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Vasilyeva OY, Tolmacheva EN, Dmitriev AE, Darkova YA, Sazhenova EA, Nikitina TV, Lebedev IN, Vasilyev SA. Aberrant methylation of placental development genes in chorionic villi of spontaneous abortions with trisomy 16. Vavilovskii Zhurnal Genet Selektsii 2024; 28:198-203. [PMID: 38680176 PMCID: PMC11043499 DOI: 10.18699/vjgb-24-24] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/18/2024] [Accepted: 01/18/2023] [Indexed: 05/01/2024] Open
Abstract
In humans, aneuploidy is incompatible with the birth of healthy children and mainly leads to the death of embryos in the early stages of development in the first trimester of pregnancy. Trisomy 16 is the most common aneuploidy among spontaneous abortions of the first trimester of pregnancy. However, the mechanisms leading to the death of embryos with trisomy 16 remain insufficiently investigated. One of these potential mechanisms is abnormal placental development, including aberrant remodeling of spiral arteries. Spiral artery remodeling involves the migration of trophoblast cells into the maternal spiral arteries, replacing their endothelium and remodeling to ensure a stable embryonic nutrition and oxygen supply. This is a complex process which depends on many factors from both the embryo and the mother. We analyzed the methylation level of seven genes (ADORA2B, NPR3, PRDM1, PSG2, PHTLH, SV2C, and TICAM2) involved in placental development in the chorionic villi of spontaneous abortions with trisomy 16 (n = 14), compared with spontaneous abortions with a normal karyotype (n = 31) and the control group of induced abortions (n = 10). To obtain sequencing libraries, targeted amplification of individual gene regions using designed oligonucleotide primers for bisulfite-converted DNA was used. The analysis was carried out using targeted bisulfite massive parallel sequencing. In the group of spontaneous abortions with trisomy 16, the level of methylation of the PRDM1 and PSG2 genes was significantly increased compared to induced abortions (p = 0.0004 and p = 0.0015, respectively). In the group of spontaneous abortions, there was no increase in the level of methylation of the PRDM1 and PSG2 genes, but the level of methylation of the ADORA2B gene was significantly increased compared to the induced abortions (p = 0.032). The results obtained indicate the potential mechanisms of the pathogenetic effect of trisomy 16 on the placental development with the participation of the studied genes.
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Affiliation(s)
- O Yu Vasilyeva
- Research Institute of Medical Genetics of the Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - E N Tolmacheva
- Research Institute of Medical Genetics of the Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - A E Dmitriev
- National Research Tomsk State University, Tomsk, Russia
| | - Ya A Darkova
- National Research Tomsk State University, Tomsk, Russia
| | - E A Sazhenova
- Research Institute of Medical Genetics of the Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - T V Nikitina
- Research Institute of Medical Genetics of the Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - I N Lebedev
- Research Institute of Medical Genetics of the Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - S A Vasilyev
- Research Institute of Medical Genetics of the Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
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Yudanova SS, Dorogina OV, Vasilyeva OY. Morphological and molecular analysis of rose cultivars from the Grandiflora and Kordesii garden groups. Vavilovskii Zhurnal Genet Selektsii 2024; 28:55-62. [PMID: 38465252 PMCID: PMC10917683 DOI: 10.18699/vjgb-24-07] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 12/11/2023] [Accepted: 12/11/2023] [Indexed: 03/12/2024] Open
Abstract
The breeding of remontant rose cultivars that are resistant to diseases and adverse conditions, with high decorative value and continuous flowering is the most important task during work with the gene pool of garden roses. Currently, intercultivar hybridization within a single garden group has largely outlived its usefulness. It is necessary to breed for highly decorative forms or cultivars that have outstanding resistance, morphological characters and patterns of seasonal rhythms, and use these plants as parental forms in further breeding. This study represents a comparative analysis of rose cultivars from two garden groups, Grandiflora (Gurzuf, Lezginka, Korallovy Syurpriz, Queen Elizabeth, Komsomolsky Ogonyok, Love) and Rosa Kordesii (Letniye Zvyozdy, Dortmund, Gutsulochka). These cultivars proved themselves during many years of testing in harsh climatic conditions. The objectives of the study were to determine the genetic relationship within the groups and to assign phenotypically different cultivars to one or another garden group. The analysis was carried out by morphological, phenological and ISSR markers. According to the phenological observations on the Grandiflora cultivars, Komsomolsky Ogonyok had later budding and flowering stages. Polymorphic data generated from the ISSR markers showed that this cultivar was the most distant from the others and formed a separate cluster on the dendrogram. A comparison of the morphological characters (flower diameter, number of petals, peduncle length, bush height) showed a significant difference ( p < 0.05) between Komsomolsky Ogonyok and the other Grandiflora cultivars. A dendrogram based on a molecular analysis showed a lack of close relationships between Komsomolsky Ogonyok and the Kordesii group, which formed a separate cluster. A pairwise comparison of the morphological characters in Komsomolsky Ogonyok with the Kordesii group revealed a significant ( p <0.05) difference in three of the four characters studied. The exceptions were flower diameter when comparing with Dortmund and Letniye Zvyozdy and peduncle length when comparing with Gutsulochka. Although Komsomolsky Ogonyok has a pattern of seasonal development similar to Dortmund in the Kordesii group, the molecular analysis did not assign the former to this group of roses. The cultivars that have valuable characters that no average rose does and that are phenotypically different from such roses represent the most valuable breeding material.
