GEO DataSets

(Submitter supplied) Only a subset of patients responds to immune checkpoint blockade in melanoma. A preclinical model recapitulating the clinical activity of ICB would provide a valuable platform for mechanistic studies. We used melanoma tumors arising from an Hgftg;Cdk4R24C/R24C genetically engineered mouse (GEM) model to evaluate the efficacy of an anti-mouse PD-L1 antibody similar to the anti-human PD-L1 antibodies durvalumab and atezolizumab. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

90 Samples

Download data: CEL

(Submitter supplied) Response to immune checkpoint inhibitors may be improved through combinations with each other and other therapies, raising questions about non-redundancy and resistance. We report results from parallel studies of melanoma patients and mice treated with anti-CTLA4 and radiation (RT). Although combined treatment improved responses, resistance was common. Computational analyses of immune and transcriptomic profiles (provided here) revealed that resistance in mice was due to upregulation of tumor PD-L1 that drives T cell exhaustion. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platforms:

GPL6246 GPL16570

14 Samples

Download data: CEL

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

Organism:

Homo sapiens

Type:

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

Platform:

GPL24676

44 Samples

Download data: BW, CSV, NARROWPEAK, TXT

(Submitter supplied) Immune therapies have had limited efficacy in high grade serous ovarian cancer (HGSC). The cellular targets and mechanism(s) of action of these agents in HGSC are unknown. Here we performed immune functional and single cell RNA sequencing transcriptional profiling on novel HGSC organoid/immune cell co-cultures treated with a variety of immune checkpoint blockade (ICB) antibodies compared to controls.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

1 Sample

Download data: CSV

(Submitter supplied) Immune therapies have had limited efficacy in high grade serous ovarian cancer (HGSC). The cellular targets and mechanism(s) of action of these agents in HGSC are unknown. Here we performed immune functional and single cell RNA sequencing transcriptional profiling on novel HGSC organoid/immune cell co-cultures treated with a variety of immune checkpoint blockade (ICB) antibodies compared to controls.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

1 Sample

Download data: CSV

(Submitter supplied) Immune therapies have had limited efficacy in high grade serous ovarian cancer (HGSC). The cellular targets and mechanism(s) of action of these agents in HGSC are unknown. Here we performed immune functional and single cell RNA sequencing transcriptional profiling on novel HGSC organoid/immune cell co-cultures treated with a variety of immune checkpoint blockade (ICB) antibodies compared to controls.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

16 Samples

Download data: TXT

(Submitter supplied) Immune therapies have had limited efficacy in high grade serous ovarian cancer (HGSC). The cellular targets and mechanism(s) of action of these agents in HGSC are unknown. Here we performed immune functional and single cell RNA sequencing transcriptional profiling on novel HGSC organoid/immune cell co-cultures treated with a variety of immune checkpoint blockade (ICB) antibodies compared to controls.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

22 Samples

Download data: TXT

(Submitter supplied) Immune therapies have had limited efficacy in high grade serous ovarian cancer (HGSC). The cellular targets and mechanism(s) of action of these agents in HGSC are unknown. Here we performed immune functional and single cell RNA sequencing transcriptional profiling on novel HGSC organoid/immune cell co-cultures treated with a variety of immune checkpoint blockade (ICB) antibodies compared to controls.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

4 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Immunotherapies have shown remarkable, albeit tumor-selective therapeutic benefits in the clinic. Here we evaluated the effects of the immunocytokine PD1-IL2v in a mouse model of de novo pancreatic neuroendocrine cancer resistant to checkpoint and other immunotherapies. PD1-IL2v is a bi-specific molecule based on a bivalent PD-1 antibody, serving as a targeting moiety, fused to an immuno-stimulatory IL-2 variant (IL2v) to precisely deliver IL2v to PD-1+ T-cells in the tumor microenvironment. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

24 Samples

Download data: CSV, MTX, TSV, TXT

(Submitter supplied) Differential responses to immune checkpoint inhibitors (ICI) may be attributed to tumor-intrinsic factors or environmental cues; however, these mechanisms cannot fully explain the variable ICI responses in different individuals. Here, we investigate the potential contribution of immunological heterogeneity with a focus on differences in T-cell receptor (TCR) repertoire to ICI responses, which has not been defined previously.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24247

