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Chiang Morales MD, Chang CY, Le VL, Huang IT, Tsai IL, Shih HJ, Huang CJ. High-Fructose/High-Fat Diet Downregulates the Hepatic Mitochondrial Oxidative Phosphorylation Pathway in Mice Compared with High-Fat Diet Alone. Cells 2022; 11:3425. [PMID: 36359820 PMCID: PMC9656843 DOI: 10.3390/cells11213425] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/20/2022] [Accepted: 10/27/2022] [Indexed: 05/06/2024] Open
Abstract
Both high-fat diet (HFD) alone and high-fructose plus HFD (HFr/HFD) cause diet-induced non-alcoholic fatty liver disease in murine models. However, the mechanisms underlying their impacts on inducing different levels of liver injury are yet to be elucidated. This study employed a proteomic approach to elucidate further on this issue. Adult male C57BL/6J mice were allocated to the HFD or the HFr/HFD group. After feeding for 12 weeks, all mice were euthanized and samples were collected. The proteomic profiles in liver tissues were analyzed using liquid chromatography-tandem mass spectrometry followed by canonical pathway analysis. We demonstrated that the mitochondrial oxidative phosphorylation (OXPHOS) pathway was the most significantly downregulated canonical pathway in the HFr/HFD group when compared with the HFD group. Within the OXPHOS pathway, the HFr/HFD group demonstrated significant downregulation of complexes I and III and significant upregulation of complex IV when compared with the HFD group. Moreover, the HFr/HFD group had lower protein levels of NADH: ubiquinone oxidoreductase subunits S3, S6, A5, and A12 in complex I (p < 0.001, =0.03, <0.001, and <0.001, respectively), lower protein level of cytochrome C in complex III (p < 0.001), and higher protein level of cytochrome C oxidase subunit 2 in complex IV (p = 0.002), when compared with the HFD group. To summarize, we have demonstrated that the hepatic mitochondrial OXPHOS pathway is significantly downregulated in long-term HFr/HFD feeding when compared with long-term HFD feeding. These data support the concept that the hepatic mitochondrial OXPHOS pathway should be involved in mediating the effects of HFr/HFD on inducing more severe liver injury than HFD alone.
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Affiliation(s)
- Milton D. Chiang Morales
- International Ph.D. Program in Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
| | - Chao-Yuan Chang
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- Department of Medical Research, Wan Fang Hospital, Taipei Medical University, Taipei 116, Taiwan
- Integrative Research Center for Critical Care, Wan Fang Hospital, Taipei Medical University, Taipei 116, Taiwan
| | - Van Long Le
- International Ph.D. Program in Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- Department of Anesthesiology and Critical Care, Hue University of Medicine and Pharmacy, Hue City 52000, Vietnam
| | - I-Tao Huang
- Emergency Department, Redcliffe Hospital, Redcliffe, QLD 4020, Australia
- School of Public Health, Faculty of Medicine, University of Queensland, Herston, QLD 4006, Australia
| | - I-Lin Tsai
- Department of Biochemistry and Molecular Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
| | - Hung-Jen Shih
- Division of Urology, Department of Surgery, Changhua Christian Hospital, Changhua 500, Taiwan
- Department of Urology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
| | - Chun-Jen Huang
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- Integrative Research Center for Critical Care, Wan Fang Hospital, Taipei Medical University, Taipei 116, Taiwan
- Department of Anesthesiology, Wan Fang Hospital, Taipei Medical University, Taipei 116, Taiwan
- Department of Anesthesiology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
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2
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Guerrero L, Paradela A, Corrales FJ. Targeted Proteomics for Monitoring One-Carbon Metabolism in Liver Diseases. Metabolites 2022; 12:metabo12090779. [PMID: 36144184 PMCID: PMC9501948 DOI: 10.3390/metabo12090779] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
Liver diseases cause approximately 2 million deaths per year worldwide and had an increasing incidence during the last decade. Risk factors for liver diseases include alcohol consumption, obesity, diabetes, the intake of hepatotoxic substances like aflatoxin, viral infection, and genetic determinants. Liver cancer is the sixth most prevalent cancer and the third in mortality (second in males). The low survival rate (less than 20% in 5 years) is partially explained by the late diagnosis, which remarks the need for new early molecular biomarkers. One-carbon metabolism integrates folate and methionine cycles and participates in essential cell processes such as redox homeostasis maintenance and the regulation of methylation reactions through the production of intermediate metabolites such as cysteine and S-Adenosylmethionine. One-carbon metabolism has a tissue specific configuration, and in the liver, the participating enzymes are abundantly expressed—a requirement to maintain hepatocyte differentiation. Targeted proteomics studies have revealed significant differences in hepatocellular carcinoma and cirrhosis, suggesting that monitoring one-carbon metabolism enzymes can be useful for stratification of liver disease patients and to develop precision medicine strategies for their clinical management. Here, reprogramming of one-carbon metabolism in liver diseases is described and the role of mass spectrometry to follow-up these alterations is discussed.
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Affiliation(s)
- Laura Guerrero
- Centro Nacional de Biotecnología (CNB), CSIC. C/Darwin 3, 28049 Madrid, Spain
| | - Alberto Paradela
- Centro Nacional de Biotecnología (CNB), CSIC. C/Darwin 3, 28049 Madrid, Spain
| | - Fernando J. Corrales
- Centro Nacional de Biotecnología (CNB), CSIC. C/Darwin 3, 28049 Madrid, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-91-585-46-96
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3
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Kim SQ, Mohallem R, Franco J, Buhman KK, Kim KH, Aryal UK. Multi-Omics Approach Reveals Dysregulation of Protein Phosphorylation Correlated with Lipid Metabolism in Mouse Non-Alcoholic Fatty Liver. Cells 2022; 11:cells11071172. [PMID: 35406736 PMCID: PMC8997945 DOI: 10.3390/cells11071172] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/24/2022] [Accepted: 03/26/2022] [Indexed: 02/04/2023] Open
Abstract
Obesity caused by overnutrition is a major risk factor for non-alcoholic fatty liver disease (NAFLD). Several lipid intermediates such as fatty acids, glycerophospholipids and sphingolipids are implicated in NAFLD, but detailed characterization of lipids and their functional links to proteome and phosphoproteome remain to be elucidated. To characterize this complex molecular relationship, we used a multi-omics approach by conducting comparative proteomic, phoshoproteomic and lipidomic analyses of high fat (HFD) and low fat (LFD) diet fed mice livers. We quantified 2447 proteins and 1339 phosphoproteins containing 1650 class I phosphosites, of which 669 phosphosites were significantly different between HFD and LFD mice livers. We detected alterations of proteins associated with cellular metabolic processes such as small molecule catabolic process, monocarboxylic acid, long- and medium-chain fatty acid, and ketone body metabolic processes, and peroxisome organization. We observed a significant downregulation of protein phosphorylation in HFD fed mice liver in general. Untargeted lipidomics identified upregulation of triacylglycerols, glycerolipids and ether glycerophosphocholines and downregulation of glycerophospholipids, such as lysoglycerophospholipids, as well as ceramides and acylcarnitines. Analysis of differentially regulated phosphosites revealed phosphorylation dependent deregulation of insulin signaling as well as lipogenic and lipolytic pathways during HFD induced obesity. Thus, this study reveals a molecular connection between decreased protein phosphorylation and lipolysis, as well as lipid-mediated signaling in diet-induced obesity.
