scholarly journals Understanding human gut diseases at single-cell resolution

2020 ◽  
Vol 29 (R1) ◽  
pp. R51-R58 ◽  
Author(s):  
Emilia Bigaeva ◽  
Werna T C Uniken Venema ◽  
Rinse K Weersma ◽  
Eleonora A M Festen
Keyword(s):  
Single Cell ◽  
Digestive System ◽  
Cell Types ◽  
Specific Cell ◽  
Human Gut ◽  
The Past ◽  
Distinct Cell ◽  
Transcriptional Variation ◽  
Single Cell Rna Sequencing ◽  
Inflammatory Bowel

Abstract Our understanding of gut functioning and pathophysiology has grown considerably in the past decades, and advancing technologies enable us to deepen this understanding. Single-cell RNA sequencing (scRNA-seq) has opened a new realm of cellular diversity and transcriptional variation in the human gut at a high, single-cell resolution. ScRNA-seq has pushed the science of the digestive system forward by characterizing the function of distinct cell types within complex intestinal cellular environments, by illuminating the heterogeneity within specific cell populations and by identifying novel cell types in the human gut that could contribute to a variety of intestinal diseases. In this review, we highlight recent discoveries made with scRNA-seq that significantly advance our understanding of the human gut both in health and across the spectrum of gut diseases, including inflammatory bowel disease, colorectal carcinoma and celiac disease.

scholarly journals High Resolution Single Cell Maps Reveals Distinct Cell Organization and Function Across Different Regions of the Human Intestine

2021 ◽  
Author(s):  
John W Hickey ◽  
Winston R Becker ◽  
Stephanie A Nevins ◽  
Aaron M Horning ◽  
Almudena Espin Perez ◽  
...  
Keyword(s):  
Single Cell ◽  
Immune Surveillance ◽  
Cell Types ◽  
Open Chromatin ◽  
Specific Cell ◽  
Symbiotic Relationships ◽  
Distinct Cell ◽  
Cell Organization ◽  
Reference Map ◽  
And Function

The colon is a complex organ that promotes digestion, extracts nutrients, participates in immune surveillance, maintains critical symbiotic relationships with microbiota, and affects overall health. To better understand its organization, functions, and its regulation at a single cell level, we performed CODEX multiplexed imaging, as well as single nuclear RNA and open chromatin assays across eight different intestinal sites of four donors. Through systematic analyses we find cell compositions differ dramatically across regions of the intestine, demonstrate the complexity of epithelial subtypes, and find that the same cell types are organized into distinct neighborhoods and communities highlighting distinct immunological niches present in the intestine. We also map gene regulatory differences in these cells suggestive of a regulatory differentiation cascade, and associate intestinal disease heritability with specific cell types. These results describe the complexity of the cell composition, regulation, and organization for this organ, and serve as an important reference map for understanding human biology and disease.

scholarly journals Distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data

2018 ◽  
Author(s):  
Aaron T. L. Lun ◽  
Samantha Riesenfeld ◽  
Tallulah Andrews ◽  
Tomas Gomes ◽  
John C. Marioni ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Real Data ◽  
Cell Types ◽  
Sequencing Data ◽  
Minimum Threshold ◽  
False Discovery ◽  
Distinct Cell ◽  
Single Cell Rna Sequencing ◽  
Unique Molecular Identifier

AbstractDroplet-based single-cell RNA sequencing protocols have dramatically increased the throughput and efficiency of single-cell transcriptomics studies. A key computational challenge when processing these data is to distinguish libraries for real cells from empty droplets. Existing methods for cell calling set a minimum threshold on the total unique molecular identifier (UMI) count for each library, which indiscriminately discards cell libraries with low UMI counts. Here, we describe a new statistical method for calling cells from droplet-based data, based on detecting significant deviations from the expression profile of the ambient solution. Using simulations, we demonstrate that our method has greater power than existing approaches for detecting cell libraries with low UMI counts, while controlling the false discovery rate among detected cells. We also apply our method to real data, where we show that the use of our method results in the retention of distinct cell types that would otherwise have been discarded.

scholarly journals XYZeq: Spatially resolved single-cell RNA sequencing reveals expression heterogeneity in the tumor microenvironment

2021 ◽  
Vol 7 (17) ◽  
pp. eabg4755
Author(s):  
Youjin Lee ◽  
Derek Bogdanoff ◽  
Yutong Wang ◽  
George C. Hartoularos ◽  
Jonathan M. Woo ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Spatial Organization ◽  
Cell Types ◽  
Mouse Tumor ◽  
Spatially Resolved ◽  
Distinct Cell ◽  
Single Cell Rna Sequencing ◽  
A Cell ◽  
Anatomical Space

