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Administration of azithromycin after allogeneic hematopoietic stem cell transplantation for hematologic malignancies has been associated with relapse in a randomized phase 3 controlled clinical trial. Studying 240 samples from patients randomized in this trial is a unique opportunity to better understand the mechanisms underlying relapse, the first cause of mortality after transplantation. We used multi-omics on patients’ samples to decipher immune alterations associated with azithromycin intake and post-transplantation relapsed malignancies. Azithromycin was associated with a network of altered energy metabolism pathways and immune subsets, including T cells biased toward immunomodulatory and exhausted profiles. In vitro, azithromycin exposure inhibited T-cell cytotoxicity against tumor cells and impaired T-cell metabolism through glycolysis inhibition, down-regulation of mitochondrial genes, and up-regulation of immunomodulatory genes, notably SOCS1. These results highlight that azithromycin directly affects immune cells that favor relapse, which raises caution about long-term use of azithromycin treatment in patients at high risk of malignancies. The ALLOZITHRO trial was registered at www.clinicaltrials.gov as #NCT01959100.

Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is the most effective treatment for selected patients with acute myeloid leukemia (AML) and relies on a “graft-versus-leukemia” effect (GVL) where donor T lymphocytes mediate control of malignant cell growth. However, relapse remains the major cause of death after allo-HSCT. In various malignancies, several immunoregulatory mechanisms have been shown to restrain antitumor immunity, including ligand-mediated engagement of inhibitory receptors (IRs) on effector cells, and induction of immunosuppressive cell subsets, such as regulatory T cells (Tregs) or myeloid-derived suppressor cells (MDSCs). Relapse after HSCT remains a major therapeutic challenge, but immunoregulatory mechanisms involved in restraining the GVL effect must be better deciphered in humans. We used mass cytometry to comprehensively characterize circulating leukocytes in 2 cohorts of patients after allo-HSCT. We first longitudinally assessed various immunoregulatory parameters highlighting specific trends, such as opposite dynamics between MDSCs and Tregs. More generally, the immune landscape was stable from months 3 to 6, whereas many variations occurred from months 6 to 12 after HSCT. Comparison with healthy individuals revealed that profound alterations in the immune equilibrium persisted 1 year after HSCT. Importantly, we found that high levels of TIGIT and CD161 expression on CD4 T cells at month 3 after HSCT were distinct features significantly associated with subsequent AML relapse in a second cross-sectional cohort. Altogether, these data provide global insights into the reconstitution of the immunoregulatory landscape after HSCT and highlight non-canonical IRs associated with relapse, which could open the path to new prognostic tools or therapeutic targets to restore subverted anti-AML immunity.

The mechanisms underlying operational tolerance after hematopoietic stem cell transplantation in humans are poorly understood. We studied two independent cohorts of patients who underwent allogeneic hematopoietic stem cell transplantation from human leukocyte antigen–identical siblings. Primary tolerance was associated with long-lasting reshaping of the recipients’ immune system compared to their healthy donors with an increased proportion of regulatory T cell subsets and decreased T cell activation, proliferation, and migration. Transcriptomics profiles also identified a role for nicotinamide adenine dinucleotide biosynthesis in the regulation of immune cell functions. We then compared individuals with operational tolerance and nontolerant recipients at the phenotypic, transcriptomic, and metabolomic level. We observed alterations centered on CD38+-activated T and B cells in nontolerant patients. In tolerant patients, cell subsets with regulatory functions were prominent. RNA sequencing analyses highlighted modifications in the tolerant patients’ transcriptomic profiles, particularly with overexpression of the ectoenzymeNT5E(encoding CD73), which could counterbalance CD38 enzymatic functions by producing adenosine. Further, metabolomic analyses suggested a central role of androgens in establishing operational tolerance. These data were confirmed using an integrative approach to evaluating the immune landscape associated with operational tolerance. Thus, balance between a CD38-activated immune state and CD73-related production of adenosine may be a key regulator of operational tolerance.

SUMMARYAcquired mutations in theUBA1gene, occurring in myeloid cells and resulting in expression of a catalytically impaired isoform of the enzyme E1, were recently identified in patients with severe adult-onset auto-inflammatory syndrome called VEXAS (vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic). The precise physiological and clinical impact of these mutations remains poorly defined.Here, we studied a unique prospective cohort of individuals with severe autoinflammatory disease with (VEXAS) or without (VEXAS-like)UBA1somatic mutations and compared with low-risk myelodysplastic syndromes (MDS) and aged gender-matched healthy controls. We performed an integrated immune analysis including multiparameter phenotyping of peripheral blood leukocytes, cytokines profiling, bulk and single-cell gene expression analyses and skin tissue imaging mass cytometry.Focusing on myeloid cells, we show that monocytes fromUBA1-mutated individuals were quantitatively and qualitatively impaired and displayed features of exhaustion with aberrant expression of chemokine receptors. Within affected tissues, pathological skin biopsies from VEXAS patients showed an abundant enrichment of CD16+CD163+monocytes adjacent to blood vessels and M1 macrophages, possibly promoting local inflammation in part through STAT3 activation. In peripheral blood from VEXAS patients, we identified a significant increase in circulating levels of many proinflammatory cytokines, including IL-1β and IL-18 which reflect inflammasome activation and markers of myeloid cells dysregulation. Gene expression analysis of whole blood confirmed the role of circulating cells in the IL-1β and IL-18 dysregulation in VEXAS patients and revealed a significant enrichment of TNF-α and NFκB signaling pathways that could mediate cell death and inflammation. Single-cell analysis confirmed the inflammatory state of monocytes from VEXAS patients and allowed us to identify specific molecular pathways that could explain monocytopenia, especially the activation of PANoptosis and a deficiency in the TYROBP/DAP12 axis and β-catenin signaling pathway. Together, these findings on monocytes from patients withUBA1mutations provide important insights into the molecular mechanisms involving the mature myeloid commitment in VEXAS syndrome and suggest that the control of the undescribed inflammasome activation and PANoptosis could be novel therapeutic targets in this condition.GRAPHICAL ABSTRACT

