Development Of Antigen-specific Immunotherapy Research Articles

Dynamics-Based Peptide–MHC Binding Optimization by a Convolutional Variational Autoencoder: A Use-Case Model for CASTELO

An unsolved challenge in the development of antigen-specific immunotherapies is determining the optimal antigens to target. Comprehension of antigen-major histocompatibility complex (MHC) binding is paramount toward achieving this goal. Here, we apply CASTELO, a combined machine learning-molecular dynamics (ML-MD) approach, to identify per-residue antigen binding contributions and then design novel antigens of increased MHC-II binding affinity for a type 1 diabetes-implicated system. We build upon a small-molecule lead optimization algorithm by training a convolutional variational autoencoder (CVAE) on MD trajectories of 48 different systems across four antigens and four HLA serotypes. We develop several new machine learning metrics including a structure-based anchor residue classification model as well as cluster comparison scores. ML-MD predictions agree well with experimental binding results and free energy perturbation-predicted binding affinities. Moreover, ML-MD metrics are independent of traditional MD stability metrics such as contact area and root-mean-square fluctuations (RMSF), which do not reflect binding affinity data. Our work supports the role of structure-based deep learning techniques in antigen-specific immunotherapy design.

Advancement of antigen-specific immunotherapy: knowledge transfer between allergy and autoimmunity.

SummaryTargeted restoration of immunological tolerance to self-antigens or innocuous environmental allergens represents the ultimate aim of treatment options in autoimmune and allergic disease. Antigen-specific immunotherapy (ASI) is the only intervention that has proven disease-modifying efficacy as evidenced by induction of long-term remission in a number of allergic conditions. Mounting evidence is now indicating that specific targeting of pathogenic T cells in autoinflammatory and autoimmune settings enables effective restoration of immune homeostasis between effector and regulatory cells and alters the immunological course of disease. Here, we discuss the key lessons learned during the development of antigen-specific immunotherapies and how these can be applied to inform future interventions. Armed with this knowledge and current high-throughput technology to track immune cell phenotype and function, it may no longer be a matter of ‘if’ but ‘when’ this ultimate aim of targeted tolerance restoration is realised.

Identification of neoantigens and development of antigen-specific immunotherapy

Cancer cells harboring somatic mutations give rise to neoantigens, which are immunologically foreign in nature to be distinguished from itself, showing high immunogenicity and, thus, induce specific T-cell responses against cancer. Therefore, neoantigens are expected to be promising targets for anti-cancer immunotherapy. The general methods used to identify candidate neoantigens are as follows: (1) non-synonymous mutations are identified by whole exome and RNA sequencing; (2) neoantigens from the mutations are predicted based on in silico MHC ligand prediction algorithm; (3) specific T-cell responses toward the candidate neoantigens are verified using tumor infiltrating T cells or peripheral blood mononuclear cells. In hematological malignancy, several neoantigens have been identified as an important treatment target. In contrast with solid malignancies, the occurrence of frameshift mutations and fusion genes producing neoantigens are high. A shared neoantigen derived from frameshift mutation of nucleophosmin I, which is often observed in acute myeloid leukemia, was reported to induce specific immune responses in vitro and in vivo. We should examine neoantigens as possible target of novel immunotherapy despite several issues to be addressed for clinical application.

Antigen-specific immunotherapies in rheumatic diseases.

The main goal of antigen-specific immunotherapy (ASI) in autoimmune and rheumatic diseases is to reprogramme or remove autoreactive cells and/or induce immune tolerance to self-antigens. Current therapies in these diseases either treat symptoms or slow down disease progression but are not yet curative or preventative - disease-specific treatments are urgently needed. In contrast to the nonspecific treatments in current use that induce generalized immune suppression, which is associated with several adverse effects including increased risk of infections, ASIs target a restricted subset of B cells or T cells, and thus do not compromise systemic immunity and host defence. This Review provides a summary of novel approaches for identifying autoepitopes and detecting and targeting autoreactive cells that might help in the development of ASIs. Promising approaches include the use of tolerizing peptides coupled to MHC constructs and/or nanocompounds, tolerizing dendritic cells and antigen-specific vaccines. Following studies in animal models of rheumatoid arthritis and systemic lupus erythematosus, several of these strategies have now entered clinical trials. However, to use these approaches in humans, several important limitations must first be addressed, such as; selecting the proper immunodominant autoantigen; identifying the optimal timing, dosing and route of administration; finding biomarkers for monitoring the therapy; and optimizing methodology.

Delineation of autoantibody repertoire through differential proteogenomics in hepatitis C virus-induced cryoglobulinemia.

