Mus musculus strain:C57BL/6
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1124061 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29519662_1.fastq.gz | Fastqsanger.gz | |||
| SRR29519662_2.fastq.gz | Fastqsanger.gz | |||
| SRR29510479_1.fastq.gz | Fastqsanger.gz | |||
| SRR29510479_2.fastq.gz | Fastqsanger.gz | |||
| SRR29510480_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 6 |
Similar Datasets
Project description:Differential tumor immune microenvironment coupled with tumor progression or tumor eradication in HPV-antigen expressing squamous cell carcinoma (SCC) models.
| PRJNA1131003 | ENA
Project description:Human papilloma virus (HPV) is an etiological factor of head and neck squamous cell carcinoma (HNSCC). To investigate the role of HPV antigen in anti-tumor immunity, we established mouse models by expressing HPV16 E6 and E7 in a SCC tumor cell line. We obtained two HPV antigen-expressing clones (C-225 and C-100) transplantable into C57BL/6 recipients. We found that C-225 elicited complete eradication in C57BL/6 mice (eradicated), whereas C-100 grew progressively (growing). We examined immune tumor microenvironment (TME) using flow cytometry and found that eradicated or growing tumors exhibited differential immune profiles that may influence the outcome of anti-tumor immunity. Surprisingly, the percentage of CD8 and CD4 tumor-infiltrating lymphocytes (TILs) was much higher in growing (C-100) than eradicated (C-225) tumor. However, the TILs upregulated PD-1 and LAG-3 more potently and exhibited impaired effector functions in growing tumor compared to their counterparts in eradicated tumor. C-225 TME is highly enriched with myeloid cells, especially polymorphonuclear (PMN) myeloid-derived suppressor cells (MDSC), whereas the percentage of M-MDSC and tumor-associated macrophages (TAMs) was much higher in C-100 TME, especially M2-TAMs (CD206+). The complete eradication of C-225 depended on CD8 T cells and elicited anti-tumor memory responses upon secondary tumor challenge. We employed DNA sequencing to identify differences in the T cell receptor of peripheral blood lymphocytes pre- and post-secondary tumor challenge. Lastly, C-225 and C-100 tumor lines harbored different somatic mutations. Overall, we uncovered differential immune TME that may underlie the divergent outcomes of anti-tumor immunity by establishing two SCC tumor lines, both of which express HPV16 E6 and E7 antigens. Our experimental models may provide a platform for pinpointing tumor-intrinsic versus host-intrinsic differences in orchestrating an immunosuppressive TME in HNSCCs and for identifying new targets that render tumor cells vulnerable to immune attack.
2024-07-09 | GSE271371 | GEO
Project description:Although adenocarcinoma of the cervix (ADC) exhibits a more malignant phenotype and poorer prognosis than squamous cell carcinoma (SCC), they are treated identically. This clinical dilemma calls for deeper investigation into differences between SCC and ADC. We studied 3 human papillomavirus (HPV)-positive SCC, 3 HPV-associated (HPVA) and 2 non-HPV-associated (NHPVA) ADC samples with single-cell RNA and T cell receptor sequencing plus 3D organoid verification. Notably, we revealed the malignant origin of epithelial cells characterized by stemness and poor differentiation and the potential mechanism of HPVA and NHPVA oncogenesis, deciphering differences between SCC and ADC. Additionally, we discovered the key role of tip cells in sprouting angiogenesis, the protumoral effects of cancer-associated fibroblasts and the functional dysregulation of T lymphocytes. We highlighted tumor microenvironment differences between different histologic subtypes through cellular interaction analysis. Importantly, we discovered novel precise treatment strategies specifically for HPV-positive SCC, HPVA and NHPVA-ADC, providing tremendous clinical value.
2023-12-01 | GSE197461 | GEO
Project description:We describe a function of focal adhesion kinase (FAK) in driving anti-tumor immune evasion. The kinase activity of nuclear-targeted FAK in squamous cancer cells drives exhaustion of CD8+ T-cells and recruitment of regulatory T-cells by transcriptionally regulating chemokine/cytokine and ligand-receptor networks, including transcription of Ccl5 that is crucial. These changes inhibit antigen-primed cytotoxic CD8+ T-cell activity, permitting growth of FAK-expressing tumors. To address how FAK activity in squamous cell carcinoma (SCC) cancer cells promotes elevated intra-tumoral regulatory T-cells, we analyzed global transcriptional profiles of SCC cells expressing or not expressing FAK.
2015-09-29 | GSE71662 | GEO
Project description:Oncogenic human papillomaviruses (HPVs) are associated with nearly all carcinomas of the uterine cervix and have also become an increasingly important factor in the etiology of a subset of oropharyngeal tumors. HPV-associated head and neck cancers (HNSCCs) have a distinct risk profile and appreciate a prognostic advantage compared to HPV-negative HNSCC. We analyzed the genome-wide expression patterns in two HPV(+) and two HPV(-) squamous cell carcinoma (SCC) cell lines. The Affymetrix Human Genome U133 Plus 2.0 Array platform was used to assess genome-wide expression differences between the HPV(+) and HPV(-) cell lines utilizing the RMA normalization package available for R. Cell lines analyzed: UM-SCC-4, UM-SCC-47, UM-SCC-74A, and CaSki.
