Single-nuclei analysis reveals depot-specific transcriptional heterogeneity and depot-specific cell types in adipose tissue of dairy cows

Multi-omics integrated analysis reveals the molecular mechanism of tail fat deposition differences in sheep with different tail types

BACKGROUND

The accumulation of tail fat in sheep is a manifestation of adaptive evolution to the environment. Sheep with different tail types show significant differences in physiological functions and tail fat deposition. Although these differences reflect the developmental mechanism of tail fat under different gene regulation, the situation of sheep tail fat tissue at the single cell level has not been explored, and its molecular mechanism still needs to be further elucidated.

RESULTS

Here, we characterized the genomic features of sheep with different tail types, detected the transcriptomic differences in tail adipose tissue between fat-tailed and thin-tailed sheep, established a single-cell atlas of sheep tail adipose tissue, and screened potential molecular markers (SESN1, RPRD1A and RASGEF1B) that regulate differences in sheep tail fat deposition through multi-omics integrated analysis. We found that the differential mechanism of sheep tail fat deposition not only involves adipocyte differentiation and proliferation, but is also closely related to cell-specific communication networks (When adipocytes act as signal outputters, LAMININ and other signal pathways are strongly expressed in guangling large tailed sheep and hu sheep), including interactions with immune cells and tissue remodeling to drive the typing of tail fat. In addition, we revealed the differentiation trajectory of sheep tail adipocytes through pseudo-time analysis and constructed the cell communication network of sheep tail adipose tissue.

CONCLUSIONS

Our results provide insights into the molecular mechanisms of tail fat deposition in sheep with different tail types, and provide a deeper explanation for the development and functional regulation of adipocytes.

Towards a consensus atlas of human and mouse adipose tissue at single-cell resolution

Adipose tissue (AT) is a complex connective tissue with a high relative proportion of adipocytes, which are specialized cells with the ability to store lipids in large droplets. AT is found in multiple discrete depots throughout the body, where it serves as the primary repository for excess calories. In addition, AT has an important role in functions as diverse as insulation, immunity and regulation of metabolic homeostasis. The Human Cell Atlas Adipose Bionetwork was established to support the generation of single-cell atlases of human AT as well as the development of unified approaches and consensus for cell annotation. Here, we provide a first roadmap from this bionetwork, including our suggested cell annotations for humans and mice, with the aim of describing the state of the field and providing guidelines for the production, analysis, interpretation and presentation of AT single-cell data.

Adipose tissue oxylipin profile changes with subclinical ketosis and depot in postpartum dairy cows

Lipolysis of adipose tissue is a natural occurrence during the periparturient period in dairy cows. However, when lipolysis rates exceed the capacity of other tissues to used nonesterified fatty acids, it may lead to the development of ketosis and other diseases. Additionally, PUFA can become oxidized into oxylipins, which modulate inflammation and metabolism. The objective of this work was to identify depot-specific differences on adipose tissue oxylipin profile in dairy cows with and without subclinical ketosis and assess the effects of oxylipins on adipocyte function in vitro. Subcutaneous adipose tissue from the flank (SAT) and visceral adipose tissue from the omentum (VAT) were collected through laparotomy from multiparous dairy cows (5-14 DIM) and grouped according to blood BHB into nonketotic (NK; n = 5; BHB ≤ 0.8 mmol/L) and subclinical ketotic (SCK; n = 5; BHB 1.4 and ≤ 2.6 mmol/L). A targeted lipidome capable of detecting a 154 oxylipins was performed in paired SAT and VAT samples from all animals. Data were analyzed using the PROC GLIMMIX procedure in SAS (v9.4, SAS Institute Inc., Cary, NC) for the effect of depot (SAT, VAT), ketosis status (SCK, NK), and their interaction (depot × ketosis status) on oxylipin abundance. The oxylipins thromboxane-B2 (TXB2), prostaglandin-A2 (PGA2), and 5-hydroxeicostretanoic acid (5-HETE) were selected from lipidomic data based on effects of ketosis status and depot-specificity to further investigate their effects on SAT and VAT adipocyte function. Lipidomic data revealed 50 oxylipins across both adipose tissue depots. SCK was associated with a decreased abundance of TXB2 and tended to associate with an increase in PGA2 and prostaglandin-E1 (PGE1). Additionally, PGE1, 15-keto-prostaglandin-E2, 13,14-dihydro-15-keto-prostaglandin-E2, 5-HETE, and 15-HETE were increased in SAT. Although VAT had a greater abundance of 9,10-dihydroxy-12Z-octadecenoic acid, 12,13-dihydroxy-9Z-octadecenoic acid, 9-oxo-10E,12Z,15Z-octadecatrienoic acid, and 13S-hydroxy-9Z,11E,15Z-octadecatrienoic acid (13[s]-HOTrE). In vitro, an average (AVG) dose of 5-HETE on VAT cells tended to increase proliferation at d 7 compared with the control, HGH dose of TXB2 tended to decrease lipid accumulation in SAT compared with control, and AVG dose of PGA2 on VAT cells tended to lower ROS compared with the control. Overall, postpartum dairy cows have depot-specific adipose tissue lipidomic profiles which are associated with changes in ketosis status.

