CMN Weekly (21 February 2025) - Your Weekly CRISPR Medicine News

Top picks

• Japanese scientists have succeeded in CRISPR-Cas9 allele-specific chromosome elimination to rescue trisomy 21 - responsible for Down syndrome - in human cells. By selectively targeting the extra chromosome in induced pluripotent stem cells and fibroblasts, researchers achieved efficient removal, restoring gene expression and cellular function. Temporary knockdown of DNA damage response genes enhanced chromosome loss. This approach, applicable to nondividing cells, could pave the way for future trisomy 21 interventions.
• Using CRISPR-Cas9, researchers developed a rat model of Cri du Chat Syndrome (CdCS) with a 2q22 deletion, replicating key patient traits. The model exhibits cognitive, social, and anxiety-related deficits linked to neuronal and immune dysfunction in the hippocampus and medial prefrontal cortex. Early AAV-Ctnnd2 gene therapy improves cognition but has limited efficacy. This study advances CdCS research and therapeutic prospects.

Research

• Researchers used CRISPR-Cas9 to correct a common EZH2 variant causing Weaver syndrome in humanised mouse embryonic stem cells. While Streptococcus pyogenes Cas9 achieved the highest correction (70.5%), it also altered the nonvariant allele significantly. Staphylococcus aureus Cas9 provided a balanced approach, correcting 52.5% with minimal off-target effects (2.0%), making it a promising candidate for future therapeutic development.
• SCISSOR, an engineered type III CRISPR system, bypasses the 6-nt cleavage rule using gRNAs with bulge loops, enabling flexible RNA excision. It repairs pathogenic frameshift mutations and modifies open reading frames to generate immunogenic poly-epitopes. This approach expands RNA editing capabilities beyond single-base changes, offering potential applications in RNA therapy and biomedical research.
• A new technique developed by Jennifer Doudna and colleagues at Unviversity of California, Berkely, achieves single-molecule resolution imaging of endogenous RNA in live cells. The new approach, smLiveFISH, uses the RNA-targeting CRISPR–Csm complex for real-time tracking of native transcripts without genetic modifications, revealing distinct RNA localisation mechanisms.
• An American study shows, that overexpressed reverse transcriptase (RT) or prime editors (PEs) alter DNA repair in mammalian cells, increasing short insertions and reducing homology-directed repair after Cas9 cleavage. RT is rapidly recruited to DNA damage sites, influencing repair independently of known sensors. A compact PE lacking the RNase H domain reduces this activity, suggesting potential clinical advantages.
• A new CRISPR-Cas9 nucleofection method enables efficient gene editing in iPSC-derived microglia, identifying key lipid regulators. APOE knockout increased lipid accumulation, while a targeted screen confirmed mTORC1, lysosomal, and autophagy-related genes as critical modulators. This study highlights CRISPR-Cas9’s potential for dissecting lipid dysregulation pathways linked to Alzheimer’s disease and neuroinflammation.
• A CRISPR-Cas9 screen identified HOXB13, GATA2, and TFAP2C as key regulators of an androgen receptor (AR) enhancer in metastatic castration-resistant prostate cancer. These factors promote enhancer activation by increasing H3K27 acetylation, chromatin accessibility, and enhancer-promoter looping. HOXB13 also facilitates FOXA1 binding, highlighting its role in AR transcription and resistance to therapy.
• A German study highlights a unique anti-CRISPR strategy by AcrVIB1 that converts Cas13b into a crRNA sink, effectively suppressing CRISPR immunity. AcrVIB1 inhibits CRISPR-Cas13b by binding Cas13b before crRNA association, promoting unproductive crRNA binding and subsequent degradation. This prevents crRNA processing and target RNA cleavage. Cryo-EM analysis shows AcrVIB1 interacts with Cas13b’s helical-2 domain, preventing crRNA stabilisation.
• Using optimised guide RNAs for SpCas9-HF1-plus and AsCas12a, Russian researchers have achieved 60–72% CCR5 knockout efficiency with undetectable off-target effects. Bioinformatics-assisted gRNA design improved target site cleavage, highlighting potential candidates for HIV gene therapy. These findings support the development of precise CRISPR-based strategies to disrupt CCR5, a key co-receptor for HIV entry.

Industry

• Spotlight Therapeutics, known for its cell-specific CRISPR-Cas platform, has shut down. Despite aiming to deliver gene editing therapies without lipid nanoparticles or viral vectors, the company’s approach faced challenges. In preclinical studies, in vivo gene editing achieved low efficiency—around 7% in mice and under 1% in minipigs. With systemic administration hurdles and limited success in local applications like ophthalmology, Spotlight has ended operations, reflecting broader struggles in the biotech sector.

