The Golgi Glycoprotein MGAT4D Is an Intrinsic Protector of Testicular
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Integrative Genomic and Epigenomic Analyses Identified IRAK1 As a Novel Target for Chronic Inflammation-Driven Prostate Tumorigenesis
bioRxiv preprint doi: https://doi.org/10.1101/2021.06.16.447920; this version posted June 16, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Integrative genomic and epigenomic analyses identified IRAK1 as a novel target for chronic inflammation-driven prostate tumorigenesis Saheed Oluwasina Oseni1,*, Olayinka Adebayo2, Adeyinka Adebayo3, Alexander Kwakye4, Mirjana Pavlovic5, Waseem Asghar5, James Hartmann1, Gregg B. Fields6, and James Kumi-Diaka1 Affiliations 1 Department of Biological Sciences, Florida Atlantic University, Florida, USA 2 Morehouse School of Medicine, Atlanta, Georgia, USA 3 Georgia Institute of Technology, Atlanta, Georgia, USA 4 College of Medicine, Florida Atlantic University, Florida, USA 5 Department of Computer and Electrical Engineering, Florida Atlantic University, Florida, USA 6 Department of Chemistry & Biochemistry and I-HEALTH, Florida Atlantic University, Florida, USA Corresponding Author: [email protected] (S.O.O) Running Title: Chronic inflammation signaling in prostate tumorigenesis bioRxiv preprint doi: https://doi.org/10.1101/2021.06.16.447920; this version posted June 16, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract The impacts of many inflammatory genes in prostate tumorigenesis remain understudied despite the increasing evidence that associates chronic inflammation with prostate cancer (PCa) initiation, progression, and therapy resistance. -
A Multistep Bioinformatic Approach Detects Putative Regulatory
BMC Bioinformatics BioMed Central Research article Open Access A multistep bioinformatic approach detects putative regulatory elements in gene promoters Stefania Bortoluzzi1, Alessandro Coppe1, Andrea Bisognin1, Cinzia Pizzi2 and Gian Antonio Danieli*1 Address: 1Department of Biology, University of Padova – Via Bassi 58/B, 35131, Padova, Italy and 2Department of Information Engineering, University of Padova – Via Gradenigo 6/B, 35131, Padova, Italy Email: Stefania Bortoluzzi - [email protected]; Alessandro Coppe - [email protected]; Andrea Bisognin - [email protected]; Cinzia Pizzi - [email protected]; Gian Antonio Danieli* - [email protected] * Corresponding author Published: 18 May 2005 Received: 12 November 2004 Accepted: 18 May 2005 BMC Bioinformatics 2005, 6:121 doi:10.1186/1471-2105-6-121 This article is available from: http://www.biomedcentral.com/1471-2105/6/121 © 2005 Bortoluzzi et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Searching for approximate patterns in large promoter sequences frequently produces an exceedingly high numbers of results. Our aim was to exploit biological knowledge for definition of a sheltered search space and of appropriate search parameters, in order to develop a method for identification of a tractable number of sequence motifs. Results: Novel software (COOP) was developed for extraction of sequence motifs, based on clustering of exact or approximate patterns according to the frequency of their overlapping occurrences. -
Comparative Biochemistry and Physiology, Part D, Vol. 5, Pp. 45-54 (2010)
