The complexities of obesity can be more effectively addressed through a multiomics approach to identify obesity biomarkers. This method illuminates the intricate links between organ systems, phenotypes, and clinical presentations, providing a deeper understanding of the molecular mechanisms underlying obesity [8]. Thorough and systematic biomarker analysis provides a framework for exploring the physiological domains influencing the susceptibility to obesity. Notably, research utilizing multiomics technologies to identify novel obesity biomarkers is still in its early stages, often hindered by methodological limitations such as small sample sizes, incomplete omics coverage, high costs, and suboptimal data analysis methods. However, with rapid advances in high-throughput sequencing and the emergence of artificial intelligence (AI), this field is well-positioned to accelerate the resolution of clinically relevant challenges [9]. This review summarizes obesity-associated biomarkers and attempts to characterize obesity from a multiomics perspective, incorporating epigenetics, transcriptomics, proteomics, metabolomics, and the microbiome. This approach aims to understand the complexity of obesity and advance the application of precision medicine.
Epigenetic changes include DNA methylation, histone modifications, and RNA methylation. Environmental factors influence epigenetics, leading to dynamic, heritable changes that are not permanent mutations. Given that obesity is a complex disease closely associated with environmental factors, it is not surprising that epigenomic changes induced by extrinsic factors contribute to the susceptibility of developing obesity.
Gene methylation has been extensively implicated in the regulation of obesity and related biological functions such as appetite, insulin signaling, immunity, inflammation, development, and circadian rhythm. In a comprehensive study by Casas-Castillo et al., a positive correlation was discovered between DNA methylation levels of peroxisome proliferator-activated receptor alpha (PPAR-α) and the metabolic syndrome index, triglyceride levels, and IR [10]. Notably, methylation patterns of PPAR-γ were found to have an inverse relationship with diastolic blood pressure but a positive correlation with BMI, highlighting the gene's role in adipocyte differentiation and metabolic regulation [11]. These findings suggest that epigenetic changes may significantly impact an individual's susceptibility to metabolic syndrome.
DNA methyltransferase 3a (DNMT3A) has been linked to human growth and obesity. DNMT3A-induced DNA methylation is pivotal in determining body size and susceptibility to obesity in humans. Studies have shown that heterozygous DNMT3A-deficient mice exhibit overeating, obesity, and increased body length [12]. Further research indicates a negative association between retinoid X receptor alpha (RXRA) methylation in adipose tissue and anthropometric indicators such as BMI and waistline [10]. Conversely, positive correlations have been observed between the methylation of low-density lipoprotein cholesterol receptor 1 and lipoprotein lipase with metabolic syndrome [10]. In addition, methylation levels of the tumor necrosis factor (TNF) gene are reduced in patients with obesity and metabolic syndrome, emphasizing the critical role of epigenetic control of inflammatory markers in the dysregulation of lipid metabolism observed in obesity and related metabolic disorders [13].
Histone modifications are implicated in the epigenetic regulation of obesity and may significantly contribute to its development and progression. These modifications, such as histone methylation, acetylation, ubiquitination, and lactylation, can induce changes in chromatin structure, resulting in either gene expression or gene silencing.
Histone methylation occurs primarily on the basic amino acids lysine and arginine, in the form of mono-methylation (me1), dimethylation (me2), or trimethylation (me3). The effects of histone methylation depend on the specific methylation site and status (activation or inhibition). For instance, methylation on H3K4, H3K36, and H3K79 activates gene transcription, while methylation on H3K9, H3K27, and H4K20 is inhibitory [14].
Methylation of H3K4 is associated with disruptions in the endocrine system, such as precocious puberty and obesity. Methylation on H3K9 is closely related to energy metabolism and methylation on both H3K4 and H3K9 affects the development of brown and beige fat. Conversely, methylation on H3K27 inhibits gene transcription, and mice with increased H3K27me3 experience significant weight gain [15]. Demethylation of H3K27 can regulate fatty acid oxidation in the liver and positively influence the thermogenic program in brown fat cells [16]. The absence of KDM6A in brown fat promotes high-fat diet (HFD)-induced obesity [17], while inhibiting H3K27 demethylation generally increases energy metabolism in metabolic organs. Inhibiting methylation of H4K20 worsens metabolic phenotypes, affects the expression of thermogenic genes, and ultimately reduces fat thermogenic capacity, contributing to obesity [18].
Histone acetylation expands chromatin conformation and allows transcription; histone deacetylation compresses chromatin and represses transcription. Histone acetylation and deacetylation are catalyzed by histone acetyltransferases (HAT) and histone deacetylases (HDAC), respectively. Studies have reported the role of histone acetylation in the pathogenesis of obesity and its associated risk factors.
