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Links from GEO DataSets

Items: 20

1.

Molecular role of the PAX5-ETV6 oncoprotein in promoting B cell acute lymphoblastic leukemia

(Submitter supplied) PAX5 is a tumor suppressor in B-ALL, while the role of PAX5 fusion proteins in B-ALL development is largely unknown. Here we studied the function of PAX5-ETV6 and PAX5- FOXP1 in mice expressing these proteins from the Pax5 locus. Both proteins arrested Blymphopoiesis at the pro-B-to-pre-B cell transition and, contrary to their proposed dominantnegative role, did not interfere with the expression of most Pax5 target genes. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL17021 GPL11002 GPL13112
36 Samples
Download data: BW, TXT
Series
Accession:
GSE84987
ID:
200084987
2.

EBF1 and PAX5 control pro-B cell expansion via oppose regulation of the Myc gene

(Submitter supplied) Lineage restricted transcription factors are frequently found mutated in B-lymphoid leukemia, suggesting a close link between normal and malignant B-cell development. One of these transcription factors is EBF1, a protein of critical importance for specification but also survival of B-lymphoid progenitors. We here report that impaired EBF1 function in mouse B-cell progenitors results in reduced expression of Myc. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other
Platform:
GPL19057
24 Samples
Download data: TXT
Series
Accession:
GSE159957
ID:
200159957
3.

PAX5 belongs to a functional transcription factor network commonly targeted in B-lineage leukemia (murine)

(Submitter supplied) One of the most frequently mutated proteins in human B-lineage leukemia, mutated in about one third of all cases, is the transcription factor PAX5. While reduced function of PAX5 has a clear connection to human malignancy there is limited evidence of a direct impact on the development and function of B-cell progenitors. One possible explanation to this comes from the finding that PAX5 mutated B-ALL display complex karyotypes and additional mutations, indicating that PAX5 might be just one component of a larger transcription factor network targeted in B-ALL. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19057
38 Samples
Download data: TXT
Series
Accession:
GSE126375
ID:
200126375
4.

PAX5 belongs to a functional transcription factor network commonly targeted in B-lineage leukemia

(Submitter supplied) One of the most frequently mutated proteins in human B-lineage leukemia is the transcription factor PAX5 mutated in about one third of all cases. While reduced function of PAX5 has a clear link to human malignancy there is limited evidence for that the this directly impact the development of function of B-cell progenitors. One possible explanation to this comes from the finding that PAX5 mutated B-ALL display complex karyotypes and additional mutations. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing; Other
Platform:
GPL18573
22 Samples
Download data: BED, TXT
Series
Accession:
GSE126300
ID:
200126300
5.

Single-cell RNASeq analysis to unravel molecular networks driving leukemia in Ebf1+/-Pax5+/- (dHet) B-ALL mice

(Submitter supplied) Here, we report that EBF1 and Pax5 collaborate in a dose-dependent manner to regulate the IL-7-STAT5 signaling pathway and one-carbon metabolism, whereby we found both diminished and enhanced binding of EBF1 and Pax5 to target genes in compound heterozygous mutant mice. Moreover, single-cell RNA sequencing analysis identified a small subset of wild-type pro-B cells on the trajectory to pre-B cells that share gene expression signatures with leukemic Ebf1+/−Pax5+/− pro-B cells. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
68 Samples
Download data: CSV
Series
Accession:
GSE158827
ID:
200158827
6.

EBF1 and Pax5 safeguard leukemic transformation by limiting IL-7 signaling, Myc expression and folate metabolism

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by array; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
5 related Platforms
110 Samples
Download data: BEDGRAPH, CSV, TXT
Series
Accession:
GSE158673
ID:
200158673
7.

ATACSeq and genome-wide binding profile of EBF1 and Pax5 to unravel molecular networks driving leukemia in Ebf1+/-Pax5+/- (dHet) B-ALL mice.

(Submitter supplied) ATACSeq, EBF1 ChIPSeq and Pax5 ChIPSeq of dHet B-ALL, dHet proB and wt proB cells.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL17021 GPL21493 GPL19057
21 Samples
Download data: BEDGRAPH
Series
Accession:
GSE158671
ID:
200158671
8.

RNASeq analysis to unravel molecular networks driving leukemia in Ebf1+/-Pax5+/- (dHet) B-ALL mice

(Submitter supplied) To profile gene expression changes in Ebf1+/-Pax5+/- (dHet) leukemic mice, we performed RNASeq analysis in dHet B-ALL, dHet proB and wt proB cells.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24247
11 Samples
Download data: TXT
Series
Accession:
GSE158661
ID:
200158661
9.

