Comprehensive multi-omics single-cell data integration reveals greater heterogeneity in the human immune system
Congmin Xu,
Junkai Yang,
Astrid Kosters,
Benjamin R. Babcock,
Peng Qiu,
Eliver E.B. Ghosn
Affiliations
Congmin Xu
Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
Junkai Yang
Department of Medicine, Division of Immunology, Lowance Center for Human Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
Astrid Kosters
Department of Medicine, Division of Immunology, Lowance Center for Human Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
Benjamin R. Babcock
Department of Medicine, Division of Immunology, Lowance Center for Human Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
Peng Qiu
Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA; Corresponding author
Eliver E.B. Ghosn
Department of Medicine, Division of Immunology, Lowance Center for Human Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA; Emory Vaccine Center, Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, GA 30322, USA; Corresponding author
Summary: Single-cell transcriptomics enables the definition of diverse human immune cell types across multiple tissues and disease contexts. Further deeper biological understanding requires comprehensive integration of multiple single-cell omics (transcriptomic, proteomic, and cell-receptor repertoire). To improve the identification of diverse cell types and the accuracy of cell-type classification in multi-omics single-cell datasets, we developed SuPERR, a novel analysis workflow to increase the resolution and accuracy of clustering and allow for the discovery of previously hidden cell subsets. In addition, SuPERR accurately removes cell doublets and prevents widespread cell-type misclassification by incorporating information from cell-surface proteins and immunoglobulin transcript counts. This approach uniquely improves the identification of heterogeneous cell types and states in the human immune system, including rare subsets of antibody-secreting cells in the bone marrow.
