1
|
Patil AR, Schug J, Liu C, Lahori D, Descamps HC, Naji A, Kaestner KH, Faryabi RB, Vahedi G. Modeling type 1 diabetes progression using machine learning and single-cell transcriptomic measurements in human islets. Cell Rep Med 2024; 5:101535. [PMID: 38677282 PMCID: PMC11148720 DOI: 10.1016/j.xcrm.2024.101535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 01/22/2024] [Accepted: 04/07/2024] [Indexed: 04/29/2024]
Abstract
Type 1 diabetes (T1D) is a chronic condition in which beta cells are destroyed by immune cells. Despite progress in immunotherapies that could delay T1D onset, early detection of autoimmunity remains challenging. Here, we evaluate the utility of machine learning for early prediction of T1D using single-cell analysis of islets. Using gradient-boosting algorithms, we model changes in gene expression of single cells from pancreatic tissues in T1D and non-diabetic organ donors. We assess if mathematical modeling could predict the likelihood of T1D development in non-diabetic autoantibody-positive donors. While most autoantibody-positive donors are predicted to be non-diabetic, select donors with unique gene signatures are classified as T1D. Our strategy also reveals a shared gene signature in distinct T1D-associated models across cell types, suggesting a common effect of the disease on transcriptional outputs of these cells. Our study establishes a precedent for using machine learning in early detection of T1D.
Collapse
Affiliation(s)
- Abhijeet R Patil
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jonathan Schug
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Chengyang Liu
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Deeksha Lahori
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Hélène C Descamps
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Ali Naji
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Klaus H Kaestner
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Robert B Faryabi
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Golnaz Vahedi
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
| |
Collapse
|
2
|
Guo X, Ning J, Chen Y, Liu G, Zhao L, Fan Y, Sun S. Recent advances in differential expression analysis for single-cell RNA-seq and spatially resolved transcriptomic studies. Brief Funct Genomics 2024; 23:95-109. [PMID: 37022699 DOI: 10.1093/bfgp/elad011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 12/09/2022] [Accepted: 03/10/2023] [Indexed: 04/07/2023] Open
Abstract
Differential expression (DE) analysis is a necessary step in the analysis of single-cell RNA sequencing (scRNA-seq) and spatially resolved transcriptomics (SRT) data. Unlike traditional bulk RNA-seq, DE analysis for scRNA-seq or SRT data has unique characteristics that may contribute to the difficulty of detecting DE genes. However, the plethora of DE tools that work with various assumptions makes it difficult to choose an appropriate one. Furthermore, a comprehensive review on detecting DE genes for scRNA-seq data or SRT data from multi-condition, multi-sample experimental designs is lacking. To bridge such a gap, here, we first focus on the challenges of DE detection, then highlight potential opportunities that facilitate further progress in scRNA-seq or SRT analysis, and finally provide insights and guidance in selecting appropriate DE tools or developing new computational DE methods.
Collapse
Affiliation(s)
- Xiya Guo
- School of Public Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
- Key Laboratory of Trace Elements and Endemic Diseases, Center for Single Cell Omics and Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Jin Ning
- School of Public Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
- Key Laboratory of Trace Elements and Endemic Diseases, Center for Single Cell Omics and Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Yuanze Chen
- School of Public Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
- Key Laboratory of Trace Elements and Endemic Diseases, Center for Single Cell Omics and Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Guoliang Liu
- School of Public Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
- Key Laboratory of Trace Elements and Endemic Diseases, Center for Single Cell Omics and Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Liyan Zhao
- School of Public Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
- Key Laboratory of Trace Elements and Endemic Diseases, Center for Single Cell Omics and Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Yue Fan
- School of Public Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
- Key Laboratory of Trace Elements and Endemic Diseases, Center for Single Cell Omics and Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Shiquan Sun
- School of Public Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
- Key Laboratory of Trace Elements and Endemic Diseases, Center for Single Cell Omics and Health, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| |
Collapse
|
3
|
