Plasma microRNAs are associated with acute exacerbation in idiopathic pulmonary fibrosis

Novel Biomarker Panel of Let-7d-5p and MiR-140-5p Can Distinguish Latent Tuberculosis Infection from Active Tuberculosis Patients

Background

Mycobacterium tuberculosis (Mtb) survives inside a human host for a long time in the form of latent tuberculosis infection (LTBI). Latent infection of tuberculosis has the opportunity of developing into active tuberculosis (ATB), which has greatly endangered human health. The existing diagnostic methods cannot effectively distinguish LTBI from ATB. Therefore, more effective diagnostic biomarkers and methods are urgently needed.

Methods

Here, we screened the GEO data set, conducted joint differential analysis and target gene enrichment analysis, after filtering the disease-related database, we screened the differential miRNA related to TB. The qPCR was used to verify the miRNAs in 84 serum samples. Different combinations of biomarkers were evaluated by logistic regression to obtain a biomarker panel with good performance for diagnosing LTBI.

Results

A panel with two miRNAs (hsa-let-7d-5p, hsa-miR-140-5p) was established to differentiate LTBI from ATB. Receiver operating characteristic (ROC) curve showed that the area under the curve (AUC) are 0.930 (sensitivity = 100%, specificity = 88.5%) and 0.923 (sensitivity = 100%, specificity = 92.3%) with the biomarker panel for the training set and test set respectively.

Conclusion

The findings indicated that the logistic regression model built by let-7d-5p and miR-140-5p has the ability to distinguish LTBI from active TB patients.

Acute Exacerbations of Interstitial Lung Diseases: Focus on Biomarkers

Interstitial lung diseases (ILDs) are a large group of pulmonary disorders characterized histologically by the cardinal involvement of the pulmonary interstitium. The prototype of ILDs is idiopathic pulmonary fibrosis (IPF), an incurable disease characterized by progressive distortion and loss of normal lung architecture through unchecked collagen deposition. Acute exacerbations are dramatic events during the clinical course of ILDs, associated with high morbidity and mortality. Infections, microaspiration, and advanced lung disease might be involved in the pathogenesis of acute exacerbations. Despite clinical scores, the prediction of the onset and outcome of acute exacerbations is still inaccurate. Biomarkers are necessary to characterize acute exacerbations better. We review the evidence for alveolar epithelial cell, fibropoliferation, and immunity molecules as potential biomarkers for acute exacerbations of interstitial lung disease.

Exosomes in pathogenesis, diagnosis, and treatment of pulmonary fibrosis

Pulmonary fibrosis (PF) is a group of interstitial lung diseases that seriously endanger human life and health. Despite the current advances in research on the pathogenesis and treatment of PF, the overall quality of survival and survival rates of PF patients remain low, prompting the search for more effective therapeutic approaches. Exosomes are nanoscale vesicles with diameters ranging from approximately 30–150 nm, capable of transporting a variety of molecules in the body and mediating intercellular communication. There is an increasing number of studies focusing on the role of exosomes in PF. This review demonstrates the significance of exosomes in the pathogenesis, diagnosis, and treatment of PF. Exosomes are able to influence inflammatory, immune, and extracellular matrix deposition processes in PF and regulate the corresponding cytokines. Some exosomes detected in sputum, blood, and bronchoalveolar lavage fluid may be used as potential diagnostic and prognostic biomarkers for PF. Exosomes derived from several cells, such as mesenchymal stem cells, have demonstrated potential as PF therapeutic agents. Drug delivery systems using exosomes may also provide new insights into PF therapy.

Roles of exosomes and exosome-derived miRNAs in pulmonary fibrosis

Pulmonary fibrosis is a chronic, progressive fibrosing interstitial lung disease of unknown etiology that leads rapidly to death. It is characterized by the replacement of healthy tissue through an altered extracellular matrix and damage to the alveolar structure. New pharmacological treatments and biomarkers are needed for pulmonary fibrosis to ensure better outcomes and earlier diagnosis of patients. Exosomes are nanoscale vesicles released by nearly all cell types that play a central role as mediators of cell-to-cell communication. Moreover, exosomes are emerging as a crucial factor in antigen presentation, immune response, immunomodulation, inflammation, and cellular phenotypic transformation and have also shown promising therapeutic potential in pulmonary fibrosis. This review summarizes current knowledge of exosomes that may promote pulmonary fibrosis and be utilized for diagnostics and prognostics. In addition, the utilization of exosomes and their cargo miRNAs as novel therapeutics and their potential mechanisms are also discussed. This review aims to elucidate the role of exosomes in the pathogenesis of pulmonary fibrosis and paves the way for developing novel therapeutics for pulmonary fibrosis. Further in-depth research and clinical trials on this topic are encouraged in the future.

