Single-cell analysis of human adipose tissue identifies depot- and disease-specific cell types

Immune cells are vital constituents of the adipose microenvironment that influence both local and systemic lipid metabolism. Mice lacking IL10 have enhanced thermogenesis, but the roles of specific cell types in the metabolic response to IL10 remain to be defined. We demonstrate here that selective loss of IL10 receptor α in adipocytes recapitulates the beneficial effects of global IL10 deletion, and that local crosstalk between IL10-producing immune cells and adipocytes is a determinant of thermogenesis and systemic energy balance. Single Nuclei Adipocyte RNA-sequencing (SNAP-seq) of subcutaneous adipose tissue defined a metabolically-active mature adipocyte subtype characterized by robust expression of genes involved in thermogenesis whose transcriptome was selectively responsive to IL10Rα deletion. Furthermore, single-cell transcriptomic analysis of adipose stromal populations identified lymphocytes as a key source of IL10 production in response to thermogenic stimuli. These findings implicate adaptive immune cell-adipocyte communication in the maintenance of adipose subtype identity and function.

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Methods and sensors for functional genomic studies of cell-cycle transitions in single cells

Physiological Genomics ◽

10.1152/physiolgenomics.00065.2020 ◽

2020 ◽

Vol 52 (10) ◽

pp. 468-477

Author(s):

Alexander C. Zambon ◽

Tom Hsu ◽

Seunghee Erin Kim ◽

Miranda Klinck ◽

Jennifer Stowe ◽

...

Keyword(s):

Cell Cycle ◽

Single Cell ◽

Single Cell Analysis ◽

Imaging System ◽

Single Cells ◽

Cell Types ◽

Cell Analysis ◽

Mcf7 Cells ◽

Genomic Studies ◽

Cell Subpopulations

Much of our understanding of the regulatory mechanisms governing the cell cycle in mammals has relied heavily on methods that measure the aggregate state of a population of cells. While instrumental in shaping our current understanding of cell proliferation, these approaches mask the genetic signatures of rare subpopulations such as quiescent (G0) and very slowly dividing (SD) cells. Results described in this study and those of others using single-cell analysis reveal that even in clonally derived immortalized cancer cells, ∼1–5% of cells can exhibit G0 and SD phenotypes. Therefore to enable the study of these rare cell phenotypes we established an integrated molecular, computational, and imaging approach to track, isolate, and genetically perturb single cells as they proliferate. A genetically encoded cell-cycle reporter (K67p-FUCCI) was used to track single cells as they traversed the cell cycle. A set of R-scripts were written to quantify K67p-FUCCI over time. To enable the further study G0 and SD phenotypes, we retrofitted a live cell imaging system with a micromanipulator to enable single-cell targeting for functional validation studies. Single-cell analysis revealed HT1080 and MCF7 cells had a doubling time of ∼24 and ∼48 h, respectively, with high duration variability in G1 and G2 phases. Direct single-cell microinjection of mRNA encoding (GFP) achieves detectable GFP fluorescence within ∼5 h in both cell types. These findings coupled with the possibility of targeting several hundreds of single cells improves throughput and sensitivity over conventional methods to study rare cell subpopulations.

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A chromatin immunoprecipitation (ChIP) protocol for use in whole human adipose tissue

AJP Endocrinology and Metabolism ◽

10.1152/ajpendo.00598.2012 ◽

2013 ◽

Vol 305 (9) ◽

pp. E1172-E1177 ◽

Cited By ~ 14

Author(s):

Yulia Haim ◽

Tanya Tarnovscki ◽

Dana Bashari ◽

Assaf Rudich

Keyword(s):

