IMCBio International PhD Program

The acto-myosin cytoskeleton shapes cells and tissues. They direct the formation of embryos such as C. elegans, Drosophila, mouse as well as the structures of single cells and tissues in vitro. Their physics has been described with the active gel descriptions. However, their regulations by the small Rho GTPases were missing so far although they are known to be essential.
The Riveline team is involved in an international network with scientists from the field aiming at understanding the self-organisation rules of these regulated active gels, i.e. acto-myosin cytoskeleton under the regulation of the small Rho GTPases. We compare cells in vitro, cells in vivo, and theory in an integrated manner. We use microfabrication, cell biology, quantitative imaging and theory to characterize their generic rules of self-organisations.
The PhD will consist in designing new directions to study these regulated active gels with controlled conditions. Acto-myosin cytoskeleton structures and their regulations by Rho GTPases will be monitored by live microscopy, quantitative biology and cryo-EM tomography. Stress generation will be evaluated in each situation from molecular to mesoscopic scales. The topic could be oriented to different directions depending on the background and tastes of the applicant.
Collaborations have started along these directions and they will continue with Florian Faessler (IGBMC) for cryo-EM and Karsten Kruse (Geneva University) for theoretical physics.

Keywords: cytoskeleton, acto-myosin, polarity, biological physics, cryo-EM

Relevant publications:

- Linjie Lu, Tristan Guyomar, Quentin Vagne, Rémi Berthoz, Alejandro Torres-Sánchez, Michèle Lieb, Cecilie Martin-Lemaitre, Kobus van Unen, Alf Honigmann, Olivier Pertz, Daniel Riveline*, Guillaume Salbreux*, Polarity-driven three-dimensional spontaneous rotation of a cell doublet, Nature Physics 20, 1194–1203 (2024).
- Karsten Kruse*, Rémi Berthoz, Luca Barberi, Anne-Cécile Reymann, Daniel Riveline*, Acto-myosin clusters as active units shaping living matter, Current Biology 34, 1045-1058 (2024).
- V. Wollrab, R. Thiagarajan, A. Wald, K. Kruse, D. Riveline, Still and rotating myosin clusters determine cytokinetic ring constriction. Nat. Commun. 7, 11860 (2016).
 

Financial support of this subject is allocated by the Research Cluster / LabEx INRT based on applicant's merit.

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:

- Classification of human actin pathological variants using C. elegans CRISPR-generated models. Hecquet T., Arbogast N., Suhner D., Goetz A., Amann G., Yürekli S., Marangoni F., S. Quintin, N. Greve J., Di Donato N., Reymann AC, iScience, Ocober 2025, https://doi.org/10.1016/j.isci.2025.113652

- In vivo detection of ALFA-tagged proteins in C. elegans with a transgenic fluorescent nanobody. Quintin S, Saad MI, Amann G, Reymann AC. MicroPubl Biol. 2025 Apr 18;2025:10.17912/micropub.biology.001542. doi: 10.17912/micropub.biology.001542.

- The kinesin Kif21b regulates radial migration of cortical projection neurons through a non-canonical function on actin cytoskeleton. Rivera RA, Asselin L, Tilly P, Benoit R, Batisse C, Richert L, Batisse J, Morlet B, Levet F, Schwaller N, Mély Y, Ruff M, Reymann AC, Godin J, Cell Reports, July 2023. doi: 10.1016/j.celrep.2023.112744

Financial support of this subject is allocated by the Research Cluster / LabEx INRT based on applicant's merit.

This project explores how the brain regulates energy balance and metabolism through molecular mechanisms linking neuronal calcium signaling to feeding behavior. Energy homeostasis depends on hypothalamic circuits that integrate hormonal and nutritional cues to control appetite and energy expenditure. Dysregulation of these systems contributes to obesity and type 2 diabetes.

Our previous work identified CaMK1D, a gene associated with type 2 diabetes, as a key regulator in AgRP neurons, modulating responses to fasting and hormones such as ghrelin. This reveals a signaling pathway connecting neuronal activity to metabolic regulation.

