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Yang R, Ji J, Ding L, Yuan X, Qu L, Wu Y, Li Y. CRISPR-Enhanced Photocurrent Polarity Switching for Dual-lncRNA Detection Combining Deep Learning for Cancer Diagnosis. Anal Chem 2024. [PMID: 39092917 DOI: 10.1021/acs.analchem.4c02617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Abnormal expression in long noncoding RNAs (lncRNAs) is closely associated with cancers. Herein, a novel CRISPR/Cas13a-enhanced photocurrent-polarity-switching photoelectrochemical (PEC) biosensor was engineered for the joint detection of dual lncRNAs, using deep learning (DL) to assist in cancer diagnosis. After target lncRNA-activated CRISPR/Cas13a cleaves to induce DNAzyme bidirectional walkers with the help of cofactor Mg2+, nitrogen-doped carbon-Cu/Cu2O octahedra are introduced into the biosensor, producing a photocurrent in the opposite direction of CdS quantum dots (QDs). The developed PEC biosensor shows high specificity and sensitivity with limits of detection down to 25.5 aM for lncRNA HOTAIR and 53.1 aM for lncRNA MALAT1. More importantly, this platform for the lncRNA joint assay in whole blood can successfully differentiate cancers from healthy people. Furthermore, the DL model is applied to explore the potential pattern hidden in data of the established technology, and the accuracy of DL cancer diagnosis can acquire 93.3%. Consequently, the developed platform offers a new avenue for lncRNA joint detection and early intelligent diagnosis of cancer.
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Affiliation(s)
- Ruiying Yang
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Jiangying Ji
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Lihua Ding
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Xinxin Yuan
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Lingbo Qu
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Yongjun Wu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Yuling Li
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
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Zhou Y, Zhang J, Sun S, Chen W, Wang Y, Shi H, Yang R, Qing Z. Amplified Biosensors Powered by Endogenous Molecules for Intracellular Fluorescence Imaging. Anal Chem 2024; 96:8078-8090. [PMID: 38622818 DOI: 10.1021/acs.analchem.4c00329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Affiliation(s)
- Yibo Zhou
- Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, P.R. China
| | - Jun Zhang
- Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, P.R. China
| | - Shuanghong Sun
- Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, P.R. China
| | - Weiju Chen
- Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, P.R. China
| | - Yuping Wang
- Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, P.R. China
| | - Huiqiu Shi
- Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, P.R. China
| | - Ronghua Yang
- Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, P.R. China
| | - Zhihe Qing
- Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, P.R. China
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Wang L, Wan P, Xu Z. A novel PANoptosis-related long non-coding RNA index to predict prognosis, immune microenvironment and personalised treatment in hepatocellular carcinoma. Aging (Albany NY) 2024; 16:2410-2437. [PMID: 38284890 PMCID: PMC10911344 DOI: 10.18632/aging.205488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/26/2023] [Indexed: 01/30/2024]
Abstract
BACKGROUND PANoptosis is involved in the interaction of apoptosis, necroptosis and pyroptosis, playing a role in programmed cell death. Moreover, long non-coding RNAs (lncRNAs) regulate the PCD. This work aims to explore the role of PANoptosis-associated lncRNAs in hepatocellular carcinoma (HCC). METHODS Co-expression analysis identified PANoptosis-associated lncRNAs in HCC. Cox and Least Absolute Shrinkage and Selection Operator (LASSO) algorithms were utilised to filter lncRNAs and establish a PANoptosis-related lncRNA index (PANRI). Additionally, Cox, Kaplan-Meier and receiver operating characteristic (ROC) curves were utilised to systematically evaluate the PANRI. Furthermore, Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data (ESTIMATE), single sample gene set enrichment analysis (ssGSEA) and immune checkpoints were performed to analyse the potential of the PANRI in differentiating different tumour immune microenvironment (TIME) populations. The consensus clustering algorithm was used to distinguish individuals with HCC having different TIME subtypes. Finally, HCC cell lines HepG2 were utilised for further validation in in vitro experiments. RESULTS The PANRI differentiates patients according to risk. Notably, ESTIMATE and ssGSEA algorithms revealed a high immune infiltration status in high-risk patients. Additionally, consensus clustering divided the patients into three clusters to identify different subtypes of TIME. Moreover, in vitro results showed that siRNA-mediated silencing of AL049840.4 inhibited the viability and migration of HepG2 cells and promoted apoptosis. CONCLUSIONS This is the first PANoptosis-related, lncRNA-based risk index in HCC to assess patient prognosis, TIME and response to immunotherapy. This study offers novel perspectives on the role of PANoptosis-associated lncRNAs in HCC.
