Abstract PR03: Nongenomic BAP1 aberrancy drives highly aggressive cutaneous melanoma phenotype

The purpose of this study was to determine the role of BAP1 levels in cutaneous melanoma (CM). BAP1 is a tumor suppressor in which loss of heterozygosity (LOH) from mutation and copy number alteration is well described in germline and somatic cancers. Although BAP1 genomic alterations in CM are extremely rare (2% of 665 samples from 5 datasets), marked variability in BAP1 expression is observed in CM. We show that low nuclear BAP1 levels portend a significantly worse clinical outcome in stage III CM (n=37, log rank p ≤0.01 for both overall survival and progression-free survival). Gene Set Enrichment Analysis (GSEA) revealed low BAP1 expression to be most highly ranked with an increased epithelial–mesenchymal transition (EMT) gene expression profile in CM tumors (n=379, FDR q = 1.34E-26) and cell lines (n=53, FDR q = 2.86E-116). We identify the expression of ZEB1, a master regulator of EMT, to be significantly associated with low BAP1 expression in CM tumors and cell lines (p= 1.5E-04 and 3.3E-05, respectively). Analysis of the BAP1 promoter indicates three canonical ZEB1 binding sites. Functional experiments show ZEB1 to bind to the BAP1 promoter, and luciferase activity assays indicate that ZEB1 acts as a transcriptional suppressor of BAP1 expression with differential utilization of the promoter binding sites. Targeted reduction of endogenous ZEB1 caused increased BAP1 levels, while targeted reduction of BAP1 did not modulate ZEB1 levels, consistent with ZEB1 having a suppressive effect on BAP1. Phenotypically, targeted reduction of BAP1 in CM cells resulted in a switch from a more differentiated, melanocytic state, to a less differentiated, more migratory and invasive phenotype. Extinguishing melanocyte-specific BAP1 in mice with a BRAF V600E mutant genetic background resulted in the emergence of primary melanoma tumors, with a marked EMT gene expression profile, and resultant metastases. Given the phenotypic changes associated with BAP1 levels in our mouse and human studies, we then tested the effect of modulating BAP1 on BRAF targeted therapy. Exogenous expression of BAP1 sensitized BRAF inhibitor (vemurafenib)-resistant melanoma cells, while the targeted reduction of BAP1 desensitized BRAF inhibitor-sensitive melanoma cells. BRAF mutant/BAP1 loss mice failed to exhibit a marked response to vemurafenib treatment compared to control mice. These data implicate regulation of BAP1 to be a major mechanism that characterizes a highly malignant and treatment-resistant subset of tumors. Our study indicates that nongenomic reduction in BAP1 through ZEB1 transcriptional modulation may be a key factor in aggressive CM.

This abstract is also being presented as Poster A30.

Citation Format: Haifeng Zhu, Junna Oba, Xiaoxing Yu, Caitlin A. Creasy, Marie-Andrée Forget, Fernando Carapeto, Cara L. Haymaker, Chang-Jiun Wu, Tatiana V. Karpinets, Wei-Lien Wang, Michael T. Tetzlaff, Alexander J. Lazar, Gordon B. Mills, Amanda R. Moore, Yu Chen, Jianhua Zhang, Jeffrey E. Gershenwald, Jennifer A. Wargo, Chantale Bernatchez, Patrick Hwu, P. Andrew Futreal, Scott E. Woodman. Nongenomic BAP1 aberrancy drives highly aggressive cutaneous melanoma 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 PR03.

Abstract CT134: Tilsotolimod engages the TLR9 pathway to promote antigen presentation and Type-I IFN signaling in solid tumors

Background: Tilsotolimod, an investigational Toll-like receptor 9 (TLR9) agonist, modulates the tumor immune microenvironment and has single-agent antitumor activity in preclinical models. The ILLUMINATE-101 phase 1b study (NCT03052205) explored the safety, efficacy, and immune effects of intratumoral tilsotolimod in multiple solid tumors.

Methods: Adults with a histologically- or cytologically-confirmed diagnosis of cancer not amenable to curative therapies received intratumoral tilsotolimod 8, 16, 23, or 32 mg into a single lesion on Days 1, 8, and 15 of Cycle 1 and Day 1 of each subsequent 3-week cycle, for up to 17 cycles. Additionally, patients with advanced melanoma were enrolled into an expansion cohort at the recommended phase 2 dose of 8 mg. The primary objective was to characterize safety (dose escalation cohort) and efficacy (expansion cohort). Secondary objectives included pharmacokinetics of tilsotolimod. Immunological assessment of injected and non-injected tumors was an exploratory objective. Blood samples and tumor biopsies of injected lesions were obtained at baseline and 24 hours post treatment for immune analyses.

Results: A total of 54 patients were enrolled. Of the 38 patients in the dose escalation cohort, 35 had metastatic disease. Patients in this cohort had a median of 7 prior lines of treatment, and the most common cancer types were pancreatic (12 patients) and colorectal (7 patients). All 16 patients in the melanoma cohort had metastatic disease with a median of 3 lines of prior therapy, and 10 patients had elevated LDH. Injected lesions were deep and required interventional radiology in 52 of 54 patients. No dose-limiting toxicities were observed. The most common treatment-related adverse events were pyrexia, fatigue, chills, nausea, and vomiting. Compared to pretreatment, biopsies of injected tumors at 24 hours showed increased activation of the Type-I IFN pathway, upregulation of MHC class I/II, IFNγ expression, and expression of multiple immune checkpoints (i.e. PD-1, LAG3). Of the 35 evaluable patients in the dose escalation cohort, 12 (34%) achieved a best overall response of stable disease (SD). Of the 16 evaluable patients in the melanoma cohort, 3 had SD, 1 who had a 35% tumor reduction with no confirmatory scan.

Conclusions: Tilsotolimod was generally well tolerated and induced alterations in the tumor microenvironment, including immune checkpoint upregulation, activation of dendritic cells, and induction of Type-I IFN signaling. Additional clinical studies of tilsotolimod in combination with checkpoint inhibitors are underway (NCT03445533, NCT03865082, and NCT02644967).