The project combines molecular, imaging, and physiological approaches to study how calcium-dependent mechanisms shape hypothalamic control of metabolism. In vivo studies in diet-induced obesity models will assess how manipulating this pathway affects feeding behavior and energy expenditure.

Conducted at IGBMC, a world-leading institute in neuroscience and metabolic research, this project offers an exceptional environment for training in cutting-edge techniques, interdisciplinary collaboration, and high-impact research. By linking cellular signaling to whole-body energy homeostasis, it aims to uncover novel therapeutic targets for obesity and metabolic disorders, providing an exciting opportunity to contribute to translational neuroscience research.

Keywords: Energy Homeostasis, Hypothalamus, Calcium Signaling, AgRP Neurons, Obesity

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

Financial support of this subject is allocated by the Research Cluster / LabEx INRT based on applicant's merit.

The immense contractile force generated by skeletal muscle is transmitted and dissipated at the muscle–tendon junction (MTJ), a highly specialized interface between muscle and tendon. This site is particularly vulnerable to injury during exercise, and its architecture undergoes significant remodeling with sustained physical activity and ageing. Understanding how the unique cellular structure and function of the MTJ are established and regulated is therefore of fundamental importance.

Our previous single-nucleus RNA sequencing (snRNA-Seq) studies revealed that myonuclei positioned at the MTJ adopt a distinct transcriptomic identity compared to other myonuclei within the same muscle fiber. Interestingly, these transcriptomes remained largely unchanged despite structural remodeling and functional improvement after exercise, pointing to a critical role for post-transcriptional regulation.

To address this, our team has developed innovative genetic and molecular tools to selectively profile the translatome and manipulate gene expression at the MTJ. This PhD project aims to: (i) map translational changes in the MTJ during exercise and ageing, (ii) elucidate how specific transcripts are selected for local translation, and (iii) identify tendon-derived signals that regulate this process. This work will uncover new mechanisms of subcellular specialization and muscle adaptation.

Keywords: skeletal muscle, protein translation, muscle-tendon junction, ageing, exercise

Relevant publications:

- Kim, M*., Franke, V*., Brandt, B., Lowenstein, E.D., Schowel, V., Spuler S., Akaline, A., and Birchmeier, C. (2020) Single-nucleus transcriptomics reveals functional compartmentalization in syncytial skeletal muscle cells. Nature Communications. 11, 6375. *, co-first authors.

- Cristofer Calvo*, Coalesco Smith*, Taejeong Song, Sakthivel Sadayappan, Douglas P. Millay# and Minchul Kim#. Loss of Ufsp1 does not cause major changes at the neuromuscular junction. Plos One. *, co-first authors. #, co-correspondence.

- Kim, M*., Wende, H.,*, Walcher, J., Cheret, C., Kempa, S., Lewin, G., and Birchmeier, C. (2018) Maf links Neuregulin1 signaling to cholesterol synthesis in myelinating Schwann cells. Genes & Development. 2018. May 1;32(9-10):645-657. (Cover paper). *, co-first authors.

Financial support of this subject is allocated by the Research Cluster / LabEx INRT based on applicant's merit.

During immune responses, B cells diversify their immunoglobulin (Ig) genes through somatic hypermutation (SHM) and class switch recombination (CSR), processes that refine antibody affinity and alter isotype without changing antigen specificity. SHM introduces mutations into Ig variable regions, generating clonal variants selected for improved antigen binding. CSR recombines the Ig heavy chain variable region with distinct constant regions, switching the expressed antibody from IgM to IgG, IgE, or IgA.

Both reactions are initiated by Activation-Induced Cytidine Deaminase (AID), which deaminates cytosines in DNA. The resulting uracils are recognized mainly by Uracil-DNA glycosylase (Ung), leading to mutations during SHM or double-strand breaks during CSR.

