Submitted:
21 March 2024
Posted:
22 March 2024
You are already at the latest version
Abstract
Keywords:
1. Introduction
2. Material and Methods
2.1. Rat Model
2.2. Mass Spectrometry Analysis of Proteins
2.2.1. Protein Extraction, Digestion and TMT-Labelling
2.2.2. Nano Liquid Chromatography Tandem Mass Spectrometry (nLC-MS/MS)
2.2.3. Proteomics Data Analysis
2.3. Statistical Analysis of Protein Expression Data
2.4. Ingenuity Pathway Analysis
3. Results
3.1. Group-Specific (Unique) Proteins
3.2. Age-Related Proteins
3.3. Dose-Related Proteins
3.4. IPA Analysis
3.5. Histological Evaluation of Rat Thyroid Tissue
4. Discussion
5. Conclusion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Ethical Permission
References
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| Young | Adult | ||||
|---|---|---|---|---|---|
| Protein | Log2 ratio (Y50; Y500) |
Protein | Log2 ratio (A50; A500) |
Protein | Log2 ratio (A50; A500) |
| FDPS | -0.60; -0.72 | AHNAK 1 (Fragment) | -0.66; -0.72 | LCN2 | 0.98; 0.69 |
| GNPTAB | -0.63; -0.66 | ALDH1A7 | 1.3; 1.0 | LGALS5 | 0.89; 2.0 |
| JAK1 | -0.63; -0.69 | APOBEC2 | 1.1; 0.88 | NCAPG2 | -1.1; -0.69 |
| LSAMP | -0.59; -0.82 | APOD | --1.3; -0.81 | NHSL1 | -0.85; -1.1 |
| MAOB | -0.61; -0.73 | ATPSCKMT | 0.81; 0.63 | NR2F2 | -0.93; -0.75 |
| REEP6 | -0.58; -0.96 | BLOC1S6 | -0.82; -0.97 | PATZ1 | -0.64; -0.92 |
| RGD1566265 | -0.60; -1.0 | BUD23 | -1.1; -1.4 | PDLIM4 | -0.73; -0.61 |
| TBC1D10A | -0.66; -0.65 | CACNG1 | -1.8; -1.2 | PHKG2 | -0.59; -0.63 |
| COX3 | -0.85; -1.1 | PISD | -0.68; -0.65 | ||
| CSTF1 | -0.73; -0.74 | PLSCR1 | -0.86; -0.73 | ||
| DHRS7B | -1.2; -0.61 | PPP1R10 | -0.96; -0.99 | ||
| DNAH6 | -0.59; -1.6 | PRR33 | 1.9; 1.4 | ||
| DPH6 | -1.4; -2.1 | PSMB8 | 1.8; 1.2 | ||
| DVL1 | -0.62; -0.93 | RAC2 | -0.68; -0.61 | ||
| ECI1 | -1.3; 0.90 | RB1 | -1.1; -0.62 | ||
| FBXW17 | -0.65; -1.0 | RT1-A1B | 4.4; 1.4 | ||
| FCGBP | -0.83; -0.78 | SNPH | -1.0; -0.82 | ||
| FXYD1 | --0.99; -0.59 | TAP2 | -0.59; -1.0 | ||
| HAT1 | -0.67; -0.63 | TAP2C | 1.5; 1.3 | ||
| IGFBP6 | --0.69; -0.65 | TFE3 | -0.59; 0.99 | ||
| IGHG | 0.67; 0.71 | Titin protein homolog (Fragment) | -1.3; -0.60 | ||
