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| 2. |
- Atienza-Párraga, Alba, et al.
(författare)
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Epigenomic re-configuration of primary multiple myeloma underlies the synergistic effect of combined DNMT and EZH2 inhibition.
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Multiple myeloma (MM) is characterized by an overexpression of EZH2 and a subsequent increase in H3K27me3-mediated silencing. However, the genome-wide redistribution of this mark in context with other epigenetic tags remains largely unexplored. Here, we show that EZH2 physically interacts with DNMT1 and that combined inhibition leads to a reduced G2/M arrest and increased apoptosis in MM. In addition, we present a catalogue of the genomic regulatory regions in normal plasma cells (NPC) as defined by their individual combination of histone marks. We used ChIP-seq and ATAC-seq data to generate whole-genome NPC chromatin annotations which we further analysed using DNA methylation arrays and RNA-seq. Comparison between NPC and MM demonstrated that, despite the global hypomethylation, enhancers show a tendency towards a higher DNA methylation levels in MM, whereas Polycomb and heterochromatic sites, highly methylated in NPC, show intermediate levels of the mark. Across all examined regulatory regions, 5-azacytidine treatment strongly reduced DNA methylation in MM. Furthermore, we find an extensive re-structuration of the global histone patterns in MM. We noticed a widespread increase in H3K27me3 except at active TSSs/promoters and enhancers, where we found a selective gain of the mark, suggestive of a directed silencing. In contrast, poised TSSs lose H3K27me3 and gain the activation mark H3K27ac, reflecting potential activation. Taken together, we present a comprehensive map of the epigenomic changes in MM as compared to NPC and provide insights into the interplay between EZH2 and DNMT1 in MM.
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| 3. |
- Kalushkova, Antonia, et al.
(författare)
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One Omics Approach Does Not Rule Them All : The Metabolome and the Epigenome Join Forces in Haematological Malignancies
- 2021
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Ingår i: EPIGENOMES. - : MDPI. - 2075-4655. ; 5:4
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Tidskriftsartikel (refereegranskat)abstract
- Aberrant DNA methylation, dysregulation of chromatin-modifying enzymes, and microRNAs (miRNAs) play a crucial role in haematological malignancies. These epimutations, with an impact on chromatin accessibility and transcriptional output, are often associated with genomic instability and the emergence of drug resistance, disease progression, and poor survival. In order to exert their functions, epigenetic enzymes utilize cellular metabolites as co-factors and are highly dependent on their availability. By affecting the expression of metabolic enzymes, epigenetic modifiers may aid the generation of metabolite signatures that could be utilized as targets and biomarkers in cancer. This interdependency remains often neglected and poorly represented in studies, despite well-established methods to study the cellular metabolome. This review critically summarizes the current knowledge in the field to provide an integral picture of the interplay between epigenomic alterations and the cellular metabolome in haematological malignancies. Our recent findings defining a distinct metabolic signature upon response to enhancer of zeste homolog 2 (EZH2) inhibition in multiple myeloma (MM) highlight how a shift of preferred metabolic pathways may potentiate novel treatments. The suggested link between the epigenome and the metabolome in haematopoietic tumours holds promise for the use of metabolic signatures as possible biomarkers of response to treatment.
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| 4. |
- Nylund, Niklas, et al.
(författare)
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Rethinking game heritage - towards reflexivity in game preservation
- 2021
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Ingår i: International Journal of Heritage Studies (IJHS). - : Taylor & Francis. - 1352-7258 .- 1470-3610. ; 27:3, s. 268-280
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Tidskriftsartikel (refereegranskat)abstract
- While games and the cultures that have sprung up around them are diverse and vastly different from each other, most exhibitions dealing with them are based on a limited understanding of games that relies on symbolic brands on one hand and on the centrality of playable experiences on the other. This bias is potentially replicated by heritage institution collections starting to define how games become cultural heritage. While games research has shown that games are firmly nestled in a participatory grassroots culture, these kinds of perspectives are curiously lacking in exhibitions. By connecting previous work on critical and intangible heritage with game studies literature, this paper emphasises the importance of various productive communities for game heritage. The concepts of intangible and critical heritage suggest that the inclusion of players and communities into the game heritage process could offer a more diverse heritage discourse. But participatory practices in collector run museums tend to produce game heritage which is implicitly working towards the same kind of one-sided understanding of games that has been criticised heavily in game studies. The critical expertise of museum professionals is needed in order to start incorporating the varicoloured practices of communities into our understanding of game heritage.
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| 5. |
- Nylund, Patrick, et al.