Despite extensive studies, how AID-induced lesions are funneled to an error-prone DNA repair pathway remains unclear. Through a genome-wide CRISPR/Cas9 screen, we identified Fam72a as a key regulator of this balance. Fam72a controls UNG2, the nuclear isoform of Ung, by limiting its protein levels (Rogier et al. Nature. 2021 ; rdcu.be/cBYhU)

Building on these findings, we will perform a focused CRISPR screen targeting genes encoding Fam72a- and UNG2-interacting proteins (identified by co-immunoprecipitation and mass spectrometry) using an UNG2–EGFP knock-in B cell line. Promising hits will be individually disrupted to explore their mechanistic roles. Finally, we aim to generate conditional knockout mouse models to dissect candidate gene functions 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).

Thomas-Claudepierre, A.S., et al. Mediator facilitates transcriptional activation and dynamic long-range contacts at the IgH locus during class switch recombination. J Exp Med 213, 303-312 (2016).

Financial support of this subject is allocated by the Research Cluster / LabEx INRT based on applicant's merit.

Transcription factors are key molecular determinants of cellular identity during development and in human diseases. They interpret our genome via recognition of specific DNA sequences, resulting in target genes being switched ‘on’ or ‘off’. Our recent research revealed a new type of gene regulation based on sensing of A/T nucleotide content (Pantier et al, 2021). In particular, the transcription factor SALL4 binds to short AT-rich motifs on the genome, and its function is essential for stem cell identity in vitro and embryonic development in vivo.

In this PhD project, you will exploit state-of-the-art genomics techniques in genetically engineered embryonic stem cells to dissect the molecular function of SALL4: regulation of transcription via long range enhancer-promoter looping (1), regulation of 3D genome structure via modulation of lamina-associated domains (2). These investigations will help us better understand how transcription factors interact across different genomic scales in order to control cell identity.

Keywords: embryonic stem cells, transcription, genome architecture, transcription factors, SALL4, CRISPR/Cas9 engineering, next-generation sequencing

Relevant publications:

- R. Pantier, K. Chhatbar, T. Quante, K. Skourti-Stathaki, J. Cholewa-Waclaw, G. Alston, B. Alexander-Howden, H.Y. Lee, A.G. Cook, C.G. Spruijt, M. Vermeulen, J. Selfridge, A. Bird, SALL4 controls cell fate in response to DNA base composition, Molecular Cell 81 (2021) 845–858. https://doi.org/10.1016/j.molcel.2020.11.046

- J.A. Watson*, R. Pantier*, U. Jayachandran, K. Chhatbar, B. Alexander-Howden, V. Kruusvee, M. Prendecki, A. Bird, A.G. Cook, Structure of SALL4 zinc finger domain reveals link between AT-rich DNA binding and Okihiro syndrome, Life Science Alliance 6 (2023) e202201588. *Co-fist authorship. https://doi.org/10.26508/lsa.202201588

- T. Quante, A. Bird, Do short, frequent DNA sequence motifs mould the epigenome?, Nat Rev Mol Cell Biol 17 (2016) 257–262. https://doi.org/10.1038/nrm.2015.31

Financial support of this subject is allocated by the Research Cluster / LabEx INRT based on applicant's merit.

This project aims to identify the epigenetic mechanisms that control the diversification of macrophages using the model of Drosophila melanogaster. Macrophages are innate immune cells known for phagocytosing debris and pathogens, acting as first responders during embryonic development, and continuing to serve important roles in various tissues into adulthood. Their responses in diseases, such as neurodegenerative disorders and cancers, can either help or worsen symptoms, depending on their behaviour, which is influenced by their environmental conditioning and previous immune challenges. Studies have shown that macrophages can retain a "memory" of immune challenges, affecting their future responses.

Previous work by the laboratory has characterized macrophages at different developmental stages, showing their diversification, which includes chromatin remodelling. The project will examine how the epigenetic landscape of macrophages changes from the embryonic to larval stages using single-cell ATACseq data and will characterize the molecular mechanisms behind the development of macrophage subpopulations, focusing on the impact of a key transcription factor, Gcm, and its interactions with non-coding RNA (ncRNA) on the chromatin remodelling.

