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Ahi EP, Brunel M, Tsakoumis E, Chen J, Schmitz M. Appetite regulating genes in zebrafish gut; a gene expression study. PLoS One 2022; 17:e0255201. [PMID: 35853004 PMCID: PMC9295983 DOI: 10.1371/journal.pone.0255201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 05/16/2022] [Indexed: 11/19/2022] Open
Abstract
The underlying molecular pathophysiology of feeding disorders, particularly in peripheral organs, is still largely unknown. A range of molecular factors encoded by appetite-regulating genes are already described to control feeding behaviour in the brain. However, the important role of the gastrointestinal tract in the regulation of appetite and feeding in connection to the brain has gained more attention in the recent years. An example of such inter-organ connection can be the signals mediated by leptin, a key regulator of body weight, food intake and metabolism, with conserved anorexigenic effects in vertebrates. Leptin signals functions through its receptor (lepr) in multiple organs, including the brain and the gastrointestinal tract. So far, the regulatory connections between leptin signal and other appetite-regulating genes remain unclear, particularly in the gastrointestinal system. In this study, we used a zebrafish mutant with impaired function of leptin receptor to explore gut expression patterns of appetite-regulating genes, under different feeding conditions (normal feeding, 7-day fasting, 2 and 6-hours refeeding). We provide evidence that most appetite-regulating genes are expressed in the zebrafish gut. On one hand, we did not observed significant differences in the expression of orexigenic genes (except for hcrt) after changes in the feeding condition. On the other hand, we found 8 anorexigenic genes in wild-types (cart2, cart3, dbi, oxt, nmu, nucb2a, pacap and pomc), as well as 4 genes in lepr mutants (cart3, kiss1, kiss1r and nucb2a), to be differentially expressed in the zebrafish gut after changes in feeding conditions. Most of these genes also showed significant differences in their expression between wild-type and lepr mutant. Finally, we observed that impaired leptin signalling influences potential regulatory connections between anorexigenic genes in zebrafish gut. Altogether, these transcriptional changes propose a potential role of leptin signal in the regulation of feeding through changes in expression of certain anorexigenic genes in the gastrointestinal tract of zebrafish.
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Shaheen A. Can ketone bodies inactivate coronavirus spike protein? The potential of biocidal agents against SARS-CoV-2. Bioessays 2021; 43:e2000312. [PMID: 33857328 PMCID: PMC8250295 DOI: 10.1002/bies.202000312] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 03/19/2021] [Accepted: 03/24/2021] [Indexed: 12/15/2022]
Abstract
Biocidal agents such as formaldehyde and glutaraldehyde are able to inactivate several coronaviruses including SARS-CoV-2. In this article, an insight into one mechanism for the inactivation of these viruses by those two agents is presented, based on analysis of previous observations during electron microscopic examination of several members of the orthocoronavirinae subfamily, including the new virus SARS-CoV-2. This inactivation is proposed to occur through Schiff base reaction-induced conformational changes in the spike glycoprotein leading to its disruption or breakage, which can prevent binding of the virus to cellular receptors. Also, a new prophylactic and therapeutic measure against SARS-CoV-2 using acetoacetate is proposed, suggesting that it could similarly break the viral spike through Schiff base reaction with lysines of the spike protein. This measure needs to be confirmed experimentally before consideration. In addition, a new line of research is proposed to help find a broad-spectrum antivirus against several members of this subfamily.
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Affiliation(s)
- Alaa Shaheen
- Shiwah Al Gharbeyah Medical Center, Aga, Dakahlia, Egypt
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3
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Abstract
Recent advances in proteomics allow the accurate measurement of abundances for thousands of proteins and phosphoproteins from multiple samples in parallel. Therefore, for the first time, we have the opportunity to measure the proteomic profiles of thousands of patient samples or disease model cell lines in a systematic way, to identify the precise underlying molecular mechanism and discover personalized biomarkers, networks and treatments. Here, we review examples of successful use of proteomics and phosphoproteomics data sets in as well as their integration other omics data sets with the aim of precision medicine. We will discuss the bioinformatics challenges posed by the generation, analysis and integration of such large data sets and present potential reasons why proteomics profiling and biomarkers are not currently widely used in the clinical setting. We will finally discuss ways to contribute to the better use of proteomics data in precision medicine and the clinical setting.
