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Inflammatory response signature score model for predicting immunotherapy response and pan-cancer prognosis.

作者信息

Chen Shuzhao, Huang Mayan, Zhang Limei, Huang Qianqian, Wang Yun, Liang Yang

机构信息

Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, Guangdong, China.

Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), Shantou, Guangdong, China.

出版信息

Comput Struct Biotechnol J. 2023 Dec 6;23:369-383. doi: 10.1016/j.csbj.2023.12.001. eCollection 2024 Dec.


DOI:10.1016/j.csbj.2023.12.001
PMID:38226313
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10788202/
Abstract

BACKGROUND: Inflammatory responses influence the outcome of immunotherapy and tumorigenesis by modulating host immunity. However, systematic inflammatory response assessment models for predicting cancer immunotherapy (CIT) responses and survival across human cancers remain unexplored. Here, we investigated an inflammatory response score model to predict CIT responses and patient survival in a pan-cancer analysis. METHODS: We retrieved 12 CIT response gene expression datasets from the Gene Expression Omnibus database (GSE78220, GSE19423, GSE100797, GSE126044, GSE35640, GSE67501, GSE115821 and GSE168204), Tumor Immune Dysfunction and Exclusion database (PRJEB23709, PRJEB25780 and phs000452.v2.p1), European Genome-phenome Archive database (EGAD00001005738), and IMvigor210 cohort. The tumor samples from six cancers types: metastatic urothelial cancer, metastatic melanoma, gastric cancer, primary bladder cancer, renal cell carcinoma, and non-small cell lung cancer.We further established a binary classification model to predict CIT responses using the least absolute shrinkage and selection operator (LASSO) computational algorithm. FINDINGS: The model had high predictive accuracy in both the training and validation cohorts. During sub-group analysis, area under the curve (AUC) values of 0.82, 0.80, 0.71, 0.7, 0.67, and 0.64 were obtained for the non-small cell lung cancer, gastric cancer, metastatic urothelial cancer, primary bladder cancer, metastatic melanoma, and renal cell carcinoma cohorts, respectively. CIT response rates were higher in the high-scoring training cohort subjects (51%) than the low-scoring subjects (27%). The five-year survival rates in the high- and low score groups of the training cohorts were 62% and 21%, respectively, while those of the validation cohorts were 54% and 22%, respectively ( < 0·001 in all cases). Inflammatory response signature score derived from on-treatment tumor specimens are highly predictive of response to CIT in patients with metastatic melanoma. A significant correlation was observed between the inflammatory response scores and tumor purity. Regardless of the tumor purity, patients in the low score group had a significantly poorer prognosis than those in the high score group. Immune cell infiltration analysis indicated that in the high score cohort, tumor-infiltrating lymphocytes were significantly enriched, particularly effector and natural killer cells. Inflammatory response scores were positively correlated with immune checkpoint genes, suggesting that immune checkpoint inhibitors may have benefited patients with high scores. Analysis of signature scores across different cancer types from The Cancer Genome Atlas revealed that the prognostic performance of inflammatory response scores for survival in patients who have not undergone immunotherapy can be affected by tumor purity. Interleukin 21 (IL21) had the highest weight in the inflammatory response model, suggesting its vital role in the prediction mode. Since the number of metastatic melanoma patients (n = 429) was relatively large among CIT cohorts, we further performed a co-culture experiment using a melanoma cell line and CD8 + T cell populations generated from peripheral blood monocytes. The results showed that IL21 therapy combined with anti-PD1 (programmed cell death 1) antibodies (trepril monoclonal antibodies) significantly enhanced the cytotoxic activity of CD8 + T cells against the melanoma cell line. CONCLUSION: In this study, we developed an inflammatory response gene signature model that predicts patient survival and immunotherapy response in multiple malignancies. We further found that the predictive performance in the non-small cell lung cancer and gastric cancer group had the highest value among the six different malignancy subgroups. When compared with existing signatures, the inflammatory response gene signature scores for on-treatment samples were more robust predictors of the response to CIT in metastatic melanoma.

摘要
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cfe0/10788202/950ac72a1dbc/gr9.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cfe0/10788202/e62de4723ea7/gr1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cfe0/10788202/97f06d6c0bde/gr2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cfe0/10788202/ef1ba1b431f4/gr3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cfe0/10788202/ddbb7297e37c/gr4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cfe0/10788202/b67abb5c4554/gr6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cfe0/10788202/27a52567f4d0/gr7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cfe0/10788202/5dd26594f9e2/gr8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cfe0/10788202/950ac72a1dbc/gr9.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cfe0/10788202/e62de4723ea7/gr1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cfe0/10788202/97f06d6c0bde/gr2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cfe0/10788202/ef1ba1b431f4/gr3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cfe0/10788202/ddbb7297e37c/gr4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cfe0/10788202/b67abb5c4554/gr6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cfe0/10788202/27a52567f4d0/gr7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cfe0/10788202/5dd26594f9e2/gr8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cfe0/10788202/950ac72a1dbc/gr9.jpg

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引用本文的文献

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Prognostic immunotherapy score (PIS) in patients with advanced urothelial carcinoma treated with pembrolizumab: real-world data and validation from ARON-2 dataset.

Clin Exp Metastasis. 2025-9-6

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[3]
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[4]
Comprehensive bioinformatics and immunohistochemical analyses identify phosphoinositide metabolism and PNPLA7 as potential biomarkers in urological cancers.

Sci Rep. 2025-4-12

[5]
Integration of graph neural networks and transcriptomics analysis identify key pathways and gene signature for immunotherapy response and prognosis of skin melanoma.

BMC Cancer. 2025-4-9

[6]
Circadian rhythm genes contribute to the prognosis prediction and potential therapeutic target in gastric cancer.

Sci Rep. 2024-10-25

[7]
Immunogenic cell death signatures from on-treatment tumor specimens predict immune checkpoint therapy response in metastatic melanoma.

Sci Rep. 2024-10-2

本文引用的文献

[1]
A tumor-associated endothelial signature score model in immunotherapy and prognosis across pan-cancers.

Front Pharmacol. 2023-8-31

[2]
Extending support for mouse data in the Molecular Signatures Database (MSigDB).

Nat Methods. 2023-11

[3]
Comprehensive analysis of glycoprotein VI-mediated platelet activation signaling pathway for predicting pan-cancer survival and response to anti-PD-1 immunotherapy.

Comput Struct Biotechnol J. 2023-4-15

[4]
Functional Gene Expression Signatures from On-Treatment Tumor Specimens Predict Anti-PD1 Blockade Response in Metastatic Melanoma.

Biomolecules. 2022-12-27

[5]
Intratumoral plasma cells predict outcomes to PD-L1 blockade in non-small cell lung cancer.

Cancer Cell. 2022-3-14

[6]
Pathway signatures derived from on-treatment tumor specimens predict response to anti-PD1 blockade in metastatic melanoma.

Nat Commun. 2021-10-15

[7]
IL-21 Is an Accomplice of PD-L1 in the Induction of PD-1-Dependent Treg Generation in Head and Neck Cancer.

Front Oncol. 2021-5-5

[8]
Conserved pan-cancer microenvironment subtypes predict response to immunotherapy.

Cancer Cell. 2021-6-14

[9]
Pan-cancer analysis of NLRP3 inflammasome with potential implications in prognosis and immunotherapy in human cancer.

Brief Bioinform. 2021-7-20

[10]
A gene expression signature of TREM2 macrophages and γδ T cells predicts immunotherapy response.

Nat Commun. 2020-10-8

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