ABSTRACT
BACKGROUND: Lung cancer is one of the most common malignancies across the world. Long noncoding RNAs (lncRNAs) play an important role in the pathology. This study was to compare the lncRNA and mRNA of lung cancer. The aim of this study was to compare the lncRNA and mRNA expression profiles, their related biological functions, and pathways in lung cancer. METHODS: Human lung cancer mRNA expression datasets were searched and downloaded from NCBI-GEO. LncRNA expression profiles in lung cancer were detected by the Agilent Human LncRNA Microarray V3.0. Differential expression analysis was conducted between cases and controls in mRNA and lncRNA. The starBase web server v2.0 was used to decipher lncRNA-protein interactions. DAVID Bioinformatics Resources 6.7 was used to perform GO Biological Processes and KEGG pathway enrichment analysis of these dysregulated mRNA and lncRNA target genes. RESULTS: The study showed that differentially expressed lncRNA target genes included almost all of the differential expression genes from mRNA. Furthermore, these dysregulated lncRNAs reflected more comprehensive impairment in functional enrichment than dysregulated mRNAs. In addition, five top downregulated lncRNAs had more remarkable fold changes than top downregulated mRNAs, especially FENDRR. CONCLUSIONS: Amount of lncRNAs and mRNAs were differentially expressed in lung cancer. The degrees of difference in lncRNAs were more than mRNAs. It may provide valuable help for an effective strategy in diagnosis and prevention.
Subject(s)
Biomarkers, Tumor/genetics , Lung Neoplasms/genetics , RNA, Long Noncoding/genetics , RNA, Messenger/genetics , Transcriptome , Computational Biology , Databases, Genetic , Gene Expression Profiling/methods , Gene Expression Regulation, Neoplastic , Gene Regulatory Networks , Genetic Predisposition to Disease , Humans , Lung Neoplasms/pathology , Oligonucleotide Array Sequence Analysis , PhenotypeABSTRACT
BACKGROUND: Matrix-assisted laser desorption ionization/time-of-flight (MALDI-TOF) mass spectrometry has been successfully used to detect trace albumin in urine for the diagnosis of albuminuria. However, only the monomeric form of albumin was detected with this approach. METHODS: Trypsin was used to digest urinary albumin and its related compounds in urine to produce characteristic peptides. The digest solution was subsequently analyzed by MALDI-TOF MS to obtain peptide ion signals which were used as diagnostic biomarkers for albuminuria. RESULTS: The analytical protocol was optimized for efficient digestion and high-performance MALDI-TOF MS analysis. The limit of detection (LOD) of albumin in urine was about 5×10(-7)M. CONCLUSIONS: Trypsin digestion combined with MALDI-TOF MS analysis is an efficient and simple approach for rapidly diagnosing albuminuria.
Subject(s)
Albumins/metabolism , Albuminuria/diagnosis , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Trypsin/metabolism , Humans , Limit of Detection , Peptides/urineABSTRACT
BACKGROUND: Matrix-assisted laser desorption ionization/time-of-flight (MALDI-TOF) mass spectrometric analysis of albumin (ALB) biomarkers is an alternative approach toward the rapid diagnosis of proteinuria for screening a large number of samples. The aim of this study is to reveal if interfering factors in urinary dipstick approach would affect the results of diagnosing albuminuria by MALDI-TOF MS. METHODS: The effects of various interfering chemicals on the diagnosis of albumin in urine were examined using both MALDI-TOF mass spectrometric and dipstick approaches. Semi-quantification of albumin was performed by using MALDI-TOF MS. RESULTS: Interferences from various drugs, detergents, vitamins and their metabolites, alkaline, and blood, which often cause false-positive and false-negative results in conventional urinary dipstick analysis, are avoided when using this MALDI-TOF MS approach. It was found that the intensity of +1 and +2 albumin ions varies with the albumin concentration. A log/log plot of the intensity ratio vs. albumin concentration is then used as a calibration curve for semi-quantifying the albumin in urines. CONCLUSIONS: MALDI-TOF MS is an effective approach toward avoiding interferences caused by various chemical compounds during the rapid diagnosis of albumin in urine. Semi-quantification of albuminuria is also achieved by this MALDI-TOF MS approach.
