JBiSE  Vol.2 No.3 , June 2009
Descriptively probabilistic relationship between mutated primary structure of von Hippel-Lindau protein and its clinical outcome
Author(s) Shao-Min Yan, Guang Wu*
ABSTRACT
In this study, we use the cross-impact analysis to build a descriptively probabilistic relationship between mutant von Hippel-Lindau protein and its clinical outcome after quantifying mutant von Hippel-Lindau proteins with the amino-acid distribution probability, then we use the Bayes-ian equation to determine the probability that the von Hippel-Lindau disease occurs under a mutation, and finally we attempt to distinguish the classifications of clinical outcomes as well as the endocrine and nonendocrine neoplasia induced by mutations of von Hippel-Lindau protein. The results show that a patient has 9/10 chance of being von Hippel-Lindau disease when a new mutation occurs in von Hippel- Lindau protein, the possible distinguishing of classifications of clinical outcomes using mod-eling, and the explanation of the endocrine and nonendocrine neoplasia in modeling view.

Cite this paper
nullYan, S. and Wu, G. (2009) Descriptively probabilistic relationship between mutated primary structure of von Hippel-Lindau protein and its clinical outcome. Journal of Biomedical Science and Engineering, 2, 190-199. doi: 10.4236/jbise.2009.23032.
References
[1]   K. C. Chou, (2004) Structure bioinformatics and its impact to biomedical science, Curr. Med. Chem, 11, 2105-2134.

[2]   G. Wu and S. Yan, (2002) Randomness in the primary structure of protein: Methods and implications, Mol. Biol. Today, 3, 55-69.

[3]   G. Wu and S. Yan, (2006) Mutation trend of hemagglutinin of influenza A virus: A review from computational mutation viewpoint, Acta Pharmacol. Sin., 27, 513-526.

[4]   G. Wu and S. Yan, (2008) Lecture notes on computational mutation, Nova Science Publishers, New York, 2008.

[5]   Von Hippel, (1911) Die anatomische Grund lage der von mir beschriebenen ‘sehr seltenen Erkrankung der Netzhaut’, Graefes. Arch. Ophthalmol., 79, 350-377.

[6]   A. Lindau, (1926) Studien uber kleinhirncysten, bau, pathogenese und bezoejimgem zur angiomatosis retinae, Acta Pathol. Microbiol. Scand., Suppl 1, 1-128.

[7]   K. L. Melmon and S. W. Rosen, (1964) Lindau’s disease, Am. J. Med., 36, 595-617.

[8]   V. V. Michels, (1988) Investigative studies in von Hippel-Lindau disease, Neurofibromatosis, 1, 159-163.

[9]   H. P. Neumann, (1987) Basic criteria for clinical diagnosis and genetic counselling in von Hippel-Lindau syndrome, Vasa, 16, 220-226.

[10]   R. R. Lonser, G. M. Glenn, M. Walther, E. Y. Chew, S. K. Libutti, W. M. Linehan, and E. H. Oldfield, (2003) von Hippel-Lindau disease, Lancet, 361, 2059-2067.

[11]   E. R. Maher, A. R. Webster, F. M. Richards, J. S. Green, P. A. Crossey, S. J. Payne, and A. T. Moore, (1996) Phenotypic expression in von Hippel-Lindau disease: Correlations with germline VHL gene mutations, J. Med. Genet., 33, 328-332.

[12]   F. M. Richards, S. J. Payne, B. Zbar, N. A. Affara, M. A. Ferguson-Smith, and E. R. Maher, (1995) Molecular analysis of de novo germline mutations in the von Hippel-Lindau disease gene, Hum. Mol. Genet., 4, 2139-2143.

[13]   F. Latif, K. Tory, J. Gnarra, M. Yao, F. M. Duh, M. L. Orcutt, et al., (1993) Identification of the von Hippel-Lindau disease tumor suppressor gene, Science, 260, 1317-1320.

[14]   P. O. Schnell, M. L. Ignacak, A. L. Bauer, J. B. Striet, W. R. Paulding, and M. F. Czyzyk-Krzeska, (2003) Regulation of tyrosine hydroxylase promoter activity by the von Hippel-Lindau tumor suppressor protein and hypoxia-inducible transcription factors, J. Neurochem., 85, 483-491.

