Preclinical childhood sarcoma models: Drug efficacy biomarker identification and validation

Frontiers in Oncology

Volumn 5, Issue Aug, 2015, Pages

  Geier, Brian ^a   Kurmashev, Dias ^b   Kurmasheva, Raushan T ^b   Houghton, Peter J ^b  

^a NATIONWIDE CHILDREN S HOSPITAL   (United States)

^b UNIVERSITY OF TEXAS HEALTH SCIENCE CENTER AT SAN ANTONIO   (United States)

Author keywords

Bioinformatics; Biomarkers; Copy number variation; Drug efficacy; Drug sensitivity; Expression profiling; Human tumor xenografts; Preclinical pharmacology

Indexed keywords

8 [4 (1 AMINOCYCLOBUTYL)PHENYL] 9 PHENYL 1,2,4 TRIAZOLO[3,4 F][1,6]NAPHTHYRIDIN 3(2H) ONE; ALISERTIB; ALKYLATING AGENT; AZD 8055; BIOLOGICAL MARKER; CABAZITAXEL; CABOZANTINIB; CISPLATIN; CRIZOTINIB; CX 5461; DASATINIB; DOCETAXEL; ERIBULIN; GENZ 644282; GLEMBATUMUMAB VEDOTIN; NTX 010; ONCOLYTIC VIRUS; PACLITAXEL; PILARALISIB; PR 104; RAPAMYCIN; SELINEXOR; SELUMETINIB; SORAFENIB; SUNITINIB; TALAZOPARIB; TEMOZOLOMIDE; UNCLASSIFIED DRUG; VINCRISTINE; VOLASERTIB;

ACUTE LYMPHOBLASTIC LEUKEMIA; ANTINEOPLASTIC ACTIVITY; BIOINFORMATICS; CHILDHOOD CANCER; CLINICAL TRIAL (TOPIC); COPY NUMBER VARIATION; DRUG EFFICACY; DRUG RESPONSE; EVENT FREE SURVIVAL; GENE EXPRESSION PROFILING; GENETIC ASSOCIATION; HUMAN; IC50; LEUKEMIA RELAPSE; MICROARRAY ANALYSIS; NONHUMAN; PICORNAVIRIDAE; PROTEIN LOCALIZATION; REVIEW; SARCOMA; SENECA VALLEY VIRUS; SIGNAL TRANSDUCTION; SOLID TUMOR; TUMOR GROWTH; TUMOR XENOGRAFT;

EID: 84940990395     PISSN: None     EISSN: 2234943X     Source Type: Journal    
DOI: 10.3389/fonc.2015.00193     Document Type: Review

References (124)

1. Smith MA, Altekruse SF, Adamson PC, Reaman GH, Seibel NL. Declining childhood and adolescent cancer mortality. Cancer (2014) 120(16):2497-506. doi:10.1002/cncr.28748.
2. Oeffinger KC, Mertens AC, Sklar CA, Kawashima T, Hudson MM, Meadows AT, et al. Chronic health conditions in adult survivors of childhood cancer. N Engl J Med (2006) 355(15):1572-82. doi:10.1056/NEJMsa060185.
3. Hirschfeld S, Ho PT, Smith M, Pazdur R. Regulatory approvals of pediatric oncology drugs: previous experience and new initiatives. J Clin Oncol (2003) 21(6):1066-73.
4. Horowitz ME, Etcubanas E, Christensen ML, Houghton JA, George SL, Green AA, et al. Phase II testing of melphalan in children with newly diagnosed rhabdomyosarcoma: a model for anticancer drug development. J Clin Oncol (1988) 6(2):308-14.
5. Houghton PJ, Adamson PC, Blaney S, Fine HA, Gorlick R, Haber M, et al. Testing of new agents in childhood cancer preclinical models: meeting summary. Clin Cancer Res (2002) 8(12):3646-57.
6. Houghton PJ, Morton CL, Tucker C, Payne D, Favours E, Cole C, et al. The pediatric preclinical testing program: description of models and early testing results. Pediatr Blood Cancer (2007) 49(7):928-40. doi:10.1002/pbc.21078.
7. Whiteford CC, Bilke S, Greer BT, Chen Q, Braunschweig TA, Cenacchi N, et al. Credentialing preclinical pediatric xenograft models using gene expression and tissue microarray analysis. Cancer Res (2007) 67(1):32-40. doi:10.1158/0008-5472.CAN-06-0610.
8. Neale G, Su X, Morton CL, Phelps D, Gorlick R, Lock RB, et al. Molecular characterization of the pediatric preclinical testing panel. Clin Cancer Res (2008) 14(14):4572-83. doi:10.1158/1078-0432.CCR-07-5090.