Citation Format: Hani M. Babiker, Vivek Subbiah, Asim Ali, Alain Algazi, Jacob Schachter, Michal Lotem, Corinne Maurice-Dror, Daniel Hendler, Shah Rahimian, Hans Minderman, Cara Haymaker, Chantale Bernatchez, Ravi Murthy, Rolf Hultsch, Nadia Caplan, Gregory Woodhead, Charles Hennemeyer, Sri Chunduru, Peter Anderson, Adi Diab, Erkut Borazanci, Igor Puzanov. Tilsotolimod engages the TLR9 pathway to promote antigen presentation and Type-I IFN signaling in solid tumors [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr CT134.

Bempegaldesleukin (NKTR-214) plus Nivolumab in Patients with Advanced Solid Tumors: Phase I Dose-Escalation Study of Safety, Efficacy, and Immune Activation (PIVOT-02)

This single-arm, phase I dose-escalation trial (NCT02983045) evaluated bempegaldesleukin (NKTR-214/BEMPEG), a CD122-preferential IL2 pathway agonist, plus nivolumab in 38 patients with selected immunotherapy-naïve advanced solid tumors (melanoma, renal cell carcinoma, and non-small cell lung cancer). Three dose-limiting toxicities were reported in 2 of 17 patients during dose escalation [hypotension (n = 1), hyperglycemia (n = 1), metabolic acidosis (n = 1)]. The most common treatment-related adverse events (TRAE) were flu-like symptoms (86.8%), rash (78.9%), fatigue (73.7%), and pruritus (52.6%). Eight patients (21.1%) experienced grade 3/4 TRAEs; there were no treatment-related deaths. Total objective response rate across tumor types and dose cohorts was 59.5% (22/37), with 7 complete responses (18.9%). Cellular and gene expression analysis of longitudinal tumor biopsies revealed increased infiltration, activation, and cytotoxicity of CD8⁺ T cells, without regulatory T-cell enhancement. At the recommended phase II dose, BEMPEG 0.006 mg/kg plus nivolumab 360 mg every 3 weeks, the combination was well tolerated and demonstrated encouraging clinical activity irrespective of baseline PD-L1 status. SIGNIFICANCE: These data show that BEMPEG can be successfully combined with a checkpoint inhibitor as dual immunotherapy for a range of advanced solid tumors. Efficacy was observed regardless of baseline PD-L1 status and baseline levels of tumor-infiltrating lymphocytes, suggesting therapeutic potential for patients with poor prognostic risk factors for response to PD-1/PD-L1 blockade.See related commentary by Rouanne et al., p. 1097.This article is highlighted in the In This Issue feature, p. 1079.

Peripheral cytokines are not influenced by the type of surgical approach for non-small cell lung cancer by four weeks postoperatively

OBJECTIVES

The influence of surgical approach on systemic inflammatory response and the subsequent oncologic impact for non-small cell lung cancer is debated. We aimed to measure the effects of thoracic surgical approach on peripheral cytokine milieu over time.

METHODS

Patients undergoing primary lung resection without neoadjuvant therapy (2016-2018) were evaluated. A panel of 43 cytokines, angiogenic factors, and inflammatory molecules (CAFs) were evaluated in peripheral blood preoperatively, at 24 -hs and 4-weeks postoperatively. Differences between CAFs in patients undergoing thoracotomy versus video-assisted thoracoscopic surgery (VATS) at all timepoints were assessed using Student's t-test.

RESULTS

76 patients with available peripheral CAF panels met inclusion criteria. Thoracotomy was performed in 53 (70 %) patients while VATS was undertaken in 23 (30 %). Upon examination of known inflammatory CAFs, including IL-1β, IL-6, IL-8, IL-10, IFN-γ, and soluble (s) CD27, no differences were detected at 24 h or 4 weeks postoperatively between surgical groups. Examination of trends over time did not demonstrate any temporal derangements for these CAFs, with return to baseline levels by 4 weeks postoperatively for both groups. Evaluation of soluble (s) checkpoint molecules, including sPD-1, sPD-L1, sTIM-3, and sCTLA-4, did not reveal any differences in the immediate postoperative or long-term recovery period.

CONCLUSIONS

Peripheral immune profiles following pulmonary resection do not appear to differ between VATS and thoracotomy postoperatively. CAF fluctuations are transient and recover rapidly. These results, at the peripheral cytokine level, suggest that the surgical approach for lung cancer is unlikely to alter the effectiveness of novel immune-modulating systemic therapies, although more studies are needed to validate these findings.

Histone Deacetylase Inhibitors and IL21 Cooperate to Reprogram Human Effector CD8+ T Cells to Memory T Cells

Clinical response rates after adoptive cell therapy (ACT) are highly correlated with in vivo persistence of the infused T cells. However, antigen-specific T cells found in tumor sites are often well-differentiated effector cells with limited persistence. Central memory CD8+ T cells, capable of self-renewal, represent desirable ACT products. We report here that exposure to a histone deacetylase inhibitor (HDACi) and IL21 could reprogram differentiated human CD8+ T cells into central memory-like T cells. Dedifferentiation of CD8+ T cells was initiated by increased H3 acetylation and chromatin accessibility at the CD28 promoter region. This led to IL21-mediated pSTAT3 binding to the CD28 region, and subsequent upregulation of surface CD28 and CD62L (markers of central memory T cells). The reprogrammed cells exhibited enhanced proliferation in response to both IL2 and IL15, and a stable memory-associated transcriptional signature (increased Lef1 and Tcf7). Our findings support the application of IL21 and HDACi for the in vitro generation of highly persistent T-cell populations that can augment the efficacy of adoptively transferred T cells.

