GEO DataSets

(Submitter supplied) The presence of B cells in tumors have been recently reported to predict the better prognosis of patients with cancer. B cells were found primarily in so-called tertiary lymphoid structures (TLSs) in tumor. TLSs are ectopic lymphoid aggregates that form at sites of micro-secondary lymphoid organs, including a B cell follicle with a network of follicular dendritic cells (FDCs) surrounded by T cell zone composed of CD4+ T follicular helper (Tfh) cells and CD8+ T cells and high endothelial venules (HEVs). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23479

6 Samples

Download data: TXT

(Submitter supplied) Human papillomavirus (HPV) positive HNSCC patients generally have a favorable survival and promising responsiveness to radiotherapy, chemoradiotherapy and checkpoint blockades. However, HPV negative patients, the majority of HNSCC patients, have been largely overlooked. Cell death has been involved in the therapeutic resistance of cancers. We constructed a cell death index (CDI), based on autophagy, apoptosis and pyroptosis related genes, to predict the prognosis for HNSCC using TCGA dataset, and validated in a cohort from Qilu Hospital of Shandong University. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

28 Samples

Download data: TXT

(Submitter supplied) DSP protein profiling using the nanostring immuno-oncology kit was performed on head and neck tumor tissue samples De proteins were identified in tumour and stromal compartments

Organism:

Homo sapiens

Type:

Other

Platform:

GPL34246

375 Samples

Download data: CSV

(Submitter supplied) DSP RNA profling using the whole transcriptome atlas kit was performed on a tissue sample perior to immunotherapy from a patient with head and neck cancer.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

9 Samples

Download data: CSV, PKC

(Submitter supplied) Head and neck squamous cell carcinoma (HNSCC) arises through exposure to environmental carcinogens or malignant transformation by human papillomavirus (HPV). Here, we assessed the transcriptional profiles of 131,224 single cells from peripheral and intra-tumoral CD45+ immune populations from HPV– and HPV+ HNSCC and healthy donors. A spectrum of transcriptional signatures in immune lineages ranging from similar to highly divergent was present in the tumor microenvironments (TME) in HPV– and HPV+ HNSCC. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

63 Samples

Download data: MTX, TSV

(Submitter supplied) Our study showed that TLS enhanced anti-tumor immunity in ESCC.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Third-party reanalysis

Download data: RDS

(Submitter supplied) Nanostring DSP was performed on 187 ROIS from 17 HNSCC patients and differential analysis was performed by patient response groups to immunotherapy. DE proteins were identified in both tumour and stromal tissue compartments

Organism:

Homo sapiens

Type:

Other

Platform:

GPL29263

187 Samples

Download data: CSV

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

11 Samples

Download data: H5

(Submitter supplied) We previously identified stress keratin 17 (K17) as a host factor that contributes to immune evasion in the context of mouse papillomavirus-induced disease. Analyses of head and neck squamous cell carcinoma (HNSCC) patient TCGA and tissue microarray data revealed that K17 can be overexpressed in both HPV+ and HPV- human cancer samples, with a more profound upregulation in HPV- HNSCC samples. In this report, we investigated the role of K17 in regulating immune response in HPV- head and neck cancer. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

7 Samples

Download data: TXT

(Submitter supplied) We previously identified stress keratin 17 (K17) as a host factor that contributes to immune evasion in the context of mouse papillomavirus-induced disease. Analyses of head and neck squamous cell carcinoma (HNSCC) patient TCGA and tissue microarray data revealed that K17 can be overexpressed in both HPV+ and HPV- human cancer samples, with a more profound upregulation in HPV- HNSCC samples. In this report, we investigated the role of K17 in regulating immune response in HPV- head and neck cancer. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

4 Samples

Download data: H5

(Submitter supplied) The advent of immunotherapy in the clinical practice of non-small cell lung cancer (NSCLC) have highlighted the impact of the tumor immune microenvironment in the control of the tumor progression, as well as in the response to immune checkpoint blockade (ICB) therapy. Tertiary Lymphoid Structures (TLS), determinants of antitumor immunity, are associated with a favorable clinical outcome in NSCLC patients and with the effectiveness of ICB in several tumors. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

