Prognostic value of the expression of chemokines and their receptors in regional lymph nodes of melanoma patients

Identification of a distinctive immunogenomic gene signature in stage-matched colorectal cancer

BACKGROUND

Colorectal cancer (CRC) remains one of the leading causes of cancer-related mortality worldwide. Despite advances in diagnosis and treatment, including surgery, chemotherapy, and immunotherapy, accurate clinical markers are still lacking. The development of prognostic and predictive indicators, particularly in the context of personalized medicine, could significantly improve CRC patient management.

METHOD

In this retrospective study, we used FFPE blocks of tissue samples from CRC patients at Augusta University (AU) to quantify a custom 15-gene panel. To differentiate the tumor and adjacent normal regions (NAT), H&E staining was utilized. For the quantification of transcripts, we used the NanoString nCounter platform. Kaplan-Meier and Log-rank tests were used to perform survival analyses. Several independent datasets were explored to validate the gene signature. Orthogonal analyses included single-cell profiling, differential gene expression, immune cell deconvolution, neoantigen prediction, and biological pathway assessment.

RESULTS

A 3-gene signature (GTF3A, PKM, and VEGFA) was found to be associated with overall survival in the AU cohort (HR = 2.26, 95% CI 1.05-4.84, p = 0.02, 93 patients), TCGA cohort (HR = 1.57, 95% CI 1.05-2.35, p < 0.02, 435 patients) and four other GEO datasets. Independent single-cell analysis identified relatively higher expression of the 3-gene signature in the tumor region. Differential analysis revealed dysregulated tissue inflammation, immune dysfunction, and neoantigen load of cell cycle processes among high-risk patients compared to low-risk patients.

CONCLUSION

We developed a 3-gene signature with the potential for prognostic and predictive clinical assessment of CRC patients. This gene-based stratification offers a cost-effective approach to personalized cancer management. Further research using similar methods could identify therapy-specific gene signatures to strengthen the development of personalized medicine for CRC patients.

Molecular signature of immune-related new survival predictions for subtype of renal cell carcinomas

Background

Kidney renal papillary cell carcinoma (KIRP), kidney chromophobe (KICH), and kidney renal clear cell carcinoma (KIRC) are three most common subtypes of renal cell carcinomas (RCC), and its development is a multifaceted process that intricately involves the interplay of numerous genes. Despite recent advances in research on renal cell carcinoma, the prognosis of KIRC patients remains dismal. Therefore, there is an urgent need to explore new prognostic biomarkers and treatment strategies to help clinicians choose more effective treatment methods and accurately predict long-term efficacy. Our study aimed to systematically evaluate the gene expression profiles of three RCC subtypes, especially KIRC, and to identify survival-related biomarker.

Methods

In our present study, we systematically evaluate the genes expression profile difference among three subtypes of RCC, and identify the survival-related key genes signature based on GEPIA2. GeneMANIA was used to identify the functionality-related differentially expressed genes (DEGs). Furthermore, focusing on KIRC, we intersected functionality-related and survival-related DEGs based on two datasets.

Results

We ascertained five DEGs (ANK3, FREM2, KIF13B, MPP7 and SOX6) as key survival-related genes in KIRC. High levels of these five DEGs expressions were strongly associated with favorable prognosis, but not correlated to metastasis. Downregulation of these five DEGs expressions was closely associated with immunomodulators, chemokines, and infiltrating levels of different immune cells, which indicated that these five DEGs were key immune-related novel prognostic biomarkers for KIRC.

Conclusions

The five identified DEGs serve as potential novel prognostic biomarkers for KIRC. However, the crucial factors that lead to the downregulation and functional inactivation of these five key genes need to be explored in future studies.

Construction of a novel prognostic model in skin cutaneous melanoma based on chemokines-related gene signature

Skin cutaneous melanoma, SKCM, is one of the most aggressive treatment-resistant tumours. Despite the fact that the BRAF oncogene and immunological checkpoints such as PD-1/PD-L1 and CTLA-4 have enhanced the therapeutic efficacy of SKCM, the subsequent resistance mechanisms and remedies have raised concerns. Chemokines have a significant role in the immunological milieu of tumor, which may increase the efficacy of checkpoint blockade and serve as a possible therapeutic intervention route. However, there is still no chemokine-based typing and risk model to provide a prognosis and therapeutic efficacy assessment for SKCM patients. In this study, we verified the distinct differences of prognostic stratification as well as immune characteristics between two chemokine-related clusters in SKCM patients. Two clusters of DEGs were discovered to be primarily enriched in B and T cell receptor signaling pathways as well as TNF signaling via NF-kappa-B. Based on 14 prognosis-related DEGs from aforementioned two clusters (CCL8, GBP2, GBP4, SRNG, HLA-DMB, RARRES3, HLA-DQA1, PARP12, APOL3, IRF1, HLA-DRA, UBE2L6, IL2RA and CD38), a chemokine-related 14-gene prognostic model was established. At the same time, researchers explored differences between the low-risk and high-risk groups in clinical traits, the proportion of infiltration of 22 different types of immune cells, and how well medications worked. The risk score model's immunotherapy and prognostic predictions were also confirmed in testing groups. Based on the finding, we can claim that there is a clear link between chemokines and TME in SKCM. The risk score may perform as a trustworthy prediction model, giving therapeutic benefits for both chemotherapy and immunotherapy, as well as being beneficial for clinical decision making in SKCM patients.

