peptide-MHC Class Research Articles

IFI30 as a key regulator of PDL1 immunotherapy prognosis in breast cancer

BackgroundIFI30 is a lysosomal thiol reductase involved in antigen presentation and immune regulation in various cancers, including breast cancer. Despite its known involvement, the precise mechanism, function, and relationship with the PD-L1 axis and immune response remain unclear. MethodsWe conducted an extensive investigation into IFI30 mRNA expression in breast cancer utilizing data from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases. Furthermore, we characterized IFI30 mRNA expression across various cell types using publicly available single-cell RNA sequencing datasets, and assessed protein expression through immunohistochemistry using an in-house breast cancer tissue microarray. Functional experiments were performed to elucidate the effects of IFI30 overexpression on PD-L1 expression and inhibitory efficacy in both macrophages and breast tumor cells. ResultsOur study unveiled a marked upregulation of IFI30 expression in breast cancer tissues compared to their normal counterparts, with notable associations identified with tumor stage and prognosis. Additionally, IFI30 expression demonstrated significant correlations with various immune-related signaling pathways, encompassing peptide antigen binding, cytokine binding, and MHC class II presentation. Notably, breast cancer samples exhibiting high IFI30 expression in tumor cells displayed high PD-L1 expression on corresponding cells, alongside a diminished ratio of CD8 + T cell infiltration within the tumor microenvironment. Furthermore, ectopic knockdown of IFI30 in both tumor cells and macrophages resulted in a reduction of PD-L1 expression, while conversely, overexpression of IFI30 led to an increase in PD-L1 expression. ConclusionsThis study offers new insights into the involvement of IFI30 in breast cancer, elucidating its interplay with the PD-L1 axis and immune response dynamics. Our findings suggest that modulation of the IFI30-PD-L1 axis could serve as a promising strategy for regulating T cells infiltration in breast cancer thus treating breast cancer.

Sensitization with Fungal Protease Allergen Establishes Long-Lived, Allergenic Th Cell Memory in the Lung.

Allergic asthma is a chronic inflammatory disease that affects millions of individuals worldwide. Exposure to allergens produced by a variety of otherwise harmless microbes, including fungi, predisposes individuals to immunopathologic disease upon subsequent encounters with allergen. We developed a mouse model that employs a purified protease produced by Aspergillus (Asp f 13) to investigate the contributions of CD4+ Th cells to recurrent lung inflammation. Notably, memory CD4+ T cells enhanced the eosinophil response of sensitized/rechallenged animals. In addition, memory CD4+ T cells maintained allergenic features, including expression of GATA-binding protein 3 and IL-5. Th2 memory T cells persisted in the peribronchiolar interstitium of the lung and expressed markers of tissue residence, such as CD69, CCR8, and IL-33R. Lastly, we identified a peptide epitope contained within Asp f 13 and generated a peptide-MHC class II tetramer. Using these tools, we further demonstrated the durability and exquisite sensitivity of memory T cells in promoting lung eosinophilia. Our data highlight important features of memory T cells that strengthen the notion that memory T cells are principal drivers of eosinophilic disease in murine models of allergic sensitization and episodic airway inflammation.

Recruitment of naive CD4+ T cells by the recombinant zoster vaccine correlates with persistent immunity.

Herpes zoster (HZ) is a substantial problem for people with decreased cell-mediated immunity, including older adults. The first vaccine approved for HZ prevention, the zoster vaccine live (ZVL), which provided limited and short-lived protection, has been supplanted by the superior recombinant zoster vaccine (RZV), which provides robust and durable protection. To understand the mechanisms underlying the differential immunologic characteristics of the 2 vaccines, we used T cell receptor β chain sequencing and peptide-MHC class II tetramer staining to analyze recombinant glycoprotein E-specific (gE-specific) CD4+ T cell clonotypes in RZV and ZVL recipients. Compared with ZVL, RZV expanded more gE-specific CD4+ clonotypes, with greater breadth and higher frequency of public clonotypes. RZV recruited a higher proportion of clonotypes from naive than from memory cells, while ZVL recruited equally from memory and naive compartments. Compared with memory-derived, naive-derived clonotypes were more likely to last 5 or more years after immunization. Moreover, the frequency of tetramer+ persistent clones correlated with the frequency of tetramer+ naive CD4+ prevaccination T cells. We conclude that the ability of RZV to recruit naive CD4+ T cells into the response may contribute to the durability of its effect. The abundance, breadth, and frequency of public clonotypes may further add to its protective effect.