9. Kolb EA, Gorlick R, Houghton PJ, Morton CL, Neale G, Keir ST, et al. Initial testing (stage 1) of AZD6244 (ARRY-142886) by the pediatric preclinical testing program. Pediatr Blood Cancer (2010) 55(4):668-77. doi:10.1002/pbc.22576.
10. Suryani S, Bracken LS, Harvey RC, Sia KC, Carol H, Chen IM, et al. Evaluation of the in vitro and in vivo efficacy of the JAK inhibitor AZD1480 against JAK-mutated acute lymphoblastic leukemia. Mol Cancer Ther (2015) 14(2):364-74. doi:10.1158/1535-7163.MCT-14-0647.
11. Gutschner T, Diederichs S. The hallmarks of cancer: a long non-coding RNA point of view. RNA Biol (2012) 9(6):703-19. doi:10.4161/rna.20481.
12. Pe'er D, Hacohen N. Principles and strategies for developing network models in cancer. Cell (2011) 144(6):864-73. doi:10.1016/j.cell.2011.03.001.
13. Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov (2012) 2(5):401-4. doi:10.1158/2159-8290.CD-12-0095.
14. Houghton JA, Cook RL, Lutz PJ, Houghton PJ. Melphalan: a potential new agent in the treatment of childhood rhabdomyosarcoma. Cancer Treat Rep (1985) 69(1):91-6.
15. Houghton PJ, Cheshire PJ, Hallman JD II, Lutz L, Friedman HS, Danks MK, et al. Efficacy of topoisomerase I inhibitors, topotecan and irinotecan, administered at low dose levels in protracted schedules to mice bearing xenografts of human tumors. Cancer Chemother Pharmacol (1995) 36(5):393-403. doi:10.1007/BF00686188.
16. Thompson J, George EO, Poquette CA, Cheshire PJ, Richmond LB, de Graaf SS, et al. Synergy of topotecan in combination with vincristine for treatment of pediatric solid tumor xenografts. Clin Cancer Res (1999) 5(11):3617-31.
17. Houghton PJ, Stewart CF, Cheshire PJ, Richmond LB, Kirstein MN, Poquette CA, et al. Antitumor activity of temozolomide combined with irinotecan is partly independent of O6-methylguanine-DNA methyltransferase and mismatch repair phenotypes in xenograft models. Clin Cancer Res (2000) 6(10):4110-8.
18. Thompson J, Zamboni WC, Cheshire PJ, Lutz L, Luo X, Li Y, et al. Efficacy of systemic administration of irinotecan against neuroblastoma xenografts. Clin Cancer Res (1997) 3(3):423-31.
19. Houghton PJ, Santana VM. Clinical trials using irinotecan. J Pediatr Hematol Oncol (2002) 24(2):84-5. doi:10.1097/00043426-200202000-00002.
20. Santana VM, Furman WL, Billups CA, Hoffer F, Davidoff AM, Houghton PJ, et al. Improved response in high-risk neuroblastoma with protracted topotecan administration using a pharmacokinetically guided dosing approach. J Clin Oncol (2005) 23(18):4039-47. doi:10.1200/JCO.2005.02.097.
21. Furman WL, Stewart CF, Poquette CA, Pratt CB, Santana VM, Zamboni WC, et al. Direct translation of a protracted irinotecan schedule from a xenograft model to a phase I trial in children. J Clin Oncol (1999) 17(6):1815-24.
22. Pappo AS, Lyden E, Breitfeld P, Donaldson SS, Wiener E, Parham D, et al. Two consecutive phase II window trials of irinotecan alone or in combination with vincristine for the treatment of metastatic rhabdomyosarcoma: the Children's Oncology Group. J Clin Oncol (2007) 25(4):362-9. doi:10.1200/JCO.2006.07.1720.
23. Liem NL, Papa RA, Milross CG, Schmid MA, Tajbakhsh M, Choi S, et al. Characterization of childhood acute lymphoblastic leukemia xenograft models for the preclinical evaluation of new therapies. Blood (2004) 103(10):3905-14. doi:10.1182/blood-2003-08-2911.
24. Santana VM, Zamboni WC, Kirstein MN, Tan M, Liu T, Gajjar A, et al. A pilot study of protracted topotecan dosing using a pharmacokinetically guided dosing approach in children with solid tumors. Clin Cancer Res (2003) 9(2):633-40.
25. Houghton PJ, Cheshire PJ, Hallman JC III, Gross JL, McRipley RJ, Sun JH, et al. Evaluation of a novel bis-naphthalimide anticancer agent, DMP 840, against human xenografts derived from adult, juvenile, and pediatric cancers. Cancer Chemother Pharmacol (1994) 33(4):265-72. doi:10.1007/BF00685898.
