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Genome-Wide Transcriptome Analysis of Laminar Tissue During the Early Stages of Experimentally Induced Equine Laminitis

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GENOME-WIDE TRANSCRIPTOME ANALYSIS OF LAMINAR TISSUE DURING THE EARLY STAGES OF EXPERIMENTALLY INDUCED EQUINE LAMINITIS A Dissertation by JIXIN WANG Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY December 2010 Major Subject: Biomedical Sciences GENOME-WIDE TRANSCRIPTOME ANALYSIS OF LAMINAR TISSUE DURING THE EARLY STAGES OF EXPERIMENTALLY INDUCED EQUINE LAMINITIS A Dissertation by JIXIN WANG Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Approved by: Chair of Committee, Bhanu P. Chowdhary Committee Members, Terje Raudsepp Paul B. Samollow Loren C. Skow Penny K. Riggs Head of Department, Evelyn Tiffany-Castiglioni December 2010 Major Subject: Biomedical Sciences iii ABSTRACT Genome-wide Transcriptome Analysis of Laminar Tissue During the Early Stages of Experimentally Induced Equine Laminitis. (December 2010) Jixin Wang, B.S., Tarim University of Agricultural Reclamation; M.S., South China Agricultural University; M.S., Texas A&M University Chair of Advisory Committee: Dr. Bhanu P. Chowdhary Equine laminitis is a debilitating disease that causes extreme sufferring in afflicted horses and often results in a lifetime of chronic pain. The exact sequence of pathophysiological events culminating in laminitis has not yet been characterized, and this is reflected in the lack of any consistently effective therapeutic strategy. For these reasons, we used a newly developed 21,000 element equine-specific whole-genome oligoarray to perform transcriptomic analysis on laminar tissue from horses with experimentally induced models of laminitis: carbohydrate overload (CHO), hyperinsulinaemia (HI), and oligofructose (OF). Samples were collected during the developmental (DEV) and Obel grade 1 (OG1) stages of laminitis for the CHO model. For the HI model, samples were collected at the Obel grade 2 (OG2) stage. For the OF model, samples were collected at the 12 h and 24 h time points. Appropriate control samples were obtained for all models. This is the first genome-wide transcriptome analysis of laminar tissue using an equine 21,000 70-mer long oligoarray approach in CHO, HI and OF induced laminitis. iv Overall, we identified the differential expression of genes encoding S100 calcium binding proteins, extracellular matrix proteins, glycoproteins, transporters, olfactory receptors, genes involved in signal transduction, body‟s homeostasis, apoptosis, and immune response. Between CHO and OF models of laminitis, there were more shared genes. We discovered several common differentially expressed genes (i.e., ADAMTS1, CYCS and CXCL14) among all three models that are likely important to the pathogenesis of equine laminitis. We also discovered what appear to be central roles of apoptosis, inflammatory response, and intracellular ion homeostasis molecular processes in CHO and OF models of laminitis. Pathway analysis detected the NOD-like receptor signaling pathway, which is involved in recognition of intracellular bacteria in both the CHO and OF models of laminitis. Genetic network analysis indicated convergent pathway core molecules present in equine acute laminitis: p38 MAPK and NF-κB. Most importantly, our results of overexpression of anti-microbial genes (i.e., DEFB4, PI3, and CXCL14) suggest the central involvement of these genes in the progression of early equine laminitis and will allow refinement of current hypotheses of disease pathogenesis. v DEDICATION This work is dedicated to my parents who have supported me so many years for my education. vi ACKNOWLEDGEMENTS I would like to thank my advisor, Dr. Bhanu Chowdhary, for his great supervision, guidance, patience, and support throughout my graduate studies. He not only cares about his students‟ professional development but also their personal growth. He also told us to learn things well, to do our best and keep the hunger for learning. These teachings have made a great impact on my academic life. Also, I would like to thank my committee members, Dr. Terje Raudsepp, Dr. Loren Skow, Dr. Paul Samollow, and Dr. Penny Riggs for their insightful suggestions and guidance throughout my graduate project. I gratefully acknowledge Dr. Hannah L. Galantino-Homer and Dr. Rebecca Carter at the Laminitis Institute at the University of Pennsylvania, Dr. Christopher C. Pollitt, Dr. Andrew Van Eps and Ms. Melody De Laat at the Australian Equine Laminitis Research Unit, University of Queensland and Dr. James Belknap and Ms. Mauria Watts at the Department of Veterinary Clinical Sciences at Ohio State University for kindly providing the laminar tissue samples for the study. I also want to extend my gratitude to Dr. Ashley Seabury, Dr. Samantha