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1.
Int J Mol Sci ; 24(23)2023 Dec 03.
Article in English | MEDLINE | ID: mdl-38069407

ABSTRACT

Neuroblastoma (NB), a childhood cancer arising from the neural crest, poses significant clinical challenges, particularly in cases featuring amplification of the MYCN oncogene. Epigenetic factors play a pivotal role in normal neural crest and NB development, influencing gene expression patterns critical for tumorigenesis. This review delves into the multifaceted interplay between MYCN and known epigenetic modifications during NB genesis, shedding light on the intricate regulatory networks underlying the disease. We provide an extensive survey of known epigenetic mechanisms, encompassing DNA methylation, histone modifications, non-coding RNAs, super-enhancers (SEs), bromodomains (BET), and chromatin modifiers in MYCN-amplified (MNA) NB. These epigenetic changes collectively contribute to the dysregulated gene expression landscape observed in MNA NB. Furthermore, we review emerging therapeutic strategies targeting epigenetic regulators, including histone deacetylase inhibitors (HDACi), histone methyltransferase inhibitors (HMTi), and DNA methyltransferase inhibitors (DNMTi). We also discuss and summarize current drugs in preclinical and clinical trials, offering insights into their potential for improving outcomes for MNA NB patients.


Subject(s)
Epigenesis, Genetic , Neuroblastoma , Humans , DNA Methylation , Gene Expression Regulation, Neoplastic , Genes, myc , N-Myc Proto-Oncogene Protein/genetics , Neuroblastoma/genetics
2.
Nature ; 609(7929): 975-985, 2022 09.
Article in English | MEDLINE | ID: mdl-36104561

ABSTRACT

Understanding cell state transitions and purposefully controlling them is a longstanding challenge in biology. Here we present cell state transition assessment and regulation (cSTAR), an approach for mapping cell states, modelling transitions between them and predicting targeted interventions to convert cell fate decisions. cSTAR uses omics data as input, classifies cell states, and develops a workflow that transforms the input data into mechanistic models that identify a core signalling network, which controls cell fate transitions by influencing whole-cell networks. By integrating signalling and phenotypic data, cSTAR models how cells manoeuvre in Waddington's landscape1 and make decisions about which cell fate to adopt. Notably, cSTAR devises interventions to control the movement of cells in Waddington's landscape. Testing cSTAR in a cellular model of differentiation and proliferation shows a high correlation between quantitative predictions and experimental data. Applying cSTAR to different types of perturbation and omics datasets, including single-cell data, demonstrates its flexibility and scalability and provides new biological insights. The ability of cSTAR to identify targeted perturbations that interconvert cell fates will enable designer approaches for manipulating cellular development pathways and mechanistically underpinned therapeutic interventions.


Subject(s)
Cell Differentiation , Models, Biological , Signal Transduction , Cell Proliferation , Datasets as Topic , Phenotype , Single-Cell Analysis , Workflow
3.
Sci Rep ; 12(1): 10851, 2022 06 27.
Article in English | MEDLINE | ID: mdl-35761023

ABSTRACT

Extracellular vesicles (EVs) are nanoparticles found in all biological fluids, capable of transporting biological material around the body. Extensive research into the physiological role of EVs has led to the development of the Minimal Information for Studies of Extracellular Vesicles (MISEV) framework in 2018. This framework guides the standardisation of protocols in the EV field. To date, the focus has been on EVs of human origin. As comparative medicine progresses, there has been a drive to study similarities between diseases in humans and animals. To successfully research EVs in felines, we must validate the application of the MISEV guidelines in this group. EVs were isolated from the plasma of healthy humans and felines. EV characterisation was carried out according to the MISEV guidelines. Human and feline plasma showed a similar concentration of EVs, comparable expression of known EV markers and analogous particle to protein ratios. Mass spectrometry analyses showed that the proteomic signature of EVs from humans and felines were similar. Asymmetrical flow field flow fractionation, showed two distinct subpopulations of EVs isolated from human plasma, whereas only one subpopulation was isolated from feline plasma. Metabolomic profiling showed similar profiles for humans and felines. In conclusion, isolation, and characterisation of EVs from humans and felines show that MISEV2018 guidelines may also be applied to felines. Potential comparative medicine studies of EVs may provide a model for studying naturally occurring diseases in both humans and felines.


Subject(s)
Extracellular Vesicles , Fractionation, Field Flow , Animals , Biological Transport , Cats , Humans , Plasma , Proteomics
4.
Bioengineering (Basel) ; 10(1)2022 Dec 21.
Article in English | MEDLINE | ID: mdl-36671585

ABSTRACT

Melanin, a light and free radical absorbing pigment, is produced in melanocyte cells that are found in skin, but also in hair follicles, eyes, the inner ear, heart, brain and other organs. Melanin synthesis is the result of a complex network of signaling and metabolic reactions. It therefore comes as no surprise that mutations in many of the genes involved are associated with various types of pigmentation diseases and phenotypes ('pigmentation genes'). Here, we used bioinformatics tools to first reconstruct gene-disease/phenotype associations for all pigmentation genes. Next, we reconstructed protein-protein interaction (PPI) networks centered around pigmentation gene products ('pigmentation proteins') and supplemented the PPI networks with protein expression information obtained by mass spectrometry in a panel of melanoma cell lines (both pigment producing and non-pigment producing cells). The analysis provides a systems network representation of all genes/ proteins centered around pigmentation and melanin biosynthesis pathways ('pigmentation network map'). Our work will enable the pigmentation research community to experimentally test new hypothesis arising from the pigmentation network map and to identify new targets for drug discovery.

