Table 1 Transcripts that are commonly changed by WD, aging, and FXR KO are associated with the overall survival rate in HCC patients (p value < 0.05). The “high” and “low” expression was defined as the upper and lower quartiles of expression for each gene (n = 108, 50% as a cutoff for both lower and upper quartiles)
Gene | Full Name | HCC vs. Normal WD vs. CD 15 vs. 5 FXR KO vs. WT | Association | Function |
|---|---|---|---|---|
PLEKHH1 | pleckstrin homology, MyTH4 and FERM domain containing H1 | Up | Unfavored | Unknown |
TTC39A | tetratricopeptide repeat domain 39A | Up | Unfavored | Unknown |
ATP6V0D2 | ATPase H+ transporting V0 subunit d2 | Up | Unfavored | It is a subunit of the integral membrane V0 complex of vacuolar ATPase which is responsible for acidifying a variety of intracellular compartments in eukaryotic cells, thus providing most of the energy required for transport processes in the vacuolar system. Regulator of osteoclast fusion and bone formation |
CENPE | centrosome-associated protein E | Up | Unfavored | Microtubule motor activity |
KIF20A | kinesin family member 20A | Up | Unfavored | Microtubule motor activity |
ASPM | abnormal spindle microtubule assembly | Up | Unfavored | Involved in mitotic spindle regulation and coordination of mitotic processes (36) |
CKAP2L | cytoskeleton associated protein 2 like | Up | Unfavored | Microtubule-associated protein required for mitotic spindle formation and cell-cycle progression in neural progenitor cells |
HMMR | hyaluronan mediated motility receptor | Up | Unfavored | Involved in cell motility (30) |
ECT2 | epithelial cell transforming 2 | Up | Unfavored | A guanine nucleotide exchange factor and transforming protein that is related to Rho-specific exchange factors and yeast cell cycle regulators (34) |
TOP2A | DNA topoisomerase II alpha | Up | Unfavored | A DNA topoisomerase, an enzyme that controls and alters the topologic states of DNA during transcription (33) |
KIF18B | kinesin family member 18B | Up | Unfavored | Mitotic cell cycle; Microtubule motor activity; Protein binding; ATP binding; Kinesin binding (32) |
TPX2 | TPX2 microtubule nucleation factor | Up | Unfavored | Apoptotic process; Mitotic nuclear division; Cell proliferation; Activation of protein kinase activity; Regulation of Mitotic spindle organization (28) |
NUF2 | NUF2 component of NDC80 kinetochore complex | Up | Unfavored | A component of a conserved protein complex associated with the centromere (31) |
TRIM59 | tripartite motif containing 59 | Up | Unfavored | Negative regulation of I-kappaB kinase/NF-kappaB signaling (27) |
FRZB | frizzled related protein | Up | Unfavored | Negative regulation of cell proliferation; Negative regulation of the Wnt signaling pathway |
E2F8 | E2F transcription factor 8 | Up | Unfavored | Regulates progression from G1 to S phase by ensuring the nucleus divides at the proper time (35) |
TREM2 | triggering receptor expressed on myeloid cells 2 | Up | Unfavored | Functions in immune response and may be involved in chronic inflammation by triggering the production of constitutive inflammatory cytokines |
MTHFD1L | methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1 like | Up | Unfavored | Involved in the synthesis of tetrahydrofolate (THF) in the mitochondrion. THF is important in the de novo synthesis of purines and thymidylate and in the regeneration of methionine from homocysteine. |
PCK1 | phosphoenolpyruvate carboxykinase 1 | Down | Favored | A main control point for the regulation of gluconeogenesis (37) |
TSC22D3 | TSC22 domain family member 3 | Down | Favored | Function as transcriptional regulators in the anti-inflammatory and immunosuppressive effects of this steroid and chemokine |
SLC22A7 | solute carrier family 22 member 7 | Down | Favored | Involved in the sodium-independent transport and excretion of organic anions, some of which are potentially toxic. |
CYP2U1 | cytochrome p450 family 2 subfamily U member 1 | Down | Favored | Xenobiotic metabolic process; Cell death; Arachidonic acid metabolic process |
SARDH | sarcosine dehydrogenase | Down | Favored | An enzyme localized to the mitochondrial matrix which catalyzes the oxidative demethylation of sarcosine |
TTC36 | tetratricopeptide repeat domain 36 | Down | Favored | May function as a tumor suppressor in hepatocellular carcinoma (HCC) since it promotes apoptosis but is downregulated in HCC. |
APOC1 | apolipoprotein C1 | Down | Favored | High-density lipoprotein and very low-density lipoprotein metabolism; Inhibits cholesteryl ester transfer protein in plasma |