Development of Biomarkers for Screening Hepatocellular Carcinoma Using Global Data Mining and Multiple Reaction Monitoring

PLoS ONE

Volumn 8, Issue 5, 2013, Pages

  Kim, Hyunsoo ^a   Kim, Kyunggon ^a   Yu, Su Jong ^a   Jang, Eun Sun ^a   Yu, Jiyoung ^a   Cho, Geunhee ^b   Yoon, Jung Hwan ^a   Kim, Youngsoo ^a  

^a Seoul National University College of Medicine   (South Korea)

^b Yonsei University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA FETOPROTEIN; ANILINE; BIOLOGICAL MARKER; COMPLEMENT COMPONENT C4A; FILAMIN B; UNCLASSIFIED DRUG;

ADULT; AGED; ARTICLE; BLOOD ANALYSIS; CANCER SCREENING; CANCER THERAPY; CHEMOEMBOLIZATION; CLINICAL ARTICLE; CONTROLLED STUDY; COPY NUMBER VARIATION; DATA ANALYSIS; DATA MINING; DNA MICROARRAY; EPIGENETICS; FEMALE; HUMAN; LIVER CELL CARCINOMA; MALE; MULTIPLE REACTION MONITORING; PERCUTANEOUS ETHANOL INJECTION THERAPY; PROTEOMICS; SOMATIC MUTATION; WESTERN BLOTTING;

AGED; AGED, 80 AND OVER; ALPHA-FETOPROTEINS; CARCINOMA, HEPATOCELLULAR; COMPLEMENT C4A; CONTRACTILE PROTEINS; DATA MINING; DNA COPY NUMBER VARIATIONS; EPIGENOMICS; FEMALE; FILAMINS; HUMANS; LIVER NEOPLASMS; MALE; MICROFILAMENT PROTEINS; MIDDLE AGED; MUTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEOME; PROTEOMICS; TUMOR MARKERS, BIOLOGICAL;

EID: 84878032994     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0063468     Document Type: Article

References (48)

