A panel of miRNAs derived from plasma extracellular vesicles as novel diagnostic biomarkers of lung adenocarcinoma

All-in-one multiple extracellular vesicle miRNA detection on a miniaturized digital microfluidic workstation

Extracellular vesicles (EVs) and EV-derived microRNAs (EV-miRNAs) are emerging as promising circulating biomarkers for early detection of malignant tumors such as non-small cell lung cancer (NSCLC). However, utilization of the gold standard method of RNA detection, the reverse transcription - quantitative polymerase chain reaction (RT-qPCR), on EV-miRNAs is hindered by laborious sample purification requirements and time-consuming multi-step procedures. Herein, we propose and demonstrate a miniaturized digital microfluidic (DMF) workstation for all-in-one EV-miRNA detection based on RT-qPCR. In comparison with the previously reported DMF platform for EV isolation, the system further integrates parallel on-chip real-time PCR capability with a comparable detection sensitivity with in-vitro RT-qPCR (limit of detection = 2 copies/μL), realizing automated, miniaturized, and facile EV-miRNA detection. Meanwhile, major methodological improvements were made, including one-step stem-looped RT-qPCR for miRNAs with both high sensitivity and specificity, and a simplified DMF substrate rework strategy for cost-effectiveness. As a demonstration, the detection of NSCLC-related EV-miRNAs within 20 μL of plasma samples was implemented, indicating the potential applicability of the DMF workstation and its automated protocol on point-of-care diagnosis of a wide range of diseases.

Wildfire-relevant woodsmoke and extracellular vesicles (EVs): Alterations in EV proteomic signatures involved in extracellular matrix degradation and tissue injury in airway organotypic models

Wildfires adversely impact air quality and public health worldwide. Exposures to wildfire smoke are linked to adverse health outcomes, including cardiopulmonary diseases. Critical research gaps remain surrounding the underlying biological pathways leading to wildfire-induced health effects. The regulation of intercellular communication and downstream toxicity driven by extracellular vesicles (EVs) is an important, understudied biological mechanism. This study investigated EVs following a wildfire smoke-relevant in vitro exposure. We hypothesized that woodsmoke (WS) would alter the proteomic content of EVs secreted in organotypic in vitro airway models. Exposures were carried out using a tri-culture model of alveolar epithelial cells, fibroblasts, and endothelial cells and a simplified co-culture model of alveolar epithelial cells and fibroblasts to inform responses across different cell populations. Epithelial cells were exposed to WS condensate and EVs were isolated from basolateral conditioned medium following 24 h exposure. WS exposure did not influence EV particle characteristics, and it moderately increased EV count. Exposure caused the differential loading of 25 and 35 proteins within EVs collected from the tri- and co-culture model, respectively. EV proteins involved in extracellular matrix degradation and wound healing were consistently modulated across both models. However, distinct proteins involved in the wound healing pathway were altered between models, suggesting unique but concerted efforts across cell types to communicate in response to injury. These findings demonstrate that a wildfire-relevant exposure alters the EV proteome and suggest an impact on EV-mediated intercellular communication. Overall, results demonstrate the viability of organotypic approaches in evaluating EVs to investigate exposure-induced biomarkers and underlying mechanisms. Findings also highlight the impact of differences in the biological complexity of in vitro models used to evaluate the effects of inhaled toxicants.

Exosomal Micro RNA Isolation in White-Tailed Deer (Odocoileus virginianus) for Diagnostic Biomarker Discovery

Molecular approaches are becoming more prevalent for the diagnosis of neurodegenerative diseases in human medicine and can be extended to diagnosis of wildlife diseases such as chronic wasting disease and other prion diseases. These diseases have been associated with exosome-bound molecular biomarkers of disease progression, such as proteins and micro RNA molecules (miRNA). We tested and optimized a method for exosomal miRNA isolation from minimally invasive, small-volume serum samples obtained from white-tailed deer (Odocoileus virginianus). We confirmed the isolation of exosomes and optimized a commercially available benchtop kit to obtain sufficient and pure RNA for miRNA sequencing. The selected method for RNA extraction combines two 500-μL serum aliquots into one elution column and re-eluting the final product of the column. We identified 137 miRNA present in healthy white-tailed deer that can be used as a baseline to identify putative miRNA biomarkers of disease progression and mechanisms of infection in future comparative disease studies. This approach to biomarker discovery may help to inform biological processes in wildlife populations and provide alternatives to invasive or postmortem samples.

Exosomal non-coding RNAs (ncRNAs) as potential biomarkers in tumor early diagnosis

Exosomes, extracellular vesicles carrying a cargo rich in various non-coding RNAs (ncRNAs), have emerged as crucial mediators of intercellular communication. Their stability, abundance, and specificity make exosomal ncRNAs promising candidates for biomarker discovery. The discovery of exosomal ncRNAs has unveiled a novel avenue for the exploration of biomarkers in tumor early diagnosis. This review consolidates current knowledge on the role of exosomal ncRNAs as potential biomarkers in the early detection of various tumors. We provide an overview of recent studies demonstrating the diagnostic potential of exosomal ncRNAs across multiple cancer types, highlighting their sensitivity, specificity, and feasibility for early detection. This review underscores the potential of exosomal ncRNAs as non-invasive biomarkers for early tumor diagnosis, paving the way for improved clinical outcomes through timely intervention and personalized management strategies.

The diagnostic and prognostic value of exosomal microRNAs in lung cancer: a systematic review

BACKGROUND

Studies have shown that many exosomal microRNAs (miRNAs) can be used as non-invasive biomarkers of lung cancer, but their diagnostic and prognostic values need to be further clarified.