26. Middlemas DS, Stewart CF, Kirstein MN, Poquette C, Friedman HS, Houghton PJ, et al. Biochemical correlates of temozolomide sensitivity in pediatric solid tumor xenograft models. Clin Cancer Res (2000) 6(3):998-1007.
27. Brent TP, Houghton PJ, Houghton JA. O6-alkylguanine-DNA alkyltransferase activity correlates with the therapeutic response of human rhabdomyosarcoma xenografts to 1-(2-chloroethyl)-3-(trans-4-methylcyclohexyl)-1-nitrosourea. Proc Natl Acad Sci U S A (1985) 82(9):2985-9. doi:10.1073/pnas.82.9.2985.
28. Kolb EA, Gorlick R, Reynolds CP, Kang MH, Carol H, Lock R, et al. Initial testing (stage 1) of eribulin, a novel tubulin binding agent, by the pediatric preclinical testing program. Pediatr Blood Cancer (2013) 60(8):1325-32. doi:10.1002/pbc.24517.
29. Houghton PJ, Kurmasheva RT, Kolb EA, Gorlick R, Maris JM, Wu J, et al. Initial testing (stage 1) of the tubulin binding agent nanoparticle albumin-bound (nab) paclitaxel (abraxane) by the pediatric preclinical testing program (PPTP). Pediatr Blood Cancer (2015) 62(7):1214-21. doi:10.1002/pbc.25474.
30. Houghton PJ, Lock R, Carol H, Morton CL, Phelps D, Gorlick R, et al. Initial testing of the hypoxia-activated prodrug PR-104 by the pediatric preclinical testing program. Pediatr Blood Cancer (2011) 57(3):443-53. doi:10.1002/pbc.22921.
31. Jamieson SM, Gu Y, Manesh DM, El-Hoss J, Jing D, Mackenzie KL, et al. A novel fluorometric assay for aldo-keto reductase 1C3 predicts metabolic activation of the nitrogen mustard prodrug PR-104A in human leukaemia cells. Biochem Pharmacol (2014) 88(1):36-45. doi:10.1016/j.bcp.2013.12.019.
32. Bid HK, Kibler A, Phelps DA, Manap S, Xiao L, Lin J, et al. Development, characterization, and reversal of acquired resistance to the MEK1 inhibitor selumetinib (AZD6244) in an in vivo model of childhood astrocytoma. Clin Cancer Res (2013) 19(24):6716-29. doi:10.1158/1078-0432.CCR-13-0842.
33. Kolb EA, Gorlick R, Houghton PJ, Morton CL, Lock RB, Tajbakhsh M, et al. Initial testing of dasatinib by the pediatric preclinical testing program. Pediatr Blood Cancer (2008) 50(6):1198-206. doi:10.1002/pbc.21368.
34. Kolb EA, Gorlick R, Houghton PJ, Morton CL, Lock R, Carol H, et al. Initial testing (stage 1) of a monoclonal antibody (SCH 717454) against the IGF-1 receptor by the pediatric preclinical testing program. Pediatr Blood Cancer (2008) 50(6):1190-7. doi:10.1002/pbc.21450.
35. Houghton PJ, Morton CL, Gorlick R, Kolb EA, Keir ST, Reynolds CP, et al. Initial testing of a monoclonal antibody (IMC-A12) against IGF-1R by the pediatric preclinical testing program. Pediatr Blood Cancer (2010) 54(7):921-6. doi:10.1002/pbc.22367.
36. Mosse YP, Laudenslager M, Longo L, Cole KA, Wood A, Attiyeh EF, et al. Identification of ALK as a major familial neuroblastoma predisposition gene. Nature (2008) 455(7215):930-5. doi:10.1038/nature07261.
37. Bresler SC, Wood AC, Haglund EA, Courtright J, Belcastro LT, Plegaria JS, et al. Differential inhibitor sensitivity of anaplastic lymphoma kinase variants found in neuroblastoma. Sci Transl Med (2011) 3(108):108ra14. doi:10.1126/scitranslmed.3002950.
38. Peterson JK, Houghton PJ. Integrating pharmacology and in vivo cancer models in preclinical and clinical drug development. Eur J Cancer (2004) 40(6):837-44. doi:10.1016/j.ejca.2004.01.003.
39. McShane LM, Altman DG, Sauerbrei W, Taube SE, Gion M, Clark GM, et al. Reporting recommendations for tumor marker prognostic studies (REMARK). J Natl Cancer Inst (2005) 97(16):1180-4. doi:10.1093/jnci/dji446.
40. McShane LM, Altman DG, Sauerbrei W, Taube SE, Gion M, Clark GM, et al. REporting recommendations for tumour MARKer prognostic studies (REMARK). Eur J Cancer (2005) 41(12):1690-6. doi:10.1016/j.ejca.2005.03.032.
