1
|
Merz MP, Seal SV, Grova N, Mériaux S, Guebels P, Kanli G, Mommaerts E, Nicot N, Kaoma T, Keunen O, Nazarov PV, Turner JD. Early-life influenza A (H1N1) infection independently programs brain connectivity, HPA AXIS and tissue-specific gene expression profiles. Sci Rep 2024; 14:5898. [PMID: 38467724 PMCID: PMC10928197 DOI: 10.1038/s41598-024-56601-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 03/08/2024] [Indexed: 03/13/2024] Open
Abstract
Early-life adversity covers a range of physical, social and environmental stressors. Acute viral infections in early life are a major source of such adversity and have been associated with a broad spectrum of later-life effects outside the immune system or "off-target". These include an altered hypothalamus-pituitary-adrenal (HPA) axis and metabolic reactions. Here, we used a murine post-natal day 14 (PND 14) Influenza A (H1N1) infection model and applied a semi-holistic approach including phenotypic measurements, gene expression arrays and diffusion neuroimaging techniques to investigate HPA axis dysregulation, energy metabolism and brain connectivity. By PND 56 the H1N1 infection had been resolved, and there was no residual gene expression signature of immune cell infiltration into the liver, adrenal gland or brain tissues examined nor of immune-related signalling. A resolved early-life H1N1 infection had sex-specific effects. We observed retarded growth of males and altered pre-stress (baseline) blood glucose and corticosterone levels at PND42 after the infection was resolved. Cerebral MRI scans identified reduced connectivity in the cortex, midbrain and cerebellum that were accompanied by tissue-specific gene expression signatures. Gene set enrichment analysis confirmed that these were tissue-specific changes with few common pathways. Early-life infection independently affected each of the systems and this was independent of HPA axis or immune perturbations.
Collapse
Affiliation(s)
- Myriam P Merz
- Immune Endocrine and Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, 4354, Esch-Sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, 2 Avenue de Université, L-4365, Esch-Sur-Alzette, Luxembourg
- Central Biobank Charité, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Snehaa V Seal
- Immune Endocrine and Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, 4354, Esch-Sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, 2 Avenue de Université, L-4365, Esch-Sur-Alzette, Luxembourg
| | - Nathalie Grova
- Immune Endocrine and Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, 4354, Esch-Sur-Alzette, Luxembourg
- Inserm U1256, NGERE, Nutrition-Génétique Et Exposition Aux Risques Environnementaux, Université de Lorraine, 54000, Nancy, France
| | - Sophie Mériaux
- Immune Endocrine and Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, 4354, Esch-Sur-Alzette, Luxembourg
| | - Pauline Guebels
- Immune Endocrine and Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, 4354, Esch-Sur-Alzette, Luxembourg
| | - Georgia Kanli
- In Vivo Imaging Platform, Luxembourg Institute of Health, 1445, Strassen, Luxembourg
- Translational Radiomics, Department of Cancer Research, Luxembourg Institute of Health, 1526, Luxembourg, Luxembourg
| | - Elise Mommaerts
- LuxGen Genome Center, Laboratoire National de Santé, Luxembourg Institute of Health, 3555, Dudelange, Luxembourg
| | - Nathalie Nicot
- LuxGen Genome Center, Laboratoire National de Santé, Luxembourg Institute of Health, 3555, Dudelange, Luxembourg
| | - Tony Kaoma
- Bioinformatics Platform, Data Integration and Analysis Unit, Luxembourg Institute of Health, 1445, Strassen, Luxembourg
| | - Olivier Keunen
- In Vivo Imaging Platform, Luxembourg Institute of Health, 1445, Strassen, Luxembourg
- Translational Radiomics, Department of Cancer Research, Luxembourg Institute of Health, 1526, Luxembourg, Luxembourg
| | - Petr V Nazarov
- Bioinformatics Platform, Data Integration and Analysis Unit, Luxembourg Institute of Health, 1445, Strassen, Luxembourg
- Multiomics Data Science Research Group, Department of Cancer Research, Luxembourg Institute of Health, 1445, Strassen, Luxembourg
| | - Jonathan D Turner
- Immune Endocrine and Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, 4354, Esch-Sur-Alzette, Luxembourg.
| |
Collapse
|
2
|
Pinto LM, Pailas A, Bondarchenko M, Sharma AB, Neumann K, Rizzo AJ, Jeanty C, Nicot N, Racca C, Graham MK, Naughton C, Liu Y, Chen CL, Meakin PJ, Gilbert N, Britton S, Meeker AK, Heaphy CM, Larminat F, Van Dyck E. DAXX promotes centromeric stability independently of ATRX by preventing the accumulation of R-loop-induced DNA double-stranded breaks. Nucleic Acids Res 2024; 52:1136-1155. [PMID: 38038252 PMCID: PMC10853780 DOI: 10.1093/nar/gkad1141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 11/08/2023] [Accepted: 11/13/2023] [Indexed: 12/02/2023] Open
Abstract
Maintaining chromatin integrity at the repetitive non-coding DNA sequences underlying centromeres is crucial to prevent replicative stress, DNA breaks and genomic instability. The concerted action of transcriptional repressors, chromatin remodelling complexes and epigenetic factors controls transcription and chromatin structure in these regions. The histone chaperone complex ATRX/DAXX is involved in the establishment and maintenance of centromeric chromatin through the deposition of the histone variant H3.3. ATRX and DAXX have also evolved mutually-independent functions in transcription and chromatin dynamics. Here, using paediatric glioma and pancreatic neuroendocrine tumor cell lines, we identify a novel ATRX-independent function for DAXX in promoting genome stability by preventing transcription-associated R-loop accumulation and DNA double-strand break formation at centromeres. This function of DAXX required its interaction with histone H3.3 but was independent of H3.3 deposition and did not reflect a role in the repression of centromeric transcription. DAXX depletion mobilized BRCA1 at centromeres, in line with BRCA1 role in counteracting centromeric R-loop accumulation. Our results provide novel insights into the mechanisms protecting the human genome from chromosomal instability, as well as potential perspectives in the treatment of cancers with DAXX alterations.
Collapse
Affiliation(s)
- Lia M Pinto
- DNA Repair and Chemoresistance Group, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210 Luxembourg, Luxembourg
- Faculty of Science, Technology and Communication, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg
- Discovery & Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Alexandros Pailas
- DNA Repair and Chemoresistance Group, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210 Luxembourg, Luxembourg
- Faculty of Science, Technology and Communication, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg
| | - Max Bondarchenko
- DNA Repair and Chemoresistance Group, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210 Luxembourg, Luxembourg
- Faculty of Science, Technology and Communication, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg
| | - Abhishek Bharadwaj Sharma
- DNA Repair and Chemoresistance Group, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210 Luxembourg, Luxembourg
| | - Katrin Neumann
- DNA Repair and Chemoresistance Group, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210 Luxembourg, Luxembourg
| | - Anthony J Rizzo
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Céline Jeanty
- DNA Repair and Chemoresistance Group, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210 Luxembourg, Luxembourg
| | - Nathalie Nicot
- Translational Medicine Operations Hub, Luxembourg Institute of Health (LIH), Luxembourg, Luxembourg
| | - Carine Racca
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), 31077 Toulouse Cedex 4, France
| | - Mindy K Graham
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Catherine Naughton
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 1QY, UK
| | - Yaqun Liu
- Institut Curie, PSL Research University, CNRS UMR3244, Dynamics of Genetic Information, Sorbonne Université, 75248 Paris Cedex 05, France
| | - Chun-Long Chen
- Institut Curie, PSL Research University, CNRS UMR3244, Dynamics of Genetic Information, Sorbonne Université, 75248 Paris Cedex 05, France
| | - Paul J Meakin
- Discovery & Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Nick Gilbert
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 1QY, UK
| | - Sébastien Britton
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), 31077 Toulouse Cedex 4, France
| | - Alan K Meeker
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Christopher M Heaphy
- Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Florence Larminat
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), 31077 Toulouse Cedex 4, France
| | - Eric Van Dyck
- DNA Repair and Chemoresistance Group, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210 Luxembourg, Luxembourg
| |
Collapse
|
3
|
Rigg E, Wang J, Xue Z, Lunavat TR, Liu G, Hoang T, Parajuli H, Han M, Bjerkvig R, Nazarov PV, Nicot N, Kreis S, Margue C, Nomigni MT, Utikal J, Miletic H, Sundstrøm T, Ystaas LAR, Li X, Thorsen F. Inhibition of extracellular vesicle-derived miR-146a-5p decreases progression of melanoma brain metastasis via Notch pathway dysregulation in astrocytes. J Extracell Vesicles 2023; 12:e12363. [PMID: 37759347 PMCID: PMC10533779 DOI: 10.1002/jev2.12363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 08/04/2023] [Accepted: 08/20/2023] [Indexed: 09/29/2023] Open
Abstract
Melanoma has the highest propensity of all cancers to metastasize to the brain with a large percentage of late-stage patients developing metastases in the central nervous system (CNS). It is well known that metastasis establishment, cell survival, and progression are affected by tumour-host cell interactions where changes in the host cellular compartments likely play an important role. In this context, miRNAs transferred by tumour derived extracellular vesicles (EVs) have previously been shown to create a favourable tumour microenvironment. Here, we show that miR-146a-5p is highly expressed in human melanoma brain metastasis (MBM) EVs, both in MBM cell lines as well as in biopsies, thereby modulating the brain metastatic niche. Mechanistically, miR-146a-5p was transferred to astrocytes via EV delivery and inhibited NUMB in the Notch signalling pathway. This resulted in activation of tumour-promoting cytokines (IL-6, IL-8, MCP-1 and CXCL1). Brain metastases were significantly reduced following miR-146a-5p knockdown. Corroborating these findings, miR-146a-5p inhibition led to a reduction of IL-6, IL-8, MCP-1 and CXCL1 in astrocytes. Following molecular docking analysis, deserpidine was identified as a functional miR-146a-5p inhibitor, both in vitro and in vivo. Our results highlight the pro-metastatic function of miR-146a-5p in EVs and identifies deserpidine for targeted adjuvant treatment.
