The role of tapasin in MHC class I antigen assembly

Allele-Specific Thresholds of Eluted Ligands for T-Cell Epitope Prediction

A common strategy for predicting candidate human leukocyte antigen class I T-cell epitopes is to use an affinity-based threshold of 500 nM. Although a 500 nM threshold across alleles effectively identifies most epitopes across alleles, findings showing that major histocompatibility complex repertoire sizes vary by allele indicate that using thresholds specific to individual alleles may improve epitope identification. In this work, we compare different strategies utilizing common and allele-specific thresholds to identify an optimal approach for T-cell epitope prediction. First, we confirmed previous observations that different human leukocyte antigen class I alleles correspond with varying repertoire sizes. Here, we define general and allele-specific thresholds that capture 80% of eluted ligands and a different set of thresholds associated with capturing 9-mer T-cell epitopes at 80% sensitivity. Our analysis revealed that allele-specific threshold performance was roughly equivalent to that of a common threshold when considering a relatively large number of alleles. However, when predicting epitopes for only a few alleles, the use of allele-specific thresholds would be preferable. Finally, we present here for public use a set of allele-specific thresholds that may be used to identify T-cell epitopes at 80% sensitivity.

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Confirmed findings that different HLA class I alleles have varying repertoire sizes.

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Defined common and allele-specific thresholds that capture 80% of eluted ligands.

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Defined common and allele-specific thresholds that capture 80% of T-cell epitopes.

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Allele-specific thresholds perform more consistently when analyzing a few alleles.

Insights into the role of ERp57 in cancer

Endoplasmic reticulum resident protein 57 (ERp57) has a molecular weight of 57 kDa, belongs to the protein disulfide-isomerase (PDI) family, and is primarily located in the endoplasmic reticulum (ER). ERp57 functions in the quality control of nascent synthesized glycoproteins, participates in major histocompatibility complex (MHC) class I molecule assembly, regulates immune responses, maintains immunogenic cell death (ICD), regulates the unfolded protein response (UPR), functions as a 1,25-dihydroxy vitamin D3 (1,25(OH)2D3) receptor, regulates the NF-κB and STAT3 pathways, and participates in DNA repair processes and cytoskeletal remodeling. Recent studies have reported ERp57 overexpression in various human cancers, and altered expression and aberrant functionality of ERp57 are associated with cancer growth and progression and changes in the chemosensitivity of cancers. ERp57 may become a potential biomarker and therapeutic target to combat cancer development and chemoresistance. Here, we summarize the available knowledge of the role of ERp57 in cancer and the underlying mechanisms.

MicroRNA Mediated Chemokine Responses in Human Airway Smooth Muscle Cells

Airway smooth muscle (ASM) cells play a critical role in the pathophysiology of asthma due to their hypercontractility and their ability to proliferate and secrete inflammatory mediators. microRNAs (miRNAs) are gene regulators that control many signaling pathways and thus serve as potential therapeutic alternatives for many diseases. We have previously shown that miR-708 and miR-140-3p regulate the MAPK and PI3K signaling pathways in human ASM (HASM) cells following TNF-α exposure. In this study, we investigated the regulatory effect of these miRNAs on other asthma-related genes. Microarray analysis using the Illumina platform was performed with total RNA extracted from miR-708 (or control miR)-transfected HASM cells. Inhibition of candidate inflammation-associated gene expression was further validated by qPCR and ELISA. The most significant biologic functions for the differentially expressed gene set included decreased inflammatory response, cytokine expression and signaling. qPCR revealed inhibition of expression of CCL11, CXCL10, CCL2 and CXCL8, while the release of CCL11 was inhibited in miR-708-transfected cells. Transfection of cells with miR-140-3p resulted in inhibition of expression of CCL11, CXCL12, CXCL10, CCL5 and CXCL8 and of TNF-α-induced CXCL12 release. In addition, expression of RARRES2, CD44 and ADAM33, genes known to contribute to the pathophysiology of asthma, were found to be inhibited in miR-708-transfected cells. These results demonstrate that miR-708 and miR-140-3p exert distinct effects on inflammation-associated gene expression and biological function of ASM cells. Targeting these miRNA networks may provide a novel therapeutic mechanism to down-regulate airway inflammation and ASM proliferation in asthma.

