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Abu-Toamih-Atamni HJ, Lone IM, Binenbaum I, Mott R, Pilalis E, Chatziioannou A, Iraqi FA. Mapping novel QTL and fine mapping of previously identified QTL associated with glucose tolerance using the collaborative cross mice. Mamm Genome 2024; 35:31-55. [PMID: 37978084 DOI: 10.1007/s00335-023-10025-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 10/08/2023] [Indexed: 11/19/2023]
Abstract
A chronic metabolic illness, type 2 diabetes (T2D) is a polygenic and multifactorial complicated disease. With an estimated 463 million persons aged 20 to 79 having diabetes, the number is expected to rise to 700 million by 2045, creating a significant worldwide health burden. Polygenic variants of diabetes are influenced by environmental variables. T2D is regarded as a silent illness that can advance for years before being diagnosed. Finding genetic markers for T2D and metabolic syndrome in groups with similar environmental exposure is therefore essential to understanding the mechanism of such complex characteristic illnesses. So herein, we demonstrated the exclusive use of the collaborative cross (CC) mouse reference population to identify novel quantitative trait loci (QTL) and, subsequently, suggested genes associated with host glucose tolerance in response to a high-fat diet. In this study, we used 539 mice from 60 different CC lines. The diabetogenic effect in response to high-fat dietary challenge was measured by the three-hour intraperitoneal glucose tolerance test (IPGTT) test after 12 weeks of dietary challenge. Data analysis was performed using a statistical software package IBM SPSS Statistic 23. Afterward, blood glucose concentration at the specific and between different time points during the IPGTT assay and the total area under the curve (AUC0-180) of the glucose clearance was computed and utilized as a marker for the presence and severity of diabetes. The observed AUC0-180 averages for males and females were 51,267.5 and 36,537.5 mg/dL, respectively, representing a 1.4-fold difference in favor of females with lower AUC0-180 indicating adequate glucose clearance. The AUC0-180 mean differences between the sexes within each specific CC line varied widely within the CC population. A total of 46 QTL associated with the different studied phenotypes, designated as T2DSL and its number, for Type 2 Diabetes Specific Locus and its number, were identified during our study, among which 19 QTL were not previously mapped. The genomic interval of the remaining 27 QTL previously reported, were fine mapped in our study. The genomic positions of 40 of the mapped QTL overlapped (clustered) on 11 different peaks or close genomic positions, while the remaining 6 QTL were unique. Further, our study showed a complex pattern of haplotype effects of the founders, with the wild-derived strains (mainly PWK) playing a significant role in the increase of AUC values.
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Affiliation(s)
- Hanifa J Abu-Toamih-Atamni
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel-Aviv University, Ramat Aviv, 69978, Tel-Aviv, Israel
| | - Iqbal M Lone
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel-Aviv University, Ramat Aviv, 69978, Tel-Aviv, Israel
| | - Ilona Binenbaum
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, Soranou Ephessiou Str, 11527, Athens, Greece
- Division of Pediatric Hematology-Oncology, First Department of Pediatrics, National and Kapodistrian University of Athens, Athens, Greece
| | - Richard Mott
- Department of Genetics, University College of London, London, UK
| | | | - Aristotelis Chatziioannou
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, Soranou Ephessiou Str, 11527, Athens, Greece
- e-NIOS Applications PC, 196 Syggrou Ave., 17671, Kallithea, Greece
| | - Fuad A Iraqi
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel-Aviv University, Ramat Aviv, 69978, Tel-Aviv, Israel.
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Koutsandreas T, Felden B, Chevet E, Chatziioannou A. Protein homeostasis imprinting across evolution. NAR Genom Bioinform 2024; 6:lqae014. [PMID: 38486886 PMCID: PMC10939379 DOI: 10.1093/nargab/lqae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 10/07/2023] [Accepted: 01/24/2024] [Indexed: 03/17/2024] Open
Abstract
Protein homeostasis (a.k.a. proteostasis) is associated with the primary functions of life, and therefore with evolution. However, it is unclear how cellular proteostasis machines have evolved to adjust protein biogenesis needs to environmental constraints. Herein, we describe a novel computational approach, based on semantic network analysis, to evaluate proteostasis plasticity during evolution. We show that the molecular components of the proteostasis network (PN) are reliable metrics to deconvolute the life forms into Archaea, Bacteria and Eukarya and to assess the evolution rates among species. Semantic graphs were used as new criteria to evaluate PN complexity in 93 Eukarya, 250 Bacteria and 62 Archaea, thus representing a novel strategy for taxonomic classification, which provided information about species divergence. Kingdom-specific PN components were identified, suggesting that PN complexity may correlate with evolution. We found that the gains that occurred throughout PN evolution revealed a dichotomy within both the PN conserved modules and within kingdom-specific modules. Additionally, many of these components contribute to the evolutionary imprinting of other conserved mechanisms. Finally, the current study suggests a new way to exploit the genomic annotation of biomedical ontologies, deriving new knowledge from the semantic comparison of different biological systems.
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Affiliation(s)
- Thodoris Koutsandreas
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- e-NIOS Applications PC, Kallithea-Athens, Greece
| | - Brice Felden
- University of Rennes, INSERM U1230, Rennes, France
| | - Eric Chevet
- INSERM U1242, University of Rennes, Rennes, France
- Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France
| | - Aristotelis Chatziioannou
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- e-NIOS Applications PC, Kallithea-Athens, Greece
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Obacz J, Archambeau J, Lafont E, Nivet M, Martin S, Aubry M, Voutetakis K, Pineau R, Boniface R, Sicari D, Pelizzari-Raymundo D, Ghukasyan G, McGrath E, Vlachavas EI, Le Gallo M, Le Reste PJ, Barroso K, Fainsod-Levi T, Obiedat A, Granot Z, Tirosh B, Samal J, Pandit A, Négroni L, Soriano N, Monnier A, Mosser J, Chatziioannou A, Quillien V, Chevet E, Avril T. IRE1 endoribonuclease signaling promotes myeloid cell infiltration in glioblastoma. Neuro Oncol 2023:noad256. [PMID: 38153426 DOI: 10.1093/neuonc/noad256] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Indexed: 12/29/2023] Open
Abstract
BACKGROUND Intrinsic or environmental stresses trigger the accumulation of improperly folded proteins in the endoplasmic reticulum (ER), leading to ER stress. To cope with this, cells have evolved an adaptive mechanism named the unfolded protein response (UPR) which is hijacked by tumor cells to develop malignant features. Glioblastoma (GB), the most aggressive and lethal primary brain tumor, relies on UPR to sustain growth. We recently showed that IRE1 alpha (referred to IRE1 hereafter), one of the UPR transducers, promotes GB invasion, angiogenesis and infiltration by macrophage. Hence, high tumor IRE1 activity in tumor cells predicts worse outcome. Herein, we characterized the IRE1-dependent signaling that shapes the immune microenvironment towards monocytes/macrophages and neutrophils. METHODS We used human and mouse cellular models in which IRE1 was genetically or pharmacologically invalidated and which were tested in vivo. Publicly available datasets from GB patients were also analyzed to confirm our findings. RESULTS We showed that IRE1 signaling, through both the transcription factor XBP1s and the regulated IRE1-dependent decay (RIDD) controls the expression of the ubiquitin-conjugating E2 enzyme UBE2D3. In turn, UBE2D3 activates the NFκB pathway, ensuing chemokine production and myeloid infiltration in tumors. CONCLUSION Our work identifies a novel IRE1/UBE2D3 pro-inflammatory axis that plays an instrumental role in GB immune regulation.
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Affiliation(s)
- Joanna Obacz
- INSERM U1242, Rennes, France
- Centre Eugène Marquis, Rennes
| | | | - Elodie Lafont
- INSERM U1242, Rennes, France
- Centre Eugène Marquis, Rennes
| | - Manon Nivet
- INSERM U1242, Rennes, France
- Centre Eugène Marquis, Rennes
| | - Sophie Martin
- INSERM U1242, Rennes, France
- Centre Eugène Marquis, Rennes
| | | | | | - Raphael Pineau
- INSERM U1242, Rennes, France
- Centre Eugène Marquis, Rennes
| | | | - Daria Sicari
- INSERM U1242, Rennes, France
- Centre Eugène Marquis, Rennes
| | | | | | - Eoghan McGrath
- INSERM U1242, Rennes, France
- Centre Eugène Marquis, Rennes
| | | | | | - Pierre Jean Le Reste
- INSERM U1242, Rennes, France
- Centre Eugène Marquis, Rennes
- Hospital of St Malo, France
| | - Kim Barroso
- IGBMC, Illkirch, France
- CNRS UMR7104, Illkirch
- INSERM U1258, Illkirch
- Université de Strasbourg, France
| | - Tanya Fainsod-Levi
- Department of Developmental Biology and Cancer Research, Hebrew University of Jerusalem, Israel
| | | | - Zvi Granot
- Department of Developmental Biology and Cancer Research, Hebrew University of Jerusalem, Israel
| | | | | | | | - Luc Négroni
- IGBMC, Illkirch, France
- CNRS UMR7104, Illkirch
- INSERM U1258, Illkirch
- Université de Strasbourg, France
| | | | | | | | | | | | - Eric Chevet
- INSERM U1242, Rennes, France
- Centre Eugène Marquis, Rennes
| | - Tony Avril
- INSERM U1242, Rennes, France
- Centre Eugène Marquis, Rennes
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4
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Batsi Y, Antonopoulou G, Fotopoulou T, Koumaki K, Kritsi E, Potamitis C, Goulielmaki M, Skarmalioraki S, Papalouka C, Poulou-Sidiropoulou E, Kosmidou V, Douna S, Vidali MS, Gkotsi EF, Chatziioannou A, Souliotis VL, Pletsa V, Papadodima O, Zoumpourlis V, Georgiadis P, Zervou M, Pintzas A, Kostas ID. Design and Synthesis of Novel 2-Acetamido, 6-Carboxamide Substituted Benzothiazoles as Potential BRAFV600E Inhibitors - In vitro Evaluation of their Antiproliferative Activity. ChemMedChem 2023; 18:e202300322. [PMID: 37792577 DOI: 10.1002/cmdc.202300322] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 10/02/2023] [Accepted: 10/03/2023] [Indexed: 10/06/2023]
Abstract
The oncogenic BRAFV600E kinase leads to abnormal activation of the MAPK signaling pathway and thus, uncontrolled cellular proliferation and cancer development. Based on our previous virtual screening studies which issued 2-acetamido-1,3 benzothiazole-6-carboxamide scaffold as active pharmacophore displaying selectivity against the mutated BRAF, eleven new substituted benzothiazole derivatives were designed and synthesized by coupling of 2-acetamidobenzo[d]thiazole-6-carboxylic acid with the appropriate amines in an effort to provide even more efficient inhibitors and tackle drug resistance often developed during cancer treatment. All derived compounds bore the benzothiazole scaffold substituted at position-2 by an acetamido moiety and at position-6 by a carboxamide functionality, the NH moiety of which was further linked through an alkylene linker to a sulfonamido (or amino) aryl (or alkyl) functionality or a phenylene linker to a sulfonamido aromatic (or non-aromatic) terminal pharmacophore in the order -C6 H4 -NHSO2 -R or reversely -C6 H4 -SO2 N(H)-R. These analogs were subsequently biologically evaluated as potential BRAFV600E inhibitors and antiproliferative agents in several colorectal cancer and melanoma cell lines. In all assays applied, one analog, namely 2-acetamido-N-[3-(pyridin-2-ylamino)propyl]benzo[d]thiazole-6-carboxamide (22), provided promising results in view of its use in drug development.
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Affiliation(s)
- Yakinthi Batsi
- Institute of Chemical Biology, National Hellenic Research Foundation, Vas. Constantinou Ave. 48, 11635, Athens, Greece
| | - Georgia Antonopoulou
- Institute of Chemical Biology, National Hellenic Research Foundation, Vas. Constantinou Ave. 48, 11635, Athens, Greece
| | - Theano Fotopoulou
- Institute of Chemical Biology, National Hellenic Research Foundation, Vas. Constantinou Ave. 48, 11635, Athens, Greece
| | - Kassandra Koumaki
- Institute of Chemical Biology, National Hellenic Research Foundation, Vas. Constantinou Ave. 48, 11635, Athens, Greece
| | - Eftichia Kritsi
- Institute of Chemical Biology, National Hellenic Research Foundation, Vas. Constantinou Ave. 48, 11635, Athens, Greece
| | - Constantinos Potamitis
- Institute of Chemical Biology, National Hellenic Research Foundation, Vas. Constantinou Ave. 48, 11635, Athens, Greece
| | - Maria Goulielmaki
- Institute of Chemical Biology, National Hellenic Research Foundation, Vas. Constantinou Ave. 48, 11635, Athens, Greece
| | - Salomi Skarmalioraki
- Institute of Chemical Biology, National Hellenic Research Foundation, Vas. Constantinou Ave. 48, 11635, Athens, Greece
| | - Chara Papalouka
- Institute of Chemical Biology, National Hellenic Research Foundation, Vas. Constantinou Ave. 48, 11635, Athens, Greece
| | - Eleni Poulou-Sidiropoulou
- Institute of Chemical Biology, National Hellenic Research Foundation, Vas. Constantinou Ave. 48, 11635, Athens, Greece
| | - Vivian Kosmidou
- Institute of Chemical Biology, National Hellenic Research Foundation, Vas. Constantinou Ave. 48, 11635, Athens, Greece
| | - Stavroula Douna
- Institute of Chemical Biology, National Hellenic Research Foundation, Vas. Constantinou Ave. 48, 11635, Athens, Greece
| | - Maria-Sofia Vidali
- Institute of Chemical Biology, National Hellenic Research Foundation, Vas. Constantinou Ave. 48, 11635, Athens, Greece
| | - Eleni-Fani Gkotsi
- Institute of Chemical Biology, National Hellenic Research Foundation, Vas. Constantinou Ave. 48, 11635, Athens, Greece
| | - Aristotelis Chatziioannou
- Institute of Chemical Biology, National Hellenic Research Foundation, Vas. Constantinou Ave. 48, 11635, Athens, Greece
| | - Vassilis L Souliotis
- Institute of Chemical Biology, National Hellenic Research Foundation, Vas. Constantinou Ave. 48, 11635, Athens, Greece
| | - Vasiliki Pletsa
- Institute of Chemical Biology, National Hellenic Research Foundation, Vas. Constantinou Ave. 48, 11635, Athens, Greece
| | - Olga Papadodima
- Institute of Chemical Biology, National Hellenic Research Foundation, Vas. Constantinou Ave. 48, 11635, Athens, Greece
| | - Vassilis Zoumpourlis
- Institute of Chemical Biology, National Hellenic Research Foundation, Vas. Constantinou Ave. 48, 11635, Athens, Greece
| | - Panagiotis Georgiadis
- Institute of Chemical Biology, National Hellenic Research Foundation, Vas. Constantinou Ave. 48, 11635, Athens, Greece
| | - Maria Zervou
- Institute of Chemical Biology, National Hellenic Research Foundation, Vas. Constantinou Ave. 48, 11635, Athens, Greece
| | - Alexander Pintzas
- Institute of Chemical Biology, National Hellenic Research Foundation, Vas. Constantinou Ave. 48, 11635, Athens, Greece
| | - Ioannis D Kostas
- Institute of Chemical Biology, National Hellenic Research Foundation, Vas. Constantinou Ave. 48, 11635, Athens, Greece
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5
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Pelizzari-Raymundo D, Doultsinos D, Pineau R, Sauzay C, Koutsandreas T, Langlais T, Carlesso A, Gkotsi E, Negroni L, Avril T, Chatziioannou A, Chevet E, Eriksson LA, Guillory X. A novel IRE1 kinase inhibitor for adjuvant glioblastoma treatment. iScience 2023; 26:106687. [PMID: 37216120 PMCID: PMC10192531 DOI: 10.1016/j.isci.2023.106687] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 12/01/2022] [Revised: 02/27/2023] [Accepted: 04/13/2023] [Indexed: 05/24/2023] Open
Abstract
Inositol-requiring enzyme 1 (IRE1) is a major mediator of the unfolded protein response (UPR), which is activated upon endoplasmic reticulum (ER) stress. Tumor cells experience ER stress due to adverse microenvironmental cues, a stress overcome by relying on IRE1 signaling as an adaptive mechanism. Herein, we report the discovery of structurally new IRE1 inhibitors identified through the structural exploration of its kinase domain. Characterization in in vitro and in cellular models showed that they inhibit IRE1 signaling and sensitize glioblastoma (GB) cells to the standard chemotherapeutic, temozolomide (TMZ). Finally, we demonstrate that one of these inhibitors, Z4P, permeates the blood-brain barrier (BBB), inhibits GB growth, and prevents relapse in vivo when administered together with TMZ. The hit compound disclosed herein satisfies an unmet need for targeted, non-toxic IRE1 inhibitors and our results support the attractiveness of IRE1 as an adjuvant therapeutic target in GB.