Collapse
Affiliation(s)
- Emma Rigg
- Department of BiomedicineUniversity of BergenBergenNorway
| | - Jiwei Wang
- Department of Neurosurgery, Qilu Hospital of Shandong University and Institute of Brain and Brain‐Inspired Science, Cheeloo College of MedicineShandong UniversityJinanChina
- Department of BiomedicineUniversity of BergenBergenNorway
- Shandong Key Laboratory of Brain Function RemodelingJinanChina
| | - Zhiwei Xue
- Department of BiomedicineUniversity of BergenBergenNorway
- Shandong Key Laboratory of Brain Function RemodelingJinanChina
| | - Taral R. Lunavat
- Department of BiomedicineUniversity of BergenBergenNorway
- Department of Neurology, Molecular Neurogenetics Unit‐West, Massachusetts General HospitalHarvard Medical SchoolCharlestownMassachusettsUSA
| | - Guowei Liu
- Department of BiomedicineUniversity of BergenBergenNorway
- Shandong Key Laboratory of Brain Function RemodelingJinanChina
| | - Tuyen Hoang
- Department of Neurosurgery, Qilu Hospital of Shandong University and Institute of Brain and Brain‐Inspired Science, Cheeloo College of MedicineShandong UniversityJinanChina
| | - Himalaya Parajuli
- Department of Neurosurgery, Qilu Hospital of Shandong University and Institute of Brain and Brain‐Inspired Science, Cheeloo College of MedicineShandong UniversityJinanChina
| | - Mingzhi Han
- Department of Neurosurgery, Qilu Hospital of Shandong University and Institute of Brain and Brain‐Inspired Science, Cheeloo College of MedicineShandong UniversityJinanChina
- Department of BiomedicineUniversity of BergenBergenNorway
- Shandong Key Laboratory of Brain Function RemodelingJinanChina
| | - Rolf Bjerkvig
- Department of Neurosurgery, Qilu Hospital of Shandong University and Institute of Brain and Brain‐Inspired Science, Cheeloo College of MedicineShandong UniversityJinanChina
| | - Petr V. Nazarov
- Bioinformatics Platform and Multiomics Data Science Research Group, Department of Cancer ResearchLuxembourg Institute of HealthLuxembourg
| | - Nathalie Nicot
- LuxGen Genome Center, Luxembourg Institute of HealthLaboratoire National de SantéDudelangeLuxembourg
| | - Stephanie Kreis
- Department of Life Sciences and MedicineUniversity of LuxembourgLuxembourg
| | - Christiane Margue
- Department of Life Sciences and MedicineUniversity of LuxembourgLuxembourg
| | | | - Jochen Utikal
- Skin Cancer UnitGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Department of Dermatology, Venereology and AllergologyUniversity Medical Center Mannheim, Ruprecht‐Karl University of HeidelbergMannheimGermany
- DKFZ Hector Cancer Institute at the University Medical Center MannheimMannheimGermany
| | - Hrvoje Miletic
- Department of Neurosurgery, Qilu Hospital of Shandong University and Institute of Brain and Brain‐Inspired Science, Cheeloo College of MedicineShandong UniversityJinanChina
- Department of PathologyHaukeland University HospitalBergenNorway
| | - Terje Sundstrøm
- Department of NeurosurgeryHaukeland University HospitalBergenNorway
- Department of Clinical MedicineUniversity of BergenBergenNorway
| | - Lars A. R. Ystaas
- Department of Neurosurgery, Qilu Hospital of Shandong University and Institute of Brain and Brain‐Inspired Science, Cheeloo College of MedicineShandong UniversityJinanChina
| | - Xingang Li
- Department of BiomedicineUniversity of BergenBergenNorway
- Shandong Key Laboratory of Brain Function RemodelingJinanChina
| | - Frits Thorsen
- Department of Neurosurgery, Qilu Hospital of Shandong University and Institute of Brain and Brain‐Inspired Science, Cheeloo College of MedicineShandong UniversityJinanChina
- Department of BiomedicineUniversity of BergenBergenNorway
- Department of NeurosurgeryHaukeland University HospitalBergenNorway
- Molecular Imaging Center, Department of BiomedicineUniversity of BergenBergenNorway
| |
Collapse
|
4
|
Pavlou MAS, Singh K, Ravichandran S, Halder R, Nicot N, Birck C, Grandbarbe L, Del Sol A, Michelucci A. Transcriptional and Chromatin Accessibility Profiling of Neural Stem Cells Differentiating into Astrocytes Reveal Dynamic Signatures Affected under Inflammatory Conditions. Cells 2023; 12:cells12060948. [PMID: 36980289 PMCID: PMC10047363 DOI: 10.3390/cells12060948] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/14/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Astrocytes arise from multipotent neural stem cells (NSCs) and represent the most abundant cell type of the central nervous system (CNS), playing key roles in the developing and adult brain. Since the differentiation of NSCs towards a gliogenic fate is a precisely timed and regulated process, its perturbation gives rise to dysfunctional astrocytic phenotypes. Inflammation, which often underlies neurological disorders, including neurodevelopmental disorders and brain tumors, disrupts the accurate developmental process of NSCs. However, the specific consequences of an inflammatory environment on the epigenetic and transcriptional programs underlying NSCs' differentiation into astrocytes is unexplored. Here, we address this gap by profiling in mice glial precursors from neural tissue derived from early embryonic stages along their astrocytic differentiation trajectory in the presence or absence of tumor necrosis factor (TNF), a master pro-inflammatory cytokine. By using a combination of RNA- and ATAC-sequencing approaches, together with footprint and integrated gene regulatory network analyses, we here identify key differences during the differentiation of NSCs into astrocytes under physiological and inflammatory settings. In agreement with its role to turn cells resistant to inflammatory challenges, we detect Nrf2 as a master transcription factor supporting the astrocytic differentiation under TNF exposure. Further, under these conditions, we unravel additional transcriptional regulatory hubs, including Stat3, Smad3, Cebpb, and Nfkb2, highlighting the interplay among pathways underlying physiological astrocytic developmental processes and those involved in inflammatory responses, resulting in discrete astrocytic phenotypes. Overall, our study reports key transcriptional and epigenetic changes leading to the identification of molecular regulators of astrocytic differentiation. Furthermore, our analyses provide a valuable resource for understanding inflammation-induced astrocytic phenotypes that might contribute to the development and progression of CNS disorders with an inflammatory component.
Collapse
Affiliation(s)
- Maria Angeliki S Pavlou
- Department of Life Sciences and Medicine, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg
- Neuro-Immunology Group, Department of Cancer Research, Luxembourg Institute of Health, L-1210 Luxembourg, Luxembourg
| | - Kartikeya Singh
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg
| | - Srikanth Ravichandran
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg
| | - Rashi Halder
- Scientific Central Services, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg
| | - Nathalie Nicot
- Translational Medicine Operations Hub, Luxembourg Institute of Health, L-3555 Dudelange, Luxembourg
- LuxGen Genome Center, Luxembourg Institute of Health & Laboratoire National de Santé, L-3555 Dudelange, Luxembourg
| | - Cindy Birck
- Department of Life Sciences and Medicine, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg
| | - Luc Grandbarbe
- Department of Life Sciences and Medicine, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg
| | - Antonio Del Sol
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg
- Computational Biology Group, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), 48160 Derio, Spain
- IKERBASQUE, Basque Foundation for Science, 48009 Bilbao, Spain
| | - Alessandro Michelucci
- Neuro-Immunology Group, Department of Cancer Research, Luxembourg Institute of Health, L-1210 Luxembourg, Luxembourg
- Scientific Central Services, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg
| |
Collapse
|
5
|
Rigg EK, Wang J, Xue Z, Lunavat T, Hoang T, Parajuli H, Han M, Liu G, Bjerkvig R, Nazarov P, Nicot N, Kreis S, Wurth C, Miletic H, Sundstrøm T, Li X, Thorsen F. P12.09.B Extracellular vesicle derived-miR-146a increases melanoma brain metastasis progression via Notch signalling pathway dysregulation. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac174.274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Melanoma has the highest tropism of any cancer to metastasize to the brain, and 40% of late-stage patients develop brain metastasis. Invasion, survival, and progression of tumors is dependent on the support of the surrounding microenvironment; therefore, modulation of neighboring cells is a key factor in metastasis. Extracellular vesicles (EVs) are important in cell-to-cell signalling, shuttling proteins, RNA and DNA to alter the surroundings into a favorable tumor microenvironment. Our aims were to investigate the role of melanoma brain metastasis (MBM) derived EVs in MBM development to find possible contributing mechanisms to cancer progression for eventual therapeutic targeting.
Material and Methods
MBM-EVs isolated via sequential ultracentrifugation were injected into mice as a pre-treatment prior to intracardial injection of MBM cells. EVs were co-cultured with normal human astrocytes (NHA) to investigate phenotypic changes. MiRNA sequencing was performed on EVs collected from MBM cells and compared to NHA and melanocytes to determine a candidate miRNA for targeting. In situ hybridization was utilized to evaluate the level of miRNA in clinical patient MBM samples. Functional in vivo validation was performed by injecting miRNA knockout MBM cells into mice. Sequencing of NHA in the presence or absence of target miRNA mimic was used to determine downstream targets.
Results
Mice primed with EVs had a significant increase in MBM tumor burden, compared to non-primed mice. Co-culture with MBM-EVs resulted in NHA activation in vitro, with increased proliferation, invasion, cytokine production, and upregulation of GFAP. MiR-146a was highly upregulated in MBM EVs, and miR-146a mimics activated NHA. Patient samples had a significant increase in miR-146a expression, compared to healthy brain controls. MiR-146a knockdown in MBM mice models reduced MBM burden and prolonged animal survival. Sequencing of NHA determined NUMB, an inhibitor of the Notch signalling pathway, as a target of miR-146a. Numb and other downstream Notch proteins expression was significantly altered in NHA in the presence of both MBM-EVs and miR-146a.
Conclusion
In conclusion, EVs are important regulators of MBM and establish tumor-supporting reactive astrocytes by delivery of miR-146a. MiR-146a alters Notch signalling in astrocytes via inhibition of the tumor suppressor gene NUMB. Elevated miR-146a levels in patients suggests a potential clinical intervention is possible via miR-146a targeting.
Collapse
Affiliation(s)
- E K Rigg
- Department of Biomedicine, University of Bergen , Bergen , Norway
| | - J Wang
- Department of Neurosurgery, Qilu Hospital of Shandong University and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine , Jinan , China
- Shandong Key Laboratory of Brain Function Remodeling , Jinan , China
- Department of Biomedicine, University of Bergen , Bergen , Norway
| | - Z Xue
- Department of Neurosurgery, Qilu Hospital of Shandong University and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine , Jinan , China
- Shandong Key Laboratory of Brain Function Remodeling , Jinan , China
| | - T Lunavat
- Department of Biomedicine, University of Bergen , Bergen , Norway
| | - T Hoang
- Department of Biomedicine, University of Bergen , Bergen , Norway
| | - H Parajuli
- Department of Biomedicine, University of Bergen , Bergen , Norway
| | - M Han
- Department of Biomedicine, University of Bergen , Bergen , Norway
- Department of Neurosurgery, Qilu Hospital of Shandong University and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine , Jinan , China
- Shandong Key Laboratory of Brain Function Remodeling , Jinan , China
| | - G Liu
- Department of Neurosurgery, Qilu Hospital of Shandong University and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine , Jinan , China
- Shandong Key Laboratory of Brain Function Remodeling , Jinan , China
| | - R Bjerkvig
- Department of Biomedicine, University of Bergen , Bergen , Norway
| | - P Nazarov
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health , Luxembourg , Luxembourg
| | - N Nicot
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health , Luxembourg , Luxembourg
| | - S Kreis
- Signal Transduction Group, Department of Life Sciences and Medicine, University of Luxembourg , Luxembourg , Luxembourg
| | - C Wurth
- Signal Transduction Group, Department of Life Sciences and Medicine, University of Luxembourg , Luxembourg , Luxembourg
| | - H Miletic
- Department of Biomedicine, University of Bergen , Bergen , Norway
| | - T Sundstrøm
- Department of Neurosurgery, Haukeland University Hospital , Bergen , Norway
| | - X Li
- Department of Neurosurgery, Qilu Hospital of Shandong University and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine , Jinan , China
- Shandong Key Laboratory of Brain Function Remodeling , Jinan , China
| | - F Thorsen
- Molecular Imaging Center, Department of Biomedicine, University of Bergen , Bergen , Norway
- Department of Biomedicine, University of Bergen , Bergen , Norway
| |
Collapse
|
6
|
Garcia P, Jürgens‐Wemheuer W, Uriarte Huarte O, Michelucci A, Masuch A, Brioschi S, Weihofen A, Koncina E, Coowar D, Heurtaux T, Glaab E, Balling R, Sousa C, Kaoma T, Nicot N, Pfander T, Schulz‐Schaeffer W, Allouche A, Fischer N, Biber K, Kleine‐Borgmann F, Mittelbronn M, Ostaszewski M, Schmit KJ, Buttini M. Neurodegeneration and neuroinflammation are linked, but independent of alpha‐synuclein inclusions, in a seeding/spreading mouse model of Parkinson's disease. Glia 2022; 70:935-960. [PMID: 35092321 PMCID: PMC9305192 DOI: 10.1002/glia.24149] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/07/2022] [Accepted: 01/13/2022] [Indexed: 12/16/2022]
Abstract
A key pathological process in Parkinson's disease (PD) is the transneuronal spreading of α‐synuclein. Alpha‐synuclein (α‐syn) is a presynaptic protein that, in PD, forms pathological inclusions. Other hallmarks of PD include neurodegeneration and microgliosis in susceptible brain regions. Whether it is primarily transneuronal spreading of α‐syn particles, inclusion formation, or other mechanisms, such as inflammation, that cause neurodegeneration in PD is unclear. We used a model of spreading of α‐syn induced by striatal injection of α‐syn preformed fibrils into the mouse striatum to address this question. We performed quantitative analysis for α‐syn inclusions, neurodegeneration, and microgliosis in different brain regions, and generated gene expression profiles of the ventral midbrain, at two different timepoints after disease induction. We observed significant neurodegeneration and microgliosis in brain regions not only with, but also without α‐syn inclusions. We also observed prominent microgliosis in injured brain regions that did not correlate with neurodegeneration nor with inclusion load. Using longitudinal gene expression profiling, we observed early gene expression changes, linked to neuroinflammation, that preceded neurodegeneration, indicating an active role of microglia in this process. Altered gene pathways overlapped with those typical of PD. Our observations indicate that α‐syn inclusion formation is not the major driver in the early phases of PD‐like neurodegeneration, but that microglia, activated by diffusible, oligomeric α‐syn, may play a key role in this process. Our findings uncover new features of α‐syn induced pathologies, in particular microgliosis, and point to the necessity for a broader view of the process of α‐syn spreading.
