Abstracts tagged "Bioinformatics"

Abstract Number: 2267 • ACR Convergence 2024
A Novel Blood-based Assay That Predicts Clinical Response to TNFα Inhibitors or Janus Kinase Inhibitors in Patients with Rheumatoid Arthritis
Maggie Louie¹, Signe Fransen², Katherine Dilger¹, Kevin Lai¹, Diana Abdueva³, David Chernoff⁴ and Jeffrey Curtis⁵, ¹Aqtual Inc, Hayward, CA, ²Aqtual Inc., sf, CA, ³Aqtual Inc., Hayward, CA, ⁴SetPoint Medical, Sausalito, CA, ⁵University of Alabama at Birmingham, Hoover, AL
Background/Purpose: Current rheumatoid arthritis (RA) treatments, including TNFa inhibitors (TNFi) and JAK inhibitors (JAKi), have transformed the management of RA by controlling symptoms and slowing…
Abstract Number: 0063 • ACR Convergence 2024
Splicing into Action:Investigating the Role of Alternative Splicing in Rheumatoid Arthritis Neutrophils
Rayan Najjar¹, Noga Rogel² and Tomas Mustelin³, ¹University of Washington, Seattle, ²University of Washinton, Seattle, ³University of Washington, Seattle, WA
Background/Purpose: Rheumatoid arthritis (RA) is a systemic autoimmune disease characterized by a variable response to therapies, reflecting its complex and incompletely understood pathogenesis. Emerging research suggests…
Abstract Number: 0869 • ACR Convergence 2024
Deciphering Pathogenic Phenotypes by Multi-modal Deep Single-cell Blood Immunophenotyping in Individuals At-risk for Rheumatoid Arthritis
Jun Inamo¹, Joshua Keegan², Alec Griffith², Tusharkanti Ghosh¹, Alice Horisberger², Kaitlyn Howard², John Pulford², Ekaterina Murzin², Brandon Hancock², Thomas Eisenhaure³, Salina Dominguez⁴, Miranda Gurra⁵, Siddarth Gurajala³, Anna Helena Jonsson¹, Jennifer Seifert⁶, Marie Feser⁷, Jill Norris⁸, Ye Cao², William Apruzzese⁹, S. Louis Bridges¹⁰, Vivian Bykerk¹¹, Susan Goodman¹², Laura Donlin¹¹, Gary S. Firestein¹³, Joan Bathon¹⁴, Laura B. Hughes¹⁵, Darren Tabechian¹⁶, Andrew Filer¹⁷, Costantino Pitzalis¹⁸, Jennifer Anolik¹⁹, Larry Moreland²⁰, Nir Hacohen²¹, Joel Guthridge²², Judith James²², Carla Cuda⁵, Harris Perlman⁵, Michael B. Brenner², Soumya Raychaudhuri²³, Jeffrey Sparks²⁴, Michael Holers⁷, Kevin Deane²⁵, James A. Lederer²⁶, Deepak Rao²⁶ and Fan Zhang²⁷, and the Accelerating Medicines Partnership RA/SLE Network, ¹University of Colorado School of Medicine, Aurora, CO, ²Brigham and Women's Hospital and Harvard Medical School, Boston, MA, ³Broad Institute of MIT and Harvard, Cambridge, ⁴Northwestern University, Chicago, ⁵Northwestern University, Chicago, IL, ⁶University of Colorado and Oklahoma Medical Research Foundation, Aurora, CO, ⁷Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO, ⁸Colorado School of Public Health, Denver, CO, ⁹Accelerating Medicines Partnership® Program: Rheumatoid Arthritis and Systemic Lupus Erythematosus (AMP® RA/SLE) Network, Boston, MA, ¹⁰Division of Rheumatology, Weill Cornell Medical College, New York, NY, ¹¹Hospital For Special Surgery, New York, NY, ¹²Hospital for Special Surgery, New York 10025, NY, ¹³University of California, San Diego, La Jolla, ¹⁴Columbia University, New York, NY, ¹⁵University of Alabama at Birmingham Medicine, Birmingham, AL, ¹⁶University of Rochester Medical Center, Rochester, ¹⁷Rheumatology Research Group, Institute for Inflammation and Ageing, NIHR Birmingham Biomedical