Proteomic study of advanced cirrhosis based on HCV to reveal potential biomarkers
Gastroenterology and Hepatology from Bed to Bench,
,
9 December 2020
https://doi.org/10.22037/ghfbb.v13i1.2219
Abstract
Background. Cirrhosis is a condition that liver damage and loses its function that follows the high rate of mortality in the world. Proteome profiling may help to identify important proteins and find the pathogenesis.
Aim. Proteomic assessment of long term effects of hepatitis C on liver is aim of this study.
Methods. Here, by the application two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), combined with (MALDI-TOF-TOF MS), proteome profile of decompensated HCV cirrhosis compared to healthy matched controls is determined. Furthermore, Cytoscape has used network analysis. The proteome comparison between two groups identified proteins with the significant expression changes (p<0.05 and fold change ≥ 1.5).
Results. Our results include of upregulation of IGHA1, C3, A1BG, IGKC and one isoform of HP. It also has been shown the decreased in the expression of APOA4 and the other spot of HP in advanced cirrhosis patients based on HCV compared to matched controls. According to network analysis, ALB has been introduced as key protein, which may play important role in pathogenesis.
Conclusion. Finally, integration of the proteomics with protein interaction data led to the identification of several novel key proteins related to the immune system that may reflect the long-term effects of hepatitis C virus on the liver and can introduce as therapeutic targets for advanced HCV- cirrhosis.
Keyword: Proteomic, liver cirrhosis, hepatitis C, Two-dimensional gel electrophoresis (2DE), Protein –protein interaction
Keywords:
- Proteomic, liver cirrhosis, hepatitis C, Two-dimensional gel electrophoresis (2DE), Protein –protein interaction
References
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11. Zali H, Ahmadi G, Bakhshandeh R, Rezaei-Tavirani M. Proteomic analysis of gene expression during human esophagus cancer. Journal of Paramedical Sciences. 2011;2(3).
12. Rezaie-Tavirani M, Fayazfar S, Heydari-Keshel S, Rezaee MB, Zamanian-Azodi M, Rezaei-Tavirani M, et al. Effect of essential oil of Rosa Damascena on human colon cancer cell line SW742. Gastroenterology and Hepatology from bed to bench. 2013;6(1).
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14. Rezaei-Tavirani M, Rahmati-Rad S, Rezaei-Tavirani M. Ethanol and Cancer Induce Similar Changes on Protein Expression Pattern of Human Fibroblast Cell. Iranian Journal of Pharmaceutical Research. 2016;15:175-84.
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16. Craven RA, Stanley AJ, Hanrahan S, Dods J, Unwin R, Totty N, et al. Proteomic analysis of primary cell lines identifies protein changes present in renal cell carcinoma. Proteomics. 2006;6(9):2853-64.
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19. Ahmad J, Downey KK, Akoad M, Cacciarelli TV. Impact of the MELD score on waiting time and disease severity in liver transplantation in United States veterans. Liver Transplantation. 2007;13(11):1564-9.
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21. Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, et al. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics. 2009;25(8):1091-3.
22. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome research. 2003;13(11):2498-504.
23. Malekzadeh R, Mohamadnejad M, Rakhshani N, Nasseri-Moghaddam S, Merat S, Tavangar SM, et al. Reversibility of cirrhosis in chronic hepatitis B. Clinical Gastroenterology and Hepatology. 2004;2(4):344-7.
24. Rossi E, Adams LA, Bulsara M, Jeffrey GP. Assessing liver fibrosis with serum marker models. Clinical Biochemist Reviews. 2007;28(1):3.
25. Xue R, Dong L, Wu H, Liu T, Wang J, Shen X. Gas chromatography/mass spectrometry screening of serum metabolomic biomarkers in hepatitis B virus infected cirrhosis patients. Clin Chem Lab Med. 2009;47(3):305-10.
26. Montaser-Kouhsari L. Plasma myeloperoxidase activity and apolipoprotein A-1 expression in chronic hepatitis B patients. Archives of Iranian medicine. 2011;14(4):254.
