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Hergalant S, Casse JM, Oussalah A, Houlgatte R, Helle D, Rech F, Vallar L, Guéant JL, Vignaud JM, Battaglia-Hsu SF, Gauchotte G. MicroRNAs miR-16 and miR-519 control meningioma cell proliferation via overlapping transcriptomic programs shared with the RNA-binding protein HuR. Front Oncol 2023; 13:1158773. [PMID: 37601663 PMCID: PMC10433742 DOI: 10.3389/fonc.2023.1158773] [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: 02/04/2023] [Accepted: 07/14/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction Meningiomas are the most common type of primary central nervous system tumors. In about 80% cases, these tumors are benign and grow very slowly, but the remainder 20% can unlock higher proliferation rates and become malignant. In this study we examined two miRs, miR-16 and miR-519, and evaluated their role in tumorigenesis and cell growth in human meningioma. Methods A cohort of 60 intracranial grade 1 and grade 2 human meningioma plus 20 healthy meningeal tissues was used to quantify miR-16 and miR-519 expressions. Cell growth and dose-response assays were performed in two human meningioma cell lines, Ben-Men-1 (benign) and IOMM-Lee (aggressive). Transcriptomes of IOMM-lee cells were measured after both miR-mimics transfection, followed by integrative bioinformatics to expand on available data. Results In tumoral tissues, we detected decreased levels of miR-16 and miR-519 when compared with arachnoid cells of healthy patients (miR-16: P=8.7e-04; miR-519: P=3.5e-07). When individually overexpressing these miRs in Ben-Men-1 and IOMM-Lee, we observed that each showed reduced growth (P<0.001). In IOMM-Lee cell transcriptomes, downregulated genes, among which ELAVL1/HuR (miR-16: P=6.1e-06; miR-519:P=9.38e-03), were linked to biological processes such as mitotic cell cycle regulation, pre-replicative complex, and brain development (FDR<1e-05). Additionally, we uncovered a specific transcriptomic signature of miR-16/miR-519-dysregulated genes which was highly enriched in HuR targets (>6-fold; 79.6% of target genes). Discussion These results were confirmed on several public transcriptomic and microRNA datasets of human meningiomas, hinting that the putative tumor suppressor effect of these miRs is mediated, at least in part, via HuR direct or indirect inhibition.
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Affiliation(s)
- Sébastien Hergalant
- INSERM, U1256, NGERE – Nutrition, Genetics, and Environmental Risk Exposure, Faculty of Medicine of Nancy, University of Lorraine, Vandoeuvre-lès-Nancy, France
| | - Jean-Matthieu Casse
- INSERM, U1256, NGERE – Nutrition, Genetics, and Environmental Risk Exposure, Faculty of Medicine of Nancy, University of Lorraine, Vandoeuvre-lès-Nancy, France
| | - Abderrahim Oussalah
- INSERM, U1256, NGERE – Nutrition, Genetics, and Environmental Risk Exposure, Faculty of Medicine of Nancy, University of Lorraine, Vandoeuvre-lès-Nancy, France
- Department of Molecular Medicine and Personalized Therapeutics, University Hospital of Nancy (CHRU), Vandoeuvre-lès-Nancy, France
- Department of Biochemistry, Molecular Biology, Nutrition, and Metabolism, University Hospital of Nancy (CHRU), Vandoeuvre-lès-Nancy, France
| | - Rémi Houlgatte
- INSERM, U1256, NGERE – Nutrition, Genetics, and Environmental Risk Exposure, Faculty of Medicine of Nancy, University of Lorraine, Vandoeuvre-lès-Nancy, France
| | - Déborah Helle
- INSERM, U1256, NGERE – Nutrition, Genetics, and Environmental Risk Exposure, Faculty of Medicine of Nancy, University of Lorraine, Vandoeuvre-lès-Nancy, France
| | - Fabien Rech
- Department of Neurosurgery, University Hospital of Nancy (CHRU), Nancy, France
- CNRS, UMR7039, CRAN - Centre de Recherche en Automatique de Nancy, Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Laurent Vallar
- Genomics and Proteomics, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Jean-Louis Guéant
- INSERM, U1256, NGERE – Nutrition, Genetics, and Environmental Risk Exposure, Faculty of Medicine of Nancy, University of Lorraine, Vandoeuvre-lès-Nancy, France
- Department of Molecular Medicine and Personalized Therapeutics, University Hospital of Nancy (CHRU), Vandoeuvre-lès-Nancy, France
- Department of Biochemistry, Molecular Biology, Nutrition, and Metabolism, University Hospital of Nancy (CHRU), Vandoeuvre-lès-Nancy, France
| | - Jean-Michel Vignaud
- INSERM, U1256, NGERE – Nutrition, Genetics, and Environmental Risk Exposure, Faculty of Medicine of Nancy, University of Lorraine, Vandoeuvre-lès-Nancy, France
- Department of Biopathology Institut De Cancérologie de Lorraine (CHRU-ICL), University Hospital of Nancy (CHRU), Nancy, France
- Centre de Ressources Biologiques BB-0033-00035, University Hospital of Nancy (CHRU), Nancy, France
| | - Shyue-Fang Battaglia-Hsu
- Department of Molecular Medicine and Personalized Therapeutics, University Hospital of Nancy (CHRU), Vandoeuvre-lès-Nancy, France
- Department of Biochemistry, Molecular Biology, Nutrition, and Metabolism, University Hospital of Nancy (CHRU), Vandoeuvre-lès-Nancy, France
- CNRS, UMR7039, CRAN - Centre de Recherche en Automatique de Nancy, Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Guillaume Gauchotte
- INSERM, U1256, NGERE – Nutrition, Genetics, and Environmental Risk Exposure, Faculty of Medicine of Nancy, University of Lorraine, Vandoeuvre-lès-Nancy, France
- Department of Biopathology Institut De Cancérologie de Lorraine (CHRU-ICL), University Hospital of Nancy (CHRU), Nancy, France
- Centre de Ressources Biologiques BB-0033-00035, University Hospital of Nancy (CHRU), Nancy, France
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Gallet P, Oussalah A, Pouget C, Dittmar G, Chery C, Gauchotte G, Jankowski R, Gueant JL, Houlgatte R. Integrative genomics analysis of nasal intestinal-type adenocarcinomas demonstrates the major role of CACNA1C and paves the way for a simple diagnostic tool in male woodworkers. Clin Epigenetics 2021; 13:179. [PMID: 34563241 PMCID: PMC8467244 DOI: 10.1186/s13148-021-01122-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 01/03/2021] [Accepted: 06/27/2021] [Indexed: 11/23/2022] Open
Abstract
Background Nasal intestinal-type adenocarcinomas (ITAC) are strongly related to chronic wood dust exposure: The intestinal phenotype relies on CDX2 overexpression but underlying molecular mechanisms remain unknown. Our objectives were to investigate transcriptomic and methylation differences between healthy non-exposed and tumor olfactory cleft mucosae and to compare transcriptomic profiles between non-exposed, wood dust-exposed and ITAC mucosa cells.
Methods We conducted a prospective monocentric study (NCT0281823) including 16 woodworkers with ITAC, 16 healthy exposed woodworkers and 13 healthy, non-exposed, controls. We compared tumor samples with healthy non-exposed samples, both in transcriptome and in methylome analyses. We also investigated wood dust-induced transcriptome modifications of exposed (without tumor) male woodworkers’ samples and of contralateral sides of woodworkers with tumors. We conducted in parallel transcriptome and methylome analysis, and then, the transcriptome analysis was focused on the genes highlighted in methylome analysis. We replicated our results on dataset GSE17433. Results Several clusters of genes enabled the distinction between healthy and ITAC samples. Transcriptomic and IHC analysis confirmed a constant overexpression of CDX2 in ITAC samples, without any specific DNA methylation profile regarding the CDX2 locus. ITAC woodworkers also exhibited a specific transcriptomic profile in their contralateral (non-tumor) olfactory cleft, different from that of other exposed woodworkers, suggesting that they had a different exposure or a different susceptibility. Two top-loci (CACNA1C/CACNA1C-AS1 and SLC26A10) were identified with a hemimethylated profile, but only CACNA1C appeared to be overexpressed both in transcriptomic analysis and in immunohistochemistry. Conclusions Several clusters of genes enable the distinction between healthy mucosa and ITAC samples even in contralateral nasal fossa thus paving the way for a simple diagnostic tool for ITAC in male woodworkers. CACNA1C might be considered as a master gene of ITAC and should be further investigated. Trial registration: NIH ClinicalTrials, NCT0281823, registered May 23d 2016, https://www.clinicaltrials.gov/NCT0281823. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01122-5.
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Affiliation(s)
- Patrice Gallet
- INSERM U1256, NGERE-Nutrition, Genetics, and Environmental Risk Exposure, Faculty of Medicine of Nancy, University of Lorraine, 54000, Nancy, Vandoeuvre-lès-Nancy, France. .,ENT Department, CHRU NANCY, 54511, Vandoeuvre-lès-Nancy, France.
| | - Abderrahim Oussalah
- INSERM U1256, NGERE-Nutrition, Genetics, and Environmental Risk Exposure, Faculty of Medicine of Nancy, University of Lorraine, 54000, Nancy, Vandoeuvre-lès-Nancy, France
| | - Celso Pouget
- Pathology Department, CHRU NANCY, 54511, Vandoeuvre-lès-Nancy, France
| | - Gunnar Dittmar
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Celine Chery
- INSERM U1256, NGERE-Nutrition, Genetics, and Environmental Risk Exposure, Faculty of Medicine of Nancy, University of Lorraine, 54000, Nancy, Vandoeuvre-lès-Nancy, France
| | - Guillaume Gauchotte
- INSERM U1256, NGERE-Nutrition, Genetics, and Environmental Risk Exposure, Faculty of Medicine of Nancy, University of Lorraine, 54000, Nancy, Vandoeuvre-lès-Nancy, France
| | - Roger Jankowski
- ENT Department, CHRU NANCY, 54511, Vandoeuvre-lès-Nancy, France
| | - Jean Louis Gueant
- INSERM U1256, NGERE-Nutrition, Genetics, and Environmental Risk Exposure, Faculty of Medicine of Nancy, University of Lorraine, 54000, Nancy, Vandoeuvre-lès-Nancy, France
| | - Rémi Houlgatte
- INSERM U1256, NGERE-Nutrition, Genetics, and Environmental Risk Exposure, Faculty of Medicine of Nancy, University of Lorraine, 54000, Nancy, Vandoeuvre-lès-Nancy, France
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Muller M, Broséus J, Feugier P, Thieblemont C, Beaugerie L, Danese S, Arnone D, Ndiaye NC, Kokten T, Houlgatte R, Peyrin-Biroulet L. Characteristics of Lymphoma in Patients with Inflammatory Bowel Disease: A Systematic Review. J Crohns Colitis 2021; 15:827-839. [PMID: 32949235 DOI: 10.1093/ecco-jcc/jjaa193] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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] [Indexed: 12/16/2022]
Abstract
BACKGROUND Lymphoma is a dreaded complication of inflammatory bowel diseases [IBD]. Knowledge about lymphoma in patients with IBD is limited to epidemiological data and the description of risk factors. We performed a systematic review to describe the clinical characteristics and prognosis of lymphoma in patients with IBD. METHODS Electronic databases were searched up to June 1, 2020. All published clinical characteristics of lymphoma occurring in patients with IBD were collected. RESULTS Eleven studies were included. A total of 589 lymphomas were described in patients with IBD. As seen in de novo lymphoma, non-Hodgkin's lymphoma [NHL] was the most common histological subtype [83.9%]. Diffuse large B-cell lymphoma [DLBCL] and follicular lymphoma were the most well-represented NHL in patients with IBD [30% and 13% respectively]. Two main differences were observed in comparison with de novo lymphoma: primary intestinal lymphoma [PIL] represented a large proportion of lymphoma in patients with IBD [22-75%] whereas mucosa-associated lymphoid tissue [MALT] lymphoma was under-represented. Epstein-Barr virus [EBV]-positive status was observed in a large proportion of tumours [44-75%]. Survival data of lymphoma in patients with IBD were similar to those of de novo lymphoma. DISCUSSION This systematic review first highlights that PIL [especially DLBCL subtype] is significantly more frequent in patients with IBD and represents the most common entity. Conversely, MALT lymphoma is extremely rare in the IBD population. However, the overall quality of the evidence is low. Further studies are required to better define lymphoma characteristics in patients with IBD.
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Affiliation(s)
- Marie Muller
- Department of Gastroenterology, Nancy University Hospital, University of Lorraine, Nancy, France
| | - Julien Broséus
- University of Lorraine, Inserm U1256 'Nutrition-Genetics and exposure to environmental risks-NGERE', Nancy, France.,University of Lorraine, CHRU-Nancy Hematology Laboratory, Laboratory department, Nancy, France
| | - Pierre Feugier
- University of Lorraine, Inserm U1256 'Nutrition-Genetics and exposure to environmental risks-NGERE', Nancy, France.,Department of Clinical Hematology, Nancy University Hospital, University of Lorraine, Nancy, France
| | | | - Laurent Beaugerie
- Sorbonne Université, AP-HP, Hôpital Saint-Antoine, Department of Gastroenterology, Paris, France
| | - Silvio Danese
- IBD Center, Department of Gastroenterology, Humanitas Clinical and Research Center-IRCCS, Rozzano Milan, Italy
| | - Djésia Arnone
- University of Lorraine, Inserm U1256 'Nutrition-Genetics and exposure to environmental risks-NGERE', Nancy, France
| | - Ndeye Coumba Ndiaye
- University of Lorraine, Inserm U1256 'Nutrition-Genetics and exposure to environmental risks-NGERE', Nancy, France
| | - Tunay Kokten
- University of Lorraine, Inserm U1256 'Nutrition-Genetics and exposure to environmental risks-NGERE', Nancy, France
| | - Rémi Houlgatte
- University of Lorraine, Inserm U1256 'Nutrition-Genetics and exposure to environmental risks-NGERE', Nancy, France
| | - Laurent Peyrin-Biroulet
- Department of Gastroenterology, Nancy University Hospital, University of Lorraine, Nancy, France.,University of Lorraine, Inserm U1256 'Nutrition-Genetics and exposure to environmental risks-NGERE', Nancy, France
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Muller M, Hansmannel F, Arnone D, Choukour M, Ndiaye NC, Kokten T, Houlgatte R, Peyrin-Biroulet L. Genomic and molecular alterations in human inflammatory bowel disease-associated colorectal cancer. United European Gastroenterol J 2020; 8:675-684. [PMID: 32268844 DOI: 10.1177/2050640620919254] [Citation(s) in RCA: 17] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Patients with inflammatory bowel disease are at increased risk of colorectal cancer, which has worse prognosis than sporadic colorectal cancer. Until recently, understanding of pathogenesis in inflammatory bowel disease-associated colorectal cancer was restricted to the demonstration of chromosomic/microsatellite instabilities and aneuploidy. The advance of high-throughput sequencing technologies has highlighted the complexity of the pathobiology and revealed recurrently mutated genes involved in the RTK/RAS, PI3K, WNT, and TGFβ pathways, leading to potentially new targetable mutations. Moreover, alterations of mitochondrial DNA and the dysregulation of non-coding sequences have also been described, as well as several epigenetic modifications. Although recent studies have brought new insights into pathobiology and raised the prospect of innovative therapeutic approaches, the understanding of colorectal carcinogenesis in inflammatory bowel disease and how it differs from sporadic colorectal cancer remains not fully elucidated. Further studies are required to better understand the pathogenesis and molecular alterations leading to human inflammatory bowel disease-associated colorectal cancer.
