Advances and challenges of precision epigenetic therapy in treating genomic imprinting diseases

Introduction

Genomic imprinting is a canonical form of epigenetic regulation in mammals that establishes parent-of-origin-dependent monoallelic gene expression essential for normal development (1). Perturbations in this process give rise to a class of rare congenital conditions known as imprinting disorders (IDs) (2). While their molecular etiologies are diverse—encompassing genetic lesions such as large-scale deletions or uniparental disomy (UPD) (3)—a significant portion of cases arise from epimutations (4). These are defined as aberrant DNA methylation patterns at key regulatory loci, or imprinting control regions (ICRs), that disrupt the expression of imprinted gene clusters without altering the underlying DNA sequence (5). This dynamic nature of epigenetic dysregulation poses a fundamental challenge for conventional therapeutic strategies, such as hormone replacement, which are often limited to symptomatic management, providing a static correction that fails to address the root defect in dynamic gene regulation (6).

This limitation underscores the need for novel therapeutic modalities. Epigenome editing has emerged as a promising strategy, as it offers the potential to restore the natural epigenetic state by rewriting aberrant marks (7,8). These approaches, which typically involve fusing epigenetic effector domains to a nuclease-deactivated Cas9 (dCas9) protein, are designed to re-establish the cell’s endogenous capacity for physiological gene control, rather than merely altering protein levels (9,10). The field of epigenome editing has recently progressed from conceptual demonstrations in cell culture to a validated therapeutic modality supported by compelling preclinical evidence in animal models (11). This rapid maturation stems from several convergent technological advancements. A new generation of more potent, specific, and durable epigenetic editors has been engineered (12,13), capable of establishing and maintaining heritable epigenetic states that mimic natural imprinting mechanisms. Concurrently, significant advances in vector engineering and non-viral delivery systems have begun to address the challenge of delivering these large molecular constructs to target tissues, including the central nervous system (CNS) (14).

This review provides a critical analysis of recent progress in epigenome editing for IDs. It first details the expanded toolkit of state-of-the-art epigenetic editors, with a focus on systems designed for durable epigenetic memory, enhanced potency, and improved deliverability. The discussion then moves to a systematic examination of delivery platforms, contrasting advances in adeno-associated virus (AAV) vector engineering with the emergence of lipid nanoparticles (LNPs) as a powerful alternative. The core of this review is a critical evaluation of the growing body of disease-specific preclinical data, with a focus on the well-studied neurological disorders Angelman syndrome (AS) and Prader-Willi syndrome (PWS). The final section discusses the remaining challenges for the clinical translation of these technologies from the laboratory to the bedside.

The expanded toolkit: next-generation epigenetic editors

The therapeutic efficacy of epigenome editing depends on the molecular capabilities of the editor platforms (15). For IDs, the primary therapeutic goal is to restore the endogenous, dynamic regulatory circuits disrupted by epimutation, rather than to simply achieve static normalization of gene expression (6). Early editing tools, however, often fell short of this objective. For example, early editors that induce transcriptional blockade (clustered regularly interspaced short palindromic repeat interference, CRISPRi) without depositing DNA methylation achieve only transient repression and fail to establish the epigenetic memory required for a durable therapeutic effect (16). Furthermore, the large size of constructs frequently exceeds the packaging capacity of AAV vectors, necessitating complex dual-vector strategies that can limit in vivo efficacy (9). Finally, the transcriptional output of a targeted epigenetic modification is highly dependent on the local chromatin and genetic context, an interplay that early tools could not predictably control (17). To address these limitations, recent advances in protein and systems engineering have produced next-generation editors designed to improve deliverability, enhance potency, and establish durable epigenetic memory (Figure 1).

Figure 1 The development of epigenetic editors in imprinting disease therapy. The development of next-generation epigenetic editors provides advantages for epigenetic therapy in imprinting disease research. (A) The classic multi-domain architecture is mechanistically synergistic: one dCas combines with the transcriptional repressor such as the KRAB domain initiates rapid transcriptional silencing by recruiting endogenous corepressors (e.g., KAP1) and another dCas recruits the DNMT3A/3L complex. (B) To overcome the packaging limitation, single dCas fuse a DNA-binding domain to the catalytic domains of DNMT3A, DNMT3L, and KRAB domain. (C) Pairing synergistic effectors with smaller Cas proteins, such as dSaCas9. (D) The recruitment of endogenous epigenetic machinery, such as the Coupled Histone tail for Autoinhibition Release of Methyltransferase system, consists of a DNA binding domain (e.g., a ZFP) fused to two functional components: the non-catalytic DNMT3L domain and a short peptide mimic of the histone H3 tail. By Figdraw. DNMT, DNA methyltransferase; dSaCas9, Staphylococcus aureus dCas9; KRAB, Krüppel-associated box.

