1
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Sprang M, Möllmann J, Andrade-Navarro MA, Fontaine JF. Overlooked poor-quality patient samples in sequencing data impair reproducibility of published clinically relevant datasets. Genome Biol 2024; 25:222. [PMID: 39152483 PMCID: PMC11328481 DOI: 10.1186/s13059-024-03331-6] [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: 06/13/2023] [Accepted: 07/08/2024] [Indexed: 08/19/2024] Open
Abstract
BACKGROUND Reproducibility is a major concern in biomedical studies, and existing publication guidelines do not solve the problem. Batch effects and quality imbalances between groups of biological samples are major factors hampering reproducibility. Yet, the latter is rarely considered in the scientific literature. RESULTS Our analysis uses 40 clinically relevant RNA-seq datasets to quantify the impact of quality imbalance between groups of samples on the reproducibility of gene expression studies. High-quality imbalance is frequent (14 datasets; 35%), and hundreds of quality markers are present in more than 50% of the datasets. Enrichment analysis suggests common stress-driven effects among the low-quality samples and highlights a complementary role of transcription factors and miRNAs to regulate stress response. Preliminary ChIP-seq results show similar trends. Quality imbalance has an impact on the number of differential genes derived by comparing control to disease samples (the higher the imbalance, the higher the number of genes), on the proportion of quality markers in top differential genes (the higher the imbalance, the higher the proportion; up to 22%) and on the proportion of known disease genes in top differential genes (the higher the imbalance, the lower the proportion). We show that removing outliers based on their quality score improves the resulting downstream analysis. CONCLUSIONS Thanks to a stringent selection of well-designed datasets, we demonstrate that quality imbalance between groups of samples can significantly reduce the relevance of differential genes, consequently reducing reproducibility between studies. Appropriate experimental design and analysis methods can substantially reduce the problem.
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Affiliation(s)
- Maximilian Sprang
- Faculty of Biology, Johannes Gutenberg-Universität Mainz, Biozentrum I, Hans-Dieter-Hüsch-Weg 15, Mainz, 55128, Germany
| | - Jannik Möllmann
- Faculty of Biology, Johannes Gutenberg-Universität Mainz, Biozentrum I, Hans-Dieter-Hüsch-Weg 15, Mainz, 55128, Germany
| | - Miguel A Andrade-Navarro
- Faculty of Biology, Johannes Gutenberg-Universität Mainz, Biozentrum I, Hans-Dieter-Hüsch-Weg 15, Mainz, 55128, Germany.
| | - Jean-Fred Fontaine
- Faculty of Biology, Johannes Gutenberg-Universität Mainz, Biozentrum I, Hans-Dieter-Hüsch-Weg 15, Mainz, 55128, Germany
- Central Institute for Decision Support Systems in Crop Protection (ZEPP), Rüdesheimer Str. 60-68, Bad Kreuznach, 55545, Germany
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2
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Saraswathy VM, Zhou L, Mokalled MH. Single-cell analysis of innate spinal cord regeneration identifies intersecting modes of neuronal repair. Nat Commun 2024; 15:6808. [PMID: 39147780 PMCID: PMC11327264 DOI: 10.1038/s41467-024-50628-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 07/11/2024] [Indexed: 08/17/2024] Open
Abstract
Adult zebrafish have an innate ability to recover from severe spinal cord injury. Here, we report a comprehensive single nuclear RNA sequencing atlas that spans 6 weeks of regeneration. We identify cooperative roles for adult neurogenesis and neuronal plasticity during spinal cord repair. Neurogenesis of glutamatergic and GABAergic neurons restores the excitatory/inhibitory balance after injury. In addition, a transient population of injury-responsive neurons (iNeurons) show elevated plasticity 1 week post-injury. We found iNeurons are injury-surviving neurons that acquire a neuroblast-like gene expression signature after injury. CRISPR/Cas9 mutagenesis showed iNeurons are required for functional recovery and employ vesicular trafficking as an essential mechanism that underlies neuronal plasticity. This study provides a comprehensive resource of the cells and mechanisms that direct spinal cord regeneration and establishes zebrafish as a model of plasticity-driven neural repair.
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Affiliation(s)
- Vishnu Muraleedharan Saraswathy
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Lili Zhou
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - Mayssa H Mokalled
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA.
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3
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Leduc A, Xu Y, Shipkovenska G, Dou Z, Slavov N. Limiting the impact of protein leakage in single-cell proteomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.26.605378. [PMID: 39091738 PMCID: PMC11291177 DOI: 10.1101/2024.07.26.605378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Limiting artifacts during sample preparation can significantly increase data quality in single-cell proteomics experiments. Towards this goal, we characterize the impact of protein leakage by analyzing thousands of primary single cells that were prepared either fresh immediately after dissociation or cryopreserved and prepared at a later date. We directly identify permeabilized cells and use the data to define a signature for protein leakage. We use this signature to build a classifier for identifying damaged cells that performs accurately across cell types and species.
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Affiliation(s)
- Andrew Leduc
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, Northeastern University, Boston, MA 02115, USA
| | - Yanxin Xu
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Gergana Shipkovenska
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Zhixun Dou
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Nikolai Slavov
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, Northeastern University, Boston, MA 02115, USA
- Parallel Squared Technology Institute, Watertown, MA 02472, USA
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4
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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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5
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Moerkens R, Mooiweer J, Ramírez-Sánchez AD, Oelen R, Franke L, Wijmenga C, Barrett RJ, Jonkers IH, Withoff S. An iPSC-derived small intestine-on-chip with self-organizing epithelial, mesenchymal, and neural cells. Cell Rep 2024; 43:114247. [PMID: 38907996 DOI: 10.1016/j.celrep.2024.114247] [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: 02/23/2024] [Revised: 04/10/2024] [Accepted: 05/02/2024] [Indexed: 06/24/2024] Open
Abstract
Human induced pluripotent stem cell (hiPSC)-derived intestinal organoids are valuable tools for researching developmental biology and personalized therapies, but their closed topology and relative immature state limit applications. Here, we use organ-on-chip technology to develop a hiPSC-derived intestinal barrier with apical and basolateral access in a more physiological in vitro microenvironment. To replicate growth factor gradients along the crypt-villus axis, we locally expose the cells to expansion and differentiation media. In these conditions, intestinal epithelial cells self-organize into villus-like folds with physiological barrier integrity, and myofibroblasts and neurons emerge and form a subepithelial tissue in the bottom channel. The growth factor gradients efficiently balance dividing and mature cell types and induce an intestinal epithelial composition, including absorptive and secretory lineages, resembling the composition of the human small intestine. This well-characterized hiPSC-derived intestine-on-chip system can facilitate personalized studies on physiological processes and therapy development in the human small intestine.
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Affiliation(s)
- Renée Moerkens
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Joram Mooiweer
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Aarón D Ramírez-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Roy Oelen
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands; Oncode Institute, 3521 AL Utrecht, the Netherlands
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands; Oncode Institute, 3521 AL Utrecht, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Robert J Barrett
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; F. Widjaja Foundation Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Iris H Jonkers
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Sebo Withoff
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands.
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6
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Chen Y, Li E, Chang Z, Zhang T, Song Z, Wu H, Cheng ZJ, Sun B. Identifying potential therapeutic targets in lung adenocarcinoma: a multi-omics approach integrating bulk and single-cell RNA sequencing with Mendelian randomization. Front Pharmacol 2024; 15:1433147. [PMID: 39092217 PMCID: PMC11291359 DOI: 10.3389/fphar.2024.1433147] [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: 05/15/2024] [Accepted: 06/25/2024] [Indexed: 08/04/2024] Open
Abstract
Our research aimed to identify new therapeutic targets for Lung adenocarcinoma (LUAD), a major subtype of non-small cell lung cancer known for its low 5-year survival rate of 22%. By employing a comprehensive methodological approach, we analyzed bulk RNA sequencing data from 513 LUAD and 59 non-tumorous tissues, identifying 2,688 differentially expressed genes. Using Mendelian randomization (MR), we identified 74 genes with strong evidence for a causal effect on risk of LUAD. Survival analysis on these genes revealed significant differences in survival rates for 13 of them. Our pathway enrichment analysis highlighted their roles in immune response and cell communication, deepening our understanding. We also utilized single-cell RNA sequencing (scRNA-seq) to uncover cell type-specific gene expression patterns within LUAD, emphasizing the tumor microenvironment's heterogeneity. Pseudotime analysis further assisted in assessing the heterogeneity of tumor cell populations. Additionally, protein-protein interaction (PPI) network analysis was conducted to evaluate the potential druggability of these identified genes. The culmination of our efforts led to the identification of five genes (tier 1) with the most compelling evidence, including SECISBP2L, PRCD, SMAD9, C2orf91, and HSD17B13, and eight genes (tier 2) with convincing evidence for their potential as therapeutic targets.
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Affiliation(s)
- Youpeng Chen
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Enzhong Li
- Department of Endocrinology, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhenglin Chang
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Tingting Zhang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhenfeng Song
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Haojie Wu
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Zhangkai J. Cheng
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Baoqing Sun
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
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7
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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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8
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Chen R, Nie P, Wang J, Wang GZ. Deciphering brain cellular and behavioral mechanisms: Insights from single-cell and spatial RNA sequencing. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1865. [PMID: 38972934 DOI: 10.1002/wrna.1865] [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: 01/31/2024] [Revised: 05/05/2024] [Accepted: 05/14/2024] [Indexed: 07/09/2024]
Abstract
The brain is a complex computing system composed of a multitude of interacting neurons. The computational outputs of this system determine the behavior and perception of every individual. Each brain cell expresses thousands of genes that dictate the cell's function and physiological properties. Therefore, deciphering the molecular expression of each cell is of great significance for understanding its characteristics and role in brain function. Additionally, the positional information of each cell can provide crucial insights into their involvement in local brain circuits. In this review, we briefly overview the principles of single-cell RNA sequencing and spatial transcriptomics, the potential issues and challenges in their data processing, and their applications in brain research. We further outline several promising directions in neuroscience that could be integrated with single-cell RNA sequencing, including neurodevelopment, the identification of novel brain microstructures, cognition and behavior, neuronal cell positioning, molecules and cells related to advanced brain functions, sleep-wake cycles/circadian rhythms, and computational modeling of brain function. We believe that the deep integration of these directions with single-cell and spatial RNA sequencing can contribute significantly to understanding the roles of individual cells or cell types in these specific functions, thereby making important contributions to addressing critical questions in those fields. This article is categorized under: RNA Evolution and Genomics > Computational Analyses of RNA RNA in Disease and Development > RNA in Development RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Renrui Chen
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Pengxing Nie
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jing Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Guang-Zhong Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
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9
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Martin-Martin C, Suarez-Alvarez B, González M, Torres IB, Bestard O, Martín JE, Barceló-Coblijn G, Moreso F, Aransay AM, Lopez-Larrea C, Rodriguez RM. Exploring kidney allograft rejection: A proof-of-concept study using spatial transcriptomics. Am J Transplant 2024; 24:1161-1171. [PMID: 38692412 DOI: 10.1016/j.ajt.2024.04.015] [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: 11/06/2023] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/03/2024]
Abstract
In this proof-of-concept study, spatial transcriptomics combined with public single-cell ribonucleic acid-sequencing data were used to explore the potential of this technology to study kidney allograft rejection. We aimed to map gene expression patterns within diverse pathologic states by examining biopsies classified across nonrejection, T cell-mediated acute rejection, interstitial fibrosis, and tubular atrophy. Our results revealed distinct immune cell signatures, including those of T and B lymphocytes, monocytes, mast cells, and plasma cells, and their spatial organization within the renal interstitium. We also mapped chemokine receptors and ligands to study immune cell migration and recruitment. Finally, our analysis demonstrated differential spatial enrichment of transcription signatures associated with kidney allograft rejection across various biopsy regions. Interstitium regions displayed higher enrichment scores for rejection-associated gene expression patterns than tubular areas, which had negative scores. This implies that these signatures are primarily driven by processes unfolding in the renal interstitium. Overall, this study highlights the value of spatial transcriptomics for revealing cellular heterogeneity and immune signatures in renal transplant biopsies and demonstrates its potential for studying the molecular and cellular mechanisms associated with rejection. However, certain limitations must be borne in mind regarding the development and future applications of this technology.
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Affiliation(s)
- Cristina Martin-Martin
- Translational Immunology, Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain; RICORS2040, Kidney Disease Research Network, ISCIII, Madrid, Spain
| | - Beatriz Suarez-Alvarez
- Translational Immunology, Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain; RICORS2040, Kidney Disease Research Network, ISCIII, Madrid, Spain
| | - Monika González
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 bld., 48160, Derio, Bizkaia, Spain
| | - Irina B Torres
- Department of Nephrology, Hospital Universitari Vall d'Hebron, Barcelona, Spain; Nephrology and Renal Transplant Laboratory, Vall Hebron Research Institute (VHIR), Barcelona, Spain; Department of Medicine, Autonomous University of Barcelona, Barcelona, Spain
| | - Oriol Bestard
- Department of Nephrology, Hospital Universitari Vall d'Hebron, Barcelona, Spain; Nephrology and Renal Transplant Laboratory, Vall Hebron Research Institute (VHIR), Barcelona, Spain; Department of Medicine, Autonomous University of Barcelona, Barcelona, Spain
| | - José E Martín
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 bld., 48160, Derio, Bizkaia, Spain
| | - Gwendolyn Barceló-Coblijn
- Lipids in Human Pathology, Institut d'Investigació Sanitària Illes Balears (IdISBa), Ctra. Valldemossa 79, E-07120 Palma, Balearic Islands, Spain; Research Unit, University Hospital Son Espases, Ctra. Valldemossa 79, E-07120 Palma, Balearic Islands, Spain
| | - Francesc Moreso
- Department of Nephrology, Hospital Universitari Vall d'Hebron, Barcelona, Spain; Nephrology and Renal Transplant Laboratory, Vall Hebron Research Institute (VHIR), Barcelona, Spain; Department of Medicine, Autonomous University of Barcelona, Barcelona, Spain
| | - Ana M Aransay
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 801 bld., 48160, Derio, Bizkaia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Carlos Lopez-Larrea
- Translational Immunology, Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011, Oviedo, Asturias, Spain; RICORS2040, Kidney Disease Research Network, ISCIII, Madrid, Spain; Department of Immunology, Hospital Universitario Central de Asturias, 33011, Oviedo, Spain.
| | - Ramon M Rodriguez
- Lipids in Human Pathology, Institut d'Investigació Sanitària Illes Balears (IdISBa), Ctra. Valldemossa 79, E-07120 Palma, Balearic Islands, Spain; Research Unit, University Hospital Son Espases, Ctra. Valldemossa 79, E-07120 Palma, Balearic Islands, Spain
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10
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Chen EZ, Kannan S, Murphy S, Farid M, Kwon C. Protocol for quantifying stem-cell-derived cardiomyocyte maturity using transcriptomic entropy score. STAR Protoc 2024; 5:103083. [PMID: 38781077 PMCID: PMC11145390 DOI: 10.1016/j.xpro.2024.103083] [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: 12/08/2023] [Revised: 03/15/2024] [Accepted: 05/01/2024] [Indexed: 05/25/2024] Open
Abstract
The inability to quantify cardiomyocyte (CM) maturation remains a significant barrier to evaluating the effects of ongoing efforts to produce adult-like CMs from pluripotent stem cells (PSCs). Here, we present a protocol to quantify stem-cell-derived CM maturity using a single-cell RNA sequencing-based metric "entropy score." We describe steps for generating an entropy score using customized R code. This tool can be used to quantify maturation levels of PSC-CMs and potentially other cell types. For complete details on the use and execution of this protocol, please refer to Kannan et al.1.
