Table 3.

Median fold changes for genes selected preclinically for RT-PCR follow-up in patient samples from the clinical trial

Probe set IDGene symbolGene titleEntrez gene IDAffymetrix median fold changes (preclinical; compared with 0 h)RT-PCR median fold changes for all patients in cohort 6A (clinical; compared with pretreatment)
HCT116DU145PBMCCycle 1Cycle 2
2 h24 h2 h24 h2 h24 h302 (3 h)303 (24 h)305 (3 h)306 (24 h)
227322_s_atBCCIPBRCA2 and CDKN1A interacting protein56647−1.20−1.221.14−1.57−1.211.161.441.141.551.03
201457_x_atBUB3BUB3 budding uninhibited by benzimidazoles 3 homologue (yeast)9184−1.12−2.22−1.01−3.94−1.51−1.08−1.03−1.131.22−1.16
207243_s_atCALM2Calmodulin 2805−1.26−1.451.00−6.54−1.03−1.11−1.521.37−1.041.37
208075_s_atCCL7Chemokine (C-C motif) ligand 763541.141.071.011.471.7011.07NANANANA
214710_s_atCCNB1Cyclin B18911.357.161.1424.331.281.101.481.181.221.12
210895_s_atCD86CD86 molecule9421.061.131.091.061.531.894.051.163.571.16
221555_x_atCDC14BCDC14 cell division cycle 14 homologue B8555−1.07−1.12−1.53−8.02−1.20−1.601.121.131.331.02
209616_s_atCES1Carboxylesterase 11066−1.051.13−1.061.331.944.901.051.93−1.452.06
213385_atCHN2Chimerin (chimaerin) 21124−1.011.08−1.10−1.16−2.18−2.14−1.181.13−1.331.05
227404_s_atEGR1Early growth response 119581.141.0510.5012.821.031.531.701.131.531.25
226419_s_atFLJ44342Hypothetical LOC6454606454601.561.122.001.553.692.373.491.343.811.07
202814_s_atHEXIM1Hexamethylene bisacetamide inducible 1106141.861.881.964.103.833.451.311.211.961.31
201464_x_atJUNJun oncogene37251.171.885.426.941.441.051.661.001.701.11
226534_atKITLGKIT ligand4254−1.07−1.29−1.11−6.978.712.331.561.412.431.38
214352_s_atKRASv-Ki-ras2 Kirsten rat sarcoma viral oncogene homologue3845−1.20−1.39−1.38−8.62−1.051.38−1.101.511.161.36
209348_s_atMAFv-maf musculoaponeurotic fibrosarcoma oncogene homologue40941.031.04−1.021.27−1.99−2.18−1.30−1.17−1.23−1.07
203836_s_atMAP3K5Mitogen-activated protein kinase kinase kinase 542171.17−1.411.02−3.551.01−1.181.291.251.741.48
212021_s_atMKI67Antigen identified by monoclonal antibody Ki-6742881.276.701.034.211.021.121.301.361.771.12
214748_atPFAAP5NEDD4 binding protein 2-like 2104431.101.201.021.172.152.482.351.431.651.26
201577_atNME1Nonmetastatic cells 1, protein (NM23A)4830−1.091.121.101.262.192.21−1.431.44−1.521.32
209064_x_atPAIP1Poly(A) binding protein interacting protein 110605−1.47−1.54−1.08−19.18−2.78−2.011.06−1.021.141.17
225842_atPHLDA1Pleckstrin homology-like domain, family A, member 122822−1.331.07−1.99−6.162.982.90−1.13−1.11−1.27−1.07
205277_atPRDM2PR domain containing 2, with ZNF domain77991.291.41−1.051.282.432.191.28−1.231.64−1.17
204900_x_atSAP30Sin3A-associated protein, 30 kDa8819−1.53−3.721.10−5.95−2.49−2.321.631.221.351.34
208991_atSTAT3Signal transducer and activator of transcription 36774−1.111.461.041.36−1.29−1.01−1.371.341.101.75
212533_atWEE1WEE1 homologue (Schizosaccharomyces pombe)7465−3.77−4.77−2.75−10.88−1.39−1.39−1.26−1.151.301.12

NOTE: Boldface indicates selection as top biomarker. Fold changes are up-regulation, except where denoted by (−) to signify down-regulation. See Materials and Methods for discussion of time points assayed.