Neoadjuvant durvalumab plus radiation versus durvalumab alone in stages I-III non-small cell lung cancer: survival outcomes and molecular correlates of a randomized phase II trial

We previously reported the results of a randomized phase II trial (NCT02904954) in patients with early-stage non-small cell lung cancer (NSCLC) who were treated with either two preoperative cycles of the anti-PD-L1 antibody durvalumab alone or combined with immunomodulatory doses of stereotactic radiation (DRT). The trial met its primary endpoint of major pathological response, which was significantly higher following DRT with no new safety signals. Here, we report on the prespecified secondary endpoint of disease-free survival (DFS) regardless of treatment assignment and the prespecified exploratory analysis of DFS in each arm of the trial. DFS at 2 and 3 years across patients in both arms of the trial were 73% (95% CI: 62.1-84.5) and 65% (95% CI: 52.5-76.9) respectively. For the exploratory endpoint of DFS in each arm of the trial, three-year DFS was 63% (95% CI: 46.0-80.4) in the durvalumab monotherapy arm compared to 67% (95% CI: 49.6-83.4) in the dual therapy arm. In addition, we report post hoc exploratory analysis of progression-free survival as well as molecular correlates of response and recurrence through high-plex immunophenotyping of sequentially collected peripheral blood and gene expression profiles from resected tumors in both treatment arms. Together, our results contribute to the evolving landscape of neoadjuvant treatment regimens for NSCLC and identify easily measurable potential biomarkers of response and recurrence.

Systematic elucidation and pharmacological targeting of tumor-infiltrating regulatory T cell master regulators

Due to their immunosuppressive role, tumor-infiltrating regulatory T cells (TI-Tregs) represent attractive immuno-oncology targets. Analysis of TI vs. peripheral Tregs (P-Tregs) from 36 patients, across four malignancies, identified 17 candidate master regulators (MRs) as mechanistic determinants of TI-Treg transcriptional state. Pooled CRISPR-Cas9 screening in vivo, using a chimeric hematopoietic stem cell transplant model, confirmed the essentiality of eight MRs in TI-Treg recruitment and/or retention without affecting other T cell subtypes, and targeting one of the most significant MRs (Trps1) by CRISPR KO significantly reduced ectopic tumor growth. Analysis of drugs capable of inverting TI-Treg MR activity identified low-dose gemcitabine as the top prediction. Indeed, gemcitabine treatment inhibited tumor growth in immunocompetent but not immunocompromised allografts, increased anti-PD-1 efficacy, and depleted MR-expressing TI-Tregs in vivo. This study provides key insight into Treg signaling, specifically in the context of cancer, and a generalizable strategy to systematically elucidate and target MR proteins in immunosuppressive subpopulations.

Abstract 4115: KLRG1 marks tumor-infiltrating CD4 T cell subsets associated with immune escape and immunotherapy response

Current methods for biomarker discovery and target identification in immuno-oncology rely on static snapshots of tumor immunity. To better capture the dynamic and compartmentalized nature of antitumor immune responses, we generated longitudinal “temporal atlases” of productive versus non-productive antitumor immune responses in murine tumor models. We utilized a 34-parameter full spectrum flow cytometry panel to comprehensively profile immune composition within tumors, draining and non-draining lymph nodes, and blood in and around key inflection points of tumor regression or progression. We leveraged two distinct preclinical models for this; the NPK-C1 ectopic prostate cancer model to map dynamics of spontaneous cancer immunoediting, and anti-PD-1 treated MC38 tumors to study response or non-response to immune checkpoint blockade (ICB). We utilized UMAP and FlowSOM algorithms for iterative dimensionality reduction and clustering, respectively, to reveal novel phenotypes associated with productive versus non-productive immunity across model systems, tissues, and time points. We discovered expression of KLRG1 within the intratumoral CD4 T cell compartment was highly associated with tumor progression and response to ICB. Specifically, both FoxP3+ Tregs and FoxP3- Tconv cells within tumors accumulated KLRG1 expression through disease progression, but this was not observed in CD4 T cell or other immune subsets residing in lymph nodes or circulating in blood. Among all intratumoral clusters, KLRG1+ Tconv were the only subset significantly correlated with tumor burden at each time point tested and across both models. KLRG1+ Tconv were significantly enriched in NPK-C1 tumors undergoing progression to escape versus those under immune-mediated equilibrium (p=0.0004) and were lost in animals undergoing curative responses to ICB (p=0.003). In the Treg compartment, unsupervised clustering revealed a KLRG1+Helios- tumor Treg subset that was positively correlated with transition from equilibrium to escape in the NPK-C1 model (p=0.005). Also indicating a potential functional significance, this phenotype was absent in tumors undergoing curative responses to ICB (p=0.0002). Systematic investigation of the functional characteristics, transcriptional programming, and translational significance of intratumoral KLRG1+ CD4 T cell subsets is ongoing. Together, these findings identify KLRG1+ CD4 T cell populations as subsets for further investigation in cancer and demonstrate the utility of longitudinal full spectrum flow cytometry profiling as an engine of dynamic biomarker and/or target discovery in immuno-oncology.

Citation Format: Casey Ager, Matthew Chaimowitz, Shruti Bansal, Meri Rogava, Johannes Melms, Catherine Spina, Cory Abate-Shen, Charles G. Drake, Matthew Dallos, Benjamin Izar. KLRG1 marks tumor-infiltrating CD4 T cell subsets associated with immune escape and immunotherapy response. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4115.

