Screening of gene markers related to the prognosis of metastatic skin cutaneous melanoma based on Logit regression and survival analysis

Jia, Guoliang; Song, Zheyu; Xu, Zhijun; Tao, Youmao; Wu, Yue; Wang, Xiaoyu

doi:10.1186/s12920-021-00923-0

Cited by 4 publications

(5 citation statements)

References 34 publications

(21 reference statements)

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“…[24] Furthermore, the methylation of gene CALML5 has a high predictive capability in the poor OS of HPV-positive oropharyngeal cancer patients. [25] In CM, study indicated that CALML5 was involved in the pathway of “hsa04916: Melanogenesis.” [18] Mac et al [26] also found that calmodulin-like protein could promote the progression of CM sample, which was is in line with our discoveries that the expression of CALML5 was negative associated with the OS of patients with CM. This finding may be related to the modulation of immune cells and pathways.…”

Section: Discussionsupporting

confidence: 87%

“…WAS is a member of WASP family which has been proved to play a virtual role in melanoma cells migration and invasion through reorganizing actin cytoskeleton. [16,17] However, concerning the role of CALML5 in CM, there is currently only 1 reference indicating the differential expression of CALML5 in the CM clusters, [18] its specific prognostic value and modulation mechanism in CM remains unclear. Thus, in this study, we ultimately chose CALML5 for subsequent prognostic analysis.…”

Section: Resultsmentioning

confidence: 99%

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Identification of lactylation gene CALML5 and its correlated lncRNAs in cutaneous melanoma by machine learning

Feng,

Chen,

Zhang

2023

Medicine

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As a product of glycolysis, lactate contributes to cancer proliferation, immunosuppression, and metastasis via histone lactylation. However, the relationship between cutaneous melanoma (CM) and lactylation-associated genes and lncRNAs has remained unclear. In this study, 4 mechanism learning algorithms and integrated bioinformatic analyses were employed to identify the core lactylation-associated genes and lncRNAs. Subsequently, 2 risk signatures based on the hub lactylation-associated genes and lncRNAs were constructed for CM patients. As a result, CALML5 was identified as a core lactylation-associated gene in CM, and its expression was found to be associated with patients survival and immune infiltration, suggesting its relevance as a potential therapeutic target. Additionally, this study provided clarification on hub CALML5-associated lncRNAs in CM, offering insights into their roles in the disease. Meanwhile, 2 identified risk signatures were both strongly linked to the prognosis and cancer growth of CM, underscoring their potential as valuable prognostic indicators. Furthermore, mechanistic analyses suggested a significant association between the risk signature and the immune microenvironment in CM, highlighting potential immune-related implications in disease progression. In conclusion, we propose that lactylation-associated genes and lncRNAs hold promise as potential targets in CM. Moreover, our findings revealed a significant correlation between lactylation and the immune microenvironment, providing crucial insights for guiding individualized treatment strategies in CM.

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Section: Discussionsupporting

confidence: 87%

Section: Resultsmentioning

confidence: 99%

Identification of lactylation gene CALML5 and its correlated lncRNAs in cutaneous melanoma by machine learning

Feng,

Chen,

Zhang

2023

Medicine

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“…In other types of cancer, such as skin cutaneous melanoma, the low expression of NLRP6 is associated with poor prognosis 79 .…”

Section: Nlrp6 In Cancermentioning

confidence: 99%

Physiological and pathophysiological functions of NLRP6: pro- and anti-inflammatory roles

2022

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The nucleotide-binding oligomerization and leucine-rich repeat receptor (NLR) protein family consists of important immune sensors that form inflammasomes, a cytosolic multi-protein platform that induces caspase-1 activation and is involved in different inflammatory pathologies. The NLR family pyrin domain containing 6 (NLRP6) is a receptor that can signal by forming inflammasomes, but which can also play an important role without forming inflammasomes. NLRP6 regulates intestinal homeostasis and inflammation, but also is involved in cancer, the nervous system or liver diseases, with both protective and deleterious consequences. In the present article, we review the different roles of NLRP6 in these processes and offer new insights into NLRP6 activation.

