CMN Weekly (13 December 2024) - Your Weekly CRISPR Medicine News

Top picks

• Researchers at HuidaGene Therapeutics have developed hfCas13Y, a high-fidelity RNA-targeting system, to reduce MECP2 protein levels in MECP2 duplication syndrome (MDS). Delivered via AAV9, hfCas13Y-gMECP2 corrected gene expression, improved behaviour, and extended survival in transgenic mice. In monkeys, a single injection reduced MECP2 expression by ~52% across the brain. The approach offers a promising strategy for treating MDS and other dosage-sensitive conditions.
• Scientists have developed a novel circular single-stranded DNA technology that enables highly efficient gene integration in various cell types, achieving up to 70% successful gene integration. The system can carry genetic sequences of up to 20 kb in length, showing promise for CAR-T cell therapy development. Read our interview with the study's corresponding author, Howard Wu, at Full Circles Therapeutics.

Research

• CRISPR-Cas9 screening has identified 406 melanoma genes, enabling subtyping (C1-C3) with distinct prognoses and immune profiles. Hot tumour subtype C1 showed the best survival, while cold tumour C3 had the poorest outcomes. A gene model, including RABIF, linked low-risk, hot tumours to longer survival. RABIF inhibition reduced melanoma growth, offering insights for improved immunotherapy strategies.
• In vivo CRISPR screening has revealed a novel role for cancer cell CD28 in promoting immune escape by stabilising Cd274 mRNA and upregulating PD-L1. CD28 deletion activated cDC1 and CD8+ T cells, inhibiting tumour growth and overcoming anti-PD-1 resistance in TNBC models. Targeting CD28 offers a promising strategy to enhance breast cancer immunotherapy.
• Researchers at the University of California San Diego have developed the SCHEMATIC resource, a systematic approach leveraging combinatorial CRISPR gene knockouts to identify synthetic lethal gene interactions across various cancer contexts. This method integrates gene interaction screens with pharmacogenomics to enhance precision oncology.
• A novel strategy for CRISPR array assembly enables efficient multiplexing, assembling up to 12 crRNAs for AsCas12a and 15 for RfxCas13d in a single reaction. Pol II and Pol III promoter-driven arrays showed distinct expression patterns, optimised for specific applications. This approach streamlines multiplex CRISPR for dissecting complex cellular networks and advancing multi-target gene therapies.
• CRISPR-Cas9 has been used to delete non-coding GWAS loci near the RUNX1 gene in human iPSCs, demonstrating the regulatory role of non-coding variants in bone formation and the potential for genome editing in treating bone disorders. These edits enhanced osteogenesis in vitro and bone regeneration in vivo, likely by upregulating RUNX1 long isoform and other targets like SETD4.
• A dual-vector system using third-generation adenoviruses (AdVs) for CRISPR-Cas9 delivery and single-stranded AAVs for donor DNA enables precise transgene insertion via homologous recombination or HMEJ, achieving up to 93% efficiency. High-fidelity nucleases minimise off-target AAV insertions, offering a coordinated, selection-free approach for versatile and effective genome editing.
• CRISPR-Cas12a diagnostics has been optimised for single-nucleotide variant (SNV) detection using ARTEMIS, an in silico tool identifying SNVs in Cas12a seed regions. Synthetic mismatches in crRNAs enhanced specificity, detecting 928 clinically relevant variants, including BRAFV600E and TP53V272M. Cas12a reliably identified SNVs in patient-derived cfDNA, advancing precise, cost-effective cancer diagnostics and personalised medicine.
• CRISPR base-editing screens have identified lysine mutations and genes affecting DNA damage response. The C17orf53 K494 mutation increased cisplatin sensitivity by disrupting RPA interactions, while STK35 emerged as a novel DDR regulator. These findings provide insights into genomic stability mechanisms and highlight variants with potential relevance for cancer therapies.
• CRISPR-Cas9 dual editing of BCL11A +58 and +55 enhancers has been shown to enhance HbF induction in HSPCs by disrupting key regulatory motifs. Editing quiescent cells avoided long deletions and micronuclei, preserving HSC engraftment and HbF efficacy in SCD models. This strategy offers improved safety and potency for β-hemoglobinopathy therapies.
• A cascade repair system combining iMXene catalysis and CRISPR/dCas9 delivery enhances probiotics for inflammatory bowel disease. It neutralises reactive oxygen species, activates anti-inflammatory NLRP12, and promotes Lactobacillus rhamnosus colonisation, reducing inflammation and restoring gut flora. Experimental models showed significant intestinal repair and improved health, highlighting the potential for innovative inflammatory disease treatments.
• CRISPR-Cas9-mediated homology-directed repair corrected TSC2 pathogenic variants in patient-derived iPSCs, including a splice acceptor mutation and a missense mutation in the GAP domain. These isogenic lines provide valuable tools for modelling tuberous sclerosis complex and advancing therapeutic development for this autosomal dominant disorder.

