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Durante IM, La Spina PE, Carmona SJ, Agüero F, Buscaglia CA. High-resolution profiling of linear B-cell epitopes from mucin-associated surface proteins (MASPs) of Trypanosoma cruzi during human infections. PLoS Negl Trop Dis 2017; 11:e0005986. [PMID: 28961244 PMCID: PMC5636173 DOI: 10.1371/journal.pntd.0005986] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/11/2017] [Accepted: 09/21/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The Trypanosoma cruzi genome bears a huge family of genes and pseudogenes coding for Mucin-Associated Surface Proteins (MASPs). MASP molecules display a 'mosaic' structure, with highly conserved flanking regions and a strikingly variable central and mature domain made up of different combinations of a large repertoire of short sequence motifs. MASP molecules are highly expressed in mammal-dwelling stages of T. cruzi and may be involved in parasite-host interactions and/or in diverting the immune response. METHODS/PRINCIPLE FINDINGS High-density microarrays composed of fully overlapped 15mer peptides spanning the entire sequences of 232 non-redundant MASPs (~25% of the total MASP content) were screened with chronic Chagasic sera. This strategy led to the identification of 86 antigenic motifs, each one likely representing a single linear B-cell epitope, which were mapped to 69 different MASPs. These motifs could be further grouped into 31 clusters of structurally- and likely antigenically-related sequences, and fully characterized. In contrast to previous reports, we show that MASP antigenic motifs are restricted to the central and mature region of MASP polypeptides, consistent with their intracellular processing. The antigenicity of these motifs displayed significant positive correlation with their genome dosage and their relative position within the MASP polypeptide. In addition, we verified the biased genetic co-occurrence of certain antigenic motifs within MASP polypeptides, compatible with proposed intra-family recombination events underlying the evolution of their coding genes. Sequences spanning 7 MASP antigenic motifs were further evaluated using distinct synthesis/display approaches and a large panel of serum samples. Overall, the serological recognition of MASP antigenic motifs exhibited a remarkable non normal distribution among the T. cruzi seropositive population, thus reducing their applicability in conventional serodiagnosis. As previously observed in in vitro and animal infection models, immune signatures supported the concurrent expression of several MASPs during human infection. CONCLUSIONS/SIGNIFICANCE In spite of their conspicuous expression and potential roles in parasite biology, this study constitutes the first unbiased, high-resolution profiling of linear B-cell epitopes from T. cruzi MASPs during human infection.
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Affiliation(s)
- Ignacio M. Durante
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECh), Universidad Nacional de San Martín (UNSAM) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Buenos Aires, Argentina
| | - Pablo E. La Spina
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECh), Universidad Nacional de San Martín (UNSAM) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Buenos Aires, Argentina
| | - Santiago J. Carmona
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECh), Universidad Nacional de San Martín (UNSAM) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Buenos Aires, Argentina
| | - Fernán Agüero
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECh), Universidad Nacional de San Martín (UNSAM) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Buenos Aires, Argentina
- * E-mail: (FA); (CAB)
| | - Carlos A. Buscaglia
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECh), Universidad Nacional de San Martín (UNSAM) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET); Buenos Aires, Argentina
- * E-mail: (FA); (CAB)
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202
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Luan X, Cao Z, Xing Z, Liu M, Gao M, Meng B, Fan R. Comparative proteomic analysis of pituitary glands from Huoyan geese between pre-laying and laying periods using an iTRAQ-based approach. PLoS One 2017; 12:e0185253. [PMID: 28945779 PMCID: PMC5612699 DOI: 10.1371/journal.pone.0185253] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 09/08/2017] [Indexed: 12/31/2022] Open
Abstract
In this study, we performed a comprehensive evaluation of the proteomic profile of the pituitary gland of the Huoyan goose during the laying period compared to the pre-laying period using an iTRAQ-based approach. Protein samples were prepared from pituitary gland tissues of nine pre-laying period and nine laying period geese. Then the protein samples from three randomly selected geese within each period were pooled in equal amounts to generate one biological sample pool. We identified 684 differentially expressed proteins, including 418 up-regulated and 266 down-regulated proteins. GO annotation and KEGG pathway analyses of these proteins were conducted. Some of these proteins were found to be associated with hormone and neurotransmitter secretion and transport, neuropeptide signalling and GnRH signalling pathways, among others. Subsequently, the modification of the abundance of three proteins (prolactin, chromogranin-A and ITPR3) was verified using western blotting. Our results will provide a new source for mining genes and gene products related to the egg-laying performance of Huoyan geese, and may provide important information for the conservation and utilization of local goose breeds.
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Affiliation(s)
- Xinhong Luan
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P.R. China
- * E-mail:
| | - Zhongzan Cao
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P.R. China
| | - Zhe Xing
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P.R. China
| | - Mei Liu
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P.R. China
| | - Ming Gao
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P.R. China
| | - Bo Meng
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P.R. China
| | - Ruiming Fan
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P.R. China
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203
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Miro Estruch I, Melchers D, Houtman R, de Haan LHJ, Groten JP, Louisse J, Rietjens IMCM. Characterization of the differential coregulator binding signatures of the Retinoic Acid Receptor subtypes upon (ant)agonist action. Biochim Biophys Acta Proteins Proteom 2017; 1865:1195-1206. [PMID: 28642153 DOI: 10.1016/j.bbapap.2017.06.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 12/09/2016] [Revised: 06/02/2017] [Accepted: 06/17/2017] [Indexed: 10/19/2022]
Abstract
Retinoic Acid Receptor alpha (RARα/NR1B1), Retinoic Acid Receptor beta (RARβ/NR1B2) and Retinoic Acid Receptor gamma (RARγ/NR1B3) are transcription factors regulating gene expression in response to retinoids. Within the RAR genomic pathways, binding of RARs to coregulators is a key intermediate regulatory phase. However, ligand-dependent interactions between the wide variety of coregulators that may be present in a cell and the different RAR subtypes are largely unknown. The aim of this study is to characterize the coregulator binding profiles of RARs in the presence of the pan-agonist all-trans-Retinoic Acid (AtRA); the subtype-selective agonists Am80 (RARα), CD2314 (RARβ) and BMS961 (RARγ); and the antagonist Ro415253. To this end, we used a microarray assay for coregulator-nuclear receptor interactions to assess RAR binding to 154 motifs belonging to >60 coregulators. The results revealed a high number of ligand-dependent RAR-coregulator interactions among all RAR variants, including many binding events not yet described in literature. Next, this work confirmed a greater ligand-independent activity of RARβ compared to the other RAR subtypes based on both higher basal and lower ligand-driven coregulator binding. Further, several coregulator motifs showed selective binding to a specific RAR subtype. Next, this work showed that subtype-selective agonists can be successfully discriminated by using coregulator binding assays. Finally this study demonstrated the possible applications of a coregulator binding assay as a tool to discriminate between agonistic/antagonistic actions of ligands. The RAR-coregulator interactions found will be of use to direct further studies to better understand the mechanisms driving the eventual actions of retinoids.
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Affiliation(s)
- Ignacio Miro Estruch
- Division of Toxicology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
| | - Diana Melchers
- PamGene International B.V., Wolvenhoek 10, 5211 HH 's-Hertogenbosch, The Netherlands
| | - René Houtman
- PamGene International B.V., Wolvenhoek 10, 5211 HH 's-Hertogenbosch, The Netherlands
| | - Laura H J de Haan
- Division of Toxicology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - John P Groten
- Division of Toxicology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands; PamGene International B.V., Wolvenhoek 10, 5211 HH 's-Hertogenbosch, The Netherlands
| | - Jochem Louisse
- Division of Toxicology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Ivonne M C M Rietjens
- Division of Toxicology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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Fei X, Zavorka ME, Malik G, Connelly CM, MacDonald RG, Berkowitz DB. General Linker Diversification Approach to Bivalent Ligand Assembly: Generation of an Array of Ligands for the Cation-Independent Mannose 6-Phosphate Receptor. Org Lett 2017; 19:4267-4270. [PMID: 28753028 PMCID: PMC6208139 DOI: 10.1021/acs.orglett.7b01914] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A generalized strategy is presented for the rapid assembly of a set of bivalent ligands with a variety of linking functionalities from a common monomer. Herein, an array of phosphatase-inert mannose-6-phosphonate-presenting ligands for the cation-independent-mannose 6-phosphate receptor (CI-MPR) is constructed. Receptor binding affinity varies with linking functionality-the simple amide and 1,5-triazole(tetrazole) being preferred over the 1,4-triazole. This approach is expected to find application across chemical biology, particularly in glycoscience, wherein multivalency often governs molecular recognition.
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Affiliation(s)
- Xiang Fei
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Megan E. Zavorka
- Department of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68198-5870, United States
| | - Guillaume Malik
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Christopher M. Connelly
- Department of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68198-5870, United States
| | - Richard G. MacDonald
- Department of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68198-5870, United States
| | - David B. Berkowitz
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
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205
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Sereni MI, Baldelli E, Gambara G, Ravaggi A, Hodge KA, Alberts DS, Guillen-Rodriguez JM, Dong T, Memo M, Odicino F, Angioli R, Liotta LA, Pecorelli SL, Petricoin EF, Pierobon M. Kinase-driven metabolic signalling as a predictor of response to carboplatin-paclitaxel adjuvant treatment in advanced ovarian cancers. Br J Cancer 2017; 117:494-502. [PMID: 28664915 PMCID: PMC5558684 DOI: 10.1038/bjc.2017.195] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 05/19/2017] [Accepted: 06/01/2017] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The biological mechanisms underlying early- and advanced-stage epithelial ovarian cancers (EOCs) are still poorly understood. This study explored kinase-driven metabolic signalling in early and advanced EOCs, and its role in tumour progression and response to carboplatin-paclitaxel treatment. METHODS Tumour epithelia were isolated from two independent sets of primary EOC (n=72 and 30 for the discovery and the validation sets, respectively) via laser capture microdissection. Reverse phase protein microarrays were used to broadly profile the kinase-driven metabolic signalling of EOC with particular emphasis on the LBK1-AMPK and AKT-mTOR axes. Signalling activation was compared between early and advanced lesions, and carboplatin-paclitaxel-sensitive and -resistant tumours. RESULTS Advanced EOCs were characterised by a heterogeneous kinase-driven metabolic signature and decreased phosphorylation of the AMPK-AKT-mTOR axis compared to early EOC (P<0.05 for AMPKα T172, AMPKα1 S485, AMPKβ1 S108, AKT S473 and T308, mTOR S2448, p70S6 S371, 4EBP1 S65, GSK-3 α/β S21/9, FOXO1 T24/FOXO3 T32, and FOXO1 S256). Advanced tumours with low relative activation of the metabolic signature and increased FOXO1 T24/FOXO3 T32 phosphorylation (P=0.041) were associated with carboplatin-paclitaxel resistance. CONCLUSIONS If validated in a larger cohort of patients, the decreased AMPK-AKT-mTOR activation and phosphorylation of FOXO1 T24/FOXO3 T32 may help identify carboplatin-paclitaxel-resistant EOC patients.
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Affiliation(s)
- Maria Isabella Sereni
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, Manassas, VA 20110, USA
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
- Department of Obstetrics and Gynecology, Campus Bio-Medico University of Rome, Via Alvaro del Portillo 21, 00128 Roma, Italy
| | - Elisa Baldelli
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, Manassas, VA 20110, USA
| | - Guido Gambara
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, Manassas, VA 20110, USA
| | - Antonella Ravaggi
- Division of Gynecologic Oncology, ‘Angelo Nocivelli’ Institute of Molecular Medicine, University of Brescia, Piazzale Spedali Civili 1, 25123 Brescia, Italy
| | - K Alex Hodge
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, Manassas, VA 20110, USA
| | - David S Alberts
- The University of Arizona Cancer Center, 3838N Campbell Ave, Tucson, AZ 85719, USA
| | | | - Ting Dong
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, Manassas, VA 20110, USA
| | - Maurizio Memo
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Franco Odicino
- Division of Gynecologic Oncology, ‘Angelo Nocivelli’ Institute of Molecular Medicine, University of Brescia, Piazzale Spedali Civili 1, 25123 Brescia, Italy
| | - Roberto Angioli
- Department of Obstetrics and Gynecology, Campus Bio-Medico University of Rome, Via Alvaro del Portillo 21, 00128 Roma, Italy
| | - Lance A Liotta
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, Manassas, VA 20110, USA
| | - Sergio L Pecorelli
- Division of Gynecologic Oncology, ‘Angelo Nocivelli’ Institute of Molecular Medicine, University of Brescia, Piazzale Spedali Civili 1, 25123 Brescia, Italy
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, Manassas, VA 20110, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, Manassas, VA 20110, USA
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206
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Lucas JL, Tacheny EA, Ferris A, Galusha M, Srivastava AK, Ganguly A, Williams PM, Sachs MC, Thurin M, Tricoli JV, Ricker W, Gildersleeve JC. Development and validation of a Luminex assay for detection of a predictive biomarker for PROSTVAC-VF therapy. PLoS One 2017; 12:e0182739. [PMID: 28771597 PMCID: PMC5542629 DOI: 10.1371/journal.pone.0182739] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 07/24/2017] [Indexed: 11/19/2022] Open
Abstract
Cancer therapies can provide substantially improved survival in some patients while other seemingly similar patients receive little or no benefit. Strategies to identify patients likely to respond well to a given therapy could significantly improve health care outcomes by maximizing clinical benefits while reducing toxicities and adverse effects. Using a glycan microarray assay, we recently reported that pretreatment serum levels of IgM specific to blood group A trisaccharide (BG-Atri) correlate positively with overall survival of cancer patients on PROSTVAC-VF therapy. The results suggested anti-BG-Atri IgM measured prior to treatment could serve as a biomarker for identifying patients likely to benefit from PROSTVAC-VF. For continued development and clinical application of serum IgM specific to BG-Atri as a predictive biomarker, a clinical assay was needed. In this study, we developed and validated a Luminex-based clinical assay for measuring serum IgM specific to BG-Atri. IgM levels were measured with the Luminex assay and compared to levels measured using the microarray for 126 healthy individuals and 77 prostate cancer patients. This assay provided reproducible and consistent results with low %CVs, and tolerance ranges were established for the assay. IgM levels measured using the Luminex assay were found to be highly correlated to the microarray results with R values of 0.93–0.95. This assay is a Laboratory Developed Test (LDT) and is suitable for evaluating thousands of serum samples in CLIA certified laboratories that have validated the assay. In addition, the study demonstrates that discoveries made using neoglycoprotein-based microarrays can be readily migrated to a clinical assay.