1. Stefaniuk P, Cianciara J, Wiercinska-Drapalo A, (2010) Present and future possibilities for early diagnosis of hepatocellular carcinoma. World J Gastroenterol 16: 418-424.
2. Wang B, Chen D, Chen Y, Hu Z, Cao M, et al. (2012) Metabonomic profiles discriminate hepatocellular carcinoma from liver cirrhosis by ultraperformance liquid chromatography-mass spectrometry. J Proteome Res 11: 1217-1227.
3. Omata M, Lesmana LA, Tateishi R, Chen PJ, Lin SM, et al. (2010) Asian Pacific Association for the Study of the Liver consensus recommendations on hepatocellular carcinoma. Hepatol Int 4: 439-474.
4. Park JW, Korean Liver Cancer Study G, National Cancer C, (2004) [Practice guideline for diagnosis and treatment of hepatocellular carcinoma]. Korean J Hepatol 10: 88-98.
5. European Association For The Study Of The L, European Organisation For R, Treatment Of C, (2012) EASL-EORTC clinical practice guidelines: management of hepatocellular carcinoma. J Hepatol 56: 908-943.
6. Duffy MJ, (2001) Clinical uses of tumor markers: a critical review. Crit Rev Clin Lab Sci 38: 225-262.
7. Daniele B, Bencivenga A, Megna AS, Tinessa V, (2004) Alpha-fetoprotein and ultrasonography screening for hepatocellular carcinoma. Gastroenterology 127: S108-112.
8. Colli A, Fraquelli M, Casazza G, Massironi S, Colucci A, et al. (2006) Accuracy of ultrasonography, spiral CT, magnetic resonance, and alpha-fetoprotein in diagnosing hepatocellular carcinoma: a systematic review. Am J Gastroenterol 101: 513-523.
9. Kim K, Kim SJ, Yu HG, Yu J, Park KS, et al. (2010) Verification of biomarkers for diabetic retinopathy by multiple reaction monitoring. J Proteome Res 9: 689-699.
10. Gerber SA, Rush J, Stemman O, Kirschner MW, Gygi SP, (2003) Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc Natl Acad Sci U S A 100: 6940-6945.
11. Bruix J, Sherman M, American Association for the Study of Liver D, (2011) Management of hepatocellular carcinoma: an update. Hepatology 53: 1020-1022.
12. Stergachis AB, MacLean B, Lee K, Stamatoyannopoulos JA, MacCoss MJ, (2011) Rapid empirical discovery of optimal peptides for targeted proteomics. Nat Methods 8: 1041-1043.
13. Kirkpatrick DS, Gerber SA, Gygi SP, (2005) The absolute quantification strategy: a general procedure for the quantification of proteins and post-translational modifications. Methods 35: 265-273.
14. Kakehashi A, Ishii N, Shibata T, Wei M, Okazaki E, et al. (2011) Mitochondrial prohibitins and septin 9 are implicated in the onset of rat hepatocarcinogenesis. Toxicol Sci 119: 61-72.
15. Ren F, Wu H, Lei Y, Zhang H, Liu R, et al. (2010) Quantitative proteomics identification of phosphoglycerate mutase 1 as a novel therapeutic target in hepatocellular carcinoma. Mol Cancer 9: 81.
16. Lee HJ, Na K, Choi EY, Kim KS, Kim H, et al. (2010) Simple method for quantitative analysis of N-linked glycoproteins in hepatocellular carcinoma specimens. J Proteome Res 9: 308-318.
17. Zhang J, Niu D, Sui J, Ching CB, Chen WN, (2009) Protein profile in hepatitis B virus replicating rat primary hepatocytes and HepG2 cells by iTRAQ-coupled 2-D LC-MS/MS analysis: Insights on liver angiogenesis. Proteomics 9: 2836-2845.
18. Niu D, Sui J, Zhang J, Feng H, Chen WN, (2009) iTRAQ-coupled 2-D LC-MS/MS analysis of protein profile associated with HBV-modulated DNA methylation. Proteomics 9: 3856-3868.
19. Sun Y, Mi W, Cai J, Ying W, Liu F, et al. (2008) Quantitative proteomic signature of liver cancer cells: tissue transglutaminase 2 could be a novel protein candidate of human hepatocellular carcinoma. J Proteome Res 7: 3847-3859.
20. Chen N, Sun W, Deng X, Hao Y, Chen X, et al. (2008) Quantitative proteome analysis of HCC cell lines with different metastatic potentials by SILAC. Proteomics 8: 5108-5118.
21. Mannova P, Fang R, Wang H, Deng B, McIntosh MW, et al. (2006) Modification of host lipid raft proteome upon hepatitis C virus replication. Mol Cell Proteomics 5: 2319-2325.
22. Yan W, Lee H, Yi EC, Reiss D, Shannon P, et al. (2004) System-based proteomic analysis of the interferon response in human liver cells. Genome Biol 5: R54.
23. Li C, Hong Y, Tan YX, Zhou H, Ai JH, et al. (2004) Accurate qualitative and quantitative proteomic analysis of clinical hepatocellular carcinoma using laser capture microdissection coupled with isotope-coded affinity tag and two-dimensional liquid chromatography mass spectrometry. Mol Cell Proteomics 3: 399-409.
