1
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Junaid M, Lee EJ, Lim SB. Single-cell and spatial omics: exploring hypothalamic heterogeneity. Neural Regen Res 2025; 20:1525-1540. [PMID: 38993130 DOI: 10.4103/nrr.nrr-d-24-00231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 06/03/2024] [Indexed: 07/13/2024] Open
Abstract
Elucidating the complex dynamic cellular organization in the hypothalamus is critical for understanding its role in coordinating fundamental body functions. Over the past decade, single-cell and spatial omics technologies have significantly evolved, overcoming initial technical challenges in capturing and analyzing individual cells. These high-throughput omics technologies now offer a remarkable opportunity to comprehend the complex spatiotemporal patterns of transcriptional diversity and cell-type characteristics across the entire hypothalamus. Current single-cell and single-nucleus RNA sequencing methods comprehensively quantify gene expression by exploring distinct phenotypes across various subregions of the hypothalamus. However, single-cell/single-nucleus RNA sequencing requires isolating the cell/nuclei from the tissue, potentially resulting in the loss of spatial information concerning neuronal networks. Spatial transcriptomics methods, by bypassing the cell dissociation, can elucidate the intricate spatial organization of neural networks through their imaging and sequencing technologies. In this review, we highlight the applicative value of single-cell and spatial transcriptomics in exploring the complex molecular-genetic diversity of hypothalamic cell types, driven by recent high-throughput achievements.
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Affiliation(s)
- Muhammad Junaid
- Department of Biochemistry & Molecular Biology, Ajou University School of Medicine, Suwon, South Korea
- Department of Biomedical Sciences, Graduate School of Ajou University, Suwon, South Korea
| | - Eun Jeong Lee
- Department of Biomedical Sciences, Graduate School of Ajou University, Suwon, South Korea
- Department of Brain Science, Ajou University School of Medicine, Suwon, South Korea
| | - Su Bin Lim
- Department of Biochemistry & Molecular Biology, Ajou University School of Medicine, Suwon, South Korea
- Department of Biomedical Sciences, Graduate School of Ajou University, Suwon, South Korea
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2
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Borowa A, Rymarczyk D, Żyła M, Kańdula M, Sánchez-Fernández A, Rataj K, Struski Ł, Tabor J, Zieliński B. Decoding phenotypic screening: A comparative analysis of image representations. Comput Struct Biotechnol J 2024; 23:1181-1188. [PMID: 38510976 PMCID: PMC10951426 DOI: 10.1016/j.csbj.2024.02.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 03/22/2024] Open
Abstract
Biomedical imaging techniques such as high content screening (HCS) are valuable for drug discovery, but high costs limit their use to pharmaceutical companies. To address this issue, The JUMP-CP consortium released a massive open image dataset of chemical and genetic perturbations, providing a valuable resource for deep learning research. In this work, we aim to utilize the JUMP-CP dataset to develop a universal representation model for HCS data, mainly data generated using U2OS cells and CellPainting protocol, using supervised and self-supervised learning approaches. We propose an evaluation protocol that assesses their performance on mode of action and property prediction tasks using a popular phenotypic screening dataset. Results show that the self-supervised approach that uses data from multiple consortium partners provides representation that is more robust to batch effects whilst simultaneously achieving performance on par with standard approaches. Together with other conclusions, it provides recommendations on the training strategy of a representation model for HCS images.
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Affiliation(s)
- Adriana Borowa
- Jagiellonian University, Faculty of Mathematics and Computer Science, Kraków, Poland
- Jagiellonian University, Doctoral School of Exact and Natural Sciences, Kraków, Poland
- Ardigen SA, Kraków, Poland
| | - Dawid Rymarczyk
- Jagiellonian University, Faculty of Mathematics and Computer Science, Kraków, Poland
- Ardigen SA, Kraków, Poland
| | | | | | | | | | - Łukasz Struski
- Jagiellonian University, Faculty of Mathematics and Computer Science, Kraków, Poland
| | - Jacek Tabor
- Jagiellonian University, Faculty of Mathematics and Computer Science, Kraków, Poland
| | - Bartosz Zieliński
- Jagiellonian University, Faculty of Mathematics and Computer Science, Kraków, Poland
- Ardigen SA, Kraków, Poland
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3
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Liu Y, Yang C. Computational methods for alignment and integration of spatially resolved transcriptomics data. Comput Struct Biotechnol J 2024; 23:1094-1105. [PMID: 38495555 PMCID: PMC10940867 DOI: 10.1016/j.csbj.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 03/02/2024] [Accepted: 03/04/2024] [Indexed: 03/19/2024] Open
Abstract
Most of the complex biological regulatory activities occur in three dimensions (3D). To better analyze biological processes, it is essential not only to decipher the molecular information of numerous cells but also to understand how their spatial contexts influence their behavior. With the development of spatially resolved transcriptomics (SRT) technologies, SRT datasets are being generated to simultaneously characterize gene expression and spatial arrangement information within tissues, organs or organisms. To fully leverage spatial information, the focus extends beyond individual two-dimensional (2D) slices. Two tasks known as slices alignment and data integration have been introduced to establish correlations between multiple slices, enhancing the effectiveness of downstream tasks. Currently, numerous related methods have been developed. In this review, we first elucidate the details and principles behind several representative methods. Then we report the testing results of these methods on various SRT datasets, and assess their performance in representative downstream tasks. Insights into the strengths and weaknesses of each method and the reasons behind their performance are discussed. Finally, we provide an outlook on future developments. The codes and details of experiments are now publicly available at https://github.com/YangLabHKUST/SRT_alignment_and_integration.
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Affiliation(s)
- Yuyao Liu
- Department of Automation, School of Information Science and Technology, Tsinghua University, Beijing, China
| | - Can Yang
- Department of Mathematics, The Hong Kong University of Science and Technology, Hong Kong, China
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4
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Rachid Zaim S, Pebworth MP, McGrath I, Okada L, Weiss M, Reading J, Czartoski JL, Torgerson TR, McElrath MJ, Bumol TF, Skene PJ, Li XJ. MOCHA's advanced statistical modeling of scATAC-seq data enables functional genomic inference in large human cohorts. Nat Commun 2024; 15:6828. [PMID: 39122670 PMCID: PMC11316085 DOI: 10.1038/s41467-024-50612-6] [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: 07/04/2023] [Accepted: 07/13/2024] [Indexed: 08/12/2024] Open
Abstract
Single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) is being increasingly used to study gene regulation. However, major analytical gaps limit its utility in studying gene regulatory programs in complex diseases. In response, MOCHA (Model-based single cell Open CHromatin Analysis) presents major advances over existing analysis tools, including: 1) improving identification of sample-specific open chromatin, 2) statistical modeling of technical drop-out with zero-inflated methods, 3) mitigation of false positives in single cell analysis, 4) identification of alternative transcription-starting-site regulation, and 5) modules for inferring temporal gene regulatory networks from longitudinal data. These advances, in addition to open chromatin analyses, provide a robust framework after quality control and cell labeling to study gene regulatory programs in human disease. We benchmark MOCHA with four state-of-the-art tools to demonstrate its advances. We also construct cross-sectional and longitudinal gene regulatory networks, identifying potential mechanisms of COVID-19 response. MOCHA provides researchers with a robust analytical tool for functional genomic inference from scATAC-seq data.
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Affiliation(s)
| | | | | | - Lauren Okada
- Allen Institute for Immunology, Seattle, WA, USA
| | - Morgan Weiss
- Allen Institute for Immunology, Seattle, WA, USA
| | | | - Julie L Czartoski
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | | | - Xiao-Jun Li
- Allen Institute for Immunology, Seattle, WA, USA.
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5
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Nabi IR, Cardoen B, Khater IM, Gao G, Wong TH, Hamarneh G. AI analysis of super-resolution microscopy: Biological discovery in the absence of ground truth. J Cell Biol 2024; 223:e202311073. [PMID: 38865088 PMCID: PMC11169916 DOI: 10.1083/jcb.202311073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 04/02/2024] [Accepted: 05/21/2024] [Indexed: 06/13/2024] Open
Abstract
Super-resolution microscopy, or nanoscopy, enables the use of fluorescent-based molecular localization tools to study molecular structure at the nanoscale level in the intact cell, bridging the mesoscale gap to classical structural biology methodologies. Analysis of super-resolution data by artificial intelligence (AI), such as machine learning, offers tremendous potential for the discovery of new biology, that, by definition, is not known and lacks ground truth. Herein, we describe the application of weakly supervised paradigms to super-resolution microscopy and its potential to enable the accelerated exploration of the nanoscale architecture of subcellular macromolecules and organelles.
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Affiliation(s)
- Ivan R. Nabi
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, Canada
| | - Ben Cardoen
- School of Computing Science, Simon Fraser University, Burnaby, Canada
| | - Ismail M. Khater
- School of Computing Science, Simon Fraser University, Burnaby, Canada
- Department of Electrical and Computer Engineering, Faculty of Engineering and Technology, Birzeit University, Birzeit, Palestine
| | - Guang Gao
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Timothy H. Wong
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Ghassan Hamarneh
- School of Computing Science, Simon Fraser University, Burnaby, Canada
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6
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Fischer F, Fischer DS, Mukhin R, Isaev A, Biederstedt E, Villani AC, Theis FJ. scTab: Scaling cross-tissue single-cell annotation models. Nat Commun 2024; 15:6611. [PMID: 39098889 PMCID: PMC11298532 DOI: 10.1038/s41467-024-51059-5] [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: 11/26/2023] [Accepted: 07/25/2024] [Indexed: 08/06/2024] Open
Abstract
Identifying cellular identities is a key use case in single-cell transcriptomics. While machine learning has been leveraged to automate cell annotation predictions for some time, there has been little progress in scaling neural networks to large data sets and in constructing models that generalize well across diverse tissues. Here, we propose scTab, an automated cell type prediction model specific to tabular data, and train it using a novel data augmentation scheme across a large corpus of single-cell RNA-seq observations (22.2 million cells). In this context, we show that cross-tissue annotation requires nonlinear models and that the performance of scTab scales both in terms of training dataset size and model size. Additionally, we show that the proposed data augmentation schema improves model generalization. In summary, we introduce a de novo cell type prediction model for single-cell RNA-seq data that can be trained across a large-scale collection of curated datasets and demonstrate the benefits of using deep learning methods in this paradigm.
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Affiliation(s)
- Felix Fischer
- Department of Computational Health, Institute of Computational Biology, Helmholtz, Munich, Germany
- School of Computing, Information and Technology, Technical University of Munich, Munich, Germany
| | - David S Fischer
- Department of Computational Health, Institute of Computational Biology, Helmholtz, Munich, Germany
- Eric and Wendy Schmidt Center, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | | | | | - Evan Biederstedt
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA, 02129, USA
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Alexandra-Chloé Villani
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA, 02129, USA
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Fabian J Theis
- Department of Computational Health, Institute of Computational Biology, Helmholtz, Munich, Germany.
- School of Computing, Information and Technology, Technical University of Munich, Munich, Germany.
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany.
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7
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Wang S, Li H, Liu Y, Pang S, Qiao S, Su J, Wang S, Zhang Y. Connectivity Network Feature Sharing in Single-Cell RNA Sequencing Data Identifies Rare Cells. J Chem Inf Model 2024. [PMID: 39096508 DOI: 10.1021/acs.jcim.4c00796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2024]
Abstract
Single-cell RNA sequencing is a valuable technique for identifying diverse cell subtypes. A key challenge in this process is that the detection of rare cells is often missed by conventional methods due to low abundance and subtle features of these cells. To overcome this, we developed SCLCNF (Local Connectivity Network Feature Sharing in Single-Cell RNA sequencing), a novel approach that identifies rare cells by analyzing features uniquely expressed in these cells. SCLCNF creates a cellular connectivity network, considering how each cell relates to its neighbors. This network helps to pinpoint coexpression patterns unique to rare cells, utilizing a rarity score to confirm their presence. Our method performs better in detecting rare cells than existing techniques, offering enhanced robustness. It has proven to be effective in human gastrula data sets for accurately pinpointing rare cells, and in sepsis data sets where it uncovers previously unidentified rare cell populations.
