1
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Short SP, Brown RE, Chen Z, Pilat JM, McElligott BA, Meenderink LM, Bickart AC, Blunt KM, Jacobse J, Wang J, Simmons AJ, Xu Y, Yang Y, Parang B, Choksi YA, Goettel JA, Lau KS, Hiebert SW, Williams CS. MTGR1 is required to maintain small intestinal stem cell populations. Cell Death Differ 2024; 31:1170-1183. [PMID: 39048708 PMCID: PMC11369156 DOI: 10.1038/s41418-024-01346-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 07/03/2024] [Accepted: 07/10/2024] [Indexed: 07/27/2024] Open
Abstract
Undifferentiated intestinal stem cells (ISCs) are crucial for maintaining homeostasis and resolving injury. Lgr5+ cells in the crypt base constantly divide, pushing daughter cells upward along the crypt axis where they differentiate into specialized cell types. Coordinated execution of complex transcriptional programs is necessary to allow for the maintenance of undifferentiated stem cells while permitting differentiation of the wide array of intestinal cells necessary for homeostasis. Previously, members of the myeloid translocation gene (MTG) family have been identified as transcriptional co-repressors that regulate stem cell maintenance and differentiation programs in multiple organ systems, including the intestine. One MTG family member, myeloid translocation gene related 1 (MTGR1), has been recognized as a crucial regulator of secretory cell differentiation and response to injury. However, whether MTGR1 contributes to the function of ISCs has not yet been examined. Here, using Mtgr1-/- mice, we have assessed the effects of MTGR1 loss specifically in ISC biology. Interestingly, loss of MTGR1 increased the total number of cells expressing Lgr5, the canonical marker of cycling ISCs, suggesting higher overall stem cell numbers. However, expanded transcriptomic and functional analyses revealed deficiencies in Mtgr1-null ISCs, including deregulated ISC-associated transcriptional programs. Ex vivo, intestinal organoids established from Mtgr1-null mice were unable to survive and expand due to aberrant differentiation and loss of stem and proliferative cells. Together, these results indicate that the role of MTGR1 in intestinal differentiation is likely stem cell intrinsic and identify a novel role for MTGR1 in maintaining ISC function.
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Affiliation(s)
- Sarah P Short
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Cancer Biology, Vanderbilt University, Nashville, TN, USA
- Department of Internal Medicine, University of Iowa, Iowa City, IA, USA
| | - Rachel E Brown
- Program in Cancer Biology, Vanderbilt University, Nashville, TN, USA
- Vanderbilt University School of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Zhengyi Chen
- Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN, USA
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jennifer M Pilat
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Cancer Biology, Vanderbilt University, Nashville, TN, USA
| | | | - Leslie M Meenderink
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Health Care System, Nashville, TN, 37232, USA
| | - Alexander C Bickart
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Koral M Blunt
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- The Ohio State University College of Medicine, Columbus, OH, USA
| | - Justin Jacobse
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Health Care System, Nashville, TN, 37232, USA
- Willem-Alexander Children's Hospital, Department of Pediatrics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jing Wang
- Department of Biostatistics, Vanderbilt University, Nashville, TN, USA
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alan J Simmons
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Yanwen Xu
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Yilin Yang
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Bobak Parang
- Program in Cancer Biology, Vanderbilt University, Nashville, TN, USA
- Vanderbilt University School of Medicine, Vanderbilt University, Nashville, TN, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Yash A Choksi
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Cancer Biology, Vanderbilt University, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Health Care System, Nashville, TN, 37232, USA
| | - Jeremy A Goettel
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Cancer Biology, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ken S Lau
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Scott W Hiebert
- Vanderbilt University School of Medicine, Vanderbilt University, Nashville, TN, USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
| | - Christopher S Williams
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
- Program in Cancer Biology, Vanderbilt University, Nashville, TN, USA.
- Vanderbilt University School of Medicine, Vanderbilt University, Nashville, TN, USA.
- Veterans Affairs Tennessee Valley Health Care System, Nashville, TN, 37232, USA.
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2
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Li J, Simmons AJ, Hawkins CV, Chiron S, Ramirez-Solano MA, Tasneem N, Kaur H, Xu Y, Revetta F, Vega PN, Bao S, Cui C, Tyree RN, Raber LW, Conner AN, Pilat JM, Jacobse J, McNamara KM, Allaman MM, Raffa GA, Gobert AP, Asim M, Goettel JA, Choksi YA, Beaulieu DB, Dalal RL, Horst SN, Pabla BS, Huo Y, Landman BA, Roland JT, Scoville EA, Schwartz DA, Washington MK, Shyr Y, Wilson KT, Coburn LA, Lau KS, Liu Q. Identification and multimodal characterization of a specialized epithelial cell type associated with Crohn's disease. Nat Commun 2024; 15:7204. [PMID: 39169060 PMCID: PMC11339313 DOI: 10.1038/s41467-024-51580-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 08/13/2024] [Indexed: 08/23/2024] Open
Abstract
Crohn's disease (CD) is a complex chronic inflammatory disorder with both gastrointestinal and extra-intestinal manifestations associated immune dysregulation. Analyzing 202,359 cells from 170 specimens across 83 patients, we identify a distinct epithelial cell type in both terminal ileum and ascending colon (hereon as 'LND') with high expression of LCN2, NOS2, and DUOX2 and genes related to antimicrobial response and immunoregulation. LND cells, confirmed by in-situ RNA and protein imaging, are rare in non-IBD controls but expand in active CD, and actively interact with immune cells and specifically express IBD/CD susceptibility genes, suggesting a possible function in CD immunopathogenesis. Furthermore, we discover early and late LND subpopulations with different origins and developmental potential. A higher ratio of late-to-early LND cells correlates with better response to anti-TNF treatment. Our findings thus suggest a potential pathogenic role for LND cells in both Crohn's ileitis and colitis.
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Affiliation(s)
- Jia Li
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alan J Simmons
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Caroline V Hawkins
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sophie Chiron
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Marisol A Ramirez-Solano
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Naila Tasneem
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Harsimran Kaur
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Yanwen Xu
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Frank Revetta
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Paige N Vega
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Shunxing Bao
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
| | - Can Cui
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Regina N Tyree
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Larry W Raber
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Anna N Conner
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jennifer M Pilat
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Justin Jacobse
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kara M McNamara
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Margaret M Allaman
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Gabriella A Raffa
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alain P Gobert
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mohammad Asim
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jeremy A Goettel
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yash A Choksi
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Dawn B Beaulieu
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Robin L Dalal
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sara N Horst
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Baldeep S Pabla
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yuankai Huo
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Bennett A Landman
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Joseph T Roland
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Elizabeth A Scoville
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
| | - David A Schwartz
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - M Kay Washington
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yu Shyr
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Keith T Wilson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA.
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA.
| | - Lori A Coburn
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA.
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA.
| | - Ken S Lau
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA.
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Qi Liu
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA.
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3
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Wathieu C, Lavergne A, Xu X, Rolot M, Nemazanyy I, Shostak K, El Hachem N, Maurizy C, Leemans C, Close P, Nguyen L, Desmet C, Tielens S, Dewals BG, Chariot A. Loss of Elp3 blocks intestinal tuft cell differentiation via an mTORC1-Atf4 axis. EMBO J 2024:10.1038/s44318-024-00184-4. [PMID: 39085648 DOI: 10.1038/s44318-024-00184-4] [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: 09/19/2023] [Revised: 06/25/2024] [Accepted: 07/12/2024] [Indexed: 08/02/2024] Open
Abstract
Intestinal tuft cells are critical for anti-helminth parasite immunity because they produce IL-25, which triggers IL-13 secretion by activated group 2 innate lymphoid cells (ILC2s) to expand both goblet and tuft cells. We show that epithelial Elp3, a tRNA-modifying enzyme, promotes tuft cell differentiation and is consequently critical for IL-25 production, ILC2 activation, goblet cell expansion and control of Nippostrongylus brasiliensis helminth infection in mice. Elp3 is essential for the generation of intestinal immature tuft cells and for the IL-13-dependent induction of glycolytic enzymes such as Hexokinase 1 and Aldolase A. Importantly, loss of epithelial Elp3 in the intestine blocks the codon-dependent translation of the Gator1 subunit Nprl2, an mTORC1 inhibitor, which consequently enhances mTORC1 activation and stabilizes Atf4 in progenitor cells. Likewise, Atf4 overexpression in mouse intestinal epithelium blocks tuft cell differentiation in response to intestinal helminth infection. Collectively, our data define Atf4 as a negative regulator of tuft cells and provide insights into promotion of intestinal type 2 immune response to parasites through tRNA modifications.
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Affiliation(s)
- Caroline Wathieu
- Interdisciplinary Cluster for Applied Genoproteomics, Liege, Belgium
- Laboratory of Cancer Biology, GIGA, University of Liege, Liege, Belgium
| | | | - Xinyi Xu
- Interdisciplinary Cluster for Applied Genoproteomics, Liege, Belgium
- Laboratory of Cancer Biology, GIGA, University of Liege, Liege, Belgium
| | - Marion Rolot
- Laboratory of Immunology-Vaccinology, Fundamental and Applied Research in Animals and Health (FARAH), University of Liege, Liege, Belgium
| | - Ivan Nemazanyy
- Platform for Metabolic Analyses, Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS 3633, Paris, France
| | - Kateryna Shostak
- Interdisciplinary Cluster for Applied Genoproteomics, Liege, Belgium
- Laboratory of Cancer Biology, GIGA, University of Liege, Liege, Belgium
| | - Najla El Hachem
- Interdisciplinary Cluster for Applied Genoproteomics, Liege, Belgium
- Laboratory of Cancer Signaling, GIGA, University of Liege, Liege, Belgium
| | - Chloé Maurizy
- Interdisciplinary Cluster for Applied Genoproteomics, Liege, Belgium
- Laboratory of Cancer Biology, GIGA, University of Liege, Liege, Belgium
| | - Charlotte Leemans
- Interdisciplinary Cluster for Applied Genoproteomics, Liege, Belgium
- Laboratory of Cancer Signaling, GIGA, University of Liege, Liege, Belgium
| | - Pierre Close
- Interdisciplinary Cluster for Applied Genoproteomics, Liege, Belgium
- Laboratory of Cancer Signaling, GIGA, University of Liege, Liege, Belgium
- WELBIO department, WEL Research Institute, avenue Pasteur, 6, 1300, Wavre, Belgium
| | - Laurent Nguyen
- Interdisciplinary Cluster for Applied Genoproteomics, Liege, Belgium
- WELBIO department, WEL Research Institute, avenue Pasteur, 6, 1300, Wavre, Belgium
- Laboratory of Molecular Regulation of Neurogenesis, University of Liege, Liege, Belgium
| | - Christophe Desmet
- Interdisciplinary Cluster for Applied Genoproteomics, Liege, Belgium
- Laboratory of Cellular and Molecular Immunology, University of Liege, Liege, GIGA-I3, Belgium
| | - Sylvia Tielens
- Interdisciplinary Cluster for Applied Genoproteomics, Liege, Belgium
- Laboratory of Cancer Biology, GIGA, University of Liege, Liege, Belgium
| | - Benjamin G Dewals
- Laboratory of Immunology-Vaccinology, Fundamental and Applied Research in Animals and Health (FARAH), University of Liege, Liege, Belgium
| | - Alain Chariot
- Interdisciplinary Cluster for Applied Genoproteomics, Liege, Belgium.
- Laboratory of Cancer Biology, GIGA, University of Liege, Liege, Belgium.
- WELBIO department, WEL Research Institute, avenue Pasteur, 6, 1300, Wavre, Belgium.
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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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Yao S, Yu X, Wang X. SmartImpute: A Targeted Imputation Framework for Single-cell Transcriptome Data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.15.603649. [PMID: 39071378 PMCID: PMC11275709 DOI: 10.1101/2024.07.15.603649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of cellular heterogeneity and tissue transcriptomic complexity. However, the high frequency of dropout events in scRNA-seq data complicates downstream analyses such as cell type identification and trajectory inference. Existing imputation methods address the dropout problem but face limitations such as high computational cost and risk of over-imputation. We present SmartImpute, a novel computational framework designed for targeted imputation of scRNA-seq data. SmartImpute focuses on a predefined set of marker genes, enhancing the biological relevance and computational efficiency of the imputation process while minimizing the risk of model misspecification. Utilizing a modified Generative Adversarial Imputation Network architecture, SmartImpute accurately imputes the missing gene expression and distinguishes between true biological zeros and missing values, preventing overfitting and preserving biologically relevant zeros. To ensure reproducibility, we also provide a function based on the GPT4 model to create target gene panels depending on the tissue types and research context. Our results, based on scRNA-seq data from head and neck squamous cell carcinoma and human bone marrow, demonstrate that SmartImpute significantly enhances cell type annotation and clustering accuracy while reducing computational burden. Benchmarking against other imputation methods highlights SmartImpute's superior performance in terms of both accuracy and efficiency. Overall, SmartImpute provides a lightweight, efficient, and biologically relevant solution for addressing dropout events in scRNA-seq data, facilitating deeper insights into cellular heterogeneity and disease progression. Furthermore, SmartImpute's targeted approach can be extended to spatial omics data, which also contain many missing values.
