CoHIT: a one-pot ultrasensitive ERA-CRISPR system for detecting multiple same-site indels

• Published in: Nature communications 2024-06, Vol.15 (1), p.5014-14
• Main Authors: Liu, Yin, Liu, Xinyi, Wei, Dongyi, Dang, Lu, Xu, Xiaoran, Huang, Shisheng, Li, Liwen, Wu, Sanyun, Wu, Jinxian, Liu, Xiaoyan, Sun, Wenjun, Tao, Wanyu, Wei, Yongchang, Huang, Xingxu, Li, Kui, Wang, Xinjie, Zhou, Fuling
• Format: Article
• Language: English
• Subjects: 45/22; 45/23; 45/41; 45/77; 631/1647/1513/2192; 631/208/4041; 631/67/2322; 692/700/139/1512; 82/83; Acute myeloid leukemia; Adaptability; Bacterial Proteins; Cancer; CRISPR; CRISPR-Associated Proteins; CRISPR-Cas Systems; Cross-reactivity; Endodeoxyribonucleases; ErbB Receptors - genetics; Genetic screening; Genetic testing; Genetic Testing - methods; Humanities and Social Sciences; Humans; INDEL Mutation; Leukemia; Leukemia, Myeloid, Acute - diagnosis; Leukemia, Myeloid, Acute - genetics; Microfluidics; Minimal residual disease; multidisciplinary; Multiplexing; Neoplasm, Residual - diagnosis; Neoplasm, Residual - genetics; Nuclear Proteins - genetics; Nucleophosmin; Proto-Oncogene Proteins B-raf - genetics; Science; Science (multidisciplinary)
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-49414-7

Genetic testing is crucial for precision cancer medicine. However, detecting multiple same-site insertions or deletions (indels) is challenging. Here, we introduce CoHIT (Cas12a-based One-for-all High-speed Isothermal Test), a one-pot CRISPR-based assay for indel detection. Leveraging an engineered AsCas12a protein variant with high mismatch tolerance and broad PAM scope, CoHIT can use a single crRNA to detect multiple NPM1 gene c.863_864 4-bp insertions in acute myeloid leukemia (AML). After optimizing multiple parameters, CoHIT achieves a detection limit of 0.01% and rapid results within 30 minutes, without wild-type cross-reactivity. It successfully identifies NPM1 mutations in 30 out of 108 AML patients and demonstrates potential in monitoring minimal residual disease (MRD) through continuous sample analysis from three patients. The CoHIT method is also competent for detecting indels of KIT , BRAF , and EGFR genes. Integration with lateral flow test strips and microfluidic chips highlights CoHIT’s adaptability and multiplexing capability, promising significant advancements in clinical cancer diagnostics. Genetic testing is crucial for precision cancer medicine. Here, the authors develop a one-pot ERA-CRISPR assay to detect variable same-site indels, using an engineered AsCas12a variant with improved mismatch tolerance and broadened PAM scope.