Adipose Tissue ◽

Chromatin Immunoprecipitation ◽

High Sensitivity ◽

Human Adipose Tissue ◽

Cell Types ◽

Dna Interaction ◽

Specific Cell ◽

Fresh Tissue ◽

Subcutaneous Adipose

Chromatin immunoprecipitation (ChIP) has become a central method when studying in vivo protein-DNA interactions, with the major challenge being the hope to capture “authentic” interactions. While ChIP protocols have been optimized for use with specific cell types and tissues including adipose tissue-derived cells, a working ChIP protocol addressing the challenges imposed by fresh whole human adipose tissue has not been described. Utilizing human paired omental and subcutaneous adipose tissue obtained during elective abdominal surgeries, we have carefully identified and optimized individual steps in the ChIP protocol employed directly on fresh tissue fragments. We describe a complete working protocol for using ChIP on whole adipose tissue fragments. Specific steps required adaptation of the ChIP protocol to human whole adipose tissue. In particular, a cross-linking step was performed directly on fresh small tissue fragments. Nuclei were isolated before releasing chromatin, allowing better management of fat content; a sonication protocol to obtain fragmented chromatin was optimized. We also demonstrate the high sensitivity of immunoprecipitated chromatin from adipose tissue to freezing. In conclusion, we describe the development of a ChIP protocol optimized for use in studying whole human adipose tissue, providing solutions for the unique challenges imposed by this tissue. Unraveling protein-DNA interaction in whole human adipose tissue will likely contribute to elucidating molecular pathways contributing to common human diseases such as obesity and type 2 diabetes.

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Stratification of chemotherapy-treated stage III colorectal cancer patients using multiplexed imaging and single-cell analysis of T-cell populations

Modern Pathology ◽

10.1038/s41379-021-00953-0 ◽

2021 ◽

Author(s):

Xanthi Stachtea ◽

Maurice B. Loughrey ◽

Manuela Salvucci ◽

Andreas U. Lindner ◽

Sanghee Cho ◽

...

Keyword(s):

Colorectal Cancer ◽

Overall Survival ◽

Single Cell ◽

Immune Cell ◽

Single Cell Analysis ◽

Cell Types ◽

Cell Segmentation ◽

Stage Iii ◽

Cell Analysis ◽

Increased Risk

AbstractColorectal cancer (CRC) has one of the highest cancer incidences and mortality rates. In stage III, postoperative chemotherapy benefits <20% of patients, while more than 50% will develop distant metastases. Biomarkers for identification of patients at increased risk of disease recurrence following adjuvant chemotherapy are currently lacking. In this study, we assessed immune signatures in the tumor and tumor microenvironment (TME) using an in situ multiplexed immunofluorescence imaging and single-cell analysis technology (Cell DIVETM) and evaluated their correlations with patient outcomes. Tissue microarrays (TMAs) with up to three 1 mm diameter cores per patient were prepared from 117 stage III CRC patients treated with adjuvant fluoropyrimidine/oxaliplatin (FOLFOX) chemotherapy. Single sections underwent multiplexed immunofluorescence staining for immune cell markers (CD45, CD3, CD4, CD8, FOXP3, PD1) and tumor/cell segmentation markers (DAPI, pan-cytokeratin, AE1, NaKATPase, and S6). We used annotations and a probabilistic classification algorithm to build statistical models of immune cell types. Images were also qualitatively assessed independently by a Pathologist as ‘high’, ‘moderate’ or ‘low’, for stromal and total immune cell content. Excellent agreement was found between manual assessment and total automated scores (p < 0.0001). Moreover, compared to single markers, a multi-marker classification of regulatory T cells (Tregs: CD3+/CD4+FOXP3+/PD1−) was significantly associated with disease-free survival (DFS) and overall survival (OS) (p = 0.049 and 0.032) of FOLFOX-treated patients. Our results also showed that PD1− Tregs rather than PD1+ Tregs were associated with improved survival. These findings were supported by results from an independent FOLFOX-treated cohort of 191 stage III CRC patients, where higher PD1− Tregs were associated with an increase overall survival (p = 0.015) for CD3+/CD4+/FOXP3+/PD1−. Overall, compared to single markers, multi-marker classification provided more accurate quantitation of immune cell types with stronger correlations with outcomes.

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Transduction of rat and human adipose-tissue derived mesenchymal stromal cells by adeno-associated viral vector serotype DJ

Biology Open ◽

10.1242/bio.058461 ◽

2021 ◽

Author(s):

E.S. Zubkova ◽

I.B. Beloglazova ◽

E.I. Ratner ◽

D.T. Dyikanov ◽

K.V. Dergilev ◽

...

