1
|
Mayr CH, Santacruz D, Jarosch S, Bleck M, Dalton J, McNabola A, Lempp C, Neubert L, Rath B, Kamp JC, Jonigk D, Kühnel M, Schlüter H, Klimowicz A, Doerr J, Dick A, Ramirez F, Thomas MJ. Spatial transcriptomic characterization of pathologic niches in IPF. SCIENCE ADVANCES 2024; 10:eadl5473. [PMID: 39121212 PMCID: PMC11313858 DOI: 10.1126/sciadv.adl5473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 07/08/2024] [Indexed: 08/11/2024]
Abstract
Despite advancements in antifibrotic therapy, idiopathic pulmonary fibrosis (IPF) remains a medical condition with unmet needs. Single-cell RNA sequencing (scRNA-seq) has enhanced our understanding of IPF but lacks the cellular tissue context and gene expression localization that spatial transcriptomics provides. To bridge this gap, we profiled IPF and control patient lung tissue using spatial transcriptomics, integrating the data with an IPF scRNA-seq atlas. We identified three disease-associated niches with unique cellular compositions and localizations. These include a fibrotic niche, consisting of myofibroblasts and aberrant basaloid cells, located around airways and adjacent to an airway macrophage niche in the lumen, containing SPP1+ macrophages. In addition, we identified an immune niche, characterized by distinct lymphoid cell foci in fibrotic tissue, surrounded by remodeled endothelial vessels. This spatial characterization of IPF niches will facilitate the identification of drug targets that disrupt disease-driving niches and aid in the development of disease relevant in vitro models.
Collapse
Affiliation(s)
- Christoph H. Mayr
- Boehringer Ingelheim Pharma GmbH & Co. KG, Department Immunology and Respiratory Disease research, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Diana Santacruz
- Boehringer Ingelheim Pharma GmbH & Co. KG, Global Computational Biology and Digital Sciences, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Sebastian Jarosch
- Boehringer Ingelheim Pharma GmbH & Co. KG, Department Drug Discovery Sciences, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Marina Bleck
- Boehringer Ingelheim Pharmaceuticals Inc., Department of Immunology and Respiratory Diseases Research, 900 Ridgebury Road, Ridgefield, CT 06877 USA
| | - John Dalton
- Boehringer Ingelheim Pharmaceuticals Inc., Department of Immunology and Respiratory Diseases Research, 900 Ridgebury Road, Ridgefield, CT 06877 USA
| | - Angela McNabola
- Boehringer Ingelheim Pharmaceuticals Inc., Department of Immunology and Respiratory Diseases Research, 900 Ridgebury Road, Ridgefield, CT 06877 USA
| | - Charlotte Lempp
- Boehringer Ingelheim Pharma GmbH & Co. KG, Department Drug Discovery Sciences, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Lavinia Neubert
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Hannover, Germany
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Berenice Rath
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Hannover, Germany
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Jan C. Kamp
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Hannover, Germany
- Department of Respiratory Medicine and Infectious Diseases, Hannover Medical School, Hannover, Germany
| | - Danny Jonigk
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Hannover, Germany
- Institute of Pathology, Hannover Medical School, Hannover, Germany
- Institute of Pathology, University Medical Center RWTH University of Aachen, Aachen, Germany
| | - Mark Kühnel
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Hannover, Germany
- Institute of Pathology, University Medical Center RWTH University of Aachen, Aachen, Germany
| | - Holger Schlüter
- Boehringer Ingelheim Pharma GmbH & Co. KG, Department Immunology and Respiratory Disease research, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Alexander Klimowicz
- Boehringer Ingelheim Pharmaceuticals Inc., Department of Immunology and Respiratory Diseases Research, 900 Ridgebury Road, Ridgefield, CT 06877 USA
| | - Jonas Doerr
- Boehringer Ingelheim Pharma GmbH & Co. KG, Department Drug Discovery Sciences, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Alec Dick
- Boehringer Ingelheim Pharma GmbH & Co. KG, Global Computational Biology and Digital Sciences, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Fidel Ramirez
- Boehringer Ingelheim Pharma GmbH & Co. KG, Global Computational Biology and Digital Sciences, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Matthew J. Thomas
- Boehringer Ingelheim Pharma GmbH & Co. KG, Department Immunology and Respiratory Disease research, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| |
Collapse
|
2
|
Dandavate V, Bolshette N, Van Drunen R, Manella G, Bueno-Levy H, Zerbib M, Kawano I, Golik M, Adamovich Y, Asher G. Hepatic BMAL1 and HIF1α regulate a time-dependent hypoxic response and prevent hepatopulmonary-like syndrome. Cell Metab 2024:S1550-4131(24)00274-2. [PMID: 39106859 DOI: 10.1016/j.cmet.2024.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 05/28/2024] [Accepted: 07/05/2024] [Indexed: 08/09/2024]
Abstract
The transcriptional response to hypoxia is temporally regulated, yet the molecular underpinnings and physiological implications are unknown. We examined the roles of hepatic Bmal1 and Hif1α in the circadian response to hypoxia in mice. We found that the majority of the transcriptional response to hypoxia is dependent on either Bmal1 or Hif1α, through shared and distinct roles that are daytime determined. We further show that hypoxia-inducible factor (HIF)1α accumulation upon hypoxia is temporally regulated and Bmal1 dependent. Unexpectedly, mice lacking both hepatic Bmal1 and Hif1α are hypoxemic and exhibit increased mortality upon hypoxic exposure in a daytime-dependent manner. These mice display mild liver dysfunction with pulmonary vasodilation likely due to extracellular signaling regulated kinase (ERK) activation, endothelial nitric oxide synthase, and nitric oxide accumulation in lungs, suggestive of hepatopulmonary syndrome. Our findings indicate that hepatic BMAL1 and HIF1α are key time-dependent regulators of the hypoxic response and can provide molecular insights into the pathophysiology of hepatopulmonary syndrome.
Collapse
Affiliation(s)
- Vaishnavi Dandavate
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Nityanand Bolshette
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Rachel Van Drunen
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Gal Manella
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Hanna Bueno-Levy
- Department of the Veterinary Resources, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Mirie Zerbib
- Department of the Veterinary Resources, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Ippei Kawano
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Marina Golik
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Yaarit Adamovich
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Gad Asher
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel.
| |
Collapse
|
3
|
Renaud L, Wilson CL, Lafyatis R, Schnapp LM, Feghali-Bostwick CA. Transcriptomic characterization of lung pericytes in systemic sclerosis-associated pulmonary fibrosis. iScience 2024; 27:110010. [PMID: 38868196 PMCID: PMC11167435 DOI: 10.1016/j.isci.2024.110010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 02/09/2024] [Accepted: 05/14/2024] [Indexed: 06/14/2024] Open
Abstract
Systemic sclerosis (SSc) is a chronic disease characterized by fibrosis and vascular abnormalities in the skin and internal organs, including the lung. SSc-associated pulmonary fibrosis (SSc-PF) is the leading cause of death in SSc patients. Pericytes are key regulators of vascular integrity and endothelial function. The role that pericytes play in SSc-PF remains unclear. We compared the transcriptome of pericytes from SSc-PF lungs (SScL) to pericytes from normal lungs (NORML). We identified 1,179 differentially expressed genes in SScL pericytes. Pathways enriched in SScL pericytes included prostaglandin, PI3K-AKT, calcium, and vascular remodeling signaling. Decreased cyclic AMP production and altered phosphorylation of AKT in response to prostaglandin E2 in SScL pericytes demonstrate the functional consequence of changes in the prostaglandin pathway that may contribute to fibrosis. The transcriptomic signature of SSc lung pericytes suggests that they promote vascular dysfunction and contribute to the loss of protection against lung inflammation and fibrosis.
Collapse
Affiliation(s)
- Ludivine Renaud
- Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Carole L. Wilson
- Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
- Department of Medicine, University of Wisconsin, Madison, WI 53705, USA
| | - Robert Lafyatis
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Lynn M. Schnapp
- Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
- Department of Medicine, University of Wisconsin, Madison, WI 53705, USA
| | | |
Collapse
|
4
|
WANG Y, LUO B, WANG Z, QUE Z, JIANG L, TIAN J. [Advancements in Single-cell RNA Sequencing Technology
in the Study of the Tumor Microenvironment in Lung Cancer]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2024; 27:441-450. [PMID: 39026495 PMCID: PMC11258646 DOI: 10.3779/j.issn.1009-3419.2024.101.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Indexed: 07/20/2024]
Abstract
The immune microenvironment plays a key role in the development and progression of tumors. In recent years, with the rapid advancement of high-throughput sequencing technologies, researchers have gained a deeper understanding of the composition and function of immune cells in the tumor microenvironment. However, traditional bulk sequencing technologies are limited in resolving heterogeneity at the single-cell level, constraining a comprehensive understanding of the complexity of the tumor microenvironment. The advent of single-cell RNA sequencing technology has brought new opportunities to uncover the heterogeneity of the immune microenvironment in lung cancer. Currently, T-cell-centered immunotherapy in clinical settings is prone to side effects affecting prognosis, such as immunogenic drug resistance or immune-related pneumonia, with the key factor being changes in the interactions between immune cells and tumor cells in the tumor microenvironment. Single-cell RNA sequencing technology can reveal the origins and functions of different subgroups within the tumor microenvironment from perspectives such as intercellular interactions and pseudotime analysis, thereby discovering new cell subgroups or novel biomarkers, providing new avenues for uncovering resistance to immunotherapy and monitoring therapeutic efficacy. This review comprehensively discusses the newest research techniques and advancements in single-cell RNA sequencing technology for unveiling the heterogeneity of the tumor microenvironment after lung cancer immunotherapy, offering insights for enhancing the precision and personalization of immunotherapy.
