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Target Identification of 22-(4-Pyridinecarbonyl) Jorunnamycin A, a Tetrahydroisoquinoline Derivative from the Sponge Xestospongia sp., in Mediating Non-Small-Cell Lung Cancer Cell Apoptosis. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248948. [PMID: 36558080 PMCID: PMC9782168 DOI: 10.3390/molecules27248948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
A dysregulation of the cell-death mechanism contributes to poor prognosis in lung cancer. New potent chemotherapeutic agents targeting apoptosis-deregulating molecules have been discovered. In this study, 22-(4-pyridinecarbonyl) jorunnamycin A (22-(4'py)-JA), a synthetic derivative of bistetrahydroisoquinolinequinone from the Thai blue sponge, was semisynthesized by the Steglich esterification method, and its pharmacological mechanism in non-small-cell lung cancer (NSCLC) was elucidated by a network pharmacology approach. All predicted targets of 22-(4'py)-JA and genes related to NSCLC were retrieved from drug-target and gene databases. A total of 78 core targets were identified, and their associations were analyzed by STRING and Cytoscape. Gene ontology and KEGG pathway enrichment analyses revealed that molecules in mitogen-activated protein kinase (MAPK) signaling were potential targets of 22-(4'py)-JA in the induction of NSCLC apoptosis. In silico molecular docking analysis displayed a possible interaction of ERK1/2 and MEK1 with 22-(4'py)-JA. In vitro anticancer activity showed that 22-(4'py)-JA has strong cytotoxic and apoptosis-inducing effects in H460, H292 and A549 NSCLC cells. Furthermore, immunoblotting confirmed that 22-(4'py)-JA induced apoptotic cell death in an ERK/MEK/Bcl-2-dependent manner. The present study demonstrated that 22-(4'py)-JA exhibited a potent anticancer effect that could be further developed for clinical application and showed that network pharmacology approaches are a powerful tool to illustrate the molecular pathways of new drugs or compounds.
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DNA walker for signal amplification in living cells. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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3
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Song L, Zhuge Y, Zuo X, Li M, Wang F. DNA Walkers for Biosensing Development. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2200327. [PMID: 35460209 PMCID: PMC9366574 DOI: 10.1002/advs.202200327] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/07/2022] [Indexed: 05/07/2023]
Abstract
The ability to design nanostructures with arbitrary shapes and controllable motions has made DNA nanomaterials used widely to construct diverse nanomachines with various structures and functions. The DNA nanostructures exhibit excellent properties, including programmability, stability, biocompatibility, and can be modified with different functional groups. Among these nanoscale architectures, DNA walker is one of the most popular nanodevices with ingenious design and flexible function. In the past several years, DNA walkers have made amazing progress ranging from structural design to biological applications including constructing biosensors for the detection of cancer-associated biomarkers. In this review, the key driving forces of DNA walkers are first summarized. Then, the DNA walkers with different numbers of legs are introduced. Furthermore, the biosensing applications of DNA walkers including the detection- of nucleic acids, proteins, ions, and bacteria are summarized. Finally, the new frontiers and opportunities for developing DNA walker-based biosensors are discussed.
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Affiliation(s)
- Lu Song
- Department of CardiologyShanghai General HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200800China
- Institute of Molecular MedicineShanghai Key Laboratory for Nucleic Acid Chemistry and NanomedicineSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Ying Zhuge
- Department of CardiologyShanghai General HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200800China
| | - Xiaolei Zuo
- Institute of Molecular MedicineShanghai Key Laboratory for Nucleic Acid Chemistry and NanomedicineSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Min Li
- Institute of Molecular MedicineShanghai Key Laboratory for Nucleic Acid Chemistry and NanomedicineSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Fang Wang
- Department of CardiologyShanghai General HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200800China
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4
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Cui X, Qin F, Song L, Wang T, Geng B, Zhang W, Jin L, Wang W, Li S, Tian X, Zhang H, Cai J. Novel Biomarkers for the Precisive Diagnosis and Activity Classification of Takayasu Arteritis. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2020; 12:e002080. [PMID: 30645172 DOI: 10.1161/circgen.117.002080] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Establishing the diagnosis and determining disease activity of Takayasu arteritis (TA) remains challenging. Novel biomarkers might help to solve this problem. METHODS In the screening phase, by using large-scale protein arrays detecting samples from 90 subjects (TA active, 29; TA inactive 31; and controls, 30). In the validation phase, by using enzyme-linked immunosorbent assay (ELISA), potential biomarkers for TA diagnosis, and activity classification were measured in independent cohorts, respectively. RESULTS In the screening phase, 18 cytokines significantly differentially enriched between TA patients and controls and another 15 cytokines significantly differentially enriched between TA patient in active and inactive status were identified (adjusted P<0.05). In the validation phase, TIMP (tissue inhibitor of metalloproteinases)-1 was identified as a specific biomarker for TA diagnosis that a cutoff value of 221.86 μg/L could provide a specificity of 89.58% and a positive predictive value of 0.92. Meanwhile, we found it unreliable to use a single biomarker for TA activity classification. Considering this, we further built a logistic regression model based on multiple cytokines, including CA (cancer antigen) 125, FLRG (follistatin-related protein), IGFBP (insulin-like growth factor-binding protein)-2, CA15-3, GROa (growth-regulated alpha protein), LYVE (lymphatic vessel endothelial hyaluronic acid receptor)-1, ULBP (UL16-binding protein)-2, and CD (cluster of differentiation) 99, with an area under the curve reaching 0.909 for discriminating TA activity status. CONCLUSIONS This study suggested TIMP-1 as a specific biomarker for TA diagnosis with a cutoff value of 221.86 μg/L. Furthermore, we provided a logistic regression model based on 8 biomarkers for the precisive activity classification of TA with an area under the curve of 0.909.