Extracellular matrix modulates depot-specific adipogenic capacity in adipose tissue of dairy cattle

Adipose tissue (AT) expands through both hyperplasia and hypertrophy. During adipogenesis, adipose stromal and progenitor cells (ASPC) proliferate and then accumulate lipids, influenced by the local AT microenvironment. Increased adipogenic capacity is desirable as it relates to metabolic health, especially in transition dairy cows where excess free fatty acids in circulation can compromise metabolic and immune health. Our aim was to elucidate the depot-specific adipogenic capacity and extracellular matrix (EMX) properties of subcutaneous (SAT) and visceral (VAT) AT of dairy cows and define how the EMX affects adipogenesis. Flank SAT and omental VAT samples were collected from dairy cows in a local abattoir. Tissue samples were used for transcriptome analysis, targeted real-time quantitative PCR (RT-qPCR) for adipogenic markers, adipocyte sizing, assessment of viscoelastic properties and collagen accumulation, and then decellularized for native EMX isolation. For in vitro analyses, SAT and VAT samples were digested via collagenase, and ASPC cultured for metabolic analysis. Adipogenic capacity was assessed by adipocyte size, quantification of ASPC in stromal vascular fraction (SVF) via flow cytometry, and gene expression of adipogenic markers. In addition, functional assays including lipolysis and glucose uptake were performed to further characterize SAT and VAT adipocyte metabolic function. Data were analyzed using SAS (version 9.4; SAS Institute Inc., Cary, NC) and GraphPad Prism 9. Subcutaneous AT adipogenic capacity was greater than VAT's, as indicated by increased ASPC abundance, increased magnitude of adipocyte ADIPOQ and FASN expression during differentiation, and higher adipocyte lipid accumulation as shown by an increased proportion of larger adipocytes and abundance of lipid droplets. Rheologic analysis revealed that VAT is stiffer than SAT, which led us to hypothesize that differences between SAT and VAT adipogenic capacity were partly mediated by depot-specific EMX microenvironment. Thus, we studied depot-specific EMX-adipocyte crosstalk using a 3-dimensional model with native EMX (decellularized AT). Subcutaneous AT and VAT ASPC were cultured and differentiated into adipocytes within depot-matched and mismatched EMX for 14 d, followed by ADIPOQ expression analysis. Visceral AT EMX impaired ADIPOQ expression in SAT cells. Our results demonstrate that SAT is more adipogenic than VAT and suggest that divergences between SAT and VAT adipogenesis are partially mediated by the depot-specific EMX microenvironment.