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Affiliation(s)
- Liangliang Wang
- Department of Chemoradiotherapy, The Affiliated People’s Hospital of Ningbo University, Ningbo, China
- Chemoradiotherapy Center of Oncology, The Affiliated People’s Hospital of Ningbo University, Ningbo, China
| | - Peng Wan
- Department of Chemoradiotherapy, The Affiliated People’s Hospital of Ningbo University, Ningbo, China
- Chemoradiotherapy Center of Oncology, The Affiliated People’s Hospital of Ningbo University, Ningbo, China
| | - Zhengyang Xu
- Department of Chemoradiotherapy, The Affiliated People’s Hospital of Ningbo University, Ningbo, China
- Chemoradiotherapy Center of Oncology, The Affiliated People’s Hospital of Ningbo University, Ningbo, China
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Wang F, Ma X, Ye J, Shi C, Chen Y, Yu Z, Li T, Yang D, Li M, Wang P. Precise Detection of Viral RNA by Programming Multiplex Rolling Circle Amplification and Strand Displacement. Anal Chem 2023; 95:17699-17707. [PMID: 37971750 DOI: 10.1021/acs.analchem.3c03548] [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: 11/19/2023]
Abstract
Detection of viral infections (e.g., SARS-CoV-2) with high precision is critical to disease control and treatment. There is an urgent need to develop point-of-care detection methods to complement the gold standard laboratory-based PCR assay with comparable sensitivity and specificity. Herein, we developed a method termed mCAD to achieve ultraspecific point-of-care detection of SARS-CoV-2 RNA while maintaining high sensitivity by programming multiplex rolling circle amplification and toehold-mediated strand displacement reactions. RCA offers sufficient amplification of RNA targets for subsequent detection. Most importantly, a multilayer of detection specificity is implemented into mCAD via sequence-specific hybridization of nucleic acids across serial steps of this protocol to fully eliminate potential false-positive detections. Using mCAD, we demonstrated a highly specific, sensitive, and convenient visual detection of SARS-CoV-2 RNA from both synthetic and clinical samples, exhibiting performance comparable to qPCR. We envision that mCAD will find its broad applications in clinical prospects for nucleic acid detections readily beyond SARS-CoV-2 RNA.
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Affiliation(s)
- Fukai Wang
- College of Chemistry and Materials Science, Shanghai Normal University, Shanghai 200233, China
| | - Xiaowei Ma
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Jing Ye
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Chenzhi Shi
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yun Chen
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Zhicai Yu
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Tianming Li
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Donglei Yang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Min Li
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Pengfei Wang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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Huang R, Liu K, Yue C, Wang Y, Zeng Z, Xiao L, Dong L, Ke R, Yang C, Liu D. Chromogenic Visualization of Single RNA Molecules In Situ with Duplex Capability by Rolling Circle Amplification with Alkaline Phosphatase. Anal Chem 2023; 95:12161-12168. [PMID: 37523480 DOI: 10.1021/acs.analchem.3c02443] [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: 08/02/2023]
Abstract
Visualizing spatial patterns of gene expression by optical microscopy at single-molecule resolution represents a long-standing challenge for imaging and molecular engineering technologies. In this study, we developed a method for visualizing mRNA with duplex capability by optical microscopy using rolling circle amplification with streptavidin-modified alkaline phosphatase (SA-ALP) to provide highly selective and sensitive RNA detection. ALP-based RNA detection provides comparable sensitivity and specificity to fluorescence-based in situ assays and similar performance to the current RNAscope technique for single-molecule RNA detection, but with improved ease of operation. This versatile and relatively user-friendly method of single-molecule RNA visualization can also overcome common problems of background interference. Our findings show that the red spots generated by the Fast Red staining in situ are readily quantified by image analysis, even in samples with heavy melanin deposition, supporting the clinical translation of this assay to improve diagnostic assays for recalcitrant tissues. This system was adaptable for duplex assays with multiple probes and multiple stains, which is ALP with horseradish peroxidase to produce red and brown signals to simultaneously visualize two different RNA targets. The duplex assay can be successfully applied to quantify mRNA expression from two genes in situ within single cells and multiple cell types. With the advantages of high sensitivity and low hardware requirements, this versatile and user-friendly method of RNA visualization may enable low-resource institutions to conduct previously inaccessible diagnostic or research questions about the in situ expression and distribution of RNAs at single-molecule resolution.
