CMN Weekly (17 January 2025) - Your Weekly CRISPR Medicine News

Some of the best links we picked up around the internet

By: Karen O'Hanlon Cohrt - Jan. 17, 2025

Top picks

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Research

Huntington's disease (HD) is a devastating neurodegenerative disorder caused by the expansion of CAG repeats in exon 1 of the huntingtin-encoding gene, HTT. Strategies to silence the expression of mutated huntingtin protein have been explored as a new therapeutic avenue to treat HD, and recent advances in gene-editing and RNA-targeting raise hopes that new treatments are on the horizon for HD patients. In a recent study, researchers in China sought to silence mutant human HTT exon 1 using CasRx – a programmable CRISPR–Cas system that targets RNA for efficient knockdown and splicing modulation – in conjunction with target-specific guide RNAs. In an article published this week in Molecular Regeneration, they report that targeting mutant HTT RNA with CRISPR/CasRx reduces the expression of diseased huntingtin protein and improves symptoms in multiple models of Huntington's disease.
Type III CRISPR and CRISPR-associated (Cas) systems (type III CRISPR-Cas systems) use guide RNAs to recognise RNA transcripts of foreign genetic elements, and this triggers the generation of cyclic oligoadenylate (cOA) second messengers by the Cas10 subunit of the type III effector complex. In an article published in Nucleic Acids Research, researchers in Switzerland report new insights into the dynamics of cOA synthesis in type III CRISPR-Cas systems and reveal key determinants of second messenger product selectivity, which offer potential new avenues for their engineering.
The CRISPR-derived endoribonuclease Csy4 is a popular tool for controlling transgene expression in various therapeutically relevant settings, but the impact of non-specific RNA cleavage remains poorly understood. To address this gap, researchers in China developed a split-Csy4 architecture that was carefully optimised for in vivo usage. First, they separated Csy4 into two independent protein moieties whose full catalytic activity can be restored via various constitutive or conditional protein dimerisation systems. They then showed that introduction of split-Csy4 into human cells caused fewer perturbations to the endogenous transcriptome compared to full-length Csy4. They demonstrated that the split-Csy4 module was effective in engineering inducible CRISPR- and translation-level gene switches regulated by the FDA-approved drug grazoprevir. Their findings were published in Nucleic Acids Research.
Achondroplasia is the most prevalent short-stature disorder and is caused by missense variants that lead to overactivation of the fibroblast growth factor receptor 3 (FGFR3). While surgical and pharmaceutical treatments can partially improve some disease features, the disease remains incurable. In an article published yesterday in Journal of Clinical Investigation, researchers in the United States describe a genetic approach to treating the disease based on Fgfr3 enhancer deletion, which improves all skeletal features in a mouse model of achondroplasia. Amongst other findings, the team found that deletion of the Fgfr3 enhancer in mice harbouring the orthologue of the most common human achondroplasia variant largely normalised long bone and vertebral body growth, markedly reduced spinal canal and foramen magnum stenosis, and improved craniofacial defects. These findings, together with high conservation of the enhancer in humans, raise the possibility of Fgfr3 enhancer deletion as a novel therapeutic approach for achondroplasia.
Natural killer (NK) cells have gained significant attention as an off-the-shelf, allogeneic cellular therapy due to their cytotoxic profile. However, their activity against solid tumours remains sub-optimal in part due to the upregulation of NK-inhibitory ligands, such as HLA-E, within the tumour microenvironment. In an article published in Molecular Therapy, researchers at various institutes in the United States report that virus-free CRISPR-Cas9-mediated knock-in of a chimeric antigen receptor into KLRC1 gene — which encodes the HLA-E-binding NKG2A receptor — generates potent GD2-specific NK cells, using NK cells isolated from human peripheral blood. They report that genome editing with CRISPR-Cas9 ribonucleoprotein complexes yields efficient genomic disruption of the KLRC1 gene with 98% knockout efficiency and specific knock-in of the GD2 CAR transgene as high as 23%, with minimal off-target activity as shown by various sequencing methods.
In an article published in Nature Reviews Cardiology, researchers from University of Edinburgh (UK) report a CRISPR-based method to manipulate complex genetic regions containing multiple non-coding RNAs (ncRNA). In contrast to traditional approaches that target individual ncRNA transcripts — which typically involve exogenous delivery of synthetic antisense oligonucleotides or small interfering RNAs for downregulation, or miRNA mimics and gene delivery vectors for overexpression — their solution leverages CRISPR activation (CRISPRa) using a catalytically-dead Cas9 and a single guide RNA to target regulatory regions, activating multiple transcripts simultaneously while maintaining natural expression patterns. They tested their method with success on vascular-related genes both in vitro and in vivo, and present their findings as a simpler, more physiologically-relevant approach to genetic manipulation with potential applications in stem cell-based precision medicine.
The development of epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) such as abivertinib has improved the prognosis for certain lung cancer patients with EGFR-driven mutations. However, acquired resistance to EGFR-TKIs poses a significant challenge to the treatment. Using a genome-wide CRISPR-Cas9 screen in lung adenocarcinoma cells, researchers in China identifies integrin subunit alpha 8 (ITGA8) as being a key gene responsible for abivertinib sensitivity. Following its identification in the screen, the team demonstrated that ITGA8 inhibits the proliferation, invasion and migration of lung adenocarcinoma cells, enhances the sensitivity to EGFR-TKIs, improves treatment efficacy, and delays the progression of acquired resistance in H1975 cell xenograft mouse models. Their findings were published this week in Acta Pharmacologica Sinica.
Structural variations (SVs) play important roles in genetic diversity, evolution, and carcinogenesis and are, as such, important for human health. However, it is unclear how spatial proximity of double-strand breaks (DSBs) affects the formation of SVs. To investigate if spatial proximity between two DSBs affects DNA repair, researchers in Denmark used data from 3C experiments (Hi-C, ChIA-PET, and ChIP-seq) to identify highly interacting loci on six different chromosomes. The target regions correlate with the borders of mega-base sized Topologically Associated Domains (TADs), and they used CRISPR-Cas9 nuclease and pairs of single guide RNAs (sgRNAs) against these targets to generate DSBs in both K562 cells and H9 human embryonic stem cells (hESC). In an article published this week in Genome Research, they report that spatial proximity between DSBs is a significant predictor of large-scale deletion and inversion frequency induced by CRISPR-Cas9 in K562 cells, and that this finding has implications for understanding SVs in the human genome and for the future application of CRISPR-Cas9 in gene editing and the modelling of rare SVs.

