Human genomic diversity, viral genomics and proteomics, as exemplified by human papillomaviruses and H5N1 influenza viruses
Tóm tắt
The diversity of hosts, pathogens and host-pathogen relationships reflects the influence of selective pressures that fuel diversity through ongoing interactions with other rapidly evolving molecules in the environment. This paper discusses specific examples illustrating the phenomenon of diversity of hosts and pathogens, with special reference to human papillomaviruses and H5NI influenza viruses. We also review the influence of diverse host-pathogen interactions that determine the pathophysiology of infections, and their responses to drugs or vaccines.
Tài liệu tham khảo
Goldstein DB, Cavalleri GL: Genomics: Understanding human diversity. Nature. 2005, 437: 1241-1242. 10.1038/4371241a.
A haplotype map of the human genome. Nature. 2005, International HapMap Consortium, 437: 1299-1320. 10.1038/nature04226.
Brookes AJ: The essence of SNPs. Gene. 1999, 234: 177-186. 10.1016/S0378-1119(99)00219-X.
Hoehe MR, Timmermann B, Lehrach H: Human inter-individual DNA sequence variation in candidate genes, drug targets, the importance of haplotypes and pharmacogenomics. Curr Pharm Biotechnol. 2003, 4: 351-378. 10.2174/1389201033377300.
Maitland ML, DiRienzo A, Ratain MJ: Interpreting disparate responses to cancer therapy: The role of human population genetics. J Clin Oncol. 2006, 24: 2151-2157. 10.1200/JCO.2005.05.2282.
Masood E: As consortium plans free SNP map of human genome. Nature. 1999, 398: 545-546.
Vitkup D, Sander C, Church GM: The amino-acid mutational spectrum of human genetic disease. Genome Biol. 2003, 4: R72-10.1186/gb-2003-4-11-r72.
Wang Z, Moult J: SNPs, protein structure, and disease. Hum Mutat. 2001, 17: 263-270. 10.1002/humu.22.
Zanotti G, Berni R: Plasma retinol-binding protein: structure and interactions with retinol, retinoids, and transthyretin. Vitam Horm. 2004, 69: 271-295.
Seelinger MW, Biesalski HK, Wissinger B, Gollnick H, et al: Phenotype in retinol deficiency due to a hereditary defect in the retinol binding protein synthesis. Invest Ophthalmol Vis Sci. 1999, 40: 3-11.
Yao-Borengasser A, Varma V, Bodles AM, Rasouli N, et al: Retinol binding protein 4 expression in humans: Relationship to insulin resistance, inflammation, and response to pioglitazone. J Clin Endocrinol Metab. 2007, 92: 2590-2597. 10.1210/jc.2006-0816.
Hash RB: Hereditary hemochromatosis. J Am Board Fam Pract. 2001, 14: 266-273.
Kim S, Misra A: SNP genotyping: Technologies and bio-medical applications. Annu Rev Biomed Eng. 2007, 9: 289-320. 10.1146/annurev.bioeng.9.060906.152037.
Delrieu O, Bowman C: Visualizing gene determinants of disease in drug discovery. Pharmacogenomics. 2006, 7: 311-329. 10.2217/14622416.7.3.311.
Giacomini KM, Brett CM, Altman RB, Benowitz NL, et al: The pharmacogenetics research network: From SNP discovery to clinical drug response. Clin Pharmacol Ther. 2007, 81: 328-345. 10.1038/sj.clpt.6100087.
McLeod HL, Evans WE: Pharmacogenomics: Unlocking the human genome for better drug therapy. Annu Rev Pharmacol Toxicol. 2001, 41: 101-121. 10.1146/annurev.pharmtox.41.1.101.
Evans WE, Johnson JA: Pharmacogenomics: The inherited basis for interindividual differences in drug response. Annu Rev Genomics Hum Genet. 2001, 2: 9-39. 10.1146/annurev.genom.2.1.9.
Shah RR: Mechanistic basis of adverse drug reactions: The perils of inappropriate dose schedules. Expert Opin Drug Saf. 2005, 4: 103-128. 10.1517/14740338.4.1.103.
Rane A: Postgenomic prospects of success in drug development and pharmacotherapy. Pharmacogenomics J. 2001, 1: 6-9. 10.1038/sj.tpj.6500013.
Bosch TM, Meijerman I, Beijnen JH, Schellens JH: Genetic polymorphisms of drug-metabolising enzymes and drug transporters in the chemotherapeutic treatment of cancer. Clin Pharmacokinet. 2006, 45: 253-285. 10.2165/00003088-200645030-00003.
Lai E: Application of SNP technologies in medicine: Lessons learned and future challenges. Genome Res. 2001, 11: 927-929. 10.1101/gr.192301.
Klein TE, Chang JT, Cho MK, Easton KL, et al: Integrating genotype and phenotype information: An overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base. Pharmacogenomics J. 2001, 1: 167-170. 10.1038/sj.tpj.6500035.
Ustav M, Stenlund A: Transient replication of BPV-1 requires two viral polypeptides encoded by the E1 and E2 open reading frames. EMBOJ. 1991, 10: 449-457.