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Affiliation(s)
- Shudong Wang
- Qingdao Institute of Software, College of Computer Science and Technology, China University of Petroleum (East China), Qingdao 266580, China
| | - Hengxiao Li
- Qingdao Institute of Software, College of Computer Science and Technology, China University of Petroleum (East China), Qingdao 266580, China
| | - Yahui Liu
- College of Science, China University of Petroleum (East China), Qingdao 266580, China
| | - Shanchen Pang
- Qingdao Institute of Software, College of Computer Science and Technology, China University of Petroleum (East China), Qingdao 266580, China
| | - Sibo Qiao
- The College of Software, Tiangong University, Tianjin 300387, China
| | - Jionglong Su
- School of AI and Advanced Computing, XJTLU Entrepreneur College (Taicang), Xi'an Jiaotong-Liverpool University, Suzhou 215123, Jiangsu, China
| | - Shaoqiang Wang
- School of Information and Control Engineering, Qingdao University of Technology, Qingdao 266525, China
| | - Yulin Zhang
- College of Mathematics and Systems Science, Shandong University of Science and Technology, Qingdao 266590, China
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8
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Madrigal A, Lu T, Soto LM, Najafabadi HS. A unified model for interpretable latent embedding of multi-sample, multi-condition single-cell data. Nat Commun 2024; 15:6573. [PMID: 39097589 PMCID: PMC11298001 DOI: 10.1038/s41467-024-50963-0] [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: 09/03/2023] [Accepted: 07/23/2024] [Indexed: 08/05/2024] Open
Abstract
Single-cell analysis across multiple samples and conditions requires quantitative modeling of the interplay between the continuum of cell states and the technical and biological sources of sample-to-sample variability. We introduce GEDI, a generative model that identifies latent space variations in multi-sample, multi-condition single-cell datasets and attributes them to sample-level covariates. GEDI enables cross-sample cell state mapping on par with state-of-the-art integration methods, cluster-free differential gene expression analysis along the continuum of cell states, and machine learning-based prediction of sample characteristics from single-cell data. GEDI can also incorporate gene-level prior knowledge to infer pathway and regulatory network activities in single cells. Finally, GEDI extends all these concepts to previously unexplored modalities that require joint consideration of dual measurements, such as the joint analysis of exon inclusion/exclusion reads to model alternative cassette exon splicing, or spliced/unspliced reads to model the mRNA stability landscapes of single cells.
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Affiliation(s)
- Ariel Madrigal
- Department of Human Genetics, McGill University, Montreal, QC, H3A 0C7, Canada
- Victor P. Dahdaleh Institute of Genomic Medicine, Montreal, QC, H3A 0G1, Canada
| | - Tianyuan Lu
- Lady Davis Institute for Medical Research, Montreal, QC, H3T 1E2, Canada
- Department of Statistical Sciences, University of Toronto, Toronto, ON, M5S 1A1, Canada
- Department of Population Health Sciences, University of Wisconsin-Madison, Madison, WI, 53726, USA
| | - Larisa M Soto
- Department of Human Genetics, McGill University, Montreal, QC, H3A 0C7, Canada
- Victor P. Dahdaleh Institute of Genomic Medicine, Montreal, QC, H3A 0G1, Canada
| | - Hamed S Najafabadi
- Department of Human Genetics, McGill University, Montreal, QC, H3A 0C7, Canada.
- Victor P. Dahdaleh Institute of Genomic Medicine, Montreal, QC, H3A 0G1, Canada.
- McGill Centre for RNA Sciences, McGill University, Montreal, Canada.
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9
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Bhayana S, Schytz PA, Bisgaard Olesen ET, Soh K, Das V. Single-Cell Advances in Investigating and Understanding Chronic Kidney Disease and Diabetic Kidney Disease. THE AMERICAN JOURNAL OF PATHOLOGY 2024:S0002-9440(24)00273-6. [PMID: 39097167 DOI: 10.1016/j.ajpath.2024.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/04/2024] [Accepted: 07/09/2024] [Indexed: 08/05/2024]
Abstract
Chronic kidney disease (CKD) and its subset diabetic kidney disease are progressive conditions that affect >850 million people worldwide. Diabetes, hypertension, and glomerulonephritis are the most common causes of CKD, which is associated with significant patient morbidity and an increased risk of cardiovascular events, such as heart failure, ultimately leading to premature death. Despite newly approved drugs, increasing evidence shows that patients respond to treatment differently given the complexity of disease heterogeneity and complicated pathophysiology. This review article presents an integrative approach to understanding and addressing CKD through the lens of precision medicine and therapeutics. Leveraging advancements in single-cell omics technologies and artificial intelligence, we can explore the intricate cellular mechanisms underlying CKD and diabetic kidney disease pathogenesis. By dissecting the cellular heterogeneity and identifying rare cell populations using single-cell approaches, it will be possible to uncover novel therapeutic targets and biomarkers for personalized treatment strategies. Finally, we discuss the potential of artificial intelligence-driven analyses in predicting disease progression and treatment response, thereby paving the way for tailored interventions.
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Affiliation(s)
- Sagar Bhayana
- Kidney Biology, Global Drug Development, Novo Nordisk A/S, Denmark
| | - Philip Andreas Schytz
- Cardiovascular, Kidney and Alzheimer Disease, Medical and Science, Novo Nordisk A/S, Denmark
| | | | - Keng Soh
- Integrated Omics, AI and Analytics, Development, Novo Nordisk A/S, Denmark
| | - Vivek Das
- Integrated Omics, AI and Analytics, Development, Novo Nordisk A/S, Denmark.
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10
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Arevalo J, Su E, Ewald JD, van Dijk R, Carpenter AE, Singh S. Evaluating batch correction methods for image-based cell profiling. Nat Commun 2024; 15:6516. [PMID: 39095341 PMCID: PMC11297288 DOI: 10.1038/s41467-024-50613-5] [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: 08/29/2023] [Accepted: 07/13/2024] [Indexed: 08/04/2024] Open
Abstract
High-throughput image-based profiling platforms are powerful technologies capable of collecting data from billions of cells exposed to thousands of perturbations in a time- and cost-effective manner. Therefore, image-based profiling data has been increasingly used for diverse biological applications, such as predicting drug mechanism of action or gene function. However, batch effects severely limit community-wide efforts to integrate and interpret image-based profiling data collected across different laboratories and equipment. To address this problem, we benchmark ten high-performing single-cell RNA sequencing (scRNA-seq) batch correction techniques, representing diverse approaches, using a newly released Cell Painting dataset, JUMP. We focus on five scenarios with varying complexity, ranging from batches prepared in a single lab over time to batches imaged using different microscopes in multiple labs. We find that Harmony and Seurat RPCA are noteworthy, consistently ranking among the top three methods for all tested scenarios while maintaining computational efficiency. Our proposed framework, benchmark, and metrics can be used to assess new batch correction methods in the future. This work paves the way for improvements that enable the community to make the best use of public Cell Painting data for scientific discovery.
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Affiliation(s)
- John Arevalo
- Imaging Platform, Broad Institute of MIT and Harvard, 02142, Cambridge, MA, USA
| | - Ellen Su
- Imaging Platform, Broad Institute of MIT and Harvard, 02142, Cambridge, MA, USA
| | - Jessica D Ewald
- Imaging Platform, Broad Institute of MIT and Harvard, 02142, Cambridge, MA, USA
| | - Robert van Dijk
- Imaging Platform, Broad Institute of MIT and Harvard, 02142, Cambridge, MA, USA
| | - Anne E Carpenter
- Imaging Platform, Broad Institute of MIT and Harvard, 02142, Cambridge, MA, USA
| | - Shantanu Singh
- Imaging Platform, Broad Institute of MIT and Harvard, 02142, Cambridge, MA, USA.
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11
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Li MM, Huang Y, Sumathipala M, Liang MQ, Valdeolivas A, Ananthakrishnan AN, Liao K, Marbach D, Zitnik M. Contextual AI models for single-cell protein biology. Nat Methods 2024; 21:1546-1557. [PMID: 39039335 PMCID: PMC11310085 DOI: 10.1038/s41592-024-02341-3] [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: 08/17/2023] [Accepted: 06/10/2024] [Indexed: 07/24/2024]
Abstract
Understanding protein function and developing molecular therapies require deciphering the cell types in which proteins act as well as the interactions between proteins. However, modeling protein interactions across biological contexts remains challenging for existing algorithms. Here we introduce PINNACLE, a geometric deep learning approach that generates context-aware protein representations. Leveraging a multiorgan single-cell atlas, PINNACLE learns on contextualized protein interaction networks to produce 394,760 protein representations from 156 cell type contexts across 24 tissues. PINNACLE's embedding space reflects cellular and tissue organization, enabling zero-shot retrieval of the tissue hierarchy. Pretrained protein representations can be adapted for downstream tasks: enhancing 3D structure-based representations for resolving immuno-oncological protein interactions, and investigating drugs' effects across cell types. PINNACLE outperforms state-of-the-art models in nominating therapeutic targets for rheumatoid arthritis and inflammatory bowel diseases and pinpoints cell type contexts with higher predictive capability than context-free models. PINNACLE's ability to adjust its outputs on the basis of the context in which it operates paves the way for large-scale context-specific predictions in biology.
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Affiliation(s)
- Michelle M Li
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Yepeng Huang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Marissa Sumathipala
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Man Qing Liang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Alberto Valdeolivas
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Ashwin N Ananthakrishnan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Katherine Liao
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Boston, MA, USA
| | - Daniel Marbach
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Marinka Zitnik
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Kempner Institute for the Study of Natural and Artificial Intelligence, Harvard University, Allston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Data Science Initiative, Cambridge, MA, USA.
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12
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Rosen Y, Brbić M, Roohani Y, Swanson K, Li Z, Leskovec J. Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN. Nat Methods 2024; 21:1492-1500. [PMID: 38366243 PMCID: PMC11310084 DOI: 10.1038/s41592-024-02191-z] [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: 02/03/2023] [Accepted: 01/22/2024] [Indexed: 02/18/2024]
Abstract
Analysis of single-cell datasets generated from diverse organisms offers unprecedented opportunities to unravel fundamental evolutionary processes of conservation and diversification of cell types. However, interspecies genomic differences limit the joint analysis of cross-species datasets to homologous genes. Here we present SATURN, a deep learning method for learning universal cell embeddings that encodes genes' biological properties using protein language models. By coupling protein embeddings from language models with RNA expression, SATURN integrates datasets profiled from different species regardless of their genomic similarity. SATURN can detect functionally related genes coexpressed across species, redefining differential expression for cross-species analysis. Applying SATURN to three species whole-organism atlases and frog and zebrafish embryogenesis datasets, we show that SATURN can effectively transfer annotations across species, even when they are evolutionarily remote. We also demonstrate that SATURN can be used to find potentially divergent gene functions between glaucoma-associated genes in humans and four other species.
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Affiliation(s)
- Yanay Rosen
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Maria Brbić
- School of Computer and Communication Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Yusuf Roohani
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Kyle Swanson
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Ziang Li
- Department of Computer Science and Technology, Tsinghua University, Beijing, China
| | - Jure Leskovec
- Department of Computer Science, Stanford University, Stanford, CA, USA.
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13
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Szałata A, Hrovatin K, Becker S, Tejada-Lapuerta A, Cui H, Wang B, Theis FJ. Transformers in single-cell omics: a review and new perspectives. Nat Methods 2024; 21:1430-1443. [PMID: 39122952 DOI: 10.1038/s41592-024-02353-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 06/07/2024] [Indexed: 08/12/2024]
Abstract
Recent efforts to construct reference maps of cellular phenotypes have expanded the volume and diversity of single-cell omics data, providing an unprecedented resource for studying cell properties. Despite the availability of rich datasets and their continued growth, current single-cell models are unable to fully capitalize on the information they contain. Transformers have become the architecture of choice for foundation models in other domains owing to their ability to generalize to heterogeneous, large-scale datasets. Thus, the question arises of whether transformers could set off a similar shift in the field of single-cell modeling. Here we first describe the transformer architecture and its single-cell adaptations and then present a comprehensive review of the existing applications of transformers in single-cell analysis and critically discuss their future potential for single-cell biology. By studying limitations and technical challenges, we aim to provide a structured outlook for future research directions at the intersection of machine learning and single-cell biology.
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Affiliation(s)
- Artur Szałata
- Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- School of Computing, Information and Technology, Technical University of Munich, Munich, Germany
| | - Karin Hrovatin
- Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Sören Becker
- Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- School of Computing, Information and Technology, Technical University of Munich, Munich, Germany
- Munich Center of Machine Learning, Munich, Germany
| | - Alejandro Tejada-Lapuerta
- Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- School of Computing, Information and Technology, Technical University of Munich, Munich, Germany
| | - Haotian Cui
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Vector Institute for Artificial Intelligence, Toronto, Ontario, Canada
- Peter Munk Cardiac Center, University Health Network, Toronto, Ontario, Canada
| | - Bo Wang
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Vector Institute for Artificial Intelligence, Toronto, Ontario, Canada
- Peter Munk Cardiac Center, University Health Network, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- AI Hub, University Health Network, Toronto, Ontario, Canada
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
- School of Computing, Information and Technology, Technical University of Munich, Munich, Germany.
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany.