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Affiliation(s)
- Sora Q. Kim
- Department of Nutrition Science, Purdue University, West Lafayette, IN 47907, USA; (S.Q.K.); (K.K.B.)
| | - Rodrigo Mohallem
- Bindley Bioscience Center, Purdue Proteomics Facility, Purdue University, West Lafayette, IN 47907, USA; (R.M.); (J.F.)
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA
| | - Jackeline Franco
- Bindley Bioscience Center, Purdue Proteomics Facility, Purdue University, West Lafayette, IN 47907, USA; (R.M.); (J.F.)
| | - Kimberly K. Buhman
- Department of Nutrition Science, Purdue University, West Lafayette, IN 47907, USA; (S.Q.K.); (K.K.B.)
| | - Kee-Hong Kim
- Department of Food Science, Purdue University, West Lafayette, IN 47907, USA;
| | - Uma K. Aryal
- Bindley Bioscience Center, Purdue Proteomics Facility, Purdue University, West Lafayette, IN 47907, USA; (R.M.); (J.F.)
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA
- Correspondence: ; Tel.: +1-765-494-4960
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4
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Li T, Hentschel A, Ahrends R. Analytical comparison of absolute quantification strategies to investigate the Insulin signaling pathway in fat cells. Proteomics 2021; 22:e2100136. [PMID: 34964541 DOI: 10.1002/pmic.202100136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/08/2022]
Abstract
So far, mass spectrometry based targeted proteomics is the most sensitive approach to answer and address specific biological questions in an accurate and quantitative fashion. However, the data analysis design used for such quantification varies in the field leading to discrepancies in the reported values. In this study, different quantification strategies based on calibration curves were evaluated and compared. The best accuracy and coefficient of variation was achieved by ratio to ratio calibration curves. We applied the ratio to ratio quantification approach to analyze very low abundant insulin signaling proteins such as PIK3RA (0.10-0.93 fmol/μg), AKT1 (0.1-0.39 fmol/μg) and the Insulin receptor (0.22 -2.62 fmol/μg) in a fat cell model and demonstrated the adaptation of this pathway at different states of insulin sensitivity. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Tingting Li
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e. V., Otto-Hahn-Straße 6b, Dortmund, 44227, Germany
| | - Andreas Hentschel
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e. V., Otto-Hahn-Straße 6b, Dortmund, 44227, Germany
| | - Robert Ahrends
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e. V., Otto-Hahn-Straße 6b, Dortmund, 44227, Germany.,Department of Analytical Chemistry, University of Vienna, Währinger Straße 38, Vienna, 1090, Austria
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5
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Pinterić M, Podgorski II, Popović Hadžija M, Tartaro Bujak I, Tadijan A, Balog T, Sobočanec S. Chronic High Fat Diet Intake Impairs Hepatic Metabolic Parameters in Ovariectomized Sirt3 KO Mice. Int J Mol Sci 2021; 22:ijms22084277. [PMID: 33924115 PMCID: PMC8074326 DOI: 10.3390/ijms22084277] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 12/12/2022] Open
Abstract
High fat diet (HFD) is an important factor in the development of metabolic diseases, with liver as metabolic center being highly exposed to its influence. However, the effect of HFD-induced metabolic stress with respect to ovary hormone depletion and sirtuin 3 (Sirt3) is not clear. Here we investigated the effect of Sirt3 in liver of ovariectomized and sham female mice upon 10 weeks of feeding with standard-fat diet (SFD) or HFD. Liver was examined by Folch, gas chromatography and lipid hydroperoxide analysis, histology and oil red staining, RT-PCR, Western blot, antioxidative enzyme and oxygen consumption analyses. In SFD-fed WT mice, ovariectomy increased Sirt3 and fatty acids synthesis, maintained mitochondrial function, and decreased levels of lipid hydroperoxides. Combination of ovariectomy and Sirt3 depletion reduced pparα, Scd-1 ratio, MUFA proportions, CII-driven respiration, and increased lipid damage. HFD compromised CII-driven respiration and activated peroxisomal ROS scavenging enzyme catalase in sham mice, whereas in combination with ovariectomy and Sirt3 depletion, increased body weight gain, expression of NAFLD- and oxidative stress-inducing genes, and impaired response of antioxidative system. Overall, this study provides evidence that protection against harmful effects of HFD in female mice is attributed to the combined effect of female sex hormones and Sirt3, thus contributing to preclinical research on possible sex-related therapeutic agents for metabolic syndrome and associated diseases.
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Affiliation(s)
- Marija Pinterić
- Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (M.P.); (I.I.P.); (M.P.H.); (A.T.); (T.B.)
| | - Iva I. Podgorski
- Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (M.P.); (I.I.P.); (M.P.H.); (A.T.); (T.B.)
| | - Marijana Popović Hadžija
- Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (M.P.); (I.I.P.); (M.P.H.); (A.T.); (T.B.)
| | - Ivana Tartaro Bujak
- Division of Materials Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia;
| | - Ana Tadijan
- Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (M.P.); (I.I.P.); (M.P.H.); (A.T.); (T.B.)
| | - Tihomir Balog
- Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (M.P.); (I.I.P.); (M.P.H.); (A.T.); (T.B.)
| | - Sandra Sobočanec
- Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (M.P.); (I.I.P.); (M.P.H.); (A.T.); (T.B.)
- Correspondence: ; Tel.: +385-1-4561-172
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6
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Zembroski AS, Buhman KK, Aryal UK. Proteome and phosphoproteome characterization of liver in the postprandial state from diet-induced obese and lean mice. J Proteomics 2020; 232:104072. [PMID: 33309929 DOI: 10.1016/j.jprot.2020.104072] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/30/2020] [Accepted: 11/30/2020] [Indexed: 02/07/2023]
Abstract
A metabolic consequence of obesity is hepatosteatosis, which can develop into more serious diseases in the non-alcoholic fatty liver disease (NAFLD) spectrum. The goal of this study was to identify the protein signature of liver in the postprandial state in obesity compared to leanness. The postprandial state is of interest due to the central role of the liver in regulating macronutrient and energy homeostasis during the fed-fast cycle and lack of previously reported controlled studies in the postprandial state. Therefore, we assessed the proteome and phosphoproteome of liver in the postprandial state from diet-induced obese (DIO) and lean mice using untargeted LC-MS/MS analysis. We identified significant alterations in the levels of proteins involved in fatty acid oxidation, activation, and transport, as well as proteins involved in energy metabolism including ketogenesis, tricarboxylic acid cycle, and electron transport chain in liver of DIO compared to lean mice. Additionally, phosphorylated proteins in liver of DIO and lean mice reflect possible regulatory mechanisms controlling fatty acid metabolism and gene expression that may contribute to hepatic metabolic alterations in obesity. Our data indicates PPARα-mediated transcriptional regulation of lipid metabolism and adaptation to hepatic lipid overload. The results of this study expand our knowledge of the molecular changes that occur in liver in the postprandial state in obesity compared to leanness. SIGNIFICANCE: Proteome and phosphoproteome studies of liver in a controlled postprandial state in obesity and leanness are lacking; however, this information is crucial to understanding how obesity-associated hepatosteatosis influences postprandial nutrient and energy metabolism. In this global shotgun proteome and phosphoproteome analysis, we identified unique protein signatures defining obesity and leanness in liver in the postprandial state and identified potential mechanisms contributing to hepatic metabolic alterations in obesity. The results of this study provide a foundation to focus future experiments on the contribution of altered protein and phosphorylation patterns to postprandial metabolism in obesity-associated hepatosteatosis.
