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Wang C, Zhang Y, Wang X, Zhou J, Wang X, Song G, Sun Y, Gu K, Xu A, Huang J. Neutrophil-associated Proteins as Novel Biomarkers Elevated in Cerebrospinal Fluid of Neurosyphilis Patients. J Infect Dis 2024:jiae078. [PMID: 38427829 DOI: 10.1093/infdis/jiae078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 02/03/2024] [Accepted: 02/27/2024] [Indexed: 03/03/2024] Open
Abstract
BACKGROUND The immunopathological mechanisms underlying neurosyphilis remain incompletely elucidated, and the diagnosis of neurosyphilis presents challenges. METHODS We used an antibody microarray to detect 640 proteins in cerebrospinal fluid (CSF) samples collected from 6 non-neurosyphilis and 10 neurosyphilis patients. The levels of CSF CXCL1, CXCL8, G-CSF, LCN2, MMP8, and MMP9 in 46 non-neurosyphilis, 51 untreated neurosyphilis, and 31 post-treatment neurosyphilis patients were quantified using enzyme-linked immunosorbent assay. The associations between the levels of these proteins and clinical parameters in neurosyphilis were evaluated using Spearman's analysis, and the diagnostic performance of these proteins in neurosyphilis was assessed using receiver operating characteristic curve. RESULTS A total of 102 differentially expressed proteins between neurosyphilis and non-neurosyphilis were identified. The levels of significantly elevated neutrophil-associated proteins (CXCL1, CXCL8, G-CSF, LCN2, MMP8, and MMP9) in neurosyphilis were positive correlations with WBC counts, RPR titer, and protein concentration in CSF. The combination of CSF CXCL8, MMP9, and LCN2 yielded an AUC of 0.92 for diagnosing neurosyphilis, surpassing that of CSF RPR. CONCLUSIONS CXCL1, CXCL8, G-CSF, LCN2, MMP8, and MMP9 could be associated with central nervous system damage of neurosyphilis. The combination of CSF CXCL8, MMP9, and LCN2 is a promising biomarker for diagnosing neurosyphilis.
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Affiliation(s)
- Cuini Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Zhang
- Center of Clinical Laboratory, Hangzhou XiXi Hospital, Hangzhou, China
| | - Xiang Wang
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiajun Zhou
- Department of Neurology, Hangzhou XiXi Hospital, Hangzhou, China
| | - Xiaoyan Wang
- Center of Clinical Laboratory, Huzhou Hospital, Huzhou, China
| | - Gang Song
- Center of Clinical Laboratory, Huzhou Third People's Hospital, Huzhou, China
| | - Yu Sun
- Center of Clinical Laboratory, Huzhou Hospital, Huzhou, China
| | - Kailong Gu
- Center of Clinical Laboratory, Hangzhou XiXi Hospital, Hangzhou, China
| | - Aifang Xu
- Center of Clinical Laboratory, Hangzhou XiXi Hospital, Hangzhou, China
| | - Jian Huang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
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Jozwik C, Eidelman O, Srivastava M. Discovery of a Hidden Proinflammatory Signaling Proteome Using a Large-Scale, Targeted Antibody Microarray Platform. Methods Mol Biol 2023; 2660:219-233. [PMID: 37191800 DOI: 10.1007/978-1-0716-3163-8_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Dynamic post-translational processes regulate protein expression in eukaryotic cells. However, the processes are difficult to assess on a proteomic scale because protein levels actually reflect the sum of individual biosynthesis and degradation rates. These rates are presently hidden from the conventional proteomic technologies. We present here a novel and dynamic, antibody microarray-based time-resolved approach to simultaneously measure not only the total protein changes but also the rates of biosynthesis of low abundance proteins in the proteome of lung epithelial cells. In this chapter, we describe the feasibility of this technique by investigating the complete proteomic kinetics of 507 low abundance proteins in cultured cystic fibrosis (CF) lung epithelial cells using 35[S] methionine or 32[P] and the consequences of repair by gene therapy with [wildtype] CFTR. This novel antibody microarray-based technology identifies relevant, hidden proteins whose regulation by the CF genotype would never have been detected by simple measurements of total proteomic masses.
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Affiliation(s)
- Catherine Jozwik
- Department of Anatomy, Physiology and Genetics, and Institute for Molecular Medicine, Uniformed Services University School of Medicine (USUHS), Bethesda, MD, USA
| | - Ofer Eidelman
- Department of Anatomy, Physiology and Genetics, and Institute for Molecular Medicine, Uniformed Services University School of Medicine (USUHS), Bethesda, MD, USA
| | - Meera Srivastava
- Department of Anatomy, Physiology and Genetics, and Institute for Molecular Medicine, Uniformed Services University School of Medicine (USUHS), Bethesda, MD, USA.
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Gumanova NG, Vasilyev DK, Bogdanova NL, Havrichenko YI, Kots AY, Metelskaya VA. Application of an antibody microarray for serum protein profiling of coronary artery stenosis. Biochem Biophys Res Commun 2022; 631:55-63. [PMID: 36166954 DOI: 10.1016/j.bbrc.2022.09.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 09/13/2022] [Indexed: 11/29/2022]
Abstract
Protein expression profiling in the serum is used to identify novel biomarkers and investigate the signaling pathways in various diseases. The aim of the present study was to evaluate serum biomarkers associated with coronary artery stenosis resulting from atherosclerosis. The study included 4 groups of subjects: group A and B with and without coronary lesions, respectively, were selected from a previously reported cohort study on coronary atherosclerosis, control group C comprised of asymptomatic subjects and group D was used for independent validation of the microarray data by ELISA. Labeled serum proteins were profiled by an Explorer antibody array, which included 656 specific antibodies in two replicates (FullMoon Biosystems, USA). Cadherin-P, interleukin-5, glutathione S-transferase Mu, and neuronal nitric oxide synthase were sex-independently increased in Group A compared with those in group B. The microarray data on cadherin-P were externally validated in an independent group D using ELISA. Fibroblast growth factor-1, FGF-2, collagen II, granulocyte-macrophage colony-stimulating factor, IL-1 alpha, angiopoietin-2, granulocyte colony-stimulating factor, lymphocyte cell-specific protein tyrosine kinase, and IkappaB kinase b were increase in men in group A compared with group B. Cyclin-dependent kinase 1, DNA fragmentation factor subunit alpha DFF45/ICAD, adenovirus type 2 E1A, calponin, ADP-ribosylation factor-6, muscle-specific actin, thyroid hormone receptor alpha, and alpha-methylacyl-CoA racemase were specifically increased in women in Group A compared with group B. Alterations in the levels of specific proteins may point to the signaling pathways contributing to coronary atherosclerosis, and these proteins will be useful biomarkers for the progression of cardiovascular diseases.
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Affiliation(s)
- Nadezhda G Gumanova
- National Research Center for Preventive Medicine (NRCPM), Petroverigsky, 10, Building 3, 101990, Moscow, Russian Federation.
| | - Dmitry K Vasilyev
- National Research Center for Preventive Medicine (NRCPM), Petroverigsky, 10, Building 3, 101990, Moscow, Russian Federation
| | - Natalya L Bogdanova
- National Research Center for Preventive Medicine (NRCPM), Petroverigsky, 10, Building 3, 101990, Moscow, Russian Federation
| | - Yaroslav I Havrichenko
- National Research Center for Preventive Medicine (NRCPM), Petroverigsky, 10, Building 3, 101990, Moscow, Russian Federation
| | - Alexander Ya Kots
- National Research Center for Preventive Medicine (NRCPM), Petroverigsky, 10, Building 3, 101990, Moscow, Russian Federation
| | - Victoria A Metelskaya
- National Research Center for Preventive Medicine (NRCPM), Petroverigsky, 10, Building 3, 101990, Moscow, Russian Federation
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Adderley J, Wang T, Ma G, Zheng Y, Young ND, Doerig C, Gasser RB. Repurposing of a human antibody-based microarray to explore conserved components of the signalome of the parasitic nematode Haemonchus contortus. Parasit Vectors 2022; 15:273. [PMID: 35907892 DOI: 10.1186/s13071-022-05400-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 07/14/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gaining insight into molecular signalling pathways of socioeconomically important parasitic nematodes has implications for understanding their molecular biology and for developing novel anthelmintic interventions. METHODS Here, we evaluated the use of a human antibody-based microarray to explore conserved elements of the signalome in the barber's pole worm Haemonchus contortus. To do this, we prepared extracts from mixed-sex (female and male) adult worms and third-stage larvae (L3s), incubated these extracts on the antibody microarray and then measured the amounts of antibody-bound proteins ('signal intensity'). RESULTS In total, 878 signals were classified into two distinct categories: signals that were higher for adults than for larvae of H. contortus (n = 376), and signals that were higher for larvae than for adults of this species (n = 502). Following a data-filtering step, high confidence ('specific') signals were obtained for subsequent analyses. In total, 39 pan-specific signals (linked to antibodies that recognise target proteins irrespective of their phosphorylation status) and 65 phosphorylation-specific signals were higher in the adult stage, and 82 pan-specific signals and 183 phosphorylation-specific signals were higher in L3s. Thus, notably more signals were higher in L3s than in the adult worms. Using publicly available information, we then inferred H. contortus proteins that were detected (with high confidence) by specific antibodies directed against human homologues, and revealed relatively high structural conservation between the two species, with some variability for select proteins. We also in silico-matched 763 compound structures (listed in the DrugBank and Kinase SARfari public databases) to four H. contortus proteins (designated HCON_00005760, HCON_00079680, HCON_00013590 and HCON_00105100). CONCLUSIONS We conclude that the present antibody-based microarray provides a useful tool for comparative analyses of signalling pathways between/among developmental stages and/or species, as well as opportunities to explore nematocidal target candidates in H. contortus and related parasites.
