Cilia-AI will train a new generation of multidisciplinary biomedical researchers and entrepreneurs, and those specializing in emerging machine learning technologies, a subset of AI. The focus is the study of primary cilia, microtubule-based projections on cell surfaces that play a pivotal role in coordinating cellular signalling pathways during development and homeostasis of cells, tissues and organs. These tiny structures are essential for various physiological functions such as hearing, smell, respiration, excretion and reproduction. Dysfunctional cilia can lead to >35 severe human diseases known as ciliopathies, exhibiting diverse and overlapping phenotypes, affecting up to 1 in 400 people. To unravel the multi-level organisation and regulation of cilia in health and disease, Cilia-AI employs a multidisciplinary approach, integrating cutting edge technologies like structural biology, omics- and organoid technologies. Advanced imaging techniques, including super-resolution microscopy, cryo-electron tomography and expansion microscopy, will be used to generate high-resolution and versatile datasets. Processing such data requires sophisticated computational methods. Cilia-AI is at the forefront of implementing and developing machine learning approaches to decipher these high-content datasets and integrate diverse multidisciplinary data. Cilia-AI offers unparalleled training opportunities for 14 Doctoral Candidates (DCs) in both academic and industrial settings. The training involves individual research projects, secondments, and network-wide sessions. This training equips DCs with skills attractive to both industrial and academic sectors, enhancing their career prospects in these domains. Overall, Cilia-AI’s research and training activities contribute to advancing the understanding of cilia in health and disease while fostering a new generation of skilled professionals with broad competences.

Coeliac disease is a chronic autoimmune-like enteropathy induced by dietary gluten in 0.5-2% Europeans. A rare but specific complication is the onset of invasive enteropathy-associated lymphomas. The host laboratory has demonstrated that in approximately 70% of CD patients, invasive lymphomas are preceded by a clonal low-grade intraepithelial lymphoproliferation, usually called type II refractory CD (RCDII). I intend to take advantage of my experience in cellular immunology and single-cell analyses: 1- to analyse the peri-tumor microenvironment and search for anti-tumoral T cell response in RCDII; and 2- to analyse the functional intra-clonal heterogeneity among RCDII malignant cells. The results should provide further insight into the mechanisms, which control disease progression and will help us to assess therapeutic strategies. This project will complete and extend the on-going genomic analysis of lymphomas complicating CD. It will notably help to assess if the JAK1/STAT3 pathway is a pertinent therapeutic target and the possible interest of checkpoint inhibitors. To achieve the aims of the innovative translational project, I will integrate one of the European leader research center in genetic diseases, giving me the opportunity to gain experience in translational immunology and human genetics, as well as to reinforce my expertise in cutting-edge single cell technologies and bioinformatics. Overall this project represents a unique stepping-stone to complete my training in pathophysiology and establish collaborations, which should put me in excellent position to establish as an independent researcher.

Type I interferonopathies (T1IFNs) are rare genetic diseases associated with an inappropriate upregulation of type I interferon (IFN) signalling. IFNs represent the first line of defence against viruses, and are induced by sensing of viral nucleic acids. Definition of the genetic basis of the T1IFNs has led to a coherent understanding of underlying pathology, involving previously unappreciated pathways of nucleic acid metabolism, and enabled the introduction of rational therapy targeted at blocking IFN signalling. Thus, it is important to identify new T1IFNs and determine their molecular and cellular basis. Beyond their role in energy metabolism, mitochondria are also recognised to play a role in the immune response to infection. Interestingly, both mitochondrial (mt) DNA and mtRNA have the potential to trigger IFN. Indeed, loss of mt integrity promoting pathogenic IFN induction, through mt nucleic acids released into the cytosol, is a novel topic of high clinical and scientific interest. We have identified patients with mutations in a gene encoding a mt protein, in which we consider the observed enhanced IFN signalling directly relevant to the associated neuropathology. My project aims to better understand the link between mt homeostasis and IFN induction, thereby defining novel pathways relating to mt integrity, mt nucleic acids and innate immune surveillance. Specifically, I will study these relationships in the context of human disease, and I will search for further novel determinants of mt function linked to innate immune homeostasis using our unique clinical screening protocol. I will bring my expertise in mt biology to the host laboratory. At the same time, this project will place me at the leading edge of clinically-directed research on nucleic acid sensing and autoinflammation. Thus, this training opportunity is designed to lead me towards independence through the acquisition of new skills and the discovery of novel research paths for my future career.

SCilS will create a multidisciplinary and intersectoral European training network focusing on ciliary signalling in development and disease. Primary cilia are microtubule-based cell surface projections that have evolved to be key signalling hubs of our cells, as they concentrate or segregate components of major cellular signalling pathways. Control of ciliary signaling output requires a high degree of regulation and critical feedback, which is needed for robustness in development and cellular homeostasis of different tissues and organs. Dysfunctional cilia can therefore lead to >35 severe human genetic traits (ciliopathies) with highly heterogeneous, overlapping phenotypes. Ciliopathies affect as many as 1 in 400 people, and for the majority of cases efficient therapeutic interventions are currently unavailable. SCilS research aims to uncover the multi-level organization and regulation of cilia-mediated signalling pathways in order to understand ciliopathy disease etiology and identify novel therapeutic targets. This challenging task will be accomplished by integrating unique expertise and cutting edge technology available within the SCilS network, including structural biology, super resolution imaging and cryo-electron tomography, state-of-the-art genomics, proteomics and bioinformatics, (stem) cell biology and biochemistry, as well as organoid technology and zebrafish models. SCilS training will give Early Stage Researchers (ESRs) unparalleled training opportunities in outstanding academic and industrial settings through training-by-research via individual research projects, secondments, and network-wide training sessions. All individual training and research activities have been designed to provide each ESR with the necessary broad competences in state‐of‐the art academic and industrial research. The network will thereby make a career in both industry and academia attractive to the ESRs and improve their career prospects in both private and public sectors.

Sickle cell disease (SCD) is one of the most prevalent monogenic diseases in Europe. A single amino acid substitution in the beta-globin chain of the adult hemoglobin (Hb) drives red blood cell sickling and multi-organ damage. The clinical severity of SCD is alleviated by the co-inheritance of mutations causing expression of fetal gamma-globin in adult life ? a condition termed hereditary persistence of fetal hemoglobin (HPFH). Transplantation of autologous, genetically modified hematopoietic stem/progenitor cells (HSPCs) is an attractive therapeutic option for SCD patients. To this end, genome editing approaches based on the use of site-specific nucleases or, more recently, base editors have been explored by many groups, including teams in our consortium. These approaches either correct the single point mutation causing SCD or reactivate fetal gamma-globin expression by mimicking HPFH mutations. On the other hand, (pre)clinical data from SCD patients or SCD mouse models, as well as preliminary data from our labs suggest that SCD HSPCs are characterized by a high mutational burden, oxidative stress and expression of inflammatory genes. This can alter HSPC properties as well as their interactions within the bone marrow niche. In the context of gene therapy, it is essential to understand the mechanisms underlying SCD HSPC dysfunction and assess the impact of genome editing approaches on SCD HSPCs. In this proposal, we have assembled a multidisciplinary team to: (i) understand the molecular and cellular mechanisms underlying SCD HSPC autonomous and non-cell-autonomous dysfunctions and (ii) evaluate the impact of established and novel genome editing approaches on SCD HSPC properties and genome integrity. This study will lay the foundation of an improved gene therapy strategy to treat SCD and provide best practice tools and protocols for genome editing-based therapies in HSPCs.