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Affiliation(s)
- Sijie Yao
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institution, Tampa, Florida, 33612, USA
| | - Xiaoqing Yu
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institution, Tampa, Florida, 33612, USA
| | - Xuefeng Wang
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institution, Tampa, Florida, 33612, USA
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6
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Raveenthiraraj S, Awanis G, Chieppa M, O’Connell AE, Sobolewski A. M1 and M2 Macrophages Differentially Regulate Colonic Crypt Renewal. Inflamm Bowel Dis 2024; 30:1138-1150. [PMID: 38001043 PMCID: PMC11219479 DOI: 10.1093/ibd/izad270] [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: 05/24/2023] [Indexed: 11/26/2023]
Abstract
BACKGROUND The colonic epithelium is the most rapidly renewing tissue in the body and is organized into a single cell layer of invaginations called crypts. Crypt renewal occurs through Lgr5 + gut stem cells situated at the crypt base, which divide, produce daughter cells that proliferate, migrate, differentiate into all the cells required for normal gut function, and are finally shed into the crypt lumen. In health, this rapid renewal helps maintain barrier function next to the hostile gut microbial luminal environment. Inflammation results in an influx of immune cells including inflammatory M1 macrophages into the gut mucosa next to the crypt epithelium, but the direct effect of macrophages on crypt regeneration and renewal are poorly understood. METHODS Using an in vitro macrophage-crypt coculture model, we show that homeostatic M2 macrophages and inflammatory M1 macrophages confer different effects on the crypt epithelium. RESULTS Both M1 and M2 increase crypt cell proliferation, with M2 macrophages requiring physical contact with the crypt epithelium, whereas M1 macrophages exert their effect through a secreted factor. Only M1 macrophages reduce goblet and Tuft cell numbers and increase Lgr5 + crypt stem cell numbers, all dependent on physical contact with the crypt epithelium. Further studies showed that M1 macrophages increase the Wnt signaling pathways cyclin D1 and LEF1 through physical contact rather than a secreted factor. CONCLUSIONS These findings highlight the importance of understanding distinct cellular interactions and direct dialogue between cells and increase our understanding of the contribution of different immune cell subtypes on crypt cell biology during inflammation.
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Affiliation(s)
- Sathuwarman Raveenthiraraj
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
- Division of Newborn Medicine, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Griselda Awanis
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - Marcello Chieppa
- Department of Biological and Environmental Sciences and Technologies, University of Solento, Centro Ecotekne, 73043, Monteroni, Lecce, Italy
| | - Amy E O’Connell
- Division of Newborn Medicine, Boston Children’s Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Anastasia Sobolewski
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
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7
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Sipos F, Műzes G. Colonic Tuft Cells: The Less-Recognized Therapeutic Targets in Inflammatory Bowel Disease and Colorectal Cancer. Int J Mol Sci 2024; 25:6209. [PMID: 38892399 PMCID: PMC11172904 DOI: 10.3390/ijms25116209] [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: 04/28/2024] [Revised: 06/02/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
Tuft cells are more than guardian chemosensory elements of the digestive tract. They produce a variety of immunological effector molecules in response to stimulation; moreover, they are essential for defense against protozoa and nematodes. Beyond the description of their characteristics, this review aims to elucidate the potential pathogenic and therapeutic roles of colonic tuft cells in inflammatory bowel disease and colorectal cancer, focusing on their primarily immunomodulatory action. Regarding inflammatory bowel disease, tuft cells are implicated in both maintaining the integrity of the intestinal epithelial barrier and in tissue repair and regeneration processes. In addition to maintaining intestinal homeostasis, they display complex immune-regulatory functions. During the development of colorectal cancer, tuft cells can promote the epithelial-to-mesenchymal transition, alter the gastrointestinal microenvironment, and modulate both the anti-tumor immune response and the tumor microenvironment. A wide variety of their biological functions can be targeted for anti-inflammatory or anti-tumor therapies; however, the adverse side effects of immunomodulatory actions must be strictly considered.
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Affiliation(s)
- Ferenc Sipos
- Immunology Division, Department of Internal Medicine and Hematology, Semmelweis University, 1088 Budapest, Hungary
| | - Györgyi Műzes
- Immunology Division, Department of Internal Medicine and Hematology, Semmelweis University, 1088 Budapest, Hungary
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8
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Contreras-Panta EW, Lee SH, Won Y, Norlander AE, Simmons AJ, Peebles RS, Lau KS, Choi E, Goldenring JR. Interleukin 13 Promotes Maturation and Proliferation in Metaplastic Gastroids. Cell Mol Gastroenterol Hepatol 2024; 18:101366. [PMID: 38815928 PMCID: PMC11292363 DOI: 10.1016/j.jcmgh.2024.101366] [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: 10/12/2023] [Revised: 05/18/2024] [Accepted: 05/20/2024] [Indexed: 06/01/2024]
Abstract
BACKGROUND & AIMS Type 2 innate lymphoid cells (ILC2s) and interleukin-13 (IL-13) promote the onset of spasmolytic polypeptide-expressing metaplasia (SPEM) cells. However, little is known about molecular effects of IL-13 in SPEM cells. We now sought to establish a reliable organoid model, Meta1 gastroids, to model SPEM cells in vitro. We evaluated cellular and molecular effects of ILC2s and IL-13 on maturation and proliferation of SPEM cells. METHODS We performed single-cell RNA sequencing to characterize Meta1 gastroids, which were derived from stomachs of Mist1-Kras transgenic mice that displayed pyloric metaplasia. Cell sorting was used to isolate activated ILC2s from stomachs of IL-13-tdTomato reporter mice treated with L635. Three-dimensional co-culture was used to determine the effects of ILC2s on Meta1 gastroids. Mouse normal or metaplastic (Meta1) and human metaplastic gastroids were cultured with IL-13 to evaluate cell responses. Air-Liquid Interface culture was performed to test long-term culture effects of IL-13. In silico analysis determined possible STAT6-binding sites in gene promoter regions. STAT6 inhibition was performed to corroborate STAT6 role in SPEM cells maturation. RESULTS Meta1 gastroids showed the characteristics of SPEM cell lineages in vitro even after several passages. We demonstrated that co-culture with ILC2s or IL-13 treatment can induce phosphorylation of STAT6 in Meta1 and normal gastroids and promote the maturation and proliferation of SPEM cell lineages. IL-13 up-regulated expression of mucin-related proteins in human metaplastic gastroids. Inhibition of STAT6 blocked SPEM-related gene expression in Meta1 gastroids and maturation of SPEM in both normal and Meta1 gastroids. CONCLUSIONS IL-13 promotes the maturation and proliferation of SPEM cells consistent with gastric mucosal regeneration.
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Affiliation(s)
- Ela W Contreras-Panta
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Su-Hyung Lee
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee; Section of Surgical Sciences, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yoonkyung Won
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee; Section of Surgical Sciences, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Allison E Norlander
- Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Alan J Simmons
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - R Stokes Peebles
- Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee; Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee; Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee; Nashville VA Medical Center, Nashville, Tennessee
| | - Ken S Lau
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee; Section of Surgical Sciences, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Eunyoung Choi
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - James R Goldenring
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee; Section of Surgical Sciences, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee; Nashville VA Medical Center, Nashville, Tennessee.
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9
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Strine MS, Fagerberg E, Darcy PW, Barrón GM, Filler RB, Alfajaro MM, D'Angelo-Gavrish N, Wang F, Graziano VR, Menasché BL, Damo M, Wang YT, Howitt MR, Lee S, Joshi NS, Mucida D, Wilen CB. Intestinal tuft cell immune privilege enables norovirus persistence. Sci Immunol 2024; 9:eadi7038. [PMID: 38517952 DOI: 10.1126/sciimmunol.adi7038] [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: 05/12/2023] [Accepted: 02/28/2024] [Indexed: 03/24/2024]
Abstract
The persistent murine norovirus strain MNVCR6 is a model for human norovirus and enteric viral persistence. MNVCR6 causes chronic infection by directly infecting intestinal tuft cells, rare chemosensory epithelial cells. Although MNVCR6 induces functional MNV-specific CD8+ T cells, these lymphocytes fail to clear infection. To examine how tuft cells promote immune escape, we interrogated tuft cell interactions with CD8+ T cells by adoptively transferring JEDI (just EGFP death inducing) CD8+ T cells into Gfi1b-GFP tuft cell reporter mice. Unexpectedly, some intestinal tuft cells partially resisted JEDI CD8+ T cell-mediated killing-unlike Lgr5+ intestinal stem cells and extraintestinal tuft cells-despite seemingly normal antigen presentation. When targeting intestinal tuft cells, JEDI CD8+ T cells predominantly adopted a T resident memory phenotype with decreased effector and cytotoxic capacity, enabling tuft cell survival. JEDI CD8+ T cells neither cleared nor prevented MNVCR6 infection in the colon, the site of viral persistence, despite targeting a virus-independent antigen. Ultimately, we show that intestinal tuft cells are relatively resistant to CD8+ T cells independent of norovirus infection, representing an immune-privileged niche that can be leveraged by enteric microbes.
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Affiliation(s)
- Madison S Strine
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Eric Fagerberg
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Patrick W Darcy
- Laboratory of Mucosal Immunology, Rockefeller University, New York, NY, USA
| | - Gabriel M Barrón
- Program in Immunology, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Renata B Filler
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Mia Madel Alfajaro
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | | | - Fang Wang
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Vincent R Graziano
- Department of Immunology, School of Medicine, UConn Health, Farmington, CT, USA
| | - Bridget L Menasché
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Martina Damo
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Ya-Ting Wang
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Tsinghua University School of Medicine, Beijing, China
| | - Michael R Howitt
- Program in Immunology, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Sanghyun Lee
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| | - Nikhil S Joshi
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Daniel Mucida
- Laboratory of Mucosal Immunology, Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Rockefeller University, New York, NY, USA
| | - Craig B Wilen
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
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10
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Eshleman EM, Rice T, Potter C, Waddell A, Hashimoto-Hill S, Woo V, Field S, Engleman L, Lim HW, Schumacher MA, Frey MR, Denson LA, Finkelman FD, Alenghat T. Microbiota-derived butyrate restricts tuft cell differentiation via histone deacetylase 3 to modulate intestinal type 2 immunity. Immunity 2024; 57:319-332.e6. [PMID: 38295798 PMCID: PMC10901458 DOI: 10.1016/j.immuni.2024.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 10/14/2023] [Accepted: 01/05/2024] [Indexed: 02/03/2024]
Abstract
Tuft cells in mucosal tissues are key regulators of type 2 immunity. Here, we examined the impact of the microbiota on tuft cell biology in the intestine. Succinate induction of tuft cells and type 2 innate lymphoid cells was elevated with loss of gut microbiota. Colonization with butyrate-producing bacteria or treatment with butyrate suppressed this effect and reduced intestinal histone deacetylase activity. Epithelial-intrinsic deletion of the epigenetic-modifying enzyme histone deacetylase 3 (HDAC3) inhibited tuft cell expansion in vivo and impaired type 2 immune responses during helminth infection. Butyrate restricted stem cell differentiation into tuft cells, and inhibition of HDAC3 in adult mice and human intestinal organoids blocked tuft cell expansion. Collectively, these data define a HDAC3 mechanism in stem cells for tuft cell differentiation that is dampened by a commensal metabolite, revealing a pathway whereby the microbiota calibrate intestinal type 2 immunity.
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Affiliation(s)
- Emily M Eshleman
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Taylor Rice
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Crystal Potter
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Division of Immunology, Allergy and Rheumatology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Amanda Waddell
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Seika Hashimoto-Hill
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Vivienne Woo
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Sydney Field
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Laura Engleman
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Hee-Woong Lim
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Michael A Schumacher
- The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA; Department of Pediatrics and Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Mark R Frey
- The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA; Department of Pediatrics and Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Lee A Denson
- Division of Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Fred D Finkelman
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Division of Immunology, Allergy and Rheumatology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Theresa Alenghat
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
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11
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Silverman JB, Vega PN, Tyska MJ, Lau KS. Intestinal Tuft Cells: Morphology, Function, and Implications for Human Health. Annu Rev Physiol 2024; 86:479-504. [PMID: 37863104 PMCID: PMC11193883 DOI: 10.1146/annurev-physiol-042022-030310] [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: 10/22/2023]
Abstract
Tuft cells are a rare and morphologically distinct chemosensory cell type found throughout many organs, including the gastrointestinal tract. These cells were identified by their unique morphologies distinguished by large apical protrusions. Ultrastructural data have begun to describe the molecular underpinnings of their cytoskeletal features, and tuft cell-enriched cytoskeletal proteins have been identified, although the connection of tuft cell morphology to tuft cell functionality has not yet been established. Furthermore, tuft cells display variations in function and identity between and within tissues, leading to the delineation of distinct tuft cell populations. As a chemosensory cell type, they display receptors that are responsive to ligands specific for their environment. While many studies have demonstrated the tuft cell response to protists and helminths in the intestine, recent research has highlighted other roles of tuft cells as well as implicated tuft cells in other disease processes including inflammation, cancer, and viral infections. Here, we review the literature on the cytoskeletal structure of tuft cells. Additionally, we focus on new research discussing tuft cell lineage, ligand-receptor interactions, tuft cell tropism, and the role of tuft cells in intestinal disease. Finally, we discuss the implication of tuft cell-targeted therapies in human health and how the morphology of tuft cells may contribute to their functionality.
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Affiliation(s)
- Jennifer B Silverman
- Epithelial Biology Center and Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; ,
| | - Paige N Vega
- Epithelial Biology Center and Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; ,
| | - Matthew J Tyska
- Epithelial Biology Center and Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; ,
| | - Ken S Lau
- Epithelial Biology Center and Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; ,
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12
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Zhu X, Meng S, Li G, Wang J, Peng X. AGImpute: imputation of scRNA-seq data based on a hybrid GAN with dropouts identification. Bioinformatics 2024; 40:btae068. [PMID: 38317025 PMCID: PMC10877090 DOI: 10.1093/bioinformatics/btae068] [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: 02/19/2024] [Revised: 02/19/2024] [Accepted: 02/19/2024] [Indexed: 02/07/2024] Open
Abstract
MOTIVATION Dropout events bring challenges in analyzing single-cell RNA sequencing data as they introduce noise and distort the true distributions of gene expression profiles. Recent studies focus on estimating dropout probability and imputing dropout events by leveraging information from similar cells or genes. However, the number of dropout events differs in different cells, due to the complex factors, such as different sequencing protocols, cell types, and batch effects. The dropout event differences are not fully considered in assessing the similarities between cells and genes, which compromises the reliability of downstream analysis. RESULTS This work proposes a hybrid Generative Adversarial Network with dropouts identification to impute single-cell RNA sequencing data, named AGImpute. First, the numbers of dropout events in different cells in scRNA-seq data are differentially estimated by using a dynamic threshold estimation strategy. Next, the identified dropout events are imputed by a hybrid deep learning model, combining Autoencoder with a Generative Adversarial Network. To validate the efficiency of the AGImpute, it is compared with seven state-of-the-art dropout imputation methods on two simulated datasets and seven real single-cell RNA sequencing datasets. The results show that AGImpute imputes the least number of dropout events than other methods. Moreover, AGImpute enhances the performance of downstream analysis, including clustering performance, identifying cell-specific marker genes, and inferring trajectory in the time-course dataset. AVAILABILITY AND IMPLEMENTATION The source code can be obtained from https://github.com/xszhu-lab/AGImpute.
