IMCBio International PhD Program

Call is closed.

The Integrative Molecular and Cellular Biology (IMCBio) graduate school wishes to attract talented PhD students to the University of Strasbourg to start innovative research projects in 2021. The IMCBio graduate school builds on the strong research developed in five research institutes: IGBMC, IBMC, IBMP, GMGM and the Institute for Viral and Liver Disease, which covers all areas of molecular and cellular biology at the levels of molecular factors, genes, cells and organisms from model systems to diseases.

Networking teams of these five Institutes, four Laboratories of Excellence (LabEx), INRT (Integrative biology: Nuclear dynamics, Regenerative and Translational medicine), MitoCross (Mitochondria-nucleus Cross-talk), NetRNA (Networks of regulatory RNAs) and HepSYS (Functional genomics of viral hepatitis and liver disease) provide a unique opportunity to get a broad overview of every aspects of gene regulation covering nuclear organization, epigenetics, transcriptional, translational, post-transcriptional and post-translational events as well as crosstalks between the nucleus, cytoplasm and organelles in eukaryotes and cell-to-cell communication..

The training community of IMCBio PhD students builds on the expertise of LabEx researchers working in synergy. Trainees also benefit from outstanding technology infrastructure and platforms to develop high-level research projects in a stimulating and interdisciplinary environment. The IMCBio graduate school offers this year up to 13 PhD fellowships for highly motivated applicants of academic excellence. So if you want to start an innovative research project in 2021, then register down below to candidate and join the IMCBio graduate school!
GMGM logo
IVLD logo
IGBMC logo
IBMP logo
IBMC logo

Architecture and Reactivity of RNA (LabEx NetRNA)

PhD 2021-1 Characterization of bacterial stress response at single-cell resolution

LabEx NetRNA - Networks of Regulatory RNAs across kingdoms and dynamical responses to biotic and abiotic stresses, http://labex-ibmc.u-strasbg.fr/NetRNA/index.php

Team : Digital Biology of RNA.

Team leader: Michael Ryckelynck, m.ryckelynck@unistra.fr, IBMC-CNRS 2, Allée Konrad Roentgen, 67 084 Strasbourg Cedex, http://labex-ibmc.u-strasbg.fr/NetRNA/team.php?id=4

Bacteria are constantly exposed to changing environment and a variety of stress to which they have to adapt their gene expression landscape. In pathogenic bacteria such adaptation is also often linked to virulence. Several stress response pathways have now been identified, one of them, the stringent response, being involved in the adaptation to nutrient starvation. The main steps of this pathway have been deciphered, in particular those involving the production and effect of the nucleotide-derived ppGpp, an alarmone mediating the whole process. Yet, thought the biochemistry of the process is well understood, the degree to which the pathway is activated within individuals of a population remains unclear and largely unexplored. Said differently, do all the bacteria activate the pathway homogeneously throughout the population or are there different sub-populations (some activating it and others staying inactive). If so, what are the dynamics and kinetics of such population heterogeneity? Such information is of prime importance to properly understand bacteria adaptation.  

This PhD project will start to address these questions by combining innovative imaging tools, RNA engineering and microfluidics. Indeed, our group is currently working at developing a genetically encoded ppGpp biosensor (i.e., an RNA molecule becoming highly fluorescent in the presence of ppGpp). The thesis work will first consist in characterizing and refining the performances of this RNA biosensor. Then, the molecule will be expressed in bacteria and the ppGpp production monitored (e.g., by time-lapse imaging) in cell populations growing in various conditions. The collected data will shed new lights on how bacteria adapt to stress and possibly open new ways of interfering with this pathway. 

Key words: Single-cell analysis, microfluidics, ppGpp biosensor, light-up RNA aptamer, structure-function characterization, in vitro selection. 

  • PhD supervisors: Michael Ryckelynck, m.ryckelynck@unistra.fr, http://labex-ibmc.u-strasbg.fr/NetRNA/team.php?id=4
  • Team members: 2 post-docs, 3 PhD students, 1 engineer.
  • 3 relevant publications: 1) Bouhedda, F.; Fam, K.T.; Collot, M.; Autour, A.; Marzi, S.; Klymchenko, A.; Ryckelynck, M.* (2020) A dimerization-based fluorogenic dye-aptamer module for RNA imaging in live cells. Nature Chemical Biology, 16, 69-76.2) Trachman, R.; Autour, A; Jeng, S. C. ; Abdolahzadeh, A.; Andreoni, A.; Cojocaru, R.; Dolgosheina, L.; Knutson, J.R.; Ryckelynck, M.; Unrau, P.J.; Ferre-D'Amare, A. (2019) Structure and functional reselection of the Mango-III fluorogenic RNA aptamer. Nature Chemical Biology, 15, 472-479. 3) Autour, A.; Jeng, S.C.; Cawte, A.; Abdolahzadeh, A.; Galli, A.; Panchapakesan, S.S.; Rueda, D.*; Ryckelynck, M.*; Unrau, P.J.* (2018) Fluorogenic RNA Mango Aptamers for Imaging Small noncoding RNAs in Mammalian Cells. Nature Communications, 9, 656. 
  • Number of PhDs in progress: 3 PhDs in progress: from 01-Oct-2018 to 30-Sept-2021, from 01-Dec-2017 to 30-Nov-2021, from 01-Oct -2020 to 30-Sept-2023.
PhD 2021-2 A functional study of small proteins and of RNA chaperone proteins in translational control in Staphylococcus aureus: a focus on small ORF genes, the hidden part of the genome

LabEx NetRNA - Networks of Regulatory RNAs across kingdoms and dynamical responses to biotic and abiotic stresses, http://labex-ibmc.u-strasbg.fr/NetRNA/index.php

Team : mRNAs and regulatory RNAs in bacteria.

Team leader: Pascale Romby, p.romby@ibmc-cnrs.unistra.fr, + 33 (0)3 88 41 70 68, IBMC-CNRS 2, Allée Konrad Roentgen, 67 084 Strasbourg Cedex, http://labex-ibmc.u-strasbg.fr/NetRNA/team.php?id=3

Staphylococcus aureus is a major opportunistic human pathogen, which has evolved many strategies to regulate the synthesis of its virulence factors in response to the host, stress and environmental changes. Our team has demonstrated that translation regulation mediated by regulatory RNAs and/or RNA-binding proteins, contributed to these adaptive processes. Recent advancement in mass-spectrometry and RNA-seq approaches have allowed genome-wide identification of translation initiation sites and the annotation of thousands of small proteins (50 or fewer amino acids) acting as regulators of larger proteins in the model bacteria Escherichia coli and eukaryotes. Their discovery and characterization of their functions have not yet been attempted in S. aureus. Using combination of genome-wide approaches, bioinformatics, genetics and biochemical analyses, the project will characterize the small open reading frames (sORF), the hidden regions of the genome of S. aureus, and will give an integrated view of the function of RNA-binding proteins in translational regulation. We will also provide a global estimation of the trans- and cis-acting regulatory signals including upstream sORFs, SD-lacking mRNAs, leaderless mRNAs, recoding events, dual-functional sRNAs, mRNA structures and their interplay with RNA chaperones. This work will bring the missing information required to better understand S. aureus physiopathology.  

Key words: Staphylococcus aureus; translation regulation; sORF; RNA chaperone; Regulatory networks; Ribosome profiling. 

  • PhD supervisor: Stefano Marzi, s.marzi@ibmc-cnrs.unistra.fr, + 33 (0)3 88 41 70 62, http://labex-ibmc.u-strasbg.fr/NetRNA/team.php?id=3
  • Team members: 12.
  • 3 relevant publications: 1) Lalaouna D., Baude J., Wu Z., Tomasini A., Chicher J., Marzi S., Vandenesch F., Romby P., Caldelari I. and Karen Moreau. RsaC sRNA modulates the oxidative stress response of Staphylococcus aureus during manganese starvation (2019). Nucleic Acids Research, 47(18):9871-9887. doi: 10.1093/nar/gkz728. 2) Bronesky D, Desgranges E, Corvaglia A, François P, Caballero CJ, Prado L, Toledo-Arana A, Lasa I, Moreau K, Vandenesch F, Marzi S, Romby P, Caldelari I. A multifaceted small RNA modulates gene expression upon glucose limitation in Staphylococcus aureus. (2019). EMBO J. pii: e99363. doi: 10.15252/embj.201899363. 3) Georg J., Lalaouna D., Hou S., Lott S. C., Caldelari I., Marzi S., Hess W. R., Romby P. The power of cooperation: Experimental and computational approaches in the functional characterization of bacterial sRNAs (2019). Mol Microbiol. doi: 10.1111/mmi.14420.     
  • Number of PhDs in progress: 4 (2017, 2019, 2019, 2020).
PhD 2021-3 Regulation of endogenous dsRNA sensing upon viral infections

LabEx NetRNA - Networks of Regulatory RNAs across kingdoms and dynamical responses to biotic and abiotic stresses, http://labex-ibmc.u-strasbg.fr/NetRNA/index.php

Team : Non-coding RNAs and viral infections.

Team leader: Dr Sébastien Pfeffer, s.pfeffer@ibmc-cnrs.unistra.fr, + 33 (0)3 88 41 70 60, IBMC-CNRS 2, Allée Konrad Roentgen, 67 084 Strasbourg Cedex, http://labex-ibmc.u-strasbg.fr/NetRNA/team.php?id=2

Viral infections represent a significant health, social and economic burden worldwide. The full understanding of the crosstalk between virus and host innate immunity is crucial to better prepare and find treatments in the future. Foreign double stranded (ds)RNA sensing by cellular factors is a conserved mechanism in antiviral innate immunity. Endogenous (endo) dsRNAs also accumulate under specific conditions and their sensing has been so far linked to human autoimmune diseases. Whether endo dsRNA sensing plays a role during viral infection remains to be fully explored.  

The overall goal of this thesis project is to study the endo dsRNA regulation in human cells upon viral infection. The main objectives are to characterize the endo dsRNAs accumulating during viral infection in human cells and to elucidate whether endo dsRNA sensing contributes to the antiviral response. 

The doctoral student will contribute to the project by using both genome-wide approaches (RNA-Seq, proteomics, etc.) and classical molecular biology techniques to study RNA-RNA or RNA-protein interactions. In addition, he/ she will be involved in the development of dCas-13-based live imaging approaches to track RNA targets of interest. Moreover, he/she will gain practical laboratory experience in molecular virology of emerging viruses such as Sindbis virus, Chikungunya virus and Zika virus. 

Key words: dsRNA, RNA sensing, virus, innate immunity, gene expression regulation.

  • PhD supervisors: Dr Sébastien Pfeffer and Dr Erika Girardi, s.pfeffer@ibmc-cnrs.unistra.fr / e.girardi@ibmc-cnrs.unistra.fr, + 33 (0)3 88 41 70 60 / + 33 (0)3 88 41 70 67, IBMC-CNRS 2, Allée Konrad Roentgen, 67 084 Strasbourg Cedex, http://labex-ibmc.u-strasbg.fr/NetRNA/team.php?id=2
  • Team members: Erika Girardi (MCU), Aurélie Fender (CR CNRS), Mélanie Messmer (IE CNRS), Monika Vilimova (PhD Student 3rd year), Morgane Baldaccini (PhD student 2nd year), Yasmine Amrani (PhD student 1st year), Charline Pasquier (M2 student). 
  • 3 relevant publications: 1) Petitjean O, Girardi E, Ngondo RP, Lupashin V, Pfeffer S. Genome-Wide CRISPR-Cas9 Screen Reveals the Importance of the Heparan Sulfate Pathway and the Conserved Oligomeric Golgi Complex for Synthetic Double-Stranded RNA Uptake and Sindbis Virus Infection. mSphere. 2020 Nov 11;5(6):e00914-20. doi: 10.1128/mSphere.00914-20. 2) López P, Girardi E, Mounce BC, Weiss A, Chane-Woon-Ming B, Messmer M, Kaukinen P, Kopp A, Bortolamiol-Becet D, Fendri A, Vignuzzi M, Brino L, Pfeffer S. High-Throughput Fluorescence-Based Screen Identifies the Neuronal MicroRNA miR-124 as a Positive Regulator of Alphavirus Infection. J Virol. 2020 Apr 16;94(9):e02145-19. doi: 10.1128/JVI.02145-19. 3) Girardi E, Lefèvre M, Chane-Woon-Ming B, Paro S, Claydon B, Imler JL, Meignin C, Pfeffer S. Cross-species comparative analysis of Dicer proteins during Sindbis virus infection. Sci Rep. 2015 May 29;5:10693. doi: 10.1038/srep10693. 
  • Number of PhDs in progress: Monika Vilimova (start date: Oct 2018), Morgane Baldaccini (start date: Oct 2019), Yasmine Amrani (start date: Oct 2020).

Development and Stem Cells (LabEx INRT)

PhD 2021-4 Deciphering the origin of aging: quantitative analysis of extrachromosomal rDNA circles dynamics during entry into replicative senescence

LabEx INRT (IGBMC) - Integrative Biology : Nuclear Dynamics, Regenerative and Translational Medecine, http://igbmc.fr/

Team : Biophysics of cell growth

Team leader: Gilles Charvin, charvin@igbmc.fr  +33 (0)3 88 65 35 88, IGBMC, 1 rue Laurent Fries, 67400 Illkirch-Graffenstaden Cedex, http://charvin.igbmc.science

 

Context

Aging is a ubiquitous feature of living organisms, yet its fundamental origin still remains to be deciphered. Over the last twenty years, budding yeast has emerged as a simple yet powerful simple model to identify and characterize the molecular mechanisms that drive age-associated physiological declines: indeed, following an asymmetrical pattern of division, mother cells can generate a limited number of daughter cells (typically 25) before entering senescence and eventually dying. The main model of aging in yeast proposes that genomic instability at the rDNA locus leads to the accumulation of deleterious extrachromosomal rDNA circles (ERCs), yet the underlying mechanism remains unclear.

Objectives

We will use high-throughput image acquisition and deep learning-based image processing in a microfluidic device to detect rare recombination events leading to ERCs formation during the replicative lifespan of individual yeast cells. We will investigate the genetic determinism of ERC formation and characterize whether and how ERCs alter cellular function. Importantly, we believe that this work may contribute to understanding the fundamental causes of aging in a single-celled eukaryotic model.

Team

We are an interdisciplinary group of researchers that develops quantitative methods to understand how cellular proliferation is controlled in various contexts, such as aging and stress response. We have recently developed a new high throughput imaging device combined with a deep-learning image processing pipeline to monitor the entry into senescence of thousands of individual cells in parallel. Our team also has a strong expertise in yeast molecular biology, redox and cell cycle biology.

Key words:aging, cell division, genomic instability,  microscopy, high throughput live cell imaging, microfluidics, deep-learning,

  • PhD supervisor: Gilles Charvin, charvin@igbmc.fr  +33 (0)3 88 65 35 88, IGBMC, 1 rue Laurent Fries, 67400 Illkirch-Graffenstaden Cedex, http://charvin.igbmc.science
  • Team members:  7
  • 3 relevant publications: 1) Proteostasis collapse, a hallmark of aging, hinders the chaperone-Start network and arrests cells in G1 Moreno DF, Jenkins K, Morlot S, Charvin G, Csikasz-Nagy A, Aldea M eLife, e48240, 2019, 2) Excessive rDNA transcription drives the disruption in nuclear homeostasis during entry into senescence in budding yeast Morlot S, Jia S, Léger I, Matifas A, Gadal O, Charvin G Cell Rep, 28(2):408-422, 2019 3) Nonlinear feedback drives homeostatic plasticity in H2O2 stress response.  Goulev Y, Morlot S, Matifas A, Huang B, Molin M, Toledano MB, Charvin G  eLife, 6, e23971, 2017

 

PhD 2021-5 Role of retinoid signaling in the ontogeny and functions of microglial cells

LabEx INRT (IGBMC) - Integrative Biology : Nuclear Dynamics, Regenerative and Translational Medecine, http://igbmc.fr/

Team : Brain development and physiology

Team leader: Pascal Dollé, dolle@igbmc.fr, +33 (0)3 88 65 33 34, IGBMC, 1 rue Laurent Fries, 67404 Illkirch-Graffenstaden Cedex, http://www.igbmc.fr/research/department/1/team/3/     

Retinoid receptors are transcription factors activated upon binding of retinoic acid well known for its multiple developmental functions including ontogenesis of different neural cell types. Surprisingly, little is known on their role in ontogenesis of microglial cells (MGCs), a class of brain macrophages important for brain development, maintenance and functions of brain microcircuits, but also key regulators of neuroinflammation. Our preliminary data support important role of retinoid receptors in control of development and specification of MGCs subtypes. The project will focus on characterization of such MGC subtypes and mechanism of their development using dedicated mouse genetic models, genomic analyses, life imaging, and primary, and organotypic cultures. To understand functional relevance of such regulations we will ask how specific MGCs contribute to brain development in physiological conditions and during maternal inflammation. We will also address the role of these MGCs in the physiology of adult brain, but also physiopathology of depression and specific neurodegenerative diseases, known to be critically impacted by neuroinflammation and/or abnormal MGC functions. To this end we will attempt to genetically and pharmacologically manipulate these MGC populations in mice models of specific disorders and monitor beneficial effects of such manipulations using behavioral tests, cellular and molecular analyses.

Key words: retinoid receptors, microglial cells, development, neuropsychiatric disorders

  • PhD supervisor: Wojciech KREZEL,  krezel@igbmc.fr, +33 3 88 65 33 49, http://www.igbmc.fr/research/department/1/team/3/                                                                   
  • Team members: 8
  • 3 relevant publications: 1) Krężel, W., Rühl, R., and de Lera, A.R. (2019). Alternative retinoid X receptor (RXR) ligands. Mol Cell Endocrinol 491, 110436, 2) Niewiadomska-Cimicka, A., Krzyżosiak, A., Ye, T., Podleśny-Drabiniok, A., Dembélé, D., Dollé, P., and Krężel, W. (2017). Genome-wide Analysis of RARβ Transcriptional Targets in Mouse Striatum Links Retinoic Acid Signaling with Huntington's Disease and Other Neurodegenerative Disorders. Mol Neurobiol 54, 3859-3878, 3) Krzyzosiak, A., Szyszka-Niagolov, M., Wietrzych, M., Gobaille, S., Muramatsu, S., and Krezel, W. (2010). Retinoid x receptor gamma control of affective behaviors involves dopaminergic signaling in mice. Neuron 66, 908-920.
  • Number of PhDs in progress: 3
PhD 2021-6 Molecular analysis of a human mutation in the gene coding for the TAF8 TFIID subunit using the mouse model

LabEx INRT (IGBMC) - Integrative Biology : Nuclear Dynamics, Regenerative and Translational Medecine, http://igbmc.fr/

Team : Dynamics of chromatin structure and transcription regulation.

