE genotypes in etiology of Alzheimer's disease.
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Grigorenko AP, Borinskaya SA, Yankovsky NK, Rogaev EI. Achievements and Peculiarities in Studies of Ancient DNA and DNA from Complicated Forensic Specimens. Acta Naturae 2009. [DOI: 10.32607/20758251-2009-1-3-58-69] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Grigorenko AP, Borinskaya SA, Yankovsky NK, Rogaev EI. Achievements and Peculiarities in Studies of Ancient DNA and DNA from Complicated Forensic Specimens. Acta Naturae 2009. [DOI: 10.32607/actanaturae.10766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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45
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Underhill PA, Myres NM, Rootsi S, Metspalu M, Zhivotovsky LA, King RJ, Lin AA, Chow CET, Semino O, Battaglia V, Kutuev I, Järve M, Chaubey G, Ayub Q, Mohyuddin A, Mehdi SQ, Sengupta S, Rogaev EI, Khusnutdinova EK, Pshenichnov A, Balanovsky O, Balanovska E, Jeran N, Augustin DH, Baldovic M, Herrera RJ, Thangaraj K, Singh V, Singh L, Majumder P, Rudan P, Primorac D, Villems R, Kivisild T. Separating the post-Glacial coancestry of European and Asian Y chromosomes within haplogroup R1a. Eur J Hum Genet 2009; 18:479-84. [PMID: 19888303 DOI: 10.1038/ejhg.2009.194] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Human Y-chromosome haplogroup structure is largely circumscribed by continental boundaries. One notable exception to this general pattern is the young haplogroup R1a that exhibits post-Glacial coalescent times and relates the paternal ancestry of more than 10% of men in a wide geographic area extending from South Asia to Central East Europe and South Siberia. Its origin and dispersal patterns are poorly understood as no marker has yet been described that would distinguish European R1a chromosomes from Asian. Here we present frequency and haplotype diversity estimates for more than 2000 R1a chromosomes assessed for several newly discovered SNP markers that introduce the onset of informative R1a subdivisions by geography. Marker M434 has a low frequency and a late origin in West Asia bearing witness to recent gene flow over the Arabian Sea. Conversely, marker M458 has a significant frequency in Europe, exceeding 30% in its core area in Eastern Europe and comprising up to 70% of all M17 chromosomes present there. The diversity and frequency profiles of M458 suggest its origin during the early Holocene and a subsequent expansion likely related to a number of prehistoric cultural developments in the region. Its primary frequency and diversity distribution correlates well with some of the major Central and East European river basins where settled farming was established before its spread further eastward. Importantly, the virtual absence of M458 chromosomes outside Europe speaks against substantial patrilineal gene flow from East Europe to Asia, including to India, at least since the mid-Holocene.
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Affiliation(s)
- Peter A Underhill
- Division of Child and Adolescent Psychiatry and Child Development, Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, 1201 Welch Road, Stanford, CA 94304-5485, USA.
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Abstract
The "royal disease," a blood disorder transmitted from Queen Victoria to European royal families, is a striking example of X-linked recessive inheritance. Although the disease is widely recognized to be a form of the blood clotting disorder hemophilia, its molecular basis has never been identified, and the royal disease is now likely extinct. We identified the likely disease-causing mutation by applying genomic methodologies (multiplex target amplification and massively parallel sequencing) to historical specimens from the Romanov branch of the royal family. The mutation occurs in F9, a gene on the X chromosome that encodes blood coagulation factor IX, and is predicted to alter RNA splicing and to lead to production of a truncated form of factor IX. Thus, the royal disease is the severe form of hemophilia, also known as hemophilia B or Christmas disease.
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Affiliation(s)
- Evgeny I Rogaev
- University of Massachusetts Medical School, 303 Belmont Street, Worcester, MA 01604, USA.
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Grigorenko AP, Borinskaya SA, Yankovsky NK, Rogaev EI. Achievements and peculiarities in studies of ancient DNA and DNA from complicated forensic specimens. Acta Naturae 2009; 1:58-69. [PMID: 22649615 PMCID: PMC3347533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Studies of ancient DNA specimens started 25 years ago. At that time short mitochondrial DNA (mtDNA) fragments were the main targets in ancient DNA studies. The last three years were especially productive in the development of new methods of DNA purification and analysis. Complete mtDNA molecules and relatively large fragments of nuclear DNA are the targets of ancient DNA studies today. Ancient DNA studies allowed us to study organisms that went extinct more than ten thousand years ago, to reconstruct their phenotypic traits and evolution. Ancient DNA analyses can help understand the development of ancient human populations and how they migrated. A new evolutionary hypothesis and reconstruction of the biota history have been re-created from recent ancient DNA data. Some peculiarities and problems specific to the study of ancient DNA were revealed, such as very limited amounts of DNA available for study, the short length of the DNA fragments, breaks and chemical modifications in DNA molecules that result in "postmortem" mutations or complete blockage of DNA replication in vitro. The same specific features of DNA analysis were revealed for specimens from complicated forensic cases that result in the lack of experimental data or interpretation problems.. Here, we list the specific features of ancient DNA methodology and describe some achievements in fundamental and applied research of ancient DNA, including our own work in the field.