Molecular machinations of the MHC-I peptide loading complex

The acquisition of an optimal peptide ligand by MHC class I molecules is crucial for the generation of immunity to viruses and tumors. This process is orchestrated by a molecular machine known as the peptide loading complex (PLC) that consists of specialized and general ER-resident molecules. These proteins collaborate to ensure the loading of an optimal peptide ligand into the antigen binding cleft of class I molecules. The surprising diversity of peptides bound to MHC class I molecules and recapitulation of class I assembly in vitro have provided new insights into the molecular machinations of peptide loading. Coupled with the extraordinary polymorphism of class I molecules and their differential dependence on various components of the PLC for cell surface expression, a picture of peptide loading at the molecular level has recently emerged and will be discussed herein.

Differential Requirement for Tapasin in the Presentation of Leader- and Insulin-Derived Peptide Antigens to Qa-1b-Restricted CTLs

The loading of MHC class I molecules with peptides involves a variety of accessory proteins, including TAP-associated glycoprotein (tapasin), which tethers empty MHC class I molecules to the TAP peptide transporter. We have evaluated the role of tapasin for the assembly of peptides with the class Ib molecule Qa-1b. In normal cells, Qa-1b is predominantly bound by a peptide, the Qa-1 determinant modifier (Qdm), derived from the signal sequence of class Ia molecules. Our results show that tapasin links Qa-1b to the TAP peptide transporter, and that tapasin facilitates the delivery of Qa-1b molecules to the cell surface. Tapasin was also required for the presentation of endogenous Qdm peptides to Qdm-specific, Qa-1b-restricted CTLs. In sharp contrast, tapasin expression was dispensable for the presentation of an insulin peptide to insulin-specific, Qa-1b-restricted CTL isolated from TCR transgenic mice. However, tapasin deficiency significantly impaired the positive selection of these insulin-specific, Qa-1b-restricted transgenic CD8+ T cells. These findings reveal that tapasin plays a differential role in the loading of Qdm and insulin peptides onto Qa-1b molecules, and that tapasin is dispensable for retention of empty Qa-1b molecules in the endoplasmic reticulum, and are consistent with the proposed peptide-editing function of tapasin.

Cloning and functional analyses of the mouse tapasin promoter

The expression of tapasin is critical for an optimized MHC class I assembly and stable MHC class I surface expression. Thus, impaired MHC class I antigen expression of tumors can be attributable to tapasin downregulation. In order to understand the molecular mechanisms of deficient tapasin expression, the mouse tapasin promoter region and its 5'-flanking sequences were characterized. The mouse tapasin promoter lacks the TATA box and its transcription is initiated at multiple sites within a 51-nucleotide stretch. Sequence analyses revealed transcription factor binding motifs for NF-kappaB, GATA, E2F, p300, AP1, SP1 and IRF-1/2. Detailed analysis of deletion mutants and elimination of transcription factor binding motifs demonstrated an important role of NF-kappaB at position -468 for its basal activity, whereas E2F at position -229 represses constitutive promoter activity. Furthermore, the IRF-1/2 binding site is required for gamma interferon inducibility of the tapasin promoter in vitro, but also negatively interferes with its constitutive activity. Thus, characterization of the tapasin promoter represents the molecular basis for the understanding of the heterogeneous expression levels of tapasin under physiological and pathophysiological conditions.

Accessory proteins and the assembly of human class I MHC molecules: a molecular and structural perspective

The cell-surface presentation of antigenic peptides by class I major histocompatibility complex (MHC) molecules to CD8+ T-cell receptors is part of an immune surveillance mechanism aimed at detecting foreign antigens. This process is initiated in the endoplasmic reticulum (ER) with the folding and assembly of class I MHC molecules which are then transported to the cell surface via the secretory pathway. In recent years, several accessory proteins have been identified as key components of the class I maturation process in the ER. These proteins include the lectin chaperones calnexin (CNX) and calreticulin (CRT), the thiol-dependent oxidoreductase ERp57, the transporter associated with antigen processing (TAP), and the protein tapasin. This review presents the most recent advances made in characterizing the biochemical and structural properties of these proteins, and discusses how this knowledge advances our current understanding of the molecular events underlying the folding and assembly of human class I MHC molecules in the ER.

