The human genome: Its modifications and interactions with those of the microbiome, and the practice of genomic medicine

Discovery Medicine

Volumn 15, Issue 84, 2013, Pages 283-290

  Li Wan Po, Alain ^a  

^a National Genetics Education and Development Centre   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DRUG DERIVATIVE; SORIVUDINE; URACIL ARABINOSIDE;

ARTICLE; DISORDERS OF MITOCHONDRIAL FUNCTIONS; GENOMICS; HUMAN; HUMAN GENOME; METAGENOME;

ARABINOFURANOSYLURACIL; GENOME, HUMAN; GENOMICS; HUMANS; METAGENOME; MITOCHONDRIAL DISEASES;

EID: 84886236796     PISSN: 15396509     EISSN: 19447930     Source Type: Journal    
DOI: None     Document Type: Article

References (67)

1. Andrei G, Snoeck R, Reymen D, Liesnard C, Goubau P, Desmyter J, De Clercq E. Comparative activity of selected antiviral compounds against clinical isolates of varicella-zoster virus. Eur J Clin Microbiol Infect Dis 14(4):318-329, 1995.
2. Cappelli B, Aiuti A. Gene therapy for adenosine deaminase deficiency. Immunol Allergy Clin North Am 30(2):249-260, 2009.
3. Chan S. Targeting the mammalian target of rapamycin (mTOR): a new approach to treating cancer. Br J Cancer 91(8):1420-1424, 2004.
4. Chin L, Gray JW. Translating insights from the cancer genome into clinical practice. Nature 452(7187):553-563, 2008.
5. Chung WH, Hung SI, Hong HS, Hsih MS, Yang LC, Ho HC, Wu JY, Chen YT. Medical genetics: a marker for Stevens-Johnson syndrome. Nature 428(6982):486, 2004.
6. D'herelle F. Sur un microbe invisible antagoniste des bacilles dysentériques. Comptes Rendus hebdomadaires des séances de l'Académie des Sciences 165:373-375, 1917.
7. De Gussem KL, inventor; Huvepharma AD, assignee. Paromomycin-supplemented feed stuff for turkey and use thereof for prophylaxis of histomoniasis, reduction of the horizontal spreading of histomoniasis, and for improved weight gain and feed conversion. United States patent 8293266. 2012.
8. Desnick RJ, Schuchman EH. Enzyme replacement therapy for lysosomal diseases: lessons from 20 years of experience and remaining challenges. Annu Rev Genomics Hum Genet 13:307-335, 2012.
9. Eiseman B, Silen W, Bascom GS, Kauvar AJ. Fecal enema as an adjunct in the treatment of pseudomembranous enterocolitis. Surgery 44(5):854-859, 1958.
10. Fleming A. On the antibacterial action of cultures of a penicillium, with special reference to their use in the isolation of B. influenzae. Br J Exp Pathol 10:226-236, 1929.
11. Gaspar HB, Cooray S, Gilmour KC, Parsley KL, Zhang F, Adams S, Bjorkegren E, Bayford J, Brown L, Davies EG, Veys P, Fairbanks L, Bordon V, Petropoulou T, Kinnon C, Thrasher AJ. Hematopoietic stem cell gene therapy for adenosine deaminase-deficient severe combined immunodeficiency leads to long-term immunological recovery and metabolic correction. Sci Transl Med 3(97):97ra80, 2011.
12. Grice EA, Segre JA. The human microbiome: our second genome. Annu Rev Genomics Hum Genet 13:151-170, 2012.
13. Hacein-Bey-Abina S, Hauer J, Lim A, Picard C, Wang GP, Berry CC, Martinache C, Rieux-Laucat F, Latour S, Belohradsky BH, Leiva L, Sorensen R, Debre M, Casanova JL, Blanche S, Durandy A, Bushman FD, Fischer A, Cavazzana-Calvo M. Efficacy of gene therapy for X-linked severe combined immunodeficiency. N Engl J Med 363(4):355-364, 2010.
14. Hacein-Bey-Abina S, Von Kalle C, Schmidt M, Mccormack MP, Wulffraat N, Leboulch P, Lim A, Osborne CS, Pawliuk R, Morillon E, Sorensen R, Forster A, Fraser P, Cohen JI, De Saint Basile G, Alexander I, Wintergerst U, Frebourg T, Aurias A, Stoppa-Lyonnet D, et al. LMO2-associated clonal T cell proliferation in two patients after gene therapy for SCID-X1. Science 302(5644):415-419, 2003.
