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1.
Cancer Immunol Res ; 11(7): 925-945, 2023 07 05.
Article in English | MEDLINE | ID: mdl-37172100

ABSTRACT

IMA101 is an actively personalized, multi-targeted adoptive cell therapy (ACT), whereby autologous T cells are directed against multiple novel defined peptide-HLA (pHLA) cancer targets. HLA-A*02:01-positive patients with relapsed/refractory solid tumors expressing ≥1 of 8 predefined targets underwent leukapheresis. Endogenous T cells specific for up to 4 targets were primed and expanded in vitro. Patients received lymphodepletion (fludarabine, cyclophosphamide), followed by T-cell infusion and low-dose IL2 (Cohort 1). Patients in Cohort 2 received atezolizumab for up to 1 year (NCT02876510). Overall, 214 patients were screened, 15 received lymphodepletion (13 women, 2 men; median age, 44 years), and 14 were treated with T-cell products. IMA101 treatment was feasible and well tolerated. The most common adverse events were cytokine release syndrome (Grade 1, n = 6; Grade 2, n = 4) and expected cytopenias. No patient died during the first 100 days after T-cell therapy. No neurotoxicity was observed. No objective responses were noted. Prolonged disease stabilization was noted in three patients lasting for 13.7, 12.9, and 7.3 months. High frequencies of target-specific T cells (up to 78.7% of CD8+ cells) were detected in the blood of treated patients, persisted for >1 year, and were detectable in posttreatment tumor tissue. Individual T-cell receptors (TCR) contained in T-cell products exhibited broad variation in TCR avidity, with the majority being low avidity. High-avidity TCRs were identified in some patients' products. This study demonstrates the feasibility and tolerability of an actively personalized ACT directed to multiple defined pHLA cancer targets. Results warrant further evaluation of multi-target ACT approaches using potent high-avidity TCRs. See related Spotlight by Uslu and June, p. 865.


Subject(s)
Immunotherapy, Adoptive , Neoplasms , Adult , Female , Humans , Male , CD8-Positive T-Lymphocytes , Feasibility Studies , Immunotherapy, Adoptive/adverse effects , Immunotherapy, Adoptive/methods , Neoplasms/therapy , Neoplasms/etiology , Receptors, Antigen, T-Cell/genetics
2.
Sci Transl Med ; 14(660): eabo6135, 2022 08 31.
Article in English | MEDLINE | ID: mdl-36044599

ABSTRACT

T cell receptor (TCR)-based immunotherapy has emerged as a promising therapeutic approach for the treatment of patients with solid cancers. Identifying peptide-human leukocyte antigen (pHLA) complexes highly presented on tumors and rarely expressed on healthy tissue in combination with high-affinity TCRs that when introduced into T cells can redirect T cells to eliminate tumor but not healthy tissue is a key requirement for safe and efficacious TCR-based therapies. To discover promising shared tumor antigens that could be targeted via TCR-based adoptive T cell therapy, we employed population-scale immunopeptidomics using quantitative mass spectrometry across ~1500 tumor and normal tissue samples. We identified an HLA-A*02:01-restricted pan-cancer epitope within the collagen type VI α-3 (COL6A3) gene that is highly presented on tumor stroma across multiple solid cancers due to a tumor-specific alternative splicing event that rarely occurs outside the tumor microenvironment. T cells expressing natural COL6A3-specific TCRs demonstrated only modest activity against cells presenting high copy numbers of COL6A3 pHLAs. One of these TCRs was affinity-enhanced, enabling transduced T cells to specifically eliminate tumors in vivo that expressed similar copy numbers of pHLAs as primary tumor specimens. The enhanced TCR variants exhibited a favorable safety profile with no detectable off-target reactivity, paving the way to initiate clinical trials using COL6A3-specific TCRs to target an array of solid tumors.


Subject(s)
Immunotherapy, Adoptive , Receptors, Antigen, T-Cell , T-Lymphocytes , Antigens, Neoplasm , Cell Line, Tumor , Cell- and Tissue-Based Therapy , Humans , Immunotherapy, Adoptive/methods , Proteomics , Receptors, Antigen, T-Cell/metabolism , Receptors, Antigen, T-Cell/therapeutic use
3.
Mol Cell Proteomics ; 20: 100110, 2021.
Article in English | MEDLINE | ID: mdl-34129939