International audience; Myasthenia gravis (MG) is an autoimmune neuromuscular disorder due to autoantibodies directed against the neuromuscular junction. Conventional treatments are limited by hefty adverse effects mandating the set-up of novel therapies. Mesenchymal Stromal Cells (MSC) are multipotent progenitors that modulate immune and inflammatory responses through soluble factors, extracellular vesicles and cell-cell contacts. Our team demonstrated that the transfer of research grade (RG-) MSC conditioned by a co-culture step with peripheral blood mononucleated cells (PBMC) improved the clinical outcomes in a humanized MG mouse model (NSG-MG) (Sudres et al., JCI Insight, 2017). To shift towards a clinical perspective, RG-MSC were replaced by clinical grade (CG-) MSC (grown using human platelet lysate). Here, we aim to characterize the phenotypic and gene expression profiles of resting and conditioned CG-MSC, compared to a classical conditioning approach (IFN-γ activation), as well as to validate their functional capacities in vitro and in vivo. Therefore, CG-MSC derived from adipose tissue were conditioned by PBMC (cMSC), activated by IFN-γ (γ-MSC), or left untreated (rMSC). Their phenotype was assessed by flow cytometry (65 antibodies) and mass cytometry (CyTOF, Fluidigm) (31 antibodies). Gene expression was analyzed by RNA-seq (Illumina). Results showed that rMSC and cMSC had close phenotypic profiles whereas major phenotypic changes were found in γ-MSC. Some markers were modulated by all conditioning treatments, while others exclusively by one of them, thus conferring specific signatures. Gene expression profiles also differed between tested conditions, suggesting that different pathways are involved. In vitro immunomodulating capacities of CG-MSC supernatants were evaluated by PBMC proliferation inhibition assay and we observed higher responses upon cellular conditioning. Proteomic analyses (PEA methodology, Olink) were carried out using PBMC-MSC coculture supernatants and potential conditioning molecules were identified. Finally, the in vivo efficacy of CG cMSC was challenged in our humanized preclinical mouse model. cMSC-treated mice presented lower MG scores than untreated mice as early as 2 weeks post-injection, and a better survival. Our work unveiled treatment-dependent phenotypic markers of MSC, it demonstrates that immunomodulation capacities in vitro and in vivo are enhanced by cellular conditioning and it enlights their potential mechanisms of action

Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in children is generally milder than in adults, but a proportion of cases result in hyperinflammatory conditions often including myocarditis. Methods To better understand these cases, we applied a multiparametric approach to the study of blood cells of 56 children hospitalized with suspicion of SARS-CoV-2 infection. Plasma cytokine and chemokine levels and blood cellular composition were measured, alongside gene expression at the bulk and single-cell levels. Findings The most severe forms of multisystem inflammatory syndrome in children (MIS-C) related to SARS-CoV-2 that resulted in myocarditis were characterized by elevated levels of pro-angiogenesis cytokines and several chemokines. Single-cell transcriptomics analyses identified a unique monocyte/dendritic cell gene signature that correlated with the occurrence of severe myocarditis characterized by sustained nuclear factor κB (NF-κB) activity and tumor necrosis factor alpha (TNF-α) signaling and associated with decreased gene expression of NF-κB inhibitors. We also found a weak response to type I and type II interferons, hyperinflammation, and response to oxidative stress related to increased HIF-1α and Vascular endothelial growth factor (VEGF) signaling. Conclusions These results provide potential for a better understanding of disease pathophysiology. Funding Agence National de la Recherche (Institut Hospitalo-Universitaire Imagine, grant ANR-10-IAHU-01; Recherche Hospitalo-Universitaire, grant ANR-18-RHUS-0010; Laboratoire d’Excellence ‘‘Milieu Intérieur,” grant ANR-10-LABX-69-01; ANR-flash Covid19 “AIROCovid” and “CoVarImm”), Institut National de la Santé et de la Recherche Médicale (INSERM), and the “URGENCE COVID-19” fundraising campaign of Institut Pasteur., Graphical abstract, Context and significance Children with SARS-CoV-2 infection were initially thought to have only mild COVID-19 symptoms. However, several weeks into the first wave of SARS-CoV-2 infections, there was a surge of a postacute pathology called multisystem inflammatory syndrome in children (MIS-C). The authors recruited a cohort of children with suspicion of SARS-CoV-2 infection and uncovered hyperinflammation, hypoxic conditions, exacerbation of TNF-α signaling via NF-κB, and absence of responses to type I and type II IFN secretion in the most severe forms of MIS-C with severe myocarditis. This work led the authors to identify in monocytes and validate in peripheral blood mononuclear cells a molecular signature of 25 genes that allows discrimination of the most severe forms of MIS-C with myocarditis., Multiparametric analysis identifies, in monocytes and dendritic cells, a molecular signature of the most severe forms of multisystem inflammatory syndrome in children caused by SARS-CoV-2 infection. Severe myocarditis is characterized by an excess of TNF-α signaling via NF-κB, hypoxic conditions, and hyperinflammation in the absence of type I and type II interferon responses.

Zika virus (ZIKV) is a mosquito-borne flavivirus that has emerged as a global concern because of its impact on human health. ZIKV infection during pregnancy can cause microcephaly and other severe brain defects in the developing fetus and there have been reports of the occurrence of Guillain-Barré syndrome in areas affected by ZIKV. NK cells are activated during acute viral infections and their activity contributes to a first line of defense because of their ability to rapidly recognize and kill virus-infected cells. To provide insight into NK cell function during ZIKV infection, we have profiled, using mass cytometry, the NK cell receptor-ligand repertoire in a cohort of acute ZIKV-infected female patients. Freshly isolated NK cells from these patients contained distinct, activated, and terminally differentiated, subsets expressing higher levels of CD57, NKG2C, and KIR3DL1 as compared with those from healthy donors. Moreover, KIR3DL1+ NK cells from these patients produced high levels of IFN-γ and TNF-α, in the absence of direct cytotoxicity, in response to in vitro stimulation with autologous, ZIKV-infected, monocyte-derived dendritic cells. In ZIKV-infected patients, overproduction of IFN-γ correlated with STAT-5 activation (r = 0.6643; p = 0.0085) and was mediated following the recognition of MHC class 1–related chain A and chain B molecules expressed by ZIKV-infected monocyte-derived dendritic cells, in synergy with IL-12 production by the latter cells. Together, these findings suggest that NK cells contribute to the generation of an efficacious adaptive anti-ZIKV immune response that could potentially affect the outcome of the disease and/or the development of persistent symptoms.

