Clonal Neoantigens Research Articles

1980TiP - Homogenisation of leftover surgical tissue across multiple cancer types: A feasibility study (HoLST-F)

BackgroundIntratumour heterogeneity is recognised across different tumour types and has implications for therapeutic resistance. At present, clinical practice often relies upon molecular information derived from a single biopsy of a primary or metastatic tumour. This information guides treatment choice but may not be representative of the diversity of the tumour. It is currently difficult to evaluate how effectively a single region guides treatment decisions because the formalin-fixed residual surgical sample that is not paraffin embedded for diagnostic purposes is typically thrown away. Retention and homogenisation – ‘blending’- of this residual formalin-fixed leftover tumour tissue creates a more representative sample for analysis. DNA may be extracted from this sample for sequencing. Pilot data in kidney cancer has demonstrated the potential of this methodology for robust mutational calling, accurate determination of cancer cell fraction and the ability to discern clonal from subclonal variants. Such information may be clinically relevant; for example, discerning resistant subclones prior to treatment, or identifying clonal neoantigens worth targeting with immunotherapy. Trial designIn order to establish the feasibility of homogenization as a potential companion diagnostic tool, our study aims to 1) identify the proportion of primary tumour cases that have left over tissue amenable to homogenization across multiple tumour types and 2) pilot homogenization across multiple tumour types. The molecular profile of the homogenate will be compared to that obtained from the diagnostic specimen using next generation sequencing techniques. This is a prospective non-interventional study (NCT03832062). Patients undergoing surgical intervention at The Royal Marsden Hospital (NHS Foundation Trust) with leftover tumour tissue from primary breast, colorectal, gastric, pancreatic, ovarian, renal cancer and sarcoma surgeries, as well as melanoma lymph node dissections will be included in the feasibility assessment. We plan to homogenise 500 cases across different tumour types. The study opened in September 2018 and is expected to run for 2 years. Clinical trial identificationNCT03832062; Release date: February 2019. Legal entity responsible for the studyRoyal Marsden NHS Foundation Trust. FundingVentana Medical Systems (a subsidiary of Roche). DisclosureL. Gallegos: Full / Part-time employment: Roche. S. Hill: Full / Part-time employment: Roche. A. Barhoumi: Full / Part-time employment: Roche. S. Stanislaw: Full / Part-time employment: Roche. M. Mendoza: Full / Part-time employment: Roche. J.M.G. Larkin: Research grant / Funding (institution): Roche; Advisory / Consultancy: Roche. N. Alexander: Full / Part-time employment: Roche; Shareholder / Stockholder / Stock options: Roche. S. Turajlic: Research grant / Funding (institution): Ventana Medical Systems (subsidiary of Roche). All other authors have declared no conflicts of interest.

Cancer Immunotherapy Is More Effective in Irradiated Tumors in Preclinical Mouse Model of Melanoma

Post-radiotherapy local recurrence is a common challenge in cancer management. Since radiotherapy induces DNA damage, tumor cells that survived radiotherapy have higher mutation burden. It is recognized that high mutation burden and high clonal neoantigen burden are associated with checkpoint inhibitor sensitivity. Therefore, we hypothesized that tumors that survived radiotherapy are more responsive to immune checkpoint treatment and cancer immunotherapy maybe an effective treatment for local recurrences after radiotherapy. To simulate recurrent tumor post radiotherapy, we irradiated B16F10 melanoma cells with 5 Gy and selected the surviving colonies for further passage. This process was repeated twice to obtain the final irradiated B16F10 cells. These irradiated B16F10 cells and parent B16F10 cells were used to generate flank xenograft tumors (5*104) in B57BL/6 mice. The mice were then treated with saline, αPD-L1 (10mg/kg), αCTLA4(5mg/kg) or αPD-L1+αCTLA4 on days 3, 6 and 9. Tumor volumes were obtained for each mouse. The tumor volumes were assessed every 2–3 days starting day 3. In the irradiated B16F10 melanoma model, our results demonstrate that both αCTLA4 alone and combination groups achieved tumor growth control (p<0.005), and there is also significant survival difference (p<0.005) with median survival 22.5, 26, 35 and 38.5 days in control, αPD-L1, αCTLA4, and combination subgroups. In the parent B16F10 melanoma model, immunotherapy treatments improved survival, though the increases were not statistically significant. Immunotherapy treatment arms were significantly more effective in irradiated B16F10 model (p value<0.005). We demonstrated that irradiated B16F10 tumors are more responsive to checkpoint inhibitor treatment than non-irradiated tumors. This finding suggest that immunotherapy may be effective for recurrent tumors after radiation. Our results are preliminary and further preclinical and clinical validation are needed.

Neoantigen quality, not quantity.

Prioritizing expressed clonal neoantigens in genes required for cancer cell survival may reduce the likelihood of resistance to neoantigen therapies.

