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Pediatric malignancies, in particular Ewing sarcoma (EwS), are characterized by low mutational load, low immunogenicity, and early metastasis. They recapitulate the embryonic immune tolerance setting and remain a challenge for established immunotherapies. These immunotherapies are not sufficient to target metastasis. Ideally, targeted therapies address gene products required for metastasis. We completed in vivo functional analyses for metastasis of 9/37 genes that we had shown to be overexpressed in EwS (Staege at al., Cancer Res 2004) and generated HLA class I restricted cytotoxic T cells against these gene products. All targets were involved in fetal development and 8/9 demonstrated functional relevance for metastasis. Allorepertoire-derived TCRs against 8/9 targets were cloned and sequenced; one target (DKK2) was nonimmunogenic. 7/8 TCRs were crossreactive, caused fratricide, or clonal TCR expansion failed (EZH2, STEAP1, PAPP-A, GPR64, ADRB3, LIPI, HOX-D1). In the tumor microenvironment we found an immunosuppressive (M0 and M2) transcriptomic signature and evidence for an immunosuppressive inflammation-associated activation of endogenous retroviral sequences. Among these most selectively expressed (n=9) and metastasis sustaining (n=8) targets, the BRICHOS chaperon domain containing antiangiogenetic bone protein chondromodulin-I (CHM1) was addressable by a non-crossreactive TCR. CHM1 is a direct downstream target of the oncogenic driver EWS-FLI1. We clinically assessed HLAA* 02:01/CHM1-specific TCR transgenic CD8+ T cells against EwS utilizing a TCR complementary determining region 3 (CDR3) recognition-sequence for the CHM1319 peptide with a Koff half-life of 113.2 ± 38.2 s. The CHM1319 motive was 130 times less homologous as compared to the 9mer ADRB3CHM1295, a crossreactive EwS target identified before. Four refractory HLA-A2+ EwS patients (pts) were treated with CHM1319-specific TCR-CDR3 transgenic T cells. Pt-derived cell lines (PDCL) were established in all cases. Pts received up to 107/kg TCR transgenic CD8+ T cells. All pts were treated with the same TCR-CDR3 recognition-sequence for CHM1. All PDCLs displayed persistent HLA-A2 expression. Transgenic T cells showed specific in vitro lysis of all PDCLs. Therapy was well tolerated and did not cause graft-versus-host disease (GvHD). Pts #1 #3 and #4 showed delayed progression, whereas pt #2, while having bone marrow (BM) involvement and accessible multifocal disease, showed partial metastatic regression associated with T-cell homing to involved lesions. In conclusion, CHM1319-TCR transgenic T cells may home to affected BM and may cause partial remission. CHM1-TCR transgenic T cells address a persistently expressed target required for metastasis, suggesting lack of immunoediting selection pressure. They proliferate in vivo without causing GvHD. This abstract is also being presented as Poster A07. Citation Format: Stefan Burdach, Guenther Richter, David Schirmer, Andreas Kirschner, Sebastian Schober, Valentina Evdokimova, Hendrik Gassmann, Elvira D’Ippolito, Maxim Barenboim, Dirk Busch, Poul Sorensen, Uwe Thiel. T-cell receptor (TCR)-based immunotherapy in pediatric malignancy: Addressing the challenge of early metastasis and low immunogenicity [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr PR05.

Immunotherapy can revolutionize anti-cancer therapy if specific targets are available. Recurrent somatic mutations in the exome can create highly specific neo-antigens. However, especially pediatric cancers are oligo-mutated and hardly exhibit recurrent neo-antigens. Yet, immunogenic peptides encoded by cancer-specific genes (CSGs), which are virtually not expressed in normal tissues, may enable a targeted immunotherapy of such cancers. Here, we describe an algorithm and provide a user-friendly software named RAVEN (Rich Analysis of Variable gene Expressions in Numerous tissues), which automatizes the systematic and fast identification of CSG-encoded peptides highly affine to Major Histocompatibility Complexes (MHC) starting from publicly available gene expression data. We applied RAVEN to a dataset assembled from more than 2,700 simultaneously normalized gene expression microarrays comprising 50 tumor entities, with a focus on sarcomas and pediatric cancers, and 71 normal tissue types. RAVEN performed a transcriptome-wide scan in each cancer entity for gender-specific CSGs. As a proof-of-concept we identified several established CSGs, but also many novel candidates potentially suitable for targeting multiple cancer types. The specific expression of the most promising CSGs was validated by qRT-PCR in cancer cell lines and by immunohistochemistry in a comprehensive tissue-microarray comprising 412 samples. Subsequently, RAVEN identified likely immunogenic peptides encoded by these CSGs by predicting the affinity to MHCs. Putative highly affine peptides were automatically crosschecked with the UniProt protein-database to exclude sequence identity with abundantly expressed proteins. The predicted affinity of selected peptides was validated in T2-cell peptide-binding assays in which many showed similar kinetics to a very immunogenic influenza control peptide.Collectively, we provide a comprehensive, exquisitely curated and validated catalogue of cancer-specific and highly MHC-affine peptides across 50 cancer entities. In addition, we developed an intuitive and freely available software to easily apply our algorithm to any gene expression dataset (https://github.com/JSGerke/RAVENsoftware). We anticipate that our peptide libraries and software constitute a rich resource to accelerate the development of novel immunotherapies.