[15]   W. G. Jr. Kaelin, (2002) Molecular basis of the VHL hereditary cancer syndrome, Nat. Rev. Cancer, 2, 673-682.

[16]   W. G. Jr. Kaelin, (2003) The von Hippel-Lindau gene, kidney cancer, and oxygen sensing, J. Am. Soc. Nephrol., 14, 2703 -2711.

[17]   T. Shuin, I. Yamasaki, K. Tamura, H. Okuda, M. Furihata, and S. Ashida, (2006) Von Hippel-Lindau disease: Molecular pathological basis, clinical criteria, genetic testing, clinical features of tumors and treatment, Jpn. J. Clin. Oncol., 36, 337-343.

[18]   M. Ohh, (2006) Ubiquitin pathway in VHL cancer syndrome, Neoplasia, 8, 623-629.

[19]   F. Chen, T. Kishida, M. Yao, T. Hustad, D. Glavac, M. Dean, J. R. Gnarra, M. L. Orcutt, F. M. Duh, G. Glenn, J. Green, Y. E. Hsia, J. Lamiell, H. Li, M. H. Wei, L. Schmidt, K. Tory, I. Kuzmin, T. Stackhouse, F. Latif, W. M. Linehan, M. Lerman, and B. Zbar, (1995) Germline mutations in the von Hippel-Lindau disease tumor suppressor gene: Correlations with phenotype, Hum. Mutat., 5, 66-75.

[20]   S. Lee, E. Nakamura, H. Yang, W. Wei, M. S. Linggi, M. P. Sajan, R. V. Farese, R. S. Freeman, B. D. Carter, W. G. Jr. Kaelin, and S. Schlisio, (2005) Neuronal apoptosis linked to EglN3 prolyl hydroxylase and familial phaeochromocytoma genes: developmental culling and cancer. Cancer Cell, 8, 1-13.

[21]   Clinical Research Group for VHL in Japan, (1995) Germline mutations in the von Hippel-Lindau disease (VHL) gene in Japanese VHL, Hum. Mol. Genet., 4, 2233-2237.

[22]   H. P. Neumann, B. Bender, I. Zauner, D. P. Berger, C. Eng, H. Brauch, and B. Zbar, (1996) Monogenetic hypertension and pheochromocytoma, Am. J. Kidney Dis., 28, 329-333.

[23]   S. Olschwang, S. Richard, C. Boisson, S. Giraud, P. Laurent- Puig, F. Resche, and G. Thomas, (1998) Germline mutation profile of the VHL gene in von Hippel-Lindau disease and in sporadic hemangioblastoma, Hum. Mutat., 12, 424-430.

[24]   C. Stolle, G. Glenn, B. Zbar, J. S. Humphrey, P. Choyke, M. Walther, S. Pack, K. Hurley, C. Andrey, R. Klausner, and W. M. Linehan, (1998) Improved detection of germline mutations in the von Hippel-Lindau disease tumor suppressor gene, Hum. Mutat., 12, 417-423.

[25]   A. Bairoch and R. Apweiler, (2000) The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 2000, Nucleic Acids Res., 28, 45-48.

[26]   N. Gao, S. Yan, and G. Wu, (2006) Pattern of positions sensitive to mutations in human haemoglobin ?-chain, Protein Pept. Lett., 13, 101-107.

[27]   G. Wu and S. Yan, (2000) Prediction of distributions of amino acids and amino acid pairs in human haemoglobin ?-chain and its seven variants causing-thalassemia from their occurrences according to the random mechanism, Comp. Haematol. Int, 10, 80-84.

[28]   G. Wu and S. Yan, (2001) Analysis of distributions of amino acids, amino acid pairs and triplets in human insulin precursor and four variants from their occurrences according to the random mechanism, J. Biochem. Mol. Biol. Biophys., 5, 293-300.

[29]   G. Wu and S. Yan, (2001) Analysis of distributions of amino acids and amino acid pairs in human tumor necrosis factor precursor and its eight variants according to random mechanism, J. Mol. Model, 7, 318-323.

[30]   G. Wu and S. Yan, (2002) Random analysis of presence and absence of two-and three-amino-acid sequences and distributions of amino acids, two- and three-amino-acid sequences in bovine p53 protein, Mol. Biol. Today, 3, 31-37.