The findings of this study will provide deeper insights into the molecular mechanisms regulating macrophage diversification, will lead to future researches on macrophage behaviour in pathological conditions like infections and cancer as well as on the role of ncRNA in the mammalian macrophages.

Keywords: Drosophila, macrophage, non coding RNA, 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.

Financial support of this subject is allocated by the Research Cluster / LabEx INRT based on applicant's merit.

Eukaryotic DNA is compacted by assembly into chromatin. Processes like gene transcription and DNA damage response (DDR) require localized changes in chromatin compaction. The mammalian SWI/SNF complex (mSWI/SNF), a multisubunit ATP‐dependent chromatin remodeling complex that slides or evicts nucleosomes from the chromatin fibre is in part responsible for regulating DNA accessibility in these contexts. The importance of mSWI/SNF in human health is underscored by the fact that its deregulation, by point mutations or misexpression, is associated to numerous diseases including cancer. Consequently, it is of paramount importance to fully understand at the molecular level how mSWI/SNF functions, but this goal has not been attained yet. mSWI/SNF comprises recently identified ‘auxiliary’ subunits, the molecular function and atomic structure of which remain largely unknown. Mounting evidence shows that those genes deregulation (mutations or alterations in expression levels) have an important impact on cancer, but the molecular basis explaining their relationship to cancer remains unknown. By using a combination of cryo-EM, biochemistry, live cell imaging and genomic, we aim to gain a better understanding of the function of the auxiliary subunits within the SWI/SNF complex. The project is expected to establish phenotype-genotype-therapy correlations, identify novel drug targets and provide structural insights into mutants SWI/SNF complexes. Ultimately this project will bridge fundamental chromatin biology with translational oncology, paving the way for precision medicine strategies.

Keywords:

Relevant publications: chromatin remodeling, disease, molecular mechanism

Financial support of this subject is allocated by the Research Cluster / LabEx INRT based on applicant's merit.

The cohesin complex is a major player in the 3D organization of eukaryotic genomes and is involved in sister chromatid cohesion, chromosome segregation, DNA replication and repair, and the regulation of gene transcription. Mutations in cohesin are found in numerous cancers and cause neurodevelopmental diseases called cohesinopathies, such as the Cornelia de Lange Syndrome (CdLS).
Cohesin’s functions are entirely dependent on its ATPase activity. How this activity contributes to cohesin's functions remains poorly understood. We have identified specific mechanisms underlying the cohesin ATPase cycle as well as specific regions and residues within the cohesin ATPase domain that are essential for this activity (Vitoria Gomes et al., 2024; doi:10.1016/j.celrep.2024.114656).
The proposed thesis project will study in detail the impact of the characterized regions and residues on cohesin's ATPase activity. Mutants of these regions and residues, but also mutants from CdLS patients, will be tested for their ability to bind ATP, form the ATPase domain, and hydrolyze ATP. These studies will be complemented by structural analyses by cryo-EM to understand the conformational impacts of these regions and residues on cohesin. This project will further be complemented by studies of these mutants by our collaborators through genome-wide analyses in iPSCs and using the zebrafish.

Keywords: Cohesin, ATPase, SMC complexes, Sister chromatid cohesion, Chromatin loops

Relevant publications:

- Vitoria Gomes et al. (2024) The cohesin ATPase cycle is mediated by specific
conformational dynamics and interface plasticity of SMC1A and SMC3 ATPase
domains. Cell Rep., 43, 114656. doi: 10.1016/j.celrep.2024.114656.
- Marek et al. (2021) Species-selective targeting of pathogens revealed by the atypical structure and active site of Trypanosoma cruzi histone deacetylase DAC2. Cell Rep., 37, 110129. doi: 10.1016/j.celrep.2021.110129.
- Ramos-Morales et al. (2021) The structure of the mouse ADAT2/ADAT3 complex reveals the molecular basis for mammalian tRNA wobble adenosine-to-inosine deamination. Nucl. Acids Res., 49, 6529-6548. doi: 10.1093/nar/gkab436.

