Disruptions of Circadian Genes in Cutaneous Melanoma-An In Silico Analysis of Transcriptome Databases.

Circadian genes are a set of genes that regulate the body's internal clock and influence various physiological processes, including sleep-wake cycles, metabolism and immune function. Skin cutaneous melanoma (SKCM) is a type of skin cancer that arises from the pigment-producing cells in the skin and is the most deadly form of skin cancer. This study has investigated the relevance of circadian gene expression and immune infiltrations in the outcomes of cutaneous melanoma patients. In the present study, in silico methods based on the GEPIa, TIMER 2.0 and cBioPortal databases were performed, so as to investigate the transcript level and prognostic value of 24 circadian genes in SKCM and their relationship with the immune infiltration level. The in silico analysis showed that significantly more than half of the investigated circadian genes have an altered transcript pattern in cutaneous melanoma compared to normal skin. The mRNA levels of TIMELES and BHLHE41 were upregulated, whereas those of NFIL3, BMAL1, HLF, TEF, RORA, RORC, NR1D1, PER1, PER2, PER3, CRY2 and BHLHE40 were downregulated. The presented research shows that SKCM patients with at least one alteration of their circadian genes have decreased overall survival. Additionally, majority of the circadian genes are significantly corelated with the immune cells' infiltration level. The strongest correlation was found for neutrophils and was followed by circadian genes: NR1D2 r = 0.52 p < 0.0001, BMAL1 r = 0.509 p < 0.0001; CLOCK r = 0.45 p < 0.0001; CSNKA1A1 r = 0.45 p < 0.0001; RORA r = 0.44 p < 0.0001. The infiltration level of immune cells in skin tumors has been associated with patient prognosis and treatment response. Circadian regulation of immune cell infiltration may further contribute to these prognostic and predictive markers. Examining the correlation between circadian rhythm and immune cell infiltration can provide valuable insights into disease progression and guide personalized treatment decisions.

B4GALT5 high expression associated with poor prognosis of hepatocellular carcinoma.

BACKGROUND: B4GALT5 is postulated to be an important protein in sugar metabolism that catalyzes the synthesis of lactosylceramide (LacCer). However, its role in hepatocellular carcinoma (HCC) remains unknown. METHOD: We characterized the expression of B4GALT5 in HCC tissue compared to normal tissue, and explored its function of B4GALT5 in HCC by enrichment analysis based on its co-expressed gene set. Next, we checked whether B4GALT5 expression is correlated to immune infiltration level and clinical prognosis in hepatocellular carcinoma. Finally, we verified the expression of B4GALT5 using clinical samples evaluated by RT-PCR, and conducted in vitro experiments with B4GALT5-knockdown HCC cells to investigate the function of B4GALT5 in the HCC cell proliferation, migration and invasion. RESULTS: We found B4GALT5 mRNA and protein expression levels were significantly high in HCC tissue compared to normal tissue. The enrichment analysis of the gene sets that co-expressed with B4GALT5 showed specificity in HCC-related pathways and functions. Also, the expression pattern of B4GALT5 was significantly related to the immune infiltration level, especially CD4+ T cell and macrophage cells. B4GALT5 higher mRNA expression was associated with poor overall survival (OS) in HCC patients. Furthermore, In vitro experiments showed that depletion of B4GALT5 significantly inhibited HCC cell proliferation, migration and invasion. This study revealed the function and its mediated pathways of B4GALT5 in HCC, indicating that B4GALT5 may serve as a prognostic biomarker of HCC.

UCP1 modulates immune infiltration level and survival outcome in ovarian cancer patients.

