CRISPR Epigenome Editing Without Base Sequence Cleavage Opens New Horizons for Treating Intractable Diseases
Background
Conventional gene therapy aims to prevent the production of abnormal proteins that cause disease by directly cutting and correcting the deoxyribonucleic acid (DNA) sequence, which contains genetic information. The third-generation CRISPR technology, which emerged after Zinc Finger and TALEN, has dramatically improved efficiency, but it has a critical drawback: it leaves unexpected physical traces throughout the genome. When gene scissors cut the double-stranded DNA, random deletions or insertions occur, causing genotoxicity or large-scale chromosomal rearrangements. Moreover, most intractable diseases are caused by abnormalities in gene expression regulation or the breakdown of epigenetic states, rather than changes in the gene sequence itself. Therefore, there is an urgent need for a regulatory tool that can precisely block or activate gene expression switches without damaging the sequence information.
Key Findings
Recently, the academic community has made progress in developing epigenome editing technology, which applies CRISPR technology to reprogram the epigenetic code. Researchers have fused inactive CRISPR proteins (dCas), which lack DNA cleavage activity, with effector domains that attach or remove epigenetic marks such as methylation or acetylation. This complex controls the initiation of transcription of target genes in cell nuclei, adjusting the expression level and duration to the desired level. For example, it delivers a methyltransferase to block the transcription of a specific gene, or delivers an acetyltransferase to a target region to awaken a dormant gene.
To ensure the in vivo efficacy of epigenome editing tools, researchers have discovered several small Cas variants with reduced protein size. Significant progress has also been made in gene engineering to optimize the size of the effector to be less than half, so that it can be easily loaded into existing adeno-associated viruses (AAV) or lipid nanoparticles (LNP). The development of highly selective effector domains that minimize off-target editing of unintended sites and do not exhibit immune rejection or cytotoxicity is also underway, bringing it closer to clinical application. In several experimental groups, it has been proven that complex three-dimensional structures within the genome and symmetrical repetitive sequence regions, which are difficult for CRISPR to access, can be safely regulated without genotoxicity.
Significance and Prospects
This technology does not involve DNA strand cleavage, which significantly reduces the risk of genotoxicity and raises the standard for evaluating the safety of therapeutic agents. Thanks to its ability to freely change the state and characteristics of cells, it is expected to accelerate next-generation regenerative medicine research, including induced pluripotent stem cells and tissue regeneration. The launch of epigenome editing pipelines, which have undergone thorough safety reviews by regulatory agencies and have begun Phase 1 clinical trials, signifies that new treatment options for patients are not far off. Of course, the development of an efficient delivery system that delivers the effector gene to the target organ without leakage and the establishment of conditions under which the epigenome correction effect is not lost in the long term are essential steps. A verification process that monitors safety to prevent epigenetic changes from spreading to unintended sites must also be included.
Why It Matters
This research has opened the way for treating Huntington's disease and certain neurodegenerative diseases, which were previously difficult to treat with conventional gene scissors due to excessive repetitive sequences or abnormal transcriptional regulation. A representative example is the design of precision anticancer therapies that selectively inhibit oncogenes that are overexpressed in cancer cells or reactivate tumor suppressor genes that are inactive. In addition, it can be immediately applied to the manufacturing process of next-generation cell and gene therapies (CGT), in which immune cells are precisely edited ex vivo and administered to patients. This is expected to contribute to reducing the production cost of personalized therapies and shortening complex engineering steps.
CRISPR/Cas-based epigenome editing technologies hold great promise for identifying novel therapeutic targets, improving gene and cell therapies, and directly addressing the underlying issues in many diseases, all while minimizing risks of genotoxicity often associated with conventional genome editing. Exciting recent advances in CRISPR/Cas-based epigenome editing technologies have drastically enhanced the ability to precisely control the timing, levels, and durations of endogenous gene expression and reprogram epigenetic states in human cells. As a result, epigenome editing is now poised to unlock new biomedical discoveries and treatments for diseases driven by transcriptional and epigenetic dysregulation as well as those stemming from aberrantly repetitive genomic regions or complex genomic arrangements that are difficult to target using conventional genome editing. Additionally, the power of epigenome editors is generating new strategies to control cell fate and function, which has direct and important implications for cell therapies and regenerative medicines. Here, as the first wave of CRISPR/Cas-based epigenome editors move into clinical trials, we cover recent advances as the field looks to address pressing hurdles facing widespread clinical deployment of epigenome editing technologies including delivery, performance, and safety. For instance, the discovery of compact Cas chassis, engineering efforts to reduce effector sizes for efficient delivery, and campaigns to tailor the targeting discrimination of epigenome editors are rapidly progressing, as is research into the development of new effector domains with high specificity, robust performance, and a lack of immunogenicity and cytotoxicity. This exciting progress is quickly moving the community closer to fulfilling the promise of CRISPR/Cas-based epigenome editing as a powerful class of platform technologies for biological discoveries, biotechnological innovations, and medicines.
This study has paved the way for treating Huntington's disease and specific neurodegenerative disorders, which were previously challenging for conventional gene editing due to excessive repetitive sequences or abnormal transcriptional regulation. A prime example is the design of precision cancer therapies that selectively suppress overexpressed oncogenes or reactivate inactive tumor suppressor genes. Furthermore, it can be readily incorporated into the manufacturing process of next-generation cell and gene therapies (CGT), where immune cells are precisely edited ex vivo and administered to patients. This is expected to contribute to reducing the production cost of personalized therapies and streamlining complex engineering steps.