IMCBio International PhD Program IMCBio PhD Call 2024

Call is open from Jan. 8, 2024, 6 a.m. (Paris time) to March 17, 2024, 6 p.m. (Paris time).

Registration is open until March 10, 2024, 6 p.m. (Paris time).

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 2024. The IMCBio graduate school builds on the strong research developed in five research institutes: IGBMC, IBMC, IBMP, GMGM and ILVD, which covers all areas of molecular and cellular biology at the levels of molecular factors, genes, cells and organisms from model systems to diseases.

The network of these five Institutes comprising four Research Clusters (aka 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 aspect of gene regulation covering nuclear organization, epigenetics, transcriptional, translational, post-transcriptional and post-translational events as well as crosstalk 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 PhD fellowships for highly motivated applicants of academic excellence. The 2024 call for applications will be open from January 8 - March 17, 2024. Please make sure to register by March 10, 2024, as this is the registration deadline, and you might complete and submit your application on March 17, 2024.
Please note that projects can be uploaded during all the duration of the call.
We accept applications from all students, i.e. requiring a Master's degree equivalency at the University of Strasbourg (including all students studying toward a Master level diploma in 2024 from foreign Universities) and from students already holding a Master's Degree.

If you want to start an innovative research project in 2024 and fit with the application criteria above, then register down below to candidate and join the IMCBio graduate school!
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Genomes expression and cross-talk in mitochondiral function and dysfunction (LabEx MitoCross)/Regulatory RNA networks in response to biotic and abiotic stresses (LabEx NetRNA)

Molecular Biology in Plants (LabEx MitoCross)/Architecture and Reactivity of RNA (LabEx NetRNA)

Name 1: Architecture and Reactivity of RNA (ARN, IBMC)

Team: Genome biology of viruses

Team leader: Redmond SMYTH

Email: redmond.smyth@helmholtz-hiri.de

 

Name 2: Institute of Molecular Biology in Plants (IBMP)

Platfrom: Gene expression analysis (AEG)

Platform leader: Abdelmalek ALIOUA

Email: malek.alioua@ibmp-cnrs.unistra.fr

 

PhD supervisors: Redmond SMYTH, Abdelmalek ALIOUA & Anne-Sophie GRIBLING-BURRER

Email: redmond.smyth@helmholtz-hiri.demalek.alioua@ibmp-cnrs.unistra.fr & anne-sophie.gribling@helmholtz-hiri.de

RNA can undergo over 170 different types of modifications. These modifications affect metabolic processes like mRNA stability, translation and can also impact the folding of RNA, all of which are critical for post transcriptional gene regulation. Notably, they are concentrated and regulated on important cellular components such as tRNAs and ribosomes. Moreover, viral RNAs tend to have more modifications than their cellular counterparts. Whilst several RNA modifications can – in principle – be detected by nanopore direct RNA sequencing, such methods are in their infancy, and the currently available algorithms yield discordant modification profiles. A major roadblock is the lack of training data for the development of improved deep learning algorithms used to convert raw data into sequence information. This project will leverage our recent advances in long read RNA structural probing on nanopores to generate this training data for the development of custom nanopore basecallers that are able to recognize either chemical or natural base modifications.

 

Keywords: RNA, modifications, nanopore

 

Relevant publications:

- Bohn P*, Gribling-Burrer AS*, Ambi U, Smyth RP# Nano-DMS-MaP-seq allows isoform specific RNA structure determination (2023) Nature Methods 20, 849-859

- Pekarek L, Zimmer MM, Gribling-Burrer A-S, Buck S, Smyth RP#, Caliskan N# Cis-mediated interactions of the SARS-CoV-2 frameshift RNA alter its conformations and affect function (2022) Nucleic Acids Research Jan 25;51(2):728-743

- Ye L, Gribling A-S, Bohn P., Kibe A, Börtlein C, Ambi U, Ahmad S, Olguin-Nava M, Smith M., Caliskan N., von Kleist M., Smyth RP# Short and long-range interactions in the HIV-1 5’UTR regulate genome dimerization and packaging. (2022) Nature Structural & Molecular Biology Apr;29(4):306-319

- Joly A.C., Garcia S., Hily J.M., Koechler S., Demangeat G., Garcia D., Vigne E., Lemaire O., Zuber H. and Gagliardi D. An extensive survey of phytoviral RNA 3' uridylation identifies extreme variations and virus-specific patterns. Plant Physiology, kiad278, 2023.

- Arsène-Ploetze F., Rompais M., Alioua A., Cognat V., Erhardt M., Graindorge S., Koechler S., Mutterer J., Carapito C. and Schaller H. Streptomyces cocklensis DSM 42063 and Actinacidiphila bryophytorum DSM 42138 colonize Arabidopsis thaliana and modulate its proteome. Published Online:16 Aug 2023 https://doi.org/10.1094/PHYTOFR-12-22-0149-R

- Méteignier L.V., Ghandour R., Meierhoff K., Zimmermann A., Chicher J., Baumberger N., Alioua A., Meureu J., Zoschke R. and Hammani K. The Arabidopsis mTERF-repeat MDA1 protein plays a dual function in transcription and stabilization of specific chloroplast transcripts within the psbE and ndhH operons. New Phytologist, 227(5):1376–1391, 2020.

Molecular Genetics, Genomics and Microbiology (LabEx MitoCross)/Architecture and Reactivity of RNA (LabEx NetRNA)

Name 1: Molecular Genetics, Genomics, Microbiology (GMGM)

Team 1: Dynamics and Plasticity of Synthetases

Team leader: Hubert BECKER

Email: h.becker@unistra.fr

 

Name 2: Architecture and Reactivity of RNA (ARN, IBMC)

Team 2: mRNAs and regulatory RNAs in bacteria

Team leader: Pascale ROMBY

Email: p.romby@ibmc-cnrs.unistra.fr

 

PhD supervisors: Hubert BECKER & Stefano MARZI

Emails: h.becker@unistra.frs.marzi@ibmc-cnrs.unistra.fr

Aminoacyl-tRNAs are commonly used by the translational machinery to achieve protein synthesis. However, aa-tRNAs can also be rerouted away from translation and used as substrates in various other processes. Proteins of the aminoacyl-tRNA transferase (ATT) family use them and transfer the amino acid (aa) moiety onto target substrates, such as lipids or the peptidoglycan.

Fem ligases are essential enzymes found in the Gram positive and pathogenic bacterium Staphylococcus aureusthat use Gly-tRNAGly to modify the peptidoglycan (PG) with glycine chains, increasing its antimicrobial resistance. In addition, in Gram-negative bacteria such as Pseudomonas aeruginosa, other types of ATTs (discovered by the laboratory) do exist that use other aa-tRNA substrates to modify membrane lipids. This pathway also participates in antimicrobial resistance and pathogenicity. Our laboratories aim to decipher, from a molecular and structural point of view, how aa-tRNAs are directed to and interact with ATTs to ensure proper modification of cell wall constituents.

In S. aureus, in addition to the canonical tRNAsGly that serve in protein synthesis, 3 non-canonical tRNAsGly with unique sequence features exist. Upon glycylation, these Gly-tRNAsGly escape translation (they are termed non-proteinogenic) and used by 3 Fem ligases in the PG modification process. Our results suggest that, beyond sequence idiosyncrasies, the modification status of tRNAs may play a role in substrate selection by Fem ligases. In the case of P. aeruginosa, it is Ala-tRNAAla that is used to modify membrane lipids, but no non-proteinogenic tRNAsAla have been identified that could ensure proper channeling, raising the question of possible RNA modification signatures. The possibility that aminoacyl-tRNA synthetases (aaRSs) —that produce aa-tRNAs— and ATTs form complexes in which the aa-tRNA is channeled between the enzymes is also a hypothesis. Understanding these pathway may shed light on molecular events that strongly influence pathogenicity of both Gram-positive and Gram-negative bacteria.

During the IMCBIO internship, the candidate will use a variety of approaches and techniques from biochemistry and molecular biology(SDS-PAGE, Western blot, total lipids extraction, sub-cellular fractionation, thin layer chromatography, PCR, RNA-Seq approaches,LC-MSMS on RNA to detect modifications, enzymology, in vitro transcription, etc.), structural biology (Cryo-EM and X-ray studies) and microbiology (manipulation of S. aureus and P. aeruginosa under BSL-2 biosafety conditions, construction of mutant strains using standard genetic methods, phenotyping, etc.). The candidate should get strong knowledge at the interface of microbiology and biochemistry, molecular and structural biology.

 

Keywords: Aminoacyl-tRNA transferases, cell wall modification, tRNA, RNA modification, pathogenic bacteria, antimicrobial resistance

 

Relevant publications:

- Yakobov N, Fischer F, Mahmoudi N, Saga Y, Grube CD, Roy H, Senger B, Grob G, Tatematsu S, Yokokawa D, Mouyna I, Latgé JP, Nakajima H, Kushiro T, Becker HD. RNA-dependent sterol aspartylation in fungi. Proc Natl Acad Sci U S A. 2020 Jun 30;117(26):14948-14957. doi: 10.1073/pnas.2003266117.

- Yakobov N, Mahmoudi N, Grob G, Yokokawa D, Saga Y, Kushiro T, Worrell D, Roy H, Schaller H, Senger B, Huck L, Riera Gascon G, Becker HD, Fischer F. RNA-dependent synthesis of ergosteryl-3β-O-glycine in Ascomycota expands the diversity of steryl-amino acids. J Biol Chem. 2022 Mar;298(3):101657. doi: 10.1016/j.jbc.2022.101657.

- Grob, G., Hemmerle, M., Yakobov, N., Mahmoudi, N., Fischer, F., Senger B. & Becker, H. D. (2022) tRNA-dependent addition of amino acids to cell wall and membrane components. Biochimie (doi: 10.1016/j.biochi.2022.09.017).

- Ribosome Profiling Methods Adapted to the Study of RNA-Dependent Translation Regulation in Staphylococcus aureus. Kohl MP, Chane-Woon-Ming B, Bahena-Ceron R, Jaramillo-Ponce J, Antoine L, Herrgott L, Romby P, Marzi S. Methods Mol Biol. 2024;2741:73-100. doi: 10.1007/978-1-0716-3565-0_5. PMID: 38217649

- RlmQ: A Newly Discovered rRNA Modification Enzyme Bridging RNA Modification and Virulence Traits in Staphylococcus aureus. Bahena-Ceron R, Teixeira C, Jaramillo Ponce JR, Wolff P, Couzon F, François P, Klaholz B, Vandenesch F, Romby P, Moreau K, Marzi S. RNA. 2023 Dec 19:rna.079850.123. doi: 10.1261/rna.079850.123. Online ahead of print. PMID: 38164596

- Mapping post-transcriptional modifications in Staphylococcus aureus tRNAs by nanoLC/MSMS. Antoine L, Wolff P, Westhof E, Romby P, Marzi S. Biochimie. 2019 Sep;164:60-69. doi: 10.1016/j.biochi.2019.07.003. Epub 2019 Jul 8. PMID: 31295507

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

Molecular Biology in Plants (LabEx MitoCross)

Name: Intitue of Molecular Biology in Plants (IBMP)

Team: Functions of PPR proteins

Team leader: Philippe GIEGE

Email: giege@unistra.fr

 

PhD supervisor: Philippe GIEGE

Email: giege@unistra.fr

Mitochondrial translation is of considerable interest because it combines bacterial traits with specific features that have evolved in eukaryotes. In plants, its mechanism remains elusive. Its ribosome contains specific RNA domains and specific protein subunits.
The characterization of plant mitochondrial ribosomes (mitoribosomes) carried out in our laboratory has identified proteins specific to plant mitoribosomes, among which 12 are pentatricopeptide repeat (PPR) proteins. Moreover, immuno-precipitation as well as proximity labelling approaches identified
further PPR proteins that might participate in translation initiation.
The research project focuses on the functional characterization of some of these new PPR proteins which could be involved in translation initiation, a process still poorly understood in plant mitochondria. In particular, the protein called rPPR2 could be involved in this process because it is located in the mRNA channel, at a distance from the decoding center, compatible with the binding to a conserved motif found in some mitochondrial mRNAs 5'UTRs. Since the gene coding for rPPR2 is essential, its expression will be deregulated by VIGS and / or amiRNA. Likewise, a truncated version of
the protein will also be expressed in planta. These mutants will be analyzed by ribosome profiling (RiboSeq) approaches. Other candidate PPR proteins will be analyzed by similar reverse genetics approaches.
Altogether, this project should reveal new functions for PPR proteins and should help to understand the diversity and specialization of translation systems in eukaryotes.

 

Keywords: Ribosome, translation initiation, PPR proteins, mitochondria, RiboSeq

 

Relevant publications:
- Waltz, F., Nguyen, T., Arrivé, M., Bochler, A., Chicher, J., Hammann, P., Kuhn, L., Quadrado, M., Mireau, H., Hashem, Y. and Giegé, P. (2019) Small is big in Arabidopsis mitochondrial ribosome. Nature Plants 5, 106-117.
- Gobert, A., Quan, Y., Arrivé, M., Waltz, F., Da Silva, N., Jomat, L., Cohen, M., Jupin, I. and Giegé, P. (2021) Towards plant resistance to viruses using protein-only RNase P. Nature comm 12, 1007.
- Arrivé, M., Bruggeman, M., Skaltsogiannis, V., Coudray, L., Quan, Y.F., Schelcher, C., Cognat, V., Hammann, P., Chicher, J., Wolff, P., Gobert, A. and Giegé, P. (2023) A tRNA modifying enzyme facilitates RNase P activity in
Arabidopsis nuclei. Nature Plants (in press).

