DOCSLIB.ORG

SYSTEMS BIOLOGY and BIOMEDICINE (Sbiomed-2018) Symposium

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
SYSTEMS BIOLOGY and BIOMEDICINE (Sbiomed-2018) Symposium Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences Research Institute of Clinical and Experimental Lymphology – Branch of the Institute of Cytology and Genetics SB RAS Novosibirsk State University BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE\SYSTEMS BIOLOGY (BGRS\SB-2018) The Eleventh International Conference SYSTEMS BIOLOGY AND BIOMEDICINE (SBioMed-2018) Symposium Abstracts 21–22 August, 2018 Novosibirsk, Russia Novosibirsk ICG SB RAS 2018 УДК 575 S98 Systems Biology and Biomedicine (SBioMed-2018) : Symposium (21–22 Aug. 2018, Novosibirsk, Russia); Abstracts / Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences; Research Institute of Clinical and Experimental Lymphology – Branch of the Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences. – Novosibirsk: ICG SB RAS, 2018. – 174 pp. – ISBN 978-5-91291-040-1. Program committee Chairman A.Y. Letyagin, Professor, Novosibirsk Executive Secretary V.V. Klimontov, Professor, Novosibirsk Members D.A. Afonnikov, Novosibirsk, Russia A.V. Baranova, Fairfast, USA N.P. Bgatova, Novosibirsk, Russia V.I. Konenkov, Novosibirsk, Russia A.V. Kochetov, Novosibirsk, Russia A.A. Lagunin, Moscow, Russia L. Lipovich, Detroit, USA T.I. Merculova, Novosibirsk, Russia V.A. Mordvinov, Novosibirsk, Russia M.P. Moshkin, Novosibirsk, Russia Yu.L. Orlov, Novosibirsk, Russia S.E. Peltek, Novosibirsk, Russia A.G. Pokrovsky, Novosibirsk, Russia T.I. Pospelova, Novosibirsk, Russia O.V. Poveschenko, Novosibirsk, Russia V.P. Puzyrev, Tomsk, Russia S.V. Sennikov, Novosibirsk, Russia M.Yu. Skoblov, Moscow, Russia V.A. Stepanov, Tomsk, Russia Yu.I. Ragino, Novosibirsk, Russia A.N. Tulpakov, Moscow, Russia M.I. Voevoda, Novosibirsk, Russia Organizing committee Chairman M.A. Korolev, Novosibirsk, Rissia Members S.A. Velikanov, Novosibirsk, Russia N.V. Vlasova, Novosibirsk, Russia S.V. Zubova, Novosibirsk, Russia O.V. Petrovskaya, Novosibirsk, Russia E.V. Kostjashkina-Kushchina, Novosibirsk, Russia Contacts: [email protected] ISBN 978-5-91291-040-1 © ICG SB RAS, 2018 Organizers • Ministry of Science and High Education of Russian Federation • Siberian Branch of the Russian Academy of Sciences (SB RAS) • Institute of Cytology and Genetics SB RAS (ICIG SB RAS) • Research Institute of Clinical and Experimental Lymphology – Branch of the Institute of Cytology and Genetics SB RAS • Novosibirsk State University (NSU) • The Federal Agency for Scientific Organizations (FASO Russia) Sponsors Russian Foundation Federal Agency Ministry of Education and for Basic Research for Scientific Science of the Russian Grant No. 18-04-20047 Organizations Federation (Minobrnauki of FASO Russia Russia) Grant No. ДНИТ 28.12487.2018/12.1 GOLD SPONSORS SILVER SPONSORS MP Biomedicals Albiogen Roche Diagnostics Rus Ltd. Skygen, Ltd Bioline, Llc Khimexpert Ltd. DIA-M, Ltd BASIC SPONSORS geneXplain GmbH IOS Press Contents Dynamic modelling of CFTR receptor maturation in cystic fibrosis: What controls the receptor concentration in the plasma membrane? D. Astapenko, H.M. Botelho, A. Kolodkin, H.V. Westerhoff , M.D. Amaral 15 Association rs189037 in the ATM gene with bronchial asthma taking into account environmental factors. N. Babushkina, A. Postrigan, A. Kucher 16 Model melanocortin obesity: immunohistochemical examination of