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Affiliation(s)
- Alyssa S Zembroski
- Department of Nutrition Science, Purdue University, West Lafayette, IN 47907, USA
| | - Kimberly K Buhman
- Department of Nutrition Science, Purdue University, West Lafayette, IN 47907, USA
| | - Uma K Aryal
- Purdue Proteomics Facility, Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA; Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA..
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7
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Dittmann A, Kennedy NJ, Soltero NL, Morshed N, Mana MD, Yilmaz ÖH, Davis RJ, White FM. High-fat diet in a mouse insulin-resistant model induces widespread rewiring of the phosphotyrosine signaling network. Mol Syst Biol 2020; 15:e8849. [PMID: 31464373 PMCID: PMC6674232 DOI: 10.15252/msb.20198849] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 07/08/2019] [Accepted: 07/09/2019] [Indexed: 12/17/2022] Open
Abstract
Obesity-associated type 2 diabetes and accompanying diseases have developed into a leading human health risk across industrialized and developing countries. The complex molecular underpinnings of how lipid overload and lipid metabolites lead to the deregulation of metabolic processes are incompletely understood. We assessed hepatic post-translational alterations in response to treatment of cells with saturated and unsaturated free fatty acids and the consumption of a high-fat diet by mice. These data revealed widespread tyrosine phosphorylation changes affecting a large number of enzymes involved in metabolic processes as well as canonical receptor-mediated signal transduction networks. Targeting two of the most prominently affected molecular features in our data, SRC-family kinase activity and elevated reactive oxygen species, significantly abrogated the effects of saturated fat exposure in vitro and high-fat diet in vivo. In summary, we present a comprehensive view of diet-induced alterations of tyrosine signaling networks, including proteins involved in fundamental metabolic pathways.
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Affiliation(s)
- Antje Dittmann
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Norman J Kennedy
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Nina L Soltero
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nader Morshed
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Miyeko D Mana
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ömer H Yilmaz
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Roger J Davis
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.,Howard Hughes Medical Institute, Worcester, MA, USA
| | - Forest M White
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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8
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Luo M, Willis WT, Coletta DK, Langlais PR, Mengos A, Ma W, Finlayson J, Wagner GR, Shi CX, Mandarino LJ. Deletion of the Mitochondrial Protein VWA8 Induces Oxidative Stress and an HNF4α Compensatory Response in Hepatocytes. Biochemistry 2019; 58:4983-4996. [PMID: 31702900 DOI: 10.1021/acs.biochem.9b00863] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
von Willebrand A domain-containing protein 8 (VWA8) is a poorly characterized, mitochondrial matrix-targeted protein with an AAA ATPase domain and ATPase activity that increases in livers of mice fed a high-fat diet. This study was undertaken to use CRISPR/Cas9 to delete VWA8 in cultured mouse hepatocytes and gain insight into its function. Unbiased omics techniques and bioinformatics were used to guide subsequent assays, including the assessment of oxidative stress and the determination of bioenergetic capacity. Metabolomics analysis showed VWA8 null cells had higher levels of oxidative stress and protein degradation; assays of hydrogen peroxide production revealed higher levels of production of reactive oxygen species (ROS). Proteomics and transcriptomics analyses showed VWA8 null cells had higher levels of expression of mitochondrial proteins (electron transport-chain Complex I, ATP synthase), peroxisomal proteins, and lipid transport proteins. The pattern of higher protein abundance in the VWA8 null cells could be explained by a higher level of hepatocyte nuclear factor 4 α (HNF4α) expression. Bioenergetic assays showed higher rates of carbohydrate oxidation and mitochondrial and nonmitochondrial lipid oxidation in intact and permeabilized cells. Inhibitor assays localized sites of ROS production to peroxisomes and NOX1/4. The rescue of VWA8 protein restored the wild-type phenotype, and treatment with antioxidants decreased the level of HNF4α expression. Thus, loss of VWA8 produces a mitochondrial defect that may be sensed by NOX4, leading to an increase in the level of ROS that results in a higher level of HNF4α. The compensatory HNF4α response results in a higher oxidative capacity and an even higher level of ROS production. We hypothesize that VWA8 is an AAA ATPase protein that plays a role in mitochondrial protein quality.
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Affiliation(s)
- Moulun Luo
- Division of Endocrinology, Department of Medicine , University of Arizona College of Medicine , Tucson , Arizona 85724 , United States
| | - Wayne T Willis
- Division of Endocrinology, Department of Medicine , University of Arizona College of Medicine , Tucson , Arizona 85724 , United States
| | - Dawn K Coletta
- Division of Endocrinology, Department of Medicine , University of Arizona College of Medicine , Tucson , Arizona 85724 , United States
| | - Paul R Langlais
- Division of Endocrinology, Department of Medicine , University of Arizona College of Medicine , Tucson , Arizona 85724 , United States
| | - April Mengos
- Mayo Clinic in Arizona , Scottsdale , Arizona 85259 , United States
| | - Wuqiong Ma
- Division of Endocrinology, Department of Medicine , University of Arizona College of Medicine , Tucson , Arizona 85724 , United States
| | - Jean Finlayson
- Division of Endocrinology, Department of Medicine , University of Arizona College of Medicine , Tucson , Arizona 85724 , United States
| | - Gregory R Wagner
- Metabolon, Inc. , Research Triangle Park , North Carolina 27709 , United States
| | - Chang-Xin Shi
- Mayo Clinic in Arizona , Scottsdale , Arizona 85259 , United States
| | - Lawrence J Mandarino
- Division of Endocrinology, Department of Medicine , University of Arizona College of Medicine , Tucson , Arizona 85724 , United States
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Caiola E, Falcetta F, Giordano S, Marabese M, Garassino MC, Broggini M, Pastorelli R, Brunelli L. Co-occurring KRAS mutation/LKB1 loss in non-small cell lung cancer cells results in enhanced metabolic activity susceptible to caloric restriction: an in vitro integrated multilevel approach. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2018; 37:302. [PMID: 30514331 PMCID: PMC6280460 DOI: 10.1186/s13046-018-0954-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/07/2018] [Indexed: 12/13/2022]
Abstract
Background Non–small-cell lung cancer (NSCLC) is a heterogeneous disease, with multiple different oncogenic mutations. Approximately 25–30% of NSCLC patients present KRAS mutations, which confer poor prognosis and high risk of tumor recurrence. About half of NSCLCs with activating KRAS lesions also have deletions or inactivating mutations in the serine/threonine kinase 11 (LKB1) gene. Loss of LKB1 on a KRAS-mutant background may represent a significant source of heterogeneity contributing to poor response to therapy. Methods Here, we employed an integrated multilevel proteomics, metabolomics and functional in-vitro approach in NSCLC H1299 isogenic cells to define their metabolic state associated with the presence of different genetic background. Protein levels were obtained by label free and single reaction monitoring (SRM)-based proteomics. The metabolic state was studied coupling targeted and untargeted mass spectrometry (MS) strategy. In vitro metabolic dependencies were evaluated using 2-deoxy glucose (2-DG) treatment or glucose/glutamine nutrient limitation. Results Here we demonstrate that co-occurring KRAS mutation/LKB1 loss in NSCLC cells allowed efficient exploitation of glycolysis and oxidative phosphorylation, when compared to cells with each single oncologic genotype. The enhanced metabolic activity rendered the viability of cells with both genetic lesions susceptible towards nutrient limitation. Conclusions Co-occurrence of KRAS mutation and LKB1 loss in NSCLC cells induced an enhanced metabolic activity mirrored by a growth rate vulnerability under limited nutrient conditions relative to cells with the single oncogenetic lesions. Our results hint at the possibility that energy stress induced by calorie restriction regimens may sensitize NSCLCs with these co-occurring lesions to cytotoxic chemotherapy. Electronic supplementary material The online version of this article (10.1186/s13046-018-0954-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elisa Caiola
- Laboratory of Molecular Pharmacology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Francesca Falcetta
- Laboratory of Cancer Pharmacology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Silvia Giordano
- Laboratory of Mass Spectrometry, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156, Milan, Italy
| | - Mirko Marabese
- Laboratory of Molecular Pharmacology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Marina C Garassino
- Thoracic Oncology, Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Massimo Broggini
- Laboratory of Molecular Pharmacology, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Roberta Pastorelli
- Laboratory of Mass Spectrometry, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156, Milan, Italy
| | - Laura Brunelli
- Laboratory of Mass Spectrometry, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156, Milan, Italy.