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Affiliation(s)
- Girolamo Giudice
- European Molecular Biology Laboratory European Bioinformatics Institute
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4
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Cuevas-Fernández B, Fuentes-Almagro C, Peragón J. Proteomics Analysis Reveals the Implications of Cytoskeleton and Mitochondria in the Response of the Rat Brain to Starvation. Nutrients 2019; 11:nu11020219. [PMID: 30678170 PMCID: PMC6412446 DOI: 10.3390/nu11020219] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/17/2019] [Accepted: 01/18/2019] [Indexed: 12/20/2022] Open
Abstract
Long-term starvation provokes a metabolic response in the brain to adapt to the lack of nutrient intake and to maintain the physiology of this organ. Here, we study the changes in the global proteomic profile of the rat brain after a seven-day period of food deprivation, to further our understanding of the biochemical and cellular mechanisms underlying the situations without food. We have used two-dimensional electrophoresis followed by mass spectrometry (2D-MS) in order to identify proteins differentially expressed during prolonged food deprivation. After the comparison of the protein profiles, 22 brain proteins were found with altered expression. Analysis by peptide mass fingerprinting and MS/MS (matrix-assisted laser desorption-ionization-time of flight mass spectrometer, MALDI-TOF/TOF) enabled the identification of 14 proteins differentially expressed that were divided into 3 categories: (1) energy catabolism and mitochondrial proteins; (2) chaperone proteins; and (3) cytoskeleton, exocytosis, and calcium. Changes in the expression of six proteins, identified by the 2D-MS proteomics procedure, were corroborated by a nanoliquid chromatography-mass spectrometry proteomics procedure (nLC-MS). Our results show that long-term starvation compromises essential functions of the brain related with energetic metabolism, synapsis, and the transmission of nervous impulse.
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Affiliation(s)
- Beatriz Cuevas-Fernández
- Biochemistry and Molecular Biology Section, Department of Experimental Biology, University of Jaén, Campus Las Lagunillas, 23071 Jaén, Spain.
| | - Carlos Fuentes-Almagro
- Proteomics Unit, Central Service of Support to Research, University of Córdoba (SCAI), 14014 Córdoba, Spain.
| | - Juan Peragón
- Biochemistry and Molecular Biology Section, Department of Experimental Biology, University of Jaén, Campus Las Lagunillas, 23071 Jaén, Spain.
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Kononikhin AS, Starodubtseva NL, Pastushkova LK, Kashirina DN, Fedorchenko KY, Brhozovsky AG, Popov IA, Larina IM, Nikolaev EN. Spaceflight induced changes in the human proteome. Expert Rev Proteomics 2016; 14:15-29. [PMID: 27817217 DOI: 10.1080/14789450.2017.1258307] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
INTRODUCTION Spaceflight is one of the most extreme conditions encountered by humans: Individuals are exposed to radiation, microgravity, hypodynamia, and will experience isolation. A better understanding of the molecular processes induced by these factors may allow us to develop personalized countermeasures to minimize risks to astronauts. Areas covered: This review is a summary of literature searches from PubMed, NASA, Roskosmos and the authors' research experiences and opinions. The review covers the available proteomic data on the effects of spaceflight factors on the human body, including both real space missions and ground-based model experiments. Expert commentary: Overall, the authors believe that the present background, methodology and equipment improvements will enhance spaceflight safety and support accumulation of new knowledge on how organisms adapt to extreme conditions.