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14
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Qin L, Zhang G, Zhang S, Chen Y. Deep Batch Integration and Denoise of Single-Cell RNA-Seq Data. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308934. [PMID: 38778573 PMCID: PMC11304254 DOI: 10.1002/advs.202308934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 03/14/2024] [Indexed: 05/25/2024]
Abstract
Numerous single-cell transcriptomic datasets from identical tissues or cell lines are generated from different laboratories or single-cell RNA sequencing (scRNA-seq) protocols. The denoising of these datasets to eliminate batch effects is crucial for data integration, ensuring accurate interpretation and comprehensive analysis of biological questions. Although many scRNA-seq data integration methods exist, most are inefficient and/or not conducive to downstream analysis. Here, DeepBID, a novel deep learning-based method for batch effect correction, non-linear dimensionality reduction, embedding, and cell clustering concurrently, is introduced. DeepBID utilizes a negative binomial-based autoencoder with dual Kullback-Leibler divergence loss functions, aligning cell points from different batches within a consistent low-dimensional latent space and progressively mitigating batch effects through iterative clustering. Extensive validation on multiple-batch scRNA-seq datasets demonstrates that DeepBID surpasses existing tools in removing batch effects and achieving superior clustering accuracy. When integrating multiple scRNA-seq datasets from patients with Alzheimer's disease, DeepBID significantly improves cell clustering, effectively annotating unidentified cells, and detecting cell-specific differentially expressed genes.
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Affiliation(s)
- Lu Qin
- College of Computer and Information EngineeringTianjin Normal UniversityTianjin300387China
| | - Guangya Zhang
- College of Computer and Information EngineeringTianjin Normal UniversityTianjin300387China
| | - Shaoqiang Zhang
- College of Computer and Information EngineeringTianjin Normal UniversityTianjin300387China
| | - Yong Chen
- Department of Biological and Biomedical SciencesRowan UniversityNJ08028USA
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15
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Hozumi Y, Wei GW. Analyzing Single Cell RNA Sequencing with Topological Nonnegative Matrix Factorization. JOURNAL OF COMPUTATIONAL AND APPLIED MATHEMATICS 2024; 445:115842. [PMID: 38464901 PMCID: PMC10919214 DOI: 10.1016/j.cam.2024.115842] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Single-cell RNA sequencing (scRNA-seq) is a relatively new technology that has stimulated enormous interest in statistics, data science, and computational biology due to the high dimensionality, complexity, and large scale associated with scRNA-seq data. Nonnegative matrix factorization (NMF) offers a unique approach due to its meta-gene interpretation of resulting low-dimensional components. However, NMF approaches suffer from the lack of multiscale analysis. This work introduces two persistent Laplacian regularized NMF methods, namely, topological NMF (TNMF) and robust topological NMF (rTNMF). By employing a total of 12 datasets, we demonstrate that the proposed TNMF and rTNMF significantly outperform all other NMF-based methods. We have also utilized TNMF and rTNMF for the visualization of popular Uniform Manifold Approximation and Projection (UMAP) and t -distributed stochastic neighbor embedding (t -SNE).
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Affiliation(s)
- Yuta Hozumi
- Department of Mathematics, Michigan State University, East Lansing, MI 48824, USA
| | - Guo-Wei Wei
- Department of Mathematics, Michigan State University, East Lansing, MI 48824, USA
- Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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16
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Hao M, Gong J, Zeng X, Liu C, Guo Y, Cheng X, Wang T, Ma J, Zhang X, Song L. Large-scale foundation model on single-cell transcriptomics. Nat Methods 2024; 21:1481-1491. [PMID: 38844628 DOI: 10.1038/s41592-024-02305-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 05/10/2024] [Indexed: 08/10/2024]
Abstract
Large pretrained models have become foundation models leading to breakthroughs in natural language processing and related fields. Developing foundation models for deciphering the 'languages' of cells and facilitating biomedical research is promising yet challenging. Here we developed a large pretrained model scFoundation, also named 'xTrimoscFoundationα', with 100 million parameters covering about 20,000 genes, pretrained on over 50 million human single-cell transcriptomic profiles. scFoundation is a large-scale model in terms of the size of trainable parameters, dimensionality of genes and volume of training data. Its asymmetric transformer-like architecture and pretraining task design empower effectively capturing complex context relations among genes in a variety of cell types and states. Experiments showed its merit as a foundation model that achieved state-of-the-art performances in a diverse array of single-cell analysis tasks such as gene expression enhancement, tissue drug response prediction, single-cell drug response classification, single-cell perturbation prediction, cell type annotation and gene module inference.
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Affiliation(s)
- Minsheng Hao
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, Beijing, China
- BioMap, Beijing, China
| | | | | | | | | | | | | | - Jianzhu Ma
- Department of Electrical Engineering, Tsinghua University, Beijing, China.
- Institute for AI Industry Research, Tsinghua University, Beijing, China.
| | - Xuegong Zhang
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, Beijing, China.
- School of Life Sciences and School of Medicine, Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China.
| | - Le Song
- BioMap, Beijing, China.
- Mohamed bin Zayed University of Artificial Intelligence, Abu Dhabi, UAE.
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17
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Kapetanou E, Malamas S, Leventis D, Karantanas AH, Klontzas ME. Developing a Radiomics Atlas Dataset of normal Abdominal and Pelvic computed Tomography (RADAPT). JOURNAL OF IMAGING INFORMATICS IN MEDICINE 2024; 37:1273-1281. [PMID: 38383807 PMCID: PMC11300734 DOI: 10.1007/s10278-024-01028-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/13/2024] [Accepted: 01/17/2024] [Indexed: 02/23/2024]
Abstract
Atlases of normal genomics, transcriptomics, proteomics, and metabolomics have been published in an attempt to understand the biological phenotype in health and disease and to set the basis of comprehensive comparative omics studies. No such atlas exists for radiomics data. The purpose of this study was to systematically create a radiomics dataset of normal abdominal and pelvic radiomics that can be used for model development and validation. Young adults without any previously known disease, aged > 17 and ≤ 36 years old, were retrospectively included. All patients had undergone CT scanning for emergency indications. In case abnormal findings were identified, the relevant anatomical structures were excluded. Deep learning was used to automatically segment the majority of visible anatomical structures with the TotalSegmentator model as applied in 3DSlicer. Radiomics features including first order, texture, wavelet, and Laplacian of Gaussian transformed features were extracted with PyRadiomics. A Github repository was created to host the resulting dataset. Radiomics data were extracted from a total of 531 patients with a mean age of 26.8 ± 5.19 years, including 250 female and 281 male patients. A maximum of 53 anatomical structures were segmented and used for subsequent radiomics data extraction. Radiomics features were derived from a total of 526 non-contrast and 400 contrast-enhanced (portal venous) series. The dataset is publicly available for model development and validation purposes.
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Affiliation(s)
- Elisavet Kapetanou
- Biomedical Engineering Graduate Programme, School of Medicine, University of Crete, Heraklion, Greece
- Department of Radiology, School of Medicine, University of Crete, Heraklion, Greece
| | - Stylianos Malamas
- Department of Computer Science-University of Crete, Heraklion, Greece
| | - Dimitrios Leventis
- Department of Medical Imaging, University Hospital of Heraklion, Crete, Greece
- Department of Radiology, School of Medicine, University of Crete, Heraklion, Greece
| | - Apostolos H Karantanas
- Department of Medical Imaging, University Hospital of Heraklion, Crete, Greece
- Department of Radiology, School of Medicine, University of Crete, Heraklion, Greece
- Computational Biomedicine Laboratory, Institute of Computer Science, Foundation for Research and Technology (FORTH), Heraklion, Crete, Greece
| | - Michail E Klontzas
- Department of Medical Imaging, University Hospital of Heraklion, Crete, Greece.
- Department of Radiology, School of Medicine, University of Crete, Heraklion, Greece.
- Computational Biomedicine Laboratory, Institute of Computer Science, Foundation for Research and Technology (FORTH), Heraklion, Crete, Greece.
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18
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Cui H, Wang C, Maan H, Pang K, Luo F, Duan N, Wang B. scGPT: toward building a foundation model for single-cell multi-omics using generative AI. Nat Methods 2024; 21:1470-1480. [PMID: 38409223 DOI: 10.1038/s41592-024-02201-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 01/30/2024] [Indexed: 02/28/2024]
Abstract
Generative pretrained models have achieved remarkable success in various domains such as language and computer vision. Specifically, the combination of large-scale diverse datasets and pretrained transformers has emerged as a promising approach for developing foundation models. Drawing parallels between language and cellular biology (in which texts comprise words; similarly, cells are defined by genes), our study probes the applicability of foundation models to advance cellular biology and genetic research. Using burgeoning single-cell sequencing data, we have constructed a foundation model for single-cell biology, scGPT, based on a generative pretrained transformer across a repository of over 33 million cells. Our findings illustrate that scGPT effectively distills critical biological insights concerning genes and cells. Through further adaptation of transfer learning, scGPT can be optimized to achieve superior performance across diverse downstream applications. This includes tasks such as cell type annotation, multi-batch integration, multi-omic integration, perturbation response prediction and gene network inference.
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Affiliation(s)
- Haotian Cui
- Peter Munk Cardiac Centre, University Health Network, Toronto, Ontartio, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
| | - Chloe Wang
- Peter Munk Cardiac Centre, University Health Network, Toronto, Ontartio, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
| | - Hassaan Maan
- Peter Munk Cardiac Centre, University Health Network, Toronto, Ontartio, Canada
- Vector Institute, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Kuan Pang
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
| | - Fengning Luo
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
| | - Nan Duan
- Microsoft Research, Redmond, WA, USA
| | - Bo Wang
- Peter Munk Cardiac Centre, University Health Network, Toronto, Ontartio, Canada.
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.
- Vector Institute, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
- AI Hub, University Health Network, Toronto, Ontario, Canada.
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19
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Hie BL, Kim S, Rando TA, Bryson B, Berger B. Scanorama: integrating large and diverse single-cell transcriptomic datasets. Nat Protoc 2024; 19:2283-2297. [PMID: 38844552 DOI: 10.1038/s41596-024-00991-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 01/11/2024] [Indexed: 08/07/2024]
Abstract
Merging diverse single-cell RNA sequencing (scRNA-seq) data from numerous experiments, laboratories and technologies can uncover important biological insights. Nonetheless, integrating scRNA-seq data encounters special challenges when the datasets are composed of diverse cell type compositions. Scanorama offers a robust solution for improving the quality and interpretation of heterogeneous scRNA-seq data by effectively merging information from diverse sources. Scanorama is designed to address the technical variation introduced by differences in sample preparation, sequencing depth and experimental batches that can confound the analysis of multiple scRNA-seq datasets. Here we provide a detailed protocol for using Scanorama within a Scanpy-based single-cell analysis workflow coupled with Google Colaboratory, a cloud-based free Jupyter notebook environment service. The protocol involves Scanorama integration, a process that typically spans 0.5-3 h. Scanorama integration requires a basic understanding of cellular biology, transcriptomic technologies and bioinformatics. Our protocol and new Scanorama-Colaboratory resource should make scRNA-seq integration more widely accessible to researchers.
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Affiliation(s)
- Brian L Hie
- Department of Chemical Engineering, Stanford University School, Stanford, CA, USA.
- Stanford Data Science, Stanford University, Stanford, CA, USA.
- Arc Institute, Palo Alto, CA, USA.
| | - Soochi Kim
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Thomas A Rando
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
- Department of Neurology, UCLA, Los Angeles, CA, USA
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, USA
| | - Bryan Bryson
- Department of Biological Engineering, MIT, Cambridge, MA, USA.
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA.
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA.
- Department of Mathematics, MIT, Cambridge, MA, USA.
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20
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Netskar H, Pfefferle A, Goodridge JP, Sohlberg E, Dufva O, Teichmann SA, Brownlie D, Michaëlsson J, Marquardt N, Clancy T, Horowitz A, Malmberg KJ. Pan-cancer profiling of tumor-infiltrating natural killer cells through transcriptional reference mapping. Nat Immunol 2024; 25:1445-1459. [PMID: 38956379 PMCID: PMC11291284 DOI: 10.1038/s41590-024-01884-z] [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: 10/25/2023] [Accepted: 05/30/2024] [Indexed: 07/04/2024]
Abstract
The functional diversity of natural killer (NK) cell repertoires stems from differentiation, homeostatic, receptor-ligand interactions and adaptive-like responses to viral infections. In the present study, we generated a single-cell transcriptional reference map of healthy human blood- and tissue-derived NK cells, with temporal resolution and fate-specific expression of gene-regulatory networks defining NK cell differentiation. Transfer learning facilitated incorporation of tumor-infiltrating NK cell transcriptomes (39 datasets, 7 solid tumors, 427 patients) into the reference map to analyze tumor microenvironment (TME)-induced perturbations. Of the six functionally distinct NK cell states identified, a dysfunctional stressed CD56bright state susceptible to TME-induced immunosuppression and a cytotoxic TME-resistant effector CD56dim state were commonly enriched across tumor types, the ratio of which was predictive of patient outcome in malignant melanoma and osteosarcoma. This resource may inform the design of new NK cell therapies and can be extended through transfer learning to interrogate new datasets from experimental perturbations or disease conditions.
