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Open AccessArticle

Temozolomide-Induced RNA Interactome Uncovers Novel LncRNA Regulatory Loops in Glioblastoma

1
NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg L-1526, Luxembourg
2
Quantitative Biology Unit, Luxembourg Institute of Health, Luxembourg L-1526, Luxembourg
3
Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, USA
4
Faculty of Science, Technology and Medicine, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg
5
Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique, UMR7104, Institut National de la Santé et de la Recherche Médicale, U964, Université de Strasbourg, 67404 Illkirch, France
6
DNA Repair and Chemoresistance, Department of Oncology, Luxembourg Institute of Health, Luxembourg L-1526, Luxembourg
7
Experimental Neurosurgery, Department of Neurosurgery, University of Heidelberg, 69120 Heidelberg, Germany
8
School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
9
Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway
*
Author to whom correspondence should be addressed.
Cancers 2020, 12(9), 2583; https://doi.org/10.3390/cancers12092583
Received: 17 July 2020 / Revised: 4 September 2020 / Accepted: 8 September 2020 / Published: 10 September 2020
(This article belongs to the Special Issue Resistance Mechanisms in Malignant Brain Tumors)
Glioblastoma (GBM) is the most aggressive brain tumor and most resistant to therapy. The identification of novel predictive biomarkers or targets to counteract chemoresistance, requires a better understanding of the GBM primary response to therapy. The aim of our study was to assess the molecular response of GBM to the standard of care chemotherapy by temozolomide (TMZ). We established a comprehensive map of gene expression changes after treatment and discovered that GBM cells elicit a coordinated gene expression program after chemotherapy that differs between sensitive and resistant cells. We found that a novel class of genes expressed as long non-coding RNAs (lncRNAs) is involved in gene regulatory circuits in GBM and could represent novel markers of GBM patient prognosis. By shedding light on the involvement of the non-coding genome in GBM, our results may provide new mechanistic insight on lncRNAs and their importance in chemoresistance.
Resistance to chemotherapy by temozolomide (TMZ) is a major cause of glioblastoma (GBM) recurrence. So far, attempts to characterize factors that contribute to TMZ sensitivity have largely focused on protein-coding genes, and failed to provide effective therapeutic targets. Long noncoding RNAs (lncRNAs) are essential regulators of epigenetic-driven cell diversification, yet, their contribution to the transcriptional response to drugs is less understood. Here, we performed RNA-seq and small RNA-seq to provide a comprehensive map of transcriptome regulation upon TMZ in patient-derived GBM stem-like cells displaying different drug sensitivity. In a search for regulatory mechanisms, we integrated thousands of molecular associations stored in public databases to generate a background “RNA interactome”. Our systems-level analysis uncovered a coordinated program of TMZ response reflected by regulatory circuits that involve transcription factors, mRNAs, miRNAs, and lncRNAs. We discovered 22 lncRNAs involved in regulatory loops and/or with functional relevance in drug response and prognostic value in gliomas. Thus, the investigation of TMZ-induced gene networks highlights novel RNA-based predictors of chemosensitivity in GBM. The computational modeling used to identify regulatory circuits underlying drug response and prioritizing gene candidates for functional validation is applicable to other datasets. View Full-Text
Keywords: glioblastoma; temozolomide; lncRNA; regulatory circuit; chemoresistance; transcriptome glioblastoma; temozolomide; lncRNA; regulatory circuit; chemoresistance; transcriptome
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MDPI and ACS Style

Fritah, S.; Muller, A.; Jiang, W.; Mitra, R.; Sarmini, M.; Dieterle, M.; Golebiewska, A.; Ye, T.; Van Dyck, E.; Herold-Mende, C.; Zhao, Z.; Azuaje, F.; Niclou, S.P. Temozolomide-Induced RNA Interactome Uncovers Novel LncRNA Regulatory Loops in Glioblastoma. Cancers 2020, 12, 2583. https://doi.org/10.3390/cancers12092583

AMA Style

Fritah S, Muller A, Jiang W, Mitra R, Sarmini M, Dieterle M, Golebiewska A, Ye T, Van Dyck E, Herold-Mende C, Zhao Z, Azuaje F, Niclou SP. Temozolomide-Induced RNA Interactome Uncovers Novel LncRNA Regulatory Loops in Glioblastoma. Cancers. 2020; 12(9):2583. https://doi.org/10.3390/cancers12092583

Chicago/Turabian Style

Fritah, Sabrina; Muller, Arnaud; Jiang, Wei; Mitra, Ramkrishna; Sarmini, Mohamad; Dieterle, Monika; Golebiewska, Anna; Ye, Tao; Van Dyck, Eric; Herold-Mende, Christel; Zhao, Zhongming; Azuaje, Francisco; Niclou, Simone P. 2020. "Temozolomide-Induced RNA Interactome Uncovers Novel LncRNA Regulatory Loops in Glioblastoma" Cancers 12, no. 9: 2583. https://doi.org/10.3390/cancers12092583

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