758 High-potency synthetic STING agonists rewire the myeloid stroma in the tumour microenvironment to amplify immune checkpoint blockade efficacy in refractory pancreatic ductal adenocarcinoma

Background

Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignancies and is clinically unresponsive to immune checkpoint blockade (ICB) immunotherapy.1 2 High densities of immunosuppressive myeloid cells,3 a paucity of antigen-presenting cells4–6 and T cell exclusion from tumour microenvironment7 all contribute to the refractory nature of PDAC to immune-based therapies. We and others have shown that innate immune activation of myeloid stroma via engagement of the STING (Stimulator of Interferon Genes) pathway can mediate proinflammatory remodeling and trigger a flood of T cell infiltration into otherwise 'cold' tumours.8–11 To that end, intratumoral injection of cyclic dinucleotide (CDN) agonists of the STING pathway has been shown to foster local and abscopal tumor immunity.8–10 Despite proven therapeutic efficacy in preclinical models, the mechanistic basis at a cellular level of how CDNs reprogram the suppressive myeloid stroma to sensitise tumours to ICB is poorly understood.

Methods

Using RNA sequencing and protein arrays we profiled myeloid-derived suppressor cell (MDSC) and M2 macrophage function following stimulation with CDNs of ascending potency. We describe the effects of CDN STING agonists on cell cycle dynamics, metabolic reprogramming and c-Myc expression in MDSCs. Next, in an orthotopic Kras+/G12DTP53+/R172HPdx1-Cre (KPC)-derived model of PDAC, we determined the ability of intratumorally-administered CDNs to sensitise PDAC to checkpoint blockade using bioluminescent in vivo imaging and multi-parameter flow cytometry of tumor stroma post-therapy.

Results

Multi-omics profiling of MDSCs and M2 Macrophages of human and murine origin show that high-potency synthetic STING agonists rewire these populations from immunosuppressive to immune-permissive phenotypes in part through inhibition of c-Myc signaling, energy metabolic modulation, and antagonism of cell cycle. Intratumoral injection of the STING agonist, IACS-8803 resulted in an amplified therapeutic response to checkpoint blockade that was dependent on T/NK cell infiltration into the tumour. Furthermore, dimensionality reduction analyses of multiparameter flow cytometry data show proinflammatory remodeling of the myeloid stroma and enhanced T cell function as salient features of synthetic agonists versus natural CDNs in orchestrating the in vivo therapeutic benefit.

Conclusions

This study uncovers molecular and cellular mechanisms by which STING agonists drive proinflammatory conversion of tumour myeloid stroma. We are the first to report that synthetic CDN STING agonists affect MDSC and M2 macrophage repolarization through altering energy metabolism and c-Myc signalling. Lastly, we demonstrate the potential for high-potency STING agonists to overcome resistance to checkpoint blockade in an aggressive orthotopic tumour model of PDAC.

References

Royal RE, Levy C, et al. Phase 2 trial of single agent Ipilimumab (anti-CTLA-4) for locally advanced or metastatic pancreatic adenocarcinoma. J Immunother 2010;33(8):828–33.

Brahmer JR, Tykodi SS, et al. Safety and activity of anti-PD-L1 antibody in patients with advanced cancer. N Engl J Med 2012;366(26):2455–65.

Karakhanova S, Link J. Characterization of myeloid leukocytes and soluble mediators in pancreatic cancer: importance of myeloid-derived suppressor cells. Oncoimmunology 2015;4:e998519.

Dallal RM, Christakos P, et al. Paucity of dendritic cells in pancreatic cancer. Surgery 2002;131:135–138.

Yamamoto T, Yanagimoto H, et al. Circulating myeloid dendritic cells as prognostic factors in patients with pancreatic cancer who have undergone surgical resection. J Surg Res 2012;173:299–308.

Hegde S, Krisnawan V, et al. Dendritic cell paucity leads to dysfunctional immune surveillance in pancreatic cancer. Cancer Cell 2020;37(3):289–307.

Beatty GL, Winograd R, et al. Exclusion of T cells from pancreatic carcinomas in mice is regulated by Ly6Clow F4/80+ extratumoral macrophages. Gastroenterology 2015;149(1):201–210.

Baird JR, Friedman D, et al. Radiotherapy combined with novel STING-Targeting oligonucleotides results in regression of established tumors. Cancer Res 2016;76(1):50–61.

Ager CR, Reilley MJ, et al. Intratumoral STING activation with T-cell checkpoint modulation generates systemic antitumor immunity. Cancer Immunol Res 2017;5(8):676–84.

Smith TT, Moffett HF, et al. Biopolymers codelivering engineered T cells and STING agonists can eliminate heterogeneous tumors. J Clin Invest 2017;127(6):2176–91.

Jing W, McAllister D, et al. STING agonist inflames the pancreatic cancer immune microenvironment and reduces tumor burden in mouse models. J Immunother Cancer 2019;7(1):115.

Single-cell protein activity analysis identifies recurrence-associated renal tumor macrophages

Clear cell renal carcinoma (ccRCC) is a heterogeneous disease with a variable post-surgical course. To assemble a comprehensive ccRCC tumor microenvironment (TME) atlas, we performed single-cell RNA sequencing (scRNA-seq) of hematopoietic and non-hematopoietic subpopulations from tumor and tumor-adjacent tissue of treatment-naive ccRCC resections. We leveraged the VIPER algorithm to quantitate single-cell protein activity and validated this approach by comparison to flow cytometry. The analysis identified key TME subpopulations, as well as their master regulators and candidate cell-cell interactions, revealing clinically relevant populations, undetectable by gene-expression analysis. Specifically, we uncovered a tumor-specific macrophage subpopulation characterized by upregulation of TREM2/APOE/C1Q, validated by spatially resolved, quantitative multispectral immunofluorescence. In a large clinical validation cohort, these markers were significantly enriched in tumors from patients who recurred following surgery. The study thus identifies TREM2/APOE/C1Q-positive macrophage infiltration as a potential prognostic biomarker for ccRCC recurrence, as well as a candidate therapeutic target.