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Paquet-Mercier F, Juncker D, Bergeron S. Precise Chip-to-Chip Reagent Transfer for Cross-Reactivity-Free Multiplex Sandwich Immunoassays. Methods Mol Biol 2021; 2237:141-149. [PMID: 33237415 DOI: 10.1007/978-1-0716-1064-0_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Common multiplex sandwich immunoassays suffer from cross-reactivity due to the mixing of detection antibodies and the combinatorial, undesired interaction between all reagents and analytes. Here we present the snap chip to perform antibody colocalization microarrays that eliminates undesirable interactions by running an array of singleplex assays realized by sequestering detection antibodies in individual nanodroplets. When detecting proteins in biological fluids, the absence of cross-reactivity allows a higher level of multiplexing, reduced background, increased sensitivity, and ensures accurate and specific results. The use of the snap chip is illustrated by measuring highly related analytes such as proteins isoforms and phospho-proteins, both particularly prone to cross-reactivity, in a single experiment. The main steps of the protocol are preparation of sample, incubation on an assay slide harboring the microarrayed capture antibodies, transfer of the microarrayed detection antibodies on their cognate spots, and measurement of the assay results by fluorescence.
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Affiliation(s)
| | - David Juncker
- McGill University and Génome Québec Innovation Centre, Montreal, QC, Canada
- Biomedical Engineering Department, McGill University, Montreal, QC, Canada
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Qiang D, Wang J, Ci C, Tang B, Ke G, Chang X, Ji B, Shao X. Evaluation of serum cytokines to predict serofast in syphilis patients. J Infect Chemother 2020; 26:970-976. [PMID: 32414686 DOI: 10.1016/j.jiac.2020.04.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 04/11/2020] [Accepted: 04/21/2020] [Indexed: 11/24/2022]
Abstract
BACKGROUND Syphilis serofast has been increasing in recent years and has resulted in a dramatic increase in medical expenses. However, there are not effective methods for serofast prediction in syphilis patients prior to treatment. AIMS AND OBJECTIVES The present study investigated novel serum biomarkers for the prediction of serofast in syphilis patients prior to treatment. MATERIALS AND METHODS Pre-treatment serum from patients with syphilis serofast and patients with syphilis serological cure were measured using antibody microarrays. The results generated from the antibody arrays were validated using ELISA. Healthy subjects were used as the controls. RESULTS Compared to serologically cured patients, six cytokines (IL-17F, TNF RI, TNF RII, IL-16, OPN, and MCSFR) were significantly lower, while five factors (MCP-3, LIF, G-CSF, MIP-3a, and GH) were higher in serofast patients. ELISA validation was in-line with the results generated from antibody arrays. Of significance, these cytokines were firstly observed to the differentially expressed in pre-treatment serofast patient serum samples. CONCLUSIONS The differentially expressed cytokines may be novel serum biomarkers for serofast prediction. These identified proteins play significant roles in the immune response, suggesting immune dysfunction may be the cause for syphilis serofast.
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Affiliation(s)
- Di Qiang
- Department of Dermatology and STD, Yi-Ji Shan Hospital, Wannan Medical College, Wuhu, China.
| | - Jingjing Wang
- Department of Dermatology and STD, Yi-Ji Shan Hospital, Wannan Medical College, Wuhu, China
| | - Chao Ci
- Department of Dermatology and STD, Yi-Ji Shan Hospital, Wannan Medical College, Wuhu, China
| | - Biao Tang
- Department of Dermatology and STD, Yi-Ji Shan Hospital, Wannan Medical College, Wuhu, China
| | - Guoling Ke
- Department of Dermatology and STD, Yi-Ji Shan Hospital, Wannan Medical College, Wuhu, China
| | - Xiaoli Chang
- Department of Dermatology and STD, Yi-Ji Shan Hospital, Wannan Medical College, Wuhu, China
| | - Bihua Ji
- Department of Dermatology and STD, Yi-Ji Shan Hospital, Wannan Medical College, Wuhu, China
| | - Xuefei Shao
- Department of Neurosurgery, Yi-Ji Shan Hospital of Wannan Medical College, Wuhu, Anhui, China.
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Hong S, Park KH, Kim YM, Lee YE, Park Y, Lee JE. A Protein Microarray Analysis of Plasma Proteins for the Prediction of Spontaneous Preterm Delivery in Women with Preterm Labor. Reprod Sci 2020; 27:1187-1196. [PMID: 32046457 DOI: 10.1007/s43032-019-00114-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 10/21/2019] [Indexed: 10/25/2022]
Abstract
We aimed to identify novel biomarkers in maternal plasma that predict spontaneous preterm delivery (SPTD) in women with preterm labor (PTL) using an antibody microarray and to develop the best prediction model for SPTD based on these biomarkers in combination with clinical and ultrasound factors. This retrospective cohort study included 215 women with singleton pregnancies and PTL (23-33 weeks) who gave plasma samples. In a nested case-control study design, plasma proteomes from SPTD (case subjects, n = 15) and term delivery (control subjects, n = 15) groups were differentially profiled using a membrane-based antibody microarray. Six candidate biomarkers of interest were validated by enzyme-linked immunosorbent assay (ELISA) in the total cohort (n = 215). Cervical lengths were also measured. The primary outcome measure was SPTD within 48 h after sampling. Twenty of the molecules studied displayed significant intergroup differences. Validation by ELISA confirmed significantly higher levels of plasma endostatin and lipopolysaccharide binding protein (LBP) in women who had SPTD within 48 h than in those delivering after 48 h. However, plasma macrophage inflammatory protein (MIP)-1α levels were significantly lower in women who delivered within 48 h. A combined model was developed to predict SPTD within 48 h using a stepwise regression procedure, which included plasma endostatin and LBP levels, nulliparity, and cervical length (area under the curve = 0.920). Plasma LBP, endostatin, and MIP-1α are potential new biomarkers for predicting imminent SPTD and a combined noninvasive model based on these biomarkers and clinical and ultrasound factors can accurately predict imminent SPTD in women with PTL.
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Affiliation(s)
- Subeen Hong
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, South Korea.,Department of Obstetrics and Gynecology, Seoul National University Bundang Hospital, 82, Gumi-ro 173 Beon-gil, Seongnam-si, Kyeonggido, 463-707, South Korea
| | - Kyo Hoon Park
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, South Korea. .,Department of Obstetrics and Gynecology, Seoul National University Bundang Hospital, 82, Gumi-ro 173 Beon-gil, Seongnam-si, Kyeonggido, 463-707, South Korea.
| | - Yu Mi Kim
- Department of Obstetrics and Gynecology, Seoul National University Bundang Hospital, 82, Gumi-ro 173 Beon-gil, Seongnam-si, Kyeonggido, 463-707, South Korea
| | - Young Eun Lee
- Department of Obstetrics and Gynecology, Seoul National University Bundang Hospital, 82, Gumi-ro 173 Beon-gil, Seongnam-si, Kyeonggido, 463-707, South Korea
| | - Yehyon Park
- Department of Obstetrics and Gynecology, Seoul National University Bundang Hospital, 82, Gumi-ro 173 Beon-gil, Seongnam-si, Kyeonggido, 463-707, South Korea
| | - Ji Eun Lee
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul, South Korea
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Lee SM, Park KH, Hong S, Kim YM, Park YH, Lee YE, Jeon SJ. Identification of Cultivable Bacteria in Amniotic Fluid Using Cervicovaginal Fluid Protein Microarray in Preterm Premature Rupture of Membranes. Reprod Sci 2020; 27:1008-17. [PMID: 31942709 DOI: 10.1007/s43032-020-00143-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 07/23/2019] [Indexed: 01/07/2023]
Abstract
We aimed to identify cervicovaginal fluid (CVF) protein biomarkers of microbial invasion of the amniotic cavity (MIAC) in women with preterm premature rupture of membranes (PPROM), using an antibody microarray. This retrospective cohort study included 99 consecutive women with singleton pregnancies and PPROM (23-33 weeks) who underwent amniocentesis and who gave CVF samples. CVF proteomes from the MIAC (n = 20) versus non-MIAC groups (n = 20) were comparatively profiled by an antibody microarray using a nested case-control study design. The seven candidate biomarkers of interest were validated in the total cohort (n = 99) by enzyme-linked immunosorbent assays (ELISA). For comparison with candidate markers, amniotic fluid (AF) white blood cell (WBC) count was also measured. The primary outcome measure was MIAC (defined as positive AF culture). Thirty of the proteins studied exhibited significant intergroup differences. Measurements of the total cohort with ELISA confirmed a significant increase in the levels of CVF IL-8, lipocalin-2, MIP-1α, MMP-9, and TIMP-1 in women with MIAC, independent of gestational age at sampling. A combined, non-invasive model was developed by using a stepwise regression procedure, which included CVF IL-8 and CVF MMP-9 (area under the curve [AUC] = 0.763), and this AUC was comparable with the AUC of AF WBC. Using protein-antibody microarray technology, we found several novel, independent, non-invasive biomarkers to identify MIAC in women with PPROM: IL-8, lipocalin-2, MIP-1α, MMP-9, and TIMP-1. Furthermore, the combined non-invasive model (IL-8 and MMP-9) was a useful independent predictor for MIAC with good discriminatory power, similar to AF WBC count.