Collapse
Affiliation(s)
- Pierre Garcia
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
- Luxembourg Center of Neuropathology Dudelange Luxembourg
| | - Wiebke Jürgens‐Wemheuer
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
- Institute of Neuropathology Saarland University Clinic (UKS) Homburg Germany
| | - Oihane Uriarte Huarte
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
- Luxembourg Center of Neuropathology Dudelange Luxembourg
| | - Alessandro Michelucci
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
- Department of Cancer Research Luxembourg Institute of Health Strassen Luxembourg
| | - Annette Masuch
- Department of Psychiatry University of Freiburg Medical Center Freiburg Germany
| | - Simone Brioschi
- Department of Psychiatry University of Freiburg Medical Center Freiburg Germany
| | | | - Eric Koncina
- Department of Life Science and Medicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
| | - Djalil Coowar
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
| | - Tony Heurtaux
- Luxembourg Center of Neuropathology Dudelange Luxembourg
- Department of Life Science and Medicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
| | - Enrico Glaab
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
| | - Rudi Balling
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
| | - Carole Sousa
- Department of Cancer Research Luxembourg Institute of Health Strassen Luxembourg
| | - Tony Kaoma
- Department of Cancer Research Luxembourg Institute of Health Strassen Luxembourg
| | - Nathalie Nicot
- Department of Cancer Research Luxembourg Institute of Health Strassen Luxembourg
| | - Tatjana Pfander
- Institute of Neuropathology Saarland University Clinic (UKS) Homburg Germany
| | | | | | | | - Knut Biber
- Department of Psychiatry University of Freiburg Medical Center Freiburg Germany
| | - Felix Kleine‐Borgmann
- Luxembourg Center of Neuropathology Dudelange Luxembourg
- Department of Cancer Research Luxembourg Institute of Health Strassen Luxembourg
- Faculty of Science, Technology and Medicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
| | - Michel Mittelbronn
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
- Luxembourg Center of Neuropathology Dudelange Luxembourg
- Department of Cancer Research Luxembourg Institute of Health Strassen Luxembourg
- Department of Life Science and Medicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
- Faculty of Science, Technology and Medicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
| | - Marek Ostaszewski
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
| | - Kristopher J. Schmit
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
- Luxembourg Center of Neuropathology Dudelange Luxembourg
| | - Manuel Buttini
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
- Luxembourg Center of Neuropathology Dudelange Luxembourg
| |
Collapse
|
7
|
Bosc C, Saland E, Bousard A, Gadaud N, Sabatier M, Cognet G, Farge T, Boet E, Gotanègre M, Aroua N, Mouchel PL, Polley N, Larrue C, Kaphan E, Picard M, Sahal A, Jarrou L, Tosolini M, Rambow F, Cabon F, Nicot N, Poillet-Perez L, Wang Y, Su X, Fovez Q, Kluza J, Argüello RJ, Mazzotti C, Avet-Loiseau H, Vergez F, Tamburini J, Fournié JJ, Tiong IS, Wei AH, Kaoma T, Marine JC, Récher C, Stuani L, Joffre C, Sarry JE. Mitochondrial inhibitors circumvent adaptive resistance to venetoclax and cytarabine combination therapy in acute myeloid leukemia. Nat Cancer 2021; 2:1204-1223. [PMID: 35122057 DOI: 10.1038/s43018-021-00264-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/31/2021] [Indexed: 04/23/2023]
Abstract
Therapy resistance represents a major clinical challenge in acute myeloid leukemia (AML). Here we define a 'MitoScore' signature, which identifies high mitochondrial oxidative phosphorylation in vivo and in patients with AML. Primary AML cells with cytarabine (AraC) resistance and a high MitoScore relied on mitochondrial Bcl2 and were highly sensitive to venetoclax (VEN) + AraC (but not to VEN + azacytidine). Single-cell transcriptomics of VEN + AraC-residual cell populations revealed adaptive resistance associated with changes in oxidative phosphorylation, electron transport chain complex and the TP53 pathway. Accordingly, treatment of VEN + AraC-resistant AML cells with electron transport chain complex inhibitors, pyruvate dehydrogenase inhibitors or mitochondrial ClpP protease agonists substantially delayed relapse following VEN + AraC. These findings highlight the central role of mitochondrial adaptation during AML therapy and provide a scientific rationale for alternating VEN + azacytidine with VEN + AraC in patients with a high MitoScore and to target mitochondrial metabolism to enhance the sensitivity of AML cells to currently approved therapies.
Collapse
Affiliation(s)
- Claudie Bosc
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Estelle Saland
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Aurélie Bousard
- Department of Oncology, Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, Leuven, Belgium
| | - Noémie Gadaud
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
- University of Toulouse, Toulouse, France
- Service d'Hématologie, Institut Universitaire du Cancer de Toulouse-Oncopole, CHU de Toulouse, Toulouse, France
| | - Marie Sabatier
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Guillaume Cognet
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Thomas Farge
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Emeline Boet
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Mathilde Gotanègre
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Nesrine Aroua
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Pierre-Luc Mouchel
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
- University of Toulouse, Toulouse, France
- Service d'Hématologie, Institut Universitaire du Cancer de Toulouse-Oncopole, CHU de Toulouse, Toulouse, France
| | - Nathaniel Polley
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Clément Larrue
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Eléonore Kaphan
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Muriel Picard
- Réanimation Polyvalente IUCT-oncopole, CHU de Toulouse, Toulouse, France
| | - Ambrine Sahal
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Latifa Jarrou
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Marie Tosolini
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
| | - Florian Rambow
- Department of Oncology, Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, Leuven, Belgium
| | - Florence Cabon
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Nathalie Nicot
- LuxGen, Quantitative Biology Unit, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Laura Poillet-Perez
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Yujue Wang
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Xiaoyang Su
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Quentin Fovez
- Cancer Heterogeneity Plasticity and Resistance to Therapies (CANTHER), University of Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277, Lille, France
| | - Jérôme Kluza
- Cancer Heterogeneity Plasticity and Resistance to Therapies (CANTHER), University of Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277, Lille, France
| | - Rafael José Argüello
- Aix Marseille University, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Céline Mazzotti
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - Hervé Avet-Loiseau
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - François Vergez
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
- University of Toulouse, Toulouse, France
- Service d'Hématologie, Institut Universitaire du Cancer de Toulouse-Oncopole, CHU de Toulouse, Toulouse, France
| | | | - Jean-Jacques Fournié
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
| | - Ing S Tiong
- Department of Clinical Haematology, The Alfred Hospital and Monash University, Melbourne, Victoria, Australia
| | - Andrew H Wei
- Department of Clinical Haematology, The Alfred Hospital and Monash University, Melbourne, Victoria, Australia
| | - Tony Kaoma
- Computational Biomedicine Research Group, Quantitative Biology Unit, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Jean-Christophe Marine
- Department of Oncology, Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, Leuven, Belgium
| | - Christian Récher
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
- University of Toulouse, Toulouse, France
- Service d'Hématologie, Institut Universitaire du Cancer de Toulouse-Oncopole, CHU de Toulouse, Toulouse, France
| | - Lucille Stuani
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Carine Joffre
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Jean-Emmanuel Sarry
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France.
- LabEx Toucan, Toulouse, France.
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France.
| |
Collapse
|
8
|
Capeyron O, Squinazi F, Dumoulin P, Destras G, Dorin J, Dalmasso M, Nicot N, Liguori S, Blanc V. A simple method for SARS-CoV-2 RNA detection in the air of an enclosed space. J Hosp Infect 2021; 119:199-200. [PMID: 34547322 PMCID: PMC8450221 DOI: 10.1016/j.jhin.2021.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 11/28/2022]
Affiliation(s)
- O Capeyron
- Equipe Opérationnelle en Hygiène Hospitalière, Centre Hospitalier d'Antibes Juan les Pins, Antibes, France
| | - F Squinazi
- Haut Conseil de Santé Publique France, Paris, France
| | - P Dumoulin
- Equipe Opérationnelle en Hygiène Hospitalière, Centre Hospitalier d'Antibes Juan les Pins, Antibes, France
| | - G Destras
- Centre National de référence des virus des infections respiratoires Sud, Lyon, France
| | - J Dorin
- Service de Biologie, Centre Hospitalier d'Antibes Juan les Pins, Antibes, France
| | - M Dalmasso
- Service de Biologie, Centre Hospitalier d'Antibes Juan les Pins, Antibes, France
| | - N Nicot
- Service de Biologie, Centre Hospitalier d'Antibes Juan les Pins, Antibes, France
| | - S Liguori
- Service de Biologie, Centre Hospitalier d'Antibes Juan les Pins, Antibes, France
| | - V Blanc
- Service de Biologie, Centre Hospitalier d'Antibes Juan les Pins, Antibes, France.
| |
Collapse
|
9
|
Ramberger E, Sapozhnikova V, Kowenz-Leutz E, Zimmermann K, Nicot N, Nazarov PV, Perez-Hernandez D, Reimer U, Mertins P, Dittmar G, Leutz A. PRISMA and BioID disclose a motifs-based interactome of the intrinsically disordered transcription factor C/EBPα. iScience 2021; 24:102686. [PMID: 34189442 PMCID: PMC8220391 DOI: 10.1016/j.isci.2021.102686] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 05/17/2021] [Accepted: 05/30/2021] [Indexed: 01/27/2023] Open
Abstract
C/EBPα represents a paradigm intrinsically disordered transcription factor containing short linear motifs and post-translational modifications (PTM). Unraveling C/EBPα protein interaction networks is a prerequisite for understanding the multi-modal functions of C/EBPα in hematopoiesis and leukemia. Here, we combined arrayed peptide matrix screening (PRISMA) with BioID to generate an in vivo validated and isoform specific interaction map of C/EBPα. The myeloid C/EBPα interactome comprises promiscuous and PTM-regulated interactions with protein machineries involved in gene expression, epigenetics, genome organization, DNA replication, RNA processing, and nuclear transport. C/EBPα interaction hotspots coincide with homologous conserved regions of the C/EBP family that also score as molecular recognition features. PTMs alter the interaction spectrum of C/EBP-motifs to configure a multi-valent transcription factor hub that interacts with multiple co-regulatory components, including BAF/SWI-SNF or Mediator complexes. Combining PRISMA and BioID is a powerful strategy to systematically explore the PTM-regulated interactomes of intrinsically disordered transcription factors. Combining peptide arrays and BioID refines the C/EBPα interactome Hotspots of protein interactions in C/EBPα mostly occur in conserved regions The interaction with the BAF/SWI-SNF complex is modulated by C/EBPα methylation Experimental design suits interactome studies of intrinsically disordered proteins
Collapse
Affiliation(s)
- Evelyn Ramberger
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Valeria Sapozhnikova
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Elisabeth Kowenz-Leutz
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Karin Zimmermann
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Nathalie Nicot
- Quantitative Biology Unit, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg
| | - Petr V Nazarov
- Quantitative Biology Unit, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg
| | - Daniel Perez-Hernandez
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.,Quantitative Biology Unit, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg
| | - Ulf Reimer
- JPT Peptide Technologies GmbH, Volmerstrasse 5, 12489 Berlin, Germany
| | - Philipp Mertins
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Gunnar Dittmar
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.,Quantitative Biology Unit, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg
| | - Achim Leutz
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.,Institute of Biology, Humboldt University of Berlin, 10115 Berlin, Germany
| |
Collapse
|
10
|
Hendrickx DM, Garcia P, Ashrafi A, Sciortino A, Schmit KJ, Kollmus H, Nicot N, Kaoma T, Vallar L, Buttini M, Glaab E. A New Synuclein-Transgenic Mouse Model for Early Parkinson's Reveals Molecular Features of Preclinical Disease. Mol Neurobiol 2021; 58:576-602. [PMID: 32997293 PMCID: PMC8219584 DOI: 10.1007/s12035-020-02085-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/21/2020] [Indexed: 12/14/2022]
Abstract
Understanding Parkinson's disease (PD), in particular in its earliest phases, is important for diagnosis and treatment. However, human brain samples are collected post-mortem, reflecting mainly end-stage disease. Because brain samples of mouse models can be collected at any stage of the disease process, they are useful in investigating PD progression. Here, we compare ventral midbrain transcriptomics profiles from α-synuclein transgenic mice with a progressive, early PD-like striatal neurodegeneration across different ages using pathway, gene set, and network analysis methods. Our study uncovers statistically significant altered genes across ages and between genotypes with known, suspected, or unknown function in PD pathogenesis and key pathways associated with disease progression. Among those are genotype-dependent alterations associated with synaptic plasticity and neurotransmission, as well as mitochondria-related genes and dysregulation of lipid metabolism. Age-dependent changes were among others observed in neuronal and synaptic activity, calcium homeostasis, and membrane receptor signaling pathways, many of which linked to G-protein coupled receptors. Most importantly, most changes occurred before neurodegeneration was detected in this model, which points to a sequence of gene expression events that may be relevant for disease initiation and progression. It is tempting to speculate that molecular changes similar to those changes observed in our model happen in midbrain dopaminergic neurons before they start to degenerate. In other words, we believe we have uncovered molecular changes that accompany the progression from preclinical to early PD.
