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1.  Hyper-Activation of Notch3 Amplifies the Proliferative Potential of Rhabdomyosarcoma Cells 
PLoS ONE  2014;9(5):e96238.
Rhabdomyosarcoma (RMS) is a pediatric myogenic-derived soft tissue sarcoma that includes two major histopathological subtypes: embryonal and alveolar. The majority of alveolar RMS expresses PAX3-FOXO1 fusion oncoprotein, associated with the worst prognosis. RMS cells show myogenic markers expression but are unable to terminally differentiate. The Notch signaling pathway is a master player during myogenesis, with Notch1 activation sustaining myoblast expansion and Notch3 activation inhibiting myoblast fusion and differentiation. Accordingly, Notch1 signaling is up-regulated and activated in embryonal RMS samples and supports the proliferation of tumor cells. However, it is unable to control their differentiation properties. We previously reported that Notch3 is activated in RMS cell lines, of both alveolar and embryonal subtype, and acts by inhibiting differentiation. Moreover, Notch3 depletion reduces PAX3-FOXO1 alveolar RMS tumor growth in vivo. However, whether Notch3 activation also sustains the proliferation of RMS cells remained unclear. To address this question, we forced the expression of the activated form of Notch3, Notch3IC, in the RH30 and RH41 PAX3-FOXO1-positive alveolar and in the RD embryonal RMS cell lines and studied the proliferation of these cells. We show that, in all three cell lines tested, Notch3IC over-expression stimulates in vitro cell proliferation and prevents the effects of pharmacological Notch inhibition. Furthermore, Notch3IC further increases RH30 cell growth in vivo. Interestingly, knockdown of Notch canonical ligands JAG1 or DLL1 in RMS cell lines decreases Notch3 activity and reduces cell proliferation. Finally, the expression of Notch3IC and its target gene HES1 correlates with that of the proliferative marker Ki67 in a small cohort of primary PAX-FOXO1 alveolar RMS samples. These results strongly suggest that high levels of Notch3 activation increase the proliferative potential of RMS cells.
doi:10.1371/journal.pone.0096238
PMCID: PMC4010457  PMID: 24797362
2.  17β-Estradiol Enhances Signalling Mediated by VEGF-A-Delta-Like Ligand 4-Notch1 Axis in Human Endothelial Cells 
PLoS ONE  2013;8(8):e71440.
Estrogens play a protective role in coronary artery disease. The mechanisms of action are still poorly understood, although a role for estrogens in stimulation of angiogenesis has been suggested. In several cell types, estrogens modulate the Notch pathway, which is involved in controlling angiogenesis downstream of vascular endothelial growth factor A (VEGF-A). The goal of our study was to establish whether estrogens modulate Notch activity in endothelial cells and the possible consequences on angiogenesis. Human umbilical vein endothelial cells (HUVECs) were treated with 17β-estradiol (E2) and the effects on Notch signalling were evaluated. E2 increased Notch1 processing as indicated by i) decreased levels of Notch1 transmembrane subunit ii) increased amount of Notch1 in nuclei iii) unaffected level of mRNA. Similarly, E2 increased the levels of the active form of Notch4 without altering Notch4 mRNA. Conversely, protein and mRNA levels of Notch2 were both reduced suggesting transcriptional repression of Notch2 by E2. Under conditions where Notch was activated by upregulation of Delta-like ligand 4 (Dll4) following VEGF-A treatment, E2 caused a further increase of the active form of Notch1, of the number of cells with nuclear Notch1 and of Hey2 mRNA. Estrogen receptor antagonist ICI 182.780 antagonized these effects suggesting that E2 modulation of Notch1 is mediated by estrogen receptors. E2 treatment abolished the increase in endothelial cells sprouting caused by Notch inhibition in a tube formation assay on 3D Matrigel and in mouse aortic ring explants. In conclusion, E2 affects several Notch pathway components in HUVECs, leading to an activation of the VEGF-A-Dll4-Notch1 axis and to a modulation of vascular branching when Notch signalling is inhibited. These results contribute to our understanding of the molecular mechanisms of cardiovascular protection exerted by estrogens by uncovering a novel role of E2 in the Notch signalling-mediated modulation of angiogenesis.
doi:10.1371/journal.pone.0071440
PMCID: PMC3742772  PMID: 23967210
3.  An Integrative Genomics Approach for Associating GWAS Information with Triple-Negative Breast Cancer 
Cancer Informatics  2013;12:1-20.