Team leader: László Tora,  laszlo@igbmc.fr, +33 (0)3 88 65 34 44,  IGBMC, 1 rue Laurent Fries, 67404 Illkirch-Graffenstaden Cedex,   http://www.igbmc.fr/research/department/1/team/29/

RNA polymerase II (Pol II) transcription initiation is controlled by the sequential assembly of the General Transcription Factors (GTF) at promoters. TFIID is the first GTF to bind the promoter. In Metazoans, TFIID is composed of the TATA binding protein (TBP) and 13 TBP-associated factors (TAFs). Interestingly, it has been shown that while many cells required the canonical TFIID complex, some others are less affected by depletion of some TAFs subunits. The development of the neural system seems particularly sensitive to TFIID requirement as mutations in genes coding for TFIID subunits have been associated with neurological disorders and intellectual disability in human patients.

In the mouse, Taf8 loss of function is lethal at the implantation stage. We have recently identified a homozygous splice site mutation in TAF8 in a patient with intellectual disability, developmental delay and mild microcephaly[1]. Analysis in fibroblasts derived from this patient have surprisingly shown that while the mutant TAF8 protein was not detectable and TFIID assembly was impaired, transcription is not significantly affected. 

The goal of this PhD project is to analyze the molecular consequences of the human mutation during development and in relevant cell types. To that extend, we have obtained a funding from Phenomin 2020 to generate a Taf8H mouse mutant carrying the patient mutation.  

The candidate will 1/ analyze the developmental phenotype of the homozygous mutant embryos and fetuses to study the origins of the developmental delay and microcephaly. 2/ If these mutants survive, she/he will also perform behavioral studies in collaboration with the Institut Clinique de la Souris to determine the learning abilities of the Taf8H/H mice. 3/ She/he will derive mES cells from Taf8H/H blastocysts and use in vitro differentiated neuronal cells in order to analyze TFIID assembly by immunoprecipitation associated with mass spectrometry (IP-MS) and nascent Pol II transcription. 4/ In parallel, the candidate will use CRISPR/Cas9 to generate mES lines carrying Taf mutations associated with neurological disorders in human (i.e; TAF2), in order to generate differentiated neuronal cells and analyze TFIID assembly by IP-MS and nascent Pol II transcription, in comparison to the Taf8H mutation.

[1] El-Saafin et al. (2018) Hum Mol Genet, 27(12):2171-2186 

Key words: TFIID, mouse, transcription, human mutation, RNA polymerase II, neurological disorders.

  • PhD supervisor: László Tora & Stéphane D. Vincent, laszlo@igbmc.fr / vincent@igbmc.fr,  +33 (0)3 88 65 34 44 / +33 (0)3 88 65 34 25, http://www.igbmc.fr/research/department/1/team/29/
  • Team members: 11.
  • 3 relevant publications: 1) Yu et al., TBPL2/TFIIA complex establishes the maternal transcriptome by an oocyte-specific promoter usage, Nature Commun, in press, (https://doi.org/10.1038/s41467-020-20239-4) – https://www.biorxiv.org/content/10.1101/2020.06.08.118984v2). 2) Kamenova & Mukherjee et al., Nat Commun (2019), Co-translational assembly of mammalian nuclear multisubunit complexes, 10(1):1740. 3) El-Saafin et al., Homozygous TAF8 mutation in a patient with intellectual disability results in undetectable TAF8 protein, but preserved RNA polymerase II transcription (2018) Hum Mol Genet, 27(12):2171-218
  • Number of PhDs in progress: Kenny Schumacher (October 2017),Vincent Hisler (October 2017) & Emmanuel Garcia-Sanchez (October 2020).
PhD 2021-7 Determination of the GRNs underlying a natural transdifferentiation event and analysis of the conserved modules with other transdifferentiation processes in C. elegans

LabEx INRT (IGBMC) - Integrative Biology : Nuclear Dynamics, Regenerative and Translational Medecine, http://igbmc.fr/

Team : In vivo cellular plasticity and direct reprogrammin.

Team leader: Sophie Jarriault,  sophie@igbmc.fr, +33 388653392,  IGBMC, 1 rue Laurent Fries, 67400 Illkirch-Graffenstaden Cedex, http://www.igbmc.fr/research/department/1/team/8/

It is now established that differentiated cells can change their identity. This fascinating event is called transdifferentiation (Td) when a differentiated cell is changed into another type of differentiated cell. We use as a model a natural Td event, which is remarkably 100% efficient, to understand the cellular and molecular mechanisms that allow a differentiated cell to change its identity. We propose here a thesis project to determine the nature and architecture of the Gene Regulatory Networks that drive the reprogramming of a cell, naturally, in vivo. We have already purified single transdifferentiating cells, focusing on one specific Td event, and determined their expression programme over time by scRNA-Seq. A number of candidate transcription factors have been identified that may drive different phases of this process. The project will consist of 1) Validating that the identified genes are necessary for Td and at what step. 2) Identifying their potential targets using our transcriptomic data. 3) Examining the hierarchical relationships that these genes may have with each other (e.g. transcriptional, subcellular localisation regulations) in order to propose a model of the molecular cascades involved in enabling a cell to be reprogrammed. And 4) Determining which factors and parts of these GRNs are conserved in various Td events. The results will have important implications for the understanding of the basis of certain cancers, or to improve the safety and efficiency of our reprogramming strategies for regenerative therapies.

Key words: Cellular plasticity, transdifferentiation, SOX2, C. elegans, scRNA Seq, GRN.

  • PhD supervisor: Sophie Jarriault & Christelle Gally, sophie@igbmc.fr / gally@igbmc.fr,  +33 388653392 / +33 388653391,  http://www.igbmc.fr/research/department/1/team/8/
  • Team members: 8.
  • 3 relevant publications: 1) Tissue-Specific Transcription Footprinting Using RNA PoI DamID (RAPID) in Caenorhabditis elegans. Gómez-Saldivar G, Osuna-Luque J, Semple JI, Glauser DA*, Jarriault S*, Meister P*. Genetics. vol. 216 no. 4 931-945. (2020)   * co-last author. 2) Sequential histone-modifying activities determine the robustness of transdifferentiation. Zuryn S., Ahier A., Portoso M., Redhouse White E., Margueron R., Morin M.C. & Jarriault S. Science 345(6198):826-829.  (2014)  Cited « Recommended» by Faculty 1000. 3) A C. elegans model for epithelial-neuronal transdifferentiatioN. Jarriault S.*, Schwab Y. & Greenwald I. PNAS 105(10) : 3790-5. (2008)    *, corresponding author  -  Cited « Must Read » and ranked in  « Top 10 Developmental Biology Papers »  by Faculty 1000. 
  • Number of PhDs in progress: 1 (October 2020).
PhD 2021-8 Dissecting the molecular mechanisms of immunoglobulin class switch recombination using CRISPR/Cas9

LabEx INRT (IGBMC) - Integrative Biology : Nuclear Dynamics, Regenerative and Translational Medecine, http://igbmc.fr/

Team : Molecular Biology of B cells.

Team leader: Bernardo Reina San Martin, reinab@igbmc.fr, +33 (0)3 88 65 34 46, IGBMC, 1 rue Laurent Fries, 67400 Illkirch-Graffenstaden Cedex, http://www.igbmc.fr/research/department/1/team/24/

During the course of immune responses B cells diversify their immunoglobulin (Ig) genes by somatic hypermutation (SHM) and class switch recombination (CSR). These reactions establish highly specific and adapted humoral responses by increasing antibody affinity and by allowing the expression of a different antibody isotype with unique immunological functions. SHM diversifies the variable region Immunoglobulin heavy (IgH) and light (IgL) chain genes, producing families of related clones bearing mutated receptors that are positively selected on the basis of antigen binding affinity. CSR diversifies the B cell repertoire by combining a single heavy chain variable region with a different constant region, switching the antibody isotype expressed (from IgM to IgG, IgE or IgA) while retaining the antigen specificity of the receptor. Both of these reactions are initiated by Activation Induced Cytidine Deaminase (AID), an enzyme that deaminates cytosines in DNA. AID-induced lesions are recognized by the DNA repair machinery and are processed in different ways to trigger mutations or double stranded DNA break intermediates during CSR. AID has the potential to induce significant collateral DNA damage and has been implicated in the generation of B cell malignancies. At present in is not understood how AID is specifically targeted to immunoglobulin genes or how collateral genomic damage is restricted. We have recently conducted a genome-wide CRISPR/Cas9 knockout screen using CH12 cells (a cell line that undergoes CSR very efficiently in vitro). In this screen, we have identified a number of candidate genes potentially regulating CSR and/or AID's activity. The project's goal is to generate individual knockouts in CH12 cells for the most interesting candidates to verify the phenotype and conduct initial mechanistic studies. Based on these results, conditional knockout mouse models will be generated to study SHM and CSR in vivo.

Skills required: Experience in molecular biology, biochemistry and tissue culture.

Skills that will be acquired: Training in immunology, molecular biology, biochemistry and Genome Editing (CRISPR/cas9).

Keywords: Antibody diversification, DNA Repair, Class Switch recombination, CRISPR/Cas9.

  • PhD supervisor: Bernardo Reina San Martin, reinab@igbmc.fr, +33 (0)3 88 65 34 46, http://www.igbmc.fr/research/department/1/team/24/
  • Team members: Jacques Moritz, Mélanie Rogier, Vincent Heyer, Nour El Ayoubi, Caroline Hillenbrand.  
  • 3 relevant publications: 1) Thomas-Claudepierre, A.S., I. Robert, P.P. Rocha, R. Raviram, E. Schiavo, V. Heyer, R. Bonneau, V.M. Luo, J.K. Reddy, T. Borggrefe, J.A. Skok and B. REINA-SAN-MARTIN. 2016. Mediator facilitates transcriptional activation and dynamic long-range contacts at the IgH locus during class switch recombination. J Exp Med 213:303-312. 16. 2) Tsouroula, K., A. Furst, M. Rogier, V. Heyer, A. Maglott-Roth, A. Ferrand, B. REINA-SAN-MARTIN* and E. Soutoglou*. 2016. Temporal and Spatial Uncoupling of DNA Double Strand Break Repair Pathways within Mammalian Heterochromatin. Mol Cell 63:293-305. * Co-Last Author. 3) Thomas-Claudepierre, A.S., E. Schiavo, V. Heyer, M. Fournier, A. Page, I. Robert, and B. REINA-SAN-MARTIN. 2013. The cohesin complex regulates immunoglobulin class switch recombination. J Exp Med 210:2495-2502. 
  • Number of PhDs in progress: 2 (2020).
PhD 2021-9 Nuclear Organisation and Division

LabEx INRT (IGBMC) - Integrative Biology : Nuclear Dynamics, Regenerative and Translational Medecine, http://igbmc.fr/

Team : Nuclear Organisation and Division.

Team leader: Manuel Mendoza, mendozam@igbmc.fr, +33 (0)3 88 65 33 86,  IGBMC, 1 rue Laurent Fries, 67400 Illkirch-Graffenstaden Cedex, http://www.igbmc.fr/mendoza/

Living cells have a fascinating ability to generate complex and dynamic internal structures. Nowhere is this property more evident than during cell division: in only a few minutes, cells alter their shape, duplicate and partition their internal components, and divide into two apparently identical halves, which in many cases go on to acquire distinct identities. These dramatic changes need to be carefully coordinated with each other in space and time. To gain insight into these processes, we focus on two major cell cycle transitions. First, we study how chromosome replication and cell division are coordinated with each other. In particular, we study how the Aurora-B-dependent “NoCut” checkpoint regulates cytokinesis abscission when chromatin bridges are delayed in the cell division site. Second, we are interested in mechanisms that establish differences in nuclear organization after asymmetric cell division, and specifically on how nuclear pore complexes control the establishment of cell identity. Our favourite experimental system is budding yeast. We then use mammalian cell culture systems, such as cancer and stem cells, to test for the conservation of molecular mechanisms identified in yeast. Multiple projects in are available in the lab. 

Key words: nuclear pore complexes – chromosome organisation – cytokinesis – cell cycle – budding yeast – stem cells.

  • PhD supervisor: Manuel Mendoza, mendozam@igbmc.fr, +33 (0)3 88 65 33 86, http://www.igbmc.fr/mendoza/
  • Team members: Faezeh Forouzanfar, Monica Dam, Vasilisa Pozharskaia, Céline Ziegler-Birling.
  • 3 relevant publications: 1) Ivanova, T., Maier, M., Missarova, A., Ziegler-Birling, C., Dam, M. Gomar-Alba, M., Carey, L. B., and Mendoza, M. (2020). Budding yeast complete DNA synthesis after chromosome segregation begins. Nat. Commun. 11, 2267. 2) Gomar-Alba, M., and Mendoza, M. (2020). Modulation of Cell Identity by Modification of Nuclear Pore Complexes. Frontiers in Genetics 10. doi:10.3389/fgene.2019.01301. 3) Kumar A, Sharma P, Gomar-Alba M, Shcheprova Z, Daulny A, Sanmartin T, Matucci I, Funaya C, Beato M, Mendoza M (2018). Daughter-cell-specific modulation of nuclear pore complexes controls cell cycle entry during asymmetric division. Nature Cell Biology 20, 432-442.      
  • Number of PhDs in progress: 2 (Monica Dam since 2018, Vasilisa Pozharskaia since Oct 2018).
PhD 2021-10 The role of CaMK1D in energy homestasis

LabEx INRT (IGBMC) - Integrative Biology : Nuclear Dynamics, Regenerative and Translational Medecine, http://igbmc.fr/

Team : Signal transduction in metabolism and inflammation

Team leader: Roméo Ricci, romeo.ricci@igbmc.fr, +33 (0) 3 88 65 35 67, IGBMC, 1 rue Laurent Fries, 67404 Illkirch-Graffenstaden Cedex,  http://www.igbmc.fr/ricci/

Regulation of energy homeostasis is key for organisms to cope with changes in food availability. NPY/AgRP and POMC neurons in the arcuate nucleus of the hypothalamus emerged as major control points translating hormonal inputs into alterations in feeding behavior and energy metabolism. Dysregulation of this intricate system contributes to obesity and type 2 diabetes (T2D). Using conditional knockout mice, we identified CaMK1D – encoded by a gene located in one of the established risk loci associated with T2D – to be required in neuronal control of food intake. We have set up a collaborative network to corroborate a specific function of CaMK1D in AgRP neurons using state-of-the-art stereotactic and chemogenetic tools. We also propose innovative strategies to identify a precise mechanism downstream of CaMK1D. Finally, we developed tools to test effects of pharmacological inhibition of CaMK1D on obesity, thus preparing the ground for new therapeutic avenues.

The project mainly involves usage of primary neuron culture systems and tools related to the analysis of cellular signaling covering a wide range of biochemical and cell biological tools. Expertise in mouse handling is not required as the project will be assisted by a technician experienced in animal handling.

Key words: CaMK1D, AgRP/NPY, Energy homeostasis, Obesity, CNS, Cellular signaling

  • PhD supervisor: Roméo Ricci, romeo.ricci@igbmc.fr, +33 (0) 3 88 65 35 67,  http://www.igbmc.fr/ricci/
  • Team members: Mengdi Qu, Eric Erbs, Marta Puig-Gamez, Zhirong Zhang, Taozhi Ye, Kevin Vivot, Li Ran
  • 3 relevant publications: 1) Pasquier A, Vivot K, Erbs E, Spiegelhalter C, Zhang Z, Aubert V, Liu Z, Senkara M, Maillard E, Pinget M, Kerr-Conte J, Pattou F, Marciniak G, Ganzhorn A, Ronchi P, Schieber NL, Schwab Y, Saftig P, Goginashvili A, Ricci R. Lysosomal degradation of newly formed insulin granules contributes to β cell failure in diabetes. Nat Commun. 2019. 2) Zhang, Z., Meszaros, M., He, W., Magliarelli, HdF., Mihlan, M., Liu, Y., Puig Gamez, M., Xu, Y., Goginashvili, A., Pasquier, A., Neven, B., Quartier, P., Aebersold, R., Han, J. and Ricci, R. PKD at the Golgi controls NLRP3 inflammasome activation. Journal of Experimental Medicine, 2017. 3) Goginashvili, A., Zhang, Z., Erbs, E., Spiegelhalter, C., Kessler, P., Mihlan, M., Pasquier, A., Krupina, K., Schieber, N., Cinque, L., Morvan, J., Sumara, I., Schwab, Y., Settembre, C., Ricci, R. Insulin secretory granules control autophagy in pancreatic b cells. Science, 2015.
  • Number of PhD in progress: 4 Marta Puig-Gamez: October 1 2016, Li Ran: October 1 2018, Taozhi Ye: December 1 2018, Mengdi Qu: October 2020
PhD 2021-11 Modeling Gene Regulation with an Interpretable Variational Autoencoder

LabEx INRT (IGBMC) - Integrative Biology : Nuclear Dynamics, Regenerative and Translational Medecine, http://igbmc.fr/

Team : Stochastic Systems Biology of Gene Regulation.