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Lee SM, Park KH, Kim SY, Kim YM, Hong S, Shin S. Cervicovaginal Fluid Protein Microarray for Detection of Microbial Invasion of the Amniotic Cavity in Preterm Labor. Reprod Sci 2020; 27:713-21. [PMID: 32046420 DOI: 10.1007/s43032-019-00077-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/03/2019] [Indexed: 01/09/2023]
Abstract
We aimed to identify cervicovaginal fluid (CVF) biomarkers that can detect microbial invasion of the amniotic cavity (MIAC) in women with preterm labor (PTL) with an antibody microarray and to develop the best combined model for detection of MIAC using these biomarkers in combination with conventional clinical variables. This retrospective cohort study included 168 singleton pregnant women with PTL (23-34 weeks) who underwent amniocentesis. AF was cultured, and CVF samples were obtained at the time of amniocentesis. An antibody microarray was used to analyze the CVF proteome (n = 40). The validation of four candidate biomarkers of interest was performed by enzyme-linked immunosorbent assay (ELISA) in the final cohort (n = 168). For comparison with candidate markers, CVF IL-6 concentration was also measured. Twenty-seven molecules studied exhibited intergroup differences. Validation by ELISA confirmed significantly higher levels of CVF DKK3, M-CSF, and TIMP-1, but not of IGFBP-2, independent of gestational age, in CVF of women with MIAC. The area under the curve (AUC) of DKK3, M-CSF, and TIMP-1 from CVF was not significantly different from the AUC of IL-6 from CVF for detecting MIAC in women with PTL. By using a stepwise regression analysis, a combined detection model was developed, which included the CVF M-CSF, TIMP-1, and gestational age at sampling (AUC = 0.823). An antibody microarray identified useful biomarkers (DKK3, M-CSF, and TIMP-1) in CVF for detection of MIAC, and a combined model including these biomarkers and gestational age can accurately detect MIAC in women with PTL.
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Shang Z, Niu X, Zhang K, Qiao Z, Liu S, Jiang X, Cao C, Lu S, Xiao H. FGA isoform as an indicator of targeted therapy for EGFR mutated lung adenocarcinoma. J Mol Med (Berl) 2019; 97:1657-68. [PMID: 31776635 DOI: 10.1007/s00109-019-01848-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 09/26/2019] [Accepted: 10/29/2019] [Indexed: 01/29/2023]
Abstract
Epidermal growth factor receptor (EGFR) gene is frequently mutated in non-small cell lung cancer (NSCLC), which can be targeted by EGFR tyrosine kinase inhibitors (TKIs). It is hard, however, to monitor the performance of EGFR-TKI therapy dynamically. Therefore, therapeutic indicators are urgently needed. Novel antibody microarray, containing 41,472 antibodies, was used for comprehensive analyzing of serum samples from 9 normal subjects and 9 EGFR mutated lung adenocarcinoma patients at three EGFR-TKI treatment time points, including before treatment (Baseline), partial response (PR) during treatment, and disease progression (PD) after resistance. Through microarray data analysis, five candidate antibodies were screened out for confirmation in serum samples and the verified one was utilized for candidate protein identification through immunoprecipitation-mass spectrometry strategy. A novel protein, isoform 2 of fibrinogen alpha chain (FGA2), was revealed and verified in the discovery sample set. Its performance as therapy indicator was further evaluated in another pre-validation sample set (n = 60). Our data confirmed that serum FGA2 level was correlated with EGFR-TKI response (p < 0.05). The expression and secretion of FGA2 in hepatocytes were inhibited by EGFR-TKI, partially explaining the downregulation of FGA2 in serum. Our results demonstrate that FGA2 is an indicator of targeted therapy for EGFR mutated lung adenocarcinoma. KEY MESSAGES: Antibody microarray was coupled with mass spectrometry for proteomics research. FGA2 was discovered as an indicator of EGFR-TKI targeted therapy. FGA2's expression/secretion in hepatocytes was dramatically inhibited by EGFR-TKI.
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Blanco Y, de Diego-Castilla G, Viúdez-Moreiras D, Cavalcante-Silva E, Rodríguez-Manfredi JA, Davila AF, McKay CP, Parro V. Effects of Gamma and Electron Radiation on the Structural Integrity of Organic Molecules and Macromolecular Biomarkers Measured by Microarray Immunoassays and Their Astrobiological Implications. Astrobiology 2018; 18:1497-1516. [PMID: 30070898 PMCID: PMC6276817 DOI: 10.1089/ast.2016.1645] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 04/10/2018] [Indexed: 05/20/2023]
Abstract
High-energy ionizing radiation in the form of solar energetic particles and galactic cosmic rays is pervasive on the surface of planetary bodies with thin atmospheres or in space facilities for humans, and it may seriously affect the chemistry and the structure of organic and biological material. We used fluorescent microarray immunoassays to assess how different doses of electron and gamma radiations affect the stability of target compounds such as biological polymers and small molecules (haptens) conjugated to large proteins. The radiation effect was monitored by measuring the loss in the immunoidentification of the target due to an impaired ability of the antibodies for binding their corresponding irradiated and damaged epitopes (the part of the target molecule to which antibodies bind). Exposure to electron radiation alone was more damaging at low doses (1 kGy) than exposure to gamma radiation alone, but this effect was reversed at the highest radiation dose (500 kGy). Differences in the dose-effect immunoidentification patterns suggested that the amount (dose) and not the type of radiation was the main factor for the cumulative damage on the majority of the assayed molecules. Molecules irradiated with both types of radiation showed a response similar to that of the individual treatments at increasing radiation doses, although the pattern obtained with electrons only was the most similar. The calculated radiolysis constant did not show a unique pattern; it rather suggested a different behavior perhaps associated with the unique structure of each molecule. Although not strictly comparable with extraterrestrial conditions because the irradiations were performed under air and at room temperature, our results may contribute to understanding the effects of ionizing radiation on complex molecules and the search for biomarkers through bioaffinity-based systems in planetary exploration.
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Affiliation(s)
- Yolanda Blanco
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Torrejón de Ardoz, Madrid, Spain
| | - Graciela de Diego-Castilla
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Torrejón de Ardoz, Madrid, Spain
| | - Daniel Viúdez-Moreiras
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Torrejón de Ardoz, Madrid, Spain
| | - Erika Cavalcante-Silva
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Torrejón de Ardoz, Madrid, Spain
| | | | - Alfonso F. Davila
- Space Science Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Christopher P. McKay
- Space Science Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Victor Parro
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Torrejón de Ardoz, Madrid, Spain
- Address correspondence to: Victor Parro, Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Carretera de Ajalvir km 4, Torrejón de Ardoz, Madrid 28850, Spain
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Iwadate Y, Suganami A, Tamura Y, Matsutani T, Hirono S, Shinozaki N, Hiwasa T, Takiguchi M, Saeki N. The Pluripotent Stem-Cell Marker Alkaline Phosphatase is Highly Expressed in Refractory Glioblastoma with DNA Hypomethylation. Neurosurgery 2018; 80:248-256. [PMID: 28173571 DOI: 10.1093/neuros/nyw026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 10/27/2016] [Indexed: 11/14/2022] Open
Abstract
Background Hypomethylation of genomic DNA induces stem-cell properties in cancer cells and contributes to the treatment resistance of various malignancies. Objective To examine the correlation between the methylation status of stem-cell-related genes and the treatment outcomes in patients with glioblastoma (GBM). Methods The genome-wide DNA methylation status was determined using HumanMethylation450 BeadChips, and the methylation status was compared between a group of patients with good prognosis (survival > 4 yr) and a group with poor prognosis (survival < 1 yr). Immunohistochemistry for proteins translated from hypomethylated genes, including alkaline phosphatase (ALPL), CD133, and CD44, was performed in 70 GBMs and 60 oligodendroglial tumors. Results The genomic DNA in refractory GBM was more hypomethylated than in GBM from patients with relatively long survival (P = .0111). Stem-cell-related genes including ALPL, CD133, and CD44 were also significantly hypomethylated. A validation study using immunohistochemistry showed that DNA hypomethylation was strongly correlated with high protein expression of ALPL, CD133, and CD44. GBM patients with short survival showed high expression of these stem-cell markers. Multivariate analysis confirmed that co-expression of ALPL + CD133 or ALPL + CD44 was a strong predictor of short survival. Anaplastic oligodendroglial tumors without isocitrate dehydrogenase 1 mutation were significantly correlated with high ALPL expression and poor survival. Conclusion Accumulation of stem-cell properties due to aberrant DNA hypomethylation is associated with the refractory nature of GBM.
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Affiliation(s)
- Yasuo Iwadate
- Department of Neurological Surgery, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Akiko Suganami
- Department of Bioinformatics, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Yutaka Tamura
- Department of Bioinformatics, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Tomoo Matsutani
- Department of Neurological Surgery, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Seiichiro Hirono
- Department of Neurological Surgery, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Natsuki Shinozaki
- Department of Neurological Surgery, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Takaki Hiwasa
- Department of Biochemistry and Genetics, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Masaki Takiguchi
- Department of Biochemistry and Genetics, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Naokatsu Saeki
- Department of Neurological Surgery, Chiba University Graduate School of Medicine, Chiba, Japan
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Abstract
The concept of antibody microarrays is one of the most versatile approaches within multiplexed immunoassay technologies. These types of arrays have increasingly become an attractive tool for the exploratory detection and study of protein abundance, function, pathways, and potential drug targets. Due to the properties of the antibody microarrays and their potential use in basic research and clinical analytics, various types of antibody microarrays have already been developed. In spite of the growing number of studies utilizing this technique, few reviews about antibody microarray technology have been presented to reflect the quality and future uses of the generated data. In this review, we provide a summary of the recent applications of antibody microarray techniques in basic biology and clinical studies, providing insights into the current trends and future of protein analysis.
