CMN Weekly (26 January 2024) - Your Weekly CRISPR Medicine News

Top picks

• Optimization of CRISPR-Cas9 gene editing in human thyrocyte cells (Nthy-Ori) has been achieved by employing lentivirus and chemical lipids for delivery, and using both classical Cas9 nuclease for double-strand breaks and modified Cas9 for single-strand breaks. The double nickase system, combined with HR vector and chemical transfection, proved effective for precise gene insertion, highlighting the importance of break type in determining repair pathways and reducing off-target effects.

Research

• Using structural similarity and gene co-occurrence analyses on over 66 million viral proteins and 330,000 genomes, researchers have identified novel anti-phage systems, including a Bacteroidota phage protein that inhibits Cas12a and a unique anti-phage protein from Akkermansia muciniphila, termed BxaP. BxaP, independent of BREX and restriction-modification systems, underscores the value of integrating protein structure and gene context in uncovering host-phage dynamics.
• A new study questions the safety of base editing. C-to-G base editing (CGBE) can lead to double-strand breaks (DSBs), central to unintended byproducts. Due to imperfect end-joining processes, CGBE might result in small deletions, aberrant transversions, and chromosomal translocations. Significant small deletions, ranging from 4.0% to 29.2% of total sequencing reads, were found in cell lines and primary cells. The translocations occur at sites between the editing target and off-targets related to Cas9 or deaminase activities.
• Researchers in America have developed a CRISPR-Cas9 strategy to correct a Col1a2 gene mutation in a mouse model of severe Osteogenesis Imperfecta (OI), using adeno-associated viruses (AAVs) for delivery. This approach enhanced bone cell gene editing, effectively reversing OI symptoms by improving bone quality and reducing fractures. It marks a pioneering demonstration of in vivo gene correction for collagen mutations in OI.
• Light-inducible base editing enables precise gene regulation. A new light-inducible RNA base editing tool, padCas13, combines the specificity of CRISPR-Cas13 with the control of light activation and allows for precise, reversible RNA targeting and degradation in mammalian cells, both in vitro and in vivo. This method is particularly relevant for diseases where transient gene expression modulation can have therapeutic benefits.
• A study on compact CRISPR-Cas12m proteins from subtype V-M has revealed their unique interference mechanism in prokaryotic immunity, relying on DNA binding rather than cleavage to block bacteriophage and plasmid invasions. Biochemical and cryo-EM analyses showed how Cas12m effectors act as transcription and replication inhibitors. Further, fusing Cas12m with adenine deaminase enabled efficient A-to-G DNA editing in E. coli and human cells, highlighting the potential of Cas12m for developing novel gene editing tools.
• An American study introduces a new model for CRISPR-Cas9 and DNA deaminase synergy in base editing, showing how Cas9 exposure to DNA enhances deaminase action. This interaction defines editing boundaries and efficiency, creating advanced base editors capable of broad-spectrum genomic edits, promising for precise gene modification.
• A CRISPR-Cas9 strategy activates the FGF18 gene in osteoarthritis chondrocytes using CAP-incorporated exosomes within HAMA hydrogel microspheres, creating an injectable system for sustained gene editing and joint lubrication. This approach promotes cartilage regeneration, reduces inflammation, and prevents ECM degradation, showing promise for osteoarthritis treatment.

