GEO DataSets

(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) 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) 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) 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) Significant response rates have been reported in patients with relapsed/refractory B-cell acute lymphoblastic leukemia (B-ALL), diffuse large B-cell lymphomas (DLBCL), mantle cell lymphomas and follicular lymphomas. In contrast, in CTL019 trials, only 26% of CLL patients had durable antitumor responses with dramatic mechanisms of resistance to anti-CD19.CAR T-cell therapy. Low expression of programmed cell death protein 1 (PD1) has been identified as pre-treatment predictor of response in these trials, though the mechanisms responsible for a limited efficacy in CLL remain poorly understood. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL30311

4 Samples

Download data: RCC

(Submitter supplied) ATAC-seq analysis of CD8 T cell subsets. The goal of this study was to understand the chromatin states associated to the effect of IL-10 in preventing activation-induced exhaustion of CD8+ T cells in the context of mouse tumor. The chromatin accessibility changes induced upon α-IL-10R antibody treatment in tumor-bearing mice were studied using ATACseq.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21103

16 Samples

Download data: BED, BROADPEAK

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL21103 GPL16570

40 Samples

Download data: BROADPEAK, CEL

(Submitter supplied) Analysis of the effect IL-10R blockade on PD-1hi effector CD8+ T-cells isolated from the TCL1-AT model of CLL

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL16570

8 Samples

Download data: CEL

(Submitter supplied) Analysis of the effect of CLL development on differentation and gene expression of CD8 T-cells

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL16570

16 Samples

Download data: CEL

(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:

Expression profiling by high throughput sequencing

Platform:

GPL24247

4 Samples

Download data: H5

(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) Analysis of T-cells isolated from CD3+ T-cells of patients with B-cell chronic lymphocytic leukemia (B-CLL). In contrast to other types of cancers, the non-malignant T-cell compartment of B CLL patients is expanded. Results provide insights into the role of T-cells in B-CLL.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL96

33 Samples

Download data: CEL

(Submitter supplied) Immune deficiency is common in cancer, but the biological basis for this and ways to reverse it remains elusive. Here we present a mouse model of B cell chronic lymphocytic leukemia (CLL) that recapitulates changes in the non-malignant circulating T cells seen in patients with this illness.1 To validate this model, we examined changes in T cell gene expression, protein expression and function in Em-TCL1 transgenic mice as they developed CLL 2,3 and demonstrate that development of CLL in these transgenic mice is associated with changes in impaired T cell function and in gene expression in CD4 and CD8 T cells similar to those observed in patients with this disease. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

56 Samples

Download data: CEL, TXT

(Submitter supplied) We report the alteration in H3K4me3 profile in Eµ-TCL1A leukemic splenocytes with or without KDM1A knockdown.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

24 Samples

Download data: BED, BW

(Submitter supplied) Chimeric antigen receptor (CAR) T cell therapy has yielded unprecedented outcomes in some patients with hematological malignancies; however, inhibition by the tumor microenvironment has prevented the broader success of CART cell therapy. We used chronic lymphocytic leukemia (CLL) as a model to investigate the interactions between the tumor microenvironment and CART cells. CLL is characterized by an immunosuppressive microenvironment, an abundance of systemic extracellular vesicles (EVs), and a relatively lower durable response rate to CART cell therapy. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

8 Samples

Download data: CSV, TXT

(Submitter supplied) mRNA profiles were generated by 3'-sequencing, in triplicate from different regulatory T cells populations of 8-week-old Foxp3-EGFP mice, healthy (Ctrl) or leukemia-bearing (TCL1) .

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21626

9 Samples

Download data: TXT

(Submitter supplied) mRNA profiles of T cells from 8-week-old wild-type (Foxp3 YFP/cre) or Ebi3-KO (Foxp3 YFP/cre Ebi3-/-) mice were generated by 3'-sequencing, in triplicate.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21626

18 Samples

Download data: TXT