The function of non-coding RNAs in idiopathic pulmonary fibrosis

Non-coding ribonucleic acids (ncRNAs) are a diverse group of RNA molecules that are mostly not translated into proteins after transcription, including long non-coding RNAs (lncRNAs) with longer than 200 nucleotides non-coding transcripts and microRNAs (miRNAs) which are only 18–22 nucleotides. As families of evolutionarily conserved ncRNAs, lncRNAs activate and repress genes via a variety of mechanisms at both transcriptional and translational levels, whereas miRNAs regulate protein-coding gene expression mainly through mRNA silencing. ncRNAs are widely involved in biological functions, such as proliferation, differentiation, migration, angiogenesis, and apoptosis. Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease with a poor prognosis. The etiology of IPF is still unclear. Increasing evidence shows the close correlations between the development of IPF and aberrant expressions of ncRNAs than thought previously. In this study, we provide an overview of ncRNAs participated in pathobiology of IPF, seeking the early diagnosis biomarker and aiming for potential therapeutic applications for IPF.

Identification of candidate lncRNA biomarkers for renal fibrosis: A systematic review

AIMS

To combine the results of dysregulated lncRNAs in individual renal fibrosis lncRNA expression profiling studies and to identify potential lncRNA biomarkers.

MATERIALS AND METHODS

We systematically searched three databases to identify lncRNA expression studies of renal fibrosis in animal models and humans. The lncRNA expression data were extracted from 24 included studies, and a lncRNA vote-counting strategy was applied to identify significant lncRNA biomarkers. The lncLocator algorithm was utilized to predict the potential subcellular localization of these lncRNAs. The predicted targets of the identified lncRNA biomarkers were obtained by searching LncBase v.2 and catRAPID. Finally, GO enrichment and KEGG pathway analyses were performed.

KEY FINDINGS

We recognized a significant lncRNA signature of 95 differentially expressed lncRNAs in 731 samples from rodent models of renal fibrosis and CKD patients, among which TCONS_01181049 and TCONS_01496394 were commonly upregulated in both urine and renal tissues, while lncRNA-Cancer Susceptibility Candidate 2 was downregulated in both blood and renal tissues. About 73.33% dysregulated lncRNAs in renal fibrosis animal models and 81.82% dysregulated lncRNAs in CKD patients were predicted to be localized to the cytoplasm. The most relevant biological processes and molecular functions associated with these lncRNAs were mRNA processing and RNA binding.

SIGNIFICANCE

The present systematic review identified 95 significantly dysregulated lncRNAs from 24 studies and future investigations should focus on exploring their potential effects on renal fibrosis and their clinical utility as biomarkers or therapeutic targets.

Biomarkers and their potential functions in idiopathic pulmonary fibrosis

Introduction: Idiopathic pulmonary fibrosis (IPF) is a chronic, devastating, and progressive lung disease that is characterized by fibrosis and respiratory failure. IPF holds high morbidity and poor prognosis and still faces considerable problems of reliable diagnosis and valid prognosis. A growing body of literature have reported changes in the level of various biomarkers in IPF patients, which means that they are expected to become a new tool for the clinical practice of IPF.Areas covered: We reviewed the recent literature about biomarkers and focus on the role they play in IPF. We systematically searched Medline/PubMed through February 2020. Many works of literature have shown that a variety of biomolecules and genomics played multiple roles in the diagnosis or differential diagnosis, prognosis, and indication of acute deterioration of IPF and so on.Expert opinion: Significant advances have been made in the role of biomarkers for IPF these years; however, current data indicate that a single biomarker is unlikely to have a transformative effect on clinical practice; therefore, the combined effect of various biomarkers can be considered to improve the accuracy of diagnosis and prognosis. Further research of biomarkers may provide new insights for the diagnosis, prognosis, and even therapy of IPF.

