Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1099447 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28640123_1.fastq.gz | Fastqsanger.gz | |||
| SRR28640123_2.fastq.gz | Fastqsanger.gz | |||
| SRR28640124_1.fastq.gz | Fastqsanger.gz | |||
| SRR28640124_2.fastq.gz | Fastqsanger.gz | |||
| SRR28640125_1.fastq.gz | Fastqsanger.gz |
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Project description:Genetic disruption of class I HLA is a common mechanism of immune evasion and immunotherapy resistance in many other cancers but has not yet been characterized in cutaneous T-cell lymphoma (CTCL). We performed single-cell RNA sequencing (scRNA-seq) on tumor samples from patients with CTCL to demonstrate the tumor-specificity and intratumoral heterogeneity of such abnormalities.
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Project description:The clinical use of human pluripotent stem cells and their derivatives is limited by the rejection of transplanted cells due to differences in their HLA genes. This has led to the proposed use of histocompatible, patient-specific stem cells, however the preparation of many different stem cell lines for clinical use is a daunting task. Here we develop two distinct genetic engineering approaches that address this problem. First, we use a combination of gene targeting and mitotic recombination to derive HLA-homozygous embryonic stem cell (ESC) subclones from an HLA-heterozygous parental line. A small bank of HLA-homozygous stem cells with common haplotypes would match a significant proportion of the population. Second, we derive HLA class I-negative cells by targeted disruption of both alleles of the B2M gene in ESCs. Mixed leukocyte reactions and peptide-specific HLA-restricted CD8+ T cell responses were reduced in class I-negative cells that had undergone differentiation in embryoid bodies. These B2M-/- ESCs could act as universal donor cells in applications where the transplanted cells do not express HLA class II genes. Both approaches used adeno-associated virus (AAV) vectors for efficient gene targeting in the absence of potentially genotoxic nucleases, and produced pluripotent, transgene-free cell lines.
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Project description:We studied gene expression profiles of 17 cutaneous B-cell lymphomas that were collected with 4-6 millimeter skin punch biopsies. We also included tissue from 2 cases of mycosis fungoides (MF), 3 normal skin biopsies and 3 tonsils to create a framework for further interpretation. A hierarchical cluster algorithm was applied for data analysis. Our results indicate that small amounts of skin tissue can be used successfully to perform microarray analysis and result in distinct gene expression patterns. Duplicate specimens clustered together demonstrating a reproducible technique. Within the cutaneous B-cell lymphoma specimens two specific B-cell differentiation stage signatures of germinal center B-cells and plasma cells could be identified. Primary cutaneous follicular and primary cutaneous diffuse large B-cell lymphomas had a germinal center B-cell signature while a subset of marginal zone lymphomas demonstrated a plasma cell signature. Primary and secondary follicular B-cell lymphoma of the skin were closely related, despite previously reported genetic and phenotypic differences. In contrast primary and secondary cutaneous diffuse large B-cell lymphoma were less related to each other. This pilot study allows a first glance into the complex and unique microenvironment of B-cell lymphomas of the skin and provides a basis for future studies, that may lead to the identification of potential histologic and prognostic markers as well as therapeutic targets. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Computed
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