bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract B62: DDB2 represses ovarian cancer cell dedifferentiation by suppressing ALDH1A1
Authors: Cui Tiantian , Srivastava Amit Kumar , Han Chunhua , Zhang Xiaoli , Wani Altaf A. , Wang Qi-En
Published: August 2018

Cancer stem cells (CSCs), representing the root of many solid tumors including ovarian cancer, have been implicated in disease recurrence, metastasis, and therapeutic resistance. Our previous study has demonstrated that DNA damage-binding protein 2 (DDB2) is able to reduce the abundance of CSCs in the bulk ovarian cancer cells, providing a novel mechanism to explain the DDB2-mediated suppression of tumorigenicity and metastasis, and also suggesting that low expression of DDB2 is required for the maintenance of CSCs. However, the underlying mechanisms still remain unclear. By using the Tet-On DDB2 modulation system, we have confirmed our previous finding that downregulation of DDB2 expands the CSC population in the 2008 ovarian cancer cell line. We also found that DDB2 is able to suppress non-CSC-to-CSC conversions in this cancer cell line. DDB2 has been recognized as a transcriptional regulator. Our microarray analysis has identified ALDH1A1 to be targeted and regulated by DDB2. Downregulation of ALDH1A1 expression by DDB2 at both mRNA and protein levels has been validated in various ovarian cancer cell lines. The mechanistic investigation demonstrated that DDB2 can bind to the promoter region of the ALDH1A1 gene, facilitating the enrichment of histone H3K27me3 by recruiting EZH2 to the promoter region, eventually inhibiting the promoter activity of the ALDH1A1 gene. In addition, we also found that DDB2 competes with transcription factor C/EBPβ for binding to the ALDH1A1 promoter, indirectly inhibiting the ALDH1A1 promoter activity. Finally, we knocked down the expression of DDB2 and ALDH1A1 individually or simultaneously in the 2008 ovarian cancer cell line, and analyzed their tumorigenicity. We found that downregulation of ALDH1A1 is able to block DDB2 silencing-induced expansion of the CSC population, indicating that ALDH1A1 plays a critical role in DDB2-mediated suppression of the CSC population in ovarian cancer cells. We further showed that treatment with a selective ALDH1A1 inhibitor blocked DDB2 silencing-induced expansion of CSCs, and halted orthotopic xenograft tumor growth. In summary, our data demonstrated that DDB2, functioning as a transcription repressor, is able to abrogate ovarian CSC properties by downregulating ALDH1A1 expression. This study provides a novel mechanism underlying the regulation of the CSC population, and would facilitate the development of efficient strategies for eliminating CSCs to prevent tumor relapse and metastasis in ovarian cancers. (Supported by NIH R01CA151248, R01CA211175.)

Citation Format: Tiantian Cui, Amit Kumar Srivastava, Chunhua Han, Xiaoli Zhang, Altaf A. Wani, Qi-En Wang. DDB2 represses ovarian cancer cell dedifferentiation by suppressing ALDH1A1. [abstract]. In: Proceedings of the AACR Conference: Addressing Critical Questions in Ovarian Cancer Research and Treatment; Oct 1-4, 2017; Pittsburgh, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(15_Suppl):Abstract nr B62.
Abstract B68: Adnexal tumors associated with endometriosis: Experience from an academic institution
Authors: Desouki Mohamed Mokhtar
Published: August 2018

Background: Endometriosis affect pelvic organs in ~10% of cases. The question of endometriosis being a precancerous lesion versus an incidental association with adnexal (fallopian tubes and ovaries) tumors is a point of debate. This study aimed to determine the frequency of adnexal tumors in cases with histologically proven endometriosis of adnexal structures at our institution.

Methods: A retrospective chart review of patients diagnosed with adnexal endometriosis from 2013-2017 was performed. Patients’ age, demographic data, and associated ipsilateral benign or malignant adnexal tumors were obtained from the pathology notes.

Results: 151 cases with a histologically verified endometriosis of fallopian tubes and/or ovaries were retrieved. The average age of the patients was 42 years (range of 22-78 years). The race/ethnic groups of the patients were white, black, and others in 120 (79%), 17 (11%) and 14 (9%), respectively. Associated malignant tumors were identified in 8 (5.3%) cases while 10 (6.6%) cases were found to have benign neoplasms in the ipsilateral site of endometriosis. The malignant tumors were endometrioid adenocarcinoma (n=4), high-grade serous carcinoma (n=3), and clear cell carcinoma (n=1). The benign neoplasms were serous cystadenoma/ cystadenofibroma (n=7) and seromucinous tumors (n=3).

Conclusions: The incidence of malignant neoplasms, especially endometrioid and high-grade serous carcinoma, is relatively high in cases with histologically verified endometriosis in our experience. Among benign tumors, serous cystadenoma and seromucinous neoplasms appear to be frequently associated with endometriosis. More studies are needed to further highlight the significance of adnexal endometriosis in causation of malignant and benign adnexal tumors.