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Affiliation(s)
- Julie L. Lucas
- MRIGlobal, Gaithersburg, Maryland, United States of America
| | | | - Allison Ferris
- MRIGlobal, Gaithersburg, Maryland, United States of America
| | | | - Apurva K. Srivastava
- Pharmacodynamics Biomarker Program, Applied/Developmental Research Directorate Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, United States of America
| | - Aniruddha Ganguly
- Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - P. Mickey Williams
- Molecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Michael C. Sachs
- Biostatistics Branch, Biometric Research Program, NCI, NIH, Bethesda, Maryland, United States of America
| | - Magdalena Thurin
- Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - James V. Tricoli
- Diagnostic Biomarkers and Technology Branch, Cancer Diagnosis Program Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, Maryland, United States of America
| | - Winnie Ricker
- Information Management Services, Inc., Rockville, Maryland, United States of America
| | - Jeffrey C. Gildersleeve
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, United States of America
- * E-mail:
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207
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Abstract
Numerous cellular proteins interact with membrane surfaces to affect essential cellular processes. These interactions can be directed towards a specific lipid component within a membrane, as in the case of phosphoinositides (PIPs), to ensure specific subcellular localization and/or activation. PIPs and cellular PIP-binding domains have been studied extensively to better understand their role in cellular physiology. We applied a pH modulation assay on supported lipid bilayers (SLBs) as a tool to study protein-PIP interactions. In these studies, pH sensitive ortho-Sulforhodamine B conjugated phosphatidylethanolamine is used to detect protein-PIP interactions. Upon binding of a protein to a PIP-containing membrane surface, the interfacial potential is modulated (i.e. change in local pH), shifting the protonation state of the probe. A case study of the successful usage of the pH modulation assay is presented by using phospholipase C delta1 Pleckstrin Homology (PLC-δ1 PH) domain and phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) interaction as an example. The apparent dissociation constant (Kd,app) for this interaction was 0.39 ± 0.05 µM, similar to Kd,app values obtained by others. As previously observed, the PLC-δ1 PH domain is PI(4,5)P2 specific, shows weaker binding towards phosphatidylinositol 4-phosphate, and no binding to pure phosphatidylcholine SLBs. The PIP-on-a-chip assay is advantageous over traditional PIP-binding assays, including but not limited to low sample volume and no ligand/receptor labeling requirements, the ability to test high- and low-affinity membrane interactions with both small and large molecules, and improved signal to noise ratio. Accordingly, the usage of the PIP-on-a-chip approach will facilitate the elucidation of mechanisms of a wide range of membrane interactions. Furthermore, this method could potentially be used in identifying therapeutics that modulate protein's capacity to interact with membranes.
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Affiliation(s)
- Djoshkun Shengjuler
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University;
| | - Simou Sun
- Department of Chemistry, The Pennsylvania State University
| | - Paul S Cremer
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University; Department of Chemistry, The Pennsylvania State University;
| | - Craig E Cameron
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University;
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Fonseca AM, Quinto L, Jiménez A, González R, Bardají A, Maculuve S, Dobaño C, Rupérez M, Vala A, Aponte JJ, Sevene E, Macete E, Menéndez C, Mayor A. Multiplexing detection of IgG against Plasmodium falciparum pregnancy-specific antigens. PLoS One 2017; 12:e0181150. [PMID: 28715465 PMCID: PMC5513451 DOI: 10.1371/journal.pone.0181150] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 06/27/2017] [Indexed: 11/18/2022] Open
Abstract
Background Pregnant women exposed to Plasmodium falciparum generate antibodies against VAR2CSA, the parasite protein that mediates adhesion of infected erythrocytes to the placenta. There is a need of high-throughput tools to determine the fine specificity of these antibodies that can be used to identify immune correlates of protection and exposure. Here we aimed at developing a multiplex-immunoassay to detect antibodies against VAR2CSA antigens. Methods and findings We constructed two multiplex-bead arrays, one composed of 3 VAR2CSA recombinant-domains (DBL3X, DBL5Ɛ and DBL6Ɛ) and another composed of 46 new peptides covering VAR2CSA conserved and semi-conserved regions. IgG reactivity was similar in multiplexed and singleplexed determinations (Pearson correlation, protein array: R2 = 0.99 and peptide array: R2 = 0.87). IgG recognition of 25 out of 46 peptides and all recombinant-domains was higher in pregnant Mozambican women (n = 106) than in Mozambican men (n = 102) and Spanish individuals (n = 101; p<0.05). Agreement of IgG levels detected in cryopreserved plasma and in elutions from dried blood spots was good after exclusion of inappropriate filter papers. Under heterogeneous levels of exposure to malaria, similar seropositivity cutoffs were obtained using finite mixture models applied to antibodies measured on pregnant Mozambican women and average of antibodies measured on pregnant Spanish women never exposed to malaria. The application of the multiplex-bead array developed here, allowed the assessment of higher IgG levels and seroprevalences against VAR2CSA-derived antigens in women pregnant during 2003–2005 than during 2010–2012, in accordance with the levels of malaria transmission reported for these years in Mozambique. Conclusions The multiplex bead-based immunoassay to detect antibodies against selected 25 VAR2CSA new-peptides and recombinant-domains was successfully implemented. Analysis of field samples showed that responses were specific among pregnant women and dependent on the level of exposure to malaria. This platform provides a high-throughput approach to investigating correlates of protection and identifying serological markers of exposure for malaria in pregnancy.
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Affiliation(s)
- Ana Maria Fonseca
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
- Graduate Program in Areas of Basic and Applied Biology (GABBA), Universidade do Porto, Porto, Portugal
| | - Llorenç Quinto
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Alfons Jiménez
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
- Spanish Consortium for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Raquel González
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
- Centro de Investigação em Saúde da Manhiça (CISM), Maputo, Mozambique
| | - Azucena Bardají
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
- Centro de Investigação em Saúde da Manhiça (CISM), Maputo, Mozambique
| | - Sonia Maculuve
- Centro de Investigação em Saúde da Manhiça (CISM), Maputo, Mozambique
| | - Carlota Dobaño
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
- Centro de Investigação em Saúde da Manhiça (CISM), Maputo, Mozambique
| | - Maria Rupérez
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
- Centro de Investigação em Saúde da Manhiça (CISM), Maputo, Mozambique
| | - Anifa Vala
- Centro de Investigação em Saúde da Manhiça (CISM), Maputo, Mozambique
| | - John J. Aponte
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
- Centro de Investigação em Saúde da Manhiça (CISM), Maputo, Mozambique
| | - Esperanza Sevene
- Centro de Investigação em Saúde da Manhiça (CISM), Maputo, Mozambique
- Eduardo Mondlane University, Maputo, Mozambique
| | - Eusebio Macete
- Centro de Investigação em Saúde da Manhiça (CISM), Maputo, Mozambique
| | - Clara Menéndez
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
- Centro de Investigação em Saúde da Manhiça (CISM), Maputo, Mozambique
| | - Alfredo Mayor
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
- Centro de Investigação em Saúde da Manhiça (CISM), Maputo, Mozambique
- * E-mail:
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209
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Abstract
Cells are covered with a cloak of carbohydrate chains (glycans) that is commonly altered in cancer and that includes variations in sialic acid (Sia) expression. These are acidic sugars that have a 9-carbon backbone and that cap vertebrate glycans on cell surfaces. Two of the major Sia forms in mammals are N-acetylneuraminic acid (Neu5Ac) and its hydroxylated form, N-glycolylneuraminic acid (Neu5Gc). Humans cannot produce endogenous Neu5Gc due to the inactivation of the gene encoding cytidine 5'monophosphate-Neu5Ac (CMP-Neu5Ac) hydroxylase (CMAH). Foreign Neu5Gc is acquired by human cells through the dietary consumption of red meat and dairy and subsequently appears on diverse glycans on the cell surface, accumulating mostly on carcinomas. Consequently, humans have circulating anti-Neu5Gc antibodies that play diverse roles in cancer and other chronic inflammation-mediated diseases and that are becoming potential diagnostic and therapeutic targets. Here, we describe a high-throughput sialoglycan microarray assay to assess such anti-Neu5Gc antibodies in the human sera. Neu5Gc-containing glycans and their matched pairs of controls (Neu5Ac-containing glycans), each with a core primary amine, are covalently linked to epoxy-coated glass slides. We exemplify the printing of 56 slides in a 16-well format using a specific nano-printer capable of generating up to 896 arrays per print. Each slide can be used to screen 16 different human sera samples for the evaluation of anti-Neu5Gc antibody specificity, intensity, and diversity. The protocol describes the complexity of this robust tool and provides a basic guideline for those aiming to investigate the response to Neu5Gc dietary carbohydrate antigen in diverse clinical samples in an array format.
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Affiliation(s)
| | - Hai Yu
- Department of Chemistry, University of California-Davis
| | - Xi Chen
- Department of Chemistry, University of California-Davis
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210
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Moschen S, Di Rienzo JA, Higgins J, Tohge T, Watanabe M, González S, Rivarola M, García-García F, Dopazo J, Hopp HE, Hoefgen R, Fernie AR, Paniego N, Fernández P, Heinz RA. Integration of transcriptomic and metabolic data reveals hub transcription factors involved in drought stress response in sunflower (Helianthus annuus L.). Plant Mol Biol 2017; 94:549-564. [PMID: 28639116 DOI: 10.1007/s11103-017-0625-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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: 03/18/2017] [Accepted: 06/12/2017] [Indexed: 05/19/2023]
Abstract
By integration of transcriptional and metabolic profiles we identified pathways and hubs transcription factors regulated during drought conditions in sunflower, useful for applications in molecular and/or biotechnological breeding. Drought is one of the most important environmental stresses that effects crop productivity in many agricultural regions. Sunflower is tolerant to drought conditions but the mechanisms involved in this tolerance remain unclear at the molecular level. The aim of this study was to characterize and integrate transcriptional and metabolic pathways related to drought stress in sunflower plants, by using a system biology approach. Our results showed a delay in plant senescence with an increase in the expression level of photosynthesis related genes as well as higher levels of sugars, osmoprotectant amino acids and ionic nutrients under drought conditions. In addition, we identified transcription factors that were upregulated during drought conditions and that may act as hubs in the transcriptional network. Many of these transcription factors belong to families implicated in the drought response in model species. The integration of transcriptomic and metabolomic data in this study, together with physiological measurements, has improved our understanding of the biological responses during droughts and contributes to elucidate the molecular mechanisms involved under this environmental condition. These findings will provide useful biotechnological tools to improve stress tolerance while maintaining crop yield under restricted water availability.
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Affiliation(s)
- Sebastián Moschen
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Julio A Di Rienzo
- Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Janet Higgins
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Takayuki Tohge
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Mutsumi Watanabe
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Sergio González
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Máximo Rivarola
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Francisco García-García
- Computational Genomics Department, Centro de Investigación Príncipe Felipe. Functional Genomics Node (INB-ELIXIR-es). Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Valencia, 46012, Spain
| | - Joaquin Dopazo
- Computational Genomics Department, Centro de Investigación Príncipe Felipe. Functional Genomics Node (INB-ELIXIR-es). Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Valencia, 46012, Spain
| | - H Esteban Hopp
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Rainer Hoefgen
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - Norma Paniego
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Paula Fernández
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
- Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
| | - Ruth A Heinz
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina.
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.
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211
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Kumar A, Vijayakumar P, Gandhale PN, Ranaware PB, Kumar H, Kulkarni DD, Raut AA, Mishra A. Genome-wide gene expression pattern underlying differential host response to high or low pathogenic H5N1 avian influenza virus in ducks. Acta Virol 2017; 61:66-76. [PMID: 28161961 DOI: 10.4149/av_2017_01_66] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The differences in the influenza viral pathogenesis observed between different pathogenic strains are associated with distinct properties of virus strains and the host immune responses. In order to determine the differences in the duck immune response against two different pathogenic strains, we studied genome-wide host immune gene response of ducks infected with A/duck/India/02CA10/2011 and A/duck/Tripura/103597/2008 H5N1 viruses using custom-designed microarray. A/duck/India/02CA10/2011 is highly pathogenic virus (HP) to ducks, whereas A/duck/Tripura/103597/2008 is a low pathogenic (LP) virus strain. Comparative lung tissue transcriptome analysis of differentially expressed genes revealed that 686 genes were commonly expressed, 880 and 1556 genes are expressed uniquely to infection with HP and LP virus, respectively. The up-regulation of chemokines (CCL4 and CXCR4) and IFN-stimulated genes (IFITM2, STAT3, TGFB1 and TGFB3) was observed in the lung tissues of ducks infected with HP virus. The up-regulation of other immune genes (IL17, OAS, SOCS3, MHC I and MHC II) was observed in both infection conditions. The expression of important antiviral immune genes MX, IFIT5, IFITM5, ISG12, β-defensins, RSAD2, EIF2AK2, TRIM23 and SLC16A3 was observed in LP virus infection, but not in HP virus infection. Several immune-related gene ontology terms and pathways activated by both the viruses were qualitatively similar but quantitatively different. Based on these findings, the differences in the host immune response might explain a part of the difference observed in the viral pathogenesis of high and low pathogenic influenza strains in ducks.
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212
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Abstract
Soluble amyloid-beta (Aβ) oligomers are the prime causative agents of cognitive deficits during early stages of Alzheimer's disease (AD). The transient nature of the oligomers makes them difficult to characterize by traditional techniques, suggesting that advanced approaches are necessary. Previously developed fluorescence-based tethered approach for probing intermolecular interactions (TAPIN) and AFM-based single-molecule force spectroscopy are capable of probing dimers of Aβ peptides. In this paper, a novel polymer nanoarray approach to probe trimers and tetramers formed by the Aβ(14-23) segment of Aβ protein at the single-molecule level is applied. By using this approach combined with TAPIN and AFM force spectroscopy, the impact of pH on the assembly of these oligomers was characterized. Experimental results reveal that pH affects the oligomer assembly process. At neutral pH, trimers and tetramers assemble into structures with a similar stability, while at acidic conditions (pH 3.7), the oligomers adopt a set of structures with different lifetimes and strengths. Models for the assembly of Aβ(14-23) trimers and tetramers based on the results obtained is proposed.
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Affiliation(s)
- Sibaprasad Maity
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA.
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213
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Terry C, Bailey M, Mitry RR, Lehec SC, Dhawan A, Hughes RD. Analysis of the Effects of Cryopreservation on Rat Hepatocytes Using SELDI-TOF Mass Spectrometry. Cell Transplant 2017; 15:35-43. [PMID: 16700328 DOI: 10.3727/000000006783982269] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Successful cryopreservation of hepatocytes is essential to the future of hepatocyte transplantation as a treatment for liver disease, and also for the improved in vitro use of hepatocytes for research. However, hepatocyte function is adversely affected by even the best cryopreservation protocols. To investigate possible mechanisms for these changes, total cell lysates were prepared from fresh and cryopreserved rat hepatocytes and the proteome profiles compared using SELDI-TOF-MS ProteinChip? technology. In addition, in vitro functional assays (viability, attachment efficiency, and lactate dehydrogenase leakage) were performed on the corresponding fresh and cryopreserved hepatocytes. Sixty-one peptides were identified as being significantly changed after cryopreservation. Thirty-seven peaks were significantly increased and 24 were significantly decreased after cryopreservation. The peak intensity of a number of these peptides was found to correlate with the in vitro function of the hepatocytes. Seven peptides correlated with in vitro function after cryopreservation and 10 peptides correlated with both fresh and cryopreserved function. The peptides significantly decreased after cryopreservation could include cytosolic enzymes or cofactors, which leaked out of the cells due to cryopreservation-induced membrane damage. The peptides significantly increased after cryopreservation could be retained products of cleavage of larger intracellular polypeptides and proteins or the result of aggregation of peptides caused by physical changes in the cell due to the cryopreservation process. Proteome profiling using SELDI-TOF-MS could be a useful tool to assess the effects of isolation and cryopreservation of hepatocytes, particularly if the findings are extended to human hepatocytes.