| KRT1 | -1.0; -0.97 | TMEM47 | -0.63; -0.58 | ||
| KRT10 | -1.1; -0.83 | TPCR12 | -0.94; -1.2 | ||
| KRT16 | -1.6; -1.4 | TXLNB | -2.0; -1.9 | ||
| KRT80 | -0.65; -0.70 | Uncharacterized protein | -1.9; -1.7 | ||
| LAMC2 | -0.76; -0.69 | ||||
| 50 kBq | 500 kBq | ||||
|---|---|---|---|---|---|
| Protein | Log2 ratio (young; adult) |
Protein | Log2 ratio (young; adult) |
Protein | Log2 ratio (young; adult) |
| BICD2 |
-0.62; -0.59 |
ABCC8 |
-1.1; -0.90 |
MEF2D |
-0.67; -0.70 |
| HABP4 |
-0.61; -0.63 |
ADGRG2 |
-0.98; -0.78 |
MOCOS |
-1.1; -0.68 |
| HBB-B1 |
0.65; -0.71 |
ALDH1A2 |
-0.65; -0.66 |
MTM1 |
-0.85; -0.88 |
| NME3 |
0.60; 2.0 |
BHMT |
-2.7; -0.77 |
MYL3 |
1.6; -0.73 |
| PALM2 |
0.63; 0.70 |
CDC40 |
-1.1; -0.84 |
PKP1 |
1.2; -1.1 |
| CLCC1 |
0.84; 1.0 |
PRKCZ |
-0.79; -0.62 |
||
| CNST |
-0.62; -1.3 |
PSMF1 |
-0.95; -0.66 |
||
| CPT2 |
1.1; 0.90 |
RBM3 |
-0.64; -1.86 |
||
| CSRP3 |
0.99; -0.73 |
SERPINB12 |
3.1; -0.64 |
||
| DAB2 |
-0.81; -0.74 |
SLC25A15 |
-0.89; -0.74 |
||
| DNAJC17 |
-0.60; -0.69 |
SMPD3 |
1.5; -2.9 |
||
| DUSP22 |
-1.1; -0.69 |
THBS4 |
0.72; -1.0 |
||
| FLT4 |
-0.88; -1.3 |
TMEM106B |
-1.2; -1.3 |
||
| HEG1 |
-0.72; -0.60 |
TP53I11 |
-0.77; -1.1 |
||
| HP |
0.87; 0.74 |
UBAC1 |
-0.78; -0.82 |
||
| IGSF8 |
-0.89; -0.80 |
VASN |
-1.1; -0.78 |
||
| LEAP2 |
-1.0; -0.85 |
WIZ |
-0.67; -0.94 |
||
| Ingenuity canonical pathways | p | z | Molecules |
|---|---|---|---|
| Y50 | |||
| tRNA Splicing | 1.7E-02 | 2.0 | PDE10A,PDE1B,PDE5A,TSEN2 |
| Stearate Biosynthesis I (Animals) | 2.5E-02 | -2.0 | CYP2E1,DHCR24,GNPAT,SLC27A5 |
| Superpathway of Methionine Degradation | 1.0E-02 | -2.0 | BHMT,BHMT2,CTH,MAT1A |
| Thyroid Hormone Metabolism II (via Conjugation and/or Degradation) | 7.4E-03 | -2.0 | SULT1B1,UGT1A1,Ugt2b17,UGT2B28 |
| Gluconeogenesis I | 1.4E-03 | -2.0 | ALDOB,ENO3,FBP1,PGAM2 |
| Glycolysis I | 2.6E-04 | -2.2 | ALDOB,ENO3,FBP1,PGAM2,PKLR |
| Bile Acid Biosynthesis, Neutral Pathway | 7.9E-06 | -2.2 | AKR1D1,BAAT,CYP27A1,CYP3A4,SLC27A5 |
| Xenobiotic Metabolism PXR Signaling Pathway | 3.7E-06 | -2.5 | ALDH1L1,ALDH1L2,ALDH8A1,CAMK2G,CYP2C19,CYP2C9,CYP3A4,GSTA5,MAOB,PPP1R11,PRKCE,SULT1B1, SULT1E1,UGT1A1,UGT2B28,UGT8 |
