Chromatin accessibility landscape of stromal subpopulations reveals distinct metabolic and inflammatory features of porcine subcutaneous and visceral adipose tissue

Chromatin landscape in paired human visceral and subcutaneous adipose tissue and its impact on clinical variables in obesity

BACKGROUND

Obesity is a global health challenge and adipose tissue exhibits distinct depot-specific characteristics impacting differentially on the risk of metabolic comorbidities.

METHODS

Here, we integrate chromatin accessibility (ATAC-seq) and gene expression (RNA-seq) data from intra-individually paired human subcutaneous (SAT) and omental visceral adipose tissue (OVAT) samples to unveil depot-specific regulatory mechanisms.

FINDINGS

We identified twice as many depot-specific differentially accessible regions (DARs) in OVAT compared to SAT. SAT-specific regions showed enrichment for adipose tissue enhancers involving genes controlling extracellular matrix organization and metabolic processes. In contrast, OVAT-specific regions showed enrichment in promoters linked to genes associated with cardiomyopathies. Moreover, OVAT-specific regions were enriched for bivalent transcription start site and repressive chromatin states, suggesting a "lingering" regulatory state. Motif analysis identified CTCF and BACH1 as most significantly enriched motifs in SAT and OVAT-specific DARs, respectively. Distinct gene sets correlated with important clinical variables of obesity, fat distribution measures, as well as insulin, glucose, and lipid metabolism.

INTERPRETATION

We provide an integrated analysis of chromatin accessibility and transcriptional profiles in paired human SAT and OVAT samples, offering new insights into the regulatory landscape of adipose tissue and highlighting depot-specific mechanisms in obesity pathogenesis.

FUNDING

SS received EU-Scientia postdoctoral Fellowship and project funding from the European Union's Horizon 2020 Research and Innovation program under the Marie Skłodowska-Curie Grant, (agreement No. 801133). LlCP and TR were supported by Helse Sør-Øst grants to Y.B (ID 2017079, ID 278908). MB received funding from grants from the DFG (German Research Foundation)-Projekt number 209933838-SFB 1052 (project B1) and by Deutsches Zentrum für Diabetesforschung (DZD, Grant: 82DZD00601).

Comparative epigenetics of domestic animals: focusing on DNA accessibility and its impact on gene regulation and traits

IMPORTANCE

Chromatin accessibility is vital for gene regulation, determining the ability of DNA-binding proteins to access the genomic regions and drive transcriptional activity, reflecting environmental changes. Although human and murine studies have advanced the understanding of chromatin dynamics, domestic animals remain comparatively underexplored despite their importance in agriculture and veterinary medicine. Investigating the accessibility of chromatin in these species is crucial for improving traits such as productivity, disease resistance, and environmental adaptation. This review assessed chromatin accessibility research in domestic animals, highlighting its significance in understanding and improving livestock traits.

OBSERVATIONS

This review outlines chromatin accessibility research in domestic animals, focusing on critical developmental processes, tissue-specific regulation, and economically significant traits. Advances in techniques, such as Assay for Transposase-Accessible Chromatin using sequencing, have enabled detailed mapping of regulatory elements, shedding light on epigenetic regulation of traits, such as muscle development and productivity. Comparative studies have uncovered conserved and species-specific cis-regulatory elements across multiple species. These findings offer insights into regulatory mechanisms that can enhance breeding strategies and animal management. In addition, high-throughput techniques, such as single-cell analysis and deep-learning models, have advanced the study of chromatin accessibility in lesser-studied species.

CONCLUSIONS AND RELEVANCE

Chromatin accessibility is crucial in gene regulation in domestic animals, influencing development, immune response, and productivity. Despite the progress, more comprehensive epigenomic datasets and cross-species analytical tools are needed to harness chromatin accessibility in domestic animal research. Understanding these mechanisms has practical applications in improving livestock traits, advancing breeding programs, and developing disease-resistant animals, highlighting the importance of integrating epigenetic and genomic tools for enhancing animal health and productivity.