Jain A, Kim BR, Yu W, Moninger TO, Karp PH, Wagner BA, Welsh MJ. Mitochondrial uncoupling proteins protect human airway epithelial ciliated cells from oxidative damage. Proc Natl Acad Sci U S A 2024; 121:e2318771121. [PMID: 38416686 DOI: 10.1073/pnas.2318771121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/12/2024] [Indexed: 03/01/2024] Open
Abstract
Apical cilia on epithelial cells defend the lung by propelling pathogens and particulates out of the respiratory airways. Ciliated cells produce ATP that powers cilia beating by densely grouping mitochondria just beneath the apical membrane. However, this efficient localization comes at a cost because electrons leaked during oxidative phosphorylation react with molecular oxygen to form superoxide, and thus, the cluster of mitochondria creates a hotspot for oxidant production. The relatively high oxygen concentration overlying airway epithelia further intensifies the risk of generating superoxide. Thus, airway ciliated cells face a unique challenge of producing harmful levels of oxidants. However, surprisingly, highly ciliated epithelia produce less reactive oxygen species (ROS) than epithelia with few ciliated cells. Compared to other airway cell types, ciliated cells express high levels of mitochondrial uncoupling proteins, UCP2 and UCP5. These proteins decrease mitochondrial protonmotive force and thereby reduce production of ROS. As a result, lipid peroxidation, a marker of oxidant injury, decreases. However, mitochondrial uncoupling proteins exact a price for decreasing oxidant production; they decrease the fraction of mitochondrial respiration that generates ATP. These findings indicate that ciliated cells sacrifice mitochondrial efficiency in exchange for safety from damaging oxidation. Employing uncoupling proteins to prevent oxidant production, instead of relying solely on antioxidants to decrease postproduction oxidant levels, may offer an advantage for targeting a local area of intense ROS generation.
Collapse
Affiliation(s)
- Akansha Jain
- Department of Internal Medicine, Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242
- Department of Molecular Physiology and Biophysics, Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242
| | - Bo Ram Kim
- Department of Internal Medicine, Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242
- HHMI, Department of Internal Medicine, University of Iowa, Iowa City, IA 52242
| | - Wenjie Yu
- Department of Internal Medicine, Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242
- HHMI, Department of Internal Medicine, University of Iowa, Iowa City, IA 52242
| | - Thomas O Moninger
- Department of Internal Medicine, Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242
| | - Philip H Karp
- Department of Internal Medicine, Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242
- HHMI, Department of Internal Medicine, University of Iowa, Iowa City, IA 52242
| | - Brett A Wagner
- Free Radical and Radiation Biology Program, Department of Radiation Oncology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242
| | - Michael J Welsh
- Department of Internal Medicine, Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242
- Department of Molecular Physiology and Biophysics, Pappajohn Biomedical Institute, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242
- HHMI, Department of Internal Medicine, University of Iowa, Iowa City, IA 52242
| |
Collapse
|
4
|
Vu LT, Ahmed F, Zhu H, Iu DSH, Fogarty EA, Kwak Y, Chen W, Franconi CJ, Munn PR, Tate AE, Levine SM, Stevens J, Mao X, Shungu DC, Moore GE, Keller BA, Hanson MR, Grenier JK, Grimson A. Single-cell transcriptomics of the immune system in ME/CFS at baseline and following symptom provocation. Cell Rep Med 2024; 5:101373. [PMID: 38232699 PMCID: PMC10829790 DOI: 10.1016/j.xcrm.2023.101373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 08/10/2023] [Accepted: 12/14/2023] [Indexed: 01/19/2024]
Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a serious and poorly understood disease. To understand immune dysregulation in ME/CFS, we use single-cell RNA sequencing (scRNA-seq) to examine immune cells in patient and control cohorts. Postexertional malaise (PEM), an exacerbation of symptoms following strenuous exercise, is a characteristic symptom of ME/CFS. To detect changes coincident with PEM, we applied scRNA-seq on the same cohorts following exercise. At baseline, ME/CFS patients display classical monocyte dysregulation suggestive of inappropriate differentiation and migration to tissue. We identify both diseased and more normal monocytes within patients, and the fraction of diseased cells correlates with disease severity. Comparing the transcriptome at baseline and postexercise challenge, we discover patterns indicative of improper platelet activation in patients, with minimal changes elsewhere in the immune system. Taken together, these data identify immunological defects present at baseline in patients and an additional layer of dysregulation in platelets.
