Combined Omics Reveals That Disruption of the Selenocysteine Lyase Gene Affects Amino Acid Pathways in Mice
Abstract
:1. Introduction
2. Materials and Methods
2.1. Animals and Diets
2.2. Reagents and Antibodies
2.3. RNA Extraction and Sequencing
2.4. Quantitative PCR (qPCR)
2.5. Metabolomics Analysis
2.6. Bioinformatics Analysis
2.7. Western Blot
2.8. Amino Acid Assays
2.9. Statistical Analysis
3. Results
3.1. Effect of Scly Disruption on the Hepatic Transcriptome
3.2. Sex Differences in Hepatic Metabolites of Scly KO Mice
3.3. Pathway Enrichment Analysis of the Livers of Scly KO Mice
3.4. Glycine Metabolism in the Scly KO Mice
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Gene | 0.08 g/g Se | 0.25 g/g Se | 2-Way ANOVA | ||||
---|---|---|---|---|---|---|---|
WT (n = 5) | Scly KO (n = 5) | WT (n = 4) | Scly KO (n = 4) | pinteraction | pSe | pgenotype | |
Abcb1a | 0.403 ± 0.016 | 0.302 ± 0.052 | 0.43 ± 0.038 | 0.571 ± 0.06 | 0.0193 | 0.0063 | 0.6606 |
Abcc3 | 0.556 ± 0.034 | 0.498 ± 0.077 | 0.476 ± 0.235 | 1.205 ± 0.143 | 0.0003 | 0.0019 | 0.0012 |
Acot3 | 0.402 ± 0.177 | 0.278 ± 0.205 | 0.526 ± 0.384 | 0.638 ± 0.190 | 0.3654 | 0.0783 | 0.9596 |
Angptl6 | 0.56 ± 0.049 | 0.501 ± 0.127 | 0.622 ± 0.172 | 0.584 ± 0.2 | 0.8866 | 0.3468 | 0.5221 |
Arl4d | 0.86 ± 0.287 | 0.858 ± 0.092 | 0.408 ± 0.135 | 1.275 ± 0.604 | 0.0321 | 0.9247 | 0.0329 |
Cesg1 | 5.394 ± 0.903 | 3.382 ± 0.158 | 2.399 ± 0.873 | 4.382 ± 1.778 | 0.0043 | 0.1055 | 0.9801 |
Eif4ebp3 | 1.118 ± 0.234 | 0.436 ± 0.108 | 1.482 ± 0.4 | 0.518 ± 0.198 | 0.316 | 0.123 | <0.0001 |
Inhbe | 3.332 ± 0.484 | 1.187 ± 0.241 | 3.815 ± 0.739 | 2.297 ± 0.454 | 0.2633 | 0.0114 | <0.0001 |
Lcn2 | 0.428 ± 0.297 | 0.348 ± 0.099 | 0.642 ± 0.357 | 0.426 ± 0.187 | 0.6491 | 0.3353 | 0.3292 |
Mt1 | 0.709 ± 0.322 | 0.133 ± 0.044 | 0.201 ± 0.096 | 0.304 ± 0.207 | 0.01 | 0.1562 | 0.0551 |
Mt2 | 0.688 ± 0.292 | 0.177 ± 0.054 | 0.25 ± 0.112 | 0.344 ± 0.13 | 0.0088 | 0.1869 | 0.0524 |
Pparg | 0.166 ± 0.052 | 0.692 ± 0.103 | 0.193 ± 0.082 | 0.683 ± 0.087 | 0.8335 | 0.9209 | <0.0001 |
Ppl | 0.089 ± 0.022 | 0.112 ± 0.059 | 0.151 ± 0.03 | 0.196 ± 0.028 | 0.5362 | 0.0011 | 0.0754 |
Selenbp2 | 13.92 ± 7.954 | 6.691 ± 1.122 | 20.88 ± 10.12 | 6.224 ± 1.178 | 0.3281 | 0.3504 | 0.008 |
Slc25a25 | 6.697 ± 0.888 | 3.163 ± 0.958 | 6.147 ± 3.191 | 4.869 ± 0.781 | 0.1732 | 0.5319 | 0.0357 |
Gene | 0.08 g/g Se | 0.25 g/g Se | 2-Way ANOVA | ||||
---|---|---|---|---|---|---|---|
WT (n = 4) | Scly KO (n = 5) | WT (n = 4) | Scly KO (n = 5) | pinteraction | pSe | pgenotype | |
Abcb1a | 0.579 ± 0.203 | 1.065 ± 0.503 | 0.727 ± 0.265 | 1.77 ± 0.707 | 0.2541 | 0.0914 | 0.0065 |
Abcc3 | 1.075 ± 0.578 | 1.496 ± 0.741 | 1.401 ± 0.605 | 1.673 ± 0.556 | 0.8063 | 0.4129 | 0.2647 |
Acot3 | 0.251 ± 0.043 | 0.114 ± 0.066 | 0.124 ± 0.029 | 0.106 ± 0.057 | 0.0323 | 0.0163 | 0.0074 |
Angptl6 | 0.012 ± 0.002 | 0.014 ± 0.007 | 0.009 ± 0.001 | 0.016 ± 0.006 | 0.3646 | 0.7616 | 0.0713 |
Arl4d | 0.561 ± 0.235 | 0.382 ± 0.171 | 1.147 ± 0.662 | 0.852 ± 0.541 | 0.7996 | 0.0345 | 0.3081 |
