MicroRNAs in Type 1 Diabetes: Complex Interregulation of the Immune System, β Cell Function and Viral Infections

Text mining-based identification of promising miRNA biomarkers for diabetes mellitus

Introduction

MicroRNAs (miRNAs) are small, non-coding RNAs that play a critical role in diabetes development. While individual studies investigating the mechanisms of miRNA in diabetes provide valuable insights, their narrow focus limits their ability to provide a comprehensive understanding of miRNAs' role in diabetes pathogenesis and complications.

Methods

To reduce potential bias from individual studies, we employed a text mining-based approach to identify the role of miRNAs in diabetes and their potential as biomarker candidates. Abstracts of publications were tokenized, and biomedical terms were extracted for topic modeling. Four machine learning algorithms, including Naïve Bayes, Decision Tree, Random Forest, and Support Vector Machines (SVM), were employed for diabetes classification. Feature importance was assessed to construct miRNA-diabetes networks.

Results

Our analysis identified 13 distinct topics of miRNA studies in the context of diabetes, and miRNAs exhibited a topic-specific pattern. SVM achieved a promising prediction for diabetes with an accuracy score greater than 60%. Notably, miR-146 emerged as one of the critical biomarkers for diabetes prediction, targeting multiple genes and signal pathways implicated in diabetic inflammation and neuropathy.

Conclusion

This comprehensive approach yields generalizable insights into the network miRNAs-diabetes network and supports miRNAs' potential as a biomarker for diabetes.

Persistent coxsackievirus B infection and pathogenesis of type 1 diabetes mellitus

Enteroviruses are believed to trigger or accelerate islet autoimmunity in genetically susceptible individuals, thereby resulting in loss of functional insulin-producing β-cells and type 1 diabetes mellitus (T1DM). Although enteroviruses are primarily involved in acute and lytic infections in vitro and in vivo, they can also establish a persistent infection. Prospective epidemiological studies have strongly associated the persistence of enteroviruses, especially coxsackievirus B (CVB), with the appearance of islet autoantibodies and an increased risk of T1DM. CVB can persist in pancreatic ductal and β-cells, which leads to structural or functional alterations of these cells, and to a chronic inflammatory response that promotes recruitment and activation of pre-existing autoreactive T cells and β-cell autoimmune destruction. CVB persistence in other sites, such as the intestine, blood cells and thymus, has been described; these sites could serve as a reservoir for infection or reinfection of the pancreas, and this persistence could have a role in the disturbance of tolerance to β-cells. This Review addresses the involvement of persistent enterovirus infection in triggering islet autoimmunity and T1DM, as well as current strategies to control enterovirus infections for preventing or reducing the risk of T1DM onset.

Fighting Enteroviral Infections to Prevent Type 1 Diabetes

Enteroviruses (EVs), especially coxsackieviruses B (CVB), are believed to trigger or accelerate islet autoimmunity in genetically susceptible individuals that results in type 1 diabetes (T1D). Therefore, strategies are needed to fight against EV infections. There are no approved antiviral drugs currently available, but various antiviral drugs targeting viral or host cell proteins and vaccines have recently shown potential to combat CVB infections and may be used as new therapeutic strategies to prevent or reduce the risk of T1D and/or preserve β-cell function among patients with islet autoantibodies or T1D.

Viruses and Type 1 Diabetes: From Enteroviruses to the Virome

For over a century, viruses have left a long trail of evidence implicating them as frequent suspects in the development of type 1 diabetes. Through vigorous interrogation of viral infections in individuals with islet autoimmunity and type 1 diabetes using serological and molecular virus detection methods, as well as mechanistic studies of virus-infected human pancreatic β-cells, the prime suspects have been narrowed down to predominantly human enteroviruses. Here, we provide a comprehensive overview of evidence supporting the hypothesised role of enteroviruses in the development of islet autoimmunity and type 1 diabetes. We also discuss concerns over the historical focus and investigation bias toward enteroviruses and summarise current unbiased efforts aimed at characterising the complete population of viruses (the “virome”) contributing early in life to the development of islet autoimmunity and type 1 diabetes. Finally, we review the range of vaccine and antiviral drug candidates currently being evaluated in clinical trials for the prevention and potential treatment of type 1 diabetes.

