| Literature DB >> 30105281 |
L J Britton1,2,3,4, Kim Bridle1,2, Lesley-Anne Jaskowski1,2, Jingjing He4, Choaping Ng4,5, Jayde E Ruelcke6, Ahmed Mohamed6,7, Janske Reiling1,2,8, Nishreen Santrampurwala1,2, Michelle M Hill6,7, Jonathan P Whitehead4,5, V Nathan Subramaniam9, Darrell H G Crawford1,2.
Abstract
Entities:
Keywords: ApoE, apolipoprotein E; FAC, ferric ammonium citrate; KO, knockout; NASH, nonalcoholic steatohepatitis; SGBS, Simpson-Golabi-Behmel Syndrome; SILAC, stable isotope labeled amino acids in cell culture; mRNA, messenger RNA
Mesh:
Substances:
Year: 2018 PMID: 30105281 PMCID: PMC6085534 DOI: 10.1016/j.jcmgh.2018.04.005
Source DB: PubMed Journal: Cell Mol Gastroenterol Hepatol ISSN: 2352-345X
Supplementary Figure 1Optimization of iron loading in SGBS cells. (A) Iron assay, P = .004 (1-way analysis of variance [ANOVA]), *P < .01 (Dunnett multiple comparisons test compared with 0 μmol/L FAC, n = 2 per group). (B) Total RNA (P = NS by 1-way ANOVA, N = 3 per group). (C) Total lysate protein (P = NS by 1-way ANOVA, n = 3 per group). (D) Total secretome protein (P = NS by 1-way ANOVA, N = 3 per group). (E) Viability assay (MTS) (P = NS by 1-way ANOVA, N = 3 per group). Data are presented as means and SEM. MTS, [3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium].
Supplementary Figure 2Volcano plot of relative signal intensity of proteins identified in the adipocyte secretome. The x-axis denotes log2 of the ratio of iron/vehicle-treated cells, with proteins to the left of zero representing those down-regulated by iron and those to the right representing up-regulation by iron. The y-axis denotes statistical significance with a line representing a P value of .05. Proteins above this line have a P value <.05. SILAC-labeled adipocytes generated 338 proteins that were identified in the secretome by mass spectrometry. Of these, 213 had reduced signal intensity in response to iron, whereas 125 had increased signal intensity. Of the 213 proteins with reduced signal intensity, 61 had a statistically significant (P < .05) down-regulation in response to iron. Of these, 53 had a greater than 2-fold decrease in response to iron. Of the 125 proteins with increased signal intensity, 11 had a statistically significant (P < .05) up-regulation in response to iron. Of these, 7 proteins had a greater than 2-fold increase response to iron. Those proteins containing signal peptide (as determined by signal peptide annotations on the UniProt database) are shown in red. Those without signal peptide are shown in blue.
List of SGBS Secretome Proteins With Significantly Altered Signal Intensity in Response to Iron
| Accession number | Gene name | Protein name | Mean signal intensity ratio, iron/vehicle | SD | |
|---|---|---|---|---|---|
| P61353 | 60S ribosomal protein L27 | 0.060 | 0.005 | .001 | |
| Q9NQH7 | Probable Xaa-Pro aminopeptidase 3 | 0.076 | 0.004 | .001 | |
| Q76M96 | Coiled-coil domain-containing protein 80 | 0.090 | 0.031 | .001 | |
| P78539 | Sushi repeat-containing protein SRPX | 0.096 | 0.620 | .001 | |
| Q9UHI8 | A disintegrin and metalloproteinase with thrombospondin motifs 1 | 0.114 | 0.090 | .002 | |
| Q92538 | Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 | 0.118 | 0.024 | .004 | |
| P08238 | Heat shock protein (HSP) 90-β | 0.125 | 0.038 | .004 | |
| Q15113 | Procollagen C-endopeptidase enhancer 1 | 0.155 | 0.088 | .001 | |
| Q9NTX5 | Ethylmalonyl-CoA decarboxylase | 0.158 | 0.068 | .001 | |
| P25788 | Proteasome subunit α type 3 | 0.176 | 0.442 | .001 | |
| Q12931 | Heat shock protein 75 kilodaltons, mitochondrial | 0.186 | 0.028 | .018 | |
| P30101 | Protein disulfide-isomerase A3 | 0.198 | 0.059 | .001 | |
| Q6NZI2 | Polymerase I and transcript release factor | 0.210 | 0.134 | .001 | |
| Q8TAV4 | Stomatin-like protein 3 | 0.220 | 0.084 | .006 | |
| Q9UKZ9 | Procollagen C-endopeptidase enhancer 2 | 0.226 | 0.030 | .001 | |
| Q05469 | Hormone-sensitive lipase | 0.231 | 0.196 | .023 | |
| Q13642 | Four and a half LIM domains protein 1 | 0.263 | 0.006 | .029 | |
| P02749 | β2-glycoprotein 1 | 0.286 | 0.310 | .048 | |
| P02462 | Collagen α-1(IV) chain | 0.286 | 0.351 | .001 | |
| P15311 | Ezrin | 0.296 | 0.077 | .003 | |
