Presentation Of Viral Peptides Research Articles

HLA-C Peptide Repertoires as Predictors of Clinical Response during Early SARS-CoV-2 Infection.

The human leukocyte antigen (HLA) system plays a pivotal role in the immune response to viral infections, mediating the presentation of viral peptides to T cells and influencing both the strength and specificity of the host immune response. Variations in HLA genotypes across individuals lead to differences in susceptibility to viral infection and severity of illness. This study uses observations from the early phase of the COVID-19 pandemic to explore how specific HLA class I molecules affect clinical responses to SARS-CoV-2 infection. By analyzing paired high-resolution HLA types and viral genomic sequences from 60 patients, we assess the relationship between predicted HLA class I peptide binding repertoires and infection severity as measured by the sequential organ failure assessment score. This approach leverages functional convergence across HLA-C alleles to identify relationships that may otherwise be inaccessible due to allelic diversity and limitations in sample size. Surprisingly, our findings show that severely symptomatic infection in this cohort is associated with disproportionately abundant binding of SARS-CoV-2 structural and non-structural protein epitopes by patient HLA-C molecules. In addition, the extent of overlap between a given patient's predicted HLA-C and HLA-A peptide binding repertoires correlates with worse prognoses in this cohort. The findings highlight immunologic mechanisms linking HLA-C molecules with the human response to viral pathogens that warrant further investigation.

Abstract 904: AI platform provides an EDGE and enables state-of-the-art identification of peptide-HLAs for the development of T cell inducing vaccines

Abstract T cell inducing vaccines are key for the development of effective therapies against cancer and infectious diseases. Peptides, presented by Human Leukocyte Antigens (HLAs), are the targets of T cells, and their identification is therefore critical to the development of such vaccines. Here, we present the latest improvement in our EDGETM (Epitope Discovery for GEnomes) platform to address this critical need. EDGE is comprised of AI models that can predict peptide presentation by HLA class I and class II. Although the models are trained primarily using immunopeptidomics data, EDGE scores are predictive of peptide-HLA immunogenicity. There are three class I presentation models in EDGE: an allele-specific model, a pan-specific model, and a model specific for infectious diseases. The allele-specific model is applicable to a large but pre-defined set of HLA alleles. On a large test dataset, the allele-specific model achieved an average precision (AP) of 63% (PPV40=79%) compared to the AP of a standard best-available public model of 21% (PPV40=28%). A Ph1/2 clinical study of personalized cancer vaccines encoding neoantigens predicted from the allele-specific model demonstrated a ~50% molecular response (defined as >=30% reduction in circulating tumor DNA relative to baseline) rate with associated extended overall survival (vs non-responders) in metastatic, microsatellite stable colorectal cancer patients. We observed that >50% of the mutations were able to elicit T cell responses. The pan-specific class I model uses HLA sequences as input feature when training and, therefore, is applicable to any HLA. On the same test dataset as above, it achieved an AP of 65% (PPV40=81%) and performed better on average for ~40 less-common HLA alleles. Prediction of viral peptide presentation by HLA class I is challenging due to the lack of immunopeptidomics data. The class I model for infectious diseases was specifically optimized to predict for viral peptides and, therefore, performed better than available class I models on published HIV and Influenza A datasets. Prediction of peptide presentation by HLA class II is challenging due to the flexibility in how the longer peptides interact with open HLA grooves as well as the lack of immunopeptidomics data as compared to the class I peptides. The class II model in EDGE, EDGE-II, uses the latest developments in protein large language models, a novel learned HLA allele-deconvolution strategy, and in-house immunopeptidomics data, resulting in improved prediction of peptide presentation by HLA class II and immunogenicity driven by CD4+ T cells. On a benchmark validation dataset, EDGE-II achieved an AP of 71% as compared to AP of 62% of a leading published model. In summary, EDGETM provides a comprehensive state-of-the-art platform for the development of vaccines that can induce both CD8+ and CD4+ T cell responses to provide durable benefit to patients. Citation Format: Joshua Klein, Daniel Sprague, Monica Lane, Meghan Hart, Olivia Petrillo, Italo Faria do Valle, Matthew Davis, Andrew Ferguson, Andrew Allen, Karin Jooss, Ankur Dhanik. AI platform provides an EDGE and enables state-of-the-art identification of peptide-HLAs for the development of T cell inducing vaccines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 904.

