Abstracts tagged "Bioinformatics"

Abstract Number: 55 • 2019 ACR/ARP Annual Meeting
A Novel Subclass of Intravascular Non-classical, Tissue Resident Synovial Monocyte Is Critical for Rheumatoid Arthritis Pathogenesis
Anna Montgomery ¹, Shang-Yang Chen ¹, Deborah Winter ² and Harris Perlman², ¹Northwestern University, Chicago, ²Northwestern University Feinberg School of Medicine, Division of Rheumatology, Chicago
Background/Purpose: There are at least three populations of circulating monocytes; classical, intermediate and non-classical. We demonstrated that circulating non-classical monocytes are required for the effector…
Abstract Number: 110 • 2019 ACR/ARP Annual Meeting
Bioinformatics Analysis of Transcriptomics Data Reveals That SRSF1 Is a Novel Molecular Brake for the T Cell Activation Program and Controls Key Cytokine Signaling Genes Implicated in Systemic Lupus Erythematosus
Rhea Bhargava¹, Michelle S. Lee ², Takayuki Katsuyama ³ and Vaishali R. Moulton ³, ¹Beth Israel Deaconess Medical Center Harvard Medical School, Boston, MA, ²Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, ³Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
Background/Purpose: T cells from systemic lupus erythematosus (SLE) patients exhibit a hyperactive phenotype with defects in homeostasis, signaling and cytokine production. By discovery approaches, we…
Abstract Number: 200 • 2019 ACR/ARP Annual Meeting
A Validated Text-mining Algorithm to Extract Rheumatoid Arthritis Medication Contained in Format-free Fields of Electronic Medical Records
Tjardo Maarseveen¹, Thomas Huizinga ¹, Marcel J.T. Reinders ¹, Erik van den Akker ¹ and Rachel Knevel ¹, ¹Leiden University Medical Center, Leiden, Netherlands
Background/Purpose: Rapidly expanding collections of Electronic Medical Records (EMR) form a valuable resource for clinical research. Besides entries with a standardized format, EMRs often also…
Abstract Number: 976 • 2019 ACR/ARP Annual Meeting
Identification of Novel Genes Associated with Dysregulation of B Cells in Patients with Primary Sjögren’s Syndrome
Jun Inamo¹, Katsuya Suzuki ², Masaru Takeshita ², Yoshiaki Kassai ³, Maiko Takigchi ⁴, Rina Kurisu ⁴, Yuumi Okuzono ⁴, Shinya Tasaki ⁵ and Tsutomu Takeuchi ⁶, ¹Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Tokyo, Japan, ²Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan, ³Immunology Unit, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Shinjuku-ku, Tokyo, Japan, ⁴Immunology Unit, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Shinjuku-ku, Japan, ⁵Integrated Technology Research Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Shinjuku-ku, Japan, ⁶Keio University School of Medicine, Tokyo, Japan
Background/Purpose: Dysregulation of B cells play a critical role in the pathogenesis of primary Sjögren’s syndrome (pSS). Long non-coding RNAs (lncRNAs), which have become the…
Abstract Number: 1930 • 2019 ACR/ARP Annual Meeting
Analysis of Lupus Nephritis Gene Expression Reveals Dysregulation of Pathogenic Pathways Activated Within Infiltrating Cells
Adam Labonte¹, Jackson Xu ², Sarah Heuer ², Robert Robl ², Prathyusha Bachali ¹, Michelle Catalina ¹, Peter Lipsky ³ and Amrie Grammer ⁴, ¹AMPEL Biosolutions and the RILITE Research Institute, Charlottesville, VA, ²AMPEL BioSolutions, Charlottesville, VA, ³AMPEL BioSolutions, LLC, Charlottesville, VA, ⁴AMPEL BioSolutions and RILITE Research Institute, Charlottesville, VA
Background/Purpose: LN is a serious complication of SLE that affects about 20-40% of all lupus patients and leads to kidney damage, end-stage renal disease, and…
Abstract Number: 1933 • 2019 ACR/ARP Annual Meeting
Tumorigenesis Related Gene Identification in Dermatomyositis Using Meta-Analysis
