Proteomics analysis of tumor microenvironment: Implications of metabolic and oxidative stresses in tumorigenesis

Mass Spectrometry Reviews

Volumn 32, Issue 4, 2013, Pages 267-311

  Zhao, Xia ^b   Zhou, Shengtao ^a,b   Liu, Rui ^a   Yuan, Kefei ^a   Yi, Tao ^b   Huang, Canhua ^a   Wei, Yuquan ^a  

^a SICHUAN UNIVERSITY   (China)

^b SICHUAN UNIVERSITY   (China)

Author keywords

metabolic stress; oxidative stress; proteomics; tumorigenesis

Indexed keywords

APOPTOTIC CELL DEATH; GLUCOSE CONSUMPTION; METABOLIC STRESS; OXIDATIVE PHOSPHORYLATION; PROTEOMICS; REACTIVE OXYGEN SPECIES; TUMOR MICROENVIRONMENT; TUMORIGENESIS;

BIOELECTRIC POTENTIALS; CELL DEATH; CYTOTOXICITY; ENZYME ACTIVITY; METABOLISM; MOLECULAR BIOLOGY; OXIDATIVE STRESS; PATHOLOGY; PROTEINS;

TUMORS;

REACTIVE OXYGEN METABOLITE;

ANIMAL; CARCINOGENESIS; HUMAN; MASS SPECTROMETRY; METABOLISM; METHODOLOGY; OXIDATIVE STRESS; PATHOLOGY; PROTEOMICS; REVIEW; TUMOR MICROENVIRONMENT;

ANIMALS; CARCINOGENESIS; HUMANS; MASS SPECTROMETRY; OXIDATIVE STRESS; PROTEOMICS; REACTIVE OXYGEN SPECIES; TUMOR MICROENVIRONMENT;

EID: 84878773449     PISSN: 02777037     EISSN: 10982787     Source Type: Journal    
DOI: 10.1002/mas.21362     Document Type: Review

References (275)