The Role of MicroRNAs in Diabetes-Related Oxidative Stress

Cellular stress, combined with dysfunctional, inadequate mitochondrial phosphorylation, produces an excessive amount of reactive oxygen species (ROS) and an increased level of ROS in cells, which leads to oxidation and subsequent cellular damage. Because of its cell damaging action, an association between anomalous ROS production and disease such as Type 1 (T1D) and Type 2 (T2D) diabetes, as well as their complications, has been well established. However, there is a lack of understanding about genome-driven responses to ROS-mediated cellular stress. Over the last decade, multiple studies have suggested a link between oxidative stress and microRNAs (miRNAs). The miRNAs are small non-coding RNAs that mostly suppress expression of the target gene by interaction with its 3'untranslated region (3'UTR). In this paper, we review the recent progress in the field, focusing on the association between miRNAs and oxidative stress during the progression of diabetes.

The miRNAs miR-211-5p and miR-204-5p modulate ER stress in human beta cells

miRNAs are a class of small non-coding RNAs that regulate gene expression. Type 1 diabetes is an autoimmune disease characterized by insulitis (islets inflammation) and pancreatic beta cell destruction. The pro-inflammatory cytokines interleukin 1 beta (IL1B) and interferon gamma (IFNG) are released during insulitis and trigger endoplasmic reticulum (ER) stress and expression of pro-apoptotic members of the BCL2 protein family in beta cells, thus contributing to their death. The nature of miRNAs that regulate ER stress and beta cell apoptosis remains to be elucidated. We have performed a global miRNA expression profile on cytokine-treated human islets and observed a marked downregulation of miR-211-5p. By real-time PCR and Western blot analysis, we confirmed cytokine-induced changes in the expression of miR-211-5p and the closely related miR-204-5p and downstream ER stress related genes in human beta cells. Blocking of endogenous miRNA-211-5p and miR-204-5p by the same inhibitor (it is not possible to block separately these two miRs) increased human beta cell apoptosis, as measured by Hoechst/propidium Iodide staining and by determination of cleaved caspase-3 activation. Interestingly, miRs-211-5p and 204-5p regulate the expression of several ER stress markers downstream of PERK, particularly the pro-apoptotic protein DDIT3 (also known as CHOP). Blocking CHOP expression by a specific siRNA partially prevented the increased apoptosis observed following miR-211-5p/miR-204-5p inhibition. These observations identify a novel crosstalk between miRNAs, ER stress and beta cell apoptosis in early type 1 diabetes.

Sensitive Plasmonic Detection of miR-10b in Biological Samples Using Enzyme-Assisted Target Recycling and Developed LSPR Probe

A portable and nonlabeled plasmonic biosensor was advanced to enable the sensitive and selective detection of microRNA (miRNA) in a biological sample. miRNAs can act on several key cellular processes, including cell differentiation, cell cycle progression, and function as oncogenes. Detection of circulating miRNAs, especially in blood or urine samples, allows noninvasive and simple diagnosis of diseases. Herein, we report a localized surface plasmon resonance sensor (LSPR) based on an enzyme-assisted target recycling system and a developed LSPR probe for the detection of gastric cancer relevant miRNAs, miR-10b. The sensitivity of the sensor was improved by increasing the concentration of the signal-amplifying agent using the duplex-specific nuclease and by strongly binding the developed LSPR probe, tannic acid capping gold nanoparticles, to the DNA. Under optimal conditions, miR-10b detection could be realized in the range of 5 pM-10 nM with a detection limit of 2.45 pM. This integrated detection system represents an approach to sensitive detection of miRNAs and offers great applications in personalized medicine and monitoring of cancer.