Team leader: Nacho Molina, nacho.molina@igbmc.fr, +33 (0)3 88 65 33 47, IGBMC, 1 rue Laurent Fries, 67404 Illkirch-Graffenstaden Cedex, http://www.igbmc.fr/molina/

Biology is going through an incredible revolution: current experimental techniques allows us to generate GBs of data in each experiment. In addition, international consortiums are formed to comprehensively address specific problems in biology.  For instance, the Human Cell Atlas Project aims to map and characterize all cells types in the human body using single-cell genomic techniques as a basis for both understanding human health and discovering new treatments for disease. This goal represents new exciting challenges in Mathematics and Computer Science as novel approaches are required to identify patterns, extract valuable information and produce reliable predictions. Machine Learning techniques have been proven to be a very powerful tool for these tasks. In particular, variational autoencoders have been used to learn reduced dimensional latent spaces from genomic data. However, the black-box nature of the methods hinders the interpretability of the latent variables. In this project we aim to develop an interpretable variational autoencoder to model gene regulation from single-cell transcriptomic data. Briefly, imposing prior knowledge on gene interactions through the network structure of the decoder will allows us to interpret latent variables as activities of regulatory proteins. Thus, we will be able to infer the key regulators that are responsible for the specific transcriptome in each single cell. Furthermore, using optimal transport theory on the latent regulatory space we will be able to predict the minimum number of regulators that need to be modified to promote a transition from one particular cell type to another. Ultimately, the result of this project may serve as a valuable computational tool to assist in the design of new cell therapies. 

We are looking for a candidate with a MSc in Computational Biology, Machine Learning, Data Science or similar. Excellent programming skills will be required. Good background in mathematics will be a plus. Prior knowledge in biology and gene regulation will not be essential but certain degree of curiosity to learn new fields will be desirable. 

Key words:  Computational Biology, Machine Learning, Variational Autocencoders, Gene regulation, Single-cell Transcriptomics.

  • PhD supervisor: Nacho Molina,  nacho.molina@igbmc.fr, +33 (0)3 88 65 33 47, http://www.igbmc.fr/molina/
  • Team members: Andrea RIBA, Oliver, TASSY, Guilherme MONTEIRO, Karen AMRAL.
  • Number of PhDs in progress: 2.5 (2017, 2018, 2019).
PhD 2021-12 Computational modeling of transcription regulation by co-activator complexes

LabEx INRT (IGBMC) - Integrative Biology : Nuclear Dynamics, Regenerative and Translational Medecine, http://igbmc.fr/

Team : Stochastic Systems Biology of Gene Regulation.

Team leader: Nacho Molina, nacho.molina@igbmc.fr,  +33 (0)3 88 65 33 47, IGBMC, 1 rue Laurent Fries, 67400 Illkirch-Graffenstaden Cedex, http://www.igbmc.fr/molina/

Transcription is a critical step in gene expression and is controlled by many different factors, including chromatin-modifying and –remodelling complexes. Despite much research, defining the principles underlying their gene-specific regulatory roles remains surprisingly challenging. For instance, genome-wide analyses reveal a large disconnect between the localization and effect on gene expression of chromatin factors, likely because we are lacking direct and dynamic measurements of their activities. The overall objective of this project is to tackle this problem and identify the cis- and trans-acting elements that determine the quantitative effect of chromatin factors on transcription. To this end, three labs have established a tight interdisciplinary collaboration (Helmlinger from CRBM, Tora and Molina from IGBMC) to combine innovative experimental approaches, including nascent transcriptomics and inducible perturbations, with computational modelling to address the following questions: 1) What are the effects of chromatin factors on the temporal dynamics of transcription? 2) How do these effects relate to the dynamics of chromatin factor binding and activities? 3) What mechanisms govern the gene-specific recruitment and function of chromatin factors?

The PhD student supervised by Nacho MOLINA will analysed the genomic sequencing data generated by the Helmlinger and Tora labs.  To gain an integrated view we will develop a biophysical model that describes the dynamics of coactivator recruitment to promoters, nucleosome modifications and remodelling, PIC assembly, and RNAPII initiation and elongation. Moreover, applying Bayesian model selection, we will evaluate alternative models describing different possible interactions between all these regulatory processes, aiming to discriminate causative from correlative effects. Overall, we expect that our systems biology approach will provide a dynamic and integrated view of co-activator function in the regulation of transcription.

The ideal candidate should hold a MSc degree in Computational Biology, Bioinformatics, Data Science, Mathematics, Computer Science or similar. Excellent programming skills will be required. Good background in mathematics will be a plus. Prior knowledge analyzing genomic sequencing data will be a plus.

Key words: Computational Biology, Systems Biology, Gene Regulation, Epigenetics, Transcription, Coactivators.

  • PhD supervisor: Nacho Molina, nacho.molina@igbmc.fr,  +33 (0)3 88 65 33 47, http://www.igbmc.fr/molina/
  • Team members: Andrea Riba, Oliver Tassy, Guilherme Monteiro, Karen Amral.
  • Number of PhDs in progress: 2.5 (2017, 2018, 2019).

Development and Stem Cells (LabEx INRT) / Genomes expression and cross-talk in mitochondrial function and dysfunction (LabEx MitoCross)

PhD 2021-13 Role of rDNA genomic instability on replicative senescence in natural yeast populations

LabEx INRT (IGBMC) - Integrative Biology : Nuclear Dynamics, Regenerative and Translational Medecine, http://igbmc.fr/

Team 1 : Biophysics of cell growth.

Team leader : Gilles Charvin, charvin@igbmc.fr, +33 (0)3 88 65 35 88, IGBMC, 1 rue Laurent Fries, 67404 Illkirch Graffenstaden LabEx MitoCross Genomes expression and cross-talk in mitochondrial function and dysfunction, https://mitocross.unistra.fr/

 LabEx MitoCross - Genomes expression and cross-talk in mitochondrial function and dysfunction, https://mitocross.unistra.fr/

Team 2 : Variation intra-spécifique et évolution des génomes.

Team  leader : Joseph Schacherer, schacherer@unistra.fr, +33 (0)3 68 85 18 21, GMGM, 15 rue René Descartes, 67000 Strasbourg, http://ttps://mitocross.unistra.fr/partners/gmgm/team-7-intraspecific-variation-and-genome-evolution/

Aging is a ubiquitous feature of living organisms, yet its fundamental origin still remains to be deciphered. Over the last twenty years, budding yeast has emerged as a powerful model to identify and characterize the molecular mechanisms that drive age-associated physiological declines. Previous work, including recent contributions from the host lab, has identified and characterized the instability of ribosomal DNA (rDNA) as the main driver of entry into replicative senescence. However, previous studies were all based on lab strains derived from very specific selection processes. Therefore, the effects associated with large genetic variations observed in natural isolates have been largely ignored. Yet, such analyses are likely to provide unprecedented advances about how genome stability controls longevity, knowing that the organization of the rDNA locus greatly differs among the variants. This project combines the experience of the Charvin lab in replicative aging studies with the unique expertise of the Schacherer lab with the analysis of structure-function relationships in intra-species genetic variants.

Key words: Replicative aging, intra-species genetic variations, microfluidics, single cell imaging.

  • PhD supervisor 1: Gilles Charvin, charvin@igbmc.fr, +33 (0)3 88 65 35 88, http://charvin.igbmc.science
  • Team members: 7.
  •  3 relevant publications: 1) Proteostasis collapse, a hallmark of aging, hinders the chaperone-Start network and arrests cells in G1 Moreno DF, Jenkins K, Morlot S, Charvin G, Csikasz-Nagy A, Aldea M, eLife, e48240, 2019. 2) Excessive rDNA transcription drives the disruption in nuclear homeostasis during entry into senescence in budding yeast, Morlot S, Jia S, Léger I, Matifas A, Gadal O, Charvin G, Cell Rep, 28(2):408-422, 2019. 3) Nonlinear feedback drives homeostatic plasticity in H2O2 stress response, Goulev Y, Morlot S, Matifas A, Huang B, Molin M, Toledano MB, Charvin G, eLife, 6, e23971, 2017.  
  • Number of PhDs in progress: 1 (starting date : 10/18)
  • PhD supervisor 2: Joseph Schacherer, / schacherer@unistra.fr, / +33 (0)3 68 85 18 21,  http://ttps://mitocross.unistra.fr/partners/gmgm/team-7-intraspecific-variation-and-genome-evolution/
  • Team members: 14.
  • 3 relevant publications: 1) Extensive impact of low-frequency variants on the phenotypic landscape at population-scale, Fournier T, Abou Saada O, Hou J, Peter J, Caudal E, Schacherer J, elife, 8 e49258, 2019. 2) Genome evolution across 1,011 Saccharomyces cerevisiae isolates. Peter J, De Chiara M, Friedrich A, Yue JX, Pflieger D, Bergström A, Sigwalt A, Barre B, Freel K, Llored A, Cruaud C, Labadie K, Aury JM, Istace B, Lebrigand K, Barbry P, Engelen S, Lemainque A, Wincker P, Liti G, Schacherer J. Nature, 2018, 7701:339-344, 2018. 3) Fitness trade-offs lead to suppressor tolerance in yeast. Hou J, Schacherer J. Mol Biol Evol, 34(1):110-118, 2017.
  • Number of PhDs in progress: 4 (starting dates: 10/207 ; 10/2017; 10/2019; 10/2019).

Functional Genomics and Cancer (LabEx INRT)

PhD 2021-14 Understanding gene regulation in blood cell development and disease

LabEx INRT (IGBMC) - Integrative Biology : Nuclear Dynamics, Regenerative and Translational Medecine, http://igbmc.fr/

Team : Hematopoiesis and leukemogenesis

Team leader: Philippe Kastner and Susan Chan, scpk@igbmc.fr, +33 (0)3 88 65 34 61 IGBMC, 1 rue Laurent Fries, 67400 Illkirch-Graffenstaden Cedex, http://www.igbmc.fr/research/department/2/team/18/

Hematopoiesis begins with pluripotent stem cells and ends in the production of lymphoid, myeloid and erythroid cells. This process occurs throughout life, and is controlled by transcriptional regulators required for cell identity and function. Our lab studies the Ikaros family of transcription factors, which are important as differentiation agents and tumor suppressors, and whose mutations are implicated in leukemias, immunodeficiencies and autoimmune diseases. How Ikaros proteins modulate gene expression in hematopoiesis, and why deregulation of Ikaros function leads to disease, remain unclear. The PhD candidate will choose from three thesis projects focused on stem cells and lymphocytes, which aim to elucidate how Ikaros proteins work as transcriptional activators and repressors at the physiological and molecular levels. The student will learn a variety of approaches including in vivo studies of mutant mouse models, in vitro engineering of cell lines, CRISPR/Cas9 genome editing, high throughput genomic analyses, flow cytometry, and biochemistry to study protein-DNA and protein-protein interactions.

Key words : hematopoiesis, development, transcriptional regulation, single cell analysis

  • PhD supervisor: Philippe Kastner and Susan Chan, scpk@igbmc.fr, +33 (0)3 88 65 34 61 IGBMC, 1 rue Laurent Fries, 67400 Illkirch-Graffenstaden Cedex, http://www.igbmc.fr/research/department/2/team/18/
  • Team members: 11 Susan Chan, Philippe Kastner, Céline Charvet, Beate Heizmann, Peggy Kirstetter, Ekatarina Baranova (post-doc), Marie-Céline Deau (PhD student), Guillaume Morel (PhD student), Chiara Taroni (PhD student), Adina Aukenova (master student), Patricia Marchal (engineer)              
  • 3 relevant publications: 1) Mastio J, Simand C, Cova G, Kastner P, Chan S, Kirstetter P. Ikaros cooperates with Notch activation and antagonizes TGFβ signaling to promote pDC development. PLoS Genet. 2018;14(7):e1007485. 2) Heizmann B, Kastner P, Chan S. The Ikaros family in lymphocyte development. Curr Opin Immunol. 2018;51:14-23. 3) Oravecz A, Apostolov A, Polak K, Jost B, Le Gras S, Chan S, Kastner P. Ikaros mediates gene silencing in T cells through Polycomb repressive complex 2. Nat Commun. 2015 Nov 9;6:8823. doi: 10.1038/ncomms9823.
  • Number of PhDs in progress: 3 (starting dates 2016, 2018, 2019)
PhD 2021-15 Role of immune cells on development and homeostasis

LabEx INRT (IGBMC) - Integrative Biology : Nuclear Dynamics, Regenerative and Translational Medecine, http://igbmc.fr/

Team : Immune and neural development.

Team leader: Angela Giangrande, angela@igbmc.fr, 0388653381,  IGBMC, 1 rue Laurent Fries, 67400 Illkirch-Graffenstaden Cedex, http://www-igbmc.u-strasbg.fr/Giangrande

Macrophages represent our first line of defense against internal and external challenges. In addition, it has become clear that these cells also put in contact distant tissues, hence providing ideal sensors of the internal state. The project aims at understanding in vivo the role and mode of action of immune cells during development and in homeostasis using Drosophila as a model system. Our recent findings indicate that hematopoiesis is necessary for morphogenesis and tissue development. We have also recently shown that the Drosophila immune cells are heterogeneous and are subdivided in clusters based on their transcriptional landscapes. A major aim will be to identify the function of the different subgroups in morphogenesis and in the adult. 

The project will involve a multidisciplinary approach and use genetics, molecular biology, high throughput assays, imaging and cell biology. 

Key words: hematopoiesis, neural development, stem cells, Drosophila, RNA seq, genetics, imaging.

  • PhD supervisor: Angela Giangrande, angela@igbmc.fr, 0671147850, http://www-igbmc.u-strasbg.fr/Giangrande
  • Team members: Dr P Cattenoz, CRCN, Dr S Monticelli, R Sakr PhD student4th year, A Pablidaki PhD student 4th year, T Boutet IMCbio PhD student (co-tutorship with N Matt) 2nd year, C Delaporte IE INSERM, C Riet AI Université.  
  • 3 relevant publications: 1) P.B. Cattenoz, R. Sakr, A. Pavlidaki, C. Delaporte, A. Riba, N. Molina, N. Hariharan, T. Mukherjee, and A. Giangrande (2020). Temporal specificity and heterogeneity of the fly immune cells’ transcriptional landscape. Deposited to BioRxiv. EMBO J. e104486 http://doi/10.15252/embj.202010448 2) G. Trébuchet, P. Cattenoz, J. Zsámboki, D. Mazaud, Darja Siekhaus,,  M. Fanto and A Giangrande (2019). The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate. J Neurosci. Jan 9;39(2):238-255. 3) W. Bazzi, P.B. Cattenoz, C. Delaporte, V. Dasari, R. Sakr, Y. Yuasa and A. Giangrande (2018). Embryonic hematopoiesis modulates the inflammatory response and larval hematopoiesis in Drosophila. eLife 2018;7:e34890 doi: http://10.7554/eLife.34890 
  • Number of PhDs in progress: 3 (starting date: 2017, 2017, 2019).
PhD 2021-16 Histone H3.3 mutations and pediatric high grade glioma

LabEx INRT (IGBMC) - Integrative Biology : Nuclear Dynamics, Regenerative and Translational Medecine, http://igbmc.fr/

Team : Chromatin an epigenetic regulation.

Team leader: Ali Hamiche, hamiche@igbmc.fr, +33 (0)3 88 65 32 50,  IGBMC, 1 rue Laurent Fries, 67400 Illkirch-Graffenstaden Cedex, http://www.igbmc.fr/research/department/2/team/22/

Pediatric high-grade glioma (HGG) is a devastating disease that accounts for ~15 % of the pediatric brain tumors. Recently, sequencing of tumor cells revealed that the histone variant H3.3 is frequently mutated in pediatric HGG, with up to 80 % of diffuse intrinsic pontine gliomas (DIPGs) carrying K27M mutation and 36 % of non-brainstem gliomas carrying either K27M or G34R/V mutations. This was the first demonstration that histone mutations may be drivers of disease, but the mechanistic aspects of H3.3 mutation functions remain largely unknown. 

Here we aim to shed light on the H3.3 mutation-related origin of pediatric HGG and DIPG. Our objectives are: to develop mouse ES cell and organoids models carrying H3.3 mutations, to immunopurify the in vivo H3.3 chromatin associated and nuclear soluble complexes from mES cells and MEF cells carrying H3.3 K27M or H3.3 G34R/V mutations, to characterize their members and to solve their structures by Cryo-EM microscopy. Using these unique models, we will follow the differentiation of ES cells into neuronal progenitors and characterize at molecular and structural levels the alterations in the epigenetic landscape due to the H3.3 somatic mutations.  

We anticipate that this project will allow the development of effective therapies for patients and to improve our understanding of the fascinating biology of the histone variant H3.3.

Key words: Cancer epigenetics, chromatin, histone variant, brain tumors. 

  • PhD supervisor: Ali Hamiche, hamiche@igbmc.fr, +33 (0)3 88 65 32 50, http://www.igbmc.fr/research/department/2/team/22/
  • Team members: Ali Hamiche, DR1, CNRS, Philippe Ramain, DR2 CNRS, Christian Bronner, CRCN, INSERM, Christophe Papin, CRCN INSERM, Catherine Ramain, CRCN INSERM, Isabelle Stoll, IE, INSERM, Abdulkhaleg IBRAHIM, Postdoc, Tajith Shaik, Postdoc, Hatem Salem, IR, Dimitra Vlachokosta, PhD Student (Supervisor : Ali Hamiche), Naif Almalaki, PhD Student (Supervisor : Christian Bronner).
  • 3 relevant publications: 1) Combinatorial DNA methylation code at repetitive elements. Papin C, Ibrahim A, Bronner C, Stoll I, Le Gras S, Dimitrov S, Bronner C, Hamiche A.  Genome Res. 2017 Mar 27. pii: gr.213983.116. doi: 10.1101/gr.213983.116. [Epub ahead of print]. Impact factor (IF) = 14, 6. 2) Latrick CM, Marek M, Ouararhni K, Papin C, Stoll I, Ignatyeva M, Obri A, Ennifar E, Dimitrov S, Romier C and Hamiche A. Molecular basis and specificity of H2A.Z-H2B recognition and deposition by the histone chaperone YL1. Nat Struct Mol Biol. 2016 Apr;23(4):309-16. Impact factor (IF) = 13.3. 3) Obri A, Ouararhni K, Papin C, Diebold M, Padmanabhan K, Marek M, Stoll I, Roy L, T. Reilly P, W. Mak T, Dimitrov S, Romier C and Hamiche A. « Anp32e, a histone chaperone specialized in the removal of H2A.Z from chromatin ». Nature 2014, doi:10.1038/nature12922. Published online 22 January 2014. Impact factor (IF) = 43.
  • Number of PhDs in progress: Dimitra Vlachokosta (Start 2018, End 2021, supervisor Ali Hamiche), Naif Almalaki PhD Student (Start 2017, End 2021; supervisor Christian Bronner).
PhD 2021-17 Transcriptional repression in melanoma

LabEx INRT (IGBMC) - Integrative Biology : Nuclear Dynamics, Regenerative and Translational Medecine, http://igbmc.fr/

Team : Genome expression and repair.