HAT consists mainly of the general control histone acetyltransferase GCN5 and the CREB-binding protein (CBP) of the p300/cyclic adenosine monophosphate response element-binding protein [14]. Overexpression of GCN5 in mouse myoblast tubules leads to inhibition of peroxisome proliferator-activated receptor γ coactivator 1-α in mitochondrial and fatty acid metabolism genes [19], and GCN5 has also been shown to promote brown adipogenesis and beige adipocyte differentiation in vitro [20]. CBP knockout mice exhibit pronounced brown remodeling of the inguinal white adipose tissue after cold exposure, and double knockout of CBP and p300 leads to severe lipodystrophy as well as pronounced hepatic steatosis, hyperglycemia, and hyperlipidemia [21]. Overexpression of HDAC4 in adipocytes leads to beige adipocyte expansion and reduced obesity [22], and feeding HDAC6-deficient mice with an HFD leads to a decreased abundance of Lactobacillus and an increased abundance of Anabaena and Anabaena parapsilosis, with changes leading to the development of obesity [23]. HDAC11 deletion enhances brown and beige adipose activity, resulting in increased energy expenditure and lean body mass [24].
Numerous studies of HAT and HDAC have highlighted the critical role of histone acetylation and deacetylation in linking epigenetic, transcriptional, and signaling phenomena to obesity metabolism. This could provide opportunities for the identification of inhibitors and activators of HDACs for the treatment of obesity.
Lactate-induced lactylation and cardiometabolic diseases (including obesity, T2DM, and hypertension) cause a range of chronic and devastating cardiovascular abnormalities. Yin et al. demonstrated that histone H2B (K6) and H4 (K80) lactylation was observed after Huazhuo Tiaozhi Granule treatment, verifying that lactylation modifications have a role in regulating lipid metabolism[25]. Elevated fasting lactate levels have been observed in obesity and T2DM [26]. In addition, reducing H3K18 lactylation attenuates reactive oxygen species production and neutrophil responses to injury and inflammation [27], suggesting that lactylation holds significant promise in treating diseases associated with obesity and diabetes.
Ubiquitination involves the covalent attachment of ubiquitin monomers or ubiquitin chains to lysine residues of proteins. Dysfunction of the ubiquitin-proteasome system can lead to metabolic disorders associated with obesity, such as diabetes and fatty liver [28]. Chronic insulin stimulation inhibits hepatocyte ubiquitination through activation of ubiquitin-specific peptidase 14 (USP14) and increases nuclear translocation of the adipogenic sterol regulatory element-binding transcription factor 1c (SREBP-1c) to inhibit mature SREBP-1c [29]. Overexpression of mitsugumin 53 (MG53) induces muscular IR and metabolic syndrome [30], while the E3 ubiquitin ligase murine double minute-2 (MDM2) promotes high glucose-induced epithelial-mesenchymal transition and oxidative stress injury, possibly through downregulation of liver kinase B1 (LKB1) [31]. Adiponectin ubiquitination is increased in the visceral fat of pregnant women with obesity compared to their lean counterparts, and it is a key mechanism through which obesity curtails adiponectin secretion during pregnancy [32]. Chen et al. showed that an inhibitor of NF-κB kinase could inactivate the deubiquitinating activity of cylindromatosis proteins by activating their phosphorylation, which promotes ubiquitination of nuclear factor erythroid 2-related factor 2 (Nrf2) and exacerbates oxidative stress injury to the kidney in obesity-associated nephropathy [33].
In summary, post-translational modifications (PTMs) play an important role in obesity and related diseases, offering numerous potential targets for therapeutic intervention. Further experimental studies are needed to investigate the roles and mechanisms of different PTMs in regulating the expression of metabolism-related genes and their impact on obesity.
RNA methylation is a crucial factor in the regulation of RNA splicing, stability, and translation, constituting around 60% of RNA modifications. Among these, modification with N6-methyladenine (m6A) is the most prevalent internal modification in messenger RNAs (mRNAs) and noncoding RNAs (ncRNAs). Inhibition of m6A modification reduces energy expenditure in mice, rendering them more susceptible to obesity and metabolic syndrome [34]. In addition, modification with 5-methylcytosine (m5C), a recently discovered and abundant mRNA modification, is linked to energy metabolism by inhibiting lipid accumulation and promoting myogenic differentiation [35]. Certain mRNAs with m5C modifications, such as Y-box binding protein 2 (YBX2) and smoothened (SMO), are recognized by Aly export factor and exported from the nucleus to the cytoplasm, leading to increased expression of YBX2 and SMO proteins. These proteins, in turn, inhibit adipogenesis and promote myogenesis [35]. Furthermore, obesity is positively associated with N1-methyladenosine (M1A), and enlarged fat cells can create an environment favorable for the M1 phenotype in vitro [36]. Decreased M1A levels have been shown to alleviate cellular inflammation, reduce weight, improve metabolic characteristics, and mitigate fat cell enlargement [37].
In summary, despite being in its early stages, the study of RNA methylation presents an exciting and essential journey toward unraveling its secrets. It has the potential to deepen our understanding of the molecular foundations of life, opening doors for innovative biomarker discovery and therapeutic development. As advancements in RNA methylation continue rapidly, new and promising biomarkers for obesity and its complications are being unearthed, offering novel approaches for preventing and treating obesity.