Molecular Genetic Genomic and Microbiology (LabEx MitoCross)

Name: Molecular Genetics, Genomics, Microbiology (GMGM)

Team: MITO

Team leader: Ivan TARASSOV

Email: i.tarassov@unistra.fr

 

PhD supervisors: Ivan TARASSOV, co-supervisor Marie SISSLER

Emails: i.tarassov@unistra.fr, m.sissler@unistra.fr

Mitochondrial diseases are a clinically heterogeneous group of disorders caused by mitochondrial dysfunctions. They may be caused by mutations of either the nuclear or the mitochondrial genomes and are mostly incurable. In the scope of the present project we are considering two frequent situations: (1) mutations within a single tRNA lead to several disorders and (2) mutations convert a sense codon into a non-sense one leading to premature termination (PTC). In both, we propose that the targeting of a single tRNA into mitochondria will allow counteracting the molecular defects at the origin of the diseases. In the first situation, the therapeutic agent is a replacement tRNA, whose role is to switch the ratio mutant tRNA/wild-type tRNA below the fateful threshold where the disease is triggered. In the second, it is a suppressor tRNA, able to decode a nonsense codon, to read-through the PTC and thus restore the synthesis of a full-length protein. Basing on recent discoveries, we propose to model gene therapy in cultured immortalized and human patients' cells. The design of therapeutic tRNAs will be rationalized according to our strong knowledge in tRNA identity and codon/anticodon recognition rules. Proof of concept series of experiments will assess for the efficacy of model cells' transfection with the therapeutic tRNA. Finally, rescue of phenotypes in cybrids and patient-derived cells upon tRNA transfection will demonstrate a therapeutic potential of tRNA PTC suppressor or replacement methodologies.

 

Keywords: Mitochondrial diseases, Mitochondrial DNA mutations, suppressor tRNA, gene therapy modeling

 

Relevant publications:

- D. Jeandard, A. Smirnova, A. M. Fasemore, L. Coudray, N. Entelis, K. U. Forstner, I. Tarassov, A. Smirnov, CoLoC-seq probes the global topology of organelle transcriptomes. Nucleic acids research 51, e16 (2023); published online EpubFeb 22 (10.1093/nar/gkac1183).

- K. Aure, G. Fayet, I. Chicherin, B. Rucheton, S. Filaut, A. M. Heckel, J. Eichler, F. Caillon, Y. Pereon, N. Entelis, I. Tarassov, A. Lombes, Homoplasmic mitochondrial tRNA(Pro) mutation causing exercise-induced muscle swelling and fatigue. Neurology. Genetics 6, e480 (2020); published online EpubAug (10.1212/NXG.0000000000000480).

- O. A. Kolesnikova, N. S. Entelis, H. Mireau, T. D. Fox, R. P. Martin, I. A. Tarassov, Suppression of mutations in mitochondrial DNA by tRNAs imported from the cytoplasm. Science 289, 1931-1933 (2000); published online EpubSep 15 (10.1126/science.289.5486.1931).

 

Name: Molecular Genetic, Genomic and Microbiology (GMGM)

Team: Intraspecific variation and genome evolution

Team leader: Joseph SCHACHERER

Email: schacherer@unistra.fr

 

PhD supervisor: Joseph SCHACHERER

Email: schacherer@unistra.fr

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.

 

Keywords: genetics, population genomics, phenotypic variation, mitochondrion, yeast

 

Relevant publications:

- Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae. O'Donnell S, Yue JX, Saada OA, Agier N, Caradec C, Cokelaer T, De Chiara M, Delmas S, Dutreux F, Fournier T, Friedrich A, Kornobis E, Li J, Miao Z, Tattini L, Schacherer J*, Liti G*, Fischer G*. Nat Genet., 2023, 55(8):1390-1399.

- Loss-of-function mutation survey revealed that genes with background-dependent fitness are rare and functionally related in yeast. Caudal E, Friedrich A, Jallet A, Garin M, Hou J, Schacherer J. Proc Natl Acad Sci USA, 2022, 119(37):e2204206119.

- 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

Name: Institute of Molecular Biology in Plants (IBMP)

Team: Maintenance and segregation of the mitochondrial genome

Team leader: José Manuel GUALBERTO

Email: jose.gualberto@ibmp-cnrs.unistra.fr

 

PhD supervisor: José Manuel GUALBERTO

Email: jose.gualberto@ibmp-cnrs.unistra.fr

 

The maintenance, integrity and proper expression of the plant mitochondrial genome (mtDNA) are fundamental for plant fitness and survival, and are under the control of nuclear-encoded factors that are targeted to mitochondria. We have recently characterized the plant-specific 5'-3' exonuclease OEX1, whose loss has dramatic effects on mtDNA genome stability and plant development. OEX1 has preference for RNA:DNA hybrids and is likely responsible for the degradation of Okazaky primers during mtDNA replication, as well as for the elimination of R-loops that compromise genome stability. It further has Flap-endonuclease activity, implying additional roles in base excision repair and the processing of recombination intermediates. In animal mitochondria, the same functions are accomplished by mito-targeted RNase H and Flap-endonuclease FEN1. In addition to OEX1, an RNase H and FEN1 have also been found in plant mitochondria, and the interplay of these apparently redundant proteins in plant mtDNA maintenance is not understood.

We propose to study the specific functions of these nucleases in plant mtDNA replication, recombination and repair. This will be done using available Arabidopsis thaliana mutants, genetic complementation and co-immunoprecipitation approaches, coupled to DNA-seq analysis of mtDNA replication and stability. The replication of a specific mitochondrial episome that is a good model of mtDNA replication will be followed, using biochemical approaches. We will also study the interplay with the corresponding OEX and RNase H chloroplast homologs.

 

Keywords: Mitochondrial genome, Arabidopsis, recombination, exonucleases, RNase

 

Relevant publications:

- Chevigny N., Weber-Lotfi F., Le Blevenec A., Nadiras C.; Fertet A., Bichara M., Erhardt M., Dietrich A., Raynaud C. and Gualberto J.M. (2022). RADA-dependent branch migration has a predominant role in plant mitochondria and its defect leads to mtDNA instability and cell cycle arrest. PLoS Genet., e1010202. doi: 10.1371/journal.pgen.1010202.

- Fertet A., Graindorge S., Koechler S., De Boer G.J., Guilloteau-Fonteny E. and Gualberto J.M. (2021). Sequence of the mitochondrial genome of Lactuca virosa suggests an unexpected role in Lactuca sativa’s evolution. Frontiers in Plant Science, 12. doi: 10.3389/fpls.2021.697136

- Gualberto J.M. and Newton K.J. (2017). Plant mitochondrial genomes: dynamics and mechanisms of mutation. Annu. Rev. Plant Biol., 68: 225-252

Integrative Biology - Nuclear Dynamics, Regenerative and Translational Medicine (LabEx INRT)

Development and Stem Cells (LabEx INRT)

Name: Institue of Genetics, Molecular and Cellular Biology (IGBMC)

Team: Dynamics of chromatin structure and transcription regulation

Team leader: László TORA

Email: laszlo@igbmc.fr

 

PhD supervisor: Stéphane VINCENT

Email: vincent@igbmc.fr

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. In particular, we have shown that in the mouse embryo, TAF10 depletion severely affects TFIID assembly but differentially impacts the nascent mesoderm with the lateral plate mesoderm being very sensitive compared to the paraxial mesoderm [1]. We have also shown that in proliferating mouse embryonic stem cells (mESCs), depletion of either TAF7 or TAF10 leads to holo-TFIID depletion and production of different partially assembled TFIID submodules but has a very limited effect on Pol II nascent transcription [2]. Altogether, these data suggest that depending on the cellular context, partially assembled TFIID sub modules can mediate Pol II transcription initiation. The goal of this PhD project is to explore the cell context dependency of the TAF proteins during differentiation. The PhD candidate will engineer various dTAG mESCs cell lines using CRISPR/Cas9 to perform acute depletion of different TAF proteins. He/she will differentiate these cells into paraxial and lateral plate mesoderm cells and will carry out a comprehensive analysis of TFIID assembly, chromatin binding and nascent transcription profiling. This project will bring new knowledge in the basic mechanisms of Pol II transcription.

[1] Bardot & Vincent, et al., Development (2017) 44(20):808-3818, 10.1242/dev.146902

[2] Hisler, ... and Vincent, BIORXIV (2023) 10.1101/2023.11.27.567046

 

Keywords: RNA polymerase II, transcription initiation, differentiation, mESCs, IP-MS, CUT&RUN, nascent RNA-seq

 

Relevant publications:
- A. Bernardini, P. Mukherjee, E. Scheer, I. Kamenova, S. Antonova, P.K. Mendoza Sanchez, G. Yayli, B. Morlet, H.T.M. Timmers, L. Tora, Hierarchical TAF1-dependent co-translational assembly of the basal transcription factor TFIID(2023), Nat Struct Mol Biol. 30(8):1141-1152, 10.1038/s41594-023-01026-3

- V. Fischer, V. Hisler, E. Scheer, E. Lata, B. Morlet, D. Plassard, D. Helmlinger, D. Devys, L. Tora and S.D. Vincent, SUPT3H-less SAGA coactivator can assemble and function without significantly perturbing RNA polymerase II transcription in mammalian cells (2022), Nucleic Acids Res., 14(50):7972-7990, 10.1093/nar/gkac637

- C. Yu, N. Cvetesic, V. Hisler, K. Gupta, T. Ye, E. Gazdag, L. Negroni, I. Berger, P. Hajkova, B. Lenhard, F. Müller and S.D. Vincent & L. Tora, TBPL2/TFIIA complex overhauls oocyte transcriptome during oocyte growth (2020), Nature Commun, 11:6439, 10.1038/s41467-020-20239-4 

Name: Institute of Genetics, Molecular and Cellular Biology (IGBMC)

Team: Cell cycle and ubiquitin signaling

Team leader: Izabela SUMARA

Email: sumara@igbmc.fr

 

PhD supervisor: Izabela SUMARA

Email: sumara@igbmc.fr

Cancer cells differ from normal cells displaying high level of proliferative capacity. That creates cancer cell vulnerabilities, which can be targeted therapeutically. One of the cellular machineries which are “hijacked” by cancer cells are the nuclear pore complexes (NPCs). NPCs constitute the sole communication gates between the nucleus and the cytoplasm and ensure cellular function and survival. Nucleoporins (Nups) are the building protein units of the NPCs and represent an “achilles heel” of cancer cells. Cancer cells increase their NPC number to adapt to proliferative demand and depletion of Nups required for NPC assembly can selectively kill cancer cells and reduce tumor growth, providing a strong proof of principle for targeting Nups in cancer disease. However, the molecular mechanisms on how rapid spatial assembly of the NPCs can be achieved in cancer cells and how exactly misregulation of Nups homeostasis can cause cancer disease remain largely unknown. Our published findings identified a novel mechanism on how spatial assembly and increased biogenesis of NPCs can be achieved in cancer cells. We plan to characterize the role of newly identified factors in Nups homeostasis in relevant cellular cancer models. Inhibition of these factors should selectively reduce viability of cancer cells. This research may create unprecedented therapeutic perspectives for cancer patients.

 

Keywords: cancer, nuclear pore complexes, nucleoporins, nucleocytoplasmic transport, cancer-specific vulnerabilities

 

Relevant publications:

- Krupina K., Kleiss C., Metzger T., Fournane S., Schmucker S., Hofmann K., Fischer B., Paul N., Porter I.M., Raffelsberger W., Poch O., Swedlow J.R., Brino L. and Sumara I. (2016) Ubiquitin receptor protein UBASH3B drives Aurora B recruitment to mitotic microtubules. Developmental Cell. Jan 11, 36 (1): 63–78.

- Agote-Aran A., Schmucker S., Jerabkova K., Boyer I.J., Berto A., Pacini L., Ronchi P., Kleiss C., Guerard L., Schwab Y., Moine H., Mandel J-L., Jacquemont S., Bagni C. and Sumara I. (2020) Spatial control of nucleoporin condensation by fragile X-related proteins. EMBO Journal. Oct 15; 39 (20): e104467

- Pangou E., Bielska O., Guerber L., Schmucker S., Agote-Arán A., Ye T., Liao Y., Puig-Gamez M., Grandgirard E., Kleiss C., Liu Y., Compe E., Zhang Z., Aebersold R., Ricci R. and Sumara I. (2021) A PKD-MFF signaling axis couples mitochondrial fission to mitotic progression. Cell Reports. May 18; 35 (7): 109129

Name: Institute of Genetics, Molecular and Cellular Biology (IGBMC)

Team: Signal transduction in metabolism and inflammation

Team leader: Roméo RICCI

Email: ricci@igbmc.fr

 

PhD supervisor: Roméo RICCI

Email: ricci@igbmc.fr

The inflammasome is an intracellular multiprotein complex that senses sterile tissue damage and infectious agents to initiate innate immune responses. Distinct inflammasomes containing specific sensing molecules exist. The NLRP3 inflammasome is unique as it detects a broad range of cellular stress signals but a primary and converging sensing mechanism initiating inflammasome assembly remains ill-defined. We found that NLRP3 binds altered endomembranes as a result of disruption of inter-organelle contact
sites in response to danger signals. However, little is known about this fundamentally new mechanism of pattern recognition linking organelle spatial organization and innate immunity. The organelle-generated signals sensed by NLRP3 and the mechanisms underlying membrane recruitment and activation of the inflammasome remain largely unexplored and thus will be subject of this proposal. The major limit hampering their identification is the difficulty to disentangle the complex cell response to the variety of stimuli leading to NLRP3 activation. We aim to push this limit through an unprecedented
combination of approaches ranging from in vitro reconstitution studies with isolated organelles and artificial liposomes and proteo-lipidomics, to cryo-FIB and cryo-ET imaging, molecular modelling, and in vivo testing of the physiological relevance of in vitro findings. This project will lay the foundation for how altered endomembranes serve as dangerassociated molecular patterns to trigger innate immune responses.


