Insulin-resistance and depression cohort data mining to identify nutraceutical related DNA methylation biomarker for type 2 diabetes

Oral Akkermansia muciniphila Biomimetic Nanotherapeutics for Ulcerative Colitis Targeted Treatment by Repairing Intestinal Epithelial Barrier and Restoring Redox Homeostasis

The structural disruption of intestinal barrier and excessive reactive oxygen/nitrogen species (RONS) generation are two intertwined factors that drive the occurrence and development of ulcerative colitis (UC). Synchronously restoring the intestinal barrier and mitigating excess RONS is a promising strategy for UC management, but its treatment outcomes are still hindered by low drug accumulation and retention in colonic lesions. Inspired by intestine colonizing bacterium, we developed a mucoadhesive probiotic Akkermansia muciniphila-mimic entinostat-loaded hollow mesopores prussian blue (HMPB) nanotherapeutic (AM@HMPB@E) for UC-targeted therapy via repairing intestinal barrier and scavenging RONS. After oral administration, the negatively charged AM@HMPB@E specifically bind to the positively charged inflamed colon lesions via electrostatic interactions and Akkermansia muciniphila membrane-mediated bioadhesion mechanism. Subsequently, the superoxide dismutase (SOD)-, and catalase (CAT)-like HMPB eliminated RONS, thereby alleviating RONS-mediated inflammation and intestinal epithelial damage. Meanwhile, the UC-site locally released entinostat could repair the damaged intestinal epithelial barrier by inhibiting intestinal endothelial cell apoptosis and up-regulating the expression of tight junctions. Both in vitro and in vivo results shown that AM@HMPB@E not only exhibited an exceptional retention in the colitis site but also demonstrated superior therapeutic efficacy compared to the first-line drug sulfasalazine, as evidenced by the longer colon, less rectal bleeding and body weight loss. Collectively, our findings highlight the clinical application prospects of this synchronous nanotherapeutic strategy for UC treatment, offering a paradigm for the rational design of oral nanomedicine.

Sex differences in the association between the muscle quality index and the incidence of depression: A cross-sectional study

BACKGROUND

Depression presents significant challenges to mental health care. Although physical activity is highly beneficial to mental and physical health, relatively few studies have conducted on the relationship between them.

AIM

To investigate the association between muscle quality index (MQI) and incidence of depression.

METHODS

The data used in this cross-sectional study were obtained from the 2011-2014 National Health and Nutritional Examination Survey, which included information on MQI, depression, and confounding factors. Multivariable logistic regression models were employed, while taking into account the complex multi-stage sampling design. A restricted cubic spline model was utilized to investigate the non-linear relationship between the MQI and depression. Additionally, subgroup analyses were performed to identify influential factors.

RESULTS

The prevalence of depression in this population was 8.44%. With the adjusted model, the MQI was associated with depression in females (odds ratio = 0.68, 95% confidence interval: 0.49-0.95) but not in males (odds ratio = 1.08, 95% confidence interval: 0.77-1.52). Restricted cubic spline adjustment of all covariates showed a significant negative non-linear relationship between depression and the MQI in females. The observed trend indicated an 80% decrease in the risk of depression for each unit increase in MQI, until a value of 2.2. Subsequently, when the MQI exceeded 2.2, the prevalence of depression increased by 20% for every unit increase in the MQI. Subgroup analyses further confirmed that the MQI was negatively associated with depression.

CONCLUSION

The MQI was inversely correlated with depression in females but not males, suggesting that females with a higher MQI might decrease the risk of depression.

Key Nutrients for Optimal Blood Glucose Control and Mental Health in Individuals with Diabetes: A Review of the Evidence

Diabetes is associated with an increased risk of mental disorders, including depression, anxiety, and cognitive decline. Mental disorders can also contribute to the development of diabetes through various mechanisms including increased stress, poor self-care behaviors, and adverse effects on glucose metabolism. Consequently, individuals suffering from either of these conditions frequently experience comorbidity with the other. Nutrition plays an important role in both diabetes and mental health disorders including depression and anxiety. Deficiencies in specific nutrients such as omega-3 fatty acids, vitamin D, B vitamins, zinc, chromium, magnesium, and selenium have been implicated in the pathogenesis of both diabetes and mental disorders. While the impact of nutrition on the progression and control of diabetes and mental disorders is broadly acknowledged, there is a notable knowledge gap concerning the implications of distinct nutrients in preventing and mitigating symptoms of both conditions when they coexist. The aim of this study was to examine the role of nutrition in improving glucose homeostasis and promoting mental well-being among individuals with diabetes. Further, we evaluated the preventive or delaying effects of key nutrients on the simultaneous manifestation of these conditions when one of them is present. Our findings indicated that the use of personalized dietary interventions and targeted nutrient supplementation can improve metabolic and mental health outcomes in patients with type 2 diabetes.