Abstract 3229: Radiation and chemotherapies result in increasing neoantigen intratumor heterogeneity and resistance to nivolumab in a patient with pleomorphic lung cancer

Abstract BACKGROUND:Immune checkpoint inhibitors (ICIs) have significantly changed the landscape of cancer treatment, but the response rate of non-small-cell lung carcinoma (NSCLC) to ICIs is less than 30%. Tumor mutational burden (TMB) is the most promising predictive biomarker for NSCLC immunotherapies. However, some NSCLC patients with high-TMB have little response to ICIs. The neoantigen intratumor heterogeneity (ITH), which determined by the ratio of subclonal neoantigen in the tumor, has been verified to be a potential therapeutic biomarker for immunotherapies in some cancer types. Pulmonary pleomorphic carcinoma, a rare subtype of pulmonary sarcomatoid carcinoma, has been shown to respond remarkably to ICIs, but the biomarkers for ICIs in pulmonary pleomorphic carcinoma have not been fully proven. CASE PRESENTATION:A 57 years old female pulmonary pleomorphic carcinoma patient, who underwent surgery, chemotherapy, anti-angiogenic therapy, radiotherapy, and anti-PD1 therapy, with disease relapse at the last, was included in this study. Primary and relapse tumor samples were collected for gene sequencing by a target sequencing panel which covered 811 cancer genes, during ICIs treatment. Peripheral bloods were collected for ctDNA and T cell receptor sequencing every two months. The results showed that the TMB (&amp;gt;10 muts/Mb) was high, but the clonal neoantigen load (1.33 neos/Mb) was low. The neoantigen ITH was increased after chemotherapy and radiotherapy with a score at nearly 0% in the primary tumor but increased to 85.72% in relapse tissues. The clonal neoantigen ratio detected by ctDNA was increased ~0.8 fold, while the high-frequency clonotypes of TCR to neoantigens dropped during ICIs treatment. CONCLUSIONS:Our results indicated that cytotoxic chemotherapy and radiotherapy can induce the subclonal neoantigens production and increase the neoantigen ITH, thus might negatively regulating patients’ response to ICIs therapy. These results highlight that the neoantigen ITH might be an important auxiliary to TMB in predicting patient response to immune therapies. More studies and clinical trials are needed to further validate these results. Citation Format: Xiaohua Hong, Yuting Liu, Yiying Liu, Yue Hu, Qifan Yang, Di Wu, Kai Zhang, Yongchao Li, Jinsong Yang, Jiaqian Wang, Jun Liu, Li Liu. Radiation and chemotherapies result in increasing neoantigen intratumor heterogeneity and resistance to nivolumab in a patient with pleomorphic lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3229.

Abstract 4949: Immunological ignorance is an enabling feature of the oligo-clonal T cell response to melanoma neoantigen

Abstract The impact of intratumor heterogeneity (ITH) and the neoantigen landscape on T cell immunity is poorly understood. ITH is a widely recognized feature of solid tumors and poses distinct challenges related to the development of effective therapeutic strategies, including cancer immunotherapy. Cutaneous melanoma is characterized by C-&amp;gt;T transitions caused by UV exposure which leads to a large mutational burden encoding putative neoantigens. Here, we performed ultra-deep DNA sequencing of multiple metastases from melanoma patients and observed ubiquitious sharing of clonal and subclonal single nucleotide variants (SNV) encoding putative HLA class I restricted neoantigen epitopes among tumors. MEL66, a reference melanoma patient with a large mutational burden (53 SNV/Mb), provided six resected metastases for study. The spontaneous T-cell response features an oligo/monoclonal T cell-receptor (TCR) repertoire which targets a few clonal neoantigens; most neoantigen-specific T cell clones ignore the tumor. CD8+ T cells to additional HLA class I restricted neoantigens can be elicited by DC vaccination (NCT03092453) with tumor-encoded amino acid substituted (mutated) peptides resulting in a diverse, high frequency TCR repertoire. Isolation of T cell clones by limiting dilution from blood and TIL permits functional validation regarding neoantigen-specificity. Gene transfer of paired abTCR heterodimers specific for clonal neoantigens confirmed correct clonotype assignments based on high throughput CDR3 sequencing. Additional melanoma patients with 2-6 resected metastases were investigated and similar observations were found. Our observations implicate ineffective neoantigen cross-presentation as the basis for immunological ignorance. We postulate that therapeutic vaccination is required to increase the breadth and diversity of neoantigen-specific CD8+ T cells as an adjunct to checkpoint inhibitor treatment for cancer. Citation Format: Gerald P. Linette, Beatriz M. Carreno, Zackary L. Skidmore, Jasreet Hundel, Obi L. Griffith, Malachi Griffith, Vincent Magrini, Elaine R. Mardis. Immunological ignorance is an enabling feature of the oligo-clonal T cell response to melanoma neoantigen [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4949.

