CMN Weekly (16 February 2024) - Your Weekly CRISPR Medicine News

Top picks

• In an article published this week in Frontiers in Pharmacology, a team led by Professor Stephanie Cherqui at UCSD’s School of Medicine reports that CRISPR-Cas9-mediated excision of the GAA repeats in the fratraxin-encoding gene, FXN, in iPSCs derived from Friedreich's ataxia patients led to rescue of mitochondrial defects and apoptotic phenotypes. These results build upon previous studies carried out by the same team, which demonstrated that autologous stem cell transplantation using CRISPR-Cas9-mediated excision of the GAA repeats in patients’ CD34⁺ HSPCs led to increased FXN expression and improved mitochondrial functions. Professor Stephanie Cherqui at UCSD’s School of Medicine has spent much of her career dedicated to developing a novel therapy for Friedreich's ataxia, which you can read about in a recent interview with CRISPR Medicine News here.

Research

• Sangamo Therapeutics has shared details of its newest genome-editing platform, a compact zinc finger base editor. In this study, which was published yesterday in Nature Communications, the team demonstrates highly efficient editing of human T cells with favourable specificity by discovering a novel deaminase and pairing it with a zinc finger nickase. The team proposes that the compact size of their zinc finger base editors makes them amenable to packaging within a single adeno-associated virus vector, which raises hope for their potential in future in vivo therapeutic applications.
• Scientists at various institutions in China have developed machine learning-based prediction models to guide the selection of Cas9 variants for efficient gene editing. Using synthetic gRNA-target paired libraries and next-gen sequencing, they compared the activity and specificity of gRNAs used with four SpCas9 variants. Based on their findings, they developed machine learning models to predict the gRNA efficiency and specificity for the four Cas9 variants. Their findings were published in Cell Reports and the machine learning models are available here.
• A team of researchers in the US has presented an exhaustive investigation of 23 Cas12a orthologs, with a focus on their cis- and trans-cleavage activities in combination with non-canonical crRNAs. Through biochemical assays, the team observed that some non-canonical crRNA:Cas12a effector complexes outperform their corresponding wild-type crRNA:Cas12a. Moreover, they observed that the tolerance of Cas12a to non-canonical crRNA is also observed in mammalian cells through INDEL formation. They applied the adaptability of Cas12a:crRNA complexes to detect SARS-CoV-2 in clinical nasopharyngeal swabs, saliva samples, and tracheal aspirates. The findings were published earlier this week in Cell Reports.
• In an article published in Methods in Cell Biology, scientists based at Washington University School of Medicine discuss a high-throughput flow-based approach to study genetic interactions. By using two different Cas9 orthologs and monitoring cell viability at multiple time points, they propose that their approach helps to mitigate the limitations of Cas9 competition and enables assessment of genetic interactions with both essential and non-essential genes at a high temporal resolution.
• To determine whether or not histone deacetylase 2 (HDAC2) function is associated with gastric cancer progression, researchers in Iran deployed CRISPR-Cas9 to knock out the gene encoding HDAC2 in a human gastric cancer cell line (EPG85.257) and evaluated tumourigenesis pathways in the resulting knock-out cells. They found that cell proliferation, colony formation, wound healing and transwell invasion were inhibited in the edited cells, while apoptotic pathways were upregulated. The findings were published yesterday in Epigenomics.
• Targeting the HIV-1 genome using CRISPR-Cas9 has shown great promise towards eliminating HIV-1 viral reservoirs, but whether or not these approaches are effective in removing HIV-1 viral proteins from mixed glia has until now not been systematically evaluated. Scientists in the US report this week that HIV-1 mRNA knockdown with CRISPR-CAS9 enhances neurocognitive function. They evaluated the efficacy of adeno-associated virus 9-CRISPR/Cas9 gene editing for eliminating HIV-1 mRNA from cortical mixed glia in vitro and in vivo (in rats) and found that treatment with CRISPR-Cas9 protractedly, although not permanently, restored the developmental trajectory of temporal processing. Their findings were published this week in the Journal of NeuroVirology.

