Gene expression profile at single cell level of tumor infiltrating myeloid antigen presenting cells from tonsillar cancer patients
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ABSTRACT: Myeloid antigen presenting cells are a heterogeneous population, and their identity is greatly influenced by niche specific cues. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of myeloid antigen presenting cells in tonsillar cancer tissue and paired contralateral healthy tissue.
Project description:The goal of this study is to compare tumor-infiltrating antigen presenting cell populations by global transcriptome profiling (RNA-seq) to help further delineate sub-populations of infiltrating myeloid cells in tumor. Methods: Four tumor antigen presenting cell populations were sorted from digested B78chOVA (melanoma variant) tumors in biological triplicate Results: RNA was extracted from the 4 groups (n=3 per group) and prepared for RNAseq. Sequencing yielded ~405 million reads with an average read depth of 33.7 million reads/sample. Reads were then aligned to the mouse genome (UCSC mm10) and those that mapped uniquely to known mRNAs were used to assess differential expression.
Project description:Transcriptional profiles of four different myeloid antigen presenting cell (APC) subsets (BDCA-1+ circulating myeloid dendritic cells, CD14+ monocytes, and in vitro generated immature and mature monocyte-derived dendritic cells) were used for comprehensive transcriptome analysis. Based on the gene expression profiling data, a quantitative relationship between myeloid APC in functionally related gene spaces was established. Keywords = myeloid antigen presenting cells Keywords = dendritic cell subsets Keywords: repeat sample
Project description:Dr. van Kooyk's laboratory is exploring the function of antigen presenting cells, such as dendritic cells (DC), that regulate viral-antigen recognition, DC trafficking and T cell binding--all processes that initiate immunity or tolerance. Essential in this is the recognition of ligands by C-type lectins and the functional consequences of differential terminal glycosylation that may regulate DC function. In this study, the gene expression profile of glycosylation-related genes is examined in relation to the maturation of human antigen-presenting cells. Two pooled RNA samples, one each from immature and mature human monocyte-derived dendritic cells, were prepared and sent to Microarray Core (E). The RNA was amplified, labeled, and hybridized to the GLYCOv3 microarrays.
Project description:Lung antigen presenting cells isolated from wild type but not Spp1-/- mice induce Th1 and Th17 cells differentiation. The goal of this study is to identify the genes differentially expressed by lung antigen presenting cells from cigarette smoke exposed mice. These genes may play crucial roles in directing Th1 and Th17 cells differentiation. Lung antigen presenting cells were isolated from lungs of two groups of wild type and Spp1-/- mice that have been exposed to cigarette smoke for 4 months. Total mRNA was extracted from these samples.
Project description:P25 is the major T cell epitope for Ag85B and enables them to induce P25-specific CD4+ Th1 cells. We used microarrays to examine the gene expression of antigen-presenting cells (APCs) stimulated with P25 and P25-specific CD4+ T cells.