Abstract PO009: Single-cell protein activity inference identifies tumor-enriched macrophages associated with early post-surgical disease recurrence

Primary Clear Cell Renal Carcinoma (ccRCC) is a highly heterogenous disease with a variable disease course post-surgery. To elucidate the cellular and transcriptional mechanisms driving disease recurrence, we aimed in this study to transcriptionally profile single-cell populations enriched in the Tumor Micro-Environment (TME) and assess their key regulatory proteins as biomarkers of recurrence. We performed scRNASeq on immune and non-immune populations from tumor compared to tumor-adjacent tissue in primary resections of treatment-naïve ccRCC patients (n=11), thus producing a complete atlas of the ccRCC tumor microenvironment. In order to mitigate gene dropout inherent to scRNASeq and commonly preventing detection of >80% of genes, we leveraged the VIPER algorithm to infer proteomic regulators of cell state. This approach relies on construction of lineage-specific gene regulatory networks with ARACNe, the Algorithm for Reconstruction of Accurate Cellular Networks, and infers protein activity from expression of hundreds of downstream transcriptional targets. By VIPER, we recover key regulatory proteins not significantly detected by gene expression alone, and improve resolution of cell subtypes. VIPER-inferred protein activity systematically abrogated gene dropout effects on a repertoire of >6,000 regulatory proteins, comparing favorably with antibody-based measurements for a subset of proteins profiled by spectral flow cytometry. This helped comprehensively characterize the individual cellular sub-populations comprising the ccRCC tumor and peri-tumor microenvironment, as well as their specific master regulators and candidate cell-cell interactions, revealing several populations undetectable by gene expression analysis. Specifically, we uncovered a novel tumor-specific macrophage subpopulation characterized by significant upregulation of TREM2, APOE, and C1Q, further validated by spatially-resolved quantitative multispectral immunofluorescence (qmIF). These tumor-specific macrophages were significantly over-represented in an exploratory cohort of patients who recurred following surgery compared to patients who did not recur (n=8), predictive of time-to-recurrence with a p-value of 0.0067. In a larger validation cohort (n=157), enrichment of tumor-specific macrophage population markers was associated with early post-surgical recurrence with a p-value of 0.0029. This study highlights the substantial increase in resolution of scRNASeq analysis afforded by VIPER and identifies TREM2/APOE/C1Q-positive macrophage infiltration as a potential biomarker for ccRCC recurrence and a candidate target for intervention to reduce post-surgical recurrence rates.

Citation Format: Aleksandar Obradovic, Nivedita Chowdhury, Casey Ager, Vinson Wang, Lukas Vlahos, Xinzheng Guo, David Aggen, Andrea Califano, Charles Drake. Single-cell protein activity inference identifies tumor-enriched macrophages associated with early post-surgical disease recurrence [abstract]. In: Proceedings of the AACR Virtual Special Conference on the Evolving Tumor Microenvironment in Cancer Progression: Mechanisms and Emerging Therapeutic Opportunities; in association with the Tumor Microenvironment (TME) Working Group; 2021 Jan 11-12. Philadelphia (PA): AACR; Cancer Res 2021;81(5 Suppl):Abstract nr PO009.

The SPARC-1 trial: A phase I study of neoadjuvant combination interleukin-1 beta and PD-1 blockade in localized clear cell renal cell carcinoma

TPS373

Background: Immune checkpoint blockade has significantly improved outcomes for patients with renal cell carcinoma (RCC) in the metastatic setting. However, there is currently no neoadjuvant systemic therapy that improves outcomes for patients with localized RCC. Emerging data suggests that immunosuppressive myeloid cell populations within the tumor microenvironment (TME) represent a key mechanism of adaptive immune resistance. In pre-clinical models, targeting interleukin 1 beta (IL-1beta) can successfully re-establish anti-tumor immunity by shifting the myeloid cells towards M1-like tumor associated macrophages (TAM) and decreasing infiltration of immunosuppressive myeloid-derived suppressor cells (MDSCs). The SPARC-1 study is testing the hypothesis that neoadjuvant therapy with combined IL-1beta blockade (canakinumab) plus PD-1 blockade (spartalizumab) is safe and can successfully remodel the myeloid compartment towards a pro-inflammatory state in patients with localized RCC. Methods: This is a single-center, single-arm, phase I trial of patients with localized clear cell RCC (ccRCC) planned for nephrectomy (stage T1b-T4NanyM0). 14 patients will receive immunotherapy with combination canakinumab (300mg IV) plus spartalizumab (400mg IV) every 4 weeks x 2 doses given 6 weeks prior to nephrectomy. The primary endpoints are safety and feasibility. Secondary endpoints include tumor CD8 T cell infiltration, tumor MDSC infiltration and objective response rate. SPARC-1 offers a unique opportunity to utilize fresh tumor tissue to identify changes in the immune TME with single-cell discrimination following therapy. Therefore, correlative studies will include single-cell RNA-sequencing, multi-color flow cytometry and multiplexed immunofluorescence to quantify changes in the density and spatial proximity of distinct immune cell populations within the TME. The study is open with 4 patient currently enrolled at the time of submission. Clinical trial information: NCT04028245 .