.
Collapse
|
5
|
Hill ABT, Murphy YM, Polkoff KM, Edwards L, Walker DM, Moatti A, Greenbaum A, Piedrahita JA. A gene edited pig model for studying LGR5 + stem cells: implications for future applications in tissue regeneration and biomedical research. Front Genome Ed 2024; 6:1401163. [PMID: 38903529 PMCID: PMC11187295 DOI: 10.3389/fgeed.2024.1401163] [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: 03/14/2024] [Accepted: 05/15/2024] [Indexed: 06/22/2024] Open
Abstract
Recent advancements in genome editing techniques, notably CRISPR-Cas9 and TALENs, have marked a transformative era in biomedical research, significantly enhancing our understanding of disease mechanisms and helping develop novel therapies. These technologies have been instrumental in creating precise animal models for use in stem cell research and regenerative medicine. For instance, we have developed a transgenic pig model to enable the investigation of LGR5-expressing cells. The model was designed to induce the expression of H2B-GFP under the regulatory control of the LGR5 promoter via CRISPR/Cas9-mediated gene knock-in. Notably, advancements in stem cell research have identified distinct subpopulations of LGR5-expressing cells within adult human, mouse, and pig tissues. LGR5, a leucine-rich repeat-containing G protein-coupled receptor, enhances WNT signaling and these LGR5+ subpopulations demonstrate varied roles and anatomical distributions, underscoring the necessity for suitable translational models. This transgenic pig model facilitates the tracking of LGR5-expressing cells and has provided valuable insights into the roles of these cells across different tissues and species. For instance, in pulmonary tissue, Lgr5+ cells in mice are predominantly located in alveolar compartments, driving alveolar differentiation of epithelial progenitors via Wnt pathway activation. In contrast, in pigs and humans, these cells are situated in a unique sub-basal position adjacent to the airway epithelium. In fetal stages a pattern of LGR5 expression during lung bud tip formation is evident in humans and pigs but is lacking in mice. Species differences with respect to LGR5 expression have also been observed in the skin, intestines, and cochlea further reinforcing the need for careful selection of appropriate translational animal models. This paper discusses the potential utility of the LGR5+ pig model in exploring the role of LGR5+ cells in tissue development and regeneration with the goal of translating these findings into human and animal clinical applications.
Collapse
Affiliation(s)
- Amanda B. T. Hill
- College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, United States
| | - Yanet M. Murphy
- College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, United States
| | - Kathryn M. Polkoff
- College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, United States
| | - Laura Edwards
- College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, United States
| | - Derek M. Walker
- College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, United States
| | - Adele Moatti
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, United States
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, and North Carolina State University, Raleigh, NC, United States
| | - Alon Greenbaum
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, United States
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, and North Carolina State University, Raleigh, NC, United States
| | - Jorge A. Piedrahita
- College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, and North Carolina State University, Raleigh, NC, United States
| |
Collapse
|
6
|
Yin Y, Koenitzer JR, Patra D, Dietmann S, Bayguinov P, Hagan AS, Ornitz DM. Identification of a myofibroblast differentiation program during neonatal lung development. Development 2024; 151:dev202659. [PMID: 38602479 PMCID: PMC11165721 DOI: 10.1242/dev.202659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 03/25/2024] [Indexed: 04/12/2024]
Abstract
Alveologenesis is the final stage of lung development in which the internal surface area of the lung is increased to facilitate efficient gas exchange in the mature organism. The first phase of alveologenesis involves the formation of septal ridges (secondary septae) and the second phase involves thinning of the alveolar septa. Within secondary septa, mesenchymal cells include a transient population of alveolar myofibroblasts (MyoFBs) and a stable but poorly described population of lipid-rich cells that have been referred to as lipofibroblasts or matrix fibroblasts (MatFBs). Using a unique Fgf18CreER lineage trace mouse line, cell sorting, single-cell RNA sequencing and primary cell culture, we have identified multiple subtypes of mesenchymal cells in the neonatal lung, including an immature progenitor cell that gives rise to mature MyoFB. We also show that the endogenous and targeted ROSA26 locus serves as a sensitive reporter for MyoFB maturation. These studies identify a MyoFB differentiation program that is distinct from other mesenchymal cell types and increases the known repertoire of mesenchymal cell types in the neonatal lung.
Collapse
Affiliation(s)
- Yongjun Yin
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jeffrey R. Koenitzer
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Debabrata Patra
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sabine Dietmann
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Institute for Informatics, Data Science and Biostatistics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Peter Bayguinov
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Andrew S. Hagan
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David M. Ornitz
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| |
Collapse
|
7
|
Zhang H, Mulqueen RM, Iannuzo N, Farrera DO, Polverino F, Galligan JJ, Ledford JG, Adey AC, Cusanovich DA. txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility. Genome Biol 2024; 25:78. [PMID: 38519979 PMCID: PMC10958877 DOI: 10.1186/s13059-023-03150-1] [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: 05/12/2023] [Accepted: 12/20/2023] [Indexed: 03/25/2024] Open
Abstract
We develop a large-scale single-cell ATAC-seq method by combining Tn5-based pre-indexing with 10× Genomics barcoding, enabling the indexing of up to 200,000 nuclei across multiple samples in a single reaction. We profile 449,953 nuclei across diverse tissues, including the human cortex, mouse brain, human lung, mouse lung, mouse liver, and lung tissue from a club cell secretory protein knockout (CC16-/-) model. Our study of CC16-/- nuclei uncovers previously underappreciated technical artifacts derived from remnant 129 mouse strain genetic material, which cause profound cell-type-specific changes in regulatory elements near many genes, thereby confounding the interpretation of this commonly referenced mouse model.
Collapse
Affiliation(s)
- Hao Zhang
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
- Asthma & Airway Disease Research Center, University of Arizona, Tucson, AZ, USA
| | - Ryan M Mulqueen
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Natalie Iannuzo
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
| | - Dominique O Farrera
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ, USA
| | - Francesca Polverino
- Asthma & Airway Disease Research Center, University of Arizona, Tucson, AZ, USA
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Arizona, Tucson, AZ, USA
- Banner - University Medicine North, Pulmonary - Clinic F, Tucson, AZ, USA
| | - James J Galligan
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ, USA
| | - Julie G Ledford
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
- Asthma & Airway Disease Research Center, University of Arizona, Tucson, AZ, USA
| | - Andrew C Adey
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA.
- Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR, USA.
- Oregon Health & Science University, Knight Cancer Institute, Portland, OR, USA.
- Oregon Health & Science University, Knight Cardiovascular Institute, Portland, OR, USA.
| | - Darren A Cusanovich
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA.
- Asthma & Airway Disease Research Center, University of Arizona, Tucson, AZ, USA.
| |
Collapse
|
8
|
Janas PP, Chauché C, Shearer P, Perona-Wright G, McSorley HJ, Schwarze J. Cold dispase digestion of murine lungs improves recovery and culture of airway epithelial cells. PLoS One 2024; 19:e0297585. [PMID: 38271372 PMCID: PMC10810513 DOI: 10.1371/journal.pone.0297585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/08/2024] [Indexed: 01/27/2024] Open
Abstract
Airway epithelial cells (AECs) play a key role in maintaining lung homeostasis, epithelium regeneration and the initiation of pulmonary immune responses. To isolate and study murine AECs investigators have classically used short and hot (1h 37°C) digestion protocols. Here, we present a workflow for efficient AECs isolation and culture, utilizing long and cold (20h 4°C) dispase II digestion of murine lungs. This protocol yields a greater number of viable AECs compared to an established 1h 37°C dispase II digestion. Using a combination of flow cytometry and immunofluorescent microscopy, we demonstrate that compared to the established method, the cold digestion allows for recovery of a 3-fold higher number of CD45-CD31-EpCAM+ cells from murine lungs. Their viability is increased compared to established protocols, they can be isolated in larger numbers by magnetic-activated cell sorting (MACS), and they result in greater numbers of distal airway stem cell (DASC) KRT5+p63+ colonies in vitro. Our findings demonstrate that temperature and duration of murine lung enzymatic digestion have a considerable impact on AEC yield, viability, and ability to form colonies in vitro. We believe this workflow will be helpful for studying lung AECs and their role in the biology of lung.