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Affiliation(s)
- S S Yudanova
- Central Siberian Botanical Garden of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - O V Dorogina
- Central Siberian Botanical Garden of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - O Yu Vasilyeva
- Central Siberian Botanical Garden of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Sivtsev AA, Zhalsanova IZ, Postrigan AE, Fonova EA, Vasilyeva OY, Zarubin AA, Minaicheva LI, Agafonova AA, Petrova VV, Ravzhaeva EG, Salyukova OA, Skryabin NA. Analysis of mutations spectrum in the ATP7B gene in patients with Wilson disease using massively parallel sequencing. Klin Lab Diagn 2022; 67:250-256. [PMID: 35575400 DOI: 10.51620/0869-2084-2022-67-4-250-256] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The study aimed to search for mutations in the ATP7B gene using massively parallel sequencing in patients with Wilson disease in the Tomsk region. For 42 patients with suspected Wilson's disease (aged from 1 to 33 years) was performed molecular genetic analysis. Enrichment of the interest genome regions was carried out by the long-range PCR. DNA libraries with ligated adapters were constructed with Nextera DNA Flex (Illumina, USA) kit. Sequencing was performed on the Illumina MiSeq platform (Illumina, USA). As a result of this work, we identified 9 pathogenic genetic variants. All variants were previously described in the literature and were found in patients with Wilson's disease. Five missense mutations, one splice site mutation, and 3 frameshift mutations were identified. In patients with Wilson's disease in the Tomsk region, the most common variant was c.3207C>A, this variant is the most common both in the Russian Federation and in other European populations. Also, a pathogenic variant c.3036dupC was found, which is probably endemic to the Russian Federation.
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Affiliation(s)
- A A Sivtsev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Science
| | - I Zh Zhalsanova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Science
| | - A E Postrigan
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Science
| | - E A Fonova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Science
| | - O Yu Vasilyeva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Science
| | - A A Zarubin
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Science
| | - L I Minaicheva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Science
| | - A A Agafonova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Science
| | - V V Petrova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Science
| | - E G Ravzhaeva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Science
| | - O A Salyukova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Science
| | - N A Skryabin
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Science
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Zhigalina DI, Malakhova AA, Vasilyeva OY, Grigor'eva EV, Sivtsev AA, Kolesnikov NA, Lopatkina ME, Savchenko RR, Zhalsanova IZ, Postrigan' AE, Zarubin AA, Nikitina TV, Bueverov AO, Bogomolov PO, Zakian SM, Skryabin NA. Generation of an induced pluripotent stem cell line ICGi030-A from a Wilson's disease patient carrying a frameshift mutation p.Lys1013fs and missense mutation p.H1069Q in the ATP7B gene. Stem Cell Res 2021; 57:102556. [PMID: 34736038 DOI: 10.1016/j.scr.2021.102556] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 09/26/2021] [Indexed: 11/30/2022] Open
Abstract
Wilson's disease is a rare autosomal recessive disorder of copper metabolism. The copper accumulation in the viscera appears due to the functional impairment of copper-transporting ATPase, which is encoded by the ATP7B gene. In this study, PBMCs of a patient with two ATP7B mutations were reprogrammed. The first mutation is a missense mutation p.H1069Q, which is the most frequent mutation in the human population. At the same time, the second one is a frameshift mutation p.Lys1013fs. The generated iPSC line had a normal karyotype, maintained the original genotype, expressed pluripotency markers, and demonstrated the ability to differentiate into derivatives of the three germ layers.