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Affiliation(s)
- Herman Netskar
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Precision Immunotherapy Alliance, University of Oslo, Oslo, Norway
| | - Aline Pfefferle
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden.
| | | | - Ebba Sohlberg
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Olli Dufva
- Wellcome Sanger Institute, Wellcome Genome Clymphoid cells (ILCs)ampus, Hinxton, Cambridge, UK
| | - Sarah A Teichmann
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Demi Brownlie
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Huddinge, Sweden
| | - Jakob Michaëlsson
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Nicole Marquardt
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Huddinge, Sweden
| | - Trevor Clancy
- Oslo Cancer Cluster, NEC OncoImmunity AS, Oslo, Norway
- Department of Vaccine Informatics, Institute for Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Amir Horowitz
- Department of Immunology & Immunotherapy, Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Karl-Johan Malmberg
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.
- Precision Immunotherapy Alliance, University of Oslo, Oslo, Norway.
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden.
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21
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Lotfollahi M. Toward learning a foundational representation of cells and genes. Nat Methods 2024; 21:1416-1417. [PMID: 39122939 DOI: 10.1038/s41592-024-02367-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2024]
Affiliation(s)
- Mohammad Lotfollahi
- Wellcome Trust Sanger Institute, Cambridge, UK.
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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22
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Kim GD, Lim C, Park J. A practical handbook on single-cell RNA sequencing data quality control and downstream analysis. Mol Cells 2024:100103. [PMID: 39094968 DOI: 10.1016/j.mocell.2024.100103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 07/19/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024] Open
Abstract
Advancements in single-cell analysis have facilitated high-resolution observation of the transcriptome in individual cells. However, standards for obtaining high-quality cells and data analysis pipeline remain variable. Here, we provide the groundwork for improving the quality of single-cell analysis by delineating guidelines for selecting high-quality cells and considerations throughout the analysis. This review will streamline researchers' access to single-cell analysis and serve as a valuable guide for analysis.
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Affiliation(s)
- Gyeong Dae Kim
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Chaemin Lim
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Jihwan Park
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea.
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23
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Ramirez A, Orcutt-Jahns BT, Pascoe S, Abraham A, Remigio B, Thomas N, Meyer AS. Integrative, high-resolution analysis of single cells across experimental conditions with PARAFAC2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.29.605698. [PMID: 39131377 PMCID: PMC11312543 DOI: 10.1101/2024.07.29.605698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Effective tools for exploration and analysis are needed to extract insights from large-scale single-cell measurement data. However, current techniques for handling single-cell studies performed across experimental conditions (e.g., samples, perturbations, or patients) require restrictive assumptions, lack flexibility, or do not adequately deconvolute condition-to-condition variation from cell-to-cell variation. Here, we report that the tensor decomposition method PARAFAC2 (Pf2) enables the dimensionality reduction of single-cell data across conditions. We demonstrate these benefits across two distinct contexts of single-cell RNA-sequencing (scRNA-seq) experiments of peripheral immune cells: pharmacologic drug perturbations and systemic lupus erythematosus (SLE) patient samples. By isolating relevant gene modules across cells and conditions, Pf2 enables straightforward associations of gene variation patterns across specific patients or perturbations while connecting each coordinated change to certain cells without pre-defining cell types. The theoretical grounding of Pf2 suggests a unified framework for many modeling tasks associated with single-cell data. Thus, Pf2 provides an intuitive universal dimensionality reduction approach for multi-sample single-cell studies across diverse biological contexts. Highlights PARAFAC2 enables tensor-based analysis of single-cell experiments across conditions.PARAFAC2 separates condition-specific effects from cell-to-cell variation.PARAFAC2 provides intuitive isolation of patterns into condition-, cell-, and gene-specific patterns.
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24
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Yang X, Mann KK, Wu H, Ding J. scCross: a deep generative model for unifying single-cell multi-omics with seamless integration, cross-modal generation, and in silico exploration. Genome Biol 2024; 25:198. [PMID: 39075536 PMCID: PMC11285326 DOI: 10.1186/s13059-024-03338-z] [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: 12/15/2023] [Accepted: 07/16/2024] [Indexed: 07/31/2024] Open
Abstract
Single-cell multi-omics data reveal complex cellular states, providing significant insights into cellular dynamics and disease. Yet, integration of multi-omics data presents challenges. Some modalities have not reached the robustness or clarity of established transcriptomics. Coupled with data scarcity for less established modalities and integration intricacies, these challenges limit our ability to maximize single-cell omics benefits. We introduce scCross, a tool leveraging variational autoencoders, generative adversarial networks, and the mutual nearest neighbors (MNN) technique for modality alignment. By enabling single-cell cross-modal data generation, multi-omics data simulation, and in silico cellular perturbations, scCross enhances the utility of single-cell multi-omics studies.
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Affiliation(s)
- Xiuhui Yang
- School of Software, Shandong University, 1500 Shunhua, Jinan, 250101, Shandong, China
- Meakins-Christie Laboratories, Department of Medicine, McGill University Health Centre, Montreal, H4A 3J1, QC, Canada
- Quantitative Life Sciences, Faculty of Medicine & Health Sciences, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Koren K Mann
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Hao Wu
- School of Software, Shandong University, 1500 Shunhua, Jinan, 250101, Shandong, China.
| | - Jun Ding
- Meakins-Christie Laboratories, Department of Medicine, McGill University Health Centre, Montreal, H4A 3J1, QC, Canada.
- Quantitative Life Sciences, Faculty of Medicine & Health Sciences, McGill University, Montreal, QC, H3G 1Y6, Canada.
- Mila-Quebec AI Institute, Montreal, QC, H2S 3H1, Canada.
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25
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Lin Y, Pan Z, Zeng Y, Yang Y, Dai Z. Detecting novel cell type in single-cell chromatin accessibility data via open-set domain adaptation. Brief Bioinform 2024; 25:bbae370. [PMID: 39073828 DOI: 10.1093/bib/bbae370] [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: 04/17/2024] [Revised: 06/27/2024] [Accepted: 07/15/2024] [Indexed: 07/30/2024] Open
Abstract
Recent advances in single-cell technologies enable the rapid growth of multi-omics data. Cell type annotation is one common task in analyzing single-cell data. It is a challenge that some cell types in the testing set are not present in the training set (i.e. unknown cell types). Most scATAC-seq cell type annotation methods generally assign each cell in the testing set to one known type in the training set but neglect unknown cell types. Here, we present OVAAnno, an automatic cell types annotation method which utilizes open-set domain adaptation to detect unknown cell types in scATAC-seq data. Comprehensive experiments show that OVAAnno successfully identifies known and unknown cell types. Further experiments demonstrate that OVAAnno also performs well on scRNA-seq data. Our codes are available online at https://github.com/lisaber/OVAAnno/tree/master.
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Affiliation(s)
- Yuefan Lin
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China
| | - Zixiang Pan
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yuansong Zeng
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yuedong Yang
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhiming Dai
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China
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26
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Linneberg-Agerholm M, Sell AC, Redó-Riveiro A, Perera M, Proks M, Knudsen TE, Barral A, Manzanares M, Brickman JM. The primitive endoderm supports lineage plasticity to enable regulative development. Cell 2024; 187:4010-4029.e16. [PMID: 38917790 PMCID: PMC11290322 DOI: 10.1016/j.cell.2024.05.051] [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: 05/19/2023] [Revised: 02/27/2024] [Accepted: 05/28/2024] [Indexed: 06/27/2024]
Abstract
Mammalian blastocyst formation involves the specification of the trophectoderm followed by the differentiation of the inner cell mass into embryonic epiblast and extra-embryonic primitive endoderm (PrE). During this time, the embryo maintains a window of plasticity and can redirect its cellular fate when challenged experimentally. In this context, we found that the PrE alone was sufficient to regenerate a complete blastocyst and continue post-implantation development. We identify an in vitro population similar to the early PrE in vivo that exhibits the same embryonic and extra-embryonic potency and can form complete stem cell-based embryo models, termed blastoids. Commitment in the PrE is suppressed by JAK/STAT signaling, collaborating with OCT4 and the sustained expression of a subset of pluripotency-related transcription factors that safeguard an enhancer landscape permissive for multi-lineage differentiation. Our observations support the notion that transcription factor persistence underlies plasticity in regulative development and highlight the importance of the PrE in perturbed development.
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Affiliation(s)
- Madeleine Linneberg-Agerholm
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Annika Charlotte Sell
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Alba Redó-Riveiro
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Marta Perera
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Martin Proks
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Teresa E Knudsen
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Antonio Barral
- Centro de Biología Molecular Severo Ochoa (CBM), CSIC-UAM, 28049 Madrid, Spain
| | - Miguel Manzanares
- Centro de Biología Molecular Severo Ochoa (CBM), CSIC-UAM, 28049 Madrid, Spain
| | - Joshua M Brickman
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200 Copenhagen N, Denmark.
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27
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Abedini A, Levinsohn J, Klötzer KA, Dumoulin B, Ma Z, Frederick J, Dhillon P, Balzer MS, Shrestha R, Liu H, Vitale S, Bergeson AM, Devalaraja-Narashimha K, Grandi P, Bhattacharyya T, Hu E, Pullen SS, Boustany-Kari CM, Guarnieri P, Karihaloo A, Traum D, Yan H, Coleman K, Palmer M, Sarov-Blat L, Morton L, Hunter CA, Kaestner KH, Li M, Susztak K. Single-cell multi-omic and spatial profiling of human kidneys implicates the fibrotic microenvironment in kidney disease progression. Nat Genet 2024:10.1038/s41588-024-01802-x. [PMID: 39048792 DOI: 10.1038/s41588-024-01802-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 05/15/2024] [Indexed: 07/27/2024]
Abstract
Kidneys are intricate three-dimensional structures in the body, yet the spatial and molecular principles of kidney health and disease remain inadequately understood. We generated high-quality datasets for 81 samples, including single-cell, single-nuclear, spot-level (Visium) and single-cell resolution (CosMx) spatial-RNA expression and single-nuclear open chromatin, capturing cells from healthy, diabetic and hypertensive diseased human kidneys. Combining these data, we identify cell types and map them to their locations within the tissue. Unbiased deconvolution of the spatial data identifies the following four distinct microenvironments: glomerular, immune, tubule and fibrotic. We describe the complex organization of microenvironments in health and disease and find that the fibrotic microenvironment is able to molecularly classify human kidneys and offers an improved prognosis compared to traditional histopathology. We provide a comprehensive spatially resolved molecular roadmap of the human kidney and the fibrotic process, demonstrating the clinical utility of spatial transcriptomics.
