Author: "Xavier Gidrol" / Topic: humans - Searchworks@Jio Institute Digital Library Search Results

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1. Characterization of the epidermal-dermal junction in hiPSC-derived skin organoids

Author: Veronika Ramovs, Hans Janssen, Ignacia Fuentes, Amandine Pitaval, Walid Rachidi, Susana M. Chuva de Sousa Lopes, Christian Freund, Xavier Gidrol, Christine L. Mummery, and Karine Raymond
Subjects: EXPRESSION, Keratinocytes, VII COLLAGEN, Induced Pluripotent Stem Cells, PROTEIN, Cell Biology, Biochemistry, INTEGRINS, Organoids, FETAL SKIN, Genetics, Humans, CELL, Epidermis, Epidermolysis Bullosa, Skin, Developmental Biology
Abstract: Human induced pluripotent stem cell (hiPSC)-derived hair-bearing skin organoids offer exciting new possibilities for modeling diseases like epidermolysis bullosa (EB). These inherited diseases affect 1 in 30,000 people worldwide and result from perturbed expression and/or structure of components of the epidermal-dermal junction (EDJ). To establish whether hiPSC-derived skin organoids might be able to capture salient features of EB, it is thus important to characterize their EDJ. Here, we report successful generation of hair-bearing skin organoids from two hiPSC lines that exhibited fully stratified interfollicular epidermis. Using immunofluorescence and electron microscopy, we showed that basal keratinocytes in organoids adhere to laminin-332 and type IV collagen-rich basement membrane via type I hemidesmosomes and integrin 81-based adhesion complexes. Importantly, we demonstrated that EDJs in organoids are almost devoid of type VII collagen, a fibril that mediates anchorage of the epidermis to dermis. This should be considered when using skin organoids for EB modeling.
Published: 2022

2. [Generating pancreatic islets organoids: Langerhanoids]

Author: Anastasia, Papoz, Flora, Clément, Camille, Laporte, Emily, Tubbs, Xavier, Gidrol, and Amandine, Pitaval
Subjects: Organoids, Islets of Langerhans, Insulin-Secreting Cells, Islets of Langerhans Transplantation, Humans, Insulin
Abstract: The extension of islet transplantation to a wider number of Type 1 diabetic patients is compromised by the scarcity of donors, the reduced ex vivo survival of pancreatic islets and the use of immunosuppressive treatments. Islets of Langerhans isolated from brain-dead donors are currently the only cell source for transplantation. Thus, it is crucial to find an alternative and an abundant source of functional insulin secreting cells not only for clinical use but also for the development of research dedicated to the screening of drugs and to the development of new therapeutic targets. Several groups around the world, including ours, develop 3D culture models as Langerhanoids that closely mimick human pancreatic islets physiology. In this review, we describe recent advances to mimic the pancreatic niche (extracellular matrix, vascularization, microfluidics) allowing better functionality of Langerhanoids.Les Langerhanoïdes, des organoïdes d’îlots pancréatiques.Les îlots de Langerhans isolés de donneurs en état de mort encéphalique constituent actuellement la seule source de cellules pour la transplantation de patients atteints de diabète de type 1. Cette approche thérapeutique reste cependant compromise par la rareté des donneurs et par certains aspects techniques. L’utilisation de sources alternatives de cellules productrices d’insuline est donc un enjeu tant thérapeutique que pour la recherche pharmacologique. Plusieurs équipes dans le monde, dont la nôtre, développent des modèles de culture cellulaire en 3D, les Langerhanoïdes, qui sont physiologiquement proches des îlots pancréatiques humains. Dans cette revue, nous décrivons les récentes avancées mimant la niche pancréatique (matrice extracellulaire, vascularisation, microfluidique), permettant ainsi d’accroître la fonctionnalité de ces Langerhanoïdes.
Published: 2022

3. Mechanical stress shapes the cancer cell response to neddylation inhibition

Author: Frédérique Mittler, Patricia Obeïd, Vincent Haguet, Cédric Allier, Sophie Gerbaud, Anastasia V. Rulina, Xavier Gidrol, Maxim Y. Balakirev, Biomicrotechnologie et génomique fonctionnelle (BIOMICS), BioSanté (UMR BioSanté), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), and Genetics and Chemogenomics (GenChem)
Subjects: Male, Cancer Research, NEDD8 Protein, Oncology, Neoplasms, [SDV]Life Sciences [q-bio], Humans, Apoptosis, Stress, Mechanical, Cell Proliferation
Abstract: Background The inhibition of neddylation by the preclinical drug MLN4924 represents a new strategy to combat cancer. However, despite being effective against hematologic malignancies, its success in solid tumors, where cell–cell and cell-ECM interactions play essential roles, remains elusive. Methods Here, we studied the effects of MLN4924 on cell growth, migration and invasion in cultured prostate cancer cells and in disease-relevant prostate tumoroids. Using focused protein profiling, drug and RNAi screening, we analyzed cellular pathways activated by neddylation inhibition. Results We show that mechanical stress induced by MLN4924 in prostate cancer cells significantly affects the therapeutic outcome. The latter depends on the cell type and involves distinct Rho isoforms. In LNCaP and VCaP cells, the stimulation of RhoA and RhoB by MLN4924 markedly upregulates the level of tight junction proteins at cell–cell contacts, which augments the mechanical strain induced by Rho signaling. This “tight junction stress response” (TJSR) causes the collapse of cell monolayers and a characteristic rupture of cancer spheroids. Notably, TJSR is a major cause of drug-induced apoptosis in these cells. On the other hand, in PC3 cells that underwent partial epithelial-to-mesenchymal transition (EMT), the stimulation of RhoC induces an adverse effect by promoting amoeboid cell scattering and invasion. We identified complementary targets and drugs that allow for the induction of TJSR without stimulating RhoC. Conclusions Our finding that MLN4924 acts as a mechanotherapeutic opens new ways to improve the efficacy of neddylation inhibition as an anticancer approach. Graphical Abstract
Published: 2022
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4. Leaky gut model of the human intestinal mucosa for testing siRNA-based nanomedicine targeting JAK1

Author: Olga Hartwig, Brigitta Loretz, Adrien Nougarede, Dorothée Jary, Eric Sulpice, Xavier Gidrol, Fabrice Navarro, Claus-Michael Lehr, Biomicrotechnologie et génomique fonctionnelle (BIOMICS), BioSanté (UMR BioSanté), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)
Subjects: [SDV]Life Sciences [q-bio], Pharmaceutical Science, Janus Kinase 1, Inflammatory Bowel Diseases, STAT Transcription Factors, Nanomedicine, Animals, Humans, Janus Kinase Inhibitors, Caco-2 Cells, Intestinal Mucosa, RNA, Small Interfering, ComputingMilieux_MISCELLANEOUS, Janus Kinases, Signal Transduction
Abstract: Complex in vitro models of human immune cells and intestinal mucosa may have a translation-assisting role in the assessment of anti-inflammatory compounds. Chronic inflammation of the gastrointestinal tract is a hallmark of inflammatory bowel diseases (IBD). In both IBD entities, Crohn's disease and ulcerative colitis, impaired immune cell activation and dysfunctional epithelial barrier are the common pathophysiology. Current therapeutic approaches are targeting single immune modulator molecules to stop disease progression and reduce adverse effects. Such molecular targets can be difficult to assess in experimental animal models of colitis, due to the disease complexity and species differences. Previously, a co-culture model based on human epithelial cells and monocytes arranged in a physiological microenvironment was used to mimic inflamed mucosa for toxicological and permeability studies. The leaky gut model described here, a co-culture of Caco-2, THP-1 and MUTZ-3 cells, was used to mimic IBD-related pathophysiology and for combined investigations of permeability and target engagement of two Janus kinase (JAK) inhibitors, tofacitinib (TOFA) and a JAK1-targeting siRNA nanomedicine. The co-culture just before reaching confluency of the epithelium was used to mimic the compromised intestinal barrier. Delivery efficacy and target engagement against JAK1 was quantified via downstream analysis of STAT1 protein phosphorylation after IFN-γ stimulation. Compared to a tight barrier, the leaky gut model showed 92 ± 5% confluence, a barrier function below 200 Ω*cm
Published: 2021
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5. CRISPR-Cas9 Technology for the Creation of Biological Avatars Capable of Modeling and Treating Pathologies: From Discovery to the Latest Improvements

Author: Ali Nasrallah, Eric Sulpice, Farah Kobaisi, Xavier Gidrol, Walid Rachidi, Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), and ANR-18-CE17-0017,PGI2Heal,La voie de la PGI2 pour améliorer la cicatrisation des plaies du pied diabétique(2018)
Subjects: Gene Editing, Technology, Transcription Activator-Like Effector Nucleases, [SDV]Life Sciences [q-bio], Humans, General Medicine, CRISPR-Cas Systems, Zinc Finger Nucleases
Abstract: International audience; This is a spectacular moment for genetics to evolve in genome editing, which encompasses the precise alteration of the cellular DNA sequences within various species. One of the most fascinating genome-editing technologies currently available is Clustered Regularly Interspaced Palindromic Repeats (CRISPR) and its associated protein 9 (CRISPR-Cas9), which have integrated deeply into the research field within a short period due to its effectiveness. It became a standard tool utilized in a broad spectrum of biological and therapeutic applications. Furthermore, reliable disease models are required to improve the quality of healthcare. CRISPR-Cas9 has the potential to diversify our knowledge in genetics by generating cellular models, which can mimic various human diseases to better understand the disease consequences and develop new treatments. Precision in genome editing offered by CRISPR-Cas9 is now paving the way for gene therapy to expand in clinical trials to treat several genetic diseases in a wide range of species. This review article will discuss genome-editing tools: CRISPR-Cas9, Zinc Finger Nucleases (ZFNs), and Transcription Activator-Like Effector Nucleases (TALENs). It will also encompass the importance of CRISPR-Cas9 technology in generating cellular disease models for novel therapeutics, its applications in gene therapy, and challenges with novel strategies to enhance its specificity.
Published: 2022
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6. Isoconazole and Clemizole Hydrochloride Partially Reverse the Xeroderma Pigmentosum C Phenotype

Author: Nour Fayyad, Caroline Barette, Bassam Badran, Walid Rachidi, Mohammad Fayyad-Kazan, Xavier Gidrol, Marie-Odile Fauvarque, Farah Kobaisi, Eric Sulpice, Hussein Fayyad-Kazan, Biomicrotechnologie et génomique fonctionnelle (BIOMICS), BioSanté (UMR BioSanté), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Genetics and Chemogenomics (GenChem), SYstèmes Moléculaires et nanoMatériaux pour l’Energie et la Santé (SYMMES), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Lebanese University [Beirut] (LU), and ANR-18-CE17-0017,PGI2Heal,La voie de la PGI2 pour améliorer la cicatrisation des plaies du pied diabétique(2018)
Subjects: 0301 basic medicine, Xeroderma pigmentosum, Miconazole, QH301-705.5, DNA damage, DNA repair, Cell Survival, Ultraviolet Rays, [SDV]Life Sciences [q-bio], XPC, Pyrimidine dimer, Skin Diseases, Catalysis, Article, Cell Line, Inorganic Chemistry, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Isoconazole, chemical screen, medicine, Humans, Pyrimidone, Biology (General), Physical and Theoretical Chemistry, QD1-999, Molecular Biology, Spectroscopy, Xeroderma Pigmentosum, skin cancer, Organic Chemistry, Drug Repositioning, General Medicine, medicine.disease, Computer Science Applications, Clemizole, UV, Chemistry, 030104 developmental biology, chemistry, Apoptosis, 030220 oncology & carcinogenesis, Cancer research, Benzimidazoles
Abstract: Xeroderma Pigmentosum protein C (XPC) is involved in recognition and repair of bulky DNA damage such as lesions induced by Ultra Violet (UV) radiation. XPC-mutated cells are, therefore, photosensitive and accumulate DNA damage leading to increased cancer incidence. Here, we performed a high-throughput screen to identify chemicals capable of normalizing the XP-C phenotype (hyper-photosensitivity and accumulation of photoproducts). Fibroblasts from XP-C patients were treated with a library of approved chemical drugs. Out of 1280 tested chemicals, 16 showed ≥ 25% photo-resistance with RZscore above 2.6 and two drugs were able to favor repair of 6 − 4 pyrimidine pyrimidone photoproducts (6-4PP). Among these two compounds, Isoconazole could partially inhibit apoptosis of the irradiated cells especially when cells were post-treated directly after UV irradiation while Clemizole Hydrochloride-mediated increase in viability was dependent on both pre and post-treatment. No synergistic effect was recorded following combined drug treatment and the compounds exerted no effect on the proliferative capacity of the cells post UV exposure. Amelioration of XP-C phenotype is a pave way towards understanding the accelerated skin cancer initiation in XP-C patients. Further examination is required to decipher the molecular mechanisms targeted by these two chemicals.
Published: 2021
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7. A new ultradian rhythm in mammalian cell dry mass observed by holography

Author: Xavier Gidrol, Jean-Yves Fortin, Patricia Obeid, Maxim Y Balakirev, Cédric Allier, Lamya Ghenim, Lionel Hervé, Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Commissariat à l'énergie atomique et aux énergies alternatives - Laboratoire d'Electronique et de Technologie de l'Information (CEA-LETI), Direction de Recherche Technologique (CEA) (DRT (CEA)), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Institut Jean Lamour (IJL), Université de Lorraine (UL)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Biomicrotechnologie et génomique fonctionnelle (BIOMICS ), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Laboratoire d'Exploration Fonctionnelle des Génomes (LEFG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7), Ghenim, Lamya, BioSanté (UMR BioSanté), Laboratoire de Physique et Chimie Théoriques (LPCT), Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), and Biomicrotechnologie et génomique fonctionnelle (BIOMICS)
Subjects: 0301 basic medicine, Science, [SDV]Life Sciences [q-bio], Cell, Holography, 01 natural sciences, Article, [PHYS] Physics [physics], 010309 optics, 03 medical and health sciences, Rhythm, Mammalian cell, 0103 physical sciences, medicine, Humans, Oscillators, Circadian rhythm, Interphase, Ultradian rhythm, Cell Proliferation, [PHYS]Physics [physics], Multidisciplinary, Proteasome, Chemistry, Temperature, Ultradian Rhythm, Cell cycle, Cell biology, [SDV] Life Sciences [q-bio], 030104 developmental biology, Proteostasis, medicine.anatomical_structure, Medicine, Single-Cell Analysis, HeLa Cells
Abstract: We have discovered a new 4 h ultradian rhythm that occurs during the interphase of the cell cycle in a wide range of individual mammalian cells, including both primary and transformed cells. The rhythm was detected by holographic lens-free microscopy that follows the histories of the dry mass of thousands of single live cells simultaneously, each at a resolution of five minutes. It was vital that the rhythm was observed in inherently heterogeneous cell populations, thus eliminating synchronization and labeling bias. The rhythm is independent of circadian rhythm, and is temperature-compensated. We show that the amplitude of the fundamental frequency provides a way to quantify the effects of, chemical reagents on cells, thus shedding light on its mechanism. The rhythm is suppressed by proteostasis disruptors and is detected only in proliferating cells, suggesting that it represents a massive degradation and re-synthesis of protein every 4 h in growing cells.
Published: 2020
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8. High-throughput synthetic rescue for exhaustive characterization of suppressor mutations in human genes

