Mutational Analysis and Predicting Response to Immunotherapy最新文献

{"title":"Abstract B085: High mutation burden and response to immune checkpoint inhibitors in angiosarcomas of the scalp and face","authors":"C. Painter, Esha Jain, Michael Dunphy, E. Anastasio, Mary McGillicuddy, Rachel E. Stoddard, Beena S. Thomas, Sara Balch, K. Anderka, K. Larkin, N. Lennon, Yen-Lin E Chen, A. Zimmer, Esme O. Baker, Simone Maiwald, J. Lapan, J. Hornick, C. Raut, G. Demetri, E. Lander, T. Golub","doi":"10.1158/2326-6074.CRICIMTEATIAACR18-B085","DOIUrl":"https://doi.org/10.1158/2326-6074.CRICIMTEATIAACR18-B085","url":null,"abstract":"Objective: Angiosarcoma (AS) is a rare soft tissue sarcoma, with an incidence of 300 cases/yr and a 5-year DSS of 30%. The low incidence has impeded large-scale research efforts. To address this, we launched a patient-partnered genomics study which seeks to empower patients to accelerate research by remotely sharing their samples and clinical information. Methods: We developed a website (ASCproject.org) to allow remote acquisition of medical records (MR), saliva, blood, and archival tissue from patients in the US and Canada. Whole-exome sequencing (WES) of ~20,000 genes is performed on tumor and matched germline DNA. Transcriptome analysis is performed on tumor RNA. Ultra-low pass whole-genome sequencing (ULP-WGS) and in some cases WES is performed on cell free DNA (cfDNA) obtained from blood samples. Clinical data including information about demographics, diagnosis, treatments, and responses are obtained via patient-reported data (PRD) and through MR abstraction. The resulting clinically annotated genomic database is shared widely to identify genomic drivers and mechanisms of response and resistance to therapies. Results: Since launch on March 13 2017, 321 patients with AS have registered. The average age of patients is 56 yrs (range 22-89). Primary locations of AS were primary breast (24%), breast with prior radiation (20%), head/face/neck/scalp (HFNS) (21%), bone/limb (9%), abdominal (3%), heart (3%), lung (1%), liver (1%), lymph (0.5%), multiple locations (11%), and other locations (5%). 142 (48%) reported being disease free at the time of enrollment. To date, 153 saliva kits, 167 MRs, 43 blood samples, and 97 tissue samples have been obtained. WES analysis is complete for 14 samples.ULP-WGS is complete for 10 cfDNA samples, and WES on 4 cfDNA samples. Transcriptome sequencing is complete for 9 tumor samples. We identified several previously described genes known to be altered in AS, including recurrent alterations in KDR and TP53. Tumor mutational burden (TMB) and mutational signature activities were quantified for each tumor sample. All three of the AS from the HFNS in the initial cohort exhibited a high TMB (>150 mutations) and dominant UV light signature (COSMIC Signature 7). Based on this, we hypothesized that HFNS AS might respond well to immune checkpoint inhibitors. We identified through PRD 56 patients with HFNS AS who reported what medications they received. Of these, 2 reported receiving immune checkpoint inhibitors for the treatment of metastatic disease. Both patients had refractory metastatic HFNS AS and reported receiving off-label anti-PD1 therapy. Both had complete or near-complete responses following immunotherapy, and currently report having no evidence of disease. Clinical responses were confirmed through review of MRs. Sequencing is currently being performed on tumor samples from both patients. Conclusion: A patient-partnered approach enabled rapid identification and enrollment of over 300 patients with AS, an exceedingly","PeriodicalId":433681,"journal":{"name":"Mutational Analysis and Predicting Response to Immunotherapy","volume":"249 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125777201","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Abstract B070: Neoepitope and mutation load as a biomarker in a broad cohort of cancer patients treated with immunotherapy","authors":"Anne-Mette Bjerregaard, Vinicius Araujo Barbosa de Lima, A. Borch, O. Oestrup, U. Lassen, S. Hadrup","doi":"10.1158/2326-6074.CRICIMTEATIAACR18-B070","DOIUrl":"https://doi.org/10.1158/2326-6074.CRICIMTEATIAACR18-B070","url":null,"abstract":"Various