Universal and highly accurate detection of circulating tumor DNA mutation in non-small cell lung cancer based on CRISPR/Cas12a system

Wang, Xueliang; Song, Jian; Fan, Xiaoyu; Shi, Chunwei; Zeng, Bingjie; Xiao, Yanqun; Sun, Fenyong

doi:10.1016/j.snb.2023.133493

Cited by 8 publications

(3 citation statements)

References 43 publications

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“…In our study, MARPLES methods are constructed and then used to diagnose HFMD and identify the subtypes of H1N1 and H3N2 based on quadruplex and quintuplex RPA assays, respectively, and the results show that MARPLES methods can detect the target genes of HFMDcausing pathogens and H1N1 and H3N2 subtypes sensitively, specifically, and accurately in 1 h, suggesting that MARPLES could realize the purposes of disease diagnosis and pathogen identification. Additionally, MARPLES may also be used to diagnose cancer by the detection of cancer-associated mutations 55 and identify drug-resistant bacteria by the detection of a specific gene and drug-resistant gene of bacteria. 47 Noteworthily, when a MARPLES method is constructed, the usage of RPA primer pairs must be optimized to achieve high efficiency in amplifying target genes, and the optimal primer pair and crRNA sequence for each gene should be screened from several candidates to achieve a robust detection signal.…”

Section: ■ Discussionmentioning

confidence: 99%

Infectious Disease Diagnosis and Pathogen Identification Platform Based on Multiplex Recombinase Polymerase Amplification-Assisted CRISPR-Cas12a System

Lin,

Sun,

Yang

et al. 2023

ACS Infect. Dis.

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Controlling and mitigating infectious diseases caused by multiple pathogens or pathogens with several subtypes require multiplex nucleic acid detection platforms that can detect several target genes rapidly, specifically, sensitively, and simultaneously. Here, we develop a detection platform, termed Multiplex Assay of RPA and Collateral Effect of Cas12a-based System (MARPLES), based on multiplex nucleic acid amplification and Cas12a ssDNase activation to diagnose these diseases and identify their pathogens. We use the clinical specimens of hand, foot, and mouth disease (HFMD) and influenza A to evaluate the feasibility of MARPLES in diagnosing the disease and identifying the pathogen, respectively, and find that MARPLES can accurately diagnose the HFMD associated with enterovirus 71, coxsackievirus A16 (CVA16), CVA6, or CVA10 and identify the exact types of H1N1 and H3N2 in an hour, showing high sensitivity and specificity and 100% predictive agreement with qRT-PCR. Collectively, our findings demonstrate that MARPLES is a promising multiplex nucleic acid detection platform for disease diagnosis and pathogen identification.

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Section: ■ Discussionmentioning

confidence: 99%

Infectious Disease Diagnosis and Pathogen Identification Platform Based on Multiplex Recombinase Polymerase Amplification-Assisted CRISPR-Cas12a System

Lin,

Sun,

Yang

et al. 2023

ACS Infect. Dis.

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“…When the crRNA recognizes the mutation site, Cas12a cleaves the substrate strand, generating an electrochemical signal. Wang et al 46 also proposed a method for detecting mutations in ctDNA from NSCLC patients. They designed a crRNA library targeting various gene mutation sites, such as those in EGFR, KRAS, and TP53.…”

Section: Detection Of Exosomesmentioning

confidence: 99%

Advances in CRISPR Based Biosensing Strategies for Cancer Diagnosis

Yang,

Zhong,

Zhong

et al. 2024

Cancer Screen Prev

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With the development of gene editing technology, its application in tumor diagnosis is becoming increasingly widespread. The CRISPR/Cas system is an important gene editing tool that can significantly improve the early detection rate and precision diagnosis level, enabling high-throughput and high-sensitivity detection of tumors. This article focuses on CRISPR/Cas system for detecting various tumor-related targets and elaborates on its applications in tumor diagnosis from five aspects: (1) detection of tumor-derived exosomes: by recognizing the surface proteins or nucleic acids of exosomes secreted by tumor cells into blood or other samples through adaptors, the CRISPR system is activated, achieving non-invasive liquid biopsy of tumors; (2) detection of circulating tumor DNA tumor cells disseminate DNA into the circulatory system to trigger nucleic acid reactions involving gene editing enzymes, enabling the monitoring of tumor dynamic states; (3) detection of circulating tumor cells (CTCs): by using aptamers to recognize surface proteins of tumor cells or directly detecting tumor-related nucleic acids, the integrated CRISPR system allows for the detection of circulating tumor cells even in trace amounts, achieving precise diagnosis; (4) detection of tumor markers: high sensitivity is achieved through the coupling of various tumor marker aptamers and gene editing systems; (5) detection and identification of tumor microenvironments: by activating gene editing enzyme activity through differential factors in the tumor tissue microenvironment and triggering nucleic acid reactions, the diagnosis and dynamic monitoring of tumors can be achieved. The progress and bottlenecks of the CRISPR/Cas system in tumor diagnosis in the future are also discussed.

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“…[19][20][21] It allows for early screening of low copy number viruses and tumor nucleic acid biomarkers. 29,33,34 However, integrating the isothermal ampli cation system with the CRISPR reaction in a single tube can hinder nucleic acid ampli cation e cacy due to the trans-cleavage activity of the Cas12a protein, particularly with low copy number inputs. This can impair ampli cation e ciency and decrease detection sensitivity.…”

Section: Introductionmentioning

confidence: 99%

Enhancement of CRISPR-Cas12a System through Universal Circular RNA Design

Liu,

Wang,

Zhang

et al. 2024

Preprint

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The combination of isothermal amplification and CRISPR-Cas12a system is a valuable tool for detecting nucleic acids, especially in emergency situations or disease outbreaks. However, achieving compatibility between these technologies has been a challenge because the CRISPR reaction eagerly cleaves nucleic acid amplification template before isothermal amplification is complete. This study presents a method called CIRCLE, which effectively addresses the compatibility issue by dividing crRNA into a universal circular DR region with a PC linker and a replaceable spacer region. Different targets could be detected in a single separate way by changing the spacer region. Furthermore, DNA modifications were firstly introduced into circular crRNA to regulate CRISPR-Cas12a system using base excision repair (BER) enzymes. The programmable strategy showed potential to detect different BER enzymes and regulate Cas12a gene-editing activity by adjusting BER enzyme levels. In the future, it holds promise for selectively editing genes in cells that express high levels of specific BER enzymes, such as UDG, in colon cancer cells. The findings of this study contribute to advancing the field of nucleic acid detection and gene editing. The CIRCLE method is a programmable and resource efficient approach for medical diagnostic applications, making it particularly valuable in future clinical settings.

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Universal and highly accurate detection of circulating tumor DNA mutation in non-small cell lung cancer based on CRISPR/Cas12a system

Cited by 8 publications

References 43 publications

Infectious Disease Diagnosis and Pathogen Identification Platform Based on Multiplex Recombinase Polymerase Amplification-Assisted CRISPR-Cas12a System

Infectious Disease Diagnosis and Pathogen Identification Platform Based on Multiplex Recombinase Polymerase Amplification-Assisted CRISPR-Cas12a System

Advances in CRISPR Based Biosensing Strategies for Cancer Diagnosis

Enhancement of CRISPR-Cas12a System through Universal Circular RNA Design

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