ABSTRACT

Knowledge about the peptide repertoire presented by human leukocyte antigens (HLA) holds the key to unlock target-specific cancer immunotherapies such as adoptive cell therapies or bispecific T cell engaging receptors. Therefore, comprehensive and accurate characterization of HLA peptidomes by mass spectrometry (immunopeptidomics) across tissues and disease states is essential. With growing numbers of immunopeptidomics datasets and the scope of peptide identification strategies reaching beyond the canonical proteome, the likelihood for erroneous peptide identification as well as false annotation of HLA-independent peptides as HLA ligands is increasing. Such "fake ligands" can lead to selection of nonexistent targets for immunotherapeutic development and need to be recognized as such as early as possible in the preclinical pipeline. Here we present computational and experimental methods that enable the identification of "fake ligands" that might be introduced at different steps of the immunopeptidomics workflow. The statistics presented herein allow discrimination of true HLA ligands from coisolated HLA-independent proteolytic fragments. In addition, we describe necessary steps to ensure system suitability of the chromatographic system. Furthermore, we illustrate an algorithm for detection of source fragmentation events that are introduced by electrospray ionization during mass spectrometry. For confirmation of peptide sequences, we present an experimental pipeline that enables high-throughput sequence verification through similarity of fragmentation pattern and coelution of synthetic isotope-labeled internal standards. Based on these methods, we show the overall high quality of existing datasets but point out limitations and pitfalls critical for individual peptides and how they can be uncovered in order to identify true ligands.


Subject(s)
HLA Antigens , Peptides , Humans , Ligands , Proteolysis , Proteome , Proteomics
5.
Nature ; 565(7738): 240-245, 2019 01.
Article in English | MEDLINE | ID: mdl-30568303

ABSTRACT

Patients with glioblastoma currently do not sufficiently benefit from recent breakthroughs in cancer treatment that use checkpoint inhibitors1,2. For treatments using checkpoint inhibitors to be successful, a high mutational load and responses to neoepitopes are thought to be essential3. There is limited intratumoural infiltration of immune cells4 in glioblastoma and these tumours contain only 30-50 non-synonymous mutations5. Exploitation of the full repertoire of tumour antigens-that is, both unmutated antigens and neoepitopes-may offer more effective immunotherapies, especially for tumours with a low mutational load. Here, in the phase I trial GAPVAC-101 of the Glioma Actively Personalized Vaccine Consortium (GAPVAC), we integrated highly individualized vaccinations with both types of tumour antigens into standard care to optimally exploit the limited target space for patients with newly diagnosed glioblastoma. Fifteen patients with glioblastomas positive for human leukocyte antigen (HLA)-A*02:01 or HLA-A*24:02 were treated with a vaccine (APVAC1) derived from a premanufactured library of unmutated antigens followed by treatment with APVAC2, which preferentially targeted neoepitopes. Personalization was based on mutations and analyses of the transcriptomes and immunopeptidomes of the individual tumours. The GAPVAC approach was feasible and vaccines that had poly-ICLC (polyriboinosinic-polyribocytidylic acid-poly-L-lysine carboxymethylcellulose) and granulocyte-macrophage colony-stimulating factor as adjuvants displayed favourable safety and strong immunogenicity. Unmutated APVAC1 antigens elicited sustained responses of central memory CD8+ T cells. APVAC2 induced predominantly CD4+ T cell responses of T helper 1 type against predicted neoepitopes.


Subject(s)
Cancer Vaccines/immunology , Cancer Vaccines/therapeutic use , Glioblastoma/diagnosis , Glioblastoma/therapy , Precision Medicine/methods , Adult , Aged , Antigens, Neoplasm/immunology , CD8-Positive T-Lymphocytes/immunology , Epitopes, T-Lymphocyte/immunology , Female , Glioblastoma/immunology , HLA-A Antigens/immunology , Humans , Immunologic Memory/immunology , Male , Middle Aged , T-Lymphocytes, Helper-Inducer/immunology , Treatment Outcome
6.
Nat Commun ; 9(1): 3919, 2018 09 25.
Article in English | MEDLINE | ID: mdl-30254248

ABSTRACT

In addition to genomic mutations, RNA editing is another major mechanism creating sequence variations in proteins by introducing nucleotide changes in mRNA sequences. Deregulated RNA editing contributes to different types of human diseases, including cancers. Here we report that peptides generated as a consequence of RNA editing are indeed naturally presented by human leukocyte antigen (HLA) molecules. We provide evidence that effector CD8+ T cells specific for edited peptides derived from cyclin I are present in human tumours and attack tumour cells that are presenting these epitopes. We show that subpopulations of cancer patients have increased peptide levels and that levels of edited RNA correlate with peptide copy numbers. These findings demonstrate that RNA editing extends the classes of HLA presented self-antigens and that these antigens can be recognised by the immune system.


