Human serum proteome analysis: New source of markers in metabolic disorders

Biomarkers in Medicine

Volumn 6, Issue 6, 2012, Pages 759-773

  Di Girolamo, Francesco ^a   Del Chierico, Federica ^a   Caenaro, Gianfranco ^b   Lante, Isabella ^b   Muraca, Maurizio ^a   Putignani, Lorenza ^a  

^a BAMBINO GESÙ CHILDREN S HOSPITAL   (Italy)

^b SAN CAMILLO HOSPITAL   (Italy)

Author keywords

biomarkers; metabolic disorders; metaproteomics; serum proteomics; SWATH MS

Indexed keywords

BIOLOGICAL MARKER; PROTEOME;

BIOREACTOR; BLOOD CHEMISTRY; CARDIOVASCULAR RISK; COMBINATORIAL CHEMISTRY; EARLY DIAGNOSIS; HUMAN; INSULIN DEPENDENT DIABETES MELLITUS; INSULIN RESISTANCE; INTESTINE FLORA; LIQUID CHROMATOGRAPHY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; METABOLIC DISORDER; NON INSULIN DEPENDENT DIABETES MELLITUS; NONALCOHOLIC FATTY LIVER; NONHUMAN; PEPTIDE LIBRARY; PROGNOSIS; PROTEIN ANALYSIS; PROTEIN BLOOD LEVEL; PROTEOMICS; QUANTITATIVE ANALYSIS; REVIEW; RISK ASSESSMENT; RISK FACTOR; SURFACE ENHANCED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; TWO DIMENSIONAL GEL ELECTROPHORESIS;

ANIMALS; BIOLOGICAL MARKERS; HUMANS; INTESTINES; METABOLIC DISEASES; METAGENOME; PROTEOME; PROTEOMICS;

EID: 84870922664     PISSN: 17520363     EISSN: 17520371     Source Type: Journal    
DOI: 10.2217/bmm.12.92     Document Type: Review

References (108)

