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Identification and Validation of Potential New Biomarkers for Prostate Cancer Diagnosis and Prognosis Using 2D-DIGE and MS

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BIOMED RESEARCH INTERNATIONAL 2015年第0期2015卷 454256-454256页

作者： Geisler, Cordelia Gaisa, Nadine T. Pfister, David Fuessel, Susanne Kristiansen, Glen Braunschweig, Till Gostek, Sonja Beine, Birte Diehl, Hanna C. Jackson, Angela M. Borchers, Christoph H. Heidenreich, Axel Meyer, Helmut E. Knuechel, Ruth Henkel, Corinna Rhein Westfal TH Aachen Inst Pathol D-52074 Aachen Germany Rhein Westfal TH Aachen Dept Urol D-52074 Aachen Germany Univ Hosp Carl Gustav Carus Dept Urol D-01307 Dresden Germany Univ Hosp Bonn UKB Inst Pathol D-53127 Bonn Germany Ruhr Univ Bochum Med Proteom Ctr D-44801 Bochum Germany Leibniz Inst Analyt Wissensch ISAS eV D-44139 Dortmund Germany Univ Victoria Univ Victoria Genome British Columbia Prote Ctr Victoria BC V8Z 7X8 Canada Univ Victoria Dept Biochem & Microbiol Victoria BC V8W 2Y2 Canada

This study was designed to identify and validate potential new biomarkers for prostate cancer and to distinguish patients with and without biochemical relapse. Prostate tissue samples analyzed by 2D-DIGE (two-dimensional difference in gel electrophoresis) and mass spectrometry (MS) revealed downregulation of secernin-1 (P < 0.044) in prostate cancer, while vinculin showed significant upregulation (P < 0.001). Secernin-1 overexpression in prostate tissue was validated using Western blot and immunohistochemistry while vinculin expression was validated using immunohistochemistry. These findings indicate that secernin-1 and vinculin are potential new tissue biomarkers for prostate cancer diagnosis and prognosis, respectively. For validation, protein levels in urine were also examined by Western blot analysis. Urinary vinculin levels in prostate cancer patients were significantly higher than in urine from nontumor patients (P = 0.006). Using multiple reaction monitoring-MS (MRM-MS) analysis, prostatic acid phosphatase (PAP) showed significant higher levels in the urine of prostate cancer patients compared to controls (P - 0.012), while galectin-3 showed significant lower levels in the urine of prostate cancer patients with biochemical relapse, compared to those without relapse (P = 0.017). Three proteins were successfully differentiated between patients with and without prostate cancer and patients with and without relapse by using MRM. Thus, this technique shows promise for implementation as a noninvasive clinical diagnostic technique.

关键词： PROSTATE tumors PROGNOSIS DIAGNOSIS BIOCHEMICAL markers IMMUNOHISTOCHEMISTRY MASS spectrometry PROSTATECTOMY PROTEINS PULSED-field gel electrophoresis FINANCING of research WESTERN immunoblotting DATA analysis software microarray technology MANN Whitney U Test

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A lateral flow paper microarray for rapid allergy point of care diagnostics

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ANALYST 2014年第10期139卷 2348-2354页

作者： Chinnasamy, Thiruppathiraja Segerink, Loes I. Nystrand, Mats Gantelius, Jesper Svahn, Helene Andersson KTH Royal Inst Technol Div Prote & Nanobiotechnol Sci Life Lab S-17121 Stockholm Sweden Univ Twente MESA Inst Nanotechnol BIOS LabChip Grp NL-7500 AE Enschede Netherlands Thermo Fisher Sci Uppsala Sweden

There is a growing need for multiplexed specific IgE tests that can accurately evaluate patient sensitization profiles. However, currently available commercial tests are either single/low-plexed or require sophisticated instrumentation at considerable cost per assay. Here, we present a novel convenient lateral flow microarray-based device that employs a novel dual labelled gold nanoparticle-strategy for rapid and sensitive detection of a panel of 15 specific IgE responses in 35 clinical serum samples. Each gold nanoparticle was conjugated to an optimized ratio of HRP and anti-IgE, allowing significant enzymatic amplification to improve the sensitivity of the assay as compared to commercially available detection reagents. The mean inter-assay variability of the developed LFM assay was 12% CV, and analysis of a cohort of clinical samples (n = 35) revealed good general agreement with ImmunoCAP, yet with a varying performance among allergens (AUC = [0.54-0.88], threshold 1 kU). Due to the rapid and simple procedure, inexpensive materials and read-out by means of a consumer flatbed scanner, the presented assay may provide an interesting low-cost alternative to existing multiplexed methods when thresholds > 1 kU are acceptable.

