High-throughput interrogation of immune responses using the Human Immune Profiling Pipeline

Guanning Wang; Olga Lyudovyk; Justin Y Kim; Ya-Hui Lin; Yuval Elhanati; Divij Mathew; E John Wherry; Ramin S Herati; Allison R Greenplate; Benjamin Greenbaum; Santosha A Vardhana; Alexander C Huang

doi:10.1016/j.xpro.2023.102289

High-throughput interrogation of immune responses using the Human Immune Profiling Pipeline

STAR Protoc. 2023 May 8;4(2):102289. doi: 10.1016/j.xpro.2023.102289. Online ahead of print.

Authors

Affiliations

¹ Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
² Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Tri-institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA.
³ Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA.
⁴ Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
⁵ Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
⁶ Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
⁷ Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
⁸ Department of Medicine, New York University School of Medicine, New York, NY, USA.
⁹ Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
¹⁰ Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Physiology, Biophysics & Systems Biology, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA. Electronic address: greenbab@mskcc.org.
¹¹ Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Lymphoma Service, Division of Hematologic Malignancies, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA. Electronic address: vardhans@mskcc.org.
¹² Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA. Electronic address: alexander.huang@pennmedicine.upenn.edu.

Abstract

The current abundance of immunotherapy clinical trials presents an opportunity to learn about the underlying mechanisms and pharmacodynamic effects of novel drugs on the human immune system. Here, we present a protocol to study how these immune responses impact clinical outcomes using large-scale high-throughput immune profiling of clinical cohorts. We describe the Human Immune Profiling Pipeline, which comprises an end-to-end solution from flow cytometry results to computational approaches and unsupervised patient clustering based on lymphocyte landscape. For complete details on the use and execution of this protocol, please refer to Lyudovyk et al. (2022).¹.

Keywords: Flow Cytometry/Mass Cytometry; Health Sciences; Immunology.

Abstract

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