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Lee AJ, Chang I, Burel JG, Lindestam Arlehamn CS, Mandava A, Weiskopf D, Peters B, Sette A, Scheuermann RH, Qian Y. DAFi: A directed recursive data filtering and clustering approach for improving and interpreting data clustering identification of cell populations from polychromatic flow cytometry data. Cytometry A 2018; 93:597-610. [PMID: 29665244 PMCID: PMC6030426 DOI: 10.1002/cyto.a.23371] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 02/05/2018] [Accepted: 03/15/2018] [Indexed: 11/10/2022]
Abstract
Computational methods for identification of cell populations from polychromatic flow cytometry data are changing the paradigm of cytometry bioinformatics. Data clustering is the most common computational approach to unsupervised identification of cell populations from multidimensional cytometry data. However, interpretation of the identified data clusters is labor-intensive. Certain types of user-defined cell populations are also difficult to identify by fully automated data clustering analysis. Both are roadblocks before a cytometry lab can adopt the data clustering approach for cell population identification in routine use. We found that combining recursive data filtering and clustering with constraints converted from the user manual gating strategy can effectively address these two issues. We named this new approach DAFi: Directed Automated Filtering and Identification of cell populations. Design of DAFi preserves the data-driven characteristics of unsupervised clustering for identifying novel cell subsets, but also makes the results interpretable to experimental scientists through mapping and merging the multidimensional data clusters into the user-defined two-dimensional gating hierarchy. The recursive data filtering process in DAFi helped identify small data clusters which are otherwise difficult to resolve by a single run of the data clustering method due to the statistical interference of the irrelevant major clusters. Our experiment results showed that the proportions of the cell populations identified by DAFi, while being consistent with those by expert centralized manual gating, have smaller technical variances across samples than those from individual manual gating analysis and the nonrecursive data clustering analysis. Compared with manual gating segregation, DAFi-identified cell populations avoided the abrupt cut-offs on the boundaries. DAFi has been implemented to be used with multiple data clustering methods including K-means, FLOCK, FlowSOM, and the ClusterR package. For cell population identification, DAFi supports multiple options including clustering, bisecting, slope-based gating, and reversed filtering to meet various autogating needs from different scientific use cases. © 2018 International Society for Advancement of Cytometry.
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Affiliation(s)
| | - Ivan Chang
- J. Craig Venter Institute, La Jolla, California
| | - Julie G. Burel
- La Jolla Institute for Allergy and Immunology, La Jolla, California
| | | | | | - Daniela Weiskopf
- La Jolla Institute for Allergy and Immunology, La Jolla, California
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, La Jolla, California
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, California
- Department of Medicine, University of California, San Diego, California
| | - Richard H. Scheuermann
- J. Craig Venter Institute, La Jolla, California
- Department of Pathology, University of California, San Diego, California
| | - Yu Qian
- J. Craig Venter Institute, La Jolla, California
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Chinthrajah RS, Purington N, Sampath V, Andorf S, Manohar M, Prunicki M, Zhou X, Tupa D, Nadeau KC. High dimensional immune biomarkers demonstrate differences in phenotypes and endotypes in food allergy and asthma. Ann Allergy Asthma Immunol 2018; 121:117-119.e1. [PMID: 29705381 DOI: 10.1016/j.anai.2018.04.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 04/17/2018] [Accepted: 04/23/2018] [Indexed: 01/28/2023]
Affiliation(s)
- R Sharon Chinthrajah
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford University School of Medicine, Stanford, California; Department of Medicine, Stanford University School of Medicine, Stanford, California; Departments of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Natasha Purington
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford University School of Medicine, Stanford, California; Quantitative Sciences Unit, Stanford University School of Medicine, Stanford, California
| | - Vanitha Sampath
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford University School of Medicine, Stanford, California; Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Sandra Andorf
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford University School of Medicine, Stanford, California; Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Monali Manohar
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford University School of Medicine, Stanford, California; Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Mary Prunicki
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford University School of Medicine, Stanford, California; Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Xiaoying Zhou
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford University School of Medicine, Stanford, California; Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Dana Tupa
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford University School of Medicine, Stanford, California; Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Kari C Nadeau
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford University School of Medicine, Stanford, California; Department of Medicine, Stanford University School of Medicine, Stanford, California; Departments of Pediatrics, Stanford University School of Medicine, Stanford, California.
