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The genes regulated by SOX11 in mantle cell lymphoma

ABSTRACT: The genes regulated by SOX11 in MCL was investigated in MCL cell line Granta 519 by siRNA knock down system. Cells were transfected using the LONZA electroporation system. Results represent cells harvested after 20 hours. Details of the experiment is published in PMID 21124928. Gene expression profiles (Human Gene 1.0 ST) of mantle cell lymphoma (MCL) cell line Granta 519 treated with SOX11 siRNA. Data analyses were performed using the Affymetrix Expression Console (v. 1.1)

ORGANISM(S): Homo sapiens

SUBMITTER: Birgitta Sander

PROVIDER: E-GEOD-25621 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Gene expression profiling and chromatin immunoprecipitation identify DBN1, SETMAR and HIG2 as direct targets of SOX11 in mantle cell lymphoma.

Wang Xiao X Björklund Stefan S Wasik Agata M AM Grandien Alf A Andersson Patrik P Kimby Eva E Dahlman-Wright Karin K Zhao Chunyan C Christensson Birger B Sander Birgitta B

PloS one 20101122 11

The SRY (sex determining region Y)-box 11 (SOX11) gene, located on chromosome 2p25, encodes for a transcription factor that is involved in tissue remodeling during embryogenesis and is crucial for neurogenesis. The role for SOX11 in hematopoiesis has not yet been defined. Two genes under direct control of SOX11 are the class- III β-tubulin gene (TUBB3) in neural cells and the transcription factor TEA domain family member 2 (TEAD2) in neural and mesenchymal progenitor cells. Normal, mature lympho ...[more]

PMID: 21124928

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High resolution ChIP sequencing reveals novel bindings targets and prognostic role for SOX11 in Mantle cell lymphoma (RNA-Seq)

Project description:SOX11 (Sex determining region Y-box 11) expression is specific for MCL as compared to other Non-HodgkinM-bM-^@M-^Ys lymphomas. However, the function and direct binding targets of SOX11 in MCL are largely unknown. We used high-resolution ChIP-Seq to identify the direct target genes of SOX11 in a genome-wide, unbiased manner and elucidate its functional significance. Pathway analysis identified WNT, PKA and TGF-beta signaling pathways as significantly enriched by SOX11 target genes. qCHIP confirmed that SOX11 directly binds to individual genes in these pathways in both MCL cell lines and patients. Interrogation of an eighty-two patientM-BM- gene-expression dataset demonstrated that SOX11 mRNA expression was inversely proportional to Ki-67, a marker of cell proliferation. Functional studies using RNA interference demonstrate that SOX11 directly regulates WNT signaling and modulates chemotherapy sensitivity to cytarabine in MCL. We analyzed SOX11 expression in three independent well-annotated tissue microarrays from the University of Wisconsin (UW), Karolina Institute and British Columbia Cancer Agency (BCCA). Our findings suggest that high SOX11 expression is associated with improved survival in a subset of MCL patients, particularly those treated with intensive chemotherapy incorporating cytarabine. Transcriptional regulation of WNT and other biological pathways affects by SOX11 target genes may help explain the impact of SOX11 expression on patient outcomes. RNA-seq experiments studying SOX11-mediated regulation of gene transcription by examining genes differentially expressed following SOX11 depletion in 3 MCL cell lines, Granta-519, Z138 and JEKO-1

2014-08-07 | E-GEOD-52148 | biostudies-arrayexpress

The genes regulated by SOX11 in mantle cell lymphoma

Project description:The genes regulated by SOX11 in MCL was investigated in MCL cell line Granta 519 by siRNA knock down system. Cells were transfected using the LONZA electroporation system. Results represent cells harvested after 20 hours. Details of the experiment is published in PMID 21124928.

2010-11-29 | GSE25621 | GEO

SOX11 Gene Expression Profiling

Project description:The neural transcription factor SOX11 is overexpressed in aggressive lymphoid neoplasms mainly in mantle cell lymphoma (MCL), but its functional role in malignant B-cells is unknown. To identify target genes transcriptionally regulated by SOX11 in malignant lymphoid cells, we have used Gene Expression Profiling (GEP) after SOX11 silencing in MCL cell lines. Differential gene expression between Z138-shSOX11 and Z138-shControl MCL cell lines. To determine the transcriptional programs regulated by SOX11, we first generated an MCL cellular model with reduced SOX11 protein levels by infecting MCL cell lines with lentiviral particles carrying shRNA plasmids specifically targeting SOX11 (shSOX11.1 and shSOX11.3). Next, we compared the GEP of shSOX11 and shControl Z138 stable transduced clones using the Affymetrix U133+2.0 microarrays.

