bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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.
Abstract B38: Ewing sarcoma regression without GVHD by allo-MHC/CHM1 specific T cells
Authors: Thiel Uwe , Schober Sebastian J. , Einspieler Ingo , Kirschner Andreas , Schirmer David , Gall Katja , Schmidt Oxana , Grunewald Thomas G. P. , Sorensen Poul H. , Richter Guenther H. S. , Luettichau Irene Teichert von , Busch Dirk H. , Burdach Stefan 
Published: August 2018

Abstract
Background: Chondromodulin-I (CHM1) sustains malignancy in Ewing sarcoma (ES). Refractory ES carries a dismal prognosis and patients with bone-marrow (BM) metastases do not survive irrespective of therapy. We assessed HLA-A*02:01/CHM1 specific allorestricted T-cell receptor (TCR) wild-type and transgenic cytotoxic (CD8+) T cells against ES.
Patients and Methods: Three refractory HLA-A2+ ES patients were treated with HLA-A*02:01/peptide specific allorepertoire-derived (i.e., allorestricted) CD8+ T cells. Patient #1 received up to 4.8 x 105/kg body weight HLA-A*02:0 allorestricted donor-derived wild type CD8+ T cells. Patient #2 received up to 8.2 x 106/kg HLA-A*02:01 donor-derived and patient #3 up to 6 x 106/kg autologous allorestricted TCR transgenic CD8+ T cells. All patients were treated with the same TCR complementary determining region 3 allorecognition sequence for CHM1 peptide 319 (CHM1319).
Findings: HLA-A*02:01/CHM1319 specific allorestricted CD8+ T cells showed specific in vitro lysis of all patient-derived ES cell lines. Therapy was well tolerated and did not cause graft-versus-host disease (GVHD). Patients #1 and #3 showed slow progression, whereas patient #2, while having BM involvement, showed partial metastatic regression associated with T-cell homing to involved lesions. CHM1319 TCR transgenic T cells could be tracked in his BM for weeks.
Interpretation: HLA-A*02:01/antigen specific allorestricted T cells proliferate in vivo without causing GVHD. CHM1319 TCR transgenic T cells home to affected BM and are associated with partial disease regression.
Funding: Wilhelm Sander-Stiftung (2006.109.1), Else Kröner-Stiftung (GR & SB; P31/08//A123/07), BMBF (GR, UT and SB, TranSarNet 01GM1104B; SB, PROVABES 01KT1311) and Cura Placida Children's Cancer Research Foundation. PHS is funded by the Excellenzinitiative at TUM/CCC Munich.
Citation Format: Uwe Thiel, Sebastian J. Schober, Ingo Einspieler, Andreas Kirschner, David Schirmer, Katja Gall, Oxana Schmidt, Thomas G. P. Grunewald, Poul H. Sorensen, Guenther H. S. Richter, Irene Teichert von Luettichau, Dirk H. Busch, Stefan Burdach. Ewing sarcoma regression without GVHD by allo-MHC/CHM1 specific T cells [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 B38.
Abstract IA13: Dynamic cell populations are responsible for sarcoma propagating potential
Authors: Tang Jackie , David Kirsch , Alman Benjamin 
Published: August 2018

Abstract
Self-renewal can maintain tumor viability and play a role in recurrence and metastasis, yet little is known about the control of self-renewal in sarcomas. We previously found that cells that exclude Hoechst dye (side population or SP cells) are enriched for tumor propagating potential in serial transplantations in a variety of sarcoma types, and thus might be enriched for renewal capacity. Here we used a mouse in which soft tissue sarcomas were driven by Trp53 deletion and Kras overexpression to trace individual clones of cells. Expression of a confetti allele or expression of barcoding in the Rosa26 locus was used to trace clones. Tumors were observed in situ in the mice, and in serial translations. Intravital microscopy in transplantations of tumors from mice expressing the confetti allele was also undertaken. While there were multiple fluorescent colors in the primary tumors, over time a dominant clone was apparent. This usually arises from a small population of cells in the early tumor. This finding was verified with serial intravital microscopy, as well as tracing the clones using barcoding. SP cells were sorted from the tumors and found to be significantly enriched for tumor propagating potential as demonstrated using serial transplantations. Over multiple transplantations, the fluorescent color expressed by cells that sorted to the SP, and were enhanced for tumor propagating potential, changed. This suggests that the tumor propagating population is dynamic, rather than being limited to a specific clone. Barcoding in additional experiments showed the same result. This was further verified by genetically expressing different-colored fluorescent markers in SP and non-SP cells. While at a given time the SP expressed one fluorescent color, over serial transplantations, they expressed different colors. Taken together, this shows that the small subpopulation of cells that are enhanced for tumor propagating potential are not derived from the same clone, but a dynamic population that changes over time. Similar to findings in human sarcoma SP cells, RNA sequencing data showed that the murine SP cells were enhanced for Wnt and Notch signaling, even in different clones over time from the same initial population. Blocking these pathways suppresses the tumor propagating potential. Thus, epigenetic changes that activate Wnt and Notch in dynamic cell populations derived from different clones in the initial tumor are likely responsible for enhancing tumor propagating potential and for cells to achieve an SP cell phenotype.
Citation Format: Jackie Tang, Kirsch David, Benjamin Alman. Dynamic cell populations are responsible for sarcoma propagating potential [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 IA13.
Abstract IA19: Emerging genetic mechanisms in undifferentiated round cell sarcomas
Authors: Antonescu Cristina 
Published: August 2018

