FTO Obesity Variant Circuitry and Adipocyte Browning in Humans

Obesity and its management in primary care setting

Obesity is a worldwide epidemic affecting adults and children, regardless of their socioeconomic status. Significant progress has been made in understanding the genetic causes contributing to obesity, shedding light on a portion of cases worldwide. In young children with severe obesity however, recessive mutations, i.e., leptin or leptin receptor deficiency should be sought. Much more has been learned about the far-reaching impact of obesity on complications, including cardiovascular disease, liver and kidney dysfunction, diabetes, inflammation, hypertension, sleep, cancer, and the eye. Preventive strategies, particularly in children, are crucial for reducing obesity rates and mitigating its long-term complications. While dietary modifications and lifestyle changes remain the cornerstone of obesity prevention or treatment, recent advancements have introduced highly effective pharmacological options complementing weight-reduction surgery. Newer medications, like incretin-based therapies including glucagon-like peptide-1 agonists (GLP-1RA), have demonstrated remarkable efficacy in promoting weight loss, offering new insights into margining obesity-related conditions. Primary care providers, whether treating adults or children, play a pivotal role in preventing obesity, initiating treatment, and making onward referrals to specialists to assist in managing obesity and obesity-related complications.

m6A methylation modification of RNA plays a significant role in the occurrence and development of colorectal cancer

Colorectal cancer is the third most common malignant tumor worldwide and ranks second in terms of mortality. N6-methyladenosine (m6A) modification is the most prevalent internal covalent modification in eukaryotic mRNA and is involved in various stages of RNA processing, including splicing, degradation, and export, playing a crucial role in the onset and progression of many diseases. The m6A modification is co-regulated by methyltransferases, demethylases, and methyl-binding proteins, and it has become a hot topic in cancer research. Based on a systematic review of existing studies on the role of m6A modification in colorectal cancer, this article further expands the research horizon in this field and effectively overcomes the limitations of existing reviews that only focus on discussing a single or a class of methylation regulators.

The emerging roles of N6-methyladenosine (m6A) deregulation in polycystic ovary syndrome

Polycystic ovary syndrome (PCOS) is an endocrine metabolic syndrome characterized by ovulation disorders, hyperandrogenemia, and polycystic ovaries, which seriously affect the psychological and physical health of childbearing women. N6-methyladenosine (m6A), as the most common mRNA epigenetic modification in eukaryotes, is vital for developing the female reproductive system and reproductive diseases. In recent years, an increasing number of studies have revealed the mechanisms by which m6A modifications and their related proteins are promoting the development of PCOS, including writers, erasers and readers. In this work, we reviewed the research progress of m6A in the pathophysiological development of PCOS from the starting point of PCOS clinical features, included the recent studies or those with significant findings related to m6A and PCOS, summarized the current commonly used therapeutic methods in PCOS and the possible targeted therapies against the m6A mechanism, and looked forward to future research directions of m6A in PCOS. With the gradual revelation of the m6A mechanism, m6A and its related proteins are expected to become a great field for PCOS treatment.

High-Fat Diet and Metabolic Diseases: A Comparative Analysis of Sex-Dependent Responses and Mechanisms

Sex differences in metabolic disorders and susceptibility to chronic diseases induced by a high-fat diet (HFD) exhibit significant dimorphic characteristics. A long-standing male-centric bias in medical research and healthcare, predominantly focused on male physiological traits, has hindered the precise treatment of metabolic diseases in female patients. A comprehensive understanding of sex differences in metabolic health and their underlying mechanisms is crucial for advancing personalized health promotion and precision medicine. This review systematically elucidates sex-specific manifestations in high-fat diet-associated metabolic disorders: males predominantly develop visceral adiposity, insulin resistance, and dyslipidemia, accompanied by a significantly elevated risk of cardiovascular and metabolic syndromes. Premenopausal females maintain metabolic homeostasis through the estrogen-mediated optimization of glucose and lipid metabolism and oxidative stress buffering mechanisms, whereas postmenopausal-phase females experience dramatic metabolic vulnerability due to z loss of protective barriers. Furthermore, we emphasize multidimensional mechanistic interpretations of metabolic sexual dimorphism from perspectives including sex chromosome complement, sex hormone signaling pathways, epigenetic regulation, gut microbiota composition, and neuroendocrine dimorphism. This work provides critical theoretical foundations for rectifying unisex research paradigms and optimizing sex-specific early warning systems and precision therapeutic strategies for metabolic disorders.

Polygenic Risk and Nutrient Intake Interactions on Obesity Outcomes: A Systematic Review and Meta-Analysis of Observational Studies

BACKGROUND

Diet is an important determinant of body weight and may modulate genetic susceptibility to obesity.

OBJECTIVE

This systematic review and meta-analysis aimed to synthesize evidence related to interactions between polygenic risk and nutrient intakes on obesity outcomes.

METHODS

MEDLINE, EMBASE, Web of Science, and Cochrane Library were systematically searched to identify observational studies that assessed interactions between polygenic risk and nutrient intakes on obesity-related outcomes. Random effects meta-analyses were performed for pooled polygenic risk score (PRS)-total fat intake and PRS-protein intake interaction coefficients on body mass index (BMI).

RESULTS

Twenty-six publications were retrieved with studies conducted among European, Asian, and African samples. Dietary fats (saturated fat, omega-3, and trans fat) and energy intake were most frequently reported to interact with PRS on obesity outcomes, but the total number of studies available was low. No significant interactions were identified in meta-analyses of PRS interactions with total fat intake and protein intake on BMI. Several studies were rated as low quality, heterogeneity was high, and although study samples were racially diverse, PRSs tended to be based on samples of European ancestry.

CONCLUSION

Evidence of interactions between polygenic risk and nutrient intakes on obesity outcomes is limited and inconsistent. Further research addressing limitations related to study quality and polygenic risk characterization is needed.

Gene-environment interaction modifies the association between hyperinsulinemia and serum urate levels through SLC22A12

BACKGROUNDHyperinsulinemia and insulin resistance often accompany elevated serum urate levels (hyperuricemia), a highly heritable condition that triggers gout; however, the underlying mechanisms are unclear.METHODSWe evaluated the association between the index of hyperinsulinemia and the fractional excretion of urate (FEUA) in 162 outpatients. The underlying mechanisms were investigated through single-cell data analysis and kinase screening combined with cell culture experiments. In 377,358 participants of the UK Biobank (UKBB), we analyzed serum urate, hyperinsulinemia, and salt intake. We also examined gene-environment interactions using single nucleotide variants in SLC22A12, which encodes urate transporter 1 (URAT1).RESULTSThe index of hyperinsulinemia was inversely associated with FEUA independently of other covariates. Mechanistically, URAT1 cell-surface abundance and urate transport activity were regulated by URAT1-Thr408 phosphorylation, which was stimulated by hyperinsulinemia via AKT. Kinase screening and single-cell data analysis revealed that serum and glucocorticoid-regulated kinase 1 (SGK1), induced by high salt, activated the same pathway, increasing URAT1. Arg405 was essential for these kinases to phosphorylate URAT1-Thr408. In UKBB participants, hyperinsulinemia and high salt intake were independently associated with increased serum urate levels. We found that SLC22A12 expression quantitative trait locus (eQTL) rs475688 synergistically enhanced the positive association between serum urate and hyperinsulinemia.CONCLUSIONURAT1 mediates the association between hyperinsulinemia and hyperuricemia. Our data provide evidence for the role of gene-environment interactions in determining serum urate levels, paving the way for personalized management of hyperuricemia.FUNDINGACRO Research Grants of Teikyo University; Japan Society for the Promotion of Science; the Japanese Society of Gout and Uric & Nucleic Acids; Fuji Yakuhin; Nanken-Kyoten; Medical Research Center Initiative for High Depth Omics.