32 Samples

Download data: TAR

(Submitter supplied) Tumor associated CD4+ and CD8+ T cells were sorted from B16f10 OVA expressing tumors in miR-155 flox, miR-155 flox CD4Cre+, and miR-155 flox CD4Cre+ mice treated with immune checkpoint blocking (ICB) antibodies by flow sorting on CD45+CD3+CD4+ cells and CD45+ CD3+CD8+ cells. RNA was collected from these cells to perform RNA sequencing of total RNA.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

18 Samples

Download data: TXT

(Submitter supplied) Immune checkpoint blockade (ICB) has led to durable clinical responses in multiple cancer types; however, biomarkers that identify which patients are most likely to respond to ICB are not well defined. Many putative biomarkers developed from a small number of samples often fail to maintain their predictive status in larger validation cohorts. We show across multiple human malignancies and syngeneic murine tumor models that neither pre-treatment T cell receptor (TCR) clonality nor changes in clonality after ICB correlate with response. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

48 Samples

Download data: TXT

(Submitter supplied) Immune checkpoint inhibitors (ICIs) have revolutionized cancer treatment; however, the responses to ICI treatment are highly variable in different individuals and the underlying mechanisms remain poorly understood.

Organism:

Mus musculus

Type:

Other

Platform:

GPL21103

7 Samples

Download data: TSV

(Submitter supplied) Recently, we have elucidated a novel role for the oncometabolite spermidine; intracellular spermidine is well-characterized as an essential metabolic fuel in growing cancer cells, but extracellular spermidine, released by dying cancer cells, also contributes to tumor progression by impairing effector activities of CD8+ T cells through the interference with proximal TCR signal transduction. In order to decipher how spermidine modulates T cell signaling and effector programs, we conducted a comprehensive gene expression analysis by microarray for in vitro cultured mouse CD8+ T cells treated with or without spermidine.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL23038

4 Samples

Download data: CEL, CHP

(Submitter supplied) To explore the effect of SIRPA perturbation on the expression changes of melanoma differentiation antigens (MDA), which directly mediates the immunogenicity of melanoma cells, we profiled the transcriptomes of B16F10 cells with SIRPA knockdown, overexpression, or control.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

9 Samples

Download data: TXT

(Submitter supplied) Here we perform QuantSeq 3' mRNA sequencing of RNA extracted from flow sorted splenic T cell from Tg4 Nr4a3-Tocky Tiger mice that had been immunised with 80ug of 4Y MBP peptide for 24 hours. After 24 hours mice were re-stimulated with 8ug 4Y MBP in the presence of isotype, anti-PD1 or anti-Lag3 antibodies for 4 hours. The results show that anti-PD1 but not anti-Lag3 imparts a unique transcriptional signature on responding T cells, indicative of stronger TCR signalling.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

6 Samples

Download data: CSV, TXT

(Submitter supplied) Here we perform QuantSeq 3' mRNA sequencing of RNA extracted from flow sorted splenic T cell from Tg4 Nr4a3-Tocky Tiger mice immunised with a high or low dose of MBP 4Y peptide, enabling identification of time and dose dependent transcriptional signatures

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

21 Samples

Download data: CSV, TXT

(Submitter supplied) Patients with advanced melanoma have shown an improved outlook after receiving anti-PD1 therapy, but the low response rate restricts clinical benefit; therefore, enhancing anti-PD1 therapy efficacy remains a major challenge. Here, our findings show significantly higher abundance of α-KG in healthy controls, anti-PD1-sensitive melanoma-bearing mice, and anti-PD1-sensitive melanoma patients; moreover, supplementation with α-KG enhanced the efficacy of anti-PD1 immunotherapy and increased PD-L1 expression in melanomas via STAT1/3. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23479

16 Samples

Download data: TXT

(Submitter supplied) Immunotherapy with checkpoint inhibitors is an efficient treatment for metastatic melanoma. Development of vitiligo upon immunotherapy represents a specific immune-related adverse event (irAE) diagnosed in 15% of patients and associated with a positive clinical response. Therefore, a detailed characterization of immune cells during vitiligo onset in melanoma patients would give insight into the immune mechanisms mediating both this irAE and the anti-tumor response. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL21697

42 Samples

Download data: CSV

(Submitter supplied) NMU-induced sprague dawley rat model of breast cancer treated with immunotherapy to prevent tumor progression

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20084 GPL25947

115 Samples

Download data: CSV