Abstract D075: Investigating the immuno-biology underlying differential response to immunotherapy in White and non-White patients with metastatic acral melanoma

Background: Acral melanoma (ACML), the rarest form of melanoma (MEL) represents 4-6% of all MEL cases however it is the most common subtype darker pigmented individuals accounting for up to 70% of all cases. Checkpoint inhibitors (CPI) have emerged as an efficacious treatment option. In cutaneous melanoma (CtMEL), tumor mutational burden (TMB) correlates with response rate. Despite low TMB in AMEL, responses to CPI parallel those in CtMEL. Given the differences in ethnicity among ACML patients compared CtMEL patients we aimed to study: (i) the correlation between response and TMB, (ii) the relationship between ethnicity and response and (iii) the underlying immune-biology accounting for differential responses. Method: All advanced and metastatic ACML patients (pts) treated with anti-CTLA4 (ipilimumab) or anti-PD1 (pembrolizumab or nivolumab) immunotherapy between March 2011 and January 2019 at MD Anderson Cancer Center, Texas, were included in this retrospective analysis. Clinical response, progression free survival and overall survival (PFS and OS) and their correlation to ethnicity and TMB were evaluated. Objective response was measured using RECIST 1.1 and analyzed using logistic regression. PFS and OS were assessed using the Kaplan Meir method and log-rank test. TMB was predicted using validated algorithm based on a defined gene mutation set obtained using next generation sequencing. Results: 44 pts with Stages III-IV ACML (IIIA: 2%, IIIB 9%, IIIC 27%, IV-M1A: 16%, IV-M1B: 25%, IV-M1C: 20%, IV-M1D2%) were included in the analysis. Median age was 63 years old (39-88) and 60% were men. Of 44 patients 12 (27%) self-identified as Hispanic, 2 as (5%) Asian and 30 (68%) as White. The overall response rate was nearly 5 times times higher in Hispanic compared to White pts (OR 4.60, p-value 0.04). The median TMB in Hispanic patients was 16 mutations/mb compared to 7 mutations/mb in White pts. The median PFS and OS for White pts were 7.2 months and 34.3 months respectively while for Hispanic pts the median PFS and OS were 6.7 (log-rank p=0.69) and 26.1 months (log-rank p=0.38) respectively. In addition to this data deep immune analysis of tumor tissue including nanostring, gene expression and TCR sequencing will be assessed and reported. Conclusions: The data from this small retrospective study suggests that White pts with ACML had low response rates to CPI presumably due to low TMB while interestingly, Hispanic pts, despite relatively low TMB have high response rates paralleling those seen in the overall CtMEL population. Despite higher response rates in Hispanic patients, there was no significant difference in OS. This data together with further immune analysis provides the rationale to design prospective studies to investigate how tumor micro-environment varies with ethnicity. Additionally we will investigate the social and biological determinants that limit survival in Hispanic pts despite higher response rates.

Citation Format: Kaysia Ludford, Chantal Saberian, Sara K Nabhan, Stephen Gruschkus, Chantale Bernatchez, Natalie Jackson, Cara L Haymaker, Patrick Hwu, Adi Diab. Investigating the immuno-biology underlying differential response to immunotherapy in White and non-White patients with metastatic acral melanoma [abstract]. In: Proceedings of the Twelfth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2019 Sep 20-23; San Francisco, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl_2):Abstract nr D075.

CIMAC-CIDC CyTOF harmonization

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Background: The Cancer Immune Monitoring and Analysis Centers – Cancer Immunology Data Commons (CIMAC-CIDC) network is a National Cancer Institute-funded initiative to identify biomarkers of mechanisms and response to cancer immunotherapy clinical trials, using state-of-the-art assay technologies. A primary platform for CIMAC-CIDC biomarker studies is CyTOF mass cytometry, which is performed at all four CIMAC laboratories. Methods: To test the ability to generate comparable data across labs, a cross-site harmonization effort was undertaken. We first harmonized SOPs between centers. Because of a new acquisition protocol introduced by the vendor (Fluidigm), we also tested this protocol across sites before finalizing the harmonized SOP. We then performed a cross-site assay harmonization experiment, using 5 shared cryopreserved PBMC samples and one lyophilized control cell preparation, along with a shared lyophilized antibody cocktail consisting of 14 markers, as validated in the HIPC consortium, plus CD45. These reagents and samples were distributed to the four sites, and FCS files were centrally analyzed by both manual gating and automated methods (Astrolabe). Results: Average CVs across sites for each cell population were reported and compared to a previous multisite CyTOF study. Once a cell recovery issue at two sites was resolved, this experiment resulted in inter-site reproducibility of under 20% CV for most cell subsets, very similar to the previous study. Conclusions: These results emphasize the ability to reproduce CyTOF across sites, and also highlights procedures, such as use of spike-in control samples, useful for tracking variability in this assay.

Successful tumor-infiltrating lymphocyte (TIL) growth from uveal melanoma (UM) using a three-signal (3.0) method

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Background: Metastatic UM is a rare cancer with poor response rates to systemic therapy. Adoptive transfer of patient-specific TIL may represent the best strategy for treatment. TIL are harvested from primary or metastatic tumors and initially expanded in culture with high dose IL-2 prior to undergoing rapid expansion protocol and therapeutic administration. Here, we report improved rates of initial expansion using a previously described TIL 3.0 method which utilizes dual agonistic antibodies to TCR and 4-1BB (Urelumab) for stimulation, respectively, with high dose IL-2, compared to the traditional method. Methods: Between 2006 and 2019, patients were consented for TIL harvest from either primary or metastatic UM tumors. Demographics, clinical features, and outcomes of the TIL initial expansion were collected. Success rates, number of cells expanded, and days in culture for the two methods were analyzed using partially overlapping samples t-tests and z-tests. Results: There were 85 harvests and expansions from 76 patients using the traditional method and 32 expansions from 30 patients using TIL 3.0. Initial TIL expansion was successful in 97% of TIL 3.0 harvests compared to 35% for the traditional method (p < 0.001). More TIL were expanded with TIL 3.0 compared to the traditional method (291.3 million cells vs. 88.6 million cells, p < 0.001), and fewer days were required in culture (18.5 vs. 29.0, p < 0.001). Both primary UM harvests and metastatic harvests were more successful with TIL 3.0 (90% vs. 12% for primary, p < 0.001, and 100% vs. 42% for metastatic, p < 0.001). Conclusions: Expansion of UM tumors via the TIL 3.0 method led to successful growth in 97% of harvests. Therapeutic administration to patients with TIL 3.0 is under active investigation. [Table: see text]

