CMN Weekly (29 April 2022) - Your Weekly CRISPR Medicine News

Top picks

• China focuses on ethics to deter another ‘CRISPR babies’ scandal. This writeup in Nature looks at China’s current efforts to implement better ethics training in research institutions. The new directive, which is one of several detailed in a comprehensive ethics statement, is intended to address gaps that were exposed when Chinese researcher He Jiankui created the so-called CRISPR babies - the first babies with edited genomes - in 2018.
• In an article published in Cell this week, scientists from the Center for Genome Engineering, Institute for Basic Science in Republic of Korea presented their findings on transcription-activator-like effector (TALE)-linked deaminases (TALEDs). The newly-developed TALEDs are composed of custom-designed TALE DNA-binding arrays, a catalytically impaired, full-length DddA variant or split DddA originated from Burkholderia cenocepacia, and an engineered deoxyadenosine deaminase derived from the E. coli TadA protein. The authors report that the new enzymes induce targeted A-to-G editing in human mitochondria, and that custom-designed TALEDs were highly efficient in human cells, catalysing A-to-G conversions at a total of 17 target sites in various mitochondrial genes with editing frequencies of up to 49%.

Research

• A new study led by Claudia Kutter at Karolinska Institute in Sweden finds that CRISPR-Cas9 deletions induce adverse on-target genomic effects that lead to functional DNA in human cells. To charactise Cas9-induced genotypic abnormalities in human cells, the team used a droplet-based target enrichment approach followed by long-read sequencing and coupled it to a customised de novo sequence assembly. They uncovered extensive genomic disruptions by Cas9, which involved a genomic duplication and inversion of the target region as well as integrations of exogenous DNA and interchromosomal DNA fragment rearrangements at the double-strand break sites, often at the same time. Despite the altered genomic composition of the target site, the team found that the aberrant fragments were still functional and impacted cell proliferation in vitro. The findings were shared this week on the pre-print server bioRxiv.
• Researchers in Switzerland and Spain report this week that optimised adenine base editing can efficiently restore function in Fanconi Anaemia (FA) patient cells without double-stranded DNA breaks. In a manuscript shared on the pre-print server bioRxiv, the authors describe a proof-of-concept base-editing strategy to address two of the most prevalent disease-causing mutations (in the FANCA gene) in FA patient cells. They found that optimisation of the base editor construct, vector type, guide RNA format, and delivery condition in primary haematopoietic stem and progenitor cells from an FA patient resulted in restored FANCA expression and normal phenoypes.
• A team in China describe in Nature Communications this week how machine learning-coupled combinatorial mutagenesis could aid researchers in the CRISPR field by enabling resource-efficient high-throughput engineering of genome editor activity. Following the generation and cross-validation of ten in silico and experimental datasets of multi-domain combinatorial mutagenesis libraries for Cas9 engineering, the team demonstrated that its approach reduces the experimental screening burden by as high as 95% while enriching top-performing variants by ∼7.5-fold in comparison to the null model.
• In an article published in BMC Biology this week, a team in China reports the use of structure-guided protein engineering to develop AsCas12a-Plus, an engineered AsCas12a variant (from Acidaminococcus sp.) that exhibits increased activity (1.5~2.0-fold improvement) and specificity (reducing off-targets from 29 to 23 and specificity index increased from 92% to 94% with 33 sgRNAs) compared to its wild-type counterpart. These improved properties were retained in multiplex editing and transcriptional activation studies, and disruption of the oncogenic BRAF^V600E mutant with AsCas12a-Plus revealed less off-target activity compared to wild-type AsCas12a without compromising editing efficiency and BRAF^V600E cancer cell killing. The team also report a similar strategy for Cas12a from Lachnospiraceae bacterium (LbCas12a).
• To address mitochondrial deafness, a team in China applied CRISPR-Cas9 gene editing to correct a c.28G > T mutation in induced pluripotent stem cell (iPSCs) lines derived from a hearing-impaired individual. The team report that correction of the pathogenic mutation led to morphologic and functional recovery of patient-derived hair cells, which are the primary sensory receptor cells within the inner ear. The authors argue that their findings provide new insights into the pathophysiology of maternally-inherited deafness and represent a step toward therapies for this disease. The findings were published in Human Molecular Genetics earlier this week.
• Scientists at Wake Forest University Health Sciences recently developed hybrid particles for the co-delivery of Cas9 mRNA and single-guide RNA with normal capsid assembly efficiency. They also report improving lenteviral (LV) vectors for integrated gene expression by including an aptamer sequence in lentiviral genomic RNA, which improved LV particle production and enhanced LV genomic RNA packaging. The findings were recently published in International Journal of Biological Macromolecules.

