1
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Ryazansky SS, Chen C, Potters M, Naumenko AN, Lukyanchikova V, Masri RA, Brusentsov II, Karagodin DA, Yurchenko AA, Dos Anjos VL, Haba Y, Rose NH, Hoffman J, Guo R, Menna T, Kelley M, Ferrill E, Schultz KE, Qi Y, Sharma A, Deschamps S, Llaca V, Mao C, Murphy TD, Baricheva EM, Emrich S, Fritz ML, Benoit JB, Sharakhov IV, McBride CS, Tu Z, Sharakhova MV. The chromosome-scale genome assembly for the West Nile vector Culex quinquefasciatus uncovers patterns of genome evolution in mosquitoes. BMC Biol 2024; 22:16. [PMID: 38273363 PMCID: PMC10809549 DOI: 10.1186/s12915-024-01825-0] [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: 08/25/2023] [Accepted: 01/11/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Understanding genome organization and evolution is important for species involved in transmission of human diseases, such as mosquitoes. Anophelinae and Culicinae subfamilies of mosquitoes show striking differences in genome sizes, sex chromosome arrangements, behavior, and ability to transmit pathogens. However, the genomic basis of these differences is not fully understood. METHODS In this study, we used a combination of advanced genome technologies such as Oxford Nanopore Technology sequencing, Hi-C scaffolding, Bionano, and cytogenetic mapping to develop an improved chromosome-scale genome assembly for the West Nile vector Culex quinquefasciatus. RESULTS We then used this assembly to annotate odorant receptors, odorant binding proteins, and transposable elements. A genomic region containing male-specific sequences on chromosome 1 and a polymorphic inversion on chromosome 3 were identified in the Cx. quinquefasciatus genome. In addition, the genome of Cx. quinquefasciatus was compared with the genomes of other mosquitoes such as malaria vectors An. coluzzi and An. albimanus, and the vector of arboviruses Ae. aegypti. Our work confirms significant expansion of the two chemosensory gene families in Cx. quinquefasciatus, as well as a significant increase and relocation of the transposable elements in both Cx. quinquefasciatus and Ae. aegypti relative to the Anophelines. Phylogenetic analysis clarifies the divergence time between the mosquito species. Our study provides new insights into chromosomal evolution in mosquitoes and finds that the X chromosome of Anophelinae and the sex-determining chromosome 1 of Culicinae have a significantly higher rate of evolution than autosomes. CONCLUSION The improved Cx. quinquefasciatus genome assembly uncovered new details of mosquito genome evolution and has the potential to speed up the development of novel vector control strategies.
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Affiliation(s)
- Sergei S Ryazansky
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA
- Department of Molecular Genetics of Cell, NRC "Kurchatov Institute", Moscow, Russia
| | - Chujia Chen
- Genetics, Bioinformatics, Computational Biology Program, Virginia Polytechnic and State University, Blacksburg, VA, USA
| | - Mark Potters
- Department of Biochemistry, Virginia Polytechnic and State University, Blacksburg, USA
| | - Anastasia N Naumenko
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA
- Department of Entomology, University of Maryland, College Park, MD, USA
| | - Varvara Lukyanchikova
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA
- Group of Genomic Mechanisms of Development, Institute of Cytology and Genetics, Novosibirsk, Russia
- Laboratory of Structural and Functional Genomics, Novosibirsk State University, Novosibirsk, Russia
| | - Reem A Masri
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA
| | - Ilya I Brusentsov
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Dmitriy A Karagodin
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Andrey A Yurchenko
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA
| | - Vitor L Dos Anjos
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Yuki Haba
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Noah H Rose
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Jinna Hoffman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Rong Guo
- Department of Entomology, University of Maryland, College Park, MD, USA
| | - Theresa Menna
- Department of Entomology, University of Maryland, College Park, MD, USA
| | - Melissa Kelley
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Emily Ferrill
- County of San Diego Vector Control Program, San Diego, CA, USA
| | - Karen E Schultz
- Mosquito and Vector Management District of Santa Barbara County, Santa Barbara, CA, USA
| | - Yumin Qi
- Department of Biochemistry, Virginia Polytechnic and State University, Blacksburg, USA
| | - Atashi Sharma
- Department of Biochemistry, Virginia Polytechnic and State University, Blacksburg, USA
| | | | | | - Chunhong Mao
- Biocomplexity Institute & Initiative University of Virginia, Charlottesville, VA, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Elina M Baricheva
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Scott Emrich
- Department of Electrical Engineering & Computer Science, the University of Tennessee, Knoxville, TN, USA
| | - Megan L Fritz
- Department of Entomology, University of Maryland, College Park, MD, USA
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Igor V Sharakhov
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA
- Fralin Life Sciences Institute, Virginia Polytechnic and State University, Blacksburg, VA, USA
- Department of Genetics and Cell Biology, Tomsk State University, Tomsk, Russia
| | - Carolyn S McBride
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Zhijian Tu
- Genetics, Bioinformatics, Computational Biology Program, Virginia Polytechnic and State University, Blacksburg, VA, USA
- Department of Biochemistry, Virginia Polytechnic and State University, Blacksburg, USA
- Fralin Life Sciences Institute, Virginia Polytechnic and State University, Blacksburg, VA, USA
| | - Maria V Sharakhova
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA.
