Using functional signatures to identify repositioned drugs for breast, myelogenous leukemia and prostate cancer

PLoS Computational Biology

Volumn 8, Issue 2, 2012, Pages

  Shigemizu, Daichi ^a   Hu, Zhenjun ^a   Hung, Jui Hung ^a   Huang, Chia Ling ^a   Wang, Yajie ^b   DeLisi, Charles ^a  

^a BOSTON UNIVERSITY   (United States)

^b CAPITAL MEDICAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

GENE EXPRESSION; INVERSE PROBLEMS; UROLOGY;

BIOACTIVE COMPOUNDS; BREAST CANCER; DRUG CANDIDATES; FUNCTIONAL SIGNATURES; GENOMICS REVOLUTION; HIGH-THROUGHPUT; INVERSE CORRELATION; PROSTATE CANCERS; RAPID IDENTIFICATION; SYSTEMATIC IDENTIFICATION;

DISEASES;

ARTICLE; BREAST CANCER; CELL FUNCTION; CONTROLLED STUDY; DATA ANALYSIS; DRUG IDENTIFICATION; DRUG RECALL; DRUG REPOSITIONING; GENE EXPRESSION; GENE IDENTIFICATION; MYELOID LEUKEMIA; PROSTATE CANCER; BIOLOGY; BREAST TUMOR; DRUG DEVELOPMENT; FACTUAL DATABASE; FEMALE; GENE EXPRESSION PROFILING; GENETICS; HUMAN; MALE; METABOLISM; METHODOLOGY; PROSTATE TUMOR; SIGNAL TRANSDUCTION;

BREAST NEOPLASMS; COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; DRUG DISCOVERY; DRUG REPOSITIONING; FEMALE; GENE EXPRESSION PROFILING; HUMANS; LEUKEMIA, MYELOID; MALE; PROSTATIC NEOPLASMS; SIGNAL TRANSDUCTION;

EID: 84861150677     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002347     Document Type: Article

References (53)