Key questions and gaps in understanding adipose tissue macrophages and early-life metabolic programming

The global obesity epidemic, with its associated comorbidities and increased risk of early mortality, underscores the urgent need for enhancing our understanding of the origins of this complex disease. It is increasingly clear that metabolism is programmed early in life and that metabolic programming can have life-long health consequences. As a critical metabolic organ sensitive to early-life stimuli, proper development of adipose tissue (AT) is crucial for life-long energy homeostasis. Early-life nutrients, especially fatty acids (FAs), significantly influence the programming of AT and shape its function and metabolism. Of growing interest are the dynamic responses during pre- and postnatal development to proinflammatory omega-6 (n6) and anti-inflammatory omega-3 (n3) FA exposures in AT. In the US maternal diet, the ratio of "pro-inflammatory" n6- to "anti-inflammatory" n3-FAs has grown dramatically due to the greater prevalence of n6-FAs. Notably, AT macrophages (ATMs) form a significant population within adipose stromal cells, playing not only an instrumental role in AT formation and maintenance but also acting as key mediators of cell-to-cell lipid and cytokine signaling. Despite rapid advances in ATM and immunometabolism fields, research has focused on responses to obesogenic diets and during adulthood. Consequently, there is a significant gap in identifying the mechanisms contributing metabolic health, especially regarding lipid exposures during the establishment of ATM physiology. Our review highlights the current understanding of ATM diversity, their critical role in AT, their potential role in early-life metabolic programming, and the broader implications for metabolism and health.

The Effect of Subclinical Ketosis on the Peripheral Blood Mononuclear Cell Inflammatory Response and Its Crosstalk with Depot-Specific Preadipocyte Function in Dairy Cows

During the periparturient period, cows undergo heightened energy demands at lactation onset, paired with reduced dry matter intake, leading to negative energy balance (NEB). Excessive lipolysis-driven adipose tissue remodeling, triggered by NEB, significantly contributes to ketosis in periparturient dairy cows. However, the role of peripheral blood mononuclear cells (PBMCs) in the pathogenesis of ketosis and in modulating adipose tissue function remains poorly understood. Here, we investigated how ketosis affects the transcriptional profile and secretome of PBMCs and its influence on preadipocyte function in visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT). Twenty-one postpartum Holstein dairy cows were categorized as either subclinical ketosis (SCK; BHB ≥ 1.0 mM) or control (CON; BHB < 0.8 mM) based on blood beta-hydroxybutyrate (BHB) concentration screening. Blood samples were collected intravenously for the isolation of PBMCs and serum metabolic profiling. Ketosis elevated circulating NEFA and BHB levels but reduced total WBC and neutrophil counts. Isolated PBMCs were evaluated for gene expression and used to produce conditioned media (PBMC-CM), during which PBMCs were stimulated with 10 ng/mL LPS. The overall phenotype of PBMCs was largely consistent between SCK and CON cows, with minimal differences detected in immunomodulatory cytokine expression and PBMC-CM composition following stimulation. Preadipocytes isolated from non-ketotic cows were treated with PBMC-CM to assess the effect of PBMC secretomes on adipose cell function. Preadipocytes treated with SCK PBMC-CM showed reduced lipid accumulation compared to those treated with CON PBMC-CM regardless of the depot. SAT preadipocytes had heightened expression of lipid metabolism-related genes, including DGAT1, LIPE, and FASN, compared to VAT when treated with SCK PBMC-CM. Preadipocytes treated with CM from PBMC stimulated by LPS exhibited upregulation in IL1B and IL6 regardless of the depot or source of PBMCs. Together, these results indicate that although PBMC profiles showed minimal differences, preadipocytes treated with PBMC-CM may be influenced by additional factors, leading to altered preadipocyte function and gene expression that may contribute to adipose cellular dysfunction.

