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van Caloen G, Schmitz S, El Baroudi M, Caignet X, Pyr Dit Ruys S, Roger PP, Vertommen D, Machiels JP. Preclinical Activity of Ribociclib in Squamous Cell Carcinoma of the Head and Neck. Mol Cancer Ther 2020; 19:777-789. [PMID: 31924739 DOI: 10.1158/1535-7163.mct-19-0695] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 11/06/2019] [Accepted: 01/03/2020] [Indexed: 11/16/2022]
Abstract
Cell-cycle pathway impairments resulting in CDK4 and 6 activation are frequently observed in human papillomavirus (HPV)-negative squamous cell carcinoma of the head and neck (SCCHN). We investigated the activity of ribociclib, a CDK4/6 inhibitor, in SCCHN models with the aim of identifying predictive biomarkers of response. HPV-negative or HPV-positive SCCHN cell lines (n = 8) and patient-derived tumor xenograft (PDTX) models (n = 6) were used. The models were classified according to their sensitivity to ribociclib to investigate potential predictive biomarkers. Ribociclib had a cytostatic effect in some HPV-negative SCCHN models but had no effect in HPV-positive models. In SCCHN cell lines and PDTXs, the retinoblastoma (Rb) protein expression level correlated with ribociclib activity. Rb knockdown was, however, not sufficient to block G0-G1 arrest induced by ribociclib in Detroit-562 where p107, p130, and Forkhead BOX M1 (FOXM1) were also implicated in ribociclib activity. Cell lines harboring epithelial-to-mesenchymal transition (EMT) features were less sensitive to ribociclib than those with an epithelial phenotype. Rb downregulation induced EMT in our Rb-expressing SCCHN cell lines. However, ribociclib still had significant activity in one PDTX model with high Rb and vimentin expression, suggesting that the presence of vimentin alone is not enough to induce ribociclib resistance. These findings suggest that CDK4/6 inhibitors should be investigated in patients with HPV-negative SCCHN with high Rb expression and an epithelial phenotype. Although these biomarkers are not predictive in all cases, they may enrich the population that could benefit from CDK4/6 inhibitors.
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Affiliation(s)
- Gabrielle van Caloen
- Institut de Recherche Clinique et Expérimentale (Pole MIRO), Université Catholique de Louvain (UCLouvain), Brussels, Belgium
| | - Sandra Schmitz
- Institut de Recherche Clinique et Expérimentale (Pole MIRO), Université Catholique de Louvain (UCLouvain), Brussels, Belgium.,Institut Roi Albert II, Department of Medical Oncology, Cliniques Universitaires Saint-Luc, Brussels, Belgium.,Department of Head and Neck Surgery, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Mariama El Baroudi
- Institut de Recherche Clinique et Expérimentale (Pole MIRO), Université Catholique de Louvain (UCLouvain), Brussels, Belgium
| | - Xavier Caignet
- Institut de Recherche Clinique et Expérimentale (Pole MIRO), Université Catholique de Louvain (UCLouvain), Brussels, Belgium
| | - Sébastien Pyr Dit Ruys
- Protein Phosphorylation Unit, de Duve Institute, Université Catholique de Louvain (UCLouvain), Brussels, Belgium
| | - Pierre P Roger
- ULB-Cancer Research Center (U-CRC) Université Libre de Bruxelles, Brussels, Belgium
| | - Didier Vertommen
- Protein Phosphorylation Unit, de Duve Institute, Université Catholique de Louvain (UCLouvain), Brussels, Belgium
| | - Jean-Pascal Machiels
- Institut de Recherche Clinique et Expérimentale (Pole MIRO), Université Catholique de Louvain (UCLouvain), Brussels, Belgium. .,Institut Roi Albert II, Department of Medical Oncology, Cliniques Universitaires Saint-Luc, Brussels, Belgium.,Department of Head and Neck Surgery, Cliniques Universitaires Saint-Luc, Brussels, Belgium
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El Baroudi M, Machiels JP, Schmitz S. Expression of SESN1, UHRF1BP1, and miR-377-3p as prognostic markers in mutated TP53 squamous cell carcinoma of the head and neck. Cancer Biol Ther 2017; 18:775-782. [PMID: 28886272 DOI: 10.1080/15384047.2017.1373212] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
The tumor suppressor gene TP53 is the most frequently mutated gene in human papillomavirus (HPV)-negative head and neck squamous cell carcinoma (HNSCC). It represents a known transcription factor that controls different microRNAs (miRNA) and target genes involved in the regulation of cellular stress, apoptosis and response to DNA damage. We used The Cancer Genome Atlas database to investigate the difference in transcriptome and proteome levels between mutated and wild-type TP53 HPV-negative HNSCC. Using different databases and an extensive literature review, we built the transcriptional and post-transcriptional network regulated by TP53. TP53 mutation was associated with poor overall survival in 203 HPV-negative patients compared to 40 patients with TP53 wild-type tumors. Using the enrichment analysis, we found that UHRF1BP1 and SESN1 mRNA were linked to prognosis in the TP53 mutated group. This is also the case for miR-377-3p, an important miRNA regulator of SESN1. Our study shows that SESN1 mRNA, UHRF1BP11 mRNA and miRNA-377-3p levels are prognostically relevant in HPV-negative HNSCC patients. This finding may help with patient stratification and the development of potential new therapeutic targets to treat patients with HNSCC.