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Affiliation(s)
- Claire Terry
- Institute of Liver Studies, King's College London School of Medicine, London, UK
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214
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Abstract
The last few years have seen breakthroughs that will transform our ability to measure important analytes. Miniaturization of reaction volumes and confinement of analytes of interest into ultrasmall containers have greatly enhanced the sensitivity and throughput of many detection methods. Fabrication of microwell arrays and implementation of bead-based assays have been instrumental in the development of methods for measuring relevant biomolecules, with applications to both diagnostics and fundamental biological studies. In this review, we describe how microwell arrays are fabricated and utilized for measuring analytes of interest. We then discuss the fundamental concepts of digital enzyme-linked immunosorbent assay (ELISA) using single-molecule arrays and applications of microwell arrays to ultrasensitive protein measurements. We also explore the utility of microwell arrays for nucleic acid detection and applications for single-cell studies.
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Affiliation(s)
- Limor Cohen
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155;
| | - David R Walt
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155;
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215
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Yıldırım K, Kaya Z. Gene regulation network behind drought escape, avoidance and tolerance strategies in black poplar (Populus nigra L.). Plant Physiol Biochem 2017; 115:183-199. [PMID: 28376411 DOI: 10.1016/j.plaphy.2017.03.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [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: 01/15/2017] [Revised: 03/27/2017] [Accepted: 03/27/2017] [Indexed: 05/01/2023]
Abstract
Drought is the major environmental problem limiting the productivity and survival of plant species. Here, previously identified three black poplar genotypes having contrasting response to drought were subjected to gradual soil water depletion in a pot trial to identify their physiological, morphological and antioxidation related adaptations. We also performed a microarray based transcriptome analyses on the leaves of genotypes by using Affymetrix poplar Genome Array containing 56,000 transcripts. Phenotypic analyses of each genotype confirmed their differential adaptations to drought that could be classified as drought escape, avoidance and tolerance. Comparative transcriptomic analysis indicated highly divergent gene expression patterns among the genotypes in response to drought and post drought re-watering (PDR). We identified 10641, 3824 and 9411 transcripts exclusively regulated in drought escape, avoidance and tolerant genotypes, respectively. The key genes involved in metabolic pathways, such as carbohydrate metabolism, photosynthesis, lipid metabolism, generation of precursor metabolites/energy, protein folding, redox homeostasis, secondary metabolic process and cell wall component biogenesis, were affected by drought stresses in the leaves of these genotypes. Transcript isoforms showed increased expression specificity in the genes coding for bark storage proteins and small heat shock proteins in drought tolerant genotype. On the other hand, drought-avoiding genotype specifically induced the transcripts annotated to the genes functional in secondary metabolite production that linked to enhanced leaf water content and growth performance under drought stress. Transcriptome profiling of drought escape genotype indicated specific regulation of the genes functional in programmed cell death and leaf senescence. Specific upregulation of GTP cyclohydrolase II and transcription factors (WRKY and ERFs) in only this genotype were associated to ROS dependent signalling pathways and gene regulation network responsible in induction of many degrading enzymes acting on cell wall carbohydrates, fatty acids and proteins under drought stress. Our findings provide new insights into the transcriptome dynamics and components of regulatory network associated with drought adaptation strategies.
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Affiliation(s)
- Kubilay Yıldırım
- Department of Bioengineering, Gaziosmanpasa University, 60100 Tokat, Turkey; Department of Biological Sciences, Middle East Technical University, 06531 Ankara, Turkey
| | - Zeki Kaya
- Department of Biological Sciences, Middle East Technical University, 06531 Ankara, Turkey.
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216
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Park YM, Kim MA, Jung HT, Kang HJ, Yoo HS, Kang IC. Nutriproteomic Analysis of Hwangmaemok-Induced Antiangiogenic Effect Using Antibody-Arrayed Protein Chip Assay. J Med Food 2017; 20:586-591. [PMID: 28581882 DOI: 10.1089/jmf.2016.3775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 11/13/2022] Open
Abstract
We investigated the antiangiogenic effects of Lindera obtusiloba Blume (Hwangmaemok, HMM), which is a plant in the Lauraceae family that is commonly used to treat colds and gastritis. Moreover, given that a recent study reported the inhibitory effects of HMM extract on cancer metastasis, we hypothesized that HMM extract might possess and antiangiogenic function. Thus, this study was conducted to investigate the effects of HMM extract on endothelial cell proliferation, migration, and neovascularization in chick chorioallantoic membrane (CAM), and investigated the molecular mechanism of antiangiogenesis using a ProteoChip-based proteomics technology. To examine the effects of HMM extracts on endothelial cell proliferation and migration, we conducted basic fibroblast growth factor (bFGF)-induced human umbilical vein endothelial cell (HUVEC) proliferation and migration. To assess the molecular mechanism of the antiangiogenic effects of HMM extract, a ProteoChip-based forwarded phase antibody array was employed to identify the differential expression of cell cycle proteins in HMM-treated HUVECs. HMM extract inhibited bFGF-induced HUVEC proliferation and migration in a dose-dependent manner and CAM angiogenesis. The ProteoChip-based antibody microarray data showed upregulation of Nibrin/NBS1 and downregulation of Plk-1 and Cyclin E, which are involved in cell division and controlling the cell cycle in bFGF-induced HUVECs. These data suggest that HMM may be a potent antitumor medicinal herb. The present study demonstrates that the antiangiogenic effect of HMM may be due to suppression of endothelial cell proliferation and migration. Taken together, these results emphasize the potential to use HMM extract as a potent angiogenesis inhibitor to treat cancer.
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Affiliation(s)
- Yu Mi Park
- 1 Department of Biological Science, College of Life and Health Sciences, Hoseo University , Asan, Korea
| | - Min-A Kim
- 1 Department of Biological Science, College of Life and Health Sciences, Hoseo University , Asan, Korea
| | - Hee Tae Jung
- 2 East-West Cancer Center, Dunsan Korean Medical Hospital of Daejeon University , Daejeon, Korea
| | - Hwa Jeong Kang
- 1 Department of Biological Science, College of Life and Health Sciences, Hoseo University , Asan, Korea
| | - Hwa-Seung Yoo
- 2 East-West Cancer Center, Dunsan Korean Medical Hospital of Daejeon University , Daejeon, Korea
| | - In-Cheol Kang
- 1 Department of Biological Science, College of Life and Health Sciences, Hoseo University , Asan, Korea
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217
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Kanaya N, Somlo G, Wu J, Frankel P, Kai M, Liu X, Wu SV, Nguyen D, Chan N, Hsieh MY, Kirschenbaum M, Kruper L, Vito C, Badie B, Yim JH, Yuan Y, Hurria A, Peiguo C, Mortimer J, Chen S. Characterization of patient-derived tumor xenografts (PDXs) as models for estrogen receptor positive (ER+HER2- and ER+HER2+) breast cancers. J Steroid Biochem Mol Biol 2017; 170:65-74. [PMID: 27154416 PMCID: PMC5094906 DOI: 10.1016/j.jsbmb.2016.05.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 04/26/2016] [Accepted: 05/02/2016] [Indexed: 12/18/2022]
Abstract
The research was to appraise the utility of the patient-derived tumor xenografts (PDXs) as models of estrogen receptor positive (ER+HER2- and ER+HER2+) breast cancers. We compared protein expression profiles by Reverse Phase Protein Array (RPPA) in tumors that resulted in PDXs compared to those that did not. Our overall PDX intake rate for ER+ breast cancer was 9% (9/97). The intake rate for ER+HER2+ tumors (3/16, 19%) was higher than for ER+HER2- tumors (6/81, 7%). Heat map analyses of RPPA data showed that ER+HER2- tumors were divided into 2 groups by luminal A/B signature [protein expression of ER, AR, Bcl-2, Bim (BCL2L11), GATA3 and INPP4b], and this expression signature was also associated with the rate of PDX intake. Cell survival pathways such as the PI3K/AKT signaling and RAS/ERK pathways were more activated in the specimens that could be established as PDX in both classes. Expression of the ER protein itself may have a bearing on the potential success of an ER+ PDX model. In addition, HER2 and its downstream protein expressions were up-regulated in the ER+HER2+ patient tumors that were successfully established as PDX models. Moreover, the comparison of RPPA data between original and PDX tumors suggested that the selection/adaptation process required to grow the tumors in mice is unavoidable for generation of ER+ PDX models, and we identified differences between patient tumor samples and paired PDX tumors. A better understanding of the biological characteristics of ER+PDX would be the key to using PDX models in assessing treatment strategies in a preclinical setting.
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Affiliation(s)
- Noriko Kanaya
- Department of Cancer Biology, City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA
| | - George Somlo
- Department of Medical Oncology, City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA
| | - Jun Wu
- Department of Comparative Medicine, City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA
| | - Paul Frankel
- Department of Information Sciences, City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA
| | - Masaya Kai
- Department of Cancer Biology, City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA
| | - Xueli Liu
- Department of Information Sciences, City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA
| | - Shang Victoria Wu
- Department of Cancer Biology, City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA
| | - Duc Nguyen
- Department of Cancer Biology, City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA
| | - Nymph Chan
- Department of Cancer Biology, City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA
| | - Meng-Yin Hsieh
- Department of Comparative Medicine, City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA
| | - Michele Kirschenbaum
- Clinical Trials Office, City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA
| | - Laura Kruper
- Department of Surgery, City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA
| | - Courtney Vito
- Department of Surgery, City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA
| | - Behnam Badie
- Department of Surgery, City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA
| | - John H Yim
- Department of Surgery, City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA
| | - Yuan Yuan
- Department of Medical Oncology, City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA
| | - Arti Hurria
- Department of Medical Oncology, City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA
| | - Chu Peiguo
- Department of Pathology, City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA
| | - Joanne Mortimer
- Department of Medical Oncology, City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA
| | - Shiuan Chen
- Department of Cancer Biology, City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA.
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218
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Yim JH, Yun JM, Kim JY, Lee IK, Nam SY, Kim CS. Phosphoprotein profiles of candidate markers for early cellular responses to low-dose γ-radiation in normal human fibroblast cells. J Radiat Res 2017; 58:329-340. [PMID: 28122968 PMCID: PMC5440887 DOI: 10.1093/jrr/rrw126] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 08/24/2016] [Accepted: 12/09/2016] [Indexed: 05/24/2023]
Abstract
Ionizing radiation causes biological damage that leads to severe health effects. However, the effects and subsequent health implications caused by exposure to low-dose radiation are unclear. The objective of this study was to determine phosphoprotein profiles in normal human fibroblast cell lines in response to low-dose and high-dose γ-radiation. We examined the cellular response in MRC-5 cells 0.5 h after exposure to 0.05 or 2 Gy. Using 1318 antibodies by antibody array, we observed ≥1.3-fold increases in a number of identified phosphoproteins in cells subjected to low-dose (0.05 Gy) and high-dose (2 Gy) radiation, suggesting that both radiation levels stimulate distinct signaling pathways. Low-dose radiation induced nucleic acid-binding transcription factor activity, developmental processes, and multicellular organismal processes. By contrast, high-dose radiation stimulated apoptotic processes, cell adhesion and regulation, and cellular organization and biogenesis. We found that phospho-BTK (Tyr550) and phospho-Gab2 (Tyr643) protein levels at 0.5 h after treatment were higher in cells subjected to low-dose radiation than in cells treated with high-dose radiation. We also determined that the phosphorylation of BTK and Gab2 in response to ionizing radiation was regulated in a dose-dependent manner in MRC-5 and NHDF cells. Our study provides new insights into the biological responses to low-dose γ-radiation and identifies potential candidate markers for monitoring exposure to low-dose ionizing radiation.
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Affiliation(s)
- Ji-Hye Yim
- Radiation Health Institute, Korea Hydro & Nuclear Power Co. Ltd, Seongnam-si, Gyeonggi-do, 13605, Korea
| | - Jung Mi Yun
- Radiation Health Institute, Korea Hydro & Nuclear Power Co. Ltd, Seongnam-si, Gyeonggi-do, 13605, Korea
| | - Ji Young Kim
- Radiation Health Institute, Korea Hydro & Nuclear Power Co. Ltd, Seongnam-si, Gyeonggi-do, 13605, Korea
| | - In Kyung Lee
- Radiation Health Institute, Korea Hydro & Nuclear Power Co. Ltd, Seongnam-si, Gyeonggi-do, 13605, Korea
| | - Seon Young Nam
- Radiation Health Institute, Korea Hydro & Nuclear Power Co. Ltd, Seongnam-si, Gyeonggi-do, 13605, Korea
| | - Cha Soon Kim
- Radiation Health Institute, Korea Hydro & Nuclear Power Co. Ltd, Seongnam-si, Gyeonggi-do, 13605, Korea
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219
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Mendonca P, Taka E, Bauer D, Cobourne-Duval M, Soliman KFA. The attenuating effects of 1,2,3,4,6 penta-O-galloyl-β-d-glucose on inflammatory cytokines release from activated BV-2 microglial cells. J Neuroimmunol 2017; 305:9-15. [PMID: 28284353 PMCID: PMC5351774 DOI: 10.1016/j.jneuroim.2017.01.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [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: 07/05/2016] [Revised: 11/01/2016] [Accepted: 01/17/2017] [Indexed: 12/29/2022]
Abstract
Alzheimer's disease (AD) is the most common cause of neurodegeneration and dementia in the elderly. Dysregulated, chronic activation of microglia, the brain's resident macrophages, induces the release of excessive amounts of pro-inflammatory cytokines which has been implicated in the early stages of AD pathology. Therefore, suppressing the expression of these inflammatory mediators may decrease or delay the progression of AD. Many natural compounds derived from plants have shown anti-inflammatory activity. The naturally occurring 1,2,3,4,6 Penta-O-Galloyl-β-d-Glucose (PGG), is a polyphenolic compound highly enriched in Rhus chinensis Millplant. It is a potent anti-inflammatory agent that act through the inhibition of many cytokines in different experimental models. In the present study, we investigated the role of PGG as an anti-inflammatory agent in LPS/IFNγ activated BV-2 microglia cells. Mouse cytokine antibody arrays were used to assess the effect of PGG on the release of pro-inflammatory cytokines, and ELISA experiments were performed to validate the results from the arrays. The results obtained from the cytokine arrays, and ELISA assays showed that PGG decreased the expression of monocyte chemotactic protein-5 (MCP-5) 8-fold, and pro-matrix metalloproteinase 9 (Pro MMP-9) 10-fold. Both of these cytokines are upregulated during the inflammatory process and have been shown to be involved in brain injury, inflammation, and neurodegeneration. Therefore, these findings suggest that the anti-inflammatory effect of PGG on activated microglia involving the attenuation of MCP-5 and Pro MMP-9 cytokines.
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Affiliation(s)
- Patricia Mendonca
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL 32307, United States
| | - Equar Taka
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL 32307, United States
| | - David Bauer
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL 32307, United States
| | - Makini Cobourne-Duval
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL 32307, United States
| | - Karam F A Soliman
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL 32307, United States.