HLA-A*11:01 and HLA-C*04:01 are associated with severe COVID-19.

We analyzed the association between HLA polymorphisms and susceptibility to SARS-CoV-2 infection and disease severity. Genotyping data from a total of 9373 COVID-19-positive cases from the Spanish Coalition to Unlock Research on Host Genetics on COVID-19 (SCOURGE) consortium and 5943 population controls were included in the study. We found an association of the alleles HLA-B*14:02 and HLA-C*08:02 with a lower risk to COVID-19 infection (p = 0.006, OR = 0.84, 95% CI = [0.75-0.95], p = 0.024, OR = 0.86, 95% CI = [0.78-0.95], respectively). We also found the alleles HLA-A*11:01 and HLA-C*04:01 associated with disease severity (p = 0.033, OR = 1.16, 95% CI = [1.04-1.31], p = 0.045, OR = 1.14, 95% CI = [1.05-1.25], respectively). These results suggest that an effective presentation of viral peptides by HLA class I alleles involve a faster infection clearance, decreasing the susceptibility and severity of COVID-19.

Inhibited MHC Class I and MHC Class II antigen processing and presentation upon Sars-CoV-2 infection

Abstract Major histocompatibility (MHC) bound viral peptides are the immune signatures to initiate the selective and cross-reactive T cell responses. Identifying the antigenic targets of adaptive immunity to SARS-CoV-2 is a key towards understanding the pathogenesis of Sars-CoV-2 and the rapidly evolving mutants. We isolated the immunopeptidomes to identify naturally processed and presented MHC-II (HLA-DR, HLA-DP) and MHC-I (HLA-ABC) bound canonical and out-of-frame viral peptides. We identified 5 HLA-DR canonical epitopes (13 peptides) from spike protein, 2 HLA-DP canonical epitopes (4 peptides) from spike and membrane proteins, 1 canonical MHC-Class I peptides and 5 out-of-frame MHC-I peptides from different ORF proteins. The viral peptides were presented in lower abundances as compared to host peptides obscuring the identification of the MHC bound viral peptides. Some of these peptides were shown to recall T cell responses in COVID-19 donors in other reported studies. We observed the downregulation of surface and total HLA-ABC, HLA-DR and HLA-DP expression upon Sars-CoV-2 infection possibly restricting the presentation of viral peptides and therefore delaying the immune response. The mechanisms by which SARS-CoV-2 evades adaptive immune responses mediated by MHC-I are studied in detail by different groups. Hence, we further investigating the modulators of the MHC-II pathway using proteomics-based approach. We observed significant downregulation of CD74 protein, CIITA protein and cathepsins in infected cells affecting the processing and presentation of viral peptides. These results may help in understanding significantly altered antigen presentation in Sars-CoV-2 infected cells.

Precise activation of antiviral memory T cells in solid tumors triggers a multi-cytokine response that ultimately drives tumor clearance.

Abstract The reactivation of CD8 +tissue-resident memory T cells (T RM) triggers a broad, yet local response that mobilizes adaptive and innate immune cells. This immunostimulatory process can be initiated in solid tumors when infiltrating antiviral memory T cells are reactivated. The intratumoral delivery of viral peptides is sufficient to clear poorly immunogenic tumors in mice and synergizes with immune checkpoint therapy. This study investigated the mechanisms required for this anti-tumor response and novel “Peptide Alarm Therapy” that is currently being tested in a Phase I clinical trial. In contrast to expectations, viral peptide presentation by cancer cells was not required for treatment efficacy, and while NK and CD4 T cells are activated and/or recruited to the tumor microenvironment (TME) following antiviral memory T cell activation, depletion of either population did not limit tumor clearance. Interestingly, inflammatory monocytes were greatly increased in both the TME and tumor-draining lymph node (tdLN) following therapy. Moreover, antigen presenting cells (APCs) containing tumor-derived antigen accumulated within the tdLN. TNFα, IFNγ, and IL-2 are cytokines that can signal to APC populations and are produced by activated T RM. When these cytokines were blocked collectively, but not independently, the treatment efficacy of Peptide Alarm Therapy was greatly reduced. Further, when these cytokines were intratumorally injected, they recapitulated some phenomena achieved by antiviral T cell activation. Thus, local reactivation of antiviral memory T cells, which infiltrate tumors and possess known specificities, drives a multi-cytokine response that promotes the immune-stimulation that effectuates tumor clearance. 1R01CA238439-01A1, 1F30CA253992-01

Ancestral origins are associated with SARS-CoV-2 susceptibility and protection in a Florida patient population.