Comparative genomics and proteomics of vertebrate diacylglycerol acyltransferase (DGAT), acyl CoA wax alcohol acyltransferase (AWAT) and monoacylglycerol acyltransferase (MGAT) Author Holmes, Roger S Published 2010 Journal Title Comparative Biochemistry and Physiology, Part D DOI https://doi.org/10.1016/j.cbd.2009.09.004 Copyright Statement © 2010 Elsevier. This is the author-manuscript version of this paper. Reproduced in accordance with the copyright policy of the publisher. Please refer to the journal's website for access to the definitive, published version. Downloaded from http://hdl.handle.net/10072/36786 Griffith Research Online https://research-repository.griffith.edu.au Comparative Biochemistry and Physiology, Part D, Vol. 5, pp. 45-54 (2010) COMPARATIVE GENOMICS AND PROTEOMICS OF VERTEBRATE DIACYLGLYCEROL ACYLTRANSFERASE (DGAT), ACYL CoA WAX ALCOHOL ACYLTRANSFERASE (AWAT) AND MONOACYLGLYCEROL ACYLTRANSFERASE (MGAT) Roger S Holmes School of Biomolecular and Physical Sciences, Griffith University, Nathan 4111 Brisbane Queensland Australia Email: [email protected] Keywords: Diacylglycerol acyltransferase-Monoacylglycerol transferase-Human- Mouse-Opossum-Zebrafish-Genetics-Evolution-X chromosome Running Head: Genomics and proteomics of vertebrate acylglycerol acyltransferases ABSTRACT BLAT (BLAST-Like Alignment Tool) analyses of the opossum (Monodelphis domestica) and zebrafish (Danio rerio) genomes were undertaken using amino acid sequences of the acylglycerol acyltransferase (AGAT) superfamily. Evidence is reported for 8 opossum monoacylglycerol acyltransferase-like (MGAT) (E.C. 2.3.1.22) and diacylglycerol acyltransferase-like (DGAT) (E.C. 2.3.1.20) genes and proteins, including DGAT1, DGAT2, DGAT2L6 (DGAT2-like protein 6), AWAT1 (acyl-CoA wax alcohol acyltransferase 1), AWAT2, MGAT1, MGAT2 and MGAT3. Three of these genes (AWAT1, AWAT2 and DGAT2L6) are closely localized on the opossum X chromosome. -
3313.Full.Pdf
[CANCER RESEARCH Vol. 6, 3313–3319, June 15, 2000] New Evidence for an Extra-Hepatic Role of N-acetylglucosaminyltransferase III in the Progression of Diethylnitrosamine-induced Liver Tumors in Mice1 Xiaoping Yang, Mantu Bhaumik, Riddhi Bhattacharyya, Shih Gong, Charles E. Rogler, and Pamela Stanley2 Departments of Cell Biology [X. Y., M. B., R. B., P. S.] and Medicine and Microbiology/Immunology [S. G., C. E. R.], Albert Einstein College of Medicine, New York, New York 10461 ABSTRACT exhibit reduced experimental metastasis (10). Overexpression of Gl- cNAc-TIII in PC12 cells perturbs their ability to respond to nerve N-acetylglucosaminyltransferase III (GlcNAc-TIII) is encoded by the growth factor (11), and overexpression in a glioma cell line inhibits Mgat3 gene and catalyzes the addition of the bisecting GlcNAc to the core of N-glycans. Mice lacking GlcNAc-TIII due to the insertion mutation epidermal growth factor receptor function (12). K562 cells expressing Mgat3tm1Pst (termed Mgat3neo), exhibit retarded progression of liver tu- a transfected Mgat3 gene are comparatively resistant to natural killer mors induced by diethylnitrosamine (DEN; M. Bhaumik et al., Cancer cell cytotoxicity and colonize spleen more effectively (13). In mice Res., 58: 2881–2887, 1998). This phenotype seemed to be due to a reduc- overexpressing a Mgat3 transgene in hepatocytes, a reduction in tion, in activity or amount, of a circulating glycoprotein(s) that enhances secretion of apolipoprotein and lipids from liver was reported (14). DEN-induced liver tumor progression. Here, we provide new evidence to Transgenic mice overexpressing a Mgat3 transgene in hematopoietic support this hypothesis. First, we show that mice with a deletion mutation ⌬ cells were found to have a defect in stroma-dependent hemopoiesis of the Mgat3 gene coding exon (Mgat3tmlJxm, termed Mgat3 ) also exhibit retarded progression of DEN-induced liver tumors. -
Network Inference from Glycoproteomics Data Reveals New Reactions in the Igg Glycosylation Pathway
