Peptide-MHC-I from Endogenous Antigen Outnumber Those from Exogenous Antigen, Irrespective of APC Phenotype or Activation

<div><p>Naïve anti-viral CD8⁺ T cells (T_CD8+) are activated by the presence of peptide-MHC Class I complexes (pMHC-I) on the surface of professional antigen presenting cells (pAPC). Increasing the number of pMHC-I <i>in vivo</i> can increase the number of responding T_CD8+. Antigen can be presented directly or indirectly (cross presentation) from virus-infected and uninfected cells, respectively. Here we determined the relative importance of these two antigen presenting pathways in mousepox, a natural disease of the mouse caused by the poxvirus, ectromelia (ECTV). We demonstrated that ECTV infected several pAPC types (macrophages, B cells, and dendritic cells (DC), including DC subsets), which directly presented pMHC-I to naïve T_CD8+ with similar efficiencies <i>in vitro</i>. We also provided evidence that these same cell-types presented antigen <i>in vivo</i>, as they form contacts with antigen-specific T_CD8+. Importantly, the number of pMHC-I on infected pAPC (direct presentation) vastly outnumbered those on uninfected cells (cross presentation), where presentation only occurred in a specialized subset of DC. In addition, prior maturation of DC failed to enhance antigen presentation, but markedly inhibited ECTV infection of DC. These results suggest that direct antigen presentation is the dominant pathway in mice during mousepox. In a broader context, these findings indicate that if a virus infects a pAPC then the presentation by that cell is likely to dominate over cross presentation as the most effective mode of generating large quantities of pMHC-I is on the surface of pAPC that endogenously express antigens. Recent trends in vaccine design have focused upon the introduction of exogenous antigens into the MHC Class I processing pathway (cross presentation) in specific pAPC populations. However, use of a pantropic viral vector that targets pAPC to express antigen endogenously likely represents a more effective vaccine strategy than the targeting of exogenous antigen to a limiting pAPC subpopulation.</p></div

RNA-Seq and CyTOF immuno-profiling of regenerating lacrimal glands identifies a novel subset of cells expressing muscle-related proteins

<div><p>The purpose of the present studies was to use CyTOF and RNA-Seq technologies to identify cells and genes involved in lacrimal gland repair that could be targeted to treat diseases of lacrimal gland dysfunction. Lacrimal glands of female BALB/c mice were experimentally injured by intra-glandular injection of interleukin 1 alpha (IL-1α). The lacrimal glands were harvested at various time points following injury (1 to 14 days) and used to either prepare single cell suspensions for CyTOF immuno-phenotyping analyses or to extract RNA for gene expression studies using RNA-Seq. CyTOF immuno-phenotyping identified monocytes and neutrophils as the major infiltrating populations 1 and 2 days post injury. Clustering of significantly differentially expressed genes identified 13 distinct molecular signatures: 3 associated with immune/inflammatory processes included genes up-regulated at days 1–2 and 3 associated with reparative processes with genes up-regulated primarily between days 4 and 5. Finally, clustering identified 65 genes which were specifically up-regulated 2 days post injury which was enriched for muscle specific genes. The expression of select muscle-related proteins was confirmed by immunohistochemistry which identified a subset of cells expressing these proteins. Double staining experiments showed that these cells are distinct from the myoepithelial cells. We conclude that experimentally induced injury to the lacrimal gland leads to massive infiltration by neutrophils and monocytes which resolved after 3 days. RNAseq and immunohistochemistry identified a group of cells, other than myoepithelial cells, that express muscle-related proteins that could play an important role in lacrimal gland repair.</p></div

DC subsets are equally efficient in direct antigen presentation.