METHODS

We conducted a systematic literature search in Web of Science, PubMed, and ScienceDirect databases, obtained relevant articles and extracted data, and used statistical methods and statistical software to comprehensively evaluate the diagnostic and prognostic value of exosomal miRNAs in lung cancer.

REGISTRATION NUMBER

PROSPERO CRD42023447398.

RESULTS

In terms of diagnosis, two exosomal miRNAs (miR-486-5p and miR-451a) were reported with the highest frequency in lung cancer patients, both of which had good diagnostic value. Compared with the control group, the pooled sensitivities of miR-486-5p and miR-451a were 0.80 (95% CI: 0.73-0.86) and 0.76 (95% CI: 0.60-0.87), specificities: 0.93 (95% CI: 0.63-0.99) and 0.85 (95% CI: 0.72-0.92), and AUCs: 0.85 (95% CI: 0.81-0.88) and 0.88 (95% CI: 0.84-0.90), for the respective miRNAs. For prognosis, in lung cancer patients with abnormally expressed exosomal miRNAs, miR-1290 was associated with PFS outcome; miR-382, miR-1246, miR-23b-3p, miR-21-5p, and miR-10b-5p were associated with OS outcome; miR-21 and miR-4257 were associated with DFS outcome; miR-125a-3p and miR-625-5p were associated with PFS and OS outcomes; miR-216b and miR-451a were associated with OS and DFS outcomes.

CONCLUSIONS

Exosomal miRNAs are valuable biomarkers in lung cancer patients. Exosomal miR-486-5p and miR-451a can be used as new diagnostic biomarkers for lung cancer. Dysregulated exosomal miRNAs could serve as indicators of survival outcomes in lung cancer patients.

The role of MAPK, notch and Wnt signaling pathways in papillary thyroid cancer: Evidence from a systematic review and meta-analyzing microarray datasets employing bioinformatics knowledge and literature

Papillary thyroid cancer (PTC) is a prevalent kind of thyroid cancer (TC), with the risk of metastasis increasing faster than any other malignancy. So, understanding the role of PTC in pathogenesis requires studying the various gene expressions to find out which particular molecular biomarkers will be helpful. The authors conducted a comprehensive search on the PubMed microarray database and a meta-analysis approach on the remaining ones to determine the differentially expressed genes between PTC and normal tissues, along with the analyses of overall survival (OS) and recurrence-free survival (RFS) rates in patients with PTC. We considered the associated genes with MAPK, Wnt, and Notch signaling pathways. Two GEO datasets have been included in this research, considering inclusion and exclusion criteria. Nineteen genes were found to have higher differences through the meta-analysis procedure. Among them, ten genes were upregulated, and nine genes were downregulated. The expression of 19 genes was examined using the GEPIA2 database, and the Kaplan-Meier plot statistics were used to analyze RFS and the OS rates. We discovered seven significant genes with the validation: PRICKLE1, KIT, RPS6KA5, GADD45B, FGFR2, FGF7, and DTX4. To further explain these findings, it was discovered that the mRNA expression levels of these seven genes and the remaining 12 genes were shown to be substantially linked with the results of the experimental literature investigations on the PTC. Our research found nineteen panels of genes that could be involved in the PTC progression and metastasis and the immune system infiltration of these cancers.

The diagnostic performance of micro-RNA and metabolites in lung cancer: A meta-analysis

BACKGROUND

The diagnosis of lung cancer is based on the microscopic exam of tissue or liquid. During the recent decade, many biomarkers have been pointed to have a potential diagnostic role. These biomarkers may be assessed in blood, pleural effusion or sputum and they could avoid biopsies or other risky procedures. The authors aimed to assess the diagnostic performances of biomarkers focusing on micro-RNA and metabolites.

METHODS

This meta-analysis was conducted under the PRISMA guidelines during a nine-year-period (2013-2022). the Meta-Disc software 5.4 (free version) was used. Q test and I2 statistics were carried out to explore the heterogeneity among studies. Meta-regression was performed in case of significant heterogeneity. Publication bias was assessed using the funnel plot test and the Egger's test (free version JASP).

RESULTS

According to our inclusion criteria, 165 studies from 79 articles were included. The pooled SEN, SPE and dOR accounted, respectively, for 0.76, 0.79 and 13.927. The AUC was estimated to 0.859 suggesting a good diagnostic accuracy. The heterogeneity in the pooled SEN and SPE was statistically significant. The meta-regression analysis focusing on the technique used, the sample, the number of biomarkers, the biomarker subtype, the tumor stage and the ethnicity revealed the biomarker number (p  =  0.009) and the tumor stage (p  =  0.0241) as potential sources of heterogeneity.

CONCLUSION

Even if this meta-analysis highlighted the potential diagnostic utility of biomarkers, more prospective studies should be performed, especially to assess the biomarkers' diagnostic potential in early-stage lung cancers.

Circulating microRNA Panels for Detection of Liver Cancers and Liver-Metastasizing Primary Cancers

Malignant liver tumors, including primary malignant liver tumors and liver metastases, are among the most frequent malignancies worldwide. The disease carries a poor prognosis and poor overall survival, particularly in cases involving liver metastases. Consequently, the early detection and precise differentiation of malignant liver tumors are of paramount importance for making informed decisions regarding patient treatment. Significant research efforts are currently directed towards the development of diagnostic tools for different types of cancer using minimally invasive techniques. A prominent area of focus within this research is the evaluation of circulating microRNA, for which dysregulated expression is well documented in different cancers. Combining microRNAs in panels using serum or plasma samples derived from blood holds great promise for better sensitivity and specificity for detection of certain types of cancer.