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Affiliation(s)
- Elaine Zhelan Chen
- Division of Cardiology, Department of Medicine, Johns Hopkins School of Medicine; Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins School of Medicine; Baltimore, MD, USA; Department of Cell Biology, Johns Hopkins School of Medicine; Baltimore, MD, USA; Institute for Cell Engineering, Johns Hopkins School of Medicine; Baltimore, MD, USA
| | - Suraj Kannan
- Division of Cardiology, Department of Medicine, Johns Hopkins School of Medicine; Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins School of Medicine; Baltimore, MD, USA; Department of Cell Biology, Johns Hopkins School of Medicine; Baltimore, MD, USA; Institute for Cell Engineering, Johns Hopkins School of Medicine; Baltimore, MD, USA
| | - Sean Murphy
- Division of Cardiology, Department of Medicine, Johns Hopkins School of Medicine; Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins School of Medicine; Baltimore, MD, USA; Department of Cell Biology, Johns Hopkins School of Medicine; Baltimore, MD, USA; Institute for Cell Engineering, Johns Hopkins School of Medicine; Baltimore, MD, USA
| | - Michael Farid
- Division of Cardiology, Department of Medicine, Johns Hopkins School of Medicine; Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins School of Medicine; Baltimore, MD, USA; Department of Cell Biology, Johns Hopkins School of Medicine; Baltimore, MD, USA; Institute for Cell Engineering, Johns Hopkins School of Medicine; Baltimore, MD, USA
| | - Chulan Kwon
- Division of Cardiology, Department of Medicine, Johns Hopkins School of Medicine; Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins School of Medicine; Baltimore, MD, USA; Department of Cell Biology, Johns Hopkins School of Medicine; Baltimore, MD, USA; Institute for Cell Engineering, Johns Hopkins School of Medicine; Baltimore, MD, USA.
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11
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Zaragoza MV, Bui TA, Widyastuti HP, Mehrabi M, Cang Z, Sha Y, Grosberg A, Nie Q. LMNA -Related Dilated Cardiomyopathy: Single-Cell Transcriptomics during Patient-derived iPSC Differentiation Support Cell type and Lineage-specific Dysregulation of Gene Expression and Development for Cardiomyocytes and Epicardium-Derived Cells with Lamin A/C Haploinsufficiency. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598335. [PMID: 38915555 PMCID: PMC11195187 DOI: 10.1101/2024.06.12.598335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
LMNA -Related Dilated Cardiomyopathy (DCM) is an autosomal-dominant genetic condition with cardiomyocyte and conduction system dysfunction often resulting in heart failure or sudden death. The condition is caused by mutation in the Lamin A/C ( LMNA ) gene encoding Type-A nuclear lamin proteins involved in nuclear integrity, epigenetic regulation of gene expression, and differentiation. Molecular mechanisms of disease are not completely understood, and there are no definitive treatments to reverse progression or prevent mortality. We investigated possible mechanisms of LMNA -Related DCM using induced pluripotent stem cells derived from a family with a heterozygous LMNA c.357-2A>G splice-site mutation. We differentiated one LMNA mutant iPSC line derived from an affected female (Patient) and two non-mutant iPSC lines derived from her unaffected sister (Control) and conducted single-cell RNA sequencing for 12 samples (4 Patient and 8 Control) across seven time points: Day 0, 2, 4, 9, 16, 19, and 30. Our bioinformatics workflow identified 125,554 cells in raw data and 110,521 (88%) high-quality cells in sequentially processed data. Unsupervised clustering, cell annotation, and trajectory inference found complex heterogeneity: ten main cell types; many possible subtypes; and lineage bifurcation for Cardiac Progenitors to Cardiomyocytes (CM) and Epicardium-Derived Cells (EPDC). Data integration and comparative analyses of Patient and Control cells found cell type and lineage differentially expressed genes (DEG) with enrichment to support pathway dysregulation. Top DEG and enriched pathways included: 10 ZNF genes and RNA polymerase II transcription in Pluripotent cells (PP); BMP4 and TGF Beta/BMP signaling, sarcomere gene subsets and cardiogenesis, CDH2 and EMT in CM; LMNA and epigenetic regulation and DDIT4 and mTORC1 signaling in EPDC. Top DEG also included: XIST and other X-linked genes, six imprinted genes: SNRPN , PWAR6 , NDN , PEG10 , MEG3 , MEG8 , and enriched gene sets in metabolism, proliferation, and homeostasis. We confirmed Lamin A/C haploinsufficiency by allelic expression and Western blot. Our complex Patient-derived iPSC model for Lamin A/C haploinsufficiency in PP, CM, and EPDC provided support for dysregulation of genes and pathways, many previously associated with Lamin A/C defects, such as epigenetic gene expression, signaling, and differentiation. Our findings support disruption of epigenomic developmental programs as proposed in other LMNA disease models. We recognized other factors influencing epigenetics and differentiation; thus, our approach needs improvement to further investigate this mechanism in an iPSC-derived model.
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12
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Shaw DK, Saraswathy VM, McAdow AR, Zhou L, Park D, Mote R, Johnson AN, Mokalled MH. Elevated phagocytic capacity directs innate spinal cord repair. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.11.598515. [PMID: 38915507 PMCID: PMC11195157 DOI: 10.1101/2024.06.11.598515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Immune cells elicit a continuum of transcriptional and functional states after spinal cord injury (SCI). In mammals, inefficient debris clearance and chronic inflammation impede recovery and overshadow pro-regenerative immune functions. We found that, unlike mammals, zebrafish SCI elicits transient immune activation and efficient debris clearance, without causing chronic inflammation. Single-cell transcriptomics and inducible genetic ablation showed zebrafish macrophages are highly phagocytic and required for regeneration. Cross-species comparisons between zebrafish and mammalian macrophages identified transcription and immune response regulator ( tcim ) as a macrophage-enriched zebrafish gene. Genetic deletion of zebrafish tcim impairs phagocytosis and regeneration, causes aberrant and chronic immune activation, and can be rescued by transplanting wild-type immune precursors into tcim mutants. Conversely, genetic expression of human TCIM accelerates debris clearance and regeneration by reprogramming myeloid precursors into activated phagocytes. This study establishes a central requirement for elevated phagocytic capacity to achieve innate spinal cord repair.
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13
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van Blokland IV, Oelen R, Groot HE, Benjamins JW, Pekayvaz K, Losert C, Knottenberg V, Heinig M, Nicolai L, Stark K, van der Harst P, Franke L, van der Wijst MG. Single-Cell Dissection of the Immune Response After Acute Myocardial Infarction. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2024; 17:e004374. [PMID: 38752343 PMCID: PMC11188632 DOI: 10.1161/circgen.123.004374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 04/17/2024] [Indexed: 06/20/2024]
Abstract
BACKGROUND The immune system's role in ST-segment-elevated myocardial infarction (STEMI) remains poorly characterized but is an important driver of recurrent cardiovascular events. While anti-inflammatory drugs show promise in reducing recurrence risk, their broad immune system impairment may induce severe side effects. To overcome these challenges, a nuanced understanding of the immune response to STEMI is needed. METHODS For this, we compared peripheral blood mononuclear single-cell RNA-sequencing (scRNA-seq) and plasma protein expression over time (hospital admission, 24 hours, and 6-8 weeks post-STEMI) in 38 patients and 38 controls (95 995 diseased and 33 878 control peripheral blood mononuclear cells). RESULTS Compared with controls, classical monocytes were increased and CD56dim natural killer cells were decreased in patients with STEMI at admission and persisted until 24 hours post-STEMI. The largest gene expression changes were observed in monocytes, associating with changes in toll-like receptor, interferon, and interleukin signaling activity. Finally, a targeted cardiovascular biomarker panel revealed expression changes in 33/92 plasma proteins post-STEMI. Interestingly, interleukin-6R, MMP9 (matrix metalloproteinase-9), and LDLR (low-density lipoprotein receptor) were affected by coronary artery disease-associated genetic risk variation, disease status, and time post-STEMI, indicating the importance of considering these aspects when defining potential future therapies. CONCLUSIONS Our analyses revealed the immunologic pathways disturbed by STEMI, specifying affected cell types and disease stages. Additionally, we provide insights into patients expected to benefit most from anti-inflammatory treatments by identifying the genetic variants and disease stage at which these variants affect the outcome of these (drug-targeted) pathways. These findings advance our knowledge of the immune response post-STEMI and provide guidance for future therapeutic studies.
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Affiliation(s)
- Irene V. van Blokland
- Department of Cardiology (I.V.B., H.E.G., J.W.B.), University Medical Center Groningen, Groningen, the Netherlands
- Department of Genetics (I.V.B., R.O., L.F., M.G.P.v.d.W.), University Medical Center Groningen, Groningen, the Netherlands
| | - Roy Oelen
- Department of Genetics (I.V.B., R.O., L.F., M.G.P.v.d.W.), University Medical Center Groningen, Groningen, the Netherlands
| | - Hilde E. Groot
- Department of Cardiology (I.V.B., H.E.G., J.W.B.), University Medical Center Groningen, Groningen, the Netherlands
| | - Jan Walter Benjamins
- Department of Cardiology (I.V.B., H.E.G., J.W.B.), University Medical Center Groningen, Groningen, the Netherlands
| | - Kami Pekayvaz
- Medizinische Klinik und Poliklinik I, University Hospital, Ludwig-Maximilian University, Munich, Germany (K.P., V.K., L.N., K.S.)
- German Center for Cardiovascular Research, Munich Heart Alliance, Munich, Germany (K.P., V.K., L.N., K.S.)
| | - Corinna Losert
- Institute of Computational Biology, German Research Center for Environmental Health, Helmholtz Zentrum München, Neuherberg, Germany (C.L., M.H.)
- Department of Computer Science, TUM School of Computation, Information & Technology, Garching, Germany (C.L., M.H.)
| | - Viktoria Knottenberg
- Medizinische Klinik und Poliklinik I, University Hospital, Ludwig-Maximilian University, Munich, Germany (K.P., V.K., L.N., K.S.)
- German Center for Cardiovascular Research, Munich Heart Alliance, Munich, Germany (K.P., V.K., L.N., K.S.)
| | - Matthias Heinig
- Institute of Computational Biology, German Research Center for Environmental Health, Helmholtz Zentrum München, Neuherberg, Germany (C.L., M.H.)
- Department of Computer Science, TUM School of Computation, Information & Technology, Garching, Germany (C.L., M.H.)
- Department of Informatics, Ludwig-Maximilians Universität München, Munich, Germany (M.H.)
| | - Leo Nicolai
- Medizinische Klinik und Poliklinik I, University Hospital, Ludwig-Maximilian University, Munich, Germany (K.P., V.K., L.N., K.S.)
- German Center for Cardiovascular Research, Munich Heart Alliance, Munich, Germany (K.P., V.K., L.N., K.S.)
| | - Konstantin Stark
- Medizinische Klinik und Poliklinik I, University Hospital, Ludwig-Maximilian University, Munich, Germany (K.P., V.K., L.N., K.S.)
- German Center for Cardiovascular Research, Munich Heart Alliance, Munich, Germany (K.P., V.K., L.N., K.S.)
| | - Pim van der Harst
- Department of Cardiology, University Medical Center Utrecht, Utrecht, the Netherlands (P.v.d.H.)
| | - Lude Franke
- Department of Genetics (I.V.B., R.O., L.F., M.G.P.v.d.W.), University Medical Center Groningen, Groningen, the Netherlands
| | - Monique G.P. van der Wijst
- Department of Genetics (I.V.B., R.O., L.F., M.G.P.v.d.W.), University Medical Center Groningen, Groningen, the Netherlands
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14
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Ehrlich A, Xu AA, Luminari S, Kidd S, Treiber CD, Russo J, Blau J. Tango-seq: overlaying transcriptomics on connectomics to identify neurons downstream of Drosophila clock neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595372. [PMID: 38826334 PMCID: PMC11142192 DOI: 10.1101/2024.05.22.595372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Knowing how neural circuits change with neuronal plasticity and differ between individuals is important to fully understand behavior. Connectomes are typically assembled using electron microscopy, but this is low throughput and impractical for analyzing plasticity or mutations. Here, we modified the trans-Tango genetic circuit-tracing technique to identify neurons synaptically downstream of Drosophila s-LNv clock neurons, which show 24hr plasticity rhythms. s-LNv target neurons were labeled specifically in adult flies using a nuclear reporter gene, which facilitated their purification and then single cell sequencing. We call this Tango-seq, and it allows transcriptomic data - and thus cell identity - to be overlayed on top of anatomical data. We found that s-LNvs preferentially make synaptic connections with a subset of the CNMa+ DN1p clock neurons, and that these are likely plastic connections. We also identified synaptic connections between s-LNvs and mushroom body Kenyon cells. Tango-seq should be a useful addition to the connectomics toolkit.
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Affiliation(s)
- Alison Ehrlich
- Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Angelina A Xu
- Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Sofia Luminari
- Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Simon Kidd
- Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Christoph D Treiber
- Centre for Neural Circuits and Behaviour, University of Oxford, UK
- Current address: Department of Biology, University of Oxford, UK
| | - Jordan Russo
- Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Justin Blau
- Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE
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15
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O'Callaghan A, Eling N, Marioni JC, Vallejos CA. BASiCS workflow: a step-by-step analysis of expression variability using single cell RNA sequencing data. F1000Res 2024; 11:59. [PMID: 38779464 PMCID: PMC11109695 DOI: 10.12688/f1000research.74416.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/26/2024] [Indexed: 05/25/2024] Open
Abstract
Cell-to-cell gene expression variability is an inherent feature of complex biological systems, such as immunity and development. Single-cell RNA sequencing is a powerful tool to quantify this heterogeneity, but it is prone to strong technical noise. In this article, we describe a step-by-step computational workflow that uses the BASiCS Bioconductor package to robustly quantify expression variability within and between known groups of cells (such as experimental conditions or cell types). BASiCS uses an integrated framework for data normalisation, technical noise quantification and downstream analyses, propagating statistical uncertainty across these steps. Within a single seemingly homogeneous cell population, BASiCS can identify highly variable genes that exhibit strong heterogeneity as well as lowly variable genes with stable expression. BASiCS also uses a probabilistic decision rule to identify changes in expression variability between cell populations, whilst avoiding confounding effects related to differences in technical noise or in overall abundance. Using a publicly available dataset, we guide users through a complete pipeline that includes preliminary steps for quality control, as well as data exploration using the scater and scran Bioconductor packages. The workflow is accompanied by a Docker image that ensures the reproducibility of our results.
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Affiliation(s)
- Alan O'Callaghan
- MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Nils Eling
- Institute for Molecular Health Sciences, ETH Zürich, Zürich, 8093, Switzerland
- Department of Quantitative Biomedicine, University of Zurich, Zürich, CH-8057, Switzerland
| | - John C. Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, CB10 1SD, UK
| | - Catalina A. Vallejos
- MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
- The Alan Turing Institute, The Alan Turing Institute, London, NW1 2DB, UK
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16
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Kotliar D, Curtis M, Agnew R, Weinand K, Nathan A, Baglaenko Y, Zhao Y, Sabeti PC, Rao DA, Raychaudhuri S. Reproducible single cell annotation of programs underlying T-cell subsets, activation states, and functions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592310. [PMID: 38746317 PMCID: PMC11092745 DOI: 10.1101/2024.05.03.592310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
T-cells recognize antigens and induce specialized gene expression programs (GEPs) enabling functions including proliferation, cytotoxicity, and cytokine production. Traditionally, different classes of helper T-cells express mutually exclusive responses - for example, Th1, Th2, and Th17 programs. However, new single-cell RNA sequencing (scRNA-Seq) experiments have revealed a continuum of T-cell states without discrete clusters corresponding to these subsets, implying the need for new analytical frameworks. Here, we advance the characterization of T-cells with T-CellAnnoTator (TCAT), a pipeline that simultaneously quantifies pre-defined GEPs capturing activation states and cellular subsets. From 1,700,000 T-cells from 700 individuals across 38 tissues and five diverse disease contexts, we discover 46 reproducible GEPs reflecting the known core functions of T-cells including proliferation, cytotoxicity, exhaustion, and T helper effector states. We experimentally characterize several novel activation programs and apply TCAT to describe T-cell activation and exhaustion in Covid-19 and cancer, providing insight into T-cell function in these diseases.
