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1. IL-23 tunes inflammatory functions of human mucosal-associated invariant T cells

Author: Laetitia Camard, Tharshana Stephen, Hanane Yahia-Cherbal, Vincent Guillemot, Sébastien Mella, Victoire Baillet, Hélène Lopez-Maestre, Daniele Capocefalo, Laura Cantini, Claire Leloup, Julie Marsande, Katherine Garro, Juan Sienes Bailo, Ambre Dangien, Natalia Pietrosemoli, Milena Hasan, Huimeng Wang, Sidonia B.G. Eckle, Anne M. Fourie, Carrie Greving, Barbara Joyce-Shaikh, Raphaelle Parker, Daniel J. Cua, Elisabetta Bianchi, and Lars Rogge
Subjects: Immunology, Transcriptomics, Science
Abstract: Summary: IL-23 signaling plays a key role in the pathogenesis of chronic inflammatory and infectious diseases, yet the cellular targets and signaling pathways affected by this cytokine remain poorly understood. We show that IL-23 receptors are expressed on the large majority of human mucosal-associated invariant T (MAIT), but not of conventional T cells. Protein and transcriptional profiling at the population and single cell level demonstrates that stimulation with IL-23 or the structurally related cytokine IL-12 drives distinct functional profiles, revealing a high level of plasticity of MAIT cells. IL-23, in particular, affects key molecules and pathways related to autoimmunity and cytotoxic functions. Integrated analysis of transcriptomes and chromatin accessibility, supported by CRISPR-Cas9 mediated deletion, shows that AP-1 transcription factors constitute a key regulatory node of the IL-23 pathway in MAIT cells. In conclusion, our findings indicate that MAIT cells are key mediators of IL-23 functions in immunity to infections and chronic inflammatory diseases.
Published: 2025
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2. Prion protein alters viral control and enhances pathology after perinatal cytomegalovirus infection

Author: Dubravka Karner, Daria Kvestak, Paola Kucan Brlic, Maja Cokaric Brdovcak, Berislav Lisnic, Ilija Brizic, Vanda Juranic Lisnic, Mijo Golemac, Jelena Tomac, Astrid Krmpotic, Esma Karkeni, Valentina Libri, Sebastien Mella, Giuseppe Legname, Hermann C. Altmeppen, Milena Hasan, Stipan Jonjic, and Tihana Lenac Rovis
Subjects: Science
Abstract: Abstract Cytomegalovirus (CMV) infection poses risks to newborns, necessitating effective therapies. Given that the damage includes both viral infection of brain cells and immune system-related damage, here we investigate the involvement of cellular prion protein (PrP), which plays vital roles in neuroprotection and immune regulation. Using a murine model, we show the role of PrP in tempering neonatal T cell immunity during CMV infection. PrP-null mice exhibit enhanced viral control through elevated virus-specific CD8 T cell responses, leading to reduced viral titers and pathology. We further unravel the molecular mechanisms by showing CMV-induced upregulation followed by release of PrP via the metalloproteinase ADAM10, impairing CD8 T cell response specifically in neonates. Additionally, we confirm PrP downregulation in human CMV (HCMV)-infected fibroblasts, underscoring the broader relevance of our observations beyond the murine model. Furthermore, our study highlights how PrP, under the stress of viral pathogenesis, reveals its impact on neonatal immune modulation.
Published: 2024
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3. Differential predictive value of resident memory CD8+T cell subpopulations in patients with non-small-cell lung cancer treated by immunotherapy

Author: Hang Phuong Pham, Diane Damotte, Stéphanie Corgnac, Ludger Johannes, Eric Tartour, Léa Paolini, Fathia Mami-Chouaib, Karen Leroy, Pascaline Boudou-Rouquette, Helene Blons, Francois Goldwasser, Pierre Laurent-Puig, Isabelle Cremer, Milena Hasan, Thi Tran, Nadege Gruel, Laure Gibault, Elizabeth Fabre, Marie Wislez, Patrice Ravel, Valentin Quiniou, Jennifer Arrondeau, Aziza Caidi, Jean-Philippe Villemin, Jonathan Ulmer, Louis-Victorien Vieillard, Joséphine Pineau, Alain Gey, Pierre Barennes, Valentina Libri, Sebastien Mella, Sixtine De Percin, and Hortense De Saint Basile
Subjects: Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract: Background A high density of resident memory T cells (TRM) in tumors correlates with improved clinical outcomes in immunotherapy-treated patients. In most clinical studies, TRM are defined by the CD103 marker. However, it is clearly established that not all TRM express CD103, but can be defined by other markers (CD49a, CD69, etc). The frequency of these subpopulations of TRM expressing or not CD103 varies according to the location of the cancer. Little is known about their functionality and their predictive impact on response to immunotherapy. In preclinical models, only some subpopulations of TRM are associated with cancer vaccine efficacy.Methods Multiparametric cytometry analyses were used to demonstrate the presence of TRM subpopulations in the lung in mice after vaccination and in fresh ex vivo human non-small cell lung cancer (NSCLC). An analysis of the T-cell repertoire of these TRM was conducted to search for their relationships. Multiplex immunofluorescence techniques were used to quantify intratumor infiltration of TRM subpopulations in two cohorts of patients with NSCLC. The impact on the clinical outcome of the TRM tumor infiltration was also investigated.Results We identified two main TRM subpopulations in tumor-infiltrating lymphocytes derived from patients with NSCLC: one co-expressing CD103 and CD49a (double positive (DP)), and the other expressing only CD49a (simple positive (SP)); both exhibiting additional TRM surface markers like CD69. Despite higher expression of inhibitory receptors, DP TRM exhibited greater functionality compared with SP TRM. Analysis of T-cell receptor (TCR) repertoire and expression of the stemness marker TCF1 revealed shared TCRs between populations, with the SP subset appearing more progenitor-like phenotype. In the training cohort, PD-L1 (Programmed Death-Ligand 1) and TCF1+CD8+T cells predict response to anti-PD-1. In patient with NSCLC validation cohorts, only DP TRM predicted PD-1 blockade response. Multivariate analysis, including various biomarkers associated with responses to anti-PD-(L)1, such as total CD8, TCF1+CD8+T cells, and PD-L1, showed that only intratumoral infiltration by DP TRM remained significant.Conclusions This study highlights the non-equivalence of TRM subpopulations. The population of TRM co-expressing CD103 and CD49a appears to be the most functional and has the most significant capacity for predicting response to immunotherapy in multivariate analysis in patients with NSCLC.
Published: 2024
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4. Beyond 40 fluorescent probes for deep phenotyping of blood mononuclear cells, using spectral technology

Author: Sandrine Schmutz, Pierre-Henri Commere, Nicolas Montcuquet, Ana Cumano, Cédric Ait-Mansour, Sophie Novault, and Milena Hasan
Subjects: spectral cytometry, autofluorescence, high-dimension, unsupervised analysis, immunophenotyping, Immunologic diseases. Allergy, RC581-607
Abstract: The analytical capability of flow cytometry is crucial for differentiating the growing number of cell subsets found in human blood. This is important for accurate immunophenotyping of patients with few cells and a large number of parameters to monitor. Here, we present a 43-parameter panel to analyze peripheral blood mononuclear cells from healthy individuals using 41 fluorescence-labelled monoclonal antibodies, an autofluorescent channel, and a viability dye. We demonstrate minimal population distortions that lead to optimized population identification and reproducible results. We have applied an advanced approach in panel design, in selection of sample acquisition parameters and in data analysis. Appropriate autofluorescence identification and integration in the unmixing matrix, allowed for resolution of unspecific signals and increased dimensionality. Addition of one laser without assigned fluorochrome resulted in decreased fluorescence spill over and improved discrimination of cell subsets. It also increased the staining index when autofluorescence was integrated in the matrix. We conclude that spectral flow cytometry is a highly valuable tool for high-end immunophenotyping, and that fine-tuning of major experimental steps is key for taking advantage of its full capacity.
Published: 2024
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5. Integrated analysis of whole blood oxylipin and cytokine responses after bacterial, viral, and T cell stimulation reveals new immune networks

Author: Etienne Villain, Aurélie Chanson, Malwina Mainka, Nadja Kampschulte, Pauline Le Faouder, Justine Bertrand-Michel, Marion Brandolini-Bulon, Bruno Charbit, Munyaradzi Musvosvi, Nicole Bilek, Thomas J. Scriba, Lluis Quintana-Murci, Nils Helge Schebb, Darragh Duffy, Cécile Gladine, Laurent Abel, Andres Alcover, Hugues Aschard, Philippe Bousso, Nollaig Bourke, Petter Brodin, Pierre Bruhns, Nadine Cerf-Bensussan, Ana Cumano, Christophe D’Enfert, Ludovic Deriano, Marie-Agnès Dillies, James Di Santo, Gérard Eberl, Jost Enninga, Jacques Fellay, Ivo Gomperts-Boneca, Milena Hasan, Gunilla Karlsson Hedestam, Serge Hercberg, Molly A. Ingersoll, Olivier Lantz, Rose Anne Kenny, Mickaël Ménager, Hugo Mouquet, Cliona O'Farrelly, Etienne Patin, Sandra Pellegrini, Antonio Rausell, Frédéric Rieux-Laucat, Lars Rogge, Magnus Fontes, Anavaj Sakuntabhai, Olivier Schwartz, Benno Schwikowski, Spencer Shorte, Frédéric Tangy, Antoine Toubert, Mathilde Touvier, Marie-Noëlle Ungeheuer, Christophe Zimmer, and Matthew L. Albert
Subjects: Immunology, Immune response, Microbiology, Science
Abstract: Summary: Oxylipins are major immunomodulating mediators, yet studies of inflammation focus mainly on cytokines. Here, using a standardized whole-blood stimulation system, we characterized the oxylipin-driven inflammatory responses to various stimuli and their relationships with cytokine responses. We performed a pilot study in 25 healthy individuals using 6 different stimuli: 2 bacterial stimuli (LPS and live BCG), 2 viral stimuli (vaccine-grade poly I:C and live H1N1 attenuated influenza), an enterotoxin superantigen and a Null control. All stimuli induced a strong production of oxylipins but most importantly, bacterial, viral, and T cell immune responses show distinct oxylipin signatures. Integration of the oxylipin and cytokine responses for each condition revealed new immune networks improving our understanding of inflammation regulation. Finally, the oxylipin responses and oxylipin-cytokine networks were compared in patients with active tuberculosis or with latent infection. This revealed different responses to BCG but not LPS stimulation highlighting new regulatory pathways for further investigations.
Published: 2023
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6. T cell migration and effector function differences in familial adenomatous polyposis patients with APC gene mutations

Author: Céline Cuche, Marta Mastrogiovanni, Marie Juzans, Hélène Laude, Marie-Noëlle Ungeheuer, Daniel Krentzel, Maria Isabella Gariboldi, Daniel Scott-Algara, Marianne Madec, Sophie Goyard, Camille Floch, Gaëlle Chauveau-Le Friec, Pierre Lafaye, Charlotte Renaudat, Muriel Le Bidan, Christine Micallef, Sandrine Schmutz, Sébastien Mella, Sophie Novault, Milena Hasan, Darragh Duffy, Vincenzo Di Bartolo, and Andrés Alcover
Subjects: Adenomatous polyposis coli, APC, familial adenomatous polyposis, T cell activation, T cell migration, cytokines, Immunologic diseases. Allergy, RC581-607
Abstract: Familial adenomatous polyposis (FAP) is an inherited disease characterized by the development of large number of colorectal adenomas with high risk of evolving into colorectal tumors. Mutations of the Adenomatous polyposis coli (APC) gene is often at the origin of this disease, as well as of a high percentage of spontaneous colorectal tumors. APC is therefore considered a tumor suppressor gene. While the role of APC in intestinal epithelium homeostasis is well characterized, its importance in immune responses remains ill defined. Our recent work indicates that the APC protein is involved in various phases of both CD4 and CD8 T cells responses. This prompted us to investigate an array of immune cell features in FAP subjects carrying APC mutations. A group of 12 FAP subjects and age and sex-matched healthy controls were studied. We characterized the immune cell repertoire in peripheral blood and the capacity of immune cells to respond ex vivo to different stimuli either in whole blood or in purified T cells. A variety of experimental approaches were used, including, pultiparamater flow cytometry, NanosString gene expression profiling, Multiplex and regular ELISA, confocal microscopy and computer-based image analyis methods. We found that the percentage of several T and natural killer (NK) cell populations, the expression of several genes induced upon innate or adaptive immune stimulation and the production of several cytokines and chemokines was different. Moreover, the capacity of T cells to migrate in response to chemokine was consistently altered. Finally, immunological synapses between FAP cytotoxic T cells and tumor target cells were more poorly structured. Our findings of this pilot study suggest that mild but multiple immune cell dysfunctions, together with intestinal epithelial dysplasia in FAP subjects, may facilitate the long-term polyposis and colorectal tumor development. Although at an initial discovery phase due to the limited sample size of this rare disease cohort, our findings open new perspectives to consider immune cell abnormalities into polyposis pathology.
Published: 2023
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7. Comprehensive Analysis of Soluble Mediator Profiles in Congenital CMV Infection Using an MCMV Model

Author: Dubravka Karner, Daria Kvestak, Berislav Lisnic, Maja Cokaric Brdovcak, Vanda Juranic Lisnic, Paola Kucan Brlic, Milena Hasan, and Tihana Lenac Rovis
Subjects: congenital human cytomegalovirus infection, HCMV, MCMV, cytokine, chemokine, Microbiology, QR1-502
Abstract: Congenital human cytomegalovirus (HCMV) infection may cause life-threatening disease and permanent damage to the central nervous system. The mouse model of CMV infection is most commonly used to study mechanisms of infection and pathogenesis. While essential to limit mouse CMV (MCMV) replication, the inflammatory responses, particularly IFNγ and TNFα, cause neurodevelopmental abnormalities. Other soluble mediators of the immune response in most tissues remain largely unexplored. To address this gap, we quantified 48 soluble mediators of the immune response, including 32 cytokines, 10 chemokines, 3 growth factors/regulators, and 3 soluble receptors in the spleen, liver, lungs, and brain at 9 and 14 days postinfection (dpi). Our analysis found 25 induced molecules in the brain at 9 dpi, with an additional 8 showing statistically elevated responses at 14 dpi. Specifically, all analyzed CCL group cytokines (CCL2, CCL3, CCL4, CCL5, CCL7, and CCL11) were upregulated at 14 dpi in the brain. Furthermore, data revealed differentially regulated analytes across tissues, such as CCL11, CXCL5, and IL-10 in the brain, IL-33/IL-33R in the liver, and VEGF-a and IL-5 in the lungs. Overall, this study provides an overview of the immune dynamics of soluble mediators in congenital CMV.
Published: 2024
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8. Low CCR5 expression protects HIV-specific CD4+ T cells of elite controllers from viral entry

Author: Mathieu Claireaux, Rémy Robinot, Jérôme Kervevan, Mandar Patgaonkar, Isabelle Staropoli, Anne Brelot, Alexandre Nouël, Stacy Gellenoncourt, Xian Tang, Mélanie Héry, Stevenn Volant, Emeline Perthame, Véronique Avettand-Fenoël, Julian Buchrieser, Thomas Cokelaer, Christiane Bouchier, Laurence Ma, Faroudy Boufassa, Samia Hendou, Valentina Libri, Milena Hasan, David Zucman, Pierre de Truchis, Olivier Schwartz, Olivier Lambotte, and Lisa A. Chakrabarti
Subjects: Science
Abstract: Here, Claireaux et al. show that people who naturally control HIV infection express lower levels of the viral co-receptor CCR5 in specific CD4+ T cells, and that this results from mutations or receptor internalization by CD4+ T cell-produced chemokines.
Published: 2022
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9. Changes in Systemic Regulatory T Cells, Effector T Cells, and Monocyte Populations Associated With Early-Life Stunting

Author: Zo Andriamanantena, Fanirisoa Randrianarisaona, Maheninasy Rakotondrainipiana, Prisca Andriantsalama, Ravaka Randriamparany, Rindra Randremanana, Frédérique Randrianirina, Sophie Novault, Darragh Duffy, François Huetz, Milena Hasan, Matthieu Schoenhals, Philippe J. Sansonetti, Pascale Vonaesch, Inès Vigan-Womas, Afribiota Investigators, Laurence Barbot-Trystram, Robert Barouki, Alexandra Bastaraud, Jean-Marc Collard, Maria Doria, Serge Ghislain Djorie, Tamara Giles-Vernick, Bolmbaye Privat Gondje, Jean-Chrysostome Gody, Jean-Michel Héraud, Francis Allan Hunald, Nathalie Kapel, Jean-Pierre Lombart, Alexandre Manirakiza, Synthia Nazita Nigatoloum, Laura Wegener Parfrey, Lisette Raharimalala, Rindra Vatosoa Randremanana, Harifetra Mamy Richard Randriamizao, Frédérique Randrianirina, Annick Lalaina Robinson, Pierre-Alain Rubbo, Philippe Sansonetti, Laura Schaeffer, Ionela Gouandjika-Vassilache, Sonia Sandrine Vondo, and Inès Vigan-Womas
Subjects: stunting, environmental enteric dysfunction, flow cytometry, monocytes, regulatory T cells, Madagascar, Immunologic diseases. Allergy, RC581-607
Abstract: Stunting and environmental enteric dysfunction (EED) may be responsible for altered gut and systemic immune responses. However, their impact on circulating immune cell populations remains poorly characterized during early life. A detailed flow cytometry analysis of major systemic immune cell populations in 53 stunted and 52 non-stunted (2 to 5 years old) children living in Antananarivo (Madagascar) was performed. Compared to age-matched non-stunted controls, stunted children aged 2-3 years old had a significantly lower relative proportion of classical monocytes. No significant associations were found between stunting and the percentages of effector T helper cell populations (Th1, Th2, Th17, Th1Th17, and cTfh). However, we found that HLA-DR expression (MFI) on all memory CD4+ or CD8+ T cell subsets was significantly lower in stunted children compared to non-stunted controls. Interestingly, in stunted children compared to the same age-matched non-stunted controls, we observed statistically significant age-specific differences in regulatory T cells (Treg) subsets. Indeed, in 2- to 3-year-old stunted children, a significantly higher percentage of memory Treg, whilst a significantly lower percentage of naive Treg, was found. Our results revealed that both innate and adaptive systemic cell percentages, as well as activation status, were impacted in an age-related manner during stunting. Our study provides valuable insights into the understanding of systemic immune system changes in stunted children.
Published: 2022
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10. Single-Cell and Bulk RNA-Sequencing Reveal Differences in Monocyte Susceptibility to Influenza A Virus Infection Between Africans and Europeans