5.
Front Cell Dev Biol ; 9: 612518, 2021.
Article in English | MEDLINE | ID: mdl-33968920

ABSTRACT

Although a rare disease, neuroblastoma accounts for the highest proportion of childhood cancer deaths. There is a lack of recurrent somatic mutations in neuroblastoma embryonal tumours, suggesting a possible role for epigenetic alterations in driving this cancer. While an increasing number of reports suggest an association of MYCN with epigenetic machinery, the mechanisms of these interactions are poorly understood in the neuroblastoma setting. Utilising chemo-genomic approaches we revealed global MYCN-epigenetic interactions and identified numerous epigenetic proteins as MYCN targets. The epigenetic regulators HDAC2, CBX8 and CBP (CREBBP) were all MYCN target genes and also putative MYCN interactors. MYCN-related epigenetic genes included SMARCs, HDACs, SMYDs, BRDs and CREBBP. Expression levels of the majority of MYCN-related epigenetic genes showed predictive ability for neuroblastoma patient outcome. Furthermore, a compound library screen targeting epigenetic proteins revealed broad susceptibility of neuroblastoma cells to all classes of epigenetic regulators, belonging to families of bromodomains, HDACs, HATs, histone methyltransferases, DNA methyltransferases and lysin demethylases. Ninety-six percent of the compounds reduced MYCN-amplified neuroblastoma cell viability. We show that the C646 (CBP-bromodomain targeting compound) exhibits switch-like temporal and dose response behaviour and is effective at reducing neuroblastoma viability. Responsiveness correlates with MYCN expression, with MYCN-amplified cells being more susceptible to C646 treatment. Thus, exploiting the broad vulnerability of neuroblastoma cells to epigenetic targeting compounds represents an exciting strategy in neuroblastoma treatment, particularly for high-risk MYCN-amplified tumours.

6.
NPJ Syst Biol Appl ; 7(1): 10, 2021 02 12.
Article in English | MEDLINE | ID: mdl-33580066

ABSTRACT

Ras is a plasma membrane (PM)-associated signaling hub protein that interacts with its partners (effectors) in a mutually exclusive fashion. We have shown earlier that competition for binding and hence the occurrence of specific binding events at a hub protein can modulate the activation of downstream pathways. Here, using a mechanistic modeling approach that incorporates high-quality proteomic data of Ras and 56 effectors in 29 (healthy) human tissues, we quantified the amount of individual Ras-effector complexes, and characterized the (stationary) Ras "wiring landscape" specific to each tissue. We identified nine effectors that are in significant amount in complex with Ras in at least one of the 29 tissues. We simulated both mutant- and stimulus-induced network re-configurations, and assessed their divergence from the reference scenario, specifically discussing a case study for two stimuli in three epithelial tissues. These analyses pointed to 32 effectors that are in significant amount in complex with Ras only if they are additionally recruited to the PM, e.g. via membrane-binding domains or domains binding to activated receptors at the PM. Altogether, our data emphasize the importance of tissue context for binding events at the Ras signaling hub.


Subject(s)
Computational Biology/methods , Proto-Oncogene Proteins c-raf/metabolism , ras Proteins/metabolism , Guanosine Triphosphate/metabolism , Humans , Membrane Proteins/metabolism , Models, Theoretical , Phosphatidylinositol 3-Kinases/metabolism , Protein Binding/physiology , Proteomics/methods , Signal Transduction/physiology , ras Proteins/genetics , ras Proteins/physiology
7.
Mol Omics ; 17(1): 72-85, 2021 02 01.
Article in English | MEDLINE | ID: mdl-33325943