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Affiliation(s)
- Amin Abedini
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Penn/CHOP Kidney Innovation Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Jonathan Levinsohn
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Penn/CHOP Kidney Innovation Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Konstantin A Klötzer
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Penn/CHOP Kidney Innovation Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Bernhard Dumoulin
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Penn/CHOP Kidney Innovation Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Ziyuan Ma
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Penn/CHOP Kidney Innovation Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Julia Frederick
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Penn/CHOP Kidney Innovation Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Poonam Dhillon
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Penn/CHOP Kidney Innovation Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Michael S Balzer
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Penn/CHOP Kidney Innovation Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Nephrology, Charité - Universitätsmedizin, Berlin, Germany
| | - Rojesh Shrestha
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Penn/CHOP Kidney Innovation Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Hongbo Liu
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Penn/CHOP Kidney Innovation Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Steven Vitale
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Penn/CHOP Kidney Innovation Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Andi M Bergeson
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Penn/CHOP Kidney Innovation Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | | | - Paola Grandi
- Genomic Sciences, GSK-Cellzome, Heidelberg, Germany
| | | | - Erding Hu
- Research and Development, GSK, Crescent Drive, Philadelphia, PA, USA
| | - Steven S Pullen
- Department of Cardiometabolic Diseases Research, Boehringer Ingelheim Pharmaceuticals, Ridgefield, CT, USA
| | - Carine M Boustany-Kari
- Department of Cardiometabolic Diseases Research, Boehringer Ingelheim Pharmaceuticals, Ridgefield, CT, USA
| | - Paolo Guarnieri
- Department of Cardiometabolic Diseases Research, Boehringer Ingelheim Pharmaceuticals, Ridgefield, CT, USA
| | | | - Daniel Traum
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Hanying Yan
- Department of Epidemiology, Biostatistics and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Kyle Coleman
- Department of Epidemiology, Biostatistics and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Matthew Palmer
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Lea Sarov-Blat
- Research and Development, GSK, Crescent Drive, Philadelphia, PA, USA
| | - Lori Morton
- Cardiovascular and Renal Research, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Christopher A Hunter
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA
| | - Klaus H Kaestner
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Mingyao Li
- Department of Epidemiology, Biostatistics and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Katalin Susztak
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
- Penn/CHOP Kidney Innovation Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
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28
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Garyn CM, Bover O, Murray JW, Ma J, Salas-Briceno K, Ross SR, Snoeck HW. G2 arrest primes hematopoietic stem cells for megakaryopoiesis. Cell Rep 2024; 43:114388. [PMID: 38935497 DOI: 10.1016/j.celrep.2024.114388] [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: 10/12/2023] [Revised: 04/22/2024] [Accepted: 06/06/2024] [Indexed: 06/29/2024] Open
Abstract
In contrast to most hematopoietic lineages, megakaryocytes (MKs) can derive rapidly and directly from hematopoietic stem cells (HSCs). The underlying mechanism is unclear, however. Here, we show that DNA damage induces MK markers in HSCs and that G2 arrest, an integral part of the DNA damage response, suffices for MK priming followed by irreversible MK differentiation in HSCs, but not in progenitors. We also show that replication stress causes DNA damage in HSCs and is at least in part due to uracil misincorporation in vitro and in vivo. Consistent with this notion, thymidine attenuated DNA damage, improved HSC maintenance, and reduced the generation of CD41+ MK-committed HSCs. Replication stress and concomitant MK differentiation is therefore one of the barriers to HSC maintenance. DNA damage-induced MK priming may allow rapid generation of a lineage essential to immediate organismal survival, while also removing damaged cells from the HSC pool.
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Affiliation(s)
- Corey M Garyn
- Columbia Center for Human Development/Center for Stem Cell Therapies, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Department of Genetics and Development, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Oriol Bover
- Columbia Center for Human Development/Center for Stem Cell Therapies, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - John W Murray
- Columbia Center for Human Development/Center for Stem Cell Therapies, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Jing Ma
- Department of Microbiology and Immunology, University of Illinois at Chicago College of Medicine, Chicago, IL 60612, USA
| | - Karen Salas-Briceno
- Department of Microbiology and Immunology, University of Illinois at Chicago College of Medicine, Chicago, IL 60612, USA
| | - Susan R Ross
- Department of Microbiology and Immunology, University of Illinois at Chicago College of Medicine, Chicago, IL 60612, USA
| | - Hans-Willem Snoeck
- Columbia Center for Human Development/Center for Stem Cell Therapies, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
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29
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Sun F, Li H, Sun D, Fu S, Gu L, Shao X, Wang Q, Dong X, Duan B, Xing F, Wu J, Xiao M, Zhao F, Han JDJ, Liu Q, Fan X, Li C, Wang C, Shi T. Single-cell omics: experimental workflow, data analyses and applications. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2561-0. [PMID: 39060615 DOI: 10.1007/s11427-023-2561-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/18/2024] [Indexed: 07/28/2024]
Abstract
Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome, proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial scRNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field, offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.
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Affiliation(s)
- Fengying Sun
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China
| | - Haoyan Li
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Dongqing Sun
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Shaliu Fu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Lei Gu
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Shao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China
| | - Qinqin Wang
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Dong
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Bin Duan
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Feiyang Xing
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jun Wu
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Minmin Xiao
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, China.
| | - Qi Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China.
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China.
| | - Xiaohui Fan
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China.
- Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China.
| | - Chen Li
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Chenfei Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Tieliu Shi
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
- Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, School of Statistics, East China Normal University, Shanghai, 200062, China.
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30
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Missarova A, Dann E, Rosen L, Satija R, Marioni J. Leveraging neighborhood representations of single-cell data to achieve sensitive DE testing with miloDE. Genome Biol 2024; 25:189. [PMID: 39026254 PMCID: PMC11256449 DOI: 10.1186/s13059-024-03334-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 07/10/2024] [Indexed: 07/20/2024] Open
Abstract
Single-cell RNA-sequencing enables testing for differential expression (DE) between conditions at a cell type level. While powerful, one of the limitations of such approaches is that the sensitivity of DE testing is dictated by the sensitivity of clustering, which is often suboptimal. To overcome this, we present miloDE-a cluster-free framework for DE testing (available as an open-source R package). We illustrate the performance of miloDE on both simulated and real data. Using miloDE, we identify a transient hemogenic endothelia-like state in mouse embryos lacking Tal1 and detect distinct programs during macrophage activation in idiopathic pulmonary fibrosis.
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Affiliation(s)
- Alsu Missarova
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Emma Dann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Leah Rosen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Rahul Satija
- Center for Genomics and Systems Biology, NYU, New York, USA.
- New York Genome Center, New York, USA.
| | - John Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
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31
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Liang NE, Parker JB, Lu JM, Januszyk M, Wan DC, Griffin M, Longaker MT. Understanding the Foreign Body Response via Single-Cell Meta-Analysis. BIOLOGY 2024; 13:540. [PMID: 39056733 PMCID: PMC11273435 DOI: 10.3390/biology13070540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 07/12/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024]
Abstract
Foreign body response (FBR) is a universal reaction to implanted biomaterial that can affect the function and longevity of the implant. A few studies have attempted to identify targets for treating FBR through the use of single-cell RNA sequencing (scRNA-seq), though the generalizability of these findings from an individual study may be limited. In our study, we perform a meta-analysis of scRNA-seq data from all available FBR mouse studies and integrate these data to identify gene signatures specific to FBR across different models and anatomic locations. We identify subclusters of fibroblasts and macrophages that emerge in response to foreign bodies and characterize their signaling pathways, gene ontology terms, and downstream mediators. The fibroblast subpopulations enriched in the setting of FBR demonstrated significant signaling interactions in the transforming growth factor-beta (TGF-β) signaling pathway, with known pro-fibrotic mediators identified as top expressed genes in these FBR-derived fibroblasts. In contrast, FBR-enriched macrophage subclusters highly expressed pro-fibrotic and pro-inflammatory mediators downstream of tumor necrosis factor (TNF) signaling. Cell-cell interactions were additionally interrogated using CellChat, with identification of key signaling interactions enriched between fibroblasts and macrophages in FBR. By combining multiple FBR datasets, our meta-analysis study identifies common cell-specific gene signatures enriched in foreign body reactions, providing potential therapeutic targets for patients requiring medical implants across a myriad of devices and indications.
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Affiliation(s)
- Norah E. Liang
- Hagey Laboratory of Pediatric Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; (N.E.L.); (J.B.P.); (J.M.L.); (M.J.); (D.C.W.); (M.G.)
- Division of General Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jennifer B. Parker
- Hagey Laboratory of Pediatric Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; (N.E.L.); (J.B.P.); (J.M.L.); (M.J.); (D.C.W.); (M.G.)
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - John M. Lu
- Hagey Laboratory of Pediatric Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; (N.E.L.); (J.B.P.); (J.M.L.); (M.J.); (D.C.W.); (M.G.)
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael Januszyk
- Hagey Laboratory of Pediatric Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; (N.E.L.); (J.B.P.); (J.M.L.); (M.J.); (D.C.W.); (M.G.)
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Derrick C. Wan
- Hagey Laboratory of Pediatric Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; (N.E.L.); (J.B.P.); (J.M.L.); (M.J.); (D.C.W.); (M.G.)
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michelle Griffin
- Hagey Laboratory of Pediatric Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; (N.E.L.); (J.B.P.); (J.M.L.); (M.J.); (D.C.W.); (M.G.)
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael T. Longaker
- Hagey Laboratory of Pediatric Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; (N.E.L.); (J.B.P.); (J.M.L.); (M.J.); (D.C.W.); (M.G.)
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
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32
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Coppard V, Szep G, Georgieva Z, Howlett SK, Jarvis LB, Rainbow DB, Suchanek O, Needham EJ, Mousa HS, Menon DK, Feyertag F, Mahbubani KT, Saeb-Parsy K, Jones JL. FlowAtlas: an interactive tool for high-dimensional immunophenotyping analysis bridging FlowJo with computational tools in Julia. Front Immunol 2024; 15:1425488. [PMID: 39086484 PMCID: PMC11288863 DOI: 10.3389/fimmu.2024.1425488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 07/02/2024] [Indexed: 08/02/2024] Open
Abstract
As the dimensionality, throughput and complexity of cytometry data increases, so does the demand for user-friendly, interactive analysis tools that leverage high-performance machine learning frameworks. Here we introduce FlowAtlas: an interactive web application that enables dimensionality reduction of cytometry data without down-sampling and that is compatible with datasets stained with non-identical panels. FlowAtlas bridges the user-friendly environment of FlowJo and computational tools in Julia developed by the scientific machine learning community, eliminating the need for coding and bioinformatics expertise. New population discovery and detection of rare populations in FlowAtlas is intuitive and rapid. We demonstrate the capabilities of FlowAtlas using a human multi-tissue, multi-donor immune cell dataset, highlighting key immunological findings. FlowAtlas is available at https://github.com/gszep/FlowAtlas.jl.git.
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Affiliation(s)
- Valerie Coppard
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | - Grisha Szep
- Randall Centre for Cell & Molecular Biophysics, King’s College London, London, United Kingdom
| | - Zoya Georgieva
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | - Sarah K. Howlett
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | - Lorna B. Jarvis
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | - Daniel B. Rainbow
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | - Ondrej Suchanek
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Edward J. Needham
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | - Hani S. Mousa
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | - David K. Menon
- Department of Anaesthesia, University of Cambridge, Cambridge, United Kingdom
| | | | - Krishnaa T. Mahbubani
- Department of Surgery, University of Cambridge, Cambridge, United Kingdom
- Collaborative Biorepository for Translational Medicine (CBTM), Cambridge NIHR Biomedical Research Centre, Cambridge, United Kingdom
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, Cambridge, United Kingdom
- Collaborative Biorepository for Translational Medicine (CBTM), Cambridge NIHR Biomedical Research Centre, Cambridge, United Kingdom
| | - Joanne L. Jones
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
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33
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Almet AA, Liu Y, Nie Q, Plikus MV. Integrated Single-Cell Analysis Reveals Spatially and Temporally Dynamic Heterogeneity in Fibroblast States During Wound Healing. J Invest Dermatol 2024:S0022-202X(24)01884-0. [PMID: 39019149 DOI: 10.1016/j.jid.2024.06.1281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 06/14/2024] [Accepted: 06/26/2024] [Indexed: 07/19/2024]
Abstract
Wound healing is a dynamic process over temporal and spatial scales. Key to repair outcomes are fibroblasts, yet how they modulate healing across time and in different wound regions remains incompletely understood. By integrating single-cell RNA-sequencing datasets of mouse skin and wounds, we infer that fibroblasts are the most transcriptionally dynamic skin-resident cells, evolving during postnatal skin maturation, and rapidly after injury towards distinct late scar states. We show that transcriptional dynamics in fibroblasts are largely driven by genes encoding extracellular matrix and signaling factors. Lineage trajectory inference and spatial gene mapping reveal that Prg4-expressing fibroblasts transiently emerge along early wound edges. Within days, they become replaced by long-lasting and likely non-interconverting fibroblast populations, including Col25a1-expressing and Pamr1-expressing fibroblasts that occupy subepidermal and deep scar regions, respectively, where they engage in reciprocal signaling with immune cells. Signaling inference shows that fibroblast-immune crosstalk repeatedly uses some signaling pathways across wound healing time, while use of other signaling pathways is time- and space-limited. Collectively, we uncovered high transcriptional plasticity by wound fibroblasts, with early states transiently forming distinct micro-niches along wound edges and in the fascia, followed by stable states, that stratify scar tissue into molecularly dissimilar upper and lower layers.
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Affiliation(s)
- Axel A Almet
- Department of Mathematics, University of California, Irvine, Irvine, CA 92617, USA; NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA 92617, USA
| | - Yingzi Liu
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92617, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92617, USA
| | - Qing Nie
- Department of Mathematics, University of California, Irvine, Irvine, CA 92617, USA; NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA 92617, USA; Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92617, USA.
| | - Maksim V Plikus
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA 92617, USA; Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92617, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92617, USA.
