Consensus Clustering and Survival-Related Genes of Cuproptosis in Cutaneous Melanoma

Qin, Wentao; Gan, Fu; Jike, Yiji; Jiang, Mingyang; Li, Ang

doi:10.1155/2023/3615688

Cited by 5 publications

(4 citation statements)

References 46 publications

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“…Previous studies have indicated the involvement of 12 genes (FDX1, LIAS, LIPT1, DLD, DLAT, PDHA1, PDHB, MTF1, GLS, CDKN2A, SLC31A1 and ATP7B) in regulating copper-induced cell death, and their abnormal expression in SKCM ( Tsvetkov et al, 2022 ; Qin et al, 2023 ). Our research also identified abnormal expression of 18 Hippo pathway-related genes in SKCM ( Figure 2A ).…”

Section: Resultsmentioning

confidence: 99%

“…Recent study found a significant difference in the expression of copper death-related genes between SKCM and normal tissues, suggesting an association between cuproptosis and the occurrence of SKCM. Additionally, they indicate that prognostic model constructed based on cuproptosis-related genes can effectively predict prognosis information for SKCM patients, highlighting the value of copper death-related genes in melanoma prognosis prediction (Qin et al, 2023). Zhou et al also develop a novel risk model based on cuproptosis-related lncRNAs, which predicted prognosis and indicated immune microenvironment landscape of patients with SKCM (Zhou et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

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Role of hippo pathway and cuproptosis-related genes in immune infiltration and prognosis of skin cutaneous melanoma

Lv,

Liu,

et al. 2024

Front. Pharmacol.

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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.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Role of hippo pathway and cuproptosis-related genes in immune infiltration and prognosis of skin cutaneous melanoma

Lv,

Liu,

et al. 2024

Front. Pharmacol.

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“…To address this issue, several studies ( Brière et al 2021 , Qin et al 2023 ) strongly advocated for the integration of modules from various methods to create more accurate and robust results. However, there is a lack of consensus clustering tools or websites that can integrate gene modules identified by different methods.…”

Section: Introductionmentioning

confidence: 99%

COMMO: a web server for the identification and analysis of consensus gene modules across multiple methods

Wu,

Han,

Song

et al. 2023

Bioinformatics

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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.

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“…Melanoma, classified as a malignant melanocytic proliferation, can originate from melanocytes in the skin, mucosal tissues, or nervous system (3). Cutaneous melanoma is the most common form of melanoma and is characterized by aggressive behavior, propensity for metastasis, and significant impact on the patient's overall prognosis, particularly when early detection proves elusive (6)(7)(8)(9).…”

Section: Introductionmentioning

confidence: 99%

Quantitative melanoma diagnosis using spectral phasor analysis of hyperspectral imaging from label-free slices

Schuty,

Martínez,

Guerra

et al. 2023

Front. Oncol.

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IntroductionMelanoma 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.MethodsUsing 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. ResultsOur 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.DiscussionThis 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.

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Consensus Clustering and Survival-Related Genes of Cuproptosis in Cutaneous Melanoma

Cited by 5 publications

References 46 publications

Role of hippo pathway and cuproptosis-related genes in immune infiltration and prognosis of skin cutaneous melanoma

Role of hippo pathway and cuproptosis-related genes in immune infiltration and prognosis of skin cutaneous melanoma

COMMO: a web server for the identification and analysis of consensus gene modules across multiple methods

Quantitative melanoma diagnosis using spectral phasor analysis of hyperspectral imaging from label-free slices

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