Genome-wide association studies (GWAS) have identified genetic variants associated with an increased risk of developing breast cancer. However, the association of genetic variants and their associated genes with the most aggressive subset of breast cancer, the triple-negative breast cancer (TNBC), remains a central puzzle in molecular epidemiology. The objective of this study was to determine whether genes containing single nucleotide polymorphisms (SNPs) associated with an increased risk of developing breast cancer are connected to and could stratify different subtypes of TNBC. Additionally, we sought to identify molecular pathways and networks involved in TNBC. We performed integrative genomics analysis, combining information from GWAS studies involving over 400,000 cases and over 400,000 controls, with gene expression data derived from 124 breast cancer patients classified as TNBC (at the time of diagnosis) and 142 cancer-free controls. Analysis of GWAS reports produced 500 SNPs mapped to 188 genes. We identified a signature of 159 functionally related SNP-containing genes which were significantly (P <10−5) associated with and stratified TNBC. Additionally, we identified 97 genes which were functionally related to, and had similar patterns of expression profiles, SNP-containing genes. Network modeling and pathway prediction revealed multi-gene pathways including p53, NFkB, BRCA, apoptosis, DNA repair, DNA mismatch, and excision repair pathways enriched for SNPs mapped to genes significantly associated with TNBC. The results provide convincing evidence that integrating GWAS information with gene expression data provides a unified and powerful approach for biomarker discovery in TNBC.
doi:10.4137/CIN.S10413
PMCID: PMC3565545  PMID: 23423317
triple negative breast cancer GWAS gene expression
5.  Notch signals in the endothelium and cancer "stem-like" cells: opportunities for cancer therapy 
Vascular Cell  2012;4:7.
Anti-angiogenesis agents and the identification of cancer stem-like cells (CSC) are opening new avenues for targeted cancer therapy. Recent evidence indicates that angiogenesis regulatory pathways and developmental pathways that control CSC fate are intimately connected, and that endothelial cells are a key component of the CSC niche. Numerous anti-angiogenic therapies developed so far target the VEGF pathway. However, VEGF-targeted therapy is hindered by clinical resistance and side effects, and new approaches are needed. One such approach may be direct targeting of tumor endothelial cell fate determination. Interfering with tumor endothelial cells growth and survival could inhibit not only angiogenesis but also the self-replication of CSC, which relies on signals from surrounding endothelial cells in the tumor microenvironment. The Notch pathway is central to controlling cell fate both during angiogenesis and in CSC from several tumors. A number of investigational Notch inhibitors are being developed. Understanding how Notch interacts with other factors that control endothelial cell functions and angiogenesis in cancers could pave the way to innovative therapeutic strategies that simultaneously target angiogenesis and CSC.
doi:10.1186/2045-824X-4-7
PMCID: PMC3348040  PMID: 22487493
6.  Integrative Analysis of Response to Tamoxifen Treatment in ER-Positive Breast Cancer Using GWAS Information and Transcription Profiling 
Variable response and resistance to tamoxifen treatment in breast cancer patients remains a major clinical problem. To determine whether genes and biological pathways containing SNPs associated with risk for breast cancer are dysregulated in response to tamoxifen treatment, we performed analysis combining information from 43 genome-wide association studies with gene expression data from 298 ER+ breast cancer patients treated with tamoxifen and 125 ER+ controls. We identified 95 genes which distinguished tamoxifen treated patients from controls. Additionally, we identified 54 genes which stratified tamoxifen treated patients into two distinct groups. We identified biological pathways containing SNPs associated with risk for breast cancer, which were dysregulated in response to tamoxifen treatment. Key pathways identified included the apoptosis, P53, NFkB, DNA repair and cell cycle pathways. Combining GWAS with transcription profiling provides a unified approach for associating GWAS findings with response to drug treatment and identification of potential drug targets.
