Role of elastin peptides in epigenetic regulation of cell proliferation- and invasivity-related genes in human tumour cells

Les propriétés invasives des cellules cancéreuses sont liées à des modulations importantes de l’expression de gènes. Des protéases doivent être exprimées afin de permettre la dégradation de la matrice extracellulaire (MEC), l’activation protéolytique de protéines matricielles et la libération de facteurs de croissance, de cytokines, de récepteurs et de molécules d’adhérence. Parmi ces protéases, les métalloprotéinases matricielles (MMPs) jouent un rôle crucial dans la dégradation de la MEC et dans le remodelage tissulaire observéau cours de l’invasion tumorale. L’émergence de thérapeutiques anticancéreuses basées sur des stratégies épigénétiques nécessitent d’évaluer leurs effets sur les propriétés des cellules tumorales. Ce travail a pour objectif d’analyser les effets de modulateurs épigénétiques (un agent hypométhylant de l’ADN et des inhibiteurs d’histone désacétylases (inhibiteursd’HDACs ou HDIs)) sur l’expression des MMP-1, -2 et -9 dans la lignée cellulaire de fibrosarcome humain HT1080. Dans un premier temps, il apparaît que l’agenthypométhylant de l’ADN, la 5-aza-2’désoxycytidine (5-azadC), augmente l’expressiongénique et protéique des MMP-1, -2 et -9. Ces modifications de l’expression sont associées à (i) une déméthylation globale de l’ADN et (ii) des modifications de la supra-organisation chromatinienne correspondant globalement à une chromatine moins condensée. De plus, la5-azadC est capable d’accroître les propriétés invasives des cellules par l’intermédiaire,notamment, d’une augmentation de l’expression de la MMP-1 par un mécanisme transcriptionnel. Cette augmentation de la transcription implique le recrutement du facteurSp1 et un remodelage chromatinien au niveau du promoteur du gène de la MMP-1.Néanmoins, une déméthylation totale de ce promoteur n’est pas nécessaire à cette induction. De manière complémentaire, le traitement des cellules HT1080 par différents HDIs révèle le rôle potentiel d’HDACs dans la régulation de l’expression de la MMP-1. Un HDIà large spectre, la trichostatine A (TSA), est capable de moduler l’expression de la MMP-1 et la texture nucléaire, mais uniquement après déméthylation préalable de l’ADN par la 5-azadC. Par contre, l’HDI spécifique des HDACs de classe I, le MS-275, est capable d’induire, à lui seul, l’expression génique et protéique de la MMP-1. Cette expression génique requiert un remodelage de la chromatine et le recrutement de l’histone acétyltransférase p300 au niveau du promoteur du gène de la MMP-1. L’ensemble de ces résultats suggèrent que des mécanismes épigénétiques jouent un rôle crucial dans le contrôle de l’expression de laMMP-1 dans les cellules HT1080, influençant ainsi les propriétés invasives de ces cellules.Invasive properties of cancer cells require critical changes in gene expression. Proteasesmust be expressed for the degradation of the extracellular matrix (ECM), the proteolyticactivation of matrix proteins and the release of bioactive molecules such as growth factors,cytokines, receptors and adhesion molecules. Among these proteases, the matrixmetalloproteinase (MMP) family members play a crucial role in the ECM breakdown andremodeling of tissues during tumor invasion. The introduction of epigenetic strategies in thetherapeutic arsenal against cancer led to the need to evaluate the effects of suchtherapeutic approaches on cell behavior. Here we focused our attention on the effects ofepigenetic modulators, a DNA hypomethylating agent and histone deacetylase inhibitors(HDAC inhibitors or HDI), on the expressions of MMP-1,-2, and -9 in the human HT1080fibrosarcoma cell line. First, we showed that the DNA hypomethylating drug 5-aza-2’deoxycytidine (5-azadC) increases MMP-1, -2, -9 expressions both at the mRNA andprotein levels. These changes in gene expression are associated with (i) a global DNAdemethylation and with (ii) modifications in chromatin supra-organization which globally correspond to a more decondensed chromatin. Moreover, 5-azadC is able to increase theinvasive properties capability of the HT1080 cells mainly via MMP-1 transcription-dependent expression. This enhancement of transcription occurs through (i) Sp1 recruitment, (ii)chromatin remodeling and (iii) in absence of full demethylation on the MMP-1 genepromoter. Using different HDIs reveals that HDACs could potentially play a role in MMP-1expression. The pan-HDI trichostatin A (TSA) act in synergy with 5-azadC and is able tomodulate MMP-1 expression and nuclear texture, but only after DNA demethylation. Incontrast, the HDAC class I inhibitor, MS-275, which display additive effect with 5-azadC, isable to induce, alone, MMP-1 gene expression through chromatin remodeling and p300recruitment to its promoter. These data suggest that epigenetic mechanisms play a crucialrole in MMP-1 expression control in HT1080 cells thus influencing the invasive potential ofthese cells

