Epigenetic information is written in chromatin. But how exactly do epigenetic mechanisms operate on the molecular level? How do chromatin alterations contribute to cell fate transitions? How does the environment influence these processes? And how does the metabolic state of a cell impact on its chromatin structure and its epigenetic memory?
These are the questions we address in the lab. Studying stem cells and cancer we focus on molecular aspects of epigenetic regulation and on the question of whether we can translate this knowledge into diagnostic and therapeutic tools for the management of diseases such as acute myeloid leukemia and myelodysplastic syndrome.
Research
In our scientific approach we combine biochemical techniques, genetic manipulation of cell cultures and sequencing of enriched chromatin fractions to address mechanistic and functional aspects of epigenetics. Key findings are validated in vivo. For the study of cancer we combine established cell lines, primary cultures and other patient samples.
Ongoing projects in the lab are related to the several of the following themes:
The link between metabolism and epigenetic regulation.
The regulation and molecular function of histone variants.
Nuclear organization and 3D chromatin architecture
Chromatin regulators as drug targets in myeloid diseases.
Below you can find examples of fundamental and more applied projects that we are doing in the lab. For a more general overview on the research lines in the lab, we invite you to watch the recording of a recent webinar given by the group leader Marcus Buschbeck:
These are two examples of ongoing projects:
How do histone variants connect 3D chromatin architecture and metabolism?
The modular building block of chromatin structure is the nucleosome that contains a core of histone proteins. Histone variants replace replication-coupled canonical histones and thus endow local chromatin environments with unique properties. The histone variants macroH2A are unique in having a tripartite structure consisting of a N-terminal histone-fold, an intrinsically unstructured linker domain and a C-terminal macro domain (see Figure below). Recently, we have made two major discoveries. First, macroH2A proteins have a major role in the nuclear organization mediated by the linker domain (Douet et al., 2017, JCS; Kozlowski, Corujo et al., 2018, EMBO Rep). Second, by directly binding metabolites and metabolic effector proteins through their macrodomain, they impact on the metabolic regulation (discussed in Hurtado-Bagès, 2020, Mol Metab). The challenge for us now is to understand how these molecular functions mediate cellular functions in cancer, differentiation and somatic cell reprogramming (discussed in Buschbeck and Hake, 2017, Nature Reviews MCB).
A particular exciting aspect for us is to understand how macroH2As link metabolism to 3D chromatin structure. So far we know that the macrodomain of macroH2A1.1 binds the NAD+ derived metabolite ADP-ribose and ADP-ribosylated proteins such as SirT7 and PARP-1. When macroH2A1.1 is abundant, one of the net effects is PARP-1 inhibition and consequentially less NAD+ consumption by PARP-1 in the nucleus. Thereby, macroH2A1.1 facilitates NAD+ dependent respiration in mitochondria (Posavec Marjanovic, Hurtado-Bagès et al., 2017, NSMB). We are now addressing the inverse question and interested to understand how direct metabolite binding affects the function of macroH2A in 3D chromatin architecture. In addition to NAD+ metabolism and ADP-ribose, we are now turning our attention to other metabolic pathways and how they interact with chromatin through macroH2A histone variants.
To have a broader view of the role of histone variants in chromatin remodelling, consider joining us in the next EMBO Workshop "Physiology and function of histone variants", held in our institution on September 22nd-24th 2021. More information in the link below:
We are looking for a postdoc or a very skilled and independent PhD student for this project! If you are interested in the intersection between chromatin and metabolism please contact us.
Chromatin modifiers as drug targets in MDS and cancer
We believe that chromatin modifiers have great potential as drug targets. Why that? First, epigenetic changes contribute to cancer but are reversible. Second, chromatin modifiers are at the basis of epigenetic regulation and as enzymes amenable to inhibition by small molecules. Third, altering chromatin structure has great potential to sensitize to established drugs acting in the context of chromatin such as genotoxic chemotherapy.
Intrinsic and acquired resistances are the main reason for failure of current cancer treatments. We coordinate the national mini-network RESPONSE (PIE16/00011) that aims to identify urgently needed response-predicting biomarkers and new combinatorial drug targets to increase rate and durability of response. Focusing on blood cancers we are studying chromatin regulators that affect the sensitivity of cells to azanucleosides, frequently referred to as hypomethylating drugs as they inhibit DNA methyltransferases.
In 2021, we have started to coordinate the MSCA innovative training network INTERCEPT-MDS in which we pose the question if epigenetic regulation can be used to intercept early disease cells before the disease would manifest with symptoms. Please find more info on INTERCEPT-MDS here:
Michael Maher, Jeannine Diesch, Marguerite-Marie Le Pannérer, Marcus Buschbeck
Epigenetics in a Spectrum of Myeloid Diseases and Its Exploitation for Therapy
Cancers 2021, 13(7), 17466 Abr 2021, .
Mutations in genes encoding chromatin regulators are early events contributing to developing asymptomatic clonal hematopoiesis of indeterminate potential and its frequent progression to myeloid diseases with increasing severity. We focus on the subset of myeloid diseases encompassing myelodysplastic syndromes and their transformation to secondary acute myeloid leukemia. We introduce the major concepts of chromatin regulation that provide the basis of epigenetic regulation. In greater detail, we discuss those chromatin regulators that are frequently mutated in myelodysplastic syndromes. We discuss their role in the epigenetic regulation of normal hematopoiesis and the consequence of their mutation. Finally, we provide an update on the drugs interfering with chromatin regulation approved or in development for myelodysplastic syndromes and acute myeloid leukemia.