Author: Farah, Kobaisi, Nour, Fayyad, Eric, Sulpice, Bassam, Badran, Hussein, Fayyad-Kazan, Walid, Rachidi, and Xavier, Gidrol
Subjects: Cell phenotype, Suppressor mutation, Review, Gene Knockout Techniques, Suppression, Genetic, Mutagenesis, Gene Knockdown Techniques, Neoplasms, Genetic screening, Animals, Humans, RNA Interference, CRISPR-Cas Systems, Synthetic rescue
Abstract: Inherited or acquired mutations can lead to pathological outcomes. However, in a process defined as synthetic rescue, phenotypic outcome created by primary mutation is alleviated by suppressor mutations. An exhaustive characterization of these mutations in humans is extremely valuable to better comprehend why patients carrying the same detrimental mutation exhibit different pathological outcomes or different responses to treatment. Here, we first review all known suppressor mutations’ mechanisms characterized by genetic screens on model species like yeast or flies. However, human suppressor mutations are scarce, despite some being discovered based on orthologue genes. Because of recent advances in high-throughput screening, developing an inventory of human suppressor mutations for pathological processes seems achievable. In addition, we review several screening methods for suppressor mutations in cultured human cells through knock-out, knock-down or random mutagenesis screens on large scale. We provide examples of studies published over the past years that opened new therapeutic avenues, particularly in oncology.
Published: 2019

9. Signaling Pathways, Chemical and Biological Modulators of Nucleotide Excision Repair: The Faithful Shield against UV Genotoxicity

Author: B. Badran, Xavier Gidrol, H. Fayyad-Kazan, Hamid Reza Rezvani, Nour Fayyad, Farah Kobaisi, Walid Rachidi, Eric Sulpice, M. Fayyad-Kazan, Biomicrotechnologie et génomique fonctionnelle (BIOMICS), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Chimie Interface Biologie pour l’Environnement, la Santé et la Toxicologie (CIBEST ), SYstèmes Moléculaires et nanoMatériaux pour l’Energie et la Santé (SYMMES), Institut de Chimie du CNRS (INC)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux (UB), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and ANR-18-CE17-0017,PGI2Heal,La voie de la PGI2 pour améliorer la cicatrisation des plaies du pied diabétique(2018)
Subjects: congenital, hereditary, and neonatal diseases and abnormalities, Aging, Xeroderma pigmentosum, DNA Repair, Ultraviolet Rays, DNA repair, DNA damage, [SDV]Life Sciences [q-bio], Trichothiodystrophy, Review Article, Genotoxic Stress, Biology, Biochemistry, Cockayne syndrome, 03 medical and health sciences, 0302 clinical medicine, medicine, Animals, Humans, Trichothiodystrophy Syndromes, lcsh:QH573-671, Cockayne Syndrome, skin and connective tissue diseases, PI3K/AKT/mTOR pathway, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Xeroderma Pigmentosum, 0303 health sciences, lcsh:Cytology, nutritional and metabolic diseases, Cell Biology, General Medicine, medicine.disease, 3. Good health, enzymes and coenzymes (carbohydrates), 030220 oncology & carcinogenesis, biological sciences, Cancer research, DNA Damage, Signal Transduction, Nucleotide excision repair
Abstract: The continuous exposure of the human body’s cells to radiation and genotoxic stresses leads to the accumulation of DNA lesions. Fortunately, our body has several effective repair mechanisms, among which is nucleotide excision repair (NER), to counteract these lesions. NER includes both global genome repair (GG-NER) and transcription-coupled repair (TC-NER). Deficiencies in the NER pathway underlie the development of several DNA repair diseases, such as xeroderma pigmentosum (XP), Cockayne syndrome (CS), and trichothiodystrophy (TTD). Deficiencies in GG-NER and TC-NER render individuals to become prone to cancer and neurological disorders, respectively. Therefore, NER regulation is of interest in fine-tuning these risks. Distinct signaling cascades including the NFE2L2 (NRF2), AHR, PI3K/AKT1, MAPK, and CSNK2A1 pathways can modulate NER function. In addition, several chemical and biological compounds have proven success in regulating NER’s activity. These modulators, particularly the positive ones, could therefore provide potential treatments for genetic DNA repair-based diseases. Negative modulators, nonetheless, can help sensitize cells to killing by genotoxic chemicals. In this review, we will summarize and discuss the major upstream signaling pathways and molecules that could modulate the NER’s activity.
Published: 2019
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10. MicroRNA degeneracy and pluripotentiality within a Lavallière-tie architecture confers robustness to gene expression networks

Author: Ricky Bhajun, Laurent Guyon, Xavier Gidrol, Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])
Subjects: 0301 basic medicine, [SDV]Life Sciences [q-bio], Gene regulatory network, Computational biology, Biology, 03 medical and health sciences, Cellular and Molecular Neuroscience, Gene expression, microRNA, Humans, Gene Regulatory Networks, Degeneracy (biology), Molecular Biology, ComputingMilieux_MISCELLANEOUS, Pharmacology, Regulation of gene expression, Genetics, Visions and Reflections, Models, Genetic, Gene Expression Profiling, Robustness (evolution), Cell Biology, Gene expression profiling, MicroRNAs, 030104 developmental biology, Gene Expression Regulation, Molecular Medicine, Signal transduction
Abstract: Modularity, feedback control, functional redundancy and bowtie architecture have been proposed as key factors that confer robustness to complex biological systems. MicroRNAs (miRNAs) are highly conserved but functionally dispensable. These antinomic properties suggest that miRNAs fine-tune gene expression rather than act as genetic switches. We synthesize published and unpublished data and hypothesize that miRNA pluripotentiality acts to buffer gene expression, while miRNA degeneracy tunes the expression of targets, thus providing robustness to gene expression networks. Furthermore, we propose a Lavallière-tie architecture by integrating signal transduction, miRNAs and protein expression data to model complex gene expression networks.
Published: 2016
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11. Lens-free microscopy for 3D + time acquisitions of 3D cell culture

Author: Cédric Allier, Anthony Berdeu, Thomas Bordy, Ondrej Mandula, Sophie Morales, Xavier Gidrol, Bastien Laperrousaz, Nathalie Picollet-D'hahan, Laboratoire Imagerie et Systèmes d'Acquisition (LISA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire de Physique de l'ENS Lyon (Phys-ENS), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Biomicrotechnologie et génomique fonctionnelle (BIOMICS), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Commissariat à l'énergie atomique et aux énergies alternatives - Laboratoire d'Electronique et de Technologie de l'Information (CEA-LETI), Direction de Recherche Technologique (CEA) (DRT (CEA)), Nanostructures et Rayonnement Synchrotron (NRS ), Modélisation et Exploration des Matériaux (MEM), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])
Subjects: 0301 basic medicine, [SDV]Life Sciences [q-bio], Cell Culture Techniques, lcsh:Medicine, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Time-Lapse Imaging, Article, Cell Line, law.invention, 03 medical and health sciences, 3D cell culture, Imaging, Three-Dimensional, law, Microscopy, Humans, lcsh:Science, ComputingMilieux_MISCELLANEOUS, Cell Aggregation, Lenses, Physics, Multidisciplinary, lcsh:R, Large aggregate, Cell migration, Cell aggregation, Lens (optics), 030104 developmental biology, Cell culture, Biophysics, lcsh:Q, Extracellular Space
Abstract: Thanks to a novel three-dimensional imaging platform based on lens-free microscopy, it is possible to perform multi-angle acquisitions and holographic reconstructions of 3D cell cultures directly into the incubator. Being able of reconstructing volumes as large as ~5 mm3 over a period of time covering several days, allows us to observe a broad range of migration strategies only present in 3D environment, whether it is single cell migration, collective migrations of cells and dispersal of cells. In addition we are able to distinguish new interesting phenomena, e.g. large-scale cell-to-matrix interactions (>1 mm), fusion of cell clusters into large aggregate (~10,000 µm2) and conversely, total dissociation of cell clusters into clumps of migrating cells. This work on a novel 3D + time lens-free microscopy technique thus expands the repertoire of phenomena that can be studied within 3D cell cultures.
Published: 2018
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12. MYPT1 is targeted by miR-145 inhibiting viability, migration and invasion in 2D and 3D HeLa cultures

Author: Alejandro González-Torres, Evelyn Gabriela Bañuelos-Villegas, Eric Sulpice, Xavier Gidrol, Luis Marat Alvarez-Salas, Natalia Martinez-Acuña, Biomicrotechnologie et génomique fonctionnelle (BIOMICS), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])
Subjects: 0301 basic medicine, Keratinocytes, Small interfering RNA, Myosin Light Chains, Cell Survival, [SDV]Life Sciences [q-bio], Biophysics, Cell Culture Techniques, medicine.disease_cause, Biochemistry, HeLa, 03 medical and health sciences, Myosin-Light-Chain Phosphatase, Cell Movement, Spheroids, Cellular, Myosin, medicine, Humans, Neoplasm Invasiveness, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Viability assay, Phosphorylation, RNA, Small Interfering, Molecular Biology, Tumor Stem Cell Assay, ComputingMilieux_MISCELLANEOUS, Gene knockdown, biology, Base Sequence, Chemistry, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Cell Biology, Transfection, biology.organism_classification, Cell biology, MicroRNAs, 030104 developmental biology, Tumor progression, Gene Knockdown Techniques, Carcinogenesis, HeLa Cells
Abstract: The miR-143/145 cluster is down-regulated in cervical tumor cells suggesting a role in tumorigenesis including cytoskeleton remodeling, a key event for tumor progression. The aim of the present work was to determine the role of miR-143/145 in the modulation of the myosin regulator phospho-myosin light chain (pMLC). HeLa monolayer and tridimensional cultures were transfected with miR-143 or miR-145 mimics inhibiting cell viability, proliferation, migration and invasion, mainly through miR-145. MiR-145 transfection increased pMLC levels by targeting the MYPT1 subunit of the regulatory myosin phosphatase. MYPT1 knockdown by siRNAs reproduced miR-145 effects suggesting miR-145 as a tumor suppressor through MYPT1 targeting, leading to a subsequent increase of pMLC levels with implications for cervical cell viability, migration and invasion.
Published: 2018
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13. Direct transfection of clonal organoids in matrigel microbeads : a promising approach toward organoid-based genetic screens

Author: Frédéric Bottausci, Stephanie Porte, Sophie Gerbaud, Nathalie Picollet-D'hahan, Xavier Gidrol, Bastien Laperrousaz, Virginie Hourtane, Frédérique Kermarrec, Ville Härmä, Biomicrotechnologie et génomique fonctionnelle (BIOMICS), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Commissariat à l'énergie atomique et aux énergies alternatives - Laboratoire d'Electronique et de Technologie de l'Information (CEA-LETI), Direction de Recherche Technologique (CEA) (DRT (CEA)), CEA [Plan de couplage DSV-DRT] Grenoble Alps Metropole (Proof of Concept program of Canceropole CLARA (PROscan3D project)), ANR-11-NANB-0002,FACSBIOMARKER,Identification et validation de biomarqueurs du cancer de la prostate par ARN interférence à haut débit couplée au FACS(2011), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Leriche, Marianne, and Nanobiologies - Identification et validation de biomarqueurs du cancer de la prostate par ARN interférence à haut débit couplée au FACS - - FACSBIOMARKER2011 - ANR-11-NANB-0002 - NANB - VALID
Subjects: 0301 basic medicine, Male, [SPI] Engineering Sciences [physics], Transgene, Biology, Transfection, Cell Line, Extracellular matrix, 03 medical and health sciences, [SPI]Engineering Sciences [physics], 0302 clinical medicine, Cell Line, Tumor, Lab-On-A-Chip Devices, Spheroids, Cellular, Genetics, Organoid, Humans, Breast, RNA, Small Interfering, Matrigel, Electroporation, Tumor Suppressor Proteins, Spheroid, PTEN Phosphohydrolase, Prostate, Microspheres, Cell biology, Organoids, Drug Combinations, 030104 developmental biology, 030220 oncology & carcinogenesis, Methods Online, Female, Proteoglycans, RNA Interference, Collagen, Laminin, Genetic screen, Transcription Factors
Abstract: International audience; Organoid cultures in 3D matrices are relevant models to mimic the complex in vivo environment that supports cell physiological and pathological behaviors. For instance, 3D epithelial organoids recapitulate numerous features of glandular tissues including the development of fully differentiated acini that maintain apico-basal polarity with hollow lumen. Effective genetic engineering in organoids would bring new insights in organogenesis and carcinogenesis. However, direct 3D transfection on already formed organoids remains challenging. One limitation is that organoids are embedded in extracellular matrix and grow into compact structures that hinder transfection using traditional techniques. To address this issue, we developed an innovative approach for transgene expression in 3D organoids by combining single-cell encapsulation in Matrigel microbeads using a microfluidic device and electroporation. We demonstrate that direct electroporation of encapsulated organoids reaches up to 80% of transfection efficiency. Using this technique and a morphological read-out that recapitulate the different stages of tumor development, we further validate the role of p63 and PTEN as key genes in acinar development in breast and prostate tissues. We believe that the combination of controlled organoid generation and efficient 3D transfection developed here opens new perspectives for flow-based high-throughput genetic screening and functional genomic applications.
Published: 2018
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14. Lens-free Video Microscopy for the Dynamic and Quantitative Analysis of Adherent Cell Culture

Author: Lionel Hervé, Michel Bornens, Xavier Gidrol, Lamya Ghenim, Fabrice Navarro, Mathilde Menneteau, Olivier Cioni, Sophie Morales, Yves Usson, Thomas Bordy, Romaric Vincent, Sabine Bardin, Cédric Allier, Commissariat à l'énergie atomique et aux énergies alternatives - Laboratoire d'Electronique et de Technologie de l'Information (CEA-LETI), Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Biomicrotechnologie et génomique fonctionnelle (BIOMICS), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Mécanismes moléculaires du transport intracellulaire, Compartimentation et dynamique cellulaires (CDC), Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-Université Pierre et Marie Curie - Paris 6 (UPMC), Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-Université Pierre et Marie Curie - Paris 6 (UPMC), Dynamique Cellulaire et Tissulaire- Interdisciplinarité, Modèles & Microscopies (TIMC-IMAG-DyCTiM), Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble - UMR 5525 (TIMC-IMAG), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Institut Laue-Langevin (ILL), ILL, Laboratoire de biologie à grande échelle, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Curie [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Curie [Paris]-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Curie [Paris]-Centre National de la Recherche Scientifique (CNRS), Dynamique Cellulaire et Tissulaire- Interdisciplinarité, Modèles & Microscopies (TIMC-DyCTiM), Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble - UMR 5525 (TIMC), and Dynamiques Cellulaire et Tissulaire - Interdisciplinarité, Modélisation & Microscopie (TIMC-IMAG-DyCTiM2)
Subjects: 0301 basic medicine, Microscope, Cell division, Computer science, General Chemical Engineering, [SDV]Life Sciences [q-bio], Holography, Cell Culture Techniques, Video microscopy, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, law.invention, 010309 optics, 03 medical and health sciences, law, 0103 physical sciences, Humans, ComputingMilieux_MISCELLANEOUS, Microscopy, Video, General Immunology and Microbiology, General Neuroscience, This Month in JoVE, Cell cycle, Lens (optics), 030104 developmental biology, Cell culture, Quantitative Microscopy, Biomedical engineering
Abstract: Here, we demonstrate that lens-free video microscopy enables us to simultaneously capture the kinetics of thousands of cells directly inside the incubator and that it is possible to monitor and quantify single cells along several cell cycles. We describe the full protocol used to monitor and quantify a HeLa cell culture for 2.7 days. First, cell culture acquisition is performed with a lens-free video microscope, and then the data is analyzed following a four-step process: multi-wavelength holographic reconstruction, cell-tracking, cell segmentation and cell division detection algorithms. As a result, we show that it is possible to gather a dataset featuring more than 10,000 cell cycle tracks and more than 2 x 10(6) cell morphological measurements.
Published: 2018
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15. Microtubule stabilization drives 3D centrosome migration to initiate primary ciliogenesis