Potential of miR-181a-5p and miR-630 as clinical biomarkers in NSCLC

BACKGROUND

The development of drug resistance and high mortality rates are the major problems observed in non-small cell lung cancer (NSCLC). Biomarkers indicating and predicting disease development towards these unfavorable directions are therefore on high demand. Many studies have demonstrated that changes in miRNAs expression may be associated with a response to treatment and disease prognosis, thus suggesting its potential biomarker value for a broad spectrum of clinical applications. The aim of the present study was to investigate the expression level of miR-181a-5p, miR-630, and its targets in NSCLC tumor tissue and plasma samples; and to analyze its association with NSCLC patient's response to treatment and disease prognosis.

METHODS

The study was performed in 89 paired tissue specimens and plasma samples obtained from NSCLC patients who underwent surgical treatment at the Department of Thoracic Surgery and Oncology of the National Cancer Institute. Analysis of miR-181a-5p and miR-630 expression was performed by qRT-PCR using TaqMan miRNA specific primers. Whereas BCL2, LMO3, PTEN, SNAI2, WIF1 expression levels were identified with KAPA SYBR FAST qPCR Kit. Each sample was examined in triplicate and calculated following the 2-ΔΔCt method. When the p-value was less than 0.05, the differences were considered statistically significant.

RESULTS

It was found that miR-181a-5p and miR-630 expression levels in NSCLC tissue and plasma samples were significantly decreased compared with control samples. Moreover, patients with low miR-181a-5p expression in tumor tissue and plasma had longer PFS rates than those with high miRNA expression. Decreased miR-630 expression in tumor was statistically significantly associated with better NSCLC patients' OS. In addition, the expression of miR-181a-5p, as well as miR-630 in tumor tissue, are the statistically significant variables for NSCLC patients' OS. Moreover, in NSCLC patient plasma samples circulating miR-181a-5p can be evaluated as significant independent prognostic factors for OS and PFS.

CONCLUSIONS

Our findings indicate the miR-181a-5p and miR-630 expression levels have the potential to prognose and predict and therefore improve the treatment individualization and the outcome of NSCLC patients. Circulating miR-181a-5p has the potential clinical value as a non-invasive biomarker for NSCLC.

Circulating noncoding RNAs: promising biomarkers in liquid biopsy for the diagnosis, prognosis, and therapy of NSCLC

As the second most common malignant tumor in the world, lung cancer is a great threat to human health. In the past several decades, the role and mechanism of ncRNAs in lung cancer as a class of regulatory RNAs have been studied intensively. In particular, ncRNAs in body fluids have attracted increasing attention as biomarkers for lung cancer diagnosis and prognosis and for the evaluation of lung cancer treatment due to their low invasiveness and accessibility. As emerging tumor biomarkers in lung cancer, circulating ncRNAs are easy to obtain, independent of tissue specimens, and can well reflect the occurrence and progression of tumors due to their correlation with some biological processes in tumors. Circulating ncRNAs have a very high potential to serve as biomarkers and hold promise for the development of ncRNA-based therapeutics. In the current study, there has been extensive evidence that circulating ncRNA has clinical significance and value as a biomarker. In this review, we summarize how ncRNAs are generated and enter the circulation, remaining stable for subsequent detection. The feasibility of circulating ncRNAs as biomarkers in the diagnosis and prognosis of non-small cell lung cancer is also summarized. In the current systematic treatment of non-small cell lung cancer, circulating ncRNAs can also predict drug resistance, adverse reactions, and other events in targeted therapy, chemotherapy, immunotherapy, and radiotherapy and have promising potential to guide the systematic treatment of non-small cell lung cancer.

Secreted proteins MDK, WFDC2, and CXCL14 as candidate biomarkers for early diagnosis of lung adenocarcinoma

BACKGROUND

Early diagnosis of lung adenocarcinoma (LUAD), one of the most common types of lung cancer, is very important to improve the prognosis of patients. The current methods can't meet the requirements of early diagnosis. There is a pressing need to identify novel diagnostic biomarkers. Secretory proteins are the richest source for biomarker research. This study aimed to identify candidate secretory protein biomarkers for early diagnosis of LUAD by integrated bioinformatics analysis and clinical validation.

METHODS

Differentially expressed genes (DEGs) of GSE31210, gene expression data of early stage of LUAD, were analyzed by GEO2R. Upregulated DEGs predicted to encode secreted proteins were obtained by taking the intersection of the DEGs list with the list of genes encoding secreted proteins predicted by the majority decision-based method (MDSEC). The expressions of the identified secreted proteins in the lung tissues of early-stage LUAD patients were further compared with the healthy control group in mRNA and protein levels by using the UALCAN database (TCGA and CPTAC). The selected proteins expressed in plasma were further validated by using Luminex technology. The diagnostic value of the screened proteins was evaluated by receiver operating characteristic (ROC) analysis. Cell counting kit-8 assay was carried out to investigate the proliferative effects of these screened proteins.

RESULTS

A total of 2183 DEGs, including 1240 downregulated genes and 943 upregulated genes, were identified in the GSE31210. Of the upregulated genes, 199 genes were predicted to encode secreted proteins. After analysis using the UALCAN database, 16 molecules were selected for further clinical validation. Plasma concentrations of three proteins, Midkine (MDK), WAP four-disulfide core domain 2 (WFDC2), and C-X-C motif chemokine ligand 14 (CXCL14), were significantly higher in LUAD patients than in healthy donors. The area under the curve values was 0.944, 0.881, and 0.809 for MDK, WFDC2, and CXCL14, 0.962 when combined them. Overexpression of the three proteins enhanced the proliferation activity of A549 cells.

CONCLUSIONS

MDK, WFDC2, and CXCL14 were identified as candidate diagnostic biomarkers for early-stage LUAD and might also play vital roles in tumorigenesis.