Author: Mary B. O’Neill, Hélène Quach, Julien Pothlichet, Yann Aquino, Aurélie Bisiaux, Nora Zidane, Matthieu Deschamps, Valentina Libri, Milena Hasan, Shen-Ying Zhang, Qian Zhang, Daniela Matuozzo, Aurélie Cobat, Laurent Abel, Jean-Laurent Casanova, Nadia Naffakh, Maxime Rotival, and Lluis Quintana-Murci
Subjects: Monocytes, single-cell ‘omics, transcriptomics, ancestry, population, influenza virus, Immunologic diseases. Allergy, RC581-607
Abstract: There is considerable inter-individual and inter-population variability in response to viruses. The potential of monocytes to elicit type-I interferon responses has attracted attention to their role in viral infections. Here, we use single-cell RNA-sequencing to characterize the role of cellular heterogeneity in human variation of monocyte responses to influenza A virus (IAV) exposure. We show widespread inter-individual variability in the percentage of IAV-infected monocytes. Notably, individuals with high cellular susceptibility to IAV are characterized by a lower activation at basal state of an IRF/STAT-induced transcriptional network, which includes antiviral genes such as IFITM3, MX1 and OAS3. Upon IAV challenge, we find that cells escaping viral infection display increased mRNA expression of type-I interferon stimulated genes and decreased expression of ribosomal genes, relative to both infected cells and those never exposed to IAV. We also uncover a stronger resistance of CD16+ monocytes to IAV infection, together with CD16+-specific mRNA expression of IL6 and TNF in response to IAV. Finally, using flow cytometry and bulk RNA-sequencing across 200 individuals of African and European ancestry, we observe a higher number of CD16+ monocytes and lower susceptibility to IAV infection among monocytes from individuals of African-descent. Based on these data, we hypothesize that higher basal monocyte activation, driven by environmental factors and/or weak-effect genetic variants, underlies the lower cellular susceptibility to IAV infection of individuals of African ancestry relative to those of European ancestry. Further studies are now required to investigate how such cellular differences in IAV susceptibility translate into population differences in clinical outcomes and susceptibility to severe influenza.
Published: 2021
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11. Corrigendum: Unveiling Interindividual Variability of Human Fibroblast Innate Immune Response Using Robust Cell-Based Protocols

Author: Audrey Chansard, Nelly Dubrulle, Mathilde Poujol de Molliens, Pierre B. Falanga, Tharshana Stephen, Milena Hasan, Ger van Zandbergen, Nathalie Aulner, Spencer L. Shorte, Brigitte David-Watine, the Milieu Intérieur Consortium, Laurent Abel, Andres Alcover, Hugues Aschard, Kalla Astrom, Philippe Bousso, Pierre Bruhns, Ana Cumano, Caroline Demangel, Ludovic Deriano, James Di Santo, Françoise Dromer, Gérard Eberl, Jost Enninga, Jacques Fellay, Ivo Gomperts-Boneca, Serge Hercberg, Olivier Lantz, Hugo Mouquet, Etienne Patin, Sandra Pellegrini, Stanislas Pol, Antonio Rausell, Lars Rogge, Anavaj Sakuntabhai, Olivier Schwartz, Benno Schwikowski, Spencer Shorte, Frédéric Tangy, Antoine Toubert, Mathilde Trouvier, Marie-Noëlle Ungeheuer, Darragh Duffy, Matthew L. Albert, and Lluis Quintana-Murci
Subjects: immortalization, HSV-1, FACS, cytokines, human primary cells, NF-kB, Immunologic diseases. Allergy, RC581-607
Published: 2021
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12. Unveiling Interindividual Variability of Human Fibroblast Innate Immune Response Using Robust Cell-Based Protocols

Author: Audrey Chansard, Nelly Dubrulle, Mathilde Poujol de Molliens, Pierre B. Falanga, Tharshana Stephen, Milena Hasan, Ger van Zandbergen, Nathalie Aulner, Spencer L. Shorte, Brigitte David-Watine, the Milieu Intérieur Consortium, Laurent Abel, Andres Alcover, Hugues Aschard, Kalla Astrom, Philippe Bousso, Pierre Bruhns, Ana Cumano, Caroline Demangel, Ludovic Deriano, James Di Santo, Françoise Dromer, Gérard Eberl, Jost Enninga, Jacques Fellay, Ivo Gomperts-Boneca, Serge Hercberg, Olivier Lantz, Hugo Mouquet, Etienne Patin, Sandra Pellegrini, Stanislas Pol, Antonio Rausell, Lars Rogge, Anavaj Sakuntabhai, Olivier Schwartz, Benno Schwikowski, Spencer Shorte, Frédéric Tangy, Antoine Toubert, Mathilde Trouvier, Marie-Noëlle Ungeheuer, Darragh Duffy, Matthew L. Albert, and Lluis Quintana-Murci
Subjects: immortalization, HSV-1, FACS, cytokines, human primary cells, NF-κB, Immunologic diseases. Allergy, RC581-607
Abstract: The LabEx Milieu Interieur (MI) project is a clinical study centered on the detailed characterization of the baseline and induced immune responses in blood samples from 1,000 healthy donors. Analyses of these samples has lay ground for seminal studies on the genetic and environmental determinants of immunologic variance in a healthy cohort population. In the current study we developed in vitro methods enabling standardized quantification of MI-cohort-derived primary fibroblasts responses. Our results show that in vitro human donor cohort fibroblast responses to stimulation by different MAMPs analogs allows to characterize individual donor immune-phenotype variability. The results provide proof-of-concept foundation to a new experimental framework for such studies. A bio-bank of primary fibroblast lines was generated from 323 out of 1,000 healthy individuals selected from the MI-study cohort. To study inter-donor variability of innate immune response in primary human dermal fibroblasts we chose to measure the TLR3 and TLR4 response pathways, both receptors being expressed and previously studied in fibroblasts. We established high-throughput automation compatible methods for standardized primary fibroblast cell activation, using purified MAMPS analogs, poly I:C and LPS that stimulate TLR3 and TLR4 pathways respectively. These results were in turn compared with a stimulation method using infection by HSV-1 virus. Our “Add-only” protocol minimizes high-throughput automation system variability facilitating whole process automation from cell plating through stimulation to recovery of cell supernatants, and fluorescent labeling. Images were acquired automatically by high-throughput acquisition on an automated high-content imaging microscope. Under these methodological conditions standardized image acquisition provided for quantification of cellular responses allowing biological variability to be measured with low system noise and high biological signal fidelity. Optimal for automated analysis of immuno-phenotype of primary human cell responses our method and experimental framework as reported here is highly compatible to high-throughput screening protocols like those necessary for chemo-genomic screening. In context of primary fibroblasts derived from donors enrolled to the MI-clinical-study our results open the way to assert the utility of studying immune-phenotype characteristics relevant to a human clinical cohort.
Published: 2021
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13. Identifying the etiology and pathophysiology underlying stunting and environmental enteropathy: study protocol of the AFRIBIOTA project

Author: Pascale Vonaesch, Rindra Randremanana, Jean-Chrysostome Gody, Jean-Marc Collard, Tamara Giles-Vernick, Maria Doria, Inès Vigan-Womas, Pierre-Alain Rubbo, Aurélie Etienne, Emilson Jean Andriatahirintsoa, Nathalie Kapel, Eric Brown, Kelsey E. Huus, Darragh Duffy, B.Brett Finlay, Milena Hasan, Francis Allen Hunald, Annick Robinson, Alexandre Manirakiza, Laura Wegener-Parfrey, Muriel Vray, Philippe J. Sansonetti, and for the AFRIBIOTA Investigators
Subjects: Stunting, Pediatric environmental enteropathy, Madagascar, Central African Republic, Microbiota, Immunology, Pediatrics, RJ1-570
Abstract: Abstract Background Globally one out of four children under 5 years is affected by linear growth delay (stunting). This syndrome has severe long-term sequelae including increased risk of illness and mortality and delayed psychomotor development. Stunting is a syndrome that is linked to poor nutrition and repeated infections. To date, the treatment of stunted children is challenging as the underlying etiology and pathophysiological mechanisms remain elusive. We hypothesize that pediatric environmental enteropathy (PEE), a chronic inflammation of the small intestine, plays a major role in the pathophysiology of stunting, failure of nutritional interventions and diminished response to oral vaccines, potentially via changes in the composition of the pro- and eukaryotic intestinal communities. The main objective of AFRIBIOTA is to describe the intestinal dysbiosis observed in the context of stunting and to link it to PEE. Secondary objectives include the identification of the broader socio-economic environment and biological and environmental risk factors for stunting and PEE as well as the testing of a set of easy-to-use candidate biomarkers for PEE. We also assess host outcomes including mucosal and systemic immunity and psychomotor development. This article describes the rationale and study protocol of the AFRIBIOTA project. Methods AFRIBIOTA is a case-control study for stunting recruiting children in Bangui, Central African Republic and in Antananarivo, Madagascar. In each country, 460 children aged 2–5 years with no overt signs of gastrointestinal disease are recruited (260 with no growth delay, 100 moderately stunted and 100 severely stunted). We compare the intestinal microbiota composition (gastric and small intestinal aspirates; feces), the mucosal and systemic immune status and the psychomotor development of children with stunting and/or PEE compared to non-stunted controls. We also perform anthropological and epidemiological investigations of the children’s broader living conditions and assess risk factors using a standardized questionnaire. Discussion To date, the pathophysiology and risk factors of stunting and PEE have been insufficiently investigated. AFRIBIOTA will add new insights into the pathophysiology underlying stunting and PEE and in doing so will enable implementation of new biomarkers and design of evidence-based treatment strategies for these two syndromes.
Published: 2018
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14. Quantitative genetic analysis deciphers the impact of cis and trans regulation on cell-to-cell variability in protein expression levels.

Author: Michael D Morgan, Etienne Patin, Bernd Jagla, Milena Hasan, Lluís Quintana-Murci, and John C Marioni
Subjects: Genetics, QH426-470
Abstract: Identifying the factors that shape protein expression variability in complex multi-cellular organisms has primarily focused on promoter architecture and regulation of single-cell expression in cis. However, this targeted approach has to date been unable to identify major regulators of cell-to-cell gene expression variability in humans. To address this, we have combined single-cell protein expression measurements in the human immune system using flow cytometry with a quantitative genetics analysis. For the majority of proteins whose variability in expression has a heritable component, we find that genetic variants act in trans, with notably fewer variants acting in cis. Furthermore, we highlight using Mendelian Randomization that these variability-Quantitative Trait Loci might be driven by the cis regulation of upstream genes. This indicates that natural selection may balance the impact of gene regulation in cis with downstream impacts on expression variability in trans.
Published: 2020
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15. Standardized Whole-Blood Transcriptional Profiling Enables the Deconvolution of Complex Induced Immune Responses

Author: Alejandra Urrutia, Darragh Duffy, Vincent Rouilly, Céline Posseme, Raouf Djebali, Gabriel Illanes, Valentina Libri, Benoit Albaud, David Gentien, Barbara Piasecka, Milena Hasan, Magnus Fontes, Lluis Quintana-Murci, Matthew L. Albert, Laurent Abel, Andres Alcover, Kalla Astrom, Philippe Bousso, Pierre Bruhns, Ana Cumano, Caroline Demangel, Ludovic Deriano, James Di Santo, Françoise Dromer, Gérard Eberl, Jost Enninga, Jacques Fellay, Antonio Freitas, Odile Gelpi, Ivo Gomperts-Boneca, Serge Hercberg, Olivier Lantz, Claude Leclerc, Hugo Mouquet, Sandra Pellegrini, Stanislas Pol, Lars Rogge, Anavaj Sakuntabhai, Olivier Schwartz, Benno Schwikowski, Spencer Shorte, Vassili Soumelis, Frédéric Tangy, Eric Tartour, Antoine Toubert, and Marie-Noëlle Ungeheuer
Subjects: Biology (General), QH301-705.5
Abstract: Systems approaches for the study of immune signaling pathways have been traditionally based on purified cells or cultured lines. However, in vivo responses involve the coordinated action of multiple cell types, which interact to establish an inflammatory microenvironment. We employed standardized whole-blood stimulation systems to test the hypothesis that responses to Toll-like receptor ligands or whole microbes can be defined by the transcriptional signatures of key cytokines. We found 44 genes, identified using Support Vector Machine learning, that captured the diversity of complex innate immune responses with improved segregation between distinct stimuli. Furthermore, we used donor variability to identify shared inter-cellular pathways and trace cytokine loops involved in gene expression. This provides strategies for dimension reduction of large datasets and deconvolution of innate immune responses applicable for characterizing immunomodulatory molecules. Moreover, we provide an interactive R-Shiny application with healthy donor reference values for induced inflammatory genes.
Published: 2016
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16. Tissue tropism and target cells of NSs-deleted rift valley fever virus in live immunodeficient mice.

Author: Céline Gommet, Agnès Billecocq, Grégory Jouvion, Milena Hasan, Tânia Zaverucha do Valle, Laurent Guillemot, Charlène Blanchet, Nico van Rooijen, Xavier Montagutelli, Michèle Bouloy, and Jean-Jacques Panthier
Subjects: Arctic medicine. Tropical medicine, RC955-962, Public aspects of medicine, RA1-1270
Abstract: BACKGROUND: Rift Valley fever virus (RVFV) causes disease in livestock and humans. It can be transmitted by mosquitoes, inhalation or physical contact with the body fluids of infected animals. Severe clinical cases are characterized by acute hepatitis with hemorrhage, meningoencephalitis and/or retinitis. The dynamics of RVFV infection and the cell types infected in vivo are poorly understood. METHODOLOGY/PRINCIPAL FINDINGS: RVFV strains expressing humanized Renilla luciferase (hRLuc) or green fluorescent protein (GFP) were generated and inoculated to susceptible Ifnar1-deficient mice. We investigated the tissue tropism in these mice and the nature of the target cells in vivo using whole-organ imaging and flow cytometry. After intraperitoneal inoculation, hRLuc signal was observed primarily in the thymus, spleen and liver. Macrophages infiltrating various tissues, in particular the adipose tissue surrounding the pancreas also expressed the virus. The liver rapidly turned into the major luminescent organ and the mice succumbed to severe hepatitis. The brain remained weakly luminescent throughout infection. FACS analysis in RVFV-GFP-infected mice showed that the macrophages, dendritic cells and granulocytes were main target cells for RVFV. The crucial role of cells of the monocyte/macrophage/dendritic lineage during RVFV infection was confirmed by the slower viral dissemination, decrease in RVFV titers in blood, and prolonged survival of macrophage- and dendritic cell-depleted mice following treatment with clodronate liposomes. Upon dermal and nasal inoculations, the viral dissemination was primarily observed in the lymph node draining the injected ear and in the lungs respectively, with a significant increase in survival time. CONCLUSIONS/SIGNIFICANCE: These findings reveal the high levels of phagocytic cells harboring RVFV during viral infection in Ifnar1-deficient mice. They demonstrate that bioluminescent and fluorescent viruses can shed new light into the pathogenesis of RVFV infection.
Published: 2011
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17. A role for the immediate early gene product c-fos in imprinting T cells with short-term memory for signal summation.

Author: Carolyn E Clark, Milena Hasan, and Philippe Bousso
Subjects: Medicine, Science
Abstract: T cells often make sequential contacts with multiple DCs in the lymph nodes and are likely to be equipped with mechanisms that allow them to sum up the successive signals received. We found that a period of stimulation as short as two hours could imprint on a T cell a "biochemical memory" of that activation signal that persisted for several hours. This was evidenced by more rapid induction of activation markers and earlier commitment to proliferation upon subsequent stimulation, even when that secondary stimulation occurred hours later. Upregulation of the immediate early gene product c-fos, a component of the AP-1 transcription factor, was maximal by 1-2 hours of stimulation, and protein levels remained elevated for several hours after stimulus withdrawal. Moreover, phosphorylated forms of c-fos that are stable and transcriptionally active persisted for a least a day. Upon brief antigenic stimulation in vivo, we also observed a rapid upregulation of c-fos that could be boosted by subsequent stimulation. Accumulation of phosphorylated c-fos may therefore serve as a biochemical fingerprint of previous suboptimal stimulation, leaving the T cell poised to rapidly resume its activation program upon its next encounter with an antigen-bearing DC.
Published: 2011
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18. Supplementary Figure from Plasma CD27, a Surrogate of the Intratumoral CD27–CD70 Interaction, Correlates with Immunotherapy Resistance in Renal Cell Carcinoma

Author: Eric Tartour, Stéphane Oudard, Yann A. Vano, Olivier Adotevi, Arnaud Mejean, Julien Adam, Sandrine Katsahian, Laurence Albiges, Nathalie Chaput, Bernd Jabla, Dominique Helley, Laetitia Mauge, Eléonore De Guillebon, Patrice Ravel, Chloe Broudin, Clémence Granier, Sebastien Mella, Valentina Libri, Virginie Verkarre, Camille Nevoret, Valentin Quiniou, Milena Hasan, Joséphine Pineau, Antonin Saldmann, Nadège Gruel, Hang Phuong Pham, Letuan Phan, Alain Gey, Nicolas Epaillard, Ikuan Sam, and Nadine Benhamouda
Abstract: Supplementary Figure from Plasma CD27, a Surrogate of the Intratumoral CD27–CD70 Interaction, Correlates with Immunotherapy Resistance in Renal Cell Carcinoma
Published: 2023
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19. Data from Plasma CD27, a Surrogate of the Intratumoral CD27–CD70 Interaction, Correlates with Immunotherapy Resistance in Renal Cell Carcinoma

Author: Eric Tartour, Stéphane Oudard, Yann A. Vano, Olivier Adotevi, Arnaud Mejean, Julien Adam, Sandrine Katsahian, Laurence Albiges, Nathalie Chaput, Bernd Jabla, Dominique Helley, Laetitia Mauge, Eléonore De Guillebon, Patrice Ravel, Chloe Broudin, Clémence Granier, Sebastien Mella, Valentina Libri, Virginie Verkarre, Camille Nevoret, Valentin Quiniou, Milena Hasan, Joséphine Pineau, Antonin Saldmann, Nadège Gruel, Hang Phuong Pham, Letuan Phan, Alain Gey, Nicolas Epaillard, Ikuan Sam, and Nadine Benhamouda
Abstract: Purpose:CD70 is a costimulatory molecule known to activate CD27-expressing T cells. CD27–CD70 interaction leads to the release of soluble CD27 (sCD27). Clear-cell renal cell carcinoma (ccRCC) expresses the highest levels of CD70 among all solid tumors; however, the clinical consequences of CD70 expression remain unclear.Experimental Design:Tumor tissue from 25 patients with ccRCC was assessed for the expression of CD27 and CD70 in situ using multiplex immunofluorescence. CD27+ T-cell phenotypes in tumors were analyzed by flow cytometry and their gene expression profile were analyzed by single-cell RNA sequencing then confirmed with public data. Baseline sCD27 was measured in 81 patients with renal cell carcinoma (RCC) treated with immunotherapy (35 for training cohort and 46 for validation cohort).Results:In the tumor microenvironment, CD27+ T cells interacted with CD70-expressing tumor cells. Compared with CD27− T cells, CD27+ T cells exhibited an apoptotic and dysfunctional signature. In patients with RCC, the intratumoral CD27–CD70 interaction was significantly correlated with the plasma sCD27 concentration. High sCD27 levels predicted poor overall survival in patients with RCC treated with anti–programmed cell death protein 1 in both the training and validation cohorts but not in patients treated with antiangiogenic therapy.Conclusions:In conclusion, we demonstrated that sCD27, a surrogate marker of T-cell dysfunction, is a predictive biomarker of resistance to immunotherapy in RCC. Given the frequent expression of CD70 and CD27 in solid tumors, our findings may be extended to other tumors.
Published: 2023
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20. Supplementary Table from Plasma CD27, a Surrogate of the Intratumoral CD27–CD70 Interaction, Correlates with Immunotherapy Resistance in Renal Cell Carcinoma