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Affiliation(s)
- Diana Pelizzari-Raymundo
- INSERM U1242, Université de Rennes, Rennes, France
- Centre de Lutte contre le Cancer Eugène Marquis, Rennes, France
| | - Dimitrios Doultsinos
- INSERM U1242, Université de Rennes, Rennes, France
- Centre de Lutte contre le Cancer Eugène Marquis, Rennes, France
| | - Raphael Pineau
- INSERM U1242, Université de Rennes, Rennes, France
- Centre de Lutte contre le Cancer Eugène Marquis, Rennes, France
| | - Chloé Sauzay
- INSERM U1242, Université de Rennes, Rennes, France
- Centre de Lutte contre le Cancer Eugène Marquis, Rennes, France
| | - Thodoris Koutsandreas
- e-NIOS PC, Kallithea-Athens, Greece
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | | | - Antonio Carlesso
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
| | - Elena Gkotsi
- e-NIOS PC, Kallithea-Athens, Greece
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Luc Negroni
- Proteomics platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)/INSERM U964/CNRS UMR 7104/Université de Strasbourg, Illkirch, France
| | - Tony Avril
- INSERM U1242, Université de Rennes, Rennes, France
- Centre de Lutte contre le Cancer Eugène Marquis, Rennes, France
| | - Aristotelis Chatziioannou
- e-NIOS PC, Kallithea-Athens, Greece
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Eric Chevet
- INSERM U1242, Université de Rennes, Rennes, France
- Centre de Lutte contre le Cancer Eugène Marquis, Rennes, France
| | - Leif A. Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
| | - Xavier Guillory
- INSERM U1242, Université de Rennes, Rennes, France
- Centre de Lutte contre le Cancer Eugène Marquis, Rennes, France
- Univ Rennes, CNRS, ISCR – UMR 6226, 35000 Rennes, France
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6
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Ricordel C, Chaillot L, Vlachavas EI, Logotheti M, Jouannic A, Desvallees T, Lecuyer G, Aubry M, Kontogianni G, Mastrokalou C, Jouan F, Jarry U, Corre R, Le Guen Y, Guillaudeux T, Lena H, Chatziioannou A, Pedeux R. Genomic characteristics and clinical significance of CD56+ circulating tumor cells in small cell lung cancer. Sci Rep 2023; 13:3626. [PMID: 36869231 PMCID: PMC9984363 DOI: 10.1038/s41598-023-30536-9] [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] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 02/24/2023] [Indexed: 03/05/2023] Open
Abstract
Circulating tumor cells (CTC) have been studied in various solid tumors but clinical utility of CTC in small cell lung cancer (SCLC) remains unclear. The aim of the CTC-CPC study was to develop an EpCAM-independent CTC isolation method allowing isolation of a broader range of living CTC from SCLC and decipher their genomic and biological characteristics. CTC-CPC is a monocentric prospective non-interventional study including treatment-naïve newly diagnosed SCLC. CD56+ CTC were isolated from whole blood samples, at diagnosis and relapse after first-line treatment and submitted to whole-exome-sequencing (WES). Phenotypic study confirms tumor lineage and tumorigenic properties of isolated cells for the 4 patients analyzed with WES. WES of CD56+ CTC and matched tumor biopsy reveal genomic alteration frequently impaired in SCLC. At diagnosis CD56+ CTC were characterized by a high mutation load, a distinct mutational profile and a unique genomic signature, compared to match tumors biopsies. In addition to classical pathways altered in SCLC, we found new biological processes specifically affected in CD56+ CTC at diagnosis. High numeration of CD56+ CTC (> 7/ml) at diagnosis was associated with ES-SCLC. Comparing CD56+ CTC isolated at diagnosis and relapse, we identify differentially altered oncogenic pathways (e.g. DLL3 or MAPK pathway). We report a versatile method of CD56+ CTC detection in SCLC. Numeration of CD56+ CTC at diagnosis is correlated with disease extension. Isolated CD56+ CTC are tumorigenic and show a distinct mutational profile. We report a minimal gene set as a unique signature of CD56+ CTC and identify new affected biological pathways enriched in EpCAM-independent isolated CTC in SCLC.
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Affiliation(s)
- Charles Ricordel
- INSERM, OSS (Oncogenesis Stress Signaling), UMR_S 1242, CLCC Eugene Marquis, Univ Rennes 1, 35000, Rennes, France.
- Service de Pneumologie, Hôpital Pontchaillou, CHU Rennes, 2 Rue Henri Le Guilloux, 35033, Rennes, France.
| | - L Chaillot
- INSERM, OSS (Oncogenesis Stress Signaling), UMR_S 1242, CLCC Eugene Marquis, Univ Rennes 1, 35000, Rennes, France
| | - E I Vlachavas
- e-NIOS PC, Kallithea-Athens, Greece
- Division of Molecular Genome Analysis (B050), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | | | - A Jouannic
- INSERM, OSS (Oncogenesis Stress Signaling), UMR_S 1242, CLCC Eugene Marquis, Univ Rennes 1, 35000, Rennes, France
| | - T Desvallees
- CNRS, INSERM, BIOSIT UAR 3480, US_S 018, Oncotrial, Univ Rennes, 35000, Rennes, France
- Unité De Pharmacologie Préclinique, Biotrial Pharmacology, Rennes, France
| | - G Lecuyer
- INSERM, OSS (Oncogenesis Stress Signaling), UMR_S 1242, CLCC Eugene Marquis, Univ Rennes 1, 35000, Rennes, France
| | - M Aubry
- INSERM, OSS (Oncogenesis Stress Signaling), UMR_S 1242, CLCC Eugene Marquis, Univ Rennes 1, 35000, Rennes, France
| | - G Kontogianni
- Centre of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou Street, 11527, Athens, Greece
| | | | - F Jouan
- INSERM, OSS (Oncogenesis Stress Signaling), UMR_S 1242, CLCC Eugene Marquis, Univ Rennes 1, 35000, Rennes, France
| | - U Jarry
- CNRS, INSERM, BIOSIT UAR 3480, US_S 018, Oncotrial, Univ Rennes, 35000, Rennes, France
- Unité De Pharmacologie Préclinique, Biotrial Pharmacology, Rennes, France
| | - R Corre
- Service de Pneumologie, Hôpital Pontchaillou, CHU Rennes, 2 Rue Henri Le Guilloux, 35033, Rennes, France
| | - Y Le Guen
- Service de Pneumologie, Hôpital Pontchaillou, CHU Rennes, 2 Rue Henri Le Guilloux, 35033, Rennes, France
| | - T Guillaudeux
- INSERM, OSS (Oncogenesis Stress Signaling), UMR_S 1242, CLCC Eugene Marquis, Univ Rennes 1, 35000, Rennes, France
- CNRS, INSERM, BIOSIT UAR 3480, US_S 018, Oncotrial, Univ Rennes, 35000, Rennes, France
| | - H Lena
- INSERM, OSS (Oncogenesis Stress Signaling), UMR_S 1242, CLCC Eugene Marquis, Univ Rennes 1, 35000, Rennes, France
- Service de Pneumologie, Hôpital Pontchaillou, CHU Rennes, 2 Rue Henri Le Guilloux, 35033, Rennes, France
| | - A Chatziioannou
- e-NIOS PC, Kallithea-Athens, Greece
- Centre of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou Street, 11527, Athens, Greece
| | - Rémy Pedeux
- INSERM, OSS (Oncogenesis Stress Signaling), UMR_S 1242, CLCC Eugene Marquis, Univ Rennes 1, 35000, Rennes, France.
- CNRS, INSERM, BIOSIT UAR 3480, US_S 018, Oncotrial, Univ Rennes, 35000, Rennes, France.
- CLCC Eugène Marquis, INSERM U1242-OSS, Université Rennes 1, Rue Bataille Flandres Dunkerque, 35042, Rennes, France.
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7
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Meligova AK, Siakouli D, Stasinopoulou S, Xenopoulou DS, Zoumpouli M, Ganou V, Gkotsi EF, Chatziioannou A, Papadodima O, Pilalis E, Alexis MN, Mitsiou DJ. ERβ1 Sensitizes and ERβ2 Desensitizes ERα-Positive Breast Cancer Cells to the Inhibitory Effects of Tamoxifen, Fulvestrant and Their Combination with All-Trans Retinoic Acid. Int J Mol Sci 2023; 24:ijms24043747. [PMID: 36835157 PMCID: PMC9959521 DOI: 10.3390/ijms24043747] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/07/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023] Open
Abstract
Adjuvant endocrine therapy (AET) is the treatment of choice for early-stage estrogen receptor alpha (ERα)-positive breast cancer (BC). However, almost 40% of tamoxifen-treated cases display no response or a partial response to AET, thus increasing the need for new treatment options and strong predictors of the therapeutic response of patients at high risk of relapse. In addition to ERα, BC research has focused on ERβ1 and ERβ2 (isoforms of ERβ), the second ER isotype. At present, the impact of ERβ isoforms on ERα-positive BC prognosis and treatment remains elusive. In the present study, we established clones of MCF7 cells constitutively expressing human ERβ1 or ERβ2 and investigated their role in the response of MCF7 cells to antiestrogens [4-hydroxytamoxifen (OHΤ) and fulvestrant (ICI182,780)] and retinoids [all-trans retinoic acid (ATRA)]. We show that, compared to MCF7 cells, MCF7-ERβ1 and MCF7-ERβ2 cells were sensitized and desensitized, respectively, to the antiproliferative effect of the antiestrogens, ATRA and their combination and to the cytocidal effect of the combination of OHT and ATRA. Analysis of the global transcriptional changes upon OHT-ATRA combinatorial treatment revealed uniquely regulated genes associated with anticancer effects in MCF7-ERβ1 cells and cancer-promoting effects in MCF7-ERβ2 cells. Our data are favorable to ERβ1 being a marker of responsiveness and ERβ2 being a marker of resistance of MCF7 cells to antiestrogens alone and in combination with ATRA.
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Affiliation(s)
- Aggeliki K. Meligova
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Dimitra Siakouli
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Sotiria Stasinopoulou
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Despoina S. Xenopoulou
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Maria Zoumpouli
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Vassiliki Ganou
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Eleni-Fani Gkotsi
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Aristotelis Chatziioannou
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Olga Papadodima
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | | | - Michael N. Alexis
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
- Correspondence: (M.N.A.); (D.J.M.)
| | - Dimitra J. Mitsiou
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
- Correspondence: (M.N.A.); (D.J.M.)
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8
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Lhomond S, Avril T, Dejeans N, Voutetakis K, Doultsinos D, McMahon M, Pineau R, Obacz J, Papadodima O, Jouan F, Bourien H, Logotheti M, Jégou G, Pallares‐Lupon N, Schmit K, Le Reste P, Etcheverry A, Mosser J, Barroso K, Vauléon E, Maurel M, Samali A, Patterson JB, Pluquet O, Hetz C, Quillien V, Chatziioannou A, Chevet E. Dual IRE1 RNase functions dictate glioblastoma development. EMBO Mol Med 2023; 15:e16731. [PMID: 36752056 PMCID: PMC9906329 DOI: 10.15252/emmm.202216731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/06/2022] [Indexed: 02/09/2023] Open
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9
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Kontogianni G, Voutetakis K, Piroti G, Kypreou K, Stefanaki I, Vlachavas EI, Pilalis E, Stratigos A, Chatziioannou A, Papadodima O. A Comprehensive Analysis of Cutaneous Melanoma Patients in Greece Based on Multi-Omic Data. Cancers (Basel) 2023; 15:cancers15030815. [PMID: 36765773 PMCID: PMC9913631 DOI: 10.3390/cancers15030815] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 02/01/2023] Open
Abstract
Cutaneous melanoma (CM) is the most aggressive type of skin cancer, and it is characterised by high mutational load and heterogeneity. In this study, we aimed to analyse the genomic and transcriptomic profile of primary melanomas from forty-six Formalin-Fixed, Paraffin-Embedded (FFPE) tissues from Greek patients. Molecular analysis for both germline and somatic variations was performed in genomic DNA from peripheral blood and melanoma samples, respectively, exploiting whole exome and targeted sequencing, and transcriptomic analysis. Detailed clinicopathological data were also included in our analyses and previously reported associations with specific mutations were recognised. Most analysed samples (43/46) were found to harbour at least one clinically actionable somatic variant. A subset of samples was profiled at the transcriptomic level, and it was shown that specific melanoma phenotypic states could be inferred from bulk RNA isolated from FFPE primary melanoma tissue. Integrative bioinformatics analyses, including variant prioritisation, differential gene expression analysis, and functional and gene set enrichment analysis by group and per sample, were conducted and molecular circuits that are implicated in melanoma cell programmes were highlighted. Integration of mutational and transcriptomic data in CM characterisation could shed light on genes and pathways that support the maintenance of phenotypic states encrypted into heterogeneous primary tumours.
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Affiliation(s)
- Georgia Kontogianni
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
- Centre of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | | | - Georgia Piroti
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Katerina Kypreou
- 1st Department of Dermatology, Andreas Syggros Hospital, Medical School, National and Kapodistrian University of Athens, 16121 Athens, Greece
| | - Irene Stefanaki
- 1st Department of Dermatology, Andreas Syggros Hospital, Medical School, National and Kapodistrian University of Athens, 16121 Athens, Greece
| | | | | | - Alexander Stratigos
- 1st Department of Dermatology, Andreas Syggros Hospital, Medical School, National and Kapodistrian University of Athens, 16121 Athens, Greece
| | - Aristotelis Chatziioannou
- Centre of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
- e-NIOS Applications Private Company, 17671 Kallithea, Greece
- Correspondence: (A.C.); (O.P.); Tel.: +30-210-727-3721 (A.C. & O.P.)
| | - Olga Papadodima
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
- Correspondence: (A.C.); (O.P.); Tel.: +30-210-727-3721 (A.C. & O.P.)
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10
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Buocikova V, Tyciakova S, Pilalis E, Mastrokalou C, Urbanova M, Matuskova M, Demkova L, Medova V, Longhin EM, Rundén-Pran E, Dusinska M, Rios-Mondragon I, Cimpan MR, Gabelova A, Soltysova A, Smolkova B, Chatziioannou A. Decitabine-induced DNA methylation-mediated transcriptomic reprogramming in human breast cancer cell lines; the impact of DCK overexpression. Front Pharmacol 2022; 13:991751. [PMID: 36278182 PMCID: PMC9585938 DOI: 10.3389/fphar.2022.991751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Decitabine (DAC), a DNA methyltransferase (DNMT) inhibitor, is tested in combination with conventional anticancer drugs as a treatment option for various solid tumors. Although epigenome modulation provides a promising avenue in treating resistant cancer types, more studies are required to evaluate its safety and ability to normalize the aberrant transcriptional profiles. As deoxycytidine kinase (DCK)-mediated phosphorylation is a rate-limiting step in DAC metabolic activation, we hypothesized that its intracellular overexpression could potentiate DAC’s effect on cell methylome and thus increase its therapeutic efficacy. Therefore, two breast cancer cell lines, JIMT-1 and T-47D, differing in their molecular characteristics, were transfected with a DCK expression vector and exposed to low-dose DAC (approximately IC20). Although transfection resulted in a significant DCK expression increase, further enhanced by DAC exposure, no transfection-induced changes were found at the global DNA methylation level or in cell viability. In parallel, an integrative approach was applied to decipher DAC-induced, methylation-mediated, transcriptomic reprogramming. Besides large-scale hypomethylation, accompanied by up-regulation of gene expression across the entire genome, DAC also induced hypermethylation and down-regulation of numerous genes in both cell lines. Interestingly, TET1 and TET2 expression halved in JIMT-1 cells after DAC exposure, while DNMTs’ changes were not significant. The protein digestion and absorption pathway, containing numerous collagen and solute carrier genes, ranking second among membrane transport proteins, was the top enriched pathway in both cell lines when hypomethylated and up-regulated genes were considered. Moreover, the calcium signaling pathway, playing a significant role in drug resistance, was among the top enriched in JIMT-1 cells. Although low-dose DAC demonstrated its ability to normalize the expression of tumor suppressors, several oncogenes were also up-regulated, a finding, that supports previously raised concerns regarding its broad reprogramming potential. Importantly, our research provides evidence about the involvement of active demethylation in DAC-mediated transcriptional reprogramming.
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Affiliation(s)
- Verona Buocikova
- Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Bratislava, Slovakia
| | - Silvia Tyciakova
- Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Bratislava, Slovakia
| | | | | | - Maria Urbanova
- Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Bratislava, Slovakia
| | - Miroslava Matuskova
- Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Bratislava, Slovakia
| | - Lucia Demkova
- Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Bratislava, Slovakia
| | - Veronika Medova
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | | | - Elise Rundén-Pran
- Health Effects Laboratory, NILU-Norwegian Institute for Air Research, Kjeller, Norway
| | - Maria Dusinska
- Health Effects Laboratory, NILU-Norwegian Institute for Air Research, Kjeller, Norway
| | | | | | - Alena Gabelova
- Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Bratislava, Slovakia
| | - Andrea Soltysova
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Bozena Smolkova
- Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Bratislava, Slovakia
- *Correspondence: Bozena Smolkova,
| | - Aristotelis Chatziioannou
- e-NIOS Applications P.C., Athens, Greece
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
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11
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Ricordel C, Chaillot L, Vlachavas EI, Logotheti M, Desvallees T, Aubry M, Kontogianni G, Mastrokalou C, Jouan F, Jarry U, Guillaudeux T, Léna H, Chatziioannou A, Pedeux R. EP16.02-004 Clinical Significance and Genomic Characteristics of CD56+ Circulating Tumor Cells in Small Cell Lung Carcinoma. J Thorac Oncol 2022. [DOI: 10.1016/j.jtho.2022.07.1035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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Almanza A, Mnich K, Blomme A, Robinson CM, Rodriguez-Blanco G, Kierszniowska S, McGrath EP, Le Gallo M, Pilalis E, Swinnen JV, Chatziioannou A, Chevet E, Gorman AM, Samali A. Regulated IRE1α-dependent decay (RIDD)-mediated reprograming of lipid metabolism in cancer. Nat Commun 2022; 13:2493. [PMID: 35524156 PMCID: PMC9076827 DOI: 10.1038/s41467-022-30159-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 04/05/2022] [Indexed: 12/13/2022] Open
Abstract
IRE1α is constitutively active in several cancers and can contribute to cancer progression. Activated IRE1α cleaves XBP1 mRNA, a key step in production of the transcription factor XBP1s. In addition, IRE1α cleaves select mRNAs through regulated IRE1α-dependent decay (RIDD). Accumulating evidence implicates IRE1α in the regulation of lipid metabolism. However, the roles of XBP1s and RIDD in this process remain ill-defined. In this study, transcriptome and lipidome profiling of triple negative breast cancer cells subjected to pharmacological inhibition of IRE1α reveals changes in lipid metabolism genes associated with accumulation of triacylglycerols (TAGs). We identify DGAT2 mRNA, encoding the rate-limiting enzyme in TAG biosynthesis, as a RIDD target. Inhibition of IRE1α, leads to DGAT2-dependent accumulation of TAGs in lipid droplets and sensitizes cells to nutritional stress, which is rescued by treatment with the DGAT2 inhibitor PF-06424439. Our results highlight the importance of IRE1α RIDD activity in reprograming cellular lipid metabolism. IRE1α cleaves several mRNAs upon accumulation of misfolded proteins. Here the authors show that active IRE1α cleaves DGAT2 mRNA encoding the rate-limiting enzyme in the synthesis of triacylglycerols, suggesting a role of IRE1α in reprogramming lipid metabolism in cancer cells.