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Affiliation(s)
- Alexey S Kononikhin
- a Institute of Biomedical Problems - Russian Federation State Scientific Research Center, Laboratory of proteomics , Russian Academy of Sciences , Moscow , Russia.,b Moscow Institute of Physics and Technology , Laboratory of ion and molecular physics , Moscow , Russia.,d V.L. Talrose Institute for Energy Problems of Chemical Physics , Laboratory of ion and molecular physics, Russian Academy of Sciences , Moscow , Russia
| | - Natalia L Starodubtseva
- b Moscow Institute of Physics and Technology , Laboratory of ion and molecular physics , Moscow , Russia.,c V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology , Laboratory of proteomics and metabolomics, Ministry of Healthcare of the Russian Federation , Moscow , Russia.,d V.L. Talrose Institute for Energy Problems of Chemical Physics , Laboratory of ion and molecular physics, Russian Academy of Sciences , Moscow , Russia
| | - Lyudmila Kh Pastushkova
- a Institute of Biomedical Problems - Russian Federation State Scientific Research Center, Laboratory of proteomics , Russian Academy of Sciences , Moscow , Russia
| | - Daria N Kashirina
- a Institute of Biomedical Problems - Russian Federation State Scientific Research Center, Laboratory of proteomics , Russian Academy of Sciences , Moscow , Russia
| | | | - Alexander G Brhozovsky
- a Institute of Biomedical Problems - Russian Federation State Scientific Research Center, Laboratory of proteomics , Russian Academy of Sciences , Moscow , Russia
| | - Igor A Popov
- b Moscow Institute of Physics and Technology , Laboratory of ion and molecular physics , Moscow , Russia.,c V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology , Laboratory of proteomics and metabolomics, Ministry of Healthcare of the Russian Federation , Moscow , Russia.,d V.L. Talrose Institute for Energy Problems of Chemical Physics , Laboratory of ion and molecular physics, Russian Academy of Sciences , Moscow , Russia
| | - Irina M Larina
- a Institute of Biomedical Problems - Russian Federation State Scientific Research Center, Laboratory of proteomics , Russian Academy of Sciences , Moscow , Russia
| | - Evgeny N Nikolaev
- d V.L. Talrose Institute for Energy Problems of Chemical Physics , Laboratory of ion and molecular physics, Russian Academy of Sciences , Moscow , Russia.,e Emanuel Institute for Biochemical Physics , Russian Academy of Sciences , Moscow , Russia.,f Skolkovo Institute of Science and Technology, Space Cluster , Skolkovo , Russia
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6
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Koo SJ, Spratt HM, Soman KV, Stafford S, Gupta S, Petersen JR, Zago MP, Kuyumcu-Martinez MN, Brasier AR, Wiktorowicz JE, Garg NJ. S-Nitrosylation Proteome Profile of Peripheral Blood Mononuclear Cells in Human Heart Failure. Int J Proteomics 2016; 2016:1384523. [PMID: 27635260 PMCID: PMC5007369 DOI: 10.1155/2016/1384523] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 04/07/2016] [Accepted: 05/16/2016] [Indexed: 01/05/2023]
Abstract
Nitric oxide (NO) protects the heart against ischemic injury; however, NO- and superoxide-dependent S-nitrosylation (S-NO) of cysteines can affect function of target proteins and play a role in disease outcome. We employed 2D-GE with thiol-labeling FL-maleimide dye and MALDI-TOF MS/MS to capture the quantitative changes in abundance and S-NO proteome of HF patients (versus healthy controls, n = 30/group). We identified 93 differentially abundant (59-increased/34-decreased) and 111 S-NO-modified (63-increased/48-decreased) protein spots, respectively, in HF subjects (versus controls, fold-change | ≥1.5|, p ≤ 0.05). Ingenuity pathway analysis of proteome datasets suggested that the pathways involved in phagocytes' migration, free radical production, and cell death were activated and fatty acid metabolism was decreased in HF subjects. Multivariate adaptive regression splines modeling of datasets identified a panel of proteins that will provide >90% prediction success in classifying HF subjects. Proteomic profiling identified ATP-synthase, thrombospondin-1 (THBS1), and vinculin (VCL) as top differentially abundant and S-NO-modified proteins, and these proteins were verified by Western blotting and ELISA in different set of HF subjects. We conclude that differential abundance and S-NO modification of proteins serve as a mechanism in regulating cell viability and free radical production, and THBS1 and VCL evaluation will potentially be useful in the prediction of heart failure.
