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Single cell functional genomics reveals plasticity of subcutaneous white adipose tissue (WAT) during early postnatal development

ABSTRACT: Single cell functional genomics reveals plasticity of subcutaneous white adipose tissue (WAT) during early postnatal development

PROVIDER: PRJNA748747 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15209918.fastq.gz	Fastqsanger.gz
	SRR15209919.fastq.gz	Fastqsanger.gz
	SRR15209920.fastq.gz	Fastqsanger.gz
	SRR15209921.fastq.gz	Fastqsanger.gz
	SRR15209922.fastq.gz	Fastqsanger.gz

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Single cell functional genomics reveals plasticity of subcutaneous white adipose tissue (WAT) during early postnatal development

Project description:We performed a large-scale single cell transcriptomic (scRNA-seq) and epigenomic (snATAC-seq) characterization of cellular subtypes (adipose stromal cells (ASC) and adipocyte nuclei) during inguinal WAT (subcutaneous; iWAT) development in mice, capturing the early postnatal period (postnatal days (PND) 06 and 18) through adulthood (PND56).

2021-09-08 | GSE180589 | GEO

Single cell functional genomics reveals plasticity of subcutaneous white adipose tissue (WAT) during early postnatal development.

Project description:ObjectiveThe current study addresses the cellular complexity and plasticity of subcutaneous (inguinal) white adipose tissue (iWAT) in mice during the critical periods of perinatal growth and establishment.MethodsWe performed a large-scale single cell transcriptomic (scRNA-seq) and epigenomic (snATAC-seq) characterization of cellular subtypes (adipose stromal cells (ASC) and adipocyte nuclei) during inguinal WAT (subcutaneous; iWAT) development in mice, capturing the early postnatal period (postnatal days (PND) 06 and 18) through adulthood (PND56).ResultsPerinatal and adult iWAT contain 3 major ASC subtypes that can be independently identified by RNA expression profiles and DNA transposase accessibility. Furthermore, the transcriptomes and enhancer landscapes of both ASC and adipocytes dynamically change during postnatal development. Perinatal ASC (PND06) are highly enriched for several imprinted genes (IGs; e.g., Mest, H19, Igf2) and extracellular matrix proteins whose expression then declines prior to weaning (PND18). By comparison, adult ASC (PND56) are more enriched for transcripts associated with immunoregulation, oxidative stress, and integrin signaling. Two clusters of mature adipocytes, identified through single nuclei RNA sequencing (snRNA-seq), were distinctive for proinflammatory/immune or metabolic gene expression patterns that became more transcriptionally diverse in adult animals. Single nuclei assay for transposase-accessible chromatin (snATAC-seq) revealed that differences in gene expression were associated with developmental changes in chromatin accessibility and predicted transcription factor motifs (e.g., Plagl1, Ar) in both stromal cells and adipocytes.ConclusionsOur data provide new insights into transcriptional and epigenomic signaling networks important during iWAT establishment at a single cell resolution, with important implications for the field of metabolic programming.

| S-EPMC8385178 | biostudies-literature

Cold-Induced Adaptations to the Proteome of Mouse Subcutaneous White Adipose Tissue (scWAT) Reveal Proteins Relevant for Tissue Remodeling and Plasticity

Project description:White adipose tissue (WAT) is one of the most dynamic and plastic organs or tissues in the body, capable of expanding its mass in response to positive energy balance (either by proliferation of adipocytes - hyperphasia, or by increasing adipoycyte size - hypertrophy), developing inducible brown adipocytes through a process termed "browning", and changing its mitochondrial mass in response to stimuli such as cold exposure. Most notably, cold stimulation and release of norepinephrine from sympathetic nerve terminals is able to drive lipolysis in WAT (and thus smaller lipid droplet size and adipocyte size), as well as promote sympathetic nerve branching and increased neurite density, as well as development of pockets of browning around these neurite-dense regions of tissue. While several RNA-sequencing (including newer single cell RNAseq studies) have been done in WAT across situations of positive energy balance (such as high fat diet, obesity) or negative energy balance (such as cold stimulation of energy expenditure), very little work has been done to investigate changes to the adipose proteome while the tissue is actively remodeling. Here, we have carried out proteomics analysis on inguinal subcutaneous (sc)WAT of C57BL/6 mice after 24 or 72hrs of cold stimulation, a period during which UCP1 is actively turned on during the browning process. Through these data, we have found that numerous protein pathways changed by cold stimulation relate to tissue remodeling and plasticity, including changes to mitochondrial dynamics, tissue immune cells, and peripheral nerves.

