International conference on bioinformatics of genome regulation
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Key words: DNA repair, database, genomic uracil Generally, the molecular events in successive steps of DNA repair are much better un- derstood than their regulation. Base excision repair (BER) is regulated at several levels, including posttranslational modifications, protein interactions, protein stability and cell cycle expression. We have focused our research on genomic uracil and it’s repair. Ge- nomic uracil may result from spontaneous or enzymatic deamination of cytosine, giving rise to mutagenic U:G mismatches, or from incorporation of dUMP during replication, giving rise to U:A pairs that are potentially mutagenic through errors in BER. Three ma- jor DNA glycosylases, UNG, TDG and SMUG1, initiate BER of genomic uracil. These proteins have different functions, as reflected by their catalytic properties, interactions and cell cycle regulation [1,2]. We recently established a database on the cell cycle regu- lation of all known DNA repair and chromatin remodeling proteins (www.dnarepair- genes.com) [3] and demonstrated that DNA glycosylases are differentially expressed. In most cells, BER supports essentially error-free repair of genomic uracil. However, in B-cells enzymatic deamination of cytosine to uracil by AID in Ig-genes is required for adaptive immunity, in which UNG has a non-canonical mutagenic role. Although essential as an immunological defense mechanism, this is also a risky process. Thus, we found that genomic uracil is significantly higher in B-cell lymphoma cell lines com- pared to non-lymphoma cancer cell lines and normal circulating lymphocytes, suggest- ing off-target deamination of cytosine to uracil by AID [4]. The genomic uracil levels correlated with AID mRNA and protein expression, but not with expression of other APOBECs. Accordingly, AID knockdown significantly reduced genomic uracil content. B-cells stimulated to express endogenous AID and undergo class switch recombination displayed a several-fold increase in total genomic uracil, indicating that B cells may undergo widespread cytosine deamination after stimulation. In line with this, we found that clustered mutations (kataegis) in B-cell lymphoma and chronic lymphocytic leuke- mia predominantly carry AID-hotspot mutational signatures. Moreover, we observed an inverse correlation of genomic uracil with uracil excision activity and expression of the uracil-DNA glycosylases UNG and SMUG1[4]. In conclusion, AID-induced mutagenic U:G mismatches in DNA may be a fundamental and common cause of mutations in B-cell malignancies. 1. Krokan H.E. and Bjørås M. (2013) Base Excision Repair. Cold Spring Harb. Perspect. Biol. 2013 Apr 1;5(4). a012583. 2. Krokan H.E., Sætrom P., Aas P.A., Pettersen,H.S., Kavli B. and Slupphaug G. (2014) Error-free versus mutagenic processing of genomic uracil – relevance to cancer. DNA Repair (Amst.)19:38-47. 3. Mjelle, R., Hegre, S.A., Aas, P.A. Slupphaug, G., Drabløs, F., Sætrom, P. and , Krokan, H.E. (2015) Cell cycle regulation of human DNA repair and chromatin remodeling genes. DNA Repair (Amst) 30:53-67. 4. Pettersen HS, Galashevskaya A., Doseth B., Sousa1 M.M.L., Sarno A., Visnes T., Aas P.A., Liabakk N.B., Slupphaug G., Sætrom P., Kavli B. and Krokan H.E. (2015) AID expression in B-cell lymphomas causes accumulation of genomic uracil and a distinct AID mutational signature. DNA Repair (Amst.) 25:60-71. 161 THE TENTH INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE\SYSTEMS BIOLOGY EFFECT OF LENTIVIRUS-MEDIATED SHRNA INACTIVATION OF HK1, HK2, AND HK3 GENES IN COLORECTAL CANCER AND MELANOMA CELLS A.V. Kudryavtseva 1, 2 *, M.S. Fedorova 1 , O.L. Kardymon 1 , A.A. Dmitriev 1 , A.I. Afre- mova 1 , D.V. Kochetkov 1 , A.V. Lipatova 1 , A.F. Sadritdinova 1, 2 , I.Y. Karpova 1 , K.M. Nyushko 2 , D.V. Kalinin 3 , N.N. Volchenko 2 , N.V. Melnikova 1 , A.A. Belova 1, 2 , M.A. Chernichenko 2 , K.M. Klimina 4 , N.V. Nasedkina 1 , A.S. Zasedatelev 1 , D.V. Sidorov 2 , A.Y. Popov 2 , G.S. Krasnov 1 , A.V. Snezhkina 1 1 Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia 2 Herzen Moscow Cancer Research Institute, Ministry of Health of the Russian Federation, Moscow, Russia 3 A.V. Vishnevsky Institute of Surgery, Moscow, Russia 4 Vavilov Institute of General Genetics, Russian Academy of Sciences Moscow, Russia * Corresponding author: