Supplementary Table 2.Differentially expressed genes (ANOVA p≤0.05 and 1.5-fold cutoff) between Post-treatment Failures and Complete Responders associated with specific categories of: “Genome Stability/Genetic Instability/Genome Instability,” “Mitosis/Cell Cycle,” and “DNA Damage/DNA Repair.”

Genome Stability/Genetic Instability/Genome Instability

Gene Symbol / Gene Name / P-t Fail vs. CR
ARHGAP1 / Rho GTPase activating protein 1 / 1.50
ATMIN / ATM interactor / 1.53
BARD1 / BRCA1 associated RING domain 1 / -1.60
CCNB1 / cyclin B1 / -2.05
FANCD2 / Fanconi anemia, complementation group D2 / -1.75
FBXO5 / F-box protein 5 / -1.73
FEN1 / flap structure-specific endonuclease 1 / -1.67
H2AFZ / H2A histone family, member Z / -1.78
HIF1A / hypoxia inducible factor 1, alpha subunit / 1.82
HMOX1 / hemeoxygenase (decycling) 1 / 2.99
MCM2 / minichromosome maintenance complex component 2 / -2.65
MCM3 / minichromosome maintenance complex component 3 / -1.74
MCM4 / minichromosome maintenance complex component 4 / -2.06
MCM6 / minichromosome maintenance complex component 6 / -2.02
MECOM / MDS1 and EVI1 complex locus / -2.08
MSH6 / mutS homolog 6 (E. coli) / -1.68
MYB / v-mybmyeloblastosis viral oncogene homolog (avian) / -1.71
PARP1 / poly (ADP-ribose) polymerase 1 / -1.57
PCNA / proliferating cell nuclear antigen / -1.72
PTEN / phosphatase and tensin homolog / 1.95
PTTG1 / pituitary tumor-transforming 1 / -2.08
RAD51 / RAD51 homolog (RecA homolog, E. coli) (S. cerevisiae) / -1.68
RAD51AP1 / RAD51 associated protein 1 / -1.78
RAD54B / RAD54 homolog B (S. cerevisiae) / -1.58
SGOL1 / shugoshin-like 1 (S. pombe) / -1.96
TTK / TTK protein kinase / -1.79

Mitosis/Cell Cycle

Gene Symbol / Gene Name / P-t Fail vs. CR
AGR2 / anterior gradient homolog 2 (Xenopuslaevis) / -2.23
ARRB1 / arrestin, beta 1 / 2.63
ATMIN / ATM interactor / 1.53
BARD1 / BRCA1 associated RING domain 1 / -1.60
CASP9 / caspase 9, apoptosis-related cysteine peptidase / -1.58
CCNB1 / cyclin B1 / -2.05
CENPF / centromere protein F, 350/400ka (mitosin) / -2.10
CYP24A1 / cytochrome P450, family 24, subfamily A, polypeptide 1 / -4.19
DCUN1D3 / DCN1, defective in cullinneddylation 1, domain containing 3 (S. cerevisiae) / 2.02
DTL / denticleless homolog (Drosophila) / -2.75
EFHD2 / EF-hand domain family, member D2 / -1.70
FANCD2 / Fanconi anemia, complementation group D2 / -1.75
FBXO5 / F-box protein 5 / -1.73
FEN1 / flap structure-specific endonuclease 1 / -1.67
GAB2 / GRB2-associated binding protein 2 / 2.00
H2AFZ / H2A histone family, member Z / -1.78
HES1 / hairy and enhancer of split 1, (Drosophila) / -1.65
HIF1A / hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor) / 1.82
HJURP / Holliday junction recognition protein / -1.58
HMOX1 / hemeoxygenase (decycling) 1 / 2.99
ING4 / inhibitor of growth family, member 4 / -1.51
ITGA2 / integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor) / -2.26
KRT18 / keratin 18 / -1.71
KRT19 / keratin 19 / -3.13
LAPTM4B / lysosomal protein transmembrane 4 beta / -2.01
LIN9 / lin-9 homolog (C. elegans) / -1.54
LMNB1 / lamin B1 / -1.89
LRIG1 / leucine-rich repeats and immunoglobulin-like domains 1 / -1.83
MAP3K3 / mitogen-activated protein kinase kinasekinase 3 / 1.53
MCM2 / minichromosome maintenance complex component 2 / -2.65
MCM3 / minichromosome maintenance complex component 3 / -1.74
MCM4 / minichromosome maintenance complex component 4 / -2.06
MCM6 / minichromosome maintenance complex component 6 / -2.02
MDK / midkine (neurite growth-promoting factor 2) / -3.47
MECOM / MDS1 and EVI1 complex locus / -2.08
METAP1 / methionylaminopeptidase 1 / -1.60
MLF1 / myeloid leukemia factor 1 / -1.92
MSH6 / mutS homolog 6 (E. coli) / -1.68
MSR1 / macrophage scavenger receptor 1 / 2.66
MYB / v-mybmyeloblastosis viral oncogene homolog (avian) / -1.71
MYO5A / myosin VA (heavy chain 12, myoxin) / 2.10
NCAPH / non-SMC condensin I complex, subunit H / -1.79
NDEL1 / nudE nuclear distribution gene E homolog (A. nidulans)-like 1 / 1.59
NEK2 / NIMA (never in mitosis gene a)-related kinase 2 / -1.87
NOX4 / NADPH oxidase 4 / 1.59
NUF2 / NUF2, NDC80 kinetochore complex component, homolog (S. cerevisiae) / -1.69
NUP155 / nucleoporin 155kDa / -1.62
NUP210 / nucleoporin 210kDa / -2.22
OIP5 / Opa interacting protein 5 / -1.68
PARP1 / poly (ADP-ribose) polymerase 1 / -1.57
PCNA / proliferating cell nuclear antigen / -1.72
PEG10 / paternally expressed 10 / -2.13
PER1 / period homolog 1 (Drosophila) / 1.62
PKIA / protein kinase (cAMP-dependent, catalytic) inhibitor alpha / -1.98
PLD2 / phospholipase D2 / 1.67
PTEN / phosphatase and tensin homolog / 1.95
PTTG1 / pituitary tumor-transforming 1 / -2.08
RAD51 / RAD51 homolog (RecA homolog, E. coli) (S. cerevisiae) / -1.68
RAD51AP1 / RAD51 associated protein 1 / -1.78
RAD54B / RAD54 homolog B (S. cerevisiae) / -1.58
RASSF3 / Ras association (RalGDS/AF-6) domain family member 3 / 1.71
RBBP8 / retinoblastoma binding protein 8 / -1.69
RPA2 / replication protein A2, 32kDa / -1.65
SESN3 / sestrin 3 / 2.15
SGOL1 / shugoshin-like 1 (S. pombe) / -1.96
SMC2 / structural maintenance of chromosomes 2 / -1.80
SSBP2 / single-stranded DNA binding protein 2 / -1.77
STMN1 / stathmin 1 / -1.81
TFDP2 / transcription factor Dp-2 (E2F dimerization partner 2) / -1.94
TK1 / thymidine kinase 1, soluble / -1.82
TPPP3 / tubulin polymerization-promoting protein family member 3 / -3.49
TTK / TTK protein kinase / -1.79
UHMK1 / U2AF homology motif (UHM) kinase 1 / -1.53

