Screening the Molecular Targets of Ovarian Cancer Based on Bioinformatics Analysis

Spatial characterisation of β-catenin-mutated hepatocellular adenoma subtypes by proteomic profiling of the tumour rim

Background & Aims

Hepatocellular adenomas (HCAs) are rare, benign, liver tumours classified at the clinicopathological, genetic, and proteomic levels. The β-catenin-activated (b-HCA) subtypes harbour several mutation types in the β-catenin gene (CTNNB1) associated with different risks of malignant transformation or bleeding. Glutamine synthetase is a surrogate marker of β-catenin pathway activation associated with the risk of malignant transformation. Recently, we revealed an overexpression of glutamine synthetase in the rims of exon 3 S45-mutated b-HCA and exon 7/8-mutated b-HCA compared with the rest of the tumour. A difference in vascularisation was found in this rim shown by diffuse CD34 staining only at the tumour centre. Here, we aimed to characterise this tumour heterogeneity to better understand its physiopathological involvement.

Methods

Using mass spectrometry imaging, genetic, and proteomic analyses combined with laser capture microdissection, we compared the tumour centre with the tumour rim and with adjacent non-tumoural tissue.

Results

The tumour rim harboured the same mutation as the tumour centre, meaning both parts belong to the same tumour. Mass spectrometry imaging showed different spectral profiles between the rim and the tumour centre. Proteomic profiling revealed the significant differential expression of 40 proteins at the rim compared with the tumour centre. The majority of these proteins were associated with metabolism, with an expression profile comparable with a normal perivenous hepatocyte expression profile.

Conclusions

The difference in phenotype between the tumour centres and tumour rims of exon 3 S45-mutated b-HCA and exon 7/8-mutated b-HCA does not depend on CTNNB1 mutational status. In a context of sinusoidal arterial pathology, tumour heterogeneity at the rim harbours perivenous characteristics and could be caused by a functional peripheral venous drainage.

Impact and implications

Tumour heterogeneity was revealed in β-catenin-mutated hepatocellular adenomas (b-HCAs) via the differential expression of glutamine synthase at tumour rims. The combination of several spatial approaches (mass spectrometry imaging, genetic, and proteomic analyses) after laser capture microdissection allowed identification of a potential role for peripheral venous drainage underlying this difference. Through this study, we were able to illustrate that beyond a mutational context, many factors can downstream regulate gene expression and contribute to different clinicopathological phenotypes. We believe that the combinations of spatial analyses that we used could be inspiring for all researchers wanting to access heterogeneity information of liver tumours.

Effects of prometryn on oxidative stress, immune response and apoptosis in the hepatopancreas of Eriocheir sinensis (Crustacea: Decapoda)

Prometryn, a triazine pesticide product used to control weed growth, poses a high risk to aquatic organisms in the environment. Several toxicological evaluations have been performed on bony fish and shrimp exposed to prometryn. However, there have been no reports conducted on the toxic mechanism of prometryn with regard to Eriocheir sinensis. In this study, our research evaluated the toxic effects of prometryn via in vitro and in vivo toxicity tests on E. sinensis. Firstly, we estimated the exposure toxicity of prometryn to E. sinensis, and then we constructed a 6 h transcriptional profile and conducted an enrichment analysis. To further reveal the toxicity of prometryn, the hepatopancreas (hepatopancreatic cells) was analyzed for antioxidant, immune and lipid-metabolism-related enzymes, antioxidant- and apoptosis-related gene expression, histopathology and TUNEL. From the results, we determined that the 96 h-LD50 was 70.059 mg/kg, and using RNA-seq, we identified 933 differentially expressed genes (DEGs), which were mainly enriched in the amino and fatty acid metabolism and the cell-fate-determination-related signaling pathway. The results of the biochemical assays showed that prometryn could significantly decrease the activities/levels of CAT, SOD, GSH, AKP and ACP, reduce the levels of T-AOC, TG, TCH, C3 and C4, and increase the MDA content. In addition, the expression levels of Nrf2, GSTs and HO-1 were first upregulated and then downregulated with increasing time. Histopathology showed that prometryn damaged the structure of the hepatopancreas cells and induced apoptosis, suggesting that the PI3K-Akt signaling pathway may be involved in the damage process of hepatopancreas cells (PI3K, PDK and Akt were downregulated whereas Bax was upregulated), leading to their apoptosis. The above results indicated that prometryn could cause injury of the hepatopancreas through oxidative stress, induce cell apoptosis, disrupt the lipid metabolism and cause immune damage. This study provided useful data for understanding and evaluating the toxicity of prometryn to aquatic crustacea.

