Salil Garg

Apolipoprotein-mediated pathways of lipid antigen presentation

Peptide antigens are presented to T cells by major histocompatibility complex (MHC) molecules, with endogenous peptides presented by MHC class I and exogenous peptides presented by MHC class II. In contrast to the MHC system, CD1 molecules bind lipid antigens that are presented at the antigen-presenting cell (APC) surface to lipid antigen-reactive T cells. Because CD1 molecules survey endocytic compartments, it is self-evident that they encounter antigens from extracellular sources. However, the mechanisms of exogenous lipid antigen delivery to CD1-antigen-loading compartments are not known. Serum apolipoproteins are mediators of extracellular lipid transport for metabolic needs. Here we define the pathways mediating markedly efficient exogenous lipid antigen delivery by apolipoproteins to achieve T-cell activation. Apolipoprotein E binds lipid antigens and delivers them by receptor-mediated uptake into endosomal compartments containing CD1 in APCs. Apolipoprotein E mediates the presentation of serum-borne lipid antigens and can be secreted by APCs as a mechanism to survey the local environment to capture antigens or to transfer microbial lipids from infected cells to bystander APCs. Thus, the immune system has co-opted a component of lipid metabolism to develop immunological responses to lipid antigens.

Antigen Presentation by CD1: Lipids, T Cells, and NKT Cells in Microbial Immunity

The discovery of molecules capable of presenting lipid antigens, the CD1 family, and of the T cells that recognize them, has opened a new dimensionin our understanding of cell-mediated immunity against infection. Like MHC Class I molecules, CD1 isoforms (CD1a, b, c and d) are assembled in the ER and sent to the cell surface. However, in contrast to MHC molecules, CD1 complexes are then re-internalized into specific endocytic compartments where they can bind lipid antigens. These include a broad scope of both self and foreign molecules that range from simple fatty acids or phospholipids, to more complex glycolipids, isoprenoids, mycolates and lipopeptides. Lipid-loaded CD1 molecules are then delivered to the cell surface and can be surveyed by CD1-restricted T cells expressing alphabeta or gammadelta T Cell Receptors (TCR). It has become clear that T cell-mediated lipid antigen recognition plays an important role in detection and clearance of pathogens. CD1a, b and c-restricted T cells have been found to recognize a number of lipid antigens from M. tuberculosis. CD1d-restricted T cells are the only CD1-restricted T cell subset present in mice, which lack the genes encoding CD1a, b and c. Evidence from experiments in CD1d-restricted T cell-deficient mice indicates that these cells play an important role in the immune response against awide range of pathogens including several bacteria, viruses and parasites. One subset of CD1d-restricted T cells in particular, invariant Natural Killer T (iNKT) cells, has been extensively studied. iNKT cells are characterized by the expression of a semi-invariant TCR composed of a strictly conserved alpha chain paired with a limited repertoire of beta chains. During infection, iNKT cells are rapidly elicited. Activated iNKT cells can produce a vast array of cytokines that profoundly affect both the innate and the adaptive arms of the immune response. In this review, we describe the pathways and mechanisms of lipid antigen binding and presentation by CD1 in detail, as well as the diverse roles played by CD1-restricted T cells in the context of microbial infection.

CD1a and MHC Class I Follow a Similar Endocytic Recycling Pathway

CD1 proteins are a family of major histocompatibility complex (MHC) class I‐like antigen‐presenting molecules that present lipids to T cells. The cytoplasmic tails (CTs) of all human CD1 isoforms, with the exception of CD1a, contain tyrosine‐based sorting motifs, responsible for the internalization of proteins by the clathrin‐mediated pathway. The role of the CD1a CT, which does not possess any sorting motifs, as well as its mode of internalization are not known. We investigated the internalization and recycling pathways followed by CD1a and the role of its CT. We found that CD1a can be internalized by a clathrin‐ and dynamin‐independent pathway and that it follows a Rab22a‐ and ADP ribosylation factor (ARF)6‐dependent recycling pathway, similar to other cargo internalized independent of clathrin. We also found that the CD1a CT is S‐acylated. However, this posttranslational modification does not determine the rate of internalization or recycling of the protein or its localization to detergent‐resistant membrane microdomains (DRMs) where we found CD1a to be enriched. We also show that plasma membrane DRMs are essential for efficient CD1a‐mediated antigen presentation. These findings place CD1a closer to MHC class I in its trafficking and potential antigen‐loading compartments among CD1 isoforms. Furthermore, we identify CD1a as a new marker for the clathrin‐ and dynamin‐independent and DRM‐dependent pathway of internalization as well as the Rab22a‐ and ARF6‐dependent recycling pathway.

