| 1. |
- Bouderlique, Thibault, et al.
(author)
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The Concerted Action of E2-2 and HEB Is Critical for Early Lymphoid Specification
- 2019
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In: Frontiers in Immunology. - : Frontiers Media SA. - 1664-3224. ; 10
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Journal article (peer-reviewed)abstract
- The apparition of adaptive immunity in Gnathostomata correlates with the expansion of the E-protein family to encompass E2-2, HEB, and E2A. Within the family, E2-2 and HEB are more closely evolutionarily related but their concerted action in hematopoiesis remains to be explored. Here we show that the combined disruption of E2-2 and HEB results in failure to express the early lymphoid program in Common lymphoid precursors (CLPs) and a near complete block in B-cell development. In the thymus, Early T-cell progenitors (ETPs) were reduced and T-cell development perturbed, resulting in reduced CD4 T- and increased γδ T-cell numbers. In contrast, hematopoietic stem cells (HSCs), erythro-myeloid progenitors, and innate immune cells were unaffected showing that E2-2 and HEB are dispensable for the ancestral hematopoietic lineages. Taken together, this E-protein dependence suggests that the appearance of the full Gnathostomata E-protein repertoire was critical to reinforce the gene regulatory circuits that drove the emergence and expansion of the lineages constituting humoral immunity.
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| 2. |
- De Paepe, Ayla
(author)
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Elucidating regulatory elements : studies in chronic lymphocytic leukemia and multiple myeloma
- 2018
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Doctoral thesis (other academic/artistic)abstract
- With next generation sequencing taking center stage in genetic and epigenetic research, its applications and challenges are many. This work revolves around the application of bioinformatics in different contexts: basic research in the understanding of diseases (biology), the effect of treatment on the target cells (clinics) and the assessment of a new wet-lab method (lab). Biology. Two studies fall under this topic, one on chronic lymphocytic leukemia, the other on multiple myeloma. Many coding mutations and chromosomal aberrations have long been identified in both diseases, yet they are only present in subsets of patients, and so it is puzzling that all this diversity results in a single diagnosis. We hypothesized that instead of a common genetic background, they might present with a common epigenetic background. For this we aimed to collect paired RNA-seq, histone ChIP-seq and ATAC-seq for patients and healthy controls, and had the following specific hypotheses: 1. Using H3K4me2 and H3K27Ac, we will be able to identify the regulatory elements altered between health and disease. 2. By looking at the interplay between those regulatory elemets, RNA-seq, ATAC-seq and database information, we will be able to describe the aberrant regulation in terms of transciption factors, regulatory elements and their target genes. Clinics Ibrutinib is a novel drug used in chronic lymphocytic leukemia treatment. Though it is shown to be beneficial to many patients, a lot of the early effects the treatment has on the malignant cells, especially in different parts of the body, are still unknown. We hypothesized that relevant changes in blood and lymph nodes would be visible soon after treatment, and collected RNA-seq data from both compartments, in additions to plasma values of inflammatory cytokines. We had to following specific hypotheses: 1. Early changes are visible, maybe even just hours after first treatment. 2. There will be differences in treatment effect between blood and lymph node compartments. Lab ChIP-seq is a very useful method to look at proteins bound to DNA, which, depending on the protein checked, can give a multitude of information. Yet, the amount of cells needed to perform these experiments is high, even in improved protocols like ChIPmentation. We hypothesized that the ChIPmentation protocol could be optimized, and that reducing time and steps would yield better data. For this we performed ChIP-seq with the original ChIPmentation protocol and with our adaptation, testing the following specific hypotheses: 1. Our version, high-throughput ChIPmentation, will perform equally well as the original method when high cell numbers are used, but be faster. 2. When low cell numbers are used, our method will give better results, as it involves less loss of material. My contribution lies in the development and execution of bioinformatics, pipelines, data handling etc, to test these hypotheses, which also includes discussions and planning of projects, samples and feasibility.
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| 3. |
- Palma, Marzia, et al.
