Frontiers in Immunology (Sep 2023)
Cyclone: an accessible pipeline to analyze, evaluate, and optimize multiparametric cytometry data
- Ravi K. Patel,
- Rebecca G. Jaszczak,
- Kwok Im,
- Kwok Im,
- Kwok Im,
- Nicholas D. Carey,
- Nicholas D. Carey,
- Nicholas D. Carey,
- Tristan Courau,
- Tristan Courau,
- Tristan Courau,
- Tristan Courau,
- Daniel G. Bunis,
- Bushra Samad,
- Lia Avanesyan,
- Lia Avanesyan,
- Lia Avanesyan,
- Lia Avanesyan,
- Nayvin W. Chew,
- Nayvin W. Chew,
- Nayvin W. Chew,
- Sarah Stenske,
- Sarah Stenske,
- Jillian M. Jespersen,
- Jillian M. Jespersen,
- Jean Publicover,
- Jean Publicover,
- Austin W. Edwards,
- Mohammad Naser,
- Arjun A. Rao,
- Leonard Lupin-Jimenez,
- Matthew F. Krummel,
- Matthew F. Krummel,
- Matthew F. Krummel,
- Stewart Cooper,
- Stewart Cooper,
- Stewart Cooper,
- Jody L. Baron,
- Jody L. Baron,
- Jody L. Baron,
- Alexis J. Combes,
- Alexis J. Combes,
- Alexis J. Combes,
- Alexis J. Combes,
- Alexis J. Combes,
- Gabriela K. Fragiadakis,
- Gabriela K. Fragiadakis
Affiliations
- Ravi K. Patel
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
- Rebecca G. Jaszczak
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
- Kwok Im
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
- Kwok Im
- Department of Pathology, University of California San Francisco, San Francisco, CA, United States
- Kwok Im
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, United States
- Nicholas D. Carey
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
- Nicholas D. Carey
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, United States
- Nicholas D. Carey
- UCSF Liver Center, University of California San Francisco, San Francisco, CA, United States
- Tristan Courau
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
- Tristan Courau
- Department of Pathology, University of California San Francisco, San Francisco, CA, United States
- Tristan Courau
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, United States
- Tristan Courau
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA, United States
- Daniel G. Bunis
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
- Bushra Samad
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
- Lia Avanesyan
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, United States
- Lia Avanesyan
- UCSF Liver Center, University of California San Francisco, San Francisco, CA, United States
- Lia Avanesyan
- The Ibrahim El-Hefni Liver Biorepository at California Pacific Medical Center (IELBC), San Francisco, CA, United States
- Lia Avanesyan
- Division of General and Transplant Hepatology, California Pacific Medical Center & Research Institute, San Francisco, CA, United States
- Nayvin W. Chew
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
- Nayvin W. Chew
- Department of Pathology, University of California San Francisco, San Francisco, CA, United States
- Nayvin W. Chew
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, United States
- Sarah Stenske
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, United States
- Sarah Stenske
- UCSF Liver Center, University of California San Francisco, San Francisco, CA, United States
- Jillian M. Jespersen
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, United States
- Jillian M. Jespersen
- UCSF Liver Center, University of California San Francisco, San Francisco, CA, United States
- Jean Publicover
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, United States
- Jean Publicover
- UCSF Liver Center, University of California San Francisco, San Francisco, CA, United States
- Austin W. Edwards
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
- Mohammad Naser
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
- Arjun A. Rao
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
- Leonard Lupin-Jimenez
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
- Matthew F. Krummel
- Department of Pathology, University of California San Francisco, San Francisco, CA, United States
- Matthew F. Krummel
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, United States
- Matthew F. Krummel
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA, United States
- Stewart Cooper
- UCSF Liver Center, University of California San Francisco, San Francisco, CA, United States
- Stewart Cooper
- The Ibrahim El-Hefni Liver Biorepository at California Pacific Medical Center (IELBC), San Francisco, CA, United States
- Stewart Cooper
- Division of General and Transplant Hepatology, California Pacific Medical Center & Research Institute, San Francisco, CA, United States
- Jody L. Baron
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, United States
- Jody L. Baron
- UCSF Liver Center, University of California San Francisco, San Francisco, CA, United States
- Jody L. Baron
- The Ibrahim El-Hefni Liver Biorepository at California Pacific Medical Center (IELBC), San Francisco, CA, United States
- Alexis J. Combes
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
- Alexis J. Combes
- Department of Pathology, University of California San Francisco, San Francisco, CA, United States
- Alexis J. Combes
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, United States
- Alexis J. Combes
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, United States
- Alexis J. Combes
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA, United States
- Gabriela K. Fragiadakis
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, United States
- Gabriela K. Fragiadakis
- Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, United States
- DOI
- https://doi.org/10.3389/fimmu.2023.1167241
- Journal volume & issue
-
Vol. 14
Abstract
In the past decade, high-dimensional single-cell technologies have revolutionized basic and translational immunology research and are now a key element of the toolbox used by scientists to study the immune system. However, analysis of the data generated by these approaches often requires clustering algorithms and dimensionality reduction representation, which are computationally intense and difficult to evaluate and optimize. Here, we present Cytometry Clustering Optimization and Evaluation (Cyclone), an analysis pipeline integrating dimensionality reduction, clustering, evaluation, and optimization of clustering resolution, and downstream visualization tools facilitating the analysis of a wide range of cytometry data. We benchmarked and validated Cyclone on mass cytometry (CyTOF), full-spectrum fluorescence-based cytometry, and multiplexed immunofluorescence (IF) in a variety of biological contexts, including infectious diseases and cancer. In each instance, Cyclone not only recapitulates gold standard immune cell identification but also enables the unsupervised identification of lymphocytes and mononuclear phagocyte subsets that are associated with distinct biological features. Altogether, the Cyclone pipeline is a versatile and accessible pipeline for performing, optimizing, and evaluating clustering on a variety of cytometry datasets, which will further power immunology research and provide a scaffold for biological discovery.
Keywords
