Mathematical prognostic biomarker models for treatment response and survival in epithelial ovarian cancer

Cancer Informatics

Volumn 10, Issue , 2011, Pages 233-247

  Nikas, Jason B ^a,b   Boylan, Kristin L M ^a   Skubitz, Amy P N ^a,b   Low, Walter C ^a,b  

^a UNIVERSITY OF MINNESOTA MEDICAL SCHOOL   (United States)

^b UNIVERSITY OF MINNESOTA   (United States)

Author keywords

Biomarkers; Global gene expression analysis; Mathematical models; Ovarian cancer; Prognostic biomarker models; Survival; Treatment response

Indexed keywords

ATORVASTATIN; BESTATIN; CALCIUM; CALMODULIN; CAMPTOTHECIN; COLCHICINE; DOCETAXEL; EPOTHILONE B; EPOTHILONE DERIVATIVE; ESTRADIOL; IMATINIB; INDOMETACIN; INFLIXIMAB; IXABEPILONE; MILATAXEL; NAVELBINE; PACLITAXEL; PLATINUM COMPLEX; PODOPHYLLOTOXIN; RAPAMYCIN; SIMVASTATIN; SULINDAC; TAXANE DERIVATIVE; TOPOTECAN; TUMOR MARKER; UNINDEXED DRUG; VALPROIC ACID; VINBLASTINE; VINCRISTINE; VINFLUNINE;

ACCURACY; ADVANCED CANCER; ARTICLE; CANCER CHEMOTHERAPY; CANCER STAGING; CANCER SURGERY; CANCER SURVIVAL; CONTROLLED STUDY; CYTOSKELETON; GENE EXPRESSION; GENE IDENTIFICATION; GENETIC SCREENING; HISTOPATHOLOGY; HUMAN; HUMAN TISSUE; MAJOR CLINICAL STUDY; MATHEMATICAL MODEL; OBSTETRIC OPERATION; OVARY CANCER; PROGNOSIS; RANDOMIZED CONTROLLED TRIAL; SENSITIVITY AND SPECIFICITY; SURVIVAL TIME; TREATMENT RESPONSE;

EID: 80755142832     PISSN: None     EISSN: 11769351     Source Type: Journal    
DOI: 10.4137/CIN.S8104     Document Type: Article

References (49)