Citation Format: Mohamed Mokhtar Desouki. Adnexal tumors associated with endometriosis: Experience from an academic institution. [abstract]. In: Proceedings of the AACR Conference: Addressing Critical Questions in Ovarian Cancer Research and Treatment; Oct 1-4, 2017; Pittsburgh, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(15_Suppl):Abstract nr B68.
Abstract B74: Identification of prognostic molecular subtypes of ovarian serous cystadenocarcinoma by isoform-level gene expression analysis
Authors: Shilpi Arunima , Seagle Brandon L. , Kandpal Manoj , Shahabi Shohreh , Davuluri Ramana V.
Published: August 2018

Characterization of molecular aberrations in ovarian serous cystadenocarcinoma (OVSC) is highly crucial for developing precision medicine approaches. While gene-level analysis of gene expression profiles of The Cancer Genome Atlas (TCGA) OVSC samples revealed four molecular subgroups (differentiated, proliferative, mesenchymal, and immunoreactive), the association of the derived subtypes with the clinical and pathologic features, such as stage, cytoreduction, and chemotherapy, is not statistically significant. Considering the fact that the majority of human genes produce multiple transcript-variants that could be involved in different functional pathways, we reanalyzed the TCGA exon-array expression profiles at the transcript variant or isoform level by following the novel informatics methodology we developed and successfully applied for glioblastoma (Pal et al., Nucleic Acids Res 2014). Non-negative matrix factorization (NMF) clustering of TCGA ovarian serous adenocarcinoma samples, based on isoform-level gene-expression profiles, recaptured the four known molecular subgroups but switched the subtype for 26% of the samples, resulting in significant (p=0.009) survival differences among the refined subgroups. The survival analysis was further extended to multivariate Cox proportional hazard model considering the different subgroups, and the clinical parameters as the predictor variables. Patients classified under mesenchymal group (HR = 1.44; 95% CI, 0.99-2.08; P < 0.05) and in stage III (HR = 2.39, 95%of CI, 1.25-4.56, P < 0.05), IV (HR= 3.16; 95% of CI, 1.58-6.32, P < 0.05) were identified to be at high risk or decreased survival, while those receiving intraperitoneal (IP) chemotherapy (HR, 0.63; 95% of CI, 0.38-1.03, P < 0.1) were associated with longer survival. We are in the process of translating the isoform-level gene signature into clinically adaptable molecular subtyping assay and validating on an independent patient cohort, with potential implications for developing robust diagnostic assays for OVSC patient stratification.

Citation Format: Arunima Shilpi, Brandon L. Seagle, Manoj Kandpal, Shohreh Shahabi, Ramana V. Davuluri. Identification of prognostic molecular subtypes of ovarian serous cystadenocarcinoma by isoform-level gene expression analysis. [abstract]. In: Proceedings of the AACR Conference: Addressing Critical Questions in Ovarian Cancer Research and Treatment; Oct 1-4, 2017; Pittsburgh, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(15_Suppl):Abstract nr B74.
Abstract IA01: PARP inhibitors as single agents and in combinations for ovarian cancer: What lies ahead?
Authors: Matulonis Ursula A.
Published: August 2018

Poly (ADP ribose) polymerase (PARP) inhibitors are an exciting and promising new class of anticancer drugs. Initial clinical trials of PARP inhibitors began over a decade ago following the discovery that PARP inhibitors in vitro had heightened anticancer activity in BRCA mutated cancer cells compared to BRCA wild-type cells. PARP inhibitor clinical development has taken several strategies, including single-agent and combination testing. Single-agent PARP inhibitors have been used as either primary treatment of recurrent ovarian cancer or as maintenance treatment following anticancer response after platinum-based chemotherapy. Three PARP inhibitors are now FDA approved for recurrent ovarian cancer, all as single agents: 1) olaparib for patients with recurrent germline BRCA mutated ovarian cancer who have received 3 or more prior lines of chemotherapy and also as maintenance therapy post-platinum therapy for patients with platinum sensitive recurrence who are in response to platinum-based chemotherapy and regardless of BRCA or tumor HR status; 2) rucaparib for patients with BRCA mutated ovarian cancer (either deleterious tumor or germline mutation) who have received at least 2 prior lines of chemotherapy; and 3) niraparib for platinum-sensitive recurrent ovarian cancer patients as maintenance therapy who are in response to platinum-based chemotherapy and regardless of BRCA or tumor HR status. Because of the myelosuppression observed with PARP inhibitors, combining these agents with chemotherapy has been difficult and has required lowering the doses of either the PARP inhibitor and/or the chemotherapy agents and often abbreviating the treatment schedule; several negative phase III studies have been reported. Combining PARP inhibitors with biologic agents is another strategy currently being tested in clinical trials and one that avoids overlapping toxicities. The combination of the PARP inhibitor olaparib and the antivascular endothelial growth factor receptor agent cediranib has shown promising phase II results against olaparib alone, especially in BRCA wild-type ovarian cancer. These results have led to phase III studies comparing the olaparib and cediranib combination to standard therapies (NCT02502266 and NCT02446600). Other studies are under way testing PARP inhibitors with other biologic agents such as immunotherapy agents and other targeted agents such as ATR inhibitors, PI3 kinase inhibitors, and heat shock protein 90 inhibitors.

Citation Format: Ursula A. Matulonis. PARP inhibitors as single agents and in combinations for ovarian cancer: What lies ahead? [abstract]. In: Proceedings of the AACR Conference: Addressing Critical Questions in Ovarian Cancer Research and Treatment; Oct 1-4, 2017; Pittsburgh, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(15_Suppl):Abstract nr IA01.
Abstract IA13: Systems approach to drug development
Authors: Mills Gordon B.
Published: August 2018

One of the key lessons of the last century of cancer therapy is that combination therapy is, in most cases, necessary, particularly in advanced disease and complex epithelial tumors, to increase tumor control. However, as we have matured in the era of precision oncology which includes small-molecule targeted therapeutics and immuno-oncology agents, while response to targeted therapies are relatively frequent, durable responses are rare and in contrast responses to immuno-oncology agents are less frequent but are commonly durable and can approximate cures. It is thus clear that rational combination therapy approaches not only within a single modality but across different therapy approaches such as targeted and immunotherapy will be necessary to fulfill the promise of precision medicine.