Industry

• Editas Medicine announced this week that the U.S. Food and Drug Administration has granted Rare Paediatric Disease Designation to EDIT-301, a CRISPR-Cas9-edited cell therapy currently under development for the treatment of transfusion-dependent beta thalassemia and sickle cell disease. Read more in our news update here.
• ERS Genomics, Dublin announced this week that it had finalised a licence agreement with Sumitomo Pharma Co., Ltd., Japan. The agreements grants Sumitomo Pharma non-exclusive access to ERS Genomics' fundamental CRISPR-Cas9 intellectual property portfolio.
• Verve Therapeutics will present comprehensive analyses of off-target editing risk for VERVE-101 at Precision Genome Engineering Keystone Symposia in Keystone, Colorado on April 29^th. VERVE-101 is a single-dose in vivo liver gene-editing treatment candidate designed to edit a single base pair in the PCSK9 gene without creating double-stranded DNA breaks, to reduce disease-driving low density lipoprotein cholesterol (LDL-C). The complans plans to investigate VERVE-101 as a treatment for heterozygous familial hypercholesterolemia, a genetic form of atherosclerotic cardiovascular disease.
• Cellectis announced this week that it had received a $20 Million convertible note under a collaboration agreement with its partner Cytovia Therapeutics. Cellectis is developing custom TALEN® editors for Cytovia to develop gene-edited iPSC-derived natural killer cells for cancer therapy.
• Cellectis announced yesterday the publication of two articles in Nature Communications, providing strong pre-clinical validation of UCART123 to treat acute myeloid leukaemia and blastic plasmacytoid dendritic cell neoplasm. You can read the articles here and here.
• Allogene Therapeutics has received FDA Orphan Drug Designation for ALLO-605, its first TurboCAR™ T cell product candidate, for the treatment of multiple myeloma. You can read more about ALLO-605 in an earlier clinical update here.

Detection

• In an article published this week in Experimental Biology and Medicine, researchers in Thailand present case findings on SARS-CoV-2 detection with their newly designed saliva collection funnel used in combination with a safe, simple, cost-effective and efficient self-collection protocol for the COVID-19 screening process. They show that a sampling and detection workflow that included their previously developed Cas12a-based detection assay could detect variants of concern seen in Thailand during 2021 with high sensitivity and specificity.
• Researchers in the U.S. report in the pre-print server Research Square that sequence-specific capture and concentration of viral RNA by a Type III CRISPR system from Thermus thermophilus enhances the diagnostic capability. Their study advances the possibility of using Type III systems for diagnostics by significantly enhancing the sensitivity of SARS-CoV-2 RNA detection directly from patient samples.
• In an article published this week in ACS Synthetic Biology, scientists in China report the development of a portable one-pot detection assay for Toxoplasma gondii, an opportuntistic parasite that poses a threat to human health and has a signifciant economic impact on the livestock industry. By combining recombinase polymerase amplification (RPA) with Cas12a, the team successed in developing an assay with high selectivity toward the B1 gene amplicon of T. gondii over other parasites with a limit of detection of 3.3 copies/μL. The visual signal readout can be easily realised by a fluorometer or lateral-flow strip. Furthermore, the authors optimised their workflow to extract T. gondii from low-concentration samples, run the assay on a low-cost thermal controller and transport the assay equipment and lyophilised samples in a portable suitcase for rapid on-site detection for field applications in remote areas.

Reviews

• Call for review articles: Frontiers in Genome Editing are now welcoming research and review articles on the topic of gene repair, addition, and replacement strategies for therapeutic genome editing. The submission deadline is August 31^st. See here for more information.
• An Insight into Modern Targeted Genome-Editing Technologies with a Special Focus on CRISPR/Cas9 and its Applications. In this review, scientists in Pakistan discuss and describe the range of currently available genome-editing tools with a particular focus on CRISPR technology and its widespread applications in humans, plants, animals, and microbes. The review also touches upon the challenges currently facing the CRISPR field as well as future perspectives.
• Current and future direction in treatment of HPV-related cervical disease. This review by scientists in Iran details the current treatment approaches to human papilloma virus (HPV)-related cervical pre-cancerous and cancerous diseases. The author discuss the likely future direction of treatment, including vaccines and genome-editing strategies currently being evaluated in clinical trials.

Conferences, podcasts, interviews, and webinars

• CRISPR 2022 - the 15^th annual CRISPR meeting is getting close! This international meeting, which will be held in Cambridge, Massachusetts, will feature exciting research from leaders in the CRISPR field, including discovery and characterisation of new CRISPR-Cas and related systems, structural and mechanistic insights, evolutionary and ecological considerations, as well as genome editing and other applications. Read more and register abstracts and attendance here.
• How CRISPR-Cas9 gene editing is transforming healthcare and agriculture, a decade after its discovery. In this podcast by The Economist entitled: 'Babbage: Editing the code of life', Nobel Laureate Jennifer Doudna explains how CRISPR could revolutionise healthcare and the global food supply as well as how it could contribute in the fight against climate change.

News from CRISPR Medicine News

• For this week's feature article, we spoke with Lucie Guo, MD PhD from Lei Stanley Qi's lab at Stanford University, who recently demonstrated that a newly engineered hyper-active Cas12a variant can regulate the expression of multiple genes in mammalian retinas. Read the interview here.
• In Wednesday's clinical update, we reported that Editas Medicine's CRISPR-edited beta thalassesmia cell therapy candidate EDI-301 has received FDA Rare Paediatric Disease Designation for the treatment of beta thalassemia in children. Read more here.
• On Wednesday, we hosted a very successful webinar on the topic of 'Controllable Genome Editing With Split-Engineered Base Editors'. Our guest speaker was Kiara N. Berríos, who recently obtained a Ph.D. in Biochemistry and Molecular Biophysics from the University of Pennsylvania. You can watch the webinar on-demand for free right here.