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Affiliation(s)
- Aitor Almanza
- Apoptosis Research Centre, National University of Ireland, Galway, H91 W2TY, Ireland.,School of Biological and Chemical Sciences, National University of Ireland, Galway, H91 W2TY, Ireland
| | - Katarzyna Mnich
- Apoptosis Research Centre, National University of Ireland, Galway, H91 W2TY, Ireland.,School of Biological and Chemical Sciences, National University of Ireland, Galway, H91 W2TY, Ireland
| | - Arnaud Blomme
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Claire M Robinson
- Apoptosis Research Centre, National University of Ireland, Galway, H91 W2TY, Ireland.,School of Biological and Chemical Sciences, National University of Ireland, Galway, H91 W2TY, Ireland
| | | | | | - Eoghan P McGrath
- Apoptosis Research Centre, National University of Ireland, Galway, H91 W2TY, Ireland.,School of Biological and Chemical Sciences, National University of Ireland, Galway, H91 W2TY, Ireland
| | - Matthieu Le Gallo
- Inserm U1242, University of Rennes, Rennes, France.,Centre de lutte contre le cancer Eugène Marquis, Rennes, France
| | | | - Johannes V Swinnen
- Department of Oncology, Laboratory of Lipid Metabolism and Cancer, KU Leuven Cancer Institute, Leuven, Belgium
| | - Aristotelis Chatziioannou
- e-NIOS Applications PC, 25 Alexandros Pantou str., 17671, Kallithea, Greece.,Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou str, 11527, Athens, GR, Greece
| | - Eric Chevet
- Inserm U1242, University of Rennes, Rennes, France.,Centre de lutte contre le cancer Eugène Marquis, Rennes, France
| | - Adrienne M Gorman
- Apoptosis Research Centre, National University of Ireland, Galway, H91 W2TY, Ireland.,School of Biological and Chemical Sciences, National University of Ireland, Galway, H91 W2TY, Ireland
| | - Afshin Samali
- Apoptosis Research Centre, National University of Ireland, Galway, H91 W2TY, Ireland. .,School of Biological and Chemical Sciences, National University of Ireland, Galway, H91 W2TY, Ireland.
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13
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Buocikova V, Longhin EM, Pilalis E, Mastrokalou C, Miklikova S, Cihova M, Poturnayova A, Mackova K, Babelova A, Trnkova L, El Yamani N, Zheng C, Rios-Mondragon I, Labudova M, Csaderova L, Kuracinova KM, Makovicky P, Kucerova L, Matuskova M, Cimpan MR, Dusinska M, Babal P, Chatziioannou A, Gabelova A, Rundén-Pran E, Smolkova B. Decitabine potentiates efficacy of doxorubicin in a preclinical trastuzumab-resistant HER2-positive breast cancer models. Biomed Pharmacother 2022; 147:112662. [DOI: 10.1016/j.biopha.2022.112662] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/14/2022] [Accepted: 01/19/2022] [Indexed: 12/22/2022] Open
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14
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Lhomond S, Avril T, Dejeans N, Voutetakis K, Doultsinos D, McMahon M, Pineau R, Obacz J, Papadodima O, Jouan F, Bourien H, Logotheti M, Jégou G, Pallares-Lupon N, Schmit K, Le Reste PJ, Etcheverry A, Mosser J, Barroso K, Vauléon E, Maurel M, Samali A, Patterson JB, Pluquet O, Hetz C, Quillien V, Chatziioannou A, Chevet E. Dual IRE1 RNase functions dictate glioblastoma development. EMBO Mol Med 2022; 14:e15622. [PMID: 35014200 DOI: 10.15252/emmm.202115622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 11/09/2022] Open
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15
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Le Reste P, Pilalis E, Aubry M, McMahon M, Cano L, Etcheverry A, Chatziioannou A, Chevet E, Fautrel A. Integration of Raman spectra with transcriptome data in glioblastoma multiforme defines tumour subtypes and predicts patient outcome. J Cell Mol Med 2021; 25:10846-10856. [PMID: 34773369 PMCID: PMC8642677 DOI: 10.1111/jcmm.16902] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 08/13/2021] [Accepted: 08/20/2021] [Indexed: 12/24/2022] Open
Abstract
Raman spectroscopy is an imaging technique that has been applied to assess molecular compositions of living cells to characterize cell types and states. However, owing to the diverse molecular species in cells and challenges of assigning peaks to specific molecules, it has not been clear how to interpret cellular Raman spectra. Here, we provide firm evidence that cellular Raman spectra (RS) and transcriptomic profiles of glioblastoma can be computationally connected and thus interpreted. We find that the dimensions of high-dimensional RS and transcriptomes can be reduced and connected linearly through a shared low-dimensional subspace. Accordingly, we were able to predict global gene expression profiles by applying the calculated transformation matrix to Raman spectra and vice versa. From these analyses, we extract a minimal gene expression signature associated with specific RS profiles and predictive of disease outcome.
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Affiliation(s)
- Pierre‐Jean Le Reste
- Department of NeurosurgeryUniversity HospitalRennesFrance
- INSERM U1242University of RennesRennesFrance
- REACT – Rennes Brain Cancer TeamRennesFrance
| | | | - Marc Aubry
- REACT – Rennes Brain Cancer TeamRennesFrance
- IGDR CNRSUniversity of RennesRennesFrance
| | - Mari McMahon
- INSERM U1242University of RennesRennesFrance
- REACT – Rennes Brain Cancer TeamRennesFrance
- Centre de Lutte Contre le Cancer Eugene MarquisRennesFrance
| | - Luis Cano
- H2P2 PlatformUMS CNRS 3480 – INSERM 018University of RennesRennesFrance
| | - Amandine Etcheverry
- REACT – Rennes Brain Cancer TeamRennesFrance
- IGDR CNRSUniversity of RennesRennesFrance
| | | | - Eric Chevet
- INSERM U1242University of RennesRennesFrance
- REACT – Rennes Brain Cancer TeamRennesFrance
- Centre de Lutte Contre le Cancer Eugene MarquisRennesFrance
| | - Alain Fautrel
- H2P2 PlatformUMS CNRS 3480 – INSERM 018University of RennesRennesFrance
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16
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Dorman A, Binenbaum I, Abu-Toamih Atamni HJ, Chatziioannou A, Tomlinson I, Mott R, Iraqi FA. Genetic mapping of novel modifiers for Apc Min induced intestinal polyps' development using the genetic architecture power of the collaborative cross mice. BMC Genomics 2021; 22:566. [PMID: 34294033 PMCID: PMC8299641 DOI: 10.1186/s12864-021-07890-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 07/14/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Familial adenomatous polyposis is an inherited genetic disease, characterized by colorectal polyps. It is caused by inactivating mutations in the Adenomatous polyposis coli (Apc) gene. Mice carrying a nonsense mutation in the Apc gene at R850, which is designated ApcMin/+ (Multiple intestinal neoplasia), develop intestinal adenomas. Several genetic modifier loci of Min (Mom) were previously mapped, but so far, most of the underlying genes have not been identified. To identify novel modifier loci associated with ApcMin/+, we performed quantitative trait loci (QTL) analysis for polyp development using 49 F1 crosses between different Collaborative Cross (CC) lines and C57BL/6 J-ApcMin/+mice. The CC population is a genetic reference panel of recombinant inbred lines, each line independently descended from eight genetically diverse founder strains. C57BL/6 J-ApcMin/+ males were mated with females from 49 CC lines. F1 offspring were terminated at 23 weeks and polyp counts from three sub-regions (SB1-3) of small intestinal and colon were recorded. RESULTS The number of polyps in all these sub-regions and colon varied significantly between the different CC lines. At 95% genome-wide significance, we mapped nine novel QTL for variation in polyp number, with distinct QTL associated with each intestinal sub-region. QTL confidence intervals varied in width between 2.63-17.79 Mb. We extracted all genes in the mapped QTL at 90 and 95% CI levels using the BioInfoMiner online platform to extract, significantly enriched pathways and key linker genes, that act as regulatory and orchestrators of the phenotypic landscape associated with the ApcMin/+ mutation. CONCLUSIONS Genomic structure of the CC lines has allowed us to identify novel modifiers and confirmed some of the previously mapped modifiers. Key genes involved mainly in metabolic and immunological processes were identified. Future steps in this analysis will be to identify regulatory elements - and possible epistatic effects - located in the mapped QTL.
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Affiliation(s)
- Alexandra Dorman
- Department of Clinical Microbiology & Immunology, Sackler Faculty of Medicine, Ramat Aviv, 69978 Tel-Aviv, Israel
| | - Ilona Binenbaum
- Department of Biology, University of Patras, Patras, Greece
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Hanifa J. Abu-Toamih Atamni
- Department of Clinical Microbiology & Immunology, Sackler Faculty of Medicine, Ramat Aviv, 69978 Tel-Aviv, Israel
| | | | - Ian Tomlinson
- Cancer Research UK Edinburgh Centre, Charles and Ethel Barr Chair of Cancer Research, University of Edinburgh, Edinburgh, UK
| | - Richard Mott
- Department of Genetics, University Collage of London, London, UK
| | - Fuad A. Iraqi
- Department of Clinical Microbiology & Immunology, Sackler Faculty of Medicine, Ramat Aviv, 69978 Tel-Aviv, Israel
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17
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Dlamini Z, Hull R, Mbatha SZ, Alaouna M, Qiao YL, Yu H, Chatziioannou A. Prognostic Alternative Splicing Signatures in Esophageal Carcinoma. Cancer Manag Res 2021; 13:4509-4527. [PMID: 34113176 PMCID: PMC8186946 DOI: 10.2147/cmar.s305464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 02/05/2021] [Accepted: 04/06/2021] [Indexed: 01/10/2023] Open
Abstract
Alternative splicing (AS) is a method of increasing the number of proteins that the genome is capable of coding for, by altering the pre-mRNA during its maturation. This process provides the ability of a broad range of proteins to arise from a single gene. AS events are known to occur in up to 94% of human genes. Cumulative data have shown that aberrant AS functionality is a major factor in human diseases. This review focuses on the contribution made by aberrant AS functionality in the development and progression of esophageal cancer. The changes in the pattern of expression of alternately spliced isoforms in esophageal cancer can be used as diagnostic or prognostic biomarkers. Additionally, these can be used as targets for the development of new treatments for esophageal cancer.
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Affiliation(s)
- Zodwa Dlamini
- SAMRC Precision Prevention & Novel Drug Targets for HIV-Associated Cancers Extramural Unit, Pan African Cancer Research Institute, University of Pretoria, Pretoria, South Africa
| | - Rodney Hull
- SAMRC Precision Prevention & Novel Drug Targets for HIV-Associated Cancers Extramural Unit, Pan African Cancer Research Institute, University of Pretoria, Pretoria, South Africa
| | - Sikhumbuzo Z Mbatha
- Department of Surgery, Steve Biko Academic Hospital, University of Pretoria, Pretoria, South Africa
| | - Mohammed Alaouna
- SAMRC Precision Prevention & Novel Drug Targets for HIV-Associated Cancers Extramural Unit, Pan African Cancer Research Institute, University of Pretoria, Pretoria, South Africa.,Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - You-Lin Qiao
- SAMRC Precision Prevention & Novel Drug Targets for HIV-Associated Cancers Extramural Unit, Pan African Cancer Research Institute, University of Pretoria, Pretoria, South Africa.,Cancer Institute/Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, People's Republic of China
| | - Herbert Yu
- SAMRC Precision Prevention & Novel Drug Targets for HIV-Associated Cancers Extramural Unit, Pan African Cancer Research Institute, University of Pretoria, Pretoria, South Africa.,University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Aristotelis Chatziioannou
- SAMRC Precision Prevention & Novel Drug Targets for HIV-Associated Cancers Extramural Unit, Pan African Cancer Research Institute, University of Pretoria, Pretoria, South Africa.,Center of Systems Biology, Biomedical Research Foundation Academy of Athens, Athens, Greece.,e-NIOS Applications PC, Kallithea, Athens, 17676, Greece
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18
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Mitra D, Vega-Rubin-de-Celis S, Royla N, Bernhardt S, Wilhelm H, Tarade N, Poschet G, Buettner M, Binenbaum I, Borgoni S, Vetter M, Kantelhardt EJ, Thomssen C, Chatziioannou A, Hell R, Kempa S, Müller-Decker K, Wiemann S. Abrogating GPT2 in triple-negative breast cancer inhibits tumor growth and promotes autophagy. Int J Cancer 2021; 148:1993-2009. [PMID: 33368291 DOI: 10.1002/ijc.33456] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 11/09/2020] [Accepted: 11/30/2020] [Indexed: 12/16/2022]
Abstract
Uncontrolled proliferation and altered metabolic reprogramming are hallmarks of cancer. Active glycolysis and glutaminolysis are characteristic features of these hallmarks and required for tumorigenesis. A fine balance between cancer metabolism and autophagy is a prerequisite of homeostasis within cancer cells. Here we show that glutamate pyruvate transaminase 2 (GPT2), which serves as a pivot between glycolysis and glutaminolysis, is highly upregulated in aggressive breast cancers, particularly the triple-negative breast cancer subtype. Abrogation of this enzyme results in decreased tricarboxylic acid cycle intermediates, which promotes the rewiring of glucose carbon atoms and alterations in nutrient levels. Concordantly, loss of GPT2 results in an impairment of mechanistic target of rapamycin complex 1 activity as well as the induction of autophagy. Furthermore, in vivo xenograft studies have shown that autophagy induction correlates with decreased tumor growth and that markers of induced autophagy correlate with low GPT2 levels in patient samples. Taken together, these findings indicate that cancer cells have a close network between metabolic and nutrient sensing pathways necessary to sustain tumorigenesis and that aminotransferase reactions play an important role in maintaining this balance.
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Affiliation(s)
- Devina Mitra
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Silvia Vega-Rubin-de-Celis
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Cell Biology (Cancer Research), University Hospital Essen, Essen, Germany
| | - Nadine Royla
- Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Stephan Bernhardt
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Heike Wilhelm
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nooraldeen Tarade
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Gernot Poschet
- Centre for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
| | - Michael Buettner
- Centre for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
| | - Ilona Binenbaum
- Department of Biology, University of Patras, Patras, Greece
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
- Division of Medical Informatics for Translational Oncology, German Cancer Research Centre, Heidelberg, Germany
- Division of Pediatric Hematology-Oncology, First Department of Pediatrics, National and Kapodistrian University of Athens, Greece
| | - Simone Borgoni
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Martina Vetter
- Department of Gynaecology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Eva Johanna Kantelhardt
- Department of Gynaecology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Christoph Thomssen
- Department of Gynaecology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Aristotelis Chatziioannou
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
- e-NIOS PC, Athens, Greece
| | - Rüdiger Hell
- Centre for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
| | - Stefan Kempa
- Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute of Health (BIH), Berlin, Germany
| | - Karin Müller-Decker
- DKFZ Tumor Models Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Wiemann
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
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19
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Maglogiannis I, Kontogianni G, Papadodima O, Karanikas H, Billiris A, Chatziioannou A. An Integrated Platform for Skin Cancer Heterogenous and Multilayered Data Management. J Med Syst 2021; 45:10. [PMID: 33404959 DOI: 10.1007/s10916-020-01679-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 11/23/2020] [Indexed: 01/22/2023]
Abstract
Electronic health record (EHR) systems improve health care services by allowing the combination of health data with clinical decision support features and clinical image analyses. This study presents a modular and distributed platform that is able to integrate and accommodate heterogeneous, multidimensional (omics, histological images and clinical) data for the multi-angled portrayal and management of skin cancer patients. The proposed design offers a layered analytical framework as an expansion of current EHR systems, which can integrate high-volume molecular -omics data, imaging data, as well as relevant clinical observations. We present a case study in the field of dermatology, where we attempt to combine the multilayered information for the early detection and characterization of melanoma. The specific architecture aspires to lower the barrier for the introduction of personalized therapeutic approaches, towards precision medicine. The paper describes the technical issues of implementation, along with an initial evaluation of the system and discussion.
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Affiliation(s)
- Ilias Maglogiannis
- Department of Digital Systems, University of Piraeus, 126 Grigoriou Lambraki, 18534, Piraeus, Greece.
| | - Georgia Kontogianni
- Department of Digital Systems, University of Piraeus, 126 Grigoriou Lambraki, 18534, Piraeus, Greece
- National Hellenic Research Foundation, 48 Vassileos Constantinou Ave, 11635, Athens, Greece
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou, 11527, Athens, Greece
| | - Olga Papadodima
- National Hellenic Research Foundation, 48 Vassileos Constantinou Ave, 11635, Athens, Greece
| | | | | | - Aristotelis Chatziioannou
- National Hellenic Research Foundation, 48 Vassileos Constantinou Ave, 11635, Athens, Greece
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou, 11527, Athens, Greece
- e-NIOS Applications Private Company, 17671, Kallithea, Greece
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20
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Berdiel-Acer M, Maia A, Hristova Z, Borgoni S, Vetter M, Burmester S, Becki C, Michels B, Abnaof K, Binenbaum I, Bethmann D, Chatziioannou A, Hasmann M, Thomssen C, Espinet E, Wiemann S. Stromal NRG1 in luminal breast cancer defines pro-fibrotic and migratory cancer-associated fibroblasts. Oncogene 2021; 40:2651-2666. [PMID: 33692466 PMCID: PMC8049869 DOI: 10.1038/s41388-021-01719-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 05/10/2020] [Revised: 02/10/2021] [Accepted: 02/18/2021] [Indexed: 01/31/2023]
Abstract
HER3 is highly expressed in luminal breast cancer subtypes. Its activation by NRG1 promotes activation of AKT and ERK1/2, contributing to tumour progression and therapy resistance. HER3-targeting agents that block this activation, are currently under phase 1/2 clinical studies, and although they have shown favorable tolerability, their activity as a single agent has proven to be limited. Here we show that phosphorylation and activation of HER3 in luminal breast cancer cells occurs in a paracrine manner and is mediated by NRG1 expressed by cancer-associated fibroblasts (CAFs). Moreover, we uncover a HER3-independent NRG1 signaling in CAFs that results in the induction of a strong migratory and pro-fibrotic phenotype, describing a subtype of CAFs with elevated expression of NRG1 and an associated transcriptomic profile that determines their functional properties. Finally, we identified Hyaluronan Synthase 2 (HAS2), a targetable molecule strongly correlated with NRG1, as an attractive player supporting NRG1 signaling in CAFs.