Variant-to-function approaches for adipose tissue: Insights into cardiometabolic disorders

Genome-wide association studies (GWASs) have identified thousands of genetic loci associated with cardiometabolic disorders. However, the functional interpretation of these loci remains a daunting challenge. This is particularly true for adipose tissue, a critical organ in systemic metabolism and the pathogenesis of various cardiometabolic diseases. We discuss how variant-to-function (V2F) approaches are used to elucidate the mechanisms by which GWAS loci increase the risk of cardiometabolic disorders by directly influencing adipose tissue. We outline GWAS traits most likely to harbor adipose-related variants and summarize tools to pinpoint the putative causal variants, genes, and cell types for the associated loci. We explain how large-scale perturbation experiments, coupled with imaging and multi-omics, can be used to screen variants' effects on cellular phenotypes and how these phenotypes can be tied to physiological mechanisms. Lastly, we discuss the challenges and opportunities that lie ahead for V2F research and propose a roadmap for future studies.

Trans-eQTL hotspots shape complex traits by modulating cellular states

Regulatory genetic variation shapes gene expression, providing an important mechanism connecting DNA variation and complex traits. The causal relationships between gene expression and complex traits remain poorly understood. Here, we integrated transcriptomes and 46 genetically complex growth traits in a large cross between two strains of the yeast Saccharomyces cerevisiae. We discovered thousands of genetic correlations between gene expression and growth, suggesting potential functional connections. Local regulatory variation was a minor source of these genetic correlations. Instead, genetic correlations tended to arise from multiple independent trans-acting regulatory loci. Trans-acting hotspots that affect the expression of numerous genes accounted for particularly large fractions of genetic growth variation and of genetic correlations between gene expression and growth. Genes with genetic correlations were enriched for similar biological processes across traits but with heterogeneous direction of effect. Our results reveal how trans-acting regulatory hotspots shape complex traits by altering cellular states.

Leveraging chicken embryos for studying human enhancers

The dynamic activity of complex gene regulatory networks stands at the core of all cellular functions that define cell identity and behaviour. Gene regulatory networks comprise transcriptional enhancers, acted upon by cell-specific transcription factors to control gene expression in a spatial and temporal specific manner. Enhancers are found in the non-coding genome; pathogenic variants can disrupt enhancer activity and lead to disease. Correlating non-coding variants with aberrant enhancer activity remains a significant challenge. Due to their clinical significance, there is a longstanding interest in understanding enhancer function during early embryogenesis. With the onset of the omics era, it is now feasible to identify putative tissue-specific enhancers from epigenome data. However, such predictions in vivo require validation. The early stages of chick embryogenesis closely parallel those of human, offering an accessible in vivo model in which to assess the activity of putative human enhancer sequences. This review explores the unique advantages and recent advancements in employing chicken embryos to elucidate the activity of human transcriptional enhancers and the potential implications of these findings in human disease.

Mapping disease loci to biological processes via joint pleiotropic and epigenomic partitioning

Genome-wide association studies (GWAS) have identified thousands of disease-associated loci, yet their interpretation remains limited by the heterogeneity of underlying biological processes. We propose Joint Pleiotropic and Epigenomic Partitioning (J-PEP), a clustering framework that integrates pleiotropic SNP effects on auxiliary traits and tissue-specific epigenomic data to partition disease-associated loci into biologically distinct clusters. To benchmark J-PEP against existing methods, we introduce a metric-Pleiotropic and Epigenomic Prediction Accuracy (PEPA)-that evaluates how well the clusters predict SNP-to-trait and SNP-to-tissue associations using off-chromosome data, avoiding overfitting. Applying J-PEP to GWAS summary statistics for 165 diseases/traits (average N = 290 K ), we attained 16-30% higher PEPA than pleiotropic or epigenomic partitioning approaches with larger improvements for well-powered traits, consistent with simulations; these gains arise from J-PEP's tendency to upweight correlated structure-signals present in both auxiliary trait and tissue data-thereby emphasizing shared components. For type 2 diabetes (T2D), J-PEP identified clusters refining canonical pathological processes while revealing underexplored immune and developmental signals. For hypertension (HTN), J-PEP identified stromal and adrenal-endocrine processes that were not identified in prior analyses. For neutrophil count, J-PEP identified hematopoietic, hepatic-inflammatory, and neuroimmune processes, expanding biological interpretation beyond classical immune regulation. Notably, integrating single-cell chromatin accessibility data refined bulk-based clusters, enhancing cell-type resolution and specificity. For T2D, single-cell data refined a bulk endocrine cluster to pancreatic islet β -cells, consistent with established β -cell dysfunction in insulin deficiency; for HTN, single-cell data refined a bulk endocrine cluster to adrenal cortex cells, consistent with a GO enrichment for neutrophil-mediated inflammation that implicates feedback between aldosterone production in the adrenal gland and local immune signaling. In conclusion, J-PEP provides a principled framework for partitioning GWAS loci into interpretable, tissue-informed clusters that provide biological insights on complex disease.

m6A deficiency impairs hypothalamic neurogenesis of feeding-related neurons in mice and human organoids and leads to adult obesity in mice

N6-methyladenosine (m6A), the most prevalent internal modification on mRNAs, plays important roles in the nervous system. Whether neurogenesis in the hypothalamus, a region critical for controlling appetite, is regulated by m6A signaling, especially in humans, remains unclear. Here, we showed that deletion of m6A writer Mettl14 in the mouse embryonic hypothalamus led to adult obesity, with impaired glucose-insulin homeostasis and increased energy intake. Mechanistically, deletion of Mettl14 leads to hypothalamic arcuate nucleus neurogenesis deficits with reduced generation of feeding-related neurons and dysregulation of neurogenesis-related m6A-tagged transcripts. Deletion of m6A writer Mettl3 or m6A reader Ythdc1 shared similar phenotypes. METTL14 or YTHDC1 knockdown also led to reduced generation of feeding-related neurons in human brain subregion-specific arcuate nucleus organoids. Our studies reveal a conserved role of m6A signaling in arcuate nucleus neurogenesis in mice and human organoids and shed light on the developmental basis of epitranscriptomic regulation of food intake and energy homeostasis.

Cold atmospheric plasma control metabolic syndromes via targeting fat mass and obesity-associated protein

Both obesity and metabolic disorders are global medical problems. Driven by prolonged inflammation, obesity increases the risk of developing metabolic syndromes such as fatty liver, diabetes, cardiovascular diseases and cancers. The fat mass and obesity-associated protein (FTO) is an m6A demethylase, elevated activity of which is known to promote the pathogenesis of many metabolic disorders, leading to the establishment of various FTO inhibitors. By combing through intrinsic connections among obesity and the four primary metabolic problems, we attribute their shared pathological cause to prolonged inflammation. By reviewing the roles of FTO in promoting these disorders and the current status of existing FTO inhibitors in treating these syndromes, we underpinned the paramount potential of resolving these clinical issues by targeting FTO and the urgent need of establishing novel FTO inhibitors with maximized efficacy and minimized side effect. Cold atmospheric plasma (CAP) is the fourth state of matter with demonstrated efficacy in treating various diseases associated with chronic inflammation. By introducing the medical characteristics of CAP, we proposed it as a possible solution to unresolved issues of current FTO inhibitors given its anti-inflammation feature and demonstrated clinical safety. We also emphasized the need of intensive investigations in exploring the feasibility of using CAP in treating obesity and associated metabolic syndromes that might function through targeting FTO.

FTO rs9939609 polymorphism is associated with dietary quality in Korean females

PURPOSE

Variation in fat mass and obesity-associated gene (FTO) is a critical risk factor in the etiology of obesity. FTO is associated with preference and sensory perception of nutrients and dietary intake. However, the effect of genetic variation on overall dietary quality has not yet been fully elucidated. This study examined whether FTO rs9939609 (T > A) was associated with dietary quality in Koreans.

METHODS

Data of 46,928 individuals from the Korean Genome and Epidemiology Study were analyzed according to FTO rs9939609 genotype, general characteristics, and diet quality based on the Korean Healthy Eating Index (KHEI), employing sex- and age-stratified approaches.

