Skip to main content
Dryad logo

Fat distribution in women associates with depot-specific transcriptomics signatures and chromatin structure

Citation

Divoux, Adeline et al. (2020), Fat distribution in women associates with depot-specific transcriptomics signatures and chromatin structure, Dryad, Dataset, https://doi.org/10.5061/dryad.7sqv9s4pb

Abstract

Preferential accumulation of fat in the upper body (apple shape) is associated with higher risk of developing metabolic syndrome relative to lower body fat (pear shape). We previously discovered that chromatin openness defined partially the transcriptome of pre-adipocytes isolated from abdominal and gluteofemoral fat. However, the molecular mechanisms underlying inter individual fat repartition variation are unknown. Adipocyte fraction was isolated from abdominal and gluteofemoral fat biopsies of premenopausal women (age and BMI-matched) segregated initially only by their waist to hip ratio. We evaluated transcriptomic and chromatin accessibility using RNA-seq and ATAC-seq along with key clinical parameters. Our data showed that higher lower body fat mass was associated with better lipid profile and free fatty acid turnover after glucose administration. Lipid and glucose metabolic pathways genes were expressed at higher levels in gluteofemoral adipocyte fraction in pears, while genes associated with inflammation were higher in both abdominal and gluteofemoral apple adipocyte fraction. Gluteofemoral adipocyte chromatin from pear-shaped women contained a significantly higher number of differentially open ATAC-seq peaks relative to chromatin from the apple-shaped gluteofemoral adipocytes. In contrast, abdominal adipocyte chromatin openness showed few differences between apple and pear-shaped women. We revealed a correlation between gene transcription and open chromatin at the proximity of the TSS of some of the differentially expressed genes.

Usage Notes

Figure S1: Depot-specific gene expression in adipocytes. (A and B) - Heat map representation of depot-specific gene expression determined by RNA-seq from the abdominal (ABD) and gluteofemoral (GF) depots in the 5 apple (left side, in red) and 5 pear-shaped women (right side, in blue). (C and D) - Venn diagrams depict number of genes up-regulated in each depot only in apples (red circle), only in pears (blue circle) or in both groups (intersection).

Figure S2: ATAC-seq peaks in ABD and GF depots for both groups of body shape women. A- Read distribution plot of open chromatin regions in apple and pear adipocytes isolated from ABD and GF depot from each subject. Sub=Subject; Rep=Replicate. (B-C) Correlation plot of all the accessible chromatin regions defined by ATAC-seq from the 10 participants (Apples and Pears) in Abdominal (B) and gluteofemoral (C) depot. D- Genomic distribution of the accessible chromatin regions in abdominal and GF depot. E- Graphic representation of the genomic distribution of the apple and pear-specific open chromatin regions observed in the GF depot (p value<0.05).

Figure S3: Differential binding analysis identifies depot-specific chromatin accessibility in adipocytes isolated from apple and pear-shaped women. A- Correlation plot of accessible chromatin regions defined by ATAC-seq from fat depots (Gluteofemoral-GF, Abdominal-ABD) in apple women (left side, in red) and pear women (right side, in blue). B- Volcano plot representation of abdominal and GF-specific open chromatin regions in adipocytes isolated from apples (left side, p≤0.05) and pear (right side, p≤0.1) women. Abdominal- (highlighted in darker red and darker blue) and GF-specific (highlighted in lighter red and lighter blue) open chromatin regions are represented. C- Promoter analysis of differentially expressed genes in ABD and GF. Boxplot representation of the average RPKM calculated from the 5 apple participants (left side) or from the 5 pear participants (right side) *p<0.05, **p<0.01, ***p<0.001 paired t-test.

Figure S4: Heat map representation of the individual gene expression data of the nuclear receptor ligand identified in abdominal (ABD) and gluteo-femoral (GF) adipocyte fraction isolated from apple- and pear-shaped subjects. In red are the nuclear receptor ligand the most expressed.

SUPPLEMENTAL TABLES

Table S1. Clinical characteristics of the 10 participants used for RNA-seq and ATAC-seq analysis.

Table S2. Computational tools, docker images and Common Workflows Language used to process the RNA-Seq data.

Table S3. List of genes differentially regulated between ABD and GF depot in apple- and pear-shaped women.

Table S4. List of genes differentially regulated between apple and pear group in ABD and GF depots.

Table S5. List of genes up-regulated in apple-shaped women in the GF depot and involved in inflammatory/immune pathways with the associated average TPM values (average from 5 apple and 5 pear subjects).

Table S6. List of ATAC-seq peaks body-shape specific in ABD and GF depots.

Table S7. List of ATAC-seq peaks depot-specific in apple- and pear-shaped women.

Funding

National Institutes of Health, Award: R01DK107009-02

Hungarian Scientific Research Fund, Award: NKFIH K-129166,GINOP-2.3.3-15-2016-00007

Debrecen Venture Catapult Program, Award: EFOP-3.6.1-16-2016-00022