Background: Chondromodulin-I (CHM1) sustains malignancy in Ewing sarcoma (ES). Refractory ES carries a dismal prognosis and patients with bone marrow (BM) metastases do not survive irrespective of therapy. We assessed HLA-A*02:01/CHM1-specific allorestricted T cell receptor (TCR) wild-type and transgenic cytotoxic (CD8+) T cells against ES. Patients and Methods: Three refractory HLA-A2+ ES patients were treated with HLA-A*02:01/peptide-specific allorepertoire-derived (i.e., allorestricted) CD8+ T cells. Patient #1 received up to 4.8 × 105/kg body weight HLA-A*02:01− allorestricted donor-derived wild-type CD8+ T cells. Patient #2 received up to 8.2 × 106/kg HLA-A*02:01− donor-derived and patient #3 up to 6 × 106/kg autologous allorestricted TCR transgenic CD8+ T cells. All patients were treated with the same TCR complementary determining region 3 allorecognition sequence for CHM1 peptide 319 (CHM1319). Results: HLA-A*02:01/CHM1319-specific allorestricted CD8+ T cells showed specific in vitro lysis of all patient-derived ES cell lines. Therapy was well tolerated and did not cause graft versus host disease (GvHD). Patients #1 and #3 showed slow progression, whereas patient #2, while having BM involvement, showed partial metastatic regression associated with T cell homing to involved lesions. CHM1319 TCR transgenic T cells could be tracked in his BM for weeks. Conclusions: CHM1319-TCR transgenic T cells home to affected BM and may cause partial disease regression. HLA-A*02:01/antigen-specific allorestricted T cells proliferate in vivo without causing GvHD.

// Andreas Kirschner 1 , Melanie Thiede 1 , Franziska Blaeschke 1, 2 , Gunther H.S. Richter 1 , Julia S. Gerke 3 , Michaela C. Baldauf 3 , Thomas G.P. Grunewald 3, 4, 5 , Dirk H. Busch 6 , Stefan Burdach 1, * , Uwe Thiel 1, * 1 Laboratory for Functional Genomics and Transplantation Biology, Departments of Pediatrics and Children’s Cancer Research Center, Klinikum rechts der Isar, Technische Universitat Munchen, Munich, Germany 2 Laboratory for Immunotherapy, Dr. von Hauner Children’s Hospital, Medical center of the LMU Munich, Munich, Germany 3 Laboratory for Pediatric Sarcoma Biology, Institute of Pathology of the LMU Munich, Munich, Germany 4 German Cancer Consortium (DKTK), Heidelberg, Germany 5 German Cancer Research Center (DKFZ), Heidelberg, Germany 6 Institute for Medical Microbiology, Immunology and Hygiene, Technische Universitat Munchen, Munich, Germany * Share senior authorship Correspondence to: Andreas Kirschner, email: andi.kirschner@tum.de Keywords: fratricide, CD107a, TCR transgenic T cells, cross reactivity, amino-acid exchange scan Received: April 18, 2016 Accepted: May 30, 2016 Published: July 18, 2016 ABSTRACT Aim: Autologous as well as allogeneic CD8 + T cells transduced with tumor antigen specific T cell receptors (TCR) may cause significant tumor lysis upon adoptive transfer. Besides unpredictable life-threatening off-target effects, these TCRs may unexpectedly commit fratricide. We hypothesized lysosome-associated membrane glycoprotein 1 (LAMP1, CD107a) to be a marker for fratricide in TCR transgenic CD8 + T cells. Methods: We identified HLA-A*02:01/peptide-restricted T cells directed against ADRB3 295 . After TCR identification, we generated HLA-A*02:01/peptide restricted TCR transgenic T cells by retroviral transduction and tested T cell expansion rates as well as A*02:01/peptide recognition and ES killing in ELISpot and xCELLigence assays. Expansion arrest was analyzed via Annexin and CD107a staining. Results were compared to CHM1 319 -TCR transgenic T cells. Results: Beta-3-adrenergic receptor (ADRB3) as well as chondromodulin-1 (CHM1) are over-expressed in Ewing Sarcoma (ES) but not on T cells. TCR transgenic T cells demonstrated HLA-A*02:01/ADRB3 295 mediated ES recognition and killing in ELISpot and xCELLigence assays. 24h after TCR transduction, CD107a expression correlated with low expansion rates due to apoptosis of ADRB3 specific T cells in contrast to CHM1 specific transgenic T cells. Amino-acid exchange scans clearly indicated the cross-reactive potential of HLA-A*02:01/ADRB3 295 - and HLA-A*02:01/CHM1 319 -TCR transgenic T cells. Comparison of peptide motive binding affinities revealed extended fratricide among ADRB3 295 specific TCR transgenic T cells in contrast to CHM1 319 . Conclusion: Amino-acid exchange scans alone predict TCR cross-reactivity with little specificity and thus require additional assessment of potentially cross-reactive HLA-A*02:01 binding candidates. CD107a positivity is a marker for fratricide of CD8 + TCR transgenic T cells.

