Advanced mass spectrometry-based multi-omics technologies for exploring the pathogenesis of hepatocellular carcinoma

Mass Spectrometry Reviews

Volumn 35, Issue 3, 2016, Pages 331-349

  Nie, Wenna ^a   Yan, Leyu ^a   Lee, Yie H ^b   Guha, Chandan ^c,d   Kurland, Irwin J ^d   Lu, Haitao ^a,e  

^a CHONGQING UNIVERSITY   (China)

^b SINGAPORE MIT ALLIANCE FOR RESEARCH AND TECHNOLOGY   (Singapore)

^c MONTEFIORE MEDICAL CENTER   (United States)

^d ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

^e QUEENSLAND UNIVERSITY OF TECHNOLOGY   (Australia)

Author keywords

DNA damage adducts; hepatocellular carcinoma; metabolomics; omics technology; proteomics; RNA modifications

Indexed keywords

DIAGNOSIS; KNOWLEDGE BASED SYSTEMS; MOLECULAR BIOLOGY; NUCLEIC ACIDS; RNA; SPECTROMETRY;

DNA DAMAGES; HEPATOCELLULAR CARCINOMA; METABOLOMICS; OMICS TECHNOLOGIES; PROTEOMICS; RNA MODIFICATIONS;

MASS SPECTROMETRY;

DNA ADDUCT; RNA;

ANALYSIS; CHEMISTRY; DNA ADDUCT; DNA DAMAGE; GENETICS; HUMAN; LIVER CELL CARCINOMA; LIVER TUMOR; MASS SPECTROMETRY; METABOLISM; METABOLOMICS; PATHOLOGY; PROCEDURES; PROTEOMICS;

CARCINOMA, HEPATOCELLULAR; DNA ADDUCTS; DNA DAMAGE; HUMANS; LIVER NEOPLASMS; MASS SPECTROMETRY; METABOLOMICS; PROTEOMICS; RNA;

EID: 84901738126     PISSN: 02777037     EISSN: 10982787     Source Type: Journal    
DOI: 10.1002/mas.21439     Document Type: Review

References (83)