different treatments of immunotherapy have in recent years made their mark in mainstream oncology, but it is still uncertain which patients will benefit and why. To determine this, different biomarkers have been investigated including tumor specific peptides originating from somatic mutations and recognized by T-cells, neoepitopes. Recent studies show that clinical benefit of immunotherapy correlate with both high mutational burden and high neoantigen load in defined patient groups, melanoma and lung cancer, underlining the possibility to use these measurements as biomarkers, and driving the hypothesis that neoantigen-responsive T-cells are the main drivers to cancer-cell elimination. We propose to investigate if a high mutational load and a high amount of neoepitopes are correlated with a general respond to immunotherapy across different cancer types and immunotherapy treatments. To examine this correlation, we studied 19 patients who have been treated with different kinds of immunotherapy. The data consist of Whole Exome Sequencing (WXS) data from blood and tumor, as well as tumor mRNA sequencing from all patients. Neoepitope load was predicted using Mutant peptide extractor and informer (MuPeXI) to find possible neoepitopes and score the neopeptides by their potential immunogenicity. The analysis of the sequencing data from the 19 patients revealed that even though these patients have cancers of varying origin and treated with different immunotherapies, a significant correlation was observed between a high number of neoepitopes as well as high mutational load with an increased possibility of a clinical benefit to immunotherapy. These findings showed that overall a clinical benefit is correlated with increased mutational load and neoepitopes independent of the cancer type and treatment which if used as a biomarker can possibly stratify patients determining who is likely to respond to cancer immunotherapy. Furthermore, we examined the tumor mRNA for T-cell recpetor sequences, and interestingly patients with high level of predeicted neoepitopes show enhanced oligoclonality of TCRs at the tumor site. Citation Format: Anne-Mette Bjerregaard, Vinicius Araujo Barbosa de Lima, Annie Borch, Olga Araujo Barbosa de Oestrup, Ulrik Lassen, Sine Reker Hadrup. Neoepitope and mutation load as a biomarker in a broad cohort of cancer patients treated with immunotherapy [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B070.","PeriodicalId":433681,"journal":{"name":"Mutational Analysis and Predicting Response to Immunotherapy","volume":"26 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123005862","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Abstract B073: A pan-HLA predictor of neoantigen processing and presentation to the tumor cell surface","authors":"T. Clancy, R. Stratford","doi":"10.1158/2326-6074.CRICIMTEATIAACR18-B073","DOIUrl":"https://doi.org/10.1158/2326-6074.CRICIMTEATIAACR18-B073","url":null,"abstract":"Currently, neoantigens are often predicted using algorithms predominantly based on knowledge of the key peptide binding affinity difference between HLA alleles. Although HLA binding algorithms predict binding affinity of a peptide to HLA reasonably well, they do not predict processing and presentation of to the cell surface (i.e., the immunopeptidome). In fact, only 15%–20% of “predicted” peptide binders are processed or presented, and therefore contribute to the immunopeptidome. Erroneous predictions may be addressed with time-consuming and laborious experiments, such as mass-spectrometry (MS). However, in silico predictions may also prove to be very useful in prioritizing therapeutically relevant immunogenic peptides. Previous in silico studies that predict naturally processed and presented peptides to the cell surface have focused on only one of the many steps in the antigen processing and presentation pathway (such as TAP transport or proteasome cleavage, etc.). Additionally, previous antigen processing prediction tools have been trained and are therefore applicable to specific HLA alleles, making it challenging to make predictions for