Predicting hepatitis B virus–positive metastatic hepatocellular carcinomas using gene expression profiling and supervised machine learning

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Abstract

Hepatocellular carcinoma (HCC) is one of the most common and aggressive human malignancies. Its high mortality rate is mainly a result of intra-hepatic metastases. We analyzed the expression profiles of HCC samples without or with intra-hepatic metastases. Using a supervised machine-learning algorithm, we generated for the first time a molecular signature that can classify metastatic HCC patients and identified genes that were relevant to metastasis and patient survival. We found that the gene expression signature of primary HCCs with accompanying metastasis was very similar to that of their corresponding metastases, implying that genes favoring metastasis progression were initiated in the primary tumors. Osteopontin, which was identified as a lead gene in the signature, was over-expressed in metastatic HCC; an osteopontin-specific antibody effectively blocked HCC cell invasion in vitro and inhibited pulmonary metastasis of HCC cells in nude mice. Thus, osteopontin acts as both a diagnostic marker and a potential therapeutic target for metastatic HCC.

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Figure 1: Classification of hepatocellular carcinoma, with or without metastasis, by gene expression.
Figure 2: Prediction of metastasis and survival with metastasis predictor model derived from leave-one-out cross-validated CCP classification.
Figure 3: Candidate genes associated with metastatic HCC.
Figure 4: Immunohistochemical analysis of osteopontin in normal liver and hepatocellular carcinoma.
Figure 5: Role of osteopontin in promoting HCC metastasis.

References

  1. 1

    Parkin, D.M., Pisani, P. & Ferlay, J. Global cancer statistics. CA Cancer J. Clin. 49, 33–64 (1999).

  2. 2

    Pisani, P., Parkin, D.M., Bray, F. & Ferlay, J. Estimates of the worldwide mortality from 25 cancers in 1990. Int. J. Cancer 83, 18–29 (1999).

  3. 3

    El-Serag, H.B. & Mason, A.C. Rising incidence of hepatocellular carcinoma in the United States. N. Engl. J. Med. 340, 745–750 (1999).

  4. 4

    Taylor-Robinson, S.D., Foster, G.R., Arora, S., Hargreaves, S. & Thomas, H.C. Increase in primary liver cancer in the UK, 1979-94. Lancet 350, 1142–1143 (1997).

  5. 5

    Curley, S.A. et al. Identification and screening of 416 patients with chronic hepatitis at high risk to develop hepatocellular cancer. Ann. Surg. 222, 375–380 (1995).

  6. 6

    Larcos, G., Sorokopud, H., Berry, G. & Farrell, G.C. Sonographic screening for hepatocellular carcinoma in patients with chronic hepatitis or cirrhosis: an evaluation. AJR Am. J. Roentgenol. 171, 433–435 (1998).

  7. 7

    Yang, B. et al. Prospective study of early detection for primary liver cancer. J. Cancer Res. Clin. Oncol. 123, 357–360 (1997).

  8. 8

    Izzo, F. et al. Outcome of 67 patients with hepatocellular cancer detected during screening of 1125 patients with chronic hepatitis. Ann. Surg. 227, 513–518 (1998).

  9. 9

    Bolondi, L. et al. Surveillance programme of cirrhotic patients for early diagnosis and treatment of hepatocellular carcinoma: a cost effectiveness analysis. Gut 48, 251–259 (2001).

  10. 10

    Tang, Z.Y. Hepatocellular carcinoma-cause, treatment and metastasis. World J. Gastroenterol. 7, 445–454 (2001).

  11. 11

    Zhou, X.D. et al. Experience of 1000 patients who underwent hepatectomy for small hepatocellular carcinoma. Cancer 91, 1479–1486 (2001).

  12. 12

    Yuki, K., Hirohashi, S., Sakamoto, M., Kanai, T. & Shimosato, Y. Growth and spread of hepatocellular carcinoma. A review of 240 consecutive autopsy cases. Cancer 66, 2174–2179 (1990).

  13. 13

    Genda, T. et al. Cell motility mediated by rho and rho-associated protein kinase plays a critical role in intrahepatic metastasis of human hepatocellular carcinoma. Hepatology 30, 1027–1036 (1999).

  14. 14

    Mitsunobu, M., Toyosaka, A., Oriyama, T., Okamoto, E. & Nakao, N. Intrahepatic metastases in hepatocellular carcinoma: the role of the portal vein as an efferent vessel. Clin. Exp. Metastasis 14, 520–529 (1996).

  15. 15

    Lindsay, C.K., Sinha, C.C. & Thorgeirsson, U.P. Morphological study of vascular dissemination in a metastatic hepatocellular carcinoma model in the monkey. Hepatology 26, 1209–1215 (1997).

  16. 16

    Kuriyama, S. et al. Analysis of intrahepatic invasion of hepatocellular carcinoma using fluorescent dye-labeled cells in mice. Anticancer Res. 18, 4181–4188 (1998).

  17. 17

    Osada, T. et al. E-cadherin is involved in the intrahepatic metastasis of hepatocellular carcinoma. Hepatology 24, 1460–1467 (1996).

  18. 18

    Guo, X.Z. et al. KAI1, a new metastasis suppressor gene, is reduced in metastatic hepatocellular carcinoma. Hepatology 28, 1481–1488 (1998).

  19. 19

    Hui, A.M., Li, X., Makuuchi, M., Takayama, T. & Kubota, K. Over-expression and lack of retinoblastoma protein are associated with tumor progression and metastasis in hepatocellular carcinoma. Int. J. Cancer 84, 604–608 (1999).