Small extravesicular microRNA in head and neck squamous cell carcinoma and its potential as a liquid biopsy for early detection

BACKGROUND

The objective was to assess secretion of small extracellular vesicular microRNA (exo-miRNA) in head and neck squamous cell carcinoma (HNSCC) according to human papillomavirus (HPV) status, and determine the translational potential as a liquid biopsy for early detection.

METHODS

This study employed a combination of cell culture and case-control study design using archival pretreatment serum. Small extracellular vesicles (sEV) were isolated from conditioned culture media and human serum samples via differential ultracentrifugation. miRNA-sequencing was performed on each sEV isolate.

RESULTS

There were clear exo-miRNA profiles that distinguished HNSCC cell lines from nonpathologic oral epithelial control cells. While there was some overlap among profiles across all samples, there were apparent differences in exo-miRNA profiles according to HPV-status. Importantly, differential exo-miRNA profiles were also apparent in serum from early-stage HNSCC cases relative to cancer-free controls.

CONCLUSIONS

Our findings indicate that exo-miRNA are highly dysregulated in HNSCC and support the potential of exo-miRNA as biomarkers for HNSCC.

Status quo of Extracellular Vesicle isolation and detection methods for clinical utility

Extracellular vesicles (EVs) are nano-sized particles that hold tremendous potential in the clinical space, as their biomolecular profiles hold a key to non-invasive liquid biopsy for cancer diagnosis and prognosis. EVs are present in most bodily fluids, hence are easily obtainable from patients, advantageous to that of traditional, invasive tissue biopsies and imaging techniques. However, there are certain constraints that hinder clinical use of EVs. The translation of EV biomarkers from "bench-to-bedside" is encumbered by the methods of EV isolation and subsequent biomarker detection currently implemented in laboratories. Although current isolation and detection methods are effective, they lack practicality, with their requirement for high bodily fluid volumes, low equipment availability, slow turnaround times and high costs. The high demand for techniques that overcome these limitations has resulted in significant advancements in nanotechnological devices. These devices are designed to integrate EV isolation and biomarker detection into a one-step method of direct EV detection from bodily fluids. This provides promise for the acceleration of EVs into current clinical standards. This review highlights the importance of EVs as cancer biomarkers, the methodological obstacles currently faced in clinical studies and how novel nanodevices could advance clinical translation.

Plasma Extracellular Vesicle miRNA Profiles Distinguish Chronic Obstructive Pulmonary Disease Exacerbations and Disease Severity

Purpose

Molecular biomarkers for chronic obstructive pulmonary disease (COPD) severity have been difficult to identify. We aimed to assess extracellular vesicle miRNAs’ potential as a blood biomarker in discriminating disease severity in participants with COPD.

Patients and Methods

Plasma extracellular vesicles (EVs) were obtained from two COPD cohorts (n = 20 during an exacerbation event, n = 20 during stable state), with varying disease severity (GOLD stages). The miRCURY LNA miRNA Serum/Plasma assay, specific to 179 targets, was used to evaluate EV miRNA expression. The miRNAs that were significantly dysregulated were further assessed for discriminatory power using ROC curve analysis, as well as their role in relevant biological pathways.

Results

One miRNA was significantly dysregulated between moderate GOLD participants compared to severe/very severe GOLD participants, with an AUC of 0.798, p = 0.01 for miR-374b-5p. Five miRNAs were significantly dysregulated between exacerbating and stable COPD participants, with miR-223-3p resulting in the highest AUC (0.755, p = 0.006) for a single miRNA, with a combination of three miRNAs (miR-92b-3p, miR-374a-5p and miR-106b-3p) providing the highest discriminatory power (AUC 0.820, p = 0.001). The “cytokine–cytokine receptor interaction” (hsa04060 pathway) was the most significant KEGG pathway enriched for three out of the five miRNAs associated with COPD exacerbations.

Conclusion

This initial small-scale study suggests that the bioactive cargo (miRNAs) in plasma EVs holds specific biological information for the severity of airflow obstruction and COPD exacerbations, warranting further investigation.

Circ_0001058 represses the progression of lung adenocarcinoma through governing of the miR-486-5p/TEK signaling axis

The most common type of lung cancer is lung adenocarcinoma. Emerging views believe that circular RNA (circRNA) participates in its pathogenesis. The objective of this study is to find out the potential functions and mechanisms of circ_0001058 in lung adenocarcinoma pathogenesis. To detect circ_0001058, miR-486-5p and TEK tyrosine kinase (TEK) receptor tyrosine kinase expressions, real-time quantitative PCR (RT-qPCR) and western blotting were performed. Cell functions, including proliferation, apoptosis and invasion, were then evaluated using cell counting kit-8, caspase-3 activity and transwell assays, respectively. To establish the role of circ_0001058 in tumorigenesis, nude mice were utilized as in-vivo models. The predicted binding relationships of miR-486-5p to circ_0001058 or TEK were further verified by performing a dual-luciferase assay and ribonucleoprotein immunoprecipitation (RIP) analysis. Decreased circ_0001058 expression was observed in lung adenocarcinoma cells and tissue specimens. Circ_0001058 was predominantly situated in the cytoplasm and was greatly resistant to RNase R digestion. Circ_0001058 overexpression restrained A549 and PC9 cells' abilities to proliferate, survive and invade, and it also repressed tumorigenesis in the animal models. Circ_0001058 directly targeted miR-486-5p and depleted its expression. Restoring miR-486-5p could invert the inhibitory effects of circ_0001058 in the cancer cell phenotypes. Furthermore, miR-486-5p targeted TEK, so the inhibitory effects of TEK overexpression on the malignant behaviors of A549 and PC9 cells could also be abolished by miR-486-5p restoration. Circ_0001058 overexpression blocked the malignant development of lung adenocarcinoma via modulation of the miR-486-5p/TEK pathway. These results contribute new insights on the pathogenesis of lung adenocarcinoma.

