Recognition of vaccinia virus-encoded major histocompatibility complex class I antigens by virus immune cytotoxic T cells is independent of the polymorphism of the peptide transporters

Identification of DDX60 as a Regulator of MHC-I Class Molecules in Colorectal Cancer

Immune checkpoint blockade (ICB) therapies induce durable responses in approximately 15% of colorectal cancer (CRC) patients who exhibit microsatellite instability-high (MSI-H) or deficient mismatch repair (dMMR). However, more than 80% of CRC patients do not respond to current immunotherapy. The main challenge with these patients is lack of MHC-I signaling to unmask their cancer cells so the immune cells can detect them. Here, we started by comparing IFNγ signature genes and MHC-I correlated gene lists to determine the potential candidates for MHC-I regulators. Then, the protein expression level of listed potential candidates in normal and cancer tissue was compared to select final candidates with enough disparity between the two types of tissues. ISG15 and DDX60 were further tested by wet-lab experiments. Overexpression of DDX60 upregulated the expression of MHC-I, while knockdown of DDX60 reduced the MHC-I expression in CRC cells. Moreover, DDX60 was downregulated in CRC tissues, and lower levels of DDX60 were associated with a poor prognosis. Our data showed that DDX60 could regulate MHC-I expression in CRC; thus, targeting DDX60 may improve the effects of immunotherapy in some patients.

Variable region of the 3' UTR is a critical virulence factor in the Far-Eastern subtype of tick-borne encephalitis virus in a mouse model

Tick-borne encephalitis virus (TBEV) is a major arbovirus that causes thousands of cases of severe neurological illness in humans annually. However, virulence factors and pathological mechanisms of TBEV remain largely unknown. To identify the virulence factors, we constructed chimeric viruses between two TBEV strains of the Far-Eastern subtype, Sofjin-HO (highly pathogenic) and Oshima 5-10 (low pathogenic). The replacement of the coding region for the structural and non-structural proteins from Sofjin into Oshima showed a partial increase of the viral pathogenicity in a mouse model. Oshima-based chimeric viruses with the variable region of the 3' UTR of Sofjin, which had a deletion of 207 nt, killed 100 % of mice and showed almost the same virulence as Sofjin. Replacement of the variable region of the 3' UTR from Sofjin into Oshima did not increase viral multiplication in cultured cells and a mouse model at the early phase of viral entry into the brain. At the terminal phase of viral infection in mice, the virus titre of the Oshima-based chimeric virus with the variable region of the 3' UTR of Sofjin reached a level identical to that of Sofjin and showed a similar histopathological change in the brain tissue. This is the first report to show that the variable region of the 3' UTR is a critical virulence factor in mice. These findings encourage further study to understand the mechanisms of the pathogenicity of TBEV, and to develop preventative and therapeutic strategies for tick-borne encephalitis.

Immunological functions of the proteasome

Proteasomes are highly abundant cytosolic and nuclear protease complexes that degrade most intracellular proteins in higher eukaryotes and appear to play a major role in the cytosolic steps of MHC class I antigen processing. This review summarizes the knowledge of the role of proteasomes in antigen processing and the impact of proteasomal proteolysis on T cell-mediated immunity.

Novel Splicing of the Human MHC-Encoded Peptide Transporter Confers Unique Properties

Presentation of intracellularly derived antigenic peptides to T cells requires their assembly together with MHC class I molecules in the endoplasmic reticulum (ER). Such peptides are delivered to the ER by an MHC-encoded transporter composed of TAP1 and TAP2 protein delivery. Here, the first alternative splicing of Tap2 is described. The human splice variant, termed Tap2iso, lacks exon 11 and original 3′ untranslated region and contains a newly identified exon 12 and 3′ untranslated region. The full-length Tap2iso cDNA (2496 bp) predicts a protein of 653 amino acids. Tap2iso mRNA was normally coexpressed with Tap2 mRNA in all human lymphocyte cell lines examined. Function of TAP2iso was evaluated at multilevel in TAP1/2iso and TAP1/2 cotransfected T2 cells, a mutant cell line deplete of endogenous Tap gene products. The TAP1-TAP2iso transporter facilitated the maturation of MHC class I molecules in the ER and restored surface expression of class I. Importantly, TAP1-TAP2iso transporters expressed in T2 cells exhibited distinct and opposing influences on peptide selectivities, at times exceeding 30-fold differences in competition experiments and attributable to diversity in the 3′-COOH tail. The common coexpression of an alternative splice product of the Tap2 gene may contribute to broaden immune diversity, a mechanism previously described to occur predominantly at the level of the TCR and MHC class I gene products.

Hypothesis: MHC class I, rather than just a flagpole for CD8+ T cells is also a protease in its own right

Ever since the discovery of MHC class I restriction and the onslaught of the dual receptor hypothesis, MHC class I has been perceived as a passive entity in TCR recognition and the appropriate antigen processing and presentation pathways. However, numerous experimental observations and theoretical considerations are difficult or unable to be explained by the accepted mechanism of class I antigen presentation. Proteases within and outside the endoplasmic reticulum (ER) are evoked to be solely responsible for the generation of the appropriate 8-10 amino acid-long peptides associated with MHC class I. A MHC class I with site-restricted ER protease activity would overcome most of the present difficulties in explaining MHC class I antigen presentation.