1. American Cancer Society. Cancer Facts and Figures 2010. Atlanta: American Cancer Society; 2010.
2. Jemal A, Siegel R, Xu J, Ward E. Cancer statistics, 2010. CA Cancer J Clin. 2010;60:277-300.
3. Cannistra SA. Cancer of the ovary. N Engl J Med. 2004;351:2519-9.
4. Vergote I, Trope CG, Amant F, Kristensen GB, Ehlen T, Johnson N, et al. Neoadjuvant chemotherapy or primary surgery in stage IIIC or IV ovarian cancer. N Engl J Med. 2010;363:943-53.
5. Du Bois A, Luck HJ, Meier W, Adams HP, Mobus V, Costa S, et al. A randomized clinical trial of cisplatin/paclitaxel versus carboplatin/ paclitaxel as frst-line treatment of ovarian cancer. J Natl Cancer Inst. 2003;95:1320-9.
6. Ozols RF, Bundy BN, Greer BE, Fowler JM, Clarke-Pearson D, Burger RA, et al. Phase III trial of carboplatin and paclitaxel compared with cisplatin and paclitaxel in patients with optimally resected stage III ovarian cancer: a Gynecologic Oncology Group study. J ClinOncol. 2003;21: 3194-200.
7. Berchuck A, Iversen ES, Lancaster JM, Pittman J, Luo J, Lee P, et al. Patterns of gene expression that characterize long-term survival in advanced stage serous ovarian cancers. Clin Cancer Res. 2005;11(10):3686-696.
8. Nikas JB, Keene CD, Low WC. Comparison of analytical mathematical approaches for identifying key nuclear magnetic resonance spectroscopy biomarkers in the diagnosis and assessment of clinical change of diseases. Journal of Comparative Neurology. 2010;518:4091-112.
9. Nikas JB, Low WC. ROC-supervised principal component analysis in connection with the diagnosis of diseases. American Journal of Translational Research. 2011;3(2):180-96.
10. Nikas JB, Low WC. Application of clustering analyses to the diagnosis of Huntington disease in mice and other diseases with well-defned group boundaries. Computer Methods and Programs in Biomedicine. 2011; doi:10.1016/j.cmpb.2011.03.004.
11. Lim R, Lappas M, Ahmed N, Permezel M, Quinn MA, Rice GE. 2D-PAGE of ovarian cancer: Analysis of soluble and insoluble fractions using medium-range immobilized pH gradients. Biochemical and Biophysical Research Communications. 2011;406:408-13.
12. Kaneko K, Satoh K, Masamune A, Satoh A, Shimosegawa T. Myosin light chain kinase inhibitors can block invasion and adhesion of human pancreatic cancer cell lines. Pancreas. 2002;24:34-41.
13. Ridley AJ, Schwartz MA, Burridge K, Firtel RA, Ginsberg MH, Borisy G, et al. Cell migration: Integrating signals from front to back. Science. 2003;302:1704-9.
14. Albiges-Rizo C, Destaing O, Fourcade B, Planus E, Block MR. Actin machinery and mechanosensitivity in invadopodia, podosomes and focal adhesions. Journal of Cell Science. 2009;122:3037-49.
15. Schmidt A, Hall MN. Signaling to the actin cytoskeleton. Annu Rev Cell Dev Biol. 1998;14:305-38.
16. Liu Z, Adams HC, Whitehead IP. The Rho-specifc guanine nucleotide exchange factor Dbs regulates breast cancer cell migration. The Journal of Biological Chemistry. 2009;284(23):15771-80.
17. Keely PJ, Westwick JK, Whitehead IP, Der CJ, Parise LV. Cdc42 and Rac1 induce integrin-mediated cell motility and invasiveness through PI(3)K. Nature. 1997;390:632-6.
18. Stowers L, Yelon D, Berg LJ, Chant J. Regulation of the polarization of T cells toward antigen-presenting cells by Ras-related GTPase CDC42. Proc. Natl. Acad. Sci. 1995;92:5027-31.
19. Sato S, Tomomori-Sato C, Parmely TJ, Florens L, Zybailov B, Swanson SK, et al. A set of consensus mammalian mediator subunits identifed by multidimensional protein identifcation technology. Molecular Cell. 2004; 14:685-91.
20. Gu W, Malik S, Ito M, Yuan CX, Fondell JD, Zhang X, et al. A novel human SRB/MED-containing cofactor complex, SMCC, involved in transcription regulation. Molecular Cell. 1999;3:97-108.
21. Musante L, Bartsch O, Ropers HH, Kalscheuer VM. CDNA cloning and characterization of the human THRAP2 gene which maps to chromosome 12q24, and its mouse ortholog Thrap2. Gene. 2004;332:119-27.
22. Daoud SS, Munson PJ, Reinhold W, Young L, Prabhu V V, Yu Q, et al. Impact of p53 knockout and topotecan treatment on gene expression pro-fles in human colon carcinoma cells: A pharmacogenomic study. Cancer Research. 2003;63:2782-93.
23. Hartman E, Prehn S. The N-terminal region of the a-subunit of the TRAP complex has a conserved cluster of negative charges. FEBS Letters. 1994; 349:324-326.
24. Fons RD, Bogert BA, Hegde RS. Substrate-specifc function of the trans-locon-associated protein complex during translocation across the ER membrane. The Journal of Cell Biology. 2003;160(4):529-39.