1. Garrod AE. Alkaptonuria. In: Inborn Errors of Metabolism. Garrod AE (Ed.). Oxford University Press, UK, 43-64 (1923
2. Powers AC. Diabetes mellitus. In: Harrison's Principles of Internal Medicine. Kasper DL, Braunwald E, Fauci AS et al. (Eds). McGraw-Hill, NY, USA, 2152-2180 (2005
3. Knip M, Simell O. Environmental triggers of Type 1 diabetes. Cold Spring Harb. Perspect. Med. 2, a007690 (2012
4. Masharani U, German MS. Pancreatic hormones and diabetes mellitus. In: Greenspan's Basic & Clinical Endocrinology. Gardner D, Shoback D (Eds). McGraw-Hill, NY, USA, 573-655 (2011
5. Berends LM, Ozanne SE. Early determinants of Type-2 diabetes. Best Pract. Res. Clin. Endocrinol. Metab. 28, 569-580 (2012
6. Fasanmade OA, Odeniyi IA, Ogbera AO. Diabetic ketoacidosis: Diagnosis and management. Afr. J. Med. Med. Sci. 37, 99-105 (2008
7. Pasquier F. Diabetes and cognitive impairment: How to evaluate the cognitive status? Diabetes Metab. 36(SUPPL3), S100-S105 (2010
8. Ripsin CM, Kang H, Urban RJ. Management of blood glucose in Type 2 diabetes mellitus. Am. Fam. Physician 79, 29-36 (2009
9. Risérus U, Willett WC, Hu FB. Dietary fats and prevention of Type 2 diabetes. Prog. Lipid Res. 48, 44-51 (2009
10. Christian P, Stewart CP. Maternal micronutrient deficiency, fetal development, and the risk of chronic disease. J. Nutr. 140, 437-445 (2010
11. Herder C, Roden M. Genetics of Type 2 diabetes: Pathophysiologic and clinical relevance. Eur. J. Clin. Invest. 41, 679-692 (2011
12. McCarthy MI. Genomics, Type 2 diabetes, and obesity. N. Engl. J. Med. 363, 2339-2350 (2012
13. Grundy SM, Brewer HB Jr, Cleeman JI, Smith SC Jr, Lenfant C; American Heart Association; National Heart, Lung, and Blood Institute. Definition of metabolic syndrome: Report of the National Heart, Lung, and Blood Institute/American Heart Association conference on scientific issues related to definition. Circulation 109, 433-438 (2004
14. den Boer M, Voshol PJ, Kuipers F, Havekes LM, Romijn JA. Hepatic steatosis: A mediator of the metabolic syndrome. Lessons from animal models. Arterioscler. Thromb. Vasc. Biol. 24, 644-649 (2004
15. Wisse BE. The inflammatory syndrome: The role of adipose tissue cytokines in metabolic disorders linked to obesity. J. Am. Soc. Nephrol. 15, 2792-2800 (2004
16. Vernon G, Baranova A, Younossi ZM. Systematic review: The epidemiology and natural history of non-Alcoholic fatty liver disease and non-Alcoholic steatohepatitis in adults. Aliment Pharmacol. Ther. 34, 274-285 (2011
17. Alisi A, Carsetti R, Nobili V. Pathogen- or damage-Associated molecular patterns during nonalcoholic fatty liver disease development. Hepatology 54, 1500-1502 (2011
18. Tilg H, Moschen AR. Insulin resistance, inflammation, and non-Alcoholic fatty liver disease. Trends Endocrinol. Metab. 19, 371-379 (2008
19. Malaguarnera M, Di Rosa M, Nicoletti F, Malaguarnera L. Molecular mechanisms involved in NAFLD progression. J. Mol. Med. (Berl.) 87, 679-695 (2009
20. Manco M, Putignani L, Bottazzo GF. Gut microbiota, lipopolysaccharides, and innate immunity in the pathogenesis of obesity and cardiovascular risk. Endocr. Rev. 31, 817-844 (2010
21. Del Chierico F, Vernocchi P, Bonizzi L et al. Early-life gut microbiota under physiological and pathological conditions: The central role of combined meta-omics-based approaches. J. Proteomics 75, 4580-4587 (2012
22. Musso G, Gambino R, Cassader M. Gut microbiota as a regulator of energy homeostasis and ectopic fat deposition: Mechanisms and implications for metabolic disorders. Curr. Opin. Lipidol. 21, 76-83 (2010