Upper Respiratory Symptoms, Gut Health and Mucosal Immunity in Athletes

Upper respiratory symptoms remain the most common illness in athletes. Upper respiratory symptoms during heavy training and competition may impair performance. Preventing illness is the primary reason for the use of supplements, such as probiotics and prebiotics, for maintaining or promoting gut health and immune function. While exercise-induced perturbations in the immune system may increase susceptibility to illness and infection, growing evidence indicates that upper respiratory symptoms are related to a breakdown in the homeostatic regulation of the mucosal immune system of the airways. Balancing protection of the respiratory tract with normal physiological functioning requires dynamic orchestration between a wide array of immune parameters. The intestinal microbiota regulates extra-intestinal immunity via the common mucosal immune system and new evidence implicates the microbiota of the nose, mouth and respiratory tract in upper respiratory symptoms. Omics’ approaches now facilitate comprehensive profiling at the molecular and proteomic levels to reveal new pathways and molecules of immune regulation. New targets may provide for personalised nutritional and training interventions to maintain athlete health.

Expression of miR-155, miR-146a, and miR-326 in T1D patients from Chile: relationship with autoimmunity and inflammatory markers

Objective The aim of this research was to analyze the expression profile of miR-155, miR-146a, and miR-326 in peripheral blood mononuclear cells (PBMC) of 47 patients with type 1 diabetes mellitus (T1D) and 39 control subjects, as well as the possible association with autoimmune or inflammatory markers. Subjects and methods Expression profile of miRs by means of qPCR using TaqMan probes. Autoantibodies and inflammatory markers by ELISA. Statistical analysis using bivariate correlation. Results The analysis of the results shows an increase in the expression of miR-155 in T1D patients in basal conditions compared to the controls (p < 0.001) and a decreased expression level of miR-326 (p < 0.01) and miR-146a (p < 0.05) compared T1D patients to the controls. miR-155 was the only miRs associated with autoinmmunity (ZnT8) and inflammatory status (vCAM). Conclusion Our data show a possible role of miR-155 related to autoimmunity and inflammation in Chilean patients with T1D.

Circulating miRNAs, isomiRs and small RNA clusters in human plasma and breast milk

Circulating small RNAs, including miRNAs but also isomiRs and other RNA species, have the potential to be used as non-invasive biomarkers for communicable and non-communicable diseases. This study aims to characterize and compare small RNA profiles in human biofluids. For this purpose, RNA was extracted from plasma and breast milk samples from 15 healthy postpartum mothers. Small RNA libraries were prepared with the NEBNext® small RNA library preparation kit and sequenced in an Illumina HiSeq2000 platform. miRNAs, isomiRs and clusters of small RNAs were annotated using seqBuster/seqCluster framework in 5 plasma and 10 milk samples that passed the initial quality control. The RNA yield was 81 ng/mL [standard deviation (SD): 41] and 3985 ng/mL (SD: 3767) for plasma and breast milk, respectively. Mean number of good quality reads was 4.04 million (M) (40.01% of the reads) in plasma and 12.5M (89.6%) in breast milk. One thousand one hundred eighty two miRNAs, 12,084 isomiRs and 1,053 small RNA clusters that included piwi-interfering RNAs (piRNAs), tRNAs, small nucleolar RNAs (snoRNA) and small nuclear RNAs (snRNAs) were detected. Samples grouped by biofluid, with 308 miRNAs, 1,790 isomiRs and 778 small RNA clusters differentially detected. In summary, plasma and milk showed a different small RNA profile. In both, miRNAs, piRNAs, tRNAs, snRNAs, and snoRNAs were identified, confirming the presence of non-miRNA species in plasma, and describing them for the first time in milk.

miR-23b Suppresses Leukocyte Migration and Pathogenesis of Experimental Autoimmune Encephalomyelitis by Targeting CCL7

