A Whole-Transcriptomic Analysis of Canine Oral Melanoma: A Chance to Disclose the Radiotherapy Effect and Outcome-Associated Gene Signature
Abstract
:1. Introduction
2. Materials and Methods
2.1. Animal Recruitment, Clinico-Pathological Features, Therapy, and Sample Acquisition
2.2. RNA Isolation from Biopsies and Blood Samples
2.3. RNA-Seq Library Preparation and Sequencing
2.4. Differential Expression Analysis and Functional Analysis
2.5. Spearman’s Correlation
2.6. Statistical Analysis
3. Results
3.1. Clinico-Pathological Features
3.2. Differential Expression Analysis and Functional Analysis
3.3. Spearman’s Correlation
4. Discussion
4.1. Transcriptomic Effect of RT on Blood and Tumour Samples
4.2. Transcriptomic Differences Associated with Overall Survival Time
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Ensembl Gene ID | Gene Name | Gene Description | lfc | logCPM | BHp |
---|---|---|---|---|---|
ENSCAFG00845016275 | GNGT1 | G protein subunit γ transducin 1 | −1.88 | 5.07 | 0.01 |
ENSCAFG00845030209 | SLCO2A1 | solute carrier organic anion transporter family member 2A1 | 2.79 | 3.23 | 0.01 |
ENSCAFG00845011968 | DDX43 | DEAD-box helicase 43 | −6.15 | 0.54 | 0.03 |
ENSCAFG00845009606 1 | (CDKN1A) 2 | 1.03 | 5.43 | 0.03 | |
ENSCAFG00845027527 1 | (LOC612587) 2 | 4.63 | 1.32 | 0.03 | |
ENSCAFG00845009602 | CENPK | centromere protein K | −1.25 | 3.51 | 0.03 |
ENSCAFG00845003828 | MT1E | metallothionein 1E | 1.05 | 6.40 | 0.03 |
ENSCAFG00845015023 1 | (C20H3orf14) 2 | −2.13 | 0.85 | 0.03 |
Ensembl Gene ID | Gene Name | Gene Description | lfc | logCPM | BHp |
---|---|---|---|---|---|
ENSCAFG00845008674 | ADAMTS2 | ADAM metallopeptidase with thrombospondin type 1 motif 2 | 3.09 | 1.78 | 0.001 |
ENSCAFG00845007491 | PROK2 | prokineticin 2 | −1.77 | 6.79 | 0.023 |
ENSCAFG00845016746 | XKRX | XK related X-linked | −1.35 | −0.59 | 0.003 |
ENSCAFG00845005455 | SLC28A3 | solute carrier family 28 member 3 | −1.26 | 4.00 | 0.002 |
ENSCAFG00845026869 | AMIGO2 | adhesion molecule with Ig-like domain 2 | −1.24 | −0.90 | 0.038 |
ENSCAFG00845001908 | KANK1 | KN motif and ankyrin repeat domains 1 | −1.21 | −0.27 | 0.001 |
ENSCAFG00845008460 | TNFAIP6 | TNF α-induced protein 6 | −1.17 | 1.25 | 0.008 |
ENSCAFG00845008349 | CD72 | CD72 molecule | −1.14 | 0.70 | 0.027 |
ENSCAFG00845016972 | MYBPC2 | myosin binding protein C2 | −1.13 | −0.58 | 0.012 |
ENSCAFG00845015333 | COL4A4 | collagen type IV α 4 chain | −1.10 | −0.50 | 0.029 |
ENSCAFG00845028251 | MYO18B | myosin XVIIIB | 1.08 | 0.85 | 0.023 |
ENSCAFG00845015341 | DLGAP3 | DLG-associated protein 3 | −1.06 | 1.19 | 0.000 |
ENSCAFG00845008907 | CRIP3 | cysteine-rich protein 3 | −1.05 | −0.22 | 0.018 |