A comprehensive review of chemokine CXC17 (VCC1) in cancer, infection, and inflammation

A crucial component of the immune system are chemokiness. Chemokine's dysregulation has been linked to a number of pathological diseases. Recently, CXCL17, a chemokine belonging to the CXC subfamily, was identified. With regard to a number of physiological conditions and disorders, CXCL17 either has homeostatic or pathogenic effects. Some research suggests that CXCL17 is an orphan ligand, despite the fact that G protein-coupled receptor (GPR) 35 has been suggested as a possible receptor for CXCL17. Since CXCL17 is primarily secreted by mucosal epithelia, such as those in the digestive and respiratory tracts, under physiological circumstances, this chemokine is referred to as a mucosal chemokine. Macrophages and monocytes are the cells that express GPR35 and hence react to CXCL17. In homeostatic conditions, this chemokine has anti-inflammatory, antibacterial, and chemotactic properties. CXCL17 promotes angiogenesis, metastasis, and cell proliferation in pathologic circumstances like malignancies. However, other studies suggest that CXCL17 may have anti-tumor properties. Additionally, studies have shown that CXCL17 may have a role in conditions such as idiopathic pulmonary fibrosis, multiple sclerosis, asthma, and systemic sclerosis. Additionally, deregulation of CXCL17 in some diseases may serve as a biomarker for diagnosis and prognosis. Clarifying the underlying mechanism of CXCL17's activity in homeostatic and pathological situations may thus increase our understanding of its role and hold promise for the development of novel treatment strategies.

FLG Is a Potential Biomarker of Prognosis and Immunotherapy in Skin Cutaneous Melanoma

Background

Skin cutaneous melanoma is one of most aggressive type of cancers worldwide. Therefore, the identification of SKCM biomarkers is of great importance. FLG gene is one of the genes that encode proteins involved in epidermal formation. This was the first time to study the role of FLG in the prognosis and immune infiltrates of skin cutaneous melanoma.

Methods

We downloaded the somatic mutation data of 471 SKCM patients from the Cancer Genome Atlas (TCGA) database and analyzed the mutation profiles with "MafTools" package. The expression of FLG and the overall survival in SKCM were analyzed by GEPIA. Additionally, univariate and multivariate Cox analyses were used to compare several clinical features with survival rates. We used TIMER to investigate FLG expression and collection of immune infiltration levels in SKCM, as well as cumulative survival in SKCM. Meanwhile, we also used CIBERSORT to investigate the association between FLG and cancer immune infiltration. In addition, gene set enrichment analysis (GSEA) was performed using the TCGA dataset. Furthermore, data from GEO and HPA was used to validate the results.

Results

Single nucleotide polymorphism (SNP) happened more frequently than insertion or deletion, and C > T was the most common of SNV in SKCM. We selected the first 15 mutated genes by analyzing 471 melanoma samples, and the prognosis analysis showed that only the high expression of mutated FLG gene was significantly correlated with the poor prognosis of SKCM. Multivariate Cox analysis showed that age, the worse tumor status, less lymph node metastasis, and FLG expression were independent factors for prognosis. Specifically, lower infiltration levels of B cell, CD8+ T cells, neutrophils, and dendritic cells correlated with poor survival outcomes in SKCM. GSEA revealed that FLG is closely related to cancer pathways and epidermal cell proliferation. In addition, the previous conclusions can be verified from external data from GEO and HPA.

Conclusion

The discovery of mutant gene FLG as a biomarker of SKCM helps elucidate how changes in the immune environment promote the occurrence of cutaneous melanoma. Further analysis suggested that FLG might be a new predictor of SKCM prognosis.

