Periodic Reporting for period 1 - TABANK (Targeting B cell Activation driven by Natural Killer cells)
Okres sprawozdawczy: 2023-10-01 do 2025-09-30
Autoimmune diseases affect nearly 4% of the world’s population and can be life-threatening. Among them, Sjögren’s Disease (SjD) is the most common systemic autoimmune disease. Unfortunately, to date, treatments are focusing on relieving symptoms. It is of public relevance to find potential new biomarkers for treatments. B cells are one key player in SjD and promising drugs targeting B cell activation are currently under phase 3 clinical trials. Restraining B cell hyperactivity is central to treat SjD permanently. Hence, instead of targeting B cell activation, SjD treatments would also benefit from targeting signals or interactions leading to B cell activation.
Targeting interaction leading to B cell hyperactivity will enable the first-ever study investigating B cell hyperactivity in relation to other immune cells in SjD. Our main hypothesis is that treatment should focus on Targeting B cell Activation driven by Natural Killer (NK) cells (TABANK), a cell type (i) located within the inflamed tissues; (ii) involved in the first line of defense against pathogen; (iii) that produce cytokines and chemokines known to act on B cells (BAFF, FLT3, IFN) and (iv) which could directly interact with B cells.
TABANK proposes to investigate this unique “marriage” of immune cells using cutting-edge technologies (high-parameter flow cytometry, single-cell sequencing technologies and unsupervised analysis) to interrogate the immune network in the circulation of SjD donors as well as in the inflamed environment of impaired salivary glands. This overarching goal will be achieved by i) Compiling a comprehensive database of immune cell profile in SjD using cutting both-single cell sequencing on high-parameter mass and flow cytometry; ii) Determining potential interaction of immune cells leading to B cell-activation using a novel computational approach; and iii) Defining and validating these interactions using ex vivo culture.
This new approach will provide a critical, and as yet still-missing, link needed to refine uncertainties on the cellular and molecular interactions that lead to an exacerbated immune response. TABANK results could then be used to find potential new treatments to cure SjD.
Targeting interaction leading to B cell hyperactivity will enable the first-ever study investigating B cell hyperactivity in relation to other immune cells in SjD. Our main hypothesis is that treatment should focus on Targeting B cell Activation driven by Natural Killer (NK) cells (TABANK), a cell type (i) located within the inflamed tissues; (ii) involved in the first line of defense against pathogen; (iii) that produce cytokines and chemokines known to act on B cells (BAFF, FLT3, IFN) and (iv) which could directly interact with B cells.
TABANK proposes to investigate this unique “marriage” of immune cells using cutting-edge technologies (high-parameter flow cytometry, single-cell sequencing technologies and unsupervised analysis) to interrogate the immune network in the circulation of SjD donors as well as in the inflamed environment of impaired salivary glands. This overarching goal will be achieved by i) Compiling a comprehensive database of immune cell profile in SjD using cutting both-single cell sequencing on high-parameter mass and flow cytometry; ii) Determining potential interaction of immune cells leading to B cell-activation using a novel computational approach; and iii) Defining and validating these interactions using ex vivo culture.
This new approach will provide a critical, and as yet still-missing, link needed to refine uncertainties on the cellular and molecular interactions that lead to an exacerbated immune response. TABANK results could then be used to find potential new treatments to cure SjD.
The first task of the project was to select patients with biobanked tissues and peripheral blood to analyze. These patients were selected from an already established cohort of over 800 patients: the Diagnosis of Primary Sjögren's Syndrome (DIApSS, NCT03681964). 60 patients were selected (20 sicca donors: i.e.: donors with similar symptoms but without the disease and 40 SjD patients) with matching clinical criteria (age, gender, duration of symptoms and absence of other diseases). Then, we generated a high-quality single-cell transcriptomics dataset on both peripheral blood (PBMCs) and in the tissue (minor salivary glands) from both SjD patients and sicca donors.
