Arquitectura Nuclear de la Leucemia

ICO - Germans Trias i Pujol

Josep Carreras Leukaemia Research Institute
Ctra. de Can Ruti, Camí de les Escoles s/n
08916 Badalona, Barcelona
Spain

Directions

Summary

The main goal of our lab is to understand the molecular mechanisms that induce and control the malignancy of leukemic cells. For that, we combine and integrate state-of-the-art genomics technology, genome-engineering tools, optogenetic and advanced microscopy imaging to study gene regulatory network in human leukemic cells. We focus particularly in the role of the three-dimensional (3D) genome organization in leukemic phenotype and how fusion protein induced by chromosomal translocation can alter the chromatin organization. Beyond our fundamental discoveries, we aim to uncover new targets and biomedical applications for the treatment of lymphoid malignancies.

 

Research

Understanding the mechanisms that control cell identity and gene regulation and whether they can be used therapeutically are fundamental objectives of current biomedical science. Indeed, the precise regulation of gene expression is crucial to guarantee tissue homeostasis and its alteration drives cell disorders and diseases. In addition to transcription factors and chromatin modifiers, the 3D genome organization has recently emerged as an instrumental player of gene regulation. Indeed, the genome is highly organized into the nucleus into various structures including compartments, domains and loops. These structures are crucial to maintain the physical interactions between regulatory regions and the gene expression. The comprehensive integration of the 3D genome organization with other layers of the gene regulatory network is therefore crucial to uncover the molecular mechanisms beyond the disease and identify new potential therapeutic targets. 

Important efforts have been made to define the basis of acute lymphoblastic leukemia (ALL) and identify the genetic lesions contributing to leukemogenesis. The most common mutations affect transcription factors or chromatin modifiers. Particularly, chromosomal translocations that create chimeric transcription factors are often associated to ALL. These mutations alter the protein functions, modify the transcriptional program and initiate the leukemogenesis. In the lab we investigate the multiple layers of the gene regulatory network to understand the dysregulation provoked by mutant proteins and its role in the pathogenesis.

 

More specifically, the research in our lab is developed around the following axes: 

  •   Uncovering the biophysical properties of the chimeric E2A-PBX1 oncogene and its role on 3D genome alteration and pathogenesis of B cell acute leukemia

We are developing new research lines to explore the molecular mechanisms driving nuclear organization of cancer cells, focusing on chimeric transcription factors generated by chromosomal translocation and its impact on 3D genome organization and pathogenesis. Our recent findings suggest that the chimeric protein E2A-PBX1, associated with one of the most frequent B-acute lymphoid leukaemia (B-ALL) translocations, has liquid-liquid phase separation (LLPS) properties that can drive the alteration of the 3D genome organization and induce leukemogenesis. We combine and integrate multi-omics experimental and computational approaches encompassing state-of-the-art technologies (chromatin conformation capture, NGS, genome editing, degron system, optogenetic, advance microscopy) to elucidate the role of the chimeric protein E2A-PBX1 on 3D chromatin organization and B-ALL malignancy. Understanding how translocation can affect biochemical properties of protein and alter the genome organization and the gene expression will offer potential new biomedical applications for the treatment of haematological malignancies.

 

  •   Identification and characterization of genome topology alteration in B cell acute lymphoblastic leukaemia

Recent advances in the molecular approaches to capture the chromosome 3D conformation are improving the current appreciation of how genome architecture affect its function in distinct tissues and diseases. Long-range chromatin interactions are organized in different layers from chromatin compartments to topologically associated domains and chromatin loops at the highest resolution. These 3D features are known to play a role in constraining gene expression patterns. In cancer cells, alteration of the genome topology also impacts gene regulation. Our lab uses a unique model of “cell normalization” of human leukemic cells via transcription factor-mediated transdifferentiation. This process leads to a rewiring of the gene expression pattern, including several oncogenes. We employ genomics technologies on leukemic cells undergoing a conversion to non-tumorigenic macrophages to study the dynamical interplay between oncogenes expression and key epigenetic regulatory mechanisms including genome topology. The impact of proposed 3D genome features on the leukemic phenotype using genome editing techniques followed by in vitro and in vivo assays. Our study aims to generate significant insights about the role of architectural features of the genome during cancer development and to contribute in designing novel therapeutic strategies to treat cancer. 

