OSskcm: an online survival analysis webserver for skin cutaneous melanoma based on 1085 transcriptomic profiles

Metformin regulates the proliferation and motility of melanoma cells by modulating the LINC00094/miR-1270 axis

BACKGROUND

Melanoma is an aggressive tumor with a high mortality rate. Metformin, a commonly prescribed diabetes medication, has shown promise in cancer prevention and treatment. Long noncoding RNAs (lncRNAs) are non-protein-coding RNA molecules that play a key role in tumor development by interacting with cellular chromatins. Despite the benefits of metformin, the anticancer mechanism underlying its effect on the regulation of lncRNAs in melanoma remains unclear.

METHODS

We investigated the lncRNA profiles of human melanoma cells with and without metformin treatment using a next-generation sequencing approach (NGS). Utilizing public databases, we analyzed the expression levels and clinical impacts of LINC00094 and miR-1270 in melanoma. The expression levels of LINC00094 and miR-1270 were verified in human cell lines and clinical samples by real-time PCR and in situ hybridization. The biological roles of LINC00094 and miR-1270 in cell growth, proliferation, cell cycle, apoptosis, and motility were studied using in vitro assays.

RESULTS

We identify a novel long noncoding RNA, namely LINC00094, whose expression considerably decreased in melanoma cells after metformin treatment. In situ hybridization analysis revealed substantially higher expression of LINC00094 in cutaneous melanoma tissue compared with adjacent normal epidermis and normal control tissues (P < 0.001). In nondiabetic patients with melanoma, the overall survival of high LINC00094 expression group was shorter than the low LINC00094 expression group with borderline statistical significance (log-rank test, P = 0.057). Coexpression analysis of LINC00094 indicated its involvement in the mitochondrial respiratory pathway, with its knockdown suppressing genes associated with mitochondrial oxidative phosphorylation, glycolysis, antioxidant production, and metabolite levels. Functional analysis revealed that silencing-LINC00094 inhibited the proliferation, colony formation, invasion, and migration of melanoma cells. Cell cycle analysis following LINC00094 knockdown revealed G1 phase arrest with reduced cell cycle protein expression. Combined TargetScan and reporter assays revealed a direct link between miR-1270 and LINC00094. Ectopic miR-1270 expression inhibited melanoma cell growth and motility while inducing apoptosis. Finally, through in silico analysis, we identified two miR-1270 target genes, CD276 and centromere protein M (CENPM), which may be involved in the biological functions of LINC00094.

CONCLUSIONS

Overall, LINC00094 expression may regulate melanoma cell growth and motility by modulating the expression of miR-1270, and targeting genes of CD276 and CENPM indicating its therapeutic potential in melanoma treatment.

Identification of genomic-wide genetic links between cutaneous melanoma and obesity-related physical traits via cFDR

BACKGROUND

Both epidemiological and clinical studies have suggested the comorbidity between cutaneous melanoma (CM) and obesity-related physical traits. However, it remains unclear about their shared genetic architecture.

OBJECTIVE

To determine the shared genetic architecture between CM and obesity-related physical traits through conditional false discovery rate (cFDR) analysis.

METHOD

Quantile-quantile plots were firstly built to assess the pleiotropic enrichment of shared single nucleotide polymorphisms between CM and each trait. Then, cFDR and conjunctional cFDR (ccFDR) were used to identify the shared risk loci between CM and each trait. Moreover, the functional evaluation of shared risk genes was carried out through analyses of expression quantitative trait loci (eQTL), Kyoto Encyclopedia of Genes and Genomes and gene ontology, respectively. Finally, single-cell sequence analysis was performed to locate the expression of eQTL-mapped genes in tissues.

RESULTS

Successive pleiotropic enrichment was found between CM and 5 obesity-related traits or height. 24 shared risk loci were identified between CM and 13 traits except appendicular lean mass using ccFDR analysis, with 17 novel and 4 validated loci. The functions of ccFDR-identified and eQTL-mapped genes were revealed to be mainly involved in cellular senescence, proliferation, meiotic nuclear division, cell cycle, and the metabolism of lipid, cholesterol and glucose. Single-cell sequence analysis showed that keratinocytes contribute to the occurrence and aggressiveness of CM through secreting paracrine cytokines.

CONCLUSION

Our findings demonstrate the significant genetic correlation between CM and obesity-related physical traits, which may provide a novel genetical basis for the pathogenesis and treatment of CM.