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Affiliation(s)
- Xiaoshu Zhu
- School of Computer and Information Security, Guangxi Key Laboratory of Trusted Software, Guilin University of Electronic Technology, Guilin 541004, China
| | - Shuang Meng
- School of Computer Science and Engineering, Guangxi Normal University, Guilin 541006, China
| | - Gaoshi Li
- School of Computer Science and Engineering, Guangxi Normal University, Guilin 541006, China
| | - Jianxin Wang
- School of Computer Science and Engineering, Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha 400083, China
| | - Xiaoqing Peng
- School of Life Sciences, Center for Medical Genetics, Central South University, Changsha 400083, China
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13
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Yang H, Huang YX, Xiong PY, Li JQ, Chen JL, Liu X, Gong YJ, Ding WJ. Possible connection between intestinal tuft cells, ILC2s and obesity. Front Immunol 2024; 14:1266667. [PMID: 38283340 PMCID: PMC10811205 DOI: 10.3389/fimmu.2023.1266667] [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: 07/26/2023] [Accepted: 12/21/2023] [Indexed: 01/30/2024] Open
Abstract
Intestinal tuft cells (TCs) are defined as chemosensory cells that can "taste" danger and induce immune responses. They play a critical role in gastrointestinal parasite invasion, inflammatory bowel diseases and high-fat diet-induced obesity. Intestinal IL-25, the unique product of TCs, is a key activator of type 2 immunity, especially to promote group 2 innate lymphoid cells (ILC2s) to secret IL-13. Then the IL-13 mainly promotes intestinal stem cell (ISCs) proliferation into TCs and goblet cells. This pathway formulates the circuit in the intestine. This paper focuses on the potential role of the intestinal TC, ILC2 and their circuit in obesity-induced intestinal damage, and discussion on further study and the potential therapeutic target in obesity.
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Affiliation(s)
- Hong Yang
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yu-Xing Huang
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Pei-Yu Xiong
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jin-Qian Li
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ji-Lan Chen
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xia Liu
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yan-Ju Gong
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Wei-Jun Ding
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
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14
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Sakahara M, Okamoto T, Srivastava U, Natsume Y, Yamanaka H, Suzuki Y, Obama K, Nagayama S, Yao R. Paneth-like cells produced from OLFM4 + stem cells support OLFM4 + stem cell growth in advanced colorectal cancer. Commun Biol 2024; 7:27. [PMID: 38182890 PMCID: PMC10770338 DOI: 10.1038/s42003-023-05504-8] [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: 11/15/2022] [Accepted: 10/25/2023] [Indexed: 01/07/2024] Open
Abstract
Tumor tissues consist of heterogeneous cells that originate from stem cells; however, their cell fate determination program remains incompletely understood. Using patient-derived organoids established from patients with advanced colorectal cancer (CRC), we evaluated the potential of olfactomedin 4 (OLFM4)+ stem cells to produce a bifurcated lineage of progenies with absorptive and secretory properties. In the early phases of organoid reconstruction, OLFM4+ cells preferentially gave rise to secretory cells. Additionally, we found that Paneth-like cells, which do not exist in the normal colon, were induced in response to Notch signaling inhibition. Video recordings of single OLFM4+ cells revealed that organoids containing Paneth-like cells were effectively propagated and that their selective ablation led to organoid collapse. In tumor tissues, Paneth-like cells were identified only in the region where tumor cells lost cell adhesion. These findings indicate that Paneth-like cells are directly produced by OLFM4+ stem cells and that their interaction contributes to tumor formation by providing niche factors. This study reveals the importance of the cell fate specification program for building a complete tumor cellular ecosystem, which might be targeted with novel therapeutics.
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Affiliation(s)
- Mizuho Sakahara
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Takuya Okamoto
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Upasna Srivastava
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
- Child Study Center, Yale School of Medicine, New Haven, CT, USA
| | - Yasuko Natsume
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Hitomi Yamanaka
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Kazutaka Obama
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Satoshi Nagayama
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Surgery, Uji-Tokushukai Medical Center, Kyoto, Japan
| | - Ryoji Yao
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan.
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15
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Lu H, Yan H, Li X, Xing Y, Ye Y, Jiang S, Ma L, Ping J, Zuo H, Hao Y, Yu C, Li Y, Zhou G, Lu Y. Single-cell map of dynamic cellular microenvironment of radiation-induced intestinal injury. Commun Biol 2023; 6:1248. [PMID: 38071238 PMCID: PMC10710489 DOI: 10.1038/s42003-023-05645-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
Intestine is a highly radiation-sensitive organ that could be injured during the radiotherapy for pelvic, abdominal, and retroperitoneal tumors. However, the dynamic change of the intestinal microenvironment related to radiation-induced intestine injury (RIII) is still unclear. Using single-cell RNA sequencing, we pictured a dynamic landscape of the intestinal microenvironment during RIII and regeneration. We showed that the various cell types of intestine exhibited heterogeneous radiosensitivities. We revealed the distinct dynamic patterns of three subtypes of intestinal stem cells (ISCs), and the cellular trajectory analysis suggested a complex interconversion pattern among them. For the immune cells, we found that Ly6c+ monocytes can give rise to both pro-inflammatory macrophages and resident macrophages after RIII. Through cellular communication analysis, we identified a positive feedback loop between the macrophages and endothelial cells, which could amplify the inflammatory response induced by radiation. Besides, we identified different T cell subtypes and revealed their role in immunomodulation during the early stage of RIII through inflammation and defense response relevant signaling pathways. Overall, our study provides a valuable single-cell map of the multicellular dynamics during RIII and regeneration, which may facilitate the understanding of the mechanism of RIII.
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Affiliation(s)
- Hao Lu
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Hua Yan
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Xiaoyu Li
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Yuan Xing
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Yumeng Ye
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Siao Jiang
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
- College of Life Sciences, Hebei University, Baoding City, Hebei Province, 071002, China
| | - Luyu Ma
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Jie Ping
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Hongyan Zuo
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Yanhui Hao
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Chao Yu
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Yang Li
- Beijing Institute of Radiation Medicine, Beijing, 100850, China.
- Academy of Life Sciences, Anhui Medical University, Hefei City, Anhui Province, 230032, China.
| | - Gangqiao Zhou
- Beijing Institute of Radiation Medicine, Beijing, 100850, China.
- Collaborative Innovation Center for Personalized Cancer Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing City, Jiangsu Province, 211166, China.
| | - Yiming Lu
- Beijing Institute of Radiation Medicine, Beijing, 100850, China.
- College of Life Sciences, Hebei University, Baoding City, Hebei Province, 071002, China.
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16
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Schumacher MA. The emerging roles of deep crypt secretory cells in colonic physiology. Am J Physiol Gastrointest Liver Physiol 2023; 325:G493-G500. [PMID: 37697924 PMCID: PMC10887841 DOI: 10.1152/ajpgi.00093.2023] [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: 05/02/2023] [Revised: 08/18/2023] [Accepted: 09/03/2023] [Indexed: 09/13/2023]
Abstract
Deep crypt secretory (DCS) cells are a population of epithelial cells located at the colonic crypt base that share some similarities to Paneth and goblet cells. They were initially defined as c-Kit expressing cells, though subsequent work showed that they are more specifically marked by Reg4 in the murine colon. The best-understood function of DCS cells at present is supporting the stem cell niche by generating Notch and EGF ligands. However, as these cells also express immunoregulatory (e.g., Ccl6) and host defense (e.g., Retnlb) genes, it is likely they have additional functions in maintaining colonic health outside of maintenance of the stem niche. Recent advances in single-cell transcriptomic profiling hint at additional epithelial and immune roles that may exist for these cells and have aided in elucidating their developmental lineage. This review highlights the emerging evidence supporting a crucial role for DCS cells in intestinal physiology, the current understanding of how these cells are regulated, and their potential role(s) in colonic disease.
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Affiliation(s)
- Michael A Schumacher
- Department of Pediatrics, University of Southern California Keck School of Medicine, Los Angeles, California, United States
- The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California, United States
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17
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Hou W, Ji Z, Chen Z, Wherry EJ, Hicks SC, Ji H. A statistical framework for differential pseudotime analysis with multiple single-cell RNA-seq samples. Nat Commun 2023; 14:7286. [PMID: 37949861 PMCID: PMC10638410 DOI: 10.1038/s41467-023-42841-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 10/24/2023] [Indexed: 11/12/2023] Open
Abstract
Pseudotime analysis with single-cell RNA-sequencing (scRNA-seq) data has been widely used to study dynamic gene regulatory programs along continuous biological processes. While many methods have been developed to infer the pseudotemporal trajectories of cells within a biological sample, it remains a challenge to compare pseudotemporal patterns with multiple samples (or replicates) across different experimental conditions. Here, we introduce Lamian, a comprehensive and statistically-rigorous computational framework for differential multi-sample pseudotime analysis. Lamian can be used to identify changes in a biological process associated with sample covariates, such as different biological conditions while adjusting for batch effects, and to detect changes in gene expression, cell density, and topology of a pseudotemporal trajectory. Unlike existing methods that ignore sample variability, Lamian draws statistical inference after accounting for cross-sample variability and hence substantially reduces sample-specific false discoveries that are not generalizable to new samples. Using both real scRNA-seq and simulation data, including an analysis of differential immune response programs between COVID-19 patients with different disease severity levels, we demonstrate the advantages of Lamian in decoding cellular gene expression programs in continuous biological processes.
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Affiliation(s)
- Wenpin Hou
- Department of Biostatistics, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA
| | - Zhicheng Ji
- Department of Biostatistics, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Zeyu Chen
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - E John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Stephanie C Hicks
- Department of Biostatistics, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA.
| | - Hongkai Ji
- Department of Biostatistics, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA.
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18
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Campillo Poveda M, Britton C, Devaney E, McNeilly TN, Gerbe F, Jay P, Maizels RM. Tuft Cells: Detectors, Amplifiers, Effectors and Targets in Parasite Infection. Cells 2023; 12:2477. [PMID: 37887321 PMCID: PMC10605326 DOI: 10.3390/cells12202477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/12/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
Tuft cells have recently emerged as the focus of intense interest following the discovery of their chemosensory role in the intestinal tract, and their ability to activate Type 2 immune responses to helminth parasites. Moreover, they populate a wide range of mucosal tissues and are intimately connected to immune and neuronal cells, either directly or through the release of pharmacologically active mediators. They are now recognised to fulfil both homeostatic roles, in metabolism and tissue integrity, as well as acting as the first sensors of parasite infection, immunity to which is lost in their absence. In this review we focus primarily on the importance of tuft cells in the intestinal niche, but also link to their more generalised physiological role and discuss their potential as targets for the treatment of gastrointestinal disorders.
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Affiliation(s)
- Marta Campillo Poveda
- Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, Glasgow G12 8TA, UK;
| | - Collette Britton
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow G61 1QH, UK; (C.B.); (E.D.)
| | - Eileen Devaney
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow G61 1QH, UK; (C.B.); (E.D.)
| | - Tom N. McNeilly
- Disease Control Department, Moredun Research Institute, Penicuik EH26 0PZ, UK;
| | - François Gerbe
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, INSERM, F-34094 Montpellier, France; (F.G.); (P.J.)
| | - Philippe Jay
- Institute of Functional Genomics (IGF), University of Montpellier, CNRS, INSERM, F-34094 Montpellier, France; (F.G.); (P.J.)
| | - Rick M. Maizels
- Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, Glasgow G12 8TA, UK;
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19
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Li J, Simmons AJ, Chiron S, Ramirez-Solano MA, Tasneem N, Kaur H, Xu Y, Revetta F, Vega PN, Bao S, Cui C, Tyree RN, Raber LW, Conner AN, Beaulieu DB, Dalal RL, Horst SN, Pabla BS, Huo Y, Landman BA, Roland JT, Scoville EA, Schwartz DA, Washington MK, Shyr Y, Wilson KT, Coburn LA, Lau KS, Liu Q. A Specialized Epithelial Cell Type Regulating Mucosal Immunity and Driving Human Crohn's Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.30.560293. [PMID: 37873404 PMCID: PMC10592875 DOI: 10.1101/2023.09.30.560293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Crohn's disease (CD) is a complex chronic inflammatory disorder that may affect any part of gastrointestinal tract with extra-intestinal manifestations and associated immune dysregulation. To characterize heterogeneity in CD, we profiled single-cell transcriptomics of 170 samples from 65 CD patients and 18 non-inflammatory bowel disease (IBD) controls in both the terminal ileum (TI) and ascending colon (AC). Analysis of 202,359 cells identified a novel epithelial cell type in both TI and AC, featuring high expression of LCN2, NOS2, and DUOX2, and thus is named LND. LND cells, confirmed by high-resolution in-situ RNA imaging, were rarely found in non-IBD controls, but expanded significantly in active CD. Compared to other epithelial cells, genes defining LND cells were enriched in antimicrobial response and immunoregulation. Moreover, multiplexed protein imaging demonstrated that LND cell abundance was associated with immune infiltration. Cross-talk between LND and immune cells was explored by ligand-receptor interactions and further evidenced by their spatial colocalization. LND cells showed significant enrichment of expression specificity of IBD/CD susceptibility genes, revealing its role in immunopathogenesis of CD. Investigating lineage relationships of epithelial cells detected two LND cell subpopulations with different origins and developmental potential, early and late LND. The ratio of the late to early LND cells was related to anti-TNF response. These findings emphasize the pathogenic role of the specialized LND cell type in both Crohn's ileitis and Crohn's colitis and identify novel biomarkers associated with disease activity and treatment response.