Expression and clinical significance of CXCL17 and GPR35 in endometrial carcinoma

Endometrial carcinoma is one of the most common gynecologic malignancies. CXCL17-CXCR8 (GPR35) axis is reported to play an indispensability role in tumors. Our purpose is to screen possible prognostic and immune-related factors in endometrial carcinoma by detecting the mRNA and protein expression of CXCL17 and CXCR8. We use the qRT-PCR method to test the mRNA expression of CXCL17 and CXCR8 in 35 pairs of endometrial carcinoma and adjacent tissue. The protein expression of CXCL17 and CXCR8 in 30 cases of normal proliferative endometrium, 30 cases of endometrial atypical hyperplasia and 50 cases of endometrial carcinoma was detected by tissue microarray immunohistochemistry. There was no significant difference in the positive expression rate between endometrial adenocarcinoma tissue and endometrial atypical hyperplasia tissue (P > 0.05). But significantly better than normal proliferative tissue (P < 0.001). Correlation analysis of CXCR8 and CXCL17 in endometrial carcinoma showed a positive correlation (r = 0.9123, P < 0.0001). For patients with endometrial cancer, the overall survival (OS) of patients with high CXCL17 expression was significantly higher than that low CXCL17 expression (log-rank test, P < 0.0001), whereas CXCR8 had no statistical significance. But the expression of CXCR8 is an independent prognostic factor of OS in endometrial carcinoma patients. Our study showed that CXCL17 and CXCR8 may be involved in the occurrence and development of endometrial cancer. High expression of CXCL17 may be used as a biomarker for predicting survival. Because CXCL17 and CXCL18 are related to lymphocytes and immune regulation, they are expected to become potential targets for immunotherapy.

Anti-melanoma effects of concomitant inhibition of SIRT1 and SIRT3 in BrafV600E/PtenNULL mice

Novel therapeutic strategies are required for the effective and lasting treatment of metastatic melanoma, one of the deadliest skin malignancies. In this study, we determined the anti-melanoma efficacy of 4'-bromo-resveratrol (4'-BR), which is a small molecule dual inhibitor of SIRT1 and SIRT3 in a Braf^V600E/Pten^NULL mouse model that recapitulates human disease, including metastases. Tumors were induced by topical application of 4-hydroxy-tamoxifen on shaved backs of 10-week-old mice, and the effects of 4'-BR (5-30 mg/kg b.wt.; intraperitoneally; 3d/week for 5 weeks) were assessed on melanoma development and progression. We found that 4'-BR at a dose of 30 mg/kg significantly reduced size and volume of primary melanoma tumors, as well as lung metastasis, with no adverse effects. Further, mechanistic studies on tumors showed significant modulation in markers of proliferation, survival and melanoma progression. As SIRT1 and SIRT3 are linked to immunomodulation, we performed differential gene expression analysis via NanoString PanCancer Immune Profiling panel (770 genes). Our data demonstrated that 4'-BR significantly downregulated genes related to metastasis-promotion, chemokine/cytokine-regulation, and innate/adaptive immune functions. Overall, inhibition of SIRT1 and SIRT3 by 4'-BR is a promising anti-melanoma therapy with anti-metastatic and immunomodulatory activities warranting further detailed studies, including clinical investigations.

Contribution of CXCR3-mediated signaling in the metastatic cascade of solid malignancies

Metastasis is a significant cause of the mortality resulting from solid malignancies. The process of metastasis is complex and is regulated by numerous cancer cell-intrinsic and -extrinsic factors. CXCR3 is a chemokine receptor that is frequently expressed by cancer cells, endothelial cells and immune cells. CXCR3A signaling in cancer cells tends to promote the invasive and migratory phenotype of cancer cells. Indirectly, CXCR3 modulates the anti-tumor immune response resulting in variable effects that can permit or inhibit metastatic progression. Finally, the activity of CXCR3B in endothelial cells is generally angiostatic, which limits the access of cancer cells to key conduits to secondary sites. However, the interaction of these activities within a tumor and the presence of opposing CXCR3 splice variants clouds the picture of the role of CXCR3 in metastasis. Consequently, thorough analysis of the contributions of CXCR3 to cancer metastasis is necessary. This review is an in-depth examination of the involvement of CXCR3 in the metastatic process of solid malignancies.

Identification and validation of tumor microenvironment-related lncRNA prognostic signature for uveal melanoma

AIM

To investigate the role of tumor microenvironment (TME)-related long non-coding RNA (lncRNA) in uveal melanoma (UM), probable prognostic signature and potential small molecule drugs using bioinformatics analysis.

METHODS

UM expression profile data were downloaded from the Cancer Genome Atlas (TCGA) and bioinformatics methods were used to find prognostic lncRNAs related to UM immune cell infiltration. The gene expression profile data of 80 TCGA specimens were analyzed using the single sample Gene Set Enrichment Analysis (ssGSEA) method, and the immune cell infiltration of a single specimen was evaluated. Finally, the specimens were divided into high and low infiltration groups. The differential expression between the two groups was analyzed using the R package 'edgeR'. Univariate, multivariate and Least Absolute Shrinkage and Selection Operator (LASSO) Cox regression analyses were performed to explore the prognostic value of TME-related lncRNAs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional analyses were also performed. The Connectivity Map (CMap) data set was used to screen molecular drugs that may treat UM.

