bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract IA09: Targeting the CRL4CRBN E3 ligases for treatment of hematologic cancers
Authors: Chopra Rajesh
Published: August 2018

Manipulation of the ubiquitin-proteasome system to achieve targeted degradation of proteins within cells using chemical tools and drugs has the potential to transform pharmacologic and therapeutic approaches in cancer and other diseases. Thalidomide and its analogues lenalidomide and pomalidomide exert their mechanism of action through the modulation of the CRL4CRBN E3 ligase family. Binding of the thalidomide to analogues Cereblon (CRBN) results in the degradation of neomorphic protein such as Aiolos and iKaros in multiple myeloma. This degradation explains the antitumor activity as well as the immunomodulatory effects of these drugs. The degradation of multiple context-specific proteins by the thalidomide analogues provides a means to uncover new cell biology as well as generate future drug molecules against currently undruggable targets. In parallel, the development of larger bifunctional molecules that bring together highly specific protein targets in complexes with Cereblon, von Hippel-Lindau or other E3 ligases to promote ubiquitin-dependent degradation has progressed to generate selective chemical compounds with potent effects in cells and in vivo models, providing valuable tools for biological target validation and with future potential for therapeutic use. This presentation will survey recent breakthroughs achieved in these two complementary methods, with a greater focus of CRL4CRBN modulation.

Citation Format: Rajesh Chopra. Targeting the CRL4CRBN E3 ligases for treatment of hematologic cancers [abstract]. In: Proceedings of the Second AACR Conference on Hematologic Malignancies: Translating Discoveries to Novel Therapies; May 6-9, 2017; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(24_Suppl):Abstract nr IA09.
Abstract IA15: Genetic predisposition to hematopoietic malignancies
Authors: Godley Lucy A.
Published: August 2018

There is a growing appreciation for the impact of baseline genetic variants in the development of hematopoietic malignancies, and the germline risk factors that make an individual more susceptible to developing bone marrow-derived cancers are being defined through highly informative families and next-generation sequencing with increasing frequency. At the University of Chicago, we use a rigorous pipeline for clinical testing of individuals comprising next-generation sequencing-based molecular testing to detect point mutations as well as microarrays to detect chromosomal rearrangements. Overall, we are now able to identify the causative germline mutation in about 20% of cases, a level commensurate with other cancer risk clinics, but hinting that additional predisposition alleles remain to be discovered. Many of our patients/families also contribute to research by banking samples for future studies designed to identify new predisposition syndromes. This presentation will include a discussion of the new insights into hematopoietic biology that can be appreciated by studying these emerging predisposition syndromes.

Citation Format: Lucy A. Godley. Genetic predisposition to hematopoietic malignancies [abstract]. In: Proceedings of the Second AACR Conference on Hematologic Malignancies: Translating Discoveries to Novel Therapies; May 6-9, 2017; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(24_Suppl):Abstract nr IA15.
Abstract A31: Mutant p53 increases integrin-ECM interactions in early HGSOC
Authors: Lecker Laura SM , Trevisan Caterina , Delaine-Smith Robin , Maniati Eleni , Pearce Oliver , Meinert Christoph , Iwanicki Marcin , Drapkin Ronny , Loessner Daniela , Balkwill Frances
Published: August 2018

Until recently, it was thought that high-grade serous ovarian cancer (HGSOC) arises from the ovarian surface epithelium (OSE). Now, it has become clear that the epithelium of the fallopian tube fimbriae is the starting point of many HGSOCs. Serous tubal intraepithelial carcinomas (STICs) are suggested to be the earliest form of HGSOC and show mutations in the p53 gene. Part of the neoplastic transformation into invasive HGSOC may be the initial adhesion of STIC cells to the surface of the ovary as a first site of metastasis. To examine the role of mutant p53 immortalized fallopian tube secretory epithelial (FTSE) cells in the early onset of HGSOC, we used mechanically tunable hydrogels and developed a protocol to obtain decellularized human ovary scaffolds for 3D cell cultures. Stable expression of mutant p53 in FTSE cells promoted adhesion to hydrogel matrices and invasion into decellularized ovary scaffolds. Next, we sought to analyze the extracellular matrix (ECM) landscape of human fallopian tube and ovary tissues and identified proteins with a high affinity to integrin αvβ3. Mutant p53 FTSE cells had increased levels of integrin αvβ3 and decreased adhesive potential upon integrin αvβ3 blockage compared to wild-type FTSE cells. The results indicate that FTSE cells expressing mutant p53 upregulate integrin expression, which in turn alters their tissue-specific ECM interactions. Our findings give new insights in the early onset of HGSOC and may help to understand the role of p53 in the cells of origin of HGSOC.

Citation Format: Laura SM Lecker, Caterina Trevisan, Robin Delaine-Smith, Eleni Maniati, Oliver Pearce, Christoph Meinert, Marcin Iwanicki, Ronny Drapkin, Daniela Loessner, Frances Balkwill. Mutant p53 increases integrin-ECM interactions in early HGSOC. [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 A31.
Abstract B08: Urinary PGE-M levels and risk of ovarian cancer
Authors: Barnard Mollie E. , Eliassen A. Heather , Rosner Bernard A. , Terry Kathryn L. , Milne Ginger L. , Tworoger Shelley S.
Published: August 2018

Introduction: Prostaglandin E2 (PGE2) is thought to influence ovarian carcinogenesis by increasing cell proliferation, tumor cell invasiveness, and angiogenesis. PGE-M is the major metabolite of PGE2 and a marker of systemic PGE2 production. Prior research has reported positive associations between urinary PGE-M and risk of colorectal, gastric, lung, pancreatic, and breast cancer; however, this is the first study to evaluate the association between urinary PGE-M and risk of ovarian cancer.