1. Abdalla MA, Haj-Ahmad Y,. 2012. Promising urinary protein biomarkers for the early detection of hepatocellular carcinoma among high-risk hepatitis C virus Egyptian patients. J Cancer 3: 390-403.
2. Aebersold R, Mann M,. 2003. Mass spectrometry-based proteomics. Nature 422: 198-207.
3. Agris PF, Vendeix FA, Graham WD,. 2007. tRNA's wobble decoding of the genome: 40 years of modification. J Mol Biol 366: 1-13.
4. Barsnes H, Vizcaino JA, Eidhammer I, Martens L,. 2009. PRIDE Converter: Making proteomics data-sharing easy. Nat Biotechnol 27: 598-599.
5. Bjork GR, Durand JM, Hagervall TG, Leipuviene R, Lundgren HK, Nilsson K, Chen P, Qian Q, Urbonavicius J,. 1999. Transfer RNA modification: Influence on translational frameshifting and metabolism. FEBS Lett 452: 47-51.
6. Budhu A1, Roessler S, Zhao X, Yu Z, Forgues M, Ji J, Karoly E, Qin LX, Ye QH, Jia HL, Fan J, Sun HC, Tang ZY, Wang XW,. 2013. Integrated metabolite and gene expression profiles identify lipid biomarkers associated with progression of hepatocellular carcinoma and patient outcomes. Gastroenterology 144: 1066-1075, e1061.
7. Cantara WA, Crain PF, Rozenski J, McCloskey JA, Harris KA, Zhang X, Vendeix FA, Fabris D, Agris PF,. 2011. The RNA modification database, RNAMDB: 2011 update. Nucleic Acids Res 39: D195-D201.
8. Chan CT, Dyavaiah M, DeMott MS, Taghizadeh K, Dedon PC, Begley TJ,. 2010. A quantitative systems approach reveals dynamic control of tRNA modifications during cellular stress. PLoS Genet 6: e1001247.
9. Chan CT, Pang YL, Deng W, Babu IR, Dyavaiah M, Begley TJ, Dedon PC,. 2012. Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins. Nat Commun 3: 937.
10. Chen F, Xue J, Zhou L, Wu S, Chen Z,. 2011a. Identification of serum biomarkers of hepatocarcinoma through liquid chromatography/mass spectrometry-based metabonomic method. Anal Bioanal Chem 401: 1899-1904.
11. Chen T, Xie G, Wang X, Fan J, Qiu Y, Zheng X, Qi X, Cao Y, Su M, Wang X, Xu LX, Yen Y, Liu P, Jia W,. 2011b. Serum and urine metabolite profiling reveals potential biomarkers of human hepatocellular carcinoma. Mol Cell Proteomics 10: M110004945.
12. Chignard N, Beretta L,. 2004. Proteomics for hepatocellular carcinoma marker discovery. Gastroenterology 127: S120-S125.
13. Chionh YH, Ho CH, Pruksakorn D, Ramesh Babu I, Ng CS, Hia F, McBee ME, Su D, Pang YL, Gu C, Dong H, Prestwich EG, Shi PY, Preiser PR, Alonso S, Dedon PC,. 2013. A multidimensional for the purification of non-coding RNA species. Nucleic Acids Res 41: e168.
14. Chuma M, Hige S, Nakanishi M, Ogawa K, Natsuizaka M, Yamamoto Y, Asaka M,. 2008. 8-Hydroxy-2′-deoxy-guanosine is a risk factor for development of hepatocellular carcinoma in patients with chronic hepatitis C virus infection. J Gastroenterol Hepatol 23: 1431-1436.
15. Chung YT, Chen CL, Wu CC, Chan SA, Chi CW, Liu TY,. 2008. Safrole-DNA adduct in hepatocellular carcinoma associated with betel quid chewing. Toxicol Lett 183: 21-27.
16. Clayton TA, Lindon JC, Cloarec O, Antti H, Charuel C, Hanton G, Provost JP, Le Net JL, Baker D, Walley RJ, Everett JR, Nicholson JK,. 2006. Pharmaco-metabonomic phenotyping and personalized drug treatment. Nature 440: 1073-1077.
17. Codarin E, Renzone G, Poz A, Avellini C, Baccarani U, Lupo F, di Maso V, Crocè SL, Tiribelli C, Arena S, Quadrifoglio F, Scaloni A, Tell G,. 2009. Differential proteomic analysis of subfractioned human hepatocellular carcinoma tissues. J Proteome Res 8: 2273-2284.