COVID-19 is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The severity of COVID-19 is highly variable and related to known (e.g., age, obesity, immune deficiency) and unknown risk factors. The widespread clinical symptoms encompass a large group of asymptomatic COVID-19 patients, raising a crucial question regarding genetic susceptibility, e.g., whether individual differences in immunity play a role in patient symptomatology and how much human leukocyte antigen (HLA) contributes to this. To reveal genetic determinants of susceptibility to COVID-19 severity in the population and further explore potential immune-related factors, we performed a genome-wide association study on 284 confirmed COVID-19 patients (cases) and 95 healthy individuals (controls). We compared cases and controls of European (EUR) ancestry and African American (AFR) ancestry separately. We identified two loci on chromosomes 5q32 and 11p12, which reach the significance threshold of suggestive association (p<1x10-5 threshold adjusted for multiple trait testing) and are associated with the COVID-19 susceptibility in the European ancestry (index rs17448496: odds ratio[OR] = 0.173; 95% confidence interval[CI], 0.08-0.36 for G allele; p = 5.15× 10-5 and index rs768632395: OR = 0.166; 95% CI, 0.07-0.35 for A allele; p = 4.25×10-6, respectively), which were associated with two genes, PPP2R2B at 5q32, and LRRC4C at 11p12, respectively. To explore the linkage between HLA and COVID-19 severity, we applied fine-mapping analysis to dissect the HLA association with mild and severe cases. Using In-silico binding predictions to map the binding of risk/protective HLA to the viral structural proteins, we found the differential presentation of viral peptides in both ancestries. Lastly, extrapolation of the identified HLA from the cohort to the worldwide population revealed notable correlations. The study uncovers possible differences in susceptibility to COVID-19 in different ancestral origins in the genetic background, which may provide new insights into the pathogenesis and clinical treatment of the disease.

Relationship of Covid-19 Severity with SARS-CoV-2 NS8 Protein Mutations Depending on Virus Strain

In mid-2021, the Delta strain of SARS-CoV-2 caused the third wave of the COVID-19 pandemic. Huge efforts have been devoted to studying the effect of its mutations on the effectiveness of neutralizing antibodies. Much less attention was paid to the individual features of the presentation of its peptides by molecules of the major histocompatibility complex class I (MCHC-I). In this study, the correlation of the HLA-I genotype of patients under the age of 60 years with the severity of COVID-19 caused by the two most common variants of the SARS-CoV-2 Delta strain in the summer of 2021: AY.122 and B.1.617.2 was studied. Analysis of the severity of the course of COVID-19 revealed a more severe course of the disease caused by the AY.122 variant. Comparison of the mutation profile of the two most common variants of the Delta strain showed that that the G8R mutation in the NS8 protein makes the greatest contribution to the ability of MHC-I to present viral peptides. Given that the NS8 protein is able to suppress the maturation of MHC-I molecules, the appearance of a mutation in one of its immunogenic epitopes could make a significant contribution to the prevalence of the AY.122 variant in the Russian population.

Inhibition of major histocompatibility complex-I antigen presentation by sarbecovirus ORF7a proteins

Viruses employ a variety of strategies to escape or counteract immune responses, including depletion of cell surface major histocompatibility complex class I (MHC-I), that would ordinarily present viral peptides to CD8+ cytotoxic T cells. As part of a screen to elucidate biological activities associated with individual severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) viral proteins, we found that ORF7a reduced cell surface MHC-I levels by approximately fivefold. Nevertheless, in cells infected with SARS-CoV-2, surface MHC-I levels were reduced even in the absence of ORF7a, suggesting additional mechanisms of MHC-I down-regulation. ORF7a proteins from a sample of sarbecoviruses varied in their ability to induce MHC-I down-regulation and, unlike SARS-CoV-2, the ORF7a protein from SARS-CoV lacked MHC-I downregulating activity. A single amino acid at position 59 (T/F) that is variable among sarbecovirus ORF7a proteins governed the difference in MHC-I downregulating activity. SARS-CoV-2 ORF7a physically associated with the MHC-I heavy chain and inhibited the presentation of expressed antigen to CD8+ T cells. Specifically, ORF7a prevented the assembly of the MHC-I peptide loading complex and caused retention of MHC-I in the endoplasmic reticulum. The differential ability of ORF7a proteins to function in this way might affect sarbecovirus dissemination and persistence in human populations, particularly those with infection- or vaccine-elicited immunity.

