bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract B01: Alternative splicing as a therapeutic vulnerability in pediatric rhabdomyosarcoma
Authors: Khurshid Safiya , Montes Matias , Roberts Ryan , Rigo Frank , Chandler Dawn S. 
Published: August 2020

Abstract
Rhabdomyosarcoma (RMS) is the most common pediatric soft-tissue sarcoma, and children who present with metastatic disease at the time of diagnosis have a poor prognosis and survival rate. The molecular events distinguishing these tumors are poorly understood. Comprehensive genetic analysis of pediatric RMS samples has revealed that these tumors are “quiet” at the genomic level and have a relatively low mutation rate. Thus, we have turned our attention to the RMS spliceome, the alternatively or aberrantly spliced transcripts, to identify new therapeutic targets. Indeed, recent advances in high-throughput sequencing technologies have uncovered a surprising number of alternatively spliced variants associated with tumorigenesis, implicating regulated splicing in the tumor phenotype. We hypothesize that differentially spliced isoforms provide a novel opportunity to modulate splicing as a therapeutic intervention in these cancers. We have identified two major splicing networks that are altered in response to tumor specific physiologic changes in RMS. We have identified RNA binding protein and their specific cis-regulatory sequence binding sites that control the splicing changes. In collaboration with Ionis Pharmaceuticals, we have designed splice-switching oligonucleotides that target the specific sequences in the pre-mRNA transcript to occlude protein binding and engineer splicing away from the tumorigenic isoforms. The splice switching oligonucleotides (SSOs) have been successful in targeting the desired transcripts to change the splice isoform, repressing RMS cell growth, and preventing migration, invasion, and angiogenesis. We are currently testing the SSOs in RMS xenograft models as well as in genetically engineered mice to assess their efficacy in vivo. Our long-term goal is to understand the role of alternative splicing in cancer and to target pre-mRNA splicing pathway as a therapeutic intervention point. From these studies, we expect to better understand the cellular events that activate alternative splicing in the pathway to tumorigenesis and how to target transcripts for therapeutic benefit in the future. Furthermore, our findings implement a new splice-modulating paradigm for cancer treatment and pioneer a strategy that may be applied throughout the spliceome to treat cancer and provide a new avenue of rational therapy design.
Citation Format: Safiya Khurshid, Matias Montes, Ryan Roberts, Frank Rigo, Dawn S. Chandler. Alternative splicing as a therapeutic vulnerability in pediatric rhabdomyosarcoma [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 B01.
Abstract B16: MECOM dysregulation is associated with poor outcome in pediatric therapy-related myeloid neoplasms
Authors: Lamprecht Tamara , Schwartz Jason R. , Ma Jing , Walsh Michael P. , Klco Jeffery M. 
Published: August 2020

Abstract
Therapy-related myeloid neoplasms (tMN) occur in children as a consequence of cytotoxic therapies used to treat childhood malignancies, are typically resistant to conventional chemotherapies, require hematopoietic cell transplantation as the only curative option, and typically have a dismal prognosis. While the genomic alterations that drive tMN in children have yet to be comprehensively described, alterations involving the MECOM locus have been described in some myeloid neoplasms like tMN. Overexpression of MECOM is associated with poor prognosis in myeloid malignancies, is present in ~10% of adult cases, and occurs at an increased frequency in pediatric AML with KMT2A rearrangements (KMT2Ar). RNA sequencing from a cohort of 56 pediatric tMN cases collected at St. Jude shows that 24 (43%) cases within our cohort express high levels of MECOM (FPKM value &gt;5). In these 24 cases, we identified one with a canonical fusion (RUNX1-MECOM), one with a NUP98 fusion (NUP98-HHEX), and 18 with KMT2Ar. Whole-genome sequencing demonstrated that two of the remaining MECOMHigh cases have a t(2;3)(p21;q26.2) involving MECOM on chromosome 3 and noncoding regions of chromosome 2 adjacent to ZFP36L2, a gene highly expressed in hematopoietic cells. Further, ENCODE data support that this region of the genome is an active enhancer, suggesting a proximity effect in which this enhancer has been hijacked to drive high levels of MECOM expression. The two remaining cases with aberrant and unexplained MECOM expression are currently under evaluation. In our cohort, MECOM expression levels are predictive of a worse outcome (overall survival at 2 years: MECOMHigh=12.5% vs. MECOMLow=40.6%; log rank p&lt;0.01). Although KMT2Ar was frequently present in our cohort 28/56 (50%) and enriched in the MECOMHigh group (MECOMHigh=75% (18/24) vs. MECOMLow=31% (10/32; p&lt;0.01), high MECOM expression did not confer a significant survival difference within the KMT2Ar group (overall survival at 2 years: MECOMHigh=16.7% vs. MECOMLow=40%; log rank p=0.33). In conclusion, we report a large cohort of pediatric tMN and show that high levels of MECOM expression predicts a worse outcome. Additionally, we identify enhancer hijacking as the mechanism through which at least a portion of high MECOM expression may be explained.