Author: Eric Tartour, Stéphane Oudard, Yann A. Vano, Olivier Adotevi, Arnaud Mejean, Julien Adam, Sandrine Katsahian, Laurence Albiges, Nathalie Chaput, Bernd Jabla, Dominique Helley, Laetitia Mauge, Eléonore De Guillebon, Patrice Ravel, Chloe Broudin, Clémence Granier, Sebastien Mella, Valentina Libri, Virginie Verkarre, Camille Nevoret, Valentin Quiniou, Milena Hasan, Joséphine Pineau, Antonin Saldmann, Nadège Gruel, Hang Phuong Pham, Letuan Phan, Alain Gey, Nicolas Epaillard, Ikuan Sam, and Nadine Benhamouda
Abstract: Supplementary Table from Plasma CD27, a Surrogate of the Intratumoral CD27–CD70 Interaction, Correlates with Immunotherapy Resistance in Renal Cell Carcinoma
Published: 2023
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21. Supplementary Data from Plasma CD27, a Surrogate of the Intratumoral CD27–CD70 Interaction, Correlates with Immunotherapy Resistance in Renal Cell Carcinoma

Author: Eric Tartour, Stéphane Oudard, Yann A. Vano, Olivier Adotevi, Arnaud Mejean, Julien Adam, Sandrine Katsahian, Laurence Albiges, Nathalie Chaput, Bernd Jabla, Dominique Helley, Laetitia Mauge, Eléonore De Guillebon, Patrice Ravel, Chloe Broudin, Clémence Granier, Sebastien Mella, Valentina Libri, Virginie Verkarre, Camille Nevoret, Valentin Quiniou, Milena Hasan, Joséphine Pineau, Antonin Saldmann, Nadège Gruel, Hang Phuong Pham, Letuan Phan, Alain Gey, Nicolas Epaillard, Ikuan Sam, and Nadine Benhamouda
Abstract: Supplementary Data from Plasma CD27, a Surrogate of the Intratumoral CD27–CD70 Interaction, Correlates with Immunotherapy Resistance in Renal Cell Carcinoma
Published: 2023
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22. Environmental and genetic drivers of population differences in SARS-CoV-2 immune responses

Author: Yann Aquino, Aurélie Bisiaux, Zhi Li, Mary O’Neill, Javier Mendoza-Revilla, Sarah Hélène Merkling, Gaspard Kerner, Milena Hasan, Valentina Libri, Vincent Bondet, Nikaïa Smith, Camille de Cevins, Mickaël Ménager, Francesca Luca, Roger Pique-Regi, Giovanna Barba-Spaeth, Stefano Pietropaoli, Olivier Schwartz, Geert Leroux-Roels, Cheuk-Kwong Lee, Kathy Leung, Joseph T.K. Wu, Malik Peiris, Roberto Bruzzone, Laurent Abel, Jean-Laurent Casanova, Sophie A. Valkenburg, Darragh Duffy, Etienne Patin, Maxime Rotival, Lluis Quintana-Murci, Génétique Evolutive Humaine - Human Evolutionary Genetics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Collège Doctoral, Sorbonne Université (SU), Interactions Virus-Insectes - Insect-Virus Interactions (IVI), Cytometrie et Biomarqueurs – Cytometry and Biomarkers (UTechS CB), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Immunologie Translationnelle - Translational Immunology lab, Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Inflammatory Responses and Transcriptomic Networks in diseases (Equipe Inserm U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Wayne State University [Detroit], University of Rome 'Tor Vergeta', Università degli Studi di Roma Tor Vergata [Roma], Virologie Structurale - Structural Virology, Virus et Immunité - Virus and immunity (CNRS-UMR3569), Universiteit Gent = Ghent University (UGENT), Ghent University Hospital, Hong Kong Red Cross Blood Transfusion Service, Hospital Authority, The University of Hong Kong (HKU), Rockefeller University [New York], CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Human genetics of infectious diseases: Complex predisposition (Equipe Inserm U1163), Howard Hughes Medical Institute (HHMI), University of Melbourne, Hong Kong Science and Technology Parks Corporation (HKSTP), Collège de France - Chaire Génomique humaine et évolution, Collège de France (CdF (institution)), The Human Evolutionary Genetics Laboratory is supported by the Institut Pasteur, the Collège de France, the Centre Nationale de la Recherche Scientifique (CNRS), the Agence Nationale de la Recherche (ANR) grants COVID-19-POPCELL (ANR-21-CO14-0003-01), POPCELL-REG (ANR-22-CE12-0030-01) and COVIFERON (ANR-21-RHUS-0008), the EU HORIZON-HLTH-2021-DISEASE-04-07 grant UNDINE (no. 101057100), the French Government’s Investissement d’Avenir program, Laboratoires d’Excellence 'Integrative Biology of Emerging Infectious Diseases' (ANR-10- LABX-62-IBEID) and 'Milieu Intérieur' (ANR-10-LABX-69-01), the Fondation pour la Recherche Médicale (Equipe FRM DEQ20180339214), the Fondation Allianz-Institut de France, and the Fondation de France (no. 00106080). K.L., J.T.K.W. and M.P. are supported by the Health and Medical Research Fund Commissioned Research on the Novel Coronavirus Disease, Hong Kong SAR (COVID190126), S.A.V by the Theme-based Research Scheme of the Research Grants Council of the Hong Kong SAR (T11-705/21-N, SAV: T11-712/19-N), and M.P., R.B. and D.D. by InnoHK, an initiative of the Innovation and Technology Commission, the Government of the Hong Kong SAR., ANR-21-CO14-0003,COVID-19-POPCELL,Facteurs génétiques et infectieux à l'origine de la variabilité populationnelle de la réponse immunitaire à l'infection par le SARS-CoV-2(2021), ANR-22-CE12-0030,popCell-REG,Variation populationnelle des profils d'accessibilité de la chromatine à l'échelle unicellulaire(2022), ANR-21-RHUS-0008,COVIFERON,Covid-19 and interferons: from discovery to therapy(2021), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), and ANR-10-LABX-0069,MILIEU INTERIEUR,GENETIC & ENVIRONMENTAL CONTROL OF IMMUNE PHENOTYPE VARIANCE: ESTABLISHING A PATH TOWARDS PERSONALIZED MEDICINE(2010)
Subjects: [SDV]Life Sciences [q-bio]
Abstract: The RNA sequencing data generated and analyzed in this study have been deposited in the Institut Pasteur data repository, OWEY, which can be accessed via the following link: https://doi.org/XXXX. The genome-wide genotyping data generated or used in this study have been deposited in OWEY and can be accessed at the following URL: https://doi.org/XXXX. Data access and use is restricted to academic research related to the variability of the human immune response.; Humans display vast clinical variability upon SARS-CoV-2 infection 1–3 , partly due to genetic and immunological factors 4 . However, the magnitude of population differences in immune responses to SARS-CoV-2 and the mechanisms underlying such variation remain unknown. Here we report single-cell RNA-sequencing data for peripheral blood mononuclear cells from 222 healthy donors of various ancestries stimulated with SARS-CoV-2 or influenza A virus. We show that SARS-CoV-2 induces a weaker, but more heterogeneous interferon-stimulated gene activity than influenza A virus, and a unique pro-inflammatory signature in myeloid cells. We observe marked population differences in transcriptional responses to viral exposure that reflect environmentally induced cellular heterogeneity, as illustrated by higher rates of cytomegalovirus infection, affecting lymphoid cells, in African-descent individuals. Expression quantitative trait loci and mediation analyses reveal a broad effect of cell proportions on population differences in immune responses, with genetic variants having a narrower but stronger effect on specific loci. Additionally, natural selection has increased immune response differentiation across populations, particularly for variants associated with SARS-CoV-2 responses in East Asians. We document the cellular and molecular mechanisms through which Neanderthal introgression has altered immune functions, such as its impact on the myeloid response in Europeans. Finally, colocalization analyses reveal an overlap between the genetic architecture of immune responses to SARS-CoV-2 and COVID-19 severity. Collectively, these findings suggest that adaptive evolution targeting immunity has also contributed to current disparities in COVID-19 risk.
Published: 2023

23. Early IFNβ secretion determines variable downstream IL-12p70 responses upon TLR4 activation

Author: Celine Posseme, Alba Llibre, Bruno Charbit, Vincent Bondet, Vincent Rouilly, Violaine Saint-André, Jeremy Boussier, Jacob Bergstedt, Nikaïa Smith, Liam Townsend, Jamie A. Sugrue, Clíona Ní Cheallaigh, Niall Conlon, Maxime Rotival, Michael S. Kobor, Estelle Mottez, Stanislas Pol, Etienne Patin, Matthew L. Albert, Lluis Quintana-Murci, Darragh Duffy, Laurent Abel, Andres Alcover, Hugues Aschard, Philippe Bousso, Nollaig Bourke, Petter Brodin, Pierre Bruhns, Nadine Cerf-Bensussan, Ana Cumano, Caroline Demangel, null Christophe d’Enfert, Ludovic Deriano, Marie-Agnès Dillies, James Di Santo, Françoise Dromer, Gérard Eberl, Jost Enninga, Jacques Fellay, Ivo Gomperts-Boneca, Milena Hasan, Magnus Fontes, Gunilla Karlsson Hedestam, Serge Hercberg, Molly A. Ingersoll, Rose Anne Kenny, Olivier Lantz, Mickael Ménager, Frédérique Michel, Hugo Mouquet, Cliona O'Farrelly, Sandra Pellegrini, Antonio Rausell, Frédéric Rieux-Laucat, Lars Rogge, Anavaj Sakuntabhai, Olivier Schwartz, Benno Schwikowski, Spencer Shorte, Frédéric Tangy, Antoine Toubert, Mathilde Touvier, Marie-Noëlle Ungeheuer, Christophe Zimmer, Immunologie Translationnelle - Translational Immunology lab, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Ecole Doctorale Frontiere de l’Innovation en Recherche et Education (ED 474 FIRE), Université Paris Cité (UPCité)-Université Paris sciences et lettres (PSL), Cytometrie et Biomarqueurs – Cytometry and Biomarkers (UTechS CB), Datactix, Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Génétique Evolutive Humaine - Human Evolutionary Genetics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), St James’s Hospital [Dublin, Ireland], Trinity College Dublin, University of British Columbia [Vancouver], Hôpital Cochin [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), HIBIO [South San Francisco], Collège de France - Chaire Génomique humaine et évolution, Collège de France (CdF (institution)), This study was funded with support from the French Governments Investissement dAvenir Program, Laboratoire Excellence Milieu Interieur Grant ANR-10-LABX-69-01 and by an Agence National de Recherche foundation grant (CE17001002)., The Milieu Intérieur Consortium is composed of the following team leaders: Laurent Abel (Hôpital Necker), Andres Alcover, Hugues Aschard, Philippe Bousso, Nollaig Bourke (Trinity College Dublin), Petter Brodin (Karolinska Institutet), Pierre Bruhns, Nadine Cerf-Bensussan (INSERM UMR 1163 – Institut Imagine), Ana Cumano, Caroline Demangel, Christophe d’Enfert, Ludovic Deriano, Marie-Agnès Dillies, James Di Santo, Françoise Dromer, Gérard Eberl, Jost Enninga, Jacques Fellay (EPFL, Lausanne), Ivo Gomperts-Boneca, Milena Hasan, Magnus Fontes (Institut Roche), Gunilla Karlsson Hedestam (Karolinska Institutet), Serge Hercberg (Université Paris 13), Molly Ingersoll, Rose Anne Kenny (Trinity College Dublin), Olivier Lantz (Institut Curie), Frédérique Michel, Hugo Mouquet, Cliona O'Farrelly (Trinity College Dublin), Etienne Patin, Sandra Pellegrini, Stanislas Pol (Hôpital Côchin), Antonio Rausell (INSERM UMR 1163 – Institut Imagine), Frédéric Rieux-Laucat (INSERM UMR 1163 – Institut Imagine), Lars Rogge, Anavaj Sakuntabhai, Olivier Schwartz, Benno Schwikowski, Spencer Shorte, Frédéric Tangy, Antoine Toubert (Hôpital Saint-Louis), Mathilde Touvier (Université Paris 13), Marie-Noëlle Ungeheuer, Christophe Zimmer, Matthew L. Albert (In Sitro), Darragh Duffy, Lluis Quintana-Murci, ANR-10-LABX-0069,MILIEU INTERIEUR,GENETIC & ENVIRONMENTAL CONTROL OF IMMUNE PHENOTYPE VARIANCE: ESTABLISHING A PATH TOWARDS PERSONALIZED MEDICINE(2010), ANR-20-CE17-0010,ELECTRO,Inhibition de l'Exchange Protein directly activated by cAMP -1 pour traiter la Fibrillation Atrial(2020), Institut Pasteur [Paris] (IP), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute-University of British Columbia (UBC), University of Cape Town, Département d'hépatologie [CHU Cochin], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Insitro [San Francisco], St James's University Hospital, Leeds Teaching Hospitals NHS Trust, University of British Columbia (UBC), This study was funded with support from the French Government’s Investissement d’Avenir Program, Laboratoire d’Excellence 'Milieu Intérieur' grant ANR-10-LABX-69-01, and by an Agence National de Recherche Foundation grant (CE17001002). We thank the UTechS CB of the Center for Translational Research, Institut Pasteur for supporting data generation, Pierre-Henri Commere for help with flow cytometry sorting, Aurelie Bisiaux for flow cytometry advice, and Dr. Molly Ingersoll for scientific advice and critical reading of the manuscript. D.D. thanks Immunoqure for provision of the mAbs under an MTA for the Simoa IFNα assay. We thank the STTAR-Bioresource of TCD-SJH-TUH COVID-19 bioresource, which supported collection of COVID-19 patient samples, and the 'URGENCE COVID-19' fundraising campaign of the Institut Pasteur (CoVarImm and Steroid Response) for supporting data generation of COVID-19 samples. N.S. is a recipient of the Pasteur-Roux-Cantarini Fellowship. N.C. and C.N.C. are part funded by a Science Foundation Ireland (SFI) grant, grant code 20/SPP/3685. L.T. is supported by the Irish Clinical Academic Training (ICAT) Program, supported by the Wellcome Trust and the Health Research Board (grant number 203930/B/16/Z), the Health Service Executive, National Doctors Training and Planning, and the Health and Social Care, Research and Development Division, Northern Ireland., Milieu Intérieur Consortium: Laurent Abel, Andres Alcover, Hugues Aschard, Philippe Bousso, Nollaig Bourke, Petter Brodin, Pierre Bruhns, Nadine Cerf-Bensussan, Ana Cumano, Caroline Demangel, Christophe d'Enfert, Ludovic Deriano, Marie-Agnès Dillies, James Di Santo, Françoise Dromer, Gérard Eberl, Jost Enninga, Jacques Fellay, Ivo Gomperts-Boneca, Milena Hasan, Magnus Fontes, Gunilla Karlsson Hedestam, Serge Hercberg, Molly A Ingersoll, Rose Anne Kenny, Olivier Lantz, Mickael Ménager, Frédérique Michel, Hugo Mouquet, Cliona O'Farrelly, Etienne Patin, Sandra Pellegrini, Stanislas Pol, Antonio Rausell, Frédéric Rieux-Laucat, Lars Rogge, Anavaj Sakuntabhai, Olivier Schwartz, Benno Schwikowski, Spencer Shorte, Frédéric Tangy, Antoine Toubert, Mathilde Touvier, Marie-Noëlle Ungeheuer, Christophe Zimmer, Matthew L Albert, Darragh Duffy, Lluis Quintana-Murci, and ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010)
Subjects: Lipopolysaccharides, Proteomics, History, Polymers and Plastics, [SDV]Life Sciences [q-bio], medicine.medical_treatment, Disease, systems immunology, Biology, General Biochemistry, Genetics and Molecular Biology, Industrial and Manufacturing Engineering, Immune system, medicine, Humans, Secretion, Epigenetics, Business and International Management, Epigenomics, TLR4 immune responses, Systems immunology, SARS-CoV-2, COVID-19, CP: Immunology, Interferon-beta, Interleukin-12, Toll-Like Receptor 4, Cytokine, IL-12p70, type I interferons, Immunology, TLR4, Cytokine variability, [SDV.IMM]Life Sciences [q-bio]/Immunology, Cytokines
Abstract: International audience; The interleukin-12 (IL-12) family comprises the only heterodimeric cytokines mediating diverse functional effects. We previously reported a striking bimodal IL-12p70 response to lipopolysaccharide (LPS) stimulation in healthy donors. Herein, we demonstrate that interferon β (IFNβ) is a major upstream determinant of IL-12p70 production, which is also associated with numbers and activation of circulating monocytes. Integrative modeling of proteomic, genetic, epigenomic, and cellular data confirms IFNβ as key for LPS-induced IL-12p70 and allowed us to compare the relative effects of each of these parameters on variable cytokine responses. Clinical relevance of our findings is supported by reduced IFNβ-IL-12p70 responses in patients hospitalized with acute severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection or chronically infected with hepatitis C (HCV). Importantly, these responses are resolved after viral clearance. Our systems immunology approach defines a better understanding of IL-12p70 and IFNβ in healthy and infected persons, providing insights into how common genetic and epigenetic variation may impact immune responses to bacterial infection.
Published: 2021
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24. Immune Profiling Enables Stratification of Patients With Active Tuberculosis Disease or Mycobacteriu m tuberculosis Infection

Author: Françoise Dromer, Antonio Rausell, Elizabeth Filander, Bruno Charbit, Odile Gelpi, Kalla Astrom, Stanislas Pol, Elisa Nemes, Vincent Rouilly, Mark Hatherill, Hadn Africa, Humphrey Mulenga, Ana Cumano, Hugo Mouquet, Etienne Patin, Lluis Quintana-Murci, Lungisa Jaxa, Laurent Abel, Milena Hasan, James P. Di Santo, Claude Leclerc, Spencer L. Shorte, Vassili Soumelis, Stéphanie Thomas, Caroline Demangel, Mathilde Touvier, Andrés Alcover, Thomas J. Scriba, Matthew L. Albert, Anavaj Sakuntabhai, Hugues Aschard, Nikaïa Smith, Serge Hercberg, Darragh Duffy, Jost Enninga, Olivier Schwartz, Ivo Gomperts-Boneca, Marie-Noëlle Ungeheuer, Simbarashe Mabwe, Ludovic Deriano, Frédéric Tangy, Gérard Eberl, Sandra Pellegrini, Antoine Toubert, Lars Rogge, Stephanus T. Malherbe, Gerhard Walzl, Michele Tameris, Munyaradzi Musvosvi, Alba Llibre, Benno Schwikowski, Olivier Lantz, Nicole Bilek, Philippe Bousso, Pierre Bruhns, Jacques Fellay, and Eric Tartour
Subjects: 0301 basic medicine, Microbiology (medical), Tuberculosis, Enzyme-Linked Immunosorbent Assay, Disease, Asymptomatic, QuantiFERON, Mycobacterium tuberculosis, Interferon-gamma, 03 medical and health sciences, 0302 clinical medicine, Antigen, Latent Tuberculosis, medicine, Humans, 030212 general & internal medicine, Online only Articles, Whole blood, biology, business.industry, immune profiling, biomarkers, patient stratification, bacterial infections and mycoses, medicine.disease, biology.organism_classification, cytokines, 3. Good health, AcademicSubjects/MED00290, 030104 developmental biology, Infectious Diseases, Cohort, Immunology, medicine.symptom, business, Interferon-gamma Release Tests
Abstract: Background Tuberculosis (TB) is caused by Mycobacterium tuberculosis (Mtb) infection and is a major public health problem. Clinical challenges include the lack of a blood-based test for active disease. Current blood-based tests, such as QuantiFERON (QFT) do not distinguish active TB disease from asymptomatic Mtb infection. Methods We hypothesized that TruCulture, an immunomonitoring method for whole-blood stimulation, could discriminate active disease from latent Mtb infection (LTBI). We stimulated whole blood from patients with active TB and compared with LTBI donors. Mtb-specific antigens and live bacillus Calmette-Guérin (BCG) were used as stimuli, with direct comparison to QFT. Protein analyses were performed using conventional and digital enzyme-linked immunosorbent assay (ELISA), as well as Luminex. Results TruCulture showed discrimination of active TB cases from LTBI (P < .0001, AUC = .81) compared with QFT (P = .45, AUC = .56), based on an interferon γ (IFNγ) readout after Mtb antigen (Ag) stimulation. This result was replicated in an independent cohort (AUC = .89). In exploratory analyses, TB stratification could be further improved by the Mtb antigen to BCG IFNγ ratio (P < .0001, AUC = .91). Finally, the combination of digital ELISA and transcriptional analysis showed that LTBI donors with high IFNγ clustered with patients with TB, suggesting the possibility to identify subclinical disease. Conclusions TruCulture offers a next-generation solution for whole-blood stimulation and immunomonitoring with the possibility to discriminate active and latent infection., We tested TruCulture, an immunomonitoring tool, to identify active disease from latent Mtb infection. TruCulture showed improved discrimination of tuberculosis cases from LTBI as compared with QuantiFERON. Tuberculosis stratification could be further improved by the Mtb Ag:BCG IFNγ ratio.
Published: 2020
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25. Dengue virus NS1 protein conveys pro‐inflammatory signals by docking onto high‐density lipoproteins

