Molecular, Metabolic, and Subcellular Mapping of the Tumor Immune Microenvironment via 3D Targeted and Non-Targeted Multiplex Multi-Omics Analyses

Most platforms used for the molecular reconstruction of the tumor-immune microenvironment (TIME) of a solid tumor fail to explore the spatial context of the three-dimensional (3D) space of the tumor at a single-cell resolution, and thus lack information about cell-cell or cell-extracellular matrix (ECM) interactions. To address this issue, a pipeline which integrated multiplex spatially resolved multi-omics platforms was developed to identify crosstalk signaling networks among various cell types and the ECM in the 3D TIME of two FFPE (formalin-fixed paraffin embedded) gynecologic tumor samples. These platforms include non-targeted mass spectrometry imaging (glycans, metabolites, and peptides) and Stereo-seq (spatial transcriptomics) and targeted seqIF (IHC proteomics). The spatially resolved imaging data in a two- and three-dimensional space demonstrated various cellular neighborhoods in both samples. The collection of spatially resolved analytes in a voxel (3D pixel) across serial sections of the tissue was also demonstrated. Data collected from this analytical pipeline were used to construct spatial 3D maps with single-cell resolution, which revealed cell identity, activation, and energized status. These maps will provide not only insights into the molecular basis of spatial cell heterogeneity in the TIME, but also novel predictive biomarkers and therapeutic targets, which can improve patient survival rates.

Spatial Immunoprofiling of Adenoid Cystic Carcinoma Reveals B7-H4 Is a Therapeutic Target for Aggressive Tumors

PURPOSE

Adenoid cystic carcinoma (ACC) is a heterogeneous malignancy, and no effective systemic therapy exists for metastatic disease. We previously described two prognostic ACC molecular subtypes with distinct therapeutic vulnerabilities, ACC-I and ACC-II. In this study, we explored the ACC tumor microenvironment (TME) using RNA-sequencing and spatial biology to identify potential therapeutic targets.

EXPERIMENTAL DESIGN

Tumor samples from 62 ACC patients with available RNA-sequencing data that had been collected as part of previous studies were stained with a panel of 28 validated metal-tagged antibodies. Imaging mass cytometry (IMC) was performed using the Fluidigm Helios CyTOF instrument and analyzed with Visiopharm software. The B7-H4 antibody-drug conjugate AZD8205 was tested in ACC patient-derived xenografts (PDX).

RESULTS

RNA deconvolution revealed that most ACCs are immunologically "cold," with approximately 30% being "hot." ACC-I tumors with a poor prognosis harbored a higher density of immune cells; however, spatial analysis by IMC revealed that ACC-I immune cells were significantly restricted to the stroma, characterizing an immune-excluded TME. ACC-I tumors overexpressed the immune checkpoint B7-H4, and the degree of immune exclusion was directly correlated with B7-H4 expression levels, an independent predictor of poor survival. Two ACC-I/B7-H4-high PDXs obtained 90% complete responses to a single dose of AZD8205, but none were observed with isotype-conjugated payload or in an ACC-II/B7-H4 low PDX.

CONCLUSIONS

Spatial analysis revealed that ACC subtypes have distinct TMEs, with enrichment of ACC-I immune cells that are restricted to the stroma. B7-H4 is highly expressed in poor-prognosis ACC-I subtype and is a potential therapeutic target.

Microfibril-associated protein 5 and the regulation of skin scar formation

Many factors regulate scar formation, which yields a modified extracellular matrix (ECM). Among ECM components, microfibril-associated proteins have been minimally explored in the context of skin wound repair. Microfibril-associated protein 5 (MFAP5), a small 25 kD serine and threonine rich microfibril-associated protein, influences microfibril function and modulates major extracellular signaling pathways. Though known to be associated with fibrosis and angiogenesis in certain pathologies, MFAP5's role in wound healing is unknown. Using a murine model of skin wound repair, we found that MFAP5 is significantly expressed during the proliferative and remodeling phases of healing. Analysis of existing single-cell RNA-sequencing data from mouse skin wounds identified two fibroblast subpopulations as the main expressors of MFAP5 during wound healing. Furthermore, neutralization of MFAP5 in healing mouse wounds decreased collagen deposition and refined angiogenesis without altering wound closure. In vitro, recombinant MFAP5 significantly enhanced dermal fibroblast migration, collagen contractility, and expression of pro-fibrotic genes. Additionally, TGF-ß1 increased MFAP5 expression and production in dermal fibroblasts. Our findings suggest that MFAP5 regulates fibroblast function and influences scar formation in healing wounds. Our work demonstrates a previously undescribed role for MFAP5 and suggests that microfibril-associated proteins may be significant modulators of wound healing outcomes and scarring.

Spatial Transcriptomics Depict Ligand-Receptor Cross-talk Heterogeneity at the Tumor-Stroma Interface in Long-Term Ovarian Cancer Survivors

Advanced high-grade serous ovarian cancer (HGSC) is an aggressive disease that accounts for 70% of all ovarian cancer deaths. Nevertheless, 15% of patients diagnosed with advanced HGSC survive more than 10 years. The elucidation of predictive markers of these long-term survivors (LTS) could help identify therapeutic targets for the disease, and thus improve patient survival rates. To investigate the stromal heterogeneity of the tumor microenvironment (TME) in ovarian cancer, we used spatial transcriptomics to generate spatially resolved transcript profiles in treatment-naïve advanced HGSC from LTS and short-term survivors (STS) and determined the association between cancer-associated fibroblasts (CAF) heterogeneity and survival in patients with advanced HGSC. Spatial transcriptomics and single-cell RNA-sequencing data were integrated to distinguish tumor and stroma regions, and a computational method was developed to investigate spatially resolved ligand-receptor interactions between various tumor and CAF subtypes in the TME. A specific subtype of CAFs and its spatial location relative to a particular ovarian cancer cell subtype in the TME correlated with long-term survival in patients with advanced HGSC. Also, increased APOE-LRP5 cross-talk occurred at the stroma-tumor interface in tumor tissues from STS compared with LTS. These findings were validated using multiplex IHC. Overall, this spatial transcriptomics analysis revealed spatially resolved CAF-tumor cross-talk signaling networks in the ovarian TME that are associated with long-term survival of patients with HGSC. Further studies to confirm whether such cross-talk plays a role in modulating the malignant phenotype of HGSC and could serve as a predictive biomarker of patient survival are warranted.

SIGNIFICANCE

Generation of spatially resolved gene expression patterns in tumors from patients with ovarian cancer surviving more than 10 years allows the identification of novel predictive biomarkers and therapeutic targets for better patient management. See related commentary by Kelliher and Lengyel, p. 1383.

Comparative Tumor Microenvironment Analysis of Primary and Recurrent Ovarian Granulosa Cell Tumors

Adult-type granulosa cell tumors (aGCT) are rare ovarian sex cord tumors with few effective treatments for recurrent disease. The objective of this study was to characterize the tumor microenvironment (TME) of primary and recurrent aGCTs and to identify correlates of disease recurrence. Total RNA sequencing (RNA-seq) was performed on 24 pathologically confirmed, cryopreserved aGCT samples, including 8 primary and 16 recurrent tumors. After read alignment and quality-control filtering, DESeq2 was used to identify differentially expressed genes (DEG) between primary and recurrent tumors. Functional enrichment pathway analysis and gene set enrichment analysis was performed using "clusterProfiler" and "GSVA" R packages. TME composition was investigated through the analysis and integration of multiple published RNA-seq deconvolution algorithms. TME analysis results were externally validated using data from independent previously published RNA-seq datasets. A total of 31 DEGs were identified between primary and recurrent aGCTs. These included genes with known function in hormone signaling such as LHCGR and INSL3 (more abundant in primary tumors) and CYP19A1 (more abundant in recurrent tumors). Gene set enrichment analysis revealed that primarily immune-related and hormone-regulated gene sets expression was increased in recurrent tumors. Integrative TME analysis demonstrated statistically significant depletion of cancer-associated fibroblasts in recurrent tumors. This finding was confirmed in multiple independent datasets.