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk, Russia.
- Fralin Life Sciences Institute, Virginia Polytechnic and State University, Blacksburg, VA, USA.
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2
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Brusentsov II, Gordeev MI, Yurchenko AA, Karagodin DA, Moskaev AV, Hodge JM, Burlak VA, Artemov GN, Sibataev AK, Becker N, Sharakhov IV, Baricheva EM, Sharakhova MV. Patterns of genetic differentiation imply distinct phylogeographic history of the mosquito species Anopheles messeae and Anopheles daciae in Eurasia. Mol Ecol 2023; 32:5609-5625. [PMID: 37702976 DOI: 10.1111/mec.17127] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 08/17/2023] [Accepted: 08/24/2023] [Indexed: 09/14/2023]
Abstract
Detailed knowledge of phylogeography is important for control of mosquito species involved in the transmission of human infectious diseases. Anopheles messeae is a geographically widespread and genetically diverse dominant vector of malaria in Eurasia. A closely related species, An. daciae, was originally distinguished from An. messeae based on five nucleotide substitutions in its ribosomal DNA (rDNA). However, the patterns of phylogeographic history of these species in Eurasia remain poorly understood. Here, using internal transcribed spacer 2 (ITS2) of rDNA and karyotyping for the species identification we determined the composition of five Anopheles species in 28 locations in Eurasia. Based on the frequencies of 11 polymorphic chromosomal inversions used as genetic markers, a large-scale population genetics analysis was performed of 1932 mosquitoes identified as An. messeae, An. daciae and their hybrids. The largest genetic differences between the species were detected in the X sex chromosome suggesting a potential involvement of this chromosome in speciation. The frequencies of autosomal inversions in the same locations differed by 13%-45% between the species demonstrating a restricted gene flow between the species. Overall, An. messeae was identified as a diverse species with a more complex population structure than An. daciae. The clinal gradients in frequencies of chromosomal inversions were determined in both species implicating their possible involvement in climate adaptations. The frequencies of hybrids were low ~1% in northern Europe but high up to 50% in south-eastern populations. Thus, our study revealed critical differences in patterns of phylogeographic history between An. messeae and An. daciae in Eurasia. This knowledge will help to predict the potential of the malaria transmission in the northern territories of the continent.