Analysis of the Interaction Network of Hub miRNAs-Hub Genes, Being Involved in Idiopathic Pulmonary Fibers and Its Emerging Role in Non-small Cell Lung Cancer

Idiopathic pulmonary fibrosis (IPF) is a fibrotic interstitial lung disease with lesions confined to the lungs. To identify meaningful microRNA (miRNA) and gene modules related to the IPF progression, GSE32537 (RNA-sequencing data) and GSE32538 (miRNA-sequencing data) were downloaded and processed, and then weighted gene co-expression network analysis (WGCNA) was applied to construct gene co-expression networks and miRNA co-expression networks. GSE10667, GSE70866, and GSE27430 were used to make a reasonable validation for the results and evaluate the clinical significance of the genes and the miRNAs. Six hub genes (COL3A1, COL1A2, OGN, COL15A1, ASPN, and MXRA5) and seven hub miRNAs (hsa-let-7b-5p, hsa-miR-26a-5p, hsa-miR-25-3p, hsa-miR-29c-3p, hsa-let-7c-5p, hsa-miR-29b-3p, and hsa-miR-26b-5p) were clarified and validated. Meanwhile, iteration network of hub miRNAs-hub genes was constructed, and the emerging role of the network being involved in non-small cell lung cancer (NSCLC) was also analyzed by several webtools. The expression levels of hub genes were different between normal lung tissues and NSCLC tissues. Six genes (COL3A1, COL1A2, OGN, COL15A1, ASPN, and MXRA5) and three miRNAs (hsa-miR-29c-3p, hsa-let-7c-5p, and hsa-miR-29b-3p) were related to the survival time of lung adenocarcinoma (LUAD). The interaction network of hub miRNAs-hub genes might provide common mechanisms involving in IPF and NSCLC. More importantly, useful clues were provided for clinical treatment of both diseases based on novel molecular advances.

Circulating lung biomarkers in idiopathic lung fibrosis and interstitial lung diseases associated with connective tissue diseases: Where do we stand?

Interstitial lung diseases (ILDs) are complex diseases with various courses where personalized medicine is highly expected. Biomarkers are indicators of physiological, pathological processes or of pharmacological response to therapeutic interventions. They can be used for diagnosis, risk-stratification, prediction and monitoring of treatment response. To better delineate the input and pitfalls of biomarkers in ILDs, we performed a systematic review and meta-analysis of literature in MEDLINE and Embase databases from January 1960 to February 2019. We focused on circulating biomarkers as having the highest generalizability. Overall, 70 studies were included in the review and 20 studies could be included in the meta-analysis. This review highlights that ILD associated with connective tissue diseases (CTD-ILD) and idiopathic pulmonary fibrosis (IPF) share common biomarkers, suggesting common pathophysiological pathways. KL-6 and SP-D, could diagnose lung fibrosis in both IPF and CTD-ILD, with KL-6 having the strongest value (OR: 520.95[110.07-2465.58], p<0.001 in IPF and OR:26.43[7.15-97.68], p<0.001 in CTD-ILD), followed by SPD (OR: 33.81[3.20-357.52], p = 0.003 in IPF and 13.24 [3.84-45.71] in SSc-ILD), MMP7 appeared as interesting for IPF diagnosis (p<0.001), whereas in SSc, CCL18 was associated with ILD diagnosis. Both CCL18 and KL-6 were predictive for the outcomes of ILDs, with higher predictive values for CCL18 in both IPF (OR:10.22[4.72-22.16], p<0.001 and in SSc [2.62[1.71-4.03], p<0.001). However, disease specific biomarkers are lacking and large longitudinal studies are needed before the translational use of the potential biomarkers in clinical practice. With the recent availability of new effective therapies in ILDs, further studies should assess response to treatment.

MicroRNA 3113-5p is a novel marker for early cardiac ischemia/reperfusion injury

BACKGROUND

Ischemia/reperfusion (I/R) injury of heart is one of the major causes of acute cardiac injury, which may result in worsening or even loss of heart function. With novel microRNAs being evolutionarily discovered, numbers of them remained functionally unknown. We aimed to discover novel microRNAs with therapeutic or diagnostic potential in the setting of early cardiac I/R injury.