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Affiliation(s)
- Jia Li
- Center for Quantitative Sciences, Vanderbilt Univerity Medical Center, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt Univerity Medical Center, Nashville, TN, USA
| | - Alan J. Simmons
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Sophie Chiron
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Marisol A. Ramirez-Solano
- Center for Quantitative Sciences, Vanderbilt Univerity Medical Center, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt Univerity Medical Center, Nashville, TN, USA
| | - Naila Tasneem
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Harsimran Kaur
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Yanwen Xu
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Frank Revetta
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Paige N. Vega
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Shunxing Bao
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Can Cui
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Regina N. Tyree
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Larry W. Raber
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Anna N. Conner
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dawn B. Beaulieu
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Robin L. Dalal
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sara N. Horst
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Baldeep S. Pabla
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yuankai Huo
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Bennett A. Landman
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Joseph T. Roland
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Surgery, Vanderbilt University Medical Center, Nashville TN, USA
| | - Elizabeth A. Scoville
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center; Nashville, TN, USA
| | - David A. Schwartz
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - M. Kay Washington
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center; Nashville, TN, USA
| | - Yu Shyr
- Center for Quantitative Sciences, Vanderbilt Univerity Medical Center, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt Univerity Medical Center, Nashville, TN, USA
| | - Keith T. Wilson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center; Nashville, TN, USA
| | - Lori A. Coburn
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center; Nashville, TN, USA
| | - Ken S. Lau
- Center for Quantitative Sciences, Vanderbilt Univerity Medical Center, Nashville, TN, USA
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Surgery, Vanderbilt University Medical Center, Nashville TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center; Nashville, TN, USA
| | - Qi Liu
- Center for Quantitative Sciences, Vanderbilt Univerity Medical Center, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt Univerity Medical Center, Nashville, TN, USA
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20
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Yammine SZ, Burns I, Gosio J, Peluso A, Merritt DM, Innes B, Coles BLK, Yan WR, Bader GD, Morshead CM, van der Kooy D. Fate Specification of GFAP-Negative Primitive Neural Stem Cells and Their Progeny at Clonal Resolution. Stem Cells Dev 2023; 32:606-621. [PMID: 37551982 DOI: 10.1089/scd.2023.0038] [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: 08/09/2023] Open
Abstract
The mature brain contains an incredible number and diversity of cells that are produced and maintained by heterogeneous pools of neural stem cells (NSCs). Two distinct types of NSCs exist in the developing and adult mouse brain: Glial Fibrillary Acidic Protein (GFAP)-negative primitive (p)NSCs and downstream GFAP-positive definitive (d)NSCs. To better understand the embryonic functions of NSCs, we performed clonal lineage tracing within neurospheres grown from either pNSCs or dNSCs to enrich for their most immediate downstream neural progenitor cells (NPCs). These clonal progenitor lineage tracing data allowed us to construct a hierarchy of progenitor subtypes downstream of pNSCs and dNSCs that were then validated using single-cell transcriptomics. Further, we identify Nexn as required for neuronal specification from neuron/astrocyte progenitor cells downstream of rare pNSCs. Combined, these data provide single-cell resolution of NPC lineages downstream of rare pNSCs that likely would be missed from population-level analyses in vivo.
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Affiliation(s)
- Samantha Z Yammine
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Ian Burns
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Jessica Gosio
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Andrew Peluso
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Daniel M Merritt
- Institute of Medical Science, University of Toronto, Toronto, Canada
| | - Brendan Innes
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Brenda L K Coles
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Wen Rui Yan
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Gary D Bader
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- The Donnelly Centre and University of Toronto, Toronto, Canada
| | - Cindi M Morshead
- The Donnelly Centre and University of Toronto, Toronto, Canada
- Department of Surgery, University of Toronto, Toronto, Canada
| | - Derek van der Kooy
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- The Donnelly Centre and University of Toronto, Toronto, Canada
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21
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Williams C, Brown R, Zhao Y, Wang J, Chen Z, Blunt K, Pilat J, Parang B, Choksi Y, Lau K, Hiebert S, Short S, Jacobse J, Xu Y, Yang Y, Goettel J. MTGR1 is required to maintain small intestinal stem cell populations. RESEARCH SQUARE 2023:rs.3.rs-3315071. [PMID: 37790452 PMCID: PMC10543309 DOI: 10.21203/rs.3.rs-3315071/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Undifferentiated intestinal stem cells (ISCs), particularly those marked by Lgr5, are crucial for maintaining homeostasis and resolving injury. Lgr5+ cells in the crypt base constantly divide, pushing daughter cells upward along the crypt axis, where they differentiate into a variety of specialized cell types. This process requires coordinated execution of complex transcriptional programs, which allow for the maintenance of undifferentiated stem cells while permitting differentiation of the wide array of intestinal cells necessary for homeostasis. Thus, disrupting these programs may negatively impact homeostasis and response to injury. Previously, members of the myeloid translocation gene (MTG) family have been identified as transcriptional co-repressors that regulate stem cell maintenance and differentiation programs in multiple organ systems, including the intestine. One MTG family member, myeloid translocation gene related 1 (MTGR1), has been recognized as a crucial regulator of secretory cell differentiation and response to injury. However, whether MTGR1 contributes to the function of ISCs has not yet been examined. Here, using Mtgr1-/- mice, we have assessed the effects of MTGR1 loss on ISC biology and differentiation programs. Interestingly, loss of MTGR1 increased the total number of cells expressing Lgr5, the canonical marker of cycling ISCs, suggesting higher overall stem cell numbers. However, expanded transcriptomic analyses revealed MTGR1 loss may instead promote stem cell differentiation into transit-amplifying cells at the expense of cycling ISC populations. Furthermore, ex vivo intestinal organoids established from Mtgr1 null were found nearly completely unable to survive and expand, likely due to aberrant ISC differentiation, suggesting that Mtgr1 null ISCs were functionally deficient as compared to WT ISCs. Together, these results identify a novel role for MTGR1 in ISC function and suggest that MTGR1 is required to maintain the undifferentiated state.
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Affiliation(s)
| | | | | | - Jing Wang
- Vanderbilt University Medical Center
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22
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Li H, Zhang Z, Squires M, Chen X, Zhang X. scMultiSim: simulation of single cell multi-omics and spatial data guided by gene regulatory networks and cell-cell interactions. RESEARCH SQUARE 2023:rs.3.rs-3301625. [PMID: 37790516 PMCID: PMC10543280 DOI: 10.21203/rs.3.rs-3301625/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Simulated single-cell data is essential for designing and evaluating computational methods in the absence of experimental ground truth. Existing simulators typically focus on modeling one or two specific biological factors or mechanisms that affect the output data, which limits their capacity to simulate the complexity and multi-modality in real data. Here, we present scMultiSim, an in silico simulator that generates multi-modal single-cell data, including gene expression, chromatin accessibility, RNA velocity, and spatial cell locations while accounting for the relationships between modalities. scMultiSim jointly models various biological factors that affect the output data, including cell identity, within-cell gene regulatory networks (GRNs), cell-cell interactions (CCIs), and chromatin accessibility, hile also incorporating technical noises. Moreover, it allows users to adjust each factor's effect easily. We validated scMultiSim's simulated biological effects and demonstrated its applications by benchmarking a wide range of computational tasks, including multi-modal and multi-batch data integration, RNA velocity estimation, GRN inference and CCI inference using spatially resolved gene expression data, many of them were not benchmarked before due to the lack of proper tools. Compared to existing simulators, scMultiSim can benchmark a much broader range of existing computational problems and even new potential tasks.
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Affiliation(s)
- Hechen Li
- Georgia Institute of Technology, Atlanta, USA
| | - Ziqi Zhang
- Georgia Institute of Technology, Atlanta, USA
| | | | - Xi Chen
- Southern University of Science and Technology, Shenzhen, China
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23
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Groves SM, Quaranta V. Quantifying cancer cell plasticity with gene regulatory networks and single-cell dynamics. FRONTIERS IN NETWORK PHYSIOLOGY 2023; 3:1225736. [PMID: 37731743 PMCID: PMC10507267 DOI: 10.3389/fnetp.2023.1225736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/25/2023] [Indexed: 09/22/2023]
Abstract
Phenotypic plasticity of cancer cells can lead to complex cell state dynamics during tumor progression and acquired resistance. Highly plastic stem-like states may be inherently drug-resistant. Moreover, cell state dynamics in response to therapy allow a tumor to evade treatment. In both scenarios, quantifying plasticity is essential for identifying high-plasticity states or elucidating transition paths between states. Currently, methods to quantify plasticity tend to focus on 1) quantification of quasi-potential based on the underlying gene regulatory network dynamics of the system; or 2) inference of cell potency based on trajectory inference or lineage tracing in single-cell dynamics. Here, we explore both of these approaches and associated computational tools. We then discuss implications of each approach to plasticity metrics, and relevance to cancer treatment strategies.
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Affiliation(s)
- Sarah M. Groves
- Department of Pharmacology, Vanderbilt University, Nashville, TN, United States
| | - Vito Quaranta
- Department of Pharmacology, Vanderbilt University, Nashville, TN, United States
- Department of Biochemistry, Vanderbilt University, Nashville, TN, United States
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24
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Kolev HM, Kaestner KH. Mammalian Intestinal Development and Differentiation-The State of the Art. Cell Mol Gastroenterol Hepatol 2023; 16:809-821. [PMID: 37507088 PMCID: PMC10520362 DOI: 10.1016/j.jcmgh.2023.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023]
Abstract
The development of the mammalian intestine, from its earliest origins as a morphologically uniform sheet of endoderm cells during gastrulation into the complex organ system that is essential for the life of the organism, is a truly fascinating process. During midgestation development, reciprocal interactions between endoderm-derived epithelium and mesoderm-derived mesenchyme enable villification, or the conversion of a radially symmetric pseudostratified epithelium into the functional subdivision of crypts and villi. Once a mature crypt-villus axis is established, proliferation and differentiation of new epithelial cells continue throughout life. Spatially localized signals including the wingless and Int-1, fibroblast growth factor, and Hippo systems, among others, ensure that new cells are being born continuously in the crypt. As cells exit the crypt compartment, a gradient of bone morphogenetic protein signaling limits proliferation to allow for the specification of multiple mature cell types. The first major differentiation decision is dependent on Notch signaling, which specifies epithelial cells into absorptive and secretory lineages. The secretory lineage is subdivided further into Paneth, goblet, tuft, and enteroendocrine cells via a complex network of transcription factors. Although some of the signaling molecules are produced by epithelial cells, critical components are derived from specialized crypt-adjacent mesenchymal cells termed telocytes, which are marked by Forkhead box l1, GLI Family Zinc Finger 1, and platelet-derived growth factor receptor α. The crucial nature of these processes is evidenced by the multitude of intestinal disorders such as colorectal cancer, short-bowel syndrome, and inflammatory bowel disease, which all reflect perturbations of the development and/or differentiation of the intestine.
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Affiliation(s)
- Hannah M Kolev
- Department of Genetics and Center for Molecular Studies in Digestive and Liver Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Klaus H Kaestner
- Department of Genetics and Center for Molecular Studies in Digestive and Liver Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
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25
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Taufalele PV, Wang W, Simmons AJ, Southard-Smith AN, Chen B, Greenlee JD, King MR, Lau KS, Hassane DC, Bordeleau F, Reinhart-King CA. Matrix stiffness enhances cancer-macrophage interactions and M2-like macrophage accumulation in the breast tumor microenvironment. Acta Biomater 2023; 163:365-377. [PMID: 35483629 PMCID: PMC9592676 DOI: 10.1016/j.actbio.2022.04.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 03/17/2022] [Accepted: 04/20/2022] [Indexed: 02/07/2023]
Abstract
The role of intratumor heterogeneity is becoming increasingly apparent in part due to expansion in single cell technologies. Clinically, tumor heterogeneity poses several obstacles to effective cancer therapy dealing with biomarker variability and treatment responses. Matrix stiffening is known to occur during tumor progression and contribute to pathogenesis in several cancer hallmarks, including tumor angiogenesis and metastasis. However, the effects of matrix stiffening on intratumor heterogeneity have not been thoroughly studied. In this study, we applied single-cell RNA sequencing to investigate the differences in the transcriptional landscapes between stiff and compliant MMTV-PyMT mouse mammary tumors. We found similar compositions of cancer and stromal subpopulations in compliant and stiff tumors but differential intercellular communication and a significantly higher concentration of tumor-promoting, M2-like macrophages in the stiffer tumor microenvironments. Interestingly, we found that cancer cells seeded on stiffer substrates recruited more macrophages. Furthermore, elevated matrix stiffness increased Colony Stimulating Factor 1 (CSF-1) expression in breast cancer cells and reduction of CSF-1 expression on stiffer substrates reduced macrophage recruitment. Thus, our results demonstrate that tissue phenotypes were conserved between stiff and compliant tumors but matrix stiffening altered cell-cell interactions which may be responsible for shifting the phenotypic balance of macrophages residing in the tumor microenvironment towards a pro-tumor progression M2 phenotype. STATEMENT OF SIGNIFICANCE: Cells within tumors are highly heterogeneous, posing challenges with treatment and recurrence. While increased tissue stiffness can promote several hallmarks of cancer, its effects on tumor heterogeneity are unclear. We used single-cell RNA sequencing to investigate the differences in the transcriptional landscapes between stiff and compliant MMTV-PyMT mouse mammary tumors. We found similar compositions of cancer and stromal subpopulations in compliant and stiff tumors but differential intercellular communication and a significantly higher concentration of tumor-promoting, M2-like macrophages in the stiffer tumor microenvironments. Using a biomaterial-based platform, we found that cancer cells seeded on stiffer substrates recruited more macrophages, supporting our in vivo findings. Together, our results demonstrate a key role of matrix stiffness in affecting cell-cell communication and macrophage recruitment.