The foundation of epigenetic editing: the CRISPRoff/on system

A primary objective for the clinical translation of epigenetic therapies is the development of tools that establish a specific and durable gene expression state that persists through mitosis and cellular differentiation long after the editor itself has been cleared (9,18). While early “hit-and-run” strategies utilizing multi-component editor cocktails demonstrated the feasibility of this approach (16), recent research has yielded substantial advances in the design of compact, potent, and safe single-protein systems capable of writing and erasing heritable epigenetic memory (10).

A key advance was the development of CRISPRoff, a single fusion protein comprising a catalytically dCas9 linked to the repressive KRAB domain and the DNA methyltransferase (DNMT) domains DNMT3A and DNMT3L (19). This system is distinguished by its capacity to establish a robust and heritable silenced state following only transient expression. A temporary pulse of CRISPRoff was shown to be sufficient to initiate highly specific DNA methylation and repressive histone marks at a target promoter. This newly written epigenetic program was then faithfully maintained by the cell’s endogenous machinery for over 450 cell divisions and, critically, persisted through the differentiation of induced pluripotent stem cells (iPSCs) into neurons. From a clinical perspective, this demonstration of heritable silencing after transient editor delivery is a crucial step. This establishes a viable path toward “one-and-done” therapies for IDs, where a single administration could lead to lifelong correction of gene expression without the risks associated with permanent transgene integration (20).

Genome-wide screens revealed that CRISPRoff can heritably silence the vast majority of human genes, including those that lack the canonical CpG islands traditionally associated with methylation-based silencing. This broad applicability substantially expands the repertoire of potential targets for epigenetic therapy (19). Furthermore, a vital feature of this system is its reversibility. A complementary tool, CRISPRon, was developed as an optimized fusion of dCas9 and the demethylase ten-eleven translocation1 (TET1), leveraging a principle established by foundational studies that first demonstrated targeted DNA demethylation using dCas9-TET1 fusions (21). CRISPRon can be targeted to a previously silenced locus to actively erase methylation marks and robustly reactivate gene expression. This “on-switch” provides a crucial safety mechanism, offering a means to reverse the therapeutic intervention if unforeseen adverse effects arise—a feature unavailable in DNA-based gene editing modalities, which carry risks associated with permanent genomic alterations (22). Both CRISPRoff and CRISPRon need to concern off-target methylation, R-loop formation and immune recognition. Off-target methylation may induce bystander methylation and spreading effects (23,24). R-loop can collide with replication forks and cause DNA damage and trigger ATM/ATR activation (25). Immune recognition includes foreign DNA recognition, RNA-DNA hybrid sensing and methylation pattern recognition which may limit in vivo applications (26).

Advances in epigenome editor design for potency and in vivo delivery

The complex chromatin architecture of certain genomic loci, such as the densely methylated ICRs, often renders single-effector strategies insufficient for inducing stable changes in epigenetic state and gene expression (27). Concurrently, the large size of many dCas9-effector fusions exceeds the packaging capacity of AAV vectors (~4.7 kb), which are a currently preferred vehicle for clinical gene therapy (28). Recent innovations have focused on addressing these challenges through the development of combinatorial and minimalist editor platforms (29).

The design of multi-effector editors has been informed by the observation that endogenous gene silencing often involves the coordinated action of multiple protein complexes. This approach aims to develop “hit-and-run” editors that establish a stable and heritable epigenetic state following transient expression (12,16). Key developments in this area include the engineering of single-construct editors that fuse a DNA-binding domain to the catalytic domains of DNMT3A, its cofactor DNMT3L, and a transcriptional repressor such as the Krüppel-associated box (KRAB) domain (30). This multi-domain architecture is mechanistically synergistic: the KRAB domain initiates rapid transcriptional silencing by recruiting endogenous corepressors (e.g., KAP1), which in turn recruit histone methyltransferases (e.g., SETDB1) that deposit repressive histone marks like H3K9me3 (31). This initial remodeling establishes a heterochromatic state that is permissive for, and may actively recruit, the DNMT3A/3L complex to install durable and heritable DNA methylation (32). The clinical potential of this strategy was validated in a non-human primate study, where a single administration of a LNP-formulated editor composed of dCas9-DNMT3A-DNMT3L-KRAB resulted in a durable (~90%) reduction in circulating PCSK9 protein and a concomitant ~70% reduction in low density lipoprotein cholesterol. Importantly, studies in mice demonstrated that this epigenetically-mediated silencing was faithfully propagated through hepatocyte division following partial hepatectomy, confirming the heritability of the engineered epigenetic state (13).