Methods: We conducted a prospective case-control study nested in the Nurses’ Health Study (NHS) and NHSII cohorts. We included 194 cases of invasive epithelial ovarian cancer and 387 matched controls. All cases were diagnosed between the time of urine specimen collection (1996-97 NHSII; 2000-2002 NHS) and the end of follow-up (2015). Controls were selected using incidence density sampling and matched to cases on year of birth, menopausal status at collection and diagnosis, date and time of day of collection, hormone therapy use at collection, and fasting status. We measured PGE-M levels using LC/MS methods, and used the PGE-M distribution among controls to identify tertile cutpoints. We estimated the association between prediagnosis urinary PGE-M (in tertiles) and risk of ovarian cancer using conditional logistic regression.

Results: We observed a suggestively lower risk of ovarian cancer for those with the highest PGE-M levels in NHS (OR=0.66; 95%CI=0.36-1.21; p-trend=0.15; n=123 cases), and no association in NHSII (OR=1.15; 95%CI=0.50-2.67; p-trend=0.75; n=71 cases). When results from the two cohorts were pooled, we observed nonsignificant, lower odds of ovarian cancer among those in the highest tertile of PGE-M compared to the lowest tertile (OR=0.80; 95%CI=0.50-1.27; p-trend=0.34), particularly after restricting our analysis to study participants who provided first morning urine samples (OR=0.68; 95%CI=0.40-1.14; p-trend=0.13). However, when we examined quartiles, no clear association was observed, although power was limited.

Conclusions: Overall, our results suggest that higher prediagnosis PGE-M levels are not associated with an increased risk of ovarian cancer. Further analyses are under way to evaluate the potential for effect modification by menopausal status, BMI, and NSAID use.

Citation Format: Mollie E. Barnard, A. Heather Eliassen, Bernard A. Rosner, Kathryn L. Terry, Ginger L. Milne, Shelley S. Tworoger. Urinary PGE-M levels and risk 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 B08.
Abstract B25: Hormone receptor expression and response in ovarian tumors of low malignant potential
Authors: Taylor Sarah E. , Andersen Courtney L. , Bhargava Rohit , Tseng George , Oesterreich Steffi , Edwards Robert P. , Lee Adrian V.
Published: August 2018

Objective: Primary treatment for ovarian low malignant potential (LMP) tumors is surgical resection with little proven effect of cytotoxic chemotherapy. New therapeutic strategies are needed to prevent and treat recurrence. The objective of this study is to investigate the role of hormone receptors in ovarian low malignant potential tumors.

Methods: We obtained formalin-fixed, paraffin embedded (FFPE) tissue samples from patients with ovarian LMP tumors. Clinicopathologic data were collected for all available specimens. Immunohistochemistry (IHC) was performed to determine protein expression. Gene expression was measured using the NanoString nCounter platform. Differences in expression between histologic subtypes were by t-test, followed by a Bonferroni adjustment for multiple comparisons (p<0.01).

Results: Thirty-eight patients were included in this study. The histologic subtypes were divided between 20 serous and 18 mucinous tumors. All serous tumors were ERα and PR positive by IHC and 6 of 20 (30%) were ERβ positive. Only one of the 18 mucinous tumors (5.6%) was positive for both ERα and PR, and all the samples were negative for ERβ. ERβ mRNA levels were elevated in the mucinous LMP tumors and ERα mRNA was higher in the serous samples. ERα and PR protein expression correlated with mRNA expression of ESR1 (r2=0.5606) and PR (r2=0.42), respectively. ERβ expression did not correlate with mRNA expression of ESR2 (r2=0.038). Measurement of estrogen-regulated genes and genes involved in ER signaling (n=236) revealed a clear separation of serous from mucinous subtypes, with 44 genes showing a statistically significant difference (p<0.01) between the serous and mucinous subtypes.

Conclusion: High levels of ERα, PR, and downstream ERα targets in serous LMP tumors suggest hormone responsiveness and that these tumors are potentially treatable with endocrine therapy. Mucinous tumors largely did not express hormone receptors. In light of this, differences in gene expression observed are more likely attributable to underlying lineage differences than differences in estrogen signaling. Additional large-scale analyses are warranted to better understand the differences between subtypes and to identify avenues for targeted therapy in mucinous LMPs.

Citation Format: Sarah E. Taylor, Courtney L. Andersen, Rohit Bhargava, George Tseng, Steffi Oesterreich, Robert P. Edwards, Adrian V. Lee. Hormone receptor expression and response in ovarian tumors of low malignant potential. [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 B25.
Abstract B71: New directions in gynecologic cancer research utilizing Text Information Extraction System (TIES) Cancer Research Network
Authors: Linkov Faina Y. , Schwenk Melissa , Davis Michael , Edwards Robert , Becich Michael
Published: August 2018

Gynecologic cancers pose significant morbidity and mortality burden for US women. Endometrial cancer is the most common gynecologic malignancy in the US, while ovarian cancer is one of the deadliest. Since research funding for some of the gynecologic malignancies has been limited, novel research on the existing datasets needs to be harnessed to improve the health of the women affected by these conditions. We aim to evaluate if Text Information Extraction System (TIES) Cancer Research Network, a federated network that facilitates data and biospecimen sharing among member institutions, has capabilities for conducting research in the area of gynecologic cancers.

