Integrative analysis of T cell-associated markers in Ewing sarcoma reveals prognostic signatures and immune dynamics
BackgroundEwing sarcoma (ES) is a rare and aggressive pediatric bone malignancy with poor prognosis, driven by therapy-resistant tumor microenvironments (TME). The TME plays a critical role in tumor progression through a complex and dynamic network of reciprocal interactions among immune cells (dysf...
Saved in:
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2025-06-01
|
| Series: | Frontiers in Immunology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fimmu.2025.1586544/full |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850219106180005888 |
|---|---|
| author | Umair Ali Khan Saddozai Umair Ali Khan Saddozai Chenxu Liu Chenxu Liu Fei Yan Zhendong Lu Muhammad Babar Khawar Muhammad Babar Khawar Muhammad Usman Akbar Saadullah Khattak Haibo Sun Haibo Sun Ping Yang |
| author_facet | Umair Ali Khan Saddozai Umair Ali Khan Saddozai Chenxu Liu Chenxu Liu Fei Yan Zhendong Lu Muhammad Babar Khawar Muhammad Babar Khawar Muhammad Usman Akbar Saadullah Khattak Haibo Sun Haibo Sun Ping Yang |
| author_sort | Umair Ali Khan Saddozai |
| collection | DOAJ |
| description | BackgroundEwing sarcoma (ES) is a rare and aggressive pediatric bone malignancy with poor prognosis, driven by therapy-resistant tumor microenvironments (TME). The TME plays a critical role in tumor progression through a complex and dynamic network of reciprocal interactions among immune cells (dysfunctional T cells, immunosuppressive macrophages), stromal components (cancer-associated fibroblasts), and tumor cells. These interactions collectively shape the immune landscape, promote immune evasion, and contribute to therapeutic resistance. Identifying reliable prognostic markers remains a critical challenge.MethodsHere we performed an integrated single-cell RNA sequencing, WGCNA, and bulk RNA-seq analyses to investigate tumor-immune interactions. Differentially expressed genes (DEGs) intersected with T cell markers identified a total of 174 T cell-associated genes. Functional enrichment analysis and molecular subtyping were performed to explore immune-related pathways. A prognostic model based on CLEC11A, BDP1, and ID3 was constructed using Cox regression and validated in external datasets. Immune infiltration was assessed using the CIBERSORT algorithm.ResultsT cell marker analyses revealed key roles in pathways such as PI3K-Akt signaling and immune modulation. Molecular subtyping identified two clusters with distinct immune microenvironments: Cluster C1 (immunosuppressive phenotype and poorer prognosis) and Cluster C2 (functionally active immune profile associated with better prognosis). The prognostic model demonstrated high predictive accuracy for 1-, 3-, and 5-year survival (AUC: 0.85, 0.82, 0.78). Additionally, a higher tumor mutation burden (TMB) with low survival rate has been observed in High-risk group. Immune infiltration analysis showed higher CD8+ T cell and dendritic cell activity and immune checkpoint expression in low-risk groups. Experimental validation demonstrated that ID3 silencing inhibited tumor cell proliferation and induced cell cycle arrest in ES cell lines.ConclusionTogether, our study identified CLEC11A, BDP1, and ID3 as key T cell associated prognostic markers and developed a validated model to predict survival outcomes in ES. Insights into T cell markers and tumor-immune dynamics offer promising advances in prognostic assessment and immunotherapy for ES. Furthermore, the role of ID3 in immune evasion and tumor proliferation underscores its potential as a therapeutic target, providing new avenues for immune checkpoint regulation and personalized treatment strategies. |
| format | Article |
| id | doaj-art-b763529178da4852aff64c447f3bc8ee |
| institution | OA Journals |
| issn | 1664-3224 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Immunology |
| spelling | doaj-art-b763529178da4852aff64c447f3bc8ee2025-08-20T02:07:30ZengFrontiers Media S.A.Frontiers in Immunology1664-32242025-06-011610.3389/fimmu.2025.15865441586544Integrative analysis of T cell-associated markers in Ewing sarcoma reveals prognostic signatures and immune dynamicsUmair Ali Khan Saddozai0Umair Ali Khan Saddozai1Chenxu Liu2Chenxu Liu3Fei Yan4Zhendong Lu5Muhammad Babar Khawar6Muhammad Babar Khawar7Muhammad Usman Akbar8Saadullah Khattak9Haibo Sun10Haibo Sun11Ping Yang12Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, Jiangsu, ChinaJiangsu Key Laboratory of Experimental and, Translational Non-Coding RNA Research, Yangzhou, ChinaInstitute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, Jiangsu, ChinaJiangsu Key Laboratory of Experimental and, Translational Non-Coding RNA Research, Yangzhou, ChinaDepartment of Oncology, The Eighth People’s Hospital of Shanghai, Shanghai, ChinaDepartment of Medical Oncology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, ChinaInstitute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, Jiangsu, ChinaJiangsu Key Laboratory of Experimental and, Translational Non-Coding RNA Research, Yangzhou, ChinaOujiang Laboratory; Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of Aging, Wenzhou Medical University, Wenzhou, ChinaDepartment of Preventive Medicine, Institute of Biomedical Informatics, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Henan University, Kaifeng, Henan, ChinaInstitute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, Jiangsu, ChinaJiangsu Key Laboratory of Experimental and, Translational Non-Coding RNA Research, Yangzhou, ChinaDepartment of Oncology, The Eighth People’s Hospital of Shanghai, Shanghai, ChinaBackgroundEwing sarcoma (ES) is a rare and aggressive pediatric bone malignancy with poor prognosis, driven by therapy-resistant tumor microenvironments (TME). The TME plays a critical role in tumor progression through a complex and dynamic network of reciprocal interactions among immune cells (dysfunctional T cells, immunosuppressive macrophages), stromal components (cancer-associated fibroblasts), and tumor cells. These interactions collectively shape the immune landscape, promote immune evasion, and contribute to therapeutic resistance. Identifying reliable prognostic markers remains a critical challenge.MethodsHere we performed an integrated single-cell RNA sequencing, WGCNA, and bulk RNA-seq analyses to investigate tumor-immune interactions. Differentially expressed genes (DEGs) intersected with T cell markers identified a total of 174 T cell-associated genes. Functional enrichment analysis and molecular subtyping were performed to explore immune-related pathways. A prognostic model based on CLEC11A, BDP1, and ID3 was constructed using Cox regression and validated in external datasets. Immune infiltration was assessed using the CIBERSORT algorithm.ResultsT cell marker analyses revealed key roles in pathways such as PI3K-Akt signaling and immune modulation. Molecular subtyping identified two clusters with distinct immune microenvironments: Cluster C1 (immunosuppressive phenotype and poorer prognosis) and Cluster C2 (functionally active immune profile associated with better prognosis). The prognostic model demonstrated high predictive accuracy for 1-, 3-, and 5-year survival (AUC: 0.85, 0.82, 0.78). Additionally, a higher tumor mutation burden (TMB) with low survival rate has been observed in High-risk group. Immune infiltration analysis showed higher CD8+ T cell and dendritic cell activity and immune checkpoint expression in low-risk groups. Experimental validation demonstrated that ID3 silencing inhibited tumor cell proliferation and induced cell cycle arrest in ES cell lines.ConclusionTogether, our study identified CLEC11A, BDP1, and ID3 as key T cell associated prognostic markers and developed a validated model to predict survival outcomes in ES. Insights into T cell markers and tumor-immune dynamics offer promising advances in prognostic assessment and immunotherapy for ES. Furthermore, the role of ID3 in immune evasion and tumor proliferation underscores its potential as a therapeutic target, providing new avenues for immune checkpoint regulation and personalized treatment strategies.https://www.frontiersin.org/articles/10.3389/fimmu.2025.1586544/fullEwing sarcomaT cell associated genesimmune infiltrationprognostic signatureproliferation |
| spellingShingle | Umair Ali Khan Saddozai Umair Ali Khan Saddozai Chenxu Liu Chenxu Liu Fei Yan Zhendong Lu Muhammad Babar Khawar Muhammad Babar Khawar Muhammad Usman Akbar Saadullah Khattak Haibo Sun Haibo Sun Ping Yang Integrative analysis of T cell-associated markers in Ewing sarcoma reveals prognostic signatures and immune dynamics Frontiers in Immunology Ewing sarcoma T cell associated genes immune infiltration prognostic signature proliferation |
| title | Integrative analysis of T cell-associated markers in Ewing sarcoma reveals prognostic signatures and immune dynamics |
| title_full | Integrative analysis of T cell-associated markers in Ewing sarcoma reveals prognostic signatures and immune dynamics |
| title_fullStr | Integrative analysis of T cell-associated markers in Ewing sarcoma reveals prognostic signatures and immune dynamics |
| title_full_unstemmed | Integrative analysis of T cell-associated markers in Ewing sarcoma reveals prognostic signatures and immune dynamics |
| title_short | Integrative analysis of T cell-associated markers in Ewing sarcoma reveals prognostic signatures and immune dynamics |
| title_sort | integrative analysis of t cell associated markers in ewing sarcoma reveals prognostic signatures and immune dynamics |
| topic | Ewing sarcoma T cell associated genes immune infiltration prognostic signature proliferation |
| url | https://www.frontiersin.org/articles/10.3389/fimmu.2025.1586544/full |
| work_keys_str_mv | AT umairalikhansaddozai integrativeanalysisoftcellassociatedmarkersinewingsarcomarevealsprognosticsignaturesandimmunedynamics AT umairalikhansaddozai integrativeanalysisoftcellassociatedmarkersinewingsarcomarevealsprognosticsignaturesandimmunedynamics AT chenxuliu integrativeanalysisoftcellassociatedmarkersinewingsarcomarevealsprognosticsignaturesandimmunedynamics AT chenxuliu integrativeanalysisoftcellassociatedmarkersinewingsarcomarevealsprognosticsignaturesandimmunedynamics AT feiyan integrativeanalysisoftcellassociatedmarkersinewingsarcomarevealsprognosticsignaturesandimmunedynamics AT zhendonglu integrativeanalysisoftcellassociatedmarkersinewingsarcomarevealsprognosticsignaturesandimmunedynamics AT muhammadbabarkhawar integrativeanalysisoftcellassociatedmarkersinewingsarcomarevealsprognosticsignaturesandimmunedynamics AT muhammadbabarkhawar integrativeanalysisoftcellassociatedmarkersinewingsarcomarevealsprognosticsignaturesandimmunedynamics AT muhammadusmanakbar integrativeanalysisoftcellassociatedmarkersinewingsarcomarevealsprognosticsignaturesandimmunedynamics AT saadullahkhattak integrativeanalysisoftcellassociatedmarkersinewingsarcomarevealsprognosticsignaturesandimmunedynamics AT haibosun integrativeanalysisoftcellassociatedmarkersinewingsarcomarevealsprognosticsignaturesandimmunedynamics AT haibosun integrativeanalysisoftcellassociatedmarkersinewingsarcomarevealsprognosticsignaturesandimmunedynamics AT pingyang integrativeanalysisoftcellassociatedmarkersinewingsarcomarevealsprognosticsignaturesandimmunedynamics |