Supplemental Table 1Pathway analysis for differentially expressed genes (≥ 2) in treated primary cells, as compared to the cells in the corresponding control culture (TREATED vs CONTROL). Significant changes in expression (≥ 2) are marked as follows: “positive value” – increase; “negative value” – reduction; “blank” – unaltered (non-significant fold changes of ≤ 2).
FOLD REGULATION (TREATED vs CONTROL)GENES / SENSITIVE RESISTANT / PATHWAY / FUNCTION
CRC-4 / CRC-2 / CRC-3 / CRC-1
TYMS / 2.8 / 2.8 / 5-FU drug metabolism / TYMS catalyzes thymidine synthesis (necessary for DNA replication and repair). 5-FU inhibits TYMS and causes disruption of nucleotide levels resulting in DNA damage. TYMS upregulation causes 5-FU resistance.
DPYD / -3.0 / -2.4 / -2.7 / 5-FU drug metabolism / DPYD rapidly degrades 5-FU to inactive compounds. DPYDupregulation causes 5-FU resistance.
TYMP / 2.3 / 5-FU drug metabolism / TYMP converts 5-FU to FdUMP (which inhibits TYMS). TYMPupregulation increases 5-FU sensitivity.
UPP1 / 2.3 / 5.0 / 5-FU drug metabolism / 5-FU is converted to FUR by UPP1. FUR is then converted to FUMP by UMPS. FUMP forms cytotoxic metabolites (dUTP and FdUTP) causing cell death (via DNA damage). UPP1upregulation increases 5-FU sensitivity.
DHFR / -2.2 / -3.4 / 5-FU drug metabolism / Converts dihydrofolate (DHF) into tetrahydrofolate (THF) which is required for thymidine synthesis. Increased DHFR increases 5-FU resistance.
ERCC1 / -2.1 / L-OHP drug metabolism / DNA repair / DNA repair (Nucleotide excision repair) gene. ERCC1upregulation causes L-OHP resistance.
ERCC2 / -2.0 / L-OHP drug metabolism / DNA repair / DNA repair (Nucleotide excision repair) gene. ERCC2 upregulation causes L-OHP resistance.
ERCC4 / 3.1 / L-OHP drug metabolism / DNA repair / DNA repair (Nucleotide excision repair) gene. ERCC4upregulation causes L-OHP resistance.
BAX / 2.1 / 2.7 / Apoptosis / Accelerates apoptosis. BAXupregulation increases drug sensitivity.
BCL2 / -3.0 / -2.4 / Apoptosis / Suppresses apoptosis. BCL2upregulation causes drug resistance.
BCL2L1 / 5.6 / Apoptosis / Anti-apoptotic gene. Potent inhibitor of cell death. Inhibits activation of caspases. BCL2L1upregulation causes drug resistance.
BAD / 2.8 / Apoptosis / Promotes cell death. Reverse the death repressor activity of BCL2L1. BADupregulation increases drug sensitivity.
FAS / 2.9 / 2.2 / Apoptosis / Receptor for FASLG. p53-dependent apoptotic promoter. FAS upregulation increases drug sensitivity.
FASLG / 2.8 / Apoptosis / Cytokine that binds to FAS, a receptor that transduces the apoptotic signal into cells. FASLGupregulation increases drug sensitivity.
TNFRSF10A / 2.3 / 3.8 / Apoptosis / Receptor for the cytotoxic TRAILligand; transmits intracellular death signal on ligand binding in TRAIL pathway. TNFRSF10Aupregulation increases drug sensitivity.
TNFRSF10B / 2.0 / Apoptosis / Receptor for the cytotoxic TRAIL ligand; transmits intracellular death signal on ligand binding in TRAIL pathway. TNFRSF10Bupregulation increases drug sensitivity.
TNF / 2.6 / Apoptosis / Cytokine that binds to TNFR1 and TNFBR; transduces the apoptotic signal into cells. TNF upregulation increases drug sensitivity.
MSH3 / -2.5 / DNA repair / DNA repair (Mismatch repair) gene. MSH3upregulation causes drug resistance.
XPC / 2.2 / 2.5 / 3.4 / L-OHP drug metabolism / DNA repair / DNA repair (Nucleotide excision repair) gene. XPC upregulation causes L-OHP resistance.