1. Chong CR, Sullivan DJ Jr, (2007) New uses for old drugs. Nature 448: 645-646.
2. Kamb A, Wee S, Lengauer C, (2007) Why is cancer drug discovery so difficult? Nat Rev Drug Discov 6: 115-120.
3. Schneider G, (2010) Virtual screening: an endless staircase? Nat Rev Drug Discov 9: 273-276.
4. Hopkins AL, (2008) Network pharmacology: the next paradigm in drug discovery. Nat Chem Biol 4: 682-690.
5. Berger SI, Iyengar R, (2009) Network analyses in systems pharmacology. Bioinformatics 25: 2466-2472.
6. Lamb J, (2007) The Connectivity Map: a new tool for biomedical research. Nat Rev Cancer 7: 54-60.
7. Schadt EE, Friend SH, Shaywitz DA, (2009) A network view of disease and compound screening. Nat Rev Drug Discov 8: 286-295.
8. Yang TH, Kon M, Hung JH, Delisi C, (2011) Combinations of newly confirmed Glioma-Associated loci link regions on chromosomes 1 and 9 to increased disease risk. BMC Med Genomics 4: 63.
9. Keiser MJ, Setola V, Irwin JJ, Laggner C, Abbas AI, et al. (2009) Predicting new molecular targets for known drugs. Nature 462: 175-181.
10. Iorio F, Bosotti R, Scacheri E, Belcastro V, Mithbaokar P, et al. (2010) Discovery of drug mode of action and drug repositioning from transcriptional responses. Proc Natl Acad Sci U S A 107: 14621-14626.
11. Chiang AP, Butte AJ, (2009) Systematic evaluation of drug-disease relationships to identify leads for novel drug uses. Clin Pharmacol Ther 86: 507-510.
12. Hu G, Agarwal P, (2009) Human disease-drug network based on genomic expression profiles. PLoS One 4: e6536.
13. Campillos M, Kuhn M, Gavin AC, Jensen LJ, Bork P, (2008) Drug target identification using side-effect similarity. Science 321: 263-266.
14. Lamb J, Crawford ED, Peck D, Modell JW, Blat IC, et al. (2006) The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science 313: 1929-1935.
15. Dudley JT, Sirota M, Shenoy M, Pai RK, Roedder S, et al. (2011) Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease. Sci Transl Med 3: 96ra76.
16. Sirota M, Dudley JT, Kim J, Chiang AP, Morgan AA, et al. (2011) Discovery and preclinical validation of drug indications using compendia of public gene expression data. Sci Transl Med 3: 96ra77.
17. Barrett T, Suzek TO, Troup DB, Wilhite SE, Ngau WC, et al. (2005) NCBI GEO: mining millions of expression profiles-database and tools. Nucleic Acids Res 33: D562-566.
18. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, et al. (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36: D480-484.
19. Linghu B, Snitkin ES, Hu Z, Xia Y, Delisi C, (2009) Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network. Genome Biol 10: R91.
20. Sun X, Shikata Y, Wang L, Ohmori K, Watanabe N, et al. (2009) Enhanced interaction between focal adhesion and adherens junction proteins: involvement in sphingosine 1-phosphate-induced endothelial barrier enhancement. Microvasc Res 77: 304-313.
21. Lu H, Ouyang W, Huang C, (2006) Inflammation, a key event in cancer development. Mol Cancer Res 4: 221-233.
22. Franklin MC, Carey KD, Vajdos FF, Leahy DJ, de Vos AM, et al. (2004) Insights into ErbB signaling from the structure of the ErbB2-pertuzumab complex. Cancer Cell 5: 317-328.
23. Golubovskaya VM, Zheng M, Zhang L, Li JL, Cance WG, (2009) The direct effect of focal adhesion kinase (FAK), dominant-negative FAK, FAK-CD and FAK siRNA on gene expression and human MCF-7 breast cancer cell tumorigenesis. BMC Cancer 9: 280.
24. Alvarez RH, (2010) Present and future evolution of advanced breast cancer therapy. Breast Cancer Res 12 (Suppl 2): S1.
25. Liu S, Huang H, Lu X, Golinski M, Comesse S, et al. (2003) Down-regulation of thiamine transporter THTR2 gene expression in breast cancer and its association with resistance to apoptosis. Mol Cancer Res 1: 665-673.
26. Rao PN, Levine E, Myers MO, Prakash V, Watson J, et al. (1999) Elevation of serum riboflavin carrier protein in breast cancer. Cancer Epidemiol Biomarkers Prev 8: 985-990.
27. Rajaraman P, Bhatti P, Doody MM, Simon SL, Weinstock RM, et al. (2008) Nucleotide excision repair polymorphisms may modify ionizing radiation-related breast cancer risk in US radiologic technologists. Int J Cancer 123: 2713-2716.
28. Milne RL, Ribas G, Gonzalez-Neira A, Fagerholm R, Salas A, et al. (2006) ERCC4 associated with breast cancer risk: a two-stage case-control study using high-throughput genotyping. Cancer Res 66: 9420-9427.
29. Smith ML, Chen IT, Zhan Q, Bae I, Chen CY, et al. (1994) Interaction of the p53-regulated protein Gadd45 with proliferating cell nuclear antigen. Science 266: 1376-1380.