41. Garnett MJ, Edelman EJ, Heidorn SJ, Greenman CD, Dastur A, Lau KW, et al. Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature (2012) 483(7391):570-5. doi:10.1038/nature11005.
42. Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, et al. The cancer cell line encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature (2012) 483(7391):603-7. doi:10.1038/nature11003.
43. Sharma SV, Haber DA, Settleman J. Cell line-based platforms to evaluate the therapeutic efficacy of candidate anticancer agents. Nat Rev Cancer (2010) 10(4):241-53. doi:10.1038/nrc2820.
44. Zou H, Hastie T. Regularization and variable selection via the elastic net. J R Stat Soc B (2005) 67(2):301-20. doi:10.1093/brain/awv075.
45. Hastie T, Tibshirani R, Friedman J. The Elements of Statistical Learning. New York, NY: Springer (2009).
46. Carol H, Boehm I, Reynolds CP, Kang MH, Maris JM, Morton CL, et al. Efficacy and pharmacokinetic/pharmacodynamic evaluation of the aurora kinase A inhibitor MLN8237 against preclinical models of pediatric cancer. Cancer Chemother Pharmacol (2011) 68(5):1291-304. doi:10.1007/s00280-011-1618-8.
47. Maris JM, Morton CL, Gorlick R, Kolb EA, Lock R, Carol H, et al. Initial testing of the aurora kinase A inhibitor MLN8237 by the pediatric preclinical testing program (PPTP). Pediatr Blood Cancer (2010) 55(1):26-34. doi:10.1002/pbc.22430.
48. Gorlick R, Kolb EA, Keir ST, Maris JM, Reynolds CP, Kang MH, et al. Initial testing (stage 1) of the polo-like kinase inhibitor volasertib (BI 6727), by the pediatric preclinical testing program. Pediatr Blood Cancer (2014) 61(1):158-64. doi:10.1002/pbc.24616.
49. Carol H, Lock R, Houghton PJ, Morton CL, Kolb EA, Gorlick R, et al. Initial testing (stage 1) of the kinesin spindle protein inhibitor ispinesib by the pediatric preclinical testing program. Pediatr Blood Cancer (2009) 53(7):1255-63. doi:10.1002/pbc.22056.
50. Lock RB, Carol H, Morton CL, Keir ST, Reynolds CP, Kang MH, et al. Initial testing of the CENP-E inhibitor GSK923295A by the pediatric preclinical testing program. Pediatr Blood Cancer (2012) 58(6):916-23. doi:10.1002/pbc.23176.
51. Krzanowski WJ, Hand DJ. ROC Curves for Continuous Data. Boca Raton, FL: CRC Press (2009). xiv, 241 p.
52. Kolb EA, Gorlick R, Billups CA, Hawthorne T, Kurmasheva RT, Houghton PJ, et al. Initial testing (stage 1) of glembatumumab vedotin (CDX-011) by the pediatric preclinical testing program. Pediatr Blood Cancer (2014) 61(10):1816-21. doi:10.1002/pbc.25099.
53. Casanova M, Ferrari A, Spreafico F, Terenziani M, Massimino M, Luksch R, et al. Vinorelbine in previously treated advanced childhood sarcomas: evidence of activity in rhabdomyosarcoma. Cancer (2002) 94(12):3263-8. doi:10.1002/cncr.10600.
54. Hayashi K, Suzuki A, Hirai S, Kurihara Y, Hoogenraad CC, Ohno S. Maintenance of dendritic spine morphology by partitioning-defective 1b through regulation of microtubule growth. J Neurosci (2011) 31(34):12094-103. doi:10.1523/JNEUROSCI.0751-11.2011.
55. Bai RL, Paull KD, Herald CL, Malspeis L, Pettit GR, Hamel E. Halichondrin B and homohalichondrin B, marine natural products binding in the vinca domain of tubulin. Discovery of tubulin-based mechanism of action by analysis of differential cytotoxicity data. J Biol Chem (1991) 266(24):15882-9.
56. Towle MJ, Salvato KA, Wels BF, Aalfs KK, Zheng W, Seletsky BM, et al. Eribulin induces irreversible mitotic blockade: implications of cell-based pharmacodynamics for in vivo efficacy under intermittent dosing conditions. Cancer Res (2011) 71(2):496-505. doi:10.1158/0008-5472.CAN-10-1874.
57. Jordan MA, Wilson L. Microtubules as a target for anticancer drugs. Nat Rev Cancer (2004) 4(4):253-65. doi:10.1038/nrc1317.