Team leader: Frédéric Coin, fredr@igbmc.fr, +33 (0)3 88 65 32 70,  IGBMC, 1 rue Laurent Fries, 67400 Illkirch-Graffenstaden Cedex, http://www.igbmc.fr/research/department/2/team/20/

TFIIH is a basal transcription factor involved in the expression of class II genes. The complex contains nine subunits including the CDK7 kinase that is involved in the phosphorylation of RNA Polymerase II. Recently, chemical inhibition of CDK7 has been shown to be highly effective in targeting cancer cells due to the specific involvement of CDK7 in expression of super-enhancer dependent genes such as the oncogene cMYC. Melanoma cells are broadly divided in proliferative cells showing high protein level of the oncogene MITF and invasive melanoma cells that show low level of MITF. Our team has shown that targeting CDK7 was highly effective against proliferative melanoma cells expressing MITF. However, we also observed that prolonged exposure to CDK7 inhibition caused a transcriptional reprograming of proliferative melanoma cells to invasive cells poorly expressing MITF and showing significant resistance to targeted therapies. By seeking to unveil the molecular details of this resistance, we have shown that MITF represses the expression of the transcription factor GATA6, involved in drug resistance, by binding to an intronic region of the gene. A repressive function for MITF has been proposed but has never been studied in detail. Our goal is now to use our model of MITF repression of GATA6 to unveil the molecular basis of this mechanism and to broaden this knowledge to the set of genes potentially suppressed by MITF in proliferative melanoma cells and activated in invasive after the loss of MITF.   

Key words: TFIIH, CDK7, MITF, melanoma, repression.

PhD 2021- 18 Understanding the function of inter-organelle contact site remodeling

LabEx INRT (IGBMC) - Integrative Biology : Nuclear Dynamics, Regenerative and Translational Medecine, http://igbmc.fr/

Team : Molecular and cellular biology of breast cancer.

Team leader: Catherine Tomasetto, catherine-laure.tomasetto@igbmc.fr, +33 (0)3 88 65 34 24,  IGBMC, 1 rue Laurent Fries, 67400 Illkirch-Graffenstaden Cedex, http://www.igbmc.fr/research/department/2/team/25/

Eukaryotic cells are compartmentalized into organelles that allow a division of labor. Organelles are not independent units: they depend on exchanges to fulfill their role. The formation of membrane contact sites (MCS), where organelle membranes come in contact, allows the exchange of molecules and information between organelles. Indeed, electron microscopy shows that organelles are in physical contact with each other. Using an unbiased approach, we have identified novel proteins that form protein complexes to construct contact sites between the endoplasmic reticulum (ER) and other cellular organelles (Di Mattia et al, EMBO report, 2018; Wilhelm et al, EMBO J, 2017). Recently, we showed that phosphorylation regulates the formation of contacts (Di Mattia, Martinet, Ikhlef et al, EMBO J, 2020). 

The proposed project consists in the functional characterization of contacts between the ER and other organelles. We surmise that inter-organelle contacts allow the cells to adapt to different challenges. The project will be to follow the dynamics of contact sites using innovative imaging methods, and to understand how contact remodeling helps the cells to adapt. 

This project will lead to a better understanding of the role of ER-organelle contacts in cellular function. 

Key words: Cell biology; inter-organelle contacts; endoplasmic reticulum.

  • PhD supervisor: Fabien Alpy, fabien.alpy@igbmc.fr,  +33 (0)3 88 65 35 19, http://www.igbmc.fr/research/department/2/team/25/
  • Team members: Researcher: Catherine-Laure Tomasetto; Fabien Alpy; Clinicians: Thien-Nga Chamaraux-Tran ; Marie-Pierre Chenard ; Carole Mathelin; Phd Students : Amélie Jaulin; Arthur Martinet; Mehdi Zouiouich; Massimo Lodi; Sébastien Molière; Engineers & Technicians Corinne Wendling; Master Student: Julie Eichler.
  • 3 relevant publications: 1) Di Mattia T, Martinet A, Ikhlef S, McEwen AG, Nominé Y, Wendling C, Poussin-Courmontagne P, Voilquin L, Eberling P, Ruffenach F, Cavarelli J, Slee J, Levine TP, Drin G, Tomasetto C*, Alpy F*. FFAT motif phosphorylation controls formation and lipid transfer function of inter-organelle contacts. EMBO J. 2020 Dec 1;39(23):e104369. https://doi.org/10.15252/embj.2019104369. 2) Di Mattia T, Wilhelm LP, Ikhlef S, Wendling C, Spehner D, Nominé Y, Giordano F, Mathelin C, Drin G, Tomasetto C*, Alpy F*. (2018). Identification of MOSPD2, a novel scaffold for endoplasmic reticulum membrane contact sites. EMBO Rep. Jul;19(7). pii: e45453. Epub 2018 Jun 1. https://doi.org/10.15252/embr.201745453. 3) Wilhelm LP, Wendling C, Védie B, Kobayashi T, Chenard MP, Tomasetto C*, Drin G, Alpy F*. (2017). STARD3 mediates endoplasmic reticulum-to-endosome cholesterol transport at membrane contact sites. EMBO J. 2017 May 15;36(10):1412-1433. https://doi.org/10.15252/embj.201695917
  • Number of PhDs in progress: Amélie Jaulin (2017); Arthur Martinet (2018); Mehdi Zouiouich (2019); Massimo Lodi (Clinician/MD; PhD starting date: 2019); Sébastien Molière (Clinician/MD; PhD starting date: 2019).
PhD 2021-19 Role of androgens in muscle precursor cell fate

LabEx INRT (IGBMC) - Integrative Biology : Nuclear Dynamics, Regenerative and Translational Medecine, http://igbmc.fr/

Team : Pathophysiological function of nuclear receptor signaling.

Team leader: Daniel Metzger, metzger@igbmc.fr, +33 (0)3 88 65 34 63,  IGBMC, 1 rue Laurent Fries, 67400 Illkirch-Graffenstaden Cedex, http://www.igbmc.fr/research/department/2/team/23/

Androgens are steroid hormones that play a key role in the control of the development of male sexual organs. They also exert anabolic effects in skeletal muscles, and reduced testosterone levels in elderly men are associated with decreased musculature. Androgen effects are mediated by the androgen receptor (AR), a member of the ligand-dependent nuclear receptor superfamily. Unexpectedly, we showed that AR in mouse muscle fibers controls the strength but not the mass of muscles after puberty.  

Satellite cells (SCs) are muscle stem cells residing in a quiescent state in a microenvironment located at the periphery of myofibers. At puberty, the androgen peak induces SC quiescence to establish a stem cell pool. Upon injury, SCs are mobilized to ensure proper muscle regeneration. However, the mechanisms that drive SCs myogenesis remain poorly understood. Thus, the aim of this project is to characterize the mechanisms by which androgens regulate SC fate and subsequently muscle regeneration, combining mouse studies and molecular biology methods, such as genome-wide sequencing. Understanding the molecular underpinnings by which androgens regulate SCs will open innovative perspectives to develop therapeutic strategies for muscle regeneration after injury, or for muscle dystrophies and aging.

Key words: Androgens, satellite cells, skeletal muscle, myopathies.

  • PhD supervisor: Daniel Metzger & Delphine Duteil, metzger@igbmc.fr / duteild@igbmc.fr ,  +33 (0)3 88 65 34 63 / +33 (0)3 88 65 34 69, http://www.igbmc.fr/research/department/2/team/23/
  • Team members: Delphine DUTEIL, Gilles LAVERNY, Daniel METZGER, Mohamed ABOUELMAATY, Beatriz GERMAN FALCON, Daniela ROVIT, Kamar GHAIBOUR, Kateryna LEN, Julie TERZIC, Darya YANUSHKO, Regis LUTZING. 
  • 3 relevant publications: 1) Rovito D, et al. Myofiber transcriptional repertoire driven by collaboration of glucocorticoid receptor, Nrf1 and Myod. Nuclei Acid Research, in revision. 2) Gali Ramamoorthy T, et al. 2015. The transcriptional coregulator PGC-1beta controls mitochondrial function and anti-oxidant defence in skeletal muscles. Nat Commun 6: 10210. 3) Chambon C, et al. 2010. Myocytic androgen receptor controls the strength but not the mass of limb muscles. Proc Natl Acad Sci U S A 107: 14327-14332. 
  • Number of PhDs in progress: Kamar GHAIBOUR (10/2019), Kateryna LEN (10/2020), Julie TERZIC (11/2020).
PhD 2021-20 Controlling gene expression: function of the major deadenylase complex regulating eukaryotic mRNA decay

LabEx INRT (IGBMC) - Integrative Biology : Nuclear Dynamics, Regenerative and Translational Medecine, http://igbmc.fr/

Team : Protein networks and complexes regulating eukaryotic mRNA decay.

Team leader: Bertrand Seraphin, seraphin@igbmc.fr, +33 (0)3 88 65 33 36,  IGBMC, 1 rue Laurent Fries, 67400 Illkirch-Graffenstaden Cedex, http://www.igbmc.fr/research/department/2/team/27/

The regulation of gene expression is particularly complex in eukaryotes that  allows cells to adapt to changing conditions and / or differentiate. This regulation occurs largely by changes in the rates of transcription or degradation of messenger RNAs (mRNAs) that adapt the synthesis of proteins to quantities needed by cells. 

Our work on the degradation of mRNAs led to the characterization of several protein complexes involved in critical steps of this process. Among them, the CCR4-NOT complex, composed of a core conserved in all eukaryotes associated species specific subunits, is a large assembly that regulates eukaryotic gene expression at multiple levels. The best-studied function of CCR4-NOT complex relates to its role in shortening the poly(A) tail of cytoplasmic mRNAs, or deadenylation. This process is indeed a key step in the constitutive and regulated turnover of mRNAs. It is therefore key to understand the biological role of the CCR4-NOT complex in deadenylation and the regulation of this process. This entails determining the organization of the complex, the role of individual subunits and identification of interacting partners modulating its activity.  

Our preliminary data provide new insights into the organization of the CCR4-NOT complex and identify new partners of this essential cellular assembly. The biological roles of these interactions will be investigated through in vivo analyses (characterization of mutants, analyses of reporter genes...) and biochemical assays (activity tests, protein-protein interaction studies...). This project will provide a molecular and functional understanding of the CCR4-NOT complex and of its role at the interface between degradation of mRNAs, translation and protein stability. In particular, the involvement of such a process in quality control mechanisms eliminating faulty mRNAs will be explored. These analyses contribute to elucidate the physiological role of the CCR4-NOT complex, including its involvement in genetic diseases and cancer. 

Key words: mRNA, poly(A) tail, regulation of gene expression, RNA decay, translation, diseases.

  • PhD supervisor: Bertrand Seraphin, seraphin@igbmc.fr, +33 (0)3 88 65 33 36, http://www.igbmc.fr/research/department/2/team/27/
  • Team members: Eric Huntzinger, Fabienne Mauxion, Bertrand Seraphin, Jérémy Scutenaire, Monica Pena-Luna, Claudine Gaudon-Plesse, Mélody Matelot, Yasmine Amrani.
  • 3 relevant publications: 1) Charenton et al. Structure of the active form of Dcp1-Dcp2 decapping enzyme bound to m7GDP and its Edc3 activator. Nat Struct Mol Biol. 2016 Nov;23(11):982-986. 2) Stupfler et al. BTG2 bridges PABPC1 RNA-binding domains and CAF1 deadenylase to control cell proliferation. Nat Commun. 2016 Feb 25;7:10811. 3) Lebreton et al. Endonucleolytic RNA cleavage by a eukaryotic exosome. Nature. 2008 Dec 18;456(7224):993-6. 
  • Number of PhDs in progress: 2, Yasmine Amrani (started 2020, co-direction), Monica Pena-Luna (started 2017).
PhD 2021-21 Uncovering the molecular mechanisms by which retinoic acid receptors control male germ cell differentiation

LabEx INRT (IGBMC) - Integrative Biology : Nuclear Dynamics, Regenerative and Translational Medecine, http://igbmc.fr/

Team : Retinoic acid signaling pathways driving stem spermatogonia ontogenesis and differentiation.

Team leaders: Norbert Ghyselinck and Manuel Mark, norbert.ghyselinck@igbmc.fr / manuel.mark@igbmc.fr, +33 (0)3 88 65 56 46 / +33 (0)3 88 65 56 36,  IGBMC, 1 rue Laurent Fries, 67400 Illkirch-Graffenstaden Cedex, http://www.igbmc.fr/research/department/2/team/10/

We aredeciphering the physiological role played by retinoic acid (ATRA) nuclear receptors(RAR), by using a large variety of techniques ranging from biochemistry, through mouse genetics, to molecular biology and imaging (1). We usethe seminiferous epithelium (SE) of the testis as a model system because ATRA is required forbothits differentiation and maintenance (2). Our previous work indicates that RARA isotype is required in Sertoli cells, the supporting somatic cells of the SE,to allow proper spermiation i.e., the release of spermatozoafrom the SE(3). However, the genetic cascade controlled by RARA is not yet defined. Evidence indicate thatSertoli cells cyclically change their functions in a coordinated manner with germ cell differentiation to support the entire process of spermatogenesis.We hypothesized that RARA exerts complementary roles in Sertoli cells by alternatively repressing genes during the stages of SE cycle preceding spermiation, when unliganded,and activating genes for spermiation and during the following stagesof SE cycle, when ATRA-liganded.The thesis project is aimed at deciphering the molecular mechanisms by which RARA is able to alternatively repressand activatetranscriptionin Sertoli cells.

(1)Mark et al., (2006) Annu. Rev. Pharmacol. Toxicol.46:451;

(2)Teletin et al., (2017) Curr. Top. Dev. Biol.125:191;

(3)Vernet et al., (2006) EMBO J.25:5816

Key words: Nuclear receptors, gene regulation (RNA-seq, single cell), epigenetics (ChiP-seq, ATAC-seq), cell differentiation, cell morphogenesis, stem cell niche, mouse genetics, bioinformatics.

  • PhD supervisor: Norbert Ghyselinck and Manuel Mark, norbert.ghyselinck@igbmc.fr / manuel.mark@igbmc.fr, +33 (0)3 88 65 56 46 / +33 (0)3 88 65 56 36, http://www.igbmc.fr/research/department/2/team/10/
  • Team members: Researchers : Norbert B. GHYSELINCK, Manuel MARK, Marius TELETIN, Nadège VERNET, PhD student : Diana CONDREA, Technicians : Betty FERET, Muriel KLOPFENSTEI.
  • 3 relevant publications: 1) Vernet N et al., (2020). Meiosis occursnormally in the fetal ovary of mice lacking all retinoic acid receptors. Sci. Adv.6(21):eaaz1139. https://pubmed.ncbi.nlm.nih.gov/32917583/. 2) Teletin Met al.,(2019). Two functionally redundant sources of retinoic acid secure spermatogonia differentiation in the seminiferous epithelium. Development146(1). pii: dev170225. https://pubmed.ncbi.nlm.nih.gov/30487180/. 3) Ghyselinck NB, Duester G. (2019). Retinoic acid signaling pathways. Development146(13):dev167502. https://pubmed.ncbi.nlm.nih.gov/31273085/.
  • Number of PhDs in progress: 1PhD (since Oct. 2019).
PhD 2021-22 Enhancer-promoter communication in transcription

LabEx INRT (IGBMC) - Integrative Biology : Nuclear Dynamics, Regenerative and Translational Medecine, http://igbmc.fr/

Team : Spatial Organization of the Genome.

Team leader: Tom Sexton, sexton@igbmc.fr, +33 (0)3 88 65 35 80,  IGBMC, 1 rue Laurent Fries, 67400 Illkirch-Graffenstaden Cedex, http://www.igbmc.fr/sexton

Description: The complex expression patterns of most genes cannot be conferred by promoter sequence alone; genes are often under “remote control” from distal regulatory elements such as enhancers. It is still unclear exactly how enhancers “find” and regulate their target genes: chromosome conformation capture studies including our own suggest that chromatin loops bring genes into direct physical proximity with enhancers, but recent microscopy experiments bring this simple model into question, suggesting that such interactions may be very transient. We are delving into this mystery with three different approaches, and a keen PhD student is welcome in any one (or more) : 

  • Capture Hi-C (Ben Zouari et al., 2019) approaches to globally map promoter interactions, which we can now do in smaller cell numbers to assess rarer cell types and developmental transitions; 
  • In silico computational biology approaches to perform meta-analyses on existing (Capture)Hi-C datasets; 
  • Live microscopy approaches we have recently developed to tag and follow promoter-enhancer communication in real-time. 

Key words: Chromatin topology; enhancer; transcriptional regulation.

  • PhD supervisor: Tom Sexton, sexton@igbmc.fr, +33 (0)3 88 65 35 80, http://www.igbmc.fr/sexton
  • Team members: Natalia Sikorska (postdoc), Nezih Karasu (PhD), Angeliki Platania (PhD), Cathie Erb (engineer).
  • 3 relevant publications: 1) Ben Zouari et al. Genome Biol 20 102 (2019). 2) Sexton and Cavalli. Cell 160 1049 (2015). 3) Sexton et al. Cell 148 458 (2012).
  • Number of PhDs in progress: 2 (started Oct 2016 and Feb 2017).
PhD 2021-23 Structural and functional studies of chromatin remodeling enzymes

LabEx INRT (IGBMC) - Integrative Biology : Nuclear Dynamics, Regenerative and Translational Medecine, http://igbmc.fr/

Team : Structural and functional basis of chromatin remodeling.

