Investigation Title Transcription profiling of human non anaplastic T-cell lymphoma Comment[Submitted Name] Transcription profiling of Non Anaplastic T-cell Lymphoma (35 tumor samples) Experimental Design co-expression_design transcription profiling by array transcription profiling by array transcription profiling by array transcription profiling by array Experimental Design Term Source REF The MGED Ontology EFO EFO EFO EFO Comment[ArrayExpressReleaseDate] 2009-09-22 Comment[SecondaryAccession] Comment[AEMIAMESCORE] 4 Comment[ArrayExpressAccession] E-TABM-783 Comment[MAGETAB TimeStamp_Version] 2010-08-13 12:24:15 Last Changed Rev: 13058 Experimental Factor Name Age(years) DiseaseState SampleType Age DiseaseStage Experimental Factor Type age(years) disease_state sample_type age disease_stage Experimental Factor Term Source REF Person Last Name de Reynies Person First Name Aurelien Person Mid Initials Person Email reyniesa@ligue-cancer.fr Person Phone Person Fax Person Address Person Affiliation Ligue Nationale Contre le Cancer, Paris, France Person Roles submitter Person Roles Term Source REF The MGED Ontology Quality Control Type Quality Control Term Source REF Replicate Type Replicate Term Source REF Normalization Type Normalization Term Source REF Date of Experiment Public Release Date 2009-09-22 PubMed ID 17284527 Publication DOI 17284527 Publication Author List Laurence de Leval, David S. Rickman, Caroline Thielen, Aurelien de Reynies, Yen-Lin Huang, Georges Delsol, Laurence Lamant, Karen Leroy, Josette Briere, Thierry Molina, Fran�oise Berger, Christian Gisselbrecht, Luc Xerri, and Philippe Gaulard Publication Title The gene expression profile of nodal peripheral T-cell lymphoma demonstrates a molecular link between angioimmunoblastic T-cell lymphoma (AITL) and follicular helper T (TFH) cells. Publication Status journal_article Publication Status Term Source REF Experiment Description A ﾑCartes dﾒIdentite des Tumeursﾒ (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net) | Affymetrix HG-U133 Plus 2.0 : 17 AITL biopsies, 2 AITL sorted cells, 16 PTCL NOS biopsies | The molecular alterations underlying the pathogenesis of angioimmunoblastic T-cell lymphoma (AITL) and peripheral T-cell lymphoma, unspecified (PTCL-u) are largely unknown. In order to characterize the ontogeny and molecular differences between both entities, a series of AITLs (n = 18) and PTCLs-u (n = 16) was analyzed using gene expression profiling. Unsupervised clustering correlated with the pathological classification and with CD30 expression in PTCL-u. The molecular profile of AITLs was characterized by a strong microenvironment imprint (overexpression of B-cell- and follicular dendritic cell-related genes, chemokines, and genes related to extracellular matrix and vascular biology), and overexpression of several genes characteristic of normal follicular helper T (T(FH)) cells (CXCL13, BCL6, PDCD1, CD40L, NFATC1). By gene set enrichment analysis, the AITL molecular signature was significantly enriched in published T(FH)-specific genes. The enrichment was higher for sorted AITL cells than for tissue samples. Overexpression of several T(FH) genes was validated by immunohistochemistry in AITLs. A few cases with molecular T(FH)-like features were identified among CD30(-) PTCLs-u. Our findings strongly support that T(FH) cells represent the normal counterpart of AITL, and suggest that the AITL spectrum may be wider than suspected, as a subset of CD30(-) PTCLs-u may derive from or be related to AITL.| Submitter : Aurelien de Reynies | Project leader : Philippe Gaulard Protocol Name P-TABM-4192 P-TABM-4194 P-TABM-4193 P-AFFY-6 P-TABM-4196 Protocol Type nucleic_acid_extraction labeling hybridization feature_extraction bioassay_data_transformation Protocol Description All samples were stored at -80C. Total RNA extraction using TRIZOL reagent (Invitrogen) according to the manufacturer's instructions. The quality of RNA was controlled by an Agilent 2100 Bioanalyser. RNAs were qualified if the 28S/18S ratio was more than 1.5. 3 ug of total RNA of each sample as starting material.Enzo BioArray High Yield RNA Transcript Labeling kit, Affymetrix, P/N 900182; T7 RNA polymerase; one-cycle target labeling protocol; see http://www.affymetrix.com/support/downloads/manuals/expression_s2_manual.pdf; one-cycle EukGE-WS2v5 target labeling protocol 20 ug cRNA per Hybridization; In vitro transcription with Enzo BioArray High Yield RNA Transcript Labeling kit, Affymetrix, P/N 900182; Incubation under rotation (60 rpm); GeneChip Fluidics Station 400; Affymetrix HG-U133 Plus 2.0 GeneChip arrays Title: Affymetrix CEL analysis. Description: RMA normalization Protocol Parameters product;IPI_Scoring;PercentTumoralTCells;CD30; amount of nucleic acid labeled;amplification;label used; volume;quantity of labeled extract used;chamber type;hyb temp;duration; Protocol Hardware Protocol Software MicroArraySuite 5.0 Protocol Contact Protocol Term Source REF The MGED Ontology SDRF File E-TABM-783.sdrf.txt Term Source Name EFO mo NCI_thesaurus ArrayExpress nci_meta The MGED Ontology EFO Term Source File http://www.ebi.ac.uk/efo/ http://mged.sourceforge.net/ontologies/MGEDontology.php ncithesaurus.obo.alt http://www.ebi.ac.uk/arrayexpress http://ncimeta.nci.nih.gov/indexMetaphrase.html http://mged.sourceforge.net/ontologies/MGEDontology.php http://www.ebi.ac.uk/efo/ Term Source Version