RESULTS

A total of 2393 differentially expressed genes were identified and met the criteria for the low and high immune cell infiltration groups. Univariate Cox analysis of lncRNA genes with differential expression identified 186 genes associated with prognosis. Eight prognostic markers of TME-included lncRNA genes were established as potentially independent prognostic elements. Among 269 differentially expressed lncRNAs, 69 were up-regulated and 200 were down-regulated. Univariate Cox regression analysis of the risk indicators and clinical characteristics of the 8 lncRNA gene constructs showed that age, TNM stage, tumor base diameter, and low and high risk indices had significant prognostic value. We screened the potential small-molecule drugs for UM, including W-13, AH-6809 and Imatinib.

CONCLUSION

The prognostic markers identified in this study are reliable biomarkers of UM. This study expands our current understanding of the role of TME-related lncRNAs in UM genesis, which may lay the foundations for future treatment of this disease.

CXC Chemokines as Therapeutic Targets and Prognostic Biomarkers in Skin Cutaneous Melanoma Microenvironment

Background

Skin Cutaneous Melanoma (SKCM) is a tumor of the epidermal melanocytes induced by gene activation or mutation. It is the result of the interaction between genetic, constitutional, and environmental factors. SKCM is highly aggressive and is the most threatening skin tumor. The incidence of the disease is increasing year by year, and it is the main cause of death in skin tumors around the world. CXC chemokines in the tumor microenvironment can regulate the transport of immune cells and the activity of tumor cells, thus playing an anti-tumor immunological role and affecting the prognosis of patients. However, the expression level of CXC chemokine in SKCM and its effect on prognosis are still unclear.

Method

Oncomine, UALCAN, GEPIA, STRING, GeneMANIA, cBioPortal, TIMER, TRRUST, DAVID 6.8, and Metascape were applied in our research.

Result

The transcription of CXCL1, CXCL5, CXCL8, CXCL9, CXCL10, and CXCL13 in SKCM tissues were significantly higher than those in normal tissues. The pathological stage of SKCM patients is closely related to the expression of CXCL4, CXCL9, CXCL10, CXCL11, CXCL12, and CXCL13. The prognosis of SKCM patients with low transcription levels of CXCL4, CXCL9, CXCL10, CXCL11, and CXCL13 is better. The differential expression of CXC chemokines is mainly associated with inflammatory response, immune response, and cytokine mediated signaling pathways. Our data indicate that the key transcription factors of CXC chemokines are RELA, NF-κB1 and SP1. The targets of CXC chemokines are mainly LCK, LYN, SYK, MAPK2, MAPK12, and ART. The relationship between CXC chemokine expression and immune cell infiltration in SKCM was closed.

Conclusions

Our research provides a basis for screening SKCM biomarkers, predicting prognosis, and choosing immunotherapy.

Prognostic value of the expression of chemokines and their receptors in regional lymph nodes of melanoma patients

Chemokines and their receptors have been reported to drive immune cells into tumours or to be directly involved in the promotion or inhibition of the development of tumours. However, their expression in regional lymph node (LN) tissues in melanoma patients remains unknown. The present study investigated the relationship between the expression of mRNA of chemokines and their receptors and clinicopathology of the regional LN tissues of skin cutaneous melanoma (SKCM) patients available in The Cancer Genome Atlas. The relationship between chemokines and their receptors and the composition of immune cells within the tumour was analysed. In SKCM regional LN tissues, the high expression of 32 types of chemokines and receptors, namely CCL2, 4‐5, 7‐8, 13, 22‐25, CCR1‐9, CXCL9‐13, 16, CXCR3, 5, 6, XCL1‐2 and XCR1 in LN was associated with favourable patient prognosis. Conversely, high expression of CXCL17 was an indicator of poor prognosis. The expression of mRNA for CXCL9‐11, 13, CXCR3, 6, CCL2, 4, 5, 7, 8, 25, CCR1, 2, 5, and XCL1, 2 in regional LN tissues was positively correlated with the fraction of CD8‐positive T cells and M1 macrophages, and was negatively correlated with M0 macrophages. CCR4, 6‐9, CCL13, 22, 23 and XCR1 were positively correlated with the fraction of memory B cells and naive T cells, and negatively correlated with M0 macrophages and resting mast cells, suggesting that chemokines and their receptors may affect the prognosis of patients by guiding immune cells into the tumour microenvironment to eliminate tumour cells.