1. Expression Map of the Human Exome in CD34+ Cells and Blood Cells: Increased Alternative Splicing in Cell Motility and Immune Response Genes
- Author
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S Tondeur, Said Assou, Céline Pangault, Thierry Fest, Jean-François Schved, Tanguy Le Carrour, Samir Hamamah, Bernard Klein, Yoann Lannay, Aurélie Cubizolle, John De Vos, Rima Benmahdi, Véronique Pantesco, Institut de recherche en biothérapie (IRB), Université Montpellier 1 (UM1)-Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Service d'hématologie clinique, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Hôpital Pontchaillou, Microenvironnement et cancer (MiCa), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Unité d'AMP/DPI, Département de Médecine et biologie de la reproduction, Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Hôpital Arnaud de Villeneuve, Laboratoire d'immunologie, Université Montpellier 1 (UM1)-Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), This work was supported by Roche, the Groupe Ouest Est des Leuce´mies et Autres Maladies du Sang (GOELAMS) group and the Socie´te´ Franc¸aise d'He´matologie (SFH)., Frei, Monique, Université de Rennes (UR)-Hôpital Pontchaillou, Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), and This work was supported by Roche, the Groupe Ouest Est des Leucémies et Autres Maladies du Sang (GOELAMS) group and the Société Française d'Hématologie (SFH).
- Subjects
Male ,Cellular differentiation ,CD34 ,Antigens, CD34 ,[SDV.GEN] Life Sciences [q-bio]/Genetics ,Kidney ,Exon ,0302 clinical medicine ,Cell Movement ,Breast ,Oligonucleotide Array Sequence Analysis ,Principal Component Analysis ,0303 health sciences ,Multidisciplinary ,Reverse Transcriptase Polymerase Chain Reaction ,Prostate ,Genetics and Genomics/Gene Expression ,Hematology ,Exons ,Cell biology ,Haematopoiesis ,medicine.anatomical_structure ,Liver ,030220 oncology & carcinogenesis ,Medicine ,Female ,Algorithms ,Research Article ,Science ,Biology ,CD19 ,03 medical and health sciences ,[SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology ,medicine ,Humans ,Computational Biology/Alternative Splicing ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Progenitor cell ,030304 developmental biology ,[SDV.GEN]Life Sciences [q-bio]/Genetics ,Blood Cells ,Gene Expression Profiling ,Alternative splicing ,Immunity ,Hematopoietic Stem Cells ,Molecular biology ,Alternative Splicing ,biology.protein ,Bone marrow - Abstract
International audience; BACKGROUND: Hematopoietic cells are endowed with very specific biological functions, including cell motility and immune response. These specific functions are dramatically altered during hematopoietic cell differentiation, whereby undifferentiated hematopoietic stem and progenitor cells (HSPC) residing in bone marrow differentiate into platelets, red blood cells and immune cells that exit into the blood stream and eventually move into lymphoid organs or inflamed tissues. The contribution of alternative splicing (AS) to these functions has long been minimized due to incomplete knowledge on AS events in hematopoietic cells. PRINCIPAL FINDINGS: Using Human Exon ST 1.0 microarrays, the entire exome expression profile of immature CD34+ HSPC and mature whole blood cells was mapped, compared to a collection of solid tissues and made freely available as an online exome expression atlas (Amazonia Exon! : http://amazonia.transcriptome.eu/exon.php). At a whole transcript level, HSPC strongly expressed EREG and the pluripotency marker DPPA4. Using a differential splicing index scheme (dsi), a list of 849 transcripts differentially expressed between hematopoietic cells and solid tissues was computed, that included NEDD9 and CD74. Some of these genes also underwent alternative splicing events during hematopoietic differentiation, such as INPP4B, PTPLA or COMMD6, with varied contribution of CD3+ T cells, CD19+ B cells, CD14+ or CD15+ myelomonocytic populations. Strikingly, these genes were significantly enriched for genes involved in cell motility, cell adhesion, response to wounding and immune processes. CONCLUSION: The relevance and the precision provided by this exon expression map highlights the contribution of alternative splicing to key feature of blood cells differentiation and function.
- Published
- 2010