For the PBMCs, the dataset comprises 15 sicca donors and 30 SjD patients. The analyses are still ongoing using bioinformatics pipelines on Rstudio and will provide a detailed overview of NK cell heterogeneity and their potential dysregulation in SjD. In parallel of the transcriptional information, we have designed a spectral flow cytometry panel to comprehensively analyze over 30 proteins expressed at the surface of NK cells. This panel of 30 proteins will also used to characterize the phenotype of NK cells in other autoimmune diseases thus expanding the scope of our study to better understand the role of NK cells in other autoimmune diseases (lupus, vasculitis, sclerodermia).
Tissues were analyzed with the most recent and cutting-edge techniques to study the inflamed environment of impaired salivary glands. Specifically, we performed spatial transcriptomics which enables to obtain transcriptional information at a single cell level and the spatial localization of the cells. This method is key to understand interaction between cells within tissue. The dataset comprises 3 sicca donors and 7 SjD patients. The analyses are still ongoing using bioinformatics pipelines on Rstudio. In parallel, we performed multiplex immunofluorescence (with 14-protein) to localize and characterize NK cells within inflamed salivary gland tissue. This integrative spatial approach will enable the identification of NK cell niches and their potential cellular partners within the tissue microenvironment.
Furthermore, we established in vitro assays to assess NK cell functionality directly from PBMC samples, allowing us to evaluate their cytotoxic and immunoregulatory capacity under controlled conditions.
Together, these achievements have established a unique and multidimensional dataset combining phenotypic, spatial, and functional information on NK cells in SjD, setting the stage for the identification of novel cellular interactions driving disease pathogenesis.
For the PBMCs, the dataset comprises 15 sicca donors and 30 SjD patients. The analyses are still ongoing using bioinformatics pipelines on Rstudio and will provide a detailed overview of NK cell heterogeneity and their potential dysregulation in SjD. In parallel of the transcriptional information, we have designed a spectral flow cytometry panel to comprehensively analyze over 30 proteins expressed at the surface of NK cells. This panel of 30 proteins will also used to characterize the phenotype of NK cells in other autoimmune diseases thus expanding the scope of our study to better understand the role of NK cells in other autoimmune diseases (lupus, vasculitis, sclerodermia).
Tissues were analyzed with the most recent and cutting-edge techniques to study the inflamed environment of impaired salivary glands. Specifically, we performed spatial transcriptomics which enables to obtain transcriptional information at a single cell level and the spatial localization of the cells. This method is key to understand interaction between cells within tissue. The dataset comprises 3 sicca donors and 7 SjD patients. The analyses are still ongoing using bioinformatics pipelines on Rstudio. In parallel, we performed multiplex immunofluorescence (with 14-protein) to localize and characterize NK cells within inflamed salivary gland tissue. This integrative spatial approach will enable the identification of NK cell niches and their potential cellular partners within the tissue microenvironment.
Furthermore, we established in vitro assays to assess NK cell functionality directly from PBMC samples, allowing us to evaluate their cytotoxic and immunoregulatory capacity under controlled conditions.
Together, these achievements have established a unique and multidimensional dataset combining phenotypic, spatial, and functional information on NK cells in SjD, setting the stage for the identification of novel cellular interactions driving disease pathogenesis.
The TABANK project has achieved results that extend well beyond the current state of the art in the field of Sjögren’s Disease (SjD). Scientifically, the project has generated multidimensional datasets that combine high-parameter flow cytometry, multiplex immunofluorescence (14-plex), and spatial transcriptomics using three distinct technologies. This integrative approach has enabled, for the first time, a comprehensive mapping of NK cell phenotype, tissue localization, and functionality in both blood and salivary glands of SjD patients. In addition, ex vivo functional assays have provided unique insights into the cytotoxic and immunoregulatory capacity of NK cells, highlighting their potential contribution to pathogenic immune networks.
Beyond the purely scientific outputs, the project has created strong conditions for long-term research impact. First, it has helped Dr. Marie Frutoso to secure new funding to support continuity and expansion of her research, including the Labex IGO Young Investigator Grant (2024, 15 K€) for comparative studies of NK cell function in systemic sclerosis and SjD, and an ATIP-Avenir Grant (2025-2030, 300 K€) which goal is to extend the investigation of NK cells interaction with other cell types and in other autoimmune diseases. Dr. Marie Frutoso is also the lead of one work package in an ANR joint project which was obtained in January 2026. This joint ANR between Graz University and the LBAI-UMR1227 Research Laboratory from the University of Western Brittany (UBO) intends to study the “pre-disease” state of SjD. A PhD has been recruited for this project and will be supervised by Pr. Divi Cornec and Dr. Marie Frutoso.