not so well-characterized alleles. Here, we outline a machine learning approach trained on MS elution data that predicts, in a pan-HLA manner, natural processing and presentation of neoantigens to the cell surface. The predictor is integrated with multiple immune parameters in a deep learning layer to predict neoantigens, and may be used for more accurate neoantigen predictions for any HLA allele, in both the class I and class II systems. Further, by analyzing previously published clinical data we illustrate that its application leads to a significantly improved identification of neoantigen targets for personalized cancer immunotherapy. Citation Format: Trevor Clancy, Richard Stratford. A pan-HLA predictor of neoantigen processing and presentation to the tumor cell surface [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B073.","PeriodicalId":433681,"journal":{"name":"Mutational Analysis and Predicting Response to Immunotherapy","volume":"318 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121198220","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Abstract B081: Serum antibody against NY-ESO-1 and XAGE1 predicts clinical responses to anti-PD-1 therapy in non-small cell lung cancer","authors":"K. Kurose, Y. Ohue, T. Karasaki, J. Futami, I. Irei, T. Masuda, M. Fukuda, A. Kinoshita, H. Matsushita, K. Shimizu, H. Yamaguchi, M. Fukuda, K. Kakimi, M. Oka","doi":"10.1158/2326-6074.CRICIMTEATIAACR18-B081","DOIUrl":"https://doi.org/10.1158/2326-6074.CRICIMTEATIAACR18-B081","url":null,"abstract":"Introduction: Lung cancer is the leading cause of death from cancer worldwide. Most lung cancers, especially non-small-cell lung cancer (NSCLC), are diagnosed in the advanced stages and are resistant to conventional chemotherapy, resulting in poor prognosis. Programmed death-1 (PD-1) inhibitors effectively treat NSCLC; however, robust biomarkers for predicting clinical benefits with anti-PD-1 therapy have yet to be identified. NSCLC expresses NY-ESO-1 and/or XAGE1 antigens which belongs to cancer-testis (CT) antigen. NY-ESO-1 is broadly expressed in various human malignancies and has been extensively investigated as a target of cancer vaccines and T-cell therapy, because it exhibits the highest immunogenicity among CT antigens. XAGE1 is expressed in approximately 40~60% of lung adenocarcinoma (LAD), and the XAGE1 serum antibody is a good prognostic marker in advanced LAD patients, as we reported previously. Thus, NY-ESO-1 and XAGE1 may be major immuno-dominant antigens in NSCLC, and spontaneous immune responses against these antigens are considered to play important roles in the immune surveillance of NSCLC. Then, we hypothesized that NY-ESO-1 and XAGE1 antibody have potential as response and monitoring biomarkers in anti-PD-1 therapy for NSCLC, and conducted a prospective study to verify this hypothesis. Methods: A prospective study of biomarkers for anti-PD-1 therapy was performed using patients with advanced NSCLC from five medical centers in Japan. Prior to the administration of nivolumab or pembrolizumab, serum NY-ESO-1 and XAGE1 antibody responses were measured using ELISA, and patients in the discovery cohort were then stratified by their antibody status for enrollment in observational study. To assess the status of the antibody response, sera from patients were collected within two months before anti-PD-1 therapy, and antibody titers were serially measured during anti-PD-1 therapy. In the multicenter study (the validation and the additional cohorts), clinical responses to anti-PD-1 therapy and the antibody status were double-blinded with each other by clinicians and laboratory scientists. The primary endpoint was the objective responses rate (ORR) to anti-PD-1 therapy according to the NY-ESO-1 and XAGE1 antibody status. Secondary endpoints included progression-free survival (PFS) and overall survival (OS). Results: In the discovery cohort (n=13), NY-ESO-1 and/or XAGE1 antibody-positive NSCLC responded to anti-PD-1 therapy, whereas antibody-negative NSCLC did not. Furthermore, the antibody titers before anti-PD-1 therapy strongly correlated with tumor reduction rates (P Citation Format: Koji Kurose, Yoshihiro