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10
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Manes NP, Nita-Lazar A. Application of targeted mass spectrometry in bottom-up proteomics for systems biology research. J Proteomics 2018; 189:75-90. [PMID: 29452276 DOI: 10.1016/j.jprot.2018.02.008] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/25/2018] [Accepted: 02/07/2018] [Indexed: 02/08/2023]
Abstract
The enormous diversity of proteoforms produces tremendous complexity within cellular proteomes, facilitates intricate networks of molecular interactions, and constitutes a formidable analytical challenge for biomedical researchers. Currently, quantitative whole-proteome profiling often relies on non-targeted liquid chromatography-mass spectrometry (LC-MS), which samples proteoforms broadly, but can suffer from lower accuracy, sensitivity, and reproducibility compared with targeted LC-MS. Recent advances in bottom-up proteomics using targeted LC-MS have enabled previously unachievable identification and quantification of target proteins and posttranslational modifications within complex samples. Consequently, targeted LC-MS is rapidly advancing biomedical research, especially systems biology research in diverse areas that include proteogenomics, interactomics, kinomics, and biological pathway modeling. With the recent development of targeted LC-MS assays for nearly the entire human proteome, targeted LC-MS is positioned to enable quantitative proteomic profiling of unprecedented quality and accessibility to support fundamental and clinical research. Here we review recent applications of bottom-up proteomics using targeted LC-MS for systems biology research. SIGNIFICANCE: Advances in targeted proteomics are rapidly advancing systems biology research. Recent applications include systems-level investigations focused on posttranslational modifications (such as phosphoproteomics), protein conformation, protein-protein interaction, kinomics, proteogenomics, and metabolic and signaling pathways. Notably, absolute quantification of metabolic and signaling pathway proteins has enabled accurate pathway modeling and engineering. Integration of targeted proteomics with other technologies, such as RNA-seq, has facilitated diverse research such as the identification of hundreds of "missing" human proteins (genes and transcripts that appear to encode proteins but direct experimental evidence was lacking).
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Affiliation(s)
- Nathan P Manes
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aleksandra Nita-Lazar
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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11
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Caira S, Iannelli A, Sciarrillo R, Picariello G, Renzone G, Scaloni A, Addeo P. Differential representation of liver proteins in obese human subjects suggests novel biomarkers and promising targets for drug development in obesity. J Enzyme Inhib Med Chem 2017; 32:672-682. [PMID: 28274171 PMCID: PMC6009959 DOI: 10.1080/14756366.2017.1292262] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The proteome of liver biopsies from human obese (O) subjects has been compared to those of nonobese (NO) subjects using two-dimensional gel electrophoresis (2-DE). Differentially represented proteins were identified by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS)-based peptide mass fingerprinting (PMF) and nanoflow-liquid chromatography coupled to electrospray-tandem mass spectrometry (nLC-ESI-MS/MS). Overall, 61 gene products common to all of the liver biopsies were identified within 65 spots, among which 25 ones were differently represented between O and NO subjects. In particular, over-representation of short-chain acyl-CoA dehydrogenase, Δ(3,5)-Δ(2,4)dienoyl-CoA isomerase, acetyl-CoA acetyltransferase, glyoxylate reductase/hydroxypyruvate reductase, fructose-biphosphate aldolase B, peroxiredoxin I, protein DJ-1, catalase, α- and β-hemoglobin subunits, 3-mercaptopyruvate S-transferase, calreticulin, aminoacylase 1, phenazine biosynthesis-like domain-containing protein and a form of fatty acid-binding protein, together with downrepresentation of glutamate dehydrogenase, glutathione S-transferase A1, S-adenosylmethionine synthase 1A and a form of apolipoprotein A-I, was associated with the obesity condition. Some of these metabolic enzymes and antioxidant proteins have already been identified as putative diagnostic markers of liver dysfunction in animal models of steatosis or obesity, suggesting additional investigations on their role in these syndromes. Their differential representation in human liver was suggestive of their consideration as obesity human biomarkers and for the development of novel antiobesity drugs.
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Affiliation(s)
- Simonetta Caira
- a Proteomics and Mass Spectrometry Laboratory , ISPAAM, National Research Council , Naples , Italy
| | - Antonio Iannelli
- b Département de Chirurgie Digestive , Centre Hospitalier Universitarie de Nice , Nice , France
| | - Rosaria Sciarrillo
- c Dipartimento di Scienze e Tecnologie , Università degli Studi del Sannio , Benevento , Italy
| | | | - Giovanni Renzone
- a Proteomics and Mass Spectrometry Laboratory , ISPAAM, National Research Council , Naples , Italy
| | - Andrea Scaloni
- a Proteomics and Mass Spectrometry Laboratory , ISPAAM, National Research Council , Naples , Italy
| | - Pietro Addeo
- e Service de Chirurgie Hépatique, Pancréatique, Biliaire et Transplantation, Pôle des Pathologies Digestives, Hépatiques et de la Transplantation, Hôpital de Hautepierre , Université de Strasbourg, Hôpitaux Universitaires de Strasbourg , Strasbourg , France
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12
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Terfve C, Sabidó E, Wu Y, Gonçalves E, Choi M, Vaga S, Vitek O, Saez-Rodriguez J, Aebersold R. System-Wide Quantitative Proteomics of the Metabolic Syndrome in Mice: Genotypic and Dietary Effects. J Proteome Res 2017; 16:831-841. [PMID: 27936760 DOI: 10.1021/acs.jproteome.6b00815] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Advances in mass spectrometry have made the quantitative measurement of proteins across multiple samples a reality, allowing for the study of complex biological systems such as the metabolic syndrome. Although the deregulation of lipid metabolism and increased hepatic storage of triacylglycerides are known to play a part in the onset of the metabolic syndrome, its molecular basis and dependency on dietary and genotypic factors are poorly characterized. Here, we used an experimental design with two different mouse strains and dietary and metabolic perturbations to generate a compendium of quantitative proteome data using three mass spectrometric techniques. The data reproduce known properties of the metabolic system and indicate differential molecular adaptation of the two mouse strains to perturbations, contributing to a better understanding of the metabolic syndrome. We show that high-quality, high-throughput proteomic data sets provide an unbiased broad overview of the behavior of complex systems after perturbation.