Indeed, in terms of the emerging fields of target therapy and immuno-oncology, we are at the end of the beginning. A number of monotherapies have demonstrated remarkable activity. However, only a portion of patients with our best biomarkers respond and responses are in general short for monotherapy with targeted therapies. Responses to immuno-oncology monotherapy and even initial attempts at combination therapy are extremely exciting in that although only subpopulations of patients still benefit, responses can be remarkably durable, approximating cures. Given the intrinsic heterogeneity of tumors as well as the many mechanisms underlying resistance to targeted and immunotherapy, the limited benefit from monotherapy is to be expected.

The short term of response to therapy for most patients is due to a major degree to the almost inevitable emergence of resistance. We have used PARP inhibitors as an effective emerging therapy to explore genomic and adaptive mechanisms of resistance. Importantly, the tumor as well as the tumor ecosystem adapts to the stress induced by targeted or immunotherapy agents. These adaptive responses, which can be observed in tissue culture, animal models, and patient samples, offer therapeutic opportunities that can be targeted to increase the fraction of patients who will benefit as well as the depth and duration of responses. Based on this paradigm, we have identified a series of unexpected mechanisms of resistance to PARP inhibitors and have developed rational combination therapies to interdict emerging resistance. Based on these preclinical studies, we have promoted a number of therapies to clinical trials and have demonstrated exciting preliminary responses.

Citation Format: Gordon B. Mills. Systems approach to drug development. [abstract]. In: Proceedings of the AACR Conference: Addressing Critical Questions in Ovarian Cancer Research and Treatment; Oct 1-4, 2017; Pittsburgh, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(15_Suppl):Abstract nr IA13.
Abstract IA17: Physical and in silico methods for improving sensitivity of detection of ctDNA for personalized medicine in high-grade serous ovarian cancer
Authors: Brenton James D.
Published: August 2018

Early detection of high-grade serous ovarian cancer (HGSOC) remains a major challenge owing to early metastasis from the fallopian tube and lack of specific symptoms or clinical signs. Noninvasive analysis of circulating tumor DNA (ctDNA) for common mutations has the potential to provide highly specific tests for detecting ovarian cancer. We have previously shown that TP53 ctDNA is highly correlated with total volume of disease using 3D volumetric reconstruction of CT images. However, detection of ctDNA requires ctDNA concentration to be greater than 0.5% for adequate sensitivity. Improved methods for detection of ctDNA are also required for reliable response monitoring during treatment and detection of minimal residual disease after surgery and systemic therapy.

I will discuss recent approaches in our lab that have investigated whether size selection of DNA fragments from plasma can increase the detection of ctDNA by enrichment away from cell free DNA of non-tumor origin. The majority of HGSOC ctDNA is in a size range of 90-150 bp based on whole-genome sequencing of cell free DNA from women with relapsed HGSOC and from HGSOC mouse xenografts. Using physical size selection in 35 patients with recurrent HGSOC and 16 additional patients with other cancer types yielded enrichment of mutated DNA fractions by a median of 4.3-fold allowing improved analysis by targeted, whole-exome, and whole-genome sequencing. This allowed identification of new mutations that otherwise were not observed.

Size selection allows detection of tumor alterations masked by non-tumor DNA in plasma, and could improve the sensitivity of liquid biopsy for applications in early diagnosis, detection of minimal residual disease and for establishing mutational signatures from ctDNA.

Citation Format: James D. Brenton. Physical and in silico methods for improving sensitivity of detection of ctDNA for personalized medicine in high-grade serous ovarian cancer. [abstract]. In: Proceedings of the AACR Conference: Addressing Critical Questions in Ovarian Cancer Research and Treatment; Oct 1-4, 2017; Pittsburgh, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(15_Suppl):Abstract nr IA17.
Abstract IA19: Granulosa cell and other rare ovarian cancers: Genomic-derived diagnostics and emergent management strategies
Authors: Huntsman David
Published: August 2018

Granulosa cell tumors, Sertoli-Leydig tumors, and small cell hypercalcemic ovarian cancers are clinically and biologically distinct. In the past few years the key mutations underpinning these mutations have been discovered. This has led to improved diagnostics for granulosa cell tumors and small cell hypercalcemic ovarian cancer. The discovery of pathognomonic mutations has led to the development of model systems and a better understanding of all three cancer types and for small cell ovarian cancer new treatment strategies.

Citation Format: David Huntsman. Granulosa cell and other rare ovarian cancers: Genomic-derived diagnostics and emergent management strategies. [abstract]. In: Proceedings of the AACR Conference: Addressing Critical Questions in Ovarian Cancer Research and Treatment; Oct 1-4, 2017; Pittsburgh, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(15_Suppl):Abstract nr IA19.
Abstract IA20: Therapeutic targeting of ARID1A mutation in ovarian cancer
Authors: Zhang Rugang
Published: August 2018

SWI/SNF chromatin remodeling complexes regulate gene transcription by changing chromatin structure through hydrolyzing ATP. Cancer genome sequencing found that mutations in genes encoding for the subunits of the SWI/SNF complexes collectively occur in ~20% of all human cancers. For example, saturation analysis of The Cancer Genome Atlas (TCGA) cancer mutational profile reveals that the ARID1A subunit of the SWI/SNF complex shows one of the highest mutation rates among epigenetic regulators. Most notably, ARID1A is mutated in over 50% of ovarian clear cell carcinomas and 30% of ovarian endometrioid carcinomas. ARID1A mutation is a known genetic driver of ovarian cancer. Over 90% of the ARID1A mutations observed in ovarian cancer are frame-shift or nonsense mutations that result in loss of ARID1A protein expression. Loss of ARID1A correlates with late-stage disease and predicts early recurrence of ovarian clear cell carcinoma. Ovarian clear cell carcinoma ranks second as the cause of death from epithelial ovarian cancer and is associated with the worst prognosis among the major ovarian cancer subtypes when diagnosed at advanced stages. Additionally, for advanced-stage disease, there is currently no effective therapy. Here we will discuss emerging opportunities for therapeutic targeting of ARID1A mutation based on the genetic makeup of ARID1-mutated ovarian cancer with precision. They include synthetic lethality, the mutual exclusivity between ARID1A and TP53 mutations in ovarian cancer, and mechanism-guided combinatory approaches.

