Expression analysis of extracellular microRNA in bronchoalveolar lavage fluid from patients with pulmonary sarcoidosis

Kishore, Amit; Navratilova, Zdenka; Kolek, Vı́tězslav; Novosadová, Eva; Čépe, Klára; Bois, Roland M. du; Petřek, Martin

doi:10.1111/resp.13364

Cited by 27 publications

(17 citation statements)

References 35 publications

(100 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…If dysregulated miRNAs are discoveried in patients with NDs, this may be used as a biomarker for the earlier diagnosis and monitoring of disease progression (Kamal et al, 2015 ). MiRNA can also be transcriptional regulators participated in pulmonary sarcoidosis and packaged in extracellular vesicles (EV) during cellular communication (Kishore et al, 2018 ). In biomedical research, identification of disease-associated miRNAs has become an important filed, which will accelerate people's understanding of disease pathogenesis at the molecular level and disease diagnosis, treatment and prevention in medical(Chen et al, 2017d ).…”

Section: Discussionmentioning

confidence: 99%

Identifying and Exploiting Potential miRNA-Disease Associations With Neighborhood Regularized Logistic Matrix Factorization

Zhao

2018

Front. Genet.

View full text Add to dashboard Cite

With the rapid development of biological research, microRNAs (miRNA) have become an attractive topic because lots of experimental studies have revealed the significant associations between miRNAs and diseases. However, considering that experiments are expensive and time-consuming, computational methods for predicting associations between miRNAs and diseases have become increasingly crucial. In this study, we proposed a neighborhood regularized logistic matrix factorization method for miRNA-disease association prediction (NRLMFMDA) by integrating miRNA functional similarity, disease semantic similarity, Gaussian interaction profile kernel similarity, and experimentally validation of disease-miRNA association. We used Gaussian interaction profile kernel similarity to cover the shortage of the traditional similarity to make it more reasonable and complete. Furthermore, NRLMFMDA also considered the important influences of the neighborhood information and took full advantage of them to improve the accuracy of the miRNA-disease association prediction. We also improved the accuracy by giving higher weights to the known association data in the process of calculating the potential association probabilities. In the global and the local leave-one-out cross validation, NRLMFMDA got the AUCs of 0.9068 and 0.8239, respectively. Moreover, the average AUC of NRLMFMDA in 5-fold cross validation was 0.8976 ± 0.0034. All the three kinds of cross validations have shown significant advantages to a number of previous models. In the case studies of breast neoplasms, esophageal neoplasms and lymphoma according to known miRNA-disease associations in the recent version of HMDD database, there were 78, 80, and 74% of top 50 predicted related miRNAs verified to have associations with these three diseases, respectively. In the further case studies for new disease without any known related miRNAs and the previous version of HMDD database, there were also high proportions of the predicted miRNAs verified by experimental reports. All the validation experiment results have demonstrated the effectiveness and practicability of NRLFMDA to predict the potential miRNA-disease associations.

show abstract

Section: Discussionmentioning

confidence: 99%

Identifying and Exploiting Potential miRNA-Disease Associations With Neighborhood Regularized Logistic Matrix Factorization

Zhao

2018

Front. Genet.

View full text Add to dashboard Cite

show abstract

“…Several studies report changes in the molecular content of EVs isolated from bronchoalveolar lavage fluid (BALF) in asthma (19)(20)(21), COPD (22), and sarcoidosis (23)(24)(25)(26).…”

Section: Extracellular Vesicles From Unknown Cellular Originmentioning

confidence: 99%

“…Thereby, all three diseases have been associated with an aberrant miRNA content of BALF EVs compared with healthy controls ( 20 , 22 , 26 ). However, these miRNAs have already been reported to be dysregulated in other diseases, meaning that they are unlikely suitable as a biomarker, unless combined with other markers.…”

Section: Extracellular Vesicles From Unknown Cellular Originmentioning

confidence: 99%

Extracellular Vesicles as Mediators of Cellular Cross Talk in the Lung Microenvironment

et al. 2020

View full text Add to dashboard Cite

The human lung is a complex tissue subdivided into several regions that differ in size, function, and resident cell types. Despite years of intensive research, we still do not fully understand the cross talk between these different regions and diverse cell populations in the lung and how this is altered in the development of chronic respiratory disease. The discovery of extracellular vesicles (EVs), small membrane vesicles released from cells for intercellular communication, has added another layer of complexity to cellular cross talk in the complex lung microenvironment. EVs from patients with chronic obstructive pulmonary disease, asthma, or sarcoidosis have been shown to carry microRNAs, proteins, and lipids that may contribute to inflammation or tissue degeneration. Here, we summarize the contribution of these small vesicles in the interplay of several different cell types in the lung microenvironment, with a focus on the development of chronic respiratory diseases. Although there are already many studies demonstrating the adverse effects of EVs in the diseased lung, we still have substantial knowledge gaps regarding the concrete role of EV involvement in lung disease, which should be addressed in future studies.

show abstract

“…To date, the phenotyping system of Wurm‐Scadding should be overcome because despite a simple reproducibility across populations, it poorly correlates with disease severity or number of systems involved . New potential biomarkers for patients affected by sarcoidosis have been proposed such as micro‐RNA (miRNA) and expression analysis of extracellular miRNA provided that miR‐146a and miR‐150 were negatively correlated with pulmonary function, but the real significance of these findings on disease progression requires further investigations …”

Section: Sarcoidosismentioning

confidence: 99%

Contemporary Concise Review 2018: Interstitial lung disease

2019

View full text Add to dashboard Cite

Expression analysis of extracellular microRNA in bronchoalveolar lavage fluid from patients with pulmonary sarcoidosis

Cited by 27 publications

References 35 publications

Identifying and Exploiting Potential miRNA-Disease Associations With Neighborhood Regularized Logistic Matrix Factorization

Identifying and Exploiting Potential miRNA-Disease Associations With Neighborhood Regularized Logistic Matrix Factorization

Extracellular Vesicles as Mediators of Cellular Cross Talk in the Lung Microenvironment

Contemporary Concise Review 2018: Interstitial lung disease

Contact Info

Product

Resources

About