cyclooxygenase-2 and macrophages in the kidney of Ay mice. N.V. Baginskaya, N.S. Logvinenko 17 Ultrastructutal organization of hepatocytes in distant tumor growth. S. Bakhbaeva, N. Bgatova, Yu. Taskaeva, V. Makarova, Yu. Borodin 18 Regenerative technologies in the treatment of knee osteoarthritis. N. Banshсhikova, V. Omelchenko, E. Letjagina, A. Akimova, O. Poveshchenko, A. Lykov, M. Surovtseva, A. Evsyukov, A. Yezhov, A. Zobnin, M. Korolev 19 IL4 (rs 2243250) gene polymorphism depending on the clinical features psoriatic disease. A. Barilo, S. Smirnova, M. Smolnikova 20 Possible mechanisms of therapeutic effects of mesenchymal stromal cells conditioned medium on the model of cryptorchidism in rats. N.A. Basalova, G.D. Sagaradze, E.S. Kuznetsova, V.I. Kirpatovsky, D.A. Ohobotov, A.A. Kamalov, A.Yu. Efimenko 21 Design of vaccine constructs capable of inducing a cross protective effect against different strains of the influenza virus A. S. Bazhan, D. Antonets, L. Karpenko, T. Ilyicheva, O. Kaplina, V. Marchenko, S. Oreshkova 22 “Mining” for the alpha-1-antitrypsin deficiency in the population of Serbia – experience in the implementation of an integrative diagnostic algorithm. A. Beletic, I. Moric, V. Djordjevic 23 Neuroprotective effects of lithium carbonate in conditions of tumor growth. N. Bgatova, Yu. Taskaeva, V. Makarova, O. Solovjeva, N. Khotskin, A. Docenko, E. Zavyalov, S. Shatskaya, V. Isupov, Yu. Borodin 24 Investigation of meningioma samples by multi-omics analysis. K. Bocharov, A. Sorokin, V. Shurhkhay, I. Popov, E. Zhvansky, A. Potapov, E. Nikolaev 25 Potential genetic markers of Alzheimer’s disease, which play a significant role in aging. A. Bocharova, K. Vagaitseva, O. Makeeva, A. Marusin, N. Zhukova, I. Zhukova, V. Alifirova, M. Matveeva, V. Stepanov 26 Computer method for image enhancement in fish diagnostics.A.G. Bogomolov, T.V. Karamysheva, N.B. Rubtsov 27 The use of mesenchymal stem cells and erythropoietin in lower limb ischemia. N. Bondarenko, A. Lykov, M. Surovtseva, O. Poveschenko, A. Kabakov, I. Kim, O. Kazakov, A. Poveschenko 28 4 SBioMed-2018 Modified sorbents for pharmacology. Yu.I. Borodin, L.N. Rachkovskaya, T.V. Popova, А.А. Kotlyarova, S.V. Michurina, A.V. Shurlygina, E.E. Rachkovsky, M.V. Robinson, P.G. Madonov, M.A. Korolev, A.Yu. Letyagin, V.I. Konenkov 29 A search for molecular relationships between bronchial asthma and hypertension as an example of comorbid diseases. E.Yu. Bragina, M.B. Freidin, I.A. Goncharova, O.V. Saik, O.I. Zolotareva, V.A. Ivanisenko, V.E. Dosenko, R. Hofestaedt 30 Serum levels of adipokines in type 2 diabetic subjects: the relationships with adipose tissue distribution and microvasculature. D.M. Bulumbaeva, N.P. Bgatova, Yu.S. Taskaeva, O.N. Fazullina, N.B. Orlov, V.I. Konenkov, S.V. Savchenko 31 The use of melatonina in patients older than 60 years in the preoperative period. P. Bulychev, D. Khabarov, I. Siutkina, A. Smagin, A. Demura 32 Morphology and proteomic analysis of human placental exosomes. E. Burkova, G. Nevinsky 33 The possibility of colonization of spongy collagen plate by mesenchymal stromal cells. N.N. Butorina, O.N. Sheveleva, O.V. Payushina, E.I. Domaratskaya, E.V. Istranova, L.P. Istranov 34 25 leading laboratories in Russia and abroad are successfully using GenSeq™ DNA Library Kit v1.1 for targeted sequencing on the routine basis. M. Chukhryaeva 35 The role of Wip1 phosphatase in tumor cells, in the tumor microenvironment and anti-cancer