Author: Gaëlle Letort, Fabrice Senger, Xavier Gidrol, Laurent Guyon, Manuel Théry, Amandine Pitaval, James Sillibourne, Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Physiologie cellulaire et végétale (LPCV), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Biologie du Cancer et de l'Infection (BCI ), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut National de la Santé et de la Recherche Médicale (INSERM), Alloimmunité-Autoimmunité-Transplantation (A2T), Institut Universitaire d'Hématologie (IUH), Université Paris Diderot - Paris 7 (UPD7)-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), European Project: 310472,EC:FP7:ERC,ERC-2012-StG_20111109,SPICY(2012), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Universitaire d'Hématologie (IUH), Université Paris Diderot - Paris 7 (UPD7)-Université Paris Diderot - Paris 7 (UPD7), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG)
Subjects: 0301 basic medicine, Axoneme, Time Factors, Cytoskeleton organization, Centrosome cycle, Retinal Pigment Epithelium, Microtubule dynamics, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, Transfection, Mechanotransduction, Cellular, Microtubules, Spindle pole body, Article, Cell Line, 03 medical and health sciences, 0302 clinical medicine, Primary ciliogenesis, Centrosome migration, Intraflagellar transport, Microtubule, Ciliogenesis, Humans, Actin network, Cilia, Cytoskeleton, Research Articles, 030304 developmental biology, Microtubule nucleation, Centrosome, 0303 health sciences, Protein Stability, Tumor Suppressor Proteins, Epithelial Cells, Cell Biology, Actin cytoskeleton, Human cells, Cell biology, Actin Cytoskeleton, 030104 developmental biology, Microtubule Proteins, RNA Interference, Centrosome positioning regulation, 030217 neurology & neurosurgery
Abstract: The classical view of centrosome decentering and migration to the cell periphery during ciliogenesis is that it is pulled toward its final destination. Here, Pitaval et al. argue that microtubule stabilization in the early stages of ciliogenesis generates pushing forces that propel the centrosome toward the apical pole., Primary cilia are sensory organelles located at the cell surface. Their assembly is primed by centrosome migration to the apical surface, yet surprisingly little is known about this initiating step. To gain insight into the mechanisms driving centrosome migration, we exploited the reproducibility of cell architecture on adhesive micropatterns to investigate the cytoskeletal remodeling supporting it. Microtubule network densification and bundling, with the transient formation of an array of cold-stable microtubules, and actin cytoskeleton asymmetrical contraction participate in concert to drive apical centrosome migration. The distal appendage protein Cep164 appears to be a key actor involved in the cytoskeleton remodeling and centrosome migration, whereas intraflagellar transport 88’s role seems to be restricted to axoneme elongation. Together, our data elucidate the hitherto unexplored mechanism of centrosome migration and show that it is driven by the increase and clustering of mechanical forces to push the centrosome toward the cell apical pole.
Published: 2017
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16. Deciphering Cell Intrinsic Properties: A Key Issue for Robust Organoid Production

Author: Xavier Gidrol, Nathalie Picollet-D'hahan, Donald K. Martin, Delphine Freida, Monika E. Dolega, Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire Interdisciplinaire de Physique [Saint Martin d’Hères] (LIPhy), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Systèmes Nanobiotechnologiques et Biomimétiques (TIMC-IMAG-SyNaBi), Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble - UMR 5525 (TIMC-IMAG), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])
Subjects: 0301 basic medicine, Cell type, Stromal cell, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, [SDV]Life Sciences [q-bio], Cell Culture Techniques, Bioengineering, Genomics, Nanotechnology, Computational biology, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, Regenerative Medicine, Regenerative medicine, 03 medical and health sciences, Organoid, Animals, Humans, Microfluidic Analytical Techniques, 3. Good health, Organoids, 030104 developmental biology, Drug development, Functional genomics, Function (biology), Biotechnology
Abstract: International audience; We highlight the disposition of various cell types to self-organize into complexorgan-like structures without necessarily the support of any stromal cells,provided they are placed into permissive 3D culture conditions. The goal ofgenerating organoids reproducibly and efficiently has been hampered by poorunderstanding of the exact nature of the intrinsic cell properties at the origin oforganoid generation, and of the signaling pathways governing their differen-tiation. Using microtechnologies like microfluidics to engineer organoidswould create opportunities for single-cell genomics and high-throughputfunctional genomics to exhaustively characterize cell intrinsic properties. Amore complete understanding of the development of organoids wouldenhance their relevance as models to study organ morphology, function,and disease and would open new avenues in drug development and regener-ative medicine.
Published: 2017
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17. Label-free analysis of prostate acini-like 3D structures by lensfree imaging

Author: Pierre Marcoux, Frédérique Kermarrec, Xavier Gidrol, Sophie Gerbaud, Nathalie Picollet-D'hahan, Monika E. Dolega, Jean-Marc Dinten, Cédric Allier, and Srikanth Vinjimore Kesavan
Subjects: Male, Cell Culture Techniques, Biomedical Engineering, Biophysics, Morphogenesis, Acinar Cells, Biology, medicine.disease_cause, Cell Line, Metastasis, 3D cell culture, Prostate, Cell Line, Tumor, Spheroids, Cellular, Image Processing, Computer-Assisted, Electrochemistry, medicine, Humans, Microscopy, Spheroid, Cell Polarity, Epithelial Cells, Equipment Design, General Medicine, medicine.disease, Cell biology, medicine.anatomical_structure, Carcinogenesis, Biotechnology, Transforming growth factor, Lumen (unit)
Abstract: We present a lensfree imaging method to analyze polarity in RWPE1 prostate epithelial cells that form polarized acini with lumen under standard tridimensional (3D) culture conditions. The first event in epithelial carcinogenesis is loss of polarity, followed by uncontrolled proliferation leading to metastasis. We demonstrate that it is possible to use optical signatures to discriminate 3D objects with distinct polarities in a large field of view. The three metrics we present here are designed as image processing tools to discriminate acini from spheroids without any 3D reconstruction. To demonstrate that our lensfree imaging platform may be used to study the 3D organization of epithelial cells, we analyzed and quantified the modulation of dynamic processes, e.g., the polarity of acini and the merging of polarized structures, upon transforming growth factor beta-1 (TGF beta-1) addition to the culture media. Hence, coupling lensfree microscopy with 3D cell culture provides an innovative tool to study epithelial tissue morphogenesis in a large field of view and to elucidate the regulation of growth, morphogenesis and differentiation in normal and cancerous human prostate cells. Moreover, such biosensor would be a powerful tool to follow cancer progression and to evaluate anti-cancer drugs.
Published: 2013
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18. Label-Free Electric Monitoring of Human Cancer Cells as a Potential Diagnostic Tool

Author: Xavier Gidrol, Frédérique Kermarrec, Thibault Honegger, David Peyrade, Clarisse Vaillier, Laboratoire des technologies de la microélectronique (LTM ), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])
Subjects: Electrophoresis, Static Electricity, Nanotechnology, 02 engineering and technology, 01 natural sciences, Analytical Chemistry, Cell Movement, Cell Line, Tumor, Lab-On-A-Chip Devices, Neoplasms, Humans, Early Cancer Detection, Electrodes, Early Detection of Cancer, ComputingMilieux_MISCELLANEOUS, Label free, [PHYS]Physics [physics], Chemistry, 010401 analytical chemistry, Equipment Design, Human cell, Dielectrophoresis, 021001 nanoscience & nanotechnology, 0104 chemical sciences, On cells, Neoplasms diagnosis, 0210 nano-technology, Biological system, Electrorotation, Human cancer
Abstract: Dielectrophoresis is widely used for cell characterization, and the exerted force on cells depends on the difference of polarizability between the latter and the surrounding medium. This physical phenomenon is translated by the real part of the Clausius-Mossotti factor. It is mostly modeled from the imaginary part, measured by electrorotation. The method described here measures experimentally the real part of the Clausius-Mossotti factor. It relies on the cell velocity when submitted to pure dielectrophoresis, and it was conducted on several human cell lines, at different times. A variety of cell lines was evaluated, from different organs or representative of different stages of cancer, with promising findings for early cancer detection.
Published: 2016
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19. Distinct outcomes of CRL-Nedd8 pathway inhibition reveal cancer cell plasticity

Author: Anastasia V, Rulina, Frédérique, Mittler, Patricia, Obeid, Sophie, Gerbaud, Laurent, Guyon, Eric, Sulpice, Frédérique, Kermarrec, Nicole, Assard, Monika E, Dolega, Xavier, Gidrol, and Maxim Y, Balakirev
Subjects: Male, NEDD8 Protein, Transcription, Genetic, Cell Survival, Ubiquitin-Protein Ligases, Cell Plasticity, Prostatic Neoplasms, Cyclopentanes, Models, Biological, Pyrimidines, Transcriptional Regulator ERG, Receptors, Androgen, Cell Line, Tumor, Gene Knockdown Techniques, Spheroids, Cellular, Humans, Cell Lineage, Original Article, Ubiquitins, Cell Proliferation, Signal Transduction
Abstract: Inhibition of protein degradation by blocking Cullin-RING E3 ligases (CRLs) is a new approach in cancer therapy though of unknown risk because CRL inhibition may stabilize both oncoproteins and tumor suppressors. Probing CRLs in prostate cancer cells revealed a remarkable plasticity of cells with TMPRSS2-ERG translocation. CRL suppression by chemical inhibition or knockdown of RING component RBX1 led to reversible G0/G1 cell cycle arrest that prevented cell apoptosis. Conversely, complete blocking of CRLs at a higher inhibitor dose-induced cytotoxicity that was amplified by knockdown of CRL regulator Cand1. We analyzed cell signaling to understand how varying degrees of CRL inhibition translated to distinct cell fates. Both tumor suppressor and oncogenic cell signaling pathways and transcriptional activities were affected, with pro-metastatic Wnt/β-catenin as the most upregulated. Suppression of the NF-κB pathway contributed to anti-apoptotic effect, and androgen receptor (AR) and ERG played decisive, though opposite, roles: AR was involved in protective quiescence, whereas ERG promoted apoptosis. These data define AR–ERG interaction as a key plasticity and survival determinant in prostate cancer and suggest supplementary treatments that may overcome drug resistance mechanisms regulated by AR–ERG interaction.
Published: 2016

20. Characterization of the transcriptional signature of C/EBPbeta isoforms (LAP/LIP) in Hep3B cells: Implication of LIP in pro-survival functions

Author: Xavier Gidrol, Jean-Louis Danan, Eric Sulpice, Martine Hiron, Jean-Philippe Salier, Simon Tendil, Gaëlle Saint-Auret, Maryvonne Daveau, and Celine A. Blache
Subjects: Gene isoform, Carcinoma, Hepatocellular, Paclitaxel, Transcription, Genetic, Cell Survival, Biology, Models, Biological, Transcriptome, Transcription (biology), Cell Line, Tumor, Humans, Protein Isoforms, Gene, Transcription factor, Cell Proliferation, Oligonucleotide Array Sequence Analysis, Cell Death, Hepatology, CCAAT-Enhancer-Binding Protein-beta, Gene Expression Profiling, Liver Neoplasms, digestive, oral, and skin physiology, Staurosporine, Cell biology, Gene expression profiling, Cell culture, Immunology, Genetic Engineering, Chromatin immunoprecipitation
Abstract: Background & Aims C/EBPbeta is an important mediator of several cellular processes, such as differentiation, proliferation, and survival of hepatic cells. However, a complete catalog of the targets of C/EBPbeta or the mechanism by which this transcription factor regulates certain liver-dependent pathways has not been clearly determined. Two major natural isoforms of this transcription factor exist: the liver-enriched activating protein (LAP) and the liver-enriched inhibitory protein (LIP), a functional LAP antagonist. In this study, we used the opposing transcriptional effects driven by LAP and LIP to determine the genuine C/EBPbeta molecular signature in the Hep3B human hepatoma cell line. We subsequently investigated the role of each of the LAP and LIP isoforms in drug-induced Hep3B cell death. Methods We engineered Hep3B cells with regulated LAP or LIP expression using the Tet-off expression system. The genes that showed inverse regulation by LAP and LIP were identified by cDNA array analysis. The cohort of direct-C/EBPbeta-targets was distinguished from indirect-targets by ChIP-on-chip analysis. Results We characterized 676 genes by this approach. Among these genes, 39 are novel direct targets of C/EBPbeta. Eleven of these new direct targets are involved in cell survival, suggesting critical roles for LAP/LIP isoforms in this cellular process. Therefore, we examined the effects of LAP and LIP over-expression on cell survival. We show that LIP promotes survival in staurosporine- or taxol-induced Hep3B cell death. Conclusions Our study provides new molecular and cellular insights into the role of C/EBPbeta in cells of hepatic origin.
Published: 2011
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21. Large scale RNAi screen reveals that the inhibitor of DNA binding 2 (ID2) protein is repressed by p53 family member p63 and functions in human keratinocyte differentiation

Author: Paul-Henri Romeo, Olivier Alibert, M A Viganò, David Castel, Ning Wu, Xavier Gidrol, Marie-Anne Debily, Kristiina Iljin, and Roberto Mantovani
Subjects: Keratinocytes, Cellular differentiation, Mitosis, Cell Cycle Proteins, Biology, Biochemistry, SDG 3 - Good Health and Well-being, E2F1, Gene silencing, Humans, Gene Regulation, RNA, Small Interfering, Promoter Regions, Genetic, Molecular Biology, Gene, Transcription factor, Inhibitor of Differentiation Protein 2, Regulation of gene expression, Tumor Suppressor Proteins, Nuclear Proteins, Promoter, Cell Differentiation, Cell Biology, Cell cycle, Phosphoproteins, Molecular biology, DNA-Binding Proteins, HEK293 Cells, Gene Expression Regulation, Tumor Suppressor Protein p53, Transcription Factors
Abstract: The inhibitor of DNA binding 2, dominant negative helix-loop-helix protein, ID2, acts as an oncogene and elevated levels of ID2 have been reported in several malignancies. Whereas some inducers of the ID2 gene have been characterized, little is known regarding the proteins capable to repress its expression. We developed siRNA microarrays to perform a large scale loss-of-function screen in human adult keratinocytes engineered to express GFP under the control of the upstream region of ID2 gene. We screened the effect of siRNA-dependent inhibition of 220 cancer-associated genes on the expression of the ID2::GFP reporter construct. Three genes NBN, RAD21, and p63 lead to a repression of ID2 promoter activity. Strikingly NBN and RAD21 are playing on major role in cell cycle progression and mitosis arrest. These results underline the pregnant need to silence ID2 expression at transcript level to promote cell cycle exit. Central to this inhibitory mechanism we find p63, a key transcription factor in epithelial development and differentiation, which binds specific cis-acting sequence within the ID2 gene promoter both in vitro and in vivo. P63 would not suppress ID2 expression, but would rather prevent excessive expression of that protein to enable the onset of keratinocyte differentiation.
Published: 2011
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22. 2D and 3D cell microarrays in pharmacology

