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BMC Cancer
Published in: BMC Cancer 1/2021

Open Access 01-12-2021 | Lymphoma | Research

The identification of gene signatures in patients with extranodal NK/T-cell lymphoma from a pair of twins

Authors: Yang Wang, Huaicheng Tan, Ting Yu, Xuelei Ma, Xiaoxuan Chen, Fangqi Jing, Liqun Zou, Huashan Shi

Published in: BMC Cancer | Issue 1/2021

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Abstract

Background

There 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.

Methods

We 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.

Results

We 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.

Conclusion

We identified four ENKTL markers (ZNF141, FCGR2C, NES and CDC27) in patients with extranodal NK/T-cell lymphoma.
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Metadata
Title
The identification of gene signatures in patients with extranodal NK/T-cell lymphoma from a pair of twins
Authors
Yang Wang
Huaicheng Tan
Ting Yu
Xuelei Ma
Xiaoxuan Chen
Fangqi Jing
Liqun Zou
Huashan Shi
Publication date
01-12-2021
Publisher
BioMed Central
Keyword
Lymphoma
Published in
BMC Cancer / Issue 1/2021
Electronic ISSN: 1471-2407
DOI
https://doi.org/10.1186/s12885-021-09023-9

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