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Affiliation(s)
- Dylan Kotliar
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA
| | - Michelle Curtis
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ryan Agnew
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kathryn Weinand
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Aparna Nathan
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Yuriy Baglaenko
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Center for Autoimmune Genetics and Etiology and Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH 45219, USA
| | - Yu Zhao
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Pardis C. Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Deepak A. Rao
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
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17
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Chun J, Moon JH, Kwack KH, Jang EY, Lee S, Kim HK, Lee JH. Single-cell RNA sequencing reveals the heterogeneity of adipose tissue-derived mesenchymal stem cells under chondrogenic induction. BMB Rep 2024; 57:232-237. [PMID: 37915134 PMCID: PMC11139680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 10/03/2023] [Accepted: 10/12/2023] [Indexed: 11/03/2023] Open
Abstract
This study investigated how adipose tissue-derived mesenchymal stem cells (AT-MSCs) respond to chondrogenic induction using droplet-based single-cell RNA sequencing (scRNA-seq). We analyzed 37,219 high-quality transcripts from control cells and cells induced for 1 week (1W) and 2 weeks (2W). Four distinct cell clusters (0-3), undetectable by bulk analysis, exhibited varying proportions. Cluster 1 dominated in control and 1W cells, whereas clusters (3, 2, and 0) exclusively dominated in control, 1W, and 2W cells, respectively. Furthermore, heterogeneous chondrogenic markers expression within clusters emerged. Gene ontology (GO) enrichment analysis of differentially expressed genes unveiled cluster-specific variations in key biological processes (BP): (1) Cluster 1 exhibited up-regulation of GO-BP terms related to ribosome biogenesis and translational control, crucial for maintaining stem cell properties and homeostasis; (2) Additionally, cluster 1 showed up-regulation of GO-BP terms associated with mitochondrial oxidative metabolism; (3) Cluster 3 displayed up-regulation of GO-BP terms related to cell proliferation; (4) Clusters 0 and 2 demonstrated similar up-regulation of GO-BP terms linked to collagen fibril organization and supramolecular fiber organization. However, only cluster 0 showed a significant decrease in GO-BP terms related to ribosome production, implying a potential correlation between ribosome regulation and the differentiation stages of AT-MSCs. Overall, our findings highlight heterogeneous cell clusters with varying balances between proliferation and differentiation before, and after, chondrogenic stimulation. This provides enhanced insights into the single-cell dynamics of AT-MSCs during chondrogenic differentiation. [BMB Reports 2024; 57(5): 232-237].
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Affiliation(s)
- Jeewan Chun
- Department of Oral Microbiology, College of Dentistry, Kyung Hee University, Seoul 02447, Korea
- Department of Dentistry, Graduate School, Kyung Hee University, Seoul 02447, Korea
| | - Ji-Hoi Moon
- Department of Oral Microbiology, College of Dentistry, Kyung Hee University, Seoul 02447, Korea
| | - Kyu Hwan Kwack
- Department of Oral Microbiology, College of Dentistry, Kyung Hee University, Seoul 02447, Korea
| | - Eun-Young Jang
- Department of Oral Microbiology, College of Dentistry, Kyung Hee University, Seoul 02447, Korea
- Department of Dentistry, Graduate School, Kyung Hee University, Seoul 02447, Korea
| | - Saebyeol Lee
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea
| | - Hak Kyun Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea
| | - Jae-Hyung Lee
- Department of Oral Microbiology, College of Dentistry, Kyung Hee University, Seoul 02447, Korea
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18
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Ouwendijk WJD, Roychoudhury P, Cunningham AL, Jerome KR, Koelle DM, Kinchington PR, Mohr I, Wilson AC, Verjans GGMGM, Depledge DP. Reanalysis of single-cell RNA sequencing data does not support herpes simplex virus 1 latency in non-neuronal ganglionic cells in mice. J Virol 2024; 98:e0185823. [PMID: 38445887 PMCID: PMC11019907 DOI: 10.1128/jvi.01858-23] [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: 11/28/2023] [Accepted: 02/14/2024] [Indexed: 03/07/2024] Open
Abstract
Most individuals are latently infected with herpes simplex virus type 1 (HSV-1), and it is well-established that HSV-1 establishes latency in sensory neurons of peripheral ganglia. However, it was recently proposed that latent HSV-1 is also present in immune cells recovered from the ganglia of experimentally infected mice. Here, we reanalyzed the single-cell RNA sequencing (scRNA-Seq) data that formed the basis for that conclusion. Unexpectedly, off-target priming in 3' scRNA-Seq experiments enabled the detection of non-polyadenylated HSV-1 latency-associated transcript (LAT) intronic RNAs. However, LAT reads were near-exclusively detected in mixed populations of cells undergoing cell death. Specific loss of HSV-1 LAT and neuronal transcripts during quality control filtering indicated widespread destruction of neurons, supporting the presence of contaminating cell-free RNA in other cells following tissue processing. In conclusion, the reported detection of latent HSV-1 in non-neuronal cells is best explained using compromised scRNA-Seq datasets.IMPORTANCEMost people are infected with herpes simplex virus type 1 (HSV-1) during their life. Once infected, the virus generally remains in a latent (silent) state, hiding within the neurons of peripheral ganglia. Periodic reactivation (reawakening) of the virus may cause fresh diseases such as cold sores. A recent study using single-cell RNA sequencing (scRNA-Seq) proposed that HSV-1 can also establish latency in the immune cells of mice, challenging existing dogma. We reanalyzed the data from that study and identified several flaws in the methodologies and analyses performed that invalidate the published conclusions. Specifically, we showed that the methodologies used resulted in widespread destruction of neurons which resulted in the presence of contaminants that confound the data analysis. We thus conclude that there remains little to no evidence for HSV-1 latency in immune cells.
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Affiliation(s)
- Werner J. D. Ouwendijk
- HerpesLabNL, Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Anthony L. Cunningham
- Centre for Virus Research, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Keith R. Jerome
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - David M. Koelle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Translational Research, Benaroya Research Institute, Seattle, Washington, USA
| | - Paul R. Kinchington
- Department of Ophthalmology and of Molecular Microbiology and Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Ian Mohr
- Department of Microbiology, New York University School of Medicine, New York, New York, USA
| | - Angus C. Wilson
- Department of Microbiology, New York University School of Medicine, New York, New York, USA
| | | | - Daniel P. Depledge
- Department of Microbiology, New York University School of Medicine, New York, New York, USA
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF) partner site Hannover-Braunschweig, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
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Salcher S, Heidegger I, Untergasser G, Fotakis G, Scheiber A, Martowicz A, Noureen A, Krogsdam A, Schatz C, Schäfer G, Trajanoski Z, Wolf D, Sopper S, Pircher A. Comparative analysis of 10X Chromium vs. BD Rhapsody whole transcriptome single-cell sequencing technologies in complex human tissues. Heliyon 2024; 10:e28358. [PMID: 38689972 PMCID: PMC11059509 DOI: 10.1016/j.heliyon.2024.e28358] [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: 08/14/2023] [Revised: 03/14/2024] [Accepted: 03/18/2024] [Indexed: 05/02/2024] Open
Abstract
The development of single-cell omics tools has enabled scientists to study the tumor microenvironment (TME) in unprecedented detail. However, each of the different techniques may have its unique strengths and limitations. Here we directly compared two commercially available high-throughput single-cell RNA sequencing (scRNA-seq) technologies - droplet-based 10X Chromium vs. microwell-based BD Rhapsody - using paired samples from patients with localized prostate cancer (PCa) undergoing a radical prostatectomy. Although high technical consistency was observed in unraveling the whole transcriptome, the relative abundance of cell populations differed. Cells with low mRNA content such as T cells were underrepresented in the droplet-based system, at least partly due to lower RNA capture rates. In contrast, microwell-based scRNA-seq recovered less cells of epithelial origin. Moreover, we discovered platform-dependent variabilities in mRNA quantification and cell-type marker annotation. Overall, our study provides important information for selection of the appropriate scRNA-seq platform and for the interpretation of published results.
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Affiliation(s)
- Stefan Salcher
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck (MUI), Innsbruck, Austria
| | - Isabel Heidegger
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Gerold Untergasser
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck (MUI), Innsbruck, Austria
| | - Georgios Fotakis
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Austria
| | - Alexandra Scheiber
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck (MUI), Innsbruck, Austria
| | - Agnieszka Martowicz
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck (MUI), Innsbruck, Austria
| | - Asma Noureen
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Austria
| | - Anne Krogsdam
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Austria
| | - Christoph Schatz
- Department of Pathology, Medical University Innsbruck, Innsbruck, Austria
| | - Georg Schäfer
- Department of Pathology, Medical University Innsbruck, Innsbruck, Austria
| | - Zlatko Trajanoski
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Austria
| | - Dominik Wolf
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck (MUI), Innsbruck, Austria
| | - Sieghart Sopper
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck (MUI), Innsbruck, Austria
| | - Andreas Pircher
- Department of Internal Medicine V, Haematology & Oncology, Comprehensive Cancer Center Innsbruck (CCCI) and Tyrolean Cancer Research Institute (TKFI), Medical University of Innsbruck (MUI), Innsbruck, Austria
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20
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Feng DC, Zhu WZ, Wang J, Li DX, Shi X, Xiong Q, You J, Han P, Qiu S, Wei Q, Yang L. The implications of single-cell RNA-seq analysis in prostate cancer: unraveling tumor heterogeneity, therapeutic implications and pathways towards personalized therapy. Mil Med Res 2024; 11:21. [PMID: 38605399 PMCID: PMC11007901 DOI: 10.1186/s40779-024-00526-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 03/25/2024] [Indexed: 04/13/2024] Open
Abstract
In recent years, advancements in single-cell and spatial transcriptomics, which are highly regarded developments in the current era, particularly the emerging integration of single-cell and spatiotemporal transcriptomics, have enabled a detailed molecular comprehension of the complex regulation of cell fate. The insights obtained from these methodologies are anticipated to significantly contribute to the development of personalized medicine. Currently, single-cell technology is less frequently utilized for prostate cancer compared with other types of tumors. Starting from the perspective of RNA sequencing technology, this review outlined the significance of single-cell RNA sequencing (scRNA-seq) in prostate cancer research, encompassing preclinical medicine and clinical applications. We summarize the differences between mouse and human prostate cancer as revealed by scRNA-seq studies, as well as a combination of multi-omics methods involving scRNA-seq to highlight the key molecular targets for the diagnosis, treatment, and drug resistance characteristics of prostate cancer. These studies are expected to provide novel insights for the development of immunotherapy and other innovative treatment strategies for castration-resistant prostate cancer. Furthermore, we explore the potential clinical applications stemming from other single-cell technologies in this review, paving the way for future research in precision medicine.
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Affiliation(s)
- De-Chao Feng
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Division of Surgery & Interventional Science, University College London, London, WC1E 6BT, UK.
| | - Wei-Zhen Zhu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jie Wang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Deng-Xiong Li
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xu Shi
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Qiao Xiong
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jia You
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ping Han
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Shi Qiu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Qiang Wei
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Lu Yang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China.
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Gibson Hughes TA, Dona MSI, Sobey CG, Pinto AR, Drummond GR, Vinh A, Jelinic M. Aortic Cellular Heterogeneity in Health and Disease: Novel Insights Into Aortic Diseases From Single-Cell RNA Transcriptomic Data Sets. Hypertension 2024; 81:738-751. [PMID: 38318714 DOI: 10.1161/hypertensionaha.123.20597] [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] [Indexed: 02/07/2024]
Abstract
Aortic diseases such as atherosclerosis, aortic aneurysms, and aortic stiffening are significant complications that can have significant impact on end-stage cardiovascular disease. With limited pharmacological therapeutic strategies that target the structural changes in the aorta, surgical intervention remains the only option for some patients with these diseases. Although there have been significant contributions to our understanding of the cellular architecture of the diseased aorta, particularly in the context of atherosclerosis, furthering our insight into the cellular drivers of disease is required. The major cell types of the aorta are well defined; however, the advent of single-cell RNA sequencing provides unrivaled insights into the cellular heterogeneity of each aortic cell type and the inferred biological processes associated with each cell in health and disease. This review discusses previous concepts that have now been enhanced with recent advances made by single-cell RNA sequencing with a focus on aortic cellular heterogeneity.
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Affiliation(s)
- Tayla A Gibson Hughes
- Centre for Cardiovascular Biology and Disease Research, Department of Microbiology, Anatomy Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC, Australia (T.A.G.H., C.G.S., A.R.P., G.R.D., A.V., M.J.)
| | - Malathi S I Dona
- Baker Heart and Diabetes Research Institute, Melbourne, Victoria, Australia (M.S.I.D., A.R.P.)
| | - Christopher G Sobey
- Centre for Cardiovascular Biology and Disease Research, Department of Microbiology, Anatomy Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC, Australia (T.A.G.H., C.G.S., A.R.P., G.R.D., A.V., M.J.)
| | - Alexander R Pinto
- Centre for Cardiovascular Biology and Disease Research, Department of Microbiology, Anatomy Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC, Australia (T.A.G.H., C.G.S., A.R.P., G.R.D., A.V., M.J.)
- Baker Heart and Diabetes Research Institute, Melbourne, Victoria, Australia (M.S.I.D., A.R.P.)
| | - Grant R Drummond
- Centre for Cardiovascular Biology and Disease Research, Department of Microbiology, Anatomy Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC, Australia (T.A.G.H., C.G.S., A.R.P., G.R.D., A.V., M.J.)
| | - Antony Vinh
- Centre for Cardiovascular Biology and Disease Research, Department of Microbiology, Anatomy Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC, Australia (T.A.G.H., C.G.S., A.R.P., G.R.D., A.V., M.J.)
| | - Maria Jelinic
- Centre for Cardiovascular Biology and Disease Research, Department of Microbiology, Anatomy Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC, Australia (T.A.G.H., C.G.S., A.R.P., G.R.D., A.V., M.J.)
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22
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Chea S, Kreger J, Lopez-Burks ME, MacLean AL, Lander AD, Calof AL. Gastrulation-stage gene expression in Nipbl+/- mouse embryos foreshadows the development of syndromic birth defects. SCIENCE ADVANCES 2024; 10:eadl4239. [PMID: 38507484 PMCID: PMC10954218 DOI: 10.1126/sciadv.adl4239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 02/15/2024] [Indexed: 03/22/2024]
Abstract
In animal models, Nipbl deficiency phenocopies gene expression changes and birth defects seen in Cornelia de Lange syndrome, the most common cause of which is Nipbl haploinsufficiency. Previous studies in Nipbl+/- mice suggested that heart development is abnormal as soon as cardiogenic tissue is formed. To investigate this, we performed single-cell RNA sequencing on wild-type and Nipbl+/- mouse embryos at gastrulation and early cardiac crescent stages. Nipbl+/- embryos had fewer mesoderm cells than wild-type and altered proportions of mesodermal cell subpopulations. These findings were associated with underexpression of genes implicated in driving specific mesodermal lineages. In addition, Nanog was found to be overexpressed in all germ layers, and many gene expression changes observed in Nipbl+/- embryos could be attributed to Nanog overexpression. These findings establish a link between Nipbl deficiency, Nanog overexpression, and gene expression dysregulation/lineage misallocation, which ultimately manifest as birth defects in Nipbl+/- animals and Cornelia de Lange syndrome.
