Networks In Tumorigenesis Research Articles

Endogenous Enzyme‐Operated Spherical Nucleic Acids for Cell‐Selective Protein Capture and Localization Regulation

AbstractPrecise regulation of protein activity and localization in cancer cells is crucial to dissect the function of the protein‐involved cellular network in tumorigenesis, but there is a lack of suitable methodology. Here we report the design of enzyme‐operated spherical nucleic acids (E‐SNAs) for manipulation of the nucleocytoplasmic translocation of proteins with cancer‐cell selectivity. The E‐SNAs are constructed by programmable engineering of aptamer‐based modules bearing enzyme‐responsive units in predesigned sites and further combination with SNA nanotechnology. We demonstrate that E‐SNAs are able to regulate cytoplasmic‐to‐nuclear shuttling of RelA protein efficiently and specifically in tumor cells, while they remain inactive in normal cells due to insufficient enzyme expression. We further confirmed the generality of this strategy by investigating the enzyme‐modulated inhibition/activation of thrombin activity by varying the aptamer‐based design.

Endogenous Enzyme-Operated Spherical Nucleic Acids for Cell-Selective Protein Capture and Localization Regulation.

Precise regulation of protein activity and localization in cancer cells is crucial to dissect the function of the protein-involved cellular network in tumorigenesis, but there is a lack of suitable methodology. Here we report the design of enzyme-operated spherical nucleic acids (E-SNAs) for manipulation of the nucleocytoplasmic translocation of proteins with cancer-cell selectivity. The E-SNAs are constructed by programmable engineering of aptamer-based modules bearing enzyme-responsive units in predesigned sites and further combination with SNA nanotechnology. We demonstrate that E-SNAs are able to regulate cytoplasmic-to-nuclear shuttling of RelA protein efficiently and specifically in tumor cells, while they remain inactive in normal cells due to insufficient enzyme expression. We further confirmed the generality of this strategy by investigating the enzyme-modulated inhibition/activation of thrombin activity by varying the aptamer-based design.

Construction of novel lncRNA-miRNA-mRNA ceRNA networks associated with prognosis of hepatitis C virus related hepatocellular carcinoma

BackgroundHepatitis C virus (HCV) infection contribute to liver fibrosis and cirrhosis, which significantly increases the risk of hepatocellular carcinoma (HCC) development. Previous studies have demonstrated the pivotal role of competitive endogenous RNA (ceRNA) networks in tumorigenesis and cancer progression. Consequently, we herein seek to identify and evaluate the prognostic relevance of a novel ceRNA network associated with HCV-related HCC. MethodsDifferentially expressed genes (DEGs) in GSE140846 dataset from GEO were identified using Network Analyst, and GO, KEGG and Reactome analyses were performed. Furthermore, a protein-protein interaction network was generated, and hub genes were detected. Hub gene expression levels, as well as those of their upstream lncRNAs and miRNAs and associated survival analyses were conducted using appropriate bioinformatics databases. Predicted target relationships were used to establish putative ceRNA networks for HCV-related HCC. ResultsA total of 372 and 360 up- and down-regulated DE-mRNA were identified, which were associated with nuclear division, cell cycle, and ATPase activity. A PPI network containing 704 DE-mRNAs was constructed, and the 6 hub gene with the highest degree of connectivity were selected for subsequent analysis. We discovered that 22 miRNAs and 4 lncRNAs upstream of 11 hub gene were significantly associated with poor prognosis of HCV-related HCC, and used them to constructe a prognostic ceRNA network. Further experiments confirmed the ceRNA-regulatory relationship of BUB1-hsa-miR-193a-3p-MALAT1. ConclusionThis study provides novel insights into the lncRNA-miRNA-mRNA ceRNA network, and reveals potential lncRNA biomarkers in HCV related HCC.

Meta-Analysis and Systematic Review of the Genomics of Mucosal Melanoma.

