CMN Weekly (15 December 2023) - Your Weekly CRISPR Medicine News

Top picks

• Marking a new era in the treatment of rare disease, Vertex Pharmaceuticals and CRISPR Therapeutics announced last Friday that the US FDA has approved their joint CRISPR-based therapy CASGEVY™ (exagamglogene autotemcel, exa-cel) for the treatment of severe sickle disease. Approximately 16,000 patients 12 years of age and older with severe sickle cell disease may now be eligible for this one-time treatment in the United States, and multiple authorised treatment centers have been activated. Exa-cel is a one-time gene-edited cell therapy. Specifically, CRISPR-Cas9 is used to disrupt the BCL11A gene in a patient’s own haematopoietic stem cells ex vivo, and the engineered cells are then transplanted back into the patient where they express foetal haemoglobin to restore healthy red blood cell levels. A decision from the FDA regarding the approval of exa-cel for the treatment of beta-thalassemia is expected early next year.

Research

• Researchers at various institutions in the US address the challenges in developing predictive and interpretable models that can improve our understanding of how enzymatic pathways function as well as how their dysregulation contributes to disease. In an article published yesterday in Nature Computational Science, they introduce Elektrum, a deep learning framework based upon in vitro kinetic assays to rapidly hypothesise an ensemble of high-quality kinetically interpretable neural networks (KINNs) that predict reaction rates. It then employs a transfer learning step, where the KINNs are inserted as intermediary layers into deeper convolutional neural networks, fine-tuning the predictions for reaction-dependent in vivo outcomes. When applied to predict CRISPR–Cas9 off-target editing probabilities, the team could show that Elektrum achieves improved performance, regularises neural network architectures and maintains physical interpretability.
• Researchers at the Gladstone Institutes in San Francisco have created the most detailed and intricate map to date of how the human immune system functions. The team, led by Alex Marson, MD, PhD who is a senior investigator at Gladstone, used base editing to probe the detailed molecular structures that regulate human T cells. Specifically, they focused on more than 100,000 genomic sites spanning almost 400 genes in T cells, to uncover exactly which nucleotides govern how immune cells respond to stimuli. Their findings, published this week in Nature, may offer explanations to help address and overcome the limitations of current immunotherapies as well as identify new drug targets for cancer and autoimmune diseases.
• Researchers in Australia and the US have used genome-wide CRISPR screening to identify a role for ARRDC3 in TRP53-mediated immune responses. Using lymphoma cells, they conducted the screen to identify novel inhibitors of tumour expansion that are induced by the tumour suppressor TRP53. They discovered that disruption of Arrestin domain containing 3 (ARRDC3) increases the survival and long-term competitiveness of MYC-driven lymphoma cells when treated with anti-cancer agents that activate TRP53. Arrdc3 deletion in mice caused perinatal lethality due to various developmental abnormalities, including cardiac defects. They note that the absence of ARRDC3 markedly accelerated MYC-driven lymphoma development, and propose that ARRDC3 is a new mediator of TRP53-mediated suppression of tumour expansion, which may open new avenues to harness this process for cancer therapy. Their findings were published yesterday in Nature Cell Death and Differentiation.
• Recombination-activating genes (RAG1 and RAG2) are critical in lymphoid cell development, and mutations in either of these genes lead to diseased states ranging from immune dysregulation to severe combined immunodeficiencies (SCID), causing life-threatening infections and death early in life without haematopoietic cell transplantation (HCT). In an article published yesterday in Blood Advances, a team of scientists from multiple US institutes report a feasibility study using the CRISPR-Cas9-based "universal gene-correction" approach for the RAG2 locus in human haematopoietic stem/progenitor cells (HSPCs) from healthy donors and one RAG2-SCID patient. They demonstrate restoration of RAG-mediated recombination following gene correction of RAG2-SCID-derived HSPCs, resulting in the development of TCR ab and gd CD3+ cells and single-positive CD4+ and CD8+ lymphocytes. They also demonstrate in vivo rescue of B-cell development, with normal IgM surface expression and a significant decrease in CD56bright NK cells. The authors propose that their findings support the development of a gene-correction therapy to benefit RAG2-deficient patients.
• In an article published online this week in Cell Systems, a team in the US report their efforts to improve our understanding of guide RNA design rules and cellular toxicity resulting from off-target or collateral RNA cleavage. They quantified the performance of over 127,000 RfxCas13d (CasRx) guide RNAs and systematically evaluated seven machine learning models to build a guide efficiency prediction algorithm orthogonally validated across multiple human cell types. Deep learning model interpretation revealed preferred sequence motifs and secondary features for highly efficient guides. They then identified and screened 46 novel Cas13d orthologs, finding that DjCas13d achieves low cellular toxicity and high specificity-even when targeting abundant transcripts in sensitive cell types, including stem cells and neurons. Finally, they could apply the new Cas13d guide efficiency model to DjCas13d, illustrating the power of combining machine learning with ortholog discovery to advance RNA targeting in human cells.