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Affiliation(s)
- Stephenson Chea
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA
| | - Jesse Kreger
- Department of Quantitative and Computational Biology, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Martha E. Lopez-Burks
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA
| | - Adam L. MacLean
- Department of Quantitative and Computational Biology, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Arthur D. Lander
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA
| | - Anne L. Calof
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA
- Department of Anatomy and Neurobiology, School of Medicine, University of California Irvine, Irvine, CA 92697, USA
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23
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Ham SD, Abraham MN, Deutschman CS, Taylor MD. Single-cell RNA sequencing reveals Immune Education promotes T cell survival in mice subjected to the cecal ligation and puncture sepsis model. Front Immunol 2024; 15:1366955. [PMID: 38562928 PMCID: PMC10982361 DOI: 10.3389/fimmu.2024.1366955] [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: 01/07/2024] [Accepted: 03/06/2024] [Indexed: 04/04/2024] Open
Abstract
Background Individual T cell responses vary significantly based on the microenvironment present at the time of immune response and on prior induced T cell memory. While the cecal ligation and puncture (CLP) model is the most commonly used murine sepsis model, the contribution of diverse T cell responses has not been explored. We defined T cell subset responses to CLP using single-cell RNA sequencing and examined the effects of prior induced T cell memory (Immune Education) on these responses. We hypothesized that Immune Education prior to CLP would alter T cell responses at the single cell level at a single, early post-CLP time point. Methods Splenic T cells were isolated from C57BL/6 mice. Four cohorts were studied: Control, Immune-Educated, CLP, and Immune-Educated CLP. At age 8 weeks, Immune-Educated and Immune-Educated CLP mice received anti-CD3ϵ antibody; Control and CLP mice were administered an isotype control. CLP (two punctures with a 22-gauge needle) was performed at 12-13 weeks of life. Mice were sacrificed at baseline or 24-hours post-CLP. Unsupervised clustering of the transcriptome library identified six distinct T cell subsets: quiescent naïve CD4+, primed naïve CD4+, memory CD4+, naïve CD8+, activated CD8+, and CD8+ cytotoxic T cell subsets. T cell subset specific gene set enrichment analysis and Hurdle analysis for differentially expressed genes (DEGs) were performed. Results T cell responses to CLP were not uniform - subsets of activated and suppressed T cells were identified. Immune Education augmented specific T cell subsets and led to genomic signatures favoring T cell survival in unoperated and CLP mice. Additionally, the combination of Immune Education and CLP effected the expression of genes related to T cell activity in ways that differed from CLP alone. Validating our finding that IL7R pathway markers were upregulated in Immune-Educated CLP mice, we found that Immune Education increased T cell surface IL7R expression in post-CLP mice. Conclusion Immune Education enhanced the expression of genes associated with T cell survival in unoperated and CLP mice. Induction of memory T cell compartments via Immune Education combined with CLP may increase the model's concordance to human sepsis.
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Affiliation(s)
- Steven D. Ham
- The Division of Critical Care Medicine, Department of Pediatrics, Cohen Children’s Medical Center/Northwell Health, New Hyde Park, NY, United States
- Sepsis Research Laboratory, The Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Mabel N. Abraham
- The Division of Critical Care Medicine, Department of Pediatrics, Cohen Children’s Medical Center/Northwell Health, New Hyde Park, NY, United States
- Sepsis Research Laboratory, The Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Clifford S. Deutschman
- The Division of Critical Care Medicine, Department of Pediatrics, Cohen Children’s Medical Center/Northwell Health, New Hyde Park, NY, United States
- Sepsis Research Laboratory, The Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Matthew D. Taylor
- The Division of Critical Care Medicine, Department of Pediatrics, Cohen Children’s Medical Center/Northwell Health, New Hyde Park, NY, United States
- Sepsis Research Laboratory, The Feinstein Institutes for Medical Research, Manhasset, NY, United States
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24
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Wilson CA, Batzel P, Postlethwait JH. Direct male development in chromosomally ZZ zebrafish. Front Cell Dev Biol 2024; 12:1362228. [PMID: 38529407 PMCID: PMC10961373 DOI: 10.3389/fcell.2024.1362228] [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: 12/27/2023] [Accepted: 02/20/2024] [Indexed: 03/27/2024] Open
Abstract
The genetics of sex determination varies across taxa, sometimes even within a species. Major domesticated strains of zebrafish (Danio rerio), including AB and TU, lack a strong genetic sex determining locus, but strains more recently derived from nature, like Nadia (NA), possess a ZZ male/ZW female chromosomal sex-determination system. AB fish pass through a juvenile ovary stage, forming oocytes that survive in fish that become females but die in fish that become males. To understand mechanisms of gonad development in NA zebrafish, we studied histology and single cell transcriptomics in developing ZZ and ZW fish. ZW fish developed oocytes by 22 days post-fertilization (dpf) but ZZ fish directly formed testes, avoiding a juvenile ovary phase. Gonads of some ZW and WW fish, however, developed oocytes that died as the gonad became a testis, mimicking AB fish, suggesting that the gynogenetically derived AB strain is chromosomally WW. Single-cell RNA-seq of 19dpf gonads showed similar cell types in ZZ and ZW fish, including germ cells, precursors of gonadal support cells, steroidogenic cells, interstitial/stromal cells, and immune cells, consistent with a bipotential juvenile gonad. In contrast, scRNA-seq of 30dpf gonads revealed that cells in ZZ gonads had transcriptomes characteristic of testicular Sertoli, Leydig, and germ cells while ZW gonads had granulosa cells, theca cells, and developing oocytes. Hematopoietic and vascular cells were similar in both sex genotypes. These results show that juvenile NA zebrafish initially develop a bipotential gonad; that a factor on the NA W chromosome, or fewer than two Z chromosomes, is essential to initiate oocyte development; and without the W factor, or with two Z doses, NA gonads develop directly into testes without passing through the juvenile ovary stage. Sex determination in AB and TU strains mimics NA ZW and WW zebrafish, suggesting loss of the Z chromosome during domestication. Genetic analysis of the NA strain will facilitate our understanding of the evolution of sex determination mechanisms.
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25
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Peng Y, Huang Q, Liu D, Kong S, Kamada R, Ozato K, Zhang Y, Zhu J. A single-cell genomic strategy for alternative transcript start sites identification. Biotechnol J 2024; 19:e2300516. [PMID: 38472100 DOI: 10.1002/biot.202300516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 01/20/2024] [Accepted: 01/30/2024] [Indexed: 03/14/2024]
Abstract
Alternative transcription start sites (TSSs) usage plays a critical role in gene transcription regulation in mammals. However, precisely identifying alternative TSSs remains challenging at the genome-wide level. We report a single-cell genomic technology for alternative TSSs annotation and cell heterogeneity detection. In the method, we utilize Fluidigm C1 system to capture individual cells of interest, SMARTer cDNA synthesis kit to recover full-length cDNAs, then dual priming oligonucleotide system to specifically enrich TSSs for genomic analysis. We apply this method to a genome-wide study of alternative TSSs identification in two different IFN-β stimulated mouse embryonic fibroblasts (MEFs). The data clearly discriminate two IFN-β stimulated MEFs. Moreover, our results indicate 81% expressed genes in these two cell types containing multiple TSSs, which is much higher than previous predictions based on Cap-Analysis Gene Expression (CAGE) (58%) or empirical determination (54%) in various cell types. This indicates that alternative TSSs are more pervasive than expected and implies our strategy could position them at an unprecedented sensitivity. It would be helpful for elucidating their biological insights in future.
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Affiliation(s)
- Yanling Peng
- Animal Functional Genomics Group, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Qitong Huang
- Animal Functional Genomics Group, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands
| | - Danli Liu
- Animal Functional Genomics Group, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Siyuan Kong
- Animal Functional Genomics Group, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Rui Kamada
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Keiko Ozato
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Yubo Zhang
- Animal Functional Genomics Group, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
| | - Jun Zhu
- DNA Sequencing and Genomics Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
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26
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Gezelius H, Enblad AP, Lundmark A, Åberg M, Blom K, Rudfeldt J, Raine A, Harila A, Rendo V, Heinäniemi M, Andersson C, Nordlund J. Comparison of high-throughput single-cell RNA-seq methods for ex vivo drug screening. NAR Genom Bioinform 2024; 6:lqae001. [PMID: 38288374 PMCID: PMC10823582 DOI: 10.1093/nargab/lqae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/22/2023] [Accepted: 01/24/2024] [Indexed: 01/31/2024] Open
Abstract
Functional precision medicine (FPM) aims to optimize patient-specific drug selection based on the unique characteristics of their cancer cells. Recent advancements in high throughput ex vivo drug profiling have accelerated interest in FPM. Here, we present a proof-of-concept study for an integrated experimental system that incorporates ex vivo treatment response with a single-cell gene expression output enabling barcoding of several drug conditions in one single-cell sequencing experiment. We demonstrate this through a proof-of-concept investigation focusing on the glucocorticoid-resistant acute lymphoblastic leukemia (ALL) E/R+ Reh cell line. Three different single-cell transcriptome sequencing (scRNA-seq) approaches were evaluated, each exhibiting high cell recovery and accurate tagging of distinct drug conditions. Notably, our comprehensive analysis revealed variations in library complexity, sensitivity (gene detection), and differential gene expression detection across the methods. Despite these differences, we identified a substantial transcriptional response to fludarabine, a highly relevant drug for treating high-risk ALL, which was consistently recapitulated by all three methods. These findings highlight the potential of our integrated approach for studying drug responses at the single-cell level and emphasize the importance of method selection in scRNA-seq studies. Finally, our data encompassing 27 327 cells are freely available to extend to future scRNA-seq methodological comparisons.
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Affiliation(s)
- Henrik Gezelius
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala 751 85, Sweden
| | - Anna Pia Enblad
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala 751 85, Sweden
- Department of Women's and Children's Health, Uppsala University, Uppsala 751 85, Sweden
| | - Anders Lundmark
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala 751 85, Sweden
| | - Martin Åberg
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala 751 85, Sweden
- Department of Clinical Chemistry and Pharmacology, Uppsala University Hospital, Uppsala 751 85, Sweden
| | - Kristin Blom
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala 751 85, Sweden
- Department of Clinical Chemistry and Pharmacology, Uppsala University Hospital, Uppsala 751 85, Sweden
| | - Jakob Rudfeldt
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala 751 85, Sweden
- Department of Clinical Chemistry and Pharmacology, Uppsala University Hospital, Uppsala 751 85, Sweden
| | - Amanda Raine
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala 751 85, Sweden
| | - Arja Harila
- Department of Women's and Children's Health, Uppsala University, Uppsala 751 85, Sweden
| | - Verónica Rendo
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 751 85, Sweden
| | - Merja Heinäniemi
- School of Medicine, University of Eastern Finland, 70210 Kuopio, Finland
| | - Claes Andersson
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala 751 85, Sweden
- Department of Clinical Chemistry and Pharmacology, Uppsala University Hospital, Uppsala 751 85, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala 751 85, Sweden
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Ghaffari S, Saleh M, Akbari B, Ramezani F, Mirzaei HR. Applications of single-cell omics for chimeric antigen receptor T cell therapy. Immunology 2024; 171:339-364. [PMID: 38009707 DOI: 10.1111/imm.13720] [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: 07/02/2023] [Accepted: 11/13/2023] [Indexed: 11/29/2023] Open
Abstract
Chimeric antigen receptor (CAR) T cell therapy is a promising cancer treatment modality. The breakthroughs in CAR T cell therapy were, in part, possible with the help of cell analysis methods, such as single-cell analysis. Bulk analyses have provided invaluable information regarding the complex molecular dynamics of CAR T cells, but their results are an average of thousands of signals in CAR T or tumour cells. Since cancer is a heterogeneous disease where each minute detail of a subclone could change the outcome of the treatment, single-cell analysis could prove to be a powerful instrument in deciphering the secrets of tumour microenvironment for cancer immunotherapy. With the recent studies in all aspects of adoptive cell therapy making use of single-cell analysis, a comprehensive review of the recent preclinical and clinical findings in CAR T cell therapy was needed. Here, we categorized and summarized the key points of the studies in which single-cell analysis provided insights into the genomics, epigenomics, transcriptomics and proteomics as well as their respective multi-omics of CAR T cell therapy.
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Affiliation(s)
- Sasan Ghaffari
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Mahshid Saleh
- Wisconsin National Primate Research Center, University of Wisconsin Graduate School, Madison, Wisconsin, USA
| | - Behnia Akbari
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Faezeh Ramezani
- Department of Medical Biotechnology, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Medical Laboratory Sciences, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hamid Reza Mirzaei
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Molecular Imaging and Therapy Service, Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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28
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Gosch A, Banemann R, Dørum G, Haas C, Hadrys T, Haenggi N, Kulstein G, Neubauer J, Courts C. Spitting in the wind?-The challenges of RNA sequencing for biomarker discovery from saliva. Int J Legal Med 2024; 138:401-412. [PMID: 37847308 PMCID: PMC10861700 DOI: 10.1007/s00414-023-03100-3] [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: 07/31/2023] [Accepted: 09/25/2023] [Indexed: 10/18/2023]
Abstract
Forensic trace contextualization, i.e., assessing information beyond who deposited a biological stain, has become an issue of great and steadily growing importance in forensic genetic casework and research. The human transcriptome encodes a wide variety of information and thus has received increasing interest for the identification of biomarkers for different aspects of forensic trace contextualization over the past years. Massively parallel sequencing of reverse-transcribed RNA ("RNA sequencing") has emerged as the gold standard technology to characterize the transcriptome in its entirety and identify RNA markers showing significant expression differences not only between different forensically relevant body fluids but also within a single body fluid between forensically relevant conditions of interest. Here, we analyze the quality and composition of four RNA sequencing datasets (whole transcriptome as well as miRNA sequencing) from two different research projects (the RNAgE project and the TrACES project), aiming at identifying contextualizing forensic biomarker from the forensically relevant body fluid saliva. We describe and characterize challenges of RNA sequencing of saliva samples arising from the presence of oral bacteria, the heterogeneity of sample composition, and the confounding factor of degradation. Based on these observations, we formulate recommendations that might help to improve RNA biomarker discovery from the challenging but forensically relevant body fluid saliva.
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Affiliation(s)
- Annica Gosch
- Institute of Legal Medicine, University Hospital of Cologne, Cologne, Germany
| | - Regine Banemann
- Federal Criminal Police Office, Forensic Science Institute, Wiesbaden, Germany
| | - Guro Dørum
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Cordula Haas
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Thorsten Hadrys
- State Criminal Police Office, Forensic Science Institute, Munich, Germany
| | - Nadescha Haenggi
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Galina Kulstein
- Federal Criminal Police Office, Forensic Science Institute, Wiesbaden, Germany
| | - Jacqueline Neubauer
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Cornelius Courts
- Institute of Legal Medicine, University Hospital of Cologne, Cologne, Germany.
