International Multiconference “Bioinformatics of Genome Regulation and Structure\Systems Biology”

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Systems Biology and Biomedicine symposium

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Systems Biology and Biomedicine symposiumGenetic Causes of Rare Forms of Inherited Retinal Distrophy

Genetic Causes of Rare Forms of Inherited Retinal Distrophy

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Tatyana Vasilyeva1, Andrey Marakhonov2, Vitaly Kadyshev3, Rena Zinchenko4
1Research Center for Medical Genetics, valyeva_debrie@mail.ru
2Research Centre for Medical Genetics, marakhonov@generesearch.ru
3Research Centre for Medical Genetics, vvh.kad@gmail.com
4Research Centre for Medical Genetics, renazinchenko@mail.ru

Retinal dystrophy is highly heterogeneous,  this “frequent among rare” inherited eye pathologies which result in blindness due to photoreceptors death. Though some common forms of retinal dystrophy are associated with well-known and years ago established genes, hundreds of others are found and kept being revealed to be involved in its pathogenesis. We reported 6 solved using next generation sequencing technology (whole exom sequencing) cases of hereditary retinitis pigmentosa in an advanced stage of the disease progression which were found to be associated with pathogenic nucleotide sequence variants in known genes PRPF31, IFT140, RGS9, RPGR, RP1, and IMPG2. All 6 analyzed cases were characterized by a similar clinical picture of the deisease at its terminal stage. NGS analysis is the only method for DNA-diagnostics of genetically diverse and clinically homogeneous forms of inherited retinal dystrophy. 

 

Systems Biology and Biomedicine symposiumQuantitative differences in the proteomic composition of the blood serum of patients with simple and paranoid schizophrenia

Quantitative differences in the proteomic composition of the blood serum of patients with simple and paranoid schizophrenia

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[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/363.pdf”]
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Liudmila Snirnova1
1Mental Health Research Institute, Tomsk National Researc Medical Center of the Russian Academy of Sciences, lpsmirnova@yandex.ru

The work analyzed the protein spectrum of blood serum of simple and paranoid schizophrenia. A set of proteins in schizophrenia was mainly associated with responsible for protein synthesis and the processes of transduction and translation; immune response, oxidative stress and apotosis, cell compataminization and cell contacts. In the blood serum of patients in the general group of schizophrenia, a significant increase in the number of RIPK1, mGluR6 receptors was revealed in comparison with healthy people. In addition, the amount of mGluR6 was significantly higher in patients with a simple form of schizophrenia than in patients with a paranoid form (p = 0.021). A quantitative assessment of the specific minor proteins that we studied using labeled standard peptides showed an increase in their number depending on the severity of the disease (a simple form of schizophrenia, leading negative symptoms)

Systems Biology and Biomedicine symposiumThe analysis of different longitudinal biomarkers association with the overall survival in non-small cell lung cancer by means of joint modeling

The analysis of different longitudinal biomarkers association with the overall survival in non-small cell lung cancer by means of joint modeling

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[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/350.pdf”]
Alina Sofronova1, Sergey Gavrilov2, Oleg Stepanov3, Kirill Peskov4, Kirill Zhudenkov5
1M&S decisions LLC, Moscow, Russia, alina.sofronova@msdecisions.ru
2M&S decisions LLC, Moscow, Russia, sergey.gavrilov@msdecisions.ru
3M&S decisions LLC, Moscow, Russia, oleg.stepanov@msdecisions.ru
4M&S decisions LLC, Moscow, Russia; Computational Oncology Group, I.M. Sechenov First Moscow State Medical University, Moscow, Russia, kirill.peskov@msdecisions.ru
5M&S decisions LLC, Moscow, Russia, kirill.zhudenkov@msdecisions.ru

It is well-known that tumor size is predictive of overall survival for patients with non-small cell lung cancer (NSCLC). Joint modeling is an advanced approach to quantify the association between longitudinal biomarkers and overall survival. The obtained results suggest that assessment of biomarker dynamics improved the accuracy of survival prediction in comparison with consideration of only baseline biomarker values for investigated patients with NSCLC.

