1
|
Li YY, Jiang S, Pan TT, Wang Y, Zhang CY. A simple "mix-and-detection" method based on template-free amplification for sensitive measurement of human cellular FEN1. Talanta 2024; 281:126863. [PMID: 39260254 DOI: 10.1016/j.talanta.2024.126863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 08/23/2024] [Accepted: 09/08/2024] [Indexed: 09/13/2024]
Abstract
Flap endonuclease 1 (FEN1) is a structure-specific nuclease that can specially identify and cleave 5' flap of branched duplex DNA, and it plays a critical role in DNA metabolic pathways and human diseases. Herein, we propose a simple "mix-and-detection" strategy for sensitive measurement of human cellular FEN1 on basis of template-free amplification. We design a dumbbell probe with 5' flap as a substrate of FEN1 and a NH2-labeled 3' termini to prevent nonspecific amplification. When FEN1 is present, the 5' flap is cleaved to release a free 3'-OH termini, initiating Ribonuclease HII (RNase HII)-assisted terminal deoxynucleotidyl transferase (TdT)-induced amplification for the production of a significant fluorescence signal. Due to the high exactitude of TdT-mediated extension reaction and RNase HII-induced single ribonucleotide excise, this assay shows excellent specificity and high sensitivity with a detection limit of 5.64 × 10-6 U/μL. Importantly, it can detect intracellular FEN1 activity with single-cell sensitivity under isothermal condition in a "mix-and-detection" manner, screen the FEN1 inhibitors, and even discriminate tumor cells from normal cells, offering a new platform for disease diagnosis and drug discovery.
Collapse
Affiliation(s)
- Yue-Ying Li
- School of Food and Health, Beijing Technology and Business University, Beijing, 100048, China; Henan Institute of Medical and Pharmaceutical Sciences & BGI College, Zhengzhou University, Zhengzhou, 450052, China
| | - Su Jiang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China
| | - Ting-Ting Pan
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China
| | - Yanbo Wang
- School of Food and Health, Beijing Technology and Business University, Beijing, 100048, China.
| | - Chun-Yang Zhang
- School of Chemistry and Chemical Engineering, State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing, 211189, China.
| |
Collapse
|
2
|
Chen W, Zhang H, Zhang Y, Hui M, Chen H, Ren C, Di D, Zhang H. Construction of dual exponential amplification accompanied by multi-terminal signal output method for convenient detection of tumor biomarker FEN1 activity. Anal Chim Acta 2023; 1263:341275. [PMID: 37225333 DOI: 10.1016/j.aca.2023.341275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 04/23/2023] [Indexed: 05/26/2023]
Abstract
As an important 5'-nuclease in DNA replication and damage repair, Flap endonuclease 1 (FEN1) has been considered as a potential tumor biomarker due to its overexpression in different human cancer cells. Here, we developed a convenient fluorescent method based on dual enzymatic repairing exponential amplification accompanied by multi-terminal signal output to realize the rapid and sensitive detection of FEN1. In the presence of FEN1, the double-branched substrate could be cleaved to produce 5' flap single strand DNA (ssDNA) which subsequently was used as a primer to initiate the dual exponential amplification (EXPAR) to generate abundant ssDNAs (X' and Y'), then the ssDNAs can respectively hybridize with the 3' and 5' ends of the signal probe to form partially complementary double strands (dsDNAs). Subsequently, the signal probe on the dsDNAs could be digested under the assistance of Bst. polymerase and T7 exonuclease, as well as releasing the fluorescence signals. The method displayed high sensitivity with the detection limit of 9.7 × 10-3 U mL-1 (1.94 × 10-4 U) and also exhibited good selectivity towards FEN1 under the challenge from complicated samples including extracts of normal and cancer cells. Furthermore, it was successfully applied to screen FEN1 inhibitors, holding great promise in the screening of potential drugs targeting FEN1. This sensitive, selective and convenient method could be used for FEN1 assay without the complicated nanomaterial synthesis/modification, showing great potential in FEN1- related prediction and diagnosis.
