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Article

The Effect of Genomic DNA Contamination on the Detection of Circulating Long Non-Coding RNAs: The Paradigm of MALAT1

1
Analysis of Circulating Tumor Cells Lab, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece
2
8th Department of Pulmonary Diseases, ‘Sotiria’ General Hospital for Chest Diseases, 11527 Athens, Greece
*
Author to whom correspondence should be addressed.
Academic Editor: Francesco Sessa
Diagnostics 2021, 11(7), 1160; https://doi.org/10.3390/diagnostics11071160
Received: 19 April 2021 / Revised: 24 May 2021 / Accepted: 21 June 2021 / Published: 25 June 2021
The presence of contaminating gDNA in RNA preparations is a frequent cause of false positives in RT-PCR-based analysis. However, in some cases, this cannot be avoided, especially when there are no exons–intron junctions in the lncRNA sequences. Due to the lack of exons in few of long noncoding RNAs (lncRNAs) and the lack of DNAse treatment step in most studies reported so far, serious questions are raised about the specificity of lncRNA detection and the potential of reporting false-positive results. We hypothesized that minute amounts of gDNA usually co-extracted with RNA could give false-positive signals since primers would specifically bind to gDNA due to the lack of junction. In the current study, we evaluated the effect of gDNA and other forms of DNA like extrachromosomal circular DNAs (eccDNAs) contamination and the importance of including a DNAse treatment step on lncRNAsexpression.As a model, we have chosen as one of the most widely studied lncRNAs in cancer namely MALAT1, which lacks exons. When we tested this hypothesis in plasma and primary tissue samples from NSCLC patients, our findings clearly indicated that results on MALAT1 expression are highly affected by the presence of DNA contamination and that the DNAse treatment step is absolutely necessary to avoid false positive results. View Full-Text
Keywords: MALAT1; non-long coding RNA; DNAse treatment; cfRNA; tumor biomarkers; false positive results; gDNA MALAT1; non-long coding RNA; DNAse treatment; cfRNA; tumor biomarkers; false positive results; gDNA
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MDPI and ACS Style

Markou, A.N.; Smilkou, S.; Tsaroucha, E.; Lianidou, E. The Effect of Genomic DNA Contamination on the Detection of Circulating Long Non-Coding RNAs: The Paradigm of MALAT1. Diagnostics 2021, 11, 1160. https://doi.org/10.3390/diagnostics11071160

AMA Style

Markou AN, Smilkou S, Tsaroucha E, Lianidou E. The Effect of Genomic DNA Contamination on the Detection of Circulating Long Non-Coding RNAs: The Paradigm of MALAT1. Diagnostics. 2021; 11(7):1160. https://doi.org/10.3390/diagnostics11071160

Chicago/Turabian Style

Markou, Athina N., Stavroula Smilkou, Emilia Tsaroucha, and Evi Lianidou. 2021. "The Effect of Genomic DNA Contamination on the Detection of Circulating Long Non-Coding RNAs: The Paradigm of MALAT1" Diagnostics 11, no. 7: 1160. https://doi.org/10.3390/diagnostics11071160

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