A bioinformatics analysis of the contribution of m6A methylation to the occurrence of diabetes mellitus

Insights into RNA N6-methyladenosine in Glucose and Lipid Metabolic Diseases and Their Therapeutic Strategies

The incidence of glucose and lipid metabolism diseases, including type 2 diabetes, obesity, metabolic syndrome, and nonalcoholic fatty liver disease, is rising, which places an enormous burden on people around the world. However, the mechanism behind these disorders remains incompletely understood. N6-methyladenosine (m6A) is 1 type of posttranscriptional RNA modification, and research has shown that it plays a crucial role in several metabolic diseases. m6A methylation is reversibly and dynamically regulated by methyltransferases (writers), demethylases (erasers), and m6A binding proteins (readers). Dysregulation of RNA m6A modification is related to different metabolic processes. Targeting RNA m6A methylation is a potential treatment strategy for these chronic metabolic diseases. This review discusses studies on RNA m6A modification in metabolic diseases and existing therapeutic drugs, with the aim of providing a concise perspective on its potential applications in managing metabolic disorders.

METTL14 promotes the development of diabetic kidney disease by regulating m6A modification of TUG1

BACKGROUND

Diabetic kidney disease (DKD) is one of the most common diabetic complications. Endoplasmic reticulum stress (ERS) is an important step for renal tubular epithelial cell apoptosis during DKD progression. Herein, the role and regulatory mechanism of METTL14 in ERS during DKD progression were investigated.

METHODS

DKD animal and cell models were established by streptozotocin (STZ) and high glucose (HG), respectively. HE and Masson staining were performed to analyze renal lesions in DKD mouse. Cell viability and proliferation were determined by MTT and EdU staining, respectively. HK2 cell apoptosis was analyzed by flow cytometry. TUG1 m6A level was determined by Me-RIP. The interaction between TUG1, LIN28B and MAPK1 was analyzed by RIP and RNA pull-down assays.

RESULTS

HG stimulation promoted apoptosis and increased ERS marker proteins (GRP78, CHOP and caspase12) expression in HK2 cells, while these changes were reversed by METTL14 knockdown. METTL14 inhibited TUG1 stability and expression level in an m6A-dependent manner. As expected, TUG1 knockdown abrogated METTL14 knockdown's inhibition on HG-induced HK2 cell apoptosis and ERS. In addition, TUG1 inactivated MAPK1/ERK signaling by binding with LIN28B. And TUG1 overexpression's repression on HG-induced HK2 cell apoptosis and ERS was abrogated by MAPK1 signaling activation. Meanwhile, METTL14 knockdown or TUG1 overexpression protected against STZ-induced renal lesions and renal fibrosis in DKD mouse.

CONCLUSION

METTL14 promoted renal tubular epithelial cell apoptosis and ERS by activating MAPK/ERK pathway through m6A modification of TUG1, thereby accelerating DKD progression.

Bulk and single-cell transcriptome analyses of islet tissue unravel gene signatures associated with pyroptosis and immune infiltration in type 2 diabetes

INTRODUCTION

Type 2 diabetes (T2D) is a common chronic heterogeneous metabolic disorder. However, the roles of pyroptosis and infiltrating immune cells in islet dysfunction of patients with T2D have yet to be explored. In this study, we aimed to explore potential crucial genes and pathways associated with pyroptosis and immune infiltration in T2D.

METHODS

To achieve this, we performed a conjoint analysis of three bulk RNA-seq datasets of islets to identify T2D-related differentially expressed genes (DEGs). After grouping the islet samples according to their ESTIMATE immune scores, we identified immune- and T2D-related DEGs. A clinical prediction model based on pyroptosis-related genes for T2D was constructed. Weighted gene co-expression network analysis was performed to identify genes positively correlated with pyroptosis-related pathways. A protein-protein interaction network was established to identify pyroptosis-related hub genes. We constructed miRNA and transcriptional networks based on the pyroptosis-related hub genes and performed functional analyses. Single-cell RNA-seq (scRNA-seq) was conducted using the GSE153885 dataset. Dimensionality was reduced using principal component analysis and t-distributed statistical neighbor embedding, and cells were clustered using Seurat. Different cell types were subjected to differential gene expression analysis and gene set enrichment analysis (GSEA). Cell-cell communication and pseudotime trajectory analyses were conducted using the samples from patients with T2D.

