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INNOSC Theranostics and
Pharmacological Sciences Enhancers and SEs in cancer treatment

produced from. 67-69 Furthermore, research indicates that 5. Limitations and future perspectives of
eRNA presence can be indicative of enhancer activity, 70,71 enhancer-targeted cancer therapy
and the levels of eRNA transcription can reflect the degree
of enhancer or promoter activity. Thus, eRNAs may After almost 40 years since the first discovery of enhancers
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serve as biological markers for active enhancer regions. 73-75 in the Simian virus 40 genome, the precise mechanisms
Moreover, studies show that eRNAs stabilize enhancer- by which enhancers exert their effect on gene activation
promoter loops by attracting cohesin complexes, which are remain elusive. The limitations arise from the intrinsic
essential for the formation and stabilization of chromatin complexity of enhancers and our limited knowledge,
loop structure. 76 which needs further advances in molecular techniques for
elucidation. As discussed earlier, the locations of enhancer
Increasing lines of evidence gradually revealed the elements can be identified by genome-wide profiling of
regulatory role of eRNAs in various diseases, including histone marks, with H3K4me1 and H3K27ac being the
cancer. 77-80 For instance, Jiao et al. identified a SE and its two major histone marks flanking active enhancers.
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derived eRNA that facilitated the expression of heparanase Recently, the application of molecular biology techniques
(HPSE), an endo-β-D-glucuronidase essential for cancer such as chromatin immunoprecipitation (ChIP) followed
invasion and metastasis. They demonstrated that HPSE by high-throughput sequencing has proven beneficial for
eRNA was highly expressed and positively correlated with genome-wide enhancer identification. 89,90 Nevertheless, the
HPSE levels in cancer tissues, promoting tumorigenesis discovery of enhancers throughout the genome remains
and aggressiveness of cancer cells both in vitro and in vivo. limited, and determining their target gene is even more
In addition, HPSE eRNA was shown to promote cancer challenging.
progression by driving chromatin looping and regulating
hnRNPU/p300/EGR1/HPSE axis. Consequently, HPSE Next-generation sequencing technologies, such as
eRNA serves as an important prognostic marker for mapping RNA interactome in vivo (MARIO), in situ
cancer patients with poor outcomes. Qin et al. applied mapping of RNA-genome interactome (iMARGI),
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genome-wide profiling of eRNAs in Chinese lung multinucleic acid interaction mapping in single cells
adenocarcinoma patients, integrating RNA-seq data analysis (MUSIC), CAGE, global RNA interactions with DNA
to present a comprehensive description of eRNAs in lung by deep sequencing (GRID-seq), and global run-on
adenocarcinoma. They discovered that highly upregulated sequencing (GRO-seq), open new horizons for
eRNAs identified upstream of TERT may contribute to lung understanding the interactions of genomic regions with
cancer development by upregulating TERT expression. TERT RNA. Despite the broad spectrum of applications for RNA-
is a well-known predisposition gene for lung cancer, encoding seq technology, its utilization in the detection of eRNAs
human telomere reverse transcriptase, which maintains on a large scale has been limited primarily due to the
telomere ends. 83-85 Intriguingly, they discovered that FOXO6 poor stability of eRNAs and insensitivity of the RNA-seq
expression was elevated in lung adenocarcinoma, attributed technique. The MARIO technique involves cross-linking
to the copy number amplification of FOXO6 eRNA in lung RNA molecules with their associated proteins before
adenocarcinoma patients. ligating them to a biotinylated RNAlinker, resulting in a
chimeric RNA in the form of RNA1-Linker-RNA2. These
Another study showed that CCAT1, an enhancer-
templated RNA, forms a complex with TFs TP63 and SOX2, linker-containing chimeric RNAs are then separated
using streptavidin-coated magnetic beads and subjected
regulating EGFR expression by binding to the SEs of EGFR. to paired-end sequencing. This technology allows for
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This interaction activates both the MEK/ERK1/2 and an equitable selection of interacting RNAs, enabling
PI3K/AKT signaling pathways in squamous cancer cells, comprehensive mapping of an RNA-RNA interactome on
promoting tumorigenesis. Similarly, NET1e, an eRNA a global scale. This approach bypasses the necessity of
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located about 90 kb downstream of the oncogene NET1, having a specific antibody for a protein and eliminates the
was highly expressed in breast cancer. In addition, in the constraint of studying only one RNA-binding protein at a
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study, CRISPR activation of NET1e was found to accelerate given time. In addition, this technique exclusively captures
cell growth in MCF7 breast cancer cell lines. Conversely, RNA molecules that are co-bound with a solitary protein
its knockdown by locked nucleic acids antisense RNA molecule, preventing the capture of RNA molecules
significantly reduced cell proliferation in the MCF7 breast
cancer cell line, suggesting its therapeutic potential in bound independently to multiple copies of a protein. This
clinical eRNA-targeted therapy. Therefore, eRNAs offer precautionary measure ensures the avoidance of reporting
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considerable therapeutic potential and warrant further false interaction.
intense investigations for their roles in cancer and other The IMARGI method is employed for the identification
diseases. of chromatin-associated RNAs (caRNAs) and the elucidation

Volume 7 Issue 3 (2024) 6 doi: 10.36922/itps.3654