CMN Weekly (20 December 2024) - Your Weekly CRISPR Medicine News

Top picks

• CRISPR genome-editing grows up: advanced therapies head for the clinic. This news article in Nature discusses recent developments in gene-editing presented at this year's American Society of Hematology’s annual meeting recently held in San Diego. While celebrating that the first and only approved CRISPR therapy, Casgevy, is working well after one year of approval - showing benefits lasting up to 5 years for blood disorder patients - it highlights a growing tension in the field. Even as new gene-editing treatments are advancing, there's a serious challenge in making these effective but expensive ($2.2 million) and complex treatments available to the patients who need them.

Research

• While capable of targeting oncogenic RNAs, CRISPR-Cas13 typically lacks single-base precision due to mismatch tolerance. By strategically introducing synthetic mismatches in the spacer sequence, researchers at Peter MacCallum Cancer Centre (Australia) designed guide RNAs that selectively silence point-mutated transcripts while sparing wild-type sequences. The used this approach to successfully target oncogenic mutations including KRAS G12, NRAS G12D, and BRAF V600E. Surprisingly, these SNV-selective crRNAs also reduced the collateral activity of RfxCas13d. This advance demonstrates that CRISPR-Cas13 can be reprogrammed for single-nucleotide precision, opening new possibilities for personalised transcriptome editing in cancer treatment. The findings were published this week in Science Advances.
• Optical pooled screening uses fluorescence microscopy to analyse cellular phenotypes at scale, but current methods are limited by their dependence on cytosolic transcript detection. In an article published in Nature Biotechnology yesterday, researchers in Germany introduce Nuclear In-Situ Sequencing (NIS-Seq) as a solution to that challenge. NIS-Seq works by generating bright sequencing signals directly from nuclear DNA, using an inverted phage promoter downstream of the sgRNA to produce multiple RNA copies independently of cellular transcription. The authors demonstrated the versatility of NIS-Seq across eight cell types from two species, enabling genome-scale screens that identified key inflammation pathway regulators.
• In an article published earlier this week in Nature Biotechnology, scientists in Austria introduced CRISPR-StAR, a novel screening technique that addresses the challenges of genetic screening in complex in vivo models by using internally controlled single-cell-level analysis. This method mitigates the noise of heterogeneous growth environments and bottlenecks, enabling robust identification of genetic dependencies in diverse tumour settings. Read the full article here.
• A genome-wide CRISPR-Cas9 screen carried out by researchers in China has identified METTL8 as a key gene driving resistance to lenvatinib, an important first-line treatment for hepatocellular carcinoma (HCC). Subsequent validation experiments found that higher METTL8 expression in lenvatinib-resistant HCC cells and patient tissues correlated with reduced treatment sensitivity. Through compound screening, the researchers discovered Rabdosiin as an effective METTL8 inhibitor that could overcome resistance to lenvatinib. The team propose that METTL8 could serve as both a therapeutic target and a biomarker for lenvatinib treatment in HCC patients. The findings were published in Experimental Cell Research.
• In an article published in PLoS One, researchers in the United States describe a potential genetic targeting approach for metastatic cancer by leveraging naturally occurring mutations that create CRISPR-Cas9 targetable PAM sites. Through whole genome sequencing of pancreatic cancer patients' primary tumours and metastases, the team found that 90% of PAM targets were preserved across tumour sites. Importantly, PAM sites in regions of loss of heterozygosity (LOH) in primary tumours were consistently maintained in metastases, while those in heterozygous regions could be lost. This suggests that targeting truncal LOH regions with CRISPR-based therapy could be a promising strategy for treating metastatic pancreatic cancer.
• A study led by Jennifer Doudna has uncovered how Cas12a initiates DNA target recognition. Through structural and biochemical analyses, the researchers discovered that Cas12a bends DNA and causes nucleotides to temporarily flip out, exposing them for RNA hybridisation. Using cryo-EM imaging and fluorescence techniques, they showed that this DNA destabilisation is essential for target finding and binding. Interestingly, this mechanism is similar to CRISPR-Cas9's approach, despite these protein families having different evolutionary origins and RNA-DNA binding patterns. The findings suggest that RNA-guided DNA interference generally begins with CRISPR-Cas proteins temporarily binding and distorting the DNA helix structure. The findings were published yesterday in Nucleic Acids Research.