ABSTRACT

Triple negative breast cancer (TNBC) has poor clinical outcomes and limited treatment options. Chemotherapy, while killing some cancer cells, can result in therapeutic-induced-senescent (TIS) cells. Senescent cells release significantly more extracellular vesicles (EVs) than non-senescent cells. Recently, N- and O-linked glycosylation alterations have been associated with senescence. We aimed to profile the N-linked glycans of whole cells, membrane, cytoplasm and EVs harvested from TIS TNBC cells and to compare these to results from non-senescent cells. TIS was induced in the Cal51 TNBC cells using the chemotherapeutic agent paclitaxel (PTX). Ultra-performance liquid chromatography (UPLC) analysis of exoglycosidase digested N-linked glycans was carried out on TIS compared to non-treated control cells. LC-Mass spectrometry (MS) analysis of the N-linked glycans and lectin blotting of samples was carried out to confirm the UPLC results. Significant differences were found in the N-glycan profile of the Cal51 membrane, cytoplasm and EV progeny of TIS compared to non-senescent cells. Protein mass spectrometry showed that the TIS cells contain different glycan modifying enzymes. The lectin, calnexin demonstrated a lower kDa size (∼58 kDa) in TIS compared to control cells (∼90 kDa) while Galectin 3 demonstrated potential proteolytic cleavage with 32 kDa and ∼22 kDa bands evident in TIS compared to non-senescent control cells with a major 32 kDa band only. TIS CAL51 cells also demonstrated a reduced adhesion to collagen I compared to control non-senescent cells. This study has shown that therapeutic-induced-senescent TNBC cells and their EV progeny, display differential N-glycan moieties compared to non-senescent Cal51 cells and their resultant EV progeny. For the future, N-glycan moieties on cancer senescent cells and their EV progeny hold potential for (i) the monitoring of treatment response as a liquid biopsy, and (ii) cancer senescent cell targeting with lectin therapies.


Subject(s)
Cellular Senescence , Extracellular Vesicles/metabolism , Glycosylation , Polysaccharides/metabolism , Triple Negative Breast Neoplasms/metabolism , Antineoplastic Agents/pharmacology , Chromatography, High Pressure Liquid , Chromatography, Liquid , Drug Resistance, Neoplasm , Female , Glycosylation/drug effects , Humans , Mass Spectrometry , Paclitaxel/pharmacology , Triple Negative Breast Neoplasms/drug therapy , Triple Negative Breast Neoplasms/pathology
8.
Biology (Basel) ; 9(5)2020 May 01.
Article in English | MEDLINE | ID: mdl-32370057

ABSTRACT

Tumour necrosis factor-related apoptosis-inducing ligand (TRAIL), is a selective anticancer cytokine capable of exerting a targeted therapy approach. Disappointingly, recent research has highlighted the development of TRAIL resistance in cancer cells, thus minimising its usefulness in clinical settings. However, several recent studies have demonstrated that cancer cells can be sensitised to TRAIL through the employment of a combinatorial approach, utilizing TRAIL in conjunction with other natural or synthetic anticancer agents. In the present study, the chemo-sensitising effect of curcumin on TRAIL-induced apoptosis in renal carcinoma cells (RCC) was investigated. The results indicate that exposure of kidney cancer ACHN cells to curcumin sensitised the cells to TRAIL, with the combination treatment of TRAIL and curcumin synergistically targeting the cancer cells without affecting the normal renal proximal tubular epithelial cells (RPTEC/TERT1) cells. Furthermore, this combination treatment was shown to induce caspase-dependent apoptosis, inhibition of the proteasome, induction of ROS, upregulation of death receptor 4 (DR4), alterations in mitogen-activated protein kinase (MAPK) signalling and induction of endoplasmic reticulum stress. An in vivo zebrafish embryo study demonstrated the effectiveness of the combinatorial regime to inhibit tumour formation without affecting zebrafish embryo viability or development. Overall, the results arising from this study demonstrate that curcumin has the ability to sensitise TRAIL-resistant ACHN cells to TRAIL-induced apoptosis.

9.
Sci Rep ; 7(1): 3091, 2017 06 08.
Article in English | MEDLINE | ID: mdl-28596528

ABSTRACT

Adverse side effects of cancer agents are of great concern in the context of childhood tumors where they can reduce the quality of life in young patients and cause life-long adverse effects. Synergistic drug combinations can lessen potential toxic side effects through lower dosing and simultaneously help to overcome drug resistance. Neuroblastoma is the most common cancer in infancy and extremely heterogeneous in clinical presentation and features. Applying a systematic pairwise drug combination screen we observed a highly potent synergy in neuroblastoma cells between the EGFR kinase inhibitor lapatinib and the anticancer compound YM155 that is preserved across several neuroblastoma variants. Mechanistically, the synergy was based on a lapatinib induced inhibition of the multidrug-resistance efflux transporter ABCB1, which is frequently expressed in resistant neuroblastoma cells, which allowed prolonged and elevated cytotoxicity of YM155. In addition, the drug combination (i.e. lapatinib plus YM155) decreased neuroblastoma tumor size in an in vivo model.