Author: Xavier Gidrol, Nathalie Picollet-D'hahan, Lamya Ghenim, Vincent Haguet, Brigitte Fouque, and Béatrice Schaack
Subjects: Automation, Laboratory, Pharmacology, Miniaturization, Microarray, Drug discovery, Microarray analysis techniques, Cell, Cell Culture Techniques, Nanotechnology, Biology, Microarray Analysis, High-Throughput Screening Assays, medicine.anatomical_structure, Cell culture, Drug Discovery, medicine, Animals, Humans, Biological Assay, DNA microarray
Abstract: To analyze the phenotypic consequences of perturbing mammalian cells with drugs, there is an increasing need for systematic cell-based assays in an HTS format. Cell microarrays provide an attractive solution as they offer more than a simple miniaturization and mechanization of conventional microtiter plates. While standard monolayer two-dimensional culture conditions are poor mimics of the cellular environment in situ, microfabricated systems enable three-dimensional organotypic cell cultures and have the potential to provide biological insight not achievable before. This article compares different cell microarray formats and evaluates their potential use in the drug discovery process.
Published: 2009
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23. A 3D Toolbox to Enhance Physiological Relevance of Human Tissue Models

Author: Christophe A. Marquette, Xavier Gidrol, Nathalie Picollet-D'hahan, Séverine Le Gac, Monika E. Dolega, Donald K. Martin, and Lavinia Liguori
Subjects: 0301 basic medicine, Tissue Engineering, Tissue Scaffolds, Computer science, Cell Culture Techniques, METIS-321608, Bioengineering, Nanotechnology, 3d model, Computational biology, Microfluidic Analytical Techniques, Models, Biological, Toolbox, Extracellular Matrix, Molecular analysis, Organoids, 03 medical and health sciences, 030104 developmental biology, Tissue engineering, Tissue scaffolds, Tissue Array Analysis, Humans, Relevance (information retrieval), Cells, Cultured, Biotechnology
Abstract: We discuss the current challenges and future prospects of flow-based organoid models and 3D self-assembling scaffolds. The existing paradigm of 3D culture suffers from a lack of control over organoid size and shape; can be an obstacle for cell harvesting and extended cellular and molecular analysis; and does not provide access to the function of exocrine glands. Moreover, existing organ-on-chip models are mostly composed of 2D extracellular matrix (ECM)-coated elastomeric membranes that do not mimic real organ architectures. A new comprehensive 3D toolbox for cell biology has emerged to address some of these issues. Advances in microfabrication and cell-culturing approaches enable the engineering of sophisticated models that mimic organ 3D architectures and physiological conditions, while supporting flow-based drug screening and secretomics-based diagnosis.
Published: 2016

24. Time-lapse contact microscopy of cell cultures based on non-coherent illumination

Author: François Perraut, Nathalie Picollet-D'hahan, Francois Chatelain, Marion Gabriel, Vincent Haguet, Cyrille Pornin, Marc R. Block, Stéphane Gétin, Dorothée Balle, Stéphanie Bigault, Xavier Gidrol, Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Département d'Optronique (DOPT), Laboratoire d'Electronique et des Technologies de l'Information (CEA-LETI), Université Grenoble Alpes (UGA)-Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Direction de Recherche Technologique (CEA) (DRT (CEA)), Département Microtechnologies pour la Biologie et la Santé (DTBS), Institute for Advanced Biosciences / Institut pour l'Avancée des Biosciences (Grenoble) (IAB), Centre Hospitalier Universitaire [Grenoble] (CHU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Etablissement français du sang - Auvergne-Rhône-Alpes (EFS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives - Laboratoire d'Electronique et de Technologie de l'Information (CEA-LETI), Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Technologique (CEA) (DRT (CEA)), Dynamique des systèmes d'adhérence et différenciation (DySAD), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie structurale (IBS - UMR 5075 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Materials science, [SDV]Life Sciences [q-bio], Population, Cell Culture Techniques, Holography, Video microscopy, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Time-Lapse Imaging, Article, law.invention, Optics, Cell Movement, law, Microscopy, Cell Adhesion, Humans, Image sensor, education, Cells, Cultured, ComputingMilieux_MISCELLANEOUS, Cell Proliferation, education.field_of_study, Microscopy, Video, Multidisciplinary, business.industry, Ray, Pinhole (optics), Photonics, business
Abstract: Video microscopy offers outstanding capabilities to investigate the dynamics of biological and pathological mechanisms in optimal culture conditions. Contact imaging is one of the simplest imaging architectures to digitally record images of cells due to the absence of any objective between the sample and the image sensor. However, in the framework of in-line holography, other optical components, e.g., an optical filter or a pinhole, are placed underneath the light source in order to illuminate the cells with a coherent or quasi-coherent incident light. In this study, we demonstrate that contact imaging with an incident light of both limited temporal and spatial coherences can be achieved with sufficiently high quality for most applications in cell biology, including monitoring of cell sedimentation, rolling, adhesion, spreading, proliferation, motility, death and detachment. Patterns of cells were recorded at various distances between 0 and 1000 μm from the pixel array of the image sensors. Cells in suspension, just deposited or at mitosis focalise light into photonic nanojets which can be visualised by contact imaging. Light refraction by cells significantly varies during the adhesion process, the cell cycle and among the cell population in connection with every modification in the tridimensional morphology of a cell.
Published: 2015
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25. A kinome-targeted RNAi-based screen links FGF signaling to H2AX phosphorylation in response to radiation

Author: Vincent Frouin, Ning Wu, Amandine Pitaval, Paul-Henri Romeo, Xavier Gidrol, Claudie Lemercier, Alexandre Papine, Sami Benzina, Françoise Soussaline, Celine Lustremant, Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire de Neuroimagerie Assistée par Ordinateur (LNAO), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), IMSTAR, IMSTAR S.A., Institut Cochin (UMR_S567 / UMR 8104), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)
Subjects: Keratinocytes, DNA Repair, [SDV]Life Sciences [q-bio], Cell Cycle Proteins, DNA-Activated Protein Kinase, environment and public health, DSB, Phosphorylation cascade, Histones, 0302 clinical medicine, DNA Breaks, Double-Stranded, Kinome, γH2AX, Phosphorylation, RNA, Small Interfering, ComputingMilieux_MISCELLANEOUS, 0303 health sciences, Radiation, biology, Kinase, Nuclear Proteins, Chromatin, DNA-Binding Proteins, Histone, 030220 oncology & carcinogenesis, Molecular Medicine, RNA Interference, Signal transduction, biological phenomena, cell phenomena, and immunity, Research Article, Signal Transduction, DNA repair, Cell Line, 03 medical and health sciences, Cellular and Molecular Neuroscience, Humans, Mitogen-Activated Protein Kinase 8, Receptor, Fibroblast Growth Factor, Type 4, Molecular Biology, 030304 developmental biology, Pharmacology, JNK1, Cell Biology, Fibroblast Growth Factors, enzymes and coenzymes (carbohydrates), ATM, FGFR4, biology.protein, Cancer research
Abstract: A general radioprotective effect by fibroblast growth factor (FGF) has been extensively described since the early 1990s; however, the molecular mechanisms involved remain largely unknown. Radiation-induced DNA double-strand breaks (DSBs) lead to a complex set of responses in eukaryotic cells. One of the earliest consequences is phosphorylation of histone H2AX to form nuclear foci of the phosphorylated form of H2AX (γH2AX) in the chromatin adjacent to sites of DSBs and to initiate the recruitment of DNA-repair molecules. Upon a DSB event, a rapid signaling network is activated to coordinate DNA repair with the induction of cell-cycle checkpoints. To date, three kinases (ATM, ATR, and DNA-PK) have been shown to phosphorylate histone H2AX in response to irradiation. Here, we report a kinome-targeted small interfering RNA (siRNA) screen to characterize human kinases involved in H2AX phosphorylation. By analyzing γH2AX foci at a single-nucleus level, we identified 46 kinases involved either directly or indirectly in H2AX phosphorylation in response to irradiation in human keratinocytes. Furthermore, we demonstrate that in response to irradiation, the FGFR4 signaling cascade promotes JNK1 activation and direct H2AX phosphorylation leading, in turn, to more efficient DNA repair. This can explain, at least partially, the radioprotective effect of FGF. Electronic supplementary material The online version of this article (doi:10.1007/s00018-015-1901-7) contains supplementary material, which is available to authorized users.
Published: 2015
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26. Involvement of membrane proteins and ion channels on the self-rotation of human cells in a non-rotating AC electric field

Author: Clarisse Vaillier, Frédérique Kermarrec, David Peyrade, Xavier Gidrol, Thibault Honegger, Laboratoire des technologies de la microélectronique (LTM), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Clot, Marielle, Université Joseph Fourier - Grenoble 1 (UJF)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), and Laboratoire des technologies de la microélectronique [2001-2015] (LTM [2001-2015])
Subjects: Rotation, Cell Survival, [SDV]Life Sciences [q-bio], Clinical Biochemistry, Cell Culture Techniques, Nanotechnology, Biochemistry, Ion Channels, Analytical Chemistry, [PHYS] Physics [physics], Electricity, Humans, Ion channel, ComputingMilieux_MISCELLANEOUS, [PHYS]Physics [physics], Chemistry, HEK 293 cells, Membrane Proteins, Dielectrophoresis, Transmembrane protein, Membrane, HEK293 Cells, Membrane protein, Cytoplasm, Gene Knockdown Techniques, Cancer cell, Biophysics, RNA Interference
Abstract: International audience; Dielectrophoresis is a force that has been exploited in microsystems for label‐free characterization and separation of cells, when their electrical signature is known. However, the polarization effect of cells at the transmembrane protein level is not well established. In this work, we have use the self‐rotation effect of cells in a non‐rotating field, known as the “Quincke effect,” in order to measure the maximum rotation frequency (frotmax) of different cell populations when modifying the composition of their membrane. We investigated the influence of active ionic transportation of membrane protein concentration on frotmax of HEK cells. Our results show that ionic transportation is responsible for the reduction of conductivity within the cytoplasm, which results in higher frotmax. However, the influence of the concentration of proteins in the membrane, achieved by silencing gene expression in cancer cells, changes significantly frotmax, which is not explained by the changes of ionic conductivity within the cell.
Published: 2015
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27. Cell microarrays in drug discovery

Author: Marie-Anne Debily, Xavier Gidrol, Amandine Pitaval, and David Castel
Subjects: High-throughput screening, Cell, Protein Array Analysis, Gene Expression, Nanotechnology, Large range, Computational biology, Pharmaceutical technology, Drug Discovery, Cell Adhesion, medicine, Animals, Humans, Microtechnology, RNA, Small Interfering, Cells, Cultured, Oligonucleotide Array Sequence Analysis, Pharmacology, Extracellular Matrix Proteins, Drug discovery, business.industry, Reproducibility of Results, medicine.anatomical_structure, Tissue Array Analysis, Drug Design, RNA Interference, DNA microarray, business
Abstract: There is an increasing need for systematic cell-based assays in a high-throughput screening (HTS) format to analyze the phenotypic consequences of perturbing mammalian cells with drugs, genes, interfering RNA. Taking advantage of the recent progress in microtechnology, new cell microarrays are being developed and applied to a large range of issues in metazoan cells. This article compares different approaches and evaluates their potential use in the drug discovery process. Although still an emerging technology, cell microarrays hold great promise to optimize the efficiency:cost ratio in cell-based HTS.
Published: 2006
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28. DNA microarray allows molecular profiling of rheumatoid arthritis and identification of pathophysiological targets

Author: Xavier Gidrol, Amandine Pitaval, Gilles Chiocchia, Carlo Lucchesi, Sylvie Mistou, Maxime Breban, S Marion, P Anract, G Falgarone, Valérie Devauchelle, M Hamadouche, Franck Letourneur, O Alibert, M Dougados, X Ayral, Nicolas Cagnard, and Catherine Fournier
Subjects: Adult, Male, Microarray, Cathepsin L, Immunology, Gene Expression, Arthritis, Computational biology, Biology, Bioinformatics, Polymerase Chain Reaction, law.invention, Arthritis, Rheumatoid, DEAD-box RNA Helicases, GTP-Binding Proteins, law, Osteoarthritis, Synovial Fluid, Gene expression, Genetics, medicine, Humans, RNA, Messenger, Gene, Cells, Cultured, Genetics (clinical), Polymerase chain reaction, Aged, DNA Primers, Glycoproteins, Oligonucleotide Array Sequence Analysis, Aged, 80 and over, Reverse Transcriptase Polymerase Chain Reaction, Lactoylglutathione Lyase, Membrane Proteins, Nucleic Acid Hybridization, Middle Aged, medicine.disease, Cathepsins, Cysteine Endopeptidases, Clusterin, Real-time polymerase chain reaction, Gene chip analysis, Female, DNA microarray, RNA Helicases, Molecular Chaperones
Abstract: This study was undertaken to evaluate the possibility to obtain a molecular signature of rheumatoid arthritis (RA) comparatively osteoarthritis (OA), and to lay the bases to develop new diagnostic tools and identify new targets. Microarray technology was used for such an analysis. The gene expression profiles of synovial tissues from patients with confirmed RA, and patients with OA were established and compared. A set of 63 genes was selected, based, more specifically, on their overexpression or underexpression in RA samples compared to OA. Results for six of these genes have been verified by quantitative PCR using both samples identical to those used in the microarray experiments and entirely separate samples. Expression profile of the 48 known genes allowed the correct classification of additional RA and OA patients. Furthermore, the distinct expression of three of the selected genes was also studied by quantitative RT-PCR in cultured synovial cells. Detailed analysis of the expression profile of the selected genes provided evidence for dysregulated biological pathways, pointed out to chromosomal location and revealed novel genes potentially involved in RA. It is proposed that such an approach allows valuable diagnosis/prognostics tools in RA to be established and potential targets for combating the disease to be identified.
Published: 2004
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29. Point-of-care diagnostics for ricin exposure