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Keasey SL, Pugh CL, Jensen SMR, Smith JL, Hontz RD, Durbin AP, Dudley DM, O'Connor DH, Ulrich RG. Antibody Responses to Zika Virus Infections in Environments of Flavivirus Endemicity. Clin Vaccine Immunol 2017; 24:e00036-17. [PMID: 28228395 PMCID: PMC5382833 DOI: 10.1128/cvi.00036-17] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 02/18/2017] [Indexed: 12/20/2022]
Abstract
Zika virus (ZIKV) infections occur in areas where dengue virus (DENV), West Nile virus (WNV), yellow fever virus (YFV), and other viruses of the genus Flavivirus cocirculate. The envelope (E) proteins of these closely related flaviviruses induce specific long-term immunity, yet subsequent infections are associated with cross-reactive antibody responses that may enhance disease susceptibility and severity. To gain a better understanding of ZIKV infections against a background of similar viral diseases, we examined serological immune responses to ZIKV, WNV, DENV, and YFV infections of humans and nonhuman primates (NHPs). Using printed microarrays, we detected very specific antibody responses to primary infections with probes of recombinant E proteins from 15 species and lineages of flaviviruses pathogenic to humans, while high cross-reactivity between ZIKV and DENV was observed with 11 printed native viruses. Notably, antibodies from human primary ZIKV or secondary DENV infections that occurred in areas where flavivirus is endemic broadly recognized E proteins from many flaviviruses, especially DENV, indicating a strong influence of infection history on immune responses. A predictive algorithm was used to tentatively identify previous encounters with specific flaviviruses based on serum antibody interactions with the multispecies panel of E proteins. These results illustrate the potential impact of exposure to related viruses on the outcome of ZIKV infection and offer considerations for development of vaccines and diagnostics.
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Affiliation(s)
- Sarah L Keasey
- Department of Biology, University of Maryland-Baltimore County, Baltimore, Maryland, USA
- Molecular and Translational Sciences Division, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
| | - Christine L Pugh
- Molecular and Translational Sciences Division, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
| | - Stig M R Jensen
- Molecular and Translational Sciences Division, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
| | - Jessica L Smith
- Molecular and Translational Sciences Division, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
| | - Robert D Hontz
- Naval Medical Research Center, Silver Spring, Maryland, USA, and U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru
| | - Anna P Durbin
- Center for Immunization Research, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Dawn M Dudley
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Robert G Ulrich
- Molecular and Translational Sciences Division, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
- Virology Division, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
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221
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Ford B, Bateman LA, Gutierrez-Palominos L, Park R, Nomura DK. Mapping Proteome-wide Targets of Glyphosate in Mice. Cell Chem Biol 2017; 24:133-140. [PMID: 28132892 DOI: 10.1016/j.chembiol.2016.12.013] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [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] [Received: 08/19/2016] [Revised: 11/14/2016] [Accepted: 12/21/2016] [Indexed: 12/30/2022]
Abstract
Glyphosate, the active ingredient in the herbicide Roundup, is one of the most widely used pesticides in agriculture and home garden use. Whether glyphosate causes any mammalian toxicity remains highly controversial. While many studies have associated glyphosate with numerous adverse health effects, the mechanisms underlying glyphosate toxicity in mammals remain poorly understood. Here, we used activity-based protein profiling to map glyphosate targets in mice. We show that glyphosate at high doses can be metabolized in vivo to reactive metabolites such as glyoxylate and react with cysteines across many proteins in mouse liver. We show that glyoxylate inhibits liver fatty acid oxidation enzymes and glyphosate treatment in mice increases the levels of triglycerides and cholesteryl esters, likely resulting from diversion of fatty acids away from oxidation and toward other lipid pathways. Our study highlights the utility of using chemoproteomics to identify novel toxicological mechanisms of environmental chemicals such as glyphosate.
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Affiliation(s)
- Breanna Ford
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, CA 94720, USA
| | - Leslie A Bateman
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, CA 94720, USA
| | - Leilani Gutierrez-Palominos
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, CA 94720, USA
| | - Robin Park
- Integrated Proteomics Applications, Inc., 12707 High Bluff Drive Suite 200, San Diego, CA 92130, USA
| | - Daniel K Nomura
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, CA 94720, USA.
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222
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Israeli-Ruimy V, Bule P, Jindou S, Dassa B, Moraïs S, Borovok I, Barak Y, Slutzki M, Hamberg Y, Cardoso V, Alves VD, Najmudin S, White BA, Flint HJ, Gilbert HJ, Lamed R, Fontes CMGA, Bayer EA. Complexity of the Ruminococcus flavefaciens FD-1 cellulosome reflects an expansion of family-related protein-protein interactions. Sci Rep 2017; 7:42355. [PMID: 28186207 PMCID: PMC5301203 DOI: 10.1038/srep42355] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 01/08/2017] [Indexed: 11/25/2022] Open
Abstract
Protein-protein interactions play a vital role in cellular processes as exemplified by assembly of the intricate multi-enzyme cellulosome complex. Cellulosomes are assembled by selective high-affinity binding of enzyme-borne dockerin modules to repeated cohesin modules of structural proteins termed scaffoldins. Recent sequencing of the fiber-degrading Ruminococcus flavefaciens FD-1 genome revealed a particularly elaborate cellulosome system. In total, 223 dockerin-bearing ORFs potentially involved in cellulosome assembly and a variety of multi-modular scaffoldins were identified, and the dockerins were classified into six major groups. Here, extensive screening employing three complementary medium- to high-throughput platforms was used to characterize the different cohesin-dockerin specificities. The platforms included (i) cellulose-coated microarray assay, (ii) enzyme-linked immunosorbent assay (ELISA) and (iii) in-vivo co-expression and screening in Escherichia coli. The data revealed a collection of unique cohesin-dockerin interactions and support the functional relevance of dockerin classification into groups. In contrast to observations reported previously, a dual-binding mode is involved in cellulosome cell-surface attachment, whereas single-binding interactions operate for cellulosome integration of enzymes. This sui generis cellulosome model enhances our understanding of the mechanisms governing the remarkable ability of R. flavefaciens to degrade carbohydrates in the bovine rumen and provides a basis for constructing efficient nano-machines applied to biological processes.
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Affiliation(s)
- Vered Israeli-Ruimy
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Pedro Bule
- CIISA – Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Sadanari Jindou
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Bareket Dassa
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Sarah Moraïs
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Ilya Borovok
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Yoav Barak
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
- Chemical Research Support, The Weizmann Institute of Science, Rehovot, Israel
| | - Michal Slutzki
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Yuval Hamberg
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Vânia Cardoso
- CIISA – Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Victor D. Alves
- CIISA – Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Shabir Najmudin
- CIISA – Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Bryan A. White
- Department of Animal Sciences, Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Champaign, IL, USA
- Department of Animal Sciences, University of Illinois at Urbana–Champaign, Champaign, IL, USA
| | - Harry J. Flint
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen, Scotland, UK
| | - Harry J. Gilbert
- Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Newcastle upon Tyne NE2 4HH, UK
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Carlos M. G. A. Fontes
- CIISA – Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Edward A. Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
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Santacatterina F, Sánchez-Aragó M, Catalán-García M, Garrabou G, de Arenas CN, Grau JM, Cardellach F, Cuezva JM. Pyruvate kinase M2 and the mitochondrial ATPase Inhibitory Factor 1 provide novel biomarkers of dermatomyositis: a metabolic link to oncogenesis. J Transl Med 2017; 15:29. [PMID: 28183315 PMCID: PMC5301421 DOI: 10.1186/s12967-017-1136-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 02/03/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Metabolic alterations play a role in the development of inflammatory myopathies (IMs). Herein, we have investigated through a multiplex assay whether proteins of energy metabolism could provide biomarkers of IMs. METHODS A cohort of thirty-two muscle biopsies and forty plasma samples comprising polymyositis (PM), dermatomyositis (DM) and sporadic inclusion body myositis (sIBM) and control donors was interrogated with monoclonal antibodies against proteins of energy metabolism using reverse phase protein microarrays (RPPA). RESULTS When compared to controls the expression of the proteins is not significantly affected in the muscle of PM patients. However, the expression of β-actin is significantly increased in DM and sIBM in consistence with muscle and fiber regeneration. Concurrently, the expression of some proteins involved in glucose metabolism displayed a significant reduction in muscle of sIBM suggesting a repression of glycolytic metabolism in these patients. In contrasts to these findings, the expression of the glycolytic pyruvate kinase isoform M2 (PKM2) and of the mitochondrial ATPase Inhibitor Factor 1 (IF1) and Hsp60 were significantly augmented in DM when compared to other IMs in accordance with a metabolic shift prone to cancer development. PKM2 alone or in combination with other biomarkers allowed the discrimination of control and IMs with very high (>95%) sensitivity and specificity. Unfortunately, plasma levels of PKM2 were not significantly altered in DM patients to recommend its use as a non-invasive biomarker of the disease. CONCLUSIONS Expression of proteins of energy metabolism in muscle enabled discrimination of patients with IMs. RPPA identified the glycolysis promoting PKM2 and IF1 proteins as specific biomarkers of dermatomyositis, providing a biochemical link of this IM with oncogenesis.
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Affiliation(s)
- Fulvio Santacatterina
- Departamento de Biología Molecular, Centro de Biología Molecular Severo, Ochoa, CSIC-UAM, Universidad Autónoma de Madrid, c/Nicolás Cabrera 1, 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Instituto de Investigación Hospital 12 de Octubre, ISCIII, Madrid, Spain
| | - María Sánchez-Aragó
- Departamento de Biología Molecular, Centro de Biología Molecular Severo, Ochoa, CSIC-UAM, Universidad Autónoma de Madrid, c/Nicolás Cabrera 1, 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Instituto de Investigación Hospital 12 de Octubre, ISCIII, Madrid, Spain
| | - Marc Catalán-García
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Muscle Research and Mitochondrial Function Laboratory, CELLEX-IDIBAPS, Faculty of Medicine-University of Barcelona, Internal Medicine Department-Hospital Clinic of Barcelona, Barcelona, Spain
| | - Glòria Garrabou
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Muscle Research and Mitochondrial Function Laboratory, CELLEX-IDIBAPS, Faculty of Medicine-University of Barcelona, Internal Medicine Department-Hospital Clinic of Barcelona, Barcelona, Spain
| | - Cristina Nuñez de Arenas
- Departamento de Biología Molecular, Centro de Biología Molecular Severo, Ochoa, CSIC-UAM, Universidad Autónoma de Madrid, c/Nicolás Cabrera 1, 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Instituto de Investigación Hospital 12 de Octubre, ISCIII, Madrid, Spain
| | - Josep M. Grau
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Muscle Research and Mitochondrial Function Laboratory, CELLEX-IDIBAPS, Faculty of Medicine-University of Barcelona, Internal Medicine Department-Hospital Clinic of Barcelona, Barcelona, Spain
| | - Francesc Cardellach
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Muscle Research and Mitochondrial Function Laboratory, CELLEX-IDIBAPS, Faculty of Medicine-University of Barcelona, Internal Medicine Department-Hospital Clinic of Barcelona, Barcelona, Spain
| | - José M. Cuezva
- Departamento de Biología Molecular, Centro de Biología Molecular Severo, Ochoa, CSIC-UAM, Universidad Autónoma de Madrid, c/Nicolás Cabrera 1, 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Instituto de Investigación Hospital 12 de Octubre, ISCIII, Madrid, Spain
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Korashy HM, Attafi IM, Famulski KS, Bakheet SA, Hafez MM, Alsaad AMS, Al-Ghadeer ARM. Gene expression profiling to identify the toxicities and potentially relevant human disease outcomes associated with environmental heavy metal exposure. Environ Pollut 2017; 221:64-74. [PMID: 27916491 DOI: 10.1016/j.envpol.2016.10.058] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [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: 04/21/2016] [Revised: 10/09/2016] [Accepted: 10/19/2016] [Indexed: 06/06/2023]
Abstract
Heavy metals are the most commonly encountered toxic substances that increase susceptibility to various diseases after prolonged exposure. We have previously shown that healthy volunteers living near a mining area had significant contamination with heavy metals associated with significant changes in the expression of some detoxifying genes, xenobiotic metabolizing enzymes, and DNA repair genes. However, alterations of most of the molecular target genes associated with diseases are still unknown. Thus, the aims of this study were to (a) evaluate the gene expression profile and (b) identify the toxicities and potentially relevant human disease outcomes associated with long-term human exposure to environmental heavy metals in mining area using microarray analysis. For this purpose, 40 healthy male volunteers who were residents of a heavy metal-polluted area (Mahd Al-Dhahab city, Saudi Arabia) and 20 healthy male volunteers who were residents of a non-heavy metal-polluted area were included in the study. Total RNA was isolated from whole blood using PAXgene Blood RNA tubes and then reversed transcribed and hybridized to the gene array using the Affymetrix U219 GeneChip. Microarray analysis showed about 2129 genes were identified and differentially altered, among which a shared set of 425 genes was differentially expressed in the heavy metal-exposed groups. Ingenuity pathway analysis revealed that the most altered gene-regulated diseases in heavy metal-exposed groups included hematological and developmental disorders and mostly renal and urological diseases. Quantitative real-time polymerase chain reaction closely matched the microarray data for some genes tested. Importantly, changes in gene-related diseases were attributed to alterations in the genes encoded for protein synthesis. Renal and urological diseases were the diseases that were most frequently associated with the heavy metal-exposed group. Therefore, there is a need for further studies to validate these genes, which could be used as early biomarkers to prevent renal injury.
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Affiliation(s)
- Hesham M Korashy
- Department of Pharmacology & Toxicology, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia.
| | - Ibraheem M Attafi
- Department of Pharmacology & Toxicology, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Konrad S Famulski
- Alberta Transplant Applied Genomics Centre, University of Alberta, Edmonton, AB T6G 2S2, Canada
| | - Saleh A Bakheet
- Department of Pharmacology & Toxicology, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Mohammed M Hafez
- Department of Pharmacology & Toxicology, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Abdulaziz M S Alsaad
- Department of Pharmacology & Toxicology, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Abdul Rahman M Al-Ghadeer
- Central Laboratory, Research Center, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
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Lessa-Aquino C, Lindow JC, Randall A, Wunder E, Pablo J, Nakajima R, Jasinskas A, Cruz JS, Damião AO, Nery N, Ribeiro GS, Costa F, Hagan JE, Reis MG, Ko AI, Medeiros MA, Felgner PL. Distinct antibody responses of patients with mild and severe leptospirosis determined by whole proteome microarray analysis. PLoS Negl Trop Dis 2017; 11:e0005349. [PMID: 28141801 PMCID: PMC5302828 DOI: 10.1371/journal.pntd.0005349] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 02/10/2017] [Accepted: 01/22/2017] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Leptospirosis is an important zoonotic disease worldwide. Humans usually present a mild non-specific febrile illness, but a proportion of them develop more severe outcomes, such as multi-organ failure, lung hemorrhage and death. Such complications are thought to depend on several factors, including the host immunity. Protective immunity is associated with humoral immune response, but little is known about the immune response mounted during naturally-acquired Leptospira infection. METHODS AND PRINCIPAL FINDINGS Here, we used protein microarray chip to profile the antibody responses of patients with severe and mild leptospirosis against the complete Leptospira interrogans serovar Copenhageni predicted ORFeome. We discovered a limited number of immunodominant antigens, with 36 antigens specific to patients, of which 11 were potential serodiagnostic antigens, identified at acute phase, and 33 were potential subunit vaccine targets, detected after recovery. Moreover, we found distinct antibody profiles in patients with different clinical outcomes: in the severe group, overall IgM responses do not change and IgG responses increase over time, while both IgM and IgG responses remain stable in the mild patient group. Analyses of individual patients' responses showed that >74% of patients in the severe group had significant IgG increases over time compared to 29% of patients in the mild group. Additionally, 90% of IgM responses did not change over time in the mild group, compared to ~51% in the severe group. CONCLUSIONS In the present study, we detected antibody profiles associated with disease severity and speculate that patients with mild disease were protected from severe outcomes due to pre-existing antibodies, while patients with severe leptospirosis demonstrated an antibody profile typical of first exposure. Our findings represent a significant advance in the understanding of the humoral immune response to Leptospira infection, and we have identified new targets for the development of subunit vaccines and diagnostic tests.