关键词： microarray technology PLASMA diagnostics ALLERGY SCANNING systems SENSITIZATION (Neuropsychology)

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The Evidence of Glioblastoma Heterogeneity

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SCIENTIFIC REPORTS 2015年第1期5卷 7979-7979页

作者： Soeda, Akio Hara, Akira Kunisada, Takahiro Yoshimura, Shin-ichi Iwama, Toru Park, Deric M. Gifu Univ Sch Med Dept Neurosurg Gifu 500 Japan Gifu Univ Sch Med Dept Tumor Pathol Gifu 500 Japan Gifu Univ Sch Med Dept Tissue & Organ Regenerat Gifu 500 Japan Univ Virginia Dept Neurol Surg Charlottesville VA USA

Cancers are composed of heterogeneous combinations of cells that exhibit distinct phenotypic characteristics and proliferative potentials. Because most cancers have a clonal origin, cancer stem cells (CSCs) must generate phenotypically diverse progenies including mature CSCs that can self-renew indefinitely and differentiated cancer cells that possess limited proliferative potential. However, no convincing evidence exists to suggest that only single CSCs are representative of patients' tumors. To investigate the CSCs' diversity, we established 4 subclones from a glioblastoma patient. These subclones were subsequently propagated and analyzed. The morphology, the self-renewal and proliferative capacities of the subclones differed. Fluorescence-activated cell sorting and cDNA-microarray analyses revealed that each subclone was composed of distinct populations of cells. Moreover, the sensitivities of the subclones to an inhibitor of epidermal growth factor receptor were dissimilar. In a mouse model featuring xenografts of the subclones, the progression and invasion of tumors and animal survival were also different. Here, we present clear evidence that a brain tumor contains heterogeneous subclones that exhibit dissimilar morphologies and self-renewal and proliferative capacities. Our results suggest that single cell-derived subclones from a patient can produce phenotypically heterogeneous self-renewing progenies in both in vitro and in vivo settings.

关键词： AUTOPOIESIS HETEROGENEITY ANTISENSE DNA CANCER stem cells microarray technology GLIOBLASTOMA multiforme

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PExFInS: An Integrative Post-GWAS Explorer for Functional Indels and SNPs

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SCIENTIFIC REPORTS 2015年第1期5卷 17302-17302页

作者： Cheng, Zhongshan Chu, Hin Fan, Yanhui Li, Cun Song, You-Qiang Zhou, Jie Yuen, Kwok-Yung Univ Hong Kong Dept Microbiol Hong Kong Hong Kong Peoples R China Univ Hong Kong State Key Lab Emerging Infect Dis Hong Kong Hong Kong Peoples R China Univ Hong Kong Res Ctr Infect & Immunol Hong Kong Hong Kong Peoples R China Univ Hong Kong Carol Yu Ctr Infect Hong Kong Hong Kong Peoples R China Univ Hong Kong Dept Biochem Hong Kong Hong Kong Peoples R China Univ Hong Kong Ctr Genom Sci Hong Kong Hong Kong Peoples R China

Expression quantitative trait loci (eQTLs) mapping and linkage disequilibrium (LD) analysis have been widely employed to interpret findings of genome-wide association studies (GWAS). With the availability of deep sequencing data of 423 lymphoblastoid cell lines (LCLs) from six global populations and the microarray expression data, we performed eQTL analysis, identified more than 228 K SNP cis-eQTLs and 21 K indel cis-eQTLs and generated a LCL cis-eQTL database. We demonstrate that the percentages of population-shared and population-specific cis-eQTLs are comparable;while indel cis-eQTLs in the population-specific subsection make more contribution to gene expression variations than those in the population-shared subsection. We found cis-eQTLs, especially the population-shared cis-eQTLs are significantly enriched toward transcription start site. Moreover, the National Human Genome Research Institute cataloged GWAS SNPs are enriched for LCL cis-eQTLs. Specifically, 32.8% GWAS SNPs are LCL cis-eQTLs, among which 12.5% can be tagged by indel cis-eQTLs, suggesting the fundamental contribution of indel cis-eQTLs to GWAS association signals. To search for functional indels and SNPs tagging GWAS SNPs, a pipeline Post-GWAS Explorer for Functional Indels and SNPs (PExFInS) has been developed, integrating LD analysis, functional annotation from public databases, cis-eQTL mapping with our LCL cis-eQTL database and other published cis-eQTL datasets.