Collapse
Affiliation(s)
- Luyen Tien Vu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Faraz Ahmed
- Genomics Innovation Hub and TREx Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA
| | - Hongya Zhu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - David Shing Huk Iu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Elizabeth A Fogarty
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Yeonui Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Weizhong Chen
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Carl J Franconi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Paul R Munn
- Genomics Innovation Hub and TREx Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA
| | - Ann E Tate
- Genomics Innovation Hub and TREx Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA
| | | | | | - Xiangling Mao
- Department of Radiology, Weill Cornell Medicine, New York, NY, USA
| | - Dikoma C Shungu
- Department of Radiology, Weill Cornell Medicine, New York, NY, USA
| | - Geoffrey E Moore
- Department of Exercise Science and Athletic Training, Ithaca College, Ithaca, NY, USA
| | - Betsy A Keller
- Department of Exercise Science and Athletic Training, Ithaca College, Ithaca, NY, USA
| | - Maureen R Hanson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jennifer K Grenier
- Genomics Innovation Hub and TREx Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA.
| | - Andrew Grimson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
| |
Collapse
|
5
|
Kong Y, Yang N, Luo Z, Huang R, Li Q. Key Cell Types and Biomarkers in Heart Failure Identified through Analysis of Single-Cell and Bulk RNA Sequencing Data. Mediators Inflamm 2023; 2023:8384882. [PMID: 38169915 PMCID: PMC10761229 DOI: 10.1155/2023/8384882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/26/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024] Open
Abstract
Heart failure (HF) is a complex clinical syndrome resulting from various cardiac diseases and a significant medical issue worldwide. Although the role of inflammation in HF pathogenesis is well-known, the specific cell types and regulatory molecules involved remain poorly understood. Here, we identified key cell types and novel biomarkers via an analysis of single-cell and bulk RNA sequencing data obtained from patients with two major HF types of ischemic cardiomyopathy and dilated cardiomyopathy. Myeloid cells were identified as the primary cell population involved in HF through cellular fraction and gene set enrichment analysis. Additionally, differential analysis of myeloid cells revealed crosstalk between cellular communication and cytokine-regulated immune responses in HF, with the MIF pathway emerging as a crucial immune regulatory pathway. The CD74/CXCR4 receptor complex in myeloid cell subgroup Mφ2 was significantly upregulated, potentially acting as a crucial regulator in HF. Upon receiving the MIF signal molecule, the CD74/CXCR4 receptor can activate NF-κB signaling to produce chemokines and thereby enhance the inflammatory response. CD74 and CXCR4 may serve as biomarkers and treatment targets for HF.
Collapse
Affiliation(s)
- Ying Kong
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, Guangdong, China
- Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, South China University of Technology, Guangzhou 510006, Guangdong, China
| | - Ning Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, Guangdong, China
| | - Zhiqing Luo
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, Guangdong, China
| | - Ruiting Huang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, Guangdong, China
| | - Quhuan Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, Guangdong, China
- Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, South China University of Technology, Guangzhou 510006, Guangdong, China
| |
Collapse
|
6
|
Heumos L, Schaar AC, Lance C, Litinetskaya A, Drost F, Zappia L, Lücken MD, Strobl DC, Henao J, Curion F, Schiller HB, Theis FJ. Best practices for single-cell analysis across modalities. Nat Rev Genet 2023; 24:550-572. [PMID: 37002403 PMCID: PMC10066026 DOI: 10.1038/s41576-023-00586-w] [Citation(s) in RCA: 127] [Impact Index Per Article: 127.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2023] [Indexed: 04/03/2023]
Abstract
Recent advances in single-cell technologies have enabled high-throughput molecular profiling of cells across modalities and locations. Single-cell transcriptomics data can now be complemented by chromatin accessibility, surface protein expression, adaptive immune receptor repertoire profiling and spatial information. The increasing availability of single-cell data across modalities has motivated the development of novel computational methods to help analysts derive biological insights. As the field grows, it becomes increasingly difficult to navigate the vast landscape of tools and analysis steps. Here, we summarize independent benchmarking studies of unimodal and multimodal single-cell analysis across modalities to suggest comprehensive best-practice workflows for the most common analysis steps. Where independent benchmarks are not available, we review and contrast popular methods. Our article serves as an entry point for novices in the field of single-cell (multi-)omic analysis and guides advanced users to the most recent best practices.
Collapse
Affiliation(s)
- Lukas Heumos
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center, Helmholtz Munich; Member of the German Center for Lung Research (DZL), Munich, Germany
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Anna C Schaar
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Munich Center for Machine Learning, Technical University of Munich, Garching, Germany
| | - Christopher Lance
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- Department of Paediatrics, Dr von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Anastasia Litinetskaya
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Felix Drost
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Luke Zappia
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Malte D Lücken
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- Institute of Lung Health and Immunity, Helmholtz Munich, Munich, Germany
| | - Daniel C Strobl
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
| | - Juan Henao
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
| | - Fabiola Curion
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Herbert B Schiller
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center, Helmholtz Munich; Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Department of Computational Health, Helmholtz Munich, Munich, Germany.