Financial support of this subject is allocated by the Research Cluster / LabEx INRT based on applicant's merit.

Eukaryotic ribosomes are complex molecular machines whose assembly is tightly controlled to ensure faithful protein biosynthesis. Ribosome assembly is initiated in the nucleolus by the transcription and processing of ribosomal RNAs, which together with ribosomal proteins form pre-60S ribosomal particles. The pre-60S particles mature by transiently interacting with various assembly factors during cytosolic export. The nearly 5000 residues long maturation factor Rea1 is vital for the export of the pre-60S particles. Rea1 belongs to the AAA+ protein family and harnesses the energy of ATP hydrolysis to remove assembly factors from pre-60S particles. ATP hydrolysis in the Rea1 hexameric AAA+ ring drives the remodeling of the ≈1700aa linker extension of the AAA+ ring, which in turn creates the mechanical force for assembly factor removal. Rea1 mechanism is poorly, despite its key importance for ribosome maturation. We have recently characterized ATP dependent linker remodeling by low-resolution negative stain electron microscopy. In this project, we aim for high-resolution cryoEM investigations on ATP dependent Rea1 linker remodeling. The PhD student will be trained in the recombinant expression and purification of Rea1 mutants as well as in state-of-the-art cryoEM. These structural investigations will be complemented by in-vitro as well in-vivo activity assays carried out in collaboration with external partners. He/she will also learn to work in a highly international environment and to develop project management skills. Furthermore, presentation skills will be acquired due to regular progress meetings and the attendance of international conferences.

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

Relevant publications:

- Remodelling of Rea1 linker domain drives the removal of assembly factors from pre-ribosomal particles. Busselez J, Koenig G, Dominique C, Klos T ,Velayudhan D, Sosnowski P, Marechal N, Crucifix C,  ,Gizardin-Fredon H ,Cianferani S, Benjamin A, Henry Y, Anthony H, Schmidt H. Nat Commun 2024

- The CryoEM structure of the Saccharomyces cerevisiae ribosome maturation factor Rea1. Sosnowski P, Urnavicius L, Boland A, Fagiewicz R, Busselez J, Papai G, Schmidt H. Elife 2018.

- Structure of human cytoplasmic dynein-2 primed for its power stroke. Schmidt H, Zalyte R, Urnavicius L, Carter AP. Nature 2015.

Financial support of this subject is allocated by the Research Cluster / LabEx INRT based on applicant's merit.

Type 2 DNA topoisomerases (Topo2) control DNA topology during replication, transcription and chromosome segregation. Essential for cell proliferation, these enzymes serve as targets for various classes of antineoplastic agents used in current cancer therapies. Resistance or non-response to cancer treatments highlights the need for personalized therapeutic strategies and a deeper understanding of their mechanisms of action.

We obtained high resolution cryoEM reconstruction of the human Topo2a isoform, in complex with DNA and anti-cancer molecules (Vanden Broeck et al, Nat. Comm 2021). Recent results from our team on the homologous bacterial enzyme showed that forming nucleoprotein complexes requires the use of more physiologically-relevant DNA substrates to capture functional conformational states (Vayssieres et al, Science 2024; Vanden Broeck et al, Nat. Comm 2019). The Topo2 are part of large complexes associated with chromatin factors and regulated by post-translational modifications (Bedez et al, Sci. Rep. 2018; Lotz et al., Can. Drug. Resist. 2020, Mazzoleni et al., J Mol Biol 2025 ahead of print). This thesis proposal aims at providing functional and structural knowledge on the enzymatic mechanisms and on cellular complexes of Topo2 in the context of chromatin. Our team has established international collaborations on complementary technologies, and cellular models to investigate the molecular architecture of Topo2 cellular complexes, as well as the interplay between drug resistance and the post-translational modifications of the Topo2.