The endochondral bone protein Chondromodulin-I (CHM1) provides oncogene addiction in Ewing sarcoma (ES). We pre-clinically tested the targetability of CHM1 by TCR transgenic, allo-restricted, peptide specific T cells to treat ES. We previously generated allo-restricted wildtype CD8+ T cells directed against the ES specific antigen CHM1319 causing specific responses against ES. However, utilization of these cells in current therapy protocols is hampered due to high complexity in production, relatively low cell numbers, and rapid T cell exhaustion. In order to provide off-the-shelf products in the future, we successfully generated HLA-A*02:01-restricted T cell receptor (TCR) transgenic T cells directed against CHM1319 by retroviral transduction. After short-term expansion a 100% purified CHM1319-TCR-transgenic T cell population expressed a CD62L+/CD45RO and CD62L+/CD45RA+ phenotype. These cells displayed specific in vitro IFNg and granzyme B release in co-culture with HLA-A*02:01+ ES cell lines expressing CHM1. When co-injected with ES cells in Rag2−/−ɣc−/− mice, CHM1-specific TCR-transgenic T cells significantly inhibited the formation of lung and liver metastases in contrast to control mice. Lungs and livers of representative mice displayed CD8+ T cell infiltration in the presence (control group treated with unspecific T cells) and in the absence (study group) of metastatic disease, respectively. Furthermore, mice receiving unspecific T cells showed signs of graft-versus-host-disease in contrast to all mice, receiving CHM1319-TCR-transgenic T cells. CHM1319 specific TCR-transgenic T cells were successfully generated causing anti-ES responses in vitro and in vivo. In the future, CHM1319-TCR-transgenic T cells may control minimal residual disease rendering donor lymphocyte infusions more efficacious and less toxic.

