Cell-specific epigenetic editing holds very high therapeutic value for atherosclerosis, cardiomyopathy, and fibrosis, provided that delivery, specificity, and safety challenges are also addressed.
Abstract
BACKGROUND
Cell-specific epigenetic editing provides a new approach to the therapy of cardiovascular disease (CVD) by rewriting pathological chromatin and RNA marks in exactly those cell populations responsible for causing disease. CVD is caused by interactions of genetics and environment on cell-type-specific epigenomic programs. Interventions that alter DNA methylation, histone marks, or RNA modifications can therefore correct maladaptive gene expression without altering DNA sequence.
SUMMARY
Recently developed technologies such as dCas9 fused to writers/erasers allow programmable, locus-directed modulation of promoters, enhancers, and transcripts. Proof-of-principle in vivo work has shown durable target silencing, illustrating both the potency and persistence of epigenetic edits. To achieve therapeutic benefit, cell-targeting strategies and rigorous single-cell/multi-omic validation of on-target activity and off-target safety will be required. Major translational challenges include scalable, cardiac-selective delivery, immune responses to vectors/editors, long-term monitoring for unintended chromatin changes, and regulatory pathways for nongenotoxic but durable interventions.
KEY MESSAGES
Altogether, cell-specific epigenetic editing holds very high therapeutic value for atherosclerosis, cardiomyopathy, and fibrosis, provided that delivery, specificity, and safety challenges are also addressed.
Although cells within an organism share nearly identical genomes, their transcriptional programs differ markedly due to reversible chemical modifications known as epigenetic marks. These marks, including DNA methylation and histone modifications, regulate gene expression without altering DNA sequence and play a central role in development and disease. While epigenetic drugs such as DNA methyltransferase inhibitors have shown clinical benefit, their genome-wide activity often results in off-target toxicity limiting broader therapeutic applications. This has driven the development of locus-specific epigenetic editing strategies. Programmable epigenetic modifiers (PEMs) combine customizable DNA-binding platforms, such as CRISPR-dCas systems, transcription activator-like effectors (TALEs), or zinc fingers, with epigenetic effector domains to precisely install or remove regulatory marks at defined genomic loci. Because effective editing depends on the pre-existing epigenetic landscape, detection and characterization of target-site epigenetic states is a prerequisite for rational editor design, increasingly aided by machine-learning models that predict editing outcomes. In this review, we summarize current technologies for epigenetic mark detection and discuss the transition from global pharmacological approaches to programmable, modular editing systems that enable spatial and temporal control of gene regulation. We further address heritability and delivery constraints. Reversible, site-specific epigenetic editing represents a promising therapeutic paradigm for cancer, genetic disorders, and regenerative medicine.
Epigenetic editing achieves durable gene silencing through targeted modification of chromatin and DNA methylation states without altering the genomic sequence-modifications that remain fundamentally reversible compared with genome editing. Long constrained by transient efficacy, insufficient precision, and delivery bottlenecks, the field reached a critical inflection point in 2024-2025, measurable through three quantifiable criteria: (1) mechanistic durability-silencing maintained across ≥ 450 cell divisions in vitro and ≥ 12 months in vivo without continued editor expression; (2) delivery competence-tissue-selective transduction at > 50% efficiency in liver, muscle, and whole brain via engineered lipid nanoparticle and AAV platforms; and (3) clinical validation-advancement of multiple first-in-human trials. The inaugural trial in epigenetic editing was OTX-2002 (targeting MYC-driven malignancies, MYCHELANGELO study), initiated in October 2022, followed by TUNE-401 for chronic hepatitis B (Phase Ib, November 2024) and EPI-321 for facioscapulohumeral muscular dystrophy (Phase I/II, first patient dosed August 2025). Artificial intelligence contributes at distinct levels: deep learning platforms have directly accelerated clinical-stage LNP formulation screening and AAV capsid prediction; AlphaFold3 has optimized protein-DNA interaction validation without yet entering clinical programs; and the 2025 de novo design of DNA-binding proteins smaller than 65 amino acids represents a proof-of-concept breakthrough with zero clinical precedent. This review comprehensively analyzes epigenetic editing's technological maturation, provides a tiered assessment of AI's realized and anticipated contributions, critically evaluates the emerging clinical landscape, and identifies decisive unresolved challenges-including long-term stability in non-dividing cells, the lack of monitoring systems and intervention protocols needed to implement reversibility in clinical practice, and manufacturing access barriers. We argue that epigenetic editing is progressively establishing itself as a distinctive therapeutic modality characterized by durable efficacy and sequence-independent safety-reversibility as a theoretical safety mechanism has been validated preclinically, but the monitoring and intervention infrastructure required for its clinical implementation remains to be established. Long-term human validation remains the outstanding core question.
Shiqi Chang, Di Lu, Yuyuan Jin et al.· Clinical Epigenetics· 0 citations
DNA methylation can function as a toxic alkylation reaction exploited by chemotherapeutic agents to induce cancer cell death. However, finely tuned DNA methylation plays a fundamental role in cellular physiology, particularly in the epigenetic regulation of gene expression. Once thought to act solely as a repressor of gene transcription, its functional role has since been elucidated as genomic locus-specific and deeply connected with other epigenetic factors. Following the clinical approval of DNA methyltransferase inhibitors, such as Azacitidine and Decitabine, for the treatment of hematological malignancies, considerable efforts have been devoted to developing pharmacological tools that modulate epigenetic DNA methylation. However, the lack of gene selectivity in these agents limits their therapeutic efficacy and increases off-target toxicity. Moreover, the non-gene-selective nature of current DNA methylation-targeting molecules fails to meet the standards required to discern the nuanced roles of DNA methylation across diverse pathophysiological contexts and genomic loci, particularly in an era where next-generation sequencing and omics technologies enable high-resolution epigenetic analyses. In this review, we examine the mechanisms and roles of DNA methylation in epigenetic regulation, evaluate the current landscape of DNA methylation modulators, from traditional DNMT inhibitors to cutting-edge CRISPR-dCas9 fusion systems and protein-protein interaction disruptors, and discuss their clinical relevance. Finally, we emphasize the need for precise, locus-specific tools to advance both cancer research and therapeutic strategies.
