A four-gene transcript score to predict metastatic-lethal progression in men treated for localized prostate cancer: Development and validation studies

Identification and validation of cigarette smoking-related genes in predicting prostate cancer development through bioinformatic analysis and experiments

The morbidity and mortality rates of prostate cancer (PCa) are high among elderly men worldwide. Several factors, such as heredity, obesity, and environment are associated with the occurrence of PCa. Cigarette smoking, which is also an important factor in the development of PCa, can lead to genetic alterations and consequently promote PCa development. However, the smoking-induced genetic alterations in PCa are unclear. This study aimed to identify the potential smoking-related genes associated with PCa development. The smoking-related differentially expressed genes (DEGs) were identified using the Gene Expression Omnibus (GEO) which included lots of PCa datasets. DEGs were subjected to protein-protein interaction (PPI) network analysis to identify the hub genes. The pathways in which these hub genes were enriched were identified. The Cancer Genome Atlas (TCGA) dataset was used to examine the expression of smoking-related genes in PCa samples and estimate their value in predicting tumor progression and prognosis. In total, 110 smoking-related DEGs were got from GSE68135 dataset which included microarray data of PCa patients with smoking or not and 14 smoking-related key genes associated with PCa were identified from PPI network. The expression of the following seven key genes was altered in TCGA PCa patients: EWSR1, SRSF6, COL6A3, FBLN1, DCN, CYP2J2, and PLA2G2A. EWSR1, SRSF6, FBLN1, and CYP2J2 also influenced PCa progression. Additionally, EWSR1 influenced disease-free survival. In the logistic regression model, CYP2J2, which exhibited the highest risk scores, was identified as the risk gene for PCa. We also found one of the smoking-related genes: EWSR1 was truly upregulated in clinical PCa patients and influenced PCa cells invasion and proliferation. This study identified the function of smoking-related genes involved in the progression of PCa.

CST2 promotes cell proliferation and regulates cell cycle by activating Wnt-β-catenin signalling pathway in serous ovarian cancer

BACKGROUND

Cystatin SA (CST2) plays multiple roles in different types of malignant tumours; however, its role in serous ovarian cancer (SOC) remains unclear. Therefore, we aimed to investigate the expression levels, survival outcomes, immune cell infiltration, proliferation, cell cycle, and underlying molecular mechanisms associated with the CST2 signature in SOC.

METHODS

The Cancer Genome Atlas database was used to acquire clinical information and CST2 expression profiles from patients with SOC. Wilcoxon rank-sum tests were used to compare CST2 expression levels between SOC and normal ovarian tissues. A prognostic assessment of CST2 was conducted using Cox regression analysis and the Kaplan-Meier method. Differentially expressed genes were identified using functional enrichment analysis. Immune cell infiltration was examined using a single-sample gene set enrichment analysis. Cell cycle characteristics and proliferation were assessed using a colony formation assay, flow cytometry, and a cell counting kit-8 assay. Western blots and quantitative reverse transcription PCR analyses were employed to examine CST2 expressions and related genes involved in the cell cycle and the Wnt-β-catenin signalling pathway.

RESULTS

Our findings revealed significant upregulation of CST2 in SOC, and elevated CST2 expression was correlated with advanced clinicopathological characteristics and unfavourable prognoses. Pathway enrichment analysis highlighted the association between the cell cycle and the Wnt signalling pathway. Moreover, increased CST2 levels were positively correlated with immune cell infiltration. Functionally, CST2 played vital roles in promoting cell proliferation, orchestrating the G1-to-S phase transition, and driving malignant SOC progression through activating the Wnt-β-catenin signalling pathway.

CONCLUSIONS

The elevated expression of CST2 may be related to the occurrence and progression of SOC by activating the Wnt-β-catenin pathway. Additionally, our findings suggest that CST2 is a promising novel biomarker with potential applications in therapeutic, prognostic, and diagnostic strategies for SOC.