18. Corona G, De Lorenzo E, Elia C, Simula MP, Avellini C, Baccarani U, Lupo F, Tiribelli C, Colombatti A, Toffoli G,. 2010. Differential proteomic analysis of hepatocellular carcinoma. Int J Oncol 36: 93-99.
19. Cox J, Mann M,. 2007. Is proteomics the new genomics ? Cell 130: 395-398.
20. Craig JR,. 2002. Tumors of the liver. In:, Zakim D, Boyer TD, editors. Hepatology, a textbook of liver disease. Vol. 2. Philadelphia: Elsevier Science USA. p. 1355.
21. Cravatt BF, Simon GM, Yates JR III., 2007. The biological impact of mass-spectrometry-based proteomics. Nature 450: 991-1000.
22. Cui JF, Liu YK, Pan BS, Song HY, Zhang Y, Sun RX, Chen J, Feng JT, Tang ZY, Yu YL, Shen HL, Yang PY,. 2004. Differential proteomic analysis of human hepatocellular carcinoma cell line metastasis-associated proteins. J Cancer Res Clin Oncol 130: 615-622.
23. D'Alessandro LA, Meyer R, Klingmuller U,. 2013. Hepatocellular carcinoma: A systems biology perspective. Front Physiol 4: 28.
24. Dominissini D, Moshitch-Moshkovitz S, Schwartz S, Salmon-Divon M, Ungar L, Osenberg S, Cesarkas K, Jacob-Hirsch J, Amariglio N, Kupiec M, Sorek R, Rechavi G,. 2012. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature 485: 201-206.
25. Dunin-Horkawicz S, Czerwoniec A, Gajda MJ, Feder M, Grosjean H, Bujnicki JM,. 2006. MODOMICS: A database of RNA modification pathways. Nucleic Acids Res 34: D145-D149.
26. El-Aneed A, Banoub J,. 2006. Proteomics in the diagnosis of hepatocellular carcinoma: Focus on high risk hepatitis B and C patients. Anticancer Res 26: 3293-3300.
27. Fan ST, Cheung ST, Lo CM,. 2000. Indications for liver transplantation in patients with chronic hepatitis B and C virus infection and hepatocellular carcinoma. J Gastroenterol Hepatol 15 (Suppl): E181-E186.
28. Farber E,. 1996. Alcohol and other chemicals in the development of hepatocellular carcinoma. Clin Lab Med 16: 377-394.
29. Feitelson MA, Sun B, Satiroglu Tufan NL, Liu J, Pan J, Lian Z,. 2002a. Genetic mechanisms of hepatocarcinogenesis. Clin Lab Med 16: 377-394.
30. Feitelson MA, Sun B, Satiroglu Tufan NL, Liu J, Pan J, Lian Z,. 2002b. Genetic mechanisms of hepatocarcinogenesis. Oncogene 21: 2593-2604.
31. Gronbaek H,. 2006. Hepatocellular carcinoma and other liver tumors. The Danish Society of Hepatology (DASL). Ugeskr Laeger 168: 1219.
32. Gstaiger M, Aebersold R,. 2009. Applying mass spectrometry-based proteomics to genetics, genomics and network biology. Nat Rev Genet 10: 617-627.
33. Holmes E, Loo RL, Stamler J, Bictash M, Yap IK, Chan Q, Ebbels T, De Iorio M, Brown IJ, Veselkov KA, Daviglus ML, Kesteloot H, Ueshima H, Zhao L, Nicholson JK, Elliott P,. 2008. Human metabolic phenotype diversity and its association with diet and blood pressure. Nature 453: 396-400.
34. Hu J, Wang Z, Fan J, Dai Z, He YF, Qiu SJ, Huang XW, Sun J, Xiao YS, Song K, Shi YH, Sun QM, Yang XR, Shi GM, Yu L, Yang GH, Ding ZB, Gao Q, Tang ZY, Zhou J,. 2011. Genetic variations in plasma circulating DNA of HBV-related hepatocellular carcinoma patients predict recurrence after liver transplantation. PLoS ONE 6: e26003.
35. Jia G, Fu Y, Zhao X, Dai Q, Zheng G, Yang Y, Yi C, Lindahl T, Pan T, Yang YG, He C,. 2011. N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat Chem Biol 7: 885-887.