Ohue, Takahiro Karasaki, Junichiro Futami, Isao Irei, Takeshi Masuda, Masaaki Fukuda, Akitoshi Kinoshita, Hirokazu Matsushita, Katsuhiko Shimizu, Hiroyuki Yamaguchi, Minoru Fukuda, Kazuhiro Kakimi, Mikio Oka. Serum antibody against NY-ESO-1 and XAGE1 predicts clinical responses to anti-PD-1 therapy in non-small cell lung cancer [abstr","PeriodicalId":433681,"journal":{"name":"Mutational Analysis and Predicting Response to Immunotherapy","volume":"8 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134171429","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Abstract B075: Modeling response and resistance to immune checkpoint blockade in syngeneic mouse glioma","authors":"Katrin Deumelandt, Jens Blobner, J. Sonner, M. Friedrich, E. Green, M. Breckwoldt, M. Fischer, Jochen Meyer, F. Sahm, D. Schrimpf, A. Deimling, M. Plattén","doi":"10.1158/2326-6074.CRICIMTEATIAACR18-B075","DOIUrl":"https://doi.org/10.1158/2326-6074.CRICIMTEATIAACR18-B075","url":null,"abstract":"Immune checkpoint inhibitors are now implemented into the standard therapy of an increasing number of tumor entities and elicit remarkable durable therapy responses. However, gliomas seem resistant to checkpoint inhibition as recent evidence from a randomized clinical trial did not show a therapeutic benefit of PD-1 blockade in an unselected population of patients with recurrent glioblastoma. The blood-brain barrier per se does not seem to be a hurdle in transducing an effective peripheral immune response into tumors as evidenced by responses seen in selected glioma patients and patients with brain metastases treated with checkpoint inhibitors. This project investigates the mechanisms of response and resistance to checkpoint blockade targeting CTLA-4 and PD-1 in an experimental syngeneic Gl261 glioma model, where we found a clear and unanticipated dichotomy between responders and non-responders. We demonstrate that response to PD-1 and CTLA-4 blockade is driven by increased numbers and effector function of cytotoxic tumor-infiltrating T-cells as well as an enhanced TCRβ repertoire clonality of tumor infiltrating CD8 T-cells. Surprisingly, little overlap of the TCRβ repertoire between responder CD8 TILs was detected with only one shared TCRβ sequence motif, suggestive of a common tumor-antigen driving the expansion of reactive clones in responding mice. Moreover, we identified putative tumor neoepitopes that were predominantly abundant in non-responding tumors and thus might have undergone effective targeting by tumor-reactive T-cell in responding tumors. Resistance to PD-1 and CTLA-4 blockade was associated with increased frequencies of intratumoral macrophages (TAMs) expressing high levels of immunosuppressive markers such as PD-L1, CD38 and CD73. TAMs of nonresponding mice induced enhanced suppression of CD4 T-cell proliferation which was partially restored by PD-L1 blockade. Strikingly, additional PD-L1 blockade enhanced response rates to PD-1 and CTLA-4 blockade in Gl261-bearing mice, potentially by inhibiting the ligation of PD-L1 on TAMs to its alternative interaction partner CD80 on TILs. Collectively, we suggest a syngeneic mouse model for assessing mechanisms of response and resistance to checkpoint blockade in gliomas demonstrating a surprising heterogeneity of the TCRβ repertoire of tumor-infiltrating CD8 T-cells despite strict syngeneicity. We also provide evidence for a suppressive TAM subset associated with resistance to immune checkpoint inhibition in glioma, providing a rationale for combinatorial therapy strategies to overcome resistance to checkpoint blockade. Citation Format: Katrin Deumelandt, Jens Blobner, Jana K. Sonner, Mirco Friedrich, Edward Green, Michael O. Breckwoldt, Manuel Fischer, Jochen Meyer, Felix Sahm, Daniel Schrimpf, Andreas von Deimling, Michael Platten. Modeling response and resistance to immune checkpoint blockade in syngeneic mouse glioma [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR Interna","PeriodicalId":433681,"journal":{"name":"Mutational Analysis and Predicting Response to Immunotherapy","volume":"42 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123163390","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Abstract