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Affiliation(s)
- Camille Terfve
- European Molecular Biology Laboratory, European Bioinformatics Institute , Cambridge, U.K
| | - Eduard Sabidó
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich , Zürich 8093, Switzerland
| | - Yibo Wu
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich , Zürich 8093, Switzerland
| | - Emanuel Gonçalves
- European Molecular Biology Laboratory, European Bioinformatics Institute , Cambridge, U.K
| | - Meena Choi
- College of Science and College of Computer and Information Science, Northeastern University , Boston, Massachusetts 02115, United States
| | - Stefania Vaga
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich , Zürich 8093, Switzerland
| | - Olga Vitek
- College of Science and College of Computer and Information Science, Northeastern University , Boston, Massachusetts 02115, United States
| | - Julio Saez-Rodriguez
- European Molecular Biology Laboratory, European Bioinformatics Institute , Cambridge, U.K.,RWTH-Aachen, Faculty of Medicine, Joint Research Center for Computational Biomedicine , Aachen D-52074, Germany
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich , Zürich 8093, Switzerland.,Department of Science, Faculty of Science, University of Zürich , Zürich CH-8006, Switzerland
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13
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A large-scale targeted proteomics assay resource based on an in vitro human proteome. Nat Methods 2016; 14:251-258. [PMID: 28267743 DOI: 10.1038/nmeth.4116] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 11/07/2016] [Indexed: 01/15/2023]
Abstract
Targeted proteomics approaches are of value for deep and accurate quantification of protein abundance. Extending such methods to quantify large numbers of proteins requires the construction of predefined targeted assays. We developed a targeted proteomics platform-in vitro proteome-assisted multiple reaction monitoring (MRM) for protein absolute quantification (iMPAQT)-by using >18,000 human recombinant proteins, thus enabling protein absolute quantification on a genome-wide scale. Our platform comprises experimentally confirmed MRM assays of mass tag (mTRAQ)-labeled peptides to allow for rapid and straightforward measurement of the absolute abundance of predefined sets of proteins by mass spectrometry. We applied iMPAQT to delineate the quantitative metabolic landscape of normal and transformed human fibroblasts. Oncogenic transformation gave rise to relatively small but global changes in metabolic pathways resulting in aerobic glycolysis (Warburg effect) and increased rates of macromolecule synthesis. iMPAQT should facilitate quantitative biology studies based on protein abundance measurements.
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14
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Röst HL, Malmström L, Aebersold R. Reproducible quantitative proteotype data matrices for systems biology. Mol Biol Cell 2016; 26:3926-31. [PMID: 26543201 PMCID: PMC4710225 DOI: 10.1091/mbc.e15-07-0507] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Historically, many mass spectrometry–based proteomic studies have aimed at compiling an inventory of protein compounds present in a biological sample, with the long-term objective of creating a proteome map of a species. However, to answer fundamental questions about the behavior of biological systems at the protein level, accurate and unbiased quantitative data are required in addition to a list of all protein components. Fueled by advances in mass spectrometry, the proteomics field has thus recently shifted focus toward the reproducible quantification of proteins across a large number of biological samples. This provides the foundation to move away from pure enumeration of identified proteins toward quantitative matrices of many proteins measured across multiple samples. It is argued here that data matrices consisting of highly reproducible, quantitative, and unbiased proteomic measurements across a high number of conditions, referred to here as quantitative proteotype maps, will become the fundamental currency in the field and provide the starting point for downstream biological analysis. Such proteotype data matrices, for example, are generated by the measurement of large patient cohorts, time series, or multiple experimental perturbations. They are expected to have a large effect on systems biology and personalized medicine approaches that investigate the dynamic behavior of biological systems across multiple perturbations, time points, and individuals.
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Affiliation(s)
- Hannes L Röst
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, CH-8093 Zurich, Switzerland Department of Genetics, Stanford University, Stanford, CA 94305
| | - Lars Malmström
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, CH-8093 Zurich, Switzerland S3IT, University of Zurich, CH-8057 Zurich, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, CH-8093 Zurich, Switzerland Faculty of Science, University of Zurich, CH-8057 Zurich, Switzerland
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15
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Shi T, Song E, Nie S, Rodland KD, Liu T, Qian WJ, Smith RD. Advances in targeted proteomics and applications to biomedical research. Proteomics 2016; 16:2160-82. [PMID: 27302376 PMCID: PMC5051956 DOI: 10.1002/pmic.201500449] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 05/09/2016] [Accepted: 06/10/2016] [Indexed: 12/17/2022]
Abstract
Targeted proteomics technique has emerged as a powerful protein quantification tool in systems biology, biomedical research, and increasing for clinical applications. The most widely used targeted proteomics approach, selected reaction monitoring (SRM), also known as multiple reaction monitoring (MRM), can be used for quantification of cellular signaling networks and preclinical verification of candidate protein biomarkers. As an extension to our previous review on advances in SRM sensitivity (Shi et al., Proteomics, 12, 1074-1092, 2012) herein we review recent advances in the method and technology for further enhancing SRM sensitivity (from 2012 to present), and highlighting its broad biomedical applications in human bodily fluids, tissue and cell lines. Furthermore, we also review two recently introduced targeted proteomics approaches, parallel reaction monitoring (PRM) and data-independent acquisition (DIA) with targeted data extraction on fast scanning high-resolution accurate-mass (HR/AM) instruments. Such HR/AM targeted quantification with monitoring all target product ions addresses SRM limitations effectively in specificity and multiplexing; whereas when compared to SRM, PRM and DIA are still in the infancy with a limited number of applications. Thus, for HR/AM targeted quantification we focus our discussion on method development, data processing and analysis, and its advantages and limitations in targeted proteomics. Finally, general perspectives on the potential of achieving both high sensitivity and high sample throughput for large-scale quantification of hundreds of target proteins are discussed.
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Affiliation(s)
- Tujin Shi
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ehwang Song
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Song Nie
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Karin D Rodland
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Tao Liu
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Wei-Jun Qian
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Richard D Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
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16
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Mass spectrometry-based absolute quantification reveals rhythmic variation of mouse circadian clock proteins. Proc Natl Acad Sci U S A 2016; 113:E3461-7. [PMID: 27247408 DOI: 10.1073/pnas.1603799113] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Absolute values of protein expression levels in cells are crucial information for understanding cellular biological systems. Precise quantification of proteins can be achieved by liquid chromatography (LC)-mass spectrometry (MS) analysis of enzymatic digests of proteins in the presence of isotope-labeled internal standards. Thus, development of a simple and easy way for the preparation of internal standards is advantageous for the analyses of multiple target proteins, which will allow systems-level studies. Here we describe a method, termed MS-based Quantification By isotope-labeled Cell-free products (MS-QBiC), which provides the simple and high-throughput preparation of internal standards by using a reconstituted cell-free protein synthesis system, and thereby facilitates both multiplexed and sensitive quantification of absolute amounts of target proteins. This method was applied to a systems-level dynamic analysis of mammalian circadian clock proteins, which consist of transcription factors and protein kinases that govern central and peripheral circadian clocks in mammals. Sixteen proteins from 20 selected circadian clock proteins were successfully quantified from mouse liver over a 24-h time series, and 14 proteins had circadian variations. Quantified values were applied to detect internal body time using a previously developed molecular timetable method. The analyses showed that single time-point data from wild-type mice can predict the endogenous state of the circadian clock, whereas data from clock mutant mice are not applicable because of the disappearance of circadian variation.