Contributions of Circulating microRNAs for Early Detection of Lung Cancer

There is unmet need to develop circulating biomarkers that would enable earlier interception of lung cancer when more effective treatment options are available. Here, a set of 30 miRNAs, selected from a review of the published literature were assessed for their predictive performance in identifying lung cancer cases in the pre-diagnostic setting. The 30 miRNAs were assayed using sera collected from 102 individuals diagnosed with lung cancer within one year following blood draw and 212 controls matched for age, sex, and smoking status. The additive performance of top-performing miRNA candidates in combination with a previously validated four-protein marker panel (4MP) consisting of the precursor form of surfactant protein B (Pro-SFTPB), cancer antigen 125 (CA125), carcinoembryonic antigen (CEA) and cytokeratin-19 fragment (CYFRA21-1) was additionally assessed. Of the 30 miRNAs evaluated, five (miR-320a-3p, miR-210-3p, miR-92a-3p, miR-21-5p, and miR-140-3p) were statistically significantly (Wilcoxon rank sum test p < 0.05) elevated in case sera compared to controls, with individual AUCs ranging from 0.57−0.62. Compared to the 4MP alone, the combination of 3-miRNAs + 4MP improved sensitivity at 95% specificity by 19.1% ((95% CI of difference 0.0−28.6); two-sided p: 0.006). Our findings demonstrate utility for miRNAs for early detection of lung cancer in combination with a four-protein marker panel.

Fucosylated exosomal miRNAs as promising biomarkers for the diagnosis of early lung adenocarcinoma

Background

Considering the absence of apparent symptoms at the early stage, most patients with lung adenocarcinoma (LUAD) present at an advanced stage, leading to a dismal 5-year survival rate of <20%. Thus, finding perspective non-invasive biomarkers for early LUAD is very essential.

Methods

We developed a fucose-captured strategy based on lentil lectin-magnetic beads to isolate fucosylated exosomes from serum. Then, a prospective study was conducted to define the diagnostic value of serum exosomal miRNAs for early LUAD. A total of 310 participants were enrolled, including 146 LUAD, 98 benign pulmonary nodules (BPNs), and 66 healthy controls (HCs). Firstly, exosome miRNAs in the discovery cohort (n = 24) were profiled by small RNA sequencing. Secondly, 12 differentially expressed miRNAs (DEmiRs) were selected for further screening in a screening cohort (n = 64) by qRT-PCR. Finally, four candidate miRNAs were selected for further validation in a validating cohort (n = 222).

Results

This study demonstrated the feasibility of a fucose-captured strategy for the isolation of fucosylated exosomes from serum, evidenced with exosomal characteristics identified by transmission electron microscopy (TEM), nanoparticle tracking analysis (NTA), and Western blotting, as well as rapid and convenient operation of <10 min. Furthermore, a miRNA panel for early LUAD composed of miR4732-5p, miR451a, miR486-5p, and miR139-3p was defined with an AUC of 0.8554 at 91.07% sensitivity and 66.36% specificity.

Conclusions

The fucose-captured strategy provides a reliable, as well as rapid and convenient, approach for the isolation of tumor-derived exosomes from serum. A four-fucosylated exosomal miRNA panel presents good performance for early LUAD diagnosis.

Blood-based transcriptomic signature panel identification for cancer diagnosis: benchmarking of feature extraction methods

Liquid biopsy has shown promise for cancer diagnosis due to its minimally invasive nature and the potential for novel biomarker discovery. However, the low concentration of relevant blood-based biosources and the heterogeneity of samples (i.e. the variability of relative abundance of molecules identified), pose major challenges to biomarker discovery. Moreover, the number of molecular measurements or features (e.g. transcript read counts) per sample could be in the order of several thousand, whereas the number of samples is often substantially lower, leading to the curse of dimensionality. These challenges, among others, elucidate the importance of a robust biomarker panel identification or feature extraction step wherein relevant molecular measurements are identified prior to classification for cancer detection. In this work, we performed a benchmarking study on 12 feature extraction methods using transcriptomic profiles derived from different blood-based biosources. The methods were assessed both in terms of their predictive performance and the robustness of the biomarker panels in diagnosing cancer or stratifying cancer subtypes. While performing the comparison, the feature extraction methods are categorized into feature subset selection methods and transformation methods. A transformation feature extraction method, namely partial least square discriminant analysis, was found to perform consistently superior in terms of classification performance. As part of the benchmarking study, a generic pipeline has been created and made available as an R package to ensure reproducibility of the results and allow for easy extension of this study to other datasets (https://github.com/VafaeeLab/bloodbased-pancancer-diagnosis).

Diagnostic and prognostic value of microRNA-486 in patients with lung cancer: A systematic review and meta-analysis

PURPOSE

There are conflicting opinions on whether miR-486 could be used for cancer diagnosis and prognosis. Therefore, this present study investigated the potential effect of miR-486 on lung cancer diagnosis and prognosis.

METHODS

We researched PubMed, Embase, Wanfang and Chinese National Knowledge Infrastructure databases to select relevant publications. Specificity and sensitivity were obtained for the pooled and subgroup diagnostic meta-analysis while the hazard ratio was for prognostic meta-analysis. Publication analyses and sensitivity analyses were conducted to investigate possible sources of heterogeneity.