Prioritization and Meta-analysis of regulatory SNPs identified IL6, TGFB1, TLR9 and MMP7 as significantly associated with cervical cancer

Cervical cancer is a leading women cancer globally with respect to both incidence and mortality. Its increased risk has been linked with HPV infection and genetic variations like single nucleotide polymorphisms (SNPs). Although, studies have been published which evaluates the effect of SNPs in a few candidate genes, however the role of number of regulatory SNPs (rSNPs) in cervical cancer is not available. As literature evidence has shown that non-coding rSNPs are related with increasing cervical cancer risk, we undertook this study to prioritize the important rSNPs and elucidate their role. A search was conducted in PubMed up to December 2020, which led to the identification of 263 articles and 969 SNPs in the non-coding region. These 969 SNPs were analysed through rSNPBase and RegulomeDB, leading to identification of 105 rSNPs. Afterwards, a regulatory module was constructed using protein-protein interaction data and a hub of highly interacting 23 target genes (corresponding to 34 rSNPs) was identified using MCODE. To further understand the mechanism of action of the 34 rSNPs, their transcription factor information with respect to cervical cancer was retrieved. To evaluate the pooled effect of these prioritized polymorphisms in cervical cancer patients, a meta-analysis was performed on 10,537 cases and 11,252 controls from 30 studies corresponding to 8 rSNPs. It led to identification of polymorphisms in IL6 (rs2069837), TGFB1 (rs1800469), TLR9 (rs187084) and MMP7 (rs11568818) which are significantly (p < 0.05) associated with increased cervical cancer risk at the population level. Overall, the study demonstrates that rSNPs targeting immune and inflammatory genes (IL1B, IL6, IL10, IL18, TGFB1, CCR5, CD40, TLR9, and MMP7) are associated with cervical cancer.

Screening the key genes of prognostic value in the microenvironment for head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) is the sixth common malignancy worldwide. The tumor microenvironment is highly related to tumor initiation, progression, and prognosis. This study aims to screen the tumor microenvironment related key genes of prognostic value for HNSCC.The gene expression and clinical data for HNSCC were downloaded from the cancer genome atlas (TCGA). The immune/stromal/ESTIMATE scores were downloaded from the website of the MD Anderson Cancer Center. Correlation of patient gender and tumor grade with immune/stromal/ESTIMATE score was tested. Patients were divided into low and high immune/stromal/ESTIMATE score subgroups. Survival analysis was performed to evaluate the prognostic value of the immune/stromal/ESTIMATE score. Tumor microenvironment related differentially expressed genes were determined and applied for functional enrichment analysis and protein-protein interaction network was predicted. The prediction value of the common differentially expressed genes on patient survival was tested.Four hundred eighty samples with complete clinical, expression data, and immune/stromal/ESTIMATE scores were enrolled for analysis. Immune/stromal/ESTIMATE score was higher in female patients than males. A total of 44 common differentially expressed genes were screened in high and low immune/stromal/ESTIMATE score subgroups. Of the 44 genes, 7 genes (ADGRG7, CSN3, CST8, KRT81, MUC7, MYH6, and SEZ6) were found to be closely related to patient survival. Enrichment analysis showed that the differentially expressed genes mainly enriched in the protein-coupled receptor signaling pathway, extracellular region, G-protein coupled receptor activity, salivary secretion, and regulation of lipolysis in adipocytes. Protein-protein interaction analysis revealed that POSTN and OGN were crucial microenvironments related genes.Tumor microenvironment related genes ADGRG7, CSN3, CST8, KRT81, MUC7, MYH6, and SEZ6 are valuable predictors for HNSCC patient survival. POSTN and OGN are crucial in modulating the microenvironment and tumor biology for HNSCC.