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Affiliation(s)
- Sue-jie Koo
- Department of Pathology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
| | - Heidi M. Spratt
- Department Preventive Medicine and Community Health, UTMB, Galveston, TX 77555, USA
- Institute for Translational Sciences, UTMB, Galveston, TX 77555, USA
| | - Kizhake V. Soman
- Department of Biochemistry and Molecular Biology, Sealy Center of Molecular Medicine, UTMB, Galveston TX 77555, USA
| | - Susan Stafford
- Department of Biochemistry and Molecular Biology, Sealy Center of Molecular Medicine, UTMB, Galveston TX 77555, USA
| | - Shivali Gupta
- Department of Microbiology and Immunology, UTMB, Galveston, TX 77555, USA
| | - John R. Petersen
- Department of Pathology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
| | - Maria P. Zago
- Instituto de Patología Experimental, CONICET-UNSa, 4400 Salta, Argentina
| | - Muge N. Kuyumcu-Martinez
- Department of Biochemistry and Molecular Biology, Sealy Center of Molecular Medicine, UTMB, Galveston TX 77555, USA
| | - Allan R. Brasier
- Institute for Translational Sciences, UTMB, Galveston, TX 77555, USA
- Department of Internal Medicine-Endocrinology, UTMB, Galveston, TX 77555, USA
| | - John E. Wiktorowicz
- Institute for Translational Sciences, UTMB, Galveston, TX 77555, USA
- Department of Biochemistry and Molecular Biology, Sealy Center of Molecular Medicine, UTMB, Galveston TX 77555, USA
- Institute for Human Infections and Immunity, UTMB, Galveston, TX 77555, USA
| | - Nisha Jain Garg
- Department of Pathology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
- Department of Microbiology and Immunology, UTMB, Galveston, TX 77555, USA
- Institute for Human Infections and Immunity, UTMB, Galveston, TX 77555, USA
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7
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Nishad S., Ghosh A. Dynamic changes in the proteome of human peripheral blood mononuclear cells with low dose ionizing radiation. Mutation Research/Genetic Toxicology and Environmental Mutagenesis 2016; 797:9-20. [DOI: 10.1016/j.mrgentox.2016.01.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 12/30/2015] [Accepted: 01/05/2016] [Indexed: 02/07/2023]
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Marengo E, Robotti E, Demartini M. The Use of Legendre and Zernike Moment Functions for the Comparison of 2-D PAGE Maps. Methods Mol Biol 2016; 1384:271-288. [PMID: 26611420 DOI: 10.1007/978-1-4939-3255-9_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The comparison of 2-D maps is not trivial, the main difficulties being the high complexity of the sample and the large experimental variability characterizing 2-D gel electrophoresis. The comparison of maps from control and treated samples is usually performed by specific software, providing the so-called spot volume dataset where each spot of a specific map is matched to its analogous in other maps, and they are described by their optical density, which is supposed to be related to the underlying protein amount. Here, a different approach is presented, based on the direct comparison of 2-D map images: each map is decomposed in terms of moment functions, successively applying the multivariate tools usually adopted in image analysis problems. The moments calculated are then treated with multivariate classification techniques. Here, two types of moment functions are presented (Legendre and Zernike moments), while linear discriminant analysis and partial least squares discriminant analysis are exploited as classification tools to provide the classification of the samples. The procedure is applied to a sample dataset to prove its effectiveness.
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Affiliation(s)
- Emilio Marengo
- Department of Sciences and Technological Innovation, University of Piedmont Orientale, Viale Michel 11, 15121, Alessandria, Italy.
| | - Elisa Robotti
- Department of Sciences and Technological Innovation, University of Piedmont Orientale, Viale Michel 11, 15121, Alessandria, Italy.
| | - Marco Demartini
- Department of Sciences and Technological Innovation, University of Piedmont Orientale, Viale Michel 11, 15121, Alessandria, Italy
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9
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Abstract
Biomarkers are the measurable changes associated with physiological or pathophysiological processes. Urine, unlike blood, lacks mechanisms for maintaining homeostasis: it is therefore an ideal source of biomarkers that can reflect systemic changes. Urinary proteome and metabolome have been studied for their diagnostic capabilities, ability to monitor disease and prognostic utility. In this review, the effects of common physiological conditions such as gender, age, diet, daily rhythms, exercise, hormone status, lifestyle and extreme environments on human urine are discussed. These effects should be considered when biomarker studies of diseases are conducted. More importantly, if physiological changes can be reflected in urine, we have reason to expect that urine will become widely used to detect small and early changes in pathological and/or pharmacological conditions.