Clinical

Caribou Biosciences announced earlier this week that it has initiated the GALLOP Phase 1 clinical trial evaluating CB-010 in patients with lupus nephritis (LN) and extrarenal lupus (ERL). In the same press release, the company also highlighted successful execution across its three clinical-stage allogeneic CAR-T cell therapy programmes in haematologic malignancies over the past year and provided an outlook on multiple clinical data catalysts planned for 2025. CB-010 is an allogeneic anti-CD19 CAR-T cell therapy with a PD-1 knockout that is currently being evaluated the ANTLER Phase 1 trial for relapsed or refractory B cell non-Hodgkin lymphoma. During an interview with CRISPR Medicine News, Caribou's Chief Scientific Officer Steve Kanner explained that lupus occurs when B cells produce anti-DNA antibodies, and that lupus patients are often treated with chemotherapy. Studies carried out elsewhere found that lymphodepletion in lupus patients followed by CAR-T cell therapy led to improvements in disease outcome. This can be explained by the fact that the diseased B cells that cause lupus become depleted and then replaced by healthy B cells when the bone marrow replenishes itself after lymphodepletion and CAR-T cell treatment. Read more about Caribou's latest updates in the official press release here.
Korro Bio announced on Monday that dosing is underway in its REWRITE study investigating KRRO-110 as a potential treatment for individuals with alpha-1 antitrypsin deficiency (AATD). You can read more about KRRO-110 in a recent clinical trial update here. See the official press release for the latest updates on the REWRITE study and pipeline updates from Korro Bio.