1. Adam J, Hatipoglu E, O'Flaherty L, Ternette N, Sahgal N, Lockstone H, Baban D, Nye E, Stamp GW, Wolhuter K, Stevens M, Fischer R, Carmeliet P, Maxwell PH, Pugh CW, Frizzell N, Soga T, Kessler BM, El-Bahrawy M, Ratcliffe PJ, Pollard PJ,. 2011. Renal cyst formation in Fh1-deficient mice is independent of the Hif/Phd pathway: Roles for fumarate in Keap1 succination and Nrf2 signaling. Cancer Cell 20: 524-537.
2. Addona TA, Abbatiello SE, Schilling B, Skates SJ, Mani DR, Bunk DM, Spiegelman CH, Zimmerman LJ, Ham AJ, Keshishian H, Hall SC, Allen S, Blackman RK, Borchers CH, Buck C, Cardasis HL, Cusack MP, Dodder NG, Gibson BW, Held JM, Hiltke T, Jackson A, Johansen EB, Kinsinger CR, Li J, Mesri M, Neubert TA, Niles RK, Pulsipher TC, Ransohoff D, Rodriguez H, Rudnick PA, Smith D, Tabb DL, Tegeler TJ, Variyath AM, Vega-Montoto LJ, Wahlander A, Waldemarson S, Wang M, Whiteaker JR, Zhao L, Anderson NL, Fisher SJ, Liebler DC, Paulovich AG, Regnier FE, Tempst P, Carr SA,. 2009. Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat Biotechnol 27: 633-641.
3. Airley RE, Mobasheri A,. 2007. Hypoxic regulation of glucose transport, anaerobic metabolism and angiogenesis in cancer: Novel pathways and targets for anticancer therapeutics. Chemotherapy 53: 233-256. (Pubitemid 47074647)
4. Albanese C, Machado FS, Tanowitz HB,. 2011. Glutamine and the tumor microenvironment: Understanding the mechanisms that fuel cancer progression. Cancer Biol Ther 12: 1098-1100.
5. Amann T, Maegdefrau U, Hartmann A, Agaimy A, Marienhagen J, Weiss TS, Stoeltzing O, Warnecke C, Schoelmerich J, Oefner PJ, Kreutz M, Bosserhoff AK, Hellerbrand C,. 2009. GLUT1 expression is increased in hepatocellular carcinoma and promotes tumorigenesis. Am J Pathol 174: 1544-1552.
6. Anastasiou D, Poulogiannis G, Asara JM, Boxer MB, Jiang J-K, Shen M, Bellinger G, Sasaki AT, Locasale JW, Auld DS, Thomas CJ, Vander Heiden MG, Cantley LC,. 2011. Inhibition of pyruvate kinase M2 by reactive oxygen species contributes to cellular antioxidant responses. Science 334: 1278-1283.
7. Ashrafian H, O'Flaherty L, Adam J, Steeples V, Chung Y-L, East P, Vanharanta S, Lehtonen H, Nye E, Hatipoglu E, Miranda M, Howarth K, Shukla D, Troy H, Griffiths J, Spencer-Dene B, Yusuf M, Volpi E, Maxwell PH, Stamp G, Poulsom R, Pugh CW, Costa B, Bardella C, Di Renzo MF, Kotlikoff MI, Launonen V, Aaltonen L, El-Bahrawy M, Tomlinson I, Pollard PJ,. 2010. Expression profiling in progressive stages of fumarate-hydratase deficiency: The contribution of metabolic changes to tumorigenesis. Cancer Res 70: 9153-9165.
8. Azad NS, Rasool N, Annunziata CM, Minasian L, Whiteley G, Kohn EC,. 2006. Proteomics in clinical trials and practice-present uses and future promise. Mol Cell Proteomics 5: 1819-1829. (Pubitemid 44688191)
9. Bae YS, Oh H, Rhee SG, Do Yoo Y,. 2011. Regulation of reactive oxygen species generation in cell signaling. Mol Cells 32: 491-509.
10. Balliet RM, Capparelli C, Guido C, Pestell TG, Martinez-Outschoorn UE, Lin Z, Whitaker-Menezes D, Chiavarina B, Pestell RG, Howell A, Sotgia F, Lisanti MP,. 2011. Mitochondrial oxidative stress in cancer-associated fibroblasts drives lactate production, promoting breast cancer tumor growth-understanding the aging and cancer connection. Cell Cycle 10: 4065-4073.
11. Bensaad K, Tsuruta A, Selak MA, Calvo Vidal MN, Nakano K, Bartrons R, Gottlieb E, Vousden KH,. 2006. TIGAR, a p53-inducible regulator of glycolysis and apoptosis. Cell 126: 107-120. (Pubitemid 44040989)
12. Birner P, Gatterbauer B, Oberhuber G, Schindl M, Rossler K, Prodinger A, Budka H, Hainfellner JA,. 2001. Expression of hypoxia-inducible factor-1 alpha in oligodendrogliomas-its impact on prognosis and on neoangiogenesis. Cancer 92: 165-171. (Pubitemid 32623053)
13. Bonuccelli G, Tsirigos A, Whitaker-Menezes D, Pavlides S, Pestell RG, Chiavarina B, Frank PG, Flomenberg N, Howell A, Martinez-Outschoorn UE, Sotgia F, Lisanti MP,. 2010. Ketones and lactate "fuel" tumor growth and metastasis Evidence that epithelial cancer cells use oxidative mitochondrial metabolism. Cell Cycle 9: 3506-3514.
14. Brar SS, Kennedy TP, Sturrock AB, Huecksteadt TP, Quinn MT, Whorton AR, Hoidal JR,. 2002. An NAD(P)H oxidase regulates growth and transcription in melanoma cells. Am J Physiol Cell Physiol 282: C1212-1224. (Pubitemid 34663069)
15. Brase JC, Mannsperger H, Sueltmann H, Korf U,. 2011. Antibody-mediated signal amplification for reverse phase protein array-based protein quantification. Methods Mol Biol 785: 55-64.
16. Brockmoeller SF, Bucher E, Mueller BM, Budczies J, Hilvo M, Griffin JL, Oresic M, Kallioniemi O, Iljin K, Loibl S, Darb-Esfahani S, Sinn BV, Klauschen F, Prinzler J, Bangemann N, Ismaeel F, Fiehn O, Dietel M, Denkert C,. 2012. Integration of metabolomics and expression of glycerol-3-phosphate acyltransferase (GPAM) in breast cancer-link to patient survival, hormone receptor status, and metabolic profiling. J Proteome Res 11: 850-860.
17. Brooks GA,. 2009. Cell-cell and intracellular lactate shuttles. J Physiol 587: 5591-5600.
18. Brown M, Dunn WB, Dobson P, Patel Y, Winder CL, Francis-McIntyre S, Begley P, Carroll K, Broadhurst D, Tseng A, Swainston N, Spasic I, Goodacre R, Kell DB,. 2009. Mass spectrometry tools and metabolite-specific databases for molecular identification in metabolomics. Analyst 134: 1322-1332.
19. Cairns RA, Harris IS, Mak TW,. 2011. Regulation of cancer cell metabolism. Nat Rev Cancer 11: 85-95.
20. Cannito S, Novo E, Compagnone A, Valfre di Bonzo L, Busletta C, Zamara E, Paternostro C, Povero D, Bandino A, Bozzo F, Cravanzola C, Bravoco V, Colombatto S, Parola M,. 2008. Redox mechanisms switch on hypoxia-dependent epithelial-mesenchymal transition in cancer cells. Carcinogenesis 29: 2267-2278.
21. Cao Z, Song JH, Kang YW, Yoon JH, Nam SW, Lee JY, Park WS,. 2010. Analysis of succinate dehydrogenase subunit B gene alterations in gastric cancers. Pathol Int 60: 559-565.
22. Celis JE, Gromov P, Cabezon T, Moreira JMA, Ambartsumian N, Sandelin K, Rank F, Gromova I,. 2004. Proteomic characterization of the interstitial fluid perfusing the breast tumor microenvironment-A novel resource for biomarker and therapeutic target discovery. Mol Cell Proteomics 3: 327-344. (Pubitemid 38702087)
23. Chan HL, Gharbi S, Gaffney PR, Cramer R, Waterfield MD, Timms JF,. 2005. Proteomic analysis of redox- and ErbB2-dependent changes in mammary luminal epithelial cells using cysteine- and lysine-labelling two-dimensional difference gel electrophoresis. Proteomics 5: 2908-2926. (Pubitemid 41059768)
24. Chan HL, Sinclair J, Timms JF,. 2012. Proteomic analysis of redox-dependent changes using cysteine-labeling 2D DIGE. Methods Mol Biol 854: 113-128.
25. Chang KP, Yu JS, Chien KY, Lee CW, Liang Y, Liao CT, Yen TC, Lee LY, Huang LL, Liu SC, Chang YS, Chi LM,. 2011. Identification of PRDX4 and P4HA2 as metastasis-associated proteins in oral cavity squamous cell carcinoma by comparative tissue proteomics of microdissected specimens using iTRAQ technology. J Proteome Res 10: 4935-4947.
26. Chen EI, Yates JR,. 2007. Cancer proteomics by quantitative shotgun proteomics. Mol Oncol 1: 144-159. (Pubitemid 47208627)
27. Chen R, Brentnall TA, Pan S, Cooke K, Moyes KW, Lane Z, Crispin DA, Goodlett DR, Aebersold R, Bronner MP,. 2007. Quantitative proteomics analysis reveals that proteins differentially expressed in chronic pancreatitis are also frequently involved in pancreatic cancer. Mol Cell Proteomics 6: 1331-1342. (Pubitemid 47365432)
28. Chen QR, Song YK, Yu LR, Wei JS, Chung JY, Hewitt SM, Veenstra TD, Khan J,. 2010a. Global genomic and proteomic analysis identifies biological pathways related to high-risk neuroblastoma. J Proteome Res 9: 373-382.
29. Chen YT, Chen CL, Chen HW, Chung T, Wu CC, Chen CD, Hsu CW, Chen MC, Tsui KH, Chang PL, Chang YS, Yu JS,. 2010b. Discovery of novel bladder cancer biomarkers by comparative urine proteomics using iTRAQ technology. J Proteome Res 9: 5803-5815.
30. Chiang KP, Niessen S, Saghatelian A, Cravatt BF,. 2006. An enzyme that regulates ether lipid signaling pathways in cancer annotated by multidimensional profiling. Chem Biol 13: 1041-1050. (Pubitemid 44557068)
31. Chiurchiu V, Maccarrone M,. 2011. Chronic inflammatory disorders and their redox control: From molecular mechanisms to therapeutic opportunities. Antioxid Redox Signal 15: 2605-2641.
32. Choe LH, Lee KH,. 2003. Quantitative and qualitative measure of intralaboratory two-dimensional protein gel reproducibility and the effects of sample preparation, sample load, and image analysis. Electrophoresis 24: 3500-3507. (Pubitemid 38089154)
33. Chong PK, Gan CS, Pham TK, Wright PC,. 2006. Isobaric tags for relative and absolute quantitation (iTRAQ) reproducibility: Implication of multiple injections. J Proteome Res 5: 1232-1240. (Pubitemid 43727802)
34. Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, Walther TC, Olsen JV, Mann M,. 2009. Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science 325: 834-840.
35. Chowdhury R, Yeoh KK, Tian Y-M, Hillringhaus L, Bagg EA, Rose NR, Leung IKH, Li XS, Woon ECY, Yang M, McDonough MA, King ON, Clifton IJ, Klose RJ, Claridge TDW, Ratcliffe PJ, Schofield CJ, Kawamura A,. 2011. The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases. EMBO Rep 12: 463-469.