Team leader: Elisa Bergamin, bergamie@igbmc.fr, +33 (0)3 88 65 32 58,  IGBMC, 1 rue Laurent Fries, 67400 Illkirch-Graffenstaden Cedex, http://www.igbmc.fr/research/department/2/team/137/

In eukaryotes, DNA is made to fit inside the cell nucleus througha high degree of compaction that is enabled by assembly into chromatin. Processes such as DNA damagerepair and transcription require localized changes in chromatin compaction. Re-organization of nucleosomesto regulate accessibility is mediated by a set of multi-subunit ATP-dependent chromatinremodeling complexesthat slide or evict nucleosomes from the chromatin fiber. Deregulation of these complexes canseverely impact gene expression, cell identity and genome integrity. The mammalian SWI/SNF complex comprisesa set of evolutionary conserved ‘core and enzymatic’ subunits, but also ‘auxiliary’ subunits presentonly in mammalians,thought to reflect increasing biological complexity. Although the topology and 3D structureof the SWI/SNF complex are becoming clearer, the structure, the molecular details of interaction and thefunction of these auxiliary yet important subunits are poorly defined at best. Despite some evidence thatcertain auxiliary subunits are involved in DNA damage repair (DDR), our knowledge of their actual functionin this process is very limited. Intriguingly, several of these proteins are predicted to be intrinsically disordered(ID), suggesting they may undergo liquid-liquid phase separation (LLPS). By using a combination of cryo-EM, x-raycrystallography,biochemistryandin cell experiments, this project aims to definethe structure and function of auxiliary subunits of the mammalian SWI/SNF complex, determine how theyinteractwith the core subunitsand with the nucleosome and better understand their roles at sites of DNAdamage, keeping into consideration their potential for phase separation.

Key words: Chromatin remodeling, Epigenetic, Cryo-EM, X-ray crystallography.

  • PhD supervisor: Elisa Bergamin, bergamie@igbmc.fr, +33 (0)3 88 65 32 58, http://www.igbmc.fr/research/department/2/team/137/
  • Team members: Dana DIAZ and Franck MARTIN (PhD students), Asgar Abbas KAZRANI (postdoc), Stephanie SIEBERT (technician), Julie LAFOUGE (M2 student).
  • 3 relevant publications: 1) Molecular basis for the methylation specificity of ATXR5 forhistone H3. Elisa Bergamin, Sarvan S, Mallette J, Eram MS, YeungS, Mongeon V, Joshi M, Brunzelle JS, Michaels SD, Blais A, VedadiM, Couture JF. Nucleic Acids Research. 2017. 2) Selective methylation of histone H3 variant H3.1 regulatesheterochromatin replication.Jacob Y*, Elisa Bergamin*, DonoghueMT, Mongeon V, LeBlanc C, Voigt P, Underwood CJ, Brunzelle JS,Michaels SD, Reinberg D, Couture JF, Martienssen RA. Science.2014* denotes co-first authorship. 3) The Cytoplasmic Adapter-Protein Dok7 Activates the Receptor Tyrosine KinaseMuSK via Dimerization.Elisa Bergamin, Peter T. Hallock, Steven J. Burden, and Stevan R. Hubbard.Molecular Cell. 2010, 39: 100-109.  
  • Number of PhDs in progress: 2 PhD students; respective starting dates 2018 and 2020.

Functional Genomics and Cancer (LabEx INRT) / Viral hepatitis and liver diseases (LabEx HepSYS)

PhD 2021-24 Claudin-1 as a driver and therapeutic target in cancer

LabEx HepSYS - Functional genomics of viral hepatitis and liver disease, http://www.labex-hepsys.fr/index.php/en

Team leader : Thomas Baumert,  thomas.baumert@unistra.fr, +33 (0)6 11 58 23 87,  IVH, 3 Rue Koeberlé, 67000 Strasbourg, http://www.u1110.inserm.fr

LabEx INRT (IGBMC) - Integrative Biology : Nuclear Dynamics, Regenerative and Translational Medecine, http://igbmc.fr/

Team  leader : Irwin Davidson, irwin@igbmc.fr, +33 (0)3 88 65 34 45, IGBMC, 1 rue Laurent Fries, 67404 Illkirch Graffenstaden Cedex, http://www.igbmc.fr/davidson/

Claudin 1 (CLDN1) is membrane protein of the tight junction family involved cell-cell contact, signaling and cell fate. CLDN1 is also highly expressed in many different types of cancers such as hepatocellular carcinoma, renal cancer and de-differentiated, therapy resistant invasive melanoma. In the liver CLDN1 is a host factor and signal transducer for entry of hepatitis C virus – a major cause of liver cancer world-wide. The host laboratories have developed a monoclonal antibody (mAb) specifically targeting nonjunctional CLDN1 expressed on the cell membrane (Mailly et al. Nature Biotech 2015). In a new collaboration, the partnering teams have obtained robust data showing that the mAb can block cancer cell growth in cell-based tumorspheroid systems and PDX and CDX xenograft in vivo models without detectable adverse effects. The candidate in this thesis project will use a combination of cellular, biochemical, molecular biology and genomics approaches to unravel the molecular mechanism by which antibody-mediated targeting of CLDN1 affects downstream signaling pathways and gene expression programs resulting in inhibition of tumor growth using hepatocellular carcinoma, melanoma and renal cell carcinoma models. Furthermore, the candidate will develop innovative preclinical approaches to investigate the potential of the CLDN1-targeting approaches for treatment of human solid tumors.    

Key words: hepatocellular carcinoma; melanoma, renal cell carcinoma, signaling pathways, control of gene expression, cancer therapeutics.

  • PhD supervisor 1:Thomas Baumert,  thomas.baumert@unistra.fr, +33 (0)6 11 58 23 8745, http://www.u1110.inserm.fr /
  • Team  members: Baumert Thomas, MD, PU-PH, HDR; Schuster Catherine, PhD DR1, HDR; Lupberger Joachim, PhD, CR1, HDR, Emilie Crouchet, PhD, Scientist, Laurent Mailly, PhD, IR, animal model expert, Pessaux Patrick, MD, PU-PH, HDR. 
  • 3 relevant publications: 1) Jühling F, Hamdane N, Crouchet E, Li S, El Saghire H, Mukherji A, Fujiwara N, Oudot MA, Thumann C, Saviano A, Roca Suarez AA, Goto K, Masia R, Sojoodi M, Arora G, Aikata H, Ono A, Tabrizian P, Schwartz M, Polyak SJ, Davidson I, Schmidl C, Bock C, Schuster C, Chayama K, Pessaux P, Tanabe KK, Hoshida Y, Zeisel MB, Duong FH, Fuchs BC, Baumert TF. Targeting clinical epigenetic reprogramming for chemoprevention of metabolic and viral hepatocellular carcinoma. Gut. 2020 Mar 26;gutjnl-2019-318918. doi: 10.1136/gutjnl-2019-318918. Online ahead of print. PMID: 32217639. (IF=19.82). 2) Aizarani N, Saviano A #, Sagar #,  Mailly L,  Durand S, Herman J.S., Pessaux P., Baumert T.F.**, Grün D.*A Human Liver Cell Atlas reveals Heterogeneity and Epithelial Progenitors. Nature. 2019 Aug;572(7768):199-204. doi: 10.1038/s41586-019-1373-2. Jul 10. PMID: 31292543. (IF=42.79). **Co-senior and co-corresponding authors *Co-corresponding authors #Co-second authors. 3) Mailly L, Xiao F*, Lupberger J*, Wilson GK, Leboeuf C, Aubert P, Duong FHT, Fofana I, Thumann C, Bandiera S, Lutgehetmann M, Volz T, Davis C, Harris HJ, Girardi E, Chane-Woon-Ming B, Fletcher N, Bartenschlager R, Pessaux P, Meuleman P, Villa P, Pfeffer S, Heim MH, Zeisel MB, Neunlist M, Dandri M, McKeating JA, Robinet E#, Baumert TF#. Clearance of persistent hepatitis C virus infection using a monoclonal antibody specific for tight junction protein claudin-1. Nat. Biotechnol., 2015, 33(5), 549-54 (IF=28.44).*Authors contributed equally, #Authors contributed equally
  • Number of PhDs in progress: 4 - N. Almeida (Oct 2019-50%); M. Dachraoui (Dec 2017); F. Del Zompo (Nov 2020); M. Muller (Oct 2019 – 50%); N. Roehlen (Oct 2018).
  • PhD supervisor 2: Irwin Davidson, irwin@igbmc.fr, +33 (0)3 88 65 34, http://www.igbmc.fr/davidson/
  • Team members: Davidson Irwin, DRCE; Malouf Gabriel, PUPH; Mengus Gabrielle CRCN; Martianov Igor CRCN; Haller Alexandre PhD; Helleux Alexandra PhD; Davidson Guillaume, PhD; Gantzer Justine, MD PhD; Baltzinger Philippe, MD PhD; Gambi Giovanni, PhD; Berico Pietro, PhD; Vokshi Bujamin, Post-Doc; Bazai-Khan Serhish Post-doc, Michel Isabelle IE.
  • 3 relevant publications: 1) Laurette P, Coassolo S, Davidson G, Michel I, Gambi G, Yao W,  Sohier P, Li M, Larue L, Mengus, G and Davidson I. (2020). Chromatin remodellers Brg1 and Bptf are required for normal gene expression and progression of oncogenic Braf-driven mouse melanoma. Cell Death and Differentiation, 2020 Jan;27(1):29-43. (IF10.7). 2) Ennen M, Keime C, Gambi, G, Kieny A, Coassolo S, Thibault-Carpentier C, Margerin-Schaller F, Davidson G, Vagne C, Lipsker D and Davidson I. (2017). MITF-high and MITF-low cells and a novel subpopulation expressing genes of both cell states contribute to intra and inter-tumoral heterogeneity of primary melanoma. Clinical Cancer Research 15;23(22):7097-7107. (IF10.1). 3) Langer D., Alpern D., Rhinn M., Martianov I., Keime C., Dollé P., Mengus G., and Davidson I. (2016) Essential role of the TFIID subunit TAF4 in murine embryogenesis and embryonic stem cell differentiation. Nature Communications. Mar 30;7:11063. doi: 10.1038/ncomms11063 (IF12.5).
  • Number of PhDs in progress: 4 - Giovanni Gambi (01/01/2017; thesis defense march 2021), Pietro Berico (co-direction 01/10/2016- thesis defense March 2021), Alexandre Haller (01/10/2020). Alexandra Helleux (co-direction; 01/10/2019).

Genomes expression and cross-talk in mitochondrial function and dysfunction (LabEx MitoCross)

PhD 2021-25 Pathogenic mutations of the mitochondrial protein ND5: investigation of molecular mechanisms of pathogenesis and development of novel gene therapy strategies

LabEx MitoCross - Genomes expression and cross-talk in mitochondrial function and dysfunction https://mitocross.unistra.fr/

Team : Intracellular traffic of RNA and mitochondrial diseases

Team leaders: Nina Entelis & Ivan Tarassov,  n.entelis@unistra.fr / i.tarassov@unistra.fr,  IPCB, 21 rue René Descartes, 67084 Strasbourg Cedex, https://mitocross.unistra.fr/partners/gmgm/team-1-intracellular-traffic-of-rna-and-mitochondrial-pathologies/

Mitochondria are essential organelles of eukaryotic cells due to their participation in many crucial cellular functions. Although most macromolecules present in the organelle are encoded in the nuclear genome, mitochondria also contain their own genome, mtDNA. More than 250 pathogenic mtDNA mutations have been identified so far which are associated with severe, incurable neuromuscular diseases. Our team possesses an important experience in the field of molecular genetics of mitochondrial pathologies. Currently, we study the consequences of point mutations in mtDNA encoded ND5 gene associated with MELAS-like syndromes. The objectives of the PhD project will be: 1) to characterize molecular and cellular mechanisms of pathogenesis, with a focus on a possible synthesis of truncated forms of ND5 protein and the defects in the assembly of the respiratory Complex I; 2) to develop therapeutic strategies based on the anti-replicative approach and on the various CRISPR/Cas systems adapted for targeting into human mitochondria. The candidate will employ molecular, cellular and biochemical approaches, such as cell culture, mitochondria purification, respiration, mitochondrial translation, CRISPR-Cas systems, immunoblotting, immunoprecipitation, molecular hybridization, fluorescent microscopy, etc.  

This project will contribute to better understanding of the mechanisms of neurodegenerative diseases caused by mtDNA mutations and to develop novel therapeutic strategies.

Key words:  mtDNA, mitochondrial diseases, respiratory complexes, molecular therapy.

  • PhD supervisor: Dr Nina Entelis, n.entelis@unistra.fr,  +33 (0) 368851481, https://mitocross.unistra.fr/partners/gmgm/team-1-intracellular-traffic-of-rna-and-mitochondrial-pathologies/
  • Team members: 4 Researchers, 2 Engineers, 1 Technician, 2 PostDocs, 1 PhD student
  • 3 relevant publications: 1) K. Auré, G. Fayet, I. Chicherin, B. Rucheton, S. Filaut, A.-M. Heckel, J. Eichler, F. Caillon, Y. Péréon, N. Entelis, I. Tarassov, A. Lombès. A homoplasmic mitochondrial tRNAPro mutation causing exercise-induced muscle swelling and fatigue. Neurology: Genetics 2020 Jul 15;6(4):e480. 2) D. Jeandard, A. Smirnova, I. Tarassov, E. Barrey, A. Smirnov, N. Entelis. Import of non-coding RNAs into human mitochondria: a critical review and emerging approaches. Cells 2019, 8, 286. 3) R Loutre, AM Heckel, A Smirnova, N Entelis, I Tarassov. Can mitochondrial DNA be CRISPRized: pro and contra. IUBMB Life, 2018, Dec;70(12):1233-1239.
  • Number of PhDs in progress: 1, co-supervised, starting date Oct 2019.
PhD 2021-26 Imaging cellular processes using synchrotron radiation

LabEx MitoCross Genomes expression and cross-talk in mitochondrial function and dysfunction https://mitocross.unistra.fr/

Team : Intracellular traffic of RNA and mitochondrial diseases

Team leaders: Nina Entelis & Ivan Tarassov,  n.entelis@unistra.fr / i.tarassov@unistra.fr,  IPCB, 21 rue René Descartes, 67084 Strasbourg Cedex, https://mitocross.unistra.fr/partners/gmgm/team-1-intracellular-traffic-of-rna-and-mitochondrial-pathologies/

In the crowded cellular environment, cellular processes rely on organellar and granular compartmentalization. Methods based on cell extraction spuriously mix together components, otherwise separated. Moreover, microscopy images usually rely on large beacons to label molecules (GFP, aptamers) that may interfere with cellular processes. Technics relying on detection of very low amounts of tiny labels constitute promising developments to decipher cellular processes. Elements heavier than aluminium are detected very effectively (attogram range (10-18 g)) using synchrotron X-ray fluorescence (XRF). At beamline Nanoscopium (synchrotron Soleil, Paris), bidimensional samples such as cells monolayers can be imaged using XRF. Each pixel yields a full XRF spectrum allowing detection of dozens of elements. Each XRF peak can be viewed as an individual color channel. Images of natural elemental distributions lead to unprecedented relationships between ionic content and physiological states. Elemental labeling also offers the opportunity to analyze the localization of labeled molecules. We want to analyze import of brominated RNAs in mitochondria where the TOM70 outer membrane transporter has been his-tagged to selectively bind nickel ions. Our results indicate we are close to a proof of concept. Bromine and nickel detection by XRF should report on RNA mitochondrial import in an unprecedented framework. This method could be adapted to any process, provided labeling is achieved. The PhD student will develop labeling strategies, contribute to XRF visualization of the yeast S. cerevisiae mitochondrial network, and transfer the technology to human cells.


Key words: X-ray Fluorescence, cellular imaging, molecular beacons, elemental distribution

  • PhD supervisor: Dr Benoît Masquida, b.masquida@unistra.fr,  +33 670237950, https://www.researchgate.net/profile/Benoit_Masquida2
  • Team members: Christelle Gruffaz, Anne-Marie Heckel, Natalia Nikitchina, Dr Benoît Masquida, Dr Cédric Schelcher, Diana Sibrikova, Dr Alexandre Smirnov, Dr Anna Smirnova, Dr. Ivan Tarassov, Dr. N. Entelis.
  • Number of PhDs in progress: Natalia Nikitchina (October 2019)
PhD 2021-27 Inheritance, epistasis, missing heritability hidden behind the mitochondrial genome variation

 LabEx MitoCross - Genomes expression and cross-talk in mitochondrial function and dysfunction, https://mitocross.unistra.fr/

Team : Variation intra-spécifique et évolution des génomes.

Team  leader : Joseph Schacherer, schacherer@unistra.fr, +33 (0)3 68 85 18 21, GMGM, 15 rue René Descartes, 67000 Strasbourg, http://ttps://mitocross.unistra.fr/partners/gmgm/team-7-intraspecific-variation-and-genome-evolution/

 

Elucidating the causes of the awesome phenotypic diversity observed in natural populations is a major challenge in biology. To date quantitative genetics has mainly been focused on the identification of the nuclear determinants of complex trait, leaving mitochondrial DNA aside. The mitochondrial genome has been considered to study specific mitochondrial traits, but its contribution to common complex traits has been largely ignored. There is a growing number of evidence that genetic variations of the mitochondrion (considered alone or through interactions with nuclear variations) account for much of the heritability of complex traits. In this context, we would like to identify mitochondrial genetic determinants of multiple complex traits (including molecular traits like gene expression levels). Moreover, we will characterize the genetic architecture of the interaction between the mitochondrial and nuclear genomes, with respect with those traits. Beyond the description of mitochondrial genetic associations, we want to uncover the molecular mechanisms underlying them, i.e. what are the genes/proteins involved and how are they contribute together to a phenotype. To achieve this, we will develop genetic and genomic approaches (experimental and computational) in the budding yeast Saccharomyces cerevisiae. Reaching a system comprehension of the genetic and molecular mechanisms underlying the nuclear-mitochondrial interactions requires a deep understanding of both molecular and computational biology. Therefore, we will work at the interface between genetics, genomics and computational biology.