关键词： LINKAGE disequilibrium POPULATION genetics LINKAGE (Genetics) LYMPHOBLASTOID cell lines microarray technology BIOLOGICAL apparatus & supplies NANOtechnology

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Synergistic anti-tumor therapy by a comb-like multifunctional antibody nanoarray with exceptionally potent activity

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SCIENTIFIC REPORTS 2015年第1期5卷 15712-15712页

作者： Li, Huafei Sun, Yun Chen, Di Zhao, He Zhao, Mengxin Zhu, Xiandi Ke, Changhong Zhang, Ge Jiang, Cheng Zhang, Li Zhang, Fulei Wei, Huafeng Li, Wei Second Mil Med Univ Int Joint Canc Inst Shanghai 200433 Peoples R China State Key Lab Antibody Med Shanghai 200433 Peoples R China Shanghai Key Lab Cell Engn Shanghai 200433 Peoples R China Peoples Liberat Army Gen Hosp PLA Grad Sch Med Ctr Canc Beijing 100853 Peoples R China

Simultaneously blocking multiple mediators offers new hope for the treatment of complex diseases. However, the curative potential of current combination therapy by chronological administration of separate monoclonal antibodies (mAbs) or multi-specific mAbs is still moderate due to inconvenient manipulation, low cooperative effectors, poor pharmacokinetics and insufficient tumor accumulation. Here, we describe a facile strategy that arms distinct mAbs with cooperative effectors onto a long chain to form a multicomponent comb-like nano mAb. Unlike dissociative parental mAbs, the multifunctional mAb nanoarray (PL-RB) constructed from type I/II anti-CD20 mAbs shows good pharmacokinetics. This PL-RB simultaneously targets distinct epitopes on a single antigen (Ag) and neighboring Ags on different lymphocytes. This unique intra-and intercellular Ag cross-linking endows the multifunctional mAb nanoarray with potent apoptosis activity. The exceptional apoptosis, complement-dependent cytotoxicity (CDC), antibody-dependent cellular cytotoxicity (ADCC) that are synchronously evoked by the nano PL-RB are further synergistically promoted via enhanced permeability and retention (EPR), which resulted in high intratumor accumulation and excellent anti-lymphoma efficiency.

关键词： ANTINEOPLASTIC agents MONOCLONAL antibodies microarray technology LYMPHOCYTES APOPTOSIS PHARMACOKINETICS

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Controllable high-throughput high-quality femtosecond laser-enhanced chemical etching by temporal pulse shaping based on electron density control

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SCIENTIFIC REPORTS 2015年第1期5卷 13202-13202页

作者： Zhao, Mengjiao Hu, Jie Jiang, Lan Zhang, Kaihu Liu, Pengjun Lu, Yongfeng Beijing Inst Technol Sch Mech Engn Laser Micro Nano Fabricat Lab Beijing 100081 Peoples R China Univ Nebraska Dept Elect Engn Lincoln NE 68588 USA

We developed an efficient fabrication method of high-quality concave microarrays on fused silica substrates based on temporal shaping of femtosecond (fs) laser pulses. This method involves exposures of fs laser pulse trains followed by a wet etching process. Compared with conventional single pulses with the same processing parameters, the temporally shaped fs pulses can enhance the etch rate by a factor of 37 times with better controllability and higher quality. Moreover, we demonstrated the flexibility of the proposed method in tuning the profile of the concave microarray structures by changing the laser pulse delay, laser fluence, and pulse energy distribution ratio. Micro-Raman spectroscopy was conducted to elucidate the stronger modification induced by the fs laser pulse trains in comparison with the single pulses. Our calculations show that the controllability is due to the effective control of localized transient free electron densities by temporally shaping the fs pulses.

