GEO DataSets

(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) 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) Background: Anti-tumor immunity is highly heterogeneous between individuals; however, underlying mechanisms remain elusive, despite their potential to improve personalized cancer immunotherapy. Head and neck squamous cell carcinomas (HNSCCs) vary significantly in immune infiltration and therapeutic responses between patients, demanding a mouse model with appropriate heterogeneity to investigate mechanistic differences. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL24247 GPL23479

19 Samples

Download data: RDS, TSV, TXT, ZIP

(Submitter supplied) Depletion of CD4+ cells by anti-CD4 monoclonal antibody (anti-CD4 mAb) induces expansion of tumor-reactive CD8+ T cells and exhibits strong antitumor effects in several murine tumor models. However, whether the anti-CD4 mAb treatment activates particular or a broad variety of tumor-reactive CD8+ T cell clones is not answered. To investigate the changes of TCR repertoire induced by the anti-CD4 mAb treatment, we performed unbiased high throughput TCR sequencing in a B16F10 mouse subcutaneous melanoma model.

Organism:

Mus musculus

Type:

Other

Platform:

GPL18635

69 Samples

Download data: TXT

(Submitter supplied) Adoptive cell therapy (ACT) using in vitro expanded tumor-infiltrating lymphocytes (TILs) has inconsistent clinical responses. To better understand determinants of therapeutic success, we tracked TIL clonotypes from baseline tumors to ACT products and post-ACT blood and tumor samples in melanoma patients using single-cell RNA and T cell receptor (TCR) sequencing. Patients with clinical responses had baseline tumors enriched in tumor-reactive TILs, and these were more effectively mobilized upon in vitro expansion, yielding products enriched in tumor-specific CD8+ cells that preferentially infiltrated tumors post-ACT. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL24676

3 Samples

Download data: H5, TSV

(Submitter supplied) Adoptive cell therapy (ACT) using in vitro expanded tumor-infiltrating lymphocytes (TILs) has inconsistent clinical responses. To better understand determinants of therapeutic success, we tracked TIL clonotypes from baseline tumors to ACT products and post-ACT blood and tumor samples in melanoma patients using single-cell RNA and T cell receptor (TCR) sequencing. Patients with clinical responses had baseline tumors enriched in tumor-reactive TILs, and these were more effectively mobilized upon in vitro expansion, yielding products enriched in tumor-specific CD8+ cells that preferentially infiltrated tumors post-ACT. more...

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL22790 GPL16791 GPL15520

63 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

4 related Platforms

89 Samples

Download data: CSV, TSV, TXT

(Submitter supplied) Adoptive cell therapy (ACT) using in vitro expanded tumor-infiltrating lymphocytes (TILs) has inconsistent clinical responses. To better understand determinants of therapeutic success, we tracked TIL clonotypes from baseline tumors to ACT products and post-ACT blood and tumor samples in melanoma patients using single-cell RNA and T cell receptor (TCR) sequencing. Patients with clinical responses had baseline tumors enriched in tumor-reactive TILs, and these were more effectively mobilized upon in vitro expansion, yielding products enriched in tumor-specific CD8+ cells that preferentially infiltrated tumors post-ACT. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

13 Samples

Download data: CSV

(Submitter supplied) Adoptive cell therapy (ACT) using in vitro expanded tumor-infiltrating lymphocytes (TILs) has inconsistent clinical responses. To better understand determinants of therapeutic success, we tracked TIL clonotypes from baseline tumors to ACT products and post-ACT blood and tumor samples in melanoma patients using single-cell RNA and T cell receptor (TCR) sequencing. Patients with clinical responses had baseline tumors enriched in tumor-reactive TILs, and these were more effectively mobilized upon in vitro expansion, yielding products enriched in tumor-specific CD8+ cells that preferentially infiltrated tumors post-ACT. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

13 Samples

Download data: TSV

(Submitter supplied) CD8 T cells are the main effectors of the adaptive immune response against intracellular pathogens and cancer. Chronic antigen stimulation and inflammation lead to CD8 T cell differentiation and function that differ from those generated during acute infections. A comprehensive definition of the heterogeneity existing within both tumor-specific and total CD8 tumor-infiltrating T cells remains to be clearly established. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

7 Samples

Download data: TAR

(Submitter supplied) We report the gene expression profiles of MACS-sorted tumor-infiltrating CD8 T cells in hepatocellular carcinoma.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

10 Samples

Download data: TXT

(Submitter supplied) We report the gene expression profiles of FACS-sorted 4-1BB+PD-1-high, 4-1BB-PD-1-high, and PD-1-int tumor-infiltrating CD8 T cells in hepatocellular carcinoma.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

15 Samples

Download data: TXT

(Submitter supplied) Using murine models that exclude variation in host genetics, environmental factors and tumour mutation burden, limiting variation between animals to naturally diverse TCRβ repertoires, we applied bulk TCRseq to study TCRβ repertoire dynamics in ICT responders and non-responders

Organism:

Mus musculus

Type:

Other

Platform:

GPL16417

225 Samples

Download data: TSV

(Submitter supplied) Tumor-infiltrating lymphocytes (TIL) were spatial heterogeneous within a single tumor. To investigate whether the gene expression approach relate to TILs diversity of local tumor region, we have employed whole genome microarray expression profiling as a discovery platform to identify different gene expression pattern of each tumor region from five primary liver cancer patients. To collect information reflecting the molecular phenotype in a more robust manner from the mRNA transcriptome profiling data, the GSVA scores of the GO gene sets provided by the Molecular Signatures Database were calculated for each of the 25 tumor samples to evaluate their activities. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

25 Samples

Download data: TXT

(Submitter supplied) Lack of reliable predictive biomarkers is a major limitation of combination therapy with chemotherapy and anti-PD-1 therapy (chemo-immunotherapy). The increase of peripheral blood (PB) CD8+ T cells expressing CX3CR1, a marker of differentiation, correlates with response to anti-PD-1 therapy; however, the predictive and prognostic value of T-cell CX3CR1 expression during chemo-immunotherapy remains elusive. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24676

6 Samples

Download data: CSV, MTX, TSV

(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) To investigate the phenotypic differences between high and low avidity tumor-specific CD8+ tumor-infiltrating lymphocytes (TILs) following anti-PD-1 therapy, we performed bulk RNA-seq on tetramer sorted GSW11-specific T cells from three regressing and three progressing CT26 tumors: giving three groups of total TethiCD8+CD44+ TILs from the progressing tumors (TetHighProg), TetloCD8+CD44+ TILs from the progressing tumors (TetLowProg) and TetloCD8+CD44+ TILs from the regressing tumors (TetLowReg), total 9 samples.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

9 Samples

Download data: TXT

(Submitter supplied) CD8+ tumor infiltrating lymphocytes can have a range of binding strengths for a single tumor associated antigen. The impact this has on the transcriptional profile of the diverse CD8+ tumor infiltrating lymphocyte population was investigated by single cell RNA sequencing.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

6 Samples

Download data: MTX, TSV

(Submitter supplied) This study reveals supeior efficiacy of triple combination treatment (TCT) based on anti-PD-(L)1 and anti-4-1BB/OX40 and describes immunological mechanisms underlying synergism between the treatment components

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

27 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19057 GPL24247

32 Samples

Download data: MTX, TSV