Playing hide and seek: tumor cells in control of MHC class I antigen presentation

MHC class I (MHC-I) molecules present a blueprint of the intracellular proteome to T cells allowing them to control infection or malignant transformation. As a response, pathogens and tumor cells often downmodulate MHC-I mediated antigen presentation to escape from immune surveillance. Although the fundamental rules of antigen presentation are known in detail, the players in this system are not saturated and new modules of regulation have recently been uncovered. Here, we update the understanding of antigen presentation by MHC-I molecules and how this can be exploited by tumors to prevent exposure of the intracellular proteome. This knowledge can provide new ways to improve immune responses against tumors and pathogens.Chemical Immunolog

T cells expanded from renal cell carcinoma display tumor-specific CD137 expression but lack significant IFN-gamma, TNF-alpha or IL-2 production

Metastatic renal cell carcinoma (RCC) has a poor prognosis. Recent advances have shown beneficial responses to immune checkpoint inhibitors, such as anti-PD-1/PD-L1 antibodies. As only a subset of RCC patients respond, alternative strategies should be explored. Patients refractory to anti-PD-1 therapy may benefit from autologous tumor-infiltrating lymphocyte (TIL) therapy. Even though efficient TIL expansion was reported from RCC lesions, it is not well established how many RCC TIL products are tumor-reactive, how well they produce pro-inflammatory cytokines in response to autologous tumors, and whether their response correlates with the presence of specific immune cells in the tumor lesions. We here compared the immune infiltrate composition of RCC lesions with that of autologous kidney tissue of 18 RCC patients. Tcell infiltrates were increased in the tumor lesions, and CD8(+) Tcell infiltrates were primarily of effector memory phenotype. Nine out of 16 (56%) tested TIL products we generated were tumor-reactive, as defined by CD137 upregulation after exposure to autologous tumor digest. Tumor reactivity was found in particular in TIL products originating from tumors with ahigh percentage of infiltrated Tcells compared to autologous kidney, and increased CD25 expression on CD8(+) Tcells. Importantly, although TIL products had the capacity to produce the key effector cytokines IFN-gamma, TNF-alpha or IL-2, they failed to produce significant amounts in response to autologous tumor digests. In conclusion, TIL products from RCC lesions contain tumor-reactive Tcells. Their restricted tumor-specific cytokine production requires further investigation of immunosuppressive factors in RCC and subsequent optimization of RCC-derived TIL culture conditions.Immunobiology of allogeneic stem cell transplantation and immunotherapy of hematological disease

Healthy cells functionally present TAP-independent SSR1 peptides: implications for selection of clinically relevant antigens

Tumors with an impaired transporter associated with antigen processing (TAP) present several endoplasmic reticulum-derived self-antigens on HLA class I (HLA-I) which are absent on healthy cells. Selection of such TAP-independent antigens for T cell-based immunotherapy should include analysis of their expression on healthy cells to prevent therapy-induced adverse toxicities. However, it is unknown how the absence of clinically relevant antigens on healthy cells needs to be validated. Here, we monitored TAP-independent antigen presentation on various healthy cells after establishing a T cell tool recognizing a TAP-independent signal sequence receptor 1-derived antigen. We found that most but not all healthy cells present this antigen under normal and inflammatory conditions, indicating that TAP-independent antigen presentation is a variable phenomenon. Our data emphasize the necessity of extensive testing of a wide variety of healthy cell types to define clinically relevant TAP-independent antigens that can be safely targeted by immunotherapy.Immunobiology of allogeneic stem cell transplantation and immunotherapy of hematological disease

PAKC: a novel panel of HLA class I antigen presentation machinery knockout cells from the same genetic origin

A single model system for integrative studies on multiple facets of antigen presentation is lacking. PAKC is a novel panel of ten cell lines knocked out for individual components of the HLA class I antigen presentation pathway. PAKC will accelerate HLA-I research in the fields of oncology, infectiology, and autoimmunity.Proteomic

The SPPL3-defined glycosphingolipid repertoire orchestrates HLA class I-mediated immune responses (vol 54, 132.e1, 2021)

Chemical Immunolog

Novel strategies for identification and therapeutic application of minor histocompatibility antigens