58. Smith JA, Wilson L, Azarenko O, Zhu X, Lewis BM, Littlefield BA, et al. Eribulin binds at microtubule ends to a single site on tubulin to suppress dynamic instability. Biochemistry (2010) 49(6):1331-7. doi:10.1021/bi901810u.
59. Jordan MA, Kamath K, Manna T, Okouneva T, Miller HP, Davis C, et al. The primary antimitotic mechanism of action of the synthetic halichondrin E7389 is suppression of microtubule growth. Mol Cancer Ther (2005) 4(7):1086-95. doi:10.1158/1535-7163.MCT-04-0345.
60. Raemaekers T, Ribbeck K, Beaudouin J, Annaert W, Van Camp M, Stockmans I, et al. NuSAP, a novel microtubule-associated protein involved in mitotic spindle organization. J Cell Biol (2003) 162(6):1017-29. doi:10.1083/jcb.200302129.
61. Vanden Bosch A, Raemaekers T, Denayer S, Torrekens S, Smets N, Moermans K, et al. NuSAP is essential for chromatin-induced spindle formation during early embryogenesis. J Cell Sci (2010) 123(Pt 19):3244-55. doi:10.1242/jcs.063875.
62. Zhu C, Zhao J, Bibikova M, Leverson JD, Bossy-Wetzel E, Fan JB, et al. Functional analysis of human microtubule-based motor proteins, the kinesins and dyneins, in mitosis/cytokinesis using RNA interference. Mol Biol Cell (2005) 16(7):3187-99. doi:10.1091/mbc.E05-02-0167.
63. Mayr MI, Hummer S, Bormann J, Gruner T, Adio S, Woehlke G, et al. The human kinesin Kif18A is a motile microtubule depolymerase essential for chromosome congression. Curr Biol (2007) 17(6):488-98. doi:10.1016/j.cub.2007.02.036.
64. Jain S, Vahdat LT. Eribulin mesylate. Clin Cancer Res (2011) 17(21):6615-22. doi:10.1158/1078-0432.CCR-11-1807.
65. Warner SL, Gray PJ, Von Hoff DD. Tubulin-associated drug targets: aurora kinases, polo-like kinases, and others. Semin Oncol (2006) 33(4):436-48. doi:10.1053/j.seminoncol.2006.04.007.
66. Cowley DO, Rivera-Perez JA, Schliekelman M, He YJ, Oliver TG, Lu L, et al. Aurora-A kinase is essential for bipolar spindle formation and early development. Mol Cell Biol (2009) 29(4):1059-71. doi:10.1128/MCB.01062-08.
67. Wysong DR, Chakravarty A, Hoar K, Ecsedy JA. The inhibition of aurora A abrogates the mitotic delay induced by microtubule perturbing agents. Cell Cycle (2009) 8(6):876-88. doi:10.4161/cc.8.6.7897.
68. Vader G, Lens SM. The aurora kinase family in cell division and cancer. Biochim Biophys Acta (2008) 1786(1):60-72. doi:10.1016/j.bbcan.2008.07.003.
69. Macurek L, Lindqvist A, Lim D, Lampson MA, Klompmaker R, Freire R, et al. Polo-like kinase-1 is activated by aurora A to promote checkpoint recovery. Nature (2008) 455(7209):119-23. doi:10.1038/nature07185.
70. Seki A, Coppinger JA, Jang CY, Yates JR, Fang G. Bora and the kinase aurora a cooperatively activate the kinase Plk1 and control mitotic entry. Science (2008) 320(5883):1655-8. doi:10.1126/science.1157425.
71. Zhou H, Kuang J, Zhong L, Kuo W, Gray J, Sahin A, et al. Tumour amplified kinase STK15/BTAK induces centrosome amplification, aneuploidy and transformation. Nat Genet (1998) 20(2):189-93. doi:10.1038/2496.
72. Gautschi O, Heighway J, Mack PC, Purnell PR, Lara PN Jr, Gandara DR. Aurora kinases as anticancer drug targets. Clin Cancer Res (2008) 14(6):1639-48. doi:10.1158/1078-0432.CCR-07-2179.
73. Wetmore C, Boyett J, Li S, Lin T, Bendel A, Gajjar A, et al. Alisertib is active as single agent in recurrent atypical teratoid rhabdoid tumors in 4 children. Neuro Oncol (2015) 17(6):882-8. doi:10.1093/neuonc/nov017.
74. Rudolph D, Steegmaier M, Hoffmann M, Grauert M, Baum A, Quant J, et al. BI 6727, a polo-like kinase inhibitor with improved pharmacokinetic profile and broad antitumor activity. Clin Cancer Res (2009) 15(9):3094-102. doi:10.1158/1078-0432.CCR-08-2445.