Subject(s)
Antigens, Neoplasm/immunology , Epitopes/immunology , Immune System/immunology , Neoplasms/immunology , RNA Editing/immunology , Antigen Presentation/immunology , CD8-Positive T-Lymphocytes/immunology , CD8-Positive T-Lymphocytes/metabolism , Cell Line, Tumor , Cells, Cultured , Cyclin I/genetics , Cyclin I/immunology , Cyclin I/metabolism , Cytotoxicity, Immunologic/immunology , HLA Antigens/immunology , Humans , Neoplasms/genetics , Neoplasms/metabolism , Peptides/genetics , Peptides/immunology , Peptides/metabolism , Proteogenomics/methods
7.
Proteomics ; 18(12): e1700284, 2018 06.
Article in English | MEDLINE | ID: mdl-29505699

ABSTRACT

Immunotherapy is revolutionizing cancer treatment and has shown success in particular for tumors with a high mutational load. These effects have been linked to neoantigens derived from patient-specific mutations. To expand efficacious immunotherapy approaches to the vast majority of tumor types and patient populations carrying only a few mutations and maybe not a single presented neoepitope, it is necessary to expand the target space to non-mutated cancer-associated antigens. Mass spectrometry enables the direct and unbiased discovery and selection of tumor-specific human leukocyte antigen (HLA) peptides that can be used to define targets for immunotherapy. Combining these targets into a warehouse allows for multi-target therapy and accelerated clinical application. For precise personalization aimed at optimally ensuring treatment efficacy and safety, it is necessary to assess the presence of the target on each individual patient's tumor. Here we show how LC-MS paired with gene expression data was used to define mRNA biomarkers currently being used as diagnostic test IMADETECT™ for patient inclusion and personalized target selection within two clinical trials (NCT02876510, NCT03247309). Thus, we present a way how to translate HLA peptide presentation into gene expression thresholds for companion diagnostics in immunotherapy considering the peptide-specific correlation to its encoding mRNA.


Subject(s)
Antigens, Neoplasm/metabolism , HLA Antigens/metabolism , Immunotherapy , Neoplasms/metabolism , Peptide Fragments/metabolism , Precision Medicine , Proteogenomics/methods , Antigen Presentation/immunology , Antigens, Neoplasm/analysis , Antigens, Neoplasm/immunology , Decision Making , Epitopes/immunology , Epitopes/metabolism , HLA Antigens/analysis , HLA Antigens/immunology , High-Throughput Nucleotide Sequencing , Humans , Mass Spectrometry/methods , Neoplasms/immunology , Peptide Fragments/analysis , Peptide Fragments/immunology , RNA, Messenger/analysis , RNA, Messenger/genetics , RNA, Messenger/immunology
8.
Clin Cancer Res ; 22(19): 4776-4785, 2016 Oct 01.
Article in English | MEDLINE | ID: mdl-27225692

ABSTRACT

PURPOSE: To perform a two-cohort, phase I safety and immunogenicity study of IMA950 in addition to standard chemoradiotherapy and adjuvant temozolomide in patients with newly diagnosed glioblastoma. IMA950 is a novel glioblastoma-specific therapeutic vaccine containing 11 tumor-associated peptides (TUMAP), identified on human leukocyte antigen (HLA) surface receptors in primary human glioblastoma tissue. EXPERIMENTAL DESIGN: Patients were HLA-A*02-positive and had undergone tumor resection. Vaccination comprised 11 intradermal injections with IMA950 plus granulocyte macrophage colony-stimulating factor (GM-CSF) over a 24-week period, beginning 7 to 14 days prior to initiation of chemoradiotherapy (Cohort 1) or 7 days after chemoradiotherapy (Cohort 2). Safety was assessed according to NCI CTCAE Version 4.0 and TUMAP-specific T-cell immune responses determined. Secondary observations included progression-free survival (PFS), pretreatment regulatory T cell (Treg) levels, and the effect of steroids on T-cell responses. RESULTS: Forty-five patients were recruited. Related adverse events included minor injection site reactions, rash, pruritus, fatigue, neutropenia and single cases of allergic reaction, anemia and anaphylaxis. Two patients experienced grade 3 dose-limiting toxicity of fatigue and anaphylaxis. Of 40 evaluable patients, 36 were TUMAP responders and 20 were multi-TUMAP responders, with no important differences between cohorts. No effect of pretreatment Treg levels on IMA950 immunogenicity was observed, and steroids did not affect TUMAP responses. PFS rates were 74% at 6 months and 31% at 9 months. CONCLUSIONS: IMA950 plus GM-CSF was well-tolerated with the primary immunogenicity endpoint of observing multi-TUMAP responses in at least 30% of patients exceeded. Further development of IMA950 is encouraged. Clin Cancer Res; 22(19); 4776-85. ©2016 AACRSee related commentary by Lowenstein and Castro, p. 4760.