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Unique phenotypes and clonal expansions of human CD4 effector memory T cells re-expressing CD45RA. Nat Commun 2017; 8:1473. [PMID: 29133794 PMCID: PMC5684192 DOI: 10.1038/s41467-017-01728-5] [Citation(s) in RCA: 159] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 10/12/2017] [Indexed: 12/01/2022] Open
Abstract
The expression of CD45RA is generally associated with naive T cells. However, a subset of effector memory T cells re-expresses CD45RA (termed TEMRA) after antigenic stimulation with unknown molecular characteristics and functions. CD4 TEMRA cells have been implicated in protective immunity against pathogens such as dengue virus (DENV). Here we show that not only the frequency but also the phenotype of CD4 TEMRA cells are heterogeneous between individuals. These cells can be subdivided into two major subsets based on the expression of the adhesion G protein-coupled receptor GPR56, and GPR56+ TEMRA cells display a transcriptional and proteomic program with cytotoxic features that is distinct from effector memory T cells. Moreover, GPR56+ TEMRA cells have higher levels of clonal expansion and contain the majority of virus-specific TEMRA cells. Overall, this study reveals the heterogeneity of CD4 TEMRA cells and provides insights into T-cell responses against DENV and other viral pathogens. Memory T cells are essential for combating recurring infection by promoting prompt and effective immune responses. Here the authors show, via system biology approaches, that human CD4 memory T cells contains a CD45RA-rexpressing pool that can be further subsetted by the expression of GPR56 for distinct functionalities.
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Pedersen NW, Chandran PA, Qian Y, Rebhahn J, Petersen NV, Hoff MD, White S, Lee AJ, Stanton R, Halgreen C, Jakobsen K, Mosmann T, Gouttefangeas C, Chan C, Scheuermann RH, Hadrup SR. Automated Analysis of Flow Cytometry Data to Reduce Inter-Lab Variation in the Detection of Major Histocompatibility Complex Multimer-Binding T Cells. Front Immunol 2017; 8:858. [PMID: 28798746 PMCID: PMC5526901 DOI: 10.3389/fimmu.2017.00858] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 07/07/2017] [Indexed: 12/22/2022] Open
Abstract
Manual analysis of flow cytometry data and subjective gate-border decisions taken by individuals continue to be a source of variation in the assessment of antigen-specific T cells when comparing data across laboratories, and also over time in individual labs. Therefore, strategies to provide automated analysis of major histocompatibility complex (MHC) multimer-binding T cells represent an attractive solution to decrease subjectivity and technical variation. The challenge of using an automated analysis approach is that MHC multimer-binding T cell populations are often rare and therefore difficult to detect. We used a highly heterogeneous dataset from a recent MHC multimer proficiency panel to assess if MHC multimer-binding CD8+ T cells could be analyzed with computational solutions currently available, and if such analyses would reduce the technical variation across different laboratories. We used three different methods, FLOw Clustering without K (FLOCK), Scalable Weighted Iterative Flow-clustering Technique (SWIFT), and ReFlow to analyze flow cytometry data files from 28 laboratories. Each laboratory screened for antigen-responsive T cell populations with frequency ranging from 0.01 to 1.5% of lymphocytes within samples from two donors. Experience from this analysis shows that all three programs can be used for the identification of high to intermediate frequency of MHC multimer-binding T cell populations, with results very similar to that of manual gating. For the less frequent populations (<0.1% of live, single lymphocytes), SWIFT outperformed the other tools. As used in this study, none of the algorithms offered a completely automated pipeline for identification of MHC multimer populations, as varying degrees of human interventions were needed to complete the analysis. In this study, we demonstrate the feasibility of using automated analysis pipelines for assessing and identifying even rare populations of antigen-responsive T cells and discuss the main properties, differences, and advantages of the different methods tested.
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Affiliation(s)
- Natasja Wulff Pedersen
- Division of Immunology and Vaccinology, Veterinary Institute, Technical University of Denmark, Copenhagen, Denmark
| | - P. Anoop Chandran
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Yu Qian
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, United States
| | - Jonathan Rebhahn
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, NY, United States
| | - Nadia Viborg Petersen
- Division of Immunology and Vaccinology, Veterinary Institute, Technical University of Denmark, Copenhagen, Denmark
| | - Mathilde Dalsgaard Hoff
- Division of Immunology and Vaccinology, Veterinary Institute, Technical University of Denmark, Copenhagen, Denmark
| | - Scott White
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, United States
| | - Alexandra J. Lee
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, United States
| | - Rick Stanton
- Human Longevity Inc., San Diego, CA, United States
| | | | | | - Tim Mosmann
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, NY, United States
| | - Cécile Gouttefangeas
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Cliburn Chan
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, United States
| | - Richard H. Scheuermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, United States
- Department of Pathology, University of California, San Diego, La Jolla, CA, United States
| | - Sine Reker Hadrup
- Division of Immunology and Vaccinology, Veterinary Institute, Technical University of Denmark, Copenhagen, Denmark
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