CMN Weekly (7 October 2022) - Your Weekly CRISPR Medicine News

Top picks

• Scientists at Yale University report in vivo correction of cystic fibrosis (CF) using non-nuclease-based peptide nucleic acid (PNA) nanoparticles. CF arises as a result of mutations in the CF transmembrane conductance regulator (CFTR) gene, and the team set out to correct the multiple organ dysfunction associated with one particular CF-causing mutation, F508del, by systemically delivering PNA gene-editing technology mediated by biocompatible polymeric nanoparticles. Following encouraging in vitro findings, the team observed that in vivo treatment led to a partial gain of CFTR function in mouse epithelia as well as correction of CFTR in both airway and gastrointestinal tissues with no off-target effects above background. The study findings were published earlier this week in Science Advances.

Research

• A team of chemists based at Northwestern University (Illinois, U.S.) have reported this week the design and evaluation of a new class of CRISPR spherical nucleic acids (SNAs). SNAs are nanostructures that provide privileged access to and across tissues and cell membranes, and this study marks the first time these structures have been explored as a means of facilitating gene editing. Specifically, the team synthesised Cas9 ProSNAs that were comprised of Cas9 cores densely modified with DNA on their exteriors and preloaded with single-guide RNA, and evaluated these for their genome-editing capabilities in multiple cell lines. Full details of the approach and findings were published yesterday in Journal of the American Chemical Society.
• A study published yesterday in Nature Biotechnology demonstrates that a particular variant of SpCas9, known as SpRY, is PAMless in vitro. The study, which was led by Benjamin Kleinstiver at Massachusetts General Hospital and Harvard Medical School, explored the potential of the team's previously reported near-PAMless SpCas9 variant SpRY to serve as a universal DNA cleavage tool for various cloning applications. By performing SpRY DNA digests using more than 130 guide RNAs sampling a wide diversity of PAMs, the team found that SpRY is PAMless in vitro and can cleave DNA at any sequence, including sites that are refractory to cleavage with wild-type SpCas9.
• Scientists in Denmark have solved the crystal structure of the TnsB transposase of type V-K of CRISPR-associated transposons (CASTs). CASTs are mobile genetic elements that co-opted CRISPR-Cas systems for RNA-guided transposition. In an article published earlier this week in Nature Communications, the team present the 2.4 Å cryo-EM structure of the Scytonema hofmannii (sh) TnsB transposase bound to the strand transfer DNA. The findings offers new insights into the mechanisms and events underlying CAST transposition.
• In a not-yet peer-reviewed manuscript shared on the pre-print server bioRxiv earlier this week, researchers in Germany and Amsterdam report CasTuner, a CRISPR-based toolkit that allows analog tuning of endogenous gene expression. In the CasTuner system, the activity of Cas-derived repressors is controlled through a FKBP12^F36V degron domain and can thereby be quantitatively tuned by titrating the small molecule degrader dTAG-13. CasTuner can be applied at the transcriptional level, using the histone deacetylase hHDAC4 fused to dCas9, or at the post-transcriptional level, using the RNA-targeting CasRx.

Industry

• Danish microbiome engineering company SNIPR Biome has launched a non-profit patent licensing programme to enable the field of CRISPR editing in prokaryotes. The company's patent portfolio, which contains more than 20 granted patents in the US and Europe, covers a technology platform that uses CRISPR-Cas to precisely target and edit prokaryotes, such as bacteria. SNIPR Biome's lead programme SNIPR001 is a CRISPR-armed bacteriophage cocktail that targets antibiotic-resistant E. coli infections in blood cancer patients, and the first patients were recently dosed in a Phase 1 trial in the U.S. Read more about SNIPR001 in a previous CMN clinical update here.
• In a press release published this week, Sestina Bio announced using Inscripta’s ONYX® platform to develop a microbial strain ready for scale-up in less than 12 months. The microbial strain in question produces Bakuchiol, a natural retinol replacement. Bakuchiol is a natural and effective skincare ingredient shown to deliver many of the same benefits as retinol, but with antioxidant properties and reduced side effects.
• Allogene Therapeutics announced in a press release published yesterday that it has initiated a potentially pivotal Phase 2 clinical trial of ALLO-501A (ALPHA2 trial) in patients with relapsed or refractory large B-cell lymphoma. ALLO-501A is an anti-CD19 CAR T-cell therapy that is made from healthy donor cells using TALEN-based gene editing, and the company expects to provide an update on the programme toward the end of 2022. Read more about ALLO-501A in a previous CMN clinical trial update here.
• Eligo Bioscience announced this week in a press release the issuance by the U.S. Patent and Trademark Office (USPTO) of an additional landmark patent in the field of CRISPR-based killing of bacteria. US Patent #11,452,765 is the third patent being granted from the WO2014124226 patent family owned by The Rockefeller University and exclusively licensed to Eligo Bioscience. While the two previous granted patents covered pharmaceutical compositions comprising CRISPR delivered by non-replicative vectors, the new patent covers pharmaceutical compositions comprising CRISPR delivered by replicative vectors (engineered phages).

