Molecular Characterisation of Canine Osteosarcoma in High Risk Breeds
Abstract
:1. Introduction
2. Results
2.1. RNAseq Gene Expression
2.2. qRT-PCR and Immunohistochemistry Validation
2.3. Cohort Epidemiology
2.4. Androgen polyQ Analysis
3. Discussion
4. Materials and Methods
4.1. Samples and Ethics
4.2. RNA Extraction and Next Generation Sequencing
4.3. Quantitative Reverse Transcriptase PCR
4.4. Immunohistochemistry
4.5. PolyQ Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Gene_ID | Gene | Log2 Fold Change | p Value |
---|---|---|---|
ENSCAFG00000007134 | MYBPC1 | −14.4441 | 0.01395 |
ENSCAFG00000001705 | MB | −13.3627 | 0.0081 |
ENSCAFG00000013875 | MYL1 | −13.1689 | 0.00085 |
ENSCAFG00000008253 | ACTA1 | −12.3844 | 0.003 |
ENSCAFG00000011103 | NRAP | −12.1537 | 0.00015 |
ENSCAFG00000005717 | ENSCAFG00000005717 | −12.0616 | 0.00035 |
ENSCAFG00000014281 | PYGM | −11.6411 | 0.0057 |
ENSCAFG00000011619 | MYH7 | −11.4064 | 0.0001 |
ENSCAFG00000002620 | TNNT1 | −11.3052 | 0.0119 |
ENSCAFG00000001016 | TRDN | −11.034 | 0.0005 |
ENSCAFG00000009333 | CESDD1 | −10.7269 | 0.04655 |
ENSCAFG00000005896 | RYR1 | −9.83487 | 0.01135 |
ENSCAFG00000009404 | TNNC1 | −9.61599 | 0.0317 |
ENSCAFG00000015475 | DES | −9.54008 | 0.0062 |
ENSCAFG00000005358 | HHATL | −9.49779 | 0.0023 |
ENSCAFG00000008707 | CKMT2 | −9.43202 | 0.00015 |
ENSCAFG00000017254 | ATP2A1 | −9.34349 | 0.01225 |
ENSCAFG00000001140 | MYOT | −9.08389 | 0.0191 |
ENSCAFG00000012927 | ALPK3 | −9.01117 | 0.0005 |
ENSCAFG00000005343 | KLHL40 | −8.96012 | 0.0234 |
ENSCAFG00000002982 | MYBPC2 | −8.66855 | 0.01675 |
ENSCAFG00000012432 | MYOZ2 | −8.62006 | 0.00415 |
ENSCAFG00000011638 | SPTA1 | −8.56014 | 0.00135 |
ENSCAFG00000001161 | OBSCN | −8.44333 | 0.01045 |
ENSCAFG00000011418 | HFE2 | −8.31185 | 0.0051 |
Gene_ID | Gene | Log2 Fold Change | p Value |
---|---|---|---|
ENSCAFG00000010484 | PKP2 | 3.54183 | 0.00095 |
ENSCAFG00000005510 | EOMES | 3.56165 | 0.04155 |
ENSCAFG00000012983 | GPR64 | 3.66911 | 0.0009 |
ENSCAFG00000013448 | COLGALT2 | 3.69448 | 0.0007 |
ENSCAFG00000007845 | DKK3 | 3.76815 | 0.0013 |
ENSCAFG00000009722 | TOX3 | 3.77935 | 0.0002 |
ENSCAFG00000023615 | MMP-12 | 3.78547 | 0.0001 |
ENSCAFG00000002589 | COL9A1 | 3.84351 | 0.0001 |
ENSCAFG00000003503 | ARHGEF5 | 3.84945 | 0.0006 |
ENSCAFG00000005101 | RPSA | 3.86821 | 0.00135 |
ENSCAFG00000019918 | FOXF1 | 3.8936 | 0.0005 |
ENSCAFG00000017309 | RPL4 | 3.92678 | 0.00015 |
ENSCAFG00000018123 | ARSI | 3.92752 | 0.0004 |
ENSCAFG00000007280 | RNF180 | 4.12335 | 0.00015 |
ENSCAFG00000010205 | ID4 | 4.12517 | 0.0108 |
ENSCAFG00000006073 | POSTN | 4.15174 | 0.03365 |
ENSCAFG00000009756 | ELOVL2 | 4.23619 | 0.00035 |
ENSCAFG00000002307 | ASPN | 4.25607 | 0.02175 |
ENSCAFG00000009135 | SAA1 | 4.42549 | 0.0053 |
ENSCAFG00000019036 | LIPG | 4.44654 | 0.0061 |
ENSCAFG00000016731 | MSX2 | 4.46357 | 0.0337 |
ENSCAFG00000015063 | MMP3 | 4.56236 | 0.0337 |
ENSCAFG00000018597 | LAMA1 | 4.58776 | 0.00025 |
ENSCAFG00000029131 | HAPLN1 | 4.61072 | 0.00015 |
ENSCAFG00000031443 | EREG | 5.61347 | 0.02875 |
Gene Set | Database | Description | Size | Expect | Ratio | False Discovery Rate (FDR) |
---|---|---|---|---|---|---|