Collapse
Affiliation(s)
- Piotr Pawel Janas
- Centre for Inflammation Research, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh BioQuarter, Edinburgh, United Kingdom
| | - Caroline Chauché
- Centre for Inflammation Research, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh BioQuarter, Edinburgh, United Kingdom
| | - Patrick Shearer
- Institute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Georgia Perona-Wright
- Institute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Henry J. McSorley
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Jürgen Schwarze
- Centre for Inflammation Research, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh BioQuarter, Edinburgh, United Kingdom
| |
Collapse
|
9
|
Yin Y, Koenitzer JR, Patra D, Dietmann S, Bayguinov P, Hagan AS, Ornitz DM. Identification of a myofibroblast differentiation program during neonatal lung development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.28.573370. [PMID: 38234814 PMCID: PMC10793446 DOI: 10.1101/2023.12.28.573370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Alveologenesis is the final stage of lung development in which the internal surface area of the lung is increased to facilitate efficient gas exchange in the mature organism. The first phase of alveologenesis involves the formation of septal ridges (secondary septae) and the second phase involves thinning of the alveolar septa. Within secondary septa, mesenchymal cells include a transient population of alveolar myofibroblasts (MyoFB) and a stable but poorly described population of lipid rich cells that have been referred to as lipofibroblasts or matrix fibroblasts (MatFB). Using a unique Fgf18CreER lineage trace mouse line, cell sorting, single cell RNA sequencing, and primary cell culture, we have identified multiple subtypes of mesenchymal cells in the neonatal lung, including an immature progenitor cell that gives rise to mature MyoFB. We also show that the endogenous and targeted ROSA26 locus serves as a sensitive reporter for MyoFB maturation. These studies identify a myofibroblast differentiation program that is distinct form other mesenchymal cells types and increases the known repertoire of mesenchymal cell types in the neonatal lung.
Collapse
Affiliation(s)
- Yongjun Yin
- Departments of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110
| | | | - Debabrata Patra
- Departments of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110
| | - Sabine Dietmann
- Departments of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110
- Institute for Informatics, Data Science & Biostatistics, Washington University School of Medicine, St. Louis, MO 63110
| | - Peter Bayguinov
- Neuroscience, Washington University School of Medicine, St. Louis, MO 63110
| | - Andrew S. Hagan
- Departments of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110
| | - David M. Ornitz
- Departments of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110
| |
Collapse
|
10
|
Zhu JH, Guan XC, Yi LL, Xu H, Li QY, Cheng WJ, Xie YX, Li WZ, Zhao HY, Wei HJ, Zhao SM. Single-nucleus transcriptome sequencing reveals hepatic cell atlas in pigs. BMC Genomics 2023; 24:770. [PMID: 38087243 PMCID: PMC10717992 DOI: 10.1186/s12864-023-09765-9] [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: 07/21/2023] [Accepted: 10/24/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND As the largest substantive organ of animals, the liver plays an essential role in the physiological processes of digestive metabolism and immune defense. However, the cellular composition of the pig liver remains poorly understood. This investigation used single-nucleus RNA sequencing technology to identify cell types from liver tissues of pigs, providing a theoretical basis for further investigating liver cell types in pigs. RESULTS The analysis revealed 13 cells clusters which were further identified 7 cell types including endothelial cells, T cells, hepatocytes, Kupffer cells, stellate cells, B cells, and cholangiocytes. The dominant cell types were endothelial cells, T cells and hepatocytes in the liver tissue of Dahe pigs and Dahe black pigs, which accounts for about 85.76% and 82.74%, respectively. The number of endothelial cells was higher in the liver tissue of Dahe pigs compared to Dahe black pigs, while the opposite tendency was observed for T cells. Moreover, functional enrichment analysis demonstrated that the differentially expressed genes in pig hepatic endothelial cells were significantly enriched in the protein processing in endoplasmic reticulum, MAPK signaling pathway, and FoxO signaling pathway. Functional enrichment analysis demonstrated that the differentially expressed genes in pig hepatic T cells were significantly enriched in the thyroid hormone signaling pathway, B cell receptor signaling pathway, and focal adhesion. Functional enrichment analysis demonstrated that the differentially expressed genes in pig hepatic hepatocytes were significantly enriched in the metabolic pathways. CONCLUSIONS In summary, this study provides a comprehensive cell atlas of porcine hepatic tissue. The number, gene expression level and functional characteristics of each cell type in pig liver tissue varied between breeds.
Collapse
Affiliation(s)
- Jun-Hong Zhu
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, 650201, China
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China
| | - Xuan-Cheng Guan
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, 650201, China
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China
| | - Lan-Lan Yi
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, 650201, China
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China
| | - Hong Xu
- School of Public Finance and Economics, Yunnan University of Finance and Economics, Kunming, 650221, China
| | - Qiu-Yan Li
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, 650201, China
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China
| | - Wen-Jie Cheng
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, 650201, China
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China
| | - Yu-Xiao Xie
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, 650201, China
- College of Biology and Agriculture, Zunyi Normal University, Zunyi, 563006, China
| | - Wei-Zhen Li
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, China
| | - Hong-Ye Zhao
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, China
| | - Hong-Jiang Wei
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China.
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, China.
| | - Su-Mei Zhao
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, 650201, China.
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Yunnan Agricultural University, Kunming, 650201, China.
| |
Collapse
|
11
|
Hume DA, Millard SM, Pettit AR. Macrophage heterogeneity in the single-cell era: facts and artifacts. Blood 2023; 142:1339-1347. [PMID: 37595274 DOI: 10.1182/blood.2023020597] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/09/2023] [Accepted: 08/09/2023] [Indexed: 08/20/2023] Open
Abstract
In this spotlight, we review technical issues that compromise single-cell analysis of tissue macrophages, including limited and unrepresentative yields, fragmentation and generation of remnants, and activation during tissue disaggregation. These issues may lead to a misleading definition of subpopulations of macrophages and the expression of macrophage-specific transcripts by unrelated cells. Recognition of the technical limitations of single-cell approaches is required in order to map the full spectrum of tissue-resident macrophage heterogeneity and assess its biological significance.
Collapse
Affiliation(s)
- David A Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Susan M Millard
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Allison R Pettit
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| |
Collapse
|
12
|
Liao P, Huang Q, Zhang J, Su Y, Xiao R, Luo S, Wu Z, Zhu L, Li J, Hu Q. How single-cell techniques help us look into lung cancer heterogeneity and immunotherapy. Front Immunol 2023; 14:1238454. [PMID: 37671151 PMCID: PMC10475738 DOI: 10.3389/fimmu.2023.1238454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 08/03/2023] [Indexed: 09/07/2023] Open
Abstract
Lung cancer patients tend to have strong intratumoral and intertumoral heterogeneity and complex tumor microenvironment, which are major contributors to the efficacy of and drug resistance to immunotherapy. From a new perspective, single-cell techniques offer an innovative way to look at the intricate cellular interactions between tumors and the immune system and help us gain insights into lung cancer and its response to immunotherapy. This article reviews the application of single-cell techniques in lung cancer, with focuses directed on the heterogeneity of lung cancer and the efficacy of immunotherapy. This review provides both theoretical and experimental information for the future development of immunotherapy and personalized treatment for the management of lung cancer.
Collapse
Affiliation(s)
- Pu Liao
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qi Huang
- Department of Respiratory and Critical Care Medicine, Hubei Province Clinical Research Center for Major Respiratory Diseases, National Health Commission (NHC) Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jiwei Zhang
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuan Su
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Respiratory and Critical Care Medicine, Hubei Province Clinical Research Center for Major Respiratory Diseases, National Health Commission (NHC) Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Rui Xiao
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Pathophysiology, School of Basic Medicine; Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shengquan Luo
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Pathophysiology, School of Basic Medicine; Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zengbao Wu
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Liping Zhu
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Pathophysiology, School of Basic Medicine; Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiansha Li
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qinghua Hu
- Key Laboratory of Pulmonary Diseases of Ministry of Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Pathophysiology, School of Basic Medicine; Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| |
Collapse
|
13
|
Zhu R, Pan X, Wang S, Qiu Z, Gu C, Yao X, Li W. Updated skin transcriptomic atlas depicted by reciprocal contribution of single-nucleus RNA sequencing and single-cell RNA sequencing. J Dermatol Sci 2023; 111:22-31. [PMID: 37407342 DOI: 10.1016/j.jdermsci.2023.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 06/13/2023] [Accepted: 06/17/2023] [Indexed: 07/07/2023]
Abstract
BACKGROUND Single-cell RNA sequencing (scRNA-seq) has advanced our understanding of skin biology, but its utility is restricted by the requirement of fresh samples, inadequate dissociation-induced cell loss or death, and activation during tissue digestion. Single-nucleus RNA sequencing (snRNA-seq) can use frozen, hard-to-dissociate materials, which might be a promising method to circumvent the limitations of scRNA-seq for the skin tissue. OBJECTIVE To profile skin cells using snRNA-seq in parallel with scRNA-seq. METHODS We performed snRNA-seq in parallel with scRNA-seq for the bisected skin sample of one person and integrated previously published scRNA-seq data for analysis. We comparatively analyzed the differences in cell proportions and gene expression between the two methods. The differentiation trajectories of keratinocytes and fibroblasts were analyzed by Slingshot analysis. RESULTS snRNA-seq was less susceptible to contamination from mitochondrial and ribosomal RNA, and exhibited a greater capacity to detect transcription factors. snRNA-seq identified more spatially and functionally relevant keratinocyte clusters that constitute cell trajectories with expected differentiation dynamics. Novel markers, e.g., LYPD3, EMP2, and CSTB, were revealed for different differentiation stages of keratinocytes, and NFIB and GRHL1 were identified as transcription factors involving in the proliferation and functional differentiation of keratinocytes. Fibroblasts were found in a state of activation in scRNA-seq. And scRNA-seq detected a greater number of immune cells. CONCLUSIONS We generated an updated atlas of the skin transcriptome based on the reciprocal contribution of scRNA-seq and snRNA-seq.