36. Chung KH, Lee DH, Kim Y, Kim TH, Huh JH, Chung SG, Lee S, Lee C, Ko JJ, An HJ,. 2010. Proteomic identification of overexpressed PRDX1 and its clinical implications in ovarian carcinoma. J Proteome Res 9: 451-457.
37. Cortesi L, Barchetti A, De Matteis E, Rossi E, Della Casa L, Marcheselli L, Tazzioli G, Lazzaretti MG, Ficarra G, Federico M, Iannone A,. 2009. Identification of protein clusters predictive of response to chemotherapy in breast cancer patients. J Proteome Res 8: 4916-4933.
38. Cottingham K,. 2006. NCI CPTI: Technologies for proteomics. J Proteome Res 5: 2502.
39. Crighton D, Wilkinson S, O'Prey J, Syed N, Smith P, Harrison PR, Gasco M, Garrone O, Crook T, Ryan KM,. 2006. DRAM, a p53-induced modulator of autophagy, is critical for apoptosis. Cell 126: 121-1134.
40. Dall'Agnol M, Bernstein C, Bernstein H, Garewal H, Payne CM,. 2006. Identification of S-nitrosylated proteins after chronic exposure of colon epithelial cells to deoxycholate. Proteomics 6: 1654-1662.
41. Dang CV,. 2007. The interplay between MYC and HIF in the Warburg effect. Ernst Schering Found Symp Proc 4: 35-53.
42. Dang CV,. 2010. Glutaminolysis-supplying carbon or nitrogen or both for cancer cells? Cell Cycle 9: 3884-3886.
43. Dang CV, Le A, Gao P,. 2009. MYC-induced cancer cell energy metabolism and therapeutic opportunities. Clin Cancer Res 15: 6479-6483.
44. Dang L, White DW, Gross S, Bennett BD, Bittinger MA, Driggers EM, Fantin VR, Jang HG, Jin S, Keenan MC, Marks KM, Prins RM, Ward PS, Yen KE, Liau LM, Rabinowitz JD, Cantley LC, Thompson CB, Heiden MGV, Su SM,. 2009. Cancer-associated IDH1 mutations produce 2-hydroxyglutarate. Nature 462: 739-744.
45. Das SK, Eder S, Schauer S, Diwoky C, Temmel H, Guertl B, Gorkiewicz G, Tamilarasan KP, Kumari P, Trauner M, Zimmermann R, Vesely P, Haemmerle G, Zechner R, Hoefler G,. 2011. Adipose triglyceride lipase contributes to cancer-associated cachexia. Science 333: 233-238.
46. De Marco F, Bucaj E, Foppoli C, Fiorini A, Blarzino C, Filipi K, Giorgi A, Schinina ME, Di Domenico F, Coccia R, Butterfield DA, Perluigi M,. 2012. Oxidative stress in HPV-driven viral carcinogenesis: Redox proteomics analysis of HPV-16 dysplastic and neoplastic tissues. PLoS ONE 7: e34366.
47. de Molina AR, Sormentero-Estrada J, Beldo-Iniesta C, Taron M, de Molina VR, Cejas P, Skrzypski M, Gallego-Ortega D, de Castro J, Casado E, Garcia-Cabezas MA, Sanchez JJ, Nistal M, Rosell R, Gonzalez-Baron M, Lacal JC,. 2007. Expression of choline kinase alpha to predict outcome in patients with early-stage non-small-cell lung cancer: A retrospective study. Lancet Oncol 8: 889-897. (Pubitemid 47488053)
48. de Souza GA, Godoy LMF, Teixeira VR, Otake AH, Sabino A, Rosa JC, Dinarte AR, Pinheiro DG, Silva WA, Eberlin MN, Chammas R, Greene LJ,. 2006. Proteomic and SAGE profiling of murine melanoma progression indicates the reduction of proteins responsible for ROS degradation. Proteomics 6: 1460-1470.
49. de Wit M, Jimenez CR, Carvalho B, Belien JAM, Delis-van Diemen PM, Mongera S, Piersma SR, Vikas M, Navani S, Ponten F, Meijer GA, Fijneman RJA,. 2012. Cell surface proteomics identifies glucose transporter type 1 and prion protein as candidate biomarkers for colorectal adenoma-to-carcinoma progression. Gut 61: 855-864.
50. DeBerardinis RJ, Cheng T,. 2010. Q's next: The diverse functions of glutamine in metabolism, cell biology and cancer. Oncogene 29: 313-324.
51. DeBerardinis RJ, Lum JJ, Hatzivassiliou G, Thompson CB,. 2008. The biology of cancer: Metabolic reprogramming fuels cell growth and proliferation. Cell Metab 7: 11-20.
52. Dengjel J, Hoyer-Hansen M, Nielsen MO, Eisenberg T, Harder LM, Schandorff S, Farkas T, Kirkegaard T, Becker AC, Schroeder S, Vanselow K, Lundberg E, Nielsen MM, Kristensen AR, Akimov V, Bunkenborg J, Madeo F, Jaattela M, Andersen JS,. 2012. Identification of autophagosome-associated proteins and regulators by quantitative proteomic analysis and genetic screens. Mol Cell Proteomics 11: M111.014035.
53. Denko NC,. 2008. Hypoxia, HIF1 and glucose metabolism in the solid tumour. Nat Rev Cancer 8: 705-713.
54. Ding SJ, Li Y, Shao XX, Zhou H, Zeng R, Tang ZY, Xia QC,. 2004. Proteome analysis of hepatocellular carcinoma cell strains, MHCC97-H and MHCC97-L, with different metastasis potentials. Proteomics 4: 982-994. (Pubitemid 38445958)
55. Dowling P, Clynes M,. 2011. Conditioned media from cell lines: A complementary model to clinical specimens for the discovery of disease-specific biomarkers. Proteomics 11: 794-804.
56. Drabovich AP, Pavlou MP, Dimitromanolakis A, Diamandis EP,. 2012. Quantitative analysis of energy metabolic pathways in MCF-7 breast cancer cells by selected reaction monitoring assay. Mol Cell Proteomics 4: 422-434.
57. Elschenbroich S, Ignatchenko V, Clarke B, Kalloger SE, Boutros PC, Gramolini AO, Shaw P, Jurisica I, Kislinger T,. 2011. In-depth proteomics of ovarian cancer ascites: Combining shotgun proteomics and selected reaction monitoring mass spectrometry. J Proteome Res 10: 2286-2299.
58. Eng CH, Abraham RT,. 2011. The autophagy conundrum in cancer: Influence of tumorigenic metabolic reprogramming. Oncogene 30: 4687-4696.
59. Fernandez-Irigoyen J, Santamaria E, Sesma L, Munoz J, Riezu JI, Caballeria J, Lu SC, Prieto J, Mato JM, Avila MA, Corrales FJ,. 2005. Oxidation of specific methionine and tryptophan residues of apolipoprotein A-I in hepatocarcinogenesis. Proteomics 5: 4964-4972. (Pubitemid 43016915)
60. Figueroa ME, Abdel-Wahab O, Lu C, Ward PS, Patel J, Shih A, Li Y, Bhagwat N, Vasanthakumar A, Fernandez HF, Tallman MS, Sun Z, Wolniak K, Peeters JK, Liu W, Choe SE, Fantin VR, Paietta E, Lowenberg B, Licht JD, Godley LA, Delwel R, Valk PJM, Thompson CB, Levine RL, Melnick A,. 2010. Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation. Cancer Cell 18: 553-567.
61. Filomeni G, Desideri E, Cardaci S, Rotilio G, Ciriolo MR,. 2010. Under the ROS. thiol network is the principal suspect for autophagy commitment. Autophagy 6: 999-1005.
62. Fratelli M, Demol H, Puype M, Casagrande S, Villa P, Eberini I, Vandekerckhove J, Gianazza E, Ghezzi P,. 2003. Identification of proteins undergoing glutathionylation in oxidatively stressed hepatocytes and hepatoma cells. Proteomics 3: 1154-1161. (Pubitemid 36929537)
63. Fu TY, Hou YY, Chu ST, Liu CF, Huang CH, Chen HC, Hsiao M, Lu PJ, Wang JS, Ger LP,. 2011. Manganese superoxide dismutase and glutathione peroxidase as prognostic markers in patients with buccal mucosal squamous cell carcinomas. Head Neck 33: 1606-1615.
64. Fukai T, Ushio-Fukai M,. 2011. Superoxide dismutases: Role in redox signaling, vascular function, and diseases. Antioxid Redox Signal 15: 1583-1606.
65. Gallego-Ortega D, Gomez del Pulgar T, Valdes-Mora F, Cebrian A, Carlos Lacal J,. 2011. Involvement of human choline kinase alpha and beta in carcinogenesis: A different role in lipid metabolism and biological functions. Adv Enzyme Regul 51: 183-194.
66. Gao P, Tchernyshyov I, Chang TC, Lee YS, Kita K, Ochi T, Zeller KI, De Marzo AM, Van Eyk JE, Mendell JT, Dang CV,. 2009. c-Myc suppression of miR-23a/b enhances mitochondrial glutaminase expression and glutamine metabolism. Nature 458: 762-765.
67. Gardie B, Remenieras A, Kattygnarath D, Bombled J, Lefevre S, Perrier-Trudova V, Rustin P, Barrois M, Slama A, Avril M-F, Bessis D, Caron O, Caux F, Collignon P, Coupier I, Cremin C, Dollfus H, Dugast C, Escudier B, Faivre L, Field M, Gilbert-Dussardier B, Janin N, Leport Y, Leroux D, Lipsker D, Malthieu F, McGilliwray B, Maugard C, Mejean A, Mortemousque I, Plessis G, Poppe B, Pruvost-Balland C, Rooker S, Roume J, Soufir N, Steinraths M, Tan M-H, Theodore C, Thomas L, Vabres P, Van Glabeke E, Meric J-B, Verkarre V, Lenoir G, Joulin V, Deveaux S, Cusin V, Feunteun J, Teh BT, Bressac-de Paillerets B, Richard S, French National Cancer Institute. 2011. Novel FH mutations in families with hereditary leiomyomatosis and renal cell cancer (HLRCC) and patients with isolated type 2 papillary renal cell carcinoma. J Med Genet 48: 226-234.
68. Gatenby RA, Gillies RJ,. 2004. Why do cancers have high aerobic glycolysis? Nat Rev Cancer 4: 891-899. (Pubitemid 39472955)
69. Giannoni E, Parri M, Chiarugi P,. 2012. EMT and oxidative stress: A bidirectional interplay affecting tumor malignancy. Antioxid Redox Signal 16: 1248-1263.
70. Gill AJ, Pachter NS, Chou A, Young B, Clarkson A, Tucker KM, Winship IM, Earls P, Benn DE, Robinson BG, Fleming S, Clifton-Bligh RJ,. 2011. Renal tumors associated with germline SDHB mutation show distinctive morphology. Am J Surg Pathol 35: 1578-1585.
71. Gloire G, Legrand-Poels S, Piette J,. 2006. NF-kappaB activation by reactive oxygen species: Fifteen years later. Biochem Pharmacol 72: 1493-1505. (Pubitemid 44666727)
72. Gromov PS, Ostergaard M, Gromova I, Celis JE,. 2002. Human proteomic databases: A powerful resource for functional genomics in health and disease. Prog Biophys Mol Biol 80: 3-22. (Pubitemid 35255010)
73. Gruber G, Greiner RH, Hlushchuk R, Aebersold DM, Altermatt HJ, Berclaz G, Djonov V,. 2004. Hypoxia-inducible factor 1 alpha in high-risk breast cancer: An independent prognostic parameter? Breast Cancer Res 6: R191-R198.