Spatially resolved analyses link genomic and immune diversity and reveal unfavorable neutrophil activation in melanoma

Complex tumor microenvironmental (TME) features influence the outcome of cancer immunotherapy (IO). Here we perform immunogenomic analyses on 67 intratumor sub-regions of a PD-1 inhibitor-resistant melanoma tumor and 2 additional metastases arising over 8 years, to characterize TME interactions. We identify spatially distinct evolution of copy number alterations influencing local immune composition. Sub-regions with chromosome 7 gain display a relative lack of leukocyte infiltrate but evidence of neutrophil activation, recapitulated in The Cancer Genome Atlas (TCGA) samples, and associated with lack of response to IO across three clinical cohorts. Whether neutrophil activation represents cause or consequence of local tumor necrosis requires further study. Analyses of T-cell clonotypes reveal the presence of recurrent priming events manifesting in a dominant T-cell clonotype over many years. Our findings highlight the links between marked levels of genomic and immune heterogeneity within the physical space of a tumor, with implications for biomarker evaluation and immunotherapy response.

Bempegaldesleukin selectively depletes intratumoral Tregs and potentiates T cell-mediated cancer therapy

High dose interleukin-2 (IL-2) is active against metastatic melanoma and renal cell carcinoma, but treatment-associated toxicity and expansion of suppressive regulatory T cells (Tregs) limit its use in patients with cancer. Bempegaldesleukin (NKTR-214) is an engineered IL-2 cytokine prodrug that provides sustained activation of the IL-2 pathway with a bias to the IL-2 receptor CD122 (IL-2Rβ). Here we assess the therapeutic impact and mechanism of action of NKTR-214 in combination with anti-PD-1 and anti-CTLA-4 checkpoint blockade therapy or peptide-based vaccination in mice. NKTR-214 shows superior anti-tumor activity over native IL-2 and systemically expands anti-tumor CD8⁺ T cells while inducing Treg depletion in tumor tissue but not in the periphery. Similar trends of intratumoral Treg dynamics are observed in a small cohort of patients treated with NKTR-214. Mechanistically, intratumoral Treg depletion is mediated by CD8⁺ Teff-associated cytokines IFN-γ and TNF-α. These findings demonstrate that NKTR-214 synergizes with T cell-mediated anti-cancer therapies.

Interleukin-2 can induce an anti-tumour response, but is associated with toxicity. Here, the authors demonstrate that an engineered interleukin-2 promotes intratumoral T regulatory cell depletion while enhancing effective anti-tumour CD8⁺ T cell responses that result in potent tumor suppression.

Persistence of adoptively transferred T cells with a kinetically engineered IL-2 receptor agonist

Interleukin-2 (IL-2) is a component of most protocols of adoptive cell transfer (ACT) therapy for cancer, but is limited by short exposure and high toxicities. NKTR-214 is a kinetically-engineered IL-2 receptor βγ (IL-2Rβγ)-biased agonist consisting of IL-2 conjugated to multiple releasable polyethylene glycol chains resulting in sustained signaling through IL-2Rβγ. We report that ACT supported by NKTR-214 increases the proliferation, homing and persistence of anti-tumor T cells compared to ACT with IL-2, resulting in superior antitumor activity in a B16-F10 murine melanoma model. The use of NKTR-214 increases the number of polyfunctional T cells in murine spleens and tumors compared to IL-2, and enhances the polyfunctionality of T and NK cells in the peripheral blood of patients receiving NKTR-214 in a phase 1 trial. In conclusion, NKTR-214 may have the potential to improve the antitumor activity of ACT in humans through increased in vivo expansion and polyfunctionality of the adoptively transferred T cells.

Combining Immune Checkpoint Blockade and Tumor-Specific Vaccine for Patients With Incurable Human Papillomavirus 16-Related Cancer: A Phase 2 Clinical Trial

Importance

In recurrent human papilloma virus (HPV)-driven cancer, immune checkpoint blockade with anti-programmed cell death 1 (PD-1) antibodies produces tumor regression in only a minority of patients. Therapeutic HPV vaccines have produced strong immune responses to HPV-16, but vaccination alone has been ineffective for invasive cancer.

Objective

To determine whether the efficacy of nivolumab, an anti-PD-1 immune checkpoint antibody, is amplified through treatment with ISA 101, a synthetic long-peptide HPV-16 vaccine inducing HPV-specific T cells, in patients with incurable HPV-16-positive cancer.

Design, Setting, and Participants

In this single-arm, single-center phase 2 clinical trial, 24 patients with incurable HPV-16-positive cancer were enrolled from December 23, 2015, to December 12, 2016. Duration of follow-up for censored patients was 12.2 months through August 31, 2017.

Interventions

The vaccine ISA101, 100 μg/peptide, was given subcutaneously on days 1, 22, and 50. Nivolumab, 3 mg/kg, was given intravenously every 2 weeks beginning day 8 for up to 1 year.

Main Outcomes and Measures

Assessment of efficacy reflected in the overall response rate (per Response Evaluation Criteria in Solid Tumors, version 1.1).

Results

Of the 24 patients (4 women and 20 men; 22 with oropharyngeal cancer; median age, 60 years [range, 36-73 years]), the overall response rate was 33% (8 patients; 90% CI, 19%-50%). Median duration of response was 10.3 months (95% CI, 10.3 months to inestimable). Five of 8 patients remain in response. Median progression-free survival was 2.7 months (95% CI, 2.5-9.4 months). Median overall survival was 17.5 months (95% CI, 17.5 months to inestimable). Grades 3 to 4 toxicity occurred in 2 patients (asymptomatic grade 3 transaminase level elevation in 1 patient and grade 4 lipase elevation in 1 patient), requiring discontinuation of nivolumab therapy.

