The global obesity epidemic is driving a parallel surge in obesity-related comorbidities, including type 2 diabetes (T2D), coronary artery disease (CAD), nonalcoholic fatty liver disease (NAFLD), and severe COVID-19 outcomes. While genetic predisposition plays a role, as evidenced by polygenic risk scores (PRSs) associated with BMI and increased comorbidity risk, not all individuals with high BMI develop these adverse health outcomes. This variability underscores the importance of understanding the interplay between genetic factors, environmental influences, and their interactions in shaping metabolic and immunological responses to obesity. Chronic low-grade inflammation is a hallmark of obesity, contributing to insulin resistance and atherosclerosis. While adipose macrophages are known players, evidence increasingly implicates preadipocytes in dysfunctional adipose tissue and the pro-inflammatory state. Preadipocytes can secrete pro-inflammatory cytokines and exhibit gene expression profiles similar to macrophages, but the underlying mechanisms driving this contribution in obese individuals remain unclear. This study hypothesized that an obesogenic environment disrupts preadipocyte function through altered chromatin co-accessibility. Using BMI-discordant MZ twin pairs, which control for genetic variation, researchers investigated epigenetic (ATAC-sequencing) and transcriptomic (RNA-sequencing) changes associated with increased BMI. This unique design allows researchers to isolate the effects of environmental factors from genetic influences, providing a powerful approach to understand BMI's impact on preadipocyte function and inflammation.

Existing literature establishes a strong link between obesity and chronic low-grade inflammation, which is a critical driver of obesity-related complications such as insulin resistance and atherosclerosis. The role of adipose tissue macrophages in this process is well-documented, with these immune cells contributing significantly to the pro-inflammatory milieu. However, recent research has increasingly highlighted the involvement of preadipocytes, the progenitor cells of adipocytes, in this inflammatory response. Studies have shown that preadipocytes can produce pro-inflammatory cytokines and express genes that overlap with those found in macrophages. This suggests that preadipocytes actively participate in shaping the inflammatory environment within adipose tissue. Previous research has demonstrated the importance of epigenetic modifications in the regulation of gene expression in preadipocytes. Alterations in DNA methylation, histone modifications, and chromatin accessibility have been linked to preadipocyte differentiation and function. However, a comprehensive understanding of how these epigenetic changes contribute to the inflammatory response in obesity remains elusive. This gap in knowledge motivated the current study to investigate the link between BMI, chromatin accessibility, and inflammation in preadipocytes using a unique twin study design that minimizes confounding genetic factors.

This study employed a unique design utilizing monozygotic (MZ) twins discordant for BMI (ΔBMI ≥3 kg/m²). Subcutaneous preadipocytes (PAd) were isolated from adipose biopsies of 10 MZ twin pairs (20 individuals). Nine pairs passed quality control for subsequent analysis. The lower BMI twin served as a control for each pair. The following data were generated: * **ATAC-seq:** Assay for Transposase-Accessible Chromatin sequencing was conducted on preadipocytes from each twin to identify regions of open chromatin, reflecting active regulatory elements. * **RNA-seq:** RNA sequencing was performed to measure gene expression levels in the preadipocytes. * **pCHi-C:** Promoter Capture Hi-C data, from an independent source of human primary preadipocytes, was used to identify promoter-enhancer interactions. Data analysis involved several steps: 1. **A/B Compartment Identification:** ATAC-seq data were used to infer active (A) and inactive (B) genomic compartments based on chromatin co-accessibility. The A compartments were characterized by shorter lengths, higher gene density, and enrichment for enhancer and promoter chromatin states compared to B compartments. pCHi-C data confirmed that promoter-enhancer interactions are significantly enriched within A compartments. 2. **Co-accessibility Analysis:** A compartment co-accessibility, a measure of the correlation between a given A compartment and all other A compartments, was calculated for each A compartment. This metric was found to be strongly associated with gene expression and other markers of active gene regulation. 3. **BMI-Discordant Twin Comparison:** Co-accessibility measures were compared between lower and higher BMI twins within each MZ pair. Significant differences in A compartment co-accessibility were observed between the two groups, highlighting changes in chromatin activity associated with increased BMI. 4. **UK Biobank Analysis:** To assess the functional relevance of the identified regions, the study performed partitioned LD-score regression (LDSC) on UK Biobank data to examine the heritability of CRP and other traits explained by the A compartments. A GxE scan in the UK Biobank was conducted to test for interactions between SNPs within these regions and BMI on CRP levels. 5. **A Compartment Clustering and Functional Enrichment:** A compartment clustering through UMAP and Louvain clustering identified functionally distinct regions within the genome. Gene ontology (GO) enrichment and transcription factor (TF) motif enrichment analyses were used to characterize the functions associated with each cluster. 6. **Differentially Expressed Genes and Accessibility Peaks:** Genes differentially expressed between higher and lower BMI twins were identified. The accessibility of ATAC-seq peaks in the regions of these genes was also assessed. The correlation between peak accessibility and gene expression was examined to identify regulatory elements influenced by BMI.

