bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract A64: Functional genomics of metastatic Ewing sarcoma
Authors: Jawhar Wajih , Waterhouse Paul , Khokha Rama , Ishii Takeaki , Turcotte Robert , Jabado Nada , Garzia Livia 
Published: August 2020

Abstract
Ewing sarcoma (ES) is a poorly differentiated bone and soft tissue tumor of high metastatic potential. ES mainly affects children, adolescents, and young adults (AYAs) at a frequency of ~1.5 cases per million globally. Ewing neoplasms strikingly converge on a single recurrent initiating event, which is a chromosomal translocation that generates a fusion transcript between the EWSR1 gene and a gene of the ETS family of transcription factors, most commonly FLi1 (85%). After 20 years since the discovery of the EWS-FLi1 fusion, ES remains a clinical challenge with unacceptably low survival rates, primarily due to metastasis. The bulk of research conducted to date (&gt;95%) being focused on the primary tumor has resulted in a critical knowledge gap. To address this issue and unravel the dysregulated pathways in ES tumor evolution and metastatic dissemination, we harnessed the genome-wide insertional mechanism of transposons and the transduction efficiency of lentiviruses to engineer ES cell models. Human mesenchymal stem cells (hMSC), the putative cells of origin of ES, were engineered to constitutively express EWS-Fli1 accompanied by the inducible expression of a highly active transposase. Upon activation of the former, transposon-mediated mutagenesis will activate oncogenes and inactivate tumor suppressor genes, to mediate transformation of the transduced that can now engraft when implanted in recipient mice. Xenografted tumors are resected and the mice observed for development of distant metastases. Matching primary and metastatic tumors are sequenced to uncover the genes commonly affected by transposition in the two compartments. Pathway-oriented bioinformatic analysis will further reveal candidate metastatic driver genes. Matching of the targeted pathways with drugs will be used to validate the candidates by in vitro and in vivo metastasis assays.
Citation Format: Wajih Jawhar, Paul Waterhouse, Rama Khokha, Takeaki Ishii, Robert Turcotte, Nada Jabado, Livia Garzia. Functional genomics of metastatic Ewing sarcoma [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr A64.
Abstract A65: Alveolar soft part sarcoma in children and adolescents: A single-institute retrospective analysis
Authors: Kang Se Na , Choi Jung Yoon , Kim Bo Kyung , Ahn Hong Yul , Hong Kyung Taek , Kang Hyoung Jin , Kim Han Soo , Cheon Jung Eun , Park Sung Hye , Shin Hee Young 
Published: August 2020

Abstract
Background: Alveolar soft part sarcoma (ASPS) is a rare soft tissue tumor that typically affects young patients. Because of the rarity of the disease, the standard treatment is not established. The aim of this study is to evaluate the clinical characteristics and treatment outcomes of pediatric ASPS.
Method: A retrospective study was conducted on children and adolescents treated for ASPS at a single center between 2000 and 2018.
Results: A total number of 11 patients were evaluated. Median age at diagnosis was 12.6 (range 3.8-16.3) years. Nine (82%) were female. The most common primary sites were limbs (64%). IRS postsurgical clinical group (IRS CG) was I in 2 (18%), III in 3 (27%), and IV in 6 (55%) patients. Of 9 patients with IRS CG III and IV who received chemotherapy, one had a complete response, two had a partial response, and six had progressive disease. One patient showed SD to sunitinib. The 5-year event-free survival (EFS) and overall survival (OS) rates were 31% and 88%, respectively. The 5-year EFS rate by primary site was 50% for the 7 patients with extremity and 0% for the 4 patients with head and neck (P-value = 0.001). The 5-year OS rate by the primary site was 100% for the 7 patients with extremity and 50% for the 4 patients with head and neck (P-value = 0.027).
Conclusion: Localized ASPS has a good prognosis after total resection. If the primary site is head and neck, the prognosis is poor due to difficulty in surgical resection. Chemotherapy and radiation therapy have limitations in the cure for patients with metastatic disease. Further studies of ASPS need to achieve development in treatment.
Citation Format: Se Na Kang, Jung Yoon Choi, Bo Kyung Kim, Hong Yul Ahn, Kyung Taek Hong, Hyoung Jin Kang, Han Soo Kim, Jung Eun Cheon, Sung Hye Park, Hee Young Shin. Alveolar soft part sarcoma in children and adolescents: A single-institute retrospective analysis [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr A65.
Abstract A77: Targeting lymphocyte exclusion in metastatic osteosarcoma
Authors: Sorenson Laurie , McEachron Troy A. 
Published: August 2020