| LPS/IL-1 Mediated Inhibition of RXR Function | 1.2E-07 | 2.6 | ACOX2,ALDH1L1,ALDH1L2,ALDH8A1,CPT2,CYP2A6 (includes others),CYP2C19,CYP2C9,CYP3A4,Cyp4a14, FABP1,ABP3,FMO4,GSTA5,HMGCS2,MAOB,MYD88,SLC27A5,SULT1B1,SULT1E1 |
| Serotonin Degradation | 4.3E-04 | -2.6 | ADH1C,ADH4,MAOB,SULT1B1,UGT1A1,Ugt2b17,UGT2B28 |
| Acetone Degradation I (to Methylglyoxal) | 4.0E-06 | -2.6 | CYP2A6 (includes others),CYP2C18,CYP2C19,CYP2C9, CYP2E1,CYP2U1,CYP3A4 |
| Bupropion Degradation | 9.8E-07 | -2.6 | CYP2A6 (includes others),CYP2C18,CYP2C19,CYP2C9, CYP2E1,CYP2U1,CYP3A4 |
| Xenobiotic Metabolism CAR Signaling Pathway | 1.4E-05 | -2.8 | ALDH1L1,ALDH1L2,ALDH8A1,Cyp2b13/Cyp2b9,CYP2C19,CYP2C9,CYP3A4,FMO4,GSTA5,PRKCE,SULT1B1,SULT1E1, UGT1A1,UGT2B28,UGT8 |
| Nicotine Degradation II | 2.4E-08 | -2.9 | AOX1,CYP2A6 (includes others),CYP2C18,CYP2C19, CYP2C9,CYP2E1,CYP2U1,CYP3A4,FMO4,UGT1A1,Ugt2b17, UGT2B28 |
| Estrogen Biosynthesis | 2.5E-07 | -3,0 | CYP2A6 (includes others),CYP2C18,CYP2C19,CYP2C9, CYP2E1,CYP2U1,CYP3A4,HSD17B13,HSD17B2 |
| Melatonin Degradation I | 4.5E-08 | -3.3 | CYP2A6 (includes others),CYP2C18,CYP2C19,CYP2C9, CYP2E1,CYP2U1,CYP3A4,SULT1B1,UGT1A1,Ugt2b17,UGT2B28 |
| Nicotine Degradation III | 4.5E-08 | -3.3 | AOX1,CYP2A6 (includes others),CYP2C18,CYP2C19, CYP2C9,CYP2E1,CYP2U1,CYP3A4,UGT1A1,Ugt2b17,UGT2B28 |
| Superpathway of Melatonin Degradation | 8.9E-09 | -3.5 | CYP2A6 (includes others),CYP2C18,CYP2C19,CYP2C9, CYP2E1,CYP2U1,CYP3A4,MAOB,SULT1B1,UGT1A1, Ugt2b17,UGT2B28 |
| Y500 | |||
| Thyroid Hormone Metabolism II (via Conjugation and/or Degradation) | 2.0E-03 | -2.0 | SULT1B1,UGT1A1,Ugt2b17,UGT2B28 |
| Retinoate Biosynthesis I | 1.8E-03 | -2.0 | ADH1C,ADH4,ALDH8A1,Rdh7 |
| Noradrenaline and Adrenaline Degradation | 1.6E-03 | -2.0 | ADH1C,ADH4,ADHFE1,MAOB |
| Superpathway of Cholesterol Biosynthesis | 1.2E-03 | -2.0 | CYP51A1,DHCR24,FDPS,HMGCS2 |
| Bile Acid Biosynthesis, Neutral Pathway | 4.6E-05 | -2.0 | AKR1D1,BAAT,CYP3A4,SLC27A5 |
| Citrulline Biosynthesis | 8.3E-06 | -2.0 | ARG1,GLS,LOC102724788/PRODH,OTC |
| Superpathway of Citrulline Metabolism | 3.0E-06 | -2.2 | ARG1,CPS1,GLS,LOC102724788/PRODH,OTC |