METHODS

Cardiac electrical activity, biochemical detection and histopathology analysis were performed to reveal early changes of cardiac I/R injury. A microRNA array was performed to screen differential microRNAs in the mouse model of cardiac I/R injury. The differentially expressed microRNAs were validated in cardiac tissues and in serum samples.

RESULTS

The abnormality in electrocardiogram and increases in serum cTnI levels suggested the successful establishment of cardiac I/R injury in mice. A total of 1882 microRNAs were identified, of which 11 were significantly down-regulated and 41 were significantly up-regulated at 3 h post reperfusion. microRNA 223-3p and microRNA 3113-5p were among the mostly altered microRNAs and were validated to be up-regulated within the early hours of I/R injury in heart tissues. In the circulating system, cTnI, a sensitive marker of cardiac injury, or microRNA 223-3p only increased within the first 6 h post I/R injury. However, microRNA 3113-5p stably increased in the serum, keeping an increase of 2.5-fold throughout the 24 h. In the human serum samples, microRNA 3113-5p was detected to be significantly upregulated as soon as 3 h after I/R stimuli and kept significantly higher levels within the 48 h.

CONCLUSION

This is the first study that reported the functional roles of microRNA 3113-5p in cardiovascular system. Our data suggested that cardiac microRNA 3113-5p might be a useful target for therapeutic purposes and circulating microRNA 3113-5p might serve as a stable marker for early diagnosis of cardiac I/R injury.

The role of microRNAs in chronic respiratory disease: recent insights

Chronic respiratory diseases encompass a group of diverse conditions affecting the airways, which all impair lung function over time. They include cystic fibrosis (CF), idiopathic pulmonary fibrosis (IPF), chronic obstructive pulmonary disease (COPD) and asthma, which together affect hundreds of millions of people worldwide. MicroRNAs (miRNAs), a class of small non-coding RNAs involved in post-transcriptional gene repression, are now recognized as major regulators in the development and progression of chronic lung disease. Alterations in miRNA abundance occur in lung tissue, inflammatory cells, and freely circulating in blood and are thought to function both as drivers and modifiers of disease. Their importance in lung pathology has prompted the development of miRNA-based therapies and biomarker tools. Here, we review the current literature on miRNA expression and function in chronic respiratory disease and highlight further research that is needed to propel miRNA treatments for lung disorders towards the clinic.

lncRNA PFAL promotes lung fibrosis through CTGF by competitively binding miR-18a

Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, fibrotic parenchymal lung disease of unknown etiology and lacks an effective intervention. Long noncoding RNAs (lncRNAs) participate in organ fibrosis and various pulmonary diseases, but the role of lncRNAs in lung fibrosis is not fully understood. In the present study, we identified that lncRNA NONMMUT021928, designated as pulmonary fibrosis-associated lncRNA (PFAL), was up-regulated in the lungs of mice with experimental lung fibrosis, and in TGF-β1-induced fibrotic lung fibroblasts. Further study showed that overexpression of PFAL promoted cell proliferation, migration, and fibroblast-myofibroblast transition. Overexpression further resulted in extracellular matrix deposition and fibrogenesis in lung fibroblasts through regulation of microRNA-18a (miR-18a). Importantly, knockdown of PFAL alleviated lung fibrosis both in vitro and in vivo. Mechanistically, our study showed that PFAL promoted lung-fibroblast activation and fibrogenesis by acting as a competing endogenous RNA for miR-18a: forced expression of PFAL inhibited the expression and activity of miR-18a, whereas silencing of PFAL had the opposite effect. Furthermore, we found that miR-18a was decreased during lung fibrosis in vitro and in vivo, as well as in patients with IPF. Moreover, knockdown of miR-18a led to fibrogenesis in lung fibroblasts, whereas enhanced expression of miR-18a attenuated TGF-β1-induced lung fibrosis by directly targeting the regulation of connecting tissue growth factor. Taken together, these results revealed the effect and mechanism of lncRNA PFAL in pulmonary fibrosis and suggested that PFAL depletion may provide a novel strategy for the treatment of lung fibrosis.-Li, X., Yu, T., Shan, H., Jiang, H., Sun, J., Zhao, X., Su, W., Yang, L., Shan, H., Liang, H. lncRNA PFAL promotes lung fibrosis through CTGF by competitively binding miR-18a.