Single cell approaches to address adipose tissue stromal cell heterogeneity

A central function of adipose tissue is in the management of systemic energy homeostasis that is achieved through the co-ordinated regulation of energy storage and mobilization, adipokine release, and immune functions. With the dramatic increase in the prevalence of obesity and obesity-related metabolic disease over the past 30 years, there has been extensive interest in targeting adipose tissue for therapeutic benefit. However, in order for this goal to be achieved it is essential to establish a comprehensive atlas of adipose tissue cellular composition and define mechanisms of intercellular communication that mediate pathologic and therapeutic responses. While traditional methods, such as fluorescence-activated cell sorting (FACS) and genetic lineage tracing, have greatly advanced the field, these approaches are inherently limited by the choice of markers and the ability to comprehensively identify and characterize dynamic interactions among stromal cells within the tissue microenvironment. Single cell RNA sequencing (scRNAseq) has emerged as a powerful tool for deconvolving cellular heterogeneity and holds promise for understanding the development and plasticity of adipose tissue under normal and pathological conditions. scRNAseq has recently been used to characterize adipose stem cell (ASC) populations and has provided new insights into subpopulations of macrophages that arise during anabolic and catabolic remodeling in white adipose tissue. The current review summarizes recent findings that use this technology to explore adipose tissue heterogeneity and plasticity.

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Thermogenic adipocytes: lineage, function and therapeutic potential

Biochemical Journal ◽

10.1042/bcj20200298 ◽

2020 ◽

Vol 477 (11) ◽

pp. 2071-2093 ◽

Cited By ~ 2

Author(s):

Alice E. Pollard ◽

David Carling

Keyword(s):

Adipose Tissue ◽

Single Cell ◽

Energy Homeostasis ◽

Environmental Changes ◽

Therapeutic Potential ◽

Human Adipose Tissue ◽

Lineage Tracing ◽

Metabolic Demand ◽

The Metabolic Syndrome ◽

Metabolic Inflexibility

Metabolic inflexibility, defined as the inability to respond or adapt to metabolic demand, is now recognised as a driving factor behind many pathologies associated with obesity and the metabolic syndrome. Adipose tissue plays a pivotal role in the ability of an organism to sense, adapt to and counteract environmental changes. It provides a buffer in times of nutrient excess, a fuel reserve during starvation and the ability to resist cold-stress through non-shivering thermogenesis. Recent advances in single-cell RNA sequencing combined with lineage tracing, transcriptomic and proteomic analyses have identified novel adipocyte progenitors that give rise to specialised adipocytes with diverse functions, some of which have the potential to be exploited therapeutically. This review will highlight the common and distinct functions of well-known adipocyte populations with respect to their lineage and plasticity, as well as introducing the most recent members of the adipocyte family and their roles in whole organism energy homeostasis. Finally, this article will outline some of the more preliminary findings from large data sets generated by single-cell transcriptomics of mouse and human adipose tissue and their implications for the field, both for discovery and for therapy.

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Impact of Local Alloimmunity and Recipient Cells in Transplant Arteriosclerosis

Circulation Research ◽

10.1161/circresaha.119.316470 ◽

2020 ◽

Vol 127 (8) ◽

pp. 974-993 ◽

Cited By ~ 1

Author(s):

Jingjing Cai ◽

Jiacheng Deng ◽

Wenduo Gu ◽

Zhichao Ni ◽

Yuanyuan Liu ◽

...