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34
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Rautenstrauch P, Ohler U. Liam tackles complex multimodal single-cell data integration challenges. Nucleic Acids Res 2024; 52:e52. [PMID: 38842910 PMCID: PMC11229356 DOI: 10.1093/nar/gkae409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 03/08/2024] [Accepted: 05/29/2024] [Indexed: 06/07/2024] Open
Abstract
Multi-omics characterization of single cells holds outstanding potential for profiling the dynamics and relations of gene regulatory states of thousands of cells. How to integrate multimodal data is an open problem, especially when aiming to combine data from multiple sources or conditions containing both biological and technical variation. We introduce liam, a flexible model for the simultaneous horizontal and vertical integration of paired single-cell multimodal data and mosaic integration of paired with unimodal data. Liam learns a joint low-dimensional representation of the measured modalities, which proves beneficial when the information content or quality of the modalities differ. Its integration accounts for complex batch effects using a tunable combination of conditional and adversarial training, which can be optimized using replicate information while retaining selected biological variation. We demonstrate liam's superior performance on multiple paired multimodal data types, including Multiome and CITE-seq data, and in mosaic integration scenarios. Our detailed benchmarking experiments illustrate the complexities and challenges remaining for integration and the meaningful assessment of its success.
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Affiliation(s)
- Pia Rautenstrauch
- Humboldt-Universität zu Berlin, Department of Computer Science, 10099 Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Uwe Ohler
- Humboldt-Universität zu Berlin, Department of Computer Science, 10099 Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Humboldt-Universität zu Berlin, Department of Biology, 10099 Berlin, Germany
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35
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Curion F, Rich-Griffin C, Agarwal D, Ouologuem S, Rue-Albrecht K, May L, Garcia GEL, Heumos L, Thomas T, Lason W, Sims D, Theis FJ, Dendrou CA. Panpipes: a pipeline for multiomic single-cell and spatial transcriptomic data analysis. Genome Biol 2024; 25:181. [PMID: 38978088 PMCID: PMC11229213 DOI: 10.1186/s13059-024-03322-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/25/2024] [Indexed: 07/10/2024] Open
Abstract
Single-cell multiomic analysis of the epigenome, transcriptome, and proteome allows for comprehensive characterization of the molecular circuitry that underpins cell identity and state. However, the holistic interpretation of such datasets presents a challenge given a paucity of approaches for systematic, joint evaluation of different modalities. Here, we present Panpipes, a set of computational workflows designed to automate multimodal single-cell and spatial transcriptomic analyses by incorporating widely-used Python-based tools to perform quality control, preprocessing, integration, clustering, and reference mapping at scale. Panpipes allows reliable and customizable analysis and evaluation of individual and integrated modalities, thereby empowering decision-making before downstream investigations.
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Affiliation(s)
- Fabiola Curion
- Department of Computational Health, Institute of Computational Biology, Helmholtz Munich, Germany
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Munich, Germany
| | - Charlotte Rich-Griffin
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Devika Agarwal
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Sarah Ouologuem
- Department of Computational Health, Institute of Computational Biology, Helmholtz Munich, Germany
| | - Kevin Rue-Albrecht
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Lilly May
- Department of Computational Health, Institute of Computational Biology, Helmholtz Munich, Germany
| | - Giulia E L Garcia
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- Doctoral Training Centre, University of Oxford, Oxford, UK
| | - Lukas Heumos
- Department of Computational Health, Institute of Computational Biology, Helmholtz Munich, Germany
- Comprehensive Pneumology Center With the CPC-M bioArchive, Helmholtz Zentrum Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Tom Thomas
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Wojciech Lason
- Nuffield Department of Medicine, Respiratory Medicine Unit, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - David Sims
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Fabian J Theis
- Department of Computational Health, Institute of Computational Biology, Helmholtz Munich, Germany.
- Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Munich, Germany.
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany.
| | - Calliope A Dendrou
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, UK.
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK.
- NIHR Oxford Biomedical Research Centre, Oxford, UK.
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36
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Gondal MN, Shah SUR, Chinnaiyan AM, Cieslik M. A systematic overview of single-cell transcriptomics databases, their use cases, and limitations. FRONTIERS IN BIOINFORMATICS 2024; 4:1417428. [PMID: 39040140 PMCID: PMC11260681 DOI: 10.3389/fbinf.2024.1417428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Accepted: 06/11/2024] [Indexed: 07/24/2024] Open
Abstract
Rapid advancements in high-throughput single-cell RNA-seq (scRNA-seq) technologies and experimental protocols have led to the generation of vast amounts of transcriptomic data that populates several online databases and repositories. Here, we systematically examined large-scale scRNA-seq databases, categorizing them based on their scope and purpose such as general, tissue-specific databases, disease-specific databases, cancer-focused databases, and cell type-focused databases. Next, we discuss the technical and methodological challenges associated with curating large-scale scRNA-seq databases, along with current computational solutions. We argue that understanding scRNA-seq databases, including their limitations and assumptions, is crucial for effectively utilizing this data to make robust discoveries and identify novel biological insights. Such platforms can help bridge the gap between computational and wet lab scientists through user-friendly web-based interfaces needed for democratizing access to single-cell data. These platforms would facilitate interdisciplinary research, enabling researchers from various disciplines to collaborate effectively. This review underscores the importance of leveraging computational approaches to unravel the complexities of single-cell data and offers a promising direction for future research in the field.
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Affiliation(s)
- Mahnoor N. Gondal
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, United States
| | - Saad Ur Rehman Shah
- Gies College of Business, University of Illinois Business College, Champaign, MI, United States
| | - Arul M. Chinnaiyan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, United States
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
- Department of Urology, University of Michigan, Ann Arbor, MI, United States
- Howard Hughes Medical Institute, Ann Arbor, MI, United States
- University of Michigan Rogel Cancer Center, Ann Arbor, MI, United States
| | - Marcin Cieslik
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, United States
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
- University of Michigan Rogel Cancer Center, Ann Arbor, MI, United States
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37
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Guimarães GR, Maklouf GR, Teixeira CE, de Oliveira Santos L, Tessarollo NG, de Toledo NE, Serain AF, de Lanna CA, Pretti MA, da Cruz JGV, Falchetti M, Dimas MM, Filgueiras IS, Cabral-Marques O, Ramos RN, de Macedo FC, Rodrigues FR, Bastos NC, da Silva JL, Lummertz da Rocha E, Chaves CBP, de Melo AC, Moraes-Vieira PMM, Mori MA, Boroni M. Single-cell resolution characterization of myeloid-derived cell states with implication in cancer outcome. Nat Commun 2024; 15:5694. [PMID: 38972873 PMCID: PMC11228020 DOI: 10.1038/s41467-024-49916-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 06/19/2024] [Indexed: 07/09/2024] Open
Abstract
Tumor-associated myeloid-derived cells (MDCs) significantly impact cancer prognosis and treatment responses due to their remarkable plasticity and tumorigenic behaviors. Here, we integrate single-cell RNA-sequencing data from different cancer types, identifying 29 MDC subpopulations within the tumor microenvironment. Our analysis reveals abnormally expanded MDC subpopulations across various tumors and distinguishes cell states that have often been grouped together, such as TREM2+ and FOLR2+ subpopulations. Using deconvolution approaches, we identify five subpopulations as independent prognostic markers, including states co-expressing TREM2 and PD-1, and FOLR2 and PDL-2. Additionally, TREM2 alone does not reliably predict cancer prognosis, as other TREM2+ macrophages show varied associations with prognosis depending on local cues. Validation in independent cohorts confirms that FOLR2-expressing macrophages correlate with poor clinical outcomes in ovarian and triple-negative breast cancers. This comprehensive MDC atlas offers valuable insights and a foundation for futher analyses, advancing strategies for treating solid cancers.
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Affiliation(s)
- Gabriela Rapozo Guimarães
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
| | - Giovanna Resk Maklouf
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
| | - Cristiane Esteves Teixeira
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
| | - Leandro de Oliveira Santos
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
| | - Nayara Gusmão Tessarollo
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
| | - Nayara Evelin de Toledo
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
| | - Alessandra Freitas Serain
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
| | - Cristóvão Antunes de Lanna
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
| | - Marco Antônio Pretti
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
| | - Jéssica Gonçalves Vieira da Cruz
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
| | - Marcelo Falchetti
- Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Mylla M Dimas
- Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Igor Salerno Filgueiras
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo,(USP), São Paulo, Brazil
| | - Otavio Cabral-Marques
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo,(USP), São Paulo, Brazil
- Instituto D'Or de Ensino e Pesquisa, São Paulo, Brazil
- Department of Medicine, Division of Molecular Medicine, Laboratory of Medical Investigation 29, School of Medicine, University of São Paulo (USP), São Paulo, Brazil
| | - Rodrigo Nalio Ramos
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo,(USP), São Paulo, Brazil
- Instituto D'Or de Ensino e Pesquisa, São Paulo, Brazil
- Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology (LIM-31), Departament of Hematology and Cell Therapy, Hospital das Clínicas HCFMUSP, School of Medicine, University of São Paulo (USP), São Paulo, Brazil
| | | | | | - Nina Carrossini Bastos
- Division of Pathology, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
| | - Jesse Lopes da Silva
- Division of Clinical Research and Technological Development, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
| | - Edroaldo Lummertz da Rocha
- Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Cláudia Bessa Pereira Chaves
- Division of Clinical Research and Technological Development, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
- Gynecologic Oncology Section, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
| | - Andreia Cristina de Melo
- Division of Clinical Research and Technological Development, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil
| | - Pedro M M Moraes-Vieira
- Laboratory of Immunometabolism, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, Universidade Estadual de Campinas, Campinas, SP, Brazil
- Obesity and Comorbidities Research Center (OCRC), Universidade Estadual de Campinas, Campinas, SP, Brazil
- Experimental Medicine Research Cluster (EMRC), Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Marcelo A Mori
- Obesity and Comorbidities Research Center (OCRC), Universidade Estadual de Campinas, Campinas, SP, Brazil
- Experimental Medicine Research Cluster (EMRC), Universidade Estadual de Campinas, Campinas, SP, Brazil
- Laboratory of Aging Biology, Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Mariana Boroni
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, RJ, Brazil.
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38
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Drost F, An Y, Bonafonte-Pardàs I, Dratva LM, Lindeboom RGH, Haniffa M, Teichmann SA, Theis F, Lotfollahi M, Schubert B. Multi-modal generative modeling for joint analysis of single-cell T cell receptor and gene expression data. Nat Commun 2024; 15:5577. [PMID: 38956082 PMCID: PMC11220149 DOI: 10.1038/s41467-024-49806-9] [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: 10/10/2023] [Accepted: 05/23/2024] [Indexed: 07/04/2024] Open
Abstract
Recent advances in single-cell immune profiling have enabled the simultaneous measurement of transcriptome and T cell receptor (TCR) sequences, offering great potential for studying immune responses at the cellular level. However, integrating these diverse modalities across datasets is challenging due to their unique data characteristics and technical variations. Here, to address this, we develop the multimodal generative model mvTCR to fuse modality-specific information across transcriptome and TCR into a shared representation. Our analysis demonstrates the added value of multimodal over unimodal approaches to capture antigen specificity. Notably, we use mvTCR to distinguish T cell subpopulations binding to SARS-CoV-2 antigens from bystander cells. Furthermore, when combined with reference mapping approaches, mvTCR can map newly generated datasets to extensive T cell references, facilitating knowledge transfer. In summary, we envision mvTCR to enable a scalable analysis of multimodal immune profiling data and advance our understanding of immune responses.
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Affiliation(s)
- Felix Drost
- Computational Health Center, Helmholtz Munich, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
- School of Life Sciences Weihenstephan, Technical University of Munich, Alte Akademie 8, 85354, Freising, Germany
| | - Yang An
- Computational Health Center, Helmholtz Munich, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
- School of Computation, Information and Technology, Technical University of Munich, Boltzmannstraße 3, 85748, Garching bei München, Germany
| | - Irene Bonafonte-Pardàs
- Computational Health Center, Helmholtz Munich, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Lisa M Dratva
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Rik G H Lindeboom
- The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Physics, Cavendish Laboratory, University of Cambridge, 19 JJ Thomson Avenue, Cambridge, UK
| | - Fabian Theis
- Computational Health Center, Helmholtz Munich, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
- School of Life Sciences Weihenstephan, Technical University of Munich, Alte Akademie 8, 85354, Freising, Germany
- School of Computation, Information and Technology, Technical University of Munich, Boltzmannstraße 3, 85748, Garching bei München, Germany
| | - Mohammad Lotfollahi
- Computational Health Center, Helmholtz Munich, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
| | - Benjamin Schubert
- Computational Health Center, Helmholtz Munich, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.
- School of Computation, Information and Technology, Technical University of Munich, Boltzmannstraße 3, 85748, Garching bei München, Germany.
