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Table 2 Lists of genes significantly altered by exposure to pristine CeO 2 (Part A), NB-DA (Part B) and NB-DL (Part C), and belonging to the canonical pathway “mitochondrial dysfunction”

From: Toxicity evaluation of manufactured CeO2 nanoparticles before and after alteration: combined physicochemical and whole-genome expression analysis in Caco-2 cells

Part A: genes altered by pristine CeO2 (n = 27)
Symbol Entrez Gene Name Fold Change p-value ID Agilent
ATP5J ATP synthase, H + transporting, mitochondrial F0 complex, subunit F6 −1,935 8,67E-03 A_23_P154832
COX4I1 cytochrome c oxidase subunit IV isoform 1 −2,313 4,97E-03 A_23_P141029
COX5B cytochrome c oxidase subunit Vb −2,312 4,98E-03 A_23_P51069
COX6A1 cytochrome c oxidase subunit VIa polypeptide 1 −2,312 4,99E-03 A_32_P168247
COX6B1 cytochrome c oxidase subunit VIb polypeptide 1 (ubiquitous) −2,306 4,87E-03 A_23_P108244
COX6C cytochrome c oxidase subunit VIc −2,088 3,08E-03 A_23_P8900
COX7A2 cytochrome c oxidase subunit VIIa polypeptide 2 (liver) −2,311 4,99E-03 A_23_P81690
COX7C cytochrome c oxidase subunit VIIc −2,312 4,99E-03 A_23_P110811
COX8A cytochrome c oxidase subunit 8A (ubiquitous) −2,312 5,00E-03 A_23_P52639
CYB5R3 cytochrome b5 reductase 3 −2,312 4,99E-03 A_23_P502224
NDUFA3 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 3, 9 kDa −2,052 4,57E-03 A_23_P208540
NDUFA4 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4, 9 kDa −2,312 4,98E-03 A_23_P145777
NDUFA6 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 6, 14 kDa −2,037 6,10E-03 A_23_P91769
NDUFA8 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 8, 19 kDa −2,200 4,97E-03 A_23_P43566
NDUFB2 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 2, 8 kDa −2,175 2,93E-03 A_24_P406301
NDUFB4 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 4, 15 kDa −2,301 4,77E-03 A_23_P69468
NDUFB8 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 8, 19 kDa −1,963 4,31E-03 A_24_P346886
NDUFB9 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 9, 22 kDa −2,311 4,99E-03 A_23_P157669
NDUFS2 NADH dehydrogenase (ubiquinone) Fe-S protein 2, 49 kDa (NADH-coenzyme Q reductase) −1,561 5,68E-04 A_23_P149470
NDUFS5 NADH dehydrogenase (ubiquinone) Fe-S protein 5, 15 kDa (NADH-coenzyme Q reductase) −2,311 4,98E-03 A_23_P10463
NDUFS7 NADH dehydrogenase (ubiquinone) Fe-S protein 7, 20 kDa (NADH-coenzyme Q reductase) −2,079 3,89E-03 A_23_P165086
NDUFS8 NADH dehydrogenase (ubiquinone) Fe-S protein 8, 23 kDa (NADH-coenzyme Q reductase) −1,904 7,63E-03 A_23_P86774
NDUFV1 NADH dehydrogenase (ubiquinone) flavoprotein 1, 51 kDa −1,704 1,08E-02 A_23_P127353
OGDH oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide) −1,513 3,02E-03 A_23_P123133
PRDX5 peroxiredoxin 5 −1,946 5,32E-03 A_24_P155378
UQCRFS1 ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1 −2,031 3,93E-03 A_23_P153586
UQCRH ubiquinol-cytochrome c reductase hinge protein −2,312 4,99E-03 A_32_P54137
Part B: genes altered by NB-DA (n = 10)
Symbol Entrez Gene Name Fold Change p-value ID Agilent
ATP5B ATP synthase, H + transporting, mitochondrial F1 complex, beta polypeptide −1,575 2,48E-02 A_23_P33216
ATP5C1 ATP synthase, H + transporting, mitochondrial F1 complex, gamma polypeptide 1 −1,525 3,84E-02 A_23_P63655
COX6A2 cytochrome c oxidase subunit VIa polypeptide 2 −2,028 4,43E-02 A_23_P401524
COX6B2 cytochrome c oxidase subunit VIb polypeptide 2 (testis) −1,522 2,45E-02 A_23_P78571
CYCS cytochrome c, somatic −1,674 3,09E-02 A_24_P376556
NDUFA5 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 5, 13 kDa −1,815 2,45E-02 A_32_P96641
PRDX3 peroxiredoxin 3 −2,65 2,51E-02 A_23_P63751
PSEN2 presenilin 2 (Alzheimer disease 4) −1,647 2,98E-02 A_23_P96985
SDHB succinate dehydrogenase complex, subunit B, iron sulfur (Ip) −1,646 2,46E-02 A_23_P149649
SDHD succinate dehydrogenase complex, subunit D, integral membrane protein −1,841 2,39E-02 A_23_P138967
Part C: genes altered by NB-DL (n = 3)
Symbol Entrez Gene Name Fold Change p-value ID Agilent
COX11 COX11 cytochrome c oxidase assembly homolog (yeast) −1,723 3,28E-02 A_24_P404204
SDHC succinate dehydrogenase complex, subunit C, integral membrane protein, 15 kDa −2,264 3,53E-02 A_24_P233850
SDHD succinate dehydrogenase complex, subunit D, integral membrane protein −2,03 4,62E-02 A_32_P60185
  1. Although the same pathway is activated, there are, stricto sensu, no common genes altered by pristine CeO2 and NB-DA or NB-DL in the mitochondrial dysfunction pathway. This demonstrates the interest of a pathway-driven analysis compared to the usual gene-driven analysis.