Subject(s)
Brain Neoplasms/drug therapy , Cancer Vaccines/therapeutic use , Glioblastoma/drug therapy , Peptides/therapeutic use , Adult , Aged , Antigens, Neoplasm/immunology , Antigens, Neoplasm/therapeutic use , Antineoplastic Agents/therapeutic use , Brain Neoplasms/mortality , Chemoradiotherapy/methods , Disease-Free Survival , Female , Glioblastoma/mortality , Humans , Kaplan-Meier Estimate , Lymphocyte Activation/drug effects , Male , Middle Aged , T-Lymphocytes/drug effects , United Kingdom , Young Adult
9.
J Neurooncol ; 111(3): 285-94, 2013 Feb.
Article in English | MEDLINE | ID: mdl-23263746

ABSTRACT

Glioblastoma multiforme is the most frequent and most malignant primary brain tumor with poor prognosis despite surgical removal and radio-chemotherapy. In this setting, immunotherapeutical strategies have great potential, but the reported repertoire of tumor associated antigens is only for HLA-A 02 positive tumors. We describe the first analysis of HLA-peptide presentation patterns in HLA-A 02 negative glioma tissue combined with gene expression profiling of the tumor samples by oligonucleotide microarrays. We identified numerous candidate peptides for immunotherapy. These are peptides derived from proteins with a well-described role in glioma tumor biology and suitable gene expression profiles such as PTPRZ1, EGFR, SEC61G and TNC. Information obtained from complementary analyses of HLA-A 02 negative tumors not only contributes to the discovery of novel shared glioma antigens, but most importantly provides the opportunity to tailor a patient-individual cocktail of tumor-associated peptides for a personalized, targeted immunotherapeutic approach in HLA-A 02 negative patients.


Subject(s)
Brain Neoplasms/pathology , Gene Expression Regulation, Neoplastic/physiology , Glioblastoma/pathology , HLA Antigens/metabolism , Brain Neoplasms/classification , Brain Neoplasms/metabolism , ErbB Receptors/metabolism , Glial Fibrillary Acidic Protein/metabolism , Glioblastoma/classification , Glioblastoma/metabolism , Humans , Ligands , Membrane Proteins/metabolism , Peptides/metabolism , Receptor-Like Protein Tyrosine Phosphatases, Class 5/metabolism , SEC Translocation Channels , Tandem Mass Spectrometry
10.
Nat Med ; 18(8): 1254-61, 2012 Aug.
Article in English | MEDLINE | ID: mdl-22842478

ABSTRACT

IMA901 is the first therapeutic vaccine for renal cell cancer (RCC) consisting of multiple tumor-associated peptides (TUMAPs) confirmed to be naturally presented in human cancer tissue. We treated a total of 96 human leukocyte antigen A (HLA-A)*02(+) subjects with advanced RCC with IMA901 in two consecutive studies. In the phase 1 study, the T cell responses of the patients to multiple TUMAPs were associated with better disease control and lower numbers of prevaccine forkhead box P3 (FOXP3)(+) regulatory T (T(reg)) cells. The randomized phase 2 trial showed that a single dose of cyclophosphamide reduced the number of T(reg) cells and confirmed that immune responses to multiple TUMAPs were associated with longer overall survival. Furthermore, among six predefined populations of myeloid-derived suppressor cells, two were prognostic for overall survival, and among over 300 serum biomarkers, we identified apolipoprotein A-I (APOA1) and chemokine (C-C motif) ligand 17 (CCL17) as being predictive for both immune response to IMA901 and overall survival. A randomized phase 3 study to determine the clinical benefit of treatment with IMA901 is ongoing.


Subject(s)
Cancer Vaccines/therapeutic use , Carcinoma, Renal Cell/therapy , Cyclophosphamide/therapeutic use , Immunosuppressive Agents/therapeutic use , Immunotherapy, Active , Kidney Neoplasms/therapy , T-Lymphocytes, Regulatory/immunology , Vaccines, Subunit/therapeutic use , Antigens, Neoplasm/immunology , Apolipoprotein A-I/blood , Biomarkers , CD8-Positive T-Lymphocytes/immunology , Carcinoma, Renal Cell/blood , Carcinoma, Renal Cell/drug therapy , Carcinoma, Renal Cell/immunology , Chemokine CCL17/blood , Combined Modality Therapy , Cyclophosphamide/administration & dosage , Cyclophosphamide/pharmacology , Female , Granulocyte-Macrophage Colony-Stimulating Factor/therapeutic use , HLA-A2 Antigen/immunology , Humans , Immunosuppressive Agents/administration & dosage , Immunosuppressive Agents/pharmacology , Kaplan-Meier Estimate , Kidney Neoplasms/blood , Kidney Neoplasms/drug therapy , Kidney Neoplasms/immunology , Lymphocyte Depletion , Male , Middle Aged , Predictive Value of Tests , Prognosis , T-Lymphocytes, Regulatory/drug effects , Treatment Outcome
11.
Brain ; 135(Pt 4): 1042-54, 2012 Apr.
Article in English | MEDLINE | ID: mdl-22418738