Mucosal melanoma is a rare subtype of melanoma. To date, there has been no comprehensive systematic collation and statistical analysis of the aberrations and aggregated frequency of driver events across multiple studies. Published studies using whole genome, whole exome, targeted gene panel, or individual gene sequencing were identified. Datasets from these studies were collated to summarize mutations, structural variants, and regions of copy-number alteration. Studies using next-generation sequencing were divided into the "main" cohort (n = 173; fresh-frozen samples), "validation" cohort (n = 48; formalin-fixed, paraffin-embedded samples) and a second "validation" cohort comprised 104 tumors sequenced using a targeted panel. Studies assessing mutations in BRAF, KIT, and NRAS were summarized to assess hotspot mutations. Statistical analysis of the main cohort variant data revealed KIT, NF1, BRAF, NRAS, SF3B1, and SPRED1 as significantly mutated genes. ATRX and SF3B1 mutations occurred more commonly in lower anatomy melanomas and CTNNB1 in the upper anatomy. NF1, PTEN, CDKN2A, SPRED1, ATM, CHEK2, and ARID1B were commonly affected by chromosomal copy loss, while TERT, KIT, BRAF, YAP1, CDK4, CCND1, GAB2, MDM2, SKP2, and MITF were commonly amplified. Further notable genomic alterations occurring at lower frequencies indicated commonality of signaling networks in tumorigenesis, including MAPK, PI3K, Notch, Wnt/β-catenin, cell cycle, DNA repair, and telomere maintenance pathways. This analysis identified genomic aberrations that provide some insight to the way in which specific pathways may be disrupted. IMPLICATIONS: Our analysis has shown that mucosal melanomas have a diverse range of genomic alterations in several biological pathways. VISUAL OVERVIEW: http://mcr.aacrjournals.org/content/molcanres/19/6/991/F1.large.jpg.

Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma

SummaryTo define the cellular composition and architecture of cutaneous squamous cell carcinoma (cSCC), we combined single-cell RNA sequencing with spatial transcriptomics and multiplexed ion beam imaging from a series of human cSCCs and matched normal skin. cSCC exhibited four tumor subpopulations, three recapitulating normal epidermal states, and a tumor-specific keratinocyte (TSK) population unique to cancer, which localized to a fibrovascular niche. Integration of single-cell and spatial data mapped ligand-receptor networks to specific cell types, revealing TSK cells as a hub for intercellular communication. Multiple features of potential immunosuppression were observed, including T regulatory cell (Treg) co-localization with CD8 T cells in compartmentalized tumor stroma. Finally, single-cell characterization of human tumor xenografts and in vivo CRISPR screens identified essential roles for specific tumor subpopulation-enriched gene networks in tumorigenesis. These data define cSCC tumor and stromal cell subpopulations, the spatial niches where they interact, and the communicating gene networks that they engage in cancer.

LncRNA LINC00857 regulates lung adenocarcinoma progression, apoptosis and glycolysis by targeting miR-1179/SPAG5 axis.

Long non-coding RNA (lncRNA), a member of non-coding RNA family with over 200 nucleotides in length, typically serves as an oncogene or tumor suppressor in tumor progression, such as cancer cell proliferation, apoptosis and glycolysis. Recent studies manifested lncRNA LINC00857 was involved in cell cycle regulation of lung cancer. Due to complicated networks in tumorigenesis, the potential roles of LINC00857 underlying lung cancer progression still need further investigation. In this study, we explored the expression of LINC00857 in lung adenocarcinoma (LUAD) tissues and LUAD cell lines and found a dramatical upregulation of LINC00857 compared with the adjacent normal lung tissues and BEAS-2B cell line, respectively. Then, LINC00857 knockdown led to the cell proliferation and glycolysis was repressed, while the apoptosis was elevated in LUAD cell lines. Furthermore, we identified a direct interaction between LINC00857 and miR-1179 in LUAD cells using bioinformatic method and report assay. Finally, we evidenced LINC00857 promoted cell growth and glycolysis and repressed apoptosis via sponging miR-1179 and further regulating sperm-associated antigen 5 (SPAG5) expression in LUAD cell lines. Hence, our results authenticated that lncRNA LINC00857 regulated the cell proliferation, glycolysis and apoptosis of LUAD cells mainly through targeting the miR-1179/SPAG5 axis, which might be a novel insight into lung cancer progression and provided a potential target for clinical treatment of LUAD patients.

Abstract 773: Analysis of oncogene affected networks in tumorigenesis of lung cancer

