CMN Weekly (6 June 2025) - Your Weekly CRISPR Medicine News

Top picks

• KJ Muldoon, the infant who received the first personalised CRISPR gene editing therapy, was discharged from hospital earlier this week. KJ, who was born with the rare and severe genetic condition severe carbamoyl phosphate synthetase 1 (CPS1) deficiency, received two doses of a base editor bound to a bespoke targeting guide sequence using lipid nanoparticles when he was 7 and 8 months old. His treatment, targeting carbamoyl phosphate synthetase 1 (CPS1) deficiency, was administered under a single-patient emergency protocol, and the positive early results were published in May in The New England Journal of Medicine. Read our coverage of that story here.
• In an article published in Cell Reports Medicine, a team in Italy, Germany and Canada investigated how gene editing using homology-directed repair (HDR) affects the functioning of haematopoietic stem cells (HSCs). They found that HDR-based editing via CRISPR-Cas9 and adeno-associated virus 6 (AAV6) but not single-stranded oligodeoxynucleotide activates stress responses in HSCs; this includes inflammation and features of senescence, both of which are known to compromise their functionality in transplantation settings. Surprisingly, the team discovered that HSCs “remember” the stress of the ex vivo editing procedure even months after transplantation and they raise the possibility of HSC memory and plasticity that they plan to investigate further.

Research

• In an article published in Nature Biotechnology, scientists at The University of Texas Southwestern Medical Center and ReCode Therapeutics report Dual Selective ORgan-Targeting lipid nanoparticles (SORT LNPs) to deliver base editors to the liver and lungs. They show that the new SORT LNPs corrects the PiZ mutation in the SERPINA1 gene (which causes alpha-1 antitrypsin deficiency (AATD)), achieving 40% correction in liver cells and 10% in lung alveolar epithelial type II cells. They report that the liver maintains stable editing for 32 weeks, reducing Z-A1AT levels by more than 80% and restoring a normal liver phenotype. In parallel, they observed 89% neutrophil elastase inhibition in lung bronchoalveolar lavage fluid. They present Dual SORT LNP therapy as a promising approach for long-lasting genome correction for multi-organ diseases such as AATD.
• A team at Yale University and Yale School of Medicine tested the ability of six Cas12a-derived base-editing systems to process multiple gRNAs from a single transcript. They identified base editor variants capable of multiplexed base editing and improved the design of the respective gRNA array expression cassette, which enabled multiplexed editing of 15 target sites in multiple human cell lines. To reduce bystander mutations, the team also developed a Cas12a gRNA engineering approach that directs editing outcomes towards a single base-pair conversion. The team then combined those advances to demonstrate that both strategies can be used together to drive multiplex base editing with greater precision and reduced bystander mutation rates. Their findings were published in Nature Biotechnology.
• Estrogen receptor alpha (ERα) is a master regulator of transcription in healthy and cancerous mammary (breast) cells. Drugs or other exogenous agents that stimulate ER transcriptional activation have been shown to increase breast cancer risk, while inhibition of ER activity (via so-called endocrine therapy) is a very effective anti-cancer therapeutic strategy. While a number of ER-inhibiting hormone therapies have been developed as systemic treatments for ER+ breast cancers, treatment resistance is a significant problem. This is often linked with somatic mutations including loss-of-function mutations in the gene encoding neurofibromin 1 (NF1). Exactly how NF1 loss promotes endocrine resistance remains poorly understood. Using CRISPR-Cas9 screens, researchers in the United States, Belgium and China have identified NR2F2 as a key driver of endocrine resistance in breast cancer. Their findings, published in Science Translational Medicine, open new avenues for "endocrine sensitisers" to augment existing endocrine therapies.
• Earlier this week, researchers in researchers in South Korea announced a method to selectively install N4-acetylcytidine (ac4C) modifications on specific RNA transcripts using engineered CRISPR-Cas13 systems. The study demonstrates precise RNA acetylation that enhances translation efficiency and reveals new regulatory functions of RNA modifications. The work was published in Nature Chemical Biology.
• Existing A-to-G base editors for mitochondrial DNA (mtDNA) are limited by low efficiency. To address this, a team in China used directed evolution to discover variants of the TadA-8e base editors that have increased activity and expanded targeting compatibility for nuclear and mtDNA adenine base editing, especially in previously unfavoured sequence contexts. Their attempts resulted in engineered mtDNA editors (eTd-mtABEs) that showed up to 87% editing efficiency in human cells, with greatly reduced DNA and RNA off-target effects. Strand-selective A-to-G editing was enhanced by an average of 3.2-fold with substitution of DddA to DNA nickases in eTd-mtABE backbones compared to mitochondrial adenine base editors. Their findings were published this week in Nature Biotechnology. Using the newly-developed eTd-mtABE, the team generated rat models of Leigh syndrome that exhibit the severe defects associated with that disease. To correct that mutation, they engineered a precise mtDNA C-to-T base editor that was injected into mutated embryos. This achieved restoration of wild-type alleles to an average of 53%, leading to amelioration of disease symptoms. Their findings were published as a Brief Communication in Nature Biotechnology.
• Researchers at University Hospital Tübingen investigated single-guide RNA CRISPR-Cas9 approaches to correct the pathogenic USH2A:c.7595-2144A>G deep-intronic variant that causes mis-splicing in inherited conditions. They compared Cas9 with EDCas9 (in which Cas9 is fused with TREX2 exonuclease) to restore correct splicing in minigene assays and patient-derived fibroblasts. While Cas9 generated variable small indels with inconsistent splicing rescue, EDCas9 produced consistent, directional deletions that effectively disrupted mis-splicing sequences and ensured robust splicing correction. Off-target assessments showed safe profiles for both systems, with EDCas9 additionally preventing targeted translocations. Using virus-like particles for delivery, the team demonstrated EDCas9's suitability as a transient therapeutic approach for addressing this pathogenic variant. Their findings were published in Molecular Therapy Nucleic Acids.
• Scientists based at The Chinese Academy of Sciences have developed inverse prime editors (iPEs) that work upstream of cleavage sites, overcoming limitations of conventional prime editing by replacing nCas9-H840A with nCas9-D10A. The team first created circular RNA-mediated inverse prime editors (ciPEs) that achieved editing efficiencies of 0.1% to 24.7%. Subsequent optimisation using Rep-X helicase further increased efficiencies to 2.7%–55.4% at previously difficult-to-target genomic sites. The team found that the Rep-X-assisted ciPE system yields fewer unwanted by-products as a result of more precise cleavage activity and suggests that it has the potential to significantly extend the genomic DNA target range of prime editing. Their findings were published recently in Nature Communications.