Cesg1 | 4.006 ± 1.288 | 4.223 ± 1.249 | 4.339 ± 0.751 | 5.236 ± 1.125 | 0.537 | 0.231 | 0.3175 |
Eif4ebp3 | 0.016 ± 0.008 | 0.017 ± 0.0146 | 0.011 ± 0.003 | 0.016 ± 0.007 | 0.6982 | 0.5723 | 0.5054 |
Inhbe | 1.899 ± 0.719 | 3.481 ± 0.845 | 2.338 ± 0.949 | 4.11 ± 0.961 | 0.8286 | 0.2351 | 0.0018 |
Lcn2 | 0.026 ± 0.01 | 0.017 ± 0.006 | 0.025 ± 0.009 | 0.016 ± 0.005 | 0.9079 | 0.7187 | 0.024 |
Mt1 | 0.314 ± 0.092 | 0.154 ± 0.12 | 0.205 ± 0.124 | 0.073 ± 0.062 | 0.7741 | 0.0696 | 0.0092 |
Mt2 | 0.397 ± 0.135 | 0.186 ± 0.121 | 0.259 ± 0.18 | 0.1 ± 0.063 | 0.6717 | 0.0844 | 0.0082 |
Pparg | 0.524 ± 0.246 | 0.465 ± 0.234 | 0.753 ± 0.165 | 0.6 ± 0.208 | 0.6549 | 0.098 | 0.319 |
Ppl | 0.004 ± 0.003 | 0.003 ± 0.002 | 0.003 ± 0.002 | 0.003 ± 0.001 | 0.5335 | 0.6621 | 0.4059 |
Selenbp2 | 0.122 ± 0.048 | 0.069 ± 0.038 | 0.077 ± 0.022 | 0.057 ± 0.017 | 0.3098 | 0.0889 | 0.0338 |
Slc25a25 | 0.209 ± 0.064 | 0.043 ± 0.013 | 0.087 ± 0.054 | 0.111 ± 0.06 | 0.0015 | 0.27 | 0.0109 |
Ingenuity Canonical Pathways | −log (p-Value) | Ratio |
---|---|---|
PXR/RXR Activation | 4.11 | 0.0462 |
LPS/IL-1 Mediated Inhibition of RXR Function | 3.76 | 0.018 |
Xenobiotic Metabolism Signaling | 3.32 | 0.0138 |
Nicotine Degradation III | 2.65 | 0.0364 |
Melatonin Degradation I | 2.52 | 0.0312 |
Nicotine Degradation II | 2.52 | 0.0312 |
Superpathway of Melatonin Degradation | 2.45 | 0.029 |
Acyl-CoA Hydrolysis | 1.82 | 0.0833 |
Hepatic Cholestasis | 1.75 | 0.0125 |
Ubiquinol-10 Biosynthesis (Eukaryotic) | 1.62 | 0.0526 |
Biological Pathways | Hits | p-Value |
---|---|---|
Alanine, aspartate and glutamate metabolism | 10 | 0.000285 |
D-glutamine and D-glutamate metabolism | 4 | 0.000299 |
Galactose metabolism | 9 | 0.000886 |
Aminoacyl-tRNA biosynthesis | 12 | 0.000907 |
Biosynthesis of unsaturated fatty acids | 6 | 0.002 |
Pantothenate and CoA biosynthesis | 5 | 0.021 |
Valine, leucine and isoleucine biosynthesis | 3 | 0.022 |
Glyoxylate and dicarboxylate metabolism | 6 | 0.045 |
Taurine and hypotaurine metabolism | 3 | 0.051 |
Glycine, serine and threonine metabolism | 7 | 0.053 |
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Seale, L.A.; Khadka, V.S.; Menor, M.; Xie, G.; Watanabe, L.M.; Sasuclark, A.; Guirguis, K.; Ha, H.Y.; Hashimoto, A.C.; Peplowska, K.; et al. Combined Omics Reveals That Disruption of the Selenocysteine Lyase Gene Affects Amino Acid Pathways in Mice. Nutrients 2019, 11, 2584. https://doi.org/10.3390/nu11112584
Seale LA, Khadka VS, Menor M, Xie G, Watanabe LM, Sasuclark A, Guirguis K, Ha HY, Hashimoto AC, Peplowska K, et al. Combined Omics Reveals That Disruption of the Selenocysteine Lyase Gene Affects Amino Acid Pathways in Mice. Nutrients. 2019; 11(11):2584. https://doi.org/10.3390/nu11112584
Chicago/Turabian StyleSeale, Lucia A., Vedbar S. Khadka, Mark Menor, Guoxiang Xie, Ligia M. Watanabe, Alexandru Sasuclark, Kyrillos Guirguis, Herena Y. Ha, Ann C. Hashimoto, Karolina Peplowska, and et al. 2019. "Combined Omics Reveals That Disruption of the Selenocysteine Lyase Gene Affects Amino Acid Pathways in Mice" Nutrients 11, no. 11: 2584. https://doi.org/10.3390/nu11112584