Keywords: Inflammasome, NLRP3, endosome, PI4P, innate immunity, macrophages, inflammation

 

Relevant publications:

- KCNN4 links Piezo-dependent mechanotransduction to NLRP3 inflammasome activation. Li R, et al. Science Immunolog. 2023

- Distinct changes in endosomal composition promote NLRP3 inflammasome
activation. Zhang Z, et al. Nat Immunol. 2023

- Protein kinase D at the Golgi controls NLRP3 inflammasome activation. Zhang Z, et al. J. Exp. Med. 2017

Name: Institute of Genetics, Molecular and Cellular Biology (IGBMC)

Team: Syncytial cell biology

Team leader: Minchul KIM

Email: kimm@igbmc.fr

 

PhD supervisor: Minchul KIM

Email: kimm@igbmc.fr

Skeletal muscle cells represent an intriguing and peculiar system in tissue biology owing to their unique cellular structure as syncytium (many nuclei in a shared cytoplasm). We previously showed by single-nucleus RNA-Sequencing that subsets of muscle nuclei have distinct transcriptional programs, similar to differentiated cell types in multi-cellular tissues. Furthermore, new nuclear subtypes were identified in diseased and aged muscles. This raises important questions on how such diverse nuclear identities are formed and maintained as well as their functional importance in muscle function. To this end, my team has established innovative genetic tools where one can manipulate specific nuclear subset inside the shared cytoplasm. The successful candidate will utilize these tools to better understand the principles by which intracellular space of muscle syncytium is organized and to tease out gene functions in different muscle domains. In addition, our team has on-going projects on other aspects of muscle biology, for instance on the mechanism of repairing micro-lesions on sarcomeres and quality control of damaged muscle nuclei. The ideal candidate is expected to show autonomy, independence, and enthusiasm to lead one of our many exciting projects. 

 

Keywords: Skeletal muscle, cell fate, heterogeneity, mouse genetics

 

Relevant publications:

- https://www.nature.com/articles/s41467-020-20064-9

- https://elifesciences.org/articles/81843

 

Name: Institute of Genetics, Molecular and Cellular Biology (IGBMC)

Team: Cell physics

Team leader: Daniel RIVELINE

Email: riveline@igbmc.fr

 

PhD supervisor: Daniel RIVELINE

Email: riveline@igbmc.fr

Morphogenesis results from the relevant spatio-temporal expression of genes associated with self-organisation rules for cells. Cells move, adhere to their neighbours and to the environment, proliferate. These collective effects lead to changes in shapes of cells and tissues.
The Cell Physics team has characterised these dynamics – elongation, flows, pulsations, ring rotation (see publication list). The simple MDCK epithelial system can recapitulate most of these canonical morphogenetic events with generic physical rules. In this context, the acto-myosin and its regulation by the small Rho GTPases play key roles but their connexions to setting cell shapes and motion remain unclear.
The PhD topic consists in characterising the relations between cell shapes/states and morphogenetic events, using microfabrication, cell biology, quantitative biology, experimental and theoretical physics. The systems will be MDCK cells and several organoids. Single cell sequencing and spatial transcriptomics will be developed to characterise the quantitative links between expressions of relevant genes, physical forces, self-organisation rules and morphogenesis. It is expected that generic rules revealed by the team will be generalised for organoids with relevant modifications.
The candidate will interact with an international and interdisciplinary network composed of scientists with various backgrounds in cell and developmental biology and in theoretical physics.


Keywords: morphogenesis, acto-myosin, small Rho GTPases, self-organisation, microfabrication, topological defects, quantitative biology, biological physics

 

Relevant publications:

- S. Lo Vecchio, O. Pertz, M. Szopos, L. Navoret, D. Riveline, Spontaneous rotations in epithelia as an interplay between cell polarity and boundaries, to appear in Nature Physics (2024) BioRxiv.

- J. Comelles, S.S. Soumya, L. Lu, E. Le Maout, S. Anvitha, G. Salbreux, F. Jülicher, M.M. Inamdar, D. Riveline, Epithelial colonies in vitro elongate through collective effects. eLife 10, e57730 (2021).

- V. Wollrab, R. Thiagarajan, A. Wald, K. Kruse, D. Riveline, Still and rotating myosin clusters determine cytokinetic ring constriction. Nat. Commun. 7, 11860 (2016).

Name: Institute of Genetics, Molecular and Cellular Biology (IGBMC)

Team: Actin dynamics and biomechanics of the early embryo

Team leader: Anne-Cécile REYMANN

Email: reymanna@igbmc.fr

 

PhD supervisor: Anne-Cécile REYMANN

Email: reymanna@igbmc.fr

Actin, a self-assembling biopolymer, plays a crucial role via the formation of dynamic networks that determine cellular shape and mechanical properties. De novo mutations in cytoskeletal actin (ACTB and ACTG1 genes) lead to a wide range of rare diseases, termed non-muscle actinopathies (NMA). Neurological impairment is the most frequent feature across the whole NMA spectrum. The mechanisms linking precisely actin disfunction to these neurological symptoms, the extent of their severity as well as their progression remain so far unknown. Together with collaborators, the Reymann team aims to understand the molecular to functional consequences of these cytoplasmic actin variants using the model organism C. elegans.

Nine human substitutions, chosen to span a large range of severity in patients, were successfully recapitulated in C. elegans actin-coding gene using CRISPR/Cas9 editing. The main objective of the proposed PhD project is to identify the cellular and molecular mechanisms at play associated with the observed neurodevelopment disorders. We will specifically probe neurogenesis, neuronal migration and neuronal maturation including axonal growth capacities. One of the advantages, is that C. elegans invariance in lineage, cell fate acquisition and body plan is enabling to detect subtle developmental defects due to our ability to identify single neurons. We will notably rely on the very advantageous NeuroPAL transgene, including 41 neuronal fate markers in the form of fluorescent reporters, that enables to unambiguously identify each individual neuron.

 

Keywords: actin, C. elegans, neurodevelopmental disorders, rare disease

 

Relevant publications:

- The kinesin Kif21b regulates radial migration of cortical projection neurons through a non-canonical function on actin cytoskeleton. José Alvarez Rivera, Laure Asselin, Peggy Tilly, Roxane Benoit, Claire Batisse, Ludovic Richert, Julien Batisse, Bastien Morlet, Florian Levet, Noémie Schwaller, Yves Mély, Marc Ruff, Anne-Cécile Reymann, Juliette Godin, Cell Reports, July 2023. DOI: 10.1016/j.celrep.2023.112744

- Rapid assembly of a polar network architecture drives efficient actomyosin contractility. Costache V, Prigent Garcia S, Plancke C, Li J, Begnaud S, Kumar Suman S, Reymann AC, Kim T, Robin F., Cell Reports, May 2022. DOI: 10.1016/j.celrep.2022.110868

- Anterior-enriched filopodia create illusion of asymmetric membrane microdomains in polarizing C. elegans zygotes. Hirani N., Illukkumbura R., Bland T., Mathonnet G., Suhner D., Reymann AC, Goehring N.W., Journal of Cell Science, July 2019. DOI: 10.1242/jcs.230714

Name: Institute of Genetics, Molecular and Cellular Biology (IGBMC)

Team: Signal transduction in metabolism and inflammation

Team leader: Roméo RICCI

Email: ricci@igbmc.fr

 

PhD supervisors: Roméo RICCI & Karl VIVOT

Emails: ricci@igbmc.frvivotk@igbmc.fr

Maintaining energy homeostasis is a vital process for living organisms to cope with changes in energy demand. The intricate balance between energy intake, expenditure, and storage is regulated within the Central Nervous System. Malfunction of the energy balance can lead to pathology such as obesity which is the main risk factor of Type 2 Diabetes (T2D). It has been established that obesity is associated with low-grade inflammation, but it is still unclear what are the molecular mechanisms involved in obesity-induced neuroinflammation.

In our recent publication in Nature Metabolism, we have uncovered an unexpected function of the Calcium/calmodulin-dependent protein kinase ID (CaMK1D) protein in hypothalamic AgRP neurons. CaMK1D represents one of the more than 100 loci genetically associated with T2D.

Based on a single cell transcriptomic analysis, we found that CaMK1D is particularly highly expressed in microglia. Our new data from microglial specific CaMK1D knockout mice provide compelling evidence for a role of CaMK1D in obesity-induced inflammation.

We hypothesize that CaMK1D acts as a central key player to control obesity-induced inflammation. Based on our data, this project will aim to confirm a specific role of CaMK1D in neuroinflammation and to explore how microglial cells promote the neuroinflammatory processes.

 

Keywords: Obesity, Neuroinflammation, Hypothalamus, Microglia

 

Relevant publications:

- CaMK1D signalling in AgRP neurons promotes ghrelin-mediated food intake. Vivot K et al. Nat Metab. 2023

- Lysosomal degradation of newly formed insulin granules contributes to β cell failure in diabetes. Pasquier A et al. Nat Commun. 2019

- Distinct changes in endosomal composition promote NLRP3 inflammasome activation. Zhang Z, et al. Nat Immunol. 2023

Name: Institute of Genetics, Molecular and Cellular Biology (IGBMC)

Team: In vivo cellular plasticity and direct reprogramming

Team leader: Sophie JARRIAULT

Email: sophie@igbmc.fr

 

PhD supervisor: Sophie JARRIAULT

Email: sophie@igbmc.fr

Our life expectancy has greatly increased over the last century. Unfortunately, age- and disease-related brain damage takes a heavy toll on the well-being and autonomy of individuals, and ultimately on our society, with significant public health costs. Recovering from brain damage or aging while remaining autonomous is therefore a crucial issue for our society. The brain is undoubtedly one of our most complex organs, and its endogenous repair capacities are very limited. Repair strategies therefore rely on the introduction or generation of new neurons. To overcome the limitations of transplantation, we propose here to improve our ability to generate new neurons in situ. Indeed, work over the last few decades has shown that adult cells can change their identity and be converted into another cell type, such as neurons. This process is called cellular reprogramming. The conversion of epithelial cells into neurons can now be induced by cellular reprogramming. However, the efficiency of this conversion remains very low, and the final neuron is not mature, suggesting the existence of brakes. The aim of the proposed project is to use an in vivo physiological model in which neuronal reprogramming occurs naturally, with 100% efficiency, to understand the mechanisms that inhibit cellular reprogramming on the one hand, and those that promote it, on the other. Taking advantage of our preliminary data, this project will focus in particular on the epigenetic mechanisms at work, in 4 aims : 1- Mine the scRNAseq data obtained by the team to identify all the epigenetic factors (~ 300) expressed in 1 reprogramming cell. 2- Test whether these factors facilitate or block the reprogramming into a neuron. 3- Characterization the exact role of identified candidates and their partners.  4- Test the ability of identified candidates to induce, or facilitate, the reprogramming of neighboring cells.  Ultimately, we aim to identify chromatin-modulating molecular targets which activity we can influence to improve the efficiency of cellular reprogramming across species.

 

Relevant publications:

- Riva C., Gally C., Hajduskova M., Suman S.K., Ahier A. & Jarriault S. (2021) A natural transdifferentiation event involving mitosis is empowered by integrating signaling inputs with conserved plasticity factors. Cell Rep. 40(12):111365. doi: 10.1016/j.celrep.2022.111365

- 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

- 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.

Name: Institute of Genetics, Molecular and Cellular Biology (IGBMC)

Team: Molecular biology of B cells

Team leader: Bernardo REINA SAN MARTIN

Email: reinab@igbmc.fr

 

PhD supervisor: Bernardo REINA SAN MARTIN

Email: reinab@igbmc.fr

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 mainly by Uracil DNA glycosylase (Ung) and are processed in different ways to trigger mutations during SHM and/or double stranded DNA breaks during CSR.

Currently, the mechanisms underlying AID-induced DNA damage and its correlation with error-prone DNA repair remain unclear. We have performed a comprehensive genome-wide CRISPR/Cas9 knockout screen targeting genes associated with CSR in which, Fam72a emerged as a pivotal regulator influencing the balance between error-prone and error-free DNA repair. Specifically, we highlighted Fam72a's role in negatively regulating the protein levels of Ung2, the nuclear isoform of Ung (Rogier et al., Nature 2021).

Building on these findings, we will undertake a targeted CRISPR/Cas9 screen focusing on genes encoding for proteins that interact with Fam72a and/or Ung2 (identified through co-immunoprecipitation and mass spectrometry) and using an established Ung2EGFP knockin B cell line. We will then generate individual knockouts for the most promising candidate genes to conduct initial mechanistic studies. To further advance our understanding, we intend to develop conditional knockout mouse models, which will allow us to explore the role of candidate genes in SHM and CSR in vivo.

This comprehensive approach seeks to unravel the intricate connections between Fam72a, Ung2, and their interacting partners, shedding light on the molecular processes underlying error-prone DNA repair in the context of AID-induced DNA damage during antibody diversification.

 

Keywords: Antibody diversification, Somatic Hypermutation, Class Switch recombination, programmed DNA Damage/Repair, CRISPR/Cas9 screening, Genome Editing, AID, Fam72a, Uracil DNA glycosylase

 

Relevant publications:

- Rogier, M. et al. Fam72a enforces error-prone DNA repair during antibody diversification. Nature 600, 329, doi:10.1038/s41586- 021-04093-y (2021).

- Yilmaz, D. et al. Activation of homologous recombination in G1 preserves centromeric integrity. Nature, doi:10.1038/s41586-021- 04200-z (2021).

- Amoretti-Villa, R., Rogier, M., Robert, I., Heyer, V. & Reina-San-Martin, B. A novel regulatory region controls IgH locus transcription and switch recombination to a subset of isotypes. Cell Mol Immunol 16, 887-889 (2019).