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Affiliation(s)
- Paul V Taufalele
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Wenjun Wang
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Alan J Simmons
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Austin N Southard-Smith
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bob Chen
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA; Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Joshua D Greenlee
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Michael R King
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Ken S Lau
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA; Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Duane C Hassane
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - François Bordeleau
- Cancer Research Center and Centre de Recherche du CHU de Québec, Université Laval, Canada
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Nadjsombati MS, Niepoth N, Webeck LM, Kennedy EA, Jones DL, Billipp TE, Baldridge MT, Bendesky A, von Moltke J. Genetic mapping reveals Pou2af2/OCA-T1-dependent tuning of tuft cell differentiation and intestinal type 2 immunity. Sci Immunol 2023; 8:eade5019. [PMID: 37172102 PMCID: PMC10308849 DOI: 10.1126/sciimmunol.ade5019] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 04/18/2023] [Indexed: 05/14/2023]
Abstract
Chemosensory epithelial tuft cells contribute to innate immunity at barrier surfaces, but their differentiation from epithelial progenitors is not well understood. Here, we exploited differences between inbred mouse strains to identify an epithelium-intrinsic mechanism that regulates tuft cell differentiation and tunes innate type 2 immunity in the small intestine. Balb/cJ (Balb) mice had fewer intestinal tuft cells than C57BL/6J (B6) mice and failed to respond to the tuft cell ligand succinate. Most of this differential succinate response was determined by the 50- to 67-Mb interval of chromosome 9 (Chr9), such that congenic Balb mice carrying the B6 Chr9 interval had elevated baseline numbers of tuft cells and responded to succinate. The Chr9 locus includes Pou2af2, which encodes the protein OCA-T1, a transcriptional cofactor essential for tuft cell development. Epithelial crypts expressed a previously unannotated short isoform of Pou2af2 predicted to use a distinct transcriptional start site and encode a nonfunctional protein. Low tuft cell numbers and the resulting lack of succinate response in Balb mice were explained by a preferential expression of the short isoform and could be rescued by expression of full-length Pou2af2. Physiologically, Pou2af2 isoform usage tuned innate type 2 immunity in the small intestine. Balb mice maintained responsiveness to helminth pathogens while ignoring commensal Tritrichomonas protists and reducing norovirus burdens.
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Affiliation(s)
- Marija S Nadjsombati
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
| | - Natalie Niepoth
- Zuckerman Mind Brain Behavior Institute, Columbia University, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, NY, USA
| | - Lily M Webeck
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
| | - Elizabeth A Kennedy
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Danielle L Jones
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
| | - Tyler E Billipp
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
| | - Megan T Baldridge
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Andres Bendesky
- Zuckerman Mind Brain Behavior Institute, Columbia University, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, NY, USA
| | - Jakob von Moltke
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
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27
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Li H, Zhang Z, Squires M, Chen X, Zhang X. scMultiSim: simulation of multi-modality single cell data guided by cell-cell interactions and gene regulatory networks. RESEARCH SQUARE 2023:rs.3.rs-2675530. [PMID: 36993284 PMCID: PMC10055660 DOI: 10.21203/rs.3.rs-2675530/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Simulated single-cell data is essential for designing and evaluating computational methods in the absence of experimental ground truth. Existing simulators typically focus on modeling one or two specific biological factors or mechanisms that affect the output data, which limits their capacity to simulate the complexity and multi-modality in real data. Here, we present scMultiSim, an in silico simulator that generates multi-modal single-cell data, including gene expression, chromatin accessibility, RNA velocity, and spatial cell locations while accounting for the relationships between modalities. scMultiSim jointly models various biological factors that affect the output data, including cell identity, within-cell gene regulatory networks (GRNs), cell-cell interactions (CCIs), and chromatin accessibility, while also incorporating technical noises. Moreover, it allows users to adjust each factor's effect easily. We validated scMultiSim's simulated biological effects and demonstrated its applications by benchmarking a wide range of computational tasks, including cell clustering and trajectory inference, multi-modal and multi-batch data integration, RNA velocity estimation, GRN inference and CCI inference using spatially resolved gene expression data. Compared to existing simulators, scMultiSim can benchmark a much broader range of existing computational problems and even new potential tasks.
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Affiliation(s)
- Hechen Li
- Georgia Institute of Technology, Atlanta, USA
| | - Ziqi Zhang
- Georgia Institute of Technology, Atlanta, USA
| | | | - Xi Chen
- Southern University of Science and Technology, China
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28
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Kotas ME, O'Leary CE, Locksley RM. Tuft Cells: Context- and Tissue-Specific Programming for a Conserved Cell Lineage. ANNUAL REVIEW OF PATHOLOGY 2023; 18:311-335. [PMID: 36351364 PMCID: PMC10443898 DOI: 10.1146/annurev-pathol-042320-112212] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Tuft cells are found in tissues with distinct stem cell compartments, tissue architecture, and luminal exposures but converge on a shared transcriptional program, including expression of taste transduction signaling pathways. Here, we summarize seminal and recent findings on tuft cells, focusing on major categories of function-instigation of type 2 cytokine responses, orchestration of antimicrobial responses, and emerging roles in tissue repair-and describe tuft cell-derived molecules used to affect these functional programs. We review what is known about the development of tuft cells from epithelial progenitors under homeostatic conditions and during disease. Finally, we discuss evidence that immature, or nascent, tuft cells with potential for diverse functions are driven toward dominant effector programs by tissue- or perturbation-specific contextual cues, which may result in heterogeneous mature tuft cell phenotypes both within and between tissues.
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Affiliation(s)
- Maya E Kotas
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, California, USA
- Department of Medicine, University of California, San Francisco, California, USA
| | - Claire E O'Leary
- Department of Medicine, University of California, San Francisco, California, USA
- Current affiliation: Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Richard M Locksley
- Department of Medicine, University of California, San Francisco, California, USA
- Department of Microbiology and Immunology, University of California, San Francisco, California, USA;
- Howard Hughes Medical Institute, University of California, San Francisco, California, USA
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29
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Du Y, Gao H, He C, Xin S, Wang B, Zhang S, Gong F, Yu X, Pan L, Sun F, Wang W, Xu J. An update on the biological characteristics and functions of tuft cells in the gut. Front Cell Dev Biol 2023; 10:1102978. [PMID: 36704202 PMCID: PMC9872863 DOI: 10.3389/fcell.2022.1102978] [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: 11/23/2022] [Accepted: 12/27/2022] [Indexed: 01/11/2023] Open
Abstract
The intestine is a powerful digestive system and one of the most sophisticated immunological organs. Evidence shows that tuft cells (TCs), a kind of epithelial cell with distinct morphological characteristics, play a significant role in various physiological processes. TCs can be broadly categorized into different subtypes depending on different molecular criteria. In this review, we discuss its biological properties and role in maintaining homeostasis in the gastrointestinal tract. We also emphasize its relevance to the immune system and highlight its powerful influence on intestinal diseases, including inflammations and tumors. In addition, we provide fresh insights into future clinical diagnostic and therapeutic strategies related to TCs.
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Affiliation(s)
- Yixuan Du
- Department of Oral Medicine, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Han Gao
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Chengwei He
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Shuzi Xin
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Boya Wang
- Undergraduate Student of 2018 Eight Program of Clinical Medicine, Peking University People’s Hospital, Beijing, China
| | - Sitian Zhang
- Department of Clinical Medicine, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Fengrong Gong
- Department of Clinical Medicine, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Xinyi Yu
- Department of Clinical Medicine, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Luming Pan
- Department of Clinical Medicine, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Fanglin Sun
- Department of Laboratory Animal Research, Xuan Wu Hospital, Capital Medical University, Beijing, China
| | - Wen Wang
- Department of Laboratory Animal Research, Xuan Wu Hospital, Capital Medical University, Beijing, China
| | - Jingdong Xu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China,*Correspondence: Jingdong Xu,
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30
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Babcock B, Malawsky D. scRNA-seq for Microcephaly Research [III]: Computational Analysis of scRNA-seq Data. Methods Mol Biol 2023; 2583:105-121. [PMID: 36418729 DOI: 10.1007/978-1-0716-2752-5_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Single-cell transcriptomic analysis (scRNA-seq) can enable researchers to explore the gene expression patterns of thousands of individual cells simultaneously. Processing the complex data generated by scRNA-seq requires specialized computational tools. This chapter focuses on the analytical aspect of scRNA-seq workflow, with a focus on resolving biological signals from large-scale scRNA-seq data produced by the Drop-Seq platform.
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Affiliation(s)
- Benjamin Babcock
- Department of Medicine, Division of Immunology, Lowance Center for Human Immunology, Emory University School of Medicine, Atlanta, GA, USA.
- Department of Neurology, University of North Carolina Medical School, Chapel Hill, NC, USA.
| | - Daniel Malawsky
- Department of Neurology, University of North Carolina Medical School, Chapel Hill, NC, USA
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
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31
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Li L, Ma M, Duan T, Sui X. The critical roles and therapeutic implications of tuft cells in cancer. Front Pharmacol 2022; 13:1047188. [PMID: 36569325 PMCID: PMC9780677 DOI: 10.3389/fphar.2022.1047188] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022] Open
Abstract
Tuft cells are solitary chemosensory epithelial cells with microvilli at the top, which are found in hollow organs such as the gastrointestinal tract, pancreas, and lungs. Recently, an increasing number of studies have revealed the chemotactic abilities and immune function of the tuft cells, and numerous efforts have been devoted to uncovering the role of tuft cells in tumors. Notably, accumulating evidence has shown that the specific genes (POU2F3, DCLK1) expressed in tuft cells are involved in vital processes related with carcinogenesis and cancer development. However, the interaction between the tuft cells and cancer remains to be further elucidated. Here, based on an introduction of biological functions and specific markers of the tuft cells, we have summarized the functional roles and potential therapeutic implications of tuft cells in cancers, including pancreatic cancer, lung cancer, gastric cancer, colon cancer, and liver cancer, which is in the hope of inspiring the future research in validating tuft cells as novel strategies for cancer therapies.
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Affiliation(s)
- Lin Li
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China
| | - Mengmeng Ma
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China
| | - Ting Duan
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China
| | - Xinbing Sui
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China
- Department of Medical Oncology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou, China
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32
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Gustafsson JK, Johansson MEV. The role of goblet cells and mucus in intestinal homeostasis. Nat Rev Gastroenterol Hepatol 2022; 19:785-803. [PMID: 36097076 DOI: 10.1038/s41575-022-00675-x] [Citation(s) in RCA: 153] [Impact Index Per Article: 76.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/04/2022] [Indexed: 12/08/2022]
Abstract
The intestinal tract faces numerous challenges that require several layers of defence. The tight epithelium forms a physical barrier that is further protected by a mucus layer, which provides various site-specific protective functions. Mucus is produced by goblet cells, and as a result of single-cell RNA sequencing identifying novel goblet cell subpopulations, our understanding of their various contributions to intestinal homeostasis has improved. Goblet cells not only produce mucus but also are intimately linked to the immune system. Mucus and goblet cell development is tightly regulated during early life and synchronized with microbial colonization. Dysregulation of the developing mucus systems and goblet cells has been associated with infectious and inflammatory conditions and predisposition to chronic disease later in life. Dysfunctional mucus and altered goblet cell profiles are associated with inflammatory conditions in which some mucus system impairments precede inflammation, indicating a role in pathogenesis. In this Review, we present an overview of the current understanding of the role of goblet cells and the mucus layer in maintaining intestinal health during steady-state and how alterations to these systems contribute to inflammatory and infectious disease.
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Affiliation(s)
- Jenny K Gustafsson
- Department of Physiology, Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden
| | - Malin E V Johansson
- Department of Medical Biochemisty and Cell biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.
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33
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Ishikawa K, Sugimoto S, Oda M, Fujii M, Takahashi S, Ohta Y, Takano A, Ishimaru K, Matano M, Yoshida K, Hanyu H, Toshimitsu K, Sawada K, Shimokawa M, Saito M, Kawasaki K, Ishii R, Taniguchi K, Imamura T, Kanai T, Sato T. Identification of Quiescent LGR5 + Stem Cells in the Human Colon. Gastroenterology 2022; 163:1391-1406.e24. [PMID: 35963362 DOI: 10.1053/j.gastro.2022.07.081] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 07/16/2022] [Accepted: 07/19/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS In the mouse intestinal epithelium, Lgr5+ stem cells are vulnerable to injury, owing to their predominantly cycling nature, and their progenies de-differentiate to replenish the stem cell pool. However, how human colonic stem cells behave in homeostasis and during regeneration remains unknown. METHODS Transcriptional heterogeneity among colonic epithelial cells was analyzed by means of single-cell RNA sequencing analysis of human and mouse colonic epithelial cells. To trace the fate of human colonic stem or differentiated cells, we generated LGR5-tdTomato, LGR5-iCasase9-tdTomato, LGR5-split-Cre, and KRT20-ERCreER knock-in human colon organoids via genome engineering. p27+ dormant cells were further visualized with the p27-mVenus reporter. To analyze the dynamics of human colonic stem cells in vivo, we orthotopically xenotransplanted fluorescence-labeled human colon organoids into immune-deficient mice. The cell cycle dynamics in xenograft cells were evaluated using 5-ethynyl-2'-deoxyuridine pulse-chase analysis. The clonogenic capacity of slow-cycling human stem cells or differentiated cells was analyzed in the context of homeostasis, LGR5 ablation, and 5-fluorouracil-induced mucosal injury. RESULTS Single-cell RNA sequencing analysis illuminated the presence of nondividing LGR5+ stem cells in the human colon. Visualization and lineage tracing of slow-cycling LGR5+p27+ cells and orthotopic xenotransplantation validated their homeostatic lineage-forming capability in vivo, which was augmented by 5-FU-induced mucosal damage. Transforming growth factor-β signaling regulated the quiescent state of LGR5+ cells. Despite the plasticity of differentiated KRT20+ cells, they did not display clonal growth after 5-FU-induced injury, suggesting that occupation of the niche environment by LGR5+p27+ cells prevented neighboring differentiated cells from de-differentiating. CONCLUSIONS Our results highlight the quiescent nature of human LGR5+ colonic stem cells and their contribution to post-injury regeneration.