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Affiliation(s)
- D I Zhigalina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia.
| | - A A Malakhova
- Federal Research Center Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia; E.N. Meshalkin National Medical Research Center, Ministry of Health of the Russian Federation, Novosibirsk, Russia; Institute of Chemical Biology and Fundamental Medicine, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - O Yu Vasilyeva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia
| | - E V Grigor'eva
- Federal Research Center Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia; E.N. Meshalkin National Medical Research Center, Ministry of Health of the Russian Federation, Novosibirsk, Russia; Institute of Chemical Biology and Fundamental Medicine, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A A Sivtsev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia
| | - N A Kolesnikov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia
| | - M E Lopatkina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia
| | - R R Savchenko
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia
| | - I Zh Zhalsanova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia
| | - A E Postrigan'
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia
| | - A A Zarubin
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia
| | - T V Nikitina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia
| | - A O Bueverov
- M.F. Vladimirsky Moscow Regional Research Clinical Institute, Moscow, Russia; I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, Russia
| | - P O Bogomolov
- M.F. Vladimirsky Moscow Regional Research Clinical Institute, Moscow, Russia
| | - S M Zakian
- Federal Research Center Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia; E.N. Meshalkin National Medical Research Center, Ministry of Health of the Russian Federation, Novosibirsk, Russia; Institute of Chemical Biology and Fundamental Medicine, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - N A Skryabin
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia
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Malakhova AA, Grigor'eva EV, Vasilyeva OY, Zhigalina DI, Skryabin NA, Sivtcev AA, Kolesnikov NA, Bueverov AO, Lebedev IN, Bogomolov PO, Zakian SM. Generation of two induced pluripotent stem cell lines from peripheral blood mononuclear cells of a patient with Wilson's disease. Stem Cell Res 2020; 47:101922. [PMID: 32738633 DOI: 10.1016/j.scr.2020.101922] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/25/2020] [Accepted: 07/19/2020] [Indexed: 11/16/2022] Open
Abstract
Wilson's disease is an inherited disorder associated with copper accumulation in the liver, brain and other vital organs. Wilson's disease is caused by mutations in the ATP7B gene. Over 300 mutations of ATP7B have been described. Despite the disease is autosomal recessive, the patient whose PBMCs were reprogrammed in the study harbours heterozygous mutation c.3207C > A (p.H1069Q). Detailed analysis of the ATP7B complete gene sequencing data has not revealed other known disease associated mutation. The generated iPSC lines maintained the original genotype, expressed pluripotency markers, had normal karyotype and demonstrated the ability to differentiate into derivatives of the three germ layers.
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Affiliation(s)
- A A Malakhova
- Federal Research Center Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia; E.N. Meshalkin National Medical Research Center, Ministry of Health of the Russian Federation, Novosibirsk, Russia; Institute of Chemical Biology and Fundamental Medicine, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia; Novosibirsk State University, Novosibirsk, Russia.
| | - E V Grigor'eva
- Federal Research Center Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia; E.N. Meshalkin National Medical Research Center, Ministry of Health of the Russian Federation, Novosibirsk, Russia; Institute of Chemical Biology and Fundamental Medicine, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia; Novosibirsk State University, Novosibirsk, Russia
| | - O Yu Vasilyeva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia
| | - D I Zhigalina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia
| | - N A Skryabin
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia
| | - A A Sivtcev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia
| | - N A Kolesnikov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia
| | - A O Bueverov
- M.F. Vladimirsky Moscow Regional Research Clinical Institute, Moscow, Russia; I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, Russia
| | - I N Lebedev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia
| | - P O Bogomolov
- M.F. Vladimirsky Moscow Regional Research Clinical Institute, Moscow, Russia
| | - S M Zakian
- Federal Research Center Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia; E.N. Meshalkin National Medical Research Center, Ministry of Health of the Russian Federation, Novosibirsk, Russia; Institute of Chemical Biology and Fundamental Medicine, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia; Novosibirsk State University, Novosibirsk, Russia
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