IMPLICATIONS

Recurrent aGCTs exhibit alterations in hormone pathway gene expression as well as decreased infiltration of cancer-associated fibroblasts, suggesting dual roles for hormonal signaling and TME remodeling underpinning disease relapse.

Abstract 5918: Interrogating host-intratumoral microbial interactions in pancreatic cancer

Cancer is increasingly becoming a rising cause of mortality worldwide. Microbiota, both within the gut and tumors, has emerged as a significant player influencing tumor growth and responses to therapies. The tumor niche provides a privileged microenvironment for microbial colonization. Recent evidence links microbiota and pancreatic tumorigenesis. Pancreatic ductal adenocarcinoma (PDAC), is an aggressive cancer surrounded by a highly immuno-suppressive tumor microenvironment (TME) which limits efficacy of most available therapies. We have previously reported that rare long-term survival in pancreatic cancer is associated with an intratumoral microbial signature which correlates with enhanced TME immunoactivation, suggestive of microbial mediated immune cell recruitment. A gut-to-tumor microbial crosstalk was also found in a human-to-mouse Fecal Microbiota Transplant (FMT) tumor model. While we have identified the vital role of microbiota in affecting tumor immunity, there is still a gap of knowledge about local microbial interactions within TME. Deeper understanding of the microbial mediated events that are triggered and follow PDAC development, which act to induce and support tumor growth, would provide us with potential novel targets that could be blocked to reverse PDAC immunosuppression and tumor growth. To interrogate the features of the pancreatic tumor microbial niche, we performed spatial co-detection of microbial and host targets to identify the cellular compartment which interacts with microbes inside the TME in clinical samples. We developed novel qualitative and quantitative imaging methodologies for evaluating crosstalk between the host and microbes. We also evaluated the effect of microbial burden on transcriptomic changes in host cells through multiple spatial sequencing approaches. Overall, we dissect the functional role of microbes in orchestrating TME organization and their effect on tumor signaling.

Citation Format: Vidhi Chandra, Hajar Rajaei, Seyda Baydogan, Javier Gomez, Sammy Ferri-Borgogno, Anirban Maitra, Erick Riquelme, Ismet Sahin, Jared Burks, Michael Kim, Florencia McAllister. Interrogating host-intratumoral microbial interactions in pancreatic cancer [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 5918.

Abstract B31: Depicting spatially-resolved immune landscapes in long-term ovarian cancer survivors by imaging mass cytometry

High-grade serous ovarian cancer (HGSC) is the most common subtype of ovarian cancer, accounting for 70% of all ovarian cancer deaths. Most patients with HGSC are diagnosed at advanced stages with the tumors spread beyond the pelvis. HGSC is notable sensitive to platinum/taxane-based chemotherapy before or following debulking surgery. Despite the high response rate, most patients will develop recurrent chemoresistant disease, and die from the disease within 2 years (short-term survivors, STS). Despite these dismal statistics, 10-15% of patients with advanced stage HGSC will survive 7 or more years following the diagnosis (long-term survivors, LTS). Immune cells in the tumor microenvironment (TME) have been shown to modulate the malignant phenotypes of HGSC. However, the mechanisms by which these cells interact with other cell types in the TME to modulate patient survival rates remain unclear. We hypothesize that spatially-resolved immune signatures associated with survival in STS and LTS patients can be identified, which may serve as a new generation of prognostic biomarkers for HGSC. To test this, we used 35 metal-tagged antibodies, which detect various cell specific and immune related markers, and imaging mass cytometry (IMC) to generate immune landscapes from a total of 47 advanced stage, and treatment naïve HGSC tumors (obtained from 21 LTS and 26 STS optimally debulked patients). Formalin fixed paraffin embedded (FFPE) tissue sections were stained. Images of each tissue section were acquired by the Fluidigm Helios CyTOF instrument utilizing the laser ablation module of the Hyperion Imaging System, and analyzed with the Visiopharm software. Tumor and stromal areas were first separated based on the presence or absence of Keratin 8/18 and SMA respectively. Cells boundaries and phenotypes were determined by a pretrained Artificial Intelligence algorithm using Visiopharm’s unbiased autoclustering module. Cell densities and spatial relationships of identified phenotypes and statistical analysis were then calculated in R. Our results demonstrated significantly higher intratumoral cell densities of NK (CD56+CD25+) and activated T cells (CD8+CD44+Granzyme B+ and CD4+CD25+) in LTS than STS. Moreover, we showed that densities of multiple subpopulations of immunosuppressive macrophages (CD68+CD163+) expressing both TIM3 and CXCR5 markers were higher in STS than LTS, suggesting that the macrophages were actively engulfing CD8+ and CD4+ T cells in the TME. Furthermore, spatial analysis showed that increased densities of TIM3+CXCR5+ macrophages and increased number of neighborhoods between these macrophages and a variety of TME cells in the STS compared to LTS. In conclusions, our findings depict distinct spatially-resolved immune landscapes that are associated with LTS in HGSC patients. Further studies on the crosstalk networks established between specific immune cell types and their neighboring cells in STS and LTS will allow the identification of novel therapeutic targets that can improve patient survival and are warranted.

Citation Format: Sammy Ferri-Borgogno, Javier A Gomez, Ivo Veletic, Jared K Burks, Samuel C Mok. Depicting spatially-resolved immune landscapes in long-term ovarian cancer survivors by imaging mass cytometry [abstract]. In: Proceedings of the AACR Special Conference: Tumor Immunology and Immunotherapy; 2022 Oct 21-24; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2022;10(12 Suppl):Abstract nr B31.

Ryanodine receptor 1-mediated Ca2+ signaling and mitochondrial reprogramming modulate uterine serous cancer malignant phenotypes

Background

Uterine serous cancer (USC) is the most common non-endometrioid subtype of uterine cancer, and is also the most aggressive. Most patients will die of progressively chemotherapy-resistant disease, and the development of new therapies that can target USC remains a major unmet clinical need. This study sought to determine the molecular mechanism by which a novel unfavorable prognostic biomarker ryanodine receptor 1 (RYR1) identified in advanced USC confers their malignant phenotypes, and demonstrated the efficacy of targeting RYR1 by repositioned FDA-approved compounds in USC treatment.

Methods

TCGA USC dataset was analyzed to identify top genes that are associated with patient survival or disease stage, and can be targeted by FDA-approved compounds. The top gene RYR1 was selected and the functional role of RYR1 in USC progression was determined by silencing and over-expressing RYR1 in USC cells in vitro and in vivo. The molecular mechanism and signaling networks associated with the functional role of RYR1 in USC progression were determined by reverse phase protein arrays (RPPA), Western blot, and transcriptomic profiling analyses. The efficacy of the repositioned compound dantrolene on USC progression was determined using both in vitro and in vivo models.

Results

High expression level of RYR1 in the tumors is associated with advanced stage of the disease. Inhibition of RYR1 suppressed proliferation, migration and enhanced apoptosis through Ca²⁺-dependent activation of AKT/CREB/PGC-1α and AKT/HK1/2 signaling pathways, which modulate mitochondrial bioenergetics properties, including oxidative phosphorylation, ATP production, mitochondrial membrane potential, ROS production and TCA metabolites, and glycolytic activities in USC cells. Repositioned compound dantrolene suppressed USC progression and survival in mouse models.

Conclusions

These findings provided insight into the mechanism by which RYR1 modulates the malignant phenotypes of USC and could aid in the development of dantrolene as a repurposed therapeutic agent for the treatment of USC to improve patient survival.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13046-022-02419-w.