Collapse
Affiliation(s)
- Diana M. Hendrickx
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Pierre Garcia
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
- Laboratoire National de Santé (LNS), Neuropathology Unit, Dudelange, Luxembourg
| | - Amer Ashrafi
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
- Present Address: Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA USA
| | - Alessia Sciortino
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Kristopher J. Schmit
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Heike Kollmus
- Department of Infection Genetics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Nathalie Nicot
- Quantitative Biology Unit, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Tony Kaoma
- Department of Oncology, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Laurent Vallar
- Genomics Research Unit, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Manuel Buttini
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Enrico Glaab
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| |
Collapse
|
11
|
Kirchmeyer M, Servais F, Ginolhac A, Nazarov PV, Margue C, Philippidou D, Nicot N, Behrmann I, Haan C, Kreis S. Systematic Transcriptional Profiling of Responses to STAT1- and STAT3-Activating Cytokines in Different Cancer Types. J Mol Biol 2020; 432:5902-5919. [PMID: 32950480 DOI: 10.1016/j.jmb.2020.09.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 07/20/2020] [Revised: 09/14/2020] [Accepted: 09/14/2020] [Indexed: 02/06/2023]
Abstract
Cytokines orchestrate responses to pathogens and in inflammatory processes, but they also play an important role in cancer by shaping the expression levels of cytokine response genes. Here, we conducted a large profiling study comparing miRNome and mRNA transcriptome data generated following different cytokine stimulations. Transcriptomic responses to STAT1- (IFNγ, IL-27) and STAT3-activating cytokines (IL6, OSM) were systematically compared in nine cancerous and non-neoplastic cell lines of different tissue origins (skin, liver and colon). The largest variation in our datasets was seen between cell lines of the three different tissues rather than stimuli. Notably, the variability in miRNome datasets was a lot more pronounced than in mRNA data. Our data also revealed that cells of skin, liver and colon tissues respond very differently to cytokines and that the cell signaling networks activated or silenced in response to STAT1- or STAT3-activating cytokines are specific to the tissue and the type of cytokine. However, globally, STAT1-activating cytokines had stronger effects than STAT3-inducing cytokines with most significant responses in liver cells, showing more genes upregulated and with higher fold change. A more detailed analysis of gene regulations upon cytokine stimulation in these cells provided insights into STAT1- versus STAT3-driven processes in hepatocarcinogenesis. Finally, independent component analysis revealed interconnected transcriptional networks distinct between cancer cells and their healthy counterparts.
Collapse
Affiliation(s)
- Mélanie Kirchmeyer
- Signal Transduction Laboratory, Department of Life Sciences and Medicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Florence Servais
- Signal Transduction Laboratory, Department of Life Sciences and Medicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Aurélien Ginolhac
- Signal Transduction Laboratory, Department of Life Sciences and Medicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Petr V Nazarov
- Quantitative Biology Unit, Luxembourg Institute of Health, 1AB rue Thomas Edison, L-1445 Strassen, Luxembourg
| | - Christiane Margue
- Signal Transduction Laboratory, Department of Life Sciences and Medicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Demetra Philippidou
- Signal Transduction Laboratory, Department of Life Sciences and Medicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Nathalie Nicot
- Quantitative Biology Unit, Luxembourg Institute of Health, 1AB rue Thomas Edison, L-1445 Strassen, Luxembourg
| | - Iris Behrmann
- Signal Transduction Laboratory, Department of Life Sciences and Medicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Claude Haan
- Signal Transduction Laboratory, Department of Life Sciences and Medicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Stephanie Kreis
- Signal Transduction Laboratory, Department of Life Sciences and Medicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg.
| |
Collapse
|
12
|
Aroua N, Boet E, Ghisi M, Nicolau-Travers ML, Saland E, Gwilliam R, de Toni F, Hosseini M, Mouchel PL, Farge T, Bosc C, Stuani L, Sabatier M, Mazed F, Larrue C, Jarrou L, Gandarillas S, Bardotti M, Picard M, Syrykh C, Laurent C, Gotanègre M, Bonnefoy N, Bellvert F, Portais JC, Nicot N, Azuaje F, Kaoma T, Joffre C, Tamburini J, Récher C, Vergez F, Sarry JE. Extracellular ATP and CD39 Activate cAMP-Mediated Mitochondrial Stress Response to Promote Cytarabine Resistance in Acute Myeloid Leukemia. Cancer Discov 2020; 10:1544-1565. [PMID: 32641297 DOI: 10.1158/2159-8290.cd-19-1008] [Citation(s) in RCA: 18] [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] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 05/09/2020] [Accepted: 07/02/2020] [Indexed: 11/16/2022]
Abstract
Relapses driven by chemoresistant leukemic cell populations are the main cause of mortality for patients with acute myeloid leukemia (AML). Here, we show that the ectonucleotidase CD39 (ENTPD1) is upregulated in cytarabine-resistant leukemic cells from both AML cell lines and patient samples in vivo and in vitro. CD39 cell-surface expression and activity is increased in patients with AML upon chemotherapy compared with diagnosis, and enrichment in CD39-expressing blasts is a marker of adverse prognosis in the clinics. High CD39 activity promotes cytarabine resistance by enhancing mitochondrial activity and biogenesis through activation of a cAMP-mediated adaptive mitochondrial stress response. Finally, genetic and pharmacologic inhibition of CD39 ecto-ATPase activity blocks the mitochondrial reprogramming triggered by cytarabine treatment and markedly enhances its cytotoxicity in AML cells in vitro and in vivo. Together, these results reveal CD39 as a new residual disease marker and a promising therapeutic target to improve chemotherapy response in AML. SIGNIFICANCE: Extracellular ATP and CD39-P2RY13-cAMP-OxPHOS axis are key regulators of cytarabine resistance, offering a new promising therapeutic strategy in AML.This article is highlighted in the In This Issue feature, p. 1426.
Collapse
Affiliation(s)
- Nesrine Aroua
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France
| | - Emeline Boet
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France
| | - Margherita Ghisi
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France
| | - Marie-Laure Nicolau-Travers
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France.,Service d'Hématologie, Institut Universitaire du Cancer de Toulouse-Oncopole, CHU de Toulouse, Toulouse, France
| | - Estelle Saland
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France
| | - Ryan Gwilliam
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France
| | - Fabienne de Toni
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France
| | - Mohsen Hosseini
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France
| | - Pierre-Luc Mouchel
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France.,Service d'Hématologie, Institut Universitaire du Cancer de Toulouse-Oncopole, CHU de Toulouse, Toulouse, France
| | - Thomas Farge
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France
| | - Claudie Bosc
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France
| | - Lucille Stuani
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France
| | - Marie Sabatier
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France
| | - Fetta Mazed
- Institut Cochin, Département Développement, Reproduction, Cancer, UMR8104-CNRS, U1016-INSERM, Paris.,Translational Research Centre in Onco-Hematology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Clément Larrue
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France
| | - Latifa Jarrou
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France
| | - Sarah Gandarillas
- Centre Régional d'Exploration Fonctionnelle et Ressources Expérimentales, Service d'Expérimentation Animale, UMS006, Inserm, Toulouse, France
| | - Massimiliano Bardotti
- Centre Régional d'Exploration Fonctionnelle et Ressources Expérimentales, Service d'Expérimentation Animale, UMS006, Inserm, Toulouse, France
| | - Muriel Picard
- University of Toulouse, Toulouse, France.,Intensive Care Unit, Institut Universitaire du Cancer de Toulouse-Oncopole, CHU de Toulouse, Toulouse, France
| | - Charlotte Syrykh
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France.,Service d'Anatomopathologie, Institut Universitaire du Cancer de Toulouse-Oncopole, CHU de Toulouse, Toulouse, France
| | - Camille Laurent
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France.,Service d'Anatomopathologie, Institut Universitaire du Cancer de Toulouse-Oncopole, CHU de Toulouse, Toulouse, France
| | - Mathilde Gotanègre
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France
| | - Nathalie Bonnefoy
- Institut de Recherche en Cancérologie de Montpellier, U1194, Inserm, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | | | | | - Nathalie Nicot
- LuxGene, Quantitative Biology Unit, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Francisco Azuaje
- Computational Biomedicine Research Group, Quantitative Biology Unit, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Tony Kaoma
- Computational Biomedicine Research Group, Quantitative Biology Unit, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Carine Joffre
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France
| | - Jérome Tamburini
- Institut Cochin, Département Développement, Reproduction, Cancer, UMR8104-CNRS, U1016-INSERM, Paris.,Translational Research Centre in Onco-Hematology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Christian Récher
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France.,Service d'Hématologie, Institut Universitaire du Cancer de Toulouse-Oncopole, CHU de Toulouse, Toulouse, France
| | - François Vergez
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France.,Service d'Hématologie, Institut Universitaire du Cancer de Toulouse-Oncopole, CHU de Toulouse, Toulouse, France
| | - Jean-Emmanuel Sarry
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France. .,University of Toulouse, Toulouse, France
| |
Collapse
|
13
|
Ullmann P, Nurmik M, Schmitz M, Rodriguez F, Weiler J, Qureshi-Baig K, Felten P, Nazarov PV, Nicot N, Zuegel N, Haan S, Letellier E. Tumor suppressor miR-215 counteracts hypoxia-induced colon cancer stem cell activity. Cancer Lett 2019; 450:32-41. [PMID: 30790680 DOI: 10.1016/j.canlet.2019.02.030] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 02/08/2019] [Accepted: 02/14/2019] [Indexed: 12/11/2022]
Abstract
Cancer stem cells, also known as tumor-initiating cells (TICs), are a population of aggressive and self-renewing cells that are responsible for the initiation and progression of many cancers, including colorectal carcinoma. Intratumoral hypoxia, i.e. reduced oxygen supply following uncontrolled proliferation of cancer cells, is thought to support TIC activity by inducing specific hypoxia-responsive mechanisms that are not yet entirely understood. Using previously established and fully characterized patient-derived TIC cultures, we could observe increased sphere and colony formation under hypoxic conditions. Mechanistically, microRNA (miRNA)-profiling experiments allowed us to identify miR-215 as one of the main hypoxia-induced miRNAs in primary colon TICs. Through stable overexpression of miR-215, followed by a set of functional in vitro and in vivo investigations, miR-215 was pinpointed as a negative feedback regulator, working against the TIC-promoting effects of hypoxia. Furthermore, we could single out LGR5, a bona fide marker of non-neoplastic intestinal stem cells, as a downstream target of hypoxia/miR-215 signaling. The strong tumor- and TIC-suppressor potential of miR-215 and the regulatory role of the hypoxia/miR-215/LGR5 axis may thus represent interesting points of attack for the development of innovative anti-CSC therapy approaches.