Citation Format: Tamara Lamprecht, Jason R. Schwartz, Jing Ma, Michael P. Walsh, Jeffery M. Klco. MECOM dysregulation is associated with poor outcome in pediatric therapy-related myeloid neoplasms [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 B16.
Abstract B28: A cross-species enhancer activity analysis approach to identify the Ewing sarcoma cell of origin
Authors: Grissenberger Sarah , Poetsch Anna , Heinzl Monika , Morelli Luisa , Sheffield Nathan , Popitsch Niko , Kovar Heinrich , Distel Martin 
Published: August 2020

Abstract
Ewing sarcoma is a malignant bone and soft tissue tumor in children and adolescents. In 85% of all cases the formation of Ewing sarcoma is caused by a chromosomal translocation, leading to the expression of the oncogene EWS-FLI1. This aberrant transcription factor is the main driver of the disease and leads to massive transcriptional dysregulation. Although the genetic mechanism driving Ewing sarcoma is well understood, an animal model adequately mimicking the disease is still lacking. One reason why modeling attempts have remained difficult is the elusive cell of origin in Ewing sarcoma. Several cell types including neural crest progenitor cells and mesenchymal stem cells have been proposed, but none of them has yet been confirmed as cell of origin of Ewing sarcoma. Towards identifying this cell of origin, we are currently following a novel cross-species approach by exploring the use of enhancers, which are specifically active in Ewing sarcoma cells, but were not created de novo by EWS-FLI1. Injection of reporter constructs into zebrafish embryos allows for visualization of cell types with activity of the selected enhancers and provides us with cell-of-origin candidate cell types. To investigate which of these candidate cells are permissive for development of Ewing-like tumors, we will also express EWS-FLI1 in these cells. If successful, this approach will not only reveal the Ewing sarcoma cell of origin but also result in a zebrafish Ewing sarcoma model, which will help to understand tumor initiation and progression and, furthermore, will be a valuable tool to develop novel therapeutic strategies.
Citation Format: Sarah Grissenberger, Anna Poetsch, Monika Heinzl, Luisa Morelli, Nathan Sheffield, Niko Popitsch, Heinrich Kovar, Martin Distel. A cross-species enhancer activity analysis approach to identify the Ewing sarcoma cell of origin [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 B28.
Abstract B37: Menin and EWS/FLI1 activate serine biosynthesis via ATF4 in Ewing sarcoma
Authors: Jiménez Jennifer A. , Ruiz Ramon Ocadiz , Apfelbaum April , Kumar Abhijay , Kerk Samuel , Grembecka Jolanta , Lyssiotis Costas A. , Lawlor Elizabeth R. 