Abstract 1551: miR-625-3p enhances chemosensitivity in ovarian cancer cells through exosomal export of cisplatin and paclitaxel

Although a majority of women with high-grade serous ovarian cancer (HGSC) achieve a complete response to first-line platinum- and paclitaxel-based chemotherapy, around thirty percent of patients are identified as incomplete responders. Their diseases typically either does not respond or progresses during treatment (refractory) or recurs within 6 months of completing treatment (resistant), suggesting the inherit or intrinsic characteristics of the tumor. Currently, there are no biomarkers that can predict intrinsic resistance, which can avoid unnecessary treatment and toxicity. MicroRNAs (miRNAs) provide a novel master layer of regulation of gene expression. However, the molecular mechanisms by which miRNAs confer a chemoresistant phenotype in ovarian cancer have not been elucidated. To identify miRNAs that are associated with intrinsic chemoresistance in HGSC, Ion Torrent next-generation sequencing analysis of miRNAs was performed on microdissected chemosensitive and chemorefractory primary HGSC cases. Amongst all the miRNAs that were significantly down-regulated in chemorefractory cases, lower miR-625-3p expression was found to be associated with poorer overall and progression-free survivals. Further functional studies showed that overexpression of miR-625-3p significantly decreased cisplatin and paclitaxel resistance in ovarian cancer cells in vitro and in vivo. Online target prediction algorithms together with transcriptome profiling of HGSC cells transfected with miR-625-3p mimics or control mimics identified SSX2IP as a direct target of miR-625-3p, suggesting that SSX2IP may play a role in conferring cisplatin/paclitaxel resistance in HGSC by mediating the effect of miR-625-3p. SSX2IP is a microtubule anchoring and centriolar satellite protein, which plays a critical role in controlling microtubule length and orientation, and centrosome maturation. We demonstrated that HGSC cells transfected with SSX2IP had marked increases in microtubule masses, intracellular multivesicular body trafficking and exosomal cisplatin level; and a decrease in intracellular cisplatin level. In conclusion, down-regulation of miR-625-3p confers cisplatin/paclitaxel resistance in ovarian cancer cells via its novel direct target SSX2IP. SSX2IP alters the microtubule dynamics and subsequently mediates inter-organelle crosstalks between microtubules and multivesicular bodies, which facilitate exosomal export of cisplatin and paclitaxel of HGSC cells. This study is crucial for developing new predictive biomarkers for intrinsic chemoresistance, and new treatment strategies for HGSC based on upregulating miR-625-3p or downregulating SSX2IP expression in ovarian cancer cells, which will enhance cisplatin and paclitaxel sensitivity, and improve patient survival rates.

Citation Format: Chi Lam Au Yeung, Tetsushi Tsuruga, Kay-Pong Yip, Sammy Ferri-Borgogno, Samuel Mok. miR-625-3p enhances chemosensitivity in ovarian cancer cells through exosomal export of cisplatin and paclitaxel [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1551.

Abstract 1248: Predictors of innate resistance to pembrolizumab in patients with microsatellite instability-high endometrial cancer

Introduction: Despite FDA approval of pembrolizumab in microsatellite instability-high (MSI-H)/mismatch repair deficient solid tumors, approximately half of patients with MSI-H endometrial cancer are treatment-refractory. We sought to evaluate pre-treatment MSI-H endometrial tumor samples to examine cell subpopulation differences in the tumor microenvironment (TME) associated with resistance to pembrolizumab.

Methods: Archival tumor samples from MSI-H endometrial cancer patients treated with pembrolizumab at MD Anderson Cancer Center were obtained under an IRB-approved protocol. Twenty-one patients were identified, and pre-treatment archival tumor samples were collected and submitted for RNA-seq and imaging mass cytometry (IMC) with an optimized 38-antibody panel to identify predictive immuno-genomic signatures and cell subpopulations associated with treatment response.

Results: Among the 21 patients treated with pembrolizumab, there were 14 responders and 7 non-responders. Based on transcriptomic signatures, TME heterogeneity was observed. The 14 responders consisted of samples with immunologically “hot” (5/5; 100%), “cold” (6/8; 75%), and “warm” TMEs (3/8; 37.5%) while the 7 non-responders consisted of only “cold” (2/8; 25%) and “warm” (5/8; 62.5%) TME samples. There was an enrichment of fibroblasts and endothelial cell transcriptomic signatures in the samples of the non-responders compared to responders (p=0.018) with a trend of increasing enrichment in those signatures as response strength decreased. IMC performed on archival tissue from 20 patients demonstrated similar trend of higher population of activated fibroblasts (SMA+, MFAP5+) and endothelial cells (CD31+) in non-responders. Furthermore, non-responders had significantly higher total regulatory T cells (CD4+FOXP3+) in the tumor (p=0.027) and stroma (p=0.0282) compared to responders. Additionally, significantly higher activated regulatory T cells (CD4+FOXP3+CD25+) were observed in the tumor (p=0.016) and stroma (p=0.008) of non-responders compared to responders. Similar abundance of total and subpopulations of CD8+ T cells were observed between responders and non-responders.

Conclusion: The MSI-H endometrial TME is heterogeneous. Increased presence of fibroblasts, endothelial cells, and regulatory T-cells in the TME correlate with innate resistance to pembrolizumab. Treatment aimed toward the reduction of these cellular subpopulations may improve sensitivity to PD-1 inhibitors. Future studies are needed to validate these findings.

Citation Format: Jeffrey A. How, Minghao Dang, Sammy Ferri-Borgogno, Elizabeth Euscher, Melinda S. Yates, Weiyi Peng, Shrina D. Patel, Jared J. Burks, Ivo Vletic, Javier Gomez, Karen Lu, Samuel C. Mok, Linghua Wang, Amir A. Jazaeri. Predictors of innate resistance to pembrolizumab in patients with microsatellite instability-high endometrial cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1248.

Spontaneous tumor regression following COVID-19 vaccination

Vaccination against COVID-19 is critical for immuno-compromised individuals, including patients with cancer. Systemic reactogenicity, a manifestation of the innate immune response to vaccines, occurs in up to 69% of patients following vaccination with RNA-based COVID-19 vaccines. Tumor regression can occur following an intense immune-inflammatory response and novel strategies to treat cancer rely on manipulating the host immune system. Here, we report spontaneous regression of metastatic salivary gland myoepithelial carcinoma in a patient who experienced grade 3 systemic reactogenicity, following vaccination with the mRNA-1273 COVID-19 vaccine. Histological and immunophenotypic inspection of the postvaccination lung biopsy specimens showed a massive inflammatory infiltrate with scant embedded tumor clusters (<5%). Highly multiplexed imaging mass cytometry showed that the postvaccination lung metastasis samples had remarkable immune cell infiltration, including CD4+ T cells, CD8+ T cells, natural killer cells, B cells, and dendritic cells, which contrasted with very low levels of these cells in the prevaccination primary tumor and lung metastasis samples. CT scans obtained 3, 6, and 9 months after the second vaccine dose demonstrated persistent tumor shrinkage (50%, 67%, and 73% reduction, respectively), suggesting that vaccination stimulated anticancer immunity. Insight: This case suggests that the mRNA-1273 COVID-19 vaccine stimulated anticancer immunity and tumor regression.

CES2 sustains HNF4α expression to promote pancreatic adenocarcinoma progression through an epoxide hydrolase-dependent regulatory loop

Objective

Intra-tumoral expression of the serine hydrolase carboxylesterase 2 (CES2) contributes to the activation of the pro-drug irinotecan in pancreatic ductal adenocarcinoma (PDAC). Given other potential roles of CES2, we assessed its regulation, downstream effects, and contribution to tumor development in PDAC.

Methods

Association between the mRNA expression of CES2 in pancreatic tumors and overall survival was assessed using The Cancer Genome Atlas. Cell viability, clonogenic, and anchorage-independent growth assays as well as an orthotopic mouse model of PDAC were used to evaluate the biological relevance of CES2 in pancreatic cancer. CES2-driven metabolic changes were determined by untargeted and targeted metabolomic analyses.