Abstract 2250: Combinational markers of neoantigen intratumor heterogeneity and neoantigen burden predict progression-free survival for lenvatinib plus PD-1 blockade in patients with intrahepatic cholangiocarcinoma

Abstract Intrahepatic cholangiocarcinoma (ICC) is an aggressive malignant neoplasm derived from biliary epithelial cells. Although many targetable gene alterations have been identified, there has no molecular targeted drug available for these patients at present, which may be due to the high intratumor heterogeneity (ITH) of ICC. Previous studies have demonstrated that some ICC patients could be benefited from immune checkpoint inhibitors (ICIs), but the predictive biomarkers are still unknown. We used whole exome sequencing to evaluate the impact of neoantigen ITH and tumor neoantigen burden (TNB) in 45 ICC patients, in which 15 patients were treated by anti-PD1 inhibitor combined with lenvatinib. The median neoantigen and clonal neoantigen load of these patients were 0.65 and 0.29 per Mb, respectively. The median neoantigen ITH index was 0.45, with a range from 0.02 to 1. Survival analysis of those patients who received the combined treatment revealed significantly longer progression-free survival (PFS) in patients with higher TNB and low neoantigen ITH (9.5 vs 3.5 months, p=0.00583). Among the 30 patients without anti-PD1 combined therapy, there were 36.7% (11/30) ICC patients with high TNB and low neoantigen ITH, indicating these patients might be benefited from this combined therapy. One of these 45 patients had the highest TMB and TNB with high MSI and dMMR has the longest PFS (12 months) after the combined treatment. Besides, we found that the clonal KRAS mutation (G12D) occurred exclusively in patients with shorter PFS and OS and lower TMB and TNB, while the FLG mutation occurred only in patients with longer PFS and OS and higher TMB and TNB. These results indicated the potential relationship between mutations in KRAS and FLG and the levels of TMB and TNB, which needs to further investigation. Therefore, these data revealed that the high TNB and lower neoantigen ITH might be a promising marker for predicting the efficacy of the combination therapy of anti-PD1 inhibitor and lenvatinib in ICC patients. Citation Format: Jianzhen Lin, Yiying Liu, Xu Yang, Yi Bai, Junyu Long, Junyu Long, Yongchao Li, Jiaqian Wang, Dongxu Wang, Xiaobo Yang, Mei Guan, Li Huo, Jie Pan, Ke Hu, Zhibo Gao, Haitao Zhao. Combinational markers of neoantigen intratumor heterogeneity and neoantigen burden predict progression-free survival for lenvatinib plus PD-1 blockade in patients with intrahepatic cholangiocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2250.

High spatiotemporal heterogeneity, clonal selection and neoantigen evolution in acquired sorafenib-resistant patient-derived xenograft models of hepatocellular carcinoma.

e15641 Background: Patient-derived xenograft (PDX) models have been regarded as valuable preclinical models for oncology drug development and exploring underlying mechanism of drug resistance. As the standard treatment option for advanced hepatocellular carcinoma (HCC), the survival benefit of sorafenib is modest. Even among those who initially responded well to sorafenib treatment, most patients ultimately develop progressive disease owing to acquired drug resistance. Understanding how selective pressure from sorafenib directs the evolution of HCC and shapes its clonal architecture is a central biological question with important clinical implications to combat acquired drug resistance. Methods: Three sorafenib-resistant PDX models were generated by continuous sorafenib treament for more than six months. Whole exome sequencing (WES) and RNA sequencing were performed. The subclone of mutation, fusion genes, and the evolving landscape of tumor neoantigens were further explored. Finally, the antitumor efficacy of recombinant mouse PD-1 antibody was evaluated in sorafenib resistance syngeneic tumors model by immune-competent C57BL/6J mice with Hepa 1-6. Results: High spatiotemporal heterogeneity was observed in engraftment among pre- and post- sorafenib resistance in established acquired-resistance PDX models. Clonal selection on engraftment was observed in established acquired-resistance PDX models. There are many high expressed genes, which showed subclone expansion with the emergence of sorafenib resistance. There is vary difference of neoantigens between pre- and post-resistance engraftment as well as sampling points in same tissues. It was presented that a high burden of clonal neoantigens in sorafenib resistant tissues (P &lt; 0.05), while there has no difference in tumor mutation burden. Moreover, the intra-tumor heterogeneity upon the neoantigen landscape was much bigger than that upon tumor mutation burden. We found that fusion subclone sizes were increased significantly after sorafenib resistance (P &lt; 0.05). Finally, the antitumor efficacy of recombinant mouse PD-1 antibody was confirmed in sorafenib resistance syngeneic tumors mice model (P &lt; 0.001). Conclusions: High spatiotemporal heterogeneity, clonal selection and neoantigen evolution was observed in acquired sorafenib-resistant PDX model of HCC. Immunotherapy such as immune checkpoint inhibitors might be a promising strategy for HCC patients with acquired sorafenib resistance. .

Neoantigen-directed immune escape in lung cancer evolution.