TNFSF10, an autophagy related gene, was a prognostic and immune infiltration marker in skin cutaneous melanoma

Autophagy exerts a pivotal effect on skin cutaneous melanoma (SKCM). This study was aimed to investigate the expression of autophagy related genes (ARGs) in SKCM as well as its clinical value. Differentially expressed (DE) ARGs were downloaded from the intersection of SKCM data in GEPIA2 database and ARGs in Human Autophagy Database (HADB) database, and were verified in SKCM datasets GSE46517 and GSE15605. DE ARGs were enriched by Metascape online tools. According to GEPIA2 database, tumor necrosis factor-related apoptosis-inducing ligand (TNFSF10) was identified as a closely related factor and prognostic marker of SKCM. Then the correlation analysis of clinicopathological characteristics between TNFSF10 and SKCM was completed by several online tools such as TISCH, HPA, BEST and qRT-PCR. Subsequently, we investigated TNFSF10 related functions and signal pathways with LinkedOmics online tool, and immune infiltration using Assistant for Clinical Bioinformatics online tool. Furthermore, correlation analysis between TNFSF10 expression and immunotherapy response was performed by TIDE algorithm and BEST online tool. And Kaplan-Meier Plotter was used to assessing the prognosis of SKCM patients receiving immunotherapy. Finally, the correlation analysis among TNFSF10 methylation, TNFSF10 expression and patient prognosis was completed by the DiseaseMeth version 2.0, UCSC XENA and qRT-PCR. ARGs are DE in SKCM and participate in the ERBB signaling pathway, as well as the processing and presentation of antigens. Moreover, TNFSF10's expression along with methylation expression were significantly associated with the prognosis. Low expression of TNFSF10 was associated with malignant clinicopathological features, lower immune signal activity and lower immunocytes abundance in patients with SKCM. As an ARG, TNFSF10 has a potential capacity in predicting the prognosis of SKCM patients, meanwhile, may be a novel immunotherapy marker for SKCM.

BS148 Reduces the Aggressiveness of Metastatic Melanoma via Sigma-2 Receptor Targeting

The management of advanced-stage melanoma is clinically challenging, mainly because of its resistance to the currently available therapies. Therefore, it is important to develop alternative therapeutic strategies. The sigma-2 receptor (S2R) is overexpressed in proliferating tumor cells and represents a promising vulnerability to target. Indeed, we have recently identified a potent S2R modulator (BS148) that is effective in melanoma. To elucidate its mechanism of action, we designed and synthesized a BS148 fluorescent probe that enters SK-MEL-2 melanoma cells as assessed using confocal microscopy analysis. We show that S2R knockdown significantly reduces the anti-proliferative effect induced by BS148 administration, indicating the engagement of S2R in BS148-mediated cytotoxicity. Interestingly, BS148 treatment showed similar molecular effects to S2R RNA interference-mediated knockdown. We demonstrate that BS148 administration activates the endoplasmic reticulum stress response through the upregulation of protein kinase R-like ER kinase (PERK), activating transcription factor 4 (ATF4) genes, and C/EBP homologous protein (CHOP). Furthermore, we show that BS148 treatment downregulates genes related to the cholesterol pathway and activates the MAPK signaling pathway. Finally, we translate our results into patient-derived xenograft (PDX) cells, proving that BS148 treatment reduces melanoma cell viability and migration. These results demonstrate that BS148 is able to inhibit metastatic melanoma cell proliferation and migration through its interaction with the S2R and confirm its role as a promising target to treat cancer.

OSppc: A web server for online survival analysis using proteome of pan-cancers

Prognostic biomarker, as a feasible and objective indicator, is valuable in the assessment of cancer risk. With the development of high-throughput sequencing technology, the screening of prognostic biomarkers has become easy, but it is difficult to screen prognostic markers based on proteomic data. In this study we developed a tool named Online consensus Survival analysis web server based on Proteome of Pan-cancers, abbreviated as OSppc, to evaluate the prognostic values of protein biomarkers. >8000 cancer cases with proteomic data, transcriptomic data and clinical follow-up information were collected from TCGA and CPTAC. 14,038 proteins (including proteins and their phosphorylated forms) analyzed by reverse-phase protein arrays and mass spectrometry in 33 types of cancers were collected. In OSppc, three analysis modules are provided, including Survival Analysis, Differential Analysis and Correlation Analysis. Survival analysis module exhibits HR with 95% CI and KM curves with log-rank p value of protein and mRNA levels of input genes. Differential analysis module shows the box plots of protein expression levels in different tissues. Correlation analysis module provides scatter plot with pearson's and spearman's correlation coefficient of the protein and its corresponding mRNA. OSppc can be accessed at http://bioinfo.henu.edu.cn/Protein/OSppc.html. SIGNIFICANCE: OSppc can analyze the association between protein, mRNA and prognosis, the correlation between proteome data and gene expression profiles, the differential expression of proteome data between subgroups such as normal and cancer as well. OSppc is registration-free and very valuable to evaluate the prognostic potency of protein of interests. OSppc is very valuable for researchers and clinicians to screen, develop and validate potential protein prognostic biomarkers in pan-cancers, and offers the opportunities to investigate the clinical important functional genes and therapeutic targets of cancers.