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Affiliation(s)
- Marie Muller
- Department of Gastroenterology, Nancy University Hospital, University of Lorraine, France
| | - Franck Hansmannel
- Inserm U1256 "Nutrition - Genetics and exposure to environmental risks - NGERE", Nancy, France
| | - Djesia Arnone
- Inserm U1256 "Nutrition - Genetics and exposure to environmental risks - NGERE", Nancy, France
| | - Myriam Choukour
- Department of Gastroenterology, Nancy University Hospital, University of Lorraine, France
| | - Ndeye Coumba Ndiaye
- Inserm U1256 "Nutrition - Genetics and exposure to environmental risks - NGERE", Nancy, France
| | - Tunay Kokten
- Inserm U1256 "Nutrition - Genetics and exposure to environmental risks - NGERE", Nancy, France
| | - Rémi Houlgatte
- Inserm U1256 "Nutrition - Genetics and exposure to environmental risks - NGERE", Nancy, France
| | - Laurent Peyrin-Biroulet
- Department of Gastroenterology, Nancy University Hospital, University of Lorraine, France.,Inserm U1256 "Nutrition - Genetics and exposure to environmental risks - NGERE", Nancy, France
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Pouget C, Hergalant S, Lardenois E, Lacomme S, Houlgatte R, Carpentier C, Dehais C, Rech F, Taillandier L, Sanson M, Appay R, Colin C, Figarella-Branger D, Battaglia-Hsu SF, Gauchotte G. Ki-67 and MCM6 labeling indices are correlated with overall survival in anaplastic oligodendroglioma, IDH1-mutant and 1p/19q-codeleted: a multicenter study from the French POLA network. Brain Pathol 2019; 30:465-478. [PMID: 31561286 DOI: 10.1111/bpa.12788] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 05/23/2019] [Accepted: 09/19/2019] [Indexed: 12/14/2022] Open
Abstract
Anaplastic oligodendroglioma (AO), IDH-mutant and 1p/19q codeleted (IDHmut+/1p19qcodel), is a high-grade glioma with only limited prognostic markers. The primary objective of this study was to evaluate, by immunohistochemistry, the prognostic value of two proliferation markers, MCM6 and Ki-67, in a large series of IDHmut+/1p19qcodel AO included in the POLA ("Prise en charge des Oligodendrogliomes Anaplasiques") French national multicenter network. We additionally examined the transcriptome obtained from this series to understand the functional pathways dysregulated with the mRNA overexpression of these two markers. The labeling indices (LI) of MCM6 and Ki-67 were obtained via computer-assisted color image analyses on immunostained AO tissues of the cohort (n = 220). Furthermore, a subgroup of AO (n = 68/220) was used to perform transcriptomic analyses. A high LI of either MCM6 (≥50%) or Ki-67 (≥15%) correlated with shorter overall survival, both in univariate (P = 0.013 and P = 0.004, respectively) and multivariate analyses (P = 0.027; multivariate Cox model including age, mitotic index, MCM6 and Ki-67). MCM6 and Ki-67 LI also correlated with overall survival in an additional retrospective cohort of 30 grade II IDHmut+/1p19qcodel oligodendrogliomas. The prognostic value of MCM6 mRNA level was confirmed in The Cancer Genome Atlas (TCGA) IDHmut+/1p19qcodel gliomas. The transcriptomic approach revealed that high transcriptional expressions of MCM6 and MKI67 were both linked positively with cell cycle progression, DNA replication, mitosis, pro-neural phenotype as well as neurogenesis, and negatively with microglial cell activation, immune response, positive regulation of myelination, oligodendrocyte development, beta-amyloid binding and postsynaptic specialization. In conclusion, the overexpression of MCM6 and/or Ki-67 is independently associated to shorter overall survival in IDHmut+/1p19qcodel AO. These two easy-to-use and cost-effective markers could thus be used concurrently in routine pathology practice. Additionally, the transcriptomic analyses showed that AO with high proliferation index have down-regulated immune response and lower microglial cells activation, and bears pro-neural phenotype.
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Affiliation(s)
- Celso Pouget
- Department of Pathology, CHRU, Nancy, France.,INSERM U1256, NGERE, Faculté de Médecine de Nancy, Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Sébastien Hergalant
- INSERM U1256, NGERE, Faculté de Médecine de Nancy, Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Emilie Lardenois
- Department of Pathology, CHRU, Nancy, France.,INSERM U1256, NGERE, Faculté de Médecine de Nancy, Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Stéphanie Lacomme
- Centre de Ressources Biologiques, CHRU, BB-0033-00035, Nancy, France
| | - Rémi Houlgatte
- INSERM U1256, NGERE, Faculté de Médecine de Nancy, Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Catherine Carpentier
- Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Inserm U 1127, CNRS UMR 7225, ICM, F-75013, Paris, France
| | - Caroline Dehais
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Neurologie 2-Mazarin, 75013, Paris, France
| | - Fabien Rech
- Department of Neurosurgery, CHRU, Nancy, France.,Institut des Neurosciences, INSERM U1051, Montpellier, France
| | | | - Marc Sanson
- Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Inserm U 1127, CNRS UMR 7225, ICM, F-75013, Paris, France.,AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Neurologie 2-Mazarin, 75013, Paris, France.,Onconeurotek, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Romain Appay
- Aix-Marseille Univ, CNRS, INP, Inst. Neurophysiopathol, Marseille, France.,AP-HM, Hôpital de la Timone, Service d'Anatomie Pathologique et de Neuropathologie and Centre de Ressources Biologiques CRB-TBM, BB-0033-00097, Marseille, France
| | - Carole Colin
- Aix-Marseille Univ, CNRS, INP, Inst. Neurophysiopathol, Marseille, France
| | - Dominique Figarella-Branger
- Aix-Marseille Univ, CNRS, INP, Inst. Neurophysiopathol, Marseille, France.,AP-HM, Hôpital de la Timone, Service d'Anatomie Pathologique et de Neuropathologie and Centre de Ressources Biologiques CRB-TBM, BB-0033-00097, Marseille, France
| | - Shyue-Fang Battaglia-Hsu
- INSERM U1256, NGERE, Faculté de Médecine de Nancy, Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Guillaume Gauchotte
- Department of Pathology, CHRU, Nancy, France.,INSERM U1256, NGERE, Faculté de Médecine de Nancy, Université de Lorraine, Vandoeuvre-lès-Nancy, France.,Centre de Ressources Biologiques, CHRU, BB-0033-00035, Nancy, France
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Safar R, Houlgatte R, Le Faou A, Ronzani C, Wu W, Ferrari L, Dubois-Pot-Schneider H, Rihn BH, Joubert O. Encapsulation of S-nitrosoglutathione: a transcriptomic validation. Drug Dev Ind Pharm 2018; 45:423-429. [DOI: 10.1080/03639045.2018.1546313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Ramia Safar
- EA 3452 CITHÉFOR, Université de Lorraine, Faculté de Pharmacie, Nancy, France
| | - Rémi Houlgatte
- INSERM U1256, Université de Lorraine, Faculté de Médecine, Nancy, France
- Hematology Laboratory, University Hospital of Nancy, Nancy, France
| | - Alain Le Faou
- EA 3452 CITHÉFOR, Université de Lorraine, Faculté de Pharmacie, Nancy, France
- Faculté de Médecine, Université de Lorraine, Nancy, France
| | - Carole Ronzani
- UMR 7199 CNRS, Université de Strasbourg, Faculté de Pharmacie, Strasbourg, France
| | - Wen Wu
- EA 3452 CITHÉFOR, Université de Lorraine, Faculté de Pharmacie, Nancy, France
| | - Luc Ferrari
- EA 3452 CITHÉFOR, Université de Lorraine, Faculté de Pharmacie, Nancy, France
- Institut Jean-Lamour, UMR CNRS 7198, Université de Lorraine, Nancy, France
| | | | - Bertrand H. Rihn
- EA 3452 CITHÉFOR, Université de Lorraine, Faculté de Pharmacie, Nancy, France
- Institut Jean-Lamour, UMR CNRS 7198, Université de Lorraine, Nancy, France
| | - Olivier Joubert
- EA 3452 CITHÉFOR, Université de Lorraine, Faculté de Pharmacie, Nancy, France
- Institut Jean-Lamour, UMR CNRS 7198, Université de Lorraine, Nancy, France
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Battaglia-Hsu SF, Ghemrawi R, Coelho D, Dreumont N, Mosca P, Hergalant S, Gauchotte G, Sequeira JM, Ndiongue M, Houlgatte R, Alberto JM, Umoret R, Robert A, Paoli J, Jung M, Quadros EV, Guéant JL. Inherited disorders of cobalamin metabolism disrupt nucleocytoplasmic transport of mRNA through impaired methylation/phosphorylation of ELAVL1/HuR. Nucleic Acids Res 2018; 46:7844-7857. [PMID: 30016500 PMCID: PMC6125644 DOI: 10.1093/nar/gky634] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [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: 05/04/2017] [Revised: 06/26/2018] [Accepted: 07/12/2018] [Indexed: 12/12/2022] Open
Abstract
The molecular mechanisms that underlie the neurological manifestations of patients with inherited diseases of vitamin B12 (cobalamin) metabolism remain to date obscure. We observed transcriptomic changes of genes involved in RNA metabolism and endoplasmic reticulum stress in a neuronal cell model with impaired cobalamin metabolism. These changes were related to the subcellular mislocalization of several RNA binding proteins, including the ELAVL1/HuR protein implicated in neuronal stress, in this cell model and in patient fibroblasts with inborn errors of cobalamin metabolism and Cd320 knockout mice. The decreased interaction of ELAVL1/HuR with the CRM1/exportin protein of the nuclear pore complex and its subsequent mislocalization resulted from hypomethylation at R-217 produced by decreased S-adenosylmethionine and protein methyl transferase CARM1 and dephosphorylation at S221 by increased protein phosphatase PP2A. The mislocalization of ELAVL1/HuR triggered the decreased expression of SIRT1 deacetylase and genes involved in brain development, neuroplasticity, myelin formation, and brain aging. The mislocalization was reversible upon treatment with siPpp2ca, cobalamin, S-adenosylmethionine, or PP2A inhibitor okadaic acid. In conclusion, our data highlight the key role of the disruption of ELAVL1/HuR nuclear export, with genomic changes consistent with the effects of inborn errors of Cbl metabolisms on brain development, neuroplasticity and myelin formation.
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Affiliation(s)
- Shyue-Fang Battaglia-Hsu
- INSERM UMRS 954 NGERE – Nutrition, Genetics, and Environmental Risk Exposure and National Center of Inborn Errors of Metabolism, Faculty of Medicine of Nancy, University of Lorraine and University Regional Hospital Center of Nancy, Vandoeuvre-lès-Nancy, F-54000, France
| | - Rose Ghemrawi
- INSERM UMRS 954 NGERE – Nutrition, Genetics, and Environmental Risk Exposure and National Center of Inborn Errors of Metabolism, Faculty of Medicine of Nancy, University of Lorraine and University Regional Hospital Center of Nancy, Vandoeuvre-lès-Nancy, F-54000, France
| | - David Coelho
- INSERM UMRS 954 NGERE – Nutrition, Genetics, and Environmental Risk Exposure and National Center of Inborn Errors of Metabolism, Faculty of Medicine of Nancy, University of Lorraine and University Regional Hospital Center of Nancy, Vandoeuvre-lès-Nancy, F-54000, France
| | - Natacha Dreumont
- INSERM UMRS 954 NGERE – Nutrition, Genetics, and Environmental Risk Exposure and National Center of Inborn Errors of Metabolism, Faculty of Medicine of Nancy, University of Lorraine and University Regional Hospital Center of Nancy, Vandoeuvre-lès-Nancy, F-54000, France
| | - Pauline Mosca
- INSERM UMRS 954 NGERE – Nutrition, Genetics, and Environmental Risk Exposure and National Center of Inborn Errors of Metabolism, Faculty of Medicine of Nancy, University of Lorraine and University Regional Hospital Center of Nancy, Vandoeuvre-lès-Nancy, F-54000, France
| | - Sébastien Hergalant
- INSERM UMRS 954 NGERE – Nutrition, Genetics, and Environmental Risk Exposure and National Center of Inborn Errors of Metabolism, Faculty of Medicine of Nancy, University of Lorraine and University Regional Hospital Center of Nancy, Vandoeuvre-lès-Nancy, F-54000, France
| | - Guillaume Gauchotte
- INSERM UMRS 954 NGERE – Nutrition, Genetics, and Environmental Risk Exposure and National Center of Inborn Errors of Metabolism, Faculty of Medicine of Nancy, University of Lorraine and University Regional Hospital Center of Nancy, Vandoeuvre-lès-Nancy, F-54000, France
| | - Jeffrey M Sequeira
- Division of Hematology/Oncology, Department of Medicine, SUNY-Downstate Medical Center, Brooklyn, New York, NY, USA
| | - Mariam Ndiongue
- INSERM UMRS 954 NGERE – Nutrition, Genetics, and Environmental Risk Exposure and National Center of Inborn Errors of Metabolism, Faculty of Medicine of Nancy, University of Lorraine and University Regional Hospital Center of Nancy, Vandoeuvre-lès-Nancy, F-54000, France
| | - Rémi Houlgatte
- INSERM UMRS 954 NGERE – Nutrition, Genetics, and Environmental Risk Exposure and National Center of Inborn Errors of Metabolism, Faculty of Medicine of Nancy, University of Lorraine and University Regional Hospital Center of Nancy, Vandoeuvre-lès-Nancy, F-54000, France
| | - Jean-Marc Alberto
- INSERM UMRS 954 NGERE – Nutrition, Genetics, and Environmental Risk Exposure and National Center of Inborn Errors of Metabolism, Faculty of Medicine of Nancy, University of Lorraine and University Regional Hospital Center of Nancy, Vandoeuvre-lès-Nancy, F-54000, France
| | - Remy Umoret
- INSERM UMRS 954 NGERE – Nutrition, Genetics, and Environmental Risk Exposure and National Center of Inborn Errors of Metabolism, Faculty of Medicine of Nancy, University of Lorraine and University Regional Hospital Center of Nancy, Vandoeuvre-lès-Nancy, F-54000, France
| | - Aurélie Robert
- INSERM UMRS 954 NGERE – Nutrition, Genetics, and Environmental Risk Exposure and National Center of Inborn Errors of Metabolism, Faculty of Medicine of Nancy, University of Lorraine and University Regional Hospital Center of Nancy, Vandoeuvre-lès-Nancy, F-54000, France
| | - Justine Paoli
- INSERM UMRS 954 NGERE – Nutrition, Genetics, and Environmental Risk Exposure and National Center of Inborn Errors of Metabolism, Faculty of Medicine of Nancy, University of Lorraine and University Regional Hospital Center of Nancy, Vandoeuvre-lès-Nancy, F-54000, France
| | - Martin Jung
- Department of Medical Biochemistry and Molecular Biology, Saarland University, Building 44, Homburg 66421, Germany
| | - Edward V Quadros
- Division of Hematology/Oncology, Department of Medicine, SUNY-Downstate Medical Center, Brooklyn, New York, NY, USA
| | - Jean-Louis Guéant
- INSERM UMRS 954 NGERE – Nutrition, Genetics, and Environmental Risk Exposure and National Center of Inborn Errors of Metabolism, Faculty of Medicine of Nancy, University of Lorraine and University Regional Hospital Center of Nancy, Vandoeuvre-lès-Nancy, F-54000, France
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8
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Dumont S, Le Pennec S, Donnart A, Teusan R, Steenman M, Chevalier C, Houlgatte R, Savagner F. Transcriptional orchestration of mitochondrial homeostasis in a cellular model of PGC-1-related coactivator-dependent thyroid tumor. Oncotarget 2018; 9:15883-15894. [PMID: 29662614 PMCID: PMC5882305 DOI: 10.18632/oncotarget.24633] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 11/08/2017] [Accepted: 02/26/2018] [Indexed: 12/03/2022] Open
Abstract
The PGC-1 (Peroxisome proliferator-activated receptor Gamma Coactivator-1) family of coactivators (PGC-1α, PGC-1β, and PRC) plays a central role in the transcriptional control of mitochondrial biogenesis and oxidative phosphorylation (OXPHOS) processes. These coactivators integrate mitochondrial energy production into cell metabolism using complementary pathways. The XTC.UC1 cell line is a mitochondria-rich model of thyroid tumors whose biogenesis is almost exclusively dependent on PRC. Here we aim to propose an integrative view of the cellular pathways regulated by PRC through integration of cDNA and miRNA microarray data and chromatin immunoprecipitation results obtained from XTC.UC1 cells invalidated for PRC. This study showes that PRC induces a complex network of cellular functions interacting with at least one to five of the studied transcription factors (Estrogen Related Receptor alpha, ERR1; Nuclear-Respiratory Factors, NRF1 and NRF2; cAMP Response Element Binding, CREB; and Ying Yang, YY1). Our data confirm that ERR1 is a key partner of PRC in the regulation of mitochondrial functions and suggest a potential role of this complex in RNA processing. PRC is also involved in transcriptional regulatory complexes targeting 12 miRNAs, five of which are involved in the control of the OXPHOS process. Our findings demonstrate that the PRC coactivator can act in complex with several transcription factors and regulate miRNA expression to control the fine regulation of main metabolic functions in the cell. Therefore, in PGC-1α/β-associated pathologies, PRC, as a metabolic sensor, may ensure mitochondrial homeostasis.
