Comment[ArrayExpressAccession] E-GEOD-14895 Investigation Title The trait of MS: Altered transcription regulation of nuclear receptors networks operate in the pre-disease state Comment[Submitted Name] The trait of MS: Altered transcription regulation of nuclear receptors networks operate in the pre-disease state Publication Title Microarray analysis identifies altered regulation of nuclear receptor family members in the pre-disease state of multiple sclerosis. Publication Author List Achiron A, Grotto I, Balicer R, Magalashvili D, Feldman A, Gurevich M Publication DOI 10.1016/j.nbd.2009.12.029 PubMed ID 20079437 Experimental Design transcription profiling by array Experimental Design Term Source REF EFO Public Release Date 2010-02-17 Experiment Description Molecular mechanisms that influence susceptibility to multiple sclerosis are poorly understood. We conducted a gene expression study in healthy subjects that subsequently developed the disease. Gene expression profiles (HG U133A and A2, Affymetrix, 22,215 transcripts) of peripheral blood mononuclear cells were analyzed in 9 healthy subjects (mean age 19.8+1.1 years) up to 9 years (mean 5.1±1.2 years) before onset of MS (MS to be, MS2b), 11 age-, gender-, and origin-matched subjects that remained MS-free (MSf), and 31 clinically isolated syndrome (CIS) patients. Most informative genes (p<0.05) and significant biological processes were compared. 1051 genes (611 up-regulated, 440 down-regulated) were significantly different between MS2b and MSf subjects. MS2b signature was characterized by down-regulation of the nuclear receptor (NR) family genes including NR subfamily 4 group A member1 (NR4A1, p=0.01), member 3 (NR4A3, p=0.01), NR subfamily 2 group F member 2 (NR2F1, p=0.03) and vitamin D receptor (VDR, p=0.02), all known to be involved in T-cell regulation by apoptosis. Comparison between MS2b and CIS operating networks demonstrated evolution of the altered NR dependent apoptosis regulation. Decreased NR4A1 expression was verified at the mRNA and protein level in an independent cohort of 20 relapsing-remitting MS patients. The identified MS trait is associated with suppressed transcription of NR networks that leads to altered apoptosis of activated T cells and the development of clinical disease. MS2b subjects have already an ongoing process that eventually will lead to clinical disease and our finding are of importance as they suggest the possibility of early detection and prevention of MS. Keywords: disease state analysis Blood samples of healthy subjects that later developed MS (MS-to-be, MS2b, N=9) were identified and used for gene expression study. For each sample of MS2b subject, a sample of an age and gender matched subject that remained MS-free (MSf, N=11) was randomly selected. A cohort of 31 CIS patients who gave blood sample for gene expression analysis within 3 months of the onset of their first neurological event, was used for comparison with the MS2b gene expression signature. For establishment of the CIS gene expression signature, microarray data from 13 age- and sex- matched healthy subjects were used. Date of Experiment Term Source Name EFO Term Source Version Term Source File Person Last Name Gurevich Achiron Grotto alicer Magalashvili Feldman Gurevich Person First Name Michael Anat Itamar Ran David Anna Michael Person Mid Initials Person Email Michael.Gurevich@sheba.health.gov.il Person Affiliation Sheba Medical Center Person Phone Person Fax Person Address Sheba Medical Center, Tel Hashomer 64, Ramat Gan, Israel Person Roles submitter Person Roles Term Source REF Person Roles Term Accession Number Normalization Type Normalization Term Accession Number Normalization Term Source REF Replicate Type Replicate Term Accession Number Replicate Term Source REF Quality Control Type Quality Control Term Accession Number Quality Control Term Source REF Protocol Name P-GSE14895-1 P-GSE14895-6 P-GSE14895-3 P-GSE14895-8 P-GSE14895-7 P-GSE14895-2 P-GSE14895-4 P-GSE14895-5 Protocol Description ID_REF =
VALUE = RMA signal cDNA was synthesized, labeled, hybridized to HG-U133A-2 array containing 22,215 gene-transcripts according to Affymetrix (Inc, Santa Clara, CA) protocol N/A Data analysis was performed by Partek Genomics Solution software (www.partek.com ). Expression values were computed from raw CEL files by applying the Robust Multi-Chip Average (RMA) background correction algorithm. The RMA correction included: 1) values background correction; 2) quantile normalization; 3) log2 transformation; 4) median polish summarization. In order to avoid the noise caused by variable set effects we normalized each set to pre-saved distribution pattern of a well balanced set used as a reference distribution. Hewlett Packard, GeneArray-TM scanner G2500A Peripheral blood mononuclear cells (PBMC) were separated on ficoll-hypaque gradient Total RNA was isolated using the TRIzol Reagent (Invitrogen, Carlsbad, CA) Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA Protocol Software Protocol Hardware Protocol Contact Protocol Type bioassay_data_transformation hybridization grow feature_extraction image_aquisition specified_biomaterial_action nucleic_acid_extraction labeling Protocol Term Source REF Protocol Term Accession Number Experimental Factor Name disease Experimental Factor Type disease Experimental Factor Term Source REF Experimental Factor Term Accession Number Comment[SecondaryAccession] GSE14895 Comment[GEOLastUpdateDate] 2009-02-19 Comment[GEOReleaseDate] 2010-02-17 Comment[ArrayExpressSubmissionDate] 2009-02-18 SDRF File E-GEOD-14895.sdrf.txt Comment[AEExperimentType] transcription profiling by array