Results

Elevated tumoral CES2 mRNA expression was a statistically significant predictor of poor overall survival in PDAC patients. Knockdown of CES2 in PDAC cells reduced cell viability, clonogenic capacity, and anchorage-independent growth in vitro and attenuated tumor growth in an orthotopic mouse model of PDAC. Mechanistically, CES2 was found to promote the catabolism of phospholipids resulting in HNF4α activation through a soluble epoxide hydrolase (sEH)-dependent pathway. Targeting of CES2 via siRNA or small molecule inhibitors attenuated HNF4α protein expression and reduced gene expression of classical/progenitor markers and increased basal-like markers. Targeting of the CES2-sEH-HNF4α axis using small molecule inhibitors of CES2 or sEH reduced cell viability.

Conclusions

We establish a novel regulatory loop between CES2 and HNF4α to sustain the progenitor subtype and promote PDAC progression and highlight the potential utility of CES2 or sEH inhibitors for the treatment of PDAC as part of non-irinotecan-containing regimens.

Oncogenic KRAS Requires Complete Loss of BAP1 Function for Development of Murine Intrahepatic Cholangiocarcinoma

Intrahepatic cholangiocarcinoma (ICC) is a primary biliary malignancy that harbors a dismal prognosis. Oncogenic mutations of KRAS and loss-of-function mutations of BRCA1-associated protein 1 (BAP1) have been identified as recurrent somatic alterations in ICC. However, an autochthonous genetically engineered mouse model of ICC that genocopies the co-occurrence of these mutations has never been developed. By crossing Albumin-Cre mice bearing conditional alleles of mutant Kras and/or floxed Bap1, Cre-mediated recombination within the liver was induced. Mice with hepatic expression of mutant Kras^G12D alone (KA), bi-allelic loss of hepatic Bap1 (B^homoA), and heterozygous loss of Bap1 in conjunction with mutant Kras^G12D expression (B^hetKA) developed primary hepatocellular carcinoma (HCC), but no discernible ICC. In contrast, mice with homozygous loss of Bap1 in conjunction with mutant Kras^G12D expression (B^homoKA) developed discrete foci of HCC and ICC. Further, the median survival of B^homoKA mice was significantly shorter at 24 weeks when compared to the median survival of ≥40 weeks in B^hetKA mice and approximately 50 weeks in B^homoA and KA mice (p < 0.001). Microarray analysis performed on liver tissue from KA and B^homoKA mice identified differentially expressed genes in the setting of BAP1 loss and suggests that deregulation of ferroptosis might be one mechanism by which loss of BAP1 cooperates with oncogenic Ras in hepato-biliary carcinogenesis. Our autochthonous model provides an in vivo platform to further study this lethal class of neoplasm.

Abstract 2749: The unique tumor immune microenvironment of clear cell ovarian carcinoma

Based on differences in chemosensitivity and clinical outcomes, we hypothesize that clear cell ovarian carcinoma (CCCO) displays a unique tumor immune microenvironment (TIME) compared to high grade serous ovarian carcinoma (HGSOC). Microsatellite instability and ARID1DA mutations are more common in clear cell ovarian carcinoma suggesting improved outcomes with checkpoint blockade immunotherapy use. Our objective is to compare the TIME of CCCO to HGSOC using imaging mass cytometry (IMC).

Primary untreated ovarian tumors were collected under an IRB-approved protocol. Formalin fixed paraffin embedded (FFPE) tissue sections were stained with 34 metal-tagged antibodies to detect various cell specific and immune related markers using the Fluidigm protocol. IMC data was obtained by the Fluidigm Helios CyTOF instrument utilizing the Hyperion Imaging System laser ablation module. Images from a 1mm2 area of each tissue section were processed and converted to tiff files using MCD Viewer (Fluidigm). Images were analyzed using a deep learning based data analytic pipeline beginning with cell segmentation then multiple rounds of phenotype clustering for cell type annotation. Various cell phenotypes were then measured for cell density analysis within a tumor enriched area. Spearman correlation was performed between cell densities of CCCO and HGSOC.

Samples from 51 patients were used for the study: 10 with CCCO and 41 with HGSOC. In the CCCO group, stage of disease ranged from stage I (70%) to III (10%), but all the HGSOC had stage III (92.7%) or IV (7.3%) disease (p&lt;0.001).

Images were analyzed using 18 markers based on high signal-to-noise ratios. Following cell segmentation and phenotype clustering, 39 cell subtype clusters were identified including 6 macrophage cell subtypes, 11 T cell subtypes, and 12 tumor cell subtypes.

CCCO had a lower density of intratumoral activated CD8+ T cells (CD44+CD8a+CD45RO+) than the HGSOC (p=0.048). Tumor cell subtypes in the tumor-enriched areas differed between the two groups. CCCO had a higher density of B7-H4midKi67hi tumor cells (p=0.004), but had a lower density B7-H4hiKi67midKeratin8_18+ (p=0.027), B7-H4hiKeratin8_18+ (p=0.004), and B7-H4hiKi67midKeratin8_18+ tumor cells (p=0.007). CCCO had a lower density of CD31+CD73mid cells (p=0.034) but higher density of CD73hi (p=0.024) compared to HGSOC.

CCCO have a distinct TIME compared to HGSOC. In our cohort, despite most having stage I disease, CCCO showed features associated with poor prognosis including decreased intratumoral CD8+ T cells, higher density of a subtype of actively dividing B7-H4mid ki67hi cancer cells, and higher density of CD73hi cells. Since B7-H4 and CD73 both act as immune checkpoint inhibitors that can confer chemoresistance, therapeutic strategies to target these molecules may enhance CD8+ T cell mediated anti-tumor immune response and chemosensitivity to improve survival in patients with CCCO.

Citation Format: Han T. Cun, Ying Zhu, Sammy Ferri-Borgogno, Jianting Sheng, Rita Cheng, Jae-hoon Kim, Gwan Hee Han, Stephen T. Wong, Karen H. Lu, Samuel C. Mok. The unique tumor immune microenvironment of clear cell ovarian carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2749.

Abstract 2744: The immune landscape of recurrent ovarian carcinoma

By examining the immune landscape in recurrent ovarian carcinoma, we can characterize the evolution of the tumor immune microenvironment (TIME) to understand its disease progression and response to therapy. Thus, the objective of this study is to evaluate the differences in the TIME in primary HGSOC compared to recurrent disease by utilizing imaging mass cytometry (IMC).

Treatment naive primary HGSOC along with matched first recurrence tumors from the same patient were collected under an IRB-approved protocol. Formalin fixed paraffin embedded tissue sections were stained with 18 metal-tagged antibodies to detect various cell specific and immune related markers using the Fluidigm protocol. IMC data was obtained by the Fluidigm Helios CyTOF instrument utilizing the Hyperion Imaging System laser ablation module. Images from a 1mm2 area of each tissue section were processed and converted to tiff files using MCD Viewer (Fluidigm). Multiplex image analysis was performed with Visiopharm software, where tumor and stromal areas were separated based on presence or absence of Keratin 8/18, Collagen-I, and SMA respectively. Cells boundaries were determined by a pretrained Artificial Intelligence algorithm and phenotyped by Visiopharm unbiased autoclustering module using only the top 20% of pixel values per cell. Statistical analysis was performed using wilcoxon signed-rank test between cell densities of the primary and paired recurrent tumors.

Paired primary and recurrent HGSOC samples were assessed from 27 patients. Stage of disease ranged from I to IV, but most were stage III (81.5%). The median time to first recurrence was 28 months (IQR 34). The image analysis showed that recurrent tumors had a lower density of stromal CD8a+ (p&lt;0.01), CD8+granzymeB+CD45RO+, (p&lt;0.01) and CD8+granzymeB+CD44+CD45RO+ cells (p&lt;0.01) compared to primary tumors. Both stromal and intratumoral CD20+ cells were higher in recurrent tumors (p=0.03, p&lt;0.01). Stromal CD73+Coll-I+ cells were lower in recurrent tumors (p&lt;0.01).

