CMN Weekly (14 June 2024) - Your Weekly CRISPR Medicine News

Top picks

• Hope, despair and CRISPR — the race to save one woman’s life: an article published this week in Nature describes the story of one woman’s diagnosis and the powerful efforts made by researchers in India to rapidly develop a gene-editing therapeutic to halt the progression of the rare, genetic central nervous system disorder familial encephalopathy with neuroserpin inclusion bodies (FENIB) and safe her life. The article touches on the challenges faced in developing a timely cure, such as FDA approval and the race to reduce costs for gene therapies, as well as the efforts currently underway to streamline the process.
• Researchers at the University of Texas Southwestern Medical Center have reported a new breakthrough in gene editing of lung stem cells in mice that showcases the potentials of base-editing to treat cystic fibrosis. The team used lung-targeting lipid nanoparticles to deliver CRISPR-Cas9 and adenine base editors to lung stem cells in a mouse model of cystic fibrosis, achieving 70% genome editing efficiency and sustained gene expression. They corrected over 95% of CFTR DNA, restoring protein function to levels comparable with current therapies. The study focused on correcting the common R553X mutation in CFTR, achieving significant restoration of CFTR function in over 50% of lung stem cells. Results were validated in human CF patient cells, showing substantial CFTR protein restoration, with potential for clinical application pending further safety and efficacy validation. The findings were published yesterday in an article in Science. Read our highlight about the study here.

