Targeted gene expression profiling of inverted papilloma and squamous cell carcinoma

Background Inverted papilloma (IP) is a sinonasal tumor with a well‐known potential for malignant transformation. The purpose of this study was to identify the genes and pathways associated with IP, with progression to carcinoma‐in‐situ and invasive carcinoma. Methods To determine genes and molecular pathways that may indicate progression and correlate with histologic changes, we analyzed six IP without dysplasia, five IP with carcinoma‐in‐situ, and 13 squamous cell carcinoma ex‐IP by targeted sequencing. The HTG EdgeSeq Oncology Biomarker Panel coupled with next‐generation sequencing was used to evaluate 2560 transcripts associated with solid tumors. Results Progressive upregulation of 11 genes were observed (CALD1, COL1A1, COL3A1, COL4A2, COL5A2, FN1, ITGA5, LGALS1, MMP11, SERPINH1, SPARC) in the order of invasive carcinoma > carcinoma‐in‐situ > IP without dysplasia. When compared with IP without dysplasia, more genes are differentially expressed in invasive carcinoma than carcinoma‐in‐situ samples (341 downregulated/333 upregulated vs. 195 downregulated/156 upregulated). Gene set enrichment analysis determined three gene sets in common between the cohorts (epithelial mesenchymal transition, extracellular matrix organization, and coagulation). Conclusions Progressive upregulation of genes specific to IP malignant degeneration has significant clinical implications. This panel of 11 genes will improve concordance of histologic classification, which can directly impact treatment and patient outcomes. Additionally, future studies on larger tumor sets may observe upregulation in the gene panel that preceded histologic changes, which may be useful for further risk stratification.