Research Center and Clinical Research Facility, University of Birmingham, Birmingham, United Kingdom, ¹⁸QMUL, Bromley Kent, United Kingdom, ¹⁹University of Rochester Medical Center, Rochester, NY, ²⁰University of Colorado, Denver, CO, ²¹Broad Institute of MIT and Harvard, Boston, MA, ²²Oklahoma Medical Research Foundation, Oklahoma City, OK, ²³Brigham and Women's Hospital, Boston, MA, ²⁴Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA, Boston, MA, ²⁵University of Colorado Denver Anschutz Medical Campus, Aurora, CO, ²⁶Brigham and Women's Hospital, Harvard Medical School, Boston, MA, ²⁷University of Colorado, Aurora, CO
Background/Purpose: Rheumatoid arthritis (RA) is a systemic autoimmune disease with currently no effective prevention strategies. Single-cell technologies have been recently used to investigate established RA…
Abstract Number: 1712 • ACR Convergence 2024
Transcriptome Analysis Characterizes the Role of Monocytes in Ankylosing Spondylitis with TNF-blocker Treatment
Yulong Tang¹, Jiangnan Xie², Dachun Zhuo¹, Qi ZHU³, Jiucun Wang¹ and Jing Liu², ¹Fudan University, Shanghai, China (People's Republic), ²Fudan University, Shanghai, Shanghai, China (People's Republic), ³Shanghai Guanghua Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai, China (People's Republic)
Background/Purpose: Ankylosing spondylitis (AS) is an autoimmune and auto-inflammatory disease characterized by chronic inflammation of the spine, sacroiliac joint, and occasionally peripheral joints. TNF-α inhibitor…
Abstract Number: 2280 • ACR Convergence 2024
Development of a Blood-based Cell-free DNA Classifier Assay to Predict Biologic and Targeted Synthetic DMARDs Response in Rheumatoid Arthritis Patients (PRIMA-102)
Peter C. Taylor¹, Kevin Lai², Hsin-Ta Wu², Jason Carlson², Diana Abdueva³, Signe Fransen⁴, Alan Kivitz⁵, Gordon Lam⁶ and David Chernoff⁷, ¹University of Oxford, Oxford, United Kingdom, ²Aqtual Inc, Hayward, CA, ³Aqtual Inc., Hayward, CA, ⁴Aqtual Inc., sf, CA, ⁵Altoona Center for Clinical Research, Duncansville, PA, ⁶Arthritis and Osteoporosis Consultants of the Carolinas, Cornelius, NC, ⁷SetPoint Medical, Sausalito, CA
Background/Purpose: Matching most beneficial targeted therapy to rheumatoid arthritis (RA) patients with inadequate response or intolerance to current treatment is an important unmet clinical need. The…
Abstract Number: L01 • ACR Convergence 2023
Analysis of 245,388 Diverse Participants in the NIH All of Us Cohort Identifies VEXAS Resiliency in UBA1 M41L Somatic Mutation Carriers
Robert Corty¹ and Alexander Bick², ¹Vanderbilt University Medical Center, Nashville, TN, ²Vanderbilt University, Nashville, TN
Background/Purpose: VEXAS syndrome is a recently-discovered systemic auto-inflammatory disease caused by somatic mutation at position 41 in the X-linked gene UBA1.1 First, 25 older men…
Abstract Number: 0024 • ACR Convergence 2023
Detection of Synovial Signatures in Peripheral Blood of Patients with Rheumatoid Arthritis via a Novel Blood-Based DNA Capture Assay
Peter C. Taylor¹, Jenya Antonova², Jennifer Geis³, Katharine Dilger³, David Chernoff⁴, Diana Abdueva³, Nancy Shadick⁵ and Michael Weinblatt⁶, ¹Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom, ²Compass Strategy and Research, Inc., San Francisco, CA, ³Aqtual Inc., Hayward, CA, ⁴Chernoff Consulting, Sausalito, CA, ⁵Brigham and Women's Hospital, Boston, MA, ⁶Harvard Medical School, Waban, MA