27. Körmöczi G, Säemann M, Buchta C, Peck‐Radosavljevic M, Mayr W, Schwartz D, et al. Influence of clinical factors on the haemolysis marker haptoglobin. European journal of clinical investigation. 2006;36(3):202-9.
28. Cooksley W, Powell L, Halliday J. Reticuloendothelial phagocytic function in human liver disease and its relationship to haemolysis. British journal of haematology. 1973;25(2):147-64.
29. Hiramatsu S, Kojima J, Okada T, Inai S, Ohmori K. The serum protein profile in chronic hepatitis, cirrhosis and liver cancer. Acta hepato-gastroenterologica. 1976;23(3):177-82.
30. Mondal G, Saroha A, Bose PP, Chatterjee B. Altered glycosylation, expression of serum haptoglobin and alpha-1-antitrypsin in chronic hepatitis C, hepatitis C induced liver cirrhosis and hepatocellular carcinoma patients. Glycoconjugate journal. 2016;33(2):209-18.
31. Gangadharan B, Bapat M, Rossa J, Antrobus R, Chittenden D, Kampa B, et al. Discovery of novel biomarker candidates for liver fibrosis in hepatitis C patients: a preliminary study. PLoS One. 2012;7(6):e39603.
32. Rossi E, Adams L, Prins A, Bulsara M, de Boer B, Garas G, et al. Validation of the FibroTest biochemical markers score in assessing liver fibrosis in hepatitis C patients. Clinical chemistry. 2003;49(3):450-4.
33. Zhang Z, Bast RC, Yu Y, Li J, Sokoll LJ, Rai AJ, et al. Three biomarkers identified from serum proteomic analysis for the detection of early stage ovarian cancer. Cancer research. 2004;64(16):5882-90.
34. Chrostek L, Supronowicz L, Panasiuk A, Cylwik B, Gruszewska E, Flisiak R. The effect of the severity of liver cirrhosis on the level of lipids and lipoproteins. Clinical and experimental medicine. 2014;14(4):417-21.
35. Pollo-Flores P, Cásseres D, Zampier L, Adnet G, Shiroma M, Padua L, et al. Lipid Metabolism and Interleukin 28B Polymorphism in Hepatitis C. Journal of Infectious Diseases and Treatment. 2016.
36. Ellison III RT, Horsburgh Jr CR, Curd J. Complement levels in patients with hepatic dysfunction. Digestive diseases and sciences. 1990;35(2):231-5.
37. Homann C, Varming K, Høgåsen K, Mollnes T, Graudal N, Thomsen AC, et al. Acquired C3 deficiency in patients with alcoholic cirrhosis predisposes to infection and increased mortality. Gut. 1997;40(4):544-9.
38. Baumann M, Witzke O, Canbay A, Patschan S, Treichel U, Gerken G, et al. Serum C3 complement concentrations correlate with liver function in patients with liver cirrhosis. Hepato-gastroenterology. 2003;51(59):1451-3.
39. Mas VR, Fassnacht R, Archer KJ, Maluf D. Molecular mechanisms involved in the interaction effects of alcohol and hepatitis C virus in liver cirrhosis. Mol Med. 2010;16(7-8):287-97.
40. Dillon ST, Bhasin MK, Feng X, Koh DW, Daoud SS. Quantitative proteomic analysis in HCV-induced HCC reveals sets of proteins with potential significance for racial disparity. Journal of translational medicine. 2013;11(1):1.
41. Bernardi M, Maggioli C, Zaccherini G. Human albumin in the management of complications of liver cirrhosis. Critical Care. 2012;16(2):1.
42. Hueging K, Weller R, Doepke M, Vieyres G, Todt D, Wölk B, et al. Several human liver cell expressed apolipoproteins complement HCV virus production with varying efficacy conferring differential specific infectivity to released viruses. PLoS One. 2015;10(7):e0134529.
43. White IR, Patel K, Symonds WT, Dev A, Griffin P, Tsokanas N, et al. Serum proteomic analysis focused on fibrosis in patients with hepatitis C virus infection. Journal of translational medicine. 2007;5(1):1.