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Affiliation(s)
- Ziqing Chen
- Key Laboratory of Systems Biomedicine, (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 China
| | - Tea Dodig-Crnković
- Affinity Proteomics, SciLifeLab, KTH - Royal Institute of Technology, 171 65 Solna, Sweden
| | - Jochen M. Schwenk
- Affinity Proteomics, SciLifeLab, KTH - Royal Institute of Technology, 171 65 Solna, Sweden
| | - Sheng-ce Tao
- Key Laboratory of Systems Biomedicine, (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240 China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai, 200240 China
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14
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Khvastunova AN, Al-Radi LS, Fedyanina OS, Kuznetsova SA. Simultaneous finding of chronic lymphocytic leukemia and residual hairy cell leukemia using a lymphocyte-binding anti-CD antibody microarray. Clin Case Rep 2018; 6:753-755. [PMID: 29636954 PMCID: PMC5889256 DOI: 10.1002/ccr3.1416] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 12/04/2017] [Accepted: 12/05/2017] [Indexed: 11/06/2022] Open
Abstract
The morphologic diagnosis of hairy cell leukemia coexisting with another lymphoproliferative disorder is hindered by the small size of hairy cell population. It can be simplified by presorting peripheral blood mononuclear cell using an anti-CD antibody microarray on transparent support (including anti-CD11c, CD25, CD103, and CD123) before their morphology analysis.
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Affiliation(s)
- Alina N Khvastunova
- Dmitry Rogachev National Research Centre of Pediatric Hematology Oncology and Immunology, Russian Ministry of Health 1 Samory Mashela st. Moscow 117997 Russia.,Centre for Theoretical Problems of Physicochemical Pharmacology RAS4 Kosygina st.Moscow 119991 Russia
| | - Liubov S Al-Radi
- Research Center for Hematology Russian Ministry of Health 4 Novy Zykovsky proezd Moscow 125167 Russia
| | - Olga S Fedyanina
- Dmitry Rogachev National Research Centre of Pediatric Hematology Oncology and Immunology, Russian Ministry of Health 1 Samory Mashela st. Moscow 117997 Russia.,Centre for Theoretical Problems of Physicochemical Pharmacology RAS4 Kosygina st.Moscow 119991 Russia
| | - Sofya A Kuznetsova
- Dmitry Rogachev National Research Centre of Pediatric Hematology Oncology and Immunology, Russian Ministry of Health 1 Samory Mashela st. Moscow 117997 Russia.,Centre for Theoretical Problems of Physicochemical Pharmacology RAS4 Kosygina st.Moscow 119991 Russia
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15
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Shlyapnikov YM, Morozov VN. Titration of trace amounts of immunoglobulins in a microarray-based assay with magnetic labels. Anal Chim Acta 2017; 966:47-53. [PMID: 28372726 DOI: 10.1016/j.aca.2017.02.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 02/24/2017] [Indexed: 10/20/2022]
Abstract
The existing immunoassay format that combines the electrophoretic collection of charged analytes on an antibody microarray with the detection of the bound analytes by magnetic beads coated with secondary antibodies displays extreme sensitivity and speed, but suffers from low precision because of high signal scatter and low signal-to-concentration ratio. Here we report three innovations that substantially improve the precision of this method and enable quantitative measurements of analyte concentrations as low as 10 fg/ml. The improvements were achieved by (i) employing parallel titration of analytes by measuring signal response to a series of sample dilutions with increasing analyte concentration, (ii) internally normalizing the signal (by relating signal intensity to that of positive controls on the same microarray) and (iii) taking measurements in the linear range of the calibration curve at concentrations close to the limit of detection. This improved method was used to quantitatively measure in human serum the titer of immunoglobulins specific to antigens secreted by Mycobacterium tuberculosis.
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Affiliation(s)
- Yuri M Shlyapnikov
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
| | - Victor N Morozov
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia; National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, VA 20110, United States
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16
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Meinert C, Kohse F, Böhme I, Gembardt F, Tetzner A, Wieland T, Greenberg B, Walther T. Further intracellular proteins and signaling pathways regulated by angiotensin-(1-7) in human endothelial cells. Data Brief 2016; 10:354-363. [PMID: 28018949 PMCID: PMC5167237 DOI: 10.1016/j.dib.2016.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Revised: 11/27/2016] [Accepted: 12/02/2016] [Indexed: 11/13/2022] Open
Abstract
In 2016, Meinert et al. (doi: 10.1016/j.jprot.2015.09.020) published the first 25 proteins in a protein array regulated in Human Umbilical Vein Endothelial Cells (HUVEC) by the heptapeptide angiotensin (Ang)-(1–7) and the first 10 intracellular signaling cascades at different time points. This supporting data article shows further proteins and pathways stimulated by Ang-(1–7) in human endothelial cells at time points of 1 h, 3 h, 6 h, and 9 h. HUVECs were stimulated with Ang-(1–7), and regulated proteins were identified via antibody microarray. Bioinformatics software IPA was used for association of regulated proteins to metabolic pathways.
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Affiliation(s)
- Christian Meinert
- Institute of Experimental and Clinical Pharmacology and Toxicology, Medical Faculty Mannheim, Universität Heidelberg, Mannheim, Germany; Department of Pharmacology and Therapeutics, University College Cork, Cork, Ireland
| | - Franziska Kohse
- Departments of Obstetrics and Pediatric Surgery, Division of Women and Child Health, Universität Leipzig, Leipzig, Germany
| | - Ilka Böhme
- Departments of Obstetrics and Pediatric Surgery, Division of Women and Child Health, Universität Leipzig, Leipzig, Germany
| | - Florian Gembardt
- Division of Nephrology, Department of Internal Medicine III, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Anja Tetzner
- Department of Pharmacology and Therapeutics, University College Cork, Cork, Ireland; Departments of Obstetrics and Pediatric Surgery, Division of Women and Child Health, Universität Leipzig, Leipzig, Germany
| | - Thomas Wieland
- Institute of Experimental and Clinical Pharmacology and Toxicology, Medical Faculty Mannheim, Universität Heidelberg, Mannheim, Germany
| | - Barry Greenberg
- Division of Cardiology, University of California, San Diego, USA
| | - Thomas Walther
- Institute of Experimental and Clinical Pharmacology and Toxicology, Medical Faculty Mannheim, Universität Heidelberg, Mannheim, Germany; Department of Pharmacology and Therapeutics, University College Cork, Cork, Ireland; Departments of Obstetrics and Pediatric Surgery, Division of Women and Child Health, Universität Leipzig, Leipzig, Germany
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17
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Sukri A, Hanafiah A, Kosai NR, Mohamed Taher M, Mohamed Rose I. Surface Antigen Profiling of Helicobacter pylori-Infected and -Uninfected Gastric Cancer Cells Using Antibody Microarray. Helicobacter 2016; 21:417-27. [PMID: 26807555 DOI: 10.1111/hel.12295] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND Comprehensive immunophenotyping cluster of differentiation (CD) antigens in gastric adenocarcinoma, specifically between Helicobacter pylori-infected and -uninfected gastric cancer patients by using DotScan(™) antibody microarray has not been conducted. Current immunophenotyping techniques include flow cytometry and immunohistochemistry are limited to the use of few antibodies for parallel examination. We used DotScan(™) antibody microarray consisting 144 CD antibodies to determine the distribution of CD antigens in gastric adenocarcinoma cells and to elucidate the effect of H. pylori infection toward CD antigen expression in gastric cancer. METHODS Mixed leukocytes population derived from gastric adenocarcinoma patients were immunophenotyped using DotScan(™) antibody microarray. AGS cells were infected with H. pylori strains and cells were captured on DotScan(™) slides. RESULTS Cluster of differentiation antigens involved in perpetuating the tolerance of immune cells to tumor cells was upregulated in gastric adenocarcinoma cells compared to normal cells. CD279 which is essential in T cells apoptosis was found to be upregulated in normal cells. Remarkably, H. pylori-infected gastric cancer patients exhibited upregulated expression of CD27 that important in maintenance of T cells. Infection of cagA+ H. pylori with AGS cells increased CD antigens expression which involved in cancer stem cell while cagA- H. pylori polarized AGS cells to express immune-regulatory CD antigens. Increased CD antigens expression in AGS cells infected with cagA+ H. pylori were also detected in H. pylori-infected gastric cancer patients. CONCLUSION This study suggests the tolerance of immune system toward tumor cells in gastric cancer and distinct mechanisms of immune responses exploited by different H. pylori strains.
