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Immune classification and identification of prognostic genes for uveal melanoma based on six immune cell signatures

Cutaneous melanoma could be treated by immunotherapy, which only has limited efficacy on uveal melanoma (UM). UM immunotyping for predicting immunotherapeutic responses and guiding immunotherapy should be better understood. This study identified molecular subtypes and key genetic markers associated...

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Autores principales: Gao, Guohong, Yu, Zhilong, Zhao, Xiaoyan, Fu, Xinyi, Liu, Shengsheng, Liang, Shan, Deng, Aijun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8593069/
https://www.ncbi.nlm.nih.gov/pubmed/34782661
http://dx.doi.org/10.1038/s41598-021-01627-2
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author Gao, Guohong
Yu, Zhilong
Zhao, Xiaoyan
Fu, Xinyi
Liu, Shengsheng
Liang, Shan
Deng, Aijun
author_facet Gao, Guohong
Yu, Zhilong
Zhao, Xiaoyan
Fu, Xinyi
Liu, Shengsheng
Liang, Shan
Deng, Aijun
author_sort Gao, Guohong
collection PubMed
description Cutaneous melanoma could be treated by immunotherapy, which only has limited efficacy on uveal melanoma (UM). UM immunotyping for predicting immunotherapeutic responses and guiding immunotherapy should be better understood. This study identified molecular subtypes and key genetic markers associated with immunotherapy through immunosignature analysis. We screened a 6-immune cell signature simultaneously correlated with UM prognosis. Three immune subtypes (IS) were determined based on the 6-immune cell signature. Overall survival (OS) of IS3 was the longest. Significant differences of linear discriminant analysis (LDA) score were detected among the three IS types. IS3 with the highest LDA score showed a low immunosuppression. IS1 with the lowest LDA score was more immunosuppressive. LDA score was significantly negatively correlated with most immune checkpoint-related genes, and could reflect UM patients’ response to anti-PD1 immunotherapy. Weighted correlation network analysis (WGCNA) identified that salmon, purple, yellow modules were related to IS and screened 6 prognostic genes. Patients with high-expressed NME1 and TMEM255A developed poor prognosis, while those with high-expressed BEX5 and ROPN1 had better prognosis. There was no notable difference in OS between patients with high-expressed LRRN1 and ST13 and those with low-expressed LRRN1 and ST13. NME1, TMEM255A, Bex5 and ROPN1 showed potential prognostic significance in UM.
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spelling pubmed-85930692021-11-16 Immune classification and identification of prognostic genes for uveal melanoma based on six immune cell signatures Gao, Guohong Yu, Zhilong Zhao, Xiaoyan Fu, Xinyi Liu, Shengsheng Liang, Shan Deng, Aijun Sci Rep Article Cutaneous melanoma could be treated by immunotherapy, which only has limited efficacy on uveal melanoma (UM). UM immunotyping for predicting immunotherapeutic responses and guiding immunotherapy should be better understood. This study identified molecular subtypes and key genetic markers associated with immunotherapy through immunosignature analysis. We screened a 6-immune cell signature simultaneously correlated with UM prognosis. Three immune subtypes (IS) were determined based on the 6-immune cell signature. Overall survival (OS) of IS3 was the longest. Significant differences of linear discriminant analysis (LDA) score were detected among the three IS types. IS3 with the highest LDA score showed a low immunosuppression. IS1 with the lowest LDA score was more immunosuppressive. LDA score was significantly negatively correlated with most immune checkpoint-related genes, and could reflect UM patients’ response to anti-PD1 immunotherapy. Weighted correlation network analysis (WGCNA) identified that salmon, purple, yellow modules were related to IS and screened 6 prognostic genes. Patients with high-expressed NME1 and TMEM255A developed poor prognosis, while those with high-expressed BEX5 and ROPN1 had better prognosis. There was no notable difference in OS between patients with high-expressed LRRN1 and ST13 and those with low-expressed LRRN1 and ST13. NME1, TMEM255A, Bex5 and ROPN1 showed potential prognostic significance in UM. Nature Publishing Group UK 2021-11-15 /pmc/articles/PMC8593069/ /pubmed/34782661 http://dx.doi.org/10.1038/s41598-021-01627-2 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This 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/) .
spellingShingle Article
Gao, Guohong
Yu, Zhilong
Zhao, Xiaoyan
Fu, Xinyi
Liu, Shengsheng
Liang, Shan
Deng, Aijun
Immune classification and identification of prognostic genes for uveal melanoma based on six immune cell signatures
title Immune classification and identification of prognostic genes for uveal melanoma based on six immune cell signatures
title_full Immune classification and identification of prognostic genes for uveal melanoma based on six immune cell signatures
title_fullStr Immune classification and identification of prognostic genes for uveal melanoma based on six immune cell signatures
title_full_unstemmed Immune classification and identification of prognostic genes for uveal melanoma based on six immune cell signatures
title_short Immune classification and identification of prognostic genes for uveal melanoma based on six immune cell signatures
title_sort immune classification and identification of prognostic genes for uveal melanoma based on six immune cell signatures
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8593069/
https://www.ncbi.nlm.nih.gov/pubmed/34782661
http://dx.doi.org/10.1038/s41598-021-01627-2
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