36. Khan DH, Jahan S, Davie JR,. 2012. Pre-mRNA splicing: Role of epigenetics and implications in disease. Adv Biol Regul 52: 377-388.
37. Kurland IJ, Accili D, Burant C, Fischer SM, Kahn BB, Newgard CB, Ramagiri S, Ronnett GV, Ryals JA, Sanders M, Shambaugh J, Shockcor J, Gross SS,. 2013. Application of combined omics platforms to accelerate biomedical discovery in diabesity. Ann NY Acad Sci 1287: 1-16.
38. Lee IN, Chen CH, Sheu JC, Lee HS, Huang GT, Yu CY, Lu FJ, Chow LP,. 2005. Identification of human hepatocellular carcinoma-related biomarkers by two-dimensional difference gel electrophoresis and mass spectrometry. J Proteome Res 4: 2062-2069.
39. Lee JS, Thorgeirsson SS,. 2004. Genome-scale profiling of gene expression in hepatocellular carcinoma: Classification, survival prediction, and identification of therapeutic targets. Gastroenterology 127: S51-55.
40. Lee YH, Lin Q, Boelsterli UA, Chung MC,. 2010. The Sod2 mutant mouse as a model for oxidative stress: A functional proteomics perspective. Mass Spectrom Rev 29: 179-196.
41. Li Z, Zhang H, Yang J, Hao T, Li S,. 2012. Promoter hypermethylation of DNA damage response genes in hepatocellular carcinoma. Cell Biol Int 36: 427-432.
42. Limbach PA, Crain PF, McCloskey JA,. 1994. Summary: The modified nucleosides of RNA. Nucleic Acids Res 22: 2183-2196.
43. Lleonart ME, Kirk GD, Villar S, Lesi OA, Dasgupta A, Goedert JJ, Mendy M, Hollstein MC, Montesano R, Groopman JD, Hainaut P, Friesen MD,. 2005. Quantitative analysis of plasma TP53 249Ser-mutated DNA by electrospray ionization mass spectrometry. Cancer Epidemiol Biomarkers Prev 14: 2956-2962.
44. Lv H,. 2013. Mass spectrometry-based metabolomics towards understanding of gene functions with a diversity of biological contexts. Mass Spectrom Rev 32: 118-128.
45. Machnicka MA, Milanowska K, Osman Oglou O, Purta E, Kurkowska M, Olchowik A, Januszewski W, Kalinowski S, Dunin-Horkawicz S, Rother KM, et al., 2013. MODOMICS: A database of RNA modification pathways-2013 update. Nucleic Acids Res 41: D262-D267.
46. McCloskey JA, Crain PF,. 1998. The RNA modification database-1998. Nucleic Acids Res 26: 196-197.
47. Meng Z, Limbach PA,. 2006. Mass spectrometry of RNA: Linking the genome to the proteome. Brief Funct Genomic Proteomic 5: 87-95.
48. Murakami Y, Yasuda T, Saigo K, Urashima T, Toyoda H, Okanoue T, Shimotohno K,. 2006. Comprehensive analysis of microRNA expression patterns in hepatocellular carcinoma and non-tumorous tissues. Oncogene 25: 2537-2545.
49. Nishimura S,. 1977. Modified nucleosides in tRNA: Its structure, biosynthesis and function (author's transl). Tanpakushitsu Kakusan Koso 22: Spec No: 922-930.
50. Ohata K, Hamasaki K, Toriyama K, Ishikawa H, Nakao K, Eguchi K,. 2004. High viral load is a risk factor for hepatocellular carcinoma in patients with chronic hepatitis B virus infection. J Gastroenterol Hepatol 19: 670-675.
51. Orimo T, Ojima H, Hiraoka N, Saito S, Kosuge T, Kakisaka T, Yokoo H, Nakanishi K, Kamiyama T, Todo S, et al., 2008. Proteomic profiling reveals the prognostic value of adenomatous polyposis coli-end-binding protein 1 in hepatocellular carcinoma. Hepatology 48: 1851-1863.