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Affiliation(s)
- Xiao Cui
- Hypertension Center, Fuwai Hospital, State Key Laboratory of Cardiovascular Diseases, National Center for Cardiovascular Diseases (X.C., F.Q., L.S., B.G., W.Z., L.J., W.W., S.L., H.Z., J.C.), Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P.R. China.,Cardiovascular Disease Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, P.R. China (X.C.)
| | - Fang Qin
- Hypertension Center, Fuwai Hospital, State Key Laboratory of Cardiovascular Diseases, National Center for Cardiovascular Diseases (X.C., F.Q., L.S., B.G., W.Z., L.J., W.W., S.L., H.Z., J.C.), Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P.R. China.,Department of Cardiology, Chongqing Cardiac Arrhythmias Therapeutic Service Center, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, P.R. China (F.Q.)
| | - Lei Song
- Hypertension Center, Fuwai Hospital, State Key Laboratory of Cardiovascular Diseases, National Center for Cardiovascular Diseases (X.C., F.Q., L.S., B.G., W.Z., L.J., W.W., S.L., H.Z., J.C.), Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P.R. China
| | - Tian Wang
- Department of Rheumatology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart, Lung and Blood Vessel Disease, Beijing, P.R. China (T.W.)
| | - Bin Geng
- Hypertension Center, Fuwai Hospital, State Key Laboratory of Cardiovascular Diseases, National Center for Cardiovascular Diseases (X.C., F.Q., L.S., B.G., W.Z., L.J., W.W., S.L., H.Z., J.C.), Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P.R. China
| | - Weili Zhang
- Hypertension Center, Fuwai Hospital, State Key Laboratory of Cardiovascular Diseases, National Center for Cardiovascular Diseases (X.C., F.Q., L.S., B.G., W.Z., L.J., W.W., S.L., H.Z., J.C.), Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P.R. China
| | - Ling Jin
- Hypertension Center, Fuwai Hospital, State Key Laboratory of Cardiovascular Diseases, National Center for Cardiovascular Diseases (X.C., F.Q., L.S., B.G., W.Z., L.J., W.W., S.L., H.Z., J.C.), Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P.R. China
| | - Wenjie Wang
- Hypertension Center, Fuwai Hospital, State Key Laboratory of Cardiovascular Diseases, National Center for Cardiovascular Diseases (X.C., F.Q., L.S., B.G., W.Z., L.J., W.W., S.L., H.Z., J.C.), Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P.R. China
| | - Shuangyue Li
- Hypertension Center, Fuwai Hospital, State Key Laboratory of Cardiovascular Diseases, National Center for Cardiovascular Diseases (X.C., F.Q., L.S., B.G., W.Z., L.J., W.W., S.L., H.Z., J.C.), Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P.R. China
| | - Xinping Tian
- Department of Rheumatology, Peking Union Medical College Hospital (X.T.), Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P.R. China
| | - Huimin Zhang
- Hypertension Center, Fuwai Hospital, State Key Laboratory of Cardiovascular Diseases, National Center for Cardiovascular Diseases (X.C., F.Q., L.S., B.G., W.Z., L.J., W.W., S.L., H.Z., J.C.), Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P.R. China
| | - Jun Cai
- Hypertension Center, Fuwai Hospital, State Key Laboratory of Cardiovascular Diseases, National Center for Cardiovascular Diseases (X.C., F.Q., L.S., B.G., W.Z., L.J., W.W., S.L., H.Z., J.C.), Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P.R. China
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Yuwen L, Ciqiu Y, Yi S, Ruilei L, Yuanhui L, Bo L, Songqi L, Weiming L, Jie L. A Pilot Study of Protein Microarray for Simultaneous Analysis of 274 Cytokines Between Abdominal Aortic Aneurysm and Normal Aorta. Angiology 2019; 70:830-837. [PMID: 31018647 DOI: 10.1177/0003319719844678] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Cytokines play an important role in the pathogenesis of abdominal aortic aneurysm (AAA). We evaluated the cytokine expression profile of large AAA walls using a 274-cytokine protein array. We hypothesized that AAAs are characterized by an inflammatory, chemotactic cytokine profile. We investigated the cytokine expression profile of 12 patients with AAA and 6 nonaneurysmal controls using an antibody-based protein array. The array generated antibodies against homogenized human aortic tissues to validate the cytokines differentially expressed in AAAs and normal aortas. Data were quantified using fluorescent signal intensities and statistically analyzed by the t test. Fifty-nine cytokines were differentially expressed between the AAA and control samples. Of the 35 selected cytokines that had relative expression >1000, 29 were significantly higher and 6 were lower in AAA samples than in controls. They respectively belonged to CC chemokines, CXC chemokines, pro-inflammatory cytokines, growth factors, proteolytic proteins and inhibitors, and cell adhesion cytokines. Our results show that distinct cytokines are involved in AAAs and suggest that the pathways involving these cytokines may be associated with the pathogenesis and development of AAAs. These findings, if confirmed by larger studies, may suggest treatment targets.
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Affiliation(s)
- Li Yuwen
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Yang Ciqiu
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People’s Hospital & Guangdong Academy of Medical Sciences, Guangzhou, Guangdong Province, China
| | - Shi Yi
- Division of Vascular Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Liu Ruilei
- Department of Breast and Thyroid Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Lai Yuanhui
- Division of Vascular Surgery, The Eastern Hospital of the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Lin Bo
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Li Songqi
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Lv Weiming
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Li Jie
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong Province, China
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Lv H, Ye L, Liu Q, Li SG, Li T, Huang NL, Gao Y, Fan LB, Du WD. S-S-PEG-COOH Self-Assembled Monolayer on Gold Surface Enabled a Combined Assay for Serological EBV Antibody Isotypes. Proteomics Clin Appl 2018; 13:e1800067. [PMID: 30311429 DOI: 10.1002/prca.201800067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 09/13/2018] [Indexed: 11/09/2022]
Abstract
PURPOSE Epstein-Barr virus (EBV) is a ubiquitous human gamma herpes virus that infects human epithelial cells and B lymphocytes. It would be potentially valuable to develop novel combined assays to benefit screening for large panels of samples of EBV infectious diseases. EXPERIMENTAL DESIGN A simple antigen-probed biochip that is modified with S-S-PEG-COOH and is used as a label-free high-throughput screening method for a combined detection of EBV capsid antigen IgM antibody, capsid antigen IgG antibody, and nuclear antigen IgG antibody. RESULTS This protein biochip has similar feasibility, sensitivity, and specificity in comparison with Liaison chemiluminescent immunoassay (CLIA). Detection limit of the EBV antibodies by the biochip is almost identical to that by CLIA-L (2.91 U mL-1 vs 3.00 U mL-1 for EBNA-1 IgG, 8 U mL-1 vs10 U mL-1 for EBV-VCA IgG, and 3.5 U mL-1 vs 10 U mL-1 for EBV-VCA IgM). Tests of the three serological antibodies against EBV by the biochip are consistent with the CLIA-L method in 274 clinical sera, respectively. Finally, the combined biochip is successfully utilized for diagnostic identification of EBV infection in 14 patients with infectious mononucleosis (IM) and 25 patients with systemic lupus erythematosus SLE, as well as additional 10 known real-time PCR positive patients. CONCLUSIONS AND CLINICAL RELEVANCE This biochip format will enable concurrent detection of antibodies against EBV infection and confirm infection status of EBV. It will be a versatile tool for large-scale epidemiological screening in view of its miniaturization and high throughput.
