Active vitamin D induces gene-specific hypomethylation in prostate cancer cells developing vitamin D resistance

Establishment and Validation of a Tumor Microenvironment Prognostic Model for Predicting Bladder Cancer Survival Status Based on Integrated Bioinformatics Analyses

This study was designed to analyze the characteristics of bladder cancer-related genes and establish a prognostic model of bladder cancer. The model passed an independent external validation set test. Differentially expressed genes (DEGs) related to bladder cancer were obtained from the Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA), and Genotype-Tissue Expression (GTEx) databases. WGCNA was used to fit the GSE188715, TCGA, and GTEx RNA-Seq data. Fusing the module genes with the high significance in tumor development extracted from WGCNA and DEGs screened from multiple databases. 709 common prognostic-related genes were obtained. The 709 genes were enriched in the Gene Ontology database. Univariate Cox and LASSO regression analyses were used to screen out 21 prognostic-related genes and further multivariate Cox regression established a bladder cancer prognostic model consisting of 8 genes. After the eight-gene prognostic model was established, the Human Protein Atlas (HPA) database, GEPIA 2, and quantitative real-time PCR (qRT-PCR) verified the differential expression of these genes. Gene Set Enrichment Analysis and immune infiltration analysis found biologically enrichment pathways and cellular immune infiltration related to this bladder cancer prognostic model. Then, we selected bladder cancer patients in the TCGA database to evaluate the predictive ability of the model on the training set and validation set. The overall survival status of the two TCGA patient groups in the training and the test sets was obtained by Kaplan–Meier survival analysis. Three-year survival rates in the training and test sets were 37.163% and 25.009% for the low-risk groups and 70.000% and 62.235% for the high-risk groups, respectively. Receiver operating characteristic curve (ROC) analysis showed that the areas under the curve (AUCs) for the training and test sets were above 0.7. In an external independent validation database GSE13507, Kaplan–Meier survival analysis showed that the three-year survival rates of the high-risk and the low-risk groups in this database were 56.719% and 76.734%, respectively. The AUCs of the ROC drawn in the external validation set were both above 0.65. Here, we constructed a prognostic model of bladder cancer based on data from the GEO, TCGA, and GTEx databases. This model has potential prognostic and clinical auxiliary diagnostic value.

Environmental Factors and the Risk of Developing Type 1 Diabetes-Old Disease and New Data

Simple Summary

Despite many studies, the risk factors of type 1 diabetes (T1DM) in children and adolescents are still not fully understood and remain a big challenge. Therefore, an extensive online search for scientific research on factors related to diabetes has been performed for the identification of new factors of unexplained etiology. A better understanding of the role of viral, bacterial, and yeast-like fungi infections related to the risk of T1DM in children and adolescents and the identification of new risk factors, especially those spread by the droplet route, is of great importance for people and families with diabetes.

Abstract

The incidence of type 1 diabetes (T1D) is increasing worldwide. The onset of T1D usually occurs in childhood and is caused by the selective destruction of insulin-producing pancreatic islet cells (β-cells) by autoreactive T cells, leading to insulin deficiency. Despite advanced research and enormous progress in medicine, the causes of T1D are still not fully understood. Therefore, an extensive online search for scientific research on environmental factors associated with diabetes and the identification of new factors of unexplained etiology has been carried out using the PubMed, Cochrane, and Embase databases. The search results were limited to the past 11 years of research and discovered 143 manuscripts published between 2011 and 2022. Additionally, 21 manuscripts from between 2000 and 2010 and 3 manuscripts from 1974 to 2000 were referenced for historical reference as the first studies showcasing a certain phenomenon or mechanism. More and more scientists are inclined to believe that environmental factors are responsible for the increased incidence of diabetes. Research results show that higher T1D incidence is associated with vitamin D deficiency, a colder climate, and pollution of the environment, as well as the influence of viral, bacterial, and yeast-like fungi infections. The key viral infections affecting the risk of developing T1DM are rubella virus, mumps virus, Coxsackie virus, cytomegalovirus, and enterovirus. Since 2020, i.e., from the beginning of the COVID-19 pandemic, more and more studies have been looking for a link between Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and diabetes development. A better understanding of the role of viral, bacterial, and yeast-like fungi infections related to the risk of T1DM in children and adolescents and the identification of new risk factors, especially those spread by the droplet route, is of great importance for people and families with diabetes.

25-Hydroxyvitamin D status is associated with interleukin-6 methylation in adipose tissue from patients with colorectal cancer

A dysfunctional visceral adipose tissue (VAT) is characterized by increased production of proinflammatory cytokines, which may increase the risk of colorectal cancer (CRC). However, the epigenetic contribution to the inflammatory status is poorly understood. In our study, we hypothesized that a dysfunctional VAT may be a risk factor for CRC, through epigenetic modifications. Therefore, we aimed to study the transcriptional/methylation profile of proinflammatory cytokines and genes related to vitamin D metabolism in VAT from CRC patients, and evaluate their association with serum 25-hydroxyvitamin D (25(OH)D). We included 129 participants (68 healthy participants and 61 CRC patients). We found that the majority of the studied genes are upregulated and hypomethylated in CRC patients, when compared to the healthy subjects (p < 0.05). In addition, serum 25(OH)D was associated with both mRNA gene expression and methylation of key genes, such as interleukin (IL)6, IL10, vitamin D receptor (VDR) or cytochrome P450 subfamily 27 type B1 (CYP27B1) (p < 0.05). Interestingly, while high IL6 expression was related to poor survival in CRC (p < 0.05), IL6 methylation was associated with an increased risk of CRC, in which 25(OH)D partially mediated this association (p < 0.05). Our study suggests a potential association between epigenetic regulation of inflammatory mediators in VAT - such as IL6 - in the CRC context, in which 25(OH)D may mediate this risk. Therefore, vitamin D could affect the epigenetic status of IL6, which can be considered for additional preventive strategies.

