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Zhu B, Chen S, Bai Y, Chen H, Liao G, Mukherjee N, Vazquez G, McIlwain DR, Tzankov A, Lee IT, Matter MS, Goltsev Y, Ma Z, Nolan GP, Jiang S. Robust single-cell matching and multimodal analysis using shared and distinct features. Nat Methods 2023; 20:304-315. [PMID: 36624212 PMCID: PMC9911356 DOI: 10.1038/s41592-022-01709-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 10/31/2022] [Indexed: 01/10/2023]
Abstract
The ability to align individual cellular information from multiple experimental sources is fundamental for a systems-level understanding of biological processes. However, currently available tools are mainly designed for single-cell transcriptomics matching and integration, and generally rely on a large number of shared features across datasets for cell matching. This approach underperforms when applied to single-cell proteomic datasets due to the limited number of parameters simultaneously accessed and lack of shared markers across these experiments. Here, we introduce a cell-matching algorithm, matching with partial overlap (MARIO) that accounts for both shared and distinct features, while consisting of vital filtering steps to avoid suboptimal matching. MARIO accurately matches and integrates data from different single-cell proteomic and multimodal methods, including spatial techniques and has cross-species capabilities. MARIO robustly matched tissue macrophages identified from COVID-19 lung autopsies via codetection by indexing imaging to macrophages recovered from COVID-19 bronchoalveolar lavage fluid by cellular indexing of transcriptomes and epitopes by sequencing, revealing unique immune responses within the lung microenvironment of patients with COVID.
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Affiliation(s)
- Bokai Zhu
- grid.168010.e0000000419368956Department of Microbiology and Immunology, Stanford University, Stanford, CA USA ,grid.168010.e0000000419368956Department of Pathology, Stanford University, Stanford, CA USA
| | - Shuxiao Chen
- grid.25879.310000 0004 1936 8972Department of Statistics and Data Science, The Wharton School, University of Pennsylvania, PA, USA
| | - Yunhao Bai
- grid.168010.e0000000419368956Department of Pathology, Stanford University, Stanford, CA USA ,grid.168010.e0000000419368956Department of Chemistry, Stanford University, Stanford, CA USA
| | - Han Chen
- grid.168010.e0000000419368956Department of Pathology, Stanford University, Stanford, CA USA
| | - Guanrui Liao
- grid.239395.70000 0000 9011 8547Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA USA
| | - Nilanjan Mukherjee
- grid.168010.e0000000419368956Department of Pathology, Stanford University, Stanford, CA USA
| | - Gustavo Vazquez
- grid.168010.e0000000419368956Department of Pathology, Stanford University, Stanford, CA USA
| | - David R. McIlwain
- grid.168010.e0000000419368956Department of Pathology, Stanford University, Stanford, CA USA
| | - Alexandar Tzankov
- grid.6612.30000 0004 1937 0642Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Ivan T. Lee
- grid.168010.e0000000419368956Department of Pathology, Stanford University, Stanford, CA USA
| | - Matthias S. Matter
- grid.6612.30000 0004 1937 0642Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Yury Goltsev
- grid.168010.e0000000419368956Department of Pathology, Stanford University, Stanford, CA USA
| | - Zongming Ma
- Department of Statistics and Data Science, The Wharton School, University of Pennsylvania, PA, USA.
| | - Garry P. Nolan
- grid.168010.e0000000419368956Department of Pathology, Stanford University, Stanford, CA USA
| | - Sizun Jiang
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA. .,Department of Pathology, Dana Farber Cancer Institute, Boston, MA, USA. .,Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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