Name: Institute of Genetics, Molecular and Cellular Biology (IGBMC)

Team: Nuclear organisation and division

Team leader: Manuel MENDOZA

Email: mendozam@igbmc.fr

 

PhD supervisor: Manuel MENDOZA

Email: mendozam@igbmc.fr

Gene expression requires ordered and efficient processing of messenger RNA (mRNA) molecules from their sites of synthesis in the nucleus to the cytoplasm, where they are translated into proteins. Yet, we know little about the cellular processes that orchestrate the flux of mRNA in time and space. We study how lysine acetyl-transferase (KAT) and deacetylase (KDAC) protein complexes regulate multiple processes in the life cycle of RNA, from its synthesis in the nucleus until its degradation in the cytoplasm. In this project, we will use state-of-the-art methods in budding yeast and mouse embryonic stem cells to determine how the NuA4 KAT complex and associated KDAC proteins control the synthesis, nuclear export, and degradation kinetics of mRNA molecules to either maintain cell fate stability or trigger cell state transitions.

 

Keywords: Nuclear pore complexes, acetylation, gene expression, mRNA synthesis and export, budding yeast, stem cells

 

Relevant publications:

- Gomar-Alba, M., Pozharskaia, V., Cichocki, B., Schaal, C., Kumar, A., Jacquel, B., et al. (2022). Nuclear pore complex acetylation regulates mRNA export and cell cycle commitment in budding yeast. EMBO J. 41, e110271.

- 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. Nature Communications 11, 2267. First version posted to bioRxiv, https://doi.org/10.1101/407957

- 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. First version posted to bioRxiv, https://doi.org/10.1101/203232

Name: Institute of Genetics, Molecular and Cellular Biology (IGBMC)

Team: Common mechanisms of development, cancer and aging

Team leader: Bill KEYES

Email: bill.keyes@igbmc.fr

 

PhD supervisor: Bill KEYES

Email: bill.keyes@igbmc.fr

Cellular senescence is a form of irreversible cell cycle arrest induced by a variety of stimuli, including aging and chemotherapy. However, work from our lab has also shown how senescence, when present transiently, can have beneficial functions in embryonic development, plasticity and regeneration (e.g. Storer et al, Cell, 2013; Ristchka et al, Genes Dev., 2017). Our lab is interested in studying the cell biology of the senescence program in different settings: in physiological settings such as development and regeneration, and in pathological settings such as aging, disease and cancer.

Using a new senescence-reporter mouse model generated by us, we have performed high-resolution profiling of senescent cells during embryonic development, to identify potential new regulators of senescence. By comparing this with other models of senescence including following chemotherapy and in aging tissues, we have identified a list of potential new senescence markers and mediators. We aim to recruit a Ph.D. student to investigate these novel genes in cellular senescence, in models such as in cancer cells after therapy, in tissue regeneration, or in aging models. The project will be tailored to the students’ research interests, but will broadly involve the study of senescence in vivo and in vitro using a variety of cell and molecular approaches, in addition to mouse models, in vivo imaging, single cell sequencing approaches.

 

Keywords: cellular senescence, cancer,  plasticity, development, regeneration, reprogramming, aging

 

Relevant publications:

- Durik, M., Sampaio Gonçalves, D., Spiegelhalter, C., Messaddeq, N., Keyes, W.M. Senescent cells deposit intracellular contents through adhesion-dependent fragmentation (2023) BioRxiv doi: https://doi.org/10.1101/2023.01.11.523642

- Ritschka, B., Knauer-Meyer, T., Sampaio-Conçalves, D., Mas, A., Plassat, J.L., Durik, M., Jacobs, H., Pedone, E., Di Vicino, U., Cosma, M.P. Keyes, W.M. (2020) The senotherapeutic drug ABT-737 disrupts aberrant p21 expression to restore liver regeneration in adult mice. Genes & Development, 34(7-8):489-494.

- Ritschka, B., Storer, M., Mas, A., Heinzmann, F., Ortells, M.C., Morton, J.P., Sansom, O.J., Zender, L. and Keyes, W.M. (2017) The senescence-associated secretory phenotype induces cellular plasticity and tissue regeneration Genes & Development, 31(2):172-183

Functional Genomics and Cancer (LabEx INRT)

Name: Institue of Genetics, Molecular and Cellular Biology (IGBMC)

Team: Genome expression and repair

Team leader: Frédéric COIN

Email: fredr@igbmc.fr

 

PhD supervisor: Frédéric COIN

Email: fredr@igbmc.fr

Malignant melanoma is responsible for 70% of skin cancer deaths in Western countries. The 5-year survival rate is only 16% for distant stage disease, demonstrating that metastasis is responsible for patient mortality. Treatment options for patients with metastatic melanoma have evolved considerably over the past decade. Combination therapies with inhibitors targeting BRAF (i.e., Vemurafenib and Dabrafenib) and MEK kinases (i.e., Trametinib) have emerged and show high efficacy but are limited by the development of resistance and subsequent progression. The proposed PhD project represents a pioneering endeavor to delve into the intricate molecular landscape of melanoma, focusing on the phenomenon of transcriptional addiction within melanoma cells. With the relentless rise in melanoma incidence worldwide, understanding the molecular underpinnings of this aggressive skin cancer is paramount. This research seeks to unravel the intricacies of transcriptional addiction, a phenomenon wherein cancer cells become heavily reliant on specific transcriptional programs for their survival and proliferation. By employing cutting-edge genomic and bioinformatic approaches, the project aims to identify key transcription factors and regulatory elements that are crucial for the sustained growth and survival of melanoma cells. This investigation will not only shed light on the fundamental biology of melanoma but also holds potential implications for the development of targeted therapeutic interventions. Furthermore, the project's comprehensive approach involves the integration of high-throughput sequencing data, functional genomics, and advanced computational analyses to construct a detailed map of the transcriptional networks driving melanoma progression. Ultimately, the outcomes of this research endeavor have the potential to pave the way for novel therapeutic strategies, providing a deeper understanding of the molecular dependencies that fuel melanoma and offering new avenues for precision medicine in the battle against this formidable malignancy.

 

Keywords: Melanoma, Transcription addiction, new drugs, TFIIH

 

Relevant publications:

- Berico, P., Nogaret, M., Cigrang, M., Lallement, A., Vand-Rajabpour, F., Flores-Yanke, A., Gambi, G., Davidson, G., Seno, L., Obid, J., Bujamin H., V, Stephanie Le Gras, Gabrielle Mengus, Tao Ye, Carlos Fernandez Cordero, Mélanie Dalmasso, Emmanuel Compe, Corine Bertolotto, Eva Hernando, Irwin Davidson, Coin. F*. 2023. Super-enhancer-driven expression of BAHCC1 promotes melanoma cell proliferation and genome stability. Cell Reports, Nov 2;42(11):113363. DOI: 10.1016/j.celrep.2023.113363

- Sandoz, J., Cigrang, M., Zachayus, A., Catez, P., Donnio L.M., Elly, C., Nieminuszczy, J., Berico, P., Braun, C., Alekseev, S., Egly, J.M., Niedzwiedz W., Mari-Giglia, G., Compe, E., and Coin, F*. 2023. Active mRNA degradation by EXD2 nuclease elicits recovery of transcription after genotoxic stress. Nature Communications, Jan 20;14(1):341. doi: 10.1038/s41467-023-35922-5.

- Sandoz, J., Nagy, Z., Catez, P., Caliskan, G., Geny, S., Renaud, J.B., Concordet, J.P., Poterszman, A., Tora, L., Egly, J.M., Le May, N., Coin, F*., 2019. Functional interplay between TFIIH and KAT2A regulates higher-order chromatin structure and class II gene expression. Nature Communications 10, 1288. https://doi.org/10.1038/s41467-019-09270-2

Name: Institute of Genetics, Molecular and Cellular Biology (IGBMC)

Team: Molecular and translational oncology

Team leader: Gabriel MALOUF

Email: maloufg@igbmc.fr

 

PhD supervisor: Gabriel MALOUF

Email: maloufg@igbmc.fr

Translocation Renal Cell Carcinoma (TRCC) is a rare kidney cancer arising essentially in children and young adults, and characterized by translocations affecting MiTF family transcription factors, in particular TFE3 and TFEB. TRCC comprise 15% of RCC in patients under 40 years old and presents a treatment challenge due to limited understanding of its development and characteristics. For patients in metastatic disease, no treatment is approved in the metastatic setting. TFE3 often fuses with different fusion partners leading to different transcriptomic program and distinct unique tumor microenvironment. We have generated three novel genetically engineered mice models of TFE3 TRCC. The goal of the PhD thesis is to 1) Characterize these various murine models. We will focus in particular on the difference between kinetics of tumor development. In addition, we will analyze early steps of oncogenesis, characterize the tumor microenvironment and identify therapeutic targets. 2) Compare the oncogenic pathways and tumor microenvironment in murine and human TRCC with the goal to identify novel therapeutic targets. 3) Identify and validate a novel therapeutic target in TRCC, allowing to generate strong rational for a clinical trial;

 

Keywords: Transcription factors, renal cell carcinomas, TFE3, single-cell renal cell carcinomas, animal models

 

Relevant publications:

- Lu X, Vano YA, Su X, Helleux A, Lindner V, Mouawad R, Spano JP, Rouprêt M, Compérat E, Verkarre V, Sun CM, Bennamoun M, Lang H, Barthelemy P, Cheng W, Xu L, Davidson I, Yan F, Fridman WH, Sautes-Fridman C, Oudard S, Malouf GG. Silencing of genes by promoter hypermethylation shapes tumor microenvironment and resistance to immunotherapy in clear-cell renal cell carcinomas. Cell Rep Med. 2023 Nov 21;4(11):101287. doi: 10.1016/j.xcrm.2023.101287. Epub 2023 Nov 14. PMID: 37967556.

- Davidson G, Helleux A, Vano YA, Lindner V, Fattori A, Cerciat M, Elaidi RT, Verkarre V, Sun C, Chevreau C, Bennamoun M, Lang H, Tricard T, Fridman WH, Sautes-Fridman C, Su X, Plassard D, Keime C, Thibault-Carpentier C, Barthelemy P, Oudard S, Davidson I, Malouf GG. Roles of mesenchymal-like tumour cells and myofibroblastic cancer-associated fibroblasts in progression and therapeutic response of clear-cell renal cell carcinoma. Cancer Research, 2023 Sep 1;83(17):2952-2969.

- Vokshi BH*, Davidson G*, Tawanaie Pour Sedehi N, Helleux A, Rippinger M, Haller A, Gantzer J, Thouvenin J, Baltzinger P, Bouarich R, Manriquez V, Zaidi S, Rao P, Msaouel P, Su X, Lang H, Tricard T, Lindner V, Surdez D, Kurtz JE, Bourdeaut F, Tannir NM, Davidson I and Malouf GG. SMARCB1 regulates a TFCP2L1-MYC transcriptional switch promoting renal medullary carcinoma transformation and ferroptosis resistance. Nat Commun. 2023 May 26;14(1):3034.

Name: Institute of Genetics, Molecular and Cellular Biology (IGBMC)

Team: Pathogenesis of inflammatory diseases

Team leader: Mei LI

Email: mei@igbmc.fr

 

PhD supervisor: Mei LI

Email: mei@igbmc.fr

Dysregulated immune responses at skin lead to inflammation involved in the development of allergies, autoimmune disorders, cutaneous infections, and cancers. The team is interested in deciphering dendritic cell (DC) -T cell axes implicated in different inflammatory pathologies. DC have specialized subsets whose local development and functions are shaped by tissue microenvironmental cues. In homeostatic and inflammatory conditions, specific DC subsets migrate into draining lymph nodes to present antigen and prime proinflammatory or tolerogenic responses. The latter can generate regulatory T cells (Treg), which are vital to the preservation of immune tolerance and suppression of exacerbated immune responses to foreign antigens, but underlying mechanisms stay poorly understood. The project will focus on a newly identified tolerogenic DC subset, to delineate its upstream activation signals, its tissue localization and dynamics in skin and other barrier tissues, and its function in driving Treg responses and crosstalking with other DC-T axes in steady state and inflammatory contexts. The study will use mouse genetic tools, immunological approaches (­­flow cytometry, cell sorting, adoptive cell transfer, in vitro cell differentiation and cell co-culture), and molecular biology tools particularly single cell RNA-sequencing and bioinformatic analyses. Results are expected to reveal novel tolerogenic mechanisms, and to identify potential therapeutic targets for allergy and autoimmunity.

 

Keywords: Immune response, inflammation; dendritic cell, T cell, tolerance, allergy, autoimmune, skin

 

Relevant publications:

- Marschall, P, Wei, R., Segaud, J., Yao, W., Hener, P., German Falcon, B., Meyer, P., Hugel, C., Silva, G., Braun, R., Kaplan, D. and Li, M. (2020) Dual function of Langerhans cells in skin TSLP-promoted Tfh cell differentiation in mouse atopic dermatitis. J. Allergy Clinic. Immunol.S0091-6749(20)31408-1. doi: 10.1016/j.jaci.2020.10.006. PMID: 33068561.

- Segaud. J.*, Yao, W.*, Marschall, P., Daubeuf, F. Lehalle, C., German B., Meyer, P., Hener, P., Hugel, C., Flatter, E., Guivarch, M., Clauss, L., Martin, S., Oulad-Abdelghani, M and Li, M. Context-dependent role of TSLP and IL-1β in skin allergic sensitization and atopic march. (2022) Nat. Commun. DOI: 10.1038/s41467-022-32196-1. PMID: 36050303. *, co-first.

- Yao, W.*, German B.*, Chraa, D.*, Braud, A., Hugel, C., Meyer, P., Davidson, G., Laurette, P., Mengus, G., Flatter, E., Marschall, P., Segaud, J., Guivarch, M., Hener, P., Birling, M, Lipsker, D., Davison, I. and Li, M. Keratinocyte-derived cytokine TSLP promotes growth and metastasis of melanoma by regulating the tumour-associated immune microenvironment. (2022) JCI Insight. DOI: 10.1172/jci.insight.161438. PMID: 36107619. *, co-first.