RESULTS

The FTO genotype did not significantly influence overall diet quality; however, female carriers of the obesity risk allele A (TA + AA) showed significantly higher KHEI scores for balance of energy nutrient consumption, especially for carbohydrate ratio (2.00 ± 1.99 versus 1.90 ± 1.98, Padjusted <0.001) and fat ratio (2.87 ± 2.15 versus 2.76 ± 2.17, Padjusted <0.001) than A-allele non-carriers (TT). Furthermore, when the females were grouped based on their median age (51 years), such an association between the FTO genotype and energy nutrient ratio was only evident in the younger group. However, such an effect of the genetic variant on diet quality and energy nutrient consumption was not evident in males, and the interactive effect of FTO and sex and age was not statistically significant.

CONCLUSION

The FTO rs9939609 (T > A) polymorphism is associated with dietary quality, particularly influencing the balance of energy nutrient intake in Korean females.

Prioritizing Parkinson's disease risk genes in genome-wide association loci

Many drug targets in ongoing Parkinson's disease (PD) clinical trials have strong genetic links. While genome-wide association studies (GWAS) nominate regions associated with disease, pinpointing causal genes is challenging. Our aim was to prioritize additional druggable genes underlying PD GWAS signals. The polygenic priority score (PoPS) integrates genome-wide information from MAGMA gene-level associations and over 57,000 gene-level features. We applied PoPS to East Asian and European PD GWAS data and prioritized genes based on PoPS, distance to the GWAS signal, and non-synonymous credible set variants. We prioritized 46 genes, including well-established PD genes (SNCA, LRRK2, GBA1, TMEM175, VPS13C), genes with strong literature evidence supporting a mechanistic link to PD (RIT2, BAG3, SCARB2, FYN, DYRK1A, NOD2, CTSB, SV2C, ITPKB), and genes relatively unexplored in PD. Many hold potential for drug repurposing or development. We prioritized high-confidence genes with strong links to PD pathogenesis that may represent our next-best candidates for developing disease-modifying therapeutics.

Visceral adiposity index, premature mortality, and life expectancy in US adults

IMPORTANCE

Visceral adiposity index (VAI) vividly reflects body fat distribution through comprehensively integrating body mass index, sex, waist circumference, triglycerides, and high-density lipoprotein cholesterol. While VAI is an established predictor of various clinical outcomes, its relationship with premature mortality and life expectancy remains unclear.

OBJECTIVE

To explore the association between VAI and premature mortality or life expectancy in a nationally representative cohort of US adults.

METHODS

This study included adults who participated in the National Health and Nutrition Examination Survey (NHANES) from 1999 to 2018, linked to the National Death Index through December 31, 2019. Data were analyzed from August to October, 2024. VAI was categorized into quartiles from the lowest Q1 to the highest Q4. Primary endpoints were premature mortality (death before 80 years of age) and life expectancy.

RESULTS

A total of 43,672 participants (women: 22,164; men: 21,508) aged > 20 years were included. Over a median follow-up of 9.2 years (IQR: 4.9-13.8), 3,187 premature deaths were documented. Higher VAI quartiles were significantly associated with increased multi-adjusted premature mortality risk compared to Q1 (Q3 vs. Q1: hazard ratio [HR], 95% confidence interval [CI]: 1.30, 1.05 to 1.61; Q4 vs. Q1: 1.68, 1.34 to 2.11). This association was particularly pronounced in women (Q3 vs. Q1: 1.53, 1.01 to 2.30; Q4 vs. Q1: 2.36, 1.52 to 3.68), with significant linear trends (P < 0.001). Estimated life expectancy at age 40 years was 41.45 (95% CI: 41.24 to 41.66), 41.32 (41.11 to 41.53), 40.55 (40.35 to 40.75), and 39.26 (39.08 to 39.45) years in Q1, Q2, Q3, and Q4 of VAI, respectively. By sex, estimated life expectancy at age 40 in Q4 was reduced by 3.33 years in women and 1.24 years in men, compared to Q1. By race and ethnicity, it was shortened by 3.90 years in Black participants and 1.68 years in White participants in Q4 group, compared to Q1.

CONCLUSIONS

In this nationwide cohort study, higher VAI was significantly associated with an increased risk of premature mortality and reduced life expectancy at age 40 among US adults. These associations we heterogeneous by sex, race and ethnicity, more pronounced in women and Black participants.

Whole genome sequencing analysis of body mass index identifies novel African ancestry-specific risk allele

Obesity is a major public health crisis associated with high mortality rates. Previous genome-wide association studies (GWAS) investigating body mass index (BMI) have largely relied on imputed data from European individuals. This study leveraged whole-genome sequencing (WGS) data from 88,873 participants from the Trans-Omics for Precision Medicine (TOPMed) Program, of which 51% were of non-European population groups. We discovered 18 BMI-associated signals (P < 5 × 10-9), including two secondary signals. Notably, we identified and replicated a novel low-frequency single nucleotide polymorphism (SNP) in MTMR3 that was common in individuals of African descent. Using a diverse study population, we further identified two novel secondary signals in known BMI loci and pinpointed two likely causal variants in the POC5 and DMD loci. Our work demonstrates the benefits of combining WGS and diverse cohorts in expanding current catalog of variants and genes confer risk for obesity, bringing us one step closer to personalized medicine.

Exploring the genetic influences on equine analgesic efficacy through genome-wide association analysis of ranked pain responses

Multimodal analgesic administration is a promising strategy for mitigating side effects typically associated with analgesia; nevertheless, variation in analgesic effectiveness still poses a considerable safety concern for both horses and veterinarians. Pharmacogenomic studies have started delving into genetic influences on varying drug effectiveness and related side effects. However, current findings have narrow implications and are limited in their ability to individualize analgesic dosages in horses. Hydromorphone and detomidine were administered to a cohort of 48 horses at standardized time intervals, with dosage rates recorded. Analgesic effectiveness was scored (1-3) based on pain response to dura penetration during cerebrospinal fluid centesis. Genome-wide association (GWA) analyses identified two SNVs passing the nominal significance threshold (P < 1 ×10-5) in association with analgesic effectiveness. One SNV identified on chromosome 27 (rs1142378599) is contained within the LOC100630731 disintegrin and metalloproteinase domain-containing protein 5 gene. The second identified SNV is an intergenic variant located on chromosome 29 (rs3430772468) These SNVs accounted for 26.11 % and 31.72 % of explained variation in analgesic effectiveness respectively, with all eight of the horses with the lowest analgesic effectiveness expressing the A/C genotype at rs3430772468, with six of which also expressing the C/T genotype at rs1142872965. Whilst highlighting the multifactorial nature of analgesic efficacy, this study serves as an important step in the application of genome-wide approaches to better understand genetic factors underpinning commonly observed variation in analgesic effectiveness in horses, with the goal of tailoring analgesic dosage to minimize commonly observed side effects and improve the outcomes of equine pain management.

Active regulatory elements recruit cohesin to establish cell specific chromatin domains

As the 3D structure of the genome is analysed at ever increasing resolution it is clear that there is considerable variation in the 3D chromatin architecture across different cell types. It has been proposed that this may, in part, be due to increased recruitment of cohesin to activated cis-elements (enhancers and promoters) leading to cell-type specific loop extrusion underlying the formation of new sub-TADs. Here we show that cohesin correlates well with the presence of active enhancers and that this varies in an allele-specific manner with the presence or absence of polymorphic enhancers which vary from one individual to another. Using the alpha globin cluster as a model, we show that when all enhancers are removed, peaks of cohesin disappear from these regions and the erythroid specific sub-TAD is no longer formed. Re-insertion of the major alpha globin enhancer (R2) is associated with re-establishment of recruitment and increased interactions. In complementary experiments insertion of the R2 enhancer element into a "neutral" region of the genome recruits cohesin, induces transcription and creates a new large (75 kb) erythroid-specific domain. Together these findings support the proposal that active enhancers recruit cohesin, stimulate loop extrusion and promote the formation of cell specific sub-TADs.