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Affiliation(s)
| | - Janet C. Lindow
- Fiocruz, Gonçalo Moniz Research Institute, Brazilian Ministry of Health, Salvador, BA, Brazil
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, United States of America
| | - Arlo Randall
- Antigen Discovery Inc, Irvine, CA, United States of America
| | - Elsio Wunder
- Fiocruz, Gonçalo Moniz Research Institute, Brazilian Ministry of Health, Salvador, BA, Brazil
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, United States of America
| | - Jozelyn Pablo
- Department of Medicine, Division of Infectious Disease, University of California Irvine, Irvine, California, United States of America
| | - Rie Nakajima
- Department of Medicine, Division of Infectious Disease, University of California Irvine, Irvine, California, United States of America
| | - Algis Jasinskas
- Department of Medicine, Division of Infectious Disease, University of California Irvine, Irvine, California, United States of America
| | - Jaqueline S. Cruz
- Fiocruz, Gonçalo Moniz Research Institute, Brazilian Ministry of Health, Salvador, BA, Brazil
| | - Alcineia O. Damião
- Fiocruz, Gonçalo Moniz Research Institute, Brazilian Ministry of Health, Salvador, BA, Brazil
| | - Nívison Nery
- Fiocruz, Gonçalo Moniz Research Institute, Brazilian Ministry of Health, Salvador, BA, Brazil
| | - Guilherme S. Ribeiro
- Institute of Collective Health, Federal University of Bahia, Salvador, BA, Brazil
| | - Federico Costa
- Fiocruz, Gonçalo Moniz Research Institute, Brazilian Ministry of Health, Salvador, BA, Brazil
- Institute of Collective Health, Federal University of Bahia, Salvador, BA, Brazil
| | - José E. Hagan
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, United States of America
| | - Mitermayer Galvão Reis
- Fiocruz, Gonçalo Moniz Research Institute, Brazilian Ministry of Health, Salvador, BA, Brazil
| | - Albert I. Ko
- Fiocruz, Gonçalo Moniz Research Institute, Brazilian Ministry of Health, Salvador, BA, Brazil
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, United States of America
| | | | - Philip L. Felgner
- Department of Medicine, Division of Infectious Disease, University of California Irvine, Irvine, California, United States of America
- * E-mail:
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Sauer U. Analytical Protein Microarrays: Advancements Towards Clinical Applications. Sensors (Basel) 2017; 17:E256. [PMID: 28146048 PMCID: PMC5335935 DOI: 10.3390/s17020256] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/13/2017] [Accepted: 01/23/2017] [Indexed: 01/28/2023]
Abstract
Protein microarrays represent a powerful technology with the potential to serve as tools for the detection of a broad range of analytes in numerous applications such as diagnostics, drug development, food safety, and environmental monitoring. Key features of analytical protein microarrays include high throughput and relatively low costs due to minimal reagent consumption, multiplexing, fast kinetics and hence measurements, and the possibility of functional integration. So far, especially fundamental studies in molecular and cell biology have been conducted using protein microarrays, while the potential for clinical, notably point-of-care applications is not yet fully utilized. The question arises what features have to be implemented and what improvements have to be made in order to fully exploit the technology. In the past we have identified various obstacles that have to be overcome in order to promote protein microarray technology in the diagnostic field. Issues that need significant improvement to make the technology more attractive for the diagnostic market are for instance: too low sensitivity and deficiency in reproducibility, inadequate analysis time, lack of high-quality antibodies and validated reagents, lack of automation and portable instruments, and cost of instruments necessary for chip production and read-out. The scope of the paper at hand is to review approaches to solve these problems.
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Affiliation(s)
- Ursula Sauer
- AIT Austrian Institute of Technology GmbH, Center for Health and Bioresources, 3430 Tulln, Austria.
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227
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Lagatie O, Van Dorst B, Stuyver LJ. Identification of three immunodominant motifs with atypical isotype profile scattered over the Onchocerca volvulus proteome. PLoS Negl Trop Dis 2017; 11:e0005330. [PMID: 28125577 PMCID: PMC5295699 DOI: 10.1371/journal.pntd.0005330] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 02/07/2017] [Accepted: 01/14/2017] [Indexed: 01/30/2023] Open
Abstract
Understanding the immune response upon infection with the filarial nematode Onchocerca volvulus and the mechanisms that evolved in this parasite to evade immune mediated elimination is essential to expand the toolbox available for diagnostics, therapeutics and vaccines development. Using high-density peptide microarrays we scanned the proteome-wide linear epitope repertoire in Cameroonian onchocerciasis patients and healthy controls from Southern Africa which led to the identification of 249 immunodominant antigenic peptides. Motif analysis learned that 3 immunodominant motifs, encompassing 3 linear epitopes, are present in 70, 43, and 31 of these peptides, respectively and appear to be scattered over the entire proteome in seemingly non-related proteins. These linear epitopes are shown to have an atypical isotype profile dominated by IgG1, IgG3, IgE and IgM, in contrast to the commonly observed IgG4 response in chronic active helminth infections. The identification of these linear epitope motifs may lead to novel diagnostic development but further evaluation of cross-reactivity against common co-infecting human nematode infections will be needed. Infection with the filarial parasite Onchocerca volvulus is the cause of river blindness. We analyzed the immune response against this parasite in infected individuals in order to identify linear epitopes. Using high-density peptide microarrays we discovered three immunodominant motifs in the Onchocerca volvulus proteome that induce a broad IgG response, but the typical IgG4 immune response against parasites was absent. Our study led to the identification of novel potential epitope sequences that can potentially be used for detection of infection with Onchocerca volvulus.
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Affiliation(s)
- Ole Lagatie
- Janssen Diagnostics, Janssen Pharmaceutica NV, Beerse, Belgium
- * E-mail:
| | - Bieke Van Dorst
- Janssen Diagnostics, Janssen Pharmaceutica NV, Beerse, Belgium
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Kayum MA, Park JI, Nath UK, Biswas MK, Kim HT, Nou IS. Genome-wide expression profiling of aquaporin genes confer responses to abiotic and biotic stresses in Brassica rapa. BMC Plant Biol 2017; 17:23. [PMID: 28122509 PMCID: PMC5264328 DOI: 10.1186/s12870-017-0979-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 01/17/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND Plants contain a range of aquaporin (AQP) proteins, which act as transporter of water and nutrient molecules through living membranes. AQPs also participate in water uptake through the roots and contribute to water homeostasis in leaves. RESULTS In this study, we identified 59 AQP genes in the B. rapa database and Br135K microarray dataset. Phylogenetic analysis revealed four distinct subfamilies of AQP genes: plasma membrane intrinsic proteins (PIPs), tonoplast intrinsic proteins (TIPs), NOD26-like intrinsic proteins (NIPs) and small basic intrinsic proteins (SIPs). Microarray analysis showed that the majority of PIP subfamily genes had differential transcript abundance between two B. rapa inbred lines Chiifu and Kenshin that differ in their susceptibility to cold. In addition, all BrPIP genes showed organ-specific expression. Out of 22 genes, 12, 7 and 17 were up-regulated in response to cold, drought and salt stresses, respectively. In addition, 18 BrPIP genes were up-regulated under ABA treatment and 4 BrPIP genes were up-regulated upon F. oxysporum f. sp. conglutinans infection. Moreover, all BrPIP genes showed down-regulation under waterlogging stress, reflecting likely the inactivation of AQPs controlling symplastic water movement. CONCLUSIONS This study provides a comprehensive analysis of AQPs in B. rapa and details the expression of 22 members of the BrPIP subfamily. These results provide insight into stress-related biological functions of each PIP gene of the AQP family, which will promote B. rapa breeding programs.
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Affiliation(s)
- Md. Abdul Kayum
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922 South Korea
| | - Jong-In Park
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922 South Korea
| | - Ujjal Kumar Nath
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922 South Korea
| | - Manosh Kumar Biswas
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922 South Korea
| | - Hoy-Taek Kim
- University-Industry Cooperation Foundation, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922 South Korea
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922 South Korea
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229
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Zhao L, Zou H, Zhang H, Sun H, Wang T, Pan T, Li X, Bai Y, Qiao S, Luo Q, Xu J, Hou C, Liu J. Enzyme-Triggered Defined Protein Nanoarrays: Efficient Light-Harvesting Systems to Mimic Chloroplasts. ACS Nano 2017; 11:938-945. [PMID: 28051843 DOI: 10.1021/acsnano.6b07527] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The elegance and efficiency by which chloroplasts harvest solar energy and conduct energy transfer have been a source of inspiration for chemists to mimic such process. However, precise manipulation to obtain orderly arranged antenna chromophores in constructing artificial chloroplast mimics was a great challenge, especially from the structural similarity and bioaffinity standpoints. Here we reported a design strategy that combined covalent and noncovalent interactions to prepare a protein-based light-harvesting system to mimic chloroplasts. Cricoid stable protein one (SP1) was utilized as a building block model. Under enzyme-triggered covalent protein assembly, mutant SP1 with tyrosine (Tyr) residues at the designated sites can couple together to form nanostructures. Through controlling the Tyr sites on the protein surface, we can manipulate the assembly orientation to respectively generate 1D nanotubes and 2D nanosheets. The excellent stability endowed the self-assembled protein architectures with promising applications. We further integrated quantum dots (QDs) possessing optical and electronic properties with the 2D nanosheets to fabricate chloroplast mimics. By attaching different sized QDs as donor and acceptor chromophores to the negatively charged surface of SP1-based protein nanosheets via electrostatic interactions, we successfully developed an artificial light-harvesting system. The assembled protein nanosheets structurally resembled the natural thylakoids, and the QDs can achieve pronounced FRET phenomenon just like the chlorophylls. Therefore, the coassembled system was meaningful to explore the photosynthetic process in vitro, as it was designed to mimic the natural chloroplast.
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Affiliation(s)
- Linlu Zhao
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, China
| | - Haoyang Zou
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, China
| | - Hao Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, China
| | - Hongcheng Sun
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, China
| | - Tingting Wang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, China
| | - Tiezheng Pan
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, China
| | - Xiumei Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, China
| | - Yushi Bai
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, China
| | - Shanpeng Qiao
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, China
| | - Quan Luo
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, China
| | - Jiayun Xu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, China
| | - Chunxi Hou
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, China
| | - Junqiu Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, China
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Zhu H, Liu M, Yu H, Liu X, Zhong Y, Shu J, Fu X, Cai G, Chen X, Geng W, Yang X, Wu M, Li Z, Zhang D. Glycopatterns of Urinary Protein as New Potential Diagnosis Indicators for Diabetic Nephropathy. J Diabetes Res 2017; 2017:5728087. [PMID: 28401167 PMCID: PMC5376433 DOI: 10.1155/2017/5728087] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Revised: 12/24/2016] [Accepted: 01/04/2017] [Indexed: 11/17/2022] Open
Abstract
Diabetic nephropathy is a major cause of chronic kidney disease and end-stage kidney disease. However, so little is known about alterations of the glycopatterns in urine with the development of diabetic nephropathy. Presently, we interrogated glycopatterns in urine specimens using a lectin microarray. The results showed that expression levels of Siaα2-6Gal/GalNAc recognized by SNA exhibited significantly increased tendency with the development of diabetic nephropathy; moreover, SNA blotting indicated glycoproteins (90 kDa, 70 kDa, and 40 kDa) in urine may contribute to this alteration. Furthermore, the glycopatterns of (GlcNAc)2-4 recognized by STL exhibited difference between diabetic and nondiabetic nephropathy. The results of urinary protein microarray fabricated by another 48 urine specimens also indicated (GlcNAc)2-4 is a potential indictor to differentiate the patients with diabetic nephropathy from nondiabetic nephropathy. Furtherly, STL blotting showed that the 50 kDa glycoproteins were correlated with this alteration. In conclusion, our data provide pivotal information to monitor the development of diabetic nephropathy and distinguish between diabetic nephropathy and nondiabetic renal disease based on precise alterations of glycopatterns in urinary proteins, but further studies are needed in this regard.
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Affiliation(s)
- Hanyu Zhu
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center of Kidney Diseases, Beijing Key Laboratory of Kidney Disease, Beijing, China
| | - Moyan Liu
- Department of Nephrology, General Hospital of Jinan Military Command, Jinan, China
| | - Hanjie Yu
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
| | - Xiawei Liu
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
| | - Yaogang Zhong
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
| | - Jian Shu
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
| | - Xinle Fu
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
| | - Guangyan Cai
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center of Kidney Diseases, Beijing Key Laboratory of Kidney Disease, Beijing, China
| | - Xiangmei Chen
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center of Kidney Diseases, Beijing Key Laboratory of Kidney Disease, Beijing, China
| | - Wenjia Geng
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center of Kidney Diseases, Beijing Key Laboratory of Kidney Disease, Beijing, China
| | - Xiaoli Yang
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center of Kidney Diseases, Beijing Key Laboratory of Kidney Disease, Beijing, China
| | - Minghui Wu
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center of Kidney Diseases, Beijing Key Laboratory of Kidney Disease, Beijing, China
| | - Zheng Li
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
- *Zheng Li: and
| | - Dong Zhang
- Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center of Kidney Diseases, Beijing Key Laboratory of Kidney Disease, Beijing, China
- *Dong Zhang:
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Abstract
Studies of the interaction of bacteria with mucus-secreting cells can be complemented at a more mechanistic level by exploring the interaction of bacteria with purified mucins. Here we describe a far Western blotting approach to show how C. jejuni proteins separated by SDS PAGE and transferred to a membrane or slot blotted directly onto a membrane can be probed using biotinylated mucin. In addition we describe the use of novel mucin microarrays to assess bacterial interactions with mucins in a high-throughput manner.
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Affiliation(s)
- Marguerite Clyne
- Conway Institute, School of Medicineand Medical Science, University College Dublin, Dublin, Ireland
| | - Gina Duggan
- Conway Institute, School of Medicineand Medical Science, University College Dublin, Dublin, Ireland
| | - Julie Naughton
- Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Billy Bourke
- Conway Institute, School of Medicineand Medical Science, University College Dublin, Dublin, Ireland.