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Affiliation(s)
- Hui Lv
- Department of Biology, School of Life Sciences, Anhui Medical University, Hefei, 230032, China
| | - Lei Ye
- Department of Pathology, Anhui Medical University, Hefei, 230032, China
| | - Qian Liu
- Department of Pathology, Anhui Medical University, Hefei, 230032, China
| | - Song-Guo Li
- Department of Pathology, Anhui Medical University, Hefei, 230032, China
| | - Tao Li
- Department of Clinical Laboratory, The First Affiliated Hospital, Anhui Medical University, Hefei, 230022, China
| | - Na-Li Huang
- Department of Biology, School of Life Sciences, Anhui Medical University, Hefei, 230032, China
| | - Yi Gao
- Department of Pathology, Anhui Medical University, Hefei, 230032, China
| | - Li-Bin Fan
- Department of Biology, School of Life Sciences, Anhui Medical University, Hefei, 230032, China
| | - Wei-Dong Du
- Department of Pathology, Anhui Medical University, Hefei, 230032, China
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7
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Sola L, Gagni P, D’Annessa I, Capelli R, Bertino C, Romanato A, Damin F, Bergamaschi G, Marchisio E, Cuzzocrea A, Bombaci M, Grifantini R, Chiari M, Colombo G, Gori A, Cretich M. Enhancing Antibody Serodiagnosis Using a Controlled Peptide Coimmobilization Strategy. ACS Infect Dis 2018; 4:998-1006. [PMID: 29570266 DOI: 10.1021/acsinfecdis.8b00014] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Antigen immunoreactivity is often determined by surface regions defined by the 3D juxtapositions of amino acids stretches that are not continuous in the linear sequence. As such, mimicking an antigen immunoreactivity by means of putative linear peptide epitopes for diagnostic purposes is not trivial. Here we present a straightforward and robust method to extend the reach of immune-diagnostic probes design by copresenting peptides belonging to the same antigenic surface. In this case study focused on a computationally predicted Zika virus NS1 protein putative antigenic region, we reached a diagnostic confidence by the oriented and spatially controlled coimmobilization of peptide sequences found adjacent within the protein fold, that cooperatively interacted to provide enhanced immunoreactivity with respect to single linear epitopes. Through our method, we were able to differentiate Zika infected individuals from healthy controls. Remarkably, our strategy fits well with the requirements to build high-throughput screening platforms of linear and mixed peptide libraries, and it could possibly facilitate the rapid identification of conformational immunoreactive regions.
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Affiliation(s)
- Laura Sola
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Paola Gagni
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Ilda D’Annessa
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Riccardo Capelli
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Camilla Bertino
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Alessandro Romanato
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Francesco Damin
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Greta Bergamaschi
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Edoardo Marchisio
- Diagnostic Bioprobes s.r.l. (DiaPro), via G. Carducci 27, 20090 Sesto San Giovanni, Italy
| | - Angela Cuzzocrea
- Diagnostic Bioprobes s.r.l. (DiaPro), via G. Carducci 27, 20090 Sesto San Giovanni, Italy
| | - Mauro Bombaci
- Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi” (INGM), Via Francesco Sforza. 35, 20122 Milano, Italy
| | - Renata Grifantini
- Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi” (INGM), Via Francesco Sforza. 35, 20122 Milano, Italy
| | - Marcella Chiari
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Giorgio Colombo
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
- Dipartimento di Chimica, Università di Pavia, V.le Taramelli 12, 27100 Pavia, Italy
| | - Alessandro Gori
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
| | - Marina Cretich
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Via Mario Bianco, 9, 20131 Milano, Italy
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Sakaguchi I, Fukasawa T, Fujimoto K, Inouye M. Immobilization of Crosslinked Peptides that Possess High Helical Contents and Their Binding to Target DNAs on Au Surfaces. CHEM LETT 2018. [DOI: 10.1246/cl.171153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ikumi Sakaguchi
- Graduate School of Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Toshiaki Fukasawa
- Graduate School of Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Kazuhisa Fujimoto
- Department of Applied Chemistry and Biochemistry, Kyushu Sangyo University, Fukuoka 813-8503, Japan
| | - Masahiko Inouye
- Graduate School of Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
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9
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Kathera C, Zhang J, Janardhan A, Sun H, Ali W, Zhou X, He L, Guo Z. Interacting partners of FEN1 and its role in the development of anticancer therapeutics. Oncotarget 2017; 8:27593-27602. [PMID: 28187440 PMCID: PMC5432360 DOI: 10.18632/oncotarget.15176] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 01/24/2017] [Indexed: 11/25/2022] Open
Abstract
Protein-protein interaction (PPI) plays a key role in cellular communication, Protein-protein interaction connected with each other with hubs and nods involved in signaling pathways. These interactions used to develop network based biomarkers for early diagnosis of cancer. FEN1(Flap endonuclease 1) is a central component in cellular metabolism, over expression and decrease of FEN1 levels may cause cancer, these regulation changes of Flap endonuclease 1reported in many cancer cells, to consider this data may needs to develop a network based biomarker. The current review focused on types of PPI, based on nature, detection methods and its role in cancer. Interacting partners of Flap endonuclease 1 role in DNA replication repair and development of anticancer therapeutics based on Protein-protein interaction data.
