Long, Noncoding RNA Dysregulation in Glioblastoma
Abstract
:Simple Summary
Abstract
1. Noncoding RNAs Are Transcribed from a Large Proportion of the Genome
1.1. Noncoding RNA Nomenclature and Biogenesis
1.2. Evolutionary Conservation of Noncoding Transcripts
1.3. Long, Noncoding RNAs in the Central Nervous System
2. General Mechanisms of lncRNAs
2.1. Guides
2.2. Scaffolds
2.3. Sponges
2.4. Peptides
2.5. Considering Structural Determinants of lncRNA Function
3. Glioblastoma Is an Aggressive, Fatal Brain Tumor
4. Tumor Heterogeneity and Therapeutic Resistance in GBM
4.1. Defining Transcriptional Subtypes in GBM
4.2. Neurodevelopmental Signatures in GBM Heterogeneity and Therapeutic Resistance
4.3. Influence of Tumor Microenvironment
5. Noncoding Aberrations Are Understudied Molecular Players in GBM
5.1. Somatic Drivers and Structural Variants in lncRNAs
5.2. lncRNA Expression Deregulation
6. RNA-Based Therapeutics
7. Conclusions and Perspectives
Supplementary Materials
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Cell Type | lncRNA Signature | mRNA Signature | Functional Ontologies |
---|---|---|---|
Endothelia | LINC-MILR1-3, SLC38A3, LINC00152, RP11-401P9.4, MIR4435-HG, LINC00339, AP000459.4, AC127904.2, RP11-161M6.2, RP11-417F21.1, TRIM52-AS1, CTD-2081C10.7, RP11-296I10.3, RP11-532M24.1 | GPR116, ITM2A, C1orf54, GNG11, COL4A1, ECSCR, EMCN, LAMA4, ECM1, RAPGEF4, A2M, IGFBP7, CD93, FLT1, RNF144B | Angiogenesis Regulation of vasculature development Hemostasis Response to oxygen levels Blood coagulation Coagulation Regulation of angiogenesis Response to decreased oxygen levels Response to hypoxia Extracellular matrix organization |
Radial Glia | Z83001.1, RP11-731J8.2, LINC00943, RP3-418C23.2, RP11-1002K11.1, MAGI2-AS3, RP11-421L21.3, LINC-FZD3-3, LINC-FZD8-1, LINC00263, EIF3J-AS1, LOC646329, LINC-KREMEN1-1, RUSC1-AS1, DGKK | GPX3, ATP1A2, BCAN, MOXD1, LIPG, CLU, FAM107A, ANXA2, VIM, GFAP, PPAP2B, ZFP36L1, GATM, TNC, HES1 | Negative regulation of nervous system development Negative regulation of neuron development Negative regulation of neurogenesis Glial cell differentiation Response to mechanical stimulus Regulation of neuron differentiation Extracellular matrix organization Extracellular structure organization Positive regulation of neuroblast proliferation |
Dividing Radial Glia | UHRF1, CTB-175P5.4, RP11-138A9.1, RP11-143K11.1, AC004447.2, SNORA59B, CTC-503J8.6, RP11-138A9.2, RP11-95D17.1, THAP9-AS1, SNHG1, CTD-2017D11.1, RP11-58B17.2, DYNLL1-AS1 | MKI67, KIF15, CCNB2, CDK1, UBE2C, FAM64A, NDC80, AURKB, MELK, TPX2, CDCA5, HIST1H1B, BIRC5, ZWINT, TOP2A | Mitotic cell cycle Nuclear division Organelle fission Mitotic nuclear division Chromosome segregation Regulation of cell cycle process Cell cycle checkpoint Chromosome organization DNA repair Microtubule-based process |