therapy. O. Demidov, E. Imyanitov, N. Barlev, B. Grigorash, E. Kochetkova, B. Uyanik, C. Garrido 36 Drug-drug interactions severity prediction based on xenobiotic structural formulas and PASS prediction algorithm. A. Dmitriev, D. Filimonov, A. Lagunin, A. Rudik, D. Karasev, K. Murtazalieva, V. Poroikov 37 Selective killing of cancer cells by ultrasound assisted by biopolymer-coated metal nanoparticles. Y.A. Dyakov, O.K. Kosheleva, T.C. Lai, M. Hsiao, N.G. Chen, C.H. Chen 38 Cancer stem cells: Emergent nature of tumor emergency. Y.R. Efremov, A.S. Proskurina, E.A. Potter, E.V. Dolgova, O.V. Efremova, S.S. Bogachev 39 Real-time lipidomic analysis of biological tissue samples. V. Eliferov, E. Zhvansky, A. Sorokin, V. Shurkhay, I. Popov, E. Nikolaev 40 Fluctuating asymmetry of gene expression in embryos derived by in vitro fertilization. N.A. Feofanova, G.V. Kontsevaya, M.V. Anisimova, Y.L. Gon, Y.M. Moshkin 41 Clinical case: rare mutations in the CYP1B1 gene in a patient with primary congenital glaucoma. V. Fishman, O. Fenkova, M. Voevoda, A. Fursova, D. Ivanoshchuk 42 SBioMed-2018 5 Analysis of transcripts and expression of hox genes in the holothuria Eupentacta fraudatrix during regeneration. V.A. Garipova, A.S. Girich, I.Y. Dolmatov 43 Hox genes in the holothurian Eupentacta fraudatrix and their participation in the regeneration. V.A. Garipova, A.S. Girich, I.Y. Dolmatov 44 DNA methylation level in regulatory regions of mtDNA and three mitochondria-related nuclear genes in atherosclerosis. M.V. Golubenko, A.V. Markov, A.A. Zarubin, A.A. Sleptsov, A.N. Kazantsev, O.A. Makeeva, V.V. Markova, I.A. Koroleva, M.S. Nazarenko, O.L. Barbarash, V.P. Puzyrev 45 Possibilities of lymph nodes phytostimulation in the old age. V. Gorchakov, Yu. Kolmogorov, O. Gorchakova 46 New lymphotropic properties of herbal remedy Silymarin at liver pathology O. Gorchakova, T. Gaskina, V. Gorchakov 47 Characterization of cell division in primary hippocampal cultures derived from kaiso deficient mice.N.B. Illarionova, E.Y. Bazhenova, D.V. Fursenko, N.V. Khotskin, I.E. Sorokin, A.V. Kulikov 48 Nanoparticles of manganese oxide induce stress granule formation in human glioblastoma cells. N.B. Illarionova, K.N. Morozova, Y.B. Dorofeeva, D.V. Petrovski, A.V. Romaschenko, E.L. Zavyalov, E. Kiseleva, Y.M. Moshkin, M.P. Moshkin 49 The spectrum of common and rare CYP1B1 gene variants in Russia patients with congenital and juvenile open angle glaucoma. D. Ivanoshchuk, O. Fenkova, S. Mikhailova, I. Bychkov, N. Konovalova, O. Konovalova, M. Voevoda, A. Fursova, A. Romaschenko 50 The association of single nucleotide variations Rs6582147 and Rs2136810 with sudden cardiac death. A. Ivanova, V. Maksimov, S. Malyutina, V. Novoselov, M. Voevoda 51 Molecular-genetic phenotype of experimental breast cancer. A.V. Kabakov, A.P. Lykov, D.V. Morozov, O.V. Kazakov, A.F. Poveshchenko, T.V. Rayter, D.N. Strunkin, V.I. Konenkov 52 Evaluation of circulating tumor cells with epithelial-mesenchymal transition properties in the blood of breast cancer patients with different effect of neoadjuvant chemotherapy. E. Kaigorodova, V. Perelmuter, N. Tarabanovskaya, E. Simolina, E. Choynzonov 53 Serum markers in head and neck squamous cell carcinoma. G.V. Kakurina, О.V. Cheremisina, I.V. Kondakova, Е.L. Choynzonov 54 The relationship of the genes expression of actin-binding proteins with metastasis in squamous cell carcinoma of the head and neck and non-small cell lung cancer.