Industry

• Biotech startup Tome Biosciences emerged from stealth this week with $213 million in venture funding to develop a new gene-editing technology it believes can overcome some of the limitations of existing methods. Tome's technology, which is called programmable genomic integration (PGI), is based on research licensed from MIT, and allows insertion of varying sizes of genetic material anywhere in the genome without damaging or breaking DNA. Tome initially plans to develop gene therapies for liver disorders and cell therapies for autoimmune disease.
• Editas Medicine announced this week that it had entered into a licence agreement with Vertex Pharmaceuticals. Under the terms of the agreement, Vertex will obtain a non-exclusive license for Editas Medicine’s Cas9 gene-editing technology for ex vivo gene-editing medicines targeting the BCL11A gene in the fields of sickle cell disease and beta thalassemia, including CASGEVY™ (exagamglogene autotemcel). This agreement extends Editas Medicine’s cash runway into 2026.
• Arbor Biotechnologies has announced a collaboration with Ginkgo Bioworks to advance the discovery and development of precision gene editors. The collaboration will leverage Ginkgo’s R&D services to further optimise Arbor’s novel precision editors towards the development of new therapies. Arbor's gene editors demonstrate unique protospacer adjacent motifs, varied cut types, smaller editing technology, and high specificity.
• Earlier this week at the annual American Society of Hematology (ASH) meeting, Vertex Pharmaceuticals shared positive results from the pivotal trials of CASGEVY^™ (exagamglogene autotemcel) in two oral presentations. The data pertains to 96 patients (44 sickle cell disease and 52 transfusion-dependent beta thalassemia patients) treated with CASGEVY, with the longest follow-up of more than four years, and continues to demonstrate the durability of the treatment. New data illustrating improvements in patient-reported outcomes after treatment with CASGEVY were also featured in poster presentations at ASH.
• At this year's annual ASH meeting, Allogene Therapeutics presented a comprehensive review of all patients in the ongoing Phase 1 ALPHA/ALPHA2 trials demonstrating that adding investigational ALLO-647 to the standard lymphodepletion regimen can yield durable responses and a safety profile in line with approved autologous CAR-T cell therapies. ALLO-647 is an anti-CD52 monoclonal antibody designed to suppress the host immune system and allow CAR-T cells to stay engrafted in order to achieve full therapeutic impact.
• Precision BioSciences announced earlier this week the approval of the first clinical trial application of the ARCUS gene-insertion programme by its partner iECURE. Precision is advancing its proprietary ARCUS® platform to develop in vivo gene-editing therapies for gene insertion, excision, and elimination, and its partner iECURE has now received approval from the Australian Therapeutic Goods Administration for the initiation of a first-in-human Phase 1/2 trial evaluating ECUR-506, which incorporates an ARCUS nuclease, for the treatment of ornithine transcarbamylase deficiency in paediatric or neonatal patients.
• Poseida Therapeutics presented positive early efficacy and safety data from its ongoing Phase 1 trial of P-BCMA-ALLO1 in relapsed or refractory multiple myeloma (MM) at this year's ASH meeting. P-BCMA-ALLO1 is an allogeneic gene-edited CAR-T cell therapy engineered to target the B cell maturation antigen, which is primarily expressed by malignant and normal plasma cells and by some mature B cells, and which is the most widely studied target in CAR-T approaches to MM.
• ERS Genomics Limited, which was formed to provide broad access to the foundational CRISPR-Cas9 intellectual property co-owned by Dr. Emmanuelle Charpentier, has announced that its second Japanese Patent (JP6692856) was upheld for the second time, in response to an invalidation challenge. The patent, filed by Dr. Charpentier, together with The Regents of the University of California and University of Vienna, was also upheld previously by the Japanese Patent Office (JPO) in 2021. Read the full press release here.