15. Hankin ME. Les microbes des rivières de l'Inde. Annales de l'Institut Pasteur 10:175-176, 1896.
16. Hayashida K, Omagari K, Masuda J, Hazama H, Kadokawa Y, Ohba K, Kohno S. The sperm mitochondria-specific translocator has a key role in maternal mitochondrial inheritance. Cell Biol Int 29(6):472-481, 2005.
17. Hehemann JH, Correc G, Barbeyron T, Helbert W, Czjzek M, Michel G. Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature 464(7290):908-912, 2010.
18. Huebner RJ, Todaro GJ. Oncogenes of RNA tumor viruses as determinants of cancer. Proc Natl Acad Sci U S A 64(3):1087-1094, 1969.
19. Jacob F, Monod J. Gènes de structure et gène de régulation dans la biosynthese de protéines [Genes of structure and genes of regulation in the biosynthesis of proteins.] C R Hebd Seances Acad Sci 249:1282-1284, 1959.
20. Jacob F, Monod J. Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 3:318-356, 1961.
21. Kajita J, Fuse E, Kuwabara T, Kobayashi H. The contribution of cytochrome P450 to the metabolism of tegafur in human liver. Drug Metab Pharmacokinet 18(5):303-309, 2003.
22. Kanamitsu SI, Ito K, Okuda H, Ogura K, Watabe T, Muro K, Sugiyama Y. Prediction of in vivo drug-drug interactions based on mechanism-based inhibition from in vitro data: inhibition of 5-fluorouracil metabolism by (E)-5-(2-Bromovinyl)uracil. Drug Metab Dispos 28(4):467-474, 2000.
23. Kelly CP. Fecal microbiota transplantation - an old therapy comes of age. N Engl J Med 368:474-475, 2013.
24. Kelly CR, De Leon L, Jasutkar N. Fecal microbiota transplantation for relapsing Clostridium difficile infection in 26 patients: methodology and results. J Clin Gastroenterol 46(2):145-149, 2012.
25. Koch R. Die ätiologie der Milzbrandkrankheit, begründet auf die Entwicklungsgeschichte des Bacillus anthracis. Beiträge zur Biologie der Pflanzen 2:277-310, 1876.
26. Kwak EL, Bang YJ, Camidge DR, Shaw AT, Solomon B, Maki RG, Ou SH, Dezube BJ, Janne PA, Costa DB, Varella-Garcia M, Kim WH, Lynch TJ, Fidias P, Stubbs H, Engelman JA, Sequist LV, Tan W, Gandhi L, Mino-Kenudson M, et al. Anaplastic lymphoma kinase inhibition in non-small-cell lung cancer. N Engl J Med 363(18):1693-1703, 2010.
27. Li-Wan-Po A, Farndon P. Barking up the wrong genome-we are not alone. J Clin Pharm Ther 36(2):125-127, 2011.
28. Li-Wan-Po A, Farndon PA, Kobayashi S, Mitsudomi T, Potter VA. The pharmacogenetic rescue of side-lined anticancer drugs to the front-line: gefitinib as a case example. Ann Pharmacother 45(2):263-275, 2011.
29. Lindenbaum J, Rund DG, Butler VP Jr, Tse-Eng D, Saha JR. Inactivation of digoxin by the gut flora: reversal by antibiotic therapy. N Engl J Med 305(14):789-794, 1981.
30. Lu TK, Koeris MS. The next generation of bacteriophage therapy. Curr Opin Microbiol 14(5):524-531, 2011.
31. Mallal S, Phillips E, Carosi G, Molina JM, Workman C, Tomazic J, Jagel-Guedes E, Rugina S, Kozyrev O, Cid JF, Hay P, Nolan D, Hughes S, Hughes A, Ryan S, Fitch N, Thorborn D, Benbow A. HLA-B5701 screening for hypersensitivity to abacavir. N Engl J Med 358(6):568-579, 2008.
32. McNulty NP, Yatsunenko T, Hsiao A, Faith JJ, Muegge BD, Goodman AL, Henrissat B, Oozeer R, Cools-Portier S, Gobert G, Chervaux C, Knights D, Lozupone CA, Knight R, Duncan AE, Bain JR, Muehlbauer MJ, Newgard CB, Heath AC, Gordon JI. The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. Sci Transl Med 3(106):106ra106, 2011.
33. Morrow JF, Cohen SN, Chang AC, Boyer HW, Goodman HM, Helling RB. Replication and transcription of eukaryotic DNA in Escherichia coli. Proc Natl Acad Sci U S A 71(5):1743-1747, 1974.