Load more

Recommended publications
  • Transcriptome Analysis Uncovers the Diagnostic Value of Mir-192-5P/HNF1A-AS1/VIL1 Panel in Cervical Adenocarcinoma
    www.nature.com/scientificreports OPEN Transcriptome analysis uncovers the diagnostic value of miR‑192‑5p/ HNF1A‑AS1/VIL1 panel in cervical adenocarcinoma Junfen Xu1*, Jian Zou1, Luyao Wu1 & Weiguo Lu1,2* Despite the fact that the incidence of cervical squamous cell carcinoma has decreased, there is an increase in the incidence of cervical adenocarcinoma. However, our knowledge on cervical adenocarcinoma is largely unclear. Transcriptome sequencing was conducted to compare 4 cervical adenocarcinoma tissue samples with 4 normal cervical tissue samples. mRNA, lncRNA, and miRNA signatures were identifed to discriminate cervical adenocarcinoma from normal cervix. The expression of VIL1, HNF1A‑AS1, MIR194‑2HG, SSTR5‑AS1, miR‑192‑5p, and miR‑194‑5p in adenocarcinoma were statistically signifcantly higher than that in normal control samples. The Receiver Operating Characteristic (ROC) curve analysis indicated that combination of miR‑192‑5p, HNF1A‑AS1, and VIL1 yielded a better performance (AUC = 0.911) than any single molecule -and could serve as potential biomarkers for cervical adenocarcinoma. Of note, the combination model also gave better performance than TCT test for cervical adenocarcinoma diagnosis. However, there was no correlation between miR‑192‑5p or HNF1A‑AS1 and HPV16/18 E6 or E7. VIL1 was weakly correlated with HPV18 E7 expression. In summary, our study has identifed miR‑192‑5p/HNF1A‑AS1/VIL1 panel that accurately discriminates adenocarcinoma from normal cervix. Detection of this panel may provide considerable clinical value in the diagnosis of cervical adenocarcinoma. Abbreviations SCC Cervical squamous cell carcinoma NcRNA Non-coding RNA MiRNA MicroRNA LncRNA Long non-coding RNA ROC Receiver operating characteristic AUC​ Area under the ROC curve RT-qPCR Quantitative reverse-transcriptase PCR HNF1A-AS1 LncRNA HNF1A antisense RNA 1 VIL1 Villin 1 Cervical cancer ranks fourth for both cancer incidence and mortality in women worldwide 1.
    [Show full text]
  • Genomic and Transcriptome Analysis Revealing an Oncogenic Functional Module in Meningiomas
    Neurosurg Focus 35 (6):E3, 2013 ©AANS, 2013 Genomic and transcriptome analysis revealing an oncogenic functional module in meningiomas XIAO CHANG, PH.D.,1 LINGLING SHI, PH.D.,2 FAN GAO, PH.D.,1 JONATHAN RUssIN, M.D.,3 LIYUN ZENG, PH.D.,1 SHUHAN HE, B.S.,3 THOMAS C. CHEN, M.D.,3 STEVEN L. GIANNOTTA, M.D.,3 DANIEL J. WEISENBERGER, PH.D.,4 GAbrIEL ZADA, M.D.,3 KAI WANG, PH.D.,1,5,6 AND WIllIAM J. MAck, M.D.1,3 1Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California; 2GHM Institute of CNS Regeneration, Jinan University, Guangzhou, China; 3Department of Neurosurgery, Keck School of Medicine, University of Southern California, Los Angeles, California; 4USC Epigenome Center, Keck School of Medicine, University of Southern California, Los Angeles, California; 5Department of Psychiatry, Keck School of Medicine, University of Southern California, Los Angeles, California; and 6Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California Object. Meningiomas are among the most common primary adult brain tumors. Although typically benign, roughly 2%–5% display malignant pathological features. The key molecular pathways involved in malignant trans- formation remain to be determined. Methods. Illumina expression microarrays were used to assess gene expression levels, and Illumina single- nucleotide polymorphism arrays were used to identify copy number variants in benign, atypical, and malignant me- ningiomas (19 tumors, including 4 malignant ones). The authors also reanalyzed 2 expression data sets generated on Affymetrix microarrays (n = 68, including 6 malignant ones; n = 56, including 3 malignant ones).