Author: Souheyla Benfrid, Kyu‐Ho Park, Mariano Dellarole, James E Voss, Carole Tamietti, Gérard Pehau‐Arnaudet, Bertrand Raynal, Sébastien Brûlé, Patrick England, Xiaokang Zhang, Anastassia Mikhailova, Milena Hasan, Marie‐Noëlle Ungeheuer, Stéphane Petres, Scott B Biering, Eva Harris, Anavaj Sakuntabhai, Philippe Buchy, Veasna Duong, Philippe Dussart, Fasséli Coulibaly, François Bontems, Félix A Rey, Marie Flamand, Virologie Structurale - Structural Virology, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Université Paris Descartes, Sorbonne Paris Cité, Plateforme BioImagerie Ultrastructurale – Ultrastructural BioImaging Platform (UTechS UBI), Institut Pasteur [Paris] (IP), Biophysique Moléculaire (plateforme) - Molecular Biophysics (platform), HIV, Inflammation et persistance - HIV, Inflammation and Persistence, Cytometrie et Biomarqueurs – Cytometry and Biomarkers (UTechS CB), Investigation Clinique et d’Accès aux Ressources Biologiques (Plate-forme) - Clinical Investigation and Access to BioResources (ICAReB), Plateforme technologique Production et purification de protéines recombinantes – Production and Purification of Recombinant Proteins Technological Platform (PPR), University of California [Berkeley] (UC Berkeley), University of California (UC), Génétique du Développement humain - Human developmental genetics, Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur (RIIP), Monash University [Clayton], Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), This study benefited from the financial support of the Institut Pasteur ACIP-27-16 (P.D., V.D., M.F.), the Institut Pasteur Dengue Task Force (to MF), the Institut Pasteur INNOV-44-19 (M.F), the National Natural Science Foundation of China 31600606 (X.Z.), the National Key R&D Program of China 2016YFA0501100 (X.Z.), Guangdong Provincial Key Laboratory of Brain Connectome and Behavior 2017B030301017 (X.Z.), CAS Key Laboratory of Brain Connectome and Manipulation 2019DP173024 (X.Z.), the NIAID/NIH R01 AI24493 (E.H.) and R21 AI146464 (E.H.), ANR Equipex CACSICE ANR-11-EQPX-0008 (G.P.-A.)., The authors gratefully acknowledge the staff of the Kampong Cham Referral Hospital, the patients and parents who participated in the study, and the Arbovirus Team in the Virology Unit at the Institut Pasteur du Cambodge who contributed to this study. We acknowledge the participation of the ICAReB facility in setting up the recruitment of donors and the acquisition of blood samples, in particular Gloria Morizot, Bianca Liliana Perlaza, Sophie Chaouche, Linda Sangari, Céline Chapel, Philippe Esterre and Hélène Laude. We are most grateful to Christine Girard-Blanc and Evelyne Dufour for their contribution in producing and purifying the recombinant DENV NS1 protein, to Béatrice Poirier-Beaudouin and Cartini Mardi for their help in setting up the cytokine quantification assay, to Arvind Sharma for providing purified anti-E MAbs, to Mathilde Ban for preparing Fab-bound NS1-HDL complexes and to Xavier Montagutelli and Etienne Simon-Lorière for testing an in vivo protection assay. We thank M. Nilges and the Equipex CACSICE for providing the Falcon II direct detector and David Veesler for his help in acquiring the first electron microscopy images of the bovine NS1-HDL complex. Finally, we thank Sébastien Quesney, Alexandre Pachot and Karine Kaiser for their support. The synopsis figure was created with BioRender.com., and ANR-11-EQPX-0008,CACSICE,Centre d'analyse de systèmes complexes dans les environnements complexes(2011)
Subjects: Arbovirus, lipoprotein particle, viruses, accessory protein, virus diseases, Dengue Virus, Viral Nonstructural Proteins, biochemical phenomena, metabolism, and nutrition, Biochemistry, virulence factor, Dengue, molecular pathogenesis, Phagocytosis, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Genetics, Humans, [SDV.IMM]Life Sciences [q-bio]/Immunology, lipids (amino acids, peptides, and proteins), Lipoproteins, HDL, Molecular Biology, hemorrhagic fever
Abstract: International audience; The dengue virus nonstructural protein 1 (NS1) is a secreted virulence factor that modulates complement, activates immune cells and alters endothelial barriers. The molecular basis of these events remains incompletely understood. Here we describe a functional high affinity complex formed between NS1 and human high-density lipoproteins (HDL). Collapse of the soluble NS1 hexamer upon binding to the lipoprotein particle leads to the anchoring of amphipathic NS1 dimeric subunits into the HDL outer layer. The stable complex can be visualized by electron microscopy as a spherical HDL with rod-shaped NS1 dimers protruding from the surface. We further show that the assembly of NS1-HDL complexes triggers the production of pro-inflammatory cytokines in human primary macrophages while NS1 or HDL alone do not. Finally, we detect NS1 in complex with HDL and low-density lipoprotein (LDL) particles in the plasma of hospitalized dengue patients and observe NS1-apolipoprotein E-positive complexes accumulating overtime. The functional reprogramming of endogenous lipoprotein particles by NS1 as a means to exacerbate systemic inflammation during viral infection provides a new paradigm in dengue pathogenesis.
Published: 2022
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26. Biological differences between FIM2 and FIM3 fimbriae of Bordetella pertussis: not just the serotype

Author: Soraya Matczak, Valérie Bouchez, Pauline Leroux, Thibaut Douché, Nils Collinet, Annie Landier, Quentin Giai Gianetto, Sophie Guillot, Julia Chamot-Rooke, Milena Hasan, Mariette Matondo, Sylvain Brisse, Julie Toubiana, Biodiversité et Epidémiologie des Bactéries pathogènes - Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Plateforme de Protéomique / Proteomics platform, Université Paris Cité (UPCité)-Spectrométrie de Masse pour la Biologie – Mass Spectrometry for Biology (UTechS MSBio), Institut Pasteur [Paris] (IP)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut Pasteur [Paris] (IP)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Centre national de Référence de la Coqueluche et autres Bordetelloses - National Reference Center for Whooping Cough and other Bordetella infections (CNR), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Spectrométrie de Masse pour la Biologie – Mass Spectrometry for Biology (UTechS MSBio), Institut Pasteur [Paris] (IP)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Cytometrie et Biomarqueurs – Cytometry and Biomarkers (UTechS CB), Département de Pédiatrie et maladies infectieuses [CHU Necker], CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), JT received funding from Ville de Paris as part of the EMERGENCE program. SM received funding from la Fondation pour la Recherche Médicale (FRM). SB received funding from INCEPTION program (ANR-16-CONV-0005)., and ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016)
Subjects: Infectious Diseases, [SDV]Life Sciences [q-bio], Immunology, Microbiology, Microbes and Infection
Abstract: International audience; Introduction: Bordetella pertussis still circulates worldwide despite vaccination. Fimbriae are components of some acellular pertussis vaccines. Population fluctuations of B. pertussis fimbrial serotypes (FIM2 and FIM3) are observed, and fim3 alleles (fim3-1 [clade 1] and fim3-2 [clade 2]) mark a major phylogenetic subdivision of B. pertussis. Objectives: To compare microbiological characteristics and expressed protein profiles between fimbrial serotypes FIM2 and FIM3 and genomic clades. Methods: A total of 23 isolates were selected. Absolute protein abundance of the main virulence factors, autoagglutination and biofilm formation, bacterial survival in whole blood, induced blood cell cytokine secretion, and global proteome profiles were assessed. Results: Compared to FIM3, FIM2 isolates produced more fimbriae, less cellular pertussis toxin subunit 1 and more biofilm, but auto-agglutinated less. FIM2 isolates had a lower survival rate in cord blood, but induced higher levels of IL-4, IL-8 and IL-1 secretion. Global proteomecomparisons uncovered 15 differentially produced proteins between FIM2 and FIM3 isolates, involved in adhesion and metabolism of metals. FIM3 isolates of clade 2 produced more FIM3 and more biofilm compared to clade 1. Conclusion: FIM serotype and fim3 clades are associated with proteomic and other biological differences, which may have implications on pathogenesis and epidemiological emergence.
Published: 2023
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27. Plasma CD27, a Surrogate of the Intratumoral CD27-CD70 Interaction, Correlates with Immunotherapy Resistance in Renal Cell Carcinoma

Author: Nadine Benhamouda, Ikuan Sam, Nicolas Epaillard, Alain Gey, Letuan Phan, Hang Phuong Pham, Nadège Gruel, Antonin Saldmann, Joséphine Pineau, Milena Hasan, Valentin Quiniou, Camille Nevoret, Virginie Verkarre, Valentina Libri, Sebastien Mella, Clémence Granier, Chloe Broudin, Patrice Ravel, Eléonore De Guillebon, Laetitia Mauge, Dominique Helley, Bernd Jabla, Nathalie Chaput, Laurence Albiges, Sandrine Katsahian, Julien Adam, Arnaud Mejean, Olivier Adotevi, Yann A. Vano, Stéphane Oudard, Eric Tartour, Paris-Centre de Recherche Cardiovasculaire (PARCC (UMR_S 970/ U970)), Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), Parean biotechnologies, Unité de génétique et biologie des cancers (U830), Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Cytometrie et Biomarqueurs – Cytometry and Biomarkers (UTechS CB), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Centre de Recherche des Cordeliers (CRC (UMR_S_1138 / U1138)), École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Paris Cité (UPCité), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut de Recherche en Cancérologie de Montpellier (IRCM - U1194 Inserm - UM), CRLCC Val d'Aurelle - Paul Lamarque-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Institut Curie [Paris], Institut Gustave Roussy (IGR), Centre d'Investigation Clinique de Besançon (Inserm CIC 1431), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Etablissement français du sang [Bourgogne-Franche-Comté] (EFS BFC)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), This work was funded by the Fondation ARC pour la Recherche sur le Cancer (Grant number SIGN'IT20181007747 and PGA12019110000946_1581 to E. Tartour), the INCA (Institut National du Cancer) (Grant number 2016–1-PL BIO-05–1 to E. Tartour), the Agence Nationale de la Recherche (Labex Immuno-Oncology to E. Tartour), the Institut National du Cancer (Grant SIRIC CARPEM to E. Tartour, S. Oudard), FONCER (to E. Tartour and S. Oudard), IDEX Université de Paris (Grant number AMI-CD27CD70BLOC to E. Tartour), and Inserm Transfert (Grant number: MAT-PI-20278–1-02 to E. Tartour), We thank the staff of the tumor banks of HEGP (B. Vedie and D. Geromin) for providing the sample materials and the Histology platform of PARCC (C. Lesaffre). We thank Franck Pages and Florence Marliot for providing access to the Halo software platform., and ANR-10-LABX-0015,ImmunoOnco,Immuno-Oncology(2010)
Subjects: Cancer Research, Oncology, [SDV]Life Sciences [q-bio], Tumor Microenvironment, Humans, Immunotherapy, Carcinoma, Renal Cell, Kidney Neoplasms, CD27 Ligand, Tumor Necrosis Factor Receptor Superfamily, Member 7
Abstract: Purpose:CD70 is a costimulatory molecule known to activate CD27-expressing T cells. CD27–CD70 interaction leads to the release of soluble CD27 (sCD27). Clear-cell renal cell carcinoma (ccRCC) expresses the highest levels of CD70 among all solid tumors; however, the clinical consequences of CD70 expression remain unclear.Experimental Design:Tumor tissue from 25 patients with ccRCC was assessed for the expression of CD27 and CD70 in situ using multiplex immunofluorescence. CD27+ T-cell phenotypes in tumors were analyzed by flow cytometry and their gene expression profile were analyzed by single-cell RNA sequencing then confirmed with public data. Baseline sCD27 was measured in 81 patients with renal cell carcinoma (RCC) treated with immunotherapy (35 for training cohort and 46 for validation cohort).Results:In the tumor microenvironment, CD27+ T cells interacted with CD70-expressing tumor cells. Compared with CD27− T cells, CD27+ T cells exhibited an apoptotic and dysfunctional signature. In patients with RCC, the intratumoral CD27–CD70 interaction was significantly correlated with the plasma sCD27 concentration. High sCD27 levels predicted poor overall survival in patients with RCC treated with anti–programmed cell death protein 1 in both the training and validation cohorts but not in patients treated with antiangiogenic therapy.Conclusions:In conclusion, we demonstrated that sCD27, a surrogate marker of T-cell dysfunction, is a predictive biomarker of resistance to immunotherapy in RCC. Given the frequent expression of CD70 and CD27 in solid tumors, our findings may be extended to other tumors.
Published: 2022
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28. SCHNAPPs - Single Cell sHiNy APPlication(s)

Author: Bernd, Jagla, Valentina, Libri, Claudia, Chica, Vincent, Rouilly, Sebastien, Mella, Michel, Puceat, Milena, Hasan, Cytometrie et Biomarqueurs – Cytometry and Biomarkers (UTechS CB), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Datactix, Marseille medical genetics - Centre de génétique médicale de Marseille (MMG), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), We would like to thank the members of Single-cell working group Pasteur/Paris for helpful discussions: Anna Barcons, Eric Tartour, Antonin Saldmann, Mandar Patgaonkar, Lisa Chakrabarti, and James Di Santo for testing and working with scShinyHub and SCHNAPPs. Kenneth Smith and Christian Vosshenrich for careful reading of the manuscript. We thank the ICAReB platform of the Institut Pasteur for providing blood samples from healthy individuals., Institut Pasteur [Paris], Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Aix Marseille Université (AMU), and Chica, Claudia
Subjects: MESH: Humans, Sequence Analysis, RNA, CITE-Seq, Shiny application, MESH: Leukocytes, Mononuclear, MESH: Software, scRNA-seq, Leukocytes, Mononuclear, MESH: Sequence Analysis, RNA, Humans, Single-Cell Analysis, multi-omics data analysis, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Software, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], MESH: Single-Cell Analysis
Abstract: International audience; Single-cell RNA-sequencing (scRNAseq) experiments are becoming a standard tool for bench-scientists to explore the cellular diversity present in all tissues. Data produced by scRNAseq is technically complex and requires analytical workflows that are an active field of bioinformatics research, whereas a wealth of biological background knowledge is needed to guide the investigation. Thus, there is an increasing need to develop applications geared towards bench-scientists to help them abstract the technical challenges of the analysis so that they can focus on the science at play. It is also expected that such applications should support closer collaboration between bioinformaticians and bench-scientists by providing reproducible science tools. We present SCHNAPPs, a Graphical User Interface (GUI), designed to enable bench-scientists to autonomously explore and interpret scRNAseq data and associated annotations. The R/Shiny-based application allows following different steps of scRNAseq analysis workflows from Seurat or Scran packages: performing quality control on cells and genes, normalizing the expression matrix, integrating different samples, dimension reduction, clustering, and differential gene expression analysis. Visualization tools for exploring each step of the process include violin plots, 2D projections, Box-plots, alluvial plots, and histograms. An R-markdown report can be generated that tracks modifications and selected visualizations. The modular design of the tool allows it to easily integrate new visualizations and analyses by bioinformaticians. We illustrate the main features of the tool by applying it to the characterization of T cells in a scRNAseq and Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-Seq) experiment of two healthy individuals.
Published: 2021
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29. P09.05 Plasma CD27, a surrogate of intratumoral CD27-CD70 interaction, correlates with immunotherapy resistance in renal cancer

Author: Virginie Verkarre, Valentina Libri, I Sam, B Jabla, Alain Gey, C. Granier, Nicolas Epaillard, Patrice Ravel, Eric Tartour, Milena Hasan, Nathalie Chaput, S Mella, J Pineau, Stéphane Oudard, Laurence Albiges, A Saldmann, Nadine Benhamouda, Olivier Adotevi, Yann-Alexandre Vano, and C Broudin
Subjects: Tumor microenvironment, LAG3, business.industry, medicine.medical_treatment, T cell, Immunotherapy, Gene signature, medicine.disease, Clear cell renal cell carcinoma, medicine.anatomical_structure, medicine, Cancer research, Antigen-presenting cell, business, Memory T cell
Abstract: Background CD70, a costimulatory molecule on antigen presenting cells, is known to activate CD27-expressing T cells. CD27-CD70 interaction leads to the release of soluble CD27 (sCD27). However, persistent interaction of CD27 and CD70 such as in chronic infection may exhaust the T cell pool and promote apoptosis. Surprisingly, our analysis based on TCGA database show that clear cell renal cell carcinoma (ccRCC) expresses the highest levels of CD70 among all solid tumors. Despite the important clinical efficacy of immunotherapy by anti-PD-1 in RCC patients, the overall response to anti-PD1 remains modest. The relationship between the CD27-CD70 interaction in the RCC and the response to immunotherapy is still unclear. Materials and Methods To study the CD27 and CD70 expression in the tumor microenvironment (TME), FFPE tumor tissues from 25 RCC patients were analysed using multiplex in situ immunofluorescence. 10 fresh RCC tumor samples were collected to analyse the phenotype of CD27+ T cells by flow cytometry and 4 samples were proceeded for single-cell RNA-seq analysis. A cohort of metastatic RCC patients (n = 35) treated by anti-PD-1 were enrolled for the measurement of plasma sCD27 by ELISA and the survival analysis is also realized. Results In the TME, we demonstrated that CD27+ T cells interact with CD70-expressing tumor cells. In fresh tumors from RCC patients, CD27+ T cells express higher levels of cleaved caspase 3 (a classical marker of apoptosis) than CD27- T cells. We confirmed the apoptotic signature (BAX, FASLG, BCL2L11, CYCS, FBXO32, LGALS1, PIK3R1, TERF1, TXNIP, CDKN2A) of CD27+ T cells by single-cell RNAseq analysis. CD27+T cells also had a tissue resident memory T cell phenotype with enriched gene expression of ITGAE, PRDM1, RBPJ and ZNF683. Moreover, CD27+T cells display an exhaustion phenotype with the expression of multiple inhibitory receptors gene signature (PDCD1, CTLA4, HAVCR2, LAG3, etc). Besides, intratumoral CD27-CD70 interaction significantly correlates with plasma sCD27 concentration in RCC (p = 0.0017). In metastatic RCC patients treated with anti-PD-1, higher levels of sCD27 predict poor overall survival (p = 0.037), while it did not correlate with inflammatory markers or clinical prognostic criteria. Conclusions In conclusion, we demonstrated that sCD27, a surrogate of T cell dysfunction in tumors likely induced by persistent interactions of CD27+T cells and CD70-expressing tumor cells, is a predictive biomarker of resistance to immunotherapy in mRCC. To our knowledge, this is the first report showing that a peripheral blood biomarker may reflect certain aspects of the tumor-host interaction in the tumor microenvironment. Given the frequent expression of CD70 and CD27 in solid tumors, our findings may be further extended to other types of tumors. CD70-CD27 interaction could thus be considered as a mechanism of tumor escape, but also a novel therapeutic target in cancers. Disclosure Information N. Benhamouda: None. I. Sam: None. N. Epaillard: None. A. Gey: None. A. Saldmann: None. J. Pineau: None. M. Hasan: None. V. Verkarre: None. V. Libri: None. S. Mella: None. C. Granier: None. C. Broudin: None. P. Ravel: None. B. Jabla: None. N. Chaput: None. L. Albiges: None. Y. Vano: None. O. Adotevi: None. S. Oudard: B. Research Grant (principal investigator, collaborator or consultant and pending grants as well as grants already received); Modest; SIRIC CARPEM, FONCER. E. Tartour: B. Research Grant (principal investigator, collaborator or consultant and pending grants as well as grants already received); Modest; Fondation ARC, INCA PLBio, Labex Immuno-Oncology, SIRIC CARPEM, FONCER, IDEX universite de Paris, Inserm Transfert.
Published: 2021
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30. Milieu Intérieur

