Coexpression network analysis in abdominal and gluteal adipose tissue reveals regulatory genetic loci for metabolic syndrome and related phenotypes

Metabolic Syndrome (MetS) is highly prevalent and has considerable public health impact, but its underlying genetic factors remain elusive. To identify gene networks involved in MetS, we conducted whole-genome expression and genotype profiling on abdominal (ABD) and gluteal (GLU) adipose tissue, and whole blood (WB), from 29 MetS cases and 44 controls. Co-expression network analysis for each tissue independently identified nine, six, and zero MetS–associated modules of coexpressed genes in ABD, GLU, and WB, respectively. Of 8,992 probesets expressed in ABD or GLU, 685 (7.6%) were expressed in ABD and 51 (0.6%) in GLU only. Differential eigengene network analysis of 8,256 shared probesets detected 22 shared modules with high preservation across adipose depots (D_ABD-GLU = 0.89), seven of which were associated with MetS (FDR P<0.01). The strongest associated module, significantly enriched for immune response–related processes, contained 94/620 (15%) genes with inter-depot differences. In an independent cohort of 145/141 twins with ABD and WB longitudinal expression data, median variability in ABD due to familiality was greater for MetS–associated versus un-associated modules (ABD: 0.48 versus 0.18, P = 0.08; GLU: 0.54 versus 0.20, P = 7.8×10⁻⁴). Cis-eQTL analysis of probesets associated with MetS (FDR P<0.01) and/or inter-depot differences (FDR P<0.01) provided evidence for 32 eQTLs. Corresponding eSNPs were tested for association with MetS–related phenotypes in two GWAS of >100,000 individuals; rs10282458, affecting expression of RARRES2 (encoding chemerin), was associated with body mass index (BMI) (P = 6.0×10⁻⁴); and rs2395185, affecting inter-depot differences of HLA-DRB1 expression, was associated with high-density lipoprotein (P = 8.7×10⁻⁴) and BMI–adjusted waist-to-hip ratio (P = 2.4×10⁻⁴). Since many genes and their interactions influence complex traits such as MetS, integrated analysis of genotypes and coexpression networks across multiple tissues relevant to clinical traits is an efficient strategy to identify novel associations.     

Exploring the cellular network of metabolic flexibility in the adipose tissue

Background

Metabolic flexibility is the ability of cells to change substrates for energy production based on the nutrient availability and energy requirement. It has been shown that metabolic flexibility is impaired in obesity and chronic diseases such as type 2 diabetes mellitus, cardiovascular diseases, and metabolic syndrome, although, whether it is a cause or an effect of these conditions remains to be elucidated.

Main body

In this paper, we have reviewed the literature on metabolic flexibility and curated pathways and processes resulting in a network resource to investigate the interplay between these processes in the subcutaneous adipose tissue. The adipose tissue has been shown to be responsible, not only for energy storage but also for maintaining energy homeostasis through oxidation of glucose and fatty acids. We highlight the role of pyruvate dehydrogenase complex–pyruvate dehydrogenase kinase (PDC-PDK) interaction as a regulatory switch which is primarily responsible for changing substrates in energy metabolism from glucose to fatty acids and back. Baseline gene expression of the subcutaneous adipose tissue, along with a publicly available obesity data set, are visualised on the cellular network of metabolic flexibility to highlight the genes that are expressed and which are differentially affected in obesity.

Conclusion

We have constructed an abstracted network covering glucose and fatty acid oxidation, as well as the PDC-PDK regulatory switch. In addition, we have shown how the network can be used for data visualisation and as a resource for follow-up studies.

     

结核分枝杆菌酸抗性基因及其调控网络

病原菌在宿主细胞内的持留分子机理是目前研究的热点和难点。病原菌的抗酸能力与此密切相关。结核分枝杆菌感染导致的结核病仍然是全球公共卫生的重大威胁,这与结核分枝杆菌抗酸并在宿主巨噬细胞内持留有关。结核分枝杆菌抗酸主要通过调控质子进出、代谢调控胞内酸碱平衡和双组份信号系统调控。本文综述了结核分枝杆菌在酸胁迫下的整体调控网络,阐述了在酸性环境中结核分枝杆菌的具体调控机理,旨在为持留结核分枝杆菌的治疗提供新的全局性思路,寻找新的结核病防控靶标。     

Analysis of an expression profile of genes in the human adipose tissue

Increasing evidence suggests that in addition to storing excess energy as fat, adipose tissue acts as an endocrine organ secreting various factors into the blood stream. Every time a new factor is found in adipose tissue, however, its implication is discussed independently, and a systematic analyses based upon a global view of gene expression of this tissue has not been performed. To describe the function of this tissue in terms of gene expression, and to find new factors, we performed random complementary DNA (cDNA) sequencing using a 3'-directed cDNA library that faithfully represents the composition of the messenger RNA (mRNA). Various well-known but unexpected genes, including those for gelsolin, plasma glutathione peroxidase (GPX-3) and carboxypeptidase E (CPE) were shown to be very active. By comparing the expression profile of active genes in the adipose with those of other tissues and with data in dbEST, we identified seven new genes that are specifically expressed in adipose tissue. Among these, one encoded a protein with collagen-like repeats and a putative secretion signal. These data can be used as new tools for analyses of the physiology of this tissue, as well as the etiology and complications of obesity.