Keyword(s):

Immune Response ◽

Single Cell ◽

Lineage Tracing ◽

Cellular Heterogeneity ◽

Lymphoid Tissues ◽

Genetic Lineage ◽

Solid Organ ◽

Term Survival ◽

Cell Clusters ◽

Transplant Arteriosclerosis

Rationale: Transplant arteriosclerosis is the major limitation to long-term survival of solid organ transplantation. Although both immune and nonimmune cells have been suggested to contribute to this process, the complex cellular heterogeneity within the grafts, and the underlying mechanisms regulating the disease progression remain largely uncharacterized. Objective: We aimed to delineate the cellular heterogeneity within the allografts, and to explore possible mechanisms underlying this process. Methods and Results: Here, we reported the transcriptional profiling of 11 868 cells in a mouse model of transplant arteriosclerosis by single-cell RNA sequencing. Unbiased clustering analyses identified 21 cell clusters at different stages of diseases, and focused analysis revealed several previously unknown subpopulations enriched in the allografts. Interestingly, we found evidence of the local formation of tertiary lymphoid tissues and suggested a possible local modulation of alloimmune responses within the grafts. Intercellular communication analyses uncovered a potential role of several ligands and receptors, including Ccl21a and Cxcr3 , in regulating lymphatic endothelial cell-induced early chemotaxis and infiltration of immune cells. In vivo mouse experiments confirmed the therapeutic potential of CCL21 and CXCR3 neutralizing antibodies in transplant arteriosclerosis. Combinational use of genetic lineage tracing and single-cell techniques further indicate the infiltration of host-derived c-Kit + stem cells as heterogeneous populations in the allografts. Finally, we compared the immune response between mouse allograft and atherosclerosis models in single-cell RNA-seq analysis. By analyzing susceptibility genes of disease traits, we also identified several cell clusters expressing genes associated with disease risk. Conclusions: Our study provides a transcriptional and cellular landscape of transplant arteriosclerosis, which could be fundamental to understanding the initiation and progression of this disease. CCL21/CXCR3 was also identified as important regulators of immune response and may serve as potential therapeutic targets in disease treatment.

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Quantitative lineage analysis identifies a long-term progenitor niche for the hepato-pancreato-biliary organ system

10.1101/2020.08.06.240176 ◽

2020 ◽

Author(s):

David Willnow ◽

Uwe Benary ◽

Anca Margineanu ◽

Maria Lillina Vignola ◽

Igor M. Pongrac ◽

...

Keyword(s):

Single Cell ◽

Cell Fate ◽

Computational Modelling ◽

Lineage Tracing ◽

Organ System ◽

Cellular Heterogeneity ◽

Genetic Lineage ◽

Genetic Syndromes ◽

Progenitor Compartment

SummarySingle cell-based studies have revealed tremendous cellular heterogeneity in stem cell and progenitor compartments, suggesting continuous differentiation trajectories with intermixing of cells at various states of lineage commitment and notable degree of plasticity during organogenesis1–5.The hepato-pancreato-biliary organ system relies on a small endoderm progenitor compartment that gives rise to a variety of different adult tissues, including liver, pancreas, gallbladder, and extra-hepatic bile ducts6, 7. Experimental manipulation of various developmental signals in the mouse embryo underscored an important cellular plasticity in this embryonic territory6, 8. This is also reflected in the existence of human genetic syndromes as well as congenital or environmentally-caused human malformations featuring multiorgan phenotypes in liver, pancreas and gallbladder6, 8. Nevertheless, the precise lineage hierarchy and succession of events leading to the segregation of an endoderm progenitor compartment into hepatic, biliary, and pancreatic structures are not yet established. Here, we combine computational modelling approaches with genetic lineage tracing to assess the tissue dynamics accompanying the ontogeny of the hepato-pancreato-biliary organ system. We show that a long-term multipotent progenitor domain persists at the border between liver and pancreas, even after pancreatic fate is specified, contributing to the formation of several organ derivatives, including the liver. Moreover, using single-cell RNA sequencing we define a specialized niche that possibly supports such long-term cell fate plasticity.