Deciphering Mechanisms of Adipocyte Differentiation in Abdominal Fat of Broilers

The excessive deposition of abdominal fat tissue (AFT) in broilers has emerged as a major concern in the poultry industry. Despite some progress in recent years, the molecular mechanisms underlying AFT development remain ambiguous. The current study combined RNA-seq with transposase-accessible chromatin sequencing (ATAC-seq) to map the dynamic profiling of chromatin accessibility and transcriptional reprogramming in AFT adipocyte differentiation in broilers at day 3 (D3) and D14. Our results found that the levels of CDK1 and PCNA were down-regulated at D14, D28, and D42 compared to D3, while the levels of C/EBPα and FABP4 were up-regulated at D14 and D42 compared to D3. Meanwhile, PPARγ was significantly up-regulated at D28 and D42. RNA-seq of AFT identified 1705 up-regulated and 1112 down-regulated differential expression genes (DEGs) between D3 and D14. Pathways based on up-regulated DEGs mainly enriched some pathways related to adipocyte differentiation, while down-regulated DEGs pointed to DNA replication, cell cycle, and gap junction. Gene set enrichment analysis (GSEA) revealed that DNA replication and the cell cycle were down-regulated at D14, while the insulin signaling pathway was up-regulated. In the OA-induced immortalized chicken preadipocyte (ICP2) model, protein dynamic changes were consistent with AFT from D3 to D14. Same pathways were enriched in ICP2. In addition, based on overlapped DEGs from AFT and ICP2, enriched pathways related to adipocyte differentiation or proliferation mentioned above were all involved. A total of 1600 gain and 16727 loss differential peaks (DPs) were identified in ICP2 by ATAC-seq. Predicted genes from DPs at the promoter regions were enriched in glycerophospholipid metabolism, TGF-β signaling, FoxO signaling, and ubiquitin-mediated proteolysis. DNA motifs predicted 159 transcription factors (TFs) based on gain and loss peaks from the promoter regions, where 1 and 10 TFs were overlapped with up or down TFs from DEGs. Overall, this study presents a framework for the comprehension of the epigenetic regulatory mechanisms of adipocyte differentiation and identifies candidate genes and potential TFs involved in AFT adipocyte differentiation in broilers.

The correlation between visceral fat/subcutaneous fat area ratio and monocyte/high-density lipoprotein ratio in patients with type 2 diabetes mellitus and albuminuria

OBJECTIVE

This study aims to observe the correlation between the visceral fat/subcutaneous fat area ratio (VSR) and peripheral blood monocyte/high-density lipoprotein ratio (MHR) in patients with type 2 diabetes mellitus (T2DM) and albuminuria.

METHODS

Based on the urinary albumin/creatinine ratio (UACR), 89 T2DM patients were divided into normo-albuminuria group (n = 49, UACR <30 mg/g) and albuminuria group (n = 40, UACR ≥30 mg/g). Gender, age, body mass index (BMI), duration of T2DM, blood pressure, visceral fat area (VA), subcutaneous fat area (SA), biochemical indexes of blood serum and urinary were collected and compared between the two groups, and the relationship between VSR and MHR was analyzed in albuminuria group.

RESULTS

No significant differences existed in gender, age, BMI, duration of diabetes, blood pressure, serum lipids, and hemoglobin Alc between the two groups. The levels of VA, VSR, MHR, and UACR were higher in the albuminuria group (P < 0.05). VSR was positively correlated with MHR (r = 0.39, P < 0.01), whereas VA was not significantly correlated with MHR in the albuminuria group.

CONCLUSION

Compared with VA, VSR was significantly correlated with MHR, suggesting that VSR is more closely related to the occurrence of chronic inflammation in type 2 diabetics with albuminuria.