Network Analyses of the Differential Expression of Heat Shock Proteins in Glioma

Heat shock protein (HSP) is a family of highly conserved protein, which exists widely in various organisms and has a variety of important physiological functions. Currently, there is no systematic analysis of HSPs in human glioma. The aim of this study was to investigate the characteristics of HSPs through constructing protein-protein interaction network (PPIN) considering the expression level of HSPs in glioma. After the identification of the differentially expressed HSPs in glioma tissues, a specific PPIN was constructed and found that there were many interactions between the differentially expressed HSPs in glioma. Subcellular localization analysis shows that HSPs and their interacting proteins distribute from the cell membrane to the nucleus in a multilayer structure. By functional enrichment analysis, gene ontology analysis, and Kyoto Encyclopedia of Genes and Genomes pathway analysis, the potential function of HSPs and two meaningful enrichment pathways was revealed. In addition, nine HSPs (DNAJA4, DNAJC6, DNAJC12, HSPA6, HSP90B1, DNAJB1, DNAJB6, DNAJC10, and SERPINH1) are prognostic markers for human brain glioma. These analyses provide a full view of HSPs about their expression, biological process, as well as clinical significance in glioma.

Wnt/β-catenin signalling in ovarian cancer: Insights into its hyperactivation and function in tumorigenesis

Epithelial ovarian cancer (EOC) is the deadliest female malignancy. The Wnt/β-catenin pathway plays critical roles in regulating embryonic development and physiological processes. This pathway is tightly regulated to ensure its proper activity. In the absence of Wnt ligands, β-catenin is degraded by a destruction complex. When the pathway is stimulated by a Wnt ligand, β-catenin dissociates from the destruction complex and translocates into the nucleus where it interacts with TCF/LEF transcription factors to regulate target gene expression. Aberrant activation of this pathway, which leads to the hyperactivity of β-catenin, has been reported in ovarian cancer. Specifically, mutations of CTNNB1, AXIN, or APC, have been observed in the endometrioid and mucinous subtypes of EOC. In addition, upregulation of the ligands, abnormal activation of the receptors or intracellular mediators, disruption of the β-catenin destruction complex, inhibition of the association of β-catenin/E-cadherin on the cell membrane, and aberrant promotion of the β-catenin/TCF transcriptional activity, have all been reported in EOC, especially in the high grade serous subtype. Furthermore, several non-coding RNAs have been shown to regulate EOC development, in part, through the modulation of Wnt/β-catenin signalling. The Wnt/β-catenin pathway has been reported to promote cancer stem cell self-renewal, metastasis, and chemoresistance in all subtypes of EOC. Emerging evidence also suggests that the pathway induces ovarian tumor angiogenesis and immune evasion. Taken together, these studies demonstrate that the Wnt/β-catenin pathway plays critical roles in EOC development and is a strong candidate for the development of targeted therapies.

Prognostic and clinicopathological value of ZIC1 in patients with cervical squamous cell carcinoma

The aim of the present study was to analyze the differences in zinc finger of the cerebellum 1 (ZIC1) expression between cervical cancer tissue, precancer tissue and normal cervical tissue to determine its clinicopathological and prognostic value in cervical squamous cell carcinoma (CSCC). Reverse transcription-quantitative PCR was used to determine the mRNA expression levels of ZIC1 in 569 fresh-frozen biopsy tissues, and immunohistochemistry was performed to detect ZIC1 protein expression in 80 CSCC tissues and 320 cervical intraepithelial neoplasia (CIN) grade III samples. The association of ZIC1 expression with the clinicopathological characteristics of CSCC was then analyzed using Cox regression analysis, and Kaplan-Meier curves were used to analyze the prognostic value. The level of ZIC1 mRNA expression in CSCC was significantly lower compared with normal cervical tissues and CIN I–III tissues (P<0.001). There was a negative correlation between ZIC1 immunoreactivity score (IRS) in CSCC tissue and adjacent noncancerous tissue (R=−0.279; P=0.012); the mean IRS of ZIC1 in CSCC tissue was 5.36±3.48, which was significantly lower compared with the corresponding adjacent noncancerous tissues (11.31±5.68; P<0.001) and CIN III samples (10.42±1.54; P<0.001). In addition, expression of ZIC1 was negatively associated with International Federation of Gynecology and Obstetrics (FIGO) stage (P=0.027) and lymph node metastasis (P<0.001). In Cox regression analysis, ZIC1 expression [hazard ratio (HR), 0.61; 95% confidence interval (CI), 0.40–0.92; P=0.018), FIGO staging (HR, 3.55; 95% CI, 2.35–5.37; P<0.001) and lymph node metastasis (HR, 2.50; 95% CI, 1.62–3.86; P<0.001) were three independent prognostic factors of overall survival. Furthermore, ZIC1 expression was also associated with disease-free survival (P=0.003). These results suggest that ZIC1 expression in CSCC may be lower than in normal cervical tissues or CIN tissues, and high expression of ZIC1 may be negatively associated with FIGO stage and lymph node metastasis. Therefore, ZIC1 may be a promising biomarker for the prognosis of CSCC.

