The Circular RNA Landscape of Non-Small Cell Lung Cancer Cells
1
Division of Cancer Research, Department of Thoracic Surgery, Medical Center―University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
2
German Cancer Consortium (DKTK), Partner Site Freiburg, 79106 Freiburg, Germany
3
Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
*
Author to whom correspondence should be addressed.
†
Authors contributed equally.
Cancers 2020, 12(5), 1091; https://doi.org/10.3390/cancers12051091
Received: 30 March 2020
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Revised: 22 April 2020
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Accepted: 23 April 2020
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Published: 28 April 2020
(This article belongs to the Special Issue Non-Coding RNAs as Emerging Regulators of Signalling Pathways and Novel Therapeutic Targets in Human Cancers)
The class of circular RNA (circRNA) is characterized by head-to-tail bonds between exons formed by backsplicing. Here, we provide a resource of circRNA expression in a comprehensive panel of 60 lung cancer and non-transformed cell lines (FL3C dataset). RNA sequencing after depletion of ribosomal RNA quantified the expression of circRNA and linear RNA. We detected 148,811 circular RNAs quantified by 2.8 million backsplicing reads originating from 12,251 genes. The number of identified circRNAs was markedly higher using rRNA depletion compared to public polyA-enriched RNA-seq datasets. CircRNAs almost never started in the first exon nor ended in the last exon and started more frequently in earlier exons. Most circRNAs showed high cell line specificity and correlated positively with their linear RNA counterpart. Known cancer genes produced more circRNAs than non-cancer genes. Subsets of circRNAs correlated with cell proliferation, histological subtype or genotype. CircTNFRSF21 was translated crossing the backsplice site in two different reading frames. Overexpression of circPVT1, circERBB2, circHIPK3, circCCNB1, circSMAD2, circTNFRSF21 and circKIF5B significantly increased colony formation. In conclusion, our data provide a comprehensive map of circRNA expression in lung cancer cells and global patterns of circRNA production as a useful resource for future research into lung cancer circRNAs.
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Keywords:
circular RNA; circRNA; NSCLC; lung cancer; lung adenocarcinoma
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MDPI and ACS Style
Van Der Steen, N.; Lyu, Y.; Hitzler, A.K.; Becker, A.C.; Seiler, J.; Diederichs, S. The Circular RNA Landscape of Non-Small Cell Lung Cancer Cells. Cancers 2020, 12, 1091. https://doi.org/10.3390/cancers12051091
AMA Style
Van Der Steen N, Lyu Y, Hitzler AK, Becker AC, Seiler J, Diederichs S. The Circular RNA Landscape of Non-Small Cell Lung Cancer Cells. Cancers. 2020; 12(5):1091. https://doi.org/10.3390/cancers12051091
Chicago/Turabian StyleVan Der Steen, Nele, Yanhong Lyu, Anne K. Hitzler, Andrea C. Becker, Jeanette Seiler, and Sven Diederichs. 2020. "The Circular RNA Landscape of Non-Small Cell Lung Cancer Cells" Cancers 12, no. 5: 1091. https://doi.org/10.3390/cancers12051091
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