Integrating allele-specific PCR with CRISPR-Cas13a for sensitive KRAS mutation detection in pancreatic cancer

The clustered regulatory interspaced short palindromic repeats (CRISPR)-Cas13a system has strong potential for highly sensitive detection of exogenous sequences. The detection of KRAS point mutations with low allele frequencies may prove powerful for the formal diagnosis of pancreatic ductal adenoca...

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Bibliographic Details
Published in:Journal of biological engineering 2024-10, Vol.18 (1), p.53-11, Article 53
Main Authors: Amintas, Samuel, Cullot, Grégoire, Boubaddi, Mehdi, Rébillard, Julie, Karembe, Laura, Turcq, Béatrice, Prouzet-Mauléon, Valérie, Bedel, Aurélie, Moreau-Gaudry, François, Cappellen, David, Dabernat, Sandrine
Format: Article
Language:English
Subjects:
Cancer
Cas13a
CRISPR
Diagnosis
Discrimination
DNA
Enzymes
Gene mutations
Genetic aspects
KRAS
Life Sciences
Liquid biopsy
Methodology
Pancreatic cancer
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Summary:The clustered regulatory interspaced short palindromic repeats (CRISPR)-Cas13a system has strong potential for highly sensitive detection of exogenous sequences. The detection of KRAS point mutations with low allele frequencies may prove powerful for the formal diagnosis of pancreatic ductal adenocarcinoma (PDAC). We implemented preamplification of KRAS alleles (wild-type and mutant) to reveal the presence of mutant KRAS with CRISPR-Cas13a. The discrimination of KRAS from KRAS was poor for the generic KRAS preamplification templates and depended on the crRNA design, the secondary structure of the target templates, and the nature of the mismatches between the guide and the templates. To improve the specificity, we used an allele-specific PCR preamplification method called CASPER (Cas13a Allele-Specific PCR Enzyme Recognition). CASPER enabled specific and sensitive detection of KRAS with low DNA input. CASPER detected KRAS mutations in DNA extracted from patients' pancreatic ultrasound-guided fine-needle aspiration fluid. CASPER is easy to implement and is a versatile and reliable method that is virtually adaptable to any point mutation.
ISSN:1754-1611
1754-1611
DOI:10.1186/s13036-024-00450-3