Antibodies cross-reactive to pathogens and autoantigens are considered pivotal in both infection control and accompanying autoimmunity. However, the pathogenic roles of autoantibodies largely remain elusive without a priori knowledge of disease-specific autoantigens. Here, through a novel quantitative proteogenomics approach, we demonstrated a successful identification of immunoglobulin variable heavy chain (VH) sequences highly enriched in pathological immune complex from clinical specimens obtained from a patient with hepatitis C virus-induced cryoglobulinemia (HCV-CG). Reconstructed single-domain antibodies were reactive to both HCV antigens and potentially liver-derived human proteins. Moreover, over the course of antiviral therapy, a substantial “de-evolution” of a distinct sub-repertoire was discovered, to which proteomically identified cryoprecipitation-prone autoantibodies belonged. This sub-repertoire was characterized by IGHJ6*03-derived, long, hydrophobic complementarity determining region (CDR-H3). This study provides a proof-of-concept of de novo mining of autoantibodies and corresponding autoantigen candidates in a disease-specific context in human, thus facilitating future reverse-translational research for the discovery of novel biomarkers and the development of antigen-specific immunotherapy against various autoantibody-related disorders.

Natural killer cells facilitate PRAME-specific T-cell reactivity against neuroblastoma.

Neuroblastoma is the most common solid tumor in children with an estimated 5-year progression free survival of 20-40% in stage 4 disease. Neuroblastoma actively avoids recognition by natural killer (NK) cells and cytotoxic T lymphocytes (CTLs). Although immunotherapy has gained traction for neuroblastoma treatment, these immune escape mechanisms restrain clinical results. Therefore, we aimed to improve neuroblastoma immunogenicity to further the development of antigen-specific immunotherapy against neuroblastoma. We found that neuroblastoma cells significantly increase surface expression of MHC I upon exposure to active NK cells which thereby readily sensitize neuroblastoma cells for recognition by CTLs. We show that oncoprotein PRAME serves as an immunodominant antigen for neuroblastoma as NK-modulated neuroblastoma cells are recognized by PRAMESLLQHLIGL/A2-specific CTL clones. Furthermore, NK cells induce MHC I upregulation in neuroblastoma through contact-dependent secretion of IFNγ. Our results demonstrate remarkable plasticity in the peptide/MHC I surface expression of neuroblastoma cells, which is reversed when neuroblastoma cells experience innate immune attack by sensitized NK cells. These findings support the exploration of NK cells as adjuvant therapy to enforce neuroblastoma-specific CTL responses.

Prevention and treatment of allergic inflammation by an Fcγ-Der f2 fusion protein in a murine model of dust mite-induced asthma

The immunoglobulin E (IgE) high-affinity receptor FcεRI expressed on mast cells and basophils plays a critical role in triggering allergic disease. The co-aggregation of the FcεRI and FcγRIIb receptors is inhibitory to FcεRI signaling and holds great potential for the treatment of IgE-mediated allergies. In China, Dermatophagoides farinae is a common anaphylaxis trigger. Therefore, in this study, the FcγRIIb-mediated immunomodulating activity of recombinant Fcγ-Der f2 fusion protein was tested in a Der f2-allergic murine model. Following the treatment, bronchoalveolar lavage fluid (BALF) was collected to measure the expression of several Th1/Th2-type cytokines (IL-5, TNF-α, IL-12p70, IL-4, IL-10, IFN-γ and IL-18) and histamine, while blood was used to detect the specific IgE and IgG-types anti-Der f2 antibodies, for measurement. In contrast to the saline-treated allergic mice, the levels of Der f2-specific IgE, cytokines and histamine were lowered in the Fcγ-Der f2-treated allergic mice, in addition to the rare inflammatory cell infiltration in the airways and blood vessels revealed by histopathological examination. The recombinant Fcγ-Der f2 protein was demonstrated to function as an effective immunotherapeutic agent, suggesting that chimeric human Fcγ-allergen proteins could be used in the development of antigen-specific immunotherapy for human allergic diseases.

Cancer immunotherapy via dendritic cells

Cancer immunotherapy attempts to harness the power and specificity of the immune system to treat tumours. The molecular identification of human cancer-specific antigens has allowed the development of antigen-specific immunotherapy. In one approach, autologous antigen-specific T cells are expanded ex vivo and then re-infused into patients. Another approach is through vaccination; that is, the provision of an antigen together with an adjuvant to elicit therapeutic T cells in vivo. Owing to their properties, dendritic cells (DCs) are often called 'nature's adjuvants' and thus have become the natural agents for antigen delivery. After four decades of research, it is now clear that DCs are at the centre of the immune system owing to their ability to control both immune tolerance and immunity. Thus, DCs are an essential target in efforts to generate therapeutic immunity against cancer.