Collapse
Affiliation(s)
- Pit Ullmann
- Molecular Disease Mechanisms Group, Life Sciences Research Unit, University of Luxembourg, 6 Avenue Du Swing, L-4367, Belvaux, Luxembourg
| | - Martin Nurmik
- Molecular Disease Mechanisms Group, Life Sciences Research Unit, University of Luxembourg, 6 Avenue Du Swing, L-4367, Belvaux, Luxembourg
| | - Martine Schmitz
- Molecular Disease Mechanisms Group, Life Sciences Research Unit, University of Luxembourg, 6 Avenue Du Swing, L-4367, Belvaux, Luxembourg
| | - Fabien Rodriguez
- Molecular Disease Mechanisms Group, Life Sciences Research Unit, University of Luxembourg, 6 Avenue Du Swing, L-4367, Belvaux, Luxembourg
| | - Jil Weiler
- Molecular Disease Mechanisms Group, Life Sciences Research Unit, University of Luxembourg, 6 Avenue Du Swing, L-4367, Belvaux, Luxembourg
| | - Komal Qureshi-Baig
- Molecular Disease Mechanisms Group, Life Sciences Research Unit, University of Luxembourg, 6 Avenue Du Swing, L-4367, Belvaux, Luxembourg
| | - Paul Felten
- Molecular Disease Mechanisms Group, Life Sciences Research Unit, University of Luxembourg, 6 Avenue Du Swing, L-4367, Belvaux, Luxembourg
| | - Petr V Nazarov
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, 1A-B Rue Thomas Edison, L-1445, Strassen, Luxembourg
| | - Nathalie Nicot
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, 1A-B Rue Thomas Edison, L-1445, Strassen, Luxembourg
| | - Nikolaus Zuegel
- Centre Hospitalier Emile Mayrisch, Rue Emile Mayrisch, L-4240, Esch-sur-Alzette, Luxembourg
| | - Serge Haan
- Molecular Disease Mechanisms Group, Life Sciences Research Unit, University of Luxembourg, 6 Avenue Du Swing, L-4367, Belvaux, Luxembourg
| | - Elisabeth Letellier
- Molecular Disease Mechanisms Group, Life Sciences Research Unit, University of Luxembourg, 6 Avenue Du Swing, L-4367, Belvaux, Luxembourg.
| |
Collapse
|
14
|
Rolvering C, Zimmer AD, Ginolhac A, Margue C, Kirchmeyer M, Servais F, Hermanns HM, Hergovits S, Nazarov PV, Nicot N, Kreis S, Haan S, Behrmann I, Haan C. The PD-L1- and IL6-mediated dampening of the IL27/STAT1 anticancer responses are prevented by α-PD-L1 or α-IL6 antibodies. J Leukoc Biol 2018; 104:969-985. [PMID: 30040142 DOI: 10.1002/jlb.ma1217-495r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 01/12/2018] [Revised: 06/15/2018] [Accepted: 06/18/2018] [Indexed: 12/19/2022] Open
Abstract
Interleukin-27 (IL27) is a type-I cytokine of the IL6/IL12 family and is predominantly secreted by activated macrophages and dendritic cells. We show that IL27 induces STAT factor phosphorylation in cancerous cell lines of different tissue origin. IL27 leads to STAT1 phosphorylation and recapitulates an IFN-γ-like response in the microarray analyses, with up-regulation of genes involved in antiviral defense, antigen presentation, and immune suppression. Like IFN-γ, IL27 leads to an up-regulation of TAP2 and MHC-I proteins, which mediate increased tumor immune clearance. However, both cytokines also upregulate proteins such as PD-L1 (CD274) and IDO-1, which are associated with immune escape of cancer. Interestingly, differential expression of these genes was observed within the different cell lines and when comparing IL27 to IFN-γ. In coculture experiments of hepatocellular carcinoma (HCC) cells with peripheral blood mononuclear cells, pre-treatment of the HCC cells with IL27 resulted in lowered IL2 production by anti-CD3/-CD28 activated T-lymphocytes. Addition of anti-PD-L1 antibody, however, restored IL2 secretion. The levels of other TH 1 cytokines were also enhanced or restored upon administration of anti-PD-L1. In addition, we show that the suppression of IL27 signaling by IL6-type cytokine pre-stimulation-mimicking a situation occurring, for example, in IL6-secreting tumors or in tumor inflammation-induced cachexia-can be antagonized by antibodies against IL6-type cytokines or their receptors. Therapeutically, the antitumor effects of IL27 (mediated, e.g., by increased antigen presentation) might thus be increased by combining IL27 with blocking antibodies against PD-L1 or/and IL6-type cytokines.
Collapse
Affiliation(s)
- Catherine Rolvering
- University of Luxembourg, Life Sciences Research Unit-Signal Transduction Laboratory, Belvaux, Luxembourg
| | - Andreas D Zimmer
- University of Luxembourg, Life Sciences Research Unit-Signal Transduction Laboratory, Belvaux, Luxembourg
| | - Aurélien Ginolhac
- University of Luxembourg, Life Sciences Research Unit-Bioinformatics Core Facility, Belvaux, Luxembourg
| | - Christiane Margue
- University of Luxembourg, Life Sciences Research Unit-Signal Transduction Laboratory, Belvaux, Luxembourg
| | - Mélanie Kirchmeyer
- University of Luxembourg, Life Sciences Research Unit-Signal Transduction Laboratory, Belvaux, Luxembourg
| | - Florence Servais
- University of Luxembourg, Life Sciences Research Unit-Signal Transduction Laboratory, Belvaux, Luxembourg
| | - Heike M Hermanns
- University Hospital Würzburg, Medical Clinic II, Division of Hepatology, Würzburg, Germany
| | - Sabine Hergovits
- University Hospital Würzburg, Medical Clinic II, Division of Hepatology, Würzburg, Germany
| | - Petr V Nazarov
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Nathalie Nicot
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Stephanie Kreis
- University of Luxembourg, Life Sciences Research Unit-Signal Transduction Laboratory, Belvaux, Luxembourg
| | - Serge Haan
- University of Luxembourg, Life Sciences Research Unit-Molecular Disease Mechanisms Laboratory, Belvaux, Luxembourg
| | - Iris Behrmann
- University of Luxembourg, Life Sciences Research Unit-Signal Transduction Laboratory, Belvaux, Luxembourg
| | - Claude Haan
- University of Luxembourg, Life Sciences Research Unit-Signal Transduction Laboratory, Belvaux, Luxembourg
| |
Collapse
|
15
|
Nazarov PV, Muller A, Kaoma T, Nicot N, Maximo C, Birembaut P, Tran NL, Dittmar G, Vallar L. RNA sequencing and transcriptome arrays analyses show opposing results for alternative splicing in patient derived samples. BMC Genomics 2017; 18:443. [PMID: 28587590 PMCID: PMC5461714 DOI: 10.1186/s12864-017-3819-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [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: 01/05/2017] [Accepted: 05/25/2017] [Indexed: 01/29/2023] Open
Abstract
Background RNA sequencing (RNA-seq) and microarrays are two transcriptomics techniques aimed at the quantification of transcribed genes and their isoforms. Here we compare the latest Affymetrix HTA 2.0 microarray with Illumina 2000 RNA-seq for the analysis of patient samples - normal lung epithelium tissue and squamous cell carcinoma lung tumours. Protein coding mRNAs and long non-coding RNAs (lncRNAs) were included in the study. Results Both platforms performed equally well for protein-coding RNAs, however the stochastic variability was higher for the sequencing data than for microarrays. This reduced the number of differentially expressed genes and genes with predictive potential for RNA-seq compared to microarray data. Analysis of this variability revealed a lack of reads for short and low abundant genes; lncRNAs, being shorter and less abundant RNAs, were found especially susceptible to this issue. A major difference between the two platforms was uncovered by analysis of alternatively spliced genes. Investigation of differential exon abundance showed insufficient reads for many exons and exon junctions in RNA-seq while the detection on the array platform was more stable. Nevertheless, we identified 207 genes which undergo alternative splicing and were consistently detected by both techniques. Conclusions Despite the fact that the results of gene expression analysis were highly consistent between Human Transcriptome Arrays and RNA-seq platforms, the analysis of alternative splicing produced discordant results. We concluded that modern microarrays can still outperform sequencing for standard analysis of gene expression in terms of reproducibility and cost. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3819-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Petr V Nazarov
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg.
| | - Arnaud Muller
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Tony Kaoma
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Nathalie Nicot
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Cristina Maximo
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | | | - Nhan L Tran
- Departments of Cancer Biology and Neurosurgery, Mayo Clinic Arizona, Phoenix, USA
| | - Gunnar Dittmar
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Laurent Vallar
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| |
Collapse
|
16
|
Rolvering C, Zimmer AD, Kozar I, Hermanns HM, Letellier E, Vallar L, Nazarov PV, Nicot N, Ginolhac A, Haan S, Behrmann I, Haan C. Crosstalk between different family members: IL27 recapitulates IFNγ responses in HCC cells, but is inhibited by IL6-type cytokines. Biochim Biophys Acta Mol Cell Res 2016; 1864:516-526. [PMID: 27939431 DOI: 10.1016/j.bbamcr.2016.12.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 12/02/2016] [Accepted: 12/07/2016] [Indexed: 01/10/2023]
Abstract
Interleukin-27 (IL27) is a type-I-cytokine of the IL6/IL12 family predominantly secreted by activated macrophages and dendritic cells. In the liver, IL27 expression was observed to be upregulated in patients with hepatitis B, and sera of hepatocellular carcinoma (HCC) patients contain significantly elevated levels of IL27 compared to healthy controls or patients with hepatitis and/or liver cirrhosis. In this study, we show that IL27 induces STAT1 and STAT3 phosphorylation in 5 HCC lines and 3 different types of non-transformed liver cells. We were especially interested in the relevance of the IL27-induced STAT3 activation in liver cells. Thus, we compared the IL27 responses with those induced by IFNγ (STAT1-dominated response) or IL6-type cytokines (IL6, hyper-IL6 (hy-IL6) or OSM) (STAT3-dominated response) by microarray analysis and find that in HCC cells, IL27 induces an IFNγ-like, STAT1-dependent transcriptional response, but we do not find an effective STAT3-dependent response. Validation experiments corroborate the finding from the microarray evaluation. Interestingly, the availability of STAT1 seems critical in the shaping of the IL27 response, as the siRNA knock-down of STAT1 revealed the ability of IL27 to induce the acute-phase protein γ-fibrinogen, a typical IL6 family characteristic. Moreover, we describe a crosstalk between the signaling of IL6-type cytokines and IL27: responses to the gp130-engaging cytokine IL27 (but not those to IFNs) can be inhibited by IL6-type cytokine pre-stimulation, likely by a SOCS3-mediated mechanism. Thus, IL27 recapitulates IFNγ responses in liver cells, but differs from IFNγ by its sensitivity to SOCS3 inhibition.