74. Gulubova M, Vlaykova T,. 2010. Expression of the xenobiotic- and reactive oxygen species-detoxifying enzymes, GST-pi, Cu/Zn-SOD, and Mn-SOD in the endocrine cells of colorectal cancer. Int J Colorectal Dis 25: 1397-1405.
75. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R,. 1999. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 17: 994-999. (Pubitemid 29474856)
76. Halligan BD, Ruotti V, Jin W, Laffoon S, Twigger SN, Dratz EA,. 2004. ProMoST (Protein Modification Screening Tool): A web-based tool for mapping protein modifications on two-dimensional gels. Nucleic Acids Res 32: W638-W644. (Pubitemid 38997414)
77. Hanahan D, Weinberg RA,. 2011. Hallmarks of cancer: The next generation. Cell 144: 646-674.
78. Hanke NT, Finch JS, Bowden GT,. 2008. Loss of catalase increases malignant mouse keratinocyte cell growth through activation of the stress activated JNK pathway. Mol Carcinog 47: 349-360. (Pubitemid 351614575)
79. Hardie DG,. 2011. AMP-activated protein kinase-An energy sensor that regulates all aspects of cell function. Genes Dev 25: 1895-1908.
80. Hashimoto T, Hussien R, Cho HS, Kaufer D, Brooks GA,. 2008. Evidence for the mitochondrial lactate oxidation complex in rat neurons: Demonstration of an essential component of brain lactate shuttles. PLoS ONE 3: e2915.
81. Hegde PS, Rusnak D, Bertiaux M, Alligood K, Strum J, Gagnon R, Gilmer TM,. 2007. Delineation of molecular mechanisms of sensitivity to lapatinib in breast cancer cell lines using global gene expression profiles. Mol Cancer Ther 6: 1629-1640. (Pubitemid 46954030)
82. Held JM, Gibson BW,. 2012. Regulatory control or oxidative damage? Proteomic approaches to interrogate the role of cysteine oxidation status in biological processes. Mol Cell Proteomics 11: R111.013037.
83. Held JM, Danielson SR, Behring JB, Atsriku C, Britton DJ, Puckett RL, Schilling B, Campisi J, Benz CC, Gibson BW,. 2010. Targeted quantitation of site-specific cysteine oxidation in endogenous proteins using a differential alkylation and multiple reaction monitoring mass spectrometry approach. Mol Cell Proteomics 9: 1400-1410.
84. Hirayama A, Kami K, Sugimoto M, Sugawara M, Toki N, Onozuka H, Kinoshita T, Saito N, Ochiai A, Tomita M, Esumi H, Soga T,. 2009. Quantitative metabolome profiling of colon and stomach cancer microenvironment by capillary electrophoresis time-of-flight mass spectrometry. Cancer Res 69: 4918-4925.
85. Hitosugi T, Kang S, Heiden MGV, Chung TW, Elf S, Lythgoe K, Dong S, Lonial S, Wang X, Chen GZ, Xie J, Gu TL, Polakiewicz RD, Roesel JL, Boggon TJ, Khuri FR, Gilliland DG, Cantley LC, Kaufman J, Chen J,. 2009. Tyrosine phosphorylation inhibits PKM2 to promote the Warburg effect and tumor growth. Sci Signal 2: ra73.
86. Holmgren A, Lu J,. 2010. Thioredoxin and thioredoxin reductase: Current research with special reference to human disease. Biochem Biophys Res Commun 396: 120-124.
87. Hu S, Arellano M, Boontheung P, Wang J, Zhou H, Jiang J, Elashoff D, Wei R, Loo JA, Wong DT,. 2008. Salivary proteomics for oral cancer biomarker discovery. Clin Cancer Res 14: 6246-6252.
88. Hu W, Zhang C, Wu R, Sun Y, Levine A, Feng Z,. 2010. Glutaminase 2, a novel p53 target gene regulating energy metabolism and antioxidant function. Proc Natl Acad Sci USA 107: 7455-7460.
89. Hu H, Deng C, Yang T, Dong Q, Chen Y, Nice EC, Huang C, Wei Y,. 2011. Proteomics revisits the cancer metabolome. Expert Rev Proteomics 8: 505-533.
90. Hu Y, Lu W, Chen G, Wang P, Chen Z, Zhou Y, Ogasawara M, Trachootham D, Feng L, Pelicano H, Chiao PJ, Keating MJ, Garcia-Manero G, Huang P,. 2012. K-ras(G12V) transformation leads to mitochondrial dysfunction and a metabolic switch from oxidative phosphorylation to glycolysis. Cell Res 22: 399-412.
91. Huang LJ, Chen SX, Huang Y, Luo WJ, Jiang HH, Hu QH, Zhang PF, Yi H,. 2006. Proteomics-based identification of secreted protein dihydrodiol dehydrogenase as a novel serum markers of non-small cell lung cancer. Lung Cancer 54: 87-94.
92. 2+-induced choline kinase activation and prostate cancer cell proliferation. Int J Cancer 128: 2833-2842.
93. Hughes C, Langridge J, Nirmalan N, Banks RE, McKenna T,. 2010. The proteomic analysis of human FFPE tissue by on-line 2D-LC-MS. J Biomol Tech 21 (3 Suppl.): S52.
94. Hurt EM, Thomas SB, Peng B, Farrar WL,. 2007. Integrated molecular profiling of SOD2 expression in multiple myeloma. Blood 109: 3953-3962. (Pubitemid 46641748)
95. Hwang TS, Choi HK, Han HS,. 2007. Differential expression of manganese superoxide dismutase, copper/zinc superoxide dismutase, and catalase in gastric adenocarcinoma and normal gastric mucosa. Eur J Surg Oncol 33: 474-479. (Pubitemid 46591167)
96. Hyoudou K, Nishikawa M, Ikemura M, Kobayashi Y, Mendelsohn A, Miyazaki N, Tabata Y, Yamashita F, Hashida M,. 2009. Prevention of pulmonary metastasis from subcutaneous tumors by binary system-based sustained delivery of catalase. J Control Release 137: 110-115.
97. Isaacs JS, Jung YJ, Mole DR, Lee S, Torres-Cabala C, Chung YL, Merino M, Trepel J, Zbar B, Toro J, Ratcliffe PJ, Linehan WM, Neckers L,. 2005. HIF overexpression correlates with biallelic loss of fumarate hydratase in renal cancer: Novel role of fumarate in regulation of HIF stability. Cancer Cell 8: 143-153. (Pubitemid 41132743)
98. Issaq HJ, Waybright TJ, Veenstra TD,. 2011. Cancer biomarker discovery: Opportunities and pitfalls in analytical methods. Electrophoresis 32: 967-975.
99. Janardhan S, Srivani P, Sastry GN,. 2006. Choline kinase: An important target for cancer. Curr Med Chem 13: 1169-1186.
100. Jiang H, Feng Y,. 2006. Hypoxia-inducible factor 1 alpha (HIF-1 alpha) correlated with tumor growth and apoptosis in ovarian cancer. Int J Gynecol Cancer 16: 405-412.
101. Jin S, White E,. 2007. Role of autophagy in cancer-Management of metabolic stress. Autophagy 3: 28-31. (Pubitemid 46100707)
102. Johnson MT, Freeman EA, Gardner DK, Hunt PA,. 2007. Oxidative metabolism of pyruvate is required for meiotic maturation of murine oocytes in vivo. Biol Reprod 77: 2-8. (Pubitemid 46986390)
103. Jones DP, Go Y-M,. 2011. Mapping the cysteine proteome: Analysis of redox-sensing thiols. Curr Opin Chem Biol 15: 103-112.
104. Jones T, Price P,. 2012. Development and experimental medicine applications of PET in oncology: A historical perspective. Lancet Oncol 13: E116-E125.
105. Jones RG, Thompson CB,. 2009. Tumor suppressors and cell metabolism: A recipe for cancer growth. Genes Dev 23: 537-548.
106. Kahlos K, Soini Y, Sormunen R, Kaarteenaho-Wiik R, Paakko P, Linnainmaa K, Kinnula VL,. 2001. Expression and prognostic significance of catalase in malignant mesothelioma. Cancer 91: 1349-1357. (Pubitemid 32267047)
107. Kaller M, Liffers S-T, Oeljeklaus S, Kuhlmann K, Roeh S, Hoffmann R, Warscheid B, Hermeking H,. 2011. Genome-wide characterization of miR-34a induced changes in protein and mRNA expression by a combined pulsed SILAC and microarray analysis. Mol Cell Proteomics 10: M111.010462.
108. Kang UB, Ahn Y, Lee JW, Kim YH, Kim J, Yu MH, Noh DY, Lee C,. 2010. Differential profiling of breast cancer plasma proteome by isotope-coded affinity tagging method reveals biotinidase as a breast cancer biomarker. BMC Cancer 10: 114.
109. Kang JH, Li M, Chen X, Yin XM,. 2011. Proteomics analysis of starved cells revealed Annexin A1 as an important regulator of autophagic degradation. Biochem Biophys Res Commun 407: 581-586.
110. Karisch R, Fernandez M, Taylor P, Virtanen C, St-Germain JR, Jin LL, Harris IS, Mori J, Mak TW, Senis YA, Ostman A, Moran MF, Neel BG,. 2011. Global proteomic assessment of the classical protein-tyrosine phosphatome and "redoxome ". Cell 146: 826-840.
111. Keith B, Johnson RS, Simon MC,. 2012. HIF1alpha and HIF2alpha: Sibling rivalry in hypoxic tumour growth and progression. Nat Rev Cancer 12: 9-22.
112. Kim JW, Dang CV,. 2006. Cancer's molecular sweet tooth and the Warburg effect. Cancer Res 66: 8927-8930. (Pubitemid 44521105)
113. Kim J, Kim SH, Lee SU, Ha GH, Kang DG, Ha NY, Ahn JS, Cho HY, Kang SJ, Lee YJ, Hong SC, Ha WS, Bae JM, Lee CW, Kim JW,. 2002. Proteome analysis of human liver tumor tissue by two-dimensional gel electrophoresis and matrix assisted laser desorption/ionization-mass spectrometry for identification of disease-related proteins. Electrophoresis 23: 4142-4156. (Pubitemid 36131469)
114. Kim SC, Sprung R, Chen Y, Xu Y, Ball H, Pei J, Cheng T, Kho Y, Xiao H, Xiao L, Grishin NV, White M, Yang X-J, Zhao Y,. 2006. Substrate and functional diversity of lysine acetylation revealed by a proteomics survey. Mol Cell 23: 607-618. (Pubitemid 44205490)
115. Klose J,. 1975. 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.
116. Kondo Y, Kanzawa T, Sawaya R, Kondo S,. 2005. The role of autophagy in cancer development and response to therapy. Nat Rev Cancer 5: 726-734. (Pubitemid 41486365)
117. Kosanam H, Makawita S, Judd B, Newman A, Diamandis EP,. 2011. Mining the malignant ascites proteome for pancreatic cancer biomarkers. Proteomics 11: 4551-4558.
118. Kroemer G, Pouyssegur J,. 2008. Tumor cell metabolism: Cancer's achilles' heel. Cancer Cell 13: 472-482. (Pubitemid 351766797)