RESULTS

The overall sensitivity and specificity with 95% confidence intervals were 0.8 (0.8-0.9) and 0.9 (0.9-0.9). Results of subgroup analysis showed that high diagnostic efficacy might be obtained by miR-486 combined with other microRNAs (area under the curve (AUC): 0.9 (0.9-1.0)) to distinguish lung cancer patients from healthy controls (AUC: 1.0 (0.9-1.0)), especially for lung adenocarcinoma (AUC: 1.0 (1.0-1.0)) in the Asian population (AUC: 0.9 (0.9-1.0)). For prognosis prediction of miR-486 in overall non-small cell lung cancer, the overall hazard ratio with 95% confidence interval was 1.15 (0.85-1.54) for high versus low expression of miR-486, which indicated that a high miR-486 level was not related to the high risk of poor outcome. However, for the subgroup of progression-free survival and patients with chemotherapy, the hazard ratio was 0.41 (0.21-0.77), indicating that the higher miR-486 level would decrease the risk of poor progression-free survival for lung cancer patients with chemotherapy.

CONCLUSION

This study suggested circulating miR-486 combined with other microRNAs could be used as ideal biomarkers in early diagnosis and prognosis prediction for lung cancer, especially for lung adenocarcinoma in the Asian population.

Bioinformatics strategies for studying the molecular mechanisms of fungal extracellular vesicles with a focus on infection and immune responses

Fungal extracellular vesicles (EVs) are released during pathogenesis and are found to be an opportunistic infection in most cases. EVs are immunocompetent with their host and have paved the way for new biomedical approaches to drug delivery and the treatment of complex diseases including cancer. With computing and processing advancements, the rise of bioinformatics tools for the evaluation of various parameters involved in fungal EVs has blossomed. In this review, we have complied and explored the bioinformatics tools to analyze the host-pathogen interaction, toxicity, omics and pathogenesis with an array of specific tools that have depicted the ability of EVs as vector/carrier for therapeutic agents and as a potential theme for immunotherapy. We have also discussed the generation and pathways involved in the production, transport, pathogenic action and immunological interactions of EVs in the host system. The incorporation of network pharmacology approaches has been discussed regarding fungal pathogens and their significance in drug discovery. To represent the overview, we have presented and demonstrated an in silico study model to portray the human Cryptococcal interactions.

Identification of Two Exosomal miRNAs in Circulating Blood of Cancer Patients by Using Integrative Transcriptome and Network Analysis

Exosomes carry molecules of great biological and clinical interest, such as miRNAs. The contents of exosomes vary between healthy controls and cancer patients. Therefore, miRNAs and other molecules transported in exosomes are considered a potential source of diagnostic and prognostic biomarkers in cancer. Many miRNAs have been detected in recent years. Consequently, a substantial amount of miRNA-related data comparing patients and healthy individuals is available, which contributes to a better understanding of the initiation, development, malignancy, and metastasis of cancer using non-invasive sampling procedures. However, a re-analysis of available ncRNA data is rare. This study used available data about miRNAs in exosomes comparing healthy individuals and cancer patients to identify possible global changes related to the presence of cancer. A robust transcriptomic analysis identified two common miRNAs (miR-495-3p and miR-543) deregulated in five cancer datasets. They had already been implicated in different cancers but not reported in exosomes circulating in blood. The study also examined their target genes and the implications of these genes for functional processes.

EVAtlas: a comprehensive database for ncRNA expression in human extracellular vesicles

Extracellular vesicles (EVs) packing various molecules play vital roles in intercellular communication. Non-coding RNAs (ncRNAs) are important functional molecules and biomarkers in EVs. A comprehensive investigation of ncRNAs expression in EVs under different conditions is a fundamental step for functional discovery and application of EVs. Here, we curated 2030 small RNA-seq datasets for human EVs (1506 sEV and 524 lEV) in 24 conditions and over 40 diseases. We performed a unified reads dynamic assignment algorithm (RDAA) considering mismatch and multi-mapping reads to quantify the expression profiles of seven ncRNA types (miRNA, snoRNA, piRNA, snRNA, rRNA, tRNA and Y RNA). We constructed EVAtlas (http://bioinfo.life.hust.edu.cn/EVAtlas), a comprehensive database for ncRNA expression in EVs with four functional modules: (i) browse and compare the distribution of ncRNAs in EVs from 24 conditions and eight sources (plasma, serum, saliva, urine, sperm, breast milk, primary cell and cell line); (ii) prioritize candidate ncRNAs in condition related tissues based on their expression; (iii) explore the specifically expressed ncRNAs in EVs from 24 conditions; (iv) investigate ncRNA functions, related drugs, target genes and EVs isolation methods. EVAtlas contains the most comprehensive ncRNA expression in EVs and will be a key resource in this field.

The roles of small extracellular vesicles in lung cancer: Molecular pathology, mechanisms, diagnostics, and therapeutics

Small extracellular vesicles (sEVs) are submicron-sized, lipid-bilayer-enclosed particles that are released from cells. A variety of tissue-specific molecules, including proteins, DNA fragments, RNA, lipids, and metabolites, can be selectively encapsulated into sEVs and delivered to nearby and distant recipient cells. Incontestable and growing evidence shows the important biological roles and the clinical relevance of sEVs in tumors. In particular, recent studies validate sEVs can be used for early tumor diagnostics, staging, and treatment monitoring. Moreover, sEVs have been used as drug delivery nanocarriers, cancer vaccines, and antigen conferrers. While still in its infancy, the field of sEV-based fundamental and translational studies has been rapidly advancing. This review comprehensively examines the latest sEV-related studies in lung cancers, encompassing extracellular vesicles and their roles in lung cancer pathophysiology, diagnostics, and therapeutics. The state-of-the-art technologies for sEV isolation, downstream molecular analyses, and sEV-based therapies indicate their potency as tools for understanding the pathology and promising clinical management of lung cancers.