TIES system provides effective tools for searching deidentified structured and unstructured data for gynecologic cancers with capabilities to explore pathology and radiology records. We used TIES system to identify records of patients with ovarian, endometrial, and cervical cancers. We used temporal search features to identify patients who developed ovarian tumors after being diagnosed with endometrial tumors. We examined records for completeness of information on diagnosis, age, and procedure year.

We found that TIES system has 13,762 records for endometrial cancer, 7,692 records for ovarian cancer, and 10,826 records for cervical cancer for Pittsburgh site. 306 records have been identified for patients who had both ovarian and endometrial malignancies. Nearly 100% of the records had information on age of the patient, year of the procedure, and exact diagnosis.

TIES is a promising tool for conducting research in the area of gynecologic malignancies, especially for rare diseases such as concurrent endometrial and ovarian cancers. Existing data repositories like TIES need to be further explored for novel research questions in the area of gynecologic cancer.

Citation Format: Faina Y. Linkov, Melissa Schwenk, Michael Davis, Robert Edwards, Michael Becich. New directions in gynecologic cancer research utilizing Text Information Extraction System (TIES) Cancer Research Network. [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 B71.
Abstract IA10: Deconstructing and reconstructing the ovarian cancer microenvironment
Authors: Balkwill Frances R.
Published: August 2018

The tumor microenvironment (TME) is critical for cancer growth and spread. However, the relationships between molecular components of the TME and higher-order features, tissue stiffness, extent of disease, and cellularity are not known. Using clinical samples of metastatic high-grade serous ovarian cancer (HGSOC) that ranged from minimal to extensive disease, we have defined RNA and protein profiles that evolved with these higher-order features.

We obtained a unique profile of the evolving metastatic microenvironment of HGSOC that includes data not only on gene expression and proteomics but also cytokine/chemokine expression, ECM organization, and biophysical properties. This “deconstruction” of a metastatic microenvironment provides a critical reference for our mouse model systems and a template for reconstruction of 3D multicellular human ovarian cancer models as will be detailed in this presentation.

Although our work was conducted on omental metastases of HGSOC, we found evidence for a conserved mechanism that may be relevant to many human solid tumors: a pattern of matrix-associated gene expression that we termed the matrix index. In the HGSOC samples, the matrix index significantly associated with various leukocyte signaling pathways of cells associated with poor prognosis including Th2 cells and macrophage-associated genes and correlated with extent of disease and tissue stiffness. Interrogating transcriptional datasets from a wide range of human solid cancers, including HGSOC, we found that the matrix index had prognostic significance irrespective of patient age, stage of disease, or first response to therapy. This led us to suggest that there may be a common matrix response to human cancer.

Citation Format: Frances R. Balkwill. Deconstructing and reconstructing the ovarian cancer microenvironment. [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 IA10.
Abstract A33: Histone demethylase KDM3A in rhabdomyosarcoma
Authors: Sobral Lays M. , Jedlicka Paul
Published: August 2018

Rhabdomyosarcoma (RMS) is the most common soft-tissue sarcoma in children, adolescents, and young adults, presenting a myogenic phenotype. RMS can be divided into two major histopathologic subtypes: driver oncofusion (PAX3/7-FOXO1) positive, alveolar (ARMS), and oncofusion-negative embryonal (ERMS). Histone methylation is a key element of chromatin-based modifications that regulates a number of cellular processes, including DNA replication, DNA repair, and gene transcription. Histone demethylase gene family members (HDMs) regulate gene expression by removing methyl marks on histone tails to activate or repress transcription. KDM3A (lysine-specific demethylase 3A or JMJD1A) is a histone demethylase belonging to the Jumonji C-terminal domain (JmjC)-containing histone demethylases that selectively removes mono- and dimethyl groups from H3K9. It has been demonstrated that KDM3A is overexpressed in many kinds of cancer, such as bladder, lung, and breast cancer, and, previously shown by our laboratory, in Ewing sarcoma, contributing to carcinogenesis. We and others have identified KDM3A as overexpressed in RMS, but the functional consequences of this overexpression have not been examined. The aim of this study was to analyze the influence of KDM3A on RMS biology. Two different RMS cells lines were used, RH30 (ARMS) and RD (ERMS), to perform stable shRNA-mediated KDM3A knockdown. The protein and RNA levels were analyzed by Western blotting and RT-qPCR, respectively. The phenotypic effects of KDM3A knockdown were analyzed by proliferation assays (MTT and clonogenic assay) and cell migration (transwell migration assay). KDM3A knockdown was able to inhibit the proliferation, colony formation, and migration of RMS cell lines, demonstrating an important role in RMS biology.