119. Kumar HR, Zhong X, Hoelz DJ, Rescorla FJ, Hickey RJ, Malkas LH, Sandoval JA,. 2008. Three-dimensional neuroblastoma cell culture: Proteomic analysis between monolayer and multicellular tumor spheroids. Pediatr Surg Int 24: 1229-1234.
120. Le A, Cooper CR, Gouw AM, Dinavahi R, Maitra A, Deck LM, Royer RE, Jagt DLV, Semenza GL, Dang CV,. 2010. Inhibition of lactate dehydrogenase A induces oxidative stress and inhibits tumor progression. Proc Natl Acad Sci USA 107: 2037-2042.
121. Le Floch R, Chiche J, Marchiq I, Naiken T, Ilk K, Murray CM, Critchlow SE, Roux D, Simon M-P, Pouyssegur J,. 2011. CD147 subunit of lactate/H+ symporters MCT1 and hypoxia-inducible MCT4 is critical for energetics and growth of glycolytic tumors. Proc Natl Acad Sci USA 108: 16663-16668.
122. Lee JD, Yang WI, Park YN, Kim KS, Choi JS, Yun MJ, Ko DH, Kim TS, Cho AEH, Kim HM, Han KH, Im SS, Ahn YH, Choi CW, Park JH,. 2005. Different glucose uptake and glycolytic mechanisms between hepatocellular carcinoma and intrahepatic mass-forming cholangiocarcinoma with increased F-18-FDG uptake. J Nucl Med 46: 1753-1759. (Pubitemid 46211600)
123. Lee S, Nakamura E, Yang HF, Wei WY, Linggi MS, Sajan MP, Farese RV, Freeman RS, Carter BD, Kaelin WG, Schlisio S,. 2005. Neuronal apoptosis linked to EgIN3 prolyl hydroxylase and familial pheochromocytoma genes: Developmental culling and cancer. Cancer Cell 8: 155-167. (Pubitemid 41132744)
124. Lee J, Giordano S, Zhang J,. 2012. Autophagy, mitochondria and oxidative stress: Cross-talk and redox signalling. Biochem J 441: 523-540.
125. Lehtonen R, Kiuru M, Vanharanta S, Sjoberg J, Aaltonen LM, Aittomaki K, Arola J, Butzow R, Eng C, Husgafvel-Pursiainen K, Isola J, Jarvinen H, Koivisto P, Mecklin JP, Peltomaki P, Salovaara R, Wasenius VM, Karhu A, Launonen V, Nupponen NN, Aaltonen LA,. 2004. Biallelic inactivation of fumarate hydratase (FH) occurs in nonsyndromic uterine leiomyomas but is rare in other tumors. Am J Pathol 164: 17-22. (Pubitemid 38364585)
126. Lei Y, Huang K, Gao C, Lau QC, Pan H, Xie K, Li J, Liu R, Zhang T, Xie N, Nai HS, Wu H, Dong Q, Zhao X, Nice EC, Huang C, Wei Y,. 2011. Proteomics identification of ITGB3 as a key regulator in reactive oxygen species-induced migration and invasion of colorectal cancer cells. Mol Cell Proteomics 10: M110.005397.
127. Leichert LI, Gehrke F, Gudiseva HV, Blackwell T, Ilbert M, Walker AK, Strahler JR, Andrews PC, Jakob U,. 2008. Quantifying changes in the thiol redox proteome upon oxidative stress in vivo. Proc Natl Acad Sci USA 105: 8197-8202. (Pubitemid 351904734)
128. Leonard SE, Reddie KG, Carroll KS,. 2009. Mining the thiol proteome for sulfenic acid modifications reveals new targets for oxidation in cells. ACS Chem Biol 4: 783-799.
129. Levine AJ, Puzio-Kuter AM,. 2010. The control of the metabolic switch in cancers by oncogenes and tumor suppressor genes. Science 330: 1340-1344.
130. Li Z, Zhao X, Bai S, Wang Z, Chen L, Wei Y, Huang C,. 2008. Proteomics identification of cyclophilin A as a potential prognostic factor and therapeutic
131. Li J, Liu R, Lei Y, Wang K, Lau QC, Xie N, Zhou S, Nie C, Chen L, Wei Y, Huang C,. 2010. Proteomic analysis revealed association of aberrant ROS signaling with suberoylanilide hydroxamic acid-induced autophagy in Jurkat T-leukemia cells. Autophagy 6: 711-724.
132. Lim SO, Gu JM, Kim MS, Kim HS, Park YN, Park CK, Cho JW, Park YM, Jung G,. 2008. Epigenetic changes induced by reactive oxygen species in hepatocellular carcinoma: Methylation of the E-cadherin promoter. Gastroenterol 135: 2128-2140.
133. Lisanti MP, Martinez-Outschoorn UE, Chiavarina B, Pavlides S, Whitaker-Menezes D, Tsirigos A, Witkiewicz A, Lin Z, Balliet R, Howell A, Sotgia F,. 2010. Understanding the "lethal" drivers of tumor-stroma co-evolution: Emerging role(s) for hypoxia, oxidative stress and autophagy/mitophagy in the tumor micro-environment. Cancer Biol Ther 10: 537-542.
134. Liu H, Zhang Y, Wang J, Wang D, Zhou C, Cai Y, Qian X,. 2006. Method for quantitative proteomics research by using metal element chelated tags coupled with mass spectrometry. Anal Chem 78: 6614-6621. (Pubitemid 44413616)
135. Liu B, Chen Y, Clair DKS,. 2008. ROS and p53: A versatile partnership. Free Radic Biol Med 44: 1529-1535.
136. Liu L, Wang S, Zhang Q, Ding Y,. 2008. Identification of potential genes/proteins regulated by Tiam1 in colorectal cancer by microarray analysis and proteome analysis. Cell Biol Int 32: 1215-1222.
137. Liu R, Li Z, Bai S, Zhang H, Tang M, Lei Y, Chen L, Liang S, Zhao Y-L, Wei Y, Huang C,. 2009. Mechanism of cancer cell adaptation to metabolic stress: Proteomics identification of a novel thyroid hormone-mediated gastric carcinogenic signaling pathway. Mol Cell Proteomics 8: 70-85.
138. Liu B, Cheng Y, Liu Q, Bao JK, Yang JM,. 2010. Autophagic pathways as new targets for cancer drug development. Acta Pharmacol Sin 31: 1154-1164.
139. Lock R, Debnath J,. 2011. Ras, autophagy and glycolysis. Cell Cycle 10: 1516-1517.
140. Long J, Lang ZW, Wang HG, Wang TL, Wang BE, Liu SQ,. 2010. Glutamine synthetase as an early marker for hepatocellular carcinoma based on proteomic analysis of resected small hepatocellular carcinomas. Hepatobiliary Pancreat Dis Int 9: 296-305.
141. Lopez-Lazaro M,. 2007. Dual role of hydrogen peroxide in cancer: Possible relevance to cancer chemoprevention and therapy. Cancer Lett 252: 1-8. (Pubitemid 46734550)
142. Lu Y, Liu P, Wen W, Grubbs CJ, Townsend RR, Malone JP, Lubet RA, You M,. 2010. Cross-species comparison of orthologous gene expression in human bladder cancer and carcinogen-induced rodent models. Am J Transl Res 3: 8-27.
143. Lu C, Ward PS, Kapoor GS, Rohle D, Turcan S, Abdel-Wahab O, Edwards CR, Khanin R, Figueroa ME, Melnick A, Wellen KE, O'Rourke DM, Berger SL, Chan TA, Levine RL, Mellinghoff IK, Thompson CB,. 2012. IDH mutation impairs histone demethylation and results in a block to cell differentiation. Nature 483: 474-478.
144. Luo Z, Zang M, Guo W,. 2010. AMPK as a metabolic tumor suppressor: Control of metabolism and cell growth. Future Oncol 6: 457-470.
145. Lv L, Li D, Zhao D, Lin R, Chu Y, Zhang H, Zha Z, Liu Y, Li Z, Xu Y, Wang G, Huang Y, Xiong Y, Guan KL, Lei QY,. 2011. Acetylation targets the M2 isoform of pyruvate kinase for degradation through chaperone-mediated autophagy and promotes tumor growth. Mol Cell 42: 719-730.
146. Ma W, Sung HJ, Park JY, Matoba S, Hwang PM,. 2007. A pivotal role for p53: Balancing aerobic respiration and glycolysis. J Bioenerg Biomembr 39: 243-246. (Pubitemid 47619376)
147. Madan E, Gogna R, Bhatt M, Pati U, Kuppusamy P, Mahdi AA,. 2011. Regulation of glucose metabolism by p53: Emerging new roles for the tumor suppressor. Oncotarget 2: 948-957.
148. Makridakis M, Vlahou A,. 2010. Secretome proteomics for discovery of cancer biomarkers. J Proteomics 73: 2291-2305.
149. Mannsperger HA, Gade S, Henjes F, Beissbarth T, Korf U,. 2010. RPPanalyzer: Analysis of reverse-phase protein array data. Bioinformatics 26: 2202-2203.
150. Mardis ER, Ding L, Dooling DJ, Larson DE, McLellan MD, Chen K, Koboldt DC, Fulton RS, Delehaunty KD, McGrath SD, Fulton LA, Locke DP, Magrini VJ, Abbott RM, Vickery TL, Reed JS, Robinson JS, Wylie T, Smith SM, Carmichael L, Eldred JM, Harris CC, Walker J, Peck JB, Du F, Dukes AF, Sanderson GE, Brummett AM, Clark E, McMichael JF, Meyer RJ, Schindler JK, Pohl CS, Wallis JW, Shi X, Lin L, Schmidt H, Tang Y, Haipek C, Wiechert ME, Ivy JV, Kalicki J, Elliott G, Ries RE, Payton JE, Westervelt P, Tomasson MH, Watson MA, Baty J, Heath S, Shannon WD, Nagarajan R, Link DC, Walter MJ, Graubert TA, DiPersio JF, Wilson RK, Ley TJ,. 2009. Recurring mutations found by sequencing an acute myeloid leukemia genome. N Engl J Med 361: 1058-1066.
151. Martinez-Outschoorn UE, Balliet RM, Rivadeneira DB, Chiavarina B, Pavlides S, Wang C, Whitaker-Menezes D, Daumer KM, Lin Z, Witkiewicz AK, Flomenberg N, Howell A, Pestell RG, Knudsen ES, Sotgia F, Lisanti MP,. 2010a. Oxidative stress in cancer associated fibroblasts drives tumor-stroma co-evolution A new paradigm for understanding tumor metabolism, the field effect and genomic instability in cancer cells. Cell Cycle 9: 3256-3276.
152. Martinez-Outschoorn UE, Whitaker-Menezes D, Pavlides S, Chiavarina B, Bonuccelli G, Trimmer C, Tsirigos A, Migneco G, Witkiewicz AK, Balliet R, Mercier I, Wang C, Flomenberg N, Howell A, Lin Z, Caro J, Pestell RG, Sotgia F, Lisanti MP,. 2010b. The autophagic tumor stroma model of cancer or "battery-operated tumor growth" A simple solution to the autophagy paradox. Cell Cycle 9: 4297-4306.
153. Martinez-Outschoorn UE, Pestell RG, Howell A, Tykocinski ML, Nagajyothi F, Machado FS, Tanowitz HB, Sotgia F, Lisanti MP,. 2011a. Energy transfer in "parasitic" cancer metabolism Mitochondria are the powerhouse and Achilles' heel of tumor cells. Cell Cycle 10: 4208-4216.
154. Martinez-Outschoorn UE, Prisco M, Ertel A, Tsirigos A, Lin Z, Pavlides S, Wang C, Flomenberg N, Knudsen ES, Howell A, Pestell RG, Sotgia F, Lisanti MP,. 2011b. Ketones and lactate increase cancer cell "stemness", driving recurrence, metastasis and poor clinical outcome in breast cancer. Cell Cycle 10: 1271-1286.