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany.
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.
- Munich Center for Machine Learning, Technical University of Munich, Garching, Germany.
| |
Collapse
|
7
|
Liu Y, Huang J, Pandey R, Liu P, Therani B, Qiu Q, Rao S, Geurts AM, Cowley AW, Greene AS, Liang M. Robustness of single-cell RNA-seq for identifying differentially expressed genes. BMC Genomics 2023; 24:371. [PMID: 37394518 PMCID: PMC10316566 DOI: 10.1186/s12864-023-09487-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/27/2023] [Indexed: 07/04/2023] Open
Abstract
BACKGROUND A common feature of single-cell RNA-seq (scRNA-seq) data is that the number of cells in a cell cluster may vary widely, ranging from a few dozen to several thousand. It is not clear whether scRNA-seq data from a small number of cells allow robust identification of differentially expressed genes (DEGs) with various characteristics. RESULTS We addressed this question by performing scRNA-seq and poly(A)-dependent bulk RNA-seq in comparable aliquots of human induced pluripotent stem cells-derived, purified vascular endothelial and smooth muscle cells. We found that scRNA-seq data needed to have 2,000 or more cells in a cluster to identify the majority of DEGs that would show modest differences in a bulk RNA-seq analysis. On the other hand, clusters with as few as 50-100 cells may be sufficient for identifying the majority of DEGs that would have extremely small p values or transcript abundance greater than a few hundred transcripts per million in a bulk RNA-seq analysis. CONCLUSION Findings of the current study provide a quantitative reference for designing studies that aim for identifying DEGs for specific cell clusters using scRNA-seq data and for interpreting results of such studies.
Collapse
Affiliation(s)
- Yong Liu
- Department of Physiology, Center of Systems Molecular Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Physiology, University of Arizona College of Medicine - Tucson, Tucson, AZ, USA
| | - Jing Huang
- Department of Physiology, Center of Systems Molecular Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Physiology, University of Arizona College of Medicine - Tucson, Tucson, AZ, USA
| | - Rajan Pandey
- Department of Physiology, Center of Systems Molecular Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Pengyuan Liu
- Department of Physiology, Center of Systems Molecular Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Physiology, University of Arizona College of Medicine - Tucson, Tucson, AZ, USA
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Bhavika Therani
- Department of Physiology, Center of Systems Molecular Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Physiology, University of Arizona College of Medicine - Tucson, Tucson, AZ, USA
| | - Qiongzi Qiu
- Department of Physiology, Center of Systems Molecular Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Physiology, University of Arizona College of Medicine - Tucson, Tucson, AZ, USA
| | - Sridhar Rao
- Versiti Blood Research Institute, Milwaukee, WI, USA
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
- Division of Pediatric Hematology/Oncology/Transplantation, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Aron M Geurts
- Department of Physiology, Center of Systems Molecular Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Allen W Cowley
- Department of Physiology, Center of Systems Molecular Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Mingyu Liang
- Department of Physiology, Center of Systems Molecular Medicine, Medical College of Wisconsin, Milwaukee, WI, USA.
- Department of Physiology, University of Arizona College of Medicine - Tucson, Tucson, AZ, USA.
| |
Collapse
|
8
|
Cao Y, Ghazanfar S, Yang P, Yang J. Benchmarking of analytical combinations for COVID-19 outcome prediction using single-cell RNA sequencing data. Brief Bioinform 2023; 24:7140296. [PMID: 37096588 DOI: 10.1093/bib/bbad159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/30/2023] [Accepted: 04/03/2023] [Indexed: 04/26/2023] Open
Abstract
The advances of single-cell transcriptomic technologies have led to increasing use of single-cell RNA sequencing (scRNA-seq) data in large-scale patient cohort studies. The resulting high-dimensional data can be summarized and incorporated into patient outcome prediction models in several ways; however, there is a pressing need to understand the impact of analytical decisions on such model quality. In this study, we evaluate the impact of analytical choices on model choices, ensemble learning strategies and integrate approaches on patient outcome prediction using five scRNA-seq COVID-19 datasets. First, we examine the difference in performance between using single-view feature space versus multi-view feature space. Next, we survey multiple learning platforms from classical machine learning to modern deep learning methods. Lastly, we compare different integration approaches when combining datasets is necessary. Through benchmarking such analytical combinations, our study highlights the power of ensemble learning, consistency among different learning methods and robustness to dataset normalization when using multiple datasets as the model input.