ABSTRACT

Peptides presented at the cell surface reflect the protein content of the cell; those on HLA class I molecules comprise the critical peptidome elements interacting with CD8 T lymphocytes. We hypothesize that peptidomes from ex vivo tumour samples encompass immunogenic tumour antigens. Here, we uncover >6000 HLA-bound peptides from HLA-A*02(+) glioblastoma, of which over 3000 were restricted by HLA-A*02. We prioritized in-depth investigation of 10 glioblastoma-associated antigens based on high expression in tumours, very low or absent expression in healthy tissues, implication in gliomagenesis and immunogenicity. Patients with glioblastoma showed no T cell tolerance to these peptides. Moreover, we demonstrated specific lysis of tumour cells by patients' CD8(+) T cells in vitro. In vivo, glioblastoma-specific CD8(+) T cells were present at the tumour site. Overall, our data show the physiological relevance of the peptidome approach and provide a critical advance for designing a rational glioblastoma immunotherapy. The peptides identified in our study are currently being tested as a multipeptide vaccine (IMA950) in patients with glioblastoma.


Subject(s)
Antigens, Neoplasm/immunology , Brain Neoplasms/immunology , Glioblastoma/immunology , Peptides/immunology , Antigen Presentation/physiology , Antigens, CD/metabolism , Antigens, Neoplasm/chemistry , Antigens, Neoplasm/therapeutic use , Brain Neoplasms/pathology , Brain Neoplasms/therapy , CD8-Positive T-Lymphocytes/immunology , Chromatography, Liquid , Cytokines/metabolism , Flow Cytometry , Gene Expression Profiling , Glial Fibrillary Acidic Protein/metabolism , Glioblastoma/pathology , Glioblastoma/therapy , HLA-A Antigens/analysis , HLA-A Antigens/chemistry , HLA-A Antigens/immunology , Humans , Mass Spectrometry , Oligonucleotide Array Sequence Analysis , Peptides/analysis , Platelet Endothelial Cell Adhesion Molecule-1/metabolism , RNA, Messenger/metabolism , Receptor-Like Protein Tyrosine Phosphatases, Class 5/metabolism , Sequence Analysis, Protein
12.
Cancer Res ; 68(7): 2447-54, 2008 Apr 01.
Article in English | MEDLINE | ID: mdl-18381453

ABSTRACT

Vascular endothelial growth factor (VEGF) is involved in various physiologic processes, such as angiogenesis or wound healing, but is also crucial in pathologic events, such as tumor growth. Thus, clinical anti-VEGF treatments have been developed that could already show beneficial effects for cancer patients. In this article, we describe the first VEGF-derived CD8(+) T-cell epitope. The natural HLA ligand SRFGGAVVR was identified by differential mass spectrometry in two primary renal cell carcinomas (RCC) and was significantly overpresented on both tumor tissues. SRFGGAVVR is derived from a cryptic translated region of VEGF presumably by initiation of translation at the nonclassic start codon CUG(499). SRFGGAVVR-specific T cells were generated in vitro using peptide-loaded dendritic cells or artificial antigen-presenting cells. SRFGGAVVR-specific CD8(+) T cells, identified by HLA tetramer analysis after in vitro stimulation, were fully functional T effector cells, which were able to secrete IFN-gamma on stimulation and killed tumor cells in vitro. Additionally, we have quantitatively analyzed VEGF mRNA and protein levels in RCC tumor and normal tissue samples by gene chip analysis, quantitative reverse transcription-PCR, in situ hybridization, and bead-based immunoassay. In the future, T cells directed against VEGF as a tumor-associated antigen may represent a possible way of combining peptide-based anti-VEGF immunotherapy with already existent anti-VEGF cancer therapies.


Subject(s)
CD8-Positive T-Lymphocytes/immunology , Epitopes, T-Lymphocyte/immunology , Vascular Endothelial Growth Factor A/immunology , Amino Acid Sequence , Animals , Carcinoma, Renal Cell/genetics , Carcinoma, Renal Cell/immunology , Dendritic Cells/immunology , HLA Antigens/immunology , Humans , Kidney Neoplasms/genetics , Kidney Neoplasms/immunology , Mice , Molecular Sequence Data , Multiple Myeloma/genetics , Multiple Myeloma/immunology , Peptide Fragments/immunology , RNA, Messenger/biosynthesis , RNA, Messenger/genetics , Reverse Transcriptase Polymerase Chain Reaction , Spectrometry, Mass, Electrospray Ionization/methods , Transfection , Vascular Endothelial Growth Factor A/biosynthesis , Vascular Endothelial Growth Factor A/genetics
13.
Mol Cell Proteomics ; 6(1): 102-13, 2007 Jan.
Article in English | MEDLINE | ID: mdl-17074750