2010-12-01 | E-GEOD-24089 | biostudies-arrayexpress
Project description:The tumor microenvironment (TME) is a complex mixture of tumor cells, immune cells, endothelial cells and fibroblastic stroma cells (FSC). While cancer-associated fibroblasts are generally seen as a tumor-promoting entity, it is conceivable that distinct FSC populations within the TME contribute to immune-mediated tumor control. Here, we show that intra-tumoral injection of a recombinant LCMV-based vaccine vector (r3LCMV) expressing the melanocyte differentiation antigen TRP2 results in T cell-dependent eradication of melanomas. Analysis of the TME revealed that viral vector transduction precipitates activation of particular FSC subsets. Using single-cell RNA-seq analysis, we identified a Cxcl13-expressing FSC population with a pronounced immune-stimulatory signature and increased expression of the inflammatory cytokine IL-33. Genetic ablation of Il33 in Cxcl13-Cre+ FSC impeded functionality of intratumoral T cells and consequently tumor control. Thus, reprogramming of distinct FSC subsets in the TME through LCMV-based vectors efficiently promotes tumor eradication by locally sustaining the activity of tumor-specific T cells.
2021-07-03 | E-MTAB-9407 | biostudies-arrayexpress
Project description:Lip is an anatomical junction between skin and mucosa and the squamous cell carcinoma (SCC) is the most frequent lip cancers. Lip SCC is frequently developed from actinic cheilitis, presented as ulcerative lesions. However, changes in transcriptomes and tumor microenvironment driving oncogenic transformation from actinic cheilitis to lip SCC and determinants of differentiation of lip SCC are largely unknown. This study aimed to investigate differences between lip SCC and its premalignant actinic cheilitis and factors related to tumor differentiation.
2024-10-28 | GSE280136 | GEO
Project description:Genome wide DNA methylation profiling of normal and primary oropharyngeal squamous cell carcinoma tissue samples, some infected with the human papilloma virus (HPV). The Illumina Infinium 27k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 27,000 CpGs in tissue samples. Samples included 46 oropharyngeal SCC primary tumors and 46 normal adjacent mucosal samples. For each tumor sample, HPV status (positivity based on both DNA and E6/E7 RNA) and p16 immunohistochemistry status is included.
2014-06-07 | GSE58272 | GEO
Project description:Lung squamous cell carcinoma (SCC) is a deadly disease for which current treatments are inadequate. We demonstrate that bi-allelic inactivation of Lkb1 and Pten in the mouse lung led to SCC that recapitulated the histology, gene expression and microenvironment found in human disease. Lkb1/Pten-null (LP) tumors expressed the squamous markers Krt5, p63 and Sox2, and transcriptionally resembled the basal subtype of human SCC. In contrast to mouse adenocarcinomas, the LP tumors contained immune populations enriched for tumor-associated neutrophils. Sca1+/Ngfr+ fractions were enriched for tumor propagating cells (TPCs) that could serially transplant the disease in orthotopic assays. TPCs in the LP model and Ngfr+ cells in human SCCs highly expressed Pdl1, suggesting a novel mechanism of immune escape for TPCs. We used microarrays to detail the gene expression profles among lung SCC tumor epitheial cell, lung ADC tumor epithelia cell and normal epithelial cells. Kras tumor stroma cells and LP tumor stroma cells were sorted by FACS, the cells were gated as EpCAM-/CD45+/CD31+
2014-01-24 | E-GEOD-54352 | biostudies-arrayexpress
Project description:Lung squamous cell carcinoma (SCC) is a deadly disease for which current treatments are inadequate. We demonstrate that bi-allelic inactivation of Lkb1 and Pten in the mouse lung led to SCC that recapitulated the histology, gene expression and microenvironment found in human disease. Lkb1/Pten-null (LP) tumors expressed the squamous markers Krt5, p63 and Sox2, and transcriptionally resembled the basal subtype of human SCC. In contrast to mouse adenocarcinomas, the LP tumors contained immune populations enriched for tumor-associated neutrophils. Sca1+/Ngfr+ fractions were enriched for tumor propagating cells (TPCs) that could serially transplant the disease in orthotopic assays. TPCs in the LP model and Ngfr+ cells in human SCCs highly expressed Pdl1, suggesting a novel mechanism of immune escape for TPCs. We used microarrays to detail the gene expression profles among lung SCC tumor epitheial cell, lung ADC tumor epithelia cell and normal epithelial cells. Normal EpCAM+, Kras tumor EpCAM+ and LP tumor EpCAM+ were sorted by FACS, the cells were gating as EpCAM+/CD45-/CD31-
2014-01-24 | E-GEOD-54351 | biostudies-arrayexpress