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Home › Dataset Library › Transcription profiling of human multiple myelome samples reveals up-regulation of translational machinery and distinct genetic subgroups...

Dataset: Transcription profiling of human multiple myelome samples reveals up-regulation of translational machinery and distinct genetic subgroups characterize hyperdiploidy

Karyotypic instability, including numerical and structural chromosomal aberrations, represents a distinct feature of multiple myeloma...

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Karyotypic instability, including numerical and structural chromosomal aberrations, represents a distinct feature of multiple myeloma (MM). 40-50% of patients displayed hyperdiploidy, defined by recurrent trisomies of non-random chromosomes. To characterize hyperdiploid (H) and nonhyperdiploid (NH) MM molecularly, we analyzed the gene expression profiles of 66 primary tumors, and used FISH to investigate the major chromosomal alterations. The differential expression of 225 genes mainly involved in protein biosynthesis, transcriptional machinery and oxidative phosphorylation distinguished the 28 H-MM from the 38 NH-MM cases. The 204 upregulated genes in H-MM mapped mainly to the chromosomes involved in hyperdiploidy, and the29% up-regulated genes in NH-MM mapped to 16q. The identified transcriptional fingerprint was robustly validated on a publicly available gene expression dataset of 64 MM cases; and the global expression modulation of regions on the chromosomes involved in hyperdiploidy was verified using a self-developed non-parametric statistical method. We showed that H-MM could be further divided into two distinct molecular and transcriptional entities, characterized by the presence of trisomy 11 and 1q-extracopies/chromosome 13 deletion, respectively. Our data reinforce the importance of combining molecular cytogenetics and gene expression profiling to define a genomic framework for the study of MM pathogenesis and clinical management. Experiment Overall Design: This series of microarray experiments contains the gene expression profiles of purified plasma cells (PCs) obtained from 102 newly diagnosed multiple myeloma (MM). PCs were purified from bone marrow specimens, after red blood cell lysis with 0.86% ammonium chloride, using CD138 immunomagnetic microbeads. The purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases. 5 micrograms of total RNA was processed and, in accordance with the manufacturer's protocols, 15 micrograms of fragmented biotin-labelled cRNA were hybridized on GeneChip Human Genome U133A Arrays (Affymetrix Inc.). The arrays were scanned using the Agilent GeneChip Scanner G2500A. The images were acquired using Affymetrix MicroArray Suite (MAS) 5.0 software and the probe level data converted to expression values using the Bioconductor function for the Robust Multi-Array average (RMA) procedure (Irizarry et al, 2003), in which perfect match intensities are background adjusted and quantile-quantile normalised.

Species:
human

Samples:
102

Source:
E-GEOD-6401

PubMed:
17367409

Updated:
Dec.12, 2014

Registered:
Jun.19, 2014


Factors: (via ArrayExpress)
Sample
GSE6401GSM147576
GSE6401GSM147626
GSE6401GSM147640
GSE6401GSM147657
GSE6401GSM147618
GSE6401GSM147571
GSE6401GSM147565
GSE6401GSM147590
GSE6401GSM147587
GSE6401GSM147581
GSE6401GSM147600
GSE6401GSM147646
GSE6401GSM147621
GSE6401GSM147566
GSE6401GSM147560
GSE6401GSM147650
GSE6401GSM147585
GSE6401GSM147577
GSE6401GSM147636
GSE6401GSM147604
GSE6401GSM147645
GSE6401GSM147578
GSE6401GSM147563
GSE6401GSM147605
GSE6401GSM147596
GSE6401GSM147593
GSE6401GSM147633
GSE6401GSM147562
GSE6401GSM147556
GSE6401GSM147559
GSE6401GSM147591
GSE6401GSM147643
GSE6401GSM147627
GSE6401GSM147653
GSE6401GSM147629
GSE6401GSM147632
GSE6401GSM147623
GSE6401GSM147631
GSE6401GSM147599
GSE6401GSM147642
GSE6401GSM147639
GSE6401GSM147628
GSE6401GSM147597
GSE6401GSM147603
GSE6401GSM147567
GSE6401GSM147610
GSE6401GSM147611
GSE6401GSM147575
GSE6401GSM147635
GSE6401GSM147569
GSE6401GSM147654
GSE6401GSM147614
GSE6401GSM147583
GSE6401GSM147589
GSE6401GSM147647
GSE6401GSM147557
GSE6401GSM147638
GSE6401GSM147622
GSE6401GSM147609
GSE6401GSM147595
GSE6401GSM147564
GSE6401GSM147558
GSE6401GSM147584
GSE6401GSM147572
GSE6401GSM147630
GSE6401GSM147608
GSE6401GSM147568
GSE6401GSM147612
GSE6401GSM147582
GSE6401GSM147644
GSE6401GSM147561
GSE6401GSM147651
GSE6401GSM147619
GSE6401GSM147580
GSE6401GSM147617
GSE6401GSM147602
GSE6401GSM147598
GSE6401GSM147601
GSE6401GSM147655
GSE6401GSM147588
GSE6401GSM147579
GSE6401GSM147652
GSE6401GSM147570
GSE6401GSM147620
GSE6401GSM147649
GSE6401GSM147648
GSE6401GSM147634
GSE6401GSM147637
GSE6401GSM147606
GSE6401GSM147656
GSE6401GSM147641
GSE6401GSM147573
GSE6401GSM147607
GSE6401GSM147586
GSE6401GSM147615
GSE6401GSM147594
GSE6401GSM147616
GSE6401GSM147625
GSE6401GSM147592
GSE6401GSM147574
GSE6401GSM147613
GSE6401GSM147624

Tags

  • blood cell
  • bone
  • bone marrow
  • cell
  • chromosome
  • genome
  • multiple myeloma
  • myeloma
  • protein

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