75. Ackermann S, Goeser F, Schulte JH, Schramm A, Ehemann V, Hero B, et al. Polo-like kinase 1 is a therapeutic target in high-risk neuroblastoma. Clin Cancer Res (2011) 17(4):731-41. doi:10.1158/1078-0432.CCR-10-1129.
76. Smith MR, Wilson ML, Hamanaka R, Chase D, Kung H, Longo DL, et al. Malignant transformation of mammalian cells initiated by constitutive expression of the polo-like kinase. Biochem Biophys Res Commun (1997) 234(2):397-405. doi:10.1006/bbrc.1997.6633.
77. Strebhardt K, Ullrich A. Targeting polo-like kinase 1 for cancer therapy. Nat Rev Cancer (2006) 6(4):321-30. doi:10.1038/nrc1841.
78. Weichert W, Ullrich A, Schmidt M, Gekeler V, Noske A, Niesporek S, et al. Expression patterns of polo-like kinase 1 in human gastric cancer. Cancer Sci (2006) 97(4):271-6. doi:10.1111/j.1349-7006.2006.00170.x.
79. Hu K, Lee C, Qiu D, Fotovati A, Davies A, Abu-Ali S, et al. Small interfering RNA library screen of human kinases and phosphatases identifies polo-like kinase 1 as a promising new target for the treatment of pediatric rhabdomyosarcomas. Mol Cancer Ther (2009) 8(11):3024-35. doi:10.1158/1535-7163.MCT-09-0365.
80. Grinshtein N, Datti A, Fujitani M, Uehling D, Prakesch M, Isaac M, et al. Small molecule kinase inhibitor screen identifies polo-like kinase 1 as a target for neuroblastoma tumor-initiating cells. Cancer Res (2011) 71(4):1385-95. doi:10.1158/0008-5472.CAN-10-2484.
81. Duan Z, Ji D, Weinstein EJ, Liu X, Susa M, Choy E, et al. Lentiviral shRNA screen of human kinases identifies PLK1 as a potential therapeutic target for osteosarcoma. Cancer Lett (2010) 293(2):220-9. doi:10.1016/j.canlet.2010.01.014.
82. Wu ZQ, Liu X. Role for Plk1 phosphorylation of Hbo1 in regulation of replication licensing. Proc Natl Acad Sci U S A (2008) 105(6):1919-24. doi:10.1073/pnas.0712063105.
83. Bader JR, Kasuboski JM, Winding M, Vaughan PS, Hinchcliffe EH, Vaughan KT. Polo-like kinase1 is required for recruitment of dynein to kinetochores during mitosis. J Biol Chem (2011) 286(23):20769-77. doi:10.1074/jbc.M111.226605.
84. Xiong F, Lin Y, Han Z, Shi G, Tian L, Wu X, et al. Plk1-mediated phosphorylation of UAP56 regulates the stability of UAP56. Mol Biol Rep (2012) 39(2):1935-42. doi:10.1007/s11033-011-0940-x.
85. Chen J, Dai G, Wang YQ, Wang S, Pan FY, Xue B, et al. Polo-like kinase 1 regulates mitotic arrest after UV irradiation through dephosphorylation of p53 and inducing p53 degradation. FEBS Lett (2006) 580(15):3624-30. doi:10.1016/j.febslet.2006.05.047.
86. Seong YS, Kamijo K, Lee JS, Fernandez E, Kuriyama R, Miki T, et al. A spindle checkpoint arrest and a cytokinesis failure by the dominant-negative polo-box domain of Plk1 in U-2 OS cells. J Biol Chem (2002) 277(35):32282-93. doi:10.1074/jbc.M202602200.
87. Okano-Uchida T, Okumura E, Iwashita M, Yoshida H, Tachibana K, Kishimoto T. Distinct regulators for Plk1 activation in starfish meiotic and early embryonic cycles. EMBO J (2003) 22(20):5633-42. doi:10.1093/emboj/cdg535.
88. Nakajima H, Toyoshima-Morimoto F, Taniguchi E, Nishida E. Identification of a consensus motif for Plk (polo-like kinase) phosphorylation reveals Myt1 as a Plk1 substrate. J Biol Chem (2003) 278(28):25277-80. doi:10.1074/jbc.C300126200.
89. Kohn KW. Molecular interaction map of the mammalian cell cycle control and DNA repair systems. Mol Biol Cell (1999) 10(8):2703-34. doi:10.1091/mbc.10.8.2703.
90. Wells NJ, Watanabe N, Tokusumi T, Jiang W, Verdecia MA, Hunter T. The C-terminal domain of the Cdc2 inhibitory kinase Myt1 interacts with Cdc2 complexes and is required for inhibition of G(2)/M progression. J Cell Sci (1999) 112(Pt 19):3361-71.