Key words: genetics, population genomics, phenotypic variation, mitochondrion, yeast

  • PhD supervisor: Joseph Schacherer, / schacherer@unistra.fr, / +33 (0)3 68 85 18 21,  http://ttps://mitocross.unistra.fr/partners/gmgm/team-7-intraspecific-variation-and-genome-evolution/
  • Team members: 14.
  • 3 relevant publications: 1) Discordant evolution of mitochondrial and nuclear yeast genomes at population level. De Chiara M, Friedrich A, Barré B, Breitenbach M, Schacherer J*, Liti G* BMC Biol. 2020, 18(1):49 2) Extensive impact of low-frequency variants on the phenotypic landscape at population-scale, Fournier T, Abou Saada O, Hou J, Peter J, Caudal E, Schacherer J, Elife. 2019, 8 e49258 3) Genome evolution across 1,011 Saccharomyces cerevisiae isolates, Peter J, De Chiara M, Friedrich A, Yue JX, Pflieger D, Bergström A, Sigwalt A, Barre B, Freel K, Llored A, Cruaud C, Labadie K, Aury JM, Istace B, Lebrigand K, Barbry P, Engelen S, Lemainque A, Wincker P, Liti G, Schacherer J, Nature, 2018, 7701:339-344.
  • Number of PhDs in progress: 4 (starting dates: 10/207 ; 10/2017; 10/2019; 10/2019).

Insect Models of Innate Immunity (LabEx NetRNA)

PhD 2021-28 Antiviral STING signaling in drosophila

LabEx NetRNA - Networks of Regulatory RNAs across kingdoms and dynamical responses to biotic and abiotic stresses, http://labex-ibmc.u-strasbg.fr/NetRNA/index.php

Team : Signaling and antiviral effectors.

Team leader: Jean-Luc Imler, jl.imler@ibmc-cnrs.unistra.fr, + 33 (0)3 88 41 70 37, IBMC-CNRS 2, Allée Konrad Roentgen, 67 084 Strasbourg Cedex, http://labex-ibmc.u-strasbg.fr/NetRNA/team.php?id=5

Innate immunity is the first barrier to infection in all animals. Recognition of the intruding microbes involves the detection of microbe-associated molecular patterns (MAMPs) by pattern recognition receptors (PRRs). Sensing by PRRs initiates signaling which leads to activation of transcription factors and ultimately expression of immune related genes. Although insect PRRs recognizing bacterial and fungal ligands have long been identified and characterized, recognition of viruses by insect innate immune systems remains poorly characterized. Our laboratory is investigating the evolutionarily ancient STING molecule in the model organism Drosophila melanogaster, and has connected it to NF-[Symbole]B signaling. We have recently shown that the cyclic dinucleotide 2’3’-cGAMP, which is produced in mammals by the enzyme cGAS, a receptor for intracytoplasmic DNA, triggers broad antiviral immunity in flies. Following up on these findings, we have identified candidate PRRs operating upstream of STING in drosophila. The PhD project aims at characterizing these candidates in vivo. The selected applicant will generate mutant flies and will characterize their phenotypes with the aim of understanding (i) the function and the regulation of the receptors activating STING, and (ii) how these receptors integrate with RNA interference, a major defense pathway in insects, to control viral infections.  

Key words: STING, cGAS, innate immunity, virus, genetics, antiviral, signaling, drosophila.

  • PhD supervisor: Jean-Luc Imler, jl.imler@ibmc-cnrs.unistra.fr, + 33 (0)3 88 41 70 37, http://labex-ibmc.u-strasbg.fr/NetRNA/team.php?id=5
  • Team members: G. Haas (scientist), L. dos Santos (post-doc), Y. Benamrouche (research engineer), F. Schlotter (assistant engineer), E. Lefebvre (assistant engineer), M. Seiler (assistant engineer), J. Schneider (PhD student), L. Hédelin (PhD student).
  • 3 relevant publications: 1) Lamiable O, Kellenberger C, Kemp C, Troxler L, Pelte N, Boutros M, Marques JT, Daeffler L, Hoffmann JA, Roussel A & Imler JL (2016) “Cytokine Diedel and a viral homologue suppress deleterious IMD-dependent gene expression in Drosophila” Proc. Natl. Acad. Sci USA, 113: 698-703. 2) Goto A, Okado K, Martins N, Cai H, Barbier V, Lamiable O, Troxler L, Santiago E, Kuhn L, Paik D, Silverman N, Holleufer A, Hartmann R, Liu J, Peng T, Hoffmann JA, Meignin C, Daeffler L & Imler JL (2018) “The kinase IKK[Symbole] regulates a STING and NF-[Symbole]B-dependent antiviral response pathway in Drosophila” Immunity, 49: 225-234. 3) Cai H, Holleufer A, Simonsen B, Schneider J, Lemoine A, Gad HH, Huang J, Huang J, Chen D, Peng T, Marques JT, Hartmann R, Martins N & Imler JL (2020) 2’3’-cGAMP triggers a STING and NF-kB dependent broad antiviral response in Drosophila. Science Signaling, 13: eabc4537.   
  • Number of PhDs in progress: 2 (Oct. 2018; Oct. 2019).
PhD 2021-29 A Gene drive carrying an antiviral gene as a tool to fight dengue and Zika viruses in Aedes mosquitoes

LabEx NetRNA - Networks of Regulatory RNAs across kingdoms and dynamical responses to biotic and abiotic stresses, http://labex-ibmc.u-strasbg.fr/NetRNA/index.php

Team : Antiviral Immunity in Aedes mosquitoes.

Team leader: Joao Trindade Marques, joao.marques@unistra.fr, + 33 (0)3 88 41 70 37, IBMC-CNRS 2, Allée Konrad Roentgen, 67 084 Strasbourg Cedex, http://labex-ibmc.u-strasbg.fr/NetRNA/team.php?id=16

Dengue (DENV) and Zika (ZIKV) are mosquito borne viruses that infect millions of people worldwide. Aedes aegypti mosquitoes are the major vectors for these viruses and can be an important target for transmission blocking strategies. We have previously described a novel antiviral gene named Loqs2 that can make mosquitoes resistant to DENV and ZIKV when ectopically expressed in the gut. The objective of this project is to design CRISPR-based gene drive (GD) systems in Aedes mosquitoes that contain the Loqs2 gene (and potentially other antiviral genes of interest). GDs are synthetic genetic elements possessing the property to spread and invade populations of a target species that would allow our transgene to modify mosquitoes in the wild. GDs have not yet been developed for mosquitoes of the Aedes genus. Here, we will generate mosquito strains carrying GDs that will be tested in the laboratory for their efficiency both in terms of gene drive and of pathogen resistance phenotype. We will also use them to address specific concerns regarding the safety of GDs. Our study will contribute to the generation of a strategy that could be applied in the field to effectively control the transmission of mosquito borne viruses.

Key words: Dengue and Zika viruses, Aedes mosquitoes, antiviral immunity, gene-drive.

  • PhD supervisors: Joao Trindade Marques and Eric Marois, joao.marques@unistra.fr / e.marois@unistra.fr, + 33 (0)3 88 41 71 13, http://labex-ibmc.u-strasbg.fr/NetRNA/team.php?id=16
  • Team members: Roenick Olmo (Postdoc), Fabien Aubry (Postdoc), Diwas Srivastava(Postdoc), Antinea Babarit (PhD student), Jeremy Esnault (tech), Illona-Marie Bouleté (Tech).
  • 3 relevant publications: 1) A single unidirectional piRNA cluster similar to the flamenco locus is the major source of EVE-derived transcription and small RNAs in Aedes aegypti mosquitoes. Aguiar ERGR, Almeida JPP, Queiroz LR, Oliveira LS, Olmo RP, Faria IJS, Imler JL, Gruber A, Matthews BJ, Marques JT.RNA. 2020 Jan 29. pii: rna.073965.119. doi: 10.1261/rna.073965.119. [Epub ahead of print] PMID: 31996404. 2) Control of dengue virus in the midgut of Aedes aegypti by ectopic expression of the dsRNA-binding protein Loqs2. Olmo RP, Ferreira AGA, Izidoro-Toledo TC, Aguiar ERGR, de Faria IJS, de Souza KPR, Osório KP, Kuhn L, Hammann P, de Andrade EG, Todjro YM, Rocha MN, Leite THJF, Amadou SCG, Armache JN, Paro S, de Oliveira CD, Carvalho FD, Moreira LA, Marois E, Imler JL, Marques JT. Nat Microbiol. 2018 3(12):1385-1393. doi: 10.1038/s41564-018-0268-6. PMID: 30374169. 3) Sequence-independent characterization of viruses based on the pattern of viral small RNAs produced by the host. Aguiar ER, Olmo RP, Paro S, Ferreira FV, de Faria IJ, Todjro YM, Lobo FP, Kroon EG, Meignin C, Gatherer D, Imler JL, Marques JT. Nucleic Acids Res. 2015 Jul 27;43(13):6191-206. doi: 10.1093/nar/gkv587. PMID: 26040701.    
  • Number of PhDs in progress: 1 (started August 2019).
PhD 2021-30 Impact of the viral RNA epitranscriptome during infection in insects

LabEx NetRNA - Networks of Regulatory RNAs across kingdoms and dynamical responses to biotic and abiotic stresses, http://labex-ibmc.u-strasbg.fr/NetRNA/index.php

Team : RNAi and receptors.

Team leader: Carine Meignin, c.meignin@unistra.fr, + 33 (0)3 88 41 71 15, IBMC-CNRS 2, Allée Konrad Roentgen, 67 084 Strasbourg Cedex, http://labex-ibmc.u-strasbg.fr/NetRNA/team.php?id=13

RNA modifications, commonly called epitranscriptome, are observed on specific residues of cellular RNAs and play a key role in maturation and functionality of these RNAs. Among over 150 chemical modifications described in RNA, the methylation of nucleotides at different positions is the most abundant. Over the past decade, the development of new detection approaches based on high-throughput genome-wide sequencing has led to the identification of methylation of also mRNAs bringing a new level in gene expression regulation.  

However, only few studies have been so far dedicated to modifications of viral RNA and, despite the identification of certain modifications of RNA present in viruses, little is known about their roles in infection and the spread of viruses. Today, certain modifications of the viral RNA appear to be fundamental for the regulation of the viral RNA metabolism for arboviruses like ZIKA and Dengue viruses. This project has an integrative dimension, since it combines the mapping of the epitranscriptome of viral RNA, as well as genetics and molecular virology.

Key words: RNA viruses, epitranscriptomics, insect cells, Drosophila melanogaster.

  • PhD supervisor: Carine Meignin, c.meignin@unistra.fr, + 33 (0)3 88 41 71 15, http://labex-ibmc.u-strasbg.fr/NetRNA/team.php?id=13
  • Team members: Claire Rousseau (PhD student), Matthieu Bellet (PhD student), Emilie Lauret (Engineer Assistant).
  • 3 relevant publications: 1) In vitro studies provide insight into effects of Dicer-2 helicase mutations in Drosophila melanogaster. Donelick HM, Talide L, Bellet M, Aruscavage PJ, Lauret E, Aguiar ERGR, Marques JT, Meignin C, Bass BL. RNA. 2020 Dec;26(12):1847-1861. doi: 10.1261/rna.077289.120. Epub 2020 Aug 25. PMID: 32843367. 2) A Transgenic Flock House Virus Replicon Reveals an RNAi Independent Antiviral Mechanism Acting in Drosophila Follicular Somatic Cells. Martins N, Lemoine A, Santiago E, Paro S, Imler JL, Meignin C. G3 (Bethesda). 2019 Feb 7;9(2):403-412. doi: 10.1534/g3.118.200872. PMID: 30530643 Free PMC article. 3) Cross-species comparative analysis of Dicer proteins during Sindbis virus infection. Girardi E, Lef√èvre M, Chane-Woon-Ming B, Paro S, Claydon B, Imler JL, Meignin C, Pfeffer S. Sci Rep. 2015 May 29;5:10693. doi: 10.1038/srep10693. PMID: 26024431 Free PMC article.    
  • Number of PhDs in progress: 2 (started October 2018 and September 2019).

Integrated Structural Biology (LabEx INRT)

PhD 2021-31 Structural study of eukaryotic transcription initiation

LabEx INRT (IGBMC) - Integrative Biology : Nuclear Dynamics, Regenerative and Translational Medecine, http://igbmc.fr/

Team : Architecture of nucleoprotein systems by 3D electron microscopy.

Team leader: Patrick Schultz, patrick.schultz@igbmc.fr, +33 (0)3 69 48 52 99,  IGBMC, 1 rue Laurent Fries, 67400 Illkirch-Graffenstaden Cedex, http://igbmc.fr/research/department/3/team/39/

A key regulatory step for transcription of protein coding genes by RNA polymerase II is the assembly of the Pre-Initiation Complex (PIC) at the gene promoter. The interaction of the TATA-binding protein (TBP) with the promoter DNA and the subsequent DNA bending is essential for PIC assembly. TBP binding to promoter DNA is therefore highly regulated and several multiprotein complexes modulate this step. The molecular mechanisms by which TFIID or SAGA, two major TBP-binding complexes, recognize the promoter DNA, deposit TBP and regulate transcription initiation are poorly understood. The thesis project aims at studying the mechanism of TBP deposition onto promoter DNA by SAGA and TFIID complexes, and in particular the role of the general transcription factor TFIIA and of the promoter sequence. The binding interfaces transcriptional activators will be determined and associated allosteric regulations will be analyzed. The recruitment of SAGA and TFIID to promoters will be studied in vitro through by analysing the structure of chromatin-bound SAGA and TFIID, and in vivo by the identification of in vivo interaction partners and the isolate intact endogenous preinitiation complexes. The candidate will have access to state of the art equipment in molecular biology, protein production and cryo-electron microscopy. 

Key words: Eukaryotic transcription initiation, cryogenic electron microscopy, biochemistry, SAGA, TFIID, TFIIA, TBP.

  • PhD supervisor: Gabor Papai, gabor.papai@igbmc.fr, +33 (0)3 69 48 52 88, http://igbmc.fr/research/department/3/team/39/
  • Team members: 4 permanent researchers (3HDR), 1 emeritus, 1 postdoctoral fellow, 3 PhD students, 4 engineers/technicians.
  • 3 relevant publications: 1) Papai G, Frechard A, Kolesnikova O, Crucifix C, Schultz P, Ben-Shem A. Structure of SAGA and mechanism of TBP deposition on gene promoters. Nature. 2020; 577(7792):711-716. 2) Kolesnikova O, Ben-Shem A, Luo J, Ranish J, Schultz P, Papai G. Molecular structure of promoter-bound yeast TFIID. Nat Commun. 2018; 9(1):4666. 3) Bieniossek C, Papai G, Schaffitzel C, Garzoni F, Chaillet M, Scheer E, Papadopoulos P, Tora L, Schultz P, Berger I. The architecture of human general transcription factor TFIID core complex. Nature. 2013; 493(7434):699-702.   
  • Number of PhDs in progress: 3 PhD students (Maximilien Werderer - 2018, Victor Hanss – 2020, Amelie Zachayus - 2020).
PhD 2021-32 Structural dynamics of nuclear hormone receptors: integrated computational and experimental studies

LabEx INRT (IGBMC) - Integrative Biology : Nuclear Dynamics, Regenerative and Translational Medecine, http://igbmc.fr/

Team : Chemical biophysics of transcriptional signaling.

Team leader: Annick Dejaegere, annick@igbmc.fr, +33 (0)3 68 85 47 21,  IGBMC, 1 rue Laurent Fries, 67400 Illkirch-Graffenstaden Cedex, http://www.igbmc.fr/research/department/3/team/34/

Nuclear receptors (NRs) form an important family of transcription factors that regulate transcriptional programs in response to binding of their cognate ligands (e.g. hormones, vitamins, or metabolites, etc.). They play a central role in cell signaling and dysfunctions in their regulatory actions are associated with a vast range of pathologies, thus making NRs important drug targets.  

NRs transduce the chemical signal encoded in their ligands into the modulation of gene networks. A large number of biochemical and structural studies have focused on revealing the molecular details of ligand-receptor interactions and subsequent conformational changes leading to gene regulation. 

Recently, mass spectrometry hydrogen-deuterium exchange (HDX) studies have emphasized that ligand binding has a profound effect on the structural dynamics of NRs. There are remarkable examples where dissimilar ligand binding results in similar 3D structures, yet the dynamics are distinct, which suggests a contribution of dynamics to selective targeting of different regulatory pathways.  

This thesis project aims to develop and apply new models that can provide a molecular interpretation of HDX experiments using molecular dynamics simulations and advanced sampling methods to identify transient conformations not accessible to conventional structural studies.  Bringing these methods together in the study of nuclear receptors will provide new insight into the role of structural dynamics in ligand-specific signaling and could provide a molecular interpretation for selective targeting of gene-regulatory pathways.  

Key words: molecular dynamics simulations – hydrogen/deuterium exchange – nuclear receptors.

  • PhD supervisor: Annick Dejaegere, annick@igbmc.fr, +33 (0)3 68 85 47 21, http://www.igbmc.fr/research/department/3/team/34/
  • Team members: 7.
  • 3 relevant publications: 1) L. Bianchetti et al. BBA General Subjects 2018 doi 10.1016/j.bbagen.2018.04.022, S.J. Wodak et al. Structure 2019 doi: 10.1016/j.str.2019.01.003 ; N. Rochel et al. Nat Commun., 2019, doi: 10.1038/s41467-018-08157- y .
  • Number of PhDs in progress: 1 (Ana Milinski, January 2021).
PhD 2021-33 Structure-function study of human ribosome complexes

LabEx INRT (IGBMC) - Integrative Biology : Nuclear Dynamics, Regenerative and Translational Medecine, http://igbmc.fr/

Team : Large complexes involved in gene expression.