Citation Format: Rugang Zhang. Therapeutic targeting of ARID1A mutation in ovarian cancer. [abstract]. In: Proceedings of the AACR Conference: Addressing Critical Questions in Ovarian Cancer Research and Treatment; Oct 1-4, 2017; Pittsburgh, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(15_Suppl):Abstract nr IA20.
Abstract IA21: Small cell carcinomas of the ovary: Strengths and weaknesses
Authors: Levine Douglas A.
Published: August 2018

Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is a rare and very aggressive malignancy that occurs mostly in young women. We and others previously described SCCOHT as a SMARCA4-mutated monogenic disease and unraveled other important molecular features, including apparent universal loss of SMARCA2 through epigenetic silencing. Typically, SMARCA4 and SMARCA2 are redundant catalytic subunits of the SWI/SNF complex and loss of either will result in the overexpression of the other. However, SCCOHT is unique in having concomitant loss of both subunits with restoration of either leading to tumor suppression. Nonetheless, despite these advances in understanding the biology of SCCOHT, there are few effective treatment options and survival rates remain poor.

In this presentation we will discuss the role of SMARCA4 and SMARCA2 on tumor growth. We will also present therapeutic options to manipulate SWI/SNF complex dependencies. We will present case histories of patients who have had positive responses to targeted therapies. We will also discuss responses to anti-PD1 immunotherapy and characterize the immune landscape of SCCOHT tumors using quantitative immunofluorescence and gene expression profiling. Unexpectedly for a low mutation burden cancer, the majority of the tumors demonstrated PD-L1 expression with strong associated T-cell infiltration. PD-L1 expression can be detected in both tumor and stromal cells, with macrophages being the most abundant PD-L1 positive cells in some tumors. These findings suggest that although SCCOHT are low-mutational-burden tumors, their immunogenic microenvironment that resembles the landscape of tumors that respond well to treatment with PD-1/PD-L1 blockade.

Citation Format: Douglas A. Levine. Small cell carcinomas of the ovary: Strengths and weaknesses. [abstract]. In: Proceedings of the AACR Conference: Addressing Critical Questions in Ovarian Cancer Research and Treatment; Oct 1-4, 2017; Pittsburgh, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(15_Suppl):Abstract nr IA21.
Abstract PR04: Tumor-derived indoleamine 2,3-dioxygenase regulates density of tumor-infiltrating CD8+ T cells and myeloid-derived suppressor cells in a murine model of ovarian cancer
Authors: Amobi Adaobi E. , Tsuji Takemasa , McGray Robert , Odunsi Kunle
Published: August 2018

The catabolism of the essential amino-acid tryptophan by indoleamine 2,3-dioxygenase (IDO1) is a central pathway that contributes to an immunosuppressive microenvironment in many types of cancer. Our lab has previously shown that IDO1 expression in human ovarian tumor correlates with poor prognosis and poor tumor infiltration by CD8+ T cells, and that improved survival is associated with increased tumor-infiltrating lymphocytes. Thus, IDO1 inhibition represents an attractive target for cancer immunotherapy.

To establish the mechanism by which IDO1 inhibition augments immune responses in a murine model of metastatic ovarian cancer, we generated a stable IDO1-overexpressing cell line (IE9mp1-mIDO1) and confirmed functional IDO1 enzyme activity. C57BL/6 mice were challenged intraperitoneally with IE9mp1-mIDO1 or IE9mp1-Empty Vector as a control. IE9mp1-mIDO1 tumor-bearing mice displayed earlier onset of tumor burden and decreased overall survival.

To delineate the role of host- and tumor-derived IDO1 on immune cell infiltration in the tumor, IDO1 genetic knockout and C57BL/6 mice were challenged with IE9mp1-EV or -mIDO1 tumor cells. All mice challenged with IE9mp1-mIDO1 demonstrate decreased CD8+ T cells in the tumor compared to IDO1KO mice challenged with IE9mp1-EV tumor cells. Moreover, tumor-derived IDO1 mediates increased CD11b+Gr1+ myeloid derived suppressor cells (MDSC) in tumor ascites.

From these data, we conclude that abrogation of IDO1 enzyme function will promote antitumor immune responses by permitting increased effector T cells decrease MDSCs in the tumor microenvironment. Ongoing experiments will characterize the mechanism by which IDO1 inhibition may augment vaccine-induced immune responses in ovarian cancer.

This abstract is also being presented as Poster A19.

