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      MicroRNA Signatures Associated with Bronchopulmonary Dysplasia Severity in Tracheal Aspirates of Preterm Infants

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          Abstract

          Bronchopulmonary dysplasia (BPD) is a form of chronic lung disease that develops in neonates as a consequence of preterm birth, arrested fetal lung development, and inflammation. The incidence of BPD remains on the rise as a result of increasing survival of extremely preterm infants. Severe BPD contributes to significant health care costs and is associated with prolonged hospitalizations, respiratory infections, and neurodevelopmental deficits. In this study, we aimed to detect novel biomarkers of BPD severity. We collected tracheal aspirates (TAs) from preterm babies with mild/moderate ( n = 8) and severe ( n = 17) BPD, and we profiled the expression of 1048 miRNAs using a PCR array. Associations with biological pathways were determined with the Ingenuity Pathway Analysis (IPA) software. We found 31 miRNAs differentially expressed between the two disease groups (2-fold change, false discovery rate (FDR) < 0.05). Of these, 4 miRNAs displayed significantly higher expression levels, and 27 miRNAs had significantly lower expression levels in the severe BPD group when compared to the mild/moderate BPD group. IPA identified cell signaling and inflammation pathways associated with miRNA signatures. We conclude that TAs of extremely premature infants contain miRNA signatures associated with severe BPD. These may serve as potential biomarkers of disease severity in infants with BPD.

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          Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.

          The two most commonly used methods to analyze data from real-time, quantitative PCR experiments are absolute quantification and relative quantification. Absolute quantification determines the input copy number, usually by relating the PCR signal to a standard curve. Relative quantification relates the PCR signal of the target transcript in a treatment group to that of another sample such as an untreated control. The 2(-Delta Delta C(T)) method is a convenient way to analyze the relative changes in gene expression from real-time quantitative PCR experiments. The purpose of this report is to present the derivation, assumptions, and applications of the 2(-Delta Delta C(T)) method. In addition, we present the derivation and applications of two variations of the 2(-Delta Delta C(T)) method that may be useful in the analysis of real-time, quantitative PCR data. Copyright 2001 Elsevier Science (USA).
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            limma powers differential expression analyses for RNA-sequencing and microarray studies

            limma is an R/Bioconductor software package that provides an integrated solution for analysing data from gene expression experiments. It contains rich features for handling complex experimental designs and for information borrowing to overcome the problem of small sample sizes. Over the past decade, limma has been a popular choice for gene discovery through differential expression analyses of microarray and high-throughput PCR data. The package contains particularly strong facilities for reading, normalizing and exploring such data. Recently, the capabilities of limma have been significantly expanded in two important directions. First, the package can now perform both differential expression and differential splicing analyses of RNA sequencing (RNA-seq) data. All the downstream analysis tools previously restricted to microarray data are now available for RNA-seq as well. These capabilities allow users to analyse both RNA-seq and microarray data with very similar pipelines. Second, the package is now able to go past the traditional gene-wise expression analyses in a variety of ways, analysing expression profiles in terms of co-regulated sets of genes or in terms of higher-order expression signatures. This provides enhanced possibilities for biological interpretation of gene expression differences. This article reviews the philosophy and design of the limma package, summarizing both new and historical features, with an emphasis on recent enhancements and features that have not been previously described.
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              Bronchopulmonary dysplasia.

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                Author and article information

                Contributors
                Role: Academic Editor
                Journal
                Biomedicines
                Biomedicines
                biomedicines
                Biomedicines
                MDPI
                2227-9059
                05 March 2021
                March 2021
                : 9
                : 3
                : 257
                Affiliations
                [1 ]Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA; rsiddaiah@ 123456pennstatehealth.psu.edu (R.S.); cojimmuo@ 123456pennstatehealth.psu.edu (C.N.O.-M.); dspear@ 123456pennstatehealth.psu.edu (D.S.); adonnelly@ 123456pennstatehealth.psu.edu (A.D.)
                [2 ]Biobehavioral Laboratory, School of Nursing, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; dmontes@ 123456email.unc.edu
                [3 ]National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; nathalie.fuentesortiz@ 123456nih.gov
                [4 ]Department of Environmental and Occupational Health, School of Public Health, Indiana University, Bloomington, IN 47405, USA
                Author notes
                [* ]Correspondence: psilveyr@ 123456iu.edu
                [†]

                These authors have contributed equally to this work.

                Author information
                https://orcid.org/0000-0002-8897-9203
                https://orcid.org/0000-0001-7083-8915
                Article
                biomedicines-09-00257
                10.3390/biomedicines9030257
                8000397
                dbea128c-9d69-4a48-a354-ba12b80b3ea1
                © 2021 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 04 February 2021
                : 01 March 2021
                Categories
                Article

                bronchopulmonary dysplasia,prematurity,mirna,biomarkers,tracheal aspirates

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