The interplay between an evolving cancer and adynamic immune microenvironment remains unclear. Here we analyse 258 regions from 88 early-stage, untreated non-small-cell lung cancers using RNA sequencing and histopathology-assessed tumour-infiltrating lymphocyte estimates. Immune infiltration varied both between and within tumours, with different mechanisms of neoantigen presentation dysfunction enriched in distinct immune microenvironments. Sparsely infiltrated tumours exhibited a waning of neoantigen editing during tumour evolution, indicative of historical immune editing, or copy-number loss of previously clonal neoantigens. Immune-infiltrated tumour regions exhibited ongoing immunoediting, with either loss of heterozygosity in human leukocyte antigens or depletion of expressed neoantigens. We identified promoter hypermethylation of genes that contain neoantigenic mutations as an epigenetic mechanism of immunoediting. Our results suggest that the immune microenvironment exerts a strong selection pressure in early-stage, untreated non-small-cell lung cancers that produces multiple routes to immune evasion, which are clinically relevant and forecast poor disease-free survival.

Dynamic Evolution of Clonal Composition and Neoantigen Landscape in Recurrent Metastatic Melanoma with a Rare Combination of Driver Mutations

In melanoma, initiating oncogenic mutations in BRAF or NRAS are detected in premalignant lesions that accumulate additional mutations and genomic instability as the tumor evolves to the metastatic state. Here we investigate evolution of clonal composition and neoantigen landscape in an atypical melanoma displaying recurrent cutaneous lesions over a 6-year period without development of extracutaneous metastases. Whole exome sequencing of four cutaneous lesions taken during the 6-year period identified a collection of single nucleotide variants and small insertions and deletions shared among all tumors, along with progressive selection of subclones displaying fewer single nucleotide variants. Later tumors also displayed lower neoantigen burden compared to early tumors, suggesting that clonal evolution was driven, at least in part, by counter selection of subclones with high neoantigen burdens. Among the selected mutations are a missense mutation in MAP2K1 (F53Y) and an inversion on chromosome 7 generating a AKAP9-BRAF fusion. The mutant proteins cooperatively activate the MAPK signaling pathway confirming they are potential driver mutations of this tumor. We therefore describe the long-term genetic evolution of cutaneous metastatic melanoma characterized by an unexpected phenotypic stability and neoantigen-driven clonal selection.

Impaired Cytolytic Activity and Loss of Clonal Neoantigens in Elderly Patients With Lung Adenocarcinoma

IntroductionWhether the efficacy of programmed death 1 (PD-1)/programmed death ligand 1 (PD-L1) inhibitors declines with senescence remains controversial for lung adenocarcinoma (LUAD). Responsiveness to anti–PD-1/PD-L1 therapy is thought to rely on neoantigen exposure and immune elements in the tumor microenvironment. In this study, we explored the features of the tumor immune microenvironment in elderly patients with treatment-naïve LUAD. MethodsTranscriptome profiles and clinical characteristics of patients with LUAD were retrieved from The Cancer Genome Atlas as a discovery cohort. Immune cell infiltration (quantified by a single-sample gene set enrichment analysis), immunoregulatory molecule expression, and mutational patterns (from The Cancer Immunome Atlas) were compared between young and elderly patients. Immune cell infiltration was verified by immunohistochemistry using a validation cohort including 105 treatment-naïve patients with LUAD. A tissue microarray consisting of 120 LUAD patients was used in the immunohistochemistry validation. ResultsActivated CD8+ T cell numbers increased slightly with age, but cytolytic molecules in T cells (granzyme B [GZMB], perforin 1 [PRF1], granzyme A [GZMA], granzyme M [GZMM], and granulysin [GNLY]) gradually declined. PD-L1 expression was not associated with age; however, a number of immunosuppressive elements beyond PD-L1 were upregulated in aging patients, including regulatory T cells and co-inhibitory molecules, for example, TIM-3, TIGIT, and HHLA2. Finally, senescence was accompanied by a loss of clonal neoantigens, which is believed to be correlated with responsiveness to immune checkpoint inhibitors. ConclusionsElderly patients were characterized by increased numbers of CD8+ T cells and impaired cytolytic molecule expression. The observed immune signature was also associated with a loss of clonal neoantigens and the accumulation of immunosuppressive elements. These findings show a unique immune microenvironment in senescence and support biomarker-guided candidate identification for anti–PD-1/PD-L1 therapeutic strategies for elderly patients with LUAD.

Immunotherapy with checkpoint inhibitors in non-small cell lung cancer: insights from long-term survivors.