Citation Format: Adaobi E. Amobi, Takemasa Tsuji, Robert McGray, Kunle Odunsi. Tumor-derived indoleamine 2,3-dioxygenase regulates density of tumor-infiltrating CD8+ T cells and myeloid-derived suppressor cells in a murine model of ovarian cancer. [abstract]. In: Proceedings of the AACR Conference: Addressing Critical Questions in Ovarian Cancer Research and Treatment; Oct 1-4, 2017; Pittsburgh, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(15_Suppl):Abstract nr PR04.
Abstract A06: BRCA-like phenotype as a hallmark of osteosarcoma's converging evolution
Authors: Kovac Michal , Ribi Sebastian , Blattmann Claudia , Nathrath Michaela , Baumhoer Daniel
Published: August 2018

Background: Osteosarcomas are aggressive bone tumors with a high degree of genetic heterogeneity, which has historically limited treatment options in patients who do not respond to standard chemotherapy.

Methods: We sequenced exomes and genomes of 32 pretherapeutic osteosarcomas, 6 time-series consisting of chemotherapy-naïve biopsies, resection specimens, recurring tumors and/or metastases, and 15 unpaired metastases from (mainly) poor responders. We then interrogated signatures of mutation processes in cancer genomes and reconciled clonal maps with phylogenetic trees, thus building an evolutionary history of each tumor. Where possible, we searched for evidence of selection acting on the tumors and hallmarks that could be therapeutically exploited.

Results: We identified pathogenic mutations in at least 14 cancer drivers, some of which were formerly unknown in the context of osteosarcoma. However, there was no single cancer driver gene that could explain the majority of cases. Instead, >80% of osteosarcomas exhibited a specific combination of single-base substitutions, LOH, or large-scale genome instability characteristic of BRCA1/2-deficient tumors. The BRCA-like phenotype developed through parallel evolution by deleterious mutations affecting the BRCA1/2 genes and their binding partners such as PALB2 or CHEK2. We therefore investigated the sensitivity of a panel of osteosarcoma cell lines to the poly(ADP)-ribose polymerase inhibitor talazoparib alone and in combination with chemotherapeutic drugs. We identified an association between homologous recombination repair deficiency and the response of osteosarcoma cell lines to talazoparib. In combination with temozolomide, talazoparib led to the activation of BAX and BAK, loss of mitochondrial membrane potential, DNA fragmentation, and caspase-dependent cell death.

Conclusion: The acquisition of a BRCA-like phenotype through converging evolution has important implications for the development of novel treatment strategies in osteosarcoma using PARP inhibitors alone or together with standard chemotherapy.

Citation Format: Michal Kovac, Sebastian Ribi, Claudia Blattmann, Michaela Nathrath, Daniel Baumhoer. BRCA-like phenotype as a hallmark of osteosarcoma's converging evolution [abstract]. In: Proceedings of the AACR Conference on Advances in Sarcomas: From Basic Science to Clinical Translation; May 16-19, 2017; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(2_Suppl):Abstract nr A06.
Abstract A11: Arginine deprivation alters global lipid metabolism in ASS1-deficient sarcomas
Authors: Kremer Jeff , Prudner Bethany , Chang Samuel , Rogers Lenny , Tine Brian Van
Published: August 2018

Objective: Argininosuccinate Synthetase 1 (ASS1) is silenced in ~90% of sarcomas. This deficiency in the urea cycle causes sarcomas to become dependent on extracellular arginine for continued cell growth and survival, a condition named arginine auxotrophy. Arginine starvation induced by pegylated arginine deiminase (ADI-PEG20) induces dramatic alterations in global metabolism as well as an induction of autophagy. We investigated the specific changes in the lipidome of leiomyosarcoma cell lines induced by ADI-PEG20. By examining the alterations in esterified and nonesterified fatty acid metabolism we sought to understand the changes in the lipidome that are capable of being therapeutically exploited.

Methods: The cell lines SKLMS1 and SKUT1 were treated with ADI-PEG20. Cell pellets were collected and 33 esterified and nonesterified fatty acids were measured using GC/MS. Pathway analysis was then performed. Cell lines were then treated with a combination of ADI-PEG20 and TOFA (an acetyl CoA carboxylase inhibitor) or etoxomir/perhexiline (beta-oxidation inhibitors) to determine synthetic lethality.

Results: There were clear alterations in lipid metabolism induced by arginine deprivation. The fluctuations in lipid metabolism indicated pathways susceptible to inhibition by a variety of small-molecule inhibitors, namely that arginine deprivation sensitizes to inhibition of beta-oxidation. Cell culture experiments with ADI-PEG20 and a number of different small-molecule inhibitors demonstrated synthetic lethality upon cotreatment with ADI-PEG20 and beta-oxidation inhibitors.

Conclusion: Arginine deprivation causes global changes in lipid metabolism. The changes in metabolism are capable of being targeted by small-molecule inhibitors with the result being an induction of a synthetic lethality. By understanding the changes in the lipidome induced by arginine deprivation, we are building a multiagent synthetic lethal therapy for sarcoma based on metabolism that avoids chemotherapy.

Citation Format: Jeff Kremer, Bethany Prudner, Samuel Chang, Lenny Rogers, Brian Van Tine. Arginine deprivation alters global lipid metabolism in ASS1-deficient sarcomas [abstract]. In: Proceedings of the AACR Conference on Advances in Sarcomas: From Basic Science to Clinical Translation; May 16-19, 2017; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(2_Suppl):Abstract nr A11.
Abstract A13: Genome-wide transcriptional analysis of HDAC inhibition-induced apoptosis in synovial sarcoma
Authors: Laporte Aimee N. , Poulin Neal M. , Lorzadeh Alireza , Wang Xiu Qing , werff Ryan Vander , Barrott Jared J. , Moska Michelle , Hughes Christopher , Morin Gregg , Jones Kevin B. , Hirst Martin , Underhill T. Michael , Nielsen Torsten O.
Published: August 2018

Introduction: Conventional cytotoxic therapies for synovial sarcoma provide limited benefit, and no drugs specifically targeting its driving SS18-SSX fusion oncoprotein are currently available. HDAC inhibition has been shown in previous studies to disrupt the driving complex implicated in synovial sarcoma, resulting in apoptosis induction.

