Multifaceted genome-wide study identifies novel regulatory loci in SLC22A11 and ZNF45 for body mass index in Indians

The complex web of obesity: from genetics to precision medicine

INTRODUCTION

Obesity is a growing public health concern affecting both children and adults. Since it involves both genetic and environmental components, the management of obesity requires both, an understanding of the underlying genetics and changes in lifestyle. The knowledge of obesity genetics will enable the possibility of precision medicine in anti-obesity medications.

AREAS COVERED

Here, we explore health complications and the prevalence of obesity. We discuss disruptions in energy balance as a symptom of obesity, examining evolutionary theories, its multi-factorial origins, and heritability. Additionally, we discuss monogenic and polygenic obesity, the converging biological pathways, potential pharmacogenomics applications, and existing anti-obesity medications - specifically focussing on the leptin-melanocortin and incretin pathways. Comparisons between childhood and adult obesity genetics are made, along with insights into structural variants, epigenetic changes, and environmental influences on epigenetic signatures.

EXPERT OPINION

With recent advancements in anti-obesity drugs, genetic studies pinpoint new targets and allow for repurposing existing drugs. This creates opportunities for genotype-informed treatment options. Also, lifestyle interventions can help in the prevention and treatment of obesity by altering the epigenetic signatures. The comparison of genetic architecture in adults and children revealed a significant overlap. However, more robust studies with diverse ethnic representation is required in childhood obesity.

Genetics and Epigenetics in Obesity: What Do We Know so Far?

PURPOSE OF REVIEW

Enormous progress has been made in understanding the genetic architecture of obesity and the correlation of epigenetic marks with obesity and related traits. This review highlights current research and its challenges in genetics and epigenetics of obesity.

RECENT FINDINGS

Recent progress in genetics of polygenic traits, particularly represented by genome-wide association studies, led to the discovery of hundreds of genetic variants associated with obesity, which allows constructing polygenic risk scores (PGS). In addition, epigenome-wide association studies helped identifying novel targets and methylation sites being important in the pathophysiology of obesity and which are essential for the generation of methylation risk scores (MRS). Despite their great potential for predicting the individual risk for obesity, the use of PGS and MRS remains challenging. Future research will likely discover more loci being involved in obesity, which will contribute to better understanding of the complex etiology of human obesity. The ultimate goal from a clinical perspective will be generating highly robust and accurate prediction scores allowing clinicians to predict obesity as well as individual responses to body weight loss-specific life-style interventions.

Epigenome-wide methylation study identified two novel CpGs associated with T2DM risk and a network of co-methylated CpGs capable of patient's classifications

Prevention of Type 2 diabetes mellitus (T2DM) pandemic needs markers that can precisely predict the disease risk in an individual. Alterations in DNA methylations due to exposure towards environmental risk factors are widely sought markers for T2DM risk prediction. To identify such individual DNA methylation signatures and their effect on disease risk, we performed an epigenome-wide association study (EWAS) in 844 Indian individuals of Indo-European origin. We identified and validated methylation alterations at two novel CpG sites in MIR1287 (cg01178710) and EDN2-SCMH1 (cg04673737) genes associated with T2DM risk at the epigenome-wide-significance-level (P < 1.2 × 10-7). Further, we also replicated the association of two known CpG sites in TXNIP, and CPT1A in the Indian population. With 535 EWAS significant CpGs (P < 1.2 × 10-7) identified in the discovery phase samples, we created a co-methylation network using weighted correlation network analysis and identified four modules among the CpGs. We observed that methylation of one of the module associates with T2DM risk factors (e.g. BMI, insulin and C-peptide) and can be used as markers to segregate T2DM patients with good glycemic control (e.g. low HbA1c) and dyslipidemia (low HDL and high TG) from the other patients. Additionally, an intronic SNP (rs6503650) in the JUP gene, a member of the same module, associated with methylation at all the 14 hub CpG sites of that module as methQTL. Our network-assisted EWAS is the first to systematically explore DNA methylation variations conferring risks to T2DM in Indians and use the identified risk CpG sites for patient segregation with different clinical outcomes. These findings can be useful for better stratification of patients to improve the clinical management and treatment effects.