    [Show full text]
  • Understanding the Role of Transforming Growth Factor Beta Signalling and Epigenomics in Osteoarthritis
    Understanding the role of Transforming Growth Factor Beta signalling and Epigenomics in Osteoarthritis by ©Erfan Aref-Eshghi A thesis submitted to the School of Graduate Studies In partial fulfilment of the requirements for the degree of Doctor of Philosophy in Medicine - Human Genetics Discipline of Genetics, Faculty of Medicine Memorial University of Newfoundland St. John’s, Newfoundland and Labrador, Canada May 2016 i Abstract Osteoarthritis (OA) is the most common form of arthritis with a high socioeconomic burden, with an incompletely understood etiology. Evidence suggests a role for the transforming growth factor beta (TGF-ß) signalling pathway and epigenomics in OA. The aim of this thesis was to understand the involvement of the TGF-ß pathway in OA and to determine the DNA methylation patterns of OA-affected cartilage as compared to the OA-free cartilage. First, I found that a common SNP in the BMP2 gene, a ligand in the Bone morphogenetic protein (BMP) subunit of TGF-ß pathway, was associated with OA in the Newfoundland population. I also showed a genetic association between SMAD3 - a signal transducer in the TGF-ß subunit of the TGF-ß signalling pathway - and the total radiographic burden of OA. I further demonstrated that SMAD3 is over-expressed in OA cartilage, suggesting an over activation of the TGF-ß signalling in OA. Next, I examined the connection of these genes in the regulation of matrix metallopeptidase 13 (MMP13) - an enzyme known to destroy extracellular matrix in OA cartilage - in the context of the ‎TGF-ß signalling. The analyses showed that TGF-ß, MMP13, and SMAD3 were overexpressed in OA cartilage, whereas the expression of BMP2 was significantly reduced.
    [Show full text]
  • Qt38n028mr Nosplash A3e1d84
    ! ""! ACKNOWLEDGEMENTS I dedicate this thesis to my parents who inspired me to become a scientist through invigorating scientific discussions at the dinner table even when I was too young to understand what the hippocampus was. They also prepared me for the ups and downs of science and supported me through all of these experiences. I would like to thank my advisor Dr. Elizabeth Blackburn and my thesis committee members Dr. Eric Verdin, and Dr. Emmanuelle Passegue. Liz created a nurturing and supportive environment for me to explore my own ideas, while at the same time teaching me how to love science, test my questions, and of course provide endless ways to think about telomeres and telomerase. Eric and Emmanuelle both gave specific critical advice about the proper experiments for T cells and both volunteered their lab members for further critical advice. I always felt inspired with a sense of direction after thesis committee meetings. The Blackburn lab is full of smart and dedicated scientists whom I am thankful for their support. Specifically Dr. Shang Li and Dr. Brad Stohr for their stimulating scientific debates and “arguments.” Dr. Jue Lin, Dana Smith, Kyle Lapham, Dr. Tet Matsuguchi, and Kyle Jay for their friendships and discussions about what my data could possibly mean. Dr. Eva Samal for teaching me molecular biology techniques and putting up with my late night lab exercises. Beth Cimini for her expertise with microscopy, FACs, singing, and most of all for being a caring and supportive friend. Finally, I would like to thank Dr. Imke Listerman, my scientific partner for most of the breast cancer experiments.
    [Show full text]
  • A Genome-Wide Association Study for Irinotecan-Related Severe Toxicities in Patients with Advanced Non-Small-Cell Lung Cancer
    The Pharmacogenomics Journal (2013) 13, 417 -- 422 & 2013 Macmillan Publishers Limited All rights reserved 1470-269X/13 www.nature.com/tpj ORIGINAL ARTICLE A genome-wide association study for irinotecan-related severe toxicities in patients with advanced non-small-cell lung cancer J-Y Han1, ES Shin2, Y-S Lee3, HY Ghang4, S-Y Kim3, J-A Hwang3, JY Kim1 and JS Lee1 The identification of patients who are at high risk for irinotecan-related severe diarrhea and neutropenia is clinically important. We conducted the first genome-wide association study (GWAS) to search for novel susceptibility genes for irinotecan-related severe toxicities, such as diarrhea and neutropenia, in non-small-cell lung cancer (NSCLC) patients treated with irinotecan chemotherapy. The GWAS putatively identified 49 single-nucleotide polymorphisms (SNPs) associated with grade 3 diarrhea (G3D) and 32 SNPs associated with grade 4 neutropenia (G4N). In the replication series, the SNPs rs1517114 (C8orf34), rs1661167 (FLJ41856) and rs2745761 (PLCB1) were confirmed as being associated with G3D, whereas rs11128347 (PDZRN3) and rs11979430 and rs7779029 (SEMAC3) were confirmed as being associated with G4N. The final imputation analysis of our GWAS and replication study showed significant overlaps of association signals within these novel variants. This GWAS screen, along with subsequent validation and imputation analysis, identified novel SNPs associated with irinotecan-related severe toxicities. The Pharmacogenomics Journal (2013) 13, 417--422; doi:10.1038/tpj.2012.24; published online 5 June 2012 Keywords: C8orf34; FLJ41856; PLCB1; PDZRN3; SEMA3C; irinotecan INTRODUCTION technologies has paved the way for a genome-wide association 13 Irinotecan is one of the most active chemotherapeutic agents for study (GWAS) to identify novel susceptibility genes.