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Affiliation(s)
- Jianqiang Wu
- a 1 Department of Pathophysiology, National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Youhe Gao
- a 1 Department of Pathophysiology, National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China.,b 2 Department of Biochemistry and Molecular Biology, Beijing Normal University, Gene Engineering and Biotechnology Beijing Key Laboratory, Beijing, 100875, China
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10
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Wojczynski MK, Parnell LD, Pollin TI, Lai CQ, Feitosa MF, O'Connell JR, Frazier-Wood AC, Gibson Q, Aslibekyan S, Ryan KA, Province MA, Tiwari HK, Ordovas JM, Shuldiner AR, Arnett DK, Borecki IB. Genome-wide association study of triglyceride response to a high-fat meal among participants of the NHLBI Genetics of Lipid Lowering Drugs and Diet Network (GOLDN). Metabolism 2015; 64:1359-71. [PMID: 26256467 PMCID: PMC4573277 DOI: 10.1016/j.metabol.2015.07.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [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: 12/04/2014] [Revised: 05/19/2015] [Accepted: 07/01/2015] [Indexed: 12/21/2022]
Abstract
OBJECTIVE The triglyceride (TG) response to a high-fat meal (postprandial lipemia, PPL) affects cardiovascular disease risk and is influenced by genes and environment. Genes involved in lipid metabolism have dominated genetic studies of PPL TG response. We sought to elucidate common genetic variants through a genome-wide association (GWA) study in the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN). METHODS The GOLDN GWAS discovery sample consisted of 872 participants within families of European ancestry. Genotypes for 2,543,887 variants were measured or imputed from HapMap. Replication of our top results was performed in the Heredity and Phenotype Intervention (HAPI) Heart Study (n = 843). PPL TG response phenotypes were constructed from plasma TG measured at baseline (fasting, 0 hour), 3.5 and 6 hours after a high-fat meal, using a random coefficient regression model. Association analyses were adjusted for covariates and principal components, as necessary, in a linear mixed model using the kinship matrix; additional models further adjusted for fasting TG were also performed. Meta-analysis of the discovery and replication studies (n = 1715) was performed on the top SNPs from GOLDN. RESULTS GOLDN revealed 111 suggestive (p < 1E-05) associations, with two SNPs meeting GWA significance level (p < 5E-08). Of the two significant SNPs, rs964184 demonstrated evidence of replication (p = 1.20E-03) in the HAPI Heart Study and in a joint analysis, was GWA significant (p = 1.26E-09). Rs964184 has been associated with fasting lipids (TG and HDL) and is near ZPR1 (formerly ZNF259), close to the APOA1/C3/A4/A5 cluster. This association was attenuated upon additional adjustment for fasting TG. CONCLUSION This is the first report of a genome-wide significant association with replication for a novel phenotype, namely PPL TG response. Future investigation into response phenotypes is warranted using pathway analyses, or newer genetic technologies such as metabolomics.
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Affiliation(s)
- Mary K Wojczynski
- Department of Genetics, Washington University School of Medicine, St. Louis, MO.
| | - Laurence D Parnell
- Nutrition and Genomics Laboratory, Jean Mayer-US Department of Agriculture Human Nutrition Research Center on Aging, Tufts University, Boston, MA
| | - Toni I Pollin
- Program in Personalized and Genomic Medicine, and Departments of Medicine and Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD
| | - Chao Q Lai
- Nutrition and Genomics Laboratory, Jean Mayer-US Department of Agriculture Human Nutrition Research Center on Aging, Tufts University, Boston, MA
| | - Mary F Feitosa
- Department of Genetics, Washington University School of Medicine, St. Louis, MO
| | - Jeff R O'Connell
- Program in Personalized and Genomic Medicine, and Departments of Medicine and Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD
| | | | - Quince Gibson
- Program in Personalized and Genomic Medicine, and Departments of Medicine and Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD
| | - Stella Aslibekyan
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL
| | - Kathy A Ryan
- Program in Personalized and Genomic Medicine, and Departments of Medicine and Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD
| | - Michael A Province
- Department of Genetics, Washington University School of Medicine, St. Louis, MO
| | - Hemant K Tiwari
- Section on Statistical Genetics, Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL
| | - Jose M Ordovas
- Nutrition and Genomics Laboratory, Jean Mayer-US Department of Agriculture Human Nutrition Research Center on Aging, Tufts University, Boston, MA
| | - Alan R Shuldiner
- Program in Personalized and Genomic Medicine, and Departments of Medicine and Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD; Geriatric Research and Education Clinical Center, Veterans Administration Medical Center, Baltimore, MD
| | - Donna K Arnett
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL
| | - Ingrid B Borecki
- Department of Genetics, Washington University School of Medicine, St. Louis, MO
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Andreeva AM, Lamas NE, Serebryakova MV, Ryabtseva IP, Bolshakov VV. Reorganization of low-molecular-weight fraction of plasma proteins in the annual cycle of cyprinidae. Biochemistry (Mosc) 2015; 80:208-18. [PMID: 25756535 DOI: 10.1134/s0006297915020078] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Reorganization of the low-molecular-weight fraction of cyprinid plasma was analyzed using various electrophoretic techniques (disc electrophoresis, electrophoresis in polyacrylamide concentration gradient, in polyacrylamide with urea, and in SDS-polyacrylamide). The study revealed coordinated changes in the low-molecular-weight protein fractions with seasonal dynamics and related reproductive rhythms of fishes. We used cultured species of the Cyprinidae family with sequenced genomes for the detection of these interrelations in fresh-water and anadromous cyprinid species. The common features of organization of fish low-molecular-weight plasma protein fractions made it possible to make reliable identification of their proteins. MALDI mass-spectrometry analysis revealed the presence of the same proteins (hemopexin, apolipoproteins, and serpins) in the low-molecular-weight plasma fraction in wild species and cultured species with sequenced genomes (carp, zebrafish). It is found that the proteins of the first two classes are organized as complexes made of protein oligomers. Stoichiometry of these complexes changes in concordance with the seasonal and reproductive rhythms.