Published: August 2020

Abstract
Ewing sarcoma (ES) is an aggressive bone and soft-tissue tumor, most commonly driven by the EWS/FLI1 fusion oncogene. Previous work has revealed that the scaffolding protein menin functions to promote ES tumorgenicity. Additionally, our recent studies revealed a previously undescribed role for menin in the activation of the serine biosynthetic pathway (SSP), a critical metabolic pathway that is aberrantly activated in many human cancers. The transcription factor ATF4 has been identified in other tumor types as a master transcriptional regulator of the SSP. Furthermore, regulation of the SSP by EWS/FLI1 has been described, although the mechanism of this regulation remains unknown. The biologic functions of menin are largely determined by its protein-binding partners, the best characterized of which is MLL in epigenetic trithorax complexes. In the current study, we are investigating the mechanistic link between menin, EWS/FLI1, and SSP hyperactivation to test the hypothesis that, in the context of ES, these transcriptional regulators cooperate to promote metabolic reprogramming via ATF4. Through gain- and loss-of-function studies, our results show that ATF4 regulates the SSP in ES cells, and that loss of ATF4 impairs ES cell proliferation. Additionally, both pharmacologic inhibition with the menin:MLL interaction inhibitor, MI-503, and doxycycline-inducible shRNA knockdown of menin lead to loss of ATF4, coincident with loss of SSP expression. Knockdown of EWS/FLI1 similarly results in loss of both ATF4 and SSP expression. Interrogation of publicly available ChIP-seq data further shows enrichment for EWS/FLI1 binding at the ATF4 gene promoter that is lost with EWS/FLI1 knockdown, and ChIP-qPCR shows menin binding at the ATF4 gene promoter in association with H3K4me3 enrichment. ChIP-qPCR also shows enrichment of ATF4 binding at SSP gene promoters, which is diminished upon menin inhibition with MI-503. Preliminary studies suggest that ATF4 overexpression may rescue the effects of menin loss of function on the SSP. Together these findings support the hypothesis that menin hijacks the SSP via aberrant activation of ATF4, and that this depends on cooperation with EWS/FLI1. Ongoing studies are assessing whether this is mediated by trithorax-dependent or -independent functions of menin.
Citation Format: Jennifer A. Jiménez, Ramon Ocadiz Ruiz, April Apfelbaum, Abhijay Kumar, Samuel Kerk, Jolanta Grembecka, Costas A. Lyssiotis, Elizabeth R. Lawlor. Menin and EWS/FLI1 activate serine biosynthesis via ATF4 in 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 B37.
Abstract B40: EWS-FLI1 orchestrates Ewing sarcoma plasticity through a post-translational modification cascade regulating FOXM1 stability
Authors: Ban Jozef , Aryee Dave , Bierbaumer Lisa , Kovar Heinrich 
Published: August 2020

Abstract
Oscillations between proliferative and migratory/invasive cell states are at the core of the metastatic process. Transition between these states involves reversible shifts in transcriptional programs that orchestrate cytoskeletal remodeling. Ewing sarcoma pathogenesis depends on EWS-FLI1, an aberrant ETS transcription factor that drives cellular transformation and proliferation of presumably mesenchymal progenitor cells. Recently, it has been reported that transient modulation of EWS-FLI1 expression results in an epithelial-to-mesenchymal transition-like phenotype of Ewing sarcoma cells and in increased metastasis (Chaturvedi et al., 2014; Franzetti et al., 2016). It has been proposed that EWS-FLI1 low cells exist in small amounts in primary Ewing sarcoma tumors and thus provide a potential source for tumor dissemination, leading to adverse prognosis. In our studies, we investigate the mechanistic basis of EWS-FLI1 dose-dependent Ewing sarcoma plasticity and recently reported on the activation of an MRTFB/TEAD transcriptional module promoting cytoskeletal reprograming in response to low EWS-FLI1 levels (Katschnig et al., 2016). Here, we show that the proliferative state depends on the activity of nuclear beta-catenin complexed to FOXM1. We find that EWS-FLI1 not only drives FOXM1 expression on the RNA level, but also sustains nuclear FOXM1 stability by a mechanism involving FOXM1 protein demethylation by lysine-specific demethylase 1 (LSD1/KDM1A). Experimental evidence suggests that EWS-FLI1 regulates LSD1 protein stability in Ewing sarcoma cells by directly activating a ubiquitin-specific protease. Modulation of EWS-FLI1 led to loss of expression of the deubiquitinting enzyme (DUB), and consequently to rapid depletion of LSD1 and FOXM1 proteins and subcellular redistribution of beta-catenin to the cytoplasm. Genetic (siRNA) and pharmacologic inhibition of the DUB or LSD1 recapitulated the destabilizing effect on FOXM1 in EWS-FLI1-high Ewing sarcoma cells, blocking tumor cell proliferation. In addition, they led to complete loss of beta-catenin expression by a mechanism that is currently under investigation. Therefore, our study identifies targetable enzymatic activities downstream of EWS-FLI1 that are required to sustain Ewing sarcoma proliferation.
Citation Format: Jozef Ban, Dave Aryee, Lisa Bierbaumer, Heinrich Kovar. EWS-FLI1 orchestrates Ewing sarcoma plasticity through a post-translational modification cascade regulating FOXM1 stability [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 B40.
