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Kong D, Zhang S, Guo M, Li S, Wang Q, Gou J, Wu Y, Chen Y, Yang Y, Dai C, Tian Z, Wee ATS, Liu Y, Wei D. Ultra-Fast Single-Nucleotide-Variation Detection Enabled by Argonaute-Mediated Transistor Platform. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2307366. [PMID: 37805919 DOI: 10.1002/adma.202307366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/03/2023] [Indexed: 10/09/2023]
Abstract
"Test-and-go" single-nucleotide variation (SNV) detection within several minutes remains challenging, especially in low-abundance samples, since existing methods face a trade-off between sensitivity and testing speed. Sensitive detection usually relies on complex and time-consuming nucleic acid amplification or sequencing. Here, a graphene field-effect transistor (GFET) platform mediated by Argonaute protein that enables rapid, sensitive, and specific SNV detection is developed. The Argonaute protein provides a nanoscale binding channel to preorganize the DNA probe, accelerating target binding and rapidly recognizing SNVs with single-nucleotide resolution in unamplified tumor-associated microRNA, circulating tumor DNA, virus RNA, and reverse transcribed cDNA when a mismatch occurs in the seed region. An integrated microchip simultaneously detects multiple SNVs in agreement with sequencing results within 5 min, achieving the fastest SNV detection in a "test-and-go" manner without the requirement of nucleic acid extraction, reverse transcription, and amplification.
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Affiliation(s)
- Derong Kong
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, 200433, P. R. China
| | - Shen Zhang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, 200433, P. R. China
| | - Mingquan Guo
- Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 200433, P. R. China
| | - Shenwei Li
- Shanghai International Travel Healthcare Center, Shanghai, 200335, P. R. China
| | - Qiang Wang
- Shanghai International Travel Healthcare Center, Shanghai, 200335, P. R. China
| | - Jian Gou
- Department of Physics, National University of Singapore, Singapore, 117542, Singapore
| | - Yungen Wu
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, 200433, P. R. China
| | - Yiheng Chen
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, 200433, P. R. China
| | - Yuetong Yang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
| | - Changhao Dai
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, 200433, P. R. China
| | - Zhengan Tian
- Shanghai International Travel Healthcare Center, Shanghai, 200335, P. R. China
| | - Andrew Thye Shen Wee
- Department of Physics, National University of Singapore, Singapore, 117542, Singapore
| | - Yunqi Liu
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, 200433, P. R. China
- Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Dacheng Wei
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, 200433, P. R. China
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Lázaro A, Maquieira Á, Tortajada-Genaro LA. Discrimination of Single-Nucleotide Variants Based on an Allele-Specific Hybridization Chain Reaction and Smartphone Detection. ACS Sens 2022; 7:758-765. [PMID: 35188365 PMCID: PMC8961872 DOI: 10.1021/acssensors.1c02220] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
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Massive DNA testing
requires novel technologies to support a sustainable
health system. In recent years, DNA superstructures have emerged as
alternative probes and transducers. We, herein, report a multiplexed
and highly sensitive approach based on an allele-specific hybridization
chain reaction (AS-HCR) in the array format to detect single-nucleotide
variants. Fast isothermal amplification was developed before activating
the HCR process on a chip to work with genomic DNA. The assay principle
was demonstrated, and the variables for integrating the AS-HCR process
and smartphone-based detection were also studied. The results were
compared to a conventional polymerase reaction chain (PCR)-based test.
The developed multiplex method enabled higher selectivity against
single-base mismatch sequences at concentrations as low as 103 copies with a limit of detection of 0.7% of the mutant DNA
percentage and good reproducibility (relative error: 5% for intra-assay
and 17% for interassay). As proof of concept, the AS-HCR method was
applied to clinical samples, including human cell cultures and biopsied
tissues of cancer patients. Accurate identification of single-nucleotide
mutations in KRAS and NRAS genes
was validated, considering those obtained from the reference sequencing
method. To conclude, AS-HCR is a rapid, simple, accurate, and cost-effective
isothermal method that detects clinically relevant genetic variants
and has a high potential for point-of-care demands.