25. Hirama T, Miller CW, Koeffer HP. Translocon-associated protein K transcripts are induced by granulocyte-macrophage colony-stimulating factor and exhibit complex alternative polyadenylation. FEBS Letters. 1999;455:223-7.
26. Cowin P, Kapprell H-P, Franke WW, Tamkun J, Hynes RO. Plakoglobin: a protein common to different kinds of intercellular adhering junctions. Cell. 1986;46:1063-73.
27. Hofmann I, Kuhn C, Franke WW. Protein p0071, a major plaque protein of non- desmosomaladhering junctions, is a selective cell-type marker. Cell Tissue Res. 2008;334:381-99.
28. Denisenko ON, Bomsztyk K. The product of the murine homolog of the drosophila extra sex combs gene displays transcriptional repressor activity. Molecular and Cellular Biology. 1997;17(8):4707-17.
29. Van der Vlag J, Otte AP. Transcriptional repression mediated by the human polycomb-group protein EED involves histone deacetylation. Nature Genetics. 1999;23:474-8.
30. Hideshima T, Richardson P, Chauhan D, et al. The proteasome inhibitor PS-341 inhibits growth, induces apoptosis, and overcomes drug resistance in human multiple myeloma cells. Cancer Res. 2001;61:3071-6.
31. Goy A, Younes A, McLaughlin P, et al. Phase II study of proteasome inhibitor bortezomib in relapsed or refractory B-cell non-Hodgkin's lymphoma. J ClinOncol. 2005;323:667-75.
32. Kapuria V, Peterson LF, Fang D, Bornmann WG, Talpaz M, Donato NJ. Deubiquitinase inhibition by small-molecule WP1130 triggers aggresome-formation and tumor cell apoptosis. Cancer Res. 2010;70:9265-76.
33. Tisdale MJ. Tumor-host interactions. Journal of Cellular Biochemistry. 2004;93:871-7.
34. Bossola M, Muscaritoli M, Costelli P, Grieco G, Bonelli G, Pacelli F, et al. Increased muscle proteasome activity correlates with disease severity in gastric cancer patients. Ann Surg. 2003;237:384-389.
35. Hilvo M, Denkert C, Lehtinen L, Muller B, Brockmoller S, Seppanen-Laakso T, et al. Novel theranostic opportunities offered by characterization of altered membrane lipid metabolism in breast cancer progression. Cancer Res. 2011;71:3236-45.
36. Hirsch HA, Iliopoulos D, Joshi A, Zhang Y, Jaeger SA, Bulyk M, et al. A transcriptional signature and common gene networks link cancer with lipid metabolism and diverse human diseases. Cancer Cell. 2010;17:348-61.
37. Young CD, Anderson SM. Sugar and fat-that's where it's at: metabolic changes in tumors. Breast Cancer Research. 2008;10:202.
38. Papandreou I, Cairns RA, Fontana L, Lim AL, Denko NC. HIF-1 mediates adaptation to hypoxia by actively downregulating mitochondrial oxygen consumption. Cell Metabolism. 2006;3:187-97.
39. Smith HJ, Lorite MJ, Tisdale MJ. Effect of a cancer cachectic factor on protein synthesis/degradation in murine C2C12 myoblasts: Modulation by eicosapentaenoicacid. Cancer Res. 1999;59:5507-13.
40. Lehto M, Laitinen S, Chinetti G, Johansson M, Ehnholm C, Staels B, et al. The OSBP-related protein family in humans. J. Lipid Res. 2001;42:1203-13.
41. Repa JJ, Liang G, Ou J, Bashmakov Y, Lobaccaro JMA, Shimomura I, et al. Regulation of mouse sterol regulatory element-binding protein-1c gene (SREBP-1c) by oxysterol receptors, LXRα and LXRβ. Genes Dev. 2000;14:2819-30.
42. Schultz JR, Tu H, Luk A, Repa JJ, Medina JC, Li L, et al. Role of LXRs in control of lipogenesis. Genes and Development. 2000;14:2831-38.
43. Frezza C, Gottlieb E. Mitochondria in cancer: Not just innocent bystanders. Seminars in Cancer Biology. 2009;19:4-11.
44. Rahman A, Korzekwa KR, Grogan J, Gonzalez FJ, Harris JW. Selective biotransformation of taxol to 6a-hydroxytaxol by human cytochrome P450 2C8. Cancer Research. 1994;54:5543-46.
45. Rieder CL, Maiato H. Stuck in division or passing through: what happens when cells cannot satisfy the spindle assembly checkpoint. Dev. Cell. 2004;7:637-51.
46. Schiff PB, Fant J, Horwitz SB. Promotion of microtubule assembly in vitro by Taxol. Nature. 1979;277:665-67.
47. Chen JG, Horwitz SB. Differential mitotic responses to microtubule-stabilizing and -destabilizing drugs. Cancer Research. 2002;62:1935-8.
48. Cicchillitti L, Della Corte A, Di Michele M, Donati MB, Rotilio D, Scambia G. Characterisation of a multimeric protein complex associated with ERp57 within the nucleus in paclitaxel-sensitive and -resistant epithelial ovarian cancer cells: The involvement of specifc conformational states of ß-actin. International Journal of Oncology. 2010;37:445-54.
49. Xu FL, Saunders WS. Actin and microtubules: working together to control spindle polarity. Cancer Cell. 2008;14:197-99.