Name: Institute of Genetics, Molecular and Cellular Biology (IGBMC)

Team: Hematopoiesis and disease

Team leaders: Susan CHAN & Philippe KASTNER

Email: scpk@igbmc.fr

 

PhD supervisor: Céline CHARVET

Email: charvetc@igbmc.fr

Autoimmune diseases are debilitating pathologies that mainly affect women with an increasing incidence in Western countries. They are generally characterized by systemic inflammatory flare-ups that contribute to widespread tissue damage. However, the mechanisms responsible for this inflammation are only partially understood. CD4 T lymphocytes are important in the establishment of a deregulated inflammatory response by producing inflammatory cytokines (IFNg, GM-CSF, …). It is therefore important to understand how the production of these cytokines is regulated, so that it can ultimately be manipulated in therapeutic approaches. Our lab found that the transcription factor (TF) Ikaros is critical to repress the pro-inflammatory program of CD4 T lymphocytes. Ikaros physically and functionally interacts with other members of the Ikaros family, such as Aiolos, but also seems to functionally converge with TFs outside of the Ikaros family, such as Foxo1, suggesting that Ikaros takes part in multiple protein networks to regulate some CD4 T cell properties. The objectives of this PhD project will be to determine: 1) the functional interaction between Ikaros, Aiolos and Foxo1 in CD4 T cells at the molecular level 2) how they influence the protein landscape and 3) if they impact the development of CD4 T cell-related inflammatory diseases.

 

Keywords: T cells, inflammation, transcriptional regulation, protein network, autoimmune diseases

 

Relevant publications:

- CD4+ T cells require Ikaros to inhibit their differentiation toward a pathogenic cell fate. Bernardi C, Maurer G, Ye T, Marchal P, Jost B, Wissler M, Maurer U, Kastner P, Chan S, Charvet C. Proc Natl Acad Sci U S A. 2021 Apr 27;118(17):e2023172118. doi: 10.1073/pnas.2023172118. PMID: 33893236

- Helios represses megakaryocyte priming in hematopoietic stem and progenitor cells. Cova G, Taroni C, Deau MC, Cai Q, Mittelheisser V, Philipps M, Jung M, Cerciat M, Le Gras S, Thibault-Carpentier C, Jost B, Carlsson L, Thornton AM, Shevach EM, Kirstetter P, Kastner P, Chan S. J Exp Med. 2021 Oct 4;218(10):e20202317. doi: 10.1084/jem.20202317. Epub 2021 Aug 30. PMID: 34459852

- Ikaros deficiency is associated with aggressive BCR-ABL1 B-cell precursor acute lymphoblastic leukemia independent of the lineage and developmental origin. Simand C, Keime C, Cayé A, Arfeuille C, Passet M, Kim R, Cavé H, Clappier E, Kastner P, Chan S, Heizmann B. Haematologica. 2022 Jan 1;107(1):316-320. doi: 10.3324/haematol.2021.279125. PMID: 34587720

Name: Institute of Genetics, Molecular and Cellular Biology (IGBMC)

Team: Transcriptional regulation of neural and immune development

Team leader: Angela GIANGRANDE

Email: angela.giangrande@igbmc.fr

 

PhD supervisor: Pierre CATTENOZ

Email: cattenoz@igbmc.fr

During development, distinct cell types acquire their properties under the control of transcription factors called cell fate determinants. These factors act on genes necessary for the progression of cell differentiation and this is accompanied by chromatin reorganisation. The acquisition of a specific chromatin conformation is required for cell differentiation and function. These two phenomena, gene regulation and chromatin reorganisation, have been well studied independently for numerous systems however their interdependency is poorly understood.

Our laboratory is studying the differentiation of glia in the developing Drosophila embryo to understand how the differentiation program controls chromatin reshaping. Our recent data identified four histone modifiers (Gcn5, Kdn4b, Gug and Su(var)3-9) directly induced by the glia fate determinant Gcm during the differentiation of the precursor into glia. The PhD candidate will characterise how these histones modifiers promote the differentiation of glial cells using the powerful genetic tools available in Drosophila combined with imaging (confocal microscopy) and state of the art sequencing technologies (ATACseq, Cut&Run, Cut&Tag).

The completion of this project will broaden our understanding of the chromatin ballet occurring during glial differentiation and will establish a clear link between the glial developmental program and the chromatin dynamics. In addition, given the conservation of most molecular pathways from Drosophila to mammals, this project will highlight the fundamental mechanisms controlling the development of the mammalian nervous system and will provide an experimental approach for their characterisation in other models.

 

Keywords: Drosophila, chromatin, gliogenesis, Cut and Run, high throughput sequencing

 

Relevant publications:

- Sakr, R., P. B. Cattenoz, A. Pavlidaki, L. Ciapponi, M. Marzullo et al., 2022 Novel cell- and stage-specific transcriptional signatures defining Drosophila neurons, glia and hemocytes. bioRxiv: 2022.2006.2030.498263.

- Pavlidaki, A., R. Panic, S. Monticelli, C. Riet, Y. Yuasa et al., 2022 An anti-inflammatory transcriptional cascade conserved from flies to humans. Cell Rep 41: 111506.

- Cattenoz, P. B., A. Popkova, T. D. Southall, G. Aiello, A. H. Brand et al., 2016 Functional Conservation of the Glide/Gcm Regulatory Network Controlling Glia, Hemocyte, and Tendon Cell Differentiation in Drosophila. Genetics 202: 191-219.

Integrated Structural Biology (LabEx INRT)

Name: Institute of Genetics, Molecular and Cellular Biology (IGBMC)

Team: Large complexes involved in gene expression

Team leader: Bruno KLAHOLZ

Email: klaholz@igbmc.fr

 

PhD supervisor: Bruno KLAHOLZ

Email: klaholz@igbmc.fr

The ribosome is a molecular machinery that goes through different phases including 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). 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 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, as established and described in our publications (Khatter et al. Nature 2015, Natchiar et al. Nature 2017, Klaholz Acta Cryst. 2019, Fréchin et al. J Struct Biol. 2023, Barchet et al. J Struct Biol. 2023, Holvec et al. bioRxiv / 2024 in press). This project will allow a better understanding of the molecular function of the human ribosome, which is an important medical target including for cancer. 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

 

Keywords: human ribosome, structure-function, structural biology, high-resolution cryo electron microscopy

 

Relevant publications:

- Structure of the human 80S ribosome at 1.9 Å resolution - the molecular role of chemical modifications and ions in RNA. 2024, in press. https://doi.org/10.1101/2023.11.23.568509

- C. Barchet, L. Fréchin, S. Holvec, I. Hazemann, O. von Loeffelholz & B. P. Klaholz. Focused classifications and refinements in high-resolution single particle cryo-EM analysis. J Struct Biol., 2023, 215, 4, 108015. https://doi.org/10.1016/j.jsb.2023.108015

- S. K. Natchiar, A. G. Myasnikov, H. Kratzat, I. Hazemann & B. P. Klaholz. Visualization of chemical modifications in the human 80S ribosome structure. Nature, 2017, 551, 472-477. http://dx.doi.org/10.1038/nature24482

Name: Institute of Genetics, Molecular and Cellular Biology (IGBMC)

Team: mRNA processing

Team leader: Clément CHARENTON

Email: charentc@igbmc.fr

 

PhD supervisor: Clément CHARENTON

Email: charentc@igbmc.fr

This project focuses on a complex biological process, enabling humans to generate 200,000 types of proteins from only 20,000 protein-coding genes!

In eukaryotes, the spliceosome removes non-coding introns from precursor messenger RNAs during pre-mRNA splicing. Crucially, many pre-mRNAs are spliced differently depending on cellular status or external stimuli. This “alternative splicing” reshapes the genetic information from a given mRNA to encode several protein isoforms and greatly diversifies proteomes.

Splicing must be extremely precise as errors produce aberrant mRNA encoding potentially toxic proteins. Dysregulation of the splicing activity is associated with several human diseases including cancer and genetic disorder.

Hence the spliceosome has the impossible task of being very accurate to prevent splicing errors while being tolerant during alternative splicing changes.

This project consists of a mechanistic study of the human spliceosome aimed at unravelling how it ensures the fidelity of pre-mRNA splicing.

The PhD student will use a combination of biochemical and structural biology approaches to reveal the molecular organisation of splicing complexes captured during key fidelity checkpoints. These complexes contain numerous protein and RNA subunits and typically require a wide array of methods to be generated, and then, precisely characterised. In particular, the PhD student will have the opportunity to use ribonucleoprotein complexes reconstitution from cell extracts and/or recombinant sources, various biochemical and biophysical assays, cryo-EM, X-ray crystallography, mass spectrometry…

 

Keywords: Spliceosome Ribonucleoprotein Structure Splicing Fidelity cryo-EM

 

Relevant publications:

- Charenton, C.*†, Wilkinson, M.E.*†, Nagai, K.*, 2019. Mechanism of 5′ splice site transfer for human spliceosome activation. Science 364, 362–367.

- Wilkinson, M.E.*†, Charenton, C.*†, Nagai, K.†, 2020. RNA Splicing by the Spliceosome. Annual Review in Biochemistry 89, 359–388.

- Plaschka, C., Lin, P.-C., Charenton, C., Nagai, K., 2018. Prespliceosome structure provides insights into spliceosome assembly and regulation. Nature 559, 419–422.

Name: Institute of Genetics, Molecular and Cellular Biology (IGBMC)

Team: Regulation of transcription

Team leader: Albert WEIXLBAUMER

Email: albert.weixlbaumer@igbmc.fr

 

PhD supervisor: Albert WEIXLBAUMER

Email: albert.weixlbaumer@igbmc.fr

Gene expression is the initial step to convert genotype to phenotype and includes several steps: i) mRNA is transcribed from DNA by RNA polymerase; ii) mRNA is processed, and iii) translated to protein by the ribosome. The machineries executing gene expression have been mostly studied in isolation in the past but we know many of them are organized in large, supramolecular assemblies where their activities are coordinated and new functions emerge that are not predictable from the individual components. We aim to close this gap. For example, we study how the bacterial RNA polymerase cooperates with the ribosome (see Webster et al., Science 2020 for recent result) or how human RNA polymerase II cooperates with enzymes involved in mRNA processing.

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 between RNA polymerase and other key enzymes involved in gene expression.

Interested candidates will use single particle cryo-EM, the ideal method to gain mechanistic insights of large, dynamic protein nucleic acid complexes, to obtain high-resolution reconstructions. Biochemical, and in-vivo approaches will complement your results. Your work will unravel how synergism and crosstalk of distinct macromolecular machines in the context of a supramolecular assembly regulates the conversion of genotype to phenotype.

 

Keywords: RNA polymerase, ribosome, mRNA processing, molecular machines, gene expression, cryo-electron microscopy, structural biology

 

Relevant publications:

- Dey S, Batisse C, Shukla J, Webster MW, Takacs M, Saint-André C, and Weixlbaumer A (2022). Structural insights into RNA-mediated transcription regulation in bacteria.  Mol Cell 82(20), 3885–3900.

- 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 369(6509), 1355-1359

- 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

Name: Institute of Genetics, Molecular and Cellular Biology (IGBMC)

Team: Transcription co-activators

Team leader: Patrick SCHULTZ

Email: patrick.schultz@igbmc.fr

 

PhD supervisor: Gabor PAPAI

Email: gabor.papai@igbmc.fr

Myc is a master transcription activator that directly stimulates the expression of 15% of the human genome and is one of the most frequently deregulated driver gene in human cancers. Among other tumors, Myc activity is deregulated in Rhabdoid cancer, a very aggressive childhood cancer with low survival rates. In patients with Rhabdoid cancer the protein Snf5 is mutated or absent as large parts of its gene, or even the whole gene, are deleted. Snf5 is a subunit of the chromatin remodeling complex Swi/Snf. It was shown that Snf5 interacts with the DNA binding pocket of Myc and attenuates in this manner the transcriptional activity of Myc. When Snf5 is deleted, as in Rhabdoid cancer, Myc is no longer held in check, yielding a destructive alteration to the transcription program of the cell.

To understand the molecular background of this process, the goal of this project is to reconstitute the assembly between Swi/Snf and Myc, and to solve its structure using cryo-Electron Microscopy. Our team has already developed human cell lines with affinity-tagged subunits of Swi/Snf that will be instrumental in purifying this complex. Potentially, the structure will serve to guide development of anti-cancer drugs that mimic the way Snf5 blocks Myc binding to DNA.

Interested candidates will be trained for purification of low-abundance complexes from human cells, functional assays and atomic structure determination by single particle cryo-EM.

 

Keywords: Chromatin remodelers, Myc oncogene, Structural biology, cryo-electron microscopy, cancer

Name: Institute of Genetics, Molecular and Cellular Biology (IGBMC)

Team: Biomolecular condensation in nuclear organization and function

Team leader: Mikhail ELTSOV

Email: eltsovm@igbmc.fr

 

PhD supervisor: Mikhail ELTSOV

Email: eltsovm@igbmc.fr

Cryo-electron tomography (cryo-ET) has revolutionized our ability to explore the molecular mechanisms, enabling analysis of macromolecular complexes directly in their native cellular environment at near-atomic. Nevertheless, extracting information from cryo-ET reconstructions remains challenging particularly because of a high noise and anisotropic resolution resulted from electron-induced damage and a limited tilt angular range accessible in cryo-ET. New approaches based on artificial intelligence (AI) offer new opportunities to overcome these challenges to take full advantage of cryo-ET for understanding biological functions.