Engineering compact editors for AAV delivery

Although multi-domain editors exhibit enhanced potency, their large size often precludes packaging into AAV vectors (13). One primary strategy to overcome this packaging limitation is engineering more compact editor payloads, for example, by pairing synergistic effectors with smaller Cas proteins (33). By fusing the KRAB and MeCP2 repressor domains to the smaller Staphylococcus aureus dCas9 (dSaCas9), an “all-in-one” AAV vector was developed that achieved robust and sustained repression of the APOE gene in the mouse hippocampus. Such systems demonstrate that combining synergistic effectors with compact DNA-binding platforms can yield potent, AAV-deliverable tools suitable for neurological applications. These advances are particularly significant for treating neurological IDs, such as AS and PWS. For these conditions, packaging a complete editor into a single AAV vector is a critical step toward efficient delivery to the CNS (2,4).

An alternative strategy for developing compact editors involves the recruitment of endogenous epigenetic machinery, thereby obviating the need to deliver a large, exogenous catalytic domain. This approach differs from editors that rely on the delivery and expression of a constitutively active foreign enzyme. The CHARM (coupled histone tail for autoinhibition release of methyltransferase) system exemplifies this design (14). The editor consists of a DNA binding domain fused to two functional components: the non-catalytic DNMT3L domain and a short peptide mimic of the histone H3 tail. The mechanism of action is based on the targeted recruitment and activation of the endogenous DNMT3A enzyme. The DNMT3L domain serves as a scaffold to recruit endogenous DNMT3A to the target locus (34,35). Concurrently, the tethered H3 peptide, which mimics a histone tail unmethylated at lysine 4 (H3K4me0), provides the allosteric signal required to release the natural autoinhibition of the recruited DNMT3A enzyme (36). This locus-specific activation results in the targeted deposition of DNA methylation by the cell’s native enzymatic machinery (14).

This minimalist design has several potential advantages for clinical translation. First, the omission of the large DNMT3A catalytic domain results in a compact editor construct that is readily packageable within a single AAV vector (14). Second, by recruiting and activating the endogenous enzyme only at the target locus, this approach avoids the continuous, unregulated activity associated with overexpressed foreign enzymes, potentially reducing cytotoxicity and improving the off-target activity profile (37,38).

Synergistic approaches combining epigenome and sequence editing

Beyond engineering standalone epigenome editors, a new therapeutic frontier is emerging from the functional interplay between epigenetic modulation and precise DNA sequence editing (39). This is particularly relevant for IDs where the genetic etiology often involves small sequence variations, such as point mutations or microdeletions, within an ICR (40,41). These mutations can disrupt the binding of critical regulatory proteins, leading to a failure to establish or maintain the correct parent-of-origin-specific epigenetic state and resulting in aberrant gene expression (42-44). While sequence-editing technologies, including prime editors (PEs) and base editors (BEs), are well-suited for correcting such genetic defects, a significant limitation for their application in IDs is the epigenetic state of the target allele (45-47).

For example, in a subset of patients with PWS, the disorder arises from small deletions or point mutations within the paternal imprinting center, leading to aberrant hypermethylation and silencing of the paternal 15q11-q13 locus (48,49). Similarly, forms of Silver-Russell syndrome are caused by microdeletions within the paternal ICR1, resulting in the silencing of the paternally expressed IGF2 gene (50). In both scenarios, the genetic lesion resides on an allele packaged into a repressive chromatin structure, which severely restricts the access of editing machinery to the target DNA sequence (51).