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Affiliation(s)
- Asif Sukri
- Department of Medical Microbiology & Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Cheras, Kuala Lumpur, Malaysia
| | - Alfizah Hanafiah
- Department of Medical Microbiology & Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Cheras, Kuala Lumpur, Malaysia.
| | - Nik Ritza Kosai
- Department of Surgery, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Cheras, Kuala Lumpur, Malaysia
| | - Mustafa Mohamed Taher
- Department of Surgery, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Cheras, Kuala Lumpur, Malaysia
| | - Isa Mohamed Rose
- Department of Pathology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Cheras, Kuala Lumpur, Malaysia
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18
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Delfani P, Sturfelt G, Gullstrand B, Carlsson A, Kassandra M, Borrebaeck CAK, Bengtsson AA, Wingren C. Deciphering systemic lupus erythematosus-associated serum biomarkers reflecting apoptosis and disease activity. Lupus 2016; 26:373-387. [PMID: 27694630 DOI: 10.1177/0961203316669240] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Systemic lupus erythematosus (SLE) is a severe chronic inflammatory autoimmune connective tissue disease. Despite major efforts, SLE remains a poorly understood disease with unpredictable course, unknown etiology and complex pathogenesis. Apoptosis combined with deficiency in clearing apoptotic cells is an important etiopathogenic event in SLE, which could contribute to the increased load of potential autoantigen(s); however, the lack of disease-specific protein signatures deciphering SLE and the underlying biological processes is striking and represents a key limitation. In this retrospective pilot study, we explored the immune system as a specific sensor for disease, in order to advance our understanding of SLE. To this end, we determined multiplexed serum protein expression profiles of crude SLE serum samples, using antibody microarrays. The aim was to identify differential immunoprofiles, or snapshots of the immune response modulated by the disease, reflecting apoptosis, a key process in the etiology of SLE and disease activity. The results showed that multiplexed panels of SLE-associated serum biomarkers could be decoded, in particular reflecting disease activity, but potentially the apoptosis process as well. While the former biomarkers could display a potential future use for prognosis, the latter biomarkers might help shed further light on the apoptosis process taking place in SLE.
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Affiliation(s)
- P Delfani
- 1 Department of Immunotechnology and CREATE Health, Lund University, Lund, Sweden
| | - G Sturfelt
- 2 Department of Clinical Sciences, Rheumatology Section, Lund University Hospital, Lund University, Lund, Sweden
| | - B Gullstrand
- 2 Department of Clinical Sciences, Rheumatology Section, Lund University Hospital, Lund University, Lund, Sweden
| | - A Carlsson
- 1 Department of Immunotechnology and CREATE Health, Lund University, Lund, Sweden
| | - M Kassandra
- 1 Department of Immunotechnology and CREATE Health, Lund University, Lund, Sweden
| | - C A K Borrebaeck
- 1 Department of Immunotechnology and CREATE Health, Lund University, Lund, Sweden
| | - A A Bengtsson
- 2 Department of Clinical Sciences, Rheumatology Section, Lund University Hospital, Lund University, Lund, Sweden
| | - C Wingren
- 1 Department of Immunotechnology and CREATE Health, Lund University, Lund, Sweden
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19
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Kamhieh-Milz J, Mustafa SA, Sterzer V, Celik H, Keski S, Khorramshahi O, Movassaghi K, Hoheisel JD, Alhamdani MSS, Salama A. Secretome profiling of apheresis platelet supernatants during routine storage via antibody-based microarray. J Proteomics 2016; 150:74-85. [PMID: 27478071 DOI: 10.1016/j.jprot.2016.07.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 07/25/2016] [Accepted: 07/27/2016] [Indexed: 02/07/2023]
Abstract
Platelet storage lesions (PSLs) occur during platelet concentrate (PC) storage. Adverse transfusion reactions (ATRs) have been demonstrated to be more frequent in older PCs and removal of the supernatant prior to transfusion reduces their occurrence. Proteomic profiling of PC supernatants was thus performed to identify proteins associated with PSLs and ATRs. Twenty-four PCs were investigated daily from day 0 to day 9 for platelet pre-activation (PPA), platelet-derived extracellular vesicles (PEVs), and platelet function. Using antibody microarrays, 673 extracellular proteins were analysed in PC supernatants on days 0, 3, 5, 7, and 9. During 5days of storage, PPA and PEVs continuously increased (P<0.0001). Platelet function was observed to remain stable within the first 5days (P=0.1751) and decreased thereafter. Comparison of all time points to day 0 revealed the identification of 136 proteins that were significantly changed in abundance during storage, of which 72 were expressed by platelets. Network analysis identified these proteins to be predominantly associated with exosomes (P=4.61×10-8, n=45 genes) and two clusters with distinct functions were found with one being associated with haemostasis and the other with RNA binding. These findings may provide an explanation for ATRs. SIGNIFICANCE Changes in platelet concentrate (PC) supernatants during storage have been so far only poorly addressed and high abundant proteins burden the identification of quantitative changes in the secretome. We applied a high-throughput antibody microarray allowing for the sensitive quantification of 673 extracellular factors. PCs account for the highest number of adverse transfusion reactions (ATRs). ATRs have been demonstrated to be more frequent in older PCs and removal of the supernatant prior to transfusion reduces their occurrence. Comprehensive interpretation of the changing proteins in the secretome during platelet storage under blood banking conditions may help to identify mechanisms leading to the occurrence of adverse transfusion reactions.
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Affiliation(s)
- Julian Kamhieh-Milz
- Institute of Transfusion Medicine, Charité University Medicine Berlin, Augustenburger Platz 1, 13349 Berlin, Germany.
| | - Shakhawan A Mustafa
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Kurdistan Institution for Strategic Studies and Scientific Research, Gullabax 335, Shorsh St., Sulaimani, Kurdistan Region, Iraq
| | - Viktor Sterzer
- Institute of Transfusion Medicine, Charité University Medicine Berlin, Augustenburger Platz 1, 13349 Berlin, Germany
| | - Hatice Celik
- Institute of Transfusion Medicine, Charité University Medicine Berlin, Augustenburger Platz 1, 13349 Berlin, Germany
| | - Sahime Keski
- Institute of Transfusion Medicine, Charité University Medicine Berlin, Augustenburger Platz 1, 13349 Berlin, Germany
| | - Omid Khorramshahi
- Institute of Transfusion Medicine, Charité University Medicine Berlin, Augustenburger Platz 1, 13349 Berlin, Germany
| | - Kamran Movassaghi
- Institute of Transfusion Medicine, Charité University Medicine Berlin, Augustenburger Platz 1, 13349 Berlin, Germany
| | - Jörg D Hoheisel
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Mohamed S S Alhamdani
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Abdulgabar Salama
- Institute of Transfusion Medicine, Charité University Medicine Berlin, Augustenburger Platz 1, 13349 Berlin, Germany
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20
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Perera SS, Wang B, Damian A, Dyer W, Zhou L, Conceicao V, Saksena NK. Retrospective Proteomic Analysis of Cellular Immune Responses and Protective Correlates of p24 Vaccination in an HIV Elite Controller Using Antibody Arrays. ACTA ACUST UNITED AC 2016; 5:microarrays5020014. [PMID: 27600080 PMCID: PMC5003490 DOI: 10.3390/microarrays5020014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 01/14/2016] [Accepted: 01/25/2016] [Indexed: 01/22/2023]
Abstract
Background: HIV p24 is an extracellular HIV antigen involved in viral replication. Falling p24 antibody responses are associated with clinical disease progression and their preservation with non-progressive disease. Stimulation of p24 antibody production by immunization to delay progression was the basis of discontinued p24 vaccine. We studied a therapy-naive HIV+ man from Sydney, Australia, infected in 1988. He received the HIV-p24-virus like particle (VLP) vaccine in 1993, and continues to show vigorous p24 antigen responses (>4% p24-specific CD4+ T cells), coupled with undetectable plasma viremia. We defined immune-protective correlates of p24 vaccination at the proteomic level through parallel retrospective analysis of cellular immune responses to p24 antigen in CD4+ and CD8+ T cells and CD14+ monocytes at viremic and aviremic phases using antibody-array. We found statistically significant coordinated up-regulation by all three cell-types with high fold-changes in fractalkine, ITAC, IGFBP-2, and MIP-1α in the aviremic phase. TECK and TRAIL-R4 were down-regulated in the viremic phase and up-regulated in the aviremic phase. The up-regulation of fractalkine in all three cell-types coincided with protective effect, whereas the dysfunction in anti-apoptotic chemokines with the loss of immune function. This study highlights the fact that induction of HIV-1-specific helper cells together with coordinated cellular immune response (p < 0.001) might be important in immunotherapeutic interventions and HIV vaccine development.
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Affiliation(s)
- Suneth S Perera
- Department of Medicine, University of Sydney, Sydney 2000, Australia.
| | - Bin Wang
- Department of Medicine, University of Sydney, Sydney 2000, Australia.
| | - Arturo Damian
- Department of Cytogenetics, Children's Hospital at Westmead, Sydney 2000, Australia.
| | - Wayne Dyer
- Australian Red Cross Blood Service, 17 O'Riordan Street, Alexandria NSW 2015 and School of Medical Sciences, (Faculty of Medicine) University of Sydney, Sydney 2000, Australia.
| | - Li Zhou
- Department of Medicine, University of Sydney, Sydney 2000, Australia.
| | - Viviane Conceicao
- Department of Medicine, University of Sydney, Sydney 2000, Australia.
| | - Nitin K Saksena
- Department of Medicine, University of Sydney, Sydney 2000, Australia.