Single-Cell Sequencing Technology in Ruminant Livestock: Challenges and Opportunities

Advancements in single-cell sequencing have transformed the genomics field by allowing researchers to delve into the intricate cellular heterogeneity within tissues at greater resolution. While single-cell omics are more widely applied in model organisms and humans, their use in livestock species is just beginning. Studies in cattle, sheep, and goats have already leveraged single-cell and single-nuclei RNA-seq as well as single-cell and single-nuclei ATAC-seq to delineate cellular diversity in tissues, track changes in cell populations and gene expression over developmental stages, and characterize immune cell populations important for disease resistance and resilience. Although challenges exist for the use of this technology in ruminant livestock, such as the precise annotation of unique cell populations and spatial resolution of cells within a tissue, there is vast potential to enhance our understanding of the cellular and molecular mechanisms underpinning traits essential for healthy and productive livestock. This review intends to highlight the insights gained from published single-cell omics studies in cattle, sheep, and goats, particularly those with publicly accessible data. Further, this manuscript will discuss the challenges and opportunities of this technology in ruminant livestock and how it may contribute to enhanced profitability and sustainability of animal agriculture in the future.

A cell atlas of thoracic aortic perivascular adipose tissue: a focus on mechanotransducers

Perivascular adipose tissue (PVAT) is increasingly recognized for its function in mechanotransduction. However, major gaps remain in our understanding of the cells present in PVAT, as well as how different cells contribute to mechanotransduction. We hypothesized that snRNA-seq would reveal the expression of mechanotransducers, and test one (PIEZO1) to illustrate the expression and functional agreement between single-nuclei RNA sequencing (snRNA-seq) and physiological measurements. To contrast two brown tissues, subscapular brown adipose tissue (BAT) was also examined. We used snRNA-seq of the thoracic aorta PVAT (taPVAT) and BAT from male Dahl salt-sensitive (Dahl SS) rats to investigate cell-specific expression mechanotransducers. Localization and function of the mechanostransducer PIEZO1 were further examined using immunohistochemistry (IHC) and RNAscope, as well as pharmacological antagonism. Approximately 30,000 nuclei from taPVAT and BAT each were characterized by snRNA-seq, identifying eight major cell types expected and one unexpected (nuclei with oligodendrocyte marker genes). Cell-specific differential gene expression analysis between taPVAT and BAT identified up to 511 genes (adipocytes) with many (≥20%) being unique to individual cell types. Piezo1 was the most highly, widely expressed mechanotransducer. The presence of PIEZO1 in the PVAT but not the adventitia was confirmed by RNAscope and IHC in male and female rats. Importantly, antagonism of PIEZO1 by GsMTX4 impaired the PVAT's ability to hold tension. Collectively, the cell compositions of taPVAT and BAT are highly similar, and PIEZO1 is likely a mechanotransducer in taPVAT.NEW & NOTEWORTHY This study describes the atlas of cells in the thoracic aorta perivascular adipose tissue (taPVAT) of the Dahl-SS rat, an important hypertension model. We show that mechanotransducers are widely expressed in these cells. Moreover, PIEZO1 expression is shown to be restricted to the taPVAT and is functionally implicated in stress relaxation. These data will serve as the foundation for future studies investigating the role of taPVAT in this model of hypertensive disease.

Adipose Tissue Inflammation: Linking Physiological Stressors to Disease Susceptibility

The study of adipose tissue (AT) is enjoying a renaissance. White, brown, and beige adipocytes are being investigated in adult animals, and the critical roles of small depots like perivascular AT are becoming clear. But the most profound revision of the AT dogma has been its cellular composition and regulation. Single-cell transcriptomic studies revealed that adipocytes comprise well under 50% of the cells in white AT, and a substantial portion of the rest are immune cells. Altering the function of AT resident leukocytes can induce or correct metabolic syndrome and, more surprisingly, alter adaptive immune responses to infection. Although the field is dominated by obesity research, conditions such as rapid lipolysis, infection, and heat stress impact AT immune dynamics as well. Recent findings in rodents lead to critical questions that should be explored in domestic livestock as potential avenues for improved animal resilience to stressors, particularly as animals age.