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Affiliation(s)
- Mireia Berdiel-Acer
- grid.7497.d0000 0004 0492 0584Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ana Maia
- grid.7497.d0000 0004 0492 0584Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Faculty of Biosciences, Ruprecht-Karls-University, Heidelberg, Germany
| | - Zhivka Hristova
- grid.7497.d0000 0004 0492 0584Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Faculty of Biosciences, Ruprecht-Karls-University, Heidelberg, Germany
| | - Simone Borgoni
- grid.7497.d0000 0004 0492 0584Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Faculty of Biosciences, Ruprecht-Karls-University, Heidelberg, Germany
| | - Martina Vetter
- grid.9018.00000 0001 0679 2801Department of Gynecology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Sara Burmester
- grid.7497.d0000 0004 0492 0584Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Corinna Becki
- grid.7497.d0000 0004 0492 0584Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Birgitta Michels
- grid.7497.d0000 0004 0492 0584Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Khalid Abnaof
- grid.7497.d0000 0004 0492 0584Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ilona Binenbaum
- grid.7497.d0000 0004 0492 0584Division of Medical Informatics for Translational Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.11047.330000 0004 0576 5395Department of Biology, University of Patras, Patras, Greece ,grid.22459.380000 0001 2232 6894Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Daniel Bethmann
- grid.9018.00000 0001 0679 2801Institute of Pathology Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Aristotelis Chatziioannou
- grid.22459.380000 0001 2232 6894Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece ,e-NIOS PC, Kallithea-Athens, Greece
| | - Max Hasmann
- grid.424277.0Roche Diagnostics, Penzberg, Germany
| | - Christoph Thomssen
- grid.9018.00000 0001 0679 2801Department of Gynecology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Elisa Espinet
- grid.7497.d0000 0004 0492 0584Divison of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.482664.aHeidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
| | - Stefan Wiemann
- grid.7497.d0000 0004 0492 0584Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
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21
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Koumaki K, Kontogianni G, Kosmidou V, Pahitsa F, Kritsi E, Zervou M, Chatziioannou A, Souliotis VL, Papadodima O, Pintzas A. BRAF paradox breakers PLX8394, PLX7904 are more effective against BRAFV600Ε CRC cells compared with the BRAF inhibitor PLX4720 and shown by detailed pathway analysis. Biochim Biophys Acta Mol Basis Dis 2020; 1867:166061. [PMID: 33385518 DOI: 10.1016/j.bbadis.2020.166061] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 12/16/2020] [Accepted: 12/22/2020] [Indexed: 12/20/2022]
Abstract
PLX7904 and PLX8394 are novel BRAFV600E inhibitors-BRAFi that are designed to evade the paradoxical MAPK activation, a trait for the name "paradox breakers"-PB. Current FDA approved inhibitors (Vemurafenib, Dabrafenib, Encorafenib) although improved progression-free survival of mtBRAF melanoma patients suffer from this treatment related side effect. mtBRAF Colorectal Cancer (CRC) is resistant to the approved BRAF inhibitors, although combinatorial treatment co-targeting BRAF and EGFR/MEK is offering a promising prospect. In an effort to explore the potential of the novel BRAF inhibitors-PB to impede CRC cell proliferation, they were tested on RKO, HT29 and Colo-205 cells, bearing the BRAFV600E mutation. This study shows that the BRAF paradox breakers PLX7904 and PLX8394 cause a more prolonged MAPK pathway inhibition and achieve a stronger blockage of proliferation and reduced viability than PLX4720, the sister compound of Vemurafenib. In some treatment conditions, cells can undergo apoptosis. Genomic analysis on the more resistant RKO cells treated with PLX7904, PLX8394 and PLX4720 showed similar gene expression pattern, but the alterations imposed by the PB were more intense. Bioinformatic analysis resulted in a short list of genes representing potential master regulators of the cellular response to BRAF inhibitors' treatments. From our results, it is clear that the BRAF paradox breakers present a notable differential regulation of major pathways, like MAPK signalling, apoptosis, cell cycle, or developmental signalling pathways. Combinatorial treatments of BRAFi with Mcl-1 and Notch modulators show a better effect than mono-treatments. Additional pathways could be further exploited in novel efficient combinatorial treatment protocols with BRAFi.
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Affiliation(s)
- Kassandra Koumaki
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Georgia Kontogianni
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Vivian Kosmidou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Fani Pahitsa
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Eftichia Kritsi
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Maria Zervou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | | | - Vassilis L Souliotis
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Olga Papadodima
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Alexander Pintzas
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece.
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22
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Buocikova V, Rios-Mondragon I, Pilalis E, Chatziioannou A, Miklikova S, Mego M, Pajuste K, Rucins M, Yamani NE, Longhin EM, Sobolev A, Freixanet M, Puntes V, Plotniece A, Dusinska M, Cimpan MR, Gabelova A, Smolkova B. Epigenetics in Breast Cancer Therapy-New Strategies and Future Nanomedicine Perspectives. Cancers (Basel) 2020; 12:E3622. [PMID: 33287297 PMCID: PMC7761669 DOI: 10.3390/cancers12123622] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/30/2020] [Accepted: 11/30/2020] [Indexed: 12/12/2022] Open
Abstract
Epigenetic dysregulation has been recognized as a critical factor contributing to the development of resistance against standard chemotherapy and to breast cancer progression via epithelial-to-mesenchymal transition. Although the efficacy of the first-generation epigenetic drugs (epi-drugs) in solid tumor management has been disappointing, there is an increasing body of evidence showing that epigenome modulation, in synergy with other therapeutic approaches, could play an important role in cancer treatment, reversing acquired therapy resistance. However, the epigenetic therapy of solid malignancies is not straightforward. The emergence of nanotechnologies applied to medicine has brought new opportunities to advance the targeted delivery of epi-drugs while improving their stability and solubility, and minimizing off-target effects. Furthermore, the omics technologies, as powerful molecular epidemiology screening tools, enable new diagnostic and prognostic epigenetic biomarker identification, allowing for patient stratification and tailored management. In combination with new-generation epi-drugs, nanomedicine can help to overcome low therapeutic efficacy in treatment-resistant tumors. This review provides an overview of ongoing clinical trials focusing on combination therapies employing epi-drugs for breast cancer treatment and summarizes the latest nano-based targeted delivery approaches for epi-drugs. Moreover, it highlights the current limitations and obstacles associated with applying these experimental strategies in the clinics.
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Affiliation(s)
- Verona Buocikova
- Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dubravska Cesta 9, 845 05 Bratislava, Slovakia; (V.B.); (S.M.); (A.G.)
| | - Ivan Rios-Mondragon
- Department of Clinical Dentistry, University of Bergen, Aarstadveien 19, 5009 Bergen, Norway; (I.R.-M.); (M.R.C.)
| | - Eleftherios Pilalis
- e-NIOS Applications Private Company, Alexandrou Pantou 25, 17671 Kallithea, Greece; (E.P.); (A.C.)
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Aristotelis Chatziioannou
- e-NIOS Applications Private Company, Alexandrou Pantou 25, 17671 Kallithea, Greece; (E.P.); (A.C.)
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Svetlana Miklikova
- Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dubravska Cesta 9, 845 05 Bratislava, Slovakia; (V.B.); (S.M.); (A.G.)
| | - Michal Mego
- 2nd Department of Oncology, Faculty of Medicine, Comenius University and National Cancer Institute, Klenova 1, 833 10 Bratislava, Slovakia;
| | - Karlis Pajuste
- Latvian Institute of Organic Synthesis, Aizkraukles str. 21, LV-1006 Riga, Latvia; (K.P.); (M.R.); (A.S.); (A.P.)
| | - Martins Rucins
- Latvian Institute of Organic Synthesis, Aizkraukles str. 21, LV-1006 Riga, Latvia; (K.P.); (M.R.); (A.S.); (A.P.)
| | - Naouale El Yamani
- Health Effects Laboratory, NILU-Norwegian Institute for Air Research, 2007 Kjeller, Norway; (N.E.Y.); (E.M.L.); (M.D.)
| | - Eleonora Marta Longhin
- Health Effects Laboratory, NILU-Norwegian Institute for Air Research, 2007 Kjeller, Norway; (N.E.Y.); (E.M.L.); (M.D.)
| | - Arkadij Sobolev
- Latvian Institute of Organic Synthesis, Aizkraukles str. 21, LV-1006 Riga, Latvia; (K.P.); (M.R.); (A.S.); (A.P.)
| | - Muriel Freixanet
- Vall d Hebron, Institut de Recerca (VHIR), 08035 Barcelona, Spain; (M.F.); (V.P.)
| | - Victor Puntes
- Vall d Hebron, Institut de Recerca (VHIR), 08035 Barcelona, Spain; (M.F.); (V.P.)
- Institut Català de Nanosciència i Nanotecnologia (ICN2), Bellaterra, 08193 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Aiva Plotniece
- Latvian Institute of Organic Synthesis, Aizkraukles str. 21, LV-1006 Riga, Latvia; (K.P.); (M.R.); (A.S.); (A.P.)
| | - Maria Dusinska
- Health Effects Laboratory, NILU-Norwegian Institute for Air Research, 2007 Kjeller, Norway; (N.E.Y.); (E.M.L.); (M.D.)
| | - Mihaela Roxana Cimpan
- Department of Clinical Dentistry, University of Bergen, Aarstadveien 19, 5009 Bergen, Norway; (I.R.-M.); (M.R.C.)
| | - Alena Gabelova
- Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dubravska Cesta 9, 845 05 Bratislava, Slovakia; (V.B.); (S.M.); (A.G.)
| | - Bozena Smolkova
- Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dubravska Cesta 9, 845 05 Bratislava, Slovakia; (V.B.); (S.M.); (A.G.)
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23
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Le Reste PJ, Pineau R, Voutetakis K, Samal J, Jégou G, Lhomond S, Gorman AM, Samali A, Patterson JB, Zeng Q, Pandit A, Aubry M, Soriano N, Etcheverry A, Chatziioannou A, Mosser J, Avril T, Chevet E. Local intracerebral inhibition of IRE1 by MKC8866 sensitizes glioblastoma to irradiation/chemotherapy in vivo. Cancer Lett 2020; 494:73-83. [PMID: 32882336 DOI: 10.1016/j.canlet.2020.08.028] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 08/11/2020] [Accepted: 08/20/2020] [Indexed: 01/07/2023]
Abstract
Glioblastoma multiforme (GBM) is the most severe primary brain cancer. Despite an aggressive treatment comprising surgical resection and radio/chemotherapy, patient's survival post diagnosis remains short. A limitation for success in finding novel improved therapeutic options for such dismal disease partly lies in the lack of a relevant animal model that accurately recapitulates patient disease and standard of care. In the present study, we have developed an immunocompetent GBM model that includes tumor surgery and a radio/chemotherapy regimen resembling the Stupp protocol and we have used this model to test the impact of the pharmacological inhibition of the endoplasmic reticulum (ER) stress sensor IRE1, on treatment efficacy.
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Affiliation(s)
- Pierre Jean Le Reste
- Inserm U1242, University of Rennes, Rennes, France; Centre de lutte contre le cancer Eugène Marquis, Rennes, France; Rennes Brain Cancer Team (REACT), 35000, Rennes, France; Neurosurgery Dept, University Hospital of Rennes, 35000, Rennes, France
| | - Raphael Pineau
- Inserm U1242, University of Rennes, Rennes, France; Centre de lutte contre le cancer Eugène Marquis, Rennes, France; Rennes Brain Cancer Team (REACT), 35000, Rennes, France
| | - Konstantinos Voutetakis
- Institute of Chemical Biology, National Hellenic Research Foundation (N.H.R.F.), Athens, Greece; Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, 41500, Larissa, Greece
| | - Juhi Samal
- CÚRAM, Centre for Research in Medical Devices, National University of Ireland, Galway, Ireland
| | - Gwénaële Jégou
- Inserm U1242, University of Rennes, Rennes, France; Centre de lutte contre le cancer Eugène Marquis, Rennes, France; Rennes Brain Cancer Team (REACT), 35000, Rennes, France
| | - Stéphanie Lhomond
- CÚRAM, Centre for Research in Medical Devices, National University of Ireland, Galway, Ireland; Apoptosis Research Centre, National University Ireland Galway, Galway, Ireland
| | - Adrienne M Gorman
- CÚRAM, Centre for Research in Medical Devices, National University of Ireland, Galway, Ireland; Apoptosis Research Centre, National University Ireland Galway, Galway, Ireland
| | - Afshin Samali
- Apoptosis Research Centre, National University Ireland Galway, Galway, Ireland
| | - John B Patterson
- Fosun OrinovePharmaTech Inc., 3537 Old Conejo Road, Suite 104, Newbury Park, CA, 91320, USA
| | - Qingping Zeng
- Fosun OrinovePharmaTech Inc., 3537 Old Conejo Road, Suite 104, Newbury Park, CA, 91320, USA
| | - Abhay Pandit
- CÚRAM, Centre for Research in Medical Devices, National University of Ireland, Galway, Ireland
| | - Marc Aubry
- Rennes Brain Cancer Team (REACT), 35000, Rennes, France; University of Rennes, CNRS, IGDR [(Institut de Génétique et développement de Rennes)]-UMR 6290, F-35000, Rennes, France; CHU Rennes, Service de Génétique Moléculaire et Génomique Médicale, Rennes, France
| | - Nicolas Soriano
- Rennes Brain Cancer Team (REACT), 35000, Rennes, France; University of Rennes, CNRS, IGDR [(Institut de Génétique et développement de Rennes)]-UMR 6290, F-35000, Rennes, France
| | - Amandine Etcheverry
- CHU Rennes, Service de Génétique Moléculaire et Génomique Médicale, Rennes, France
| | - Aristotelis Chatziioannou
- Institute of Chemical Biology, National Hellenic Research Foundation (N.H.R.F.), Athens, Greece; e-NIOS PC, Kallithea-Athens, Greece
| | - Jean Mosser
- Rennes Brain Cancer Team (REACT), 35000, Rennes, France; University of Rennes, CNRS, IGDR [(Institut de Génétique et développement de Rennes)]-UMR 6290, F-35000, Rennes, France; CHU Rennes, Service de Génétique Moléculaire et Génomique Médicale, Rennes, France; University of Rennes, Plateforme GEH, CNRS, Inserm, BIOSIT - UMS 3480, US_S 018, F-35000, Rennes, France
| | - Tony Avril
- Inserm U1242, University of Rennes, Rennes, France; Centre de lutte contre le cancer Eugène Marquis, Rennes, France; Rennes Brain Cancer Team (REACT), 35000, Rennes, France
| | - Eric Chevet
- Inserm U1242, University of Rennes, Rennes, France; Centre de lutte contre le cancer Eugène Marquis, Rennes, France; Rennes Brain Cancer Team (REACT), 35000, Rennes, France.
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24
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25
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Sicari D, Chatziioannou A, Koutsandreas T, Sitia R, Chevet E. Role of the early secretory pathway in SARS-CoV-2 infection. J Cell Biol 2020; 219:151984. [PMID: 32725137 PMCID: PMC7480111 DOI: 10.1083/jcb.202006005] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/03/2020] [Accepted: 07/07/2020] [Indexed: 12/17/2022] Open
Abstract
Similar to other RNA viruses, SARS-CoV-2 must (1) enter a target/host cell, (2) reprogram it to ensure its replication, (3) exit the host cell, and (4) repeat this cycle for exponential growth. During the exit step, the virus hijacks the sophisticated machineries that host cells employ to correctly fold, assemble, and transport proteins along the exocytic pathway. Therefore, secretory pathway-mediated assemblage and excretion of infective particles represent appealing targets to reduce the efficacy of virus biogenesis, if not to block it completely. Here, we analyze and discuss the contribution of the molecular machines operating in the early secretory pathway in the biogenesis of SARS-CoV-2 and their relevance for potential antiviral targeting. The fact that these molecular machines are conserved throughout evolution, together with the redundancy and tissue specificity of their components, provides opportunities in the search for unique proteins essential for SARS-CoV-2 biology that could also be targeted with therapeutic objectives. Finally, we provide an overview of recent evidence implicating proteins of the early secretory pathway as potential antiviral targets with effective therapeutic applications.