Keywords: DNA topoisomerase, chromatin, Structural biology, cancer

Relevant publications:

- Vayssières M, Marechal N., Yun L., Lopez Duran  B., Murugasamy NK, Fogg  JM, Zechiedrich L., Nadal M., Lamour V. (2024). Structural basis of DNA crossover capture by Escherichia coli DNA gyrase. Science,384(6692):227-232. doi: 10.1126/science.adl5899.

- Vanden Broeck A, Lotz C, Drillien R, Bedez C, Lamour V (2021). Structural basis for the allosteric regulation of Human Topoisomerase 2α. Nat. Commun. 12, 2962. https://doi.org/10.1038/s41467-021-23136-6.

- Vanden Broeck A, Lotz C, Ortiz J, Lamour V. (2019) Cryo-EM structure of the complete E. coli DNA gyrase nucleoprotein complex. Nat. Commun., 10, 4935. https://doi.org/10.1038/s41467-019-12914-y.

Financial support of this subject is allocated by the Research Cluster / LabEx INRT based on applicant's merit.

The intricate cognitive functions of the cerebral cortex stem from a diverse network of neurons and glial cells, all generated from a uniform pool of progenitors during corticogenesis. This project seeks to elucidate how these progenitors sequentially produce distinct neuronal and glial progeny over time, shaping brain development.

While transcriptional programs have been recognized as key drivers of neuronal diversity, emerging evidence indicates that certain neuronal mRNAs are present in progenitor cells long before their corresponding proteins appear. This observation suggests that translation mechanisms may play a pivotal role in defining cell identity, alongside transcription.

We propose that dynamic regulation of tRNA pools significantly influences translation during cortical patterning, affecting progenitor competency. Our preliminary findings indicate that tRNA availability varies across cell types and developmental stages in the mouse cortex. Through cutting-edge cell labelling and sequencing techniques (tRNA sequencing, quantitative measurement of translation efficiency), the PhD candidate will resolve the tRNAs repertoires in neurons as they migrate and mature and determine whether tRNA fluctuation correlates with specific change in translational programs during cortical lineage differentiation.

By uncovering these mechanisms, this project not only advances our understanding of neural diversity but also has potential implications for neurodevelopmental disorders.

Keywords: brain development, neuronal diversity, translation, omic analysis, transfer RNA

Relevant publications:

- Del-Pozo-Rodriguez J, et al. ADAT3 variants disrupt the activity of the ADAT tRNA deaminase complex and impair neuronal migration. Brain (2025) 10.1093/brain/awaf109

- Bayam E et al.  Bi-allelic variants in WDR47 cause a complex neurodevelopmental syndrome. EMBO Mol Med (2024) 10.1038/s44321-024-00178-z.

- Ramos-Morales E et al. The structure of the mouse ADAT2/ADAT3 complex reveals the molecular basis for mammalian tRNA wobble adenosine-to-inosine deamination. Nucleic Acids Res (2021) 49: 6529-6548

Financial support of this subject is allocated by the Research Cluster / LabEx INRT based on applicant's merit.

Chikungunya virus (CHIKV) is an emerging mosquito-borne virus responsible for severe and persistent musculoskeletal pain. Although skeletal muscle has been identified as a key target tissue where the virus establishes pathology, how individual CHIKV proteins interact with and perturb host muscle factors remains poorly understood.

This PhD project aims to investigate the direct impact of individual CHIKV proteins on skeletal muscle in the absence of infection, enabling the identification of host pathways targeted by these viral factors without the confounding effects of viral replication. To do so, the PhD student will acquire broad training at the interface of cell biology and infection biology by a) generating and characterizing mouse models expressing individual CHIKV proteins in vivo using muscle-specific AAV delivery and b) validating key findings in primary cells infected with CHIKV.

The project is linked to an ANRS-funded study coordinated by Dr. Kim, who will provide expertise in muscle biology and in vivo model development. Dr. Pfeffer/Dr Girardi’s team will contribute with a complementary expertise in molecular virology and provide BSL3 infrastructure to validate the most relevant findings using primary murine cells for CHIKV infections.