Background/Purpose: In rheumatoid arthritis [RA], synovial biopsies were shown to guide therapy selection1. However, biopsies require special training for clinicians and are semi-invasive for patients.…
Abstract Number: 0734 • ACR Convergence 2023
Immune Isoform Atlas: Landscape of Alternative Splicing in Human Immune Cells and Involvement of Dysregulated Alternative Splicing in Autoimmune Diseases
Jun Inamo¹, Akari Suzuki², Mahoko Takahashi Ueda¹, Kensuke Yamaguchi¹, Hiroshi Nishida³, Katsuya Suzuki⁴, Yuko Kaneko⁵, Tsutomu Takeuchi⁶, Hiroaki Hatano⁷, Kazuyoshi Ishigaki⁸, Yasushi Ishihama³, Kazuhiko Yamamoto⁹ and Yuta Kochi¹, ¹Tokyo Medical and Dental University, Tokyo, Japan, ²RIKEN Center for Integrative Medical Science, Kanagawa, Japan, ³Kyoto University, Kyoto, Japan, ⁴Keio University, Shinjuku, Japan, ⁵Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan, ⁶Keio University School of Medicine and Saitama Medical University, Tokyo, Japan, ⁷Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan, ⁸RIKEN, Tokyo, Japan, ⁹Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo and Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
Background/Purpose: Alternative splicing events play a critical role in the immune system1,2 and one of major causal mechanisms for complex traits including immune-mediated diseases (IMDs),…
Abstract Number: 1600 • ACR Convergence 2023
Transcriptomic Characterization of Class II Lupus Nephritis and Outcomes
Jasmine Shwetar¹, Katie Preisinger¹, Devyn Zaminski², Philip Carlucci¹, Kristina Deonaraine¹, Qian Xiao³, Joseph Mears⁴, Siddarth Gurajala³, Izmirly peter⁵, Judith James⁶, Joel Guthridge⁶, Andrea Fava⁷, Brad Rovin⁸, Wade DeJager⁶, Ming Wu⁹, Deepak Rao¹⁰, Chaim Putterman¹¹, Betty Diamond¹², Derek Fine¹³, Jose Monroy-Trujillo¹³, Kristin Haag¹⁴, H Michael Belmont², William Apruzzese¹⁰, Anne Davidson¹², Fernanda Payan-Schober¹⁵, Richard Furie¹⁶, Paul Hoover¹⁰, Celine Berthier¹⁷, Maria Dall'Era¹⁸, Kerry Cho¹⁹, Diane L. Kamen²⁰, Kenneth Kalunian²¹, Jennifer Anolik²², Soumya Raychaudhuri¹⁰, Nir Hacohen²³, Michelle Petri²⁴, Robert Clancy²⁵, David Wofsy¹⁸, Arnon Arazi²⁶, Kelly Ruggles⁹, Jill Buyon²⁵ and The Accelerating Medicines Partnership SLE/RA²⁷, ¹New York University School of Medicine, New York, NY, ²NYU School of Medicine, New York, NY, ³Harvard Medical School, Boston, MA, ⁴Michigan University, Ann Arbor, MI, ⁵NYU, New York, NY, ⁶Oklahoma Medical Research Foundation, Oklahoma City, OK, ⁷Johns Hopkins University, Baltimore, MD, ⁸Ohio State University, Columbus, OH, ⁹NYU Langone, New York, NY, ¹⁰Brigham and Women's Hospital, Boston, MA, ¹¹Albert Einstein College of Medicine, Bronx, NY, ¹²Feinstein Institutes for Medical Research, Manhasset, NY, ¹³Johns Hopkins School of Medicine, Baltimore, MD, ¹⁴Thomas Jefferson University, Philadelphia, PA, ¹⁵Texas Tech University Health Sciences Center, El Paso, TX, ¹⁶Northwell Health, Manhasset, NY, ¹⁷University of Michigan, Ann Arbor, MI, ¹⁸University of California San Francisco, San Francisco, CA, ¹⁹UCSF Health, San Francisco, CA, ²⁰Medical University of South Carolina, Charleston, SC, ²¹University of California San Diego, La Jolla, CA, ²²University of Rochester Medical Center, Rochester, NY, ²³Broad Institute of MIT and Harvard, Cambridge, MA, ²⁴Department of Medicine, Division of Rheumatology, Johns Hopkins University School of Medicine, Timonium, MD, ²⁵NYU Grossman School of Medicine, New York, NY, ²⁶Broad Institute of MIT and Harvard, Melrose, MA, ²⁷University of Colorado Anschutz Medical Campus, Aurora, CO