B082: PD-1 to CD8 ratio on tumor-infiltrating lymphocytes and peripheral blood mononuclear cells as a predictor for determining response of glioblastoma patients to radiation-induced ICD-based DC vaccine therapy","authors":"Fang-Yu Lin, C. Jan, W. Tsai, H. Harn, Hsin-Man Lu, Ming-chao Liu, S. Chiu, D. Cho","doi":"10.1158/2326-6074.CRICIMTEATIAACR18-B082","DOIUrl":"https://doi.org/10.1158/2326-6074.CRICIMTEATIAACR18-B082","url":null,"abstract":"Glioblastoma multiforme (GBM) is the most common and aggressive glioma within the central nervous system in adults. Radiation-induced ICD-based DC vaccine (RICD-DC vaccine) therapy plus conventional multi-modal regimen for GBM has been demonstrated with promising outcomes in clinical trials. However, some GBM patients received RICD-DC vaccine therapy did not increased survival rates than other GBM patients who only received conventional therapy. To investigate this issue, we conducted a retrospective study to analyze clinical and laboratory data to evaluate the factors which is critical for affecting the response rate of RICD-DC vaccine treatment. Patients with de novo GBM were enrolled (n=47) and divided into two subgroups: the first subgroup received post-surgical adjuvant immunotherapy with autologous RICD-DC vaccine (n=27) and the second received conventional treatment without immunotherapy (control, n=20). Quantitative immunohistochemistry for CD45, CD4, CD8, programmed death-1 (PD-1) and programmed death ligand 1 (PD-L1) was performed on patient tumor samples and peripheral blood mononuclear cells (PBMCs) at initial resection/biopsy before treatment. Pearson’s correlation, Cox proportional hazard model, and Kaplan-Meier analyses were performed to examine the correlations between these biomarkers expression and survival rates. In the RICD-DC vaccine group, patients with a lower PD-1+/CD8+ ratio (≤0.21) on tumor infiltrating lymphocytes (TILs) had longer overall survival (OS) (median 60.97 months, P Citation Format: Fang-Yu Lin, Chia-Ing Jan, Wan-Chen Tsai, Horng-Jyh Harn, Hsin-Man Lu, Ming-Chao Liu, Shao-Chih Chiu, Der-Yang Cho. PD-1 to CD8 ratio on tumor-infiltrating lymphocytes and peripheral blood mononuclear cells as a predictor for determining response of glioblastoma patients to radiation-induced ICD-based DC vaccine therapy [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B082.","PeriodicalId":433681,"journal":{"name":"Mutational Analysis and Predicting Response to Immunotherapy","volume":"71 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127292233","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Abstract B069: Temozolomide drives mismatch repair deficiency and fosters neoantigen generation in tumor cells","authors":"V. Amodio, Giovanni Grmano, L. Barault, S. Lamba, G. Rospo, A. Magrì, F. Maione, Giovanni Crisafulli, Carlotta Cancelliere, G. Lerda, A. Bartolini, G. Siravegna, B. Mussolin, Roberta Frappolli, M. Montone, G. Randon, F. Braud, Nabil Amirouchene Angelozzi, S. Marsoni, M. D’Incalci, A. Orlandi, E. Giraudo, Andrea Satore-Bianchi, S. Siena, F. Pietrantonio, F. Nicolantonio, A. Bardelli","doi":"10.1158/2326-6074.CRICIMTEATIAACR18-B069","DOIUrl":"https://doi.org/10.1158/2326-6074.CRICIMTEATIAACR18-B069","url":null,"abstract":"The tumor mutational burden affects immune surveillance and is associated with response to immune checkpoint blockade. We recently reported that inactivation of the DNA mismatch repair (MMR) pathway in cancer cells increases the mutational burden and modifies the neoantigen landscapes of cancer cells leading to their increased recognition by the immune system. We designed a pharmacologic screening to identify FDA-approved drugs capable of differentially affecting cancer cells MMR proficient and deficient. MMR-deficienT-cells displayed lower sensitivity to the alkylating agent Temozolomide (TMZ) and to the antimetabolite 6-Thioguanine (6-TG). Cells lacking key elements of the MMR pathway such as MutL homolog1, MutS homolog2 (MSH2) or MutS homolog 6 (MSH6), displayed an increased resistance to both TMZ and 6-TG. Next we treated two mouse colorectal cancer cell lines (MC38 and CT26) with