52. Patterson AD, Maurhofer O, Beyoglu D, Lanz C, Krausz KW, Pabst T, Gonzalez FJ, Dufour JF, Idle JR,. 2011. Aberrant lipid metabolism in hepatocellular carcinoma revealed by plasma metabolomics and lipid profiling. Cancer Res 71: 6590-6600.
53. Poirier MC,. 2004. Chemical-induced DNA damage and human cancer risk. Nat Rev Cancer 4: 630-637.
54. Poirier MC,. 2012. Chemical-induced DNA damage and human cancer risk. Discov Med 14: 283-288.
55. Poulsen HE, Specht E, Broedbaek K, Henriksen T, Ellervik C, Mandrup-Poulsen T, Tonnesen M, Nielsen PE, Andersen HU, Weimann A,. 2012. RNA modifications by oxidation: A novel disease mechanism ? Free Radic Biol Med 52: 1353-1361.
56. Ressom HW, Xiao JF, Tuli L, Varghese RS, Zhou B, Tsai TH, Ranjbar MR, Zhao Y, Wang J, Di Poto C, Cheema AK, Tadesse MG, Goldman R, Shetty K,. 2012. Utilization of metabolomics to identify serum biomarkers for hepatocellular carcinoma in patients with liver cirrhosis. Anal Chim Acta 743: 90-100.
57. Santamaría E, Muñoz J, Fernandez-Irigoyen J, Sesma L, Mora MI, Berasain C, Lu SC, Mato JM, Prieto J, Avila MA, Corrales FJ,. 2006. Molecular profiling of hepatocellular carcinoma in mice with a chronic deficiency of hepatic s-adenosylmethionine: Relevance in human liver diseases. J Proteome Res 5: 944-953.
58. Schafer DF, Sorrell MF,. 1999. Hepatocellular carcinoma. Lancet 353: 1253-1257.
59. Schaffer SW, Jong CJ, Warner D, Ito T, Azuma J,. 2013. Taurine deficiency and MELAS are closely related syndromes. Adv Exp Med Biol 776: 153-165.
60. Schagdarsurengin U, Wilkens L, Steinemann D, Flemming P, Kreipe HH, Pfeifer GP, Schlegelberger B, Dammann R,. 2003. Frequent epigenetic inactivation of the RASSF1A gene in hepatocellular carcinoma. Oncogene 22: 1866-1871.
61. Sharma VK, Vouros P, Glick J,. 2011. Mass spectrometric based analysis, characterization and applications of circulating cell free DNA isolated from human body fluids. Int J Mass Spectrom 304: 172-183.
62. Song BC, Chung YH, Kim JA, Choi WB, Suh DD, Pyo SI, Shin JW, Lee HC, Lee YS, Suh DJ,. 2002. Transforming growth factor-beta1 as a useful serologic marker of small hepatocellular carcinoma. Cancer 94: 175-180.
63. Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM,. 2009. Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature 457: 910-914.
64. Sun W, Xing B, Sun Y, Du X, Lu M, Hao C, Lu Z, Mi W, Wu S, Wei H, Gao X, Zhu Y, Jiang Y, Qian X, He F,. 2007. Proteome analysis of hepatocellular carcinoma by two-dimensional difference gel electrophoresis: Novel protein markers in hepatocellular carcinoma tissues. Mol Cell Proteomics 6: 1798-1808.
65. Suzuki T, Ikeuchi Y, Noma A, Sakaguchi Y,. 2007. Mass spectrometric identification and characterization of RNA-modifying enzymes. Methods Enzymol 425: 211-229.
66. Tan Y, Yin P, Tang L, Xing W, Huang Q, Cao D, Zhao X, Wang W, Lu X, Xu Z, Wang H, Xu G,. 2012. Metabolomics study of stepwise hepatocarcinogenesis from the model rats to patients: Potential biomarkers effective for small hepatocellular carcinoma diagnosis. Mol Cell Proteomics 11: M111010694.
67. Uccello M, Malaguarnera G, Corriere T, Biondi A, Basile F, Malaguarnera M,. 2012. Risk of hepatocellular carcinoma in workers exposed to chemicals. Hepat Mon 12: e5943.
68. Urbonavicius J, Qian O, Durand JMB, Hagervall TG, Bjork GR,. 2001. Improvement of reading frame maintenance is a common function for several tRNA modifications. EMBO J 20: 4863-4873.