ERCC3 / 2.3 / L-OHP drug metabolism / DNA repair / DNA repair (Nucleotide excision repair) gene. ERCC3upregulation causes L-OHP resistance.
UNG / 2.1 / DNA repair / DNA repair (Base excision repair) gene. UNGupregulation causes drug resistance.
CDKN1A / 2.8 / 3.0 / 8.2 / 6.8 / Cell cycle / Intermediate of p53 pathway. May act as a defense mechanism in response to DNA damage.
CCND1 / -2.2 / -5.0 / 5.3 / Cell cycle / CDK inhibitor; regulates cell cycle during G1/S transition; CCND1 is reduced during S-phase and increases during G2 phase (if cell cycle continues)
CDK1 / -20.3 / -7.4 / -5.9 / -111.4 / Cell cycle / Promotes G2-M transition, and regulates G1 progress and G1-S transition via association with multiple interphasecyclins. Required in higher cells for entry into S-phase and mitosis. Reduced CDK1 causes G2 arrest and prevents apoptosis indirectly.
CDKN2A / 2.7 / -3.8 / Cell cycle / Negative regulator of cell proliferation; by interacting with CDK4 and CDK6 and inhibits their ability to interact with cyclins D. Increased CDKN2A leads to reduced cyclin expression and inactivation of cyclin D; causes G1 arrest. Reduced CDKN2A leads to increased cell proliferation
CCNA2 / -2.4 / -4.5 / -2.7 / -15.9 / Cell cycle / Essential for the control of the cell cycle at the G1/S (start) and the G2/M (mitosis) transitions. CDKN1A inhibits the activity of cyclin A/CDK2 (required for G1/S transition); leading to G1 arrest.
CCNB2 / -6.7 / -2.0 / -4.1 / -20.9 / Cell cycle / Essential for the control of the cell cycle at the G2/M (mitosis) transition.
GADD45A / 2.1 / 3.6 / 5.3 / 4.3 / Cell cycle / Involved in growth arrest and DNA damage mediated by p53.
ABCB1 / -14.3 / -3.8 / -69.0 / Drug transporters / Drug efflux transporters. ABCB1upregulation causes drug resistance.
ABCC1 / -2.1 / -2.8 / Drug transporters / Drug efflux transporters. ABCC1upregulation causes drug resistance.
ABCC2 / -3.5 / -3.9 / Drug transporters / Drug efflux transporters. ABCC2upregulation causes drug resistance.
ABCG2 / -2.4 / -3.8 / -5.7 / Drug transporters / Drug efflux transporters. ABCG2upregulation causes drug resistance.
ATP7A / -2.0 / L-OHP drug metabolism / Drug transporters / Drug efflux transporters. ATP7Aupregulation causes L-OHP resistance.
ATP7B / -2.0 / 4.3 / L-OHP drug metabolism / Drug transporters / Drug efflux transporters. ATP7Bupregulation causes L-OHP resistance.
SLC22A7 / 2.8 / Drug transporters / Drug influx transporters. SLC22A7upregulation increases drug sensitivity.
NFKBIE / 2.2 / 2.3 / Transcription factor / Inhibits NF-kappa-B activity. NFKBIEupregulation increases drug sensitivity.
FOS / 3.9 / 2.4 / 5.0 / Signal transduction / Positive growth regulator. Regulates ERCC1. FOS upregulation causes drug resistance
RAF1 / 2.0 / Signal transduction / Acts as a regulatory link determining cell fate decisions (i.e. proliferation, differentiation, apoptosis, survival and oncogenic transformation). Protect cells from apoptosis by translocating to the mitochondria where it binds BCL2 and displaces BAD/Bcl2-antagonist of cell death; restricts caspase activation. RAF1upregulation causes drug resistance.
SMAD3 / -2.5 / -3.2 / Signal transduction / Receptor-regulated SMAD; acts as an intracellular signal transducer and transcriptional modulator activated by TGF-beta. Formation of the SMAD3/SMAD4 complex activates transcription. Forms a SMAD3/SMAD4/JUN/FOS complex to regulate TGF-beta-mediated transcription. Downregulation of SMAD3 decreases apoptosis and increases drug resistance.
ZEB1 / -2.5 / EMT transition / Acts as a transcriptional repressor. Represses E-cadherin promoter and induces an epithelial-mesenchymal transition (EMT)
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