Abstract PO-024: Tumor-specific cell populations in clear cell renal carcinoma associated with clinical outcome identified using single-cell protein activity inference

Primary Clear Cell Renal Carcinoma (ccRCC) is a highly heterogenous disease with a variable disease course post-surgery, and ccRCC tumor micro-environment has thus far not been characterized at the single-cell level with the whole-transcriptome resolution enabled by single-cell RNA Sequencing (scRNASeq). To elucidate the cellular and transcriptional mechanisms driving disease recurrence, we performed scRNASeq on both hematopoietic and non-hematopoietic populations from tumor and tumor-adjacent tissue from primary resections of treatment-naïve ccRCC patients (n=11), thus producing a complete atlas of the ccRCC tumor microenvironment. Furthermore, in order to mitigate gene dropout inherent to scRNASeq and commonly preventing detection of >80% of genes, we leveraged the VIPER algorithm, which quantitates protein activity, to infer the proteomic regulators of cell state. Clustering at the gene expression level enabled construction of lineage-specific gene regulatory networks applying ARACNe, the Algorithm for Reconstruction of Accurate Cellular Networks, from which protein activity of upstream regulatory molecules could be inferred by VIPER. Comparison with protein-level expression data from antibody-based, high-parameter spectral flow cytometry in the same patients shows that VIPER-measured protein activity systematically abrogated gene dropout effects on a repertoire of >6,000 regulatory proteins, comparing favorably with antibody-based measurements. This helped comprehensively characterize the individual cellular sub-populations comprising the ccRCC tumor and peri-tumor microenvironment, as well as their specific master regulators and candidate cell-cell interactions, revealing several populations undetectable by gene expression analysis. Specifically, we uncovered a novel tumor-specific, macrophage subpopulation characterized by significant upregulation of TREM2, APOE, and C1Q, as validated by spatially-resolved, quantitative multispectral immunofluorescence (qmIF). These tumor-specific macrophages were statistically significantly over-represented in a separate validation cohort of patients who recurred following surgery (n=4) compared to patients who did not recur (n=4). This study highlights the substantial resolution increase afforded by VIPER and identifies TREM2/APOE/C1Q-positive macrophage infiltration as a potential biomarker for ccRCC recurrence and a candidate target for intervention. Furthermore, it provides a highly-generalizable methodology to study the role of rare subpopulations by leveraging VIPER on scRNASeq data.

Citation Format: Aleksandar Obradovic, Nivedita Showdhury, Casey Ager, Vinson Wang, Lukas Vlahos, Xinzheng V. Guo, David H. Aggen, James McKiernan, Andrea Califano, Charles G. Drake. Tumor-specific cell populations in clear cell renal carcinoma associated with clinical outcome identified using single-cell protein activity inference [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr PO-024.

Abstract PR02: Melanoma evolves complete immunotherapy resistance through acquisition of a hypermetabolic phenotype

Advances in our understanding of tumor immune biology and development of cancer immunotherapies have led to improved outcomes for patients who suffer from aggressive cancers such as melanoma. Despite the clinical success of immune checkpoint blockade, a majority of patients still fail to respond, and the underlying mechanisms that drive resistance remain unclear. To understand why a subset of tumors fail to respond to immunotherapy, we established a novel murine model of melanoma that is fully resistant to immune checkpoint blockade. By in vivo passaging nonresponding B16 melanoma tumor cells, we selected for a resistant variant that fails to respond to the combination of CTLA-4, PD-1, and PD-L1 blockade. In comparing gene expression of parental versus resistant tumor cells and analyzing the corresponding immune infiltrate, we determined the adaptations associated with resistance to therapy. We found that evasion of immunotherapy was associated with a “hypermetabolic” phenotype, characterized by an upregulation of glycolytic, oxidoreductase, and mitochondrial oxidative phosphorylation pathways to establish a hypoxic, metabolically hostile microenvironment. Enforced expression of two key genes associated with these pathways in parental tumor cells was sufficient to mediate resistance to triple checkpoint blockade. Flow cytometry assays determined that T cells infiltrating resistant tumors had diminished glycolytic capacity and effector function, indicating a metabolic disadvantage. Consistent with our findings, melanoma patients who failed dual checkpoint blockade exhibited similar metabolic alterations as seen in our resistant variant. Using a novel MRI-based imaging approach, we observed distinct metabolic changes that stratified responding versus nonresponding tumors in live mice. Applying this method to patients could provide insight into predicting response rates to checkpoint modulation. Overall, our data indicate that resistant melanoma tumor cells acquire a “hypermetabolic” phenotype to establish a hostile microenvironment that is capable of inhibiting the antitumor immune response.

This abstract is also being presented as Poster A24.

Citation Format: Ashvin R. Jaiswal, Arthur J. Liu, Shivanand Pudakalakatti, Prasanta Dutta, Priyamvada Jayaprakash, Todd Bartkowiak, Casey Ager, Zhiqiang Wang, Alex Reuben, Zachary Cooper, Cristina Ivan, Zhenlin Ju, Felix Nwajei, Jing Wang, Michael A. Davies, R. Eric Davis, Jennifer A. Wargo, Pratip K. Bhattacharya, David S. Hong, Michael A. Curran. Melanoma evolves complete immunotherapy resistance through acquisition of a hypermetabolic phenotype [abstract]. In: Proceedings of the AACR Special Conference on Melanoma: From Biology to Target; 2019 Jan 15-18; Houston, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(19 Suppl):Abstract nr PR02.