Background/Purpose: Lupus Nephritis (LN) significantly reduces the survival and life expectancy of patients with SLE. Given this, considerable effort has gone into characterizing the histologic…
Abstract Number: 2040 • ACR Convergence 2023
Distinguishing Multisystem Inflammatory Syndrome in Children from Typhus Using Artificial Intelligence: MISC vs. Endemic Typhus (AI-MET)
Angela Chun¹, Abraham Bautista-Castillo², Isabella Osuna¹, Kristiana Nasto¹, Flor Munoz³, Gordon Schutze¹, Sridevi Devaraj¹, Eyal Muscal⁴, Marietta De Guzman⁵, Kristen Sexson Tejtel¹, Ioannis Kakadiaris² and Tiphanie Vogel¹, ¹Baylor College of Medicine / Texas Children's Hospital, Houston, TX, ²Computational Biomedicine Lab University of Houston, Houston, TX, ³Baylor College of Medicine, Texas Children's Hospital, Houston, TX, ⁴Division of Rheumatology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, ⁵Baylor College of Medicine, Houston, TX
Background/Purpose: Multisystem inflammatory syndrome in children (MIS-C) following SARS-CoV2infection is a recognized mimic of other inflammatory disorders, including Kawasaki Disease and macrophage activation syndrome. However,…
Abstract Number: 0033 • ACR Convergence 2023
A Novel Transcriptome-Based Machine Learning Pipeline Predicts Phenotypes of Lupus Patients
Emily Leventhal¹, Andrea Daamen¹, Amrie Grammer² and Peter Lipsky², ¹AMPEL BioSolutions, LLC, and The RILITE Research Institute, Charlottesville, VA, ²AMPEL BioSolutions, Charlottesville, VA
Background/Purpose: Gene expression analysis coupled with machine learning (ML) holds the promise of identifying subsets of patients with heterogeneous diseases, such as systemic lupus erythematosus…
Abstract Number: 0736 • ACR Convergence 2023
Deciphering Complement System-dependent Cellular Pathways in Human Rheumatoid Arthritis Synovial Tissue Using Large Single-cell Computational Omics
Juan Vargas¹, Ian Mantel², Nirmal Banda¹, Anna Helena Jonsson³, Kevin Wei⁴, Deepak Rao³, Susan Goodman⁵, Kevin Deane¹, The Accelerating Medicines Partnership SLE/RA¹, Jennifer Anolik⁶, Michael Brenner⁴, Soumya Raychaudhuri³, Jennifer Seifert⁷, Michael Holer¹, Laura Donlin⁵ and Fan Zhang⁸, ¹University of Colorado Anschutz Medical Campus, Aurora, CO, ²Weill Cornell Medicine, New York, NY, ³Brigham and Women's Hospital, Boston, MA, ⁴Brigham and Women's Hospital and Harvard Medical School, Boston, MA, ⁵Hospital for Special Surgery, New York, NY, ⁶University of Rochester Medical Center, Rochester, NY, ⁷the Accelerating Medicines Partnership (AMP) RA/SLE Network, Boston, MA, ⁸University of Colorado, Aurora, CO

Background/Purpose: The complement system is a major component of innate immunity and plays a vital role in autoimmune disease pathogenesis. In patients with rheumatoid arthritis…
Abstract Number: 1608 • ACR Convergence 2023