Background: Chondromodulin-I (CHM1) sustains malignancy in Ewing sarcoma (ES). Refractory ES carries a dismal prognosis and patients with bone-marrow (BM) metastases do not survive irrespective of therapy. We assessed HLA-A*02:01/CHM1 specific allorestricted T-cell receptor (TCR) wild-type and transgenic cytotoxic (CD8+) T cells against ES. Patients and Methods: Three refractory HLA-A2+ ES patients were treated with HLA-A*02:01/peptide specific allorepertoire-derived (i.e., allorestricted) CD8+ T cells. Patient #1 received up to 4.8 x 105/kg body weight HLA-A*02:0 allorestricted donor-derived wild type CD8+ T cells. Patient #2 received up to 8.2 x 106/kg HLA-A*02:01 donor-derived and patient #3 up to 6 x 106/kg autologous allorestricted TCR transgenic CD8+ T cells. All patients were treated with the same TCR complementary determining region 3 allorecognition sequence for CHM1 peptide 319 (CHM1319). Findings: HLA-A*02:01/CHM1319 specific allorestricted CD8+ T cells showed specific in vitro lysis of all patient-derived ES cell lines. Therapy was well tolerated and did not cause graft-versus-host disease (GVHD). Patients #1 and #3 showed slow progression, whereas patient #2, while having BM involvement, showed partial metastatic regression associated with T-cell homing to involved lesions. CHM1319 TCR transgenic T cells could be tracked in his BM for weeks. Interpretation: HLA-A*02:01/antigen specific allorestricted T cells proliferate in vivo without causing GVHD. CHM1319 TCR transgenic T cells home to affected BM and are associated with partial disease regression. Funding: Wilhelm Sander-Stiftung (2006.109.1), Else Kröner-Stiftung (GR & SB; P31/08//A123/07), BMBF (GR, UT and SB, TranSarNet 01GM1104B; SB, PROVABES 01KT1311) and Cura Placida Children's Cancer Research Foundation. PHS is funded by the Excellenzinitiative at TUM/CCC Munich. Citation Format: Uwe Thiel, Sebastian J. Schober, Ingo Einspieler, Andreas Kirschner, David Schirmer, Katja Gall, Oxana Schmidt, Thomas G. P. Grunewald, Poul H. Sorensen, Guenther H. S. Richter, Irene Teichert von Luettichau, Dirk H. Busch, Stefan Burdach. Ewing sarcoma regression without GVHD by allo-MHC/CHM1 specific T cells [abstract]. In: Proceedings of the AACR Conference on Advances in Sarcomas: From Basic Science to Clinical Translation; May 16-19, 2017; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(2_Suppl):Abstract nr B38.

Pregnancy-associated plasma protein-A (PAPPA), also known as pappalysin, is a member of the insulin like growth factor (IGF) family. PAPPA acts as a protease, cleaving IGF inhibitors, i.e. IGF binding proteins (IGFBPs), thereby releasing IGFs from IGFBPs. The insulin/IGF-axis is involved in cancer in general and in Ewing sarcoma (ES) in particular. ES is a highly malignant bone tumor characterized by early metastatic spread. PAPPA stimulates normal bone growth, and is also associated with various cancers. In particular, PAPPA is overexpressed and required for proliferation in ES. We isolated HLA-A*02:01+/peptide restricted T cells from A*02:01- healthy donors directed against PAPPA, generated by priming with A*02:01+ PAPPA peptide-loaded dendritic cells. After T cell receptor (TCR) identification, retrovirally TCR transduced CD8+ T cells were assessed for their in vitro specificity and in vivo efficacy in human ES bearing Rag2-/-γc-/- mice. Engraftment in mice and tumor infiltration of TCR transgenic T cells in the mice was evaluated. The TCR transgenic T cell clone PAPPA-2G6 demonstrated specific reactivity towards HLA-A*02:01+/PAPPA+ ES cell lines. We furthermore detected circulating TCR transgenic T cells in the blood in Rag2-/-γc-/- mice and in vivo engraftment of the in bone marrow. Tumor growth in mice with xenografted ES was significantly reduced after treatment with PAPPA-2G6 TCR transgenic T cells compared to controls, and tumors from treated mice revealed tumor infiltrating PAPPA-2G6 TCR transgenic T cells. In summary, we demonstrate that PAPPA is a promising target for TCR based immunotherapy of ES. We demonstrate that TCR transgenic T cells recognize this target, home to the tumor, and causes tumor regression in a preclinical mouse model. Citation Format: Uwe Thiel, Andreas Kirschner, Melanie Thiede, Thomas GP Grünewald, Rebeca Alba Rubio, Günther Richter, Thomas Kirchner, Dirk Busch, Poul Sorensen, Stefan Burdach. Pappalysin-1 is a suitable target for T cell receptor transgenic T cells to kill Ewing sarcoma in vivo and in vitro [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 692. doi:10.1158/1538-7445.AM2017-692