23. Cani PD, Delzenne NM. The role of the gut microbiota in energy metabolism and metabolic disease. Curr. Pharm. Des. 15, 1546-1558 (2009
24. Othman M, Agüero R, Lin HC. Alterations in intestinal microbial flora and human disease. Curr. Opin. Gastroenterol. 24, 11-16 (2008
25. Compare D, Coccoli P, Rocco A et al. Gut-liver axis: The impact of gut microbiota on non alcoholic fatty liver disease. Nutr. Metab. Cardiovasc. Dis. 22, 471-476 (2012
26. De Gottardi A, McCoy KD. Evaluation of the gut barrier to intestinal bacteria in nonalcoholic fatty liver disease. J. Hepatol. 55, 1181-1183 (2011
27. Miele L, Valenza V, La Torre G et al. Increased intestinal permeability and tight junction alterations in nonalcoholic fatty liver disease. Hepatology 49, 1877-1887 (2009
28. Cani PD, Amar J, Iglesias MA et al. Metabolic endotoxemia initiates obesity and insulin resistance. Diabetes 56, 1761-1772 (2007
29. Musso G, Gambino R, Cassader M. Obesity, diabetes, and gut microbiota: The hygiene hypothesis expanded? Diabetes Care 33, 2277-2284 (2010
30. Alisi A, Manco M, Devito R, Piemonte F, Nobili V. Endotoxin and plasminogen activator inhibitor-1 serum levels associated with nonalcoholic steatohepatitis in children. J. Pediatr. Gastroenterol. Nutr. 50, 645-649 (2010
31. Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Microbial ecology: Human gut microbes associated with obesity. Nature 444, 1022-1023 (2006
32. Turnbaugh PJ, Hamady M, Yatsunenko T et al. A core gut microbiome in obese and lean twins. Nature 480, 480-484 (2009
33. Turnbaugh PJ, Gordon JI. The core gut microbiome, energy balance and obesity. J. Physiol. 587(PT17), 4153-4158 (2009
34. Bäckhed F, Ding H, Wang T et al. The gut microbiota as an environmental factor that regulates fat storage. Proc. Natl Acad. Sci. USA 101, 15718-15723 (2004
35. Towle HC. Glucose and cAMP: Adversaries in the regulation of hepatic gene expression. Proc. Natl Acad. Sci. USA 98, 13476-13478 (2001
36. Dentin R, Pégorier JP, Benhamed F et al. Hepatic glucokinase is required for the synergistic action of ChREBP and SREBP1c on glycolytic and lipogenic gene expression. J. Biol. Chem. 279, 20314-20326 (2004
37. Bäckhed F, Manchester JK, Semenkovich CF, Gordon JI. Mechanisms underlying the resistance to diet-Induced obesity in germfree mice. Proc. Natl Acad. Sci. USA 104, 979-984 (2007
38. Xue B, Kahn BB. AMPK integrates nutrient and hormonal signals to regulate food intake and energy balance through effects in the hypothalamus and peripheral tissues. J. Physiol. 574(PT1), 73-83 (2006
39. Kahn BB, Alquier T, Carling D, Hardie DG. AMP-Activated protein kinase: Ancient energy gauge provides clues to modern understanding of metabolism. Cell Metab. 1, 15-25 (2005
40. Ruderman NB, Saha AK. Metabolic syndrome: Adenosine monophosphateactivated protein kinase and malonyl coenzyme A. Obesity (Silver Spring) 14(SUPPL1), 25S-33S (2006
41. Ebert M P, Korc M, Malfertheiner P, Rocken C. Advances, challenges, and limitations in serum-proteome based cancer diagnosis. J. Proteome Res. 5, 19-25 (2006
42. Petricoin EF, Zoon KC, Kohn EC, Barrett JC, Liotta LA. Clinical proteomics: Translating benchside promise into bedside reality. Nat. Rev. Drug Discov. 1, 683-695 (2002
43. Blonder J, Issaq HJ, Veenstra TD. Proteomic biomarker discovery: It's more than just mass spectrometry. Electrophoresis 32, 1541-1548 (2011
44. Righetti PG, Boschetti E, Lomas L, Citterio A. Protein equalizer technology: The quest for a 'democratic proteome'. Proteomics 6, 3980-3992 (2006
45. Keidel EM, Ribitsch D, Lottspeich F. Equalizer technology - equal rights for disparate beads. Proteomics 10, 2089-2098 (2010
