Epigenetic Editing Steps Closer to the Clinic as Bioengineering Tools Mature

At a conference hall in Amsterdam this past October, researchers gathered for the seventh International Conference on Epigenetics and Bioengineering, known as EpiBio-24, held from October 3 to 5 under the chairmanship of Dr. Karmella Haynes of Emory University, Dr. Nate Hathaway of the University of North Carolina at Chapel Hill, and Professor Pernette Verschure of the University of Amsterdam and Amsterdam University Medical Centers. The meeting brought together multidisciplinary scientists working at the intersection of epigenetics and bioengineering, with a shared emphasis on development and disease. What emerged over three days was a clear sense that a field barely a decade old is rapidly pivoting from foundational discovery toward (pre)clinical applications of targeted epigenetic therapies, with more than ten companies now developing epigenetic editing therapies and a clinical trial already underway.

The opening keynote set an ambitious tone. Wendy Bickmore, director of the MRC Human Genetics Unit at the University of Edinburgh and a pioneer in functional three-dimensional genome organization, delivered the special EMBO Keynote lecture on how the non-coding genome regulates gene activity. She illustrated that distant enhancers do not always need direct physical contact with their target promoters to activate gene expression, but they must be located within roughly 200 to 300 nanometers of a promoter to function effectively. Bickmore showed that cohesin-mediated loop-extrusion is essential for long-range enhancer action, while also challenging the loop-extrusion model as the sole explanation, presenting evidence from her laboratory of ‘leaky’ insulation across topologically associating domain boundaries that causes bystander activation. She also unveiled a novel histone post-translational modification, H3K115 acetylation, which sits within the histone core rather than on the tail and is enriched precisely at the transcription start site in the nucleosome-depleted region, suggesting it marks a fragile nucleosome strongly associated with active transcription.

On the second day, Lei Stanley Qi, associate professor of bioengineering at Stanford University and a pioneer in CRISPR technology, offered a conceptual reframing of how scientists should interpret chromatin maps. TAD boundaries, he argued, are merely snapshots of chromatin interactions, whereas a cell functions as a living, dynamic system. He drew an evocative parallel with Leonardo da Vinci’s Vitruvian Man, which captures optional configurations of the human body, much as epigenetic figures capture the states of many cells across time and space. Qi described an epistasis mapping approach to enhancer functionality, explaining how redundant, independent, or synergistic enhancer interactions can provide compensatory, fine-tuning, or robust regulatory effects respectively, and noted that BRD4-mediated condensation can facilitate such interactions. Notably, his findings independently confirmed Bickmore’s conclusion that enhancers need spatial proximity to promoters to exert their effects.

The final keynote, from Angelo Lombardo, professor of tissue biology and regenerative medicine at Vita-Salute San Raffaele University and co-founder of Chroma Medicine, delivered perhaps the strongest evidence yet that epigenetic editing can work as a durable therapy. His laboratory discovered that stable gene repression requires simultaneous methylation of DNA and repressive histone marks, and that epigenetic regulators such as DNMT3A/3L and KRAB domains, which catalyze DNA and histone methylation, silence retroviral elements in embryonic stem cells. Inspired by this natural system, the group fused DNMT3A/3L and the KRAB domain of ZNF10 to zinc finger domains targeting specific genomic regions, achieving stable gene repression across multiple cell lines. They recently demonstrated long-term repression of PCSK9, a hepatocyte gene involved in cholesterol homeostasis, in mice for nearly one year, reducing LDL receptor presence on hepatocyte membranes. Strikingly, even after partial liver resection, the induced DNA methylation state and repressed expression were retained in the regrown tissue, showing that these modifications are faithfully inherited. Lombardo also highlighted epigenetic silencing of Hepatitis B virus via induced DNA methylation as a viable therapeutic avenue.

Beyond the keynotes, a wave of technical innovation is reshaping how epigenetic enzymes are understood and improved. Albert Jeltsch of the University of Stuttgart uses Deep Enzymology to systematically investigate the preferred flanking DNA sequences of DNA methyltransferases, finding that different DNA substrates influence DNMT1 efficacy so drastically that allele-specific DNA methylation becomes possible. Saulius Klimašauskas and colleagues at Vilnius University developed a click-chemistry technique for bioorthogonal labeling at sites where individual DNMTs catalyze methylation in live cells, enabling high-resolution chemical ‘tracks’ of epigenetic writers throughout the cell cycle. At Rice University, Jacob Goell reduced the cytotoxicity of the histone acetyltransferase P300 while preserving its enzymatic activity through a single point mutation in the P300 core, and found that P300 primes genes for activation and enhances prime editing efficiency independently of its catalytic function.

Epigenetic reader domains, which evolved over millions of years to recognize specific post-translational modifications, are also becoming central tools, particularly where high-quality antibodies are hard to develop. Tuncay Baubec of Utrecht University presented ChromID, a systematic approach in which a biotin ligase fused to a chromatin reader domain biotinylates nearby proteins; after pull-down and mass spectrometry, the epigenetic proteome at a targeted modification is mapped. EpiCypher’s Matthew Meiners described chimeric tandem reader domains and synthetic, fully chemically defined modified nucleosomes for use as spike-ins in CUT&RUN and CUT&Tag assays, allowing researchers to map reader-PTM interactions and histone modification co-occurrences. Anja Köhler of the University of Stuttgart introduced the Bimolecular Anchor Detector, or BiAD, technology, which combines a sgRNA/dCas9 DNA-binding module with reader-domain detector modules fused to complementary split fluorophore parts, reconstituting fluorescence only when both modules bind in proximity, thereby visualizing epigenetic marks at specific genomic loci in living cells. Meanwhile, Marvin Tanenbaum of the Hubrecht Institute presented stopless-ORF circular mRNAs encoding SunTag epitopes, permitting live-cell single-molecule imaging of ribosome kinetics and revealing that ribosome collisions actually facilitate translation through difficult sequences by resolving stalls.