Arl13b regulates endocytic recycling traffic

Intracellular recycling pathways play critical roles in internalizing membrane and fluid phase cargo and in balancing the inflow and outflow of membrane and cell surface molecules. To identify proteins involved in the regulation of endocytic recycling, we used an shRNA trafficking library and screened for changes in the surface expression of CD1a antigen-presenting molecules that follow an endocytic recycling route. We found that silencing of the ADP-ribosylation factor (Arf)-like small GTPase Arl13b led to a decrease in CD1a surface expression, diminished CD1a function, and delayed CD1a recycling, suggesting that Arl13b is involved in the regulation of endocytic recycling traffic. Arl13b appears to be required for the major route of endocytic trafficking, causing clustering of early endosomes and leading to the accumulation of endocytic cargo. Moreover, Arl13b colocalized with markers of the endocytic recycling pathway followed by CD1a, namely Arf6 and Rab22a. We also detected an interaction between Arl13b and the actin cytoskeleton. Arl13b was previously implicated in cilia formation and function. Our present results indicate a previously unidentified role for Arl13b in endocytic recycling traffic and suggest a link between Arl13b function and the actin cytoskeleton.

Arf-like GTPase Arl8b regulates lytic granule polarization and natural killer cell-mediated cytotoxicity

By exploiting NK cell LROs (known as lytic granules) as a model, a new role is defined for Arl8b in regulating motility and exocytosis of lytic granules of NK cells. Not only lytic granules but also the MTOC is unable to polarize toward the immune synapse formed between the NK cell and its target in Arl8b-depleted NK cells.

Synthesis and biological activity of α-galactosyl ceramide KRN7000 and galactosyl (α1→2) galactosyl ceramide

Graphical abstract The synthesis and biological activity of α-galactosyl ceramide (α-GalCer) and Gal(α1→2)GalCer is reported.

Regulation of CD1 Antigen-presenting Complex Stability

For major histocompatibility complex class I and II molecules, the binding of specific peptide antigens is essential for assembly and trafficking and is at the center of their quality control mechanism. However, the role of lipid antigen binding in stabilization and quality control of CD1 heavy chain (HC)·β2-microglobulin (β2m) complexes is unclear. Furthermore, the distinct trafficking and loading routes of CD1 proteins take them from mildly acidic pH in early endososmal compartments (pH 6.0) to markedly acidic pH in lysosomes (pH 5.0) and back to neutral pH of the cell surface (pH 7.4). Here, we present evidence that the stability of each CD1 HC·β2m complex is determined by the distinct pH optima identical to that of the intracellular compartments in which each CD1 isoform resides. Although stable at acidic endosomal pH, complexes are only stable at cell surface pH 7.4 when bound to specific lipid antigens. The proposed model outlines a quality control program that allows lipid exchange at low endosomal pH without dissociation of the CD1 HC·β2m complex and then stabilizes the antigen-loaded complex at neutral pH at the cell surface.

MHC Class II Presentation Is Controlled by the Lysosomal Small GTPase, Arl8b

Dendritic cells (DCs) are specialized APCs with the ability to prime naive T cells. DCs first sample Ags from the environment and then orchestrate their processing and loading onto MHC class II (MHC II) Ag-presenting molecules in lysosomes. Once MHC II molecules have bound a peptide, the MHC II–peptide complex is delivered to the cell surface for presentation to CD4+ T cells. Regulation of Ag uptake via macropinocytosis and phagocytosis has been extensively studied, as well as trafficking in early endocytic vesicles notably regulated by the small GTPase Rab5 and its effectors. However, little is known about the regulators of Ag delivery from early endosomes to lysosomal compartments where the proper pH, proteases, MHC II, invariant chain, and HLA-DM reside, awaiting exogenous Ags for loading. In this article, we report the crucial role of the small GTPase ADP-ribosylation factor-like 8b (Arl8b) in MHC II presentation in DCs. We show for the first time, to our knowledge, that Arl8b localizes to MHC II compartments in DCs and regulates formation of MHC II–peptide complexes. Arl8b-silenced DCs display a defect in MHC II–Ag complex formation and its delivery to the cell surface during infection resulting in a defect in T cell recognition. Our results highlight the role of Arl8b as a trafficking regulator of the late stage of complex formation and MHC II presentation in DCs.

Single-cell variability guided by microRNAs

Variability in miRNA activity, and therefore gene networks, may define cell state A single zygote with a defined DNA sequence gives rise to all the varied cells of the mammalian body. This variety of cell fates may arise in part from cell-to-cell variability in the gene expression programs of embryonic stem cells (ESCs). Three recent studies have taken different approaches to characterizing this variability in gene expression in stem cells (1–3). These results suggest that microRNAs (miRNAs) could play an important role in controlling and generating this variability.

RNAi screens of lysosomal trafficking.

Here, we describe the general principles of RNA interference screens to study lysosomal functions in mammalian cells. Lysosomes occupy a central position in the biology of numerous processes such as degradation, microbial killing, and immunological antigen presentation to T cells. Selection of a screening system, conducting pooled versus arrayed screens, and appropriate steps in assay development, validation, and verification of novel gene candidates are all discussed. We focus on our experience in developing an arrayed short hairpin RNA screen to identify novel lysosomal trafficking proteins involved in vesicle and cargo trafficking and illustrate how such a trafficking library can be applied to screens involving lysosomes.