| P42765 | 3-Ketoacyl-CoA thiolase, mitochondrial | 0.308 | 0.136 | .001 | |
| Q8IY17 | Neuropathy target esterase | 0.316 | 0.028 | .026 | |
| Q92743 | Serine protease HTRA1 | 0.324 | 0.075 | .001 | |
| Q16836 | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 0.348 | 0.207 | .011 | |
| Q99715 | Collagen α-1(XII) chain | 0.348 | 0.183 | .001 | |
| P26038 | Moesin | 0.362 | 0.110 | .034 | |
| P23284 | Peptidyl-prolyl cis-trans isomerase B | 0.374 | 0.122 | .001 | |
| O94769 | Extracellular matrix protein 2 | 0.375 | 0.060 | .005 | |
| Q16363 | Laminin subunit α-4 | 0.407 | 0.091 | .001 | |
| Q9BU40 | Chordin-like protein 1 | 0.419 | 0.264 | .001 | |
| O75390 | Citrate synthase, mitochondrial | 0.454 | 0.183 | .012 | |
| Q92626 | Peroxidasin homolog | 0.457 | 0.200 | .001 | |
| P07942 | Laminin subunit β1 | 0.484 | 0.110 | .001 | |
| Q08629 | Testican-1 | 0.497 | 0.055 | .014 | |
| O00462 | β-mannosidase | 2.180 | 2.560 | .034 | |
| Q13510 | Acid ceramidase | 2.222 | 3.135 | .048 | |
| Q02952 | A-kinase anchor protein 12 | 2.665 | 0.572 | .047 | |
| A6NCN2 | Putative keratin-87 protein | 4.113 | 0.011 | .022 | |
| P23468 | Receptor-type tyrosine-protein phosphatase δ | 10.687 | 2.199 | .003 | |
| P10586 | Receptor-type tyrosine-protein phosphatase F | 11.935 | 3.955 | .001 |
NOTE. Proteins shown had a greater than 2-fold change in signal intensity in response to iron, with P < .05. Proteins highlighted in bold represent the 20 proteins of interest after review of the UniProt protein descriptions. Data were analyzed using the online Quantitative Proteomics P value Calculator using no normalization and nonadjusted P values (N = 3 per group).
CUB, C1r/C1s, Uegf, bone morphogenetic protein-1; EGF, epidermal growth factor; HTRA, High-Temperature Requirement A.
Figure 1SGBS ApoE expression after FAC treatment. (A) ApoE mRNA (P = NS, ratio paired t test), (B) secretome ApoE densitometry (*P = .001, ratio paired t test), (C) lysate ApoE densitometry normalized to β-actin (#P = .0005, ratio paired t test), (D) secretome ApoE immunoblot, and (E) whole-cell lysate ApoE and β-actin immunoblots (N = 3 per group). Data are presented as means and SEM.
Supplementary Figure 3Mechanistic aspects of iron-related dysregulation of protein secretion. (A) Interleukin 6 (IL6) mRNA (P = NS, paired t test, N = 3 per group). (B and C) Oxidative stress (*P < .05, both N = 3 per group). (B) Heme-oxygenase (HO-1) mRNA (P = .01, paired t test). (C) Glutathione peroxidase 1 (GPX1) mRNA (P = .049, paired t test). (D–I) Endoplasmic reticulum stress (all N = 3 per group). (D) Unspliced X-box binding protein (XBP1) mRNA (P = NS, paired t test). (E) Spliced XBP1 mRNA (P = NS, paired t test). (F) Immunoglobulin binding protein (BiP) mRNA (P = NS, paired t test). (G) Endoplasmic reticulum degradation-enhancing α-mannidose-like protein (EDEM) mRNA (P = NS, paired t test). (H) Activating transcription factor 4 (ATF4) mRNA (P = NS, paired t test). (I) CCAAT/enhancer-binding protein homologous protein (CHOP) mRNA (P = NS, paired t test). (J–M) Enrichment with signal peptide and exosome proteins. (J) Proportion of proteins down-regulated significantly by iron with signal peptide vs no signal peptide. (K) Proportion of proteins not down-regulated significantly by iron with signal peptide vs no signal peptide. (L) Proportion of proteins down-regulated significantly by iron with exosome secretion vs no exosome secretion. (M) Proportion of proteins not down-regulated significantly by iron with exosome secretion vs no exosome secretion. Of the 61 proteins down-regulated significantly, 62% (38 of 61) had signal peptide, whereas of the remaining proteins only 47% (129 of 277) had signal peptide. The 1-tailed Fisher exact test showed significant enrichment with signal peptide (P = .02) among the group down-regulated significantly. In contrast, there was no significant enrichment of the exosomal pathway (P = .51, 1-tailed Fisher exact test), because 15% (9 of 61) of the proteins down-regulated significantly and 14% (39 of 277) of the remaining secretome proteins had been reported previously in the high-confidence proteins from the EVpedia database.