Industry

• Intellia Therapeutics and ReCode Therapeutics have announced a strategic collaboration to launch novel gene-editing therapies for cystic fibrosis. According to a press release published yesterday, the collaboration combines Intellia’s CRISPR-based platform, including its DNA writing technology, with ReCode’s proprietary Selective Organ Targeting (SORT) lipid nanoparticles to broaden the reach of gene editing to disease-causing targets in the lung. Read more about the SORT technology in our previous interview with ReCode's co-founder Daniel Siegwart.
• Precision BioSciences announced this week that it has received pre-IND feedback from the FDA for its hepatitis B virus (HBV) therapeutic candidate PBGENE-HBV. The feedback is reported to support a clinical development path for PBGENE-HBV, and Precision expects to file an IND application (US) and/or a clinical trial application (CTA, EU) in 2024. The candidate leverages Precision's meganuclease technology, ARCUS, and is specifically designed to eliminate cccDNA and inactivate integrated HBV DNA.
• Precision BioSciences announced in a press release published on Monday that it has received an initial $7.5 million cash payment and equity investment from TG Therapeutics for Azel-Cel in the treatment of autoimmune diseases and other indications beyond cancer. Azel-cel is an allogeneic meganuclease-edited CD19-targeting CAR-T cell therapeutic candidate initially designed to treat relapsed or refractory non-Hodgkin lymphoma. In August 2023, Precision BioSciences announced the completion of a strategic transaction with Imugene Limited for global rights to Azel-cel for cancer. Azel-cel is being evaluated in a Phase 1/2 trial for relapsed or refractory B-cell acute lymphoblastic leukaemia and non-Hodgkin lymphoma.
• The European Commission has approved CASGEVY™ (exagamglogene autotemcel), for the treatment of sickle cell disease transfusion-dependent beta thalassemia in individuals 12 years and older. Read more about CASGEVY in one of our previous articles here.
• Fate Therapeutics is to webcast a conference call on Monday, February 26, 2024 at 5:00 PM ET, reporting fourth quarter and full year financial results for 2023. See press release for more details.
• CRISPR Therapeutics announced yesterday that it will present at the Citi 2024 Virtual Oncology Leadership Summit on Wednesday, February 21, 2024, at 1:00 p.m. ET. See here for details on how to access the live webcast.
• CRISPR Therapeutics has entered into an investment agreement for the sale of approximately $280 million of its common shares to a select group of institutional investors in a registered direct offering, at a price per share of $71.50. This represents a premium of greater than 10% to CRISPR Therapeutics’ 30-day volume-weighted average price. The financing is expected to close on or about February 27, 2024, subject to customary closing conditions. Read the full details in the company's press release.
• Earlier this week, Prime Medicine announced the pricing of an underwritten upsized public offering of 19,200,001 shares of its common stock at a public offering price of $6.25 per share and, in lieu of common stock to certain investors, pre-funded warrants to purchase 3,200,005 shares of common stock at a public offering price of $6.24999 per pre-funded warrant, which represents the per share public offering price of each share of common stock less the $0.00001 per share exercise price for each pre-funded warrant. See the compny's press release for more details.

CRISPR screens

• A team in Japan reports the identification of TFDP1 as a modulator of global chromatin accessibility. According to an article published yesterday in Nature Genetics, the team carried out a genome-wide CRISPR screen combined with an optimised ATAC-see protocol to identify genes that modulate global chromatin accessibility. That screen revealed known chromatin regulators including CREBBP and EP400, as well as several previously unrecognised proteins that modulate chromatin accessibility; these include TFDP1, HNRNPU, EIF3D and THAP11, which belong to diverse biological pathways. ATAC-seq analysis following knockout of those genes revealed distinct and specific effects on chromatin accessibility. Among the main findings were that the transcription factor TFDP1 modulates global chromatin accessibility through transcriptional regulation of canonical histones.
• Poly(ADP-ribose) glycohydrolase (PARG) is a popular therapeutic target for cancer although the specific genetic vulnerabilities that would render cancer cells susceptible to such a therapy remain unclear. Loss of PARG expression has been shown to result in acquired resistance to poly(ADP-ribose) polymerase inhibitors (PARPi) in certain BRCA2;p53-deficient tumours. In an article published yesterday in EMBO Journal, scientists in Swizterland, Netherlands and Czech Republic report that PARG-deficient tumour cells exhibit increased dependence upon EXO1/FEN1-mediated DNA repair. Through whole-genome CRISPR-Cas9 drop-out screens, they identified various genes involved in DNA repair that were essential for the survival of PARG;BRCA2;p53-deficient cells. In particular, their findings reveal EXO1 and FEN1 as major synthetic lethal interactors of PARG loss.

Reviews

• The Present and Future Landscapes of Molecular Diagnostics. This review describes the current status and future directions of molecular diagnostics and encompasses four major techniques: PCR, next-generation sequencing, isothermal amplification methods such as recombinase polymerase amplification and loop-mediated isothermal amplification, and CRISPR-based detection methods. The authors explore the advantages and drawbacks of each technique, describe the overlap between techniques, and examine current clinical offerings.

News from CRISPR Medicine News

• This week's clinical trial update brought news from HuidaGene Therapeutics. The company recently announced that the FDA has granted Orphan Drug Designation to its CRISPR-based therapeutic candidate, HG302. The company is developing HG302 as a novel treatment for Duchenne muscular dystrophy. Read the update here.