ABSTRACT

The major histocompatibility complex (MHC) presents peptides derived from degraded cellular proteins to T-cells and is thus crucial for triggering specific immune responses against viral infections or cancer. Up to now, there has been no evidence for a correlation between levels of mRNA (the "transcriptome") and the density of MHC-peptide complexes (the "MHC ligandome") on cells. Because such dependences are of intrinsic importance for the detailed understanding of translation efficiency and protein turnover and thus for systems biology in general and for tumor immunotherapy in practical application, we quantitatively analyzed the levels of mRNA and corresponding MHC ligand densities in samples of renal cell carcinomas and their autologous normal kidney tissues. Relative quantification was carried out by gene chip analysis and by stable isotope peptide labeling, respectively. In comparing more than 270 pairs of gene expression and corresponding peptide presentation ratios, we demonstrate that there is no clear correlation (r = 0.32) between mRNA levels and corresponding MHC peptide levels in renal cell carcinoma. A significant number of peptides presented predominantly on tumor or normal tissue showed no or only minor changes in mRNA expression levels. In several cases, peptides could even be identified despite the virtual absence of the respective mRNA. Thus we conclude that a majority of epitopes from tumor-associated antigens will not be found in approaches based mainly on mRNA expression studies as mRNA expression reflects a distorted picture of the situation on the cell surface as visible for T-cells.


Subject(s)
Gene Dosage , Kidney/cytology , Kidney/pathology , Major Histocompatibility Complex/immunology , RNA, Messenger/genetics , Amino Acid Sequence , Antigen Presentation/genetics , HLA Antigens/chemistry , Humans , Ligands , Molecular Sequence Data , Oligonucleotide Array Sequence Analysis , Peptides/analysis , Peptides/chemistry , RNA, Messenger/analysis
14.
Clin Cancer Res ; 12(14 Pt 1): 4163-70, 2006 Jul 15.
Article in English | MEDLINE | ID: mdl-16857787

ABSTRACT

PURPOSE: To elicit a long-lasting antitumor immune response, CD8+ and CD4+ T cells should be activated. We attempted to isolate HLA-DR-presented peptides directly from dissected solid tumors, in particular from renal cell carcinoma, to identify MHC class II ligands from tumor-associated antigens (TAA) for their use in peptide-based immunotherapy. EXPERIMENTAL DESIGN: Tumor specimens were analyzed by immunohistochemical staining for their HLA class II expression. HLA class II peptides were subsequently isolated and identified by mass spectrometry. Gene expression analysis was done to detect genes overexpressed in tumor tissue. Peptides from identified TAAs were used to induce peptide-specific CD4+ T-cell responses in healthy donors and in tumor patients. RESULTS: In the absence of inflammation, expression of MHC class II molecules is mainly restricted to cells of the immune system. To our surprise, we were able to isolate and characterize hundreds of class II peptides directly from primary dissected solid tumors, especially from renal cell carcinomas, and from colorectal carcinomas and transitional cell carcinomas. Infiltrating leukocytes expressed MHC class II molecules and tumor cells, very likely under the influence of IFNgamma. Our list of identified peptides contains ligands from several TAAs, including insulin-like growth factor binding protein 3 and matrix metalloproteinase 7. The latter bound promiscuously to HLA-DR molecules and were able to elicit CD4+ T-cell responses. CONCLUSIONS: Thus, our direct approach will rapidly expand the limited number of T-helper epitopes from TAAs for their use in clinical vaccination protocols.


Subject(s)
Carcinoma, Renal Cell/immunology , Gene Expression Regulation, Neoplastic , Histocompatibility Antigens Class II/immunology , Kidney Neoplasms/immunology , Peptides/chemistry , Antigens, Neoplasm/chemistry , CD4-Positive T-Lymphocytes/metabolism , CD8-Positive T-Lymphocytes/metabolism , Carcinoma, Renal Cell/metabolism , Cell Line, Tumor , Epitopes/chemistry , HLA-DR Antigens/metabolism , Histocompatibility Antigens Class II/metabolism , Humans , Immunohistochemistry , Interferon-gamma/metabolism , Kidney Neoplasms/metabolism , RNA, Messenger/metabolism
15.
J Mol Med (Berl) ; 84(3): 194-202, 2006 Mar.
Article in English | MEDLINE | ID: mdl-16501849

ABSTRACT

Autophagy delivers cytoplasmic constituents for lysosomal degradation. Recent studies have demonstrated that this pathway mediates resistance to pathogens and is targeted for immune evasion by viruses and bacteria. Lysosomal degradation products, including pathogenic determinants, are then surveyed by the adaptive immune system to elicit antigen-specific T cell responses. CD4(+) T helper cells have been shown to recognize nuclear and cytosolic antigens via presentation by major histocompatibility complex (MHC) class II molecules after autophagy. Furthermore, some sources of natural MHC class II ligands display characteristics of autophagy substrates, and autophagosomes fuse with late endosomes, in which MHC class II loading is thought to occur. Although MHC class II antigen processing via autophagy has so far mainly been described for professional antigen-presenting cells like B cells, macrophages, and dendritic cells, it might be even more important for cells with less endocytic potential, like epithelial cells, when these express MHC class II at sites of inflammation. Therefore, autophagy might contribute to immune surveillance of intracellular pathogens via MHC class II presentation of intracellular pathogen-derived peptides.


