DNA Microarray Analysis on the Genes Differentially Expressed in the Liver of the Pufferfish, Takifugu rubripes, Following an Intramuscular Administration of Tetrodotoxin
Abstract
:1. Introduction
2. Experimental Section
2.1. Materials
2.2. TTX Administration and Sample Preparation
2.3. TTX Extraction and Quantification
2.4. RNA Extraction for Microarray Analysis
2.5. Preparation of Fluorescently-Labeled cRNA and Microarray Analysis
2.6. Quantitative Real-Time PCR
2.7. Data Analysis and Statistics
3. Results
3.1. TTX Determination
No. | Sex | Body weight (kg) | Dose (µg) | TTX concentration (µg/g) | Total amount (µg) | Accumulation (% of dose) | |||
---|---|---|---|---|---|---|---|---|---|
Liver | Skin | Ovary | Muscle | ||||||
1 | F | 1.14 | 285 | 0.48 | 0.30 | 5.43 | N.D.1 | 145 | 51 |
2 | F | 0.84 | 210 | 0.68 | 0.97 | 5.30 | N.D. | 162 | 77 |
3 | F | 1.00 | 250 | 1.12 | 0.62 | 4.97 | N.D. | 206 | 82 |
4 | F | 1.10 | 275 | 0.54 | 0.33 | 4.51 | N.D. | 124 | 45 |
5 | M | 0.86 | 215 | 1.35 | 0.79 | N.D. 1 | N.D. | 176 | 82 |
Mean ± SE | 0.99 ± 0.15 | 247 ± 15 | 0.84 ± 0.17 | 0.60 ± 0.13 | 5.05 ± 0.21 | N.D. | 163 ± 14 | 67 ± 8 |
3.2. Gene Expression Analysis
Ensemble ID | Gene name | Predicted description | Functional classification | FC |
---|---|---|---|---|
ENSTRUT00000045544 | Cela2a | Chymotrypsin-like elastase family member 2A | Enzyme, cofactor | 37.6 |
ENSTRUT00000041722 | Tmem168 | Transmembrane protein 168 | Transport vesicle | 20.0 |
ENSTRUT00000006023 | Arhgap29 | Rho GTPase-activating protein 29 | Enzyme, cofactor | 12.1 |
ENSTRUT00000034782 | Kcnma1 | T. rubripes calcium channel alpha-1 subunit homolog (AF026198.1) | Ion channel activity | 10.4 |
ENSTRUT00000004724 | Chrna9 | T. rubripes nicotinic acetylcholine receptor alpha 9d subunit (AY299471.1) | Ion channel activity | 8.1 |
ENSTRUT00000038610 | Csmd1 | CUB and sushi domain-containing protein 1 | Protein binding | 7.0 |
ENSTRUT00000036792 | Serinc4 | Serine incorporator 4 | Transporter activity | 6.8 |
ENSTRUT00000026094 | C14orf135 | Pecanex-like protein C14orf135 | Unknown | 6.6 |
ENSTRUT00000046072 | Lrp2 | Low density lipoprotein receptor-related protein 2 | Receptor activity | 5.4 |
ENSTRUT00000046718 | Col27a1 | Collagen alpha-1(XXVII) chain A-like | Structural molecule | 5.2 |
ENSTRUT00000000397 | Klhl32 | Kelch-like protein 32 | Protein binding | 4.5 |
ENSTRUT00000000173 | Elk4 | ELK4, ETS-domain protein | Transcription factor | 4.3 |
ENSTRUT00000025902 | Zbtb45 | Zinc finger and BTB domain-containing protein 45 | Transcription factor | 4.3 |
ENSTRUT00000020252 | Spsb1 | SPRY domain-containing SOCS box protein 1 | Receptor activity | 4.3 |
ENSTRUT00000032342 | Dysf | Dysferlin | Lipid binding | 4.1 |
ENSTRUT00000003310 | Scn2b | Sodium channel beta-2 subunit | Ion channel activity | 4.0 |
ENSTRUT00000011167 | Loxl2 | Lysyl oxidase homolog 2 | Enzyme, cofactor | 3.9 |
ENSTRUT00000017057 | Dmbx1 | Diencephalon/mesencephalon homeobox protein 1 | Transcription factor | 3.9 |
ENSTRUT00000023088 | Clk2 | Dual specificity protein kinase CLK2 | Enzyme, cofactor | 3.9 |
ENSTRUT00000045827 | Myo3b | Myosin-IIIb | Enzyme, cofactor | 3.8 |
ENSTRUT00000025143 | Megf11 | Multiple epidermal growth factor-like domains protein 11 | Metal ion binding | 3.7 |
ENSTRUT00000003539 | Slc44a1 | Choline transporter-like protein 1 | Transporter activity | 3.7 |
ENSTRUT00000017798 | Cc4 | Carbonic anhydrase 4 | Enzyme, cofactor | 3.5 |
ENSTRUT00000006962 | OR4563-2 | T. rubripes odorant receptor (DQ306241.1) | Receptor activity | 3.5 |
ENSTRUT00000024316 | Pitpnm2 | Membrane-associated phosphatidylinositol transfer protein 2 | Metal ion binding | 3.4 |