Recent approaches to the development of antigen-specific immunotherapies for myasthenia gravis

Acquired autoimmune myasthenia gravis (MG) is the most common disease that affects the neuromuscular junction (NMJ). MG is associated with autoantibodies (auto-Abs) to components of the NMJ. About 85–90% of MG patients have auto-Abs against the muscle nicotinic acetylcholine receptor (AChR), while about half of the remaining patients have auto-Abs against muscle-specific kinase. Auto-Abs, in combination with local deposition of complement, reduce the number of available post-synaptic nicotinic AChRs and thereby impair neuromuscular transmission. Current medications for MG are non-specific and include acetylcholinesterase inhibitors, immunosuppressants, plasma exchange, intravenous Ig administration and thymectomy. Treatments that selectively target the anti-AChR auto-Abs may prove to be more effective and free of side-effects. We here review two approaches aimed at the development of antigen-specific therapies for MG. The first is specific apheresis of Abs from patients' sera using immobilised recombinant AChR domains as immunoadsorbents. Indeed, we have recently shown that the combined recombinant extracellular domains of all human AChR subunits are capable of specifically immunoadsorbing the majority of pathogenic auto-Abs from several MG sera. The second therapeutic approach is the development of non-pathogenic anti-AChR monoclonal Abs that could potentially be used as protective agents by blocking the binding of patients' auto-Abs to the AChR.

Heat-shock protein 60 as a tool for novel therapeutic strategies that target the induction of regulatory T cells in human arthritis

In health, immune responses to self are abundantly available, but under strict control of mechanisms of peripheral tolerance. Occasionally the immune system loses control and an autoimmune disease develops. At present, treatment of autoimmune disease is based on generalised suppression of all immune responses, and is often needed to be lifelong, leading to long-term toxicities and suppression of protective immune responses against pathogens. A more targeted approach would be to reset the immune system via restoration of failing regulatory mechanisms, and redirect the immune system to a state of tolerance. Over the past decade there have been enormous advances in the understanding of basic processes that control immune tolerance, pushing regulatory T cells forward as targets for novel therapeutic strategies. This review describes the development of antigen-specific immunotherapy that targets the antigen-specific induction of regulatory T cells as a means to treat autoimmune disease. The ‘holy grail’ for autoimmunity is not the disease-causing antigen, but the disease-curing antigen.

Tumorantigen-Identifizierung: Strategien und klinische Perspektiven

The identification of tumor antigens is crucial for the development of antigen-specific immunotherapies in cancer. Ideal target antigens for immunotherapies have a tumor specific expresssion pattern. Antigen expresssion in solid tumors is typically heterogenous. Therefore an effective immunotherapy should target several antigens simultaneously (polyvalent vaccine). Here we discuss strategies how tumor antigens can be identified and further analyzed as potential target antigens for active immunotherapy (cancer vaccine).

Identification of the Main Immunogenic Region of Retinal S-Antigen: Subordinate Influence of MHC, IGH, Species or Strain Differences on the Specificity of the Antibody Response

The factors which lead to selection of dominant antigenic sites concentrated in discreet regions of proteins and polypeptides are important to the development of antigen-specific immunotherapies for autoimmune diseases and for vaccine design. In this study, the main immunogenic regions of the immunopathogenic autoantigen, retinal S-antigen, have been identified by examination of the specificity of antibody responses of different species. Using cyanogen bromide and synthetic peptides in western blots and the ELISA, the specificities of antisera from rabbits, guinea pigs, rats and 19 inbred strains of mice were tested. All animals produced high titers of antibody to S-antigen with the exception of PL/J mice. Antibodies which bound epitopes contained in peptide CB46, a 46 amino acid-containing peptide located at the C-terminus of S-antigen, were dominant in all species and strains tested. The epitopes in CB46 were multiple, overlapping, and concentrated in a stretch of approximately 30 residues. Two overlapping synthetic peptides from that region substantially competed the anti-CB46 response of all animals. Antibodies which recognized peptide CB47, a 47 residue peptide from the N-terminus, comprised the next most common group. This epitope was similar in all mice and overlapped the epitope defined by rat antibodies. All anti-CB47 antibodies mapped to an 11 residue region of CB47. Eleven strains of mice did not respond to CB47 after one immunization with S-antigen; however, multiple immunizations readily converted all animals so tested to CB47 responders. Rabbits and guinea pigs exhibited very weak responses to CB47 following one immunization; multiple immunizations increased the response minimally. Rats produced a strong antibody response to peptide CB123, which contains the known uveitogenic sites, while very little activity to CB123 was raised in rabbits and guinea pigs. Only 3 murine strains, LP, LP.R3, and B10.R3-71, responded with antibodies to CB123 and the epitope was mapped to a 30 residue region which in rats also contains two distinct pathogenic sites and an antibody epitope. Only rats and rabbits made antibody to the CB35 peptide; the epitopes were contained within an 18 residue sequence. The results show that a main immunogenic region is located in S-antigen near the C-terminus and is independent of species or MHC. Less dominant, species and strain-dependent immunogenic regions were found in three other areas, i.e. peptides CB47, CB123 and CB35.