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Affiliation(s)
- Daria Sicari
- Inserm U1242, Université de Rennes, Rennes, France.,Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France.,Università Vita-Salute San Raffaele, Milan, Italy
| | - Aristotelis Chatziioannou
- e-NIOS Applications PC, Kallithea-Athens, Greece.,Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Theodoros Koutsandreas
- e-NIOS Applications PC, Kallithea-Athens, Greece.,Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | | | - Eric Chevet
- Inserm U1242, Université de Rennes, Rennes, France.,Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France.,Università Vita-Salute San Raffaele, Milan, Italy
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26
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Maurel M, Obacz J, Avril T, Ding YP, Papadodima O, Treton X, Daniel F, Pilalis E, Hörberg J, Hou W, Beauchamp MC, Tourneur-Marsille J, Cazals-Hatem D, Sommerova L, Samali A, Tavernier J, Hrstka R, Dupont A, Fessart D, Delom F, Fernandez-Zapico ME, Jansen G, Eriksson LA, Thomas DY, Jerome-Majewska L, Hupp T, Chatziioannou A, Chevet E, Ogier-Denis E. Control of anterior GRadient 2 (AGR2) dimerization links endoplasmic reticulum proteostasis to inflammation. EMBO Mol Med 2020; 11:emmm.201810120. [PMID: 31040128 PMCID: PMC6554669 DOI: 10.15252/emmm.201810120] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [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] [Indexed: 12/24/2022] Open
Abstract
Anterior gradient 2 (AGR2) is a dimeric protein disulfide isomerase family member involved in the regulation of protein quality control in the endoplasmic reticulum (ER). Mouse AGR2 deletion increases intestinal inflammation and promotes the development of inflammatory bowel disease (IBD). Although these biological effects are well established, the underlying molecular mechanisms of AGR2 function toward inflammation remain poorly defined. Here, using a protein-protein interaction screen to identify cellular regulators of AGR2 dimerization, we unveiled specific enhancers, including TMED2, and inhibitors of AGR2 dimerization, that control AGR2 functions. We demonstrate that modulation of AGR2 dimer formation, whether enhancing or inhibiting the process, yields pro-inflammatory phenotypes, through either autophagy-dependent processes or secretion of AGR2, respectively. We also demonstrate that in IBD and specifically in Crohn's disease, the levels of AGR2 dimerization modulators are selectively deregulated, and this correlates with severity of disease. Our study demonstrates that AGR2 dimers act as sensors of ER homeostasis which are disrupted upon ER stress and promote the secretion of AGR2 monomers. The latter might represent systemic alarm signals for pro-inflammatory responses.
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Affiliation(s)
- Marion Maurel
- INSERM U1242, "Chemistry, Oncogenesis Stress Signaling", University of Rennes, Rennes, France.,Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France.,VIB Department of Medical Protein Research, UGent, Gent, Belgium.,Apoptosis Research Centre, School of Natural Sciences, NUI Galway, Galway, Ireland
| | - Joanna Obacz
- INSERM U1242, "Chemistry, Oncogenesis Stress Signaling", University of Rennes, Rennes, France.,Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France
| | - Tony Avril
- INSERM U1242, "Chemistry, Oncogenesis Stress Signaling", University of Rennes, Rennes, France.,Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France
| | - Yong-Ping Ding
- INSERM, UMR1149, Team «Gut Inflammation», Research Centre of Inflammation, Paris, France.,Université Paris-Diderot Sorbonne Paris-Cité, Paris, France.,APHP Beaujon Hospital Clichy la Garenne, Paris, France
| | - Olga Papadodima
- Institute of Biology, Medicinal Chemistry & Biotechnology, NHRF, Athens, Greece
| | - Xavier Treton
- INSERM, UMR1149, Team «Gut Inflammation», Research Centre of Inflammation, Paris, France.,Université Paris-Diderot Sorbonne Paris-Cité, Paris, France.,APHP Beaujon Hospital Clichy la Garenne, Paris, France
| | - Fanny Daniel
- INSERM, UMR1149, Team «Gut Inflammation», Research Centre of Inflammation, Paris, France.,Université Paris-Diderot Sorbonne Paris-Cité, Paris, France.,APHP Beaujon Hospital Clichy la Garenne, Paris, France
| | - Eleftherios Pilalis
- Institute of Biology, Medicinal Chemistry & Biotechnology, NHRF, Athens, Greece.,International Centre for Cancer Vaccine Science, Gdansk, Poland
| | - Johanna Hörberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
| | - Wenyang Hou
- Departments of Anatomy and Cell Biology, Human Genetics, and Pediatrics, McGill University, Montreal, QC, Canada
| | - Marie-Claude Beauchamp
- Departments of Anatomy and Cell Biology, Human Genetics, and Pediatrics, McGill University, Montreal, QC, Canada
| | - Julien Tourneur-Marsille
- INSERM, UMR1149, Team «Gut Inflammation», Research Centre of Inflammation, Paris, France.,Université Paris-Diderot Sorbonne Paris-Cité, Paris, France.,APHP Beaujon Hospital Clichy la Garenne, Paris, France
| | - Dominique Cazals-Hatem
- INSERM, UMR1149, Team «Gut Inflammation», Research Centre of Inflammation, Paris, France.,Université Paris-Diderot Sorbonne Paris-Cité, Paris, France.,APHP Beaujon Hospital Clichy la Garenne, Paris, France
| | - Lucia Sommerova
- Regional Centre for Applied Molecular Oncology (RECAMO), Brno, Czech Republic
| | - Afshin Samali
- Apoptosis Research Centre, School of Natural Sciences, NUI Galway, Galway, Ireland
| | - Jan Tavernier
- VIB Department of Medical Protein Research, UGent, Gent, Belgium
| | - Roman Hrstka
- Regional Centre for Applied Molecular Oncology (RECAMO), Brno, Czech Republic
| | - Aurélien Dupont
- Microscopy Rennes Imaging Centre, and Biosit, UMS3480 CNRS, University of Rennes 1, Rennes Cédex, France
| | | | | | - Martin E Fernandez-Zapico
- Division of Oncology Research, Department of Oncology, Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Gregor Jansen
- Biochemistry Department, McGill University Life Sciences Complex, Montréal, QC, Canada
| | - Leif A Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
| | - David Y Thomas
- Biochemistry Department, McGill University Life Sciences Complex, Montréal, QC, Canada
| | - Loydie Jerome-Majewska
- Departments of Anatomy and Cell Biology, Human Genetics, and Pediatrics, McGill University, Montreal, QC, Canada
| | - Ted Hupp
- International Centre for Cancer Vaccine Science, Gdansk, Poland.,Regional Centre for Applied Molecular Oncology (RECAMO), Brno, Czech Republic.,Edinburgh Cancer Research Centre at the Institute of Genetics and Molecular Medicine, Edinburgh University, Edimburgh, UK
| | - Aristotelis Chatziioannou
- Institute of Biology, Medicinal Chemistry & Biotechnology, NHRF, Athens, Greece .,e-NIOS PC, Kallithea-Athens, Greece
| | - Eric Chevet
- INSERM U1242, "Chemistry, Oncogenesis Stress Signaling", University of Rennes, Rennes, France .,Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France
| | - Eric Ogier-Denis
- INSERM, UMR1149, Team «Gut Inflammation», Research Centre of Inflammation, Paris, France .,Université Paris-Diderot Sorbonne Paris-Cité, Paris, France.,APHP Beaujon Hospital Clichy la Garenne, Paris, France
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27
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Soller M, Abu-Toamih Atamni HJ, Binenbaum I, Chatziioannou A, Iraqi FA. Designing a QTL Mapping Study for Implementation in the Realized Collaborative Cross Genetic Reference Population. ACTA ACUST UNITED AC 2020; 9:e66. [PMID: 31756057 DOI: 10.1002/cpmo.66] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 12/27/2022]
Abstract
The Collaborative Cross (CC) mouse resource is a next-generation mouse genetic reference population (GRP) designed for high-resolution mapping of quantitative trait loci (QTL) of large effect affecting complex traits during health and disease. The CC resource consists of a set of 72 recombinant inbred lines (RILs) generated by reciprocal crossing of five classical and three wild-derived mouse founder strains. Complex traits are controlled by variations within multiple genes and environmental factors, and their mutual interactions. These traits are observed at multiple levels of the animals' systems, including metabolism, body weight, immune profile, and susceptibility or resistance to the development and progress of infectious or chronic diseases. Herein, we present general guidelines for design of QTL mapping experiments using the CC resource-along with full step-by-step protocols and methods that were implemented in our lab for the phenotypic and genotypic characterization of the different CC lines-for mapping the genes underlying host response to infectious and chronic diseases. © 2019 by John Wiley & Sons, Inc. Basic Protocol 1: CC lines for whole body mass index (BMI) Basic Protocol 2: A detailed assessment of the power to detect effect sizes based on the number of lines used, and the number of replicates per line Basic Protocol 3: Obtaining power for QTL with given target effect by interpolating in Table 1 of Keele et al. (2019).
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Affiliation(s)
- Morris Soller
- Department of Genetics, Silverman Institute for Life Sciences, Hebrew University, Jerusalem, Israel
| | - Hanifa J Abu-Toamih Atamni
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel
| | - Ilona Binenbaum
- Department of Biology, University of Patras, Patras, Greece.,Institute of Biology, Medicinal Chemistry & Biotechnology, NHRF, Athens, Greece
| | | | - Fuad A Iraqi
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel
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28
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Cardoso Alves L, Berger MD, Koutsandreas T, Kirschke N, Lauer C, Spörri R, Chatziioannou A, Corazza N, Krebs P. Non-apoptotic TRAIL function modulates NK cell activity during viral infection. EMBO Rep 2020; 21:e48789. [PMID: 31742873 PMCID: PMC6945065 DOI: 10.15252/embr.201948789] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/16/2019] [Accepted: 10/18/2019] [Indexed: 11/29/2022] Open
Abstract
The role of death receptor signaling for pathogen control and infection-associated pathogenesis is multifaceted and controversial. Here, we show that during viral infection, tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) modulates NK cell activity independently of its pro-apoptotic function. In mice infected with lymphocytic choriomeningitis virus (LCMV), Trail deficiency led to improved specific CD8+ T-cell responses, resulting in faster pathogen clearance and reduced liver pathology. Depletion experiments indicated that this effect was mediated by NK cells. Mechanistically, TRAIL expressed by immune cells positively and dose-dependently modulates IL-15 signaling-induced granzyme B production in NK cells, leading to enhanced NK cell-mediated T cell killing. TRAIL also regulates the signaling downstream of IL-15 receptor in human NK cells. In addition, TRAIL restricts NK1.1-triggered IFNγ production by NK cells. Our study reveals a hitherto unappreciated immunoregulatory role of TRAIL signaling on NK cells for the granzyme B-dependent elimination of antiviral T cells.
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Affiliation(s)
- Ludmila Cardoso Alves
- Institute of PathologyUniversity of BernBernSwitzerland
- Graduate School for Cellular and Biomedical SciencesUniversity of BernBernSwitzerland
| | | | - Thodoris Koutsandreas
- Institute of Biology, Medicinal Chemistry & BiotechnologyNHRFAthensGreece
- e‐NIOS PCKallithea‐AthensGreece
| | - Nick Kirschke
- Institute of PathologyUniversity of BernBernSwitzerland
| | | | - Roman Spörri
- Institute of MicrobiologyETH ZurichZurichSwitzerland
| | - Aristotelis Chatziioannou
- Institute of Biology, Medicinal Chemistry & BiotechnologyNHRFAthensGreece
- e‐NIOS PCKallithea‐AthensGreece
| | - Nadia Corazza
- Institute of PathologyUniversity of BernBernSwitzerland
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29
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Abu-Toamih Atamni HJ, Kontogianni G, Binenbaum I, Mott R, Himmelbauer H, Lehrach H, Chatziioannou A, Iraqi FA. Hepatic gene expression variations in response to high-fat diet-induced impaired glucose tolerance using RNAseq analysis in collaborative cross mouse population. Mamm Genome 2019; 30:260-275. [PMID: 31650267 DOI: 10.1007/s00335-019-09816-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 10/09/2019] [Indexed: 12/14/2022]
Abstract
Hepatic gene expression is known to differ between healthy and type 2 diabetes conditions. Identifying these variations will provide better knowledge to the development of gene-targeted therapies. The aim of this study is to assess diet-induced hepatic gene expression of susceptible versus resistant CC lines to T2D development. Next-generation RNA-sequencing was performed for 84 livers of diabetic and non-diabetic mice of 41 different CC lines (both sexes) following 12 weeks on high-fat diet (42% fat). Data analysis revealed significant variations of hepatic gene expression in diabetic versus non-diabetic mice with significant sex effect, where 601 genes were differentially expressed (DE) in overall population (males and females), 718 genes in female mice, and 599 genes in male mice. Top prioritized DE candidate genes were Lepr, Ins2, Mb, Ckm, Mrap2, and Ckmt2 for the overall population; for females-only group were Hdc, Serpina12, Socs1, Socs2, and Mb, while for males-only group were Serpine1, Mb, Ren1, Slc4a1, and Atp2a1. Data analysis for sex differences revealed 193 DE genes in health (Top: Lepr, Cav1, Socs2, Abcg2, and Col5a3), and 389 genes DE between diabetic females versus males (Top: Lepr, Clps, Ins2, Cav1, and Mrap2). Furthermore, integrating gene expression results with previously published QTL, we identified significant variants mapped at chromosomes at positions 36-49 Mb, 62-71 Mb, and 79-99 Mb, on chromosomes 9, 11, and 12, respectively. Our findings emphasize the complexity of T2D development and that significantly controlled by host complex genetic factors. As well, we demonstrate the significant sex differences between males and females during health and increasing to extent levels during disease/diabetes. Altogether, opening the venue for further studies targets the discovery of effective sex-specific and personalized preventions and therapies.
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Affiliation(s)
- H J Abu-Toamih Atamni
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel-Aviv University, Ramat Aviv, 69978, Tel Aviv, Israel
| | - G Kontogianni
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - I Binenbaum
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece.,Department of Biology, University of Patras, Patras, Greece
| | - R Mott
- Department of Genetics, University College of London, London, UK
| | - H Himmelbauer
- Centre for Genomic Regulation (CRG), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - H Lehrach
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - A Chatziioannou
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece.,e-NIOS Applications PC, 17671, Kallithea, Greece
| | - Fuad A Iraqi
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel-Aviv University, Ramat Aviv, 69978, Tel Aviv, Israel.
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Vekris A, Pilalis E, Chatziioannou A, Petry KG. A Computational Pipeline for the Extraction of Actionable Biological Information From NGS-Phage Display Experiments. Front Physiol 2019; 10:1160. [PMID: 31607941 PMCID: PMC6769401 DOI: 10.3389/fphys.2019.01160] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 11/23/2018] [Accepted: 08/28/2019] [Indexed: 12/20/2022] Open
Abstract
Phage Display is a powerful method for the identification of peptide binding to targets of variable complexities and tissues, from unique molecules to the internal surfaces of vessels of living organisms. Particularly for in vivo screenings, the resulting repertoires can be very complex and difficult to study with traditional approaches. Next Generation Sequencing (NGS) opened the possibility to acquire high resolution overviews of such repertoires and thus facilitates the identification of binders of interest. Additionally, the ever-increasing amount of available genome/proteome information became satisfactory regarding the identification of putative mimicked proteins, due to the large scale on which partial sequence homology is assessed. However, the subsequent production of massive data stresses the need for high-performance computational approaches in order to perform standardized and insightful molecular network analysis. Systems-level analysis is essential for efficient resolution of the underlying molecular complexity and the extraction of actionable interpretation, in terms of systemic biological processes and pathways that are systematically perturbed. In this work we introduce PepSimili, an integrated workflow tool, which performs mapping of massive peptide repertoires on whole proteomes and delivers a streamlined, systems-level biological interpretation. The tool employs modules for modeling and filtering of background noise due to random mappings and amplifies the biologically meaningful signal through coupling with BioInfoMiner, a systems interpretation tool that employs graph-theoretic methods for prioritization of systemic processes and corresponding driver genes. The current implementation exploits the Galaxy environment and is available online. A case study using public data is presented, with and without a control selection.
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Affiliation(s)
| | - Eleftherios Pilalis
- Metabolic Engineering and Bioinformatics Program, Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece.,eNIOS Applications P.C., Athens, Greece
| | - Aristotelis Chatziioannou
- Metabolic Engineering and Bioinformatics Program, Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece.,eNIOS Applications P.C., Athens, Greece
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Malagari K, Moschouris H, Kiakidis T, Harward S, Kelekis A, Vrakas S, Koundouras D, Filipiadis D, Glantzounis G, Emmanouil E, Chatziioannou A, Vergadis V, Elefsiniotis I, Koskinas J, Dourakis S, Kelekis N. Five-Years Outcome Analysis of 142 Consecutive Hepatocellular Carcinoma Patients Treated with Doxorubicin Eluting Microspheres 30-60 μm: Results from a Single-Centre Prospective Phase II Trial. Cardiovasc Intervent Radiol 2019; 42:1551-1562. [PMID: 31321482 DOI: 10.1007/s00270-019-02260-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 06/03/2019] [Indexed: 12/19/2022]
Abstract
PURPOSE To assess prospectively long-term results of doxorubicin-loaded HepaSphere 30-60 μm in consecutive patients with hepatocellular carcinoma (HCC) not amenable to curative treatments. PATIENTS AND METHODS Single-center study from June 2011 to December 2015 in 151 patients treated with 75 mg of doxorubicin per HepaSphere vial. Baseline: Barcelona Clinic Liver Cancer BCLC A/B was 49.3%/50.7%, and median diameter 6.1 cm (mean 6.7 ± 2.0). Liver function, local response (mRECIST), liver time to progression (LTTP), progression-free survival (PFS), overall survival (OS) and adverse events (AEs) were recorded. RESULTS Final analysis included 142 patients with median follow-up of 46.8 months (range 4-72) without grade 4/5 AEs, and 30-day mortality was 0%. Mean number of scheduled treatments was 2.6 (range 1-3) and on demand 3 (range 1-8). Complete response for single tumor ≤ 5 cm was 75.0% and 66.7% for Child A and Child B, while for > 5 cm was 28.6% and 11.8%, respectively. OS was 31.0 months (mean 33.3 ± 15.2; range 8-69), notably for BCLC A 41 months (mean 41.1 ± 15.3; range 13-69) and for BCLC B 26.0 (mean 26.0 ± 10.5; range 8-51). OS at 1, 3 and 5 years: 95.8%, 75.7% and 21.4% for BCLC A, and 94.4%, 36.1% and 2.7% for BCLC B. Median LTTP for BCLC A was 11 months (mean 11.9 ± 4.7; range 3-24) and 7.5 for BCLC B (mean 7.9 ± 2.9). Local response was significant for OS and LTTP (p < 0.0001), while size and lesion number affected LPFS and OS (p < 0.001). CONCLUSIONS HepaSphere 30-60 μm loaded with doxorubicin provides a safe and effective treatment option for patients with HCC.