Protein degradation and the generation of MHC class I-presented peptides

Over the past decade there has been considerable progress in understanding how MHC class I-presented peptides are generated. The emerging theme is that the immune system has not evolved its own specialized proteolytic mechanisms but instead utilizes the phylogenetically ancient catabolic pathways that continually turnover proteins in all cells. Three distinct proteolytic steps have now been defined in MHC class I antigen presentation. The first step is the degradation of proteins by the ubiquitin-proteasome pathway into oligopeptides that either are of the correct size for presentation or are extended on their amino-termini. In the second step, aminopeptidases trim N-extended precursors into peptides of the correct length to be presented on class I molecules. The third step involves the destruction of peptides by endo- and exopeptidases, which limits antigen presentation, but is important for preventing the accumulation of peptides and recycling them back to amino acids for protein synthesis or production of energy. The immune system has evolved several components that modify the activity of these ancient pathways in ways that enhance the generation of class I-presented peptides. These include catalytically active subunits of the proteasome, the PA28 proteasome activator, and leucine aminopeptidase, all of which are upregulated by interferon-gamma. In addition to these pathways that operate in all cells, dendritic cells and macrophages can also generate class I-presented peptides from proteins internalized from the extracellular fluids by degrading them in endocytic compartments or transferring them to the cyotosol for degradation by proteasomes.

HIV type 1 abrogates TAP-mediated transport of antigenic peptides presented by MHC class I. Transporter associated with antigen presentation

Downregulation of MHC class I expression following human immunodeficiency virus 1 (HIV-1) infection is thought to play an important role in viral escape from immune recognition by cytotoxic T-lymphocytes (CTLs). Since exogenous addition of HIV-1-derived peptides restores susceptibility of HIV-1-infected cells to CTL-mediated lysis, we tested whether endogenous peptide loading is impaired in these cells. Our results show that in HIV-1-infected cells the ability of the transporter associated with antigen presentation (TAP) to translocate antigenic peptides from the cytosol to the lumen of the ER for presentation on MHC class I molecules is abolished. These data suggest that interference with the supply of antigenic peptides to the MHC class I pathway provides an additional mechanism by which HIV-1 evades the CTL-mediated immune response.

Multiple proteases process viral antigens for presentation by MHC class I molecules to CD8(+) T lymphocytes

Recognition by CD8(+) cytotoxic T lymphocytes of any intracellular viral protein requires its initial cytosolic proteolytic processing, the translocation of processed peptides to the endoplasmic reticulum via the transporters associated with antigen processing, and their binding to nascent major histocompatibility complex (MHC) class I molecules that then present the antigenic peptides at the infected cell surface. From initial assumptions that the multicatalytic and ubiquitous proteasome is the only protease capable of fully generating peptide ligands for MHC class I molecules, the last few years have seen the identification of a number of alternative proteases that contribute to endogenous antigen processing. Trimming by non-proteasomal proteases of precursor peptides produced by proteasomes is now a well-established fact. In addition, proteases that can process antigens in a fully proteasome-independent fashion have also been identified. The final level of presentation of many viral epitopes is probably the result of interplay between different proteolytic activities. This expands the number of tissues and physiological and pathological situations compatible with antigen presentation, as well as the universe of pathogen-derived sequences available for recognition by CD8(+) T lymphocytes.

Major histocompatibility complex class I-restricted antigen processing and presentation

Major histocompatibility complex (MHC) class I molecules present antigenic peptides to CD8-expressing cytotoxic T lymphocytes (CTLs). This antigen recognition system is critically important for immune surveillance against viruses and tumors. Most class I-binding peptides are generated in the cytosol, as side products from the degradation of misfolded proteins by proteasomes. A subset of the resulting peptides are translocated across the endoplasmic reticulum (ER) membrane by a dedicated peptide transporter, and these peptides are then loaded onto peptide-receptive class I molecules in the ER. The stable assembly of class I molecules with peptides is controlled by a variety of accessory proteins, including chaperones with general housekeeping functions and factors with dedicated roles in class I assembly. Peptide-filled class I molecules are then delivered to the cell surface for recognition by CTLs. This highly regulated process permits the host to rapidly counter invading pathogens with strong and sustained CTL responses and, at the same time, avoid misguided attacks. Here, how the class I antigen processing machinery accomplishes this daunting task is reviewed.