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39
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Sethi R, Ang KS, Li M, Long Y, Ling J, Chen J. ezSingleCell: an integrated one-stop single-cell and spatial omics analysis platform for bench scientists. Nat Commun 2024; 15:5600. [PMID: 38961061 PMCID: PMC11222513 DOI: 10.1038/s41467-024-48188-2] [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: 03/22/2023] [Accepted: 04/22/2024] [Indexed: 07/05/2024] Open
Abstract
ezSingleCell is an interactive and easy-to-use application for analysing various single-cell and spatial omics data types without requiring prior programing knowledge. It combines the best-performing publicly available methods for in-depth data analysis, integration, and interactive data visualization. ezSingleCell consists of five modules, each designed to be a comprehensive workflow for one data type or task. In addition, ezSingleCell allows crosstalk between different modules within a unified interface. Acceptable input data can be in a variety of formats while the output consists of publication ready figures and tables. In-depth manuals and video tutorials are available to guide users on the analysis workflows and parameter adjustments to suit their study aims. ezSingleCell's streamlined interface can analyse a standard scRNA-seq dataset of 3000 cells in less than five minutes. ezSingleCell is available in two forms: an installation-free web application ( https://immunesinglecell.org/ezsc/ ) or a software package with a shinyApp interface ( https://github.com/JinmiaoChenLab/ezSingleCell2 ) for offline analysis.
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Affiliation(s)
- Raman Sethi
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix, Singapore, 138671, Singapore
| | - Kok Siong Ang
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Mengwei Li
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Yahui Long
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Jingjing Ling
- Singapore Immunology Network (SIgN), Agency of Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos, Singapore, 138648, Singapore
| | - Jinmiao Chen
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix, Singapore, 138671, Singapore.
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore.
- Immunology Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 5 Science Drive 2, Blk MD4, Level 3, Singapore, 117545, Singapore.
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40
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Schnell J, Miao Z, Achieng M, Fausto CC, Wang V, Kuyper FD, Thornton ME, Grubbs B, Kim J, Lindström NO. Stepwise developmental mimicry generates proximal-biased kidney organoids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.601028. [PMID: 39005387 PMCID: PMC11244853 DOI: 10.1101/2024.06.28.601028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
The kidney maintains body fluid homeostasis by reabsorbing essential compounds and excreting waste. Proximal tubule cells, crucial for renal reabsorption of a range of sugars, ions, and amino acids, are highly susceptible to damage, leading to pathologies necessitating dialysis and kidney transplants. While human pluripotent stem cell-derived kidney organoids are used for modeling renal development, disease, and injury, the formation of proximal nephron cells in these 3D structures is incomplete. Here, we describe how to drive the development of proximal tubule precursors in kidney organoids by following a blueprint of in vivo human nephrogenesis. Transient manipulation of the PI3K signaling pathway activates Notch signaling in the early nephron and drives nephrons toward a proximal precursor state. These "proximal-biased" (PB) organoid nephrons proceed to generate proximal nephron precursor cells. Single-cell transcriptional analyses across the organoid nephron differentiation, comparing control and PB types, confirm the requirement of transient Notch signaling for proximal development. Indicative of functional maturity, PB organoids demonstrate dextran and albumin uptake, akin to in vivo proximal tubules. Moreover, PB organoids are highly sensitive to nephrotoxic agents, display an injury response, and drive expression of HAVCR1 / KIM1 , an early proximal-specific marker of kidney injury. Injured PB organoids show evidence of collapsed tubules, DNA damage, and upregulate the injury-response marker SOX9 . The PB organoid model therefore has functional relevance and potential for modeling mechanisms underpinning nephron injury. These advances improve the use of iPSC-derived kidney organoids as tools to understand developmental nephrology, model disease, test novel therapeutics, and for understanding human renal physiology.
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41
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Xu H, Ye Y, Duan R, Gao Y, Hu Y, Gao L. Beaconet: A Reference-Free Method for Integrating Multiple Batches of Single-Cell Transcriptomic Data in Original Molecular Space. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306770. [PMID: 38711214 PMCID: PMC11234410 DOI: 10.1002/advs.202306770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 04/02/2024] [Indexed: 05/08/2024]
Abstract
Integrating multiple single-cell datasets is essential for the comprehensive understanding of cell heterogeneity. Batch effect is the undesired systematic variations among technologies or experimental laboratories that distort biological signals and hinder the integration of single-cell datasets. However, existing methods typically rely on a selected dataset as a reference, leading to inconsistent integration performance using different references, or embed cells into uninterpretable low-dimensional feature space. To overcome these limitations, a reference-free method, Beaconet, for integrating multiple single-cell transcriptomic datasets in original molecular space by aligning the global distribution of each batch using an adversarial correction network is presented. Through extensive comparisons with 13 state-of-the-art methods, it is demonstrated that Beaconet can effectively remove batch effect while preserving biological variations and is superior to existing unsupervised methods using all possible references in overall performance. Furthermore, Beaconet performs integration in the original molecular feature space, enabling the characterization of cell types and downstream differential expression analysis directly using integrated data with gene-expression features. Additionally, when applying to large-scale atlas data integration, Beaconet shows notable advantages in both time- and space-efficiencies. In summary, Beaconet serves as an effective and efficient batch effect removal tool that can facilitate the integration of single-cell datasets in a reference-free and molecular feature-preserved mode.
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Affiliation(s)
- Han Xu
- School of Computer Science and TechnologyXidian UniversityXi'an710126China
| | - Yusen Ye
- School of Computer Science and TechnologyXidian UniversityXi'an710126China
| | - Ran Duan
- School of Electrical and Information EngineeringBeijing University of Civil Engineering and ArchitectureBeijing102616China
| | - Yong Gao
- Department of Computer ScienceThe University of British Columbia OkanaganKelownaBritish ColumbiaV1V 1V7Canada
| | - Yuxuan Hu
- School of Computer Science and TechnologyXidian UniversityXi'an710126China
| | - Lin Gao
- School of Computer Science and TechnologyXidian UniversityXi'an710126China
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Chen AA, Clark K, Dewey BE, DuVal A, Pellegrini N, Nair G, Jalkh Y, Khalil S, Zurawski J, Calabresi PA, Reich DS, Bakshi R, Shou H, Shinohara RT. PARE: A framework for removal of confounding effects from any distance-based dimension reduction method. PLoS Comput Biol 2024; 20:e1012241. [PMID: 38985831 PMCID: PMC11262650 DOI: 10.1371/journal.pcbi.1012241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 07/22/2024] [Accepted: 06/10/2024] [Indexed: 07/12/2024] Open
Abstract
Dimension reduction tools preserving similarity and graph structure such as t-SNE and UMAP can capture complex biological patterns in high-dimensional data. However, these tools typically are not designed to separate effects of interest from unwanted effects due to confounders. We introduce the partial embedding (PARE) framework, which enables removal of confounders from any distance-based dimension reduction method. We then develop partial t-SNE and partial UMAP and apply these methods to genomic and neuroimaging data. For lower-dimensional visualization, our results show that the PARE framework can remove batch effects in single-cell sequencing data as well as separate clinical and technical variability in neuroimaging measures. We demonstrate that the PARE framework extends dimension reduction methods to highlight biological patterns of interest while effectively removing confounding effects.
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Affiliation(s)
- Andrew A. Chen
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Kelly Clark
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Blake E. Dewey
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Anna DuVal
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Nicole Pellegrini
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Govind Nair
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Youmna Jalkh
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Masschusetts, United States of America
| | - Samar Khalil
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Masschusetts, United States of America
| | - Jon Zurawski
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Masschusetts, United States of America
| | - Peter A. Calabresi
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Daniel S. Reich
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Rohit Bakshi
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Masschusetts, United States of America
- Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Haochang Shou
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Center for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Russell T. Shinohara
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Center for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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Zheng Y, Liu Y, Yang J, Dong L, Zhang R, Tian S, Yu Y, Ren L, Hou W, Zhu F, Mai Y, Han J, Zhang L, Jiang H, Lin L, Lou J, Li R, Lin J, Liu H, Kong Z, Wang D, Dai F, Bao D, Cao Z, Chen Q, Chen Q, Chen X, Gao Y, Jiang H, Li B, Li B, Li J, Liu R, Qing T, Shang E, Shang J, Sun S, Wang H, Wang X, Zhang N, Zhang P, Zhang R, Zhu S, Scherer A, Wang J, Wang J, Huo Y, Liu G, Cao C, Shao L, Xu J, Hong H, Xiao W, Liang X, Lu D, Jin L, Tong W, Ding C, Li J, Fang X, Shi L. Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials. Nat Biotechnol 2024; 42:1133-1149. [PMID: 37679543 PMCID: PMC11252085 DOI: 10.1038/s41587-023-01934-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 07/31/2023] [Indexed: 09/09/2023]
Abstract
Characterization and integration of the genome, epigenome, transcriptome, proteome and metabolome of different datasets is difficult owing to a lack of ground truth. Here we develop and characterize suites of publicly available multi-omics reference materials of matched DNA, RNA, protein and metabolites derived from immortalized cell lines from a family quartet of parents and monozygotic twin daughters. These references provide built-in truth defined by relationships among the family members and the information flow from DNA to RNA to protein. We demonstrate how using a ratio-based profiling approach that scales the absolute feature values of a study sample relative to those of a concurrently measured common reference sample produces reproducible and comparable data suitable for integration across batches, labs, platforms and omics types. Our study identifies reference-free 'absolute' feature quantification as the root cause of irreproducibility in multi-omics measurement and data integration and establishes the advantages of ratio-based multi-omics profiling with common reference materials.
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Affiliation(s)
- Yuanting Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.
| | - Yaqing Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jingcheng Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
- Greater Bay Area Institute of Precision Medicine, Guangzhou, China
| | | | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, China
| | - Sha Tian
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Ying Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Luyao Ren
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Wanwan Hou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Feng Zhu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yuanbang Mai
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | | | | | | | - Ling Lin
- Zhangjiang Center for Translational Medicine, Shanghai Biotecan Medical Diagnostics Co. Ltd., Shanghai, China
| | - Jingwei Lou
- Zhangjiang Center for Translational Medicine, Shanghai Biotecan Medical Diagnostics Co. Ltd., Shanghai, China
| | - Ruiqiang Li
- Novogene Bioinformatics Institute, Beijing, China
| | - Jingchao Lin
- Metabo-Profile Biotechnology (Shanghai) Co. Ltd., Shanghai, China
| | | | | | - Depeng Wang
- Nextomics Biosciences Institute, Wuhan, China
| | | | - Ding Bao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Zehui Cao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Qiaochu Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Qingwang Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Xingdong Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yuechen Gao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - He Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Bin Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Bingying Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jingjing Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
- Nextomics Biosciences Institute, Wuhan, China
| | - Ruimei Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Tao Qing
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Erfei Shang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jun Shang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Shanyue Sun
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Haiyan Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Xiaolin Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Naixin Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Peipei Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Ruolan Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Sibo Zhu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Andreas Scherer
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- EATRIS ERIC-European Infrastructure for Translational Medicine, Amsterdam, the Netherlands
| | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jing Wang
- National Institute of Metrology, Beijing, China
| | - Yinbo Huo
- Key Laboratory of Bioanalysis and Metrology for State Market Regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai, China
| | - Gang Liu
- Key Laboratory of Bioanalysis and Metrology for State Market Regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai, China
| | - Chengming Cao
- Key Laboratory of Bioanalysis and Metrology for State Market Regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai, China
| | - Li Shao
- Key Laboratory of Bioanalysis and Metrology for State Market Regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai, China
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Wenming Xiao
- Office of Oncologic Diseases, Office of New Drugs, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Xiaozhen Liang
- Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Daru Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Weida Tong
- Key Laboratory of Bioanalysis and Metrology for State Market Regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai, China
| | - Chen Ding
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, China.
| | - Xiang Fang
- National Institute of Metrology, Beijing, China.
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Cancer Center, Fudan University, Shanghai, China.
- International Human Phenome Institutes (Shanghai), Shanghai, China.
