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Auvré F, Coutier J, Martin MT, Fortunel NO. Quantitative Detection of Low-Abundance Transcripts at Single-Cell Level in Human Epidermal Keratinocytes by Digital Droplet Reverse Transcription-Polymerase Chain Reaction. Methods Mol Biol 2018; 1879:31-41. [PMID: 29736807 DOI: 10.1007/7651_2018_149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Genetic and epigenetic characterization of the large cellular diversity observed within tissues is essential to understanding the molecular networks that ensure the regulation of homeostasis, repair, and regeneration, but also pathophysiological processes. Skin is composed of multiple cell lineages and is therefore fully concerned by this complexity. Even within one particular lineage, such as epidermal keratinocytes, different immaturity statuses or differentiation stages are represented, which are still incompletely characterized. Accordingly, there is presently great demand for methods and technologies enabling molecular investigation at single-cell level. Also, most current methods used to analyze gene expression at RNA level, such as RT-qPCR, do not directly provide quantitative data, but rather comparative ratios between two conditions. A second important need in skin biology is thus to determine the number of RNA molecules in a given cell sample. Here, we describe a workflow that we have set up to meet these specific needs, by means of transcript quantification in cellular micro-samples using flow cytometry sorting and reverse transcription-digital droplet polymerase chain reaction. As a proof-of-principle, the workflow was tested for the detection of transcription factor transcripts expressed at low levels in keratinocyte precursor cells. A linear correlation was found between quantification values and keratinocyte input numbers in a low quantity range from 40 cells to 1 cell. Interpretable signals were repeatedly obtained from single-cell samples corresponding to estimated expression levels as low as 10-20 transcript copies per keratinocyte or less. The present workflow may have broad applications for the detection and quantification of low-abundance nucleic acid species in single cells, opening up perspectives for the study of cell-to-cell genetic and molecular heterogeneity. Interestingly, the process described here does not require internal references such as house-keeping gene expression, as it is initiated with defined cell numbers, precisely sorted by flow cytometry.
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Affiliation(s)
- Frédéric Auvré
- Laboratoire de Génomique et Radiobiologie de la Kératinopoïèse, CEA/DRF/IBFJ/IRCM, Evry, France.,INSERM U967, Fontenay-aux-Roses, France.,Université Paris-Diderot, Paris 7, France.,Université Paris-Saclay, Paris 11, France
| | - Julien Coutier
- Laboratoire de Génomique et Radiobiologie de la Kératinopoïèse, CEA/DRF/IBFJ/IRCM, Evry, France.,INSERM U967, Fontenay-aux-Roses, France.,Université Paris-Diderot, Paris 7, France.,Université Paris-Saclay, Paris 11, France
| | - Michèle T Martin
- Laboratoire de Génomique et Radiobiologie de la Kératinopoïèse, CEA/DRF/IBFJ/IRCM, Evry, France.,INSERM U967, Fontenay-aux-Roses, France.,Université Paris-Diderot, Paris 7, France.,Université Paris-Saclay, Paris 11, France
| | - Nicolas O Fortunel
- Laboratoire de Génomique et Radiobiologie de la Kératinopoïèse, CEA/DRF/IBFJ/IRCM, Evry, France. .,INSERM U967, Fontenay-aux-Roses, France. .,Université Paris-Diderot, Paris 7, France. .,Université Paris-Saclay, Paris 11, France.
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Comparison of Cellular Alterations in Fat Cells Harvested With Laser-Assisted Liposuction and Suction-Assisted Liposuction. J Craniofac Surg 2016; 27:631-5. [DOI: 10.1097/scs.0000000000002589] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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Sevilla LM, Latorre V, Carceller E, Boix J, Vodák D, Mills IG, Pérez P. Glucocorticoid receptor and Klf4 co-regulate anti-inflammatory genes in keratinocytes. Mol Cell Endocrinol 2015; 412:281-9. [PMID: 26001834 DOI: 10.1016/j.mce.2015.05.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 05/14/2015] [Accepted: 05/14/2015] [Indexed: 10/23/2022]
Abstract
The glucocorticoid (GC) receptor (GR) and Kruppel-like factor Klf4 are transcription factors that play major roles in skin homeostasis. However, whether these transcription factors cooperate in binding genomic regulatory regions in epidermal keratinocytes was not known. Here, we show that in dexamethasone-treated keratinocytes GR and Klf4 are recruited to genomic regions containing adjacent GR and KLF binding motifs to control transcription of the anti-inflammatory genes Tsc22d3 and Zfp36. GR- and Klf4 loss of function experiments showed total GR but partial Klf4 requirement for full gene induction in response to dexamethasone. In wild type keratinocytes induced to differentiate, GR and Klf4 protein expression increased concomitant with Tsc22d3 and Zfp36 up-regulation. In contrast, GR-deficient cells failed to differentiate or fully induce Klf4, Tsc22d3 and Zfp36 correlating with increased expression of the epithelium-specific Trp63, a known transcriptional repressor of Klf4. The identified transcriptional cooperation between GR and Klf4 may determine cell-type specific regulation and have implications for developing therapies for skin diseases.