Abstract
Osteosarcoma (OS) is the most common bone tumor in pediatric and adolescent/young adult patients. Over the past three decades, significant improvements in the survival rates or therapeutic approaches for these patients have not been made, especially in the context of metastatic disease. While immune checkpoint blockade has revolutionized the therapeutic landscape in various adult malignancies, its impact in OS has been largely underwhelming. Currently, it is unknown whether the lack of therapeutic benefit of immune checkpoint inhibition observed in patients with OS is truly due to treatment inefficacy rather than a limited understanding of the tumor microenvironment that supports this aggressive disease. To address this knowledge gap, we have performed targeted gene expression profiling of metastatic and nonmetastatic osteosarcoma specimens. Our data demonstrate that T cells are largely excluded from the metastatic specimens and that this exclusion significantly correlates with markers of vascular instability. In a pathologic setting, such as that of cancer, VEGF and ANG2 signaling promote vascular instability, which limits leukocyte extravasation and subsequent tumor infiltration. Our data suggest that vascular destabilization mediated by VEGF/ANG2 signaling impedes T-cell infiltration specifically in metastatic OS and identify these molecules as potential targets for therapeutic intervention.
Citation Format: Laurie Sorenson, Troy A. McEachron. Targeting lymphocyte exclusion in metastatic osteosarcoma [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr A77.
Abstract B08: Beyond synthetic lethality: Multiple mechanisms can explain genetic interactions within childhood cancer
Authors: Daub Josephine T. , Amini Saman , Holstege Frank C.P. , Kemmeren Patrick 
Published: August 2020

Abstract
Even though the survival rate of childhood cancer has increased in the last decades to around 80% today, it is still a leading cause of death for children in developed countries. Cancer develops through the acquisition of multiple mutations, and it is assumed that genetic interactions between mutated genes play an important role in cancer onset and progression. One approach to find genetic interactions in cancer is to search for pairs of mutated genes that occur more (or less) often than expected given the frequency of the individual mutated genes. Highly co-occurring mutated genes suggest a cooperative role of these altered genes in cancer development. Mutually exclusive gene pairs can be a signal of synthetic lethality, where the combination of the two mutations is lethal for the cancer cells, and could therefore point to possible cancer treatments. We developed a statistical pipeline, based on two genetic interaction tests, to detect significant cases of co-occurrence and mutual exclusivity in two pediatric cancer data sets, comprising over 2,500 tumors from 23 cancer types. In total we detect 15 co-occurring and 26 mutually exclusive candidate genetic interactions. Nearly all candidate gene pairs are uniquely found in one cancer type, supporting earlier findings that genetic interactions are often cell or cancer type specific. Interestingly, we find that synthetic lethality is not the main cause of the mutual exclusivity patterns in our data set. The majority of these patterns can be attributed to cancer subtypes and within pathway relationships, where the effect of a mutated gene is similar to mutating a (downstream) gene in the same pathway. This initial map of genetic interactions in childhood cancer provides a solid starting point to select suitable candidates for experimental validation as well as extending the analyses to investigate the contribution of genetic interactions towards structural variants, genetic predisposition, and cellular pathways.
Citation Format: Josephine T. Daub, Saman Amini, Frank C.P. Holstege, Patrick Kemmeren. Beyond synthetic lethality: Multiple mechanisms can explain genetic interactions within childhood cancer [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr B08.
Abstract B09: Epigenetic changes mediated by H3.3 G34R mutation in a CRISPR-edited pediatric glioblastoma cell line
Authors: Deshmukh Shriya , Chen Carol C.L. , Ouanouki Amira , Jabado Nada 
Published: August 2020