Cystatin SA attenuates gastric cancer cells growth and increases sensitivity to oxaliplatin via PI3K/AKT signaling pathway

PURPOSE

Cystatin SA (CST2) belongs to the superfamily of cysteine protease inhibitors. Emerging research indicates that CST2 is often dysregulated across various cancers. Its role and molecular mechanisms in gastric cancer remain underexplored. This study aims to explore the expression and function of CST2 in gastric cancer.

METHODS

CST2 expression was analyzed and validated through Western blot. CST2 overexpression was induced by lentivirus in GC cells, and the correlation between CST2 expression levels and downstream signaling pathways was assessed. In addition, multiple assays, including cell proliferation, colony formation, wound-healing, and transwell migration/invasion, were considered to ascertain the influence of CST2 overexpression on gastric cancer. The cell cycle and apoptosis were detected by flow cytometry.

RESULTS

CST2 expression at the protein level was decreased to be reduced in both gastric cancer tissues and cell lines, and CST2 expression attenuate gastric cancer growth, an effect restricted to gastric cancer cells and absent in gastric epithelial GES-1 cells. Furthermore, CST2 was demonstrated to improve chemosensitivity to Oxaliplatin in gastric cancer cells through the PI3K/AKT signaling pathway.

CONCLUSION

These findings indicate that CST2 is downregulated at the protein level in gastric cancer tissues and cell lines. Additionally, CST2 was found to attenuate the growth of gastric cancer cells and to enhance sensitivity to Oxaliplatin through the PI3K/AKT signaling pathway, specific to gastric cancer cell lines. CST2 may serve as a tumor suppressor gene increasing sensitivity to Oxaliplatin in gastric cancer.

Bioinformatic analysis of cancer-associated fibroblast related gene signature as a predictive model in clinical outcomes and immune characteristics of gastric cancer

Background

Gastric cancer (GC) has a high incidence and high mortality rate among Asian countries, and distinguishing predictive prognosis biomarkers for GC are essential. Cancer-associated fibroblasts (CAFs) play a significant role in the progression, immune evasion, and therapeutic resistance of GC. Therefore, CAF-associated genes might have huge potential as prognostic biomarkers for predicting tumor progression and survival rate in GC pateints.

Methods

A sum of 1,134 GC patients from the The Cancer Genome Atlas Stomach Adenocarcinoma (TCGA-STAD), GSE62254, and GSE84437 datasets as well as GC cohorts from Xijing hospital were included. Firstly, we performed univariate Cox regression analysis to identify CAF-associated prognostic genes. Subsequently, the Least Absolute Shrinkage and Selection Operator (LASSO) regression analysis was used to develop a CAF gene signature (CAFGS) in the TCGA-STAD training cohort. CAFGS’s predictive performance was examined in both the training and validation cohorts, and the relationship between CAFGS and the tumor microenvironment (TME) was investigated by ssGSEA, CIBERSORT, TIMER, and ESTIMATE. Finally, a nomogram of CAFGS was established.

Results

Ten CAF-associated genes (ANGPTL4, CPNE8, CST2, HTR1F, IL1RAP, NR1D1, NTAN1, OLFML2B, TMEM259, and VTN) were identified to develop CAFGS. A high CAFGS score represented a worse outcome for GC patients in four cohorts, and a strong correlation was found between CAFGS and the infiltration of immune cells. We showed that CAFs contribute to immune evasion and unfavorable prognoses of GC patients by promoting the formation of an immunosuppressive microenvironment, and a high level of CAF infiltration may attenuate the efficacy of immunotherapy. The nomogram based on CAFGS showed reasonable predictive ability and may deliver great clinical net benefits.

Conclusions

We established a CAFGS model with 10 CAF-associated genes that had a great predictive value for GC prognosis and survival rate evaluation. This study could provide a novel insight for investigating the role of CAFs in GC.

