Circulating cell‐free microRNAs (miRNAs) are potential cancer biomarkers. The aim of this study was to identify miRNAs that are differentially expressed between benign pleural effusion (BPE) and lung adenocarcinoma‐associated malignant pleural effusion (LA‐MPE). The expression level of cell‐free miRNA was investigated in 107 patients with pleural effusion. Microarrays were used to screen 160 miRNAs in a discovery set comprising 20 effusion samples (ten BPEs and ten LA‐MPEs). Real‐time quantitative reverse transcription polymerase chain reaction (qRT‐PCR) was used to validate the profiling results obtained for the discovery set and those obtained for a validation set comprising 42 BPEs and 45 LA‐MPEs. The area under the receiver operating characteristic curve (AUC) was used to evaluate the diagnostic performance of the identified miRNAs and other common tumor markers, such as carcinoembryonic antigen (CEA) and cytokeratin fragment (CYFRA) 21‐1. Microarray profiling showed that miR‐198 was significantly downregulated in LA‐MPE compared with BPE (p = 0.002). The miRNA microarray analysis results were confirmed by qRT‐PCR (p < 0.001) using the validation set. The AUCs for miR‐198, CEA and CYFRA 21‐1 in the validation set were 0.887, 0.898 and 0.836, respectively. The diagnostic performance of miR‐198 was comparable with that of CEA, but better than that of CYFRA 21‐1. The AUC for all three markers combined was 0.926 (95% confidence interval, 0.843–0.973) with a sensitivity of 89.2% and a specificity of 85.0%. The present study suggests that cell‐free miR‐198 from patients with pleural effusion might have diagnostic potential for differentiating LA‐MPE from BPE.

Choi SY, et al. J Korean Med Sci. 2013 Sep;28(9):1293-1301. https://doi.org/10.3346/jkms.2013.28.9.1293

The selection of reference genes is essential for quantifying gene expression. Theoretically they should be expressed stably and not regulated by experimental or pathological conditions. However, identification and validation of reference genes for human cancer research are still being regarded as a critical point, because cancerous tissues often represent genetic instability and heterogeneity. Recent pan-cancer studies have demonstrated the importance of the appropriate selection of reference genes for use as internal controls for the normalization of gene expression; however, no stably expressed, consensus reference genes valid for a range of different human cancers have yet been identified. In the present study, we used large-scale cancer gene expression datasets from The Cancer Genome Atlas (TCGA) database, which contains 10,028 (9,364 cancerous and 664 normal) samples from 32 different cancer types, to confirm that the expression of the most commonly used reference genes is not consistent across a range of cancer types. Furthermore, we identified 38 novel candidate reference genes for the normalization of gene expression, independent of cancer type. These genes were found to be highly expressed and highly connected to relevant gene networks, and to be enriched in transcription-translation regulation processes. The expression stability of the newly identified reference genes across 29 cancerous and matched normal tissues were validated via quantitative reverse transcription PCR (RT-qPCR). We reveal that most commonly used reference genes in current cancer studies cannot be appropriate to serve as representative control genes for quantifying cancer-related gene expression levels, and propose in this study three potential reference genes (HNRNPL, PCBP1, and RER1) to be the most stably expressed across various cancerous and normal human tissues.