Network analysis of large-scale ImmGen and Tabula Muris datasets highlights metabolic diversity of tissue mononuclear phagocytes

The diversity of mononuclear phagocyte (MNP) subpopulations across tissues is one of the key physiological characteristics of the immune system. Here, we focus on understanding the metabolic variability of MNPs through metabolic network analysis applied to three large-scale transcriptional datasets: we introduce (1) an ImmGen MNP open-source dataset of 337 samples across 26 tissues; (2) a myeloid subset of ImmGen Phase I dataset (202 MNP samples); and (3) a myeloid mouse single-cell RNA sequencing (scRNA-seq) dataset (51,364 cells) assembled based on Tabula Muris Senis. To analyze such large-scale datasets, we develop a network-based computational approach, genes and metabolites (GAM) clustering, for unbiased identification of the key metabolic subnetworks based on transcriptional profiles. We define 9 metabolic subnetworks that encapsulate the metabolic differences within MNP from 38 different tissues. Obtained modules reveal that cholesterol synthesis appears particularly active within the migratory dendritic cells, while glutathione synthesis is essential for cysteinyl leukotriene production by peritoneal and lung macrophages.

Natural IgM initiates the immunological cascade against minor antigen-mismatched cells, illustrating the dependency and unique role of APC subtypes

In organ transplantation a major obstacle is the immunological response against mismatches of major and minor histocompatibility antigen (Ags). Even when MHC Ags are matched between donor and recipient, minor Ags can elicit graft rejection. To date, it is unclear how endogenous antigen-presenting cells (APCs) recognize, coordinate and induce immunological responses against minor Ag-mismatched cells, particularly in the absence of pathogen-associated molecular patterns (PAMPs). We hypothesized that each APC subtype is dependent on each other to complete an immunological response against mismatches of minor Ags. Using a well-established minor Agmismatch model, we demonstrated that the elimination of any one APC subtype (Batf3+ DCs, Irf4+ DCs, Ly6C+ monocytes or B cells) resulted in a diminished or abolished immune response against minor Ag-mismatches. Specifically, we demonstrated that this immunological response began with the recognition of minor Ag-mismatched cells by natural IgM, which resulted in an immune complex formation. This cellular immune complex was then acquired by MHC II presenting APCs, of which one was MHC II expressing Ly6C+ monocytes. Subsequently, Ly6C+ monocyte induced Ag-specific CD4+ T cells licensed Batf3+ DCs via CD40 to present mismatches of minor antigen to Ag-specific CD8+T cells, which were required for the cytotoxic elimination of minor-Ag mismatched cells. Overall, our in vivo findings suggest a sequential, coordinated immunological event is required for the rejection of minor Ag-mismatched cells.

Ly6C+ monocyte efferocytosis and cross-presentation of cell-associated antigen

Recently it was shown that circulating Ly6C+ monocytes traffic from tissue to the draining lymph nodes (LNs) with minimal alteration in their overall phenotype. Furthermore, in the steady state, Ly6C+ monocytes are as abundant as classical dendritic cells (DCs) within the draining LNs, and even more abundant during inflammation. However, little is known about the functional roles of constitutively trafficking Ly6C+ monocytes. In this study we investigated whether Ly6C+ monocytes can efferocytose (acquire dying cells) and cross-present cell-associated antigen, a functional property specially attributed to Batf3+ DCs. We demonstrated that Ly6C+ monocytes intrinsically efferocytose and cross-present cell-associated antigen to CD8+ T cells. In addition, efferocytosis was enhanced upon direct activation of the Ly6C+ monocytes through its corresponding TLRs, TLR4 and TLR7. However, only ligation of TLR7, and not TLR4, enhanced cross-presentation by Ly6C+ monocytes. Overall, this study outlines two functional roles, among others, that Ly6C+ monocytes have during an adaptive immune response.

Double-edged sword: self-acquiring Batf3-dependent dendritic cell required for anti-tumor immunity and graft rejection (APP3P.104)

One of the major obstacles for the graft acceptance of tissue and organs is the mismatch of major and minor histocompatibility (H) antigens. Minor H antigens are peptides derived from polymorphic proteins and presented by antigen-presenting cells on major histocompatibility complex (MHC) molecules. Here we hypothesized that the self-acquiring, cross-presenting Batf3-dependent dendritic cell (DC) is responsible for minor-antigen graft rejection. Using three models of minor-antigen graft rejection: 1) male antigen 2) non-sex complex minor antigen and 3) skin organ transplant, we demonstrate that Batf3-dependent DCs are responsible for minor-antigen graft rejection. However, in the presence of a TLR7 ligand, the requirement for Batf3-dependent DCs is bypassed by shifting the functionality of Batf3-independent DCs to elicit minor-antigen graft rejection. Overall our study identifies the DC subtype responsible for minor-antigen graft rejection.

Pulmonary dendritic cells require cis-activation to cross-prime T cells (APP4P.117)

Dendritic cells (DCs) are required for the induction of cytotoxic T cells (CTL). In most tissues, including the lung, the resident migratory DC fall into two types, respectively expressing the integrin markers, CD103 and CD11b. The current supposition is that DC function is predetermined by lineage, designating the CD103+ DC as the major cross-presenting DC able to induce CTL. Here we proposed that DC function might also be determined by the nature of the pathogen associated molecular pattern (PAMP) that stimulates it and to which it is able to respond. Thus, in the presence of a TLR3 (CD103+) or a TLR7 (CD11b+) agonist respectively we demonstrated in vivo that both DC subtypes did exhibit the capacity to orchestrate a CTL response. This selectivity did not extend to antigen cross-presentation for T cell proliferation but was required for induction of cytotoxicity and protection in a model of tumor metastasis.

Xanthine oxidoreductase promotes the inflammatory state of mononuclear phagocytes through effects on chemokine expression, peroxisome proliferator-activated receptor-{gamma} sumoylation, and HIF-1{alpha}

The protective effects of pharmacological inhibitors of xanthine oxidoreductase (XOR) have implicated XOR in many inflammatory diseases. Nonetheless, the role played by XOR during inflammation is poorly understood. We previously observed that inhibition of XOR within the inflammatory mononuclear phagocytes (MNP) prevented neutrophil recruitment during adoptive transfer demonstrating the role of XOR in MNP-mediated neutrophil recruitment. To further explore the role of XOR in the inflammatory state of MNP, we studied MNP isolated from inflammatory lungs combined with analyses of MNP cell lines. We demonstrated that XOR activity was increased in inflammatory MNP following insufflation of Th-1 cytokines in vivo and that activity was specifically increased by MNP differentiation. Inhibition of XOR reduced levels of CINC-1 secreted by MNP. Expression of peroxisome proliferator-activated receptor γ (PPARγ) in purified rat lung MNP and MNP cell lines reflected both the presence of PPARγ isoforms and PPARγ SUMOylation, and XOR inhibitors increased levels of SUMO-PPARγ in MNP cell lines. Both ectopic overexpression of XOR cDNA and uric acid supplementation reduced SUMO-PPARγ in MNP cells. Levels of the M2 markers CD36, CD206, and arginase-1 were modulated by uric acid and oxonic acid, whereas siRNA to SUMO-1 or PIAS-1 also reduced arginase-1 in RAW264.7 cells. We also observed that HIF-1α was increased by XOR inhibitors in inflammatory MNP and in MNP cell lines. These data demonstrate that XOR promotes the inflammatory state of MNP through effects on chemokine expression, PPARγ SUMOylation, and HIF-1α and suggest that strategies for inhibiting XOR may be valuable in modulating lung inflammatory disorders.