Our team demonstrated the effectiveness of combining cryo-ET with noise-to-noise deep learning based denoising techniques [1] for visualization of nucleosomes and DNA linkers within the functional environment of the cell nucleus, preserved in a near-native state [2]. However, these methods could not cope with information anisotropies, making it difficult to automatically annotate chromatin structure in tomograms. Recently, new approaches involving learning from simulated data and generative deep learning were presented that can address all major limitations of cryo-ET [3].

This project aims to apply and further develop this methodology to facilitate automated annotation of nucleosomes and tracing the path of chromatin fiber within the native nucleus. The comparative analysis of chromatin fibers in tomograms containing active and inactive chromatin domains will providing insights into molecular mechanisms underlying structural mechanisms of gene expression regulation.

[1] Lehtinen, J., Munkberg, J., Hasselgren, J., Laine, S., Karras, T., Aittala, M. and Aila, T. (2018) Noise2Noise: Learning Image Restoration without Clean Data. ArXiv, abs/1803.04189.

[2] Fatmaoui, F., Carrivain, P., Grewe, D., Jakob, B., Victor, J. M., Leforestier, A., & Eltsov, M. (2022). Cryo-electron tomography and deep learning denoising reveal native chromatin landscapes of interphase nuclei. bioRxiv, 2022-08.

[3] Zhang, H., Li, Y., Liu, Y., Li, D., Wang, L., Song, K., ... & Zhu, P. (2023). A method for restoring signals and revealing individual macromolecule states in cryo-ET, REST. Nature Communications, 14(1), 2937.

Keywords: cryo-electron tomography, data mining, artificial intelligence, deep learning, data simulation, chromatin, epigenetics

 

Relevant publications:

- Fatmaoui F., Carrivain P., Grewe D., Jakob B., Victor JM., LeforestierA., Eltsov M. Cryo-electron tomography and deep learning denoising reveal native chromatin landscapes of interphase nuclei. bioRxiv 2022.08.16.502515; doi: 10.1101/2022.08.16.502515

- Harastani M., Eltsov M., Leforestier A., Jonic S. TomoFlow: Analysis of Continuous Conformational Variability of Macromolecules in Cryogenic Subtomograms based on 3D Dense Optical Flow. J Mol Biol. 2022;434(2):167381. doi: 10.1016/j.jmb.2021.167381

- Harastani M., Eltsov M., Leforestier A., Jonic S. HEMNMA-3D: Cryo Electron Tomography Method Based on Normal Mode Analysis to Study Continuous Conformational Variability of Macromolecular Complexes. Front Mol Biosci. 2021 8:663121. doi: 10.3389/fmolb.2021.663121.

Translational Medecine and Neurogenetics (LabEx INRT)

Name: Institute of Genetics, Molecular and Cellular Biology (IGBMC)

Team: RNA disease

Team leader: Nicolas CHARLET

Email: ncharlet@igbmc.fr

 

PhD supervisor: Nicolas CHARLET

Email: ncharlet@igbmc.fr

We are seeking a motivated PHD student to investigate how peculiar genetic mutations, namely microsatellite expansions, which are DNA sequences typically composed of more than 50 repeats of 2 to 6 nucleotides-long DNA motifs (for example (CGG)100x, (GGGGCC)500x, etc.) cause muscle and/or neuronal diseases. Importantly these mutations are located in genomic regions annotated as “non coding” (5’ and 3’UTRs, introns, lncRNAs, etc.). We notably focus on Neuronal Intranuclear Inclusion Disease (NIID), OcculoPharyngoDistal Myopathy (OPDM) and Amyotrophic Lateral Sclerosis (ALS), which affects specifically motor neurons and that is the 3rd most common neurodegenerative disease worldwide.

Our work shows that despite being localized in “non-coding” sequences, these microsatellites repeat expansions are nonetheless translated into novel and toxic proteins (Sellier et al., Neuron 2017, Boivin et al., EMBO Journal 2020, Boivin et al., Neuron 2021, etc.).

The PHD student will investigate how these GGC and GGGGCC repeats are translated into toxic proteins using a wide range of molecular and cellular approaches (Omics, RT-qPCR, western, immunoprecipitation, immunofluorescence, transfection and cell transduction, primary cultures of mouse embryonic neurons, confocal and super resolution etc.), as well as develop novel animal models expressing these mutations through a viral strategy (AAV injection, mouse locomotor phenotyping, histology, IHC, etc.).

Overall, this proposal will help to better understand the cause of muscle and neuronal degeneration to define therapeutic strategies for these devastating diseases.

This work will take place at Institute of Genetics and Biology Molecular and Cellular (IGBMC, http://www.igbmc.fr/) a large European public research laboratory comprising ~800 persons involved in 40 research groups and 12 technological platforms, including all core services essential to the present project.

 

Keywords: human genetic diseases, molecular and cellular biology, mouse model, muscle, neurons

 

Relevant publications:

- Boivin et al., Translation of GGC repeat expansions into a toxic polyglycine protein in NIID defines a novel class of human genetic disorders. Neuron. 2021; 109(11):1825.

- 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).

- 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.

Name: Institute of Genetics, Molecular and Cellular Biology (IGBMC)

Team: Muscle and diseases

Team leader: Jocelyn LAPORTE

Email: jocelyn@igbmc.fr

 

PhD supervisors: Valérie BIANCALANA & Johann BOHM

Emails: valerie.biancalana@chru-strasbourg.fr & johann.boehm@igbmc.fr

Congenital myopathies are a class of rare genetic diseases characterized by muscle weakness from birth and abnormalities in skeletal muscle biopsies. There is currently no curative treatment for these diseases as the understanding of the pathological mechanisms remains limited.

Our team previously identified the genetic basis of several myopathies and characterized corresponding and faithful cellular and mouse models. Defects in skeletal muscle structure and function were observed but their molecular bases are unknown.

Using multi-omics approaches (single nuclei and bulk transcriptomic, proteomic, metabolomic), the PhD project aims to unravel the molecular pathways important for the normal maturation of skeletal muscles and altered in several congenital myopathies. The student will proceed to the informatic analysis of the omics data generated by the team from disease models untreated or treated with previously validated innovative therapies, in order to identify the disease and therapy molecular signatures. He/she will then combine these different multi-omics levels with quantitative imaging/histology and phenotyping into an integrated view of these pathologies using different informatic pipelines and artificial intelligence for big data analysis and heterogenous multi-layered networks. Wet-bench validation will be done by the student or other team members through alternative methods ranging from western blotting, quantitative PCR, ELISA assays and metabolite dosing.

Overall, the student will reveal the main molecular pathways commonly implicated in different myopathies. These pathways will highlight key biomarkers for diagnosis and to follow therapeutic efficiency and will be candidate for genetic or/and pharmacological manipulation to validate novel therapeutic proof-of-concepts.

 

Keywords: Bioinformatics, artificial intelligence, omics, imaging, congenital myopathies, cellular models, mouse models

 

Relevant publications:

- Djeddi S, Reiss D, Menuet A, Freismuth S, de Carvalho Neves J, Djerroud S, Massana-Muñoz X, Sosson AS, Kretz C, Raffelsberger W, Keime C, Dorchies OM, Thompson J, Laporte J. Multi-omics comparisons of different forms of centronuclear myopathies and the effects of several therapeutic strategies. Mol Ther. 2021 Aug 4;29(8):2514-2534. doi: 10.1016/j.ymthe.2021.04.033. (S Djeddi = previous PhD student) 

- 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. Science Transl Med. 2019 Mar 20;11(484). doi: 10.1126/scitranslmed.aav1866. (V Lionello = previous PhD student) 

- Gómez-Oca R, Edelweiss E, Djeddi S, Gerbier M, Massana-Muñoz X, Oulad-Abdelghani M, Crucifix C, Spiegelhalter C, Messaddeq N, Poussin-Courmontagne P, Koebel P, Cowling BS^, Laporte J^. Differential impact of ubiquitous and muscle dynamin 2 isoforms in muscle physiology and centronuclear myopathy. Nature Commun. 2022 Nov 11;13(1):6849. doi: 10.1038/s41467-022-34490-4. (R Gomez-Oca = previous PhD student) 

Name: Institute of Genetics, Molecular and Cellular Biology (IGBMC)

Team: Pathophysiology of down's syndrome and rare dose-effect diseases causing intellectual disabilities

Team leader: Yann HERAULT

Email: herault@igbmc.fr

 

PhD supervisor: Yann HERAULT

Email: herault@igbmc.fr

Dow syndrome (DS) is the most common form of intellectual disability.  DS is caused by the overdosage of a few candidate genes located on human chromosome 21. We have demonstrated that the cystathionine beta-synthase gene (Cbs) overdosage is sufficient and necessary to induce memory deficits in DS mouse and rat models displayed memory deficits. Furthermore, treatments with two chemicals targeting CBS overdose were successful in restoring recognition memories in adults. Remarkably, CBS is expressed at low levels in different regions during brain development, and then starts to be mainly restricted to astrocytes in adults.

Astrocytes are brain cells that play an important role in synaptic transmission and plasticity, notably by ensuring the optimal functioning of neurons. Thus, we hypothesize that the CBS overdosage in DS is probably taking place primary in DS brain astrocytes. In this project, we aim to understand the consequences of CBS overdosage in DS astrocytes. For this, we plan 1) to rescue the CBS dosage in DS mouse models using a genetic approach and monitor the behavior; 2) to characterize the cellular and molecular mechanisms changed in vivo by the normalization of Cbs dosage in brain astrocytes; 3) to carry a similar analysis in vitro with astrocyte-enriched cell cultures derived from DS IPS models. With this project we will continue to shed light on the consequences of CBS overdosage; a major step for the development of a therapeutic approach in DS.

 

Keywords: Genetic, therapy, animal and cellular models

 

Relevant publications:

- Nguyen TL, Duchon A, Manousopoulou A, Loaëc N, Villiers B, Pani G, Karatas M, Mechling AE, Harsan LA, Limanton E, Bazureau JP, Carreaux F, Garbis SD, Meijer L, Herault Y, Correction of cognitive deficits in mouse models of Down syndrome by a pharmacological inhibitor of DYRK1A. Dis Model Mech. 2018 11, pii: dmm.035634. doi: 10.1242/dmm.035634.

- Marechal D, Brault V, Leon A, Martin D, Lopes Pereira P, Loaec N, Birling M-C, Friocourt G, Blondel M, Herault Y. 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, PMID: 30649339

- Duchon A, MdM Muñiz Moreno, S Martin Lorenzo, MP Silva de Souza, C Chevalier, V Nalesso, H Meziane, P Loureiro de Sousa, V Noblet, J-P Armspach V Brault, Y Hérault. Multi-influential interactions alter behaviour and cognition through six main biological cascades in Down syndrome mouse models. Hum mol Genet, 2021 30, 771-788, doi: 10.1093/hmg/ddab012, PMID: 33693642

Integrative Biology - Nuclear Dynamics, Regenerative and Translational Medicine (LabEx INRT)/Regulatory RNA networks in response to biotic and abiotic stresses (LabEx NetRNA)

Functional Genomics and Cancer (LabEx INRT) / Insect Models of Innate Immunity (LabEx NetRNA)

Name 1: Institute of Genetics, Molecular and Cellular Biology (IGBMC)

Team 1: Molecular and cellular biology of breast cancer

Team leader: Catherine TOMASETTO

Email: cat@igbmc.fr

 

Name 2: Insect Models of Innate Immunity (M3I, IBMC)

Team 2: Antiviral innate immunity in insects

Team leaders: Jean-Luc IMLER & Carine MEIGNIN

Emails: jl.imler@ibmc-cnrs.unistra.fr & c.meignin@ibmc-cnrs.unistra.fr

 

PhD supervisors: Catherine TOMASETTO & Carine MEIGNIN

Emails: cat@igbmc.fr & c.meignin@ibmc-cnrs.unistra.fr

C19ORF12/Nazo are evolutionarily conserved proteins that have been identified independently by unbiased genetic approaches for their roles in a neurodegenerative disease in humans and in antiviral immunity in the model organism Drosophila. These mysterious proteins do not contain structural domains that could hint to a possible function and seem to co-localize with mitochondria and endoplasmic reticulum membranes thus suggesting that they are associated with ER-mitochondria contacts. Several observations further suggest that they are involved in vesicle trafficking and lipid metabolism. The goal of this application is to unite the findings made in flies and humans and to provide explanations for the connection of C19ORF12/Nazo proteins to seemingly unrelated physiological functions. We will combine experiments in vivo, taking advantage of the fly model (Imler/Meignin), and tissue culture cells (Tomasetto) to establish the link between C19ORF12/Nazo proteins and organelle biology to understand how they impact the biology of neurons and resistance to viral infections. State of the art cell biology techniques, coupled to structure/function studies, will contribute to the understanding of the regulation and the dynamics of these enigmatic proteins with relevance to human health. The collaboration between our two laboratories is ongoing (co-supervision of the 6-month internship of Julian Wagner B. Sc. in 2023) and our teams are technically and scientifically complementary on this project. Catherine Tomasetto has a long-standing cell biology expertise, her team made key contributions in the field of inter-organelle contact biology. JL. Imler and C. Meignin are recognized internationally for their work in the field of antiviral immunity in insects, in particular for the discovery that viral infections in drosophila triggers expression of antiviral genes regulated by the cGAS/STING pathway.

 

Keywords: Innate immunity, Virus, Cell biology, mitochondria, membrane dynamics, Inter-organelle contacts, cGAS, STING

 

Relevant publications:

- Zouiouich M, Di Mattia T, Martinet A, Eichler J, Wendling C, Tomishige N, Grandgirard E, Fuggetta N, Fromental-Ramain C, Mizzon G, Dumesnil C, Carpentier M, Reina-San-Martin B, Mathelin C, Schwab Y, Thiam AR, Kobayashi T, Drin G, Tomasetto C*, Alpy F. (2022). MOSPD2 is an endoplasmic reticulum-lipid droplet tether functioning in LD homeostasis. Journal of Cell Biology. 221 (6): e202110044. https://doi.org/10.1083/jcb.202110044 

- 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*. (2020). FFAT motif phosphorylation controls formation and lipid transfer function of inter‐organelle contacts. EMBO J. 39:e104369. https://doi.org/10.15252/embj.2019104369

- 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.