91. Liu F, Rothblum-Oviatt C, Ryan CE, Piwnica-Worms H. Overproduction of human Myt1 kinase induces a G2 cell cycle delay by interfering with the intracellular trafficking of Cdc2-cyclin B1 complexes. Mol Cell Biol (1999) 19(7):5113-23.
92. Thalhammer V, Lopez-Garcia LA, Herrero-Martin D, Hecker R, Laubscher D, Gierisch ME, et al. PLK1 phosphorylates PAX3-FOXO1, the inhibition of which triggers regression of alveolar rhabdomyosarcoma. Cancer Res (2015) 75(1):98-110. doi:10.1158/0008-5472.CAN-14-1246.
93. Tse KF, Jeffers M, Pollack VA, McCabe DA, Shadish ML, Khramtsov NV, et al. CR011, a fully human monoclonal antibody-auristatin E conjugate, for the treatment of melanoma. Clin Cancer Res (2006) 12(4):1373-82. doi:10.1158/1078-0432.CCR-05-2018.
94. Carter PJ, Senter PD. Antibody-drug conjugates for cancer therapy. Cancer J (2008) 14(3):154-69. doi:10.1097/PPO.0b013e318172d704.
95. Rose AA, Grosset AA, Dong Z, Russo C, Macdonald PA, Bertos NR, et al. Glycoprotein non-metastatic B is an independent prognostic indicator of recurrence and a novel therapeutic target in breast cancer. Clin Cancer Res (2010) 16(7):2147-56. doi:10.1158/1078-0432.CCR-09-1611.
96. Pollack VA, Alvarez E, Tse KF, Torgov MY, Xie S, Shenoy SG, et al. Treatment parameters modulating regression of human melanoma xenografts by an antibody-drug conjugate (CR011-vcMMAE) targeting GPNMB. Cancer Chemother Pharmacol (2007) 60(3):423-35. doi:10.1007/s00280-007-0490-z.
97. Ripoll VM, Irvine KM, Ravasi T, Sweet MJ, Hume DA. Gpnmb is induced in macrophages by IFN-gamma and lipopolysaccharide and acts as a feedback regulator of proinflammatory responses. J Immunol (2007) 178(10):6557-66. doi:10.4049/jimmunol.178.10.6557.
98. Tomihari M, Hwang SH, Chung JS, Cruz PD Jr, Ariizumi K. Gpnmb is a melanosome-associated glycoprotein that contributes to melanocyte/keratinocyte adhesion in a RGD-dependent fashion. Exp Dermatol (2009) 18(7):586-95. doi:10.1111/j.1600-0625.2008.00830.x.
99. Bachner D, Schroder D, Gross G. mRNA expression of the murine glycoprotein (transmembrane) nmb (Gpnmb) gene is linked to the developing retinal pigment epithelium and iris. Brain Res Gene Expr Patterns (2002) 1(3-4):159-65. doi:10.1016/S1567-133X(02)00012-1.
100. Chung JS, Sato K, Dougherty II, Cruz PD Jr, Ariizumi K. DC-HIL is a negative regulator of T lymphocyte activation. Blood (2007) 109(10):4320-7. doi:10.1182/blood-2006-11-053769.
101. Chung JS, Dougherty I, Cruz PD Jr, Ariizumi K. Syndecan-4 mediates the coinhibitory function of DC-HIL on T cell activation. J Immunol (2007) 179(9):5778-84. doi:10.4049/jimmunol.179.9.5778.
102. Schwarzbich MA, Gutknecht M, Salih J, Salih HR, Brossart P, Rittig SM, et al. The immune inhibitory receptor osteoactivin is upregulated in monocyte-derived dendritic cells by BCR-ABL tyrosine kinase inhibitors. Cancer Immunol Immunother (2012) 61(2):193-202. doi:10.1007/s00262-011-1096-1.
103. Onaga M, Ido A, Hasuike S, Uto H, Moriuchi A, Nagata K, et al. Osteoactivin expressed during cirrhosis development in rats fed a choline-deficient, L-amino acid-defined diet, accelerates motility of hepatoma cells. J Hepatol (2003) 39(5):779-85. doi:10.1016/S0168-8278(03)00361-1.
104. Rose AA, Siegel PM. Osteoactivin/HGFIN: is it a tumor suppressor or mediator of metastasis in breast cancer? Breast Cancer Res (2007) 9(6):403. doi:10.1186/bcr1791.
105. Kuan CT, Wakiya K, Dowell JM, Herndon JE II, Reardon DA, Graner MW, et al. Glycoprotein non-metastatic melanoma protein B, a potential molecular therapeutic target in patients with glioblastoma multiforme. Clin Cancer Res (2006) 12(7 Pt 1):1970-82. doi:10.1158/1078-0432.CCR-05-2797.