  20. 20

    Schena, M., Shalon, D., Davis, R.W. & Brown, P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467–470 (1995).

  21. 21

    Bittner, M. et al. Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature 406, 536–540 (2000).

  22. 22

    Alizadeh, A.A. et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403, 503–511 (2000).

  23. 23

    Perou, C.M. et al. Molecular portraits of human breast tumours. Nature 406, 747–752 (2000).

  24. 24

    Pomeroy, S.L. et al. Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature 415, 436–442 (2002).

  25. 25

    Shipp, M.A. et al. Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning. Nat. Med. 8, 68–74 (2002).

  26. 26

    Khan, J. et al. Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Nat. Med. 7, 673–679 (2001).

  27. 27

    Okabe, H. et al. Genome-wide analysis of gene expression in human hepatocellular carcinomas using cDNA microarray: identification of genes involved in viral carcinogenesis and tumor progression. Cancer Res. 61, 2129–2137 (2001).

  28. 28

    Xu, X.R. et al. Insight into hepatocellular carcinogenesis at transcriptome level by comparing gene expression profiles of hepatocellular carcinoma with those of corresponding noncancerous liver. Proc. Natl. Acad. Sci. USA 98, 15089–15094 (2001).

  29. 29

    Radmacher, M.D., McShane, L.M. & Simon, R. A paradigm for class prediction using gene expression profiles. J. Comput. Biol. 9, 505–511 (2002).

  30. 30

    Singhal, H. et al. Elevated plasma osteopontin in metastatic breast cancer associated with increased tumor burden and decreased survival. Clin. Cancer Res. 3, 605–611 (1997).

  31. 31

    Fedarko, N.S., Jain, A., Karadag, A., Van Eman, M.R. & Fisher, L.W. Elevated serum bone sialoprotein and osteopontin in colon, breast, prostate, and lung cancer. Clin. Cancer Res. 7, 4060–4066 (2001).

  32. 32

    Li, Y. et al. Establishment of a hepatocellular carcinoma cell line with unique metastatic characteristics through in vivo selection and screening for metastasis-related genes through cDNA microarray. J. Cancer Res. Clin. Oncol. (doi 10.1007/s00432-002-0396-4).

  33. 33

    Qin, L.X. et al. The association of chromosome 8p deletion and tumor metastasis in human hepatocellular carcinoma. Cancer Res. 59, 5662–5665 (1999).

  34. 34

    Hanahan, D. & Weinberg, R.A. The hallmarks of cancer. Cell 100, 57–70 (2000).

  35. 35

    Sharp, J.A., Sung, V., Slavin, J., Thompson, E.W. & Henderson, M.A. Tumor cells are the source of osteopontin and bone sialoprotein expression in human breast cancer. Lab. Invest. 79, 869–877 (1999).

  36. 36

    Urquidi, V. et al. Contrasting expression of thrombospondin-1 and osteopontin correlates with absence or presence of metastatic phenotype in an isogenic model of spontaneous human breast cancer metastasis. Clin. Cancer Res. 8, 61–74 (2002).

  37. 37

    Chen, H., Ke, Y., Oates, A.J., Barraclough, R. & Rudland, P.S. Isolation of and effector for metastasis-inducing DNAs from a human metastatic carcinoma cell line. Oncogene 14, 1581–1588 (1997).

  38. 38

    Oates, A.J., Barraclough, R. & Rudland, P.S. The identification of osteopontin as a metastasis-related gene product in a rodent mammary tumour model. Oncogene 13, 97–104 (1996).

  39. 39

    Denhardt, D.T., Giachelli, C.M. & Rittling, S.R. Role of osteopontin in cellular signaling and toxicant injury. Annu. Rev. Pharmacol. Toxicol. 41, 723–749 (2001).

  40. 40

    Weber, G.F. The metastasis gene osteopontin: a candidate target for cancer therapy. Biochim. Biophys. Acta 1552, 61–85 (2001).

  41. 41

    Medico, E. et al. Osteopontin is an autocrine mediator of hepatocyte growth factor-induced invasive growth. Cancer Res. 61, 5861–5868 (2001).

  42. 42

    Edmondson, H.A. & Steiner, P.E. Primary carcinoma of the liver. A study of 100 cases among 48900 necropsies. Cancer 7, 462–503 (1954).

  43. 43

    Wu, C.G. et al. Distinctive gene expression profiles associated with hepatitis B virus x protein. Oncogene 20, 3674–3682 (2001).

  44. 44

    Eisen, M.B., Spellman, P.T., Brown, P.O. & Botstein, D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95, 14863–14868 (1998).

  45. 45

    Brazma, A. et al. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat. Genet. 29, 365–371 (2001).

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Acknowledgements

We thank C.C. Harris and L. Varticovski for comments; D. Dudek and K. MacPherson for editorial assistance; D. Petersen, J. Powell and members of the National Cancer Institute microarray team at the Advanced Technology Center for technical support; C. Drachenberg for pathological diagnosis; and J. Fan and X.D. Zhou for help in preparing human tissues. This work was supported in part by the Intramural Research Program of the US National Cancer Institute. Q.H.Y., L.X.Q., Z.C.M., Z.Q.W., S.L.Y., Y.K.L. and Z.Y.T. were supported by research grants from the State Key Basic Research Program of China (No. G1998051210) and from the key project of the Ministry of Education of China.

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Correspondence to Xin Wei Wang.

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