Subject(s)
ATP Binding Cassette Transporter, Subfamily B, Member 1/antagonists & inhibitors , Antineoplastic Agents/pharmacology , Imidazoles/pharmacology , Lapatinib/pharmacology , Naphthoquinones/pharmacology , Protein Kinase Inhibitors/pharmacology , Animals , Antineoplastic Agents/chemistry , Apoptosis/genetics , Cell Line, Tumor , Drug Synergism , Humans , Imidazoles/chemistry , Lapatinib/chemistry , N-Myc Proto-Oncogene Protein/metabolism , Naphthoquinones/chemistry , Neuroblastoma/genetics , Neuroblastoma/metabolism , Protein Kinase Inhibitors/chemistry , RNA Interference , Receptor, trkA/metabolism , Zebrafish
10.
Genome Med ; 9(1): 15, 2017 02 10.
Article in English | MEDLINE | ID: mdl-28187790

ABSTRACT

BACKGROUND: Retinoid therapy is widely employed in clinical oncology to differentiate malignant cells into their more benign counterparts. However, certain high-risk cohorts, such as patients with MYCN-amplified neuroblastoma, are innately resistant to retinoid therapy. Therefore, we employed a precision medicine approach to globally profile the retinoid signalling response and to determine how an excess of cellular MYCN antagonises these signalling events to prevent differentiation and confer resistance. METHODS: We applied RNA sequencing (RNA-seq) and interaction proteomics coupled with network-based systems level analysis to identify targetable vulnerabilities of MYCN-mediated retinoid resistance. We altered MYCN expression levels in a MYCN-inducible neuroblastoma cell line to facilitate or block retinoic acid (RA)-mediated neuronal differentiation. The relevance of differentially expressed genes and transcriptional regulators for neuroblastoma outcome were then confirmed using existing patient microarray datasets. RESULTS: We determined the signalling networks through which RA mediates neuroblastoma differentiation and the inhibitory perturbations to these networks upon MYCN overexpression. We revealed opposing regulation of RA and MYCN on a number of differentiation-relevant genes, including LMO4, CYP26A1, ASCL1, RET, FZD7 and DKK1. Furthermore, we revealed a broad network of transcriptional regulators involved in regulating retinoid responsiveness, such as Neurotrophin, PI3K, Wnt and MAPK, and epigenetic signalling. Of these regulators, we functionally confirmed that MYCN-driven inhibition of transforming growth factor beta (TGF-ß) signalling is a vulnerable node of the MYCN network and that multiple levels of cross-talk exist between MYCN and TGF-ß. Co-targeting of the retinoic acid and TGF-ß pathways, through RA and kartogenin (KGN; a TGF-ß signalling activating small molecule) combination treatment, induced the loss of viability of MYCN-amplified retinoid-resistant neuroblastoma cells. CONCLUSIONS: Our approach provides a powerful precision oncology tool for identifying the driving signalling networks for malignancies not primarily driven by somatic mutations, such as paediatric cancers. By applying global omics approaches to the signalling networks regulating neuroblastoma differentiation and stemness, we have determined the pathways involved in the MYCN-mediated retinoid resistance, with TGF-ß signalling being a key regulator. These findings revealed a number of combination treatments likely to improve clinical response to retinoid therapy, including co-treatment with retinoids and KGN, which may prove valuable in the treatment of high-risk MYCN-amplified neuroblastoma.


Subject(s)
Anilides/therapeutic use , N-Myc Proto-Oncogene Protein/drug effects , Neuroblastoma/drug therapy , Phthalic Acids/therapeutic use , Signal Transduction , Transforming Growth Factor beta/drug effects , Tretinoin/therapeutic use , Antineoplastic Agents/therapeutic use , Cell Line, Tumor , Drug Resistance, Neoplasm , Gene Expression Regulation, Neoplastic , Humans , Neuroblastoma/genetics , Neuroblastoma/metabolism , Precision Medicine , Retinoids/therapeutic use
11.
Sci Signal ; 9(455): ra114, 2016 11 22.
Article in English | MEDLINE | ID: mdl-27879396

ABSTRACT

Signal transduction networks are often rewired in cancer cells. Identifying these alterations will enable more effective cancer treatment. We developed a computational framework that can identify, reconstruct, and mechanistically model these rewired networks from noisy and incomplete perturbation response data and then predict potential targets for intervention. As a proof of principle, we analyzed a perturbation data set targeting epidermal growth factor receptor (EGFR) and insulin-like growth factor 1 receptor (IGF1R) pathways in a panel of colorectal cancer cells. Our computational approach predicted cell line-specific network rewiring. In particular, feedback inhibition of insulin receptor substrate 1 (IRS1) by the kinase p70S6K was predicted to confer resistance to EGFR inhibition, suggesting that disrupting this feedback may restore sensitivity to EGFR inhibitors in colorectal cancer cells. We experimentally validated this prediction with colorectal cancer cell lines in culture and in a zebrafish (Danio rerio) xenograft model.