<p>(A) Mice were injected with ECTV, D-LN harvested and cells stained with antibodies to identify non-NK, non-B, non T cell, GFP⁺ CD11c⁺ DC subsets as: pDC (B220⁺CD11b^-), CD8α (B220^-CD8α ⁺CD11b^-), CD11b⁺ (B220^-CD11b⁺CD8α ^-). Nos. represent % of cells in 3 representative experiments using 3 mice per condition. (B and C) Mice were injected with NP-S-EGFP or NP-EGFP, D-LN harvested and stained as described in (A), with the addition anti- K^b-SIINFEKL. Quantification of K^b-SIINFEKL expression and efficiency was determined as described in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004941#ppat.1004941.g002" target="_blank">Fig 2C</a>. Data are pooled from 3 experiments using 3 mice per condition. (D) Mice were injected with NP-EGFP or NP-S-EGFP, then D-LN cells were FACS sorted for EGFP⁺ or EGFP^- pDC, CD8α ⁺, or CD11b⁺ DC, as above. Each population was co-cultured with OT-I T_CD8+ that were then analyzed for proliferation as above. Data are pooled from 3 experiments, using 15 mice per condition to obtain sufficient cells. (E) As in (A), except for addition of anti-CD80 and anti-CD86 antibodies. Data are pooled from 3 experiments. All graphs show (mean ± standard error), P values *p<0.05, **p<0.01, ***p<0.001, NS (not significant) using Student’s unpaired t-test.</p

Histological analysis of IL-1α injected lacrimal glands.

<p>Lacrimal gland tissue was excised 1, 2, 3, 4, and 7 days post IL-1α or saline (vehicle) injection and processed for hematoxylin and eosin staining. Scale bar represents 50 μm for all panels.</p

Representative molecular signatures of lacrimal gland inflammation and repair.

<p>Expression (log2[fold change]) pattern of clusters representative of the 8 consolidated clusters were plotted for days 1, 2, 3, 4, 5, and 7. Threshold for significant up/down-regulation (+/- 1 = log2[+/-2]) is indicated by dotted blue line.</p

Mass cytometry (CyTOF immunophenotyping) antibody panel.

<p>Mass cytometry (CyTOF immunophenotyping) antibody panel.</p

Expression pattern of significantly differentially expressed genes by day.

<p>The significantly differentially expressed genes at days 1, 2, 4, and 5 were plotted to visualize the global expression of these genes across all time points (days 3, 7, 14 and 14S data not plotted based on the small number of genes). Day 4 and 5 significantly differentially expressed genes exclude day 1 and 2 expression for visualization purposes (very few genes up/down-regulated). Data points colored based on regulation at the day of interest; green = strongly up-regulated, red, up-regulated, orange = strongly down-regulated, blue = down-regulated.</p

Differential expression of collagen chains by day.

<p>Differential expression of collagen chains by day.</p

Double-staining of β-taxilin and desmin proteins.

<p>Lacrimal gland tissue from IL-1α injected mice were double-stained for muscle related proteins desmin and β-taxilin. Panels represent staining from 2 days post IL-1α injected lacrimal glands which were counterstained with DAPI to visualize cell nuclei. Arrows represent cells expressing both proteins; arrowheads represent cells expressing β-taxilin only; stars represent cells expressing desmin only; BV represents a blood vessel. Scale bars represent 25 μm.</p

Antigen specific T cells relocate to the LN periphery where they interact with infected pAPC expressing antigen <i>in vivo</i>.

<p>(A and B) Localization of OT-I T_CD8+ following ECTV infection. Naïve OT-I T_CD8+ were labeled with cell tracker CMTMR dye (red) and adoptively transferred. Mice were injected with NP-S-EGFP or NP-EGFP i.d., and 12 h.p.i., D-LN were harvested and analyzed by fluorescence microscopy. (C, E, G, I) Mice were injected with NP-S-EGFP or NP-EGFP i.d., and 24 h.p.i. D-LN were harvested and stained for B220⁺ B cells, CD169⁺ macrophages, CD11c⁺ DC and CD103⁺ DC, and analyzed by fluorescence microscopy. (D, F, H, J) High power view of interaction of naïve OT-I T_CD8+ and ECTV-infected pAPC. The insets (D, F, H, and J) show 2-dimensional projections of one plane of the 3-dimensional datasets. Each image is representative of 3 experiments, with a minimum of 4 infected nodes per experiment.</p