Transcriptional profiling of 29 cases of diffuse large B cell lymphoma
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE21846 | GEO | 2011/08/02
SECONDARY ACCESSION(S): PRJNA129331
REPOSITORIES: GEO
Similar Datasets
Project description:29 cases of RCHOP treated DLBCL were profiled for miRNA expression. Different integrated annalysis were performed, including mirNA differential expression between cases classified according to the COO signature (see later) and correlation tests between gene and miRNA expression.
2011-08-02 | GSE21847 | GEO
Project description:29 cases of RCHOP treated DLBCL were profiled for miRNA expression. Different integrated annalysis were performed, including mirNA differential expression between cases classified according to the COO signature (see later) and correlation tests between gene and miRNA expression. Cases classified according to the cell of origin classsifer (Wright G, Tan B, Rosenwald A, Hurt EH, Wiestner A, Staudt LM. A gene expression-based method to diagnose clinically distinct subgroups of diffuse large B cell lymphoma. Proc Natl Acad Sci U S A 2003;100:9991-6.) based on gene expression were subjected to miRNA expression profiling.
2011-08-01 | E-GEOD-21847 | biostudies-arrayexpress
Project description:29 cases of RCHOP treated DLBCL were profiled for gene expression. Different integrated annalysis were performed, including mirNA differential expression between cases classified according to the COO signature (see later) and correlation tests between gene and miRNA expression. After transcriptional profiling the cases were classified according to the cell of origin based on the classifier proposed by Wright et al (Wright G, Tan B, Rosenwald A, Hurt EH, Wiestner A, Staudt LM. A gene expression-based method to diagnose clinically distinct subgroups of diffuse large B cell lymphoma. Proc Natl Acad Sci U S A 2003;100:9991-6.).
2011-08-01 | E-GEOD-21846 | biostudies-arrayexpress
Project description:miRNA expression data from 36 cases of RCHOP treated DLBCL samples were correlated with clinical variables in order to find miRNA signatures related with outcome.
2011-08-02 | GSE21848 | GEO
Project description:miRNA expression data from 36 cases of RCHOP treated DLBCL samples were correlated with clinical variables in order to find miRNA signatures related with outcome. Cases classified according to the cell of origin classsifer (Wright G, Tan B, Rosenwald A, Hurt EH, Wiestner A, Staudt LM. A gene expression-based method to diagnose clinically distinct subgroups of diffuse large B cell lymphoma. Proc Natl Acad Sci U S A 2003;100:9991-6.) based on gene expression were subjected to miRNA expression profiling.
2011-08-01 | E-GEOD-21848 | biostudies-arrayexpress
Project description:Objection: To evaluate a qPCR-based 32-gene expression assay to determine the cell-of-origin (COO) of diffuse large B-cell lymphoma (DLBCL) with formalin-fixed paraffin-embedded (FFPE) tissue. Methods: The most established subtyping algorithm, the COO model, categorizes DLBCL into activated B-cell (ABC) and germinal center B-cell (GCB)-like subgroups through gene expression profiling. Biopsy of DLBCL patients with paired FFPE and fresh frozen tissue were collected to assign COO based on the immunohistochemistry (IHC) algorithm (Han’s algorithm), qPCR-based 32-gene expression assay (DLBCL-COO assay) and global gene expression profiling with RNA-seq. Results: The DLBCL-COO assay demonstrated a significantly superior concordance of COO determination with the “gold standard” RNA-seq, comparing with the IHC assignment with Han’s algorithm (91.9% versus 77.5%; P = 0.005). Furthermore, overall survival of GCB patients defined by DLBCL-COO assay was superior significantly towards the ABC patients (Figure 2B, P = 0.023). This effect was not seen when tumors were classified by IHC algorithm. Conclusions: The DLBCL-COO assay provides flexibility and accuracy in DLBCL subtype characterization. These subtype distinctions should help guiding prognostic and therapeutic options for the patients in our daily practice.
2020-04-22 | GSE147986 | GEO
Project description:Gene expression profiling (GEP) divides DLBCL according to the cell of origin into GCB, ABC and unclassifiable, exhibiting different mutational profiles. The Hans algorithm, a surrogate of GEP, classifies cases expressing CD10, BCL6 and MUM1 as GCB but it is not clear whether all these cases correspond to GCB-type. Accordingly, LBCL with IRF4 rearrangement usually expresses GCB phenotype (CD10+, BCL6+) together with strong MUM1/IRF4.