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“…The top ten genes -EGFR, IL8, ICAM1, STAT1, CDK2, OAS2, MITF, PBK, CDKN3, and CXCL10 -were con rmed for association with melanoma through bioinformatic analysis in differentially expressed genes (DEGs) [13]. Logit regression and survival analysis were applied to detect the eleven feature DEGs -ZNF750, NLRP6, TGM3, KRTDAP, CAMSAP3, KRT6C, CALML5, SPRR2E, CD3G, RTP5, and FAM83C -related to the prognosis of metastatic cutaneous melanoma [14]. MDM2, MDM4, USP7, and PPM1D were con rmed in metastatic melanoma patients [15].…”

Section: Introductionmentioning

confidence: 99%

Transcriptome-Wide Association Study Reveals New Molecular Interactions Associated with Melanoma

Saad

Hamed

2023

Preprint

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The journey of discovering melanoma biomarkers is never ending. Under that assumption, this study is attempted to partially fill in a gap in that journey by identifying biomarkers related to melanoma. A transcriptome-wide association study (TWAS) was conducted on genome-wide association study (GWAS) summary statistics of malignant melanoma of skin (UK biobank dataset) and The Cancer Genome Atlas-Skin Cutaneous Melanoma (TCGA-SKCM) gene expression weights. Afterwards, a gene enrichment analysis was applied on the TWAS significant associations. The melanoma’s gene-microRNA (miRNA) regulatory network was constructed from the TWAS genes and their corresponding miRNAs. At last, a disease enrichment analysis was conducted on the corresponding miRNAs. The TWAS detected 27 genes associated with melanoma having P-value less than 0.05, namely, AMIGO1, GSTM3, MDM4, COPA, DENND4B, RAB13, IL1A, ANAPC13, CRIPAK, LOC389458, LOC441204, MTERFD1, CBWD1, B3GAT1, HOXC10, DDX11, PROZ, DHRS1, SPATA5L1, C16orf73, EIF3CL, FANCA, SCRN2, ALDH16A1, UPK1A, EDEM2, and TEF. After Joint/Conditional test, one gene (AMIGO1) was dropped out, resulting in 26 significant genes. The gene ontology (GO) biological process ended with the association of the extended gene set (76 genes) with protein K11-linked ubiquitination, and regulation of cell cycle phase transition. K11-linked ubiquitin chains regulates cell division. Interestingly, the extended gene set was related to different skin cancer subtypes. Moreover, the enriched pathways were nsp1 from SARS-CoV-2 inhibits translation initiation in the host cell, cell cycle, translation factors, and DNA repair pathways Full Network. The gene-miRNA regulatory network identified 10 hotspot genes: TP53, BRCA1, FANCA, BLM, USP7, MDM2, MDM4, IL1A, EIF3F, and ANAPC16; and 4 hotspot miRNAs: mir-16, mir-15a, mir-125b, and mir-146a. Melanoma was one of the top ten diseases associated with the corresponding (106) miRNAs. Our results shed light on melanoma pathogenesis and biologically significant molecular interactions. Besides, our study gives a comprehensive pipeline for the TWASs generally.

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Screening of gene markers related to the prognosis of metastatic skin cutaneous melanoma based on Logit regression and survival analysis

Cited by 4 publications

References 34 publications

Identification of lactylation gene CALML5 and its correlated lncRNAs in cutaneous melanoma by machine learning

Identification of lactylation gene CALML5 and its correlated lncRNAs in cutaneous melanoma by machine learning

Physiological and pathophysiological functions of NLRP6: pro- and anti-inflammatory roles

Transcriptome-Wide Association Study Reveals New Molecular Interactions Associated with Melanoma

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