An Epigenetic Signature is Associated with Serum 25-Hydroxyvitamin D in Colorectal Cancer Tumors

INTRODUCTION

Vitamin D has been widely associated with colorectal cancer (CRC) through different insights. This study aims to explore the association between serum 25-hydroxyvitamin D (25(OH)D) and the global DNA methylation in tumor from CRC patients.

METHODS AND RESULTS

A genome-wide DNA methylation analysis is conducted in 20 CRC patients under categorical (10 patients have 25(OH)D <30 ng mL^-1 ; 10 patients with 25(OH)D ≥30 ng mL^-1 ) and continuous models of 25(OH)D. A total of 95 differentially methylated CpGs (DMCpGs) are detected under the categorical model (false discovery rate (FDR) < 0.05), while 16 DMCpGs are found under the continuous model. Regional analysis showed eight vitamin D-associated differentially methylated regions (DMR). Between them, a DMR is the most significant at cAMP-Dependent Protein Kinase Inhibitor Alpha (PKIA) locus. Furthermore, seven genes, including PKIA gene, have more or equal than two significant DMCpGs. The protein networking analysis found pathways implicated in cell adhesion and extracellular matrix, as well as signaling transduction.

CONCLUSIONS

This study identifies novel epigenetic loci associated with serum 25(OH)D status. Interestingly, also, a positive association between vitamin D and DNA methylation in the CRC context is found, suggesting a role in CRC. Further studies are warranted to clarify and replicate these results.

Dysregulation of miR-138-5p/RPS6KA1-AP2M1 Is Associated With Poor Prognosis in AML

Acute myeloid leukemia (AML) is a malignant disease of hematopoietic stem/progenitor cells, and most AML patients are in a severe state. Internal tandem duplication mutations in FLT3 gene (FLT3-ITD) detected in AML stem cells account for 20–30 percent of AML patients. In this study, we attempted to study the impact of the interaction of FLT3-ITD mutation and the CXCL12/CXCR4 axis in AML, and the possible mechanisms caused by the impact by bioinformatics. Gene set variation analysis (GSVA) revealed that the PI3K-Akt-mTOR pathway positively correlated with the status of FLT3-ITD mutation. Multiple survival analyses were performed on TCGA-AML to screen the prognostic-related genes, and RPS6KA1 and AP2M1 are powerful prognostic candidates for overall survival in AML. WGCNA, KEGG/GO analysis, and the functional roles of RPS6KA1 and AP2M1 in AML were clarified by correlation analysis. We found that the expression levels of RPS6KA1 and AP2M1 were significantly associated with chemoresistance of AML, and the CXCL12/CXCR4 axis would regulate RPS6KA1/AP2M1 expression. Besides, miR-138-5p, regulated by the CXCL12/CXCR4 axis, was the common miRNA target of RPS6KA1 and AP2M1. Taken together, the interaction of FLT3-ITD mutation and the CXCL12/CXCR4 axis activated the PI3K-Akt-mTOR pathway, and the increased expression of RPS6KA1 and AP2M1 caused by hsa-miR-138-5p downregulation regulates the multi-resistance gene expression leading to drug indications.

Vitamin D and its Effects on DNA Methylation in Development, Aging, and Disease

DNA methylation is increasingly being recognized as a mechanism through which environmental exposures confer disease risk. Several studies have examined the association between vitamin D and changes in DNA methylation in areas as diverse as human and animal development, genomic stability, chronic disease risk, and malignancy. In many cases, they have demonstrated clear associations between vitamin D and DNA methylation in candidate disease pathways. Despite this, a clear understanding of the mechanisms by which these factors interact is unclear. This paper reviews the current understanding of the effects of vitamin D on DNA methylation. In light of current knowledge in the field, the potential mechanisms mediating vitamin D effects on DNA methylation are discussed, as are the limiting factors and future avenues for research into this exciting area.

Genome-Protecting Compounds as Potential Geroprotectors

Throughout life, organisms are exposed to various exogenous and endogenous factors that cause DNA damages and somatic mutations provoking genomic instability. At a young age, compensatory mechanisms of genome protection are activated to prevent phenotypic and functional changes. However, the increasing stress and age-related deterioration in the functioning of these mechanisms result in damage accumulation, overcoming the functional threshold. This leads to aging and the development of age-related diseases. There are several ways to counteract these changes: 1) prevention of DNA damage through stimulation of antioxidant and detoxification systems, as well as transition metal chelation; 2) regulation of DNA methylation, chromatin structure, non-coding RNA activity and prevention of nuclear architecture alterations; 3) improving DNA damage response and repair; 4) selective removal of damaged non-functional and senescent cells. In the article, we have reviewed data about the effects of various trace elements, vitamins, polyphenols, terpenes, and other phytochemicals, as well as a number of synthetic pharmacological substances in these ways. Most of the compounds demonstrate the geroprotective potential and increase the lifespan in model organisms. However, their genome-protecting effects are non-selective and often are conditioned by hormesis. Consequently, the development of selective drugs targeting genome protection is an advanced direction.