Immune checkpoint inhibitors for melanoma improve adaptive T cell immunity during COVID-19 without exacerbating inflammation., The COVID-19 pandemic has spread worldwide, yet the role of antiviral T cell immunity during infection and the contribution of immune checkpoints remain unclear. By prospectively following a cohort of 292 patients with melanoma, half of which treated with immune checkpoint inhibitors (ICIs), we identified 15 patients with acute or convalescent COVID-19 and investigated their transcriptomic, proteomic, and cellular profiles. We found that ICI treatment was not associated with severe COVID-19 and did not alter the induction of inflammatory and type I interferon responses. In-depth phenotyping demonstrated expansion of CD8 effector memory T cells, enhanced T cell activation, and impaired plasmablast induction in ICI-treated COVID-19 patients. The evaluation of specific adaptive immunity in convalescent patients showed higher spike (S), nucleoprotein (N), and membrane (M) antigen-specific T cell responses and similar induction of spike-specific antibody responses. Our findings provide evidence that ICI during COVID-19 enhanced T cell immunity without exacerbating inflammation.

Summary CD4+ T follicular helper cells (Tfh) promote B cell maturation and antibody production in secondary lymphoid organs. By using an innovative culture system based on splenocyte stimulation, we studied the dynamics of naive and memory CD4+ T cells during the generation of a Tfh cell response. We found that both naive and memory CD4+ T cells can acquire phenotypic and functional features of Tfh cells. Moreover, we show here that the transition of memory as well as naive CD4+ T cells into the Tfh cell profile is supported by the expression of pro-Tfh genes, including transcription factors known to orchestrate Tfh cell development. Using this culture system, we provide pieces of evidence that HIV infection differentially alters these newly identified pathways of Tfh cell generation. Such diversity in pathways of Tfh cell generation offers a new framework for the understanding of Tfh cell responses in physiological and pathological contexts., Graphical abstract, Highlights • In vitro stimulation of human spleen cells leads to the generation of Tfh-like cells • Splenic naive and memory CD4+ T cells can acquire Tfh cell functions • Specific programs of differentiation lead to the acquisition of Tfh cell functions • In vitro HIV infection differentially alters Tfh transcriptomic programs, Immunology; Virology; Cell biology

SARS-CoV-2 infection in children is generally milder than in adults, yet a proportion of cases result in hyperinflammatory conditions often including myocarditis. To better understand these cases, we applied a multi-parametric approach to the study of blood cells of 56 children hospitalized with suspicion of SARS-CoV-2 infection. The most severe forms of MIS-C (multisystem inflammatory syndrome in children related to SARS-CoV-2), that resulted in myocarditis, were characterized by elevated levels of pro-angiogenesis cytokines and several chemokines. Single-cell transcriptomic analyses identified a unique monocyte/dendritic cell gene signature that correlated with the occurrence of severe myocarditis, characterized by sustained NF-κB activity, TNF-α signaling, associated with decreased gene expression of NF-κB inhibitors. We also found a weak response to type-I and type-II interferons, hyperinflammation and response to oxidative stress related to increased HIF-1α and VEGF signaling. These results provide potential for a better understanding of disease pathophysiology.

International audience

Introduction La restauration immunitaire induite par les inhibiteurs de checkpoints immunitaires ont révolutionné le pronostic des cancers métastatiques [1]. La contribution de cette stratégie thérapeutique pour la prise en charge des infections reste toutefois controversée, malgré quelques études en faveur de leur utilisation, notamment dans le contexte de paralysie immunitaire au décours d’un sepsis sévère [2], [3], ou dans les situations d’épuisement immunitaire au cours des infections virales chroniques [4], [5]. Au cours de la COVID-19, des études suggèrent qu’un état d’épuisement immunitaire en lien avec une anergie et/ou une déplétion des lymphocytes T serait partiellement responsable de la virulence du SARS-CoV-2 [6], [7], [8], [9], [10]. Certains proposent donc l’utilisation des anti-PD1 comme stratégie thérapeutique tandis que d’autres suggèrent qu’au contraire, elle pourrait aggraver l’hyperinflammation [11], [12]. Patients et méthodes Nous avons suivi de façon prospective 292 patients atteints de mélanome lors de la première vague de COVID-19 (de mars à juin 2020) dont la moitié était traitée par immunothérapie (anti-PD1 ± anti-CTLA4). Les patients présentant des symptômes de COVID-19 étaient dépistés par PCR. Une sérologie SARS-CoV-2 était recherchée de façon systématique. Les patients présentant une infection symptomatique active ( 21 jours du début des symptômes, PCR négative, sérologie positive) ont été inclus pour une étude approfondie de la réponse immunitaire par une analyse transcriptionnelle (Nanostring), protéomique (SIMOA, Luminex) et cellulaire (cytométrie de masse). Résultats Quinze patients atteints de COVID-19 ont été identifiés (infection active ou convalescente) avec une estimation de la séroprévalence à 8,6 % de la cohorte. Quatre patients sur 15 ont nécessité une hospitalisation (26,7 %). Les données cliniques ne retrouvaient pas d’éléments en faveur d’une forme plus sévère de COVID-19 lors d’un traitement par anti-PD1, seul un patient ayant également une leucémie lymphoïde chronique, a développé une forme sévère de la COVID-19 et est décédé de défaillance respiratoire. L’analyse de la réponse immunitaire, en comparaison avec une cohorte de patients non traités par immunothérapie, retrouvait une réponse immunitaire innée semblable dans les deux cohortes. De même, le taux d’anticorps anti-Spike (IgG et IgA), la capacité neutralisante ainsi que la longévité des anticorps (suivi du taux sur une période d’1 an) étaient similaires en présence ou non d’un traitement par immunothérapie. En revanche, l’analyse de la réponse cellulaire mettait en évidence, chez les patients traités par immunothérapie, une expansion de la population de lymphocytes T CD8+ effecteurs mémoires, une augmentation de l’activation des lymphocytes T CD4+ et CD8+, et une augmentation la production d’IFN-gamma lors d’une stimulation ex-vivo par des peptides issus du SARS-CoV-2. Conclusion Nos résultats sont en faveur d’une augmentation de la réponse cellulaire T anti-SARS-CoV-2 lors d’un traitement par anti-PD1 chez les patients suivis pour mélanome, et de l’absence d’une exacerbation de la réponse inflammatoire. Il est nécessaire de confirmer ces résultats avec un plus grand nombre de patients, dans d’autres types de cancers et dans d’autres centres.