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Affiliation(s)
- K Malagari
- 2nd Department of Radiology, Medical School, National and Kapodistrian University of Athens, 19 Monis Kyccou, 15669, Papagou, Athens, Greece. .,Attikon Hospital, Chaidari, Greece. .,Evgenidion Hospital, Athens, Greece.
| | - H Moschouris
- Radiology Department of Tzanion General Hospital, Athens, Greece
| | - Th Kiakidis
- 2nd Department of Radiology, Medical School, National and Kapodistrian University of Athens, 19 Monis Kyccou, 15669, Papagou, Athens, Greece.,Evgenidion Hospital, Athens, Greece
| | - S Harward
- University of Massachusets Medical School, Worcester, MA, USA
| | - A Kelekis
- 2nd Department of Radiology, Medical School, National and Kapodistrian University of Athens, 19 Monis Kyccou, 15669, Papagou, Athens, Greece.,Attikon Hospital, Chaidari, Greece.,Evgenidion Hospital, Athens, Greece
| | - S Vrakas
- Tzanion Hospital, Athens, Greece
| | - D Koundouras
- 2nd Clinic of Medicine and Hepatology Medical School, National and Kapodistrian University of Athens, Athens, Greece.,2nd Clinic of Internal Medicine University of Athens Hippokration Hospital, Athens, Greece
| | - D Filipiadis
- 2nd Department of Radiology, Medical School, National and Kapodistrian University of Athens, 19 Monis Kyccou, 15669, Papagou, Athens, Greece.,Attikon Hospital, Chaidari, Greece
| | - G Glantzounis
- Department of Surgery, University Hospital of Ioannina (UOI), Ioannina, Greece
| | - E Emmanouil
- 2nd Department of Radiology, Medical School, National and Kapodistrian University of Athens, 19 Monis Kyccou, 15669, Papagou, Athens, Greece.,Evgenidion Hospital, Athens, Greece
| | - A Chatziioannou
- Evgenidion Hospital, Athens, Greece.,1st Department of Radiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - V Vergadis
- Radiology Department of Laikon University Hospital, Athens, Greece
| | - I Elefsiniotis
- Department of Internal Medicine and Hepatology Unit, Agioi Anargyroi General and Oncology Hospital of Kifissia Hospital Timiou Stavrou and Noufaron, Kalyftaki, Athens, Greece
| | - J Koskinas
- 2nd Clinic of Medicine and Hepatology Medical School, National and Kapodistrian University of Athens, Athens, Greece.,2nd Clinic of Internal Medicine University of Athens Hippokration Hospital, Athens, Greece
| | - S Dourakis
- 2nd Clinic of Medicine and Hepatology Medical School, National and Kapodistrian University of Athens, Athens, Greece.,2nd Clinic of Internal Medicine University of Athens Hippokration Hospital, Athens, Greece
| | - N Kelekis
- 2nd Department of Radiology, Medical School, National and Kapodistrian University of Athens, 19 Monis Kyccou, 15669, Papagou, Athens, Greece.,Attikon Hospital, Chaidari, Greece.,Evgenidion Hospital, Athens, Greece
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32
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Vlachavas EI, Pilalis E, Papadodima O, Koczan D, Willis S, Klippel S, Cheng C, Pan L, Sachpekidis C, Pintzas A, Gregoriou V, Dimitrakopoulou-Strauss A, Chatziioannou A. Radiogenomic Analysis of F-18-Fluorodeoxyglucose Positron Emission Tomography and Gene Expression Data Elucidates the Epidemiological Complexity of Colorectal Cancer Landscape. Comput Struct Biotechnol J 2019; 17:177-185. [PMID: 30809322 PMCID: PMC6374701 DOI: 10.1016/j.csbj.2019.01.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [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: 11/19/2018] [Revised: 01/18/2019] [Accepted: 01/19/2019] [Indexed: 02/07/2023] Open
Abstract
Purpose Transcriptomic profiling has enabled the neater genomic characterization of several cancers, among them colorectal cancer (CRC), through the derivation of genes with enhanced causal role and informative gene sets. However, the identification of small-sized gene signatures, which can serve as potential biomarkers in CRC, remains challenging, mainly due to the great genetic heterogeneity of the disease. Methods We developed and exploited an analytical framework for the integrative analysis of CRC datasets, encompassing transcriptomic data and positron emission tomography (PET) measurements. Profiling data comprised two microarray datasets, pertaining biopsy specimen from 30 untreated patients with primary CRC, coupled by their F-18-Fluorodeoxyglucose (FDG) PET values, using tracer kinetic analysis measurements. The computational framework incorporates algorithms for semantic processing, multivariate analysis, data mining and dimensionality reduction. Results Transcriptomic and PET data feature sets, were evaluated for their discrimination performance between primary colorectal adenocarcinomas and adjacent normal mucosa. A composite signature was derived, pertaining 12 features: 7 genes and 5 PET variables. This compact signature manifests superior performance in classification accuracy, through the integration of gene expression and PET data. Conclusions This work represents an effort for the integrative, multilayered, signature-oriented analysis of CRC, in the context of radio-genomics, inferring a composite signature with promising results for patient stratification.
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Key Words
- 18F-FDG PET
- ACADM, Acyl-Coenzyme A Dehydrogenase
- AUC, Area Under the Curve
- CCT7, Chaperonin Containing TCP1 Subunit 7
- CD44, CD44 Molecule (Indian Blood Group)
- CRC, Colorectal cancer
- Colorectal cancer
- DE, Differentially Expressed
- FD, Fractal Dimension
- FDG, F-18-Fluorodeoxyglucose
- GDC, Genomics Data Commons
- GEO, Gene Expression Omnibus
- GSTP1, Glutathione S-Transferase Pi 1
- KIT, Proto-Oncogene Receptor Tyrosine Kinase
- Lasso, least absolute shrinkage and selection operator
- MFA, Multiple Factor Analysis
- Microarray analysis
- PCs, Principal Components
- PET, Positron Emission Tomography
- ROC, Receiver-operator Characteristic curve
- Radiogenomics
- SUV, Standardized Uptake Value
- TCGA
- TCGA-COAD, The Cancer Genome Atlas-Colon Adenocarcinoma
- Translational bioinformatics
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Affiliation(s)
- Efstathios-Iason Vlachavas
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece.,Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Dragana, Greece.,Enios Applications Private Limited Company, A17671 Athens, Greece
| | - Eleftherios Pilalis
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece.,Enios Applications Private Limited Company, A17671 Athens, Greece
| | - Olga Papadodima
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Dirk Koczan
- Core Facility Micro-Array-Technology, Center of Medical Research, University of Rostock, Germany
| | | | - Sven Klippel
- Surgical Clinic A, Klinikum Ludwigshafen, Germany
| | - Caixia Cheng
- Clinical Cooperation Unit Nuclear Medicine, German Cancer Research Center, Heidelberg, Germany
| | - Leyun Pan
- Clinical Cooperation Unit Nuclear Medicine, German Cancer Research Center, Heidelberg, Germany
| | - Christos Sachpekidis
- Clinical Cooperation Unit Nuclear Medicine, German Cancer Research Center, Heidelberg, Germany
| | - Alexandros Pintzas
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Vasilis Gregoriou
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | | | - Aristotelis Chatziioannou
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece.,Enios Applications Private Limited Company, A17671 Athens, Greece
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33
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Obiedat A, Seidel E, Mahameed M, Berhani O, Tsukerman P, Voutetakis K, Chatziioannou A, McMahon M, Avril T, Chevet E, Mandelboim O, Tirosh B. Transcription of the NKG2D ligand MICA is suppressed by the IRE1/XBP1 pathway of the unfolded protein response through the regulation of E2F1. FASEB J 2018; 33:3481-3495. [PMID: 30452881 DOI: 10.1096/fj.201801350rr] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [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: 12/31/2022]
Abstract
The unfolded protein response (UPR) is an adaptive signaling pathway activated in response to endoplasmic reticulum (ER) stress. The effectors of the UPR are potent transcription activators; however, some genes are suppressed by ER stress at the mRNA level. The mechanisms underlying UPR-mediated gene suppression are less known. Exploration of the effect of UPR on NK cells ligand expression found that the transcription of NK group 2 member D (NKG2D) ligand major histocompatibility complex class I polypeptide-related sequence A/B (MICA/B) is suppressed by the inositol-requiring enzyme 1 (IRE1)/X-box binding protein 1 (XBP1) pathway of the UPR. Deletion of IRE1 or XBP1 was sufficient to promote mRNA and surface levels of MICA. Accordingly, NKG2D played a greater role in the killing of IRE1/XBP1 knockout target cells. Analysis of effectors downstream to XBP1s identified E2F transcription factor 1 (E2F1) as linking UPR and MICA transcription. The inverse correlation between XBP1 and E2F1 or MICA expression was corroborated in RNA-Seq analysis of 470 primary melanoma tumors. While mechanisms that connect XBP1 to E2F1 are not fully understood, we implicate a few microRNA molecules that are modulated by ER stress and possess dual suppression of E2F1 and MICA. Because of the importance of E2F1 and MICA in cancer progression and recognition, these observations could be exploited for cancer therapy by manipulating the UPR in tumor cells.-Obiedat, A., Seidel, E., Mahameed, M., Berhani, O., Tsukerman, P., Voutetakis, K., Chatziioannou, A., McMahon, M., Avril, T., Chevet, E., Mandelboim, O., Tirosh, B. Transcription of the NKG2D ligand MICA is suppressed by the IRE1/XBP1 pathway of the unfolded protein response through the regulation of E2F1.
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Affiliation(s)
- Akram Obiedat
- Institute for Drug Research, School of Pharmacy, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Einat Seidel
- The Lautenberg Center for Immunology and Cancer Research, The Biomedical Research Institute Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem Hadassah Medical School, Jerusalem, Israel
| | - Mohamed Mahameed
- Institute for Drug Research, School of Pharmacy, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Orit Berhani
- The Lautenberg Center for Immunology and Cancer Research, The Biomedical Research Institute Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem Hadassah Medical School, Jerusalem, Israel
| | - Pinchas Tsukerman
- The Lautenberg Center for Immunology and Cancer Research, The Biomedical Research Institute Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem Hadassah Medical School, Jerusalem, Israel
| | - Konstantinos Voutetakis
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation (NHRF), Athens, Greece.,Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Aristotelis Chatziioannou
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation (NHRF), Athens, Greece.,e-Noesis Inspired Operational Systems Applications Private Company PC, Kallithea-Athens, Greece
| | - Mari McMahon
- INSERM U1242, University of Rennes, Rennes, France.,Centre de Lutte contre le Cancer Eugène Marquis, Rennes, France; and.,Apoptosis Research Centre (ARC), National University of Ireland, Galway (NUIG), Galway, Ireland
| | - Tony Avril
- INSERM U1242, University of Rennes, Rennes, France.,Centre de Lutte contre le Cancer Eugène Marquis, Rennes, France; and
| | - Eric Chevet
- INSERM U1242, University of Rennes, Rennes, France.,Centre de Lutte contre le Cancer Eugène Marquis, Rennes, France; and
| | - Ofer Mandelboim
- The Lautenberg Center for Immunology and Cancer Research, The Biomedical Research Institute Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem Hadassah Medical School, Jerusalem, Israel
| | - Boaz Tirosh
- Institute for Drug Research, School of Pharmacy, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
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Petry KG, Vekris A, Pilalis E, Chatziioannou A. Innovations in molecular biology and proteomics adapted to in vivo peptide phage display define active protein domains as biomarkers in multiple sclerosis neuroinflammation. Meta Gene 2018. [DOI: 10.1016/j.mgene.2018.05.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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35
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Vermeulen R, Saberi Hosnijeh F, Bodinier B, Portengen L, Liquet B, Garrido-Manriquez J, Lokhorst H, Bergdahl IA, Kyrtopoulos SA, Johansson AS, Georgiadis P, Melin B, Palli D, Krogh V, Panico S, Sacerdote C, Tumino R, Vineis P, Castagné R, Chadeau-Hyam M, Botsivali M, Chatziioannou A, Valavanis I, Kleinjans JCS, de Kok TMCM, Keun HC, Athersuch TJ, Kelly R, Lenner P, Hallmans G, Stephanou EG, Myridakis A, Kogevinas M, Fazzo L, De Santis M, Comba P, Bendinelli B, Kiviranta H, Rantakokko P, Airaksinen R, Ruokojarvi P, Gilthorpe M, Fleming S, Fleming T, Tu YK, Lundh T, Chien KL, Chen WJ, Lee WC, Kate Hsiao C, Kuo PH, Hung H, Liao SF. Pre-diagnostic blood immune markers, incidence and progression of B-cell lymphoma and multiple myeloma: Univariate and functionally informed multivariate analyses. Int J Cancer 2018; 143:1335-1347. [PMID: 29667176 PMCID: PMC6100111 DOI: 10.1002/ijc.31536] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [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: 12/27/2017] [Revised: 03/15/2018] [Accepted: 03/19/2018] [Indexed: 12/13/2022]
Abstract
Recent prospective studies have shown that dysregulation of the immune system may precede the development of B‐cell lymphomas (BCL) in immunocompetent individuals. However, to date, the studies were restricted to a few immune markers, which were considered separately. Using a nested case–control study within two European prospective cohorts, we measured plasma levels of 28 immune markers in samples collected a median of 6 years before diagnosis (range 2.01–15.97) in 268 incident cases of BCL (including multiple myeloma [MM]) and matched controls. Linear mixed models and partial least square analyses were used to analyze the association between levels of immune marker and the incidence of BCL and its main histological subtypes and to investigate potential biomarkers predictive of the time to diagnosis. Linear mixed model analyses identified associations linking lower levels of fibroblast growth factor‐2 (FGF‐2 p = 7.2 × 10−4) and transforming growth factor alpha (TGF‐α, p = 6.5 × 10−5) and BCL incidence. Analyses stratified by histological subtypes identified inverse associations for MM subtype including FGF‐2 (p = 7.8 × 10−7), TGF‐α (p = 4.08 × 10−5), fractalkine (p = 1.12 × 10−3), monocyte chemotactic protein‐3 (p = 1.36 × 10−4), macrophage inflammatory protein 1‐alpha (p = 4.6 × 10−4) and vascular endothelial growth factor (p = 4.23 × 10−5). Our results also provided marginal support for already reported associations between chemokines and diffuse large BCL (DLBCL) and cytokines and chronic lymphocytic leukemia (CLL). Case‐only analyses showed that Granulocyte‐macrophage colony stimulating factor levels were consistently higher closer to diagnosis, which provides further evidence of its role in tumor progression. In conclusion, our study suggests a role of growth‐factors in the incidence of MM and of chemokine and cytokine regulation in DLBCL and CLL. What's new? B‐cell lymphomas (BCL) are frequent in immunocompromised individuals, but most BCL cases are thought to occur as a consequence of minor immune perturbations in otherwise immunocompetent individuals. Here the authors prospectively examined a panel of immune markers in the blood from 268 patients afflicted with BCL and paired controls. The data uncover a functional role for growth factors (i.e. FGF‐2, TGF‐alpha) in the incidence and progression of multiple myeloma, a BCL subtype, and underscore the importance of chemokine and cytokine regulation in diffuse large B‐cell lymphoma and chronic lymphocytic leukemia.
