CMN Weekly (9 June 2023) - Your Weekly CRISPR Medicine News

Top picks

• Researchers at ETH Zurich, Switzerland, have used CRISPR-Cas9 to repair non-functional transcriptional elements in the endogenous promoter region of δ-globin to increase the overall expression of adult haemoglobin 2 (HbA2). They inserted multiple transcription factor elements in HUDEP-2 immortalised erythroid progenitor cells and found increases in HBD transcript, from less than 5% to over 20% of total β-like globins. Edited CD34+ hematopoietic stem and progenitors (HSPCs) differentiated to primary human erythroblasts express up to 46% HBD in clonal populations.
• Researchers in China have developed a novel sensitive and specific off-target detection method, AID-seq (adaptor-mediated off-target identification by sequencing), that can comprehensively and faithfully detect the low-frequency off-targets generated by different CRISPR nucleases (including Cas9 and Cas12a). AID-seq is the most sensitive and specific in vitro off-target detection method to date and can be used as a rapid and high-throughput platform to select the best sgRNAs and characterise the properties of new CRISPRs.

Research

• Danish researchers have used CRISPR-Cas9 to identify genes that modulate treatment response to enzalutamide, docetaxel, and cabazitaxel in the castration-resistant prostate cancer cell line C4. Single-gene C4 knockout clones/populations for all genes could validate the effect on treatment response for five genes (IP6K2, XPO4, DRG1, PRKAB1, and RP2).
• Researchers from Repare Therapeutics and elsewhere in the USA report positive clinical results from evaluating camonsertib, a potent and selective oral small molecule inhibitor of Ataxia-Telangiectasia and Rad3-related protein kinase (ATRi) in advanced solid tumours. Patients for the clinical trial were selected using the company's chemogenomic CRISPR screening platform SNIPRx to have ATRi-sensitising mutations in their tumours.
• German researchers present CasTuner, a CRISPR-based toolkit for analogue tuning of endogenous gene expression. The system exploits Cas-derived repressors that are quantitatively tuned by ligand titration through an FKBP12F36V degron domain. CasTuner thus provides an easy-to-implement tool to study dose-responsive processes in their physiological context.
• Spanish researchers report robust CRISPR-Cas9 genetic editing of primary human malignant B cells - i.e., chronic lymphocytic leukaemia (CLL) and mantle cell lymphoma (MCL) cells. The method allows both depletion and overexpression of genes of interest in primary CLL/MCL cells and enable studying the differences underlying their clinical-biological diversity.

Industry

• Parse Biosciences have launched CRISPR Detect, a platform enabling single-cell pooled CRISPR screens at an unprecedented scale. CRISPR Detect brings the scale of existing Parse Evercode technology to single-cell CRISPR screening by allowing users to pair perturbations and transcriptional profiles in up to one million cells in a single experiment. This scale will expand the applications of single-cell CRISPR screening, particularly in drug discovery where cost has limited their use to targeted validation studies.
• Editas Medicine announced favourable initial safety and efficacy data from the first four patients with sickle cell disease (SCD) treated with EDIT-301 in the RUBY trial. Patients 1 and 2 reached normal haemoglobin levels five months post-treatment with EDIT-301. Patients 3 and 4 saw increases in total and fetal haemoglobin at three and two months of follow-up, respectively. The company also announced favourable initial safety and efficacy data from the first transfusion-dependent beta-thalassemia patient treated in the EdiTHAL trial.
• Vycellix - a Florida-based cell and gene engineering company with scientific operations in Sweden - has shown proof-of-concept for its new VY-UC allogeneic cell therapy platform. The company reports that insertion of a novel CD45-engager (VY-UC) into virtually any cell holds the potential to displace complex and costly gene-editing systems such as CRISPR-Cas9 to engineer fully immune privileged cells that in pre-clinical in vitro and in vivo models demonstrate persistence, retention of function, and avoidance of host immune rejection.
• Repare Therapeutics reports initial proof-of-concept monotherapy data from its Phase 1 MYTHIC clinical trial evaluating lunresertib (RP-6306), a first-in-class, oral PKMYT1 inhibitor in advanced solid tumours. The company used its chemogenomic CRISPR screening platform SNIPRx to selectively identify patients most likely to achieve clinical benefit from the drug.