High Survivin and Low Zinc Finger of the Cerebellum 1 Expression Indicates Poor Prognosis in Triple-negative Breast Carcinoma

Purpose

Triple-negative breast carcinoma (TNBC) is accompanied with high risk of metastasis and recurrence. The present study aimed to explore the clinicopathological and prognostic roles of putative tumor-related genes in patients with TNBC.

Methods

Thirty pairs of frozen-thawed tumors were used to select reliable indicators via real-time quantitative polymerase chain reaction (RT-qPCR). Then, 150 pathology specimens were used to evaluate the expression of proteins in TNBC through immunohistochemistry. In addition, Kaplan-Meier curves and Cox regression analysis were also performed to analyze the overall survival and disease-free survival.

Results

RT-qPCR results indicated that among all the proteins analyzed using fresh-frozen TNBC samples, the expression levels of only Survivin and zinc finger of the cerebellum 1 (ZIC1) were obviously different from those in the corresponding normal tissues. Survivin and ZIC1 expression had opposite effects on the clinicopathological diagnosis and prognostic assessment in TNBC patients. Further, there was a negative correlation between Survivin and ZIC1 expression. In addition, the “Survivin-positive ZIC1-negative group” was associated with histologic grade, lymph node metastasis, and TNM staging (p < 0.001) and this was also an independent factor for evaluating the prognosis of TNBC in patients.

Conclusion

In summary, the expression levels of Survivin and ZIC1 in TNBC are different from those in normal tissues and are negatively correlated mutually. The combined detection of Survivin and ZIC1 expression levels could allow better comprehensive diagnosis and prognostic evaluation for TNBC patients.

ZIC1 acts a tumor suppressor in breast cancer by targeting survivin

In this study, we aimed to identify the tumor suppressive roles of zinc finger of the cerebellum 1 (ZIC1) in patients with malignant breast neoplasms and to examine the association between ZIC1 and survivin expression. For this purpose, 140 invasive breast cancer specimens, 1,075 RNA breast cancer samples from The Cancer Genome Atlas (TCGA), 6 human breast cancer cell lines and MCF-10A normal breast epithelial cells were selected in order to compare the expression level of ZIC1 with that of survivin via immunohistochemistry and western blot analysis. Subsequently, the MDA-MB-231 and SK-BR3 cells with a lower ZIC1 expression were transfected with rLV-Zic1-PGK-Puro lentivirus or rLV-ZsGreen-PGK-Puro lentivirus in order to observe any alterations in cell proliferation and apoptosis through MTT assay, colony formation assay, mitochondrial membrane potential assay and flow cytometric analysis, and to analyze the modulation of molecular mechanisms by western blot analysis. In addition, xenograft mouse models were constructed to explore the role of ZIC1 in the growth of implanted tumors. The results revealed that ZIC1 negatively correlated with survivin in tumors and cells, and a higher ZIC1 RNA expression indicated a better overall survival in the 1,075 TCGA RNA breast cancer samples. In vitro, the overexpression of ZIC1 inhibited cell proliferation, reduced mitochondrial membrane potential and promoted the apoptosis of the MDA-MB-231 and SK-BR3 breast cancer cells by inactivating the Akt/mTOR/P70S6K pathway, suppressing survivin expression, modulating the cell cycle, releasing cytochrome c (Cyto-c) into the cytosol and activating caspase proteins. In vivo, an elevated ZIC1 expression suppressed the growth of implanted tumors and downregulated survivin expression in tumors. On the whole, the findings of this study demonstrate that ZIC1 plays a tumor suppressive role in breast cancer, by targeting surviving, significantly downregulating its expression.