Immune checkpoint inhibitors (ICIs) targeting the programmed cell death-1 (PD-1)-programmed cell death ligand-1 (PD-L1) axis have shown promising results in non-small cell lung cancer (NSCLC) patients, some of them with persistent responses to these agents that form a population of long-term survivors. Despite the variable definition of PD-L1 positivity in tumors, an association between expression and response has been reasonably consistent in advanced NSCLC. In addition, the clinical efficacy of ICIs seems to be related to the genomic landscape of the tumor in terms of mutational burden and clonal neoantigens. Furthermore, increasing evidence shows that excessive activation of the immune response elicited by ICIs, leading to immune-related toxicities, might be associated with an improved response to immunotherapy. There are still many unanswered questions about the proper use of these agents to maximize their efficacy, which may be improved through combination with radiation, chemotherapy, targeted therapies, or other immune mediators, including dual checkpoint blockade. To search for clues for addressing these challenges, this review focused on the characteristics and clinical features of long-term NSCLC survivors and the potential biomarkers of response to ICIs.

Abstract B111: Vaccination against TAP downregulation-induced neoantigens to prevent future tumor development in the setting of recurrence or premalignancy

Abstract Development of therapeutic strategies to prevent recurrence in cancer patients, or tumor progression in individuals at high risk of developing cancer, has been challenging given the long and often unpredictable time to the emergence of the malignant tumors. Mutation-generated neoantigens represent the most potent antigens to induce antitumor immunity, yet the ability to predict which neoantigens will be expressed in future tumors is at present not an option.To overcome the limitations of targeting mutated neoantigens, we have developed a simple and broadly applicable approach to induce neoantigens in tumor cells in situ by reducing the expression of peptide transporter TAP, whereby a TAP-specific siRNA is targeted to tumor cells in mice by conjugation to a broad-range nucleolin-binding aptamer. Nucleolin, normally expressed in the cytoplasm and nucleolus of all somatic cells, is translocated to the cell surface of most murine and human tumors and hence could serve as an almost universal target to deliver therapeutics to tumors in vivo. Previous results have demonstrated that genetic ablation of TAP not only inhibits the canonical antigen processing pathway but also upregulates alternative pathways presenting new epitopes, essentially neoantigens, that can be recognized by the immune system to elicit effective CD8+ T-cell responses. Such epitopes are shared among all (tumor) cells in which TAP is downregulated, corresponding to the functional equivalent of clonal mutation-generated neoantigens. Our study shows that transiently increasing the neoantigen burden of tumor cells in situ by targeted downregulation of TAP represent a potent way of generating antitumor immunity in the absence of measurable toxicity.Exploiting the ability to induce neoantigens in situ, we are developing a novel vaccination strategy targeting potent neoantigens to control the growth of the future tumors—whereby mice in remission or with premalignant lesions are first vaccinated against TAP downregulation-induced neoantigens, and when or if tumor develops the same antigens are induced in the tumor, termed prorapeutic vaccination (prophylactic + therapeutic). To induce an immune response against TAP downregulation-induced neoantigens, mice were vaccinated with TAP siRNAs that are targeted to DC in situ by conjugation to a short CpG oligonucleotide leading to the downregulation of TAP, expression of neoantigens, as well as activation of the DC, and thereby priming of a potent T-cell response. To induce neoantigens in the future tumors, the TAP siRNA is targeted to the developing tumor lesion by conjugation to the nucleolin (Nucl) aptamer. Both Nucl and CpG targeted siRNA are administered systemically via intraperitoneal injection to reach the disseminated tumor lesions and resident DC present throughout the body. In murine models of recurrence and premalignant disease, prorapeutic vaccination elicited an adaptive and innate antitumor immune response and inhibited tumor growth. The prorapeutic vaccination approach was more effective than vaccinating against prototypic mutated neoantigens, and did not elicit measurable autoimmune toxicity, in stark contrast to a comparatively therapeutic dose of CTLA-4.The ability to vaccinate against experimentally induced neoantigens using a broadly applicable procedure with two chemically synthesized reagents, introduces a new paradigm in cancer immunotherapy of vaccinating against neoantigens induced in future tumors, to prevent recurrence in patients in remission or preventing tumor development in individuals at high risk of developing cancer. Citation Format: Greta Garrido Hidalgo, Brett Schrand, Ailem Rabasa, Agata Levay, Tal Gefen, Giri Bhuwan Bhuwan, Anthony R. Ferrantella, Vikas Dudeja, Koen Marijt, Thorbald T. van Hall, Eli Gilboa. Vaccination against TAP downregulation-induced neoantigens to prevent future tumor development in the setting of recurrence or premalignancy [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 B111.

Abstract PR15: The oncometabolite R-2-Hydroxyglutarate suppresses the innate immune microenvironment of IDH1-mutated gliomas via aryl hydrocarbon receptor signaling