Industry

• Prime Medicine has announced that it will receive up to $15 million from the Cystic Fibrosis Foundation to support developing prime editors for treating cystic fibrosis. Prime Medicine will take two approaches: hotspot editing of multiple mutations and using the proprietary technology PASSIGE (Prime Assisted Site Specific Integrase Gene Editing) to address nearly all mutations with a single superexon insertion strategy.
• Synthego has announced a strategic partnership with SeQure Dx, a company focused on off-target analysis for preclinical and clinical gene modification customers. The partnership will provide CRISPR-based therapeutics developers with comprehensive off-target editing analytical services, including best-in-class technology and turn-key end-to-end development solutions.
• HuidaGene Therapeutics has been granted orphan drug designation from the FDA for HG302 for the potential treatment of Duchenne muscular dystrophy. HG302 is a novel, first-in-class CRISPR DNA-editing therapy with hfCas12Max targeting human DMD exon 51 splice-donor (SD) site delivered by one viral vector into the muscles.
• ProQR Therapeutics has presented new data demonstrating robust in vivo editing capabilities of its Axiomer RNA editing technology and reporting up to 70% editing of the actin beta gene ACTB in the liver of non-human primates and mice. Axiomer employs "Editing Oligonucleotides", or EONs, that mediate single nucleotide changes to RNA in a highly specific and targeted way using the molecular machinery ADAR (Adenosine Deaminase Acting on RNA) that is present in human cells.
• Locus Biosciences has received $23.9 Million in funding from BARDA to support its first Phase 2 trial of CRISPR-enhanced bacteriophage therapy, LBP-EC01, for treating urinary tract infections (UTIs) caused by drug-resistant E. coli. LBP-EC01 is a bacteriophage cocktail engineered with a CRISPR-Cas3 construct, and it has previously met all primary and secondary endpoints and demonstrated safety and tolerability in a Phase 1b trial.
• CorriXR Therapeutics has received an undisclosed amount of funding from Cortado Ventures. CorriXR focuses on oncology biotherapeutics development and utilises a proprietary CRISPR-Cas biomolecular tool to disable a tumour cell's genome while not affecting healthy cells.

CRISPR screens

• American researchers have used genome-wide epigenome profiling, epigenome editing, and phenotypic and single-cell RNA-seq CRISPR screening to identify a new class of genomic enhancers that respond to the mechanical microenvironment. These 'mechanoenhancers' could be active on either soft or stiff extracellular matrix contexts, and regulated transcription to influence critical cell functions including apoptosis, mechanotransduction, proliferation, and migration.
• A CRISPR-Cas9 screen has identified 26 genes affecting BCMA expression in Multiple Myeloma (MM), highlighting the roles of γ-secretase and N-glycosylation in regulating BCMA levels, crucial for immunotherapy efficacy. This insight into BCMA regulation may inform strategies to enhance MM treatment​​.

Reviews

• Recent Advancements in Reducing the Off-Target Effect of CRISPR-Cas9 Genome Editing. This review summarises the recent technological advancements in reducing the off-target effect of CRISPR-Cas9 genome editing.
• Data Visualization of CRISPR-Cas9 Guide RNA Design Tools. This overview discusses the importance of a good visualisation summary to interpret information and different ways to represent similar information effectively.
• Seven technologies to watch in 2024. This technology feature in Nature mentions large-fragment DNA insertion by CRISPR as one of next year's most exciting developments.
• Engineering approaches for RNA-based and cell-based osteoarthritis therapies. This review highlights modern genetic medicines that have been clinically approved for other diseases, in addition to emerging genome and cellular engineering approaches, to emphasize their potential as transformative osteoarthritis treatments.

News from CRISPR Medicine News

• At CRISPR Medicine News, we have introduced a new category in our covering of advances in CRISPR gene-editing technology: CMN Special. These are long reads based on multiple interviews with experts in a specific field. Think of them as mini-reviews where we dive deeper into a selected topic and try to educate our readers (and ourselves) about the latest discoveries and challenges. Our first shot was on delivery, and in the workings are new CMN Specials that might take a closer look at, for example, RNA editing, epigenome editing, off-targets, base editing, prime editing, infectious diseases and much more. We will strive to publish a new CMN Special approximately every month, so you can soon look forward to our next long read.
• On Monday, we brought the first article to our new CMN Special series, Gene-Editing Tools: Delivery Methods and Challenges. Gene-editing systems, especially CRISPR-Cas9, have revolutionised genome editing, offering potential cures for genetic disorders, cancers, and other diseases. However, efficient, safe, and specific delivery of these tools to target cells and tissues remains a significant hurdle. We spoke with multiple gene editing experts and discussed the benefits and limitations of the available delivery technologies.