MACE RNA Sequencing Analysis of Conjunctival Squamous Cell Carcinoma Using Formalin-Fixed Paraffin-Embedded Tumor Tissue

Abstract

Purpose : Squamous cell carcinoma (SCC) of the conjunctiva is the most common malignancy of the ocular surface and frequently requires an extensive surgical treatment. We performed transcriptome-wide gene expression profiling to investigate the transcriptional alterations in SCC compared to benign tumors of the conjunctiva or healthy tissue and to identify potential future biomarkers.

Methods : Seven subjects with SCC and seven subjects with papilloma of the conjunctiva who had been treated at the Eye Center of the University Freiburg were included in this study. Healthy conjunctival tissue from ten subjects who underwent retinal detachment surgery served as control. Following resection, tumor and control tissue samples were fixed in formalin and embedded in paraffin (FFPE) according to a standardized protocol. Total RNA was isolated from FFPE specimens and massive analysis of cDNA ends (MACE) libraries were sequenced applying TrueQuant bias elimination. Normalization and test for differential gene expression were performed using DEGSeq, prior to quantifying differential transcription as the log2 ratio of the normalized values between two groups. Gene Ontology (GO) Enrichment Analysis was performed using the web-based toolkit www.pantherdb.org.

Results : MACE analysis revealed the differential expression of 204 significantly upregulated (log2fold>2) and 148 significantly downregulated factors (log2fold<2) in SCC compared to healthy conjunctiva. According to the GO enrichment analysis, 34 of the upregulated factors belong to the GO term cornification (enrichment p value 2.85E-36) and 45 to keratinocyte differentiation (p = 2.67E-38). Two of the most strongly upregulated gene transcripts in SCC compared to both conjunctival papilloma (log2fold = 7.86 and 3.27, respectively) and healthy tissue (log2fold = 6.82 and 6.70) are SPINK6 (serine peptidase inhibitor, Kazal type 6) and SBSN (suprabasin).

Conclusions : Our results demonstrate that SPINK6 and SBSN, both known to be expressed in differentiating keratinocytes, are highly upregulated in conjunctival carcinoma when compared to benign lesions or healthy conjunctiva. Both factors may serve as biomarkers for the diagnosis of malignant conjunctival tumors in the future. Further studies with larger sample size are warranted to validate the transcripts as prognostic factors or potential treatment targets for conjunctival SCC with confidence.

This is an abstract that was submitted for the 2018 ARVO Annual Meeting, held in Honolulu, Hawaii, April 29 - May 3, 2018.