Detection

• A team in China reports a rapid extracellular vesicle (EV) aggregation induced in-situ microRNA detection technology based on cationic lipid-polymer hybrid nanoparticles encapsulating a cascade system of catalytic hairpin assembly and CRISPR-Cas12a (CLHN-CCC). The assay, which was designed to improve the possibilites for timely internal RNA detection for cancer diagnostics, allows for EV enrichment in three-dimensional space and in-situ detection of internal microRNAs in one step within 30 min. The team demonstrates enrichment efficiency of greater than 90% for artificial EVs, cell-secreted EVs and serum EVs, which is 5-fold higher than that of traditional ultracentrifugation. The findings were published in Biosensors and Bioelectronics.
• In an article published yesterday in Microchimica Acta, a team in China present a novel nucleic acid aptamer nanoprobes-mediated hairpin allosteric and aptamer-assisted CRISPR system for the detection of Streptococcus pneumoniae and Staphylococcus aureus. The fluorescence assay, which can be completed in 55 minutes, leverages the hairpin allosteric effect caused by the aptamer binding to the target bacteria, whereby the detection of S. pneumoniae is first achieved through changes in fluorescence due to FRET. Subsequently, Cas12a protein is added to detect S. aureus. The amplified output signal is triggered by two methods to ensure the sensitivity of the method: the synergistic FRET effect is achieved by the assembly of multi-aptamer through the conjugation of streptavidin–biotin, and the trans-cleavage function of CRISPR/Cas12a. Under optimised assay conditions, the team achieved high sensitivity (a detection limit of 135 cfu/mL) and broad-concentration quantification (dynamic range of 10³-10⁷ cfu/mL) of S. pneumoniae.

Reviews

• Antimicrobial resistance expansion in pathogens: a review of current mitigation strategies and advances towards innovative therapy. This review considers the specifics of some of the current antimicrobial resistance (AMR)-mitigating strategies, while noting their drawbacks, and discusses advances in CRISPR-based technology as an important point-of-care tool for tracking and curbing AMR in our fight against a looming 'post-antibiotic' era.
• Nanoparticle-mediated delivery of non-viral gene editing technology to the brain. This review introduces the three main gene-editing nucleases (zinc finger nucleases, transcription activator-like effector nucleases (TALEN), and CRISPR-Cas9) as non-viral treatments for neurologic disorders, the delivery barriers associated with brain targeting, and the current non-viral techniques used for brain-specific delivery. The authors highlight the challenges and opportunities for future research the field field that could lead to blood-brain barrier bypassing therapeutic gene editing.

Perspectives

• A CRISPR pioneer looks back as the first gene-editing therapy is approved. CRISPR pioneer Luciano Marraffini, who is credited as being one of the first scientists to elucidate how CRISPR-Cas systems work at the molecular level, shares his thoughts on the clinical applications of CRISPR, following the recent approval of the first-ever gene-edited therapy by the US, UK and Bahrain medicine regulatory authorities.

News from CRISPR Medicine News

• In this week's clinical trial update, we shared news from Caribou Biosciences, which is getting closer to Phase 3 with its gene-edited cell therapy candidate for large B-cell lymphoma, CB-010, as well as positive safety and efficacy data from Editas Medicine's ongoing haemoglobinopathy trials of EDIT-301. Read the article here.