Ontology highlight
ABSTRACT:
PROVIDER: PRJNA701144 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13674728.fastq.gz | Fastqsanger.gz | |||
| SRR13674729.fastq.gz | Fastqsanger.gz |
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Project description:Melanoma is one of the most commonly diagnosed malignancies and serves as a model for studying immunotherapy. The B16 melanoma model is characterized by low T cell infiltration in the tumor, and blocking the PD-1 pathway shows no significant anti-tumor activity, mirroring melanoma patients with a cold tumor immunophenotype. Therefore, understanding the molecular basis that prevents T cell-mediated anti-tumor activity in B16 melanoma is of great significance. In this study, we generated Tyr knockout B16 melanoma cells using CRISPR/Cas9 and discovered that tyrosinase in melanoma significantly inhibits the anti-tumor activity of T cells. Tyrosinase deficiency significantly increases T-cell infiltration and activation within the tumor. Single-cell RNA sequencing reveals an altered cold tumor immunophenotype in tyrosinase-deficient B16 melanoma. In wild-type mice, T cells in tyrosinase-deficient tumors express elevated levels of PD-1 and Foxp3. However, strikingly, in PD-1 deficient mice, the loss of tyrosinase in B16 melanoma unleashes the anti-tumor activity of PD-1 deficient T cells. This enhanced anti-tumor activity is explained by significantly increased tumor T cell infiltration accompanied by reduced frequencies of Tregs in PD-1 knockout mice. Targeting tyrosinase may enhance the anti-tumor efficacy of PD-1 blockade in cold tumors, offering a novel strategy to render cold tumors responsive to immunotherapy. Clinically, higher levels of tyrosinase expression in human melanoma are associated with a poorer prognosis, indicating that our findings could potentially improve the efficacy of immunotherapy in melanoma patients.
2025-04-28 | GSE273734 | GEO
Project description:Analysis of gene expression patterns of B-1 cells from C57BL6 wild type mice versus B-1 cells fromIL-10 Knockout mice. This study will help in the identification of factors in B-1 cells involved in changing of metastatic behavior of B16 melanoma after contacting with B-1 lymphocytes.
2017-10-28 | E-MEXP-3973 | biostudies-arrayexpress
Project description:We have shown that C57BL/6J CCR5 knockout mice develop 30.4% ± 8.6% fewer B16 F10 lung nodules compared to wild type mice after the intravenous injection of 100,000 B16 F10 cells. We sought to understand this phenomenon by comparing gene expression in the lungs of these mice at 6, 24, and 48 hours after tumor injection. There were 6 groups or conditions (CCR5 - 6 hours, WT - 6 hours, CCR5 - 24 hours, WT - 24 hours, CCR5 - 48 hours, WT - 48 hour); each group had 4 to 5 mice. All of the mice were injected with 100,000 B16 F10 melanoma cells by tail vein. At the designated time, the mice were anesthetized with Avertin and their lungs were perfused with PBS. After this, the lungs were harvested and snap frozen in liquid nitrogen. They were kept at minus 80 degrees C until processing. mRNA was extracted as described below and equivalent amounts of mRNA (by weight) was pooled by group.
2013-10-25 | E-GEOD-51422 | biostudies-arrayexpress
Project description:Vascular endothelial growth factor B (VEGFB) plays a crucial role in glucolipid metabolism and is highly associated with type 2 diabetes mellitus (T2DM). The role of VEGFB in the insulin secretion of β cells remains unverified. Thus, this study aims to discuss the effect of VEGFB on regulating insulin secretion in T2DM development, and its underlying mechanism. A high-fat diet and streptozocin were used for inducing T2DM in mice model, and VEGFB gene in islet cells of T2DM mice was knocked out by CRISPR Cas9 and overexpressed by Adeno-Associated Virus (AAV) injection. The effect of VEGFB and its underlying mechanism was assessed by light microscope, electron microscope, fluorescence confocal microscope, enzyme-linked immunosorbent assay, mass spectrometer, and western blot. The decrement of insulin secretion in islet β cell of T2DM mice are aggravated and blood glucose remains at a high level after VEGFB deletion. However, glucose tolerance and insulin sensitivity of T2DM mice were improved after the AAV-VEGFB186 injection. VEGFB knockout or overexpression can inhibit or activate PLCγ/IP3R in a VEGFR1-dependent manner. Then, the change of PLCγ/IP3R caused by VEGFB/VEGFR1 will alter the expression of key factors on the Ca2+/CaMK2 signal pathway such as PPP3CA. Moreover, VEGFB can cause altered insulin secretion by changing the calcium concentration in β cells of T2DM mice. These findings indicated that VEGFB activated the Ca2+/CaMK2 pathway via VEGFR1-PLCγ and IP3R pathway to regulate insulin secretion, which provides new insight into the regulatory mechanism of abnormal insulin secretion in T2DM.