RESULTS

We identified 17 pyroptosis-related hub genes. We determined the abundance of 13 immune cell types in the merged matrix and found that these cell types were correlated with the 17 pyroptosis-related hub genes. Analysis of the scRNA-seq dataset of 1892 islet samples from patients with T2D and controls revealed 11 clusters. INS and IAPP were determined to be pyroptosis-related and candidate hub genes among the 11 clusters. GSEA of the 11 clusters demonstrated that the myc, G2M checkpoint, and E2F pathways were significantly upregulated in clusters with several differentially enriched pathways.

DISCUSSION

This study elucidates the gene signatures associated with pyroptosis and immune infiltration in T2D and provides a critical resource for understanding of islet dysfunction and T2D pathogenesis.

Milk Exosomal microRNAs: Postnatal Promoters of β Cell Proliferation but Potential Inducers of β Cell De-Differentiation in Adult Life

Pancreatic β cell expansion and functional maturation during the birth-to-weaning period is driven by epigenetic programs primarily triggered by growth factors, hormones, and nutrients provided by human milk. As shown recently, exosomes derived from various origins interact with β cells. This review elucidates the potential role of milk-derived exosomes (MEX) and their microRNAs (miRs) on pancreatic β cell programming during the postnatal period of lactation as well as during continuous cow milk exposure of adult humans to bovine MEX. Mechanistic evidence suggests that MEX miRs stimulate mTORC1/c-MYC-dependent postnatal β cell proliferation and glycolysis, but attenuate β cell differentiation, mitochondrial function, and insulin synthesis and secretion. MEX miR content is negatively affected by maternal obesity, gestational diabetes, psychological stress, caesarean delivery, and is completely absent in infant formula. Weaning-related disappearance of MEX miRs may be the critical event switching β cells from proliferation to TGF-β/AMPK-mediated cell differentiation, whereas continued exposure of adult humans to bovine MEX miRs via intake of pasteurized cow milk may reverse β cell differentiation, promoting β cell de-differentiation. Whereas MEX miR signaling supports postnatal β cell proliferation (diabetes prevention), persistent bovine MEX exposure after the lactation period may de-differentiate β cells back to the postnatal phenotype (diabetes induction).

Alteration of m6A epitranscriptomic tagging of ribonucleic acids after spinal cord injury in mice

The m6A methylation is reported to function in multiple physiological and pathological processes. However, the functional relevance of m6A modification to post-spinal cord injured (SCI) damage is not yet clear. In the present study, methylated RNA immunoprecipitation combined with microarray analysis showed that the global RNA m6A levels were decreased following SCI. Then, gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) analyses were conducted to demonstrate the potential function of differential m6A-tagged transcripts and the altered transcripts with differential m6A levels. In addition, we found that the m6A “writer,” METTL3, significantly decreased after SCI in mice. The immunostaining validated that the expression of METTL3 mainly changed in GFAP or Iba-1+ cells. Together, this study shows the alteration of m6A modification following SCI in mice, which might contribute to the pathophysiology of the spinal cord after trauma.

Establishment and Verification of a Gene Signature for Diagnosing Type 2 Diabetics by WGCNA, LASSO Analysis, and In Vitro Experiments

Objective

The incidence and prevalence of type 2 diabetes are increasing with age. Nevertheless, there is lack of sensitive diagnostic tools and effective therapeutic regimens. We aimed to establish and verify a practical and valid diagnostic tool for this disease.

Methods

WGCNA was presented on the expression profiling of type 2 diabetic and normal islets in combined GSE25724 and GSE38642 datasets. By LASSO Cox regression analyses, a gene signature was constructed based on the genes in diabetes-related modules. ROC curves were plotted for assessing the diagnostic efficacy. Correlations between the genes and immune cell infiltration and pathways were analyzed. BST2 and BTBD1 expression was verified in glucotoxicity-induced and normal islet β cells. The influence of BST2 on β cell dysfunction was investigated under si-BST2 transfection.

Results

Totally, 14 coexpression modules were constructed, and red and cyan modules displayed the correlations to diabetes. The LASSO gene signature (BST2, BTBD1, IFIT1, IFIT3, and RTP4) was developed. The AUCs in the combined datasets and GSE20966 dataset were separately 0.914 and 0.910, confirming the excellent performance in diagnosing type 2 diabetes. Each gene in the model was distinctly correlated to immune cell infiltration and key signaling pathways (TGF-β and P53, etc.). The abnormal expression of BST2 and BTBD1 was confirmed in glucotoxicity-induced β cells. BST2 knockdown ameliorated β cell dysfunction and altered the activation of TGF-β and P53 pathways.

Conclusion

Our findings propose a gene signature with high efficacy to diagnose type 2 diabetes, which could assist and improve early diagnosis and therapy.