Abstract 5011: Targeting hypoxia-induced immune suppression to overcome immunotherapy resistance in prostate cancer

Immune checkpoint blockade is effective in “hot” tumors like melanoma with pre-existing immune infiltrates; however, “cold” tumors like prostate cancer fail to respond. We found that prostate cancers harbor regions of hypoxia that resist T cell infiltration even in the context of anti-CTLA-4 (cytotoxic T lymphocyte associated protein-4) and anti-PD-1 (programmed cell death protein 1) blockade. These hypoxic zones serve as islands of immune privilege through the recruitment and suppressive polarization of immature myeloid cells into myeloid-derived suppressor cells (MDSC) and tumor-associated macrophages (TAM). We found that targeted hypoxia ablation using TH-302, a hypoxia-activated prodrug, sensitized both transplantable and spontaneous models of prostate cancer to checkpoint blockade, coincident with enhanced T cell infiltration and effector function and loss of MDSC recruitment and suppressive function. Tumors treated with the combination of TH-302 and checkpoint blockade showed a reduced capacity to suppressively polarize new myeloid immigrants, implying a durable reconditioning of the tumor microenvironment (TME) into an immune-infiltrated, pro-inflammatory milieu. T cells infiltrating combination-treated tumors exhibited increased mitochondrial respiration, consistent with creation of a metabolically favorable milieu for T cell function. Based on these findings, we hypothesized that other approaches capable of metabolically rewiring the TME should promote anti-tumor immunity and sensitize checkpoint blockade-resistant tumors to immunotherapy. With this in mind, we performed a longitudinal study comparing a panel of different mitochondrial respiration inhibitors and a glutaminase inhibitor for their efficacy in reducing hypoxia, improving T cell infiltration and decreasing myeloid cell recruitment and suppressive polarization using immunofluorescence staining and confocal microscopy. Our preliminary data suggests that inhibitors targeting mitochondrial respiration, rather than those targeting glutamine metabolism synergize with checkpoint blockade and exhibit the highest efficacy in increasing T cell recruitment. We continue to characterize the dynamics of hypoxia reduction, duration of normalization following drug withdrawal, and impact on the immune microenvironment of these diverse approaches to metabolic reconditioning.

Citation Format: Priyamvada Jayaprakash, Midan Ai, Arthur Liu, Pratha Budhani, Todd Bartkowiak, Jie Sheng, Casey Ager, Courtney Nicholas, Ashvin Jaiswal, Yanqiu Sun, Krishna Shah, Sadhana Balasubramanyam, Nan Li, Guocan Wang, Jing Ning, Anna Zal, Tomasz Zal, Michael Curran. Targeting hypoxia-induced immune suppression to overcome immunotherapy resistance in prostate 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 5011.

Phase 1 trial of TLR9 agonist lefitolimod in combination with CTLA-4 checkpoint inhibitor ipilimumab in advanced tumors

TPS2669

Background: Drugs targeting pathogen associated molecular patterns are an attractive strategy to stimulate the immune system. Toll-like receptors (TLR) have generated significant interest as an effective means of stimulating the immune system that result in the killing of tumor cells. TLR-9 agonists can function to promote an early immune response and are an appealing partner for combination with checkpoint blockade to improve immune activation. Lefitolimod (MGN1703) is a covalently closed dumbbell-shaped DNA molecule that functions as a TLR-9 agonist. We developed a clinical trial combining lefitolimod with ipilimumab (anti-CTLA4) in patients with advanced malignancies. In the dose-escalation phase 19 patients were enrolled and no DLTs were encountered. Safety data and maximum planned dose level of lefitolimod at 120mg weekly and ipilimumab 3mg/kg every 3 weeks was previously presented. Adverse events related to the combination included fatigue, appetite loss, rash, and anemia. Methods: This trial (NCT02668770) was designed to evaluate the safety profile and maximum tolerated dose of lefitolimod with ipilimumab. A 3+3 trial design was used to establish safety of the combination at each dose level and guide the decision to escalate dose. Lefitolimod is administered via subcutaneous (SC) injection weekly while ipilimumab is given at 3mg/kg intravenous on day 8 of each 3 week cycle. Lefitolimod starting dose was 15mg SC weekly with 3 dose level escalations up to 120mg SC weekly. Patients receive treatment for 4 cycles (total 12 weeks) with the combination, and those with stable disease or response were eligible to remain on lefitolimod therapy for up to 1 year. Eligible patients have a metastatic or unresectable solid tumor refractory to standard therapies, ECOG ≤ 2, and normal organ and bone marrow function. Patients are allowed to have received prior checkpoint blockade agents. Enrollment in expansion cohorts in ongoing. To better understand relevant immunologic changes associated with treatment, paired pre- and post-treatment biopsies of target lesions and peripheral blood collection during treatment is required for target expansion cohort patient populations. In addition to evaluating target patient populations at the combination dose established during escalation, an expansion cohort for patients with cutaneous metastases involves combination treatment with intratumoral delivery of lefitolimod. Clinical trial information: NCT02668770.