(författare)
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A distinct metabolic response characterizes sensitivity to EZH2 inhibition in multiple myeloma
- 2021
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Ingår i: Cell Death and Disease. - : Springer Nature. - 2041-4889. ; 12:2
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Tidskriftsartikel (refereegranskat)abstract
- Multiple myeloma (MM) is a heterogeneous haematological disease that remains clinically challenging. Increased activity of the epigenetic silencer EZH2 is a common feature in patients with poor prognosis. Previous findings have demonstrated that metabolic profiles can be sensitive markers for response to treatment in cancer. While EZH2 inhibition (EZH2i) has proven efficient in inducing cell death in a number of human MM cell lines, we hereby identified a subset of cell lines that despite a global loss of H3K27me3, remains viable after EZH2i. By coupling liquid chromatography-mass spectrometry with gene and miRNA expression profiling, we found that sensitivity to EZH2i correlated with distinct metabolic signatures resulting from a dysregulation of genes involved in methionine cycling. Specifically, EZH2i resulted in a miRNA-mediated downregulation of methionine cycling-associated genes in responsive cells. This induced metabolite accumulation and DNA damage, leading to G2 arrest and apoptosis. Altogether, we unveiled that sensitivity to EZH2i in human MM cell lines is associated with a specific metabolic and gene expression profile post-treatment.
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| 7. |
- Nylund, Patrick, et al.
(författare)
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Empowering macrophages : the cancer fighters within the tumour microenvironment in mantle cell lymphoma
- 2024
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Ingår i: Frontiers in Immunology. - : Frontiers Media S.A.. - 1664-3224. ; 15
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Forskningsöversikt (refereegranskat)abstract
- In Mantle Cell Lymphoma (MCL), the role of macrophages within the tumour microenvironment (TME) has recently gained attention due to their impact on prognosis and response to therapy. Despite their low absolute number in MCL tumour tissue, recent findings reveal an association between the levels of macrophages and prognosis, consistent with trends observed in other lymphoma subtypes. M2-like macrophages, identified by markers such as CD163, contribute to angiogenesis and suppression of the immune response. Clinical trials with MCL patients treated with chemoimmunotherapy and targeted treatments underscore the adverse impact of high levels of M2-like macrophages. Immunomodulatory drugs like lenalidomide reduce the levels of MCL-associated CD163+ macrophages and enhance macrophage phagocytic activity. Similarly, clinical approaches targeting the CD47 “don’t eat me” signalling, in combination with the anti-CD20-antibody rituximab, demonstrate increased macrophage activity and phagocytosis of MCL tumour cells. Cell-based therapies such as chimeric antigen receptor (CAR) T-cell have shown promise but various challenges persist, leading to a potential interest in CAR-macrophages (CAR-M). When macrophages are recruited to the TME, they offer advantages including phagocytic function and responsiveness to microenvironment alterations, suggesting their potential as a manipulable and inducible alternative when CAR T-cell therapies fails in the complex landscape of MCL treatment.
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| 8. |
- Nylund, Patrick, et al.
(författare)
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PVT1 interacts with the polycomb repressive complex 2 to suppress genomic regions with pro-apoptotic and tumour suppressor functions in multiple myeloma
- 2024
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Ingår i: Haematologica. - : Ferrata Storti Foundation. - 0390-6078 .- 1592-8721. ; 109:2, s. 567-577
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Tidskriftsartikel (refereegranskat)abstract
- Multiple myeloma is a heterogeneous hematological disease that originates from the bone marrow and is characterized by the monoclonal expansion of malignant plasma cells. Despite novel therapies, multiple myeloma remains clinically challenging. A common feature among patients with poor prognosis is the increased activity of the epigenetic silencer EZH2, which is the catalytic subunit of the PRC2. Interestingly, the recruitment of PRC2 lacks sequence specificity and, to date, the molecular mechanisms that define which genomic locations are destined for PRC2-mediated silencing remain unknown. The presence of a long non-coding RNA (lncRNA)-binding pocket on EZH2 suggests that lncRNA could potentially mediate PRC2 recruitment to specific genomic regions. Here, we coupled RNA immunoprecipitation sequencing, RNA-sequencing and chromatin immunoprecipitation-sequencing analysis of human multiple myeloma primary cells and cell lines to identify potential lncRNA partners to EZH2. We found that the lncRNA plasmacytoma variant translocation 1 (PVT1) directly interacts with EZH2 and is overexpressed in patients with a poor prognosis. Moreover, genes predicted to be targets of PVT1 exhibited H3K27me3 enrichment and were associated with pro-apoptotic and tumor suppressor functions. In fact, PVT1 inhibition independently promotes the expression of the PRC2 target genes ZBTB7C, RNF144A and CCDC136. Altogether, our work suggests that PVT1 is an interacting partner in PRC2-mediated silencing of tumor suppressor and pro-apoptotic genes in multiple myeloma, making it a highly interesting potential therapeutic target.