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232
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Lee JR, Haddon DJ, Gupta N, Price JV, Credo GM, Diep VK, Kim K, Hall DA, Baechler EC, Petri M, Varma M, Utz PJ, Wang SX. High-Resolution Analysis of Antibodies to Post-Translational Modifications Using Peptide Nanosensor Microarrays. ACS Nano 2016; 10:10652-10660. [PMID: 27636738 PMCID: PMC5367622 DOI: 10.1021/acsnano.6b03786] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Autoantibodies are a hallmark of autoimmune diseases such as lupus and have the potential to be used as biomarkers for diverse diseases, including immunodeficiency, infectious disease, and cancer. More precise detection of antibodies to specific targets is needed to improve diagnosis of such diseases. Here, we report the development of reusable peptide microarrays, based on giant magnetoresistive (GMR) nanosensors optimized for sensitively detecting magnetic nanoparticle labels, for the detection of antibodies with a resolution of a single post-translationally modified amino acid. We have also developed a chemical regeneration scheme to perform multiplex assays with a high level of reproducibility, resulting in greatly reduced experimental costs. In addition, we show that peptides synthesized directly on the nanosensors are approximately two times more sensitive than directly spotted peptides. Reusable peptide nanosensor microarrays enable precise detection of autoantibodies with high resolution and sensitivity and show promise for investigating antibody-mediated immune responses to autoantigens, vaccines, and pathogen-derived antigens as well as other fundamental peptide-protein interactions.
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Affiliation(s)
- Jung-Rok Lee
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
| | - D. James Haddon
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, California 94305, United States
| | - Nidhi Gupta
- Intel Corporation, Santa Clara, California 95052, United States
| | - Jordan V. Price
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, California 94305, United States
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, Berkeley, California 94720, United States
| | - Grace M. Credo
- Intel Corporation, Santa Clara, California 95052, United States
| | - Vivian K. Diep
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, California 94305, United States
| | - Kyunglok Kim
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, United States
| | - Drew A. Hall
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, United States
- Department of Electrical and Computer Engineering, University of California, San Diego, California 92093, United States
| | - Emily C. Baechler
- Center for Immunology, University of Minnesota Medical School, Minneapolis, Minnesota 55455, United States
| | - Michelle Petri
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Madoo Varma
- Intel Corporation, Santa Clara, California 95052, United States
| | - Paul J. Utz
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, California 94305, United States
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Shan X. Wang
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, United States
- Corresponding Author.
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233
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Tian HM, Yan H, Zhang J, He P, Chen CT. [Effect of Acupuncture on Neurological Function and Related Differentially-depressed Profiles in the Brain of Middle Cerebral Artery Occlusion Rats Using Antibody Chips Technique]. Zhen Ci Yan Jiu 2016; 41:479-485. [PMID: 29071888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
OBJECTIVE To observe the effect of acupuncture on changes of neurological function and expression of proteins in the ischemic brain region in middle cerebral artery occlusion (MCAO) rats with protein chip technique, so as to reveal the profiles of cerebral proteins related to its effectiveness in improving cerebral ischemia (CI). METHODS SD rats were rando-mized into sham operation (sham), CI model, non-acupoint and acupoint groups (n=10 in each group). The CI model was established by MCAO according to modified Longa's method. For rats of the acupoint group, "Dazhui" (CV 14), "Baihui" (GV 20) and "Shuigou" (GV 26) were punctured by twirling the filiform needles for about 1 min, and repeated once again during 30 min of need-le retention, which was conducted once every 12 h, and 6 times altogether. The non-acupoints were about 3 mm away from the above-mentioned acupoints and stimulated with the same method and same procedures. The neurological deficit score was scaled according to Longa's method. The differentially-expressed proteins (≥ 1.5 folds in up- and down-regulation) in the ischemic region of the brain were detected by using Springbio 720 antibody chip technology. RESULTS Compared with the sham group, the neurological deficit score was significantly higher in the model group (P<0.01), while compared with the model group, the neurological deficit scores were considerably in both acupoint and non-acupoint groups (P<0.05, P<0.01). The therapeutic effect of acupoint group was evidently superior to that of the non-acupoint group in improving neurological function (P<0.05). Compared with the sham group, the differentially-expressed proteins in the ischemic brain including 33 up-regulated and 12 down-regulated were found in the model group, mainly functioning in cell apoptosis, cell cycle regulation, cell differentiation and proliferation, cell cytoskeleton and connection, cell signal transduction, DNA repair and transcription factors. Compared with the model group, the differentially-expressed proteins including 12 up-regulated and 31 down-regulated in the acupoint group, and 15 up-regu-lated and 17 down-regulated in the non-acupoint group were detected, functioning being the same as those mentioned above in the model group. CONCLUSIONS Manual acupuncture stimulation of GV 14, GV 20 and GV 26 can improve neurological function in CI rats, which may be associated with its function in regulating the expression of many proteins in the ischemic region of the brain.
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Affiliation(s)
- Hao-Mei Tian
- Key Lab of Correlation between Meridian Acupoints and Viscera of Hunan Administration of Traditional Chinese Medicine, Hunan University of Traditional Chinese Medicine, Changsha 410208, China
| | - Hong Yan
- Key Lab of Correlation between Meridian Acupoints and Viscera of Hunan Administration of Traditional Chinese Medicine, Hunan University of Traditional Chinese Medicine, Changsha 410208, China
| | - Juan Zhang
- Ningxiang County Hospital of Traditional Chinese Medicine, Changsha 410600
| | - Ping He
- Key Lab of Correlation between Meridian Acupoints and Viscera of Hunan Administration of Traditional Chinese Medicine, Hunan University of Traditional Chinese Medicine, Changsha 410208, China
| | - Chu-Tao Chen
- Key Lab of Internal Medicine Constructed by Chinese Ministry of Education and Provincial Government, Hunan University of Traditional Chinese Medicine, Changsha 410007.
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234
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Persson N, Jansson B, Stuhr-Hansen N, Kovács A, Welinder C, Danielsson L, Blixt O. A Combinatory Antibody-Antigen Microarray Assay for High-Content Screening of Single-Chain Fragment Variable Clones from Recombinant Libraries. PLoS One 2016; 11:e0168761. [PMID: 28002485 PMCID: PMC5176327 DOI: 10.1371/journal.pone.0168761] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 12/06/2016] [Indexed: 12/30/2022] Open
Abstract
We have developed a combinatory antibody–antigen microarray for direct screening of multiple single-chain fragment variable (scFv) clones with no need for pre-purification or enrichment before screening. The straightforward workflow allows for early selection of binders to predefined peptide and glycopeptide targets. A capture antibody is contact printed on microarray slides, side by side with the antigens of interest. A large number of scFv clones, in supernatants, are printed on top of the capture antibody and the antigen in a “spot-on-spot” print. The printed scFv clones, which bind to the capture antibody, are detected using biotinylated antigen, while the binding of scFv clones to the printed antigen is detected through a mouse anti-tag antibody. Two different analyses are thus performed on the same slide, generating two kinds of information: one on the ability of an individual scFv clone to bind to the soluble form of the antigen, which may favour selection for higher affinity rather than avidity, while the other allows the identification of large numbers of clones, simultaneously, due to the binding of scFv clones to densely presented antigens, thus providing an overall increased hit rate. The functionality of the new screening approach was illustrated through the generation of antibodies against peptides from the chaperone complex Ku70/Ku80 and the GalNAcα-serine/threonine epitope on the IgA1 alpha chain hinge region. In total, 659 scFv clones were screened with a hit rate of approximately 20%. This approach allowed the identification of functional antibodies in both cases, illustrating the usefulness and capacity of this combinatory microarray screening technique for efficient analysis and validation of antibodies at an early stage of antibody generation.
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Affiliation(s)
- Nina Persson
- Chemical Glyco-Biology Laboratory, Department of Chemistry, Copenhagen University, Copenhagen, Denmark
| | - Bo Jansson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Nicolai Stuhr-Hansen
- Chemical Glyco-Biology Laboratory, Department of Chemistry, Copenhagen University, Copenhagen, Denmark
| | - András Kovács
- Chemical Glyco-Biology Laboratory, Department of Chemistry, Copenhagen University, Copenhagen, Denmark
- Division of Clinical Chemistry and Pharmacology, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Charlotte Welinder
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Centre of Excellence in Biological and Medical Mass Spectrometry (CEBMMS), Biomedical Centre D13, Lund University, Lund, Sweden
| | - Lena Danielsson
- Division of Clinical Chemistry and Pharmacology, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Ola Blixt
- Chemical Glyco-Biology Laboratory, Department of Chemistry, Copenhagen University, Copenhagen, Denmark
- * E-mail:
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235
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Rentka A, Harsfalvi J, Szucs G, Szekanecz Z, Szodoray P, Koroskenyi K, Kemeny-Beke A. Membrane array and multiplex bead analysis of tear cytokines in systemic sclerosis. Immunol Res 2016; 64:619-26. [PMID: 26687127 DOI: 10.1007/s12026-015-8763-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [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: 01/19/2023]
Abstract
Although serious ocular manifestations of systemic sclerosis (SSc) have been described, tear analysis of patients with SSc has not been performed in previous studies. Our aim was to measure a wide panel of cytokines and chemokines in tears of patients with SSc and to assess the most significant molecules with a more sensitive and specific method. Unstimulated tear samples were collected from nine patients with SSc and 12 age- and gender-matched healthy controls. The relative levels of 102 different cytokines were determined by a cytokine array, and then absolute levels of four key cytokines were determined by a magnetic bead assay. Array results revealed shifted cytokine profile characterized by predominance of inflammatory mediators. Of the 102 analyzed molecules, nine were significantly increased in tears of patients with SSc. Based on the multiplex bead results, C-reactive protein, interferon-γ-inducible protein-10, and monocyte chemoattractant protein-1 levels were significantly higher in tears of patients with SSc. Our current data depict a group of inflammatory mediators, which play a significant role in ocular pathology of SSc; furthermore, they might function as excellent candidates for future therapeutic targets in SSc patients with ocular manifestations.
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Affiliation(s)
- Aniko Rentka
- Department of Ophthalmology, University of Debrecen, Debrecen, Hungary
| | - Jolan Harsfalvi
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Gabriella Szucs
- Department of Rheumatology, Institute of Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Zoltan Szekanecz
- Department of Rheumatology, Institute of Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Peter Szodoray
- Institute of Immunology, Rikshospitalet, Oslo University Hospital, Oslo, Norway
| | - Krisztina Koroskenyi
- Department of Biochemistry and Molecular Biology, Signaling and Apoptosis Research Group, Hungarian Academy of Sciences, Research Center of Molecular Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Adam Kemeny-Beke
- Department of Ophthalmology, University of Debrecen, Debrecen, Hungary.
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Kong F, Li Y, Hu E, Wang R, Wang J, Liu J, Zhang J, He D, Xiao X. The Characteristic of S100A7 Induction by the Hippo-YAP Pathway in Cervical and Glossopharyngeal Squamous Cell Carcinoma. PLoS One 2016; 11:e0167080. [PMID: 27907036 PMCID: PMC5132200 DOI: 10.1371/journal.pone.0167080] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 11/08/2016] [Indexed: 11/19/2022] Open
Abstract
S100A7 is expressed in many squamous cell carcinomas (SCCs). Our previous study revealed that S100A7 was dramatically induced in several SCC cells and activation of the Hippo pathway significantly promoted S100A7 in epidermoid carcinoma cells. However, whether the Hippo pathway regulates S100A7 expression in SCCs remains largely unknown. Here, we uncover that S100A7 induction by the Hippo-YAP pathway displays different characteristic in cervical and glossopharyngeal SCC. In well differentiated HCC94 cervical cells and FaDu pharyngeal cells, S100A7 is easily induced by both suspension and dense culture, which is accompanied by an increase in YAP phosphorylation and a decrease in nuclear YAP. Strikingly, these correlations of S100A7 and YAP reverse after recovery of cell attachment or relief from dense culture. Further examination finds that S100A7 induction is significantly repressed by nuclear YAP, which is validated by activation or inhibition of the Hippo pathway via loss- and/or gain-of- LATS1 and MST1 function. Subsequently, we prove that TEAD1 is required for YAP transcriptional repression of S100A7. However, S100A7 is hardly induced in poorly differentiated SiHa cervical cells and NCI-H226 pulmonary cells even in suspension or activation of the Hippo pathway. More importantly, cervical and lingual SCC tissues array analyses show that S100A7 expression displays the positive correlation with pYAP-S127 and the negative correlation with nuclear YAP in the majority of well differentiated but not in poorly differentiated tissues. Collectively, our findings demonstrate that the different induction of S100A7 toward activation of the Hippo pathway mainly depends on the degree of cell differentiation in cervical and glossopharyngeal SCC.
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Affiliation(s)
- Fei Kong
- Key laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, Beijing Normal University, Beijing, China
| | - Yunguang Li
- Key laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, Beijing Normal University, Beijing, China
| | - Enze Hu
- Key laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, Beijing Normal University, Beijing, China
| | - Rui Wang
- Key laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, Beijing Normal University, Beijing, China
| | - Junhao Wang
- Key laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, Beijing Normal University, Beijing, China
| | - Jin Liu
- Key laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, Beijing Normal University, Beijing, China
| | - Jinsan Zhang
- School of Pharmaceutical Sciences and Key Laboratory of Biotechnology and Pharmaceutical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Dacheng He
- Key laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, Beijing Normal University, Beijing, China
| | - Xueyuan Xiao
- Key laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, Beijing Normal University, Beijing, China
- * E-mail:
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237
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Peyser ND, Pendleton K, Gooding WE, Lui VWY, Johnson DE, Grandis JR. Genomic and Transcriptomic Alterations Associated with STAT3 Activation in Head and Neck Cancer. PLoS One 2016; 11:e0166185. [PMID: 27855189 PMCID: PMC5113908 DOI: 10.1371/journal.pone.0166185] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/24/2016] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Hyperactivation of STAT3 via constitutive phosphorylation of tyrosine 705 (Y705) is common in most human cancers, including head and neck squamous carcinoma (HNSCC). STAT3 is rarely mutated in cancer and the (epi)genetic alterations that lead to STAT3 activation are incompletely understood. Here we used an unbiased approach to identify genomic and epigenomic changes associated with pSTAT3(Y705) expression using data generated by The Cancer Genome Atlas (TCGA). METHODS AND FINDINGS Mutation, mRNA expression, promoter methylation, and copy number alteration data were extracted from TCGA and examined in the context of pSTAT3(Y705) protein expression. mRNA expression levels of 1279 genes were found to be associated with pSTAT3(705) expression. Association of pSTAT3(Y705) expression with caspase-8 mRNA expression was validated by immunoblot analysis in HNSCC cells. Mutation, promoter hypermethylation, and copy number alteration of any gene were not significantly associated with increased pSTAT3(Y705) protein expression. CONCLUSIONS These cumulative results suggest that unbiased approaches may be useful in identifying the molecular underpinnings of oncogenic signaling, including STAT3 activation, in HNSCC. Larger datasets will likely be necessary to elucidate signaling consequences of infrequent alterations.