Targeted hypoxia reduction restores T cell infiltration and sensitizes prostate cancer to immunotherapy

Despite the success of immune checkpoint blockade against melanoma, many "cold" tumors like prostate cancer remain unresponsive. We found that hypoxic zones were prevalent across preclinical prostate cancer and resisted T cell infiltration even in the context of CTLA-4 and PD-1 blockade. We demonstrated that the hypoxia-activated prodrug TH-302 reduces or eliminates hypoxia in these tumors. Combination therapy with this hypoxia-prodrug and checkpoint blockade cooperated to cure more than 80% of tumors in the transgenic adenocarcinoma of the mouse prostate-derived (TRAMP-derived) TRAMP-C2 model. Immunofluorescence imaging showed that TH-302 drives an influx of T cells into hypoxic zones, which were expanded by checkpoint blockade. Further, combination therapy reduced myeloid-derived suppressor cell density by more than 50%, and durably reduced the capacity of the tumor to replenish the granulocytic subset. Spontaneous prostate tumors in TRAMP transgenic mice, which completely resist checkpoint blockade, showed minimal adenocarcinoma tumor burden at 36 weeks of age and no evidence of neuroendocrine tumors with combination therapy. Survival of Pb-Cre4, Ptenpc-/-Smad4pc-/- mice with aggressive prostate adenocarcinoma was also significantly extended by this combination of hypoxia-prodrug and checkpoint blockade. Hypoxia disruption and T cell checkpoint blockade may sensitize some of the most therapeutically resistant cancers to immunotherapy.

Abstract PR08: Metabolic adaptations establish immunotherapy resistance in melanoma

Background: Despite the success of T-cell checkpoint blockade antibodies in treating an array of cancers, the majority of patients still fail to respond to these therapies, or respond transiently and then relapse. The molecular mechanisms that drive lack of response to checkpoint blockade, whether pre-existing or evolved on therapy, remain unclear.

Materials and Methods: To address this critical gap in clinical knowledge, we established a mouse model of melanoma designed to elucidate the molecular mechanisms underlying immunotherapy resistance. Through multiple in vivo passages, we selected a B16 melanoma tumor line that evolved complete resistance to combination blockade of CTLA-4, PD-1, and PD-L1, which cures ~80% of mice of the parental tumor. Using gene expression analysis, proteomics, and immunogenomics, we determined the adaptations engaged by this melanoma to become completely immunotherapy resistant. NMR spectroscopy, Seahorse XF analysis, flow cytometry, confocal microscopy, and Western blot analysis provided further insight into the mechanisms driving checkpoint blockade resistance.

Results: Acquisition of immunotherapy resistance by these melanomas was driven by coordinate upregulation of the glycolytic and aldose reductase pathways to create a metabolically hostile microenvironment in which T-cell function is profoundly suppressed. When reintroduced into the parental tumor, the genes most closely associated with these metabolic adaptations confer enhanced immunotherapy resistance. We have validated upregulation of these pathways in a unique cohort of melanoma patients who failed dual checkpoint blockade. Additionally, we employed MRI imaging to visualize metabolic changes acquired by resistant tumors in live mice. Clinical application of this technique could provide a much-needed noninvasive tool to predict immunotherapeutic sensitivity of patients.

Conclusion: Upregulation of glycolytic metabolism and the aldose reductase pathway by melanoma tumor cells cripples T cells in the microenvironment and confers resistance to checkpoint blockade.

This abstract is also being presented as Poster A71.

Citation Format: Ashvin R. Jaiswal, Shivanand Pudakalakatti, Prasanta Dutta, Arthur Liu, Todd Bartkowiak, Casey Ager, Cristina Ivan, Richard Eric Davis, Michael A. Davies, Jennifer Wargo, James P. Allison, Pratip K. Bhattacharya, David Hong, Michael A. Curran. Metabolic adaptations establish immunotherapy resistance in melanoma [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 PR08.

Abstract 1700: Metabolic adaptations confer immunotherapy resistance in melanoma

Background: Despite the success of T-cell checkpoint blockade antibodies in treating an array of cancers, the majority of patients still fail to respond to these therapies, or respond transiently and then relapse. The molecular mechanisms that drive lack of response to checkpoint blockade, whether pre-existing or evolved on therapy, remain unclear.

Materials and Methods: To address this critical gap in clinical knowledge, we established a mouse model of melanoma designed to elucidate the molecular mechanisms underlying immunotherapy resistance. Through multiple in vivo passages, we selected a B16 melanoma tumor line that evolved complete resistance to combination blockade of CTLA-4, PD-1, and PD-L1, which cures ~75% of mice of the parental tumor. Using gene expression analysis, proteomics, and immunogenomics, we determined the adaptations engaged by this melanoma to become completely immunotherapy resistant. NMR spectroscopy, Seahorse XF Analysis, flow cytometry, confocal microscopy and Western blot analysis provided further insight into the mechanisms driving checkpoint blockade resistance.

Results: Acquisition of immunotherapy resistance by these melanomas was driven by acquisition of a hypermetabolic state through coordinate upregulation of both glycolysis and oxidative phosphorylation (OxPhos). Depletion of essential nutrients from the tumor microenvironment by these resistant tumors functionally compromises infiltrating T cells to an extent that cannot be rescued by even triple checkpoint blockade. The glycolysis and OxPhos-associated genes most highly induced by these resistant melanomas were capable of conferring enhanced resistance to checkpoint blockade when reintroduced monogenically into the parental tumor. We have validated upregulation of these pathways in a unique cohort of melanoma patients who failed dual checkpoint blockade. Additionally, we employed a novel MRI imaging technique to visualize metabolic changes acquired by resistant tumors in live mice. Clinical application of this technique could provide a much-needed noninvasive tool to predict immunotherapeutic sensitivity of patient cancers.