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Affiliation(s)
- Ilya I Brusentsov
- Department of Entomology, Virginia Polytechnic Institute and State University and Fralin Life Sciences Institute, Blacksburg, Virginia, USA
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk, Russia
| | | | - Andrey A Yurchenko
- Department of Entomology, Virginia Polytechnic Institute and State University and Fralin Life Sciences Institute, Blacksburg, Virginia, USA
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Dimitriy A Karagodin
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk, Russia
| | | | - James M Hodge
- Department of Entomology, Virginia Polytechnic Institute and State University and Fralin Life Sciences Institute, Blacksburg, Virginia, USA
| | - Vladimir A Burlak
- Laboratory of Ecology, Genetics, and Environmental Protection, Tomsk State University, Tomsk, Russia
| | - Gleb N Artemov
- Laboratory of Ecology, Genetics, and Environmental Protection, Tomsk State University, Tomsk, Russia
| | - Anuarbek K Sibataev
- Department of General Biology and Genomics, L.N. Gumilyov Eurasian National University, Nur-Sultan, Kazakhstan
- Department of Agricultural Biology, Tomsk State University, Tomsk, Russia
| | - Norbert Becker
- Center for Organismal Studies, University of Heidelberg, Heidelberg, Germany
- German Mosquito Control Association, Speyer, Germany
| | - Igor V Sharakhov
- Department of Entomology, Virginia Polytechnic Institute and State University and Fralin Life Sciences Institute, Blacksburg, Virginia, USA
- Laboratory of Ecology, Genetics, and Environmental Protection, Tomsk State University, Tomsk, Russia
| | - Elina M Baricheva
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Maria V Sharakhova
- Department of Entomology, Virginia Polytechnic Institute and State University and Fralin Life Sciences Institute, Blacksburg, Virginia, USA
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk, Russia
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3
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Fedorova S, Dorogova NV, Karagodin DA, Oshchepkov DY, Brusentsov II, Klimova NV, Baricheva EM. The complex role of transcription factor GAGA in germline death during Drosophila spermatogenesis: transcriptomic and bioinformatic analyses. PeerJ 2023; 11:e14063. [PMID: 36643636 PMCID: PMC9835689 DOI: 10.7717/peerj.14063] [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: 12/19/2021] [Accepted: 08/26/2022] [Indexed: 01/11/2023] Open
Abstract
The GAGA protein (also known as GAF) is a transcription factor encoded by the Trl gene in D. melanogaster. GAGA is involved in the regulation of transcription of many genes at all stages of fly development and life. Recently, we investigated the participation of GAGA in spermatogenesis and discovered that Trl mutants experience massive degradation of germline cells in the testes. Trl underexpression induces autophagic death of spermatocytes, thereby leading to reduced testis size. Here, we aimed to determine the role of the transcription factor GAGA in the regulation of ectopic germline cell death. We investigated how Trl underexpression affects gene expression in the testes. We identified 15,993 genes in three biological replicates of our RNA-seq analysis and compared transcript levels between hypomorphic Trl R85/Trl 362 and Oregon testes. A total of 2,437 differentially expressed genes were found, including 1,686 upregulated and 751 downregulated genes. At the transcriptional level, we detected the development of cellular stress in the Trl-mutant testes: downregulation of the genes normally expressed in the testes (indicating slowed or abrogated spermatocyte differentiation) and increased expression of metabolic and proteolysis-related genes, including stress response long noncoding RNAs. Nonetheless, in the Flybase Gene Ontology lists of genes related to cell death, autophagy, or stress, there was no enrichment with GAGA-binding sites. Furthermore, we did not identify any specific GAGA-dependent cell death pathway that could regulate spermatocyte death. Thus, our data suggest that GAGA deficiency in male germline cells leads to an imbalance of metabolic processes, impaired mitochondrial function, and cell death due to cellular stress.
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Affiliation(s)
- Svetlana Fedorova
- Department of Cell Biology, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russian Federation
| | - Natalya V. Dorogova
- Department of Cell Biology, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russian Federation
| | - Dmitriy A. Karagodin
- Department of Cell Biology, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russian Federation
| | - Dmitry Yu Oshchepkov
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russian Federation
| | - Ilya I. Brusentsov
- Department of Cell Biology, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russian Federation
| | - Natalya V. Klimova
- Department of Molecular Genetics, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russian Federation
| | - Elina M. Baricheva
- Department of Cell Biology, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russian Federation
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4
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Artemov GN, Fedorova VS, Karagodin DA, Brusentsov II, Baricheva EM, Sharakhov IV, Gordeev MI, Sharakhova MV. New Cytogenetic Photomap and Molecular Diagnostics for the Cryptic Species of the Malaria Mosquitoes Anopheles messeae and Anopheles daciae from Eurasia. Insects 2021; 12:835. [PMID: 34564275 PMCID: PMC8465136 DOI: 10.3390/insects12090835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/03/2021] [Accepted: 09/13/2021] [Indexed: 11/17/2022]
Abstract
The Eurasian malaria vector Anopheles messeae is a widely spread and genetically diverse species. Five widespread polymorphic chromosomal inversions were found in natural populations of this mosquito. A cryptic species, Anopheles daciae, was differentiated from An. messeae by the presence of several nucleotide substitutions in the Internal Transcribed Spacer 2 (ITS2) region of ribosomal DNA. However, because of the absence of a high-quality reference cytogenetic map, the inversion polymorphisms in An. daciae and An. messeae remain poorly understood. Moreover, a recently determined heterogeneity in ITS2 in An. daciae questioned the accuracy of the previously used Restriction Fragment Length Polymorphism (RFLP) assay for species diagnostics. In this study, a standard-universal cytogenetic map was constructed based on orcein stained images of chromosomes from salivary glands for population studies of the chromosomal inversions that can be used for both An. messeae and An. daciae. In addition, a new ITS2-RFLP approach for species diagnostics was developed. Both methods were applied to characterize inversion polymorphism in populations of An. messeae and An. daciae from a single location in Western Siberia in Russia. The analysis demonstrates that cryptic species are remarkably different in their frequencies of chromosomal inversion variants. Our study supports previous observations that An. messeae has higher inversion polymorphism in all autosomes than the cryptic species An. daciae.