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Affiliation(s)
- Noah D. Peyser
- Department of Otolaryngology–Head and Neck Surgery, University of California San Francisco, San Francisco, CA, United States of America, 94143
| | - Kelsey Pendleton
- Department of Otolaryngology, University of Pittsburgh and the University of Pittsburgh Cancer Institute, Pittsburgh, PA, United States of America, 15213
| | - William E. Gooding
- Biostatistics Facility, University of Pittsburgh Cancer Institute, Pittsburgh, PA, United States of America, 15213
| | - Vivian W. Y. Lui
- Department of Pharmacology and Pharmacy, School of Biomedical Sciences, Li-Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong SAR, China
| | - Daniel E. Johnson
- Department of Medicine, University of Pittsburgh and the University of Pittsburgh Cancer Institute, Pittsburgh, PA, United States of America
| | - Jennifer R. Grandis
- Department of Otolaryngology–Head and Neck Surgery, University of California San Francisco, San Francisco, CA, United States of America, 94143
- * E-mail:
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238
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Lee S, Jang J, Jeon H, Lee J, Yoo SM, Park J, Lee MS. Latent Kaposi's sarcoma-associated herpesvirus infection in bladder cancer cells promotes drug resistance by reducing reactive oxygen species. J Microbiol 2016; 54:782-788. [PMID: 27796928 DOI: 10.1007/s12275-016-6388-x] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 09/19/2016] [Accepted: 09/19/2016] [Indexed: 02/05/2023]
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is the major etiologic agent of Kaposi's sarcoma, primary effusion lymphoma, and multicentric Castleman's disease. Recent studies have indicated that KSHV can be detected at high frequency in patient-derived bladder cancer tissue and might be associated with the pathogenesis of bladder cancer. Bladder cancer is the second most common cancer of the genitourinary tract, and it has a high rate of recurrence. Because drug resistance is closely related to chemotherapy failure and cancer recurrence, we investigated whether KSHV infection is associated with drug resistance of bladder cancer cells. Some KSHV-infected bladder cancer cell lines showed resistance to an anti-cancer drug, cisplatin, possibly as a result of down-regulation of reactive oxygen species. Additionally, drug resistance acquired from KSHV infection could partly be overcome by HDAC1 inhibitors. Taken together, the data suggest the possible role of KSHV in chemo-resistant bladder cancer, and indicate the therapeutic potential of HDAC1 inhibitors in drug-resistant bladder cancers associated with KSHV infection.
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Affiliation(s)
- Suhyuk Lee
- Department of Microbiology and Immunology, Eulji University School of Medicine, Daejeon, 34824, Republic of Korea
| | - Jaehyuk Jang
- Department of Microbiology and Immunology, Eulji University School of Medicine, Daejeon, 34824, Republic of Korea
| | - Hyungtaek Jeon
- Department of Microbiology and Immunology, Eulji University School of Medicine, Daejeon, 34824, Republic of Korea
| | - Jisu Lee
- Department of Microbiology and Immunology, Eulji University School of Medicine, Daejeon, 34824, Republic of Korea
| | - Seung-Min Yoo
- Department of Microbiology and Immunology, Eulji University School of Medicine, Daejeon, 34824, Republic of Korea
| | - Jinsung Park
- Department of Urology, Eulji University Hospital, Eulji University School of Medicine, Daejeon, 34824, Republic of Korea
| | - Myung-Shin Lee
- Department of Microbiology and Immunology, Eulji University School of Medicine, Daejeon, 34824, Republic of Korea.
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239
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Pin E, Stratton S, Belluco C, Liotta L, Nagle R, Hodge KA, Deng J, Dong T, Baldelli E, Petricoin E, Pierobon M. A pilot study exploring the molecular architecture of the tumor microenvironment in human prostate cancer using laser capture microdissection and reverse phase protein microarray. Mol Oncol 2016; 10:1585-1594. [PMID: 27825696 DOI: 10.1016/j.molonc.2016.09.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [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: 04/11/2016] [Revised: 09/24/2016] [Accepted: 09/28/2016] [Indexed: 12/24/2022] Open
Abstract
The cross-talk between tumor epithelium and surrounding stromal/immune microenvironment is essential to sustain tumor growth and progression and provides new opportunities for the development of targeted treatments focused on disrupting the tumor ecology. Identification of novel approaches to study these interactions is of primary importance. Using laser capture microdissection (LCM) coupled with reverse phase protein microarray (RPPA) based protein signaling activation mapping we explored the molecular interconnection between tumor epithelium and surrounding stromal microenvironment in 18 prostate cancer (PCa) specimens. Four specimen-matched cellular compartments (normal-appearing epithelium and its adjacent stroma, and malignant epithelium and its adjacent stroma) were isolated for each case. The signaling network analysis of the four compartments unraveled a number of molecular mechanisms underlying the communication between tumor cells and stroma in the context of the tumor microenvironment. In particular, differential expression of inflammatory mediators like IL-8 and IL-10 by the stroma cells appeared to modulate specific cross-talks between the tumor cells and surrounding microenvironment.
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Affiliation(s)
- Elisa Pin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA; Division of Experimental Oncology 2, CRO-IRCCS, National Cancer Institute, Aviano, Italy
| | - Steven Stratton
- Division of Cancer Prevention and Control, University of Arizona Cancer Center, Tucson, AZ, USA
| | - Claudio Belluco
- Department of Surgical Oncology, CRO-IRCCS, National Cancer Institute, Aviano, Italy
| | - Lance Liotta
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Ray Nagle
- Division of Cancer Prevention and Control, University of Arizona Cancer Center, Tucson, AZ, USA
| | - K Alex Hodge
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Jianghong Deng
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Ting Dong
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Elisa Baldelli
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Emanuel Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA.
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240
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Säll A, Persson H, Ohlin M, Borrebaeck CAK, Wingren C. Advancing the global proteome survey platform by using an oriented single chain antibody fragment immobilization approach. N Biotechnol 2016; 33:503-13. [PMID: 26703809 DOI: 10.1016/j.nbt.2015.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/27/2015] [Accepted: 12/03/2015] [Indexed: 11/17/2022]
Abstract
Increasing the understanding of a proteome and how its protein composition is affected by for example different diseases, such as cancer, has the potential to improve strategies for early diagnosis and therapeutics. The Global Proteome Survey or GPS is a method that combines mass spectrometry and affinity enrichment with the use of antibodies. The technology enables profiling of complex proteomes in a species independent manner. The sensitivity of GPS, and other methods relying on affinity enrichment, is largely affected by the activity of the exploited affinity reagent. We here present an improvement of the GPS platform by utilizing an antibody immobilization approach which ensures a controlled immobilization process of the antibody to the magnetic bead support. More specifically, we make use of an antibody format that enables site-directed biotinylation and use this in combination with streptavidin coated magnetic beads. The performance of the expanded GPS platform was evaluated by profiling yeast proteome samples. We demonstrate that the oriented antibody immobilization strategy increases the ability of the GPS platform and results in larger fraction of functional antibodies. Additionally, we show that this new antibody format enabled in-solution capture, i.e. immobilization of the antibodies after sample incubation. A workflow has been established that permit the use of an oriented immobilization strategy for the GPS platform.
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Affiliation(s)
- Anna Säll
- Department of Immunotechnology, Lund University, Medicon Village (House 406), SE-223 81 Lund, Sweden
| | - Helena Persson
- Department of Immunotechnology, Lund University, Medicon Village (House 406), SE-223 81 Lund, Sweden; Science for Life Laboratory, Royal Institute of Technology, Stockholm, Sweden
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Medicon Village (House 406), SE-223 81 Lund, Sweden
| | - Carl A K Borrebaeck
- Department of Immunotechnology, Lund University, Medicon Village (House 406), SE-223 81 Lund, Sweden.
| | - Christer Wingren
- Department of Immunotechnology, Lund University, Medicon Village (House 406), SE-223 81 Lund, Sweden.
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241
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Lu LL, Chung AW, Rosebrock TR, Ghebremichael M, Yu WH, Grace PS, Schoen MK, Tafesse F, Martin C, Leung V, Mahan AE, Sips M, Kumar MP, Tedesco J, Robinson H, Tkachenko E, Draghi M, Freedberg KJ, Streeck H, Suscovich TJ, Lauffenburger DA, Restrepo BI, Day C, Fortune SM, Alter G. A Functional Role for Antibodies in Tuberculosis. Cell 2016; 167:433-443.e14. [PMID: 27667685 DOI: 10.1016/j.cell.2016.08.072] [Citation(s) in RCA: 367] [Impact Index Per Article: 45.9] [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: 02/08/2016] [Revised: 05/04/2016] [Accepted: 08/26/2016] [Indexed: 11/18/2022]
Abstract
While a third of the world carries the burden of tuberculosis, disease control has been hindered by a lack of tools, including a rapid, point-of-care diagnostic and a protective vaccine. In many infectious diseases, antibodies (Abs) are powerful biomarkers and important immune mediators. However, in Mycobacterium tuberculosis (Mtb) infection, a discriminatory or protective role for humoral immunity remains unclear. Using an unbiased antibody profiling approach, we show that individuals with latent tuberculosis infection (Ltb) and active tuberculosis disease (Atb) have distinct Mtb-specific humoral responses, such that Ltb infection is associated with unique Ab Fc functional profiles, selective binding to FcγRIII, and distinct Ab glycosylation patterns. Moreover, compared to Abs from Atb, Abs from Ltb drove enhanced phagolysosomal maturation, inflammasome activation, and, most importantly, macrophage killing of intracellular Mtb. Combined, these data point to a potential role for Fc-mediated Ab effector functions, tuned via differential glycosylation, in Mtb control.
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Affiliation(s)
- Lenette L Lu
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
| | - Amy W Chung
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Tracy R Rosebrock
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
| | | | - Wen Han Yu
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Patricia S Grace
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Matthew K Schoen
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Fikadu Tafesse
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Constance Martin
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
| | - Vivian Leung
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
| | - Alison E Mahan
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Magdalena Sips
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Department of Biomedical Molecular Biology, Ghent University, Ghent 9000, Belgium
| | - Manu P Kumar
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | | | - Hannah Robinson
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | | | - Monia Draghi
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | | | - Hendrik Streeck
- Institute for Medical Biology, University Hospital Essen, University of Duisburg-Essen, 45141 Essen, Germany
| | - Todd J Suscovich
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Blanca I Restrepo
- School of Public Health, University of Texas Health Houston, Brownsville, TX 78520, USA
| | - Cheryl Day
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30307, USA; Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30332, USA; South African Tuberculosis Vaccine Initiative (SATVI) and School of Child and Adolescent Health, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, Cape Town 7925, South Africa
| | - Sarah M Fortune
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA.
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA.
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242
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Berntson L, Hedlund-Treutiger I, Alving K. Anti-inflammatory effect of exclusive enteral nutrition in patients with juvenile idiopathic arthritis. Clin Exp Rheumatol 2016; 34:941-945. [PMID: 27383427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 02/26/2016] [Indexed: 06/06/2023]
Abstract
OBJECTIVES There is extensive evidence for an influence of gut microbiota on the immune system, which has consequences for inflammatory diseases. Exclusive enteral nutrition (EEN), which may change the gut microbiota, is an effective anti-inflammatory treatment for Crohn's disease in children. We wanted to explore the immediate anti-inflammatory effect of EEN in children with juvenile idiopathic arthritis (JIA). METHODS Thirteen patients with JIA (7-17 years of age), in a disease flare-up, were included in the study. Six children dropped out within 1.5-2.0 weeks of treatment, and seven patients continued, constituting the study cohort. EEN was given for three to eight weeks, with clinical and laboratory status assessed before and after treatment periods. In addition to conventional laboratory tests, 92 inflammatory proteins were analysed with a multiplex system (Proseek Multiplex Inflammation I, Olink Bioscience). RESULTS EEN had a significant anti-inflammatory effect on active joints (p=0.031), JADAS27 (p=0.016) and morning stiffness (p=0.031). In the multiplex analysis of inflammatory proteins, MMP-1 (matrix metalloproteinase), involved in the degradation of collagens in chondrocytes, decreased significantly (p=0.047), as did MCP-4 (p=0.031) and 4E-BP1 (p=0.031). CONCLUSIONS Exclusive enteral nutrition for three to eight weeks had anti-inflammatory effect in all children with JIA that continued with EEN for more than two weeks. The study is only exploratory but the result supports an immunologically important role for the intestinal canal in these patients.
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Affiliation(s)
- Lillemor Berntson
- Department of Women's and Children's Health, Uppsala University, Sweden.
| | | | - Kjell Alving
- Department of Women's and Children's Health, Uppsala University, Sweden
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243
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Xu L, Li S, Ran X, Liu C, Lin R, Wang J. Apoptotic activity and gene responses in Drosophila melanogaster S2 cells, induced by azadirachtin A. Pest Manag Sci 2016; 72:1710-1717. [PMID: 26607310 DOI: 10.1002/ps.4198] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [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: 06/17/2015] [Revised: 11/22/2015] [Accepted: 11/23/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Azadirachtin has been used as an antifeedant and growth disruption agent for many insect species. Previous investigations have reported the apoptotic effects of azadirachtin on some insect cells, but the molecular mechanisms are still not clear. This study investigated the underlying molecular mechanisms for the apoptotic effects induced by azadirachtin on Drosophila melanogaster S2 cells in vitro. RESULTS The results of the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide assay demonstrated that azadirachtin exhibited significant cytotoxicity to S2 cells in a time- and dose-dependent manner. The changes in cellular morphology and the DNA fragmentation demonstrated that azadirachtin induced remarkable apoptosis of S2 cells. Expression levels of 276 genes were found to be significantly changed in S2 cells after exposure to azadirachtin, as detected by Drosophila genome array. Among these genes, calmodulin (CaM) was the most highly upregulated gene. Azadirachtin was further demonstrated to trigger intracellular Ca(2+) release in S2 cells. The genes related to the apoptosis pathway, determined from chip data, were validated by the real-time quantitative polymerase chain reaction method. CONCLUSION The results showed that azadirachtin-mediated intracellular Ca(2+) release was the primary event that triggered apoptosis in Drosophila S2 cells through both pathways of the Ca(2+) -CaM and EcR/Usp signalling cascade. © 2015 Society of Chemical Industry.