Collapse
Affiliation(s)
- Yue Cao
- School of Mathematics and Statistics, The University of Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, NSW 2006, Australia
- Sydney Precision Data Science Centre, University of Sydney, NSW 2006, Australia
- Laboratory of Data Discovery for Health Limited (D24H), Science Park, Hong Kong SAR, China
| | - Shila Ghazanfar
- School of Mathematics and Statistics, The University of Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, NSW 2006, Australia
- Sydney Precision Data Science Centre, University of Sydney, NSW 2006, Australia
| | - Pengyi Yang
- School of Mathematics and Statistics, The University of Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, NSW 2006, Australia
- Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, NSW 2145, Australia
- Sydney Precision Data Science Centre, University of Sydney, NSW 2006, Australia
- Laboratory of Data Discovery for Health Limited (D24H), Science Park, Hong Kong SAR, China
| | - Jean Yang
- School of Mathematics and Statistics, The University of Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, NSW 2006, Australia
- Sydney Precision Data Science Centre, University of Sydney, NSW 2006, Australia
- Laboratory of Data Discovery for Health Limited (D24H), Science Park, Hong Kong SAR, China
| |
Collapse
|
9
|
Patel A, Kumar S, Lai L, Chakravarthy C, Valanparambil R, Reddy ES, Gottimukkala K, Bajpai P, Raju DR, Edara VV, Davis-Gardner ME, Linderman S, Dixit K, Sharma P, Mantus G, Cheedarla N, Verkerke HP, Frank F, Neish AS, Roback JD, Davis CW, Wrammert J, Ahmed R, Suthar MS, Sharma A, Murali-Krishna K, Chandele A, Ortlund EA. Molecular basis of SARS-CoV-2 Omicron variant evasion from shared neutralizing antibody response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.10.24.513517. [PMID: 36324804 DOI: 10.1101/2022.10.13.512091] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A detailed understanding of the molecular features of the neutralizing epitopes developed by viral escape mutants is important for predicting and developing vaccines or therapeutic antibodies against continuously emerging SARS-CoV-2 variants. Here, we report three human monoclonal antibodies (mAbs) generated from COVID-19 recovered individuals during first wave of pandemic in India. These mAbs had publicly shared near germline gene usage and potently neutralized Alpha and Delta, but poorly neutralized Beta and completely failed to neutralize Omicron BA.1 SARS-CoV-2 variants. Structural analysis of these three mAbs in complex with trimeric spike protein showed that all three mAbs are involved in bivalent spike binding with two mAbs targeting class-1 and one targeting class-4 Receptor Binding Domain (RBD) epitope. Comparison of immunogenetic makeup, structure, and function of these three mAbs with our recently reported class-3 RBD binding mAb that potently neutralized all SARS-CoV-2 variants revealed precise antibody footprint, specific molecular interactions associated with the most potent multi-variant binding / neutralization efficacy. This knowledge has timely significance for understanding how a combination of certain mutations affect the binding or neutralization of an antibody and thus have implications for predicting structural features of emerging SARS-CoV-2 escape variants and to develop vaccines or therapeutic antibodies against these.