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Affiliation(s)
- Gleb N. Artemov
- Laboratory of Evolutionary Genomics of Insects, Institute of Cytology and Genetics, 630090 Novosibirsk, Russia; (G.N.A.); (D.A.K.); (I.I.B.); (I.V.S.)
- Department of Genetics and Cell Biology, Tomsk State University, 634050 Tomsk, Russia;
| | - Valentina S. Fedorova
- Department of Genetics and Cell Biology, Tomsk State University, 634050 Tomsk, Russia;
| | - Dmitriy A. Karagodin
- Laboratory of Evolutionary Genomics of Insects, Institute of Cytology and Genetics, 630090 Novosibirsk, Russia; (G.N.A.); (D.A.K.); (I.I.B.); (I.V.S.)
| | - Ilya I. Brusentsov
- Laboratory of Evolutionary Genomics of Insects, Institute of Cytology and Genetics, 630090 Novosibirsk, Russia; (G.N.A.); (D.A.K.); (I.I.B.); (I.V.S.)
| | - Elina M. Baricheva
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, 630090 Novosibirsk, Russia;
| | - Igor V. Sharakhov
- Laboratory of Evolutionary Genomics of Insects, Institute of Cytology and Genetics, 630090 Novosibirsk, Russia; (G.N.A.); (D.A.K.); (I.I.B.); (I.V.S.)
- Department of Genetics and Cell Biology, Tomsk State University, 634050 Tomsk, Russia;
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Mikhail I. Gordeev
- Department of General Biology and Ecology, Moscow Region State University, 141014 Moscow, Russia;
| | - Maria V. Sharakhova
- Laboratory of Evolutionary Genomics of Insects, Institute of Cytology and Genetics, 630090 Novosibirsk, Russia; (G.N.A.); (D.A.K.); (I.I.B.); (I.V.S.)
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
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5
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Degtyareva AO, Leberfarb EY, Efimova EG, Brusentsov II, Usova AV, Lushnikova EL, Merkulova TI. rs2072580T>A Polymorphism in the Overlapping Promoter Regions of the SART3 and ISCU Genes Associated with the Risk of Breast Cancer. Bull Exp Biol Med 2020; 169:81-84. [PMID: 32495170 DOI: 10.1007/s10517-020-04829-2] [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: 08/09/2019] [Indexed: 10/24/2022]
Abstract
We analyzed association of potentially regulatory polymorphisms (rs590352, rs11542583, rs3829202, rs207258, and rs4796672) with breast cancer. A significant association was found between this disease and rs2072580T>A (p=0.001) located in the overlapping promoter regions of the SART3 and ISCU genes. In women with AA and AT genotypes, the risk of breast cancer is higher by 6.7 times (p=0.001) and 12 times (p=0.001), respectively, in comparison with TT genotype. Under a codominant model of inheritance (AT vs AA+TT), the risk of breast cancer was increased by 4.2 times (р=0.001) for the AT genotype. Under a recessive model of inheritance (TT vs AA+TT), the risk of disease was 10-fold higher (р=0.001) for the TT genotype. It has been demonstrated that the T>A substitution affects the binding properties of transcription factors CREB1 and REST.
