Lack of Conserved miRNA Deregulation in HPV-Induced Squamous Cell Carcinomas

Abstract

Squamous cell carcinomas (SCCs) in the anogenital and head and neck regions are associated with high-risk types of human papillomaviruses (HR-HPV). Deregulation of miRNA expression is an important contributor to carcinogenesis. This study aimed to pinpoint commonly and uniquely deregulated miRNAs in cervical, anal, vulvar, and tonsillar tumors of viral or non-viral etiology, searching for a common set of deregulated miRNAs linked to HPV-induced carcinogenesis. RNA was extracted from tumors and nonmalignant tissues from the same locations. The miRNA expression level was determined by next-generation sequencing. Differential expression of miRNAs was calculated, and the patterns of miRNA deregulation were compared between tumors. The total of deregulated miRNAs varied between tumors of different locations by two orders of magnitude, ranging from 1 to 282. The deregulated miRNA pool was largely tumor-specific. In tumors of the same location, a low proportion of miRNAs were exclusively deregulated and no deregulated miRNA was shared by all four types of HPV-positive tumors. The most significant overlap of deregulated miRNAs was found between tumors which differed in location and HPV status (HPV-positive cervical tumors vs. HPV-negative vulvar tumors). Our results imply that HPV infection does not elicit a conserved miRNA deregulation in SCCs.

Keywords: human papillomavirus; microRNA; squamous cell carcinoma.

Figure 2

DE of miRNAs in tumors of different locations and HPV status. (a) Total numbers of differentially expressed miRNAs in each of the seven analyzed tumor types. (b) The miRNAs that exhibited shared deregulation across the seven studied tumor types. The values denote the total numbers of miRNAs which were deregulated specifically in one tumor type and those whose deregulation was common to two, three, four, or five tumor types. No miRNAs were deregulated in more than five tumor types. (c) Venn diagrams depicting the numbers of unique and shared differentially expressed miRNAs among the seven studied tumor types. The font size range is denoted in the legend. Zero values were omitted. The placement of the sole miRNA deregulated in HPV-positive vulvar tumors (MIR451A) is marked with a red dot. DE values were calculated with respect to normal tissues and filtered (FC ≥ 2.0, padj ≤ 0.1; see Materials and Methods). For DE values of individual miRNAs, see Table S3. Venn diagrams were created using InteractiVenn [79].

Figure 1

Clustering of tissue samples by miRNA expression profiles. (a) PCA plot; (b) heatmap plot. The heatmap color scale depicts log-transformed abundance values of individual miRNAs among total miRNA sequencing reads. Visualizations were carried out in ClustVis [41].