The potential diagnostic value of extracellular vesicle miRNA for human non-small cell lung cancer: a systematic review and meta-analysis

Background: This meta-analysis aimed to evaluate the diagnostic accuracy of extracellular vesicles (EV) miRNAs for non-small cell lung cancer (NSCLC).Methods: All eligible studies were searched in an online database. Stata 15.0, Meta-disc 14.0 and Review Manager 5.2 software packages were used to perform all statistical analysis.Results: The analysis included 16 articles and 70 studies. Pooled sensitivity (SEN) and specificity (SPE), positive predictive value and negative predictive value were 0.77 (95% CI: 0.72-0.80), 0.83 (95% CI: 0.78-0.86), 0.88 (95% CI: 0.86-0.90) and 0.63 (95% CI: 0.58-0.68), respectively. The overall diagnostic odds ratio (DOR) was 16 (95% CI: 11-21) and the area under the curve (AUC) was 0.86 (95% CI: 0.83-0.89). 3 EV miRNAs could identify metastatic NSCLC from healthy, and 10 distinguish early-stage NSCLC. The respective targets of EV miR-21, miR-210, and miR-1290 could activate PI3K/AKT-related pathway.Conclusion: EV miRNAs had high diagnostic accuracy (AUC = 0.86) for NSCLC, especially metastatic NSCLC (AUC = 0.90), and early-stage NSCLC (AUC = 0.88). Besides, multitudinous EV miRNAs combined showed higher diagnostic value than alone. EV miR-21, miR-210, and miR-1290 might be associated with PI3K/AKT-related pathway and the valuable diagnostic biomarkers for NSCLC.

A Physically Active Status Affects the Circulating Profile of Cancer-Associated miRNAs

Circulating miRNAs are ideal diagnostics and prognostics biomarkers in cancer since altered levels of specific miRNAs have been associated to development/progression of several cancers. Physical activity is a recognized preventive strategy against several cancers, but it may also modify the baseline levels of cancer-associated miRNAs and, hence, may act as a confounding pre-analytical variable. This study aimed at understanding whether physical activity-dependent changes in cancer-associated circulating miRNAs profile could act as a confounding variable. A panel comprising 179 miRNAs was assayed in plasma from 20 highly trained and 10 sedentary men. RT-qPCR data were analyzed with the 2^−2ΔΔCT methods and normalized on hsa-miR-320d, as determined by bioinformatics analysis. miRNAs associated with the diagnosis of the most prevalent cancers were considered. Only those miRNAs, relevantly associated with cancers, found ≥2-fold up- or downregulated in highly trained subjects compared to sedentary were disclosed. The results reveal that chronic physical activity determined modifications altering the baseline level of several cancer-associated miRNAs and, hence, their diagnostic and prognostic potential. In conclusion, based on our results, a physically active status emerges as an important pre-analytical variable able to alter the basal level of circulating miRNAs, and these alterations might be considered as potentially misleading the analytical output.

The mechanism by which noncoding RNAs regulate muscle wasting in cancer cachexia

Cancer cachexia (CC) is a complex metabolic syndrome that accelerates muscle wasting and affects up to 80% of patients with cancer; however, timely diagnostic methods and effective cures are lacking. Although a considerable number of studies have focused on the mechanism of CC-induced muscle atrophy, few novel therapies have been applied in the last decade. In recent years, noncoding RNAs (ncRNAs) have attracted great attention as many differentially expressed ncRNAs in cancer cachectic muscles have been reported to participate in the inhibition of myogenesis and activation of proteolysis. In addition, extracellular vesicles (EVs), which function as ncRNA carriers in intercellular communication, are closely involved in changing ncRNA expression profiles in muscle and promoting the development of muscle wasting; thus, EV-related ncRNAs may represent potential therapeutic targets. This review comprehensively describes the process of ncRNA transmission through EVs and summarizes the pathways and targets of ncRNAs that lead to CC-induced muscle atrophy.

miRNAs in lung cancer. A systematic review identifies predictive and prognostic miRNA candidates for precision medicine in lung cancer

Lung cancer (LC) is the leading cause of cancer-related death worldwide and miRNAs play a key role in LC development. To better diagnose LC and to predict drug treatment responses we evaluated 228 articles encompassing 16,697 patients and 12,582 healthy controls. Based on the criteria of ≥3 independent studies and a sensitivity and specificity of >0.8 we found blood-borne miR-20a, miR-10b, miR-150, and miR-223 to be excellent diagnostic biomarkers for non-small cell LC whereas miR-205 is specific for squamous cell carcinoma. The systematic review also revealed 38 commonly regulated miRNAs in tumor tissue and the circulation, thus enabling the prediction of histological subtypes of LC. Moreover, theranostic biomarker candidates with proven responsiveness to checkpoint inhibitor treatments were identified, notably miR-34a, miR-93, miR-106b, miR-181a, miR-193a-3p, and miR-375. Conversely, miR-103a-3p, miR-152, miR-152-3p, miR-15b, miR-16, miR-194, miR-34b, and miR-506 influence programmed cell death-ligand 1 and programmed cell death-1 receptor expression, therefore providing a rationale for the development of molecularly targeted therapies. Furthermore, miR-21, miR-25, miR-27b, miR-19b, miR-125b, miR-146a, and miR-210 predicted response to platinum-based treatments. We also highlight controversial reports on specific miRNAs. In conclusion, we report diagnostic miRNA biomarkers for in-depth clinical evaluation. Furthermore, in an effort to avoid unnecessary toxicity we propose predictive biomarkers. The biomarker candidates support personalized treatment decisions of LC patients and await their confirmation in randomized clinical trials.