Microarray analysis to unravel molecular networks driving leukemia in Ebf1+/- Pax5+/- (dHet) B-ALL mice

(Submitter supplied) To profile gene expression changes in Ebf1+/-Pax5+/- (dHet) B-ALL mice, we performed microarray analysis in dHet B-ALL, dHet proB and wt proB cells
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL7202
10 Samples
Download data: TXT
Series
Accession:
GSE158645
ID:
200158645
10.

Transcriptomic analysis of ETV6/RUNX1 KO lymphoid cell line generated by CRISPR/Cas9 showed a distinct expression signature and a deregulation of its downstream signaling genes

(Submitter supplied) The gene expression profile of E/R KO clones versus REH cells and controls clones, analysed by total RNA-sequencing, showed a total of 342 genes differentially expressed (q<0.05), 182 upregulated and 160 downregulated. The heatmap of the top50 of the most deregulated genes according to fold change (FC) values showed a distinct expression signature of E/R KO clones as compared with REH cells and control clones
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21697
6 Samples
Download data: CSV, XLSX
11.

CLIC5: a novel ETV6 target gene in childhood acute lymphoblastic leukemia

(Submitter supplied) Background: The most common rearrangement in childhood precursor B-cell acute lymphoblastic leukemia (pre-B ALL) is the t(12;21)(p13;q22) translocation resulting in the ETV6-AML1 fusion gene. A frequent concomitant event is the loss of the residual ETV6 allele suggesting a critical role for the ETV6 transcriptional repressor in the etiology of pre-B ALL. However, the precise mechanism through which loss of functional ETV6 contributes to disease pathogenesis is still unclear Results: To investigate the impact of ETV6 loss on the transcriptional network and identify new transcriptional targets of ETV6, we used whole transcriptome analysis of both pre-B leukemic cell lines and pre-B ALL patients combined with chromatin immunoprecipitation. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL16558 GPL16791
25 Samples
Download data: TXT
12.

Pax5 is a tumor suppressor in mouse mutagenesis models of acute lymphoblastic leukemia

(Submitter supplied) To examine the role of PAX5 alterations in leukemogenesis, we performed mutagenesis screens of mice heterozygous for a loss-of-function Pax5 allele. Both chemical and retroviral mutagenesis resulted in a significantly increased penetrance and reduced latency of leukemia, with a shift to B-lymphoid lineage. We observed a range of maturation of lymphoid tumors, and genomic profiling identified a high frequency of secondary genomic mutations, deletions and retroviral insertions targeting B-lymphoid development, including Pax5, and additional genes and pathways known to be mutated in ALL, including tumor suppressors, Ras and JAK-STAT signaling. more...
Organism:
Mus musculus
Type:
Genome variation profiling by genome tiling array
Platform:
GPL13131
39 Samples
Download data: TXT
Series
Accession:
GSE67611
ID:
200067611
13.

Inhibition of Inflammatory Signaling in Pax5 Mutant Cells Mitigates B-cell leukemogenesis against leukemia

(Submitter supplied) We used microarrays to investigate gene expression changes in healthy and leukemic cells from Pax5+/- and IL6+/-;Pax5+/- mice in CF and SPF housing conditions. PAX5 is one of the most frequently mutated genes in B-cell acute lymphoblastic leukemia (B-ALL), and children with inherited preleukemic PAX5 mutations are at a higher risk of developing the disease. Abnormal profiles of inflammatory markers can be detected in neonatal blood spot samples of children who later developed B-cell precursor B-ALL. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6246
22 Samples
Download data: CEL
Series
Accession:
GSE154589
ID:
200154589
14.

Gene expression analysis of Early immature and Late mature T-ALL cell lines

(Submitter supplied) Early immature T-cell acute lymphoblastic leukemias (T-ALLs) account for about 5-10% of pediatric T-ALLs and are associated with poor prognosis. However, the genetic defects that drive the biology of these tumors remain largely unknown. Analysis of microarray gene expression signatures in adult T-ALL demonstrated a high prevalence of early immature leukemias and revealed a close relationship between these tumors and myeloid leukemias. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL570
20 Samples
Download data: CEL
Series
Accession:
GSE48046
ID:
200048046
15.

Gene Expression Analyisis of T-ALL LOUCY cell lines treated with ETV6 siRNA vs. scramble control siRNA

(Submitter supplied) Transcriptional effects of ETV6 inactivation in immature T-ALL were investigated by gene expression analysis upon siRNA-mediated knockdown of ETV6 in LOUCY cells, a T-ALL cell line with a transcriptional program highly related to that of immature T-ALLs. Gene Set Enrichment Analysis (GSEA) of the ETV6 knockdown signature showed a significant enrichment in genes characteristically upregulated in ETV6 mutant immature T-ALLs including HOXA13, PRDM16, PTEN and CD33.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL10558
4 Samples
Download data: TXT
Series
Accession:
GSE33820
ID:
200033820
16.