Research

• In an article published this week in Molecular Therapy Nucleic Acids, a team in Poland report a new strategy to treat Duchenne muscular dystrophy (DMD) cardiomyopathy, which is actually the primary cause of death from DMD. They edited iPSC-derived cardiomyocytes with the CRISPR/deadCas9-VP64 system to restore utrophin expression, finding that upregulation of utrophin improved the physiological function of the cardiomyocytes and can compensate for a loss of dystrophin.
• In an article published this week in Nature Biomedical Engineering, researchers report enhancement of prime-editing-assisted site-specific integrase gene editing (PASSIGE) via phage-assisted continuous evolution. The article describes a method of using phages to continuously and periodically enhance the performance of the Bxb1 recombinase enzyme. The study presents this method as a significant advancement in gene integration methods for mammalian genomes. This approach combines the programmability of prime editing with the precision of recombinases to integrate large DNA segments over 10 kilobases. Engineered recombinase variants demonstrated up to 60% donor integration in human cell lines with pre-installed recombinase landing sites, which is a 3.2-fold increase compared to the wild-type recombinase. Notably, integration efficiencies exceeded 30% in primary human fibroblasts, and PASSIGE outperformed the PASTE method of gene integration. This method could provide an exceptionally efficient approach for targeted gene integration in mammalian cells.
• In an article published this week in JCI Insight, researchers explore TANGO2-deficiency disorder (TDD), an autosomal-recessive genetic disease caused by biallelic loss-of-function variants in the TANGO2 gene. The researchers established the first patient-derived induced pluripotent stem cell differentiated cardiomyocyte (iPSC-CM) model to study TDD that replicate key electrophysiological abnormalities seen in the disease. These abnormalities were corrected in iPSC-CMs through adenoviral expression of WT-TANGO2 or CRISPR-mediated correction of the pathogenic variant.
• Researchers in China have introduced a mouse model for spontaneous hyperuricemia, a common metabolic disorder with severe complications. In an article published in the Journal of Cardiovascular Translational Research, researchers describe using CRISPR-Cas9 to generate Uox-/- mice by deleting exons 2-4 of the Uox gene. These Uox-/- mice died by 4 weeks of age. After intervention with xanthine oxidase inhibitor allopurinol (which reduces the levels of uric acid in the body), the mice survived beyond 8 weeks but displayed multiple complications including spontaneous hyperuricemia along with urate nephropathy, cardiovascular disease and cardiometabolic disorders. The researchers present the Uox-/- mouse model as a novel tool for studying hyperuricemia-associated early-onset cardiovascular disorders in humans.
• In an article published in PLOS Genetics, researchers explored the role of long non-coding RNAs in glioblastoma, the most common malignant brain tumour in adults. Using CRISPR inhibition (CRISPRi), they screened for long non-coding RNAs (lncRNAs) critical to glioblastoma invasion and identified LINC03045 as a significant gene. Validation with cultured cancer stem cells showed that knocking down LINC03045 reduced invasion. Analysis of public databases linked LINC03045 to patient survival and tumour grade. Additionally, WASF3, part of the JAK-STAT pathway, was identified as a downstream element of LINC03045. This study positions LINC03045 as a crucial non-coding gene in glioblastoma invasion, highlighting its potential as a therapeutic target for glioblastoma treatment.
• A team of researchers in China used CRISPR-Cas9 loss-of-function screens to investigate ferroptosis as a potential treatment for ovarian cancer. However, resistance to ferroptosis remains a challenge. In an article published in Apoptosis this week, the team identified PAX8 as a ferroptosis resistance protein in GPX4-dependent ovarian cancer. Depleting PAX8 increased sensitivity to GPX4 inhibitors and combining a PAX8 inhibitor with RSL3 (which is small molecule inhibitor of glutathione peroxidase 4) suppressed cancer cell growth and induced ferroptosis in a mouse model. These findings highlight PAX8 as a key therapeutic target, suggesting that combining PAX8 inhibitors like losartan and captopril with ferroptosis inducers could be an effective new approach for ovarian cancer therapy.
• Researchers have investigated the role of non-coding RNAs in the chemoresistance of hepatocellular carcinoma (HCC) in patients infected with Hepatitis B and C viruses. In an article published by Cell Death Discovery, researchers identified several significantly downregulated micro RNAs (miRNAs) in HCC. These miRNAs target genes in the BMP signalling pathway, affecting chemoresistance, invasion, and migration of cancer cells. The study revealed that lncRNA-KCNQ1OT1 sequesters these miRNAs, promoting chemoresistance. Using CRISPR to suppress KCNQ1OT1 in HCC cells enhanced chemosensitivity and reduced metastasis, with tumour regression observed in a mouse model.
• In an article published in Human Molecular Genetics, researchers examined the role of dystrophin protein 71 (Dp71) in tumour survival, noting its dual role as a tumour suppressor in some cancers and an oncogene in others. Using CRISPR-Cas9, they specifically ablated the Dp71f variant in a sarcoma cell line lacking the canonical variant, and found that loss of Dp71f led to significant transcriptomic changes, particularly in genes related to calcium signalling and ECM-receptor interactions. These findings highlight the critical regulatory role of Dp71f in sarcoma cells, suggesting it as a target for future research on dystrophin's functions in cancer.
• Researchers in Australia have developed a highly efficient targeted insertional mutagenesis system, CRIMP, and an associated plasmid toolkit, CRIMPkit, that overcomes limitations of site-directed insertion such as low efficiency and the need for customisation for each target. Find out more in the article published in Nature Communications.
• In a study published in PLoS One this week, researchers used CRISPR-Cas9 genome editing to repair AXIN1-truncated mutations in five hepatocellular carcinoma (HCC) cell lines. AXIN1 is one of the most frequently mutated genes in HCC, but the mechanism by which AXIN1 mutations contribute to HCC development remains unclear. This study provides insights into the effects of repairing AXIN1 mutations on β-catenin signalling, cell viability, and colony formation in HCC cell lines.
• Researchers in the US have addressed efficiency issues in CRISPR prime editing in an article published in eLife this week. They discovered that sequence complementarity between the 5' and 3' regions of pegRNA can hinder its complex formation with Cas9, reducing prime editing efficiency. To overcome this, they developed a pegRNA refolding procedure, which improved efficiencies in zebrafish embryos by nearly 25-fold. Additionally, introducing point mutations to disrupt internal pegRNA interactions resulted in up to a six-fold increase in efficiency.
• In an article published by Nature Communications, researchers introduce CoHIT, a novel CRISPR-based assay that simplifies and accelerates the detection of multiple same-site indels in cancer genes. Using an engineered AsCas12a protein and a single crRNA, CoHIT rapidly identifies NPM1 mutations in acute myeloid leukaemia with high sensitivity, demonstrating its potential for clinical cancer diagnostics and monitoring minimal residual disease.
• Researchers in the US have developed base-editing strategies to convert CAG repeats to CAA in the huntingtin gene, aiming to delay the onset of Huntington's disease by shortening uninterrupted CAG repeats. These strategies use cytosine base editors and guide RNAs to efficiently convert CAG to CAA with high specificity and minimal off-target effects, significantly reducing somatic CAG repeat expansion in HD knock-in mice. Read more in the publication here.