Our study demonstrates the evolution of the TIME of HGSOC from primary tumor to first recurrence. Recurrent tumors demonstrated lower stromal CD8+ T cells, specifically activated memory T cells and resting memory T cells, compared to their primary tumors, suggesting a more immunosuppressive environment. Although recurrent tumors had a higher density of CD20+ B cells, their function was not further described. These alterations propose that recurrent HGSOC demonstrates a more suppressive TIME that warrants further characterization.

Citation Format: Han T. Cun, Sammy Ferri-Borgogno, Rita Cheng, Jae-hoon Kim, Gwan Hee Han, Jared K. Burks, Karen H. Lu, Samuel C. Mok. The immune landscape of recurrent ovarian carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2744.

Abstract 103: Spatially resolved transcriptomics identified distinct tumor-stroma crosstalk networks in long term ovarian cancer survivors

The tumor microenvironment (TME), composed primarily of fibroblasts, endothelial cells, lymphocytic infiltrates and extracellular matrix proteins, can directly affect cancer cell growth, migration, differentiation as well as immune cell landscapes, thereby presenting a unique aspect of diagnosing and treating cancer. Cancer-associated fibroblasts (CAF) and immune cells are the main orchestrators of the ovarian cancer TME. We hypothesized that spatial transcriptomics (ST), which can provide a rich spatial context to gene expression, will identify crosstalk signaling networks among various cell types in the ovarian TME. Advanced stage high-grade serous ovarian cancer (HGSC) tissue frozen sections from two treatment naïve long-term survivors (LTS, overall survival ≥ 10 years) and two short-term survivors (STS, overall survival ≤ 2 years) were placed onto a ST expression slide pre-spotted with 1000 unique barcoded RNA-capturing probes. The ST slides were then stained with H&E and imaged. Tissue permeabilization and cDNA synthesis were then performed directly on the tissue section. The derived barcoded cDNA libraries from each sample were sequenced using Illumina NextSeq500 flow cells. After RNA-Seq analysis, supervised analysis was then performed by selecting different regions (based on tissue histology) in the tumor, tumor/stroma mixture, stroma close or far away from tumor areas to identify differentially expressed genes between STS and LTS. Stromal cells from different spatial locations had unique differentially expressed genes based on their proximity (11 genes in LTS; 11 genes in STS) or remoteness (18 genes in LTS; 10 genes in STS) to cancer cell compartments. Among the major modulated gene networks, higher levels of antigen-presenting molecules were found in the stroma in close proximity to the tumor cell nest than in stroma located far away in LTS tumor samples but not in the STS samples, suggesting an increased number of activated antigen-presenting cells in LTS tumors. In addition, higher levels of adhesion molecules and angiogenetic factors were found in the stroma in close proximity to the tumor cell nest than in stroma located far away in STS tumor samples but not in LTS samples, suggesting that adhesion molecules and angiogenetic factors produced by stromal cells may facilitate the invasiveness of the tumor cells, which subsequently leads to short term survival in patients with the disease. Our findings demonstrate for the first time that spatially resolved transcriptomics allows the identification of prognostic biomarkers associated with overall survival in HGSC patients. Further studies using deconvoluted ST data to further delineate the specific stromal cell subtypes in close proximity to tumors, and imaging mass cytometry (IMC) or multiplexed immunohistochemistry to validate the protein expression of the potential biomarkers are ongoing.

Citation Format: Sammy Ferri-Borgogno, Jianting Sheng, Ying Zhu, Kwong K. Wong, Stephen T. Wong, Samuel C. Mok. Spatially resolved transcriptomics identified distinct tumor-stroma crosstalk networks in long term ovarian cancer survivors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 103.

SIO: A Spatioimageomics Pipeline to Identify Prognostic Biomarkers Associated with the Ovarian Tumor Microenvironment

Stromal and immune cells in the tumor microenvironment (TME) have been shown to directly affect high-grade serous ovarian cancer (HGSC) malignant phenotypes, however, how these cells interact to influence HGSC patients' survival remains largely unknown. To investigate the cell-cell communication in such a complex TME, we developed a SpatioImageOmics (SIO) pipeline that combines imaging mass cytometry (IMC), location-specific transcriptomics, and deep learning to identify the distribution of various stromal, tumor and immune cells as well as their spatial relationship in TME. The SIO pipeline automatically and accurately segments cells and extracts salient cellular features to identify biomarkers, and multiple nearest-neighbor interactions among tumor, immune, and stromal cells that coordinate to influence overall survival rates in HGSC patients. In addition, SIO integrates IMC data with microdissected tumor and stromal transcriptomes from the same patients to identify novel signaling networks, which would lead to the discovery of novel survival rate-modulating mechanisms in HGSC patients.

CES2 Expression in Pancreatic Adenocarcinoma Is Predictive of Response to Irinotecan and Is Associated With Type 2 Diabetes

PURPOSE

The combination chemotherapy of fluorouracil, leucovorin, irinotecan, and oxaliplatin (FOLFIRINOX) has provided clinically meaningful improvement for pancreatic ductal adenocarcinoma (PDAC). We previously uncovered a role for the serine hydrolase carboxylesterase 2 (CES2) in mediating intratumoral activation of the prodrug irinotecan, a constituent of FOLFIRINOX. We aimed to further test the predictive value of CES2 for response to irinotecan using patient-derived xenograft (PDX) models and to elucidate the determinants of CES2 expression and response to FOLFIRINOX treatment among patients with PDAC.

METHODS

PDXs were engrafted subcutaneously into nude mice and treated for 4 weeks with either saline control or irinotecan. CES2 and hepatocyte nuclear factor 4 alpha (HNF4A) expression in PDAC tissues was evaluated by immunohistochemical and Western blot analysis. Kaplan-Meier and Cox regression analyses were applied to assess the association between overall survival and hemoglobin A1C (HbA1C) levels in patients who underwent neoadjuvant FOLFIRINOX treatment.

RESULTS

High CES2 activity in PDAC PDXs was associated with increased sensitivity to irinotecan. Integrated gene expression, proteomic analyses, and in vitro genetic experiments revealed that nuclear receptor HNF4A, which is upregulated in diabetes, is the upstream transcriptional regulator of CES2 expression. Elevated CES2 protein expression in PDAC tissues was positively associated with a history of type 2 diabetes (odds ratio, 4.84; P = .02). High HbA1C levels were associated with longer overall survival in patients who received neoadjuvant FOLFIRINOX treatment (P = .04).

CONCLUSION

To our knowledge, we provide, for the first time, evidence that CES2 expression is associated with a history of type 2 diabetes in PDAC and that elevated HbA1C, by predicting tumor CES2 expression, may represent a novel marker for stratifying patients most likely to respond to FOLFIRINOX therapy.

Targeting Dopamine Receptor D2 by Imipridone Suppresses Uterine Serous Cancer Malignant Phenotype

Uterine serous cancer (USC) is an aggressive subtype of endometrial cancer, with poor survival and high recurrence rates. The development of novel and effective therapies specific to USC would aid in its management. However, few studies have focused solely on this rare subtype. The current study demonstrated that the orally bioavailable, investigational new drug and novel imipridone ONC206 suppressed USC cell proliferation and induced apoptosis both in vitro and in vivo. Disruption of the DRD2-mediated p38MAPK/ERK/PGC-1α network by ONC206 led to metabolic reprogramming and suppression of both glycolysis and oxidative phosphorylation. ONC206 also synergized with paclitaxel in reducing USC cell viability. In addition, DRD2 overexpression correlated with poor overall survival in patients. This study provides the first evidence that ONC206 induced metabolic reprogramming in USC cells and is a promising therapeutic agent for USC treatment. These findings support further development of ONC206 as a promising therapeutic agent and improves survival rates in patients with USC.

Abstract 854: An artificial intelligence pipeline for imaging mass cytometry data analysis and its application in ovarian cancer prognostic biomarker discovery

Imaging mass cytometry (IMC) is a powerful platform which enables high-dimensional, single-cell analysis of cell type and state. However, reliable methods used to analyze the IMC data remain to be developed. We seek to build an artificial intelligence (AI)-based analytics pipeline for imaging mass cytometry (IMC) to increase the accuracy of cell segmentation and spatial information extraction and apply the AI pipeline to analyze the IMC data derived from high-grade serous ovarian cancer samples for patient overall survival prediction.

