CRISPRi-based radiation modifier screen identifies long non-coding RNA therapeutic targets in glioma

• Published in: Genome Biology Vol. 21; no. 1; p. 83
• Main Authors: Liu, S. John, Malatesta, Martina, Lien, Brian V., Saha, Parna, Thombare, Shivani S., Hong, Sung Jun, Pedraza, Leslie, Koontz, Mark, Seo, Kyounghee, Horlbeck, Max A., He, Daniel, Birk, Harjus S., Jain, Miten, Olsen, Hugh E., Akeson, Mark, Weissman, Jonathan S., Monje, Michelle, Gupta, Nalin, Raleigh, David R., Ullian, Erik M., Lim, Daniel A.
• Format: Journal Article
• Language: English
• Published: London BioMed Central 31.03.2020; BMC
• Subjects: Adult; adults; Animal Genetics and Genomics; Antisense oligonucleotides; Astrocytes; Bioinformatics; Biomedical and Life Sciences; Brain; Brain Neoplasms - genetics; Brain Neoplasms - pathology; Brain Neoplasms - radiotherapy; Brain Neoplasms - therapy; Cancer therapies; Cancer therapy; Cell growth; Cell Line, Tumor; Cell proliferation; Combined Modality Therapy; CRISPR; CRISPR-Cas Systems; CRISPRi; Evolutionary Biology; fractionation; genome; Genomes; Glioblastoma; Glioblastoma - genetics; Glioblastoma - pathology; Glioblastoma - radiotherapy; Glioblastoma - therapy; Glioma; Glioma cells; Human Genetics; Humans; Invasiveness; Ionizing radiation; Life Sciences; lncRNA; Microbial Genetics and Genomics; Non-coding RNA; oligonucleotides; Oligonucleotides, Antisense; Organoids; Pediatrics; Plant Genetics and Genomics; Radiation; Radiation therapy; Radiation Tolerance; radiotherapy; RNA, Long Noncoding - antagonists & inhibitors; Therapeutic applications; Transcription; viability; lncRNA; CRISPRi; Organoids; Glioma; Cancer therapy; Radiation
• ISSN: 1474-760X; 1474-7596; 1474-760X
• DOI: 10.1186/s13059-020-01995-4

Background Long non-coding RNAs (lncRNAs) exhibit highly cell type-specific expression and function, making this class of transcript attractive for targeted cancer therapy. However, the vast majority of lncRNAs have not been tested as potential therapeutic targets, particularly in the context of currently used cancer treatments. Malignant glioma is rapidly fatal, and ionizing radiation is part of the current standard-of-care used to slow tumor growth in both adult and pediatric patients. Results We use CRISPR interference (CRISPRi) to screen 5689 lncRNA loci in human glioblastoma (GBM) cells, identifying 467 hits that modify cell growth in the presence of clinically relevant doses of fractionated radiation. Thirty-three of these lncRNA hits sensitize cells to radiation, and based on their expression in adult and pediatric gliomas, nine of these hits are prioritized as lncRNA Glioma Radiation Sensitizers ( lncGRS ). Knockdown of lncGRS-1 , a primate-conserved, nuclear-enriched lncRNA, inhibits the growth and proliferation of primary adult and pediatric glioma cells, but not the viability of normal brain cells. Using human brain organoids comprised of mature neural cell types as a three-dimensional tissue substrate to model the invasive growth of glioma, we find that antisense oligonucleotides targeting lncGRS-1 selectively decrease tumor growth and sensitize glioma cells to radiation therapy. Conclusions These studies identify lncGRS-1 as a glioma-specific therapeutic target and establish a generalizable approach to rapidly identify novel therapeutic targets in the vast non-coding genome to enhance radiation therapy.