Activation and differentiation of cognate T cells by a dextran-based antigen-presenting system for cancer immunotherapy.

Immunotherapeutic modulation of antigen-specific T-cell responses instead of the whole repertoire helps avoid immune-related adverse events. We have developed an artificial antigen-presenting system (aAPS) where multiple copies of a multimeric peptide-MHC class I complex presenting a murine class I MHC restricted ovalbumin-derived peptide (signal 1), along with a costimulatory ligand (signal 2) are chemically conjugated to a dextran backbone. Cognate naive CD8+ T cells, when treated with this aAPS underwent significant expansion and showed an activated phenotype. Furthermore, elevated expression of effector cytokines led to the differentiation of these cells to cytotoxic T lymphocytes which resulted in target cell lysis, indicative of the functional efficacy of the aAPS. CD8+ T cells with decreased proliferative potential due to repeated antigenic stimulation could also be re-expanded by the developed aAPS. Thus, the developed aAPS warrants further engineering for future application as a rapidly customizable personalized immunotherapeutic agent, incorporating patient-specific MHC-restricted tumor antigens and different costimulatory signals to modulate both naive and antigen-experienced but exhausted tumor-specific T cells in cancer.

Localization, tissue biology and T cell state - implications for cancer immunotherapy.

Tissue localization is a critical determinant of T cell immunity. CD8+ T cells are contact-dependent killers, which requires them to physically be within the tissue of interest to kill peptide-MHC class I-bearing target cells. Following their migration and extravasation into tissues, T cells receive many extrinsic cues from the local microenvironment, and these signals shape T cell differentiation, fate and function. Because major organ systems are variable in their functions and compositions, they apply disparate pressures on T cells to adapt to the local microenvironment. Additional complexity arises in the context of malignant lesions (either primary or metastatic), and this has made understanding the factors that dictate T cell function and longevity in tumours challenging. Moreover, T cell differentiation state influences how cues from the microenvironment are interpreted by tissue-infiltrating T cells, highlighting the importance of T cell state in the context of tissue biology. Here, we review the intertwined nature of T cell differentiation state, location, survival and function, and explain how dysfunctional T cell populations can adopt features of tissue-resident memory T cells to persist in tumours. Finally, we discuss how these factors have shaped responses to cancer immunotherapy.

Insights into anti-tumor immunity via the polyomavirus shared across human Merkel cell carcinomas.

Understanding and augmenting cancer-specific immunity is impeded by the fact that most tumors are driven by patient-specific mutations that encode unique antigenic epitopes. The shared antigens in virus-driven tumors can help overcome this limitation. Merkel cell carcinoma (MCC) is a particularly interesting tumor immunity model because (1) 80% of cases are driven by Merkel cell polyomavirus (MCPyV) oncoproteins that must be continually expressed for tumor survival; (2) MCPyV oncoproteins are only ~400 amino acids in length and are essentially invariant between tumors; (3) MCPyV-specific T cell responses are robust and strongly linked to patient outcomes; (4) anti-MCPyV antibodies reliably increase with MCC recurrence, forming the basis of a standard clinical surveillance test; and (5) MCC has one of the highest response rates to PD-1 pathway blockade among all solid cancers. Leveraging these well-defined viral oncoproteins, a set of tools that includes over 20 peptide-MHC class I tetramers has been developed to facilitate the study of anti-tumor immunity across MCC patients. Additionally, the highly immunogenic nature of MCPyV oncoproteins forces MCC tumors to develop robust immune evasion mechanisms to survive. Indeed, several immune evasion mechanisms are active in MCC, including transcriptional downregulation of MHC expression by tumor cells and upregulation of inhibitory molecules including PD-L1 and immunosuppressive cytokines. About half of patients with advanced MCC do not persistently benefit from PD-1 pathway blockade. Herein, we (1) summarize the lessons learned from studying the anti-tumor T cell response to virus-positive MCC; (2) review immune evasion mechanisms in MCC; (3) review mechanisms of resistance to immune-based therapies in MCC and other cancers; and (4) discuss how recently developed tools can be used to address open questions in cancer immunotherapy. We believe detailed investigation of this model cancer will provide insight into tumor immunity that will likely also be applicable to more common cancers without shared tumor antigens.