Author: Chantal Mourton-Gilles, Dorothée Jary, Jean Berthier, Cathy Philippe, Mohamed Lemine Youba Diakite, Jérôme Rollin, Didier Sauvaire, Guillaume Delapierre, Xavier Gidrol, Génétique, immunothérapie, chimie et cancer (GICC), UMR 7292 CNRS [2012-2017] (GICC UMR 7292 CNRS), Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives - Laboratoire d'Electronique et de Technologie de l'Information (CEA-LETI), Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Agence Nationale de Sécurité du Médicament et des produits de santé, ANSM, Agence nationale de sécurité du médicament et des produits de santé [Saint-Denis] (ANSM), Laboratoire d'Exploration Fonctionnelle des Génomes (LEFG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7), Département Microtechnologies pour la Biologie et la Santé (DTBS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Technologique (CEA) (DRT (CEA)), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Université de Tours-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Electronique et des Technologies de l'Information (CEA-LETI), Université Grenoble Alpes (UGA)-Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Direction de Recherche Technologique (CEA) (DRT (CEA)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG)
Subjects: Theranostic Nanomedicine, Point-of-care testing, Point-of-Care Systems, [SDV]Life Sciences [q-bio], Biomedical Engineering, Host response, Poison control, Bioengineering, Biological Warfare Agents, Ricin, Computer security, computer.software_genre, Biochemistry, chemistry.chemical_compound, Cartridge, Mice, Lab-On-A-Chip Devices, Animals, Humans, ComputingMilieux_MISCELLANEOUS, Whole blood, Mice, Inbred BALB C, Chromatography, General Chemistry, 3. Good health, Ricin toxin, chemistry, computer
Abstract: A long-sought milestone in the defense against bioterrorism is the development of rapid, simple, and near-patient assays for diagnostic and theranostic purposes. Here, we present a powerful test based on a host response to a biological weapon agent, namely the ricin toxin. A signature for exposure to ricin was extracted and characterized in mice and then integrated into a plastic microfluidic cartridge. This enabled early diagnosis of exposure to ricin in mice using a drop of whole blood in less than 1 h and 30 min. The cartridge stores the reagents and implements all of the steps of the analysis, including mRNA extraction from a drop of blood, followed by tens of parallel RT-qPCR reactions. The simple and low-cost microfluidic cartridge developed here may find other applications in point-of-care diagnostics.
Published: 2015
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30. A statistically inferred microRNA network identifies breast cancer target miR-940 as an actin cytoskeleton regulator

Author: Vincent Haguet, Stéphanie Combe, Ricky Bhajun, Christian Lajaunie, Xavier Gidrol, Amandine Pitaval, Eric Sulpice, Patricia Obeid, Laurent Guyon, Itebeddine Ghorbel, Biomicrotechnologie et génomique fonctionnelle (BIOMICS), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Centre de Bioinformatique (CBIO), MINES ParisTech - École nationale supérieure des mines de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Cancer et génome: Bioinformatique, biostatistiques et épidémiologie d'un système complexe, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), ANR et CEA, Mines Paris - PSL (École nationale supérieure des mines de Paris), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Centre de Géosciences (GEOSCIENCES), MINES ParisTech - École nationale supérieure des mines de Paris-PSL Research University (PSL), and MINES ParisTech, Bibliothèque
Subjects: Kinase, Mesenchymal Transition, [SDV]Life Sciences [q-bio], Cells, Gene regulatory network, Gene-Expression, Breast Neoplasms, Biology, Discovery, Article, Cell Movement, Myosin, microRNA, Gene expression, Humans, Gene Regulatory Networks, Disease, ComputingMilieux_MISCELLANEOUS, Cellular Senescence, Cell Proliferation, Monomeric GTP-Binding Proteins, Genetics, Regulation of gene expression, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Multidisciplinary, Gene Expression Profiling, Computational Biology, Molecular Sequence Annotation, Animal Development, Actin cytoskeleton, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Cell biology, Gene Expression Regulation, Neoplastic, Gene expression profiling, Actin Cytoskeleton, MicroRNAs, Gene Ontology, Female, Databases, Nucleic Acid, Prediction, Signal Transduction
Abstract: International audience; MiRNAs are key regulators of gene expression. By binding to many genes, they create a complex network of gene co-regulation. Here, using a network-based approach, we identified miRNA hub groups by their close connections and common targets. In one cluster containing three miRNAs, miR-612, miR-661 and miR-940, the annotated functions of the co-regulated genes suggested a role in small GTPase signalling. Although the three members of this cluster targeted the same subset of predicted genes, we showed that their overexpression impacted cell fates differently. miR-661 demonstrated enhanced phosphorylation of myosin II and an increase in cell invasion, indicating a possible oncogenic miRNA. On the contrary, miR-612 and miR-940 inhibit phosphorylation of myosin II and cell invasion. Finally, expression profiling in human breast tissues showed that miR-940 was consistently downregulated in breast cancer tissues M icroRNAs are a class of endogenous, small (19–25 nucleotides), single-stranded non-coding RNAs that regulate gene expression in all eukaryotic organisms. In metazoans, microRNAs most commonly bind to the 39 untranslated region (39UTR) of their mRNA target transcript and cause translational repression and/or mRNA degradation. Every microRNA is predicted to regulate from a dozen to thousands of genes, including transcription factors. This fine-tuning of protein expression is known to be involved in many physiological processes, such as development, apoptosis, signal transduction and even cancer progression 1,2. More than 2,000 mature human microRNAs are listed in the 20 th release of miRBase: http://www.mirbase.org (2014) (Date of access:19/08/2013), and some authors hypothesise that the majority of human genes are regulated by microRNAs 3. Since their discovery in 1993 4 , a fair understanding of their role in animal development and in the onset and progression of diseases 2 , as well as of their potential use in therapies 5 , has been gathered. However, the cooperative behaviour of microRNAs is still under investigation. A growing body of experimental evidence suggests that microRNAs can regulate genes through complementarity, meaning that microRNAs can act together to regulate individual genes or groups of genes involved in similar processes 6. For example, Hu and co-workers demonstrated that transducing a cocktail of precursor microRNAs (miR-21, miR-24 and miR-221) can result in more effective engraftment of transplanted cardiac progenitor cells 7. Consistent with these discoveries, Zhu et al. demonstrated that miR-21 and miR-221 coregulate 56 gene ontology (GO) processes 8. In the same study, the authors also showed that cotransfection of miR-1 and miR-21 increases H 2 O 2-induced myocardial apoptosis and oxidative stress. These recent findings support the idea of microRNA-mediated cooperative regulation but also argue for the use of systemic approaches, notably based on graph theory, to decipher individual and complementary roles of microRNAs. Some work has been conducted to use recent high-throughput experiment-derived data sets to infer microRNA synergistic relationships 9–12. Herein, we present a microRNA network based on target similarities among microRNAs to infer clusters of microRNAs. Clusters are defined as groups of microRNAs sharing a set of common targets, predicted by either DIANA-microT v3 13 or TargetScan v6.2 14. Some authors have used GO enrichment analysis as a confirmatory tool for their clustering approach 11. In our case, GO enrichment is not used to infer networks but as a way to estimate the probable metabolic pathway(s) a cluster of microRNAs could co-regulate. Moreover, the novelty of our approach is to consider not only clusters of microRNAs but also OPEN
Published: 2015
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31. Erratum: A large-scale RNAi screen identifies LCMR1 as a critical regulator of Tspan8-mediated melanoma invasion

Author: Odile Berthier-Vergnes, Laetitia Barbollat-Boutrand, Xavier Gidrol, T Voeltzel, Emmanuelle Berger, Eric Sulpice, Jérôme Lamartine, Manale El Kharbili, Ingrid Masse, Françoise Degoul, A de la Fouchardière, Ricky Bhajun, G Agaësse, Centre de génétique et de physiologie moléculaire et cellulaire (CGPhiMC), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, Biologie à Grande Echelle, Institut National de la Santé et de la Recherche Médicale (INSERM), Imagerie Moléculaire et Therapie Vectorisee, Université d'Auvergne - Clermont-Ferrand I (UdA), Département de Biopathologie, Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC), Cardiovasculaire, métabolisme, diabétologie et nutrition (CarMeN), Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National de la Recherche Agronomique (INRA), Centre de Recherche en Cancérologie de Lyon (UNICANCER/CRCL), Centre Léon Bérard [Lyon]-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), French Society for Dermatological Research (SRD), La Ligue Contre le Cancer (Comite Ardeche), association 'Vaincre le Melanome', Roche Company, Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université d'Auvergne (Clermont Ferrand 1) (UdA), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hospices Civils de Lyon (HCL), Centre de Recherche en Cancérologie de Lyon (CRCL), Université de Lyon-Université de Lyon-Centre Léon Bérard [Lyon]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives - Laboratoire d'Electronique et de Technologie de l'Information (CEA-LETI), Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Centre Jean Perrin [Clermont-Ferrand] (UNICANCER/CJP), UNICANCER, Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Laboratoire de Planétologie et Géodynamique [UMR 6112] (LPG), Université d'Angers (UA)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG)
Subjects: 0301 basic medicine, Male, mélanome, Cancer Research, Skin Neoplasms, Tetraspanins, [SDV]Life Sciences [q-bio], cancer de la peau, medicine.disease_cause, métastase, Molecular oncology, Mice, 0302 clinical medicine, RNA interference, Vemurafenib, Melanoma, ComputingMilieux_MISCELLANEOUS, cellular proliferation, Mediator Complex, Tumor Protein, Translationally-Controlled 1, Cell cycle, 3. Good health, 030220 oncology & carcinogenesis, invasion cellulaire, Heterografts, RNA Interference, medicine.drug, Signal Transduction, endocrine system, Mice, Nude, [SDV.CAN]Life Sciences [q-bio]/Cancer, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, Transfection, 03 medical and health sciences, Cell Line, Tumor, medicine, Genetics, PTEN, Animals, Humans, Neoplasm Invasiveness, Molecular Biology, prolifération cellulaire, medicine.disease, 030104 developmental biology, Immunology, Cancer research, biology.protein, Skin cancer, Carcinogenesis
Abstract: Melanoma is the deadliest form of skin cancer owing to its proclivity to metastasise, and recently developed therapies have not yielded the expected results, because almost all patients relapse. Therefore, understanding the molecular mechanisms that underlie early invasion by melanoma cells is crucial to improving patient survival. We have previously shown that, whereas the Tetraspanin 8 protein (Tspan8) is undetectable in normal skin and benign lesions, its expression arises with the progression of melanoma and is sufficient to increase cell invasiveness. Therefore, to identify Tspan8 transcriptional regulators that could explain the onset of Tspan8 expression, thereby conferring an invasive phenotype, we performed an innovative RNA interference-based screen, which, for the first time, identified several Tspan8 repressors and activators, such as GSK3 beta, PTEN, IQGAP1, TPT1 and LCMR1. LCMR1 is a recently identified protein that is overexpressed in numerous carcinomas; its expression and role, however, had not previously been studied in melanoma. The present study identified Tspan8 as the first LCMR1 target that could explain its function in carcinogenesis. LCMR1 modulation was sufficient to positively regulate endogenous Tspan8 expression, with concomitant in vitro phenotypic changes such as loss of melanoma cell-matrix adherence and increase in invasion, and Tspan8 expression promoted tumourigenicity in vivo. Moreover, LCMR1 and Tspan8 overexpression were shown to correlate in melanoma lesions, and both proteins could be downregulated in vitro by vemurafenib. In conclusion, this study highlights the importance of Tspan8 and its regulators in the control of early melanoma invasion and suggests that they may be promising new therapeutic targets downstream of the RAF-MEK-ERK signalling pathway.
Published: 2017
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32. High-throughput monitoring of major cell functions by means of lensfree video microscopy

Author: Fabien Momey, Xavier Gidrol, S. Vinjimore Kesavan, Nelly Dubrulle, Eric Sulpice, Jean-Marc Dinten, Brigitte David-Watine, Olivier Cioni, Bernard Chalmond, D. Freida, Spencer L. Shorte, Cédric Allier, Commissariat à l'énergie atomique et aux énergies alternatives - Laboratoire d'Electronique et de Technologie de l'Information (CEA-LETI), Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Imagerie Dynamique (Plate-Forme) (PFID), Institut Pasteur [Paris] (IP), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Centre de Mathématiques et de Leurs Applications (CMLA), École normale supérieure - Cachan (ENS Cachan)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris], Laboratoire d'Electronique et des Technologies de l'Information ( CEA-LETI ), Université Grenoble Alpes ( UGA ) -Direction de Recherche Technologique (CEA) ( DRT (CEA) ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Imagerie Dynamique (Plate-Forme) ( PFID ), Université de Cergy Pontoise ( UCP ), Université Paris-Seine, Centre de Mathématiques et de Leurs Applications ( CMLA ), École normale supérieure - Cachan ( ENS Cachan ) -Centre National de la Recherche Scientifique ( CNRS ), and Bertacchi Griffi, Nathalie
Subjects: Programmed cell death, Cell division, [SDV]Life Sciences [q-bio], Primary Cell Culture, Cell, Population, Video Recording, Cell Count, Video microscopy, Biology, Article, Cell Line, Tumor, Cell Adhesion, medicine, Humans, RNA, Small Interfering, education, [ SDV.IB.IMA ] Life Sciences [q-bio]/Bioengineering/Imaging, education.field_of_study, Microscopy, Video, Osteoblasts, Multidisciplinary, Cell Death, Mesenchymal stem cell, [ SDV.BC.BC ] Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Mesenchymal Stem Cells, Transfection, Fibroblasts, Cell biology, [SDV] Life Sciences [q-bio], medicine.anatomical_structure, Cell culture, Cell Division
Abstract: International audience; Quantification of basic cell functions is a preliminary step to understand complex cellular mechanisms, for e.g., to test compatibility of biomaterials, to assess the effectiveness of drugs and siRNAs, and to control cell behavior. However, commonly used quantification methods are label-dependent, and end-point assays. As an alternative, using our lensfree video microscopy platform to perform high-throughput real-time monitoring of cell culture, we introduce specifically devised metrics that are capable of non-invasive quantification of cell functions such as cell-substrate adhesion, cell spreading, cell division, cell division orientation and cell death. Unlike existing methods, our platform and associated metrics embrace entire population of thousands of cells whilst monitoring the fate of every single cell within the population. This results in a high content description of cell functions that typically contains 25,000 - 900,000 measurements per experiment depending on cell density and period of observation. As proof of concept, we monitored cell-substrate adhesion and spreading kinetics of human Mesenchymal Stem Cells (hMSCs) and primary human fibroblasts, we determined the cell division orientation of hMSCs, and we observed the effect of transfection of siCellDeath (siRNA known to induce cell death) on hMSCs and human Osteo Sarcoma (U2OS) Cells.
Published: 2014
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33. An EWOD-based microfluidic chip for single-cell isolation, mRNA purification and subsequent multiplex qPCR