[31]   G. Wu and S. Yan, (2002) Analysis of distributions of amino acids in the primary structure of apoptosis regulator Bcl-2 family according to the random mechanism, J. Biochem. Mol. Biol. Biophys, 6, 407-414.

[32]   G. Wu and S. Yan, (2002) Analysis of distributions of amino acids in the primary structure of tumor suppressor p53 family according to the random mechanism, J. Mol. Model, 8, 191-198.

[33]   G. Wu and S. Yan, (2004) Determination of sensitive positions to mutations in human p53 protein, Biochem. Biophys. Res. Commun., 321, 313-319.

[34]   G. Wu and S. Yan, (2005) Searching of main cause leading to severe influenza A virus mutations and consequently to influenza pandemics/epidemics, Am. J. Infect. Dis., 1, 116-123.

[35]   G. Wu and S. Yan, (2005) Prediction of mutation trend in hemagglutinins and neuraminidases from influenza A viruses by means of cross-impact analysis, Biochem. Biophys. Res. Commun., 326, 475-482.

[36]   G. Wu and S. Yan, (2006) Timing of mutation in hemagglutinins from influenza A virus by means of amino-acid distribution rank and fast Fourier transform, Protein Pept. Lett., 13, 143-148.

[37]   G. Wu and S. Yan, (2006) Prediction of possible mutations in H5N1 hemagglutinins of influenza A virus by means of logistic regression, Comp. Clin. Pathol., 15, 255-261.

[38]   G. Wu and S. Yan, (2006) Prediction of mutations in H5N1 hemagglutinins from influenza A virus, Protein Pept. Lett., 13, 971-976.

[39]   G. Wu and S. Yan, (2007) Improvement of model for prediction of hemagglutinin mutations in H5N1 influenza viruses with distinguishing of arginine, leucine and serine, Protein Pept. Lett., 14, 191-196.

[40]   G. Wu and S. Yan, (2007) Improvement of prediction of mutation positions in H5N1 hemagglutinins of influenza A virus using neural network with distinguishing of arginine, leucine and serine, Protein Pept. Lett., 14, 465-470.

[41]   G. Wu and S. Yan, (2007) Prediction of mutations engineered by randomness in H5N1 neuraminidases from influenza A virus, Amino Acids, 34, 81-90.

[42]   G. Wu and S. Yan, (2007) Prediction of mutations in H1 neuraminidases from North America influenza A virus engineered by internal randomness, Mol. Divers., 11, 131-140.

[43]   G. Wu and S. Yan, (2008) Prediction of mutations initiated by internal power in H3N2 hemagglutinins of influenza A virus from North America, Int. J. Pept. Res. Ther., 14, 41-51.

[44]   G. Wu and S. Yan, (2008) Prediction of mutation in H3N2 hemagglutinins of influenza A virus from North America based on different datasets, Protein Pept. Lett., 15, 144-152.

[45]   W. Feller, (1968) An introduction to probability theory and its applications, 3rd ed, Wiley, New York, 1, 34-40.

[46]   B. Zbar, T. Kishida, F. Chen, L. Schmidt, E. R. Maher, F. M. Richards, P. A. Crossey, A. R. Webster, N. A. Affara, M. A. Ferguson-Smith, et al., (1996) Germline mutations in the Von Hippel-Lindau disease (VHL) gene in families from North America, Europe, and Japan, Hum. Mutat., 8, 348-357.

[47]   T. G. Gordon and H. Hayward, (1968) Initial experiments with the cross-impact matrix method of forecasting, Futures, 1, 100-116.

[48]   T. G. Gordon, (1969) Cross-impact matrices - an illustration of their use for policy analysis, Futures, 2, 527-531.

[49]   S. Enzer, (1970) Delphi and cross-impact techniques: an effective combination for systematic futures analysis, Futures, 3, 48-61.

[50]   S. Enzer, (1970) Cross-impact techniques in technology assessment, Futures, 4, 30-51.

[51]   A. P. Sage, (1977) Methodology for large-scale systems, McGraw-Hill, New York, 165-203.

[52]   G. Wu, (2000) Application of cross-impact analysis to the relationship between aldehyde dehydrogenase 2 and flushing, Alcohol Alcohol., 35, 55-59.

