The Th1/Tfh-like biased responses elicited by the rASP-1 innate adjuvant are dependent on TRIF and Type I IFN receptor pathways.

Ov-ASP-1 (rASP-1), a parasite-derived protein secreted by the helminth Onchocerca volvulus, is an adjuvant which enhances the potency of the influenza trivalent vaccine (IIV3), even when used with 40-fold less IIV3. This study is aimed to provide a deeper insight into the molecular networks that underline the adjuvanticity of rASP-1. Here we show that rASP-1 stimulates mouse CD11c(+) bone marrow-derived dendritic (BMDCs) to secrete elevated levels of IL-12p40, TNF-α, IP-10 and IFN-β in a TRIF-dependent but MyD88-independent manner. rASP-1-activated BMDCs promoted the differentiation of naïve CD4(+) T cells into Th1 cells (IFN-γ(+)) that was TRIF- and type I interferon receptor (IFNAR)-dependent, and into Tfh-like cells (IL21(+)) and Tfh1 (IFN-γ(+) IL21(+)) that were TRIF-, MyD88- and IFNAR-dependent. rASP-1-activated BMDCs promoted the differentiation of naïve CD4(+) T cells into Th17 (IL-17(+)) cells only when the MyD88 pathway was inhibited. Importantly, rASP-1-activated human blood cDCs expressed upregulated genes that are associated with DC maturation, type I IFN and type II IFN signaling, as well as TLR4-TRIF dependent signaling. These activated cDCs promoted the differentiation of naïve human CD4(+) T cells into Th1, Tfh-like and Th17 cells. Our data thus confirms that the rASP-1 is a potent innate adjuvant that polarizes the adaptive T cell responses to Th1/Tfh1 in both mouse and human DCs. Notably, the rASP-1-adjuvanted IIV3 vaccine elicited protection of mice from a lethal H1N1 infection that is also dependent on the TLR4-TRIF axis and IFNAR signaling pathway, as well as on its ability to induce anti-IIV3 antibody production

Baseline immune states (BIS) associated with vaccine responsiveness and factors that shape the BIS.

Vaccines are among the greatest inventions in medicine, leading to the elimination or control of numerous diseases, including smallpox, polio, measles, rubella, and, most recently, COVID-19. Yet, the effectiveness of vaccines varies among individuals. In fact, while some recipients mount a robust response to vaccination that protects them from the disease, others fail to respond. Multiple clinical and epidemiological factors contribute to this heterogeneity in responsiveness. Systems immunology studies fueled by advances in single-cell biology have been instrumental in uncovering pre-vaccination immune cell types and genomic features (i.e., the baseline immune state, BIS) that have been associated with vaccine responsiveness. Here, we review clinical factors that shape the BIS, and the characteristics of the BIS associated with responsiveness to frequently studied vaccines (i.e., influenza, COVID-19, bacterial pneumonia, malaria). Finally, we discuss potential strategies to enhance vaccine responsiveness in high-risk groups, focusing specifically on older adults

Single Cell Analysis of Blood Mononuclear Cells Stimulated Through Either LPS or Anti-CD3 and Anti-CD28.

Immune cell activation assays have been widely used for immune monitoring and for understanding disease mechanisms. However, these assays are typically limited in scope. A holistic study of circulating immune cell responses to different activators is lacking. Here we developed a cost-effective high-throughput multiplexed single-cell RNA-seq combined with epitope tagging (CITE-seq) to determine how classic activators of T cells (anti-CD3 coupled with anti-CD28) or monocytes (LPS) alter the cell composition and transcriptional profiles of peripheral blood mononuclear cells (PBMCs) from healthy human donors. Anti-CD3/CD28 treatment activated all classes of lymphocytes either directly (T cells) or indirectly (B and NK cells) but reduced monocyte numbers. Activated T and NK cells expressed senescence and effector molecules, whereas activated B cells transcriptionally resembled autoimmune disease- or age-associated B cells (e.g., CD11c, T-bet). In contrast, LPS specifically targeted monocytes and induced two main states: early activation characterized by the expression of chemoattractants and a later pro-inflammatory state characterized by expression of effector molecules. These data provide a foundation for future immune activation studies with single cell technologies (https://czi-pbmc-cite-seq.jax.org/)

Sexual-dimorphism in human immune system aging.