Conservation of minor histocompatibility antigens between human and non-human primates

It is well accepted that minor histocompatibility antigens (mHag) can function as transplantation barriers between HLA-matched individuals. Little is known about the molecular nature and evolutionary conservation of mHag. It is only very recently that the first human mHag were identified. The HLA-A2.1-restricted mHag HA-2 and the HLA-B7-restricted mHag H-Y appeared to be peptides derived from polymorphic self proteins. Here we show that the HLA-A2.1-restricted mHag HA-1, HA-2, and the H-Y peptides are conserved between man, chimpanzees and rhesus macaques. Human cytotoxic T cell clones specific for the HLA-A2.1-restricted mHag HA-1, HA-2, and H-Y recognized HLA-A2.1 gene-transfected chimpanzee and rhesus macaque cells. High-pressure liquid chromatography fractionation of HLA-A2.1-bound peptides isolated from the HLA-A2.1-transfected chimpanzee cells revealed that the chimpanzee HA-1 and HA-2 co-eluted with the human HA-1 and HA-2. Subsequent amino acid sequencing showed that the chimpanzee HA-2 peptide is identical to the human HA-2 peptide. Our functional and biochemical results demonstrate that mHag peptides are conserved for over 35 million years.

Identification of new TAP2 alleles in gorilla: evolution of the locus within hominoids

Transporters associated with antigen processing molecules (TAP1 and TAP2) mediate the transfer of cytosolic peptides into the lumen of the endoplasmic reticulum for association with newly synthesized class I molecules of the major histocompatibility complex. Previous molecular and functional analyses of rat and human TAP2 homologues indicated major differences in gene diversification patterns and selectivity of peptides transported. Therefore, in this study, we analyzed the alleles of the gorilla TAP2 locus to determine whether the pattern of diversification resembled that in either of those two species. Sequence analysis of the TAP2 cDNAs from gorilla Epstein-Barr virus-transformed B-cell lines revealed four alleles with a genetic distance of less than 1%. The nucleotide substitutions distinguishing the alleles are confined to the 3' half of the coding region and occur individually or within two small clusters of variability. Diversification of the locus appears to have resulted from point substitutions and recombinational events. Evolutionary-rate estimates for the TAP2 gene in gorilla and human closely approximate those observed for other hominoid genes. The amino acid polymorphisms within the gorilla molecules are distinct from those in the human homologues. The absence of ancestral polymorphisms suggests that gorilla and human TAP2 genes have not evolved in a trans-species fashion but rather have diversified since the divergence of the lineages.

Polymorphic peptide transporters in MHC class I monomorphic Syrian hamster

We have already shown that in species with highly polymorphic major histocompatibility complex (MHC) class I molecules (human, mouse) no functional polymorphism of the peptide transporters TAP1 and TAP2 is detectable (Lobigs and Müllbacher 1993). Investigating the antigen-presentation machinery of the class I MHC monomorphic Syrian hamster using mouse MHC class I expression via recombinant vaccinia viruses (VV) we found that six hamster cell lines fall into two phenotypic classes. four cell lines (HaK, FF, MF-2, and HT-1) showed no defect in expressing four different H2 class I molecules (Kk, Kd, Kb, Dd) and the appropriate VV peptide recognized by mouse VV-immune cytotoxic T (Tc) cells on the cell surface. Two cell lines (BHK-21 and NIL-2) expressed Dd and Kb in association with VV peptides as recognized by VV-immune, H2-restricted Tc cells but not Kk and Kd. However, Kd was expressed on the cell surface, as shown by fluorescence-activated cell sorter (FACS) analysis and alloreactive Tc-cell recognition. Kk is only surface-expressed in these two cell lines when superinfected with two VV recombinants encoding rat TAP1 (VV-mtp1) and TAP2 (VV-mtp2). Superinfection with VV-mtp1 and VV-mtp2 rendered both cell lines, after infection with either VV-Kk and VV-Kd, susceptible to lysis by either Kk- or Kd-restricted VV-immune Tc cells. Thus Syrian hamster cell lines express functionally polymorphic peptide transporters. The TAP2 gene from FF cells was cloned and sequenced; comparison with human, mouse, and rat TAP2 sequences show 78%, 88% and 87% similarity, respectively.

Allelic variation at the TAP 1 locus influences disease phenotype in HLA-B27 positive individuals with ankylosing spondylitis

The objective was to determine the role of the TAP 1 gene in influencing the phenotype of disease in adult patients with ankylosing spondylitis (AS). The distribution of TAP 1 gene alleles was determined using the PCR RFLP method and restriction enzymes Bcl I and Acc I. The study population included 115 HLA-B27 positive patients with well-documented AS and 41 HLA-B27 positive normal controls. No significant difference in distribution of TAP 1 alleles was noted in comparisons of all AS patients with normal controls. However, AS patients with extraspinal disease were noted to have a significantly increased prevalence of the TAP 1B allele (17.0%) as compared to AS patients without extraspinal disease (2.9%) (P = 0.005) or normal controls (1.9%) (P = 0.005). Polymorphism at the TAP 1 locus may influence disease outcome in patients with AS.