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Affiliation(s)
- A M Andreeva
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, 152742, Russia.
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12
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Elliott RM, de Roos B, Duthie SJ, Bouwman FG, Rubio-Aliaga I, Crosley LK, Mayer C, Polley AC, Heim C, Coort SL, Evelo CT, Mulholland F, Daniel H, Mariman EC, Johnson IT. Transcriptome analysis of peripheral blood mononuclear cells in human subjects following a 36 h fast provides evidence of effects on genes regulating inflammation, apoptosis and energy metabolism. Genes Nutr 2014; 9:432. [PMID: 25260660 DOI: 10.1007/s12263-014-0432-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 09/20/2014] [Indexed: 12/29/2022]
Abstract
There is growing interest in the potential health benefits of diets that involve regular periods of fasting. While animal studies have provided compelling evidence that feeding patterns such as alternate-day fasting can increase longevity and reduce incidence of many chronic diseases, the evidence from human studies is much more limited and equivocal. Additionally, although several candidate processes have been proposed to contribute to the health benefits observed in animals, the precise molecular mechanisms responsible remain to be elucidated. The study described here examined the effects of an extended fast on gene transcript profiles in peripheral blood mononuclear cells from ten apparently healthy subjects, comparing transcript profiles after an overnight fast, sampled on four occasions at weekly intervals, with those observed on a single occasion after a further 24 h of fasting. Analysis of the overnight fasted data revealed marked inter-individual differences, some of which were associated with parameters such as gender and subject body mass. For example, a striking positive association between body mass index and the expression of genes regulated by type 1 interferon was observed. Relatively subtle changes were observed following the extended fast. Nonetheless, the pattern of changes was consistent with stimulation of fatty acid oxidation, alterations in cell cycling and apoptosis and decreased expression of key pro-inflammatory genes. Stimulation of fatty acid oxidation is an expected response, most likely in all tissues, to fasting. The other processes highlighted provide indications of potential mechanisms that could contribute to the putative beneficial effects of intermittent fasting in humans.
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Affiliation(s)
- R M Elliott
- Institute of Food Research, Colney Lane, Norwich, UK,
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13
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Abstract
Current toxicology studies frequently lack measurements at molecular resolution to enable a more mechanism-based and predictive toxicological assessment. Recently, a systems toxicology assessment framework has been proposed, which combines conventional toxicological assessment strategies with system-wide measurement methods and computational analysis approaches from the field of systems biology. Proteomic measurements are an integral component of this integrative strategy because protein alterations closely mirror biological effects, such as biological stress responses or global tissue alterations. Here, we provide an overview of the technical foundations and highlight select applications of proteomics for systems toxicology studies. With a focus on mass spectrometry-based proteomics, we summarize the experimental methods for quantitative proteomics and describe the computational approaches used to derive biological/mechanistic insights from these datasets. To illustrate how proteomics has been successfully employed to address mechanistic questions in toxicology, we summarized several case studies. Overall, we provide the technical and conceptual foundation for the integration of proteomic measurements in a more comprehensive systems toxicology assessment framework. We conclude that, owing to the critical importance of protein-level measurements and recent technological advances, proteomics will be an integral part of integrative systems toxicology approaches in the future.
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Abstract
AbstractLung cancer is one of the most common cancers in terms of both incidence and mortality.The major reasons for the increasing number of deaths from lung cancer are late detection and lack of effective therapies. To improve our understanding of lung cancer biology, there is urgent need for blood-based, non-invasive molecular tests to assist in its detection in a cost-effective manner at an early stage when curative interventions are still possible. Recent advances in proteomic technology have provided extensive, high throughput analytical tools for identification, characterization and functional studies of proteomes. Changes in protein expression patterns in response to stimuli can serve as indicators or biomarkers of biological and pathological processes as well as physiological and pharmacological responses to drug treatment, thus aiding in early diagnosis and prognosis of disease. However, only a few biomarkers have been approved by the FDA to date for screening and diagnostic purposes. This review provides a brief overview of currently available proteomic techniques, their applications and limitations and the current state of knowledge about important serum biomarkers in lung cancer and their potential value as prognostic and diagnostic tools.