ARTICLE DOI: 10.1038/s41467-017-01525-0 OPEN Network inference from glycoproteomics data reveals new reactions in the IgG glycosylation pathway Elisa Benedetti1, Maja Pučić-Baković2, Toma Keser 3, Annika Wahl4,5, Antti Hassinen6, Jeong-Yeh Yang7, Lin Liu7, Irena Trbojević-Akmačić2, Genadij Razdorov 2, Jerko Štambuk2, Lucija Klarić2,8,9, Ivo Ugrina 3,10,11, Maurice H.J. Selman12, Manfred Wuhrer 12, Igor Rudan 8, Ozren Polasek13,14, Caroline Hayward 9, Harald Grallert4,5,15, Konstantin Strauch16,17, Annette Peters5, Thomas Meitinger18, Christian Gieger4,5, Marija Vilaj2, Geert-Jan Boons7,19, Kelley W. Moremen7, Tatiana Ovchinnikova20, Nicolai Bovin20, Sakari Kellokumpu6, Fabian J. Theis 1,21, Gordan Lauc2,3 & Jan Krumsiek 1,14 Immunoglobulin G (IgG) is a major effector molecule of the human immune response, and aberrations in IgG glycosylation are linked to various diseases. However, the molecular mechanisms underlying protein glycosylation are still poorly understood. We present a data- driven approach to infer reactions in the IgG glycosylation pathway using large-scale mass- spectrometry measurements. Gaussian graphical models are used to construct association networks from four cohorts. We find that glycan pairs with high partial correlations represent enzymatic reactions in the known glycosylation pathway, and then predict new biochemical reactions using a rule-based approach. Validation is performed using data from a GWAS and results from three in vitro experiments. We show that one predicted reaction is enzymatically feasible and that one rejected reaction does not occur in vitro. Moreover, in contrast to previous knowledge, enzymes involved in our predictions colocalize in the Golgi of two cell lines, further confirming the in silico predictions. -
A Systems Genetics Approach to Revealing the Pdgfb Molecular Network of the Retina
Molecular Vision 2020; 26:459-471 <http://www.molvis.org/molvis/v26/459> © 2020 Molecular Vision Received 19 November 2019 | Accepted 17 June 2020 | Published 19 June 2020 A systems genetics approach to revealing the Pdgfb molecular network of the retina Shasha Li,1,2 Fuyi Xu,2 Lin Liu,1 Rong Ju,3 Jonas Bergquist,1,4 Qing Yin Zheng,5,6 Jia Mi,1 Lu Lu,2 Xuri Li,3 Geng Tian1 (The first two authors contributed equally to this work.) 1Medicine and Pharmacy Research Center, Binzhou Medical University, Yantai, Shandong, China; 2Department of Genetics, Genomics and informatics, University of Tennessee Health Science Center, Memphis, TN; 3State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, Guangdong, China; 4Analytical Chemistry and Neurochemistry, Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden; 5Transformative Otology and Neuroscience Center, Case Western Reserve University School of Medicine, Cleveland, OH; 6Departments of Otolaryngology, Case Western Reserve University School of Medicine, Cleveland, OH. Purpose: Platelet-derived growth factor (PDGF) signaling is well known to be involved in vascular retinopathies. Among the PDGF family, the subunit B (PDGFB) protein is considered a promising therapeutic target. This study aimed to identify the genes and potential pathways through which PDGFB affects retinal phenotypes by using a systems genetics approach. Methods: Gene expression data had been previously generated in a laboratory for the retinas of 75 C57BL/6J(B6) X DBA/2J (BXD) recombinant inbred (RI) strains. Using this data, the genetic correlation method was used to identify genes correlated to Pdgfb. A correlation between intraocular pressure (IOP) and Pdgfb was calculated based on the Pearson correlation coefficient. -
Glycosyltransferase B4GALNT2 As a Predictor of Good Prognosis in Colon Cancer: Lessons from Databases