Methods: Transcriptome analysis was undertaken in a panel of six human synovial sarcoma cell lines in order to uncover potential mechanisms of cell death following HDAC inhibition. By comparison studies with five additional publicly available related expression datasets, common class effects resulting from HDAC inhibition were investigated. Five human synovial sarcoma tumor samples were profiled by RNA-seq for comparison. A mouse model of synovial sarcoma was treated by HDAC inhibition and tumors were profiled for apoptotic markers.

Results: Cell cycle arrest, differentiation, and response to oxygen-containing species and cell death were common biologic responses among the panel of post-HDAC inhibitor expression studies. Specific to synovial sarcoma, reactivation of repressed tumor suppressor CDKN2A and induction of proapoptotic transcriptional patterns results in apoptosis and decreased tumor burden in vivo.

Conclusion: HDAC inhibition impedes SS18-SSX-mediated transcriptional deregulation, allowing for reactivation of normal cell cycle regulatory and apoptotic pathways. This study provides mechanistic support for a particular susceptibility of synovial sarcoma to HDAC inhibition as a means of potential clinical treatment.

Citation Format: Aimee N. Laporte, Neal M. Poulin, Alireza Lorzadeh, Xiu Qing Wang, Ryan Vander werff, Jared J. Barrott, Michelle Moska, Christopher Hughes, Gregg Morin, Kevin B. Jones, Martin Hirst, T. Michael Underhill, Torsten O. Nielsen. Genome-wide transcriptional analysis of HDAC inhibition-induced apoptosis in synovial sarcoma [abstract]. In: Proceedings of the AACR Conference on Advances in Sarcomas: From Basic Science to Clinical Translation; May 16-19, 2017; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(2_Suppl):Abstract nr A13.
Abstract A15: Modeling sporadic gastrointestinal stromal tumor with BRAFV600E mutation
Authors: Ran Leili , Murphy Devan , Sher Jessica , Cao Zhen , Wang Shangqian , Walczak Edward , Guan Youxin , Xie Yuanyuan , Shukla Shipra , Zhan Yu , Antonescu Cristina R. , Chen Yu , Chi Ping
Published: August 2018

Gastrointestinal stromal tumor (GIST) is the most common subtype of sarcoma, characterized by activating mutations in KIT, PDGFRA, BRAF, N/H/KRAS, and loss of function genetic/epigenetic alterations in NF1, SDH-complex. Despite clinical advances for KIT/PDGFRA-mutant GIST, the scientific and clinical advances for KIT/PDGFRA-wild type GISTs have remained extremely limited due to the lack of model systems. Due to the lack of ICC-lineage specific cre system, modeling for sporadic GIST has not been feasible. ETV1 has recently been described as an ICC and GIST-lineage specific master regulator. Here, using the cre-activated Rosa26CAGGS-LSL-EYFP system, we demonstrate that Etv1CREERT2 preferentially activates cre in the Etv1-expressing ICC lineage by tamoxifen. Using the BrafCA conditional allele for cre-activated BrafV600E, we observed that BrafV600E alone, while leading to development of ICC hyperplasia, is not sufficient to drive GIST tumorigenesis. Combination of BrafV600E activation and Trp53 loss not only gives rise to ICC hyperplasia, but also leads to multifocal GIST-like tumors in mouse GI tract with 100% penetrance. We further demonstrate that the BrafV600E; Tp53-/- sporadic GIST mouse models are amenable for therapeutic intervention and recapitulate clinical responses to RAF inhibitors in human GIST. Our observations provide the first in vivo model for understanding the pathogenesis and therapeutic responses in BRAF-mutant GISTs. Importantly, these observations provide the proof of principle for modeling sporadic GIST in adult mice using the Etv1CREERT2 system and establish the feasibility and utility of establishing model systems for human GISTs that do not have any model systems available for mechanistic studies and therapeutic development.

Citation Format: Leili Ran, Devan Murphy, Jessica Sher, Zhen Cao, Shangqian Wang, Edward Walczak, Youxin Guan, Yuanyuan Xie, Shipra Shukla, Yu Zhan, Cristina R. Antonescu, Yu Chen, Ping Chi. Modeling sporadic gastrointestinal stromal tumor with BRAFV600E mutation [abstract]. In: Proceedings of the AACR Conference on Advances in Sarcomas: From Basic Science to Clinical Translation; May 16-19, 2017; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(2_Suppl):Abstract nr A15.
Abstract A29: The NF1 and NF2 pharmacome project, a course in high-throughput screening to identify targets and profile the sensitivity of MPNST cells to candidate drugs
Authors: Guo Jianman , Grovola Michael , Coggins Grace , Duggan Patrick , Huang Jiale , Song Claire , Witek Gabriela , Lin Danny , Xie Hong , Schultz David , Berritt Simon , Field Jeffrey
Published: August 2018