Gene Expression Profile of 57 human T-ALL samples collected in human clinical trial E2993 (Marks et al., 2009)

(Submitter supplied) Analysis of microarray gene expression signatures in adult T-ALL demonstrated a high prevalence of early immature leukemias and revealed a close relationship between these tumors and myeloid leukemias.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL10558
57 Samples
Download data: TXT
Series
Accession:
GSE33469
ID:
200033469
17.

Activating PAX Gene Family Paralogs to Complement PAX5 Leukemia Driver Mutations

(Submitter supplied) PAX5, one of nine members of the mammalian paired box (PAX) family of transcription factors, plays an important role in B cell development. Approximately one-third of individuals with pre-B acute lymphoblastic leukemia (ALL) acquire heterozygous inactivating mutations of PAX5 in malignant cells, and heterozygous germline loss-offunction PAX5 mutations cause autosomal dominant predisposition to ALL. At least in mice, Pax5 is required for pre-B cell maturation, and leukemic remission occurs when Pax5 expression is restored in a Pax5-deficient mouse model of ALL. Together, these observations indicate that PAX5 deficiency reversibly drives leukemogenesis. PAX5 and its two most closely related paralogs, PAX2 and PAX8, which are not mutated in ALL, exhibit overlapping expression and function redundantly during embryonic development. However, PAX5 alone is expressed in lymphocytes, while PAX2 and PAX8 are predominantly specific to kidney and thyroid, respectively. We show that forced expression of PAX2 or PAX8 complements PAX5 loss-of-function mutation in ALL cells as determined by modulation of PAX5 target genes, restoration of immunophenotypic and morphological differentiation, and, ultimately, reduction of replicative potential. Activation of PAX5 paralogs, PAX2 or PAX8, ordinarily silenced in lymphocytes, may therefore represent a novel approach for treating PAX5-deficient ALL. In pursuit of this strategy, we took advantage of the fact that, in kidney, PAX2 is upregulated by extracellular hyperosmolarity. We found that hyperosmolarity, at potentially clinically achievable levels, transcriptionally activates endogenous PAX2 in ALL cells via a mechanism dependent on NFAT5, a transcription factor coordinating response to hyperosmolarity. We also found that hyperosmolarity upregulates residual wild type PAX5 expression in ALL cells and modulates gene expression, including in PAX5-mutant primary ALL cells. These findings specifically demonstrate that osmosensing pathways may represent a new therapeutic target for ALL and more broadly point toward the possibility of using gene paralogs to rescue mutations driving cancer and other diseases.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
7 Samples
Download data: CSV
18.

Genome wide genotyping and gene expression data of childhood B-cell precursor ALL without known genetic aberrations

(Submitter supplied) Acute lymphoblastic pediatric leukemia specimens without known genetic hallmarks are examined for hidden genomic aberrancies and related gene expression profiles Integration of genomic variation and gene expression profiling identifies hidden genetic lesions and novel pathways involved in BP-ALL pathogenesis Keywords: expression data
Organism:
Homo sapiens
Type:
Expression profiling by array; Genome variation profiling by SNP array; SNP genotyping by SNP array
Platforms:
GPL570 GPL2004 GPL2005
160 Samples
Download data: CEL, CHP, PDF
Series
Accession:
GSE10792
ID:
200010792
19.

Germline Aberrations of PAX5 Cause Susceptibility to pre-B cell Acute Lymphoblastic Leukemia

(Submitter supplied) A novel heterozygous germline variant, c.547G>A (p.Gly183Ser), in the paired box protein encoding gene, PAX5, was found to segregate with disease in two unrelated kindreds with autosomal dominant pre-B cell acute lymphoblastic leukemia (ALL). Leukemic cells from both families exhibited 9p deletion, with loss-of-heterozygosity and retention of the mutant PAX5 allele at 9p13. Two additional sporadic ALL cases with 9p loss demonstrated PAX5 Gly183 substitution in the leukemic cells. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL11180
40 Samples
Download data: CEL
Series
Accession:
GSE45260
ID:
200045260
20.

Infection exposure is a causal factor in B-precursor acute lymphoblastic leukemia as a result of Pax5 inherited susceptibility

(Submitter supplied) We used microarrays to investigate gene expression changes in tumor-bearing Pax5+/- mice
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6246
17 Samples
Download data: CEL
Series
Accession:
GSE62529
ID:
200062529
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