Clinical and preclinical

• Vor Bio's Phase 1/2 VBP101 trial for trem-cel - CD34+ cells modified by CRISPR/Cas9 gene-editing to lack CD33 - combined with Mylotarg in high-risk AML post-transplant patients shows promising outcomes. Data highlights include reliable engraftment (100% neutrophil recovery, median 9.5 days), preserved blood counts, and a broadened Mylotarg therapeutic window. Trem-cel manufacturing achieved a high CD33 editing efficiency (median 90%). FDA feedback supports a registrational trial design.
• Beam Therapeutics' BEAM-101 demonstrated robust efficacy in Phase 1/2 BEACON trial for severe sickle cell disease, presented at ASH 2024. All seven patients achieved >60% HbF, <40% HbS, and resolved anaemia. Rapid neutrophil (17 days) and platelet (19 days) engraftment were observed, with normalised hemolysis markers and no post-engraftment VOCs. Safety aligned with busulfan conditioning, confirming BEAM-101's potential for transforming SCD treatment.
• Beam Therapeutics has demonstrated its ESCAPE platform combining base-edited HSCs (BEAM-104) with anti-CD117 antibody (BEAM-103) conditioning in non-human primates. The approach enabled durable HbF production (>80% cells expressing γ-globin), normal hematopoietic function, and reduced toxicity versus genotoxic regimens. Clinical development is planned.
• HuidaGene Therapeutics has dosed the first patient in its MUSCLE trial for HG302, a CRISPR-based therapy targeting Duchenne muscular dystrophy (DMD). Using the proprietary hfCas12Max nuclease for precise exon51 skipping, HG302 is delivered via a single low-dose AAV vector, minimising immune-related risks. This approach aims to overcome safety concerns associated with high-dose AAV therapies, offering a potentially safer, one-time treatment to restore dystrophin production in DMD patients.
• Fate Therapeutics' FT819 - an off-the-shelf CD19-targeted CRISPR-engineered CAR T-cell therapy - showed promising Phase 1 results in moderate-to-severe systemic lupus erythematosus (SLE) with lupus nephritis. In three patients receiving fludarabine-free conditioning, rapid CD19+ B cell depletion, no severe adverse events, and durable remission were observed. The first patient achieved drug-free remission and immune reset by Month 6.
• Poseida Therapeutics has presented promising data at the ASH Annual Meeting on two of its Cas-CLOVER-edited allogeneic CAR-T therapies. Phase 1 results for P-BCMA-ALLO1 in relapsed/refractory multiple myeloma showed a 91% overall response rate in an optimised lymphodepletion arm, including 100% in BCMA-naïve patients. Preclinical findings for dual-targeting P-CD19CD20-ALLO1 revealed superior antitumour activity and demonstrated durable CAR-T reactivation using a T-cell engager.
• Vertex Pharmaceuticals presented long-term data at ASH 2024 showing the durable benefits of CRISPR-Cas9 therapy CASGEVY for sickle cell disease (SCD) and beta-thalassemia (TDT). In SCD, 93% of patients remained free from vaso-occlusive crises for a median of 30.9 months. In TDT, 98% achieved transfusion independence for a median of 34.5 months. Sustained quality-of-life improvements and stable HbF levels underline its transformative potential.
• CRISPR Therapeutics presented promising Phase 1/2 data for CTX112, an allogeneic CRISPR-Cas9-edited CAR-T therapy for relapsed/refractory CD19-positive B-cell malignancies, at ASH 2024. Across dose levels, CTX112 achieved a 67% objective response rate and a 50% complete response rate, with durable remissions over six months. The therapy showed a favourable safety profile with no dose-limiting toxicities or severe adverse events, underscoring its potential as a scalable off-the-shelf CAR-T option.
• Editas Medicine has reported positive interim data from the RUBY trial for severe sickle cell disease of reni-cel (EDIT-301) - autologous CD34+ hematopoietic stem and progenitor cells (HSPCs) edited with CRISPR-AsCas12a in HBG1/2 gene promoters. Among 28 patients, 27 were free of vaso-occlusive events post-treatment, and reni-cel led to sustained increases in total haemoglobin (mean 13.8 g/dL at 6 months) and HbF (48.1%).
• Be Biopharma will soon initiate its BeCoMe-9 trial, evaluating BE-101 for haemophilia B. BE-101 is a therapy using autologous B cells engineered with CRISPR-Cas9 to express human factor IX (hFIX), offering sustained, re-dosable hFIX levels to reduce bleeding episodes. Granted Orphan Drug and Fast Track designations, the therapy aims to demonstrate safety and efficacy in its Phase 1/2 trial, advancing B Cell Medicine as a transformative treatment platform.