There are several large-scale efforts to compare the sensitivities of tumor cells to chemotherapeutic drugs and small-molecule pathway probes. However, to date, none of these profiling efforts systematically probed malignant peripheral nerve sheet tumors (MPNST). We initiated a database of drug sensitivities of MPNST as part of a course in high-throughput screening. We first developed a panel of 130 drugs highly relevant to neurofibromatosis (NF1 and NF2) that included a comprehensive set of MEK, RAF, RAS, FTI, PAK, ERK inhibitors, a representative set of drugs against many other cancer pathways including Wnt, Hedgehog, p53, EGF, HDAC, as well as classical cytotoxic agents such as doxorubicin and taxol. Many of the drugs in our panel are in clinical trials themselves, or closely related to drugs in trials for NF1. The drugs were tested against cells in 384-well plates at eight concentrations ranging from .004 μM to 10 μM. Cells were allowed to attach overnight, incubated for 72 hours with drugs, and then analyzed for ATP content using ATPlite. To date, we have profiled nine MPNST cell lines (ST88-14, ST88-3, 90-8, SNF02.2, STS26, T265, S462TY, SNF96.2, SNF94.3) and one NF2 Schwannoma cell line (HEI193). We also tested several cell lines that were tested in other screens so that we can compare our results to the other databases. The IC50 was calculated as a common measure of how effective each drug is using GraphPad Prism software. NF1 cells were distinguished from NF2 cells and STS26 cells (a spontaneous MPNST cell line derived from a patient who did not have NF1) by their strong sensitivity to MEK and Bromodomain inhibitors. Some drugs, including cytotoxic agents, Pak inhibitors, and HDAC inhibitors, were broadly toxic, inhibiting growth regardless of NF1 and NF2 status. None of the drugs in our panel exclusively inhibited HEI193 cells. With this study we initiated a database to archive the drug sensitivities of NF1 and NF2 cells that will be expanded in future versions of our course.

Sponsored by Children's Tumor Foundation.

Citation Format: Jianman Guo, Michael Grovola, Grace Coggins, Patrick Duggan, Jiale Huang, Claire Song, Gabriela Witek, Danny Lin, Hong Xie, David Schultz, Simon Berritt, Jeffrey Field. The NF1 and NF2 pharmacome project, a course in high-throughput screening to identify targets and profile the sensitivity of MPNST cells to candidate drugs [abstract]. In: Proceedings of the AACR Conference on Advances in Sarcomas: From Basic Science to Clinical Translation; May 16-19, 2017; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(2_Suppl):Abstract nr A29.
Abstract B04: Functional characterization of IGF-IR/PI3K/Akt signaling in myxoid liposarcoma
Authors: Trautmann Marcel , Cyra Magdalene Alice , Bertling Christian , Isfort Ilka , Menzel Jasmin , Steinestel Konrad , Grünewald Inga , Altvater Bianca , Rossig Claudia , Åman Pierre , Wardelmann Eva , Huss Sebastian , Hartmann Wolfgang
Published: August 2018

Introduction: Myxoid liposarcoma (MLS) is the second most common type of liposarcoma and an aggressive disease with particular propensity to develop hematogenic metastases. Ninety percent of MLS are characterized by a reciprocal translocation t(12;16) (q13;p11), leading to the pathogenic gene fusion of FUS and DDIT3. The resulting chimeric FUS-DDIT3 fusion protein is suggested to play a crucial role in MLS pathogenesis, although the specific mechanism of action remains to be substantiated. Aiming at the preclinical identification of novel therapeutic options, we here investigate the functional relevance of FUS-DDIT3 in IGF-IR/PI3K/Akt signal transduction.

Experimental Procedures: Immunohistochemical analyses of IGF-IR/PI3K/Akt signaling effectors and modulators were performed in a comprehensive cohort of clinical MLS specimens. FUS-DDIT3-dependent activation of the IGF-IR/PI3K/Akt signaling cascade was analyzed by siRNA and immunoblotting in vitro. Cell proliferation and FACS assays were performed in multiple tumor-derived MLS cell lines. An established MLS chorioallantoic membrane model (CAM) was employed for in vivo confirmation of the preclinical in vitro data.

Results: In a significant subset of MLS specimens, immunohistochemical staining revealed elevated phosphorylation levels of various signaling components, representing a strong indication of activated IGF-IR/PI3K/Akt signaling to be a frequent feature in MLS. IGF-IR inhibition significantly suppressed the IGF-IR/PI3K/Akt signaling cascade, associated with impairment of MLS cell viability and induction of apoptosis in vitro and in vivo. Furthermore, siRNA-mediated knockdown of FUS-DDIT3 led to dephosphorylation of IGF-IR/PI3K/Akt signaling components, implying that the FUS-DDIT3 fusion protein is involved in the IGF-IR regulated signaling cascade.

Conclusions: Our preclinical study emphasizes the pivotal role of the IGF-IR/PI3K/Akt signaling pathway in MLS pathogenesis and indicates its functional dependence on the MLS-specific FUS-DDIT3 fusion protein. Furthermore, our in vitro and in vivo results demonstrate that targeting the IGF-IR/PI3K/Akt signaling pathway provides a rational, molecularly founded therapeutic strategy in the treatment of MLS.

Citation Format: Marcel Trautmann, Magdalene Alice Cyra, Christian Bertling, Ilka Isfort, Jasmin Menzel, Konrad Steinestel, Inga Grünewald, Bianca Altvater, Claudia Rossig, Pierre Åman, Eva Wardelmann, Sebastian Huss, Wolfgang Hartmann. Functional characterization of IGF-IR/PI3K/Akt signaling in myxoid liposarcoma [abstract]. In: Proceedings of the AACR Conference on Advances in Sarcomas: From Basic Science to Clinical Translation; May 16-19, 2017; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(2_Suppl):Abstract nr B04.
Abstract B20: The molecular function of ASPSCR1-TFE3 in alveolar soft part sarcoma
Authors: Tanaka Miwa , Nakamura Takuro
Published: August 2018

Alveolar soft part sarcoma (ASPS) is a soft-tissue sarcoma that affects predominantly adolescents and young adults with lower legs and buttocks as frequent primary sites. ASPS is characterized by alveolar structure of tumor cells, abundant vascularization, and high frequency of hematogenous metastasis. As for gene abnormality, ASPSCR1-TFE3 fusion gene is observed in all ASPS cases. To understand the exact mechanisms of ASPSCR1-TFE3 and tumorigenesis of ASPS, we have developed an ex vivo mouse model for human ASPS (Tanaka et al., Cancer Res 2017;77(4).