Alterations in SARS-CoV-2 Omicron and Delta peptides presentation by HLA molecules.

The T-cell immune response is a major determinant of effective SARS-CoV-2 clearance. Here, using the recently developed T-CoV bioinformatics pipeline (https://t-cov.hse.ru) we analyzed the peculiarities of the viral peptide presentation for the Omicron, Delta and Wuhan variants of SARS-CoV-2. First, we showed the absence of significant differences in the presentation of SARS-CoV-2-derived peptides by the most frequent HLA class I/II alleles and the corresponding HLA haplotypes. Then, the analysis was limited to the set of peptides originating from the Spike proteins of the considered SARS-CoV-2 variants. The major finding was the destructive effect of the Omicron mutations on PINLVRDLPQGFSAL peptide, which was the only tight binder from the Spike protein for HLA-DRB1*03:01 allele and some associated haplotypes. Specifically, we predicted a dramatical decline in binding affinity of HLA-DRB1*03:01 and this peptide both because of the Omicron BA.1 mutations (N211 deletion, L212I substitution and EPE 212-214 insertion) and the Omicron BA.2 mutations (V213G substitution). The computational prediction was experimentally validated by ELISA with the use of corresponding thioredoxin-fused peptides and recombinant HLA-DR molecules. Another finding was the significant reduction in the number of tightly binding Spike peptides for HLA-B*07:02 HLA class I allele (both for Omicron and Delta variants). Overall, the majority of HLA alleles and haplotypes was not significantly affected by the mutations, suggesting the maintenance of effective T-cell immunity against the Omicron and Delta variants. Finally, we introduced the Omicron variant to T-CoV portal and added the functionality of haplotype-level analysis to it.

T-CoV: a comprehensive portal of HLA-peptide interactions affected by SARS-CoV-2 mutations

Rapidly appearing SARS-CoV-2 mutations can affect T cell epitopes, which can help the virus to evade either CD8 or CD4 T-cell responses. We developed T-cell COVID-19 Atlas (T-CoV, https://t-cov.hse.ru) – the comprehensive web portal, which allows one to analyze how SARS-CoV-2 mutations alter the presentation of viral peptides by HLA molecules. The data are presented for common virus variants and the most frequent HLA class I and class II alleles. Binding affinities of HLA molecules and viral peptides were assessed with accurate in silico methods. The obtained results highlight the importance of taking HLA alleles diversity into account: mutation-mediated alterations in HLA-peptide interactions were highly dependent on HLA alleles. For example, we found that the essential number of peptides tightly bound to HLA-B*07:02 in the reference Wuhan variant ceased to be tight binders for the Indian (Delta) and the UK (Alpha) variants. In summary, we believe that T-CoV will help researchers and clinicians to predict the susceptibility of individuals with different HLA genotypes to infection with variants of SARS-CoV-2 and/or forecast its severity.

HLA, Immune Response, and Susceptibility to COVID-19.

The severe acute respiratory syndrome caused by Coronavirus 2 (SARS-CoV-2) that appeared in December 2019 has precipitated the global pandemic Coronavirus Disease 2019 (COVID-19). However, in many parts of Africa fewer than expected cases of COVID-19, with lower rates of mortality, have been reported. Individual human leukocyte antigen (HLA) alleles can affect both the susceptibility and the severity of viral infections. In the case of COVID-19 such an analysis may contribute to identifying individuals at higher risk of the disease and the epidemiological level to understanding the differences between countries in the epidemic patterns. It is also recognized that first antigen exposure influences the consequence of subsequent exposure. We thus propose a theory incorporating HLA antigens, the “original antigenic sin (OAS)” effect, and presentation of viral peptides which could explain with differential susceptibility or resistance to SARS-CoV-2 infections.

Crystal structure of the giant panda MHC class I complex: First insights into the viral peptide presentation profile in the bear family.