46. Anderson NL. The clinical plasma proteome: A survey of clinical assays for proteins in plasma serum. Clin. Chem. 56, 177-185 (2010
47. Shen Y, Kim J, Strittmatter EF et al. Characterization of the human blood plasma proteome. Proteomics 5, 4034-4045 (2005
48. Barelli S, Canellini G, Thadikkaran L et al. Oxidation of proteins: Basic principles and perspectives for blood proteomics. Proteomics Clin. Appl. 2, 142-157 (2008
49. D'Amici GM, Rinalducci S, Zolla L. Proteomic analysis of RBC membrane protein degradation during blood storage. J. Proteome Res. 6, 3242-3255 (2007
50. Issaq HJ, Xiao Z, Veenstra TD. Serum and plasma proteomics. Chem. Rev. 107, 3601-2360 (2007
51. Gloerich J, Wevers RA, Smeitink JA, van Engelen BG, van den Heuvel LP. Proteomics approaches to study genetic and metabolic disorders. J. Proteome Res. 6, 506-512 (2007)
52. Lilley KS, Razzaq A, Dupree P. Two dimensional gel electrophoresis: Recent advances in sample preparation, detection and quantitation. Curr. Opin. Chem. Biol. 6, 46-50 (2002
53. Issaq HJ, Veenstra TD, Conrads TP, Felschow D. The SELDI-TOF MS approach to proteomics: Protein profiling and biomarker identification. Biochem. Biophys. Res. Commun. 292, 587-592 (2002)
54. Travis J, Pannell R. Selective removal of albumin from plasma 426 by affinity chromatography. Clin. Chim. Acta 49, 49-52 (1973
55. McDonald WH, Yates JR 3rd. Shotgun proteomics and biomarker discovery. Dis. Markers 18, 99-105 (2002).
56. Picotti P, Aebersold R. Selected reaction monitoring-based proteomics: Workflows, potential, pitfalls and future directions. Nat. Methods 30, 555-566 (2012
57. Gillet LC, Navarro P, Tate S et al. Targeted data extraction of the MS/MS spectra generated by data-Independent acquisition: A new concePTfor consistent and accurate proteome analysis. Mol. Cell. Proteomics 11, O111.016717 (2012
58. Birkenmeier G, Usbeck E, Saro L, Kopperschläger G. Triazine dye binding of human alpha-fetoprotein and albumin. J. Chromatogr. 265, 27-35 (1983
59. Birkenmeier G, Kopperschläger G. Application of dye-ligand chromatography to the isolation of alpha-1-proteinase inhibitor and alpha-1-Acid glycoprotein. J. Chromatogr. 235, 237-248 (1982
60. Fang X, Zhang WW. Affinity separation and enrichment methods in proteomic analysis. J. Proteomics 71, 284-303 (2008
61. Righetti PG, Boschetti E. The ProteoMiner and the FortyNiners: Searching for gold nuggets in the proteomic arena. Mass Spectrom. Rev. 27, 596-608 (2008
62. Boschetti E, Righetti PG. The art of observing rare protein species in proteomes with peptide ligand libraries. Proteomics 9, 1492-1510 (2009
63. Boschetti E, Lomas L, Citterio A, Righetti PG. Romancing the "hidden proteome", anno domini two zero zero seven. J. Chromatogr. A 1153, 277-290 (2007
64. Steel LF, Trotter MG, Nakajima PB, Mattu TS, Gonye G, Block T. Efficient and specific removal of albumin from human serum samples. Mol. Cell. Proteomics 2, 262-270 (2003
65. Pieper R, Su Q, Gatlin CL, Huang ST, Anderson NL, Steiner S. Multi-component immunoaffinity subtraction chromatography: An innovative step towards a comprehensive survey of the human plasma proteome. Proteomics 3, 422-432 (2003
66. Stuart CA, Pietrzyk RA, Furlanetto RW, Green A. High-Affinity antibody from hens eggs directed against the human insulinreceptor and the human IGF-I receptor. Anal. Biochem. 173, 142-150 (1988
67. Gassmann M, Thömmes P, Weiser T, Hübscher U. Efficient production of chicken egg yolk antibodies against a conserved mammalian protein. FASEB J. 4, 2528-2532 (1990
68. Larsson A, Karlsson-Parra A, Sjöquist J. Use of chicken antibodies in enzyme immunoassays to avoid interference by rheumatoid factors. Clin. Chem. 37, 411-414 (1991
