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Wang Z, Feng N, Zhou Y, Cheng X, Zhou C, Ma A, Wang Q, Li Y, Chen Y. Mesophilic Argonaute-Mediated Polydisperse Droplet Biosensor for Amplification-Free, One-Pot, and Multiplexed Nucleic Acid Detection Using Deep Learning. Anal Chem 2024; 96:2068-2077. [PMID: 38259216 DOI: 10.1021/acs.analchem.3c04426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Detection of nucleic acids from a single multiplexed and amplification-free test is critical for ensuring food safety, clinical diagnostics, and environmental monitoring. In this study, we introduced a mesophilic Argonaute protein from Clostridium butyricum (CbAgo), which exhibits nucleic acid endonuclease activity, to achieve a programmable, amplification-free system (PASS) for rapid nucleic acid quantification at ambient temperatures in one pot. By using CbAgo-mediated binding with specific guide DNA (gDNA) and subsequent targeted cleavage of wild-type target DNAs complementary to gDNA, PASS can detect multiple foodborne pathogen DNA (<102 CFU/mL) simultaneously. The fluorescence signals were then transferred to polydisperse emulsions and analyzed by using deep learning. This simplifies the process and increases the suitability of polydisperse emulsions compared to traditional digital PCR, which requires homogeneous droplets for accurate detection. We believe that PASS has the potential to become a next-generation point-of-care digital nucleic acid detection method.
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Affiliation(s)
- Zhipan Wang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Niu Feng
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Yanan Zhou
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Xinrui Cheng
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Cuiyun Zhou
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Aimin Ma
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Qinyu Wang
- Department of Computer Science and Technology, Wuhan University of Science and Technology, Wuhan 430000, Hubei China
| | - Yingjun Li
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Yiping Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
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Deng Q, Su B, Ji X, Fang Q, Zhou S, Zhou C. Predictive value of unmethylated RASSF1A on disease progression in non-small cell lung cancer patients receiving pemetrexed-based chemotherapy. Cancer Biomark 2020; 27:313-323. [PMID: 31839603 DOI: 10.3233/cbm-190258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND OBJECTIVE Chemotherapy remains the basis of the treatment of lung cancer, and screening biomarkers with predictive value for chemotherapy is of great interest. The present study focused on status of genes methylation in NSCLC patients receiving pemetrexed- or gemcitabine-based chemotherapy. PATIENTS AND METHODS Promoter methylation of Ras association domain family (RASSF1A) and short stature homeobox 2 (SHOX2) was examined in bronchoalveolar lavage (BAL) from 117 NSCLC patients treated with chemotherapy. Multivariate analysis was used to identify the predictive value of gene methylation. Progression-free survival (PFS) rather than overall survival (OS) was used as the clinical outcome to minimize the impact of chemotherapy on gene methylation. RESULTS The methylation of RASSF1A and SHOX2 was significantly associated with shorter PFS (RASSF1A: HR = 2.355, 95% CI: 1.533-3.617, P< 0.0001; SHOX2: HR = 2.123, 95% CI: 1.392-3.236, P= 0.0004). After adjusting for confounding factors, RASSF1A methylation was still a predictive factor for PFS (HR = 1.765, 95% CI: 1.064-2.928, P= 0.0278). In the pemetrexed group, unmethylated RASSF1A could be used to predict longer PFS (P= 0.0001), and no predictive value was found in the gemcitabine group. CONCLUSION Unmethylated RASSF1A is a favorable prognostic indicator for patients receiving pemetrexed doublets. Because of the promoting effect of most chemotherapeutic drugs on gene methylation, unmethylated RASSF1A is not suitable as a predictor for gemcitabine doublets.
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Affiliation(s)
- Qinfang Deng
- Medical College of Soochow University, Soochow, China.,Department of Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.,Medical College of Soochow University, Soochow, China
| | - Bo Su
- Central Laboratory, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.,Medical College of Soochow University, Soochow, China
| | - Xianxiu Ji
- Department of Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qiyu Fang
- Department of Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Songwen Zhou
- Department of Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Caicun Zhou
- Medical College of Soochow University, Soochow, China.,Department of Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
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Kikuchi N, Kolpashchikov DM. A universal split spinach aptamer (USSA) for nucleic acid analysis and DNA computation. Chem Commun (Camb) 2018; 53:4977-4980. [PMID: 28425510 DOI: 10.1039/c7cc01540b] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We demonstrate how a single universal spinach aptamer (USSA) probe can be used to detect multiple (potentially any) nucleic acid sequences. USSA can be used for cost-efficient and highly selective analysis of even folded DNA and RNA analytes, as well as for the readout of outputs of DNA logic circuits.