Subject(s)
Colorectal Neoplasms/metabolism , Colorectal Neoplasms/therapy , Computer Simulation , Models, Biological , Animals , Cell Line, Tumor , Colorectal Neoplasms/pathology , ErbB Receptors/metabolism , Heterografts , Humans , Neoplasm Proteins/metabolism , Neoplasm Transplantation , Receptor, IGF Type 1 , Receptors, Somatomedin/metabolism , Ribosomal Protein S6 Kinases, 70-kDa/metabolism , Zebrafish
12.
Oncotarget ; 7(37): 60310-60331, 2016 Sep 13.
Article in English | MEDLINE | ID: mdl-27531891

ABSTRACT

Wnt signalling is involved in the formation, metastasis and relapse of a wide array of cancers. However, there is ongoing debate as to whether activation or inhibition of the pathway holds the most promise as a therapeutic treatment for cancer, with conflicting evidence from a variety of tumour types. We show that Wnt/ß-catenin signalling is a bi-directional vulnerability of neuroblastoma, malignant melanoma and colorectal cancer, with hyper-activation or repression of the pathway both representing a promising therapeutic strategy, even within the same cancer type. Hyper-activation directs cancer cells to undergo apoptosis, even in cells oncogenically driven by ß-catenin. Wnt inhibition blocks proliferation of cancer cells and promotes neuroblastoma differentiation. Wnt and retinoic acid co-treatments synergise, representing a promising combination treatment for MYCN-amplified neuroblastoma. Additionally, we report novel cross-talks between MYCN and ß-catenin signalling, which repress normal ß-catenin mediated transcriptional regulation. A ß-catenin target gene signature could predict patient outcome, as could the expression level of its DNA binding partners, the TCF/LEFs. This ß-catenin signature provides a tool to identify neuroblastoma patients likely to benefit from Wnt-directed therapy. Taken together, we show that Wnt/ß-catenin signalling is a bi-directional vulnerability of a number of cancer entities, and potentially a more broadly conserved feature of malignant cells.


Subject(s)
Gene Expression Regulation, Neoplastic , N-Myc Proto-Oncogene Protein/genetics , Neuroblastoma/genetics , Wnt Signaling Pathway/genetics , beta Catenin/genetics , Antineoplastic Agents/pharmacology , Bridged Bicyclo Compounds, Heterocyclic/pharmacology , Cell Differentiation/drug effects , Cell Differentiation/genetics , Cell Line, Tumor , Cell Proliferation/drug effects , Cell Proliferation/genetics , Gene Expression Profiling/methods , Humans , N-Myc Proto-Oncogene Protein/metabolism , Neuroblastoma/metabolism , Neuroblastoma/pathology , Proteomics/methods , Pyrimidinones/pharmacology , RNA Interference , Survival Analysis , Tretinoin/pharmacology , Wnt Proteins/antagonists & inhibitors , Wnt Proteins/genetics , Wnt Proteins/metabolism , beta Catenin/metabolism
13.
World J Gastroenterol ; 22(20): 4848-59, 2016 May 28.
Article in English | MEDLINE | ID: mdl-27239111

ABSTRACT

AIM: To investigate killer inhibitory and activating receptor expression by natural killer (NK), natural killer T-like (NKT-like) and CD8+ T lymphocytes in patients with chronic hepatitis C virus (HCV) infection with elevated and with persistently normal alanine aminotransferase (PNALT). METHODS: The percentage of peripheral blood Treg cells, KIR2DL3, ILT-2, KIR3DL1, CD160, NKG2D, NKG2C expressing NK, T and NKT-like cells, cytokine production and NK cytotoxicity were determined by flow cytometry. Twenty-one patients with chronic HCV infection with elevated alanine aminotransferase, 11 HCV carriers with persistently normal alanine aminotransferase and 15 healthy volunteers were enrolled. RESULTS: No significant differences were observed in the percentage of total T, NK or NKT-like cells between study groups. Comparing the activating and inhibitory receptor expression by NK cells obtained from HCV carriers with PNALT and chronic HCV hepatitis patients with elevated alanine aminotransferase, NKG2D activating receptor expression was the only receptor showing a significant difference. NKG2D expression of NK cells was significantly lower in patients with elevated alanine aminotransferase. The expression of CD160, NKG2D and NKG2C activating receptor by CD8+ T cells were significantly lower in patients with chronic HCV hepatitis than in healthy controls and in HCV carriers with PNALT. Plasma TGF-ß1 levels inversely correlated with NKG2D expression by NK cells. In vitroTGF-ß1 treatment inhibited NK cells cytotoxic activity and downregulated NKG2D expression. CD8+ T cells from HCV carriers with PNALT showed significantly elevated expression of CD160, NKG2D and NKG2C activating receptors compared to chronic HCV patients with elevated alanine aminotransferase. Enhanced expression of inhibitory KIR2DL3 receptor, and decreased ILT-2 expression on NK cells were also found in chronic hepatitis C patients compared to healthy controls. CONCLUSION: Our study demonstrated a complex dysregulation of activating and inhibitory receptor expression, such as decreased NKG2D and CD160 activating receptor expression and increased KIR2DL3 inhibitory receptor expression by NK and cytotoxic T cells and may provide further mechanism contributing to defective cellular immune functions in chronic hepatitis C. Increased NKG2D receptor expression in HCV patients with persistently normal ALT suggests an important pathway for sustaining NK and CD8 T cell function and a protective role against disease progression.