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Affiliation(s)
- Solenne Dumont
- L'institut du Thorax, INSERM, CNRS, UNIV Nantes, BP 70721, 44007 NANTES Cedex 1, France
| | | | - Audrey Donnart
- L'institut du Thorax, INSERM, CNRS, UNIV Nantes, BP 70721, 44007 NANTES Cedex 1, France
| | - Raluca Teusan
- L'institut du Thorax, INSERM, CNRS, UNIV Nantes, BP 70721, 44007 NANTES Cedex 1, France
| | - Marja Steenman
- L'institut du Thorax, INSERM, CNRS, UNIV Nantes, BP 70721, 44007 NANTES Cedex 1, France
| | | | - Rémi Houlgatte
- Inserm UMR 954, Faculté de Médecine, BP 184, 54505 VANDOEUVRE-LÈS-NANCY Cedex, France
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9
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Steenman M, Espitia O, Maurel B, Guyomarch B, Heymann MF, Pistorius MA, Ory B, Heymann D, Houlgatte R, Gouëffic Y, Quillard T. Identification of genomic differences among peripheral arterial beds in atherosclerotic and healthy arteries. Sci Rep 2018; 8:3940. [PMID: 29500419 PMCID: PMC5834518 DOI: 10.1038/s41598-018-22292-y] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [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: 10/05/2017] [Accepted: 02/15/2018] [Indexed: 01/07/2023] Open
Abstract
Calcification is independently associated with cardiovascular events and morbidity. The calcification burden in atherosclerotic lesions quantitatively and qualitatively differs between arterial beds. Cardiovascular risk factors (CVRF) differentially affect plaque development between arterial beds. The aim of this study was to evaluate the impact of CVRF on atherosclerotic plaque calcification and to further study the molecular arterial heterogeneity that could account for these differences. Histological analysis was performed on atherosclerotic plaques from 153 carotid, 97 femoral and 28 infrapopliteal arteries. CVRF showed minor associations with plaque calcification: age and hypertension affected only the overall presence of calcification but not the type of the calcification, which significantly differed between arterial beds. Transcriptome analysis revealed distinct gene expression profiles associated with each territory in atherosclerotic and healthy arteries. Canonical pathway analysis showed the preferential involvement of immune system-related processes in both atherosclerotic and healthy carotid arteries. Bone development-related genes were among those mostly enriched in atherosclerotic and healthy femoral arteries, which are more prone to developing endochondral calcification. This study highlights the heterogeneous nature of arteries from different peripheral vascular beds and contributes to a better understanding of atherosclerosis formation and evolution.
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Affiliation(s)
- Marja Steenman
- l'institut du thorax, INSERM, CNRS, UNIV Nantes, Nantes, France
| | - Olivier Espitia
- UMR1238 INSERM, Université de Nantes, CHU de Nantes, Nantes, France.,Department of Internal Medicine, CHU de Nantes, Nantes, France
| | - Blandine Maurel
- UMR1238 INSERM, Université de Nantes, CHU de Nantes, Nantes, France.,Department of Vascular Surgery, CHU de Nantes, Nantes, France
| | | | | | | | - Benjamin Ory
- UMR1238 INSERM, Université de Nantes, CHU de Nantes, Nantes, France
| | - Dominique Heymann
- Department of Oncology and Metabolism, University of Sheffield, INSERM, European Associated Laboratory "Sarcoma Research Unit", Sheffield, UK.,Institut de Cancérologie de l'Ouest, INSERM, U1232, Université de Nantes, Nantes, France
| | - Rémi Houlgatte
- INSERM U1256, NGERE, University of Nancy, Nancy, France.,DRCI, University Hospital of Nancy, Nancy, France
| | - Yann Gouëffic
- UMR1238 INSERM, Université de Nantes, CHU de Nantes, Nantes, France.,Department of Vascular Surgery, CHU de Nantes, Nantes, France
| | - Thibaut Quillard
- UMR1238 INSERM, Université de Nantes, CHU de Nantes, Nantes, France.
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10
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Broséus J, Chen G, Hergalant S, Ramstein G, Mounier N, Guéant JL, Feugier P, Gisselbrecht C, Thieblemont C, Houlgatte R. Relapsed diffuse large B-cell lymphoma present different genomic profiles between early and late relapses. Oncotarget 2018; 7:83987-84002. [PMID: 27276707 PMCID: PMC5356640 DOI: 10.18632/oncotarget.9793] [Citation(s) in RCA: 18] [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: 04/18/2016] [Accepted: 05/13/2016] [Indexed: 01/12/2023] Open
Abstract
Despite major advances in first-line treatment, a significant proportion of patients with diffuse large B-cell lymphoma (DLBCL) will experience treatment failure. Prognosis is particularly poor for relapses occurring less than one year after the end of first-line treatment (early relapses/ER) compared to those occurring more than one year after (late relapses/LR). To better understand genomic alterations underlying the delay of relapse, we identified copy number variations (CNVs) on 39 tumor samples from a homogeneous series of patients included in the Collaborative Trial in Relapsed Aggressive Lymphoma (CORAL) prospective study. To identify CNVs associated with ER or LR, we devised an original method based on Significance Analysis of Microarrays, a permutation-based method which allows control of false positives due to multiple testing. Deletions of CDKN2A/B (28%) and IBTK (23%) were frequent events in relapsed DLBCLs. We identified 56 protein-coding genes and 25 long non-coding RNAs with significantly differential CNVs distribution between ER and LR DLBCLs, with a false discovery rate < 0.05. In ER DLBCLs, CNVs were related to transcription regulation, cell cycle and apoptosis, with duplications of histone H1T (31%), deletions of DIABLO (26%), PTMS (21%) and CK2B (15%). In LR DLBCLs, CNVs were related to immune response, with deletions of B2M (20%) and CD58 (10%), cell proliferation regulation, with duplications of HES1 (25%) and DVL3 (20%), and transcription regulation, with MTERF4 deletions (20%). This study provides new insights into the genetic aberrations in relapsed DLBCLs and suggest pathway-targeted therapies in ER and LR DLBCLs.
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Affiliation(s)
- Julien Broséus
- Inserm U954, Faculty of Medicine, Nancy, France.,Hematology, Laboratory Department, University Hospital of Nancy, Nancy, France
| | - Gaili Chen
- ZhongNan Hospital of Wuhan University, Wuhan, China
| | | | | | - Nicolas Mounier
- Hemato-oncology, University Hospital of l'Archet, Nice, France
| | - Jean-Louis Guéant
- Inserm U954, Faculty of Medicine, Nancy, France.,Biochemistry, Laboratory Department, University Hospital of Nancy, Nancy, France
| | - Pierre Feugier
- Inserm U954, Faculty of Medicine, Nancy, France.,Hematology Department, University Hospital of Nancy, Nancy, France
| | | | - Catherine Thieblemont
- APHP, Saint-Louis Hospital, Hemato-Oncology Department, Paris, France.,Paris Diderot University-Sorbonne Paris-Cité, Paris, France
| | - Rémi Houlgatte
- Inserm U954, Faculty of Medicine, Nancy, France.,DRCI, University Hospital of Nancy, Nancy, France
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11
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Espitia O, Chatelais M, Steenman M, Charrier C, Maurel B, Georges S, Houlgatte R, Verrecchia F, Ory B, Lamoureux F, Heymann D, Gouëffic Y, Quillard T. Implication of molecular vascular smooth muscle cell heterogeneity among arterial beds in arterial calcification. PLoS One 2018; 13:e0191976. [PMID: 29373585 PMCID: PMC5786328 DOI: 10.1371/journal.pone.0191976] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [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: 10/20/2017] [Accepted: 01/15/2018] [Indexed: 11/29/2022] Open
Abstract
Vascular calcification is a strong and independent predictive factor for cardiovascular complications and mortality. Our previous work identified important discrepancies in plaque composition and calcification types between carotid and femoral arteries. The objective of this study is to further characterize and understand the heterogeneity in vascular calcification among vascular beds, and to identify molecular mechanisms underlying this process. We established ECLAGEN biocollection that encompasses human atherosclerotic lesions and healthy arteries from different locations (abdominal, thoracic aorta, carotid, femoral, and infrapopliteal arteries) for histological, cell isolation, and transcriptomic analysis. Our results show that lesion composition differs between these locations. Femoral arteries are the most calcified arteries overall. They develop denser calcifications (sheet-like, nodule), and are highly susceptible to osteoid metaplasia. These discrepancies may derive from intrinsic differences between SMCs originating from these locations, as microarray analysis showed specific transcriptomic profiles between primary SMCs isolated from each arterial bed. These molecular differences translated into functional disparities. SMC from femoral arteries showed the highest propensity to mineralize due to an increase in basal TGFβ signaling. Our results suggest that biological heterogeneity of resident vascular cells between arterial beds, reflected by our transcriptomic analysis, is critical in understanding plaque biology and calcification, and may have strong implications in vascular therapeutic approaches.
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Affiliation(s)
- Olivier Espitia
- INSERM, UMR 1238, Nantes, France; Université de Nantes, Nantes Atlantique Universités, Laboratoire « Sarcome osseux et remodelage des tissus osseux calcifiés », Faculté de Médecine, Nantes, France
- CHU Hôtel Dieu, Nantes, France
| | - Mathias Chatelais
- INSERM, UMR 1238, Nantes, France; Université de Nantes, Nantes Atlantique Universités, Laboratoire « Sarcome osseux et remodelage des tissus osseux calcifiés », Faculté de Médecine, Nantes, France
| | - Marja Steenman
- Institut du Thorax, Inserm UMR1087, Faculté de Médecine, Université de Nantes, Nantes Atlantique Universités, Nantes, France
| | - Céline Charrier
- INSERM, UMR 1238, Nantes, France; Université de Nantes, Nantes Atlantique Universités, Laboratoire « Sarcome osseux et remodelage des tissus osseux calcifiés », Faculté de Médecine, Nantes, France
| | - Blandine Maurel
- INSERM, UMR 1238, Nantes, France; Université de Nantes, Nantes Atlantique Universités, Laboratoire « Sarcome osseux et remodelage des tissus osseux calcifiés », Faculté de Médecine, Nantes, France
- CHU Hôtel Dieu, Nantes, France
| | - Steven Georges
- INSERM, UMR 1238, Nantes, France; Université de Nantes, Nantes Atlantique Universités, Laboratoire « Sarcome osseux et remodelage des tissus osseux calcifiés », Faculté de Médecine, Nantes, France
| | - Rémi Houlgatte
- Inserm U954, Faculty of Medicine, Nancy, France, DRCI, University Hospital of Nancy, Nancy, France
| | - Franck Verrecchia
- INSERM, UMR 1238, Nantes, France; Université de Nantes, Nantes Atlantique Universités, Laboratoire « Sarcome osseux et remodelage des tissus osseux calcifiés », Faculté de Médecine, Nantes, France
| | - Benjamin Ory
- INSERM, UMR 1238, Nantes, France; Université de Nantes, Nantes Atlantique Universités, Laboratoire « Sarcome osseux et remodelage des tissus osseux calcifiés », Faculté de Médecine, Nantes, France
| | - François Lamoureux
- INSERM, UMR 1238, Nantes, France; Université de Nantes, Nantes Atlantique Universités, Laboratoire « Sarcome osseux et remodelage des tissus osseux calcifiés », Faculté de Médecine, Nantes, France
| | - Dominique Heymann
- Institut de Cancérologie de l'Ouest, site René Gauducheau, Boulevard Professeur Jacques Monod, Saint-Herblain, France
- University of Sheffield, Department of Oncology and Metabolism, INSERM, European Associated Laboratory “Sarcoma Research Unit”, Medical School, Sheffield, United Kingdom
- University of Nantes, Faculty of Medicine, Nantes, France
| | - Yann Gouëffic
- INSERM, UMR 1238, Nantes, France; Université de Nantes, Nantes Atlantique Universités, Laboratoire « Sarcome osseux et remodelage des tissus osseux calcifiés », Faculté de Médecine, Nantes, France
- CHU Hôtel Dieu, Nantes, France
| | - Thibaut Quillard
- INSERM, UMR 1238, Nantes, France; Université de Nantes, Nantes Atlantique Universités, Laboratoire « Sarcome osseux et remodelage des tissus osseux calcifiés », Faculté de Médecine, Nantes, France
- CHU Hôtel Dieu, Nantes, France
- * E-mail:
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12
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Broséus J, Mourah S, Ramstein G, Bernard S, Mounier N, Cuccuini W, Gaulard P, Gisselbrecht C, Brière J, Houlgatte R, Thieblemont C. VEGF 121, is predictor for survival in activated B-cell-like diffuse large B-cell lymphoma and is related to an immune response gene signature conserved in cancers. Oncotarget 2017; 8:90808-90824. [PMID: 29207605 PMCID: PMC5710886 DOI: 10.18632/oncotarget.19385] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 06/12/2017] [Accepted: 07/03/2017] [Indexed: 02/07/2023] Open
Abstract
Tumor microenvironment including endothelial and immune cells plays a crucial role in tumor progression and has been shown to dramatically influence cancer survival. In this study, we investigated the clinical relevance of the gene expression of key mediators of angiogenesis, VEGF isoforms 121, 165, and 189, and their receptors (VEGFR-1 and R-2) in a cohort of patients (n = 37) with relapsed/refractory diffuse large B-cell lymphoma (DLBCL) from the Collaborative Trial in Relapsed Aggressive Lymphoma (CORAL). In patients with ABC-like DLBCL, but not in patients with GCB-like DLBCL, low VEGF121 expression was associated with a significantly better survival than in those with high VEGF121 level: 4-year overall survival at 100% vs 36% (p = .011), respectively. A specific gene signature including 57 genes was correlated to VEGF121 expression level and was analyzed using a discovery process in 1,842 GSE datasets of public microarray studies. This gene signature was significantly expressed in other cancer datasets and was associated with immune response. In conclusion, low VEGF121 expression level was significantly associated with a good prognosis in relapsed/refractory ABC-like DLBCL, and with a well-conserved gene-expression profiling signature related to immune response. These findings pave the way for rationalization of drugs targeting immune response in refractory/relapsed ABC-like DLBCL.