A potential solution to this challenge is the concept of “epigenetic conditioning”. A landmark study by Li et al. demonstrated that the efficiency of prime editing is strongly enhanced by active transcriptional elongation, indicating that a permissive, transcriptionally active chromatin state is required for optimal editor function (39). This observation has led to the development of a therapeutic strategy where the epigenetic state of a locus is modulated prior to sequence editing. This strategy involves a sequential, two-step approach for IDs caused by genetic defects on a silenced allele. First, an epigenetic editor designed for transcriptional activation (CRISPRa) is transiently delivered to the mutated, silenced ICR to remodel the local chromatin into an active state and initiate transcription. This initial step makes the DNA target accessible for subsequent high-efficiency correction by a PE or BE. By directly addressing this fundamental efficiency barrier, this combined “epigenetic conditioning” strategy offers a viable pathway toward a one-time, curative therapy that corrects the underlying genetic cause of many IDs.

Overcoming the delivery hurdle: precision, safety, and control

Although engineering compact and potent epigenetic editors has solved fundamental design challenges, therapeutic success ultimately depends on precise, safe, and effective in vivo delivery (52-54). The central challenge has evolved beyond merely packaging the editor construct. The current frontier is the development of delivery platforms capable of navigating complex biological barriers, targeting specific cell populations while avoiding off-target tissues, and providing tight control over the duration of editor expression to maximize therapeutic benefit while minimizing risk (55). This requires a multi-faceted approach, balancing the inherent advantages and limitations of both viral and non-viral systems to suit the specific pathophysiology of the target ID (Table 1).

Viral vectors: engineering for higher precision and immune evasion

AAV vectors remain a clinical mainstay due to their proven efficacy in transducing non-dividing cells like neurons, making them highly relevant for neurological IDs such as AS and PWS (72,73). Mechanistically, following cell entry, the single-stranded AAV genome is converted into a double-stranded circular DNA episome that persists in the nucleus of non-dividing cells without integrating into the host genome (57). This provides the basis for long-term, stable expression of the therapeutic payload, a clinically ideal scenario for congenital conditions like IDs that require a single, lifelong correction (4). However, the major obstacles for their application in epigenome editing are their limited packaging capacity (around 4.7 kb), the host immune response and genotoxic risk of transgene products and vectors (60,62). This also primes the immune system against future doses. Given that the commonly used S. pyogenes Cas9 (SpCas9) alone is ~4.2 kb, co-packaging of the dCas9-effector fusion and the necessary guide RNA (gRNA) expression cassettes into a single vector is often not feasible (67). To circumvent this size limitation, several advanced strategies are being employed. Dual-vector AAV systems, where the editor and gRNA(s) are packaged into two separate AAV particles for co-infection of the target cell, are a common approach (74). A more sophisticated version of this is the split-editor system, where the dCas9-effector protein is split into two fragments (e.g., using inteins) that are delivered by separate AAVs and reconstitute into a functional editor upon co-expression in the target cell (65). Perhaps the most streamlined approach is the adoption of smaller Cas9 orthologs, such as Staphylococcus aureus Cas9 (SaCas9) or Streptococcus thermophilus Cas9, which are approximately 1 kb shorter than SpCas9. Their compact size allows the entire epigenome editing machinery to be packaged into a single, all-in-one AAV vector, simplifying production and clinical application (67,70).

One powerful approach is directed evolution, where vast libraries of AAV capsid variants are administered in vivo and variants that successfully transduce the desired target cells are selectively recovered and amplified. This iterative process has yielded novel capsids with remarkable capabilities. For example, the landmark development of the Cre-recombination-based AAV targeted evolution (CREATE) platform led to the discovery of AAV-PHP.B, a variant exhibiting a greater than 40-fold increased efficiency in crossing the blood-brain barrier (BBB) compared to the parental AAV9 serotype (68). This discovery is critical for neurological IDs like AS and PWS, as it enables less invasive, systemic delivery routes for CNS-targeted therapies that were previously inaccessible. Further refining this, machine learning algorithms are now being used to navigate the vast sequence space of potential capsid variants. By training deep neural networks on experimental data, these models can predict the viability of highly diverse capsid sequences, dramatically accelerating the design of novel vectors with desired properties, such as specific tropism or the ability to evade immune detection (75).