2013-04-04 | E-GEOD-34763 | biostudies-arrayexpress

RNA-seq of human IMR-32 neuroblastoma cell line with SOX11 knockdown as compared to control

Project description:RNA-seq to define downstream targets of adrenergic SOX11 upon knockdown using 4 siRNAs against SOX11 in the SOX11 expressing adrenergic cell line IMR-32. Analysis was performed 48h upon after nucleofections, control samples are treated with siNTC (non-targeted control). 4 biological replicates were used.

2022-12-13 | E-MTAB-9340 | biostudies-arrayexpress

RNA-seq of human CLB-GA and NGP neuroblastoma cell lines with SOX11 knockdown as compared to control

Project description:RNA-seq upon SOX11 knockdown in the neuroblastoma cell lines CLB-GA and NGP. Cells were nucleofected with a pool of four different siRNAs targeting SOX11 and a non-targeting control (NTC). Analysis was performed 2 days upon SOX11 knockdown, including four biological replicates per condition.

2022-12-13 | E-MTAB-11883 | biostudies-arrayexpress

ATAC-seq of human CLB-GA neuroblastoma cell line with SOX11 knockdown as compared to control

Project description:ATAC-seq to define open and closed chromatin in the human CLG-GA neuroblastoma cell line upon SOX11 knockdown using siRNAs. Analysis was performed 48h upon after nucleofection, control samples are treated with siNTC (non-targeting control). 2 biological replicates were used.

2023-12-30 | E-MTAB-9463 | biostudies-arrayexpress

SOX11-positive and SOX11-knockdown xenograft derived tumor Gene Expression Profilings

2014-11-04 | GSE52892 | GEO

SOX11-positive and SOX11-knockdown xenograft derived tumor Gene Expression Profilings

Project description:The neural transcription factor SOX11 is overexpressed in aggressive lymphoid neoplasms mainly in mantle cell lymphoma (MCL). We have recently demonstrated SOX11 tumorigenic potential in vivo by showing a significant reduction on tumor growth of SOX11-knockdown MCL cells in xenograft experiments, confirming the clinical observations that SOX11 may play an important role in the aggressive behavior of MCL (Vegliante et al., 2013). However, the specific mechanisms regulated by SOX11 that promote the oncogenic and rapid tumor growth of aggressive MCL still remain to be elucidated. To further characterize the potential oncogenic mechanisms regulated by SOX11 in MCL, we have analyzed the GEP derived from the xenograft SOX11-positive and knockdown xenograft derived tumors. Differential gene expression between SOX11-positive Z138 and SOX11-negative Z138 MCL cell lines xenotransplanted in SCID mices derived tumors. To determine the transcriptional programs regulated by SOX11 we first generated a MCL cellular model with reduced SOX11 protein levels by infecting MCL cell lines with lentiviral particles carrying shRNA plasmids specifically targeting SOX11 (shSOX11.1 and shSOX11.3). Next, CB17-severe combined immunodeficient (CB17-SCID) mice (Charles River Laboratory, Wilmington, MA) were subcutaneously inoculated into their lower dorsum with Z138 shSOX11.1, shSOX11.3, shControl in Matrigel basement membrane matrix and compared the GEP of SOX11-positive and SOX11-negative MCL xenotransplant derived tumors using the Affymetrix U133+2.0 microarrays.

2014-11-04 | E-GEOD-52892 | biostudies-arrayexpress

Transcription profiling by array of human HEK293 cells overexpressing SOX11

Project description:We have carried out a cell line-based overexpression study coupled with microarray analysis to characterise the set of genes regulated by SOX11 and therefore critical for neurodevelopmental processes important in health and disease. The HEK293 cells were transiently transfected by pDEST40-SOX11 or control plasmid (pDEST40).Cells were collected at 24 hours post-transfection.Total RNA from alll samples was extracted.Biotinylated cRNA was prepared using the Illumina total Prep RNA application Kits.Hybridization, washing and scanning were performed according to the Illumina BeadStation 500* manual (revision C)

2011-06-21 | E-TABM-1025 | biostudies-arrayexpress

SOX11 Gene Expression Profiling

2013-04-04 | GSE34763 | GEO