69. Gundry RL, White MY, Nogee J, Tchernyshyov I, Van Eyk JE. Assessment of albumin removal from an immunoaffinity spin column: Critical implications for proteomic examination of the albuminome and albumin-depleted samples. Proteomics 9, 2021-2028 (2009
70. Dayarathna MK, Hancock WS, Hincapie M. A two step fractionation approach for plasma proteomics using immunodepletion of abundant proteins and multi-lectin affinity chromatography: Application to the analysis of obesity, diabetes, and hypertension diseases. J. Sep. Sci. 31, 1156-1166 (2008
71. Zhang Q, Monroe ME, Schepmoes AA et al. Comprehensive identification of glycated peptides and their glycation motifs in plasma and erythrocytes of control and diabetic subjects. J. Proteome Res. 10, 3076-3088 (2011
72. Sennels L, Salek M, Lomas L, Boschetti E, Righetti PG, Rappsilber J. Proteomic analysis of human blood serum using peptide library beads. J. Proteome Res. 6, 4055-4062 (2007
73. Righetti PG, Fasoli E, Boschetti E. Combinatorial peptide ligand libraries: The conquest of the 'hidden proteome' advances at great strides. Electrophoresis 32, 960-966 (2011
74. Zhi W, Purohit S, Carey C, Wang M, She JX. Proteomic technologies for the discovery of Type 1 diabetes biomarkers. J. Diabetes Sci. Technol. 4, 993-1002 (2010
75. O'Farrell PH. High resolution twodimensional electrophoresis of proteins. J. Biol. Chem. 250, 4007-4021 (1975
76. Klose J. Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. A novel approach to testing for induced point mutations in mammals. Humangenetik 26, 231-243 (1975
77. Tonge R, Shaw J, Middleton B et al. Validation and development of fluorescence two dimensional differential gel electrophoresis proteomics technology. Proteomics 1, 377-396 (2001
78. Kim HJ, Cho EH, Yoo JH et al. Proteome analysis of serum from Type 2 diabetics with nephropathy. J. Proteome Res. 6, 735-743 (2007
79. Liu YP, Hu SW, Wu ZF, Mei LX, Lang P, Lu XH. Proteomic analysis of human serum from diabetic retinopathy. Int. J. Ophthalmol. 4, 616-622 (2011
80. Hung PH, Chen YW, Cheng KC et al. Plasma proteomic analysis of the critical limb ischemia markers in diabetic patients with hemodialysis. Mol. Biosyst. 7, 1990-1998 (2011
81. Chen CC, Lu YC, Chen YW et al. Hemopexin is up-regulated in plasma from Type 1 diabetes mellitus patients: Role of glucose-Induced ROS. J. Proteomics 75, 3760-3777 (2012
82. Cho WC, Yip TT, Chung WS, Leung AW, Cheng CH, Yue KK. Differential expression of proteins in kidney, eye, aorta, and serum of diabetic and non-diabetic rats. J. Cell. Biochem. 99, 256-268 (2006
83. Trak-Smayra V, Dargere D, Noun R et al. Serum proteomic profiling of obese patients: Correlation with liver pathology and evolution after bariatric surgery. Gut 58, 825-832 (2009
84. Dayal B, Ertel NH. ProteinChip technology: A new and facile method for the identification and measurement of high-density lipoproteins ApoA-I and ApoA-II and their glycosylated products in patients with diabetes and cardiovascular disease. J. Proteome Res. 1, 375-380 (2002
85. Kiga C, Nakagawa T, Koizumi K et al. Expression patterns of plasma proteins in spontaneously diabetic rats after oral administration of a Kampo medicine, Hachimi-jio-gan, using SELDI ProteinChip platform. Biol. Pharm. Bull. J. 28, 1031-1037 (2005
86. Elased KM, Cool DR, Morris M. Novel mass spectrometric methods for evaluation of plasma angiotensin converting enzyme 1 and renin activity. Hypertension 46, 953-959 (2005
87. Sharma AM, Janke J, Gorzelniak K, Engeli S, Luft FC. Angiotensin blockade prevents Type 2 diabetes by formation of fat cells. Hypertension 40, 609-611 (2002
