1
|
Lv H, Liu L, He Y, Yang K, Fu Y, Bao Y. Role of hippo pathway and cuproptosis-related genes in immune infiltration and prognosis of skin cutaneous melanoma. Front Pharmacol 2024; 15:1344755. [PMID: 38515849 PMCID: PMC10955143 DOI: 10.3389/fphar.2024.1344755] [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: 11/26/2023] [Accepted: 02/19/2024] [Indexed: 03/23/2024] Open
Abstract
Melanoma is the most lethal type of skin cancer with an increasing incidence. Cuproptosis is the most recently identified copper-dependent form of cell death that relies on mitochondrial respiration. The hippocampal (Hippo) pathway functions as a tumor suppressor by regulating Yes-associated protein/transcriptional coactivator with PDZ-binding motif (YAP/TAZ) activity. However, its role in cuproptosis remains unknown. In addition, the correlation of cuproptosis-related genes and Hippo pathway-related genes with tumor prognosis warrants further investigation. In the present study, we explored the correlation of cuproptosis-related genes and Hippo pathway-related genes with the prognosis of melanoma through analysis of data from a public database and experimental verification. We found eight Hippo pathway-related genes that were downregulated in melanoma and exhibited predictive value for prognosis. There was a significant positive correlation between cuproptosis-related genes and Hippo pathway-related genes in skin cutaneous melanoma. YAP1 expression was positively correlated with ferredoxin 1 (FDX1) expression in the GSE68599 dataset and A2058 cells. Moreover, YAP1 was positively and negatively correlated with M2 macrophages and regulatory T cell infiltration, respectively. In conclusion, the present study demonstrated the prognostic value of Hippo pathway-related genes (particularly YAP1) in melanoma, revealing the correlation between the expression of Hippo pathway-related genes and immune infiltration. Thus, the present findings may provide new clues on the prognostic assessment of patients with melanoma and a new target for the immunotherapy of this disease.
Collapse
Affiliation(s)
- Haozhen Lv
- Department of Dermatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Lin Liu
- Department of Dermatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Peking Union Medical College, Beijing, China
| | - Yuexi He
- Department of Dermatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Peking Union Medical College, Beijing, China
| | - Kun Yang
- Department of Dermatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Yu Fu
- Department of Dermatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Peking Union Medical College, Beijing, China
| | - Yingqiu Bao
- Department of Dermatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| |
Collapse
|
2
|
Hsieh MY, Hsu SK, Liu TY, Wu CY, Chiu CC. Melanoma biology and treatment: a review of novel regulated cell death-based approaches. Cancer Cell Int 2024; 24:63. [PMID: 38336727 PMCID: PMC10858604 DOI: 10.1186/s12935-024-03220-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 01/09/2024] [Indexed: 02/12/2024] Open
Abstract
The incidence of melanoma, the most lethal form of skin cancer, has increased due to ultraviolet exposure. The treatment of advanced melanoma, particularly metastatic cases, remains challenging with poor outcomes. Targeted therapies involving BRAF/MEK inhibitors and immunotherapy based on anti-PD1/anti-CTLA4 antibodies have achieved long-term survival rates of approximately 50% for patients with advanced melanoma. However, therapy resistance and inadequate treatment response continue to hinder further breakthroughs in treatments that increase survival rates. This review provides an introduction to the molecular-level pathogenesis of melanoma and offers an overview of current treatment options and their limitations. Cells can die by either accidental or regulated cell death (RCD). RCD is an orderly cell death controlled by a variety of macromolecules to maintain the stability of the internal environment. Since the uncontrolled proliferation of tumor cells requires evasion of RCD programs, inducing the RCD of melanoma cells may be a treatment strategy. This review summarizes studies on various types of nonapoptotic RCDs, such as autophagy-dependent cell death, necroptosis, ferroptosis, pyroptosis, and the recently discovered cuproptosis, in the context of melanoma. The relationships between these RCDs and melanoma are examined, and the interplay between these RCDs and immunotherapy or targeted therapy in patients with melanoma is discussed. Given the findings demonstrating melanoma cell death in response to different stimuli associated with these RCDs, the induction of RCD shows promise as an integral component of treatment strategies for melanoma.
Collapse
Affiliation(s)
- Ming-Yun Hsieh
- Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
- Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung, 804, Taiwan
| | - Sheng-Kai Hsu
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
| | - Tzu-Yu Liu
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
| | - Chang-Yi Wu
- Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung, 804, Taiwan.
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, 807, Taiwan.
| | - Chien-Chih Chiu
- Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung, 804, Taiwan.
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, 807, Taiwan.
- Center for Cancer Research, Kaohsiung Medical University, Kaohsiung, 807, Taiwan.
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, 807, Taiwan.
