CMN Weekly (11 March 2022) - Your Weekly CRISPR Medicine News

Top picks

• Chinese researchers find that a new Cas9-fusion enzyme can significantly suppress chromosomal translocations and large deletions. They fused Cas9 to three prime repair exonuclease 2 (TRX2) to create an exo-endonuclease, Cas9TX, that prevents perfect DNA repair and avoids repeated cleavage.
• A new approach for Duchenne Muscular Dystrophy (DMD) therapy targets the patient cohort with multi-exon duplications in the DMD gene. Researchers in the UK show that the expression of a single CRISPR-Cas9 nuclease targeting a genomic region within a DMD duplication can restore the production of wild-type dystrophin in vitro and lead to approximately 50% dystrophin protein restoration in treated myoblasts.

Research

• Researchers in Italy have achieved efficient and inducible gene editing of the DM1 protein kinase (DMPK) gene both in vitro and in vivo in patient-derived cells and a mouse model, respectively. Mutations in DMPK cause the most common dominant neuromuscular disorder, myotonic dystrophy type 1 (DM1). The results were achieved by a dual-vector approach delivering promotor driven Cas9 nuclease and tetracycline repressor-based guide RNAs into the cells.
• American researchers have compared zinc finger nucleases (ZFNs) and CRISPR-Cas9 gene editing systems to edit hematopoietic stem and progenitor cells (HSPCs). The authors conclude that CRISPR-Cas9 RNP gene editing is more stable and efficient than ZFN mRNA-based delivery, partially due to intracellular RNase activity. They suggest co-delivered RNase inhibitors as a strategy to enhance the expression of gene-editing proteins from mRNA intermediates.
• Researchers in China have used CRISPR-Cas9 to correct concurrent α- and β-thalassemia in patient-derived hiPSCs. The authors suggest that, in the future, the corrected hiPSCs can be applied for autologous transplantation in patients with concurrent α- and β-thalassemia.
• Leveraging synthetic peptide nucleic acids (PNAs) to bind RNA with unusually high affinity to create, American researchers have created gRNA spacer-targeted, or ‘antispacer’, PNAs as a tool to modulate Cas9 binding and activity in cells. The authors also show that short PAM-proximal antispacer PNAs achieve potent cleavage inhibition (over 2000-fold reduction) and that PAM-distal PNAs modify gRNA affinity to promote on-target specificity.
• American researchers have studied the off-target effects of various CRISPR-Cas13 effectors. They find that the off-target effects of RxCas13d, a commonly used Cas13 effector, can be as strong as the level of on-target RNA knockdown. This might limit their utility in eukaryotic cells and highlights the need for caution when designing and interpreting Cas13-based knockdown experiments.
• A Chinese study finds that CRISPR-Cas9 can induce global chromosome rearrangements that reshape the genome and transcriptome of human cells. The authors used CRISPR-Cas9 to target the highly repetitive human endogenous retrotransposons, LINE-1 and Alu, resulting in a large number of DNA double-strand breaks in the chromosomes.
• American researchers have established a computational framework to guide the experimental determination of functional CRISPR-Cas system PAM sequences. Dubbed Spacer2PAM, the framework is anticipated to facilitate endogenous CRISPR-Cas systems for industrial biotechnology and synthetic biology.

Industry

• SNIPR BIOME has opened a new BSL2/GMO2-classified laboratory in Copenhagen, Denmark, among the largest of its kind in Scandinavia and Northern Europe. It will handle clinical samples from the phase 1 clinical trial with SNIPR001 and expand its CRISPR and microbiome portfolio. SNIPR BIOME uses proprietary CRISPR technologies to selectively target microbial pathogens and remodel the microbiome to address critical unmet medical needs.
• Sherlock Biosciences has raised $80 million in a Series B financing led by Novalis LifeSciences and new investors Illumina Ventures, Albany Capital and Catalio Capital Management. This new funding will drive the development of products and partnerships, enabled by the company's CRISPR-based platform for the decentralised diagnostic platform for DNA and RNA detection.
• Allogene Therapeutics announced yesterday that the FDA had granted Fast Track designation (FTD) to ALLO-316, the company's first AlloCAR T solid tumour clinical candidate for treating patients with advanced or metastatic clear cell renal cell carcinoma (RCC). ALLO-316 targets CD70, which is highly expressed in RCC with limited normal tissue expression.
• Intellia Therapeutics has stated in response to the recent US Patent and Trademark Office decision relating to CRISPR-Cas9 genome editing technology in eukaryotic cells. In short, UC Berkeley lost a years-long CRISPR patent dispute to the Broad Institute of Harvard and MIT. Intellia disagrees with the decision and will continue developing new CRISPR-Cas9-based therapeutics. The company does not expect the ruling to impact its ability to discover, develop, or commercialise future CRISPR-based medicines.
• On the upside for Intellia Therapeutics, the FDA has granted the company orphan drug designation for its ex vivo investigational T cell receptor (TCR)-T cell therapy, NTLA-5001, to treat acute myeloid leukaemia (AML). NTLA-5001 is an autologous TCR-T cell therapy designed to target the Wilms' Tumor (WT1) antigen, which is highly expressed in AML and many other hematologic and solid tumours.

