Noncoding RNA:RNA Regulatory Networks in Cancer
Abstract
1. Introduction
2. Competing Endogenous RNA (ceRNA) Networks and Regulation
3. The Links between Long Noncoding RNAs and microRNAs
3.1. Cytoplasmic lncRNAs
3.1.1. H19
3.1.2. Growth Arrest-Specific 5 (GAS5)
3.1.3. LincRNA, Regulator of Reprogramming (Linc-ROR)
3.1.4. Noncoding RNA Activated by DNA Damage (NORAD)
3.2. Nuclear LncRNAs
3.2.1. X-Inactive Transcript (XIST)
3.2.2. Nuclear Enriched Abundant Transcript 1 (NEAT1)
3.2.3. Metastasis Associated Lung Adenocarcinoma Transcript 1 (MALAT1)
3.2.4. Plasmacytoma Variant Translocation 1 (PVT1)
3.3. Antisense RNAs
3.3.1. Hox Transcript Antisense RNA (HOTAIR)
3.3.2. HOXD Antisense Growth-Associated lncRNA (HOXD-AS1)
3.4. Pseudogenes
3.4.1. Tumor Suppressive Pseudogenes
3.4.2. Oncogenic Pseudogenes
3.5. Circular RNAs
3.5.1. Cerebellar Degeneration-Related Protein 1 Antisense RNA (CDR1as)
3.5.2. Circ-ITCH (Itchy E3 Ubiquitin Protein Ligase)
3.5.3. CircHIPK3 (Homeodomain Interacting Protein Kinase 3)
3.5.4. CircPVT1
3.5.5. Other Newly Identified circRNAs
4. The Impact of Cellular Localization on miRNA-Mediated Gene Regulation
5. The Diagnostic and Prognostic Potential of ceRNA Interactions
6. Closing Remarks
Acknowledgments
Conflicts of Interest
Abbreviations
ADAR2 | adenosine deaminase, RNA specific B1 |
AGO2 | argonaute 2, RISC catalytic component |
AKT | AKT serine/threonine kinase 1/protein kinase B |
ANXA1 | annexin A1 |
AR | androgen receptor |
ARHI | DIRAS family GTPase 3 |
ATG7 | autophagy related 7 |
AVPR2 | arginine vasopressin receptor 2 |
AXL | AXL receptor tyrosine kinase |
BCL2 | B-cell lymphoma 2, apoptosis regulator |
BECN1 | beclin 1 |
BMF | Bcl2 modifying factor |
BRAF | B-Raf proto-oncogene, serine/threonine kinase |
BRAFP1 | B-Raf proto-oncogene, serine/threonine kinase pseudogene 1 |
BUB1 | BUB1 mitotic checkpoint serine/threonine kinase |
CCND1 | cyclin D1 |
CCNE1 | cyclin E1 |
CCNJ | cyclin J |
CDC42 | cell division cycle 42 |
CDK3 | cyclin dependent kinase 3 |
CDK6 | cyclin dependent kinase 6 |
ceRNA | competing endogenous RNA |
c-Kit | KIT proto-oncogene receptor tyrosine kinase |
c-Met | MET proto-oncogene, receptor tyrosine kinase |
CRC | colorectal carcinoma |
CRISPR | clustered regularly interspaced short palindromic repeats |
CTNNA1 | catenin alpha 1 |
CTNNA1P | catenin alpha 1 pseudogene |
CXCR4 | C-X-C motif chemokine receptor 4 |
CYP4Z1 | cytochrome P450 family 4 subfamily Z member 1 |
CYP4Z2P | cytochrome P450 family 4 subfamily Z member 2, pseudogene |
CYTH3 | cytohesin 3 |
DNMT3B | DNA methyltransferase 3 beta |
DRCE | drug-response related ceRNA |
DVL2 | disheveled segment polarity protein 2 |
EGFR | epidermal growth factor receptor |
EGR1 | early growth response 1 |
EMT | epithelial mesenchymal transition |
EPHA4 | EPH receptor A4 |
EZH2 | enhancer of zeste 2 polycomb repressive complex 2 subunit |
FAK | focal adhesion kinase |
FANCC | Fanconi anemia complementation group C |
FASN | fatty acid synthase |
FOXO3 | forkhead box O3 |
FOXO3P | forkhead box O3 pseudogene |
FTH1 | ferritin heavy chain 1 |
FZD4 | frizzled class receptor 4 |
GIT2 | GIT ArfGAP 2 |
HCC | hepatocellular carcinoma |
HER2 | erb-b2 receptor tyrosine kinase 2 |
HIF-1α | hypoxia-inducible factor 1-alpha |
HMGA1P6/7 | high mobility group AT-hook 1 pseudogene 6/7 |