Mining old transcriptomes to predict HSC age

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SC-RNA-seq assisted synthesis of a Boolean network to model early haematopoiesis aging

We previously analyzed 15 000 transcriptomes of mouse hematopoietic stem and progenitor cells (HSPCs) from young and aged mice and characterized the early differentiation of the hematopoietic stem cells (HSCs) according to age, thanks to cell clustering and pseudotime analysis (Herault et al, 2021). In this study, we propose an original strategy to build a Boolean gene network explaining HSC priming and homeostasis based on our previous single cell data analysis and the actual knowledge of these biological processes (graphical abstract). We first made an exhaustive analysis of the transcriptional network on selected HSPC states in the differentiation trajectory of HSCs by identifying regulons, modules formed by a transcription factor (TFs) and its targets, from the scRNA-seq data., From this global view of transcriptional regulation in early hematopoiesis, we chose to focus on 15 components, 13 selected TFs (Tal1, Fli1, Gata2, Gata1, Zfpm1, Egr1, Junb, Ikzf1, Myc, Cebpa, Bclaf1, Klf1, Spi1) and two complexes regulating the ability of HSC to cycle (CDK4/6 - Cyclines D and CIP/KIP). We then defined the relations in the differentiation dynamics we want to model ((non) reachability, attractors) between the HSPC states that are partial observations of binarized activity levels of the 15 components. Besides, we defined an influence graph of possibly involved TF interactions in the dynamic using regulon analysis on our single cell data and interactions from the literature. Next, using Answer Set Programming (ASP) and considering these inputs, we obtained a Boolean model as a final solution of a Boolean satisfiability problem. Finally, we perturbed the model according to aging differences underlined from our regulon analysis. This led us to propose new regulatory mechanisms at the origin of the differentiation bias of aged HSCs, explaining the decrease in the transcriptional priming of HSCs toward all mature cell types except megakaryocytes

A novel Boolean network inference strategy to model early hematopoiesis aging

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Single Cell Transcriptomics to Understand HSC Heterogeneity and Its Evolution upon Aging

International audienceSingle-cell transcriptomic technologies enable the uncovering and characterization of cellular heterogeneity and pave the way for studies aiming at understanding the origin and consequences of it. The hematopoietic system is in essence a very well adapted model system to benefit from this technological advance because it is characterized by different cellular states. Each cellular state, and its interconnection, may be defined by a specific location in the global transcriptional landscape sustained by a complex regulatory network. This transcriptomic signature is not fixed and evolved over time to give rise to less efficient hematopoietic stem cells (HSC), leading to a well-documented hematopoietic aging. Here, we review the advance of single-cell transcriptomic approaches for the understanding of HSC heterogeneity to grasp HSC deregulations upon aging. We also discuss the new bioinformatics tools developed for the analysis of the resulting large and complex datasets. Finally, since hematopoiesis is driven by fine-tuned and complex networks that must be interconnected to each other, we highlight how mathematical modeling is beneficial for doing such interconnection between multilayered information and to predict how HSC behave while aging

Single-cell RNA-seq reveals a concomitant delay in differentiation and cell cycle of aged hematopoietic stem cells

International audienceBackground: Hematopoietic stem cells (HSCs) are the guarantor of the proper functioning of hematopoiesis due to their incredible diversity of potential. During aging, heterogeneity of HSCs changes, contributing to the deterioration of the immune system. In this study, we revisited mouse HSC compartment and its transcriptional plasticity during aging at unicellular scale. Results: Through the analysis of 15,000 young and aged transcriptomes, we identified 15 groups of HSCs revealing rare and new specific HSC abilities that change with age. The implantation of new trajectories complemented with the analysis of transcription factor activities pointed consecutive states of HSC differentiation that were delayed by aging and explained the bias in differentiation of older HSCs. Moreover, reassigning cell cycle phases for each HSC clearly highlighted an imbalance of the cell cycle regulators of very immature aged HSCs that may contribute to their accumulation in an undifferentiated state. Conclusions: Our results establish a new reference map of HSC differentiation in young and aged mice and reveal a potential mechanism that delays the differentiation of aged HSCs and could promote the emergence of age-related hematologic diseases

Human ZKSCAN3 and Drosophila M1BP are functionally homologous transcription factors in autophagy regulation