| Estrogen Biosynthesis | 7.9E-13 | -2.3 | CYP2A6 (includes others),CYP2C18,CYP2C19,CYP2C9, CYP2E1,CYP2F1,CYP2S1,CYP2U1,CYP3A4,CYP51A1,HSD17B13,HSD17B2 |
| Nicotine Degradation II | 1.3E-12 | -2.7 | Aox3,CYP2A6 (includes others),CYP2C18,CYP2C19, CYP2C9,CYP2E1,CYP2F1,CYP2S1,CYP2U1,CYP3A4, CYP51A1,UGT1A1,Ugt2b17,UGT2B28 |
| Melatonin Degradation I | 1.3E-13 | -2.7 | CYP2A6 (includes others),CYP2C18,CYP2C19,CYP2C9, CYP2E1,CYP2F1,CYP2S1,CYP2U1,CYP3A4,CYP51A1, SULT1B1,UGT1A1,Ugt2b17,UGT2B28 |
| Nicotine Degradation III | 1.3E-13 | -2.6 | Aox3,CYP2A6 (includes others),CYP2C18,CYP2C19,CYP2C9, CYP2E1,CYP2F1,CYP2S1,CYP2U1,CYP3A4,CYP51A1, UGT1A1,Ugt2b17,UGT2B28 |
| Serotonin Degradation | 4.6E-06 | -2.8 | ADH1C,ADH4,ADHFE1,MAOB,SULT1B1,UGT1A1,Ugt2b17,UGT2B28 |
| Superpathway of Melatonin Degradation | 2.0E-14 | -2.87 | CYP2A6 (includes others),CYP2C18,CYP2C19,CYP2C9, CYP2E1,CYP2F1,CYP2S1,CYP2U1,CYP3A4,CYP51A1,MAOB, SULT1B1,UGT1A1,Ugt2b17,UGT2B28 |
| Xenobiotic Metabolism CAR Signaling Pathway | 1.3E-04 | -3.3 | ALDH1L2,ALDH8A1,Cyp2b13/Cyp2b9,CYP2C19,CYP2C9, CYP3A4,GSTA5,SULT1B1,SULT1E1,UGT1A1,UGT2B28 |
| Xenobiotic Metabolism PXR Signaling Pathway | 5.9E-06 | -3.6 | ALDH1L2,ALDH8A1,CAMK2A,CYP2C19,CYP2C9,CYP3A4, GSTA5,MAOB,Ppp1cc,SULT1B1,SULT1E1,UGT1A1,UGT2B28 |
| A50 | |||
| Xenobiotic Metabolism CAR Signaling Pathway | 3.9E-03 | 2.3 | ALDH8A1,GSTA1,GSTA5,MAP2K2,MAP2K5,SULT1B1,SULT2B1,UGT1A1,UGT2B28 |
| A500 | |||
| ILK Signaling | 1.9E-04 | -2.3 | ACTB,ACTN2,JUN,MYH1,MYH2,MYH3,MYH6,MYH7,MYH8,MYL1,MYL2,MYL3 |
| Apelin Cardiomyocyte Signaling Pathway | 2.6E-03 | -2.6 | ATP2A1,MYL1,MYL2,MYL3,MYLPF,PLCL2,SLC9A2 |
| Actin Cytoskeleton Signaling | 1.4E-05 | -2.7 | ACTB,ACTN2,APC,MPRIP,MYH1,MYH2,MYH3,MYH6, MYH7,MYH8,MYL1,MYL2,MYL3,MYLPF,TTN |
| Upstream regulator | Molecule type | p | z | Target molecules in dataset |
| Y500 | ||||
| EFNA2 | kinase | 4.5E-03 | 2.0 | KRT13,KRT4,PKP1,TGM1 |
| A50 | ||||
| let-7 | microRNA | 2.3E-02 | 2.2 | APC,BOP1,IGF1R,MYD88,STARD13 |
| IGF1 | growth factor | 2.0E-03 | -2.2 | GFAP,IGF1R,IGFBP3,PSMB8,SLC20A1 |
| A500 | ||||
| MYOCD | transcription regulator | 7.8E-10 | -2.1 | ACTN2,CASQ2,CNN1,COL1A1,HSPB7,MYH6,MYH7,MYL2,TNNC1,TNNI1,TTN |
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