9 Samples

Download data: CSV

(Submitter supplied) Head and neck squamous cell carcinoma (HNSCC) is characterized by complex relations between stromal, epithelial, and immune cells within the tumor microenvironment (TME). To enable the development of more efficacious therapies, we aim to study the heterogeneity, signatures of unique cell populations, and cell-cell interactions of suppressive non-immune and immune cell populations in 6 human papillomavirus (HPV)+ and 12 HPV- HNSCC patient tumor and matched peripheral blood specimens using single-cell RNA sequencing (scRNAseq). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

51 Samples

Download data: MTX, TSV

(Submitter supplied) Introduction Immune checkpoint blockade (ICB) is a systemic therapeutic option for advanced hepatocellular carcinoma (HCC). However, low patient response rates necessitate the development of robust predictive biomarkers that identify individuals who will benefit from ICB. A 4-gene inflammatory signature, comprising CD8, PD-L1, LAG-3, and STAT1, was recently shown to be associated with a better overall response to ICB in various cancer types. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: CSV

(Submitter supplied) While T cell accumulation in tumors is associated with response to immune checkpoint blockade (ICB), many T cell-rich tumors fail to respond to ICB. Here we leveraged a large neoadjuvant PD-1 blockade trial in hepatocellular carcinoma (HCC) to search for correlates of ICB response within T cell-rich tumors. Paired scRNAseq/TCRseq of nearly one million immune cells revealed that tumor responses to ICB correlated with significant clonal expansion of intratumoral CH25H+CXCL13+IL-21+CD4 T cells and GranzymeK+PD-1+CD8 effector T cells, whereas terminally exhausted CD39hiToxhiPD-1hi CD8 clones dominated in non-responders. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24676

510 Samples

Download data: CSV, RDA

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

124 Samples

Download data: TSV

(Submitter supplied) The comparative resistance of some cancers including head and neck squamous cell carcinoma to checkpoint blockade is speculated to derive from the low frequency of expressed somatic mutations targeted by T cells as neoantigens. SCCVII, a spontaneously arising murine squamous carcinoma resembling human HNSCC in several key features, is likewise poorly immunogenic as irradiated tumor cells alone fail to induce protective immunity within syngeneic hosts. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

123 Samples

Download data: TSV

(Submitter supplied) The comparative resistance of some cancers including head and neck squamous cell carcinoma to checkpoint blockade is speculated to derive from the low frequency of expressed somatic mutations targeted by T cells as neoantigens. SCCVII, a spontaneously arising murine squamous carcinoma resembling human HNSCC in several key features, is likewise poorly immunogenic as irradiated tumor cells alone fail to induce protective immunity within syngeneic hosts. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

1 Sample

Download data: TSV

(Submitter supplied) Glioblastomas (GBM) are aggressive primary brain tumors with an inherent resistance to T cell-centric immunotherapy imparted to their low mutational burden and immunosuppressive tumor microenvironment (TME). Examination of the GBM TME dynamics following fractionated RT revealed a 10-fold increase in T cell content, an enrichment also observed by spatial imaging mass cytometry in matched primary and recurrent human GBM. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

28 Samples

Download data: XLSX

(Submitter supplied) Objective: To better understand the immune microenvironment of pancreatic ductal adenocarcinomas (PDACs), here we explored the relevance of T and B cell compartmentalization into tertiary lymphoid structures (TLSs) for the generation of local antitumor immunity. Design: We characterized the functional states and spatial organization of PDAC-infiltrating T and B cells using single-cell RNA sequencing (scRNA-seq), flow cytometry, multicolor immunofluorescence, gene expression profiling of microdissected TLSs, as well as in vitro assays. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL33019

19 Samples

Download data: RCC

(Submitter supplied) CD8+ T cell responses are critical for anti-tumor immunity. While extensively profiled in the tumor microenvironment (TME), recent studies in mice identified responses in lymph nodes (LN) as essential; however, the role of LN in human cancer patients remains unknown. Here, we examined CD8+ T cells in human head and neck squamous cell carcinomas (HNSCC) and regional lymph node (LN) using single-cell genomics. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

18 Samples

Download data: CSV, H5AD