2023-10-24 | PXD043843 | Pride
Project description:We have shown that C57BL/6J CCR5 knockout mice develop 30.4% ± 8.6% fewer B16 F10 lung nodules compared to wild type mice after the intravenous injection of 100,000 B16 F10 cells. We sought to understand this phenomenon by comparing gene expression in the lungs of these mice at 6, 24, and 48 hours after tumor injection.
2013-10-25 | GSE51422 | GEO
Project description:The FOXC2 transcription factor regulates a variety of developmental and biological processes in both embryonic and adult tissues. Importantly, overexpression or dysregulation of FOXC2 is also associated with oncogenic activity in numerous cancer types, though the function of FOXC2 in the context of melanoma has not been previously investigated. Therefore, the goal of this study was to assess FOXC2's regulation of gene expression in melanoma cells. To this end, we employed CRISPR-Cas9 gene editing technology to disrupt the Foxc2 gene in B16-F1 melanoma, and we performed RNA-seq analysis to assess differential gene expression between the wild-type B16-F1 melanoma cell line and our novel FOXC2-deficient B16-F1ΔFOXC2 gene-edited variant cell line.
2019-10-25 | GSE134296 | GEO
Project description:The goal of this study was to compare the gene expression profiles of a highly versus poorly tumorigenic murine melanoma. B16-F1 is a well-characterized murine melanoma cell line that grows progressively in hosts, both as primary tumors in subcutaneous tissue and as metastatic lesions in internal organs. D5.1G4 is a chemically mutated variant of B16 melanoma that grows with significantly slower kinetics than its wild-type counterpart. Whole genome expression microarray analysis of RNA isolated from these murine melanoma lines was performed to provide insights into factors that regulate the growth and metastasis of these tumors, which are useful models for investigating in a murine system the outgrowth, progression, and control of a cancer type that is prevalent in humans worldwide.
2015-09-29 | GSE69908 | GEO
Project description:To investigate the impact of Card11 on TIL differentiation, we isolated TILs from B16-F10 tumors of WT mice, E134G mice, and K215M mice and performed scRNA seq. We also sorted tumor-infiltrating lymphocytes (TILs) from melanoma(B16-F10) of WT mice and conducted scRNA and scTCR sequencing. To further investigate the impact of Card11 on TCR clonal diversity, we sorted CD8 T cells from melanoma WT mice or K215M mice and performed scRNA and scTCR sequencing.
2025-04-23 | GSE292543 | GEO
Project description:VEGF family members are important regulators of vascular functions. Promoting VEGFA signalling in aged mice has been shown to delay various aging phenotypes and extend the survival of aged mice. Although there is profound knowledge on functions of VEGFA, VEGFB has not been investigated in the context of cardiac aging. Our RNA data of aged mouse hearts revealed significant downregulation of Vegfb in the heart, specifically in endothelial cells and cardiomyocytes, while VEGFB expression was reduced in endothelial cells, fibroblasts and cardiomyocytes in aged human hearts. By contrast, VEGFB expression was exclusively reduced in cardiomyocytes of patients with cardiac hypertrophy. Hence, we investigated whether Vegfb gene therapy can revert age-dependent cardiac pathologies. We overexpressed Vegfb186, the soluble VEGFB isoform, via AAV9 vector transduction into 18-month-old C57Bl/6J male mice. AAV9-Vegfb treatment prevented progression age-related diastolic dysfunction and decreased cardiac fibrosis. We further found a rescue of aging-related left ventricular denervation in the hearts of AVV9-Vegfb treated old mice which was associated with an increase in heart rate variability. However, heart to body weight ratio and cardiomyocyte hypertrophy were increased in the AAV9-Vegfb treated mouse hearts, without alteration of cardiac systolic or diastolic function. Histological and transcriptomic analyses revealed that VEGFB186 induces compensatory cardiac hypertrophy which was accompanied by a rescued length-width-ratio, reduced fibrosis and the absence of cardiac inflammation. Cardiac single-nuclei RNA sequencing further suggested that AAV9-Vegfb treatment affects cardiac hypertrophy putatively via STAT3 which was validated in vitro. In conclusion, our data reveals that Vegfb overexpression partially reverses pathological alterations in the aging heart. Despite the overall improvement of the age-related cardiac phenotype, the AAV9-Vegfb-mediated induced cardiac hypertrophy which might reflect protective hypertrophy.
2024-11-30 | E-MTAB-14595 | biostudies-arrayexpress