44. Hu J, Gao DZ. Distinction immune genes of hepatitis-induced heptatocellular carcinoma. Bioinformatics. 2012;28(24):3191-4.
45. Safaei A, Tavirani MR, Oskouei AA, Azodi MZ, Mohebbi SR, Nikzamir AR. Protein-protein interaction network analysis of cirrhosis liver disease. Gastroenterology and Hepatology from bed to bench. 2016;9(2):114.
46. Gray J, Chattopadhyay D, Beale GS, Patman GL, Miele L, King BP, et al. A proteomic strategy to identify novel serum biomarkers for liver cirrhosis and hepatocellular cancer in individuals with fatty liver disease. BMC cancer. 2009;9(1):1.
47. Martínez-Esparza M, Tristán-Manzano M, Ruiz-Alcaraz AJ, García-Peñarrubia P. Inflammatory status in human hepatic cirrhosis. World journal of gastroenterology. 2015;21(41):11522.
48. Lindgren S, Laurell AB, Eriksson S. Complement components and activation in primary biliary cirrhosis. Hepatology. 1984;4(1):9-14.
49. Tietge U, Boker K, Bahr M, Weinberg S, Pichlmayr R, Schmidt H, et al. Lipid parameters predicting liver function in patients with cirrhosis and after liver transplantation. Hepato-gastroenterology. 1997;45(24):2255-60.
2. Friedman SL. Hepatic stellate cells: protean, multifunctional, and enigmatic cells of the liver. Physiol Rev. 2008;88(1):125-72.
3. Schuppan D, Afdhal NH. Liver cirrhosis. The Lancet. 2008;371(9615):838-51.
4. Hussain SM, Semelka RC, Mitchell DG. MR imaging of hepatocellular carcinoma. Magnetic resonance imaging clinics of North America. 2002;10(1):31-52.
5. Majumdar A, Kitson MT, Roberts SK. Treatment of Hepatitis C in Patients with Cirrhosis: Remaining Challenges for Direct-Acting Antiviral Therapy. Drugs. 2015;75(8):823-34.
6. Mukerji AN, Patel V, Jain A. Improving survival in decompensated cirrhosis. International journal of hepatology. 2012;2012.
7. Fukumitsu K, Yagi H, Soto-Gutierrez A, editors. Bioengineering in organ transplantation: targeting the liver. Transplantation proceedings; 2011: Elsevier.
8. Runyon BA, editor Historical aspects of treatment of patients with cirrhosis and ascites. Seminars in liver disease; 1997: © 1997 by Thieme Medical Publishers, Inc.
9. Chandramouli K, Qian P-Y. Proteomics: challenges, techniques and possibilities to overcome biological sample complexity. Human genomics and proteomics. 2009;1(1).
10. Kalantari S, Rutishauser D, Samavat S, Nafar M, Mahmudieh L, Rezaei-Tavirani M, et al. Urinary prognostic biomarkers and classification of IgA nephropathy by high resolution mass spectrometry coupled with liquid chromatography. PLoS One. 2013;8(12):e80830.
11. Zali H, Ahmadi G, Bakhshandeh R, Rezaei-Tavirani M. Proteomic analysis of gene expression during human esophagus cancer. Journal of Paramedical Sciences. 2011;2(3).
12. Rezaie-Tavirani M, Fayazfar S, Heydari-Keshel S, Rezaee MB, Zamanian-Azodi M, Rezaei-Tavirani M, et al. Effect of essential oil of Rosa Damascena on human colon cancer cell line SW742. Gastroenterology and Hepatology from bed to bench. 2013;6(1).
13. Zamanian-Azodi M, Rezaie-Tavirani M, Heydari-Kashal S, Kalantari S, Dailian S, Zali H. Proteomics analysis of MKN45 cell line before and after treatment with Lavender aqueous extract. Gastroenterology and Hepatology from bed to bench. 2011;5(1).