Multiplexed spatial analysis of the tumor microenvironment by IMC was performed on 41 formalin fixed paraffin embedded (FFPE) tissue samples obtained from treatment naïve high- grade serous ovarian cancer patients using a panel of 24 metal-tagged antibodies that are specific to tumor, immune and stromal cell markers. IMC data was collected using a a Helios CyTOF instrument equipped with Hyperion Imaging System (Fluidigm). Mask Region-Convolution Neural Network (Mask R-CNN) model was used for cell segmentation. Cell subtypes were derived by iterative phenograph clustering with different marker combinations and different subsets of cells in each iteration. Tumor area was calculated as a thresholded Gaussian blurred image of the density map of the center-of-mass of Keratin positive tumor cells. All cells with center-of-mass located within the tumor region were classified as intratumoral cells. The average cell composition in the nearest neighborhood of each cell type (distance between the center of mass of two cells &lt; 20 μm) in the tumor cell compartment was computed.

The results showed that cell segmentation by Mask R-CNN has a higher accuracy than traditional watershed segmentation. Significantly more granzymeB+ CD8+ T cells and CD11b+ Vista+ cells were found in long-term survivors comparing to short-term survivors in both tumor and stromal cell compartments of the tumor microenvironment. Additionally, CD196+, CD45RO+ and CD73+ cell densities in the tumor cell compartment were significantly lower in long-term than short-term survivors. Our results also showed that the mean numbers of CD73+ cells adjacent to Vista- CD4+ T cells, macrophages and B cells were significantly lower in long-term than short-term survivors. The mean number of granzymeB+ CD8+ T cells adjacent to Vista- CD4+ T cells was significantly higher in long-term than short-term survivors.

These data demonstrated that the deep learning-based cell segmentation method achieved higher accuracy than the conventional watershed segmentation method. Furthermore, our AI pipeline can automatically extract cell count and cell neighborhood information in tumor. The cell count and neighborhood information could be further employed as features for machine learning to generate predictive biomarkers for ovarian cancer patient survival.

Citation Format: Ying Zhu, Jianting Sheng, Sammy Ferri-Borgogno, Tsz-Lun Yeung, Jared K. Burks, Samuel C. Mok, Stephen T. Wong. An artificial intelligence pipeline for imaging mass cytometry data analysis and its application in ovarian cancer prognostic biomarker discovery [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 854.

Abstract 3267: Identification of a novel biomarker response in a prospective clinical trial of immune checkpoint blockade in recurrent ovarian carcinoma

The role of immune checkpoint inhibitors (ICPIs) in ovarian cancer continues to be refined. The presence of intratumoral T cells in ovarian tumors correlates with improved survival and progression, suggesting that immune modulation, such as by ICPIs, may be beneficial. However, a better understanding of the immune effects following ICPI use, particularly in those with a long progression free survival, is needed. Thus, we used imaging mass cytometry (IMC) to compare the tumor immune landscape of patients with ovarian cancer before and after a CTLA4 immune checkpoint inhibitor treatment to determine the association between alterations in immune landscapes and progression free survival.

Fine needle biopsies were obtained from 8 patients with recurrent platinum-resistant ovarian carcinoma enrolled in a phase 2 randomized trial evaluating the efficacy of Tremelimumab and Durvalumab (CTLA4 and PDL1 checkpoint inhibitors, respectively) in recurrent ovarian cancer treatment. Each patient had a pre-treatment biopsy and on-treatment biopsy after 3 cycles of CTLA4 inhibitor therapy. Progression free time (PFS) was recorded with 3 patients with a long PFS (&gt;180 days) and 5 with short PFS (&lt;60 days).

Formalin fixed paraffin embedded (FFPE) tissue sections were stained for IMC analysis via Fluidigm protocol with 34 metal-tagged antibodies to detect various cell and immune related markers. The IMC data was obtained using the Fluidigm Helios CyTOF instrument and Hyperion Imaging System laser ablation module. A novel image informatics pipeline through Matlab was used to assess the image intensity of each marker and cell location.

Using the developed image informatics pipeline, cell types and locations were analyzed for 16 samples from 8 patients. In all patients, mean CD8+ T cell densities had an increased trend in on-treatment vs pre-treatment samples (205.6 v 129.9 cells/mm2, p=0.086). An analysis of cell location found that in all patients on-treatment, the mean number of CD8+ T cells adjacent to M2 macrophages increased significantly (0.09 v. 0.17 cells, p = 0.0460) as well as the mean number of CD8+ T cells adjacent to B7H4+ tumor cells (0.035 v. 0.01 cells, p = 0.046). Furthermore, patients with a long PFS had a significantly higher number of CD8+ cells neighboring B cells on-treatment than short PFS (0.12 v. 0.27 cells, p=0.028).

Using IMC and novel image informatics pipeline, we found that patients with recurrent ovarian cancer treated with Tremelimumab with a long PFS mounted a significant immune response compared to patients with a short PFS, with a higher number of CD8+ T cells neighboring B cells after treatment. For all patients, the immune landscape altered after treatment. To our knowledge, this is the first known use of IMC to demonstrate immune response in ovarian cancer following ICPI therapy. Overall, IMC and image informatics pipeline are robust tools that simultaneously analyze multiple biomarkers and spatial location of cells to better assess the tumor immune microenvironment and cellular interactions.

Citation Format: Han Cun, Emily M. Hinchcliff, Ying Zhu, Sammy Ferri-Borgogno, Rita Cheng, Jared K. Burks, Stephen T. Wong, Amir A. Jazaeri, Samuel C. Mok. Identification of a novel biomarker response in a prospective clinical trial of immune checkpoint blockade in recurrent ovarian carcinoma [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 3267.

Abstract 5321: Novel imipridone ONC206 inhibits cell proliferation and induces apoptosis in uterine serous cancer through altering MAPK/AKT signaling network and metabolic reprogramming

Uterine serous carcinoma (USC) is the most aggressive subtype of endometrial cancer. Patients with advanced stage USC have poor survival rates and new treatment regimens are lacking. ONC201 is the first clinical bitopic antagonist of dopamine receptor D2 (DRD2), that is well tolerated and currently being investigated in several clinical trials for oncology. ONC206 is a chemical derivative of ONC201 with the same impridone core structure, which is also a DRD2 antagonist that exhibits distinct receptor pharmacology and nanomolar potency in various preclinical cancer models. However, the effects of ONC206 on USC progression and the mechanism of action have not been thoroughly explored. Using both in vitro and in vivo models, and multiple USC cell lines, the effects of ONC206 on cell proliferation and apoptosis were determined. Reverse phase protein arrays (RPPAs) and Western blot analyses were used to determine the effect of ONC206 on the expression of key proteins in various signaling networks in ONC206 treated USC cells. The results showed that ONC206 suppressed USC cell proliferation and induces apoptosis in a dose-dependent manner. Luciferase labeled USC cell ARK1-bearing mice treated with 100mg/kg ONC206 had significantly lower chemiluminescent signals than those treated with the control buffer. RPPA data showed that ONC206 treated USC cells had markedly lower expression signals in p38MAPK, p-AKT, p-S6, and multiple mitochondrial proteins associated with mitochondrial ATP synthesis including MTCO1, and TFAM than the control cells did. Significantly lower ATP levels and cytochrome c oxidase activities in ONC206 treated USC cells than in control cells were demonstrated by luminescent ATP detection assay kit and the cytochrome c oxidase assay kit. These data suggest that ONC206 suppresses USC progression through inhibiting MAPK/AKT network, which subsequently leads to metabolic reprogramming and increased apoptosis. Moreover, by knocking-out DRD2, USC cells became more resistant to ONC206 treatment. This suggested that the effect of ONC206 is likely mediated through its binding to DRD2. ONC206 also showed a synergistic effect with paclitaxel in vitro. Further studies which demonstrate the optimal dosage and the efficacy of treatment of USC using ONC206 are warranted.