Steelman, Dr. Xianyao Li, Dr. Huaijun Zhou, Dr. Ivan Ivanov, Dr. Pranab Jyoti Das, Dr. Nandina Paria, Dr. Dhruva Kumar Mishra, Dr. Monika Vishnoi, Dr. Jan Janecka, and fellow graduate students Priyanka Kachroo, Jana Caldwell and Felipe Avila for their help. Finally, thanks to my parents for their love. vii NOMENCLATURE AAEP American Association of Equine Practitioners ACTB Beta Actin ADAM A Disintegrin and Metalloproteinase ADAMDEC1 ADAM-like, decysin 1 ADAMTS A Disintegrin and Metalloproteinase with Thrombospondin AGTPBP1 ATP/GTP Binding Protein 1 ANOVA Analysis of Variance AP-1 Activator Protein 1 BAX BCL2-associated X Protein BCP Bromochloropropane BEX2 Brain Expressed X-linked 2 B2M Beta-2-Microglobulin BM Basement Membrane BP Biological Process BPV-1 Bovine Papillomavirus-1 BWE Black Walnut Extract CACYBP Calcyclin Binding Protein CADS A Common Array Dye-swap CC Cellular Component CCL Chemokine (C-C motif) Ligand viii CCR Chemokine (C-C motif) Receptor CD14 Cluster of Differentiation 14 CD69 Cluster of Differentiation 69 CEBPB CCAAT/enhancer Binding Protein (C/EBP), beta CFB Complement Factor B CHO Carbohydrate Overload CIB1 Calcium and Integrin Binding 1 CILP2 Cartilage Intermediate Layer Protein 2 CITED1 Cbp/p300-interacting Transactivator CNRQ Calibrated Normalized Relative Quantity COX Cyclooxygenase CPA6 Carboxypeptidase A6 CPXM Carboxypeptidase X (M14 Family), Member 2 CRTAC1 Cartilage Acidic Protein 1 CRYAB Crystallin, Alpha B CSH Cross-species Hybridization CXCL Chemokine (C-X-C motif) Ligand Cp Crossing Point DAMP Damage-associated Molecular Pattern DAPP1 Dual Adaptor of Phosphotyrosine and 3-phosphoinositides DAVID Database for Annotation, Visualization and Integrated Discovery DDB2 Damage-specific DNA Binding Protein 2 ix DDF Deep Digital Flexor DE Differentially Expressed DEFB4 Defensin, Beta 4 DMSO Dimethylsufoxide ECD Equine Cushing‟s Disease ECEL1 Endothelin Converting Enzyme-like 1 ECM Extracellular Matrix EEF1A1 Eukaryotic Translation Elongation Factor 1 Alpha 1 EHC Euglycemic-hyperinsulinemic Clamp EHSS Equine Hindgut Streptococcal Species EMS Equine Metabolic Syndrome ERK Extracellular Signal-regulated Kinase ET-1 Endothelin-1 FAP Fibroblast Activation Protein, Alpha FGR Gardner-Rasheed Feline Sarcoma Viral Oncogene Homolog FIBIN Fin Bud Initiation Factor FOSL1 FOS-like Antigen 1 FWER Family Wise Error Rate GAPDH Glyceraldhyde-3-phosphate Dehydrogenase GI Gastrointestinal GLMN Glomulin GLUT Glucose Transporter x GNB2L1 Guanine Nucleotide Binding Protein, Beta Polypeptide 2-like 1 GO Gene Ontology GPCR G-protein Coupled Receptor GRB7 Growth Factor Receptor-bound Protein 7 GSN Gelsolin GWAS Genome Wide Association Study HMGB2 High-mobility Group Box 2 HPRT1 Hypoxanthine Phosphoribosyltransferase 1 HD Hemidesmosome HI Hyperinsulinaemia HR Heart Rate ICAM-1 Intercellular Adhesion Molecule 1 IGFBP Insulin-like Growth Factor Binding Protein IL Interleukin IL10RB Interleukin 10 Receptor, beta ING5 Inhibitor of Growth Family, Member 5 IR Insulin Resistance KRT17 Keratin 17 LFS Lavender Foal Syndrome LIMMA Linear Models for Microarray Data LOC554251 Hypothetical Protein LOC554251 LOXL1 Lysyl Oxidase-like 1 xi LOWESS Locally Weighted Scatter Plot Smoothing Regression LPS Lipopolysacccharide LTB4R Leukotriene B4 Receptor MAF V-maf Musculoaponeurotic Fibrosarcoma Oncogene Homolog MAIL Molecule Possessing Ankyrin-repeats Induced by LPS MAPK Mitogen Activated Protein Kinase MAQC Microarray Quality Control MATN2 Matrilin 2 MCP Monocyte Chemotactic Protein MF Molecular Function MIF Macrophage Migration Inhibitory Factor MMP Matrix Metalloproteinase MMPI Matrix Metalloproteinase Inhibitor MNAT1 Menage A Trois Homolog 1 MSS Musculoskeletal Syndrome MYBPC2 Myosin Binding Protein C, Fast Type MYOD Maturity Onset Diabetes of Young NDEL1 NudE Nuclear Distribution Gene E Homolog-like 1 NDUFB3 NADH Dehydrogenase (ubiquinone) 1 Beta Subcomplex, 3 NF Normalization Factor NF-κB Nuclear Factor κB NFAT Nuclear Factor of Activated T Cells xii NRQ Normalized Relative Quantity NSAID Nonsteroidal Anti-inflammatory Drug OA Osteoarthritis OF Oligofructose OR7A10 Olfactory Receptor, Family 7, Subfamily A, Member 10 PAMP Pathogen Associated Molecule Pattern P4HA3 Proline 4-hydroxylase, alpha polypeptide III PI3 Peptidase Inhibitor 3 PI3K Phosphoinositide 3-kinase PCA Principle Component Analysis PDL Primary Dermal Laminae PEL Primary Epidermal Laminae PMT Photomultiplier Tube PPA1 Pyrophosphatase 1 PPIA Peptidylprolyl Isomerase A PROM2 Prominin 2 qRT-PCR Quantitative Reverse Transcriptase PCR QSOX1 Quiescin Q6 Sulfhydryl Oxidase 1 RA Rheumatoid Arthritis RAD23B RAD23 Homolog B RAO Recurrent Airway Obstruction REEP3 Receptor Accessory Protein 3 xiii RNF144B Ring Finger 144B ROS Reactive
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  • The Plasma Peptides of Alzheimer's Disease

