Computational protocol to identify shared transcriptional risks and mutually beneficial compounds between diseases

Hua Gao; Mao Zhang; Richard A. Baylis; Fudi Wang; Johan L.M. Björkegren; Jason J. Kovacic; Arno Ruusalepp; Nicholas J. Leeper

STAR Protocols (Mar 2024)

Computational protocol to identify shared transcriptional risks and mutually beneficial compounds between diseases

Hua Gao,
Mao Zhang,
Richard A. Baylis,
Fudi Wang,
Johan L.M. Björkegren,
Jason J. Kovacic,
Arno Ruusalepp,
Nicholas J. Leeper

Affiliations

Hua Gao: Department of Surgery, Division of Vascular Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cardiovascular Institute, Stanford, CA 94305, USA; Corresponding author
Mao Zhang: Stanford Cardiovascular Institute, Stanford, CA 94305, USA
Richard A. Baylis: Department of Surgery, Division of Vascular Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cardiovascular Institute, Stanford, CA 94305, USA; Department of Medicine, Division of Cardiology, University of California, San Francisco, San Francisco, CA 94143, USA
Fudi Wang: Department of Surgery, Division of Vascular Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cardiovascular Institute, Stanford, CA 94305, USA
Johan L.M. Björkegren: Department of Medicine, Karolinska Institute, Huddinge, Sweden; Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
Jason J. Kovacic: Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA; Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia; St. Vincent’s Clinical School, University of NSW, Sydney, NSW, Australia
Arno Ruusalepp: Department of Cardiac Surgery and The Heart Clinic, Tartu University Hospital and Department of Cardiology, Institute of Clinical Medicine, Tartu University, Tartu, Estonia
Nicholas J. Leeper: Department of Surgery, Division of Vascular Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cardiovascular Institute, Stanford, CA 94305, USA; Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Corresponding author

Journal volume & issue: Vol. 5, no. 1
p. 102883

Abstract

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Summary: The accumulation of omics and biobank resources allows for a genome-wide understanding of the shared pathologic mechanisms between diseases and for strategies to identify drugs that could be repurposed as novel treatments. Here, we present a computational protocol, implemented as a Snakemake workflow, to identify shared transcriptional processes and screen compounds that could result in mutual benefit. This protocol also includes a description of a pharmacovigilance study designed to validate the effect of compounds using electronic health records.For complete details on the use and execution of this protocol, please refer to Gao et al.1 and Baylis et al.2 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Published in STAR Protocols

ISSN: 2666-1667 (Online)
Publisher: Elsevier
Country of publisher: United States
LCC subjects: Science: Science (General)
Website: https://star-protocols.cell.com/

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Abstract

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