Abstract Background: IDH1-mutated gliomas are associated with less abundant and phenotypically skewed innate and adaptive immune cell infiltrates compared to IDH1 wild-type tumors. Despite this, the most frequent mutation—IDH1R132H—represents a clonal shared neoantigen and mutations in IDH are associated with a more favorable prognosis. While the tumor cell-intrinsic consequences of the oncometabolite R-2-hydroxyglutarate (R-2-HG) accumulating in IDH1-mutated gliomas as a result of a neomorphic enzymatic function are well-characterized, potential direct paracrine effects of R-2-HG influencing the glioma immune microenvironment remain incompletely understood. Aim: This study aimed at characterizing the impact of the oncometabolite R-2-HG on the innate immune microenvironment of IDH1-mutated gliomas. Methods and Results: By means of comprehensive analyses of expression datasets from human gliomas and syngeneic murine tumor models as well as transporter studies, we demonstrate that R-2-HG is imported by both microglia and macrophages via SLC family transporters and suppresses their function in a paracrine manner. Functional analyses of microglia and macrophages indicate an R-2-HG-driven induction of tolerogenicity as evidenced by accumulation of IL10 and TGFβ and suppression of MHC-II expression, which results in impaired activation of antigen-specific T-cells and activation of immune checkpoint molecules. Multilevel signature profiling of human tumor-infiltrating as well as primary immune cells was complemented by reporter gene assays and pathway analyses and revealed that R-2-HG activates the cytosolic transcription factor aryl hydrocarbon receptor (AHR), a key immunomodulatory target of immunosuppressive tryptophan metabolism. By means of knockout models, the observed immunosuppressive phenotype was shown to be AHR-dependent. Functional relevance of R-2-HG-mediated, AHR-driven impairment of myeloid cell immunity was demonstrated in vivo by pharmacologic AHR inhibition, increasing the efficacy of checkpoint blockade. Conclusion: R-2-HG impairs antitumor immunity in IDH1-mutated gliomas by activating the AHR in innate immune cells, thus suppressing the innate immune microenvironment by compromising antigen presentation and activation of antigen-specific T-cells. This, together with recent findings on inhibitory effects on T-cell immunity, represents a novel mechanism of immune evasion of an immunogenic driver mutation and opens a novel therapeutic approach to IDH1-mutated gliomas. Citation Format: Mirco Friedrich, Lukas Bunse, Theresa Bunse, Edward Green, Tobias Kessler, Stefan Pusch, Katrin Deumelandt, Rafael Carretero, Andreas von Deimling, Francisco J Quintana, Wolfgang Wick, Michael Platten. The oncometabolite R-2-Hydroxyglutarate suppresses the innate immune microenvironment of IDH1-mutated gliomas via aryl hydrocarbon receptor signaling [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 PR15.

Neoepitopes-based vaccines: challenges and perspectives

First generations of cancer vaccines using shared tumour antigens have been associated with disappointing clinical results. However, the paradigm shift introduced by immune checkpoint inhibitors has led to a renewed interest on anti-tumoural vaccination based on mutation-associated neoantigens. First clinical results are encouraging with some signs of clinical activity associated with induction of a specific immune response. In advanced or metastatic diseases, vaccination may either enhance the response to Programmed cell death 1 (PD-1/-L1) antagonists by increasing the number of effectors within the tumour or induce an anti-tumoural T-cell response in immunologically ‘cold’ tumours. There is also a strong rationale to use cancer vaccines in an adjuvant setting to induce a long-term control of the residual disease. Prediction of neoepitopes efficiently presented by Human Leukocyte Antigen (HLA) molecules remains a challenge, as well as identification of clonal neoantigens. Some mechanisms of resistance are already identified, such as tumour loss of neoepitopes-presenting HLA class I molecules. In this context, the role of CD4+ T cells induced by different cancer vaccines should be clarified. Finally, although studies have focused on mutated epitopes corresponding to single nucleotide variants, other neoantigens could be of strong interest such as those linked to tumour specific RNA-splicing abnormalities or associated with insertions-deletions.

PC06.03 Tumor Mutation Burden - PRO

PC06.03 Tumor Mutation Burden - PRO

Abstract A69: Mutagenicity of urea cycle dysregulation and its implications for cancer immunotherapy