CD96 as a Potential Diagnostic Biomarker and New Target for Skin Cutaneous Melanoma

Skin cutaneous melanoma has high morbidity and mortality. Identification of reliable and quantitative melanoma biomarkers could facilitate an early diagnosis and improve survival and morbidity rates. CD96 has a significant role in adjusting immune function. Although the abnormal expression of CD96 has been reported to participate in carcinogenesis in many human types of cancer, the bioinformatics role of the CD96 in melanoma is unknown. Expression degrees and their underlying functions were first studied by this study. According to TCGA, GTEx, and gene expression profile interaction analysis dataset in this paper, compared with normal skin tissues, CD96 was expressed at higher levels in human cutaneous melanoma skin tissues. Meanwhile, we detected the relative CD96 expression levels by immunohistochemistry. Gene functional enrichment analyses were applied through cBioPortal database analysis. CD96 was clearly upregulated in skin cutaneous melanoma patients and carried out its effects through regulating several signaling pathways, containing the JAK-STAT, PI3K-Akt, and MAPK. Taken together, the analysis results indicated that CD96 could be used as a new clinical bioindicator as well as an underlying medicinal target for cutaneous melanoma.

A tumor-specific pro-IL-12 activates preexisting cytotoxic T cells to control established tumors

It is a challenge to effectively reactivate preexisting tumor-infiltrating lymphocytes (TILs) without causing severe toxicity. Interleukin-12 (IL-12) can potently activate lymphocytes, but its clinical use is limited by its short half-life and dose-related toxicity. In this study, we developed a tumor-conditional IL-12 (pro-IL-12), which masked IL-12 with selective extracellular receptor–binding domains of the IL-12 receptor while preferentially and persistently activating TILs after being unmasked by matrix metalloproteinases expressed by tumors. Systemic delivery of pro-IL-12 demonstrated reduced toxicity but better control of established tumors compared with IL-12-Fc. Mechanistically, antitumor responses induced by pro-IL-12 were dependent on TILs and IFNγ. Furthermore, direct binding of IL-12 to IL-12R on CD8+, not CD4+, T cells was essential for maximal effectiveness. Pro-IL-12 improved the efficacy of both immune checkpoint blockade and targeted therapy when used in combination. Therefore, our study demonstrated that pro-IL-12 could rejuvenate TILs, which then combined with current treatment modalities while limiting adverse effects for treating established tumors.

ZIP9 Is a Druggable Determinant of Sex Differences in Melanoma

Melanoma and most other cancers occur more frequently and have worse prognosis in males compared with females. Although sex steroids are thought to be involved, classical androgen and estrogen receptors are not detectable in most melanomas. Here we show that testosterone promotes melanoma proliferation by activating ZIP9 (SLC39A9), a zinc transporter that is widely expressed in human melanoma but not intentionally targeted by available therapeutics. This testosterone activity required an influx of zinc, activation of MAPK, and nuclear translocation of YAP. FDA-approved inhibitors of the classical androgen receptor also inhibited ZIP9, thereby antagonizing the protumorigenic effects of testosterone in melanoma. In male mice, androgen receptor inhibitors suppressed growth of ZIP9-expressing melanomas but had no effect on isogenic melanomas lacking ZIP9 or on melanomas in females. These data suggest that ZIP9 might be effectively targeted in melanoma and other cancers by repurposing androgen receptor inhibitors that are currently approved only for prostate cancer. SIGNIFICANCE: Testosterone signaling through ZIP9 mediates some of the sex differences in melanoma, and drugs that target AR can be repurposed to block ZIP9 and inhibit melanoma in males.