Jihad Aljabban¹, Saad Syed ², Sharjeel Syed ³, Kalyn Hoffman ⁴, Laith Hasan ⁵, Nikhil Adapa ¹, Zahir Allarakhia ⁶, Dexter Hadley ⁷, Mohamad Aljabban ⁸ and Wael Jarjour ⁹, ¹Ohio State University College of Medicine, Columbus, ²Stanford School of Medicine, Stanford, ³Stanford School of Medicine, Stanford, CA, ⁴The Ohio State University College of Medicine, Columbus, OH, ⁵Tulane School of Medicine, New Orleans, ⁶Ohio State University College of Medicine, Columbus, OH, ⁷Institute for Computational Health Sciences, San Francisco, ⁸Genesys Health Systems, Grand Blanc, MI, ⁹Ohio State College of Medicine, Columbus, OH
Background/Purpose: Dermatomyositis (DM) is a progressive, systemic autoimmune disease-causing inflammatory changes in the skin and skeletal muscles. DM is associated with carcinomas of the ovary,…
Abstract Number: 1934 • 2019 ACR/ARP Annual Meeting
Tripartite Motif (TRIM) Gene Family Expression in Dermatomyositis
Jihad Aljabban¹, Sharjeel Syed ², Saad Syed ³, Zarife Sahenk ⁴, Noah Weisleder ⁵, Kevin McElhanon ⁵, Kalyn Hoffman ⁶, Nikhil Adapa ¹, Zahir Allarakhia ⁷, Laith Hasan ⁸, Dexter Hadley ⁹, Mohamad Aljabban ¹⁰ and Wael Jarjour ¹¹, ¹Ohio State University College of Medicine, Columbus, ²Stanford School of Medicine, Stanford, CA, ³Stanford School of Medicine, Stanford, ⁴Department of Neurology, Research Institute at Nationwide Children’s Hospital, Columbus, OH, ⁵Dorothy M. Davis Heart and Lung Research Institute & Dept. of Physiology & Cell Biology, The Ohio State University Wexner Medical Center, Columbus, OH, ⁶The Ohio State University College of Medicine, Columbus, OH, ⁷Ohio State University College of Medicine, Columbus, OH, ⁸Tulane School of Medicine, New Orleans, ⁹Institute for Computational Health Sciences, San Francisco, ¹⁰Genesys Health Systems, Grand Blanc, MI, ¹¹Ohio State College of Medicine, Columbus, OH
Background/Purpose: Dermatomyositis (DM) is a progressive, systemic autoimmune disease causing inflammatory changes to the skin and skeletal muscles. TRIM family proteins are composed of approximately…
Abstract Number: 1939 • 2019 ACR/ARP Annual Meeting
Analysis of Discoid Lupus Erythematosus (DLE) Gene Expression Reveals Dysregulation of Pathogenic Pathways Associated with Infiltrating Immune/Inflammatory Cells
Frances Harris¹, Sarah Heuer ², Robert Robl ², Prathyusha Bachali ², Adam Labonte ², Benjamin Chong ³, Michelle Catalina ², Peter Lipsky ² and Amrie Grammer ², ¹RILITE Research Institute, Charlottesville, VA, ²RILITE Research Institute, Charlottesville, ³University of Texas Southwestern, Dallas
Background/Purpose: DLE is a chronic, scarring inflammatory autoimmune disease of the skin. The precise molecular pathways underlying DLE pathogenesis have not been fully delineated. To…
Abstract Number: 2022 • 2019 ACR/ARP Annual Meeting
Analysis of Gene Expression from Systemic Lupus Erythematosus Synovium Reveals Unique Pathogenic Mechanisms
Erika Hubbard¹, Michelle Catalina ², Sarah Heuer ¹, Prathyusha Bachali ², Nicholas Geraci ³, Peter Lipsky ³ and Amrie Grammer ¹, ¹AMPEL BioSolutions and RILITE Research Institute, Charlottesville, VA, ²AMPEL BioSolutions and the RILITE Research Institute, Charlottesville, VA, ³AMPEL BioSolutions, LLC, Charlottesville, VA
Background/Purpose: Arthritis is a common manifestation of SLE and the ability of a new lupus therapy often depends on its ability to suppress joint inflammation.…
Abstract Number: 2074 • 2019 ACR/ARP Annual Meeting
Automated Diagnosis Extraction from Electronic Medical Records with Machine Learning Classifiers
Tjardo Maarseveen¹, Thomas Huizinga ¹, Marcel J.T. Reinders ¹, Erik van den Akker ¹ and Rachel Knevel ¹, ¹Leiden University Medical Center, Leiden, Netherlands
Background/Purpose: The use of Electronic Medical Records (EMR) for research purposes has led to an increasing interest in Natural Language Processing (NLP) for text classification.…
Abstract Number: 1964 • 2018 ACR/ARHP Annual Meeting
Epigenetic Changes of Energy Metabolism-Related Genes in Rheumatoid Arthritis Fibroblast-like Synoviocytes
Brian Pedersen¹, Roxana Coras^1,2, Wei Wang³, Gary S. Firestein¹ and Monica Guma^1,2, ¹Medicine, University of California San Diego, La Jolla, CA, ²Medicine, Autonomous University of Barcelona, Bellatera, Spain, ³Chemistry and Biochemistry, University of California San Diego, La Jolla, CA