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Affiliation(s)
- A P Grigorenko
- Vavliov Institute of General Genetics, Russian Academy of Sciences
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Järve M, Zhivotovsky LA, Rootsi S, Help H, Rogaev EI, Khusnutdinova EK, Kivisild T, Sanchez JJ. Decreased rate of evolution in Y chromosome STR loci of increased size of the repeat unit. PLoS One 2009; 4:e7276. [PMID: 19789645 PMCID: PMC2748704 DOI: 10.1371/journal.pone.0007276] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2009] [Accepted: 09/09/2009] [Indexed: 11/18/2022] Open
Abstract
Background Polymorphic Y chromosome short tandem repeats (STRs) have been widely used in population genetic and evolutionary studies. Compared to di-, tri-, and tetranucleotide repeats, STRs with longer repeat units occur more rarely and are far less commonly used. Principal Findings In order to study the evolutionary dynamics of STRs according to repeat unit size, we analysed variation at 24 Y chromosome repeat loci: 1 tri-, 14 tetra-, 7 penta-, and 2 hexanucleotide loci. According to our results, penta- and hexanucleotide repeats have approximately two times lower repeat variance and diversity than tri- and tetranucleotide repeats, indicating that their mutation rate is about half of that of tri- and tetranucleotide repeats. Thus, STR markers with longer repeat units are more robust in distinguishing Y chromosome haplogroups and, in some cases, phylogenetic splits within established haplogroups. Conclusions Our findings suggest that Y chromosome STRs of increased repeat unit size have a lower rate of evolution, which has significant relevance in population genetic and evolutionary studies.
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Affiliation(s)
- Mari Järve
- Department of Evolutionary Biology, University of Tartu and Estonian Biocentre, Tartu, Estonia.
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Rogaev EI, Borinskaia SA, Islamgulov DV, Grigorenko AP. [Human microRNA in norm and pathology]. Mol Biol (Mosk) 2008; 42:751-764. [PMID: 18988525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
MicroRNAs (miRNAs) are a class of RNA which controls gene expression at the posttranscription level. Binding with the target RNA, a miRNA can supress translation and/or induce degradation of mRNA. The studies of miRNAs have already shown that miRNA were essential to switch the programs of gene expression during embryo development as well as to control cell functioning of the adult organism. Alteration of the miRNA expression profile may appear not less important in development of pathology than better known structural variations of the proteins. The role of miRNA has been confirmed for a range of common diseases connected to impaired balance of cell proliferation, differentiation and programmed death. This review discusses specific features of miRNA-mediated regulation of gene expression and its role in normal and pathological development of muscle, immune, and nervous systems. The evidence of miRNA involvent in neurodegenerative disorders and mental disorders is demonstrated.
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Borinskaia SA, Kal'ina NR, Sanina ED, Kozhekbaeva ZM, Gupalo EI, Garmash IV, Ogurtsov PP, Parshukova ON, Boĭko SG, Veselovskiĭ EM, Vershubskaia GG, Kozlov AI, Rogaev EI, Iankovskiĭ NK. [Polymorphism of the apolipoprotein E gene (APOE) in the populations of Russia and neighboring countries]. Genetika 2007; 43:1434-1440. [PMID: 18069348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Allele and genotype frequencies for the locus encoding apolipoprotein E, involved in the regulation of lipid metabolism (APOE), were evaluated in 16 populations representing 12 ethnic groups (a total of 1103 subjects) from Russia and neighboring countries. In the populations examined, the frequencies of allele epsilon4, which is the risk factor of Alzheimer's disease and coronary heart disease, varied from less than 5 to more than 20%, while the variation of the major epsilon3 allele in these populations ranged from less than 75 to 95%. The frequencies of alleles epsilon3 and epsilon4 were 0.714 and 0.205 in Saami, 0.734 and 0.149 in Maris, 0.841 and 0.122 in Evenks, 0.788 and 0.163 in Buryats, 0.764 and 0.202 in Chukchi, 0.875 and 0.075 in Iranians, 0.956 and 0.044 in mountain-dwellers of the Pamirs, 0.771 and 0.094 in Ukrainians, and 0.795 and 0.091 in Belarussians, respectively. In Russians from different regions of the country, the frequencies of these alleles were 0.728 and 0.139 (Kostroma), 0.795 and 0.105 (Moscow), 0.857 and 0.092 (Rostov-on-Don), and 0.824 and 0.083 (Krasnodar), respectively. The latitudinal distribution of the APOE epsilon3 and epsilon4 allele frequencies in the populations examined was comparable to the frequency distribution pattern of these alleles in other populations of Eurasia.
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