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Chen Y, Wang X, Zhang J, Jiang Q, Qiao B, He B, Yin W, Qiao J, Liu Y. Split crRNA with CRISPR-Cas12a enabling highly sensitive and multiplexed detection of RNA and DNA. Nat Commun 2024; 15:8342. [PMID: 39333528 PMCID: PMC11436650 DOI: 10.1038/s41467-024-52691-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 09/13/2024] [Indexed: 09/29/2024] Open
Abstract
The CRISPR-Cas12a system has revolutionized nucleic acid testing (NAT) with its rapid and precise capabilities, yet it traditionally required RNA pre-amplification. Here we develop rapid fluorescence and lateral flow NAT assays utilizing a split Cas12a system (SCas12a), consisting of a Cas12a enzyme and a split crRNA. The SCas12a assay enables highly sensitive, amplification-free, and multiplexed detection of miRNAs and long RNAs without complex secondary structures. It can differentiate between mature miRNA and its precursor (pre-miRNA), a critical distinction for precise biomarker identification and cancer progression monitoring. The system's specificity is further highlighted by its ability to detect DNA and miRNA point mutations. Notably, the SCas12a system can quantify the miR-21 biomarker in plasma from cervical cancer patients and, when combined with RPA, detect HPV at attomole levels in clinical samples. Together, our work presents a simple and cost-effective SCas12a-based NAT platform for various diagnostic settings.
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Affiliation(s)
- Yichuan Chen
- Pilot Base of Food Microbial Resources Utilization of Hubei Province, School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, 430023, China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, 430042, China
| | - Xinping Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, 430042, China
| | - Junqi Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, 430042, China
| | - Qingyuan Jiang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, 430042, China
| | - Bin Qiao
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450001, China
| | - Baoxia He
- Department of pharmacy, Affiliated Cancer Hospital of Zhengzhou University and Henan cancer hospital, Zhengzhou, Henan, 450003, China
| | - Wenhao Yin
- BravoVax Co. Ltd., Wuhan, Hubei, 430075, China
| | - Jie Qiao
- Pilot Base of Food Microbial Resources Utilization of Hubei Province, School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, 430023, China.
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450001, China.
| | - Yi Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, 430042, China.
- BravoVax Co. Ltd., Wuhan, Hubei, 430075, China.
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Multi-omics analysis reveals the interaction between the complement system and the coagulation cascade in the development of endometriosis. Sci Rep 2021; 11:11926. [PMID: 34099740 PMCID: PMC8185094 DOI: 10.1038/s41598-021-90112-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 04/16/2021] [Indexed: 02/05/2023] Open
Abstract
Endometriosis (EMS) is a disease that shows immune dysfunction and chronic inflammation characteristics, suggesting a role of complement system in its pathophysiology. To find out the hub genes and pathways involved in the pathogenesis of EMs, three raw microarray datasets were recruited from the Gene Expression Omnibus database (GEO). Then, a series of bioinformatics technologies including gene ontology (GO), Hallmark pathway enrichment, protein-protein interaction (PPI) network and gene co-expression correlation analysis were performed to identify hub genes. The hub genes were further verified by the Real-time quantitative polymerase chain reaction (RT-PCR) and Western Blot (WB). We identified 129 differentially expressed genes (DEGs) in EMs, of which 78 were up-regulated and 51 were down-regulated. Through GO functional enrichment analysis, we found that the DEGs are mainly enriched in cell adhesion, extracellular matrix remodeling, chemokine regulation, angiogenesis regulation, epithelial cell proliferation, et al. In Hallmark pathway enrichment analysis, coagulation pathway showed great significance and the terms in which included the central complement factors. Moreover, the genes were dominating in PPI network. Combined co-expression analysis with experimental verification, we found that the up-regulated expression of complement (C1S, C1QA, C1R, and C3) was positively related to tissue factor (TF) in EMs. In this study, we discovered the over expression complement and the positive correlation between complement and TF in EMs, which suggested that interaction of complement and coagulation system may play a role within the pathophysiology of EMS.
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Smith AE, Jnah A, Newberry D. Chromosome 16p13.11 Microdeletion Syndrome in a Newborn: A Case Study. Neonatal Netw 2019; 37:303-309. [PMID: 30567812 DOI: 10.1891/0730-0832.37.5.303] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Chromosome 16p13.11 microdeletion syndrome is a rare copy number variant that carries increased risks for complications in the neonatal period and throughout the life span. Clinical manifestations and associated defects known to present in the neonatal period include motor delay, facial dysmorphisms, microcephaly, gastroesophageal reflux disease (GERD), and congenital heart defects. Management in the neonatal period focuses on associated comorbidities, including motor delay with or without GERD, which commonly manifests as feeding difficulties. Life span implications of chromosome 16p13.11 microdeletion syndrome include developmental, speech, and language delay; psychiatric and behavioral problems; seizure disorders; and, less commonly, obesity. Nursing assessment is critical to the early identification of nonspecific abnormalities associated with de novo genetic disorders. Early identification and diagnosis of chromosome 16p13.11 microdeletion syndrome are critical to optimizing outcomes throughout infancy and across the life span. We present a case report of an infant diagnosed with chromosome 16p13.11 microdeletion. A discussion of genetic influences, associated clinical manifestations, diagnostics, management, and health promotion strategies are presented to establish core knowledge of chromosome 16p13.11 microdeletion.
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