Team leader: Bruno Klaholz, klaholz@igbmc.fr, +33 (0)3 69 48 52 78,  IGBMC, 1 rue Laurent Fries, 67404 Illkirch-Graffenstaden Cedex, http://igbmc.fr/Klaholz

The ribosome is a molecular machinery that goes through different phases, notably initiation, elongation and termination of messenger RNA translation. Protein synthesis is catalysed by the ribosome and is regulated by protein factors that bind transiently to the ribosome during the different phases. Over the past few years, our research group succeeded in purifying the human ribosome to high homogeneity and determined its three-dimensional structure to ~3 Å resolution using cryo-EM (Khatter et al., Nature 2015; Natchiar et al., Nature 2017) which represented a major scientific and technical challenge. The structure provided unprecedented insights into the detailed architecture of the human ribosome down to the atomic level with the visualization of side-chain positions and conformations of ribosomal RNAs and proteins and even chemical modifications. This now opens unique possibilities in studying the molecular mechanisms of protein synthesis in humans by analysing functional complexes of the human ribosome with mRNA, tRNAs and ribosomal factors bound. The aim of this PhD project is to address the regulatory mechanism of initiation factors binding to the human ribosome in the presence of selected mRNA sequences. The study will comprise the biochemical preparation of the human ribosome and of ribosomal factors (already available in the group), translation assays with cell extracts for functional analysis, the reconstitution and biophysical characterization of the complexes comprising the 40S ribosomal subunit or the full 80S human ribosome, and the determination of the atomic structure using cutting-edge technologies (on-site high-resolution cryo electron microscopy, single particle image processing and 3D reconstruction, atomic model refinement using structure refinement methods used in crystallography, as established and described in our publications Khatter et al., Nature 2015, Natchiar et al., Nature 2017, Natchiar et al., Protocol Exchange 2017). This project will allow a better understanding of the molecular function of the human ribosome, which is an important medical target. The project will benefit from the technological platforms in Integrated Structural Biology available as part of the infrastructures hosted at the Centre for Integrative Biology at the IGBMC including cutting-edge instrumentation in cryo-EM required for this project.

Key words: Human ribosome, ribosomal factors, 3D structure.

  • PhD supervisor: Bruno Klaholz, klaholz@igbmc.fr, +33 (0)3 69 48 52 78, http://igbmc.fr/Klaholz
  • Team members: 12. 
  • 3 relevant publications: 1) Nature 2017. 2) Nat Commun 2016. 3) Nature 2015.   
  • Number of PhDs in progress: 2 (10.2017 & 10.2019) + 2 in co-directorship (10.2018 & 11.2019).
PhD 2021-34 Structural investigations on the coupling of transcription and translation

LabEx INRT (IGBMC) - Integrative Biology : Nuclear Dynamics, Regenerative and Translational Medecine, http://igbmc.fr/

Team : Regulation of Transcription

Team leader: Albert Weixlbaumer, albert.weixlbaumer@igbmc.fr, +33 (0)3 6948 51 03,  IGBMC, 1 rue Laurent Fries, 67400 Illkirch-Graffenstaden Cedex, http://www.igbmc.fr/research/department/3/team/119

Gene expression employs at least two steps in all kingdoms of life: i) DNA is transcribed to mRNA by RNA polymerase (RNAP); and ii) the mRNA is translated to protein by the ribosome. In prokaryotes (bacteria and archaea) both processes can occur in close spatial proximity and simultaneously in a supramolecular assembly line called the expressome. The expressome consists of a transcribing RNAP coupled to a ribosome co-translating the nascent mRNA. We have recently visualized this higher-order assembly for the first time at high-resolution (Webster et al., Science 2020) and this raised many new questions. 

Students interested to tackle challenging problems and using state-of-the-art structural biology approaches, will be able to choose from a number of projects and study the allosteric crosstalk of E. coli RNAP coupled to the ribosome. 

For instance, RNAP pauses frequently and we want to understand how collisions between the ribosome and RNAP are avoided, or on the contrary, how they are used to facilitate the expression of genes further downstream? Alternatively, we know a number of transcription factors, which are involved in coupling but we lack a mechanistic understanding about their function. Finally, we identified alternative RNAP binding sites on the ribosome and want to investigate their biological role. 

Interested candidates will use single particle cryo-EM, the ideal method to gain mechanistic insights of large, dynamic complexes, to obtain high-resolution reconstructions. Biochemical, and in-vivo approaches will complement your results. Your work will unravel how synergism and crosstalk of two distinct macromolecular machines in the context of a supramolecular assembly regulates the conversion of genotype to phenotype. For more information, take a look at Webster et al., Science 2020 (doi: 10.1126/science.abb5036).

Key words: RNA polymerase, ribosome, molecular machines, gene expression, cryo-electron microscopy, structural biology.

  • PhD supervisor: Albert Weixlbaumer, albert.weixlbaumer@igbmc.fr, +33 (0)3 6948 51 03, http://www.igbmc.fr/research/department/3/team/119
  • Team members: 7 (3 students, 2 postdocs, 2 research technicians).
  • 3 relevant publications: 1) Webster MW, Takacs M, Zhu C, Vidmar V, Eduljee AD, Abdelkareem M,  Weixlbaumer A (2020). Structural basis of transcription-translation coupling and collision in bacteria. Science 10.1126/science.abb5036. 2) Abdelkareem M, Saint-André C, Takacs M, Papai G, Crucifix C, Guo X, Ortiz J, Weixlbaumer A (2019). Structural Basis of Transcription: RNA polymerase backtracking and its reactivation. Mol Cell 75(2), 298-309. 3) Guo X, Myasnikov AG, Chen J, Crucifix C, Papai G, Takacs M, Schultz P, Weixlbaumer A (2018). Structural Basis for NusA Stabilized Transcriptional Pausing. Mol Cell 69(5), 816–827 (featured on the cover).  
  • Number of PhDs in progress: 3 PhD students (Maximilien Werderer - 2018, Victor Hanss – 2020, Amelie Zachayus - 2020).
PhD 2021-35 Structural investigations on Rea1 complexes

LabEx INRT (IGBMC) - Integrative Biology : Nuclear Dynamics, Regenerative and Translational Medecine, http://igbmc.fr/

Team : Structural Biology of Molecular Machines.

Team leader: Helgo Schmidt, schmidth@igbmc.fr, +33 (0)3 69 48 52 77,  IGBMC, 1 rue Laurent Fries, 67400 Illkirch-Graffenstaden Cedex, http://www.igbmc.fr/research/department/3/team/134/

Eukaryotic ribosomes are complex molecular machines whose assembly is tightly controlled to ensure faithful protein biosynthesis. Ribosome assembly is initiated in the nucleolus by the transcription and processing of ribosomal RNAs, which together with ribosomal proteins form pre-60S ribosomal particles. The pre-60S particles mature by transiently interacting with various assembly factors during cytosolic export. The nearly 5000 residues long maturation factor Rea1 is vital for the export of the pre-60S particles. Rea1 belongs to the AAA+ protein family and harnesses the energy of ATP hydrolysis to mechanically remove assembly factors from pre-60S particles. Despite its key importance for ribosome maturation, the Rea1 structure and mechanism are poorly understood. We will carry out genetic manipulations in yeast to tag proteins for subsequent Rea1-pre-60S purification. The PhD student will be trained in state-of-the-art cryo-electron microscopy to structurally characterize these complexes. These structural investigations will be complemented by in-vitro as well in-vivo activity assays carried out in collaboration with external partners. He/she will also learn to work in a highly international environment and to develop project management skills. Furthermore, presentation skills will be acquired due to regular progress meetings and the attendance of international conferences.

Key words: Rea1, molecular machines, ribosome maturation, AAA+ proteins, cryo-electron microscopy, structural biology.

  • PhD supervisor: Helgo Schmidt, schmidth@igbmc.fr, +33 (0)3 69 48 52 77, http://www.igbmc.fr/research/department/3/team/134/
  • Team members: 4.
  • 3 relevant publications: 1) The CryoEM structure of the Saccharomyces cerevisiae ribosome maturation factor Rea1. Sosnowski P, Urnavicius L, Boland A, Fagiewicz R, Busselez J, Papai G, Schmidt H.Elife 2018. 2) Structure of human cytoplasmic dynein-2 primed for its power stroke. Schmidt H, Zalyte R, Urnavicius L, Carter AP. Nature 2015.3) Insights into dynein motor domain function from a 3.3-A crystal structure. Schmidt H, Gleave ES, Carter AP. NSMB 2012.
  • Number of PhDs in progress: 2 (01.09.2017 & 01.10.2019).

 

Integrated Structural Biology (LabEx INRT) / Genomes expression and cross-talk in mitochondrial function and dysfunction (LabEx MitoCross)

PhD 2021-36 Molecular basis of adenosine-to-inosine modification and its dysregulation in intellectual disorders

LabEx INRT (IGBMC) - Integrative Biology : Nuclear Dynamics, Regenerative and Translational Medecine, http://igbmc.fr/

Team 1 : Molecular basis of chromatin and transcription regulation.

Team leader : Christophe Romier, romier@igbmc.fr, +33 (0)3 69 48 52 94,  IGBMC, 1 rue Laurent Fries, 67404 Illkirch Graffenstaden Cedex, http://www.igbmc.fr/research/department/3/team/123/

LabEx MitoCross Genomes expression and cross-talk in mitochondrial function and dysfunction, https://mitocross.unistra.fr/

Team 2 : Metabolism and trafficking of RNA within the plant cell.

Team leaders : Laurence Drouard and Anne-Marie Duchêne, laurence.drouard@ibmp-cnrs.unistra.fr / anne-marie.duchêne@unistra.fr, +33 (0)3 67 15 53 98 / +33 (0)3 67 15 53 69, IBMP, 12 Rue du Général Zimmer, 67084 Strasbourg, https://mitocross.unistra.fr/partners/ibmp/team-3-metabolism-and-trafficking-of-rna-within-the-plant-cell/

Posttranscriptional RNA modifications expand the functions of RNAs and are often linked with the etiology of human diseases. The adenosine to inosine modification (A-to-I) plays crucial roles in RNAs. In tRNAs, wobble A-to-I is catalyzed by the essential ADAT complex that, when mutated, causes wobble inosine decrease and leads to human neurodevelopmental disorders, including intellectual disability, microcephaly, strabismus and epilepsy. The supervising teams have revealed how the mammalian ADAT complex assembles and can perform its deamination activity (manuscript in revision). However, the molecular and functional bases for ADAT dysregulation in disease remain elusive. The proposed project will make use of a biology integrated strategy to investigate tRNA recognition by ADAT and how disease mutations perturb ADAT mode of action. Notably, the project will combine biochemical, biophysical, structural and in cellulo analyzes to decipher how (i) ADAT recognizes its different cognate tRNAs, (ii) ADAT performs its catalytic mechanism, and (iii) how the wobble inosine effects on tRNA stability and function. The candidate will further collaborate with the team of Juliette Godin at IGBMC to study the consequences of the wobble inosine decrease on brain development and intellectual disorders. 

Key words: RNA modification, inosine, ADAT complex, tRNA binding, brain development, intellectual disorders.

  • PhD supervisor 1: Christophe Romier,  romier@igbmc.fr, +33 (0)3 69 48 52 94, http://www.igbmc.fr/research/department/3/team/123/
  • Team members: Pierre Antony, Marie-Laure Durand, Pauline Landwerlin, Elizabeth Ramos Morales, Christophe Romier, Edouard Troesch, Marina Vitoria Gomes.
  • 3 relevant publications: 1) Marek, M. et al. (2018) Characterization of histone deacetylase 8 (HDAC8) selective inhibition reveals specific active site structural and functional determinants. J. Med. Chem., 61, 10000-10016. 2) Latrick, C.M.et al. (2016) Molecular basis and specificity of H2A.Z–H2B recognition and deposition by the histone chaperone YL1. Nat. Struct. Mol. Biol., 23, 309-316. 3) Obri, A.et al. (2014) ANP32E is a histone chaperone that removes H2A.Z from chromatin. Nature, 505, 648-653. 
  • Number of PhDs in progress: Elizabeth Ramos Morales (start 2017), Marina Vitoria Gomes (start 2017), Pauline Landwerlin (start 2018).
  • PhD supervisor 2: Laurence Drouard, laurence.drouard@ibmp-cnrs.unistra.fr, +33 (0)3 67 15 53 98, https://mitocross.unistra.fr/partners/ibmp/team-3-metabolism-and-trafficking-of-rna-within-the-plant-cell/
  • Team members: Marjory Cherry, Laurence Drouard, Anne-Marie Duchêne, Mickaele Hemono, Herrade Meichel, Patryk Ngondo, Thalia Salinas-Giegé, Elodie Ubrig.
  • 3 relevant publications: 1) Hummel, A. et al. (2020) Epigenetic silencing of clustered tDNAs in Arabidopsis. Nucleic Acids Res, 48, 10297-10312. 2) Lalande S, et al. (2020) Arabidopsis tRNA-derived fragments as potential modulators of translation. RNA Biol, 1-12. 3) Megel C, et al. (2019). Plant RNases T2, but not Dicer-like proteins are major players of tRNA-derived fragments biogenesis. Nucleic Acids Res, 47:941-952. 
  • Number of PhDs in progress: Mickaele Hemono (start 2017), Marjorie Cherry (start 2018), Herrade Meichel (start 2019).

Plant biology (LabEx NetRNA)

PhD 2021-37 Analysis of RNA polymerase IV non-catalytic subunits required for genome surveillance in plants

LabEx NetRNA - Networks of Regulatory RNAs across kingdoms and dynamical responses to biotic and abiotic stresses, http://labex-ibmc.u-strasbg.fr/NetRNA/index.php

Team : Mechanisms of small RNA biogenesis and action.

Team leader: Todd Blevins, todd.blevins@ibmp-cnrs.unistra.fr, + 33 (0)3 67 15 53 28, IBMP, 12 rue du général Zimmer, 67084 Strasbourg cedex, https://www.polymerase.eu/blevins-lab/

Three RNA polymerases are universally conserved, essential enzymes in the cell nucleus: Pol I, Pol II and Pol III. In plants, a variant of Pol II called Pol IV produces non-coding transcripts that are processed into small interfering RNAs (siRNAs) to silence transposable elements (TEs), regulate development and mediate stress responses (Blevins et al. 2015; Rymen et al. 2020). How Pol IV protects genome integrity while also regulating certain genes is not well understood. This PhD project aims to determine the molecular functions of Pol IV subunits and domains that diverge from Pol II (Ferrafiat et al. 2019). (i) Genome editing combined with -omics approaches will be used to determine the role of Pol IV-specific domains in siRNA biogenesis, DNA methylation and TE silencing (genome surveillance). (ii) the student will use liquid chromatography + mass spectrometry (LC-MS/MS) to study immunopurified Pol IV harboring wild-type or mutated non-catalytic subunits and dissect Pol IV’s interactome. (iii) Epi-transcriptomic features that distinguish Pol IV from Pol II transcripts will be investigated using direct RNA sequencing (i.e., to detect modified RNA bases). Together, these experiments will chart the function of Pol IV non-catalytic subunits and elucidate structure-function relationships that allow paralogous enzymes (Pol II and Pol IV) to operate distinct siRNA pathways. 

Key words: non-coding RNA, transposable elements, DNA methylation, RNA polymerase IV (Pol IV).

Translational Medecine and Neurogenetics (LabEx INRT)

PhD 2021-38 Validation of novel therapeutic approaches for congenital myopathies

LabEx INRT (IGBMC) - Integrative Biology : Nuclear Dynamics, Regenerative and Translational Medecine, http://igbmc.fr/

Team : Pathophysiology of neuromuscular diseases.

Team leader: Jocelyn Laporte, jocelyn@igbmc.fr, +33 (0)3 88 65 34 12,  IGBMC, 1 rue Laurent Fries, 67400 Illkirch-Graffenstaden Cedex, http://www.igbmc.fr/Laporte/

Congenital myopathies are severe genetic diseases without current treatment. Using established cellular and murine models, the PhD candidate will investigate the mechanisms leading to such diseases and validate gene modulation and editing for therapies. We previously identified 2 targets (BIN1 and DNM2 genes) which should be modulated to rescue several forms of congenital myopathies.  

The PhD student will modulate further the activity and levels of these targets to achieve therapeutic benefit in vivo in mice. Three approaches will be developed and validated in culture muscle cells and mouse models : genetic inactivation or correction through genome editing (CRISPR/Cas9), gene modulation through exogenous gene expression using viral vectors of the adeno-associated virus type (gene therapy), and pharmacological treatments (drugs). In vivo assays will be done in our myopathies mouse models faithfully reproducing the patient phenotypes, and improvement of phenotypes will be measured by locomotor tests (activity, coordination, strength), measurement of leg muscle strength, in vivo imaging, histology and electron microscopy. 

This project will validate one or more strategies improving several forms of congenital myopathies that should be translatable to patients. 

Key words: CRISPR/Cas9, gene therapy, Adeno-associated virus vector, pharmacology, rare disease, mice.

  • PhD supervisor: Jocelyn Laporte, jocelyn@igbmc.fr, +33 (0)3 88 65 34 12, http://www.igbmc.fr/Laporte/
  • Team members: 19. 
  • 3 relevant publications: 1) Tasfaout H, Buono S, Guo S, Kretz C, Messaddeq N, Booten S, Greenlee S, Monia BP, Cowling BS*, Laporte J*. Antisense oligonucleotide-mediated Dnm2 knockdown prevents and reverts myotubular myopathy in mice. Nat Commun. 2017 Jun 7;8:15661. (H Tasfaout = previous PhD student). 2) Rabai A, Reisser L, Reina-San-Martin B, Mamchaoui K, Cowling BS, Nicot AS, Laporte J. Allele-Specific CRISPR/Cas9 Correction of a Heterozygous DNM2 Mutation Rescues Centronuclear Myopathy Cell Phenotypes. Mol Ther Nucleic Acids. 2019 Feb 27;16:246-256. (A Rabai = previous PhD student). 3) Lionello VM, Nicot AS, Sartori M, Kretz C, Kessler P, Buono S, Djerroud S, Messaddeq N, Koebel P, Prokic I, Herault Y, Romero NB, Laporte J*, Cowling BS*. Amphiphysin 2 (BIN1) modulation rescues MTM1 centronuclear myopathy and prevents focal adhesion defects. Sci Transl Med. 2019 Mar 20;11(484). (V Lionello = previous PhD student).    
  • Number of PhDs in progress: 7 PhD in progress (3 HDR in team): Gomez Oca (10/17), Silva Rojas (11/17), Djeddi (9/18), Borne (10/18), Chartreux (10/19), Giraud (10/19), Bokan (11/20).
PhD 2021-39 Mitochondrial dysfunction in Down syndrome mouse models as a new therapeutic target

LabEx INRT (IGBMC) - Integrative Biology : Nuclear Dynamics, Regenerative and Translational Medecine, http://igbmc.fr/

Team : Physiopathology of aneuploidy, gene dosage effect and Down syndrome.