Hurtado-Bagès S, Knobloch G, Ladurner AG, Buschbeck M
The taming of PARP1 and its impact on NAD
Mol MetabAgo 2020, 38100950. Epub 12 Feb 2020
Background: Poly-ADP-ribose polymerases (PARPs) are key mediators of cellular stress response. They are intimately linked to cellular metabolism through the consumption of NAD+. PARP1/ARTD1 in the nucleus is the major NAD+ consuming activity and plays a key role in maintaining genomic integrity.
Scope of review: In this review, we discuss how different organelles are linked through NAD+ metabolism and how PARP1 activation in the nucleus can impact the function of distant organelles. We discuss how differentiated cells tame PARP1 function by upregulating an endogenous inhibitor, the histone variant macroH2A1.1.
Major conclusions: The presence of macroH2A1.1, particularly in differentiated cells, raises the threshold for the activation of PARP1 with consequences for DNA repair, gene transcription, and NAD+ homeostasis.
Kozlowski M, Corujo D, Hothorn M, Guberovic I, Mandemaker IK, Blessing C, Sporn J, Gutierrez-Triana A, Smith R, Portmann T, Treier M, Scheffzek K, Huet S, Timinszky G, Buschbeck M, Ladurner AG
MacroH2A histone variants limit chromatin plasticity through two distinct mechanisms.
EMBO Rep.Oct 2018, 19(10) . Epub 3 Sep 2018
MacroH2A histone variants suppress tumor progression and act as epigenetic barriers to induced pluripotency. How they impart their influence on chromatin plasticity is not well understood. Here, we analyze how the different domains of macroH2A proteins contribute to chromatin structure and dynamics. By solving the crystal structure of the macrodomain of human macroH2A2 at 1.7 Å, we find that its putative binding pocket exhibits marked structural differences compared with the macroH2A1.1 isoform, rendering macroH2A2 unable to bind ADP-ribose. Quantitative binding assays show that this specificity is conserved among vertebrate macroH2A isoforms. We further find that macroH2A histones reduce the transient, PARP1-dependent chromatin relaxation that occurs in living cells upon DNA damage through two distinct mechanisms. First, macroH2A1.1 mediates an isoform-specific effect through its ability to suppress PARP1 activity. Second, the unstructured linker region exerts an additional repressive effect that is common to all macroH2A proteins. In the absence of DNA damage, the macroH2A linker is also sufficient for rescuing heterochromatin architecture in cells deficient for macroH2A.
Marjanović MP, Hurtado-Bagès S, Lassi M, Valero V, Malinverni R, Delage H, Navarro M, Corujo D, Guberovic I, Douet J, Gama-Perez P, Garcia-Roves PM, Ahel I, Ladurner AG, Yanes O, Bouvet P, Suelves M, Teperino R, Pospisilik JA, Buschbeck M
MacroH2A1.1 regulates mitochondrial respiration by limiting nuclear NAD(+) consumption.
Nat. Struct. Mol. Biol.9 Oct 2017, . Epub 9 Oct 2017
Histone variants are structural components of eukaryotic chromatin that can replace replication-coupled histones in the nucleosome. The histone variant macroH2A1.1 contains a macrodomain capable of binding NAD(+)-derived metabolites. Here we report that macroH2A1.1 is rapidly induced during myogenic differentiation through a switch in alternative splicing, and that myotubes that lack macroH2A1.1 have a defect in mitochondrial respiratory capacity. We found that the metabolite-binding macrodomain was essential for sustained optimal mitochondrial function but dispensable for gene regulation. Through direct binding, macroH2A1.1 inhibits basal poly-ADP ribose polymerase 1 (PARP-1) activity and thus reduces nuclear NAD(+) consumption. The resultant accumulation of the NAD(+) precursor NMN allows for maintenance of mitochondrial NAD(+) pools that are critical for respiration. Our data indicate that macroH2A1.1-containing chromatin regulates mitochondrial respiration by limiting nuclear NAD(+) consumption and establishing a buffer of NAD(+) precursors in differentiated cells.
Variants of core histones and their roles in cell fate decisions, development and cancer.
Nat. Rev. Mol. Cell Biol.1 Feb 2017, . Epub 1 Feb 2017
Histone variants endow chromatin with unique properties and show a specific genomic distribution that is regulated by specific deposition and removal machineries. These variants - in particular, H2A.Z, macroH2A and H3.3 - have important roles in early embryonic development, and they regulate the lineage commitment of stem cells, as well as the converse process of somatic cell reprogramming to pluripotency. Recent progress has also shed light on how mutations, transcriptional deregulation and changes in the deposition machineries of histone variants affect the process of tumorigenesis. These alterations promote or even drive cancer development through mechanisms that involve changes in epigenetic plasticity, genomic stability and senescence, and by activating and sustaining cancer-promoting gene expression programmes.
Drug repositioning as a fast and cost effective approach to personalized therapies. A pilot study on myelodysplastic syndrome and acute myeloid leukaemia
Dissecting the Role of Polycomb Complexes in the Pathogenesis of Myelodysplastic Syndromes (MDS) and the Evolution to Acute Myeloid Leukemia (DJCLS R 14/16)