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Affiliation(s)
- Lin Xu
- Key Laboratory of Green Pesticide and Agriculture Bioengineering of Ministry of Education, Guizhou University, Guiyang, China
| | - Sheng Li
- Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
| | - Xueqin Ran
- Faculty of Animal Science and Veterinary Medicine, Guiyang, China
| | - Chang Liu
- Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
| | - Rutao Lin
- Faculty of Animal Science and Veterinary Medicine, Guiyang, China
| | - Jiafu Wang
- Key Laboratory of Green Pesticide and Agriculture Bioengineering of Ministry of Education, Guizhou University, Guiyang, China
- Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
- Tongren College, Tongren, China
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244
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Roberts AM, Ward CC, Nomura DK. Activity-based protein profiling for mapping and pharmacologically interrogating proteome-wide ligandable hotspots. Curr Opin Biotechnol 2016; 43:25-33. [PMID: 27568596 DOI: 10.1016/j.copbio.2016.08.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 08/04/2016] [Accepted: 08/11/2016] [Indexed: 11/19/2022]
Abstract
Despite the completion of human genome sequencing efforts nearly 15 years ago that brought with it the promise of genome-based discoveries that would cure human diseases, most protein targets that control human diseases have remained largely untranslated, in-part because they represent difficult protein targets to drug. In addition, many of these protein targets lack screening assays or accessible binding pockets, making the development of small-molecule modulators very challenging. Here, we discuss modern methods for activity-based protein profiling-based chemoproteomic strategies to map 'ligandable' hotspots in proteomes using activity and reactivity-based chemical probes to allow for pharmacological interrogation of these previously difficult targets. We will showcase several recent examples of how these technologies have been used to develop highly selective small-molecule inhibitors against disease-related protein targets.
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Affiliation(s)
- Allison M Roberts
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Carl C Ward
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Daniel K Nomura
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, United States.
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245
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Klohonatz KM, Hess AM, Hansen TR, Squires EL, Bouma GJ, Bruemmer JE. Equine endometrial gene expression changes during and after maternal recognition of pregnancy. J Anim Sci 2016; 93:3364-76. [PMID: 26440005 DOI: 10.2527/jas.2014-8826] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The mechanism for maternal recognition of pregnancy (MRP) in horses is unknown. To maintain a pregnancy, a mobile conceptus must be recognized by the uterus before d 14 postovulation (PO). This recognition prevents endometrial secretion of PGF2α on d14 through 16, which would otherwise initiate luteolysis. The objective of this study was to evaluate gene expression in the endometrium of pregnant and nonpregnant mares during and after MRP to identify possible genes involved during this time. Twelve normally cycling mares were used in a crossover design and randomly assigned to a specific collection day. Endometrial samples were collected from a pregnant and nonpregnant (nonmated) mare on cycle d 12, 14, 16, and 18 (n = 3/d) PO. Microarray analysis comparing the endometrial gene expression in pregnant and nonpregnant mares revealed no differences at d 12. Ten genes were identified to have consistently higher or lower expression levels in the endometrium from pregnant versus nonpregnant mares on d 14, 16, and 18 (P < 0.001). The expression of these 10 genes was further analyzed with real-time PCR. d 14, 16, and 18 gene expression patterns were consistent with the microarray analysis, but on d 12, 4 of the 10 were identified as differentially expressed. Endometrial samples were then collected on d 13 PO (n = 3) and processed for western blot and immunohistochemical analysis of 2 proteins due to their reproductive significance. SPLA2 and DKK1 antibody specificity were confirmed via western blot analysis but were not different in samples from pregnant and nonpregnant mares (P = 0.114 and P = 0.514, respectively) and cellular localization was examined by immunohistochemical analysis. This is the first study to describe gene expression and cellular localization in the endometrium at the time of MRP for these genes and suggests that the uterus does not prepare to support a pregnancy until d 14. The function of these genes may be critical in the process of MRP.
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246
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Kogut MH, Swaggerty CL, Byrd JA, Selvaraj R, Arsenault RJ. Chicken-Specific Kinome Array Reveals that Salmonella enterica Serovar Enteritidis Modulates Host Immune Signaling Pathways in the Cecum to Establish a Persistence Infection. Int J Mol Sci 2016; 17:ijms17081207. [PMID: 27472318 PMCID: PMC5000605 DOI: 10.3390/ijms17081207] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 06/15/2016] [Accepted: 07/08/2016] [Indexed: 02/07/2023] Open
Abstract
Non-typhoidal Salmonella enterica induces an early, short-lived pro-inflammatory response in chickens that is asymptomatic of clinical disease and results in a persistent colonization of the gastrointestinal (GI) tract that transmits infections to naïve hosts via fecal shedding of bacteria. The underlying mechanisms that control this persistent colonization of the ceca of chickens by Salmonella are only beginning to be elucidated. We hypothesize that alteration of host signaling pathways mediate the induction of a tolerance response. Using chicken-specific kinomic immune peptide arrays and quantitative RT-PCR of infected cecal tissue, we have previously evaluated the development of disease tolerance in chickens infected with Salmonella enterica serovar Enteritidis (S. Enteritidis) in a persistent infection model (4-14 days post infection). Here, we have further outlined the induction of an tolerance defense strategy in the cecum of chickens infected with S. Enteritidis beginning around four days post-primary infection. The response is characterized by alterations in the activation of T cell signaling mediated by the dephosphorylation of phospholipase c-γ1 (PLCG1) that inhibits NF-κB signaling and activates nuclear factor of activated T-cells (NFAT) signaling and blockage of interferon-γ (IFN-γ) production through the disruption of the JAK-STAT signaling pathway (dephosphorylation of JAK2, JAK3, and STAT4). Further, we measured a significant down-regulation reduction in IFN-γ mRNA expression. These studies, combined with our previous findings, describe global phenotypic changes in the avian cecum of Salmonella Enteritidis-infected chickens that decreases the host responsiveness resulting in the establishment of persistent colonization. The identified tissue protein kinases also represent potential targets for future antimicrobial compounds for decreasing Salmonella loads in the intestines of food animals before going to market.
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Affiliation(s)
- Michael H Kogut
- Southern Plains Agricultural Resarch Center, United States Department of Agriculture, Agricultural Research Service, College Station, TX 77845, USA.
| | - Christina L Swaggerty
- Southern Plains Agricultural Resarch Center, United States Department of Agriculture, Agricultural Research Service, College Station, TX 77845, USA.
| | - James Allen Byrd
- Southern Plains Agricultural Resarch Center, United States Department of Agriculture, Agricultural Research Service, College Station, TX 77845, USA.
| | - Ramesh Selvaraj
- Ohio Agricultural Research Center, The Ohio State University, Wooster, OH 44691, USA.
| | - Ryan J Arsenault
- Department of Animal and Food Sciences, University of Delaware, Newark, DE 19716, USA.
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247
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Kaddi CD, Wang MD. Models for predicting stage in head and neck squamous cell carcinoma using proteomic data. Annu Int Conf IEEE Eng Med Biol Soc 2016; 2014:5216-9. [PMID: 25571169 DOI: 10.1109/embc.2014.6944801] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Head and neck squamous cell carcinoma (HNSCC) that is detected at an advanced stage is associated with much worse patient outcomes than if detected at early stages. This study uses reverse phase protein array (RPPA) data to build predictive models that discriminate between early and advanced stage HNSCC. Individual and ensemble binary classifiers, using filter-based and wrapper-based feature selection, are used to build several models which achieve moderate MCC and AUC values. This study identifies informative protein feature sets which may contribute to an increased understanding of the molecular basis of HNSCC.
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248
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Men D, Zhou J, Li W, Leng Y, Chen X, Tao S, Zhang XE. Fluorescent Protein Nanowire-Mediated Protein Microarrays for Multiplexed and Highly Sensitive Pathogen Detection. ACS Appl Mater Interfaces 2016; 8:17472-7. [PMID: 27315221 DOI: 10.1021/acsami.6b04786] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Protein microarrays are powerful tools for high-throughput and simultaneous detection of different target molecules in complex biological samples. However, the sensitivity of conventional fluorescence-labeling protein detection methods is limited by the availability of signal molecules for binding to the target molecule. Here, we built a multifunctional fluorescent protein nanowire (FNw) by harnessing self-assembly of yeast amyloid protein. The FNw integrated a large number of fluorescent molecules, thereby enhancing the fluorescent signal output in target detection. The FNw was then combined with protein microarray technology to detect proteins derived from two pathogens, including influenza virus (hemagglutinin 1, HA1) and human immunodeficiency virus (p24 and gp120). The resulting detection sensitivity achieved a 100-fold improvement over a commercially available detection reagent.
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Affiliation(s)
- Dong Men
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences , Wuhan 430071, China
- Nursing College, Henan University , Kaifeng 475004, China
| | - Juan Zhou
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences , Wuhan 430071, China
| | - Wei Li
- College of Life Sciences, Hubei University , Wuhan 430062, China
| | - Yan Leng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences , Wuhan 430071, China
| | - Xinwen Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences , Wuhan 430071, China
| | - Shengce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University , Shanghai 200240, China
| | - Xian-En Zhang
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences , Beijing 100101, China
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249
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da Silva E Silva DA, Frozino Ribeiro A, Damasceno S, Rocha CS, Berenguer de Matos AH, Boerngen-Lacerda R, Correia D, Brunialti Godard AL. Inflexible ethanol intake: A putative link with the Lrrk2 pathway. Behav Brain Res 2016; 313:30-37. [PMID: 27411784 DOI: 10.1016/j.bbr.2016.07.001] [Citation(s) in RCA: 10] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 06/28/2016] [Accepted: 07/02/2016] [Indexed: 01/10/2023]
Abstract
Alcoholism is a complex multifactorial disorder with a strong genetic influence. Although several studies have shown the impact of high ethanol intake on the striatal gene expression, few have addressed the relationship between the patterns of gene expression underlying the compulsive behaviour associated with the two major concerns in addiction: the excessive drug consumption and relapsing. In this study, we used a chronic three-bottle free-choice murine model to address striatal transcript regulation among animals with different ethanol intakes and preferences: Light Drinkers (preference for water throughout the experiment), Heavy Drinkers (preference for ethanol with a non-compulsive intake) and Inflexible Drinkers (preference for ethanol and simultaneous loss of control over the drug intake). Our aim was to correlate the intake patterns observed in this model with gene expression changes in the striatum, a brain region critical for the development of alcohol addiction. We found that the transcripts of the Lrrk2 gene, which encodes a multifunctional protein with kinase and GTPase activities, is upregulated only in Inflexible Drinkers suggesting, for the first time, that the Lrrk2 pathway plays a major role in the compulsive ethanol intake behaviour of addicted subjects.
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Affiliation(s)
| | - Andrea Frozino Ribeiro
- Programa de Pós-Graduação em Neurociências, Faculdade de Filosofia de Ciências Humanas, Universidade Federal de Minas Gerais, MG 31270-901, Brazil
| | - Samara Damasceno
- Departmento de Biologia Geral, Universidade Federal de Minas Gerais, Pampulha, Belo Horizonte, MG CEP 31270-901, Brazil
| | - Cristiane S Rocha
- Departmento de Genética Médica, Faculdade de Ciências Medicas, Universidade de Campinas, Tessália Vieira de Camargo, Cidade Universitária Zeferino Vaz, Campinas, SP, Brazil
| | - Alexandre H Berenguer de Matos
- Departmento de Genética Médica, Faculdade de Ciências Medicas, Universidade de Campinas, Tessália Vieira de Camargo, Cidade Universitária Zeferino Vaz, Campinas, SP, Brazil
| | - Roseli Boerngen-Lacerda
- Departamento de Farmacologia, Jardim das Américas, Universidade Federal do Paraná, P.O. Box 19031, Curitiba, PR 81531-990, Brazil
| | - Diego Correia
- Departmento de Biologia Geral, Universidade Federal de Minas Gerais, Pampulha, Belo Horizonte, MG CEP 31270-901, Brazil; Departamento de Farmacologia, Jardim das Américas, Universidade Federal do Paraná, P.O. Box 19031, Curitiba, PR 81531-990, Brazil
| | - Ana Lúcia Brunialti Godard
- Departmento de Biologia Geral, Universidade Federal de Minas Gerais, Pampulha, Belo Horizonte, MG CEP 31270-901, Brazil.
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250
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Gallego-Villar L, Rivera-Barahona A, Cuevas-Martín C, Guenzel A, Pérez B, Barry MA, Murphy MP, Logan A, Gonzalez-Quintana A, Martín MA, Medina S, Gil-Izquierdo A, Cuezva JM, Richard E, Desviat LR. In vivo evidence of mitochondrial dysfunction and altered redox homeostasis in a genetic mouse model of propionic acidemia: Implications for the pathophysiology of this disorder. Free Radic Biol Med 2016; 96:1-12. [PMID: 27083476 DOI: 10.1016/j.freeradbiomed.2016.04.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 04/01/2016] [Accepted: 04/02/2016] [Indexed: 12/16/2022]
Abstract
Accumulation of toxic metabolites has been described to inhibit mitochondrial enzymes, thereby inducing oxidative stress in propionic acidemia (PA), an autosomal recessive metabolic disorder caused by the deficiency of mitochondrial propionyl-CoA carboxylase. PA patients exhibit neurological deficits and multiorgan complications including cardiomyopathy. To investigate the role of mitochondrial dysfunction in the development of these alterations we have used a hypomorphic mouse model of PA that mimics the biochemical and clinical hallmarks of the disease. We have studied the tissue-specific bioenergetic signature by Reverse Phase Protein Microarrays and analysed OXPHOS complex activities, mtDNA copy number, oxidative damage, superoxide anion and hydrogen peroxide levels. The results show decreased levels and/or activity of several OXPHOS complexes in different tissues of PA mice. An increase in mitochondrial mass and OXPHOS complexes was observed in brain, possibly reflecting a compensatory mechanism including metabolic reprogramming. mtDNA depletion was present in most tissues analysed. Antioxidant enzymes were also found altered. Lipid peroxidation was present along with an increase in hydrogen peroxide and superoxide anion production. These data support the hypothesis that oxidative damage may contribute to the pathophysiology of PA, opening new avenues in the identification of therapeutic targets and paving the way for in vivo evaluation of compounds targeting mitochondrial biogenesis or reactive oxygen species production.
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Affiliation(s)
- L Gallego-Villar
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Universidad Autónoma, Madrid, Spain; CIBER de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain; Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Madrid, Spain
| | - A Rivera-Barahona
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Universidad Autónoma, Madrid, Spain; CIBER de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain; Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Madrid, Spain
| | - C Cuevas-Martín
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Universidad Autónoma, Madrid, Spain; CIBER de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | | | - B Pérez
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Universidad Autónoma, Madrid, Spain; CIBER de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain; Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Madrid, Spain
| | | | - M P Murphy
- Medical Research Council, Mitochondrial Biology Unit, Cambridge, UK
| | - A Logan
- Medical Research Council, Mitochondrial Biology Unit, Cambridge, UK
| | - A Gonzalez-Quintana
- CIBER de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain; Instituto de Investigación Hospital 12 de Octubre (i+12), Madrid, Spain
| | - M A Martín
- CIBER de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain; Instituto de Investigación Hospital 12 de Octubre (i+12), Madrid, Spain
| | - S Medina
- Department of Food Science and Technology, CEBAS-CSIC, Campus de Espinardo 25, 30100 Espinardo, Murcia, Spain
| | - A Gil-Izquierdo
- Department of Food Science and Technology, CEBAS-CSIC, Campus de Espinardo 25, 30100 Espinardo, Murcia, Spain
| | - J M Cuezva
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Universidad Autónoma, Madrid, Spain; CIBER de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - E Richard
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Universidad Autónoma, Madrid, Spain; CIBER de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain; Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Madrid, Spain
| | - L R Desviat
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Universidad Autónoma, Madrid, Spain; CIBER de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain; Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Madrid, Spain.
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