Detection

• A highly sensitive, on-site detection system for the cyanobacterial toxin microcystin-LR (MC-LR) in freshwater is described by Chinese researchers. Signal read-out of the CRISPR-Cas12a-based aptasensor platform can be achieved by either fluorometer (detection limit of ∼3 × 10^–6 μg/L) or lateral flow strips (detection limit of 1 × 10^–3μg/L).

Reviews

• A review by Spanish researchers takes a closer look at mRNA and gene editing late-breaking therapies in liver diseases. They discuss the potential of CRISPR Cas9-based technologies in vivo modification of the cellular genome with therapeutic purposes using gene supplementation, correction, or silencing. The review summarises the different gene-editing strategies applied to treating liver diseases, highlighting their therapeutic efficacy and safety concerns.
• A mini-review by Indian researchers discuss the emerging therapeutic approach using CRISPR-dCas9 to target head and neck cancer epigenetics. The authors suggest that with technological advancements and successful attempts, epigenome editing by CRISPR-dCas9 will have vast therapeutic applications and be widely employed in the near future.
• The mechanism and delivery of the CRISPR-Cas gene editing system is the subject of a review by researchers in China. The authors mainly focus on nanoparticle-mediated delivery.

Highlights from the American Association for Cancer Research (AACR) 2022 Annual Meeting

• Iovance Biotherapeutics will present a poster detailing its preclinical activity and manufacturing feasibility of TALEN modified PDCD-1 knockout (KO) tumour infiltrating lymphocyte (TIL) cell therapy.
• TCR² Therapeutics will present a poster about its CRISPR-engineered off-the-shelf anti-mesothelin T cell receptor fusion construct (TRuC®) T cells.
• CRISPR Therapeutics and Nkarta Therapeutics jointly present a poster that describes the multiplexed gene knockout of CBLB, CISH and CD70 with CRISPR-Cas9. This enhances cytotoxicity of CD70-CAR NK cells and provides greater resistance to TGF-β for cancer immunotherapy.
• Nkarta Therapeutics will present a poster describing its gene-editing strategies for immune masking to extend the pharmacokinetics of allogeneic cell therapies.
• Gracell Biotechnologies will present a poster detailing early results of a safety and efficacy study of CRISPR-edited allogeneic TruUCAR™ GC502 in patients with relapsed/refractory B-cell acute lymphoblastic leukaemia (r/r B-ALL)
• Caribou Biosciences will present preclinical data from its allogeneic anti-BCMA CAR-T cell therapy that is engineered using Cas12a chRDNA technology to treat relapsed or refractory multiple myeloma (r/r MM).

Meetings and webinars

• Integrated DNA Technologies will host a webinar entitled An improved solution for generating large CRISPR HDR knock-ins. The webinar takes place on 22 March 2022 at 10 am.
• Aarhus University, Denmark, is providing a summer course at the bachelor level entitled Genetic Engineering Using CRISPR/Cas. The course is specifically intended for students interested in biomedical research. The course will be held from 8 to 19 August 2022, and the application deadline is 21 March.

Opinions and perspectives

• A feature in Nature suggests that the recent major CRISPR patent decision won’t end the tangled dispute and that fights over who invented the gene-editing technology will become more complex and could carry on for years.

News from CRISPR Medicine News

• Wednesday, we reported that the first patient had been dosed in a CRISPR trial for acute myeloid leukaemia. Intellia Therapeutics recently announced that the first patient had been dosed in its Phase 1/2a CRISPR trial for acute myeloid leukaemia (AML). The new therapeutic candidate, NTLA-5001, is a CRISPR-edited T cell receptor therapy designed to target Wilm's Tumour (WT1) antigen, found on AML and several other blood cancers of certain types of solid cancer.
• This Monday's feature was about finding the secret ingredient for CRISPR-Cas3 editing in human cells. For years, Dr Yan Zhang at the University of Michigan wondered why scientists struggled to adapt certain type I CRISPR systems for gene editing in human cells. Then her lab discovered a hidden Cas protein, Cas11, which turns out to be critical for the function of many type I CRISPR systems.
• Our sister site CARBON - CRISPR AgroBio News - published its second newsletter last Tuesday. Here you can find links to all the latest news about CRISPR in AgroBio, e.g., gene-edited rice with over 10% yield increase, off-target edits in plants and much more.

Huh, Heh, Wow

• The efforts of Ben Lamm and George Church to recreate the woolly mammoth by CRISPR-engineering the genes of Asian elephants have got a helping hand from an additional $60 million in funding. However, a new study by Danish evolutionary biologists suggests that the efforts at best will result in a hairy Asian elephant adapted to live in the cold. The study managed to recover about 95% of the genome of an extinct relative to the Norway brown rat but missed some genes believed to be essential to smell and the immune system. The authors conclude that even a few missing genes in animals' re-created genomes could be problematic.