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Affiliation(s)
- Julien Broséus
- Inserm U954, Faculty of Medicine, University of Lorraine, Nancy, France.,University Hospital of Nancy, Hematology Laboratory, Nancy, France
| | - Samia Mourah
- Paris Diderot University, Sorbonne Paris Cité, Paris, France.,APHP, Saint Louis University Hospital, Pharmacology-Biologic Laboratory, Paris, France.,Inserm UMRS 976, France
| | | | - Sophie Bernard
- APHP, Saint-Louis University Hospital, Hemato-Oncology, Paris, France
| | | | - Wendy Cuccuini
- APHP, Saint-Louis University Hospital, Hematology Laboratory, Paris, France
| | - Philippe Gaulard
- Department of Pathology, APHP, Henri Mondor University Hospital, Creteil, France.,Inserm U955, University Paris-Est, Créteil, France
| | - Christian Gisselbrecht
- APHP, Saint-Louis University Hospital, Hemato-Oncology, Paris, France.,Lymphoma Study Association, Pierre-Bénite, France
| | - Josette Brière
- Department of Pathology, APHP, Saint-Louis University Hospital, Paris, France
| | - Rémi Houlgatte
- Inserm U954, Faculty of Medicine, University of Lorraine, Nancy, France.,University Hospital of Nancy, DRCI, Nancy, France
| | - Catherine Thieblemont
- Paris Diderot University, Sorbonne Paris Cité, Paris, France.,APHP, Saint-Louis University Hospital, Hemato-Oncology, Paris, France
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13
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Gauchotte G, Hergalant S, Vigouroux C, Casse JM, Houlgatte R, Kaoma T, Helle D, Brochin L, Rech F, Peyre M, Labrousse F, Vallar L, Guéant JL, Vignaud JM, Battaglia-Hsu SF. Cytoplasmic overexpression of RNA-binding protein HuR is a marker of poor prognosis in meningioma, and HuR knockdown decreases meningioma cell growth and resistance to hypoxia. J Pathol 2017; 242:421-434. [PMID: 28493484 DOI: 10.1002/path.4916] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [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: 03/03/2017] [Revised: 04/19/2017] [Accepted: 04/26/2017] [Indexed: 11/11/2022]
Abstract
HuR regulates cytoplasmic mRNA stability and translatability, and the HuR expression level has been shown to correlate with poor disease outcome in several cancer types; however, the prognostic value and potential pro-oncogenic properties of HuR in meningioma remain unclear. Thus, in the present study, we analysed 85 meningioma tissue samples to establish the relationship between HuR expression, tumour cell proliferation, and/or patient survival. In addition, we examined the anti-proliferative effects of HuR knockdown in two meningioma cell lines (IOMM-Lee and Ben-Men-1) and conducted transcriptome-wide analyses (IOMM-Lee cells) to elucidate the molecular consequences of HuR knockdown. The results of the present study showed HuR cytoplasmic expression to correlate positively with tumour grade (p = 1.2 × 10-8 ) and negatively with progression-free and overall survival (p = 0.01) time in human meningioma tissues. In vitro, siHuR-induced HuR knockdown was shown to reduce the growth of both Ben-Men-1 (p = 2 × 10-8 ) and IOMM-Lee (p = 4 × 10-9 ) cells. Transcriptome analyses revealed HuR knockdown in IOMM-Lee cells to deregulate the HIF1A signalling pathway (p = 1.5 × 10-6 ) and to up-regulate the expression of genes essential for the assembly of the cytoplasmic mRNA processing body, global genome nucleotide-excision repair, poly(A)-specific ribonuclease activity, the positive regulation of apoptosis and of cell cycle arrest, and the negative regulation of RNA splicing [p(FDR) < 0.001]. Interestingly, HuR knockdown under hypoxic culture conditions further potentiated the effects of HuR knockdown on cell growth, apoptosis, and HIF1A expression. We thus conclude that cytoplasmic HuR expression is a marker of poor prognosis in meningioma and that HuR is a promising potential therapeutic target for use in tumours refractory to standard therapies. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Guillaume Gauchotte
- INSERM U954, Faculty of Medicine, Université de Lorraine, Vandoeuvre-lès-Nancy, France.,Department of Pathology, CHRU, Nancy, France
| | - Sébastien Hergalant
- INSERM U954, Faculty of Medicine, Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | | | - Jean-Matthieu Casse
- INSERM U954, Faculty of Medicine, Université de Lorraine, Vandoeuvre-lès-Nancy, France.,Department of Pathology, CHRU, Nancy, France
| | - Rémi Houlgatte
- INSERM U954, Faculty of Medicine, Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Tony Kaoma
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Déborah Helle
- INSERM U954, Faculty of Medicine, Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | | | - Fabien Rech
- Department of Neurosurgery, CHRU, Nancy, France.,Institut des Neurosciences, INSERM U1051, Montpellier, France
| | - Matthieu Peyre
- Sorbonne Université, UPMC University Paris 06, INSERM, CNRS, UM 75, U 1127, UMR 7225, ICM, Paris, France.,Department of Neurosurgery, Groupe Hospitalier Pitié Salpêtrière, AP-HP, Paris, France
| | | | - Laurent Vallar
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Jean-Louis Guéant
- INSERM U954, Faculty of Medicine, Université de Lorraine, Vandoeuvre-lès-Nancy, France.,M2TP, Division of Biochemistry and Molecular Biology, CHRU, Vandoeuvre-lès-Nancy, France
| | - Jean-Michel Vignaud
- INSERM U954, Faculty of Medicine, Université de Lorraine, Vandoeuvre-lès-Nancy, France.,Department of Pathology, CHRU, Nancy, France.,Centre de Ressources Biologiques, BB-0033-00035, CHRU Nancy, France
| | - Shyue-Fang Battaglia-Hsu
- INSERM U954, Faculty of Medicine, Université de Lorraine, Vandoeuvre-lès-Nancy, France.,M2TP, Division of Biochemistry and Molecular Biology, CHRU, Vandoeuvre-lès-Nancy, France
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14
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Danger R, Chesneau M, Paul C, Guérif P, Durand M, Newell KA, Kanaparthi S, Turka LA, Soulillou JP, Houlgatte R, Giral M, Ramstein G, Brouard S. A composite score associated with spontaneous operational tolerance in kidney transplant recipients. Kidney Int 2017; 91:1473-1481. [PMID: 28242033 PMCID: PMC5432017 DOI: 10.1016/j.kint.2016.12.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [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: 08/21/2016] [Revised: 11/29/2016] [Accepted: 12/22/2016] [Indexed: 11/16/2022]
Abstract
New challenges in renal transplantation include using biological information to devise a useful clinical test for discerning high- and low-risk patients for individual therapy and ascertaining the best combination and appropriate dosages of drugs. Based on a 20-gene signature from a microarray meta-analysis performed on 46 operationally tolerant patients and 266 renal transplant recipients with stable function, we applied the sparse Bolasso methodology to identify a minimal and robust combination of six genes and two demographic parameters associated with operational tolerance. This composite score of operational tolerance discriminated operationally tolerant patients with an area under the curve of 0.97 (95% confidence interval 0.94-1.00). The score was not influenced by immunosuppressive treatment, center of origin, donor type, or post-transplant lymphoproliferative disorder history of the patients. This composite score of operational tolerance was significantly associated with both de novo anti-HLA antibodies and tolerance loss. It was validated by quantitative polymerase chain reaction using independent samples and demonstrated specificity toward a model of tolerance induction. Thus, our score would allow clinicians to improve follow-up of patients, paving the way for individual therapy.
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Affiliation(s)
- Richard Danger
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France; Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France
| | - Mélanie Chesneau
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France; Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France
| | - Chloé Paul
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France; Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France
| | - Pierrick Guérif
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France; Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France
| | - Maxim Durand
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France; Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France
| | | | | | - Laurence A Turka
- Center for Transplantation Sciences, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jean-Paul Soulillou
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France; Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France
| | - Rémi Houlgatte
- INSERM UMR 954, Nancy, France; CHU de Nancy, DRCI, Nancy, France
| | - Magali Giral
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France; Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France; Université de Nantes, Faculté de Médecine, Nantes, France; CIC Biotherapy, CHU Nantes, Nantes, France
| | - Gérard Ramstein
- LINA DUKe, UMR 6241, Université de Nantes, Ecole des Mines de Nantes and CNRS, Nantes, France
| | - Sophie Brouard
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France; Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France; CIC Biotherapy, CHU Nantes, Nantes, France.
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15
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Steenman M, Stefani M, Thebaud N, Szüts V, Varro A, Dos Remedios C, Houlgatte R. Shared gene expression profile between aging and diseased hearts in man. Archives of Cardiovascular Diseases Supplements 2017. [DOI: 10.1016/s1878-6480(17)30518-9] [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: 10/19/2022]
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16
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Sigoillot SM, Bourgeois F, Karmouch J, Molgó J, Dobbertin A, Chevalier C, Houlgatte R, Léger J, Legay C. Neuromuscular junction immaturity and muscle atrophy are hallmarks of the ColQ-deficient mouse, a model of congenital myasthenic syndrome with acetylcholinesterase deficiency. FASEB J 2016; 30:2382-99. [PMID: 26993635 DOI: 10.1096/fj.201500162] [Citation(s) in RCA: 16] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 02/26/2016] [Indexed: 12/13/2022]
Abstract
The collagen ColQ anchors acetylcholinesterase (AChE) in the synaptic cleft of the neuromuscular junction (NMJ). It also binds MuSK and perlecan/dystroglycan, 2 signaling platforms of the postsynaptic domain. Mutations in ColQ cause a congenital myasthenic syndrome (CMS) with AChE deficiency. Because the absence of AChE does not fully explain the complexity of the syndrome and there is no curative treatment for the disease, we explored additional potential targets of ColQ by conducting a large genetic screening of ColQ-deficient mice, a model for CMS with AChE deficiency, and analyzed their NMJ and muscle phenotypes. We demonstrated that ColQ controls the development and the maturation of the postsynaptic domain by regulating synaptic gene expression. Notably, ColQ deficiency leads to an up-regulation of the 5 subunits of the nicotinic acetylcholine receptor (AChR), leading to mixed mature and immature AChRs at the NMJ of adult mice. ColQ also regulates the expression of extracellular matrix (ECM) components. However, whereas the ECM mRNAs were down-regulated in vitro, compensation seemed to occur in vivo to maintain normal levels of these mRNAs. Finally, ColQ deficiency leads to a general atrophic phenotype and hypoplasia that affect fast muscles. This study points to new specific hallmarks for this CMS.-Sigoillot, S. M., Bourgeois, F., Karmouch, J., Molgó, J., Dobbertin, A., Chevalier, C., Houlgatte, R., Léger, J., Legay, C. Neuromuscular junction immaturity and muscle atrophy are hallmarks of the ColQ-deficient mouse, a model of congenital myasthenic syndrome with acetylcholinesterase deficiency.
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Affiliation(s)
- Séverine M Sigoillot
- Centre de Neurophysique, Physiologie et Pathologie, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 8119, Université Paris Descartes, Sorbonne Paris Cité, Paris France
| | - Francine Bourgeois
- Centre de Neurophysique, Physiologie et Pathologie, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 8119, Université Paris Descartes, Sorbonne Paris Cité, Paris France
| | - Jennifer Karmouch
- Centre de Neurophysique, Physiologie et Pathologie, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 8119, Université Paris Descartes, Sorbonne Paris Cité, Paris France
| | - Jordi Molgó
- Commissariat à l'énergie Atomique et aux Energies Alternatives, Institut de Biologie et Technologies de Saclay, Service d'Ingénierie Moléculaire des Protéines, Gif sur Yvette, France; Institut des Neurosciences Paris-Saclay, UMR 9197, CNRS/Université Paris-Sud, Paris, France; and
| | - Alexandre Dobbertin
- Centre de Neurophysique, Physiologie et Pathologie, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 8119, Université Paris Descartes, Sorbonne Paris Cité, Paris France
| | - Catherine Chevalier
- Institut de Recherche Thérapeutique de l'Université de Nantes, Plateforme Génomique Intégrative, Nantes, France
| | - Rémi Houlgatte
- Institut de Recherche Thérapeutique de l'Université de Nantes, Plateforme Génomique Intégrative, Nantes, France
| | - Jean Léger
- Institut de Recherche Thérapeutique de l'Université de Nantes, Plateforme Génomique Intégrative, Nantes, France
| | - Claire Legay
- Centre de Neurophysique, Physiologie et Pathologie, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 8119, Université Paris Descartes, Sorbonne Paris Cité, Paris France;
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17
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Chen G, Broséus J, Hergalant S, Donnart A, Chevalier C, Bolaños-Jiménez F, Guéant JL, Houlgatte R. Identification of master genes involved in liver key functions through transcriptomics and epigenomics of methyl donor deficiency in rat: relevance to nonalcoholic liver disease. Mol Nutr Food Res 2014; 59:293-302. [PMID: 25380481 DOI: 10.1002/mnfr.201400483] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [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: 07/18/2014] [Revised: 09/17/2014] [Accepted: 10/26/2014] [Indexed: 02/06/2023]
Abstract
SCOPE Our study aims to investigate molecular events associated to methyl donor deficiency (MDD) by analyzing the transcriptome and the methylome of MDD rats in liver. METHODS AND RESULTS Twenty-one-day-old rats born to mothers fed either with a standard diet or a MDD diet during gestation and lactation were compared. From a total of 44 000 probes for 26 456 genes, we found two gene clusters in MDD rats whose expression levels had significant differences compared with controls: 3269 overexpressed (p < 0.0009) and 2841 underexpressed (p < 0.0004) genes. Modifications of DNA methylation were found in the promoter regions of 1032 genes out of 14 981 genes. Ontological analyses revealed that these genes are mainly involved in glucose and lipid metabolism, nervous system, coagulation, ER stress, and mitochondrial function. CONCLUSION Putative master genes exhibiting changes in both gene expression and DNA methylation are limited to 266 genes and are mainly involved in the renin-angiotensin system (n = 3), mitochondrion metabolism (n = 18), and phospholipid homeostasis (n = 3). Most of these master genes participate in nonalcoholic fatty liver disease. The adverse effects of MDD on the metabolic process indicate the beneficial impact of folate and vitamin B12, especially during the perinatal period.
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Affiliation(s)
- Gaili Chen
- Institut National de la Santé et de la Recherche Médicale (INSERM), Faculté de Médecine, Vandœuvre-lès-Nancy, France
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18
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Rolland AD, Lardenois A, Goupil AS, Lareyre JJ, Houlgatte R, Chalmel F, Le Gac F. Profiling of androgen response in rainbow trout pubertal testis: relevance to male gonad development and spermatogenesis. PLoS One 2013; 8:e53302. [PMID: 23301058 PMCID: PMC3536770 DOI: 10.1371/journal.pone.0053302] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 11/27/2012] [Indexed: 12/15/2022] Open
Abstract
The capacity of testicular somatic cells to promote and sustain germ cell differentiation is largely regulated by sexual steroids and notably androgens. In fish species the importance of androgens is emphasized by their ability to induce sex reversal of the developing fries and to trigger spermatogenesis. Here we studied the influence of androgens on testicular gene expression in trout testis using microarrays. Following treatment of immature males with physiological doses of testosterone or 11-ketotestosterone, 418 genes that exhibit changes in expression were identified. Interestingly, the activity of testosterone appeared stronger than that of 11-ketotestosterone. Expression profiles of responsive genes throughout testis development and in isolated germ cells confirmed androgens to mainly affect gene expression in somatic cells. Furthermore, specific clusters of genes that exhibit regulation coincidently with changes in the natural circulating levels of androgens during the reproductive cycle were highlighted, reinforcing the physiological significance of these data. Among somatic genes, a phylogenetic footprinting study identified putative androgen response elements within the proximal promoter regions of 42 potential direct androgen target genes. Finally, androgens were also found to alter the germ line towards meiotic expression profiles, supporting the hypothesis of a role for the somatic responsive genes in driving germ cell fate. This study significantly increases our understanding of molecular pathways regulated by androgens in vertebrates. The highly cyclic testicular development in trout together with functions associated with regulated genes reveal potential mechanisms for androgen actions in tubule formation, steroid production, germ cell development and sperm secretion.
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Affiliation(s)
- Antoine D. Rolland
- INRA, UR1037 LPGP, SFR Biosit, Biogenouest, Campus de Beaulieu, Rennes, France
| | - Aurélie Lardenois
- Inserm, U1085, IRSET, Université de Rennes I, Campus de Beaulieu, Rennes, France
| | - Anne-Sophie Goupil
- INRA, UR1037 LPGP, SFR Biosit, Biogenouest, Campus de Beaulieu, Rennes, France
| | | | - Rémi Houlgatte
- Inserm, UMR1087, l’institut du thorax IRT - UN, Nantes, France
- Université de Nantes, Nantes, France
| | - Frédéric Chalmel
- Inserm, U1085, IRSET, Université de Rennes I, Campus de Beaulieu, Rennes, France
| | - Florence Le Gac
- INRA, UR1037 LPGP, SFR Biosit, Biogenouest, Campus de Beaulieu, Rennes, France
- * E-mail:
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19
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Baron D, Magot A, Ramstein G, Steenman M, Fayet G, Chevalier C, Jourdon P, Houlgatte R, Savagner F, Pereon Y. Immune response and mitochondrial metabolism are commonly deregulated in DMD and aging skeletal muscle. PLoS One 2011; 6:e26952. [PMID: 22096509 PMCID: PMC3212519 DOI: 10.1371/journal.pone.0026952] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [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: 07/25/2011] [Accepted: 10/06/2011] [Indexed: 01/12/2023] Open
Abstract
Duchenne Muscular Dystrophy (DMD) is a complex process involving multiple pathways downstream of the primary genetic insult leading to fatal muscle degeneration. Aging muscle is a multifactorial neuromuscular process characterized by impaired muscle regeneration leading to progressive atrophy. We hypothesized that these chronic atrophying situations may share specific myogenic adaptative responses at transcriptional level according to tissue remodeling. Muscle biopsies from four young DMD and four AGED subjects were referred to a group of seven muscle biopsies from young subjects without any neuromuscular disorder and explored through a dedicated expression microarray. We identified 528 differentially expressed genes (out of 2,745 analyzed), of which 328 could be validated by an exhaustive meta-analysis of public microarray datasets referring to DMD and Aging in skeletal muscle. Among the 328 validated co-expressed genes, 50% had the same expression profile in both groups and corresponded to immune/fibrosis responses and mitochondrial metabolism. Generalizing these observed meta-signatures with large compendia of public datasets reinforced our results as they could be also identified in other pathological processes and in diverse physiological conditions. Focusing on the common gene signatures in these two atrophying conditions, we observed enrichment in motifs for candidate transcription factors that may coordinate either the immune/fibrosis responses (ETS1, IRF1, NF1) or the mitochondrial metabolism (ESRRA). Deregulation in their expression could be responsible, at least in part, for the same transcriptome changes initiating the chronic muscle atrophy. This study suggests that distinct pathophysiological processes may share common gene responses and pathways related to specific transcription factors.