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Affiliation(s)
- Chandrasekhar Kathera
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jing Zhang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Avilala Janardhan
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Hongfang Sun
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wajid Ali
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaolong Zhou
- The Laboratory of Animal Genetics, Breeding, and Reproduction, College of Animal Science and Technology, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Lingfeng He
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhigang Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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10
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Palma A, Tinti M, Paoluzi S, Santonico E, Brandt BW, Hooft van Huijsduijnen R, Masch A, Heringa J, Schutkowski M, Castagnoli L, Cesareni G. Both Intrinsic Substrate Preference and Network Context Contribute to Substrate Selection of Classical Tyrosine Phosphatases. J Biol Chem 2017; 292:4942-4952. [PMID: 28159843 DOI: 10.1074/jbc.m116.757518] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 01/31/2017] [Indexed: 01/19/2023] Open
Abstract
Reversible tyrosine phosphorylation is a widespread post-translational modification mechanism underlying cell physiology. Thus, understanding the mechanisms responsible for substrate selection by kinases and phosphatases is central to our ability to model signal transduction at a system level. Classical protein-tyrosine phosphatases can exhibit substrate specificity in vivo by combining intrinsic enzymatic specificity with the network of protein-protein interactions, which positions the enzymes in close proximity to their substrates. Here we use a high throughput approach, based on high density phosphopeptide chips, to determine the in vitro substrate preference of 16 members of the protein-tyrosine phosphatase family. This approach helped identify one residue in the substrate binding pocket of the phosphatase domain that confers specificity for phosphopeptides in a specific sequence context. We also present a Bayesian model that combines intrinsic enzymatic specificity and interaction information in the context of the human protein interaction network to infer new phosphatase substrates at the proteome level.
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Affiliation(s)
- Anita Palma
- From the Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Michele Tinti
- From the Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Serena Paoluzi
- From the Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Elena Santonico
- From the Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Bernd Willem Brandt
- the Centre for Integrative Bioinformatics, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands, and
| | | | - Antonia Masch
- the Institut für Biochemie & Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, 06108 Halle, Germany
| | - Jaap Heringa
- the Centre for Integrative Bioinformatics, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands, and
| | - Mike Schutkowski
- the Institut für Biochemie & Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, 06108 Halle, Germany
| | - Luisa Castagnoli
- From the Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Gianni Cesareni
- From the Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy,
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11
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Santos A, Bueno PR. Glycoprotein assay based on the optimized immittance signal of a redox tagged and lectin-based receptive interface. Biosens Bioelectron 2016; 83:368-78. [DOI: 10.1016/j.bios.2016.04.043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 04/08/2016] [Accepted: 04/14/2016] [Indexed: 12/29/2022]
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12
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A Cell Microarray Format: A Peptide Release System Using a Photo-Cleavable Linker for Cell Toxicity and Cell Uptake Analysis. Methods Mol Biol 2016; 1352:199-210. [PMID: 26490477 DOI: 10.1007/978-1-4939-3037-1_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
There has been increasing interest in the potential use of microarray technologies to perform systematic and high-throughput cell-based assays. We are currently focused on developing more practical array formats and detection methods that will enable researchers to conduct more detailed analyses in cell microarray studies. In this chapter, we describe the construction of a novel peptide-array format system for analyzing cellular toxicity and cellular uptake. In this system, a peptide is immobilized at the bottom of a conventional 96-well plate using a photo-cleavable linker. The peptide can then be released from the bottom by irradiating the desired wells with UV light, thus allowing the cytotoxicity or cellular uptake of the peptide to be monitored. This system will facilitate the realization of high-throughput cell arrays for cellomics analyses and cell-based phenotypic drug screens.
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Syahir A, Tomizaki KY, Kajikawa K, Mihara H. Anomalous Reflection of Gold: A Novel Platform for Biochips. Methods Mol Biol 2015; 1352:97-110. [PMID: 26490470 DOI: 10.1007/978-1-4939-3037-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
The importance of protein detection system for protein functions analyses in recent post-genomic era is rising with the emergence of label-free protein detection methods. We are focusing on a simple and practical label-free optical-detection method called anomalous reflection (AR) of gold. When a molecular layer forms on the gold surface, significant reduction in reflectivity can be observed at wavelengths of 400-500 nm. This allows the detection of molecular interactions by monitoring changes in reflectivity. In this chapter, we describe the AR method with three different application platforms: (1) gold, (2) gold containing alloy/composite (AuAg2O), and (3) metal-insulator-metal (MIM) thin layers. The AuAg2O composite and MIM are implemented as important concepts for signal enhancement process for the AR technique. Moreover, the observed molecular adsorption and activity is aided by a three-dimensional surface geometry, performed using poly(amidoamine) or PAMAM dendrimer modification. The described system is suitable to be used as a platform for high-throughput detection system in a chip format.
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Affiliation(s)
- Amir Syahir
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400, Malaysia.
| | - Kin-ya Tomizaki
- Department of Materials Chemistry, Ryukoku University, Seta-Oe, Otsu, 520-2194, Japan
| | - Kotaro Kajikawa
- Department of Electronics and Applied Physics, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, Yokohama, 226-8502, Japan
| | - Hisakazu Mihara
- Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
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Label and Label-Free Detection Techniques for Protein Microarrays. MICROARRAYS 2015; 4:228-44. [PMID: 27600222 PMCID: PMC4996399 DOI: 10.3390/microarrays4020228] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 04/10/2015] [Accepted: 04/17/2015] [Indexed: 02/02/2023]
Abstract
Protein microarray technology has gone through numerous innovative developments in recent decades. In this review, we focus on the development of protein detection methods embedded in the technology. Early microarrays utilized useful chromophores and versatile biochemical techniques dominated by high-throughput illumination. Recently, the realization of label-free techniques has been greatly advanced by the combination of knowledge in material sciences, computational design and nanofabrication. These rapidly advancing techniques aim to provide data without the intervention of label molecules. Here, we present a brief overview of this remarkable innovation from the perspectives of label and label-free techniques in transducing nano-biological events.