Abstract
Undifferentiated round cell sarcomas (URCS) occurring in pediatric and young adults are defined by a primitive morphology reminiscent of Ewing sarcoma, but lack the canonical EWSR1-ETS gene fusion. More than &gt;90% of EWSR1-negative URCS are instead characterized by either a CIC-DUX4 fusion or a genetic abnormality involving BCOR. The latter group includes intra-chromosomal paracentric inversions (BCOR-CCNB3), inter-chromosomal fusions (BCOR-MAML3), or BCOR internal tandem duplications (ITD). Irrespective of their variable mechanism for dysregulation, the tumors share a similar phenotype and a BCOR upregulation at transcriptional and protein levels. In contrast, CIC-DUX4 URCS are characterized by a distinct transcriptional upregulation of PEA3 transcription factors (ETV1/4/5). For practical and treatment purposes, URCS have been regarded as “Ewing sarcoma-like” and have been managed similarly to the Ewing sarcoma family of tumors, despite their poor chemotherapy responses and aggressive clinical behavior. Alternatively these tumors are grouped by default in an “undifferentiated sarcoma category,” with their clinical management being often biased. Despite the wide spectrum of genetic abnormalities, the unifying concept is that the various gene partners or ITDs disrupt the C-terminal repressor domains of both CIC and BCOR, resulting in an oncogenic transcriptional activation of target genes. In URCS with BCOR ITD, the ITD sequences located at the C-terminal may affect the PUFD domain conformation of the BCOR protein, which might interfere with PCGF1 binding and thus could affect the PRC1-related epigenetic modifications.
Citation Format: Cristina Antonescu. Emerging genetic mechanisms in undifferentiated round cell 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 IA19.
Abstract IA24: Identification of therapies for plexiform neurofibromas, a precursor of malignant peripheral nerve sheath tumors
Authors: Clapp D. Wade 
Published: August 2018

Abstract
Plexiform neurofibromas (PNs) are complex nerve and soft tissue tumors that affect 25-50% of individuals with neurofibromatosis type 1 (NF1), the most common genetic disease in man with a predisposition to cancer. PNs cause lifelong morbidity ranging from deformity to paralysis and mortality due to organ compression, and progress to MPNST in ~8-13% of patients. The generation of genetically engineered mouse models that closely recapitulate the development of human plexiform neurofibromas has allowed our laboratory and others to pursue genetic and pharmacologic studies to identify novel therapies. Genetic and adoptive transfer studies conducted by our lab in collaboration with Dr. Luis Parada identified a key role for c-kit/kit-ligand in tumor initiation and progression. These data led to a clinical trial administering imatinib mesylate to target aberrant stem cell factor (SCF)/c-kit signaling in the tumor microenvironment, which induced the only objective clinical responses ever obtained in a therapeutic clinical trial in pNF. Based on the observation that young children with head, neck, and airway tumors were most likely to have partial tumor regression, a registration trial in this patient population is currently being pursued. Further, additional phase 2 trials using other receptor tyrosine kinases that include c-kit are under way as well. More recently, studies in GEM models informed clinical trials of MEK inhibitors led by Dr. Brigitte Widemann (Pediatric Branch of NCI) to directly inhibit aberrant Ras signaling in PN cells. Studies are ongoing to extend these promising initial clinical findings to investigate the developmental, molecular, and pharmacokinetic effects of c-kit and MEK inhibition alone and in combination in preclinical models. Specifically, studies to explore adaptive responses to MEK inhibition monotherapy in mice and patients treated with selumetinib via integrated exome, RNAseq, and kinome studies in pre- and post-treatment tumor tissue are under way.
Citation Format: D. Wade Clapp. Identification of therapies for plexiform neurofibromas, a precursor of malignant peripheral nerve sheath tumors [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 IA24.