HMGA2 | high mobility group AT-hook 2 |
HMGB1 | high mobility group box 1 |
hTERT | human telomerase reverse transcriptase |
IGF1R | insulin like growth factor 1 receptor |
IGF2 | insulin like growth factor 2 |
INST6 | integrator complex subunit 6 |
INTS6P1 | integrator complex subunit 6 pseudogene 1 |
KRAS | KRAS proto-oncogene, GTPase |
LIN28 | lin-28 homolog |
lncRNA | long noncoding RNA |
LSCC | laryngeal squamous cell carcinoma |
MCL1 | MCL1, BCL2 family apoptosis regulator |
MDR1 | ATP binding cassette subfamily B member 1 |
miRNA | microRNA |
MKI67 | marker of proliferation Ki-67 |
MMP2 | matrix metallopeptidase 2 |
MRP1 | ATP binding cassette subfamily C member 1 |
MYCN | MYCN proto-oncogene, bHLH transcription factor |
NF-κB | nuclear factor kappa B |
NSCLC | non-small cell lung cancer |
OCT4/POU5F1 | POU class 5 homeobox 1 |
OSCC | oral squamous cell carcinoma |
PDK1 | pyruvate dehydrogenase kinase 1 |
PI3K | phosphatidylinositol-4,5-bisphosphate 3-kinase |
PIK3CD | phosphatidylinositol-4,5-Bisphosphate 3-Kinase Catalytic Subunit Delta |
PLXNC1 | plexin C1 |
PPIB | peptidylprolyl isomerase B |
PRC2 | polycomb repressive complex 2 |
PTEN | phosphatase and tensin homolog |
PTENP1 | phosphatase and tensin homolog pseudogene 1 |
RELA | RELA proto-oncogene, NF-κB subunit |
RHOA | ras homolog family member A |
RISC | RNA-induced silencing complex |
ROCK2 | Rho associated coiled-coil containing protein kinase 2 |
RSU1P2 | Ras suppressor protein 1 pseudogene 2 |
SMAD7 | SMAD family member 7 |
SOCS6 | suppressor of cytokine signaling 6 |
SOX9 | SRY (sex determining region Y)-box 9 |
STAT3 | signal transducer and activator of transcription 3 |
TEAD | TEA domain transcription factor |
TIMP2/3 | tissue inhibitor of metalloproteinases 2/3 |
TNRC6 | trinucleotide repeat containing 6A |
TP53 | tumor protein p53 |
TUSC2 | tumor suppressor 2, mitochondrial calcium regulator |
TWIST1 | twist family bHLH transcription factor 1 |
UCA1 | urothelial cancer associated 1 |
VEGFA | vascular endothelial growth factor A |
VEGFR2 | kinase insert domain receptor |
VIM | vimentin |
YAP1 | Yes associated protein 1 |
YY1 | Yin Yang 1 transcription factor |
ZEB1/2 | zinc finger E-box binding homeobox 1/2 |
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Noncoding RNA Species | Competing Endogenous RNAs | Shared miRNAs | Cancer Type | References | |
---|---|---|---|---|---|
LncRNA | H19 | DNMT3B | miR-29b-3p | Bladder | [54] |
GIT2, CYTH3 | miR-200b, miR-200c, let-7b | Breast | [55] | ||
HMGA2 | let-7 | Pancreas, tongue | [56,57] | ||
VIM, ZEB1, ZEB2 | miR-138, miR-200a | Colon | [58] | ||
ROCK2 | miR-484 | Lung | [59] | ||
LIN28 | let-7 family | Breast | [60,61] | ||
GAS5 | PTEN | miR-21, miR-222 | Thyroid, gastric, endometrial, cervical, lung | [63,64,65,66,67] | |
CXCR4 | miR-301 | Esophageal | [68] | ||
Linc-ROR | SOX9 | let-7 family, miR-93, miR-145, miR-320a, miR-320b | Pancreas | [71] | |
miR-15b, miR-33a, miR-129, miR-145, and miR-206 | Esophageal | [72] | |||
NORAD | RHOA | miR-125a-3p | Pancreas | [74] | |
XIST | SMAD7 | miR-92b | Liver | [76] | |
PTEN | miR-181a | Liver | [77] | ||
PDK1 | miR-139-5p | Liver | [78] | ||
EZH2 | miR-101 | Gastric | [79] | ||
AR | miR-124 | Bladder | [80] | ||
EGFR | miR-133a | Pancreas | [81] | ||
NEAT1 | CDK6 | miR-107 | Laryngeal, glioma | [85,86] | |
