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Expression profiling of cutaneous squamous cell carcinoma with perineural invasion implicates the p53 pathway in the process

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ABSTRACT

Squamous cell carcinoma (SCC) is the second most common cancer worldwide and accounts for approximately 30% of all keratinocyte cancers. The vast majority of cutaneous SCCs of the head and neck (cSCCHN) are readily curable with surgery and/or radiotherapy unless high-risk features are present. Perineural invasion (PNI) is recognized as one of these high-risk features. The molecular changes during clinical PNI in cSCCHN have not been previously investigated. In this study, we assessed the global gene expression differences between cSCCHN with or without incidental or clinical PNI. The results of the analysis showed signatures of gene expression representative of activation of p53 in tumors with PNI compared to tumors without, amongst other alterations. Immunohistochemical staining of p53 showed cSCCHN with clinical PNI to be more likely to exhibit a diffuse over-expression pattern, with no tumors showing normal p53 staining. DNA sequencing of cSCCHN samples with clinical PNI showed no difference in mutation number or position with samples without PNI, however a significant difference was observed in regulators of p53 degradation, stability and activity. Our results therefore suggest that cSCCHN with clinical PNI may be more likely to contain alterations in the p53 pathway, compared to cSCCHN without PNI.

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Expression profiling of cSCCHN, cSCCHN with incidental PNI or clinical PNI.(a) Genes found to be differentially expressed between the three groups using one-way ANOVA, P < 0.05, were clustered using Euclidian distance metric and Ward’s linkage, for visualisation. Red – cSCCHN, blue – cSCCHN with Incidental PNI, maroon – cSCCHN with Clinical PNI. Scale below shows difference in fold expression. (b) Venn diagram comparison of differentially expressed genes for pairwise analysis using t-test, P < 0.05 with Benjamini and Hochberg False Discovery Rate. (c) Mechanistic network of upstream regulator signature for differences observed in p53 signaling pathway. (d) Mechanistic network of upstream regulator signature for differences observed in p53 signaling pathway. Both mechanistic network figures were taken from Ingenuity Pathway Analysis software.
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f1: Expression profiling of cSCCHN, cSCCHN with incidental PNI or clinical PNI.(a) Genes found to be differentially expressed between the three groups using one-way ANOVA, P < 0.05, were clustered using Euclidian distance metric and Ward’s linkage, for visualisation. Red – cSCCHN, blue – cSCCHN with Incidental PNI, maroon – cSCCHN with Clinical PNI. Scale below shows difference in fold expression. (b) Venn diagram comparison of differentially expressed genes for pairwise analysis using t-test, P < 0.05 with Benjamini and Hochberg False Discovery Rate. (c) Mechanistic network of upstream regulator signature for differences observed in p53 signaling pathway. (d) Mechanistic network of upstream regulator signature for differences observed in p53 signaling pathway. Both mechanistic network figures were taken from Ingenuity Pathway Analysis software.

Mentions: In total, 27,607 entities were expressed in at least one sample across the entire cohort, representing transcripts from 19,770 genes. One-way ANOVA analysis with multiple testing correction (Benjamini and Hochberg False Discovery Rate) identified 6,917 genes that showed significantly different expression between the groups (P ≤ 0.05). Hierarchical clustering was used to visualize these results (Fig. 1a). Genes were inversely expressed in cSCCHN without any invasion and with clinical PNI, and showed mid-level expression in disease with incidental PNI. Pairwise analyses between each pair of the three groups (t-test, P ≤ 0.05 with Benjamini and Hochberg False Discovery Rate) were performed. Comparison between the clinical and incidental PNI groups demonstrated 342 genes with significantly different expression (Supplementary Table S2). When clinical PNI and cSCCHN were compared, 7,793 significantly different genes were identified (Supplementary Table S3). Comparison between incidental PNI and SCC showed 2,412 genes with significantly different expression (Supplementary Table S4). There were many differentially expressed genes in cSCCHN with clinical PNI compared to cSCCHN without PNI that were not shared in the incidental PNI comparison (Fig. 1b). Although there were fewer differences between clinical PNI and incidental PNI, the majority of these differences were not found in the incidental PNI compared to cSCCHN (Fig. 1b). This suggests the possibility that clinical PNI of cSCCHN arises in a different manner or pathway to that of cSCCHN with incidental PNI.