Collapse
Affiliation(s)
- Catherine Rolvering
- University of Luxembourg, Life Sciences Research Unit - Signal Transduction Laboratory, 6, Avenue du Swing, L4367 Belvaux, Luxembourg.
| | - Andreas D Zimmer
- University of Luxembourg, Life Sciences Research Unit - Signal Transduction Laboratory, 6, Avenue du Swing, L4367 Belvaux, Luxembourg.
| | - Ines Kozar
- University of Luxembourg, Life Sciences Research Unit - Signal Transduction Laboratory, 6, Avenue du Swing, L4367 Belvaux, Luxembourg.
| | - Heike M Hermanns
- University Hospital Würzburg, Medical Clinic II, Division of Hepatology, Grombühlstr. 12, D-97080 Würzburg, Germany.
| | - Elisabeth Letellier
- University of Luxembourg, Life Sciences Research Unit - Molecular Disease Mechanisms Laboratory, 6, Avenue du Swing, L4367 Belvaux, Luxembourg.
| | - Laurent Vallar
- Genomics Research Laboratory, Dept. of Oncology, Luxembourg Institute of Health, 84 Val Fleuri, L1526 Luxembourg, Luxembourg.
| | - Petr V Nazarov
- Genomics Research Laboratory, Dept. of Oncology, Luxembourg Institute of Health, 84 Val Fleuri, L1526 Luxembourg, Luxembourg.
| | - Nathalie Nicot
- Genomics Research Laboratory, Dept. of Oncology, Luxembourg Institute of Health, 84 Val Fleuri, L1526 Luxembourg, Luxembourg.
| | - Aurélien Ginolhac
- University of Luxembourg, Life Sciences Research Unit - Bioinformatics Core Facility, 6, Avenue du Swing, L4367 Belvaux, Luxembourg.
| | - Serge Haan
- University of Luxembourg, Life Sciences Research Unit - Molecular Disease Mechanisms Laboratory, 6, Avenue du Swing, L4367 Belvaux, Luxembourg.
| | - Iris Behrmann
- University of Luxembourg, Life Sciences Research Unit - Signal Transduction Laboratory, 6, Avenue du Swing, L4367 Belvaux, Luxembourg.
| | - Claude Haan
- University of Luxembourg, Life Sciences Research Unit - Signal Transduction Laboratory, 6, Avenue du Swing, L4367 Belvaux, Luxembourg.
| |
Collapse
|
17
|
Bahlawane C, Schmitz M, Letellier E, Arumugam K, Nicot N, Nazarov PV, Haan S. Data on quantification of signaling pathways activated by KIT and PDGFRA mutants. Data Brief 2016; 9:828-838. [PMID: 27872880 PMCID: PMC5107687 DOI: 10.1016/j.dib.2016.10.026] [Citation(s) in RCA: 2] [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: 10/19/2016] [Revised: 10/21/2016] [Accepted: 10/26/2016] [Indexed: 12/28/2022] Open
Abstract
The present data are related to the article entitled “Insights into ligand stimulation effects on gastro-intestinal stromal tumors signaling” (C. Bahlawane, M. Schmitz, E. Letellier, K. Arumugam, N. Nicot, P.V. Nazarov, S. Haan, 2016) [1]. Constitutive and ligand-derived signaling pathways mediated by KIT and PDGFRA mutated proteins found in gastrointestinal stromal tumors (GIST) were compared. Expression of mutant proteins was induced by doxycycline in an isogenic background (Hek293 cells). Kit was identified by FACS at the cell surface and found to be quickly degraded or internalized upon SCF stimulation for both Kit Wild type and Kit mutant counterparts. Investigation of the main activated pathways in GIST unraveled a new feature specific for oncogenic KIT mutants, namely their ability to be further activated by Kit ligand, the stem cell factor (scf). We were also able to identify the MAPK pathway as the most prominent target for a common inhibition of PDGFRA and KIT oncogenic signaling. Western blotting and micro-array analysis were applied to analyze the capacities of the mutant to induce an effective STATs response. Among all Kit mutants, only Kit Ex11 deletion mutant was able to elicit an effective STATs response whereas all PDGFRA were able to do so.
Collapse
Affiliation(s)
- Christelle Bahlawane
- Molecular Disease Mechanisms group, Life Sciences Research Unit, University of Luxembourg, Campus Belval, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg
- Corresponding author. Fax: +352 4666446435.
| | - Martine Schmitz
- Molecular Disease Mechanisms group, Life Sciences Research Unit, University of Luxembourg, Campus Belval, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Elisabeth Letellier
- Molecular Disease Mechanisms group, Life Sciences Research Unit, University of Luxembourg, Campus Belval, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Karthik Arumugam
- Department of Infection and Immunity, LIH, 84 Val Fleuri, L-1526 Luxembourg
| | - Nathalie Nicot
- Genomics Research Unit, LIH, 84 Val Fleuri, L-1526 Luxembourg
| | - Petr V. Nazarov
- Genomics Research Unit, LIH, 84 Val Fleuri, L-1526 Luxembourg
| | - Serge Haan
- Molecular Disease Mechanisms group, Life Sciences Research Unit, University of Luxembourg, Campus Belval, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg
| |
Collapse
|
18
|
Youcef G, Olivier A, Nicot N, Muller A, Deng C, Labat C, Fay R, Rodriguez-Guéant RM, Leroy C, Jaisser F, Zannad F, Lacolley P, Vallar L, Pizard A. Preventive and chronic mineralocorticoid receptor antagonism is highly beneficial in obese SHHF rats. Br J Pharmacol 2016; 173:1805-19. [PMID: 26990406 DOI: 10.1111/bph.13479] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 02/17/2016] [Accepted: 02/23/2016] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND AND PURPOSE Mineralocorticoid receptor (MR) activation contributes to heart failure (HF) progression. Its overactivity in obesity is thought to accelerate cardiac remodelling and HF development. Given that MR antagonists (MRA) are beneficial in chronic HF patients, we hypothesized that early MRA treatment may target obesity-related disorders and consequently delay the development of HF. EXPERIMENTAL APPROACH Twenty spontaneously hypertensive HF dyslipidaemic obese SHHF(cp/cp) rats and 18 non-dyslipidaemic lean SHHF(+/+) controls underwent regular monitoring for their metabolic and cardiovascular phenotypes with or without MRA treatment [eplerenone (eple), 100 mg∙kg(-1) ∙day(-1) ] from 1.5 to 12.5 months of age. KEY RESULTS Eleven months of eple treatment in obese rats (SHHF(cp/cp) eple) reduced the obesity-related metabolic disorders observed in untreated SHHF(cp/cp) rats by reducing weight gain, triglycerides and total cholesterol levels and by preserving adiponectinaemia. The MRA treatment predominantly preserved diastolic and systolic functions in obese rats by alleviating the eccentric cardiac hypertrophy observed in untreated SHHF(cp/cp) animals and preserving ejection fraction (70 ± 1 vs. 59 ± 1%). The MRA also improved survival independently of these pressure effects. CONCLUSION AND IMPLICATIONS Early chronic eple treatment resulted in a delay in cardiac remodelling and HF onset in both SHHF(+/+) and SHHF(cp/cp) rats, whereas SHHF(cp/cp) rats further benefited from the MRA treatment through a reduction in their obesity and dyslipidaemia. These findings suggest that preventive MRA therapy may provide greater benefits in obese patients with additional risk factors of developing cardiovascular complications.
Collapse
Affiliation(s)
- G Youcef
- UMRS U1116 Inserm, Nancy, France.,Fédération de Recherche 3209, Nancy, France.,Université de Lorraine, Nancy, France.,Genomics Research Unit, Luxembourg Institute of Health, Luxembourg
| | - A Olivier
- UMRS U1116 Inserm, Nancy, France.,Fédération de Recherche 3209, Nancy, France.,Université de Lorraine, Nancy, France.,CHU Nancy, Nancy, France
| | - N Nicot
- Genomics Research Unit, Luxembourg Institute of Health, Luxembourg
| | - A Muller
- Genomics Research Unit, Luxembourg Institute of Health, Luxembourg
| | - C Deng
- Fédération de Recherche 3209, Nancy, France.,Université de Lorraine, Nancy, France.,UMR 7365 CNRS, Nancy, France
| | - C Labat
- UMRS U1116 Inserm, Nancy, France.,Fédération de Recherche 3209, Nancy, France.,Université de Lorraine, Nancy, France
| | - R Fay
- CHU Nancy, Nancy, France.,CIC 1433 Inserm, Pierre Drouin, Nancy, France
| | - R-M Rodriguez-Guéant
- Fédération de Recherche 3209, Nancy, France.,Université de Lorraine, Nancy, France.,CHU Nancy, Nancy, France.,U954 Inserm, Nancy, France
| | - C Leroy
- UMRS U1116 Inserm, Nancy, France.,CIC 1433 Inserm, Pierre Drouin, Nancy, France
| | - F Jaisser
- CHU Nancy, Nancy, France.,CIC 1433 Inserm, Pierre Drouin, Nancy, France
| | - F Zannad
- UMRS U1116 Inserm, Nancy, France.,Fédération de Recherche 3209, Nancy, France.,Université de Lorraine, Nancy, France.,CHU Nancy, Nancy, France.,CIC 1433 Inserm, Pierre Drouin, Nancy, France
| | - P Lacolley
- UMRS U1116 Inserm, Nancy, France.,Fédération de Recherche 3209, Nancy, France.,Université de Lorraine, Nancy, France.,CHU Nancy, Nancy, France
| | - L Vallar
- Genomics Research Unit, Luxembourg Institute of Health, Luxembourg
| | - A Pizard
- UMRS U1116 Inserm, Nancy, France.,Fédération de Recherche 3209, Nancy, France.,Université de Lorraine, Nancy, France.,CHU Nancy, Nancy, France.,CIC 1433 Inserm, Pierre Drouin, Nancy, France
| |
Collapse
|
19
|
Pacheco MP, John E, Kaoma T, Heinäniemi M, Nicot N, Vallar L, Bueb JL, Sinkkonen L, Sauter T. Integrated metabolic modelling reveals cell-type specific epigenetic control points of the macrophage metabolic network. BMC Genomics 2015; 16:809. [PMID: 26480823 PMCID: PMC4617894 DOI: 10.1186/s12864-015-1984-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 10/06/2015] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND The reconstruction of context-specific metabolic models from easily and reliably measurable features such as transcriptomics data will be increasingly important in research and medicine. Current reconstruction methods suffer from high computational effort and arbitrary threshold setting. Moreover, understanding the underlying epigenetic regulation might allow the identification of putative intervention points within metabolic networks. Genes under high regulatory load from multiple enhancers or super-enhancers are known key genes for disease and cell identity. However, their role in regulation of metabolism and their placement within the metabolic networks has not been studied. METHODS Here we present FASTCORMICS, a fast and robust workflow for the creation of high-quality metabolic models from transcriptomics data. FASTCORMICS is devoid of arbitrary parameter settings and due to its low computational demand allows cross-validation assays. Applying FASTCORMICS, we have generated models for 63 primary human cell types from microarray data, revealing significant differences in their metabolic networks. RESULTS To understand the cell type-specific regulation of the alternative metabolic pathways we built multiple models during differentiation of primary human monocytes to macrophages and performed ChIP-Seq experiments for histone H3 K27 acetylation (H3K27ac) to map the active enhancers in macrophages. Focusing on the metabolic genes under high regulatory load from multiple enhancers or super-enhancers, we found these genes to show the most cell type-restricted and abundant expression profiles within their respective pathways. Importantly, the high regulatory load genes are associated to reactions enriched for transport reactions and other pathway entry points, suggesting that they are critical regulatory control points for cell type-specific metabolism. CONCLUSIONS By integrating metabolic modelling and epigenomic analysis we have identified high regulatory load as a common feature of metabolic genes at pathway entry points such as transporters within the macrophage metabolic network. Analysis of these control points through further integration of metabolic and gene regulatory networks in various contexts could be beneficial in multiple fields from identification of disease intervention strategies to cellular reprogramming.
Collapse
Affiliation(s)
- Maria Pires Pacheco
- Life Sciences Research Unit, University of Luxembourg, 162a, Avenue de la Faïencerie, L-1511, Luxembourg, Luxembourg.
| | - Elisabeth John
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367, Belvaux, Luxembourg.
| | - Tony Kaoma
- Genomics Research Unit, Luxembourg Institute of Health, L-1526, Luxembourg, Luxembourg.
| | - Merja Heinäniemi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, 70211, Kuopio, Finland.
| | - Nathalie Nicot
- Genomics Research Unit, Luxembourg Institute of Health, L-1526, Luxembourg, Luxembourg.
| | - Laurent Vallar
- Genomics Research Unit, Luxembourg Institute of Health, L-1526, Luxembourg, Luxembourg.
| | - Jean-Luc Bueb
- Life Sciences Research Unit, University of Luxembourg, 162a, Avenue de la Faïencerie, L-1511, Luxembourg, Luxembourg.
| | - Lasse Sinkkonen
- Life Sciences Research Unit, University of Luxembourg, 162a, Avenue de la Faïencerie, L-1511, Luxembourg, Luxembourg.