- Cai H, Li L, Slavik K, Huang J, Ting Y, Ai X, Hédelin L, Haas G, Xiang Z, Yang Y, Li X, Chen Y, Wei Z, Deng H, Chen D, Jiao R, Martins N, Meignin C, Kranzusch P & Imler JL (2023) The virus-induced cyclic dinucleotide 2’3’-c-di-GMP mediates STING-dependent antiviral immunity in Drosophila. Immunity, 56: 1991-2005

- Pennemann FL, Mussabekova A, Urban C, Stukalov A, Andersen LL, Grass V, Lavacca TM, Holtze C, Oubraham L, Benamrouche Y, Girardi E, Boulos RE, Hartmann R, Superti-Furga G, Habjan M, Imler JL, Meignin C & Pichlmair A (2021) Cross-species analysis of viral nucleic acid interactors identifies TAOKs as immune regulators. Nature Communications, 12: 7009.

- Holleufer A, Winther KG, Gad HH, Ai X, Chen Y, Li L, Wei Z, Deng H, Liu J, Ahlmann Frederiksen N, Simonsen B, Kleigrewe K, Pichlmair A, Cai H, Imler JL, Hartmann R (2021) Two cGAS-like receptors induce a Sting-dependent antiviral immune response in Drosophila melanogaster. Nature, 597 : 114-118.

Integrated Structural Biology (LabEx INRT) /Architecture and Reactivity of RNA (LabEx NetRNA)

Name 1: Institute of Genetics, Molecular and Cellular Biology (IGBMC)

Team 1: Chromatin stability and DNA mobility

Team leader: Marc RUFF

Email: ruff@igbmc.fr

 

Name 2: Architecture and Reactivity of RNA (ARN, IBMC)

Team 2: Viral ribonucleoproteins genome incorporation and assembly

Team leaders: Roland MARQUET & Jean-Christophe PAILLARD

Emails: r.marquet@unistra.fr & jc.paillart@ibmc-cnrs.unistra.fr

 

PhD supervisors: Marc RUFF & Serena BERNACCHI

Email: ruff@igbmc.fr & s.bernacchi@ibmc-cnrs.unistra.fr

Packaging of gRNA is a key step for the production of infectious virus, yet, surprisingly, how HIV-1 preferentially recognizes its gRNA is poorly understood. Indeed, deciphering the molecular mechanisms governing HIV-1 gRNA packaging would further the development of antiretroviral strategies and enable the design of improved retroviral vectors. HIV-1 gRNA selection is mediated by highly specific interactions between the viral Gag protein and the Psi region in the gRNA. The assembly of the viral particle occurs at the plasma membrane. The aims of our collaborative project are i) to determine the structure of the complex formed by Gag bound to lipids mimicking the plasma membrane environment in association with the Psi RNA by cryo-EM, and ii) to investigate the role of cellular and viral ligands of Gag that might regulate the binding specificity of the precursor to gRNA. Our two teams are thus working synergically to the structure of this complex. Besides, we planned to show whether the specificity of Gag binding to gRNA is modulated by cellular (ALIX, Tsg101) or viral (Vpr) factors by comparing the binding of Gag to gRNA and spliced viral RNAs in the absence and in the presence of these ligands using biochemical and biophysical assays.

 

Keywords: HIV-1, Gag precursor, genomic RNA, protein-RNA specific interactions, viral assembly, cryo-EM

 

Relevant publications:

- Bonnard, D., Le Rouzic, E., Singer, M.R., Yu, Z., Le Strat, F., Batisse, C., Batisse, J., Amadori, C., Chasset, S., Pye, V.E., Emiliani, S., Ledoussal, B., Ruff, M., Moreau, F., Cherepanov, P., and Benarous, R. (2023). Biological and Structural Analyses of New Potent Allosteric Inhibitors of HIV-1 Integrase. Antimicrob Agents Chemother 67, e0046223, 10.1128/aac.00462-23.

- Drillien, R., Pradeau-Aubreton, K., Batisse, J., Mezher, J., Schenckbecher, E., Marguin, J., Ennifar, E., and Ruff, M. (2022). Efficient production of protein complexes in mammalian cells using a poxvirus vector. PLoS One 17, e0279038, 10.1371/journal.pone.0279038.

- Mauro, E., Lapaillerie, D., Tumiotto, C., Charlier, C., Martins, F., Sousa, S.F., Metifiot, M., Weigel, P., Yamatsugu, K., Kanai, M., Munier-Lehmann, H., Richetta, C., Maisch, M., Dutrieux, J., Batisse, J., Ruff, M., Delelis, O., Lesbats, P., and Parissi, V. (2023). Modulation of the functional interfaces between retroviral intasomes and the human nucleosome. mBio 14, e0108323, 10.1128/mbio.01083-23.

- Zinc Fingers in HIV-1 Gag Precursor Are Not Equivalent for gRNA Recruitment at the Plasma Membrane.Boutant E, Bonzi J, Anton H, Nasim MB, Cathagne R, Réal E, Dujardin D, Carl P, Didier P, Paillart JC, Marquet R, Mély Y, de Rocquigny H, Bernacchi S. Biophys J. 2020, 119(2):419-433. DOI: 10.1016/j.bpj.2020.05.035.

- The C-terminal p6 domain of the HIV-1 Pr55Gag precursor is required for specific binding to the genomic RNA. Dubois N, Khoo KK, Ghossein S, Seissler T, Wolff P, McKinstry WJ, Mak J, Paillart JC, Marquet R, Bernacchi S. RNA Biol. 2018,15(7):923-936. PMCID: PMC6161697.

- Specific recognition of the HIV-1 genomic RNA by the Gag precursor  Abd El-Wahab E. W. ,  Smyth R. P. , Mailler E. , Bernacchi S., Vivet-Boudou V. , Hijnen M. , Jossinet F.,  Mak J. ,  Paillart J.-C., Marquet R. Nat Commun. 2014 ,5:4304.   DOI: 10.1038/ncomms5304.

Regulatory RNA networks in response to biotic and abiotic stresses (LabEx NetRNA)

Architecture and Reactivity of RNA (LabEx NetRNA)

Name: Architecture and Reactivity of RNA (ARN, IBMC)

Team: Bacterial infection pathogenesis and immunity

Team leader: Benoît MARTEYN

Email: b.marteyn@ibmc-cnrs.unistra.fr

 

PhD supervisor: Patryk NGONDO

Email: patryk.ngondo@unistra.fr

Bacteria have evolved the ability to hijack host cellular processes and to dampen host defense mechanisms to their advantage. This is especially important for Shigella, a facultative-intracellular pathogenic bacterium, that invades host colonic cells to disseminate. Shigella secretes virulence factors, so far studied for their protein targeting capacity, to subvert cellular functions such as host immune defenses. Even though it is now well established that Shigella possess remarkable tools for regulating its own RNAs, Shigella’s targeting of the host transcriptome has received little attention so far. Therefore, the overall goal of this PhD thesis project will be to investigate Shigella's capacity to target and impact the fate of host RNAs rather than proteins.

The doctoral student will contribute to the project by using both genome-wide approaches and classical molecular biology techniques to study RNA-protein interactions. He/she will employ recent technological breakthroughs such as RNA metabolic labeling (Slam-seq) and protein proximity labeling (TurboID) to implement global unbiased transcriptomics and proteomics approaches. First, he/she will identify host transcripts post-transcriptionally misregulated following Shigella's invasion of cells relevant for the pathogenesis (epithelial cells, macrophages, and neutrophils). Then, using a TurboID based approach, he/she will identify RNA binding proteins, of host or bacterial origin, associated to the misregulated transcripts. Finally, using gain or loss of function approaches, he/she will assess the importance of identified factors for the Shigella pathogenesis.

 

Keywords: RNA binding proteins, post-transcriptional regulation, Shigella infection, Host gene expression regulation

 

Relevant publications:

- Shigella-mediated oxygen depletion is essential for intestinal mucosa colonization. Tinevez JY, Arena ET, Anderson M, Nigro G, Injarabian L, André A, Ferrari M, Campbell-Valois FX, Devin A, Shorte SL, Sansonetti PJ, Marteyn BS. Nat Microbiol. 2019 Nov;4(11):2001-2009. doi: 10.1038/s41564-019-0525-3.

- Shigella Diversity and Changing Landscape: Insights for the Twenty-First Century. Anderson M, Sansonetti PJ, Marteyn BS. Front Cell Infect Microbiol. 2016 Apr 19;6:45. doi: 10.3389/fcimb.2016.00045. eCollection 2016.

- The interactome of CLUH reveals its association to SPAG5 and its co-translational proximity to mitochondrial proteins. Hémono M, Haller A, Chicher J, Duchêne AM, Ngondo RP.BMC Biol. 2022 Jan 10;20(1):13. doi: 10.1186/s12915-021-01213-y.

Insect Models of Innate Immunity (LabEx NetRNA)

Name: Insect Models of Innate Immunity (M3I, IBMC)

Team: Antiviral immunity in Aedes mosquitoes

Team leader: Joao TRINADE MARQUES

Email: joao.marques@unistra.fr

 

PhD supervisor: Joao TRINADE MARQUES

Email: joao.marques@unistra.fr

Aedes aegypti mosquitoes are the major vector for many important diseases, such as Zika and dengue. Aedes mosquitoes have very high ability to acquire and transmit viruses, commonly referred to as vector competence. These mosquitoes are highly anthropophilic and display many adaptations to host seeking and human blood feeding. It is currently unknown whether host seeking cues and the changes leading to anthropophilia also affect vector competence. In this project, we will use a multi-disciplinary approach to identify and functionally characterize the connection of the olfactory system and the mechanisms used for host seeking to vector competence for viruses in Ae. aegypti mosquitoes. Combining comparative genetic, olfactory, virological and immunological analyses, we intend to address a major gap in our understanding of the impact of environmental odor sensing on the immune system and antiviral defenses. This study should shed new light on the evolution of vector competence in Ae. aegypti and could lead to the development of novel strategies to control the transmission of mosquito-borne viruses.

 

Keywords: Aedes mosquitoes, arboviruses, antiviral immunity, olfaction

 

Relevant publicaitons:

- Mosquito vector competence for dengue is modulated by insect-specific viruses. Olmo RP, Todjro YMH, Aguiar ERGR, de Almeida JPP, Ferreira FV, Armache JN, de Faria IJS, Ferreira AGA, Amadou SCG, Silva ATS, de Souza KPR, Vilela APP, Babarit A, Tan CH, Diallo M, Gaye A, Paupy C, Obame-Nkoghe J, Visser TM, Koenraadt CJM, Wongsokarijo MA, Cruz ALC, Prieto MT, Parra MCP, Nogueira ML, Avelino-Silva V, Mota RN, Borges MAZ, Drumond BP, Kroon EG, Recker M, Sedda L, Marois E, Imler JL, Marques JT. Nat Microbiol. 2023 Jan;8(1):135-149. doi: 10.1038/s41564-022-01289-4. PMID: 36604511

- Invading viral DNA triggers dsRNA synthesis by RNA polymerase II to activate antiviral RNA interference in Drosophila. de Faria IJS, Aguiar ERGR, Olmo RP, Alves da Silva J, Daeffler L, Carthew RW, Imler JL, Marques JT. Cell Rep. 2022 Jun 21;39(12):110976. doi: 10.1016/j.celrep.2022.110976. PMID: 35732126.

- 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

Molecular Biology in Plants (LabEx NetRNA)

Name: Institute of Molecular Biology in Plants (IBMP)

Team: Plant epigenetics

Team leader: Pauline JULLIEN

Email: jullien@cnrs.fr

 

PhD supervisors: Pauline JULLIEN & Philippe GIEGE

Emails: jullien@cnrs.fr & giege@unistra.fr

Plant-pathogen interactions are complex processes involving molecular and physiological changes in both the host and the pathogen. An increasing number of reports are pointing towards the role of epigenetics in plant defense against pathogens. However, the lack of spatio-temporal definition prevents us from understanding the extent of chromatin changes as well as their functions during infection. We recently showed that a bacterial virulence factor induces global changes in DNA methylation. My research group also discovered that genes encoding epigenetic factors typically expressed solely during the reproductive phase of the plant life cycle are induced by pathogen infection (abbreviated “RePat” genes). Surprisingly, mutations affecting RePat genes reduce infection. This research project focuses on the functional characterization of RePat genes during induction by virulence factors and genuine bacterial infection. We will examine the function of RePat genes during infection and assess how they alter the plant’s epigenome to benefit bacterial infection. We will use epigenomic methods, deep sequencing, bioinformatics, imaging tools, and cell-specific nuclei sorting to investigate RePat genes' cell-specific roles during infection. This will help comprehend epigenetic mechanisms behind increased resistance in RePat mutants and provide insights into infection resistance, potentially aiding in agricultural enhancement through improved plant resistance to pathogens.

 

Keywords: small RNA; DNA methylation; pseudomonas; plants

 

Relevant publications:

- Bonnet, D. M. V., Tirot, L., Grob, S. and Jullien, P. E. (2023). Methylome response to proteasome inhibition by the Pseudomonas syringae virulence factor Syringolin A. Molecular Plant-Microbe Interactions.

- Jullien, P. E., Schröder, J. A., Bonnet, D. M. V., Pumplin, N. and Voinnet, O. (2022). Asymmetric expression of Argonautes in reproductive tissues. Plant Physiol 188, 38–43.