Industry

Orna Therapeutics and Shanghai Simnova Biotech Co., Ltd. announced earlier this week an expansion of their strategic collaboration to include BCMA (B-cell maturation antigen) as a designated biological target for RNA-based therapeutics development. According to an official press release, this partnership leverages Orna’s groundbreaking circular RNA (oRNA^®) technology and Simnova’s expertise in cell therapy to deliver transformative treatments for patients worldwide.
Earlier this week, the CRISPR licensing company ERS Genomics announced the launch of its Express License platform to provide small research enterprises and start-ups with affordable and rapid access to the world’s largest foundational and essential CRISPR/Cas9 patent portfolio. The Express License has been designed for companies with <15 employees and under $10M in funding to use CRISPR/Cas9 technology for internal research. This non-exclusive license makes the technology more accessible and affordable for small organizations working in gene editing, screening, and genomics research. For more details, see the official press release here.
In a press release published on Monday, Editas Medicine announced its three-year strategic priorities, anticipated 2025 key milestones, and new in vivo preclinical proof of concept data in non-human primates editing haematopoietic stem cells (HSCs) and liver cells, as well as in vivo delivery data in humanised mice to two additional target cell types. According to that announcement, anticipated milestones for 2025 include the declaration of two in vivo development candidates, disclosure of further in vivo HSC data as well as in vivo data in one liver indication, establishment of one additional target cell type/tissue, and continued revenue generation through sublicensing of the company's foundational IP.
ArsenalBio announced on Monday that Bristol Myers Squibb (NYSE:BMY) has exercised its exclusive license option for ArsenalBio’s AB-4000 series, the lead collaboration programme generated under the multi-program agreement signed in December 2020. This milestone further strengthens the collaboration to advance next-generation T cell therapies for the treatment of solid tumours. ArsenalBio developed the AB-4000 series using its CITE technology - a CRISPR-based method that inserts DNA into T cells at a specific site. The inserted DNA contains PrimeR logic gates for selective tumour targeting and shRNA to overcome the tumour environment, aiming to create more effective and safer T cell therapies. Read more in the official press release here.
Tune Therapeutics announced on Sunday the completion of more than $175M in financing led by New Enterprise Associates, Yosemite, Regeneron Ventures and Hevolution Foundation. According to the official press release, the funding will help to speed up the development of the company’s existing pipeline, which is currently headed by TUNE-401 – a clinical-stage epigenetic silencer for chronic Hepatitis B (HBV). The funds will also support the development of additional gene-, cell-, and regenerative therapy programmes already underway at Tune, and to progress the company's broader mission of bringing the power and versatility of epigenetic therapies to bear on common and chronic diseases.
Earlier this week, CRISPR Therapeutics highlighted its strategic priorities and anticipated milestones for 2025. Among the updates were that the ongoing launch of CASGEVY^® continues to gain momentum, and that key updates across several programmes are expected in 2025. The company reports starting 2025 with a strong balance sheet with approximately $1.9 billion in cash, cash equivalents, and marketable securities. Read the official press release here.
Synthego has signed a strategic agreement with AstraZeneca which grants Synthego a global license to manufacture and distribute AstraZeneca's novel CRISPR gene-editing enzyme, eSpOT-ON, recently published as engineered ePsCas9, to the worldwide research community. This nuclease, developed by AstraZeneca, will be paired with Synthego’s best-in-class gRNA to enable improved health outcomes. Under the terms of the agreement, Synthego also receives exclusive commercialization rights including the right to sublicense this nuclease for therapeutic and commercial use. In a press release, Synthego CEO Craig Christianson said: "We are excited to offer significantly lower upfront fees for rights to a leading CRISPR enzyme enabling therapeutic developers to de-risk their fundraising process, and making overall development costs significantly less than with traditional nucleases.” See the official press release for further details.
Be Biopharma announced this week that it has closed a $92M Series C financing round that included participation from new investor Nextech with existing investors including ARCH Venture Partners, Atlas Venture, RA Capital Management, Alta Partners, Longwood Fund, Bristol Myers Squibb, and Takeda Ventures, among others. According to a press release, the funds will be used to generate clinical proof-of-concept for BE-101 in the ongoing BeCoMe-9 Phase 1/2 clinical trial for haemophilia B and to advance BE-102 for the treatment of hypophosphatasia to the clinic.