Abstract Immune checkpoint therapy leads to durable clinical responses in many cancer patients, but fails in others. To improve the clinical response to immunotherapy, it is highly important to identify predictive biomarkers. While checkpoint genes’ expression levels, tumor neo-antigen load and microsatellite instability (MSI) have been associated with enhanced response to checkpoint immunotherapies, they yet provide only a modest predictive signal and hence there is a need to identify additional predictive factors. Specifically, while there is growing evidence that metabolic alterations can affect the tumor and modulate the immune response, the potential effects of altered cancer metabolism on tumor mutagenesis and immunotherapy remain unexplored. The urea cycle (UC) converts excess nitrogen derived from the breakdown of nitrogen-containing molecules (e.g., ammonia) to urea, a relatively non-toxic and disposable nitrogenous compound. We and others have shown that silencing of the UC enzyme ASS1 promotes cancer proliferation by diverting its substrate aspartate toward CAD enzyme, which mediates the first three reactions in the pyrimidine synthesis pathway. We now demonstrate, by analysis of the TCGA data, tumor samples and cancer cell line experiments, that UC dysregulation (UCD) is a much wider common metabolic phenomenon that maximizes nitrogen utilization in cancer, favoring pyrimidine synthesis over urea disposal. Of note, while UCD is significantly associated with decreased cancer patient survival, the overall mutational load is not. Remarkably, we find that the UCD changes the 1:1 purine (R)-to-pyrimidine (Y) ratio in favor of pyrimidine in cancer cells. Moreover, in analysis of both TCGA data and UC perturbed cancer cells we find that: (a) UCD is significantly associated with a novel and unique pattern of purine-to-pyrimidine transversion mutational bias across many cancer types at the DNA coding (sense) strand, and (b) this trend becomes stronger and more significant at both the mRNA and protein levels, testifying to its functional implications. Notably, the overall mutational load in cancer is negatively correlated with UCD, testifying to their independence. To test whether the mutational bias is associated with better immunotherapy response, we analyze published data of three large melanoma cohorts. We find that responders of both anti-PD1 and anti-CTLA4 therapy exhibit significantly higher UCD and R-&amp;gt;Y mutational bias than non-responders. We further observe that the peptides carrying transverse R-&amp;gt;Y mutations are preferentially presented as neoantigens in responders independent of mutational load, and this trend becomes significant for more clonal neoantigens, promoting UCD as a potential biomarker for the success of immunotherapy. Finally, as nitrogen metabolites are excreted in the urine, we hypothesize that these changes may be detectable in urine of UCD-cancers. We observe increased levels of pyrimidine derived metabolites in the urine of mice bearing colon tumors associated with UCD in the tumors compared to normal intestine. In an analogous manner, we find significantly higher levels pyrimidine derived metabolites in the urine of human patients with prostate cancer compared to controls. Collectively, these results support our hypothesis that UCD is a prevalent metabolic phenomenon in cancer, generating mutational biased neo-peptides, worsening patients’ prognosis and yet enhancing the response to immune therapy independent of mutational load and MSI. Taken together, our findings point to the important role of UCD in a broad spectrum of cancers, to the potential use of UCD related metabolites as cancer biomarkers, and last but not least, to the role of UCD in predicting response to immune check point therapy. Broadly, our results suggest future therapeutic interventions aiming to increase UCD levels to enhance the coverage and efficiency of cancer immunotherapy. Citation Format: Joo Sang Lee, Narin Carmel, Hiren Karathia, Noam Auslander, Shiran Rabinovich, Rom Keshet, Noa Stettner, Alon Silberman, Lilach Agemy, Daniel Helbling, Raya Eilam, Qin Sun, Alexander Brandis, Hila Weiss, David Dimmock, Noam Stern-Ginossar, Avigdor Scherz, Igor Ulitsky, Sandesh CS Nagamani, Ronit Elhasid, Sridhar Hannenhalli, Eytan Ruppin, Ayelet Erez. Mutagenicity of urea cycle dysregulation and its implications for cancer immunotherapy [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2017 Oct 1-4; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2018;6(9 Suppl):Abstract nr A69.

Treatment resistance in urothelial carcinoma: an evolutionary perspective.

The emergence of treatment-resistant clones is a critical barrier to cure in patients with urothelial carcinoma. Setting the stage for the evolution of resistance, urothelial carcinoma is characterized by extensive mutational heterogeneity, which is detectable even in patients with early stage disease. Chemotherapy and immunotherapy both act as selective pressures that shape the evolutionary trajectory of urothelial carcinoma throughout the course of the disease. A detailed understanding of the dynamics of evolutionary drivers is required for the rational development of curative therapies. Herein, we describe the molecular basis of the clonal evolution of urothelial carcinomas and the use of genomic approaches to predict treatment responses. We discuss various mechanisms of resistance to chemotherapy with a focus on the mutagenic effects of the DNA dC->dU-editing enzymes APOBEC3 family of proteins. We also review the evolutionary mechanisms underlying resistance to immunotherapy, such as the loss of clonal tumour neoantigens. By dissecting treatment resistance through an evolutionary lens, the field will advance towards true precision medicine for urothelial carcinoma.

Somatic POLE exonuclease domain mutations are early events in sporadic endometrial and colorectal carcinogenesis, determining driver mutational landscape, clonal neoantigen burden and immune response.

Genomic instability, which is a hallmark of cancer, is generally thought to occur in the middle to late stages of tumourigenesis, following the acquisition of permissive molecular aberrations such as TP53 mutation or whole genome doubling. Tumours with somatic POLE exonuclease domain mutations are notable for their extreme genomic instability (their mutation burden is among the highest in human cancer), distinct mutational signature, lymphocytic infiltrate, and excellent prognosis. To what extent these characteristics are determined by the timing of POLE mutations in oncogenesis is unknown. Here, we have shown that pathogenic POLE mutations are detectable in non‐malignant precursors of endometrial and colorectal cancer. Using genome and exome sequencing, we found that multiple driver mutations in POLE‐mutant cancers show the characteristic POLE mutational signature, including those in genes conventionally regarded as initiators of tumourigenesis. In POLE‐mutant cancers, the proportion of monoclonal predicted neoantigens was similar to that in other cancers, but the absolute number was much greater. We also found that the prominent CD8+ T‐cell infiltrate present in POLE‐mutant cancers was evident in their precursor lesions. Collectively, these data indicate that somatic POLE mutations are early, quite possibly initiating, events in the endometrial and colorectal cancers in which they occur. The resulting early onset of genomic instability may account for the striking immune response and excellent prognosis of these tumours, as well as their early presentation. © 2018 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.