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BioPen: direct writing of functional materials at the point of care. Sci Rep 2014; 4:4872. [PMID: 24799039 PMCID: PMC4010928 DOI: 10.1038/srep04872] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 04/10/2014] [Indexed: 01/09/2023] Open
Abstract
Rapid and precise patterning of functional biomaterials is desirable for point-of-care (POC) tissue engineering and diagnostics. However, existing technologies such as dip-pen nanolithography and inkjet printing are currently unsuitable for POC applications due to issues of cost and portability. Here, we report the development of ‘BioPen', a portable tool for continuous, defined and scalable deposition of functional materials with micrometer spatial resolution and nanolitre volumetric resolution. BioPen is based upon the ballpoint pen but with multiple “ink sources” (functional material solutions) and with an apparatus that can be optimized for writing living cells, proteins, nucleic acids, etc. We demonstrate POC detection of human immunodeficiency virus type 1 (HIV-1) nucleic acid by writing on paper with BioPen using “ink” consisting of nucleic acid probes and nucleic acid-modified gold nanoparticles. We also demonstrate POC tissue engineering by writing a continuous pattern of living, functional, interconnected cells with a defined extracellular environment. Because it is simple, accurate, inexpensive and portable, BioPen has broad potential for POC detection of diagnostic biomarkers, and for POC engineering of tissues for a range of healing applications.
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Wong CL, Chen GCK, Li X, Ng BK, Shum P, Chen P, Lin Z, Lin C, Olivo M. Colorimetric surface plasmon resonance imaging (SPRI) biosensor array based on polarization orientation. Biosens Bioelectron 2013; 47:545-52. [DOI: 10.1016/j.bios.2013.02.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 02/06/2013] [Accepted: 02/22/2013] [Indexed: 10/27/2022]
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Kakiyama T, Usui K, Tomizaki KY, Mie M, Kobatake E, Mihara H. A peptide release system using a photo-cleavable linker in a cell array format for cell-toxicity analysis. Polym J 2013. [DOI: 10.1038/pj.2013.20] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Usui K, Kikuchi T, Tomizaki KY, Kakiyama T, Mihara H. A novel array format for monitoring cellular uptake using a photo-cleavable linker for peptide release. Chem Commun (Camb) 2013; 49:6394-6. [DOI: 10.1039/c3cc41632a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Pai J, Yoon T, Kim ND, Lee IS, Yu J, Shin I. High-throughput profiling of peptide-RNA interactions using peptide microarrays. J Am Chem Soc 2012; 134:19287-96. [PMID: 23110629 DOI: 10.1021/ja309760g] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A rapid and quantitative method to evaluate binding properties of hairpin RNAs to peptides using peptide microarrays has been developed. The microarray technology was shown to be a powerful tool for high-throughput analysis of RNA-peptide interactions by its application to profiling interactions between 111 peptides and six hairpin RNAs. The peptide microarrays were also employed to measure hundreds of dissociation constants (K(d)) of RNA-peptide complexes. Our results reveal that both hydrophobic and hydrophilic faces of amphiphilic peptides are likely involved in interactions with RNAs. Furthermore, these results also show that most of the tested peptides bind hairpin RNAs with submicromolar K(d) values. One of the peptides identified by using this method was found to have good inhibitory activity against TAR-Tat interactions in cells. Because of their great applicability to evaluation of nearly all types of RNA-peptide interactions, peptide microarrays are expected to serve as robust tools for rapid assessment of peptide-RNA interactions and development of peptide ligands against RNA targets.
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Affiliation(s)
- Jaeyoung Pai
- National Creative Research Center for Biofunctional Molecules, Department of Chemistry, Yonsei University, Seoul 120-749, Korea
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20
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Leptospiral outer membrane protein microarray, a novel approach to identification of host ligand-binding proteins. J Bacteriol 2012; 194:6074-87. [PMID: 22961849 DOI: 10.1128/jb.01119-12] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Leptospirosis is a zoonosis with worldwide distribution caused by pathogenic spirochetes belonging to the genus Leptospira. The leptospiral life cycle involves transmission via freshwater and colonization of the renal tubules of their reservoir hosts. Infection requires adherence to cell surfaces and extracellular matrix components of host tissues. These host-pathogen interactions involve outer membrane proteins (OMPs) expressed on the bacterial surface. In this study, we developed an Leptospira interrogans serovar Copenhageni strain Fiocruz L1-130 OMP microarray containing all predicted lipoproteins and transmembrane OMPs. A total of 401 leptospiral genes or their fragments were transcribed and translated in vitro and printed on nitrocellulose-coated glass slides. We investigated the potential of this protein microarray to screen for interactions between leptospiral OMPs and fibronectin (Fn). This approach resulted in the identification of the recently described fibronectin-binding protein, LIC10258 (MFn8, Lsa66), and 14 novel Fn-binding proteins, denoted Microarray Fn-binding proteins (MFns). We confirmed Fn binding of purified recombinant LIC11612 (MFn1), LIC10714 (MFn2), LIC11051 (MFn6), LIC11436 (MFn7), LIC10258 (MFn8, Lsa66), and LIC10537 (MFn9) by far-Western blot assays. Moreover, we obtained specific antibodies to MFn1, MFn7, MFn8 (Lsa66), and MFn9 and demonstrated that MFn1, MFn7, and MFn9 are expressed and surface exposed under in vitro growth conditions. Further, we demonstrated that MFn1, MFn4 (LIC12631, Sph2), and MFn7 enable leptospires to bind fibronectin when expressed in the saprophyte, Leptospira biflexa. Protein microarrays are valuable tools for high-throughput identification of novel host ligand-binding proteins that have the potential to play key roles in the virulence mechanisms of pathogens.