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Affiliation(s)
- Ana Lázaro
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Ángel Maquieira
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain
- Unidad Mixta UPV-La Fe, Nanomedicine and Sensors, Av. Fernando Abril Martorell, 46026 Valencia, Spain
| | - Luis A. Tortajada-Genaro
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain
- Unidad Mixta UPV-La Fe, Nanomedicine and Sensors, Av. Fernando Abril Martorell, 46026 Valencia, Spain
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Enhanced asymmetric blocked qPCR method for affordable detection of point mutations in KRAS oncogene. Anal Bioanal Chem 2021; 413:2961-2969. [PMID: 33619642 DOI: 10.1007/s00216-021-03229-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 10/22/2022]
Abstract
An accurate genetic diagnostic is key for adequate patient management and the suitability of healthcare systems. The scientific challenge lies in developing methods to discriminate those patients with certain genetic variations present in tumor cells at low concentrations. We report a method called enhanced asymmetric blocked qPCR (EAB-qPCR) that promotes the blocker annealing against the primer-template hybrid controlling thermal cycling and reaction conditions with nonmodified oligonucleotides. Real-time fluorescent amplification curves of wild-type alleles were delayed by about eight cycles for EAB-qPCR, compared to conventional blocked qPCR approaches. This method reduced the amplification of native DNA variants (blocking percentage 99.7%) and enabled the effective enrichment of low-level DNA mutations. Excellent performance was estimated for the detection of mutated alleles in sensitivity (up to 0.5% mutant/total DNA) and reproducibility terms, with a relative standard deviation below 2.8%. The method was successfully applied to the mutational analysis of metastatic colorectal carcinoma from biopsied tissues. The determined single-nucleotide mutations in the KRAS oncogene (codon 12-13) totally agreed with those obtained from next-generation sequencing. EAB-qPCR is an accurate cheap method and can be easily incorporated into daily routine to detect mutant alleles. Hence, these features are especially interesting to facilitate the diagnosis and prognosis of several clinical diseases.
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Chen K, Wu S, Ye S, Huang H, Zhou Y, Zhou H, Wu S, Mao Y, Shangguan F, Lan L, Chen B. Dimethyl Fumarate Induces Metabolic Crisie to Suppress Pancreatic Carcinoma. Front Pharmacol 2021; 12:617714. [PMID: 33692690 PMCID: PMC7937954 DOI: 10.3389/fphar.2021.617714] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/15/2021] [Indexed: 01/22/2023] Open
Abstract
Dimethyl fumarate (DMF) is an approved drug used in the treatment of multiple sclerosis (MS) and psoriasis therapy. Multiple studies have demonstrated other pharmacological activities of DMF such as an anti-cancer agent. In particular, studies have shown that DMF can modulate the NRF2/HO1/NQO1 antioxidant signal pathway and inactivate NF-κB to suppress the growth of colon and breast cancer cells, and induce cell death. In this study, we aimed to evaluate the anti-tumor activities of DMF in pancreatic cancer (PC) focusing on cell death as the predominant mechanism of response. We showed that both mitochondrial respiration and aerobic glycolysis were severely depressed following treatment with DMF and the effects could be abrogated by treatment with L-cysteine and N-acetyl-L-cysteine (NAC). Importantly, we verified that DMF induced metabolic crisis and that cell death was not related to alterations in ROS. Our data implied that MTHFD1 could be a potential downstream target of DMF identified by molecular docking analysis. Finally, we confirmed that MTHFD1 is up-regulated in PC and overexpression of MTHFD1 was negatively related to outcomes of PC patients. Our data indicate that DMF induces metabolic crisie to suppress cell growth and could be a potential novel therapy in the treatment of PC.
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Affiliation(s)
- Kaiyuan Chen
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Shanshan Wu
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Laboratory of Precision Medical Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Sisi Ye
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Laboratory of Precision Medical Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Huimin Huang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yi Zhou
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Hongfei Zhou
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Shijia Wu
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yefan Mao
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Fugen Shangguan
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Linhua Lan
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Bicheng Chen
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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