Conclusions and Relevance

The overall response rate of 33% and median overall survival of 17.5 months is promising compared with PD-1 inhibition alone in similar patients. A randomized clinical trial to confirm the contribution of HPV-16 vaccination to tumoricidal effects of PD-1 inhibition is warranted for further study.

Trial Registration

ClinicalTrials.gov identifier: NCT02426892.

Potential clinical application of tumor-infiltrating lymphocyte therapy for ovarian epithelial cancer prior or post-resistance to chemotherapy

BACKGROUND

Immunotherapy has become a powerful treatment option for several solid tumor types. The presence of tumor-infiltrating lymphocytes (TIL) is correlated with better prognosis in ovarian cancer, pointing at the possibility to benefit from harnessing their anti-tumor activity. This preclinical study explores the feasibility of adoptive cell therapy (ACT) with TIL using an improved culture method.

METHODS

TIL from high-grade serous ovarian cancer were cultured using a combination of IL-2 with agonistic antibodies targeting 4-1BB and CD3. The cells were phenotyped using flow cytometry in the fresh tissue and after expansion. Tumor reactivity was assessed against HLA-matched ovarian cancer cell lines via IFN-γ ELISPOT.

RESULTS

Ovarian cancer is highly infiltrated with CD8⁺ TIL that are preferentially and robustly expanded with the addition of the agonistic antibodies. With a 95% success rate, the TIL are grown to ≥ 100 × 10⁶ cells in 2-3 weeks without over differentiation. In addition, the CD8⁺ TIL grown with this method showed HLA-restricted tumor recognition.

CONCLUSIONS

These results indicate the viability of TIL ACT for refractory ovarian cancer by allowing for the large expansion of anti-tumor TIL in a short time and consistent manner.

Exposure to anti-PD-1 causes functional differences in tumor-infiltrating lymphocytes in rare solid tumors

The pervasive use of therapeutic antibodies targeting programmed cell death protein 1 (PD-1) to boost anti-tumor immunity has positioned this approach to become the standard-of-care for some solid tumor malignancies. However, little is known as to how blockade of PD-1 may alter the function or phenotype of tumor-infiltrating lymphocytes (TIL). We used our ongoing Phase II clinical trial of pembrolizumab for patients with rare solid tumors from various types (NCT02721732) with matched core biopsies taken at baseline and after initial dose of anti-PD-1 (15-21 days post-dose) to elucidate this question. One fresh core needle biopsy was used to propagate TIL ex vivo to analyze phenotype and function using flow cytometry in both CD8⁺ and CD4⁺ TIL populations. An enriched CTLA-4 expression in the CD4⁺ TIL population was observed in TIL expanded from the on-treatment samples compared to TIL expanded from the matched baseline (n = 22, p = 0.0007) but was not observed in patients who experienced tumor regression. Impact on functionality was evaluated by measuring secretion of 65 soluble factors by expanded TIL from 26 patients at baseline and on-treatment. The CD8⁺ TIL population demonstrated a diminished cytokine secretion profile post-pembrolizumab. Overall, our study assesses the ramifications of one dose of anti-PD-1 on TIL in rare solid tumor types.

The Effect of Topoisomerase I Inhibitors on the Efficacy of T-Cell-Based Cancer Immunotherapy

Background

Immunotherapy has increasingly become a staple in cancer treatment. However, substantial limitations in the durability of response highlight the need for more rational therapeutic combinations. The aim of this study is to investigate how to make tumor cells more sensitive to T-cell-based cancer immunotherapy.

Methods

Two pairs of melanoma patient-derived tumor cell lines and their autologous tumor-infiltrating lymphocytes were utilized in a high-throughput screen of 850 compounds to identify bioactive agents that could be used in combinatorial strategies to improve T-cell-mediated killing of tumor cells. RNAi, overexpression, and gene expression analyses were utilized to identify the mechanism underlying the effect of Topoisomerase I (Top1) inhibitors on T-cell-mediated killing. Using a syngeneic mouse model (n = 5 per group), the antitumor efficacy of the combination of a clinically relevant Top1 inhibitor, liposomal irinotecan (MM-398), with immune checkpoint inhibitors was also assessed. All statistical tests were two-sided.

Results

We found that Top1 inhibitors increased the sensitivity of patient-derived melanoma cell lines (n = 7) to T-cell-mediated cytotoxicity (P < .001, Dunnett’s test). This enhancement is mediated by TP53INP1, whose overexpression increased the susceptibility of melanoma cell lines to T-cell cytotoxicity (2549 cell line: P = .009, unpaired t test), whereas its knockdown impeded T-cell killing of Top1 inhibitor–treated melanoma cells (2549 cell line: P < .001, unpaired t test). In vivo, greater tumor control was achieved with MM-398 in combination with α-PD-L1 or α-PD1 (P < .001, Tukey’s test). Prolonged survival was also observed in tumor-bearing mice treated with MM-398 in combination with α-PD-L1 (P = .002, log-rank test) or α-PD1 (P = .008, log-rank test).

Conclusions

We demonstrated that Top1 inhibitors can improve the antitumor efficacy of cancer immunotherapy, thus providing the basis for developing novel strategies using Top1 inhibitors to augment the efficacy of immunotherapy.

Abstract 1176: Immunogenomic profiling identifies a subgroup of squamous cell lung cancers with immunosuppressed tumor microenvironment and correlates TGF-beta and Wnt/beta-catenin signaling as predictive of low PD-L1 expression

Introduction: immune checkpoint inhibitors have revolutionized the treatment of non-small cell lung cancer (NSCLC), but only ~15% of patients will achieve durable clinical benefit. Our group and others have focused on characterizing the interaction between tumor genomic characteristics and immune microenvironment. Genes such as PTEN, CTNNB1, STK11 and KEAP1 have been associated with intra-tumor immune depletion, but a broader understanding of other key driver genes of NSCLC and their interplay with the immune microenvironment is currently lacking. To prospectively delineate the genomic and immune landscape of NSCLC, we launched the ICON Project (Immunogenomic Profiling of NSCLC).