TMZ until resistant populations emerged. MC38 cells acquired TMZ resistance through inactivation of the MMR pathway. Bioinformatic analysis revealed that these cells had higher numbers of neoantigens compared to parental cells. Importantly, when MC38 MMRd cells were injected in syngeneic mice, they were unable to form tumors. On the contrary, CT26 cells that acquired TMZ-resistance through other mechanisms, efficiently formed tumors in mice. Therefore, TMZ-induced MMR inactivation, and not TMZ treatment per se, triggered immune surveillance. To assess whether results obtained in mouse cancer models might translate to human disease, we tested TMZ in 47 molecularly annotated colorectal cancer (CRC) cancer cell lines. Only MMR-proficienT-cells and cells in which O6-methylguanine-DNA- methyltransferase (MGMT, the enzyme responsible for repairing the DNA adducts formed by TMZ) was not expressed were sensible to TMZ. Ten sensitive cell lines were chronically treated with TMZ until resistant populations emerged; we found that MGMT re-expression and loss of MMR genes were the main mechanisms of acquired resistance. In agreement with in vitro observations, analysis of biopsies from eight patients relapsing upon TMZ-based therapeutic regimens revealed MGMT re-expression (5 patients) and MMR genes mutations (i.e., MSH2 or MSH6) as main resistance mechanism. In both cell lines and biopsies, MMR inactivation led to increased mutational load and, consequently, to higher levels of predicted neo-antigens, suggesting an augmented immunogenicity. These preclinical data led to the clinical trial Arethusa (NCT03519412; https://clinicaltrials.gov/ct2/show/NCT03519412). Within Arethusa MMR-proficient patients will be tested for (MGMT) expression (IHC) and then for MGMT promoter methylation. MGMT negative patients will be treated with temozolomide (TMZ). Patients progressing under temozolomide will be tested for tumor mutational burden (TMB) and proceed to pembrolizumab if TMB is > 20 mutations/Mb. The primary study hypothesis is that tumors with acquired resistance to temozolomide might ","PeriodicalId":433681,"journal":{"name":"Mutational Analysis and Predicting Response to Immunotherapy","volume":"75 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128618396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Abstract B078: Unbiased identification of CD4+ T-cell epitopes using novel MHC-based chimeric receptors","authors":"J. Kisielow, F. Obermair, M. Kopf","doi":"10.1158/2326-6074.CRICIMTEATIAACR18-B078","DOIUrl":"https://doi.org/10.1158/2326-6074.CRICIMTEATIAACR18-B078","url":null,"abstract":"αβT-cell receptors (TCRs) bind peptide-major histocompatibility complexes (pMHC) with low affinity, posing a considerable challenge for direct identification of αβT-cell cognate peptides (epitopes). Here, we describe a platform for the discovery of MHC class-II presented epitopes, based on screening of engineered reporter cells expressing novel pMHC-TCR (MCR) hybrid molecules carrying cDNA-derived peptides. This technology identifies natural epitopes of CD4 T-cells in an unbiased and efficient manner and allows detailed analysis of TCR cross-reactivity providing recognition patterns on top of discrete epitopes. We identify cognate peptides of virus- and tumor-specific T-cells in mouse disease models and present a proof of concept for human T-cells. Furthermore, we show that vaccination with a peptide naturally recognized by TILs can efficiently protect from tumor challenge. Thus, the MCR technology holds promise for basic research and clinical applications allowing personalized identification of T-cell antigens in patients. Citation Format: Jan Kisielow, Franz-Josef Obermair, Manfred Kopf. Unbiased identification of CD4+ T-cell epitopes using novel MHC-based chimeric receptors [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B078.","PeriodicalId":433681,"journal":{"name":"Mutational Analysis and Predicting Response to Immunotherapy","volume":"52 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"117037783","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Abstract B072: Immune checkpoint blockade enhances mutated