Industry

• SNIPR Biome secured up to €20 million from the European Investment Bank under HERA Invest to combat antimicrobial resistance. Using CRISPR-based technology, SNIPR targets multidrug-resistant bacteria like E. coli. The funding supports its lead therapy, SNIPR001, to prevent bloodstream infections, highlighting Europe's commitment to health innovation and preparedness against global biological threats.
• Cellectis has secured the final €5 million tranche of its €40 million credit facility with the European Investment Bank to advance its allogeneic CAR T-cell therapies, UCART22 and UCART20x22. The disbursement includes issuing 611,426 warrants, allowing the EIB to purchase shares at €1.70 each. The tranche matures in six years with a 6% annual interest rate, supporting Cellectis' cell therapy pipeline development.
• ProQR Therapeutics expanded its Rett Syndrome collaboration with RSRT, securing $9.1M to advance AX-2402, an Axiomer RNA editing therapy targeting the MECP2 R270X mutation, into clinical trials. This platform offers the potential to address diverse Rett mutations, impacting a broad patient population. The partnership aims to accelerate transformative therapies for this severe neurodevelopmental disorder with significant unmet needs.
• Editas Medicine is shifting its focus entirely to in vivo CRISPR-based therapies, targeting proof of concept in humans within two years. Preclinical breakthroughs include HBG1/2 promoter editing with tLNPs for HbF induction in sickle cell and beta-thalassemia and high-efficiency liver editing in primates. The company is cutting 65% of its workforce, halting reni-cel development, and extending its cash runway to Q2 2027.
• The UK Medical Research Council has launched two Centres of Research Excellence (CoRE), including the CoRE in Therapeutic Genomics, backed by up to £50 million over 14 years. In partnership with the Innovative Genomics Institute, the Centre will develop scalable, AI-driven approaches to reprogram genetic therapies for untreatable genetic disorders, aiming to reduce costs and accelerate regulatory approval. Initial targets include blood, eye, and brain disorders.
• Chroma Medicine and Nvelop Therapeutics have merged to form nChroma Bio, combining advanced epigenetic editing with programmable non-viral delivery to expand genetic medicine's scope. Backed by $75M in financing, nChroma will advance its lead candidate, CRMA-1001, for hepatitis B and D, leveraging DNA-safe modulation of gene expression. The company aims to pioneer new in vivo therapies for hepatic and extrahepatic diseases.

Detection

• A novel LAMP-CRISPR/Cas12b method enables rapid, single-tube detection of Toxoplasma gondii in environmental samples. Targeting the B1 gene, it combines isothermal amplification, CRISPR-based recognition, and lateral flow strips for visual results. Highly specific and sensitive, it detected nine T. gondii genotypes at 0.1 oocyst sensitivity and showed 100% accuracy across 112 environmental samples, offering a powerful tool for zoonotic disease monitoring.

News from CRISPR Medicine News

• On Wednesday, we published an interview with Howard Wu at Full Circles Therapeutics, who developed a novel circular single-stranded DNA technology that enables highly efficient gene integration in various cell types, achieving up to 70% successful gene integration. The system can carry genetic sequences of up to 20 kb in length, showing promise for CAR-T cell therapy development.