As the toolbox expands, so does the appetite for unbiased, high-throughput screening. Lacramioara Bintu’s laboratory at Stanford developed dCas9-mediated high-throughput recruitment, or HT-recruit, testing more than 5,000 nuclear protein Pfam domains of human and viral origin for their ability to silence or activate gene expression, alongside a library of 114,288 sequences tiling transcription factors and chromatin regulators. Her characterization was memorably vivid: transcriptional activators tend to be ‘greasy acidic noodles with a little salt, pepper and queso,’ rich in acidic and hydrophobic residues interspersed with serine, proline, or glutamine, while repressors come in more flavors, with KRAB domains the best performers across contexts, including a newly identified KRAB from ZNF705F that outperforms the commonly used ZNF10 KRAB. At UC Berkeley, Michael Herschl screened over 50,000 pairs of epigenetic editors, some with catalytic domains up to 6.3 kilobases, using the COMBINE inducible screening platform, identifying editor combinations that impart long-term epigenetic changes and a bidirectional CRISPR perturbation system capable of activating and repressing genes concurrently. A key insight: domains operating in the same or similar pathways show good perturbation synergy, mimicking their natural collaboration. Samuel Reisman of Duke University, in work toward regenerative therapies, screened over 1,600 human transcription factors with CRISPR activation followed by Perturb-seq single-cell RNA sequencing to map the fidelity and subtype-specificity of astrocyte-to-neuron reprogramming.

Computational advances featured prominently as well. Kim Kira Witetzek of Academia Sinica presented ATAC-Mass, which combines isotopic labeling, ion beam imaging at 100-nanometer resolution, and mass cytometry to integrate epigenomics, proteomics, and three-dimensional nuclear imaging at the single-cell level. Jennifer Spangle of Emory University School of Medicine described a chemoenzymatic technique using an L-methionine analogue that converts into a SAM analogue, tagging methylated proteins with a detectable alkyne; the approach resolves mono-, di-, and trimethylation, histidine methylation, and arginine methylation with site specificity, works in vivo and across the blood-brain barrier, and identified 221 proteins with novel methylation sites upon enrichment. Philipp Schnee of the University of Stuttgart showed how 3D molecular dynamics simulations can predict enzyme behavior, enabling the design of a ‘Super-Substrate’ for protein lysine methyltransferases that outcompetes natural substrates with substantially increased specificity. Kimberley Glass of Brigham and Women’s Hospital presented SPIDER, a computational modeling tool that builds gene regulatory networks from DNase-seq, ATAC-seq, or DNA methylation data, prunes false positives using chromatin states, and accurately predicts ChIP-seq transcription factor binding events lacking a corresponding sequence motif, a persistent weakness of older pipelines.

The field’s clinical momentum was matched by growing candor about its risks. Jamie Hackett of EMBL Rome used CRISPR-dCas9 perturbation screens to dissect causal regulatory roles, finding that blocking histone tail acetylation prevents transcriptional activation after H3K4me3 deposition, and that gene permissiveness to epigenetic reprogramming depends on cell type, expressed factors, and DNA sequence. Domitilla del Vecchio of MIT proposed that H3K9me3 causally follows DNA methylation, noting that KRAB alone does not confer long-term memory while DNMT3A does. Bas van Steensel of the Netherlands Cancer Institute used transposon systems to relocate enhancers, promoters, and CTCF sites across a two-megabase window, discovering that enhancers communicate with gene bodies as well as promoters. On safety, Henriette O’Geen of UC Davis showed that hundreds of CpGs retain off-target methylation 24 days after transient editing, particularly at bivalent genes poised for transcription and implicated in oncogenesis, prompting a call for a gold standard for reporting off-target effects; Majid Pahlevan Kakhki of Karolinska Institutet independently reported widespread unintended methylation across nearly all CRISPR-dCas9 tools, including CRISPRoff. In applied settings, Pernette Verschure’s group found transcription burst size predicts gene responsiveness in hormone-sensitive breast cancer, while Gabriella Ficz of Barts Cancer Institute demonstrated ex vivo epigenetic editing of CDKN2B in umbilical cord hematopoietic stem cells, with durable methylation maintained after engraftment in mice and inherited across myeloid and lymphoid lineages. Ivana Parker of the University of Florida, meanwhile, mapped the epigenetic pathways underlying BCG vaccine-induced macrophage activation. Together, the Amsterdam meeting captured a field in confident transition: from conceptual understanding of chromatin’s static architecture to the dynamic, engineered, and increasingly therapeutic manipulation of the epigenome, balanced by a maturing commitment to safety, standardization, and open collaboration between academia and industry.

Subject of Research: Epigenetic editing technologies and their translation from bioengineering innovations toward clinical therapies

Article Title: Bridging bioengineering and epigenetics: from technical innovations to clinical applications

Article References: Jacob, J., van Loosen, Q. C., van den Berg van Saparoea, A. C. H., Sarno, F., & Verschure, P. J. (2024). Bridging bioengineering and epigenetics: from technical innovations to clinical applications. Epigenetics Communications, 4(1), Article 8. https://doi.org/10.1186/s43682-024-00031-x

Image Credits: AI Generated

DOI: 10.1186/s43682-024-00031-x

Keywords: epigenetics, bioengineering, CRISPR, epigenome editing, DNA methylation, chromatin, gene regulation, clinical applications, off-target effects, high-throughput screening, transcription, gene therapy