Citation Format: Lays M. Sobral, Paul Jedlicka. Histone demethylase KDM3A in rhabdomyosarcoma [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 A33.
Abstract B13: COP1-ETS axis regulates ERK transcriptional output and modulates sensitivity to MAPK inhibitors
Authors: Xie Yuanyuan , Cao Zhen , Wong Wai Pung , Guan Youxin , Zhang Jenny , Walczak Edward , Murphy Devan , Ran Leili , Sirota Inna , Wang Shangqian , Shukla Shipra , Gao Dong , Wongvipat John , Knott Simon , Chang Kenneth , Antonescu Cristina , Hannon Gregory , Chi Ping , Chen Yu
Published: August 2018

Aberrant activation of the mitogen activate kinase (MAPK) pathway is highly prevalent in cancer and therapies targeting the pathway are approved or under active investigation in multiple malignancies. MAPK signaling leads to activation of a transcriptional program that includes general growth promoting genes, negative feedback regulators of the MAPK pathway, and lineage-specific genes. While the mechanisms of upstream signal transduction that leads to MAPK activation have been studied in detail, how MAPK activation is dynamically coupled with downstream nuclear transcriptional response is not fully understood. In gastrointestinal stomal tumor (GIST) and melanoma, two malignancies with aberrant MAPK activation, we find that Pea3 family ETS transcription factors ETV1, ETV4, and ETV5 are critical nuclear effectors of MAPK signaling. We find that the primary mechanism linking MAPK and Pea3 activity is through protein stability via the COP1 E3 ligase. The loss of COP1 leads to decoupling between upstream MAPK signaling and downstream transcription with constitutively stabilized Pea3 protein levels, constitutively high MAPK transcriptome, yet decreased upstream signaling due to Pea3-mediated transcription of negative feedback regulators. This leads to decreased therapeutic sensitivity to MAPK pathway inhibition in vitro and in vivo. These observations indicate that MAPK signaling-dependent regulation of Pea3 ETS protein stability is a crucial pathway that couples downstream transcriptional response to MAPK signaling and can shape the therapeutic sensitivity to MAPK pathway inhibition in cancer.

Citation Format: Yuanyuan Xie, Zhen Cao, Wai Pung Wong, Youxin Guan, Jenny Zhang, Edward Walczak, Devan Murphy, Leili Ran, Inna Sirota, Shangqian Wang, Shipra Shukla, Dong Gao, John Wongvipat, Simon Knott, Kenneth Chang, Cristina Antonescu, Gregory Hannon, Ping Chi, Yu Chen. COP1-ETS axis regulates ERK transcriptional output and modulates sensitivity to MAPK inhibitors [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 B13.
Abstract B14: A restricted cell population propagates MPNST growth after treatment
Authors: Sun Daochun , Parada Luis
Published: August 2018

Malignant peripheral nerve sheath tumor is a type of soft-tissue sarcoma that arises from the neural crest lineage and is commonly associated with nerve trunks. Surgical removal is the major treatment conjugated with chemo/radiation therapy when applicable. However, the complete tumor clearance is limited by the resectability, especially when tumor is associated with large peripheral nerve such as sciatic nerve, brachial plexus, and sacral plexus. The local recurrence of MPNST is 40-45% and distal recurrence is 40-48%. By harnessing our Nes-hsvTK-GFP transgene that successfully labeled the cancer stem cells in glioblastoma, we identified a small quiescent cell population in MPNSTs from both cisNf1+/-;Trp53+/- (cisNP) spontaneous model and skin progenitor (SKP)-based allograft model. Inhibition of these cells by feeding mice ganciclovir chow significantly decreased the tumor growth in both cisNP model and allograft model. We also found that the transgene-labeled GFP+ cells enrich in the sciatic nerve region compared to the distal tumor mass in MPNST allograft model. Tumor primary culture from the sciatic nerve vicinity forms significantly larger and more spheres in vitro than the distal tumor mass. The BrdU-EdU sequential labeling assay after chemotherapy in MPNST allograft model shows that the GFP+ cells can continuously repopulate tumor. These results indicate that the transgene-labeled GFP+ cells may serve as a source of tumor growth and, at the same time, a novel target to reduce MPNST relapse after treatment.

Citation Format: Daochun Sun, Luis Parada. A restricted cell population propagates MPNST growth after treatment [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 B14.
Abstract B17: Utility of MRI and PET/CT to differentiate benign versus malignant peripheral nerve sheath tumors (MPNST)
Authors: Sebro Ronnie , Niziolek Paul
Published: August 2018

Aim: To assess the utility of MRI and PET/CT to differentiate benign versus malignant peripheral nerve sheath tumors (MPNST).

Methods: We retrospectively identified 68 patients with histologically confirmed nerve sheath tumors. All of these patients had pretreatment magnetic resonance imaging (MRI) studies and 17 patients had pretreatment 18-fluorodeoxyglucose positron emission tomography (PET/CT). Age, history of neurofibromatosis, maximum size of the tumor, MR features, and maximum standardized uptake values (SUV) from PET/CT were obtained. We used Wilcoxon-Rank sum or Fisher's exact tests to compare benign versus malignant nerve sheath tumors.