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Affiliation(s)
- Keiko Ishikawa
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan; Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan
| | - Shinya Sugimoto
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan; Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan
| | - Mayumi Oda
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Masayuki Fujii
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Sirirat Takahashi
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Yuki Ohta
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Ai Takano
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Kazuhiro Ishimaru
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Mami Matano
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Kosuke Yoshida
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan; Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan
| | - Hikaru Hanyu
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Kohta Toshimitsu
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Kazuaki Sawada
- Center for Integrated Medical Research, School of Medicine, Keio University, Tokyo, Japan
| | - Mariko Shimokawa
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Megumu Saito
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan; Fujii Memorial Research Institute, Otsuka Pharmaceutical Company, Limited, Shiga, Japan
| | - Kenta Kawasaki
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan; Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan
| | - Ryota Ishii
- Department of Biostatistics, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Koji Taniguchi
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan; Department of Pathology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Takeshi Imamura
- Department of Molecular Medicine for Pathogenesis, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Takanori Kanai
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan
| | - Toshiro Sato
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan.
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34
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Actomyosin contractility as a mechanical checkpoint for cell state transitions. Sci Rep 2022; 12:16063. [PMID: 36163393 PMCID: PMC9512847 DOI: 10.1038/s41598-022-20089-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 09/08/2022] [Indexed: 11/08/2022] Open
Abstract
Cell state transitions induced by mechano-chemical cues result in a heterogeneous population of cell states. While much of the work towards understanding the origins of such heterogeneity has focused on the gene regulatory mechanisms, the contribution of intrinsic mechanical properties of cells remains unknown. In this paper, using a well-defined single cell platform to induce cell-state transitions, we reveal the importance of actomyosin contractile forces in regulating the heterogeneous cell-fate decisions. Temporal analysis of laterally confined growth of fibroblasts revealed sequential changes in the colony morphology which was tightly coupled to the progressive erasure of lineage-specific transcription programs. Pseudo-trajectory constructed using unsupervised diffusion analysis of the colony morphology features revealed a bifurcation event in which some cells undergo successful cell state transitions towards partial reprogramming. Importantly, inhibiting actomyosin contractility before the bifurcation event leads to more efficient dedifferentiation. Taken together, this study highlights the presence of mechanical checkpoints that contribute to the heterogeneity in cell state transitions.
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35
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Li Z, Wang Y, Ganan-Gomez I, Colla S, Do KA. A machine learning-based method for automatically identifying novel cells in annotating single-cell RNA-seq data. Bioinformatics 2022; 38:4885-4892. [PMID: 36083008 PMCID: PMC9801963 DOI: 10.1093/bioinformatics/btac617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 01/07/2023] Open
Abstract
MOTIVATION Single-cell RNA sequencing (scRNA-seq) has been widely used to decompose complex tissues into functionally distinct cell types. The first and usually the most important step of scRNA-seq data analysis is to accurately annotate the cell labels. In recent years, many supervised annotation methods have been developed and shown to be more convenient and accurate than unsupervised cell clustering. One challenge faced by all the supervised annotation methods is the identification of the novel cell type, which is defined as the cell type that is not present in the training data, only exists in the testing data. Existing methods usually label the cells simply based on the correlation coefficients or confidence scores, which sometimes results in an excessive number of unlabeled cells. RESULTS We developed a straightforward yet effective method combining autoencoder with iterative feature selection to automatically identify novel cells from scRNA-seq data. Our method trains an autoencoder with the labeled training data and applies the autoencoder to the testing data to obtain reconstruction errors. By iteratively selecting features that demonstrate a bi-modal pattern and reclustering the cells using the selected feature, our method can accurately identify novel cells that are not present in the training data. We further combined this approach with a support vector machine to provide a complete solution for annotating the full range of cell types. Extensive numerical experiments using five real scRNA-seq datasets demonstrated favorable performance of the proposed method over existing methods serving similar purposes. AVAILABILITY AND IMPLEMENTATION Our R software package CAMLU is publicly available through the Zenodo repository (https://doi.org/10.5281/zenodo.7054422) or GitHub repository (https://github.com/ziyili20/CAMLU). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ziyi Li
- To whom correspondence should be addressed. or
| | - Yizhuo Wang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Irene Ganan-Gomez
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Simona Colla
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Kim-Anh Do
- To whom correspondence should be addressed. or
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36
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Long T, Abbasi N, Hernandez JE, Li Y, Sayed IM, Ma S, Iemolo A, Yee BA, Yeo GW, Telese F, Ghosh P, Das S, Huang WJM. RNA binding protein DDX5 directs tuft cell specification and function to regulate microbial repertoire and disease susceptibility in the intestine. Gut 2022; 71:1790-1802. [PMID: 34853057 PMCID: PMC9156727 DOI: 10.1136/gutjnl-2021-324984] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 11/12/2021] [Indexed: 12/30/2022]
Abstract
OBJECTIVE Tuft cells residing in the intestinal epithelium have diverse functions. In the small intestine, they provide protection against inflammation, combat against helminth and protist infections, and serve as entry portals for enteroviruses. In the colon, they had been implicated in tumourigenesis. Commitment of intestinal progenitor cells to the tuft cell lineage requires Rho GTPase Cell Division Cycle 42 (CDC42), a Rho GTPase that acts downstream of the epidermal growth factor receptor and wingless-related integration site signalling cascades, and the master transcription factor POU class 2 homeobox 3 (POU2F3). This study investigates how this pathway is regulated by the DEAD box containing RNA binding protein DDX5 in vivo. DESIGN We assessed the role of DDX5 in tuft cell specification and function in control and epithelial cell-specific Ddx5 knockout mice (DDX5ΔIEC) using transcriptomic approaches. RESULTS DDX5ΔIEC mice harboured a loss of intestinal tuft cell populations, modified microbial repertoire, and altered susceptibilities to ileal inflammation and colonic tumourigenesis. Mechanistically, DDX5 promotes CDC42 protein synthesis through a post-transcriptional mechanism to license tuft cell specification. Importantly, the DDX5-CDC42 axis is parallel but distinct from the known interleukin-13 circuit implicated in tuft cell hyperplasia, and both pathways augment Pou2f3 expression in secretory lineage progenitors. In mature tuft cells, DDX5 not only promotes integrin signalling and microbial responses, it also represses gene programmes involved in membrane transport and lipid metabolism. CONCLUSION RNA binding protein DDX5 directs tuft cell specification and function to regulate microbial repertoire and disease susceptibility in the intestine.
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Affiliation(s)
- Tianyun Long
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Nazia Abbasi
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Juan E Hernandez
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Yuxin Li
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Ibrahim M Sayed
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Shengyun Ma
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Attilio Iemolo
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Brian A Yee
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Francesca Telese
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Pradipta Ghosh
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Soumita Das
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Wendy Jia Men Huang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
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37
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Gut Epithelial Inositol Polyphosphate Multikinase Alleviates Experimental Colitis via Governing Tuft Cell Homeostasis. Cell Mol Gastroenterol Hepatol 2022; 14:1235-1256. [PMID: 35988719 PMCID: PMC9579329 DOI: 10.1016/j.jcmgh.2022.08.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/11/2022] [Accepted: 08/11/2022] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS Inositol polyphosphate multikinase (IPMK), an essential enzyme for inositol phosphate metabolism, has been known to mediate major biological events such as growth. Recent studies have identified single-nucleotide polymorphisms in the IPMK gene associated with inflammatory bowel disease predisposition. Therefore, we aimed to investigate the functional significance of IPMK in gut epithelium. METHODS We generated intestinal epithelial cell (IEC)-specific Ipmk knockout (IPMKΔIEC) mice, and assessed their vulnerability against dextran sulfate sodium-induced experimental colitis. Both bulk and single-cell RNA sequencing were performed to analyze IPMK-deficient colonic epithelial cells and colonic tuft cells. RESULTS Although IPMKΔIEC mice developed normally and showed no intestinal abnormalities during homeostasis, Ipmk deletion aggravated dextran sulfate sodium-induced colitis, with higher clinical colitis scores, and increased epithelial barrier permeability. Surprisingly, Ipmk deletion led to a significant decrease in the number of tuft cells without influencing other IECs. Single-cell RNA sequencing of mouse colonic tuft cells showed 3 distinct populations of tuft cells, and further showed that a transcriptionally inactive population was expanded markedly in IPMKΔIEC mice, while neuronal-related cells were relatively decreased. CONCLUSIONS Cholinergic output from tuft cells is known to be critical for the restoration of intestinal architecture upon damage, supporting that tuft cell-defective IPMKΔIEC mice are more prone to colitis. Thus, intestinal epithelial IPMK is a critical regulator of colonic integrity and tissue regeneration by determining tuft cell homeostasis and affecting cholinergic output.
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38
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Macnair W, Gupta R, Claassen M. psupertime: supervised pseudotime analysis for time-series single-cell RNA-seq data. Bioinformatics 2022; 38:i290-i298. [PMID: 35758781 PMCID: PMC9235474 DOI: 10.1093/bioinformatics/btac227] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Motivation Improvements in single-cell RNA-seq technologies mean that studies measuring multiple experimental conditions, such as time series, have become more common. At present, few computational methods exist to infer time series-specific transcriptome changes, and such studies have therefore typically used unsupervised pseudotime methods. While these methods identify cell subpopulations and the transitions between them, they are not appropriate for identifying the genes that vary coherently along the time series. In addition, the orderings they estimate are based only on the major sources of variation in the data, which may not correspond to the processes related to the time labels. Results We introduce psupertime, a supervised pseudotime approach based on a regression model, which explicitly uses time-series labels as input. It identifies genes that vary coherently along a time series, in addition to pseudotime values for individual cells, and a classifier that can be used to estimate labels for new data with unknown or differing labels. We show that psupertime outperforms benchmark classifiers in terms of identifying time-varying genes and provides better individual cell orderings than popular unsupervised pseudotime techniques. psupertime is applicable to any single-cell RNA-seq dataset with sequential labels (e.g. principally time series but also drug dosage and disease progression), derived from either experimental design and provides a fast, interpretable tool for targeted identification of genes varying along with specific biological processes. Availability and implementation R package available at github.com/wmacnair/psupertime and code for results reproduction at github.com/wmacnair/psupplementary. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Will Macnair
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Revant Gupta
- Inner Medicine I, Faculty of Medicine, University of Tübingen, University Hospital Tübingen, 72074, Germany
| | - Manfred Claassen
- Inner Medicine I, Faculty of Medicine, University of Tübingen, University Hospital Tübingen, 72074, Germany.,Department of Computer Science, University of Tübingen, Tübingen 72074, Germany
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39
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Uniken Venema WTC, Ramírez-Sánchez AD, Bigaeva E, Withoff S, Jonkers I, McIntyre RE, Ghouraba M, Raine T, Weersma RK, Franke L, Festen EAM, van der Wijst MGP. Gut mucosa dissociation protocols influence cell type proportions and single-cell gene expression levels. Sci Rep 2022; 12:9897. [PMID: 35701452 PMCID: PMC9197976 DOI: 10.1038/s41598-022-13812-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 05/27/2022] [Indexed: 01/15/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of the cellular landscape of organs. Most single-cell protocols require fresh material, which limits sample size per experiment, and consequently, introduces batch effects. This is especially true for samples acquired through complex medical procedures, such as intestinal mucosal biopsies. Moreover, the tissue dissociation procedure required for obtaining single cells is a major source of noise; different dissociation procedures applied to different compartments of the tissue induce artificial gene expression differences between cell subsets. To overcome these challenges, we have developed a one-step dissociation protocol and demonstrated its use on cryopreserved gut mucosal biopsies. Using flow cytometry and scRNA-seq analysis, we compared this one-step dissociation protocol with the current gold standard, two-step collagenase digestion, and an adaptation of a recently published alternative, three-step cold-active Bacillus licheniformus protease digestion. Both cell viability and cell type composition were comparable between the one-step and two-step collagenase dissociation, with the former being more time-efficient. The cold protease digestion resulted in equal cell viability, but better preserves the epithelial cell types. Consequently, to analyze the rarer cell types, such as glial cells, larger total biopsy cell numbers are required as input material. The multi-step protocols affected cell types spanning multiple compartments differently. In summary, we show that cryopreserved gut mucosal biopsies can be used to overcome the logistical challenges and batch effects in large scRNA-seq studies. Furthermore, we demonstrate that using cryopreserved biopsies digested using a one-step collagenase protocol enables large-scale scRNA-seq, FACS, organoid generation and intraepithelial lymphocyte expansion.
