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The identification of gene signatures in patients with extranodal NK/T-cell lymphoma from a pair of twins
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 neoantig...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8650233/ https://www.ncbi.nlm.nih.gov/pubmed/34872521 http://dx.doi.org/10.1186/s12885-021-09023-9 |
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author | Wang, Yang Tan, Huaicheng Yu, Ting Ma, Xuelei Chen, Xiaoxuan Jing, Fangqi Zou, Liqun Shi, Huashan |
author_facet | Wang, Yang Tan, Huaicheng Yu, Ting Ma, Xuelei Chen, Xiaoxuan Jing, Fangqi Zou, Liqun Shi, Huashan |
author_sort | Wang, Yang |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-8650233 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-86502332021-12-07 The identification of gene signatures in patients with extranodal NK/T-cell lymphoma from a pair of twins Wang, Yang Tan, Huaicheng Yu, Ting Ma, Xuelei Chen, Xiaoxuan Jing, Fangqi Zou, Liqun Shi, Huashan BMC Cancer Research 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. BioMed Central 2021-12-06 /pmc/articles/PMC8650233/ /pubmed/34872521 http://dx.doi.org/10.1186/s12885-021-09023-9 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Wang, Yang Tan, Huaicheng Yu, Ting Ma, Xuelei Chen, Xiaoxuan Jing, Fangqi Zou, Liqun Shi, Huashan The identification of gene signatures in patients with extranodal NK/T-cell lymphoma from a pair of twins |
title | The identification of gene signatures in patients with extranodal NK/T-cell lymphoma from a pair of twins |
title_full | The identification of gene signatures in patients with extranodal NK/T-cell lymphoma from a pair of twins |
title_fullStr | The identification of gene signatures in patients with extranodal NK/T-cell lymphoma from a pair of twins |
title_full_unstemmed | The identification of gene signatures in patients with extranodal NK/T-cell lymphoma from a pair of twins |
title_short | The identification of gene signatures in patients with extranodal NK/T-cell lymphoma from a pair of twins |
title_sort | identification of gene signatures in patients with extranodal nk/t-cell lymphoma from a pair of twins |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8650233/ https://www.ncbi.nlm.nih.gov/pubmed/34872521 http://dx.doi.org/10.1186/s12885-021-09023-9 |
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