An evolving understanding of multiple causal variants underlying genetic association signals

Understanding how genetic variation contributes to phenotypic variation is a fundamental question in genetics. Genome-wide association studies (GWASs) have discovered numerous genetic associations with various human phenotypes, most of which contain co-inherited variants in strong linkage disequilibrium (LD) with indistinguishable statistical significance. The experimental and analytical difficulty in identifying the "causal variant" among the co-inherited variants has traditionally led mechanistic studies to focus on relatively simple loci, where a single functional variant is presumed to explain most of the association signal and affect a target gene. The notion that a single causal variant is responsible for an association signal, while other variants in LD are merely correlated, has often been assumed in functional studies. However, emerging evidence powered by high-throughput experimental tools and context-specific functional databases argues that even a single independent signal may involve multiple functional variants in strong LD, each contributing to the observed genetic association. In this perspective, we articulate this evolving understanding of causal variants through examples from both traditional locus-by-locus approaches and more recent high-throughput functional studies. We then discuss the implications and prospects of this notion in understanding the genetic architecture of complex traits and interpreting the variant-level causality in GWAS follow-up studies.

The importance of thiamine availability in the thermogenic competency of human adipocytes

Brown and beige adipocytes express uncoupling protein 1 (UCP1), which is located in the inner mitochondrial membrane and facilitates the dissipation of excess energy as heat. The activation of thermogenic adipocytes is a potential therapeutic target for treating type 2 diabetes mellitus, obesity, and related co-morbidities. Therefore, identifying novel approaches to stimulate the function of these adipocytes is crucial for advancing therapeutic strategies. Currently, there are limited amount of human adipocyte cell line models available to study the regulatory mechanisms of browning and key players in thermogenesis. The Simpson-Golabi-Behmel syndrome (SGBS) preadipocyte cell line has been proven as a valuable model to investigate human adipocyte biology. In this study, we investigated how excess thiamine (vitamin B1), and the inhibition of thiamine transporters affect the expression of thermogenic markers and functional parameters during adrenergic stimulation in SGBS adipocytes. We found that limiting thiamine availability by pharmacological inhibitors impeded the dibutyryl-cAMP (db-cAMP)-dependent induction of thiamine transporter 1 and 2 (encoded by SLC19A2 and SLC19A3), UCP1, PGC1a, and other browning markers, as well as proton leak respiration which is associated with UCP1-dependent heat generation. Contrarily, excess thiamine enhanced the db-cAMP-dependent induction of thiamine transporters, while UCP1, PGC1a, and other browning markers were upregulated. In addition, abundant amounts of thiamine increased the basal, unstimulated coupled and uncoupled respiration, and the expression of mitochondrial complex subunits. Our study highlights the critical role of excess thiamine in the thermogenic activation of SGBS adipocytes and its potential to enhance thermogenesis.

Genetic determinants of muscle health: A population-based study

BACKGROUND

Muscle mass is associated with physical and functional performance across adulthood. Its reduction plays a crucial role in the development of age-related conditions such as frailty and sarcopenia. Genetic variations potentially impact muscle health, particularly in an aged population.

OBJECTIVES

For this reason, we aimed to evaluate the association between genetic biomarkers and appendicular lean mass index (ALMI), a marker of muscle health, to identify possible risk factors for age-related sarcopenia in a population-based study.

MATERIALS AND METHODS

We cross-sectionally analyzed data collected in 2015 from the São Paulo Epidemiologic Sleep Study (EPISONO). Participants underwent bioelectrical impedance and genetic evaluations.

RESULTS

After adjusting the data for age and sex, 12 single nucleotide polymorphisms (SNP) were significantly associated with ALMI. Among them, rs9928094 (beta = -0.031 p = 0.029) and rs9930333 (beta = -0.030 p = 0.035) are located in the FTO gene, which is related to obesity and fat gain and, rs16839632 (beta = 0.038 p = 0.029) located in the FMN2 gene, responsible for actin cytoskeleton and cell polarity.

CONCLUSIONS

Poor muscle health is a multifactorial condition and genetic biomarkers can support the stratification of the risk for adverse body composition states affecting muscle and physical performance across adulthood.

Human genetics of metabolic dysfunction-associated steatotic liver disease: from variants to cause to precision treatment

Metabolic dysfunction-associated steatotic liver disease (MASLD) is characterized by increased hepatic steatosis with cardiometabolic disease and is a leading cause of advanced liver disease. We review here the genetic basis of MASLD. The genetic variants most consistently associated with hepatic steatosis implicate genes involved in lipoprotein input or output, glucose metabolism, adiposity/fat distribution, insulin resistance, or mitochondrial/ER biology. The distinct mechanisms by which these variants promote hepatic steatosis result in distinct effects on cardiometabolic disease that may be best suited to precision medicine. Recent work on gene-environment interactions has shown that genetic risk is not fixed and may be exacerbated or attenuated by modifiable (diet, exercise, alcohol intake) and nonmodifiable environmental risk factors. Some steatosis-associated variants, notably those in patatin-like phospholipase domain-containing 3 (PNPLA3) and transmembrane 6 superfamily member 2 (TM6SF2), are associated with risk of developing adverse liver-related outcomes and provide information beyond clinical risk stratification tools, especially in individuals at intermediate to high risk for disease. Future work to better characterize disease heterogeneity by combining genetics with clinical risk factors to holistically predict risk and develop therapies based on genetic risk is required.

IRX5 Promoted SREBP1-Mediated de Novo Fatty Acid Synthesis via HMGN4 in Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC), a prevalent malignant tumour, ranks highly in both morbidity and mortality, and its prevention and treatment need further studies. The transcription factor iroquois homeobox 5 (IRX5) plays an essential role in HCC, whereas little is known about its exact functions and underlying mechanisms in tumour metabolism reprogramming. Besides, as a transcription factor that mainly locates in nuclei, IRX5 lacks a nuclear localisation sequence, which makes uncovering the mechanism of IRX5 translocating into the nuclei of great significance. Here, we first found that both IRX5 and HCC development are highly expressed; IRX5 accelerates de novo fatty acid synthesis and promotes cancer cell proliferation and progression. Moreover, the GST pull-down combined with GC/MS experiments identified an interaction between IRX5 and high-mobility group nucleosomal binding domain 4 (HMGN4). Immunofluorescence analysis showed that IRX5 and HMGN4 colocalised within the nucleus. Coimmunoprecipitation further confirmed their direct interaction. The elevated expression of HMGN4 enhanced the nuclear transport of IRX5. Taken together, our observations suggest that HMGN4 driving IRX5 nuclear translocation promotes HCC development via de novo fatty acid synthesis reprogramming.

A Complex Network of Obesity-Risk Genes Revealed by Systematic Bioinformatics and Single-Cell Transcriptomic Analyses

The development of obesity is closely linked to genetic factors. Despite the identification of numerous genes associated with an increased risk of obesity in humans, a comprehensive understanding of their biological roles has not been achieved. In our extensive bioinformatics study, we identified 802 core genes implicated in obesity. Our protein-protein interaction (PPI) network analysis revealed that these genes form a tightly connected functional network primarily involved in neurological and metabolic regulatory processes. Moreover, our in-depth analysis of single-cell transcriptomic datasets from the human hypothalamus, pancreatic islets, adipose tissue, and liver has shed light on the distinct expression profiles of these obesity-linked genes across various tissue and cell types. This analysis also highlighted the biological processes they influence and the upstream transcriptional regulatory networks involved. Our study not only uncovers the complicated regulatory role of genetic factors in the pathogenesis and progression of obesity but also establishes a close link between the expression patterns and functional roles of these obesity-associated genes. This study provides crucial insights for advancing our understanding of the genetic mechanisms underlying obesity.

Genotype inference from aggregated chromatin accessibility data reveals genetic regulatory mechanisms

BACKGROUND

Understanding the genetic causes underlying variability in chromatin accessibility can shed light on the molecular mechanisms through which genetic variants may affect complex traits. Thousands of ATAC-seq samples have been collected that hold information about chromatin accessibility across diverse cell types and contexts, but most of these are not paired with genetic information and come from distinct projects and laboratories.