2021-05-25 | MSV000087516 | MassIVE

snRNA-seq data on human subcutaneous and omental white adipose tissue

Project description:We generated single nucleus transcriptomic atlas for human subcutaneous and omental white adipose tissue (WAT).

2023-02-23 | GSE225700 | GEO

LR11 knockout in BAT and WAT

Project description:To study the gene expression profiles of brown (BAT) and white (WAT) adipose tissues in wild type and LR11-deficeint mice. The four RNA sources, WT scWAT, Lr11 -/- scWAT, WT BAT and Lr11 -/- BAT, were prepared from subcutaneous WAT and BAT from wild-type mice and Lr11 -/- mice, respectively (n=3 each).

2015-11-01 | E-GEOD-69117 | biostudies-arrayexpress

snRNA-Seq from Younger and Older human abdominal subcutaneous white adipose tissue

Project description:Abstract White adipose tissue (WAT) is a robust energy storage and endocrine organ critical for maintaining metabolic health as we age. Our aim was to identify cell-specific transcriptional aberrations that occur in WAT with aging. We leveraged full-length snRNA-Seq and histology to characterize the cellular landscape of human abdominal subcutaneous WAT in a prospective cohort of 10 younger (≤30 years) and 10 older individuals (≥65 years) balanced for sex and body mass index (BMI). The older group had greater cholesterol, very-low-density lipoprotein, triglycerides, thyroid stimulating hormone, and aspartate transaminase compared to the younger group (p< 0.05). We highlight that aging WAT is associated with adipocyte hypertrophy, increased proportions of lipid-associated macrophages and mast cells, an upregulation of immune responses linked to fibrosis in pre-adipocyte, adipocyte, and vascular populations, and highlight CXCL14 as a biomarker of these processes. We show that older WAT has elevated levels of senescence marker p16 in adipocytes and identify the adipocyte subpopulation driving this senescence profile. We confirm that these transcriptional and phenotypical changes occur without overt fibrosis and in older individuals that have comparable WAT insulin sensitivity to the younger individuals.

2024-07-31 | GSE235529 | GEO

miR-30a target genes in the subcutaneous fat pad of diabetic mice

Project description:In this study, we tested the hypothesis that restoration of miR-30a expression in WAT would improve peripheral insulin sensitivity. Exogenous miR-30a expression in subcutaneous WAT depots of obese mice improved insulin sensitivity, decreased ectopic liver fat deposition, and reduced WAT inflammation compared to matched controls. We identified the target genes and pathways of miR-30a using RNA-Seq technology

2021-04-03 | GSE112691 | GEO

Membrane Metallo-Endopeptidase (Neprilysin) Regulates Inflammatory Response and Insulin Signaling in White Preadipocytes

Project description:Accumulation of visceral white adipose tissue (WAT) associates with insulin resistance, adipose tissue inflammation, and metabolic syndrome, whereas accumulation of subcutaneous WAT may be protective. We aimed to identify molecular mechanisms that might provide mechanistic insights underlying the phenotypic differences in these tissues. Membrane Metallo-Endopeptidase (MME/Neprislyin) is an extracellular, membrane-bound protease enriched in subcutaneous WAT that can target degradation of a variety of peptides, including insulin, IL6, and β-amyloids. We hypothesized that MME contributes to adipose depot-specific metabolic properties.

2019-02-25 | GSE117353 | GEO

Characterization of Mmp3 positive and negative cells from SVF of subcutaneous adipose tissue

Project description:RNA sequencing from isolated MMP3+ cells in subcutaneous WAT SVF showed higher expression of genes associated with beige progenitors.

2023-10-28 | GSE160376 | GEO

Escherichia coli strain:WAT

Project description:Escherichia coli WAT genome

| PRJNA292047 | ENA