CMN Weekly (31 March 2023) - Your Weekly CRISPR Medicine News

Top picks

• In an article published yesterday in Science, a tead led by base-editing pioneer David Liu shows that base editing can rescue spinal muscular atrophy (SMA) in cells and in mice. Their approach involved genome editing of SMN2, an insufficient copy of SMN1 (mutations in which are a major cause of SMA) harbouring a C6>T mutation, to permanently restore SMN protein levels and rescue SMA phenotypes. Adeno-associated virus (AAV)9-mediated base editor delivery in a mouse model of SMA yielded 87% average T6>C conversion, improved motor function, and extended average lifespan, which was enhanced by one-time base editor+nusinersen co-administration. Nusinersen (marketed as Spinraza) is an approved antisense oligonucleotide therapy for SMA.
• ‘Astonishing’ molecular syringe ferries proteins into human cells. This news piece in Nature describes a recent study led by CRISPR pioneer Feng Zhang, that demonstrates delivery of potentially therapeutic proteins into human cells grown in the laboratory, by exploiting a molecular ‘syringe’ that some viruses and bacteria use to infect their hosts. Although it's early days yet, the approach could hold promise for the delivery of protein-based therapeutics as well as gene-editing therapeutics to human cells. The original study was published in Nature earlier this week.

Industry

• Caribou Biosciences announced this week that it is ready to initiate the dose expansion portion of its ongoing CB-010 ANTLER Phase 1 trial in second-line large B cell lymphoma patients. CB-010 is a CRISPR-edited anti-CD19 allogeneic CAR-T cell therapy being evaluated in patients with relapsed or refractory B cell non-Hodgkin lymphoma. The candidate was well tolerated at all 3 dose levels evaluated in a recently completed dose escalation portion of the ANTLER trial.
• Caribou Biosciences also announced this week that the first patient has been dosed in the CaMMouflage Phase 1 Trial of CB-011, an allogeneic anti-BCMA CAR-T cell therapy. CB-011 is being developed for the treatment of relapsed or refractory multiple myeloma and is the second candidate from Caribou's pipeline to enter clinical trials. Read more about Caribou's unique approach to therapeutic gene editing in our recent interview with the company's chief scientific officer here.
• At the start of this week, CRISPR Therapeutics and Vertex Pharmaceuticals announced a new licensing agreement to accelerate the development of Vertex’s hypoimmune cell therapies to treat type 1 diabetes. The non-exclusive agreement will allow Vertex to access CRISPR Therapeutic's CRISPR-Cas9 gene-editing technology in exchange for an up-front payment of $100 million. CRISPR Therapeutics will be eligible for up to an additional $230 million in research and development milestones and receive royalties on any future products resulting from this agreement.
• Israel-based Trobix Bio announced that it has raised $3 Million from private-investor group Chartered Group to advance its pipline of precision microbiome oncology therapeutics. The company is utilising CRISPR, phage, and synthetic biology technologies to develop new therapies that address the gastrointestinal side effects of cancer treatments as well as other gastrointestinal diseases impacted by the microbiome.