RESULTS

We report here joint genotyping, chromatin accessibility peak calling, and discovery of quantitative trait loci which influence chromatin accessibility (caQTLs), demonstrating the capability of performing caQTL analysis on a large scale in a diverse sample set without pre-existing genotype information. Using 10,293 profiling samples representing 1454 unique donor individuals across 653 studies from public databases, we catalog 24,159 caQTLs in total. After joint discovery analysis, we cluster samples based on accessible chromatin profiles to identify context-specific caQTLs. We find that caQTLs are strongly enriched for annotations of gene regulatory elements across diverse cell types and tissues and are often linked with genetic variation associated with changes in expression (eQTLs), indicating that caQTLs can mediate genetic effects on gene expression. We demonstrate sharing of causal variants for chromatin accessibility across human traits, enabling a more complete picture of the genetic mechanisms underlying complex human phenotypes.

CONCLUSIONS

Our work provides a proof of principle for caQTL calling from previously ungenotyped samples and represents one of the largest, most diverse caQTL resources currently available, informing mechanisms of genetic regulation of gene expression and contribution to disease.

Regulatory risk loci link disrupted androgen response to pathophysiology of Polycystic Ovary Syndrome

A major challenge in deciphering the complex genetic landscape of Polycystic Ovary Syndrome (PCOS) is the limited understanding of the molecular mechanisms driven by susceptibility loci, necessitating investigation into the regulatory pathways that contribute to the diverse phenotypic manifestations of PCOS. In this study, we integrated molecular and epigenomic annotations across proposed pathogenic cell types and employed a deep learning (DL) model to infer the cell-type-specific effects of risk variants. Our analysis revealed the role of these variants in brain and endocrine cell types affecting the binding sites of key transcription factors (TFs)-FOXA1, FOXL1, WT1, SALL4, and CPEB1-which regulate ovarian development, folliculogenesis, and steroid hormone signaling, contributing to disease-associated transcriptomic profiles. Our DL model, which is strongly correlated with MPRA data, identified enhancer-disrupting activity in 20% of the risk variants, particularly affecting TFs involved in androgen-mediated signaling, shedding light on the molecular consequences of hyperandrogenemia. Using the IRX3-FTO locus as a case study, we explored the potential cell-type-specific regulatory effects of risk variants in the fetal brain, pancreas, adipocytes, and an endothelial cell-line, which suggest that disruptions in IRX3 regulation (previously linked to obesity) may contribute to PCOS pathogenesis through diverse mechanisms, including neuronal development, metabolic regulation, and folliculogenesis. Our findings underscore the value of integrating DL models with epigenomic annotations to identify disease-relevant variants, explore the pleiotropic impact of disease risk loci, and gain novel insights into cross-cell-type regulatory interactions.

The Secret Life of N1-methyladenosine: A Review on its Regulatory Functions

N1-methyladenosine (m1A) is a conserved modification on house-keeping RNAs, including tRNAs and rRNAs. With recent advancement on m1A detection and mapping, m1A is revealed to have a secret life with regulatory functions. This includes the regulation of its canonical substrate tRNAs, and expands into new territories such as tRNA fragments, mRNAs and repeat RNAs. The dynamic regulation of m1A has been shown in different biological contexts, including stress response, diet, T cell activation and aging. Interestingly, m1A can also be installed by non-enzymatic mechanisms. However, technical challenges remain in m1A site mapping; as a result, controversies have been observed across different labs or different methods. In this review we will summarize the recent development of m1A detection, its dynamic regulation, and its biological functions on diverse RNA substrates.

Both Fetal and Maternal Genotypes Affect Preeclampsia Pathogenesis in Iranian Patients

Preeclampsia is a multifactorial disorder that only occurs during pregnancy. Several genome-wide association studies (GWASs) have revealed potential susceptible variants associated with preeclampsia in different populations. GWASs findings in other ethnicities must be replicated in order to confirm the observed genotype-phenotype association. Here, we performed a replication study to investigate the association of three previously reported genome-wide signals, including FLT1rs4769612, FTO rs1421085, and ZNF831 rs259983, with preeclampsia in the Iranian population. A total of 600 subjects were recruited for this study. The maternal group included 200 preeclamptic patients and 200 healthy normotensive pregnant women. The fetal group included 100 individuals born of preeclamptic pregnancies and 100 individuals born from healthy pregnancies. The tetra-primer amplification refractory mutation system-polymerase chain reaction (TP-ARMS PCR) technique was used for genotyping the rs4769612, rs1421085, and rs259983 variants. The fetal genotype of rs4769612 (FLT1) was associated with preeclampsia risk under the recessive inheritance model. Moreover, fetal rs1421085 (FTO) increased the risk of preeclampsia under dominant and over-dominant inheritance models. Regarding ZNF831 rs259983, only the maternal genotype was associated with preeclampsia under the dominant model, and no association was detected between the fetal genotype and the disease risk. Although the present results showed discrepancies with previous studies considering the association of maternal or fetal genotypes with preeclampsia, all three studied polymorphisms were related to the disease risk in the Iranian population. Based on our study, rs4769612, rs1421085, and rs259983 were associated with the risk of preeclampsia in the Iranian population.

An obesogenic FTO allele causes accelerated development, growth and insulin resistance in human skeletal muscle cells

Human GWAS have shown that obesogenic FTO polymorphisms correlate with lean mass, but the mechanisms have remained unclear. It is counterintuitive because lean mass is inversely correlated with obesity and metabolic diseases. Here, we use CRISPR to knock-in FTOrs9939609-A into hESC-derived tissue models, to elucidate potentially hidden roles of FTO during development. We find that among human tissues, FTOrs9939609-A most robustly affect human muscle progenitors' proliferation, differentiation, senescence, thereby accelerating muscle developmental and metabolic aging. An edited FTOrs9939609-A allele over-stimulates insulin/IGF signaling via increased muscle-specific enhancer H3K27ac, FTO expression and m6A demethylation of H19 lncRNA and IGF2 mRNA, with excessive insulin/IGF signaling leading to insulin resistance upon replicative aging or exposure to high fat diet. This FTO-m6A-H19/IGF2 circuit may explain paradoxical GWAS findings linking FTOrs9939609-A to both leanness and obesity. Our results provide a proof-of-principle that CRISPR-hESC-tissue platforms can be harnessed to resolve puzzles in human metabolism.

Advances in energy balance & metabolism circuitry

Advancements in informatics, genetics, and neuroscience have greatly expanded our understanding of how the central nervous system (CNS) regulates energy balance and metabolism. This chapter explores the key neural circuits within the hypothalamus and brainstem that integrate behavioral and physiological processes to maintain metabolic homeostasis. It also examines the dynamic interplay between the CNS and peripheral organs, mediated through hormonal and neuronal signals, which fine-tune appetite, energy expenditure, and body weight. Furthermore, we highlight groundbreaking research that unveils molecular and cellular pathways governing energy regulation, representing a new frontier in addressing obesity and metabolic disorders. Innovative approaches, such as neurogenetic and neuromodulation techniques, are explored as promising strategies for improving weight management and metabolic health. By providing a comprehensive perspective on the mechanisms underlying energy balance, this chapter underscores the transformative potential of emerging therapeutic innovations.

Functionally characterizing obesity-susceptibility genes using CRISPR/Cas9, in vivo imaging and deep learning

Hundreds of loci have been robustly associated with obesity-related traits, but functional characterization of candidate genes remains a bottleneck. Aiming to systematically characterize candidate genes for a role in accumulation of lipids in adipocytes and other cardiometabolic traits, we developed a pipeline using CRISPR/Cas9, non-invasive, semi-automated fluorescence imaging and deep learning-based image analysis in live zebrafish larvae. Results from a dietary intervention show that 5 days of overfeeding is sufficient to increase the odds of lipid accumulation in adipocytes by 10 days post-fertilization (dpf, n = 275). However, subsequent experiments show that across 12 to 16 established obesity genes, 10 dpf is too early to detect an effect of CRISPR/Cas9-induced mutations on lipid accumulation in adipocytes (n = 1014), and effects on food intake at 8 dpf (n = 1127) are inconsistent with earlier results from mammals. Despite this, we observe effects of CRISPR/Cas9-induced mutations on ectopic accumulation of lipids in the vasculature (sh2b1 and sim1b) and liver (bdnf); as well as on body size (pcsk1, pomca, irs1); whole-body LDLc and/or total cholesterol content (irs2b and sh2b1); and pancreatic beta cell traits and/or glucose content (pcsk1, pomca, and sim1a). Taken together, our results illustrate that CRISPR/Cas9- and image-based experiments in zebrafish larvae can highlight direct effects of obesity genes on cardiometabolic traits, unconfounded by their - not yet apparent - effect on excess adiposity.