Abstract
Background: Pediatric glioblastomas (pGBM) are aggressive and lethal brain tumors with few effective treatment options. Since the discovery of recurrent histone H3 mutations in pGBMs, multiple groups have sought to uncover the mechanism by which these mutations drive tumorigenesis. One striking aspect of histone H3 mutations is their tumor location and age-specificity: the K27M mutation occurs in midline brain structures in infants and young children, whereas the G34R/V mutations occur in the cerebral hemisphere of adolescents. Efforts to elucidate the mechanism underlying K27M tumorigenesis have centered on K27M-mediated inhibition of the PRC2 complex and the resulting drastic loss of the repressive H3K27me3 mark in these tumors. Studies have shown that G34 mutations affect methylation of the adjacent K36 residue, resulting in a local decrease of the active H3K36me3 mark on the mutant histone. It remains uncertain whether the G34R/V mutations promote global changes in the epigenome that drive tumorigenesis.
Methods: To investigate the epigenetic consequences of the G34R mutation, we generated an isogenic in vitro model using CRISPR/Cas9 to correct the G34R mutation in a pGBM-derived cell line. We then comprehensively characterized and compared the epigenome and transcriptome of CRISPR-unedited clones (carrying the G34R mutation) and CRISPR-edited (wild-type) clones. Using ChIP-seq, we profiled H3K36me3 and H3K27me3 marks to study G34R-mediated regulation of these antagonistic marks.
Results: ChIP-seq profiling revealed that CRISPR editing of the G34R mutation had minimal effects on total levels or genomic distribution and profile of H3K36me3 and H3K27me3 marks. In contrast, we previously showed that CRISPR editing of the K27M mutation in pGBM cell lines rescued total H3K27me3 levels and genomic distribution to that of histone wild-type pGBMs. In agreement with their similar epigenetic profiles, there were very few transcriptomic differences between G34R and wildtype cells.
Conclusions: Our results suggest that the epigenome in G34R-mutant pGBM cells may be less dynamic or amenable to epigenetic perturbation from removal of the initial driver oncomutation than K27M-mutant tumors. These findings underscore that different strategies may be required to target and treat G34R and K27M-mutant pGBM tumors.
Citation Format: Shriya Deshmukh, Carol C.L. Chen, Amira Ouanouki, Nada Jabado. Epigenetic changes mediated by H3.3 G34R mutation in a CRISPR-edited pediatric glioblastoma cell line [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr B09.
Abstract B17: A C19MC-LIN28A-MYCN oncogenic circuit driven by hijacked super-enhancers is a distinct therapeutic vulnerability in ETMRs—a lethal brain tumor
Authors: Mumal Iqra , Sin-Chan Patrick , Suwal Tannu , Singh Irtisha , Li Xiao-Nan , Lin Charles , Mack Stephen , Rich Jeremy , Huang Annie 
Published: August 2020

Abstract
Embryonal tumors with multilayered rosettes (ETMRs) are distinctly challenging brain tumors of infants and very young children, with characteristic rapid progression and only 10-20% overall survival. ETMRs have characteristic amplification of Chr19q13.41 miRNA cluster (C19MC) and enrichment of pluripotency factor LIN28A. Since the discovery of C19MC, an embryonic stem cell-enriched, primate specific miRNA cluster, as a disease marker of ETMR, there has been limited progress in biologic and therapeutic understanding of this disease. In prior studies we demonstrated single C19MC oncomiRs promotes oncogenesis and inhibit neural differentiation, yet the specific mechanisms of C19MC remains unclear. Here we show expression of 5-C19MC oncomiRs cooperatively inhibits multiple cell cycle checkpoint tumor suppressors to drive cellular proliferation. We further show that C19MC oncomiRs activate a potent oncogenic circuit by upregulating MYCN and LIN28A via downregulation of RNA binding protein, Tristetraprolin. Using RNA-IP analyses, we uncovered epigenetic regulators as major targets of LIN28A and showed that LIN28A directly regulates expression of embryonic-neural DNMT3A2 and DNMT3B6 isoforms. Deep epigenetic mapping on primary tumors revealed high DNA-DNA interactions and enhancer hijacking focused on MYCN. We also discovered tumors with TTYH1-C19MC gene fusions harbored a novel hybrid super-enhancer. Lastly, super-enhancer analysis revealed MYCN/MAZ as major transcriptional regulators and that treatment with a potent MYCN and bromodomain inhibitor JQ-1 inhibited proliferation of primary cells. Collectively, our data reveal that tumor-specific genomic and epigenomic alterations of C19MC entrap and drive multiple feed-forward loops to fuel a potent C19MC-LIN28A-MYCN oncogenic circuit, that can be powerfully abrogated by bromodomain inhibitors. Our findings underscore C19MC as a critical oncogene in ETMRs and provide critical therapeutic insights and a framework for developing high-fidelity models for this orphan disease.
Citation Format: Iqra Mumal, Patrick Sin-Chan, Tannu Suwal, Irtisha Singh, Xiao-Nan Li, Charles Lin, Stephen Mack, Jeremy Rich, Annie Huang. A C19MC-LIN28A-MYCN oncogenic circuit driven by hijacked super-enhancers is a distinct therapeutic vulnerability in ETMRs—a lethal brain tumor [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr B17.
Abstract B19: Identification of physiologically relevant EWS-FLI1 target genes in Ewing’s sarcoma via CRISPRa screening
Authors: Saratov Vadim , Ngo Qui A. , Pedot Gloria , Niggli Felix K. , Schaefer Beat W. 
Published: August 2020