rhizamoeba@mail.ru Key words: Warburg effect, hexokinases, shRNA, glycolysis, melanoma, colorectal cancer The switch from oxidative phosphorylation to glycolysis in proliferating cancer cell even under aerobic conditions has been shown first in 1926 by Otto Warburg. Today “Warburg effect” is known as a metabolic phenotype, a hallmark of malignant tumors. This shift is associated with alterations in signaling pathways involved in energy metabolism, includ- ing glucose uptake and fermentation, and regulation of mitochondrial functions. It has been shown that many genes encoding glycolytic enzymes are dysregulated in cancer. Hexokinases (HKs), which catalyze the first step of glycolysis, have been identified to play a role in tumorigenesis of human colorectal cancer (CRC) and melanoma. However, the mechanisms of HKs in the promotion of tumor growth remain elusive. The pur- pose of this study is to investigate the effect of silencing hexokinase genes (HK1, HK2, and HK3) in colon cancer (HT29, RKO, HCT116, CW480, and HCT15) and melanoma (Ksen, Kor, Z, and Cher) cells using short hairpin RNA (shRNA) lentiviral vectors. shR- NA lentiviral plasmid vectors PLSLP-HK1, PLSLP-HK2, and PLSLP-HK3 were con- structed and then transfected separately or co-transfected into cells. The results indicated that shRNA-mediated attenuation of HK2 and HK3 separately, as well as one together led to increased apoptosis rates of cancer cells and decreased glucose metabolism. HK1 gene inactivation did not result to significant changes in apoptotic rate or cells growth. Co-transfection by shRNA vectors against HK1, HK2, and HK3 together resulted in a rapid cell death by apoptosis. Thus, our results suggest that HK2 and HK3 genes are the key therapeutic targets for reducing aerobic glycolysis. This study shows a promising strategy for colorectal and melanoma cancer therapy. This work was financially supported by grant 14-15-01083 from the Russian Science Foundation. Part of this work was performed using the equipment of EIMB RAS “Ge- nome” center (http://www.eimb.ru/rus/ckp/ccu_genome_c.php). 162 THE TENTH INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE\SYSTEMS BIOLOGY COMPUTER SOFTWARE FOR STATISTICAL ANALYSIS OF GENES LOCATION RELATIVE TO CHROMOSOME CONTACTS REVEALED BY CHIA-PET E.V. Kulakova*, A.M. Spitsina 1 Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia 2 Novosibirsk State University, Novosibirsk, Russia * Corresponding author: kylakovaekaterina@gmail.com Key words: sequencing, ChIA-PET, Hi-C, chromosome contacts, genome, CTCF sites Motivation and Aim: Several technologies based on chromatin immunoprecipitation (ChIP) have been developed to study the binding of transcription factors (TF) to genom- ic DNA including microarray (ChIP-chip), ChIP-PET and ChIP-Seq [1]. The challenge is to define whether such distal binding sites are functional, i.e. physically proximal to target gene promoters via chromosome loops attracting RNA polymerase II complex for gene transcription [2]. Chromatin Interaction Analysis with Paired-End-Tag sequenc- ing (ChIA-PET) method fits these demands still requiring development of specialized high-throughput software for data integration [2]. The aim of the work was to develop a computer program for statistical data analysis and test it on CTCF (CCCTC-binding factor) binding sites, genes and spatial topological domains. Methods and Algorithms: We used data on the location of CTCF binding sites clusters obtained by ChIA-PET as well as obtained experimentally by methods Hi-C, ChIA-PET [2]. Gene annotation was obtained from UCSC Genome Browser (http://genome.ucsc. edu). Results: In result has been developed computer software for statistical analysis and visu- alization of results for experimental data obtained by ChIA-PET and Hi-C. The program was developed in Java language that calls modules based on R and Matlab environment using library such as Rserve and MatlabControl. The program has graphical user inter- face. This tool has function such as identification gene location near to domains bound- ary; near to binding sites of transcription factor; visualization of heatmap based on pairs of CTCF binding sites; distributions of human genes relative CTCF binding sites and a randomly generated list of such sites. Conclusion: We considered a model the location of genes relative chromosome loops and binding sites. Genes of RefSeq are located inside the loop between the sites ac- counted for half of the total. It was revealed that most of the genes in the chromosomal loops are arranged individually Availability: Software is available from the author upon request Acknowledgements: The work is supported by ICG budget project 0324-2015-0003. References: 1. E.V. Ignatieva et al. (2015) Regulatory Genomics: Combined Experimental and Computational Ap- proaches, Russian Journal of Genetics, V. 51, 4: 334-352. 