    [Show full text]
  • C-Met As a Key Factor Responsible for Sustaining Undifferentiated Phenotype and Therapy Resistance in Renal Carcinomas
    cells Review C-Met as a Key Factor Responsible for Sustaining Undifferentiated Phenotype and Therapy Resistance in Renal Carcinomas Paulina Marona 1 , Judyta Górka 1 , Jerzy Kotlinowski 1 , Marcin Majka 2 , Jolanta Jura 1 and Katarzyna Miekus 1,* 1 Department of General Biochemistry, Faculty of Biochemistry, Biopphisics and Biotechnology, Jagiellonian University, Gronostajowa Street 7, 30-387 Krakow, Poland; [email protected] (P.M.); [email protected] (J.G.); [email protected] (J.K.); [email protected] (J.J.) 2 Department of Transplantation, Jagiellonian University Medical College, Jagiellonian University, Wielicka 265, 30-663 Krakow, Poland; [email protected] * Correspondence: [email protected] Received: 28 February 2019; Accepted: 19 March 2019; Published: 22 March 2019 Abstract: C-Met tyrosine kinase receptor plays an important role under normal and pathological conditions. In tumor cells’ overexpression or incorrect activation of c-Met, this leads to stimulation of proliferation, survival and increase of motile activity. This receptor is also described as a marker of cancer initiating cells. The latest research shows that the c-Met receptor has an influence on the development of resistance to targeted cancer treatment. High c-Met expression and activation in renal cell carcinomas is associated with the progression of the disease and poor survival of patients. C-Met receptor has become a therapeutic target in kidney cancer. However, the therapies used so far using c-Met tyrosine kinase inhibitors demonstrate resistance to treatment. On the other hand, the c-Met pathway may act as an alternative target pathway in tumors that are resistant to other therapies.
    [Show full text]
  • Development of Novel Analysis and Data Integration Systems to Understand Human Gene Regulation
    Development of novel analysis and data integration systems to understand human gene regulation Dissertation zur Erlangung des Doktorgrades Dr. rer. nat. der Fakult¨atf¨urMathematik und Informatik der Georg-August-Universit¨atG¨ottingen im PhD Programme in Computer Science (PCS) der Georg-August University School of Science (GAUSS) vorgelegt von Raza-Ur Rahman aus Pakistan G¨ottingen,April 2018 Prof. Dr. Stefan Bonn, Zentrum f¨urMolekulare Neurobiologie (ZMNH), Betreuungsausschuss: Institut f¨urMedizinische Systembiologie, Hamburg Prof. Dr. Tim Beißbarth, Institut f¨urMedizinische Statistik, Universit¨atsmedizin, Georg-August Universit¨at,G¨ottingen Prof. Dr. Burkhard Morgenstern, Institut f¨urMikrobiologie und Genetik Abtl. Bioinformatik, Georg-August Universit¨at,G¨ottingen Pr¨ufungskommission: Prof. Dr. Stefan Bonn, Zentrum f¨urMolekulare Neurobiologie (ZMNH), Referent: Institut f¨urMedizinische Systembiologie, Hamburg Prof. Dr. Tim Beißbarth, Institut f¨urMedizinische Statistik, Universit¨atsmedizin, Korreferent: Georg-August Universit¨at,G¨ottingen Prof. Dr. Burkhard Morgenstern, Weitere Mitglieder Institut f¨urMikrobiologie und Genetik Abtl. Bioinformatik, der Pr¨ufungskommission: Georg-August Universit¨at,G¨ottingen Prof. Dr. Carsten Damm, Institut f¨urInformatik, Georg-August Universit¨at,G¨ottingen Prof. Dr. Florentin W¨org¨otter, Physikalisches Institut Biophysik, Georg-August-Universit¨at,G¨ottingen Prof. Dr. Stephan Waack, Institut f¨urInformatik, Georg-August Universit¨at,G¨ottingen Tag der m¨undlichen Pr¨ufung: der 30. M¨arz2018
    [Show full text]
  • Novel Pharmacogenomic Markers of Irinotecan-Induced Severe Toxicity in Metastatic Colorectal Cancer Patients