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Affiliation(s)
- Werna T C Uniken Venema
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Aarón D Ramírez-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Emilia Bigaeva
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Sebo Withoff
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Iris Jonkers
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | | | | - Tim Raine
- Department of Gastroenterology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Eleonora A M Festen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - Monique G P van der Wijst
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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40
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New insights into tuft cell formation: Implications for structure–function relationships. Curr Opin Cell Biol 2022; 76:102082. [DOI: 10.1016/j.ceb.2022.102082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/18/2022] [Accepted: 03/24/2022] [Indexed: 11/18/2022]
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41
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Chen L, Yang Y, Sun S, Xie Y, Pan C, Li M, Li C, Liu Y, Xu Z, Liu W, Ji M. Indolepropionic acid reduces obesity‐induced metabolic dysfunction through colonic barrier restoration mediated via tuft cell‐derived IL‐25. FEBS J 2022; 289:5985-6004. [DOI: 10.1111/febs.16470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 04/06/2022] [Accepted: 05/03/2022] [Indexed: 12/19/2022]
Affiliation(s)
- Lu Chen
- Department of Pathogen Biology Nanjing Medical University China
- Jiangsu Province Engineering Research Center of Antibody Drug Nanjing China
| | - Yuxuan Yang
- Department of Pathogen Biology Nanjing Medical University China
| | - Siyu Sun
- Department of Pathogen Biology Nanjing Medical University China
| | - Yuan Xie
- Department of Endocrinology Sir Run Run Hospital Nanjing Medical University China
| | - Cailong Pan
- Department of Pathology School of Basic Medicine Nanjing Medical University China
| | - Maining Li
- Department of Pathogen Biology Nanjing Medical University China
| | - Chen Li
- Department of Pathogen Biology Nanjing Medical University China
| | - Yu Liu
- Department of Endocrinology Sir Run Run Hospital Nanjing Medical University China
| | - Zhipeng Xu
- Department of Pathogen Biology Nanjing Medical University China
| | - Wentao Liu
- Department of Pharmacology School of Basic Medicine Nanjing Medical University China
| | - Minjun Ji
- Department of Pathogen Biology Nanjing Medical University China
- Jiangsu Province Engineering Research Center of Antibody Drug Nanjing China
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42
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Vega PN, Nilsson A, Kumar MP, Niitsu H, Simmons AJ, Ro J, Wang J, Chen Z, Joughin BA, Li W, McKinley ET, Liu Q, Roland JT, Washington MK, Coffey RJ, Lauffenburger DA, Lau KS. Cancer-Associated Fibroblasts and Squamous Epithelial Cells Constitute a Unique Microenvironment in a Mouse Model of Inflammation-Induced Colon Cancer. Front Oncol 2022; 12:878920. [PMID: 35600339 PMCID: PMC9114773 DOI: 10.3389/fonc.2022.878920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
The tumor microenvironment plays a key role in the pathogenesis of colorectal tumors and contains various cell types including epithelial, immune, and mesenchymal cells. Characterization of the interactions between these cell types is necessary for revealing the complex nature of tumors. In this study, we used single-cell RNA-seq (scRNA-seq) to compare the tumor microenvironments between a mouse model of sporadic colorectal adenoma (Lrig1CreERT2/+;Apc2lox14/+) and a mouse model of inflammation-driven colorectal cancer induced by azoxymethane and dextran sodium sulfate (AOM/DSS). While both models develop tumors in the distal colon, we found that the two tumor types have distinct microenvironments. AOM/DSS tumors have an increased abundance of two populations of cancer-associated fibroblasts (CAFs) compared with APC tumors, and we revealed their divergent spatial association with tumor cells using multiplex immunofluorescence (MxIF) imaging. We also identified a unique squamous cell population in AOM/DSS tumors, whose origins were distinct from anal squamous epithelial cells. These cells were in higher proportions upon administration of a chemotherapy regimen of 5-Fluorouracil/Irinotecan. We used computational inference algorithms to predict cell-cell communication mediated by ligand-receptor interactions and downstream pathway activation, and identified potential mechanistic connections between CAFs and tumor cells, as well as CAFs and squamous epithelial cells. This study provides important preclinical insight into the microenvironment of two distinct models of colorectal tumors and reveals unique roles for CAFs and squamous epithelial cells in the AOM/DSS model of inflammation-driven cancer.
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Affiliation(s)
- Paige N Vega
- Department of Cell and Developmental Biology and Program in Developmental Biology, Vanderbilt University, Nashville, TN, United States.,Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Avlant Nilsson
- Department of Biological Engineering and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States.,Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Manu P Kumar
- Department of Biological Engineering and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Hiroaki Niitsu
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, United States.,Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Alan J Simmons
- Department of Cell and Developmental Biology and Program in Developmental Biology, Vanderbilt University, Nashville, TN, United States.,Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, United States
| | - James Ro
- Department of Cell and Developmental Biology and Program in Developmental Biology, Vanderbilt University, Nashville, TN, United States.,Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Jiawei Wang
- Department of Cell and Developmental Biology and Program in Developmental Biology, Vanderbilt University, Nashville, TN, United States.,Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Zhengyi Chen
- Department of Cell and Developmental Biology and Program in Developmental Biology, Vanderbilt University, Nashville, TN, United States.,Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Brian A Joughin
- Department of Biological Engineering and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Wei Li
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, United States.,Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Eliot T McKinley
- Department of Cell and Developmental Biology and Program in Developmental Biology, Vanderbilt University, Nashville, TN, United States.,Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Qi Liu
- Department of Biostatistics and Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Joseph T Roland
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, United States.,Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, United States
| | - M Kay Washington
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Robert J Coffey
- Department of Cell and Developmental Biology and Program in Developmental Biology, Vanderbilt University, Nashville, TN, United States.,Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, United States.,Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Douglas A Lauffenburger
- Department of Biological Engineering and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Ken S Lau
- Department of Cell and Developmental Biology and Program in Developmental Biology, Vanderbilt University, Nashville, TN, United States.,Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, United States.,Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, United States
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43
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Lindholm HT, Parmar N, Drurey C, Poveda MC, Vornewald P, Ostrop J, Díez-Sanchez A, Maizels RM, Oudhoff MJ. BMP signaling in the intestinal epithelium drives a critical feedback loop to restrain IL-13-driven tuft cell hyperplasia. Sci Immunol 2022; 7:eabl6543. [PMID: 35559665 PMCID: PMC7614132 DOI: 10.1126/sciimmunol.abl6543] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The intestinal tract is a common site for various types of infections including viruses, bacteria, and helminths, each requiring specific modes of immune defense. The intestinal epithelium has a pivotal role in both immune initiation and effector stages, which are coordinated by lymphocyte cytokines such as IFNγ, IL-13, and IL-22. Here, we studied intestinal epithelial immune responses using organoid image analysis based on a convolutional neural network, transcriptomic analysis, and in vivo infection models. We found that IL-13 and IL-22 both induce genes associated with goblet cells, but the resulting goblet cell phenotypes are dichotomous. Moreover, only IL-13-driven goblet cells are associated with classical NOTCH signaling. We further showed that IL-13 induces the bone morphogenetic protein (BMP) pathway, which acts in a negative feedback loop on immune type 2-driven tuft cell hyperplasia. This is associated with inhibiting Sox4 expression to putatively limit the tuft cell progenitor population. Blocking ALK2, a BMP receptor, with the inhibitor dorsomorphin homolog 1 (DMH1) interrupted the feedback loop, resulting in greater tuft cell numbers both in vitro and in vivo after infection with Nippostrongylus brasiliensis. Together, this investigation of cytokine effector responses revealed an unexpected and critical role for the BMP pathway in regulating type 2 immunity, which can be exploited to tailor epithelial immune responses.
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Affiliation(s)
- Håvard T. Lindholm
- CEMIR - Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, NTNU - Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Naveen Parmar
- CEMIR - Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, NTNU - Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Claire Drurey
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunology and Inflammation, University of Glasgow, G12 8TA Glasgow, United Kingdom
| | - Marta Campillo Poveda
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunology and Inflammation, University of Glasgow, G12 8TA Glasgow, United Kingdom
| | - Pia Vornewald
- CEMIR - Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, NTNU - Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Jenny Ostrop
- CEMIR - Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, NTNU - Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Alberto Díez-Sanchez
- CEMIR - Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, NTNU - Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Rick M. Maizels
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunology and Inflammation, University of Glasgow, G12 8TA Glasgow, United Kingdom
| | - Menno J. Oudhoff
- CEMIR - Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, NTNU - Norwegian University of Science and Technology, 7491 Trondheim, Norway
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44
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Brown RE, Jacobse J, Anant SA, Blunt KM, Chen B, Vega PN, Jones CT, Pilat JM, Revetta F, Gorby AH, Stengel KR, Choksi YA, Palin K, Piazuelo MB, Washington MK, Lau KS, Goettel JA, Hiebert SW, Short SP, Williams CS. MTG16 (CBFA2T3) regulates colonic epithelial differentiation, colitis, and tumorigenesis by repressing E protein transcription factors. JCI Insight 2022; 7:153045. [PMID: 35503250 PMCID: PMC9220854 DOI: 10.1172/jci.insight.153045] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/13/2022] [Indexed: 12/04/2022] Open
Abstract
Aberrant epithelial differentiation and regeneration contribute to colon pathologies including inflammatory bowel disease (IBD) and colitis-associated cancer (CAC). MTG16 (CBFA2T3) is a transcriptional corepressor expressed in the colonic epithelium. MTG16 deficiency in mice exacerbates colitis and increases tumor burden in CAC, though the underlying mechanisms remain unclear. Here, we identified MTG16 as a central mediator of epithelial differentiation, promoting goblet and restraining enteroendocrine cell development in homeostasis and enabling regeneration following dextran sulfate sodium (DSS)-induced colitis. Transcriptomic analyses implicated increased E box-binding transcription factor (E protein) activity in MTG16-deficient colon crypts. Using a novel mouse model with a point mutation that attenuates MTG16:E protein interactions (Mtg16P209T), we established that MTG16 exerts control over colonic epithelial differentiation and regeneration by repressing E protein-mediated transcription. Mimicking murine colitis, MTG16 expression was increased in biopsies from patients with active IBD compared to unaffected controls. Finally, uncoupling MTG16:E protein interactions partially phenocopied the enhanced tumorigenicity of Mtg16-/- colon in the azoxymethane(AOM)/DSS-induced model of CAC, indicating that MTG16 protects from tumorigenesis through additional mechanisms. Collectively, our results demonstrate that MTG16, via its repression of E protein targets, is a key regulator of cell fate decisions during colon homeostasis, colitis, and cancer.
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Affiliation(s)
- Rachel E Brown
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Justin Jacobse
- Willem-Alexander Children's Hospital, Leiden University Medical Center, Leiden, Netherlands
| | - Shruti A Anant
- Department of Medicine, Health, and Society, Vanderbilt University, Nashville, United States of America
| | - Koral M Blunt
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America
| | - Bob Chen
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Paige N Vega
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Chase T Jones
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America
| | - Jennifer M Pilat
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Frank Revetta
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, United States of America
| | - Aidan H Gorby
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America
| | - Kristy R Stengel
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Yash A Choksi
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America
| | - Kimmo Palin
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - M Blanca Piazuelo
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America
| | - Mary K Washington
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, United States of America
| | - Ken S Lau
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Jeremy A Goettel
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America
| | - Scott W Hiebert
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Sarah P Short
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America
| | - Christopher S Williams
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America
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45
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Nauman M, Stanley P. Glycans that regulate Notch signaling in the intestine. Biochem Soc Trans 2022; 50:689-701. [PMID: 35311893 PMCID: PMC9370068 DOI: 10.1042/bst20200782] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/23/2022] [Accepted: 03/07/2022] [Indexed: 12/12/2022]
Abstract
Intestinal homeostasis is key to the maintenance of good health. The small intestine plays important roles in absorption, digestion, hormonal and immune functions. Crypt base columnar (CBC) stem cells residing at the bottom of crypts are nurtured by Paneth cells, and together create the stem cell niche, the foundation of intestinal homeostasis. CBC stem cells replicate to replenish their number, or differentiate into a variety of epithelial cells with specialized functions. Notch signaling is a cell-cell signaling pathway that regulates both the proliferation and differentiation of CBC stem cells. NOTCH1 and NOTCH2 stimulated by canonical Notch ligands DLL1 and DLL4 mediate Notch signaling in the intestine that, in concert with other signaling pathways including the WNT and BMP pathways, determines cell fates. Importantly, interactions between Notch receptors and canonical Notch ligands are regulated by O-glycans linked to Ser/Thr in epidermal growth factor-like (EGF) repeats of the Notch receptor extracellular domain (NECD). The O-glycans attached to NECD are key regulators of the strength of Notch signaling. Imbalances in Notch signaling result in altered cell fate decisions and may lead to cancer in the intestine. In this review, we summarize the impacts of mutations in Notch pathway members on intestinal development and homeostasis, with a focus on the glycosyltransferases that transfer O-glycans to EGF repeats of NOTCH1, NOTCH2, DLL1 and DLL4.
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Affiliation(s)
- Mohd Nauman
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY 10461, U.S.A
| | - Pamela Stanley
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY 10461, U.S.A
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Duque-Correa MA, Goulding D, Rodgers FH, Gillis JA, Cormie C, Rawlinson KA, Bancroft AJ, Bennett HM, Lotkowska ME, Reid AJ, Speak AO, Scott P, Redshaw N, Tolley C, McCarthy C, Brandt C, Sharpe C, Ridley C, Moya JG, Carneiro CM, Starborg T, Hayes KS, Holroyd N, Sanders M, Thornton DJ, Grencis RK, Berriman M. Defining the early stages of intestinal colonisation by whipworms. Nat Commun 2022; 13:1725. [PMID: 35365634 PMCID: PMC8976045 DOI: 10.1038/s41467-022-29334-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 03/08/2022] [Indexed: 01/08/2023] Open
Abstract
Whipworms are large metazoan parasites that inhabit multi-intracellular epithelial tunnels in the large intestine of their hosts, causing chronic disease in humans and other mammals. How first-stage larvae invade host epithelia and establish infection remains unclear. Here we investigate early infection events using both Trichuris muris infections of mice and murine caecaloids, the first in-vitro system for whipworm infection and organoid model for live helminths. We show that larvae degrade mucus layers to access epithelial cells. In early syncytial tunnels, larvae are completely intracellular, woven through multiple live dividing cells. Using single-cell RNA sequencing of infected mouse caecum, we reveal that progression of infection results in cell damage and an expansion of enterocytes expressing of Isg15, potentially instigating the host immune response to the whipworm and tissue repair. Our results unravel intestinal epithelium invasion by whipworms and reveal specific host-parasite interactions that allow the whipworm to establish its multi-intracellular niche. Whipworms are large parasites causing chronic disease in humans and other mammals. Here, the authors show how larvae create tunnels inside the gut lining and reveal the early host response to infection via Isg15 in mice and murine caecaloids.