Keyword(s):

Adipose Tissue ◽

Cellular Response ◽

Viral Vectors ◽

Viral Vector ◽

Ex Vivo ◽

Human Adipose Tissue ◽

Cell Types ◽

Specific Cell ◽

Therapeutic Benefits ◽

Rat Adipose Tissue

Ex vivo, gene therapy is a powerful approach holding great promises for the treatment of both genetic and acquired diseases. Adeno-associated virus (AAV) vectors are safe and efficient delivery system for modification of mesenchymal stem cells (MSC) that could maximize their therapeutic benefits. Assessment to MSC viability and functional activity after infection with new AAV serotypes is necessary, due to AAV tropism to specific cell types. We infected human and rat adipose-tissue MSC with hybrid AAV-DJ serotype vectors carrying GFP and SCF genes. GFP expression from AAV-DJ was about 1.5-fold superior to that observed with AAV-2 and lasted for at least 21 days as was evaluated by flow cytometry and fluorescence microscopy. AAV-DJ proves to be suitable for the infection of rat and human MSC with a similar efficiency. Infected MSC were still viable however showing 25-30%. growth rate slowdown. Moreover, we found increase of SERPINB2 mRNA expression in human MSC whereas expression of other oxidative stress markers and extracellular matrix proteins was not affected. These results suggest that there is a differential cellular response in MSC infected with AAV viral vectors, which should be taken into account as it can affect the expected outcome for the therapeutic application.

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Novel microfluidic platform accelerates processing of tissue into single cells for molecular analysis and primary culture models

10.21203/rs.3.rs-82281/v1 ◽

2020 ◽

Author(s):

Jeremy Lombardo ◽

Marzieh Aliaghaei ◽

Quy Nguyen ◽

Kai Kessenbrock ◽

Jered Haun

Keyword(s):

Single Cell ◽

Stress Responses ◽

Single Cell Analysis ◽

Single Cells ◽

Cell Types ◽

Tissue Preparation ◽

Cell Analysis ◽

Processing Technologies ◽

Microfluidic Platform ◽

Wide Range

Abstract Tissues are composed of highly heterogeneous mixtures of cell subtypes, and this diversity is increasingly being characterized using high-throughput single cell analysis methods. However, these efforts are hindered by the fact that tissues must first be dissociated into single cell suspensions that are viable and still accurately represent phenotypes from the original tissue. Current methods for breaking down tissues are inefficient, labor-intensive, subject to high variability, and potentially biased towards cell subtypes that are easier to release. Here, we present a microfluidic platform consisting of three different tissue processing technologies that can perform the complete tissue to single cell workflow, including digestion, disaggregation, and filtration. First, we developed a new microfluidic digestion device that can be loaded with minced tissue specimens quickly and easily, and then use the combination of proteolytic enzyme activity and fluid shear forces to accelerate tissue breakdown. Next, we integrated dissociation and filter technologies into a single device, which enhanced single cell numbers and fully prepared the sample for single cell analysis. The final multi-device platform was then evaluated using a diverse array of tissue types that exhibited a wide range of properties. For murine kidney and mammary tumor, we found that microfluidic processing produced 2.5-fold more single, viable cells. Single cell RNA sequencing (scRNA-seq) further revealed that device processing enriched for endothelial cells, fibroblasts, and basal epithelium, and did not increase stress responses. For murine liver and heart, which are softer tissues containing fragile cell types, processing time could be reduced to 15 min, and even as short as 1 min. We also demonstrated that periodic recovery at defined time intervals produced substantially more hepatocytes and cardiomyocytes than continuous operation, most likely by preventing damage to fragile cell types. In future work, we will seek to integrate additional operations such as upstream tissue preparation and downstream microfluidic cell sorting and detection to create powerful point-of-care single cell diagnostic platforms.