34. Muegge BD, Kuczynski J, Knights D, Clemente JC, Gonzalez A, Fontana L, Henrissat B, Knight R, Gordon JI. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science 332(6032):970-974, 2011.
35. Murphy EF, Cotter PD, Hogan A, O'Sullivan O, Joyce A, Fouhy F, Clarke SF, Marques TM, O'Toole PW, Stanton C, Quigley EM, Daly C, Ross PR, O'Doherty RM, Shanahan F. Divergent metabolic outcomes arising from targeted manipulation of the gut microbiota in diet-induced obesity. Gut 62(2):220-226, 2013.
36. Nakayama H, Kinouchi T, Kataoka K, Akimoto S, Matsuda Y, Ohnishi Y. Intestinal anaerobic bacteria hydrolyse sorivudine, producing the high blood concentration of 5-(E)-(2-bromovinyl)uracil that increases the level and toxicity of 5-fluorouracil. Pharmacogenetics 7(1):35-43, 1997.
37. O'Brien SG, Guilhot F, Larson RA, Gathmann I, Baccarani M, Cervantes F, Cornelissen JJ, Fischer T, Hochhaus A, Hughes T, Lechner K, Nielsen JL, Rousselot P, Reiffers J, Saglio G, Shepherd J, Simonsson B, Gratwohl A, Goldman JM, Kantarjian H, et al. Imatinib compared with interferon and low-dose cytarabine for newly diagnosed chronic-phase chronic myeloid leukemia. N Engl J Med 348(11):994-1004, 2003.
38. Ogura K, Nishiyama T, Takubo H, Kato A, Okuda H, Arakawa K, Fukushima M, Nagayama S, Kawaguchi Y, Watabe T. Suicidal inactivation of human dihydropyrimidine dehydrogenase by (E)-5-(2-bromovinyl)uracil derived from the antiviral, sorivudine. Cancer Lett 122(1-2):107-113, 1998.
39. Okuda H, Nishiyama T, Ogura K, Nagayama S, Ikeda K, Yamaguchi S, Nakamura Y, Kawaguchi Y, Watabe T. Lethal drug interactions of sorivudine, a new antiviral drug, with oral 5-fluorouracil prodrugs. Drug Metab Dispos 25(5):270-273, 1997.
40. Pace NR, Sapp J, Goldenfeld N. Phylogeny and beyond: Scientific, historical, and conceptual significance of the first tree of life. Proc Natl Acad Sci U S A 109(4):1011-1018, 2012.
41. Persons DA, Baum C. Solving the problem of gamma-retroviral vectors containing long terminal repeats. Mol Ther 19(2):229-231, 2011.
42. Piccart-Gebhart MJ, Procter M, Leyland-Jones B, Goldhirsch A, Untch M, Smith I, Gianni L, Baselga J, Bell R, Jackisch C, Cameron D, Dowsett M, Barrios CH, Steger G, Huang CS, Andersson M, Inbar M, Lichinitser M, Lang I, Nitz U, et al. Trastuzumab after adjuvant chemotherapy in HER2-positive breast cancer. N Engl J Med 353(16):1659-1672, 2005.
43. Pritchard DI. Sourcing a chemical succession for cyclosporin from parasites and human pathogens. Drug Discov Today 10(10):688-691, 2005.
44. Rakyan VK, Down TA, Balding DJ, Beck S. Epigenome-wide association studies for common human diseases. Nat Rev Genet 12(8):529-541, 2011.
45. Rikova K, Guo A, Zeng Q, Possemato A, Yu J, Haack H, Nardone J, Lee K, Reeves C, Li Y, Hu Y, Tan Z, Stokes M, Sullivan L, Mitchell J, Wetzel R, MacNeill J, Ren JM, Yuan J, Bakalarski CE, et al. Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer. Cell 131(6):1190-1203, 2007.
46. Romond EH, Perez EA, Bryant J, Suman VJ, Geyer CE Jr, Davidson NE, Tan-Chiu E, Martino S, Paik S, Kaufman PA, Swain SM, Pisansky TM, Fehrenbacher L, Kutteh LA, Vogel VG, Visscher DW, Yothers G, Jenkins RB, Brown AM, Dakhil SR, et al. Trastuzumab plus adjuvant chemotherapy for operable HER2-positive breast cancer. N Engl J Med 353(16):1673-1684, 2005.
47. Rous P. A sarcoma of the fowl transmissible by an agent separable from the tumor cells. J Exp Med 13(4):397-411, 1911.
48. Schwartz R. A molecular star in the wars against cancer. N Engl J Med 347(7):462-463, 2002.
49. Shanahan F. The gut microbiota - a clinical perspective on lessons learned. Nat Rev Gastroenterol Hepatol 9(10):609-614, 2012.