BACKGROUND: The uncoupling proteins (UCPs) are critical genes associated with tumorigenesis and chemoresistance. However, little is known about the molecular mechanism of the UCPs in ovarian cancer (OV). MATERIAL AND METHODS: UCPs expression analysis was conducted using Gene Expression Profiling Interactive Analysis (GEPIA), and its potential in clinical prognosis was analyzed using Kaplan- Meier analyses. The influence of UCPs on immune infiltration was analyzed by TIMER. In addition, the correlation between UCPs expression and molecular mechanisms was investigated by TIMER and Cancer Single-cell State Atlas (CancerSEA). RESULTS: UCP1, UCP2, UCP3 and UCP5 expression levels correlated with a favorable prognosis and tumor progression. Moreover, UCP1 expression correlated to several immune cell markers and regulated tumorigenesis, such as tumor invasion, EMT, metastasis and DNA repair. In addition, UCP1 potentially involved in genes expression of SNAI2, MMP2, BRCA1 and PARP1. CONCLUSIONS: These results implied a critical role of UCP1 in the prognosis and immune infiltration of ovarian cancer. In addition, UCP1 expression participated in regulating multiple oncogenes and tumorigenesis.

Identification of Immune-Related Genes for Establishment of Prognostic Index in Hepatocellular Carcinoma.

Background: Immune checkpoint inhibitor (ICI) therapy has been proved to be a promising therapy to many types of solid tumors. However, effective biomarker for estimating the response to ICI therapy and prognosis of hepatocellular carcinoma (HCC) patients remains underexplored. The aim of this study is to build a novel immune-related prognostic index based on transcriptomic profiles. Methods: Weighted gene co-expression network analysis (WGCNA) was conducted to identify immune-related hub genes that are differentially expressed in HCC cohorts. Next, univariate Cox regression analysis and least absolute shrinkage and selection operator (LASSO) analysis were used to detect hub genes associated to overall survival (OS). To validate the immune-related prognostic index, univariate and multivariate Cox regression analysis were performed. CIBERSORT and ESTIMATE were used to explore the tumor microenvironment and immune infiltration level. Results: The differential expression analysis detected a total of 148 immune-related genes, among which 25 genes were identified to be markedly related to overall survival in HCC patients. LASSO analysis yielded 10 genes used to construct the immune-related gene prognostic index (IRGPI), by which a risk score is computed to estimate low vs. high risk indicating the response to ICI therapy and prognosis. Further analysis confirmed that this immune-related prognostic index is an effective indicator to immune infiltration level, response to ICI treatment and OS. The IRGPI low-risk patients had better overall survival (OS) than IRGPI high-risk patients on two independent cohorts. Moreover, we found that IRGPI high-risk group was correlated with high TP53 mutation rate, immune-suppressing tumor microenvironment, and these patients acquired less benefit from ICI therapy. In contrast, IRGPI-low risk group was associated with low TP53 and PIK3CA mutation rate, high infiltration of naive B cells and T cells, and these patients gained relatively more benefit from ICI therapy.

MMP25 Regulates Immune Infiltration Level and Survival Outcome in Head and Neck Cancer Patients.

Background: MMP25 is a critical gene of matrix metalloproteinases (MMPs). However, the molecular mechanism of MMP25 in head and neck cancer pathogenesis remains unclear. Methods: MMP25 expression was analyzed using The Cancer Genome Atlas (TCGA) database, and its influence on clinical prognosis was performed using Kaplan-Meier and Cox regression analyses. The correlation between MMP25 and immune infiltration was investigated by CIBERSORT, TIMER, and ESTIMATE. In addition, the relationship between MMP25 expression and molecular mechanisms was analyzed by gene set enrichment analysis (GSEA), gene ontology (GO), and weighted gene co-expression network analysis (WGCNA). Results: MMP25 expression level correlated with prognosis and immune infiltrating levels, especially activated CD4+ memory T cells, in head and neck cancer. Moreover, MMP25 expression potentially mediated genes, such as IRF8, IKZF1, and DOCK2, and tumor-associated pathways, including p53 signaling, PI3K/AKT/mTOR signaling, and JAK/STAT signaling pathway. Conclusions: These findings suggested that MMP25 plays a critical role in the prognosis and immune infiltration level of head and neck cancer. In addition, MMP25 expression significantly correlated with the regulation of various oncogenes and tumor-related pathways.