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Cellular Heterogeneity in Adipose Tissues

Annual Review of Physiology ◽

10.1146/annurev-physiol-031620-095446 ◽

2021 ◽

Vol 83 (1) ◽

pp. 257-278 ◽

Cited By ~ 1

Author(s):

Silvia Corvera

Keyword(s):

Metabolic Disease ◽

Adipose Tissue ◽

Immune Cell ◽

Nutrient Release ◽

Cell Types ◽

Experimental Models ◽

Lineage Tracing ◽

Cellular Heterogeneity ◽

Genetic Lineage ◽

Adipose Tissues

Adipose tissue depots in distinct anatomical locations mediate key aspects of metabolism, including energy storage, nutrient release, and thermogenesis. Although adipocytes make up more than 90% of adipose tissue volume, they represent less than 50% of its cellular content. Here, I review recent advances in genetic lineage tracing and transcriptomics that reveal the identities of the heterogeneous cell populations constituting mouse and human adipose tissues. In addition to mature adipocytes and their progenitors, these include endothelial and various immune cell types that together orchestrate adipose tissue development and functions. One salient finding is the identification of progenitor subtypes that can modulate adipogenic capacity through paracrine mechanisms. Another is the description of fate trajectories of monocyte/macrophages, which can respond maladaptively to nutritional and thermogenic stimuli, leading to metabolic disease. These studies have generated an extraordinary source of publicly available data that can be leveraged to explore commonalities and differences among experimental models, providing new insights into adipose tissues and their role in metabolic disease.

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Cellular heterogeneity and lineage restriction during mouse digit tip regeneration at single cell resolution

10.1101/737023 ◽

2019 ◽

Author(s):

Gemma L. Johnson ◽

Erick J. Masias ◽

Jessica A. Lehoczky

Keyword(s):

Single Cell ◽

Limb Regeneration ◽

Cell Types ◽

Cellular Heterogeneity ◽

Specific Gene ◽

Genetic Lineage ◽

Epimorphic Regeneration ◽

Related Cell ◽

Lower Vertebrates ◽

Single Cell Rna Sequencing

ABSTRACTInnate regeneration following digit tip amputation is one of the few examples of epimorphic regeneration in mammals. Digit tip regeneration is mediated by the blastema, the same structure invoked during limb regeneration in some lower vertebrates. By genetic lineage analyses in mice, the digit tip blastema has been defined as a population of heterogeneous, lineage restricted progenitor cells. These previous studies, however, do not comprehensively evaluate blastema heterogeneity or address lineage restriction of closely related cell types. In this report we present single cell RNA sequencing of over 38,000 cells from mouse digit tip blastemas and unamputated control digit tips and generate an atlas of the cell types participating in digit tip regeneration. We define the differentiation trajectories of vascular, monocytic, and fibroblastic lineages over regeneration, and while our data confirm broad lineage restriction of progenitors, our analysis reveals an early blastema fibroblast population expressing a novel regeneration-specific gene, Mest.

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Ventricular, atrial and outflow tract heart progenitors arise from spatially and molecularly distinct regions of the primitive streak

10.1101/2020.07.12.198994 ◽

2020 ◽

Author(s):

Kenzo Ivanovitch ◽

Pablo Soro-Barrio ◽

Probir Chakravarty ◽

Rebecca A Jones ◽

S. Neda Mousavy Gharavy ◽

...

Keyword(s):

