بخشی از مقاله انگلیسی:
The Emergence of lncRNAs in Cancer
Cancer is a complex disease consisting of multiple factors that lead to the development of malignant tumors . While much progress has been made in identifying the major contributors to cancer progression, the clinical picture remains bleak. Current research efforts aim to better understand the interplay between cancer cells, tumor microenvironments, and defense mechanisms involved in cancer development, immune evasion, and therapeutic susceptibility . However, the majority of these studies focus on protein-coding genes as the crucial components in disease progression, overlooking the vast landscape of noncoding genes. Among these noncoding transcripts are lncRNAs. lncRNAs are RNA species greater than 200 bp in length commonly characterized by polyadenylation, splicing of multiple exons, promoter trimethylation of histone H3 at lysine 4 (H3K4me3), and transcription by RNA polymerase II [2,3]. lncRNA-mediated biology has been implicated in a wide variety of cellular processes, including pluripotency in mouse embryonic stem cells  and X chromosome inactivation . While some lncRNAs, such as XIST (X inactive specific transcript) appear to operate exclusively in the nucleus as regulators of gene expression [5,6], others function predominantly in the cytoplasm to regulate signal transduction and the stability of mRNAs [7–9]. Several distinct mechanisms of lncRNA activity have been described. Most prominently, lncRNAs have been shown to collaborate with protein partners to form ribonucleoprotein complexes (RNP, see Glossary) . For example, XIST interacts with the Polycomb repressive complex 2 (PRC2), resulting in PRC2 recruitment and subsequent trimethylation of histone H3 at lysine 27 (H3K27me3) of the inactive X chromosome . Air and Kcnq1ot1 bind to G9a, a histone H3 lysine 9 methylase, to regulate gene expression [12,13]. ANRIL associates with PRC1 to regulate the INK4a locus . Long intergenic noncoding RNA (linc)RNA-p21 and PANDA aretwo p53-regulated lncRNAs that interact with hnRNP-K and NF-YA to regulate transcription [15,16]. lncRNA-LET is downregulated across several cancers and functions by binding to and degrading nuclear factor 90 (NF90) protein, which enhances hypoxia-induced cancer cell invasion . Given this tendency to engage proteins, lncRNAs are surfacing as decoys, scaffolds, and guides .In cancer, lncRNAs are emerging as a prominent layer of previously underappreciated transcriptional regulation that function as both oncogenes and tumor suppressors  (Table 1). For example, overexpression of the HOTAIR lncRNA correlates with aggressive breast , colorectal , hepatocellular , and gastrointestinal stromal tumors , while lncRNA TARID prevents cancer formation through promoter demethylation at tumor suppressors . In this review we discuss emerging themes of lncRNA-mediated function within major areas of cancer progression and metastasis, focusing on advances made over the past several years (Figure 1).
Cancer results from an accumulation of modified genes, either by mutation or epigenetic alterations such as methylation, acetylation, and phosphorylation . Growing evidence suggests that key cellular genes involved in proliferation, apoptosis, and stem cell differentiation are epigenetically modified in cancer . However, the mechanisms underlying precise epigenetic control are poorly understood. An evolving model of lncRNA activity centers on their ability to bind to and regulate epigenetic complexes . Specifically, several lncRNAs have been shown to function by interacting with Polycomb group complexes . This is especially relevant in cancer because PRC1 and 2 are known oncogenic drivers in several types of malignancies [27–30]. For example, FAL1 (focally amplified lncRNA on chromosome 1), a novel oncogenic lncRNA present across several epithelial tumors, associates with BMI1, a core subunit of the PRC1 complex . In ovarian cancer, FAL1 was shown to mediate cancer progression and was associated with decreased patient survival. FAL1 interaction with BMI1 stabilizes the PRC1 complex by preventing BMI1 degradation, allowing PRC1 to occupy and repress the promoters of target genes such as p21, resulting in loss of cell cycle regulation and increased tumorigenesis. Similarly, NBAT-1, lncRNA-HEIH, HOTAIR, ANRIL, TUG1, and XIST have all been shown to interact with the enzymatic subunit of the PRC2 complex, EZH2, to modulate the repressive H3K27me3 histone mark on downstream target genes. This subsequently leads to either oncogenesis or tumor suppression in a multitude of cancer types, including neuroblastoma , hepatocellular , breast , gastric , non-small cell lung carcinoma (NSCLC) , and hematologic malignancies , respectively. In fact, up to 20% of all lncRNAs have been implicated in PRC2 binding , suggesting that PRC2 promiscuously binds to lncRNAs . Recent studies have shown both specific and non-specific binding of PRC2 to lncRNAs, and emerging evidence suggests that these activities are not mutually exclusive . However, the in vivo binding specificity of PRC2 remains to be elucidated. One of the most-studied lncRNAs, HOTAIR (HOX transcript antisense RNA), recruits the PRC2 complex to a set of genes involved in suppressing breast cancer metastasis . This genomewide retargeting of PRC2 results in repression of genes that prevent cancer progression. In addition, HOTAIR-mediated genetic reprogramming results in gene expression signatures that resemble embryonic fibroblast gene signatures, and this promotes cell migration, invasion, and metastasis. lncRNAs can also interact with Polycomb group complexes indirectly. For example, PANDA (P21 associated ncRNA DNA damage activated) physically interacts with scaffoldattachment-factor-A (SAFA) to indirectly recruit both the PRC1 and PRC2 complexes to the promoters of genes involved in cellular senescence . This suggests that lncRNAs can facilitate epigenetic changes through interaction with protein intermediates. In addition to Polycomb group complexes, several lncRNAs have been linked to the SWI/SNF nucleosome-remodeling complex in cancer and other diseases [41–44]. SWI/SNF is a multisubunit complex that uses the energy of ATP hydrolysis to redistribute and rearrange nucleosomes to influence gene expression [45,46]. In cancer, SWI/SNF is widely considered to be a tumor suppressor because deleterious mutations are present in approximately 20% of all cancers [45,47–49]. Indeed, SChLAP1 (second chromosome locus associated with prostate-1), a prostate cancer-specific lncRNA that is highly expressed in 15–30% of localized and metastatic tumors , is significantly associated with poor clinical outcomes and lethal disease. Moreover, SChLAP1 expression enhances tumor invasion and metastasis, in part, by interacting with and abrogating genome-wide binding of the SWI/SNF complex. Subsequent studies have defined SChLAP1 as one of the best prognostic genes in prostate cancer and have also shown the clinical utility of SChLAP1 as both a tissue- and urine-based biomarker [50–52]. Comparably, lncTCF7 is highly expressed in hepatocellular carcinoma (HCC) and is required for the maintenance of self-renewal capacity in liver cancer stem cells (CSC) . Functionally, lncTCF7 triggers the Wnt signaling pathway by binding to and recruiting the SWI/SNF complex to the TCF7 promoter to activate gene expression. This preserves the self-renewal capabilities of liver CSCs and promotes tumor initiation in HCC. lncRNA-mediated SWI/SNF regulation has also been described in other cellular and disease processes. For example, polymerase Vtranscribed lncRNAs indirectly interact with the SWI/SNF complex to mediate transcriptional silencing . In addition, the cardio-protective lncRNA Mhrt directly interacts with BRG1, the catalytic subunit of SWI/SNF, to prevent cardiac hypertrophy . Taken together, these studies suggest that lncRNAs play an important role in SWI/SNF regulation, and systematic efforts to characterize similar lncRNA mediators of SWI/SNF in other cancers are warranted. In addition, HOTTIP (HOXA transcript at the distal tip) is another lncRNA upregulated in HCC . HOTTIP expression is associated with clinical progression of HCC and is also an independent predictor of overall survival. Mechanistically, HOTTIP regulates the HOXA locus byinteracting with the WDR5/MLL epigenetic complex to drive H3K4me3 . Previous studies have identified an RNA binding pocket on WDR5 , suggesting that direct binding of lncRNAs to WDR5/MLL may similarly promote other cancers. Epigenetic control by lncRNAs is not only exercised via interactions with chromatin remodelers. For example, TARID (TCF21 antisense RNA inducing demethylation) directs promoter demethylation of the tumor-suppressive transcription factor TCF21 . TARID is normally expressed in benign lung, oral, and ovarian epithelium but suppressed in cancer owing to hypermethylation of its promoter. TARID acts as a scaffold to recruit GADD45A, a DNA demethylator, to the TCF21 promoter, resulting in demethylation of the TCF21 promoter through the base-excision repair pathway. The physical interaction between the TCF21 promoter, TARID, and GADD45A is crucial for TCF21 expression and tumor suppression. Insight into the biology and mechanism of lncRNAs provides a basis for the understanding of the global epigenetic modifications that occur in cancer.