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21
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Díez P, Lorenzo S, Dégano RM, Ibarrola N, González-González M, Nieto W, Almeida J, González M, Orfao A, Fuentes M. Multipronged functional proteomics approaches for global identification of altered cell signalling pathways in B-cell chronic lymphocytic leukaemia. Proteomics 2016; 16:1193-203. [PMID: 26910488 DOI: 10.1002/pmic.201500372] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 12/04/2015] [Accepted: 02/09/2016] [Indexed: 11/11/2022]
Abstract
Chronic lymphocytic leukaemia (CLL) is a malignant B cell disorder characterized by its high heterogeneity. Although genomic alterations have been broadly reported, protein studies are still in their early stages. Herein, a 224-antibody microarray has been employed to study the intracellular signalling pathways in a cohort of 14 newly diagnosed B-CLL patients as a preliminary study for further investigations. Several protein profiles were differentially identified across the cytogenetic and molecular alterations presented in the samples (deletion 13q14 and 17p13.1, trisomy 12, and NOTCH1 mutations) by a combination of affinity and MS/MS proteomics approaches. Among others altered cell signalling pathways, PKC family members were identified as down-regulated in nearly 75% of the samples tested with the antibody arrays. This might explain the rapid progression of the disease when showing p53, Rb1, or NOTCH1 mutations due to PKC-proteins family plays a critical role favouring the slowly progressive indolent behaviour of CLL. Additionally, the antibody microarray results were validated by a LC-MS/MS quantification strategy and compared to a transcriptomic CLL database. In summary, this research displays the usefulness of proteomic strategies to globally evaluate the protein alterations in CLL cells and select the possible biomarkers to be further studied with larger sample sizes.
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Affiliation(s)
- Paula Díez
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain.,Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Seila Lorenzo
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Rosa M Dégano
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Nieves Ibarrola
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - María González-González
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain.,Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Wendy Nieto
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Julia Almeida
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Marcos González
- Service of Haematology, IBMCC, IBSAL, University Hospital of Salamanca, Salamanca, Spain
| | - Alberto Orfao
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain.,Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
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22
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Abstract
Fuelled by advances in our understanding of the human kinome and phosphoproteome and the increasing availability of pan- and phosphosite-specific antibodies, antibody microarrays have emerged as powerful tools for interrogating protein phosphorylation-mediated signaling systems in ex vivo studies. This economical platform permits ultra-sensitive, semiquantitative measurements of the levels of hundreds of protein kinases and their substrates along with their phosphorylation status simultaneously with minute amounts of specimens. Recent technological innovations in the design and fabrication of antibody microarrays and sample preparation have permitted further refinements of the technology to yield improvements in data quality. In this chapter, we describe a detailed protocol that we have developed for tracking the expression and phosphorylation of protein kinases and their substrates in crude cell lysate samples using a high-content antibody microarray.
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23
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Yang T, Yao H, He G, Song L, Liu N, Wang Y, Yang Y, Keller ET, Deng X. Effects of Lovastatin on MDA-MB-231 Breast Cancer Cells: An Antibody Microarray Analysis. J Cancer 2016; 7:192-9. [PMID: 26819643 PMCID: PMC4716852 DOI: 10.7150/jca.13414] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 10/27/2015] [Indexed: 12/21/2022] Open
Abstract
Despite the tremendous improvement in cancer therapeutics, treatment of late-stage breast cancer remains a challenge for both basic scientists and clinicians. Lovastatin, a natural product derived from Aspergillus terreus or Monascus ruber, has been widely used as cholesterol-lowing drug in the clinic. It also has anti-cancer properties through poorly defined molecular mechanisms. In the present study, we employed a novel antibody microarray technology to investigate the molecular mechanisms through which lovastatin inhibits breast cancer. We found that lovastatin up-regulated 17 proteins and down-regulated 20 proteins in MDA-MB-231 breast cancer cells. These included proteins that modulate apoptosis, cell proliferation, differentiation, signal transduction, epithelial-to-mesenchymal transition and tumor metastasis. Modulation of these pathways may mediate, in part, the inhibitory activity of lovastatin on breast cancer.
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Affiliation(s)
- Tao Yang
- 1. National Engineering Laboratory for Rice and Byproduct Deep Processing, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Hui Yao
- 2. Medical College, Hunan Normal University, Changsha, Hunan 410013, China
| | - Guangchun He
- 2. Medical College, Hunan Normal University, Changsha, Hunan 410013, China
| | - Liujiang Song
- 2. Medical College, Hunan Normal University, Changsha, Hunan 410013, China
| | - Ning Liu
- 2. Medical College, Hunan Normal University, Changsha, Hunan 410013, China
| | - Yan Wang
- 1. National Engineering Laboratory for Rice and Byproduct Deep Processing, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Yingke Yang
- 3. College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Evan T Keller
- 4. Department of Urology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xiyun Deng
- 2. Medical College, Hunan Normal University, Changsha, Hunan 410013, China
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Kaufman KL, Mactier S, Christopherson RI. Surface Antigen Profiling of Surgical Melanoma Specimens. Methods Mol Biol 2015. [PMID: 26659797 DOI: 10.1007/7651_2015_302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
An antibody microarray (DotScanTM) has been developed for profiling clinical melanoma specimens. Immobilized antibodies capture live cells expressing corresponding antigens to produce a dot pattern that represents the surface profile or immunophenotype. The unique signatures obtained may correlate with disease subtype, tumor progression, and clinical outcome. Here we describe the rapid analysis of surgically resected metastatic melanoma. Leukocytes are separated from tumor cells using CD45 antibody-conjugated magnetic beads and separated cell populations are profiled on the microarray. This antibody microarray may be extended to include additional antibodies for cell surface biomarkers and therapeutic antibodies.
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Affiliation(s)
- Kimberley L Kaufman
- Cancer Proteomics Laboratory, School of Molecular Bioscience, The University of Sydney, Sydney, NSW, 2006, Australia.
| | - Swetlana Mactier
- Cancer Proteomics Laboratory, School of Molecular Bioscience, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Richard I Christopherson
- Cancer Proteomics Laboratory, School of Molecular Bioscience, The University of Sydney, Sydney, NSW, 2006, Australia
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Meinert C, Gembardt F, Böhme I, Tetzner A, Wieland T, Greenberg B, Walther T. Identification of intracellular proteins and signaling pathways in human endothelial cells regulated by angiotensin-(1-7). J Proteomics 2015; 130:129-39. [PMID: 26388433 DOI: 10.1016/j.jprot.2015.09.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 08/21/2015] [Accepted: 09/12/2015] [Indexed: 10/23/2022]
Abstract
The study aimed to identify proteins regulated by the cardiovascular protective peptide angiotensin-(1-7) and to determine potential intracellular signaling cascades. Human endothelial cells were stimulated with Ang-(1-7) for 1 h, 3 h, 6 h, and 9 h. Peptide effects on intracellular signaling were assessed via antibody microarray, containing antibodies against 725 proteins. Bioinformatics software was used to identify affected intracellular signaling pathways. Microarray data was verified exemplarily by Western blot, Real-Time RT-PCR, and immunohistochemical studies. The microarray identified 110 regulated proteins after 1 h, 119 after 3 h, 31 after 6 h, and 86 after 9 h Ang-(1-7) stimulation. Regulated proteins were associated with high significance to several metabolic pathways like “Molecular Mechanism of Cancer” and “p53 signaling” in a time dependent manner. Exemplarily, Western blots for the E3-type small ubiquitin-like modifier ligase PIAS2 confirmed the microarray data and displayed a decrease by more than 50% after Ang-(1-7) stimulation at 1 h and 3 h without affecting its mRNA. Immunohistochemical studies with PIAS2 in human endothelial cells showed a decrease in cytoplasmic PIAS2 after Ang-(1-7) treatment. The Ang-(1-7) mediated decrease of PIAS2 was reproduced in other endothelial cell types. The results suggest that angiotensin-(1-7) plays a role in metabolic pathways related to cell death and cell survival in human endothelial cells.
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Affiliation(s)
- Christian Meinert
- Institute of Experimental and Clinical Pharmacology and Toxicology, Medical Faculty Mannheim, Universität Heidelberg, Germany; Department of Pharmacology and Therapeutics, University College Cork, Cork, Ireland
| | - Florian Gembardt
- Division of Nephrology, Department of Internal Medicine III, Faculty of Medicine, Technische Universität Dresden, Germany
| | - Ilka Böhme
- Department of Obstetrics, Division of Women and Child Health, Universität Leipzig, Leipzig, Germany
| | - Anja Tetzner
- Department of Pharmacology and Therapeutics, University College Cork, Cork, Ireland; Department of Obstetrics, Division of Women and Child Health, Universität Leipzig, Leipzig, Germany
| | - Thomas Wieland
- Institute of Experimental and Clinical Pharmacology and Toxicology, Medical Faculty Mannheim, Universität Heidelberg, Germany
| | - Barry Greenberg
- Division of Cardiology, University of California, San Diego, USA
| | - Thomas Walther
- Institute of Experimental and Clinical Pharmacology and Toxicology, Medical Faculty Mannheim, Universität Heidelberg, Germany; Department of Pharmacology and Therapeutics, University College Cork, Cork, Ireland; Department of Obstetrics, Division of Women and Child Health, Universität Leipzig, Leipzig, Germany.