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Affiliation(s)
- Ruolan Huang
- Engineering Research Centre of Molecular Medicine of Ministry of Education, Key Laboratory of Fujian Molecular Medicine, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, School of Medicine, Huaqiao University, Quanzhou, Fujian 362021, China
| | - Kun Liu
- Department of Pathology, Zhongshan Hospital, Fudan University, Xiamen Branch, Xiamen City, Fujian Province 361015, China
| | - Chensirong Yue
- Engineering Research Centre of Molecular Medicine of Ministry of Education, Key Laboratory of Fujian Molecular Medicine, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, School of Medicine, Huaqiao University, Quanzhou, Fujian 362021, China
| | - Ying Wang
- Engineering Research Centre of Molecular Medicine of Ministry of Education, Key Laboratory of Fujian Molecular Medicine, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, School of Medicine, Huaqiao University, Quanzhou, Fujian 362021, China
| | - Zhilong Zeng
- Engineering Research Centre of Molecular Medicine of Ministry of Education, Key Laboratory of Fujian Molecular Medicine, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, School of Medicine, Huaqiao University, Quanzhou, Fujian 362021, China
| | - Lu Xiao
- Engineering Research Centre of Molecular Medicine of Ministry of Education, Key Laboratory of Fujian Molecular Medicine, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, School of Medicine, Huaqiao University, Quanzhou, Fujian 362021, China
| | - Lei Dong
- Department of Pathology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Rongqin Ke
- Engineering Research Centre of Molecular Medicine of Ministry of Education, Key Laboratory of Fujian Molecular Medicine, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, School of Medicine, Huaqiao University, Quanzhou, Fujian 362021, China
| | - Chaoyong Yang
- The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Dan Liu
- Engineering Research Centre of Molecular Medicine of Ministry of Education, Key Laboratory of Fujian Molecular Medicine, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, School of Medicine, Huaqiao University, Quanzhou, Fujian 362021, China
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Dong Q, Ding Q, Yuan R, Yuan Y. Metal Porphyrin Complex Combined with Polymerization and Isomerization Cyclic Amplification for a Sensitive Photoelectrochemical Assay. Anal Chem 2023; 95:5126-5132. [PMID: 36897080 DOI: 10.1021/acs.analchem.3c00167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
5,10,15,20-Tetrakis(4-aminophenyl)-21H,23H-porphine (TPAPP) possesses good light-harvesting ability and photoelectrochemical (PEC) cathode response signal; however, the disadvantages of easy stacking and weak hydrophilicity limit its application as a signal probe in PEC biosensors. Based on these, we prepared a Fe3+ and Cu2+ co-coordinating photoactive material (TPAPP-Fe/Cu) with horseradish peroxidase (HRP)-like activity. The metal ions in the porphyrin center not only enabled the directional flow of photogenerated electrons between electron-rich porphyrin and positive metal ions within inner-/intermolecular layers but also accelerated electron transfer through a synergistic redox reaction of Fe(III)/Fe(II) and Cu(II)/Cu(I) as well as rapid generation of superoxide anion radicals (O2-•) by mimicking catalytically produced and dissolved oxygen, thereby providing the desired cathode photoactive material with extremely high photoelectric conversion efficiency. Accordingly, by combining with toehold-mediated strand displacement (TSD)-induced single cycle and polymerization and isomerization cyclic amplification (PICA), an ultrasensitive PEC biosensor was constructed for the detection of colon cancer-related miRNA-182-5p. The ultratrace target could be converted to abundant output DNA by TSD possessing the desirable amplifying ability to trigger PICA for forming long ssDNA with repetitive sequences, thus decorating substantial TPAPP-Fe/Cu-labeled DNA signal probes for producing high PEC photocurrent. Meanwhile, the Mn(III) meso-tetraphenylporphine chloride (MnPP) was embedded in dsDNA to further exhibit a sensitization effect toward TPAPP-Fe/Cu and an acceleration effect analogous to that of metal ions in the porphyrin center above. As a result, the proposed biosensor displayed a detection limit as low as 0.2 fM, facilitating the development of high-performance biosensors and showing great potential in early clinical diagnosis.
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Affiliation(s)
- Qingyuan Dong
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Qiao Ding
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Yali Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
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