    Novel pharmacogenomic markers of irinotecan-induced severe toxicity in metastatic colorectal cancer patients Thèse Siwen Sylvialin Chen Doctorat en sciences pharmaceutiques Philosophiae doctor (Ph.D.) Québec, Canada © Siwen Sylvialin Chen, 2015 ii Résumé L’irinotécan est un agent de chimiothérapie largement utilisé pour le traitement de tumeurs solides, particulièrement pour le cancer colorectal métastatique (mCRC). Fréquemment, le traitement par l’irinotécan conduit à la neutropénie et la diarrhée, des effets secondaires sévères qui peuvent limiter la poursuite du traitement et la qualité de vie des patients. Plusieurs études pharmacogénomiques ont évalué les risques associés à la chimiothérapie à base d’irinotécan, en particulier en lien avec le gène UGT1A, alors que peu d’études ont examiné l’impact des gènes codant pour des transporteurs. Par exemple, le marqueur UGT1A1*28 a été associé à une augmentation de 2 fois du risque de neutropénie, mais ce marqueur ne permet pas de prédire la toxicité gastrointestinale ou l’issue clinique. L’objectif de cette étude était de découvrir de nouveaux marqueurs génétiques associés au risque de toxicité induite par l’irinotécan, en utilisant une stratégie d’haplotype/SNP-étiquette permettant de maximiser la couverture des loci génétiques ciblés. Nous avons analysé les associations génétiques des loci UGT1 et sept gènes codants pour des transporteurs ABC impliqués dans la pharmacocinétique de l’irinotécan, soient ABCB1, ABCC1, ABCC2, ABCC5, ABCG1, ABCG2 ainsi que SLCO1B1. Les profils de 167 patients canadiens atteints de mCRC sous traitement FOLFIRI (à base d’irinotécan) ont été examinés et les marqueurs significatifs ont par la suite été validés dans une cohorte indépendante de 250 patients italiens.
    [Show full text]
  • Clinical, Molecular, and Immune Analysis of Dabrafenib-Trametinib
    Supplementary Online Content Chen G, McQuade JL, Panka DJ, et al. Clinical, molecular and immune analysis of dabrafenib-trametinib combination treatment for metastatic melanoma that progressed during BRAF inhibitor monotherapy: a phase 2 clinical trial. JAMA Oncology. Published online April 28, 2016. doi:10.1001/jamaoncol.2016.0509. eMethods. eReferences. eTable 1. Clinical efficacy eTable 2. Adverse events eTable 3. Correlation of baseline patient characteristics with treatment outcomes eTable 4. Patient responses and baseline IHC results eFigure 1. Kaplan-Meier analysis of overall survival eFigure 2. Correlation between IHC and RNAseq results eFigure 3. pPRAS40 expression and PFS eFigure 4. Baseline and treatment-induced changes in immune infiltrates eFigure 5. PD-L1 expression eTable 5. Nonsynonymous mutations detected by WES in baseline tumors This supplementary material has been provided by the authors to give readers additional information about their work. © 2016 American Medical Association. All rights reserved. Downloaded From: https://jamanetwork.com/ on 09/30/2021 eMethods Whole exome sequencing Whole exome capture libraries for both tumor and normal samples were constructed using 100ng genomic DNA input and following the protocol as described by Fisher et al.,3 with the following adapter modification: Illumina paired end adapters were replaced with palindromic forked adapters with unique 8 base index sequences embedded within the adapter. In-solution hybrid selection was performed using the Illumina Rapid Capture Exome enrichment kit with 38Mb target territory (29Mb baited). The targeted region includes 98.3% of the intervals in the Refseq exome database. Dual-indexed libraries were pooled into groups of up to 96 samples prior to hybridization.