Collapse
Affiliation(s)
- Anamika Patel
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Sanjeev Kumar
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Lilin Lai
- Department of Pediatrics, Emory National Primate Center, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Chennareddy Chakravarthy
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Rajesh Valanparambil
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Elluri Seetharami Reddy
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi, 110016, India
| | - Kamalvishnu Gottimukkala
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Prashant Bajpai
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Dinesh Ravindra Raju
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
- Georgia Tech, Atlanta, GA 30332, USA
| | - Venkata Viswanadh Edara
- Department of Pediatrics, Emory National Primate Center, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Meredith E Davis-Gardner
- Department of Pediatrics, Emory National Primate Center, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Susanne Linderman
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Kritika Dixit
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Pragati Sharma
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Grace Mantus
- Department of Pediatrics, Emory National Primate Center, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Narayanaiah Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Hans P Verkerke
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02215, USA
| | - Filipp Frank
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Andrew S Neish
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - John D Roback
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Carl W Davis
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Jens Wrammert
- Department of Pediatrics, Emory National Primate Center, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Rafi Ahmed
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Mehul S Suthar
- Department of Pediatrics, Emory National Primate Center, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Amit Sharma
- Structural Parasitology Group, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Kaja Murali-Krishna
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
- Department of Pediatrics, Emory National Primate Center, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Anmol Chandele
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Eric A Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| |
Collapse
|
10
|
Junttila S, Smolander J, Elo LL. Benchmarking methods for detecting differential states between conditions from multi-subject single-cell RNA-seq data. Brief Bioinform 2022; 23:6649780. [PMID: 35880426 PMCID: PMC9487674 DOI: 10.1093/bib/bbac286] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 06/07/2022] [Accepted: 06/23/2022] [Indexed: 12/13/2022] Open
Abstract
Single-cell RNA-sequencing (scRNA-seq) enables researchers to quantify transcriptomes of thousands of cells simultaneously and study transcriptomic changes between cells. scRNA-seq datasets increasingly include multisubject, multicondition experiments to investigate cell-type-specific differential states (DS) between conditions. This can be performed by first identifying the cell types in all the subjects and then by performing a DS analysis between the conditions within each cell type. Naïve single-cell DS analysis methods that treat cells statistically independent are subject to false positives in the presence of variation between biological replicates, an issue known as the pseudoreplicate bias. While several methods have already been introduced to carry out the statistical testing in multisubject scRNA-seq analysis, comparisons that include all these methods are currently lacking. Here, we performed a comprehensive comparison of 18 methods for the identification of DS changes between conditions from multisubject scRNA-seq data. Our results suggest that the pseudobulk methods performed generally best. Both pseudobulks and mixed models that model the subjects as a random effect were superior compared with the naïve single-cell methods that do not model the subjects in any way. While the naïve models achieved higher sensitivity than the pseudobulk methods and the mixed models, they were subject to a high number of false positives. In addition, accounting for subjects through latent variable modeling did not improve the performance of the naïve methods.
Collapse
Affiliation(s)
| | | | - Laura L Elo
- Corresponding author: Laura L. Elo, Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland. Tel.: +358504680795; E-mail:
| |
Collapse
|
11
|
Voigt AP, Mullin NK, Mulfaul K, Lozano LP, Wiley LA, Flamme-Wiese MJ, Boese EA, Han IC, Scheetz TE, Stone EM, Tucker BA, Mullins RF. Choroidal endothelial and macrophage gene expression in atrophic and neovascular macular degeneration. Hum Mol Genet 2022; 31:2406-2423. [PMID: 35181781 PMCID: PMC9307320 DOI: 10.1093/hmg/ddac043] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/22/2022] [Accepted: 02/06/2022] [Indexed: 11/22/2022] Open
Abstract
The human choroid is a heterogeneous, highly vascular connective tissue that dysfunctions in age-related macular degeneration (AMD). In this study, we performed single-cell RNA sequencing on 21 human choroids, 11 of which were derived from donors with early atrophic or neovascular AMD. Using this large donor cohort, we identified new gene expression signatures and immunohistochemically characterized discrete populations of resident macrophages, monocytes/inflammatory macrophages and dendritic cells. These three immune populations demonstrated unique expression patterns for AMD genetic risk factors, with dendritic cells possessing the highest expression of the neovascular AMD-associated MMP9 gene. Additionally, we performed trajectory analysis to model transcriptomic changes across the choroidal vasculature, and we identified expression signatures for endothelial cells from choroidal arterioles and venules. Finally, we performed differential expression analysis between control, early atrophic AMD, and neovascular AMD samples, and we observed that early atrophic AMD samples had high expression of SPARCL1, a gene that has been shown to increase in response to endothelial damage. Likewise, neovascular endothelial cells harbored gene expression changes consistent with endothelial cell damage and demonstrated increased expression of the sialomucins CD34 and ENCM, which were also observed at the protein level within neovascular membranes. Overall, this study characterizes the molecular features of new populations of choroidal endothelial cells and mononuclear phagocytes in a large cohort of AMD and control human donors.