14. Rezaei-Tavirani M, Rahmati-Rad S, Rezaei-Tavirani M. Ethanol and Cancer Induce Similar Changes on Protein Expression Pattern of Human Fibroblast Cell. Iranian Journal of Pharmaceutical Research. 2016;15:175-84.
15. Hasanzadeh H, Rezaie-Tavirani M, Seyyedi S, Emadi A. Proteomics Study of extremely low frequency electromagnetic field (50 Hz) on human neuroblastoma cells. Koomesh. 2015;17(1):233-8.
16. Craven RA, Stanley AJ, Hanrahan S, Dods J, Unwin R, Totty N, et al. Proteomic analysis of primary cell lines identifies protein changes present in renal cell carcinoma. Proteomics. 2006;6(9):2853-64.
17. Uto H, Kanmura S, Takami Y, Tsubouchi H. Clinical proteomics for liver disease: a promising approach for discovery of novel biomarkers. Proteome science. 2010;8(1):1.
18. Corbin I, Ryner L, Singh H, Minuk G. Quantitative hepatic phosphorus-31 magnetic resonance spectroscopy in compensated and decompensated cirrhosis. American Journal of Physiology-Gastrointestinal and Liver Physiology. 2004;287(2):G379-G84.
19. Ahmad J, Downey KK, Akoad M, Cacciarelli TV. Impact of the MELD score on waiting time and disease severity in liver transplantation in United States veterans. Liver Transplantation. 2007;13(11):1564-9.
20. Yu H, Kim PM, Sprecher E, Trifonov V, Gerstein M. The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol. 2007;3(4):e59.
21. Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, et al. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics. 2009;25(8):1091-3.
22. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome research. 2003;13(11):2498-504.
23. Malekzadeh R, Mohamadnejad M, Rakhshani N, Nasseri-Moghaddam S, Merat S, Tavangar SM, et al. Reversibility of cirrhosis in chronic hepatitis B. Clinical Gastroenterology and Hepatology. 2004;2(4):344-7.
24. Rossi E, Adams LA, Bulsara M, Jeffrey GP. Assessing liver fibrosis with serum marker models. Clinical Biochemist Reviews. 2007;28(1):3.
25. Xue R, Dong L, Wu H, Liu T, Wang J, Shen X. Gas chromatography/mass spectrometry screening of serum metabolomic biomarkers in hepatitis B virus infected cirrhosis patients. Clin Chem Lab Med. 2009;47(3):305-10.
26. Montaser-Kouhsari L. Plasma myeloperoxidase activity and apolipoprotein A-1 expression in chronic hepatitis B patients. Archives of Iranian medicine. 2011;14(4):254.
27. Körmöczi G, Säemann M, Buchta C, Peck‐Radosavljevic M, Mayr W, Schwartz D, et al. Influence of clinical factors on the haemolysis marker haptoglobin. European journal of clinical investigation. 2006;36(3):202-9.
28. Cooksley W, Powell L, Halliday J. Reticuloendothelial phagocytic function in human liver disease and its relationship to haemolysis. British journal of haematology. 1973;25(2):147-64.
29. Hiramatsu S, Kojima J, Okada T, Inai S, Ohmori K. The serum protein profile in chronic hepatitis, cirrhosis and liver cancer. Acta hepato-gastroenterologica. 1976;23(3):177-82.
30. Mondal G, Saroha A, Bose PP, Chatterjee B. Altered glycosylation, expression of serum haptoglobin and alpha-1-antitrypsin in chronic hepatitis C, hepatitis C induced liver cirrhosis and hepatocellular carcinoma patients. Glycoconjugate journal. 2016;33(2):209-18.
31. Gangadharan B, Bapat M, Rossa J, Antrobus R, Chittenden D, Kampa B, et al. Discovery of novel biomarker candidates for liver fibrosis in hepatitis C patients: a preliminary study. PLoS One. 2012;7(6):e39603.
32. Rossi E, Adams L, Prins A, Bulsara M, de Boer B, Garas G, et al. Validation of the FibroTest biochemical markers score in assessing liver fibrosis in hepatitis C patients. Clinical chemistry. 2003;49(3):450-4.