International audienceAutophagy is an essential cellular process that maintains homeostasis by recycling damaged organelles and nutrients during development and cellular stress. ZKSCAN3 is the sole identified master transcriptional repressor of autophagy in human cell lines. How ZKSCAN3 achieves autophagy repression at the mechanistic or organismal level however still remains to be elucidated. Furthermore, Zkscan3 knockout mice display no discernable autophagy-related phenotypes, suggesting that there may be substantial differences in the regulation of autophagy between normal tissues and tumor cell lines. Here, we demonstrate that vertebrate ZKSCAN3 and Drosophila M1BP are functionally homologous transcription factors in autophagy repression. Expression of ZKSCAN3 in Drosophila prevents premature autophagy onset due to loss of M1BP function and conversely, M1BP expression in human cells can prevent starvation-induced autophagy due to loss of nuclear ZKSCAN3 function. In Drosophila ZKSCAN3 binds genome-wide to sequences targeted by M1BP and transcriptionally regulates the majority of M1BP-controlled genes, demonstrating the evolutionary conservation of the transcriptional repression of autophagy. This study thus allows the potential for transitioning the mechanisms, gene targets and plethora metabolic processes controlled by M1BP onto ZKSCAN3 and opens up Drosophila as a tool in studying the function of ZKSCAN3 in autophagy and tumourigenesis

3014 – ORAL PRESENTATION: SINGLE-CELL RNA-SEQ REVEALS A CONCOMITANT DELAY IN DIFFERENTIATION AND CELL CYCLE OF AGED HEMATOPOIETIC STEM CELL

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New Insights into PLZF/Rara Mechanism during APL Onset: EZH2 on the Road

International audienceINTRODUCTION Inappropriate recruitment of functional Polycomb-Group proteins (PcG) may trigger epigenetic unbalance at very specific genomic loci that substantially contribute to the pathogenesis of Acute Myeloid Leukemia (AML). This concept was first described in Acute Promyelocytic Leukemia (APL) in which PcG proteins were abnormally addressed due to the expression of X-RARA fusion proteins and were involved in the treatment response of the disease. For instance, in the context of APL with t(11;17)(q23;q21) translocation, the resulted oncogenic fusion protein PLZF/RARA leads to abnormal recruitment of PcG at the promoters of genes involved in acid-trans-retinoic acid (ATRA) response (Boukarabila et al.). As a consequence of that and compared to other APL subtypes (e-g: PML/RARA), APL with PLZF/RARA are insensitive to ATRA. In the recent years, a repertoire of cis-regulatory enhancer elements has been dissected to reveal important insight about leukemia onset and define new subsets of the disease with different treatment responses (Bhagwat et al). As we previously reported that PLZF displayed epigenetic specificity on enhancers (Poplineau et al.) we questioned the role of PLZF/RARA on these regulatory regions during APL onset. METHODS We performed in vivo comparative epigenomic profiling (H3K27ac, H3K4me1, H3K27me3 and H3K4me3 ChIPseq) between normal myeloid progenitors (granulocyte-monocyte progenitors purified from wild-type mice) and PLZF/RARA transformed mouse progenitors (late promyelocytes purified from mice developing APL). To question the role of PcG in APL onset, we used retroviral overexpression of PLZF/RARA and transduced Lineage negative cells from a conditional KO EZH2 mouse model. Transformation was tested by replating assay and cells were characterized by FACS and morphology analyses. We also performed EZH2 pharmacological inhibition using GSK126 and UNC1999 on a human cell line expressing the fusion protein PLZF/RARA. We analyzed the impact of this inhibition on their transcriptomic signature (RNAseq) and their proliferative capacity. RESULTS Upon PLZF/RARA expression and APL progression, specific cis-regulatory enhancer elements were targeted by the H3K27me3 PcG repressive mark. This gain in poised enhancer regions, upon PLZF/RARA expression reflected a reoriented PcG activity, from enhancers regulating developmental processes to those regulating stress and immune responses. To demonstrate the importance of this H3K27me3 switch for APL progression, we investigated the effect of EZH2 loss during PLZF/RARA transformation. Using a conditional KO EZH2 mouse model, we demonstrated that PLZF/RARA required EZH2 activity to efficiently transform progenitors since EZH2 loss promoted differentiation that altered the replating capacity of the PLZF/RARA expressing cells. In addition, EZH2 inhibition by GSK126 revealed some interesting benefits since it sensitized PLZF/RARA transformed progenitors to ATRA treatment. Moreover, inhibition of EZH2 with GSK126 or UNC1999 induced a decrease in the proliferation advantage of a human PLZF/RARA-inducible cell line. This was linked to a change of its transcriptomic signature towards an expression pattern closer to the one observed in the parent cell line. CONCLUSION Taken together, our data showed that PLZF/RARA modifies H3K27me3 profiles at enhancer regions and requires EZH2 activity for APL onset. Finally, our results suggest that EZH2 inhibition could be a new promising therapeutic approach for retinoic-acid resistant APL. Disclosures No relevant conflicts of interest to declare

PLZF limits enhancer activity during hematopoietic progenitor aging

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