ENSTRUT00000030952 | Ptafr | Platelet-activating factor receptor | Receptor activity | 3.4 |
ENSTRUT00000038903 | Hepacam2 | HEPACAM family member 2 | Unknown | 3.4 |
ENSTRUT00000043658 | Gpr22 | Probable G-protein coupled receptor 22 | Receptor activity | 3.3 |
ENSTRUT00000031306 | Ptpn2 | Tyrosine-protein phosphatase non-receptor type 2 | Enzyme, cofactor | 3.3 |
ENSTRUT00000019629 | Eps15l1 | Epidermal growth factor receptor substrate 15-like 1 | Receptor activity | 3.2 |
ENSTRUT00000036590 | Zdhhc8 | Membrane-associated DHHC8 zinc finger protein (NM_001078596.1) | Enzyme, cofactor | 3.2 |
ENSTRUT00000031045 | Rheb | GTP-binding protein Rheb | Enzyme, cofactor | 3.2 |
ENSTRUT00000047583 | Agap2 | Arf GAP with GTPase domain, ankyrin repeat and PH domain 2 | Enzyme, cofactor | 3.0 |
ENSTRUT00000017824 | Ppargc1a | Peroxisome proliferator activated receptor gamma coactivator 1 alpha (DQ157766.1) | Receptor activity | 3.0 |
ENSTRUT00000027961 | Pfkp | 6-phosphofructokinase type C | Enzyme, cofactor | 3.0 |
ENSTRUT00000029743 | E2f2 | Transcription factor E2F2 | Unknown | 3.0 |
Ensemble ID | Gene name | Predicted description | Functional classification | FC | |||
---|---|---|---|---|---|---|---|
ENSTRUT00000047556 | Fusa2 | Elongation factor G 2 | Transcription factor | −3.0 | |||
ENSTRUT00000009260 | Rspo3 | R-spondin-3 | Transduction | −7.8 | |||
ENSTRUT00000029878 | Ncoa2 | Nuclear receptor coactivator 2 | Transcription factor | −7.3 | |||
ENSTRUT00000005082 | Sasb | Fatty acyl-CoA hydrolase precursor, medium chain | Enzyme, cofactor | −6.2 | |||
ENSTRUT00000042623 | Kcnj3 | G protein-activated inward rectifier potassium channel 1 | Ion channel activity | −5.9 | |||
ENSTRUT00000029012 | Galnt1 | Polypeptide N-acetylgalactosaminyltransferase 1 | Enzyme, cofactor | −5.7 | |||
ENSTRUT00000034755 | Stk11ip | Serine/threonine kinase 11-interacting protein | Protein binding | −5.5 | |||
ENSTRUT00000007314 | Unc5d | Netrin receptor UNC5D | Receptor activity | −5.3 | |||
ENSTRUT00000024559 | Dnmt3a | DNA (cytosine-5)-methyltransferase 3A | Transcription factor | −4.7 | |||
ENSTRUT00000028271 | finTRIM | Fish virus induced TRIM protein | Metal ion binding | −4.7 | |||
ENSTRUT00000021561 | Synpo2 | Synaptopodin-2 | Protein binding | −4.4 | |||
ENSTRUT00000035155 | Klhl8 | Kelch-like protein 8 | Protein binding | −4.4 | |||
ENSTRUT00000013283 | Lnx2 | Ligand of Numb protein X2 | Metal ion binding | −4.3 | |||
ENSTRUT00000005282 | Sox5 | T. rubripes transcription factor SOX5 (AY277973.1) | Transcription factor | −4.1 | |||
ENSTRUT00000004950 | Egr3 | Early growth response protein 3 | Transcription factor | −4.0 | |||
ENSTRUT00000001876 | Nme1 | Nucleoside diphosphate kinase A | Transcription factor | −4.0 | |||
ENSTRUT00000037748 | Cadm2 | Cell adhesion molecule 2 | Protein binding | −3.9 | |||
ENSTRUT00000029148 | Cln3 | Battenin | Enzyme, cofactor | −3.8 | |||
ENSTRUT00000018412 | Hecd3 | Probable E3 ubiquitin-protein ligase HECTD3 | Protein binding | −3.7 | |||
ENSTRUT00000010231 | Wipi2 | WD repeat domain phosphoinositide-interacting protein 2 | Enzyme, cofactor | −3.7 | |||
ENSTRUT00000038056 | Angpt2 | Angiopoietin-2 | Receptor activity | −3.7 | |||
ENSTRUT00000011781 | - | Putative F-type lectin | Sugar binding | −3.6 | |||
ENSTRUT00000025271 | Tyro3 | Tyrosine-protein kinase receptor TYRO3 | Transduction | −3.6 | |||
ENSTRUT00000036834 | Pcolce | T. rubripes procollagen C-endopeptidase enhancer 1 (AF016494.1) | Protein binding | −3.4 | |||
ENSTRUT00000009581 | Rims1 | Regulating synaptic membrane exocytosis protein 1 | Protein binding | −3.4 | |||
ENSTRUT00000013940 | Pdlim5 | PDZ and LIM domain protein 5 | Protein binding | −3.4 | |||
