Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data

Abstract

Resolving chromatin remodeling-linked gene expression changes at cell type resolution is important for understanding disease states. We describe MAGICAL, a hierarchical Bayesian approach that leverages paired scRNA-seq and scATAC-seq data from different conditions to map disease-associated transcription factors, chromatin sites, and genes as regulatory circuits. By simultaneously modeling signal variation across cells and conditions in both omics data types, MAGICAL achieved high accuracy on circuit inference. We applied MAGICAL to study Staphylococcus aureus sepsis from peripheral blood mononuclear single-cell data that we generated from infected subjects with bloodstream infection and from uninfected controls. MAGICAL identified sepsis-associated regulatory circuits predominantly in CD14 monocytes, known to be activated by bacterial sepsis. We addressed the challenging problem of distinguishing host regulatory circuit responses to methicillin-resistant- (MRSA) and methicillin-susceptible Staphylococcus aureus (MSSA) infections. While differential expression analysis failed to show predictive value, MAGICAL identified epigenetic circuit biomarkers that distinguished MRSA from MSSA.

Competing Interest Statement

A.G.L. is a military service member. This work was prepared as part of his official duties. Title 17, US Code 105 provides that copyright protection under this title is not available for any work of the US Government. Title 17, US code 101 defines a US Government work as a work prepared by a military service member or employee of the US Government as part of that person's official duties. The views expressed in the article are those of the authors and do not necessarily express the official policy and position of the US Navy, the Department of Defense, the US Government, or the institutions affiliated with the authors. V.G.F. reports personal fees from Novartis, Debiopharm, Genentech, Achaogen, Affinium, Medicines Co., MedImmune, Bayer, Basilea, Affinergy, Janssen, Contrafect, Regeneron, Destiny, Amphliphi Biosciences, Integrated Biotherapeutics; C3J, Armata, Valanbio; Akagera, Aridis, Roche, grants from NIH, MedImmune, Allergan, Pfizer, Advanced Liquid Logics, Theravance, Novartis, Merck; Medical Biosurfaces; Locus; Affinergy; Contrafect; Karius; Genentech, Regeneron, Deep Blue, Basilea, Janssen; Royalties from UpToDate, stock options from Valanbio and ArcBio, Honoraria from Infectious Diseases of America for his service as Associate Editor of Clinical Infectious Diseases, and a patent sepsis diagnostics pending.

Funding Statement

This study was funded by the Defense Advanced Research Projects Agency contract number N6600119C4022 (S.C.S.), Defense Health Agency grant 9700130 through the Naval Medical Research Center (A.G.L.), National Institutes of Health grant R01GM071966 (O.G.T.), and Simons Foundation grant 395506 (O.G.T.).

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I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.

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The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

The Navy COVID-19 study protocol was approved by the Naval Medical Research Center institutional review board (protocol number NMRC.2020.0006) in compliance with all applicable Federal regulations governing the protection of human subjects. The staphylococcus sepsis protocol was reviewed and approved by the Duke Medical School institutional review board (protocol number Pro00102421).

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