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Affiliation(s)
- Roel Vermeulen
- Division of Environmental Epidemiology, Utrecht University, Institute for Risk Assessment Sciences, Utrecht, The Netherlands.,MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom
| | - Fatemeh Saberi Hosnijeh
- Division of Environmental Epidemiology, Utrecht University, Institute for Risk Assessment Sciences, Utrecht, The Netherlands.,Immunology Department, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Barbara Bodinier
- MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom
| | - Lützen Portengen
- Division of Environmental Epidemiology, Utrecht University, Institute for Risk Assessment Sciences, Utrecht, The Netherlands
| | - Benoît Liquet
- Laboratoire de Mathématiques et de leurs Applications, Université de Pau et des Pays de l'Adour, UMR CNRS, Pau, France.,ARC Centre of Excellence for Mathematical and Statistical Frontiers, Queensland University of Technology (QUT), Brisbane, Australia
| | - Javiera Garrido-Manriquez
- MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom
| | - Henk Lokhorst
- Department of Hematology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ingvar A Bergdahl
- Department of Public Health and Clinical Medicine, and Department of Biobank Research, Umeå University, Umeå, Sweden
| | - Soterios A Kyrtopoulos
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, Athens, Greece
| | | | - Panagiotis Georgiadis
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, Athens, Greece
| | - Beatrice Melin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Domenico Palli
- The Institute for Cancer Research and Prevention, Florence, Italy
| | - Vittorio Krogh
- Fondazione IRCCS-Instituto Nazionale dei Tumori, Milan, Italy
| | - Salvatore Panico
- Department of Clinical Medicine and Surgery, University of Naples Frederico II, Naples, Italy
| | - Carlotta Sacerdote
- Piedmont Reference Centre for Epidemiology and Cancer Prevention (CPO Piemonte), Turin, Italy
| | - Rosario Tumino
- Cancer registry and Histopathology Unit, Azienda Ospedaliera 'Civile-M.P.Arezzo', Ragusa, Italy
| | - Paolo Vineis
- MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom.,HuGeF Foundation, Torino, Italy
| | - Raphaële Castagné
- MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom.,INSERM, UMR1027, Université Toulouse III-Paul Sabatier, Toulouse, France
| | - Marc Chadeau-Hyam
- Division of Environmental Epidemiology, Utrecht University, Institute for Risk Assessment Sciences, Utrecht, The Netherlands.,MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom
| | | | - Maria Botsivali
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Aristotelis Chatziioannou
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Ioannis Valavanis
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Jos C S Kleinjans
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | - Theo M C M de Kok
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | - Hector C Keun
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Institute of Reproductive and Developmental Biology (IRDB), Hammersmith Hospital, London, United Kingdom
| | - Toby J Athersuch
- MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom.,Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Rachel Kelly
- Immunology Department, Erasmus University Medical Center, Rotterdam, The Netherlands.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - Per Lenner
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Goran Hallmans
- Nutrition Research, Department of Public Health and Clinical Medicine, and Department of Biobank Research, Umeå University, Umeå, Sweden
| | | | - Antonis Myridakis
- Environmental Chemical Processes Laboratory, University of Crete, Heraklion, Greece
| | - Manolis Kogevinas
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
| | | | | | | | | | | | | | | | | | | | | | | | - Yu-Kang Tu
- University of Leeds, Leeds, United Kingdom
| | | | | | - Wei J Chen
- National Taiwan University, Taipei, Taiwan
| | | | | | | | - Hung Hung
- National Taiwan University, Taipei, Taiwan
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Lhomond S, Avril T, Dejeans N, Voutetakis K, Doultsinos D, McMahon M, Pineau R, Obacz J, Papadodima O, Jouan F, Bourien H, Logotheti M, Jégou G, Pallares‐Lupon N, Schmit K, Le Reste P, Etcheverry A, Mosser J, Barroso K, Vauléon E, Maurel M, Samali A, Patterson JB, Pluquet O, Hetz C, Quillien V, Chatziioannou A, Chevet E. Dual IRE1 RNase functions dictate glioblastoma development. EMBO Mol Med 2018; 10:emmm.201707929. [PMID: 29311133 PMCID: PMC5840541 DOI: 10.15252/emmm.201707929] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [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] [Indexed: 12/31/2022] Open
Abstract
Proteostasis imbalance is emerging as a major hallmark of cancer, driving tumor aggressiveness. Evidence suggests that the endoplasmic reticulum (ER), a major site for protein folding and quality control, plays a critical role in cancer development. This concept is valid in glioblastoma multiform (GBM), the most lethal primary brain cancer with no effective treatment. We previously demonstrated that the ER stress sensor IRE1α (referred to as IRE1) contributes to GBM progression, through XBP1 mRNA splicing and regulated IRE1-dependent decay (RIDD) of RNA Here, we first demonstrated IRE1 signaling significance to human GBM and defined specific IRE1-dependent gene expression signatures that were confronted to human GBM transcriptomes. This approach allowed us to demonstrate the antagonistic roles of XBP1 mRNA splicing and RIDD on tumor outcomes, mainly through selective remodeling of the tumor stroma. This study provides the first demonstration of a dual role of IRE1 downstream signaling in cancer and opens a new therapeutic window to abrogate tumor progression.
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Affiliation(s)
| | - Tony Avril
- INSERM U1242, “Chemistry, Oncogenesis, Stress, Signaling”Université de Rennes 1RennesFrance,Centre de Lutte Contre le Cancer Eugène MarquisRennesFrance
| | | | - Konstantinos Voutetakis
- Institute of Biology, Medicinal Chemistry & BiotechnologyNHRFAthensGreece,Department of Biochemistry & BiotechnologyUniversity of ThessalyLarissaGreece
| | - Dimitrios Doultsinos
- INSERM U1242, “Chemistry, Oncogenesis, Stress, Signaling”Université de Rennes 1RennesFrance,Centre de Lutte Contre le Cancer Eugène MarquisRennesFrance
| | - Mari McMahon
- INSERM U1242, “Chemistry, Oncogenesis, Stress, Signaling”Université de Rennes 1RennesFrance,Centre de Lutte Contre le Cancer Eugène MarquisRennesFrance,Apoptosis Research CentreSchool of Natural SciencesNUI GalwayGalwayIreland
| | - Raphaël Pineau
- INSERM U1242, “Chemistry, Oncogenesis, Stress, Signaling”Université de Rennes 1RennesFrance,Centre de Lutte Contre le Cancer Eugène MarquisRennesFrance
| | - Joanna Obacz
- INSERM U1242, “Chemistry, Oncogenesis, Stress, Signaling”Université de Rennes 1RennesFrance,Centre de Lutte Contre le Cancer Eugène MarquisRennesFrance
| | - Olga Papadodima
- Institute of Biology, Medicinal Chemistry & BiotechnologyNHRFAthensGreece
| | - Florence Jouan
- INSERM U1242, “Chemistry, Oncogenesis, Stress, Signaling”Université de Rennes 1RennesFrance,Centre de Lutte Contre le Cancer Eugène MarquisRennesFrance
| | - Heloise Bourien
- INSERM U1242, “Chemistry, Oncogenesis, Stress, Signaling”Université de Rennes 1RennesFrance,Centre de Lutte Contre le Cancer Eugène MarquisRennesFrance
| | - Marianthi Logotheti
- Institute of Biology, Medicinal Chemistry & BiotechnologyNHRFAthensGreece,e‐NIOS PCKallithea‐AthensGreece
| | - Gwénaële Jégou
- INSERM U1242, “Chemistry, Oncogenesis, Stress, Signaling”Université de Rennes 1RennesFrance,Centre de Lutte Contre le Cancer Eugène MarquisRennesFrance
| | | | | | - Pierre‐Jean Le Reste
- INSERM U1242, “Chemistry, Oncogenesis, Stress, Signaling”Université de Rennes 1RennesFrance,Department of NeurosurgeryUniversity Hospital PontchaillouRennesFrance
| | - Amandine Etcheverry
- Integrated Functional Genomics and Biomarkers TeamUMR6290, CNRSUniversité de Rennes 1RennesFrance
| | - Jean Mosser
- Integrated Functional Genomics and Biomarkers TeamUMR6290, CNRSUniversité de Rennes 1RennesFrance
| | - Kim Barroso
- INSERM U1242, “Chemistry, Oncogenesis, Stress, Signaling”Université de Rennes 1RennesFrance,Centre de Lutte Contre le Cancer Eugène MarquisRennesFrance
| | - Elodie Vauléon
- INSERM U1242, “Chemistry, Oncogenesis, Stress, Signaling”Université de Rennes 1RennesFrance,Centre de Lutte Contre le Cancer Eugène MarquisRennesFrance
| | - Marion Maurel
- INSERM U1242, “Chemistry, Oncogenesis, Stress, Signaling”Université de Rennes 1RennesFrance,Centre de Lutte Contre le Cancer Eugène MarquisRennesFrance,Apoptosis Research CentreSchool of Natural SciencesNUI GalwayGalwayIreland
| | - Afshin Samali
- Apoptosis Research CentreSchool of Natural SciencesNUI GalwayGalwayIreland
| | | | - Olivier Pluquet
- Institut Pasteur de LilleCNRS UMR8161 “Mechanisms of Tumourigenesis and Targeted Therapies”Université de LilleLilleFrance
| | - Claudio Hetz
- Biomedical Neuroscience InstituteFaculty of MedicineUniversity of ChileSantiagoChile,Program of Cellular and Molecular BiologyInstitute of Biomedical SciencesUniversity of ChileSantiagoChile,Center for Geroscience, Brain Health and MetabolismSantiagoChile,Buck Institute for Research on AgingNovatoCAUSA,Department of Immunology and Infectious diseasesHarvard School of Public HealthBostonMAUSA
| | - Véronique Quillien
- INSERM U1242, “Chemistry, Oncogenesis, Stress, Signaling”Université de Rennes 1RennesFrance,Centre de Lutte Contre le Cancer Eugène MarquisRennesFrance
| | - Aristotelis Chatziioannou
- Institute of Biology, Medicinal Chemistry & BiotechnologyNHRFAthensGreece,e‐NIOS PCKallithea‐AthensGreece
| | - Eric Chevet
- INSERM U1242, “Chemistry, Oncogenesis, Stress, Signaling”Université de Rennes 1RennesFrance,Centre de Lutte Contre le Cancer Eugène MarquisRennesFrance
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Yeles C, Vlachavas EI, Papadodima O, Pilalis E, Vorgias CE, Georgakilas AG, Chatziioannou A. Integrative Bioinformatic Analysis of Transcriptomic Data Identifies Conserved Molecular Pathways Underlying Ionizing Radiation-Induced Bystander Effects (RIBE). Cancers (Basel) 2017; 9:E160. [PMID: 29186820 PMCID: PMC5742808 DOI: 10.3390/cancers9120160] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [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: 11/06/2017] [Revised: 11/18/2017] [Accepted: 11/22/2017] [Indexed: 12/11/2022] Open
Abstract
Ionizing radiation-induced bystander effects (RIBE) encompass a number of effects with potential for a plethora of damages in adjacent non-irradiated tissue. The cascade of molecular events is initiated in response to the exposure to ionizing radiation (IR), something that may occur during diagnostic or therapeutic medical applications. In order to better investigate these complex response mechanisms, we employed a unified framework integrating statistical microarray analysis, signal normalization, and translational bioinformatics functional analysis techniques. This approach was applied to several microarray datasets from Gene Expression Omnibus (GEO) related to RIBE. The analysis produced lists of differentially expressed genes, contrasting bystander and irradiated samples versus sham-irradiated controls. Furthermore, comparative molecular analysis through BioInfoMiner, which integrates advanced statistical enrichment and prioritization methodologies, revealed discrete biological processes, at the cellular level. For example, the negative regulation of growth, cellular response to Zn2+-Cd2+, and Wnt and NIK/NF-kappaB signaling, thus refining the description of the phenotypic landscape of RIBE. Our results provide a more solid understanding of RIBE cell-specific response patterns, especially in the case of high-LET radiations, like α-particles and carbon-ions.
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Affiliation(s)
- Constantinos Yeles
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Zografou Campus, 15701 Athens, Greece; (C.Y.); (C.E.V.)
- Metabolic Engineering and Bioinformatics Research Team, Institute of Biology Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, 11635 Athens, Greece; (E.-I.V); (O.P.)
| | - Efstathios-Iason Vlachavas
- Metabolic Engineering and Bioinformatics Research Team, Institute of Biology Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, 11635 Athens, Greece; (E.-I.V); (O.P.)
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Dragana, Greece
- Enios Applications Private Limited Company, A17671 Athens, Greece;
| | - Olga Papadodima
- Metabolic Engineering and Bioinformatics Research Team, Institute of Biology Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, 11635 Athens, Greece; (E.-I.V); (O.P.)
| | | | - Constantinos E. Vorgias
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Zografou Campus, 15701 Athens, Greece; (C.Y.); (C.E.V.)
| | - Alexandros G. Georgakilas
- Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), Zografou, 15780 Athens, Greece;
| | - Aristotelis Chatziioannou
- Metabolic Engineering and Bioinformatics Research Team, Institute of Biology Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, 11635 Athens, Greece; (E.-I.V); (O.P.)
- Enios Applications Private Limited Company, A17671 Athens, Greece;
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38
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Georgiadis P, Liampa I, Hebels DG, Krauskopf J, Chatziioannou A, Valavanis I, de Kok TM, Kleinjans JC, Bergdahl IA, Melin B, Spaeth F, Palli D, Vermeulen R, Vlaanderen J, Chadeau-Hyam M, Vineis P, Kyrtopoulos SA. Evolving DNA methylation and gene expression markers of B-cell chronic lymphocytic leukemia are present in pre-diagnostic blood samples more than 10 years prior to diagnosis. BMC Genomics 2017; 18:728. [PMID: 28903739 PMCID: PMC5598006 DOI: 10.1186/s12864-017-4117-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 09/05/2017] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND B-cell chronic lymphocytic leukemia (CLL) is a common type of adult leukemia. It often follows an indolent course and is preceded by monoclonal B-cell lymphocytosis, an asymptomatic condition, however it is not known what causes subjects with this condition to progress to CLL. Hence the discovery of prediagnostic markers has the potential to improve the identification of subjects likely to develop CLL and may also provide insights into the pathogenesis of the disease of potential clinical relevance. RESULTS We employed peripheral blood buffy coats of 347 apparently healthy subjects, of whom 28 were diagnosed with CLL 2.0-15.7 years after enrollment, to derive for the first time genome-wide DNA methylation, as well as gene and miRNA expression, profiles associated with the risk of future disease. After adjustment for white blood cell composition, we identified 722 differentially methylated CpG sites and 15 differentially expressed genes (Bonferroni-corrected p < 0.05) as well as 2 miRNAs (FDR < 0.05) which were associated with the risk of future CLL. The majority of these signals have also been observed in clinical CLL, suggesting the presence in prediagnostic blood of CLL-like cells. Future CLL cases who, at enrollment, had a relatively low B-cell fraction (<10%), and were therefore less likely to have been suffering from undiagnosed CLL or a precursor condition, showed profiles involving smaller numbers of the same differential signals with intensities, after adjusting for B-cell content, generally smaller than those observed in the full set of cases. A similar picture was obtained when the differential profiles of cases with time-to-diagnosis above the overall median period of 7.4 years were compared with those with shorted time-to-disease. Differentially methylated genes of major functional significance include numerous genes that encode for transcription factors, especially members of the homeobox family, while differentially expressed genes include, among others, multiple genes related to WNT signaling as well as the miRNAs miR-150-5p and miR-155-5p. CONCLUSIONS Our findings demonstrate the presence in prediagnostic blood of future CLL patients, more than 10 years before diagnosis, of CLL-like cells which evolve as preclinical disease progresses, and point to early molecular alterations with a pathogenetic potential.
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MESH Headings
- Biomarkers, Tumor/genetics
- DNA Methylation
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Leukemia, Lymphocytic, Chronic, B-Cell/blood
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- MicroRNAs/genetics
- Prognosis
- Time Factors
- Humans
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Affiliation(s)
- Panagiotis Georgiadis
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48, Vassileos Constantinou Avenue, 11635 Athens, Greece
| | - Irene Liampa
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48, Vassileos Constantinou Avenue, 11635 Athens, Greece
| | - Dennie G. Hebels
- Department of Toxicogenomics, Maastricht University, 6229 Maastricht, ER Netherlands
| | - Julian Krauskopf
- Department of Toxicogenomics, Maastricht University, 6229 Maastricht, ER Netherlands
| | - Aristotelis Chatziioannou
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48, Vassileos Constantinou Avenue, 11635 Athens, Greece
| | - Ioannis Valavanis
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48, Vassileos Constantinou Avenue, 11635 Athens, Greece
| | - Theo M.C.M. de Kok
- Department of Toxicogenomics, Maastricht University, 6229 Maastricht, ER Netherlands
| | - Jos C.S. Kleinjans
- Department of Toxicogenomics, Maastricht University, 6229 Maastricht, ER Netherlands
| | - Ingvar A. Bergdahl
- Department of Biobank Research, and Occupational and Environmental Medicine, Department of Public Health and Clinical Medicine, Umeå University, 901 87 Umeå, Sweden
| | - Beatrice Melin
- Department of Radiation Sciences, Oncology, Umeå University, 901 87 Umeå, Sweden
| | - Florentin Spaeth
- Department of Radiation Sciences, Oncology, Umeå University, 901 87 Umeå, Sweden
| | - Domenico Palli
- The Institute for Cancer Research and Prevention, 50141 Florence, Italy
| | - R.C.H. Vermeulen
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, Netherlands
| | - J. Vlaanderen
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, Netherlands
| | - Marc Chadeau-Hyam
- Department of Epidemiology and Biostatistics, MRC-HPA Centre for Environment and Health, School of Public Health, Faculty of Medicine, Imperial College, London, W2 1PG UK
| | - Paolo Vineis
- Department of Epidemiology and Biostatistics, MRC-HPA Centre for Environment and Health, School of Public Health, Faculty of Medicine, Imperial College, London, W2 1PG UK
| | - Soterios A. Kyrtopoulos
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48, Vassileos Constantinou Avenue, 11635 Athens, Greece
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Vineis P, Chatziioannou A, Cunliffe VT, Flanagan JM, Hanson M, Kirsch-Volders M, Kyrtopoulos S. Epigenetic memory in response to environmental stressors. FASEB J 2017; 31:2241-2251. [PMID: 28280003 DOI: 10.1096/fj.201601059rr] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 02/21/2017] [Indexed: 12/22/2022]
Abstract
Exposure to environmental stressors, toxicants, and nutrient deficiencies can affect DNA in several ways. Some exposures cause damage and alter the structure of DNA, but there is increasing evidence that the same or other environmental exposures, including those that occur during fetal development in utero, can cause epigenetic effects that modulate DNA function and gene expression. Some epigenetic changes to DNA that affect gene transcription are at least partially reversible (i.e., they can be enzymatically reversed after cessation of exposure to environmental agents), but some epigenetic modifications seem to persist, even for decades. To explain the effects of early life experiences (such as famine and exposures to other stressors) on the long-term persistence of specific patterns of epigenetic modifications, such as DNA methylation, we propose an analogy with immune memory. We propose that an epigenetic memory can be established and maintained in self-renewing stem cell compartments. We suggest that the observations on early life effects on adult diseases and the persistence of methylation changes in smokers support our hypothesis, for which a mechanistic basis, however, needs to be further clarified. We outline a new model based on methylation changes. Although these changes seem to be mainly adaptive, they are also implicated in the pathogenesis and onset of diseases, depending on individual genotypic background and types of subsequent exposures. Elucidating the relationships between the adaptive and maladaptive consequences of the epigenetic modifications that result from complex environmental exposures is a major challenge for current and future research in epigenetics.-Vineis, P., Chatziioannou, A., Cunliffe, V. T., Flanagan, J. M., Hanson, M., Kirsch-Volders, M., Kyrtopoulos, S. Epigenetic memory in response to environmental stressors.