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Affiliation(s)
- María A Duque-Correa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK. .,Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK.
| | - David Goulding
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Faye H Rodgers
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.,Mogrify Ltd, 25 Cambridge Science Park, Milton Road, Cambridge, CB4 0FW, UK
| | - J Andrew Gillis
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
| | - Claire Cormie
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.,Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Kate A Rawlinson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Allison J Bancroft
- Lydia Becker Institute of Immunology and Inflammation, Wellcome Trust Centre for Cell Matrix Research and Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Hayley M Bennett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.,Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Magda E Lotkowska
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Adam J Reid
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.,Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Anneliese O Speak
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Paul Scott
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Nicholas Redshaw
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Charlotte Tolley
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Catherine McCarthy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Cordelia Brandt
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Catherine Sharpe
- Lydia Becker Institute of Immunology and Inflammation, Wellcome Trust Centre for Cell Matrix Research and Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK.,InstilBio, UMIC Bio-Incubator, Manchester, M13 9XX, UK
| | - Caroline Ridley
- Lydia Becker Institute of Immunology and Inflammation, Wellcome Trust Centre for Cell Matrix Research and Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK.,Prime Global Medical Communications, Knutsford, WA16 8GP, UK
| | - Judit Gali Moya
- Faculty of Biology, University of Barcelona, Barcelona, 08028, Spain
| | - Claudia M Carneiro
- Immunopathology Laboratory, NUPEB, Federal University of Ouro Preto, Campus Universitario Morro do Cruzeiro, Ouro Preto, MG, 35400-000, Brazil
| | - Tobias Starborg
- Lydia Becker Institute of Immunology and Inflammation, Wellcome Trust Centre for Cell Matrix Research and Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK.,Rosalind Franklin Institute, Harwell Campus, Didcot, OX11 0FA, UK
| | - Kelly S Hayes
- Lydia Becker Institute of Immunology and Inflammation, Wellcome Trust Centre for Cell Matrix Research and Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Nancy Holroyd
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Mandy Sanders
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - David J Thornton
- Lydia Becker Institute of Immunology and Inflammation, Wellcome Trust Centre for Cell Matrix Research and Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Richard K Grencis
- Lydia Becker Institute of Immunology and Inflammation, Wellcome Trust Centre for Cell Matrix Research and Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Matthew Berriman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.
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47
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Karabacak NM, Zheng Y, Dubash TD, Burr R, Micalizzi DS, Wittner BS, Lin M, Wiley D, Comaills V, Emmons E, Niederhoffer K, Ho U, Ukleja J, Che D, Stowe H, Nieman L, Haas W, Stott SL, Lawrence MS, Ting DT, Miyamoto DT, Haber DA, Toner M, Maheswaran S. Differential Kinase Activity Across Prostate Tumor Compartments Defines Sensitivity to Target Inhibition. Cancer Res 2022; 82:1084-1097. [PMID: 35045985 PMCID: PMC8930560 DOI: 10.1158/0008-5472.can-21-2609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/03/2021] [Accepted: 01/12/2022] [Indexed: 11/16/2022]
Abstract
Cancer therapy often results in heterogeneous responses in different metastatic lesions in the same patient. Inter- and intratumor heterogeneity in signaling within various tumor compartments and its impact on therapy are not well characterized due to the limited sensitivity of single-cell proteomic approaches. To overcome this barrier, we applied single-cell mass cytometry with a customized 26-antibody panel to PTEN-deleted orthotopic prostate cancer xenograft models to measure the evolution of kinase activities in different tumor compartments during metastasis or drug treatment. Compared with primary tumors and circulating tumor cells (CTC), bone metastases, but not lung and liver metastases, exhibited elevated PI3K/mTOR signaling and overexpressed receptor tyrosine kinases (RTK) including c-MET protein. Suppression of c-MET impaired tumor growth in the bone. Intratumoral heterogeneity within tumor compartments also arose from highly proliferative EpCAM-high epithelial cells with increased PI3K and mTOR kinase activities coexisting with poorly proliferating EpCAM-low mesenchymal populations with reduced kinase activities; these findings were recapitulated in epithelial and mesenchymal CTC populations in patients with metastatic prostate and breast cancer. Increased kinase activity in EpCAM-high cells rendered them more sensitive to PI3K/mTOR inhibition, and drug-resistant EpCAM-low populations with reduced kinase activity emerged over time. Taken together, single-cell proteomics indicate that microenvironment- and cell state-dependent activation of kinase networks create heterogeneity and differential drug sensitivity among and within tumor populations across different sites, defining a new paradigm of drug responses to kinase inhibitors. SIGNIFICANCE Single-cell mass cytometry analyses provide insights into the differences in kinase activities across tumor compartments and cell states, which contribute to heterogeneous responses to targeted therapies.
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Affiliation(s)
- Nezihi Murat Karabacak
- Center for Engineering in Medicine and Surgery, Massachusetts General Hospital, Harvard Medical School
- Shriners Hospital for Children, Boston, MA 02114
| | - Yu Zheng
- Massachusetts General Hospital Center for Cancer Research, Harvard Medical School, Charlestown, MA 02129
| | - Taronish D. Dubash
- Massachusetts General Hospital Center for Cancer Research, Harvard Medical School, Charlestown, MA 02129
| | - Risa Burr
- Massachusetts General Hospital Center for Cancer Research, Harvard Medical School, Charlestown, MA 02129
| | - Douglas S. Micalizzi
- Massachusetts General Hospital Center for Cancer Research, Harvard Medical School, Charlestown, MA 02129
| | - Ben S. Wittner
- Massachusetts General Hospital Center for Cancer Research, Harvard Medical School, Charlestown, MA 02129
| | - Maoxuan Lin
- Massachusetts General Hospital Center for Cancer Research, Harvard Medical School, Charlestown, MA 02129
| | - Devon Wiley
- Massachusetts General Hospital Center for Cancer Research, Harvard Medical School, Charlestown, MA 02129
| | - Valentine Comaills
- Massachusetts General Hospital Center for Cancer Research, Harvard Medical School, Charlestown, MA 02129
| | - Erin Emmons
- Massachusetts General Hospital Center for Cancer Research, Harvard Medical School, Charlestown, MA 02129
| | - Kira Niederhoffer
- Massachusetts General Hospital Center for Cancer Research, Harvard Medical School, Charlestown, MA 02129
| | - Uyen Ho
- Massachusetts General Hospital Center for Cancer Research, Harvard Medical School, Charlestown, MA 02129
| | - Jacob Ukleja
- Massachusetts General Hospital Center for Cancer Research, Harvard Medical School, Charlestown, MA 02129
| | - Dante Che
- Massachusetts General Hospital Center for Cancer Research, Harvard Medical School, Charlestown, MA 02129
| | - Hannah Stowe
- Center for Engineering in Medicine and Surgery, Massachusetts General Hospital, Harvard Medical School
- Shriners Hospital for Children, Boston, MA 02114
| | - Linda Nieman
- Massachusetts General Hospital Center for Cancer Research, Harvard Medical School, Charlestown, MA 02129
| | - Wilhelm Haas
- Massachusetts General Hospital Center for Cancer Research, Harvard Medical School, Charlestown, MA 02129
| | - Shannon L. Stott
- Massachusetts General Hospital Center for Cancer Research, Harvard Medical School, Charlestown, MA 02129
| | - Michael S. Lawrence
- Massachusetts General Hospital Center for Cancer Research, Harvard Medical School, Charlestown, MA 02129
| | - David T. Ting
- Massachusetts General Hospital Center for Cancer Research, Harvard Medical School, Charlestown, MA 02129
| | - David T. Miyamoto
- Massachusetts General Hospital Center for Cancer Research, Harvard Medical School, Charlestown, MA 02129
| | - Daniel A. Haber
- Massachusetts General Hospital Center for Cancer Research, Harvard Medical School, Charlestown, MA 02129
- Howard Hughes Medical Institute, Bethesda, MD, 20815
| | - Mehmet Toner
- Center for Engineering in Medicine and Surgery, Massachusetts General Hospital, Harvard Medical School
- Shriners Hospital for Children, Boston, MA 02114
| | - Shyamala Maheswaran
- Massachusetts General Hospital Center for Cancer Research, Harvard Medical School, Charlestown, MA 02129
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48
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Abstract
Although tuft cells were discovered over 60 years ago, their functions have long been enigmatic, especially in human health. Nonetheless, tuft cells have recently emerged as key orchestrators of the host response to diverse microbial infections in the gut and airway. While tuft cells are epithelial in origin, they exhibit functions akin to immune cells and mediate important interkingdom interactions between the host and helminths, protists, viruses, and bacteria. With broad intra- and intertissue heterogeneity, tuft cells sense and respond to microbes with exquisite specificity. Tuft cells can recognize helminth and protist infection, driving a type 2 immune response to promote parasite expulsion. Tuft cells also serve as the primary physiologic target of persistent murine norovirus (MNV) and promote immune evasion. Recently, tuft cells were also shown to be infected by rotavirus. Other viral infections, such as influenza A virus, can induce tuft cell–dependent tissue repair. In the context of coinfection, tuft cells promote neurotropic flavivirus replication by dampening antiviral adaptive immune responses. Commensal and pathogenic bacteria can regulate tuft cell abundance and function and, in turn, tuft cells are implicated in modulating bacterial infiltration and mucosal barrier integrity. However, the contribution of tuft cells to microbial sensing in humans and their resulting effector responses are poorly characterized. Herein, we aim to provide a comprehensive overview of microbial activation of tuft cells with an emphasis on tuft cell heterogeneity and differences between mouse and human tuft cell biology as it pertains to human health and disease.
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Affiliation(s)
- Madison S. Strine
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Craig B. Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut, United States of America
- * E-mail: ,
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49
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Burclaff J, Bliton RJ, Breau KA, Ok MT, Gomez-Martinez I, Ranek JS, Bhatt AP, Purvis JE, Woosley JT, Magness ST. A Proximal-to-Distal Survey of Healthy Adult Human Small Intestine and Colon Epithelium by Single-Cell Transcriptomics. Cell Mol Gastroenterol Hepatol 2022; 13:1554-1589. [PMID: 35176508 PMCID: PMC9043569 DOI: 10.1016/j.jcmgh.2022.02.007] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND & AIMS Single-cell transcriptomics offer unprecedented resolution of tissue function at the cellular level, yet studies analyzing healthy adult human small intestine and colon are sparse. Here, we present single-cell transcriptomics covering the duodenum, jejunum, ileum, and ascending, transverse, and descending colon from 3 human beings. METHODS A total of 12,590 single epithelial cells from 3 independently processed organ donors were evaluated for organ-specific lineage biomarkers, differentially regulated genes, receptors, and drug targets. Analyses focused on intrinsic cell properties and their capacity for response to extrinsic signals along the gut axis across different human beings. RESULTS Cells were assigned to 25 epithelial lineage clusters. Multiple accepted intestinal stem cell markers do not specifically mark all human intestinal stem cells. Lysozyme expression is not unique to human Paneth cells, and Paneth cells lack expression of expected niche factors. Bestrophin 4 (BEST4)+ cells express Neuropeptide Y (NPY) and show maturational differences between the small intestine and colon. Tuft cells possess a broad ability to interact with the innate and adaptive immune systems through previously unreported receptors. Some classes of mucins, hormones, cell junctions, and nutrient absorption genes show unappreciated regional expression differences across lineages. The differential expression of receptors and drug targets across lineages show biological variation and the potential for variegated responses. CONCLUSIONS Our study identifies novel lineage marker genes, covers regional differences, shows important differences between mouse and human gut epithelium, and reveals insight into how the epithelium responds to the environment and drugs. This comprehensive cell atlas of the healthy adult human intestinal epithelium resolves likely functional differences across anatomic regions along the gastrointestinal tract and advances our understanding of human intestinal physiology.
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Affiliation(s)
- Joseph Burclaff
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - R Jarrett Bliton
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill/North Carolina State University, Chapel Hill, North Carolina
| | - Keith A Breau
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Meryem T Ok
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill/North Carolina State University, Chapel Hill, North Carolina
| | - Ismael Gomez-Martinez
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jolene S Ranek
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Aadra P Bhatt
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jeremy E Purvis
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - John T Woosley
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Scott T Magness
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill/North Carolina State University, Chapel Hill, North Carolina; Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
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50
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Hendel SK, Kellermann L, Hausmann A, Bindslev N, Jensen KB, Nielsen OH. Tuft Cells and Their Role in Intestinal Diseases. Front Immunol 2022; 13:822867. [PMID: 35237268 PMCID: PMC8884241 DOI: 10.3389/fimmu.2022.822867] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/25/2022] [Indexed: 12/11/2022] Open
Abstract
The interests in intestinal epithelial tuft cells, their basic physiology, involvement in immune responses and relevance for gut diseases, have increased dramatically over the last fifteen years. A key discovery in 2016 of their close connection to helminthic and protozoan infection has further spurred the exploration of these rare chemosensory epithelial cells. Although very sparse in number, tuft cells are now known as important sentinels in the gastrointestinal tract as they monitor intestinal content using succinate as well as sweet and bitter taste receptors. Upon stimulation, tuft cells secrete a broad palette of effector molecules, including interleukin-25, prostaglandin E2 and D2, cysteinyl leukotriene C4, acetylcholine, thymic stromal lymphopoietin, and β-endorphins, some of which with immunomodulatory functions. Tuft cells have proven indispensable in anti-helminthic and anti-protozoan immunity. Most studies on tuft cells are based on murine experiments using double cortin-like kinase 1 (DCLK1) as a marker, while human intestinal tuft cells can be identified by their expression of the cyclooxygenase-1 enzyme. So far, only few studies have examined tuft cells in humans and their relation to gut disease. Here, we present an updated view on intestinal epithelial tuft cells, their physiology, immunological hub function, and their involvement in human disease. We close with a discussion on how tuft cells may have potential therapeutic value in a clinical context.
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Affiliation(s)
- Sebastian Kjærgaard Hendel
- Department of Gastroenterology, Herlev Hospital, University of Copenhagen, Herlev, Denmark
- *Correspondence: Sebastian Kjærgaard Hendel,
| | - Lauge Kellermann
- Department of Gastroenterology, Herlev Hospital, University of Copenhagen, Herlev, Denmark
| | - Annika Hausmann
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niels Bindslev
- Department of Biomedical Sciences , University of Copenhagen, Copenhagen, Denmark
| | - Kim Bak Jensen
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Ole Haagen Nielsen
- Department of Gastroenterology, Herlev Hospital, University of Copenhagen, Herlev, Denmark
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