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Affiliation(s)
- Mariama El Baroudi
- a Department of Medical Oncology, Institut de Recherche Expérimentale et Clinique (IREC)-Pole MIRO , Université Catholique de Louvain , Brussels , Belgium
| | - Jean-Pascal Machiels
- a Department of Medical Oncology, Institut de Recherche Expérimentale et Clinique (IREC)-Pole MIRO , Université Catholique de Louvain , Brussels , Belgium.,b Institut Roi Albert II, Department of Medical Oncology and Head and Neck Surgery , Cliniques Universitaires Saint-Luc and Institut de Recherche Clinique et Expérimentale (Pole MIRO), Université catholique de Louvain , Brussels , Belgium
| | - Sandra Schmitz
- a Department of Medical Oncology, Institut de Recherche Expérimentale et Clinique (IREC)-Pole MIRO , Université Catholique de Louvain , Brussels , Belgium.,b Institut Roi Albert II, Department of Medical Oncology and Head and Neck Surgery , Cliniques Universitaires Saint-Luc and Institut de Recherche Clinique et Expérimentale (Pole MIRO), Université catholique de Louvain , Brussels , Belgium
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El Baroudi M, Cinti C, Capobianco E. Immunomediated Pan-cancer Regulation Networks are Dominant Fingerprints After Treatment of Cell Lines with Demethylation. Cancer Inform 2016; 15:45-64. [PMID: 27147816 PMCID: PMC4849425 DOI: 10.4137/cin.s31809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 02/09/2016] [Accepted: 02/17/2016] [Indexed: 11/11/2022] Open
Abstract
Pan-cancer studies are particularly relevant not only for addressing the complexity of the inherently observed heterogeneity but also for identifying clinically relevant features that may be common to the cancer types. Immune system regulations usually reveal synergistic modulation with other cancer mechanisms and in combination provide insights on possible advances in cancer immunotherapies. Network inference is a powerful approach to decipher pan-cancer systems dynamics. The methodology proposed in this study elucidates the impacts of epigenetic treatment on the drivers of complex pan-cancer regulation circuits involving cell lines of five cancer types. These patterns were observed from differential gene expression measurements following demethylation with 5-azacytidine. Networks were built to establish associations of phenotypes at molecular level with cancer hallmarks through both transcriptional and post-transcriptional regulation mechanisms. The most prominent feature that emerges from our integrative network maps, linking pathway landscapes to disease and drug-target associations, refers primarily to a mosaic of immune-system crosslinked influences. Therefore, characteristics initially evidenced in single cancer maps become motifs well summarized by network cores and fingerprints.
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Affiliation(s)
- Mariama El Baroudi
- Laboratory of Integrative Systems Medicine (LISM), Institute of Clinical Physiology, National Research Council of Italy (CNR), Pisa, Italy.; Medical Oncology Department, MIRO, Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain, Brussels, Belgium
| | - Caterina Cinti
- Cancer Therapy UOS, Institute of Clinical Phsyiology, National Research Council of Italy (CNR), Siena, Italy
| | - Enrico Capobianco
- Laboratory of Integrative Systems Medicine (LISM), Institute of Clinical Physiology, National Research Council of Italy (CNR), Pisa, Italy.; Center for Computational Science, Miller School of Medicine, University of Miami, Miami, FL, USA
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Evangelista M, Baroudi ME, Rizzo M, Tuccoli A, Poliseno L, Pellegrini M, Rainaldi G. Alkaline Phosphatase-Positive Immortal Mouse Embryo Fibroblasts Are Cells in a Transitional Reprogramming State Induced to Face Environmental Stresses. Genet Epigenet 2016; 7:33-41. [PMID: 26740745 PMCID: PMC4694620 DOI: 10.4137/geg.s27696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 05/25/2015] [Accepted: 05/27/2015] [Indexed: 12/31/2022]
Abstract
In this study, we report that immortal mouse embryonic fibroblasts (I-MEFs) have a baseline level of cells positive for alkaline phosphatase (AP+) staining. Environmental stresses, including long-lasting growth in the absence of expansion and treatment with drugs, enhance the frequency of AP+ I-MEFs. By adapting fast red AP staining to the sorting procedure, we separated AP+ and AP− I-MEFs and demonstrated that the differentially expressed genes are consistent with a reprogrammed phenotype. In particular, we found that sestrin 1 is upregulated in AP+ I-MEFs. We focused on this gene and demonstrated that increased sestrin 1 expression is accompanied by the growth of I-MEFs in the absence of expansion and occurs before the formation of AP+ I-MEFs. Together with sestrin 1 upregulation, we found that AP+ I-MEFs accumulated in the G1 phase of the cell cycle, suggesting that the two events are causally related. Accordingly, we found that silencing sestrin 1 expression reduced the frequency and G1 accumulation of AP+ I-MEFs. Taken together, our data suggested that I-MEFs stressed by environmental changes acquire the AP+ phenotype and achieve a quiescent state characterized by a new transcriptional network.