Conclusion: Acquisition of a hypermetabolic state by melanoma tumor cells cripples T cells in the microenvironment and confers complete resistance to checkpoint blockade.

Citation Format: Ashvin R. Jaiswal, Shivanand Pudakalakatti, Dutta Prasanta, Arthur Liu, Todd Bartkowiak, Casey Ager, Michael A. Davies, Richard E. Davis, Jennifer Wargo, Pratip K. Bhattacharya, David S. Hong, Michael A. Curran. Metabolic adaptations confer immunotherapy resistance in melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1700.

Mechanisms underlying 4-1BB agonist antibody mediated hepatotoxicity

Agonist antibodies against the T cell costimulatory receptor 4-1BB have proven extraordinarily efficacious in the treatment of a multitude of pre-clinical murine tumors both in mono- and combination therapy settings. Although administration of α4-1BB in Phase I and II clinical trials has led to disease stabilization and partial remission in some cases of melanoma; high grade, dose limiting liver inflammation has slowed the progress of these agents toward FDA approval. We sought to uncover the mechanisms by which 4-1BB agonist antibodies trigger hepatotoxicity in hopes of discovering approaches by which the anti-tumor and hepatotoxic effects could be separated. We show that α4-1BB mediated liver damage initiates through stimulation of myeloid cells, followed by subsequent recruitment and activation of CD8 and CD4 T cells in the liver. Moreover, we show that the inflammatory cytokine IL-27 is essential in myeloid conversion of T cells into mediators of liver damage. Conversely, we show that Foxp3+ regulatory T cells are potent suppressors of 4-1BB agonist mediated hepatotoxicity; as depletion of Tregs exacerbates liver pathology. Our results go on to support the use of combination therapies in the treatment of tumor malignancies, in particular CTLA-4 blockade which may expand Tregs in the liver to ameliorate α4-1BB mediated toxicities while also amplifying anti-tumor immune responses.

Despite KLRG1 expression, highly cytotoxic ThEO/TcEO polarized T cells efficiently establish immunologic memory

Targeting immune inhibitory (CTLA-4, PD-1) or stimulatory (OX-40, 4-1BB) co-receptors has proven to be a potent anti-cancer therapeutic strategy, eliciting robust anti-tumor T cell responses and yielding compelling pre-clinical and clinical data in a variety of cancers. We have previously shown in pre-clinical models that 4-1BB agonist antibodies engender strong anti-tumor T cell responses capable of driving regression of established tumors and durable tumor-free survival. This impressive anti-tumor effect is due, in part, to the unique ability of 4-1BB co-stimulation to differentiate a novel subset of T cells that acquires a highly cytotoxic effector profile typically only seen in NK cells. This phenotype- known as ThEO (CD4+) or TcEO (CD8+)-is driven by the T-box transcription factor Eomesodermin, and is further characterized by expression of the inhibitory receptor KLRG1. We show here that, despite high level effector function and expression of several co-inhibitory receptors (PD-1, TIM-3, KLRG1), these ThEO/TcEO phenotype T cells efficiently establish immunologic memory and recall with high frequency upon secondary tumor challenge. Further, they maintain high effector function on recall and can traffic to tissue sites far removed from the original malignancy. These findings provide mechanistic insight into the process of memory formation and give evidence for the capacity of ThEO/TcEO cells to prevent tumor recurrence.

Identifying mechanisms of acquired resistance to immunotherapy (TUM2P.1025)

Immunotherapy has demonstrated a remarkable potential to cure established cancer, but many tumors either relapse or fail to respond. The molecular mechanisms which drive these tumor relapses remain unknown. We hypothesize that tumors evolve resistance under immunotherapeutic pressure mediated by changes in gene expression which can be selected and propagated through serial passage and then identified and targeted. We are comparing untreated B16 melanoma tumors to those expanding despite treating with combinations checkpoint blockade (CTLA-4, PD-1, and PD-L1), 4-1BB-agonist antibody, adoptive transfer of TRP-1 specific CD4 T-cells, or growth in MHC-mismatched hosts. Through multiple in vivo passages, we have already selected a B16 melanoma tumor line that has evolved almost 100% resistance to combination blockade of CTLA-4, PD-1, and PD-L1, which could cure nearly 90% of tumor-bearing mice in the first cycle. After each passage under selective pressure of combination blockade, we have observed visible signs of increased angiogenesis correlating with enhanced therapy resistance. By determining the pathways engaged by these tumors to develop resistance to tumor-specific immunity, we hope to discover novel characteristics of the mammalian immune system as well as reveal new targets for immunotherapeutic intervention in melanoma patients.

Despite KLRG1 expression, highly cytotoxic ThEO/TcEO polarized T cells efficiently establish immunologic memory (LYM5P.662)

Targeting immune inhibitory (CTLA-4, PD-1) or stimulatory (OX-40, 4-1BB) co-receptors has proven a potent anti-cancer therapeutic strategy, eliciting robust anti-tumor T cell responses and compelling pre-clinical and clinical data in a variety of cancers. We have previously shown in pre-clinical models that 4-1BB agonist antibodies engender strong anti-tumor T cell responses, imparting enhanced survival benefit in addition to evoking durable tumor regression. This impressive anti-tumor effect is due, in part, to the unique ability of 4-1BB co-stimulation to differentiate a novel subset of T cells that acquires a highly cytotoxic effector profile typically only seen in NK cells. This subset-dubbed ThEO (CD4+) or TcEO (CD8+)-is driven by the T-box transcription factor Eomesodermin, and is further characterized by expression of the inhibitory receptor KLRG1. We show here that, despite their strong effector function and expression of several co-inhibitory receptors (PD-1, TIM-3, KLRG1), the ThEO/TcEO phenotype establishes immunological memory and recalls with high frequency upon secondary tumor challenge with potent anti-tumor effector function. Further, these cells manifest characteristics of central memory (Tcm), effector memory (Tem), as well as stem cell memory (Tscm), and reside in multiple memory niches. These findings provide mechanistic insight into the process of memory formation and give evidence for the capacity of ThEO/TcEO cells to prevent tumor recurrence.