TCF-1 dictates lung tissue resident helper T cell and memory B cell development during flu

Abstract Influenza (flu) infections are a significant cause of annual human morbidity and mortality. The efficacy of seasonal flu vaccines depends on the accuracy of the prediction of the circulating strains for the upcoming season. To develop flu vaccines that are broadly effective and more sustainable, induction of a cross-reactive memory immunity is desirable. Flu infection induces cross-reactive tissue resident memory T (Trm) and B (Brm) cells which rapidly respond to reinfection. Tissue resident helper T (Trh) cells are a population of T follicular helper (Tfh)-like CD4 +Trm cells that promote the development of Brm cell responses following flu infection. The transcription factor TCF-1, encoded by Tcf7, is critical in the development of both memory T cells and Tfh cells following viral infections. However, the role of TCF-1 in Trh cell development has not been investigated. Utilizing a Tcf7 fl/flCD4 Creconditional knockout mouse model in conjunction with intravascular labeling and influenza A peptide MHC Class II tetramers, we found that TCF-1 is required for the differentiation of flu-specific Trh cells, as well as optimal Brm development following flu infections. Most significantly, upon heterosubtypic reinfection, the Trh population in the Tcf7 fl/flcontrol mice expanded while it became undetectable in the Tcf7 fl/flCD4 Cremice, coinciding with a severely impaired lung resident germinal center B cell and CD138 +plasma cell response. Together, our data indicates that TCF-1 is critical in the development of lung tissue resident helper cells and tissue resident memory B cell response following flu infections. This work has implications for the development of universal flu vaccines.

DM functions differently in thymic antigen presentation cell subsets in development of autoreactive CD4+ T cells

Abstract Autoreactive CD4+ T cells broadly exist in healthy individuals and potentially cause autoimmune diseases; however, why they can escape from thymic negative selection is still controversial. We observed that the activity of DM, a peptide epitope editor in MHC class II antigen presentation pathway, is differentially regulated in different thymic antigen presenting cells (APC). It is high in cTEC that involved in cortical positive selection, but low in mTEC, B cell, pDC and cDC that mediate negative selection in medulla, while it remains high in all types of peripheral APC. The molecular mechanism of differential regulation is still unknown. It is not directly inhibited by DO, a negative regulator of DM that directly competes DM catalytic site with peptide-MHC class II complex, since DM editing activity remains low in those thymic medulla APC in DO−/− mice. We further confirmed that presentation of autoantigen epitope MOG35–55 for thymic positive selection and in vitro activation of autoreactive CD4+ T cells in EAE, a mouse model of human multiple sclerosis disease, is DM dependent. This is also true for presentation of insulin epitope B9–23 to activate autoreactive CD4+ T cells restricted to type 1 diabetes associated HLA-DQ8. Our findings highlighted a fundamental mechanism that immune system differentially regulates DM activity in thymus to balance the efficiency of negative selection to minimize autoimmunity and the maximum of T cell repertoire to defend infection; however, the DM-dependency property of certain autoantigen epitopes accidently caused the failure deletion of autoreactive CD4+ T cells.

Binding of LAG-3 to stable peptide-MHC class II limits T cell function and suppresses autoimmunity and anti-cancer immunity

Lymphocyte activation gene-3 (LAG-3) is a potent inhibitory co-receptor; yet, its functional ligand remains elusive, with distinct potential ligands identified. Here, we investigated the relative contribution of potential ligands, stable peptide-MHC class II complexes (pMHCII) and fibrinogen-like protein 1 (FGL1), to LAG-3 activity invitro and invivo. Binding of LAG-3 to stable pMHCII but not to FGL1 induced Tcell suppression invitro. Consistently, LAG-3 mutants lacking FGL1-binding capacity but not those lacking stable pMHCII-binding capacity retained suppressive activity invitro. Accordingly, targeted disruption of stable pMHCII- but not FGL1-binding capacity of LAG-3 in NOD mice recapitulated diabetes exacerbation by LAG-3 deficiency. Additionally, the loss of stable pMHCII-binding capacity of LAG-3 augmented anti-cancer immunity comparably with LAG-3 deficiency in C57BL/6 mice. These results identify stable pMHCII as a functional ligand of LAG-3 both in autoimmunity and anti-cancer immunity. Thus, stable pMHCII-LAG-3 interaction is a potential therapeutic target in human diseases.