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17
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Engelken J, Espadas G, Mancuso FM, Bonet N, Scherr AL, Jímenez-Álvarez V, Codina-Solà M, Medina-Stacey D, Spataro N, Stoneking M, Calafell F, Sabidó E, Bosch E. Signatures of Evolutionary Adaptation in Quantitative Trait Loci Influencing Trace Element Homeostasis in Liver. Mol Biol Evol 2016; 33:738-54. [PMID: 26582562 PMCID: PMC4760079 DOI: 10.1093/molbev/msv267] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Essential trace elements possess vital functions at molecular, cellular, and physiological levels in health and disease, and they are tightly regulated in the human body. In order to assess variability and potential adaptive evolution of trace element homeostasis, we quantified 18 trace elements in 150 liver samples, together with the expression levels of 90 genes and abundances of 40 proteins involved in their homeostasis. Additionally, we genotyped 169 single nucleotide polymorphism (SNPs) in the same sample set. We detected significant associations for 8 protein quantitative trait loci (pQTL), 10 expression quantitative trait loci (eQTLs), and 15 micronutrient quantitative trait loci (nutriQTL). Six of these exceeded the false discovery rate cutoff and were related to essential trace elements: 1) one pQTL for GPX2 (rs10133290); 2) two previously described eQTLs for HFE (rs12346) and SELO (rs4838862) expression; and 3) three nutriQTLs: The pathogenic C282Y mutation at HFE affecting iron (rs1800562), and two SNPs within several clustered metallothionein genes determining selenium concentration (rs1811322 and rs904773). Within the complete set of significant QTLs (which involved 30 SNPs and 20 gene regions), we identified 12 SNPs with extreme patterns of population differentiation (FST values in the top 5% percentile in at least one HapMap population pair) and significant evidence for selective sweeps involving QTLs at GPX1, SELENBP1, GPX3, SLC30A9, and SLC39A8. Overall, this detailed study of various molecular phenotypes illustrates the role of regulatory variants in explaining differences in trace element homeostasis among populations and in the human adaptive response to environmental pressures related to micronutrients.
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Affiliation(s)
- Johannes Engelken
- †These authors contributed equally to this work. ‡Deceased October 23, 2015. Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Guadalupe Espadas
- †These authors contributed equally to this work. Proteomics Unit, Center of Genomics Regulation, Barcelona, Spain Proteomics Unit, Universitat Pompeu Fabra, Barcelona, Spain
| | - Francesco M Mancuso
- Proteomics Unit, Center of Genomics Regulation, Barcelona, Spain Proteomics Unit, Universitat Pompeu Fabra, Barcelona, Spain
| | - Nuria Bonet
- Genomics Core Facility, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Barcelona, Spain
| | - Anna-Lena Scherr
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Victoria Jímenez-Álvarez
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Marta Codina-Solà
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Daniel Medina-Stacey
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Nino Spataro
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Francesc Calafell
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Eduard Sabidó
- Proteomics Unit, Center of Genomics Regulation, Barcelona, Spain Proteomics Unit, Universitat Pompeu Fabra, Barcelona, Spain
| | - Elena Bosch
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
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18
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Pedersen BA, Wang W, Taylor JF, Khattab OS, Chen YH, Edwards RA, Yazdi PG, Wang PH. Hepatic proteomic analysis revealed altered metabolic pathways in insulin resistant Akt1(+/-)/Akt2(-/-) mice. Metabolism 2015; 64:1694-703. [PMID: 26455965 PMCID: PMC4641788 DOI: 10.1016/j.metabol.2015.09.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 08/19/2015] [Accepted: 09/08/2015] [Indexed: 10/23/2022]
Abstract
OBJECTIVE The aim of this study was to identify liver proteome changes in a mouse model of severe insulin resistance and markedly decreased leptin levels. METHODS Two-dimensional differential gel electrophoresis was utilized to identify liver proteome changes in AKT1(+/-)/AKT2(-/-) mice. Proteins with altered levels were identified with tandem mass spectrometry. Ingenuity Pathway Analysis was performed for the interpretation of the biological significance of the observed proteomic changes. RESULTS 11 proteins were identified from 2 biological replicates to be differentially expressed by a ratio of at least 1.3 between age-matched insulin resistant (Akt1(+/-)/Akt2(-/-)) and wild type mice. Albumin and mitochondrial ornithine aminotransferase were detected from multiple spots, which suggest post-translational modifications. Enzymes of the urea cycle were common members of top regulated pathways. CONCLUSION Our results help to unveil the regulation of the liver proteome underlying altered metabolism in an animal model of severe insulin resistance.
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Affiliation(s)
- Brian A Pedersen
- UC Irvine Diabetes Center, University of California at Irvine, Irvine, CA 92697, USA
- Sue and Bill Gross Stem Cell Research Center, University of California at Irvine, Irvine, CA 92697, USA
- Department of Medicine, University of California at Irvine, Irvine, CA 92697, USA
| | - Weiwen Wang
- UC Irvine Diabetes Center, University of California at Irvine, Irvine, CA 92697, USA
- Sue and Bill Gross Stem Cell Research Center, University of California at Irvine, Irvine, CA 92697, USA
- Department of Medicine, University of California at Irvine, Irvine, CA 92697, USA
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami School of Medicine, Miami, FL, 33136
| | - Jared F Taylor
- UC Irvine Diabetes Center, University of California at Irvine, Irvine, CA 92697, USA
- Sue and Bill Gross Stem Cell Research Center, University of California at Irvine, Irvine, CA 92697, USA
- Department of Medicine, University of California at Irvine, Irvine, CA 92697, USA
| | - Omar S Khattab
- UC Irvine Diabetes Center, University of California at Irvine, Irvine, CA 92697, USA
- Sue and Bill Gross Stem Cell Research Center, University of California at Irvine, Irvine, CA 92697, USA
| | - Yu-Han Chen
- UC Irvine Diabetes Center, University of California at Irvine, Irvine, CA 92697, USA
- Sue and Bill Gross Stem Cell Research Center, University of California at Irvine, Irvine, CA 92697, USA
- Department of Physiology & Biophysics, University of California at Irvine, Irvine, CA 92697, USA
| | - Robert A Edwards
- Department of Pathology, University of California at Irvine, Irvine, CA 92697, USA
| | - Puya G Yazdi
- UC Irvine Diabetes Center, University of California at Irvine, Irvine, CA 92697, USA
- Sue and Bill Gross Stem Cell Research Center, University of California at Irvine, Irvine, CA 92697, USA
- Department of Medicine, University of California at Irvine, Irvine, CA 92697, USA
| | - Ping H Wang
- UC Irvine Diabetes Center, University of California at Irvine, Irvine, CA 92697, USA
- Sue and Bill Gross Stem Cell Research Center, University of California at Irvine, Irvine, CA 92697, USA
- Department of Medicine, University of California at Irvine, Irvine, CA 92697, USA
- Department of Biological Chemistry, University of California at Irvine, Irvine, CA 92697, USA
- Department of Physiology & Biophysics, University of California at Irvine, Irvine, CA 92697, USA
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Ebhardt HA, Root A, Sander C, Aebersold R. Applications of targeted proteomics in systems biology and translational medicine. Proteomics 2015; 15:3193-208. [PMID: 26097198 PMCID: PMC4758406 DOI: 10.1002/pmic.201500004] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 04/27/2015] [Accepted: 06/09/2015] [Indexed: 01/28/2023]
Abstract
Biological systems are composed of numerous components of which proteins are of particularly high functional significance. Network models are useful abstractions for studying these components in context. Network representations display molecules as nodes and their interactions as edges. Because they are difficult to directly measure, functional edges are frequently inferred from suitably structured datasets consisting of the accurate and consistent quantification of network nodes under a multitude of perturbed conditions. For the precise quantification of a finite list of proteins across a wide range of samples, targeted proteomics exemplified by selected/multiple reaction monitoring (SRM, MRM) mass spectrometry has proven useful and has been applied to a variety of questions in systems biology and clinical studies. Here, we survey the literature of studies using SRM-MS in systems biology and clinical proteomics. Systems biology studies frequently examine fundamental questions in network biology, whereas clinical studies frequently focus on biomarker discovery and validation in a variety of diseases including cardiovascular disease and cancer. Targeted proteomics promises to advance our understanding of biological networks and the phenotypic significance of specific network states and to advance biomarkers into clinical use.