FoxO-1 contributes to the efficacy of the combination of the XPO1 inhibitor selinexor and cisplatin in ovarian carcinoma preclinical models

The XPO1/CRM1 inhibitor selinexor (KPT-330), is currently being evaluated in multiple clinical trials as an anticancer agent. XPO1 participates in the nuclear export of FoxO-1, which we previously found to be decreased in platinum-resistant ovarian carcinoma. The aim of this study was to determine whether enriching FoxO-1 nuclear localization using selinexor would increase ovarian cancer cell sensitivity to cisplatin. Selinexor, as a single agent, displayed a striking antiproliferative effect in different ovarian carcinoma cell lines. A schedule-dependent synergistic effect of selinexor in combination with cisplatin was found in cisplatin-sensitive IGROV-1, the combination efficacy being more evident in sensitive than in the resistant cells. In IGROV-1 cells, the combination was more effective when selinexor followed cisplatin exposure. A modulation of proteins involved in apoptosis (p53, Bax) and in cell cycle progression (p21WAF1) was found by Western blotting. Selinexor-treated cells exhibited enriched FoxO-1 nuclear staining. Knock-down experiments with RNA interference indicated that FOXO1-silenced cells displayed a reduced sensitivity to selinexor. FOXO1 silencing also tended to reduce the efficacy of the drug combination at selected cisplatin concentrations. Selinexor significantly inhibited tumor growth, induced FoxO-1 nuclear localization and improved the efficacy of cisplatin in IGROV-1 xenografts. Taken together, our results support FoxO-1 as one of the key factors promoting sensitivity towards selinexor and the synergistic interaction between cisplatin and selinexor in ovarian carcinoma cells with selected molecular backgrounds, highlighting the need for treatment regimens tailored to the molecular tumor features.

Attenuation of MUC4 potentiates the anticancer activity of auranofin via regulation of the Her2/Akt/FOXO3 pathway in ovarian cancer cells

Previously, we reported that auranofin induces apoptosis in SKOV3 cells via regulation of the IKKβ/FOXO3 pathway. In the present study, we reveal that the anticancer activity of auranofin in SKOV3 cells could be enhanced by the attenuation of MUC4 through the regulation of the Her2/Akt/FOXO3 pathway. Compared to the control-siRNA, siRNA transfection against MUC4 into SKOV3 cells accelerated the protein degradation of Her2. Under the same conditions, the expression level of phosphorylated Akt was also downregulated leading to an increase of FOXO3 in the nucleus. Notably, auranofin treatment in SKOV3 cells also resulted in the downregulation of the expression levels of both Her2 and phosphorylated Akt. Thus, Her2 was identified as the common molecular target protein by siRNA transfection against MUC4. Western blot analysis of total and nuclear fraction lysates from SKOV3 cells revealed that attenuation of MUC4 combined with auranofin treatment in SKOV3 cells synergistically activated FOXO3 translocation from the cytoplasm to the nucleus through the regulation of the Her2/Akt/FOXO3 pathway. Attenuation of MUC4 by siRNA transfection potentiated the antitumor effect of auranofin which was examined by performing in vitro assays such as WST-1, cell counting, colony formation, TUNEL and Annexin V staining. In addition, western blot analysis of the apoptosis‑related proteins such as PARP1, caspase-3, Bim extra large (EL), Bax and Bcl2 revealed that the attenuation of MUC4 by siRNA transfection potentiates the pro-apoptotic activity of auranofin in SKOV3 cells. Collectively, auranofin could regulate the Her2/Akt/FOXO3 signaling pathway in SKOV3 cells and be used as a potential antitumor agent considering the expression of MUC4 in ovarian cancer patients.