Abstract Genetic abnormality is one of major causes of tumorigenesis by driving the progressive transformation of normal human cells into highly malignant derivatives. Tracing the downstream pathways through which and how the effects of the oncogenic-activating mutations are transmitted is an important and challenging problem in studying disease mechanisms, diagnoses and treatments. In this study, we designed a network-based computational method, called MAXMAP, to not only predict mutation downstream affected pathways, but also quantitatively measure the dynamics of the pathway genes. We first constructed a heterogeneous network by integrating protein-protein interaction networks and signaling and regulatory networks from available up-to-date curated databases, as well as RNASeq expression data. The RNAseq dataset of these mutated cell lines has 18,096 genes whereas the Protein Protein Interaction and Signalling, regulation dataset has 14,864 genes. We then used the maximal information flow method to globally optimize the effects from the mutations to target downstream genes. The method was applied to analyze the biological network dynamics that is caused by single (TP53), double (TP53+KRAS) and triple (TP53+KRAS+STK11) mutations of HBEC30KT, an immortalized lung cell line, and revealed the core dynamical subnetworks of these mutations. Only the triple mutant is known to have tumor-like properties and as shown in earlier studies these sequential mutation accumulations lead to tumorigenesis in mouse xenograft models. The experimental validation of a small subnetwork was performed using transient knock down of the pathway genes and expression was verified using qPCR. We showed the dynamical subnetworks through which a gene, SLC7A5 was affected by sequential single, double or triple mutations. We have experimentally validated the predicted small subnetwork for SLC7A5 which is an important transporter of neutral amino acids. It is associated with bladder and bile duct adeno carcinomas and overexpressed in lung cancers. We selected the subnetwork affected due to the single mutation (TP53) for validation, including THBS1, TNFRSF11B and MAPK1 and SLC7A5. Hence, using the MAXMAP method we have successfully identified a dynamical subnetwork affected by changes in the known network of genes. These results suggest that this computational method may allow us to predict drug targets or biomarkers or to study interesting alternative paths and predict the most likely path leading to certain phenotypic outcomes. Citation Format: Adwait Sathe, Yong Chen, Hyuntae Yoo, Michael Q. Zhang. Analysis of oncogene affected networks in tumorigenesis of lung cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 773.

LncRNA UCA1-miR-507-FOXM1 axis is involved in cell proliferation, invasion and G0/G1 cell cycle arrest in melanoma.

Recently, the incidence of melanoma has been on the rise. Patients with distant metastasis share poor prognosis. Increasing studies have been conducted to clarify the molecular mechanisms as well as to investigate potential effective therapeutic targets in the development of melanoma. This study focuses on the LncRNA UCA1 and its downstream regulated factors. In our experiments, UCA1 expression was discovered to be upregulated in melanoma tissues and cells, while the depletion of UCA1 led to the inhibition of cell proliferation, invasion and cell cycle arrest. To further our understanding of the mechanisms of UCA1, a system of experiments was built. We found that miR-507 could directly bind to UCA1 at the miRNA recognition site, and that there was a negative correlation between miR-507 and UCA1. Additionally, FOXM1 is a target of miR-507 and can be downregulated by either miR-507 overexpression or UCA1 depletion. Downregulated FOXM1 was analogous to the depletion of UCA1 and the overexpression of miR-507. These results, taken together, provide evidence for a novel UCA1 interaction regulatory network in tumorigenesis of melanoma.

Delphinidin Inhibits Tumor Growth by Acting on VEGF Signalling in Endothelial Cells.

The vasculoprotective properties of delphinidin are driven mainly by its action on endothelial cells. Moreover, delphinidin displays anti-angiogenic properties in both in vitro and in vivo angiogenesis models and thereby might prevent the development of tumors associated with excessive vascularization. This study was aimed to test the effect of delphinidin on melanoma-induced tumor growth with emphasis on its molecular mechanism on endothelial cells. Delphinidin treatment significantly decreased in vivo tumor growth induced by B16-F10 melanoma cell xenograft in mice. In vitro, delphinidin was not able to inhibit VEGFR2-mediated B16-F10 melanoma cell proliferation but it specifically reduced basal and VEGFR2-mediated endothelial cell proliferation. The anti-proliferative effect of delphinidin was reversed either by the MEK1/2 MAP kinase inhibitor, U-0126, or the PI3K inhibitor, LY-294002. VEGF-induced proliferation was reduced either by U-0126 or LY-294002. Under these conditions, delphinidin failed to decrease further endothelial cell proliferation. Delphinidin prevented VEGF-induced phosphorylation of ERK1/2 and p38 MAPK and decreased the expression of the transcription factors, CREB and ATF1. Finally, delphinidin was more potent in inhibiting in vitro cyclic nucleotide phosphodiesterases (PDEs), PDE1 and PDE2, compared to PDE3-PDE5. Altogether delphinidin reduced tumor growth of melanoma cell in vivo by acting specifically on endothelial cell proliferation. The mechanism implies an association between inhibition of VEGF-induced proliferation via VEGFR2 signalling, MAPK, PI3K and at transcription level on CREB/ATF1 factors, and the inhibition of PDE2. In conjunction with our previous studies, we demonstrate that delphinidin is a promising compound to prevent pathologies associated with generation of vascular network in tumorigenesis.