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Affiliation(s)
- Lisa M Sevilla
- Instituto de Biomedicina de Valencia-Consejo Superior de Investigaciones Científicas (IBV-CSIC), Jaime Roig 11, E-46010 Valencia, Spain
| | - Víctor Latorre
- Instituto de Biomedicina de Valencia-Consejo Superior de Investigaciones Científicas (IBV-CSIC), Jaime Roig 11, E-46010 Valencia, Spain; Faculty of Human and Medical Sciences, The University of Manchester, Manchester, UK
| | - Elena Carceller
- Instituto de Biomedicina de Valencia-Consejo Superior de Investigaciones Científicas (IBV-CSIC), Jaime Roig 11, E-46010 Valencia, Spain
| | - Julia Boix
- Instituto de Biomedicina de Valencia-Consejo Superior de Investigaciones Científicas (IBV-CSIC), Jaime Roig 11, E-46010 Valencia, Spain
| | - Daniel Vodák
- Bioinformatics Core Facility, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Norway
| | - Ian Geoffrey Mills
- Prostate Cancer Research Group, Centre for Molecular Medicine (Norway), University of Oslo and Oslo University Hospitals, Oslo, Norway; Department of Molecular Oncology, Oslo University Hospitals, Oslo, Norway; Department of Urology, Oslo University Hospitals, Oslo, Norway; FASTMAN Movember Centre of Excellence, CCRCB, Queens University, Belfast, UK
| | - Paloma Pérez
- Instituto de Biomedicina de Valencia-Consejo Superior de Investigaciones Científicas (IBV-CSIC), Jaime Roig 11, E-46010 Valencia, Spain.
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Parrish JZ, Kim CC, Tang L, Bergquist S, Wang T, Derisi JL, Jan LY, Jan YN, Davis GW. Krüppel mediates the selective rebalancing of ion channel expression. Neuron 2014; 82:537-44. [PMID: 24811378 DOI: 10.1016/j.neuron.2014.03.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2014] [Indexed: 12/27/2022]
Abstract
Ion channel gene expression can vary substantially among neurons of a given type, even though neuron-type-specific firing properties remain stable and reproducible. The mechanisms that modulate ion channel gene expression and stabilize neural firing properties are unknown. In Drosophila, we demonstrate that loss of the Shal potassium channel induces the compensatory rebalancing of ion channel expression including, but not limited to, the enhanced expression and function of Shaker and slowpoke. Using genomic and network modeling approaches combined with genetic and electrophysiological assays, we demonstrate that the transcription factor Krüppel is necessary for the homeostatic modulation of Shaker and slowpoke expression. Remarkably, Krüppel induction is specific to the loss of Shal, not being observed in five other potassium channel mutants that cause enhanced neuronal excitability. Thus, homeostatic signaling systems responsible for rebalancing ion channel expression can be selectively induced after the loss or impairment of a specific ion channel.
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Affiliation(s)
- Jay Z Parrish
- Department of Biology, University of Washington, Seattle, WA 98195, USA.
| | - Charles C Kim
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA 94110, USA.