Interferons interfere with lung repair Interferons (IFNs) are central to antiviral immunity. Viral recognition elicits IFN production, which in turn triggers the transcription of IFN-stimulated genes (ISGs), which engage in various antiviral functions. Type I IFNs (IFN-α and IFN-β) are widely expressed and can result in immunopathology during viral infections. By contrast, type III IFN (IFN-λ) responses are primarily restricted to mucosal surfaces and are thought to confer antiviral protection without driving damaging proinflammatory responses. Accordingly, IFN-λ has been proposed as a therapeutic in coronavirus disease 2019 (COVID-19) and other such viral respiratory diseases (see the Perspective by Grajales-Reyes and Colonna). Broggi et al. report that COVID-19 patient morbidity correlates with the high expression of type I and III IFNs in the lung. Furthermore, IFN-λ secreted by dendritic cells in the lungs of mice exposed to synthetic viral RNA causes damage to the lung epithelium, which increases susceptibility to lethal bacterial superinfections. Similarly, using a mouse model of influenza infection, Major et al. found that IFN signaling (especially IFN-λ) hampers lung repair by inducing p53 and inhibiting epithelial proliferation and differentiation. Complicating this picture, Hadjadj et al. observed that peripheral blood immune cells from severe and critical COVID-19 patients have diminished type I IFN and enhanced proinflammatory interleukin-6– and tumor necrosis factor-α–fueled responses. This suggests that in contrast to local production, systemic production of IFNs may be beneficial. The results of this trio of studies suggest that the location, timing, and duration of IFN exposure are critical parameters underlying the success or failure of therapeutics for viral respiratory infections. Science , this issue p. 706 , p. 712 , p. 718 ; see also p. 626

Erdheim-Chester disease (ECD) is an histiocytosis of the L-group, characterised by multiorgan infiltration of histiocytes that often carry oncogenic mutations.1 In the past few years, several studies have progressively and carefully mapped ECD genome, and several mutations have been described, most of them activating the mitogen-activated protein kinases (MAPK) pathway.1 These discoveries led to new therapies targeting BRAF or MEK in patients with ECD.2 Despite these findings, ECD pathogenesis still remains undetermined. Patients with ECD present a systemic inflammatory disease, with not only macrophages but also several other immune cells infiltrating affected tissues. A few studies have tried to explore the immune phenotype of ECD, with cytokine dosage in plasma and/or immunohistochemistry analysis, suggesting a complex network of inflammatory cytokines and chemokines.3 In order to explore the inflammatory phenotype of ECD, we realised immune phenotyping of circulating immune cells of 13 patients with ECD (details on patients’ characteristics are available in online supplementary table 1) and …

BackgroundCoronavirus disease 2019 (Covid-19) is a major global threat that has already caused more than 100,000 deaths worldwide. It is characterized by distinct patterns of disease progression implying a diverse host immune response. However, the immunological features and molecular mechanisms involved in Covid-19 severity remain so far poorly known.MethodsWe performed an integrated immune analysis that included in-depth phenotypical profiling of immune cells, whole-blood transcriptomic and cytokine quantification on a cohort of fifty Covid19 patients with a spectrum of disease severity. All patient were tested 8 to 12 days following first symptoms and in absence of anti-inflammatory therapy.ResultsA unique phenotype in severe and critically ill patients was identified. It consists in a profoundly impaired interferon (IFN) type I response characterized by a low interferon production and activity, with consequent downregulation of interferon-stimulated genes. This was associated with a persistent blood virus load and an exacerbated inflammatory response that was partially driven by the transcriptional factor NFĸB. It was also characterized by increased tumor necrosis factor (TNF)-α and interleukin (IL)-6 production and signaling as well as increased innate immune chemokines.ConclusionWe propose that type-I IFN deficiency in the blood is a hallmark of severe Covid-19 and could identify and define a high-risk population. Our study provides a rationale for testing IFN administration combined with adapted anti-inflammatory therapy targeting IL-6 or TNF-α in most severe patients. These data also raise concern for utilization of drugs that interfere with the IFN pathway.

The anti-tumor immune response plays a crucial role in cancer patient outcome as well as in response to the growing family of immunotherapeutic treatments. Improving patient prognostic and therapeutic management requires a better knowledge of the tumor microenvironment, for which a deep characterization of tumor-infiltrating immune populations is instrumental. Mass cytometry represents an excellent tool in tumor Immunology, as it allows the simultaneous analysis of40 markers on single cells. In this chapter, we review challenging technical aspects of the mass cytometry phenotyping of tumor infiltrating immune cells, focusing on fresh human solid tumor samples. We first explain how to design mass cytometry experiments, then provide detailed protocols to isolate mononuclear immune cells from solid tissues and to stain them for an acquisition on a mass cytometer. We also discuss how to optimize the preparation of single immune cell samples, and how to ensure the reproducibility of data generated from distinct fresh human samples. Finally, we provide troubleshooting suggestions for difficult sample acquisitions on a mass cytometer.

The anti-tumor immune response plays a crucial role in cancer patient outcome as well as in response to the growing family of immunotherapeutic treatments. Improving patient prognostic and therapeutic management requires a better knowledge of the tumor microenvironment, for which a deep characterization of tumor-infiltrating immune populations is instrumental. Mass cytometry represents an excellent tool in tumor Immunology, as it allows the simultaneous analysis of >40 markers on single cells. In this chapter, we review challenging technical aspects of the mass cytometry phenotyping of tumor infiltrating immune cells, focusing on fresh human solid tumor samples. We first explain how to design mass cytometry experiments, then provide detailed protocols to isolate mononuclear immune cells from solid tissues and to stain them for an acquisition on a mass cytometer. We also discuss how to optimize the preparation of single immune cell samples, and how to ensure the reproducibility of data generated from distinct fresh human samples. Finally, we provide troubleshooting suggestions for difficult sample acquisitions on a mass cytometer.