Subject(s)
CD8-Positive T-Lymphocytes/immunology , Hepacivirus/immunology , Hepatitis C, Chronic/immunology , Killer Cells, Natural/immunology , Natural Killer T-Cells/immunology , Adult , Aged , Alanine Transaminase/blood , Biomarkers/blood , CD8-Positive T-Lymphocytes/virology , Case-Control Studies , Cytokines/blood , Cytotoxicity, Immunologic , Female , Hepatitis C, Chronic/blood , Hepatitis C, Chronic/diagnosis , Host-Pathogen Interactions , Humans , Killer Cells, Natural/virology , Male , Middle Aged , Natural Killer T-Cells/virology , Phenotype , Prognosis , Receptors, Immunologic/blood , Up-Regulation
14.
Sci Signal ; 8(408): ra130, 2015 Dec 22.
Article in English | MEDLINE | ID: mdl-26696630

ABSTRACT

Signaling pathways control cell fate decisions that ultimately determine the behavior of cancer cells. Therefore, the dynamics of pathway activity may contain prognostically relevant information different from that contained in the static nature of other types of biomarkers. To investigate this hypothesis, we characterized the network that regulated stress signaling by the c-Jun N-terminal kinase (JNK) pathway in neuroblastoma cells. We generated an experimentally calibrated and validated computational model of this network and used the model to extract prognostic information from neuroblastoma patient-specific simulations of JNK activation. Switch-like JNK activation mediates cell death by apoptosis. An inability to initiate switch-like JNK activation in the simulations was significantly associated with poor overall survival for patients with neuroblastoma with or without MYCN amplification, indicating that patient-specific simulations of JNK activation could stratify patients. Furthermore, our analysis demonstrated that extracting information about a signaling pathway to develop a prognostically useful model requires understanding of not only components and disease-associated changes in the abundance or activity of the components but also how those changes affect pathway dynamics.


Subject(s)
Biomarkers, Tumor/metabolism , MAP Kinase Kinase 4/metabolism , Models, Biological , Neuroblastoma/metabolism , Neuroblastoma/mortality , Nuclear Proteins/metabolism , Oncogene Proteins/metabolism , Signal Transduction , Adolescent , Animals , Cell Line, Tumor , Child , Child, Preschool , Disease-Free Survival , Female , Follow-Up Studies , Humans , Infant , Male , N-Myc Proto-Oncogene Protein , Neoplasms, Experimental/metabolism , Predictive Value of Tests , Survival Rate , Zebrafish/metabolism , Zebrafish Proteins/metabolism
15.
Oncotarget ; 6(41): 43182-201, 2015 Dec 22.
Article in English | MEDLINE | ID: mdl-26673823

ABSTRACT

Despite intensive study, many mysteries remain about the MYCN oncogene's functions. Here we focus on MYCN's role in neuroblastoma, the most common extracranial childhood cancer. MYCN gene amplification occurs in 20% of cases, but other recurrent somatic mutations are rare. This scarcity of tractable targets has hampered efforts to develop new therapeutic options. We employed a multi-level omics approach to examine MYCN functioning and identify novel therapeutic targets for this largely un-druggable oncogene. We used systems medicine based computational network reconstruction and analysis to integrate a range of omic techniques: sequencing-based transcriptomics, genome-wide chromatin immunoprecipitation, siRNA screening and interaction proteomics, revealing that MYCN controls highly connected networks, with MYCN primarily supressing the activity of network components. MYCN's oncogenic functions are likely independent of its classical heterodimerisation partner, MAX. In particular, MYCN controls its own protein interaction network by transcriptionally regulating its binding partners.Our network-based approach identified vulnerable therapeutically targetable nodes that function as critical regulators or effectors of MYCN in neuroblastoma. These were validated by siRNA knockdown screens, functional studies and patient data. We identified ß-estradiol and MAPK/ERK as having functional cross-talk with MYCN and being novel targetable vulnerabilities of MYCN-amplified neuroblastoma. These results reveal surprising differences between the functioning of endogenous, overexpressed and amplified MYCN, and rationalise how different MYCN dosages can orchestrate cell fate decisions and cancerous outcomes. Importantly, this work describes a systems-level approach to systematically uncovering network based vulnerabilities and therapeutic targets for multifactorial diseases by integrating disparate omic data types.


Subject(s)
Genes, myc/physiology , Neuroblastoma/genetics , Nuclear Proteins/physiology , Oncogene Proteins/physiology , Protein Interaction Maps/physiology , Blotting, Western , Chromatin Immunoprecipitation , Computational Biology/methods , Gene Expression Regulation, Neoplastic/physiology , High-Throughput Nucleotide Sequencing/methods , Humans , N-Myc Proto-Oncogene Protein , Neuroblastoma/metabolism , Neuroblastoma/pathology , Oligonucleotide Array Sequence Analysis , Polymerase Chain Reaction , Proteomics/methods , Signal Transduction/physiology
16.
Nat Rev Cancer ; 15(9): 515-27, 2015 Sep.
Article in English | MEDLINE | ID: mdl-26289315

ABSTRACT

Cancer is often considered a genetic disease. However, much of the enormous plasticity of cancer cells to evolve different phenotypes, to adapt to challenging microenvironments and to withstand therapeutic assaults is encoded by the structure and spatiotemporal dynamics of signal transduction networks. In this Review, we discuss recent concepts concerning how the rich signalling dynamics afforded by these networks are regulated and how they impinge on cancer cell proliferation, survival, invasiveness and drug resistance. Understanding this dynamic circuitry by mathematical modelling could pave the way to new therapeutic approaches and personalized treatments.