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| 9. |
- Nylund, Patrick
(författare)
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Targeting molecular mechanisms for epigenetic silencing in multiple myeloma : Implications for biology and precision medicine
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Multiple myeloma (MM) is a heterogeneous haematological cancer where malignant plasma cells clonally expand within the bone marrow. The transcriptional repressor PRC2 and its catalytic subunit EZH2 play a major role in MM, as PRC2 re-targeting results in a MM-specific gene silencing profile. In paper I, we explored the metabolic response to EZH2 inhibition (EZH2i). A global loss of H3K27me3 was found in all EZH2i-treated MM cell lines. EZH2i-sensitive cell lines acquired a unique metabolic signature, following the upregulation of a cluster of miRNAs which target methionine cycling-associated genes and are silenced by H3K27me3. These miRNAs were not upregulated in resistant cell lines, due to additional DNA methylation-mediated silencing.Therefore, in paper II we sought to evaluate the combinatorial effect of DNA demethylation agents and EZH2 inhibitors. Here, we provided a comprehensive map of the reconfiguration of the epigenome in primary MM samples. Furthermore, we demonstrated a direct protein-protein interaction between DNMT1 and EZH2 and showed that co-inhibition of these enzymes has an enhanced effect in synergistically activating genes regulating apoptosis and cell cycling. PRC2 lacks sequence specificity but contains a lncRNA binding pocket. In paper III, we hypothesized that PRC2 targeting to specific genomic regions could be mediated by lncRNAs in the context of MM. Coupling RIP- and RNA-seq, we identified a physical interaction between the lncRNA PVT1 and EZH2, as well as 270 genes potentially targeted by the EZH2-PVT1 axis. In addition, we found that independent inhibition of EZH2 and PVT1 resulted in the upregulation of the tumour suppressor genes ZBTB7C, RNF144A and CCDC136, suggesting a functional interdependency between these two epigenetic regulators. In paper IV we investigated the effects of dual G9a/DNMT inhibition in MM cells, resulting in suppressed expression of MM-associated oncogenes and increased tumour cell death. By coupling ChIP-seq, DNA methylation arrays and RNA-seq, we identified a group of genes silenced by G9a and/or DNMTs that when activated, blocked MM proliferative potential by activating genes with tumour suppressor function. In summary, this thesis highlights the strong interconnection between the dysregulation of epigenetic/metabolic regulatory mechanisms and MM pathogenesis, providing insights into how these mechanisms can be targeted to promote anti-MM effects.
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| 10. |
- Nylund, Patrick, et al.
(författare)
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The complex nature of lncRNA-mediated chromatin dynamics in multiple myeloma
- 2023
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Ingår i: Frontiers in Oncology. - : Frontiers Media S.A.. - 2234-943X. ; 13
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Forskningsöversikt (refereegranskat)abstract
- Extensive genome-wide sequencing efforts have unveiled the intricate regulatory potential of long non-protein coding RNAs (lncRNAs) within the domain of haematological malignancies. Notably, lncRNAs have been found to directly modulate chromatin architecture, thereby impacting gene expression and disease progression by interacting with DNA, RNA, and proteins in a tissue- or condition-specific manner. Furthermore, recent studies have highlighted the intricate epigenetic control of lncRNAs in cancer. Consequently, this provides a rationale to explore the possibility of therapeutically targeting lncRNAs themselves or the epigenetic mechanisms that govern their activity. Within the scope of this review, we will assess the current state of knowledge regarding the epigenetic regulation of lncRNAs and how, in turn, lncRNAs contribute to chromatin remodelling in the context of multiple myeloma.
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| 11. |
- Prax, Patrick, 1984-, et al.
(författare)
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Drawing Things Together : Understanding the Challenges and Opportunities of a Cross-LAM Approach to Digital Game Preservation and Exhibition
- 2019
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Ingår i: Nordisk kulturpolitisk tidskrift. - Oslo : Idunn. - 1403-3216 .- 2000-8325. ; 22:2, s. 332-354
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Tidskriftsartikel (refereegranskat)abstract
- Digital games have become a central part of contemporary culture and society. At the same time digital games provide numerous challenges for collections, preservation efforts, documentation, and exhibitions. This article investigates the challenges and opportunities implicit in LAM convergence and collaboration with actors outside of the LAM-sector itself. These actors are stakeholders of various kinds within game culture: game makers and industry, players, and rogue archives. More specifically, we turn to the collaboration in two Nordic museums in their work with digital games: The Finnish Museum of Games and the National Swedish Museum of Science and Technology. We draw on their actual efforts at collaboration between LAM-institutions and outside stakeholders and analyze them through the lens of political participation and agonistic pluralism. These concepts come from an interpretation of the participatory agenda in cultural policy that aims to resolve inconsistencies in the participatory agenda specifically around neoliberal logics of participation.The paper asks: How can the preservation of digital games be supported through participation of stakeholders inside and outside the LAM sector, and what policy changes would such collaborations require?This paper concludes that political participation and agonistic pluralism are useful concepts for the modeling and understanding of game preservation and provide a possible solution for the paradoxes of the participatory agenda in Nordic cultural policy. Our comparison of the work in two museums shows that approaches that empower participants can lead to successful and surprising exhibitions not possible without the sharing of curatorial power. Policy regulating LAM-institutions should change in order to accommodate players, makers, and rogue archives as participants in game preservation efforts. For the future the participatory agenda in cultural policy should be interpreted through the lens of political participation and agonistic pluralism as calling for truly empowering participants in order to elevate participation in game preservation from lucky accidents to a political participation policy.
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