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29
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Bhattacharya S, Myers JA, Baker C, Guo M, Danopoulos S, Myers JR, Bandyopadhyay G, Romas ST, Huyck HL, Misra RS, Dutra J, Holden-Wiltse J, McDavid AN, Ashton JM, Al Alam D, Potter SS, Whitsett JA, Xu Y, Pryhuber GS, Mariani TJ. Single-Cell Transcriptomic Profiling Identifies Molecular Phenotypes of Newborn Human Lung Cells. Genes (Basel) 2024; 15:298. [PMID: 38540357 PMCID: PMC10970229 DOI: 10.3390/genes15030298] [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: 02/01/2024] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 05/01/2024] Open
Abstract
While animal model studies have extensively defined the mechanisms controlling cell diversity in the developing mammalian lung, there exists a significant knowledge gap with regards to late-stage human lung development. The NHLBI Molecular Atlas of Lung Development Program (LungMAP) seeks to fill this gap by creating a structural, cellular and molecular atlas of the human and mouse lung. Transcriptomic profiling at the single-cell level created a cellular atlas of newborn human lungs. Frozen single-cell isolates obtained from two newborn human lungs from the LungMAP Human Tissue Core Biorepository, were captured, and library preparation was completed on the Chromium 10X system. Data was analyzed in Seurat, and cellular annotation was performed using the ToppGene functional analysis tool. Transcriptional interrogation of 5500 newborn human lung cells identified distinct clusters representing multiple populations of epithelial, endothelial, fibroblasts, pericytes, smooth muscle, immune cells and their gene signatures. Computational integration of data from newborn human cells and with 32,000 cells from postnatal days 1 through 10 mouse lungs generated by the LungMAP Cincinnati Research Center facilitated the identification of distinct cellular lineages among all the major cell types. Integration of the newborn human and mouse cellular transcriptomes also demonstrated cell type-specific differences in maturation states of newborn human lung cells. Specifically, newborn human lung matrix fibroblasts could be separated into those representative of younger cells (n = 393), or older cells (n = 158). Cells with each molecular profile were spatially resolved within newborn human lung tissue. This is the first comprehensive molecular map of the cellular landscape of neonatal human lung, including biomarkers for cells at distinct states of maturity.
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Affiliation(s)
- Soumyaroop Bhattacharya
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA; (G.B.); (S.T.R.); (H.L.H.); (R.S.M.); (G.S.P.); (T.J.M.)
| | - Jacquelyn A. Myers
- Genomic Research Center, University of Rochester Medical Center, Rochester, NY 14642, USA; (J.A.M.); (C.B.); (J.R.M.); (J.M.A.)
| | - Cameron Baker
- Genomic Research Center, University of Rochester Medical Center, Rochester, NY 14642, USA; (J.A.M.); (C.B.); (J.R.M.); (J.M.A.)
| | - Minzhe Guo
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45219, USA; (M.G.); (S.S.P.); (J.A.W.); (Y.X.)
| | - Soula Danopoulos
- Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, University of California Los Angeles, Los Angeles, CA 90024, USA; (S.D.)
| | - Jason R. Myers
- Genomic Research Center, University of Rochester Medical Center, Rochester, NY 14642, USA; (J.A.M.); (C.B.); (J.R.M.); (J.M.A.)
| | - Gautam Bandyopadhyay
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA; (G.B.); (S.T.R.); (H.L.H.); (R.S.M.); (G.S.P.); (T.J.M.)
| | - Stephen T. Romas
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA; (G.B.); (S.T.R.); (H.L.H.); (R.S.M.); (G.S.P.); (T.J.M.)
| | - Heidie L. Huyck
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA; (G.B.); (S.T.R.); (H.L.H.); (R.S.M.); (G.S.P.); (T.J.M.)
| | - Ravi S. Misra
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA; (G.B.); (S.T.R.); (H.L.H.); (R.S.M.); (G.S.P.); (T.J.M.)
| | - Jennifer Dutra
- Clinical & Translational Science Institute, University of Rochester, Rochester, NY 14642, USA; (J.D.); (J.H.-W.)
| | - Jeanne Holden-Wiltse
- Clinical & Translational Science Institute, University of Rochester, Rochester, NY 14642, USA; (J.D.); (J.H.-W.)
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY 14642, USA;
| | - Andrew N. McDavid
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY 14642, USA;
| | - John M. Ashton
- Genomic Research Center, University of Rochester Medical Center, Rochester, NY 14642, USA; (J.A.M.); (C.B.); (J.R.M.); (J.M.A.)
| | - Denise Al Alam
- Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, University of California Los Angeles, Los Angeles, CA 90024, USA; (S.D.)
| | - S. Steven Potter
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45219, USA; (M.G.); (S.S.P.); (J.A.W.); (Y.X.)
| | - Jeffrey A. Whitsett
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45219, USA; (M.G.); (S.S.P.); (J.A.W.); (Y.X.)
| | - Yan Xu
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45219, USA; (M.G.); (S.S.P.); (J.A.W.); (Y.X.)
| | - Gloria S. Pryhuber
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA; (G.B.); (S.T.R.); (H.L.H.); (R.S.M.); (G.S.P.); (T.J.M.)
| | - Thomas J. Mariani
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY 14642, USA; (G.B.); (S.T.R.); (H.L.H.); (R.S.M.); (G.S.P.); (T.J.M.)
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30
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Xu P, Peng J, Yuan T, Chen Z, He H, Wu Z, Li T, Li X, Wang L, Gao L, Yan J, Wei W, Li CT, Luo ZG, Chen Y. High-throughput mapping of single-neuron projection and molecular features by retrograde barcoded labeling. eLife 2024; 13:e85419. [PMID: 38390967 PMCID: PMC10914349 DOI: 10.7554/elife.85419] [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: 12/07/2022] [Accepted: 02/22/2024] [Indexed: 02/24/2024] Open
Abstract
Deciphering patterns of connectivity between neurons in the brain is a critical step toward understanding brain function. Imaging-based neuroanatomical tracing identifies area-to-area or sparse neuron-to-neuron connectivity patterns, but with limited throughput. Barcode-based connectomics maps large numbers of single-neuron projections, but remains a challenge for jointly analyzing single-cell transcriptomics. Here, we established a rAAV2-retro barcode-based multiplexed tracing method that simultaneously characterizes the projectome and transcriptome at the single neuron level. We uncovered dedicated and collateral projection patterns of ventromedial prefrontal cortex (vmPFC) neurons to five downstream targets and found that projection-defined vmPFC neurons are molecularly heterogeneous. We identified transcriptional signatures of projection-specific vmPFC neurons, and verified Pou3f1 as a marker gene enriched in neurons projecting to the lateral hypothalamus, denoting a distinct subset with collateral projections to both dorsomedial striatum and lateral hypothalamus. In summary, we have developed a new multiplexed technique whose paired connectome and gene expression data can help reveal organizational principles that form neural circuits and process information.
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Affiliation(s)
- Peibo Xu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Center for Brain Science and Brain-Inspired TechnologyShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jian Peng
- School of Life Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech UniversityShanghaiChina
| | - Tingli Yuan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Center for Brain Science and Brain-Inspired TechnologyShanghaiChina
| | - Zhaoqin Chen
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Center for Brain Science and Brain-Inspired TechnologyShanghaiChina
| | - Hui He
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Center for Brain Science and Brain-Inspired TechnologyShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Ziyan Wu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Center for Brain Science and Brain-Inspired TechnologyShanghaiChina
| | - Ting Li
- School of Life Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech UniversityShanghaiChina
| | - Xiaodong Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Center for Brain Science and Brain-Inspired TechnologyShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Luyue Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of ScienceShanghaiChina
| | - Le Gao
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Center for Brain Science and Brain-Inspired TechnologyShanghaiChina
| | - Jun Yan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Center for Brain Science and Brain-Inspired TechnologyShanghaiChina
- Shanghai Center for Brain Science and Brain-Inspired Intelligence TechnologyShanghaiChina
- School of Future Technology, University of Chinese Academy of SciencesBeijingChina
| | - Wu Wei
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of ScienceShanghaiChina
- Lingang LaboratoryShanghaiChina
| | - Chengyu T Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Center for Brain Science and Brain-Inspired TechnologyShanghaiChina
- Shanghai Center for Brain Science and Brain-Inspired Intelligence TechnologyShanghaiChina
- School of Future Technology, University of Chinese Academy of SciencesBeijingChina
- Lingang LaboratoryShanghaiChina
| | - Zhen-Ge Luo
- School of Life Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech UniversityShanghaiChina
| | - Yuejun Chen
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Center for Brain Science and Brain-Inspired TechnologyShanghaiChina
- Shanghai Center for Brain Science and Brain-Inspired Intelligence TechnologyShanghaiChina
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31
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Lukomska A, Theune WC, Frost MP, Xing J, Kearney A, Trakhtenberg EF. Upregulation of developmentally-downregulated miR-1247-5p promotes neuroprotection and axon regeneration in vivo. Neurosci Lett 2024; 823:137662. [PMID: 38286398 PMCID: PMC10923146 DOI: 10.1016/j.neulet.2024.137662] [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: 11/03/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 01/31/2024]
Abstract
Numerous micro-RNAs (miRNAs) affect neurodevelopment and neuroprotection, but potential roles of many miRNAs in regulating these processes are still unknown. Here, we used the retinal ganglion cell (RGC) central nervous system (CNS) projection neuron and optic nerve crush (ONC) injury model, to optimize a mature miRNA arm-specific quantification method for characterizing the developmental regulation of miR-1247-5p in RGCs, investigated whether injury affects its expression, and tested whether upregulating miR-1247-5p-mimic in RGCs promotes neuroprotection and axon regeneration. We found that, miR-1247-5p is developmentally-downregulated in RGCs, and is further downregulated after ONC. Importantly, RGC-specific upregulation of miR-1247-5p promoted neuroprotection and axon regeneration after injury in vivo. To gain insight into the underlying mechanisms, we analyzed by bulk-mRNA-seq embryonic and adult RGCs, along with adult RGCs transduced by miR-1247-5p-expressing viral vector, and identified developmentally-regulated cilial and mitochondrial biological processes, which were reinstated to their embryonic levels in adult RGCs by upregulation of miR-1247-5p. Since axon growth is also a developmentally-regulated process, in which mitochondrial dynamics play important roles, it is possible that miR-1247-5p promoted neuroprotection and axon regeneration through regulating mitochondrial functions.
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Affiliation(s)
- Agnieszka Lukomska
- Department of Neuroscience, University of Connecticut School of Medicine, 263 Farmington Ave., Farmington, CT 06030, USA
| | - William C Theune
- Department of Neuroscience, University of Connecticut School of Medicine, 263 Farmington Ave., Farmington, CT 06030, USA
| | - Matthew P Frost
- Department of Neuroscience, University of Connecticut School of Medicine, 263 Farmington Ave., Farmington, CT 06030, USA
| | - Jian Xing
- Department of Neuroscience, University of Connecticut School of Medicine, 263 Farmington Ave., Farmington, CT 06030, USA
| | - Anja Kearney
- Department of Neuroscience, University of Connecticut School of Medicine, 263 Farmington Ave., Farmington, CT 06030, USA
| | - Ephraim F Trakhtenberg
- Department of Neuroscience, University of Connecticut School of Medicine, 263 Farmington Ave., Farmington, CT 06030, USA.
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Chea S, Kreger J, Lopez-Burks ME, MacLean AL, Lander AD, Calof AL. Gastrulation-stage gene expression in Nipbl +/- mouse embryos foreshadows the development of syndromic birth defects. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.16.558465. [PMID: 37905011 PMCID: PMC10614802 DOI: 10.1101/2023.10.16.558465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
In animal models, Nipbl-deficiency phenocopies gene expression changes and birth defects seen in Cornelia de Lange Syndrome (CdLS), the most common cause of which is Nipbl-haploinsufficiency. Previous studies in Nipbl+/- mice suggested that heart development is abnormal as soon as cardiogenic tissue is formed. To investigate this, we performed single-cell RNA-sequencing on wildtype (WT) and Nipbl+/- mouse embryos at gastrulation and early cardiac crescent stages. Nipbl+/- embryos had fewer mesoderm cells than WT and altered proportions of mesodermal cell subpopulations. These findings were associated with underexpression of genes implicated in driving specific mesodermal lineages. In addition, Nanog was found to be overexpressed in all germ layers, and many gene expression changes observed in Nipbl+/- embryos could be attributed to Nanog overexpression. These findings establish a link between Nipbl-deficiency, Nanog overexpression, and gene expression dysregulation/lineage misallocation, which ultimately manifest as birth defects in Nipbl+/- animals and CdLS. Teaser Gene expression changes during gastrulation of Nipbl-deficient mice shed light on early origins of structural birth defects.
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33
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Ismail KA, Mukherjee M, Kareta MS, Lopez SMC. Enabling methanol fixation of pediatric nasal wash during respiratory illness for single cell sequencing in comparison with fresh samples. Pediatr Res 2024; 95:835-842. [PMID: 37758866 DOI: 10.1038/s41390-023-02780-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/21/2023] [Accepted: 07/24/2023] [Indexed: 09/29/2023]
Abstract
BACKGROUND Lower respiratory tract infection (LRTI) including pneumonia, bronchitis, and bronchiolitis is the sixth leading cause of mortality around the world and leading cause of death in children under 5 years. Systemic immune response to viral infection is well characterized. However, there is little data regarding the immune response at the upper respiratory tract mucosa. The upper respiratory mucosa is the site of viral entry, initial replication and the first barrier against respiratory infections. Lower respiratory tract samples can be challenging to obtain and require more invasive procedures. However, nasal wash (NW) samples from the upper respiratory tract can be obtained with minimal discomfort to the patient. METHOD In a pilot study, we developed a protocol using NW samples obtained from hospitalized children with LRTI that enables single cell RNA sequencing (scRNA-seq) after the NW sample is methanol-fixed. RESULTS We found no significant changes in scRNA-seq qualitative and quantitative parameters between methanol-fixed and fresh NW samples. CONCLUSIONS We present a novel protocol to enable scRNA-seq in NW samples from children admitted with LRTI. With the inherent challenges associated with clinical samples, the protocol described allows for processing flexibility as well as multicenter collaboration. IMPACT There are no significant differences in scRNA-seq qualitative and quantitative parameters between methanol fixed and fresh Pediatric Nasal wash samples. The study demonstrates the effectiveness of methanol fixation process on preserving respiratory samples for single cell sequencing. This enables Pediatric Nasal wash specimen for single cell RNA sequencing in pediatric patients with respiratory tract infection and allows processing flexibility and multicenter collaboration.
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Affiliation(s)
- Khaled A Ismail
- Environmental Influences on Health and Disease Group, Sanford Research, Sioux Falls, SD, USA
| | - Malini Mukherjee
- Functional Genomics and Bioinformatics Core, Sioux Falls, SD, USA
| | - Michael S Kareta
- Functional Genomics and Bioinformatics Core, Sioux Falls, SD, USA
- Genetics & Genomics Group, Sanford Research, Sioux Falls, SD, USA
- Department of Pediatrics, Sanford School of Medicine-University of South Dakota, Sioux Falls, SD, USA
| | - Santiago M C Lopez
- Environmental Influences on Health and Disease Group, Sanford Research, Sioux Falls, SD, USA.
- Department of Pediatrics, Sanford School of Medicine-University of South Dakota, Sioux Falls, SD, USA.
- Children's Health Specialty Clinic, Sanford Children's Hospital, Sioux Falls, SD, USA.
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34
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Khan MI, Easwaran M, Martinez JD, Kimura A, Erickson-DiRenzo E. Method for Collecting Single Epithelial Cells from the Mouse Larynx. Laryngoscope 2024; 134:786-794. [PMID: 37602769 PMCID: PMC10841475 DOI: 10.1002/lary.30970] [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: 03/24/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/22/2023]
Abstract
OBJECTIVE The larynx is lined by specialized epithelial cell populations. Studying molecular changes occurring in individual epithelial cell types requires a reliable method for removing these cells from the larynx. Our objective was to develop a method to harvest individual epithelial cells from the mouse larynx while minimizing contamination from non-laryngeal sites and non-epithelial laryngeal cells. METHODS Mice were euthanized, and the larynx was carefully exposed and separated from non-laryngeal sites. A small dental brush was inserted into the laryngeal inlet and rotated to obtain epithelial cells. Cells were transferred to collection media, counted, and cytospin preparations stained for laryngeal epithelial (i.e., Pan-Keratin, EpCAM, NGFR, p63, K5, β-tubulin, MUC5AC) and non-epithelial (i.e., vimentin) cell markers. Histopathology was completed on brushed laryngeal tissue sections to evaluate the depth of cell collection. Preliminary Single-cell RNA sequencing (scRNA-seq) was performed to confirm this method can capture diverse laryngeal cell types. RESULTS We collected 6000-8000 cells from a single larynx and 35000-40000 cells from combining brushings from three tissues. Histopathology demonstrated brushing removed the epithelial layer of the larynx and some underlying tissue. Immunofluorescence staining demonstrated the phenotype of harvested cells was primarily epithelial. Preliminary scRNA-seq was successfully conducted and displayed nine unique cell clusters. CONCLUSION We developed a reliable method of harvesting individual epithelial cells from the mouse larynx. This method will be useful for collection of laryngeal cells for a variety of downstream cellular and molecular assays, including scRNA-seq, protein analyses, and cell-culture-based experiments, following laryngeal injury. LEVEL OF EVIDENCE NA Laryngoscope, 134:786-794, 2024.