Industry

• Arbor Biotechnologies announced yesterday that the FDA has cleared the IND application for ABO-101, a novel gene-editing therapeutic designed to address primary hyperoxaluria type 1 (PH1). The redePHine Phase 1/2 study is designed to evaluate the safety, tolerability, pharmacokinetics, pharmacodynamics, and preliminary efficacy of ABO-101 in both adult and paediatric patients with PH1. ABO-101 is a liver-targeted gene-editing therapeutic designed to be a single-dose treatment for PH1 by causing permanent loss of function of the HAO1 gene in the liver to reduce PH1-associated oxalate production. ABO-101 consists of a lipid nanoparticle licensed from Acuitas Therapeutics, encapsulating messenger RNA expressing a novel Type V CRISPR Cas12i2 nuclease and an optimised guide RNA which specifically targets the human HAO1 gene. See the official press release for further details.
• Precision Biosciences announced earlier this week that it has received Clinical Trial Application approval in Hong Kong to study PBGENE-HBV in the ongoing ELIMINATE-B Phase I trial. PBGENE-HBV is Precision’s lead wholly owned in vivo gene-editing programme designed to cure chronic hepatitis B by eliminating cccDNA, the key source of replicating hepatitis B virus (HBV), and inactivating integrated HBV DNA in hepatocytes. According to the press release, Precision Biosciences is actively recruiting patients for the ELIMINATE-B trial in Moldova and has begun activating a top infectious disease clinical site in Hong Kong as part of its global regulatory and clinical operations strategy.

Detection

• In an article published in Analytical Chemistry yesterday, researchers in China present a new CRISPR/Cas12a-enabled multi-colour visual biosensing strategy for the rapid detection of disease biomarkers. Unlike most other CRISPR/Cas12a-based biosensors developed for point-of-care testing (POCT) which employ fluorescent systems as reporter probes, the newly described method produces a strong visual signal through the action of horseradish peroxidase (HRP) mediating the etching of gold nanobipyramids (AuNBPs) under hydrogen peroxide and 3,3',5,5'-tetramethylbenzidine. In the presence of the biomarker target, the trans-cleavage activity of CRISPR-Cas12a is activated, which results in release of HRP from the reporter probe. The researchers demonstrate the utility of the method using the breast cancer 1 gene (BRCA1) as a proof-of-principle target, sensitive (as low as 30 pM BRCA1) and fast detection (60 minutes or less).

Reviews

• Chemical engineering of CRISPR–Cas systems for therapeutic application. This review focuses on chemical modification and engineering approaches for gRNAs to enhance or enable CRISPR-based therapeutics, emphasising Cas9 and Cas12a as therapeutic paradigms. Issues that chemically-modified gRNAs seek to address, including drug delivery, physiological stability, editing efficiency and off-target effects, as well as challenges that remain, are also discussed.
• Single-molecule perspectives of CRISPR/Cas systems: target search, recognition, and cleavage. This mini review aims to offer a comprehensive overview of CRISPR/Cas molecular dynamics, offering conclusive insights into their broader potential for genome editing and biotechnological applications.

Awards

• ChristianaCare’s Gene Editing Institute’s CRISPR in a Box™ teaching toolkit has been named the #2 innovation on The Scientist’s Top 10 Innovations list for 2024. This cutting-edge toolkit has already empowered over 1,000 students this year, providing a hands-on experience with one of the most exciting technologies in modern science. Read more here.

Patent news

• Troubling Trend of “Self” Revocation In the CRISPR Space Continues in Europe. Less than two months after CVC made the surprising move to revoke two of its seminal European CRISPR patents, Sigma-Aldrich has done it too. While the facts that led to Sigma’s “self” revocation may be different than CVC’s, this en vogue trend of avoiding final decisions is troubling because it denies the public of the certainty it deserves. Read more in this piece for National Law Review here.