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Affiliation(s)
- A O Degtyareva
- Federal Research Center Institute of Cytology and Genetics, Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia.
| | - E Y Leberfarb
- Federal Research Center Institute of Cytology and Genetics, Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State Medical University, Ministry of Health of the Russian Federation, Novosibirsk, Russia
| | - E G Efimova
- Novosibirsk State Medical University, Ministry of Health of the Russian Federation, Novosibirsk, Russia
| | - I I Brusentsov
- Federal Research Center Institute of Cytology and Genetics, Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
| | - A V Usova
- Novosibirsk State Medical University, Ministry of Health of the Russian Federation, Novosibirsk, Russia
| | - E L Lushnikova
- Institute for Molecular Pathology and Pathomorphology, Federal Research Center for Fundamental and Translational Medicine, Novosibirsk, Russia
| | - T I Merkulova
- Federal Research Center Institute of Cytology and Genetics, Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk National Research State University, Novosibirsk, Russia
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6
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Leberfarb EY, Degtyareva AO, Brusentsov II, Maximov VN, Voevoda MI, Autenshlus AI, Morozov DV, Sokolov AV, Merkulova TI. Potential regulatory SNPs in the ATXN7L3B and KRT15 genes are associated with gender-specific colorectal cancer risk. Per Med 2019; 17:43-54. [PMID: 31797724 DOI: 10.2217/pme-2019-0059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 12/24/2022]
Abstract
Aim: According to the current data, a major factor for phenotypic variation of complex traits and disease susceptibility is the cis-acting effects of noncoding variants on gene expression. Our purpose was to evaluate the association between colorectal cancer (CRC) and six single nucleotide polymorphisms identified using our original bioinformatics approach as regulatory and putatively related to CRC. Materials: One hundred and sixty CRC patients and 185 healthy controls have been genotyped for rs590352, rs2072580, rs78317230, rs3829202, rs11542583 and rs4796672. Results: Genotypes and alleles distributions of rs590352 of ATXN7L3B gene were significantly different between the male CRC subjects and controls. Significant correlation of genotype with CRC is observable for women only for the rs4796672 of KRT15 gene. Analysis of haplotypes reveals that rs2072580 of the ISCU and SART3 genes can be also associated with CRC. Conclusion: We have identified three SNPs associated with CRC risk and demonstrated a gender specificity of rs590352 and rs4796672.
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Affiliation(s)
- Elena Yu Leberfarb
- Institute of Cytology & Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State Medical University, Novosibirsk, Russia
| | - Arina O Degtyareva
- Institute of Cytology & Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State Medical University, Novosibirsk, Russia
| | - Ilya I Brusentsov
- Institute of Cytology & Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Vladimir N Maximov
- Institute of Cytology & Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State Medical University, Novosibirsk, Russia
| | - Mikhail I Voevoda
- Institute of Cytology & Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | | | | | | | - Tatiana I Merkulova
- Institute of Cytology & Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
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7
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Autenshlyus AI, Golovanova AV, Studenikina AA, Brusentsov II, Proskura AV, Zhurakovskiy IP, Arkhipov SA, Sidorov SV, Vavilin VA, Lyakhovich VV. Personalized Approach to Assessing mRNA Expression of Histidine-Rich Glycoprotein and Immunohistochemical Markers in Diseases of the Breast. DOKL BIOCHEM BIOPHYS 2019; 484:59-62. [PMID: 31012015 DOI: 10.1134/s1607672919010162] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Indexed: 11/23/2022]
Abstract
Biopsy material of patients with malignant and benign breast diseases was examined. HRG mRNA expression was detected in 70% of cases in biopsy material obtained from patients with nonspecific invasive carcinoma and in 66.7% of cases in biopsy material of patients with benign breast diseases. Immunohistochemical analysis revealed expression of collagen II, the beta-1 integrin, and E-cadherin-markers of epithelial-mesenchymal transition. The use of RT-qPCR combined with immunohistochemical study made it possible to identify atypical cells, which can be regarded as precancerous changes, in individual patients.