Abstract B47: Overexpression of TLX3 or HOXA9 in association mutant IL7Rα are sufficient to generate T-ALL in vivo
Authors: Rodrigues Gisele O.L. , Hixon Julie , Winer Hila , Li Wenqing , Durum Scott 
Published: August 2020

Abstract
Background: Mutations of the IL7Rα chain occur in approximately 10% of pediatric T-cell acute lymphoblastic leukemia cases. While we have shown that mutant IL7Rα is sufficient to transform an immortalized thymocyte cell line, mutation of IL7Rα alone was insufficient to cause transformation of primary T cells, suggesting that additional genetic lesions may be present, contributing to initiate leukemia. Studies addressing the combinations of mutant IL7Rα plus TLX3 or HOXA9 overexpression indicate in vitro grow advantage, suggesting these two genes as potential collaborative candidates. Furthermore, patients with mutated IL7Rα were more likely to have TLX3 or HOXA subgroup leukemia.
Objective: We sought to determine whether combination of mutant hIL7Rα plus TLX3 or HOXA9 overexpression is sufficient to generate T-cell leukemia in vivo.
Methods: Double-negative thymocytes were isolated from C57BL/6J mice and transduced with retroviral vectors containing mutant hIL7Rα plus TLX3 or HOXA9. The same combinations were tested for the hIL7Rα wild-type. Transduced thymocytes were cultured on the OP9-DL4 bone marrow stromal cell line for 7-13 days and accessed for driver oncogenes expression and then injected into sublethally irradiated Rag-/- mice. Mice were euthanized at onset of clinical signs, and cells were immunophenotyped by flow cytometry.
Results: Thymocytes transduced with muthIL7Rα-TLX3 showed overexpression of c-Myc and Pim-1. Nonetheless, there was no difference in the protein level expression for these two proteins in either thymocytes transduced with muthIL-7Rα-HOXA9 or in the control wthIL7Rα-TLX3. Mice injected with either muthIL7Ra-TLX3 or muthIL7Rα-HOXA9 cells, but not the controls (wthIL7Rα-TLX3 or wthIL7Rα-HOXA9), developed leukemia approximately 14 days post injection, characterized by GFP-expressing T-cells in blood, spleen, liver, lymph nodes, and bone marrow.
Conclusion: Thymocytes transduced with muthIL7Rα-TLX3 showed c-Myc and Pim-1 upregulation. Cells expressing the combination muthIL7Rα-TLX3 or muthIL7Rα-HOXA9 were sufficient to trigger T-cell leukemia in vivo.
Citation Format: Gisele O.L. Rodrigues, Julie Hixon, Hila Winer, Wenqing Li, Scott Durum. Overexpression of TLX3 or HOXA9 in association mutant IL7Rα are sufficient to generate T-ALL in vivo [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 B47.
Abstract B66: Nutritional intakes are associated with HDL-cholesterol levels in survivors of childhood acute lymphoblastic leukemia
Authors: Morel Sophia , Amre Devendra , Teasdale Emma , Laverdière Caroline , Sinnett Daniel , Levy Emile , Marcil Valérie 
Published: August 2020

Abstract
Background: Survivors of childhood acute lymphoblastic leukemia (cALL) are at high risk of developing dyslipidemia (high LDL-cholesterol, high triglycerides, or low HDL-cholesterol). Studies showed that, similarly to the general population, cALL survivors do not respect dietary guidelines. However, whether nutritional intakes affect the lipid profile of this high-risk population remains unknown. This study aims to examine the associations between macro- and micronutrients and the presence of dyslipidemia in children and young adult survivors of cALL.
Methods: Participants (n=247) survivors of cALL were recruited as part of the PETALE study at Sainte-Justine University Health Center (49.4% boys; median age: 21.7 yrs, range: 8.5-41.0 yrs; median time since diagnosis: 15.2 yrs, range: 5.4-28.2 yrs). Nutritional data were collected using a validated food frequency questionnaire (FFQ) comprising 190 items. Fasting blood was used to determine participants’ lipid profile by enzymatic reactions. Multivariable logistic regression models were fitted to evaluate the associations between intakes of macro- and micronutrients and dyslipidemia. The model included the following covariables: body mass index, age at diagnosis, age at diagnosis2, sex, and total energy intake.