Systems Biology and Biomedicine symposiumPlacental transcriptome co-expression analysis reveals key biomarkers and pathways of preeclampsia

Placental transcriptome co-expression analysis reveals key biomarkers and pathways of preeclampsia

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[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/340.pdf”]
Trifonova E.1, Zarubin A.2, Babovskaya A.3, Markov A.4, Stepanov V.5
1TNRMC RAS, Tomsk, Russia; SibMed, Tomsk, Russia, ekaterina.trifonova@medgenetics.ru
2TNRMC RAS, Tomsk, Russia, aleksei.zarubin@medgenetics.ru
3TNRMC RAS, Tomsk, Russia, anastasia.babovskaya@medgenetics.ru
4TNRMC RAS, Tomsk, Russia, anton.markov@medgenetics.ru
5TNRMC RAS, Tomsk, Russia, vadim.stepanov@medgenetics.ru

Preeclampsia is a complication of pregnancy characterized by new-onset hypertension and proteinuria of gestation, with serious consequences for mother and infant. Although a vast amount of research has been performed on the pathogenesis of preeclampsia, the underlying mechanisms of this multisystemic disease have remained to be fully elucidated. We identified the significant role of disturbance of intercellular interactions and regulation of proteins modification in placental tissue during the development of the PE. Among the genes involved in these key pathways, 9 hub genes and 3 master regulators were identified from the co-expression and upstream analysis networks. The present study may provide a basis for exploring potential novel genes and pathways as therapeutic targets for preeclampsia.

Systems Biology and Biomedicine symposiumMBP-hydrolyzing abzymes as a peripheral markers associated with impaired myelination in schizophrenia

MBP-hydrolyzing abzymes as a peripheral markers associated with impaired myelination in schizophrenia

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[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/333.pdf”]
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Daria Parshukova1, Liudmila Smirnova2, Ekaterina Dmitrieva3, Arkady Semke4, Vasily Yarnykh5, Svetlana Ivanova6
1Mental Health Research Institute Tomsk National Research Medical Center RAS, Susl2008@yandex.ru
2Mental Health Research Institute Tomsk National Research Medical Center RAS, Lpsmirnova@yandex.ru
3Mental Health Research Institute Tomsk National Research Medical Center RAS, Egdtomsk@mail.ru
4Mental Health Research Institute Tomsk National Research Medical Center RAS, Asemke@mail.ru
5University of Washington, Department of Radiology, yarnykh@uw.edu
6Mental Health Research Institute Tomsk National Research Medical Center RAS, Ivanovaniipz@gmail.com

It is well-known that the pathology of myelin and oligodendrocytes is involved in the pathogenesis of schizophrenia. Anomalies in oligodendrocytes and myelin can be a source of neuronal disruption. The discovery of catalytic antibodies (abzymes) allows us to investigate their pathological role in various conditions. One of the possible ways of inducing proteolytic antibodies is the appearance in the peripheral blood of a substrate in the form of damaged protein fragments. In our previous study, it was shown that the IgG of schizophrenia patients can hydrolyze the myelin basic protein – one of the main components of the central nervous system myelin.В  The study of IgG proteases in accessible biomaterial (serum) and their association with myelination disturbance in schizophrenia may be potential criteria for monitoring the severity of mental disorders.

Systems Biology and Biomedicine symposiumPharmacological effects of recombinant FGF21 in ovariectomized mice C57Bl/6J.

Pharmacological effects of recombinant FGF21 in ovariectomized mice C57Bl/6J.