Author: Milena Hasan
Subjects: 0303 health sciences, 03 medical and health sciences, 0302 clinical medicine, Reference values, General Medicine, Biology, Humanities, 030217 neurology & neurosurgery, General Biochemistry, Genetics and Molecular Biology, 3. Good health, 030304 developmental biology
Abstract: Le projet Milieu Intérieur vise à élucider les facteurs environnementaux et héréditaires qui façonnent un système immunitaire sain, et à définir ses frontières lors de l’homéostasie et à la suite d’une stimulation immunitaire. Le projet repose sur un phénotypage immunitaire de 1 000 donneurs sains. En corrélant les mesures obtenues par analyse en cytométrie en flux de la composition des cellules immunitaires du sang périphérique en homéostasie avec les métadonnées associées, nous avons défini des valeurs de référence de phénotypes en fonction du sexe et de l’âge et constaté un impact significatif du tabagisme et de l’infection latente par le cytomégalovirus sur les phénotypes mesurés. Nous avons également identifié onze nouveaux polymorphismes (SNP, single-nucleotide polymorphism), associés à des phénotypes spécifiques de certaines cellules immunitaires. Des conduites expérimentales robustes et standardisées ont été établies pour quantifier les signatures protéiques et transcriptionnelles de la réponse immunitaire résultant de la stimulation des cellules du sang périphérique et pour explorer les déterminants génétiques et non-génétiques de la variabilité de cette réponse. Les approches analytiques établies par Milieu Intérieur et l’ensemble des données recueillies pourront ainsi servir de référence pour des études comparatives avec différentes maladies.
Published: 2019
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31. Distinct single-component adjuvants steer human DC-mediated T-cell polarization via Toll-like receptor signaling toward a potent antiviral immune response

Author: Max Bastian, Milena Hasan, Anja Ullrich, Brigitte David-Watine, Stefan Schülke, Spencer Louis Shorte, Bianca Walber, Christel Kamp, Laura Roßmann, Anna-Lisa Gerards, Tharshana Stephen, Ger van Zandbergen, Ingo Spreitzer, Katrin Bagola, Paul-Ehrlich-Institute - Federal Institute for Vaccines and Biomedicines (EPI), Cytometrie et Biomarqueurs – Cytometry and Biomarkers (UTechS CB), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), BioImagerie Photonique – Photonic BioImaging (UTechS PBI), Institut Pasteur Korea - Institut Pasteur de Corée, Réseau International des Instituts Pasteur (RIIP), Friedrich-Loeffler-Institut (FLI), Johannes Gutenberg - Universität Mainz = Johannes Gutenberg University (JGU), and This project was funded by the German Ministry of Health (BMG) to M.B. and G.v.Z.
Subjects: Adult, Male, Adolescent, T-Lymphocytes, Monophosphoryl Lipid A, Lipid A, chemistry.chemical_compound, Immunology and Inflammation, Immune system, Adjuvants, Immunologic, Interferon, TLR, medicine, Humans, primary human cells, Aged, Immunity, Cellular, Toll-like receptor, Multidisciplinary, SARS-CoV-2, Chemistry, Toll-Like Receptors, Imidazoles, COVID-19, Dendritic Cells, TLR7, biochemical phenomena, metabolism, and nutrition, Biological Sciences, Middle Aged, adjuvants, mRNA vaccines, Cell biology, TLR4, [SDV.IMM]Life Sciences [q-bio]/Immunology, Female, Resiquimod, medicine.drug
Abstract: Significance Vaccines profit from the addition of adjuvants to better and more specifically initiate, amplify, and shape immune responses. Although the number of adjuvant candidates has steadily increased, peaking in the current SARS-CoV-2 pandemic, little is known about their inherent mode of action. Using human blood immune cells, we established a multilayer method to systematically assess the adjuvants’ effects on innate and adaptive immune cells. By employing a multiplex analysis with cells from 30 different donors, we determined important patterns of adjuvant function. Moreover, we demonstrate correlates of an antiviral immune response using a Toll-like receptor 7/8 ligand adjuvant and single-stranded RNA. This knowledge about adjuvants’ distinct immune signatures supports the selection of safe and effective adjuvants for future vaccines., The COVID-19 pandemic highlights the importance of efficient and safe vaccine development. Vaccine adjuvants are essential to boost and tailor the immune response to the corresponding pathogen. To allow for an educated selection, we assessed the effect of different adjuvants on human monocyte-derived dendritic cells (DCs) and their ability to polarize innate and adaptive immune responses. In contrast to commonly used adjuvants, such as aluminum hydroxide, Toll-like receptor (TLR) agonists induced robust phenotypic and functional DC maturation. In a DC-lymphocyte coculture system, we investigated the ensuing immune reactions. While monophosphoryl lipid A synthetic, a TLR4 ligand, induced checkpoint inhibitors indicative for immune exhaustion, the TLR7/8 agonist Resiquimod (R848) induced prominent type-1 interferon and interleukin 6 responses and robust CTL, B-cell, and NK-cell proliferation, which is particularly suited for antiviral immune responses. The recently licensed COVID-19 vaccines, BNT162b and mRNA-1273, are both based on single-stranded RNA. Indeed, we could confirm that the cytokine profile induced by lipid-complexed RNA was almost identical to the pattern induced by R848. Although this awaits further investigation, our results suggest that their efficacy involves the highly efficient antiviral response pattern stimulated by the RNAs’ TLR7/8 activation.
Published: 2021
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32. Cytokine profile as a prognostic tool in coronavirus disease 2019. Comment on 'Urgent avenues in the treatment of COVID-19: Targeting downstream inflammation to prevent catastrophic syndrome' by Quartuccio et al. Joint Bone Spine. 2020;87:191–93

Author: Paul Gougis, Patrice Cacoub, Olivier Benveniste, D. Amelin, Matheus Vieira, Georgina Maalouf, Jean-Marc Lacorte, Alexandre Le Joncour, Esma Karkeni, Lucie Biard, David Saadoun, Joe-Elie Salem, Milena Hasan, Yves Allenbach, and Merwan Idir
Subjects: Oncology, 2019-20 coronavirus outbreak, medicine.medical_specialty, Coronavirus disease 2019 (COVID-19), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Cytokine profile, Inflammation, 03 medical and health sciences, 0302 clinical medicine, Rheumatology, Internal medicine, Correspondence, Medicine, Humans, 030212 general & internal medicine, Interleukin 6, 030203 arthritis & rheumatology, biology, business.industry, SARS-CoV-2, COVID-19, Joint bone, Prognosis, 3. Good health, biology.protein, Cytokines, medicine.symptom, business
Abstract: Joint Bone Spine - Sous presse. Epreuves corrigees par l'auteur. Disponible en ligne depuis le jeudi 8 octobre 2020
Published: 2021
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33. Heterogeneity of monocyte subsets and susceptibility to influenza virus contribute to inter-population variability of protective immunity

Author: Qian Zhang, Aurélie Bisiaux, Valentina Libri, Hélène Quach, Shen-Ying Zhang, Julien Pothlichet, Nadia Naffakh, Daniela Matuozzo, Laurent Abel, Milena Hasan, Yann Aquino, Nora Zidane, Mary B. O’Neill, Matthieu Deschamps, Jean-Laurent Casanova, Aurélie Cobat, Maxime Rotival, and Lluis Quintana-Murci
Subjects: Innate immune system, Monocyte, Antigen presentation, CD16, Biology, medicine.disease_cause, Virus, medicine.anatomical_structure, Interferon, Immunology, medicine, Influenza A virus, Tumor necrosis factor alpha, medicine.drug
Abstract: There is considerable inter-individual and inter-population variability in response to viruses. The potential of monocytes to elicit type-I interferon responses has attracted attention to their role in viral infections. Here, we use an ex vivo model to characterize the role of cellular heterogeneity in human variation of monocyte responses to influenza A virus (IAV) exposure. Using single-cell RNA-sequencing, we show widespread inter-individual variability in the percentage of IAV-infected monocytes. We show that cells escaping viral infection display increased mRNA expression of type-I interferon stimulated genes and decreased expression of ribosomal genes, relative to both infected cells and those never exposed to IAV. While this host defense strategy is shared between CD16+/CD16- monocytes, we also uncover CD16+-specific mRNA expression of IL6 and TNF in response to IAV, and a stronger resistance of CD16+ monocytes to IAV infection. Notably, individuals with high cellular susceptibility to IAV are characterized by a lower activation at basal state of an IRF/STAT-induced transcriptional network, which includes antiviral genes such as IFITM3, MX1, and OAS3. Finally, using flow cytometry and bulk RNA-sequencing across 200 individuals of African and European ancestry, we observe a higher number of CD16+ monocytes and lower susceptibility to IAV infection among monocytes from individuals of African-descent. Collectively, our results reveal the effects of IAV infection on the transcriptional landscape of human monocytes and highlight previously unappreciated differences in cellular susceptibility to IAV infection between individuals of African and European ancestry, which may account for the greater susceptibility of Africans to severe influenza.Significance StatementMonocytes may play a critical role during severe viral infections. Our study tackles how heterogeneity in monocyte subsets and activation contributes to shape individual differences in the transcriptional response to viral infections. Using single-cell RNA-sequencing, we reveal heterogeneity in monocyte susceptibility to IAV infection, both between CD16+/CD16- monocytes and across individuals, driven by differences in basal activation of an IRF/STAT-induced antiviral program. Furthermore, we show a decreased ability of IAV to infect and replicate in monocytes from African-ancestry individuals, with possible implications for antigen presentation and lymphocyte activation. These results highlight the importance of early cellular activation in determining an individuals’ innate immune response to viral infection.
Published: 2020
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34. In utero exposure to Azathioprine in autoimmune disease. Where do we stand?

Author: Rebecca Bromley, Laura Damian, Marianne Rivière, Hilde Kelchtermans, Katrien Devreese, Yehuda Shoenfeld, Daniel Henrion, Enrique Esteve-Valverde, Patrick Martin Mattera, Laurent Loufrani, Cristina Belizna, Alexandre Levy, Sebastián Udry, Anne-Laure Guihot, Angela Tincani, Jamilya Khizroeva, Taylor Pindi Sala, Rosario Lopez Pedrera, A. Djokovic, Milena Hasan, Nadia Bahi Buisson, Jaume Alijotas-Reig, Maria Orietta Borghi, Géraldine Gascoin, José Omar Latino, Jan Willem Cohen Tervaert, Pier Luigi Meroni, Hannah Cohen, Viktoria Bidsatze, Laurence Bernard, Cecilia Beatrice Chighizola, Johanna Gebhart, Francesca Pregnolato, N. Stanisavljevic, Marie Briet, Mathilde Saiet, Elisabeth Elefant-Amoura, Pascale Peretti, Laurence Lagarce, Ljudmila Stojanovich, Ingrid Pabinger, Jose Rakotonjanahary, Isabelle Pellier, Alexander Makatsariya, Céline Fassot, Marie Noelle Ungeheuer, Laura Andreoli, Christian Muchardt, Jan Voswinkel, Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Clinical Immunology and Rheumatology Research Department Auxologico Institute, Milan, Italy., The Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Ghent University Hospital, Vall d'Hebron University Hospital [Barcelona], Althaia Healthcare Network of Manresa, Barcelona, University College London Hospitals (UCLH), Clinique de l'Anjou [Angers], Recherches en Psychopathologie, nouveaux symptômes et lien social (EA 4050), Université de Poitiers-Université de Brest (UBO)-Université Catholique de l'Ouest (UCO)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), University of Angers, Angers Hospital, French Lupus and Other Autoimmune Disease Patients Association, Institut Pasteur [Paris], Régulation épigénétique - Epigenetic regulation, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Cytometrie et Biomarqueurs – Cytometry and Biomarkers (UTechS CB), Investigation Clinique et d’Accès aux Ressources Biologiques (Plate-forme) - Clinical Investigation and Access to BioResources (ICAReB), MitoVasc - Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), Laboratoire Recherches en psychopathologie et psychanalyse (RPPSY), Université Catholique de l'Ouest (UCO), Institut Pasteur [Paris] (IP), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Pediatrics, medicine.medical_specialty, Offspring, [SDV]Life Sciences [q-bio], Immunology, Population, Azathioprine, Autoimmune Diseases, 03 medical and health sciences, 0302 clinical medicine, Pregnancy, Genetic predisposition, Immunology and Allergy, Medicine, Humans, education, Prospective cohort study, Child, Female, Immunosuppressive Agents, Pregnancy Complications, Prenatal Exposure Delayed Effects, Retrospective Studies, 030203 arthritis & rheumatology, education.field_of_study, business.industry, Public health, Retrospective cohort study, medicine.disease, 3. Good health, 030211 gastroenterology & hepatology, business, medicine.drug
Abstract: International audience; Azathioprine (AZA), an oral immunosuppressant, is safe during pregnancy. Some reports suggested different impairments in the offspring of mothers with autoimmune diseases (AI) exposed in utero to AZA. These observations are available from retrospective studies or case reports. However, data with respect to the long-term safety in the antenatally exposed child are still lacking. The aim of this study is to summarize the current knowledge in this field and to focus on the need for a prospective study on this population. We performed a PubMed search using several search terms. The actual data show that although the risk of congenital anomalies in offspring, as well as the infertility risk, are similar to those found in general population, there is a higher incidence of prematurity, of lower weight at birth and an intra-uterine delay of development. There is also an increased risk of materno- fetal infections, especially cytomegalovirus infection. Some authors raise the interrogations about neurocognitive impairment. Even though the adverse outcomes might well be a consequence of maternal illness and disease activity, interest has been raised about a contribution of this drug. However, the interferences between the external agent (in utero exposure to AZA), with the host (child genetic susceptibility, immune system anomalies, emotional status), environment (public health, social context, availability of health care), economic, social, and behavioral conditions, cultural patterns, are complex and represent confounding factors. In conclusion, it is necessary to perform studies on the medium and long-term outcome of children born by mothers with autoimmune diseases, treated with AZA, in order to show the safety of AZA exposure. Only large-scale population studies with long-term follow-up will allow to formally conclude in this field
Published: 2020
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35. SCHNAPPs - Single Cell sHiNy APPlication(s)

Author: Bernd Jagla, Vincent Rouilly, Michel Pucéat, and Milena Hasan
Subjects: 0303 health sciences, 03 medical and health sciences, 0302 clinical medicine, medicine.anatomical_structure, Computer science, Expression data, Cell, medicine, Cluster analysis, Gene, Data science, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract: MotivationSingle-cell RNA-sequencing (scRNAseq) experiments are becoming a standard tool for bench-scientists to explore the cellular diversity present in all tissues. On one hand, the data produced by scRNASeq is technically complex, with analytical workflows that are still very much an active field of bioinformatics research, and on the other hand, a wealth of biological background knowledge is often needed to guide the investigation. Therefore, there is an increasing need to develop applications geared towards bench-scientists to help them abstract the technical challenges of the analysis, so that they can focus on the Science at play. It is also expected that such applications should support closer collaboration between bioinformaticians and bench-scientists by providing reproducible science tools.ResultsWe present SCHNAPPs, a computer program designed to enable bench-scientists to autonomously explore and interpret single cell RNA-seq expression data and associated annotations. The Shiny-based application allows selecting genes and cells of interest, performing quality control, normalization, clustering, and differential expression analyses, applying standard workflows from Seurat (Stuart et al., 2019) or Scran (Lun et al., 2016) packages, and most of the common visualizations. An R-markdown report can be generated that tracks the modifications, and selected visualizations facilitating communication and reproducibility between bench-scientist and bioinformatician. The modular design of the tool allows to easily integrate new visualizations and analyses by bioinformaticians. We still recommend that a data analysis specialist oversees the analysis and interpretation.AvailabilityThe SCHNAPPs application, docker file, and documentation are available on GitHub: https://c3bi-pasteur-fr.github.io/UTechSCB-SCHNAPPs; Example contribution are available at the following GitHub site: https://github.com/baj12/SCHNAPPsContributions.
Published: 2020
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36. Unveiling inter individual variability of human fibroblast innate immune response using robust cell-based protocols

Author: Nelly Dubrulle, Nathalie Aulner, Milena Hasan, Tharshana Stephen, Brigitte David-Watine, Audrey Chansard, Mathilde Poujol de Molliens, Pierre Barthélémy Falanga, Ger van Zandbergen, and Spencer Louis Shorte
Subjects: education.field_of_study, Innate immune system, Population, Cell, Context (language use), Computational biology, Biology, Immune system, medicine.anatomical_structure, TLR3, medicine, education, Cell activation, Fibroblast
Abstract: The LabEx Milieu Interieur (MI) project is a clinical study centered on the detailed characterization of the baseline and induced immune responses in blood samples from 1000 healthy donors. Analyses of these samples has lay ground for seminal studies on the genetic and environmental determinants of immunologic variance in a healthy cohort population. In the current study we developed in vitro methods enabling standardized quantification of MI-cohort-derived primary fibroblasts responses. Our results show that in vitro human donor cohort fibroblast responses to stimulation by different MAMPs analogs allows to characterize individual donor immune-phenotype variability. The results provide proof-of-concept foundation to a new experimental framework for such studies.A bio-bank of primary fibroblast lines was generated from 323 out of 1,000 healthy individuals selected from the MI-study cohort. To study inter-donor variability of innate immune response in primary human dermal fibroblasts we chose to measure the TLR3 and TLR4 response pathways, both receptors being expressed and previously studied in fibroblasts. We established high-throughput automation compatible methods for standardized primary fibroblast cell activation, using purified MAMPS analogs, poly I:C and LPS that stimulate TLR3 and TLR4 pathways respectively. These results were in turn compared with a stimulation method using infection by HSV-1 virus. Our “Add-only” protocol minimizes high-throughput automation system variability facilitating whole process automation from cell plating through stimulation to recovery of cell supernatants, and fluorescent labeling. Images were acquired automatically by high-throughput acquisition on an automated high-content imaging microscope. Under these methodological conditions standardized image acquisition provided for quantification of cellular responses allowing biological variability to be measured with low system noise and high biological signal fidelity. Optimal for automated analysis of immuno-phenotype of primary human cell responses our method and experimental framework as reported here is highly compatible to high-throughput screening protocols like those necessary for chemo-genomic screening. In context of primary fibroblasts derived from donors enrolled to the MI-clinical-study our results open the way to assert the utility of studying immune-phenotype characteristics relevant to a human clinical cohort.
Published: 2020
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37. Quantitative genetic analysis deciphers the impact of cis and trans regulation on cell-to-cell variability in protein expression levels