Subject(s)
Drug Resistance, Neoplasm , Neoplasms/drug therapy , Neoplasms/metabolism , Signal Transduction , Cell Proliferation , Gene Expression Regulation, Neoplastic , Humans , Neoplasms/genetics , Neoplasms/pathology
17.
Nat Cell Biol ; 16(7): 673-84, 2014 Jul.
Article in English | MEDLINE | ID: mdl-24929361

ABSTRACT

Signal transduction requires the coordination of activities between different pathways. In mammalian cells, Raf-1 regulates the MST-LATS and MEK-ERK pathways. We found that a complex circuitry of competing protein interactions coordinates the crosstalk between the ERK and MST pathways. Combining mathematical modelling and experimental validation we show that competing protein interactions can cause steep signalling switches through phosphorylation-induced changes in binding affinities. These include Akt phosphorylation of MST2 and a feedback phosphorylation of Raf-1 Ser 259 by LATS1, which enables Raf-1 to suppress both MST2 and MEK signalling. Mutation of Raf-1 Ser 259 stimulates both pathways, simultaneously driving apoptosis and proliferation, whereas concomitant MST2 downregulation switches signalling to cell proliferation, transformation and survival. Thus, competing protein interactions provide a versatile regulatory mechanism for signal distribution through the dynamic integration of graded signals into switch-like responses.


Subject(s)
Genes, Switch/physiology , Models, Biological , Protein Serine-Threonine Kinases/metabolism , Proto-Oncogene Proteins c-raf/metabolism , Signal Transduction , Animals , Apoptosis/physiology , Cell Proliferation , Cells, Cultured , Embryo, Nonmammalian , HEK293 Cells , HeLa Cells , Hippo Signaling Pathway , Humans , MAP Kinase Signaling System/physiology , MCF-7 Cells , Mice , NIH 3T3 Cells , Phosphorylation , Protein Binding , Serine-Threonine Kinase 3 , Zebrafish/embryology
18.
PLoS One ; 8(7): e67770, 2013.
Article in English | MEDLINE | ID: mdl-23874444

ABSTRACT

BACKGROUND: Chronic hepatitis C (CHC) patients achieving rapid virological response (RVR) on PEG-IFN/ribavirin (P/R) therapy have high chance of sustained virological response (SVR). To analyze host immunological factors associated with RVR, viral kinetics, phenotype distribution and Th1/Th2 cytokine production by peripheral blood mononuclear cells (PBMC) were studied prior to and during P/R therapy. METHODS: TNF-α, IFN-γ, IL-2, IL-6, IL-4 and IL-10 production by PBMC were measured after Toll-like receptor 4 (TLR-4) or phorbol myristate acetate/Ionomycin stimulation in 20 healthy controls and in 50 CHC patients before receiving and during P/R therapy. RVR was achieved by 14, complete early virological response (cEVR) by 19 patients and 17 patients were null-responders (NR). RESULTS: Patients with RVR showed an increased baseline TNF-α and IL-6 production by TLR-4 activated monocytes and increased IFN-γ, decreased IL-4 and IL-10 production by lymphocytes compared to non-RVR patients. SVR was also associated with increased baseline TNF-α production and decreased IL-10 levels compared to patients who did not achieve SVR. Baseline IL-2 production was higher in cEVR compared to NR patients. Antiviral treatment increased TNF-α, IL-6 production by monocytes and IFN-γ secretion by lymphocytes and decreased IL-4 and IL-10 production by lymphocytes in cEVR compared to NR patients. CONCLUSION: RVR was associated with increased baseline proinflammatory cytokine production by TLR-4 stimulated monocytes and by activated lymphocytes. In null-responders and in patients who did not achieve SVR both TLR-4 sensing function and proinflammatory cytokine production were impaired, suggesting that modulation of TLR activity and controlled induction of inflammatory cytokine production may provide further therapeutic strategy for CHC patients non-responding to P/R treatment.