The Osteogenic Potential of Falciform Ligament-Derived Stromal Cells-A Comparative Analysis between Two Osteogenic Induction Programs

Mesenchymal stromal cells (MSCs) have gained special relevance in bone tissue regenerative applications. MSCs have been isolated from different depots, with adipose tissue being acknowledged as one of the most convenient sources, given the wide availability, high cellular yield, and obtainability. Recently, the falciform ligament (FL) has been regarded as a potential depot for adipose tissue-derived stromal cells (FL-ADSCs) isolation. Nonetheless, the osteogenic capability of FL-ADSCs has not been previously characterized. Thus, the present study aimed the detailed characterization of FL-ADSCs' functionality upon osteogenic induction through a classic (dexamethasone-based-DEX) or an innovative strategy with retinoic acid (RA) in a comparative approach with ADSCs from a control visceral region. Cultures were characterized for cell proliferation, metabolic activity, cellular morphology, fluorescent cytoskeletal and mitochondrial organization, and osteogenic activity-gene expression analysis and cytochemical staining. FL-derived populations expressed significantly higher levels of osteogenic genes and cytochemical markers, particularly with DEX induction, as compared to control ADSCs that were more responsive to RA. FL-ADSCs were identified as a potential source for bone regenerative applications, given the heightened osteogenic functionality. Furthermore, data highlighted the importance of the selection of the most adequate osteogenic-inducing program concerning the specificities of the basal cell population.

Emerging role of T3-binding protein μ-crystallin (CRYM) in health and disease

Thyroid hormones are essential metabolic and developmental regulators that exert a huge variety of effects in different organs. Triiodothyronine (T3) and thyroxine (T4) are synthesized in the thyroid gland and constitute unique iodine-containing hormones that are constantly regulated by a homeostatic feedback mechanism. T3/T4 activity in cells is mainly determined by specific transporters, cytosolic binding proteins, deiodinases (DIOs), and nuclear receptors. Modulation of intracellular T3/T4 level contributes to the maintenance of this regulatory feedback. μ-Crystallin (CRYM) is an important intracellular high-affinity T3-binding protein that buffers the amount of T3 freely available in the cytosol, thereby controlling its action. In this review, we focus on the molecular and pathological properties of CRYM in thyroid hormone signaling, with emphasis on its critical role in malignancies.

Integration of ATAC-seq and RNA-seq analysis identifies key genes affecting intramuscular fat content in pigs

Meat quality is one of the most important economic traits in pig breeding and production, and intramuscular fat (IMF) content is the major factor in improving meat quality. The IMF deposition in pigs is influenced by transcriptional regulation, which is dependent on chromatin accessibility. However, how chromatin accessibility plays a regulatory role in IMF deposition in pigs has not been reported. Xidu black is a composite pig breed with excellent meat quality, which is an ideal research object of this study. In this study, we used the assay for transposase-accessible chromatin using sequencing (ATAC-seq) and RNA sequencing (RNA-seq) analysis to identify the accessible chromatin regions and key genes affecting IMF content in Xidu black pig breed with extremely high and low IMF content. First, we identified 21,960 differential accessible chromatin peaks and 297 differentially expressed genes. The motif analysis of differential peaks revealed several potential cis-regulatory elements containing binding sites for transcription factors with potential roles in fat deposition, including Mef2c, CEBP, Fra1, and AP-1. Then, by integrating the ATAC-seq and RNA-seq analysis results, we found 47 genes in the extremely high IMF (IMF_H) group compared with the extremely low IMF (IMF_L) group. For these genes, we observed a significant positive correlation between the differential gene expression and differential ATAC-seq signal (r² = 0.42). This suggests a causative relationship between chromatin remodeling and the resulting gene expression. We identified several candidate genes (PVALB, THRSP, HOXA9, EEPD1, HOXA10, and PDE4B) that might be associated with fat deposition. Through the PPI analysis, we found that PVALB gene was the top hub gene. In addition, some pathways that might regulate fat cell differentiation and lipid metabolism, such as the PI3K-Akt signaling pathway, MAPK signaling pathway, and calcium signaling pathway, were significantly enriched in the ATAC-seq and RNA-seq analysis. To the best of our knowledge, our study is the first to use ATAC-seq and RNA-seq to examine the mechanism of IMF deposition from a new perspective. Our results provide valuable information for understanding the regulation mechanism of IMF deposition and an important foundation for improving the quality of pork.