T cells recognizing the highly immunogenic minor histocompatibility antigens (mHags) expressed by hematopoietic and tumor cells may be powerful tools in the battle against hematological malignancies. However, mHag-specific immunotherapy is still in its infancy, since currently only few clinically useful mHags are identified, and since the exploration of T cell based immunotherapy for the treatment of cancer was initiated only a decade ago. The scope of thesis is to tackle these issues by 1) identifying and facilitating the identification of novel clinically relevant mHags and 2) investigating the immunotherapeutic potential of mHag-specific CD4+ T cells in vitro as well as in a preclinical murine model. The thesis describes the identification of the first HLA class II-restricted mHag with a truly hematopoietic tissue expression. The mHag is encoded by the CD19 gene, which is not only highly expressed on B cells, but also on their malignant derivatives. The identification of the CD19-derived mHag is performed using a novel genetic fine-mapping strategy, called zygosity-genotype correlation analysis. The genome-wide application of this strategy is easy and rapid as we demonstrate with the molecular characterization of the novel SLC19A1-derived mHag. In addition, we also outline a directed strategy to make significant progress toward wide scale application of mHag-specific immunotherapy. Furthermore, we utilize the rationale behind this directed strategy towards the identification of new mHags using a reverse identification approach. We describe the advantages of reverse identification and provide an extensive list of putative mHags that are predicted using reliable antigen-processing and HLA-binding algorithms combined with databases containing all currently known genes and genotyped SNPs. The second part of the thesis shows the feasibility of transferring a TCR derived from mHag-specific CD4+ human T cells into recall antigen (tetanus toxoid; TT)-specific CD4+ T cells. The TCR-transgenic cells acquire mHag specificity, and expand efficiently in vitro via stimulation of their intrinsic TT-specific TCR. Next, similar dual-specific T cells as well as the parent mHag-specific T cells are used as sole treatment for established multiple myeloma tumors in immunodeficient mice. This adoptive immunotherapy with sole mHag-specific CD4+ T cells is very effective against tumor in the bone marrow. However, the mice suffer from extramedullary tumor relapses, which are in vitro but not in vivo susceptible to further T cell therapy. These results seem also relevant for the clinic, since the relapse of multiple myeloma at extramedullary sites is a known complication in patients treated with DLI. Finally, the discussion describes how the current findings may contribute to the improvement of immunotherapeutic strategies based on mHag-specific (CD4+) T cells

The regulatory network behind MHC class I expression.

The MHC class I pathway, presenting endogenously derived peptides to T lymphocytes, is hijacked in many pathological conditions. This affects MHC class I levels and peptide presentation at the cell surface leading to immune escape of cancer cells or microbes. It is therefore important to identify the molecular mechanisms behind MHC class I expression, processing and antigen presentation. The identification of NLRC5 as regulator of MHC class I transcription was a huge step forward in understanding the transcriptional mechanism involved. Nevertheless, many questions concerning MHC class I transcription are yet unsolved. Here we illuminate current knowledge on MHC class I and NLRC5 transcription, we highlight some remaining questions and discuss the use of quickly developing high-content screening tools to reveal unknowns in MHC class I transcription in the near future

The Role of Glycosphingolipids in Immune Cell Functions

Proteomic

An unexplored angle: T cell antigen discoveries reveal a marginal contribution of proteasome splicing to the immunogenic MHC class I antigen pool

In the current era of T cell-based immunotherapies, it is crucial to understand which types of MHC-presented T cell antigens are produced by tumor cells. In addition to linear peptide antigens, chimeric peptides are generated through proteasome-catalyzed peptide splicing (PCPS). Whether such spliced peptides are abundantly presented by MHC is highly disputed because of disagreement in computational analyses of mass spectrometry data of MHC-eluted peptides. Moreover, such mass spectrometric analyses cannot elucidate how much spliced peptides contribute to the pool of immunogenic antigens. In this Perspective, we explain the significance of knowing the contribution of spliced peptides for accurate analyses of peptidomes on one hand, and to serve as a potential source of targetable tumor antigens on the other hand. Toward a strategy for mass spectrometry independent estimation of the contribution of PCPS to the immunopeptidome, we first reviewed methodologies to identify MHC-presented spliced peptide antigens expressed by tumors. Data from these identifications allowed us to compile three independent datasets containing 103, 74, and 83 confirmed T cell antigens from cancer patients. Only 3.9%, 1.4%, and between 0% and 7.2% of these truly immunogenic antigens are produced by PCPS, therefore providing a marginal contribution to the pool of immunogenic tumor antigens. We conclude that spliced peptides will not serve as a comprehensive source to expand the number of targetable antigens for immunotherapies.</p