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26
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Nijaguna MB, Schröder C, Patil V, Shwetha SD, Hegde AS, Chandramouli BA, Arivazhagan A, Santosh V, Hoheisel JD, Somasundaram K. Definition of a serum marker panel for glioblastoma discrimination and identification of Interleukin 1β in the microglial secretome as a novel mediator of endothelial cell survival induced by C-reactive protein. J Proteomics 2015; 128:251-61. [PMID: 26232108 DOI: 10.1016/j.jprot.2015.07.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 07/04/2015] [Accepted: 07/24/2015] [Indexed: 12/22/2022]
Abstract
Glioblastoma (GBM) is the most common malignant adult primary brain tumor. We profiled 724 cancer-associated proteins in sera of healthy individuals (n=27) and GBM (n=28) using antibody microarray. While 69 proteins exhibited differential abundance in GBM sera, a three-marker panel (LYAM1, BHE40 and CRP) could discriminate GBM sera from that of healthy donors with an accuracy of 89.7% and p<0.0001. The high abundance of C-reactive protein (CRP) in GBM sera was confirmed in 264 independent samples. High levels of CRP protein was seen in GBM but without a change in transcript levels suggesting a non-tumoral origin. Glioma-secreted Interleukin 6 (IL6) was found to induce hepatocytes to secrete CRP, involving JAK-STAT pathway. The culture supernatant from CRP-treated microglial cells induced endothelial cell survival under nutrient-deprivation condition involving CRP-FcγRIII signaling cascade. Transcript profiling of CRP-treated microglial cells identified Interleukin 1β (IL1β) present in the microglial secretome as the key mediator of CRP-induced endothelial cell survival. IL1β neutralization by antibody-binding or siRNA-mediated silencing in microglial cells reduced the ability of the supernatant from CRP-treated microglial cells to induce endothelial cell survival. Thus our study identifies a serum based three-marker panel for GBM diagnosis and provides leads for developing targeted therapies. Biological significance A complex antibody microarray based serum marker profiling identified a three-marker panel - LYAM1, BHE40 and CRP as an accurate discriminator of glioblastoma sera from that of healthy individuals. CRP protein is seen in high levels without a concomitant increase of CRP transcripts in glioblastoma. Glioma-secreted IL6 induced hepatocytes to produce CRP in a JAK-STAT signaling dependent manner. CRP induced microglial cells to release IL1β which in turn promoted endothelial cell survival. This study, besides defining a serum panel for glioblastoma discrimination, identified IL1β as a potential candidate for developing targeted therapy.
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Affiliation(s)
- Mamatha B Nijaguna
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Christoph Schröder
- Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Vikas Patil
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Shivayogi D Shwetha
- Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore 560029, India
| | - Alangar S Hegde
- Sri Satya Sai Institute of Higher Medical Sciences, Bangalore 560066, India
| | - Bangalore A Chandramouli
- Department of Neurosurgery, National Institute of Mental Health and Neuro Sciences, Bangalore 560029, India
| | - Arimappamagan Arivazhagan
- Department of Neurosurgery, National Institute of Mental Health and Neuro Sciences, Bangalore 560029, India
| | - Vani Santosh
- Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore 560029, India
| | - Jörg D Hoheisel
- Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany.
| | - Kumaravel Somasundaram
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.
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Zhou J, Belov L, Chapuis P, Chan C, Armstrong N, Kaufman KL, Solomon MJ, Clarke SJ, Christopherson RI. Surface profiles of live colorectal cancer cells and tumor infiltrating lymphocytes from surgical samples correspond to prognostic categories. J Immunol Methods 2014; 416:59-68. [PMID: 25445327 DOI: 10.1016/j.jim.2014.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 10/10/2014] [Accepted: 11/03/2014] [Indexed: 12/31/2022]
Abstract
Extensive surface profiles of colorectal cancer (CRC) cells and tumor infiltrating lymphocytes (TIL) have been obtained from 45 surgical resection samples. Live cells were captured on an antibody microarray and stained with fluorescently-labeled antibodies. Minimal panels of 11 CRC antigens (CD13, CD24, CD26, CD49d, CD138, CD166, CA-125, CA19-9, EGFR, Galectin-4 and HLA-DR) and 11 T-cell antigens (CD10, CD11b, CD11c, CD25, CD31, CD95, CD151, CD181, Galectin-4, CA19-9, TSP-1) provide signatures for relapse and survival. Hierarchical clustering of profiles from CRC cells and TIL identified groups of patients for survival, systemic relapse and death. The groups from CRC and TIL profiles for systemic relapse showed 79.2% concordance, enabling prediction of relapse after surgery. The results demonstrate communication between CRC cells and TIL.
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Affiliation(s)
- Jerry Zhou
- School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia
| | - Larissa Belov
- School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia
| | - Pierre Chapuis
- Discipline of Surgery, Sydney Clinical School, University of Sydney, Sydney, NSW 2006, Australia; Department of Colorectal Surgery, Concord Hospital, Concord West, NSW 2139, Australia
| | - Charles Chan
- Department of Anatomical Pathology, Concord Hospital, Concord West, NSW 2139, Australia; Discipline of Pathology, Concord Clinical School, University of Sydney, Sydney, NSW 2006, Australia
| | - Nicola Armstrong
- School of Mathematics and Statistics, University of Sydney, Sydney, NSW 2006, Australia
| | - Kimberley L Kaufman
- School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia
| | - Michael J Solomon
- Discipline of Surgery, Sydney Clinical School, University of Sydney, Sydney, NSW 2006, Australia; Discipline of Surgery, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
| | - Stephen J Clarke
- Bill Walsh Cancer Research Laboratories, Royal North Shore Hospital, St Leonards, NSW 2065, Australia
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Nordström M, Wingren C, Rose C, Bjartell A, Becker C, Lilja H, Borrebaeck CAK. Identification of plasma protein profiles associated with risk groups of prostate cancer patients. Proteomics Clin Appl 2014; 8:951-62. [PMID: 25196118 DOI: 10.1002/prca.201300059] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 06/19/2014] [Accepted: 08/26/2014] [Indexed: 11/06/2022]
Abstract
PURPOSE Early detection of prostate cancer (PC) using prostate-specific antigen (PSA) in blood reduces PC-death among unscreened men. However, due to modest specificity of PSA at commonly used cut-offs, there are urgent needs for additional biomarkers contributing enhanced risk classification among men with modestly elevated PSA. EXPERIMENTAL DESIGN Recombinant antibody microarrays were applied for protein expression profiling of 80 plasma samples from routine PSA-measurements, a priori divided into four risk groups, based on levels of total and %free PSA. RESULTS The results demonstrated that plasma protein profiles could be identified that pin-pointed PC (a malignant biomarker signature) and most importantly that showed moderate to high correlation with biochemically defined PC risk groups. Notably, the data also implied that the risk group with midrange PSA and low %free PSA, a priori known to be heterogeneous, could be further stratified into two subgroups, more resembling the lowest and highest risk groups, respectively. CONCLUSIONS AND CLINICAL RELEVANCE In this pilot study, we have shown that plasma protein biomarker signatures, associated with risk groups of PC, could be identified from crude plasma samples using affinity proteomics. This approach could in the longer perspective provide novel opportunities for improved risk classification of PC patients.
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Affiliation(s)
- Malin Nordström
- Department of Immunotechnology, Lund University, Medicon Village, Lund, Sweden; CREATE Health, Lund University, Medicon Village, Lund, Sweden
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29
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Schröder C, Srinivasan H, Sill M, Linseisen J, Fellenberg K, Becker N, Nieters A, Hoheisel JD. Plasma protein analysis of patients with different B-cell lymphomas using high-content antibody microarrays. Proteomics Clin Appl 2014; 7:802-12. [PMID: 24323458 DOI: 10.1002/prca.201300048] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 09/02/2013] [Accepted: 09/10/2013] [Indexed: 11/09/2022]
Abstract
PURPOSE In this study, plasma samples from a multicentric case-control study on lymphoma were analyzed for the identification of proteins useful for diagnosis. EXPERIMENTAL DESIGN The protein content in the plasma of 100 patients suffering from the three most common B-cell lymphomas and 100 control samples was studied with antibody microarrays composed of 810 antibodies that target cancer-associated proteins. Sample pools were screened for an identification of marker proteins. Then, the samples were analyzed individually to validate the usability of these markers. RESULTS More than 200 proteins with disease-associated abundance changes were found. The evaluation on individual patients confirmed some molecules as robust informative markers while others were inadequate for this purpose. In addition, the analysis revealed distinct subgroups for each of the three investigated B-cell lymphoma subtypes. With this information, we delineated a classifier that discriminates the different lymphoma entities. CONCLUSIONS AND CLINICAL RELEVANCE Variations in plasma protein abundance permit discrimination between different patient groups. After validation on a larger study cohort, the findings could have diagnostic as well as differential diagnostic potential. Beside this, methodological aspects were critically evaluated, such as the value of sample pooling for the identification of biomarkers that are useful for a diagnosis on individual patients.
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Affiliation(s)
- Christoph Schröder
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum, Heidelberg, Germany
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30
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Kaufman KL, Mactier S, Armstrong NJ, Mallawaaratchy D, Byrne SN, Haydu LE, Jakrot V, Thompson JF, Mann GJ, Scolyer RA, Christopherson RI. Surface antigen profiles of leukocytes and melanoma cells in lymph node metastases are associated with survival in AJCC stage III melanoma patients. Clin Exp Metastasis 2014; 31:407-21. [PMID: 24435119 PMCID: PMC3973954 DOI: 10.1007/s10585-014-9636-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 01/09/2014] [Indexed: 12/14/2022]
Abstract
There is an urgent need to identify more accurate prognostic biomarkers in melanoma patients, particularly in those with metastatic disease. This study aimed to identify melanoma and leukocyte surface antigens predictive of survival in a prospective series of AJCC stage IIIb/c melanoma patients (n = 29). Live cell suspensions were prepared from melanoma metastases within lymph nodes (LN). The suspensions were immuno-magnetically separated into CD45+ (leukocyte) and CD45− (non-hematopoietic, enriched melanoma cell) fractions. Surface antigens on CD45− and CD45+ cell populations were profiled using DotScan™ microarrays (Medsaic Pty. Ltd.) and showed differential abundance levels for 52 and 78 antigens respectively. Associations of the surface profiles with clinicopathologic and outcome data (median follow-up 35.4 months post LN resection) were sought using univariate (log-rank test) and multivariate (Wald’s test; modelled with patient’s age, gender and AJCC staging at LN recurrence) survival models. CD9 (p = 0.036), CD39 (p = 0.004) and CD55 (p = 0.005) on CD45+ leukocytes were independently associated with distant metastasis-free survival using multivariate analysis. Leukocytes with high CD39 levels were also significantly associated with increased overall survival (OS) in multivariate analysis (p = 0.016). LNs containing leukocytes expressing CD11b (p = 0.025), CD49d (p = 0.043) and CD79b (p = 0.044) were associated with reduced OS on univariate analysis. For enriched melanoma cells (CD45− cell populations), 11 surface antigens were significantly correlated with the disease-free interval (DFI) between diagnosis of culprit primary melanoma and LN metastasis resection. Nine antigens on CD45+ leukocytes also correlated with DFI. Following validation in independent datasets, surface markers identified here should enable more accurate determination of prognosis in stage III melanoma patients and provide better risk stratification of patients entering clinical trials.