24. Woo HG, Lee JH, Yoon JH, Kim CY, Lee HS, et al. (2010) Identification of a cholangiocarcinoma-like gene expression trait in hepatocellular carcinoma. Cancer Res 70: 3034-3041.
25. Satow R, Shitashige M, Kanai Y, Takeshita F, Ojima H, et al. (2010) Combined functional genome survey of therapeutic targets for hepatocellular carcinoma. Clin Cancer Res 16: 2518-2528.
26. Roessler S, Jia HL, Budhu A, Forgues M, Ye QH, et al. (2010) A unique metastasis gene signature enables prediction of tumor relapse in early-stage hepatocellular carcinoma patients. Cancer Res 70: 10202-10212.
27. Hoshida Y, Nijman SM, Kobayashi M, Chan JA, Brunet JP, et al. (2009) Integrative transcriptome analysis reveals common molecular subclasses of human hepatocellular carcinoma. Cancer Res 69: 7385-7392.
28. Acevedo LG, Bieda M, Green R, Farnham PJ, (2008) Analysis of the mechanisms mediating tumor-specific changes in gene expression in human liver tumors. Cancer Res 68: 2641-2651.
29. Segal E, Sirlin CB, Ooi C, Adler AS, Gollub J, et al. (2007) Decoding global gene expression programs in liver cancer by noninvasive imaging. Nat Biotechnol 25: 675-680.
30. Lee JS, Heo J, Libbrecht L, Chu IS, Kaposi-Novak P, et al. (2006) A novel prognostic subtype of human hepatocellular carcinoma derived from hepatic progenitor cells. Nat Med 12: 410-416.
31. Budhu A, Forgues M, Ye QH, Jia HL, He P, et al. (2006) Prediction of venous metastases, recurrence, and prognosis in hepatocellular carcinoma based on a unique immune response signature of the liver microenvironment. Cancer Cell 10: 99-111.
32. Ye QH, Qin LX, Forgues M, He P, Kim JW, et al. (2003) Predicting hepatitis B virus-positive metastatic hepatocellular carcinomas using gene expression profiling and supervised machine learning. Nat Med 9: 416-423.
33. Chen CF, Hsu EC, Lin KT, Tu PH, Chang HW, et al. (2010) Overlapping high-resolution copy number alterations in cancer genomes identified putative cancer genes in hepatocellular carcinoma. Hepatology 52: 1690-1701.
34. Chochi Y, Kawauchi S, Nakao M, Furuya T, Hashimoto K, et al. (2009) A copy number gain of the 6p arm is linked with advanced hepatocellular carcinoma: an array-based comparative genomic hybridization study. J Pathol 217: 677-684.
35. Hashimoto K, Mori N, Tamesa T, Okada T, Kawauchi S, et al. (2004) Analysis of DNA copy number aberrations in hepatitis C virus-associated hepatocellular carcinomas by conventional CGH and array CGH. Mod Pathol 17: 617-622.
36. Hernandez-Vargas H, Lambert MP, Le Calvez-Kelm F, Gouysse G, McKay-Chopin S, et al. (2010) Hepatocellular carcinoma displays distinct DNA methylation signatures with potential as clinical predictors. PLoS One 5: e9749.
37. De Zhu J, (2005) The altered DNA methylation pattern and its implications in liver cancer. Cell Res 15: 272-280.
38. Malaguarnera G, Giordano M, Paladina I, Berretta M, Cappellani A, et al. (2010) Serum markers of hepatocellular carcinoma. Dig Dis Sci 55: 2744-2755.
39. Cottingham K, (2009) Candidate biomarkers for liver cancer. J Proteome Res 8: 428.
40. Masuzaki R, Karp SJ, Omata M, (2012) New serum markers of hepatocellular carcinoma. Semin Oncol 39: 434-439.
41. Bertino G, Ardiri A, Malaguarnera M, Malaguarnera G, Bertino N, et al. (2012) Hepatocellualar carcinoma serum markers. Semin Oncol 39: 410-433.
42. Bertino G, Neri S, Bruno CM, Ardiri AM, Calvagno GS, et al. (2011) Diagnostic and prognostic value of alpha-fetoprotein, des-gamma-carboxy prothrombin and squamous cell carcinoma antigen immunoglobulin M complexes in hepatocellular carcinoma. Minerva Med 102: 363-371.
43. Alkofer B, Lepennec V, Chiche L, (2011) Hepatocellular cancer in the non-cirrhotic liver. J Visc Surg 148: 3-11.
44. Nguyen VT, Law MG, Dore GJ, (2009) Hepatitis B-related hepatocellular carcinoma: epidemiological characteristics and disease burden. J Viral Hepat 16: 453-463.
45. Nakagawa K, Koike S, Matsumura H, Yokoi K, Kitamura H, (2012) [alpha-fetoprotein producing rectal cancer]. Gan To Kagaku Ryoho 39: 671-674.
46. Donati M, Brancato G, Donati A, (2010) Clinical biomarkers in hepatocellular carcinoma (HCC). Front Biosci (Schol Ed) 2: 571-577.
47. Bei R, Mizejewski GJ, (2011) Alpha fetoprotein is more than a hepatocellular cancer biomarker: from spontaneous immune response in cancer patients to the development of an AFP-based cancer vaccine. Curr Mol Med 11: 564-581.
48. Robinson P (2008) Hepatocellular carcinoma: development and early detection. Cancer Imaging 8 Spec No A: S128-131.