Methods: we prospectively collected tissue specimens from patients with stage I-IIIA NSCLC undergoing surgical resection. Samples were subjected to extensive immune-genomic profiling, including whole-exome and RNA sequencing, multiplex immunofluorescence (mIF), and flow cytometry.

Results: from 2016-2018, 150 patients were accrued, with 78 samples having undergone genomic profiling. Most patients had stage I-II disease (74%) and non-squamous histology (70%). Most commonly mutated genes were TP53, EGFR, KRAS, CDKN2A, STK11, and mean TMB was 7.6 mut/Mb, which is comparable to TCGA (6.9mut/Mb, p=ns). Unsupervised clustering according to expression of CD8+ T cell related genes segregated tumors into immune-enriched (clusters 1 and 3) and immune-depleted (clusters 2 and 4) subgroups. We validated these findings through flow cytometry (CD8+GzB+ T cells) and mIF (CD8), with both methods showing CD8+ T cell infiltration to be enriched in clusters 1 and 3. Cluster 1 included squamous and non-squamous histology, tumors with epithelial and mesenchymal signatures, and high TMB. Cluster 2 included exclusively squamous histology with predominant mesenchymal tumor signature, high TMB, and was enriched for TP53 mutations. Cluster 3 had predominantly non-squamous histology, epithelial signature, and low TMB. Cluster 4 had exclusively non-squamous histology, predominant epithelial signature, low TMB, and was enriched for KEAP1 mutations. In addition, PD-L1 expression (by mIF) was negatively correlated with TGF-beta and WNT/Beta-catenin signaling pathway, as well as high EGFR and FGFR2 expression on malignant cells.

Conclusion: CD8+ T-cell gene signature identifies immunosuppressed subgroups of lung cancer, especially among squamous cell carcinomas with a mesenchymal signature, that may be associated with resistance to immune-based therapies. TGF-beta and Wnt/beta-catenin pathways are associated with an immunosuppressed tumor microenvironment, and may be potential novel targets to restore anti-tumor immunity in lung cancers with low PD-L1 expression.

Citation Format: Marcelo V. Negrao, Tatiana Karpinets, Jun Li, Alexandre Reuben, Cara Haymaker, Kyle G. Mitchell, Junya Fujimoto, Chi-Wan Chow, Edwin R. Parra, Lorenzo Federico, Jianhua Zhang, Ara A. Vaporciyan, Chantale Bernatchez, Tina Cascone, Boris Sepesi, Ignacio I. Wistuba, John V. Heymach, Jianjun Zhang, Don L. Gibbons, ICON Team. Immunogenomic profiling identifies a subgroup of squamous cell lung cancers with immunosuppressed tumor microenvironment and correlates TGF-beta and Wnt/beta-catenin signaling as predictive of low PD-L1 expression [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 1176.

Abstract 3776: Spatially resolved immunogenomic analyses reveal diverse sub tumoral microenvironments in the context of melanoma immunotherapy

Sustained periods of apparent clinical benefit despite lack of objective response are well known in a subpopulation of advanced melanoma patients. Inter-individual heterogeneity in response of separate tumors is common, characterizing complex overall response patterns. The molecular and cellular dynamics facilitating such long-term survival and heterogeneous response is poorly understood, particularly in the era of exposure to multiple potentially active therapies. We studied an exceptional case of long-term survival in a patient with non-responding metastatic melanoma in order to characterize the clonal and microenvironmental factors active across 3 time points.

We performed immunogenomic analyses of 3 metachronous tumors, including a systemic therapy-naïve mass, 67 intratumor sub-regions of a non-responding mass during PD-1 inhibitor therapy, and a post-PD-1 inhibitor mass. We profiled samples using whole exome sequencing, RNA-sequencing (RNA-seq), immunohistochemistry (IHC), and T cell receptor sequencing. Longitudinal, spatial, and cross-modal analyses were performed.

Longitudinal analyses identified mutations in several genes known to be associated with targeted or immune therapy resistance affecting distinct metastases. Genomic intratumoral heterogeneity (ITH) was primarily driven by subclonal copy number alterations that showed evidence of spatially-distinct evolution which may be in response to selective pressures at the tumor margin. RNA-seq revealed an unexpectedly high degree of ITH characterized by limited group-level gene or pathway associations with physical or immune characteristics of each site. Spatially-distinct pockets of immune activation and suppression were observed throughout the PD-1 inhibitor resistant metastasis despite a largely immune-excluded phenotype seen on IHC. A specific T cell Vβ CDR3 rearrangement was identified as dominant and recurrent not only across multiple spatial points within a single tumor mass, but also across metachronous tumors spanning the patient’s disease course. Immunophenotyping of the T cell population with single-cell RNA-seq suggested repeated T-cell priming events leading to the persistence of both activated and exhausted T cells bearing the same TCR-β at any given time.

Our findings highlight an unexpected level of genomic and immune heterogeneity in metastatic melanoma tumors of a long-term surviving patient. The observed degree of ITH across local tumor microenvironments reiterates the inherent limitations to identifying robust and reproducible predictive biomarkers of therapy response based on limited physical sampling of tumors. Further spatiotemporal analysis of metastatic lesions in the context of immune checkpoint blockade will be required to determine how the mechanisms driving convergent microenvironmental phenotypes may be harnessed for therapeutic gain.