Rewiring drug-activated p53-regulatory network from suppressing to promoting tumorigenesis

Many of oncogenes and tumor suppressor genes have been found to exert variable and even opposing roles in different kinds of tumors or at different stages of cancer development. Here we showed that tumorigenic potential of mouse embryonic carcinoma P19 cells cultured in adherent plates (attached-P19-cells) was suppressed by a chemotherapeutic agent, 5-aza-2'-deoxycytidine (ZdCyd), whereas the higher pro-tumorigenicity of P19 cells growing in suspension (detached-P19-cells) was generated by the ZdCyd treatment. Surprisingly, p53 activity was highly up-regulated by ZdCyd in both growing conditions. By our developed computational approaches, we revealed that there was a significant enrichment of apoptotic pathways in the ZdCyd-induced p53-dominant gene-regulatory network in attached P19 cells, whereas the pro-survival genes were significantly enriched in the ZdCyd-induced p53 network in detached P19 cells. The protein-protein interaction network of the ZdCyd-treated detached P19 cells was significantly different from that of ZdCyd-treated attached P19 cells. On the other hand, inhibition of p53 expression by siRNA suppressed the ZdCyd-induced tumorigenesis of detached P19 cells, suggesting that the ZdCyd-activated p53 plays oncogenic function in detached P19 cells. Taken together, these results indicate a context-dependent role for the ZdCyd-activated p53-dominant network in tumorigenesis.

Paradoxical effects of ethoxidine, a topoisomerase I inhibitor, in the cellular processes leading to angiogenesis on endothelial cells

Angiogenesis, a critical step in tumorigenesis, is defined by different processes leading to neovascularization. Topoisomerase I (Top I) is the target for some of the most successful anticancer drugs that decrease tumor cell proliferation. Ethoxidine, a benzo[c]phenanthridines derivative, camptothecin analogue, has been identified as a potent inhibitor of Top I in various cancer cell lines. This study was aimed to investigate the impact of ethoxidine on angiogenesis and cellular processes including migration, proliferation and adhesion since these processes play an important role in tumor progression. Ethoxidine was incubated for 24 h at low (10⁻⁹ M) and high (10⁻⁵ M) concentrations on two types of human endothelial cells: EaHy.926 and human umbilical endothelial cells. Vascular endothelial growth factor (VEGF, 20 ng/ml) was used as a positive control. Ethoxidine at low concentration increased cell proliferation and migration that was associated with enhanced metalloproteinase 2 expression and activity, whereas high concentration of ethoxidine inhibited all of these effects. The two concentrations of ethoxidine did not affect endothelial cell adhesion. Low concentration of ethoxidine increased VEGF expression and endothelial nitric oxide (NO) synthase expression, NO and superoxide anion productions, whereas high concentration of ethoxidine did not induce any effect. Taken together, the present results highlight paradoxical effects of ethoxidine on angiogenesis depending on the concentration used. This study underscores that in addition to its anti-proliferative properties, ethoxidine may affect the generation of vascular network in tumorigenesis.

Genome-Wide Promoter Analysis Uncovers Portions of the Cancer Methylome

DNA methylation has a role in mediating epigenetic silencing of CpG island genes in cancer and other diseases. Identification of all gene promoters methylated in cancer cells "the cancer methylome" would greatly advance our understanding of gene regulatory networks in tumorigenesis. We previously described a new method of identifying methylated tumor suppressor genes based on pharmacologic unmasking of the promoter region and detection of re-expression on microarray analysis. In this study, we modified and greatly improved the selection of candidates based on new promoter structure algorithm and microarray data generated from 20 cancer cell lines of 5 major cancer types. We identified a set of 200 candidate genes that cluster throughout the genome of which 25 were previously reported as harboring cancer-specific promoter methylation. The remaining 175 genes were tested for promoter methylation by bisulfite sequencing or methylation-specific PCR (MSP). Eighty-two of 175 (47%) genes were found to be methylated in cell lines, and 53 of these 82 genes (65%) were methylated in primary tumor tissues. From these 53 genes, cancer-specific methylation was identified in 28 genes (28 of 53; 53%). Furthermore, we tested 8 of the 28 newly identified cancer-specific methylated genes with quantitative MSP in a panel of 300 primary tumors representing 13 types of cancer. We found cancer-specific methylation of at least one gene with high frequency in all cancer types. Identification of a large number of genes with cancer-specific methylation provides new targets for diagnostic and therapeutic intervention, and opens fertile avenues for basic research in tumor biology.