Comparative Reverse Vaccinology of Piscirickettsia salmonis, Aeromonas salmonicida, Yersinia ruckeri, Vibrio anguillarum and Moritella viscosa, Frequent Pathogens of Atlantic Salmon and Lumpfish Aquaculture.

Marine finfish aquaculture is affected by diverse infectious diseases, and they commonly occur as co-infection. Some of the most frequent and prevalent Gram-negative bacterial pathogens of the finfish aquaculture include Piscirickettsia salmonis, Aeromonas salmonicida, Yersinia ruckeri, Vibrio anguillarum and Moritella viscosa. To prevent co-infections in aquaculture, polyvalent or universal vaccines would be ideal. Commercial polyvalent vaccines against some of these pathogens are based on whole inactivated microbes and their efficacy is controversial. Identification of common antigens can contribute to the development of effective universal or polyvalent vaccines. In this study, we identified common and unique antigens of P. salmonis, A. salmonicida, Y. ruckeri, V. anguillarum and M. viscosa based on a reverse vaccinology pipeline. We screened the proteome of several strains using complete available genomes and identified a total of 154 potential antigens, 74 of these identified antigens corresponded to secreted proteins, and 80 corresponded to exposed outer membrane proteins (OMPs). Further analysis revealed the outer membrane antigens TonB-dependent siderophore receptor, OMP assembly factor BamA, the LPS assembly protein LptD and secreted antigens flagellar hook assembly protein FlgD and flagellar basal body rod protein FlgG are present in all pathogens used in this study. Sequence and structural alignment of these antigens showed relatively low percentage sequence identity but good structural homology. Common domains harboring several B-cells and T-cell epitopes binding to major histocompatibility (MHC) class I and II were identified. Selected peptides were evaluated for docking with Atlantic salmon (Salmo salar) and Lumpfish MHC class II. Interaction of common peptide-MHC class II showed good in-silico binding affinities and dissociation constants between −10.3 to −6.5 kcal mol−1 and 5.10 × 10−9 to 9.4 × 10−6 M. This study provided the first list of antigens that can be used for the development of polyvalent or universal vaccines against these Gram-negative bacterial pathogens affecting finfish aquaculture.

Abstract P5-08-04: LMP7-specific inhibitor M3258 modulates the tumor microenvironment of aggressive breast cancer