doi:10.4137/BCBCR.S8652
PMCID: PMC3292850  PMID: 22399860
tamoxifen genome-wide association studies gene expression
8.  An Integrative Genomics Approach to Biomarker Discovery in Breast Cancer 
Cancer Informatics  2011;10:185-204.
Genome-wide association studies (GWAS) have successfully identified genetic variants associated with risk for breast cancer. However, the molecular mechanisms through which the identified variants confer risk or influence phenotypic expression remains poorly understood. Here, we present a novel integrative genomics approach that combines GWAS information with gene expression data to assess the combined contribution of multiple genetic variants acting within genes and putative biological pathways, and to identify novel genes and biological pathways that could not be identified using traditional GWAS. The results show that genes containing SNPs associated with risk for breast cancer are functionally related and interact with each other in biological pathways relevant to breast cancer. Additionally, we identified novel genes that are co-expressed and interact with genes containing SNPs associated with breast cancer. Integrative analysis combining GWAS information with gene expression data provides functional bridges between GWAS findings and biological pathways involved in breast cancer.
doi:10.4137/CIN.S6837
PMCID: PMC3153161  PMID: 21869864
genome-wide association studies gene expression pathway
9.  Targeting Cancer Stem Cells through Notch Signaling 
The cellular heterogeneity of neoplasms has been at the center of considerable interest since the “cancer stem cell hypothesis”, originally formulated for hematologic malignancies, was extended to solid tumors. The origins of cancer “stem” cells (CSCs) or tumor-initiating cells (TICs) (henceforth referred to as CSCs) and the methods to identify them are hotly debated topics. Nevertheless, the existence of sub-populations of tumor cells with stem-like characteristics has significant therapeutic implications. The stem-like phenotype includes indefinite self-replication, pluripotency and, importantly, resistance to chemotherapeutics. Thus, it is plausible that CSC, regardless of their origin, may escape standard therapies and cause disease recurrences and/or metastasis after apparently complete remissions. Consequently, the idea of selectively targeting CSCs with novel therapeutics is gaining considerable interest. The Notch pathway is one of the most intensively studied putative therapeutic targets in CSC, and several investigational Notch inhibitors are being developed. However, successful targeting of Notch signaling in CSC will require a thorough understanding of Notch regulation and the context-dependent interactions between Notch and other therapeutically relevant pathways. Understanding these interactions will increase our ability to design rational combination regimens that are more likely to prove safe and effective. Additionally, to determine which patients are most likely to benefit from treatment with Notch-targeting therapeutics, reliable biomarkers to measure pathway activity in CSC from specific tumors will have to be identified and validated. This article summarizes the most recent developments in the field of Notch-targeted cancer therapeutics, with emphasis on CSC.
doi:10.1158/1078-0432.CCR-09-2823
PMCID: PMC3008160  PMID: 20530696
10.  Associating GWAS Information with the Notch Signaling Pathway Using Transcription Profiling 
Cancer Informatics  2011;10:93-108.
Genome-wide association studies (GWAS) have identified SNPs associated with breast cancer. However, they offer limited insights about the biological mechanisms by which SNPs confer risk. We investigated the association of GWAS information with a major oncogenic pathway in breast cancer, the Notch signaling pathway. We first identified 385 SNPs and 150 genes associated with risk for breast cancer by mining data from 41 GWAS. We then investigated their expression, along with 32 genes involved in the Notch signaling pathway using two publicly available gene expression data sets from the Caucasian (42 cases and 143 controls) and Asian (43 cases and 43 controls) populations. Pathway prediction and network modeling confirmed that Notch receptors and genes involved in the Notch signaling pathway interact with genes containing SNPs associated with risk for breast cancer. Additionally, we identified other SNP-associated biological pathways relevant to breast cancer, including the P53, apoptosis and MAP kinase pathways.
doi:10.4137/CIN.S6072
PMCID: PMC3091413  PMID: 21584266
GWAS; gene expression; Notch signaling pathway
11.  A novel mechanism of late gene silencing drives Simian virus 40 transformation of human mesothelial cells 
Cancer research  2008;68(22):9488-9496.
