The microdissected gene expression landscape of nasopharyngeal cancer reveals vulnerabilities in FGF and noncanonical NF-κB signaling.

Abstract

Nasopharyngeal cancer (NPC) is an Epstein-Barr virus (EBV)-positive epithelial malignancy with an extensive inflammatory infiltrate. Traditional RNA-sequencing techniques uncovered only microenvironment signatures, while the gene expression of the tumor epithelial compartment has remained a mystery. Here, we use Smart-3SEQ to prepare transcriptome-wide gene expression profiles from microdissected NPC tumors, dysplasia, and normal controls. We describe changes in biological pathways across the normal to tumor spectrum and show that fibroblast growth factor (FGF) ligands are overexpressed in NPC tumors, while negative regulators of FGF signaling, including SPRY1, SPRY2, and LGALS3, are down-regulated early in carcinogenesis. Within the NF-κB signaling pathway, the critical noncanonical transcription factors, RELB and NFKB2, are enriched in the majority of NPC tumors. We confirm the responsiveness of EBV-positive NPC cell lines to targeted inhibition of these pathways, reflecting the heterogeneity in NPC patient tumors. Our data comprehensively describe the gene expression landscape of NPC and unravel the mysteries of receptor tyrosine kinase and NF-κB pathways in NPC.

• Authors: Joshua K Tay, Chunfang Zhu, June Ho Shin, Shirley X Zhu, Sushama Varma, Joseph W Foley, Sujay Vennam, Yim Ling Yip, Chuan Keng Goh, De Yun Wang, Kwok Seng Loh, Sai Wah Tsao, Quynh-Thu Le, John B Sunwoo, Robert B West
• Journal: Science advances (Sci Adv) Vol. 8 Issue 14 Pg. eabh2445 (04 08 2022) ISSN: 2375-2548 [Electronic] United States
• PMID: 35394843 (Publication Type: Journal Article)

Chemical References

• Intracellular Signaling Peptides and Proteins
• Membrane Proteins
• NF-kappa B
• SPRY2 protein, human
• Fibroblast Growth Factors

Topics

• Cell Line, Tumor
• Epstein-Barr Virus Infections (genetics, pathology)
• Fibroblast Growth Factors (metabolism)
• Gene Expression
• Herpesvirus 4, Human (genetics, metabolism)
• Humans
• Intracellular Signaling Peptides and Proteins (genetics)
• Membrane Proteins (metabolism)
• NF-kappa B (metabolism)
• Nasopharyngeal Carcinoma (genetics)
• Nasopharyngeal Neoplasms (genetics, metabolism, pathology)
• Signal Transduction
• Tumor Microenvironment