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20
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Le Pennec S, Mirebeau-Prunier D, Boutet-Bouzamondo N, Jacques C, Guillotin D, Lauret E, Houlgatte R, Malthièry Y, Savagner F. Nitric oxide and calcium participate in the fine regulation of mitochondrial biogenesis in follicular thyroid carcinoma cells. J Biol Chem 2011; 286:18229-39. [PMID: 21454643 PMCID: PMC3093895 DOI: 10.1074/jbc.m110.217521] [Citation(s) in RCA: 13] [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: 12/30/2010] [Revised: 03/29/2011] [Indexed: 11/06/2022] Open
Abstract
Members of the peroxisome proliferator-activated receptor γ coactivator-1 family (i.e. PGC-1α, PGC-1β, and the PGC-1-related coactivator (PRC)) are key regulators of mitochondrial biogenesis and function. These regulators serve as mediators between environmental or endogenous signals and the transcriptional machinery governing mitochondrial biogenesis. The FTC-133 and RO82 W-1 follicular thyroid carcinoma cell lines, which present significantly different numbers of mitochondria, metabolic mechanisms, and expression levels of PRC and PGC-1α, may employ retrograde signaling in response to respiratory dysfunction. Nitric oxide (NO) and calcium have been hypothesized to participate in this activity. We investigated the effects of the S-nitroso-N-acetyl-DL-penicillamine-NO donor, on the expression of genes involved in mitochondrial biogenesis and cellular metabolic functions in FTC-133 and RO82 W-1 cells by measuring lactate dehydrogenase and cytochrome c oxidase (COX) activities. We studied the action of ionomycin and 1,2-bis(2-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid-acetoxymethyl ester (BAPTA/AM) (i.e. a calcium ionophore and a cytosolic calcium chelator) on whole genome expression and mitochondrial biogenesis in RO82 W-1 cells. COX activity and the dynamics of endoplasmic reticulum and mitochondrial networks were analyzed in regard to calcium-modulating treatments. In the FTC-133 and RO82 W-1 cells, the mitochondrial biogenesis induced by NO was mainly related to PRC expression as a retrograde mitochondrial signaling. Ionomycin diminished COX activity and negatively regulated PRC-mediated mitochondrial biogenesis in RO82 W-1 cells, whereas BAPTA/AM produced the opposite effects with a reorganization of the mitochondrial network. This is the first demonstration that NO and calcium regulate mitochondrial biogenesis through the PRC pathway in thyroid cell lines.
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Affiliation(s)
| | - Delphine Mirebeau-Prunier
- From INSERM UMR694
- Université d'Angers, and
- Laboratoire de Biochimie, Centre Hospitalier Universitaire d'Angers, F-49033 Angers, France
| | | | | | | | | | - Rémi Houlgatte
- INSERM UMR915, l'Institut du Thorax, F-44007 Nantes, France, and
- Université de Nantes, F-44035 Nantes, France
| | - Yves Malthièry
- From INSERM UMR694
- Université d'Angers, and
- Laboratoire de Biochimie, Centre Hospitalier Universitaire d'Angers, F-49033 Angers, France
| | - Frédérique Savagner
- From INSERM UMR694
- Université d'Angers, and
- Laboratoire de Biochimie, Centre Hospitalier Universitaire d'Angers, F-49033 Angers, France
- INSERM UMR915, l'Institut du Thorax, F-44007 Nantes, France, and
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21
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Baron D, Dubois E, Bihouée A, Teusan R, Steenman M, Jourdon P, Magot A, Péréon Y, Veitia R, Savagner F, Ramstein G, Houlgatte R. Meta-analysis of muscle transcriptome data using the MADMuscle database reveals biologically relevant gene patterns. BMC Genomics 2011; 12:113. [PMID: 21324190 PMCID: PMC3049149 DOI: 10.1186/1471-2164-12-113] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Accepted: 02/16/2011] [Indexed: 12/12/2022] Open
Abstract
Background DNA microarray technology has had a great impact on muscle research and microarray gene expression data has been widely used to identify gene signatures characteristic of the studied conditions. With the rapid accumulation of muscle microarray data, it is of great interest to understand how to compare and combine data across multiple studies. Meta-analysis of transcriptome data is a valuable method to achieve it. It enables to highlight conserved gene signatures between multiple independent studies. However, using it is made difficult by the diversity of the available data: different microarray platforms, different gene nomenclature, different species studied, etc. Description We have developed a system tool dedicated to muscle transcriptome data. This system comprises a collection of microarray data as well as a query tool. This latter allows the user to extract similar clusters of co-expressed genes from the database, using an input gene list. Common and relevant gene signatures can thus be searched more easily. The dedicated database consists in a large compendium of public data (more than 500 data sets) related to muscle (skeletal and heart). These studies included seven different animal species from invertebrates (Drosophila melanogaster, Caenorhabditis elegans) and vertebrates (Homo sapiens, Mus musculus, Rattus norvegicus, Canis familiaris, Gallus gallus). After a renormalization step, clusters of co-expressed genes were identified in each dataset. The lists of co-expressed genes were annotated using a unified re-annotation procedure. These gene lists were compared to find significant overlaps between studies. Conclusions Applied to this large compendium of data sets, meta-analyses demonstrated that conserved patterns between species could be identified. Focusing on a specific pathology (Duchenne Muscular Dystrophy) we validated results across independent studies and revealed robust biomarkers and new pathways of interest. The meta-analyses performed with MADMuscle show the usefulness of this approach. Our method can be applied to all public transcriptome data.
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22
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Rolland D, Bouamrani A, Houlgatte R, Barbarat A, Ramus C, Arlotto M, Ballester B, Berger F, Felman P, Callet-Bauchu E, Baseggio L, Traverse-Glehen A, Brugière S, Garin J, Coiffier B, Berger F, Thieblemont C. Identification of proteomic signatures of mantle cell lymphoma, small lymphocytic lymphoma, and marginal zone lymphoma biopsies by surface enhanced laser desorption/ionization-time of flight mass spectrometry. Leuk Lymphoma 2011; 52:648-58. [PMID: 21438832 DOI: 10.3109/10428194.2010.549256] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Mantle cell lymphoma (MCL), small lymphocytic lymphoma (SLL), and marginal zone lymphoma (MZL) are small B-cell non-Hodgkin lymphomas (NHLs) that may be difficult to distinguish. In order to identify specific proteomic biomarkers, differential proteomic analysis of these three NHLs was performed using surface enhanced laser desorption/ionization-time of flight mass spectrometry (SELDI-TOF-MS). Whole cell lysates obtained from 18 MCL, 20 SLL, and 20 MZL biopsies were applied on two different ProteinChips (cationic and anionic). Hierarchical clustering and discriminating scores combined with an innovative bio-informatics microdissection strategy allowed us to distinguish specific lymphoma proteomic signatures based on the expression of 37 protein peaks. SELDI-assisted protein purification combined with nano-liquid chromatography (LC) quadrupole-time of flight tandem mass spectrometry (Q-TOF MS/MS) was used to identify proteins overexpressed in both MCL and SLL tumors. Among them two histones, H2B and H4, were identified in MCL tumor biopsies and the signal recognition particle 9 kDa protein, SRP9, in SLL tumor biopsies.
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Affiliation(s)
- Delphine Rolland
- INSERM U836, Equipe 7 Université Joseph Fourier, Grenoble, France
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23
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Baron D, Bihouée A, Teusan R, Dubois E, Savagner F, Steenman M, Houlgatte R, Ramstein G. MADGene: retrieval and processing of gene identifier lists for the analysis of heterogeneous microarray datasets. ACTA ACUST UNITED AC 2011; 27:725-6. [PMID: 21216776 PMCID: PMC3042180 DOI: 10.1093/bioinformatics/btq710] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [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: 11/24/2022]
Abstract
Summary: MADGene is a software environment comprising a web-based database and a java application. This platform aims at unifying gene identifiers (ids) and performing gene set analysis. MADGene allows the user to perform inter-conversion of clone and gene ids over a large range of nomenclatures relative to 17 species. We propose a set of 23 functions to facilitate the analysis of gene sets and we give two microarray applications to show how MADGene can be used to conduct meta-analyses. Availability: The MADGene resources are freely available online from http://www.madtools.org, a website dedicated to the analysis and annotation of DNA microarray data. Contact:gerard.ramstein@univ-nantes.fr Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Daniel Baron
- INSERM U915, IRT-UN, University of Nantes, France
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24
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Carat S, Houlgatte R, Bourdon J. A parallel scheme for comparing transcription factor binding sites matrices. J Bioinform Comput Biol 2010; 8:485-502. [PMID: 20556858 DOI: 10.1142/s0219720010004689] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Revised: 12/16/2009] [Accepted: 01/15/2010] [Indexed: 01/27/2023]
Abstract
Gene regulation implies many mechanisms. Their identification is a crucial task to construct regulatory networks, and is necessary to understand the pathology in many cases. This requires the identification of transcription factors that play a role in regulation. Numerous motif discovery tools are now available. Combining efficiently their results appears useful for comparing and clustering these motifs in order to reduce redundancies and to identify the corresponding transcription factor. We develop a method that produces, compares and clusters a set of motifs and identifies some close motifs in databases like JASPAR and the public version of Transfac. Unlike previous comparison methods, where each matrix column is compared independently, we have developed a global method to compare motifs that also helps to reduce the number of false positives. We also propose an original graph motif model that generalizes the classical position specific pattern matrices. Finally, we present an application of our method to study ChIP-chip data sets in the context of an eukaryotic organism.
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Affiliation(s)
- Solenne Carat
- Institut du thorax, INSERM U 915, Université de Nantes, France.
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25
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Orozco-Solís R, Matos RJB, Guzmán-Quevedo O, Lopes de Souza S, Bihouée A, Houlgatte R, Manhães de Castro R, Bolaños-Jiménez F. Nutritional programming in the rat is linked to long-lasting changes in nutrient sensing and energy homeostasis in the hypothalamus. PLoS One 2010; 5:e13537. [PMID: 20975839 PMCID: PMC2958833 DOI: 10.1371/journal.pone.0013537] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [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: 04/03/2010] [Accepted: 09/14/2010] [Indexed: 12/24/2022] Open
Abstract
Background Nutrient deficiency during perinatal development is associated with an increased risk to develop obesity, diabetes and hypertension in the adulthood. However, the molecular mechanisms underlying the developmental programming of the metabolic syndrome remain largely unknown. Methodology/Principal Findings Given the essential role of the hypothalamus in the integration of nutritional, endocrine and neuronal cues, here we have analyzed the profile of the hypothalamus transcriptome in 180 days-old rats born to dams fed either a control (200 g/kg) or a low-protein (80 g/kg) diet through pregnancy and lactation. From a total of 26 209 examined genes, 688 were up-regulated and 309 down-regulated (P<0.003) by early protein restriction. Further bioinformatic analysis of the data revealed that perinatal protein restriction permanently alters the expression of two gene clusters regulating common cellular processes. The first one includes several gate keeper genes regulating insulin signaling and nutrient sensing. The second cluster encompasses a functional network of nuclear receptors and co-regulators of transcription involved in the detection and use of lipid nutrients as fuel which, in addition, link temporal and nutritional cues to metabolism through their tight interaction with the circadian clock. Conclusions/Significance Collectively, these results indicate that the programming of the hypothalamic circuits regulating energy homeostasis is a key step in the development of obesity associated with malnutrition in early life and provide a valuable resource for further investigating the role of the hypothalamus in the programming of the metabolic syndrome.
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Affiliation(s)
- Ricardo Orozco-Solís
- INRA, UMR1280 Physiologie des Adaptations Nutritionnelles, Université de Nantes, Nantes Atlantique Université, Nantes, France
| | - Rhowena J. B. Matos
- INRA, UMR1280 Physiologie des Adaptations Nutritionnelles, Université de Nantes, Nantes Atlantique Université, Nantes, France
| | - Omar Guzmán-Quevedo
- INRA, UMR1280 Physiologie des Adaptations Nutritionnelles, Université de Nantes, Nantes Atlantique Université, Nantes, France
| | - Sandra Lopes de Souza
- Departamento de Anatomia, Centro de Ciências Biológicas, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Audrey Bihouée
- INSERM, U915, IFR26, l'institut du Thorax, Nantes, France
| | - Rémi Houlgatte
- INSERM, U915, IFR26, l'institut du Thorax, Nantes, France
| | - Raul Manhães de Castro
- Departamento de Nutriçao, Centro de Ciências da Saude, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Francisco Bolaños-Jiménez
- INRA, UMR1280 Physiologie des Adaptations Nutritionnelles, Université de Nantes, Nantes Atlantique Université, Nantes, France
- * E-mail:
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26
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Rolland D, Raharijaona M, Barbarat A, Houlgatte R, Thieblemont C. Inhibition of GST-pi nuclear transfer increases mantle cell lymphoma sensitivity to cisplatin, cytarabine, gemcitabine, bortezomib and doxorubicin. Anticancer Res 2010; 30:3951-3957. [PMID: 21036708] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
PURPOSE Mantle cell lymphoma (MCL) is a chemoresistant lymphoma overexpressing the class pi glutathione-S-transferase (GST-pi). The nuclear localisation of GST-pi is induced by chemotherapy and is correlated to cell resistance. In this study, the effect of the Agaricus bisporus lectin (ABL), a GST-pi nuclear transfer inhibitor, on the chemosensitivity of MCL cells was investigated. METHODS The proliferation of three MCL cell lines was evaluated in the presence of doxorubicin (DOX), cisplatin (CDDP), cytarabine (Ara-C), gemcitabine (GEM) or bortezomib with or without ABL pre-treatment. RESULTS The cytotoxic activities of CDDP, Ara-C, GEM and bortezomib were increased in all cell lines. The DOX cytotoxic activity was enhanced in two of three cell lines. The inhibition of GST-pi nuclear transfer led to the potentialisation of all drug combinations. CONCLUSION The inhibition of the nuclear transfer of GST-pi increases the MCL sensitivity to DOX, CDDP, Ara-C, GEM and bortezomib, alone or in combination.