Second, TABANK has contributed to improving Dr. Marie Frutoso’s mentorship, with the supervision of two Master’s students (Lisa Sériau, M2; Lou-Anna Hemon, M1), a PhD student (Rudolf Corty, ongoing PhD), and the guidance of an international visiting PhD student from the University of Graz (Pavlina Javorova, 9-month exchange). These activities strengthen the training environment and dissemination of methodological expertise.
Third, the project has promoted integration within the scientific community: Dr. Marie Frutoso’s was selected as a member of the Scientific Board of the French Society of Rheumatology (2024–2026), and presented the work at high-level scientific meetings, including the Auto-ImmunoSEM meeting (Paris, February 2024).
Fourth, TABANK has fostered collaboration and translational potential. Exploratory contacts have been initiated with InnatePharma, an industrial partner with expertise in NK cell biology, paving the way for future translational applications. Within the host laboratory, Dr. Frutoso has contributed as co-author to a publication on B cell biology in SjD, reinforcing integration into ongoing research programs. In addition, a method-focused paper describing the advanced analytical pipelines developed in TABANK has been accepted in Springer Methods in Molecular Biology, ensuring methodological dissemination to the wider scientific community.
Taken together, these achievements extend well beyond the state of the art by combining high-resolution immune profiling with spatial and functional readouts, securing funding and collaborations for future development, integrating the PI into the national and international scientific landscape, and creating a foundation for translational applications. This comprehensive progress not only advances understanding of SjD pathogenesis but also contributes to establishing Dr. Frutoso’s independent research program and long-term scientific career.
Beyond the purely scientific outputs, the project has created strong conditions for long-term research impact. First, it has helped Dr. Marie Frutoso to secure new funding to support continuity and expansion of her research, including the Labex IGO Young Investigator Grant (2024, 15 K€) for comparative studies of NK cell function in systemic sclerosis and SjD, and an ATIP-Avenir Grant (2025-2030, 300 K€) which goal is to extend the investigation of NK cells interaction with other cell types and in other autoimmune diseases. Dr. Marie Frutoso is also the lead of one work package in an ANR joint project which was obtained in January 2026. This joint ANR between Graz University and the LBAI-UMR1227 Research Laboratory from the University of Western Brittany (UBO) intends to study the “pre-disease” state of SjD. A PhD has been recruited for this project and will be supervised by Pr. Divi Cornec and Dr. Marie Frutoso.
Second, TABANK has contributed to improving Dr. Marie Frutoso’s mentorship, with the supervision of two Master’s students (Lisa Sériau, M2; Lou-Anna Hemon, M1), a PhD student (Rudolf Corty, ongoing PhD), and the guidance of an international visiting PhD student from the University of Graz (Pavlina Javorova, 9-month exchange). These activities strengthen the training environment and dissemination of methodological expertise.
Third, the project has promoted integration within the scientific community: Dr. Marie Frutoso’s was selected as a member of the Scientific Board of the French Society of Rheumatology (2024–2026), and presented the work at high-level scientific meetings, including the Auto-ImmunoSEM meeting (Paris, February 2024).
Fourth, TABANK has fostered collaboration and translational potential. Exploratory contacts have been initiated with InnatePharma, an industrial partner with expertise in NK cell biology, paving the way for future translational applications. Within the host laboratory, Dr. Frutoso has contributed as co-author to a publication on B cell biology in SjD, reinforcing integration into ongoing research programs. In addition, a method-focused paper describing the advanced analytical pipelines developed in TABANK has been accepted in Springer Methods in Molecular Biology, ensuring methodological dissemination to the wider scientific community.
Taken together, these achievements extend well beyond the state of the art by combining high-resolution immune profiling with spatial and functional readouts, securing funding and collaborations for future development, integrating the PI into the national and international scientific landscape, and creating a foundation for translational applications. This comprehensive progress not only advances understanding of SjD pathogenesis but also contributes to establishing Dr. Frutoso’s independent research program and long-term scientific career.