Citation Format: Chi Lam Au Yeung, Wen Hu, Li Zhang, Sammy Ferri-Borgogno, Rohinton S. Tarapore, Joshua E. Allen, Karen H. Lu, Samuel C. Mok. Novel imipridone ONC206 inhibits cell proliferation and induces apoptosis in uterine serous cancer through altering MAPK/AKT signaling network and metabolic reprogramming [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 5321.

Abstract C055: Novel imipridone ONC206 inhibits cell proliferation and induces apoptosis in uterine serous cancer through altering MAPK/AKT/AMPK signaling network and metabolic reprogramming

Uterine serous carcinoma (USC) is the most aggressive subtype of endometrial cancer. Patients with advanced stage USC have poor survival rates and new treatment regimens are lacking. Recent clinical studies showed that imipridones constitute a novel class of agents with antitumor activities. Among them, ONC206, a novel orally bioavailable small molecule that has recently been shown to bind G protein-coupled receptor (GPCR)-dopamine receptor D2 (DRD2) by comprehensive GPCR screening, induces apoptosis in glioblastoma cells. However, the effects of ONC206 on USC progression and the mechanism of action have not been thoroughly explored. Using both in vitro and in vivo models, and multiple USC cell lines, the effects of ONC206 on cell proliferation, cell cycle progression, and apoptosis were determined. Reverse phase protein arrays (RPPAs) and Western blot analyses were used to determine the effect of ONC206 on the expression of key proteins in various signaling networks in ONC206 treated USC cells. The results showed that ONC206 suppressed USC cell proliferation and induces apoptosis in a does dependent manner. It increased the number of USC cells in the G1 phase of the cell cycle. Luciferase labeled USC cell ARK1-bearing mice treated with 100mg/kg ONC206 had significantly lower chemiluminescent signals than those treated with the control buffer. RPPA data showed that ONC206 treated USC cells had markedly lower expression signals in p38MAPK, p-AKT, p-S6, CDKs, and multiple mitochondrial proteins associated with mitochondrial ATP synthesis including MTCO1, SDHB, and HSPD1 than the control cells did. In addition, markedly higher expression levels of p-AMPK, Bim, and cleaved caspases were also observed in ONC206 treated cells than the control did. Significantly lower ATP levels and cytochrome c oxidase activities in ONC206 treated USC cells than in control cells were demonstrated by luminescent ATP detection assay kit and the cytochrome c oxidase assay kit. These data suggest that ONC206 suppresses USC progression through inhibiting MAPK/AKT network, which subsequently leads to cell cycle arrest, metabolic reprogramming and increased apoptosis. Further studies which demonstrate the optimal dosage and the efficacy of treatment of USC using ONC206 are warranted.

Citation Format: Chi Lam Au Yeung, Wen Hu, Li Zhang, Sammy Ferri-Borgogno, Rohinton Tarapore, Karen H Lu, Samuel C Mok. Novel imipridone ONC206 inhibits cell proliferation and induces apoptosis in uterine serous cancer through altering MAPK/AKT/AMPK signaling network and metabolic reprogramming [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr C055. doi:10.1158/1535-7163.TARG-19-C055

YAP1 oncogene is a context-specific driver for pancreatic ductal adenocarcinoma

Transcriptomic profiling classifies pancreatic ductal adenocarcinoma (PDAC) into several molecular subtypes with distinctive histological and clinical characteristics. However, little is known about the molecular mechanisms that define each subtype and their correlation with clinical outcome. Mutant KRAS is the most prominent driver in PDAC, present in over 90% of tumors, but the dependence of tumors on oncogenic KRAS signaling varies between subtypes. In particular, the squamous subtype is relatively independent of oncogenic KRAS signaling and typically displays much more aggressive clinical behavior versus the progenitor subtype. Here, we identified that yes-associated protein 1 (YAP1) activation is enriched in the squamous subtype and associated with poor prognosis. Activation of YAP1 in progenitor subtype cancer cells profoundly enhanced malignant phenotypes and transformed progenitor subtype cells into squamous subtype. Conversely, depletion of YAP1 specifically suppressed tumorigenicity of squamous subtype PDAC cells. Mechanistically, we uncovered a significant positive correlation between WNT5A expression and YAP1 activity in human PDAC and demonstrated that WNT5A overexpression led to YAP1 activation and recapitulated a YAP1-dependent but Kras-independent phenotype of tumor progression and maintenance. Thus, our study identifies YAP1 oncogene as a major driver of squamous subtype PDAC and uncovers the role of WNT5A in driving PDAC malignancy through activation of the YAP pathway.

Exosomes harbor B cell targets in pancreatic adenocarcinoma and exert decoy function against complement-mediated cytotoxicity

Although B cell response is frequently found in cancer, there is little evidence that it alters tumor development or progression. The process through which tumor-associated antigens trigger humoral response is not well delineated. We investigate the repertoire of antigens associated with humoral immune response in pancreatic ductal adenocarcinoma (PDAC) using in-depth proteomic profiling of immunoglobulin-bound proteins from PDAC patient plasmas and identify tumor antigens that induce antibody response together with exosome hallmark proteins. Additional profiling of PDAC cell-derived exosomes reveals significant overlap in their protein content with immunoglobulin-bound proteins in PDAC plasmas, and significant autoantibody reactivity is observed between PDAC cell-derived exosomes and patient plasmas compared to healthy controls. Importantly, PDAC-derived exosomes induce a dose-dependent inhibition of PDAC serum-mediated complement-dependent cytotoxicity towards cancer cells. In summary, we provide evidence that exosomes display a large repertoire of tumor antigens that induce autoantibodies and exert a decoy function against complement-mediated cytotoxicity.

Abstract B13: Synthetic vulnerabilities in MLL3 deficient pancreatic tumors

Myeloid/lymphoid or mixed-lineage leukemia 3 (MLL3) is a histone 3-lysine 4 methyltransferase, frequently mutated in a variety of solid tumors including pancreatic ductal adenocarcinoma (PDAC), a nearly lethal disease due to our current inability to therapeutically target major oncogenic proteins driving this cancer. Like other tumor suppressor genes, direct targeting of MLL3 is not feasible, and thus our objective was to find biological pathways which are synthetic lethal targets in MLL3-deficient PDAC tumors. Identification of drug targets in such a specific genetic context could potentially dictate stratification of patients based on the mutational profile of their tumor. To achieve this, we generated a novel genetically engineered mouse model (GEMM) of pancreatic cancer, in which targeted mutation of Kras (G12D) and loss of functional MLL3 was driven by Cre-recombination from early pancreatic lineage-specific transcription factor, Pdx1. Our unpublished data suggests that loss of MLL3 function in exocrine pancreas cooperates with mutant Kras to accelerate the progression of invasive pancreatic neoplasia. Using cell lines generated from spontaneous tumors arising in KC (KrasG12D alone) and KMC (KrasG12D; MLL3δ/δ) mice, we performed functional genomic analyses and found several key oncogenic pathways upregulated in MLL3-deficient cells. We selected two well-known oncogenic pathways and through a series of cellular and biochemical assays, further validated their selectively activation in KMC cells, in contrast with KC cells. Next, we picked multiple pharmacological inhibitors of these pathways, which are already approved at various phases of clinical trials, and tested for their efficacy on growth of KC and KMC cells in both two- and three-dimensional growth assays. In agreement with our data showing preferential activation in KMC cells, we found KMC cells to be significantly more sensitive than KC cells to the effect of these inhibitors. Thus, identification of synthetic lethal hits in context of MLL3 functional loss could potentially enable us to design strategies to limit metastasis in patients with surgically-resectable tumors.

Citation Format: Sonal Gupta, Sammy Ferri-Borgogno, Mary R. Reisenauer, Anvita k. Gupta, Anirban Maitra. Synthetic vulnerabilities in MLL3 deficient pancreatic tumors [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr B13.