ENSTRUT00000041778 | Foxa3 | T. rubripes folkhead transcription factor FoxA3 (AB604763.1) | Transcription factor | −3.3 | |||
ENSTRUT00000026385 | Fam70a | Protein FAM70A | Unknown | −3.3 | |||
ENSTRUT00000003229 | Arhgef26 | Rho guanine nucleotide exchange factor 26 | Transcription factor | −3.2 | |||
ENSTRUT00000007982 | Kif2c | Kinesin-like protein KIF2C | Protein binding | −3.2 | |||
ENSTRUT00000013282 | Lnx2 | Ligand of Numb protein X2 | Protein binding | −3.2 | |||
ENSTRUT00000005850 | Crybb2 | Beta-crystallin A2 | Protein binding | −3.2 | |||
ENSTRUT00000003860 | Edaradd | Ectodysplasin-A receptor-associated adapter protein | Protein binding | −3.1 | |||
ENSTRUT00000015819 | Pbxip1 | Pre-B-cell leukemia transcription factor-interacting protein 1 | Transcription factor | −3.1 | |||
ENSTRUT00000011222 | Serpinh1 | Serpin H1 | Protein binding | −3.1 | |||
ENSTRUT00000020096 | Atp2b3 | Plasma membrane calcium-transporting ATPase 3 | Transporter activity | −3.1 | |||
ENSTRUT00000009874 | Plxdc1 | Plexin domain-containing protein 1 | Unknown | −3.1 | |||
ENSTRUT00000047512 | Suox | Sulfite oxidase, mitochondrial | Enzyme, cofactor | −3.1 | |||
ENSTRUT00000020028 | finTRIM | Fish virus induced TRIM protein | Metal ion binding | −3.0 | |||
ENSTRUT00000041535 | Pxn | Paxillin | Protein binding | −3.0 | |||
ENSTRUT00000033313 | Nox5 | T. rubripes NADPH oxidase 5 (BR000279.1) | Enzyme, cofactor | −3.0 | |||
ENSTRUT00000027204 | Pacs2 | Phosphofurin acidic cluster sorting protein 2 | Unknown | −3.0 | |||
ENSTRUT00000044222 | Tgfbrap1 | Transforming growth factor-beta receptor-associated protein 1 | Protein binding | −3.0 | |||
ENSTRUT00000027017 | Hnrnpk | Heterogeneous nuclear ribonucleoprotein K | Transcription factor | −3.0 | |||
ENSTRUT00000043644 | Hsp90b1 | Heat shock protein 90kDa beta member 1 | Protein binding | −3.0 | |||
ENSTRUT00000043157 | Tle3 | T. rubripes transducin-like enhancer protein 3 (AB236415.1) | Transcription factor | −3.0 | |||
ENSTRUT00000022207 | Vwa1 | Von Willebrand factor A domain-containing protein 1 | Unknown | −3.0 | |||
ENSTRUT00000026592 | Tacr3 | Neuromedin-K receptor | Receptor activity | −3.0 | |||
ENSTRUT00000028610 | Dach1 | Dachshund homolog 1 | Protein binding | −3.0 | |||
ENSTRUT00000011629 | Gas2l3 | GAS2-like protein 3 | Protein binding | −3.0 | |||
ENSTRUT00000018505 | Epha2 | Ephrin type-A receptor 4 precursor | Receptor activity | −3.0 |
4. Discussion
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Matsumoto, T.; Feroudj, H.; Kikuchi, R.; Kawana, Y.; Kondo, H.; Hirono, I.; Mochizuki, T.; Nagashima, Y.; Kaneko, G.; Ushio, H.; et al. DNA Microarray Analysis on the Genes Differentially Expressed in the Liver of the Pufferfish, Takifugu rubripes, Following an Intramuscular Administration of Tetrodotoxin. Microarrays 2014, 3, 226-244. https://doi.org/10.3390/microarrays3040226
Matsumoto T, Feroudj H, Kikuchi R, Kawana Y, Kondo H, Hirono I, Mochizuki T, Nagashima Y, Kaneko G, Ushio H, et al. DNA Microarray Analysis on the Genes Differentially Expressed in the Liver of the Pufferfish, Takifugu rubripes, Following an Intramuscular Administration of Tetrodotoxin. Microarrays. 2014; 3(4):226-244. https://doi.org/10.3390/microarrays3040226
Chicago/Turabian StyleMatsumoto, Takuya, Holger Feroudj, Ryosuke Kikuchi, Yuriko Kawana, Hidehiro Kondo, Ikuo Hirono, Toshiaki Mochizuki, Yuji Nagashima, Gen Kaneko, Hideki Ushio, and et al. 2014. "DNA Microarray Analysis on the Genes Differentially Expressed in the Liver of the Pufferfish, Takifugu rubripes, Following an Intramuscular Administration of Tetrodotoxin" Microarrays 3, no. 4: 226-244. https://doi.org/10.3390/microarrays3040226