Abstract 2617: Inducing neoantigens in therapeutic and prophylactic cancer immunotherapy

Abstract Correlation between clonal neoantigen burden (neoantigens generated early in tumorigenesis and therefore represented at high frequency in all tumor lesions) and responsiveness to checkpoint blockade has underscored the relevance of neoantigens in promoting tumor immunogenicity. Yet, the most of patients do not express, or express low numbers of, clonal neoantigens, and consequently will be less likely to benefit from checkpoint blockade. We describe strategies to generate de novo neoantigens in the patient’ disseminated tumors and show that in mouse tumor models they potentiate checkpoint blockade. We previously showed that tumor inhibition of the Nonsense-mediated mRNA decay (NMD) results in the neoantigens’ induction and reduces tumor growth (Pastor et al., 2010). We now demonstrate that tumor-targeted NMD inhibition potentiates PD-1 blockade. A general concern and potential limitation of this approach is that a significant proportion of the induced neoepitopes come from mutated products and hence will not be shared by all tumor lesions. To that end, we are exploring alternative strategies by targeting key components of antigen presentation pathways, specifically the TAP transporter, ERAAP peptidase, and Invariant chain. Studies show that downregulation of these products, not only reduces the canonical antigenic presentation but also upregulates alternative pathways that present new, otherwise silent or subdominant, epitopes. Since such epitopes are not generated by random events they are more likely to represent clonal neoepitopes. We are developing approaches to inhibit the aforementioned mediators using corresponding siRNAs targeted to tumor cells by conjugation to a nucleolin-binding aptamer. Nucleolin, a nucleolar product, is translocated to the surface the majority of tumors and thereby serves as a broad target to deliver therapeutic cargo to the disseminated tumors. We show that nucleolin aptamer-targeted downregulation of TAP, ERAAP or Invariant chain inhibits tumor growth and potentiates PD-1 blockade. Recent studies suggest that tumor neoantigen-specific T cells are dysfunctional due to constant antigenic exposure. Transiently expressed siRNA inhibition-induced neoantigens are not expected to be defective. Ongoing studies explore the combinatorial use of neoantigen induction methods with others immune potentiating strategies. Prophylactic cancer vaccination obviates the limitations of therapeutic vaccination. A major barrier for developing this modality is the choice of antigens that will appear in the future cancer. The ability to induce tumor neoantigens can serve the basis for developing a new approach to prophylactic, though not preventative, cancer vaccination whereby neoantigens are induced in the healthy individual (at risk for cancer), and if or when a cancer develops induce the same antigens in the patient’ tumor by the methods described above. Preliminary studies in mice show that the approach has merit. Citation Format: Greta Garrido Hidalgo, Agata Levay, Alexey Berezhnoy, Brett Schrand, Eli Gilboa. Inducing neoantigens in therapeutic and prophylactic cancer immunotherapy [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 2617. doi:10.1158/1538-7445.AM2017-2617

Quantitative Shotgun Proteomics Unveils Candidate Novel Esophageal Adenocarcinoma (EAC)-specific Proteins

Esophageal cancer is the eighth most common cancer worldwide and the majority of patients have systemic disease at presentation. Esophageal adenocarcinoma (OAC), the predominant subtype in western countries, is largely resistant to current chemotherapy regimens. Selective markers are needed to enhance clinical staging and to allow targeted therapies yet there are minimal proteomic data on this cancer type. After histological review, lysates from OAC and matched normal esophageal and gastric samples from seven patients were subjected to LC MS/MS after tandem mass tag labeling and OFFGEL fractionation. Patient matched samples of OAC, normal esophagus, normal stomach, lymph node metastases and uninvolved lymph nodes were used from an additional 115 patients for verification of expression by immunohistochemistry (IHC).Over six thousand proteins were identified and quantified across samples. Quantitative reproducibility was excellent between technical replicates and a moderate correlation was seen across samples with the same histology. The quantitative accuracy was verified across the dynamic range for seven proteins by immunohistochemistry (IHC) on the originating tissues. Multiple novel tumor-specific candidates are proposed and EPCAM was verified by IHC.This shotgun proteomic study of OAC used a comparative quantitative approach to reveal proteins highly expressed in specific tissue types. Novel tumor-specific proteins are proposed and EPCAM was demonstrated to be specifically overexpressed in primary tumors and lymph node metastases compared with surrounding normal tissues. This candidate and others proposed in this study could be developed as tumor-specific targets for novel clinical staging and therapeutic approaches.