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44
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MaxFuse enables data integration across weakly linked spatial and single-cell modalities. Nat Biotechnol 2024; 42:1036-1037. [PMID: 37679547 DOI: 10.1038/s41587-023-01943-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
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45
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Yuan DY, McKeague ML, Raghu VK, Schoen RE, Finn OJ, Benos PV. Cellular and transcriptional profiles of peripheral blood mononuclear cells pre-vaccination predict immune response to preventative MUC1 vaccine. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.598031. [PMID: 38948837 PMCID: PMC11212910 DOI: 10.1101/2024.06.14.598031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
A single arm trial (NCT007773097) and a double-blind, placebo controlled randomized trial ( NCT02134925 ) were conducted in individuals with a history of advanced colonic adenoma to test the safety and immunogenicity of the MUC1 tumor antigen vaccine and its potential to prevent new adenomas. These were the first two trials of a non-viral cancer vaccine administered in the absence of cancer. The vaccine was safe and strongly immunogenic in 43% (NCT007773097) and 25% ( NCT02134925 ) of participants. The lack of response in a significant number of participants suggested, for the first time, that even in a premalignant setting, the immune system may have already been exposed to some level of suppression previously reported only in cancer. Single-cell RNA-sequencing (scRNA-seq) on banked pre-vaccination peripheral blood mononuclear cells (PBMCs) from 16 immune responders and 16 non-responders identified specific cell types, genes, and pathways of a productive vaccine response. Responders had a significantly higher percentage of CD4+ naive T cells pre-vaccination, but a significantly lower percentage of CD8+ T effector memory (TEM) cells and CD16+ monocytes. Differential gene expression (DGE) and transcription factor inference analysis showed a higher level of expression of T cell activation genes, such as Fos and Jun, in CD4+ naive T cells, and pathway analysis showed enriched signaling activity in responders. Furthermore, Bayesian network analysis suggested that these genes were mechanistically connected to response. Our analyses identified several immune mechanisms and candidate biomarkers to be further validated as predictors of immune responses to a preventative cancer vaccine that could facilitate selection of individuals likely to benefit from a vaccine or be used to improve vaccine responses.
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46
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Nishide M, Shimagami H, Kumanogoh A. Single-cell analysis in rheumatic and allergic diseases: insights for clinical practice. Nat Rev Immunol 2024:10.1038/s41577-024-01043-3. [PMID: 38914790 DOI: 10.1038/s41577-024-01043-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2024] [Indexed: 06/26/2024]
Abstract
Since the advent of single-cell RNA sequencing (scRNA-seq) methodology, single-cell analysis has become a powerful tool for exploration of cellular networks and dysregulated immune responses in disease pathogenesis. Advanced bioinformatics tools have enabled the combined analysis of scRNA-seq data and information on various cell properties, such as cell surface molecular profiles, chromatin accessibility and spatial information, leading to a deeper understanding of pathology. This Review provides an overview of the achievements in single-cell analysis applied to clinical samples of rheumatic and allergic diseases, including rheumatoid arthritis, systemic lupus erythematosus, systemic sclerosis, allergic airway diseases and atopic dermatitis, with an expanded scope beyond peripheral blood cells to include local diseased tissues. Despite the valuable insights that single-cell analysis has provided into disease pathogenesis, challenges remain in translating single-cell findings into clinical practice and developing personalized treatment strategies. Beyond understanding the atlas of cellular diversity, we discuss the application of data obtained in each study to clinical practice, with a focus on identifying biomarkers and therapeutic targets.
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Affiliation(s)
- Masayuki Nishide
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.
- Department of Immunopathology, World Premier International Research Center Initiative (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan.
- Department of Advanced Clinical and Translational Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.
| | - Hiroshi Shimagami
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Immunopathology, World Premier International Research Center Initiative (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan
- Department of Advanced Clinical and Translational Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.
- Department of Immunopathology, World Premier International Research Center Initiative (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan.
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan.
- Center for Infectious Diseases for Education and Research (CiDER), Osaka University, Suita, Osaka, Japan.
- Center for Advanced Modalities and DDS (CAMaD), Osaka University, Suita, Osaka, Japan.
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47
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Bhuiyan SA, Xu M, Yang L, Semizoglou E, Bhatia P, Pantaleo KI, Tochitsky I, Jain A, Erdogan B, Blair S, Cat V, Mwirigi JM, Sankaranarayanan I, Tavares-Ferreira D, Green U, McIlvried LA, Copits BA, Bertels Z, Del Rosario JS, Widman AJ, Slivicki RA, Yi J, Sharif-Naeini R, Woolf CJ, Lennerz JK, Whited JL, Price TJ, Robert W Gereau Iv, Renthal W. Harmonized cross-species cell atlases of trigeminal and dorsal root ganglia. SCIENCE ADVANCES 2024; 10:eadj9173. [PMID: 38905344 DOI: 10.1126/sciadv.adj9173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 05/16/2024] [Indexed: 06/23/2024]
Abstract
Sensory neurons in the dorsal root ganglion (DRG) and trigeminal ganglion (TG) are specialized to detect and transduce diverse environmental stimuli to the central nervous system. Single-cell RNA sequencing has provided insights into the diversity of sensory ganglia cell types in rodents, nonhuman primates, and humans, but it remains difficult to compare cell types across studies and species. We thus constructed harmonized atlases of the DRG and TG that describe and facilitate comparison of 18 neuronal and 11 non-neuronal cell types across six species and 31 datasets. We then performed single-cell/nucleus RNA sequencing of DRG from both human and the highly regenerative axolotl and found that the harmonized atlas also improves cell type annotation, particularly of sparse neuronal subtypes. We observed that the transcriptomes of sensory neuron subtypes are broadly similar across vertebrates, but the expression of functionally important neuropeptides and channels can vary notably. The resources presented here can guide future studies in comparative transcriptomics, simplify cell-type nomenclature differences across studies, and help prioritize targets for future analgesic development.
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Affiliation(s)
- Shamsuddin A Bhuiyan
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Mengyi Xu
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Alan Edwards Center for Research on Pain and Department of Physiology, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Lite Yang
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Evangelia Semizoglou
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Parth Bhatia
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Katerina I Pantaleo
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Ivan Tochitsky
- F.M. Kirby Neurobiology Center and Department of Neurobiology, Boston Children's Hospital and Harvard Medical School, 3 Blackfan Cir., Boston, MA 02115, USA
| | - Aakanksha Jain
- F.M. Kirby Neurobiology Center and Department of Neurobiology, Boston Children's Hospital and Harvard Medical School, 3 Blackfan Cir., Boston, MA 02115, USA
| | - Burcu Erdogan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Steven Blair
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Victor Cat
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Juliet M Mwirigi
- Department of Neuroscience and Center for Advanced Pain Studies, University of Texas at Dallas, 800 W Campbell Rd, Richardson, TX, 75080, USA
| | - Ishwarya Sankaranarayanan
- Department of Neuroscience and Center for Advanced Pain Studies, University of Texas at Dallas, 800 W Campbell Rd, Richardson, TX, 75080, USA
| | - Diana Tavares-Ferreira
- Department of Neuroscience and Center for Advanced Pain Studies, University of Texas at Dallas, 800 W Campbell Rd, Richardson, TX, 75080, USA
| | - Ursula Green
- Department of Pathology, Center for Integrated Diagnostics, Massachussetts General Hospital and Havard Medical School, Boston, MA 02114, USA
| | - Lisa A McIlvried
- Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Bryan A Copits
- Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Zachariah Bertels
- Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - John S Del Rosario
- Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Allie J Widman
- Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Richard A Slivicki
- Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Jiwon Yi
- Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Reza Sharif-Naeini
- Alan Edwards Center for Research on Pain and Department of Physiology, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Clifford J Woolf
- F.M. Kirby Neurobiology Center and Department of Neurobiology, Boston Children's Hospital and Harvard Medical School, 3 Blackfan Cir., Boston, MA 02115, USA
| | - Jochen K Lennerz
- Department of Pathology, Center for Integrated Diagnostics, Massachussetts General Hospital and Havard Medical School, Boston, MA 02114, USA
| | - Jessica L Whited
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Theodore J Price
- Department of Neuroscience and Center for Advanced Pain Studies, University of Texas at Dallas, 800 W Campbell Rd, Richardson, TX, 75080, USA
| | - Robert W Gereau Iv
- Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - William Renthal
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
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Zhou M, Zhang H, Bai Z, Mann-Krzisnik D, Wang F, Li Y. Protocol to perform integrative analysis of high-dimensional single-cell multimodal data using an interpretable deep learning technique. STAR Protoc 2024; 5:103066. [PMID: 38748882 PMCID: PMC11109308 DOI: 10.1016/j.xpro.2024.103066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/21/2023] [Accepted: 04/24/2024] [Indexed: 05/25/2024] Open
Abstract
The advent of single-cell multi-omics sequencing technology makes it possible for researchers to leverage multiple modalities for individual cells. Here, we present a protocol to perform integrative analysis of high-dimensional single-cell multimodal data using an interpretable deep learning technique called moETM. We describe steps for data preprocessing, multi-omics integration, inclusion of prior pathway knowledge, and cross-omics imputation. As a demonstration, we used the single-cell multi-omics data collected from bone marrow mononuclear cells (GSE194122) as in our original study. For complete details on the use and execution of this protocol, please refer to Zhou et al.1.
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Affiliation(s)
- Manqi Zhou
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA; Institute of Artificial Intelligence for Digital Health, Weill Cornell Medicine, New York, NY 10021, USA
| | - Hao Zhang
- Division of Health Informatics, Department of Population Health Sciences, Weill Cornell Medicine, New York, NY 10021, USA
| | - Zilong Bai
- Institute of Artificial Intelligence for Digital Health, Weill Cornell Medicine, New York, NY 10021, USA; Division of Health Informatics, Department of Population Health Sciences, Weill Cornell Medicine, New York, NY 10021, USA
| | | | - Fei Wang
- Institute of Artificial Intelligence for Digital Health, Weill Cornell Medicine, New York, NY 10021, USA; Division of Health Informatics, Department of Population Health Sciences, Weill Cornell Medicine, New York, NY 10021, USA
| | - Yue Li
- Quantitative Life Science, McGill University, Montréal, QC H3A 0G4, Canada; School of Computer Science, McGill University, Montréal, QC H3A 0G4, Canada; Mila - Quebec AI Institute, Montréal, QC H2S 3H1, Canada.
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49
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Chen J, Zhou M, Wu W, Zhang J, Li Y, Li D. STimage-1K4M: A histopathology image-gene expression dataset for spatial transcriptomics. ARXIV 2024:arXiv:2406.06393v2. [PMID: 38947920 PMCID: PMC11213178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Recent advances in multi-modal algorithms have driven and been driven by the increasing availability of large image-text datasets, leading to significant strides in various fields, including computational pathology. However, in most existing medical image-text datasets, the text typically provides high-level summaries that may not sufficiently describe sub-tile regions within a large pathology image. For example, an image might cover an extensive tissue area containing cancerous and healthy regions, but the accompanying text might only specify that this image is a cancer slide, lacking the nuanced details needed for in-depth analysis. In this study, we introduce STimage-1K4M, a novel dataset designed to bridge this gap by providing genomic features for sub-tile images. STimage-1K4M contains 1,149 images derived from spatial transcriptomics data, which captures gene expression information at the level of individual spatial spots within a pathology image. Specifically, each image in the dataset is broken down into smaller sub-image tiles, with each tile paired with 15,000 - 30,000 dimensional gene expressions. With 4,293,195 pairs of sub-tile images and gene expressions, STimage-1K4M offers unprecedented granularity, paving the way for a wide range of advanced research in multi-modal data analysis an innovative applications in computational pathology, and beyond.
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Affiliation(s)
| | | | - Wenrong Wu
- University of North Carolina at Chapel Hill
| | | | - Yun Li
- University of North Carolina at Chapel Hill
| | - Didong Li
- University of North Carolina at Chapel Hill
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50
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Wang Y, Thistlethwaite W, Tadych A, Ruf-Zamojski F, Bernard DJ, Cappuccio A, Zaslavsky E, Chen X, Sealfon SC, Troyanskaya OG. Automated single-cell omics end-to-end framework with data-driven batch inference. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.01.564815. [PMID: 37961197 PMCID: PMC10635042 DOI: 10.1101/2023.11.01.564815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
To facilitate single-cell multi-omics analysis and improve reproducibility, we present SPEEDI (Single-cell Pipeline for End to End Data Integration), a fully automated end-to-end framework for batch inference, data integration, and cell type labeling. SPEEDI introduces data-driven batch inference and transforms the often heterogeneous data matrices obtained from different samples into a uniformly annotated and integrated dataset. Without requiring user input, it automatically selects parameters and executes pre-processing, sample integration, and cell type mapping. It can also perform downstream analyses of differential signals between treatment conditions and gene functional modules. SPEEDI's data-driven batch inference method works with widely used integration and cell-typing tools. By developing data-driven batch inference, providing full end-to-end automation, and eliminating parameter selection, SPEEDI improves reproducibility and lowers the barrier to obtaining biological insight from these valuable single-cell datasets. The SPEEDI interactive web application can be accessed at https://speedi.princeton.edu/.
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Affiliation(s)
- Yuan Wang
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
- These authors contributed equally
| | - William Thistlethwaite
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
- These authors contributed equally
| | - Alicja Tadych
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
| | | | - Daniel J Bernard
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Antonio Cappuccio
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elena Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xi Chen
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
| | - Stuart C. Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Olga G. Troyanskaya
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
- Lead contact
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