Comparative transcriptomic and metabolomic analysis of FTO knockout and wild-type porcine iliac artery endothelial cells

The fat mass and obesity associated (FTO) gene, previously identified as a pivotal genetic locus associated with adiposity, has recently been linked to various cancers. In this study, we established an FTO knockout (KO) cell line in porcine iliac artery endothelial cells (PIECs) utilizing CRISPR/Cas9 technology to systematically investigate the gene's function and effect through transcriptomic and metabolomic analysis. Our results revealed significant gene expression and metabolic profiles differences between the FTO KO and wild-type (WT) cells. Furthermore, enrichment analysis highlighted the involvement of differentially expressed genes in metabolic processes, cellular components, and molecular functions, as well as in complement and coagulation cascades, mineral absorption, glutathione metabolism, insulin signaling, fluid shear stress, and atherosclerosis pathways. The metabolomic profiling revealed clear distinctions between the FTO KO and WT cells, indicating profound modifications in cellular metabolism. Correlation analysis of transcriptomic and metabolomic data revealed a significant association between six metabolites and twenty genes, with melatonin showing specific correlations with the expression of several genes, indicating a complex regulatory network between gene expression and metabolic changes. This study provides a foundation for further research on the FTO gene's role in cellular processes and molecular mechanisms underlying physiological and pathological conditions.

Obesity and Cardiometabolic Disease: Insights From Genetic Studies

Obesity is a highly prevalent chronic disease and major driver of both atherosclerotic heart disease and heart failure. Obesity is also a heritable neuronal disease with heritability estimates of up to 70%. In this work I review how common genetic variants, usually with small effect sizes, contribute to the risk for developing obesity and cardiometabolic disease in the majority of people and how this can be further modulated by environmental factors. In some individuals, rare genetic variants with large effect sizes can influence the risk of developing obesity, in some cases in a Mendelian manner. I also address how identification of these rare variants has led to fundamental biologic insights into how satiety and reward are biologic processes, has led to more personalized treatments, and has identified potential novel drug treatments. Biologic insights derived from genetic studies of obesity have also improved our understanding of the causal mediators between obesity and cardiovascular disease. A major limitation of studies to date is that they involved mostly people of European ancestry. Studying more diverse populations will improve our understanding of obesity and cardiometabolic disease. Lessons derived from genetic studies make a compelling case for increasing accessibility to therapies that have sustained efficacy in managing obesity and improving health. This increased knowledge must also inform public health initiatives that will reduce the prevalence of obesity in the coming decades.

A guide to studying 3D genome structure and dynamics in the kidney

The human genome is tightly packed into the 3D environment of the cell nucleus. Rapidly evolving and sophisticated methods of mapping 3D genome architecture have shed light on fundamental principles of genome organization and gene regulation. The genome is physically organized on different scales, from individual genes to entire chromosomes. Nuclear landmarks such as the nuclear envelope and nucleoli have important roles in compartmentalizing the genome within the nucleus. Genome activity (for example, gene transcription) is also functionally partitioned within this 3D organization. Rather than being static, the 3D organization of the genome is tightly regulated over various time scales. These dynamic changes in genome structure over time represent the fourth dimension of the genome. Innovative methods have been used to map the dynamic regulation of genome structure during important cellular processes including organism development, responses to stimuli, cell division and senescence. Furthermore, disruptions to the 4D genome have been linked to various diseases, including of the kidney. As tools and approaches to studying the 4D genome become more readily available, future studies that apply these methods to study kidney biology will provide insights into kidney function in health and disease.

Dissection of type 2 diabetes: a genetic perspective

Diabetes is a leading cause of global mortality and disability, and its economic burden is substantial. This Review focuses on type 2 diabetes, which makes up 90-95% of all diabetes cases. Type 2 diabetes involves a progressive loss of insulin secretion often alongside insulin resistance and metabolic syndrome. Although obesity and a sedentary lifestyle are considerable contributors, research over the last 25 years has shown that type 2 diabetes develops on a predisposing genetic background, with family and twin studies indicating considerable heritability (ie, 31-72%). This Review explores type 2 diabetes from a genetic perspective, highlighting insights into its pathophysiology and the implications for precision medicine. More specifically, the traditional understanding of type 2 diabetes genetics has focused on a dichotomy between monogenic and polygenic forms. However, emerging evidence suggests a continuum that includes monogenic, oligogenic, and polygenic contributions, revealing their complementary roles in type 2 diabetes pathophysiology. Recent genetic studies provide deeper insights into disease mechanisms and pave the way for precision medicine approaches that could transform type 2 diabetes management. Additionally, the effect of environmental factors on type 2 diabetes, particularly from epigenetic modifications, adds another layer of complexity to understanding and addressing this multifaceted disease.

Therapeutic Potential of FTO Demethylase in Metabolism and Disease Pathways

The crucial involvement of the Fat Mass and Obesity-associated (FTO) protein in both metabolic and non-metabolic diseases has been documented since its discovery. This enzyme, known as FTO, is a demethylase that belongs to the 2-oxoglutarate-dependent nucleic acid demethylases. Its primary function is to target N6-methyladenosine (m6A) in RNA, which is crucial in regulating RNA stability, processing, and expression. This review facilitates understanding the FTO gene variations linked to Body Mass Index (BMI) and obesity, resulting in increased vulnerability to type 2 diabetes. While prior reviews have already discussed the link between FTO and BMI and its impact on type 2 diabetes, the current review additionally examines the emerging evidence suggesting a direct influence of the FTO gene on metabolism. Additionally, the paper discusses the alternative role of FTO and emphasizes the endophenotypes in neurological circuits and the demethylase function of FTO in neurodegenerative disorders. The review further examines the impact of FTO on several physiological systems and emphasizes the need to study FTO as a potential multitarget for future research and therapies.

Using omics data and genome editing methods to decipher GWAS loci associated with coronary artery disease

Coronary artery disease (CAD) is due to atherosclerosis, a pathophysiological process that involves several cell-types and results in the accumulation of lipid-rich plaque that disrupt the normal blood flow through the coronary arteries to the heart. Genome-wide association studies have identified 1000s of genetic variants robustly associated with CAD or its traditional risk factors (e.g. blood pressure, blood lipids, type 2 diabetes, smoking). However, gaining biological insights from these genetic discoveries remain challenging because of linkage disequilibrium and the difficulty to interpret the functions of non-coding regulatory elements in the human genome. In this review, we present different statistical methods (e.g. Mendelian randomization) and molecular datasets (e.g. expression or protein quantitative trait loci) that have helped connect CAD-associated variants with genes, biological pathways, and cell-types or tissues. We emphasize that these various strategies make predictions, which need to be validated in orthologous systems. We discuss specific examples where the integration of omics data with GWAS results has prioritized causal CAD variants and genes. Finally, we review how targeted and genome-wide genome editing experiments using the CRISPR/Cas9 toolbox have been used to characterize new CAD genes in human cells. Researchers now have the statistical and bioinformatic methods, the molecular datasets, and the experimental tools to dissect comprehensively the loci that contribute to CAD risk in humans.