ENSCAFG00845028917 1 | (LOC119864113) 2 | −1.02 | 0.53 | 0.044 | |
ENSCAFG00845002458 | LAYN | layilin | 1.02 | 1.32 | 0.030 |
ENSCAFG00845028881 1 | (LOC119864112) 2 | −1.01 | 7.64 | 0.000 | |
ENSCAFG00845030285 | STAB1 | stabilin 1 | 1.00 | 2.46 | 0.003 |
ENSCAFG00845003394 | MLXIPL | MLX interacting protein-like | 0.99 | −0.70 | 0.033 |
ENSCAFG00845014560 | AASS | aminoadipate–semialdehyde synthase | −0.98 | 3.14 | 0.045 |
ENSCAFG00845030320 | SLAMF1 | signalling lymphocytic activation molecule family member 1 | −0.98 | 2.49 | 0.008 |
ENSCAFG00845001649 | NIM1K | NIM1 serine/threonine protein kinase | −0.94 | 0.87 | 0.007 |
ENSCAFG00845015409 | CABLES1 | Cdk5 and Abl enzyme substrate 1 | −0.93 | 0.42 | 0.012 |
ENSCAFG00845004274 | IL21R | interleukin 21 receptor | −0.92 | 3.23 | 0.042 |
ENSCAFG00845006782 | CRISP2 | cysteine-rich secretory protein 3 | −0.91 | 3.11 | 0.006 |
ENSCAFG00845015621 | PSD3 | Pleckstrin and Sec7 domain containing 3 | −0.90 | 3.88 | 0.000 |
ENSCAFG00845029249 | LEF1 | lymphoid enhancer binding factor 1 | −0.90 | 5.77 | 0.025 |
ENSCAFG00845014724 | GCH1 | GTP cyclohydrolase 1 | −0.90 | 2.19 | 0.038 |
ENSCAFG00845007930 | CCR7 | C-C motif chemokine receptor 7 | −0.89 | 4.80 | 0.005 |
ENSCAFG00845000734 | SLC23A1 | marginal zone B and B1 cell-specific protein | 0.86 | 4.00 | 0.000 |
ENSCAFG00845008805 | SCML4 | Scm polycomb group protein-like 4 | −0.86 | 2.37 | 0.000 |
ENSCAFG00845028411 | TFDP2 | transcription factor Dp−2 | −0.85 | 6.51 | 0.004 |
ENSCAFG00845028315 | B3GALNT1 | β-1,3-N-acetylgalactosaminyltransferase 1 (globoside blood group) | 0.84 | 2.31 | 0.025 |
ENSCAFG00845009720 | TXK | TXK tyrosine kinase | −0.84 | 2.33 | 0.044 |
ENSCAFG00845021928 | TEX14 | testis-expressed 14, intercellular bridge forming factor | 0.82 | −0.08 | 0.007 |
ENSCAFG00845005503 | JAM3 | junctional adhesion molecule 3 | −0.81 | 1.22 | 0.045 |
ENSCAFG00845028387 | TOX | thymocyte selection-associated high-mobility group box | −0.81 | 2.46 | 0.021 |
ENSCAFG00845017349 | GPR84 | G protein-coupled receptor 84 | 0.80 | 2.69 | 0.038 |
ENSCAFG00845008004 | KLF10 | KLF transcription factor 10 | 0.79 | 6.22 | 0.016 |
ENSCAFG00845008786 | P2RY2 | purinergic receptor P2Y2 | 0.78 | 5.28 | 0.002 |
ENSCAFG00845002694 | G0S2 | G0/G1 switch 2 | 0.78 | 3.73 | 0.011 |
ENSCAFG00845018861 1 | (DSTN) 2 | destrin, actin depolymerizing factor | −0.75 | 1.83 | 0.000 |
ENSCAFG00845021223 | AQP3 | aquaporin 3 (Gill blood group) | 0.74 | 4.34 | 0.013 |
ENSCAFG00845014621 | SOCS3 | suppressor of cytokine signalling 3 | −0.72 | 3.24 | 0.038 |
ENSCAFG00845018321 | ATP10A | ATPase phospholipid transporting 10A (putative) | −0.72 | 3.17 | 0.002 |
ENSCAFG00845016371 | RGS10 | regulator of G protein signalling 10 | −0.70 | 4.31 | 0.001 |