Expression profiling of cutaneous squamous cell carcinoma with perineural invasion implicates the p53 pathway in the process
Expression profiling of cSCCHN, cSCCHN with incidental PNI or clinical PNI.(a) Genes found to be differentially expressed between the three groups using one-way ANOVA, P < 0.05, were clustered using Euclidian distance metric and Ward’s linkage, for visualisation. Red – cSCCHN, blue – cSCCHN with Incidental PNI, maroon – cSCCHN with Clinical PNI. Scale below shows difference in fold expression. (b) Venn diagram comparison of differentially expressed genes for pairwise analysis using t-test, P < 0.05 with Benjamini and Hochberg False Discovery Rate. (c) Mechanistic network of upstream regulator signature for differences observed in p53 signaling pathway. (d) Mechanistic network of upstream regulator signature for differences observed in p53 signaling pathway. Both mechanistic network figures were taken from Ingenuity Pathway Analysis software.
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC5035993&req=5

f1: Expression profiling of cSCCHN, cSCCHN with incidental PNI or clinical PNI.(a) Genes found to be differentially expressed between the three groups using one-way ANOVA, P < 0.05, were clustered using Euclidian distance metric and Ward’s linkage, for visualisation. Red – cSCCHN, blue – cSCCHN with Incidental PNI, maroon – cSCCHN with Clinical PNI. Scale below shows difference in fold expression. (b) Venn diagram comparison of differentially expressed genes for pairwise analysis using t-test, P < 0.05 with Benjamini and Hochberg False Discovery Rate. (c) Mechanistic network of upstream regulator signature for differences observed in p53 signaling pathway. (d) Mechanistic network of upstream regulator signature for differences observed in p53 signaling pathway. Both mechanistic network figures were taken from Ingenuity Pathway Analysis software.
Mentions: In total, 27,607 entities were expressed in at least one sample across the entire cohort, representing transcripts from 19,770 genes. One-way ANOVA analysis with multiple testing correction (Benjamini and Hochberg False Discovery Rate) identified 6,917 genes that showed significantly different expression between the groups (P ≤ 0.05). Hierarchical clustering was used to visualize these results (Fig. 1a). Genes were inversely expressed in cSCCHN without any invasion and with clinical PNI, and showed mid-level expression in disease with incidental PNI. Pairwise analyses between each pair of the three groups (t-test, P ≤ 0.05 with Benjamini and Hochberg False Discovery Rate) were performed. Comparison between the clinical and incidental PNI groups demonstrated 342 genes with significantly different expression (Supplementary Table S2). When clinical PNI and cSCCHN were compared, 7,793 significantly different genes were identified (Supplementary Table S3). Comparison between incidental PNI and SCC showed 2,412 genes with significantly different expression (Supplementary Table S4). There were many differentially expressed genes in cSCCHN with clinical PNI compared to cSCCHN without PNI that were not shared in the incidental PNI comparison (Fig. 1b). Although there were fewer differences between clinical PNI and incidental PNI, the majority of these differences were not found in the incidental PNI compared to cSCCHN (Fig. 1b). This suggests the possibility that clinical PNI of cSCCHN arises in a different manner or pathway to that of cSCCHN with incidental PNI.

View Article: PubMed Central - PubMed

ABSTRACT

Squamous cell carcinoma (SCC) is the second most common cancer worldwide and accounts for approximately 30% of all keratinocyte cancers. The vast majority of cutaneous SCCs of the head and neck (cSCCHN) are readily curable with surgery and/or radiotherapy unless high-risk features are present. Perineural invasion (PNI) is recognized as one of these high-risk features. The molecular changes during clinical PNI in cSCCHN have not been previously investigated. In this study, we assessed the global gene expression differences between cSCCHN with or without incidental or clinical PNI. The results of the analysis showed signatures of gene expression representative of activation of p53 in tumors with PNI compared to tumors without, amongst other alterations. Immunohistochemical staining of p53 showed cSCCHN with clinical PNI to be more likely to exhibit a diffuse over-expression pattern, with no tumors showing normal p53 staining. DNA sequencing of cSCCHN samples with clinical PNI showed no difference in mutation number or position with samples without PNI, however a significant difference was observed in regulators of p53 degradation, stability and activity. Our results therefore suggest that cSCCHN with clinical PNI may be more likely to contain alterations in the p53 pathway, compared to cSCCHN without PNI.

No MeSH data available.