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Affiliation(s)
- H Alexander Ebhardt
- Department of Biology, Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Alex Root
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medical College, New York, NY, USA
| | - Chris Sander
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
- Faculty of Science, University of Zurich, Zurich, Switzerland
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20
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Larance M, Pourkarimi E, Wang B, Brenes Murillo A, Kent R, Lamond AI, Gartner A. Global Proteomics Analysis of the Response to Starvation in C. elegans. Mol Cell Proteomics 2015; 14:1989-2001. [PMID: 25963834 PMCID: PMC4587315 DOI: 10.1074/mcp.m114.044289] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Indexed: 12/31/2022] Open
Abstract
Periodic starvation of animals induces large shifts in metabolism but may also influence many other cellular systems and can lead to adaption to prolonged starvation conditions. To date, there is limited understanding of how starvation affects gene expression, particularly at the protein level. Here, we have used mass-spectrometry-based quantitative proteomics to identify global changes in the Caenorhabditis elegans proteome due to acute starvation of young adult animals. Measuring changes in the abundance of over 5,000 proteins, we show that acute starvation rapidly alters the levels of hundreds of proteins, many involved in central metabolic pathways, highlighting key regulatory responses. Surprisingly, we also detect changes in the abundance of chromatin-associated proteins, including specific linker histones, histone variants, and histone posttranslational modifications associated with the epigenetic control of gene expression. To maximize community access to these data, they are presented in an online searchable database, the Encyclopedia of Proteome Dynamics (http://www.peptracker.com/epd/).
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Affiliation(s)
- Mark Larance
- From the ‡Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow St, Dundee, United Kingdom, DD15EH
| | - Ehsan Pourkarimi
- From the ‡Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow St, Dundee, United Kingdom, DD15EH
| | - Bin Wang
- From the ‡Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow St, Dundee, United Kingdom, DD15EH
| | - Alejandro Brenes Murillo
- From the ‡Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow St, Dundee, United Kingdom, DD15EH
| | - Robert Kent
- From the ‡Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow St, Dundee, United Kingdom, DD15EH
| | - Angus I Lamond
- From the ‡Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow St, Dundee, United Kingdom, DD15EH
| | - Anton Gartner
- From the ‡Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow St, Dundee, United Kingdom, DD15EH
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21
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Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps. Nat Med 2015; 21:407-13. [PMID: 25730263 PMCID: PMC4390165 DOI: 10.1038/nm.3807] [Citation(s) in RCA: 282] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 01/20/2015] [Indexed: 02/07/2023]
Abstract
Clinical specimens are each inherently unique, limited and non-renewable. As such, small samples such as tissue biopsies are often completely consumed after a limited number of analyses. Here we present a method that enables fast and reproducible conversion of a small amount of tissue (approximating the quantity obtained by a biopsy) into a single, permanent digital file representing the mass spectrometry-measurable proteome of the sample. The method combines pressure cycling technology (PCT) and SWATH mass spectrometry (MS), and the resulting proteome maps can be analyzed, re-analyzed, compared and mined in silico to detect and quantify specific proteins across multiple samples. We used this method to process and convert 18 biopsy samples from 9 renal cell carcinoma patients into SWATH-MS fragment ion maps. From these proteome maps we detected and quantified more than 2,000 proteins with a high degree of reproducibility across all samples. The identified proteins clearly separated tumorous kidney tissues from healthy tissue, and differentiated distinct histomorphological kidney cancer subtypes.
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22
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Wu Y, Williams EG, Dubuis S, Mottis A, Jovaisaite V, Houten SM, Argmann CA, Faridi P, Wolski W, Kutalik Z, Zamboni N, Auwerx J, Aebersold R. Multilayered genetic and omics dissection of mitochondrial activity in a mouse reference population. Cell 2014; 158:1415-1430. [PMID: 25215496 DOI: 10.1016/j.cell.2014.07.039] [Citation(s) in RCA: 178] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 06/02/2014] [Accepted: 07/28/2014] [Indexed: 02/06/2023]
Abstract
The manner by which genotype and environment affect complex phenotypes is one of the fundamental questions in biology. In this study, we quantified the transcriptome--a subset of the metabolome--and, using targeted proteomics, quantified a subset of the liver proteome from 40 strains of the BXD mouse genetic reference population on two diverse diets. We discovered dozens of transcript, protein, and metabolite QTLs, several of which linked to metabolic phenotypes. Most prominently, Dhtkd1 was identified as a primary regulator of 2-aminoadipate, explaining variance in fasted glucose and diabetes status in both mice and humans. These integrated molecular profiles also allowed further characterization of complex pathways, particularly the mitochondrial unfolded protein response (UPR(mt)). UPR(mt) shows strikingly variant responses at the transcript and protein level that are remarkably conserved among C. elegans, mice, and humans. Overall, these examples demonstrate the value of an integrated multilayered omics approach to characterize complex metabolic phenotypes.
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Affiliation(s)
- Yibo Wu
- Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich (ETHZ), Zurich 8093, Switzerland
| | - Evan G Williams
- Laboratory of Integrative and Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Sébastien Dubuis
- Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich (ETHZ), Zurich 8093, Switzerland
| | - Adrienne Mottis
- Laboratory of Integrative and Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Virginija Jovaisaite
- Laboratory of Integrative and Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Sander M Houten
- Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases and Department of Pediatrics, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Carmen A Argmann
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Pouya Faridi
- Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich (ETHZ), Zurich 8093, Switzerland; Department of Traditional Pharmacy, School of Pharmacy and Pharmaceutical Sciences, Shiraz University of Medical Sciences, Shiraz 71349-14693, Iran
| | - Witold Wolski
- Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich (ETHZ), Zurich 8093, Switzerland
| | - Zoltán Kutalik
- Institute of Social and Preventive Medicine (IUMSP), Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne 1010, Switzerland; Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Nicola Zamboni
- Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich (ETHZ), Zurich 8093, Switzerland
| | - Johan Auwerx
- Laboratory of Integrative and Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland.
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich (ETHZ), Zurich 8093, Switzerland; Faculty of Science, University of Zurich, Zurich 8057, Switzerland.
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23
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Diet-induced obesity modulates epigenetic responses to ionizing radiation in mice. PLoS One 2014; 9:e106277. [PMID: 25171162 PMCID: PMC4149562 DOI: 10.1371/journal.pone.0106277] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 08/05/2014] [Indexed: 01/16/2023] Open
Abstract
Both exposure to ionizing radiation and obesity have been associated with various pathologies including cancer. There is a crucial need in better understanding the interactions between ionizing radiation effects (especially at low doses) and other risk factors, such as obesity. In order to evaluate radiation responses in obese animals, C3H and C57BL/6J mice fed a control normal fat or a high fat (HF) diet were exposed to fractionated doses of X-rays (0.75 Gy ×4). Bone marrow micronucleus assays did not suggest a modulation of radiation-induced genotoxicity by HF diet. Using MSP, we observed that the promoters of p16 and Dapk genes were methylated in the livers of C57BL/6J mice fed a HF diet (irradiated and non-irradiated); Mgmt promoter was methylated in irradiated and/or HF diet-fed mice. In addition, methylation PCR arrays identified Ep300 and Socs1 (whose promoters exhibited higher methylation levels in non-irradiated HF diet-fed mice) as potential targets for further studies. We then compared microRNA regulations after radiation exposure in the livers of C57BL/6J mice fed a normal or an HF diet, using microRNA arrays. Interestingly, radiation-triggered microRNA regulations observed in normal mice were not observed in obese mice. miR-466e was upregulated in non-irradiated obese mice. In vitro free fatty acid (palmitic acid, oleic acid) administration sensitized AML12 mouse liver cells to ionizing radiation, but the inhibition of miR-466e counteracted this radio-sensitization, suggesting that the modulation of radiation responses by diet-induced obesity might involve miR-466e expression. All together, our results suggested the existence of dietary effects on radiation responses (especially epigenetic regulations) in mice, possibly in relationship with obesity-induced chronic oxidative stress.