Building on this collaborative framework, this interdisciplinary PhD project aims to:
(i) comprehensively map the interactome of CHIKV proteins with host factors in skeletal muscle,
(ii) characterize the localization and pathogenic impact of individual viral proteins, and (iii) integrate bioinformatics to identify key host pathways and therapeutic targets.

Keywords: Skeletal muscle, chikungunya virus, host-pathogen interaction

Relevant publications:

- Kim, M*., Franke, V*., Brandt, B., Lowenstein, E.D., Schowel, V., Spuler S., Akaline, A., and Birchmeier, C. (2020) Single-nucleus transcriptomics reveals functional compartmentalization in syncytial skeletal muscle cells. Nature Communications. 11, 6375. *, co-first authors.

- Cristofer Calvo*, Coalesco Smith*, Taejeong Song, Sakthivel Sadayappan, Douglas P. Millay# and Minchul Kim#. Loss of Ufsp1 does not cause major changes at the neuromuscular junction. Plos One. *, co-first authors. #, co-correspondence.

- Kim, M*., Wende, H.,*, Walcher, J., Cheret, C., Kempa, S., Lewin, G., and Birchmeier, C. (2018) Maf links Neuregulin1 signaling to cholesterol synthesis in myelinating Schwann cells. Genes & Development. 2018. May 1;32(9-10):645-657. (Cover paper). *, co-first authors.

- Messmer M, Pierson L, Pasquier C, Djordjevic N, Chicher J, Hammann P, Pfeffer S, Girardi E (2024). DEAD box RNA helicase 5 is a new pro-viral host factor for Sindbis virus infection. Virol J. 21(1):76.

- Girardi E#, Messmer M, Lopez P, Fender A, Chicher J, Chane-Woon-Ming B, Hammann P, Pfeffer S# (2023). Proteomics-based determination of double-stranded RNA interactome reveals known and new factors involved in Sindbis virus infection. RNA 29(3):361-375. #, co-correspondence.

- López, P.*, Girardi, E.*, #, Mounce, B.C., Weiss, A., Chane-Woon-Ming, B., Messmer, M., Kaukinen, P., Kopp, A., Bortolamiol-Becet, D., Fendri, A., Vignuzzi M, Brino L, Pfeffer S#. (2020). High-Throughput Fluorescence-Based Screen Identifies the Neuronal MicroRNA miR-124 as a Positive Regulator of Alphavirus Infection. J. Virol. 94, e02145-19. *, co-first authors. #, co-correspondence.

Financial support of this subject is allocated by the IMCBio Graduate School based on applicant's merit.

Shigella is a facultative intracellular bacterium that invades colonic epithelial cells and manipulates host cellular processes to promote infection. While its protein-targeting virulence strategies are well described, the impact of Shigella infection on the host transcriptome—particularly at the post-transcriptional level—remains poorly explored. Preliminary data indicate that Shigella affects host RNA metabolism at both transcriptional and post-transcriptional stages, highlighting RNA regulation as a key but underexplored aspect of infection biology.
This PhD project aims to identify and characterize host and bacterial trans-acting factors involved in post-transcriptional RNA regulation during Shigella infection. The future PhD candidate will first select and identify post-transcriptionally deregulated mRNA targets using cultured epithelial cells infected with Shigella flexneri 2a. Next, proteomics approaches such as TurboID will be employed to identify RNA-binding proteins associated with the selected transcripts. These transcripts will be specifically targeted using CRISPR–dCas13 or the MS2 stem-loop system to dissect RNA–protein interactions and validate the underlying regulatory mechanisms. Finally, gain- or loss-of-function studies will assess the
contribution of these factors to Shigella pathogenesis.
Combining RNA-seq, RIP-seq, CRISPR-based RNA targeting, and global proteomics, this exploratory project will uncover novel post-transcriptional mechanisms shaping host responses during bacterial infection.

Keywords: RNA-binding proteins, post-transcriptional regulation, Shigella infection, RNAseq, RIP-seq, TurboID, CRISPR–dCas13, MS2

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.

Financial support of this subject is guaranteed by the Research Cluster / LabEx NetRNA.