    [Show full text]
  • Robles JTO Supplemental Digital Content 1
    Supplementary Materials An Integrated Prognostic Classifier for Stage I Lung Adenocarcinoma based on mRNA, microRNA and DNA Methylation Biomarkers Ana I. Robles1, Eri Arai2, Ewy A. Mathé1, Hirokazu Okayama1, Aaron Schetter1, Derek Brown1, David Petersen3, Elise D. Bowman1, Rintaro Noro1, Judith A. Welsh1, Daniel C. Edelman3, Holly S. Stevenson3, Yonghong Wang3, Naoto Tsuchiya4, Takashi Kohno4, Vidar Skaug5, Steen Mollerup5, Aage Haugen5, Paul S. Meltzer3, Jun Yokota6, Yae Kanai2 and Curtis C. Harris1 Affiliations: 1Laboratory of Human Carcinogenesis, NCI-CCR, National Institutes of Health, Bethesda, MD 20892, USA. 2Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo 104-0045, Japan. 3Genetics Branch, NCI-CCR, National Institutes of Health, Bethesda, MD 20892, USA. 4Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan. 5Department of Chemical and Biological Working Environment, National Institute of Occupational Health, NO-0033 Oslo, Norway. 6Genomics and Epigenomics of Cancer Prediction Program, Institute of Predictive and Personalized Medicine of Cancer (IMPPC), 08916 Badalona (Barcelona), Spain. List of Supplementary Materials Supplementary Materials and Methods Fig. S1. Hierarchical clustering of based on CpG sites differentially-methylated in Stage I ADC compared to non-tumor adjacent tissues. Fig. S2. Confirmatory pyrosequencing analysis of DNA methylation at the HOXA9 locus in Stage I ADC from a subset of the NCI microarray cohort. 1 Fig. S3. Methylation Beta-values for HOXA9 probe cg26521404 in Stage I ADC samples from Japan. Fig. S4. Kaplan-Meier analysis of HOXA9 promoter methylation in a published cohort of Stage I lung ADC (J Clin Oncol 2013;31(32):4140-7). Fig. S5. Kaplan-Meier analysis of a combined prognostic biomarker in Stage I lung ADC.
    [Show full text]
  • Genome-Wide Analysis Identifies Significant Contribution of Brain-Expressed Genes in Chronic, but Not Acute, Back Pain
    medRxiv preprint doi: https://doi.org/10.1101/2020.09.04.20187575; this version posted September 7, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license . Genome-wide analysis identifies significant contribution of brain-expressed genes in chronic, but not acute, back pain Andrey V. Bortsov1,†, Marc Parisien2,†, Samar Khoury2,†, Dmitri V. Zaykin3, Amy E Martinsen5,6,7, Marie Udnesseter Lie4,5,6, Ingrid Heuch7, HUNT All-In Pain, Kristian Hveem5,8, John-Anker Zwart5,6,7, Bendik S Winsvold5,7, Luda Diatchenko2* 1. Center for Translational Pain Medicine, Department of Anesthesiology, Duke University, Durham, NC, USA. 2. Alan Edwards Centre for Research on Pain; Department of Anesthesia, School of Medicine; School of Dentistry; McGill University, Montréal, QC, Canada. 3. Biostatistics and Computational Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA. 4. Research and Communication Unit for Musculoskeletal Health (FORMI), Department of Research, Innovation and Education, Division of Clinical Neuroscience, Oslo University Hospital, Oslo, Norway. 5. K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway. 6. Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway. 7. Department of Research, Innovation and Education, Division of Clinical Neuroscience, Oslo University Hospital, Oslo, Norway. 8. HUNT Research Center, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway.
    [Show full text]
  • Vast Human-Specific Delay in Cortical Ontogenesis Associated With
    Supplementary information Extension of cortical synaptic development distinguishes humans from chimpanzees and macaques Supplementary Methods Sample collection We used prefrontal cortex (PFC) and cerebellar cortex (CBC) samples from postmortem brains of 33 human (aged 0-98 years), 14 chimpanzee (aged 0-44 years) and 44 rhesus macaque individuals (aged 0-28 years) (Table S1). Human samples were obtained from the NICHD Brain and Tissue Bank for Developmental Disorders at the University of Maryland, USA, the Netherlands Brain Bank, Amsterdam, Netherlands and the Chinese Brain Bank Center, Wuhan, China. Informed consent for use of human tissues for research was obtained in writing from all donors or their next of kin. All subjects were defined as normal by forensic pathologists at the corresponding brain bank. All subjects suffered sudden death with no prolonged agonal state. Chimpanzee samples were obtained from the Yerkes Primate Center, GA, USA, the Anthropological Institute & Museum of the University of Zürich-Irchel, Switzerland and the Biomedical Primate Research Centre, Netherlands (eight Western chimpanzees, one Central/Eastern and five of unknown origin). Rhesus macaque samples were obtained from the Suzhou Experimental Animal Center, China. All non-human primates used in this study suffered sudden deaths for reasons other than their participation in this study and without any relation to the tissue used. CBC dissections were made from the cerebellar cortex. PFC dissections were made from the frontal part of the superior frontal gyrus. All samples contained an approximately 2:1 grey matter to white matter volume ratio. RNA microarray hybridization RNA isolation, hybridization to microarrays, and data preprocessing were performed as described previously (Khaitovich et al.
    [Show full text]