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Affiliation(s)
- Paolo Vineis
- Medical Research Council-Public Health England Center for Environment and Health, Imperial College London, London, United Kingdom;
| | - Aristotelis Chatziioannou
- Institute of Biology, Medicinal Chemistry, and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Vincent T Cunliffe
- Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | - James M Flanagan
- Epigenetics Unit, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Mark Hanson
- Institute of Developmental Sciences, University Hospital Southampton, University of Southampton, United Kingdom
| | | | - Soterios Kyrtopoulos
- Institute of Biology, Medicinal Chemistry, and Biotechnology, National Hellenic Research Foundation, Athens, Greece
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40
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Zarafeta D, Moschidi D, Ladoukakis E, Gavrilov S, Chrysina ED, Chatziioannou A, Kublanov I, Skretas G, Kolisis FN. Metagenomic mining for thermostable esterolytic enzymes uncovers a new family of bacterial esterases. Sci Rep 2016; 6:38886. [PMID: 27991516 PMCID: PMC5171882 DOI: 10.1038/srep38886] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [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: 06/20/2016] [Accepted: 11/14/2016] [Indexed: 11/09/2022] Open
Abstract
Biocatalysts exerting activity against ester bonds have a broad range of applications in modern biotechnology. Here, we have identified a new esterolytic enzyme by screening a metagenomic sample collected from a hot spring in Kamchatka, Russia. Biochemical characterization of the new esterase, termed EstDZ2, revealed that it is highly active against medium chain fatty acid esters at temperatures between 25 and 60 °C and at pH values 7-8. The new enzyme is moderately thermostable with a half-life of more than six hours at 60 °C, but exhibits exquisite stability against high concentrations of organic solvents. Phylogenetic analysis indicated that EstDZ2 is likely an Acetothermia enzyme that belongs to a new family of bacterial esterases, for which we propose the index XV. One distinctive feature of this new family, is the presence of a conserved GHSAG catalytic motif. Multiple sequence alignment, coupled with computational modelling of the three-dimensional structure of EstDZ2, revealed that the enzyme lacks the largest part of the "cap" domain, whose extended structure is characteristic for the closely related Family IV esterases. Thus, EstDZ2 appears to be distinct from known related esterolytic enzymes, both in terms of sequence characteristics, as well as in terms of three-dimensional structure.
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Affiliation(s)
- Dimitra Zarafeta
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Danai Moschidi
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Efthymios Ladoukakis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Sergey Gavrilov
- Winogradsky Institute of Microbiology, Research Center for Biotechnology Russian Academy of Sciences, Moscow, Russian Federation
| | - Evangelia D. Chrysina
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Aristotelis Chatziioannou
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Ilya Kublanov
- Winogradsky Institute of Microbiology, Research Center for Biotechnology Russian Academy of Sciences, Moscow, Russian Federation
| | - Georgios Skretas
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Fragiskos N. Kolisis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
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Papadodima O, Moulos P, Koryllou A, Piroti G, Kolisis F, Chatziioannou A, Pletsa V. Modulation of Pathways Underlying Distinct Cell Death Mechanisms in Two Human Lung Cancer Cell Lines in Response to SN1 Methylating Agents Treatment. PLoS One 2016; 11:e0160248. [PMID: 27467507 PMCID: PMC4965087 DOI: 10.1371/journal.pone.0160248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 07/15/2016] [Indexed: 12/13/2022] Open
Affiliation(s)
- Olga Papadodima
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Panagiotis Moulos
- Institute of Molecular Biology and Genetics, Biomedical Sciences Research Centre ‘Alexander Fleming’, 16672 Vari, Greece
| | - Aggeliki Koryllou
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Georgia Piroti
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Fragiskos Kolisis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, 15780 Athens, Greece
| | - Aristotelis Chatziioannou
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 11635 Athens, Greece
- Enios Applications Private Company, 25 Al.Pantou str., 17671 Athens, Greece
- * E-mail: (AC); (VP)
| | - Vasiliki Pletsa
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 11635 Athens, Greece
- * E-mail: (AC); (VP)
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Trachana SP, Pilalis E, Gavalas NG, Tzannis K, Papadodima O, Liontos M, Rodolakis A, Vlachos G, Thomakos N, Haidopoulos D, Lykka M, Koutsoukos K, Kostouros E, Terpos E, Chatziioannou A, Dimopoulos MA, Bamias A. The Development of an Angiogenic Protein "Signature" in Ovarian Cancer Ascites as a Tool for Biologic and Prognostic Profiling. PLoS One 2016; 11:e0156403. [PMID: 27258020 PMCID: PMC4892506 DOI: 10.1371/journal.pone.0156403] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 05/13/2016] [Indexed: 01/07/2023] Open
Abstract
Advanced ovarian cancer (AOC) is one of the leading lethal gynecological cancers in developed countries. Based on the important role of angiogenesis in ovarian cancer oncogenesis and expansion, we hypothesized that the development of an "angiogenic signature" might be helpful in prediction of prognosis and efficacy of anti-angiogenic therapies in this disease. Sixty-nine samples of ascitic fluid- 35 from platinum sensitive and 34 from platinum resistant patients managed with cytoreductive surgery and 1st-line carboplatin-based chemotherapy- were analyzed using the Proteome ProfilerTM Human Angiogenesis Array Kit, screening for the presence of 55 soluble angiogenesis-related factors. A protein profile based on the expression of a subset of 25 factors could accurately separate resistant from sensitive patients with a success rate of approximately 90%. The protein profile corresponding to the "sensitive" subset was associated with significantly longer PFS (8 [95% Confidence Interval {CI}: 8-9] vs. 20 months [95% CI: 15-28]; Hazard ratio {HR}: 8.3, p<0.001) and OS (20.5 months [95% CI: 13.5-30] vs. 74 months [95% CI: 36-not reached]; HR: 5.6 [95% CI: 2.8-11.2]; p<0.001). This prognostic performance was superior to that of stage, histology and residual disease after cytoreductive surgery and the levels of vascular endothelial growth factor (VEGF) in ascites. In conclusion, we developed an "angiogenic signature" for patients with AOC, which can be used, after appropriate validation, as a prognostic marker and a tool for selection for anti-angiogenic therapies.
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Affiliation(s)
- Sofia-Paraskevi Trachana
- Department of Clinical Therapeutics, Medical School, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
- * E-mail:
| | - Eleftherios Pilalis
- Metabolic Engineering and Bioinformatics Program Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Nikos G. Gavalas
- Department of Clinical Therapeutics, Medical School, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
| | - Kimon Tzannis
- Department of Clinical Therapeutics, Medical School, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
| | - Olga Papadodima
- Metabolic Engineering and Bioinformatics Program Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Michalis Liontos
- Department of Clinical Therapeutics, Medical School, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
| | - Alexandros Rodolakis
- First Department of Obstetrics and Gynecology, Medical School, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
| | - Georgios Vlachos
- First Department of Obstetrics and Gynecology, Medical School, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
| | - Nikolaos Thomakos
- First Department of Obstetrics and Gynecology, Medical School, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
| | - Dimitrios Haidopoulos
- First Department of Obstetrics and Gynecology, Medical School, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
| | - Maria Lykka
- Department of Clinical Therapeutics, Medical School, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
| | - Konstantinos Koutsoukos
- Department of Clinical Therapeutics, Medical School, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
| | - Efthimios Kostouros
- Department of Clinical Therapeutics, Medical School, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
| | - Evagelos Terpos
- Department of Clinical Therapeutics, Medical School, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
| | - Aristotelis Chatziioannou
- Metabolic Engineering and Bioinformatics Program Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Meletios-Athanasios Dimopoulos
- Department of Clinical Therapeutics, Medical School, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
| | - Aristotelis Bamias
- Department of Clinical Therapeutics, Medical School, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
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Zarafeta D, Kissas D, Sayer C, Gudbergsdottir SR, Ladoukakis E, Isupov MN, Chatziioannou A, Peng X, Littlechild JA, Skretas G, Kolisis FN. Discovery and Characterization of a Thermostable and Highly Halotolerant GH5 Cellulase from an Icelandic Hot Spring Isolate. PLoS One 2016; 11:e0146454. [PMID: 26741138 PMCID: PMC4704807 DOI: 10.1371/journal.pone.0146454] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [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: 10/27/2015] [Accepted: 12/17/2015] [Indexed: 12/20/2022] Open
Abstract
With the ultimate goal of identifying robust cellulases for industrial biocatalytic conversions, we have isolated and characterized a new thermostable and very halotolerant GH5 cellulase. This new enzyme, termed CelDZ1, was identified by bioinformatic analysis from the genome of a polysaccharide-enrichment culture isolate, initiated from material collected from an Icelandic hot spring. Biochemical characterization of CelDZ1 revealed that it is a glycoside hydrolase with optimal activity at 70°C and pH 5.0 that exhibits good thermostability, high halotolerance at near-saturating salt concentrations, and resistance towards metal ions and other denaturing agents. X-ray crystallography of the new enzyme showed that CelDZ1 is the first reported cellulase structure that lacks the defined sugar-binding 2 subsite and revealed structural features which provide potential explanations of its biochemical characteristics.
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Affiliation(s)
- Dimitra Zarafeta
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Dimitrios Kissas
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Christopher Sayer
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | | | - Efthymios Ladoukakis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Michail N. Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Aristotelis Chatziioannou
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Xu Peng
- Danish Archaea Centre, Department of Biology, Copenhagen University, Copenhagen, Denmark
| | - Jennifer A. Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Georgios Skretas
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Fragiskos N. Kolisis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
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44
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Logotheti M, Pilalis E, Venizelos N, Kolisis F, Chatziioannou A. Development and validation of a skin fibroblast biomarker profile for schizophrenic patients. AIMS Bioengineering 2016. [DOI: 10.3934/bioeng.2016.4.552] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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45
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Valenciaga Y, Prout D, Chatziioannou A. SU-C-201-01: Investigation of the Effects of Scintillator Surface Treatment On Light Output Measurements with SiPM Detectors. Med Phys 2015. [DOI: 10.1118/1.4923839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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46
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Pilalis E, Koutsandreas T, Valavanis I, Athanasiadis E, Spyrou G, Chatziioannou A. KENeV: A web-application for the automated reconstruction and visualization of the enriched metabolic and signaling super-pathways deriving from genomic experiments. Comput Struct Biotechnol J 2015; 13:248-55. [PMID: 26925206 PMCID: PMC4733223 DOI: 10.1016/j.csbj.2015.03.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [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: 11/05/2014] [Revised: 03/30/2015] [Accepted: 03/31/2015] [Indexed: 01/19/2023] Open
Abstract
Gene expression analysis, using high throughput genomic technologies,has become an indispensable step for the meaningful interpretation of the underlying molecular complexity, which shapes the phenotypic manifestation of the investigated biological mechanism. The modularity of the cellular response to different experimental conditions can be comprehended through the exploitation of molecular pathway databases, which offer a controlled, curated background for statistical enrichment analysis. Existing tools enable pathway analysis, visualization, or pathway merging but none integrates a fully automated workflow, combining all above-mentioned modules and destined to non-programmer users. We introduce an online web application, named KEGG Enriched Network Visualizer (KENeV), which enables a fully automated workflow starting from a list of differentially expressed genes and deriving the enriched KEGG metabolic and signaling pathways, merged into two respective, non-redundant super-networks. The final networks can be downloaded as SBML files, for further analysis, or instantly visualized through an interactive visualization module. In conclusion, KENeV (available online at http://www.grissom.gr/kenev) provides an integrative tool, suitable for users with no programming experience, for the functional interpretation, at both the metabolic and signaling level, of differentially expressed gene subsets deriving from genomic experiments.
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Affiliation(s)
- Eleftherios Pilalis
- Metabolic Engineering and Bioinformatics Programme, Institute of Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Theodoros Koutsandreas
- Metabolic Engineering and Bioinformatics Programme, Institute of Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Ioannis Valavanis
- Metabolic Engineering and Bioinformatics Programme, Institute of Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | | | - George Spyrou
- Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Aristotelis Chatziioannou
- Metabolic Engineering and Bioinformatics Programme, Institute of Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
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47
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Pampalakis G, Obasuyi O, Papadodima O, Chatziioannou A, Zoumpourlis V, Sotiropoulou G. The KLK5 protease suppresses breast cancer by repressing the mevalonate pathway. Oncotarget 2015; 5:2390-403. [PMID: 24158494 PMCID: PMC4058013 DOI: 10.18632/oncotarget.1235] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Kallikrein-related peptidase 5 (KLK5) displays aberrant expression in cancer. However, any functional association is missing. Here, we show that reconstitution of KLK5 expression in non-expressing MDA-MB-231 breast cancer cells suppresses malignancy in vitro and in vivo dose-dependently. Reactivation of KLK5 suppressed key EMT genes. Unexpectedly, we identified altered expression of genes encoding enzymes of the mevalonate pathway typical of those observed upon cholesterol starvation. Consistently, we found that SREBF1, the master regulator of the mevalonate pathway was induced. KLK5 re-expression leads to reduced cellular cholesterol and fatty acid synthesis and enhanced uptake of LDL-cholesterol. Suppression of the mevalonate pathway in KLK5 transfectants was further shown by reduced synthesis of isoprenoids. Indeed, we found diminished levels of active RhoA, a signaling oncoprotein that requires prenylation for activation. We propose that reduced RhoA activation plays a dominant role in suppression of malignancy by KLK5, since geranylgeranyl pyrophosphate restored active RhoA in KLK5-reverted cells resulting in increased malignancy. For the first time, we suggest that a protease may suppress breast cancer by modulating the mevalonate pathway.
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Papadodima O, Chatziioannou A, Patrinou-Georgoula M, Kolisis FN, Pletsa V, Guialis A. HuR-regulated mRNAs associated with nuclear hnRNP A1-RNP complexes. Int J Mol Sci 2013; 14:20256-81. [PMID: 24152440 PMCID: PMC3821614 DOI: 10.3390/ijms141020256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [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: 07/29/2013] [Revised: 09/06/2013] [Accepted: 09/16/2013] [Indexed: 12/13/2022] Open
Abstract
Post-transcriptional regulatory networks are dependent on the interplay of many RNA-binding proteins having a major role in mRNA processing events in mammals. We have been interested in the concerted action of the two RNA-binding proteins hnRNP A1 and HuR, both stable components of immunoselected hnRNP complexes and having a major nuclear localization. Specifically, we present here the application of the RNA-immunoprecipitation (RIP)-Chip technology to identify a population of nuclear transcripts associated with hnRNP A1-RNPs as isolated from the nuclear extract of either HuR WT or HuR-depleted (KO) mouse embryonic fibroblast (MEF) cells. The outcome of this analysis was a list of target genes regulated via HuR for their association (either increased or reduced) with the nuclear hnRNP A1-RNP complexes. Real time PCR analysis was applied to validate a selected number of nuclear mRNA transcripts, as well as to identify pre-spliced transcripts (in addition to their mature mRNA counterpart) within the isolated nuclear hnRNP A1-RNPs. The differentially enriched mRNAs were found to belong to GO categories relevant to biological processes anticipated for hnRNP A1 and HuR (such as transport, transcription, translation, apoptosis and cell cycle) indicating their concerted function in mRNA metabolism.
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Affiliation(s)
- Olga Papadodima
- Division of Biological Research and Biotechnology, Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens 11635, Greece; E-Mails: (O.P.); (A.C.); (M.P.-G.)
| | - Aristotelis Chatziioannou
- Division of Biological Research and Biotechnology, Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens 11635, Greece; E-Mails: (O.P.); (A.C.); (M.P.-G.)
| | - Meropi Patrinou-Georgoula
- Division of Biological Research and Biotechnology, Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens 11635, Greece; E-Mails: (O.P.); (A.C.); (M.P.-G.)
| | - Fragiskos N. Kolisis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens 15780, Greece; E-Mail:
| | - Vasiliki Pletsa
- Division of Biological Research and Biotechnology, Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens 11635, Greece; E-Mails: (O.P.); (A.C.); (M.P.-G.)
- Authors to whom correspondence should be addressed; E-Mails: (V.P.); (A.G.); Tel.: +30-210-7273-754 (V.P. & A.G.); Fax: +30-210-7273-677 (V.P. & A.G.)
| | - Apostolia Guialis
- Division of Biological Research and Biotechnology, Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens 11635, Greece; E-Mails: (O.P.); (A.C.); (M.P.-G.)
- Authors to whom correspondence should be addressed; E-Mails: (V.P.); (A.G.); Tel.: +30-210-7273-754 (V.P. & A.G.); Fax: +30-210-7273-677 (V.P. & A.G.)
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50
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Berry-Pusey BN, Chang YC, Prince SW, Chu K, David J, Taschereau R, Silverman RW, Williams D, Ladno W, Stout D, Tsao TC, Chatziioannou A. A semi-automated vascular access system for preclinical models. Phys Med Biol 2013; 58:5351-62. [PMID: 23877111 DOI: 10.1088/0031-9155/58/16/5351] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Murine models are used extensively in biological and translational research. For many of these studies it is necessary to access the vasculature for the injection of biologically active agents. Among the possible methods for accessing the mouse vasculature, tail vein injections are a routine but critical step for many experimental protocols. To perform successful tail vein injections, a high skill set and experience is required, leaving most scientists ill-suited to perform this task. This can lead to a high variability between injections, which can impact experimental results. To allow more scientists to perform tail vein injections and to decrease the variability between injections, a vascular access system (VAS) that semi-automatically inserts a needle into the tail vein of a mouse was developed. The VAS uses near infrared light, image processing techniques, computer controlled motors, and a pressure feedback system to insert the needle and to validate its proper placement within the vein. The VAS was tested by injecting a commonly used radiolabeled probe (FDG) into the tail veins of five mice. These mice were then imaged using micro-positron emission tomography to measure the percentage of the injected probe remaining in the tail. These studies showed that, on average, the VAS leaves 3.4% of the injected probe in the tail. With these preliminary results, the VAS system demonstrates the potential for improving the accuracy of tail vein injections in mice.
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Affiliation(s)
- B N Berry-Pusey
- Crump Institute for Molecular Imaging at UCLA, 570 Westwood Plaza, Los Angeles, CA 90095, USA.
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