Equally important is managing the host immune response. Pre-existing neutralizing antibodies against common AAV serotypes can exclude a significant portion of the patient population (76). To address this, researchers are rationally engineering “stealth” AAVs. Mechanistically, this involves identifying key amino acid residues on the capsid surface that form the epitopes recognized by dominant neutralizing antibodies and mutating them to disrupt antibody binding while preserving the vector’s ability to transduce target cells (71). For congenital conditions like IDs, where a single, lifelong correction is the goal, overcoming pre-existing immunity is critical to ensure the therapy is available and effective for the broadest possible patient population.

Non-viral vectors: expanding beyond the liver

LNPs have emerged as a leading non-viral platform, offering key advantages that directly address the limitations of AAVs. Their large cargo capacity, low immunogenicity allowing for repeat dosing, and relative ease of manufacturing make them highly attractive (56,58). Crucially, LNPs are ideal for delivering editor-encoding mRNA or the fully-formed ribonucleoprotein (RNP) complex itself (77). This facilitates a transient, “hit-and-run” mechanism. Unlike DNA-based viral vectors, the mRNA or RNP cargo is active for only a short period before being naturally degraded by cellular machinery. This transient expression profile is ideal for epigenome editing, where temporary editor activity is sufficient to install a durable epigenetic mark. From a clinical safety perspective, this is a major advantage, as it dramatically shortens the time window for potential off-target effects and minimizes the long-term risk of immunogenicity against the foreign editor protein (56,59).

However, LNP-based delivery faces its own set of challenges. A major mechanistic bottleneck is endosomal escape (78). After being taken up by the cell via endocytosis, the LNP must release its cargo into the cytoplasm before it is trafficked to the lysosome and degraded. Modern LNP formulations contain advanced ionizable lipids that are engineered to be near-neutral at physiological pH but become protonated (positively charged) in the acidic environment of the late endosome. This charge switch is thought to promote interactions with anionic endosomal lipids, disrupting the membrane and facilitating cargo release (61). To further enhance this process, recent innovations have focused on optimizing the lipid architecture itself. For example, novel ionizable lipids with terminally branched tails, termed branched endosomal disruptor (BEND) lipids, have been shown to improve endosomal disruption. Molecular dynamics simulations suggest that this branched structure allows the lipid tails to penetrate more deeply into the endosomal membrane, leading to greater destabilization and more efficient cargo release into the cytosol (64).

The other primary barrier to broad LNP utility has been their intrinsic tropism to the liver, a process mediated by the adsorption of apolipoprotein E (ApoE) from the bloodstream, which then engages the low-density lipoprotein receptor (LDLR) on hepatocytes (63). Although advantageous for liver-specific diseases, this tropism is a limitation for most IDs and may cause hepatotoxicity. A key strategy to achieve this is the selective organ targeting (SORT) methodology. This approach involves incorporating a supplementary “SORT” molecule (a fifth lipid component) into the standard four-component LNP formulation, which modulates the particle’s biophysical properties to redirect delivery to other organs, such as the lungs or spleen, while de-targeting the liver (66). Another powerful strategy involves conjugating targeting ligands to the LNP surface. For example, attaching N-acetylgalactosamine (GalNAc) targets the particle to the asialoglycoprotein receptor (ASGPR) on hepatocytes with extremely high specificity (69). The same principle can be applied to target other tissues relevant to IDs; for instance, using ligands that bind to receptors highly expressed in the CNS or muscle could enable the development of therapies for neurological or growth-related syndromes. As these technologies for programming LNP tropism mature, they are poised to unlock a vast new range of therapeutic applications, particularly for systemic conditions like many IDs.

Preclinical proof-of-concept: targeting specific IDs

The convergence of next-generation editors and advanced delivery systems has enabled compelling preclinical studies for IDs. These investigations provide the first tangible evidence that precisely rewriting the epigenome can correct underlying molecular defects and rescue disease-relevant phenotypes.