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Kazantseva Antonina1, Tatyana Yakovleva2, Elena Makarova3, Nadezhda Kriklivaya4, Nadezhda Bazhan5
1ICG SB RAS, Novosibirsk, Russia, antonyna@yandex.ru
2ICG SB RAS, Novosibirsk, Russia, tatyanajakovleva@yandex.ru
3ICG SB RAS, Novosibirsk, Russia, enmakarova@gmail.com
4ICG SB RAS, Novosibirsk, Russia, nad.krikl@mail.ru
5ICG SB RAS, Novosibirsk, Russia, bazhan-nm@yandex.ru

Postmenopausal women have an increased risk of the development of the metabolic syndrome and type 2 diabetes. In pharmacological experiments it was found that hepatic hormone fibroblast growth factor 21 (FGF21) acts as a potent metabolic regulator. But the normalizing metabolic effects of FGF21 have been described only for males. Ovariectomized female mice may be considered as a model of decreased levels of estradiol in women during postmenopause. In this study we investigated the pharmacological effects of recombinant FGF21 in ovariectomized female mice. Ovariectomized animals received daily FGF21 injections (1 mkg/g body weight) for 7 days. On the 7th day, mice were tested in a glucose tolerance test. Then in mice blood levels of insulin, glucose and adiponectin were determined. Our results showed that FGF21 did not reduce body weight and adiposity, but improved carbohydrate lipid metabolism in estrogen-deficient female mice. These data allow considering FGF21 as a potential regulator for the correction of metabolic syndrome caused by a lack of estrogen in female mice.

Systems Biology and Biomedicine symposiumOpisthorchis felineus extracellular vesicles increase cell proliferation and migration rates of human H69 cholangiocytes

Opisthorchis felineus extracellular vesicles increase cell proliferation and migration rates of human H69 cholangiocytes

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[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/317.pdf”]
D.V. Ponomarev1, O. Zaparina2, M.Y. Pakharukova3, V.A. Mordvinov4
1Laboratory of Molecular Mechanisms of Pathological Processes Institute of Cytology and Genetics SB RAS, p.dmitr@outlook.com
2Laboratory of Molecular Mechanisms of Pathological Processes Institute of Cytology and Genetics SB RAS, zp.oksana.93@gmail.com
3Laboratory of Molecular Mechanisms of Pathological Processes Institute of Cytology and Genetics SB RAS, pmaria@yandex.ru
4Laboratory of Molecular Mechanisms of Pathological Processes Institute of Cytology and Genetics SB RAS, mordvin@bionet.nsc.ru

Opisthorchis felineus, is a food-borne liver trematode and the main cause of opisthorchiasis in Russia and Europe. It affects hepatobiliary system of fish-eating mammals, including humans. Opisthorchiasis is associated with chronic inflammation, biliary epithelium proliferation, liver fibrosis, and even might cause cholangiocarcinoma among chronically infected individuals. Secreted proteins and extracellular vesicles of liver flukes might play an important role in the development of pathology. We investigated the response of human H69 cholangiocytes and human hepatoma HepG2 cells to adult liver flukes and to extracellular vesicles released from the flukes. We have demonstrated high mitogenic and cell migration stimulating activity of flukes and EVs vesicles. The activity was specific for cholangiocytes, but not for HepG2 cells. Specific mitogenic effect of liver fluke extracellular vesicles on proliferation and migration of human cholangiocytes in vitro may reflect the mechanisms of development of precancerous biliary intraepithelial neoplasia during opisthorchiasis in vivo.

Systems Biology and Biomedicine symposiumWhole genome of novel Lactobacillus fermentum HFD1 strain producing various antimicrobial metabolites

Whole genome of novel Lactobacillus fermentum HFD1 strain producing various antimicrobial metabolites

No Comment on Whole genome of novel Lactobacillus fermentum HFD1 strain producing various antimicrobial metabolites

Georgii Ozhegov1, Monyr Nait Yahia2, Alexey Vasilchenko3, Natalya Gogoleva4, Dina Yarullina5, Airat Kaumov6
1Kazan Federal University, Kazan, Russia; Perm State Pharmaceutical Academy, Perm, Russia, georgii_provisor@mail.ru
2Kazan Federal University, Kazan, Russia, monyrnait94@gmail.com
3University of Tyumen, Tyumen, Russia, avasilchenko@gmail.com
4Kazan Federal University, Kazan, Russia; Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russia, NEGogoleva@kpfu.ru
5Kazan Federal University, Kazan, Russia, kasfes@gmail.com
6Kazan Federal University, Kazan, Russia, kairatr@yandex.ru