ENSCAFG00845021432 | GNAZ | G protein subunit α z | −0.70 | 2.51 | 0.005 |
ENSCAFG00845023493 | TSPAN5 | tetraspanin 5 | −0.69 | 3.71 | 0.047 |
ENSCAFG00845005802 | VASH1 | vasohibin 1 | −0.68 | 2.33 | 0.039 |
ENSCAFG00845019977 | KCNMB4 | potassium calcium-activated channel subfamily M regulatory β subunit 4 | −0.68 | 1.49 | 0.006 |
ENSCAFG00845025551 1 | (ATP13A4) 2 | ATPase 13A4 | −0.66 | 2.48 | 0.007 |
ENSCAFG00845004641 | SPOCK2 | SPARC (osteonectin)-, cwcv-, and kazal-like domains proteoglycan 2 | −0.64 | 6.09 | 0.025 |
ENSCAFG00845016402 1 | (GNG11) 2 | G protein subunit γ 11 | −0.63 | 5.82 | 0.010 |
ENSCAFG00845009033 1 | (CCL14) 2 | C-C motif chemokine ligand 14 | −0.63 | 3.34 | 0.017 |
ENSCAFG00845000866 1 | (C4H1orf198) 2 | chromosome 4 C1orf198 homolog | −0.63 | 3.29 | 0.023 |
ENSCAFG00845008023 | PSEN2 | presenilin 2 | −0.62 | 3.05 | 0.001 |
ENSCAFG00845012374 | EHD3 | EH domain containing 3 | −0.60 | 4.48 | 0.031 |
ENSCAFG00845025918 | MYL9 | myosin light chain 9 | −0.60 | 5.95 | 0.028 |
ENSCAFG00845012329 | APC2 | APC regulator of WNT signalling pathway 2 | 0.59 | 1.30 | 0.011 |
ENSCAFG00845026987 | ITGB5 | integrin subunit β 5 | −0.59 | 3.04 | 0.008 |
Ensembl Gene ID | Gene Name | Gene Description | lfc | logCPM | BHp |
---|---|---|---|---|---|
ENSCAFG00845023887 | KRT76 | keratin 76 | 8.59 | 8.08 | 0.002 |
ENSCAFG00845014426 | ITGA8 | integrin subunit α 8 | 5.64 | 6.34 | 0.002 |
ENSCAFG00845000761 | MMP13 | matrix metallopeptidase 13 | −4.29 | 6.51 | 0.009 |
ENSCAFG00845010154 | PI16 | peptidase inhibitor 16 | 8.03 | 5.88 | 0.009 |
ENSCAFG00845004266 | APOA1 | apolipoprotein A1 | 6.36 | 3.63 | 0.009 |
ENSCAFG00845029417 | MFAP5 | microfibril-associated protein 5 | 4.52 | 5.26 | 0.014 |
ENSCAFG00845013295 | SVEP1 | sushi, von Willebrand factor type A, EGF, and pentraxin domain containing 1 | 3.71 | 5.28 | 0.019 |
ENSCAFG00845023760 | ELF5 | E74-like ETS transcription factor 5 | 4.37 | 2.07 | 0.019 |
ENSCAFG00845028592 | ANKRD55 | ankyrin repeat domain 55 | 5.82 | 3.03 | 0.022 |
ENSCAFG00845005444 | CDSN | corneodesmosin | 8.82 | 5.25 | 0.023 |
ENSCAFG00845005605 | SOSTDC1 | sclerostin domain containing 1 | 4.66 | 3.25 | 0.023 |
ENSCAFG00845029513 | WNT5B | Wnt family member 5B | −2.74 | 4.04 | 0.026 |
ENSCAFG00845001685 | UOX | urate oxidase | 3.98 | 3.37 | 0.026 |
ENSCAFG00845017608 | PLA2G4F | phospholipase A2 group IVF | 3.78 | 0.59 | 0.028 |
ENSCAFG00845025826 1 | (RPTN) 2 | repetin | 7.33 | 4.39 | 0.028 |
ENSCAFG00845029411 | GDPD2 | glycerophosphodiester phosphodiesterase domain containing 2 | 4.15 | 2.21 | 0.028 |
Ensembl Gene ID | Gene Name | Gene Description | lfc | logCPM | BHp |
---|---|---|---|---|---|