33. Zhang Z, Bast RC, Yu Y, Li J, Sokoll LJ, Rai AJ, et al. Three biomarkers identified from serum proteomic analysis for the detection of early stage ovarian cancer. Cancer research. 2004;64(16):5882-90.
34. Chrostek L, Supronowicz L, Panasiuk A, Cylwik B, Gruszewska E, Flisiak R. The effect of the severity of liver cirrhosis on the level of lipids and lipoproteins. Clinical and experimental medicine. 2014;14(4):417-21.
35. Pollo-Flores P, Cásseres D, Zampier L, Adnet G, Shiroma M, Padua L, et al. Lipid Metabolism and Interleukin 28B Polymorphism in Hepatitis C. Journal of Infectious Diseases and Treatment. 2016.
36. Ellison III RT, Horsburgh Jr CR, Curd J. Complement levels in patients with hepatic dysfunction. Digestive diseases and sciences. 1990;35(2):231-5.
37. Homann C, Varming K, Høgåsen K, Mollnes T, Graudal N, Thomsen AC, et al. Acquired C3 deficiency in patients with alcoholic cirrhosis predisposes to infection and increased mortality. Gut. 1997;40(4):544-9.
38. Baumann M, Witzke O, Canbay A, Patschan S, Treichel U, Gerken G, et al. Serum C3 complement concentrations correlate with liver function in patients with liver cirrhosis. Hepato-gastroenterology. 2003;51(59):1451-3.
39. Mas VR, Fassnacht R, Archer KJ, Maluf D. Molecular mechanisms involved in the interaction effects of alcohol and hepatitis C virus in liver cirrhosis. Mol Med. 2010;16(7-8):287-97.
40. Dillon ST, Bhasin MK, Feng X, Koh DW, Daoud SS. Quantitative proteomic analysis in HCV-induced HCC reveals sets of proteins with potential significance for racial disparity. Journal of translational medicine. 2013;11(1):1.
41. Bernardi M, Maggioli C, Zaccherini G. Human albumin in the management of complications of liver cirrhosis. Critical Care. 2012;16(2):1.
42. Hueging K, Weller R, Doepke M, Vieyres G, Todt D, Wölk B, et al. Several human liver cell expressed apolipoproteins complement HCV virus production with varying efficacy conferring differential specific infectivity to released viruses. PLoS One. 2015;10(7):e0134529.
43. White IR, Patel K, Symonds WT, Dev A, Griffin P, Tsokanas N, et al. Serum proteomic analysis focused on fibrosis in patients with hepatitis C virus infection. Journal of translational medicine. 2007;5(1):1.
44. Hu J, Gao DZ. Distinction immune genes of hepatitis-induced heptatocellular carcinoma. Bioinformatics. 2012;28(24):3191-4.
45. Safaei A, Tavirani MR, Oskouei AA, Azodi MZ, Mohebbi SR, Nikzamir AR. Protein-protein interaction network analysis of cirrhosis liver disease. Gastroenterology and Hepatology from bed to bench. 2016;9(2):114.
46. Gray J, Chattopadhyay D, Beale GS, Patman GL, Miele L, King BP, et al. A proteomic strategy to identify novel serum biomarkers for liver cirrhosis and hepatocellular cancer in individuals with fatty liver disease. BMC cancer. 2009;9(1):1.
47. Martínez-Esparza M, Tristán-Manzano M, Ruiz-Alcaraz AJ, García-Peñarrubia P. Inflammatory status in human hepatic cirrhosis. World journal of gastroenterology. 2015;21(41):11522.
48. Lindgren S, Laurell AB, Eriksson S. Complement components and activation in primary biliary cirrhosis. Hepatology. 1984;4(1):9-14.
49. Tietge U, Boker K, Bahr M, Weinberg S, Pichlmayr R, Schmidt H, et al. Lipid parameters predicting liver function in patients with cirrhosis and after liver transplantation. Hepato-gastroenterology. 1997;45(24):2255-60.
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