Lactobacilli, generally recognized as safe for humans, are characterized with high antagonistic properties. Among 40 strains of Lactobacilli isolated from the faeces of healthy humans, Lactobacillus fermentum HFD1 exhibited significant antimicrobial activity against various nosocomial pathogens. The genome of L.fermentum HFD1 was sequenced on Illumina MiSeq and ONT MinION instruments. After reads assembly 2 circular contigs with respective sizes of 2101878 bp and 5386 bp have been obtained. The raw reads alignment with BWA and post-assembly assessment showed that 99.9% of Illumina reads and 99.2% of MinION reads were mapped to assembled genome. The genome was read with 575x coverage for Illumina data and 454x coverage for MinION data. Based on genome alignment L. fermentum FTDC8312 was found as closest related strain. The BLAST search identified the short contig as similar to bacterophage phiX174. In the genome 2120 coding sequences (CDS) were predicted. Among them 606 were annotated as “hypothetical” without known biological role. By using CAMPr3, ADAM and AMPA services 5 CDSs with highest summary prediction score were identified as coding for antimicrobial peptides. Further validation of their antimicrobial activity in vitro is required.

Systems Biology and Biomedicine symposiumInfluence of Immobilized Subtilisins on Perfomance Indicators of Rat Heart in Experiment

Influence of Immobilized Subtilisins on Perfomance Indicators of Rat Heart in Experiment

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Pavel Madonov1, Roman Knyazev2, Konstantin Ershov3
1Department of experimental pharamacology Research Institute of Clinical and Experimental Lymphology – Branch of the Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences Novosibirsk, Russian Federation Department of pharmacology, clinical pharmacology and evidence-based medicine Novosibirsk State Medical University Novosibirsk, Russian Federation, Pmadonov@yandex.ru
2Research Institute of Biochemistry -Branch of the Federal Research Center of Fundamental and Translational Medicine Department of pharmacology, clinical pharmacology and evidence based medicine Novosibirsk State Medical University Novosibirsk, Russian Federation, Knjazev_roman@mail.ru
3Department of pharmacology, clinical pharmacology and evidence-based medicine Novosibirsk State Medical University,Novosibirsk, Russian Federation, Ershov_k@bk.ru

Immobilized subtilisins are bacterial proteinases with high thrombolytic activity that can improve peripheral circulation by dissolving a blood clot and reducing the manifestations of endothelial dysfunction. This article presents materials on the effect of immobilized subtilisins on heart performance in an experiment. The action of these proteinases was studied on a model of an isolated rat heart according to Langendorff. For registration, heart rate (HR) and pressure developed by the left ventricle (HDL) were selected. When immobilized subtilisins were added, an increase in left ventricular contraction force and a decrease in heart rate were shown. The results show that immobilized subtilisins have positive inotropic and negative chronotropic effects.

Systems Biology and Biomedicine symposiumNegative-pressure wound therapy of purulent wounds in patients with diabetic foot syndrome

Negative-pressure wound therapy of purulent wounds in patients with diabetic foot syndrome

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[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/296.pdf”]
Oleg Shumkov1, Mikhail Smagin2, Rustam Khapaev3
1Research Institute of Clinical and Experimental Lymphology Branch ICG SB RAS Novosibirsk, Russia, shumkov2011@ngs.ru
2Research Institute of Clinical and Experimental Lymphology Branch ICG SB RAS Novosibirsk, Russia, msa85@inbox.ru
3Research Institute of Clinical and Experimental Lymphology Branch ICG SB RAS Novosibirsk, Russia, khapaers@bionet.nsc.ru

В The clinical efficacy of the Pico vacuum dressing was evaluated in the complex treatment of patients with purulent-necrotic complications of the diabetic foot syndrome. The use of negative pressure in the treatment of purulent-necrotic complications of FDS in comparison with the classical principles of treatment of purulent wounds allows you to speed up the healing process and reduce the number of reoperations. It should be noted that the method of vacuum treatment of wound defects is considered by us only in combination with other components of the treatment of chronic infected wounds, such as systemic antibiotic therapy, elimination of hemodynamically significant arterial stenosis and occlusion, unloading of the foot.