关键词： FEMTOSECOND lasers ELECTRON density ETCHING microarray technology FEMTOSECOND pulses

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Transcriptomic Analysis of mRNAs in Human Monocytic Cells Expressing the HIV-1 Nef Protein and Their Exosomes

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BIOMED RESEARCH INTERNATIONAL 2015年第0期2015卷 492395-492395页

作者： Aqil, Madeeha Mallik, Saurav Bandyopadhyay, Sanghamitra Maulik, Ujjwal Jameel, Shahid Int Ctr Genet Engn & Biotechnol Virol Grp New Delhi 110067 India Univ Illinois Coll Dent Dept Oral Med & Diagnost Sci Chicago IL 60612 USA Indian Stat Inst Machine Intelligence Unit Kolkata 700108 India Jadavpur Univ Dept Comp Sci & Engn Kolkata 700032 W Bengal India Wellcome Trust DBT India Alliance Hyderabad 500034 Andhra Pradesh India

The Nef protein of human immunodeficiency virus (HIV) promotes viral replication and progression to AIDS. Besides its well-studied effects on intracellular signaling, Nef also functions through its secretion in exosomes, which are nanovesicles containing proteins, microRNAs, and mRNAs and are important for intercellular communication. Nef expression enhances exosome secretion and these exosomes can enter uninfected CD4 T cells leading to apoptotic death. We have recently reported the first miRNome analysis of exosomes secreted from Nef-expressing U937monocytic cells. Here we show genome-wide transcriptome analysis of Nef-expressing U937 cells and their exosomes. We identified four key mRNAs preferentially retained in Nef-expressing cells;these code for MECP2, HMOX1, AARSD1, and ATF2 and are important for chromatin modification and gene expression. Interestingly, their target miRNAs are exported out in exosomes. We also identified three key mRNAs selectively secreted in exosomes from Nef-expressing U937 cells and their corresponding miRNAs being preferentially retained in cells. These are AATK, SLC27A1, and CDKAL and are important in apoptosis and fatty acid transport. Thus, our study identifies selectively expressed mRNAs in Nef-expressing U937 cells and their exosomes and supports a new mode on intercellular regulation by the HIV-1 Nef protein.

关键词： PROTEIN metabolism AIDS (Disease) APOPTOSIS CELL interaction (Biology) GENE expression HIV (Viruses) HUMAN genome MONOCYTES FINANCING of research RNA T-test (Statistics) DISEASE progression microarray technology

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Single Nucleotide Polymorphism (rs4932178) in the P1 Promoter of FURIN Is Not Prognostic to Colon Cancer

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BIOMED RESEARCH INTERNATIONAL 2015年第0期2015卷 321276-321276页

作者： Declercq, Jeroen Jacobs, Bart Biesmans, Bart Roth, Arnaud Klingbiel, Dirk Tejpar, Sabine Creemers, John W. Katholieke Univ Leuven Dept Human Genet Biochem Neuroendocrinol Lab B-3000 Leuven Belgium Katholieke Univ Leuven Dept Human Genet Digest Oncol Unit B-3000 Leuven Belgium Univ Hosp Geneva Oncosurgery Unit CH-1204 Geneva Switzerland Swiss Grp Clin Canc Res SAKK Coordinating Ctr CH-3008 Bern Switzerland

High expression of the proprotein processing enzyme FURIN has been associated with tumor progression and metastasis. A SNP (rs4932178) in the promoter of FURIN has been reported to affect expression in liver, with the T allele resulting in higher expression than the Callele. In this study we have investigated the association of this SNP with prognostic and biological subgroups of colorectal cancer (CRC). In a panel of 1382 patients with CRC, this SNP had no impact on overall survival or on postoperative risk of relapse. This SNP also could not be linked with FURIN expression levels in CRC samples from the patients. Furthermore, we demonstrate in luciferase reporter experiments in the colon cancer cell lines Caco-2 and SW480 and in the hepatocellular carcinoma cell line Huh 7 that expression is not affected by the SNP. Since, FURIN inhibition in human colon cancer cell lines has previously been shown to repress tumor metastases, association between FURIN gene expression levels and postoperative relapse-free survival was also investigated. However, no association could be found. Altogether, we could not confirm an effect of the SNP on FURIN expression in vitro and no correlations could be found in vivo with FURIN expression or outcome.