| | - Lamont Tang
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sharon Bergquist
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Tingting Wang
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Joseph L Derisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lily Yeh Jan
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Physiology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yuh Nung Jan
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Physiology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Graeme W Davis
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
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Duportets L, Bozzolan F, Abrieux A, Maria A, Gadenne C, Debernard S. The transcription factor Krüppel homolog 1 is linked to the juvenile hormone-dependent maturation of sexual behavior in the male moth, Agrotis ipsilon. Gen Comp Endocrinol 2012; 176:158-66. [PMID: 22285394 DOI: 10.1016/j.ygcen.2012.01.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 01/04/2012] [Accepted: 01/07/2012] [Indexed: 12/26/2022]
Abstract
In the male moth, Agrotis ipsilon, the behavioral response and neuronal sensitivity in the primary olfactory center, the antennal lobe (AL), to sex pheromone increase with age and juvenile hormone (JH) biosynthesis. Although JH has been shown to control this age-dependent plasticity, the underlying signaling pathway remains obscure. In this context, we cloned a full cDNA encoding the Krüppel homolog 1 transcription factor (AipsKr-h1) of A. ipsilon, which was found to be predominantly expressed in ALs, where its amount increased concomitantly with age and sex pheromone responses. Conversely, the expression of AipsKr-h1 protein in the antenna was age-independent. Moreover, the administration of JH in immature males or fluvastatin, an inhibitor of JH biosynthesis, in mature males induced an increase or a decline of the AipsKr-h1 protein level in ALs, respectively. This effect was suppressed with a combined injection of fluvastatin and JH. Our results showed that Aipskr-h1 is a JH-upregulated gene that might mediate JH action on central pheromone processing, modulating sexual behavior in A. ipsilon.
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Affiliation(s)
- Line Duportets
- UMR 1272, UPMC-INRA, Physiologie de l'Insecte: Signalisation et Communication, Université Paris VI, Bâtiment A, 7 quai Saint Bernard, 75005 Paris, France
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Bany BM, Scott CA, Eckstrum KS. Analysis of uterine gene expression in interleukin-15 knockout mice reveals uterine natural killer cells do not play a major role in decidualization and associated angiogenesis. Reproduction 2011; 143:359-75. [PMID: 22187674 DOI: 10.1530/rep-11-0325] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
During decidualization, uterine natural killer (uNK) cells are the most abundant immune cell types found in the uterus. Although it is well known that they play key roles in spiral arteriole modification and the maintenance of decidual integrity seen after mid-pregnancy, their roles in the differentiation of decidual cells and accompanying angiogenesis during the process of decidualization is less well characterized. To address this, we used whole-genome Illumina BeadChip analysis to compare the gene expression profiles in implantation segments of the uterus during decidualization on day 7.5 of pregnancy between wild-type and uNK cell-deficient (interleukin-15-knockout) mice. We found almost 300 differentially expressed genes and verified the differential expression of ~60 using quantitative RT-PCR. Notably, there was a lack of differential expression of genes involved in decidualization and angiogenesis and this was also verified by quantitative RT-PCR. Similar endothelial cell densities and proliferation indices were also found in the endometrium between the implantation site tissues of wild-type and knockout mice undergoing decidualization. Overall, the results of this study reveal that uNK cells likely do not play a major role in decidualization and accompanying angiogenesis during implantation. In addition, the study identifies a large number of genes whose expression in implantation-site uterine tissue during decidualization depends on interleukin-15 expression in mice.
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Affiliation(s)
- Brent M Bany
- Department of Physiology, Southern Illinois University School of Medicine, Carbondale, Illinois 62901, USA.
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Neumüller RA, Richter C, Fischer A, Novatchkova M, Neumüller KG, Knoblich JA. Genome-wide analysis of self-renewal in Drosophila neural stem cells by transgenic RNAi. Cell Stem Cell 2011; 8:580-93. [PMID: 21549331 PMCID: PMC3093620 DOI: 10.1016/j.stem.2011.02.022] [Citation(s) in RCA: 198] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Revised: 11/01/2010] [Accepted: 02/16/2011] [Indexed: 01/14/2023]
Abstract
The balance between stem cell self-renewal and differentiation is precisely controlled to ensure tissue homeostasis and prevent tumorigenesis. Here we use genome-wide transgenic RNAi to identify 620 genes potentially involved in controlling this balance in Drosophila neuroblasts. We quantify all phenotypes and derive measurements for proliferation, lineage, cell size, and cell shape. We identify a set of transcriptional regulators essential for self-renewal and use hierarchical clustering and integration with interaction data to create functional networks for the control of neuroblast self-renewal and differentiation. Our data identify key roles for the chromatin remodeling Brm complex, the spliceosome, and the TRiC/CCT-complex and show that the alternatively spliced transcription factor Lola and the transcriptional elongation factors Ssrp and Barc control self-renewal in neuroblast lineages. As our data are strongly enriched for genes highly expressed in murine neural stem cells, they are likely to provide valuable insights into mammalian stem cell biology as well.
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Affiliation(s)
- Ralph A Neumüller
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
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