International Journal of Molecular Sciences Article Glycosyltransferase B4GALNT2 as a Predictor of Good Prognosis in Colon Cancer: Lessons from Databases Michela Pucci, Nadia Malagolini and Fabio Dall’Olio * Department of Experimental, Diagnostic and Specialty Medicine (DIMES), General Pathology Building, University of Bologna, Via San Giacomo 14, 40126 Bologna, Italy; [email protected] (M.P.); [email protected] (N.M.) * Correspondence: [email protected]; Tel.: +39-051-2094704 Abstract: Background: glycosyltransferase B4GALNT2 and its cognate carbohydrate antigen Sda are highly expressed in normal colon but strongly downregulated in colorectal carcinoma (CRC). We previously showed that CRC patients expressing higher B4GALNT2 mRNA levels displayed longer survival. Forced B4GALNT2 expression reduced the malignancy and stemness of colon cancer cells. Methods: Kaplan–Meier survival curves were determined in “The Cancer Genome Atlas” (TCGA) COAD cohort for several glycosyltransferases, oncogenes, and tumor suppressor genes. Whole expression data of coding genes as well as miRNA and methylation data for B4GALNT2 were downloaded from TCGA. Results: the prognostic potential of B4GALNT2 was the best among the glycosyltransferases tested and better than that of many oncogenes and tumor suppressor genes; high B4GALNT2 expression was associated with a lower malignancy gene expression profile; differential methylation of an intronic B4GALNT2 gene position and miR-204-5p expression play major roles in B4GALNT2 regulation. Conclusions: high B4GALNT2 expression is a strong predictor of good prognosis in CRC as a part of a wider molecular signature that includes ZG16, ITLN1, BEST2, and Citation: Pucci, M.; Malagolini, N.; GUCA2B. Differential DNA methylation and miRNA expression contribute to regulating B4GALNT2 Dall’Olio, F. -
Epigenetic Activation of MGAT3 and Corresponding Bisecting Glcnac Shortens the Survival of Cancer Patients
www.impactjournals.com/oncotarget/ Oncotarget, Vol. 7, No. 32 Research Paper Epigenetic activation of MGAT3 and corresponding bisecting GlcNAc shortens the survival of cancer patients Reto S. Kohler1, Merrina Anugraham1, Mónica Núñez López1, Christina Xiao1, Andreas Schoetzau1, Timm Hettich2, Goetz Schlotterbeck2, André Fedier1, Francis Jacob1,3,*, Viola Heinzelmann-Schwarz1,4,* 1Ovarian Cancer Research, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland 2School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Muttenz, Switzerland 3Glyco-Oncology, Ovarian Cancer Research, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland 4Hospital for Women, Department of Gynecology and Gynecological Oncology, University Hospital Basel, Basel, Switzerland *These authors contributed equally to this work Correspondence to: Viola Heinzelmann-Schwarz, email: [email protected] Keywords: N-glycosylation, DNA methylation, long-time survival, bisecting GlcNAc, ovarian cancer Received: December 18, 2015 Accepted: June 26, 2016 Published: July 12, 2016 ABSTRACT Bisecting GlcNAc on N-glycoproteins is described in E-cadherin-, EGF-, Wnt- and integrin- cancer-associated signaling pathways. However, the mechanisms regulating bisecting GlcNAc expression are not clear. Bisecting GlcNAc is attached to N-glycans through beta 1-4 N-acetylglucosaminyl transferase III (MGAT3), which is encoded by two exons flanked by high-density CpG islands. Despite a recently described correlation of MGAT3 and bisecting GlcNAc in ovarian cancer cells, it remains unknown whether DNA methylation is causative for the presence of bisecting GlcNAc. Here, we narrow down the regulatory genomic region and show that reconstitution of MGAT3 expression with 5-Aza coincides with reduced DNA methylation at the MGAT3 transcription start site. -
Content Based Search in Gene Expression Databases and a Meta-Analysis of Host Responses to Infection