30. Ingelman-Sundberg M, Sim SC, Gomez A, Rodriguez-Antona C, (2007) Influence of cytochrome P450 polymorphisms on drug therapies: pharmacogenetic, pharmacoepigenetic and clinical aspects. Pharmacol Ther 116: 496-526.
31. Belin S, Beghin A, Solano-Gonzalez E, Bezin L, Brunet-Manquat S, et al. (2009) Dysregulation of ribosome biogenesis and translational capacity is associated with tumor progression of human breast cancer cells. PLoS One 4: e7147.
32. Lukk M, Kapushesky M, Nikkila J, Parkinson H, Goncalves A, et al. (2010) A global map of human gene expression. Nat Biotechnol 28: 322-324.
33. Pallasch CP, Schwamb J, Konigs S, Schulz A, Debey S, et al. (2008) Targeting lipid metabolism by the lipoprotein lipase inhibitor orlistat results in apoptosis of B-cell chronic lymphocytic leukemia cells. Leukemia 22: 585-592.
34. Vogler WR, Olson AC, Hajdu J, Shoji M, Raynor R, et al. (1993) Structure-function relationships of alkyl-lysophospholipid analogs in selective antitumor activity. Lipids 28: 511-516.
35. Naito M, Kudo I, Nakagawa Y, Waku K, Nojiri H, et al. (1991) Suppression of ethanolamine-containing glycerophospholipid synthesis in HL-60 cells during retinoic acid-induced differentiation. J Biochem 110: 469-471.
36. Parker C, Omine M, Richards S, Nishimura J, Bessler M, et al. (2005) Diagnosis and management of paroxysmal nocturnal hemoglobinuria. Blood 106: 3699-3709.
37. Ikushima H, Miyazono K, (2010) TGFbeta signalling: a complex web in cancer progression. Nat Rev Cancer 10: 415-424.
38. Naka K, Hoshii T, Muraguchi T, Tadokoro Y, Ooshio T, et al. (2010) TGF-beta-FOXO signalling maintains leukaemia-initiating cells in chronic myeloid leukaemia. Nature 463: 676-680.
39. Horiguchi K, Shirakihara T, Nakano A, Imamura T, Miyazono K, et al. (2009) Role of Ras signaling in the induction of snail by transforming growth factor-beta. J Biol Chem 284: 245-253.
40. Risinger GM Jr, Updike DL, Bullen EC, Tomasek JJ, Howard EW, (2010) TGF-beta suppresses the upregulation of MMP-2 by vascular smooth muscle cells in response to PDGF-BB. Am J Physiol Cell Physiol 298: C191-201.
41. Stahnke K, Eckhoff S, Mohr A, Meyer LH, Debatin KM, (2003) Apoptosis induction in peripheral leukemia cells by remission induction treatment in vivo: selective depletion and apoptosis in a CD34+ subpopulation of leukemia cells. Leukemia 17: 2130-2139.
42. Fimognari C, Lenzi M, Sciuscio D, Cantelli-Forti G, Hrelia P, (2007) Cell-cycle specificity of sulforaphane-mediated apoptosis in Jurkat T-leukemia cells. In Vivo 21: 377-380.
43. Heemskerk MH, (2010) T-cell receptor gene transfer for the treatment of leukemia and other tumors. Haematologica 95: 15-19.
44. Unsinger J, Herndon JM, Davis CG, Muenzer JT, Hotchkiss RS, et al. (2006) The role of TCR engagement and activation-induced cell death in sepsis-induced T cell apoptosis. J Immunol 177: 7968-7973.
45. Hu Z, Hung JH, Wang Y, Chang YC, Huang CL, et al. (2009) VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology. Nucleic Acids Res 37: W115-121.
46. (EBCTCG). EBCTCG (2005) Effects of chemotherapy and hormonal therapy for early breast cancer on recurrence and 15-year survival: an overview of the randomised trials. Lancet 365: 1687-1717.
47. Kuhn MA, Wang X, Payne WG, Ko F, Robson MC, (2002) Tamoxifen decreases fibroblast function and downregulates TGF(beta2) in dupuytren's affected palmar fascia. J Surg Res 103: 146-152.
48. Brandt S, Kopp A, Grage B, Knabbe C, (2003) Effects of tamoxifen on transcriptional level of transforming growth factor beta (TGF-beta) isoforms 1 and 2 in tumor tissue during primary treatment of patients with breast cancer. Anticancer Res 23: 223-229.
49. Ivanovic V, Demajo M, Krtolica K, Krajnovic M, Konstantinovic M, et al. (2006) Elevated plasma TGF-beta1 levels correlate with decreased survival of metastatic breast cancer patients. Clin Chim Acta 371: 191-193.
50. Nilsson UW, Jonsson JA, Dabrosin C, (2009) Tamoxifen decreases extracellular TGF-beta1 secreted from breast cancer cells-a post-translational regulation involving matrix metalloproteinase activity. Exp Cell Res 315: 1-9.
51. Pardali K, Moustakas A, (2007) Actions of TGF-beta as tumor suppressor and pro-metastatic factor in human cancer. Biochim Biophys Acta 1775: 21-62.
52. Beissbarth T, Speed TP, (2004) GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics 20: 1464-1465.
53. Curtis RK, Oresic M, Vidal-Puig A, (2005) Pathways to the analysis of microarray data. Trends Biotechnol 23: 429-435.