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Chiva C, Ortega M, Sabidó E. Influence of the digestion technique, protease, and missed cleavage peptides in protein quantitation. J Proteome Res 2014; 13:3979-86. [PMID: 24986539 DOI: 10.1021/pr500294d] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Quantitative determination of absolute and relative protein amounts is an essential requirement for most current bottom-up proteomics applications, but protein quantitation estimates are affected by several sources of variability such as sample preparation, mass spectrometric acquisition, and data analysis. Among them, sample digestion has attracted much attention from the proteomics community, as protein quantitation by bottom-up proteomics relies on the efficiency and reproducibility of protein enzymatic digestion, with the presence of missed cleavages, nonspecific cleavages, or even the use of different proteases having been postulated as important sources of variation in protein quantitation. Here we evaluated both in-solution and filter-aided digestion protocols and assessed their influence in the estimation of protein abundances using five E. coli mixtures with known amounts of spiked proteins. We observed that replicates of trypsin specificity digestion protocols are highly reproducible in terms of peptide quantitation, with digestion technique and the chosen proteolytic enzyme being the major sources of variability in peptide quantitation. Finally, we also evaluated the result of including peptides with missed cleavages in protein quantitation and observed no significant differences in precision, accuracy, specificity, and sensitivity compared with the use of fully tryptic peptides.
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Affiliation(s)
- Cristina Chiva
- Proteomics Unit, Centre de Regulació Genòmica (CRG) , Dr. Aiguader 88, 08003 Barcelona, Spain
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25
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Abstract
UNLABELLED Creation of lethal and synthetic lethal mutations in an experimental organism is a cornerstone of genetic dissection of gene function, and is related to the concept of an essential gene. Common inbred mouse strains carry background mutations, which can act as genetic modifiers, interfering with the assignment of gene essentiality. The inbred strain C57BL/6J, commonly known as "Black Six", stands out, as it carries a spontaneous homozygous deletion in the nicotinamide nucleotide transhydrogenase (Nnt) gene [GenBank: AH009385.2], resulting in impairment of steroidogenic mitochondria of the adrenal gland, and a multitude of indirect modifier effects, coming from alteration of glucocorticoid-regulated processes. Over time, the popular strain has been used, by means of gene targeting technology, to assign "essential" and "redundant" qualifiers to numerous genes, thus creating an internally consistent "parallel universe" of knowledge. It is unrealistic to suggest phasing-out of this strain, given the scope of shared resources built around it, however, continuing on the road of "strain-unawareness" will result in profound waste of effort, particularly where translational research is concerned. The review analyzes the historical roots of this phenomenon and proposes that building of "parallel universes" should be urgently made visible to a critical reader by obligatory use of unambiguous and persistent tags in publications and databases, such as hypertext links, pointing to a vendor's strain description web page, or to a digital object identifier (d.o.i.) of the original publication, so that any research done exclusively in C57BL/6J, could be easily identified. REVIEWERS This article was reviewed by Dr. Neil Smalheiser and Dr. Miguel Andrade-Navarro.
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Affiliation(s)
- Alexander Kraev
- Charles H, Best Institute, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G 1L6, Canada.
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26
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Bailey DJ, McDevitt MT, Westphall MS, Pagliarini DJ, Coon JJ. Intelligent data acquisition blends targeted and discovery methods. J Proteome Res 2014; 13:2152-61. [PMID: 24611583 PMCID: PMC3983381 DOI: 10.1021/pr401278j] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
![]()
A mass spectrometry (MS) method is
described here that can reproducibly
identify hundreds of peptides across multiple experiments. The method
uses intelligent data acquisition to precisely target peptides while
simultaneously identifying thousands of other, nontargeted peptides
in a single nano-LC–MS/MS experiment. We introduce an online
peptide elution order alignment algorithm that targets peptides based
on their relative elution order, eliminating the need for retention-time-based
scheduling. We have applied this method to target 500 mouse peptides
across six technical replicate nano-LC–MS/MS experiments and
were able to identify 440 of these in all six, compared with only
256 peptides using data-dependent acquisition (DDA). A total of 3757
other peptides were also identified within the same experiment, illustrating
that this hybrid method does not eliminate the novel discovery advantages
of DDA. The method was also tested on a set of mice in biological
quadruplicate and increased the number of identified target peptides
in all four mice by over 80% (826 vs 459) compared with the standard
DDA method. We envision real-time data analysis as a powerful tool
to improve the quality and reproducibility of proteomic data sets.
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Affiliation(s)
- Derek J Bailey
- Department of Chemistry, University of Wisconsin - Madison , 1101 Unviersity Avenue, Madison, Wisconsin 53706, United States
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27
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Chang CY, Sabidó E, Aebersold R, Vitek O. Targeted protein quantification using sparse reference labeling. Nat Methods 2014; 11:301-4. [DOI: 10.1038/nmeth.2806] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 12/13/2013] [Indexed: 12/22/2022]
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28
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Kiel C, Ebhardt HA, Burnier J, Portugal C, Sabidó E, Zimmermann T, Aebersold R, Serrano L. Quantification of ErbB network proteins in three cell types using complementary approaches identifies cell-general and cell-type-specific signaling proteins. J Proteome Res 2013; 13:300-13. [PMID: 24313378 DOI: 10.1021/pr400878x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Relating protein concentration to cell-type-specific responses is one of the remaining challenges for obtaining a quantitative systems level understanding of mammalian signaling. Here we used mass-spectrometry (MS)- and antibody-based quantitative proteomic approaches to measure protein abundances for 75% of a hand-curated reconstructed ErbB network of 198 proteins, in two established cell types (HEK293 and MCF-7) and in primary keratinocyte cells. Comparison with other quantitative studies allowed building a set of ErbB network proteins expressed in all cells and another which are cell-specific and could impart specific properties to the network. As a proof-of-concept of the importance of protein concentration, we generated a small simplified mathematical model encompassing ligand binding, followed by receptor dimerization, activation, and degradation. The model predicts ErbB phosphorylation in HEK293, MCF-7, and keratinocyte cells simply by incorporating cell-type-specific ErbB1, ErbB2, and caveolin-1 abundances but otherwise contains similar rate constants. Altogether, the data provide a resource for protein abundances and localization to be included in larger mathematical models, enabling the generation of cell-type-specific computational models. MS data have been deposited to the ProteomeXchange via PRIDE (with identifier PXD000623) and PASSEL (with identifier PASS00372).
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Affiliation(s)
- Christina Kiel
- EMBL/CRG Systems Biology Research Unit, ‡Proteomics Unit, §Advanced Light Microscopy Core Facility, Centre for Genomic Regulation (CRG) , Dr. Aiguader 88, 08003 Barcelona, Spain
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