Subject(s)
Adaptation, Physiological/immunology , Autophagy , Immunity, Innate , Infections/immunology , Infections/pathology , Animals , Bacterial Infections/immunology , CD4-Positive T-Lymphocytes/immunology , Cytoplasm/metabolism , Endocytosis , Endosomes/metabolism , Histocompatibility Antigens Class II/immunology , Histocompatibility Antigens Class II/metabolism , Humans , Lysosomes/metabolism
16.
Genet Vaccines Ther ; 3: 6, 2005 Aug 22.
Article in English | MEDLINE | ID: mdl-16115316

ABSTRACT

BACKGROUND: Anti-tumor vaccines targeting the entire tumor antigen repertoire represent an attractive immunotherapeutic approach. In the context of a phase I/II clinical trial, we vaccinated metastatic melanoma patients with autologous amplified tumor mRNA. In order to provide the large quantities of mRNA needed for each patient, the Stratagene Creator SMART cDNA library construction method was modified and applied to produce libraries derived from the tumors of 15 patients. The quality of those mRNA library vaccines was evaluated through sequencing and microarray analysis. RESULTS: Random analysis of bacterial clones of the library showed a rate of 95% of recombinant plasmids among which a minimum of 51% of the clones contained a full-Open Reading Frame. In addition, despite a biased amplification toward small abundant transcripts compared to large rare fragments, we could document a relatively conserved gene expression profile between the total RNA of the tumor of origin and the corresponding in vitro transcribed complementary RNA (cRNA). Finally, listing the 30 most abundant transcripts of patient MEL02's library, a large number of tumor associated antigens (TAAs) either patient specific or shared by several melanomas were found. CONCLUSION: Our results show that unlimited amounts of cRNA representing tumor's transcriptome could be obtained and that this cRNA was a reliable source of a large variety of tumor antigens.

17.
Cancer Biol Ther ; 4(9): 943-8, 2005 Sep.
Article in English | MEDLINE | ID: mdl-16082191

ABSTRACT

MAGE derived HLA ligands have repeatedly been shown to elicit T-cell responses against tumor cells. In renal cell carcinoma (RCC), however, only few T-cell epitopes from cancer testis antigens have been described. To identify potential candidates, we applied a combined approach of microarray/qPCR expression analysis and sequencing of HLA ligands from RCC by mass spectrometry. We analyzed the expression of 21 MAGE genes in ten RCC samples and two glioblastoma samples and could identify the first MHC class I ligand NIGDEALIGRW from MAGED4 presented by HLA-A*25 on RCC solid tumor tissue. MAGED4 was expressed in 30% of RCC and both glioblastoma samples. Among the other MAGE family members only MAGEB2 and -C1 and the broadly expressed MAGED1, -D2, -F1 and -H1 were expressed in RCC. Ligands from MAGED4 could thus be interesting tumor-associated antigens in a subset of RCC, even though the identified ligand is presented by a rather rare allele.


Subject(s)
Antigens, Neoplasm/metabolism , Carcinoma, Renal Cell/immunology , Genes, MHC Class I , HLA Antigens , Kidney Neoplasms/immunology , Peptides/analysis , Antigens, Neoplasm/chemistry , Antigens, Neoplasm/genetics , Case-Control Studies , Humans , Ligands , Neoplasm Proteins/chemistry , Neoplasm Proteins/genetics , Neoplasm Proteins/metabolism
18.
Proc Natl Acad Sci U S A ; 102(22): 7922-7, 2005 May 31.
Article in English | MEDLINE | ID: mdl-15894616

ABSTRACT

MHC-peptide complexes mediate key functions in adaptive immunity. In a classical view, MHC-I molecules present peptides from intracellular source proteins, whereas MHC-II molecules present antigenic peptides from exogenous and membrane proteins. Nevertheless, substantial crosstalk between these two pathways has been observed. We investigated the influence of autophagy on the MHC-II ligandome and demonstrated that peptide presentation is altered considerably upon induction of autophagy. The presentation of peptides from intracellular and lysosomal source proteins was strongly increased on MHC-II in contrast with peptides from membrane and secreted proteins. In addition, autophagy influenced the MHC-II antigen-processing machinery. Our study illustrates a profound influence of autophagy on the class II peptide repertoire and suggests that this finding has implications for the regulation of CD4(+) T cell-mediated processes.


