Comprehensive Immune Monitoring of Clinical Trials to Advance Human Immunotherapy
Felix J. Hartmann,
Joel Babdor,
Pier Federico Gherardini,
El-Ad D. Amir,
Kyle Jones,
Bita Sahaf,
Diana M. Marquez,
Peter Krutzik,
Erika O’Donnell,
Natalia Sigal,
Holden T. Maecker,
Everett Meyer,
Matthew H. Spitzer,
Sean C. Bendall
Affiliations
Felix J. Hartmann
Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA 94305, USA
Joel Babdor
Departments of Otolaryngology-Head and Neck Surgery and Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
Pier Federico Gherardini
Parker Institute for Cancer Immunotherapy, San Francisco, CA 94125, USA
El-Ad D. Amir
Astrolabe Diagnostics, Inc., Fort Lee, NJ 07024, USA
Kyle Jones
Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
Bita Sahaf
Cancer Correlative Science Unit, Cancer Institute, School of Medicine, Stanford University, Palo Alto, CA 94305, USA
Diana M. Marquez
Departments of Otolaryngology-Head and Neck Surgery and Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
Peter Krutzik
Primity Bio, Fremont, CA 94538, USA
Erika O’Donnell
Primity Bio, Fremont, CA 94538, USA
Natalia Sigal
Department of Microbiology and Immunology, Stanford University, Palo Alto, CA 94305, USA
Holden T. Maecker
Department of Microbiology and Immunology, Stanford University, Palo Alto, CA 94305, USA
Everett Meyer
Cellular Therapy Facility, Blood and Marrow Transplantation, School of Medicine, Stanford University, Palo Alto, CA 94305, USA
Matthew H. Spitzer
Departments of Otolaryngology-Head and Neck Surgery and Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA 94125, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Corresponding author
Sean C. Bendall
Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA 94305, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA 94125, USA; Corresponding author
Summary: The success of immunotherapy has led to a myriad of clinical trials accompanied by efforts to gain mechanistic insight and identify predictive signatures for personalization. However, many immune monitoring technologies face investigator bias, missing unanticipated cellular responses in limited clinical material. We present here a mass cytometry (CyTOF) workflow for standardized, systems-level biomarker discovery in immunotherapy trials. To broadly enumerate immune cell identity and activity, we established and extensively assessed a reference panel of 33 antibodies to cover major cell subsets, simultaneously quantifying activation and immune checkpoint molecules in a single assay. This assay enumerates ≥98% of peripheral immune cells with ≥4 positively identifying antigens. Robustness and reproducibility are demonstrated on multiple samples types, across two research centers and by orthogonal measurements. Using automated analysis, we identify stratifying immune signatures in bone marrow transplantation-associated graft-versus-host disease. Together, this validated workflow ensures comprehensive immunophenotypic analysis and data comparability and will accelerate biomarker discovery. : Hartmann et al. provide an experimental framework to identify and characterize all major human immune cell lineages in a single assay using mass cytometry (CyTOF). This validated and readily available workflow ensures comprehensive immunophenotypic analysis, improves data comparability, and allows identification of disease-associated immune signatures and biomarkers for human immunotherapy. Keywords: immunotherapy, cancer, phenotyping, monitoring, mass cytometry, biomarker, CyTOF, bone marrow transplantation