Results: There was no significant difference in the mean age of the patients with benign versus MPNST (P=0.85). Patients with NF1 had higher odds of MPNSTs (OR=26.7, P=2.6 x10-7). There was no difference in the mean size of the benign versus MPNSTs (P=0.44). Homogeneous enhancement of a lesion after intravenous contrast (OR=0.08, P=0.008) and the target sign (OR=0.0, P=0.041), were both associated with decreased odds of MPNST. Bone destruction seen on MRI (P=5.7x10-4) and an enlarged nerve (OR = 3.89, P=0.048) were associated with increased odds of MPNST. MPNSTs had significantly higher mean maximum SUV than benign nerve sheath tumors (P=0.0272). The previously published threshold maximum SUV of 3.5 had 100% sensitivity and 50% specificity to exclude MPNST as 50% (4/8) of the benign nerve sheath tumors had a maximum SUV >3.5.

Conclusion: MRI and PET/CT are useful for differentiating benign from MPNST, but neither is specific. A maximum SUV of 3.5 is highly sensitive for identifying MPNST; however, tissue sampling is often necessary to confirm the diagnosis since using this threshold results in a large proportion of false positives.

Citation Format: Ronnie Sebro, Paul Niziolek. Utility of MRI and PET/CT to differentiate benign versus malignant peripheral nerve sheath tumors (MPNST) [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 B17.
Abstract B24: Molecular and functional dissection of the CIC-DUX4 fusion in undifferentiated round cell sarcoma
Authors: Okimoto Ross A. , Wu Wei , Bivona Trever G.
Published: August 2018

CIC-DUX4 soft-tissue tumors are an aggressive subset of undifferentiated round cell sarcomas that arise in children and young adults. The cytogenetic hallmark, (t(4;19) or t(10;19)), of this tumor is a chromosomal translocation that fuses the transcription factor, Capicua (CIC), with the double homeobox 4 protein, DUX4. Despite morphologic similarities to Ewing sarcoma, CIC-DUX4 sarcomas are clinically distinct with rapid development of lethal metastatic disease and chemoinsensitivity. The unique cytogenetic and clinical features that distinguish CIC-DUX4 sarcomas from other small round cell tumors provide a unique opportunity to identify and rationally target this population to improve clinical outcomes.

To meet this need, we are taking a systematic functional approach to identify critical CIC-DUX4 targets that promote tumor progression and metastasis. Leveraging a comparative transcriptional analysis between cytogenetically distinct small round cell sarcomas, we reveal that the CIC-DUX4 fusion activates highly conserved molecular networks to control tumor growth and metastatic capacity. Using an orthotopic soft-tissue sarcoma model, we show that CIC-DUX4 induces ETV4 expression to drive invasion and metastasis. Genetic silencing of ETV4 in CIC-DUX4 expressing tumors limits tumor dissemination without a profound impact on tumor cell growth. These findings suggest that CIC-DUX4 enhances metastasis and tumor growth through distinct transcriptional repertoires. Consistent with this, we identify multiple components of the cell cycle machinery that are transcriptionally regulated by CIC-DUX4 expression. Specifically, the CIC-DUX4 fusion co-opts native CIC-binding specificity to transcriptionally activate these cell cycle target genes. Altogether, our molecular and functional dissection of the CIC-DUX4 fusion reveals highly conserved CIC-regulated transcriptional targets that promote tumor growth and metastasis. We aim to pharmacologically exploit these key CIC-DUX4-dependent transcriptional nodes to improve outcomes for this population with few therapeutic options.

Citation Format: Ross A. Okimoto, Wei Wu, Trever G. Bivona. Molecular and functional dissection of the CIC-DUX4 fusion in undifferentiated round cell 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 B24.
Abstract B27: Analysis of the immune infiltrate in undifferentiated pleomorphic sarcoma of the extremity and trunk in response to radiotherapy
Authors: Keung Emily Z. , Tsai Jen-Wei , Ali Ali M. , Cormier Janice N. , Bishop Andrew J. , Guadagnolo B. Ashleigh , Hunt Kelly K. , Torres Keila E. , Somaiah Neeta , Wargo Jennifer A. , Lazar Alexander , Wang Wei-Lien , Roland Cristina L.
Published: August 2018

Introduction: Undifferentiated pleomorphic sarcoma of the extremity and trunk (ET UPS) presents a unique diagnostic and therapeutic challenge. Recently, immunotherapy has been employed in the treatment of patients with advanced UPS with preliminary evidence of benefit in 40% of a small initial cohort (SARC028). However, there is currently a paucity of data characterizing the immune infiltrate population in ET UPS. Radiotherapy (RT) is associated with improved locoregional control in combination with surgery. Localized RT has been shown in other tumor types to promote tumor antigen release and enhance tumor-specific targeting by the adaptive immune system. The aim of this study was two-fold: 1) to characterize the immune infiltrate in ET UPS and 2) to evaluate the effect of preoperative RT on immune cell infiltrates in ET UPS.

Methods: We identified 17 matched ET UPS tumor samples before and after RT. Immunohistochemistry for CD8, CD4, PD-L1, PD1, CD3, CD163, and FOXP3 was performed on the matched pairs. Changes in immune infiltrate over time between the pairs were compared with a paired t-test.