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Affiliation(s)
| | | | - Milena Rizzo
- Institute of Clinical Physiology (IFC), CNR, Pisa, Italy.; Tuscan Tumor Institute (ITT), Firenze, Italy
| | - Andrea Tuccoli
- Oncogenomics Unit, Core Research Laboratory (CRL), Tuscan Tumor Institute (ITT), Pisa, Italy
| | - Laura Poliseno
- Institute of Clinical Physiology (IFC), CNR, Pisa, Italy.; Oncogenomics Unit, Core Research Laboratory (CRL), Tuscan Tumor Institute (ITT), Pisa, Italy
| | - Marco Pellegrini
- Laboratory of Integrative Systems Medicine (LISM), CNR, Pisa, Italy
| | - Giuseppe Rainaldi
- Institute of Clinical Physiology (IFC), CNR, Pisa, Italy.; Tuscan Tumor Institute (ITT), Firenze, Italy
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El Baroudi M, La Sala D, Cinti C, Capobianco E. Pathway landscapes and epigenetic regulation in breast cancer and melanoma cell lines. Theor Biol Med Model 2014; 11 Suppl 1:S8. [PMID: 25077705 PMCID: PMC4108926 DOI: 10.1186/1742-4682-11-s1-s8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Epigenetic variation is a main regulation mechanism of gene expression in various cancer histotypes, and due to its reversibility, the potential impact in therapy can be very relevant. METHODS Based on a selected pair, breast cancer (BC) and melanoma, we conducted inference analysis in parallel on a few cell lines (MCF-7 for BC and A375 for melanoma). Starting from differential expression after treatment with a demethylating agent, the 5-Aza-2'-deoxycytidine (DAC), we provided pathway enrichment analysis and gene regulatory maps with cross-linked microRNAs and transcription factors. RESULTS Several oncogenic signaling pathways altered upon DAC treatment were detected with significant enrichment. We represented the association between these cancers by depicting the landscape of common and specific variation affecting them.
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Riba A, Bosia C, El Baroudi M, Ollino L, Caselle M. A combination of transcriptional and microRNA regulation improves the stability of the relative concentrations of target genes. PLoS Comput Biol 2014; 10:e1003490. [PMID: 24586138 PMCID: PMC3937125 DOI: 10.1371/journal.pcbi.1003490] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 12/18/2013] [Indexed: 01/01/2023] Open
Abstract
It is well known that, under suitable conditions, microRNAs are able to fine tune the relative concentration of their targets to any desired value. We show that this function is particularly effective when one of the targets is a Transcription Factor (TF) which regulates the other targets. This combination defines a new class of feed-forward loops (FFLs) in which the microRNA plays the role of master regulator. Using both deterministic and stochastic equations, we show that these FFLs are indeed able not only to fine-tune the TF/target ratio to any desired value as a function of the miRNA concentration but also, thanks to the peculiar topology of the circuit, to ensure the stability of this ratio against stochastic fluctuations. These two effects are due to the interplay between the direct transcriptional regulation and the indirect TF/Target interaction due to competition of TF and target for miRNA binding (the so called "sponge effect"). We then perform a genome wide search of these FFLs in the human regulatory network and show that they are characterized by a very peculiar enrichment pattern. In particular, they are strongly enriched in all the situations in which the TF and its target have to be precisely kept at the same concentration notwithstanding the environmental noise. As an example we discuss the FFL involving E2F1 as Transcription Factor, RB1 as target and miR-17 family as master regulator. These FFLs ensure a tight control of the E2F/RB ratio which in turns ensures the stability of the transition from the G0/G1 to the S phase in quiescent cells.
