Project description:RNA sequencing was used to characterize in situ tumor infiltrating conventional type 1 dendritic cells (cDC1) in BRAFV600E melanoma tumors transplanted into C57BL/6 wildtype mice. Our analysis shows PGE2-dependent differences in the gene expression profile of intratumoral cDC1.
Project description:RNA sequencing was used to characterize PGE2-mediated changes in the gene expression profile of conventional type 1 dendritic cells (cDC1). Our analysis shows that treatment of cDC1 with PGE2 or conditioned medium from PGE2-producing tumors induces transcriptional changes in resting cDC1. cDC1 activated with a TLR3 ligand after PGE2 pre-treatment show alterations in the expression of activation induced genes.
Project description:RNA-seq of the immune-suppressed cDC1 was done to look into the mechanism underlying TLR9. It was then compared with the inflammatory cDC1 DCs.
Project description:Cytotoxic T cells confer a prognostic benefit in many tumors, including ovarian cancer. We and others have previously identified a subset of CD8+ T cells, namely CD103+CD8+ T cells, that seems to have a better prognostic effect. The aim of this study is to identify how these CD103+ T cells differ from CD103-CD8+ T cells on mRNA level in human samples of ovarian cancer.
Project description:RNA sequencing was used to characterize PGE2-mediated changes in the gene expression profile of human conventional type 1 dendritic cells (cDC1) purified from PBMCs of healthy donors. Our analysis shows that treatment of cDC1 with PGE2 induces transcriptional changes in resting cDC1. cDC1 activated with a TLR3 ligand after PGE2 pre-treatment show alterations in the expression of activation induced genes.
Project description:To identify the direct targets of Zeb1 we performed ChIP-seq of wild type cDC1 cell line in unstimulated condition. cDC1 cell line was used for Chromatin Immunoprecipitation, it was then fixed and crosslinked and then fragmented and the fragmented DNA-protein was immunoprecipated using Zeb1 antibody. The chromatin sample was then used to prepare library using NEB kit following the manufacturer's protocol
Project description:To have a mechanistic insight how the Zeb1 KD CD8+cDC1 perturbs the immune response globally. to identify the genes that are regulated by Zeb1 RNA was isolated and check for quality, then we used NEB RNA library preparation kit to prepare the library and send for sequencing on Illumina Hi-seq 2500 platform
Project description:We report the transcriptome analysis of epidermal CD8 tissue resident memory T (TRM) cells from healthy human skin. Specifically, epidermal CD8+CD103+CD49a+ and CD8+CD103+CD49- TRM cells from healthy human skin were sorted by FACS. Differential gene expression analysis revealed functional dichotomy of epidermal CD8+CD103+CD49a+ and CD8+CD103+CD49- TRM cells.
Project description:Multiple subsets of FLT3L-dependent dendritic cells (DCs) control T cell tolerance and immunity. In mouse tissues, CD8α-like DCs are identified by CD103 expression. This DC subset efficiently enters lymph nodes and cross-presents antigens, rendering CD103+ DCs promising targets for therapeutic tolerance induction or vaccination. However, only limited numbers of CD103+ DCs can be isolated with current methods. Moreover, bone marrow cultures with FLT3L produce complex mixtures of DC subsets. We developed a novel method for generating large numbers of Batf3-dependent CD103+ DCs. We used microarray analysis to compare in vitro generated CD103+ and CD103- DCs and correlated their expression patterns to published profiles and signatures of DC subsets.
Project description:A high percentage of uveal melanoma patients develop metastatic tumors that predominately occur in the liver. To identify genes associated with metastasis in this pathology, we studied 63 molecular profiles derived from gene expression microarrays performed from enuceated primary tumors. Metastasis free survival analysis was performed to obtain clinical and genomic variables associated to metastasis occurrence. We also compared within the 57 tumors with at least 36 months follow-up, 28 uveal melanoma from patients who developed liver metastases (meta1 group) with 29 tumors arising from patients without metastases (or later metastases, i.e. after 36 months) (meta0 group). The transcriptome of 63 uveal melanoma from enucleation of untreated patients were analyzed using Affymetrix U133plus2 Arrays.