Simplifying causal gene identification in GWAS loci

Genome-wide association studies (GWAS) help to identify disease-linked genetic variants, but pinpointing the most likely causal genes in GWAS loci remains challenging. Existing GWAS gene prioritization tools are powerful but often use complex black box models trained on datasets containing unaddressed biases. Here, we use a data-driven approach to construct a truth set of causal genes in 406 GWAS loci. We train a gene prioritization tool, CALDERA, that uses a simple logistic regression model with L1 regularization and corrects for potential confounders. Using three independent benchmarking datasets of resolved GWAS loci, we compare the performance of CALDERA with three other methods (FLAMES, L2G, and cS2G). CALDERA outperforms all these methods in two out of three datasets and ranks second in the remaining dataset. We demonstrate that CALDERA prioritizes genes with expected properties, such as mutation intolerance (OR = 1.751 for pLI > 90%, P = 8.45×10-3). Overall, CALDERA provides a powerful solution for prioritizing potentially causal genes in GWAS loci and may help identify novel genetics-driven drug targets.

Abundant repressor binding sites in human enhancers are associated with the fine-tuning of gene regulation

The regulation of gene expression relies on the coordinated action of transcription factors (TFs) at enhancers, including both activator and repressor TFs. We employed deep learning (DL) to dissect HepG2 enhancers into positive (PAR), negative (NAR), and neutral activity regions. Sharpr-MPRA and STARR-seq highlight the dichotomy impact of NARs and PARs on modulating and catalyzing the activity of enhancers, respectively. Approximately 22% of HepG2 enhancers, termed "repressive impact enhancers" (RIEs), are predominantly populated by NARs and transcriptional repression motifs. Genes flanking RIEs exhibit a stage-specific decline in expression during late development, suggesting RIEs' role in trimming enhancer activities. About 16.7% of human NARs emerge from neutral rhesus macaque DNA. This gain of repressor binding sites in RIEs is associated with a 30% decrease in the average expression of flanking genes in humans compared to rhesus macaque. Our work reveals modulated enhancer activity and adaptable gene regulation through the evolutionary dynamics of TF binding sites.

The relationship between dietary branched-chain and aromatic amino acids with the regulation of leptin and FTO genes in adipose tissue of patients undergoing abdominal surgery

Recent studies have suggested that the interaction between diet and an individual's genetic predisposition can determine the likelihood of obesity and various metabolic disorders. The current study aimed to examine the association of dietary branched-chain amino acids(BCAAs) and aromatic amino acids(AAAs) with the expression of the leptin and FTO genes in the visceral and subcutaneous adipose tissues of individuals undergoing surgery. This cross-sectional study was conducted on 136 Iranian adults, both men and women, aged ≥18 years. The samples were selected from patients admitted for abdominal surgeries. The dietary intake of BCAAs and AAAs was determined using a valid and reliable 168-item food frequency questionnaire. Using the quantitative PCR method, leptin and FTO mRNA expression was measured in both visceral and subcutaneous fat tissues. The mean age of the participants was 39.8 ± 12.7 years, and the mean intake of BCAAs and AAAs was 17.7 ± 0.9 and 9.3 ± 0.3% of protein per day, respectively. In overweight-obese patients(body mass index = 25-34.9 kg/m2), the intake of BCAAs(β:-0.75,95%CI:-1.47,-0.03), valine(β:-0.78,95%CI:-1.51,-0.05), and tyrosine(β:-0.81,95%CI:-1.55,-0.06) was inversely associated with FTO gene expression in subcutaneous fat tissue in adjusted model. In morbidly obese patients(body mass index ≥ 35 kg/m2), a higher intake of total BCAAs(β:1.10,95%CI:0.07-2.13), leucine(β:1.07,95%CI:0.03-2.13), and isoleucine(β:1.49,95%CI:0.46-2.52) was associated with an increase of leptin gene expression in subcutaneous fat tissue. Our findings suggest that dietary BCAA may associated with gene expression in adipose tissues, potentially influencing obesity-related metabolic pathways. Further prospective studies are warranted to validate results and elucidate the potential for dietary interventions targeting amino acids intake in obesity management.

Response eQTLs, chromatin accessibility, and 3D chromatin structure in chondrocytes provide mechanistic insight into osteoarthritis risk

Osteoarthritis (OA) poses a significant healthcare burden with limited treatment options. While genome-wide association studies (GWASs) have identified over 100 OA-associated loci, translating these findings into therapeutic targets remains challenging. To address this gap, we mapped gene expression, chromatin accessibility, and 3D chromatin structure in primary human articular chondrocytes in both resting and OA-mimicking conditions. We identified thousands of differentially expressed genes, including those associated with differences in sex and age. RNA sequencing in chondrocytes from 101 donors across two conditions uncovered 3,782 unique eGenes, including 420 that exhibited strong and significant condition-specific effects. Colocalization with OA GWAS signals revealed 13 putative OA risk genes, 6 of which have not been previously identified. Chromatin accessibility and 3D chromatin structure provided insights into the mechanisms and conditional specificity of these variants. Our findings shed light on OA pathogenesis and highlight potential targets for therapeutic development.

Systematic functional characterization of non-coding regulatory SNPs associated with central obesity

Central obesity is associated with higher risk of developing a wide range of diseases independent of overall obesity. Genome-wide association studies (GWASs) have identified more than 300 susceptibility loci associated with central obesity. However, the functional understanding of these loci is limited by the fact that most loci are in non-coding regions. To address this issue, our study first prioritized 2,034 single-nucleotide polymorphisms (SNPs) based on fine-mapping and epigenomic annotation analysis. Subsequently, we employed self-transcribing active regulatory region sequencing (STARR-seq) to systematically evaluate the enhancer activity of these prioritized SNPs. The resulting data analysis identified 141 SNPs with allelic enhancer activity. Further analysis of allelic transcription factor (TF) binding prioritized 20 key TFs mediating the central-obesity-relevant genetic regulatory network. Finally, as an example, we illustrate the molecular mechanisms of how rs8079062 acts as an allele-specific enhancer to regulate the expression of its targeted RNF157. We also evaluated the role of RNF157 in the adipogenic differentiation process. In conclusion, our results provide an important resource for understanding the genetic regulatory mechanisms underlying central obesity.

A bioinformatics toolbox to prioritize causal genetic variants in candidate regions

This review addresses the significant challenge of identifying causal genetic variants within quantitative trait loci (QTLs) for complex traits and diseases. Despite progress in detecting the ever-larger number of such loci, establishing causality remains daunting. We advocate for integrating bioinformatics and multiomics analyses to streamline the prioritization of candidate genes' variants. Our case study on the Pla2g4e gene, identified previously as a positional candidate obesity gene through genetic mapping and expression studies, demonstrates how applying multiomic data filtered through regulatory elements containing SNPs can refine the search for causative variants. This approach can yield results that guide more efficient experimental strategies, accelerating genetic research toward functional validation and therapeutic development.

PROTAC-mediated FTO protein degradation effectively alleviates diet-induced obesity and hepatic steatosis

Demethylation of N6-Methyladenosine (m6A) by fat mass and obesity-associated protein (FTO) occurs in the development of obesity and fatty liver disease. In this study, we synthesized FTO-degradation targeted chimera (FTO-DT), which exhibited excellent lipid-lowering activity at low concentration. At a concentration of 0.33 nM, the FTO-DT continuously and efficiently degraded FTO protein and reduced fat deposition. The FTO-DT improved energy metabolism and oxidative stress by increasing intracellular m6A levels, and further reduced fat deposition in hepatocytes, adipocytes, and mice fed a high-fat diet. The findings support the potential of FTO degradation by FTO-DT as a therapy for obesity and metabolic-associated fatty liver disease (MAFLD). This study provides a theoretical basis for the application of PROTACs in the treatment of metabolic disease and describes a novel approach for the development of drugs targeting metabolic disorders.

