A myeloid program associated with COVID-19 severity is decreased by therapeutic blockade of IL-6 signaling

Altered myeloid inflammation and lymphopenia are hallmarks of severe infections, including SARS-CoV-2. Here, we identified a gene program, defined by correlation with EN-RAGE ( S100A12 ) gene expression, which was up-regulated in patient airway and blood myeloid cells. The EN-RAGE program was expressed in 7 cohorts and observed in patients with both COVID-19 and acute respiratory distress syndrome (ARDS) from other causes. This program was associated with greater clinical severity and predicted future mechanical ventilation and death. EN-RAGE+ myeloid cells express features consistent with suppressor cell functionality, with low HLA-DR and high PD-L1 surface expression and higher expression of T cell-suppressive genes. Sustained EN-RAGE signature expression in airway and blood myeloid cells correlated with clinical severity and increasing expression of T cell dysfunction markers, such as PD-1. IL-6 upregulated many of the severity-associated genes in the EN-RAGE gene program in vitro , along with potential mediators of T cell suppression, such as IL-10. Blockade of IL-6 signaling by tocilizumab in a placebo-controlled clinical trial led to rapid normalization of ENRAGE and T cell gene expression. This identifies IL-6 as a key driver of myeloid dysregulation associated with worse clinical outcomes in COVID-19 patients and provides insights into shared pathophysiological mechanisms in non-COVID-19 ARDS. ### Competing Interest Statement J.A.H., H.S., J.V.H., C.O., L.O., X.G., N.W., A.Q., D.C., A.C, D.F.C., T.R, J.M.M., F.C., A.T., M.B., L.T., A.R., S.B.K., R.N.B., and C.M.R. were employees of Genentech, Inc. at the time of this study and own equity in Roche. The COMET study was supported in part by Genentech funding. C.J.Y. is a Scientific Advisory Board member for and holds equity in Related Sciences and ImmunAI, a consultant for and holds equity in Maze Therapeutics, and a consultant for TReX Bio. C.J.Y. has received research support from Chan Zuckerberg Initiative, Chan Zuckerberg Biohub, and Genentech. C.S.C. has received research funding from Roche-Genentech for an unrelated project as well as from NIH, DOD, and Quantum Leap Healthcare Collaborative. C.S.C. is a consultant for Vasomune, Quark, and Gen1e Life Sciences. C.H. is a consultant for Spring Discovery but does not have any financial interest in the company nor is the work related to what is covered in this manuscript. AR is a co-founder and equity holder of Celsius Therapeutics, an equity holder in Immunitas Therapeutics and, until 31 July 2020, was a scientific advisory board member of ThermoFisher Scientific, Syros Pharmaceuticals, Asimov and Neogene Therapeutics. AR is a named inventor on multiple patents related to single cell and spatial genomics filed by or issued to the Broad Institute. ### Clinical Trial NCT04320615 ### Funding Statement This study was supported with funding from Roche, Inc. and federal funds from the Department of Health and Human Services; Office of the Assistant Secretary for Preparedness and Response; Biomedical Advanced Research and Development Authority, under OT number: HHSO100201800036C. C.J.Y. is further supported by the NIH grants R01AR071522, R01AI136972, U01HG012192, and the Chan Zuckerberg Initiative, and is an investigator at the Chan Zuckerberg Biohub and is a member of the Parker Institute for Cancer Immunotherapy (PICI). G.C.H. was supported by the National Science Foundation Undergraduate Research Fellowship Program 1650113. C.S.C. is further supported by NIH R35HL140026. C.H. is further supported by a K23 from NHLBI K23 HL133495. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The COMET study was approved by the Institutional Review Board: UCSF Human Research Protection Program (HRPP) IRB# 20-30497 and informed consent was obtained for patients. COVACTA was conducted in accordance with Good Clinical Practice guidelines of the International Council for Harmonisation E6 and the Declaration of Helsinki or local laws and regulations, whichever afforded greater protection. Informed consent was obtained from the patient or their legally authorized representative prior to participation. The studies were approved by institutional review boards or ethics committees at each site. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes The RNAseq and proteomics data that support the findings of this study are available in the public online respositories Gene Expression Omnibus (GEO), SRA, and the European Genome-Phenome Archive (EGA). COMET: GEO GSE163668 (whole blood), GSE163426 (tracheal aspirate), GSE168453 (PBMC). Schulte-Schrepping, et al.: http://fastgenomics.org. Liao, et al.: SRA PRJNA608742. Silvin, et al.: EGA E-MTAB-9221. Delorey, et al.: Broad Single Cell Portal accession number SCP1052. Grant, et al.: GEO GSE155249. COVACTA RNA-seq, proteomics, and clinical metadata: EGA; accession number EGAS00001006688 (available to qualified researchers upon request; https://ega-archive.org/). Individual patient level clinical data for the COVACTA study is available through the clinical study data request platform (https://vivli.org/).