Detection

• Researchers from Brunei have developed a CRISPR-Cas12a-based fluorescence aptasensor for the rapid and sensitive detection of ampicillin. The ssDNA activator is bound to three ampicillin-specific aptamers through complementary base pairings. The fluorescence signal was linearly proportional to the ampicillin target concentration with a 0.01 nM detection limit and a read-out time of 30 min.

Reviews and commentaries

• An Update on the Application of CRISPR Technology in Clinical Practice. This review describes the function and applications of the CRISPR–Cas9 system and delineates how it could be utilised for gene therapy of various human disorders, including cancer and infectious diseases. Moreover, it documents current challenges and potential solutions to overcome obstacles for the effective use of CRISPR–Cas9 in clinical practice.
• CRISPR-Mediated Base Editing: Promises and Challenges for a Viable Oncotherapy Strategy. This review examines the leading base editing technologies, discusses their applications and prospects in tumour research and therapy, and elaborates on their mode of delivery.
• Progress of CRISPR-based programmable RNA manipulation and detection. This review summarises the current understanding of mechanistic and functional characteristics of various Cas effectors; gives an overview of the RNA detection and manipulation toolbox established so far, including knockdown, editing, imaging, modification, and mapping RNA-protein interactions; and discusses the future directions for CRISPR-based RNA targeting tools.
• Natural components as surface engineering agents for CRISPR delivery. This review provides an overview of current research, including the use of lipids, proteins, natural components (like leaf extracts), and polysaccharides to modify the surface of nanoparticles and nanomaterials to improve delivery efficiency, stability, and (in some cases) cellular internalisation ability.
• A systematic review of computational methods for designing efficient guides for CRISPR DNA base editor systems. This review presents the key features, capabilities and limitations of all currently available software, focusing on predictive model-based algorithms. It also summarises existing software for sgRNA design and provides a base for improving the efficiency of available software suites for precise target base editing.
• Current and prospective strategies for advancing the targeted delivery of CRISPR/Cas system via extracellular vesicles. This review focuses on the current status of extracellular vesicle (EV) based CRISPR-Cas delivery systems. It explores various strategies and methodologies to improve loading capacity, safety, stability, targeting, and tracking for EV-based CRISPR/Cas system delivery. Moreover, it discusses the future avenues for developing EV-based delivery systems that could pave the way for novel clinically valuable gene delivery approaches.
• One and Done? How CRISPR Is Changing the Clinical Outlook for Multiple Diseases. This perspective in Inside Precision Medicine discusses the race to be the first with an approved CRISPR therapy, and it evaluates the rapid progress that will likely make 2023 a big year for gene editing in terms of clinical success.

News from CRISPR Medicine News

• On Monday, we reported about new research from Carl June’s lab at the University of Pennsylvania that may be a game-changer for adoptive T-cell immunotherapies. By taking the brakes off T cells, solid tumours can be attacked with surprising efficiency in xenograft mouse models, with complete clearance of disease in some cases. Read our interview with two researchers behind the achievement, PhD candidate David Mai and Dr Neil Sheppard.
• Thursday, we brought an explainer about base editors: What Are Base Editors and How Do They Work? Here we introduce this relatively new class of gene editors that combine the powerful DNA-scanning and sequence-identification capabilities of the CRISPR-Cas9 system with a deaminase enzyme that can introduce single nucleotide polymorphisms in a target sequence, without the intentional generation of a DNA double-strand break. Also, check out our growing list of explainers describing other fundamental aspects of CRISPR and gene editing.