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Affiliation(s)
- Andrea Riba
- Department of Physics and INFN, University of Torino, Torino, Italy
- * E-mail: (AR); (CB)
| | - Carla Bosia
- Department of Physics and INFN, University of Torino, Torino, Italy
- * E-mail: (AR); (CB)
| | - Mariama El Baroudi
- National Research Council (CNR), Institute of Informatics and Telematics (IIT) and Institute of Clinical Physiology (IFC), Laboratory for Integrative System Medicine (LISM), Pisa, Italy
| | - Laura Ollino
- Department of Physics and INFN, University of Torino, Torino, Italy
| | - Michele Caselle
- Department of Physics and INFN, University of Torino, Torino, Italy
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Bosia C, Osella M, Baroudi ME, Corà D, Caselle M. Gene autoregulation via intronic microRNAs and its functions. BMC Syst Biol 2012; 6:131. [PMID: 23050836 PMCID: PMC3534558 DOI: 10.1186/1752-0509-6-131] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 10/01/2012] [Indexed: 12/05/2022]
Abstract
Background MicroRNAs, post-transcriptional repressors of gene expression, play a pivotal role in gene regulatory networks. They are involved in core cellular processes and their dysregulation is associated to a broad range of human diseases. This paper focus on a minimal microRNA-mediated regulatory circuit, in which a protein-coding gene (host gene) is targeted by a microRNA located inside one of its introns. Results Autoregulation via intronic microRNAs is widespread in the human regulatory network, as confirmed by our bioinformatic analysis, and can perform several regulatory tasks despite its simple topology. Our analysis, based on analytical calculations and simulations, indicates that this circuitry alters the dynamics of the host gene expression, can induce complex responses implementing adaptation and Weber’s law, and efficiently filters fluctuations propagating from the upstream network to the host gene. A fine-tuning of the circuit parameters can optimize each of these functions. Interestingly, they are all related to gene expression homeostasis, in agreement with the increasing evidence suggesting a role of microRNA regulation in conferring robustness to biological processes. In addition to model analysis, we present a list of bioinformatically predicted candidate circuits in human for future experimental tests. Conclusions The results presented here suggest a potentially relevant functional role for negative self-regulation via intronic microRNAs, in particular as a homeostatic control mechanism of gene expression. Moreover, the map of circuit functions in terms of experimentally measurable parameters, resulting from our analysis, can be a useful guideline for possible applications in synthetic biology.
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Affiliation(s)
- Carla Bosia
- Human Genetics Foudation, V Nizza 52, Torino I-10126, Italy.
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El Baroudi M, Corà D, Bosia C, Osella M, Caselle M. A curated database of miRNA mediated feed-forward loops involving MYC as master regulator. PLoS One 2011; 6:e14742. [PMID: 21390222 PMCID: PMC3048388 DOI: 10.1371/journal.pone.0014742] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Accepted: 02/01/2011] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The MYC transcription factors are known to be involved in the biology of many human cancer types. But little is known about the Myc/microRNAs cooperation in the regulation of genes at the transcriptional and post-transcriptional level. METHODOLOGY/PRINCIPAL FINDINGS Employing independent databases with experimentally validated data, we identified several mixed microRNA/Transcription Factor Feed-Forward Loops regulated by Myc and characterized completely by experimentally supported regulatory interactions, in human. We then studied the statistical and functional properties of these circuits and discussed in more detail a few interesting examples involving E2F1, PTEN, RB1 and VEGF. CONCLUSIONS/SIGNIFICANCE We have assembled and characterized a catalogue of human mixed Transcription Factor/microRNA Feed-Forward Loops, having Myc as master regulator and completely defined by experimentally verified regulatory interactions.
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Affiliation(s)
- Mariama El Baroudi
- Department of Theoretical Physics, University of Turin and National Institute for Nuclear Physics, Turin, Italy
- Center for Complex Systems in Molecular Biology and Medicine, University of Turin, Turin, Italy
| | - Davide Corà
- Center for Complex Systems in Molecular Biology and Medicine, University of Turin, Turin, Italy
- Systems Biology Lab, Institute for Cancer Research and Treatment (IRCC), School of Medicine, University of Turin, Turin, Italy
| | - Carla Bosia
- Department of Theoretical Physics, University of Turin and National Institute for Nuclear Physics, Turin, Italy
- Center for Complex Systems in Molecular Biology and Medicine, University of Turin, Turin, Italy
| | - Matteo Osella
- Department of Theoretical Physics, University of Turin and National Institute for Nuclear Physics, Turin, Italy
- Center for Complex Systems in Molecular Biology and Medicine, University of Turin, Turin, Italy
| | - Michele Caselle
- Department of Theoretical Physics, University of Turin and National Institute for Nuclear Physics, Turin, Italy
- Center for Complex Systems in Molecular Biology and Medicine, University of Turin, Turin, Italy
- * E-mail:
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