Collapse
Affiliation(s)
- Ronghui Zhu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai Institute of Dermatology, Shanghai, China
| | - Xiaoyu Pan
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai Institute of Dermatology, Shanghai, China
| | - Shangshang Wang
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai Institute of Dermatology, Shanghai, China
| | - Zhuoqiong Qiu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai Institute of Dermatology, Shanghai, China
| | - Chaoying Gu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai Institute of Dermatology, Shanghai, China
| | - Xu Yao
- Department of Allergy and Rheumatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Wei Li
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai Institute of Dermatology, Shanghai, China.
| |
Collapse
|
14
|
Sant P, Rippe K, Mallm JP. Approaches for single-cell RNA sequencing across tissues and cell types. Transcription 2023; 14:127-145. [PMID: 37062951 PMCID: PMC10807473 DOI: 10.1080/21541264.2023.2200721] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/30/2023] [Indexed: 04/18/2023] Open
Abstract
Single-cell sequencing of RNA (scRNA-seq) has advanced our understanding of cellular heterogeneity and signaling in developmental biology and disease. A large number of complementary assays have been developed to profile transcriptomes of individual cells, also in combination with other readouts, such as chromatin accessibility or antibody-based analysis of protein surface markers. As scRNA-seq technologies are advancing fast, it is challenging to establish robust workflows and up-to-date protocols that are best suited to address the large range of research questions. Here, we review scRNA-seq techniques from mRNA end-counting to total RNA in relation to their specific features and outline the necessary sample preparation steps and quality control measures. Based on our experience in dealing with the continuously growing portfolio from the perspective of a central single-cell facility, we aim to provide guidance on how workflows can be best automatized and share our experience in coping with the continuous expansion of scRNA-seq techniques.
Collapse
Affiliation(s)
- Pooja Sant
- Single-cell Open Lab, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Karsten Rippe
- Division Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Jan-Philipp Mallm
- Single-cell Open Lab, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| |
Collapse
|
15
|
James J, Dekan A, Niihori M, McClain N, Varghese M, Bharti D, Lawal OS, Padilla-Rodrigez M, Yi D, Dai Z, Gusev O, Rafikova O, Rafikov R. Novel Populations of Lung Capillary Endothelial Cells and Their Functional Significance. RESEARCH SQUARE 2023:rs.3.rs-2887159. [PMID: 37205391 PMCID: PMC10187412 DOI: 10.21203/rs.3.rs-2887159/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The role of the lung's microcirculation and capillary endothelial cells in normal physiology and the pathobiology of pulmonary diseases is unequivocally vital. The recent discovery of molecularly distinct aerocytes and general capillary (gCaps) endothelial cells by single-cell transcriptomics (scRNAseq) advanced the field in understanding microcirculatory milieu and cellular communications. However, increasing evidence from different groups indicated the possibility of more heterogenic structures of lung capillaries. Therefore, we investigated enriched lung endothelial cells by scRNAseq and identified five novel populations of gCaps with distinct molecular signatures and roles. Our analysis suggests that two populations of gCaps that express Scn7a(Na+) and Clic4(Cl-) ion transporters form the arterial-to-vein zonation and establish the capillary barrier. We also discovered and named mitotically-active "root" cells (Flot1+) on the interface between arterial, Scn7a+, and Clic4 + endothelium, responsible for the regeneration and repair of the adjacent endothelial populations. Furthermore, the transition of gCaps to a vein requires a venous-capillary endothelium expressing Lingo2. Finally, gCaps detached from the zonation represent a high level of Fabp4, other metabolically active genes, and tip-cell markers showing angiogenesis-regulating capacity. The discovery of these populations will translate into a better understanding of the involvement of capillary phenotypes and their communications in lung disease pathogenesis.
Collapse
|
16
|
Wang JQ, Gao MY, Gao R, Zhao KH, Zhang Y, Li X. Oligodendrocyte lineage cells: Advances in development, disease, and heterogeneity. J Neurochem 2023; 164:468-480. [PMID: 36415921 DOI: 10.1111/jnc.15728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 11/03/2022] [Accepted: 11/13/2022] [Indexed: 11/24/2022]
Abstract
Oligodendrocyte progenitor cells (OPCs) originate in the ventricular zone (VZ) of the brain and spinal cord, and their primary function is to differentiate into oligodendrocytes (OLs). Studies have shown that OPCs and OLs are pathologically and physiologically heterogeneous. Previous transcriptome analyses used Bulk RNA-seq, which compares average gene expression in cells and does not allow for heterogeneity. In recent years, the development of single-cell sequencing (scRNA-seq) and single-cell nuclear sequencing (snRNA-seq) has allowed us to study an individual cell. In this review, sc/snRNA-seq was used to study the different subpopulations of OL lineage cells, their developmental trajectories, and their applications in related diseases. These techniques can distinguish different subpopulations of cells, and identify differentially expressed genes in particular cell types under certain conditions, such as treatment or disease. It is of great significance to the study of the occurrence, prevention, and treatment of various diseases.
Collapse
Affiliation(s)
- Jia-Qi Wang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Meng-Yuan Gao
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Rui Gao
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Ke-Han Zhao
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yuan Zhang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Xing Li
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, China
| |
Collapse
|
17
|
Big Data in Gastroenterology Research. Int J Mol Sci 2023; 24:ijms24032458. [PMID: 36768780 PMCID: PMC9916510 DOI: 10.3390/ijms24032458] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 01/28/2023] Open
Abstract
Studying individual data types in isolation provides only limited and incomplete answers to complex biological questions and particularly falls short in revealing sufficient mechanistic and kinetic details. In contrast, multi-omics approaches to studying health and disease permit the generation and integration of multiple data types on a much larger scale, offering a comprehensive picture of biological and disease processes. Gastroenterology and hepatobiliary research are particularly well-suited to such analyses, given the unique position of the luminal gastrointestinal (GI) tract at the nexus between the gut (mucosa and luminal contents), brain, immune and endocrine systems, and GI microbiome. The generation of 'big data' from multi-omic, multi-site studies can enhance investigations into the connections between these organ systems and organisms and more broadly and accurately appraise the effects of dietary, pharmacological, and other therapeutic interventions. In this review, we describe a variety of useful omics approaches and how they can be integrated to provide a holistic depiction of the human and microbial genetic and proteomic changes underlying physiological and pathophysiological phenomena. We highlight the potential pitfalls and alternatives to help avoid the common errors in study design, execution, and analysis. We focus on the application, integration, and analysis of big data in gastroenterology and hepatobiliary research.
Collapse
|
18
|
Kong S, Li R, Tian Y, Zhang Y, Lu Y, Ou Q, Gao P, Li K, Zhang Y. Single-cell omics: A new direction for functional genetic research in human diseases and animal models. Front Genet 2023; 13:1100016. [PMID: 36685871 PMCID: PMC9846559 DOI: 10.3389/fgene.2022.1100016] [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: 11/16/2022] [Accepted: 12/16/2022] [Indexed: 01/06/2023] Open
Abstract
Over the past decade, with the development of high-throughput single-cell sequencing technology, single-cell omics has been emerged as a powerful tool to understand the molecular basis of cellular mechanisms and refine our knowledge of diverse cell states. They can reveal the heterogeneity at different genetic layers and elucidate their associations by multiple omics analysis, providing a more comprehensive genetic map of biological regulatory networks. In the post-GWAS era, the molecular biological mechanisms influencing human diseases will be further elucidated by single-cell omics. This review mainly summarizes the development and trend of single-cell omics. This involves single-cell omics technologies, single-cell multi-omics technologies, multiple omics data integration methods, applications in various human organs and diseases, classic laboratory cell lines, and animal disease models. The review will reveal some perspectives for elucidating human diseases and constructing animal models.
Collapse
Affiliation(s)
- Siyuan Kong
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China,*Correspondence: Siyuan Kong, ; Yubo Zhang,
| | - Rongrong Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yunhan Tian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China,College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Yaqiu Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yuhui Lu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Qiaoer Ou
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Peiwen Gao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Kui Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yubo Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China,College of Life Science and Engineering, Foshan University, Foshan, China,*Correspondence: Siyuan Kong, ; Yubo Zhang,
| |
Collapse
|
19
|
Levesque MV, Hla T. Signal Transduction and Gene Regulation in the Endothelium. Cold Spring Harb Perspect Med 2023; 13:cshperspect.a041153. [PMID: 35667710 PMCID: PMC9722983 DOI: 10.1101/cshperspect.a041153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Extracellular signals act on G-protein-coupled receptors (GPCRs) to regulate homeostasis and adapt to stress. This involves rapid intracellular post-translational responses and long-lasting gene-expression changes that ultimately determine cellular phenotype and fate changes. The lipid mediator sphingosine 1-phosphate (S1P) and its receptors (S1PRs) are examples of well-studied GPCR signaling axis essential for vascular development, homeostasis, and diseases. The biochemical cascades involved in rapid S1P signaling are well understood. However, gene-expression regulation by S1PRs are less understood. In this review, we focus our attention to how S1PRs regulate nuclear chromatin changes and gene transcription to modulate vascular and lymphatic endothelial phenotypic changes during embryonic development and adult homeostasis. Because S1PR-targeted drugs approved for use in the treatment of autoimmune diseases cause substantial vascular-related adverse events, these findings are critical not only for general understanding of stimulus-evoked gene regulation in the vascular endothelium, but also for therapeutic development of drugs for autoimmune and perhaps vascular diseases.