Citation Format: Akash Mitra, Miles C. Andrews, Whijae Roh, Mariana P. de Macedo, Alexandre Reuben, Fernando Carapeto, Feng Wang, Sangeetha M. Reddy, Khalida Wani, Christine Spencer, John Miller, Aislyn Schalck, Latasha D. Little, Donald A. Sakellariou-Thompson, Curtis Gumbs, Wen-Jen Hwu, Chantale Bernatchez, Jianhua Zhang, Patrick Hwu, Nicholas Navin, Padmanee Sharma, James P. Allison, Jennifer Wargo, Alexander J. Lazar, Philip A. Futreal. Spatially resolved immunogenomic analyses reveal diverse sub tumoral microenvironments in the context of melanoma immunotherapy [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 3776.

Abstract 4062: Activation of innate and adaptive immunity using intratumoral tilsotolimod (IMO-2125) as monotherapy in patients with refractory solid tumors: a phase Ib study (ILLUMINATE-101)

While checkpoint inhibitor therapy has transformed treatment of multiple tumor types, many patients remain refractory. Tilsotolimod, a toll-like receptor 9 agonist, has been shown in preclinical models to activate plasmacytoid dendritic cells and increase T cell infiltration to the tumor microenvironment. Preliminary results of a phase 1/2 study suggested that intratumoral injection of tilsotolimod in combination with ipilimumab may revive an immune response in patients with immune checkpoint inhibitor-resistant metastatic melanoma. To further explore the role of tilsotolimod in modulating the tumor immune microenvironment, we conducted a Phase Ib monotherapy trial (ILLUMINATE-101). Adults with histologically or cytologically confirmed diagnosis of cancer not amenable to curative therapies received intratumoral tilsotolimod in doses escalating from 8 mg to 32 mg into a single lesion at weeks 1, 2, 3, 5, 8, and 11. Objectives of the dose evaluation portion included characterizing safety and pharmacokinetics, and evaluating alterations in the tumor microenvironment. Blood samples and tumor biopsies of injected and distal lesions were obtained at baseline and on treatment. Immune analyses included evaluation using Nanostring and/or flow cytometry of activation of the type 1 interferon (IFN) pathway, IFN gamma levels, activation of dendritic cell subsets, and changes in T cell status. As of November 7, 2018, 41 patients have been enrolled, including 38 patients into the dose evaluation portion and 3 patients into a melanoma expansion cohort. No dose-limiting toxicities or treatment-related adverse events have been observed. Within 24 hours, fresh tumor biopsies showed significant increases in IFN gamma levels, activation of the type 1 IFN pathway, induction of an antigen processing gene signature (a measure of the MHC class I antigen presentation pathway), and maturation of dendritic cells as measured by expression of HLA-DR (MHC class II), compared to pretreatment biopsies. Of 25 evaluable patients who received at least 1 dose of tilsotolimod and had at least 1 post-baseline disease assessment, 12 (48%) had a RECIST v1.1 disease assessment of stable disease. For patients with at least one disease assessment following documentation of stable disease (n=8), duration of stable disease ranged from 0.53 to 4.2+ months, with 3 patients ongoing. These results demonstrate that single agent tilsotolimod was well tolerated and induced robust alterations in the tumor microenvironment.

Citation Format: Hani M. Babiker, Vivek Subbiah, Orla Maguire, Shah Rahimian, Hans Minderman, Cara L. Haymaker, Chantale Bernatchez, Erkut Borazanci, James Geib, Srinivas K. Chunduru, Peter M. Anderson, Igor Puzanov, Adi Diab. Activation of innate and adaptive immunity using intratumoral tilsotolimod (IMO-2125) as monotherapy in patients with refractory solid tumors: a phase Ib study (ILLUMINATE-101) [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 4062.

Abstract 5028: Characterization of the tumor immune microenvironment in treatment-naïve EGFR-mutant NSCLC uncovers a low IFN-gamma suppressive immune phenotype

Background: Although immune checkpoint blockade has been successfully utilized in treating patients with non-small cell lung cancer (NSCLC), the benefit of immunotherapy for patients with advanced EGFR-mutant (EGFRm) NSCLC has been limited. Data from IMpower150 trial’s subgroup analysis suggests modulation of the tumor immune microenvironment (TME) with antiangiogenic agents and chemotherapy might enhance response to anti-PD-1/PD-L1 blockade in EGFRm lung cancers. We aim to gain a deep understanding of EGFRm NSCLC TME as the first step to make EGFRm amenable to immune therapy.

Methods: We queried two cohorts of resected stage I-III lung adenocarcinomas: PROSPECT (94 tumors) and Immune Genomic Profiling of NSCLC (ICON, 76 tumors). In the PROSPECT cohort (14 EGFRm vs 80 WT), we compared 10 immune markers by IHC (PD-L1, PD-1, CD3, CD4, CD8, CD45RO, CD57, CD68, FoxP3 and Granzyme B) and 44 immune regulator genes’ expression levels and pathway signatures from microarray data. We subsequently validated the observation of differentially expressed genes in the ICON cohort (15 EGFRm vs 61 WT) using IF, RNAseq and WES.

Results: In the PROSPECT cohort, lower PD-L1 (2.2 vs 10.4 H-score, p&lt;0.01) and lower GzmB (212 vs. 358 counts/mm2, p=0.02) were observed in the EGFRm compared to WT tumors. This is validated in the ICON cohort, showing lower PD-L1 expression (0.18% vs 7.28% p=0.05) and lower TMB (1.8 vs 9.0 mut/Mb, p&lt;0.01) in EGFRm compared to WT tumors. IFN-gamma gene expression (3.89 vs 4.71 p=0.03 in PROSPECT) and signatures were low in the EGFRm tumors, suggesting a suppressive tumor microenvironment. Different than some prior reports, we found CD8+ T cells were not significantly different in EGFRm vs. WT groups. Among known immune regulators, TGFbeta was higher in the EGFRm tumors in the PROSPECT cohort, but not in the ICON cohort. Other known immune regulators, including CTLA4, LAG3, TIM3, TIGIT, IL6 and VEGFA were not differentially expressed.