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Affiliation(s)
- A I Autenshlyus
- Novosibirsk State Medical University, Ministry of Health of the Russian Federation, 630091, Novosibirsk, Russia. .,Research Institute of Molecular Biology and Biophysics, 630117, Novosibirsk, Russia.
| | - A V Golovanova
- Novosibirsk State Medical University, Ministry of Health of the Russian Federation, 630091, Novosibirsk, Russia
| | - A A Studenikina
- Novosibirsk State Medical University, Ministry of Health of the Russian Federation, 630091, Novosibirsk, Russia
| | - I I Brusentsov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - A V Proskura
- Research Institute of Molecular Biology and Biophysics, 630117, Novosibirsk, Russia
| | - I P Zhurakovskiy
- Novosibirsk State Medical University, Ministry of Health of the Russian Federation, 630091, Novosibirsk, Russia
| | - S A Arkhipov
- Novosibirsk State Medical University, Ministry of Health of the Russian Federation, 630091, Novosibirsk, Russia.,Research Institute of Molecular Biology and Biophysics, 630117, Novosibirsk, Russia
| | - S V Sidorov
- National Research Novosibirsk State University, 630090, Novosibirsk, Russia
| | - V A Vavilin
- Research Institute of Molecular Biology and Biophysics, 630117, Novosibirsk, Russia
| | - V V Lyakhovich
- Research Institute of Molecular Biology and Biophysics, 630117, Novosibirsk, Russia
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8
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Autenshlyus AI, Brusentsov II, Marinkin IO, Smirnova SA, Rukavishnikov MY, Lyakhovich VV. Messenger RNA of the Histidine-Rich Glycoprotein in Breast Tumors. DOKL BIOCHEM BIOPHYS 2018. [PMID: 29536307 DOI: 10.1134/s1607672918010106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The content of mRNA of the histidine-rich glycoprotein (HRG), a potential marker of malignant neoplasia, which can be used in differential diagnosis of breast tumors, was determined in 110 breast tumor biopsy samples. The presence of HRG mRNA did not depend on the cancer type, on the preoperative treatment or its absence, as well as on the tumor progression stage and the presence of metastases.
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Affiliation(s)
- A I Autenshlyus
- Ministry of Healthcare of the Russian Federation, Novosibirsk State Medical University, Novosibirsk, 630091, Russia. .,Research Institute of Molecular Biology and Biophysics, Novosibirsk, 630117, Russia.
| | - I I Brusentsov
- Ministry of Healthcare of the Russian Federation, Novosibirsk State Medical University, Novosibirsk, 630091, Russia.,Federal Research Center Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - I O Marinkin
- Ministry of Healthcare of the Russian Federation, Novosibirsk State Medical University, Novosibirsk, 630091, Russia
| | - S A Smirnova
- JSC Vector-Best, Kol'tsovo, Novosibirsk oblast, 633159, Russia
| | | | - V V Lyakhovich
- Research Institute of Molecular Biology and Biophysics, Novosibirsk, 630117, Russia
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Brusentsov II, Katokhin AV, Sakharovskaia ZV, Sazonov AE, Ogorodova LM, Fedorova OS, Kolchanov NA, Mordvinov VA. [DNA diagnosis of mixed invasions of Opisthorchis felineus and Metorchis bilis by polymerase chain reaction]. Med Parazitol (Mosk) 2010:10-13. [PMID: 20614520] [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: 05/29/2023]
Abstract
Opisthorchiasis is one of the significant naturofocal diseases in Russia. The diagnosis of opisthorchiasis may mask some diseases, such as opisthorchiasis, metorchiasis, and clonorchiasis - biohelminthoses that are induced by various representatives of the family Opisthorchiidae-Opisthorchis felineus/O.viverrini, Metorchis bilis, and Clonorchis sinensis, respectively. Coproovoscopy and serologic methods fail to accurately define the species-specific affiliation; in this connection the identification of opisthorchids, by using DNA diagnostic techniques, becomes urgent. The present paper gives the results of development of DNA diagnosticum, which differentiates parasitic diseases induced by O. felineus and M. bills. The ribosomal RNA gene cluster fragment incorporating internal transcribed spacer 2 (ITS2) was used as a diagnostic marker. A system for diagnosing opisthorchiasis was developed as a multiplex polymerase chain analysis and tested on 37 patients infected with various species of opisthorchids.
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