Crosstalk between Gut Microbiota and Epigenetic Markers in Obesity Development: Relationship between Ruminococcus, BMI, and MACROD2/SEL1L2 Methylation

Changes in gut microbiota composition and in epigenetic mechanisms have been proposed to play important roles in energy homeostasis, and the onset and development of obesity. However, the crosstalk between epigenetic markers and the gut microbiome in obesity remains unclear. The main objective of this study was to establish a link between the gut microbiota and DNA methylation patterns in subjects with obesity by identifying differentially methylated DNA regions (DMRs) that could be potentially regulated by the gut microbiota. DNA methylation and bacterial DNA sequencing analysis were performed on 342 subjects with a BMI between 18 and 40 kg/m2. DNA methylation analyses identified a total of 2648 DMRs associated with BMI, while ten bacterial genera were associated with BMI. Interestingly, only the abundance of Ruminococcus was associated with one BMI-related DMR, which is located between the MACROD2/SEL1L2 genes. The Ruminococcus abundance negatively correlated with BMI, while the hypermethylated DMR was associated with reduced MACROD2 protein levels in serum. Additionally, the mediation test showed that 19% of the effect of Ruminococcus abundance on BMI is mediated by the methylation of the MACROD2/SEL1L2 DMR. These findings support the hypothesis that a crosstalk between gut microbiota and epigenetic markers may be contributing to obesity development.

Diet-gut microbiota-epigenetics in metabolic diseases: From mechanisms to therapeutics

The prevalence of metabolic diseases, including obesity, dyslipidemia, type 2 diabetes mellitus (T2DM), and non-alcoholic fatty liver disease (NAFLD), is a severe burden in human society owing to the ensuing high morbidity and mortality. Various factors linked to metabolic disorders, particularly environmental factors (such as diet and gut microbiota) and epigenetic modifications, contribute to the progression of metabolic diseases. Dietary components and habits regulate alterations in gut microbiota; in turn, microbiota-derived metabolites, such as short-chain fatty acids (SCFAs), are influenced by diet. Interestingly, diet-derived microbial metabolites appear to produce substrates and enzymatic regulators for epigenetic modifications (such as DNA methylation, histone modifications, and non-coding RNA expression). Epigenetic changes mediated by microbial metabolites participate in metabolic disorders via alterations in intestinal permeability, immune responses, inflammatory reactions, and insulin resistance. In addition, microbial metabolites can trigger inflammatory immune responses and microbiota dysbiosis by directly binding to G-protein-coupled receptors (GPCRs). Hence, diet-gut microbiota-epigenetics may play a role in metabolic diseases. However, their complex relationships with metabolic diseases remain largely unknown and require further investigation. This review aimed to elaborate on the interactions among diet, gut microbiota, and epigenetics to uncover the mechanisms and therapeutics of metabolic diseases.

Epigenetics in Precision Nutrition

Precision nutrition is an emerging area of nutrition research, with primary focus on the individual variability in response to dietary and lifestyle factors, which are mainly determined by an individual’s intrinsic variations, such as those in genome, epigenome, and gut microbiome. The current research on precision nutrition is heavily focused on genome and gut microbiome, while epigenome (DNA methylation, non-coding RNAs, and histone modification) is largely neglected. The epigenome acts as the interface between the human genome and environmental stressors, including diets and lifestyle. Increasing evidence has suggested that epigenetic modifications, particularly DNA methylation, may determine the individual variability in metabolic health and response to dietary and lifestyle factors and, therefore, hold great promise in discovering novel markers for precision nutrition and potential targets for precision interventions. This review summarized recent studies on DNA methylation with obesity, diabetes, and cardiovascular disease, with more emphasis put in the relations of DNA methylation with nutrition and diet/lifestyle interventions. We also briefly reviewed other epigenetic events, such as non-coding RNAs, in relation to human health and nutrition, and discussed the potential role of epigenetics in the precision nutrition research.