General Kernel Machine Methods for Multi-Omics Integration and Genome-Wide Association Testing With Related Individuals

Integrating multi-omics data may help researchers understand the genetic underpinnings of complex traits and diseases. However, the best ways to integrate multi-omics data and use them to address pressing scientific questions remain a challenge. One important and topical problem is how to assess the aggregate effect of multiple genomic data types (e.g. genotypes and gene expression levels) on a phenotype, particularly while accommodating routine issues, such as having related subjects' data in analyses. In this paper, we extend an existing composite kernel machine regression model to integrate two multi-omics data types, while accommodating for general correlation structures amongst outcomes. Due to the kernel machine regression framework, our methods allow for the integration of high-dimensional omics data with small, nonlinear, and interactive effects, and accommodation of general study designs. Here, we focus on scientific questions that aim to assess the association between a functional grouping (such as a gene or a pathway) and a quantitative trait of interest. We use a kernel machine regression to integrate the two multi-omics data types, as they may relate to the trait, and perform a global test of association. We demonstrate the advantage of this approach over single data type association tests via simulation. Finally, we apply this method to a large, multi-ethnic data set to investigate how predicted gene expression and rare genetic variation may be related to two platelet traits.

Maximal Fat Oxidation During Exercise in Healthy Individuals: Lack of Genetic Association with the FTO rs9939609 Polymorphism

Background/Objectives: Previous studies suggest that there is a genetically determined component of fat oxidation at rest and during exercise. To date, the FTO gene has been proposed as a candidate gene to affect fat oxidation during exercise because of the association of the "at-risk" A allele with different obesity-related factors such as increased body fat, higher appetite and elevated insulin and triglyceride levels. The A allele of the FTO gene may also be linked to obesity through a reduced capacity for fat oxidation during exercise, a topic that remains largely underexplored in the current literature. The aim of this study was to analyze the association between the FTO rs9939609 polymorphism with the rate of fat oxidation during exercise and metabolic syndrome criteria in healthy participants. Methods: A total of 80 healthy participants (41 men and 39 women) underwent comprehensive assessments, including measurements of anthropometric variables, blood pressure and blood measures of fasting glucose, triglycerides, low- and high-density lipoprotein cholesterol (LDL-c and HDL-c), insulin, interleukin-6 (IL-6) and C-reactive protein (CRP) concentrations. Additionally, the Homeostatic Model Assessment (HOMA-IR) was used to evaluate insulin resistance. Peak oxygen uptake (VO2peak) and maximal fat oxidation rate (MFO) were also measured during an incremental cycling test. FTO rs9939609 genotyping (TT, AT, AA) was performed using genomic DNA samples obtained from a buccal swab and measured with PCR. Results: There were 32 participants (40.0%) with the TT genotype; 31 (38.8%) with the AT genotype; and 17 (21.2%) with the AA genotype. Age, body characteristics, VO2peak, blood pressure and blood variables were similar across all three genotypes. However, serum insulin concentration and HOMA-IR were associated with the FTO rs9939609 genotype with higher values in AA with respect to AT and TT participants (p < 0.050). Still, MFO was similar in TT, AT and AA participants (0.35 ± 0.13, 0.37 ± 0.11, 0.33 ± 0.11 g/min, p = 0.702). In the dominant model, there was no statistical difference between TT and A allele carriers. However, the recessive model revealed that AA participants had higher values of body mass, body mass index, blood insulin concentration and HOMA-IR than T allele carriers (p < 0.050), with no differences in MFO. Conclusions: In our sample of healthy individuals, the FTO rs9939609 polymorphism was associated with several phenotypes associated with obesity and insulin resistance, particularly under the AA vs. T allele/recessive model. However, the FTO rs9939609 polymorphism was not associated with MFO during exercise as fat oxidation was similar across genotypes. This suggests that reduced fat oxidation during exercise is unlikely to be a cause of the obesogenic influence of the FTO AA genotype. Clinically, these findings suggest that the obesogenic effects of the FTO AA genotype are unlikely driven by impaired fat oxidation during exercise. Instead, attention should focus on mechanisms like appetite regulation and energy intake. Moreover, exercise interventions may still effectively mitigate obesity risk, as AA individuals retain normal fat oxidation capacity during exercise.

Association between FTO gene polymorphism and obesity in down syndrome children

Children with Down syndrome (DS) have a higher incidence of overweight and obesity compared to typically developing peers. The fat mass and obesity-associated gene (FTO) is one of the early identified genes linked to obesity in various populations. To date, the FTO rs17817449 gene polymorphism has not been investigated in overweight/obese-DS (ODS) individuals. The current study aimed to explore the potential association between the FTO rs17817449 gene polymorphism and obesity-related markers, and to evaluate the ability of this polymorphism in the prediction of overweight/obesity in DS children and adolescents. This case-control study included 100 DS children under the age of 18, classified into three groups according to BMI-percentile; 50 non-obese DS (NODS), 24 overweight DS, and 26 ODS. Genotyping of FTO gene rs17817449 polymorphism was performed using the restriction fragment length polymorphism (RFLP-PCR) method. Serum lipid and thyroid profiles were also assessed. The results revealed significant increase in the frequency of the FTO rs17817449 T allele among overweight /ODS children compared to NODS children (p=0.0099). Overweight/ODS children exhibited significantly higher frequencies of the FTO rs17817449 GT and TT genotypes compared to NODS children.

CONCLUSION

There is an association between FTO rs17817449 genetic variant and overweight/obesity among the studied DS groups. The FTO rs17817449 GT and TT genotypes, as well as TGs level, were identified as independent risk factors for predicting overweight and obesity in DS children.

WHAT IS KNOWN

• Overweight and obese-DS (ODS) children displayed higher BMI and atherogenic lipid profile than non-obese DS children (NODS). FTO gene polymorphism rs17817449 contributes to obesity development in general population, but there is conflicting information about the risk allele.

WHAT IS NEW

• FTO rs17817449 TT genotype and T allele were considered as independent risk factors for overweight and obesity development in DS children, so they could be used for obesity prediction in DS children.

FTO in health and disease

Fat mass and obesity-associated (FTO) protein, a key enzyme integral to the dynamic regulation of epitranscriptomic modifications in RNAs, significantly influences crucial RNA lifecycle processes, including splicing, export, decay, and translation. The role of FTO in altering the epitranscriptome manifests across a spectrum of physiological and pathological conditions. This review aims to consolidate current understanding regarding the implications of FTO in health and disease, with a special emphasis on its involvement in obesity and non-communicable diseases associated with obesity, such as diabetes, cardiovascular disease, and cancer. It also summarizes the established molecules with FTO-inhibiting activity. Given the extensive impact of FTO on both physiology and pathophysiology, this overview provides illustrative insights into its roles, rather than an exhaustive account. A proper understanding of FTO function in human diseases could lead to new treatment approaches, potentially unlocking novel avenues for addressing both metabolic disorders and malignancies. The evolving insights into FTO's regulatory mechanisms hold great promise for future advancements in disease treatment and prevention.

Noncoding variation near UBE2E2 orchestrates cardiometabolic pathophenotypes through polygenic effectors

Mechanisms underpinning signals from genome-wide association studies remain poorly understood, particularly for noncoding variation and for complex diseases such as type 2 diabetes mellitus (T2D) where pathogenic mechanisms in multiple different tissues may be disease driving. One approach is to study relevant endophenotypes, a strategy we applied to the UBE2E2 locus where noncoding single nucleotide variants (SNVs) are associated with both T2D and visceral adiposity (a pathologic endophenotype). We integrated CRISPR targeting of SNV-containing regions and unbiased CRISPR interference (CRISPRi) screening to establish candidate cis-regulatory regions, complemented by genetic loss of function in murine diet-induced obesity or ex vivo adipogenesis assays. Nomination of a single causal gene was complicated, however, because targeting of multiple genes near UBE2E2 attenuated adipogenesis in vitro; CRISPR excision of SNV-containing noncoding regions and a CRISPRi regulatory screen across the locus suggested concomitant regulation of UBE2E2, the more distant UBE2E1, and other neighborhood genes; and compound heterozygous loss of function of both Ube2e2 and Ube2e1 better replicated pathological adiposity and metabolic phenotypes compared with homozygous loss of either gene in isolation. This study advances a model whereby regulatory effects of noncoding variation not only extend beyond the nearest gene but may also drive complex diseases through polygenic regulatory effects.