Subject(s)
Antigen Presentation/immunology , Autophagy/immunology , Cadaverine/analogs & derivatives , Gene Expression/immunology , Histocompatibility Antigens Class II/immunology , Peptides/immunology , Amino Acid Sequence , B-Lymphocytes/immunology , Cysteine Endopeptidases/metabolism , Histocompatibility Antigens Class II/metabolism , Humans , Ligands , Lysosomes/immunology , Lysosomes/metabolism , Oligonucleotide Array Sequence Analysis , Peptides/genetics , Peptides/metabolism
19.
Int Immunol ; 17(5): 591-7, 2005 May.
Article in English | MEDLINE | ID: mdl-15802306

ABSTRACT

Infection with the common pathogen Chlamydophila pneumoniae (Cpn, previously Chlamydia pneumoniae) has a high prevalence in patients suffering from arteriosclerosis and may trigger or contribute to heart disease. In mice, CD8-positive T cells are critical for the eradication of the infection and the development of immune memory against Cpn. Although several H2-class I epitopes have been described, no HLA-class I-associated peptides from Cpn are known. In order to define HLA-A*0201 epitopes from Cpn, we focused on the bacterial heat shock proteins (HSP) 60 and 70 which are known to be recognized by the immune system. Using epitope prediction, peptide binding studies and peptide-specific CTLs from HLA-A2 transgenic mice, we could define a potential HSP-70-derived epitope. The study of PBMCs from Cpn-infected individuals using fluorescent MHC tetramers revealed that some patients have CD8(+) T cells capable of recognizing the Cpn HSP-70 HLA-A*0201 epitope. Our studies pave the way to the immunomonitoring of the anti-Cpn CTL immune response present in patients suffering from different diseases potentially linked to Cpn or anti-Cpn immunity.


Subject(s)
Chaperonin 60/immunology , Chlamydophila Infections/immunology , Chlamydophila pneumoniae/immunology , Epitopes, T-Lymphocyte/immunology , HLA-A Antigens/metabolism , HSP70 Heat-Shock Proteins/immunology , T-Lymphocytes, Cytotoxic/immunology , Animals , Antibodies, Bacterial/blood , Cells, Cultured , Chaperonin 60/chemistry , HLA-A2 Antigen , HSP70 Heat-Shock Proteins/chemistry , HeLa Cells , Humans , Leukocytes, Mononuclear/immunology , Mice
20.
Clin Cancer Res ; 11(5): 1928-40, 2005 Mar 01.
Article in English | MEDLINE | ID: mdl-15756019

ABSTRACT

Dendritic cells are the most powerful antigen-presenting cells playing a decisive role for the initiation and maintenance of primary immune responses. However, signaling pathways involved in the differentiation of these cells have not been fully determined. Imatinib is a novel tyrosine kinase inhibitor effective against Abl kinases, c-Kit, and platelet-derived growth factor receptor. Using this compound, we show that human monocyte-derived dendritic cells generated in the presence of therapeutic concentrations of imatinib show a reduced expression of CD1a, MHC class I and II, and costimulatory molecules as well as decreased secretion of chemokines and cytokines resulting in an impaired capacity of dendritic cells to elicit primary T-cell responses. Using Western blot analyses, we found that these effects are mediated by inhibition of phosphatidylinositol 3-kinase/Akt pathways and a pronounced down-regulation of nuclear localized protein levels of nuclear factor-kappaB family members. Importantly, using blocking antibodies and tyrosine kinase inhibitors, we show that the inhibitory effects of imatinib on dendritic cell differentiation are not mediated via platelet-derived growth factor receptor and c-Kit. Taken together, our study reveals that imatinib inhibits dendritic cell differentiation and function via Akt and nuclear factor-kappaB signal transduction. Importantly, we show that imatinib can inhibit the function of normal, nonmalignant cells that may result in immunosuppression of these patients.


Subject(s)
Antineoplastic Agents/pharmacology , Dendritic Cells/immunology , Gene Expression Profiling , NF-kappa B/pharmacology , Piperazines/pharmacology , Protein Serine-Threonine Kinases/biosynthesis , Protein Serine-Threonine Kinases/pharmacology , Proto-Oncogene Proteins/biosynthesis , Proto-Oncogene Proteins/pharmacology , Pyrimidines/pharmacology , Benzamides , Cell Differentiation , Humans , Imatinib Mesylate , Immunosuppression Therapy , Lipopolysaccharide Receptors , Monocytes , NF-kappa B/biosynthesis , Proto-Oncogene Proteins c-akt , Signal Transduction
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