GEO DataSets

(Submitter supplied) The T-box transcription factor T-bet is encoded by Tbx21 and was identified to play a role in aging and tissue localization of B cells. T-bet expression was detected in malignant B cells but its potential role in B-cell malignancies remains largely unexplored. We used single cell RNA sequencing (scRNA-seq) and the assay for transposase accessible chromatin using sequencing (scATAC-seq) to analyze the regulatory role of T-bet in TCL1 leukemia.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

4 Samples

Download data: H5

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

8 Samples

Download data: CSV, H5, TSV

(Submitter supplied) The T-box transcription factor T-bet is encoded by Tbx21 and was identified to play a role in aging and tissue localization of B cells. T-bet expression was detected in malignant B cells but its potential role in B-cell malignancies remains largely unexplored. We used single cell RNA sequencing (scRNA-seq) and the assay for transposase accessible chromatin using sequencing (scATAC-seq) to analyze the regulatory role of T-bet in TCL1 leukemia.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

4 Samples

Download data: CSV, H5, TSV

(Submitter supplied) Redundant tumor microenvironment (TME) immunosuppressive mechanisms and epigenetic maintenance of terminal T-cell exhaustion greatly hinder functional anti-tumor T-cell responses in chronic lymphocytic leukemia (CLL). Bromodomain and extra-terminal (BET) proteins regulate key pathways contributing to CLL pathogenesis and TME interactions, including T-cell function and differentiation. Herein, we report that blocking BET protein function alleviates immunosuppressive networks in the CLL TME and repairs inherent T-cell defects. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL34315

12 Samples

Download data: RCC

(Submitter supplied) Several studies have demonstrated an impaired function of the microenvironment in chronic lymphocytic leukemia (CLL), contributing to immune evasion of tumor cells and disease progression. However, in CLL-like monoclonal B cell lymphocytosis (MBL) studies are scarce. Herein, a comprehensive characterization of the microenvironment in 59 MBL, 56 early stage CLL and 31 healthy controls was conducted. Gene expression arrays and qRT-PCR were performed on RNA from CD4+ peripheral blood cells; serum cytokines were measured by immunoassays and proteomic studies; and flow cytometry was applied to evaluate peripheral blood cytotoxic, Th1, exhausted and effector CD4+ T cells, besides monocytic CD14, CD4 and HLA-DR expression. MBL and early stage CLL showed a similar upregulation of cytotoxic and Th1-related genes, expanded perforin+ and CXCR3+ CD4+ T cells as well as PD1+ CD4+ T cells compared to controls. However, a strong inflammatory response was only identified in MBL: enhanced phagocytosis, pattern recognition receptors, IL8, HMGB1, TREM1 and acute response signaling pathways, along with increased levels of proinflammatory cytokines (remarkably IL8, IFN? and TNF?). Of note, this inflammatory drive was decreased in early stage CLL: diminished proinflammatory cytokines including IFN?, decreased IL8 signaling pathway and lower monocytic HLA-DR expression compared to MBL. Besides, this inflammation was especially reduced in IGHV mutated CLL, involving a decrease of the proinflammatory HMGB1 signaling pathway. These novel findings reveal a different pathophysiology between MBL and CLL, paving the way for the development of pre-emptive immunotherapies with optimal benefits at MBL and early stage CLL, before intense immune exhaustion.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16686

36 Samples

Download data: CEL

(Submitter supplied) Chronic Lymphocytic Leukemia (CLL) cells multiply in secondary lymphoid tissue but the mechanisms leading to their proliferation are still uncertain. In addition to BCR-triggered signals, other microenvironmental factors might well be involved. In proliferation centres, leukemic B cells are in close contact with CD4+CD40L+ T cells. Therefore, we here dissected the signals provided by autologous activated T cells (Tact) to CLL cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

21 Samples

Download data: CEL

(Submitter supplied) Tcl1 tg mice develop a chronic lymphocytic leukemia (CLL) -like disease. To investigate the contribution of the adhesion molecule CD44 to CLL pathophysiology, we developed a CD19Cre CD44flox/flox Tcl1 tg mouse with a B cell specific CD44 deficiency (CD44ΔB Tcl1 tg). We used the Clariom S mouse microarray from Affymetrix to investigate transcriptional differeneces between Tcl1 tg and CD44ΔB Tcl1 tg mice