Abstract Background: LMP7 (beta5i/PSMB8) is a proteolytic subunit of the immunoproteasome that is predominantly expressed in leukocytes and inflamed tissues. The immunoproteasome degrades ubiquitinated proteins for maintenance of cell homeostasis and generation of peptides for MHC class I presentation. LMP7 has been implicated in multiple myeloma, autoimmune and inflammatory diseases, and inflammation-related cancers. Here, we evaluated the effect of M3258, an orally bioavailable, highly-selective, and reversible inhibitor of LMP7, on the tumor microenvironment (TME) using in vitro and in vivo models of triple-negative breast cancer (TNBC) and inflammatory breast cancer (IBC). Methods: The proteolytic activity of M3258 was determined using the fluorogenic LMP7-specific peptidic substrate (Ac-ANW)2R110. Its anti-proliferation activity was determined using the CellTiter-Blue cell viability and sulforhodamine B staining assays. Expression of immunoproteasome subunits under different conditions was examined by Western blotting. All in vitro assessments were done with or without IFNγ, which is known to increase immunoproteasome expression. The in vivo anti-tumor efficacy of M3258 was evaluated using a SUM-149 PT TN-IBC xenograft mouse model implanted in humanized mice. Single-cell RNA sequencing (scRNA-seq) was used in this same study to examine the impact of M3258 on the TME. Results: M3258 inhibited LMP7 activity (IC50 = 6.5-212.8 nM) and had no effects on LMP7 protein expression in a panel of TNBC cells (DU4475, HCC1187), IBC cells (SUM190, IBC3, KPL4), and TN-IBC cells (SUM-149 PT, BCX-010, FC-IBC02). M3258 inhibited proliferation of TNBC and IBC cell lines in vitro (IC50 = 1-20 µM). In keeping with previous reports, IFNγ treatment strongly induced LMP7 expression and enhanced its proteolytic activity in these cell lines in vitro and increased M3258 sensitivity (2- to 5-fold). In the humanized SUM-149 PT xenograft mouse model, M3258 orally administered at 10 mg/kg significantly inhibited tumor growth versus vehicle (31.4%, P < 0.01) and was tolerated. ScRNA-seq analysis of the terminal tumor samples from this study revealed that M3258 reduced the abundance of CD4+ and CD8+ T cells, Tregs, M1 and M2 macrophages, and dendritic cells. Gene expression profiling indicated a particularly pronounced inhibitory effect of M3258 on M1 and M2 macrophages. Furthermore, M3258 treatment activated CD8+ T cells and suppressed expression of genes involved in inflammatory response, IFNα signaling, IFNγ signaling, and TNFα signaling in immune cells. In light of the scRNA-seq findings, we assessed the impact of M1 and M2 macrophages on the invasiveness of TN-IBC cells in vitro. Co-cultures with M1 or M2 macrophages enhanced invasiveness of SUM-149 PT cells (4.6-fold by M1, P < 0.001; 6.3-fold by M2, P < 0.01) and BCX-010 cells (2.1-fold by M1, P < 0.05; 4.0-fold by M2, P < 0.01). Since M2 macrophages showed a superior effect than M1 macrophages on TN-IBC cell invasiveness, we further assessed M3258’s ability to inhibit such activity. M3258 at 500 nM significantly inhibited M2 macrophage-induced invasion of SUM-149 PT cells (29.6%, P < 0.05) and BCX-010 (49.5%, P < 0.01). Conclusion: Using the exquisitely selective LMP7 inhibitor M3258, we were able to demonstrate for the first time that LMP7 plays an important role in the inflammatory microenvironment, proliferation and invasiveness of TNBC and IBC cells, in particular by modulating the pathogenic role of M2 macrophages. These data warrant future in vivo studies into the antitumor efficacy of M3258 when used with immunotherapy agents. Citation Format: Xuemei Xie, Jangsoon Lee, Ganiraju C Manyam, Troy Pearson, Gina Walter-Bausch, Manja Friese-Hamim, Samantha M Goodstal, Debu Tripathy, Wang Jing, Michael Sanderson, Naoto T Ueno. LMP7-specific inhibitor M3258 modulates the tumor microenvironment of aggressive breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P5-08-04.

Systematic Determination of TCR–Antigen and Peptide–MHC Binding Kinetics among Field Variants of a Theileria parva Polymorphic CTL Epitope

CTLs are known to contribute to immunity toward Theileria parva, the causative agent of East Coast fever. The Tp967-75 CTL epitope from the Muguga strain of T. parva is polymorphic in other parasite strains. Identifying the amino acids important for MHC class I binding, as well as TCR recognition of epitopes, can allow the strategic selection of Ags to induce cellular immunity toward T. parva In this study, we characterized the amino acids important for MHC class I binding and TCR recognition in the Tp967-75 epitope using alanine scanning and a series of variant peptide sequences to probe these interactions. In a peptide-MHC class I binding assay, we found that the amino acids at positions 1, 2, and 3 were critical for binding to its restricting MHC class I molecule BoLA-1*023:01. With IFN-γ ELISPOT and peptide-MHC class I Tet staining assays on two parasite-specific bovine CTL lines, we showed that amino acids at positions 5-8 in the epitope were required for TCR recognition. Only two of eight naturally occurring polymorphic Tp9 epitopes were recognized by both CTLs. Finally, using a TCR avidity assay, we found that a higher TCR avidity was associated with a stronger functional response toward one of two variants recognized by the CTL. These data add to the growing knowledge on the cross-reactivity of epitope-specific CTLs and specificities that may be required in the selection of Ags in the design of a wide-spectrum vaccine for East Coast fever.

Cross-dressing of dendritic cells strengthens antitumor immunity

Different subsets of tumor-infiltrating dendritic cells (DCs) influence immune response and tolerance in cancer settings. Duong et al. discovered that conventional DC2 subset (cDC2s) can differentiate into stimulatory interferon-stimulated gene (ISG)+ DCs by type I interferon (IFN-I) produced in regressor tumors and acquire and present tumor-derived peptide-MHC (pMHC) class I complexes to increase the protective antitumor CD8+ T cell response.