Author: Dorothée Jary, Yves Fouillet, G. Castellan, A. Bellemin-Comte, Xavier Gidrol, C. Delattre, A. Rival, Commissariat à l'énergie atomique et aux énergies alternatives - Laboratoire d'Electronique et de Technologie de l'Information (CEA-LETI), Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG)
Subjects: [SDV]Life Sciences [q-bio], Microfluidics, Biomedical Engineering, Bioengineering, Nanotechnology, 02 engineering and technology, Computational biology, Cell Separation, Cellular level, Biology, 01 natural sciences, Biochemistry, Cell Line, Single-cell analysis, Humans, Multiplex, Cell isolation, RNA, Messenger, ComputingMilieux_MISCELLANEOUS, Ability to work, 010401 analytical chemistry, General Chemistry, Equipment Design, Microfluidic Analytical Techniques, 021001 nanoscience & nanotechnology, 0104 chemical sciences, Microfluidic chip, Electrowetting, 0210 nano-technology, Multiplex Polymerase Chain Reaction
Abstract: Single cell analysis circumvents the need to average data from large populations by observing each cell individually, thus enabling the analysis of cell-to-cell variability. The ability to work on this scale presents many new opportunities for the life sciences and biomedical applications. Microfluidics has become a tool of choice for such studies and electrowetting on dielectric (EWOD) technology is well adapted for samples with reduced size and biological studies at the single cell level. In the present manuscript, for the first time, we present an integrated and automated system based on EWOD that can process the complete workflow on a single device, from the isolation of a single cell to mRNA purification and gene expression analysis.
Published: 2014
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34. Immunogenic calreticulin exposure occurs through a phylogenetically conserved stress pathway involving the chemokine CXCL8

Author: Michael Durchschlag, Lorenzo Galluzzi, Frank Madeo, Mickaël Michaud, L Zitvogel, Laura Senovilla, E Sulpice, Erika Vacchelli, Frédéric Schlemmer, Yuting Ma, Antonella Sistigu, Christoph Ruckenstuhl, Isabelle Martins, Abdul Qader Sukkurwala, Guido Kroemer, Oliver Kepp, Wang Y, Xavier Gidrol, Schlumberger, Institut de biologie et chimie des protéines [Lyon] (IBCP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Princeton University, Institut Gustave Roussy (IGR), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Service d'Oncologie Médicale [CHRU Besançon], Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Immunologie des tumeurs et immunothérapie (UMR 1015), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Gustave Roussy (IGR)-Université Paris-Sud - Paris 11 (UP11), Apoptose, cancer et immunité (U848), Université Paris-Sud - Paris 11 (UP11)-Institut Gustave Roussy (IGR)-Institut National de la Santé et de la Recherche Médicale (INSERM), Plateforme de métabolomique, Direction de la recherche [Gustave Roussy], Institut Gustave Roussy (IGR)-Institut Gustave Roussy (IGR), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)
Subjects: musculoskeletal diseases, Chemokine, Saccharomyces cerevisiae Proteins, [SDV]Life Sciences [q-bio], Chemokine CXCL2, Antineoplastic Agents, Apoptosis, Saccharomyces cerevisiae, Receptors, Interleukin-8B, Receptors, Interleukin-8A, Mice, Immune system, Cell Line, Tumor, Neoplasms, Animals, Humans, CXC chemokine receptors, Autocrine signalling, Molecular Biology, ComputingMilieux_MISCELLANEOUS, Original Paper, Mice, Inbred BALB C, biology, Interleukin-8, Dendritic Cells, Cell Biology, HCT116 Cells, Cell biology, Mice, Inbred C57BL, CXCL2, Cancer cell, biology.protein, Mitoxantrone, Signal transduction, Calreticulin, Transcriptome, HeLa Cells, Signal Transduction
Abstract: The exposure of calreticulin (CRT) on the surface of stressed and dying cancer cells facilitates their uptake by dendritic cells and the subsequent presentation of tumor-associated antigens to T lymphocytes, hence stimulating an anticancer immune response. The chemotherapeutic agent mitoxantrone (MTX) can stimulate the peripheral relocation of CRT in both human and yeast cells, suggesting that the CRT exposure pathway is phylogenetically conserved. Here, we show that pheromones can act as physiological inducers of CRT exposure in yeast cells, thereby facilitating the formation of mating conjugates, and that a large-spectrum inhibitor of G protein-coupled receptors (which resemble the yeast pheromone receptor) prevents CRT exposure in human cancer cells exposed to MTX. An RNA interference screen as well as transcriptome analyses revealed that chemokines, in particular human CXCL8 (best known as interleukin-8) and its mouse ortholog Cxcl2, are involved in the immunogenic translocation of CRT to the outer leaflet of the plasma membrane. MTX stimulated the production of CXCL8 by human cancer cells in vitro and that of Cxcl2 by murine tumors in vivo. The knockdown of CXCL8/Cxcl2 receptors (CXCR1/Cxcr1 and Cxcr2) reduced MTX-induced CRT exposure in both human and murine cancer cells, as well as the capacity of the latter-on exposure to MTX-to elicit an anticancer immune response in vivo. Conversely, the addition of exogenous Cxcl2 increased the immunogenicity of dying cells in a CRT-dependent manner. Altogether, these results identify autocrine and paracrine chemokine signaling circuitries that modulate CRT exposure and the immunogenicity of cell death.
Published: 2014
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35. Human bone marrow mesenchymal stem cells regulate biased DNA segregation in response to cell adhesion asymmetry

Author: Séverine Lecourt, Xavier Gidrol, Laurent Guyon, Valérie Vanneaux, Gaëlle Letort, Jérôme Larghero, Audrey Cras, Delphine Freida, Manuel Thery, Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Unité de Thérapie Cellulaire, Hopital St Louis, Laboratoire de physiologie cellulaire végétale (LPCV), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Institut de Biosciences et de Biotechnologies de Grenoble (ex-IRTSV) (BIG), Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), European Research Council [ERC-310472], Agence National pour la Recherche [ANR-05PRIB01103, ANR-10-IBHU-0002], Martin-Laffon, Jacqueline, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Larghero, Jerome, Thery, Manuel, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Grenoble Alpes (UGA)
Subjects: Cell type, Cell division, Cellular differentiation, micropatterns, Bone Marrow Cells, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Chromatids, Biology, General Biochemistry, Genetics and Molecular Biology, Chromosome segregation, 03 medical and health sciences, 0302 clinical medicine, Chromosome Segregation, Humans, Sister chromatids, human, Cell adhesion, lcsh:QH301-705.5, Mitosis, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, Metaphase, 030304 developmental biology, Genetics, mitosis, 0303 health sciences, mesenchymal stem cells, spatial distribution, Mesenchymal stem cell, Cell Differentiation, cell adhesion, DNA, Fibroblasts, Fibronectins, Cell biology, lcsh:Biology (General), Cell Division, 030217 neurology & neurosurgery
Abstract: International audience; Biased DNA segregation is a mitotic event in which the chromatids carrying the original template DNA strands and those carrying the template copies are not segregated randomly into the two daughter cells. Biased segregation has been observed in several cell types, but not in human mesenchymal stem cells (hMSCs), and the factors affecting this bias have yet to be identified. Here, we have investigated cell adhesion geometries as a potential parameter by plating hMSCs from healthy donors on fibronectin-coated micropatterns. On symmetric micropatterns, the segregation of sister chromatids to the daughter cells appeared random. In contrast, on asymmetric micropatterns, the segregation was biased. This sensitivity to asymmetric extracellular cues was reproducible in cells from all donors but was not observed in human skin-derived fibroblasts or in a fibroblastic cell line used as controls. We conclude that the asymmetry of cell adhesion is a major factor in the regulation of biased DNA segregation in hMSCs.
Published: 2013
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36. The opportunistic pathogen Pseudomonas aeruginosa activates the DNA double-strand break signaling and repair pathway in infected cells

Author: Véronique Collin-Faure, Sylvie Elsen, Xavier Gidrol, Claudie Lemercier, Lemercier, Claudie, Pathogénie bactérienne et réponses cellulaires, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Institut de Biosciences et de Biotechnologies de Grenoble (ex-IRTSV) (BIG), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), This work was supported by the Institut National de la Santé et de la Recherche Médicale (INSERM), the Commissariat à l'Energie Atomique et aux Energies Renouvelables (CEA), the Centre National de la Recherche Scientifique (CNRS) and the Université Joseph Fourier (UJF Grenoble)., Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Grenoble Alpes (UGA), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA)
Subjects: MESH: Signal Transduction, DNA Repair, MESH: ADP Ribose Transferases, [SDV]Life Sciences [q-bio], MESH: DNA Breaks, Double-Stranded, Ataxia Telangiectasia Mutated Proteins, medicine.disease_cause, Histones, chemistry.chemical_compound, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Chromosome instability, DNA Breaks, Double-Stranded, H2AX, Phosphorylation, MESH: Ataxia Telangiectasia Mutated Proteins, MESH: Bacterial Proteins, ADP Ribose Transferases, MESH: DNA Repair, MESH: Histones, 0303 health sciences, biology, Kinase, Intracellular Signaling Peptides and Proteins, DNA double strand breaks, 3. Good health, [SDV] Life Sciences [q-bio], Histone, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Pseudomonas aeruginosa, MESH: Pseudomonas aeruginosa, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Molecular Medicine, Signal transduction, Tumor Suppressor p53-Binding Protein 1, Infection, Signal Transduction, MESH: Cell Line, Tumor, DNA repair, Bacterial Toxins, HL-60 Cells, [SDV.CAN]Life Sciences [q-bio]/Cancer, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Microbiology, MESH: Chromosomal Instability, 03 medical and health sciences, Cellular and Molecular Neuroscience, Bacterial Proteins, [SDV.CAN] Life Sciences [q-bio]/Cancer, MESH: HL-60 Cells, Cell Line, Tumor, Chromosomal Instability, MESH: Intracellular Signaling Peptides and Proteins, medicine, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, 030304 developmental biology, Pharmacology, MESH: Humans, MESH: Phosphorylation, 030306 microbiology, Mutagenesis, JNK Mitogen-Activated Protein Kinases, Cell Biology, MESH: JNK Mitogen-Activated Protein Kinases, chemistry, MESH: Bacterial Toxins, ATM, biology.protein, DNA
Abstract: International audience; Highly hazardous DNA double-strand breaks can be induced in eukaryotic cells by a number of agents including pathogenic bacterial strains. We have investigated the genotoxic potential of Pseudomonas aeruginosa, an opportunistic pathogen causing devastating nosocomial infections in cystic fibrosis or immunocompromised patients. Our data revealed that infection of immune or epithelial cells by P. aeruginosa triggered DNA strand breaks and phosphorylation of histone H2AX (γH2AX), a marker of DNA double-strand breaks. Moreover, it induced formation of discrete nuclear repair foci similar to gamma-irradiation-induced foci, and containing γH2AX and 53BP1, an adaptor protein mediating the DNA-damage response pathway. Gene deletion, mutagenesis, and complementation in P. aeruginosa identified ExoS bacterial toxin as the major factor involved in γH2AX induction. Chemical inhibition of several kinases known to phosphorylate H2AX demonstrated that Ataxia Telangiectasia Mutated (ATM) was the principal kinase in P. aeruginosa-induced H2AX phosphorylation. Finally, infection led to ATM kinase activation by an auto-phosphorylation mechanism. Together, these data show for the first time that infection by P. aeruginosa activates the DNA double-strand break repair machinery of the host cells. This novel information sheds new light on the consequences of P. aeruginosa infection in mammalian cells. As pathogenic Escherichia coli or carcinogenic Helicobacter pylori can alter genome integrity through DNA double-strand breaks, leading to chromosomal instability and eventually cancer, our findings highlight possible new routes for further investigations of P. aeruginosa in cancer biology and they identify ATM as a potential target molecule for drug design.
Published: 2013
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37. Cardiac Glycosides Exert Anticancer Effects by Inducing Immunogenic Cell Death

Author: Laurie Menger, Lorenzo Galluzzi, Xavier Gidrol, Mickaël Michaud, Erika Vacchelli, Grégoire Mignot, Yuting Ma, Eric Sulpice, François Ghiringhelli, Nazanine Modjtahedi, Fabrice Andre, Frédéric Schlemmer, Clara Locher, Guido Kroemer, Takahiro Yamazaki, Oliver Kepp, Isabelle Martins, Sandy Adjemian, Laurence Zitvogel, Shensi Shen, Abdul Qader Sukkurwala, Laboratoire Réactions et Génie des Procédés (LRGP), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Lecor-Esitpa, DAM Île-de-France (DAM/DIF), Direction des Applications Militaires (DAM), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Centre Hospitalier de Meaux, Biomicrotechnologie et génomique fonctionnelle (BIOMICS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Département d'oncologie médicale [Centre Georges-François Leclerc], Centre Régional de Lutte contre le cancer Georges-François Leclerc [Dijon] (UNICANCER/CRLCC-CGFL), UNICANCER-UNICANCER, Radiothérapie moléculaire (UMR 1030), Université Paris-Sud - Paris 11 (UP11)-Institut Gustave Roussy (IGR)-Institut National de la Santé et de la Recherche Médicale (INSERM), Apoptose, cancer et immunité (U848), Centre de Thermique de Lyon (CETHIL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA), Service d'Oncologie Médicale [CHRU Besançon], Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Institut de biologie et chimie des protéines [Lyon] (IBCP), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), and Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Programmed cell death, Digoxin, Organoplatinum Compounds, medicine.medical_treatment, [SDV]Life Sciences [q-bio], Antineoplastic Agents, Biosensing Techniques, Biology, Pharmacology, Cardiac Glycosides, 03 medical and health sciences, Mice, 0302 clinical medicine, Immune system, Cell Line, Tumor, Neoplasms, medicine, Animals, Humans, Anthracyclines, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Chemotherapy, General Medicine, medicine.disease, 3. Good health, Oxaliplatin, Cell culture, 030220 oncology & carcinogenesis, Hepatocellular carcinoma, Cancer cell, Immunogenic cell death, medicine.drug
Abstract: Some successful chemotherapeutics, notably anthracyclines and oxaliplatin, induce a type of cell stress and death that is immunogenic, hence converting the patient's dying cancer cells into a vaccine that stimulates antitumor immune responses. By means of a fluorescence microscopy platform that allows for the automated detection of the biochemical hallmarks of such a peculiar cell death modality, we identified cardiac glycosides (CGs) as exceptionally efficient inducers of immunogenic cell death, an effect that was associated with the in- hibition of the plasma membrane Na + - and K + -dependent adenosine triphosphatase (Na + /K + -ATPase). CGs ex- acerbated the antineoplastic effects of DNA-damaging agents in immunocompetent but not immunodeficient mice. Moreover, cancer cells succumbing to a combination of chemotherapy plus CGs could vaccinate synge- neic mice against a subsequent challenge with living cells of the same type. Finally, retrospective clinical analy- ses revealed that the administration of the CG digoxin during chemotherapy had a positive impact on overall survival in cohorts of breast, colorectal, head and neck, and hepatocellular carcinoma patients, especially when they were treated with agents other than anthracyclines and oxaliplatin.
Published: 2012
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38. p63 regulates human keratinocyte proliferation via MYC-regulated gene network and differentiation commitment through cell adhesion-related gene network