Detection

To address obstacles often met in CRISPR-based multiplex biomarker detection, such as the need for multiple crRNAs and insufficient sensitivity, researchers in China developed a programmable DNA nanoswitch (NS)-regulated plasmonic CRISPR/Cas12a-gold nanostars (Au NSTs) reporter platform for detection of nucleic acid and non-nucleic acid biomarkers with the assistance of the spatial confinement effect. By programming the target recognition sequence in NS, they could run the assay with just one crRNA to detect both nucleic acid and non-nucleic acid biomarkers. Using this approach, they report that the detection limit decreased by ∼196-fold for miRNA-375 and 122-fold for prostate-specific antigen, respectively, and they could detect the same biomarkers in clinical urine samples for the identification of individuals with and without prostate cancer. Their findings were published this week in Nano Letters.
In an article published in Nanoscale, researchers in China present a graphene field-effect transistor (GFET) based on the CRISPR-Cas system for detecting Mycobacterium tuberculosis. Leveraging the ability of the CRISPR-Cas12a to specifically recognise and cleave target DNA, the team integrated that system onto the FET platform. Utilising its electrical amplification capability, they achieved rapid and sensitive detection without the need for sample pre-amplification, with a limit of detection (LoD) as low as 2.42 × 10^-18 M. They report that Cas12a-GFET devices can differentiate 30 positive cases from 56 serum samples within 5 minutes and highlight their potential in future biological analysis and clinical diagnosis.
Earlier this week in Analytical Chemistry, a team in China report the development of a multiplex digital nucleic acid assay by coupling nucleic acid amplification and Argonaute protein (Ago)-specific detection using parallel droplet fusion facilitated by a SlipChip. The SlipChip can generate a series of droplets to perform multiplex digital loop-mediated isothermal amplification (LAMP), followed by a series of droplets containing Ago reagents for parallel mixing and reactions, resulting in three distinct digital fluorescence signals (FAM, ROX, and Cy5) corresponding to each specific target sequence. The team performed viral load analysis of respiratory viruses, including influenza A, influenza B, and SARS-CoV-2, within 60 min. They also report using the digital LAMP-Ago assay to analyse viral loads in 34 clinical samples.

Reviews

CRISPR-Cas9 Targeting PCSK9: A Promising Therapeutic Approach for Atherosclerosis. This review summarises and discusses ongoing gene-editing approaches targeting PCSK9, designed to lower the risk of cardiovascular diseases via long-term regulation of low-density lipoprotein cholesterol (LDL-C).
Genome engineering with Cas9 and AAV repair templates, successes and pitfalls. The authors of this review summarise the current knowledge of recombinant adeno-associated virus (rAAV) transduction, data on its use in rodent embryos in combination with CRISPR-Cas9 to easily generate sequence replacements or insertions, the limitations of rAAV and the unexpected events observed to date, and the protocol optimisations already in place to facilitate its use in the generation of animal models.
Insights into eye genetics and recent advances in ocular gene therapy. This review provides and overview of the viral and non-viral vector systems used in ocular gene therapy, highlighting their advantages and limitations. The authors explore the potential of emerging technologies like CRISPRCas9 in treating genetic eye diseases, briefly addressing the regulatory landscape, concerns, challenges, and future directions of gene therapy in ophthalmology. Finally, the authors emphasise the need for long-term safety and efficacy data as these innovative treatments move from bench to bedside.
CRISPR detection of cardiac tumor-associated microRNAs. The authors offer a critical discussion of the advances, pitfalls, and future perspectives for CRISPR-based diagnostic systems in detecting micro RNA (miRNA), focusing on the diagnosis and prognosis of cardiac tumours.