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Single Cell Analysis of ACE2 Expression Reveals the Potential Targets for 2019-nCoV

10.20944/preprints202002.0221.v1 ◽

2020 ◽

Cited By ~ 5

Author(s):

Yanyan Zhu ◽

Miaomiao Jiang ◽

Liang Gao ◽

Xiaoyun Huang

Keyword(s):

Single Cell ◽

Single Cell Analysis ◽

Cell Types ◽

Cell Entry ◽

The Novel ◽

Cell Analysis ◽

Systematic Analysis ◽

Proximal Tubule Cells ◽

Putative Receptor ◽

Novel Coronavirus

ACE2, the putative receptor for the novel coronavirus (2019-nCoV), played an important role in cell entry of 2019-nCoV. However, it is not yet clear what cell types within the human body express ACE2. Here, a systematic analysis was undertaken using published single cell datasets. In total, our study analyzed 229652 cells, from five different organs, derived from 88 donors. The top ACE2 expressing cells include proximal tubule cells in the kidney and enterocytes in the intestine. Other major ACE2 expressing cells in the kidney include podocytes, intercalated cells and endothelial cells. Our results offer a comprehensive atlas of ACE2 expression at the single cell level and unravel the enormous potential targets of 2019-nCoVinfection beyond the lung.

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High dimensional single cell analysis reveals unexpected immune cell types, and loss of motility of alveolar macrophages regulated by PPARγ in chronic obstructive pulmonary disease

10.1055/s-0039-1678319 ◽

2019 ◽

Author(s):

W Fujii ◽

K Baßler ◽

T Kapellos ◽

AC Aschenbrenner ◽

K Händler ◽

...

Keyword(s):

Chronic Obstructive Pulmonary Disease ◽

Single Cell ◽

Alveolar Macrophages ◽

Immune Cell ◽

Single Cell Analysis ◽

Cell Types ◽

High Dimensional ◽

Chronic Obstructive ◽

Cell Analysis ◽

Obstructive Pulmonary Disease

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Single-cell analysis in situ in a Bacillus subtilis swarming community identifies distinct spatially separated subpopulations differentially expressing hag (flagellin), including specialized swarmers

Microbiology ◽

10.1099/mic.0.047159-0 ◽

2011 ◽

Vol 157 (9) ◽

pp. 2456-2469 ◽

Cited By ~ 20

Author(s):

Kassem Hamze ◽

Sabine Autret ◽

Krzysztof Hinc ◽

Soumaya Laalami ◽

Daria Julkowska ◽

...

Keyword(s):

Bacillus Subtilis ◽

Single Cell ◽

Single Cell Analysis ◽

Laboratory Strain ◽

Cell Types ◽

Spatiotemporal Pattern ◽

Cell Analysis ◽

Wide Range ◽

Low Humidity

The non-domesticated Bacillus subtilis strain 3610 displays, over a wide range of humidity, hyper-branched, dendritic, swarming-like migration on a minimal agar medium. At high (70 %) humidity, the laboratory strain 168 sfp + (producing surfactin) behaves very similarly, although this strain carries a frameshift mutation in swrA, which another group has shown under their conditions (which include low humidity) is essential for swarming. We reconcile these different results by demonstrating that, while swrA is essential for dendritic migration at low humidity (30–40 %), it is dispensable at high humidity. Dendritic migration (flagella- and surfactin-dependent) of strains 168 sfp + swrA and 3610 involves elongation of dendrites for several hours as a monolayer of cells in a thin fluid film. This enabled us to determine in situ the spatiotemporal pattern of expression of some key players in migration as dendrites develop, using gfp transcriptional fusions for hag (encoding flagellin), comA (regulation of surfactin synthesis) as well as eps (exopolysaccharide synthesis). Quantitative (single-cell) analysis of hag expression in situ revealed three spatially separated subpopulations or cell types: (i) networks of chains arising early in the mother colony (MC), expressing eps but not hag; (ii) largely immobile cells in dendrite stems expressing intermediate levels of hag; and (iii) a subpopulation of cells with several distinctive features, including very low comA expression but hyper-expression of hag (and flagella). These specialized cells emerge from the MC to spearhead the terminal 1 mm of dendrite tips as swirling and streaming packs, a major characteristic of swarming migration. We discuss a model for this swarming process, emphasizing the importance of population density and of the complementary roles of packs of swarmers driving dendrite extension, while non-mobile cells in the stems extend dendrites by multiplication.

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