Targeting the Warburg effect in cancer cells through ENO1 knockdown rescues oxidative phosphorylation and induces growth arrest

In the last 5 years, novel knowledge on tumor metabolism has been revealed with the identification of critical factors that fuel tumors. Alpha-enolase (ENO1) is commonly over-expressed in tumors and is a clinically relevant candidate molecular target for immunotherapy. Here, we silenced ENO1 in human cancer cell lines and evaluated its impact through proteomic, biochemical and functional approaches. ENO1 silencing increased reactive oxygen species that were mainly generated through the sorbitol and NADPH oxidase pathways, as well as autophagy and catabolic pathway adaptations, which together affect cancer cell growth and induce senescence. These findings represent the first comprehensive metabolic analysis following ENO1 silencing. Inhibition of ENO1, either alone, or in combination with other pathways which were perturbed by ENO1 silencing, opens novel avenues for future therapeutic approaches.

Abstract B49: Alpha-enolase knockdown reprograms metabolism and points out targetable pathways to counteract PDA growth

Pancreatic ductal adenocarcinoma (PDA), an aggressively invasive, treatment-resistant malignancy, is usually detectable only when already inevitably fatal. Despite advances in genetic screening, mapping and molecular characterization, its pathology remains largely elusive. Renewed interest in longstanding doctrines of tumor metabolism has led to the emergence of aberrant signaling pathways as critical factors modulating central metabolic networks that fuel pancreatic tumors. We have previously described α-enolase (ENO1) as a PDA-associated antigen. It is a moonlighting protein that works both as a key metabolic enzyme and a membrane plasminogen receptor. To better characterize ENO1 metabolic and fuelling role in pancreatic cancer, we have silenced ENO1 in three different human PDA cell lines (CFPAC-1, PT45 and T3M4) and evaluated its impact through proteomic, biochemical and functional approaches. Protein expression alterations following ENO1 knockdown were revealed by LC-MS/MS analysis. On the basis of a spectra count label-free quantitation approach several proteins mainly involved in cell adhesion, metabolism and proliferation were found to be differentially expressed in ENO1-silenced cells compared to the control. Indeed, ENO1-silenced PDA cells displayed a delay in proliferation, decreased survival and colony formation capabilities. The cell-cycle profile analysis revealed a strong increase in the number of PDA cells in G2/M phase, a concomitant decrease in G1 phase and no difference in the proportion of cells in S phase after ENO1 silencing as compared to control cells. Moreover, ENO1-silenced cells showed specific morphological changes that were indicative of cellular senescence, as confirmed by an increase in β-galactosidase staining. Of note, ENO1 knockdown PDA cells grew significantly less compared to control cells when injected sub cute in SCID-beige mice. The growth inhibition was partially due to an increased concentration of intracellular reactive oxygen species (ROS) mainly generated through the sorbitol and NADPH oxidase pathways. ENO1 knockdown increase autophagy, the most important stress response for cells to adapt to nutrient starvation and promotes also catabolic pathway adaptations that restore pyruvate and acetyl-CoA bulk. Furthermore, the increased entry of glutamine into the TCA cycle induce a drop in nucleotide bases synthesis and promote oxidative phosphorylation in PDA cells, switching to the aerobic glycolysis typical of cancer cells. These findings may have implications for future therapeutic approaches: the inhibition of ENO1, in fact, can potentially synergize with therapies targeting autophagy and glutamine pathway.

Citation Format: Michela Capello, Sammy Ferri-Borgogno, Moitza Principe, Michelle Samuel Chattaragada, Chiara Riganti, Weidong Zhou, Laura Follia, Lance A. Liotta, Emanuel F. Petricoin, III, Paola Cappello, Francesco Novelli. Alpha-enolase knockdown reprograms metabolism and points out targetable pathways to counteract PDA growth. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Innovations in Research and Treatment; May 18-21, 2014; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2015;75(13 Suppl):Abstract nr B49.

Abstract 1889: Can the moonlighting glycolytic enzyme α-enolase be a therapeutic target in pancreatic cancer

Aberrant metabolism together with invasion and metastasis are hallmarks of cancer. This is particularly true for pancreatic ductal adenocarcinoma (PDAC), characterized by rapid progression, invasiveness and resistance to treatments. We have previously described α-enolase (ENOA) as a PDAC-associated antigen. It is a moonlighting protein that works both as a key metabolic enzyme and as a membrane plasminogen receptor. In order to clarify its multifunctional role in pancreatic tumorigenesis we investigated the effect of ENOA knockdown in PDAC cells. Protein expression alterations following ENOA knockdown in the human PDAC cell line CFPAC-1 were revealed by LC-MS/MS analysis. On the basis of a spectra count label-free quantitation approach a large number of proteins mainly involved in cell adhesion, metabolism and proliferation were found to be differentially expressed in ENOA silenced cells compared to the control. After ENOA silencing, PDAC cells displayed a delay in proliferation and decreased survival and colony formation capabilities, even if the pyruvate production was not affected. The growth inhibition was partially due to an increased concentration of intracellular reactive oxygen species (ROS) mainly generated through the sorbitol and NADPH oxidase pathways. Moreover in ENOA silenced cells, the in vitro plasminogen-driven invasion was abolished and the number of lung tumor masses was significantly reduced in SCID-beige mice injected with ENOA silenced cells compared to mice injected with control cells. These effects are under further confirmation in other PDAC cell lines. All together, these findings propose ENOA as a promising target for developing new therapies in pancreatic cancer management.

Citation Format: Michela Capello, Moitza Principe, Michelle Samuel Chattaragada, Chiara Riganti, Weidong Zhou, Sammy Ferri-Borgogno, Simona Rolla, Lance Liotta, Emanuel Petricoin, Paola Cappello, Francesco Novelli. Can the moonlighting glycolytic enzyme α-enolase be a therapeutic target in pancreatic cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1889. doi:10.1158/1538-7445.AM2013-1889

Towards pancreatic cancer diagnosis using EIS biochips

Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive and lethal cancers in Europe and the United States. It has a very low 5 years-survival rate and its diagnosis is often late and imprecise due to the lack of specificity of currently used markers for PDAC. As previously demonstrated PDAC patients' sera may contain autoantibodies towards phosphorylated α-enolase (ENOA), which in combination with other standard markers can increase specificity in diagnosis of PDAC. In this context we realized a microfluidic platform with integrated EIS biosensors. We achieved a specific antibodies detection by immobilizing onto electrodes peptides corresponding to a portion of ENOA. Phosphorylation of peptides was found to influence the recognition of antibodies in PDAC patients' sera detected by the developed biochip thus validating the EIS technique as a strong tool for quick, cost-saving and label-free analysis of serum samples. Biochip results are in agreement with those from traditional techniques, such as ELISA and western blot, but measurements are much more sensitive and specific, increasing the possibility of PDAC diagnosis. In addition this approach is faster and more reproducible compared to traditional techniques making the developed biochips ideal for a quick, cost-saving and label-free analysis of serum samples.

α-Enolase: a promising therapeutic and diagnostic tumor target

α-enolase (ENOA) is a metabolic enzyme involved in the synthesis of pyruvate. It also acts as a plasminogen receptor and thus mediates activation of plasmin and extracellular matrix degradation. In tumor cells, ΕΝΟΑ is upregulated and supports anaerobic proliferation (Warburg effect), it is expressed at the cell surface, where it promotes cancer invasion, and is subjected to a specific array of post-translational modifications, namely acetylation, methylation and phosphorylation. Both ENOA overexpression and its post-translational modifications could be of diagnostic and prognostic value in cancer. This review will discuss recent information on the biochemical, proteomics and immunological characterization of ENOA, particularly its ability to trigger a specific humoral and cellular immune response. In our opinion, this information can pave the way for effective new therapeutic and diagnostic strategies to counteract the growth of the most aggressive human disease.