CMN Weekly (21 November 2025) - Your Weekly CRISPR Medicine News

Top picks

• Scribe Therapeutics has presented preclinical data showing durable, precise in vivo CRISPR editing across three cardiometabolic programmes. STX-1150 silenced PCSK9 without DNA modification, sustaining LDL-C reductions for over 515 days. STX-1200 inactivated LPA with >95% efficacy at sub-0.5 mg/kg doses. STX-1400 achieved saturated APOC3 editing in primates, sharply lowering triglycerides. All candidates demonstrated high specificity, supporting one-time, long-acting genetic therapies for prevalent lipid disorders.
• Using prime editing to permanently convert dispensable endogenous tRNAs into suppressor tRNAs, a team at the Broad Institute has developed a disease-agnostic strategy to rescue premature stop codon mutations. The approach, termed PERT, demonstrated efficient protein rescue in cell models of Batten disease, Tay–Sachs disease, and cystic fibrosis, and rescued disease pathology in a mouse model of Hurler syndrome without causing off-target readthrough of natural stop codons. Also, read this perspective in Nature.

Research

• Researchers at Cellectis have developed a kilobase-long circular single-stranded DNA donor template approach combined with TALEN technology. The method achieved high gene insertion frequencies in haematopoietic stem and progenitor cells. CssDNA-edited HSPCs demonstrated superior engraftment and edit maintenance compared to AAV-edited cells in female NCG mice, attributed to higher levels of primitive HSPCs, a more quiescent metabolic state and elevated bone marrow niche adhesion markers.
• A doxycycline-inducible spCas9 system in human pluripotent stem cells achieved stable INDEL efficiencies of 82–93% for single-gene knockouts and over 80% for double-gene knockouts through systematic parameter optimisation. Using this CRISPR-Cas9 platform to evaluate sgRNA scoring algorithms, the team found that Benchling provided the most accurate predictions and identified an ineffective sgRNA targeting ACE2 exon 2 that produced 80% INDELs whilst retaining protein expression.
• Researchers at the Gene Editing Institute, ChristianaCare Health System, have used CRISPR to selectively knock down a cancer-specific version of the stress-response regulator NRF2, restoring the efficacy of standard chemotherapy in mouse models of lung squamous cell carcinoma. By exploiting a tumour mutation that creates a unique PAM site, the editors achieved modest but durable editing, sufficient to slow growth and re-sensitise tumours to carboplatin–paclitaxel. Also, read our take on the study.
• A platform called MetaEdit harnesses CRISPR-associated transposases to stably integrate kilobase-sized DNA payloads into bacterial genomes directly within the gut microbiome. The approach achieved species-specific editing of Bacteroides thetaiotaomicron in mice with complex flora at over 99% on-target specificity, enabling the insertion of a 7.5-kb metabolic pathway and accomplishing the first in vivo genetic engineering of segmented filamentous bacteria.
• Researchers have used CRISPR-based haplotype editing to target common single-nucleotide polymorphisms in cis with NEFL disease mutations for gene excision in iPSC-derived motor neurons from Charcot-Marie-Tooth type 2E patients. The approach, validated in two iPSC lines with different missense mutations, achieved phenotypic rescue and therapeutic editing levels. However, gene inversion – a frequent byproduct of excision – failed to disrupt mutant allele expression reliably.
• An American study finds that neurons exhibit slow, distinct DNA repair responses after CRISPR editing, challenging assumptions based on dividing cells. The researchers demonstrate that manipulating these repair pathways in nondividing cells can direct outcomes and improve editing efficiency. Also, read our take on the study.
• A new method, BreakTag, offers a scalable next-generation sequencing approach to characterise CRISPR-Cas9 nucleases and guide RNAs by enriching DNA double-strand breaks at on- and off-target sequences. The method enables off-target nomination, nuclease activity assessment and scission profile characterisation, with companion tools including BreakInspectoR for data analysis and XGScission for predicting cleavage patterns. Library preparation takes approximately 6 hours, and the complete protocol can be achieved in around 3 days.
• Fusing a double-stranded DNA-specific cytosine deaminase, DddAE1347A, to cytidine base editors increased editing efficiency up to 93-fold compared to BE4max, with the optimised system achieving 52% efficiency at the C14 and C15 positions in cell lines. The approach, tested in cell lines, embryos, tobacco and cotton, proved compatible with various Cas9 and deaminase variants, broadening the editing window at PAM-proximal cytosine positions.
• Through systematic creation and testing of thousands of chimeric proteins, researchers explored a combinatorial landscape of over 15,000 multi-domain CRISPR activators and identified two potent variants, MHV and MMH. These activators demonstrated enhanced activity compared to the gold-standard SAM activator across diverse targets and cell types, whilst the study revealed that many activators cause substantial cellular toxicity unrelated to their gene-regulatory capacity.
• Targeting cardiac transcription factor domains to naïve genomic sites using dead Cas9 induced epigenetic remodelling that altered both local and distal promoter chromatin, significantly changing gene expression even across insulating loci. The CRISPR-dCas9 approach revealed that virtually any DNA site can become regulatory, with transcriptional activation or repression varying non-linearly with distance between the regulatory site and gene.
• Base editors built from CRISPR-Cas12f1, a miniature 422-amino-acid Cas protein, were created by fusing catalytically inactive dCas12f1 to cytosine or adenine deaminases. Testing on plasmid targets in Escherichia coli revealed efficient editing of both the displaced non-target strand and the target DNA strand – an effect not observed with UnCas12f1 base editors.
• A rapid method, termed PAM-readID, enables the accurate determination of PAM recognition profiles for CRISPR-Cas nucleases in mammalian cells by integrating double-stranded oligodeoxynucleotides at DNA breaks. The approach successfully profiled SaCas9, SaHyCas9, Nme1Cas9, SpCas9, SpG, SpRY and AsCas12a, achieving accurate PAM preference identification with as few as 500 sequence reads or via Sanger sequencing.