155. Mathew R, White E,. 2011. Autophagy in tumorigenesis and energy metabolism: Friend by day, foe by night. Curr Opin Genet Dev 21: 113-119.
156. Mathew R, Karantza-Wadsworth V, White E,. 2007. Role of autophagy in cancer. Nat Rev Cancer 7: 961-967. (Pubitemid 350165856)
157. Mathew R, Karp CM, Beaudoin B, Vuong N, Chen G, Chen HY, Bray K, Reddy A, Bhanot G, Gelinas C, Dipaola RS, Karantza-Wadsworth V, White E,. 2009. Autophagy suppresses tumorigenesis through elimination of p62. Cell 137: 1062-1075.
158. Mathivanan S, Simpson RJ,. 2009. ExoCarta: A compendium of exosomal proteins and RNA. Proteomics 9: 4997-5000.
159. Mathivanan S, Ahmed M, Ahn NG, Hainard A, Amanchy R, Andrews PC, Bader JS, Balgley BM, Bantscheff M, Bennett KL, Bjoerling E, Blagoev B, Bose R, Brahmachari SK, Burlingame AS, Bustelo XR, Cagney G, Cantin GT, Cardasis HL, Celis JE, Chaerkady R, Chu F, Cole PA, Costello CE, Cotter RJ, Crockett D, DeLany JP, De Marzo AM, DeSouza LV, Deutsch EW, Dransfield E, Drewes G, Droit A, Dunn MJ, Elenitoba-Johnson K, Ewing RM, Van Eyk J, Faca V, Falkner J, Fang X, Fenselau C, Figeys D, Gagne P, Gelfi C, Gevaert K, Gimble JM, Gnad F, Goel R, Gromov P, Hanash SM, Hancock WS, Harsha HC, Hart G, Hays F, He F, Hebbar P, Helsens K, Hermeking H, Hide W, Hjerno K, Hochstrasser DF, Hofmann O, Horn DM, Hruban RH, Ibarrola N, James P, Jensen ON, Jensen PH, Jung P, Kandasamy K, Kheterpal I, Kikuno RF, Korf U, Koerner R, Kuster B, Kwon M-S, Lee H-J, Lee Y-J, Lefevre M, Lehvaslaiho M, Lescuyer P, Levander F, Lim MS, Loebke C, Loo JA, Mann M, Martens L, Martinez-Heredia J, McComb M, McRedmond J, Mehrle A, Menon R, Miller CA, Mischak H, Mohan SS, Mohmood R, Molina H, Moran MF, Morgan JD, Moritz R, Morzel M, Muddiman DC, Nalli A, Navarro JD, Neubert TA, Ohara O, Oliva R, Omenn GS, Oyama M, Paik Y-K, Pennington K, Pepperkok R, Periaswamy B, Petricoin EF, Poirier GG, Prasad TSK, Purvine SO, Rahiman BA, Ramachandran P, Ramachandra YL, Rice RH, Rick J, Ronnholm RH, Salonen J, Sanchez J-C, Sayd T, Seshi B, Shankari K, Sheng SJ, Shetty V, Shivakumar K, Simpson RJ, Sirdeshmukh R, Siu KWM, Smith JC, Smith RD, States DJ, Sugano S, Sullivan M, Superti-Furga G, Takatalo M, Thongboonkerd V, Trinidad JC, Uhlen M, Vandekerckhove J, Vasilescu J, Veenstra TD, Vidal-Taboada J-M, Vihinen M, Wait R, Wang X, Wiemann S, Wu B, Xu T, Yates JR, Zhong J, Zhou M, Zhu Y, Zurbig P, Pandey A,. 2008. Human Proteinpedia enables sharing of human protein data. Nat Biotechnol 26: 164-167. (Pubitemid 351225942)
160. Mathivanan S, Fahner CJ, Reid GE, Simpson RJ,. 2012. ExoCarta 2012: Database of exosomal proteins, RNA and lipids. Nucleic Acids Res 40: D1241-D1244.
161. Matsumoto N, Ezaki J, Komatsu M, Takahashi K, Mineki R, Taka H, Kikkawa M, Fujimura T, Takeda-Ezaki M, Ueno T, Tanaka K, Kominami E,. 2008. Comprehensive proteomics analysis of autophagy-deficient mouse liver. Biochem Biophys Res Commun 368: 643-649.
162. Mattoon D, Michaud G, Merkel J, Schweitzer B,. 2005. Biomarker discovery using protein microarray technology platforms: Antibody-antigen complex profiling. Expert Rev Proteomics 2: 879-889. (Pubitemid 41746508)
163. Mazurek S,. 2011. Pyruvate kinase type M2: A key regulator of the metabolic budget system in tumor cells. Int J Biochem Cell Biol 43: 969-980.
164. McAllister SS, Weinberg RA,. 2010. Tumor-host interactions: A far-reaching relationship. J Clin Oncol 28: 4022-4028.
165. Meehan KL, Sadar MD,. 2004. Quantitative profiling of LNCaP prostate cancer cells using isotope-coded affinity tags and mass spectrometry. Proteomics 4: 1116-1134. (Pubitemid 38445970)
166. Melendez A, Talloczy Z, Seaman M, Eskelinen EL, Hall DH, Levine B,. 2003. Autophagy genes are essential for dauer development and life-span extension in C-elegans. Science 301: 1387-1391. (Pubitemid 37075816)
167. Meng Z, Veenstra TD,. 2011. Targeted mass spectrometry approaches for protein biomarker verification. J Proteomics 74: 2650-2659.
168. Mihaylova MM, Shaw RJ,. 2011. The AMPK signalling pathway coordinates cell growth, autophagy and metabolism. Nat Cell Biol 13: 1016-1023.
169. Mohr A, Bueneker C, Gough RP, Zwacka RM,. 2008. MnSOD protects colorectal cancer cells from TRAIL-induced apoptosis by inhibition of Smac/DIABLO release. Oncogene 27: 763-774. (Pubitemid 351186311)
170. Moldovan L, Mythreye K, Goldschmidt-Clermont PJ, Satterwhite LL,. 2006. Reactive oxygen species in vascular endothelial cell motility. Roles of NAD(P)H oxidase and Rac1. Cardiovasc Res 71: 236-246.
171. Molina H, Parmigiani G, Pandey A,. 2005. Assessing reproducibility of a protein dynamics study using in vivo labeling and liquid chromatography tandem mass spectrometry. Anal Chem 77: 2739-2744. (Pubitemid 40617319)
172. Molloy MP, Donohoe S, Brzezinski EE, Kilby GW, Stevenson TI, Baker JD, Goodlett DR, Gage DA,. 2005. Large-scale evaluation of quantitative reproducibility and proteome coverage using acid cleavable isotope coded affinity tag mass spectrometry for proteomic profiling. Proteomics 5: 1204-1208.
173. Monsef N, Soller M, Panagopoulos I, Abrahamsson PA,. 2010. HIF1 alpha isoforms in benign and malignant prostate tissue and their correlation to neuroendocrine differentiation. BMC Cancer 10: 385.
174. Muller-Delp JM, Gurovich AN, Christou DD, Leeuwenburgh C,. 2012. Redox balance in the aging microcirculation: New friends, new foes, and new clinical directions. Microcirculation 19: 19-28.
175. Murphy JP, Pinto DM,. 2011. Targeted proteomic analysis of glycolysis in cancer cells. J Proteome Res 10: 604-613.
176. Nakamura T, Lipton SA,. 2011. Redox modulation by S-nitrosylation contributes to protein misfolding, mitochondrial dynamics, and neuronal synaptic damage in neurodegenerative diseases. Cell Death Differ 18: 1478-1486.
177. Nanjundan M, Byers LA, Carey MS, Siwak DR, Raso MG, Diao L, Wang J, Coombes KR, Roth JA, Mills GB, Wistuba II, Minna JD, Heymach JV,. 2010. Proteomic profiling identifies pathways dysregulated in non-small cell lung cancer and an inverse association of AMPK and adhesion pathways with recurrence. J Thorac Oncol 5: 1894-1904.
178. Neumann CA, Fang Q,. 2007. Are peroxiredoxins tumor suppressors? Curr Opin Pharmacol 7: 375-380. (Pubitemid 47289263)
179. Neumann HPH, Pawlu C, Peczkowska M, Bausch B, MeWhinney SR, Muresan M, Buchta M, Franke G, Klisch J, Bley TA, Hoegerle S, Boedeker CC, Opocher G, Schipper J, Januszewicz A, Eng C,. 2004. Distinct clinical features of paraganglioma syndromes associated with SDHB and SDHD gene mutations. JAMA 292: 943-951. (Pubitemid 39097204)
180. Nieman KM, Kenny HA, Penicka CV, Ladanyi A, Buell-Gutbrod R, Zillhardt MR, Romero IL, Carey MS, Mills GB, Hotamisligil GS, Yamada SD, Peter ME, Gwin K, Lengyel E,. 2011. Adipocytes promote ovarian cancer metastasis and provide energy for rapid tumor growth. Nat Med 17: 1498-1503.
181. Nishikawa M, Tamada A, Hyoudou K, Umeyama Y, Takahashi Y, Kobayashi Y, Kumai H, Ishida E, Staud F, Yabe Y, Takakura Y, Yamashita F, Hashida M,. 2004. Inhibition of experimental hepatic metastasis by targeted delivery of catalase in mice. Clin Exp Metastasis 21: 213-2221.
182. Nomura DK, Dix MM, Cravatt BF,. 2010. Activity-based protein profiling for biochemical pathway discovery in cancer. Nat Rev Cancer 10: 630-638.
183. Nomura DK, Long JZ, Niessen S, Hoover HS, Ng SW, Cravatt BF,. 2010. Monoacylglycerol lipase regulates a fatty acid network that promotes cancer pathogenesis. Cell 140: 49-61.
184. Norvell A, McMahon SB,. 2010. Rise of the rival. Science 327: 964-965.
185. Olovnikov IA, Kravchenko JE, Chumakov PM,. 2009. Homeostatic functions of the p53 tumor suppressor: Regulation of energy metabolism and antioxidant defense. Semin Cancer Biol 19: 32-41.
186. Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M,. 2002. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1: 376-386.
187. Orimo A, Gupta PB, Sgroi DC, Arenzana-Seisdedos F, Delaunay T, Naeem R, Carey VJ, Richardson AL, Weinberg RA,. 2005. Stromal fibroblasts present in invasive human breast carcinomas promote tumor growth and angiogenesis through elevated SDF-1/CXCL12 secretion. Cell 121: 335-348. (Pubitemid 40692295)
188. Parsons DW, Jones S, Zhang X, Lin JC-H, Leary RJ, Angenendt P, Mankoo P, Carter H, Siu IM, Gallia GL, Olivi A, McLendon R, Rasheed BA, Keir S, Nikolskaya T, Nikolsky Y, Busam DA, Tekleab H, Diaz LA Jr, Hartigan J, Smith DR, Strausberg RL, Marie SKN, Shinjo SMO, Yan H, Riggins GJ, Bigner DD, Karchin R, Papadopoulos N, Parmigiani G, Vogelstein B, Velculescu VE, Kinzler KW,. 2008. An integrated genomic analysis of human glioblastoma Multiforme. Science 321: 1807-1812.
189. Patel JB, Shah FD, Shukla SN, Shah PM, Patel PS,. 2009. Role of nitric oxide and antioxidant enzymes in the pathogenesis of oral cancer. J Cancer Res Ther 5: 247-253.
190. Pavlides S, Tsirigos A, Migneco G, Whitaker-Menezes D, Chiavarina B, Flomenberg N, Frank PG, Casimiro MC, Wang C, Pestell RG, Martinez-Outschoorn UE, Howell A, Sotgia F, Lisanti MP,. 2010. The autophagic tumor stroma model of cancer Role of oxidative stress and ketone production in fueling tumor cell metabolism. Cell Cycle 9: 3485-3505.