Subject(s)
Antiviral Agents/therapeutic use , Cytokines/metabolism , Hepatitis C, Chronic/drug therapy , Hepatitis C, Chronic/metabolism , Inflammation Mediators/metabolism , Interferon-alpha/therapeutic use , Ribavirin/therapeutic use , Adult , Aged , Drug Therapy, Combination , Female , Genotype , Hepacivirus/genetics , Hepatitis C, Chronic/virology , Humans , Killer Cells, Natural/metabolism , Leukocytes, Mononuclear/drug effects , Leukocytes, Mononuclear/immunology , Leukocytes, Mononuclear/metabolism , Lymphocyte Activation , Male , Middle Aged , Phenotype , RNA, Viral/blood , T-Lymphocyte Subsets/immunology , T-Lymphocyte Subsets/metabolism , Toll-Like Receptor 4/metabolism , Treatment Outcome , Viral Load
19.
Cell Mol Life Sci ; 70(23): 4617-30, 2013 Dec.
Article in English | MEDLINE | ID: mdl-23807209

ABSTRACT

Invasiveness is a common feature of trophoblast and tumors; however, while tumor invasion is uncontrolled, trophoblast invasion is strictly regulated. Both trophoblast and tumor cells express high levels of the immunomodulatory progesterone-induced blocking factor (PIBF), therefore, we aimed to test the possibility that PIBF might be involved in invasion. To this aim, we used PIBF-silenced or PIBF-treated trophoblast (HTR8/Svneo, and primary trophoblast) and tumor (HT-1080, A549, HCT116, PC3) cell lines. Silencing of PIBF increased invasiveness as well as MMP-2,-9 secretion of HTR8/SVneo, and decreased those of HT-1080 cells. PIBF induced immediate STAT6 activation in both cell lines. Silencing of IL-4Rα abrogated all the above effects of PIBF, suggesting that invasion-related signaling by PIBF is initiated through the IL-4Rα/PIBF-receptor complex. In HTR-8/SVneo, PIBF induced fast, but transient Akt and ERK phosphorylation, whereas in tumor cells, PIBF triggered sustained Akt, ERK, and late STAT3 activation. The late signaling events might be due to indirect action of PIBF. PIBF induced the expression of EGF and HB-EGF in HT-1080 cells. The STAT3-activating effect of PIBF was reduced in HB-EGF-deficient HT-1080 cells, suggesting that PIBF-induced HB-EGF contributes to late STAT3 activation. PIBF binds to the promoters of IL-6, EGF, and HB-EGF; however, the protein profile of the protein/DNA complex is different in the two cell lines. We conclude that in tumor cells, PIBF induces proteins, which activate invasion signaling, while-based on our previous data-PIBF might control trophoblast invasion by suppressing proinvasive genes.


Subject(s)
Matrix Metalloproteinase 2/metabolism , Matrix Metalloproteinase 9/metabolism , Pregnancy Proteins/metabolism , Suppressor Factors, Immunologic/metabolism , Trophoblasts/metabolism , Animals , Animals, Genetically Modified , Blotting, Western , Cell Line , Cell Line, Tumor , Cell Movement , Cell Transplantation/methods , Cells, Cultured , Embryo, Nonmammalian/cytology , Embryo, Nonmammalian/metabolism , Green Fluorescent Proteins/genetics , Green Fluorescent Proteins/metabolism , HCT116 Cells , Heparin-binding EGF-like Growth Factor , Humans , Intercellular Signaling Peptides and Proteins/genetics , Intercellular Signaling Peptides and Proteins/metabolism , Matrix Metalloproteinase 2/genetics , Matrix Metalloproteinase 9/genetics , Microscopy, Confocal , Neoplasms/genetics , Neoplasms/metabolism , Neoplasms/pathology , Pregnancy Proteins/genetics , Promoter Regions, Genetic/genetics , Protein Binding , RNA Interference , Signal Transduction/genetics , Suppressor Factors, Immunologic/genetics , Transplantation, Heterologous , Trophoblasts/cytology , Trophoblasts/transplantation , Zebrafish/embryology , Zebrafish/genetics , Zebrafish/metabolism
20.
J Reprod Immunol ; 97(1): 43-50, 2013 Mar.
Article in English | MEDLINE | ID: mdl-23432871

ABSTRACT

With its genomic and non-genomic actions, progesterone plays a role in preparing the endometrium for implantation and also in regulating trophoblast invasion and migration. The genomic actions of progesterone are mediated by the classical nuclear progesterone receptors, PR-A and PR-B. In addition to their genomic actions, nuclear progesterone receptors may also trigger rapid cytoplasmic signalling events. Membrane-bound progesterone receptors have been implicated in the rapid non-genomic actions of progesterone. Both genomic and extra-nuclear actions of progesterone are crucial for adequate decidualisation and implantation. Progesterone plays a role in establishing uterine receptivity by blocking the proliferative effect of oestrogen, by inducing genes that allow the endometrium to permit embryo attachment, and also acts as a negative regulator of trophoblast invasion by controlling matrix metalloproteinase (MMP) activity.


Subject(s)
Embryo Implantation , Endometrium/metabolism , Progesterone/physiology , Receptors, Progesterone/metabolism , Trophoblasts/physiology , Animals , Cell Growth Processes , Cell Movement , Estrogens/metabolism , Female , Gene Expression Regulation, Developmental , Humans , Matrix Metalloproteinases/metabolism , Pregnancy , Signal Transduction
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