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Affiliation(s)
- Nanami Kikuchi
- Chemistry Department, University of Central Florida, Orlando, 32816, Florida, USA
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Duncan R, Kourout M, Grigorenko E, Fisher C, Dong M. Advances in multiplex nucleic acid diagnostics for blood-borne pathogens: promises and pitfalls. Expert Rev Mol Diagn 2015; 16:83-95. [PMID: 26581018 DOI: 10.1586/14737159.2016.1112272] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The large number of blood-borne viruses, bacteria and parasites currently of concern, as well as many newly emerging pathogens, presents a daunting challenge to protection of the safety of blood for transfusion and diagnosing infectious diseases. Focusing on nucleic acid diagnostic tests, multiplex devices are coming into use with many more in various developmental stages that promise to offer solutions to the clinical need. The characteristics, advantages and disadvantages of platforms in clinical use and at the research and development stage are examined here. The presence of multiple assays and associated reagents operating simultaneously on one platform, implementation in traditional clinical laboratories and regulatory review will present special challenges. Fortunately, clinical laboratories have made dramatic technical progress in the last two decades and regulatory agencies have publicly expressed support for development of multiplex devices.
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Affiliation(s)
- Robert Duncan
- a Center for Biologics Evaluation and Research , US FDA , Silver Spring , MD , USA
| | - Moussa Kourout
- a Center for Biologics Evaluation and Research , US FDA , Silver Spring , MD , USA
| | | | - Carolyn Fisher
- a Center for Biologics Evaluation and Research , US FDA , Silver Spring , MD , USA
| | - Ming Dong
- a Center for Biologics Evaluation and Research , US FDA , Silver Spring , MD , USA
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Zhang C, Niu P, Hong Y, Wang J, Zhang J, Ma X. A probe-free four-tube real-time PCR assay for simultaneous detection of twelve enteric viruses and bacteria. J Microbiol Methods 2015; 118:93-8. [PMID: 26342434 DOI: 10.1016/j.mimet.2015.08.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 08/27/2015] [Accepted: 08/27/2015] [Indexed: 12/30/2022]
Abstract
OBJECTIVES We aim to develop a multiplex real-time PCR assay to detect the most common pathogens causing community outbreaks of diarrhea. METHODS Four reaction systems of fluorescence dye-based real-time PCR assay were performed to amplify genes of norovirus, sapovirus, rotavirus, astrovirus, adenovirus, Campylobacter jejuni, Yersinia enterocolitica, Vibrio parahaemolyticus, Salmonella spp., Escherichia coli, and Shigella spp. PCR products of each pathogen were identified by characteristic peaks in melting curves. RESULTS The assay was able to achieve detection limit of 50 copies/reaction for each individual virus target, and 140-500CFU/mL for each individual bacterium target. A total of 122 clinical specimens from hospitalized children with acute diarrhea were used to evaluate the assay. The clinical sensitivity was very similar to that of reference methods. Norovirus genogroup II revealed the highest detectable rate (45/122, 36.9%). Coinfection was found in 28 out of 122 (23%) clinical specimens. CONCLUSION This assay proved to be a cost-effective, sensitive and reliable method for simultaneous detection of enteric viruses and bacteria.
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Affiliation(s)
- Chen Zhang
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Peihua Niu
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yanying Hong
- Beijing Traditional Chinese Medicine Hospital, Capital Medical University Medical Laboratory, Beijing, China
| | - Ji Wang
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jingyun Zhang
- National Institute for Infectious Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xuejun Ma
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
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Zhou W. Effect of adenovirus‑mediated uPA gene transduction on the fibrinolytic activity of human umbilical vein endothelial cells. Mol Med Rep 2014; 10:2701-5. [PMID: 25176046 DOI: 10.3892/mmr.2014.2518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Accepted: 04/25/2014] [Indexed: 11/06/2022] Open
Abstract
The present study aimed to investigate the effect of adenovirus‑mediated urokinase‑type plasminogen activator (uPA) transduction on uPA expression and fibrinolytic activity in human umbilical vein endothelial cells (HUVECs). Recombinant adenovirus vectors containing the human uPA gene were constructed and transduced into HUVECs. The expression and fibrinolytic activity of uPA was then assessed in HUVECs using western blot analysis, ELISA and colorimetric assay. The experiments were performed in three groups: The ad/uPa (n=3), ad/neg control (n=3) and blank control (n=3) groups. Western blot analysis revealed that uPA protein expression in the HUVECs in the ad/uPa group was significantly increased compared with those in the ad/neg control or blank groups (P<0.01). The uPA protein levels in the supernatant of the three groups were 379.40±2.46, 240.01±1.16 and 256.10±3.04 ng/l, respectively, showing that the uPA protein levels were significantly higher in the supernatant in the ad/uPa group compared with those in the ad/neg control or blank groups. uPA activity was determined using a colorimetric method and was found to be 40238.49±5755 IU/mg in the HUVECs in the ad/uPa group, which was significantly higher than that in the HUVECs in the ad/neg control (6180.03±942.38 IU/mg) or blank groups (3346.06±928.81 IU/mg) (both P<0.01). These findings suggested that transduction of the uPA gene increased uPA protein expression and fibrinolytic activity in HUVECs.
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Affiliation(s)
- Weimin Zhou
- Department of Vascular Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
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