Single Cell ◽

Heart Development ◽

Primitive Streak ◽

Outflow Tract ◽

Lineage Tracing ◽

Molecular Signature ◽

Genetic Lineage ◽

Cardiac Progenitors ◽

Heart Field ◽

Genetic Lineage Tracing

AbstractThe heart develops from two sources of mesoderm progenitors, the first and second heart field (FHF and SHF). Using a single cell transcriptomic assay in combination with genetic lineage tracing, we find the FHF and SHF are subdivided into distinct pools of progenitors in gastrulating mouse embryos at earlier stages than previously thought. Each subpopulation has a distinct origin in the primitive streak. The first progenitors to leave the primitive streak contribute to the left ventricle, shortly after right ventricle progenitor emigrate, followed by the outflow tract and atrial progenitors. Although cells allocated to the outflow tract and atrium leave the primitive streak at a similar stage, they arise from different regions. Outflow tract originate from distal locations in the primitive streak while atrial progenitors are positioned more proximally. Moreover, single cell RNA sequencing demonstrates that the primitive streak cells contributing to the ventricles have a distinct molecular signature from those forming the outflow tract and atrium. We conclude that cardiac progenitors are pre-patterned within the primitive streak and this prefigures their allocation to distinct anatomical structures of the heart. Together, our data provide a new molecular and spatial map of mammalian cardiac progenitors that will support future studies of heart development, function and disease.

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Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma

10.1101/2020.11.11.355693 ◽

2020 ◽

Author(s):

Karin D. Prummel ◽

Helena L. Crowell ◽

Susan Nieuwenhuize ◽

Eline C. Brombacher ◽

Stephan Daetwyler ◽

...

Keyword(s):

Gene Expression ◽

Single Cell ◽

Single Cell Analysis ◽

De Novo ◽

Primordial Germ Cells ◽

Gene Expression Signature ◽

Time Lapse ◽

Lineage Tracing ◽

Genetic Lineage ◽

Lateral Plate

AbstractThe mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration, and their dysregulation can result in congenital anomalies of the viscera, ventral wall defects, and mesothelioma tumors. Nonetheless, the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here, we combine genetic lineage tracing, in toto live imaging, and single-cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm (LPM). Our single-cell analysis uncovers a post-gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos, we chart the origin of mesothelial progenitors to the lateral-most, hand2-expressing LPM and confirm evolutionary conservation in mouse. Our time-lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation, documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally, hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium, we find de novo expression of LPM-associated transcription factors, and in particular of Hand2, indicating the re-initiation of a developmental transcriptional program in mesothelioma. Taken together, our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2, contributing to our understanding of mesothelial pathologies and mesothelioma.

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Ventricular, atrial, and outflow tract heart progenitors arise from spatially and molecularly distinct regions of the primitive streak

PLoS Biology ◽

10.1371/journal.pbio.3001200 ◽

2021 ◽

Vol 19 (5) ◽

pp. e3001200

Author(s):

Kenzo Ivanovitch ◽

Pablo Soro-Barrio ◽

Probir Chakravarty ◽

Rebecca A. Jones ◽

Donald M. Bell ◽

...

Keyword(s):

Single Cell ◽

Heart Development ◽

Primitive Streak ◽

Outflow Tract ◽

Lineage Tracing ◽

Molecular Signature ◽

Genetic Lineage ◽

Cardiac Progenitors ◽

Heart Field ◽

Genetic Lineage Tracing

The heart develops from 2 sources of mesoderm progenitors, the first and second heart field (FHF and SHF). Using a single-cell transcriptomic assay combined with genetic lineage tracing and live imaging, we find the FHF and SHF are subdivided into distinct pools of progenitors in gastrulating mouse embryos at earlier stages than previously thought. Each subpopulation has a distinct origin in the primitive streak. The first progenitors to leave the primitive streak contribute to the left ventricle, shortly after right ventricle progenitor emigrate, followed by the outflow tract and atrial progenitors. Moreover, a subset of atrial progenitors are gradually incorporated in posterior locations of the FHF. Although cells allocated to the outflow tract and atrium leave the primitive streak at a similar stage, they arise from different regions. Outflow tract cells originate from distal locations in the primitive streak while atrial progenitors are positioned more proximally. Moreover, single-cell RNA sequencing demonstrates that the primitive streak cells contributing to the ventricles have a distinct molecular signature from those forming the outflow tract and atrium. We conclude that cardiac progenitors are prepatterned within the primitive streak and this prefigures their allocation to distinct anatomical structures of the heart. Together, our data provide a new molecular and spatial map of mammalian cardiac progenitors that will support future studies of heart development, function, and disease.