Association of tapasin and COPI provides a mechanism for the retrograde transport of major histocompatibility complex (MHC) class I molecules from the Golgi complex to the endoplasmic reticulum

Tapasin is a subunit of the transporter associated with antigen processing (TAP). It associates with the major histocompatibility complex (MHC) class I. We show that tapasin interacts with beta- and gamma-subunits of COPI coatomer. COPI retrieves membrane proteins from the Golgi network back to the endoplasmic reticulum (ER). The COPI subunit-associated tapasin also interacts with MHC class I molecules suggesting that tapasin acts as the cargo receptor for packing MHC class I molecules as cargo proteins into COPI-coated vesicles. In tapasin mutant cells, neither TAP nor MHC class I are detected in association with the COPI coatomer. Interestingly, tapasin-associated MHC class I molecules are antigenic peptide-receptive and detected in both the ER and the Golgi. Our data suggest that tapasin is required for the COPI vesicle-mediated retrograde transport of immature MHC class I molecules from the Golgi network to the ER.

Accessory proteins that control the assembly of MHC molecules with peptides

The stable assembly of Major Histocompatibility Complex (MHC) molecules with peptides is controlled by a number of cofactors, including proteins with general housekeeping functions and proteins with dedicated functions in MHC assembly. Recent work in my laboratory has focused on two chaperones, tapasin (tpn) and DM, that play critical roles in the loading of peptides onto MHC class I and MHC class II molecules, respectively. Tapasin is a transmembrane protein that tethers empty class I molecules in the endoplasmic reticulum to the transporter associated with antigen processing. DM is a peptide exchange factor that binds with empty and peptide-loaded class II molecules in endosomal and lysosomal compartments. Although a number of different functions for tapasin and DM have been proposed, emerging evidence suggests that both of these chaperones retain unstable MHC molecules in peptide-loading compartments until they bind with high-affinity peptides. These cofactors therefore promote the surface expression of long-lived MHC-peptide complexes.

Assembly and antigen-presenting function of MHC class I molecules in cells lacking the ER chaperone calreticulin

MHC class I molecules expressed in a calreticulin-deficient cell line (K42) assembled with beta 2-microglobulin (beta2-m) normally, but their subsequent loading with optimal peptides was defective. Suboptimally loaded class I molecules were released into the secretory pathway. This occurred despite the ability of newly synthesized class I to interact with the transporter associated with antigen processing (TAP) loading complex. The efficiency of peptide loading was reduced by 50%-80%, and impaired T cell recognition was observed for three out of four antigens tested. The peptide-loading function was specific to calreticulin, since the defect in K42 could be rectified by transfection with calreticulin but not a soluble form of calnexin, which shares its lectin-like activity.

Tapasin enhances peptide-induced expression of H2-M3 molecules, but is not required for the retention of open conformers

H2-M3 is a class Ib MHC molecule that binds a highly restricted pool of peptides, resulting in its intracellular retention under normal conditions. However, addition of exogenous M3 ligands induces its escape from the endoplasmic reticulum (ER) and, ultimately, its expression at the cell surface. These features of M3 make it a powerful and novel model system to study the potentially interrelated functions of the ER-resident class I chaperone tapasin. The functions ascribed to tapasin include: 1) ER retention of peptide-empty class I molecules, 2) TAP stabilization resulting in increased peptide transport, 3) direct facilitation of peptide binding by class I, and 4) peptide editing. We report in this study that M3 is associated with the peptide-loading complex and that incubation of live cells with M3 ligands dramatically decreased this association. Furthermore, high levels of open conformers of M3 were efficiently retained intracellularly in tapasin-deficient cells, and addition of exogenous M3 ligands resulted in substantial surface induction that was enhanced by coexpression of either membrane-bound or soluble tapasin. Thus, in the case of M3, tapasin directly facilitates intracellular peptide binding, but is not required for intracellular retention of open conformers. As an alternative approach to define unique aspects of M3 biosynthesis, M3 was expressed in human cell lines that lack an M3 ortholog, but support expression of murine class Ia molecules. Unexpectedly, peptide-induced surface expression of M3 was observed in only one of two cell lines. These results demonstrate that M3 expression is dependent on a unique factor compared with class Ia molecules.