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367, Belvaux, Luxembourg.
| | - Thomas Sauter
- Life Sciences Research Unit, University of Luxembourg, 162a, Avenue de la Faïencerie, L-1511, Luxembourg, Luxembourg.
| |
Collapse
|
20
|
Zhang L, Hamad EA, Vausort M, Funakoshi H, Nicot N, Nazarov PV, Vallar L, Feldman AM, Wagner DR, Devaux Y. Whole transcriptome microarrays identify long non-coding RNAs associated with cardiac hypertrophy. Genom Data 2015; 5:68-71. [PMID: 26484228 PMCID: PMC4583629 DOI: 10.1016/j.gdata.2015.05.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 05/21/2015] [Indexed: 12/11/2022]
Abstract
Long non-coding RNAs (lncRNAs) have recently emerged as a novel group of non-coding RNAs able to regulate gene expression. While their role in cardiac disease is only starting to be understood, their involvement in cardiac hypertrophy is poorly known. We studied the association between lncRNAs and left ventricular hypertrophy using whole transcriptome microarrays. Wild-type mice and mice overexpressing the adenosine A2A receptor were subjected to transverse aortic constriction (TAC) to induce left ventricular hypertrophy. Expression profiles of lncRNAs in the heart were characterized using genome-wide microarrays. An analytical pipeline was specifically developed to extract lncRNA data from microarrays. We identified 2 lncRNAs up-regulated and 3 lncRNAs down-regulated in the hearts of A2A-receptor overexpressing-mice subjected to TAC compared to wild-type mice. Differential expression of these 2 lncRNAs was validated by quantitative PCR. Complete microarray dataset is available at Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/) under the accession number GSE45423. Here, we describe in details the experimental design, microarray performance and analysis.
Collapse
Affiliation(s)
- Lu Zhang
- Laboratory of Cardiovascular Research, Luxembourg Institute of Health, Luxembourg
| | - Eman A Hamad
- Department of Physiology, Cardiovascular Research Center, Temple University School of Medicine, Philadelphia, PA, United States
| | - Mélanie Vausort
- Laboratory of Cardiovascular Research, Luxembourg Institute of Health, Luxembourg
| | - Hajime Funakoshi
- Department of Cardiology, Fukuoka National Hospital, Fukuoka, Japan
| | - Nathalie Nicot
- Genomics Research Unit, Luxembourg Institute of Health, Luxembourg
| | - Petr V Nazarov
- Genomics Research Unit, Luxembourg Institute of Health, Luxembourg
| | - Laurent Vallar
- Genomics Research Unit, Luxembourg Institute of Health, Luxembourg
| | - Arthur M Feldman
- Department of Physiology, Cardiovascular Research Center, Temple University School of Medicine, Philadelphia, PA, United States
| | - Daniel R Wagner
- Laboratory of Cardiovascular Research, Luxembourg Institute of Health, Luxembourg ; Division of Cardiology, Centre Hospitalier, Luxembourg
| | - Yvan Devaux
- Laboratory of Cardiovascular Research, Luxembourg Institute of Health, Luxembourg
| | | |
Collapse
|
21
|
Naegelen I, Plançon S, Nicot N, Kaoma T, Muller A, Vallar L, Tschirhart EJ, Bréchard S. An essential role of syntaxin 3 protein for granule exocytosis and secretion of IL-1α, IL-1β, IL-12b, and CCL4 from differentiated HL-60 cells. J Leukoc Biol 2014; 97:557-71. [PMID: 25548252 DOI: 10.1189/jlb.3a0514-254rr] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Besides their roles in the killing of pathogens, neutrophils have the capacity to package a variety of cytokines into cytoplasmic granules for subsequent release upon inflammatory conditions. Because the rapid secretion of cytokines orchestrates the action of other immune cells at the infection site and thus, can contribute to the development and chronicity of inflammatory diseases, we aimed to determine the intracellular SNARE machinery responsible for the regulation of cytokine secretion and degranulation. From a constructed gene-expression network, we first selected relevant cytokines for functional validation by the CBA approach. We established a cytokine-secretion profile for human neutrophils and dHL-60 cells, underlining their similar ability to secrete a broad variety of cytokines within proinflammatory conditions mimicked by LPS stimulation. Secondly, after screening of SNARE genes by microarray experiments, we selected STX3 for further functional studies. With the use of a siRNA strategy, we show that STX3 is clearly required for the maximal release of IL-1α, IL-1β, IL-12b, and CCL4 without alteration of other cytokine secretion in dHL-60 cells. In addition, we demonstrate that STX3 is involved in MMP-9 exocytosis from gelatinase granules, where STX3 is partly localized. Our results suggest that the secretion of IL-1α, IL-1β, IL-12b, and CCL4 occurs during gelatinase degranulation, a process controlled by STX3. In summary, these findings provide first evidence that STX3 has an essential role in trafficking pathways of cytokines in neutrophil granulocytes.
Collapse
Affiliation(s)
- Isabelle Naegelen
- *University of Luxembourg, Life Sciences Research Unit, Calcium Signaling and Inflammation, Luxembourg; and Centre de Recherche Public Santé, Luxembourg
| | - Sébastien Plançon
- *University of Luxembourg, Life Sciences Research Unit, Calcium Signaling and Inflammation, Luxembourg; and Centre de Recherche Public Santé, Luxembourg
| | - Nathalie Nicot
- *University of Luxembourg, Life Sciences Research Unit, Calcium Signaling and Inflammation, Luxembourg; and Centre de Recherche Public Santé, Luxembourg
| | - Tony Kaoma
- *University of Luxembourg, Life Sciences Research Unit, Calcium Signaling and Inflammation, Luxembourg; and Centre de Recherche Public Santé, Luxembourg
| | - Arnaud Muller
- *University of Luxembourg, Life Sciences Research Unit, Calcium Signaling and Inflammation, Luxembourg; and Centre de Recherche Public Santé, Luxembourg
| | - Laurent Vallar
- *University of Luxembourg, Life Sciences Research Unit, Calcium Signaling and Inflammation, Luxembourg; and Centre de Recherche Public Santé, Luxembourg
| | - Eric J Tschirhart
- *University of Luxembourg, Life Sciences Research Unit, Calcium Signaling and Inflammation, Luxembourg; and Centre de Recherche Public Santé, Luxembourg
| | - Sabrina Bréchard
- *University of Luxembourg, Life Sciences Research Unit, Calcium Signaling and Inflammation, Luxembourg; and Centre de Recherche Public Santé, Luxembourg
| |
Collapse
|
22
|
Moussay E, Kaoma T, Baginska J, Muller A, Van Moer K, Nicot N, Nazarov PV, Vallar L, Chouaib S, Berchem G, Janji B. The acquisition of resistance to TNFα in breast cancer cells is associated with constitutive activation of autophagy as revealed by a transcriptome analysis using a custom microarray. Autophagy 2014; 7:760-70. [DOI: 10.4161/auto.7.7.15454] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
|
23
|
Van Dyck E, Nazarov PV, Muller A, Nicot N, Bosseler M, Pierson S, Van Moer K, Palissot V, Mascaux C, Knolle U, Ninane V, Nati R, Bremnes RM, Vallar L, Berchem G, Schlesser M. Bronchial airway gene expression in smokers with lung or head and neck cancer. Cancer Med 2014; 3:322-36. [PMID: 24497500 PMCID: PMC3987082 DOI: 10.1002/cam4.190] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 09/30/2013] [Accepted: 11/01/2013] [Indexed: 01/10/2023] Open
Abstract
Cigarette smoking is the major cause of cancers of the respiratory tract, including non-small cell lung cancer (NSCLC) and head and neck cancer (HNC). In order to better understand carcinogenesis of the lung and upper airways, we have compared the gene expression profiles of tumor-distant, histologically normal bronchial biopsy specimens obtained from current smokers with NSCLC or HNC (SC, considered as a single group), as well as nonsmokers (NS) and smokers without cancer (SNC). RNA from a total of 97 biopsies was used for gene expression profiling (Affymetrix HG-U133 Plus 2.0 array). Differentially expressed genes were used to compare NS, SNC, and SC, and functional analysis was carried out using Ingenuity Pathway Analysis (IPA). Smoking-related cancer of the respiratory tract was found to affect the expression of genes encoding xenobiotic biotransformation proteins, as well as proteins associated with crucial inflammation/immunity pathways and other processes that protect the airway from the chemicals in cigarette smoke or contribute to carcinogenesis. Finally, we used the prediction analysis for microarray (PAM) method to identify gene signatures of cigarette smoking and cancer, and uncovered a 15-gene signature that distinguished between SNC and SC with an accuracy of 83%. Thus, gene profiling of histologically normal bronchial biopsy specimens provided insight into cigarette-induced carcinogenesis of the respiratory tract and gene signatures of cancer in smokers.
Collapse
Affiliation(s)
- Eric Van Dyck
- Département d'Oncologie, CRP-Santé du Luxembourg, Luxembourg
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Cheng L, Huang Z, Zhou W, Wu Q, Rich J, Bao S, Baxter P, Mao H, Zhao X, Liu Z, Huang Y, Voicu H, Gurusiddappa S, Su JM, Perlaky L, Dauser R, Leung HCE, Muraszko KM, Heth JA, Fan X, Lau CC, Man TK, Chintagumpala M, Li XN, Clark P, Zorniak M, Cho Y, Zhang X, Walden D, Shusta E, Kuo J, Sengupta S, Goel-Bhattacharya S, Kulkarni S, Cochran B, Cusulin C, Luchman A, Weiss S, Wu M, Fernandez N, Agnihotri S, Diaz R, Rutka J, Bredel M, Karamchandani J, Das S, Day B, Stringer B, Al-Ejeh F, Ting M, Wilson J, Ensbey K, Jamieson P, Bruce Z, Lim YC, Offenhauser C, Charmsaz S, Cooper L, Ellacott J, Harding A, Lickliter J, Inglis P, Reynolds B, Walker D, Lackmann M, Boyd A, Berezovsky A, Poisson L, Hasselbach L, Irtenkauf S, Transou A, Mikkelsen T, deCarvalho AC, Emlet D, Del Vecchio C, Gupta P, Li G, Skirboll S, Wong A, Figueroa J, Shahar T, Hossain A, Lang F, Fouse S, Nakamura J, James CD, Chang S, Costello J, Frerich JM, Rahimpour S, Zhuang Z, Heiss JD, Golebiewska A, Stieber D, Evers L, Lenkiewicz E, Brons NHC, Nicot N, Oudin A, Bougnaud S, Hertel F, Bjerkvig R, Barrett M, Vallar L, Niclou SP, Hao X, Rahn J, Ujack E, Lun X, Cairncross G, Weiss S, Senger D, Robbins S, Harness J, Lerner R, Ihara Y, Santos R, Torre JDL, Lu A, Ozawa T, Nicolaides T, James D, Petritsch C, Higgins D, Schroeder M, Ball B, Milligan B, Meyer F, Sarkaria J, Henley J, Flavahan W, Wu Q, Hitomi M, Rahim N, Kim Y, Sloan A, Weil R, Nakano I, Sarkaria J, Stringer B, Li M, Lathia J, Rich J, Hjelmeland A, Kaluzova M, Platt S, Kent M, Bouras A, Machaidze R, Hadjipanayis C, Kang SG, Kim SH, Huh YM, Kim EH, Park EK, Chang JH, Kim SH, Hong YK, Kim DS, Lee SJ, Kim EH, Kang SG, Hitomi M, Deleyrolle L, Sinyuk M, Li M, Goan W, Otvos B, Rohaus M, Oli M, Vedam-Mai V, Schonberg D, Wu Q, Rich J, Reynolds B, Lathia J, Lee ST, Chu K, Kim SH, Lee SK, Kim M, Roh JK, Lerner R, Griveau A, Ihara Y, Reichholf B, McMahon M, Rowitch D, James D, Petritsch C, Nitta R, Mitra S, Agarwal M, Bui T, Li G, Lin J, Adamson C, Martinez-Quintanilla J, Choi SH, Bhere D, Heidari P, He D, Mahmood U, Shah K, Mitra S, Gholamin S, Feroze A, Achrol A, Kahn S, Weissman I, Cheshier S, Nakano I, Sulman EP, Wang Q, Mostovenko E, Liu H, Lichti CF, Shavkunov A, Kroes RA, Moskal JR, Conrad CA, Lang FF, Emmett MR, Nilsson CL, Osuka S, Sampetrean O, Shimizu T, Saga I, Onishi N, Sugihara E, Okubo J, Fujita S, Takano S, Matsumura A, Saya H, Saito N, Fu J, Wang S, Yung WKA, Koul D, Schmid RS, Irvin DM, Vitucci M, Bash RE, Werneke AM, Miller CR, Shinojima N, Hossain A, Takezaki T, Fueyo J, Gumin J, Gao F, Nwajei F, Marini FC, Andreeff M, Kuratsu JI, Lang FF, Singh S, Burrell K, Koch E, Agnihotri S, Jalali S, Vartanian A, Gumin J, Sulman E, Lang F, Wouters B, Zadeh G, Spelat R, Singer E, Matlaf L, McAllister S, Soroceanu L, Spiegl-Kreinecker S, Loetsch D, Laaber M, Schrangl C, Wohrer A, Hainfellner J, Marosi C, Pichler J, Weis S, Wurm G, Widhalm G, Knosp E, Berger W, Takezaki T, Shinojima N, Kuratsu JI, Lang F, Tam Q, Tanaka S, Nakada M, Yamada D, Nakano I, Todo T, Hayashi Y, Hamada JI, Hirao A, Tilghman J, Ying M, Laterra J, Venere M, Chang C, Wu Q, Summers M, Rosenfeld S, Rich J, Tanaka S, Luk S, Chang C, Iafrate J, Cahill D, Martuza R, Rabkin S, Chi A, Wakimoto H, Wirsching HG, Krishnan S, Frei K, Krayenbuhl N, Reifenberger G, Weller M, Tabatabai G, Man J, Shoemake J, Venere M, Rich J, Yu J. STEM CELLS. Neuro Oncol 2013. [DOI: 10.1093/neuonc/not190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
25
|
Nazarov PV, Reinsbach SE, Muller A, Nicot N, Philippidou D, Vallar L, Kreis S. Interplay of microRNAs, transcription factors and target genes: linking dynamic expression changes to function. Nucleic Acids Res 2013; 41:2817-31. [PMID: 23335783 PMCID: PMC3597666 DOI: 10.1093/nar/gks1471] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [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] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are ubiquitously expressed small non-coding RNAs that, in most cases, negatively regulate gene expression at the post-transcriptional level. miRNAs are involved in fine-tuning fundamental cellular processes such as proliferation, cell death and cell cycle control and are believed to confer robustness to biological responses. Here, we investigated simultaneously the transcriptional changes of miRNA and mRNA expression levels over time after activation of the Janus kinase/Signal transducer and activator of transcription (Jak/STAT) pathway by interferon-γ stimulation of melanoma cells. To examine global miRNA and mRNA expression patterns, time-series microarray data were analysed. We observed delayed responses of miRNAs (after 24-48 h) with respect to mRNAs (12-24 h) and identified biological functions involved at each step of the cellular response. Inference of the upstream regulators allowed for identification of transcriptional regulators involved in cellular reactions to interferon-γ stimulation. Linking expression profiles of transcriptional regulators and miRNAs with their annotated functions, we demonstrate the dynamic interplay of miRNAs and upstream regulators with biological functions. Finally, our data revealed network motifs in the form of feed-forward loops involving transcriptional regulators, mRNAs and miRNAs. Additional information obtained from integrating time-series mRNA and miRNA data may represent an important step towards understanding the regulatory principles of gene expression.