191. Peng XC, Gong FM, Zhao YW, Zhou LX, Xie YW, Liao HL, Lin HJ, Li ZY, Tang MH, Tong AP,. 2011. Comparative proteomic approach identifies PKM2 and Cofilin-1 as potential diagnostic, prognostic and therapeutic targets for pulmonary adenocarcinoma. PLoS ONE 6: e27309.
192. Plymoth A, Hainaut P,. 2011. Proteomics beyond proteomics: Toward clinical applications. Curr Opin Oncol 23: 77-82.
193. Pollard PJ, El-Bahrawy M, Poulsom R, Elia G, Killick P, Kelly G, Hunt T, Jeffery R, Seedhar P, Barwell J, Latif F, Gleeson MJ, Hodgson SV, Stamp GW, Tomlinson IPM, Maher ER,. 2006. Expression of HIF-1 alpha, HIF-2 alpha (EPAS1), and their target genes in paraganglioma and pheochromocytoma with VHL and SDH mutations. J Clin Endocrinol Metab 91: 4593-4598. (Pubitemid 44833443)
194. Qu W, Oya S, Lieberman BP, Ploessl K, Wang L, Wise DR, Divgi CR, Chodosh LP, Thompson CB, Kung HF,. 2012. Preparation and characterization of L-5-C-11-glutamine for metabolic imaging of tumors. J Nucl Med 53: 98-105.
195. Radisky DC, Levy DD, Littlepage LE, Liu H, Nelson CM, Fata JE, Leake D, Godden EL, Albertson DG, Nieto MA, Werb Z, Bissell MJ,. 2005. Rac1b and reactive oxygen species mediate MMP-3-induced EMT and genomic instability. Nature 436: 123-127. (Pubitemid 40966197)
196. Raimondo F, Morosi L, Chinello C, Magni F, Pitto M,. 2011. Advances in membranous vesicle and exosome proteomics improving biological understanding and biomarker discovery. Proteomics 11: 709-720.
197. Ralhan R, Masui O, DeSouza LV, Matta A, Macha M, Siu KWM,. 2011. Identification of proteins secreted by head and neck cancer cell lines using LC-MS/MS: Strategy for discovery of candidate serological biomarkers. Proteomics 11: 2363-2376.
198. Ramanathan A, Wang C, Schreiber SL,. 2005. Perturbational profiling of a cell-line model of tumorigenesis by using metabolic measurements. Proc Natl Acad Sci USA 102: 5992-5997. (Pubitemid 40594243)
199. Ren F, Wu H, Lei Y, Zhang H, Liu R, Zhao Y, Chen X, Zeng D, Tong A, Chen L, Wei Y, Huang C,. 2010. Quantitative proteomics identification of phosphoglycerate mutase 1 as a novel therapeutic target in hepatocellular carcinoma. Mol Cancer 9: 81.
200. Ritorto MS, Borlak J,. 2011. Combined serum and tissue proteomic study applied to a c-Myc transgenic mouse model of hepatocellular carcinoma identified novel disease regulated proteins suitable for diagnosis and therapeutic intervention strategies. J Proteome Res 10: 3012-3030.
201. Rustin P, Munnich A, Rotig A,. 2002. Succinate dehydrogenase and human diseases: New insights into a well-known enzyme. Eur J Hum Genet 10: 289-291. (Pubitemid 34778046)
202. Sarto C, Frutiger S, Cappellano F, Sanchez JC, Doro G, Catanzaro F, Hughes GJ, Hochstrasser DF, Mocarelli P,. 1999. Modified expression of plasma glutathione peroxidase and manganese superoxide dismutase in human renal cell carcinoma. Electrophoresis 20: 3458-3466.
203. Sattler UGA, Mueller-Klieser W,. 2009. The anti-oxidant capacity of tumour glycolysis. Int J Radiat Biol 85: 963-971.
204. Scherz-Shouval R, Elazar Z,. 2011. Regulation of autophagy by ROS: Physiology and pathology. Trends Biochem Sci 36: 30-38.
205. Scherz-Shouval R, Shvets E, Fass E, Shorer H, Gil L, Elazar Z,. 2007. Reactive oxygen species are essential for autophagy and specifically regulate the activity of Atg4. EMBO J 26: 1749-1760. (Pubitemid 46624042)
206. Schmelzer K, Fahy E, Subramaniam S, Dennis EA,. 2007. The lipid maps initiative in lipidomics. Methods Enzymol 432: 171-183.
207. Seeber LMS, Horree N, van der Groep P, van der Wall E, Verheijen RHM, van Diest PJ,. 2010. Necrosis related HIF-1 alpha expression predicts prognosis in patients with endometrioid endometrial carcinoma. BMC Cancer 10: 307.
208. Selak MA, Armour SM, MacKenzie ED, Boulahbel H, Watson DG, Mansfield KD, Pan Y, Simon MC, Thompson CB, Gottlieb E,. 2005. Succinate links TCA cycle dysfunction to oncogenesis by inhibiting HIF-alpha prolyl hydroxylase. Cancer Cell 7: 77-85. (Pubitemid 40126384)
209. Semenza GL,. 2008. Tumor metabolism: Cancer cells give and take lactate. J Clin Invest 118: 3835-3837.
210. Shiio Y, Aebersold R,. 2006. Quantitative proteome analysis using isotope-coded affinity tags and mass spectrometry. Nat Protoc 1: 139-145.
211. Shui W, Sheu L, Liu J, Smart B, Petzold CJ, Hsieh T-y, Pitcher A, Keasling JD, Bertozzi CR,. 2008. Membrane proteomics of phagosomes suggests a connection to autophagy. Proc Natl Acad Sci USA 105: 16952-16957.
212. Sigrist CJA, Cerutti L, de Castro E, Langendijk-Genevaux PS, Bulliard V, Bairoch A, Hulo N,. 2010. PROSITE, a protein domain database for functional characterization and annotation. Nucleic Acids Res 38: D161-D166.
213. Skvortsova I, Skvortsov S, Stasyk T, Raju U, Popper BA, Schiestl B, von Guggenberg E, Neher A, Bonn GK, Huber LA, Lukas P,. 2008. Intracellular signaling pathways regulating radioresistance of human prostate carcinoma cells. Proteomics 8: 4521-4533.
214. Smith CA, O'Maille G, Want EJ, Qin C, Trauger SA, Brandon TR, Custodio DE, Abagyan R, Siuzdak G,. 2005. METLIN-a metabolite mass spectral database. Ther Drug Monit 27: 747-751. (Pubitemid 44391729)
215. Smith EH, Janknecht R, Maher LJ III., 2007. Succinate inhibition of alpha-ketoglutarate-dependent enzymes in a yeast model of paraganglioma. Hum Mol Genet 16: 3136-3148. (Pubitemid 350131331)
216. Sonveaux P, Vegran F, Schroeder T, Wergin MC, Verrax J, Rabbani ZN, De Saedeleer CJ, Kennedy KM, Diepart C, Jordan BF, Kelley MJ, Gallez B, Wahl ML, Feron O, Dewhirst MW,. 2008. Targeting lactate-fueled respiration selectively kills hypoxic tumor cells in mice. J Clin Invest 118: 3930-3942.
217. Spratlin JL, Serkova NJ, Eckhardt SG,. 2009. Clinical applications of metabolomics in oncology: A review. Clin Cancer Res 15: 431-440.
218. Stewart JJ, White JT, Yan X, Collins S, Drescher CW, Urban ND, Hood L, Lin B,. 2006. Proteins associated with Cisplatin resistance in ovarian cancer cells identified by quantitative proteomic technology and integrated with mRNA expression levels. Mol Cell Proteomics 5: 433-443.
219. Suberbielle E, Gonzalez-Dunia D, Pont F,. 2008. High reproducibility of two-dimensional liquid chromatography using pH-driven fractionation with a pressure-resistant electrode. J Chromatogr B Analyt Technol Biomed Life Sci 871: 125-129.
220. Surendran S, Rajasankar S,. 2010. Parkinson's disease: Oxidative stress and therapeutic approaches. Neurol Sci 31: 531-540.
221. Tan HT, Lee YH, Chung MC,. 2012. Cancer proteomics. Mass Spectrom Rev 31: 583-605.
222. Tautenhahn R, Patti GJ, Rinehart D, Siuzdak GE,. 2012. XCMS Online: A web-based platform to process untargeted metabolomic data. Anal Chem 5: 5035-5039.
223. Thorburn J, Frankel AE, Thorburn A,. 2009. Regulation of HMGB1 release by autophagy. Autophagy 5: 247-249.
224. Tong A, Wu L, Lin Q, Lau QC, Zhao X, Li J, Chen P, Chen L, Tang H, Huang C, Wei YQ,. 2008. Proteomic analysis of cellular protein alterations using a hepatitis B virus-producing cellular model. Proteomics 8: 2012-2023. (Pubitemid 351775781)
225. Toro JR, Nickerson ML, Wei MH, Warren MB, Glenn GM, Turner ML, Stewart L, Duray P, Tourre O, Sharma N, Choyke P, Stratton P, Merino M, Walther MM, Linehan WM, Schmidt LS, Zbar B,. 2003. Mutations in the Fumarate hydratase gene cause hereditary leiomyomatosis and renal cell cancer in families in North America. Am J Hum Genet 73: 95-106. (Pubitemid 36793783)
226. Trachootham D, Alexandre J, Huang P,. 2009. Targeting cancer cells by ROS-mediated mechanisms: A radical therapeutic approach? Nat Rev Drug Discov 8: 579-591.
227. Trimmer C, Sotgia F, Whitaker-Menezes D, Balliet RM, Eaton G, Martinez-Outschoorn UE, Pavlides S, Howell A, Iozzo RV, Pestell RG, Scherer PE, Capozza F, Lisanti MP,. 2011. Caveolin-1 and mitochondrial SOD2 (MnSOD) function as tumor suppressors in the stromal microenvironment: A new genetically tractable model for human cancer associated fibroblasts. Cancer Biol Ther 11: 383-394.
228. Turcan S, Rohle D, Goenka A, Walsh LA, Fang F, Yilmaz E, Campos C, Fabius AWM, Lu C, Ward PS, Thompson CB, Kaufman A, Guryanova O, Levine R, Heguy A, Viale A, Morris LGT, Huse JT, Mellinghoff IK, Chan TA,. 2012. IDH1 mutation is sufficient to establish the glioma hypermethylator phenotype. Nature 483: 479-483.
229. Turhani D, Krapfenbauer K, Thurnher D, Langen H, Fountoulakis M,. 2006. Identification of differentially expressed, tumor-associated proteins in oral squamous cell carcinoma by proteomic analysis. Electrophoresis 27: 1417-1423.
230. Twig G, Elorza A, Molina AJA, Mohamed H, Wikstrom JD, Walzer G, Stiles L, Haigh SE, Katz S, Las G, Alroy J, Wu M, Py BF, Yuan J, Deeney JT, Corkey BE, Shirihai OS,. 2008. Fission and selective fusion govern mitochondrial segregation and elimination by autophagy. EMBO J 27: 433-446. (Pubitemid 351161653)
231. Unlu M, Morgan ME, Minden JS,. 1997. Difference gel electrophoresis: A single gel method for detecting changes in protein extracts. Electrophoresis 18: 2071-2077. (Pubitemid 27501267)
232. Ushio-Fukai M, Nakamura Y,. 2008. Reactive oxygen species and angiogenesis: NADPH oxidase as target for cancer therapy. Cancer Lett 266: 37-52. (Pubitemid 351753035)
233. Valko M, Leibfritz D, Moncol J, Cronin MT, Mazur M, Telser J,. 2007. Free radicals and antioxidants in normal physiological functions and human disease. Int J Biochem Cell Biol 39: 44-84. (Pubitemid 44566469)
