A robust immune-related gene pairs signature for predicting the overall survival of esophageal cancer

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Abstract

Background

Identifying reliable biomarkers could effectively predict esophagus carcinoma (EC) patients with poor prognosis. In this work, we constructed an immune-related gene pairs (IRGP) signature to evaluate the prognosis of EC.

Results

The IRGP signature was trained by the TCGA cohort and validated by three GEO datasets, respectively. Cox regression model together with LASSO was applied to construct the overall survival (OS) associated IRGP. 21 IRGPs consisting of 38 immune-related genes were included in our signature, according to which patients were stratified into high- and low-risk groups. The results of Kaplan-Meier survival analyses indicated that high-risk EC patients had worse OS than low-risk group in the training set, meta-validation set and all independent validation datasets. After adjustment in multivariate Cox analyses, our signature continued to be an independent prognostic factor of EC and the signature-based nomogram could effectively predict the prognosis of EC sufferers. Besides, Gene Ontology analysis revealed this signature is related to immunity. ‘CIBERSORT’ analysis revealed the infiltration levels of plasma cells and activated CD4 memory T cells in two risk groups were significantly different. Ultimately, we validated the expression levels of six selected genes from IRGP index in KYSE-150 and KYSE-450.

Conclusions

This IRGP signature could be applied to select EC patients with high mortality risk, thereby improving prospects for the treatment of EC.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-023-09496-x.

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Most cited references 56

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Global Cancer Statistics 2018: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries

Ahmedin Jemal, Lindsey A Torre, Rebecca Siegel … (2018)

This article provides a status report on the global burden of cancer worldwide using the GLOBOCAN 2018 estimates of cancer incidence and mortality produced by the International Agency for Research on Cancer, with a focus on geographic variability across 20 world regions. There will be an estimated 18.1 million new cancer cases (17.0 million excluding nonmelanoma skin cancer) and 9.6 million cancer deaths (9.5 million excluding nonmelanoma skin cancer) in 2018. In both sexes combined, lung cancer is the most commonly diagnosed cancer (11.6% of the total cases) and the leading cause of cancer death (18.4% of the total cancer deaths), closely followed by female breast cancer (11.6%), prostate cancer (7.1%), and colorectal cancer (6.1%) for incidence and colorectal cancer (9.2%), stomach cancer (8.2%), and liver cancer (8.2%) for mortality. Lung cancer is the most frequent cancer and the leading cause of cancer death among males, followed by prostate and colorectal cancer (for incidence) and liver and stomach cancer (for mortality). Among females, breast cancer is the most commonly diagnosed cancer and the leading cause of cancer death, followed by colorectal and lung cancer (for incidence), and vice versa (for mortality); cervical cancer ranks fourth for both incidence and mortality. The most frequently diagnosed cancer and the leading cause of cancer death, however, substantially vary across countries and within each country depending on the degree of economic development and associated social and life style factors. It is noteworthy that high-quality cancer registry data, the basis for planning and implementing evidence-based cancer control programs, are not available in most low- and middle-income countries. The Global Initiative for Cancer Registry Development is an international partnership that supports better estimation, as well as the collection and use of local data, to prioritize and evaluate national cancer control efforts. CA: A Cancer Journal for Clinicians 2018;0:1-31. © 2018 American Cancer Society.

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Signatures of mutational processes in human cancer

Ludmil Alexandrov, Serena Nik-Zainal, David Wedge … (2015)

All cancers are caused by somatic mutations. However, understanding of the biological processes generating these mutations is limited. The catalogue of somatic mutations from a cancer genome bears the signatures of the mutational processes that have been operative. Here, we analysed 4,938,362 mutations from 7,042 cancers and extracted more than 20 distinct mutational signatures. Some are present in many cancer types, notably a signature attributed to the APOBEC family of cytidine deaminases, whereas others are confined to a single class. Certain signatures are associated with age of the patient at cancer diagnosis, known mutagenic exposures or defects in DNA maintenance, but many are of cryptic origin. In addition to these genome-wide mutational signatures, hypermutation localized to small genomic regions, kataegis, is found in many cancer types. The results reveal the diversity of mutational processes underlying the development of cancer with potential implications for understanding of cancer etiology, prevention and therapy.

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Five-Year Survival with Combined Nivolumab and Ipilimumab in Advanced Melanoma

James Larkin, Vanna Chiarion-Sileni, Rene Gonzalez … (2019)

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Author and article information

Contributors

Dan Shi: danshi@cqmu.edu.cn

Biao Xie: kybiao@cqmu.edu.cn

Journal

Journal ID (nlm-ta): BMC Genomics

Journal ID (iso-abbrev): BMC Genomics

Title: BMC Genomics

Publisher: BioMed Central (London )

ISSN (Electronic): 1471-2164

Publication date (Electronic): 10 July 2023

Publication date PMC-release: 10 July 2023

Publication date Collection: 2023

Volume: 24

Electronic Location Identifier: 385

Affiliations

[1 ]GRID grid.452206.7, ISNI 0000 0004 1758 417X, Department of Cardiology, , The First Affiliated Hospital of Chongqing Medical University, ; Chongqing, China

[2 ]GRID grid.203458.8, ISNI 0000 0000 8653 0555, Department of Nutrition and Food Hygiene, , Chongqing Medical University, ; Chongqing, China

[3 ]GRID grid.459453.a, ISNI 0000 0004 1790 0232, Anatomy Teaching and Research Section, Basic department, , Chongqing Medical and Pharmaceutical College, ; Chongqing, China

[4 ]GRID grid.203458.8, ISNI 0000 0000 8653 0555, Department of Biostatistics, , Chongqing Medical University, ; Chongqing, China

Article

Publisher ID: 9496

DOI: 10.1186/s12864-023-09496-x

PMC ID: 10332031

SO-VID: 6ac21c0b-f7ed-4024-977a-e08cff72f851

License:

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/. The Creative Commons Public Domain Dedication waiver ( http://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.

History

Date received : 23 February 2023

Date accepted : 30 June 2023

Funding

Funded by: FundRef http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;

Award ID: 8210120502

Award ID: 82204159

Funded by: FundRef http://dx.doi.org/10.13039/100012546, Chongqing Postdoctoral Science Foundation;

Award ID: cstc2021jcyj-bshX0220

Custom metadata

ScienceOpen disciplines: Genetics

Keywords: esophageal cancer,prognosis,immune-related gene pairs,bioinformatic analysis,cells lines

Data availability:

ScienceOpen disciplines: Genetics

Keywords: esophageal cancer, prognosis, immune-related gene pairs, bioinformatic analysis, cells lines

A robust immune-related gene pairs signature for predicting the overall survival of esophageal cancer

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Abstract

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Supplementary Information

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Genome Integrity

Most cited references 56

Global Cancer Statistics 2018: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries

Signatures of mutational processes in human cancer

Five-Year Survival with Combined Nivolumab and Ipilimumab in Advanced Melanoma

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