Industry

• Epic Bio will present the highlights of the IND-enabling data package for lead its candidate EPI-321, an epigenetic therapeutic candidate for the treatment of facioscapulohumeral muscular dystrophy. Epic Bio is an epigenetic-editing company that utilises CRISPR technology to modify genes without cutting DNA. Read more in the official press release here.
• Cellectis announced a novel non-viral gene therapy to treat sickle cell disease (SCD). Cellectis leverages TALEN® technology and non-viral gene repair template delivery to develop a clinically relevant gene-editing process in haematopoietic stem and progenitor cells (HSPCs) from SCD patients which results in over 50% expression of normal adult haemoglobin in mature red blood cells. This pre-clinical data supports the therapeutic potential of autologous gene-corrected HSPCs for treating SCD. Read the press release here.

Clinical Trials

• KSQ Therapeutics announced dosing of the first patient in a clinical trial of KSQ-001EX, an experimental tumour-infiltrating lymphocyte (TIL) therapy, in which the SOCS1 gene is inactivated. Data from pre-clinical studies show the potential of KSQ-001EX, as a novel, effective solid tumour treatment through enhanced anti-tumour activity, persistence, and memory formation. Find more details in the press release here.

Reviews

• Delivery of nucleic acid based genome editing platforms via lipid nanoparticles: Clinical applications. Delivery remains a topic of conversation regarding safety and efficacy. Base- and prime-editing technologies, particularly those based on lipid nanoparticle (LNP) delivery, offer precise modifications without double-strand breaks, showing potential for safe, targeted treatments. This review evaluates the progress and challenges in using LNP-encapsulated CRISPR technologies for clinical applications.
• Multiplexed Detection Strategies for Biosensors Based on the CRISPR-Cas System. This review summarises the principles, strategies, and features of multiplexed detection using CRISPR and explores the associated challenges and future perspectives. The review outlines the ongoing challenges faced in CRISPR multiplexed detection such as nonspecific collateral cleavage activity, limited signal reporting strategies, and potential cross-reactions.

Editorials

• CRISPR cures and cancer vaccines: researchers can help to shepherd them to market. This editorial published this week highlights the evolution of personalised medicine, including the successes of CAR T-cell therapy and the potential of novel therapeutics like mRNA cancer vaccines and CRISPR-based therapies for rare disorders. It addresses the future of regulatory agencies, as well as the potential broader benefits of personalised medicine for rare diseases applied to common conditions.

Webinars

• Last week's webinar presented by CRISPR Medicine News and GeneHumdi in which Dr Annarita Miccio from the Imagine Institute in Paris discusses CRISPR Clinical Trials: current progress and future perspectives in ex vivo approaches is available to watch here.
• For the next CRISPR Medicine News and GeneHumdi webinar, Dr Paula Río from the Division of Hematopoietic Innovative Therapies will discuss CRISPR Clinical Trials: current progress and future perspectives in ex vivo approaches. The webinar airs for free on Tuesday June 25 from 15:00 – 16:00 CEST. Sign up is available here.

Billie Pang is a genomics scientist and science writer/communicator based in Dublin, Ireland.

This article was updated on 17th June 2024 to correct an error in the news item concerning KSQ Therapeutics under Clinical Trials. In the original version, it was stated that the SOCS1 gene is activated in KSQ-001EX. This was incorrect; the SOCS1 gene is inactivated in KSQ-001EX.