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Tumor Discovery RNA-protein complexes deregulated in cancer

Table 1. (Continued)
Gene Partner Target Modification Tumor References
FIRRE HnRNP U X chromosome H3K27me Set up of specific 70
chromosomal
domains
CASC11 EZH2 PTEN H3K27me CRC, HCC 71
LNMAT1 EZH2 CADM H3K27me Melanoma 72,73
ZFAT-AS1 PRC2 CDX2 H3K27me Glioma 74
LINC01271 PUB Tensin 1 promoter Upregulates tensin CRC, BC 64,75
(MaTAR25) 1 in focal adhesions,
affecting migration
Abbreviations: ANRIL: Antisense noncoding RNA in the INK4 locus; ARHGAP27: Rho GTPase activating protein 27, antisense. CASC11: Cancer
susceptibility 11; CHASERR: CHD2 Adjacent suppressive regulatory RNA; FIRRE: Functional intergenic repeating RNA element; GIHCG: Gradually
increased during hepatocarcinogenesis; IRENA: IFN-responsive nuclear factor-κB activator; LINC01271: Mammary tumor associated RNA 25
(MaTAR25) homolog; LNMAT1: Long noncoding RNA lymph node metastasis-associated transcript 1; NRAV/NRIR: Negative regulator of antiviral
response; NRIR: PVT1: Plasmacytoma variant translocation 1; HOXA-AS: Homeobox gene A, antisense; HOTTIP: HOXA transcript at the distal
tip; Xist: X-inactive specific transcript; ZFAT-AS1: Zinc finger and AT hook domain (ZFAT) antisense 1. Proteins. CADM: Cell adhesion molecule
1; CBX7: Chromobox protein homolog 7; CDKi: Cyclin-dependent kinase inhibitor; CDX2: Caudal-related homeobox transcription factor 2;
CHD2: Chromodomain helicase DNA-binding protein 2; CTCF: CCCTC-binding factor; GADD45A: Growth arrest and DNA damage-inducible alpha;
PTEN: Phosphatase and tensin homolog. Cancers. AML: Acute myeloid leukemia; BC: Breast cancer; CRC: Colorectal cancer; GC: Gastric cancer;
HCC: Hepatocellular cancer; LC: Lung cancer; MM: Multiple myeloma; NSCLC: Non-small cell lung cancer; OC: Ovarian cancer.

Table 2. LncRNAs associated with DNMTs, silencing genes through CpG methylation
ncRNA Recruitment Target Mechanism References
DACOR DNMT1 Fos, Jun, DNMT1 CpG methylation, Decoy 76
LINC0051 EZH2 PTEN CpG methylation 77
HOTAIR DNMT1 PTEN CpG methylation 78
SAMD12-AS1 DNMT1 P53 CpG 79
KIF9-AS1 DNMT1 RAI2 CpG 80
ANRIL Steric hindrance, block of Pol II binding IGF2R CpG methylated 81
HITT EZH2, PRC2 Hif-1α Triplex formation 82
CDKN2B-AS1/ANRIL PRC2 CDKN2B Triplex formation 83
Notes: A link to ncRNA databases can be found at https://lncipedia.org/db and http://www.noncode.org/; for RNAs related to biomolecular
condensates, a link can be found at https://rps.renlab.org/#/Browse
Abbreviations: ANRIL: Antisense noncoding RNA in the INK4 locus; CDKN2B: Cyclin-dependent kinase inhibitor 2B; CpG: Cytosine-phosphate-
guanine; DACOR: DNMT1-associated colon cancer repressed LncRNA; HIF-1α: Hypoxia inducible factor 1α; HITT: HIF-1α inhibitor at the
translation level; HOTAIR: HOX transcript antisense RNA; IGF2R: Insulin growth factor 2 receptor; KIF9-AS: Kinesin family member 9-antisense;
LINC0051: Long intergenic non-protein coding RNA 51; PTEN: Phosphatase and TENsin homolog deleted on chromosome 10; RAI2: Retinoic acid
induced 2; SAMD12-AS: Sterile alpha motif domain-containing 12-Antisense.

upregulated in hepatocellular carcinoma (HCC) and is in HCC and papillary thyroid cancer using small molecule
associated with poor survival outcomes. 111-117 NEAT1_2 is inhibitors. 121
also overexpressed and dysregulated in multiple cancers, Paraspeckle components have been implicated in cancer
including breast, ovarian, prostate, and lung cancers, as well development through expression analyses, knockout
as multiple myeloma. Furthermore, elevated NEAT1 levels cell studies, and RNA silencing approaches. Proteins
are linked to chemotherapy resistance and are associated such as NONO, SFPQ, and PSPC1 have been extensively
with cancer stemness. NEAT1 promotes resistance to studied. 122-129 NONO, a core paraspeckle component, is
117
cisplatin and taxol, while downregulation or silencing involved in RNA- and DNA-tethered condensates and
118
of NEAT1 sensitizes tumors to these chemotherapeutic undergoes phase separation in vitro, which is sustained
agents. NEAT1_2 also facilitates cancer progression and by nucleic acid binding. NONO plays a role in the
metastasis, particularly in thyroid cancer. 119,120 It has been transcription of super-enhancer-regulated genes, such as
suggested that NEAT1_2 could serve as a therapeutic target HAND2 and GATA2. Inhibition of the RNA-binding ability

Volume 3 Issue 4 (2024) 7 doi: 10.36922/td.4657