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, 807, Taiwan.
| |
Collapse
|
3
|
Wu X, Han M, Song X, He S, Bo X, Zhu Y. COMMO: a web server for the identification and analysis of consensus gene modules across multiple methods. Bioinformatics 2023; 39:btad708. [PMID: 37995293 PMCID: PMC10713113 DOI: 10.1093/bioinformatics/btad708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/05/2023] [Accepted: 11/22/2023] [Indexed: 11/25/2023] Open
Abstract
SUMMARY A variety of computational methods have been developed to identify functionally related gene modules from genome-wide gene expression profiles. Integrating the results of these methods to identify consensus modules is a promising approach to produce more accurate and robust results. In this application note, we introduce COMMO, the first web server to identify and analyze consensus gene functionally related gene modules from different module detection methods. First, COMMO implements eight state-of-the-art module detection methods and two consensus clustering algorithms. Second, COMMO provides users with mRNA and protein expression data for 33 cancer types from three public databases. Users can also upload their own data for module detection. Third, users can perform functional enrichment and two types of survival analyses on the observed gene modules. Finally, COMMO provides interactive, customizable visualizations and exportable results. With its extensive analysis and interactive capabilities, COMMO offers a user-friendly solution for conducting module-based precision medicine research. AVAILABILITY AND IMPLEMENTATION COMMO web is available at https://commo.ncpsb.org.cn/, with the source code available on GitHub: https://github.com/Song-xinyu/COMMO/tree/master.
Collapse
Affiliation(s)
- Xiaojing Wu
- Basic Medical School, Anhui Medical University, Hefei 230022, China
- National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Mingfei Han
- National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Xinyu Song
- Center for Artificial Intelligence in Medicine, Medical Innovation Research Division of Chinese, PLA General Hospital, Beijing 100853, China
| | - Song He
- Department of Bioinformatics, Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Xiaochen Bo
- Department of Bioinformatics, Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Yunping Zhu
- Basic Medical School, Anhui Medical University, Hefei 230022, China
- National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| |
Collapse
|
4
|
Schuty B, Martínez S, Guerra A, Lecumberry F, Magliano J, Malacrida L. Quantitative melanoma diagnosis using spectral phasor analysis of hyperspectral imaging from label-free slices. Front Oncol 2023; 13:1296826. [PMID: 38162497 PMCID: PMC10756080 DOI: 10.3389/fonc.2023.1296826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 10/31/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction Melanoma diagnosis traditionally relies on microscopic examination of hematoxylin and eosin (H&E) slides by dermatopathologists to search for specific architectural and cytological features. Unfortunately, no single molecular marker exists to reliably differentiate melanoma from benign lesions such as nevi. This study explored the potential of autofluorescent molecules within tissues to provide molecular fingerprints indicative of degenerated melanocytes in melanoma. Methods Using hyperspectral imaging (HSI) and spectral phasor analysis, we investigated autofluorescence patterns in melanoma compared to intradermal nevi. Using UV excitation and a commercial spectral confocal microscope, we acquired label-free HSI data from the whole-slice samples. Results Our findings revealed distinct spectral phasor distributions between melanoma and intradermal nevi, with melanoma displaying a broader phasor phase distribution, signifying a more heterogeneous autofluorescence pattern. Notably, longer wavelengths associated with larger phases correlated with regions identified as melanoma by expert dermatopathologists using H&E staining. Quantitative analysis of phase and modulation histograms within the phasor clusters of five melanomas (with Breslow thicknesses ranging from 0.5 mm to 6 mm) and five intradermal nevi consistently highlighted differences between the two groups. We further demonstrated the potential for the discrimination of several melanocytic lesions using center-of-mass comparisons of phase and modulation variables. Remarkably, modulation versus phase center of mass comparisons revealed strong statistical significance among the groups. Additionally, we identified the molecular endogenous markers responsible for tissue autofluorescence, including collagen, elastin, NADH, FAD, and melanin. In melanoma, autofluorescence is characterized by a higher phase contribution, indicating an increase in FAD and melanin in melanocyte nests. In contrast, NADH, elastin, and collagen dominate the autofluorescence of the nevus. Discussion This work underscores the potential of autofluorescence and HSI-phasor analysis as valuable tools for quantifying tissue molecular fingerprints, thereby supporting more effective and quantitative melanoma diagnosis.
Collapse
Affiliation(s)
- Bruno Schuty
- Unidad de Bioimagenología Avanzada, Institut Pasteur de Montevideo, Hospital de Clínicas Universidad de la República, Montevideo, Uruguay
| | - Sofía Martínez
- Unidad de Bioimagenología Avanzada, Institut Pasteur de Montevideo, Hospital de Clínicas Universidad de la República, Montevideo, Uruguay
- Unidad Academica de Dermatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Analía Guerra
- Unidad Academica de Dermatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Federico Lecumberry
- Instituto de Ingeniería Eléctrica, Facultad de Ingeniería, Universidad de la República, Montevideo, Uruguay
| | - Julio Magliano
- Unidad Academica de Dermatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Leonel Malacrida
- Unidad de Bioimagenología Avanzada, Institut Pasteur de Montevideo, Hospital de Clínicas Universidad de la República, Montevideo, Uruguay
- Unidad Academica de Fisiopatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| |
Collapse
|