In mouse ASPS, the tumor cells frequently showed tumor intravasation, with the intravascular tumor cells presenting as organoid structures covered with hemangiopericytes, which is also observed in human ASPS. Moreover, culture supernatant of mouse ASPS cells strongly induced hemangiopericyte migration in vitro. The search for hemangiopericyte-inducing factors which are released from ASPS cells is in progress.

We identified Gpnmb that plays an important role in intravasation of ASPS tumor cells as a direct target of the ASPSCR1-TFE3 fusion transcription factor. The ChIP-seq analysis detected an ASPSCR1-TFE3 binding peak at the Gpnmb promoter, and Gpnmb expression was significantly upregulated in ASPS tumors. Enhanced localization of GPNMB at the front of tumor invasion and intravasation in both mouse and human ASPS. Knockdown of Gpnmb suppressed transendothelial migration of ASPS tumor cells, indicating that Gpnmb is required for intravasation.

TFE3 is a member of the TFE/MITF family, which has been found involved in human cancer such as renal cell carcinoma and malignant melanoma. The present model enabled us to evaluate tumorigenic activity of TFE/MITF family proteins. To examine the oncogenic activity of ASPSCR1 fusion genes, artificial chimeric genes were generated consisting of the 5 ASPSCR1 and 3 TFE/MITF sequences. The ASPSCR1-TFE3 and ASPSCR1-TFEB but not ASPSCR1-TFEC and ASPSCR1-MITF induced sarcoma. The results suggest the presence of TFE3/TFEB-specific cofactors and mechanisms for tumorigenesis. In order to identify such novel cofactors and functional motifs, human ASPS cell-nuclear extract was incubated with TFE3 or MITF proteins and TFE3- or MITF-bound fractions were analyzed by mass spectrometry. The TFE3-specific interaction partners were identified and their roles in tumorigenesis, angiogenesis, and/or metastasis are subjected to the subsequent analysis. These studies will provide valuable information for our understanding of the biology of ASPS and functions of TFE/MITF family transcription factors.

Citation Format: Miwa Tanaka, Takuro Nakamura. The molecular function of ASPSCR1-TFE3 in alveolar soft part sarcoma [abstract]. In: Proceedings of the AACR Conference on Advances in Sarcomas: From Basic Science to Clinical Translation; May 16-19, 2017; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(2_Suppl):Abstract nr B20.
Abstract B33: Assessing macrophage polarization in sarcomas with PD-L1 correlates
Authors: Hostetter Galen , Sempere Lorenzo , Jewell Scott , Baylin Steve
Published: August 2018

The role of innate and adaptive immunity in a wide range of human tumors has shown critical roles, though sometimes competing, in numerous immune components in both the tumor and the tumor microenvironment (TME). The PD-1/PD-L1 interaction in both tumor and the TME has become high priority in correlative biomarkers of human disease with increasing number of targeted agents showing high levels of durable response. The in situ analysis of viral defense pathway, interferon response, and PD-L1 status has provided strong preliminary data of correlative staining by immunohistochemistry in colon and lung carcinomas. Generally, such human tumors arise in organs with frequent and high exposure to external/foreign antigens. Here we expand our IHC staining to include human tumors arising from sites with varied immune activity to include uterine wall (leiomyosarcoma), subcutaneous connective tissue to include dermatofibrosarcoma protuberans (DFSP), soft tissue sarcoma, fibrosarcoma, and osteosarcoma. IHC panel includes immune markers of CD4, CD8, CD68 (M1 macrophages), CD163 (M2 macrophages); dsRNA antibodies (J2 and K1); MDA 5, RIG 1, STAT 1, and pSTAT1; PD-L1 and PD-1; and interferon response markers IRF 3, IRF 7, and IFIT 1. Immunostaining is ongoing and supports preliminary sarcoma phenotype of quite varied PD-L1 immunoreactivity with lower prevalence than lung and colon carcinomas. Immune markers of T-cell subset and macrophage M1 and M2 are significantly lower in sarcoma samples and detailed analysis of M1 and M2 macrophages in DFSP, STS, fibrosarcomas, and osteosarcoma. Each tumor type is represented on single TMA with 8-12 samples each from the Van Andel Institute Biorepository Core. In our experience, tissue site density and macrophage subtypes and difference in polarized macrophages (M2) in relation to CD4 and CD8 markers were significant in relation to PD-L1 and require further exploration. Improved characterization of PD-L1 pathway and potential surrogate markers to compile immune competency profiles will include early results from our IHC staining for dsRNA fragments to lend support to endogenous retroviral activation in a wide range of both carcinomas and sarcomas.

Citation Format: Galen Hostetter, Lorenzo Sempere, Scott Jewell, Steve Baylin. Assessing macrophage polarization in sarcomas with PD-L1 correlates [abstract]. In: Proceedings of the AACR Conference on Advances in Sarcomas: From Basic Science to Clinical Translation; May 16-19, 2017; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(2_Suppl):Abstract nr B33.