Clinical & preclinical

• YolTech Therapeutics' YOLT-203, an in vivo CRISPR-based therapy targeting HAO1 to silence glycolate oxidase, has received FDA IND clearance for a pivotal PH1 trial. The study will assess safety and oxalate-lowering efficacy. Designed as a one-time treatment, YOLT-203 has also secured orphan and paediatric designations from both the FDA and EMA, supporting its potential for long-term renal protection in PH1 patients.

Industry

• Cassidy Bio has launched with $8M seed funding to develop an AI-driven genomic foundation model for CRISPR therapy design. By integrating proprietary wet-lab data with machine learning, the platform predicts optimal guide, enzyme, and delivery combinations, aiming to replace trial-and-error with scalable, clinically reliable genome-editing solutions. The approach seeks to enhance specificity, efficacy and speed in therapeutic development.

Screening

• A genome-wide CRISPR knockout screen identified UHRF1 as a restriction factor against HCoV-229E, with UHRF1 suppressing viral infection by downregulating the entry receptor APN via promoter hypermethylation. Follow-up CRISPR activation screens confirmed APN's critical role. The study identified additional genes, including SIGLEC1 and PLAC8, contributing to UHRF1's restrictive functions, whilst demonstrating that age-related decline in UHRF1 expression correlates with increased susceptibility to coronavirus infection.
• Functional CRISPR knockout screening with a custom sgRNA library targeting druggable genes across six ovarian and pancreatic cancer cell lines identified novel regulators of cytokine-induced PD-L1 expression. The screen uncovered KEAP1 as a key regulator, with its depletion or pharmacological inhibition reducing PD-L1 through NRF2 activation, suggesting the KEAP1/NRF2 axis as a potentially druggable immune checkpoint mechanism.
• A fluorescence microscopy-based CRISPR screening platform combining live-cell and antibody-based molecular markers enabled systematic identification of primary cilium regulators through targeted and genome-wide screens in human cells. Integration of screens focused on distinct ciliary phenotypes yielded multi-dimensional gene function profiles, identifying TZMP1 (SMIM27) as a transition zone microprotein required for ciliogenesis in human cells and ciliary function in Xenopus embryos.

Reviews

• Application of CRISPR-Based Biosensors in Analytical Chemistry. This review comprehensively introduces the biological mechanisms and classification of CRISPR-Cas systems, with particular emphasis on their analytical applications in molecular diagnostics, biosensor development, and miniaturised device integration.
• CRISPR-Based Functional Genomics in Pluripotent Stem Cells. This review provides a comprehensive evaluation of recent developments in CRISPR-Cas platforms, including gene knockouts, base and prime editing, and CRISPR activation or interference (CRISPRa/i), as applied to PSC systems.
• CRISPR-Cas9 in leukaemia immunotherapy: precision engineering of CAR-T cells and tumour-microenvironment modulation. This review examines how CRISPR-Cas9 is reshaping leukaemia therapy by enabling precise immune-cell engineering for more effective immunotherapies and refined disease modelling.
• Mechanisms of transcription-coupled repair and DNA damage surveillance in health and disease. This review explores how lesion-stalled RNA polymerase II triggers and shapes transcription-coupled repair, weaving together structural insights, Pol II processing and ubiquitylation, and emerging DNA–protein crosslink repair to illuminate why defects in these mechanisms cause distinct hereditary TC-NER disorders.
• Harnessing artificial intelligence to advance CRISPR-based genome editing technologies. This review summarises key AI methodologies underlying these advances and discusses their recent noteworthy applications to genome editing technologies.