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Series GSE87910 Query DataSets for GSE87910
Status Public on Oct 12, 2017
Title Gene expression profiles of 16 relapsed/refractory CLL patients treated with lenalidomide in a phase II clinical trial
Organism Homo sapiens
Experiment type Expression profiling by array
Summary The aim of the study is to identify differentially expressed genes between chronic lymphocytic leukemia (CLL) patients who will respond to lenalidomide treatment and non responsive patients. We performed a whole genome gene-expression analysis of pre-treatment samples collected from 16 CLL patients included in a phase II clinical trial. The pre-treatment sample comprises purified CD19 cells from peripheral blood. Ten (37%) patients achieved partial responses (PR) and were classified as responders (R), 2 (7%) stable diseases (SD) and 4 (15%) progressive diseases (PD) and were classified as non responders (NR).
Supervised analysis identified 78 genes up-regulated and 119 genes down-regulated in R compared with NR (Fold change [FC]≥2, p<0.01, Figure 4). Different expression levels of genes involved in interferon (INF) and Wnt signaling pathways characterized patients who will respond to lenalidomide. In particular, R showed a 23-fold increase in Wnt inhibitor Shisa homolog 3 (SHISA3), whereas a decrease of WISP3, CDH4, HOXB7 and WNT10A. Moreover, leukemic cells collected from R down-regulated interferon-induced proteins (IFI44, -6.6; IFI44L, -9.3; IFIT2, -2) and STAT1 (-2.4 fold change). NR group up-regulated lipoprotein lipase (LPL, +7.5). The baseline expression levels of cereblon (CRBN) were not dissimilar between R and NR subsets
 
Overall design Large-scale gene expression profiling (GEP) was performed on total RNA extracted from purified CD19+ CLL cells (RNeasy Mini kit Plus, QIAGEN, Valencia, CA, USA) from 16 individual CLL patients by hybridization on 4X44K Whole Human Genome Microarray (Agilent Technologies, Palo alto, CA). Fluorescence data were analysed with Feature Extraction Software v.10.5 (Agilent Technologies) an QC Chart tool v.1.3. Agglomerative two-dimensional clustering analysis and supervised analyses based on t-test were performed using Gene Spring GX (Agilent) software. Genes were defined as differentially expressed between groups at a significant level of p<0.05 and with a fold change cut off ± 2 in all the pair wise comparisons.
 
Contributor(s) Maffei R, Marasca R
Citation(s) 28639485
Submission date Oct 13, 2016
Last update date Feb 22, 2018
Contact name Rossana Maffei
E-mail(s) rossana.maffei@unimore.it
Phone +39 059 4222715
Organization name University of Modena and Reggio Emilia
Department Dept of Hematology and Oncology
Lab Lab of Molecular Hematology
Street address Via del Pozzo 71
City Modena
State/province Modena
ZIP/Postal code 41100
Country Italy
 
Platforms (1)
GPL4133 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Feature Number version)
Samples (16)
GSM2342917 MO001
GSM2342918 RO003
GSM2342919 SI004
Relations
BioProject PRJNA348177

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE87910_RAW.tar 41.9 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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