Suppression of the late gene expression, usually by integration of the viral DNA into the host genome, is a critical step in DNA tumor viruses carcinogenesis. Simian virus 40 (SV40) induces high rates of transformation in infected primary human mesothelial cells (S-HM) in tissue culture, leading to the formation of immortal cell lines (S-HML). The studies described here were designed to elucidate the unusual susceptibility of primary human mesothelial cells (HM) to SV40 carcinogenesis.
We found that S-HML contained wild-type, mostly episomal SV40 DNA. In these cells the early genes that code for the viral oncogenes are expressed, at he same time, the synthesis of the late genes capsid proteins is suppressed and S-HML are not lysed. Late genes suppression is achieved through the production of antisense RNA molecules. These antisense RNA molecules originate in the early region of the SV40 circular chromosome and proceed in antisense orientation into the late gene region, leading to the formation of highly unstable double strand RNA that is rapidly degraded. Our results reveal a novel biological mechanism responsible for the suppression of late viral gene products, an important step in viral carcinogenesis in humans.
doi:10.1158/0008-5472.CAN-08-2332
PMCID: PMC2666620  PMID: 19010924
12.  A Plasmid Model System Shows that Drosophila Dosage Compensation Depends on the Global Acetylation of Histone H4 at Lysine 16 and Is Not Affected by Depletion of Common Transcription Elongation Chromatin Marks▿ †  
Molecular and Cellular Biology  2007;27(22):7865-7870.
Dosage compensation refers to the equalization of most X-linked gene products between males, which have one X chromosome and a single dose of X-linked genes, and females, which have two X's and two doses of such genes. We developed a plasmid-based model of dosage compensation that allows new experimental approaches for the study of this regulatory mechanism. In Drosophila melanogaster, an enhanced rate of transcription of the X chromosome in males is dependent upon the presence of histone H4 acetylated at lysine 16. This chromatin mark occurs throughout active transcriptional units, leading us to the conclusion that the enhanced level of transcription is achieved through an enhanced rate of RNA polymerase elongation. We used the plasmid model to demonstrate that enhancement in the level of transcription does not depend on other histone marks and factors that have been associated with the process of elongation, thereby highlighting the special role played by histone H4 acetylated at lysine 16 in this process.
doi:10.1128/MCB.00397-07
PMCID: PMC2169142  PMID: 17875941
13.  The Drosophila MSL Complex Acetylates Histone H4 at Lysine 16, a Chromatin Modification Linked to Dosage Compensation 
Molecular and Cellular Biology  2000;20(1):312-318.
In Drosophila, dosage compensation—the equalization of most X-linked gene products in males and females—is achieved by a twofold enhancement of the level of transcription of the X chromosome in males relative to each X chromosome in females. A complex consisting of at least five gene products preferentially binds the X chromosome at numerous sites in males and results in a significant increase in the presence of a specific histone isoform, histone 4 acetylated at lysine 16. Recently, RNA transcripts (roX1 and roX2) encoded by two different genes have also been found associated with the X chromosome in males. We have partially purified a complex containing MSL1, -2, and -3, MOF, MLE, and roX2 RNA and demonstrated that it exclusively acetylates H4 at lysine 16 on nucleosomal substrates. These results demonstrate that the MSL complex is responsible for the specific chromatin modification characteristic of the X chromosome in Drosophila males.
PMCID: PMC85086  PMID: 10594033

Results 1-13 (13)