69. Uto H, Kanmura S, Takami Y, Tsubouchi H,. 2010. Clinical proteomics for liver disease: A promising approach for discovery of novel biomarkers. Proteome Sci 8: 70.
70. Wang B, Chen D, Chen Y, Hu Z, Cao M, Xie Q, Xu J, Zheng S, Li L,. 2012. Metabonomic profiles discriminate hepatocellular carcinoma from liver cirrhosis by ultraperformance liquid chromatography-mass spectrometry. J Proteome Res 11: 1217-1227.
71. Wang LY, Chen CJ, Zhang YJ, Tsai WY, Lee PH, Feitelson MA, Lee CS, Santella RM,. 1998. 4-Aminobiphenyl DNA damage in liver tissue of hepatocellular carcinoma patients and controls. Am J Epidemiol 147: 315-323.
72. Wang W, Peng JX, Yang JQ, Yang LY,. 2009. Identification of gene expression profiling in hepatocellular carcinoma using cDNA microarrays. Dig Dis Sci 54: 2729-2735.
73. Wang X, Zhang A, Sun H,. 2013a. Power of metabolomics in diagnosis and biomarker discovery of hepatocellular carcinoma. Hepatology 57: 2072-2077.
74. Wang XJ, Lv HT, Zhang AH, Sun WJ, Liu L, Wang P, Wu Z, Zou D, Sun H,. 2013b. Metabolite profiling and pathway analysis of acute hepatitis rats by UPLC-ESI MS combined with pattern recognition methods. Liver Int 34: 759-779.
75. Weerapana E, Wang C, Simon GM, Richter F, Khare S, Dillon MB, Bachovchin DA, Mowen K, Baker D, Cravatt BF,. 2010. Quantitative reactivity profiling predicts functional cysteines in proteomes. Nature 468: 790-795.
76. Wei SSY, Gowda GAN, Skill N, Maluccio M, Raftery D,. 2012. Differentiating hepatocellular carcinoma from hepatitis C using metabolite profiling. Metabolites 2: 701-716.
77. Wu W, Li J, Liu Y, Zhang C, Meng X, Zhou Z,. 2012. Comparative proteomic studies of serum from patients with hepatocellular carcinoma. J Invest Surg 25: 37-42.
78. Xiao JF, Varghese RS, Zhou B, Nezami Ranjbar MR, Zhao Y, Tsai TH, Di Poto C, Wang J, Goerlitz D, Luo Y, Cheema AK, Sarhan N, Soliman H, Tadesse MG, Ziada DH, Ressom HW,. 2012. LC-MS based serum metabolomics for identification of hepatocellular carcinoma biomarkers in Egyptian cohort. J Proteome Res 11: 5914-5923.
79. Xue R, Lin Z, Deng C, Dong L, Liu T, Wang J, Shen X,. 2008. A serum metabolomic investigation on hepatocellular carcinoma patients by chemical derivatization followed by gas chromatography/mass spectrometry. Rapid Commun Mass Spectrom 22: 3061-3068.
80. Yang F, Zhang L, Huo XS, Yuan JH, Xu D, Yuan SX, Zhu N, Zhou WP, Yang GS, Wang YZ, Shang JL, Gao CF, Zhang FR, Wang F, Sun SH,. 2011. Long noncoding RNA high expression in hepatocellular carcinoma facilitates tumor growth through enhancer of zeste homolog 2 in humans. Hepatology 54: 1679-1689.
81. Yarian C, Townsend H, Czestkowski W, Sochacka E, Malkiewicz AJ, Guenther R, Miskiewicz A, Agris PF,. 2002. Accurate translation of the genetic code depends on tRNA modified nucleosides. J Biol Chem 277: 16391-16395.
82. Ye G, Zhu B, Yao Z, Yin P, Lu X, Kong H, Fan F, Jiao B, Xu G,. 2012. Analysis of urinary metabolic signatures of early hepatocellular carcinoma recurrence after surgical removal using gas chromatography-mass spectrometry. J Proteome Res 11: 4361-4372.
83. Yoo BK, Santhekadur PK, Gredler R, Chen D, Emdad L, Bhutia S, Pannell L, Fisher PB, Sarkar D,. 2011. Increased RNA-induced silencing complex (RISC) activity contributes to hepatocellular carcinoma. Hepatology 53: 1538-1548.