CD8 T Cells Target Antigen Cross-Presented by Bone Marrow Derived Cells to Induce Bystander Rejection of Grafts Lacking the Cognate Peptide-MHC

CD8 T cells play a key role in cancer immunotherapy and allograft rejection. However, it is not clear how they kill cells and tissues that do not have the agonist peptide-major histocompatibility complex (MHC) on their surface, as in the settings of MHC class I deficient tumors and indirect rejection of MHC-mismatched transplants. CD8 T cells might respond to agonist antigen cross-presented on hematopoietic cells, leading to a “bystander” rejection. Alternatively, they may recognize agonist antigen cross-presented on recipient endothelial cells and kill the tissue’s vital blood supply. The latter mechanism predicts that all non-vascularized grafts, grafts dependent on in-growth of recipient blood vessels, will be susceptible to CD8 T cell mediated indirect rejection. In contrast, we show here that non-vascularized transplants, bearing the same agonist antigen, are not universally susceptible to this rejection pathway. Non-vascularized skin, but not islet or heart tissue transplants were indirectly rejected by CD8 T cells. Furthermore, CD8 T cells were able to indirectly reject skin grafts when recipient MHC class I expression was restricted to bone marrow derived cells but not when it was restricted to radioresistant cells (e.g. endothelial cells). These findings argue against a major role for endothelial cell cross-presentation in killing of tissue that does not present the agonist peptide-MHC class I. Instead, the data suggests that cross-presentation by recipient hematopoietic cells underlies the CD8 T cell mediated killing of tissue that is unable to directly present the target peptide-MHC class I.

CNN-PepPred: an open-source tool to create convolutional NN models for the discovery of patterns in peptide sets-application to peptide-MHC class II binding prediction.

SummaryThe ability to unveil binding patterns in peptide sets has important applications in several biomedical areas, including the development of vaccines. We present an open-source tool, CNN-PepPred, that uses convolutional neural networks to discover such patterns, along with its application to peptide–HLA class II binding prediction. The tool can be used locally on different operating systems, with CPUs or GPUs, to train, evaluate, apply and visualize models.Availability and implementationCNN-PepPred is freely available as a Python tool with a detailed User’s Guide at https://github.com/ComputBiol-IBB/CNN-PepPred. The site includes the peptide sets used in this study, extracted from IEDB (www.iedb.org).Supplementary information Supplementary data are available at Bioinformatics online.

Toward Guided Mutagenesis: Gaussian Process Regression Predicts MHC Class II Antigen Mutant Binding.

Antigen-specific immunotherapies (ASI) require successful loading and presentation of antigen peptides into the major histocompatibility complex (MHC) binding cleft. One route of ASI design is to mutate native antigens for either stronger or weaker binding interaction to MHC. Exploring all possible mutations is costly both experimentally and computationally. To reduce experimental and computational expense, here we investigate the minimal amount of prior data required to accurately predict the relative binding affinity of point mutations for peptide-MHC class II (pMHCII) binding. Using data from different residue subsets, we interpolate pMHCII mutant binding affinities by Gaussian process (GP) regression of residue volume and hydrophobicity. We apply GP regression to an experimental data set from the Immune Epitope Database, and theoretical data sets from NetMHCIIpan and Free Energy Perturbation calculations. We find that GP regression can predict binding affinities of nine neutral residues from a six-residue subset with an average R2 coefficient of determination value of 0.62 ± 0.04 (±95% CI), average error of 0.09 ± 0.01 kcal/mol (±95% CI), and with an receiver operating characteristic (ROC) AUC value of 0.92 for binary classification of enhanced or diminished binding affinity. Similarly, metrics increase to an R2 value of 0.69 ± 0.04, average error of 0.07 ± 0.01 kcal/mol, and an ROC AUC value of 0.94 for predicting seven neutral residues from an eight-residue subset. Our work finds that prediction is most accurate for neutral residues at anchor residue sites without register shift. This work holds relevance to predicting pMHCII binding and accelerating ASI design.