Author: Lluis Quintana-Murci, Etienne Patin, Bernd Jagla, John C. Marioni, Michael D Morgan, Milena Hasan, The Wellcome Trust Sanger Institute [Cambridge], Génétique Evolutive Humaine - Human Evolutionary Genetics, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Cytometrie et Biomarqueurs – Cytometry and Biomarkers (UTechS CB), Institut Pasteur [Paris], Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Chaire Génomique humaine et évolution, Collège de France (CdF (institution)), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, TwinsUK is funded by the Wellcome Trust, Medical Research Council, European Union, the National Institute for Health Research (NIHR)-funded BioResource, Clinical Research Facility and Biomedical Research Centre based at Guy’s and St Thomas’ NHS Foundation Trust in partnership with King’s College London., Morgan, Michael D. [0000-0003-0757-0711], Patin, Etienne [0000-0002-9911-4459], Jagla, Bernd [0000-0002-7696-0484], Quintana-Murci, Lluís [0000-0003-2429-6320], Marioni, John C. [0000-0001-9092-0852], Apollo - University of Cambridge Repository, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP), Collège de France - Chaire Génomique humaine et évolution, Morgan, Michael D [0000-0003-0757-0711], and Marioni, John C [0000-0001-9092-0852]
Subjects: Male, Cancer Research, Protein Expression, Gene Expression, QH426-470, Biochemistry, 0302 clinical medicine, Spectrum Analysis Techniques, Gene expression, Databases, Genetic, Genetics (clinical), Genetics, Regulation of gene expression, 0303 health sciences, Immune System Proteins, Flow Cytometry, Phenotype, Phenotypes, Spectrophotometry, Female, Cytophotometry, Research Article, Immunology, Quantitative Trait Loci, Biology, Polymorphism, Single Nucleotide, 03 medical and health sciences, Gene Expression and Vector Techniques, Humans, Gene Regulation, Genetic Testing, Allele, Selection, Genetic, Molecular Biology Techniques, Gene, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Alleles, 030304 developmental biology, Medicine and health sciences, Evolutionary Biology, Molecular Biology Assays and Analysis Techniques, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Population Biology, Biology and life sciences, Gene Expression Profiling, Immunity, Proteins, Human Genetics, Quantitative genetics, Human genetics, Research and analysis methods, Gene Expression Regulation, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Immune System, Genetic Polymorphism, Trans-acting, 030217 neurology & neurosurgery, Population Genetics, Genome-Wide Association Study
Abstract: Identifying the factors that shape protein expression variability in complex multi-cellular organisms has primarily focused on promoter architecture and regulation of single-cell expression in cis. However, this targeted approach has to date been unable to identify major regulators of cell-to-cell gene expression variability in humans. To address this, we have combined single-cell protein expression measurements in the human immune system using flow cytometry with a quantitative genetics analysis. For the majority of proteins whose variability in expression has a heritable component, we find that genetic variants act in trans, with notably fewer variants acting in cis. Furthermore, we highlight using Mendelian Randomization that these variability-Quantitative Trait Loci might be driven by the cis regulation of upstream genes. This indicates that natural selection may balance the impact of gene regulation in cis with downstream impacts on expression variability in trans., Author summary Genetic variation can change how much a gene is turned on or off in a tissue or a population of cells of the same type. However, this averaging of expression levels across a cell population masks an important aspect of gene expression regulation, namely its variability. Recent work in humans has indicated that nearby (cis) genetic factors minimally influence this variability. We have combined genetic measurements with flow cytometry single-cell protein levels to resolve the genetic control of gene expression variability in human immune cells. Importantly, we have demonstrated that whilst genetic variants near the target genes (cis) rarely influence variability, there is still an extensive genetic contribution from genetic loci faraway, or on a separate chromosome (trans). Furthermore, we have resolved that these trans genetic effects regulate the expression of other nearby genes, which leads to changes in gene expression variability of our target proteins. Our findings can be explained by an evolutionary balance between the cis regulation of gene expression levels, and the downstream consequences on gene expression variability.
Published: 2020
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38. Low CCR5 expression protects HIV-specific CD4+ T cells of elite controllers from viral entry

Author: Mathieu Claireaux, Rémy Robinot, Jérôme Kervevan, Mandar Patgaonkar, Isabelle Staropoli, Anne Brelot, Alexandre Nouël, Stacy Gellenoncourt, Xian Tang, Mélanie Héry, Stevenn Volant, Emeline Perthame, Véronique Avettand-Fenoël, Julian Buchrieser, Thomas Cokelaer, Christiane Bouchier, Laurence Ma, Faroudy Boufassa, Samia Hendou, Valentina Libri, Milena Hasan, David Zucman, Pierre de Truchis, Olivier Schwartz, Olivier Lambotte, Lisa A. Chakrabarti, Virus et Immunité - Virus and immunity (CNRS-UMR3569), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Laboratoire de Microbiologie Clinique [AP-HP Hôpital Necker-Enfants Malades], CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Biomics (plateforme technologique), Centre de recherche en épidémiologie et santé des populations (CESP), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Cytometrie et Biomarqueurs – Cytometry and Biomarkers (UTechS CB), Hôpital Foch [Suresnes], Hôpital Raymond Poincaré [AP-HP], Immunologie des Maladies Virales et Autoimmunes (IMVA - U1184), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM), AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), Université Paris-Sud - Paris 11 (UP11), This work was supported by grants to L.A.C. from ANRS (17218 and 19206), Institut Pasteur (PasteurInnov TETRHIS), and ANR (14 CE 16002901). The Biomics Platform is a member of the 'France Génomique' consortium (ANR10-INBS-09-08). M.C. was the recipient of a Sidaction fellowship, R.R. of a Pasteur Carnot MS and a Sidaction fellowships, M.P. of an ANRS fellowship, and S.G. of a MESR/Université de Paris fellowship., We are grateful to patients who participated in the study. We thank the investigators of the ANRS CO21 CODEX cohort and Camille Lecuroux for help with recruitment of controller patients, Morgane Marcou and Katia Bourdic for help with recruitment of treated patients, Bernard Lagane for the gift of plamids, and Sophie Novault from the Pasteur CB UTechS for advice on cell sorting. MHC class II tetramer reagents were provided by the NIH Tetramer Core facility at Emory University. The following reagent was obtained through the NIH AIDS Reagent Program, Division of AIDS, NIAID, NIH: HIV-1 PTE Gag peptide set (Cat # 11554)., ANR-14-CE16-0029,PD1VAX,Une nouvelle stratégie de vaccination par vecteur ADN PD1 pour mimer les réponses spécifiques de Gag trouvées chez les contrôleurs spontanés du VIH(2014), and ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010)
Subjects: CD4-Positive T-Lymphocytes, Viral membrane fusion, MESH: Mutation, Receptors, CXCR3, Receptors, CCR5, Science, MESH: Virus Internalization, viruses, General Physics and Astronomy, Down-Regulation, Gene Products, gag, HIV Infections, MESH: Receptors, CCR5, MESH: Down-Regulation, General Biochemistry, Genetics and Molecular Biology, Article, MESH: Receptors, CXCR3, MESH: HIV-1, MESH: Elite Controllers, Humans, MESH: Humans, Multidisciplinary, Retrovirus, Histocompatibility Antigens Class II, MESH: CD4-Positive T-Lymphocytes, virus diseases, MESH: HIV Infections, General Chemistry, Virus Internalization, MESH: Chemokines, MESH: Gene Expression Regulation, Gene Expression Regulation, MESH: Gene Products, gag, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Mutation, MESH: Histocompatibility Antigens Class II, HIV-1, Chemokines, Elite Controllers
Abstract: HIV elite controllers maintain a population of CD4 + T cells endowed with high avidity for Gag antigens and potent effector functions. How these HIV-specific cells avoid infection and depletion upon encounter with the virus remains incompletely understood. Ex vivo characterization of single Gag-specific CD4 + T cells reveals an advanced Th1 differentiation pattern in controllers, except for the CCR5 marker, which is downregulated compared to specific cells of treated patients. Accordingly, controller specific CD4 + T cells show decreased susceptibility to CCR5-dependent HIV entry. Two controllers carried biallelic mutations impairing CCR5 surface expression, indicating that in rare cases CCR5 downregulation can have a direct genetic cause. Increased expression of β-chemokine ligands upon high-avidity antigen/TCR interactions contributes to autocrine CCR5 downregulation in controllers without CCR5 mutations. These findings suggest that genetic and functional regulation of the primary HIV coreceptor CCR5 play a key role in promoting natural HIV control., Here, Claireaux et al. show that people who naturally control HIV infection express lower levels of the viral co-receptor CCR5 in specific CD4+ T cells, and that this results from mutations or receptor internalization by CD4+ T cell-produced chemokines.
Published: 2019
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39. HIBISCUS: Hydroxychloroquine for the secondary prevention of thrombotic and obstetrical events in primary antiphospholipid syndrome

Author: Patrick Blanco, Maarten Limper, Jamilya Khizroeva, Pier Luigi Meroni, Olivier Lambotte, Nadine Magy-Bertrand, Loic Sentilhes, Raquel Ferrer-Oliveras, Pieter Van Paasen, Jan Willem Cohen Tervaert, Marie Noelle Ungeheuer, Enrique Esteve-Valverde, Katrien Devreese, Ricard Cervera, Laura Andreoli, A. Djokovic, Emmanuel Andrès, Antonia Caligaro, Jean Sibilia, Daniel Henrion, Angela Tincani, Guillaume Mahé, Jose Omar Latino, N. Stanisavljevic, Sebastián Udry, Patrick Saulnier, Ljudmila Stojanovich, Şule Apraş Bilgen, Bernard Imbert, Cédric Landron, Damien Sène, Karina de Leeuw, Céline Fassot, Fatma Said, Boris Bienvenu, Laura Damian, Florence Perrinet, Jaume Alijotas-Reig, Francesca Pregnolato, Alban Godon, Estibaliz Lazaro, Thierry Martin, Viktoria Bitsadze, Laurent Arnaud, Laurent Loufrani, Gilles Pernod, Alexander Makatsariya, Gilberto Pires da Rosa, Noémie Jourde-Chiche, Pierre Yves Jeandel, Elisabeta Candrea, Maria Orietta Borghi, Milena Hasan, Jean Marie Chretien, Crina Sinescu, Cristina Belizna, Mathilde Versini, Pascale Jeannin, Thomas Le Gallou, Fréderic Tollis, Marc Antoine Pistorius, Loukman Omarjee, Valentina Canti, Mohamed Hamidou, Achile Aouba, György Nagy, Ova Shovman, Sébastien Abad, Levent Kilic, Teresa Delross, Howard Amital, Lai-Shan Tam, Zahir Amoura, Christian Muchardt, Amelia Ruffatti, Laurent Chiche, Patrick Jego, Emmanuelle Dernis, Maria Favaro, Miri Blank, Romain Lubin, Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM), Biologie Neurovasculaire et Mitochondriale Intégrée (BNMI), Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Université Paris 13 (UP13), Hôpital Avicenne [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Vall d'Hebron University Hospital [Barcelona], Sackler Faculty of Medicine, Tel Aviv University (TAU), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), University of Brescia, CHU Strasbourg, Université de Caen Normandie (UNICAEN), Normandie Université (NU), Hacettepe University = Hacettepe Üniversitesi, Hôpital Saint-Joseph [Marseille], Department of Obstetrics and Gynecology, I.M. Sechenow First Moscow State Medical University, Moscow, Russia., Immunology from Concept and Experiments to Translation (ImmunoConcept), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), Università degli Studi di Padova = University of Padua (Unipd), University of Medicine and Pharmacy, Luliu-Hatieganu, Hôpital Européen [Fondation Ambroise Paré - Marseille], Maastricht University [Maastricht], University of Alberta, Universitatea Babeş-Bolyai [Cluj-Napoca], Centre Hospitalier du Mans, Ghent University Hospital, University of Belgrade [Belgrade], Althaia Healthcare Network of Manresa, Barcelona, MitoVasc - Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), Cardiovascular Functions In Vitro (CARFI), Centre hospitalier universitaire de Nantes (CHU Nantes), Centre de Recherche Translationnelle - Center for Translational Science (CRT), Institut Pasteur [Paris] (IP), CHU Grenoble, Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Centre de Recherche en Cancérologie Nantes-Angers (CRCNA), PRES Université Nantes Angers Le Mans (UNAM)-PRES Université Nantes Angers Le Mans (UNAM)-Hôtel-Dieu de Nantes-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôpital Laennec-Centre National de la Recherche Scientifique (CNRS)-Faculté de Médecine d'Angers-Centre hospitalier universitaire de Nantes (CHU Nantes), CHU Pontchaillou [Rennes], Vascular research center of Marseille (VRCM), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre recherche en CardioVasculaire et Nutrition = Center for CardioVascular and Nutrition research (C2VN), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Department of Obstetrics and Gynecology, I.M. Sechenow First Moscow State Medical University, Moscow, Immunologie des Maladies Virales et Autoimmunes (IMVA - U1184), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM), AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), Centre hospitalier universitaire de Poitiers (CHU Poitiers), Hospital Carlos G. Durand, Hôpital Haut-Lévêque [CHU Bordeaux], CHU Bordeaux [Bordeaux], University Medical Center Groningen [Groningen] (UMCG), University Medical Center [Utrecht], Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Centre d'Investigation Clinique [Rennes] (CIC), Université de Rennes (UR)-Hôpital Pontchaillou-Institut National de la Santé et de la Recherche Médicale (INSERM), Cellules Souches et Développement / Stem Cells and Development, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Semmelweis University [Budapest], Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble - UMR 5525 (TIMC-IMAG), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Hospital de São João [Porto], Hôpital La Rabta [Tunis], Hôpital Lariboisière, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Lariboisière-Fernand-Widal [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Diderot - Paris 7 (UPD7), Service de rhumatologie [Strasbourg], CHU Strasbourg-Hôpital de Hautepierre [Strasbourg], Université de Médecine Carol Davila, The Chinese University of Hong Kong [Hong Kong], Diaverum Dialysis Center, Angers, Investigation Clinique et d’Accès aux Ressources Biologiques (Plate-forme) - Clinical Investigation and Access to BioResources (ICAReB), Institut Arnault Tzanck, Barcelona Centre for International Health Research, Hospital Clinic (CRESIB), Universitat de Barcelona (UB), The HIBISCUS study is funded for its French part of the trial by the Ministery of Health, France in 2015 (PHRC N PAPIRUS)., The investigators are very grateful to Professor Y Shoenfeld for the scientific revision of the design and very valuable remarks. The investigators are also grateful to the patients, patients' association, collaborators and networks involved in the trial and to the research staff at all participating hospitals., Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université d'Angers (UA), Hôpital avicenne, Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Université Paris 13 (UP13)-Hôpital Avicenne, Tel Aviv University [Tel Aviv], Service de médecine interne [CHU Pitié-Salpétrière], Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Pitié-Salpêtrière [APHP], Universita degli Studi di Padova, Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), Centre de Recherche Translationnelle (CRT), Institut Pasteur [Paris], Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Aix Marseille Université (AMU), Centre recherche en CardioVasculaire et Nutrition (C2VN), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Hôpital Jean Minjoz, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Hôpital Pontchaillou-Institut National de la Santé et de la Recherche Médicale (INSERM), Cellules Souches et Développement, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-IMAG-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Lariboisière-Université Paris Diderot - Paris 7 (UPD7), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB), Université Paris Diderot - Paris 7 (UPD7)-Hôpital Lariboisière-Fernand-Widal [APHP], and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)
Subjects: ANTICOAGULANT, Pediatrics, Additional Therapy, [SDV]Life Sciences [q-bio], 030204 cardiovascular system & hematology, RECOMMENDATIONS, COMPLEMENT, 0302 clinical medicine, Pregnancy, An international multicenter trial on Hydroxychloroquine for the secondary prevention of relapses in primary antiphospholipid syndrome is launched, Antiphospholipid syndrome, Immunology and Allergy, PREGNANT PATIENTS, SYSTEMIC-LUPUS-ERYTHEMATOSUS, Secondary prevention, Anticoagulant, Pregnancy Outcome, Take home messages, WOMEN, 3. Good health, [SDV.IMM]Life Sciences [q-bio]/Immunology, Female, medicine.drug, Hydroxychloroquine, Primary antiphospholipid syndrome, medicine.medical_specialty, medicine.drug_class, Immunology, Relapse rate, Relapse rate in antiphospholipid syndrome (APS) is high despite standard current therapies, 53 centers from 16 countries participate to this international trial, Orphan drug, 03 medical and health sciences, Survival rate in this population is 90.1% at 10 years and 65% at 15 years, There is a need for additional or alternative therapies in this disease, hydroxychloroquine, primary antiphospholipid syndrome, secondary prevention, medicine, MANAGEMENT, Humans, DRUGS, 030203 arthritis & rheumatology, business.industry, Thrombosis, Delivery, Obstetric, medicine.disease, ANTIBODIES, RISK-FACTORS, business
Abstract: International audience; The relapse rate in antiphospholipid syndrome (APS) remains high, i.e. around 20%–21% at 5 years in thrombotic APS and 20–28% in obstetrical APS [2, 3].Hydroxychloroquine (HCQ) appears as an additional therapy, as it possesses immunomodulatory and anti-thrombotic various effects [4–16].Our group recently obtained the orphan designation of HCQ in antiphospholipid syndrome by the European Medicine Agency.Furthermore, the leaders of the project made the proposal of an international project, HIBISCUS, about the use of Hydroxychloroquine in secondary prevention of obstetrical and thrombotic events in primary APS. This study has been launched in several countries and at now, 53 centers from 16 countries participate to this international trial.This trial consists in two parts: a retrospective and a prospective study.The French part of the trial in thrombosis has been granted by the French Minister of Health in December 2015 (the academic trial independent of the pharmaceutical industry PHRC N PAPIRUS) and is coordinated by one of the members of the leading consortium of HIBISCUS.
Published: 2018
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40. Human thymopoiesis is influenced by a common genetic variant within the TCRA-TCRD locus

