Prognostic analysis of uveal melanoma based on the characteristic genes of M2-type macrophages in the tumor microenvironment
Abstract Uveal melanoma arises from stromal melanocytes and is the most prevalent primary intraocular tumor in adults. It poses a significant diagnostic and therapeutic challenge due to its high malignancy and early onset of metastases. In recent years, there has been a growing interest in the role...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-07-01
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| Series: | BMC Bioinformatics |
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| Online Access: | https://doi.org/10.1186/s12859-023-05396-9 |
| _version_ | 1827899603707494400 |
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| author | Li Fu Qun Huang Yongfeng Wu Diang Chen |
| author_facet | Li Fu Qun Huang Yongfeng Wu Diang Chen |
| author_sort | Li Fu |
| collection | DOAJ |
| description | Abstract Uveal melanoma arises from stromal melanocytes and is the most prevalent primary intraocular tumor in adults. It poses a significant diagnostic and therapeutic challenge due to its high malignancy and early onset of metastases. In recent years, there has been a growing interest in the role of diverse immune cells in tumor cell development and metastasis. Using The Cancer Genome Atlas and the gene expression omnibus databases, and the CIBERSORT method, we investigated the topography of intra-tumor immune infiltration in uveal melanoma in this research. We evaluated the prognosis of uveal melanoma patients using the M2 macrophage immune cell infiltration score in conjunction with clinical tumor patient data. We built a prognostic model based on the distinctive genes of M2 macrophages and combined it with patients’ clinical data in the database; we ran a survival prognostic analysis to authenticate the model’s accuracy. The functional study revealed the importance of macrophage-associated genes in the development of uveal melanoma. Moreover, the reliability of our prediction model was verified by combining tumor mutational load, immune checkpoint, and drug sensitivity, respectively. Our study provides a reference for the follow-up study of uveal melanoma. |
| first_indexed | 2024-03-12T23:20:10Z |
| format | Article |
| id | doaj.art-405430d1055e4f4c85bd8ba5ccca8f75 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-03-12T23:20:10Z |
| publishDate | 2023-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-405430d1055e4f4c85bd8ba5ccca8f752023-07-16T11:29:57ZengBMCBMC Bioinformatics1471-21052023-07-0124111510.1186/s12859-023-05396-9Prognostic analysis of uveal melanoma based on the characteristic genes of M2-type macrophages in the tumor microenvironmentLi Fu0Qun Huang1Yongfeng Wu2Diang Chen3Department of Ophthalmology, Jian Yang Hospital of Traditional Chinese MedicineDepartment of Ophthalmology, Hospital of Chengdu University of Traditional Chinese MedicineDepartment of Ophthalmology, Jian Yang Hospital of Traditional Chinese MedicineDepartment of Andrology, Hospital of Chengdu University of Traditional Chinese MedicineAbstract Uveal melanoma arises from stromal melanocytes and is the most prevalent primary intraocular tumor in adults. It poses a significant diagnostic and therapeutic challenge due to its high malignancy and early onset of metastases. In recent years, there has been a growing interest in the role of diverse immune cells in tumor cell development and metastasis. Using The Cancer Genome Atlas and the gene expression omnibus databases, and the CIBERSORT method, we investigated the topography of intra-tumor immune infiltration in uveal melanoma in this research. We evaluated the prognosis of uveal melanoma patients using the M2 macrophage immune cell infiltration score in conjunction with clinical tumor patient data. We built a prognostic model based on the distinctive genes of M2 macrophages and combined it with patients’ clinical data in the database; we ran a survival prognostic analysis to authenticate the model’s accuracy. The functional study revealed the importance of macrophage-associated genes in the development of uveal melanoma. Moreover, the reliability of our prediction model was verified by combining tumor mutational load, immune checkpoint, and drug sensitivity, respectively. Our study provides a reference for the follow-up study of uveal melanoma.https://doi.org/10.1186/s12859-023-05396-9Uveal melanomaM2 macrophagesTumor microenvironment (TME)The Cancer Genome Atlas (TCGA)Gene expression omnibus (GEO) |
| spellingShingle | Li Fu Qun Huang Yongfeng Wu Diang Chen Prognostic analysis of uveal melanoma based on the characteristic genes of M2-type macrophages in the tumor microenvironment BMC Bioinformatics Uveal melanoma M2 macrophages Tumor microenvironment (TME) The Cancer Genome Atlas (TCGA) Gene expression omnibus (GEO) |
| title | Prognostic analysis of uveal melanoma based on the characteristic genes of M2-type macrophages in the tumor microenvironment |
| title_full | Prognostic analysis of uveal melanoma based on the characteristic genes of M2-type macrophages in the tumor microenvironment |
| title_fullStr | Prognostic analysis of uveal melanoma based on the characteristic genes of M2-type macrophages in the tumor microenvironment |
| title_full_unstemmed | Prognostic analysis of uveal melanoma based on the characteristic genes of M2-type macrophages in the tumor microenvironment |
| title_short | Prognostic analysis of uveal melanoma based on the characteristic genes of M2-type macrophages in the tumor microenvironment |
| title_sort | prognostic analysis of uveal melanoma based on the characteristic genes of m2 type macrophages in the tumor microenvironment |
| topic | Uveal melanoma M2 macrophages Tumor microenvironment (TME) The Cancer Genome Atlas (TCGA) Gene expression omnibus (GEO) |
| url | https://doi.org/10.1186/s12859-023-05396-9 |
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