- Tirot, L. and Jullien, P. E. (2022). Epigenetic dynamics during sexual reproduction: At the nexus of developmental control and genomic integrity. Curr Opin Plant Biol 69, 102278.

Name: Institute of Molecular Biology in Plants (IBMP)

Team: Biology and biotechnology of grapevine viruses

Team leader: Christophe RITZENTHALER

Email: ritzenth@unistra.fr

 

PhD supervisor: Christophe RITZENTHALER

Email: ritzenth@unistra.fr

RNA viruses form organized membrane-bound viral factories to replicate their genomes. This process requires virus- and host-encoded proteins and involves the production of double-stranded RNA (dsRNA) replication intermediates. A dsRNA-centered strategy performed in healthy and virus-infected Arabidopsis has allowed us to identify a small set of host proteins that may act as pro- or anti-viral factors. One candidate protein has caught our attention due to its yet unknown function despite being highly conserved during evolution in plants. Using X-ray crystallography and single-particle CryoEM, we recently showed that this protein possesses outstanding dsRNA-binding properties possibly linked to a function in innate immunity.

This PhD project aims first at deciphering the function(s) of this candidate protein in healthy plants and upon viral infection. For this, a genetic approach including CRISPR-Cas9 mutants will be exploited for phenotypic screening under various environmental conditions. Viruses deficient or not in suppression of silencing activity will also be tested. In parallel, RNA-seq data will be exploited to identify possible differences in gene expression or changes in small RNA profiles. Beyond this protein’s function, the project will also aim at elucidating the underlying molecular mechanisms using in vitro and in vivo strategies including RNase activity assays, co-immunoprecipitation and purification of native dsRNA-protein complexes for structural studies.

 

Keywords: RNA virus replication, Host-virus interactions, dsRNA-binding proteins, plant virology

 

Relevant publications:

- Incarbone, M., Clavel, M., Monsion, B., Kuhn, L., Scheer, H., Vantard, E., Poignavent, V., Dunoyer, P., Genschik, P., and Ritzenthaler, C. (2021). Immunocapture of dsRNA-bound proteins provides insight into Tobacco rattle virus replication complexes and reveals Arabidopsis DRB2 to be a wide-spectrum antiviral effector. Plant Cell 33, 3402-3420. https://www.ncbi.nlm.nih.gov/pubmed/34436604

- Incarbone, M., Scheer, H., Hily, J.M., Kuhn, L., Erhardt, M., Dunoyer, P., Altenbach, D., and Ritzenthaler, C. (2020). Characterization of a DCL2-Insensitive Tomato Bushy Stunt Virus Isolate Infecting Arabidopsis thaliana. Viruses 12, 1121. https://www.ncbi.nlm.nih.gov/pubmed/33023227

- Monsion, B., Incarbone, M., Hleibieh, K., Poignavent, V., Ghannam, A., Dunoyer, P., Daeffler, L., Tilsner, J., and Ritzenthaler, C. (2018). Efficient Detection of Long dsRNA in Vitro and in Vivo Using the dsRNA Binding Domain from FHV B2 Protein. Front Plant Sci 9, 70. https://www.ncbi.nlm.nih.gov/pubmed/29449856

Viral hepatitis and liver diseases (LabEx HepSYS)

Viral hepatitis and liver diseases (LabEx HepSYS)

Name: Institute for Viral and Liver Disease (U1110)

Team: Personalized medicine approaches for the discovery of novel therapeutic targets and biomarkers for advanced liver disease and liver cancer

Team leader: Thomas BAUMERT

Email: thomas.baumert@unistra.fr

 

PhD supervisors:  Catherine SCHUSTER (dir.), Thomas BAUMERT (co-dir.) & Emilie CROUCHET (sup.)

Emails: catherine.schuster@unistra.fr, thomas.baumert@unistra.fr & ecrouchet@unistra.fr

Fibrosis is the excessive deposition of extracellular matrix components, which results in disruption of tissue architecture and loss of organ function. It occurs during an aberrant wound healing process and shares a common pathogenesis across different organs such as the heart, liver, kidney, and lung. In developed countries, organ fibrosis accounts for up to 45% of death due to the lack of effective therapeutic strategies and is a major risk factor for tumor development across organs. A better understanding of the fibrosis mechanisms and its complications such as cancers is crucial for development of treatments.

In the liver, the major causes of fibrotic liver diseases and liver cancers are chronic hepatitis B and C, alcohol abuse, and metabolic dysfunction-associated steatohepatitis (MASH). It is estimated that up to 85-95% of liver cancer develops in fibrotic disease. Moreover, hepatocellular carcinoma (HCC) accounts for the majority of liver cancer and is a leading and fast rising cause of cancer-related death globally. Despite tremendous efforts, no approved therapy exists to treat advanced liver fibrosis and treatment options for its complications such as HCC are still unsatisfactory. Previously, we have identified a pan-etiology 186-gene clinical prognostic liver signature (PLS) in diseased liver tissues robustly predicting liver disease progression and carcinogenesis in multiple patient cohorts. Based on this study, we developed a simple and robust liver cell-based system that models the PLS, named cPLS for cell culture PLS. Our recent publications showed that the cPLS model offers unique opportunities to discover compounds for fibrotic liver disease treatment and cancers across the distinct liver cancer etiologies, in a fast-track high-throughput screening format (see relevant publications). 

Taking advantage of these discoveries and of our expertise, we aim to develop a gene signature predicting fibrosis progression to cancer across organs and to model it in vitro, using two complementary strategies. In collaboration with bioinformaticians, the candidate will participate in the identification of common fibrosis drivers between idiopathic pulmonary fibrosis, kidney fibrosis and advanced liver fibrosis by integrating transcriptomics, proteomics, and clinical data from fibrotic patients.

 In parallel, the candidate will establish novel cell-based systems modeling fibrosis. Previous studies had already suggested that certain cancer cell-based models share signaling pathways with different cell types (e.g. NIH LINCS program, https://clue.io/). The aim of the PhD candidate will be to develop and characterize triculture models using epithelial cell lines, fibroblast and macrophages in 2D and 3D systems and fibrotic cocktails to mimic fibrogenic responses. Fibrogenic process will be analyzed in these systems by RNA-Seq and Nanostring technologies to refine the fibrosis signature.

To discover novel compounds for fibrosis across-organs, the best models will be selected to perform drug screening and perturbations studies using CRISPR-Cas9 technology. Effect of the top compound and mechanism of action will be validated using cutting edge technologies already developed in our lab such as patient-derived models (organoids, spheroids…), state-of-the-art animal models for fibrosis and spatial transcriptomic.

The candidate will work in a multidisciplinary and enriching international environment, in synergy with surgeons, clinicians, cell and molecular biologists and bioinformaticians. She/he will acquire expertise in cell and molecular biology and in bio-informatic and will build expertise in translational medicine and drug discovery.

 

Keywords: Chronic liver disease, Gene signature, Drug discovery, cell culture systems.

 

Relevant publications:

- Crouchet E, Li S, Sojoodi M, Bandiera S, Fujiwara N, El Saghire H,…, Hoshida Y, Fuchs BC, Baumert TF. Hepatocellular carcinoma chemoprevention by targeting the angiotensin-converting enzyme and EGFR transactivation. JCI Insight. 2022 Jul 8; 7(13):e159254.

- Crouchet E, Bandiera S, Fujiwara N, Li S, El Saghire H,…, Heikenwälder M, Schuster C, Pochet N, Zeisel MB, Fuchs BC, Hoshida Y, Baumert TF. A human liver cell-based system modeling a clinical prognostic liver signature for therapeutic discovery. Nat Commun. 2021 Sep 17;12(1):5525.

- Jühling, F. et al. Targeting clinical epigenetic reprogramming for chemoprevention of metabolic and viral hepatocellular carcinoma. Gut 70, 157–169 (2021).

Viral hepatitis and liver diseases (LabEx HepSYS)/Integrative Biology - Nuclear Dynamics, Regenerative and Translational Medicine (LabEx INRT)

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

Name 1: Institute for Translational Medicine and Liver Diseases (ITM)

Team 1: Signaling in liver disease

Team leader: Joachim LUPBERGER

Email: joachim.lupberger@unistra.fr

 

Name 2: Institute of Genetics, Molecular and Cellular Biology (IGBMC)

Team 2: Genome expression and repair

Team leader: Frédéric COIN

Email: fredr@igbmc.fr

 

PhD supervisors: Joachim LUPBERGER & Frédéric COIN

Emails: joachim.lupberger@unistra.fr & fredr@igbmc.fr

Hepatitis D virus (HDV) causes a severe form of chronic liver injury, which progresses rapidly lead to liver complications, cancer, and death. In pilot experiments, we identified an HDV-specific transcriptional signature in the livers of infected human liver chimeric mice and profiled posttranslational histone modifications. As the HDV-infected animals show signs of liver fibrosis and perturbed hepatic DNA repair, we hypothesize that these epigenetic signatures exert a key role in the development of liver fibrosis and cancer.

The PhD thesis aims to identify the mechanism of this epigenetic viral imprinting during chronic HDV infection and its impact on DNA repair and cancer risk. Thereto, the candidate will apply perturbations studies (i.e., RNAi, CRSIP, small molecules) on infection and liver disease models in vitro to study the role of candidate drivers of HDV signatures for disease progression and cancer. Moreover, the candidate will study the impact of HDV on DNA repair components, particularly transcription factor II H (TFIIH), using recombinant expression technology and enzymatic assays. Key technologies, samples, and protocols are already established and available in the teams of both supervisors.

The research program and the embedded thesis project will have a major impact for HDV-infected patients by advancing the knowledge of HDV-associated liver complications, novel preventive strategies to attenuate liver complications in these patients, and novel biomarkers for liver disease.

 

 

Keywords: chronic hepatitis delta, virus, DNA repair, fibrosis, cancer, epigenetics

 

Relevant publications:

- Van Renne N, Roca Suarez AA, Duong FHT, Gondeau C, Calabrese D, Fontaine N, Ababsa A, Bandiera S, Croonenborghs T, Pochet N, De Blasi V, Pessaux P, Piardi T, Sommacale D, Ono A, Chayama K, Fujita M, Nakagawa H, Hoshida Y, Zeisel MB, Heim MH, Baumert TF, Lupberger J. miR-135a-5p-mediated downregulation of protein tyrosine phosphatase receptor delta is a candidate driver of HCV-associated hepatocarcinogenesis. Gut. 2018;67(5):953-962. (IF= 31.795)

- Lupberger J, Croonenborghs T, Roca Suarez AA, Van Renne N, Jühling F, Oudot MA, Virzì A, Bandiera S, Jamey C, Meszaros G, Brumaru D, Mukherji A, Durand SC, Heydmann L, Verrier ER, El Saghire H, Hamdane N, Bartenschlager R, Fereshetian S, Ramberger E, Sinha R, Nabian M, Everaert C, Jovanovic M, Mertins P, Carr SA, Chayama K, Dali-Youcef N, Ricci R, Bardeesy NM, Fujiwara N, Gevaert O, Zeisel MB, Hoshida Y, Pochet N, Baumert TF. Combined Analysis of Metabolomes, Proteomes, and Transcriptomes of Hepatitis C Virus-Infected Cells and Liver to Identify Pathways Associated With Disease Development. Gastroenterology. 2019;157(2):537-551.e9. (IF= 33.883)

- Roehlen N, Saviano A, El Saghire H, Crouchet E, Nehme Z, Del Zompo F, Jühling F, Oudot MA, Durand SC, Duong FHT, Cherradi S, Gonzalez Motos V, Almeida N, Ponsolles C, Heydmann L, Ostyn T, Lallement A, Pessaux P, Felli E, Cavalli A, Sgrignani J, Thumann C, Koutsopoulos O, Fuchs BC, Hoshida Y, Hofmann M, Vyberg M, Viuff BM, Galsgaard ED, Elson G, Toso A, Meyer M, Iacone R, Schweighoffer T, Teixeira G, Moll S, De Vito C, Roskams T, Davidson I, Heide D, Heikenwälder M, Zeisel MB, Lupberger J, Mailly L, Schuster C, Baumert TF. A monoclonal antibody targeting nonjunctional claudin-1 inhibits fibrosis in patient-derived models by modulating cell plasticity. Sci Transl Med. 2022;14(676):eabj4221. (IF= 17.100)

- Berico, P., Nogaret, M., Cigrang, M., Lallement, A., Vand-Rajabpour, F., Flores-Yanke, A., Gambi, G., Davidson, G., Seno, L., Obid, J., Bujamin H., V, Stephanie Le Gras, Gabrielle Mengus, Tao Ye, Carlos Fernandez Cordero, Mélanie Dalmasso, Emmanuel Compe, Corine Bertolotto, Eva Hernando, Irwin Davidson, Coin. F*. 2023. Super-enhancer-driven expression of BAHCC1 promotes melanoma cell proliferation and genome stability. Cell Reports, Nov 2;42(11):113363. DOI: 10.1016/j.celrep.2023.113363.

- Sandoz, J., Cigrang, M., Zachayus, A., Catez, P., Donnio L.M., Elly, C., Nieminuszczy, J., Berico, P., Braun, C., Alekseev, S., Egly, J.M., Niedzwiedz W., Mari-Giglia, G., Compe, E., and Coin, F*. 2023. Active mRNA degradation by EXD2 nuclease elicits recovery of transcription after genotoxic stress. Nature Communications, Jan 20;14(1):341. doi: 10.1038/s41467-023-35922-5.

- Alekseev, S., Nagy, Z., Sandoz, J., Weiss, A., Egly, J.M., Le May, N., Coin, F*., 2017. Transcription without XPB Establishes a Unified Helicase-Independent Mechanism of Promoter Opening in Eukaryotic Gene Expression. Molecular Cell 65, 504-514 e4. https://doi.org/10.1016/j.molcel.2017.01.012.