Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2019 Apr 24;9(1):6511.
doi: 10.1038/s41598-019-42839-x.

Genome-wide analysis of canine oral malignant melanoma metastasis-associated gene expression

Affiliations

Genome-wide analysis of canine oral malignant melanoma metastasis-associated gene expression

K L Bowlt Blacklock et al. Sci Rep. .

Abstract

Oral malignant melanoma (OMM) is the most common canine melanocytic neoplasm. Overlap between the somatic mutation profiles of canine OMM and human mucosal melanomas suggest a shared UV-independent molecular aetiology. In common with human mucosal melanomas, most canine OMM metastasise. There is no reliable means of predicting canine OMM metastasis, and systemic therapies for metastatic disease are largely palliative. Herein, we employed exon microarrays for comparative expression profiling of FFPE biopsies of 18 primary canine OMM that metastasised and 10 primary OMM that did not metastasise. Genes displaying metastasis-associated expression may be targets for anti-metastasis treatments, and biomarkers of OMM metastasis. Reduced expression of CXCL12 in the metastasising OMMs implies that the CXCR4/CXCL12 axis may be involved in OMM metastasis. Increased expression of APOBEC3A in the metastasising OMMs may indicate APOBEC3A-induced double-strand DNA breaks and pro-metastatic hypermutation. DNA double strand breakage triggers the DNA damage response network and two Fanconi anaemia DNA repair pathway members showed elevated expression in the metastasising OMMs. Cross-validation was employed to test a Linear Discriminant Analysis classifier based upon the RT-qPCR-measured expression levels of CXCL12, APOBEC3A and RPL29. Classification accuracies of 94% (metastasising OMMs) and 86% (non-metastasising OMMs) were estimated.

PubMed Disclaimer

Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Genes differentially expressed between metastasising and non-metastasising OMMs. Exon microarray-measured expression of 331 genes in 18 metastasising (M) and 10 non-metastasising (NM) OMMs. The log2-transformed NM/M fold-change (x-axis) denotes the difference in gene expression between the M and NM OMMs. The minus log10-transformed permutation testing-adjusted t-test derived p-values (y-axis) indicates the statistical significances of gene expression differences. The dotted line illustrates the -log10 PTadj. p-value corresponding to a PTadj. p-value = 0.05. Red spheres represent the 3 genes subsequently employed in class prediction analysis.
Figure 2
Figure 2
RT-qPCR-measured expression levels in OMMs of 3 genes employed in Linear Discriminant Analysis classifier. Expression values that encompass those shared by 25% and 75% of the OMMs are denoted by the bottom and top of each box, respectively. The median expression value is represented by the line within each box, and the maximum and minimum expression values are indicated by the lines extending above and below each box, respectively. M = metastasising tumour; NM = Non-metastasising OMM.
Figure 3
Figure 3
Relationship between M and NM OMMs in the context of the expression levels of the genes employed for class prediction. Principal component analysis was performed using the RT-qPCR-measured expression levels of CXCL12, APOBEC3A and RPL29 in 17 M (red circles) and 7 NM (blue circles) OMMs. The first (PC1) and second (PC2) principal components are shown.
Figure 4
Figure 4
Class Prediction by Linear Discriminant Analysis. (A) Random sampling cross-validation. On each of 20 occasions, the RT-qPCR-measured expression values of 3 genes (CXCL12, RPL29 and APOBEC3A) which displayed >two-fold differential expression between M and NM OMMs were used to predict the class (M = a square, and NM = a circle) of 3 randomly-selected OMMs (2 M OMMs and 1 NM OMM, which represent 10% of the OMMs and constituted a ‘test set’). Prior to class prediction, the LDA classifier was trained using the gene expression data obtained for the remaining 90% of the OMMs (15 M and 6 NM OMMs, which constituted a ‘training set’). (B) Leave-one-out cross-validation. The RT-qPCR-measured expression values of 3 genes (CXCL12, RPL29 and APOBEC3A) which displayed >two-fold differential expression between M and NM OMMs were used to predict the class of each of 24 OMMs (17 M = squares, 7 NM = circles). On each of 24 occasions, the class of one OMM was predicted after the LDA classifier had been trained using the gene expression data obtained for the remaining 23 OMMs. Row 1 depicts the actual class of each OMM and row 2 the predicted class of each tumour.

Similar articles

Cited by

References

    1. Todoroff RJ, Brodey RS. Oral and pharyngeal neoplasia in the dog: a retrospective survey of 361 cases. J. Am. Vet. Med. Assoc. 1979;175:567–571. - PubMed
    1. Ramos-Vara JA, et al. Retrospective study of 338 canine oral melanomas with clinical, histologic, and immunohistochemical review of 129 cases. Vet. Pathol. 2000;37:597–608. doi: 10.1354/vp.37-6-597. - DOI - PubMed
    1. Gillard M, et al. Naturally occurring melanomas in dogs as models for non-UV pathways of human melanomas. Pigment Cell Melanoma Res. 2014;27:90–102. doi: 10.1111/pcmr.12170. - DOI - PubMed
    1. Smith SH, Goldschmidt MH, McManus PM. A comparative review of melanocytic neoplasms. Vet. Pathol. 2002;39:651–678. doi: 10.1354/vp.39-6-651. - DOI - PubMed
    1. Bergman PJ. Canine oral melanoma. Clin. Tech. Small Anim. Pract. 2007;22:55–60. doi: 10.1053/j.ctsap.2007.03.004. - DOI - PubMed

Publication types

MeSH terms