Background/Purpose: Epigenetic changes contribute to the pathogenesis of rheumatoid arthritis (RA) and a comprehensive epigenomic characterization of RA fibroblast-like synoviocytes (FLS) has recently been described.…
Abstract Number: 1974 • 2018 ACR/ARHP Annual Meeting
Dynamics of Transcriptional Signatures from Synovial Macrophage Subsets during Acute and Chronic Murine Models of Inflammatory Arthritis
Philip J. Homan¹, Anna B Montgomery², Salina Dominguez³, Carla M. Cuda³, Harris Perlman³ and Deborah R. Winter³, ¹Division of Rheumatology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, ²Division of Rheumatology, Northwestern University Feinberg School of Medicine, Chicago, IL, ³Department of Medicine Division of Rheumatology, Northwestern University Feinberg School of Medicine, Chicago, IL
Background/Purpose: Macrophages play an integral role in the progression and persistence of rheumatoid arthritis (RA) through production of degradative enzymes, cytokines, and chemokines and recruitment…
Abstract Number: 2115 • 2018 ACR/ARHP Annual Meeting
Identification of Systemic Lupus Erythematosus Subgroups Using Electronic Health Record and Genetic Databases
Milena Gianfrancesco¹, Ishan Paranjpe², Julia Kay³, Joanne Nitiham⁴, Kimberly Taylor⁵, Cristina Lanata¹, Marina Sirota⁶, Lindsey A. Criswell⁷, Gabriela Schmajuk⁸ and Jinoos Yazdany², ¹Medicine/Rheumatology, University of California, San Francisco, San Francisco, CA, ²University of California, San Francisco, San Francisco, CA, ³Medicine/Rheumatology, University of California - San Francisco, San Francisco, CA, ⁴Rosalind Russell / Ephraim P. Engleman Rheumatology Research Center, University of California, San Francisco, San Francisco, CA, ⁵University of California, San Francisco, Rosalind Russell / Ephraim P. Engleman Rheumatology Research Center, San Francisco, CA, ⁶Pediatrics, Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, CA, ⁷University of California San Francisco, San Francisco, CA, ⁸San Francisco VA Medical Center, San Francisco, CA
Background/Purpose: Systemic lupus erythematosus (SLE) is a multifactorial disease with genetic and environmental risk factors, and heterogeneous manifestations that encompass a wide range of disease…
Abstract Number: 2123 • 2018 ACR/ARHP Annual Meeting
Analysis of Lupus Synovitis Gene Expression Reveals Dysregulation of Pathogenic Pathways Activated within Infiltrating Immune Cells
Erika Hubbard, Michelle Catalina, Sarah Heuer, Prathyusha Bachali, Nick Geraci, Isabella Blanco, Robert Robl, Peter Lipsky and Amrie Grammer, AMPEL BioSolutions and RILITE Research Institute, Charlottesville, VA
Background/Purpose: Arthritis is a common manifestation of SLE but the inflammatory and immune cells that infiltrate synovium and the signaling pathways activated are not well…
Abstract Number: 2804 • 2018 ACR/ARHP Annual Meeting
Identifying Lupus Patients in Electronic Health Records: Development and Validation of Machine Learning Algorithms and Application of Rule-Based Algorithms
April Jorge¹, Victor M. Castro², April Barnado³, Vivian Gainer², Chuan Hong⁴, Tianxi Cai², Robert Carroll⁵, Leslie Crofford³, Karen Costenbader⁶, Katherine P. Liao⁷, Elizabeth Karlson⁶ and Candace H. Feldman⁶, ¹Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, ²Research Information Systems and Computing, Partners Healthcare, Boston, MA, ³Division of Rheumatology and Immunology, Vanderbilt University Medical Center, Nashville, TN, ⁴Harvard T.H. Chan School of Public Health, Boston, MA, ⁵Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, ⁶Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA, ⁷Brigham and Women's Hospital, Boston, MA
Background/Purpose: To utilize electronic health records (EHR) to study SLE, phenotypic algorithms are needed to accurately identify these patients. We aimed to generate an EHR…

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