Ces dernières années ont vu une progression importante des capacités des nouveaux appareils de cytométrie. Deux sauts technologiques ont été récemment franchis avec la cytométrie couplée à la spectrométrie de masse, dans laquelle les fluorochromes ont été remplacés par des métaux rares non radioactifs de la famille des lanthanides et la cytométrie spectrale qui collecte les photons sur le spectre visible. Dans cette revue, nous décrivons schématiquement la cytométrie en flux conventionnelle et ces deux technologies ainsi que leurs avantages et adaptabilités et leurs inconvénients.

RationaleMass cytometry allows large multiplex analysis of cell cycle stages together with differentiation, activation, and exhaustion markers, allowing further assessment of the quiescence status of resting CD4 T cells. MethodsPeripheral blood CD4 T lymphocytes from 8 individuals, 4 healthy donors, and 4 HIV-infected on antiretroviral treatment (T) were stained with the same 26 monoclonal antibodies and dyes targeting surface and intracellular markers of differentiation, activation, exhaustion, and cell cycle stages. Samples were run on a CYTOF-2. ResultsPatterns of naive [TN] CD4 T cells strongly differed from all other memory subsets central-memory (CM), transitional-memory (TM), effector-memory (EM), and terminally differentiated RA-expressing (TEMRA) subsets, while stem-cell memory (SCM) and T follicular-helper cells (TfH) were close to CM and TM cells with the highest percentages in cell cycle. EM and TEMRA were the most altered by HIV infection, with an increased frequency of activated and cycling cells. Activation markers and coinhibitory receptor expression differed among cell cycle stages, with HLA-DR fitting better than CD25 or CD38 with cycle, and opposite PD-1 gradients along differentiation and cell cycle. Resting DR-CD25- CD4+ T cells contained similar amounts of cells in G1 than the activated DRCD25 +/- ones but three fold lower cells in S-G2-M. ConclusionThis broad multiplex mass cytometry analysis demonstrates some subsets of the so-called resting CD25-DR- CD4+ T cells contain noticeable amounts of cells into cycle or expressing coinhibitory receptors, opening new avenues for a redefinition of resting peripheral blood CD4 T cells harboring the HIV reservoirs.

Background Myositis is a heterogeneous group of muscular auto-immune diseases with clinical and pathological criteria that allow the classification of patients into different sub-groups. Inclusion body myositis is the most frequent myositis above fifty years of age. Diagnosing inclusion body myositis requires expertise and is challenging. Little is known concerning the pathogenic mechanisms of this disease in which conventional suppressive-immune therapies are inefficacious. Objectives Our aim was to deepen our understanding of the immune mechanisms involved in inclusion body myositis and identify specific biomarkers. Methods Using a panel of thirty-six markers and mass cytometry, we performed deep immune profiling of peripheral blood cells from inclusion body myositis patients and healthy donors, divided into two cohorts: test and validation cohorts. Potential biomarkers were compared to myositis controls (anti-Jo1-, anti-3-hydroxyl-3-methylglutaryl CoA reductase-, and anti-signal recognition particle-positive patients). Results Unsupervised analyses revealed substantial changes only within CD8+ cells. We observed an increase in the frequency of CD8+ cells that expressed high levels of T-bet, and containing mainly both effector and terminally differentiated memory cells. The senescent marker CD57 was overexpressed in CD8+T-bet+ cells of inclusion body myositis patients. As expected, senescent CD8+T-bet+ CD57+ cells of both patients and healthy donors were CD28nullCD27nullCD127null. Surprisingly, non-senescent CD8+T-bet+ CD57- cells in inclusion body myositis patients expressed lower levels of CD28, CD27, and CD127, and expressed higher levels of CD38 and HLA-DR compared to healthy donors. Using classification and regression trees alongside receiver operating characteristics curves, we identified and validated a frequency of CD8+T-bet+ cells >51.5% as a diagnostic biomarker specific to inclusion body myositis, compared to myositis control patients, with a sensitivity of 94.4%, a specificity of 88.5%, and an area under the curve of 0.97. Conclusion Using a panel of thirty-six markers by mass cytometry, we identify an activated cell population (CD8+T-bet+ CD57- CD28lowCD27lowCD127low CD38+ HLA-DR+) which could play a role in the physiopathology of inclusion body myositis, and identify CD8+T-bet+ cells as a predominant biomarker of this disease.

Mice reconstituted with a human immune system and bearing human tumors represent a promising model for developing novel cancer immunotherapies. Here, we used mass cytometry and multi-parametric flow cytometry to characterize human leukocytes infiltrating a human breast cancer tumor model in immunocompromised NOD.SCID.γc-null mice reconstituted with a human immune system and compared it to samples of breast cancer patients. We observed highly activated human CD4+ and CD8+ T cells in the tumor, as well as minor subsets of innate immune cells in both settings. We also report that ICOS+ CD4+ regulatory T cells (Treg) were enriched in the tumor relative to the periphery in humanized mice and patients, providing a target to affect Treg and tumor growth. Indeed, administration of a neutralizing mAb to human ICOS reduced Treg proportions and numbers and improved CD4+ T cell proliferation in humanized mice. Moreover, a combination of the anti-ICOS mAb with cyclophosphamide reduced tumor growth, and that was associated with an improved CD8 to Treg ratio. However, depletion of human CD8+ T cells only marginally affected tumor control whereas depletion of murine myeloid cells abrogated the effect of the combination therapy. Altogether, our results indicate that a combination of anti-ICOS mAb and chemotherapy controls tumor growth in humanized mice and highlight the crucial implication of innate immunity in treatment efficacy, opening new perspectives for the treatment of breast cancer.One sentence summaryICOS expressed on Tregs is a promising target to improve tumor immunity in humansAbbreviationsICOSInducible CostimulatoryNSGNOD.SCID.gc-nullTregregulatory T cellsCTXcyclophosphamideHuMicehumanized miceCyTOFcytometry time-of-flighttSNEtdistributed stochastic neighbor embeddingpDCsplasmacytoid dendritic cellsDCdendritic cellsICDimmunogenic cell death