Targeted immune epitope prediction to HHLA2 and MAGEB5 protein variants as therapeutic approach to related viral diseases

BackgroundTargeted immunotherapy is mostly associated with cancer treatment wherein designed molecules engage signaling pathways and mutant proteins critical to the survival of the cell. One of several genetic approaches is the use of in silico methods to develop immune epitopes targeting specific antigenic regions on related mutant proteins. In a recent study we showed a functional association between the gamma retrovirus HERV-H Long Terminal Associating (HHLA1, HHLA2 and HHLA3) proteins and melanoma associated antigen of the B class proteins (MAGEB5), with a resultant decrease in expression of HLA class I and II immune variants. HLA-C and HLA-DRB5 were the main HLA class I and II Immune variants, respectively, that showed expression changes across viral samples of interest. Specific immune variants for HLA-C and HLA-DRB5 were filtered for the top ten based on their relative frequency of counts across the samples.ResultsProtein variants for HHLA1, HHLA2, HHLA3 and MAGEB5 were used to predict antigenic epitope peptides to immune peptide-MHC class I and II binding using artificial neural networks. For IC50 peptide scores (PS) ≥ 0.5 with a transformed binding ability between 0 and 1, the top 5 epitopes identified for all targeted genes HHLA1,2 & 3 and MAGEB5 were qualified as strong or weak binders according to the threshold. Domain analysis using NCBI Conserved Domain Database (CDD) identified HHLA2 with immunoglobulin-like domains (Ig_C1-set) and MAGEB5 with the MAGE Homology Domain (MHD). Linear regression showed a statistical correlation (P < 0.001) for HHLA2 and MAGEB5 predicted epitope peptides to HLA-C but not HLA-DRB5. The prediction model identified HLA-C variant 9 (HLA-C9, BAA08825.1 HLA-B*1511) at 1.1% as the most valuable immune target for clinical considerations. Identification of the 9-mer epitope peptide within the domain showed for HHLA2: YANRTSLFY (PS = 0.5837) and VLAYYLSSSQNTIIN (PS = 0.77) for HLA-C and HLA-DRB5, respectively and for MAGEB5, peptides: FVRLTYLEY (PS = 0.5293) and YPAHYQFLWGPRAYT (PS = 0.62) for HLA-C and HLA-DRB5, respectively.ConclusionSpecific immune responses to targeted epitope peptides and their prediction models, suggested co-expression and co-evolution for HHLA2 and MAGEB5 in viral related diseases. HHLA2 and MAGEB5 could be considered markers for virus related tumors and targeted therapy for oncogenic diseases.

FVIII Proteins with a Modified Immunodominant T-Cell Epitope Exhibit Reduced Immunogenicity and Normal Procoagulant Activity