DNA Methylation Markers and Prediction Model for Depression and Their Contribution for Breast Cancer Risk

Background

Major depressive disorder (MDD) has become a leading cause of disability worldwide. However, the diagnosis of the disorder is dependent on clinical experience and inventory. At present, there are no reliable biomarkers to help with diagnosis and treatment. DNA methylation patterns may be a promising approach for elucidating the etiology of MDD and predicting patient susceptibility. Our overarching aim was to identify biomarkers based on DNA methylation, and then use it to propose a methylation prediction score for MDD, which we hope will help us evaluate the risk of breast cancer.

Methods

Methylation data from 533 samples were extracted from the Gene Expression Omnibus (GEO) database, of which, 324 individuals were diagnosed with MDD. Statistical difference of DNA Methylation between Promoter and Other body region (SIMPO) score for each gene was calculated based on the DNA methylation data. Based on SIMPO scores, we selected the top genes that showed a correlation with MDD in random resampling, then proposed a methylation-derived Depression Index (mDI) by combining the SIMPO of the selected genes to predict MDD. A validation analysis was then performed using additional DNA methylation data from 194 samples extracted from the GEO database. Furthermore, we applied the mDI to construct a prediction model for the risk of breast cancer using stepwise regression and random forest methods.

Results

The optimal mDI was derived from 426 genes, which included 245 positive and 181 negative correlations. It was constructed to predict MDD with high predictive power (AUC of 0.88) in the discovery dataset. In addition, we observed moderate power for mDI in the validation dataset with an OR of 1.79. Biological function assessment of the 426 genes showed that they were functionally enriched in Eph Ephrin signaling and beta-catenin Wnt signaling pathways. The mDI was then used to construct a predictive model for breast cancer that had an AUC ranging from 0.70 to 0.67.

Conclusion

Our results indicated that DNA methylation could help to explain the pathogenesis of MDD and assist with its diagnosis.

Mining the Selective Remodeling of DNA Methylation in Promoter Regions to Identify Robust Gene-Level Associations With Phenotype

Epigenetics is an essential biological frontier linking genetics to the environment, where DNA methylation is one of the most studied epigenetic events. In recent years, through the epigenome-wide association study (EWAS), researchers have identified thousands of phenotype-related methylation sites. However, the overlaps of identified phenotype-related DNA methylation sites between various studies are often quite small, and it might be due to the fact that methylation remodeling has a certain degree of randomness within the genome. Thus, the identification of robust gene-phenotype associations is crucial to interpreting pathogenesis. How to integrate the methylation values of different sites on the same gene and to mine the DNA methylation at the gene level remains a challenge. A recent study found that the DNA methylation difference of the gene body and promoter region has a strong correlation with gene expression. In this study, we proposed a Statistical difference of DNA Methylation between Promoter and Other Body Region (SIMPO) algorithm to extract DNA methylation values at the gene level. First, by choosing to smoke as an environmental exposure factor, our method led to significant improvements in gene overlaps (from 5 to 17%) between different datasets. In addition, the biological significance of phenotype-related genes identified by SIMPO algorithm is comparable to that of the traditional probe-based methods. Then, we selected two disease contents (e.g., insulin resistance and Parkinson's disease) to show that the biological efficiency of disease-related gene identification increased from 15.43 to 44.44% (p-value = 1.20e-28). In summary, our results declare that mining the selective remodeling of DNA methylation in promoter regions can identify robust gene-level associations with phenotype, and the characteristic remodeling of a given gene's promoter region can reflect the essence of disease.

Blood Cell DNA Methylation of Aging-Related Ubiquitination Gene DZIP3 Can Predict the Onset of Early Stage Colorectal Cancer

There is a body of evidence that the aging immune system is linked to cancer. In this study, with aging- and immune-related DNA methylation data, we investigated the DNA methylation regulation changes in promoters with other regions of genes during aging and their association with the immune-cell proportion in the circulating whole blood of individuals. The analyses for aging- and CD4+ T cell proportion-derived differential genes showed that ubiquitination plays an important role in the aging immune system and tumorigenesis. Therefore, starting from a set of pre-annotated ubiquitination genes, we found that among the differentially ubiquitinated genes, DZIP3, an E3 ubiquitin ligase with no reports on its function in immune cells and tumorigenesis, was significantly associated with both aging (P-value = 3.86e-06) and CD4+ T cell proportion (P-value = 1.97e-05) in circulating blood. By collecting a cohort of 100 colon cancer patients and 50 healthy individuals, we validated that the 1st exon DNA methylation of DZIP3 could predict the onset of early stage (AUC = 0.833, OR = 8.82) and all pTNM stages of colorectal cancer (AUC = 0.782, OR = 5.70). Thus, the epigenetically regulated ubiquitination machine plays an important role in immune aging and tumorigenesis.