Research

• In an article published yesterday in Nature Biotechnology, a team of researchers in the U.S. and Canada describe an inhalation-based method to deliver CRISPR mRNA to the mouse lung using improved lipid nanoparticles (LNPs). Using a high-throughput synthesis platform, they generated and screened a library of 720 biodegradable ionisable lipids to build inhalable delivery vehicles for mRNA and CRISPR–Cas9 gene editors. The study identified a nanoparticle formulation that achieves moderately efficient editing in the mouse lung after intratracheal delivery of CRISPR RNA–LNPs, and provides a path forward for gene-edited therapies for lung diseases.
• In an article published yesterday in Nature Communications, scientists in Korea and Singapore report that of two widely used Cas9 nickase (nCas9) variants, nCas9 (H840A) but not nCas9 (D10A) can cleave both strands of genomic DNA, producing unwanted DSBs, albeit less efficiently than wild-type Cas9. nCas9s are created in the lab by replacing key catalytic amino acid residues in one of the two nuclease domains of S. pyogenesis Cas9 (SpCas9). nCas9s produce nicks or single-strand breaks and are used for paired nicking, homology-directed repair, base editing, and prime editing. Upon introducing additional mutations and incorporating nCas9 (H840A) into a prime editor, the team observed a dramatic increase in the frequency of correct edits, but not unwanted indels in vitro.
• A team in China report the development of a new surface-enhanced Raman scattering (SERS) detection method using a catalytically-dead Cas9 (dCas9) and an enzyme catalysis amplification reaction, which achieved a simple and rapid detection of low-content human papilloma virus (HPV) genes. In the assay, the CRISPR/dCas9/guide RNA complex was anchored above a magnetic bead, which can precisely capture target DNA sequences, exhibiting high selectivity for HPV genes. When biotinylated target DNAs are present, they can bridge a streptavidin-modified horse radish peroxidase (HRP) to the magnetic bead, producing an HRP-decorated conjugate that allows rapid detection. The findings were published yesterday in Analytical Chemistry.
• Researchers at St. Jude Children's Research Hospital (U.S.) present CRIS.py, a simple and highly versatile Python-based programme for analysing next-generation sequencing data for genome-editing outcomes. The new programme can be used to analyse sequencing results for any kind of modification or multiplex modifications specified by the user. CRIS.py runs on all fastq files found in a directory, thereby concurrently analysing all uniquely indexed samples. CRIS.py results are consolidated into two summary files, which allows users to sort and filter results and quickly identify the clones (or animals) of greatest interest. The findings were published today as a chapter in the Methods in Molecular Biology book series.
• Another chapter in the Methods in Molecular Biology book series describes and illustrates a step-by-step procedure for editing the genome of skeletal muscle satellite cells in vivo, using a muscle-specific system leveraging Cre-dependent Cas9 knockin mice and adeno-associated virus (AAV)9-mediated sgRNA delivery.
• Scientists in Hong Kong describe a novel CRISPR-based approach to loss-of-function studies, by developing a pair of switches that are independently controlled by both inducible promoters and degrons. The system enables toggling between two constructs with comparable kinetics and tightness. The findings were published yesterday in Journal of Cell Science.
• A team in the UK and Brazil report CATSH, a CRISPR-assisted diagnostic test for Schistosoma haematobium, a major neglected tropical disease caused by parasitic worms that is targeted for elimination as a public health issue by 2030. Combining recombinase polymerase amplification (RPA), Cas12a-targeted cleavage and portable real-time fluorescence detection, the team showed that CATSH exhibitis high analytical sensitivity, consistent detection of a single parasitic egg and specificity for urogenital Schistosoma species. The findings were published earlier this week in Scientific Reports.
• In a preprint under review at Cell Press, a team in the U.S. and Denmark describes a simultaneous knock-out knock-in genome-editing strategy in human haematopoeitic and progenitor stem cells using CRISPR-Cas9 and homology-directed repair. The team demonstrates that their approach potently inhibits CCCR5- and CXCR4-tropic HIV-1 infection. Read the preprint here.

Reviews

• Transgenesis and Genome Engineering: A Historical Review. This review chapter summarises the milestones in the transgenesis and genome-engineering fields from the 1970s to date. Methods involving bacterial artificial chromosomes (BACs), yeast artificial chromosomes (YACs), CRISPR, TALENs, and zinc finger nucleases are discussed.
• Therapeutic perspective for children and young adults living with thalassemia and sickle cell disease. This review presents the most recent advances and future perspectives in thalassemia and sickle cell disease treatment, including new drugs, gene therapy, and gene editing, and the current clinical trial status in the paediatric populations.

Interviews

• Editing the cell’s transcripts. For cases where gene editing simply won’t work, biochemist Aseem Ansari, who is chair of chemical biology and therapeutics at St. Jude Children’s Research Hospital, is working on a new idea: changing how cells regulate genes. Read the interview in Drug Discovery News here.

News from CRISPR Medicine News

• On Monday, we published an interview with Assistant Professor Ryan Jackson of Utah State University (U.S.) and Professor Chase Beisel of the Helmholtz Institute for RNA-based Infection Research in Germany. The duo's recent collaboration led to the discoverythat upon recognition of an RNA target, Cas12a2 cleaves all the other nucleic acids present, destroying the bacterial cell and preventing bacteriophage from replicating. Check out the interview here.