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Timucin C, Gul O, Kutuk O, Basaga H. ANTIBODY ARRAY–BASED IMMUNOSENSOR FOR DETECTING CARDIOVASCULAR DISEASE RISK MARKERS. J Immunoassay Immunochem 2012; 33:275-90. [DOI: 10.1080/15321819.2011.638407] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Seehuber A, Schmidt D, Dahint R. Poly(acrylic acid)-poly(ethylene glycol) layers on positively charged surface coatings: molecular structure, protein resistance, and application to single protein deposition. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:8700-8710. [PMID: 22571171 DOI: 10.1021/la2050652] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A new copolymer (PAA-PEG2000) has been designed, consisting of a negatively charged poly(acrylic acid) (PAA) backbone to which poly(ethylene glycol) (PEG) side chains with a molecular weight of about 2 kDa were grafted in a molecular ratio of 3:10. It readily adsorbs to positively charged surfaces and may be considered to be the anionic counterpart of PEG-grafted poly(l-lysine) (PLL-PEG), which was first described by Kenausis et al. and is widely used to render negatively charged surfaces protein-resistant. The synthesis of PAA-PEG2000 can be carried out in aqueous solution at room temperature and does not require any sophisticated techniques such as handling in an inert gas atmosphere. Using ellipsometry and infrared reflection absorption spectroscopy (IRRAS), the film structure has been carefully analyzed for copolymer adsorption onto three different positively charged surfaces, namely, thin layers of poly(allylamine) (PAH), poly(ethyleneimine) (PEI) and (3-aminopropyl)triethoxysilane (APTES). Besides the film thickness, the conformation of the PEG chains and their orientation with respect to the surface normal appear to be important parameters for the protein resistance of the films. Although PAA-PEG2000 adsorbed to PAH and PEI renders the surfaces inert, only partial protein resistance has been observed if the copolymer is deposited on APTES. In a model application, we have generated heterogeneous surfaces composed of isolated small Au nanoparticles (AuNP's) embedded in a protein-resistant layer of PAA-PEG2000 and demonstrated that the AuNP's can serve as adsorption sites for single protein species. In the future, these nanopatterned surfaces may be used for the investigation of isolated proteins.
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Affiliation(s)
- Andrea Seehuber
- Applied Physical Chemistry, University of Heidelberg, 69120 Heidelberg, Germany
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Syahir A, Kajikawa K, Mihara H. Sensitive Detection of Small Molecule–Protein Interactions on a Metal–Insulator–Metal Label‐Free Biosensing Platform. Chem Asian J 2012; 7:1867-74. [DOI: 10.1002/asia.201200138] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2012] [Revised: 04/03/2012] [Indexed: 12/16/2022]
Affiliation(s)
- Amir Syahir
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226‐8501 (Japan), Fax: (+81) 45‐924‐5756
| | - Kotaro Kajikawa
- Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, Yokohama 226‐8502 (Japan)
| | - Hisakazu Mihara
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226‐8501 (Japan), Fax: (+81) 45‐924‐5756
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Sin EJ, Moon YS, Lee YK, Lim JO, Huh JS, Choi SY, Sohn YS. SURFACE MODIFICATION OF ALUMINUM OXIDE FOR BIOSENSING APPLICATION. BIOMEDICAL ENGINEERING-APPLICATIONS BASIS COMMUNICATIONS 2012. [DOI: 10.4015/s1016237212500093] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The surface modification for immobilization of antibodies on the aluminum oxide surface was developed for biosensing application. The aluminum oxide has been received much attention since it has various advantages including low cost, hardness, resistance to organic solvents, and high capacitance. In addition, the aluminum oxide can prevent the leakage current in the electrical detection. For development of the protein anchorable surface, the aluminum oxide chip was treated with oxygen plasma and directly immersed in ethanol and toluene solution of 3-aminopropyltriethoxysilane (APTES). Next, this amine modified chip was immersed in the glutaraldehyde solution that contained sodium cyanoborohydride. Finally, the fluorescent materials, the Alexa 488, and the FITC conjugated anti-IgG were reacted to the aldehyde-modified surface. To verify the modified surface, the intensity of the fluorescence was measured and compared. The higher intensity of the fluorescence was observed when the APTES was dissolved in toluene rather than in ethanol. From the highest intensity of the fluorescence observed, the FITC conjugated anti-IgG was well immobilized on the modified surface of the aluminum oxide with APTES and glutaraldehyde. Thus, the proposed surface modification method can immobilize the proteins including antibodies, and can be applied for the various biological researches including biosensors and biochips.
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Affiliation(s)
- Eun Jung Sin
- Department of Biomedical Engineering, Catholic University of Daegu, Gyeongsan-si, Gyeongbuk 712-702, Republic of Korea
| | - Young-Soon Moon
- Department of Sensors and Display Engineering, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Yeon Kyung Lee
- Department of Biomedical Engineering, Catholic University of Daegu, Gyeongsan-si, Gyeongbuk 712-702, Republic of Korea
| | - Jeong-Ok Lim
- Biomedical Research Institute, Kyungpook National University School of Medicine, Daegu 700-721, Republic of Korea
| | - Jeung-Soo Huh
- School of Material Science and Engineering, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Sie-Young Choi
- Department of Sensors and Display Engineering, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Young-Soo Sohn
- Department of Biomedical Engineering, Catholic University of Daegu, Gyeongsan-si, Gyeongbuk 712-702, Republic of Korea
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Sharivkin R, Walker MD, Soen Y. Proteomics-based dissection of human endoderm progenitors by differential cell capture on antibody array. Mol Cell Proteomics 2012; 11:586-95. [PMID: 22580589 DOI: 10.1074/mcp.m111.016840] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Heterogeneity, shortage of material, and lack of progenitor-specific cell surface markers are major obstacles to elucidating the mechanisms underlying developmental processes. Here we report a proteomics platform that alleviates these difficulties and demonstrate its effectiveness in fractionating heterogeneous cultures of early endoderm derived from human embryonic stem cells. The approach, designated differential cell-capture antibody array, is based on highly parallel, comparative screening of live cell populations using hundreds of antibodies directed against cell-surface antigens. We used this platform to fractionate the hitherto unresolved early endoderm compartment of CXCR4+ cells and identify several endoderm (CD61+ and CD63+) and non-endoderm (CD271+, CD49F+, CD44+ and B2M+) sub-populations. We provide evidence that one of these sub-populations, CD61+, is directly derived from CXCR4+ cells, displays characteristic kinetics of emergence, and exhibits a distinct gene expression profile. The results demonstrate the potential of the cell-capture antibody array as a powerful proteomics tool for detailed dissection of heterogeneous cellular systems.