STAT3 | miR-506, let-7e | Gastric, glioma | [87,88] | ||
ZEB1 | miR-204 | Nasopharyngeal | [89] | ||
CCND1 | miR-193-3p | Cervical | [90] | ||
MALAT1 | HMGB1 | miR-129-5p | Colon | [94] | |
CDC42 | miR-1 | Breast | [95] | ||
miR-206 | Gallbladder | [96] | |||
STAT3 | miR-124, miR-125b | Lung, oral | [97,98] | ||
PTEN | miR-17, miR-20a, miR-106b | Colon | [100] | ||
PVT1 | YAP1, HIF1-α | miR-186-5p | Liver, gastric | [102,103] | |
ATG7, BECN1 | miR-186 | Glioma | [104] | ||
TWIST1 | miR-186 | Prostate | [105] | ||
HIF1-α | miR-199a-5p | Lung | [106] | ||
BCL2, CCND1, FASN | miR-195 | Osteosarcoma | [107] | ||
miR-200 family | Renal, breast | [108,109] | |||
HOTAIR | c-Met, SNAIL | miR-34a | Gastric, pancreas | [115,116] | |
CCNJ | miR-205 | Bladder | [117] | ||
IGF2 | miR-663b | Pancreas | [118] | ||
HOXD-AS1 | E2F8, SOX4 | miR-130a | Glioma, liver | [119,120] | |
FZD4 | miR-608 | Ovarian | [121] | ||
Pseudogene | PTENP1 | PTEN | miR-19b, miR-20a, miR-21, miR-26a, miR-214, miR-93, miR-106b | Prostate, renal, oral, gastric | [31,124,125,126] |
SOCS6 | miR-17-5p | Esophageal | [127] | ||
TUSC2P | TUSC2, TIMP2, TIMP3 | miR-17, miR-93, miR-299-3p, miR-520a, miR-608, miR-661 | Breast, prostate | [128] | |
INTS6P1 | INTS6 | miR-17-5p | Liver | [129] | |
CTNNAP1 | CTNNA | miR-141 | Colon | [130] | |
FOXO3P | FOXO3, circ-FOXO3 | miR-22, miR-136*, miR-138, miR-149*, miR-433, miR-762, miR-3614-5p, miR-3622b-5p | Breast | [131] | |
FTH1P11, FTH1P16 | FTH1 | miR-19b, miR-181a, miR-210, miR-362, miR-616, miR-638 | Prostate | [132] | |
BRAFP1 | BRAF | miR-30a, miR-182, miR-134, miR-543, miR-653, miR-876 | Melanoma | [35] | |
KRASP1 | KRAS | let-7 family | Prostate | [31] | |
OCT4-pg1, OCT4-pg3, OCT4-pg4, OCT4-pg5 | OCT4/POU5F1 | miR-145 | Liver, endometrial | [31,133,134] | |
RSU1P2 | IGF1R, MYCN, EPHA4 | let-7a | Cervical | [135] | |
CYP4Z2P | CYP4Z1, CDK3, hTERT | miR-125a, miR-197, miR-204, miR-1226 | Breast | [136,137,138] | |
HMGA1P7 | HMGA1, H19, IGF2 | miR-15, miR-16, miR-214, miR-761 | Breast | [139,140] | |
CircRNA | CDR1as | CCNE1, PIK3CD, EGFR, IGF1R, RELA | miR-7 | Liver, colon, lung, gastric | [144,149,151,152,153,154] |
circ-ITCH | ITCH | miR-7, miR-17, miR-214 | Lung, esophageal | [156,157] | |
p21, PTEN | miR-7, miR-224 | Bladder | [158] | ||
circ-HIPK3 | FAK, IGF1R, EGFR, YY1 | miR-124 | Colon | [159] | |
circ-PVT1 | IGF2BP1, KRAS, HMGA2 | let-7 | Breast, lung | [160] | |
AURKA, MKI67, BUB1 | miR-497-5p | Head and neck | [161] | ||
circ-MYLK | VEGFA, VEGFR2 | miR-29a | Bladder | [162] | |
circ-MTO1 | p21 | miR-9 | Liver | [163] | |
circ-CCDC66 | MYC | miR-93 | Colon | [164] |
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Chan, J.J.; Tay, Y. Noncoding RNA:RNA Regulatory Networks in Cancer. Int. J. Mol. Sci. 2018, 19, 1310. https://doi.org/10.3390/ijms19051310
Chan JJ, Tay Y. Noncoding RNA:RNA Regulatory Networks in Cancer. International Journal of Molecular Sciences. 2018; 19(5):1310. https://doi.org/10.3390/ijms19051310
Chicago/Turabian StyleChan, Jia Jia, and Yvonne Tay. 2018. "Noncoding RNA:RNA Regulatory Networks in Cancer" International Journal of Molecular Sciences 19, no. 5: 1310. https://doi.org/10.3390/ijms19051310
APA StyleChan, J. J., & Tay, Y. (2018). Noncoding RNA:RNA Regulatory Networks in Cancer. International Journal of Molecular Sciences, 19(5), 1310. https://doi.org/10.3390/ijms19051310