Recombinant expression of vaccinia virus-encoded TAP1 and TAP2 promotes MHC class I-restricted antigen presentation in a Syrian hamster cell line

Transporter associated with antigen presentation (TAP) molecules supply small peptides to the lumen of the endoplasmic reticulum for assembly with MHC class I glycoproteins. Here we report that a Syrian hamster cell line, BHK, which is commonly used in cell biological and virological investigations, is deficient in antigen presentation in a xenogeneic model. Thus when the mouse MHC class I restriction element, Kd, is expressed in BHK cells via a vaccinia virus (VV) recombinant, no significant recognition by VV-immune and Kd-restricted cytotoxic T cells is induced. This defect is apparently a consequence of a deficiency in TAP-dependent peptide transport and can be repaired when rat TAP1 and TAP2 are provided by recombinant VV expression.

Tap gene associations in UK caucasoids

The authors determined the allele frequencies of the TAP1 and TAP2 transporter genes in a healthy UK Caucasoid population by ARMS-PCR. TAP1A was the most frequent TAP1 allele by far, being present in 76% of subjects. TAP1 alleles could not be assigned in 24% of subjects, since the combinations TAP1A/1b and TAP1C/1D cannot be separated. TAP2A was the most frequent TAP2 alleles (75% of subjects) followed by TAP2B (43%), TAP2C (11%), TAP2D (8%) and TAP2E (6%). The authors also identified an individual with a previously undescribed TAP2 allele, TAP2H (isoleucine at amino acid [aa] 379, alanine at aa 565, alanine at aa 665). It was not possible to assign unequivocally TAP2 alleles in 15 individuals (9%) as TAP2A/D and TAP2C/E cannot be distinguished from each other. To address this problem a separate study of families of rheumatoid arthritis (RA) patients selected for this ambiguity were studied. In all five informative families, TAP2A/2D was confirmed as the combination present. In the population studied no evidence was found for linkage disequilibrium between TAP1 and TAP2 or between the TAP genes and HLA-DP. There was no evidence for extensive linkage disequilibrium between the TAP genes and HLA-DQR, although TAP2B was associated with DRI (delta = 0.056, corrected P < 0.01) and TAP2D with DR4 (delta = 0.018). In the RA families studied, TAP2D was found on DRB1*0401-bearing haplotypes.

Evidence that transporters associated with antigen processing translocate a major histocompatibility complex class I-binding peptide into the endoplasmic reticulum in an ATP-dependent manner

We have investigated the role of the putative peptide transporters associated with antigen processing (TAP) by using a permeabilized-cell system. The main objective was to determine whether these molecules, which bear homology to the ATP-binding cassette family of transporters, translocate antigenic peptides across the endoplasmic reticulum membrane for assembly with major histocompatibility complex (MHC) class I molecules and beta 2-microglobulin light chain. The pore-forming toxin streptolysin O was used to generate permeabilized cells, and peptide translocation was determined by measuring the amount of added radiolabeled peptide bound to endogenous class I molecules. No radiolabeled peptide was associated with MHC class I glycoproteins from unpermeabilized cells. We found that efficient peptide binding to MHC class I molecules in permeabilized cells is both transporter dependent and ATP dependent. In antigen-processing mutant cells lacking a functional transporter, uptake occurs only through a less-efficient transporter and ATP-independent pathway. In addition, short peptides (8-10 amino acids) known to bind MHC class I molecules compete efficiently with a radiolabeled peptide for TAP-dependent translocation, whereas longer peptides and a peptide derived from an endoplasmic reticulum signal sequence do not compete efficiently. This result indicates that the optimal substrates for TAP possess the characteristics of MHC-binding peptides.

Presentation of numerous viral peptides to mouse major histocompatibility complex (MHC) class I-restricted T lymphocytes is mediated by the human MHC-encoded transporter or by a hybrid mouse-human transporter

The major histocompatibility complex-encoded transporter associated with antigen processing (TAP) is required for the efficient presentation of cytosolic antigens to class I-restricted T cells. TAP is thought to be formed by the interaction of two gene products, termed TAP1 and TAP2. We find that TAPs consisting either of human subunits, or mouse TAP1 and human TAP2, facilitate the presentation of numerous defined viral peptides to mouse class I-restricted T cells. As human and mouse TAP2 and TAP1 differ in 23 and 28% of their residues, respectively, this indicates that TAP1 and TAP2 can form a functional complex with partners considerably different from those they coevolved with. Moreover, these findings indicate that widely disparate TAPs facilitate delivery of the same peptides to class I molecules. These findings suggest that TAP polymorphism does not greatly influence the types of peptides presented to the immune system.

Restrictions on the use of antigenic peptides by the immune system

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