Content Based Search in Gene Expression Databases and a Meta-analysis of Host Responses to Infection A Thesis Submitted to the Faculty of Drexel University by Francis X. Bell in partial fulfillment of the requirements for the degree of Doctor of Philosophy November 2015 c Copyright 2015 Francis X. Bell. All Rights Reserved. ii Acknowledgments I would like to acknowledge and thank my advisor, Dr. Ahmet Sacan. Without his advice, support, and patience I would not have been able to accomplish all that I have. I would also like to thank my committee members and the Biomed Faculty that have guided me. I would like to give a special thanks for the members of the bioinformatics lab, in particular the members of the Sacan lab: Rehman Qureshi, Daisy Heng Yang, April Chunyu Zhao, and Yiqian Zhou. Thank you for creating a pleasant and friendly environment in the lab. I give the members of my family my sincerest gratitude for all that they have done for me. I cannot begin to repay my parents for their sacrifices. I am eternally grateful for everything they have done. The support of my sisters and their encouragement gave me the strength to persevere to the end. iii Table of Contents LIST OF TABLES.......................................................................... vii LIST OF FIGURES ........................................................................ xiv ABSTRACT ................................................................................ xvii 1. A BRIEF INTRODUCTION TO GENE EXPRESSION............................. 1 1.1 Central Dogma of Molecular Biology........................................... 1 1.1.1 Basic Transfers .......................................................... 1 1.1.2 Uncommon Transfers ................................................... 3 1.2 Gene Expression ................................................................. 4 1.2.1 Estimating Gene Expression ............................................ 4 1.2.2 DNA Microarrays ...................................................... -
Essential Role of Microphthalmia Transcription Factor for DNA Replication, Mitosis and Genomic Stability in Melanoma
Oncogene (2011) 30, 2319–2332 & 2011 Macmillan Publishers Limited All rights reserved 0950-9232/11 www.nature.com/onc ORIGINAL ARTICLE Essential role of microphthalmia transcription factor for DNA replication, mitosis and genomic stability in melanoma T Strub1,4, S Giuliano2,4,TYe1, C Bonet2, C Keime1, D Kobi1, S Le Gras1, M Cormont3, R Ballotti2, C Bertolotto2 and I Davidson1 1Institut de Ge´ne´tique et de Biologie Mole´culaire et Cellulaire, CNRS, INSERM, Universite´ de Strasbourg, Illkirch, France; 2INSERM U895 Team 1 and Department of Dermatology, CHU Nice, France and 3INSERM U895 Team 7, Nice, France Malignant melanoma is an aggressive cancer known use of internal promoters (Steingrimsson, 2008). The for its notorious resistance to most current therapies. MITF-M isoform (hereafter designated simply as The basic helix-loop-helix microphthalmia transcription MITF) is the major form produced specifically in the factor (MITF) is the master regulator determining the melanocyte lineage from an intronic promoter (Goding, identity and properties of the melanocyte lineage, and is 2000b). MITF is essential for the survival of melano- regarded as a lineage-specific ‘oncogene’ that has a blasts and postnatal melanocytes (McGill et al., 2002; critical role in the pathogenesis of melanoma. MITF Hou and Pavan, 2008), in which it also controls the promotes melanoma cell proliferation, whereas sustained expression of genes required for the melanin synthesis supression of MITF expression leads to senescence. (Bertolotto et al., 1998). By combining chromatin immunoprecipitation coupled to In addition to regulating multiple aspects of normal high throughput sequencing (ChIP-seq) and RNA sequen- melanocyte function, MITF also has a critical role in cing analyses, we show that MITF directly regulates a melanoma, in which it is required for survival, and set of genes required for DNA replication, repair and controls the proliferation, invasive and metastatic mitosis. -
University of Southern Denmark Replication of 15 Loci Involved In