Results: CD8, CD4, PD-L1, PD1, CD3, CD163, and FoxP3 positive cells were identified in all samples. The effects were variable, but there was an overall trend towards an increase in the density of tumor-infiltrating immune cells of all assayed types in ET UPS following completion of RT, with increases in the median number of CD8 (55 vs. 111 cells/mm2, p=0.17), CD4 (3 vs. 13 cells/mm2, p=0.01), CD3 (158 vs. 219 cells/mm2, p=0.06), CD163 (1363 vs. 2001 cells/mm2, p=0.76), and FOXP3 (14 vs. 25 cells/mm2, p=0.23) positive cells in RT-treated tumor sections. Interestingly, although PD-L1 was not expressed in any pre-RT ET UPS tumors, positive PD-L1 expression was observed in 21% (3/14) of tumors after RT treatment (p=0.07).

Conclusion: An immune infiltrate is present in ET UPS at the time of diagnosis, with a trend towards increased density of immune infiltrate and PD-L1 expression after completion of RT. These data support evaluating immune checkpoint inhibitors with standard of care RT in the treatment of ET UPS.

Citation Format: Emily Z. Keung, Jen-Wei Tsai, Ali M. Ali, Janice N. Cormier, Andrew J. Bishop, B. Ashleigh Guadagnolo, Kelly K. Hunt, Keila E. Torres, Neeta Somaiah, Jennifer A. Wargo, Alexander Lazar, Wei-Lien Wang, Cristina L. Roland. Analysis of the immune infiltrate in undifferentiated pleomorphic sarcoma of the extremity and trunk in response to radiotherapy [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 B27.
Abstract B36: A biomarker-guided approach to combining PARP inhibitors with radiotherapy in pediatric sarcomas
Authors: Shelat Anang A. , Tinkle Christopher L. , Stewart Elizabeth , Federico Sara Michele , Bianski Brandon , Mellado-Lagarde Marcia
Published: August 2018

Background: Ewing sarcoma (EWS) expresses high levels of Schlafen-11 (SLFN11). SLFN11 disrupts checkpoint maintenance and may serve as a biomarker to assess sensitivity to Poly (ADP-ribose) polymerase 1 and 2 inhibitors (PARPi). The goal of this study is to evaluate SLFN11 protein expression in a panel of pediatric solid tumors and correlate levels of protein with sensitivity to PARP inhibition combined with ionizing radiation (IR), a component of therapy for many pediatric sarcomas and a potent inducer of DNA damage.

Methods: SLFN11 mRNA and protein levels were assessed by quantitative RT-PCR, and immunohistochemistry, Western blot, and immunofluorescence microscopy, respectively. PARPi included talazoparib (TAL), niraparib (NIR), veliparib (VEL), and olaparib (OLA). Approximately 30 minutes after addition of systemic therapy, graded doses of radiation were delivered and viability across a panel of pediatric solid tumor cell lines was measured using the ATP-based Cell TiterGlo assay and confirmed with the colony formation assay.

Results: We found that SLFN11 mRNA and protein is expressed at high levels in EWS, and SLFN11 is also variably present in a subset of other pediatric sarcomas, including desmoplastic small round cell tumor, osteosarcoma, and rhabdomyosarcoma. In all tumor cells with detectable SLFN11 expression, viability was reduced by greater than 90% when exposed to 2 Gy IR and 1-10 nM TAL, whereas cells with undetectable levels of SLFN11 were 5-10 times less sensitive. Intriguingly, variation in the potentiation between specific PARPi and IR correlated with the ability to form drug-induced PARP-DNA adducts, with the strong PARP trapper TAL showing ~10-fold higher potency compared to the moderate trapper NIR, and ~300-fold more potency relative to the weak trapper VEL. Consistent with our PARPi findings, the toposiomerase 1 inhibitor irinotecan, which also forms DNA adducts, potentiated with IR similarly to TAL at concentrations <10 nM in tumor cells expressing detectable levels of SLFN11.

Conclusion: SLFN11 is present in select pediatric sarcomas and may induce a DNA repair defect that is best exploited by combining low doses of TAL and irinotecan with IR.

Citation Format: Anang A. Shelat, Christopher L. Tinkle, Elizabeth Stewart, Sara Michele Federico, Brandon Bianski, Marcia Mellado-Lagarde. A biomarker-guided approach to combining PARP inhibitors with radiotherapy in pediatric 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 B36.
Abstract IA01: SWI/SNF (BAF) complex mutations in cancer: Mechanisms and vulnerabilities
Authors: Roberts Charles W. M.
Published: August 2018

Data emerging over the last several years implicate SWI/SNF (BAF) chromatin remodeling complexes as a major tumor suppressor as frequent inactivating mutations in at least nine different SWI/SNF subunits, collectively identified in 20% of all cancers. These include recurrent mutations of ARID1A (BAF250a) in ovarian, endometrioid, bladder, stomach, colorectal and pancreatic cancers and neuroblastoma; of the BRG1 (SMARCA4) subunit in medulloblastomas and non-small cell lung cancers; of the PBRM1 (BAF180) subunit in renal carcinomas; of the ARID2 subunit in hepatocellular, lung, and pancreas carcinomas as well as melanomas; and of the BRD7 subunit in breast cancers. The SWI/SNF complex includes both core and lineage-specific subunits and utilizes the energy of ATP to modulate chromatin structure and regulate transcription.