Author: Lluis Quintana-Murci, Marine Germain, Magnus Fontes, Antoine Toubert, Itauá Leston Araujo, David-Alexandre Trégouët, James P. Di Santo, Emmanuel Clave, Corinne Douay, Silvia Lopez-Lastra, Milena Hasan, Bruno Charbit, Noémie Saut, Breno Luiz Melo-Lima, Darragh Duffy, Cécile Alanio, Jacob Bergstedt, Alejandra Urrutia, Cameron Ross MacPherson, Yan Li, Etienne Patin, Pierre-Emmanuel Morange, Matthew L. Albert, Institut Universitaire d'Hématologie (IUH), Université Paris Diderot - Paris 7 (UPD7), Alloimmunité-Autoimmunité-Transplantation (A2T), Université Paris Diderot - Paris 7 (UPD7)-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), Immunobiologie des Cellules dendritiques, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Recherche Translationnelle - Center for Translational Science (CRT), Institut Pasteur [Paris] (IP), Génétique Evolutive Humaine - Human Evolutionary Genetics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Lund University [Lund], Genentech, Inc., Genentech, Inc. [San Francisco], Immunité Innée - Innate Immunity, Laboratoire d'hématologie biologique [Hôpital de la Timone - Hôpital Nord - APHM], Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE), Centre recherche en CardioVasculaire et Nutrition = Center for CardioVascular and Nutrition research (C2VN), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Research Unit on Cardiovascular and Metabolic Diseases (ICAN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Institut de Cardiométabolisme et Nutrition = Institute of Cardiometabolism and Nutrition [CHU Pitié Salpêtrière] (IHU ICAN), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), International Group for Data Analysis (IGDA), Service d'Immunologie et d'Histocompatibilité, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Diderot - Paris 7 (UPD7)-Groupe Hospitalier Saint Louis - Lariboisière - Fernand Widal [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), This work was supported by the French government’s Invest in the Future Program, managed by the Agence Nationale de la Recherche (ANR, 10-LABX-69-01). I.L.A. was a recipient of the Science without Borders PhD program from Brazil Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq). J.B. is a member of the Lund Center for Control of Complex Engineering Systems (LCCC) Linnaeus Center and the Excellence Center at Linköping-Lund in Information Technology (ELLIT) Excellence Center at Lund University and is supported by the ELLIIT Excellence Center. J.P.D.S., Y.L., and S.L.-L. received funding from Institut Pasteur, INSERM, the Laboratoire d’Excellence REVIVE. A.T. and E.C. received funding from ANR grant PriCelAge (ANR-14-CE14-0030-01). Genetic investigations in the MARTHA study were supported by the GENMED Laboratory of Excellence on Medical Genomics (ANR-10-LABX-0013), We thank J. Fellay, P. Scepanovic, and C. A. W. Thorball for support with genetic analysis and J.-M. Doisne, G. M. Ranson, and H. Strick-Marchand for support with humanized mouse experiments. We thank V. Asnafi, E. Macintyre, A. Cieslak, and I. André-Schmutz for helpful discussions. We also thank the Centre d’Immunologie Humaine (Institut Pasteur, Paris, France) for support., ANR-14-CE14-0030,PriCelAge,Induction de réponses cellulaires T avec l'âge avancé(2014), ANR-10-LABX-0013,GENMED,Medical Genomics(2010), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Universitaire d'Hématologie (IUH), Université Paris Diderot - Paris 7 (UPD7)-Université Paris Diderot - Paris 7 (UPD7), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Recherche Translationnelle (CRT), Institut Pasteur [Paris], Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Immunité Innée, Centre recherche en CardioVasculaire et Nutrition (C2VN), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Institute of cardiometabolism and nutrition (ICAN), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [APHP]-Sorbonne Université (SU), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Université Paris Diderot - Paris 7 (UPD7)-Groupe Hospitalier Saint Louis - Lariboisière - Fernand Widal [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (APHP), ANR-14-CE14-0030,PriCelAge,Induction de réponses cellulaires T avec l’âge avancé(2014), ANR: PREFI-10-LABX-13/10-LABX-0013,GENMED,Medical Genomics(2010), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], and Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)
Subjects: 0301 basic medicine, education.field_of_study, T-cell receptor excision circles, T cell, Population, Genome-wide association study, Locus (genetics), General Medicine, Biology, 3. Good health, Transplantation, 03 medical and health sciences, Haematopoiesis, Thymocyte, 030104 developmental biology, 0302 clinical medicine, medicine.anatomical_structure, 030220 oncology & carcinogenesis, Immunology, medicine, [SDV.IMM]Life Sciences [q-bio]/Immunology, education
Abstract: International audience; The thymus is the primary lymphoid organ where naïve T cells are generated; however, with the exception of age, the parameters that govern its function in healthy humans remain unknown. We characterized the variability of thymic function among 1000 age- and sex-stratified healthy adults of the Milieu Intérieur cohort, using quantification of T cell receptor excision circles (TRECs) in peripheral blood T cells as a surrogate marker of thymopoiesis. Age and sex were the only nonheritable factors identified that affect thymic function. TREC amounts decreased with age and were higher in women compared to men. In addition, a genome-wide association study revealed a common variant (rs2204985) within the T cell receptor TCRA-TCRD locus, between the DD2 and DD3 gene segments, which associated with TREC amounts. Strikingly, transplantation of human hematopoietic stem cells with the rs2204985 GG genotype into immunodeficient mice led to thymopoiesis with higher TRECs, increased thymocyte counts, and a higher TCR repertoire diversity. Our population immunology approach revealed a genetic locus that influences thymopoiesis in healthy adults, with potentially broad implications in precision medicine.
Published: 2018
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41. Primary antiphospholipid syndrome and antiphospholipid syndrome associated to systemic lupus: Are they different entities?

Author: Pier Luigi Meroni, Laura Damian, Cristina Belizna, Daniel Henrion, Ljudmila Stojanovich, Laurent Loufrani, Patrick Saulnier, Guillaume Mahé, Pascal Reynier, Enrique Esteve-Valverde, Jan Willem Cohen-Tervaert, Milena Hasan, Jaume Alijotas-Reig, Ferdinando Nicoletti, Alban Godon, Laurent Arnaud, Katrien Devreese, Marie Noelle Ungeheuer, György Nagy, Loukman Omarjee, Céline Fassot, Marc Antoine Pistorius, Jean Marie Chretien, Christian Muchardt, Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université d'Angers (UA), Biologie Neurovasculaire et Mitochondriale Intégrée (BNMI), Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University of Belgrade [Belgrade], Maastricht University [Maastricht], Biologie Neurovasculaire Intégrée (BNVI), Semmelweis University [Budapest], Régulation épigénétique - Epigenetic regulation, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Cytometrie et Biomarqueurs – Cytometry and Biomarkers (UTechS CB), Institut Pasteur [Paris], Investigation Clinique et d’Accès aux Ressources Biologiques (Plate-forme) - Clinical Investigation and Access to BioResources (ICAReB), CHU Strasbourg, Universitat Autònoma de Barcelona (UAB), University of Catania [Italy], Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM), Centre d'Investigation Clinique [Rennes] (CIC), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Hôpital Pontchaillou-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Pontchaillou [Rennes], Centre hospitalier universitaire de Nantes (CHU Nantes), Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), Ghent University Hospital, MitoVasc - Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP), and Université de Rennes (UR)-Hôpital Pontchaillou-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: Primary antiphospholipid syndrome, Some limitation, ERYTHEMATOSUS, Immunology, 030204 cardiovascular system & hematology, Bioinformatics, 03 medical and health sciences, 0302 clinical medicine, Antiphospholipid syndrome, CARDIAC MANIFESTATIONS, Immunology and Allergy, Medicine, Humans, Lupus Erythematosus, Systemic, In patient, CLASSIFICATION CRITERIA, Secondary antiphospholipid syndrome, ANTIBODY TYPE, 030203 arthritis & rheumatology, Systemic lupus erythematosus, ANTICOAGULANT ACTIVITY, business.industry, Systemic lupus, SECONDARY, Genetic data, medicine.disease, 3. Good health, THROMBOGENIC MECHANISM, ANNEXIN A5, [SDV.MHEP.RSOA]Life Sciences [q-bio]/Human health and pathology/Rhumatology and musculoskeletal system, CARDIOVASCULAR-DISEASE, SYNDROME APS, Antibodies, Antiphospholipid, [SDV.IMM]Life Sciences [q-bio]/Immunology, Identification (biology), business
Abstract: International audience; Primary antiphospholipid syndrome (PAPS) and antiphospholipid syndrome associated to lupus (SAPS) have several overlapping characteristics. As systemic manifestations are also reported in patients with PAPS, and as a subgroup of PAPS patients could evaluate to a SAPS, the differentiation between the two types of APS could be performed based on the clinical experience of the medical teams and is related to a variety of clinical, biological, histological and genetic features. Several data are available in the literature with respect to the identification of distinctive features between these two entities. However, there are some limitation in the interpretation of results issued from studies performed prior to updated Sydney criteria. Based on recent data, a certain number of features more frequent in one type of APS as compared to the other could be distinguished. The major differentiation between these two entities is genetical. New genetic data allowing the identification of specific subgroups of APS are ongoing.
Published: 2018
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42. Publisher Correction: Natural variation in the parameters of innate immune cells is preferentially driven by genetic factors

Author: Vincent Rouilly, Cherie Green, Lluis Quintana-Murci, Julie Hunkapiller, Isabelle Peguillet, Magnus Fontes, Jacob Bergstedt, Alejandra Urrutia, Claire Leloup, Benoit Beitz, Friederike Jönsson, Darragh Duffy, Stéphanie Thomas, François Huetz, Lars Rogge, Cécile Alanio, Matthew L. Albert, Petar Scepanovic, Olivier Lantz, Barbara Piasecka, Yoong Wearn Lim, Jacques Fellay, Hélène Quach, Christian Hammer, Milena Hasan, Etienne Patin, Magge Zepeda, Valentina Libri, and James P. Di Santo
Subjects: 0301 basic medicine, Innate immune system, Immunology, Computational biology, Biology, Natural variation, InformationSystems_GENERAL, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, 030220 oncology & carcinogenesis, ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, Correct name, Immunology and Allergy
Abstract: In the version of this article initially published, the name of one author was incorrect (James P. Santo). The correct name is James P. Di Santo. The error has been corrected in the HTML and PDF versions of the article.
Published: 2018

43. Automated flow cytometric analysis across large numbers of samples and cell types

Author: Lluis Quintana-Murci, Valentina Libri, Bernard Chalmond, Xiaoyi Chen, Vincent Rouilly, Benoit Beitz, Alejandra Urrutia, Matthew L. Albert, Lars Rogge, Milena Hasan, Etienne Patin, Darragh Duffy, Benno Schwikowski, Biologie systémique - Systems Biology, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Analyse, Géométrie et Modélisation (AGM - UMR 8088), CY Cergy Paris Université (CY)-Centre National de la Recherche Scientifique (CNRS), Centre d'Immunologie Humaine (CIH), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Immunobiologie des Cellules Dendritiques, Immunorégulation, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Centre de Mathématiques et de Leurs Applications (CMLA), École normale supérieure - Cachan (ENS Cachan)-Centre National de la Recherche Scientifique (CNRS), Université de Cergy Pontoise (UCP), Université Paris-Seine, Génétique Evolutive Humaine - Human Evolutionary Genetics, Institut Non Linéaire de Nice Sophia-Antipolis (INLN), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), The Milieu Intérieur Consortium is composed of the following team leaders: Laurent Abel (Hôpital Necker), Andres Alcover, Philippe Bousso, Pierre Bruhns, Ana Cumano, Marc Daëron, Cécile Delval, Caroline Demangel, Ludovic Deriano, James Di Santo, Françoise Dromer, Gérard Eberl, Jost Enninga, Odile Gelpi, Antonio Freitas, Ivo Gomperts-Boneca, Serge Hercberg (Université Paris 13), Olivier Lantz (Institut Curie), Claude Leclerc, Hugo Mouquet, Sandra Pellegrini, Stanislas Pol (Hôpital Côchin), Lars Rogge, Anavaj Sakuntabhai, Olivier Schwartz, Benno Schwikowski, Spencer Shorte, Vassili Soumelis (Institut Curie), Frédéric Tangy, Eric Tartour (Hôpital Européen George Pompidou), Antoine Toubert (Hôpital Saint-Louis), Marie-Noëlle Ungeheuer, Lluis Quintana-Murci2, Matthew L. Albert3.Additional information can be found at: http://www.pasteur.fr/labex/milieu-interieur., Kop, Marie-Luce, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-CY Cergy Paris Université (CY), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Nice Sophia Antipolis (1965 - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)
Subjects: Multidimensional analysis, [SDV.IMM] Life Sciences [q-bio]/Immunology, Neutrophils, Computer science, T-Lymphocytes, Pipeline (computing), Statistics as Topic, Immunology, Flow cytometry, Gating, Bioinformatics, Monocytes, Automation, T-Lymphocyte Subsets, Bayesian information criterion, Cluster Analysis, Humans, Immunology and Allergy, Population-based cohort, Cluster analysis, Automation, Laboratory, B-Lymphocytes, business.industry, Bayes Theorem, Dendritic Cells, Reference Standards, Mixture model, Standardization, Killer Cells, Natural, Identification (information), ComputingMethodologies_PATTERNRECOGNITION, [SDV.IMM]Life Sciences [q-bio]/Immunology, Algorithms, Biological system, business, Software
Abstract: International audience; Multi-parametric flow cytometry is a key technology for characterization of immune cell phenotypes. However, robust high-dimensional post-analytic strategies for automated data analysis in large numbers of donors are still lacking. Here, we report a computational pipeline, called FlowGM, which minimizes operator input, is insensitive to compensation settings, and can be adapted to different analytic panels. A Gaussian Mixture Model (GMM)-based approach was utilized for initial clustering, with the number of clusters determined using Bayesian Information Criterion. Meta-clustering in a reference donor permitted automated identification of 24 cell types across four panels. Cluster labels were integrated into FCS files, thus permitting comparisons to manual gating. Cell numbers and coefficient of variation (CV) were similar between FlowGM and conventional gating for lymphocyte populations, but notably FlowGM provided improved discrimination of "hard-to-gate" monocyte and dendritic cell (DC) subsets. FlowGM thus provides rapid high-dimensional analysis of cell phenotypes and is amenable to cohort studies.
Published: 2015
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44. Distinctive roles of age, sex, and genetics in shaping transcriptional variation of human immune responses to microbial challenges

Author: Barbara, Piasecka, Darragh, Duffy, Alejandra, Urrutia, Hélène, Quach, Etienne, Patin, Céline, Posseme, Jacob, Bergstedt, Bruno, Charbit, Vincent, Rouilly, Cameron R, MacPherson, Milena, Hasan, Benoit, Albaud, David, Gentien, Jacques, Fellay, Matthew L, Albert, Lluis, Quintana-Murci, Centre de Recherche Translationnelle - Center for Translational Science (CRT), Institut Pasteur [Paris], Génétique Evolutive Humaine - Human Evolutionary Genetics, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Immunobiologie des Cellules dendritiques, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Genentech, Inc., Genentech, Inc. [San Francisco], Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Lund University [Lund], International Group for Data Analysis (IGDA), Plateforme de génomique [Institut Curie], Institut Curie [Paris], Ecole Polytechnique Fédérale de Lausanne (EPFL), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne (UNIL), This work was supported by the French Government’s Investissement d’Avenir Program, Laboratoire d’Excellence 'Milieu Intérieur' Grant ANR-10-LABX-69-01., We acknowledge Stephanie Thomas for managing the Milieu Intérieur Consortium. Milieu intérieur Consortium : Abel L, Alcover A, Aschard H, Aström K, Bousso P, Bruhns P, Cumano A, Duffy D, Demangel C, Deriano L, Di Santo J, Dromer F, Eberl G, Enninga J, Fellay J, Fontes M, Freitas A, Gelpi O, Gomperts-Boneca I, Hercberg S, Lantz O, Leclerc C, Mouquet H, Patin E, Pellegrini S, Pol S, Raussel A, Rogge L, Sakuntabhai A, Schwartz O, Schwikowski B, Shorte S, Soumelis V, Tangy F, Tartour E, Toubert A, Ungeheuer MN, Quintana-Murci L, Albert ML., ANR-10-LABX-0069,MILIEU INTERIEUR,GENETIC & ENVIRONMENTAL CONTROL OF IMMUNE PHENOTYPE VARIANCE: ESTABLISHING A PATH TOWARDS PERSONALIZED MEDICINE(2010), Centre de Recherche Translationnelle ( CRT ), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale ( INSERM ), Centre de Bioinformatique, Biostatistique et Biologie Intégrative ( C3BI ), International Group for Data Analysis ( IGDA ), Institut Curie, Ecole Polytechnique Fédérale de Lausanne ( EPFL ), Milieu intérieur Consortium : Abel L, Alcover A, Aschard H, Aström K, Bousso P, Bruhns P, Cumano A, Duffy D, Demangel C, Deriano L, Di Santo J, Dromer F, Eberl G, Enninga J, Fellay J, Fontes M, Freitas A, Gelpi O, Gomperts-Boneca I, Hercberg S, Lantz O, Leclerc C, Mouquet H, Patin E, Pellegrini S, Pol S, Raussel A, Rogge L, Sakuntabhai A, Schwartz O, Schwikowski B, Shorte S, Soumelis V, Tangy F, Tartour E, Toubert A, Ungeheuer MN, Quintana-Murci L, Albert ML., ANR : 10-LABX-0069,MILIEU INTERIEUR,GENETIC & ENVIRONMENTAL CONTROL OF IMMUNE PHENOTYPE VARIANCE: ESTABLISHING A PATH TOWARDS PERSONALIZED MEDICINE ( 2010 ), Vougny, Marie-Christine, Laboratoires d'excellence - GENETIC & ENVIRONMENTAL CONTROL OF IMMUNE PHENOTYPE VARIANCE: ESTABLISHING A PATH TOWARDS PERSONALIZED MEDICINE - - MILIEU INTERIEUR2010 - ANR-10-LABX-0069 - LABX - VALID, Institut Pasteur [Paris] (IP), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Lausanne = University of Lausanne (UNIL), Milieu Intérieur Consortium, Abel, L., Alcover, A., Aschard, H., Aström, K., Bousso, P., Bruhns, P., Cumano, A., Duffy, D., Demangel, C., Deriano, L., Di Santo, J., Dromer, F., Eberl, G., Enninga, J., Fellay, J., Fontes, M., Freitas, A., Gelpi, O., Gomperts-Boneca, I., Hercberg, S., Lantz, O., Leclerc, C., Mouquet, H., Patin, E., Pellegrini, S., Pol, S., Raussel, A., Rogge, L., Sakuntabhai, A., Schwartz, O., Schwikowski, B., Shorte, S., Soumelis, V., Tangy, F., Tartour, E., Toubert, A., Ungeheuer, M.N., Quintana-Murci, L., and Albert, M.L.
Subjects: Adult, Male, Aging, Genotype, [SDV.IMM] Life Sciences [q-bio]/Immunology, Quantitative Trait Loci, [ SDV.IMM.IA ] Life Sciences [q-bio]/Immunology/Adaptive immunology, Cohort Studies, Enterotoxins, Young Adult, Immunology and Inflammation, Humans, sex, genetics, [ SDV.BIBS ] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [ SDV.GEN.GH ] Life Sciences [q-bio]/Genetics/Human genetics, Aged, [ SDV.IMM.II ] Life Sciences [q-bio]/Immunology/Innate immunity, Bacteria, Fungi, Genetic Variation, Middle Aged, Biological Sciences, Bacteria/immunology, Enterotoxins/immunology, Female, Fungi/immunology, Gene Expression Regulation/immunology, Influenza A virus/immunology, age, gene expression, human immune variation, [ SDV.GEN.GPO ] Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], [ SDV.MHEP.MI ] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Gene Expression Regulation, PNAS Plus, Influenza A virus, [SDV.IMM]Life Sciences [q-bio]/Immunology
Abstract: Significance Identifying the drivers of the interindividual diversity of the human immune system is crucial to understand their consequences on immune-mediated diseases. By examining the transcriptional responses of 1,000 individuals to various microbial challenges, we show that age and sex influence the expression of many immune-related genes, but their effects are overall moderate, whereas genetic factors affect a smaller gene set but with a stronger effect. We identify numerous genetic variants that affect transcriptional variation on infection, many of which are associated with autoimmune or inflammatory disorders. These results enable additional exploration of the role of regulatory variants in the pathogenesis of immune-related diseases and improve our understanding of the respective effects of age, sex, and genetics on immune response variation., The contribution of host genetic and nongenetic factors to immunological differences in humans remains largely undefined. Here, we generated bacterial-, fungal-, and viral-induced immune transcriptional profiles in an age- and sex-balanced cohort of 1,000 healthy individuals and searched for the determinants of immune response variation. We found that age and sex affected the transcriptional response of most immune-related genes, with age effects being more stimulus-specific relative to sex effects, which were largely shared across conditions. Although specific cell populations mediated the effects of age and sex on gene expression, including CD8+ T cells for age and CD4+ T cells and monocytes for sex, we detected a direct effect of these intrinsic factors for the majority of immune genes. The mapping of expression quantitative trait loci (eQTLs) revealed that genetic factors had a stronger effect on immune gene regulation than age and sex, yet they affected a smaller number of genes. Importantly, we identified numerous genetic variants that manifested their regulatory effects exclusively on immune stimulation, including a Candida albicans-specific master regulator at the CR1 locus. These response eQTLs were enriched in disease-associated variants, particularly for autoimmune and inflammatory disorders, indicating that differences in disease risk may result from regulatory variants exerting their effects only in the presence of immune stress. Together, this study quantifies the respective effects of age, sex, genetics, and cellular heterogeneity on the interindividual variability of immune responses and constitutes a valuable resource for further exploration in the context of different infection risks or disease outcomes.
Published: 2018
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45. Natural variation in the parameters of innate immune cells is preferentially driven by genetic factors