Gloss B, Bernard HU, Seedorf K, Klock G: The upstream regulatory region of the human papilloma virus-16 contains an E2 protein-independent enhancer which is specific for cervical carcinoma cells and regulated by glucocorticoid hormones. EMBO J. 1987, 6: 3735-3743.
Wilson R, Fehrmann F, Laimins LA: Role of the E1-E4 protein in the differentiation-dependent life cycle of human papilloma-virus type 31. J Virol. 2005, 79: 6732-6740. 10.1128/JVI.79.11.6732-6740.2005.
Fehrmann F, Klumpp DJ, Laimins LA: Human papillo-mavirus type 31 E5 protein supports cell cycle progression and activates late viral functions upon epithelial differentiation. J Virol. 2003, 77: 2819-2831. 10.1128/JVI.77.5.2819-2831.2003.
Zhang B, Li P, Wang E, Brahmi Z, et al: The E5 protein of human papillomavirus type 16 perturbs MHC class II antigen maturation in human foreskin keratinocytes treated with interferon-gamma. Virology. 2003, 310: 100-108. 10.1016/S0042-6822(03)00103-X.
Snijders PJ, Steenbergen RD, Heideman DA, Meijer CJ: HPV-mediated cervical carcinogenesis: Concepts and clinical implications. J Pathol. 2006, 208: 152-164. 10.1002/path.1866.
Stanley M: Immunobiology of HPV and HPV vaccines. Gynecol Oncol. 2008, 109: S15-S21. 10.1016/j.ygyno.2008.02.003.
Chow VT, Leong PW: Complete nucleotide sequence, genomic organization and phylogenetic analysis of a novel genital human papillomavirus type, HLT7474-S. J Gen Virol. 1999, 80: 2923-2929.
de Villiers EM, Fauquet C, Broker TR, Bernard HU, et al: Classification of papillomaviruses. Virology. 2004, 324: 17-27. 10.1016/j.virol.2004.03.033.
Delius H, Saegling B, Bergmann K, Shamanin V, et al: The genomes of three of four novel HPV types, defined by differences of their L1 genes, show high conservation of the E7 gene and the URR. Virology. 1998, 240: 359-365. 10.1006/viro.1997.8943.
Forslund O, Hansson BG: Human papillomavirus type 70 genome cloned from overlapping PCR products: Complete nucleotide sequence and genomic organization. J Clin Microbiol. 1996, 34: 802-809.
Ho L, Chan SY, Chow V, Chong T, et al: Sequence variants of human papillomavirus type 16 in clinical samples permit verification and extension of epidemiological studies and construction of a phylogenetic tree. J Clin Microbiol. 1991, 29: 1765-1772.
Chan SY, Ho L, Ong CK, Chow V, et al: Molecular variants of human papillomavirus type 16 from four continents suggest ancient pandemic spread of the virus and its coevolution with humankind. J Virol. 1992, 66: 2057-2066.
Radivojac P, Iakoucheva LM, Oldfield CJ, Obradovic Z, et al: Intrinsic disorder and functional proteomics. Biophys J. 2007, 92: 1439-1456. 10.1529/biophysj.106.094045.
Shimizu K, Hirose S, Noguchi T: POODLE-S: Web application for predicting protein disorder by using physicochemical features and reduced amino acid set of a position-specific scoring matrix. Bioinformatics. 2007, 23: 2337-2338. 10.1093/bioinformatics/btm330.
Hirose S, Shimizu K, Kanai S, Kuroda Y, Noguchi T: POODLE-L: A two-level SVM prediction system for reliably predicting long disordered regions. Bioinformatics. 2007, 23: 2046-2053. 10.1093/bioinformatics/btm302.
Uversky VN, Roman A, Oldfield CJ, Dunker AK: Protein intrinsic disorder and human papillomaviruses: Increased amount of disorder in E6 and E7 oncoproteins from high risk HPVs. J Proteome Res. 2006, 5: 1829-1842. 10.1021/pr0602388.
Ma HC, Chen JM, Chen JW, Sun YX, et al: The panorama of the diversity of H5 subtype influenza viruses. Virus Genes. 2007, 34: 283-287. 10.1007/s11262-006-0018-3.
Chow VT, Tambyah PA, Goh KT: To kill a mocking bird flu?. Ann Acad Med. 2008, 37: 451-453.
Wallace RG, Hodac H, Lathrop RH, Fitch WM: A statistical phylogeography of influenza A H5N1. Proc Natl Acad Sci. 2007, USA, 104: 4473-4478. 10.1073/pnas.0700435104.
Narasaraju T, Sim MK, Ng HH, Phoon MC, et al: Adaptation of human influenza H3N2 virus in a mouse pneumonitis model: Insights into viral virulence, tissue tropism and host pathogenesis's. Microbes Infect. 2009, 11: 2-11. 10.1016/j.micinf.2008.09.013.
Zhao B, Sakharkar KR, Lim CS, Kangueane P, et al: MHC-peptide binding prediction for epitope based vaccine design. Int J Integr Biol. 2007, 1: 127-140.
Sakharkar MK, Sakharkar KR, Pervaiz S: Druggability of human disease genes. Int J Biochem Cell Biol. 2007, 39: 1156-1164. 10.1016/j.biocel.2007.02.018.