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Affiliation(s)
- D Rolland
- INSERM U836 équipe 7, Grenoble, France
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Guenin L, Raharijaona M, Houlgatte R, Baba-Aissa F. Expression profiling of prospero in the Drosophila larval chemosensory organ: Between growth and outgrowth. BMC Genomics 2010; 11:47. [PMID: 20085633 PMCID: PMC2826315 DOI: 10.1186/1471-2164-11-47] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [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: 03/17/2009] [Accepted: 01/19/2010] [Indexed: 11/11/2022] Open
Abstract
Background The antenno-maxilary complex (AMC) forms the chemosensory system of the Drosophila larva and is involved in gustatory and olfactory perception. We have previously shown that a mutant allele of the homeodomain transcription factor Prospero (prosVoila1, V1), presents several developmental defects including abnormal growth and altered taste responses. In addition, many neural tracts connecting the AMC to the central nervous system (CNS) were affected. Our earlier reports on larval AMC did not argue in favour of a role of pros in cell fate decision, but strongly suggested that pros could be involved in the control of other aspect of neuronal development. In order to identify these functions, we used microarray analysis of larval AMC and CNS tissue isolated from the wild type, and three other previously characterised prospero alleles, including the V1 mutant, considered as a null allele for the AMC. Results A total of 17 samples were first analysed with hierarchical clustering. To determine those genes affected by loss of pros function, we calculated a discriminating score reflecting the differential expression between V1 mutant and other pros alleles. We identified a total of 64 genes in the AMC. Additional manual annotation using all the computed information on the attributed role of these genes in the Drosophila larvae nervous system, enabled us to identify one functional category of potential Prospero target genes known to be involved in neurite outgrowth, synaptic transmission and more specifically in neuronal connectivity remodelling. The second category of genes found to be differentially expressed between the null mutant AMC and the other alleles concerned the development of the sensory organs and more particularly the larval olfactory system. Surprisingly, a third category emerged from our analyses and suggests an association of pros with the genes that regulate autophagy, growth and insulin pathways. Interestingly, EGFR and Notch pathways were represented in all of these three functional categories. We now propose that Pros could perform all of these different functions through the modulation of these two antagonistic and synergic pathways. Conclusions The current data contribute to the clarification of the prospero function in the larval AMC and show that pros regulates different function in larvae as compared to those controlled by this gene in embryos. In the future, the possible mechanism by which Pros could achieve its function in the AMC will be explored in detail.
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Affiliation(s)
- Laure Guenin
- Université de Bourgogne, Facultés des Sciences, Unité Mixte de Recherche 5548 Associée au Centre National de la Recherche Scientifique, 6, Bd Gabriel, 21 000 Dijon, France
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Raharijaona M, Le Pennec S, Poirier J, Mirebeau-Prunier D, Rouxel C, Jacques C, Fontaine JF, Malthiery Y, Houlgatte R, Savagner F. PGC-1-related coactivator modulates mitochondrial-nuclear crosstalk through endogenous nitric oxide in a cellular model of oncocytic thyroid tumours. PLoS One 2009; 4:e7964. [PMID: 19956726 PMCID: PMC2776512 DOI: 10.1371/journal.pone.0007964] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2009] [Accepted: 10/25/2009] [Indexed: 11/19/2022] Open
Abstract
Background The PGC-1 related coactivator (PRC), which shares structural and functional features with PGC-1α, is believed to regulate several metabolic pathways as well as mitochondrial biogenesis. Its involvement in the early programming of cell proliferation suggests the existence of finely regulated crosstalk between mitochondrial functions and the cell cycle status. Methodology/Principal Findings PRC-regulated pathways were explored in a cell-line model derived from mitochondrial-rich tumours with an essentially oxidative metabolism and specifically high PRC expression. The functional status of mitochondria was compared to the results of microarray analysis under conditions of temporal PRC inhibition. To specify the fine PRC regulation, the expression levels of the genes and proteins involved in the oxidative phosphorylation process were studied by real time quantitative PCR and western blotting. As in earlier studies on PGC-1α, we investigated the role of nitric oxide in PRC-regulated mitochondrial biogenesis and determined its action in the control of the phosphorylation status of the mitogen-activated protein kinase pathway. Conclusion/Significance We found that nitric oxide rapidly influences PRC expression at the transcriptional level. Focusing on mitochondrial energetic metabolism, we observed that PRC differentially controls respiratory chain complexes and coupling efficiency in a time-dependent manner to maintain mitochondrial homeostasis. Our results highlight the key role of PRC in the rapid modulation of metabolic functions in response to the status of the cell cycle.
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Affiliation(s)
- Mahatsangy Raharijaona
- INSERM, UMR 915, l'institut du Thorax, Nantes, France
- Université de Nantes, Nantes, France
| | - Soazig Le Pennec
- INSERM, UMR 694, Angers, France
- Université d'Angers, Angers, France
| | - Julie Poirier
- INSERM, UMR 694, Angers, France
- Université d'Angers, Angers, France
| | - Delphine Mirebeau-Prunier
- INSERM, UMR 694, Angers, France
- Université d'Angers, Angers, France
- CHU Angers, Laboratoire de Biochimie, Angers, France
| | - Clothilde Rouxel
- INSERM, UMR 694, Angers, France
- Université d'Angers, Angers, France
| | - Caroline Jacques
- INSERM, UMR 694, Angers, France
- Université d'Angers, Angers, France
| | | | - Yves Malthiery
- INSERM, UMR 694, Angers, France
- Université d'Angers, Angers, France
- CHU Angers, Laboratoire de Biochimie, Angers, France
| | - Rémi Houlgatte
- INSERM, UMR 915, l'institut du Thorax, Nantes, France
- Université de Nantes, Nantes, France
| | - Frédérique Savagner
- INSERM, UMR 915, l'institut du Thorax, Nantes, France
- INSERM, UMR 694, Angers, France
- Université d'Angers, Angers, France
- CHU Angers, Laboratoire de Biochimie, Angers, France
- * E-mail: .
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Rolland AD, Lareyre JJ, Goupil AS, Montfort J, Ricordel MJ, Esquerré D, Hugot K, Houlgatte R, Chalmel F, Le Gac F. Expression profiling of rainbow trout testis development identifies evolutionary conserved genes involved in spermatogenesis. BMC Genomics 2009; 10:546. [PMID: 19925684 PMCID: PMC2786911 DOI: 10.1186/1471-2164-10-546] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Accepted: 11/20/2009] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Spermatogenesis is a late developmental process that involves a coordinated expression program in germ cells and a permanent communication between the testicular somatic cells and the germ-line. Current knowledge regarding molecular factors driving male germ cell proliferation and differentiation in vertebrates is still limited and mainly based on existing data from rodents and human. Fish with a marked reproductive cycle and a germ cell development in synchronous cysts have proven to be choice models to study precise stages of the spermatogenetic development and the germ cell-somatic cell communication network. In this study we used 9K cDNA microarrays to investigate the expression profiles underlying testis maturation during the male reproductive cycle of the trout, Oncorhynchus mykiss. RESULTS Using total testis samples at various developmental stages and isolated spermatogonia, spermatocytes and spermatids, 3379 differentially expressed trout cDNAs were identified and their gene activation or repression patterns throughout the reproductive cycle were reported. We also performed a tissue-profiling analysis and highlighted many genes for which expression signals were restricted to the testes or gonads from both sexes. The search for orthologous genes in genome-sequenced fish species and the use of their mammalian orthologs allowed us to provide accurate annotations for trout cDNAs. The analysis of the GeneOntology terms therefore validated and broadened our interpretation of expression clusters by highlighting enriched functions that are consistent with known sequential events during male gametogenesis. Furthermore, we compared expression profiles of trout and mouse orthologs and identified a complement of genes for which expression during spermatogenesis was maintained throughout evolution. CONCLUSION A comprehensive study of gene expression and associated functions during testis maturation and germ cell differentiation in the rainbow trout is presented. The study identifies new pathways involved during spermatogonia self-renewal or rapid proliferation, meiosis and gamete differentiation, in fish and potentially in all vertebrates. It also provides the necessary basis to further investigate the hormonal and molecular networks that trigger puberty and annual testicular recrudescence in seasonally breeding species.
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Affiliation(s)
| | | | | | - Jérôme Montfort
- INRA, UR1037, IFR-140, Ouest Genopole, Rennes, 35042, France
| | | | - Diane Esquerré
- INRA, UMR 1313 de Génétique Animale et Biologie Intégrative, Domaine de Vilvert, 78350 Jouy-en-Josas, France
- CEA, DSV, iRCM, SREIT, Laboratoire de Génétique Animale et Biologie Intégrative, 78350 Jouy-en-Josas, France
- AgroParisTech, UMR de Génétique Animale et Biologie Intégrative, 78350 Jouy-en-Josas, France
| | - Karine Hugot
- INRA, UMR 1313 de Génétique Animale et Biologie Intégrative, Domaine de Vilvert, 78350 Jouy-en-Josas, France
- CEA, DSV, iRCM, SREIT, Laboratoire de Génétique Animale et Biologie Intégrative, 78350 Jouy-en-Josas, France
- AgroParisTech, UMR de Génétique Animale et Biologie Intégrative, 78350 Jouy-en-Josas, France
| | - Rémi Houlgatte
- Inserm, U915, Université de Nantes, Faculté de Médecine, Nantes, 44035, France
| | - Fréderic Chalmel
- Inserm, U625, GERHM, Université de Rennes1, IFR-140, Ouest Genopole, Rennes, 35042, France
| | - Florence Le Gac
- INRA, UR1037, IFR-140, Ouest Genopole, Rennes, 35042, France
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Van Landeghem L, Mahé MM, Teusan R, Léger J, Guisle I, Houlgatte R, Neunlist M. Regulation of intestinal epithelial cells transcriptome by enteric glial cells: impact on intestinal epithelial barrier functions. BMC Genomics 2009; 10:507. [PMID: 19883504 PMCID: PMC2778665 DOI: 10.1186/1471-2164-10-507] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [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: 02/26/2009] [Accepted: 11/02/2009] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Emerging evidences suggest that enteric glial cells (EGC), a major constituent of the enteric nervous system (ENS), are key regulators of intestinal epithelial barrier (IEB) functions. Indeed EGC inhibit intestinal epithelial cells (IEC) proliferation and increase IEB paracellular permeability. However, the role of EGC on other important barrier functions and the signalling pathways involved in their effects are currently unknown. To achieve this goal, we aimed at identifying the impact of EGC upon IEC transcriptome by performing microarray studies. RESULTS EGC induced significant changes in gene expression profiling of proliferating IEC after 24 hours of co-culture. 116 genes were identified as differentially expressed (70 up-regulated and 46 down-regulated) in IEC cultured with EGC compared to IEC cultured alone. By performing functional analysis of the 116 identified genes using Ingenuity Pathway Analysis, we showed that EGC induced a significant regulation of genes favoring both cell-to-cell and cell-to-matrix adhesion as well as cell differentiation. Consistently, functional studies showed that EGC induced a significant increase in cell adhesion. EGC also regulated genes involved in cell motility towards an enhancement of cell motility. In addition, EGC profoundly modulated expression of genes involved in cell proliferation and cell survival, although no clear functional trend could be identified. Finally, important genes involved in lipid and protein metabolism of epithelial cells were shown to be differentially regulated by EGC. CONCLUSION This study reinforces the emerging concept that EGC have major protective effects upon the IEB. EGC have a profound impact upon IEC transcriptome and induce a shift in IEC phenotype towards increased cell adhesion and cell differentiation. This concept needs to be further validated under both physiological and pathophysiological conditions.
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Royère D, Feuerstein P, Cadoret V, Puard V, Uzbekova S, Dalbies-Tran R, Teusan R, Houlgatte R, Labas V, Guérif F. Approches non invasives de l’embryon : protéomique, métabolomique, dialogue ovocyte-cumulus. ACTA ACUST UNITED AC 2009; 37:917-20. [DOI: 10.1016/j.gyobfe.2009.09.016] [Citation(s) in RCA: 7] [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: 09/03/2009] [Accepted: 09/03/2009] [Indexed: 10/20/2022]
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Fontaine JF, Mirebeau-Prunier D, Raharijaona M, Franc B, Triau S, Rodien P, Goëau-Brissonniére O, Karayan-Tapon L, Mello M, Houlgatte R, Malthiery Y, Savagner F. Increasing the number of thyroid lesions classes in microarray analysis improves the relevance of diagnostic markers. PLoS One 2009; 4:e7632. [PMID: 19893615 PMCID: PMC2764086 DOI: 10.1371/journal.pone.0007632] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [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: 05/12/2009] [Accepted: 10/05/2009] [Indexed: 11/19/2022] Open
Abstract
Background Genetic markers for thyroid cancers identified by microarray analysis have offered limited predictive accuracy so far because of the few classes of thyroid lesions usually taken into account. To improve diagnostic relevance, we have simultaneously analyzed microarray data from six public datasets covering a total of 347 thyroid tissue samples representing 12 histological classes of follicular lesions and normal thyroid tissue. Our own dataset, containing about half the thyroid tissue samples, included all categories of thyroid lesions. Methodology/Principal Findings Classifier predictions were strongly affected by similarities between classes and by the number of classes in the training sets. In each dataset, sample prediction was improved by separating the samples into three groups according to class similarities. The cross-validation of differential genes revealed four clusters with functional enrichments. The analysis of six of these genes (APOD, APOE, CLGN, CRABP1, SDHA and TIMP1) in 49 new samples showed consistent gene and protein profiles with the class similarities observed. Focusing on four subclasses of follicular tumor, we explored the diagnostic potential of 12 selected markers (CASP10, CDH16, CLGN, CRABP1, HMGB2, ALPL2, ADAMTS2, CABIN1, ALDH1A3, USP13, NR2F2, KRTHB5) by real-time quantitative RT-PCR on 32 other new samples. The gene expression profiles of follicular tumors were examined with reference to the mutational status of the Pax8-PPARγ, TSHR, GNAS and NRAS genes. Conclusion/Significance We show that diagnostic tools defined on the basis of microarray data are more relevant when a large number of samples and tissue classes are used. Taking into account the relationships between the thyroid tumor pathologies, together with the main biological functions and pathways involved, improved the diagnostic accuracy of the samples. Our approach was particularly relevant for the classification of microfollicular adenomas.
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Affiliation(s)
- Jean-Fred Fontaine
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
- INSERM, UMR 694, Angers, France
- Université d'Angers, Angers, France
| | - Delphine Mirebeau-Prunier
- INSERM, UMR 694, Angers, France
- Université d'Angers, Angers, France
- CHU Angers, Laboratoire de Biochimie, Angers, France
| | - Mahatsangy Raharijaona
- INSERM, UMR 915, l'institut du Thorax, Nantes, France
- Université de Nantes, Nantes, France
| | - Brigitte Franc
- Hôpital A Paré, Laboratoire d'Anatomie Pathologique, Boulogne, France
| | - Stephane Triau
- CHU Angers, Laboratoire de Pathologie Cellulaire et Tissulaire, Angers, France
| | - Patrice Rodien
- INSERM, UMR 694, Angers, France
- Université d'Angers, Angers, France
- CHU Angers, Département Endocrinologie-Diabétologie-Nutrition, Angers, France
| | | | | | | | - Rémi Houlgatte
- INSERM, UMR 915, l'institut du Thorax, Nantes, France
- Université de Nantes, Nantes, France
| | - Yves Malthiery
- INSERM, UMR 694, Angers, France
- Université d'Angers, Angers, France
- CHU Angers, Laboratoire de Biochimie, Angers, France
| | - Frédérique Savagner
- INSERM, UMR 694, Angers, France
- Université d'Angers, Angers, France
- CHU Angers, Laboratoire de Biochimie, Angers, France
- INSERM, UMR 915, l'institut du Thorax, Nantes, France
- * E-mail:
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Lamirault G, Meur NL, Roussel JC, Cunff MFL, Baron D, Bihouée A, Guisle I, Raharijaona M, Ramstein G, Teusan R, Chevalier C, Gueffet JP, Trochu JN, Léger JJ, Houlgatte R, Steenman M. Molecular risk stratification in advanced heart failure patients. J Cell Mol Med 2009; 14:1443-52. [PMID: 19793385 PMCID: PMC3829011 DOI: 10.1111/j.1582-4934.2009.00913.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [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: 11/29/2022] Open
Abstract
Risk stratification in advanced heart failure (HF) is crucial for the individualization of therapeutic strategy, in particular for heart transplantation and ventricular assist device implantation. We tested the hypothesis that cardiac gene expression profiling can distinguish between HF patients with different disease severity. We obtained tissue samples from both left (LV) and right (RV) ventricle of explanted hearts of 44 patients undergoing cardiac transplantation or ventricular assist device placement. Gene expression profiles were obtained using an in-house microarray containing 4217 muscular organ-relevant genes. Based on their clinical status, patients were classified into three HF-severity groups: deteriorating (n= 12), intermediate (n= 19) and stable (n= 13). Two-class statistical analysis of gene expression profiles of deteriorating and stable patients identified a 170-gene and a 129-gene predictor for LV and RV samples, respectively. The LV molecular predictor identified patients with stable and deteriorating status with a sensitivity of 88% and 92%, and a specificity of 100% and 96%, respectively. The RV molecular predictor identified patients with stable and deteriorating status with a sensitivity of 100% and 96%, and a specificity of 100% and 100%, respectively. The molecular prediction was reproducible across biological replicates in LV and RV samples. Gene expression profiling has the potential to reproducibly detect HF patients with highest HF severity with high sensitivity and specificity. In addition, not only LV but also RV samples could be used for molecular risk stratification with similar predictive power.