50. Soda M, Choi YL, Enomoto M, Takada S, Yamashita Y, Ishikawa S, Fujiwara S, Watanabe H, Kurashina K, Hatanaka H, Bando M, Ohno S, Ishikawa Y, Aburatani H, Niki T, Sohara Y, Sugiyama Y, Mano H. Identification of the transforming EML4-ALK fusion gene in non-small-cell lung cancer. Nature 448(7153):561-566, 2007.
51. Sousa AP, Amaral A, Baptista M, Tavares R, Caballero Campo P, Caballero Peregrin P, Freitas A, Paiva A, Almeida-Santos T, Ramalho-Santos J. Not all sperm are equal: functional mitochondria characterize a subpopulation of human sperm with better fertilization potential. PLoS One 6(3):e18112, 2013.
52. Stehelin D, Varmus HE, Bishop JM, Vogt PK. DNA related to the transforming gene(s) of avian sarcoma viruses is present in normal avian DNA. Nature 260(5547):170-173, 1976.
53. Stein S, Ott MG, Schultze-Strasser S, Jauch A, Burwinkel B, Kinner A, Schmidt M, Kramer A, Schwable J, Glimm H, Koehl U, Preiss C, Ball C, Martin H, Gohring G, Schwarzwaelder K, Hofmann WK, Karakaya K, Tchatchou S, Yang R, et al. Genomic instability and myelodysplasia with monosomy 7 consequent to EVI1 activation after gene therapy for chronic granulomatous disease. Nat Med 16(2):198-204, 2010.
54. Stratton MR. Exploring the genomes of cancer cells: progress and promise. Science 331(6024):1553-1558, 2011.
55. Sulakvelidze A, Alavidze Z, Morris JG Jr. Bacteriophage therapy. Antimicrob Agents Chemother 45(3):649-659, 2001.
56. Takeya T, Hanafusa H. Structure and sequence of the cellular gene homologous to the RSV src gene and the mechanism for generating the transforming virus. Cell 32(3):881-890, 1983.
57. Twort FW. An investigation on the nature of ultra-microscopic viruses. Lancet 186(4814):241-243, 1915.
58. Van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, De Vos WM, Visser CE, Kuijper EJ, Bartelsman JF, Tijssen JG, Speelman P, Dijkgraaf MG, Keller JJ. Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med 368(5):407-415, 2013.
59. Vennstrom B, Sheiness D, Zabielski J, Bishop JM. Isolation and characterization of c-myc, a cellular homolog of the oncogene (v-myc) of avian myelocytomatosis virus strain 29. J Virol 42(3):773-779, 1982.
60. Vernon JA, Golec JH, Dimasi JA. Drug development costs when financial risk is measured using the Fama-French three-factor model. Health Econ 19(8):1002-1005, 2010.
61. Vogelstein B, Fearon ER, Hamilton SR, Kern SE, Preisinger AC, Leppert M, Nakamura Y, White R, Smits AM, Bos JL. Genetic alterations during colorectal-tumor development. N Engl J Med 319(9):525-532, 1988.
62. Wallace BD, Wang H, Lane KT, Scott JE, Orans J, Koo JS, Venkatesh M, Jobin C, Yeh LA, Mani S, Redinbo MR. Alleviating cancer drug toxicity by inhibiting a bacterial enzyme. Science 330(6005):831-835, 2010.
63. Watabe T, Okuda H, Ogura K. [Lethal drug interactions of the new antiviral, sorivudine, with anticancer prodrugs of 5-fluorouracil.] Yakugaku Zasshi 117(10-11):910-921, 1997.
64. Woese CR. A proposal concerning the origin of life on the planet earth. J Mol Evol 13(2):95-101, 1979.
65. Woese CR, Fox GE. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci U S A 74(11):5088-5090, 1977.
66. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A 87(12):4576-4579, 1990.
67. Zimran A, Brill-Almon E, Chertkoff R, Petakov M, Blanco-Favela F, Munoz ET, Solorio-Meza SE, Amato D, Duran G, Giona F, Heitner R, Rosenbaum H, Giraldo P, Mehta A, Park G, Phillips M, Elstein D, Altarescu G, Szleifer M, Hashmueli S, et al. Pivotal trial with plant cell-expressed recombinant glucocerebrosidase, taliglucerase alfa, a novel enzyme replacement therapy for Gaucher disease. Blood 118(22):5767-5773, 2011.