 

  •   Characterization of transcription factor mutations and their role in 3D genome organization alteration and leukemogenesis

Somatic alterations of the lymphoid transcription factors (TFs) PAX5 and BCL11b are hallmarks of B and T cell precursor ALL, respectively.  While many of these somatic mutations have been classified, their impacts on the molecular mechanisms of the TFs remain elusive. Therefore, we focus on mutation altering domains essential to the biochemical properties of the TFs and evaluate how these mutations affect their properties and the ability of the TFs to shape the genome. We aim to precisely profile the aberrant function of the TFs and to link it to the altered gene regulatory network observed in disease. 

  

Awards

2022 Ramón y Cajal Fellowship

2019 “Investigador” Individual Fellowship from the Spanish association against the cancer (AECC).  

2017 Marie Skłodowska Curie Individual Fellowship

 

People

NombreRol
Gregoire StikGroup Leader

Selected publications

Cuartero S, Stik G, Stadhouders R

Three-dimensional genome organization in immune cell fate and function.

Nat Rev Immunol 20 Sep 2022, . Epub 20 Sep 2022
Immune cell development and activation demand the precise and coordinated control of transcriptional programmes. Three-dimensional (3D) organization of the genome has emerged as an important regulator of chromatin state, transcriptional activity and cell identity by facilitating or impeding long-range genomic interactions among regulatory elements and genes. Chromatin folding thus enables cell type-specific and stimulus-specific transcriptional responses to extracellular signals, which are essential for the control of immune cell fate, for inflammatory responses and for generating a diverse repertoire of antigen receptor specificities. Here, we review recent findings connecting 3D genome organization to the control of immune cell differentiation and function, and discuss how alterations in genome folding may lead to immune dysfunction and malignancy.
Más información
Plana-Carmona M, Stik G, Bulteau R, Segura-Morales C, Alcázar N, Wyatt CDR, Klonizakis A, de Andrés-Aguayo L, Gasnier M, Tian TV, Torcal Garcia G, Vila-Casadesús M, Plachta N, Serrano M, Francesconi M, Graf T

The trophectoderm acts as a niche for the inner cell mass through C/EBPα-regulated IL-6 signaling.

Stem Cell Reports 13 Sep 2022, 17 (9) 1991-2004. Epub 11 Ago 2022
IL-6 has been shown to be required for somatic cell reprogramming into induced pluripotent stem cells (iPSCs). However, how Il6 expression is regulated and whether it plays a role during embryo development remains unknown. Here, we describe that IL-6 is necessary for C/EBPα-enhanced reprogramming of B cells into iPSCs but not for B cell to macrophage transdifferentiation. C/EBPα overexpression activates both Il6 and Il6ra genes in B cells and in PSCs. In embryo development, Cebpa is enriched in the trophectoderm of blastocysts together with Il6, while Il6ra is mostly expressed in the inner cell mass (ICM). In addition, Il6 expression in blastocysts requires Cebpa. Blastocysts secrete IL-6 and neutralization of the cytokine delays the morula to blastocyst transition. The observed requirement of C/EBPα-regulated IL-6 signaling for pluripotency during somatic cell reprogramming thus recapitulates a physiologic mechanism in which the trophectoderm acts as niche for the ICM through the secretion of IL-6.
Más información
Stikker BS, Stik G, van Ouwerkerk AF, Trap L, Spicuglia S, Hendriks RW, Stadhouders R

Severe COVID-19-associated variants linked to chemokine receptor gene control in monocytes and macrophages.