关键词： COLON tumors PROGNOSIS CANCER relapse RESEARCH CHI-squared test CONFIDENCE intervals GENE expression GENETIC polymorphisms MASS spectrometry MEDICAL cooperation POLYMERASE chain reaction PROBABILITY theory PROTEOLYTIC enzymes REGRESSION analysis FINANCING of research SURVIVAL analysis (Biometry) T-test (Statistics) TUMOR classification RANDOMIZED controlled trials DATA analysis software microarray technology DESCRIPTIVE statistics KAPLAN-Meier estimator IRINOTECAN (Drug) ODDS ratio GENOTYPE KRUSKAL-Wallis Test GENETIC aspects

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Identification of Potential Transcriptomic Markers in Developing Ankylosing Spondylitis: A Meta-Analysis of Gene Expression Profiles

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BIOMED RESEARCH INTERNATIONAL 2015年第0期2015卷 826316-826316页

作者： Fang, Fang Pan, Jian Xu, Lixiao Li, Gang Wang, Jian Soochow Univ Childrens Hosp Pediat Res Inst Suzhou 215003 Peoples R China

The goal of this study was to identify potential transcriptomic markers in developing ankylosing spondylitis by a meta-analysis of multiple public microarray datasets. Using the INMEX (integrative meta-analysis of expression data) program, we performed the meta-analysis to identify consistently differentially expressed (DE) genes in ankylosing spondylitis and further performed functional interpretation (gene ontology analysis and pathway analysis) of the DE genes identified in the meta-analysis. Three microarray datasets (26 cases and 29 controls in total) were collected for meta-analysis. 905 consistently DE genes were identified in ankylosing spondylitis, among which 482 genes were upregulated and 423 genes were downregulated. The upregulated gene with the smallest combined rank product (RP) was GNG11 (combined RP = 299.64). The downregulated gene with the smallest combined RP was S100P (combined RP = 335.94). In the gene ontology (GO) analysis, the most significantly enriched GO term was "immune systemprocess" (P = 3.46x10(-26)). The most significant pathway identified in the pathway analysis was antigen processing and presentation (P = 8.40 x 10(-5)). The consistently DE genes in ankylosing spondylitis and biological pathways associated with those DE genes identified provide valuable information for studying the pathophysiology of ankylosing spondylitis.

关键词： ANKYLOSING spondylitis BIOCHEMICAL markers GENE expression META-analysis FINANCING of research TIME microarray technology GENE expression profiling

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Identification of Reference Genes in Human Myelomonocytic Cells for Gene Expression Studies in Altered Gravity

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BIOMED RESEARCH INTERNATIONAL 2015年第0期2015卷 363575-363575页

作者： Thiel, Cora S. Hauschild, Swantje Tauber, Svantje Paulsen, Katrin Raig, Christiane Raem, Arnold Biskup, Josefine Gutewort, Annett Huerlimann, Eva Unverdorben, Felix Buttron, Isabell Lauber, Beatrice Philpot, Claudia Lier, Hartwin Engelmann, Frank Layer, Liliana E. Ullrich, Oliver Univ Zurich Fac Med Inst Anat CH-8057 Zurich Switzerland Otto Von Guericke Univ Inst Engn Mech Dept Machine Design Engn Design & Prod Dev D-39106 Magdeburg Germany Otto Von Guericke Univ MARS D-39106 Magdeburg Germany Univ Munster Ctr Nanotechnol Arrows Biomed Deutsch GmbH D-48149 Munster Germany Space Agcy German Aerosp Ctr D-53227 Bonn Germany KEK GmbH D-06905 Bad Schmiedeberg Germany Univ Appl Sci Jena D-07745 Jena Germany Univ Zurich Zurich Ctr Integrat Human Physiol ZIHP CH-8057 Zurich Switzerland

Gene expression studies are indispensable for investigation and elucidation of molecular mechanisms. For the process of normalization, reference genes ("housekeeping genes") are essential to verify gene expression analysis. Thus, it is assumed that these reference genes demonstrate similar expression levels over all experimental conditions. However, common recommendations about reference genes were established during 1 g conditions and therefore their applicability in studies with altered gravity has not been demonstrated yet. The microarray technology is frequently used to generate expression profiles under defined conditions and to determine the relative difference in expression levels between two or more different states. In our study, we searched for potential reference genes with stable expression during different gravitational conditions (microgravity, normogravity, and hypergravity) which are additionally not altered in different hardware systems. We were able to identify eight genes (ALB, B4GALT6, GAPDH, HMBS, YWHAZ, ABCA5, ABCA9, and ABCC1) which demonstrated no altered gene expression levels in all tested conditions and therefore represent good candidates for the standardization of gene expression studies in altered gravity.

关键词： LYMPHATIC cancer DIAGNOSIS AERONAUTICS in medicine CELL culture CELL physiology GENE expression GENES GENOMES MOLECULAR biology FINANCING of research RNA technology ARTIFICIAL gravity microarray technology

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