AS

AS is a severe neurodevelopmental disorder caused by the loss of function of the maternally expressed UBE3A gene (79). In neurons, the paternal UBE3A allele is intact but epigenetically silenced by a long non-coding antisense transcript, UBE3A-ATS (80). This molecular configuration presents a clear therapeutic opportunity: if the antisense-mediated repression can be overcome, the healthy paternal allele can be reactivated to restore protein function. Recent studies have validated a genetic strategy to achieve this epigenetic outcome. By delivering a standard CRISPR/Cas9 nuclease system via AAV vectors, researchers created targeted deletions in the UBE3A-ATS gene in the mouse brain (19,81). While mechanistically a form of gene editing, this approach permanently stops the production of the antisense transcript responsible for silencing. As a result, the epigenetic repression of the paternal UBE3A allele is lifted, leading to its robust and sustained reactivation. Critically, this molecular correction led to a corresponding rescue of key disease phenotypes, including motor deficits and abnormal synaptic plasticity. While these studies represent a major step forward, the reliance on a nuclease to create a permanent DNA double-strand break (DSB) carries inherent risks, such as large deletions or complex genomic rearrangements at the target site (82). A true epigenome editing approach—using a dCas9-repressor fusion (e.g., dCas9-KRAB)—would represent a more direct and potentially safer therapeutic strategy. Such a tool could establish a heritable silenced state at the UBE3A-ATS promoter without altering the underlying DNA sequence. This strategy would achieve the same therapeutic goal—reactivation of paternal UBE3A—while avoiding the safety concerns associated with DSBs. Furthermore, an epigenetically silenced state is potentially reversible, offering a crucial safety advantage over a permanent DNA deletion.

PWS

PWS is a complex neurodevelopmental disorder that results from the loss of expression of a cluster of paternally expressed genes within the 15q11.2-q13 region (83). This locus contains several protein-coding genes (MKRN3, MAGEL2, NDN, SNURF-SNRPN) and non-coding snoRNAs; evidence from human microdeletions suggests that paternal deficiency for the SNORD116 snoRNA cluster is a primary contributor to key PWS phenotypes, including hyperphagia and obesity (84). The coordinated silencing of these genes on the intact maternal allele is governed by a master regulatory element, the Prader-Willi Imprinting Center (PWS-IC), which overlaps the SNRPN promoter and is silenced by DNA methylation (85). This architecture suggests that a therapeutic intervention targeting the PWS-IC alone could reactivate the entire gene cluster.

A recent study by Rohm et al. systematically investigated this hypothesis using CRISPR-based epigenome editing in human iPSCs (86). The authors demonstrated that targeted DNA demethylation using a dCas9-TET1 editor at the PWS-IC convincingly reactivated the maternal SNRPN gene and downstream PWS-associated transcripts. Critically, they showed that even a transient delivery of the dCas9-TET1 editor was sufficient to establish a stable and heritable activation of the PWS locus that was maintained for weeks and persisted through differentiation into neurons. This finding is a crucial proof-of-concept, establishing a viable path toward a ‘hit-and-run’ therapeutic strategy for complex, multi-gene IDs.

While the most advanced preclinical data have been generated for neurological IDs, extending these principles to other conditions, such as those affecting growth and metabolism, presents a distinct set of challenges and advantages. For neurological disorders, the primary obstacle is delivery, specifically navigating the BBB to achieve widespread distribution within the CNS (14,68). However, a key advantage is that the target cells—neurons—are post-mitotic; therefore, a successful epigenetic correction is likely to be permanent. Conversely, for systemic disorders affecting mitotically active tissues like the liver or muscle, delivery is more straightforward, but the central challenge shifts to durability. The successful targeted demethylation of the PWS-IC (86), combined with the development of editors capable of inducing heritable epigenetic silencing, suggests these distinct challenges can be met, offering a unified therapeutic paradigm for a wide range of IDs.

Challenges and ethical considerations

Despite advantages, several challenges concerning the long-term efficacy and safety, remain to be addressed for completely clinical application. First, the persistence of artificially induced methylation depends on its faithful replication by endogenous maintenance methyltransferases during DNA replication. Inefficient maintenance or editing in a subset of progenitor cells may result in the gradual dilution of the epigenetic mark over multiple cell cycles, causing therapeutic effects to wane over time (87). The long-term stability of an engineered epigenetic state against natural aging-related drift remains largely unknown. Notably, recent studies have revealed that epigenetic rejuvenation strategies can reverse age-associated epigenetic drift, offering a promising avenue to sustain induced modifications (88-90). Secondly, the immunogenicity of AAV vector and dCas9 protein is common in vivo delivery as referred above. Thirdly, there is a mismatch between AAV persistence and the “Hit-and-Run” goal. AAV genomes, especially in non-dividing or slowly dividing cells, can persist as long-lived episomes or integrated fragments, leading to sustained expression of the dCas9-effector cargo for months to years, which will prolong off-target editing risks, immunogenicity, and long-term genotoxicity. Researchers have addressed this contradiction from multiple angles such as self-inactivating AAV vector, biodegradable LNPs (91,92). Finally, while LNPs offer a non-viral, potentially re-doseable alternative to AAV, they present their own significant delivery challenges as residual hepatic tropism and dose-limiting hepatotoxicity. Overcoming this requires advanced LNP engineering to actively redirect particles away from the liver and towards the disease-relevant tissue (92).

