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New Generation RNA Sequencing of Urethral Cancer Compared with Benign Urethral Tissue: Implications for Diagnostic and Future Research Advancements
Nickolas Kinachtchouk, MD, MBA1, Samantha Freeman, MD
1, Rachael Gotlieb, MD
1, Kailey Hooper, BS
1, Travis Sullivan, MS
1, Eric Burks, MD
2, Kimberly Rieger-Christ, PhD
1, Alex J. Vanni, MD
1.
1Lahey Hospital, Burlington, MA, USA,
2Boston Medical Center, Boston, MA, USA.
Background:Primary urethral cancer is rare with a projected incidence of 4.3 and 1.5 cases per million for men and women respectively.
1 Given its rarity, there is limited data regarding diagnostic testing and treatment.
2,3 Surgery remains the mainstay of treatment as research is limited regarding other treatment modalities. Previous studies have performed genomic sequencing of urethral cancer, but none have compared it to benign tissue.
4–8 The goal of this study is to identify possible molecular targets to guide diagnosis or treatment of urethral cancer.
Methods:Cases of penile and urethral SCC were identified from a retrospective review at a single institution. All cases were reviewed by an individual pathologist to confirm diagnosis and identify malignant tissue that originated from the urethra or benign urethral tissue exclusive of disease. FFPE tissue was macrodissected from the malignant and benign urethral regions of interest. In total, there were 12 malignant samples and 10 benign samples. Total RNA was extracted using the Qiagen miRNeasy FFPE kit. Differentially expressed genes (DEGs) were identified through NGS RNA sequencing analysis.
Results: The analysis identified 525 genes differentially expressed at least two-fold (FDR<0.001) between malignant and benign urethral tissue. Of these, 309 genes were upregulated in the malignant tissue and 216 were downregulated. Gene ontology analysis of the DEGs identified functions associated with cell division, cell proliferation, cell differentiation, and angiogenesis. Several of the DEGs identified here have been associated with various types of SCC, including CDKN2A, MMP1, TNC, SPP1, LAMP3, and PRDM16: while many appear to be unique to urethral SCC.
Conclusions:The identification of DEGs between urethral cancer and benign tissues provides a framework for future research. These genes may hold promise as biomarkers of urethral cancer. Future studies looking at their function and clinical relevance may lead to diagnostic tools and novel therapeutic strategies.
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