This study's key findings include: 1. **Altered Chromatin Co-accessibility:** A significant decrease in A compartment co-accessibility was observed in preadipocytes from higher BMI MZ twins compared to their lower BMI counterparts. This effect encompassed a substantial portion of the genome (~88.5 Mb). 2. **Link to Systemic Inflammation:** The regions with altered co-accessibility were enriched for the heritability of CRP, a marker of systemic inflammation. Furthermore, these regions showed a higher accumulation of SNPs with genotype-by-BMI interaction effects on CRP levels in the UK Biobank, suggesting a functional link between altered chromatin accessibility and increased inflammation. 3. **Functional Clustering of A Compartments:** Clustering of A compartments identified distinct groups with different levels of co-accessibility and enrichment for specific gene functions and regulatory elements. Specifically, cluster 1, enriched for genes related to developmental processes, cell polarity, cell adhesion, and immune responses, showed a higher accumulation of low p-value GxE SNPs associated with CRP. 4. **BMI-Responsive Genes:** Analysis identified 52 differentially expressed genes (DEGs) between higher and lower BMI twins within cluster 1's reprogrammed A compartments. Many of these genes showed a significant enrichment of BMI-associated GWAS variants in their cis-regions. This is further supported by an enrichment analysis of the chromatin state coverage of enhancer and promoter chromatin states, super-enhancer identification, regulatory interactions, and responses to differentiation signals. 5. **INPPSK-MIR22HG Regulatory Circuit:** The study highlighted a disruption in the co-accessibility of ATAC-seq peaks in the MIR22HG/WDR81 region and INPPSK gene in higher BMI individuals, showing how changes in chromatin interaction are reflected in gene expression, potentially contributing to the observed phenotype. This finding provides a molecular mechanism by which BMI influences gene expression, potentially contributing to the development of obesity-related traits.

This study demonstrates a novel mechanism linking increased BMI to systemic inflammation through alterations in preadipocyte chromatin co-accessibility. The use of BMI-discordant MZ twin pairs effectively controls for genetic confounding, providing strong evidence for the role of environmental factors in shaping epigenetic modifications and their downstream effects on inflammation. The identification of specific genomic regions associated with both altered co-accessibility and increased inflammation provides valuable insights into the pathophysiology of obesity and its complications. The findings underscore the significance of preadipocytes, not just as passive fat storage cells, but also as active contributors to the inflammatory environment in obesity. The observed gene-environment interactions (GxEs) in the UK Biobank further strengthen the link between the identified genomic regions and human inflammation. The study's approach of integrating epigenetic and transcriptomic data with GWAS data offers a powerful strategy for identifying gene-environment interactions in complex traits. The findings have implications for developing novel therapeutic strategies targeting preadipocyte function and chromatin regulation to mitigate obesity-associated inflammation and its downstream comorbidities. Future studies should focus on the functional validation of the identified candidate genes and regulatory elements to better understand their roles in preadipocyte biology and obesity-associated inflammation.

This study provides strong evidence that increased BMI disrupts the higher-order chromatin organization in human preadipocytes, leading to alterations in gene expression and contributing to systemic inflammation. The findings highlight the importance of preadipocytes in the inflammatory response to obesity and identify novel candidate genes and regulatory elements for future investigation. The study's novel approach of combining BMI-discordant twin pairs with large-scale genomic data analysis provides a powerful strategy for understanding gene-environment interactions in complex traits. Future research should focus on functional validation of candidate genes and regulatory elements to develop potential therapeutic strategies.

The study's relatively small sample size (10 BMI-discordant MZ twin pairs) limits the statistical power to detect subtle effects. The study focused on subcutaneous adipose tissue preadipocytes; the results may not be directly generalizable to visceral adipose tissue, which may have different inflammatory characteristics. The preadipocytes were cultured in vitro; the results might not entirely reflect in vivo conditions. The heterogeneity of obesogenic environmental factors (diet, physical activity, etc.) in the MZ pairs is a limitation, warranting future research with larger sample sizes and controlled environmental conditions.