MicroRNA biomarkers of type 2 diabetes: A protocol for corroborating evidence by computational genomics and meta-analyses

lncRNA UCA1 inhibits mitochondrial dysfunction of skeletal muscle in type 2 diabetes mellitus by sequestering miR-143-3p to release FGF21

Increasing evidence suggests that insulin resistance in type 2 diabetes mellitus (T2DM) is associated with mitochondrial dysfunction in skeletal muscle, while the underlying molecular mechanisms remain elusive. This study aims to construct a ceRNA regulatory network that is involved in mitochondrial dysfunction of skeletal muscle in T2DM. Based on GEO database analysis, differentially expressed lncRNA and mRNA profiles were identified in skeletal muscle tissues of T2DM. Next, LASSO regression analysis was conducted to predict the key lncRNAs related to T2DM, which was validated by receiver operating characteristic (ROC) analysis. Moreover, the miRNAs related to skeletal muscle in T2DM were identified by WGCNA, followed by construction of gene-gene interaction network and GO and KEGG enrichment analyses. It was found that 12 lncRNAs and 6 miRNAs were related to skeletal muscle in T2DM. Moreover, the lncRNA-miRNA-mRNA ceRNA network involving UCA1, miR-143-3p, and FGF21 was constructed. UCA1, and FGF21 were downregulated, while miR-143-3p was upregulated in skeletal muscle cells (SkMCs) exposed to palmitic acid. Additionally, ectopic expression experiments were performed in SkMCs to confirm the effects of UCA1/miR-143-3p/FGF21 on mitochondrial dysfunction by determining mitochondrial ROS, oxygen consumption rate (OCR), membrane potential, and ATP level. Overexpression of miR-143-3p increased ROS accumulation and reduced the OCR, fluorescence ratio of JC-1, and ATP level, which were reversed by upregulation of UCA1 or FGF21. Collectively, lncRNA UCA1 inhibited mitochondrial dysfunction of skeletal muscle in T2DM by sequestering miR-143-3p away from FGF21, therefore providing a potential therapeutic target for alleviating mitochondrial dysfunction of skeletal muscle in T2DM.

MicroRNA biomarkers of type 2 diabetes: evidence synthesis from meta-analyses and pathway modelling

AIMS/HYPOTHESIS

MicroRNAs are being sought as biomarkers for the early identification of type 2 diabetes. This study aimed to synthesise the evidence from microRNA-type 2 diabetes association studies and microRNA-regulated type 2 diabetes pathway delineation studies that met stringent quality criteria to identify and validate microRNAs of both statistical and biological significance as type 2 diabetes biomarkers.

METHODS

Eligible controlled studies on microRNA expression profiling of type 2 diabetes were retrieved from PubMed, ScienceDirect and Web of Science. MicroRNA-regulated type 2 diabetes pathway delineation studies were conducted by integrating and cross-verifying the data from miRTarBase, TransmiR, miRecords, TargetScanHuman, the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Retraction Watch database. Before meta-analysis, quality assessment was performed according to the corresponding reporting guidelines for evidence-based medicine. To select the most statistically significant microRNAs, we conducted extensive meta-analyses according to the latest methodology. Subgroup and sensitivity analyses were carried out to further examine the microRNA candidates for their tissue specificity and blood fraction specificity and the robustness of the evidence. Signalling pathway impact analysis of dysregulated microRNAs identified from meta-analyses was performed to select biologically significant microRNAs that were enriched in our newly built microRNA-regulated pathways.

RESULTS

Of the 404 differentially expressed microRNAs identified in the 156 controlled profiling studies with a combined sample size of >15,000, only 60 were both consistently and significantly dysregulated in human type 2 diabetes. No microRNAs were both consistently and significantly dysregulated in multiple tissues according to subgroup analyses. In total, 58 microRNAs were found to be robust in sensitivity analyses. A total of 1966 pathway delineation studies were identified, including 3290 microRNA-target interactions, which were further combined with KEGG pathways, producing 225 microRNA-regulated pathways. Impact analysis found that 16 dysregulated microRNAs identified from extensive meta-analyses were statistically significantly enriched in the augmented KEGG type 2 diabetes pathway.

CONCLUSIONS/INTERPRETATION

Sixteen microRNAs met the criteria for biomarker selection. In terms of both significance and relevance, the order of priority for verification of these microRNAs is as follows: miR-29a-3p, miR-221-3p, miR-126-3p, miR-26a-5p, miR-503-5p, miR-100-5p, miR-101-3p, mIR-103a-3p, miR-122-5p, miR-199a-3p, miR-30b-5p, miR-130a-3p, miR-143-3p, miR-145-5p, miR-19a-3p and miR-311-3p.

REGISTRATION

PROSPERO registration number CRD42017081659.

Roles of Non-Coding RNAs in Primary Biliary Cholangitis

Primary biliary cholangitis (PBC) is an autoimmune-mediated chronic cholestatic liver disease, fatigue, and skin itching are the most common clinical symptoms. Its main pathological feature is the progressive damage and destruction of bile duct epithelial cells. Non-coding RNA (NcRNA, mainly including microRNA, long non-coding RNA and circular RNA) plays a role in the pathological and biological processes of various diseases, especially autoimmune diseases. Many validated ncRNAs are expected to be biomarkers for the diagnosis or treatment of PBC. This review will elucidate the pathogenesis of PBC and help to identify potential ncRNA biomarkers for PBC.