Influence of IL1B (rs16944) and IL1R2 (rs4141134) polymorphisms on aggressiveness and prognosis of cutaneous melanoma

Cutaneous melanoma is the most aggressive skin cancer with high mortality. Proinflammatory cytokines can modulate the proliferation and survival of cutaneous melanoma cells. Higher levels of interleukin-1β (IL1B) were associated with tumor cell proliferation, invasion, and migration, and the IL-1 type II receptor (IL1R2) serves as an endogenous inhibitor of IL1B signaling. Single-nucleotide variations (SNVs) in these genes (IL1B rs16944 and IL1R2 rs4141134) can modulate cytokine production and binding; however, their role in cutaneous melanoma is still unknown. Thus, we investigated the influence of the above SNVs in clinicopathological aspects and cutaneous melanoma patients' survival. In the present study, we analyzed 193 patients with cutaneous melanoma for IL1B c.-598T>C (rs16944) and IL1R2 c.-2009G>A (rs4141134) genotypes with TaqMan assays. Differences between groups were calculated using χ2 or Fisher's exact test and multiple logistic regression. Progression-free survival (PFS) and melanoma-specific survival were calculated by Kaplan-Meier and Cox methods. The prognostic value of IL1R2 was also analyzed by the online consensus survival webserver for skin cutaneous melanoma (OSskcm). We found that IL1R2 rs4141134 GG genotype was more common in patients with nodular subtype (49.1% vs. 29.8%, P = 0.01) and the frequency of IL1R2 rs4141134 GG or GA was higher in patients with Clark levels III-V (87.4% vs. 75.8%, P = 0.04). Patients with IL1R2 rs4141134 GG or GA genotypes presented lower PFS (hazard ratio: 3.12, 95% confidence interval, 1.10-8.79, P = 0.03) when compared with AA genotype, supported by OSskcm results. Thus, our study presented for the first time preliminary evidence that IL1R2 rs4141134 SNV may modulate cutaneous melanoma clinicopathological aspects and survival possible by allowing IL1B signaling.

EVI2B Is a New Prognostic Biomarker in Metastatic Melanoma with IFNgamma Associated Immune Infiltration

Simple Summary

Ecotropic viral integration site 2B (EVI2B) is a protein-coding gene known as a lymphocyte-specific marker in peripheral blood. However, the prognostic value of EVI2B expression in metastatic melanoma tissue and its detailed profile of tumor-infiltrating lymphocytes are still unclear. In publicly available datasets, we found that increased EVI2B was significantly associated with longer prognoses such as overall survival and disease-specific survival. The EVI2B-high melanoma tissue had a favorable distribution/clustering pattern of infiltrating lymphocytes with increased CD8+ T cells over regulatory T cells. Moreover, EVI2B expression correlated with multiple immunomodulatory genes including IFN-γ signature genes. In conclusion, EVI2B is a prognostic biomarker with IFN-γ associated immune infiltration in metastatic melanoma.

Abstract

Background: To assess the prognostic role and the antitumor immunological relevance of ecotropic viral integration site 2B (EVI2B) in metastatic melanoma. Methods: In this study, we integrated clinical data, mRNA expression data, and the distribution and fraction of tumor infiltrating lymphocytes (TILs) using The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets (GSE65904 and GSE19234). Results: The univariate and multivariate analyses showed that higher gene expression of EVI2B was significantly associated with longer prognoses. The EVI2B-high melanoma tissue had favorable histological parameters such as a brisk global distribution pattern and clustering structure of TILs (i.e., Banfield and Raftery index) with enriched CD8+ T cells over regulatory T cells and increased cytotoxicity scores. In addition, EVI2B expression positively correlated with IFN-γ signature genes (CXCL10, CXCL9, HLA-DRA, IDO1, IFNG, and STAT1) and other various immunomodulatory genes. Conclusion: EVI2B is a novel prognostic biomarker with IFN-γ associated immune infiltration in metastatic melanoma.

Identification of Potential Prognostic Biomarkers Associated With Cancerometastasis in Skin Cutaneous Melanoma

Skin cutaneous melanoma (SKCM) is a highly aggressive tumor. The mortality and drug resistance among it are high. Thus, exploring predictive biomarkers for prognosis has become a priority. We aimed to find immune cell-based biomarkers for survival prediction. Here 321 genes were differentially expressed in immune-related groups after ESTIMATE analysis and differential analysis. Two hundred nineteen of them were associated with the metastasis of SKCM via weighted gene co-expression network analysis. Twenty-six genes in this module were hub genes. Twelve of the 26 genes were related to overall survival in SKCM patients. After a multivariable Cox regression analysis, we obtained six of these genes (PLA2G2D, IKZF3, MS4A1, ZC3H12D, FCRL3, and P2RY10) that were independent prognostic signatures, and a survival model of them performed excellent predictive efficacy. The results revealed several essential genes that may act as significant prognostic factors of SKCM, which could deepen our understanding of the metastatic mechanisms and improve cancer treatment.