Adipose Tissue Dysfunction Determines Lipotoxicity and Triggers the Metabolic Syndrome: Current Challenges and Clinical Perspectives

The adipose tissue organ is organised as distinct anatomical depots located all along the body axis, and it is constituted of three different types of adipocytes: white, beige and brown, which are integrated with vascular, immune, neural, and extracellular stroma cells. These distinct adipocytes serve different specialised functions. The main function of white adipocytes is to ensure healthy storage of excess nutrients/energy and its rapid mobilisation to supply the demand of energy imposed by physiological cues in other organs, whereas brown and beige adipocytes are designed for heat production through uncoupling lipid oxidation from energy production. The concerted action of the three types of adipocytes/tissues ensures an optimal metabolic status. However, when one or several of these adipose depots become dysfunctional because of sustained lipid/nutrient overload, then insulin resistance and associated metabolic complications ensue. These metabolic alterations close a vicious cycle that negatively affects the adipose tissue functionality and compromises global metabolic homeostasis. Optimising white adipose tissue expandability and ensuring its functional metabolic flexibility and/or promoting brown/beige mediated thermogenic activity are complementary strategies that counteract obesity and its associated lipotoxic metabolic effects. However, the development of these therapeutic approaches requires a deep understanding of adipose tissue in all broad aspects. In this chapter, we will discuss the characteristics of the different adipose tissue depots with respect to origins and precursors recruitment, plasticity, cellular composition, and expandability capacity potential as well as molecular and metabolic characteristic signatures in both physiological and pathophysiological conditions. Current antilipotoxic strategies for future clinical application are also discussed in this chapter.

Inflammatory tone in liver and adipose tissue in dairy cows experiencing a healthy transition from late pregnancy to early lactation

The transition from late pregnancy (LP) to early lactation (EL) in dairy cows is characterized by a major reorganization of the metabolic activities of liver and adipose tissue in support of milk synthesis. This reorganization has been attributed in large part to variation in the plasma concentration and actions of growth hormone, insulin, and other metabolic hormones. A role for the immune system has also been suggested by a near-universal rise in circulating levels of liver-derived acute-phase proteins (APP) in early lactating cows. However, less attention has been devoted to the possibility that resident macrophages of liver and adipose tissue adopt a proinflammatory state (referred herein as inflammatory tone) in parallel with the rise in plasma APP. We addressed this question by measuring the expression of genes expressed predominantly in the resident macrophage population of liver and adipose tissue and indicative of a proinflammatory (tumor necrosis factor α, IL-6, IL-12, resistin, and cluster of differentiation 80 [CD80]) or anti-inflammatory state (IL-10 and chitinase-3-like protein 1 [CHI3L1]). In a first group of cows, none of these inflammatory gene markers were regulated in liver between LP on d -29 (relative to parturition) and on d 8 of EL despite 1.7 to 5.6-fold upregulation in the expression of the APP (haptoglobin, serum amyloid α, and orosomucoid 1). In a second group of healthy cows, expression of the inflammatory gene markers did not differ between livers with low (<5.3%) or high (>11.5%) triglyceride content on d 7 of EL. In adipose tissue, a modest increase in inflammatory tone was suggested between LP and EL by increased CD80 expression and decreased CHI3L1 expression in EL. To assess the possibility that inflammatory tone would be more prominent if assayed in a cell compartment enriched with macrophages, adipose tissue was obtained in LP on d -28 and in EL on d +10 from cows experiencing a healthy transition period and fractionated into its adipocyte and stromal vascular cell (SVC) compartments. Expression of inflammatory gene markers was higher in SVC than adipocytes but remained unregulated in SVC between LP and EL. Overall, these results suggest little change in the inflammatory tone of resident macrophages in liver and adipose tissue of healthy transition dairy cows and do not support a role for the local immune system in the reorganization of metabolism in these tissues at the onset of lactation.