hsa05414 | KEGG | Dilated cardiomyopathy | 90 | 5.9888 | 2.6717 | 0.04748 |
hsa05410 | KEGG | Hypertrophic cardiomyopathy | 83 | 5.523 | 2.7159 | 0.04748 |
hsa04020 | KEGG | Calcium signaling pathway | 183 | 12.177 | 2.053 | 0.04748 |
P02746 | Panther | Heme biosynthesis | 12 | 0.96911 | 7.2231 | 0.001603 |
R-HSA-397014 | Reactome | Muscle contraction | 206 | 13.605 | 2.7932 | 0.0075 |
R-HSA-189451 | Reactome | Heme biosynthesis | 11 | 0.72645 | 11.012 | 0.00 |
R-HSA-390522 | Reactome | Striated Muscle Contraction | 36 | 2.3775 | 5.468 | 0.000151 |
R-HSA-189445 | Reactome | Metabolism of porphyrins | 17 | 1.1227 | 8.0164 | 0.00017 |
R-HSA-109582 | Reactome | Hemostasis | 620 | 40.946 | 1.6363 | 0.014273 |
R-HSA-5578775 | Reactome | Ion homeostasis | 56 | 3.6983 | 3.5151 | 0.018011 |
R-HSA-5576891 | Reactome | Cardiac conduction | 141 | 9.3118 | 2.3626 | 0.037904 |
OSA Cases and Diagnosis | IWH (n = 379) | Rottweiler (n = 1019) |
---|---|---|
Number of OSA cases (%) | 0.53 | 3.04 |
Male age of diagnosis (mean, years) | 5.34 | 7.65 |
Female age of diagnosis (mean, years) | 7.00 ** | 8.50 * |
Breed | Group | Diagnosis and Age | AR1 Q-Repeat | AR2 Q-Repeat | AR Q-Repeat Number (Mean ± SEM) |
---|---|---|---|---|---|
IWH | Male | OSA | 10.25 ± 0.25 (4) | 24.50 ± 0.29 (4) | 34.75 ± 0.25 (4) |
Non OSA over 6.5 years | 10.05 ± 0.05 (19) | 24.31 ± 0.12 (16) | 34.31 ± 0.12 (16) | ||
Female | OSA | 10.13 ± 0.13 (8) | 24.57 ± 0.13 (7) | 34.57 ± 0.13 (7) | |
Non OSA over 9 years | 10.04 ± 0.04 (13) | 24.19 ± 0.16 (13) | 34.23 ± 0.15 (13) | ||
Rottweiler | Male | OSA | 11.00 ± 0.00 (12) | 23.00 ± 0.00 (12) | 34.00 ± 0.00 (12) |
Non OSA over 9 years | 11.00 ± 0.00 (49) | 23.00 ± 0.00 (50) | 34.00 ± 0.00 (49) | ||
Female | OSA | 11.03 ± 0.03 (19) | 23.00 ± 0.00 (18) | 34.03 ± 0.03 (18) | |
Non OSA over 10 years | 11.00 ± 0.00 (43) | 22.98 ± 0.02 (45) | 34.00 ± 0.00 (43) |
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Simpson, S.; Dunning, M.; de Brot, S.; Alibhai, A.; Bailey, C.; Woodcock, C.L.; Mestas, M.; Akhtar, S.; Jeyapalan, J.N.; Lothion-Roy, J.; et al. Molecular Characterisation of Canine Osteosarcoma in High Risk Breeds. Cancers 2020, 12, 2405. https://doi.org/10.3390/cancers12092405
Simpson S, Dunning M, de Brot S, Alibhai A, Bailey C, Woodcock CL, Mestas M, Akhtar S, Jeyapalan JN, Lothion-Roy J, et al. Molecular Characterisation of Canine Osteosarcoma in High Risk Breeds. Cancers. 2020; 12(9):2405. https://doi.org/10.3390/cancers12092405
Chicago/Turabian StyleSimpson, Siobhan, Mark Dunning, Simone de Brot, Aziza Alibhai, Clara Bailey, Corinne L. Woodcock, Madeline Mestas, Shareen Akhtar, Jennie N. Jeyapalan, Jennifer Lothion-Roy, and et al. 2020. "Molecular Characterisation of Canine Osteosarcoma in High Risk Breeds" Cancers 12, no. 9: 2405. https://doi.org/10.3390/cancers12092405
APA StyleSimpson, S., Dunning, M., de Brot, S., Alibhai, A., Bailey, C., Woodcock, C. L., Mestas, M., Akhtar, S., Jeyapalan, J. N., Lothion-Roy, J., Emes, R. D., Allegrucci, C., Rizvanov, A. A., Mongan, N. P., & Rutland, C. S. (2020). Molecular Characterisation of Canine Osteosarcoma in High Risk Breeds. Cancers, 12(9), 2405. https://doi.org/10.3390/cancers12092405