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL23038

8 Samples

Download data: CEL, CHP

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

22 Samples

Download data: CEL, CHP

(Submitter supplied) Tumor cell survival critically depends on heterotypic communication with benign cells in the microenvironment. Here we describe a novel survival signaling pathway activated in stromal cells by contact to B-cells from chronic lymphocytic leukemia (CLL) patients. The expression of PKC-βII and the subsequent activation of NF-κB in bone marrow stromal cells is a prerequisite to support the survival of malignant B-cells. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

14 Samples

Download data: CEL, CHP

(Submitter supplied) Tumor cell survival critically depends on heterotypic communication with benign cells in the microenvironment. Here we describe a novel survival signaling pathway activated in stromal cells by contact to B-cells from chronic lymphocytic leukemia (CLL) patients. The expression of PKC-βII and the subsequent activation of NF-κB in bone marrow stromal cells is a prerequisite to support the survival of malignant B-cells. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

8 Samples

Download data: CEL, CHP

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL18573 GPL17586 GPL20301

58 Samples

Download data: BED, CEL, CHP

(Submitter supplied) Bromodomain and extra-terminal (BET) family proteins are key regulators of gene expression in cancer. Herein, we utilize BRD4 profiling to identify critical pathways involved in pathogenesis of chronic lymphocytic leukemia (CLL). BRD4 is over-expressed in CLL and is enriched proximal to genes up-regulated or de novo expressed in CLL with known function in disease pathogenesis and progression. These genes, including key members of the BCR signaling pathway, provide rationale for this therapeutic approach to identify new targets in alternative types of cancer. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

9 Samples

Download data: CEL, CHP

(Submitter supplied) Bromodomain and extra-terminal (BET) family proteins are key regulators of gene expression in cancer. Herein, we utilize BRD4 profiling to identify critical pathways involved in pathogenesis of chronic lymphocytic leukemia (CLL). BRD4 is over-expressed in CLL and is enriched proximal to genes up-regulated or de novo expressed in CLL with known function in disease pathogenesis and progression. These genes, including key members of the BCR signaling pathway, provide rationale for this therapeutic approach to identify new targets in alternative types of cancer. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL20301 GPL18573

49 Samples

Download data: BED, XLSX

(Submitter supplied) CD84 can be expressed on stromal cells in CLL, its target gene in these cells have yet to be identified. This experiment aimed at determining the CD84 regulated genes on stroma.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL16570

2 Samples

Download data: CEL

(Submitter supplied) To elucidate effects of tumor host interactions in vivo in CLL, purified tumor cells were obtained concurrently from blood, bone marrow and/or lymph node and analyzed by gene expression profiling. Keywords: RNA

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4176

Platform:

GPL570

62 Samples

Download data: CEL

Analysis of purified CLL cells from 24 treatment-naive patients. Samples were obtained concurrently from peripheral blood (PB), bone marrow (BM) and/or lymph nodes (LN). Results provide insight into the role of the tissue microenvironment in the pathogenesis of CLL in vivo.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 24 individual, 3 tissue sets

Platform:

GPL570

Series:

GSE21029

62 Samples

Download data: CEL

(Submitter supplied) Chronic lymphocytic leukemia (CLL) cell survival and growth is fueled by aberrant activation of various pro-survival signaling pathways within tumor niches. Specifically, B-cell receptor (BCR) signaling, toll-like receptor signaling, and supportive cellular interactions drive constitutive activation of NF-κB signaling and transcription of proliferative/pro-survival genes. Directly targeting the NF-κB pathway has been a challenge, however, herein, we investigated SpiD3, a spirocyclic dimer and novel NF-κB pathway inhibitor in preclinical models of CLL. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

9 Samples

Download data: XLSX

(Submitter supplied) Enhancer profiling has emerged as a powerful approach for discovering the cis-regulatory elements that define transcriptional core regulatory circuits. Characteristic biochemical and biophysical attributes of chromatin mark active enhancer elements, which can be leveraged with genome-wide assay technologies for discovery. This includes chromatin immunoprecipitation followed by sequencing (ChIP-seq) for histone H3 acetylated lysine 27 (H3K27ac). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

36 Samples

Download data: BEDGRAPH, XLSX

(Submitter supplied) CLL cells obtained from patients with CLL were treated with MLN4924 to determine whether NFkB transcription targets were affected by the drug.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

22 Samples

Download data: TXT

(Submitter supplied) Evaluation of differential expression between CLL patients in a chemoimmunotherapy trial with age-matched controls

Organism:

Homo sapiens

Type:

Expression profiling by array

Datasets:

GDS4167 GDS4168

Platforms:

GPL96 GPL97

104 Samples

Download data: CEL