Background:The understanding of Erdheim-Chester Disease (ECD) pathogenesis has been greatly improved these past few years with the discovery of activating MAPK pathway mutations in most of ECD patients. However, the inflammatory phenotype of ECD remains widely unknown.Objectives:We aimed to explore the inflammatory phenotype of Erdheim-Chester disease (ECD) using mass cytometry.Methods:We analyzed peripheral blood mononuclear cells from 13 ECD patients and 11 healthy donors (HD) using mass cytometry with 29 metal-conjugated antibodies.Results:Compared to HD, untreated ECD patients had increased proportion of classical monocytes (90.8 [87.1-96.5] vs 81.6 [76.2-87.5] %, p=0.02) and decreased proportion of non-classical monocytes (4.7 [3.4-9.7] vs 11.8 [6.6-17.2] %, p=0.047). Untreated ECD patients had more circulating Th17 cells compared to HD (3.3 [3-5.3] vs 1.3 [0.4-2.3] %, p=0.015) and ECD patients treated with BRAF or MEK inhibitors (3.3 (3-5.3] vs 1.9 [0.6-2.4] %, p=0.005). Moreover Treg cells were lower in ECD patients than HD, with an increased Th17/Treg ratio (1.37 [0.74-1.9] vs 0.34 [0.19-0.43], p=0.0004). There was no difference regarding Th1 cells, Th2 cells, B cells, NK cells and circulating dendritic cells.Conclusion:ECD monocyte profile seems similar to what have been described in CMML. Inflammation observed in ECD may be driven through Th17 cells, and might be targeted with specific treatment.Disclosure of Interests:None declared

Myositis is a heterogeneous group of muscular auto-immune diseases with clinical and pathological criteria that allow the classification of patients into different sub-groups. Inclusion body myositis is the most frequent myositis above fifty years of age. Diagnosing inclusion body myositis requires expertise and is challenging. Little is known concerning the pathogenic mechanisms of this disease in which conventional suppressive-immune therapies are inefficacious.Our aim was to deepen our understanding of the immune mechanisms involved in inclusion body myositis and identify specific biomarkers.Using a panel of thirty-six markers and mass cytometry, we performed deep immune profiling of peripheral blood cells from inclusion body myositis patients and healthy donors, divided into two cohorts: test and validation cohorts. Potential biomarkers were compared to myositis controls (anti-Jo1-, anti-3-hydroxyl-3-methylglutaryl CoA reductase-, and anti-signal recognition particle-positive patients).Unsupervised analyses revealed substantial changes only within CD8+ cells. We observed an increase in the frequency of CD8+ cells that expressed high levels of T-bet, and containing mainly both effector and terminally differentiated memory cells. The senescent marker CD57 was overexpressed in CD8+Using a panel of thirty-six markers by mass cytometry, we identify an activated cell population (CD8+

International audience; Adult tissue repair and regeneration require stem-progenitor cells that can self-renew and generate differentiated progeny. Skeletal muscle regenerative capacity relies on muscle satellite cells (MuSCs) and their interplay with different cell types within the niche. However, our understanding of skeletal muscle tissue cellular composition is limited. Here, using a combined approach of single-cell RNA sequencing and mass cytometry, we precisely mapped 10 different mononuclear cell types in adult mouse muscle. We also characterized gene signatures and determined key discriminating markers of each cell type. We identified two previously understudied cell populations in the interstitial compartment. One expresses the transcription factor scleraxis and generated tenocytes in vitro. The second expresses markers of smooth muscle and mesenchymal cells (SMMCs) and, while distinct from MuSCs, exhibited myogenic potential and promoted MuSC engraftment following transplantation. The blueprint presented here yields crucial insights into muscle-resident cell-type identities and can be exploited to study muscle diseases.

Adult tissue repair and regeneration require the activation of resident stem and progenitor cells that can self-renew and generate differentiated progeny. The regenerative capacity of skeletal muscle relies on muscle satellite cells (MuSCs) and their interplay with different cell types within the niche. However, our understanding of the cells that compose skeletal muscle tissue is limited and molecular definitions of the principal cell types are lacking. Here, using a novel combined approach of single-cell RNA-sequencing and mass cytometry, we precisely mapped 10 different cell types in adult mouse skeletal muscle, including two previously unidentified populations. We also characterized the gene signatures and determined the key discriminating markers of each cell type. We found an unexpected complexity in the interstitial compartment, wherein two new cell populations were identified. One population expressed the transcription factor Scleraxis and generated tenocytes in vitro. The second population expressed smooth muscle and mesenchymal cell (SMMC) markers and, while distinct from MuSCs, exhibited myogenic potential and promoted MuSC engraftment following transplantation. The blueprint presented here yields crucial insights into muscle-resident cell type identities and can be exploited to study muscle ageing and diseases.

International audience; Mass cytometry is a powerful tool that allows simultaneous analysis of more than 37 markers at the single cell level. Mass cytometry is of particular interest in the identification of a wide variety of cell phenotypes in autoimmune diseases. Moreover, cells can be labelled with palladium isotopes and pooled before staining (barcoding). Nevertheless, immunolo-gists often face an important problem concerning the choice of markers to be included in a panel. This problem arises due to the incompatibility of different buffers used for the fixation and permeabilization of cells with various cell surface epitopes. In this study, we used a panel of 27 markers (19 surface markers and 8 intranuclear markers) to demonstrate disparities in the detection of cell surface antigens when comparing different buffers to stain unsti-mulated peripheral blood mononuclear cells. These disparities range from mild differences to very important differences in population frequencies depending on the buffers. Finally, we demonstrate the harmful effects of permeabilization prior to barcoding on the detection of some cell surface antigens. Here, we optimize a protocol that is suitable to use when targeting a large panel including both cell surface and intranuclear markers on unstimulated human peripheral blood mononuclear cells.

The recent introduction of mass cytometry, a technique coupling a cell introduction system generating a stream of single cells with mass spectrometry, has greatly increased the number of parameters that can be measured per single cell. As with all new technology there is a need for dissemination of standardization and quality control procedures. Here, we characterize variations in sensitivity observed across the mass range of a mass cytometer, using different lanthanide tags. We observed a five-fold difference in lanthanide detection over the mass range and demonstrated that each instrument has its own sensitivity pattern. Therefore, the selection of lanthanide combinations is a key step in the establishment of a staining panel for mass cytometry-based experiments, particularly for multicenter studies. We propose the sensitivity pattern as the basis for panel design, instrument standardization and future implementation of normalization algorithms.