Collapse
Affiliation(s)
- Wei Chen
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China
| | - Huige Zhang
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China; Key Laboratory of Special Function Materials and Structure Design (MOE), Lanzhou University, Lanzhou, 730000, China.
| | - Yanning Zhang
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Meiyi Hui
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China
| | - Hongli Chen
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China
| | - Cuiling Ren
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China
| | - Duolong Di
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources, Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Haixia Zhang
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China.
| |
Collapse
|
3
|
Ding S, Wei Y, Chen G, Du F, Cui X, Huang X, Yuan Y, Dong J, Tang Z. Detection of Cancer Marker Flap Endonuclease 1 Using One-Pot Transcription-Powered Clustered Regularly Interspaced Short Palindromic Repeat/Cas12a Signal Expansion. Anal Chem 2022; 94:13549-13555. [PMID: 36121799 DOI: 10.1021/acs.analchem.2c03054] [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: 11/29/2022]
Abstract
As a critical functional protein in DNA replication and genome stability, flap endonuclease 1 (FEN1) has been considered a promising biomarker and druggable target for multiple cancers. We report here a transcription-powered clustered regularly interspaced short palindromic repeat (CRISPR)/Cas12a signal expansion platform for rapid and sensitive detection of FEN1. In this method, the probe cleavage by FEN1 generated a free 5' flap single-stranded DNA which could hybridize with the single-stranded T7 promoter-bearing template and trigger the extension. Then, the CRISPR guide RNA (crRNA) transcribed from the extended template activated the collateral DNase activity of Cas12a, releasing the fluorophore from the quenched DNA signal probe to report the FEN1 detection result. The high specificity for FEN1 was validated by comparing with other repair-relevant proteins. The limit of detection (LOD) could be as low as 0.03 mU, which is sensitive enough to detect the FEN1 activity in biological samples. In addition, the inhibition assay of FEN1 was also successfully achieved with this platform, proving its potential in inhibitor screening. In summary, this study provides a novel biosensor for FEN1 activity analysis and provides new insights into the development of CRISPR-based biosensors for non-nucleic acid targets.
Collapse
Affiliation(s)
- Sheng Ding
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Yinghua Wei
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P. R. China
| | - Gangyi Chen
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P. R. China
| | - Feng Du
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P. R. China
| | - Xin Cui
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P. R. China
| | - Xin Huang
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P. R. China
| | - Yi Yuan
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P. R. China
| | - Juan Dong
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P. R. China
| | - Zhuo Tang
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P. R. China
| |
Collapse
|
4
|
Targeting MDC1 promotes apoptosis and sensitizes Imatinib resistance in CML cells by mainly disrupting non-homologous end-joining repair. MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2022; 39:226. [PMID: 36175703 DOI: 10.1007/s12032-022-01821-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 08/09/2022] [Indexed: 10/14/2022]
Abstract
The first-line drug Imatinib (IM) has achieved a curative effect in most chronic myeloid leukemia (CML) patients, but drug resistance remains a problem. More alternative therapeutic strategies need to explore. In recent years, targeting dysregulated DNA repair mechanisms provided promising options for cancer treatment. Here, we discovered the versatile Mediator of DNA Damage Checkpoint 1 (MDC1) interacted with γ-H2AX and 53BP1 in the early stage of the DNA damage response of cells. MDC1 overexpressed in CML cell lines and patients' bone marrow mononuclear cells. By knocking down MDC1, non-homologous end-joining pathways were mainly inhibited, leading to an intense accumulation of unrepaired intracellular DNA damage and an apparent cell apoptosis promotion. Notably, targeting MDC1 further enhanced drug sensitivity in IM-resistant CML cells. Our work revealed that MDC1 is a prospective target for CML treatment through regulating DNA damage repair mechanism, and also an alternative option for IM resistance dilemma. This study extends the understanding of regulating dysfunctional DNA repair mechanisms for cancer treatment.
Collapse
|
5
|
Small-Molecule Inhibitors Targeting FEN1 for Cancer Therapy. Biomolecules 2022; 12:biom12071007. [PMID: 35883563 PMCID: PMC9312813 DOI: 10.3390/biom12071007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/15/2022] [Accepted: 07/19/2022] [Indexed: 01/27/2023] Open
Abstract
DNA damage repair plays a key role in maintaining genomic stability and integrity. Flap endonuclease 1 (FEN1) is a core protein in the base excision repair (BER) pathway and participates in Okazaki fragment maturation during DNA replication. Several studies have implicated FEN1 in the regulation of other DNA repair pathways, including homologous recombination repair (HRR) and non-homologous end joining (NHEJ). Abnormal expression or mutation of FEN1 in cells can cause a series of pathological responses, leading to various diseases, including cancers. Moreover, overexpression of FEN1 contributes to drug resistance in several types of cancers. All this supports the hypothesis that FEN1 could be a therapeutic target for cancer treatment. Targeting FEN1 has been verified as an effective strategy in mono or combined treatment of cancer. Small-molecule compounds targeting FEN1 have also been developed and detected in cancer regression. In this review, we summarize the recent development of small-molecule inhibitors targeting FEN1 in recent years, thereby expanding their therapeutic potential and application.
Collapse
|