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Chow BA, Donahue SW, Vaughan MR, McConkey B, Vijayan MM. Serum immune-related proteins are differentially expressed during hibernation in the American black bear. PLoS One 2013; 8:e66119. [PMID: 23825529 PMCID: PMC3692520 DOI: 10.1371/journal.pone.0066119] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [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: 11/21/2012] [Accepted: 05/01/2013] [Indexed: 11/23/2022] Open
Abstract
Hibernation is an adaptation to conserve energy in the face of extreme environmental conditions and low food availability that has risen in several animal phyla. This phenomenon is characterized by reduced metabolic rate (∼25% of the active basal metabolic rate in hibernating bears) and energy demand, while other physiological adjustments are far from clear. The profiling of the serum proteome of the American black bear (Ursus americanus) may reveal specific proteins that are differentially modulated by hibernation, and provide insight into the remarkable physiological adaptations that characterize ursid hibernation. In this study, we used differential gel electrophoresis (DIGE) analysis, liquid chromatography coupled to tandem mass spectrometry, and subsequent MASCOT analysis of the mass spectra to identify candidate proteins that are differentially expressed during hibernation in captive black bears. Seventy serum proteins were identified as changing by ±1.5 fold or more, out of which 34 proteins increased expression during hibernation. The majority of identified proteins are involved in immune system processes. These included α2-macroglobulin, complement components C1s and C4, immunoglobulin μ and J chains, clusterin, haptoglobin, C4b binding protein, kininogen 1, α2-HS-glycoprotein, and apoplipoproteins A-I and A-IV. Differential expression of a subset of these proteins identified by proteomic analysis was also confirmed by immunodetection. We propose that the observed serum protein changes contribute to the maintenance of the hibernation phenotype and health, including increased capacities for bone maintenance and wound healing during hibernation in bears.
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Affiliation(s)
- Brian A. Chow
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Seth W. Donahue
- Department of Mechanical Engineering, Colorado State University, Fort Collins, Colorado, United States of America
| | - Michael R. Vaughan
- Department of Fish and Wildlife Conservation, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Brendan McConkey
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
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Abstract
The major factor in the morbidity and mortality of cancer patients is metastasis. There exists a relative lack of specific therapeutic approaches to control metastasis, and this is a fruitful area for investigation. A healthy diet and lifestyle not only can inhibit tumorigenesis but also can have a major impact on cancer progression and survival. Many chemicals found in edible plants are known to inhibit metastatic progression of cancer. While the mechanisms underlying antimetastatic activity of some phytochemicals are being delineated, the impact of diet, dietary components, and various phytochemicals on metastasis suppressor genes is underexplored. Epigenetic regulation of metastasis suppressor genes promises to be a potentially important mechanism by which dietary components can impact cancer metastasis since many dietary constituents are known to modulate gene expression. The review addresses this area of research as well as the current state of knowledge regarding the impact of diet, dietary components, and phytochemicals on metastasis suppressor genes.
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Wen JJ, Zago MP, Nuñez S, Gupta S, Burgos FN, Garg NJ. Serum proteomic signature of human chagasic patients for the identification of novel potential protein biomarkers of disease. Mol Cell Proteomics 2012; 11:435-52. [PMID: 22543060 DOI: 10.1074/mcp.m112.017640] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chagas disease is initiated upon infection by Trypanosoma cruzi. Among the health consequences is a decline in heart function, and the pathophysiological mechanisms underlying this manifestation are not well understood. To explore the possible mechanisms, we employed IgY LC10 affinity chromatography in conjunction with ProteomeLab PF2D and two-dimensional gel electrophoresis to resolve the proteome signature of high and low abundance serum proteins in chagasic patients. MALDI-TOF MS/MS analysis yielded 80 and 14 differentially expressed proteins associated with cardiomyopathy of chagasic and other etiologies, respectively. The extent of oxidative stress-induced carbonyl modifications of the differentially expressed proteins (n = 26) was increased and coupled with a depression of antioxidant proteins. Functional annotation of the top networks developed by ingenuity pathway analysis of proteome database identified dysregulation of inflammation/acute phase response signaling and lipid metabolism relevant to production of prostaglandins and arachidonic acid in chagasic patients. Overlay of the major networks identified prothrombin and plasminogen at a nodal position with connectivity to proteome signature indicative of heart disease (i.e., thrombosis, angiogenesis, vasodilatation of blood vessels or the aorta, and increased permeability of blood vessel and endothelial tubes), and inflammatory responses (e.g., platelet aggregation, complement activation, and phagocyte activation and migration). The detection of cardiac proteins (myosin light chain 2 and myosin heavy chain 11) and increased levels of vinculin and plasminogen provided a comprehensive set of biomarkers of cardiac muscle injury and development of clinical Chagas disease in human patients. These results provide an impetus for biomarker validation in large cohorts of clinically characterized chagasic patients.