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Remme CA, Scicluna BP, Verkerk AO, Amin AS, van Brunschot S, Beekman L, Deneer VHM, Chevalier C, Oyama F, Miyazaki H, Nukina N, Wilders R, Escande D, Houlgatte R, Wilde AAM, Tan HL, Veldkamp MW, de Bakker JMT, Bezzina CR. Genetically determined differences in sodium current characteristics modulate conduction disease severity in mice with cardiac sodium channelopathy. Circ Res 2009; 104:1283-92. [PMID: 19407241 DOI: 10.1161/circresaha.109.194423] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Conduction slowing of the electric impulse that drives the heartbeat may evoke lethal cardiac arrhythmias. Mutations in SCN5A, which encodes the pore-forming cardiac sodium channel alpha subunit, are associated with familial arrhythmia syndromes based on conduction slowing. However, disease severity among mutation carriers is highly variable. We hypothesized that genetic modifiers underlie the variability in conduction slowing and disease severity. With the aim of identifying such modifiers, we studied the Scn5a(1798insD/+) mutation in 2 distinct mouse strains, FVB/N and 129P2. In 129P2 mice, the mutation resulted in more severe conduction slowing particularly in the right ventricle (RV) compared to FVB/N. Pan-genomic mRNA expression profiling in the 2 mouse strains uncovered a drastic reduction in mRNA encoding the sodium channel auxiliary subunit beta4 (Scn4b) in 129P2 mice compared to FVB/N. This corresponded to low to undetectable beta4 protein levels in 129P2 ventricular tissue, whereas abundant beta4 protein was detected in FVB/N. Sodium current measurements in isolated myocytes from the 2 mouse strains indicated that sodium channel activation in myocytes from 129P2 mice occurred at more positive potentials compared to FVB/N. Using computer simulations, this difference in activation kinetics was predicted to explain the observed differences in conduction disease severity between the 2 strains. In conclusion, genetically determined differences in sodium current characteristics on the myocyte level modulate disease severity in cardiac sodium channelopathies. In particular, the sodium channel subunit beta4 (SCN4B) may constitute a potential genetic modifier of conduction and cardiac sodium channel disease.
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Affiliation(s)
- Carol Ann Remme
- Heart Failure Research Center, Department of Experimental Cardiology, Academic Medical Center, University of Amsterdam, Room K2-110, PO Box 22700, 1100 DE Amsterdam, The Netherlands.
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Nevarez L, Vasseur V, Le Dréan G, Tanguy A, Guisle-Marsollier I, Houlgatte R, Barbier G. Isolation and analysis of differentially expressed genes in Penicillium glabrum subjected to thermal stress. Microbiology (Reading) 2008; 154:3752-3765. [PMID: 19047743 DOI: 10.1099/mic.0.2008/021386-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- L. Nevarez
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Université Européenne de Bretagne, Ecole Supérieure de Microbiologie et Sécurité Alimentaire de Brest, Technopôle Brest-Iroise, 28280 Plouzané, France
| | - V. Vasseur
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Université Européenne de Bretagne, Ecole Supérieure de Microbiologie et Sécurité Alimentaire de Brest, Technopôle Brest-Iroise, 28280 Plouzané, France
| | - G. Le Dréan
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Université Européenne de Bretagne, Ecole Supérieure de Microbiologie et Sécurité Alimentaire de Brest, Technopôle Brest-Iroise, 28280 Plouzané, France
| | - A. Tanguy
- Evolution et Génétique des Populations Marines, UMR CNRS 7144, Université Pierre et Marie Curie, Station Biologique de Roscoff, Place Georges Teissier, 29682 Roscoff Cedex, France
| | - I. Guisle-Marsollier
- Plate-forme Transcriptomique Ouest-Génopôle, Institut du Thorax INSERM U533, 1 Rue Gaston Veil, BP 53508, 44035 Nantes, Cedex 1, France
| | - R. Houlgatte
- Plate-forme Transcriptomique Ouest-Génopôle, Institut du Thorax INSERM U533, 1 Rue Gaston Veil, BP 53508, 44035 Nantes, Cedex 1, France
| | - G. Barbier
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Université Européenne de Bretagne, Ecole Supérieure de Microbiologie et Sécurité Alimentaire de Brest, Technopôle Brest-Iroise, 28280 Plouzané, France
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Thieblemont C, Rolland D, Baseggio L, Felman P, Gazzo S, Callet-Bauchu E, Traverse-Glehen A, Houlgatte R, Fu K, Weisenburger D, De Jong D, Jaffe ES, Rosenwald A, Ott G, Coiffier B, Berger F. Comprehensive analysis of GST-pi expression in B-cell lymphomas: Correlation with histological subtypes and survival. Leuk Lymphoma 2008; 49:1403-6. [PMID: 18604726 DOI: 10.1080/10428190802094245] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Olivier V, Blanchard P, Chaouch S, Lallemand P, Schurr F, Celle O, Dubois E, Tordo N, Thiéry R, Houlgatte R, Ribière M. Molecular characterisation and phylogenetic analysis of Chronic bee paralysis virus, a honey bee virus. Virus Res 2008; 132:59-68. [PMID: 18079012 DOI: 10.1016/j.virusres.2007.10.014] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2007] [Revised: 10/11/2007] [Accepted: 10/17/2007] [Indexed: 11/20/2022]
Abstract
The complete sequences of the two major RNAs of Chronic bee paralysis virus (CBPV) have been determined. RNA 1 (3674nt long) and RNA 2 (2305nt long) are positive single-stranded RNAs that are capped but not polyadenylated. The 3' ends of both RNAs are unreactive to polymerisation or ligation even in denaturing conditions, a feature already observed in alphanodavirus RNAs. The three previously described smaller RNAs [Overton, H.A., Buck, K.W., Bailey, L., et al., 1982. Relationships between the RNA components of Chronic bee-paralysis virus and those of chronic bee-paralysis virus associate. J. Gen. Virol. 63, 171-179], were not detected in this study, supporting the hypothesis that they would correspond to the three RNAs of the Chronic bee paralysis satellite virus (CBPSV). RNA 1 and RNA 2 encoded three and four overlapping open reading frames (ORFs), respectively. The amino acid sequences deduced from the ORF 3 on RNA 1 shared the conserved motifs of the RNA-dependent RNA polymerase (RdRp) sequence and presented similarities with members of the Nodaviridae and Tombusviridae families. However, no similarities were found between the other CBPV deduced amino acid sequences and sequences in the NCBI databases, suggesting that CBPV is the prototype of a new family of positive single-stranded RNA viruses.
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Affiliation(s)
- Violaine Olivier
- Agence Française de Sécurité Sanitaire des Aliments, 105 route des Chappes, BP 111, 06 902 Sophia-Antipolis, France
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Baron D, Houlgatte R, Fostier A, Guiguen Y. Expression profiling of candidate genes during ovary-to-testis trans-differentiation in rainbow trout masculinized by androgens. Gen Comp Endocrinol 2008; 156:369-78. [PMID: 18299129 DOI: 10.1016/j.ygcen.2008.01.016] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2007] [Revised: 01/14/2008] [Accepted: 01/15/2008] [Indexed: 11/25/2022]
Abstract
Fish gonadal phenotype is very sensitive to sex steroid and functional masculinizations can be obtained in most species using androgen treatments. To gain insight into the molecular effects of androgen-induced masculinization we characterized, in the rainbow trout, the gonadal expression profiles of 103 candidate genes involved in sex differentiation and early gametogenesis. The androgen treatment (11beta-hydroxyandrostenedione, 10 mg/kg of food for 3 months) was administered in a genetic all-female population. Gonads were sampled at different time points in genetic all-male and all-female control populations and in the androgen-treated group. Gene expression profiles were recorded by real-time RT-PCR and biological samples and gene expressions were compared using a global clustering analysis. This analysis revealed that masculinization with androgens acts firstly by repressing granulosa cell related genes, including genes involved in ovarian differentiation (foxl2a, fst, cyp19a1a), and subsequently by repressing genes important for early oogenesis (gdf9, bcl2lb, fancl, gcl, fshb, lhb, sox23, sox24, nup62 and vtgr). However, this masculinizing treatment did not induce a testicular differentiation similar to what was observed in the control male population. This was especially noticeable for many Leydig cell genes encoding proteins involved in steroidogenesis or its control (hsd3b1, star, cyp17a1, cyp11b2.1 and nr5a1b) that were down-regulated in the androgen-treated group. Concomitantly some Sertoli cells marker genes were up-regulated by the androgen treatment (sox9a.1, nr0b1, cldn11, dmrt1) whereas others were down-regulated (amh, sox9a.2), suggesting a partial differentiation of the Sertoli cell lineage. Overall, this suggests that the crucial step of this masculinization process is the de-differentiation of the granulosa cells.
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Affiliation(s)
- Daniel Baron
- INRA, UR1037 SCRIBE, IFR140, Ouest-Genopole, Rennes, France
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Baron D, Montfort J, Houlgatte R, Fostier A, Guiguen Y. Androgen-induced masculinization in rainbow trout results in a marked dysregulation of early gonadal gene expression profiles. BMC Genomics 2007; 8:357. [PMID: 17916255 PMCID: PMC2099445 DOI: 10.1186/1471-2164-8-357] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [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: 04/04/2007] [Accepted: 10/04/2007] [Indexed: 11/27/2022] Open
Abstract
Background Fish gonadal sex differentiation is affected by sex steroids treatments providing an efficient strategy to control the sexual phenotype of fish for aquaculture purposes. However, the biological effects of such treatments are poorly understood. The aim of this study was to identify the main effects of an androgen masculinizing treatment (11β-hydroxyandrostenedione, 11βOHΔ4, 10 mg/kg of food for 3 months) on gonadal gene expression profiles of an all-female genetic population of trout. To characterize the most important molecular features of this process, we used a large scale gene expression profiling approach using rainbow trout DNA microarrays combined with a detailed gene ontology (GO) analysis. Results 2,474 genes were characterized as up-regulated or down-regulated in trout female gonads masculinized by androgen in comparison with control male or female gonads from untreated all-male and all-female genetic populations. These genes were classified in 13 k-means clusters of temporally correlated expression profiles. Gene ontology (GO) data mining revealed that androgen treatment triggers a marked down-regulation of genes potentially involved in early oogenesis processes (GO 'mitotic cell cycle', 'nucleolus'), an up-regulation of the translation machinery (GO 'ribosome') along with a down-regulation of proteolysis (GO 'proteolysis', 'peptidase' and 'metallopeptidase activity'). Genes considered as muscle fibres markers (GO 'muscle contraction') and genes annotated as structural constituents of the extracellular matrix (GO 'extracellular matrix') or related to meiosis (GO 'chromosome' and 'meiosis') were found significantly enriched in the two clusters of genes specifically up-regulated in androgen-treated female gonads. GO annotations 'Sex differentiation' and 'steroid biosynthesis' were enriched in a cluster of genes with high expression levels only in control males. Interestingly none of these genes were stimulated by the masculinizing androgen treatment. Conclusion This study provides evidence that androgen masculinization results in a marked dysregulation of early gene expression profiles when compared to natural testicular or ovarian differentiation. Based on these results we suggest that, in our experimental conditions, androgen masculinization proceeds mainly through an early inhibition of female development.
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Affiliation(s)
- Daniel Baron
- INRA, UR1037 SCRIBE, IFR140, Ouest-Genopole, F-35000 Rennes, France.
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Bertucci F, Pages C, Finetti P, Rochaix P, Lamant L, Devilard E, Nguyen C, Houlgatte R, Birnbaum D, Xerri L, Brousset P. Gene expression profiling of human melanoma cell lines with distinct metastatic potential identifies new progression markers. Anticancer Res 2007; 27:3441-3449. [PMID: 17970093] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
BACKGROUND Identification of markers associated with melanoma progression is crucial to identify new prognostic and/or therapeutic targets. MATERIALS AND METHODS By using DNA microarrays, two human melanoma cell lines, M4Be and Tw12, derived from the same tumor, but with different metastatic potential, were profiled. Western blot of cell lines, immunohistochemistry on melanoma biopsies and in silico analyses validated and extended our results. RESULTS Thirty-six clones were differentially-expressed between the two cell lines, representing 33 named genes and 2 expressed sequence tags. The most up-regulated gene in the strongly metastatic clone Tw12 was CD10. Protein analysis with anti-CD1O antibody confirmed this finding in cell lines and clinical samples with expression being more frequent in metastatic compared to primary tumors. Many up-regulated genes were involved in angiogenesis, invasion, growth and apoptosis. Down-regulated genes included tumor suppressor genes and those were involved in differentiation. CONCLUSION We identified several genes the expression of which is associated with metastatic progression in human melanoma cells. Although further analyses are warranted to clarify their exact role in tumor progression, they might lead to new prognostic markers and/or molecular therapeutic targets in metastatic melanoma.
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Affiliation(s)
- François Bertucci
- Departments of Medical Oncology, UMR599 INSERM, Institut Paoli Calmettes, Marseille, France.
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Ballester B, Ramuz O, Gisselbrecht C, Doucet G, Loï L, Loriod B, Bertucci F, Bouabdallah R, Devilard E, Carbuccia N, Mozziconacci MJ, Birnbaum D, Brousset P, Berger F, Salles G, Briére J, Houlgatte R, Gaulard P, Xerri L. Gene expression profiling identifies molecular subgroups among nodal peripheral T-cell lymphomas. Oncogene 2005; 25:1560-70. [PMID: 16288225 DOI: 10.1038/sj.onc.1209178] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The classification of peripheral T-cell lymphomas (PTCL) is still a matter of debate. To establish a molecular classification of PTCL, we analysed 59 primary nodal T-cell lymphomas using cDNA microarrays, including 56 PTCL and three T-lymphoblastic lymphoma (T-LBL). The expression profiles could discriminate angioimmunoblastic lymphoma, anaplastic large-cell lymphoma and T-LBL. In contrast, cases belonging to the broad category of 'PTCL, unspecified' (PTCL-U) did not share a single molecular profile. Using a multiclass predictor, we could separate PTCL-U into three molecular subgroups called U1, U2 and U3. The U1 gene expression signature included genes known to be associated with poor outcome in other tumors, such as CCND2. The U2 subgroup was associated with overexpression of genes involved in T-cell activation and apoptosis, including NFKB1 and BCL-2. The U3 subgroup was mainly defined by overexpression of genes involved in the IFN/JAK/STAT pathway. It comprised a majority of histiocyte-rich PTCL samples. Gene Ontology annotations revealed different functional profile for each subgroup. These results suggest the existence of distinct subtypes of PTCL-U with specific molecular profiles, and thus provide a basis to improve their classification and to develop new therapeutic targets.
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Baris O, Mirebeau-Prunier D, Savagner F, Rodien P, Ballester B, Loriod B, Granjeaud S, Guyetant S, Franc B, Houlgatte R, Reynier P, Malthiery Y. Gene profiling reveals specific oncogenic mechanisms and signaling pathways in oncocytic and papillary thyroid carcinoma. Oncogene 2005; 24:4155-61. [PMID: 15806164 DOI: 10.1038/sj.onc.1208578] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The oncogenic pathways in mitochondrial-rich thyroid carcinomas are not clearly understood. To investigate the possible implication of mitochondrial abundance in the genesis of thyroid tumors, we have explored the gene expression profile of six oncocytic carcinomas and six mitochondrial-rich papillary carcinomas using cDNA-microarray technology. A supervised approach allowed us to identify 83 genes differentially expressed in the two types of carcinoma. These genes were classified according to their ontologic profiles. Three genes, NOS3, alpha-actinin-2 and alpha-catenin, suspected of playing a role in tumor genesis, were explored by quantitative RT-PCR analysis and immunohistochemistry. Of the 59 genes overexpressed in papillary carcinomas, 51% were involved in cell communication. Of the 24 genes overexpressed in oncocytic carcinomas, 84% were involved in mitochondrial and cellular metabolism. Our results suggest that mitochondrial respiratory chain complexes III and IV play a significant role in the regulation of reactive oxygen species production by oncocytic tumors.