calreticulin-induced T-cell immunity in myeloproliferative neoplasms","authors":"C. C. Bozkus, V. Roudko, J. Finnigan, J. Mascarenhas, R. Hoffman, C. Iancu-Rubin, N. Bhardwaj","doi":"10.1158/2326-6074.cricimteatiaacr18-b072","DOIUrl":"https://doi.org/10.1158/2326-6074.cricimteatiaacr18-b072","url":null,"abstract":"","PeriodicalId":433681,"journal":{"name":"Mutational Analysis and Predicting Response to Immunotherapy","volume":"52 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125373774","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Abstract B086: Exploiting large-scale HLA peptidomics to generate novel immunotherapies: A data-driven approach to true neoantigen prioritization","authors":"A. Powlesland, Geert P. M. Mommen, R. Carreira, J. Hurst, M. J. Cundell, D. Lowne, F. Capuano, B. Jakobsen","doi":"10.1158/2326-6074.CRICIMTEATIAACR18-B086","DOIUrl":"https://doi.org/10.1158/2326-6074.CRICIMTEATIAACR18-B086","url":null,"abstract":"Purpose of Study: In this study we demonstrate accurate prediction of the impact of somatic mutations on the HLA presentation landscape achieved by interrogating a large scale database of 1.4 million unique HLA peptide sequences that have been directly identified by mass spectrometry. Background: Peptides presented to the immune system on HLA complexes are valuable targets for immunotherapeutic treatments. Identifying the full complement of peptides derived from a particular protein that are presented on major class I HLA restrictions will provide a vital step toward increasing the speed and viability of many immunotherapeutic strategies. Advances in next-generation sequencing (NGS) and single-cell technologies have enabled the accurate capture of somatic mutations accumulated by a tumor, yet a significant hurdle remains how this information can be utilized for immunotherapeutic benefit. In particular, identifying which somatic mutations produce neoantigens (peptides that contain a somatic mutation and are presented to the immune system in complex with HLA) is crucial to linking genetic changes with immunologic impact. Materials and Methods: Our approach to understanding the targetable human HLA peptidome is based on three key principles: achieving full proteome coverage, maximising individual protein coverage, and focusing on dominant HLA restrictions. By integrating novel cell biology, mass spectrometry, and bioinformatic technologies across over 1,000 individual experiments we have dramatically increased the depth of the HLA ligandome captured and achieved near total coverage of the protein-coding genome. Over 90% of the proteome has been captured for the restriction HLA-A*02:01, dominant in Caucasian populations. Our comprehensive genome coverage has enabled us to probe both directly and indirectly for the presence of neoantigens. Known somatic mutations within immortalized lines were used to generate bespoke reference databases that has led to direct identification of many hundreds of neoantigens. Results: Proteins that were found to contain neoantigens appeared to follow the same pattern of antigen processing and presentation as their unmutated equivalents. We have therefore found our HLA peptide dataset is able to offer significant value in predicting the likelihood of a somatic mutation creating a neoantigen. To test this, somatic mutations reported in 980 cell lines were probed against the database of HLA peptides. On average we find one peptide containing the mutated amino acid for every five somatic mutations reported. By incorporating the HLA background of the cell carrying the mutation, we narrow this prediction to one high-affinity HLA peptide for every fourteen somatic mutations reported. Comparing the peptides predicted in this analysis with those directly identified by mass spectrometry, we are able to show that we can prioritize mutation data by accurately predicting the presence and relative abundance of neoantigens. Our neoant","PeriodicalId":433681,"journal":{"name":"Mutational Analysis and Predicting Response to Immunotherapy","volume":"80 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126205585","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}