2023-06-05 | GSE178417 | GEO
Project description:To understand the biological function of GSTT1 deletion in diffuse large B cell lymphoma (DLBCL), we identified genes that are expressed differently in lymph node tissues from DLBCL patients collected at diagnosis with GSTT1 deletion (4 cases) compared to those without GSTT1 deletion (4 cases).
2016-05-24 | GSE47355 | GEO
Project description:Sporadic Burkitt lymphoma (sBL) can be delineated from diffuse large B-cell lymphoma (DLBCL) by a very homogeneous mRNA expression signature. However, it remained unclear whether all three BL variants – sBL, endemic BL (eBL) and immunodeficiency-associated BL (HIV-BL) – represent a uniform biological entity despite their differences in geographical occurrence, association with immunodeficiency and/or incidence of EBV infection. To address this issue, we generated micro RNA (miRNA) profiles from 18 eBL, 31 sBL and 15 HIV-BL cases. In addition, we analyzed the miRNA expression of 86 DLBCL to determine whether miRNA profiles recapitulate the molecular differences between BL and DLBCL evidenced by mRNA profiling. A signature of 38 miRNAs enriched in MYC regulated and NF-kB pathway associated miRNAs was obtained that differentiated BL from DLBCL. The miRNA profiles of sBL and eBL displayed only 6 differentially expressed miRNAs, whereas HIV and EBV infection had no impact on the miRNA profile of BL. In conclusion, miRNA profiling confirms that BL and DLBCL represent distinct lymphoma categories and demonstrates that the three BL variants are representatives of the same biological entity with only marginal miRNA expression differences between eBL and sBL. Archival tumor specimens of 86 diffuse large B-cell lymphoma (DLBCL) and 64 Burkitt lymphoma (BL) patients were obtained. The DLBCL samples have previously been reviewed by a panel of expert hematopathologists and their clinical data were published as part of the RiCOVER-60 trial. The diagnosis of all BL cases was confirmed by histopathology review according to the criteria of the WHO classification. Based on their geographical origin, 31 BL samples were designated as sporadic BL (sBL) and 18 samples as endemic BL (eBL). Fifteen BL cases were diagnosed as immunodeficiency-associated BL (HIV-BL). Of the 18 eBL 14 cases were EBV+ (87.5%), 2 samples were EBV- (12.5%) and for 2 eBL cases the EBV status was unknown. Of the sBL samples 26 were EBV- (86.7%), 4 cases were EBV+ (13.3%) and for 1 case the EBV status was not evaluable. Among the HIV-BL 5 (33.3%) were EBV+, whereas 10 (66.7%) were EBV-.
2011-07-17 | E-GEOD-22420 | biostudies-arrayexpress
Project description:The pathogenesis of diffuse large B cell lymphomas (DLBCL) is only partly understood. We analyzed 148 DLBCL by high resolution single nucleotide polymorphism (SNP)-chips to characterize genomic imbalances. Seventy-nine cases were of the germinal center B-cell like (GCB) type of DLBCL, 49 of the activated B-cell like (ABC) subtype and 20 were type 3 DLBCL. Twenty-four regions of recurrent genomic gains and 38 regions of recurrent genomic losses were identified over the whole cohort, with a median of 25 imbalances per case for ABC-DLBCL and 19 per case for GCB-DLBCL. Several recurrent copy number changes showed differential frequencies in the GCB- and ABC-DLBCL subgroups, including gains of HDAC7A predominantly in GCB-DLBCL (38% of cases) and losses of BACH2 and CASP8AP2 predominantly in ABC-DLBCL (35%), hinting at disparate pathogenetic mechanisms in these entities. Correlating gene expression and copy number revealed a strong gene dosage effect in all tumors, with 34% of probesets showing a concordant expression change in affected regions. Two new potential tumor suppressor genes emerging from the analysis, CASP3 and IL5RA, were sequenced in 10 and 16 candidate cases, respectively. However, no mutations were found, pointing to a potential haploinsufficiency effect of these genes, considering their reduced expression in cases with deletions. This work thus describes differences and similarities in the landscape of genomic aberrations in the DLBCL subgroups in a large collection of cases, confirming already known targets, but also discovering novel copy number changes with possible pathogenetic relevance.
2014-07-22 | GSE57611 | GEO