    The Plasma Peptides of Alzheimer's Disease

    Florentinus‑Mefailoski et al. Clin Proteom (2021) 18:17 https://doi.org/10.1186/s12014‑021‑09320‑2 Clinical Proteomics RESEARCH Open Access The plasma peptides of Alzheimer’s disease Angelique Florentinus‑Mefailoski1, Peter Bowden1, Philip Scheltens2, Joep Killestein3, Charlotte Teunissen4 and John G. Marshall1,5* Abstract Background: A practical strategy to discover proteins specifc to Alzheimer’s dementia (AD) may be to compare the plasma peptides and proteins from patients with dementia to normal controls and patients with neurological condi‑ tions like multiple sclerosis or other diseases. The aim was a proof of principle for a method to discover proteins and/ or peptides of plasma that show greater observation frequency and/or precursor intensity in AD. The endogenous tryptic peptides of Alzheimer’s were compared to normals, multiple sclerosis, ovarian cancer, breast cancer, female normal, sepsis, ICU Control, heart attack, along with their institution‑matched controls, and normal samples collected directly onto ice. Methods: Endogenous tryptic peptides were extracted from blinded, individual AD and control EDTA plasma sam‑ ples in a step gradient of acetonitrile for random and independent sampling by LC–ESI–MS/MS with a set of robust and sensitive linear quadrupole ion traps. The MS/MS spectra were ft to fully tryptic peptides within proteins identi‑ fed using the X!TANDEM algorithm. Observation frequency of the identifed proteins was counted using SEQUEST algorithm. The proteins with apparently increased observation frequency in AD versus AD Control were revealed graphically and subsequently tested by Chi Square analysis. The proteins specifc to AD plasma by Chi Square with FDR correction were analyzed by the STRING algorithm.
  • Supplementary File 2A Revised

    Supplementary File 2A Revised

    Supplementary file 2A. Differentially expressed genes in aldosteronomas compared to all other samples, ranked according to statistical significance. Missing values were not allowed in aldosteronomas, but to a maximum of five in the other samples. Acc UGCluster Name Symbol log Fold Change P - Value Adj. P-Value B R99527 Hs.8162 Hypothetical protein MGC39372 MGC39372 2,17 6,3E-09 5,1E-05 10,2 AA398335 Hs.10414 Kelch domain containing 8A KLHDC8A 2,26 1,2E-08 5,1E-05 9,56 AA441933 Hs.519075 Leiomodin 1 (smooth muscle) LMOD1 2,33 1,3E-08 5,1E-05 9,54 AA630120 Hs.78781 Vascular endothelial growth factor B VEGFB 1,24 1,1E-07 2,9E-04 7,59 R07846 Data not found 3,71 1,2E-07 2,9E-04 7,49 W92795 Hs.434386 Hypothetical protein LOC201229 LOC201229 1,55 2,0E-07 4,0E-04 7,03 AA454564 Hs.323396 Family with sequence similarity 54, member B FAM54B 1,25 3,0E-07 5,2E-04 6,65 AA775249 Hs.513633 G protein-coupled receptor 56 GPR56 -1,63 4,3E-07 6,4E-04 6,33 AA012822 Hs.713814 Oxysterol bining protein OSBP 1,35 5,3E-07 7,1E-04 6,14 R45592 Hs.655271 Regulating synaptic membrane exocytosis 2 RIMS2 2,51 5,9E-07 7,1E-04 6,04 AA282936 Hs.240 M-phase phosphoprotein 1 MPHOSPH -1,40 8,1E-07 8,9E-04 5,74 N34945 Hs.234898 Acetyl-Coenzyme A carboxylase beta ACACB 0,87 9,7E-07 9,8E-04 5,58 R07322 Hs.464137 Acyl-Coenzyme A oxidase 1, palmitoyl ACOX1 0,82 1,3E-06 1,2E-03 5,35 R77144 Hs.488835 Transmembrane protein 120A TMEM120A 1,55 1,7E-06 1,4E-03 5,07 H68542 Hs.420009 Transcribed locus 1,07 1,7E-06 1,4E-03 5,06 AA410184 Hs.696454 PBX/knotted 1 homeobox 2 PKNOX2 1,78 2,0E-06