Team leader: Yann Herault, herault@igbmc.fr, +33 (0)3 88 65 56 57,  IGBMC, 1 rue Laurent Fries, 67400 Illkirch-Graffenstaden Cedex, http://www.igbmc.fr/research/department/4/team/45/

Down syndrome (DS) is the first genetic cause of intellectual disability. DS is due to the trisomy of chromosome 21 (Hsa21) in human and is also associated with several comorbidities (https://go-ds21.eu/).  Studies in mice, aimed to understand the DS physiopathology, suggest that a mitochondrial dysfunction contributes to the disease (1). Among the Hsa21 genes, two genes have a major role in mitochondria: NRIP1, that codes for the nuclear receptor interacting protein 1 (NRIP1), acts on mitochondrial pathways through the negative regulation of the transcriptional coactivator PGC-1α; Cystathionine β-synthase gene (CBS), can influence mitochondrial activity by the production of hydrogen sulfide (H2S). We have shown that mouse overexpressing these genes displayed cognitive phenotypes (1,2). The goal of the PhD thesis is to characterize how NRIP1, and CBS overdosage can alter energy production in mitochondria in the brain and in other comorbidities. Taking advantage of our mouse models overexpressing NRIP1 or CBS, the student will combine behavioral, cellular and molecular approaches to describe the mitochondrial dysfunction in neurons and other tissues, and find the pathways altered by the overdosage of those two proteins. Understanding the interplay between proteins involved in DS is crucial for developing the best therapeutic approach in this pathology.    

Key words: Trisomy 21, Intellectual disability, comorbidities CBS, NRIP1.

  • PhD supervisor: Yann Herault, herault@igbmc.fr, +33 (0)3 88 65 56 57, http://www.igbmc.fr/research/department/4/team/45/
  • Team members: 17. 
  • 3 relevant publications: 1) Muñiz Moreno et al., Modeling Down syndrome in animals from the early stage to the 4.0 models and next. Prog Brain Res. 2020, 251:91-143. doi: 10.1016/bs.pbr.2019.08.001. 2) Maréchal et al., Cbs overdosage is necessary and sufficient to induce cognitive phenotypes in mouse models of Down syndrome and interacts genetically with Dyrk1a. Hum. Mol. Genet. 2019, 28(9)1561-1577. doi: 10.1093/hmg/ddy447. 3) Duchon et al., Multi-influential interactions alter behaviour and cognition through six main biological cascades in Down syndrome mouse models. bioRxiv 2020.07.08.193136; doi: 10.1101/2020.07.08.193136. .    
  • Number of PhDs in progress: 4 co-directions (2021), 1 co-direction (2023).
PhD 2021-40 Deciphering the role of HnRNP-G (RBMX) and its functional retrocopies (RBMXL1) in brain development in humans and mice

LabEx INRT (IGBMC) - Integrative Biology : Nuclear Dynamics, Regenerative and Translational Medecine, http://igbmc.fr/

Team : Regulation of cortical development in health and disease.

Team leader: Juliette Godin, godin@igbmc.fr, +33 (0)3 69 48 51 33,  IGBMC, 1 rue Laurent Fries, 67404 Illkirch-Graffenstaden Cedex, http://www.igbmc.fr/research/department/4/team/125/

The RMBX/hnRNP-G protein, encoded by RBMX on chromosome (chr) X in mammals, contributes to alternative mRNA splicing and maintenance of chromatin structure and genome stability. Remarkably, RBMX has been retrocopied several times during evolution. The most recent retrocopies, RBMXL1 on human chr1, and Rbmxl1a/b on mouse chr8 and14, occurred from independent retrotransposition events. Pathogenic variants in RBMX cause intellectual disability and microcephaly in hemizygous males through unknown mechanisms. Given their 98% identity to RBMX and their expression during brain development in humans and mice, RBMXL1/Rbmxl1 are likely functional and able to compensate RBMX loss-of-function in the brain. We aim to 1) dissect the complex mechanisms by which RBMX and its retrocopies contribute to brain development; 2) understand the impact of human pathogenic variants; and 3) unravel how recurrent retrotransposition of RBMX have contributed to shape brain size and function during evolution. The intern will evaluate the functional redundancy of RBMX and its retrocopies during mouse brain development and be in charge of the analysis of the functional consequences of identified variants in vivo. 

Key words: RBMX, retrocopies, cerebral cortex, neurodevelopment, neurogenetics.

  • PhD supervisor: Juliette Godin, godin@igbmc.fr, +33 (0)3 69 48 51 33, http://www.igbmc.fr/research/department/4/team/125/
  • Team members: GODIN J; PI, BAYAM, E; Post-Doc, FLICI, H; Post-Doc, RIVEIRA, J; PhD student, HARDION, C; PhD Student, TILLIOLE, P, M2 student, TILLY, P; Assistant ingénieur. 
  • 3 relevant publications: 1) Asselin L, et al. Mutations in the KIF21B kinesin gene cause neurodevelopmental disorders through imbalanced canonical motor activity. Nature Communication (2020) 11: 2441. 2) Kannan M et al. WD40-repeat 47, a microtubule-associated protein, is essential for brain development and autophagy. PNAS (2017) 114: E9308-E9317. 3) Laguesse S et al. A Dynamic Unfolded Protein Response Contributes to the Control of Cortical Neurogenesis. Developmental Cell (2015) 35: 553-67.    
  • Number of PhDs in progress: 2 (1/10/2018; 1/12/2019).
PhD 2021-41 Role of CHD1L in neurogenesis and its implication in neurodevelopmental diseases

LabEx INRT (IGBMC) - Integrative Biology : Nuclear Dynamics, Regenerative and Translational Medecine, http://igbmc.fr/

Team : Study of copy number variants in autism spectrum disorders and their comorbidities.

Team leader: Christelle Golzio, golzioc@igbmc.fr, +33 (0)3 88 65 33 93,  IGBMC, 1 rue Laurent Fries, 67400 Illkirch-Graffenstaden Cedex, http://www.igbmc.fr/research/department/4/team/132/

The chromatin remodeler CHD1L is an enzyme implicated in chromatin remodeling and DNA relaxation process and is known to facilitate DNA repair and pluripotency in stem cells. CHD1L has been extensively studied in the context of cancer but little is known on its role during brain development. The deletion and duplication of the 1q21.1 region (1.35 Mb; 8 genes) containing CHD1L have been found in individuals with variable phenotypes including autism, schizophrenia, cardiac defects and micro/macrocephaly. Through the study of this chromosomal region in cellular and animal models, we found that CHD1L dosage changes modulates the brain size by controlling the proliferation of the neuronal progenitors. Here we propose to follow-up our observations to investigate further the role of CHD1L during neurogenesis. The PhD student will i) identify the transcriptional targets and partners of CHD1L in IPSC-derived neurons and glial cells, ii) determine transcriptomic profiles in the context of normal and mutant conditions to identify tissue-specific gene regulation networks, iii) Study Excitatory/Inhibitory balance by performing electrophysiological experiments on normal and mutant human iPSC-derived neurons and glial cells.

Key words: CHD1L, neurodevelopment, neurogenetics, IPSC, modeling disease.

  • PhD supervisor: Christelle Golzio, golzioc@igbmc.fr, +33 (0)3 88 65 33 93, http://www.igbmc.fr/research/department/4/team/132/
  • Team members: Christelle GOLZIO; PI, Mathieu MASSONOT; PhD Student, Elodie FAURE, M2 student, Marianne LEMEE, M2 student, Chantal WEBER; Ingénieur d’Etude.
  • 3 relevant publications: 1) Arbogast T, et al. Hum Mol Genet. 28(9) :1474-1486 (2019). 2) Loviglio MN*, Arbogast T*, et al. Am J Hum Genet. 101 (4):564-577 (2017). 3) Bernier R, et al. Cell, Jul 17;158(2):263-76 (2014).  
  • Number of PhDs in progress: 1 (1/09/2020).

Translational Medecine and Neurogenetics (LabEx INRT) / Genomes expression and cross-talk in mitochondrial function and dysfunction (LabEx MitoCross)

PhD 2021-42 Study of mitochondrial dysfunctions in amyotrophic lateral sclerosis

LabEx INRT (IGBMC) - Integrative Biology : Nuclear Dynamics, Regenerative and Translational Medecine, http://igbmc.fr/

Team 1 : RNA disease.

Team leader : Nicolas Charlet, ncharlet@igbmc.fr, +33 (0)3 88 65 33 09,  IGBMC, 1 rue Laurent Fries, 67404 Illkirch Graffenstaden Cedex, http://www.igbmc.fr/research/department/4/team/42/

 LabEx MitoCross - Genomes expression and cross-talk in mitochondrial function and dysfunction, https://mitocross.unistra.fr/

Team 2 : Intracellular traffic of RNA and mitochondrial diseases.

Team leaders : Nina Entelis and Ivan Tarassov, n.entelis@unistra.fr / i.tarassov@unistra.fr, +33 (0)3 68 85 14 81, Strasbourg University, 4, allée K. Roentgen, 67000 Strasbourg, https://mitocross.unistra.fr/partners/gmgm/team-1-intracellular-traffic-of-rna-and-mitochondrial-pathologies/

Neurological disorders are the second cause of death (9 millions/ year) worldwide. Amyotrophic Lateral Sclerosis (ALS) is the third most common neurodegenerative disease. This devastating disease is characterized by degeneration of motor neurons leading to muscle wasting, ultimately resulting in paralysis and death of patients in 3 to 5 years. Importantly, disruptions of mitochondrial functions and structures alteration of their morphology has been extensively reported in ALS.

Mitochondria are cellular organelles essential for energy production, calcium homeostasis and cell death regulation. Consequently, dysfunctional mitochondria lead to oxidative stress, loss of calcium homeostasis and induce apoptosis. Thus, altered mitochondria should be swiftly and efficiently degraded. However, due to their large size, they cannot be degraded by the proteasome and dysfunctional mitochondria rely on autophagy. This catabolic process is based on the formation of a double membrane vesicle engulfing the material to eliminate, which is then directed to lysosomes for degradation. 

Recently, the most common genetic cause of ALS was identified as an expansion of GGGGCC repeats located within the C9ORF72 gene. This mutation leads to decreased expression of the C9ORF72 protein. Recent results of team 1 indicate that C9ORF72 regulates autophagy (Sellier et al., 2016; Boivin et al., 2020). Team 2 is expert in state-of-the-art methodologies aimed to characterize mitochondria integrities, functions and morphologies in vitro on isolated organelles, as well as in vivo in cultured cells or in animal/ patient tissues. Thus, the objectives of this co-supervised PhD project will be to characterize the molecular and cellular mechanisms of clearance of altered mitochondria through autophagy, with a special focus on alterations caused by the C9orf72 mutation. The candidate will employ molecular, cellular and biochemical approaches (CRISPR-Cas9, immunoblotting and immunofluorescence, immunoprecipitation, transfection, cell culture, mitochondria purification and characterization, mass spectrometry and RNA-Seq, etc.), as well as study of mouse models of ALS. 

Overall, this proposal will help contribute to better understanding of the cause mechanisms of neuronal degeneration in ALS patients, in order to define therapeutic strategies for this devastating disease.

Key words: Genetic diseases, Neurodegeneration, Mitochondria, Autophagy.

  • PhD supervisor 1: Nicolas Charlet, ncharlet@igbmc.fr, +33 (0)3 88 65 33 09, http://www.igbmc.fr/research/department/4/team/42/
  • Team  members: 6 : 2 researchers, 2 PHD, 1 Engineer, 1 Master 2.
  • 3 relevant publications: 1) Boivin et al. C9ORF72 haploinsufficiency synergizes DPR proteins toxicity, a double hit mechanism that can be prevented by drugs activating autophagy. EMBO J. 2020; 39(4). 2) Sellier et al., rbFOX1/MBNL1 competition for CCUG RNA repeats binding contributes to myotonic dystrophy type 1/ 2 differences. Nature Communications. 2018; 9(1):2009. 3) Sellier et al., Translation of Expanded CGG Repeats into FMRpolyG Is Pathogenic and May Contribute to Fragile X Tremor Ataxia Syndrome. Neuron. 2017; 93(2):331-347.
  • Number of PhDs in progress: 2 (starting dates : sept 2017 and january 2020). 

 

  • PhD supervisor 2 : Ivan Tarassov, i.tarassov@unistra.fr, +33 (0)3 68 85 14 81, https://mitocross.unistra.fr/partners/gmgm/team-1-intracellular-traffic-of-rna-and-mitochondrial-pathologies/
  • Team members: 9 : 3 DR CNRS, 1 CRCN CNRS, 1 IR UNISTRA, 1 IE CNRS, 1 PhD, 2 postdocs.
  • 3 relevant publications: 1) K. Auré, G. Fayet, I. Chicherin, B. Rucheton, S. Filaut, A.-M. Heckel, J. Eichler, F. Caillon, Y. Péréon, N. Entelis, I. Tarassov, A. Lombès. A homoplasmic mitochondrial tRNAPro mutation causing exercise-induced muscle swelling and fatigue. Neurology: Genetics 2020 Jul 15;6(4):e480. 2) D. Jeandard, A. Smirnova, I. Tarassov, E. Barrey, A. Smirnov, N. Entelis. Import of non-coding RNAs into human mitochondria: a critical review and emerging approaches. Cells 2019, 8, 286. 3) R Loutre, AM Heckel, A Smirnova, N Entelis, I Tarassov. Can mitochondrial DNA be CRISPRized: pro and contra. IUBMB Life, 2018, Dec;70(12):1233-1239.  
  • Number of PhDs in progress: 1, co-supervised, starting date Oct 2019. 

Viral hepatitis and liver diseases (LabEx HepSYS)

PhD 2021- 43 Unraveling the molecular biology of the liver circadian clock to discover novel targets for treatment of liver fibrosis and cancer

LabEx HepSYS - Functional genomics of viral hepatitis and liver disease, http://www.labex-hepsys.fr/index.php/en

Team: virus-host interactions and liver disease

Team leader : Thomas Baumert,  thomas.baumert@unistra.fr, +33 (0)6 11 58 23 87,  Institute of Viral Disease, 3 Rue Koeberlé, 67000 Strasbourg, http://www.u1110.inserm.fr

Liver cancer caused by hepatitis B and C viruses and metabolic disease are major health and economic burden world-wide. With nearly 40% of overweight population globally, non-alcoholic fatty liver disease and its advanced form non-alcoholic steatohepatitis (NASH) are becoming the most prevalent liver disease. Fibrosis is the key factor determining the outcome of liver disease progression and risk of liver cancer. Approved anti-fibrotics are absent and therapies in clinical development show only very limited efficacy. The liver circadian clock (CC) plays a key role in liver physiology and disease biology. At the heart of the CC-functioning resides the CC-oscillator, an elegantly designed transcriptional-translational feedback system. Notably, the CC-oscillator (present in every cell type) not only drives daily rhythmicity of their own synthesis, but also generate circadian phase-specific variability in the expression levels of thousands of target genes through transcriptional, post-transcriptional and post-translational mechanisms mediating disease. The molecular relationship between CC-controlled gene expression and liver fibrosis in humans is largely unknown. Using patient-derived liver primary cells, tissues and cell lines combined with scRNASeq and functional genomics, this PhD project aims to determine the regulation and the function of liver CC-controlled gene networks driving liver fibrosis and cancer at single cell level. The investigation of these pathways will enable the discovery of new targets for treatment of liver fibrosis and cancer prevention – a major unmet medical need. 

Key words: Circadian clock, NASH, Fibrosis, Functional Genomics, Liver Cancer, Virus, Single-cell analyses, drug and target discovery.

  • PhD supervisor :Thomas Baumert,  thomas.baumert@unistra.fr, +33 (0)6 11 58 23 8745,
  • PhD co-supervisor:  Atish MUKHERJI, Mukherji@unistra.fr, +33 (0)3.68.85.37.15, http://www.u1110.inserm.fr /
  • Team  members: Baumert Thomas, MD, PU-PH, HDR; Schuster Catherine, PhD DR1, HDR; Lupberger Joachim, PhD, CR1, HDR, Emilie Crouchet, PhD, Scientist, Laurent Mailly, PhD, IR, animal model expert, Pessaux Patrick, MD, PU-PH, HDR. 
  • 3 relevant publications: 1) Mukherji A*, Bailey SM, Staels B and Baumert TF*.: The Circadian Clock and Liver Function in Health and Disease. J. Hepatology (2019) 71: 200-211. (IF: 20.5), 2) Jühling F, Hamdane N, Crouchet E, Li S, El Saghire H, Mukherji A, Fujiwara N, Oudot MA, Thumann C, Saviano A, Roca Suarez AA, Goto K, Masia R, Sojoodi M, Arora G, Aikata H, Ono A, Tabrizian P, Schwartz M, Polyak SJ, Davidson I, Schmidl C, Bock C, Schuster C, Chayama K, Pessaux P, Tanabe KK, Hoshida Y, Zeisel MB, Duong FH, Fuchs BC, Baumert TF. Targeting clinical epigenetic reprogramming for chemoprevention of metabolic and viral hepatocellular carcinoma. Gut. 2020 Mar 26;gutjnl-2019-318918. doi: 10.1136/gutjnl-2019-318918. Online ahead of print. PMID: 32217639. (IF=19.82). 3) .Aizarani N, Saviano A, Sagar, Mailly L, Durand S, Herman J.S., Pessaux P., Baumert T.F.*, Grün D.*A Human Liver Cell Atlas reveals Heterogeneity and Epithelial Progenitors. Nature. 2019 Aug; 572:199-204. (IF=42.7) *corresponding authors
  • Number of PhDs in progress: 4 - N. Almeida (Oct 2019-50%); M. Dachraoui (Dec 2017); F. Del Zompo (Nov 2020); M. Muller (Oct 2019 – 50%); N. Roehlen (Oct 2018).