106. Morton CL, Houghton PJ, Kolb EA, Gorlick R, Reynolds CP, Kang MH, et al. Initial testing of the replication competent Seneca Valley virus (NTX-010) by the pediatric preclinical testing program. Pediatr Blood Cancer (2010) 55(2):295-303. doi:10.1002/pbc.22535.
107. Reddy PS, Burroughs KD, Hales LM, Ganesh S, Jones BH, Idamakanti N, et al. Seneca Valley virus, a systemically deliverable oncolytic picornavirus, and the treatment of neuroendocrine cancers. J Natl Cancer Inst (2007) 99(21):1623-33. doi:10.1093/jnci/djm198.
108. Kato H, Takeuchi O, Sato S, Yoneyama M, Yamamoto M, Matsui K, et al. Differential roles of MDA5 and RIG-I helicases in the recognition of RNA viruses. Nature (2006) 441(7089):101-5. doi:10.1038/nature04734.
109. Gitlin L, Barchet W, Gilfillan S, Cella M, Beutler B, Flavell RA, et al. Essential role of mda-5 in type I IFN responses to polyriboinosinic:polyribocytidylic acid and encephalomyocarditis picornavirus. Proc Natl Acad Sci U S A (2006) 103(22):8459-64. doi:10.1073/pnas.0603082103.
110. Storey JD, Tibshirani R. Statistical significance for genomewide studies. Proc Natl Acad Sci U S A (2003) 100(16):9440-5. doi:10.1073/pnas.1530509100.
111. Liberzon A, Subramanian A, Pinchback R, Thorvaldsdottir H, Tamayo P, Mesirov JP. Molecular signatures database (MSigDB) 3.0. Bioinformatics (2011) 27(12):1739-40. doi:10.1093/bioinformatics/btr260.
112. Liang H, Cheung LW, Li J, Ju Z, Yu S, Stemke-Hale K, et al. Whole-exome sequencing combined with functional genomics reveals novel candidate driver cancer genes in endometrial cancer. Genome Res (2012) 22(11):2120-9. doi:10.1101/gr.137596.112.
113. Rudin CM, Poirier JT, Senzer NN, Stephenson J Jr, Loesch D, Burroughs KD, et al. Phase I clinical study of Seneca Valley virus (SVV-001), a replication-competent picornavirus, in advanced solid tumors with neuroendocrine features. Clin Cancer Res (2011) 17(4):888-95. doi:10.1158/1078-0432.CCR-10-1706.
114. Monti S, Tamayo P, Mesirov J, Golub T. Consensus clustering: a resampling-based method for class discovery and visualization of gene expression microarray data. Machine Learning (2003) 52(1-2):91-118. doi:10.1023/A:1023949509487.
115. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 102(43):15545-50. doi:10.1073/pnas.0506580102.
116. Pepe MS, Longton G, Anderson GL, Schummer M. Selecting differentially expressed genes from microarray experiments. Biometrics (2003) 59(1):133-42. doi:10.1111/1541-0420.00016.
117. Brunet JP, Tamayo P, Golub TR, Mesirov JP. Metagenes and molecular pattern discovery using matrix factorization. Proc Natl Acad Sci U S A (2004) 101(12):4164-9. doi:10.1073/pnas.0308531101.
118. Witten DM, Tibshirani R, Hastie T. A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis. Biostatistics (2009) 10(3):515-34. doi:10.1093/biostatistics/kxp008.
119. Witten DM, Tibshirani RJ. Extensions of sparse canonical correlation analysis with applications to genomic data. Stat Appl Genet Mol Biol (2009) 8:Article28. doi:10.2202/1544-6115.1470.
120. Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP. GenePattern 2.0. Nat Genet (2006) 38(5):500-1. doi:10.1038/ng0506-500.
121. Kuehn H, Liberzon A, Reich M, Mesirov JP. Using GenePattern for gene expression analysis. In: Baxevanis AD, Current Protocols in Bioinformatics/Editorial Board. Chapter 7: Unit 7 12 (2008). doi:10.1002/0471250953.bi0712s22.
122. Subramanian A, Kuehn H, Gould J, Tamayo P, Mesirov JP. GSEA-P: a desktop application for gene set enrichment analysis. Bioinformatics (2007) 23(23):3251-3. doi:10.1093/bioinformatics/btm369.
123. Wettenhall JM, Smyth GK. limmaGUI: a graphical user interface for linear modeling of microarray data. Bioinformatics (2004) 20(18):3705-6. doi:10.1093/bioinformatics/bth449.
124. Center CBCaMS-KC. 2012 cBio Cancer Genomics Portal. (2012). Available from: http://www.cbioportal.org/public-portal/. Accessed 2012.