University of Southern Denmark Replication of 15 loci involved in human plasma protein N-glycosylation in 4802 samples from four cohorts Sharapov, Sodbo Zh; Shadrina, Alexandra S; Tsepilov, Yakov A; Elgaeva, Elizaveta E; Tiys, Evgeny S; Feoktistova, Sofya G; Zaytseva, Olga O; Vuckovic, Frano; Cuadrat, Rafael; Jäger, Susanne; Wittenbecher, Clemens; Karssen, Lennart C; Timofeeva, Maria; Tillin, Therese; Trbojević-Akmačić, Irena; Štambuk, Tamara; Rudman, Najda; Krištić, Jasminka; Šimunović, Jelena; Momčilović, Ana; Vilaj, Marija; Jurić, Julija; Slana, Anita; Gudelj, Ivan; Klarić, Thomas; Puljak, Livia; Skelin, Andrea; Kadić, Antonia Jeličić; Van Zundert, Jan; Chaturvedi, Nishi; Campbell, Harry; Dunlop, Malcolm; Farrington, Susan M; Doherty, Margaret; Dagostino, Concetta; Gieger, Christian; Allegri, Massimo; Williams, Frances; Schulze, Matthias B; Lauc, Gordan; Aulchenko, Yurii S Published in: Glycobiology DOI: 10.1093/glycob/cwaa053 Publication date: 2021 Document version: Accepted manuscript Citation for pulished version (APA): Sharapov, S. Z., Shadrina, A. S., Tsepilov, Y. A., Elgaeva, E. E., Tiys, E. S., Feoktistova, S. G., Zaytseva, O. O., Vuckovic, F., Cuadrat, R., Jäger, S., Wittenbecher, C., Karssen, L. C., Timofeeva, M., Tillin, T., Trbojević- Akmačić, I., Štambuk, T., Rudman, N., Krištić, J., Šimunović, J., ... Aulchenko, Y. S. (2021). Replication of 15 loci involved in human plasma protein N-glycosylation in 4802 samples from four cohorts. Glycobiology, 31(2), 82- 88. https://doi.org/10.1093/glycob/cwaa053 Go to publication entry in University of Southern Denmark's Research Portal Terms of use This work is brought to you by the University of Southern Denmark. Unless otherwise specified it has been shared according to the terms for self-archiving. If no other license is stated, these terms apply: • You may download this work for personal use only. -
Deep Evolutionary Analysis Reveals the Design Principles of Fold A
RESEARCH ARTICLE Deep evolutionary analysis reveals the design principles of fold A glycosyltransferases Rahil Taujale1,2, Aarya Venkat3, Liang-Chin Huang1, Zhongliang Zhou4, Wayland Yeung1, Khaled M Rasheed4, Sheng Li4, Arthur S Edison1,2,3, Kelley W Moremen2,3, Natarajan Kannan1,3* 1Institute of Bioinformatics, University of Georgia, Athens, Georgia; 2Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia; 3Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia; 4Department of Computer Science, University of Georgia, Athens, Georgia Abstract Glycosyltransferases (GTs) are prevalent across the tree of life and regulate nearly all aspects of cellular functions. The evolutionary basis for their complex and diverse modes of catalytic functions remain enigmatic. Here, based on deep mining of over half million GT-A fold sequences, we define a minimal core component shared among functionally diverse enzymes. We find that variations in the common core and emergence of hypervariable loops extending from the core contributed to GT-A diversity. We provide a phylogenetic framework relating diverse GT-A fold families for the first time and show that inverting and retaining mechanisms emerged multiple times independently during evolution. Using evolutionary information encoded in primary sequences, we trained a machine learning classifier to predict donor specificity with nearly 90% accuracy and deployed it for the annotation of understudied GTs. Our studies provide an evolutionary framework for investigating complex relationships connecting GT-A fold sequence, structure, function and regulation. *For correspondence: [email protected] Introduction Competing interests: The Complex carbohydrates make up a large bulk of the biomass of any living cell and play essential authors declare that no roles in biological processes ranging from cellular interactions, pathogenesis, immunity, quality con- competing interests exist.