Collapse
|
20
|
Pavan RR, Diniz F, El-Dahr S, Tortelote GG. Gene length is a pivotal feature to explain disparities in transcript capture between single transcriptome techniques. FRONTIERS IN BIOINFORMATICS 2023; 3:1144266. [PMID: 37122996 PMCID: PMC10132733 DOI: 10.3389/fbinf.2023.1144266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 04/04/2023] [Indexed: 05/02/2023] Open
Abstract
The scale and capability of single-cell and single-nucleus RNA-sequencing technologies are rapidly growing, enabling key discoveries and large-scale cell mapping operations. However, studies directly comparing technical differences between single-cell and single-nucleus RNA sequencing are still lacking. Here, we compared three paired single-cell and single-nucleus transcriptomes from three different organs (Heart, Lung and Kidney). Differently from previous studies that focused on cell classification, we explored disparities in the transcriptome output of whole cells relative to the nucleus. We found that the major cell clusters could be recovered by either technique from matched samples, but at different proportions. In 2/3 datasets (kidney and lung) we detected clusters exclusively present with single-nucleus RNA sequencing. In all three organ groups, we found that genomic and gene structural characteristics such as gene length and exon content significantly differed between the two techniques. Genes recovered with the single-nucleus RNA sequencing technique had longer sequence lengths and larger exon counts, whereas single-cell RNA sequencing captured short genes at higher rates. Furthermore, we found that when compared to the whole host genome (mouse for kidney and lung datasets and human for the heart dataset), single transcriptomes obtained with either technique skewed from the expected proportions in several points: a) coding sequence length, b) transcript length and c) genomic span; and d) distribution of genes based on exons counts. Interestingly, the top-100 DEG between the two techniques returned distinctive GO terms. Hence, the type of single transcriptome technique used affected the outcome of downstream analysis. In summary, our data revealed both techniques present disparities in RNA capture. Moreover, the biased RNA capture affected the calculations of basic cellular parameters, raising pivotal points about the limitations and advantages of either single transcriptome techniques.
Collapse
Affiliation(s)
- Ricardo R. Pavan
- Institute for Marine and Antarctic Studies (IMAS), Nubeena Crescent, Taroona, TAS, Australia
| | - Fabiola Diniz
- Section of Pediatric Nephrology, Department of Pediatrics Tulane University School of Medicine, New Orleans, LA, United States
| | - Samir El-Dahr
- Section of Pediatric Nephrology, Department of Pediatrics Tulane University School of Medicine, New Orleans, LA, United States
| | - Giovane G. Tortelote
- Section of Pediatric Nephrology, Department of Pediatrics Tulane University School of Medicine, New Orleans, LA, United States
- *Correspondence: Giovane G. Tortelote,
| |
Collapse
|
21
|
Liu J, Tran V, Vemuri VNP, Byrne A, Borja M, Kim YJ, Agarwal S, Wang R, Awayan K, Murti A, Taychameekiatchai A, Wang B, Emanuel G, He J, Haliburton J, Oliveira Pisco A, Neff NF. Concordance of MERFISH spatial transcriptomics with bulk and single-cell RNA sequencing. Life Sci Alliance 2022; 6:6/1/e202201701. [PMID: 36526371 PMCID: PMC9760489 DOI: 10.26508/lsa.202201701] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 12/23/2022] Open
Abstract
Spatial transcriptomics extends single-cell RNA sequencing (scRNA-seq) by providing spatial context for cell type identification and analysis. Imaging-based spatial technologies such as multiplexed error-robust fluorescence in situ hybridization (MERFISH) can achieve single-cell resolution, directly mapping single-cell identities to spatial positions. MERFISH produces a different data type than scRNA-seq, and a technical comparison between the two modalities is necessary to ascertain how to best integrate them. We performed MERFISH on the mouse liver and kidney and compared the resulting bulk and single-cell RNA statistics with those from the Tabula Muris Senis cell atlas and from two Visium datasets. MERFISH quantitatively reproduced the bulk RNA-seq and scRNA-seq results with improvements in overall dropout rates and sensitivity. Finally, we found that MERFISH independently resolved distinct cell types and spatial structure in both the liver and kidney. Computational integration with the Tabula Muris Senis atlas did not enhance these results. We conclude that MERFISH provides a quantitatively comparable method for single-cell gene expression and can identify cell types without the need for computational integration with scRNA-seq atlases.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Ruofan Wang
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Kyle Awayan
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Abhishek Murti
- School of Medicine, University of California, San Francisco, CA, USA
| | | | - Bruce Wang
- School of Medicine, University of California, San Francisco, CA, USA
| | | | | | | | | | | |
Collapse
|
22
|
Hu X, Wu M, Ma T, Zhang Y, Zou C, Wang R, Zhang Y, Ren Y, Li Q, Liu H, Li H, Wang T, Sun X, Yang Y, Tang M, Li X, Li J, Gao X, Li T, Zhou X. Single-cell transcriptomics reveals distinct cell response between acute and chronic pulmonary infection of Pseudomonas aeruginosa. MedComm (Beijing) 2022; 3:e193. [PMID: 36514779 PMCID: PMC9732387 DOI: 10.1002/mco2.193] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/31/2022] [Accepted: 11/09/2022] [Indexed: 12/14/2022] Open
Abstract
Knowledge of the changes in the immune microenvironment during pulmonary bacterial acute and chronic infections is limited. The dissection of immune system may provide a basis for effective therapeutic strategies against bacterial infection. Here, we describe a single immune cell atlas of mouse lungs after acute and chronic Pseudomonas aeruginosa infection using single-cell transcriptomics, multiplex immunohistochemistry, and flow cytometry. Our single-cell transcriptomic analysis revealed large-scale comprehensive changes in immune cell composition and high variation in cell-cell interactions after acute and chronic P. aeruginosa infection. Bacterial infection reprograms the genetic architecture of immune cell populations. We identified specific immune cell types, including Cxcl2+ B cells and interstitial macrophages, in response to acute and chronic infection, such as their proportions, distribution, and functional status. Importantly, the patterns of immune cell response are drastically different between acute and chronic infection models. The distinct molecular signatures highlight the importance of the highly dynamic cell-cell interaction process in different pathological conditions, which has not been completely revealed previously. These findings provide a comprehensive and unbiased immune cellular landscape for respiratory pathogenesis in mice, enabling further understanding of immunologic mechanisms in infection and inflammatory diseases.
Collapse
Affiliation(s)
- Xueli Hu
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Mingbo Wu
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Teng Ma
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Yige Zhang
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Chaoyu Zou
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Ruihuan Wang
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Yongxin Zhang
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Yuan Ren
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina,State Key Laboratory of Oral DiseasesNational Clinical Research Center for Oral DiseasesChinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and ManagementWest China Hospital of StomatologySichuan UniversityChengduChina
| | - Qianqian Li
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Huan Liu
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Heyue Li
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Taolin Wang
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Xiaolong Sun
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Yang Yang
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Miao Tang
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Xuefeng Li
- Department of Radiation OncologyThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Jing Li
- State Key Laboratory of Oral DiseasesNational Clinical Research Center for Oral DiseasesChinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and ManagementWest China Hospital of StomatologySichuan UniversityChengduChina
| | - Xiang Gao
- Department of Neurosurgery and Institute of NeurosurgeryState Key Laboratory of Biotherapy and Cancer CenterWest China HospitalWest China Medical SchoolSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Taiwen Li
- State Key Laboratory of Oral DiseasesNational Clinical Research Center for Oral DiseasesChinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and ManagementWest China Hospital of StomatologySichuan UniversityChengduChina
| | - Xikun Zhou
- State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| |
Collapse
|
23
|
Overbey EG, Das S, Cope H, Madrigal P, Andrusivova Z, Frapard S, Klotz R, Bezdan D, Gupta A, Scott RT, Park J, Chirko D, Galazka JM, Costes SV, Mason CE, Herranz R, Szewczyk NJ, Borg J, Giacomello S. Challenges and considerations for single-cell and spatially resolved transcriptomics sample collection during spaceflight. CELL REPORTS METHODS 2022; 2:100325. [PMID: 36452864 PMCID: PMC9701605 DOI: 10.1016/j.crmeth.2022.100325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) and spatially resolved transcriptomics (SRT) have experienced rapid development in recent years. The findings of spaceflight-based scRNA-seq and SRT investigations are likely to improve our understanding of life in space and our comprehension of gene expression in various cell systems and tissue dynamics. However, compared to their Earth-based counterparts, gene expression experiments conducted in spaceflight have not experienced the same pace of development. Out of the hundreds of spaceflight gene expression datasets available, only a few used scRNA-seq and SRT. In this perspective piece, we explore the growing importance of scRNA-seq and SRT in space biology and discuss the challenges and considerations relevant to robust experimental design to enable growth of these methods in the field.