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Affiliation(s)
- Revital Sharivkin
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel
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26
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Dasilva N, Díez P, Matarraz S, González-González M, Paradinas S, Orfao A, Fuentes M. Biomarker discovery by novel sensors based on nanoproteomics approaches. SENSORS 2012; 12:2284-308. [PMID: 22438764 PMCID: PMC3304166 DOI: 10.3390/s120202284] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 01/20/2012] [Accepted: 02/14/2012] [Indexed: 12/23/2022]
Abstract
During the last years, proteomics has facilitated biomarker discovery by coupling high-throughput techniques with novel nanosensors. In the present review, we focus on the study of label-based and label-free detection systems, as well as nanotechnology approaches, indicating their advantages and applications in biomarker discovery. In addition, several disease biomarkers are shown in order to display the clinical importance of the improvement of sensitivity and selectivity by using nanoproteomics approaches as novel sensors.
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Affiliation(s)
- Noelia Dasilva
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), Departamento de Medicina and Servicio General de Citometría, University of Salamanca, Salamanca 37007, Spain; E-Mails: (N.D.); (P.D.); (S.M.); (M.G.-G.); (A.O.)
| | - Paula Díez
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), Departamento de Medicina and Servicio General de Citometría, University of Salamanca, Salamanca 37007, Spain; E-Mails: (N.D.); (P.D.); (S.M.); (M.G.-G.); (A.O.)
| | - Sergio Matarraz
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), Departamento de Medicina and Servicio General de Citometría, University of Salamanca, Salamanca 37007, Spain; E-Mails: (N.D.); (P.D.); (S.M.); (M.G.-G.); (A.O.)
| | - María González-González
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), Departamento de Medicina and Servicio General de Citometría, University of Salamanca, Salamanca 37007, Spain; E-Mails: (N.D.); (P.D.); (S.M.); (M.G.-G.); (A.O.)
| | - Sara Paradinas
- Departamento de Química Analítica, Facultad de Ciencias Químicas, University of Salamanca, Salamanca 37008, Spain; E-Mail:
| | - Alberto Orfao
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), Departamento de Medicina and Servicio General de Citometría, University of Salamanca, Salamanca 37007, Spain; E-Mails: (N.D.); (P.D.); (S.M.); (M.G.-G.); (A.O.)
| | - Manuel Fuentes
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), Departamento de Medicina and Servicio General de Citometría, University of Salamanca, Salamanca 37007, Spain; E-Mails: (N.D.); (P.D.); (S.M.); (M.G.-G.); (A.O.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +34-923-294-811; Fax: +34-923-294-743
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Tomizaki KY, Obi M, Mihara H. Noncompetitive On-Chip Immunoassays for Detection of Nonlabeled Antibodies Based on the Excluded Volume Effect of the Target Itself. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2012. [DOI: 10.1246/bcsj.20110239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Kin-ya Tomizaki
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology
- Innovative Materials and Processing Research Center, Ryukoku University
- Department of Materials Chemistry, Ryukoku University
| | - Masaki Obi
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology
| | - Hisakazu Mihara
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology
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Kong DH, Jung JW, Na K, Jeong SK, Paik YK, Jung SH, Suh IB, Kim YM, Ha KS. Normalization using a tagged-internal standard assay for analysis of antibody arrays and the evaluation of serological biomarkers for liver disease. Anal Chim Acta 2012; 718:92-8. [PMID: 22305903 DOI: 10.1016/j.aca.2011.12.055] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 12/09/2011] [Accepted: 12/16/2011] [Indexed: 01/08/2023]
Abstract
For minimizing systemic experimental variation in the analysis of antibody array data, we developed a novel median-centered/IgM-tagged-internal standard (TIS) assay normalization using median-centering and TIS assay-based determination of serum IgM concentrations. We evaluated five normalization methods by analyzing correlation coefficients and coefficients of variation for six serum proteins using human serum samples from normal controls (n=25) and patients with liver cirrhosis (n=25) or hepatocellular carcinoma (HCC; n=29). Median-centered normalization improved correlation coefficients, while IgM-based normalizations improved coefficients of variation. The TIS assay was more efficient, economical, and reproducible for determining IgM concentrations than enzyme-linked immunosorbent assay. Additionally, we normalized antibody array data for six serum proteins using the median-centered/IgM-TIS assay, and evaluated serum biomarkers through distribution analysis of normalized fluorescence intensities and receiver operating characteristic analyses for the diagnosis of liver cirrhosis and HCC. Apolipoprotein A-1 and a combination of alpha-fetoprotein and C-reactive protein were determined to be potential serological biomarkers for liver cirrhosis and HCC, respectively. Thus, median-centered/IgM-TIS assay normalization is a useful approach for analyzing antibody array data and evaluating serological biomarkers for the diagnosis of liver disease or cancers.
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Affiliation(s)
- Deok-Hoon Kong
- Department of Molecular and Cellular Biochemistry, Kangwon National University School of Medicine, Chuncheon, Kangwon-Do, Republic of Korea
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Usui K, Kakiyama T, Tomizaki KY, Mie M, Kobatake E, Mihara H. Cell fingerprint patterns using designed α-helical peptides to screen for cell-specific toxicity. Bioorg Med Chem Lett 2011; 21:6281-4. [PMID: 21940168 DOI: 10.1016/j.bmcl.2011.09.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 08/29/2011] [Accepted: 09/01/2011] [Indexed: 12/16/2022]
Abstract
We conducted cell-based cytotoxicity screening of a 101-membered α-helical peptide library using cell fingerprints (CFPs). The CFP data suggested that there is a relationship between cytotoxicity and peptide characteristics, such as hydrophobicity, charge, and amino acid composition. In spite of the small size of the library used in this study, several peptides demonstrated cell-specific toxicity. The strategy of combining a designed peptide library with CFP thus shows real promise for peptide-based screening with cells.
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Affiliation(s)
- Kenji Usui
- Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan.