The viral cytotoxic T lymphocyte (CTL) epitope peptides presented by classical MHC-I molecules require the assembly of a peptide-MHC-I-β2m (pMHC-I) trimolecular complex for T cell receptor (TCR) recognition, which is the critical activation link for triggering antiviral T cell immunity. Research on T cell immunology in the Ursidae family, especially structural immunology, is still lacking. In this study, the structure of the key trimolecular complex pMHC-I, which binds a peptide from canine distemper virus, was solved for the first time using giant panda as a representative species of Ursidae. The structural characteristics of the giant panda pMHC-I complex (pAime-128), including the unique pockets in the peptide-binding groove (PBG), were analyzed in detail. Comparing the pAime-128 to others in the bear family and extending the comparison to other mammals revealed distinct features. The interaction between MHC-I and β2m, the features of pAime-128 involved in TCR docking and cluster of differentiation 8 (CD8) binding, the anchor sites in the PBG, and the CTL epitopes of potential viruses that infect pandas were clarified. Unique features of pMHC-I viral antigen presentation in the panda were revealed by solving the three-dimensional (3D) structure of pAime-128. The distinct characteristics of pAime-128 indicate an unusual event that emerged during the evolution of the MHC system in the bear family. These results provide a new platform for research on panda CTL immunity and the design of vaccines for application in the bear family.

The Loss of HLA-F/KIR3DS1 Ligation Is Mediated by Hemoglobin Peptides.

The human leukocyte antigen (HLA)-Ib molecule, HLA-F, is known as a CD4+ T-cell protein and mediator of HIV progression. While HLA-Ia molecules do not have the chance to select and present viral peptides for immune recognition due to protein downregulation, HLA-F is upregulated. Post HIV infection, HLA-F loses the affinity to its activating receptor KIR3DS1 on NK cells leading to progression of the HIV infection. Several studies aimed to solve the question of the biophysical interface between HLA ligands and their cognate receptors. It became clear that even an invariant HLA molecule can be structurally modified by the variability of the bound peptide. We recently discovered the ability of HLA-F to select and present peptides and the HLA-F allele-specific peptide selection from the proteomic content using soluble HLA (sHLA) technology and a sophisticated MS method. We established recombinant K562 cells that express membrane-bound HLA-F*01:01, 01:03 or 01:04 complexes. While a recombinant soluble form of KIR3DS1 did not bind to the peptide-HLA-F complexes, acid elution of the peptides resulted in the presentation of HLA-F open conformers, and the binding of the soluble KIR3DS1 receptor increased. We used CD4+/HIV− and CD4+/HIV+ cells and performed an MS proteome analysis. We could detect hemoglobin as significantly upregulated in CD4+ T-cells post HIV infection. The expression of cellular hemoglobin in nonerythroid cells has been described, yet HLA-Ib presentation of hemoglobin-derived peptides is novel. Peptide sequence analysis from HLA-F allelic variants featured hemoglobin peptides as dominant and shared. The reciprocal experiment of binding hemoglobin peptide fractions to the HLA-F open conformers resulted in significantly diminished receptor recognition. These results underpin the molecular involvement of HLA-F and its designated peptide ligand in HIV immune escape.

Mechanisms of “Peptide Alarm Therapy”: Can antiviral memory T cells directly kill cancer cells in an MHC Class I-dependent way?

Abstract “Peptide alarm therapy” is a novel cancer immunotherapy that repurposes antiviral memory CD8+ T cells within tumors to drive antitumor immunity. After a primary infection, antigen-specific CD8+ T cells establish a surveillance program that positions T cells throughout the entire body. In particular, resident-memory CD8+ T cells (Trm) permanently reside in all tissues after primary antigen exposure and survey their immediate surroundings for possible re-exposure. In addition to normal tissue, antiviral Trm populate solid tumors. In contrast to tumor-specific T cells, intratumoral antiviral Trm are not exhausted and demonstrate potent reactivation with cognate peptide. This re-activation of Trm in tumors leads to upregulation of effector molecules and chemokines, the local recruitment of circulating immune cells, and the increased migration of dendritic cells to the tumor-draining lymph node. The intratumoral injection of peptide, and the subsequent reactivation of antiviral Trm, induces tumor growth suppression and exhibits synergy with immune checkpoint blockade, specifically PD-L1. The mechanisms driving this antitumor immune response remain uncharacterized. In this study, we have tested whether viral peptide presentation by cancer cells is necessary for the efficacy of peptide alarm therapy. A targeted knock-out of the MHC Class I allele, H-2Kb, in the B16.F10 melanoma cell line has been generated and employed in combination with the OT-I Tg CD8+ T cells, which bind the SIINFEKL:H-2Kb peptide:MHCI complex. Our data suggest that peptide presentation by cancer cells is not necessary for the reactivation of intratumoral antiviral Trm, and does not reduce tumor growth suppression in the context of peptide alarm therapy.