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Affiliation(s)
- Mohammed Imran Khan
- Department of Otolaryngology - Head & Neck Surgery, School of Medicine, Stanford University, Stanford, CA
| | - Meena Easwaran
- Department of Otolaryngology - Head & Neck Surgery, School of Medicine, Stanford University, Stanford, CA
- Department of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - Joshua D. Martinez
- Department of Otolaryngology - Head & Neck Surgery, School of Medicine, Stanford University, Stanford, CA
| | - Akari Kimura
- Department of Otolaryngology - Head & Neck Surgery, School of Medicine, Stanford University, Stanford, CA
| | - Elizabeth Erickson-DiRenzo
- Department of Otolaryngology - Head & Neck Surgery, School of Medicine, Stanford University, Stanford, CA
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35
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Netzer C, von Arps-Aubert V, Mačinković I, von der Grün J, Küffer S, Ströbel P, von Knethen A, Weigert A, Beutner D. Association between spatial distribution of leukocyte subsets and clinical presentation of head and neck squamous cell carcinoma. Front Immunol 2024; 14:1240394. [PMID: 38322012 PMCID: PMC10844964 DOI: 10.3389/fimmu.2023.1240394] [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: 06/14/2023] [Accepted: 12/28/2023] [Indexed: 02/08/2024] Open
Abstract
Background Interactions between tumor cells and cells in the microenvironment contribute to tumor development and metastasis. The spatial arrangement of individual cells in relation to each other influences the likelihood of whether and how these cells interact with each other. Methods This study investigated the effect of spatial distribution on the function of leukocyte subsets in the microenvironment of human head and neck squamous cell carcinoma (HNSCC) using multiplex immunohistochemistry (IHC). Leukocyte subsets were further classified based on analysis of two previously published HNSCC single-cell RNA datasets and flow cytometry (FC). Results IHC revealed distinct distribution patterns of leukocytes differentiated by CD68 and CD163. While CD68hiCD163lo and CD68hiCD163hi cells accumulated near tumor sites, CD68loCD163hi cells were more evenly distributed in the tumor stroma. PD-L1hi and PD-1hi cells accumulated predominantly around tumor sites. High cell density of PD-L1hi CD68hiCD163hi cells or PD-1hi T cells near the tumor site correlated with improved survival. FC and single cell RNA revealed high variability within the CD68/CD163 subsets. CD68hiCD163lo and CD68hiCD163hi cells were predominantly macrophages (MΦ), whereas CD68loCD163hi cells appeared to be predominantly dendritic cells (DCs). Differentiation based on CD64, CD80, CD163, and CD206 revealed that TAM in HNSCC occupy a broad spectrum within the classical M1/M2 polarization. Notably, the MΦ subsets expressed predominantly CD206 and little CD80. The opposite was observed in the DC subsets. Conclusion The distribution patterns and their distinct interactions via the PD-L1/PD-1 pathway suggest divergent roles of CD68/CD163 subsets in the HNSCC microenvironment. PD-L1/PD-1 interactions appear to occur primarily between specific cell types close to the tumor site. Whether PD-L1/PD-1 interactions have a positive or negative impact on patient survival appears to depend on both the spatial localization and the entity of the interacting cells. Co-expression of other markers, particularly CD80 and CD206, supports the hypothesis that CD68/CD163 IHC subsets have distinct functions. These results highlight the association between spatial leukocyte distribution patterns and the clinical presentation of HNSCC.
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Affiliation(s)
- Christoph Netzer
- Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Vanessa von Arps-Aubert
- Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Igor Mačinković
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Jens von der Grün
- Department of Radiation Oncology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
- Department of Radiotherapy and Oncology, University Hospital Frankfurt, Frankfurt, Germany
| | - Stefan Küffer
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Philipp Ströbel
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Andreas von Knethen
- Department of Anesthesiology, Intensive Care Medicine and Pain Therapy, University Hospital Frankfurt, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Andreas Weigert
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Dirk Beutner
- Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Center Göttingen, Göttingen, Germany
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Park Y, Muttray NP, Hauschild AC. Species-agnostic transfer learning for cross-species transcriptomics data integration without gene orthology. Brief Bioinform 2024; 25:bbae004. [PMID: 38305455 PMCID: PMC10835749 DOI: 10.1093/bib/bbae004] [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: 09/13/2023] [Revised: 11/24/2023] [Accepted: 12/10/2023] [Indexed: 02/03/2024] Open
Abstract
Novel hypotheses in biomedical research are often developed or validated in model organisms such as mice and zebrafish and thus play a crucial role. However, due to biological differences between species, translating these findings into human applications remains challenging. Moreover, commonly used orthologous gene information is often incomplete and entails a significant information loss during gene-id conversion. To address these issues, we present a novel methodology for species-agnostic transfer learning with heterogeneous domain adaptation. We extended the cross-domain structure-preserving projection toward out-of-sample prediction. Our approach not only allows knowledge integration and translation across various species without relying on gene orthology but also identifies similar GO among the most influential genes composing the latent space for integration. Subsequently, during the alignment of latent spaces, each composed of species-specific genes, it is possible to identify functional annotations of genes missing from public orthology databases. We evaluated our approach with four different single-cell sequencing datasets focusing on cell-type prediction and compared it against related machine-learning approaches. In summary, the developed model outperforms related methods working without prior knowledge when predicting unseen cell types based on other species' data. The results demonstrate that our novel approach allows knowledge transfer beyond species barriers without the dependency on known gene orthology but utilizing the entire gene sets.
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Affiliation(s)
- Youngjun Park
- Department of Medical Informatics, University Medical Center Göttingen, Göttingen, Germany
- International Max Planck Research Schools for Genome Science, Georg-August-Universität Göttingen Göttingen, Germany
| | - Nils P Muttray
- Applied Statistics, Georg-August-Universität Göttingen Göttingen, Germany
| | - Anne-Christin Hauschild
- Department of Medical Informatics, University Medical Center Göttingen, Göttingen, Germany
- Campus-Institute Data Science (CIDAS), Georg-August-Universität Göttingen Göttingen, Germany
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Scott MT, Liu W, Mitchell R, Clarke CJ, Kinstrie R, Warren F, Almasoudi H, Stevens T, Dunn K, Pritchard J, Drotar ME, Michie AM, Jørgensen HG, Higgins B, Copland M, Vetrie D. Activating p53 abolishes self-renewal of quiescent leukaemic stem cells in residual CML disease. Nat Commun 2024; 15:651. [PMID: 38246924 PMCID: PMC10800356 DOI: 10.1038/s41467-024-44771-9] [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: 10/24/2022] [Accepted: 01/04/2024] [Indexed: 01/23/2024] Open
Abstract
Whilst it is recognised that targeting self-renewal is an effective way to functionally impair the quiescent leukaemic stem cells (LSC) that persist as residual disease in chronic myeloid leukaemia (CML), developing therapeutic strategies to achieve this have proved challenging. We demonstrate that the regulatory programmes of quiescent LSC in chronic phase CML are similar to that of embryonic stem cells, pointing to a role for wild type p53 in LSC self-renewal. In support of this, increasing p53 activity in primitive CML cells using an MDM2 inhibitor in combination with a tyrosine kinase inhibitor resulted in reduced CFC outputs and engraftment potential, followed by loss of multilineage priming potential and LSC exhaustion when combination treatment was discontinued. Our work provides evidence that targeting LSC self-renewal is exploitable in the clinic to irreversibly impair quiescent LSC function in CML residual disease - with the potential to enable more CML patients to discontinue therapy and remain in therapy-free remission.
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Affiliation(s)
- Mary T Scott
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Wei Liu
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Rebecca Mitchell
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Cassie J Clarke
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Ross Kinstrie
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Felix Warren
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Hassan Almasoudi
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Thomas Stevens
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Karen Dunn
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - John Pritchard
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Mark E Drotar
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Alison M Michie
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Heather G Jørgensen
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | | | - Mhairi Copland
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - David Vetrie
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, UK.
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Li J, Wang Y. nPCA: a linear dimensionality reduction method using a multilayer perceptron. Front Genet 2024; 14:1290447. [PMID: 38259616 PMCID: PMC10800564 DOI: 10.3389/fgene.2023.1290447] [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: 09/07/2023] [Accepted: 12/13/2023] [Indexed: 01/24/2024] Open
Abstract
Background: Linear dimensionality reduction techniques are widely used in many applications. The goal of dimensionality reduction is to eliminate the noise of data and extract the main features of data. Several dimension reduction methods have been developed, such as linear-based principal component analysis (PCA), nonlinear-based t-distributed stochastic neighbor embedding (t-SNE), and deep-learning-based autoencoder (AE). However, PCA only determines the projection direction with the highest variance, t-SNE is sometimes only suitable for visualization, and AE and nonlinear methods discard the linear projection. Results: To retain the linear projection of raw data and generate a better result of dimension reduction either for visualization or downstream analysis, we present neural principal component analysis (nPCA), an unsupervised deep learning approach capable of retaining richer information of raw data as a promising improvement to PCA. To evaluate the performance of the nPCA algorithm, we compare the performance of 10 public datasets and 6 single-cell RNA sequencing (scRNA-seq) datasets of the pancreas, benchmarking our method with other classic linear dimensionality reduction methods. Conclusion: We concluded that the nPCA method is a competitive alternative method for dimensionality reduction tasks.
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Affiliation(s)
- Juzeng Li
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Yi Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
- Human Phenome Institute, Fudan University, Shanghai, China
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Berges AJ, Ospino R, Mafla L, Collins S, Chan-Li Y, Ghosh B, Sidhaye V, Lina I, Hillel AT. Dysfunctional Epithelial Barrier Is Characterized by Reduced E-Cadherin in Idiopathic Subglottic Stenosis. Laryngoscope 2024; 134:374-381. [PMID: 37565709 PMCID: PMC10842128 DOI: 10.1002/lary.30951] [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: 04/06/2023] [Revised: 07/11/2023] [Accepted: 07/18/2023] [Indexed: 08/12/2023]
Abstract
OBJECTIVES To aim of the study was to characterize the molecular profile and functional phenotype of idiopathic subglottic stenosis (iSGS)-scar epithelium. METHODS Human tracheal biopsies from iSGS scar (n = 6) and matched non-scar (n = 6) regions were analyzed using single-cell RNA sequencing (scRNA-seq). Separate specimens were used for epithelial cell expansion in vitro to assess average growth rate and functional capabilities using transepithelial-electrical resistance (TEER), fluorescein isothiocyanate-dextran flux permeability assay, ciliary coverage, and cilia beating frequency (CBF). Finally, epithelial tight junction protein expression of cultured cells was quantified using immunoblot assay (n = 4) and immunofluorescence (n = 6). RESULTS scRNA-seq analysis revealed a decrease in goblet, ciliated, and basal epithelial cells in the scar iSGS cohort. Furthermore, mRNA expression of proteins E-cadherin, claudin-3, claudin-10, occludin, TJP1, and TJP2 was also reduced (p < 0.001) in scar epithelium. Functional assays demonstrated a decrease in TEER (paired 95% confidence interval [CI], 195.68-890.83 Ω × cm2 , p < 0.05), an increase in permeability (paired 95% CI, -6116.00 to -1401.99 RFU, p < 0.05), and reduced epithelial coverage (paired 95% CI, 0.1814-1.766, fold change p < 0.05) in iSGS-scar epithelium relative to normal controls. No difference in growth rate (p < 0.05) or CBF was found (paired 95% CI, -2.118 to 3.820 Hz, p > 0.05). Immunoblot assay (paired 95% CI, 0.0367-0.605, p < 0.05) and immunofluorescence (paired 95% CI, 13.748-59.191 mean grey value, p < 0.05) revealed E-cadherin reduction in iSGS-scar epithelium. CONCLUSION iSGS-scar epithelium has a dysfunctional barrier and reduced structural protein expression. These results are consistent with dysfunctional epithelium seen in other airway pathology. Further studies are warranted to delineate the causality of epithelial dysfunction on the downstream fibroinflammatory cascade in iSGS. LEVEL OF EVIDENCE NA Laryngoscope, 134:374-381, 2024.
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Affiliation(s)
- Alexandra J. Berges
- Johns Hopkins Department of Otolaryngology-Head and Neck Surgery, 1800 Orleans Street, Baltimore, MD, 21287
| | - Rafael Ospino
- Johns Hopkins University School of Medicine, 1800 Orleans Street, Baltimore, MD, 21287
| | - Laura Mafla
- Johns Hopkins University School of Medicine, 1800 Orleans Street, Baltimore, MD, 21287
| | - Samuel Collins
- Johns Hopkins Department of Otolaryngology-Head and Neck Surgery, 1800 Orleans Street, Baltimore, MD, 21287
| | - Yee Chan-Li
- Johns Hopkins Department of Otolaryngology-Head and Neck Surgery, 1800 Orleans Street, Baltimore, MD, 21287
| | - Baishakhi Ghosh
- Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD, 21205
| | - Venkataramana Sidhaye
- Johns Hopkins Division of Pulmonary and Critical Care Medicine, 1800 Orleans Street, Baltimore, MD, 21287
- Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD, 21205
| | - Ioan Lina
- Johns Hopkins Department of Otolaryngology-Head and Neck Surgery, 1800 Orleans Street, Baltimore, MD, 21287
| | - Alexander T. Hillel
- Johns Hopkins Department of Otolaryngology-Head and Neck Surgery, 1800 Orleans Street, Baltimore, MD, 21287
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Fu J, Wang Z, Martinez M, Obradovic A, Jiao W, Frangaj K, Jones R, Guo XV, Zhang Y, Kuo WI, Ko HM, Iuga A, Bay Muntnich C, Prada Rey A, Rogers K, Zuber J, Ma W, Miron M, Farber DL, Weiner J, Kato T, Shen Y, Sykes M. Plasticity of intragraft alloreactive T cell clones in human gut correlates with transplant outcomes. J Exp Med 2024; 221:e20230930. [PMID: 38091025 PMCID: PMC10720543 DOI: 10.1084/jem.20230930] [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: 05/30/2023] [Revised: 08/22/2023] [Accepted: 11/20/2023] [Indexed: 12/17/2023] Open
Abstract
The site of transition between tissue-resident memory (TRM) and circulating phenotypes of T cells is unknown. We integrated clonotype, alloreactivity, and gene expression profiles of graft-repopulating recipient T cells in the intestinal mucosa at the single-cell level after human intestinal transplantation. Host-versus-graft (HvG)-reactive T cells were mainly distributed to TRM, effector T (Teff)/TRM, and T follicular helper compartments. RNA velocity analysis demonstrated a trajectory from TRM to Teff/TRM clusters in association with rejection. By integrating pre- and post-transplantation (Tx) mixed lymphocyte reaction-determined alloreactive repertoires, we observed that pre-existing HvG-reactive T cells that demonstrated tolerance in the circulation were dominated by TRM profiles in quiescent allografts. Putative de novo HvG-reactive clones showed a transcriptional profile skewed to cytotoxic effectors in rejecting grafts. Inferred protein regulon network analysis revealed upstream regulators that accounted for the effector and tolerant T cell states. We demonstrate Teff/TRM interchangeability for individual T cell clones with known (allo)recognition in the human gut, providing novel insight into TRM biology.
