Abstract

BackgroundThere is no unified treatment standard for patients with extranodal NK/T-cell lymphoma (ENKTL). Cancer neoantigens are the result of somatic mutations and cancer-specific. Increased number of somatic mutations are associated with anti-cancer effects. Screening out ENKTL-specific neoantigens on the surface of cancer cells relies on the understanding of ENKTL mutation patterns. Hence, it is imperative to identify ENKTL-specific genes for ENKTL diagnosis, the discovery of tumor-specific neoantigens and the development of novel therapeutic strategies. We investigated the gene signatures of ENKTL patients.MethodsWe collected the peripheral blood of a pair of twins for sequencing to identify unique variant genes. One of the twins is diagnosed with ENKTL. Seventy samples were analyzed by Robust Multi-array Analysis (RMA). Two methods (elastic net and Support Vector Machine-Recursive Feature Elimination) were used to select unique genes. Next, we performed functional enrichment analysis and pathway enrichment analysis. Then, we conducted single-sample gene set enrichment analysis of immune infiltration and validated the expression of the screened markers with limma packages.ResultsWe screened out 126 unique variant genes. Among them, 11 unique genes were selected by the combination of elastic net and Support Vector Machine-Recursive Feature Elimination. Subsequently, GO and KEGG analysis indicated the biological function of identified unique genes. GSEA indicated five immunity-related pathways with high signature scores. In patients with ENKTL and the group with high signature scores, a proportion of functional immune cells are all of great infiltration. We finally found that CDC27, ZNF141, FCGR2C and NES were four significantly differential genes in ENKTL patients. ZNF141, FCGR2C and NES were upregulated in patients with ENKTL, while CDC27 was significantly downregulated.ConclusionWe identified four ENKTL markers (ZNF141, FCGR2C, NES and CDC27) in patients with extranodal NK/T-cell lymphoma.

Highlights

  • Extranodal NK/T-cell lymphoma (ENKTL) is a subtype of non-Hodgkin lymphoma characterized by progressive lesions in nasal cavities, the middle of the face, upper aerodigestive tracts and other non-nasal sites

  • Our study aims at identifying gene signatures in patients with extranodal NK/T-cell lymphoma

  • To understand the biological function of unique mutated genes, GO (Gene Ontology) enrichment analysis and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis were performed in DAVID

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Summary

Introduction

Extranodal NK/T-cell lymphoma (ENKTL) is a subtype of non-Hodgkin lymphoma characterized by progressive lesions in nasal cavities, the middle of the face, upper aerodigestive tracts and other non-nasal sites. Immunotherapy for programmed cell death protein 1 (PD-1) and programmed cell death protein ligand 1 (PD-L1) has enormously improved the therapeutic effect of ENKTL [8, 9]. Searching for tumorspecific genes is beneficial for ENKTL diagnosis, the discovery of tumor-specific neoantigens and the development of novel therapeutic strategies. These tumorspecific genes can be used as predictors of the prognosis. There is no unified treatment standard for patients with extranodal NK/T-cell lymphoma (ENKTL). Screening out ENKTL-specific neoantigens on the surface of cancer cells relies on the understanding of ENKTL mutation patterns. It is imperative to identify ENKTL-specific genes for ENKTL diagnosis, the discovery of tumor-specific neoantigens and the development of novel therapeutic strategies.

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