Generating protective immunity to severe influenza disease in Indigenous Australians

Abstract The 2009 influenza pandemic caused generally mild infections due, at least partially, to broadly cross-reactive pre-existing CD8+ T cell immunity. In contrast, severe disease was observed in Indigenous populations worldwide, as shown by disproportionate hospitalisation rates. Human leukocyte antigen-I (HLA-I) molecules present viral peptides to CD8+ T cells, eliciting anti-viral responses that contribute to accelerated viral clearance. We identified several HLA-I alleles which are highly prevalent in Indigenous Australians (HLA-A*11:01, A*24:02, A*34:01, B*13:01 and B*15:21) but largely understudied. Using specific HLA-allomorph expressing C1R cell lines, we identified influenza A and B immunopeptidomes by mass spectrometry. A total of 653 influenza peptides derived from various viral proteins were presented during infection by different HLA-Is. Using virus-specific PBMC expansions, we screened these peptides for their potential to reactivate influenza-specific memory CD8+ T cells. We identified on average 4.6 (2–8) immunogenic epitopes per HLA-I for influenza A and B. We defined epitope-specific CD8+ T cells ex vivo across different human tissues and determined their memory subsets, phenotype and activation in healthy donors and influenza-infected patients. Overall, our approach is effective in detection of immunogenic epitopes and understanding CD8+ T cell pools in Indigenous populations, thus providing potential vaccine targets to protect Indigenous populations globally, from severe influenza disease. This is the first study to identify hallmarks of immunogenic responses and reveal key targets of an effective CD8+ T cell vaccine in Indigenous people.

Peptides of endogenous retrovirus Gag gene variants are not agonistic ligands for autoreactive T cells in non-obese diabetic mice

Abstract Endogenous retroviruses (ERV) have been isolated from the pancreatic islets of non-obese diabetic (NOD) mice. We previously demonstrated that a murine leukemia retrovirus–like ERV Gag protein was secreted together with exosomes by an insulinoma and by primary islet mesenchymal stem cells. Here, we further demonstrated that Gag is an effective antigen to stimulate IFN-gamma production by autoreactive T cells using recombinant Gag protein or virus-like particles (VLPs) expressing the Gag gene. However, candidate peptides of this Gag protein were not effective in stimulating the T cells. Upon analyses of ERV Gag genes expressed in the islets of prediabetic NOD mice, we were surprised to find multiple Gag gene variants with complete open-reading frames. These results suggested the expression of different endogenous proviruses, or alternatively, the detection of point mutations incurred during viral replication. A new batch of altered peptides was synthesized reflecting the variations among the Gag gene variants, and a few of them induced detectable amount of cytokine secretion from the T cells. But, the levels of IFN-gamma induced by the peptides were much lower than that induced by the Gag protein and the VLPs, suggesting a low affinity activation. This weak T-cell-stimulating activity of the Gag peptides was further confirmed by testing diabetogenic T-cell clones, as well as by using MHC tetramers loaded with candidate peptides. The data suggest that ERV Gag or its gene variants may trigger autoimmunity via a pathway that could be independent from direct presentation of viral peptides to autoreactive T cells.

Function of the cargo sorting dileucine motif in a cytomegalovirus immune evasion protein.