Identification of ZNF704 as a Novel Oncogene and an Independent Prognostic Marker in Chondrosarcoma

Purpose

The transcription factor zinc finger protein 704 (ZNF704) is implicated in tumorigenesis. However, the underlying role of ZNF704 in the pathogenesis of chondrosarcoma remains not well delineated. This study investigates the expression level, prognostic significance and potential biological function of ZNF704 in human chondrosarcoma.

Materials and Methods

The mRNA and protein levels of ZNF704 in fresh chondrosarcomas and the paired adjacent non-tumor tissues were evaluated using real-time PCR and immunoblotting, respectively. The protein expression of ZNF704 in chondrosarcoma specimens was detected by immunohistochemistry, and the associations among its expression level, clinicopathological characteristics and prognosis were further investigated. Cell viability, colony formation and apoptosis assay were determined in chondrosarcoma cells and a xenograft model with ZNF704 knockdown.

Results

The expression levels of ZNF704 mRNA and protein in chondrosarcoma tissues were significantly higher than those in the paired adjacent non-tumor tissues and benign cartilage tumors. Clinicopathological analysis revealed that ZNF704 was expressed at higher levels in chondrosarcoma patients with higher histological grade and advanced MSTS stage. We also found that high expression of ZNF704 significantly correlated with a worse overall survival of chondrosarcoma patients. Multivariate Cox regression analysis indicated that ZNF704 was an independent prognostic marker in chondrosarcoma patients. Our in vitro studies demonstrated that knockdown of ZNF704 markedly inhibited chondrosarcoma cell viability, colony formation and induced apoptosis. In a nude mouse xenograft model, ZNF704 knockdown slowed down chondrosarcoma growth by inducing apoptosis in vivo.

Conclusion

These findings suggest that ZNF704 may act as a potent oncogene implicated in chondrosarcoma development, and serve as a independent prognostic marker, highlight the potential of ZNF704 as a novel biomarker and therapeutic target for chondrosarcoma.

Selective Nonmethylated CpG DNA Recognition Mechanism of Cysteine Clamp Domains

Methylation of DNA at CpG sites is a major mark for epigenetic regulation, but how transcription factors are influenced by CpG methylation is not well understood. Here, we report the molecular mechanisms of how the TCF (T-cell factor) and GEF (glucose transporter 4 enhancer factor) families of proteins selectively target unmethylated DNA sequences with a C-clamp type zinc finger domain. The structure of the C-clamp domain from human GEF family protein HDBP1 (C-clamp^HDBP1) in complex with DNA was determined using NMR spectroscopy, which adopts a unique zinc finger fold and selectively binds RCCGG (R = A/G) DNA sequences with an "Arg···Trp-Lys-Lys" DNA recognition motif inserted in the major groove. The CpG base pairs are central to the binding due to multiple hydrogen bonds formed with the backbone carbonyl groups of Trp378 and Lys379, as well as the side chain ε-amino groups of Lys379 and Lys380 from C-clamp^HDBP1. Consequently, methylation of the CpG dinucleotide almost abolishes the binding. Homology modeling reveals that the C-clamp domain from human TCF1E (C-clamp^TCF1E) binds DNA through essentially the same mechanism, with a similar "Arg···Arg-Lys-Lys" DNA recognition motif. The substitution of tryptophan by arginine makes C-clamp^HDBP1 prefer RCCGC DNA sequences. The two signature DNA recognition motifs are invariant in the GEF and TCF families of proteins, respectively, from fly to human. The recognition of the CpG dinucleotide through two consecutive backbone carbonyl groups is the same as that of the CXXC type unmethylated CpG DNA binding domains, suggesting a common mechanism shared by unmethylated CpG binding proteins.