Genome Biol 14 Abr 2022, 23 (1) 96. Epub 14 Abr 2022
Genome-wide association studies have identified 3p21.31 as the main risk locus for severe COVID-19, although underlying mechanisms remain elusive. We perform an epigenomic dissection of 3p21.31, identifying a CTCF-dependent tissue-specific 3D regulatory chromatin hub that controls the activity of several chemokine receptor genes. Risk SNPs colocalize with regulatory elements and are linked to increased expression of CCR1, CCR2 and CCR5 in monocytes and macrophages. As excessive organ infiltration of inflammatory monocytes and macrophages is a hallmark of severe COVID-19, our findings provide a rationale for the genetic association of 3p21.31 variants with elevated risk of hospitalization upon SARS-CoV-2 infection.
Más información
Soochit W, Sleutels F, Stik G, Bartkuhn M, Basu S, Hernandez SC, Merzouk S, Vidal E, Boers R, Boers J, van der Reijden M, Geverts B, van Cappellen WA, van den Hout M, Ozgur Z, van IJcken WFJ, Gribnau J, Renkawitz R, Graf T, Houtsmuller A, Grosveld F, Stadhouders R, Galjart N

CTCF chromatin residence time controls three-dimensional genome organization, gene expression and DNA methylation in pluripotent cells.

Nat Cell Biol Ago 2021, 23 (8) 881-893. Epub 29 Jul 2021
The 11 zinc finger (ZF) protein CTCF regulates topologically associating domain formation and transcription through selective binding to thousands of genomic sites. Here, we replaced endogenous CTCF in mouse embryonic stem cells with green-fluorescent-protein-tagged wild-type or mutant proteins lacking individual ZFs to identify additional determinants of CTCF positioning and function. While ZF1 and ZF8-ZF11 are not essential for cell survival, ZF8 deletion strikingly increases the DNA binding off-rate of mutant CTCF, resulting in reduced CTCF chromatin residence time. Loss of ZF8 results in widespread weakening of topologically associating domains, aberrant gene expression and increased genome-wide DNA methylation. Thus, important chromatin-templated processes rely on accurate CTCF chromatin residence time, which we propose depends on local sequence and chromatin context as well as global CTCF protein concentration.
Más información
Stik G, Vidal E, Barrero M, Cuartero S, Vila-Casadesús M, Mendieta-Esteban J, Tian TV, Choi J, Berenguer C, Abad A, Borsari B, le Dily F, Cramer P, Marti-Renom MA, Stadhouders R, Graf T

CTCF is dispensable for immune cell transdifferentiation but facilitates an acute inflammatory response.

Nat. Genet. 8 Jun 2020, . Epub 8 Jun 2020
Three-dimensional organization of the genome is important for transcriptional regulation
Más información
Tian TV, Di Stefano B, Stik G, Vila-Casadesús M, Sardina JL, Vidal E, Dasti A, Segura-Morales C, De Andrés-Aguayo L, Gómez A, Goldmann J, Jaenisch R, Graf T

Whsc1 links pluripotency exit with mesendoderm specification.

Nat Cell Biol Jul 2019, 21 (7) 824-834. Epub 24 Jun 2019
How pluripotent stem cells differentiate into the main germ layers is a key question of developmental biology. Here, we show that the chromatin-related factor Whsc1 (also known as Nsd2 and MMSET) has a dual role in pluripotency exit and germ layer specification of embryonic stem cells. On induction of differentiation, a proportion of Whsc1-depleted embryonic stem cells remain entrapped in a pluripotent state and fail to form mesendoderm, although they are still capable of generating neuroectoderm. These functions of Whsc1 are independent of its methyltransferase activity. Whsc1 binds to enhancers of the mesendodermal regulators Gata4, T (Brachyury), Gata6 and Foxa2, together with Brd4, and activates the expression of these genes. Depleting each of these regulators also delays pluripotency exit, suggesting that they mediate the effects observed with Whsc1. Our data indicate that Whsc1 links silencing of the pluripotency regulatory network with activation of mesendoderm lineages.
Más información
Stik G, Graf T

Hoxb5, a Trojan horse to generate T cells.

Nat Immunol Mar 2018, 19 (3) 210-212. Más información
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Current projects

Genome topology alteration in B cell acute lymphoblastic leukaemia.

Responsable:Gregoire Stik
Financiadores:
Fecha de inicio:01/01/2019
Fecha de finalización:31/12/2023