Results: Despite their young age, 41.3% of cALL survivors had dyslipidemia defined by having at least one abnormal lipid value. Specifically, 12.2% had high triglycerides and 17.4% high LDL-cholesterol and 23.1% low HDL-cholesterol. Our analysis revealed that having low HDL-cholesterol was associated with higher intakes in several nutrients (3rd vs. 1st tertile). They were proteins [odd ratio (OR): 0.27, 95%CI: 0.08-0.92, P&lt;0.05], zinc (OR: 0.26, 95%CI: 0.08-0.84, P&lt;0.05), copper (OR: 0.34, 95%CI: 0.12-0.99, P&lt;0.05), selenium (OR: 0.17, 95%CI: 0.05-0.59, P&lt;0.01), niacin (OR: 0.25, 95%CI: 0.08-0.84, P&lt;0.05), riboflavin (OR: 0.24, 95%CI: 0.07-0.84, P&lt;0.05), and vitamin B12 (OR: 0.35, 95%CI: 0.13-0.90, P&lt;0.05).
Conclusion: Our study shows the potential protective role of specific macro- and micronutrients on HDL-cholesterol levels in cALL survivors. These results stress the importance of deepening our understanding of the impact of nutrition in the development of dyslipidemia after cancer treatment. Nutritional strategies could be a valuable approach to prevent long-term cardiometabolic complications in cALL survivors.
Citation Format: Sophia Morel, Devendra Amre, Emma Teasdale, Caroline Laverdière, Daniel Sinnett, Emile Levy, Valérie Marcil. Nutritional intakes are associated with HDL-cholesterol levels in survivors of childhood acute lymphoblastic leukemia [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 B66.
Abstract B67: EGFR as a target in pediatric solid tumors
Authors: Albert Catherine M. , Pinto Navin R. , Rudzinski Erin R. , Park Julie R. 
Published: August 2020

Abstract
The epidermal growth factor receptor (EGFR or HER1) is a cell surface tyrosine kinase receptor that is expressed in a diverse group of epithelial and nonepithelial tissues and broadly associated with cell proliferation and differentiation. Expression of wild-type EGFR and activating mutations are described in many malignancies, including a variety of pediatric solid tumors. In the setting of malignancy, EGFR has been associated with aggressive disease, chemotherapy resistance, and increased metastatic potential. Employment of anti-EGFR agents has yielded some promising results, but they are not always effective against all cancer-associated aberrant EGFR expression and are frequently associated with notable off-tumor toxicities due to the expression of EGFR in normal tissue. The unique EGFR monoclonal antibody (mAb) 806 selectively binds to an epitope on the extracellular portion of human EGFR expressed on the surface of tumor cells. This antibody recognizes the deletion mutant EGFRvIII commonly present in glioblastomas and some other solid tumors as well as wild-type EGFR. We designed a phase I trial for pediatric and young adult patients with recurrent or refractory solid tumors expressing epidermal growth factor (EGFR) to examine the safety and feasibility of administering autologous, peripheral blood-derived T cells that have been genetically modified to express a second-generation (2G) EGFR806-specific chimeric antigen receptor (CAR). Literature review and evaluation of EGFR immunohistochemistry (IHC) performed on several tissue microarrays were used to estimate the percentage of EGFR positivity among common subtypes of pediatric cancer. Using these tools, we hypothesized that 15-40% of otherwise eligible patients would meet the eligibility criteria of EGFR positivity. The trial opened in August of 2018. To date, a total of 33 patient tumors have undergone EGFR IHC to determine eligibility for the trial. 9/33 (27.3%) have been EGFR+. EGFR+ histologies include BCOR fusion sarcoma (3), germ cell tumor (2), osteosarcoma, Ewing sarcoma, desmoplastic small round cell tumor, and synovial sarcoma. Our eligibility testing thus far demonstrates EGFR expression by IHC in a variety of histologies. Two rare diseases, recurrent BCOR fusion sarcoma and refractory germ cell tumors, have demonstrated a significantly higher rate of EGFR IHC positivity, (3/3)100% and (2/3) 66.7%, respectively. These early results indicate that this trial and other anti-EGFR therapies may be most effectively targeted to certain subgroups of pediatric cancer patients.
Citation Format: Catherine M. Albert, Navin R. Pinto, Erin R. Rudzinski, Julie R. Park. EGFR as a target in pediatric solid tumors [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 B67.