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      Immune signature-based risk stratification and prediction of immune checkpoint inhibitor’s efficacy for lung adenocarcinoma

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          Abstract

          Background

          Lung adenocarcinoma (LUAD) is a common pulmonary malignant disease with a poor prognosis. There were limited studies investigating the influences of the tumor immune microenvironment on LUAD patients’ survival and response to immune checkpoint inhibitors (ICIs).

          Methods

          Based on TCGA-LUAD dataset, we constructed a prognostic immune signature and validated its predictive capability in the internal as well as total datasets. Then, we explored the differences of tumor-infiltrating lymphocytes, tumor mutation burden, and patients’ response to ICI treatment between the high-risk score group and low-risk score group.

          Results

          This immune signature consisted of 17 immune-related genes, which was an independent prognostic factor for LUAD patients. In the low-risk score group, patients had better overall survival. Although the differences were non-significant, patients with low-risk scores had more tumor-infiltrating follicular helper T cells and fewer macrophages (M0), which were closely related to clinical outcomes. Additionally, the total TMB was markedly decreased in the low-risk score group. Using immunophenoscore as a surrogate of ICI response, we found that patients with low-risk scores had significantly higher immunophenoscore.

          Conclusion

          The 17-immune-related genes signature may have prognostic and predictive relevance with ICI therapy but needs prospective validation.

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          Most cited references45

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          edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

          Summary: It is expected that emerging digital gene expression (DGE) technologies will overtake microarray technologies in the near future for many functional genomics applications. One of the fundamental data analysis tasks, especially for gene expression studies, involves determining whether there is evidence that counts for a transcript or exon are significantly different across experimental conditions. edgeR is a Bioconductor software package for examining differential expression of replicated count data. An overdispersed Poisson model is used to account for both biological and technical variability. Empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference. The methodology can be used even with the most minimal levels of replication, provided at least one phenotype or experimental condition is replicated. The software may have other applications beyond sequencing data, such as proteome peptide count data. Availability: The package is freely available under the LGPL licence from the Bioconductor web site (http://bioconductor.org). Contact: mrobinson@wehi.edu.au
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            Cancer statistics, 2019

            Each year, the American Cancer Society estimates the numbers of new cancer cases and deaths that will occur in the United States and compiles the most recent data on cancer incidence, mortality, and survival. Incidence data, available through 2015, were collected by the Surveillance, Epidemiology, and End Results Program; the National Program of Cancer Registries; and the North American Association of Central Cancer Registries. Mortality data, available through 2016, were collected by the National Center for Health Statistics. In 2019, 1,762,450 new cancer cases and 606,880 cancer deaths are projected to occur in the United States. Over the past decade of data, the cancer incidence rate (2006-2015) was stable in women and declined by approximately 2% per year in men, whereas the cancer death rate (2007-2016) declined annually by 1.4% and 1.8%, respectively. The overall cancer death rate dropped continuously from 1991 to 2016 by a total of 27%, translating into approximately 2,629,200 fewer cancer deaths than would have been expected if death rates had remained at their peak. Although the racial gap in cancer mortality is slowly narrowing, socioeconomic inequalities are widening, with the most notable gaps for the most preventable cancers. For example, compared with the most affluent counties, mortality rates in the poorest counties were 2-fold higher for cervical cancer and 40% higher for male lung and liver cancers during 2012-2016. Some states are home to both the wealthiest and the poorest counties, suggesting the opportunity for more equitable dissemination of effective cancer prevention, early detection, and treatment strategies. A broader application of existing cancer control knowledge with an emphasis on disadvantaged groups would undoubtedly accelerate progress against cancer.
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              Robust enumeration of cell subsets from tissue expression profiles

              We introduce CIBERSORT, a method for characterizing cell composition of complex tissues from their gene expression profiles. When applied to enumeration of hematopoietic subsets in RNA mixtures from fresh, frozen, and fixed tissues, including solid tumors, CIBERSORT outperformed other methods with respect to noise, unknown mixture content, and closely related cell types. CIBERSORT should enable large-scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets (http://cibersort.stanford.edu).
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                Author and article information

                Contributors
                1978135000@qq.com
                li_anping@yahoo.com
                2544928065@qq.com
                qianchu@tjh.tjmu.edu.cn
                luosxrm@163.com
                kmwu@tjh.tjmu.edu.cn
                Journal
                Cancer Immunol Immunother
                Cancer Immunol Immunother
                Cancer Immunology, Immunotherapy
                Springer Berlin Heidelberg (Berlin/Heidelberg )
                0340-7004
                1432-0851
                2 January 2021
                2 January 2021
                2021
                : 70
                : 6
                : 1705-1719
                Affiliations
                [1 ]GRID grid.33199.31, ISNI 0000 0004 0368 7223, Department of Oncology, Tongji Hospital of Tongji Medical College, , Huazhong University of Science and Technology, ; Wuhan, 430030 China
                [2 ]GRID grid.414008.9, ISNI 0000 0004 1799 4638, Department of Medical Oncology, , The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, ; Zhengzhou, 450008 China
                [3 ]GRID grid.13402.34, ISNI 0000 0004 1759 700X, Bone Marrow Transplantation Center, The First Affiliated Hospital, , Zhejiang University School of Medicine, ; No. 79 Qingchun Road, Hangzhou, 310003 China
                Author information
                http://orcid.org/0000-0003-2499-1032
                Article
                2817
                10.1007/s00262-020-02817-z
                8139885
                33386920
                3a2f0b24-437a-4f03-88f8-9e41d30a9261
                © The Author(s) 2021

                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/.

                History
                : 13 June 2020
                : 1 December 2020
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: 81874120
                Award ID: 82073370
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100010888, Wuhan Municipal Science and Technology Bureau;
                Award ID: 2017060201010170
                Award Recipient :
                Categories
                Original Article
                Custom metadata
                © Springer-Verlag GmbH Germany, part of Springer Nature 2021

                Oncology & Radiotherapy
                lung adenocarcinoma,immunotherapy,the tumor immune microenvironment,immune checkpoint inhibitor,tumor mutation burden,prognostic model

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