CMN Weekly (10 June 2022) - Your Weekly CRISPR Medicine News
Some of the best links we picked up around the internet
By: Gorm Palmgren - Jun. 10, 2022
Top picks
A new CRISPR-based map ties almost every human gene to its function in the cell. Jonathan Weissman at MIT's Whitehead Institute for Biomedical Research performed genome-scale Perturb-seq targeting all expressed genes with CRISPR interference (CRISPRi) across >2.5 million human cells. In addition to assigning gene function, single-cell transcriptional phenotypes allow for in-depth dissection of complex cellular phenomena - from RNA processing to differentiation.
Humans have pre-existing adaptive immunity to the RNA-editing enzyme Cas13d from Ruminococcus flavefaciens (RfxCas13d), which should be considered in the development of Cas13d-based therapies. Researchers in Singapore found Cas13d-reactive antibodies and CD4 and CD8 T cell responses in most donors comparable to responses against Cas9 proteins from Staphylococcus aureus (SaCas9) and Streptococcus pyogenes (SpCas9).
Chinese scientists have elucidated the cause of off-target effects of CRISPR-Cas12a. They show that the nuclease can still recognise and cleave the target dsDNA sequence even with insertions (DNA bubble) or deletions (RNA bubble). Moreover, the tolerance to these bubbles is closely related to the location and size of the bubble and the GC base content of crRNA.
CRISPRedict is a new web tool for interpretable gRNA efficiency prediction model for CRISPR-Cas9 gene editing. Researchers in Greece developed the tool, and it offers (i) quick and accurate predictions across various experimental conditions; (ii) regression and classification models for scoring gRNAs and (iii) multiple visualisations to explain the obtained results.
A new attention-based deep learning framework, Apindel, can predict CRISPR-Cas9 repair outcomes. Apindel performs better and delivers more detailed prediction categories than the most advanced DNA-mutation-predicting models. In addition, the model reveals that nucleotides at different positions relative to the cleavage sites have different influences on CRISPR-Cas9 editing outcomes.
A simple and fast method for detecting bacterial antimicrobial resistance (AMR) genes is described by researchers in Sweden. Cas9 first recognises the gene of interest and linearises the circular plasmid that harbours the AMR gene. The plasmid is then stretched on a glass surface and visualised by fluorescence microscopy, allowing for detection and detailed information on the number and size of plasmids in the clinical sample.
Chinese researchers have developed a strategy for rapidly detecting the circulating tumour DNA (ctDNA) BRAF V600E related to aggressive behaviour in papillary thyroid carcinoma. The strategy is based on 3D DNA walker binding to the target ctDNA and subsequent release of large amounts of output DNAs through cyclic cleavage with the assistance of a specific endonuclease. The output DNAs then specifically bind to crRNA and activate the non-specific trans-cleavage activity of Cas12a to generate a fluorescence signal.
Scientists in China present an ultra-sensitive CRISPR-Cas12a-based assay for detecting DNA methylation. Ultra-low background interference is achieved with a novel methyl-dependent DNA endonuclease GlaI coupled with double cascaded strand displacement amplification. As a result, as low as a 0.1% methylation level can be identified in the presence of excessive unmethylated DNA in down to 38 ng of genomic DNA.
Researchers in China present a method for the rapid and specific diagnosis of the Omicron variant of SARS-CoV-2. The platform is based on CRISPR-Cas12a and surface plasmon resonance, and it can analyse viral RNA without the need for amplification within 38 min and achieve a limit of detection of 15 fM.