Differences in immune function and responses contribute to health- and life-span disparities between sexes. However, the role of sex in immune system aging is not well understood. Here, we characterize peripheral blood mononuclear cells from 172 healthy adults 22-93 years of age using ATAC-seq, RNA-seq, and flow cytometry. These data reveal a shared epigenomic signature of aging including declining naïve T cell and increasing monocyte and cytotoxic cell functions. These changes are greater in magnitude in men and accompanied by a male-specific decline in B-cell specific loci. Age-related epigenomic changes first spike around late-thirties with similar timing and magnitude between sexes, whereas the second spike is earlier and stronger in men. Unexpectedly, genomic differences between sexes increase after age 65, with men having higher innate and pro-inflammatory activity and lower adaptive activity. Impact of age and sex on immune phenotypes can be visualized at https://immune-aging.jax.org to provide insights into future studies

AMULET: a novel read count-based method for effective multiplet detection from single nucleus ATAC-seq data.

Detecting multiplets in single nucleus (sn)ATAC-seq data is challenging due to data sparsity and limited dynamic range. AMULET (ATAC-seq MULtiplet Estimation Tool) enumerates regions with greater than two uniquely aligned reads across the genome to effectively detect multiplets. We evaluate the method by generating snATAC-seq data in the human blood and pancreatic islet samples. AMULET has high precision, estimated via donor-based multiplexing, and high recall, estimated via simulated multiplets, compared to alternatives and identifies multiplets most effectively when a certain read depth of 25K median valid reads per nucleus is achieved

Systems immunology to the study of the tumour microenvironment and the fetomaternal interface

Il existe de nombreuses similarités entre le développement du foetus et celui des cellules tumorales. En effet, dans les deux cas ils requièrent une division cellulaire intense, une invasion des tissues de l’hôte ainsi qu’une vascularisation soutenue. De plus, malgré le fait que le foetus et les cellules tumorales expriment à la fois des antigènes étrangers (les antigènes paternels pour le foetus et les antigènes du soi modifiés au niveau des cellules tumorales) ils ne sont pas rejetés par le système immunitaire. Parmi plusieurs populations cellulaires impliquées dans ce phénomène de non rejet ou de tolérance, les cellules T régulatrices (Tregs) jouent un rôle primordial dans les deux processus. En effet, notre laboratoire a démontré que l’émergence des cellules tumorales ainsi que l’implantation fœtale s’accompagnent d’une activation forte et rapide des Tregs. Cette observation prend tout son sens quand l’élimination de ces Tregs a conduit à un rejet immunitaire de la tumeur ou du foetus. Afin de valider ces observations, nous avons mis au point une étude transcriptomique comparative entre le microenvironnement tumoral et l’interface foeto-maternelle. Cela a révélé une forte similarité et une importante diminution des voies de signalisation immunologiques associées à la présentation antigénique et à l’activation des cellules T. De plus, des analyses non supervisées ont mis en évidence une coévolution des signatures immunitaires inhibées et cela dés les premiers jours suivant l’implantation des tumeurs ou du foetus. Par ailleurs, l’élimination des Tregs (qui a conduit un rejet de la tumeur ou du foetus) a permis de faire basculer les mêmes signatures immunitaires d’un état d’inhibition à un état d’activation. En définitive, nous pensons que les mécanismes déployés au cours de l’évolution pour protéger les foetus du rejet immunitaire sont détournés afin de favoriser le développement des cellules tumorales.There are striking similarities between fetus and tumor development. They both require intense cell division, invasion of host tissues and sustained vascularization. Moreover, despite that fetus and tumor express foreign antigens - paternal allo-antigens for fetuses and modified auto-antigens for tumors, they are not rejected by the immune system. Among others, regulatory T cells (Tregs), which are key players in tolerance, appear to play a significant role in both processes. We showed that tumor emergence as well as embryo implantation elicit a strikingly similar brisk Treg response, which functional relevance is supported by the fact that and Treg depletion leads to fetus or tumor immune rejection. Comparison of fetal and tumor microenvironments through transcriptomics revealed strikingly similar and dramatic decrease in expression of multiple immune-related pathways, including antigen presentation and T cell response. Unsupervised analyses highlighted the co-evolution in time of downregulated immune signatures, from the very first days after tumor or embryo implantation. Treg depletion, which leads to fetus or tumor rejection, converted the very same down-modulated immune signatures to up-regulated ones. We propose that means selected during evolution to protect mammalian fetuses are hijacked to license tumor development