Julie Gilbert, Francesco Calzaferri· Chemical Research in Toxicol...· 0 citations
CRISPR has emerged as a next-generation gene-editing tool with the potential to target the molecular pathways associated with ageing and related disorders. It functions through RNA-guided Cas nucleases, directing DNA cleavage and utilizing the native DNA repair machinery for genetic manipulations. Advances in CRISPR technology have significantly enhanced the precision and flexibility of techniques for genome editing. The enzyme Cas9's ability to cut DNA at exact site has revolutionized genome editing by enabling accurate modifications within living eukaryotic cells. This review critically examines recent developments in CRISPR-based technologies, including Cas9, Cas12, base editing, prime editing, and CRISPR-mediated gene regulation. It highlights their rising applications in ageing research, with more emphasis on neurodegenerative disorders such as Alzheimer's and Parkinson's diseases. The review also discusses the major pharmacological and translational challenges that currently limit clinical applications, including inefficient tissue-specific delivery, off-target genome editing, immunogenicity, manufacturing complexity, and long-term safety concerns. Also, recent progress in both, viral and non-viral delivery methods are critically evaluated, including adeno-associated viruses, lentivirus vectors, lipid nanoparticles, gold nanoparticles, exosomes, electroporation, and microinjection, is thoroughly discussed to highlight their therapeutic potential and translational limitations. Current studies indicate that CRISPR-based approaches have preclinical potential for targeting important hallmarks of ageing, particularly genomic instability, telomere attrition, and mitochondrial dysfunction. Other hallmarks of ageing, such as stem cell exhaustion, epigenetic modifications, and microbiome changes, are at earlier stages of development. Overall, this review describes future strategies for developing safe, precise, and clinically translatable CRISPR-based treatments to promote healthy ageing.
Sakshi Rathore, Akash Gupta, Kamal Shah et al.· Ageing Research Reviews· 0 citations
Epigenetic regulators exert critical functions in cancer initiation and progression by governing key processes-such as gene expression, chromatin remodeling, and cellular differentiation-without altering the underlying DNA sequence. Given the multitude of targetable nodes within epigenetic pathways and their central roles in tumorigenesis, disease progression, and drug resistance, the advancement of epigenetic therapies holds considerable promise for augmenting existing cancer treatment modalities. Recent pharmacological innovations have yielded diverse small-molecule inhibitors directed against principal epigenetic enzymes-namely DNA methyltransferases (DNMTs), histone acetyltransferases (HATs), histone deacetylases (HDACs), and histone methyltransferases (HMTs). These agents have demonstrated potent therapeutic efficacy in both preclinical models and early-phase clinical trials by reprogramming the epigenetic landscape of malignant cells, potentiating conventional therapies, and overcoming resistance mechanisms. However, comprehensive assessments of their safety, selectivity, and resistance profiles remain incomplete, and systematic analyses of the clinical translation barriers for multitargeted epigenetic modulators are lacking. Accordingly, this review presents an in-depth analysis of the most recent advances in small-molecule epigenetic modulators, focusing on their mechanisms of action, therapeutic applications, and the challenges impeding their clinical development, with the aim of informing the rational design and optimization of next-generation epigenetic treatment strategies for cancer. FACTS.
Peng Jin, Yi Wang, Na Zhao et al.· Biochimica et biophysica act...· 0 citations
Aging and cancer reflect distinct but interconnected manifestations of cellular stress responses shaped by context-specific molecular and environmental factors. Senescence initially restrains malignancy through stable cell-cycle arrest and immune clearance, yet persistence of senescent cells and the senescence-associated secretory phenotype (SASP) paradoxically drives tumor progression, therapeutic resistance, and immune evasion via chronic inflammation and metabolic reprogramming. Functional genomic screening has evolved from bulk RNA interference to precision clustered regularly interspaced short palindromic repeats (CRISPR) modalities, including knockout, interference, activation, and base editing, and onward to single-cell and in vivo platforms. These technological advances have transformed our capacity to dissect cellular state transitions and network dependencies with unprecedented resolution. Here, we trace this technological evolution and synthesize its impact on aging and cancer research, with emphasis on chromatin regulation, metabolic rewiring, the SASP, nucleocytoplasmic transport, therapeutic response, and the tumor microenvironment. We emphasize that the current evidence derives predominantly from preclinical functional screens and computational predictions. We propose shifting from gene-centric discovery toward context-dependent network analysis. Integrating precise editing, in vivo screening, single-cell multi-omics, and emerging artificial intelligence (AI)-assisted design may provide information and a design basis for future combined strategies that simultaneously target vulnerabilities in senescent cells and malignant populations.
Bo Fan, Aiwei Wu, Xue Pan et al.· Ageing and Cancer Research &...· 0 citations
A new method for surgically removing training examples from a model reveals that as datasets grow, the link between what a model learns and what it produces dissolves.