My laboratory began studying the SWI/SNF complex when SNF5 (SMARCB1/INI1/BAF47) became the first SWI/SNF subunit linked to tumor suppression over fifteen years ago when it was found to be biallelically inactivated in nearly all cases of a highly aggressive type of pediatric cancer called malignant rhabdoid tumor (MRT). Despite the extremely aggressive and lethal nature of MRT, we have shown that these cancers are diploid and have remarkably simple genomes. We now study the complex using mouse models, cell lines, and primary human tumor samples. Insights into the normal function of SWI/SNF complexes, the mechanisms by which mutation of the complexes drive cancer formation, and potential therapeutic vulnerabilities created by mutation of the complex will be presented, including our recent efforts that identify a central role for SWI/SNF complexes in enhancer regulation.

Citation Format: Charles W. M. Roberts. SWI/SNF (BAF) complex mutations in cancer: Mechanisms and vulnerabilities [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 IA01.
Abstract IA02: Modeling sarcoma susceptibility: The Li-Fraumeni syndrome paradigm
Authors: Malkin David
Published: August 2018

The original description of Li-Fraumeni syndrome (LFS) 1969 was generated from the ascertainment of medical and death records of over 600 children with rhabdomyosarcoma. Although the clinical definition of LFS has evolved over the decades, the occurrence of sarcoma in at least one affected TP53 gene mutation carrier is common to many families. However, the genotype:cancer phenotype association of sarcomas in mutation carriers remains poorly understood. This lecture will review some of the phenotypic characterizations of sarcomas in LFS and explore recent exciting advances that suggest a role for various genetic/genomic and epigenetic modifiers of the underlying germline TP53 mutation in defining these clinical phenotypes. The challenges and opportunities to enhance early tumor detection and modify disease risk will also be discussed.

Citation Format: David Malkin. Modeling sarcoma susceptibility: The Li-Fraumeni syndrome paradigm [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 IA02.
Abstract IA04: Targeting the expression of EWS-FLI1
Authors: Sen Nirmalya , Ludwig Katelyn , Rangel-Rivera Guillermo O. , Kim Suntae , Huppi Konrad , Jenkins Lisa , Dwyer Jennifer E. , Hoover Shelley , Helman Lee , Simpson Mark , Mendoza Arnulfo , Hummon Amanda B. , Caplen Natasha J.
Published: August 2018

Post-translational modifications (PTMs) of transcription factors represent potential therapeutic targets for a variety of diseases, including cancer. In the majority of cases of the bone and soft tissue tumor Ewing sarcoma (ES), a chromosomal translocation, t(11:22), results in expression of the fusion transcription factor EWS-FLI1. Few PTMs of EWS-FLI1 have been identified. Using functional genetic methods and mass spectrometry analysis, we have identified a phosphorylated serine residue in the FLI1 domain of EWS-FLI1 that regulates the stability of the EWS-FLI1 oncoprotein. Loss of phosphorylation of this serine residue triggers ubiquitination and proteasomal degradation of EWS-FLI1, and apoptotic cell death. Xenograft studies suggest this post-translational modification of EWS-FLI1 can be targeted in vivo and that this inhibits ES tumor growth.

Citation Format: Nirmalya Sen, Katelyn Ludwig, Guillermo O. Rangel-Rivera, Suntae Kim, Konrad Huppi, Lisa Jenkins, Jennifer E. Dwyer, Shelley Hoover, Lee Helman, Mark Simpson, Arnulfo Mendoza, Amanda B. Hummon, Natasha J. Caplen. Targeting the expression of EWS-FLI1 [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 IA04.
Abstract IA20: Autophagy in alveolar soft part sarcomagenesis
Authors: Jones Kevin B.
Published: August 2018

Altered metabolism is considered to be one of the new hallmarks of cancer. Autophagy is one major avenue of altered cancer metabolism, enabling cell survival under metabolic stress and promoting chemoresistance. The nuclear localization of MiTF/TFE3 family transcription factors has associated with upregulated transcription of autophagy genes in pancreatic cancer. Alveolar soft part sarcoma is a rare but deadly soft-tissue sarcoma, with a predilection for adolescent and young adult victims. Alveolar soft part sarcoma is noteworthy for its resistance to traditional cytotoxic chemotherapies. It consistently associates with a t(X;17) chromosomal translocation that produces the ASPSCR1-TFE3 target gene, bearing the DNA-binding domain from TFE3 and protein interaction domains from ASPSCR1. We have demonstrated that conditional expression of ASPSCR1-TFE3 is sufficient to drive alveolar soft part sarcomagenesis in the mouse with complete penetrance. Mouse tumors recapitulate human alveolar soft part sarcoma histology and transcriptomes faithfully. While direct targets of ASPSCR1-TFE3 have been studied in a renal cell carcinoma cell line, they have not been studied in alveolar soft part sarcoma. We report not only the first genome-wide localization of the ASPSCR1-TFE3 oncoprotein on chromatin from alveolar soft part sarcoma cell lines and mouse tumors, but also its association with actively transcribed genes. Among these are found many genes related to autophagy, especially those related specifically to the nutrient responsive pathways that drive autophagy. We demonstrate high expression of autophagy-related lysosomes and proteins at baseline conditions in human tumors and cell lines and mouse tumors. We also demonstrate active autophagic flux even in the absence of stress conditions. Inhibition of autophagy has no apparent impact on the survival of alveolar soft part sarcoma cells alone, but profoundly impacts their protein degradation pathways and the availability of amino acids for protein assembly in stress. Inhibition of autophagy strongly synergizes with chemotherapy to kill alveolar soft part sarcoma cells, suggesting it was a source mechanism for resistance. We have therefore demonstrated the direct targets of ASPSCR1-TFE3 in alveolar soft part sarcomas, including a number of autophagy genes that are expressed in these tumors, independently from nutrient deprivation or stress, rendering cells particularly resistant to many therapy-induced stresses.