Factor VIII (FVIII) neutralizing antibodies (inhibitors) are a serious complication in hemophilia A (HA). The peptide FVIII2194-2213 (legacy FVIII numbering, sequence: SYFTNMFATWSPSKARLHLQ) has been shown to contain an immunodominant HLA-DRA*01-DRB1*01:01 (DRB1*01:01)-restricted epitope recognized by CD4+ T-effector cells isolated from HA subjects. The aim of this study was to identify amino acid substitutions to de-immunize this epitope while retaining pro-coagulant function and expression levels comparable to those of wild-type (WT) FVIII proteins. The minimal DRB1*01:01-binding motif was mapped to FVIII2194-2205 by quantitative peptide-MHC Class II (MHCII) binding assays. Further binding assays with sequence-modified FVIII peptides established that the residues important for DRB1*01:01 affinity were F2196, M2199, A2201, and S2204, corresponding to MHCII anchor positions 1, 4, 6 and 9. T-cell proliferation experiments with Ala-substituted FVIII2194-2205 peptides identified F2196A as a substitution that abrogated proliferation and cytokine secretion of five clones specific for FVIII2194-2213. The substitution F2196A was then engineered into a recombinant (r)FVIII-C2 protein. T-cell clones that were strongly stimulated by wild-type rFVIII-C2 did not proliferate when cultured with rFVIII-C2-F2196A, indicating the immunogenic synthetic peptide includes a naturally processed T-cell epitope. The measured and predicted effects of additional amino acid substitutions within this binding motif were further evaluated by peptide-MHCII binding assays, CD4+ T-cell proliferation assays, and MHCII-binding prediction algorithms. Amino acid homologs within this binding motif were evaluated with sequence homologies to FVIII and FV proteins from different species. On the basis of all these results, six rB-domain-deleted (BDD)-FVIII proteins with amino acid substitutions F2196A, F2196L, F2196K, M2199A, M2199W or M2199R, respectively, were designed and produced; all but the F2196A variant had specific activities comparable to that of rWT-BDD-FVIII. The F2196A variant also had the lowest expression level among the rBDD-FVIIII proteins produced. Peptide-MHCII binding assays confirmed that FVIII2194-2205 peptides with substitutions F2196A, F2196K, M2199A and M2199R did not bind to DRB1*01:01 or to an additional 9 HLA-DR proteins tested, with the exception of the M2199A peptide binding to DRB1*09:01. The predicted effects of these FVIII sequence modifications on binding to additional MHCII alleles included in reference sets representing ~99% of the human population HLA diversity were evaluated using ProPred and Immune Epitope Database algorithms. These programs correctly predicted that the substitutions would abrogate binding to DRB1*01:01 and also indicated that affinities for additional MHCII would be reduced by each substitution. The substitutions were predicted to increase peptide-MHCII affinities for a smaller number of MHCII alleles, indicating a possible risk of creating neo-epitopes restricted to these specific HLA alleles. Importantly, proliferation of patient-derived T-cell clones in response to rBDD-FVIII-F2196K and rBDD-FVIII-M2199A proteins was dramatically reduced compared with responses to rWT-BDD-FVIII. We have previously demonstrated that a severe HA inhibitor subject had an oligoclonal T-cell response to only one T-cell epitope within the FVIII A2, C1 and C2 domains and that one epitope was FVIII2194-2213 (Ettinger et al., Blood 2106; 128(16):2043). This observation, together with the results presented here, further suggests that modification of only a small number of immunodominant epitopes may be sufficient to significantly de-immunize FVIII and decrease FVIII inhibitors in HA patients. The present results provide proof-of-principle for the design of less immunogenic FVIII proteins targeted to specific subsets of HA patients. DisclosuresEttinger:Bloodworks NW: Patents & Royalties: Inventor on FVIII patents. James:Bloodworks NW: Patents & Royalties: inventor on FVIII patent(s). Pratt:Bloodworks NW: Patents & Royalties: inventor on FVIII patents.

Ranking-Based Convolutional Neural Network Models for Peptide-MHC Class I Binding Prediction.

T-cell receptors can recognize foreign peptides bound to major histocompatibility complex (MHC) class-I proteins, and thus trigger the adaptive immune response. Therefore, identifying peptides that can bind to MHC class-I molecules plays a vital role in the design of peptide vaccines. Many computational methods, for example, the state-of-the-art allele-specific method , have been developed to predict the binding affinities between peptides and MHC molecules. In this manuscript, we develop two allele-specific Convolutional Neural Network-based methods named and to tackle the binding prediction problem. Specifically, we formulate the problem as to optimize the rankings of peptide-MHC bindings via ranking-based learning objectives. Such optimization is more robust and tolerant to the measurement inaccuracy of binding affinities, and therefore enables more accurate prioritization of binding peptides. In addition, we develop a new position encoding method in and to better identify the most important amino acids for the binding events. We conduct a comprehensive set of experiments using the latest Immune Epitope Database (IEDB) datasets. Our experimental results demonstrate that our models significantly outperform the state-of-the-art methods including with an average percentage improvement of 6.70% on AUC and 17.10% on ROC5 across 128 alleles.

Detection of autoreactive CD4+ T cells by MHC class II multimers in HLA-linked human autoimmune diseases.

Recognition of self-peptides in association with distinct HLA class II alleles by autoreactive CD4+ T cells is central for loss of immunological tolerance leading to autoimmune disease. However, identifying immunodominant self-peptides and characterizing autoreactive T cells is challenging. In this issue of the JCI, Falta et al. identify a disease-associated complementarity-determining region 3β motif specific for beryllium-modified C-C motif ligand 4 (CCL4) and CCL3 self-peptides in patients with chronic beryllium disease (CBD), a granulomatous lung disorder with a known HLA class II allelic association. Detection of these antigen-specific CD4+ T cells by beryllium-pulsed HLA-DP2 tetramers presenting CCL4/CCL3 confirms these autoantigens in humans and mice and enables monitoring in the progress of disease. Detection of autoreactive CD4+ T cells by peptide-MHC class II multimers allows for the detailed characterization of disease-promoting T cells. This knowledge has profound implications for the monitoring and development of targeted therapies in human autoimmune disorders.