Approche immunologie des systèmes pour l'étude du microenvironnement tumoral et de l'interface foeto-maternelle

There are striking similarities between fetus and tumor development. They both require intense cell division, invasion of host tissues and sustained vascularization. Moreover, despite that fetus and tumor express foreign antigens - paternal allo-antigens for fetuses and modified auto-antigens for tumors, they are not rejected by the immune system. Among others, regulatory T cells (Tregs), which are key players in tolerance, appear to play a significant role in both processes. We showed that tumor emergence as well as embryo implantation elicit a strikingly similar brisk Treg response, which functional relevance is supported by the fact that and Treg depletion leads to fetus or tumor immune rejection. Comparison of fetal and tumor microenvironments through transcriptomics revealed strikingly similar and dramatic decrease in expression of multiple immune-related pathways, including antigen presentation and T cell response. Unsupervised analyses highlighted the co-evolution in time of downregulated immune signatures, from the very first days after tumor or embryo implantation. Treg depletion, which leads to fetus or tumor rejection, converted the very same down-modulated immune signatures to up-regulated ones. We propose that means selected during evolution to protect mammalian fetuses are hijacked to license tumor development.Il existe de nombreuses similarités entre le développement du foetus et celui des cellules tumorales. En effet, dans les deux cas ils requièrent une division cellulaire intense, une invasion des tissues de l’hôte ainsi qu’une vascularisation soutenue. De plus, malgré le fait que le foetus et les cellules tumorales expriment à la fois des antigènes étrangers (les antigènes paternels pour le foetus et les antigènes du soi modifiés au niveau des cellules tumorales) ils ne sont pas rejetés par le système immunitaire. Parmi plusieurs populations cellulaires impliquées dans ce phénomène de non rejet ou de tolérance, les cellules T régulatrices (Tregs) jouent un rôle primordial dans les deux processus. En effet, notre laboratoire a démontré que l’émergence des cellules tumorales ainsi que l’implantation fœtale s’accompagnent d’une activation forte et rapide des Tregs. Cette observation prend tout son sens quand l’élimination de ces Tregs a conduit à un rejet immunitaire de la tumeur ou du foetus. Afin de valider ces observations, nous avons mis au point une étude transcriptomique comparative entre le microenvironnement tumoral et l’interface foeto-maternelle. Cela a révélé une forte similarité et une importante diminution des voies de signalisation immunologiques associées à la présentation antigénique et à l’activation des cellules T. De plus, des analyses non supervisées ont mis en évidence une coévolution des signatures immunitaires inhibées et cela dés les premiers jours suivant l’implantation des tumeurs ou du foetus. Par ailleurs, l’élimination des Tregs (qui a conduit un rejet de la tumeur ou du foetus) a permis de faire basculer les mêmes signatures immunitaires d’un état d’inhibition à un état d’activation. En définitive, nous pensons que les mécanismes déployés au cours de l’évolution pour protéger les foetus du rejet immunitaire sont détournés afin de favoriser le développement des cellules tumorales

Regulatory T Cells Orchestrate Similar Immune Evasion of Fetuses and Tumors in Mice

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The Tsallis generalized entropy enhances the interpretation of transcriptomics datasets

International audienceBackground:Identifying differentially expressed genes between experimental conditions is still the gold-standard approach to interpret transcriptomic profiles. Alternative approaches based on diversity measures have been proposed to complement the interpretation of such datasets but are only used marginally. Methods: Here, we reinvestigated diversity measures, which are commonly used in ecology, to characterize mice pregnancy microenvironments based on a public transcriptome dataset. Mainly, we evaluated the Tsallis entropy function to explore the potential of a collection of diversity measures for capturing relevant molecular event information.Results: We demonstrate that the Tsallis entropy function provides additional information compared to the traditional diversity indices, such as the Shannon and Simpson indices. Depending on the relative importance given to the most abundant transcripts based on the Tsallis entropy function parameter, our approach allows appreciating the impact of biological stimulus on the inter-individual variability of groups of samples. Moreover, we propose a strategy for reducing the complexity of transcriptome datasets using a maximation of the beta diversity.Conclusions: We highlight that a diversity-based analysis is suitable for capturing complex molecular events occurring during physiological events. Therefore, we recommend their use through the Tsallis entropy function to analyze transcriptomics data in addition to differential expression analyses

TGF-β and VEGF cooperatively control the immunotolerant tumor environment and the efficacy of cancer immunotherapies

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