Collapse
Affiliation(s)
- Eliah G. Overbey
- Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, New York, NY, USA
| | - Saswati Das
- Department of Biochemistry, Atal Bihari Vajpayee Institute of Medical Sciences & Dr. Ram Manohar Lohia Hospital, New Delhi, India
| | - Henry Cope
- School of Medicine, University of Nottingham, Derby DE22 3DT, UK
| | - Pedro Madrigal
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Zaneta Andrusivova
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Solène Frapard
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Rebecca Klotz
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Daniela Bezdan
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen 72076, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, German
- yuri GmbH, Meckenbeuren, Germany
| | | | - Ryan T. Scott
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | | | | | - Jonathan M. Galazka
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Sylvain V. Costes
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Christopher E. Mason
- Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, New York, NY, USA
| | - Raul Herranz
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid 28040, Spain
| | - Nathaniel J. Szewczyk
- School of Medicine, University of Nottingham, Derby DE22 3DT, UK
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701, USA
| | - Joseph Borg
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta
| | - Stefania Giacomello
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| |
Collapse
|
24
|
Pennitz P, Kirsten H, Friedrich VD, Wyler E, Goekeri C, Obermayer B, Heinz GA, Mashreghi MF, Büttner M, Trimpert J, Landthaler M, Suttorp N, Hocke AC, Hippenstiel S, Tönnies M, Scholz M, Kuebler WM, Witzenrath M, Hoenzke K, Nouailles G. A pulmonologist's guide to perform and analyse cross-species single lung cell transcriptomics. Eur Respir Rev 2022; 31:31/165/220056. [PMID: 35896273 DOI: 10.1183/16000617.0056-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/16/2022] [Indexed: 11/05/2022] Open
Abstract
Single-cell ribonucleic acid sequencing is becoming widely employed to study biological processes at a novel resolution depth. The ability to analyse transcriptomes of multiple heterogeneous cell types in parallel is especially valuable for cell-focused lung research where a variety of resident and recruited cells are essential for maintaining organ functionality. We compared the single-cell transcriptomes from publicly available and unpublished datasets of the lungs in six different species: human (Homo sapiens), African green monkey (Chlorocebus sabaeus), pig (Sus domesticus), hamster (Mesocricetus auratus), rat (Rattus norvegicus) and mouse (Mus musculus) by employing RNA velocity and intercellular communication based on ligand-receptor co-expression, among other techniques. Specifically, we demonstrated a workflow for interspecies data integration, applied a single unified gene nomenclature, performed cell-specific clustering and identified marker genes for each species. Overall, integrative approaches combining newly sequenced as well as publicly available datasets could help identify species-specific transcriptomic signatures in both healthy and diseased lung tissue and select appropriate models for future respiratory research.
Collapse
Affiliation(s)
- Peter Pennitz
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany.,Both authors contributed equally to this work
| | - Holger Kirsten
- University of Leipzig, Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig, Germany.,Both authors contributed equally to this work
| | - Vincent D Friedrich
- University of Leipzig, Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig, Germany.,Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI), Leipzig, Germany
| | - Emanuel Wyler
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Cengiz Goekeri
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany.,Cyprus International University, Faculty of Medicine, Nicosia, Cyprus
| | - Benedikt Obermayer
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Core Unit Bioinformatics, Berlin, Germany
| | - Gitta A Heinz
- Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), A Leibniz Institute, Therapeutic Gene Regulation, Berlin, Germany
| | - Mir-Farzin Mashreghi
- Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), A Leibniz Institute, Therapeutic Gene Regulation, Berlin, Germany.,Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), Berlin, Germany
| | - Maren Büttner
- University of Bonn, Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, Bonn, Germany.,Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Systems Medicine, Bonn, Germany
| | - Jakob Trimpert
- Freie Universität Berlin, Institute of Virology, Berlin, Germany
| | - Markus Landthaler
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.,Humboldt-Universität zu Berlin, Institute for Biology, IRI Life Sciences, Berlin, Germany
| | - Norbert Suttorp
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Andreas C Hocke
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Stefan Hippenstiel
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Mario Tönnies
- HELIOS Clinic Emil von Behring, Department of Pneumology and Department of Thoracic Surgery, Chest Hospital Heckeshorn, Berlin, Germany
| | - Markus Scholz
- University of Leipzig, Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig, Germany
| | - Wolfgang M Kuebler
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Physiology, Berlin, Germany.,German Center for Lung Research (DZL), Berlin, Germany
| | - Martin Witzenrath
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany.,German Center for Lung Research (DZL), Berlin, Germany
| | - Katja Hoenzke
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Geraldine Nouailles
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| |
Collapse
|
25
|
TAS-Seq is a robust and sensitive amplification method for bead-based scRNA-seq. Commun Biol 2022; 5:602. [PMID: 35760847 PMCID: PMC9245575 DOI: 10.1038/s42003-022-03536-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 05/27/2022] [Indexed: 12/22/2022] Open
Abstract
Single-cell RNA-sequencing (scRNA-seq) is valuable for analyzing cellular heterogeneity. Cell composition accuracy is critical for analyzing cell–cell interaction networks from scRNA-seq data. However, droplet- and plate-based scRNA-seq techniques have cell sampling bias that could affect the cell composition of scRNA-seq datasets. Here we developed terminator-assisted solid-phase cDNA amplification and sequencing (TAS-Seq) for scRNA-seq based on a terminator, terminal transferase, and nanowell/bead-based scRNA-seq platform. TAS-Seq showed high tolerance to variations in the terminal transferase reaction, which complicate the handling of existing terminal transferase-based scRNA-seq methods. In murine and human lung samples, TAS-Seq yielded scRNA-seq data that were highly correlated with flow-cytometric data, showing higher gene-detection sensitivity and more robust detection of important cell–cell interactions and expression of growth factors/interleukins in cell subsets than 10X Chromium v2 and Smart-seq2. Expanding TAS-Seq application will improve understanding and atlas construction of lung biology at the single-cell level. Terminator-assisted solid-phase cDNA amplification and sequencing (TASseq) uses a terminator, terminal transferase and bead-based platform to improve generation of single-cell RNA-seq libraries.
Collapse
|
26
|
Lendahl U, Muhl L, Betsholtz C. Identification, discrimination and heterogeneity of fibroblasts. Nat Commun 2022; 13:3409. [PMID: 35701396 PMCID: PMC9192344 DOI: 10.1038/s41467-022-30633-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 05/04/2022] [Indexed: 12/14/2022] Open
Abstract
Fibroblasts, the principal cell type of connective tissue, secrete extracellular matrix components during tissue development, homeostasis, repair and disease. Despite this crucial role, the identification and distinction of fibroblasts from other cell types are challenging and laden with caveats. Rapid progress in single-cell transcriptomics now yields detailed molecular portraits of fibroblasts and other cell types in our bodies, which complement and enrich classical histological and immunological descriptions, improve cell class definitions and guide further studies on the functional heterogeneity of cell subtypes and states, origins and fates in physiological and pathological processes. In this review, we summarize and discuss recent advances in the understanding of fibroblast identification and heterogeneity and how they discriminate from other cell types. In this review, the authors look at how recent progress in single-cell transcriptomics complement and enrich the classical, largely morphological, portraits of fibroblasts. The detailed molecular information now available provides new insights into fibroblast identity, heterogeneity and function.
Collapse
Affiliation(s)
- Urban Lendahl
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77, Stockholm, Sweden.,Department of Neurobiology, Care sciences and Society, Karolinska Institutet, SE-14183, Huddinge, Sweden
| | - Lars Muhl
- Department of Medicine, Huddinge, Karolinska Institutet, Blickagången 16, SE-141 57, Huddinge, Sweden
| | - Christer Betsholtz
- Department of Medicine, Huddinge, Karolinska Institutet, Blickagången 16, SE-141 57, Huddinge, Sweden. .,Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Dag Hammarskjölds väg 20, SE-751 85, Uppsala, Sweden.
| |
Collapse
|
27
|
Wong BH, Mei D, Chua GL, Galam DL, Wenk MR, Torta F, Silver DL. The lipid transporter Mfsd2a maintains pulmonary surfactant homeostasis. J Biol Chem 2022; 298:101709. [PMID: 35150739 PMCID: PMC8914330 DOI: 10.1016/j.jbc.2022.101709] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 11/18/2022] Open
Abstract
Pulmonary surfactant is a lipoprotein complex essential for lung function, and insufficiency or altered surfactant composition is associated with major lung diseases, such as acute respiratory distress syndromes, idiopathic pulmonary fibrosis, and chronic obstructive pulmonary disease. Pulmonary surfactant is primarily composed of phosphatidylcholine (PC) in complex with specialized surfactant proteins and secreted by alveolar type 2 (AT2) cells. Surfactant homeostasis on the alveolar surface is balanced by the rates of synthesis and secretion with reuptake and recycling by AT2 cells, with some degradation by pulmonary macrophages and loss up the bronchial tree. However, whether phospholipid (PL) transporters exist in AT2 cells to mediate reuptake of surfactant PL remains to be identified. Here, we demonstrate that major facilitator superfamily domain containing 2a (Mfsd2a), a sodium-dependent lysophosphatidylcholine (LPC) transporter, is expressed at the apical surface of AT2 cells. A mouse model with inducible AT2 cell–specific deficiency of Mfsd2a exhibited AT2 cell hypertrophy with reduced total surfactant PL levels because of reductions in the most abundant surfactants, PC containing dipalmitic acid, and PC species containing the omega-3 fatty acid docosahexaenoic acid. These changes in surfactant levels and composition were mirrored by similar changes in the AT2 cell lipidome. Mechanistically, direct tracheal instillation of fluorescent LPC and PC probes indicated that Mfsd2a mediates the uptake of LPC generated by pulmonary phospholipase activity in the alveolar space. These studies reveal that Mfsd2a-mediated LPC uptake is quantitatively important in maintaining surfactant homeostasis and identify this lipid transporter as a physiological component of surfactant recycling.