Collapse
Affiliation(s)
- Petr V Nazarov
- Genomics Research Unit, Centre de Recherche Public de la Santé, L-1526 Luxembourg, Luxembourg
| | | | | | | | | | | | | |
Collapse
|
26
|
Van Dyck E, Nazarov P, Muller A, Nicot N, Bosseler M, Pierson S, Van Moer K, Palissot V, Nati R, Berchem G, Schlesser M. Profils d’expression génique de biopsies de muqueuse bronchique saine de fumeurs atteints ou non du cancer du poumon non à petites cellules et de non-fumeurs. Rev Mal Respir 2013. [DOI: 10.1016/j.rmr.2012.10.075] [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: 10/27/2022]
|
27
|
Ghoneim C, Kaoma T, Nicot N, François B, Nazarov P, Muller A, Birembaut P, Vallar L. Abstract 3905: Identification of new tumor-specific splice variants in NSCL cancers by whole genome exon arrays. Cancer Res 2011. [DOI: 10.1158/1538-7445.am2011-3905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Although lung cancer is one of the major causes of cancer death in men and women worldwide, the molecular pathogenesis of this disease remains elusive. The contribution of alternative splicing (AS) to cancer pathogenesis and progression is emerging as an area of considerable interest. Cancer-specific splice variants seem to play a key role in disease mechanism and etiology.
In this study, we analyzed 20 matched pairs of tumor specimens of Adenocarcinomas (AC), Squamous Cell Carcinomas (SCC) and adjacent normal tissue using Affymetrix GeneChip Exon microarrays. With this technology, it is possible to profile simultaneously gene expression and alternative splicing patterns for the entire genome using a single array. At the exon level, multiple probes for each exon enable the discrimination among different isoforms of a gene. Total RNA from tumors or normal tissue samples were amplified using the Ambion whole transcript expression kit and were hybridized onto GeneChip Human Exon 1.0 ST Array®. Data generated were normalized using RMA and were subjected to several layers of filtering (DABG filter, Multiple mRNAs filter). The delta splice index (ΔSI) was calculated, and alternative splicing events were detected using MIDAS and Rank Product method. Probesets were ranked based on their SI p-values.
By comparing tumor samples to the corresponding normal subgroups, we generated a list of 1689 splice variant candidates for SCC and 1010 for AC showing significant differential expression between normal and tumor tissues. Top candidates in each tumor subtype were selected based on their ΔSI for manual inspection and further bioinformatics analysis. Study of alternatively spliced candidates revealed that approximately 30 % of the genes were detected in both types of cancer. Gene function analysis combining text mining and knowledge-based approaches indicated that the largest subset (70 %) of these genes was related to cancer. Within this group, 30% of genes were related to lung cancers. Interestingly the major part (85%) of variant candidates was not previously associated with AS events in cancer. We focused our attention on this latter group and, through validation by RT/PCR, confirmed the existence of new specific alternative splicing events occurring in each cancer type. In addition, we identified biological pathways and gene networks that are specifically altered in AC or SCC. The cancer-specific AS variants and pathways identified in our study are promising biomarkers and targets for diagnostic or therapeutic purposes.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3905. doi:10.1158/1538-7445.AM2011-3905
Collapse
Affiliation(s)
| | - Tony Kaoma
- 1Microarray center CRP-SANTE, Luxembourg, Luxembourg
| | | | | | - Petr Nazarov
- 1Microarray center CRP-SANTE, Luxembourg, Luxembourg
| | - Arnaud Muller
- 1Microarray center CRP-SANTE, Luxembourg, Luxembourg
| | | | | |
Collapse
|
28
|
Nicot N, Hausman JF, Hoffmann L, Evers D. Housekeeping gene selection for real-time RT-PCR normalization in potato during biotic and abiotic stress. J Exp Bot 2005; 56:2907-14. [PMID: 16188960 DOI: 10.1093/jxb/eri285] [Citation(s) in RCA: 778] [Impact Index Per Article: 40.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Plant stress studies are more and more based on gene expression. The analysis of gene expression requires sensitive, precise, and reproducible measurements for specific mRNA sequences. Real-time RT-PCR is at present the most sensitive method for the detection of low abundance mRNA. To avoid bias, real-time RT-PCR is referred to one or several internal control genes, which should not fluctuate during treatments. Here, the non-regulation of seven housekeeping genes (beta-tubulin, cyclophilin, actin, elongation factor 1-alpha (ef1alpha), 18S rRNA, adenine phosphoribosyl transferase (aprt), and cytoplasmic ribosomal protein L2) during biotic (late blight) and abiotic stresses (cold and salt stress) was tested on potato plants using geNorm software. Results from the three experimental conditions indicated that ef1alpha was the most stable among the seven tested. The expression of the other housekeeping genes tested varied upon stress. In parallel, a study of the variability of expression of hsp20.2, shown to be implicated in late blight stress, was realized. The relative quantification of the hsp20.2 gene varied according to the internal control and the number of internal controls used, thus highlighting the importance of the choice of internal controls in such experiments.
Collapse
Affiliation(s)
- Nathalie Nicot
- Centre de Recherche Public-Gabriel Lippmann, Environment and Biotechnologies Research Unit, 41 rue du Brill, L-4422 Belvaux, Luxembourg
| | | | | | | |
Collapse
|
29
|
Boisson M, Mondon K, Torney V, Nicot N, Laine AL, Bahrman N, Gouy A, Daniel-Vedele F, Hirel B, Sourdille P, Dardevet M, Ravel C, Le Gouis J. Partial sequences of nitrogen metabolism genes in hexaploid wheat. Theor Appl Genet 2005; 110:932-40. [PMID: 15714330 DOI: 10.1007/s00122-004-1913-4] [Citation(s) in RCA: 18] [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] [Subscribe] [Scholar Register] [Received: 07/02/2004] [Accepted: 12/15/2004] [Indexed: 05/21/2023]
Abstract
Our objective was to partially sequence genes controlling nitrogen metabolism in wheat species in order to find sequence polymorphism that would enable their mapping. Primers were designed for nitrate reductase, nitrite reductase, glutamate dehydrogenase and glutamate synthase (GOGAT), and gene fragments were amplified on Triticum aestivum, T. durum, T. monococcum, T. speltoides and T. tauschii. We obtained more than 8 kb of gene sequences, mainly as coding regions (60%). Polymorphism was quantified by comparing two-by-two the three genomes of the hexaploid cultivar Arche and genomes of diploid wheat species. On average, the polymorphism rate was higher for non-coding regions, where it ranged from 1/60 to 1/23, than for coding regions (range: 1/110-1/40) except when the hexaploid D genome was compared to that of T. tauschii (1/800 and 1/816, respectively). Genome-specific primers were devised for the ferredoxin-dependent (Fd)-GOGAT gene, and they enabled the mapping of this gene on homoeologous chromosomes of group 2 using Chinese Spring deletion lines. A single nucleotide polymorphism (SNP) detected between the two hexaploid wheat cultivars Arche and Recital was used to genetically map Fd-GOGAT on chromosome 2D using a population of dihaploid lines. Fd-GOGAT-specific primers were used to estimate the SNP rate on a set of 11 hexaploid and nine Durum wheat genotypes leading to the estimate of 1 SNP/515 bp. We demonstrate that polymorphism detection enables heterologous, homeologous and even paralogous copies to be assigned, even if the elaboration of specific primer pairs is time-consuming and expensive because of the sequencing.
Collapse
Affiliation(s)
- M Boisson
- INRA URGAP, Domaine de Brunehaut, Péronne, BP 136, 80200, Estrées-Mons, France
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Nicot N, Chiquet V, Gandon B, Amilhat L, Legeai F, Leroy P, Bernard M, Sourdille P. Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs). Theor Appl Genet 2004; 109:800-5. [PMID: 15146317 DOI: 10.1007/s00122-004-1685-x] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2004] [Accepted: 03/31/2004] [Indexed: 05/04/2023]
Abstract
The increasing availability of expressed sequence tags (ESTs) in wheat ( Triticum aestivum) and related cereals provides a valuable resource of non-anonymous DNA molecular markers. We examined 170,746 wheat ESTs from the public (International Triticeae EST Cooperative) and Génoplante databases, previously clustered in contigs, for the presence of di- to hexanucleotide simple sequence repeats (SSRs). Analysis of 46,510 contigs identified 3,530 SSRs, which represented 7.5% of the total number of contigs. Only 74% of the sequences allowed primer pairs to be designed, 70% led to an amplification product, mainly of a high quality (68%), and 53% exhibited polymorphism for at least one cultivar among the eight tested. Even though dinucleotide SSRs were less represented than trinucleotide SSRs (15.5% versus 66.5%, respectively), the former showed a much higher polymorphism level (83% versus 46%). The effect of the number and type of repeats is also discussed. The development of new EST-SSRs markers will have important implications for the genetic analysis and exploitation of the genetic resources of wheat and related species and will provide a more direct estimate of functional diversity.
Collapse
Affiliation(s)
- N Nicot
- UMR INRA-UBP Amélioration et Santé des Plantes, 234 Avenue du Brézet, Domaine de Crouël, 63039 Clermont-Ferrand Cedex 2, France
| | | | | | | | | | | | | | | |
Collapse
|