Abstract 629: Combination hypoxia-specific chemotherapy and immunotherapy of prostate cancer

Tumor hypoxia contributes to chemotherapy and radiotherapy resistance, and helps foster metastasis. Hypoxia likely also supports tumor immune resistance by supporting development of suppressive myeloid and T cell populations by activating immunosuppressive signaling pathways in the tumor and stroma, and by creating a metabolically hostile environment for immune effector cells. TH-302 is a hypoxia-specific chemotherapeutic drug which is activated only in the hypoxic cores of tumors and remains harmless in the periphery. We hypothesized that concurrent combination therapy with TH-302 and T cell checkpoint blockade would promote inside-out tumor destruction with the drug killing at the core, releasing antigen, and diminishing suppression, while the antibodies helped expand and protect the T cells activated as a result. In the TRAMP-C2 prostatic adenocarcinoma model, we found that antibody blockade of CTLA-4 and PD-1, used in conjunction with TH-302 administration, promoted tumor rejection in a significantly larger percentage of mice than either therapy alone. The combination therapy promoted uniquely advantageous ratios of effector T cells to MDSC within the prostate cancer microenvironment. This novel combination of immunotherapy and hypoxia-specific chemotherapy has the potential to offer profound anti-tumor responses to a much greater percentage of patients than either chemotherapy or immunotherapy alone with the same or fewer side effects.

Citation Format: Midan Ai, Todd Bartkowiak, Ashvin R. Jaiswal, Krishna Shah, Casey Ager, Beatrisa Lerman, Michael A. Curran. Combination hypoxia-specific chemotherapy and immunotherapy of prostate cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 629. doi:10.1158/1538-7445.AM2014-629

Expanding the product profile of a microbial alkane biosynthetic pathway

Microbially produced alkanes are a new class of biofuels that closely match the chemical composition of petroleum-based fuels. Alkanes can be generated from the fatty acid biosynthetic pathway by the reduction of acyl-ACPs followed by decarbonylation of the resulting aldehydes. A current limitation of this pathway is the restricted product profile, which consists of n-alkanes of 13, 15, and 17 carbons in length. To expand the product profile, we incorporated a new part, FabH2 from Bacillus subtilis , an enzyme known to have a broader specificity profile for fatty acid initiation than the native FabH of Escherichia coli . When provided with the appropriate substrate, the addition of FabH2 resulted in an altered alkane product profile in which significant levels of n-alkanes of 14 and 16 carbons in length are produced. The production of even chain length alkanes represents initial steps toward the expansion of this recently discovered microbial alkane production pathway to synthesize complex fuels. This work was conceived and performed as part of the 2011 University of Washington international Genetically Engineered Machines (iGEM) project.

Dependence of exhaled breath composition on exogenous factors, smoking habits and exposure to air pollutants

Non-invasive disease monitoring on the basis of volatile breath markers is a very attractive but challenging task. Several hundreds of compounds have been detected in exhaled air using modern analytical techniques (e.g. proton-transfer reaction mass spectrometry, gas chromatography-mass spectrometry) and have even been linked to various diseases. However,the biochemical background for most of compounds detected in breath samples has not been elucidated; therefore, the obtained results should be interpreted with care to avoid false correlations. The major aim of this study was to assess the effects of smoking on the composition of exhaled breath. Additionally, the potential origin of breath volatile organic compounds (VOCs) is discussed focusing on diet, environmental exposure and biological pathways based on other's studies. Profiles of VOCs detected in exhaled breath and inspired air samples of 115 subjects with addition of urine headspace derived from 50 volunteers are presented. Samples were analyzed with GC-MS after preconcentration on multibed sorption tubes in case of breath samples and solid phase micro-extraction (SPME) in the case of urine samples. Altogether 266 compounds were found in exhaled breath of at least 10% of the volunteers. From these, 162 compounds were identified by spectral library match and retention time (based on reference standards). It is shown that the composition of exhaled breath is considerably influenced by exposure to pollution and indoor-air contaminants and particularly by smoking. More than 80 organic compounds were found to be significantly related to smoking, the largest group comprising unsaturated hydrocarbons (29 dienes, 27 alkenes and 3 alkynes). On the basis of the presented results, we suggest that for the future understanding of breath data it will be necessary to carefully investigate the potential biological origin of volatiles, e.g., by means of analysis of tissues, isolated cell lines or other body fluids. In particular, VOCs linked to smoking habit or being the results of human exposure should be considered with care for clinical diagnosis since small changes in their concentration profiles(typically in the ppt(v)–ppb(v) range) revealing that the outbreak of certain disease might be hampered by already high background.

The effects of choice and task preference on the work performance of adults with severe disabilities

We evaluated the effects of choice versus the assignment of tasks of varying preferences on the work engagement of adults with severe disabilities. The combined results of two experiments suggests that the relative preference for a task may be an important variable in the effectiveness of choice for some individuals.