Plasma Proteomic Profiling in Antiphospholipid Antibody-positive Patients with Different Clinical Phenotypes: Results from the Antiphospholipid Syndrome Alliance for Clinical Trials and International Networking (APS ACTION) Registry
Ayesha Butt¹, Rolando Garcia Milian¹, George Goshua¹, Sean Gu¹, Eugenia Chock², Valentina Restrepo¹, John Hwa¹, Hyung Chun¹, H Michael Belmont³, Kello Nina⁴, D. Ware Branch⁵, Michelle Petri⁶, Jason Knight⁷, Rohan Willis⁸, Maria Laura Bertolaccini⁹, Doruk Erkan¹⁰, Alfred lee¹, Anish Sharda¹ and Alexander Pine¹¹, ¹Yale School of Medicine, New Haven, CT, ²Yale School of Medicine, Greenwich, CT, ³NYU School of Medicine, New York, NY, ⁴Northwell Health, Brooklyn, NY, ⁵University of Utah, Salt Lake City, UT, ⁶Department of Medicine, Division of Rheumatology, Johns Hopkins University School of Medicine, Timonium, MD, ⁷University of Michigan, Ann Arbor, MI, ⁸University of Texas Medical Branch, Galveston, TX, ⁹King's College London, London, United Kingdom, ¹⁰Hospital for Special Surgery, New York, NY, ¹¹VA Connecticut/Yale School of Medicine, West Haven, CT
Background/Purpose: Antiphospholipid syndrome (APS) is an autoimmune disease with thrombotic and obstetric complications arising via a model of immunothrombosis. Patients may present with a spectrum…
Abstract Number: 2369 • ACR Convergence 2023
Investigating Macrophage Heterogeneity in the Esophagus of SSc Patients
Hadijat Makinde¹, Matthew Dapas², Salina Dominguez², Tyler Therron¹, Miranda Gurra¹, Mary Karns³, Kathleen Aren³, Alexandra Soriano², Lutfiyya Muhammad⁴, Carla Cuda¹, Dustin Carlson¹, Jane Dematte⁵, Darren Brenner¹, John Pandolfino⁶, Harris Perlman¹, Deborah Winter⁷ and Marie-Pier Tetreault¹, ¹Northwestern University, Chicago, IL, ²Northwestern University FSM Division of Rheumatology, Chicago, IL, ³Northwestern University Division of Rheumatology, Chicago, IL, ⁴Northwestern University Feinberg School of Medicine, Chicago, IL, ⁵Northwestern University, Elmhurst, IL, ⁶Northwestern University, Feinberg School of Medicine, Wilmette, IL, ⁷Northwestern University, Skokie, IL
Background/Purpose: Systemic sclerosis (SSc) is characterized by an initial inflammatory phase followed by fibrosis. Esophageal dysfunction in SSc is associated with Gastroesophageal Reflux Disease (GERD),…
Abstract Number: 0037 • ACR Convergence 2023
New Histological Approach in Spatial Transcriptomics Implicates Glandular Cell Involvement in Pathophysiology of Sjögren’s Disease
Paulina Czarnota¹, Rick Wilbrink², Bhuwan Khatri¹, Anna Stolarczyk¹, Cherilyn Pritchett Frazee¹, Chuang Li¹, Caleb Marlin¹, Kyle Wright³, Kandice Tessneer¹, Lida Radfar⁴, Judith James¹, Robert Scofield¹, Indra Adrianto⁵, Astrid Rasmussen¹, Joel Guthridge¹, A. Darise Farris¹ and Christopher Lessard¹, ¹Oklahoma Medical Research Foundation, Oklahoma City, OK, ²University Medical Center Groningen, Groningen, Netherlands, ³University of Oklahoma Health Sciences Center, Oklahoma City, OK, ⁴University of Oklahoma College of Dentistry, Oklahoma City, OK, ⁵Henry Ford Health, Detroit, MI
Background/Purpose: 10X Visium spatial transcriptomics evaluates gene expression in a 50μm tile coordinate of a sectioned tissue, yielding heterogeneous cell sampling. Spatial PCA algorithm was…

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