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Li C, Wu N, Lin X, Zhou Q, Xu M. Integrated transcriptomic and immunological profiling reveals new diagnostic and prognostic models for cutaneous melanoma. Front Pharmacol 2024; 15:1389550. [PMID: 38863979 PMCID: PMC11165152 DOI: 10.3389/fphar.2024.1389550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/13/2024] [Indexed: 06/13/2024] Open
Abstract
The mortality rate associated with cutaneous melanoma (SKCM) remains alarmingly high, highlighting the urgent need for a deeper understanding of its molecular underpinnings. In our study, we leveraged bulk transcriptome sequencing data from the SKCM cohort available in public databases such as TCGA and GEO. We utilized distinct datasets for training and validation purposes and also incorporated mutation and clinical data from TCGA, along with single-cell sequencing data from GEO. Through dimensionality reduction, we annotated cell subtypes within the single-cell data and analyzed the expression of tumor-related pathways across these subtypes. We identified differentially expressed genes (DEGs) in the training set, which were further refined using the Least Absolute Shrinkage and Selection Operator (LASSO) machine learning algorithm, employing tenfold cross-validation. This enabled the construction of a prognostic model, whose diagnostic efficacy we subsequently validated. We conducted Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses on the DEGs, and performed immunological profiling on two risk groups to elucidate the relationship between model genes and the immune responses relevant to SKCM diagnosis, treatment, and prognosis. We also knocked down the GMR6 expression level in the melanoma cells and verified its effect on cancer through multiple experiments. The results indicate that the GMR6 gene plays a role in promoting the proliferation, invasion, and migration of cancer cells in human melanoma. Our findings offer novel insights and a theoretical framework that could enhance prognosis, treatment, and drug development strategies for SKCM, potentially leading to more precise therapeutic interventions.
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Affiliation(s)
- Changchang Li
- Department of Dermatology,Wenzhou Hospital of Integrated Traditional Chinese and Western Medicine, Wenzhou, China
| | - Nanhui Wu
- Department of Dermatopathology, Shanghai Skin Disease Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaoqiong Lin
- Department of Dermatology,Wenzhou Hospital of Integrated Traditional Chinese and Western Medicine, Wenzhou, China
| | - Qiaochu Zhou
- Department of Dermatology,Wenzhou Hospital of Integrated Traditional Chinese and Western Medicine, Wenzhou, China
| | - Mingyuan Xu
- Department of Dermatopathology, Shanghai Skin Disease Hospital, Tongji University School of Medicine, Shanghai, China
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Fucikova J, Palova-Jelinkova L, Klapp V, Holicek P, Lanickova T, Kasikova L, Drozenova J, Cibula D, Álvarez-Abril B, García-Martínez E, Spisek R, Galluzzi L. Immunological control of ovarian carcinoma by chemotherapy and targeted anticancer agents. Trends Cancer 2022; 8:426-444. [PMID: 35181272 DOI: 10.1016/j.trecan.2022.01.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/05/2022] [Accepted: 01/19/2022] [Indexed: 12/24/2022]
Abstract
At odds with other solid tumors, epithelial ovarian cancer (EOC) is poorly sensitive to immune checkpoint inhibitors (ICIs), largely reflecting active immunosuppression despite CD8+ T cell infiltration at baseline. Accumulating evidence indicates that both conventional chemotherapeutics and targeted anticancer agents commonly used in the clinical management of EOC not only mediate a cytostatic and cytotoxic activity against malignant cells, but also drive therapeutically relevant immunostimulatory or immunosuppressive effects. Here, we discuss such an immunomodulatory activity, with a specific focus on molecular and cellular pathways that can be harnessed to develop superior combinatorial regimens for clinical EOC care.
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Affiliation(s)
- Jitka Fucikova
- Sotio, Prague, Czech Republic; Department of Immunology, Charles University, Second Faculty of Medicine and University Hospital Motol, Prague, Czech Republic.
| | - Lenka Palova-Jelinkova
- Department of Immunology, Charles University, Second Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Vanessa Klapp
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
| | - Peter Holicek
- Sotio, Prague, Czech Republic; Department of Immunology, Charles University, Second Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Tereza Lanickova
- Sotio, Prague, Czech Republic; Department of Immunology, Charles University, Second Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | | | - Jana Drozenova
- Department of Pathology, Third Faculty of Medicine and University Hospital Kralovske Vinohrady, Prague, Czech Republic
| | - David Cibula
- Gynecologic Oncology Center, Department of Obstetrics and Gynecology, Charles University, First Faculty of Medicine and General University Hospital, Prague, Czech Republic
| | - Beatriz Álvarez-Abril
- Department of Hematology and Oncology, Hospital Universitario Morales Meseguer, Murcia, Spain
| | - Elena García-Martínez
- Department of Hematology and Oncology, Hospital Universitario Morales Meseguer, Murcia, Spain; Instituto Murciano de Investigación Biosanitaria (IMIB-Arrixaca), Murcia, Spain; Universidad Católica San Antonio de Murcia, Guadalupe, Spain
| | - Radek Spisek
- Sotio, Prague, Czech Republic; Department of Immunology, Charles University, Second Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA; Sandra and Edward Meyer Cancer Centre, New York, NY, USA; Caryl and Israel Englander Institute for Precision Medicine, New York, NY, USA.
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