MicroRNAs (miRNAs) are small, non-coding RNAs involved in immune response regulation. Specific miRNAs have been linked to the development of various autoimmune diseases; however, their contribution to the modulation of CNS-directed cellular infiltration remains unclear. In this study, we found that miR-23b, in addition to its reported functions in the suppression of IL-17-associated autoimmune inflammation, halted the progression of experimental autoimmune encephalomyelitis (EAE), an animal model of multiple sclerosis (MS), by directly inhibiting the migration of pathogenic leukocytes to the CNS. We demonstrated that miR-23b was specifically decreased during the acute phase of EAE and that overexpression of miR-23b resulted in a defect in leukocyte migration and strong resistance to EAE. Furthermore, we found that miR-23b suppressed leukocyte migration of EAE by targeting CCL7, a chemokine that attracts monocytes during inflammation and metastasis. Finally, in the adoptive transfer model, miR-23b reduced the severity of EAE by inhibiting the migration of pathogenic T cells to the CNS rather than diminishing the encephalitogenesis of T cells. Taken together, our results characterize a novel aspect of miR-23b function in leukocyte migration, and they identify miR-23b as a potential therapeutic target in the amelioration of MS and likely other autoimmune diseases.

Persistent coxsackievirus B4 infection induces microRNA dysregulation in human pancreatic cells

Enterovirus infections are implicated in the development of type 1 diabetes (T1D). MicroRNAs as regulators of gene expression are involved in many physiological and pathological processes. Given that viral infections dysregulate cellular microRNAs, we investigated the impact of persistent coxsackievirus B4 infection on microRNA expression of human pancreatic cells. Next-generation sequencing was used to determine microRNA expression in PANC-1 cells persistently infected (for several weeks) with coxsackievirus B4 and uninfected control cells. Target prediction restricted to T1D risk genes was performed with miRWalk2.0. Functional annotation analysis was performed with DAVID6.7. Expression of selected microRNAs and T1D risk genes was measured by quantitative reverse-transcription polymerase chain reaction. Eighty-one microRNAs were dysregulated in persistently infected PANC-1 cells. Forty-nine of the known fifty-five T1D risk genes were predicted as putative targets of at least one of the dysregulated microRNAs. Most functional annotation terms that were enriched in these 49 putative target genes were related to the immune response or autoimmunity. mRNA levels of AFF3, BACH2, and IL7R differed significantly between persistently infected cells and uninfected cells. This is the first characterization of the microRNA expression profile changes induced by persistent coxsackievirus B4 infection in pancreatic cells. The predicted targeting of genes involved in the immune response and autoimmunity by the dysregulated microRNAs as well as the dysregulated expression of diabetes risk genes shows that persistent coxsackievirus B4 infection profoundly impacts the host cell. These data support the hypothesis of a possible link between persistent coxsackievirus B4 infection and the development of T1D.

Type 1 diabetes and viral infections: What is the relationship?

Type 1 diabetes (T1D) is the most common chronic metabolic disorder in children. Epigenetic and environmental factors capable of altering the penetrance of major susceptibility genes or capable of increasing the penetrance of low-risk genes are currently thought to play a role in triggering autoimmunity and T1D development. This paper discusses the current knowledge of the role of viruses in T1D. Most studies that have evaluated the potential association between viral infections and T1D have indicated that it is highly likely that some of these infectious agents play a role in T1D development. However, most T1D cases are immune-mediated, and it is supposed that the initial viral infection is capable of creating, in genetically predisposed subjects, a particular condition in which chronic local inflammation occurs through the persistence of the infecting virus in pancreatic tissue and the activation of autoimmunity by means of molecular mimicry, bystander activation, or both. Theoretically, this knowledge could lead to possible prophylaxis and therapy for T1D. Further studies devoted to evaluating which infectious agents are linked to T1D and which immune mechanisms induce or protect against the disease are needed before adequate prophylactic and therapeutic measures can be developed.