ENSCAFG00845013314 1 | (LOC111098753) 2 | −7.80 | −0.68 | 0.000004 | |
ENSCAFG00845027442 | TKTL1 | Transketolase-like 1 | 3.04 | 0.32 | 0.000004 |
ENSCAFG00845026120 | H4C4 | H4 clustered histone 4 | −7.35 | −1.10 | 0.03 |
Ensembl Gene ID | Gene Name | Gene Description | r | p |
---|---|---|---|---|
ENSCAFG00845023887 | KRT76 | keratin 76 | 0.57 | 0.15 |
ENSCAFG00845014426 | ITGA8 | integrin subunit α 8 | 0.33 | 0.43 |
ENSCAFG00845000761 | MMP13 | matrix metallopeptidase 13 | −0.79 | 0.03 |
ENSCAFG00845010154 | PI16 | peptidase inhibitor 16 | 0.33 | 0.43 |
ENSCAFG00845004266 | APOA1 | apolipoprotein A1 | 0.52 | 0.20 |
ENSCAFG00845029417 | MFAP5 | microfibril-associated protein 5 | 0.64 | 0.10 |
ENSCAFG00845013295 | SVEP1 | sushi, von Willebrand factor type A, EGF, and pentraxin domain containing 1 | 0.98 | 0.0004 |
ENSCAFG00845023760 | ELF5 | E74-like ETS transcription factor 5 | 0.62 | 0.12 |
ENSCAFG00845028592 | ANKRD55 | ankyrin repeat domain 55 | 0.45 | 0.27 |
ENSCAFG00845005444 | CDSN | corneodesmosin | 0.57 | 0.15 |
ENSCAFG00845005605 | SOSTDC1 | sclerostin domain containing 1 | 0.64 | 0.10 |
ENSCAFG00845029513 | WNT5B | Wnt family member 5B | −0.86 | 0.01 |
ENSCAFG00845001685 | UOX | urate oxidase | 0.48 | 0.24 |
ENSCAFG00845017608 | PLA2G4F | phospholipase A2 group IVF | 0.79 | 0.03 |
ENSCAFG00845025826 | RPTN | repetin | 0.36 | 0.39 |
ENSCAFG00845029411 | GDPD2 | glycerophosphodiester phosphodiesterase domain containing 2 | 0.55 | 0.17 |
ENSCAFG00845022756 | Novel gene 1 | 0.38 | 0.36 | |
ENSCAFG00845001333 | Novel gene 2 | 0.55 | 0.17 |
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Mucignat, G.; Montanucci, L.; Elgendy, R.; Giantin, M.; Laganga, P.; Pauletto, M.; Mutinelli, F.; Vascellari, M.; Leone, V.F.; Dacasto, M.; et al. A Whole-Transcriptomic Analysis of Canine Oral Melanoma: A Chance to Disclose the Radiotherapy Effect and Outcome-Associated Gene Signature. Genes 2024, 15, 1065. https://doi.org/10.3390/genes15081065
Mucignat G, Montanucci L, Elgendy R, Giantin M, Laganga P, Pauletto M, Mutinelli F, Vascellari M, Leone VF, Dacasto M, et al. A Whole-Transcriptomic Analysis of Canine Oral Melanoma: A Chance to Disclose the Radiotherapy Effect and Outcome-Associated Gene Signature. Genes. 2024; 15(8):1065. https://doi.org/10.3390/genes15081065
Chicago/Turabian StyleMucignat, Greta, Ludovica Montanucci, Ramy Elgendy, Mery Giantin, Paola Laganga, Marianna Pauletto, Franco Mutinelli, Marta Vascellari, Vito Ferdinando Leone, Mauro Dacasto, and et al. 2024. "A Whole-Transcriptomic Analysis of Canine Oral Melanoma: A Chance to Disclose the Radiotherapy Effect and Outcome-Associated Gene Signature" Genes 15, no. 8: 1065. https://doi.org/10.3390/genes15081065