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Affiliation(s)
- Jianing Fu
- Department of Medicine, Columbia Center for Translational Immunology, Columbia University, New York, NY, USA
| | - Zicheng Wang
- Department of Systems Biology, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA
| | | | - Aleksandar Obradovic
- Department of Medicine, Columbia Center for Translational Immunology, Columbia University, New York, NY, USA
| | - Wenyu Jiao
- Department of Medicine, Columbia Center for Translational Immunology, Columbia University, New York, NY, USA
| | - Kristjana Frangaj
- Department of Medicine, Columbia Center for Translational Immunology, Columbia University, New York, NY, USA
| | - Rebecca Jones
- Department of Medicine, Columbia Center for Translational Immunology, Columbia University, New York, NY, USA
| | - Xinzheng V. Guo
- Human Immune Monitoring Core, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Ya Zhang
- Human Immune Monitoring Core, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Wan-I Kuo
- Human Immune Monitoring Core, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Huaibin M. Ko
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Alina Iuga
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Constanza Bay Muntnich
- Department of Medicine, Columbia Center for Translational Immunology, Columbia University, New York, NY, USA
| | - Adriana Prada Rey
- Department of Medicine, Columbia Center for Translational Immunology, Columbia University, New York, NY, USA
| | - Kortney Rogers
- Department of Medicine, Columbia Center for Translational Immunology, Columbia University, New York, NY, USA
| | - Julien Zuber
- Department of Medicine, Columbia Center for Translational Immunology, Columbia University, New York, NY, USA
| | - Wenji Ma
- Department of Systems Biology, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA
| | - Michelle Miron
- Department of Microbiology and Immunology, Columbia University, New York, NY, USA
| | - Donna L. Farber
- Department of Microbiology and Immunology, Columbia University, New York, NY, USA
- Department of Surgery, Columbia University, New York, NY, USA
| | - Joshua Weiner
- Department of Medicine, Columbia Center for Translational Immunology, Columbia University, New York, NY, USA
- Department of Surgery, Columbia University, New York, NY, USA
| | - Tomoaki Kato
- Department of Surgery, Columbia University, New York, NY, USA
| | - Yufeng Shen
- Department of Systems Biology, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA
| | - Megan Sykes
- Department of Medicine, Columbia Center for Translational Immunology, Columbia University, New York, NY, USA
- Department of Microbiology and Immunology, Columbia University, New York, NY, USA
- Department of Surgery, Columbia University, New York, NY, USA
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Ge W, Zhang T, Zhou Y, Shen W. Data Analysis Pipeline for scRNA-seq Experiments to Study Early Oogenesis. Methods Mol Biol 2024; 2770:203-225. [PMID: 38351456 DOI: 10.1007/978-1-0716-3698-5_15] [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] [Indexed: 02/16/2024]
Abstract
Germ cells as the means for the transmission of genetic information between generations have been a hot topic of research for decades. The analysis of the transcriptomes, that is of the RNA transcripts produced by the genotype at a given time, of germ cells and the surrounding somatic cells, is essential to unravel the cellular and molecular processes regulating gametogenesis. However, the asynchronized differentiation of germ cells and high cellular heterogeneity in the developing ovary or testis represent two unsurmountable challenges for delineating the transcription regulation mechanism of germ cells using traditional bulk RNA sequencing. By performing single-cell RNA sequencing (scRNA-seq), it is now possible to dissect the transcriptome of germ cell development at single-cell resolution, and apply powerful bioinformatics methods to translate raw sequencing data into meaningful information. Here, using the 10× Genomic platform and the most widely cited bioinformatics tools, we describe how to analyze early female germ cell development using scRNA-seq data generated from mouse E11.5 to E14.5 ovaries. This pipeline will provide a guide for exploring the processes of early germ cell development at single-cell resolution.
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Affiliation(s)
- Wei Ge
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Teng Zhang
- College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Yang Zhou
- College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Wei Shen
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China.
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Qu S, Zhou X, Wang Z, Wei Y, Zhou H, Zhang X, Zhu Q, Wang Y, Yang Q, Jiang L, Ma Y, Gao Y, Kong L, Zhang L. The effects of methylphenidate and atomoxetine on Drosophila brain at single-cell resolution and potential drug repurposing for ADHD treatment. Mol Psychiatry 2024; 29:165-185. [PMID: 37957291 PMCID: PMC11078728 DOI: 10.1038/s41380-023-02314-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 10/24/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023]
Abstract
The stimulant methylphenidate (MPH) and the non-stimulant atomoxetine (ATX) are frequently used for the treatment of attention-deficit/hyperactivity disorder (ADHD); however, the function of these drugs in different types of brain cells and their effects on related genes remain largely unknown. To address these questions, we built a pipeline for the simultaneous examination of the activity behavior and transcriptional responses of Drosophila melanogaster at single-cell resolution following drug treatment. We selected the Drosophila with significantly increased locomotor activities (hyperactivity-like behavior) following the administration of each drug in comparison with the control (same food as the drug-treated groups with 5% sucrose, yeast, and blue food dye solution) using EasyFlyTracker. Subsequently, single cell RNA sequencing (scRNASEQ) was used to capture the transcriptome of 82,917 cells, unsupervised clustering analysis of which yielded 28 primary cell clusters representing the major cell types in adult Drosophila brain. Indeed, both neuronal and glial cells responded to MPH and ATX. Further analysis of differentially expressed genes (DEGs) revealed distinct transcriptional changes associated with these two drugs, such as two well-studied dopamine receptor genes (Dop2R and DopEcR) were responsive to MPH but not to ATX at their optimal doses, in addition to genes involved in dopamine metabolism pathways such as Syt1, Sytalpha, Syt7, and Ih in different cell types. More importantly, MPH also suppressed the expression of genes encoding other neurotransmitter receptors and synaptic signaling molecules in many cell types, especially those for Glu and GABA, while the responsive effects of ATX were much weaker. In addition to monoaminergic neuronal transmitters, other neurotransmitters have also shown a similar pattern with respect to a stronger effect associated with MPH than with ATX. Moreover, we identified four distinct glial cell subtypes responsive to the two drugs and detected a greater number of differentially expressed genes associated with ensheathing and astrocyte-like glia. Furthermore, our study provides a rich resource of candidate target genes, supported by drug set enrichment analysis (P = 2.10E-4; hypergeometric test), for the further exploration of drug repurposing. The whole list of candidates can be found at ADHDrug ( http://adhdrug.cibr.ac.cn/ ). In conclusion, we propose a fast and cost-efficient pipeline to explore the underlying molecular mechanisms of ADHD drug treatment in Drosophila brain at single-cell resolution, which may further facilitate drug repurposing applications.
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Affiliation(s)
- Susu Qu
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
- Chinese Institute for Brain Research, Beijing, China.
| | - Xiangyu Zhou
- Chinese Institute for Brain Research, Beijing, China
| | - Zhicheng Wang
- Chinese Institute for Brain Research, Beijing, China
| | - Yi Wei
- Chinese Institute for Brain Research, Beijing, China
| | - Han Zhou
- Chinese Institute for Brain Research, Beijing, China
| | | | - Qingjie Zhu
- Chinese Institute for Brain Research, Beijing, China
| | - Yanmin Wang
- Chinese Institute for Brain Research, Beijing, China
| | - Quanjun Yang
- Department of Pharmacy, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Likun Jiang
- Department of Computer Science, Xiamen University, Xiamen, China
| | - Yuan Ma
- Chinese Institute for Brain Research, Beijing, China
| | - Yuan Gao
- Chinese Institute for Brain Research, Beijing, China
| | - Lei Kong
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Li Zhang
- Chinese Institute for Brain Research, Beijing, China.
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Wilson CA, Batzel P, Postlethwait JH. Direct Male Development in Chromosomally ZZ Zebrafish. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.27.573483. [PMID: 38234788 PMCID: PMC10793451 DOI: 10.1101/2023.12.27.573483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
The genetics of sex determination varies across taxa, sometimes even within a species. Major domesticated strains of zebrafish ( Danio rerio ), including AB and TU, lack a strong genetic sex determining locus, but strains more recently derived from nature, like Nadia (NA), possess a ZZ male/ZW female chromosomal sex-determination system. AB strain fish pass through a juvenile ovary stage, forming oocytes that survive in fish that become females but die in fish that become males. To understand mechanisms of gonad development in NA zebrafish, we studied histology and single cell transcriptomics in developing ZZ and ZW fish. ZW fish developed oocytes by 22 days post-fertilization (dpf) but ZZ fish directly formed testes, avoiding a juvenile ovary phase. Gonads of some ZW and WW fish, however, developed oocytes that died as the gonad became a testis, mimicking AB fish, suggesting that the gynogenetically derived AB strain is chromosomally WW. Single-cell RNA-seq of 19dpf gonads showed similar cell types in ZZ and ZW fish, including germ cells, precursors of gonadal support cells, steroidogenic cells, interstitial/stromal cells, and immune cells, consistent with a bipotential juvenile gonad. In contrast, scRNA-seq of 30dpf gonads revealed that cells in ZZ gonads had transcriptomes characteristic of testicular Sertoli, Leydig, and germ cells while ZW gonads had granulosa cells, theca cells, and developing oocytes. Hematopoietic and vascular cells were similar in both sex genotypes. These results show that juvenile NA zebrafish initially develop a bipotential gonad; that a factor on the NA W chromosome or fewer than two Z chromosomes is essential to initiate oocyte development; and without the W factor or with two Z doses, NA gonads develop directly into testes without passing through the juvenile ovary stage. Sex determination in AB and TU strains mimics NA ZW and WW zebrafish, suggesting loss of the Z chromosome during domestication. Genetic analysis of the NA strain will facilitate our understanding of the evolution of sex determination mechanisms.
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Kitamoto T, Idé T, Tezuka Y, Wada N, Shibayama Y, Tsurutani Y, Takiguchi T, Inoue K, Suematsu S, Omata K, Ono Y, Morimoto R, Yamazaki Y, Saito J, Sasano H, Satoh F, Nishikawa T. Identifying primary aldosteronism patients who require adrenal venous sampling: a multi-center study. Sci Rep 2023; 13:21722. [PMID: 38081870 PMCID: PMC10713522 DOI: 10.1038/s41598-023-47967-z] [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: 03/29/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Adrenal venous sampling (AVS) is crucial for subtyping primary aldosteronism (PA) to explore the possibility of curing hypertension. Because AVS availability is limited, efforts have been made to develop strategies to bypass it. However, it has so far proven unsuccessful in applying clinical practice, partly due to heterogeneity and missing values of the cohorts. For this purpose, we retrospectively assessed 210 PA cases from three institutions where segment-selective AVS, which is more accurate and sensitive for detecting PA cases with surgical indications, was available. A machine learning-based classification model featuring a new cross-center domain adaptation capability was developed. The model identified 102 patients with PA who benefited from surgery in the present cohort. A new data imputation technique was used to address cross-center heterogeneity, making a common prediction model applicable across multiple cohorts. Logistic regression demonstrated higher accuracy than Random Forest and Deep Learning [(0.89, 0.86) vs. (0.84, 0.84), (0.82, 0.84) for surgical or medical indications in terms of f-score]. A derived integrated flowchart revealed that 35.2% of PA cases required AVS with 94.1% accuracy. The present model enabled us to reduce the burden of AVS on patients who would benefit the most.
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Affiliation(s)
- Takumi Kitamoto
- Endocrinology and Diabetes Center, Yokohama Rosai Hospital, Yokohama, 2220036, Japan.
- Department of Diabetes, Metabolism and Endocrinology, Chiba University Hospital, Chiba, 2608670, Japan.
| | - Tsuyoshi Idé
- IBM Research, T. J. Watson Research Center, Yorktown Heights, NY, 10598, USA
| | - Yuta Tezuka
- Department of Diabetes, Metabolism, and Endocrinology, Tohoku University Hospital, Sendai, 9808574, Japan
- Division of Nephrology, Rheumatology, and Endocrinology, Tohoku University Graduate School of Medicine, Sendai, 9808574, Japan
| | - Norio Wada
- Department of Diabetes and Endocrinology, Sapporo City General Hospital, Sapporo, 0608604, Japan
| | - Yui Shibayama
- Department of Diabetes and Endocrinology, Sapporo City General Hospital, Sapporo, 0608604, Japan
- Department of Rheumatology, Endocrinology and Nephrology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, 0608648, Japan
| | - Yuya Tsurutani
- Endocrinology and Diabetes Center, Yokohama Rosai Hospital, Yokohama, 2220036, Japan
| | - Tomoko Takiguchi
- Endocrinology and Diabetes Center, Yokohama Rosai Hospital, Yokohama, 2220036, Japan
| | - Kosuke Inoue
- Department of Social Epidemiology, Graduate School of Medicine, Kyoto University, Kyoto, 6048135, Japan
| | - Sachiko Suematsu
- Endocrinology and Diabetes Center, Yokohama Rosai Hospital, Yokohama, 2220036, Japan
| | - Kei Omata
- Department of Diabetes, Metabolism, and Endocrinology, Tohoku University Hospital, Sendai, 9808574, Japan
- Division of Nephrology, Rheumatology, and Endocrinology, Tohoku University Graduate School of Medicine, Sendai, 9808574, Japan
| | - Yoshikiyo Ono
- Department of Diabetes, Metabolism, and Endocrinology, Tohoku University Hospital, Sendai, 9808574, Japan
- Division of Nephrology, Rheumatology, and Endocrinology, Tohoku University Graduate School of Medicine, Sendai, 9808574, Japan
| | - Ryo Morimoto
- Division of Nephrology, Rheumatology, and Endocrinology, Tohoku University Graduate School of Medicine, Sendai, 9808574, Japan
| | - Yuto Yamazaki
- Department of Pathology, Tohoku University Graduate School of Medicine, Sendai, 9808575, Japan
| | - Jun Saito
- Endocrinology and Diabetes Center, Yokohama Rosai Hospital, Yokohama, 2220036, Japan
| | - Hironobu Sasano
- Department of Pathology, Tohoku University Graduate School of Medicine, Sendai, 9808575, Japan
| | - Fumitoshi Satoh
- Division of Nephrology, Rheumatology, and Endocrinology, Tohoku University Graduate School of Medicine, Sendai, 9808574, Japan
- Department of Pathology, Tohoku University Graduate School of Medicine, Sendai, 9808575, Japan
| | - Tetsuo Nishikawa
- Endocrinology and Diabetes Center, Yokohama Rosai Hospital, Yokohama, 2220036, Japan
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Muraleedharan Saraswathy V, Zhou L, Mokalled MH. Single-cell analysis of innate spinal cord regeneration identifies intersecting modes of neuronal repair. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.19.541505. [PMID: 37292638 PMCID: PMC10245778 DOI: 10.1101/2023.05.19.541505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Adult zebrafish have an innate ability to recover from severe spinal cord injury. Here, we report a comprehensive single nuclear RNA sequencing atlas that spans 6 weeks of regeneration. We identify cooperative roles for adult neurogenesis and neuronal plasticity during spinal cord repair. Neurogenesis of glutamatergic and GABAergic neurons restores the excitatory/inhibitory balance after injury. In addition, transient populations of injury-responsive neurons (iNeurons) show elevated plasticity between 1 and 3 weeks post-injury. Using cross-species transcriptomics and CRISPR/Cas9 mutagenesis, we found iNeurons are injury-surviving neurons that share transcriptional similarities with a rare population of spontaneously plastic mouse neurons. iNeurons are required for functional recovery and employ vesicular trafficking as an essential mechanism that underlies neuronal plasticity. This study provides a comprehensive resource of the cells and mechanisms that direct spinal cord regeneration and establishes zebrafish as a model of plasticity-driven neural repair.