Conferences

The 37^th Annual Society for Immunotherapy of Cancer will be held between the 8th and 12th November in Boston as well as virutally. This year's event will include presentations by many of the companies working in the gene-editing field. We have collected the company names and links to abstract details here:

• CRISPR Therapeutics - Poster presentation
• Century Therapeutics - Two poster presentations
• Poseida Therapeutics - Poster presentation
• Fate Therapeutics - Twelve poster presentations
• Cellectis - Two poster presentations
• Cytovia Therapeutics - Three poster presentations

Detection

• In an article published ahead of print in Analytica Chimica Acta, scientists in China report the development of a novel aptamer-based colorimetric biosensor to detect methicillin-resistant Staphylococcus aureus (MRSA) using a CRISPR-Cas12a system and recombinase polymerase amplification (RPA). The aptamer of silver ion (Ag⁺) pre-coupled to magnetic nanoparticles was employed both as the substrate of trans-cleavage in the CRISPR-Cas12a system and the modulator of a Ag⁺-3,3',5,5'-tetramethylbenzidine (TMB) chromogenic reaction, effectively integrating the CRISPR-Cas12a system with convenient colorimetry. Using triple amplification of RPA, multiple-turnover nuclease activity of Cas12a, and cytosine-Ag⁺-cytosine coordination chemistry, the team could detect MRSA down to 8 CFU mL^-1.

Reviews

• CRISPR-Cas system manipulating nanoparticles signal transduction for cancer diagnosis. This review summarises the working mechanisms of the CRISPR-Cas system for biosensing, as well as examines the strategies behind CRISPR-manipulated nanosensors based on various signal models for cancer diagnosis, including colorimetric, fluorescent, electrochemical, electrochemiluminescent, pressure, and other signals. Finally, the prospects and challenges of CRISPR-Cas-based nanosensors for cancer diagnostic are also discussed.
• CRISPR-Based Diagnostics and Microfluidics for COVID-19 Point-of-Care Testing: A Review of Main Applications. In this review, authors in Iran examine CRISPR-based diagnostic methods and present their benefits and drawbacks in relation to point-of-care testing of suspected SARS-CoV-2 infections at home or in small clinics.

News from CRISPR Medicine News

• In this week's feature article, you can read about the recent of work of researchers led by Alexander Marson at the Department of Medicine, University of California San Francisco, who have developed a new method for high-yield genome engineering in primary cells. Their method employs a hybrid ssDNA repair template and small-molecule cocktails. The use of ssDNA with Cas9 target sequences in homology-dependent repair (HDR) templates instead of dsDNA increased knock-in efficiency and cell yield by two- to three-fold. The small-molecule combinations enhanced HDR and increased knock-in efficiencies by an additional two- to three-fold. Read the full story here.
• Our recent webinar 'Epigenomic Editing Ameliorates Detrimental Effects of Adolescent Alcohol Exposure' by Subhash C. Pandey, PhD, Joseph A. Flaherty, MD Endowed Professor of Psychiatry and Director, Alcohol Research Center, University of Illinois at Chicago, USA is now available to watch on demand. See here for details.

Huh, Heh, Wow

• The key to tastier beer might be mutant yeast—with notes of banana. In a new study published earlier this week in Applied and Environmental Microbiology, Belgian scientists report improving the flavour of contemporary beer by identifying and engineering a gene in yeast and some other alcoholic drinks using CRISPR-Cas9 technology.