Author: Ingrid Masse, JÃ©rome Rollin, Xavier Gidrol, JÃ©rÃ´me Lamartine, Ning Wu, Neurobiologie génétique et intégrative (NGI), Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Exploration Fonctionnelle des Génomes (LEFG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7), Génétique moléculaire, signalisation et cancer (GMSC), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Centre de génétique et de physiologie moléculaire et cellulaire (CGPhiMC), Laboratoire Biopuces (BIOPUCES), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon
Subjects: Keratinocytes, MESH: Signal Transduction, Cell, MESH: beta Catenin, Gene regulatory network, Biochemistry, MESH: Cell Cycle Checkpoints, MESH: Down-Regulation, 0302 clinical medicine, Cell Movement, MESH: RNA, Small Interfering, Gene Regulatory Networks, RNA, Small Interfering, MESH: Cell Movement, beta Catenin, MESH: Gene Regulatory Networks, 0303 health sciences, Receptors, Notch, integumentary system, Wnt signaling pathway, Cell Differentiation, MESH: Keratinocytes, Cell biology, MESH: Wnt Proteins, medicine.anatomical_structure, Gene Knockdown Techniques, 030220 oncology & carcinogenesis, MESH: Membrane Proteins, Keratinocyte, Signal Transduction, MESH: Cell Differentiation, Notch signaling pathway, Down-Regulation, Cell fate determination, Biology, MESH: Cell Adhesion, Proto-Oncogene Proteins c-myc, 03 medical and health sciences, MESH: Cell Proliferation, Cell Adhesion, medicine, MESH: Proto-Oncogene Proteins c-myc, Humans, Gene Regulation, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Cell adhesion, Molecular Biology, Cell Proliferation, 030304 developmental biology, MESH: Humans, Cell growth, MESH: Transcriptome, Membrane Proteins, Cell Cycle Checkpoints, Cell Biology, MESH: Gene Knockdown Techniques, Wnt Proteins, stomatognathic diseases, Cancer research, sense organs, Transcriptome, MESH: Receptors, Notch
Abstract: International audience; Although p63 and MYC are important in the control of epidermal homeostasis, the underlying molecular mechanisms governing keratinocyte proliferation or differentiation downstream of these two genes are not completely understood. By analyzing the transcriptional changes and phenotypic consequences of the loss of either p63 or MYC in human developmentally mature keratinocytes, we have characterized the networks acting downstream of these two genes to control epidermal homeostasis. We show that p63 is required to maintain growth and to commit to differentiation by two distinct mechanisms. Knockdown of p63 led to down-regulation of MYC via the Wnt/β-catenin and Notch signaling pathways and in turn reduced keratinocyte proliferation. We demonstrate that a p63-controlled keratinocyte cell fate network is essential to induce the onset of keratinocyte differentiation. This network contains several secreted proteins involved in cell migration/adhesion, including fibronectin 1 (FN1), interleukin-1β (IL1B), cysteine-rich protein 61 (CYR61), and jagged-1 (JAG1), that act downstream of p63 as key effectors to trigger differentiation. Our results characterized for the first time a connection between p63 and MYC and a cell adhesion-related network that controls differentiation. Furthermore, we show that the balance between the MYC-controlled cell cycle progression network and the p63-controlled cell adhesion-related network could dictate skin cell fate.
Published: 2012
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39. The miR-17 family links p63 protein to MAPK signaling to promote the onset of human keratinocyte differentiation

Author: Ning Wu, Frédérique Kermarrec, Sami Benzina, Stéphanie Combe, Patricia Obeid, Eric Sulpice, and Xavier Gidrol
Subjects: Keratinocytes, Skin Physiology, Anatomy and Physiology, MAPK signaling cascades, MAP Kinase Signaling System, Cellular differentiation, MAPK8, lcsh:Medicine, Biology, Signal transduction, Cell Line, RNA interference, Molecular cell biology, microRNA, Keratin, Genetics, Gene silencing, Humans, Mitogen-Activated Protein Kinase 9, Mitogen-Activated Protein Kinase 8, lcsh:Science, Transcription factor, Skin, chemistry.chemical_classification, Multidisciplinary, integumentary system, Tumor Suppressor Proteins, lcsh:R, Signaling cascades, Cell Differentiation, Genomics, Keratin 1, Antigens, Differentiation, Cell biology, Functional Genomics, MicroRNAs, chemistry, lcsh:Q, Gene expression, Transcriptome, Genome Expression Analysis, Transcription Factors, Research Article, Developmental Biology
Abstract: The p63 protein plays a key role in regulating human keratinocyte proliferation and differentiation. Although some p63-regulating microRNAs (miRNAs) have been identified in the control of epidermal homeostasis, little is known about miRNAs acting downstream of p63. In this paper, we characterized multiple p63-regulated miRNAs (miR-17, miR-20b, miR-30a, miR-106a, miR-143 and miR-455-3p) and elucidated their roles in the onset of keratinocyte differentiation. We identified RB, p21 and multiple MAPKs as targets of these p63-controlled miRNAs. Upon inhibition of most of these miRNAs, we observed defects in commitment to differentiation that could be reversed by siRNA-mediated silencing of their targets. Furthermore, knockdown of MAPK8 and MAPK9 efficiently restored expression of the early differentiation markers keratin 1 and keratin 10 in p63-silenced primary human keratinocytes. These results highlight new mechanistic roles of multiple miRNAs, particularly the miR-17 family (miR-17, miR-20b and miR-106a), as regulatory intermediates for coordinating p63 with MAPK signaling in the commitment of human mature keratinocytes to early differentiation.
Published: 2012

40. Pre-microRNA and Mature microRNA in Human Mitochondria

Author: Eric Barrey, Xavier Gidrol, Orane Boyer, Blandine Bonnamy, Gaëlle Saint-Auret, Dominique Damas, Unité de biologie intégrative des adaptations à l'exercice (UBIAE), Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire Biopuces (BIOPUCES), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), This study was supported jointly by the Genopole d'Evry (ATIGE), the 'Institut National de la Sante' et de la Recherche Me' dicale' (INSERM), 'Commissariat a' l'Energie Atomique' (CEA) and the 'Institut de la Recherche Agronomique' (INRA)., Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, World Mitochondria Society. INT., AgroParisTech-Institut National de la Recherche Agronomique (INRA), Barrey, Eric, and Gidrol, Xavier
Subjects: Microfluidics, Oligonucleotides, Mitochondrion, Myoblasts, Molecular cell biology, 0302 clinical medicine, RNA interference, Gene expression, RNA Precursors, In Situ Hybridization, ComputingMilieux_MISCELLANEOUS, energetics, 0303 health sciences, Multidisciplinary, mtDNA, apoptosis, Cell Differentiation, Genomics, MESH: Genetics and Genomics, mitochondria, gene expression, microrna, Functional Genomics, Mitochondria, RNA silencing, 030220 oncology & carcinogenesis, Medicine, RNA extraction, DNA Probes, Research Article, Mitochondrial DNA, Science, MESH: Developmental Biology, Molecular Sequence Data, miRNA importation, post-transcription regulation, Biology, DNA, Mitochondrial, 03 medical and health sciences, microRNA, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, 030304 developmental biology, Base Sequence, MESH: Molecular Biology, RNA, Molecular biology, MicroRNAs, Genome, Mitochondrial, RNA transport, Digoxigenin, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Developmental Biology
Abstract: Chantier qualité GA; International audience; BACKGROUND: Because of the central functions of the mitochondria in providing metabolic energy and initiating apoptosis on one hand and the role that microRNA (miRNA) play in gene expression, we hypothesized that some miRNA could be present in the mitochondria for post-transcriptomic regulation by RNA interference. We intend to identify miRNA localized in the mitochondria isolated from human skeletal primary muscular cells. METHODOLOGY/PRINCIPAL FINDINGS: To investigate the potential origin of mitochondrial miRNA, we in-silico searched for microRNA candidates in the mtDNA. Twenty five human pre-miRNA and 33 miRNA aligments (E-value35) for the smallest RNA input concentration and 204 miRNA for the maximum RNA input concentration. In silico analysis predicted 80 putative miRNA target sites in the mitochondrial genome (E-value
Published: 2011
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41. Gene association networks from microarray data using a regularized estimation of partial correlation based on PLS regression

Author: Arthur Tenenhaus, Vincent Guillemot, Xavier Gidrol, and Vincent Frouin
Subjects: Clustering high-dimensional data, T-Lymphocytes, Genes, myc, Context (language use), Biology, Machine learning, computer.software_genre, Sensitivity and Specificity, Gene interaction, Partial least squares regression, Databases, Genetic, Genetics, Escherichia coli, Humans, Computer Simulation, Gene Regulatory Networks, Graphical model, Least-Squares Analysis, Partial correlation, Oligonucleotide Array Sequence Analysis, Covariance matrix, business.industry, Applied Mathematics, Computational Biology, Reproducibility of Results, Pattern recognition, Regression, Genes, Bacterial, Area Under Curve, Artificial intelligence, business, computer, Algorithms, Biotechnology, Signal Transduction
Abstract: Reconstruction of gene-gene interactions from large-scale data such as microarrays is a first step toward better understanding the mechanisms at work in the cell. Two main issues have to be managed in such a context: 1) choosing which measures have to be used to distinguish between direct and indirect interactions from high-dimensional microarray data and 2) constructing networks with a low proportion of false-positive edges. We present an efficient methodology for the reconstruction of gene interaction networks in a small-sample-size setting. The strength of independence of any two genes is measured, in such "high-dimensional network," by a regularized estimation of partial correlation based on Partial Least Squares Regression. We finally emphasize specific properties of the proposed method. To assess the sensitivity and specificity of the method, we carried out the reconstruction of networks from simulated data. We also tested PLS-based partial correlation network on static and dynamic real microarray data. An R implementation of the proposed algorithm is available from http://biodev.extra.cea.fr/plspcnetwork/.
Published: 2010

42. The Intracellular Localization of ID2 Expression Has a Predictive Value in Non Small Cell Lung Cancer

Author: Xavier Gidrol, C. Blechet, Arthur Tenenhaus, Serge Guyétant, Sandra Regina, Jérôme Rollin, El Rassi, Karine, Laboratoire d'Exploration Fonctionnelle des Génomes (LEFG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7), Pathologies Respiratoires : Protéolyse et Aérosolthérapie, Université de Tours (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire d'anatomie pathologique, Laboratoire, service d'hématologie-hémostase, Supélec Sciences des Systèmes (E3S), Ecole Supérieure d'Electricité - SUPELEC (FRANCE), and Université de Tours-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: Oncology, medicine.medical_specialty, Lung Neoplasms, Colorectal cancer, Cellular differentiation, Protein Array Analysis, lcsh:Medicine, Biology, 03 medical and health sciences, Prostate cancer, 0302 clinical medicine, Breast cancer, Transcription (biology), Carcinoma, Non-Small-Cell Lung, Internal medicine, Tumor Cells, Cultured, medicine, Humans, Prospective Studies, lcsh:Science, Lung cancer, Transcription factor, Oncology/Lung Cancer, Inhibitor of Differentiation Protein 2, 030304 developmental biology, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], 0303 health sciences, Multidisciplinary, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], lcsh:R, Genetics and Genomics/Gene Expression, Cell Differentiation, medicine.disease, Immunohistochemistry, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Pathology/Molecular Pathology, 3. Good health, Tumor progression, 030220 oncology & carcinogenesis, Cancer research, lcsh:Q, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Research Article
Abstract: BACKGROUND: ID2 is a member of a subclass of transcription regulators belonging to the general bHLH (basic-helix-loop-helix) family of transcription factors. In normal cells, ID2 is responsible for regulating the balance between proliferation and differentiation. More recent studies have demonstrated that ID2 is involved in tumor progression in several cancer types such as prostate or breast. METHODOLOGY/PRINCIPAL FINDINGS: In this work, we investigated, for the first time, the relationship between the expression of ID2 in non-small cell lung cancer (NSCLC) patients and the clinicopathological features and prognosis of these patients. Immunohistochemistry was performed on tissue microarrays, which included 62 NSCLC tumors. In malignant tissues, ID2 expression has been detected in both the nuclear and cytoplasmic compartments, but we have demonstrated that only nuclear expression of ID2 is inversely correlated with the differentiation grade of the tumor (p = 0.007). Interestingly, among patients with poorly differentiated tumors, high nuclear expression of ID2 was an independent and unfavorable prognostic factor for survival (p = 0.036). CONCLUSIONS: These results suggest that ID2 could be involved in tumor dedifferentiation processes of NSCLC, and could be used as prognostic marker for patients with poorly differentiated tumors.
Published: 2009

43. Prostaglandin E2 regulates B cell proliferation through a candidate tumor suppressor, Ptger4

Author: Xavier Gidrol, Olivier Alibert, Ning Wu, Jernej Murn, and Simon Tendil
Subjects: CD30, Lymphoma, Formal, Inbred C57BL, Medical and Health Sciences, Mice, hemic and lymphatic diseases, Receptors, Immunology and Allergy, 2.1 Biological and endogenous factors, Genes, Tumor Suppressor, Aetiology, B-cell lymphoma, Receptor, Inbred BALB C, Oligonucleotide Array Sequence Analysis, Cancer, Mice, Knockout, Mice, Inbred BALB C, B-Lymphocytes, Social Control, Prostaglandin E, Articles, Hematology, Survival Rate, medicine.anatomical_structure, lipids (amino acids, peptides, and proteins), Female, Signal transduction, Tumor Suppressor, Signal Transduction, Biotechnology, Lymphoma, B-Cell, Knockout, B-cell receptor, Immunology, EP4 Receptor, Biology, Article, Dinoprostone, Rare Diseases, Clinical Research, medicine, Receptors, Prostaglandin E, Animals, Humans, B cell, Cell Proliferation, Cell growth, Gene Expression Profiling, B-Cell, medicine.disease, Molecular biology, Social Control, Formal, Mice, Inbred C57BL, Gene Expression Regulation, Genes, Cancer research, EP4 Subtype, Receptors, Prostaglandin E, EP4 Subtype, Neoplasm Transplantation
Abstract: B cell receptor (BCR) signaling contributes to the pathogenesis of B cell malignancies, and most B cell lymphomas depend on BCR signals for survival. Identification of genes that restrain BCR-mediated proliferation is therefore an important goal toward improving the therapy of B cell lymphoma. Here, we identify Ptger4 as a negative feedback regulator of proliferation in response to BCR signals and show that its encoded EP4 receptor is a principal molecule conveying the growth-suppressive effect of prostaglandin E2 (PGE2). Stable knockdown of Ptger4 in B cell lymphoma markedly accelerated tumor spread in mice, whereas Ptger4 overexpression yielded significant protection. Mechanistically, we show that the intrinsic activity of Ptger4 and PGE2–EP4 signaling target a similar set of activating genes, and find Ptger4 to be significantly down-regulated in human B cell lymphoma. We postulate that Ptger4 functions in B cells as a candidate tumor suppressor whose activity is regulated by PGE2 in the microenvironment. These findings suggest that targeting EP4 receptor for prostaglandin may present a novel strategy for treatment of B cell malignancies.
Published: 2008

44. Cell microarray for functional exploration of genomes

Author: David, Castel, Marie-Anne, Debily, Amandine, Pitaval, and Xavier, Gidrol
Subjects: Genome, Tissue Array Analysis, Nucleic Acids, Green Fluorescent Proteins, Animals, Humans, Gene Silencing, Transfection, Cells, Cultured
Abstract: As more genomes are sequenced, challenge of rapidly unraveling the functions of genes was faced. To that end, cell microarrays have been recently described that permit transfection of thousands of nucleic acids in parallel and enable the analysis of phenotypic consequences of such perturbations. As many parameters can influence the efficiency of transfection and consequently protein expression or extinction, some important features in manufacturing cell microarrays for functional exploration of genomes were described.
Published: 2007

