Project description:RNA-seq of SH-SY5Y NB cells stably transduced with shETV5 compared to parental cells, cell line samples and samples of xenografted tumors
Project description:Hodgkin lymphoma (HL) is a malignancy of germinal center (GC) B-cell origin. To explore the role of long non-coding RNAs (lncRNAs) in HL, we studied lncRNA expression patterns in normal B-cell subsets, HL cell lines and tissues. Naive and memory B-cells showed a highly similar lncRNA expression pattern, distinct from GC-B cells. Significant differential expression between HL and normal GC-B cells was observed for 475 lncRNA loci. For two validated lncRNAs an enhanced expression was observed in HL, diffuse large B cell lymphoma and lymphoblastoid cell lines. For a third lncRNA, increased expression levels were observed in HL and part of Burkitt lymphoma cell lines. RNA-FISH on primary HL tissues revealed a tumor cell-specific expression pattern for all three lncRNAs. A potential cis-regulatory role was observed for 107 differentially expressed lncRNA-mRNA pairs localizing within a 60kb region. In line with a cis-acting role, we showed a preferential nuclear localization for two selected candidates. Thus, we showed dynamic lncRNA expression changes during the transit of normal B-cells through the GC reaction and widely deregulated lncRNA expression patterns in HL. Three lncRNAs showed a tumor cell-specific expression pattern in HL tissues and might therefore be of value as a biomarker.
Project description:Transcription profiling by array of Ras-induced human fibroblast cell line WI38 to analyse transcriptional changes in senescent cells
Project description:Gene expression was compared between four B-cell derived HL cell lines (L428, L1236, L591, KMH2) and GC B cells from three different patients. Experiment Overall Design: Gene expression was compared between four B-cell derived HL cell lines (L428, L1236, L591, KMH2) and GC B cells from three different patients.
Project description:Cell differentiation is associated with changes in chromatin organization and gene expression. In this study, we examine chromatin structure following differentiation of the human myeloid leukemia cell line (HL-60/S4) into granulocytes with retinoic acid (RA) or into macrophage with phorbol ester (TPA). We performed ChIP-seq of histone H3 and its modifications, analyzing changes in nucleosome occupancy, nucleosome repeat length, eu-/heterochromatin redistribution and properties of epichromatin (surface chromatin adjacent to the nuclear envelope). Nucleosome positions changed genome-wide, exhibiting a specific class of alterations involving nucleosome loss in extended (~1kb) regions, pronounced in enhancers and promoters. Genes that lost nucleosomes at their promoters showed a tendency to be upregulated. On the other hand, nucleosome gain was not systematic at functional elements and did not show simple effects on transcript levels. The average genome-wide nucleosome repeat length (NRL) did not change significantly with differentiation. However, we detected an approximate 10 bp NRL decrease around the hematopoietic transcription factor (TF) PU.1 and the architectural protein CTCF, suggesting an effect on NRL proximal to TF binding sites. Nucleosome occupancy changed in regions associated with H3K4me3 in differentiated cells, compared to untreated HL-60/S4 cells. Epichromatin regions, largely unaffected by cell differentiation, revealed an increased GC content and high nucleosome density compared to surrounding chromatin. Epichromatin showed depletion of major (permissive and repressive) histone modifications and revealed enrichment with PML body-associated genes. In general, chromatin changes during HL-60/S4 differentiation appeared to be more localized, compared to changes among diverse cell types studied elsewhere, suggesting that the cell lineage differentiation of HL-60/S4 cells involves less drastic nucleosome repositioning.
Project description:Transcription profiling of mouse bone marrow macrophages (BMM) compared to BMM co-cultured with 4T1.2 breast cancer cells, treated with tumour cell supernatant, or RAW macrophage cell line
Project description:Gene expression was compared between four B-cell derived HL cell lines (L428, L1236, L591, KMH2) and GC B cells from three different patients. Keywords: Cell type comparison