Mass cytometry allows large multiplex analysis of cell cycle stages together with differentiation, activation, and exhaustion markers, allowing further assessment of the quiescence status of resting CD4 T cells.Peripheral blood CD4 T lymphocytes from 8 individuals, 4 healthy donors, and 4 HIV-infected on antiretroviral treatment (T) were stained with the same 26 monoclonal antibodies and dyes targeting surface and intracellular markers of differentiation, activation, exhaustion, and cell cycle stages. Samples were run on a CYTOF-2.Patterns of naïve [TN] CD4 T cells strongly differed from all other memory subsets central-memory (CM), transitional-memory (TM), effector-memory (EM), and terminally differentiated RA-expressing (TEMRA) subsets, while stem-cell memory (SCM) and T follicular-helper cells (TfH) were close to CM and TM cells with the highest percentages in cell cycle. EM and TEMRA were the most altered by HIV infection, with an increased frequency of activated and cycling cells. Activation markers and coinhibitory receptor expression differed among cell cycle stages, with HLA-DR fitting better than CD25 or CD38 with cycle, and opposite PD-1 gradients along differentiation and cell cycle. "Resting" DR-CD25- CD4+ T cells contained similar amounts of cells in G1 than the activated DR ± CD25± ones but three fold lower cells in S-G2-M.This broad multiplex mass cytometry analysis demonstrates some subsets of the so-called "resting" CD25-DR- CD4+ T cells contain noticeable amounts of cells into cycle or expressing coinhibitory receptors, opening new avenues for a redefinition of resting peripheral blood CD4 T cells harboring the HIV reservoirs. © 2016 International Clinical Cytometry Society.

The recent introduction of mass cytometry, a technique coupling a cell introduction system generating a stream of single cells with mass spectrometry, has greatly increased the number of parameters that can be measured per single cell. As with all new technology there is a need for dissemination of standardization and quality control procedures. Here, we characterize variations in sensitivity observed across the mass range of a mass cytometer, using different lanthanide tags. We observed a five-fold difference in lanthanide detection over the mass range and demonstrated that each instrument has its own sensitivity pattern. Therefore, the selection of lanthanide combinations is a key step in the establishment of a staining panel for mass cytometry-based experiments, particularly for multicenter studies. We propose the sensitivity pattern as the basis for panel design, instrument standardization and future implementation of normalization algorithms.

The mucosal events of HIV transmission have been extensively studied, but the role of infected cells present in the genital and rectal secretions, and in the semen, in particular, remains a matter of debate. As a prerequisite to a thorough in vivo investigation of the early transmission events through infected cells, we characterized in detail by multi-parameter flow cytometry the changes in macaque seminal leukocytes during SIVmac251 infection, focusing on T cells, macrophages and dendritic cells. Using immunocytofluorescence targeting SIV proteins and real-time quantitative PCR targeting SIV DNA, we investigated the nature of the infected cells on sorted semen leukocytes from macaques at different stages of infection. Finally, we cocultured semen CD4+ T cells and macrophages with a cell line permissive to SIV infection to assess their infectivity in vitro. We found that primary infection induced strong local inflammation, which was associated with an increase in the number of leukocytes in semen, both factors having the potential to favor cell-associated virus transmission. Semen CD4+ T cells and macrophages were productively infected at all stages of infection and were infectious in vitro. Lymphocytes had a mucosal phenotype and expressed activation (CD69 & HLA-DR) and migration (CCR5, CXCR4, LFA-1) markers. CD69 expression was increased in semen T cells by SIV infection, at all stages of infection. Macrophages predominated at all stages and expressed CD4, CCR5, MAC-1 and LFA-1. Altogether, we demonstrated that semen contains the two major SIV-target cells (CD4+ T cells and macrophages). Both cell types can be productively infected at all stages of SIV infection and are endowed with markers that may facilitate transmission of infection during sexual exposure., Author Summary Human Immunodeficiency Virus infection is predominantly transmitted by mucosal exposure, after sexual intercourse. Although substantial progresses have been recently achieved in our understanding of the mechanisms of HIV mucosal transmission, many questions remain. Semen is one of the major sources for HIV which contains both cell-free viral particles and viral infected cells. However, today, the role of cell-associated virus has been largely understudied. We provide here a detailed characterization of the semen leukocyte populations in the highly relevant experiment model of SIV infection of macaques. We demonstrate that the major target cells for the virus, CD4+ T cells and macrophages, are present in macaques semen at all stages of infection. Both cell types are productively infected in vivo and are endowed with adhesion and migration markers that may facilitate virus transmission during sexual exposure. The acute phase of infection is associated with a strong seminal inflammation that may increase semen leukocytes infectivity. This work supports for a role of cell-associated virus in HIV transmission which needs to be considered for the design of prevention strategies.

Background Spontaneous long-term HIV/SIV control in HIV-controller patients and SIV-controller macaques (SIC) is usually associated to protective MHC-class-I alleles and efficient CD8 T-cell responses. However, many HIV-controllers efficiently control HIV-infection despite of non-protective MHC background and weak CD8 T-cell responses, raising the question of real contribution of this response in maintaining viral control. We addressed this question by depleting in vivo CD8+ cells in SIC bearing or not protective MHC and weak CD8 T-cell responses.

Methods Naive male mauritian cynomolgus macaques were immunized with auxo-GTU-MultiSIV DNA encoding Gag, Nef, Rev and Tat (n=14) or by a combination of auxo-GTUMultiSIV DNA and auxo-GTU-SIV-vifvprvpx (n=12) by the intradermal route followed by electroporation. MHC class I and class II haplotypes were determined by microsatellite analysis. T-cell epitopes were mapped by IFN-g ELISPOT in PBMC by using matrix of 15-mer (overlapping by 11) SIVmac239 Gag, Nef, Rev, Tat, Vif, Vpx and Vpr peptides. Sequence and length of candidate epitopes were further optimized.