Collapse
Affiliation(s)
- Andrew P Voigt
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
| | - Nathaniel K Mullin
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
| | - Kelly Mulfaul
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
| | - Lola P Lozano
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
| | - Luke A Wiley
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
| | - Miles J Flamme-Wiese
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
| | - Erin A Boese
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
| | - Ian C Han
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
| | - Todd E Scheetz
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
| | - Edwin M Stone
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
| | - Budd A Tucker
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
| | - Robert F Mullins
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
| |
Collapse
|
12
|
Thurman AL, Li X, Villacreses R, Yu W, Gong H, Mather SE, Romano-Ibarra GS, Meyerholz DK, Stoltz DA, Welsh MJ, Thornell IM, Zabner J, Pezzulo AA. A Single-Cell Atlas of Large and Small Airways at Birth in a Porcine Model of Cystic Fibrosis. Am J Respir Cell Mol Biol 2022; 66:612-622. [PMID: 35235762 PMCID: PMC9163647 DOI: 10.1165/rcmb.2021-0499oc] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/26/2022] [Indexed: 11/24/2022] Open
Abstract
Lack of CFTR (cystic fibrosis transmembrane conductance regulator) affects the transcriptome, composition, and function of large and small airway epithelia in people with advanced cystic fibrosis (CF); however, whether lack of CFTR causes cell-intrinsic abnormalities present at birth versus inflammation-dependent abnormalities is unclear. We performed a single-cell RNA-sequencing census of microdissected small airways from newborn CF pigs, which recapitulate CF host defense defects and pathology over time. Lack of CFTR minimally affected the transcriptome of large and small airways at birth, suggesting that infection and inflammation drive transcriptomic abnormalities in advanced CF. Importantly, common small airway epithelial cell types expressed a markedly different transcriptome than corresponding large airway cell types. Quantitative immunohistochemistry and electrophysiology of small airway epithelia demonstrated basal cells that reach the apical surface and a water and ion transport advantage. This single cell atlas highlights the archetypal nature of airway epithelial cells with location-dependent gene expression and function.
Collapse
Affiliation(s)
| | - Xiaopeng Li
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, Michigan
| | | | | | | | | | | | | | - David A. Stoltz
- Department of Internal Medicine
- Pappajohn Biomedical Institute
- Department of Molecular Physiology and Biophysics, and
- Department of Biomedical Engineering, and
| | - Michael J. Welsh
- Department of Internal Medicine
- Pappajohn Biomedical Institute
- Department of Molecular Physiology and Biophysics, and
- Department of Neurology, Roy J. and Lucille A. Carver College of Medicine
- Howard Hughes Medical Institute, University of Iowa, Iowa City, Iowa
| | | | - Joseph Zabner
- Department of Internal Medicine
- Pappajohn Biomedical Institute
| | | |
Collapse
|
13
|
Zhang M, Guo FR. BSDE: barycenter single-cell differential expression for case-control studies. Bioinformatics 2022; 38:2765-2772. [PMID: 35561165 PMCID: PMC9113363 DOI: 10.1093/bioinformatics/btac171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 03/14/2022] [Accepted: 03/23/2022] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Single-cell sequencing brings about a revolutionarily high resolution for finding differentially expressed genes (DEGs) by disentangling highly heterogeneous cell tissues. Yet, such analysis is so far mostly focused on comparing between different cell types from the same individual. As single-cell sequencing becomes cheaper and easier to use, an increasing number of datasets from case-control studies are becoming available, which call for new methods for identifying differential expressions between case and control individuals. RESULTS To bridge this gap, we propose barycenter single-cell differential expression (BSDE), a nonparametric method for finding DEGs for case-control studies. Through the use of optimal transportation for aggregating distributions and computing their distances, our method overcomes the restrictive parametric assumptions imposed by standard mixed-effect-modeling approaches. Through simulations, we show that BSDE can accurately detect a variety of differential expressions while maintaining the type-I error at a prescribed level. Further, 1345 and 1568 cell type-specific DEGs are identified by BSDE from datasets on pulmonary fibrosis and multiple sclerosis, among which the top findings are supported by previous results from the literature. AVAILABILITY AND IMPLEMENTATION R package BSDE is freely available from doi.org/10.5281/zenodo.6332254. For real data analysis with the R package, see doi.org/10.5281/zenodo.6332566. These can also be accessed thorough GitHub at github.com/mqzhanglab/BSDE and github.com/mqzhanglab/BSDE_pipeline. The two single-cell sequencing datasets can be download with UCSC cell browser from cells.ucsc.edu/?ds=ms and cells.ucsc.edu/?ds=lung-pf-control. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Mengqi Zhang
- Department of Surgery, Perelman Medical School, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | |
Collapse
|