Serum Exosomes and Their miRNA Load-A Potential Biomarker of Lung Cancer

Early detection of lung cancer in screening programs is a rational way to reduce mortality associated with this malignancy. Low-dose computed tomography, a diagnostic tool used in lung cancer screening, generates a relatively large number of false-positive results, and its complementation with molecular biomarkers would greatly improve the effectiveness of such programs. Several biomarkers of lung cancer based on different components of blood, including miRNA signatures, were proposed. However, only a few of them have been positively validated in the context of early cancer detection yet, which imposes a constant need for new biomarker candidates. An emerging source of cancer biomarkers are exosomes and other types of extracellular vesicles circulating in body fluids. Hence, different molecular components of serum/plasma-derived exosomes were tested and showed different levels in lung cancer patients and healthy individuals. Several studies focused on the miRNA component of these vesicles. Proposed signatures of exosome miRNA had promising diagnostic value, though none of them have yet been clinically validated. These signatures involved a few dozen miRNA species overall, including a few species that recurred in different signatures. It is worth noting that all these miRNA species have cancer-related functions and have been associated with lung cancer progression. Moreover, a few of them, including known oncomirs miR-17, miR-19, miR-21, and miR-221, appeared in multiple miRNA signatures of lung cancer based on both the whole serum/plasma and serum/plasma-derived exosomes.

Extracellular heat shock proteins and cancer: New perspectives

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High expression of extracellular heat shock proteins (HSPs) indicates highly aggressive tumors.

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HSP profiling of extracellular vesicles (EVs) derived from various biological fluids and released by immune cells may open new perspectives for an identification of diagnostic, prognostic and predictive biomarkers of cancer.

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Identification of specific microRNAs targeting HSPs in EVs may be a promising strategy for the discovery of novel biomarkers of cancer.

Heat shock proteins (HSPs) are a large family of molecular chaperones aberrantly expressed in cancer. The expression of HSPs in tumor cells has been shown to be implicated in the regulation of apoptosis, immune responses, angiogenesis and metastasis. Given that extracellular vesicles (EVs) can serve as potential source for the discovery of clinically useful biomarkers and therapeutic targets, it is of particular interest to study proteomic profiling of HSPs in EVs derived from various biological fluids of cancer patients. Furthermore, a divergent expression of circulating microRNAs (miRNAs) in patient samples has opened new opportunities in exploiting miRNAs as diagnostic tools. Herein, we address the current literature on the expression of extracellular HSPs with particular interest in HSPs in EVs derived from various biological fluids of cancer patients and different types of immune cells as promising targets for identification of clinical biomarkers of cancer. We also discuss the emerging role of miRNAs in HSP regulation for the discovery of blood-based biomarkers of cancer. We outline the importance of understanding relationships between various HSP networks and co-chaperones and propose the model for identification of HSP signatures in cancer. Elucidating the role of HSPs in EVs from the proteomic and miRNAs perspectives may provide new opportunities for the discovery of novel biomarkers of cancer.

Five-lncRNA signature in plasma exosomes serves as diagnostic biomarker for esophageal squamous cell carcinoma

Changes in expression of long non-coding RNAs (lncRNAs) in plasma exosomes can be useful for diagnosis of cancer patients. Here, we conducted a four-stage study to identify plasma exosome lncRNAs with diagnostic potential in esophageal squamous cell carcinoma (ESCC). First, plasma exosome lncRNA expression profiles were examined in ESCC patients, esophagitis patients, and healthy controls using RNA sequencing. Differentially expressed plasma exosome lncRNAs from the lncRNA expression profile were then evaluated by qRT-PCR in a large cohort of ESCC patients, esophagitis patients, and healthy controls. Expression levels of the lncRNAs NR_039819, NR_036133, NR_003353, ENST00000442416.1, and ENST00000416100.1 were significantly higher in exosomes from ESCC patients than non-cancer controls. We also confirmed that levels of these five plasma exosome lncRNAs decreased markedly in ESCC patients after surgery. Our results suggest that these five exosome lncRNAs may serve as highly effective, noninvasive biomarkers for ESCC diagnosis.

Novel hepatotoxicity biomarkers of extracellular vesicle (EV)-associated miRNAs induced by CCl4

Recent findings have revealed that extracellular vesicles (EVs) are secreted from cells and circulate in the blood. EVs are classified as exosomes (40-100 nm), microvesicles (50-1,000 nm) or apoptotic bodies (500-2,000 nm). EVs contain mRNAs, microRNAs, and DNAs and have the ability to transfer them from cell to cell. Recently, especially in humans, the diagnostic accuracy of tumor cell type-specific EV-associated miRNAs as biomarkers has been found to be more than 90 %. In addition, microRNAs contained in EVs in blood are being identified as specific biomarkers of chemical-induced inflammation and organ damage. Therefore, microRNAs contained in the EVs released into the blood from tissues and organs in response to adverse events such as exposure to chemical substances and drugs are expected to be useful as novel biomarkers for toxicity assessment. In this study, C57BL/6 J male mice orally dosed with carbon tetrachloride (CCl4) were used as a hepatotoxicity animal model. Here, we report that not only the known hepatotoxicity biomarkers miR-122 and miR-192 but also 42 novel EV-associated biomarkers were upregulated in mice dosed with CCl4. Some of these novel biomarkers may be expected to be able to use for better understanding the mechanism of toxicity. These results suggest that our newly developed protocol using EV-associated miRNAs as a biomarker would accelerate the rapid evaluation of toxicity caused by chemical substances and/or drugs.