234. Vander Heiden MG, Cantley LC, Thompson CB,. 2009. Understanding the Warburg effect: The metabolic requirements of cell proliferation. Science 324: 1029-1033.
235. Varghese B, Swaminathan G, Plotnikov A, Tzimas C, Yang N, Rui H, Fuchs SY,. 2010. Prolactin inhibits activity of pyruvate kinase M2 to stimulate cell proliferation. Mol Endocrinol 24: 2356-2365.
236. Verschoor ML, Wilson LA, Singh G,. 2010. Mechanisms associated with mitochondrial-generated reactive oxygen species in cancer. Can J Physiol Pharmacol 88: 204-219.
237. Vinayavekhin N, Homan EA, Saghatelian A,. 2010. Exploring disease through metabolomics. ACS Chem Biol 5: 91-103.
238. Wang P, Whiteaker JR, Paulovich AG,. 2009. The evolving role of mass spectrometry in cancer biomarker discovery. Cancer Biol Ther 8: 1083-1094.
239. Wang Q, Zhang Y, Yang C, Xiong H, Lin Y, Yao J, Li H, Xie L, Zhao W, Yao Y, Ning ZB, Zeng R, Xiong Y, Guan K-L, Zhao S, Zhao GP,. 2010. Acetylation of metabolic enzymes coordinates carbon source utilization and metabolic flux. Science 327: 1004-1007.
240. Wang L, Liu HL, Li Y, Yuan P,. 2011. Proteomic analysis of pancreatic intraepithelial neoplasia and pancreatic carcinoma in rat models. World J Gastroenterol 17: 1434-1441.
241. Warburg O,. 1956. On the origin of cancer cells. Science 123: 309-314.
242. Warburg O, Posener K, Negelein E,. 1924. Ueber den Stoffwechsel der Tumoren. Biochem Z 152: 319-344.
243. Ward PS, Thompson CB,. 2012. Metabolic reprogramming: A cancer hallmark even Warburg did not anticipate. Cancer Cell 21: 297-308.
244. Weinberg F, Chandel NS,. 2009. Reactive oxygen species-dependent signaling regulates cancer. Cell Mol Life Sci 66: 3663-3673.
245. Wellen KE, Thompson CB,. 2010. Cellular metabolic stress: Considering how cells respond to nutrient excess. Mol Cell 40: 323-332.
246. Whetstone PA, Butlin NG, Corneillie TM, Meares CF,. 2004. Element-coded affinity tags for peptides and proteins. Bioconjug Chem 15: 3-6. (Pubitemid 38165973)
247. Whitaker-Menezes D, Martinez-Outschoorn UE, Lin Z, Ertel A, Flomenberg N, Witkiewicz AK, Birbe RC, Howell A, Pavlides S, Gandara R, Pestell RG, Sotgia F, Philp NJ, Lisanti MP,. 2011. Evidence for a stromal-epithelial "lactate shuttle" in human tumors MCT4 is a marker of oxidative stress in cancer-associated fibroblasts. Cell Cycle 10: 1772-1783.
248. Wiese S, Reidegeld KA, Meyer HE, Warscheid B,. 2007. Protein labeling by iTRAQ: A new tool for quantitative mass spectrometry in proteome research. Proteomics 7: 340-350. (Pubitemid 46293976)
249. Wild P, Dikic I,. 2010. Mitochondria get a Parkin' ticket. Nat Cell Biol 12: 104-106.
250. Wishart DS, Tzur D, Knox C, Eisner R, Guo AC, Young N, Cheng D, Jewell K, Arndt D, Sawhney S, Fung C, Nikolai L, Lewis M, Coutouly M-A, Forsythe I, Tang P, Shrivastava S, Jeroncic K, Stothard P, Amegbey G, Block D, Hau DD, Wagner J, Miniaci J, Clements M, Gebremedhin M, Guo N, Zhang Y, Duggan GE, MacInnis GD, Weljie AM, Dowlatabadi R, Bamforth F, Clive D, Greiner R, Li L, Marrie T, Sykes BD, Vogel HJ, Querengesser L,. 2007. HMDB: The human metabolome database. Nucleic Acids Res 35: D521-D526. (Pubitemid 46056263)
251. Witkiewicz AK, Casimiro MC, Dasgupta A, Mercier I, Wang C, Bonuccelli G, Jasmin JF, Frank PG, Pestell RG, Kleer CG, Sotgia F, Lisanti MP,. 2009. Towards a new "stromal-based" classification system for human breast cancer prognosis and therapy. Cell Cycle 8: 1654-1658.
252. Wu CC, Peng PH, Chang YT, Huang YS, Chang KP, Hao SP, Tsang NM, Yeh CT, Chang YS, Yu JS,. 2008. Identification of potential serum markers for nasopharyngeal carcinoma from a xenografted mouse model using Cy-dye labeling combined with three-dimensional fractionation. Proteomics 8: 3605-3620.
253. Xia C, Meng Q, Lin LZ, Rojanasakul Y, Wang XR, Jiang BH,. 2007. Reactive oxygen species regulate angiogenesis and tumor growth through vascular endothelial growth factor. Cancer Res 67: 10823-10830. (Pubitemid 350145911)
254. Xu W, Yang H, Liu Y, Yang Y, Wang P, Kim SH, Ito S, Yang C, Wang P, Xiao MT, Liu LX, Jiang WQ, Liu J, Zhang JY, Wang B, Frye S, Zhang Y, Xu Y-h, Lei QY, Guan KL, Zhao SM, Xiong Y,. 2011. Oncometabolite 2-hydroxyglutarate is a competitive inhibitor of alpha-ketoglutarate-dependent dioxygenases. Cancer Cell 19: 17-30.
255. Yan H, Parsons DW, Jin G, McLendon R, Rasheed BA, Yuan W, Kos I, Batinic-Haberle I, Jones S, Riggins GJ, Friedman H, Friedman A, Reardon D, Herndon J, Kinzler KW, Velculescu VE, Vogelstein B, Bigner DD,. 2009. IDH1 and IDH2 mutations in gliomas. N Engl J Med 360: 765-773.
256. Yang W, Xia Y, Ji H, Zheng Y, Liang J, Huang W, Gao X, Aldape K, Lu Z,. 2011. Nuclear PKM2 regulates beta-catenin transactivation upon EGFR activation. Nature 480: 118-122.
257. Yeap PM, Tobias ES, Mavraki E, Fletcher A, Bradshaw N, Freel EM, Cooke A, Murday VA, Davidson HR, Perry CG, Lindsay RS,. 2011. Molecular analysis of pheochromocytoma after maternal transmission of SDHD mutation elucidates mechanism of parent-of-origin effect. J Clin Endocrinol Metab 96: E2009-E2013.
258. Yeung AT, Patel BB, Li X-M, Seeholzer SH, Coudry RA, Cooper HS, Bellacosa A, Boman BM, Zhang T, Litwin S, Ross EA, Conrad P, Crowell JA, Kopelovich L, Knudson A,. 2008. One-hit effects in cancer: Altered proteome of morphologically normal colon crypts in Familial Adenomatous Polyposis. Cancer Res 68: 7579-7586.
259. Yoo DG, Song YJ, Cho EJ, Lee SK, Park JB, Yu JH, Lim SP, Kim JM, Jeon BH,. 2008. Alteration of APEI/ref-1 expression in non-small cell lung cancer: The implications of impaired extracellular superoxide dismutase and catalase antioxidant systems. Lung Cancer 60: 277-284. (Pubitemid 351622081)
260. Yu KH, Barry CG, Austin D, Busch CM, Sangar V, Rustgi AK, Blair IA,. 2009. Stable isotope dilution multidimensional liquid chromatography-tandem mass spectrometry for pancreatic cancer serum biomarker discovery. J Proteome Res 8: 1565-1576.
261. Yuan KF, Lei YL, Huang CH,. 2010. Application of chemistry-based functional proteomics to screening for novel drug targets. Comb Chem High Throughput Screen 13: 414-421.
262. Yuneva MO, Fan TWM, Allen TD, Higashi RM, Ferraris DV, Tsukamoto T, Mates JM, Alonso FJ, Wang C, Seo Y, Chen X, Bishop JM,. 2012. The metabolic profile of tumors depends on both the responsible genetic lesion and tissue type. Cell Metab 15: 157-170.
263. Zhan XQ, Desiderio DM,. 2003. Differences of the spatial and quantitative reproducibility between two second-dimension gel electrophoresis systems. Electrophoresis 24: 1834-1846. (Pubitemid 38088971)
264. Zhang Z, Bast RC, Yu YH, Li JN, Sokoll LJ, Rai AJ, Rosenzweig JM, Cameron B, Wang YY, Meng XY, Berchuck A, van Haaften-Day C, Hacker NF, de Bruijn HWA, van der Zee AGJ, Jacobs IJ, Fung ET, Chan DW,. 2004. Three biomarkers identified from serum proteomic analysis for the detection of early stage ovarian cancer. Cancer Res 64: 5882-5890. (Pubitemid 39095590)
265. Zhang DH, Tai LK, Wong LL, Chiu LL, Sethi SK, Koay ESC,. 2005. Proteomic study reveals that proteins involved in metabolic and detoxification pathways are highly expressed in HER-2/neu-positive breast cancer. Mol Cell Proteomics 4: 1686-1696. (Pubitemid 41749262)
266. Zhang X, Wei D, Yap Y, Li L, Guo S, Chen F,. 2007. Mass spectrometry-based "omics" technologies in cancer diagnostics. Mass Spectrom Rev 26: 403-431. (Pubitemid 46750377)
267. Zhang L, Wei Q, Mao L, Liu W, Mills GB, Coombes K,. 2009. Serial dilution curve: A new method for analysis of reverse phase protein array data. Bioinformatics 25: 650-654.
268. Zhang XD, Qin ZH, Wang J,. 2010. The role of p53 in cell metabolism. Acta Pharmacol Sin 31: 1208-1212.
269. Zhang J, Wang K, Zhang J, Liu SS, Dai L, Zhang JY,. 2011. Using proteomic approach to identify tumor-associated proteins as biomarkers in human esophageal squamous cell carcinoma. J Proteome Res 10: 2863-2872.
270. Zhang W, Trachootham D, Liu J, Chen G, Pelicano H, Garcia-Prieto C, Lu W, Burger JA, Croce CM, Plunkett W, Keating MJ, Huang P,. 2012. Stromal control of cystine metabolism promotes cancer cell survival in chronic lymphocytic leukaemia. Nat Cell Biol 14: 276-286.
271. Zhao S, Xu W, Jiang W, Yu W, Lin Y, Zhang T, Yao J, Zhou L, Zeng Y, Li H, Li Y, Shi J, An W, Hancock SM, He F, Qin L, Chin J, Yang P, Chen X, Lei Q, Xiong Y, Guan KL,. 2010. Regulation of cellular metabolism by protein lysine acetylation. Science 327: 1000-1004.
272. Zhou S, Huang C, Wei Y,. 2010. The metabolic switch and its regulation in cancer cells. Sci China Life Sci 53: 942-958.
273. Zhou W, Capello M, Fredolini C, Piemonti L, Liotta LA, Novelli F, Petricoin EF,. 2010. Mass spectrometry analysis of the post-translational
274. Zhou W, Capello M, Fredolini C, Racanicchi L, Piemonti L, Liotta LA, Noveli F, Petricoin EF,. 2012. Proteomic analysis reveals Warburg effect and anomalous metabolism of glutamine in pancreatic cancer cells. J Proteome Res 11: 554-563.
275. Zoidakis J, Makridakis M, Zerefos PG, Bitsika V, Esteban S, Frantzi M, Stravodimos K, Anagnou NP, Roubelakis MG, Sanchez-Carbayo M, Vlahou A,. 2012. Profilin 1 is a potential biomarker for bladder cancer aggressiveness. Mol Cell Proteomics 11: M111.009449.