Ethical concerns also pose significant challenges for epigenomic editing in imprinting diseases. Particularly in the context of germline editing, the potential for irreversible impacts on future generations has sparked widespread ethical debates (93). The long-term safety and stability of epigenomic editing still require further evaluation. Globally, efforts are being made to establish clinical application guidelines for epigenomic editing technology to ensure its safety and efficacy, distinguishing from gene therapy (94). Balancing technological advancement with ethical considerations is a critical issue that requires collective discussion across society, thereby enhancing public understanding and acceptance of epigenomic editing.

Conclusions

The treatment paradigm for IDs is at a pivotal juncture. For decades, therapeutic options have been largely confined to supportive care and symptomatic management, which, while beneficial, fail to address the fundamental molecular lesion: the disruption of parent-of-origin-specific gene regulation. The recent, rapid maturation of epigenome editing technologies, however, heralds a new era. As detailed in this review, the field has moved beyond proof-of-concept to establish a sophisticated toolkit of editors capable of writing, erasing, and rewriting heritable epigenetic marks with increasing precision and durability. Breakthroughs over the past decade, such as the development of compact, “hit-and-run” editors like CRISPRoff/on and multi-domain fusions, have established that transient delivery can install a permanent epigenetic state—a critical prerequisite for clinical translation. This innovation in editor design has been paralleled by significant advances in delivery. Engineered AAV capsids with enhanced CNS tropism and immune-evasive properties, alongside the emergence of programmable LNP platforms for extra-hepatic targeting, are systematically dismantling the barriers to in vivo application. The convincing preclinical data in models of AS and PWS are a direct result of this technological convergence, providing concrete evidence that reactivating a silenced allele or silencing a master regulatory element can rescue disease-relevant phenotypes.

Despite this remarkable progress, the path to the clinic remains challenging. Key questions surrounding long-term durability, particularly in mitotically active tissues, and the potential for off-target epigenetic alterations must be rigorously addressed in large animal models. For allele-specificity limitation, ensuring precise control of editor expression to minimize unintended consequences is paramount. Furthermore, the prospect of combining epigenetic conditioning with sequence-specific editors for disorders rooted in microdeletions or point mutations opens a new therapeutic frontier that will require the careful orchestration of multiple advanced technologies.

In conclusion, epigenome editing offers a therapeutic philosophy that is uniquely aligned with the pathophysiology of IDs. This therapeutic philosophy does not aim for static protein replacement or permanent genetic alteration, but rather seeks to restore the cell’s endogenous capacity for dynamic, physiological gene control. The tools to achieve this are now largely in hand. The next decade will be defined by the meticulous work of refining these tools, validating their long-term safety, and translating this profound scientific potential into transformative, and potentially curative medicines for patients and families affected by these devastating conditions.

Acknowledgments

None.

Footnote

Peer Review File: Available at https://tp.amegroups.com/article/view/10.21037/tp-2025-655/prf

Funding: This work was supported by the National Natural Science Foundation of China (No. 82271738 to Y.L.), and Zhejiang Provincial Basic Public Welfare Research Projects (No. LTGY24H260003 to C.J.).

Conflicts of Interest: All authors have completed the ICMJE uniform disclosure form (available at https://tp.amegroups.com/article/view/10.21037/tp-2025-655/coif). Y.L. reports that this work was supported by the National Natural Science Foundation of China (No. 82271738). C.J. reports that this work was supported by Zhejiang Provincial Basic Public Welfare Research Projects (No. LTGY24H260003). The other author has no conflicts of interest to declare.

Ethical Statement: The authors are accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.

Open Access Statement: This is an Open Access article distributed in accordance with the Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International License (CC BY-NC-ND 4.0), which permits the non-commercial replication and distribution of the article with the strict proviso that no changes or edits are made and the original work is properly cited (including links to both the formal publication through the relevant DOI and the license). See: https://creativecommons.org/licenses/by-nc-nd/4.0/.

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