(author)
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Ibrutinib induces rapid down-regulation of inflammatory markers and altered transcription of chronic lymphocytic leukaemia-related genes in blood and lymph nodes
- 2018
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In: British Journal of Haematology. - : WILEY. - 0007-1048 .- 1365-2141. ; 183:2, s. 212-224
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Journal article (peer-reviewed)abstract
- In chronic lymphocytic leukaemia (CLL) patients, treatment with the Bruton tyrosine kinase inhibitor ibrutinib induces a rapid shift of tumour cells from lymph nodes (LN) to peripheral blood (PB). Here, we characterized in depth the dynamics of ibrutinib-induced inflammatory, transcriptional and cellular changes in different compartments immediately after treatment initiation in seven relapsed/refractory CLL patients. Serial PB and LN samples were taken before start and during the first 29 days of treatment. Changes in plasma inflammation-related biomarkers, CLL cell RNA expression, B-cell activation and migration markers expression, and PB mononuclear cell populations were assessed. A significant reduction of 10 plasma inflammation markers, the majority of which were chemokines and not CLL-derived, was observed within hours, and was paralleled by very early increase of CD19(+) circulating cells. At the RNA level, significant and continuous changes in transcription factors and signalling molecules linked to B-cell receptor signalling and CLL biology was observed in both PB and LN CLL cells already after 2 days of treatment. In conclusion, ibrutinib seems to instantly shut off an ongoing inflammatory response and interfere with diverse sensitive pathways in the LN.
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| 4. |
- Tobiasson, Magnus, et al.
(author)
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Comprehensive mapping of the effects of azacitidine on DNA methylation, repressive/permissive histone marks and gene expression in primary cells from patients with MDS and MDS-related disease
- 2017
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In: Oncotarget. - : IMPACT JOURNALS LLC. - 1949-2553. ; 8:17, s. 28812-28825
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Journal article (peer-reviewed)abstract
- Azacitidine (Aza) is first-line treatment for patients with high-risk myelodysplastic syndromes (MDS), although its precise mechanism of action is unknown. We performed the first study to globally evaluate the epigenetic effects of Aza on MDS bone marrow progenitor cells assessing gene expression (RNA seq), DNA methylation (Illumina 450k) and the histone modifications H3K18ac and H3K9me3 (ChIP seq). Aza induced a general increase in gene expression with 924 significantly upregulated genes but this increase showed no correlation with changes in DNA methylation or H3K18ac, and only a weak association with changes in H3K9me3. Interestingly, we observed activation of transcripts containing 15 endogenous retroviruses (ERVs) confirming previous cell line studies. DNA methylation decreased moderately in 99% of all genes, with a median beta-value reduction of 0.018; the most pronounced effects seen in heterochromatin. Aza-induced hypomethylation correlated significantly with change in H3K9me3. The pattern of H3K18ac and H3K9me3 displayed large differences between patients and healthy controls without any consistent pattern induced by Aza. We conclude that the marked induction of gene expression only partly could be explained by epigenetic changes, and propose that activation of ERVs may contribute to the clinical effects of Aza in MDS.
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| 5. |
- Åhsberg, Josefine, et al.
(author)
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Ebf1 heterozygosity results in increased DNA damage in pro-B cells and their synergistic transformation by Pax5 haploinsufficiency
- 2015
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In: Blood. - : American Society of Hematology. - 0006-4971 .- 1528-0020. ; 125:26, s. 4052-4059
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Journal article (peer-reviewed)abstract
- Early B-cell factor 1 (Ebf1) is a transcription factor with documented dose-dependent functions in normal and malignant B-lymphocyte development. To understand more about the roles of Ebf1 in malignant transformation, we investigated the impact of reduced functional Ebf1 dosage on mouse B-cell progenitors. Gene expression analysis suggested that Ebf1 was involved in the regulation of genes important for DNA repair and cell survival. Investigation of the DNA damage in steady state, as well as after induction of DNA damage by UV light, confirmed that pro-B cells lacking 1 functional allele of Ebf1 display signs of increased DNA damage. This correlated to reduced expression of DNA repair genes including Rad51, and chromatin immunoprecipitation data suggested that Rad51 is a direct target for Ebf1. Although reduced dosage of Ebf1 did not significantly increase tumor formation in mice, a dramatic increase in the frequency of pro-B cell leukemia was observed in mice with combined heterozygous mutations in the Ebf1 and Pax5 genes, revealing a synergistic effect of combined dose reduction of these proteins. Our data suggest that Ebf1 controls DNA repair in a dose-dependent manner providing a possible explanation to the frequent involvement of EBF1 gene loss in human leukemia.
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