Citation Format: Kevin B. Jones. Autophagy in alveolar soft part sarcomagenesis [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 IA20.
Abstract PR08: Ubiquitin-specific protease 6 (USP6) oncogene confers sensitivity of Ewing sarcoma to interferon cytotoxicity
Authors: Henrich Ian , Young Rob , Quick Laura , Wang Xiaoke , Oliveira Andre , Chou Margaret
Published: August 2018

Our goal is to identify novel targeted therapies for Ewing sarcoma (ES). ES is a devastating malignancy that predominantly affects children and young adults. It is the second most common cancer of the bone, yet in contrast to many other malignancies, survival rates have not improved for decades. For patients with localized disease, no biomarkers exist to predict recurrence or response to chemotherapy. For those with metastatic disease, chemotherapy is largely ineffective, and 5-year survival rates have stagnated at approximately 20%. Thus, there is an urgent need to identify biomarkers that can predict recurrence and response to therapy, as well as identify novel targeted therapies to combat this lethal disease.

USP6 is the key etiologic agent in several benign bone and soft tissue tumors (BSTTs), where its chromosomal translocation results in overexpression. USP6 encodes a deubiquitylating enzyme, and our prior studies identified the tyrosine kinase Jak1 as an essential substrate of USP6 during BSTT development. Jak1 levels are dramatically elevated in USP6-overexpressing cells, leading to phosphorylation and activation of STAT transcription factors.

We recently discovered that USP6 is also highly expressed in multiple sarcomas, including ES. Since Jak1-STATs play a central in mediating response to interferon (IFN), we hypothesized that USP6 might cause dysregulated IFN signaling in ES. Microarray and RNA-sequencing analysis revealed that USP6 by itself induced an IFN-response gene signature, both in immortalized, patient-derived ES cells and in primary human ES tumors. USP6+ ES cells were found to be exquisitely sensitive to exogenous IFN compared to USP6- ES cells, with both prolonged and heightened STAT1 and STAT3 activation observed. Furthermore, IFN selectively induced apoptosis of USP6+ but not USP6- ES cells. Gene expression analysis confirmed that in USP6+ ES cells, IFN synergistically induced expression of numerous IFN-stimulated genes (ISGs), including the pro-apoptotic ligand TRAIL. CRISPR-mediated depletion of TRAIL completely abrogated IFN-induced death of USP6+ ES cells. In sum, these results identify USP6 as a potential novel biomarker that may predict sensitivity of ES to targeted IFN therapy.

This abstract is also being presented as Poster B11.

Citation Format: Ian Henrich, Rob Young, Laura Quick, Xiaoke Wang, Andre Oliveira, Margaret Chou. Ubiquitin-specific protease 6 (USP6) oncogene confers sensitivity of Ewing sarcoma to interferon cytotoxicity [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 PR08.
NOS3 895G>T and CBR3 730G>A Are Associated with Recurrence Risk in Non-Muscle-Invasive Bladder Cancer with Intravesical Instillations of THP
Authors: Zhou Qidong , Ding Weihong , Weng Yingjie , Ding Guanxiong , Xia Guowei , Xu Jianfeng , Xu Ke , Ding Qiang
Published: August 2018

Objectives: To analyze the correlation between pharmacogenomic biomarkers and the efficacy of pirarubicin (THP, also named 4’-O-tetrahydropyranyl-adriamycin) and to explore potential associations of individual genetic backgrounds with the clinical outcomes of non-muscle-invasive bladder cancer (NMIBC) patients. Methods: Between July 2003 and June 2011, a total of 91 patients were treated with transurethral resection (TUR) of the bladder tumor and were histopathologically confirmed to have NMIBC. Patients received an immediate instillation and maintenance therapy with THP. All patients underwent follow-up for recurrence. We genotyped 13 single nucleotide polymorphisms (SNPs) from blood and saliva DNA samples of all patients. Results: The associations of patients’ genotypes with tumor recurrence risks were analyzed by survival analysis. A total of 16 (17.6%) of the 91 patients with NMIBC had tumor recurrences with a median follow-up of 17 months (range, 2–83 months). We confirmed the effect of the European Organization for Research and Treatment of Cancer (EORTC) risk score for predicting tumor recurrence (p = 0.002, log-rank test). We adjusted for the EORTC score and found that 2 SNPs, NOS3 895G>T (rs1799983) (p = 0.02, HR = 4.32, 95% CI, 1.30–14.39, GT+TT vs. GG) and CBR3 730G>A (rs1056892) (p = 0.04, HR = 2.57, 95% CI, 1.07–6.18, GA+AA vs. GG), were significantly associated with a higher recurrence risk after TUR and instillations of THP in NMIBC patients. Conclusions: Our results suggest that NOS3 895G>T and CBR3 730G>A are genetic markers that can be used to predict tumor recurrence in NMIBC patients receiving intravesical instillations of THP. The effects of those 2 SNPs are independent of the EORTC scores. Further studies with larger sample sizes and longer follow-ups are needed to confirm our results.