Clinical

• AccurEdit Therapeutics’ ART002, an in vivo CRISPR-Cas therapy for heterozygous familial hypercholesterolemia, has achieved over 90% PCSK9 knockdown and up to 70% LDL-C reduction in a clinical trial. Using lipid nanoparticle delivery, a single dose demonstrated long-term efficacy and an excellent safety profile. ART002 marks the first successful in vivo PCSK9-targeting gene editing therapy, potentially transforming hypercholesterolemia treatment.
• Precision BioSciences’ PBGENE-HBV, an ARCUS-based CRISPR therapy, has demonstrated safety and antiviral activity in the first cohort of the ELIMINATE-B trial for chronic Hepatitis B. A single low-dose administration reduced HBsAg levels in two of three patients without serious adverse events. Designed to eliminate cccDNA and integrated HBV DNA, PBGENE-HBV represents a potential curative approach, with dose escalation and further clinical data expected throughout 2025.

Screening

• CRISPRi screens across six cancer cell lines have identified 32 cis-regulatory elements (CREs) influencing MYC expression and cell growth. While most CREs contact MYC, only a small subset affect growth when silenced. Lineage-specific transcription factors enriched at these CREs show tumour-specific correlations with MYC expression. These findings highlight the complexity of tissue-specific gene regulation at the MYC locus.
• A genome-wide CRISPR screen in fibroblasts from patients with Néstor-Guillermo Progeria Syndrome (NGPS) identified 43 genes that mitigate multiple cellular defects associated with the disease. The findings suggest that the A12T mutation in BAF disrupts protein synthesis, contributing to cellular dysfunction and premature ageing.
• A large-scale reporter assay of 4,041 cancer-associated SNVs has identified 380 regulatory variants and their target genes, linking inherited cancer risk to mitochondrial translation, DNA repair, and Rho GTPase activity. CRISPR knockout screens confirmed some risk genes also support tumour growth. Editing SNV rs10411210 increased RHPN2 expression and RhoA activation, highlighting how single variants can drive cancer-related pathways.
• A CRISPR-based kinome-wide screen in human cardiomyocytes has identified TAOK1 as a key regulator of doxorubicin-induced cardiomyopathy (DIC). TAOK1 suppression reduced DOX-induced cell death, mitochondrial dysfunction, and p38 MAPK activation without affecting cancer cell sensitivity. AAV-mediated TAOK1 silencing improved cardiac function in a DIC mouse model, highlighting TAOK1 as a promising therapeutic target for mitigating chemotherapy-induced heart damage.

Detection

• Researchers developed a CRISPR-Cas13a-based digital detection method for influenza A viral RNA, eliminating the need for polymerase chain reaction. Using droplet microfluidics and microsphere-capture probes, the assay enhances signal intensity, achieving single-molecule sensitivity with a detection limit of 10 copies/μL in under an hour. Validated on clinical and synthetic samples, this method offers a rapid, precise tool for RNA diagnostics.
• A new electrochemical biosensor integrates roll-cycling amplification (RCA) and CRISPR-Cas12a to enhance sensitivity in detecting E. coli-2571. RCA activates Cas12a’s collateral cleavage, altering electrochemical signals on the electrode. The sensor achieves a detection limit of 5.28 CFU/mL with high accuracy. This approach improves biosensor performance and offers a versatile platform for detecting harmful bacteria.
• Chinese researchers have developed a CRISPR-Cas13a-based colorimetric assay using GO@Pt nanozymes for rapid monkeypox virus (MPXV) detection. This microfluidic system couples recombinase polymerase amplification with CRISPR-mediated reporter cleavage, triggering a visible colour change. It detects MPXV at 1 copy/μL within 60 minutes and showed 100% agreement with PCR in clinical samples, offering a sensitive, low-resource diagnostic tool for outbreak control.

Reviews

• Current trends in application of CRISPR/Cas9 in gene editing and diagnostics in Neglected tropical diseases (NTDs). This review explores the application of CRISPR-Cas9 in targeting virulent genes of neglected tropical disease (NTD) parasites, highlighting its potential for gene editing, advanced diagnostics, and associated biosafety concerns.
• Treating neuromuscular diseases: unveiling gene therapy breakthroughs and pioneering future applications. This review highlights advancements in AAV-based gene therapy for neuromuscular diseases, focusing on SMA and DMD, discussing FDA-approved treatments, preclinical progress, and the potential of CRISPR-Cas9 while addressing the need for biomarkers to optimise therapeutic outcomes.

Perspectives

• A perspective in Endpoints News highlights CRISPR’s struggle for commercial success despite scientific breakthroughs. While firms like CRISPR Therapeutics have made strides in gene editing for diseases such as sickle cell and cardiovascular conditions, market confidence has waned. Investors question high costs, competition from existing drugs, and technical challenges. The field is shifting from rare diseases to common conditions, but regulatory and financial hurdles persist.
• A Nature Methods feature explores challenges in vector-based gene delivery. Around 45–50% of lab-made plasmids contain design or sequencing errors, risking experimental validity. AAV and lentiviral vectors present immunogenicity and potential oncogenic risks. Quality control, including Sanger sequencing, is essential. Advances in AAV capsid engineering and alternative delivery methods aim to improve efficiency and safety in research and gene therapy.

News from CRISPR Medicine News

• On Wednesday, we reported that the Bahrain Oncology Centre announced the country's first successful administration of CASGEVY - the world's only approved therapy using CRISPR gene-editing technology - to treat a sickle cell disease patient. It marks the first CASGEVY administration in the Middle East region.