Industry and clinical

• Beam Therapeutics announced this week that the US FDA has granted orphan drug designation to BEAM-101 for the treatment of sickle cell disease (SCD). BEAM-101 is the first base-edited therapeutic candidate for a haemoglobinopathy. It is a patient-specific, autologous haematopoietic stem and progenitor cell-based therapy designed as a one-time treatment for SCD and beta-thalassemia. BEAM-101 is being evaluated in the BEACON Phase 1/2 clinical trial. See the press release for further details.
• YolTech Therapeutics announced today that the US FDA has cleared its IND application for YOLT-101, an in vivo base-editing therapeutic candidate designed to treat heterozygous familial hypercholesterolemia (HeFH). YOLT-101 works by permanently disrupting the PCKS9 gene for long-term reduction of harmful LDL-levels and is being evaluated in a Phase 1 investigator-led trial in China. Early clinical data from that trial, released in April 2024, revealed dose-dependent, durable LDL-C reduction in HeFH patients following a single intravenous dose of YOLT-101.
• On Sunday, Allogene Therapeutics presented new clinical data from the Phase 1 TRAVERSE trial, which is evaluating the allogeneic CAR-T cell therapeutic candidate ALLO-316 for the treatment of advanced or metastatic renal cell carcinoma. The data, presented orally at the 2025 Annual ASCO meeting held in Chicago, highlights durable responses in heavily pre-treated patients after a single dose of ALLO-316. See the official press release for further details and read our clinical trial update here.

Reviews

• Deep Learning Based Models for CRISPR/Cas Off-Target Prediction. This review provides an overview of existing off-target site (OTS) prediction tools with an emphasis on deep learning methods. The authors characterise datasets used for deep learning training and testing, evaluate six deep learning models using six public datasets, and validate OTS data from the CRISPRoffT database. The performance of these models is assessed using standardised metrics, such as Precision, Recall, F1 score, MCC, AUROC and PRAUC. The authors report that incorporating validated OTS datasets into model training enhanced overall model performance, and improved robustness of prediction, particularly with highly imbalanced datasets. While no model consistently outperforms other models across all scenarios, they found that CRISPR-Net, R-CRISPR, and Crispr-SGRU show strong overall performance.
• From Cas Proteins to Cutting-Edge Biosensors: A New Era in Clinical Pathogen Diagnostics. The authors of this review discuss the design and development of various CRISPR/Cas-based biosensors, exploring the applications of CRISPR/Cas-assisted biosensing for emerging infectious diseases. The authors highlights advantageous features for pathogen diagnostics including cost-effectiveness, multiplex detection and point-of-care-testing. Challenges and future developments of CRISPR/Cas-based biosensors for rapid and accurate pathogen detection in specialised settings are also summarised.
• Gene editing therapy as a therapeutic approach for cardiovascular diseases in animal models: A scoping review. This review explores the efficacy and safety of gene-editing therapy for the treatment of cardiovascular diseases (CVDs) and identifies opportunities for future advancements. The author investigated studies on gene-editing interventions in animal models of CVDs, retrieved from PubMed, ScienceDirect, and Web of Science up to December 2024.

Detection

• In a recent article published in Biosensors & Bioelectronics, scientists in China report a CRISPR/Cas12a-based colorimetric sensor for detecting tumour-derived exosomes using a dual-recognition strategy with EpCAM and CD63 aptamers. The newly-developed system captures lung cancer cell-derived exosomes to release trigger DNA; this activates the trans-cleavage activity of CRISPR/Cas12a to generate a sensitive colorimetric signal. They report that the sensor achieved a detection limit of 31 particles/mL and successfully distinguished healthy individuals from lung cancer patients using smartphone-based analysis, offering high sensitivity, good specificity, and low-cost on-site detection capabilities.

News from CRISPR Medicine News

• New clinical data from Allogene Therapeutics' Phase 1 TRAVERSE trial reveals durable responses in patients with heavily pre-treated advanced renal cell carcinoma. The allogeneic CAR-T cell therapeutic candidate ALLO-316 shows promise as the first of its kind to demonstrate efficacy in solid tumours, offering renewed hope for those with limited treatment options. Read more about this in Wednesday's clinical trial update here.