Abstract
Ewing’s sarcoma is an aggressive pediatric bone and soft-tissue cancer with a pathognomonic chromosomal translocation t(11;22) resulting in expression of EWS-FLI1, an “undruggable” fusion protein acting as a transcriptional modulator. Identification and ranking of repressed EWS-FLI1 target genes essential for cancer cell survival will potentially provide much-needed insights to develop novel therapeutic strategies. We performed a CRISPR activation (CRISPRa) dropout screen in Ewing cells. We generated a clonal SKNMC cell line homogenously expressing the synergistic activation mediator (SAM) CRISPRa system to functionally interrogate repressed EWS-FLI1 target genes. The systems functionality was tested using CD44, a surface marker absent on the surface of Ewing cells. We found robust and stable expression of CD44 after introduction of promoter-targeting gRNAs. The library of repressed EWS-FLI1 target genes, named LIBerty, was constructed to target 872 genes bioinformatically selected from publicly available silenced EWS-FLI1 RNA-Seq datasets as well as genes identified as repressed signature genes in Ewing’s sarcoma via meta-analysis with 3,777 unique guideRNAs. LIBerty was lentivirally delivered into SAM SKNMC cells and data from four biologic replicates were gathered at three time points: three, ten, and 21 days after infection. Cells were harvested and samples were prepared for next-generation sequencing (NGS) via PCR. The NGS data were evaluated with the analysis tool PinAPL-Py. Preliminary analysis of the screen revealed efficient selection of the positive control genes BAD and BBC3. In addition, high-ranking hits included CDKN1A and CDKN1C, both cell cycle regulators and known tumor-suppressor genes. Furthermore, we identified PCDH7 and TGFBR2, two genes already known from the literature to play a role in Ewing’s sarcoma. The presence of validated genes amid highest-ranking candidates confirms robustness of the conducted CRISPRa screen. Further analysis and validation of previously unexplored targets and pathways is currently ongoing. Our CRISPRa screen revealed both known as well as previously unknown EWS-FLI1 repressed genes whose absence of function is essential for tumor cell survival.
Citation Format: Vadim Saratov, Qui A. Ngo, Gloria Pedot, Felix K. Niggli, Beat W. Schaefer. Identification of physiologically relevant EWS-FLI1 target genes in Ewing’s sarcoma via CRISPRa screening [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr B19.
Abstract B34: Cord blood CD34+ HSPCs: An in vitro model system for characterizing NUP98 fusions
Authors: Hiltenbrand Ryan , Miller Jonathan , Klco Jeffery 
Published: August 2020