45. Broad modulation of gene expression in CD4+ lymphocyte subpopulations in response to low doses of ionizing radiation

Author: Aurélie Vaurijoux, Peggy Maltère, Gaëtan Gruel, Cyrille Petat, Xavier Gidrol, Philippe Voisin, Pascale Voisin, Sandrine Roch-Lefèvre, Eric Gregoire, Laurence Roy, Laboratoire de dosimétrie biologique (DRPH/SRBE/LDB), Institut de Radioprotection et de Sûreté Nucléaire (IRSN), Service de Génomique Fonctionnelle, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire de dosimétrie biologique (IRSN/DRPH/SRBE/LDB), Service de RadioBiologie et d'Epidémiologie (IRSN/DRPH/SRBE), and Institut de Radioprotection et de Sûreté Nucléaire (IRSN)-Institut de Radioprotection et de Sûreté Nucléaire (IRSN)
Subjects: CD4-Positive T-Lymphocytes, Male, cycline, protein synthesis, Lymphocyte, [SDV]Life Sciences [q-bio], complementary DNA, Ionizing radiation, cyclin dependent kinase inhibitor 1A, low energy radiation, human experiment, 0302 clinical medicine, Gene expression, Cells, Cultured, Whole blood, Regulation of gene expression, 0303 health sciences, Cultured, Radiation, adult, article, CD8 antigen, Middle Aged, protein DDB2, unclassified drug, medicine.anatomical_structure, priority journal, 030220 oncology & carcinogenesis, CD4 antigen, ionizing radiation, protein Bax, radiation response, Cells, CD56 antigen, Biophysics, oxidative phosphorylation, Biology, Radiation Dosage, Dose-Response Relationship, 03 medical and health sciences, medicine, Humans, Radiology, Nuclear Medicine and imaging, controlled study, Irradiation, human, normal human, protein expression, 030304 developmental biology, growth arrest and DNA damage inducible protein 45, human cell, DNA microarray, CD4 lymphocyte count, cell type, Dose-Response Relationship, Radiation, Molecular biology, human tissue, Gene Expression Regulation, Gene chip analysis, RNA, lymphocyte subpopulation, CD8
Abstract: To compare me responses of the different lymphocyte sub-types after an exposure of whole blood to low doses of ionizing radiation, we examined variations in gene expression in different lymphocyte subpopulations using microarray technology. Blood samples from five healthy donors were independently exposed to 0 (sham irradiation), 0.05 and 0.5 Gy of ionizing radiation. Three and 24 h after exposure, CD56+, CD4+ and CD8+ cells were negatively isolated. RNA from each set of experimental conditions was competitively hybridized on 25k oligonucleotide microarrays. Modifications of gene expression were measured after both intervals and in all cell types. Twenty-four hours after exposure to 0.5 Gy, we observed an induction of the expression of BAX, PCNA, GADD45, DDB2 and CDKNIA. However, the numbers of modulated genes greatly differed between cell types. In particular, 3 h after exposure to doses as low as 0.05 Gy, the number of down-modulated genes was 10 times greater for CD4+ cells than for all other cell types. Moreover, most of these repressed genes were taking part in the cell processes of protein biosynthesis and oxidative phosphorylation. The results suggest that several biological pathways in CD4+ cells could be sensitive to low doses of radiation. Therefore, specifically studying CD4+ cells could help to understand the mechanisms involved in low-dose response and allow their detection.
Published: 2007
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46. New p63 targets in keratinocytes identified by a genome-wide approach

Author: Roberto Mantovani, Eleonora Candi, Carlotta Castagnoli, Daniele Merico, Xavier Gidrol, Amelie Robert, Daniela Alotto, M. Alessandra Vigano, Gerry Melino, Jérôme Lamartine, Barbara Testoni, Centre de génétique et de physiologie moléculaire et cellulaire (CGPhiMC), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, Conservation des espèces, restauration et suivi des populations (CERSP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Toxicology Unit, University of Leicester, Laboratoire d'Exploration Fonctionnelle des Génomes (LEFG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7), Responsible for operational MIPAS mission calibration for ESA from 2002 to 2005 &ndash, Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Conservation des espèces, Restauration et Suivi des Populations (CERSP), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN), and Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Keratinocytes, Organogenesis, Transactivation, 0302 clinical medicine, Chlorocebus aethiops, MESH: Animals, MESH: Tumor Suppressor Protein p53, Skin, 0303 health sciences, p63, Targets, integumentary system, Settore BIO/11, MESH: Protein Array Analysis, General Neuroscience, Cell Differentiation, MESH: Keratinocytes, DNA-Binding Proteins, MESH: COS Cells, CpG site, 030220 oncology & carcinogenesis, COS Cells, Protein Binding, Gene isoform, Transcriptional Activation, MESH: Cell Differentiation, MESH: Trans-Activators, Protein Array Analysis, Biology, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, Animals, Humans, MESH: Protein Binding, MESH: Tumor Suppressor Proteins, Molecular Biology, Transcription factor, Gene, 030304 developmental biology, MESH: Humans, General Immunology and Microbiology, Tumor Suppressor Proteins, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, ChIP-on-chip, ChIP on chip, Molecular biology, MESH: Cercopithecus aethiops, MESH: Organogenesis, Gene chip analysis, Trans-Activators, MESH: Transcriptional Activation, Tumor Suppressor Protein p53, Chromatin immunoprecipitation, MESH: DNA-Binding Proteins, Transcription Factors
Abstract: International audience; p63 is a developmentally regulated transcription factor related to p53. It is involved in the development of ectodermal tissues, including limb, skin and in general, multilayered epithelia. The DeltaNp63alpha isoform is thought to play a 'master' role in the asymmetric division of epithelial cells. It is also involved in the pathogenesis of several human diseases, phenotypically characterized by ectodermal dysplasia. Our understanding of transcriptional networks controlled by p63 is limited, owing to the low number of bona fide targets. To screen for new targets, we employed chromatin immunoprecipitation from keratinocytes (KCs) coupled to the microarray technology, using both CpG islands and promoter arrays. The former revealed 96 loci, the latter yielded 85 additional genes. We tested 40 of these targets in several functional assays, including: (i) in vivo binding by p63 in primary KCs; (ii) expression analysis in differentiating HaCaT cells and in cells overexpressing DeltaNp63alpha; (iii) promoter transactivation and (iv) immunostaining in normal tissues, confirming their regulation by p63. We discovered several new specific targets whose functional categorization links p63 to cell growth and differentiation.
Published: 2006
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47. An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes

Author: Philippe Kastner, Philippe Dessen, Christine Bole-Feysot, Paul A. Lyons, Virginie Virolle, Philippe Rostagno, Franck Amiot, Gary Williams, Chimène Moreilhon, Pascal Barbry, Bernard Jost, Roslin Russell, Erdogan Gulari, Xavier Gidrol, Géraldine Rios, Virginie Defamie, Kevin Le Brigand, Virginie Magnone, Tom C. Freeman, Jean Marie Rouillard, Bernard Mari, Institut de pharmacologie moléculaire et cellulaire (IPMC), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), MRC Rosalind Franklin Centre for Genomics Research, Department of Chemical Engineering, University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System, Biodiscovery LLC, Institut de génétique et biologie moléculaire et cellulaire (IGBMC), Université Louis Pasteur - Strasbourg I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Service de Génomique Fonctionnelle, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire de Génétique Oncologique, Institut Gustave Roussy (IGR)-Centre National de la Recherche Scientifique (CNRS), Réseau National des Génopoles, the GIP Aventis, the French Ministry of Industry (Réseau GenHomme), the French Association Vaincre la Mucoviscidose, the INCA, the CNRS, the UK Medical Research Council, Université Nice Sophia Antipolis (... - 2019) (UNS), and Kervella, Jacqueline
Subjects: Microarray, Transcription, Genetic, MESH: Oligonucleotide Probes, In silico, [SDV.GEN] Life Sciences [q-bio]/Genetics, Biology, MESH: Databases, Nucleic Acid, MESH: Expressed Sequence Tags, Transcriptome, 03 medical and health sciences, MESH: Gene Expression Profiling, Mice, 0302 clinical medicine, Genetics, Animals, Humans, MESH: Animals, MESH: Mice, 030304 developmental biology, Oligonucleotide Array Sequence Analysis, Expressed Sequence Tags, 0303 health sciences, Expressed sequence tag, [SDV.GEN]Life Sciences [q-bio]/Genetics, Internet, MESH: Humans, Oligonucleotide, MESH: Transcription, Genetic, Gene Expression Profiling, Gene expression profiling, MESH: Internet, Oligonucleotide Microarray, 030220 oncology & carcinogenesis, MESH: Oligonucleotide Array Sequence Analysis, Methods Online, DNA microarray, Databases, Nucleic Acid, Oligonucleotide Probes
Abstract: Two collections of oligonucleotides have been designed for preparing pangenomic human and mouse microarrays. A total of 148,993 and 121,703 oligonucleotides were designed against human and mouse transcripts. Quality scores were created in order to select 25,342 human and 24,109 mouse oligonucleotides. They correspond to: (i) a BLAST-specificity score; (ii) the number of expressed sequence tags matching each probe; (iii) the distance to the 3' end of the target mRNA. Scores were also used to compare in silico the two microarrays with commercial microarrays. The sets described here, called RNG/MRC collections, appear at least as specific and sensitive as those from the commercial platforms. The RNG/MRC collections have now been used by an Anglo-French consortium to distribute more than 3500 microarrays to the academic community. Ad hoc identification of tissue-specific transcripts and a approximately 80% correlation with hybridizations performed on Affymetrix GeneChiptrade mark suggest that the RNG/MRC microarrays perform well. This work provides a comprehensive open resource for investigators working on human and mouse transcriptomes, as well as a generic method to generate new microarray collections in other organisms. All information related to these probes, as well as additional information about commercial microarrays have been stored in a freely-accessible database called MEDIANTE.
Published: 2006
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48. Human side population keratinocytes exhibit long-term proliferative potential and a specific gene expression profile and can form a pluristratified epidermis

Author: Nicolas O. Fortunel, Olivia Zobiri, Gaëlle Larderet, Peggy Maltère, Michèle T. Martin, Gilles Waksman, Marine Cegalerba, Pierre Vaigot, and Xavier Gidrol
Subjects: Adult, Keratinocytes, Cell signaling, Time Factors, Population, Cell Separation, Biology, In Vitro Techniques, Colony-Forming Units Assay, Side population, Gene expression, Humans, Progenitor cell, education, Cells, Cultured, Cell Proliferation, Oligonucleotide Array Sequence Analysis, education.field_of_study, Gene Expression Profiling, Stem Cells, Cell Differentiation, Cell Biology, Cell sorting, Molecular biology, Haematopoiesis, Epidermal Cells, Cell culture, Molecular Medicine, Female, Epidermis, Developmental Biology
Abstract: The aim of the present study was to characterize human side population (SP) epidermal keratinocytes isolated from primary cell cultures. For that purpose, keratinocytes were isolated from normal adult breast skin samples and the Hoechst 33342 exclusion assay described for hematopoietic cells was adapted to keratinocytes. Three types of keratinocytes were studied: the SP, the main population (MP), and the unsorted initial population. SP keratinocytes represented 0.16% of the total population. In short-term cultures, they exhibited an increased colony-forming efficiency and produced more actively growing colonies than did unsorted and MP keratinocytes. In long-term cultures, SP cells exhibited an extensive expansion potential, performing a mean of 44 population doublings for up to 12 successive passages after cell sorting. Moreover, even in long-term cultures, SP keratinocytes were able to form a pluristratified epidermis when seeded on a dermal substrate. Unsorted and MP keratinocytes promoted a reduced expansion: mean values of 14 population doublings for five passages and 12 population doublings for four successive passages, respectively. To further characterize SP cells, cDNA microarrays were used to identify their molecular signature. Transcriptome profiling showed that 41 genes were differentially expressed in SP (vs. MP) cells, with 37 upregulated genes and only four downregulated genes in SP cells. The majority of these genes were functionally related to the regulation of transcription and cell signaling. In conclusion, SP human keratinocytes isolated from primary cultures exhibited both short- and long-term high proliferative potential, formed a pluristratified epidermis, and were characterized by a specific gene expression profile.
Published: 2005

49. Low-dose exposure to gamma rays induces specific gene regulations in normal human keratinocytes

Author: Jérôme Lamartine, Cyrille Petat, Michèle T. Martin, Frédérick Libert, Xavier Gidrol, Vincent Frouin, Pascale Le Minter, Noreli Franco, and Jean-Jacques Leplat
Subjects: Regulation of gene expression, Keratinocytes, Radiation, Epidermis (botany), Biophysics, Dose-Response Relationship, Radiation, Biology, Radiation Dosage, Ionizing radiation, Cell biology, Gene Expression Regulation, Gamma Rays, Immunology, Dosimetry, Humans, Radiology, Nuclear Medicine and imaging, Irradiation, DNA microarray, Gene, Transcription factor, Cells, Cultured, Skin, Transcription Factors
Abstract: Skin is the organ most exposed to various environmental aggressors, including ionizing radiation. Low-dose and low-dose-rate exposures to gamma rays account for most occupational, medical or environmental irradiations. To examine whether this type of exposure triggers specific molecular responses, cultured primary keratinocytes isolated from adult normal skin were irradiated with single acute doses of 1 cGy or 2 Gy. DNA microarrays containing 10,500 probes were used to assess transcriptional changes over a time course between 3 and 72 h postirradiation. Keratinocytes were studied at a differentiated stage to mimic the response of cells from the suprabasal layers of the epidermis. A major finding of this study was the identification of an important number of low-dose-specific genes (140), most of which were modulated at 48 h. Clustering analysis also revealed low-dose-specific profiles. One of these clusters (17 known genes) was further analyzed using Gibbs sampling algorithm, which led to the identification of 7 putative promoter sequences. These results show for the first time that low-dose ionizing radiation is able to induce specific transcriptional responses in human keratinocytes. Our findings support the potential usefulness of microarrays in biological dosimetry studies after low-dose exposures.
Published: 2005

50. [Cell microarrays and functional genomics]

Author: Yoann, Roupioz, David, Castel, Amandine, Pitaval, Sandrine, Baghdoyan, and Xavier, Gidrol
Subjects: Humans, Genomics, Transfection, Cells, Cultured, Oligonucleotide Array Sequence Analysis
Abstract: With the complete sequencing of the human genome, research priorities have shifted from the identification of genes to the elucidation of their function. Methods currently used by scientists to characterize gene function, such as knock-out mice, are based upon loss of protein function and analysis of the resulting phenotypes to infer a potential role for the protein under scrutiny. Until now, these methods have been successful but time consuming and only a few genes at a time could be analyzed. Cell microarrays allow to simultaneously transfect thousands of different nucleic acid molecules, RNA or DNA, into adherent cells. It is then possible to analyze a large pallet of resulting phenotypes in clusters of transfected cells. We are currently manufacturing cell microarrays with collections of full-length cDNA cloned in expression vectors (gain of function analyses) or siRNA (loss of function studies) to unravel function of genes involved in differentiation and proliferation of human cells. Although there are still some technological difficulties to overcome, the potential for cell microarrays to speed up functional exploration of genomes is very promising.
Published: 2005

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