Single-cell RNA sequencing (scRNA-seq) of tissues has revealed remarkable heterogeneity of cell types and states but does not provide information on the spatial organization of cells. To better understand how individual cells function within an anatomical space, we developed XYZeq, a workflow that encodes spatial metadata into scRNA-seq libraries. We used XYZeq to profile mouse tumor models to capture spatially barcoded transcriptomes from tens of thousands of cells. Analyses of these data revealed the spatial distribution of distinct cell types and a cell migration-associated transcriptomic program in tumor-associated mesenchymal stem cells (MSCs). Furthermore, we identify localized expression of tumor suppressor genes by MSCs that vary with proximity to the tumor core. We demonstrate that XYZeq can be used to map the transcriptome and spatial localization of individual cells in situ to reveal how cell composition and cell states can be affected by location within complex pathological tissue.

scholarly journals Single cell RNA sequencing of theStrongylocentrotus purpuratuslarva reveals the blueprint of major cell types and nervous system of a non-chordate deuterostome

2021 ◽  
Author(s):  
Periklis Paganos ◽  
Danila Voronov ◽  
Jacob Musser ◽  
Detlev Arendt ◽  
Maria I. Arnone
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Sea Urchin ◽  
Regulatory Networks ◽  
Neuronal Cell ◽  
Cell Types ◽  
Molecular Fingerprint ◽  
Distinct Cell ◽  
Single Cell Rna Sequencing ◽  
Cell Diversity

AbstractIdentifying the molecular fingerprint of organismal cell types is key for understanding their function and evolution. Here, we use single cell RNA sequencing (scRNA-seq) to survey the cell types of the sea urchin early pluteus larva, representing an important developmental transition from non-feeding to feeding larva. We identified 21 distinct cell clusters, representing cells of the digestive, skeletal, immune, and nervous systems. Further subclustering of these revealed a highly detailed portrait of cell diversity across the larva, including the identification of 12 distinct neuronal cell types. Moreover, we corroborated co-expression of key regulatory genes previously shown to drive sea urchin gene regulatory networks, and revealed additional domains in which these regulatory networks are likely to function within the larva. Lastly, we recovered a neuronal cell type co-expressingPdx-1andBrn1/2/4, which had previously been shown to share similar gene expression with vertebrate pancreas. Our results extend this finding, revealing twenty transcription factors shared by this population of neurons in sea urchin and vertebrate pancreatic cells. Using differential expression results from Pdx-1 knockdown experiments, we generate a draft of the Pdx-1 regulatory network in these cells, and hypothesize this network was present in an ancestral deuterostome neuron before being co-opted into the pancreas developmental lineage in vertebrates.

scholarly journals Molecular taxonomy of human ocular outflow tissues defined by single cell transcriptomics

2020 ◽  
Author(s):  
Gaurang Patel ◽  
Wen Fury ◽  
Hua Yang ◽  
Maria Gomez-Caraballo ◽  
Yu Bai ◽  
...  
Keyword(s):  
Intraocular Pressure ◽  
Single Cell ◽  
Ocular Hypertension ◽  
Trabecular Meshwork ◽  
Cell Types ◽  
Specific Expression ◽  
Distinct Cell ◽  
Single Cell Rna Sequencing ◽  
Outflow Pathway

ABSTRACTThe conventional outflow pathway is a complex tissue responsible for maintaining intraocular pressure (IOP) homeostasis. The coordinated effort of multiple cells with differing responsibilities ensure healthy outflow function and IOP maintenance. Dysfunction of one or more resident cell type results in ocular hypertension and risk for glaucoma, a leading cause of blindness. In this study, single cell RNA sequencing was performed to generate a comprehensive cell atlas of human conventional outflow tissues. We obtained 17757 genes expression profiles from 8758 cells from eight eyes of four donors representing the outflow cell transcriptome. Upon clustering analysis, 12 distinct cell types were identified, and region-specific expression of candidate genes were mapped in human tissues. Significantly, we identified two distinct expression patterns (myofibroblast and fibroblast) from cells located in the trabecular meshwork (TM), the primary structural component of the conventional outflow pathway. We also located neuron and macrophage signatures in the TM. The second primary component structure, Schlemm’s canal displayed a unique combination of lymphatic/blood vascular gene expression. Other expression clusters corresponded to cells from neighboring tissues, predominantly in the ciliary muscle/scleral spur, which together correspond to the uveoscleral outflow path. Importantly, the utility of our atlas was demonstrated by mapping glaucoma-relevant genes to outflow cell clusters. Our study provides a comprehensive molecular and cellular classification of conventional and unconventional outflow pathway structures responsible for IOP homeostasis.Significance statementOcular hypertension is the primary, and only modifiable risk factor for glaucoma, the leading cause of irreversible blindness. Intraocular pressure is regulated homeostatically by resistance to aqueous humor outflow through an architecturally complex tissue, the conventional/trabecular pathway. In this study, we generated a comprehensive cell atlas of the human trabecular meshwork and neighboring tissues using single cell, RNA sequencing. We identified 12 distinct cell types, and mapped region-specific expression of candidate genes. The utility of our atlas was demonstrated by mapping glaucoma-relevant genes to conventional outflow cell clusters. Our study provides a comprehensive molecular and cellular classification of tissue structures responsible for intraocular pressure homeostasis in health, and dysregulation in disease.