[53]   G. Wu and S. Yan, (2008) Building quantitative relationship between changed sequence and changed oxygen affinity in human hemoglobin-chain, Protein Pept. Lett., 15, 341-345.

[54]   Wikipedia, (2008) Bayes’ theorem, http://en.wikipedia.org/wiki/ Bayes’_theorem.

[55]   S. O. Ang, H. Chen, K. Hirota, V. R. Gordeuk, J. Jelinek, Y. Guan, E. Liu, A. I. Sergueeva, G. Y. Miasnikova, D. Mole, P. H. Maxwell, D. W. Stockton, G. L. Semenza, and J. T. Prchal., (2002) Disruption of oxygen homeostasis underlies congenital Chuvash polycythemia, Nature Genet., 32, 614-621.

[56]   Y. Pastore, K. Jedlickova, Y. Guan, E. Liu, J. Fahner, H. Hasle, J. F. Prchal, and J. T. Prchal., (2003) Mutations of von Hippel- Lindau tumor-suppressor gene and congenital polycythemia, Am. J. Hum. Genet., 73, 412-419.

[57]   E. R. Maher, (2004) Von Hippel-Lindau disease, Curr. Mol. Med., 4, 833-842.

[58]   E. R. Woodward and E. R. Maher, (2006) Von Hippel-Lindau disease and endocrine tumour susceptibility, End. Relat. Cancer, 13, 415-425.

[59]   M. T. Sgambati, C. Stolle, P. L. Choyke, M. M. Walther, B. Zbar, W. M. Linehan, and G. M. Glenn, (2000) Mosaicism in von Hippel-Lindau disease: lessons from kindreds with germline mutations identified in offspring with mosaic parents, Am. J. Hum. Genet., 66, 84-91.

[60]   A. R. Webster, F. M. Richards, F. E. MacRonald, A. T. Moore, and E. R. Maher, (1998) An analysis of phenotypic variation in the familial cancer syndrome von Hippel-Lindau disease: evidence for modifier effects, Am. J. Hum. Genet., 63, 1025-1035.

[61]   P. A. Crossey, C. Eng, M. Ginalska-Malinowska, T. W. J. Lennard, J. R. Sampson, B. A. J. Ponder, and E. R. Maher, (1995) Molecular genetic diagnosis of von Hippel-Lindau disease in familial phaeochromocytoma, J. Med. Genet., 32, 885-886.

[62]   P. A. Crossey, F. M. Richards, K. Foster, J. S. Green, A. Prowse, F. Latif, M. I. Lerman, B. Zbar, N. A. Affara, M. A. Ferguson-Smith, and R. Maher, (1994) Buys CHCM, identification of intragenic mutations in the von Hippel-Lindau disease tumour suppressor gene and correlation with disease phenotype, Hum. Mol. Genet., 3, 1303-1308.

[63]   E. R. Maher, A. R. Webster, F. M. Richards, J. S. Green, P. A. Crossey, S. J. Payne, and A. T. Moore, (2000) Phenotypic expression in von Hippel-Lindau disease: correlations with germline VHL gene mutations, J. Med. Genet., 37, 62-63.

[64]   C. E. Stebbins, W. G. Jr. Kaelin, and N. P. Pavletich, (1999) Structure of the VHL-ElonginC-ElonginB complex: Implications for VHL tumor suppressor function, Science, 284, 455-461.

[65]   S. J. Marx and W. F. Simonds, (2005) Hereditary hormone excess: Genes, molecular pathways, and syndromes, End. Rev., 26, 615-661.

[66]   G. Wu and S. Yan, (2005) Determination of mutation trend in proteins by means of translation probability between RNA codes and mutated amino acids, Biochem. Biophys. Res. Commun., 337, 692-700.

[67]   G. Wu and S. Yan, (2006) Determination of mutation trend in hemagglutinins by means of translation probability between RNA codons and mutated amino acids, Protein Pept. Lett., 13, 601-609.

[68]   G. Wu and S. Yan, (2007) Translation probability between RNA codons and translated amino acids, and its applications to protein mutations, in: Leading-Edge Messenger RNA Research Communications, ed. Ostrovskiy M. H. Nova Science Publishers, New York, Chapter 3, 47-65.

 
 
Top