Conclusion: Our analysis showed that EGFR-mutant NSCLCs demonstrate a PD-L1 low, GzmB low, IFN-gamma low immune phenotype, suggesting a suppressive tumor microenvironment. We found that the CD8+ T cells were present in the tumor, but likely suppressed functionally by the negative regulators in the TME. These results direct future analysis of suppressive immune cell populations (CD4+ subpopulation, macrophages and dendritic cells) in EGFRm lung cancers, and represent an initial step for rationale combination of immune therapy to modulate the suppressed TME, which might lead to enhanced treatment efficacy to benefit patients with EGFR-mutant lung cancers.

Citation Format: Xiuning Le, Marcelo V. Negrao, Alexandre Reuben, Won-Chul Lee, Edwin Parra, Jun Li, Tatiana Karpinets, Carmen Behrens, Boris Sepesi, Ara Vaporiciyan, Jack Roth, Cara Haymaker, Emily Roarty, Jianhua Zhang, Chantale Bernatchez, Jianjun Zhang, Ignacio Wistuba, Don Gibbons, John Heymach. Characterization of the tumor immune microenvironment in treatment-naïve EGFR-mutant NSCLC uncovers a low IFN-gamma suppressive immune phenotype [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 5028.

Association of relative neutrophilia with a distinct immunoinhibitory milieu in non-small cell lung cancer

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Background: Elevated neutrophil-to-lymphocyte ratio (NLR) has been associated with poor prognosis in non-small cell lung cancer (NSCLC); the biological underpinnings of this observation have not been fully elucidated. We examined the relationships between peripheral neutrophil counts (PMN), NLR, circulating cytokines and angiogenic factors (CAF), and tumor microenvironment (TME) features in NSCLC. Methods: 150 patients with resectable NSCLC were enrolled in an immunoprofiling project. A panel of 43 CAFs was used to analyze preoperative plasma samples. Chemotherapy-naïve patients with CAF and a complete blood count ≤30 days preoperatively were included (n = 66; Table). For a subset, transcriptional signatures (MCP-counter, n = 50) and flow cytometry (n = 19) were used to identify TME phenotypes. Results: Increased PMNs were associated with increased pro-inflammatory CAF such as IL-1b (r = 0.392) and IL-6 (r = 0.339), as well as Th17/Tc17 associated CAF IL-17A (r = 0.320) and TNF-a (r = 0.368). Elevated NLR was inversely correlated with the lymphocyte activation marker soluble CD27 (r = -0.320, p = 0.009). This negative association was mirrored in the TME, as tumor neutrophil signatures were inversely correlated with a local IFN-g gene signature (r = -0.626, p < 0.001). Interestingly, a Th17/Tc17 peripheral signature (elevated IL-17A) was associated with an enrichment of CD8+TIM3+ cells (r = 0.623, p = 0.042) in the tumor. While this requires confirmation in a larger cohort, this correlation provides a potential rationale for targeting TIM3 in this population. Upon analysis of clinical characteristics, peripheral PMNs and NLR were higher among patients with squamous histology (PMN p = 0.009; NLR p = 0.034) and positively correlated with tumor size (PMN r = 0.344, p = 0.004; NLR r = 0.363, p = 0.003). Conclusions: A relative neutrophilia in NSCLC patients is associated with an inflammatory milieu suggestive of a Th17/Tc17 presence and decreased lymphocyte activation that is reflected within the TME. Further investigation is needed to define the role of NLR as a predictive biomarker and to identify whether neutrophils or Th17/Tc17 T cells could serve as a therapeutic target to improve immunotherapy response in NSCLC.[Table: see text]

Baseline tumor-immune signatures associated with response to bempegaldesleukin (NKTR-214) and nivolumab

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Background: PIVOT-02 is an ongoing phase 1/2 study of bempegaldesleukin (NKTR-214), a CD122-preferential IL-2 pathway agonist, plus nivolumab in patients with advanced solid tumors. Bempegaldesleukin (NKTR-214) increases proliferative tumor infiltrating lymphocytes (TIL) and cell surface PD-1 on immune cells and PD-L1 on tumor cells, demonstrating potential synergy with anti-PD-1 therapy. Pre-treatment tumor biopsies from metastatic 1L melanoma (MEL) and urothelial carcinoma (UC) patients were analyzed to correlate baseline immune phenotype to response. Methods: Pre-treatment TIL (CD8+ T cells/mm2 and %CD3+ by IHC; 29 MEL; 22 UC) were measured and divided into high and low groups based on median values. PD-L1 (% PD-L1 on tumor cells by IHC [28-8 PharmDx]; 33 MEL; 23 UC) was scored negative (<1%) or positive (≥1%). Interferon gamma gene score (IFNG; 11 MEL) was scored as high or low based on median p value of <0.1 for 15 genes (EdgeSeq). High and low groups were correlated with responses per RECIST 1.1. Results: Baseline demographics and prognostic factors were balanced in the biomarker subgroups. Response rates for response evaluable MEL and UC were 53% (SITC 2018) and 48% (ASCO-GU 2019), respectively. In MEL, median values of CD3-TIL and CD8-TIL were 19% and 203 cells/mm2, respectively. Response rate correlations were 67% and 20% with IFNG high and low, 79% and 29% with CD3-TIL high and low, 79% and 33% with CD8-TIL high and low, and 68% and 43% with PD-L1 positive and negative. Most importantly, responses were observed in patients with the least favorable tumor microenvironment, characterized as both PD-L1 negative and TIL low, with responses of 17% (1/6 CD8-TIL), and 25% (2/8 CD3-TIL), respectively. Similar correlative trends were observed in UC, with 50% (4/8 CD8-TIL) and 38% (3/8 CD3-TIL) responses in patients with least favorable microenvironment. Conclusions: The biomarker program included in PIVOT-02 identified baseline immune signatures correlated with response for MEL and UC. The response rates observed in both the favorable and unfavorable tumor microenvironments indicate the potential of this combination and support its broad development. Clinical trial information: NCT02983045.