Collapse
Affiliation(s)
- Bernice H Wong
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Ding Mei
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Geok Lin Chua
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Dwight L Galam
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Markus R Wenk
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Federico Torta
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - David L Silver
- Signature Research Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore.
| |
Collapse
|
28
|
Tran E, Shi T, Li X, Chowdhury AY, Jiang D, Liu Y, Wang H, Yan C, Wallace WD, Lu R, Ryan AL, Marconett CN, Zhou B, Borok Z, Offringa IA. Development of human alveolar epithelial cell models to study distal lung biology and disease. iScience 2022; 25:103780. [PMID: 35169685 PMCID: PMC8829779 DOI: 10.1016/j.isci.2022.103780] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 10/27/2021] [Accepted: 01/12/2022] [Indexed: 11/25/2022] Open
Abstract
Many acute and chronic diseases affect the distal lung alveoli. Alveolar epithelial cell (AEC) lines are needed to better model these diseases. We used de-identified human remnant transplant lungs to develop a method to establish AEC lines. The lines grow well in 2-dimensional (2D) culture as epithelial monolayers expressing lung progenitor markers. In 3-dimensional (3D) culture with fibroblasts, Matrigel, and specific media conditions, the cells form alveolar-like organoids expressing mature AEC markers including aquaporin 5 (AQP5), G-protein-coupled receptor class C group 5 member A (GPRC5A), and surface marker HTII280. Single-cell RNA sequencing of an AEC line in 2D versus 3D culture revealed increased cellular heterogeneity and induction of cytokine and lipoprotein signaling in 3D organoids. Our approach yields lung progenitor lines that retain the ability to differentiate along the alveolar cell lineage despite long-term expansion and provides a valuable system to model and study the distal lung in vitro.
Collapse
Affiliation(s)
- Evelyn Tran
- Department of Surgery, Keck School of Medicine, University of Southern California (USC), Los Angeles, CA 90033, USA
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
| | - Tuo Shi
- Department of Surgery, Keck School of Medicine, University of Southern California (USC), Los Angeles, CA 90033, USA
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
| | - Xiuwen Li
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
- Department of Translational Genomics, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
| | - Adnan Y. Chowdhury
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
| | - Du Jiang
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
| | - Yixin Liu
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
| | - Hongjun Wang
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
| | - Chunli Yan
- Department of Surgery, Keck School of Medicine, University of Southern California (USC), Los Angeles, CA 90033, USA
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
| | - William D. Wallace
- Department of Pathology, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
| | - Rong Lu
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
| | - Amy L. Ryan
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
| | - Crystal N. Marconett
- Department of Surgery, Keck School of Medicine, University of Southern California (USC), Los Angeles, CA 90033, USA
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
| | - Beiyun Zhou
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
| | - Zea Borok
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ite A. Offringa
- Department of Surgery, Keck School of Medicine, University of Southern California (USC), Los Angeles, CA 90033, USA
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, USC, Los Angeles, CA 90033, USA
| |
Collapse
|
29
|
Gifre-Renom L, Daems M, Luttun A, Jones EAV. Organ-Specific Endothelial Cell Differentiation and Impact of Microenvironmental Cues on Endothelial Heterogeneity. Int J Mol Sci 2022; 23:ijms23031477. [PMID: 35163400 PMCID: PMC8836165 DOI: 10.3390/ijms23031477] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/14/2022] [Accepted: 01/19/2022] [Indexed: 02/04/2023] Open
Abstract
Endothelial cells throughout the body are heterogeneous, and this is tightly linked to the specific functions of organs and tissues. Heterogeneity is already determined from development onwards and ranges from arterial/venous specification to microvascular fate determination in organ-specific differentiation. Acknowledging the different phenotypes of endothelial cells and the implications of this diversity is key for the development of more specialized tissue engineering and vascular repair approaches. However, although novel technologies in transcriptomics and proteomics are facilitating the unraveling of vascular bed-specific endothelial cell signatures, still much research is based on the use of insufficiently specialized endothelial cells. Endothelial cells are not only heterogeneous, but their specialized phenotypes are also dynamic and adapt to changes in their microenvironment. During the last decades, strong collaborations between molecular biology, mechanobiology, and computational disciplines have led to a better understanding of how endothelial cells are modulated by their mechanical and biochemical contexts. Yet, because of the use of insufficiently specialized endothelial cells, there is still a huge lack of knowledge in how tissue-specific biomechanical factors determine organ-specific phenotypes. With this review, we want to put the focus on how organ-specific endothelial cell signatures are determined from development onwards and conditioned by their microenvironments during adulthood. We discuss the latest research performed on endothelial cells, pointing out the important implications of mimicking tissue-specific biomechanical cues in culture.
Collapse
Affiliation(s)
- Laia Gifre-Renom
- Centre for Molecular and Vascular Biology, Department of Cardiovascular Sciences, Katholieke Universiteit Leuven (KU Leuven), BE-3000 Leuven, Belgium; (L.G.-R.); (M.D.); (A.L.)
| | - Margo Daems
- Centre for Molecular and Vascular Biology, Department of Cardiovascular Sciences, Katholieke Universiteit Leuven (KU Leuven), BE-3000 Leuven, Belgium; (L.G.-R.); (M.D.); (A.L.)
| | - Aernout Luttun
- Centre for Molecular and Vascular Biology, Department of Cardiovascular Sciences, Katholieke Universiteit Leuven (KU Leuven), BE-3000 Leuven, Belgium; (L.G.-R.); (M.D.); (A.L.)
| | - Elizabeth A. V. Jones
- Centre for Molecular and Vascular Biology, Department of Cardiovascular Sciences, Katholieke Universiteit Leuven (KU Leuven), BE-3000 Leuven, Belgium; (L.G.-R.); (M.D.); (A.L.)
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, 6229 ER Maastricht, The Netherlands
- Correspondence:
| |
Collapse
|
30
|
Chowdhury S, Hofree M, Lin K, Maru D, Kopetz S, Shen JP. Implications of Intratumor Heterogeneity on Consensus Molecular Subtype (CMS) in Colorectal Cancer. Cancers (Basel) 2021; 13:4923. [PMID: 34638407 PMCID: PMC8507736 DOI: 10.3390/cancers13194923] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 09/21/2021] [Accepted: 09/25/2021] [Indexed: 01/04/2023] Open
Abstract
The implications of intratumor heterogeneity on the four consensus molecular subtypes (CMS) of colorectal cancer (CRC) are not well known. Here, we use single-cell RNA sequencing (scRNASeq) to build an algorithm to assign CMS classification to individual cells, which we use to explore the distributions of CMSs in tumor and non-tumor cells. A dataset of colorectal tumors with bulk RNAseq (n = 3232) was used to identify CMS specific-marker gene sets. These gene sets were then applied to a discovery dataset of scRNASeq profiles (n = 10) to develop an algorithm for single-cell CMS (scCMS) assignment, which recapitulated the intrinsic biology of all four CMSs. The single-cell CMS assignment algorithm was used to explore the scRNASeq profiles of two prospective CRC tumors with mixed CMS via bulk sequencing. We find that every CRC tumor contains individual cells of each scCMS, as well as many individual cells that have enrichment for features of more than one scCMS (called mixed cells). scCMS4 and scCMS1 cells dominate stroma and immune cell clusters, respectively, but account for less than 3% epithelial cells. These data imply that CMS1 and CMS4 are driven by the transcriptomic contribution of immune and stromal cells, respectively, not tumor cells.
Collapse
Affiliation(s)
- Saikat Chowdhury
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Matan Hofree
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Kangyu Lin
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dipen Maru
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John Paul Shen
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| |
Collapse
|
31
|
Richter ML, Deligiannis IK, Yin K, Danese A, Lleshi E, Coupland P, Vallejos CA, Matchett KP, Henderson NC, Colome-Tatche M, Martinez-Jimenez CP. Single-nucleus RNA-seq2 reveals functional crosstalk between liver zonation and ploidy. Nat Commun 2021; 12:4264. [PMID: 34253736 PMCID: PMC8275628 DOI: 10.1038/s41467-021-24543-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 06/24/2021] [Indexed: 12/19/2022] Open
Abstract
Single-cell RNA-seq reveals the role of pathogenic cell populations in development and progression of chronic diseases. In order to expand our knowledge on cellular heterogeneity, we have developed a single-nucleus RNA-seq2 method tailored for the comprehensive analysis of the nuclear transcriptome from frozen tissues, allowing the dissection of all cell types present in the liver, regardless of cell size or cellular fragility. We use this approach to characterize the transcriptional profile of individual hepatocytes with different levels of ploidy, and have discovered that ploidy states are associated with different metabolic potential, and gene expression in tetraploid mononucleated hepatocytes is conditioned by their position within the hepatic lobule. Our work reveals a remarkable crosstalk between gene dosage and spatial distribution of hepatocytes.