Proteomic Analyses of Fibroblast- and Serum-Derived Exosomes Identify QSOX1 as a Marker for Non-invasive Detection of Colorectal Cancer

Simple Summary

Early diagnosis of colorectal cancer (CRC) is crucial to improve patient outcomes. The tumour microenvironment immediately adapts to malignant transformations, including the activation of fibroblasts in the connective tissue nearby. In this study, we investigated fibroblast activity-related protein secretion via extracellular vesicles (EVs). QSOX1, a protein identified to be significantly reduced in activated fibroblasts and derived EVs, was also found to be significantly reduced in circulating blood plasma EVs of CRC patients as compared to control patients. Hence, blood plasma EV-associated QSOX1 represents a promising platform for diagnostic CRC screening.

Abstract

The treatment of colorectal cancer (CRC) has improved during the last decades, but methods for crucial early diagnosis are yet to be developed. The influence of the tumour microenvironment on liquid biopsies for early cancer diagnostics are gaining growing interest, especially with emphasis on exosomes (EXO), a subgroup of extracellular vesicles (EVs). In this study, we established paired cancer-associated (CAFs) and normal fibroblasts (NF) from 13 CRC patients and investigated activation status-related protein abundance in derived EXOs. Immunohistochemical staining of matched patient tissue was performed and an independent test cohort of CRC patient plasma-derived EXOs was assessed by ELISA. A total of 11 differentially abundant EV proteins were identified between NFs and CAFs. In plasma EXOs, the CAF-EXO enriched protein EDIL3 was elevated, while the NF-EXO enriched protein QSOX1 was diminished compared to whole plasma. Both markers were significantly reduced in patient-matched CRC tissue compared to healthy colon tissue. In an independent test cohort, a significantly reduced protein abundance of QSOX1 was observed in plasma EXOs from CRC patients compared to controls and diagnostic ROC curve analysis revealed an AUC of 0.904. In conclusion, EXO-associated QSOX1 is a promising novel marker for early diagnosis and non-invasive risk stratification in CRC.

Proteomic Analyses of Fibroblast- and Serum-Derived Exosomes Identify QSOX1 as a Marker for Non-invasive Detection of Colorectal Cancer

The treatment of colorectal cancer (CRC) has improved during the last decades, but methods for crucial early diagnosis are yet to be developed. The influence of the tumour microenvironment on liquid biopsies for early cancer diagnostics are gaining growing interest, especially with emphasis on exosomes (EXO), a subgroup of extracellular vesicles (EVs). In this study, we established paired cancer-associated (CAFs) and normal fibroblasts (NF) from 13 CRC patients and investigated activation status-related protein abundance in derived EXOs. Immunohistochemical staining of matched patient tissue was performed and an independent test cohort of CRC patient plasma-derived EXOs was assessed by ELISA. A total of 11 differentially abundant EV proteins were identified between NFs and CAFs. In plasma EXOs, the CAF-EXO enriched protein EDIL3 was elevated, while the NF-EXO enriched protein QSOX1 was diminished compared to whole plasma. Both markers were significantly reduced in patient-matched CRC tissue compared to healthy colon tissue. In an independent test cohort, a significantly reduced protein abundance of QSOX1 was observed in plasma EXOs from CRC patients compared to controls and diagnostic ROC curve analysis revealed an AUC of 0.904. In conclusion, EXO-associated QSOX1 is a promising novel marker for early diagnosis and non-invasive risk stratification in CRC.

Does Cannabis Intake Protect Against Non-alcoholic Fatty Liver Disease? A Two-Sample Mendelian Randomization Study

BACKGROUND AND AIM

Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disease. Previous observational studies suggested that cannabis use may be associated with a lower risk for NAFLD but the causal relationship remains unclear. We aim in this study to examine the causal effect of cannabis consumption on the risk of NAFLD using a Mendelian randomization analysis. Clarifying this causal effect is important for cannabis-based drug discovery for NAFLD.

METHODS

We used data from the largest-to-date GWAS meta-analysis on lifetime use of cannabis (yes or no) consisting of three cohorts [International Cannabis Consortium (ICC), 23andMe, and the UK Biobank] of European ancestry (total N = 184,765). We also used other GWAS data on cannabis use dependence and cannabis use disorder (CUD). The NAFLD GWAS data were generated from the UK Biobank population (1,122 cases and 399,900 controls). The inverse variance weighted (IVW) method was used to assess the causal impact of cannabis lifetime use on the risk of NAFLD. We also performed a sensitivity analysis using weighted median estimator and MR-Egger.

