Table 2. Relative-Quantitation Proteomics Analysis of Protein Expression Changes with 12-D3NVP Treatment, as Compared to NVP, of Cryopreserved Human Hepatocytesa.
| changes
with 12-D3NVP treatment (in comparison to NVP) | ||||
|---|---|---|---|---|
| UniProt accession | UniProt entry | gene name | fold change | P value |
| Q16540 | 39S ribosomal protein L23, mitochondrial | MRPL23 | 8.32 ± 2.21 | 0.0159 |
| Q8Nl60 | atypical kinase ADCK3, mitochondrial | COQ8A | 1.95 ± 0.2 | 0.0168 |
| Q9HA77 | probable cysteine-tRNA ligase, mitochondrial | CARS2 | 1.85 ± 0.2 | 0.0041 |
| Q14498 | RNA-binding protein 39 | RBM39 | 1.7 ± 0.2 | 0.0339 |
| Q9Y2H5 | pleckstrin homology domain-containing family A member 6 | PLEKHA6 | 1.59 ± 0.05 | 0.0188 |
| Q8lYS2 | isoform 2 of uncharacterized protein KlAA2013 | KlAA2013 | 1.36 ± 0.01 | 0.0051 |
| P60709 | actin, cytoplasmic 1 | ACTB | –1.09 ± 0.19 | 0.4937 |
| P04406 | glyceraldehyde-3-phosphate dehydrogenase | GAPDH | –1.35 ± 0.16 | 0.1836 |
| P34897 | serine hydroxymethyltransferase, mitochondrial | SHMT2 | –1.28 ± 0.05 | 0.0225 |
| P08574 | cytochrome c1, heme protein, mitochondrial | CYC1 | –1.4 ± 0.09 | 0.0478 |
| Q15046 | isoform mitochondrial of lysine-tRNA ligase | KARS | –1.42 ± 0.06 | 0.0490 |
| Q96l24 | far upstream element-binding protein 3 | FUBP3 | –1.47 ± 0.03 | 0.0198 |
| P00167 | cytochrome b5 | CYB5A | –1.5 ± 0.11 | 0.0361 |
| Q13438 | protein os-9 | OS9 | –1.53 ± 0.09 | 0.0187 |
| Q9Y315 | deoxyribose-phosphate aldolase | DERA | –1.63 ± 0.06 | 0.0229 |
| Q4G176 | Acyl-CoA synthetase family member 3, mitochondrial | ACSF3 | –1.63 ± 0.09 | 0.0278 |
| P82979 | SAP domain-containing ribonucleoprotein | SARNP | –1.65 ± 0.07 | 0.0043 |
| O75431 | metaxin-2 | MTX2 | –1.67 ± 0.09 | 0.0465 |
| Q9H6R4 | nucleolar protein 6 | NOL6 | –1.85 ± 0.12 | 0.0121 |
| P13716 | isoform 2 of delta-aminolevulinic acid dehydratase | ALAD | –1.86 ± 0.08 | 0.0467 |
| O15321 | transmembrane 9 superfamily member 1 | TM9SF1 | –1.86 ± 0.08 | 0.0366 |
| P10635 | cytochrome P450 2D6 | CYP2D6 | –1.92 ± 0.07 | 0.0317 |
| Q9BVK6 | transmembrane emp24 domain-containing protein 9 | TMED9 | –1.93 ± 0.14 | 0.0218 |
| Q8N163 | cell cycle and apoptosis regulator protein 2 | CCAR2 | –2.05 ± 0.09 | 0.0164 |
| Q9UJ68 | mitochondrial peptide methionine sulfoxide reductase | MSRA | –2.05 ± 0.14 | 0.0358 |
| P11712 | cytochrome P450 2C9 | CYP2C9 | –2.06 ± 0.16 | 0.0498 |
| Q9NYL9 | tropomodulin-3 | TMOD3 | –2.1 ± 0.01 | 0.0356 |
| Q93096 | protein tyrosine phosphatase type IVA 1 | PTP4A1 | –2.42 ± 0.17 | 0.0466 |
| Q9Y2D5 | isoform 2 of A-kinase anchor protein 2 | AKAP2 | –2.67 ± 0.06 | 0.0249 |
| Q9Y3B2 | exosome complex component csl4 | EXOSC1 | –2.73 ± 0.09 | 0.0086 |
Cryopreserved pooled-donor (10, mixed-sex) primary human hepatocytes were treated for 48 h with 10 μM NVP or 12-D3NVP. Cell lysate was then prepared and subjected to Top10 nanoLC-MS-based proteomics with data analysis performed in Proteome Discoverer 2.1, using Sequest HT for peptide spectral matching/protein identification and precursor ion area detection for relative quantitation. Up to 10 unique or razor peptides were used in protein precursor ion-based quantitation. Statistically significant relative-quantitation changes are shown for treatment with 12-D3NVP as compared to NVP as well as the results for housekeeping proteins actin and GAPDH. UniProt proteome Homo sapiens9606 was used for protein identification profiling, with UniProt accession numbers, protein entry (protein name), and gene name’s provided. P values were generated using an unpaired t test, and the effect size was calculated using Cohen’s d equation. Data are representative of experiments with three different 10-donor pools of hepatocytes.