DNA Damage/DNA Repair

Gene Symbol / Gene Name / P-t Fail vs. CR
ADARB1 / adenosine deaminase, RNA-specific, B1 / 2.04
ARHGAP1 / Rho GTPase activating protein 1 / 1.50
ATMIN / ATM interactor / 1.53
BARD1 / BRCA1 associated RING domain 1 / -1.60
CASP9 / caspase 9, apoptosis-related cysteine peptidase / -1.58
CCNB1 / cyclin B1 / -2.05
CDA / cytidinedeaminase / 2.52
DTL / denticleless homolog (Drosophila) / -2.75
FANCD2 / Fanconi anemia, complementation group D2 / -1.75
FBXO5 / F-box protein 5 / -1.73
FEN1 / flap structure-specific endonuclease 1 / -1.67
H2AFZ / H2A histone family, member Z / -1.78
HIF1A / hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor) / 1.82
HJURP / Holliday junction recognition protein / -1.58
HMOX1 / hemeoxygenase (decycling) 1 / 2.99
ING4 / inhibitor of growth family, member 4 / -1.51
LAPTM4B / lysosomal protein transmembrane 4 beta / -2.01
LMNB1 / lamin B1 / -1.89
MCM2 / minichromosome maintenance complex component 2 / -2.65
MSH6 / mutS homolog 6 (E. coli) / -1.68
NOX4 / NADPH oxidase 4 / 1.59
PARP1 / poly (ADP-ribose) polymerase 1 / -1.57
PCNA / proliferating cell nuclear antigen / -1.72
PMAIP1 / phorbol-12-myristate-13-acetate-induced protein 1 / -2.27
PTEN / phosphatase and tensin homolog / 1.95
PTTG1 / pituitary tumor-transforming 1 / -2.08
RAD51 / RAD51 homolog (RecA homolog, E. coli) (S. cerevisiae) / -1.68
RAD51AP1 / RAD51 associated protein 1 / -1.78
RAD54B / RAD54 homolog B (S. cerevisiae) / -1.58
RBBP8 / retinoblastoma binding protein 8 / -1.69
RPA2 / replication protein A2, 32kDa / -1.65
TK1 / thymidine kinase 1, soluble / -1.82
TRIP13 / thyroid hormone receptor interactor 13 / -1.93
TTK / TTK protein kinase / -1.79
YEATS4 / YEATS domain containing 4 / -1.70