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Affiliation(s)
- Jian-Jun Wen
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas 77555-1070, USA
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Richards TJ, Kaminski N, Baribaud F, Flavin S, Brodmerkel C, Horowitz D, Li K, Choi J, Vuga LJ, Lindell KO, Klesen M, Zhang Y, Gibson KF. Peripheral blood proteins predict mortality in idiopathic pulmonary fibrosis. Am J Respir Crit Care Med 2012; 185:67-76. [PMID: 22016448 DOI: 10.1164/rccm.201101-0058oc] [Citation(s) in RCA: 267] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
RATIONALE Idiopathic pulmonary fibrosis (IPF) is a lethal lung disease of unknown etiology with a variable and unpredictable course. OBJECTIVES The aim of this study was to identify and validate plasma proteins that are predictive of outcome in IPF. METHODS Plasma samples were available for 241 patients with IPF (140 derivation and 101 validation). In the derivation cohort, concentrations of 92 proteins were analyzed using a multiplex bead-based immunoassay and concentrations of matrix metalloproteinase (MMP)-7, MMP-1, and surfactant protein D were assessed by ELISA. In the validation cohort concentrations of intercellular adhesion molecule (ICAM)-1, IL-8, and vascular cell adhesion molecule (VCAM)-1 were assessed by bead-based multiplex assay, and S100A12 and MMP-7 by ELISA. Associations of biomarkers with mortality, transplant-free survival, and disease progression were tested in the derivation and validation cohorts using nonparametric methods of survival analysis and the Cox proportional hazards model, and an integrated risk prediction score was derived and tested. MEASUREMENTS AND MAIN RESULTS High concentrations of MMP-7, ICAM-1, IL-8, VCAM-1, and S100A12 predicted poor overall survival, poor transplant-free survival, and poor progression-free survival in the derivation cohort. In the independent validation cohort high concentrations of all five were predictive of poor transplant-free survival; MMP-7, ICAM-1, and IL-8 of overall survival; and ICAM-1 of poor progression-free survival. The personal clinical and molecular mortality prediction index derived in the derivation cohort was highly predictive of mortality in the validation cohort. CONCLUSIONS Our results suggest that plasma proteins should be evaluated as a tool for prognosis determination in prioritization of patients for lung transplantation and stratification in drug studies.
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Affiliation(s)
- Thomas J Richards
- The Dorothy P. & Richard P. Simmons Center for Interstitial Lung Disease, Department of Medicine, University of Pittsburgh Medical Center, NW 628 MUH, 3459 5th Avenue, Pittsburgh, PA 15261, USA
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Bron PA, van Baarlen P, Kleerebezem M. Emerging molecular insights into the interaction between probiotics and the host intestinal mucosa. Nat Rev Microbiol 2011; 10:66-78. [PMID: 22101918 DOI: 10.1038/nrmicro2690] [Citation(s) in RCA: 413] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Probiotic bacteria can modulate immune responses in the host gastrointestinal tract to promote health. The genomics era has provided novel opportunities for the discovery and characterization of bacterial probiotic effector molecules that elicit specific responses in the intestinal system. Furthermore, nutrigenomic analyses of the response to probiotics have unravelled the signalling and immune response pathways which are modulated by probiotic bacteria. Together, these genomic approaches and nutrigenomic analyses have identified several bacterial factors that are involved in modulation of the immune system and the mucosal barrier, and have revealed that a molecular 'bandwidth of human health' could represent a key determinant in an individual's physiological responsiveness to probiotics. These approaches may lead to improved stratification of consumers and to subpopulation-level probiotic supplementation to maintain or improve health, or to reduce the risk of disease.
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Affiliation(s)
- Peter A Bron
- Top Institute Food and Nutrition, Nieuwe Kanaal 9A, 6709 PA Wageningen, The Netherlands
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