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Affiliation(s)
- Olivier Baris
- INSERM EMI-U 0018, Laboratoire de Biochimie et Biologie Moléculaire, CHU, 4 rue Larrey, Angers F-49033, France.
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Bertucci F, Finetti P, Rougemont J, Charafe-Jauffret E, Cervera N, Tarpin C, Nguyen C, Xerri L, Houlgatte R, Jacquemier J, Viens P, Birnbaum D. Gene Expression Profiling Identifies Molecular Subtypes of Inflammatory Breast Cancer. Cancer Res 2005; 65:2170-8. [PMID: 15781628 DOI: 10.1158/0008-5472.can-04-4115] [Citation(s) in RCA: 167] [Impact Index Per Article: 8.8] [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] [Indexed: 11/16/2022]
Abstract
Breast cancer is a heterogeneous disease. Comprehensive gene expression profiles obtained using DNA microarrays have revealed previously indistinguishable subtypes of noninflammatory breast cancer (NIBC) related to different features of mammary epithelial biology and significantly associated with survival. Inflammatory breast cancer (IBC) is a rare, particular, and aggressive form of disease. Here we have investigated whether the five molecular subtypes described for NIBC (luminal A and B, basal, ERBB2 overexpressing, and normal breast-like) were also present in IBC. We monitored the RNA expression of approximately 8,000 genes in 83 breast tissue samples including 37 IBC, 44 NIBC, and 2 normal breast samples. Hierarchical clustering identified the five subtypes of breast cancer in both NIBC and IBC samples. These subtypes were highly similar to those defined in previous studies and associated with similar histoclinical features. The robustness of this classification was confirmed by the use of both alternative gene set and analysis method, and the results were corroborated at the protein level. Furthermore, we show that the differences in gene expression between NIBC and IBC and between IBC with and without pathologic complete response that we have recently reported persist in each subtype. Our results show that the expression signatures defining molecular subtypes of NIBC are also present in IBC. Obtained using different patient series and different microarray platforms, they reinforce confidence in the expression-based molecular taxonomy but also give evidence for its universality in breast cancer, independently of a specific clinical form.
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Affiliation(s)
- François Bertucci
- Institut de Cancérologie de Marseille, Laboratoire d'Oncologie Moléculaire, Institut Paoli-Calmettes and UMR599 Institut National de la Santé et de la Recherche Médicale, IFR137, France
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Vey N, Mozziconacci MJ, Groulet-Martinec A, Debono S, Finetti P, Carbuccia N, Beillard E, Devilard E, Arnoulet C, Coso D, Sainty D, Xerri L, Stoppa AM, Lafage-Pochitaloff M, Nguyen C, Houlgatte R, Blaise D, Maraninchi D, Birg F, Birnbaum D, Bertucci F. Identification of new classes among acute myelogenous leukaemias with normal karyotype using gene expression profiling. Oncogene 2005; 23:9381-91. [PMID: 15543237 DOI: 10.1038/sj.onc.1207910] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Conventional cytogenetic analysis currently stratifies acute myelogenous leukaemia (AML) into prognostically relevant groups. However, approximately 50% of adult AMLs have normal cytogenetics (NC-AMLs), and represent a heterogeneous and poorly understood group. We analysed gene expression in 55 AML samples including 53 cases from adult patients with NC-AML (n = 36), trisomy 8, t(15;17), t(8;21), t(11;19), 7q deletion, and two cell lines using 9000-gene DNA microarrays. Global hierarchical clustering showed that NC-AMLs are a heterogeneous group. Supervised analysis distinguished two subgroups of NC-AML: one subgroup constituted a homogeneous NC cluster ('pure NC-AML'), and the other NC-AMLs were close to the AML cases with translocations ('translocation like'). Gene expression signatures were also derived for patients with trisomy 8, as well as FLT3 and MLL gene duplications. Importantly, samples from 24 NC-AML patients who could be evaluated for clinical outcome were analysed. In all, 43 genes that discriminated two classes of patients with significantly different prognosis were identified. The poor prognosis class contained a majority of 'pure NC-AMLs', whereas the 'translocation-like' AMLs were in the good prognosis class. Discriminator genes included genes involved in drug resistance (TOP2B), protein transport (MTX2, SLC35A2), and cell signalling (MAPK1, PRKAB2). Our results demonstrate the transcriptional heterogeneity of NC-AMLs, and suggest the existence of 'translocation-like' NC-AMLs and of a gene expression signature that may predict response to chemotherapy.
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Affiliation(s)
- Norbert Vey
- Department of Molecular Oncology, Institut Paoli-Calmettes-UMR599 Inserm, IFR137, Marseille Cancer Institute, Marseille, France
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de Fraipont F, El Atifi M, Cherradi N, Le Moigne G, Defaye G, Houlgatte R, Bertherat J, Bertagna X, Plouin PF, Baudin E, Berger F, Gicquel C, Chabre O, Feige JJ. Gene expression profiling of human adrenocortical tumors using complementary deoxyribonucleic Acid microarrays identifies several candidate genes as markers of malignancy. J Clin Endocrinol Metab 2005; 90:1819-29. [PMID: 15613424 DOI: 10.1210/jc.2004-1075] [Citation(s) in RCA: 164] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The aim of this study was to identify predictor sets of genes whose over- or underexpression in human sporadic adrenocortical tumors would help to identify malignant vs. benign tumors and to predict postsurgical metastatic recurrence. For this, we analyzed the expression of 230 candidate genes using cDNA microarrays in a series of 57 well-characterized human sporadic adrenocortical tumors (33 adenomas and 24 carcinomas). We identified two clusters of genes (the IGF-II cluster containing eight genes, including IGF-II, and the steroidogenesis cluster containing six genes encoding steroidogenic enzymes plus eight other genes) whose combined levels of expression appeared to be good predictors of malignancy. This predictive value was as strong as that of the pathological score of Weiss. The analysis of the population of carcinomas (13 tumors) for genes whose expression would be strongly different between recurring and nonrecurring tumors allowed identification of 14 genes meeting these criteria. Among these genes, there are probably new markers of tumor evolution that will deserve additional validation on a larger scale. Taken together, these results show that the parallel analysis of the expression levels of a selected group of genes on microgram quantities of tumor RNA (a quantity that can be obtained from fine needle aspirations) appears as a complementary method to histopathology for the diagnosis and prognosis of evolution of adrenocortical carcinomas.
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Affiliation(s)
- Florence de Fraipont
- Institut National de la Santé et de la Recherche Médicale, Equipe Mixte 01-05, Department of Cellular Responses and Dynamics, Angiogenesis Laboratory, Commissariat à l'Energie Atomique Grenoble, 17 rue des Martyrs, F-38054 Grenoble Cedex 9, France
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Bertucci F, Finetti P, Rougemont J, Charafe-Jauffret E, Nasser V, Loriod B, Camerlo J, Tagett R, Tarpin C, Houvenaeghel G, Nguyen C, Maraninchi D, Jacquemier J, Houlgatte R, Birnbaum D, Viens P. Gene expression profiling for molecular characterization of inflammatory breast cancer and prediction of response to chemotherapy. Cancer Res 2005; 64:8558-65. [PMID: 15574762 DOI: 10.1158/0008-5472.can-04-2696] [Citation(s) in RCA: 150] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Inflammatory breast cancer (IBC) is a rare but aggressive form of breast cancer with a 5-year survival limited to approximately 40%. Diagnosis, based on clinical and/or pathological criteria, may be difficult. Optimal systemic neoadjuvant therapy and accurate predictors of pathological response have yet to be defined for increasing response rate and survival. Using DNA microarrrays containing approximately 8,000 genes, we profiled breast cancer samples from 81 patients, including 37 with IBC and 44 with noninflammatory breast cancer (NIBC). Global unsupervised hierarchical clustering was able to some extent to distinguish IBC and NIBC cases and revealed subclasses of IBC. Supervised analysis identified a 109-gene set the expression of which discriminated IBC from NIBC samples. This molecular signature was validated in an independent series of 26 samples, with an overall performance accuracy of 85%. Discriminator genes were associated with various cellular processes possibly related to the aggressiveness of IBC, including signal transduction, cell motility, adhesion, and angiogenesis. A similar approach, with leave-one-out cross-validation, identified an 85-gene set that divided IBC patients with significantly different pathological complete response rate (70% in one group and 0% in the other group). These results show the potential of gene expression profiling to contribute to a better understanding of IBC, and to provide new diagnostic and predictive factors for IBC, as well as for potential therapeutic targets.
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Affiliation(s)
- François Bertucci
- Département d'Oncologie Moléculaire, Institut Paoli-Calmettes and UMR599 Institut National de la Santé et de la Recherche Médicale, IFR137, Marseille, France
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Lopez F, Rougemont J, Loriod B, Bourgeois A, Loï L, Bertucci F, Hingamp P, Houlgatte R, Granjeaud S. Feature extraction and signal processing for nylon DNA microarrays. BMC Genomics 2004; 5:38. [PMID: 15222896 PMCID: PMC471548 DOI: 10.1186/1471-2164-5-38] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [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: 04/21/2004] [Accepted: 06/29/2004] [Indexed: 04/30/2023] Open
Abstract
Background High-density DNA microarrays require automatic feature extraction methodologies and softwares. These can be a potential source of non-reproducibility of gene expression measurements. Variation in feature location or in signal integration methodology may be a significant contribution to the observed variance in gene expression levels. Results We explore sources of variability in feature extraction from DNA microarrays on Nylon membrane with radioactive detection. We introduce a mathematical model of the signal emission and derive methods for correcting biases such as overshining, saturation or variation in probe amount. We also provide a quality metric which can be used qualitatively to flag weak or untrusted signals or quantitatively to modulate the weight of each experiment or gene in higher level analyses (clustering or discriminant analysis). Conclusions Our novel feature extraction methodology, based on a mathematical model of the radioactive emission, reduces variability due to saturation, neighbourhood effects and variable probe amount. Furthermore, we provide a fully automatic feature extraction software, BZScan, which implements the algorithms described in this paper.
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Affiliation(s)
- F Lopez
- TAGC, INSERM-ERM 206, Parc Scientifique de Luminy, 13288 Marseille Cedex 09, France
| | - J Rougemont
- TAGC, INSERM-ERM 206, Parc Scientifique de Luminy, 13288 Marseille Cedex 09, France
| | - B Loriod
- TAGC, INSERM-ERM 206, Parc Scientifique de Luminy, 13288 Marseille Cedex 09, France
| | - A Bourgeois
- TAGC, INSERM-ERM 206, Parc Scientifique de Luminy, 13288 Marseille Cedex 09, France
| | - L Loï
- TAGC, INSERM-ERM 206, Parc Scientifique de Luminy, 13288 Marseille Cedex 09, France
| | - F Bertucci
- Département d'Oncologie Moléculaire, Institut Paoli-Calmettes, Marseille, France
- Université de la Méditerranée, Marseille, France
| | - P Hingamp
- TAGC, INSERM-ERM 206, Parc Scientifique de Luminy, 13288 Marseille Cedex 09, France
- Université de la Méditerranée, Marseille, France
| | - R Houlgatte
- TAGC, INSERM-ERM 206, Parc Scientifique de Luminy, 13288 Marseille Cedex 09, France
| | - S Granjeaud
- TAGC, INSERM-ERM 206, Parc Scientifique de Luminy, 13288 Marseille Cedex 09, France
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Thieblemont C, Nasser V, Felman P, Leroy K, Gazzo S, Callet-Bauchu E, Loriod B, Granjeaud S, Gaulard P, Haioun C, Traverse-Glehen A, Baseggio L, Bertucci F, Birnbaum D, Magrangeas F, Minvielle S, Avet-Loiseau H, Salles G, Coiffier B, Berger F, Houlgatte R. Small lymphocytic lymphoma, marginal zone B-cell lymphoma, and mantle cell lymphoma exhibit distinct gene-expression profiles allowing molecular diagnosis. Blood 2004; 103:2727-37. [PMID: 14630827 DOI: 10.1182/blood-2003-06-2160] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Non-germinal center small B-cell lymphomas represent a heterogeneous group of non-Hodgkin lymphomas, the most frequent histologic subtypes being small lymphocytic lymphoma (SLL), splenic marginal zone B-cell lymphoma (MZL), and mantle cell lymphoma (MCL). In order to identify genomic signatures specific for each disease, we analyzed 128 primary tumors using high-density microarrays. Several clusters of genes significantly discriminated the 3 histologic subtypes. Genes associated with cell adhesion, angiogenesis, and inhibition of apoptosis were up-regulated in SLL. Genes associated with intracellular signaling via the AKT1 pathway were up-regulated in splenic MZL. Genes associated with cell cycle control and multidrug resistance were up-regulated in MCL. Using 44 genes selected within the gene clusters discriminant for the 3 lymphoma subtypes, we generated a class prediction score that allowed us to classify the 3 entities in 96% of the cases, including borderline cases. Whereas specific transcriptional profiles easily distinguished all MZL samples, SLL samples, and most of the MCL samples into separate groups, few MCL cases exhibited MZL-type transcriptional profiles. This study demonstrates that SLL, splenic MZL, and MCL possess specific transcriptional profiles that may be relevant to the pathogenesis and the diagnosis of these histologic subtypes.
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MESH Headings
- Biopsy
- Diagnosis, Differential
- Gene Expression Profiling/methods
- Gene Expression Regulation, Neoplastic
- Humans
- In Situ Hybridization, Fluorescence
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Lymph Nodes/pathology
- Lymphoma, B-Cell/diagnosis
- Lymphoma, B-Cell/genetics
- Lymphoma, B-Cell/pathology
- Lymphoma, Mantle-Cell/diagnosis
- Lymphoma, Mantle-Cell/genetics
- Lymphoma, Mantle-Cell/pathology
- Multigene Family
- Oligonucleotide Array Sequence Analysis
- Palatine Tonsil/pathology
- RNA, Neoplasm/genetics
- RNA, Neoplasm/isolation & purification
- Reproducibility of Results
- Spleen/pathology
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Bertucci F, Salas S, Eysteries S, Nasser V, Finetti P, Ginestier C, Charafe-Jauffret E, Loriod B, Bachelart L, Montfort J, Victorero G, Viret F, Ollendorff V, Fert V, Giovaninni M, Delpero JR, Nguyen C, Viens P, Monges G, Birnbaum D, Houlgatte R. Gene expression profiling of colon cancer by DNA microarrays and correlation with histoclinical parameters. Oncogene 2004; 23:1377-91. [PMID: 14973550 DOI: 10.1038/sj.onc.1207262] [Citation(s) in RCA: 247] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Different diagnostic and prognostic groups of colorectal carcinoma (CRC) have been defined. However, accurate diagnosis and prediction of survival are sometimes difficult. Gene expression profiling might improve these classifications and bring new insights into underlying molecular mechanisms. We profiled 50 cancerous and noncancerous colon tissues using DNA microarrrays consisting of approximately 8000 spotted human cDNA. Global hierarchical clustering was to some extent able to distinguish clinically relevant subgroups, normal versus cancer tissues and metastatic versus nonmetastatic tumours. Supervised analyses improved these segregations by identifying sets of genes that discriminated between normal and tumour tissues, tumours associated or not with lymph node invasion or genetic instability, and tumours from the right or left colon. A similar approach identified a gene set that divided patients with significantly different 5-year survival (100% in one group and 40% in the other group; P=0.005). Discriminator genes were associated with various cellular processes. An immunohistochemical study on 382 tumour and normal samples deposited onto a tissue microarray subsequently validated the upregulation of NM23 in CRC and a downregulation in poor prognosis tumours. These results suggest that microarrays may provide means to improve the classification of CRC, provide new potential targets against carcinogenesis and new diagnostic and/or prognostic markers and therapeutic targets.
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Affiliation(s)
- François Bertucci
- Département d'Oncologie Moléculaire, Institut Paoli-Calmettes and U119 Inserm, IFR57, Marseille, France
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