Author: Petar Scepanovic, Julie Hunkapiller, Jacob Bergstedt, Alejandra Urrutia, Jacques Fellay, Lluis Quintana-Murci, Hélène Quach, Friederike Jönsson, Cherie Green, Olivier Lantz, Lars Rogge, Stéphanie Thomas, Vincent Rouilly, Barbara Piasecka, Yoong Wearn Lim, Claire Leloup, Cécile Alanio, Isabelle Peguillet, Christian Hammer, Benoit Beitz, Magnus Fontes, Magge Zepeda, Matthew L. Albert, Valentina Libri, James P. Di Santo, Etienne Patin, Milena Hasan, François Huetz, Darragh Duffy, Vougny, Marie-Christine, Laboratoires d'excellence - GENETIC & ENVIRONMENTAL CONTROL OF IMMUNE PHENOTYPE VARIANCE: ESTABLISHING A PATH TOWARDS PERSONALIZED MEDICINE - - MILIEU INTERIEUR2010 - ANR-10-LABX-0069 - LABX - VALID, Génétique Evolutive Humaine - Human Evolutionary Genetics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Centre de Recherche Translationnelle - Center for Translational Science (CRT), Institut Pasteur [Paris] (IP), Lund University [Lund], Immunobiologie des Cellules dendritiques, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Ecole Polytechnique Fédérale de Lausanne (EPFL), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne = University of Lausanne (UNIL), Anticorps en Thérapie et Pathologie, Genentech, Inc. [San Francisco], Immunorégulation, Biologie des Populations Lymphocytaires, Institut Curie [Paris], International Group for Data Analysis (IGDA), Immunité Innée - Innate Immunity, This work benefited from support of the French government’s program ‘Investissement d’Avenir’, managed by the Agence Nationale de la Recherche (reference 10-LABX-69-01). J.B. is a member of the LCCC Linnaeus Center and the ELLIIT Excellence Center at Lund University and is supported by the ELLIIT Excellence Center., The Milieu Intérieur Consortium : Laurent Abel, Andres Alcover, Kalle Astrom, Philippe Bousso, Pierre Bruhns, Ana Cumano, Caroline Demangel, Ludovic Deriano, James P. Di Santo, Françoise Dromer, Darragh Duffy, Gérard Eberl, Jost Enninga, Jacques Fellay, Antonio Freitas, Odile Gelpi, Ivo Gomperts Boneca, Serge Hercberg, Olivier Lantz, Claude Leclerc, Hugo Mouquet, Etienne Patin, Sandra Pellegrini, Stanislas Pol, Lars Rogge, Anavaj Sakuntabhai, Olivier Schwartz, Benno Schwikowski, Spencer Shorte, Vassili Soumelis, Frédéric Tangy, Eric Tartour, Antoine Toubert, Marie-Noëlle Ungeheuer, Lluís Quintana-Murci & Matthew L. Albert, ANR-10-LABX-0069,MILIEU INTERIEUR,GENETIC & ENVIRONMENTAL CONTROL OF IMMUNE PHENOTYPE VARIANCE: ESTABLISHING A PATH TOWARDS PERSONALIZED MEDICINE(2010), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris], Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Lausanne (UNIL), and Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris]
Subjects: Adult, Male, 0301 basic medicine, MESH: Immunity, Innate/genetics, [SDV.IMM] Life Sciences [q-bio]/Immunology, MESH: Immunophenotyping, MESH: Genetic Variation/immunology, Immunology, Genome-wide association study, Disease, Adaptive Immunity, Biology, Immunophenotyping, Young Adult, 03 medical and health sciences, 0302 clinical medicine, Immune system, Immunity, Genetic variation, Humans, Immunology and Allergy, Aged, Genetic association, MESH: Aged, Innate immune system, MESH: Humans, MESH: Middle Aged, Genetic Variation, MESH: Adult, Environmental exposure, Middle Aged, Immunity, Innate, MESH: Male, 3. Good health, 030104 developmental biology, MESH: Young Adult, MESH: Genome-Wide Association Study, MESH: Adaptive Immunity/genetics, [SDV.IMM]Life Sciences [q-bio]/Immunology, Female, MESH: Female, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract: A Publisher Correction to this article was published on 03 May 2018; International audience; The quantification and characterization of circulating immune cells provide key indicators of human health and disease. To identify the relative effects of environmental and genetic factors on variation in the parameters of innate and adaptive immune cells in homeostatic conditions, we combined standardized flow cytometry of blood leukocytes and genome-wide DNA genotyping of 1,000 healthy, unrelated people of Western European ancestry. We found that smoking, together with age, sex and latent infection with cytomegalovirus, were the main non-genetic factors that affected variation in parameters of human immune cells. Genome-wide association studies of 166 immunophenotypes identified 15 loci that showed enrichment for disease-associated variants. Finally, we demonstrated that the parameters of innate cells were more strongly controlled by genetic variation than were those of adaptive cells, which were driven by mainly environmental exposure. Our data establish a resource that will generate new hypotheses in immunology and highlight the role of innate immunity in susceptibility to common autoimmune diseases.
Published: 2018
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46. Human thymopoiesis is influenced by a common genetic variant within the

Author: Emmanuel, Clave, Itauá Leston, Araujo, Cécile, Alanio, Etienne, Patin, Jacob, Bergstedt, Alejandra, Urrutia, Silvia, Lopez-Lastra, Yan, Li, Bruno, Charbit, Cameron Ross, MacPherson, Milena, Hasan, Breno Luiz, Melo-Lima, Corinne, Douay, Noémie, Saut, Marine, Germain, David-Alexandre, Trégouët, Pierre-Emmanuel, Morange, Magnus, Fontes, Darragh, Duffy, James P, Di Santo, Lluis, Quintana-Murci, Matthew L, Albert, and Antoine, Toubert
Subjects: Adult, Male, Receptors, Antigen, T-Cell, alpha-beta, T-Lymphocytes, Genetic Variation, Receptors, Antigen, T-Cell, gamma-delta, Mice, SCID, Thymus Gland, Middle Aged, Cohort Studies, Young Adult, Phenotype, Genetic Loci, Animals, Humans, Female, Biomarkers, Aged, Genome-Wide Association Study
Abstract: The thymus is the primary lymphoid organ where naïve T cells are generated; however, with the exception of age, the parameters that govern its function in healthy humans remain unknown. We characterized the variability of thymic function among 1000 age- and sex-stratified healthy adults of the Milieu Intérieur cohort, using quantification of T cell receptor excision circles (TRECs) in peripheral blood T cells as a surrogate marker of thymopoiesis. Age and sex were the only nonheritable factors identified that affect thymic function. TREC amounts decreased with age and were higher in women compared to men. In addition, a genome-wide association study revealed a common variant (rs2204985) within the T cell receptor
Published: 2017

47. High level of IL-10 expression in the blood of animal models possibly relates to resistance against leptospirosis

Author: Didier Monchy, Marie-Estelle Soupé-Gilbert, Milena Hasan, Cyrille Goarant, Louise Roche, Mariko Matsui, Institut Pasteur de Nouvelle-Calédonie, Réseau International des Instituts Pasteur (RIIP), Centre de Recherche Translationnelle - Center for Translational Science (CRT), Institut Pasteur [Paris] (IP), Centre hospitalier territorial Gaston-Bourret [Nouméa], This work was supported by the French Ministry of Research and Technology, Institut Pasteur in New Caledonia, and Institut Pasteur in Paris. Position of M.M. is financed by the Government of New Caledonia, and Institut Pasteur [Paris]
Subjects: 0301 basic medicine, medicine.medical_treatment, Interleukin-1beta, 030106 microbiology, Immunology, Gene Expression, Virulence, Hamster, Biochemistry, [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity, Antibodies, Neutralization, Mice, 03 medical and health sciences, In vivo, Leptospira, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Cricetinae, medicine, Animals, Immunology and Allergy, Leptospirosis, Molecular Biology, Cytokine, Disease Resistance, biology, Tumor Necrosis Factor-alpha, Hematology, biology.organism_classification, medicine.disease, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Interleukin-10, 3. Good health, Disease Models, Animal, Interleukin 10, 030104 developmental biology, Gene Expression Regulation, IL-1β, TNF-α, IL-10
Abstract: International audience; Leptospirosis is a severe zoonosis which immunopathogenesis is poorly understood. We evaluated correlation between acute form of the disease and the ratio of the anti-inflammatory cytokine IL-10 to the pro-inflammatory TNF-α and IL-1β expression during the early phase of infection comparing resistant mice and susceptible hamsters infected with two different species of virulent Leptospira. The IL-10/TNF-α and IL-10/IL-1β expression ratios were higher in mouse compared to hamster independently of the Leptospira strain, suggesting a preponderant role of the host response and notably these cytokines in the clinical expression and survival to leptospirosis. Using an IL-10 neutralization strategy in Leptospira-infected mouse model, we also showed evidence of a possible role of this cytokine on host susceptibility, bacterial clearance and on regulation of cytokine gene expression.
Published: 2017
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48. Single-cell Gene Expression Using Multiplex RT-qPCR to Characterize Heterogeneity of Rare Lymphoid Populations

Author: Thibaut Perchet, Sylvestre Chea, Milena Hasan, Ana Cumano, Rachel Golub, Lymphopoïèse (Lymphopoïèse (UMR_1223 / U1223 / U-Pasteur_4)), Institut Pasteur [Paris]-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), Cellule Pasteur, Université Paris Diderot - Paris 7 (UPD7)-PRES Sorbonne Paris Cité, Centre d'Immunologie Humaine (CIH), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), This work was supported by the Institut Pasteur, INSERM, Université Paris Diderot and by the Ministère de la Recherche (to S.C.), the Association pour la Recherche sur le Cancer (to S.C. and R.G.), the REVIVE Future Investment Program and the Agence Nationale de Recherche (ANR, grant 'Twothyme' to A.C.), ANR grant 'Myeloten' (to R.G.), and the Institut National du Cancer (Role of the immune microenvironment during liver carcinogenesis, to R.G.)., ANR-14-CE11-0022,Twothyme,Deux progéniteurs hématopoïétiques différents établissent le compartiment de lymphocytes T: tester un nouveau paradigme du développement T.(2014), ANR-13-ISV1-0003,MYELOTEN,DEREGULATION DE L'HEMATOPOIESE PAR LA SUREXPRESSION DE L'INTERLEUKINE-10 : IMPLICATIONS DANS LE DEVELOPPEMENT DE PATHOLOGIES HEMATOLOGIQUES(2013), Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), and PRES Sorbonne Paris Cité-Université Paris Diderot - Paris 7 (UPD7)
Subjects: 0301 basic medicine, General Chemical Engineering, Cellular differentiation, Population, Biology, Real-Time Polymerase Chain Reaction, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Single-cell analysis, Gene expression, Genetics, Humans, Multiplex, Lymphocytes, education, Gene, education.field_of_study, General Immunology and Microbiology, General Neuroscience, Gene Expression Profiling, Cell Differentiation, Gene signature, 030104 developmental biology, [SDV.IMM]Life Sciences [q-bio]/Immunology, Single-Cell Analysis, Cell activation
Abstract: International audience; Gene expression heterogeneity is an interesting feature to investigate in lymphoid populations. Gene expression in these cells varies during cell activation, stress, or stimulation. Single-cell multiplex gene expression enables the simultaneous assessment of tens of genes(1)(,)(2)(,)(3). At the single-cell level, multiplex gene expression determines population heterogeneity(4)(,)(5). It allows for the distinction of population heterogeneity by determining both the probable mix of diverse precursor stages among mature cells and also the diversity of cell responses to stimuli. Innate lymphoid cells (ILC) have been recently described as a population of innate effectors of the immune response(6)(,)(7). In this protocol, cell heterogeneity of the ILC hepatic compartment is investigated during homeostasis. Currently, the most widely used technique to assess gene expression is RT-qPCR. This method measures gene expression only one gene at a time. Additionally, this method cannot estimate heterogeneity of gene expression, since multiple cells are needed for one test. This leads to the measurement of the average gene expression of the population. When assessing large numbers of genes, RT-qPCR becomes a time-, reagent-, and sample-consuming method. Hence, the trade-offs limit the number of genes or cell populations that can be evaluated, increasing the risk of missing the global picture. This manuscript describes how single-cell multiplex RT-qPCR can be used to overcome these limitations. This technique has benefited from recent microfluidics technological advances(1)(,)(2). Reactions occurring in multiplex RT-qPCR chips do not exceed the nanoliter-level. Hence, single-cell gene expression, as well as simultaneous multiple gene expression, can be performed in a reagent-, sample-, and cost-effective manner. It is possible to test cell gene signature heterogeneity at the clonal level between cell subsets within a population at different developmental stages or under different conditions(4)(,)(5). Working on rare populations with large numbers of conditions at the single-cell level is no longer a restriction.
Published: 2017
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49. Macrophage chemotactic protein-1 mRNA levels in non-Hodgkin lymphoma

Author: Antica Duletić-Načinović, David Zombori, Sanja Štifter, Nives Jonjić, Milena Hasan, Toni Valković, Blaženka Grahovac, and Ita Hadžisejdić
Subjects: Adult, Male, Cytoplasm, Pathology, medicine.medical_specialty, Chemokine, Stromal cell, Non-Hodgkin lymphoma, Monocyte chemotactic protein-1, Palatine Tonsil, Biology, General Biochemistry, Genetics and Molecular Biology, Palatine tonsil, hemic and lymphatic diseases, Internal medicine, medicine, Humans, Macrophage, Lymphocytes, RNA, Messenger, Chemokine CCL2, Aged, Aged, 80 and over, Hematology, Reverse Transcriptase Polymerase Chain Reaction, Gene Expression Profiling, Lymphoma, Non-Hodgkin, Macrophages, General Medicine, Middle Aged, medicine.disease, Immunohistochemistry, Lymphoma, medicine.anatomical_structure, Lymphatic system, biology.protein, Female
Abstract: Non-Hodgkin lymphoma (NHL) is one of the most common malignancies whose incidence increases, and the treatment results are not satisfactory. The aim of this study was to determine the capacity of NHL to produce MCP-1, chemokine that induces chemotaxis of macrophages and lymphoid cells. The mRNA expression and protein MCP-1 expression were determined in the samples of 20 patients with NHL and 8 reactive tonsils. MCP-1 mRNA was detected in 8/8 tonsils and in 19/20 patients with NHL by real-time PCR analysis. In addition, the amount of detected MCP-1 cDNA was significantly higher in patients with limited stage, good IPI, normal level of fibrinogen and LDH. Finally, in patients with aggressive NHL, the level of MCP-1 cDNA was higher than in indolent tumours. Immunohistochemical analysis revealed that majority of stromal elements such as macrophages, endothelial and smooth muscle cells in reactive as well as in neoplastic lymphoid tissue showed strong cytoplasmic MCP-1 expression. Moderate cytoplasmic MCP-1 expression was also observed in reactive lymphocytes, while tumour cells of indolent NHL were mostly pale in comparison with aggressive lymphomas which predominantly demonstrated intense MCP-1 staining. These intriguing preliminary results emphasize the need for further investigations that must be conducted on the representative sample with concordant measurement of serum MCP-1 level.
Published: 2010
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50. The herpesviral Fc receptor fcr-1 down-regulates the NKG2D ligands MULT-1 and H60

Author: Milena Hasan, Astrid Krmpotić, Hrvoje Šimić, Jurica Arapović, Ulrich H. Koszinowski, Albert Zimmermann, Stipan Jonjić, Hartmut Hengel, Tihana Lenac, Zsolt Ruzsics, Matthias Budt, and Martin Messerle
Subjects: Muromegalovirus, NK Cell Lectin-Like Receptor Subfamily K, Immunology, Fc receptor, Down-Regulation, Immunoglobulins, chemical and pharmacologic phenomena, Receptors, Fc, Ligands, Virus Replication, Immunoglobulin G, Natural killer cell, Minor Histocompatibility Antigens, Mice, Viral Proteins, fcr-1, NKG2D, MULT-1, H60, medicine, Animals, Humans, Immunology and Allergy, Receptors, Immunologic, Receptor, Mice, Inbred BALB C, Membrane Glycoproteins, biology, Histocompatibility Antigens Class I, BIOMEDICINE AND HEALTHCARE. Basic Medical Sciences, Brief Definitive Report, Membrane Proteins, Molecular biology, Protein Structure, Tertiary, Transmembrane domain, Membrane glycoproteins, medicine.anatomical_structure, Ectodomain, NIH 3T3 Cells, biology.protein, Brief Definitive Reports, Receptors, Natural Killer Cell, Carrier Proteins, Lysosomes, BIOMEDICINA I ZDRAVSTVO. Temeljne medicinske znanosti, Protein Processing, Post-Translational
Abstract: Members of the α- and β-subfamily of herpesviridae encode glycoproteins that specifically bind to the Fc part of immunoglobulin (Ig)G. Plasma membrane resident herpesviral Fc receptors seem to prevent virus-specific IgG from activating antibody-dependent effector functions. We show that the mouse cytomegalovirus (MCMV) molecule fcr-1 promotes a rapid down-regulation of NKG2D ligands murine UL16-binding protein like transcript (MULT)-1 and H60 from the cell surface. Deletion of the m138/fcr-1 gene from the MCMV genome attenuates viral replication to natural killer (NK) cell response in an NKG2D-dependent manner in vivo. A distinct N-terminal module within the fcr-1 ectodomain in conjunction with the fcr-1 transmembrane domain was required to dispose MULT-1 to degradation in lysosomes. In contrast, down-modulation of H60 required the complete fcr-1 ectodomain, implying independent modes of fcr-1 interaction with the NKG2D ligands. The results establish a novel viral strategy for down-modulating NK cell responses and highlight the impressive diversity of Fc receptor functions.
Published: 2006
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