scholarly journals Single-cell Transcriptomics Identify Extensive Heterogeneity in the Cellular Composition of Mouse Achilles Tendons

2019 ◽  
Author(s):  
Andrea J De Micheli ◽  
Jacob B Swanson ◽  
Nathaniel P Disser ◽  
Leandro M Martinez ◽  
Nicholas R Walker ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Types ◽  
Tissue Homeostasis ◽  
Cellular Heterogeneity ◽  
Cell Populations ◽  
Cellular Composition ◽  
Matrix Assembly ◽  
Distinct Cell ◽  
Single Cell Rna Sequencing ◽  
Additional Support

AbstractTendon is a connective tissue that transmits forces between muscles and bones. Cellular heterogeneity is increasingly recognized as an important factor in the biological basis of tissue homeostasis and disease, but little is known about the diversity of cells that populate tendon. Our objective was to explore the heterogeneity of cells in mouse Achilles tendons using single-cell RNA sequencing. We assembled a transcriptomic atlas and identified 11 distinct cell types in tendons, including 3 previously undescribed populations of fibroblasts. Using trajectory inference analysis, we provide additional support for the notion that pericytes are progenitor cells for the fibroblasts that compose adult tendons. We also modeled cell-interactions and identified ligand-receptor pairs involved in tendon homeostasis. Our findings highlight notable heterogeneity between and within tendon cell populations, which may contribute to our understanding of tendon extracellular matrix assembly and maintenance, and inform the design of therapies to treat tendinopathies.

scholarly journals Harnessing Single-Cell RNA Sequencing to Better Understand How Diseased Cells Behave the Way They Do in Cardiovascular Disease

2020 ◽  
Author(s):  
Farwah Iqbal ◽  
Adrien Lupieri ◽  
Masanori Aikawa ◽  
Elena Aikawa
Keyword(s):  
Cardiovascular Disease ◽  
Single Cell ◽  
Rna Sequencing ◽  
Molecular Mechanisms ◽  
Cell Types ◽  
Specific Cell ◽  
Calcific Aortic Valve Disease ◽  
Cardiovascular Tissues ◽  
Single Cell Rna Sequencing ◽  
Cell Phenotypes

The transition of healthy arteries and cardiac valves into dense, cell-rich, calcified, and fibrotic tissues is driven by a complex interplay of both cellular and molecular mechanisms. Specific cell types in these cardiovascular tissues become activated following the exposure to systemic stimuli including circulating lipoproteins or inflammatory mediators. This activation induces multiple cascades of events where changes in cell phenotypes and activation of certain receptors may trigger multiple pathways and specific alterations to the transcriptome. Modifications to the transcriptome and proteome can give rise to pathological cell phenotypes and trigger mechanisms that exacerbate inflammation, proliferation, calcification, and recruitment of resident or distant cells. Accumulating evidence suggests that each cell type involved in vascular and valvular diseases is heterogeneous. Single-cell RNA sequencing is a transforming medical research tool that enables the profiling of the unique fingerprints at single-cell levels. Its applications have allowed the construction of cell atlases including the mammalian heart and tissue vasculature and the discovery of new cell types implicated in cardiovascular disease. Recent advances in single-cell RNA sequencing have facilitated the identification of novel resident cell populations that become activated during disease and has allowed tracing the transition of healthy cells into pathological phenotypes. Furthermore, single-cell RNA sequencing has permitted the characterization of heterogeneous cell subpopulations with unique genetic profiles in healthy and pathological cardiovascular tissues. In this review, we highlight the latest groundbreaking research that has improved our understanding of the pathological mechanisms of atherosclerosis and future directions for calcific aortic valve disease.

scholarly journals Single-cell RNA-sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis

2019 ◽  
Author(s):  
Arun C. Habermann ◽  
Austin J. Gutierrez ◽  
Linh T. Bui ◽  
Stephanie L. Yahn ◽  
Nichelle I. Winters ◽  
...  
Keyword(s):  
Epithelial Cell ◽  
Pulmonary Fibrosis ◽  
Single Cell ◽  
Rna Sequencing ◽  
Cell Types ◽  
Distinct Cell ◽  
Single Cell Rna Sequencing ◽  
Epithelial Remodeling ◽  
Discrete Manner ◽  
Cell Phenotypes

AbstractPulmonary fibrosis is a form of chronic lung disease characterized by pathologic epithelial remodeling and accumulation of extracellular matrix. In order to comprehensively define the cell types, mechanisms and mediators driving fibrotic remodeling in lungs with pulmonary fibrosis, we performed single-cell RNA-sequencing of single-cell suspensions from 10 non-fibrotic control and 20 PF lungs. Analysis of 114,396 cells identified 31 distinct cell types. We report a remarkable shift in epithelial cell phenotypes occurs in the peripheral lung in PF, and identify several previously unrecognized epithelial cell phenotypes including a KRT5−/KRT17+, pathologic ECM-producing epithelial cell population that was highly enriched in PF lungs. Multiple fibroblast subtypes were observed to contribute to ECM expansion in a spatially-discrete manner. Together these data provide high-resolution insights into the complexity and plasticity of the distal lung epithelium in human disease, and indicate a diversity of epithelial and mesenchymal cells contribute to pathologic lung fibrosis.One Sentence SummarySingle-cell RNA-sequencing provides new insights into pathologic epithelial and mesenchymal remodeling in the human lung.

scholarly journals Characterizing smoking-induced transcriptional heterogeneity in the human bronchial epithelium at single-cell resolution

2018 ◽  
Author(s):  
Grant E. Duclos ◽  
Vitor H. Teixeira ◽  
Patrick Autissier ◽  
Yaron B. Gesthalter ◽  
Marjan A. Reinders-Luinge ◽  
...  
Keyword(s):  
Single Cell ◽  
Airway Remodeling ◽  
Bronchial Epithelium ◽  
Cell Types ◽  
Premalignant Lesions ◽  
Specific Cell ◽  
Cell Hyperplasia ◽  
Bronchial Epithelial ◽  
Molecular Alterations ◽  
Distinct Cell

ABSTRACTThe human bronchial epithelium is composed of multiple, distinct cell types that cooperate to perform functions, such as mucociliary clearance, that defend against environmental insults. While studies have shown that smoking alters bronchial epithelial function and morphology, the precise effects of this exposure on specific cell types are not well-understood. We used single-cell RNA sequencing to profile bronchial epithelial cells from six never- and six current smokers. Unsupervised analyses identified thirteen cell clusters defined by unique combinations of nineteen distinct gene sets. Expression of a set of toxin metabolism genes localized to ciliated cells from smokers. Smoking-induced airway remodeling was characterized by a loss of club cells and extensive goblet cell hyperplasia. Finally, we identified a novel peri-goblet epithelial subpopulation in smokers that expressed a marker of bronchial premalignant lesions. Our data demonstrates that smoke exposure drives a complex landscape of cellular and molecular alterations in the human bronchial epithelium that may contribute to the onset of smoking-associated lung diseases.

scholarly journals Characterizing smoking-induced transcriptional heterogeneity in the human bronchial epithelium at single-cell resolution

2019 ◽  
Vol 5 (12) ◽  
pp. eaaw3413 ◽  
Author(s):  
Grant E. Duclos ◽  
Vitor H. Teixeira ◽  
Patrick Autissier ◽  
Yaron B. Gesthalter ◽  
Marjan A. Reinders-Luinge ◽  
...  
Keyword(s):  
Single Cell ◽  
Bronchial Epithelium ◽  
Cell Types ◽  
Premalignant Lesions ◽  
Specific Cell ◽  
Cell Hyperplasia ◽  
Bronchial Epithelial ◽  
Distinct Cell ◽  
Complex Landscape

The human bronchial epithelium is composed of multiple distinct cell types that cooperate to defend against environmental insults. While studies have shown that smoking alters bronchial epithelial function and morphology, its precise effects on specific cell types and overall tissue composition are unclear. We used single-cell RNA sequencing to profile bronchial epithelial cells from six never and six current smokers. Unsupervised analyses led to the characterization of a set of toxin metabolism genes that localized to smoker ciliated cells, tissue remodeling associated with a loss of club cells and extensive goblet cell hyperplasia, and a previously unidentified peri-goblet epithelial subpopulation in smokers who expressed a marker of bronchial premalignant lesions. Our data demonstrate that smoke exposure drives a complex landscape of cellular alterations that may prime the human bronchial epithelium for disease.

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