Intermediate Progenitor | LINC-TMEM200C-1, RP11-798G7.8, RP11-35IJ23.1-AS1, RP3-326L13.3, CTD-2245E15.3, C1orf132, AC084018.1, RP11-73O6.3, RP11-594N15.3, RP11-436D23.1, AC0838848.8, DGCR11, RP11-456K23.1, RP6-24A23.3, RP1-20C7.6 | PPP1R17, EOMES, NHLH1, SSTR2, SETD7, CCDC129, SIPA1L2, NPR3, FAM60A, SLCO4C1, TRIM45, INHBB, UBL7, STX8, TMEM206 | Dicarboxylic acid biosynthetic process Glutamine family amino acid biosynthetic process GPI anchor metabolic process Regulation of triglyceride biosynthetic process Glutamate metabolic process Neuroblast proliferation Neuromuscular synaptic transmission GPI anchor biosynthetic process Positive regulation of triglyceride metabolic process Positive regulation of triglyceride biosynthetic process |
New Neuron | RP5-1024G6.8, LINC-PTCHD2-3, RP11-513M16.8, RP11-661O13.1, RP11-524C21.2, RP11-356K23.1, LINC01105 | SLC24A2, NRP1, RASGEF1, PALMD, SEMA3C, KCNQ3, UNC5D, SLC17A6, DOK6, SEZ6, DCC, SORBS2, FAM126A, ZNF804A, PPP2R2B | Limb bud formation Cardiac ventricle morphogenesis Cardiac chamber morphogenesis Axon extension Regulation of neuron differentiation Neuron projection extension Positive regulation of neuron differentiation Positive regulation of neurogenesis Glial cell development Regulation of neuron projection development |
Maturing Neuron | MIR137HG, LINC00599, PWAR6, SIK3-IT1, RP11-53O19.3, RP11-402L6.1, RP11-18I14.10, RP11-486F17.1, NAV2-AS3, DAPK1-IT1, RP11-397O4.1, RP11-64K12.10, LINC00643, RP3-462E2.5, LINC-TMEM182-5 | SLC44A5, GRIN2B, CCBE1, CDH13, CAMK2B, SATB2, ARPP21, ADRA2A, DAB1, GLRA2, GPR85, KIAA0319, MCTP1, ADCY1, FLRT2 | Limb bud formation Cardiac ventricle morphogenesis Cardiac chamber morphogenesis Axon extension Regulation of neuron differentiation Neuron projection extension Positive regulation of neuron differentiation Positive regulation of neurogenesis Glial cell development Regulation of neuron projection development |
Interneuron | DLX-AS1, RP11-588P7.1, SOX2-OT, GS1-18A18.1, MEG3, LINC-DKFZP761K2322-2, GRIP2, AC87393.1, LINC00966, RP11-450H6.3, RP13-514E23.1, RP11-379H18.1, RP11-69E11.4, AC012358.8, LINC-TBCC-1 | ERBB4, GAD1, MAF, DLX2, NRXN3, FAM65B, DLX5, PLS3, PDZRN3, LHX6, DLX6, THRB, SCGN, IGF1, CELF4 | GABA synthesis, release, reuptake and degradation Transmission across chemical synapses Neurotransmitter release cycle Nuclear receptor transcription pathway Signaling by ERBB2 Signaling by FGFR Signaling by FGFR in disease Neuronal system Downstream signal transduction Downstream signaling of activated FGFR |
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DeSouza, P.A.; Qu, X.; Chen, H.; Patel, B.; Maher, C.A.; Kim, A.H. Long, Noncoding RNA Dysregulation in Glioblastoma. Cancers 2021, 13, 1604. https://doi.org/10.3390/cancers13071604
DeSouza PA, Qu X, Chen H, Patel B, Maher CA, Kim AH. Long, Noncoding RNA Dysregulation in Glioblastoma. Cancers. 2021; 13(7):1604. https://doi.org/10.3390/cancers13071604
Chicago/Turabian StyleDeSouza, Patrick A., Xuan Qu, Hao Chen, Bhuvic Patel, Christopher A. Maher, and Albert H. Kim. 2021. "Long, Noncoding RNA Dysregulation in Glioblastoma" Cancers 13, no. 7: 1604. https://doi.org/10.3390/cancers13071604
APA StyleDeSouza, P. A., Qu, X., Chen, H., Patel, B., Maher, C. A., & Kim, A. H. (2021). Long, Noncoding RNA Dysregulation in Glioblastoma. Cancers, 13(7), 1604. https://doi.org/10.3390/cancers13071604