88. Sundsten T, Eberhardson M, Göransson M, Bergsten P. The use of proteomics in identifying differentially expressed serum proteins in humans with Type 2 diabetes. Proteome Sci. 4, 22 (2006
89. Sundsten T, Zethelius B, Berne C, Bergsten P. Plasma proteome changes in subjects with Type 2 diabetes mellitus with a low or high early insulin response. Clin. Sci. (Lond.) 114, 499-507 (2008
90. Yang YH, Zhang S, Cui JF et al. Diagnostic potential of serum protein pattern in Type 2 diabetic nephropathy. Diabet. Med. 24, 1386-1392 (2007
91. McGuire JN, Eising S, Wägner AM, Pociot F. Screening newborns for candidate biomarkers of Type 1 diabetes. Arch. Physiol. Biochem. 116, 227-232 (2010
92. Kim SM, Park JS, Norwitz ER et al. Identification of proteomic biomarkers in maternal plasma in the early second trimester that predict the subsequent development of gestational diabetes. Reprod. Sci. 19, 202-209 (2012
93. Floreani A, Navaglia F, Rizzotto ER et al. Mass spectrometry measurement of plasma hepcidin for the prediction of iron overload. Clin. Chem. Lab. Med. 49, 197-206 (2011
94. Mæland Nilsen M, Uleberg KE, Janssen EA, Baak JP, Andersen OK, Hjelle A. SELDI-TOF MS to protein identification by on-chip elution. J. Proteomics 74, 2995-2998 (2011
95. Jensen TM, Witte DR, Pieragostino D et al. Association between protein signals and Type 2 diabetes incidence. Acta Diabetol. doi:10.1007/s00592-012- 0376-3 (2012) (Epub ahead of print
96. Riaz S, Alam SS, Akhtar MW. Proteomic identification of human serum biomarkers in diabetes mellitus Type 2. J. Pharm. Biomed. Anal. 51, 1103-1107 (2010
97. Tang W, Shi YQ, Zou JJ et al. Serum biomarker of diabetic peripheral neuropathy indentified by differential proteomics. Front. Biosci. 16, 2671-2681 (2011
98. Gagnon H, Franck J, Wisztorski M, Day R, Fournier I, Salzet M. Targeted mass spectrometry imaging: Specific targeting mass spectrometry imaging technlogies from history to perspective. Prog. Histochem. Cytochem. 47, 133-174 (2012
99. Bischoff R, Luider TM. Methodological advances in the discovery of protein and peptide disease markers. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 803, 27-40 (2004
100. Metz TO, Qian WJ, Jacobs JM et al. Application of proteomics in the discovery of candidate protein biomarkers in a diabetes autoantibody standardization program sample subset. J. Proteome Res. 7, 698-707 (2008
101. Becker CH, Bern M. Recent developments in quantitative proteomics. Mutat. Res. 722, 171-182 (2011).
102. Imai K, Koshiyama A, Nakata K. Towards clinical proteomics analysis. Biomed. Chromatogr. 25, 59-64 (2011
103. Brun V, Masselon C, Garin J, Dupuis A. Isotope dilution strategies for absolute quantitative proteomics. J. Proteomics 72, 740-749 (2009
104. Kirkpatrick DS, Gerber SA, Gygi SP. The absolute quantification strategy: A general procedure for the quantification of proteins and post-Translational modifications. Methods 35, 265-273 (2005
105. Zhang G, Ueberheide BM, Waldemarson S et al. Protein quantitation using mass spectrometry. Methods Mol. Biol. 673, 211-222 (2010
106. Vissers JP, Langridge JI, Aerts JM. Analysis and quantification of diagnostic serum markers and protein signatures for Gaucher disease. Mol. Cell Proteomics 6, 755-766 (2007
107. Omenn GS, States DJ, Adamski M et al. Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publiclyavailable database. Proteomics 5, 3226-3245 (2005
108. Di Girolamo F, Alessandroni J, Somma P, Guadagni F. Pre-Analytical operating procedures for serum low molecular weight protein profiling. J. Proteomics 73, 667-677 (2010