GEO DataSets

(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) 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) Analysis of gene expression profiles in metastatic melanoma to validate prognostic signatures.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

214 Samples

Download data: TXT

(Submitter supplied) We isolated OSCC cells and performed single-cell RNA sequencing(scRNA-seq). Using immunohistochemistry(IHC) to analyze the relationship between TLS and prognosis. Multiple immunohistochemistry (MIHC), Flow cytometry (FCM) and Spatial analysis were used to verify the characteristics of TCF7+ T cells and their correlation with TLS. The prognostic significance, upstream regulatory network and intercellular communication of the TCF7+ T cell subpopulation were performed by multivariate analysis, Scenic and CellPhone software package analysis.We found a strong association between TCF7+ T cell subsets, TLSs and prognosis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: MTX, TSV

(Submitter supplied) Pancreatic ductal adenocarcinoma (PDAC) has complex tumor immune microenvironment (TIME), the clinical values of which remains to be explored. This study aimed to delineate the immune landscape of PDAC and determine the clinical value of immune features in TIME. There was a significant difference in immune profiles between PDAC and adjacent normal pancreatic tissues. Several novel immune features were captured by quantitative pathology analysis on mIHC, some of which were significantly correlated to the prognosis of PDAC patients. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: MTX, TSV

(Submitter supplied) Through single-cell RNA sequencing (scRNA-seq), we identify substantial transcriptomic evolution of PDOs propagated from the parental tumor, which may alter predicted drug sensitivity. In addition, we performed an integrative analyses of PDAC biopsies and provide an in-depth characterization of the heterogeneity within the tumor microenvironment, including cancer-associated fibroblast (CAF) subclasses, and predicts for a multitude of ligand-receptor interactions, revealing potential targets for immunotherapy approaches.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

17 Samples

Download data: TAR

(Submitter supplied) We treated 6 week-old KPC mice with vehicle or CA-4948 and perform scRNASeq to assess transcriptomic changes in CAFs and immune cells

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

4 Samples

Download data: MTX, TSV

(Submitter supplied) We treated FVBN/J mice bearing orthotopic KI tumors with vehicle or CA-4948 for two weeks and performed bulk RNASeq to assess transcriptomic changes in the tumor

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

8 Samples

Download data: TXT

(Submitter supplied) In this study, we performed laser capture microdissection (LCM) of PDAC samples to define their cancer- and stroma-specific molecular subtypes and identify a prognostic gene expression signature for short-term and long-term survival. LCM and RNA-seq analysis of cancer and adjacent stroma of 19 treatment-naïve PDAC tumors were performed. Gene expression signatures were tested for their robustness in a large independent validation set. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

38 Samples

Download data: TXT

(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) We examined the effects of an oral small molecule DPP inhibitor (BXCL701) on PDAC tumor growth and tumor immune landscape using mT3-2D and Pan02 subcutaneous syngeneic murine models in C57BL/6 mice

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

42 Samples

Download data: CSV, XLSX

(Submitter supplied) Pemphigus, a rare autoimmune bullous disease mediated by anti-desmoglein autoantibodies, can be controlled with systemic medication like rituximab and high-dose systemic corticosteroids combined with immunosuppressants. However, some patients continue to experience chronically recurrent blisters in a specific area, requiring long-term maintenance systemic therapy. We demonstrate the presence of skin tertiary lymphoid structures (TLSs) with desmoglein-specific B cells in chronic blisters from pemphigus patients. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL20301

8 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) PD-L1 suppresses host immunity and promotes tumor growth. We investigated how IFN-γ regulates PD-L1 in the ovarian cancer microenvironment. In clinical samples, the number of stromal CTLs in peritoneally disseminated tumors was correlated with PD-L1 expression on the tumor cells, and the lymphocyte number was significantly related to the IFN-γ signature score. In mouse models, PD-L1 was induced in peritoneal disseminated tumors, where lymphocytes were prominent, but not in subcutaneous tumors. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

12 Samples

Download data: CEL

(Submitter supplied) Ovarian cancer often progresses by disseminating to the peritoneal cavity, but how the tumor cells evade host immunity during this process is poorly understood. Programmed cell death 1 ligand 1 (PD-L1) is known to suppress immune system and to be an unfavorable prognostic factor in ovarian cancer. The purpose of this study was to elucidate the function of PD-L1 in peritoneal dissemination. Positive cytology in ascites was a significant poor prognostic factor in ovarian cancer. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

64 Samples

Download data: CEL

(Submitter supplied) Intratumoral B cell responses are associated with more favorable clinical outcomes in human pancreatic ductal adenocarcinoma cancer (PDAC). However, the antigens driving these B cell responses are largely unknown. We sought to discover these antigens by using single-cell RNA (sc-RNASeq) and immunoglobulin (Ig) sequencing of tumor-infiltrating immune cells from seven primary PDAC samples. We identified activated T and B cell responses and evidence of germinal center reactions. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL15520 GPL18573

13 Samples

Download data: CSV, FASTA, MTX, TSV

(Submitter supplied) Hidradenitis suppurativa (HS) is an inflammatory skin disease with limited therapeutic options. We and others have previously identified an abnormal B cell infiltrate within HS lesional skin. We performed scRNASequencing on CD3 negative cells from inflammatory HS skin lesions, healthy control skin and matched blood to better understand infiltrating B cells amongst other immune cells within lesional skin.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

20 Samples

Download data: MTX, TSV

(Submitter supplied) Hidradenitis suppurativa (HS) skin lesions are infiltrated by numerous inflammatory cell types, which may be subject to and can act upon surrounding tissue stroma and epithelium. Understanding how these networks are locally organized can help identify key nodes sustaining inflammatory and fibrotic processes.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

3 Samples

Download data: CSV, JPG, JSON, MTX, PNG, TSV

(Submitter supplied) Hidradenitis suppurativa (HS) is an inflammatory skin disease with limited therapeutic options. CD4 T Cells have been described as more inflammatory than T cells in healthy skin. To better understand alterations within the T cell compartment, we profiled CD4 Teffector cells and regulatory T cells (Treg) from inflammatory HS skin lesions and healthy control skin via scRNASequencing.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

14 Samples

Download data: MTX, TSV

(Submitter supplied) Hidradenitis suppurativa (HS) is an inflammatory skin disease with limited therapeutic options. Identifying transcriptional alterations within non-immune populations of HS lesions versus healthy controls could identify novel targets for therapy. We profiled subsets sorted as live, CD45 negative cells from biopsies of inflammatory lesions of three patients with HS and six specimens from healthy controls to determine what cell types and pathways were altered in HS inflammatory lesions.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

9 Samples

Download data: MTX, TSV