2. G. Li et al. (2012) Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation, Cell V.148. 1-2: 84-98. 163 THE TENTH INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE\SYSTEMS BIOLOGY SYSTEMIC ROLE OF ALLELIC VARIANTS IN A 2Q22 REGION IN MAJOR AGE-RELATED DISEASES AND LIFESPAN A.M. Kulminski*, L. He, I. Culminskaya, Y. Loika, Y. Kernogitski, K.G. Arbeev, E. Loiko, L. Arbeeva, O. Bagley, M. Duan, A. Yashkin, F. Fang, M. Kovtun, S.V. Ukraintseva, D. Wu, A.I. Yashin Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, USA * Corresponding author: kulminsk@duke.edu Key words: healthspan, lifespan, aging, geroscience Motivation and Aim: Gaining insights into genetic influences on age-related diseases and lifespan is a challenging task complicated by the elusive role of evolution in these phenotypes. Combining approaches from genome-wide and candidate-gene studies may be beneficial. Methods and Algorithms: Genome-wide scan of participants of the Atherosclerosis Risk in Communities (ARIC) Study (N = 9,573) was used to pre-select promising loci. Candi- date-gene methods were used to comprehensively analyze associations of novel uncom- mon variants in Caucasians (minor allele frequency~2.5%) located in band 2q22.3 with risks of coronary heart disease (CHD), congestive heart failure (CHF), stroke, diabetes, cancer, neurodegenerative diseases (ND), and mortality in the ARIC study, the Fram- ingham Heart Study (N = 4,434), and the Health and Retirement Study (N = 9,676). We leveraged the analyses of pleiotropy, age-related heterogeneity, and causal inferences. Results: Meta-analysis of the results from these comprehensive analyses shows that the minor allele increases risks of death by about 50% (p = 4.6×10 -9 ), CHD by 35% (p = 8.9×10 -6 ), CHF by 55% (p = 9.7×10 -5 ), stroke by 25% (p = 4.0×10 -2 ), and ND by 100% (p = 1.3×10 -3 ). This allele also antagonistically influences each of two diseases, diabetes and cancer, in different populations. Combined significance of the pleiotropic effects was p = 6.6×10 -21 . Causal mediation analyses show that endophenotypes explained only small fractions of these effects. This locus harbors an evolutionary conserved gene-des- ert region with non-coding intergenic sequences likely involved in regulation of protein- coding flanking genes ZEB2 and ACVR2A. This region is intensively studied for muta- tions causing severe developmental/genetic disorders. Conclusion: Our analyses indicate a promising target region for interventions aimed to reduce risks of many major human diseases and mortality. 164 THE TENTH INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE\SYSTEMS BIOLOGY COMPARATIVE EXPRESSION LANDSCAPES IN REPLICA- TIVE AND STRESS INDUCED PREMATURE SENESCENCE K.C. Kural 1 , N. Tandon 2 , O.V. Kel-Margoulis 2 , A. Baranova 1, 3, 4 * 1 School of Systems Biology, George Mason University, Fairfax, VA USA 2 geneXplain, Wolfenbüttel Germany 3 Federal State Budgetary Institution “Research Centre for Medical Genetics”, Moscow, Russia 4 ATLAS Biomed Group, Moscow, Russia * Corresponding author: abaranov@gmu.edu; aancha@gmail.com Key words: senescence, ageing, expression landscapes, distance analysis Motivation and Aim: Senescence is the phenomenon accompanying the cessation of cell division in population of normal diploid cells. It can happen naturally in form of repli- cative senescence or may be a consequence of external challenges such as oxidative or radiation stress. It is widely believed that the senescence provides a protection against possible tumor formation. This research aimed at identifying differentially expressed gene signatures chracteristic for replicative and stress induced senescence in human fi- broblast cells. Methods and Algorithms: We employed geneXplain bioinformatics software platform. Our approach was to classify the differentially expressed genes by their functions to dissect the involvement of these genes in various cell cycle processes