Abstract
Chromosomal translocations of the Nucleoporin 98 gene (NUP98) are associated with multiple hematopoietic malignancies. In particular, NUP98 rearrangements can be found in up to 6.6% of de novo cases of pediatric AML. Specific subpopulations of pediatric AML appear to be even more enriched for NUP98 fusions, with over 16% of cytogenetically normal pediatric AML patients and 15% of non-Down syndrome acute megakaryoblastic leukemia (AMKL) patients harboring these fusions. Clinically, the NUP98-KDM5A fusion is associated with erythroid and megakaryocytic leukemias while the NUP98-NSD1 fusion is associated with myelomonocytic leukemias. When NUP98 fusions are present in AML, they confer a poor prognosis. To better characterize the role of these fusions in human hematopoiesis, we used cord blood CD34+ (cb-CD34+) hematopoietic stem and progenitor cells (HSPCs) as an in vitro model system. We transduced cb-CD34+ HSPCs with NUP98-NSD1, NUP98-KDM5A, or empty vector control and studied the effects on cell proliferation and differentiation in liquid culture media containing cytokines (IL-6, FLT3-Ligand, SCF, TPO, and SR1 (an aryl hydrocarbon receptor antagonist)). NUP98-NSD1 and NUP98-KDM5A fusions increase the proliferation rate in liquid culture by three-fold and 19-fold, respectively (p&lt;0.05). Consistent with observations from patients with these fusions, cells expressing NUP98-KDM5A have increased expression of CD235A and CD71, consistent with erythroid differentiation (p&lt;0.05). In addition, cells expressing NUP98-NSD1 have increased expression of CD11b compared to NUP98-KDM5A (p&lt;0.01) expressing cells. When placed in methylcellulose, the NUP98 fusions tested had no effect on total colony number, but we observed more erythroid differentiation for NUP98-KDM5A compared to vector control (p&lt;0.05). Overall, the results of these in vitro studies demonstrate increased proliferation and inhibition of differentiation in HSPCs by NUP98 fusions, and cell differentiation patterns parallel the different AML subtypes observed in patients with NUP98-NSD1 and NUP98-KDM5A fusions. We propose cbCD34+ HSPCs as a promising system for in vitro modeling of NUP98 fusions.
Citation Format: Ryan Hiltenbrand, Jonathan Miller, Jeffery Klco. Cord blood CD34+ HSPCs: An in vitro model system for characterizing NUP98 fusions [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr B34.
Abstract B36: A novel model of osteosarcomagenesis reveals dysregulation of oxidative phosphorylation
Authors: Jewell Brittany E. , Xu An , Zhou Ruoji , Zhu Dandan , Lu Linchao , Zhao Ruying , Wang Lisa L. , Lee Dung-Fang 
Published: August 2020

Abstract
The purpose of this study is to develop a new model to study osteosarcoma in order to elucidate cellular pathways important in osteosarcomagenesis that are potential therapeutic targets. Osteosarcoma is the most common bone malignancy in childhood and early adolescence. Thirty percent of patients with the rare genetic disorder Type II Rothmund-Thomson syndrome (RTS) develop osteosarcoma. Patients with RTS have biallelic mutations in the RECQL4 gene, which encodes an ATP-dependent DNA helicase. Unfortunately, many attempts to model RTS-associated osteosarcoma have not been successful. Here, we describe a patient-derived induced pluripotent stem cell (iPSC) model capable of recapitulating the process of osteosarcomagenesis. Briefly, RTS patient fibroblasts are reprogrammed to iPSCs, then subsequently differentiated to mesenchymal stem cells. These cells are validated and further differentiated to early and late osteoblasts, the potential precursors of osteosarcoma. Because the iPSC-derived osteoblasts retain the genetic fidelity of the patient from which they were derived, we believe these cells are the ideal model to study the molecular mechanism associated with RTS-associated osteosarcoma. Utilizing the patient-derived osteoblasts, we have performed RNAseq and subsequent GSEA analyses to explore the transcriptome of RTS osteoblasts and found the dysregulation of oxidative phosphorylation in RTS osteoblasts. Interestingly, it has been reported that specific vacuolar ATPases are upregulated in patient cells. It has been reported that vacuolar ATPases function to increase proton concentration within the mitochondria and also within the extracellular environment. Understanding key mechanisms of osteosarcomagenesis is critical to making steps toward novel therapeutics.
Citation Format: Brittany E. Jewell, An Xu, Ruoji Zhou, Dandan Zhu, Linchao Lu, Ruying Zhao, Lisa L. Wang, Dung-Fang Lee. A novel model of osteosarcomagenesis reveals dysregulation of oxidative phosphorylation [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr B36.