As an immune evasion mechanism, cytomegaloviruses (CMVs) have evolved proteins that interfere with cell surface trafficking of MHC class-I (MHC-I) molecules to tone down recognition by antiviral CD8 T cells. This interference can affect the trafficking of recently peptide-loaded MHC-I from the endoplasmic reticulum to the cell surface, thus modulating the presentation of viral peptides, as well as the recycling of pre-existing cell surface MHC-I, resulting in reduction of the level of overall MHC-I cell surface expression. Murine cytomegalovirus (mCMV) was paradigmatic in that it led to the discovery of this immune evasion strategy of CMVs. Members of its m02-m16 gene family code for type-I transmembrane glycoproteins, proven or predicted, most of which carry cargo sorting motifs in their cytoplasmic, C-terminal tail. For the m06 gene product m06 (gp48), the cargo has been identified as being MHC-I, which is linked by m06 to cellular adapter proteins AP-1A and AP-3A through the dileucine motif EPLARLL. Both APs are involved in trans-Golgi network (TGN) cargo sorting and, based on transfection studies, their engagement by the dileucine motif was proposed to be absolutely required to prevent MHC-I exposure at the cell surface. Here, we have tested this prediction in an infection system with the herein newly described recombinant virus mCMV-m06AA, in which the dileucine motif is destroyed by replacing EPLARLL with EPLARAA. This mutation has a phenotype in that the transition of m06-MHC-I complexes from early endosomes (EE) to late endosomes (LE)/lysosomes for degradation is blocked. Consistent with the binding of the MHC-I α-chain to the luminal domain of m06, the m06-mediated disposal of MHC-I did not require the β2m chain of mature MHC-I. Unexpectedly, however, disconnecting MHC-I cargo from AP-1A/3A by the motif mutation in m06 had no notable rescuing impact on overall cell surface MHC-I, though it resulted in some improvement of the presentation of viral antigenic peptides by recently peptide-loaded MHC-I. Thus, the current view on the mechanism by which m06 mediates immune evasion needs to be revised. While the cargo sorting motif is critically involved in the disposal of m06-bound MHC-I in the endosomal/lysosomal pathway at the stage of EE to LE transition, this motif-mediated disposal is not the critical step by which m06 causes immune evasion. We rather propose that engagement of AP-1A/3A by the cargo sorting motif in m06 routes the m06-MHC-I complexes into the endosomal pathway and thereby detracts them from the constitutive cell surface transport.

A Sampling of Highlights from the Literature

Myosin II structure (from D. Goodsell via WikiMedia Commons)Tumor cells at the invasive front of primary melanomas differ from the cells elsewhere in the tumor. These amoeboid cells are rounded, enriched in phosphorylated myosin chains (indicative of high myosin II activity), and key to metastasis. Amoeboid cells secrete factors that attract monocytes and promote their differentiation into protumor macrophages. Blocking myosin II activity prevents the surrounding macrophages from supporting tumor growth. IL1α from the macrophages induces NF-κB activation in the amoeboid cells, completing a protumor loop.Georgouli M, …, Sanz-Moreno V. Cell 2019 Feb;176:757–74.Balancing treatment to hit the sweet spot (from maxpixel)One can have too much of a good thing. Although combining anti–CTLA-4 with anti–PD-1 can induce effective antitumor immunity when tumor burdens are high, when they are low, this combination increases the susceptibility of tumor-specific T cells to apoptosis. T cells in the low-tumor state are less exhausted and produce increased amounts of IFNγ but also bare more IFNγ receptors, leading to depletion of higher-frequency clones and loss of memory responses. Thus, finding the sweet spot for combination therapy may be necessary to avoid inducing immune-intrinsic resistance to treatment.Pai C.-C.S., …, Fong L. Immunity 2019 Feb;50:477–92.Cross-presentation inhibited by YTHDF1 in DCs (from R. Vatner et al. Front Oncol 2014)Cross-presentation by dendritic cells is limited by the protein YTHDF1. The binding of YTHDF1 to the 3'UTR of mRNAs that are modified with N6-adenosine methylation increases the translation of cathepsins, causing rapid degradation of endocytosed antigens. YTHDF1-deficient dendritic cells (DCs) have enhanced cross-presentation. Mice whose DCs lack YTHDF1 reject tumors more readily and respond better to checkpoint inhibitors. Thus, cross-presentation is key for antitumor immunity, and modulation of cross-presentation through YTHDF1 provides another target for cancer immunotherapy in combination with checkpoint inhibitors.Han D, …, He C. Nature 2019 Feb;566:270–74.Neutrophils travel with circulating tumor cells (from Dr Graham Beards via Wikimedia Commons)In breast cancer patients, some circulating tumor cells (CTCs) cluster with neutrophils. These CTC-neutrophil clusters are more proliferative, metastatic, and correlate with lower progression-free and overall survival than CTCs alone in mouse models. Although mutational burdens are similar to CTCs alone, the CTC-neutrophil clusters have recurrent mutations in TLE1 and MERTK, which promote myeloid infiltration into tumors. VCAM1 is required for CTC interaction with neutrophils, and blocking this prevents cluster formation, providing a potential therapeutic target to reduce metastasis.Szczerba BM, …, Aceto N. Nature 2019 Feb;566:553–57.Ribosome large and small subunits (by Vossman via Wikimedia Commons)Ribosomes contain 80 proteins involved in translation. Wei et al. deleted each one to ascertain their influence on the peptides presented by MHC class I. Two large ribosomal subunit proteins, RPL28 and RPL6, have opposite effects on presentation of viral peptides if missing (increased and decreased, respectively), and depletion of the small subunit protein RPS28 increased the presentation of host peptides. Thus, tumors can manipulate the antitumor response of T cells through their altered ribosomal composition and mutated ribosomal proteins, both of which affect the peptides presented to T cells.Wei J, …, Yewdell JW. Mol Cell 2019 Jan 31. DOI: 10.1016/j.molcel.2018.12.020.Lung commensals and T cells (via Pixabay)Effects of the lung's microbiome on tumors was studied in a mutant-Kras/p53– mouse model. Commensal microbiota promote inflammation and cancer progression through resident γδ T cells. The microbes are required for γδ T-cell expansion and activation, subsequent neutrophil infiltration, and development of lung adenocarcinomas. Disruption of the microbiota-mediated activation of γδ T cells may aid inactivating this route to lung cancer.Jin C, …, Jacks T. Cell 2019 Feb;176:998–1013.

