When CRISPR meets Dark Genome: Epigenetic Editing

Innovation happens fast in the Biotech industry and the technologies are being superseded a new technology even faster than before. When we are getting used to gene therapy, a new technology is getting attention and sizable investing, epigenetics.

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What exactly is epigenetics?

Conrad Waddington coined the term "epigenetics" 89 years ago to describe phenotypic variation that does not result from changes in genotype. Since then, significant progress has been made in understanding epigenetic mechanisms for gene control, including chromatin remodeling, DNA methylation at CpG islands, and post-translational modifications (such as methylation, acetylation, citrullination, and phosphorylation) of the N-terminal tails protruding from the core histones that package genomic DNA.

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By orchestrating internal and environmental signaling cues into transcription independent of the underlying genetic code, epigenetic regulatory mechanisms play a central role in nearly all cellular phenomena. In general, the epigenome is a collection of heritable and nonheritable sequence independent biological molecules that converge to modulate chromatin structure, genome function, and gene expression patterns. Epigenomic regulation occurs through a complex interplay of proteins that bind to genomic DNA, biochemical modifications to DNA and histones, and structural changes that allow regulatory proteins to access DNA. Despite the fact that projects like ENCODE and the Roadmap Epigenomics Mapping Consortium have accelerated our understanding of epigenetic states in health and disease, the extent to which epigenetic alterations are drivers or consequences of disease is frequently unknown.

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Which is the current state of the art on clinical setting?

For many years, pharmaceutical companies have been developing new compounds to reverse dysfunctional epigenetic states in oncology, the most recent being Epizyme's Tazverik (tazemetostat), a small-molecule EZH2 inhibitor for treating sarcoma and relapsed or refractory follicular lymphoma. There are currently eight small-molecule epigenetic drugs on the market, ranging from DNA methyl transferase inhibitors (DNMTs) to Histone deacetylase inhibitors (HDACIs). All act indiscriminately on epigenetic targets throughout the genome, and all have only mild efficacy, with dose-limiting toxicity associated with thrombocytopenia, neutropenia, nausea, and even cardiac toxicity. Given the complexities of epigenetic regulation during carcinogenesis, administering a "cocktail" of epigenetically-targeted drugs, such as vorinostat/decitabine treatments, demonstrated therapeutic advantages in pediatric patients with secondary MDS/acute myeloid leukemia (AML) associated with solid tumor recurrence, including disease stability and a good quality of life.

What is Epigenetic Editing?

The use of epigenetic enzymes to rebuild the localized epigenetic environment of an internal genomic region, usually with the goal of regulating transcription, is known as epigenetic editing. The use of nuclease-null deactivated (or dead) CRISPR/Cas systems (dCas) to perturb noncoding nucleic acid elements, such as promoters, enhancers, and transcription factor binding motifs, as well as noncoding RNAs, to gain insights into their functional roles and the resulting epigenetic changes, has significantly accelerated epigenetic editing progress.

Many important factors still limit the development of epigenome editing, preventing its use in humans. Like conventional genome editing, the clinical utility of epigenome editing is limited by targeted delivery options, potential off-targeting, and efficacy. Many factors influence these issues, including the identity of the targeted tissue, the chromatin context of the therapeutic gene of interest, and the epigenome editor's copy number.?For example, the dCas complex is delivered by AAVs, despite the fact that epigenome editing effector domains are frequently too large to be packaged together within AAV. Epic Bio is working with Stanford University on a tiny DNA-binding protein called CasMINI to solve this problem, allowing the company's gene therapies to fit on a single AAV vector. Nonetheless, challenges with immunogenicity and large-scale manufacturing persist, which many companies and universities, including the Wyss Institute, are attempting to address.

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So, who′s who in the epigenome editing game?

Chroma Medicine , Tune Therapeutics , Epicrispr Biotechnologies , and Navega Therapeutics have raised a total of $ + 200 million in funding, joining Sangamo Therapeutics, Inc. and Encoded Therapeutics Inc. in the quest to make epigenome editing a clinical reality. These startups are primarily developing platforms based on catalytically inactive CRISPR systems linked to effector domains that regulate gene expression. Unlike currently marketed epigenetic cancer drugs, which act on a genome-wide scale and have dose-limiting toxicities, the specificity of epigenome editors promises to open up a wide range of new indications beyond oncology. In a landscape crowded with small-molecule inhibitors, monoclonal antibodies, gene therapies, small interfering RNAs, antisense oligonucleotides, and traditional gene and base editing, epigenome editors' ability to restore genes silenced in disease in a tunable and durable manner may prove to be a key therapeutic niche.

Two startups have disclosed their programs: Encoded is developing a DNA-binding domain tethered to an SCN1A-specific transcription factor under the control of a regulatory element specific to GABAergic inhibitory neurons to upregulate expression of the NaV1.1 channel for Dravet syndrome, and Navega is investigating ZFPs or dCas9 targeted to SCN9A and fused to KRAB to repress the NaV1.7 channel in chronic pain. When it’s highly expressed, it sends out lots of pain signals. But it would be a bad idea to simply delete this gene because some amount of pain is useful; it signals when something is going wrong within the body. This system allowed for transient gene therapy, which is advantageous in the framework of chronic pain, because permanent pain insensitivity is not desired. Although the treatment is transient, the long duration still presents a substantial advantage compared to existing drugs, which must be taken daily or hourly, and which may have undesirable addictive effects.

Which are the funds backing these new startups?

?It is no surprise to see names like Atlas Ventures and Horizon Ventures, Newpath partners and emerson collective backing these companies, they have a long history of investing in early on in disruptive technologies like prime editing and gene and cell therapies.

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How far are we from getting this into the clinic?

Although the road ahead will be long and difficult, epigenome editing therapies will provide several novel therapeutic options. They show promise for monogenic diseases where the target genes outnumber the AAV gene therapy payload capacity and a healthy endogenous gene can be upregulated or downregulated (depending on the condition). Perhaps the most compelling therapeutic applications are restoring gene expression in congenital diseases of genome imprinting (for example, DiGeorge syndrome), autosomal dominant diseases of haploinsufficiency, or downregulating cancer cell activity, conditions that traditional gene therapy may not be able to treat.?

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References:

1 - Quratulain Babar, Ayesha Saeed, Tanveer A. Tabish, Sabrina Pricl, Helen Townley, Nanasaheb Thorat, Novel epigenetic therapeutic strategies and targets in cancer, Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, Volume 1868, Issue 12, 2022, 166552, ISSN 0925-4439, https://doi.org/10.1016/j.bbadis.2022.166552.

2- Jennifer Khirallah, Maximilan Eimbinder, Yamin Li, Qiaobing Xu, Clinical progress in genome-editing technology and in vivo delivery techniques, Trends in Genetics, Volume 39, Issue 3, 2023, Pages 208-216, ISSN 0168-9525, https://doi.org/10.1016/j.tig.2022.12.001.

3- Fine-tuning epigenome editors.?Nat Biotechnol?40, 281 (2022). https://doi.org/10.1038/s41587-022-01270-w

4 - Rittiner Joseph, Cumaran Mohanapriya, Malhotra Sahil, Kantor Boris, Therapeutic modulation of gene expression in the disease state: Treatment strategies and approaches for the development of next-generation of the epigenetic drugs . Frontiers in Bioengineering and Biotechnology; 10;2022??https://www.frontiersin.org/articles/10.3389/fbioe.2022.1035543; 10.3389/fbioe.2022.1035543

5 - Moreno et al., Sci. Transl. Med.13, eaay9056 (2021)