Recent progress in epigenetics of obesity

Nowadays, obesity is one of the largest public health problems worldwide. In the last few decades, there has been a marked increase in the obesity epidemic and its related comorbidities. Worldwide, more than 2.2 billion people (33%) are affected by overweight or obesity (712 million, 10%) and its associated metabolic complications. Although a high heritability of obesity has been estimated, the genetic variants conducted from genetic association studies only partially explain the variation of body mass index. This has led to a growing interest in understanding the potential role of epigenetics as a key regulator of gene-environment interactions on the development of obesity and its associated complications. Rapid advances in epigenetic research methods and reduced costs of epigenome-wide association studies have led to a great expansion of population-based studies. The field of epigenetics and metabolic diseases such as obesity has advanced rapidly in a short period of time. The main epigenetic mechanisms include DNA methylation, histone modifications, microRNA (miRNA)-mediated regulation and so on. DNA methylation is the most investigated epigenetic mechanism. Preliminary evidence from animal and human studies supports the effect of epigenetics on obesity. Studies of epigenome-wide association studies and genome-wide histone modifications from different biological specimens such as blood samples (newborn, children, adolescent, youth, woman, man, twin, race, and meta-analysis), adipose tissues, skeletal muscle cells, placenta, and saliva have reported the differential expression status of multiple genes before and after obesity interventions and have identified multiple candidate genes and biological markers. These findings may improve the understanding of the complex etiology of obesity and its related comorbidities, and help to predict an individual's risk of obesity at a young age and open possibilities for introducing targeted prevention and treatment strategies.

Unique attributes of obesity in India: A narrative review

Obesity has become a burgeoning epidemic in India, even though the country is still dealing with undernutrition. As a significant determinant of the Metabolic Syndrome (MetS) and non-communicable diseases (NCDs) such as type 2 diabetes mellitus (T2DM) and cardiovascular disease (CVD), understanding the Indian context of the problem and learning how to deal with the obesity epidemic in this country has gained paramount importance. This narrative review points to the unique features of the obesity epidemic in India and its associated contributing factors, including the evolving nature of the Indian diet, the peculiarity of the increased adiposity at lower BMIs, unique obesity-associated genetic variants in Indians, the contribution of the gut microbiome, the impact of chronic inflammation and the role of ambient air pollution, and the contribution of decreased physical activity levels concerning the rapid urbanisation and the built environment. We believe that disseminating our insights into these unique features influencing the development of obesity in India will help increase global awareness and pave the way for better control and management of this obesity epidemic.

Identification of candidate biomarkers and pathways associated with type 1 diabetes mellitus using bioinformatics analysis

Type 1 diabetes mellitus (T1DM) is a metabolic disorder for which the underlying molecular mechanisms remain largely unclear. This investigation aimed to elucidate essential candidate genes and pathways in T1DM by integrated bioinformatics analysis. In this study, differentially expressed genes (DEGs) were analyzed using DESeq2 of R package from GSE162689 of the Gene Expression Omnibus (GEO). Gene ontology (GO) enrichment analysis, REACTOME pathway enrichment analysis, and construction and analysis of protein–protein interaction (PPI) network, modules, miRNA-hub gene regulatory network and TF-hub gene regulatory network, and validation of hub genes were performed. A total of 952 DEGs (477 up regulated and 475 down regulated genes) were identified in T1DM. GO and REACTOME enrichment result results showed that DEGs mainly enriched in multicellular organism development, detection of stimulus, diseases of signal transduction by growth factor receptors and second messengers, and olfactory signaling pathway. The top hub genes such as MYC, EGFR, LNX1, YBX1, HSP90AA1, ESR1, FN1, TK1, ANLN and SMAD9 were screened out as the critical genes among the DEGs from the PPI network, modules, miRNA-hub gene regulatory network and TF-hub gene regulatory network. Receiver operating characteristic curve (ROC) analysis confirmed that these genes were significantly associated with T1DM. In conclusion, the identified DEGs, particularly the hub genes, strengthen the understanding of the advancement and progression of T1DM, and certain genes might be used as candidate target molecules to diagnose, monitor and treat T1DM.

Genetics of early growth traits

In recent years, genome-wide association studies have shed light on the genetics of early growth and its links with later-life health outcomes. Large-scale datasets and meta-analyses, combined with recently developed analytical methods, have enabled dissection of the maternal and fetal genetic contributions to variation in birth weight. Additionally, longitudinal approaches have shown differences between the genetic contributions to infant, childhood and adult adiposity. In contrast, studies of adult height loci have shown strong associations with early body length and childhood height. Early growth-associated loci provide useful tools for causal analyses: Mendelian randomization (MR) studies have provided evidence that early BMI and height are causally related to a number of adult health outcomes. We advise caution in the design and interpretation of MR studies of birth weight investigating effects of fetal growth on later-life cardiometabolic disease because birth weight is only a crude indicator of fetal growth, and the choice of genetic instrument (maternal or fetal) will greatly influence the interpretation of the results. Most genetic studies of early growth have to date centered on European-ancestry participants and outcomes measured at a single time-point, so key priorities for future studies of early growth genetics are aggregation of large samples of diverse ancestries and longitudinal studies of growth trajectories.