and the pathways involved in senescence. The list of genes which are exclusively up and down regulated in stress induced senescence and replicative senescence were compared. The genes unique for each of these two types of senescence were then subjected to promoter analysis. Po- tential transcription factor (TF) binding sites were used to deduce master regulators that control the activity of these downstream genes. Results: Our analysis suggests that the Aurora-A kinase pathway is the master regula- tor central to both types of cell senescence. IL-1α, GM-CSF, MKP-2, MKK3, GDNF, TRIM36, MLTK are identified as specific contributors to replicative senescence, while BTEB-2, SHIP-110, SPK, and CDP play a role in stress induced senescence. Conclusion: Our study outlines converging pathways for stress induced and replicative senescence, and connects mitochondrial stress with replicative cellular aging through accumulating failures of the centrosomal homeostasis. Availability: on request. 165 THE TENTH INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE\SYSTEMS BIOLOGY TRANSCRIPTOMICS OF THE CRYOBIOTIC LEECH OZOBRANCHUS JANTSEANUS S.V. Kuznecova 1 , D. Suzuki 2 , M.D. Logacheva 3 , O.S. Kozlova 1 , T. Kikawada 4 , R.M. Sabirov 1 , O.A. Gusev 1 1 Kazan Federal University, Kazan, Russia 2 Tokyo University of Marine Science and Technology, Tokyo, Japan 3 M.V. Lomonosov Moscow State University, Moscow, Russia 4 National Institute of Agrobiological Sciences, Tsukuba, Japan * Corresponding author: svtkuzn@gmail.com Key words: transcriptome, cyobiosis, turtle leech, Ozobranchus jantseanus Motivation and Aim: The Ozobranchus jantseanus is the turtle leech capable to survive after exposure to super-low temperature.[1] In contrast to known cryotolerant inverte- brates the turtle leeches does not require prolonged pre-conditioning and resist immediate freezing. However, in natural habitat leeches are never exposed to such low temperatures. Further understanding of the genetic mechanisms underlying such a unique ability would contribute to development of new technologies in non-toxic cryopreservation of living cells and tissues of animals. Methods and Algorithms: In the order to address the processes underlying cryotolerance ability we analyzed transcriptional changes in the leech on different stages of exposure to low temperature. We analyzed of mRNA expression in 4 groups of leeches: active animals, immediately after freezing, and further recovery for 3,5h and 24h after freezing. Results: De-novo assembly of the transcriptome resulted in 99 624 coding transcripts. Among them, we observed dramatically changes in expression between control and 3,5h group. In 3,5h group we selected a cluster with 143 most up-regulated transcripts. Sur- prisingly that among them more than 25% are orphan genes and they weren’t found in known organisms in data base. We observed increasing in RPKM value for transcripts coding tyrosinase, coadhesin, thrombospondin type 1, destabilase, properdin, brain-spe- cific angiogenesis inhibitor, alpha-2-macroglobulin and etc. A significant increase in the expression value of transcripts of heat shock protein is not detected. Conclusion: Among the most up-regulated by freezing transcripts expressed in the leech, 56% are represented by products of unknown genes. Furthermore, 25% of them are orphan, Ozobranchus-specific genes. We suppose that among them, there are some new candidate uncharacterized cryoprotectors and further in vitro studies will be done for deeper understanding of this phenomenon. Acknowledgements: The work is performed according to the Russian Government Pro- gram of Competitive Growth of Kazan Federal University References: 1. Dai Suzuki, Tomoko Miyamoto, Takahiro Kikawada, Manabu Watanabe, Toru Suzuki (2014) A Leech Capable of Surviving Exposure to Extremely Low Temperatures, PLoS ONE 9(1): e86807. doi:10.1371/journal.pone.0086807 2. 