Cytomegalovirus-Specific T Cells Restricted by HLA-Cw*0702 Increase Markedly with Age and Dominate the CD8+ T-Cell Repertoire in Older People.

Cytomegalovirus (CMV) infection elicits a strong T-cell immune response, which increases further during aging in a process termed “memory inflation.” CMV downregulates the expression of HLA-A and HLA-B on the surface of infected cells to limit presentation of viral peptides to T-cells although HLA-C is relatively spared as it also engages with inhibitory killer immunoglobulin receptor receptors and therefore reduces lysis by natural killer cells. We investigated the magnitude and functional properties of CMV-specific CD8+ T-cells specific for 10 peptides restricted by HLA-C in a cohort of 53 donors between the age of 23 and 91 years. This was achieved via peptide stimulation of PBMCs followed by multicolor flow cytometry. Three peptides, derived from proteins generated in the immediate-early period of viral replication and restricted by HLA-Cw*0702, elicited strong immune responses, which increased substantially with age such that the average aggregate response represented 37% of the CD8+ T-cell pool within donors above 70 years of age. Remarkably, a single response represented 70% of the total CD8+ T-cell pool within a 91-year-old donor. HLA-Cw*0702-restricted CD8+ T-cell responses were immunodominant over HLA-A and HLA-B-restricted CMV-specific responses and did not show features of exhaustion such as PD-1 or CD39 expression. Indeed, such CTL exhibit a polyfunctional cytokine profile with co-expression of IFN-γ and TNF-α and a strong cytotoxic phenotype with intracellular expression of perforin and granzymeB. Functionally, HLA-Cw*0702-restricted CTL show exceptionally high avidity for cognate peptide-HLA and demonstrate very early and efficient recognition of virally infected cells. These observations indicate that CD8+ T-cells restricted by HLA-C play an important role in the control of persistent CMV infection and could represent a novel opportunity for CD8+ T-cell therapy of viral infection within immunosuppressed patients. In addition, the findings provide further evidence for the importance of HLA-C-restricted T-cells in the control of chronic viral infection.

Host genotype and time dependent antigen presentation of viral peptides: predictions from theory

The rate of progression of HIV infected individuals to AIDS is known to vary with the genotype of the host, and is linked to their allele of human leukocyte antigen (HLA) proteins, which present protein degradation products at the cell surface to circulating T-cells. HLA alleles are associated with Gag-specific T-cell responses that are protective against progression of the disease. While Pol is the most conserved HIV sequence, its association with immune control is not as strong. To gain a more thorough quantitative understanding of the factors that contribute to immunodominance, we have constructed a model of the recognition of HIV infection by the MHC class I pathway. Our model predicts surface presentation of HIV peptides over time, demonstrates the importance of viral protein kinetics, and provides evidence of the importance of Gag peptides in the long-term control of HIV infection. Furthermore, short-term dynamics are also predicted, with simulation of virion-derived peptides suggesting that efficient processing of Gag can lead to a 50% probability of presentation within 3 hours post-infection, as observed experimentally. In conjunction with epitope prediction algorithms, this modelling approach could be used to refine experimental targets for potential T-cell vaccines, both for HIV and other viruses.