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Affiliation(s)
- Kimberley L Kaufman
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, 2006, Australia.
| | - Swetlana Mactier
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, 2006, Australia
| | - Nicola J Armstrong
- Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.,School of Mathematics and Statistics and Prince of Wales Clinical School, University of New South Wales, Kensington, NSW, 2052, Australia
| | | | - Scott N Byrne
- Discipline of Infectious Diseases and Immunology Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia.,Discipline of Dermatology, Bosch Institute, Faculty of Medicine, Sydney Medical School, Sydney, NSW, 2006, Australia
| | - Lauren E Haydu
- Melanoma Institute Australia, North Sydney, NSW, 2060, Australia.,Discipline of Surgery, Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Valerie Jakrot
- Melanoma Institute Australia, North Sydney, NSW, 2060, Australia
| | - John F Thompson
- Melanoma Institute Australia, North Sydney, NSW, 2060, Australia
| | - Graham J Mann
- Melanoma Institute Australia, North Sydney, NSW, 2060, Australia.,Westmead Institute of Cancer Research, The University of Sydney at Westmead Millennium Institute, Westmead, NSW, 2145, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, North Sydney, NSW, 2060, Australia.,Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, 2050, Australia.,Discipline of Pathology, Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia
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Demyanenko SV, Uzdensky AB, Sharifulina SA, Lapteva TO, Polyakova LP. PDT-induced epigenetic changes in the mouse cerebral cortex: a protein microarray study. Biochim Biophys Acta Gen Subj 2013; 1840:262-70. [PMID: 24055374 DOI: 10.1016/j.bbagen.2013.09.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Revised: 08/02/2013] [Accepted: 09/11/2013] [Indexed: 01/08/2023]
Abstract
BACKGROUND Photodynamic therapy (PDT) is used for cancer treatment including brain tumors. But the role of epigenetic processes in photodynamic injury of normal brain tissue is unknown. METHODS 5-Aminolevulinic acid (ALA), a precursor of protoporphyrin IX (PpIX), was used to photosensitize mouse cerebral cortex. PpIX accumulation in cortical tissue was measured spectrofluorometrically. Hematoxylin/eosin, gallocyanin-chromalum and immunohistochemical staining were used to study morphological changes in PDT-treated cerebral cortex. Proteomic antibody microarrays were used to evaluate expression of 112 proteins involved in epigenetic regulation. RESULTS ALA administration induced 2.5-fold increase in the PpIX accumulation in the mouse brain cortex compared to untreated mice. Histological study demonstrated PDT-induced injury of some neurons and cortical vessels. ALA-PDT induced dimethylation of histone H3, upregulation of histone deacetylases HDAC-1 and HDAC-11, and DNA methylation-dependent protein Kaiso that suppressed transcriptional activity. Upregulation of HDAC-1 and H3K9me2 was confirmed immunohistochemically. Down-regulation of transcription factor FOXC2, PABP, and hBrm/hsnf2a negatively regulated transcription. Overexpression of phosphorylated histone H2AX indicated activation of DNA repair, but down-regulation of MTA1/MTA1L1 and PML - impairment of DNA repair. Overexpression of arginine methyltransferase PRMT5 correlated with up-regulation of transcription factor E2F4 and importin α5/7. CONCLUSION ALA-PDT injures and kills some but not all neurons and caused limited microvascular alterations in the mouse cerebral cortex. It alters expression of some proteins involved in epigenetic regulation of transcription, histone modification, DNA repair, nuclear protein import, and proliferation. GENERAL SIGNIFICANCE These data indicate epigenetic markers of photo-oxidative injury of normal brain tissue.
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Affiliation(s)
- S V Demyanenko
- Southern Federal University, Rostov-on-Don 344090, Russia.
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Lee S, Kim S, Malm J, Jeong OC, Lilja H, Laurell T. Improved porous silicon microarray based prostate specific antigen immunoassay by optimized surface density of the capture antibody. Anal Chim Acta 2013; 796:108-14. [PMID: 24016590 DOI: 10.1016/j.aca.2013.06.041] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 06/10/2013] [Accepted: 06/25/2013] [Indexed: 11/20/2022]
Abstract
Enriching the surface density of immobilized capture antibodies enhances the detection signal of antibody sandwich microarrays. In this study, we improved the detection sensitivity of our previously developed P-Si (porous silicon) antibody microarray by optimizing concentrations of the capturing antibody. We investigated immunoassays using a P-Si microarray at three different capture antibody (PSA - prostate specific antigen) concentrations, analyzing the influence of the antibody density on the assay detection sensitivity. The LOD (limit of detection) for PSA was 2.5 ng mL(-1), 80 pg mL(-1), and 800 fg mL(-1) when arraying the PSA antibody, H117 at the concentration 15 μg mL(-1), 35 μg mL(-1), and 154 μg mL(-1), respectively. We further investigated PSA spiked into human female serum in the range of 800 fg mL(-1) to 500 ng mL(-1). The microarray showed a LOD of 800 fg mL(-1) and a dynamic range of 800 fg mL(-1) to 80 ng mL(-1) in serum spiked samples.
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Affiliation(s)
- SangWook Lee
- Bioengineering Laboratory, Riken Institute, Saitama, Japan; Department of Biomedical Engineering, Dongguk University, Seoul, Republic of Korea.
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Wu CX, Liu QM, Zhao XL, Wang F, Xu DK, He W. An antibody microarray assay for screening serum biomarkers for liver cancer. Shijie Huaren Xiaohua Zazhi 2010; 18:3378-3383. [DOI: 10.11569/wcjd.v18.i31.3378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To develop an antibody microarray assay for screening serum biomarkers for liver cancer.
METHODS: Antibody microarrays targeting 14 potential liver cancer biomarkers were prepared on aldehyde-coated glass slides. The prepared antibody microarrays were incubated with NHS-biotin-labeled serum samples and visualized with streptavidin-Cy3 fluorescent dye. The serum expression levels of 14 biomarkers were then compared between 44 liver cancer patients and 46 healthy individuals.
RESULTS: The accuracy and reproducibility of data from the developed antibody microarray assay were satisfactory. The serum expression levels of HSP70, CK19, GPC3, PTMA, AFU, GP73, HBxAg and CA125 differed significantly between liver cancer patients and healthy individuals (all P < 0.01).
CONCLUSION: An effective antibody microarray assay for screening serum biomarkers for liver cancer has been successfully developed.
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Albin DM, Gehring AG, Reed SA, Tu SI. Apparent thixotropic properties of saline/glycerol drops with biotinylated antibodies on streptavidin-coated glass slides: implications for bacterial capture on antibody microarrays. Sensors (Basel) 2009; 9:995-1011. [PMID: 22399952 DOI: 10.3390/s90200995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Accepted: 02/11/2009] [Indexed: 11/20/2022]
Abstract
The thixotropic-like properties of saline/glycerol drops, containing biotinylated capture antibodies, on streptavidin-coated glass slides have been investigated, along with their implications for bacterial detection in a fluorescent microarray immunoassay. The thixotropic-like nature of 60:40 saline-glycerol semisolid droplets (with differing amounts of antibodies) was observed when bacteria were captured, and their presence detected using a fluorescently-labeled antibody. Semisolid, gel-like drops of biotinylated capture antibody became liquefied and moved, and then returned to semisolid state, during the normal immunoassay procedures for bacterial capture and detection. Streaking patterns were observed that indicated thixotropic-like characteristics, and this appeared to have allowed excess biotinylated capture antibody to participate in bacterial capture and detection. When developing a microarray for bacterial detection, this must be considered for optimization. For example, with the appropriate concentration of antibody (in this study, 0.125 ng/nL), spots with increased diameter at the point of contact printing (and almost no streaking) were produced, resulting in a maximal signal. With capture antibody concentrations greater than 0.125 ng/nL, the excess biotinylated capture antibody (i.e., that which was residing in the three-dimensional, semisolid droplet space above the surface) was utilized to capture more bacteria. Similarly, when the immunoassay was performed within a hydrophobic barrier (i.e., without a coverslip), brighter spots with increased signal were observed. In addition, when higher concentrations of cells (∼108 cells/mL) were available for capture, the importance of unbound capture antibody in the semisolid droplets became apparent because washing off the excess, unbound biotinylated capture antibody before the immunoassay was performed reduced the signal intensity by nearly 50%. This reduction in signal was not observed with lower concentrations of cells (∼106 cells/mL). With increased volumes of capture antibody, abnormal spots were visualized, along with decreased signal intensity, after bacterial detection, indicating that the increased droplet volume detrimentally affected the immunoassay.
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