Data-independent acquisition-based proteome and phosphoproteome profiling across six melanoma cell lines reveals determinants of proteotypes

Human cancer cell lines are widely used in pharmacological and systems biological studies. The rapid documentation of the steady-state gene expression landscape of the cells used in a particular experiment may help to improve the reproducibility of scientific research. Here we applied a data-independent acquisition mass spectrometry (DIA-MS) method, coupled with a peptide spectral-library-free data analysis workflow, to measure both the proteome and phosphoproteome of a melanoma cell line panel with different metastatic properties. For each cell line, the single-shot DIA-MS detected 8100 proteins and almost 40 000 phosphopeptides in the respective measurements of two hours. Benchmarking the DIA-MS data towards the RNA-seq data and tandem mass tag (TMT)-MS results from the same set of cell lines demonstrated comparable qualitative coverage and quantitative reproducibility. Our data confirmed the high but complex mRNA-protein and protein-phospsite correlations. The results successfully established DIA-MS as a strong and competitive proteotyping approach for cell lines. The data further showed that all subunits of the glycosylphosphatidylinositol (GPI)-anchor transamidase complex were overexpressed in metastatic melanoma cells and identified altered phosphoprotein modules such as the BAF complex and mRNA splicing between metastatic and primary cells. This study provides a high-quality resource for calibrating DIA-MS performance, benchmarking DIA bioinformatic algorithms, and exploring the metastatic proteotypes in melanoma cells.

Expression of OPN3 in acral lentiginous melanoma and its associated with clinicohistopathologic features and prognosis

BACKGROUND

OPN3 upregulation associated with metastasis was recently described in two subtypes of lung cancers. And OPN3 identified in light-independent functions in epidermal melanocytes has already shown promise. However, in malignant melanocytic tissues, the expression and characterization of OPN3 remain uncharacterized.

OBJECTIVES

We investigated the clinico-histopathologic features in relation to OPN3 expression of acral lentiginous melanoma (ALM), which is a rare cutaneous melanoma subtype and not associated with prior sunlight exposure.

METHODS

In all, 84 samples of junctional melanocytic nevi (JMN, n = 12), primary ALMs (n = 39) and inguinal lymph node metastasis (ILNM, n = 23) from ALMs were evaluated for the immunohistochemical expression of OPN3. OPN3 messenger RNA and protein level were further determined in melanocytic tumors using quantitative real-time PCR, multiimmunofluorescence and Western blot assays. We also estimated the associations OPN3 expression between clinicopathological features and prognosis.

RESULTS

ILNMs, in contrast to JMN and ALMs, had higher OPN3 expression scores (p < .001) by immunohistochemistry analysis. High OPN3 score was associated with presence of ulceration, increased Breslow depth and Clark level (p = .025, p = .042, and p = .012, respectively). Furthermore, a remarkable difference (p = .037) of patient overall survival was found when comparing the OPN3 expression of immunohistochemical score between equal to or larger than 100 and below 100 groups. Also, Cox regression models showed that high OPN3 scores were associated with worse melanoma survival.

CONCLUSION

High OPN3 expression is significantly associated with ALMs and metastatic phenotype as well as a poor prognosis.

OSucs: An Online Prognostic Biomarker Analysis Tool for Uterine Carcinosarcoma

BACKGROUND

Uterine carcinosarcoma (UCS) is a type of rare and aggressive tumor. The standard treatment for UCS involves surgical treatment followed by radiochemotherapy. Clinical outcomes of UCS patients are poor due to high metastasis and relapse rate. Therefore, new targeted therapy strategies for UCS are needed. Because UCS is highly heterogenous, it is critical to identify and develop prognostic biomarkers to distinguish molecular subtypes of UCS for better treatment guidance.

METHODS

Using gene expression profiles and clinical follow-up data, we developed an online consensus survival analysis tool named OSucs. This web tool allows researchers to conveniently analyze the prognostic abilities of candidate genes in UCS.

RESULTS

To test the reliability of this server, we analyzed five previously reported prognostic biomarkers, all of which showed significant prognostic impacts. In addition, ETV4 (ETS variant transcription factor 4), ANGPTL4 (Angiopoietin-like protein 4), HIST1H1C (Histone cluster 1 H1 family member c) and CTSV (Cathepsin V) showed prognostic potential in a molecular subtype-specific manner.

CONCLUSION

We built a platform for researchers to analyze if genes have prognostic potentials in UCS.