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Disease-relevant single cell photonic signatures identify S100β stem cells and their myogenic progeny in vascular lesions

10.1101/2020.05.13.093518 ◽

2020 ◽

Author(s):

Claire Molony ◽

Damien King ◽

Mariana Di Luca ◽

Abidemi Olayinka ◽

Roya Hakimjavadi ◽

...

Keyword(s):

Machine Learning ◽

Stem Cells ◽

Single Cell ◽

Ex Vivo ◽

Lineage Tracing ◽

Supervised Machine Learning ◽

Vascular Lesions ◽

Cell Phenotype ◽

Genetic Lineage ◽

Collagen Iii

AbstractA hallmark of subclinical atherosclerosis is the accumulation of vascular smooth muscle cell (SMC)-like cells leading to intimal thickening and lesion formation. While medial SMCs contribute to vascular lesions, the involvement of resident vascular stem cells (vSCs) remains unclear. We evaluated single cell photonics as a discriminator of cell phenotype in vitro before the presence of vSC within vascular lesions was assessed ex vivo using supervised machine learning and further validated using lineage tracing analysis. Using a novel lab-on-a-Disk (Load) platform, label-free single cell photonic emissions from normal and injured vessels ex vivo were interrogated and compared to freshly isolated aortic SMCs, cultured Movas SMCs, macrophages, B-cells, S100β+ mVSc, bone marrow derived mesenchymal stem cells (MSC) and their respective myogenic progeny across five broadband light wavelengths (λ465 - λ670 ± 20 nm). We found that profiles were of sufficient coverage, specificity, and quality to clearly distinguish medial SMCs from different vascular beds (carotid vs aorta), discriminate normal carotid medial SMCs from lesional SMC-like cells ex vivo following flow restriction, and identify SMC differentiation of a series of multipotent stem cells following treatment with transforming growth factor beta 1 (TGF-β1), the Notch ligand Jagged1, and Sonic Hedgehog using multivariate analysis, in part, due to photonic emissions from enhanced collagen III and elastin expression. Supervised machine learning supported genetic lineage tracing analysis of S100β+ vSCs and identified the presence of S100β+ vSC-derived myogenic progeny within vascular lesions. We conclude disease-relevant photonic signatures may have predictive value for vascular disease.

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The Impact of Single-Cell Genomics on Adipose Tissue Research

International Journal of Molecular Sciences ◽

10.3390/ijms21134773 ◽

2020 ◽

Vol 21 (13) ◽

pp. 4773

Author(s):

Alana Deutsch ◽

Daorong Feng ◽

Jeffrey E. Pessin ◽

Kosaku Shinoda

Keyword(s):

Adipose Tissue ◽

Single Cell ◽

Energy Homeostasis ◽

Whole Body ◽

Diabetes Research ◽

Obesity And Diabetes ◽

Important Regulator ◽

Whole Body Metabolism ◽

Tissue Aging ◽

The Impact

Adipose tissue is an important regulator of whole-body metabolism and energy homeostasis. The unprecedented growth of obesity and metabolic disease worldwide has required paralleled advancements in research on this dynamic endocrine organ system. Single-cell RNA sequencing (scRNA-seq), a highly meticulous methodology used to dissect tissue heterogeneity through the transcriptional characterization of individual cells, is responsible for facilitating critical advancements in this area. The unique investigative capabilities achieved by the combination of nanotechnology, molecular biology, and informatics are expanding our understanding of adipose tissue’s composition and compartmentalized functional specialization, which underlie physiologic and pathogenic states, including adaptive thermogenesis, adipose tissue aging, and obesity. In this review, we will summarize the use of scRNA-seq and single-nuclei RNA-seq (snRNA-seq) in adipocyte biology and their applications to obesity and diabetes research in the hopes of increasing awareness of the capabilities of this technology and acting as a catalyst for its expanded use in further investigation.

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