Collapse
Affiliation(s)
- M L Richter
- Helmholtz Pioneer Campus (HPC), Helmholtz Zentrum München, Neuherberg, Germany
| | - I K Deligiannis
- Helmholtz Pioneer Campus (HPC), Helmholtz Zentrum München, Neuherberg, Germany
| | - K Yin
- Helmholtz Pioneer Campus (HPC), Helmholtz Zentrum München, Neuherberg, Germany
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, United Kingdom
| | - A Danese
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - E Lleshi
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, United Kingdom
| | - P Coupland
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, United Kingdom
| | - C A Vallejos
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - K P Matchett
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Little France Crescent, Edinburgh, United Kingdom
| | - N C Henderson
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Little France Crescent, Edinburgh, United Kingdom
| | - M Colome-Tatche
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany.
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.
- Biomedical Center (BMC), Physiological Chemistry, Faculty of Medicine, LMU Munich, Munich, Germany.
| | - C P Martinez-Jimenez
- Helmholtz Pioneer Campus (HPC), Helmholtz Zentrum München, Neuherberg, Germany.
- TUM School of Medicine, Technical University of Munich, Munich, Germany.
| |
Collapse
|
32
|
Li H, Humphreys BD. Single Cell Technologies: Beyond Microfluidics. KIDNEY360 2021; 2:1196-1204. [PMID: 35368355 PMCID: PMC8786099 DOI: 10.34067/kid.0001822021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/13/2021] [Indexed: 02/04/2023]
Abstract
Single-cell RNA-sequencing (scRNA-seq) has been widely adopted in recent years due to standardized protocols and automation, reliability, and standardized bioinformatic pipelines. The most widely adopted platform is the 10× Genomics solution. Although powerful, this system is limited by its high cost, moderate throughput, and the inability to customize due to fixed kit components. This study will cover new approaches that do not rely on microfluidics and thus have low entry costs, are highly customizable, and are within the reach of any laboratory possessing molecular biology expertise.
Collapse
Affiliation(s)
| | - Benjamin D. Humphreys
- Division of Nephrology, Washington University in St. Louis School of Medicine, St. Louis, Missouri,Department of Developmental Biology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| |
Collapse
|
33
|
Transcriptomic Changes of Murine Visceral Fat Exposed to Intermittent Hypoxia at Single Cell Resolution. Int J Mol Sci 2020; 22:ijms22010261. [PMID: 33383883 PMCID: PMC7795619 DOI: 10.3390/ijms22010261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 11/22/2020] [Accepted: 12/24/2020] [Indexed: 12/12/2022] Open
Abstract
Intermittent hypoxia (IH) is a hallmark of obstructive sleep apnea (OSA) and induces metabolic dysfunction manifesting as inflammation, increased lipolysis and insulin resistance in visceral white adipose tissues (vWAT). However, the cell types and their corresponding transcriptional pathways underlying these functional perturbations are unknown. Here, we applied single nucleus RNA sequencing (snRNA-seq) coupled with aggregate RNA-seq methods to evaluate the cellular heterogeneity in vWAT following IH exposures mimicking OSA. C57BL/6 male mice were exposed to IH and room air (RA) for 6 weeks, and nuclei from vWAT were isolated and processed for snRNA-seq followed by differential expressed gene (DEGs) analyses by cell type, along with gene ontology and canonical pathways enrichment tests of significance. IH induced significant transcriptional changes compared to RA across 14 different cell types identified in vWAT. We identified cell-specific signature markers, transcriptional networks, metabolic signaling pathways, and cellular subpopulation enrichment in vWAT. Globally, we also identify 298 common regulated genes across multiple cellular types that are associated with metabolic pathways. Deconvolution of cell types in vWAT using global RNA-seq revealed that distinct adipocytes appear to be differentially implicated in key aspects of metabolic dysfunction. Thus, the heterogeneity of vWAT and its response to IH at the cellular level provides important insights into the metabolic morbidity of OSA and may possibly translate into therapeutic targets.
Collapse
|
34
|
Horie M, Castaldi A, Sunohara M, Wang H, Ji Y, Liu Y, Li F, Wilkinson TA, Hung L, Shen H, Kage H, Offringa IA, Marconett CN, Flodby P, Zhou B, Borok Z. Integrated Single-Cell RNA-Sequencing Analysis of Aquaporin 5-Expressing Mouse Lung Epithelial Cells Identifies GPRC5A as a Novel Validated Type I Cell Surface Marker. Cells 2020; 9:cells9112460. [PMID: 33187367 PMCID: PMC7697677 DOI: 10.3390/cells9112460] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 10/30/2020] [Accepted: 11/05/2020] [Indexed: 12/01/2022] Open
Abstract
Molecular and functional characterization of alveolar epithelial type I (AT1) cells has been challenging due to difficulty in isolating sufficient numbers of viable cells. Here we performed single-cell RNA-sequencing (scRNA-seq) of tdTomato+ cells from lungs of AT1 cell-specific Aqp5-Cre-IRES-DsRed (ACID);R26tdTomato reporter mice. Following enzymatic digestion, CD31-CD45-E-cadherin+tdTomato+ cells were subjected to fluorescence-activated cell sorting (FACS) followed by scRNA-seq. Cell identity was confirmed by immunofluorescence using cell type-specific antibodies. After quality control, 92 cells were analyzed. Most cells expressed ‘conventional’ AT1 cell markers (Aqp5, Pdpn, Hopx, Ager), with heterogeneous expression within this population. The remaining cells expressed AT2, club, basal or ciliated cell markers. Integration with public datasets identified three robust AT1 cell- and lung-enriched genes, Ager, Rtkn2 and Gprc5a, that were conserved across species. GPRC5A co-localized with HOPX and was not expressed in AT2 or airway cells in mouse, rat and human lung. GPRC5A co-localized with AQP5 but not pro-SPC or CC10 in mouse lung epithelial cell cytospins. We enriched mouse AT1 cells to perform molecular phenotyping using scRNA-seq. Further characterization of putative AT1 cell-enriched genes revealed GPRC5A as a conserved AT1 cell surface marker that may be useful for AT1 cell isolation.
Collapse
Affiliation(s)
- Masafumi Horie
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (M.H.); (A.C.); (M.S.); (H.W.); (Y.J.); (Y.L.); (H.S.); (P.F.); (B.Z.)
| | - Alessandra Castaldi
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (M.H.); (A.C.); (M.S.); (H.W.); (Y.J.); (Y.L.); (H.S.); (P.F.); (B.Z.)
| | - Mitsuhiro Sunohara
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (M.H.); (A.C.); (M.S.); (H.W.); (Y.J.); (Y.L.); (H.S.); (P.F.); (B.Z.)
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan;
- Division for Health Service Promotion, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hongjun Wang
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (M.H.); (A.C.); (M.S.); (H.W.); (Y.J.); (Y.L.); (H.S.); (P.F.); (B.Z.)
| | - Yanbin Ji
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (M.H.); (A.C.); (M.S.); (H.W.); (Y.J.); (Y.L.); (H.S.); (P.F.); (B.Z.)
| | - Yixin Liu
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (M.H.); (A.C.); (M.S.); (H.W.); (Y.J.); (Y.L.); (H.S.); (P.F.); (B.Z.)
| | - Fan Li
- Single-Cell, Sequencing, and CyTOF Core (SC2), Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (F.L.); (T.A.W.); (L.H.)
| | - Thomas A. Wilkinson
- Single-Cell, Sequencing, and CyTOF Core (SC2), Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (F.L.); (T.A.W.); (L.H.)
| | - Long Hung
- Single-Cell, Sequencing, and CyTOF Core (SC2), Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (F.L.); (T.A.W.); (L.H.)
| | - Hua Shen
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (M.H.); (A.C.); (M.S.); (H.W.); (Y.J.); (Y.L.); (H.S.); (P.F.); (B.Z.)
| | - Hidenori Kage
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan;
| | - Ite A. Offringa
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (I.A.O.); (C.N.M.)
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Crystal N. Marconett
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (I.A.O.); (C.N.M.)
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Per Flodby
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (M.H.); (A.C.); (M.S.); (H.W.); (Y.J.); (Y.L.); (H.S.); (P.F.); (B.Z.)
| | - Beiyun Zhou
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (M.H.); (A.C.); (M.S.); (H.W.); (Y.J.); (Y.L.); (H.S.); (P.F.); (B.Z.)
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Zea Borok
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (M.H.); (A.C.); (M.S.); (H.W.); (Y.J.); (Y.L.); (H.S.); (P.F.); (B.Z.)
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Correspondence: ; Tel.: +323-409-7184; Fax: +323-226-2738
| |
Collapse
|