Background: Chondromodulin-I (CHM1) sustains malignancy in Ewing sarcoma (ES). Refractory ES carries a dismal prognosis and patients with bone marrow (BM) metastases do not survive irrespective of therapy. We assessed HLA-A*02:01/ CHM1 specific allorestricted T cell receptor (TCR) wildtype and transgenic cytotoxic (CD8+) T cells against ES. Patients and Methods: Three refractory HLA-A2+ ES patients were treated with HLA-A*02:01/peptide specific allorepertoire-derived (i.e. allorestricted) CD8+ T cells. Patient #1 received up to 4.8x105/kg body weight HLA-A*02:01- allorestricted donor derived wild type CD8+ T cells. Patient #2 received up to 8.2x106/kg HLA-A*02:01- donor derived and patient #3 up to 6x106/kg autologous allorestricted TCR transgenic CD8+ T cells. All patients were treated with the same TCR complementary determining region 3 allorecognition sequence for CHM1319. Results: HLA-A*02:01/CHM1319 specific allorestricted CD8+ T cells showed specific in vitro lysis of all patient-derived ES cell lines. Therapy was well tolerated and did not cause graft versus host disease (GVHD). Patients #1 and #3 showed slow progression, whereas patient #2, while having BM involvement, showed partial metastatic regression associated with T cell homing to involved lesions. CHM1319 TCR transgenic T cells could be tracked in his BM for weeks. Conclusions: CHM1319-TCR transgenic T cells home to affected BM and may cause partial disease regression. HLA-A*02:01/antigen specific allorestricted T cells proliferate in vivo without causing GVHD. Citation Format: Uwe Thiel, Sebastian Schober, ingo Einspieler, Andreas Kirschner, David Schirmer, Thomas Grünewald, Irene Teichert-von Lüttichau, Guenther Richter, Poul Sorensen, Stefan Burdach. Ewing Sarcoma regression by Allo-MHC/Chm1 specific T cells without GVHD [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3757. doi:10.1158/1538-7445.AM2017-3757

Pregnancy-associated plasma protein-A (PAPPA), also known as pappalysin, is a member of the insulin-like growth factor (IGF) family. PAPPA acts as a protease, cleaving IGF inhibitors, i.e., IGF binding proteins (IGFBPs), thereby setting free IGFs. The insulin/IGF-axis is involved in cancer in general and in Ewing sarcoma (ES) in particular. ES is a highly malignant bone tumor characterized by early metastatic spread. PAPPA is associated with various cancers. It is overexpressed and required for proliferation in ES. PAPPA also stimulates normal bone growth. We isolated HLA-A*02:01+/peptide-restricted T cells from A*02:01− healthy donors directed against PAPPA, generated by priming with A*02:01+ PAPPA peptide loaded dendritic cells. After TCR identification, retrovirally TCR transduced CD8+ T cells were assessed for their in vitro specificity and in vivo efficacy in human ES bearing Rag2−/−γc−/− mice. Engraftment in mice and tumor infiltration of TCR transgenic T cells in the mice was evaluated. The TCR transgenic T cell clone PAPPA-2G6 demonstrated specific reactivity toward HLA-A*02:01+/PAPPA+ ES cell lines. We furthermore detected circulating TCR transgenic T cells in the blood in Rag2−/−γc−/− mice and in vivo engraftment in bone marrow. Tumor growth in mice with xenografted ES was significantly reduced after treatment with PAPPA-2G6 TCR transgenic T cells in contrast to controls. Tumors of treated mice revealed tumor-infiltrating PAPPA-2G6 TCR transgenic T cells. In summary, we demonstrate that PAPPA is a first-rate target for TCR-based immunotherapy of ES.

BackgroundWe have previously reported that human recombinant granzyme B (grB) mediates apoptosis in membrane heat shock protein 70 (Hsp70)-positive tumor cells in a perforin-independent manner.Methodology/principal findingsOptical imaging of uptake kinetics revealed co-localization of grB with recycling endosomes (Rab9/11) as early as 5 min after internalization, with late endosomes (Rab7) after 30 min, and the lysosomal compartment (LAMP1/2) after 60 to 120 min. Active caspase-3-mediated apoptosis was induced in mouse CT26 monolayer cells and 3D tumor spheroids, but not in normal mouse endothelial cells. Granzyme B selectively reduced the proportion of membrane Hsp70-positive cells in CT26 tumor spheroids. Consecutive i.v. injections of recombinant human grB into mice bearing membrane Hsp70-positive CT26 tumors resulted in significant tumor suppression, and a detailed inspection of normal mouse organs revealed that the administration of anti-tumoral concentrations of grB elicited no clinicopathological changes.Conclusions/significanceThese findings support the future clinical evaluation of human grB as a potential adjuvant therapeutic agent, especially for treating immunosuppressed patients that bear membrane Hsp70-positive tumors.