A Cell Atlas of Thoracic Aortic Perivascular Adipose Tissue: a focus on mechanotransducers

Perivascular adipose tissue (PVAT) is increasingly recognized for its function in mechanotransduction. To examine the cell-specificity of recognized mechanotransducers we used single nuclei RNA sequencing (snRNAseq) of the thoracic aorta PVAT (taPVAT) from male Dahl SS rats compared to subscapular brown adipose tissue (BAT). Approximately 30,000 nuclei from taPVAT and BAT each were characterized by snRNAseq, identifying 8 major cell types expected and one unexpected (nuclei with oligodendrocyte marker genes). Cell-specific differential gene expression analysis between taPVAT and BAT identified up to 511 genes (adipocytes) with many (≥20%) being unique to individual cell types. Piezo1 was the most highly, widely expressed mechanotransducer. Presence of PIEZO1 in the PVAT was confirmed by RNAscope® and IHC; antagonism of PIEZO1 impaired the PVAT's ability to hold tension. Collectively, the cell compositions of taPVAT and BAT are highly similar, and PIEZO1 is likely a mechanotransducer in taPVAT.

Optimized nucleus isolation protocol from frozen mouse tissues for single nucleus RNA sequencing application

The single cell RNA sequencing technique has been particularly used during the last years, allowing major discoveries. However, the widespread application of this analysis has showed limitations. Indeed, the direct study of fresh tissues is not always feasible, notably in the case of genetically engineered mouse embryo or sensitive tissues whose integrity is affected by classical digestion methods. To overcome these limitations, single nucleus RNA sequencing offers the possibility to work with frozen samples. Thus, single nucleus RNA sequencing can be performed after genotyping-based selection on samples stocked in tissue bank and is applicable to retrospective studies. Therefore, this technique opens the field to a wide range of applications requiring adapted protocols for nucleus isolation according to the tissue considered. Here we developed a protocol of nucleus isolation from frozen murine placenta and pancreas. These two complex tissues were submitted to a combination of enzymatic and manual dissociation before undergoing different steps of washing and centrifugation. The entire protocol was performed with products usually present in a research lab. Before starting the sequencing process, nuclei were sorted by flow cytometry. The results obtained validate the efficiency of this protocol which is easy to set up and does not require the use of commercial kits. This specificity makes it adaptable to different organs and species. The association of this protocol with single nucleus RNA sequencing allows the study of complex samples that resist classical lysis methods due to the presence of fibrotic or fatty tissue, such as fibrotic kidney, tumors, embryonic tissues or fatty pancreas.

White Adipose Tissue Heterogeneity in the Single-Cell Era: From Mice and Humans to Cattle

Adipose tissue is a major modulator of metabolic function by regulating energy storage and by acting as an endocrine organ through the secretion of adipokines. With the advantage of next-generation sequencing-based single-cell technologies, adipose tissue has been studied at single-cell resolution, thus providing unbiased insight into its molecular composition. Recent single-cell RNA sequencing studies in human and mouse models have dissected the transcriptional cellular heterogeneity of subcutaneous (SAT), visceral (VAT), and intramuscular (IMAT) white adipose tissue depots and revealed unique populations of adipose tissue progenitor cells, mature adipocytes, immune cell, vascular cells, and mesothelial cells that play direct roles on adipose tissue function and the development of metabolic disorders. In livestock species, especially in bovine, significant gaps of knowledge remain in elucidating the roles of adipose tissue cell types and depots on driving the pathogenesis of metabolic disorders and the distinct fat deposition in VAT, SAT, and IMAT in meat animals. This review summarizes the current knowledge on the transcriptional and functional cellular diversity of white adipose tissue revealed by single-cell approaches and highlights the depot-specific function of adipose tissue in different mammalian species, with a particular focus on recent findings and future implications in cattle.

Master of disguise: deconvoluting adipose tissue heterogeneity and its impact on metabolic health

Adipose tissue in its different forms: white, brown, and beige, while essential in day-to-day bodily functions, leads to several disorders when present in overabundance, including obesity and type-2 diabetes. Adipose tissue function/dysfunction is largely mediated by the diversity of its cell composition, within adipocytes and cells in its stromal fraction. Owing to its heterogeneous nature, recent studies have focused on intercalating the effects of cellular diversity with adipose tissue function, particularly by employing sequencing technologies. In this review, we highlight the recent advances in utilizing single-cell and single-nuclei RNA sequencing technologies to discover novel adipose tissue cell types or subtypes, and to determine their role in mediating tissue, as well as whole-body metabolism and function.