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De Marni ML, Monegal A, Venturini S, Vinati S, Carbone R, de Marco A. Antibody purification-independent microarrays (PIM) by direct bacteria spotting on TiO2-treated slides. Methods 2011; 56:317-25. [PMID: 21736943 DOI: 10.1016/j.ymeth.2011.06.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Revised: 06/17/2011] [Accepted: 06/20/2011] [Indexed: 11/30/2022] Open
Abstract
The preparation of effective conventional antibody microarrays depends on the availability of high quality material and on the correct accessibility of the antibody active moieties following their immobilization on the support slide. We show that spotting bacteria that expose recombinant antibodies on their external surface directly on nanostructured-TiO(2) or epoxy slides (purification-independent microarray - PIM) is a simple and reliable alternative for preparing sensitive and specific microarrays for antigen detection. Variable domains of single heavy-chain antibodies (VHHs) against fibroblast growth factor receptor 1 (FGFR1) were used to capture the antigen diluted in serum or BSA solution. The FGFR1 detection was performed by either direct antigen labeling or using a sandwich system in which FGFR1 was first bound to its antibody and successively identified using a labeled FGF. In both cases the signal distribution within each spot was uniform and spot morphology regular. The signal-to-noise ratio of the signal was extremely elevated and the specificity of the system was proved statistically. The LOD of the system for the antigen was calculated being 0.4ng/mL and the dynamic range between 0.4ng/mL and 10μg/mL. The microarrays prepared with bacteria exposing antibodies remain fully functional for at least 31 days after spotting. We finally demonstrated that the method is suitable for other antigen-antibody pairs and expect that it could be easily adapted to further applications such as the display of scFv and IgG antibodies or the autoantibody detection using protein PIMs.
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Silicon biochips for dual label-free and fluorescence detection: Application to protein microarray development. Biosens Bioelectron 2011; 26:3938-43. [PMID: 21481581 DOI: 10.1016/j.bios.2011.03.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Revised: 03/15/2011] [Accepted: 03/17/2011] [Indexed: 11/23/2022]
Abstract
A new silicon chip for protein microarray development, fabrication and validation is proposed. The chip is made of two areas with oxide layers of different thicknesses: an area with a 500 nm SiO2 layer dedicated to interferometric label-free detection and quantification of proteins and an area with 100 nm SiO2 providing enhanced fluorescence. The chip allows, within a single experiment performed on the same surface, label-free imaging of arrayed protein probes coupled with high sensitivity fluorescence detection of the molecular interaction counterparts. Such a combined chip is of high practical utility during assay development process to image arrays, check consistency and quality of the protein array, quantify the amount of immobilized probes and finally detect fluorescence of bioassays.
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Takeda M, Shiku H, Ino K, Matsue T. Electrochemical chip integrating scalable ring–ring electrode array to detect secreted alkaline phosphatase. Analyst 2011; 136:4991-6. [DOI: 10.1039/c1an15620a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Protein microarrays and biomarkers of infectious disease. Int J Mol Sci 2010; 11:5165-83. [PMID: 21614200 PMCID: PMC3100839 DOI: 10.3390/ijms11125165] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 12/11/2010] [Accepted: 12/15/2010] [Indexed: 01/11/2023] Open
Abstract
Protein microarrays are powerful tools that are widely used in systems biology research. For infectious diseases, proteome microarrays assembled from proteins of pathogens will play an increasingly important role in discovery of diagnostic markers, vaccines, and therapeutics. Distinct formats of protein microarrays have been developed for different applications, including abundance-based and function-based methods. Depending on the application, design issues should be considered, such as the need for multiplexing and label or label free detection methods. New developments, challenges, and future demands in infectious disease research will impact the application of protein microarrays for discovery and validation of biomarkers.
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Abstract
In the past decade, an explosion in the number of high-throughput tools for the measurement of different cellular products has occurred. These tools have the potential to further our understanding of human disease and this development has facilitated the identification of new biomarkers in all areas of medicine. In the field of solid organ transplantation, two different areas have developed: the use of biomarkers to predict allograft tolerance for the identification of patients who can be weaned from immunosuppressive therapy, and biomarkers for the prediction of allograft rejection, so that parenchymal damage can be prevented before it becomes irreversible. In this Review, we discuss the development of biomarkers that are indicative of transplant tolerance. Identifying patients in whom donor-specific tolerance has developed would constitute a major advance in the care of organ transplant recipients. This ability would allow the minimization or even the withdrawal of immunosuppressive therapy in selected patients, thus reducing the number of adverse effects and costs, and optimizing long-term graft outcomes. The routine clinical use of these biomarkers, once validated, would bring to the fore the possibility of personalized medicine.
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Protein-protein interactions and selection: generation of molecule-binding proteins on the basis of tertiary structural information. FEBS J 2010; 277:2006-14. [PMID: 20412054 DOI: 10.1111/j.1742-4658.2010.07627.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Antibodies and their fragments are attractive binding proteins because their high binding strength is generated by several hypervariable loop regions, and because high-quality libraries can be prepared from the vast gene clusters expressed by mammalian lymphocytes. Recent explorations of new genome sequences and protein structures have revealed various small, nonantibody scaffold proteins. Accurate structural descriptions of protein-protein interactions based on X-ray and NMR analyses allow us to generate binding proteins by using grafting and library techniques. Here, we review approaches for generating binding proteins from small scaffold proteins on the basis of tertiary structural information. Identification of binding sites from visualized tertiary structures supports the transfer of function by peptide grafting. The local library approach is advantageous as a go-between technique for grafted foreign peptide sequences and small scaffold proteins. The identification of binding sites also supports the construction of efficient libraries with a low probability of denatured variants, and, in combination with the design for library diversity, opens the way to increasing library density and randomized sequence lengths without decreasing density. Detailed tertiary structural analyses of protein-protein complexes allow accurate description of epitope locations to enable the design of and screening for multispecific, high-affinity proteins recognizing multiple epitopes in target molecules.
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Ishii J, Fukuda N, Tanaka T, Ogino C, Kondo A. Protein-protein interactions and selection: yeast-based approaches that exploit guanine nucleotide-binding protein signaling. FEBS J 2010; 277:1982-95. [DOI: 10.1111/j.1742-4658.2010.07625.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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