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INNOSC Theranostics and
Pharmacological Sciences Enhancers and SEs in cancer treatment

of their specific genomic interaction sites. The IMARGI identifying enhancers and SEs and their target genes but
procedure initiates with in situ crosslinking and genome also in assessing their pathological functions and cancer-
fragmentation, then converts each nearby RNA-DNA driving potential. 100-103
pair into an RNA-linker-DNA chimeric sequence. The application of enhancer-targeting drugs, such as
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Subsequently, the chimeric sequences are transformed into BET inhibitors, is known to block the family member of
a sequencing library optimized for paired-end sequencing. BET proteins, which are preferentially located at active
To analyze paired-end sequencing data and unveil caRNA- enhancers (H3K27ac). BET proteins have the ability to
DNA interactions, researchers can utilize the standardized identify and attach to acetylated lysine residues. Inhibiting
bioinformatic software package known as iMARGI-Docker, BET proteins shows significant potential for advancing
available at https://sysbio.ucsd.edu/imargi_pipeline. 94
cancer treatment strategies in the future. For instance,
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The MUSIC GRID technique enables simultaneous in an in vitro investigation, the pharmacologic inhibitor
profiling of multiple chromatin interactions, gene GNE987 reduced NB cell growth and survival, promoted
expression, and RNA-chromatin associations at the single- apoptosis, and caused cell cycle arrest by degrading BRD4.
nucleus level. It represents an effective tool for investigating These observations were consistent with a reduction in
chromatin structure and gene expression at the cellular xenograft tumor size. Chen et al. also identified a new
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level within intricate tissues. Of significant note, GRID- oncogenic gene, FAM163A, enriched with the H3K27Ac
seq is capable of identifying both coding and ncRNAs that mark in GNE987-treated cells using RNA-seq and ChIP-
interact with tissue-specific promoters and enhancers, seq data.
particularly SEs. Consequently, it enables the generation of The application of genome engineering tools to
a comprehensive map illustrating the connectivity between produce targeted mutations across different species has
promoters and enhancers on a global scale. 96
been described in various studies. 106-108 A pioneering study
The FANTOM consortium utilized the CAGE technique using CRISPR-Cas9 enhancer correction in treating sickle
to analyze extensive transcriptomes from various cell types, cell disease and β-thalassemia resulted in patients no
leading to the identification of 43,011 enhancer elements longer needing transfusions and eliminated vaso-occlusive
that were transcribed into eRNAs. 61 episodes. These findings suggest that CRISPR genome/
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The utilization of GRO-seq, a cutting-edge methodology, epigenome editing is not only a useful tool for generating
enables the identification of the precise genomic locations and investigating chromosomal aberrations but also holds
and orientations of all RNA polymerases actively involved promise for correcting disease abnormalities, including
in transcription. This powerful approach proves invaluable cancer and age-related diseases. 110,111 For instance, it was
in monitoring the transcription of nascent enhancers. In shown that the application of CRISPR-Cas13a to knock
addition, the distinctive transcription pattern exhibited down the SMAD7 enhancer, an estrogen-responsive eRNA,
by enhancers can be utilized to identify these regulatory inhibited cell proliferation and migration while promoting
elements, even in the absence of any information regarding cell apoptosis. This knockdown led to the suppression of
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the underlying TFs. Consequently, GRO-seq proves to be a cell invasion in bladder cancer in 5637 and T24 cells.
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proficient approach for the identification, characterization, In another study, Mill et al. discovered that using the
and comprehension of enhancer transcription regulation. CRISPR/Cas9 system to disrupt the SE region related to the
The detection of enhancer transcription through GRO- RUNX1 gene promoted apoptosis in acute leukemia cells
seq analysis serves as a highly dependable method for (OCI-AML5), consequently modifying the survival rate of
identifying active enhancers. This approach can be mice with AML. Additionally, Vincent et al. demonstrated
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effectively utilized to study and characterize enhancers that epigenomic disruption of EGFR enhancers using
and is considered the most reliable indicator of enhancer CRISPRi (dCas9-KRAB) technology curtailed the invasive
activity, surpassing the histone modifications commonly and proliferative competency of glioblastoma cells and
enriched at enhancers. 16,97,98 enhanced their sensitivity to temozolomide treatment.

A more integrative approach combining ChIP The landscape of drug delivery techniques in cancer
with high-throughput molecular biology techniques treatment has undergone a remarkable revolution with
such as Hi-C, Hi-ChIP, ATAC-seq, and their single- the discovery of nanoparticles (NPs) and small-sized
cell sequencing alternatives would be more efficient in molecules. This breakthrough in nanotechnology has
uncovering the mechanisms by which enhancers and SEs completely transformed conventional methods of delivering
regulate transcription and oncogenesis. Furthermore, drugs to cancer tissues, presenting novel possibilities
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experimental validation in vitro, in vivo, and ex vivo and renewed hope for effective cancer treatment. The
using enhancer reporter vectors would not only help in distinctive characteristics of NPs, including decreased

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