IFN-gamma affects both the stability and the intracellular transport of class I MHC complexes

In accordance with the key role of major histocompatibility complex (MHC) class I molecules in the adaptive immune response against viruses, their expression can be enhanced by the potent cytokine interferon-gamma (IFN-gamma), which upregulates the expression of multiple components in the pathway of class I-restricted antigen presentation. In this study, we analyzed the effect of IFN-gamma treatment on class I formation, peptide editing, trafficking, and cell surface expression. We show that IFN-gamma treatment promotes significantly the assembly and cell surface expression of stable class I complexes. Yet the existence of large intracellular pools of both free class I heavy chains and suboptimal class I complexes indicates that the optimal peptide supply limits cell surface expression levels of class I complexes. Unexpectedly, we found that IFN-gamma appears generally to slow the maturation rates of both class I complexes and transferrin receptors. Apparently, IFN-gamma causes prolonged retention of molecules in the endoplasmic reticulum (ER) because it regulates the expression of ER-residing proteins that participate in protein maturation. Consequently, it induces more rigorous ER quality control. The significance of these effects of IFN-gamma for in vivo immune responses is discussed.

Tapasin: an ER chaperone that controls MHC class I assembly with peptide

The stable assembly of MHC class I molecules with peptides in the endoplasmic reticulum (ER) involves several accessory molecules. One of these accessory molecules is tapasin, a transmembrane protein that tethers empty class I molecules to the peptide transporter associated with antigen processing (TAP). Here, evidence is presented that tapasin retains class I molecules in the ER until they acquire high-affinity peptides.

Downregulation of the constitutive tapasin expression in human tumor cells of distinct origin and its transcriptional upregulation by cytokines

Human tumor cells frequently exhibit abnormalities in the major histocompatibility complex (MHC) class I surface expression which can be due to structural alterations and/or dysregulation of various components of the MHC class I antigen processing machinery, such as HLA class I heavy and light chains, the peptide transporter and the proteasome subunits. Although several cofactors critical for proper MHC class I assembly have been identified, their contribution to the immune escape phenotype of tumor cells has not been analyzed. In order to determine whether tapasin deficits are an integral part of immune escape mechanisms of human tumors, we studied the constitutive and cytokine-regulated expression pattern of tapasin in malignant cells of distinct histology. Heterogeneous and reduced expression levels of tapasin were found in small-cell lung carcinoma, pancreatic carcinoma, colon carcinoma, head an neck squamous cell carcinoma and renal cell carcinoma cell lines. Tapasin downregulation was also prominent in surgically removed tumor lesions when compared to normal controls. The impaired tapasin expression is often associated with low MHC class I cell surface expression. In addition, various cytokines, including interferon (IFN)-alpha, IFN-gamma, tumor necrosis factor (TNF)-alpha and interleukin (IL)-4, but not granulocyte-macrophage colony stimulating factor (GM-CSF), transcriptionally upregulate to a distinct extent and in a time-dependent manner tapasin expression in tumor cells. Thus, deficient tapasin expression appears to be a frequent event in human tumor cells. Its restoration by cytokines further suggests that impaired tapasin expression in tumors is rather due to dysregulation than to structural alterations.

Tapasin-mediated retention and optimization of peptide ligands during the assembly of class I molecules

The murine class I H-2Kb molecule achieves high level surface expression in tapasin-deficient 721.220 human cells. Compared with their behavior in wild-type cells, Kb molecules expressed on 721.220 cells are more receptive to exogenous peptide, undergo more rapid surface decay, and fail to form macromolecular peptide loading complexes. As a result, they are rapidly transported to the cell surface, reflecting a failure of endoplasmic reticulum retention mechanisms in the absence of loading complex formation. Despite the failure of Kb molecules to colocalize to the TAP and their rapid egress to the cell surface, Kb is still capable of presenting TAP-dependent peptides in the absence of tapasin. Furthermore, pool sequencing of peptides eluted from these molecules revealed strict conservation of their canonical H-2Kb-binding motif. There was a reduction in the total recovery of peptides associated with Kb molecules purified from the surface of tapasin-deficient cells. Comparison of the peptides bound to Kb in the presence and absence of tapasin revealed considerable overlap in peptide repertoire. These results indicate that in the absence of an interaction with tapasin, Kb molecules fail to assemble with calreticulin and TAP, yet they are still capable of acquiring a diverse array of peptides. However, a significant proportion of these peptides appear to be suboptimal, resulting in reduced cell surface stability of Kb complexes. Taken together, the findings indicate that tapasin plays an essential role in the formation of the class I loading complex, which retains class I heterodimers in the endoplasmic reticulum until optimal ligand selection is completed.