166 THE TENTH INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE\SYSTEMS BIOLOGY A MATHEMATICAL MODEL FOR PREDICTING OF IGD–CD27+B LYMPHOCYTES LEVELS IN DONORS’ BLOOD S.R. Kuznetsov 1 *, I.V. Kudryavtsev 2 , A.V. Orekhov 1 , A.V. Polevshchikov 2 , M.K. Serebriakova 2 , V.I. Shishkin 1 1 St. Petersburg State University, St. Petersburg, Russia 2 Institute of Experimental Medicine, St. Petersburg, Russia * Corresponding author: abxy01@yandex.ru Key words: mathematical model, systems immunology, flow cytometry, T cells, B cells Motivation and Aim: Previously we proposed to use McKendrick–von Foerster age- structured population model to describe proliferation and differentiation processes of T and B-lymphocytes in the immune response [1, 2]. In this work McKendrick–von Foerster equation is used to define parameters of IgD+CD27+ lymphocytes prolifera- tion in a healthy person. As a result, a formula was built, allowing to predict the level of IgD– CD27+ lymphocytes from the data of IgD+CD27+ B lymphocytes level and CD3+CD4+CXCR5+CXCR3–CCR6–CCR4+ Tfh2 lymphocytes level. Methods and Algorithms: We supposed that levels of IgD+CD27+, IgD–CD27+ and Tfh2 cells of a healthy person do not changes over the time, and it is possible to use a stationary solution of McKendrick–von Foerster equation. Optimal parameters of the model were determined by the Monte Carlo method, using the data on the level of lym- phocytes in the blood of 30 donors. For verification of the model, there was used data from 19 donors. Based on verifying data (in particular concentrations of IgD+CD27+ B cells and Tfh2) there were made predictions of the level of IgD–CD27+ B cells for each of 19 donors; the result was compared with experimental data. Results: The formula has been obtained to determine the level of IgD–CD27+B-lympho- cytes from the data of IgD+CD27+ and Tfh2 lymphocytes levels in the venousblood of donors. Verification revealed the comparison of experimental data with prediction made by the model; the correlation coefficient for 19 donors was 0.65. Conclusion: The proposed model reliably describes the process of IgD+CD27+B-lym- phocytes proliferation in a healthy person. Availability: The derived computational scheme for predicting the level of IgD–CD27+B cells can be applied in a clinical practice. References: 1. S.R. Kuznetsov (2015) Mathematical model of the immune response, Vestnik S.-Petersburg Univ. Ser. 10. Prikl. Mat. Inform. Prots. Upr., 4: 72–87. (In Russian). 2. S.R. Kuznetsov (2015) Mathematical Model of the Humoral Immune Response: Focusing On Thl7 Autoimmunity, Math. Biol. Bioinf., 10(2):455-472. doi: 10.17537/2015.10.45 167 THE TENTH INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE\SYSTEMS BIOLOGY TARGET ENRICHMENT TECHNOLOGIES FOR APPLIED RESEARCH D.A. Kwon Agilent Technologies Russia, Moscow, Russia * Corresponding author: dmitry.kwon@agilent.com Key words: NGS, target enrichment, amplification, hybridization, custom Motivation and Aim: (text): NGS as an approach gave a powerful breakthrough in genomics, transcriptomics and epigenetics research and provides a tool for evaluation of wide range of principles, regularities and even mechanisms of genome functioning. The current stage of NGS is an applied research for clinical and biotechnological fields. Where not whole genome\transcriptome but more discrete objectives appears. Target enrichment – is a group of methods for library preparation for NGS to study genome\ transcriptome in any scale – from single gene up to whole functionally significant part of. Methods and Algorithms: (text): Agilent Technologies, Inc. provides wide menu of target enrichment kits, using two technologies – amplification (Haloplex technology) for small amounts of starting material and hybridization (SureSelect and OneSeq). These kits are able to provide high quality NGS libraries with excellent on target index for wide range of experiments – from small number of genes up to whole-exome and NGS-based cytogenetics for comprehensive, all-in-one detection of genome-wide CNVs, copy- neutral LOH (cnLOH), SNPs, and indels analysis in one target enrichment capture. Important to mention that any of the kits above can be used with custom design for any object. Also Agilent Technologies, Inc. provides wide range of NGS-related products for - In silico Design of custom NGS Target Enrichment panels - NGS data analysis software - NGS libraries quality control - NGS workflow automation 168 THE TENTH INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE\SYSTEMS BIOLOGY CHARACTERIZATION OF NOVEL ALKANE-DEGRADING AND BIOSURFACTANT-PRODUCING STRAIN TSUKAMURELLA TYROSINOSOLVENS PS2 A.V. Laikov 1 *, E.A. Boulygina 1 , V.A. Romanova 1 , T.V. Grigorieva 1 1 Kazan Federal University, Kazan, Russia * Corresponding author: a.v.laikov@gmail.com Download 3.91 Kb. Do'stlaringiz bilan baham: |
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