Aim The CD4 depletion in the chronic phase of HIV infection is mostly due to the loss of uninfected cells. We previously showed that this lost was related to the expression of NKp44L, a cellular ligand of the natural cytotoxicity receptor NKp44, which renders CD4 cells sensitive to NK killing. NKp44L is specially induced by the highly conserved 3S motif of the HIV-1 gp41 envelope protein. We also have shown that NKp44L is present on bystander non-infected CD4 cells, but absent from HIV-infected cells, through a Nef-dependent mechanism. In this study we sought to determine whether the loss of uninfected bystander CD4 cells could be prevented by a 3S therapeutic immunization in a macaque model chronically infected with SHIV162P3.

Introduction Interferon-α response is one the first innate immune response to HIV/SIV infections during primary infection but is associated with immune suppression, chronic immune activation and pathogenesis. Cell types involved in Interferon alpha production are poorly defined as pDC activation levels are, and reasons for which IFN-α are only transiently detected during acute primary infection, and re-appear in the late clinical AIDS phase are not known. Methods Macaques were infected by SIVmac251 to further analyse the dynamics of pDC and IFN-α during primary infection. We performed a multi-parameter followup: quality and kinetic of IFN-alpha responses (mRNA levels by RT-QPCR, antiviral activity by MDBK/VSV assay, ELISA), define cell types involved in IFN-α production (9 colors flow cytometry), monitor plasmacytoid DCs (pDC) activation/IFN-α production, monitor different pDC precursor stages by flow cytometry, monitor virus loads. Results Plasma viral loads peaked on day 10–11 p.i. to progressively reach a plateau on month 2–3. IFN-α plasma concentrations peaked on day 7–9 p.i. to become rapidly undetectable after day 14–17 p.i.. pDCs were the only cell type with detectable of IFN-α levels in peripheral lymph nodes (PLN) leukocytes. IFN-α mRNA levels correlated both to viral RNA loads and % of IFN-α positive pDCs, which reached transiently 1.82% ±1.52 positive cells on day 9 p.i.. In gut mucosa, IFN-α mRNA levels were also increased in some macaques in association with a raise of BDCA-2 mRNA levels. In PLN a much higher % of pDC transiently show increased expression of activation and apoptosis markers as CCR7, HLA-DR, CD40, CD86, CD95 (on day 9 p.i, 41 ± 13% of pDCs were HLA-DR high CCR7 high and 95 ± 2.93 % were CD95 positive). In parallel we observed an increase of pDC with precursor phenotype (CD123 low HLA-DR low , 22% ± 14 on day 9 p.i.) which express Ki67+ in PLN. This subtype is reminiscent of cells normally present in the bone marrow at steady state which are not able to produce IFN-α in response to SIV in vitro . The proportion of these Ki67+ precursor pDC population circulating in blood correlated with decreased production of IFN-α by pDCs in response to SIV in vitro . Setpoint was associated with a return to baseline of IFN-α mRNA levels in lymphnodes and gut mucosa, and to lower although sustained activation of pDC in lymph nodes, with no detectable IFN-α positive pDCs. Conclusion These data: 1/support that pDC are the main contributors, if not the only, to IFN-α production in response to SIVin this phase. 2/Strongly suggest that the replacement of strongly activated pDC prone to apoptosis by non-functional bone marrow derived early pDC precursors in PLN contribute to rapid decrease of IFN-α production in primary infection, and may contribute to transient decrease of pDC responsiveness to in vitro stimulation. 3/Sustained activation of the pDC pool at set point in the absence of detectable IFN-α expression suggest different threshold of virus loads or imflammation are responsible for differential pDC functions in the chronic compared to primary phase.

Chronic immune activation (IA) is considered as the driving force of CD4+ T cell depletion and AIDS. Fundamental clues in the mechanisms that regulate IA could lie in natural hosts of SIV, such as African green monkeys (AGMs). Here we investigated the role of innate immune cells and IFN-α in the control of IA in AGMs. AGMs displayed significant NK cell activation upon SIVagm infection, which was correlated with the levels of IFN-α. Moreover, we detected cytotoxic NK cells in lymph nodes during the early acute phase of SIVagm infection. Both plasmacytoid and myeloid dendritic cell (pDC and mDC) homing receptors were increased, but the maturation of mDCs, in particular of CD16+ mDCs, was more important than that of pDCs. Monitoring of 15 cytokines showed that those, which are known to be increased early in HIV-1/SIVmac pathogenic infections, such as IL-15, IFN-α, MCP-1 and CXCL10/IP-10, were significantly increased in AGMs as well. In contrast, cytokines generally induced in the later stage of acute pathogenic infection, such as IL-6, IL-18 and TNF-α, were less or not increased, suggesting an early control of IA. We then treated AGMs daily with high doses of IFN-α from day 9 to 24 post-infection. No impact was observed on the activation or maturation profiles of mDCs, pDCs and NK cells. There was also no major difference in T cell activation or interferon-stimulated gene (ISG) expression profiles and no sign of disease progression. Thus, even after administration of high levels of IFN-α during acute infection, AGMs were still able to control IA, showing that IA control is independent of IFN-α levels. This suggests that the sustained ISG expression and IA in HIV/SIVmac infections involves non-IFN-α products., Author Summary Chronic inflammation is considered as directly involved in AIDS pathogenesis. The role of IFN-α as a driving force of chronic inflammation is under debate. Natural hosts of SIV, such as African green monkeys (AGMs), avoid chronic inflammation. We show for the first time that NK cells are strongly activated during acute SIVagm infection. This further demonstrates that AGMs mount a strong early innate immune response. Myeloid and plasmacytoid dendritic cells (mDCs and pDCs) homed to lymph nodes; however mDCs showed a stronger maturation profile than pDCs. Monitoring of cytokine profiles in plasma suggests that the control of inflammation in AGMs is starting earlier than previously considered, weeks before the end of the acute infection. We tested whether the capacity to control inflammation depends on the levels of IFN-α produced. When treated with high doses of IFN-α during acute SIVagm infection, AGMs did not show increase of immune activation or signs of disease progression. Our study provides evidence that the control of inflammation in SIVagm infection is not the consequence of weaker IFN-α levels. These data indicate that the sustained interferon-stimulated gene induction and chronic inflammation in HIV/SIVmac infections is driven by factors other than IFN-α.