RESULTS

There was no statistically significant causal effect between either the lifetime cannabis use, cannabis use dependence or CUD and the risk for NAFLD (p > 0.05 for all tests). No significant pleotropic effect was observed based on both MR-PRESSO global test (p = 0.99) and the modified Q' statistics. However, the study may be underpowered.

CONCLUSION

Our results demonstrated no evidence that cannabis consumption has a causal effect of protection against the development of NAFLD.

TROY signals through JAK1-STAT3 to promote glioblastoma cell migration and resistance

Glioblastoma (GBM) is the most common primary malignant brain tumor in adults and carries a discouraging prognosis. Its aggressive and highly infiltrative nature renders the current standard treatment of maximal surgical resection, radiation, and chemotherapy relatively ineffective. Identifying the signaling pathways that regulate GBM migration/invasion and resistance is required to develop more effective therapeutic regimens to treat GBM. Expression of TROY, an orphan receptor of the TNF receptor superfamily, increases with glial tumor grade, inversely correlates with patient overall survival, stimulates GBM cell invasion in vitro and in vivo, and increases resistance to temozolomide and radiation therapy. Conversely, silencing TROY expression inhibits GBM cell invasion, increases sensitivity to temozolomide, and prolongs survival in a preclinical intracranial xenograft model. Here, we have identified for the first time that TROY interacts with JAK1. Increased TROY expression increases JAK1 phosphorylation. In addition, increased TROY expression promotes STAT3 phosphorylation and STAT3 transcriptional activity that is dependent upon JAK1. TROY-mediated activation of STAT3 is independent of its ability to stimulate activity of NF-κB. Inhibition of JAK1 activity by ruxolitinib or knockdown of JAK1 expression by siRNA significantly inhibits TROY-induced STAT3 activation, GBM cell migration, and decreases resistance to temozolomide. Taken together, our data indicate that the TROY signaling complex may represent a potential therapeutic target with the distinctive capacity to exert effects on multiple pathways mediating GBM cell invasion and resistance.

Copy number alterations are associated with metastatic-lethal progression in prostate cancer

BACKGROUNDS

Aside from Gleason score few factors accurately identify the subset of prostate cancer (PCa) patients at high risk for metastatic progression. We hypothesized that copy number alterations (CNAs), assessed using CpG methylation probes on Illumina Infinium® Human Methylation450 (HM450K) BeadChip arrays, could identify primary prostate tumors with potential to develop metastatic progression.

METHODS

Epigenome-wide DNA methylation profiling was performed in surgically resected primary tumor tissues from two cohorts of PCa patients with clinically localized disease who underwent radical prostatectomy (RP) as primary therapy and were followed prospectively for at least 5 years: (1) a Fred Hutchinson (FH) Cancer Research Center-based cohort (n = 323 patients); and (2) an Eastern Virginia (EV) Medical School-based cohort (n = 78 patients). CNAs were identified using the R package ChAMP. Metastasis was confirmed by positive bone scan, MRI, CT or biopsy, and death certificates confirmed cause of death.

RESULTS

We detected 15 recurrent CNAs were associated with metastasis in the FH cohort and replicated in the EV cohort (p < 0.05) without adjusting for Gleason score in the model. Eleven of the recurrent CNAs were associated with metastatic progression in the FH cohort and validated in the EV cohort (p < 0.05) when adjusting for Gleason score.

CONCLUSIONS

This study shows that CNAs can be reliably detected from HM450K-based DNA methylation data. There are 11 recurrent CNAs showing association with metastatic-lethal events following RP and improving prediction over Gleason score. Genes affected by these CNAs may functionally relate to tumor aggressiveness and metastatic progression.