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Lin M, Zhong Y, Zhou D, Guan B, Hu B, Wang P, Liu F. Proximal tubule cells in blood and urine as potential biomarkers for kidney disease biopsy. PeerJ 2023; 11:e16499. [PMID: 38077419 PMCID: PMC10710128 DOI: 10.7717/peerj.16499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/31/2023] [Indexed: 12/18/2023] Open
Abstract
Early diagnosis and treatment are crucial for managing kidney disease, yet there remains a need to further explore pathological mechanisms and develop minimally invasive diagnostic methods. In this study, we employed single-cell RNA sequencing (scRNA-seq) to assess the cellular heterogeneity of kidney diseases. We analyzed gene expression profiles from renal tissue, peripheral blood mononuclear cells (PBMCs), and urine of four patients with nephritis. Our findings identified 12 distinct cell subsets in renal tissues and leukocytes. These subsets encompassed fibroblast cells, mesangial cells, epithelial cells, proximal tubule cells (PTCs), and six immune cell types: CD8+ T cells, macrophages, natural killer cells, dendritic cells, B cells, and neutrophils. Interestingly, PTCs were present in both PBMCs and urine samples but absent in healthy blood samples. Furthermore, several populations of fibroblast cells, mesangial cells, and PTCs exhibited pro-inflammatory or pro-apoptotic behaviors. Our gene expression analysis highlighted the critical role of inflammatory PTCs and fibroblasts in nephritis development and progression. These cells showed high expression of pro-inflammatory genes, which could have chemotactic and activating effect on neutrophils. This was substantiated by the widespread in these cells. Notably, the gene expression profiles of inflammatory PTCs in PBMCs, urine, and kidney tissues had high similarity. This suggests that PTCs in urine and PBMCs hold significant potential as alternative markers to invasive kidney biopsies.
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Affiliation(s)
- Minwa Lin
- Depament of Nephrology, The First People’s Hospital of Foshan, Foshan, China
| | - Yingxue Zhong
- Depament of Nephrology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Dan Zhou
- Cancer Center, The First People’s Hospital of Foshan, Foshan, China
| | - Baozhang Guan
- Depament of Nephrology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Bo Hu
- Depament of Nephrology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Panpan Wang
- Department of Traditional Chinese Medicine, the First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Fanna Liu
- Depament of Nephrology, The First Affiliated Hospital of Jinan University, Guangzhou, China
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Murphy AE, Fancy N, Skene N. Avoiding false discoveries in single-cell RNA-seq by revisiting the first Alzheimer's disease dataset. eLife 2023; 12:RP90214. [PMID: 38047913 PMCID: PMC10695556 DOI: 10.7554/elife.90214] [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] [Indexed: 12/05/2023] Open
Abstract
Mathys et al. conducted the first single-nucleus RNA-seq (snRNA-seq) study of Alzheimer's disease (AD) (Mathys et al., 2019). With bulk RNA-seq, changes in gene expression across cell types can be lost, potentially masking the differentially expressed genes (DEGs) across different cell types. Through the use of single-cell techniques, the authors benefitted from increased resolution with the potential to uncover cell type-specific DEGs in AD for the first time. However, there were limitations in both their data processing and quality control and their differential expression analysis. Here, we correct these issues and use best-practice approaches to snRNA-seq differential expression, resulting in 549 times fewer DEGs at a false discovery rate of 0.05. Thus, this study highlights the impact of quality control and differential analysis methods on the discovery of disease-associated genes and aims to refocus the AD research field away from spuriously identified genes.
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Affiliation(s)
- Alan E Murphy
- UK Dementia Research Institute at Imperial College LondonLondonUnited Kingdom
- Department of Brain Sciences, Imperial College LondonLondonUnited Kingdom
| | - Nurun Fancy
- UK Dementia Research Institute at Imperial College LondonLondonUnited Kingdom
- Department of Brain Sciences, Imperial College LondonLondonUnited Kingdom
| | - Nathan Skene
- UK Dementia Research Institute at Imperial College LondonLondonUnited Kingdom
- Department of Brain Sciences, Imperial College LondonLondonUnited Kingdom
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Xu R, Xie H, Shen X, Huang J, Zhang H, Fu Y, Zhang P, Guo S, Wang D, Li S, Zheng K, Sun W, Liu L, Cheng J, Jiang H. Impaired Efferocytosis Enables Apoptotic Osteoblasts to Escape Osteoimmune Surveillance During Aging. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303946. [PMID: 37897313 PMCID: PMC10754079 DOI: 10.1002/advs.202303946] [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: 06/15/2023] [Revised: 09/08/2023] [Indexed: 10/30/2023]
Abstract
Macrophage efferocytosis of apoptotic osteoblasts (apoOBs) is a key osteoimmune process for bone homeostasis. However, apoOBs frequently accumulate in aged bone marrow, where they may mount proinflammatory responses and progressive bone loss. The reason why apoOBs are not cleared during aging remains unclear. In this study, it is demonstrated that aged apoOBs upregulate the immune checkpoint molecule CD47, which is controlled by SIRT6-regulated transcriptional pausing, to evade clearance by macrophages. Using osteoblast- and myeloid-specific gene knockout mice, SIRT6 is further revealed to be a critical modulator for apoOBs clearance via targeting CD47-SIRPα checkpoint. Moreover, apoOBs activate SIRT6-mediated chemotaxis to recruit macrophages by releasing apoptotic vesicles. Two targeting delivery strategies are developed to enhance SIRT6 activity, resulting in rejuvenated apoOBs clearance and delayed age-related bone loss. Collectively, the findings reveal a previously unknown linkage between immune surveillance and bone homeostasis and targeting the SIRT6-regulated mechanism can be a promising therapeutic strategy for age-related bone diseases.
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Affiliation(s)
- Rongyao Xu
- Jiangsu Key Laboratory of Oral DiseasesNanjing Medical UniversityNanjingJiangsu Province210029China
- Department of Oral and Maxillofacial SurgeryAffiliated Hospital of StomatologyNanjing Medical UniversityNanjingJiangsu Province210029China
- Jiangsu Province Engineering Research Center of Stomatological Translational MedicineNanjingJiangsu Province210029China
| | - Hanyu Xie
- Jiangsu Key Laboratory of Oral DiseasesNanjing Medical UniversityNanjingJiangsu Province210029China
- Department of Oral and Maxillofacial SurgeryAffiliated Hospital of StomatologyNanjing Medical UniversityNanjingJiangsu Province210029China
- Jiangsu Province Engineering Research Center of Stomatological Translational MedicineNanjingJiangsu Province210029China
| | - Xin Shen
- Jiangsu Key Laboratory of Oral DiseasesNanjing Medical UniversityNanjingJiangsu Province210029China
- Department of Oral and Maxillofacial SurgeryAffiliated Hospital of StomatologyNanjing Medical UniversityNanjingJiangsu Province210029China
- Jiangsu Province Engineering Research Center of Stomatological Translational MedicineNanjingJiangsu Province210029China
| | - Jiadong Huang
- Jiangsu Key Laboratory of Oral DiseasesNanjing Medical UniversityNanjingJiangsu Province210029China
- Jiangsu Province Engineering Research Center of Stomatological Translational MedicineNanjingJiangsu Province210029China
| | - Hengguo Zhang
- Jiangsu Key Laboratory of Oral DiseasesNanjing Medical UniversityNanjingJiangsu Province210029China
- Jiangsu Province Engineering Research Center of Stomatological Translational MedicineNanjingJiangsu Province210029China
| | - Yu Fu
- Jiangsu Key Laboratory of Oral DiseasesNanjing Medical UniversityNanjingJiangsu Province210029China
- Department of Oral and Maxillofacial SurgeryAffiliated Hospital of StomatologyNanjing Medical UniversityNanjingJiangsu Province210029China
- Jiangsu Province Engineering Research Center of Stomatological Translational MedicineNanjingJiangsu Province210029China
| | - Ping Zhang
- Jiangsu Key Laboratory of Oral DiseasesNanjing Medical UniversityNanjingJiangsu Province210029China
- Department of Oral and Maxillofacial SurgeryAffiliated Hospital of StomatologyNanjing Medical UniversityNanjingJiangsu Province210029China
- Jiangsu Province Engineering Research Center of Stomatological Translational MedicineNanjingJiangsu Province210029China
| | - Songsong Guo
- Jiangsu Key Laboratory of Oral DiseasesNanjing Medical UniversityNanjingJiangsu Province210029China
- Department of Oral and Maxillofacial SurgeryAffiliated Hospital of StomatologyNanjing Medical UniversityNanjingJiangsu Province210029China
- Jiangsu Province Engineering Research Center of Stomatological Translational MedicineNanjingJiangsu Province210029China
| | - Dongmiao Wang
- Jiangsu Key Laboratory of Oral DiseasesNanjing Medical UniversityNanjingJiangsu Province210029China
- Department of Oral and Maxillofacial SurgeryAffiliated Hospital of StomatologyNanjing Medical UniversityNanjingJiangsu Province210029China
- Jiangsu Province Engineering Research Center of Stomatological Translational MedicineNanjingJiangsu Province210029China
| | - Sheng Li
- Jiangsu Key Laboratory of Oral DiseasesNanjing Medical UniversityNanjingJiangsu Province210029China
- Department of Oral and Maxillofacial SurgeryAffiliated Hospital of StomatologyNanjing Medical UniversityNanjingJiangsu Province210029China
- Jiangsu Province Engineering Research Center of Stomatological Translational MedicineNanjingJiangsu Province210029China
| | - Kai Zheng
- Jiangsu Key Laboratory of Oral DiseasesNanjing Medical UniversityNanjingJiangsu Province210029China
- Jiangsu Province Engineering Research Center of Stomatological Translational MedicineNanjingJiangsu Province210029China
| | - Wen Sun
- Jiangsu Key Laboratory of Oral DiseasesNanjing Medical UniversityNanjingJiangsu Province210029China
- Jiangsu Province Engineering Research Center of Stomatological Translational MedicineNanjingJiangsu Province210029China
- Department of Basic Science of StomatologyAffiliated Hospital of StomatologyNanjing Medical UniversityNanjingJiangsu211166China
| | - Laikui Liu
- Jiangsu Key Laboratory of Oral DiseasesNanjing Medical UniversityNanjingJiangsu Province210029China
- Jiangsu Province Engineering Research Center of Stomatological Translational MedicineNanjingJiangsu Province210029China
- Department of Basic Science of StomatologyAffiliated Hospital of StomatologyNanjing Medical UniversityNanjingJiangsu211166China
| | - Jie Cheng
- Jiangsu Key Laboratory of Oral DiseasesNanjing Medical UniversityNanjingJiangsu Province210029China
- Department of Oral and Maxillofacial SurgeryAffiliated Hospital of StomatologyNanjing Medical UniversityNanjingJiangsu Province210029China
- Jiangsu Province Engineering Research Center of Stomatological Translational MedicineNanjingJiangsu Province210029China
| | - Hongbing Jiang
- Jiangsu Key Laboratory of Oral DiseasesNanjing Medical UniversityNanjingJiangsu Province210029China
- Department of Oral and Maxillofacial SurgeryAffiliated Hospital of StomatologyNanjing Medical UniversityNanjingJiangsu Province210029China
- Jiangsu Province Engineering Research Center of Stomatological Translational MedicineNanjingJiangsu Province210029China
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Karmaus PWF, Tata A, Meacham JM, Day F, Thrower D, Tata PR, Fessler MB. Meta-Analysis of COVID-19 BAL Single-Cell RNA Sequencing Reveals Alveolar Epithelial Transitions and Unique Alveolar Epithelial Cell Fates. Am J Respir Cell Mol Biol 2023; 69:623-637. [PMID: 37523502 DOI: 10.1165/rcmb.2023-0077oc] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/31/2023] [Indexed: 08/02/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) of BAL cells has provided insights into coronavirus disease (COVID-19). However, reports have been limited by small patient cohorts. We performed a meta-analysis of BAL scRNA-seq data from healthy control subjects (n = 13) and patients with COVID-19 (n = 20), sourced from six independent studies (167,280 high-quality cells in total). Consistent with the source reports, increases in infiltrating leukocyte subtypes were noted, several with type I IFN signatures and unique gene expression signatures associated with transcellular chemokine signaling. Noting dramatic reductions of inferred NKX2-1 and NR4A1 activity in alveolar epithelial type II (AT-II) cells, we modeled pseudotemporal AT-II-to-AT-I progression. This revealed changes in inferred AT-II cell metabolic activity, increased transitional cells, and a previously undescribed AT-I state. This cell state was conspicuously marked by the induction of genes of the epidermal differentiation complex, including the cornified envelope protein SPRR3 (small proline-rich protein 3), upregulation of multiple KRT (keratin) genes, inferred mitochondrial dysfunction, and cell death signatures including apoptosis and ferroptosis. Immunohistochemistry of lungs from patients with COVID-19 confirmed upregulation and colocalization of KRT13 and SPRR3 in the distal airspaces. Forced overexpression of SPRR3 in human alveolar epithelial cells ex vivo did not activate caspase-3 or upregulate KRT13, suggesting that SPRR3 marks an AT-I cornification program in COVID-19 but is not sufficient for phenotypic changes.
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Affiliation(s)
| | - Aleksandra Tata
- Department of Cell Biology, School of Medicine, Duke University, Durham, North Carolina
| | | | - Frank Day
- Office of Scientific Computing, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina; and
| | - David Thrower
- Office of Scientific Computing, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina; and
| | - Purushothama Rao Tata
- Department of Cell Biology, School of Medicine, Duke University, Durham, North Carolina
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50
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Kavaliauskaite G, Madsen JS. Automatic quality control of single-cell and single-nucleus RNA-seq using valiDrops. NAR Genom Bioinform 2023; 5:lqad101. [PMID: 38025048 PMCID: PMC10657416 DOI: 10.1093/nargab/lqad101] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 10/05/2023] [Accepted: 11/01/2023] [Indexed: 12/01/2023] Open
Abstract
Single-cell and single-nucleus RNA-sequencing (sxRNA-seq) measures gene expression in individual cells or nuclei enabling comprehensive characterization of cell types and states. However, isolation of cells or nuclei for sxRNA-seq releases contaminating RNA, which can distort biological signals, through, for example, cell damage and transcript leakage. Thus, identifying barcodes containing high-quality cells or nuclei is a critical analytical step in the processing of sxRNA-seq data. Here, we present valiDrops, an automated method to identify high-quality barcodes and flag dead cells. In valiDrops, barcodes are initially filtered using data-adaptive thresholding on community-standard quality metrics, and subsequently, valiDrops uses a novel clustering-based approach to identify barcodes with distinct biological signals. We benchmark valiDrops and show that biological signals from cell types and states are more distinct, easier to separate and more consistent after filtering by valiDrops compared to existing tools. Finally, we show that valiDrops can predict and flag dead cells with high accuracy. This novel classifier can further improve data quality or be used to identify dead cells to interrogate the biology of cell death. Thus, valiDrops is an effective and easy-to-use method to improve data quality and biological interpretation. Our method is openly available as an R package at www.github.com/madsen-lab/valiDrops.
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Affiliation(s)
- Gabija Kavaliauskaite
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M 5230, Denmark
- Center for Functional Genomics and Tissue Plasticity (ATLAS), Odense M 5230, Denmark
| | - Jesper Grud Skat Madsen
- Center for Functional Genomics and Tissue Plasticity (ATLAS), Odense M 5230, Denmark
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense M 5230, Denmark
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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