bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract B46: CATACOMB: An endogenous inducible gene that antagonizes H3K27 methylation activity of Polycomb Repressive complex 2 via a H3K27M-like mechanism
Authors: Piunti Andrea , Smith Edwin , Morgan Marc , Ugarenko Michal , Khaltyan Natalia , Helmin Kathryn , Ryan Caila , Murray David , Rickels Ryan , Yilmaz Bahar , Rendleman Emily , Savas Jeffrey , Singer Benjamin , Bulun Serdar , Shilatifard Ali 
Published: August 2020

Abstract
Dysregulation of Polycomb Repressive Complex 2 (PRC2) function is a common feature of many cancer types, including both solid and hematologic malignancies. A number of chromosomal translocations involving Polycomb group proteins have been identified; however, the molecular function of these fusion proteins remains largely unexplored. Here we characterize two endometrial stromal sarcoma (ESS) associated fusion proteins: JAZF1-SUZ12 and MBTD1-CXORF67. We identify JAZF1 as a previously unreported subunit of the NuA4 complex, which when fused to SUZ12 creates a bridge between the NuA4 and PRC2 complexes. Intriguingly, the MBTD1-CXORF67 fusion binds to PRC2 and leads to strongly reduced levels of the PRC2 catalytic products H3K27me2/3. We demonstrate that this inhibitory function is mediated by the CXORF67 half of the fusion protein. Because of this striking property, we propose a new gene name: CATACOMB (CATalytic Antagosnist of polyCOMB; official gene name: EZHIP). We map CATACOMB’s inhibitory function to a short, highly conserved region and identify a single methionine residue essential for diminution of H3K27me2/3 levels. Remarkably, the amino acid sequence surrounding this critical methionine resembles that of the oncogenic histone H3 lysine-27-to-methionine (H3K27M) mutation found in high-grade pediatric gliomas. Finally, we show CATACOMB expression is silenced through DNA methylation and upon treatment with DNA demethylating agents, CATACOMB is expressed, binds to PRC2, and antagonizes its catalytic activity. In conclusion, we have identified an endogenous inducible gene, CATACOMB, which can regulate the catalytic activity of PRC2 and propose that such mechanism of regulation of histone modifications through the expression of antagonistic subunits may also exist for other histone-modifying enzyme complexes.
Citation Format: Andrea Piunti, Edwin Smith, Marc Morgan, Michal Ugarenko, Natalia Khaltyan, Kathryn Helmin, Caila Ryan, David Murray, Ryan Rickels, Bahar Yilmaz, Emily Rendleman, Jeffrey Savas, Benjamin Singer, Serdar Bulun, Ali Shilatifard. CATACOMB: An endogenous inducible gene that antagonizes H3K27 methylation activity of Polycomb Repressive complex 2 via a H3K27M-like mechanism [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 B46.
Abstract B49: Modeling a pathogenic SAMD9 mutation in human induced pluripotent stem cells
Authors: Schwartz Jason R. , Connelly Jon P. , Pruett-Miller Shondra M. , Klco Jeffery M. 
Published: August 2020

Abstract
Germline mutations in SAMD9 are the molecular determinants of some pedigrees with familial monosomy 7 and myelodysplastic syndrome (MDS) (OMIM 252270), MIRAGE syndrome (myelodysplasia, infection, restriction of growth, adrenal hypoplasia, genital phenotypes, enteropathy), and other nonsyndromic pediatric MDS. Mutations identified thus far have been associated with decreased growth of hematopoietic stem and progenitor cells (HSPCs) and bone marrow hypocellularity. Previous studies suggest that the wild-type function of SAMD9 is growth restrictive; therefore, the mutations identified in pediatric MDS have been deemed gain-of-function (GoF), given the exaggerated antiproliferative phenotype demonstrated in overexpression systems within nonhematopoietic cell lines, most commonly HEK-293T. To date, no model systems are available to study the impact of these mutations in their endogenous locus, a locus known to be induced by inflammatory stimuli, namely interferon (IFN). Here we report our development, using CRISPR/Cas9 genomic engineering, of two separate isogenic human induced pluripotent stem cell (iPSC) lines, derived from a non-neoplastic iPSC line (BJFF.6), containing a known pathogenic SAMD9 mutation (c.3406G&gt;C; p.E1136Q), which we previously identified in a family with monosomy 7 and MDS. From this mutated iPSC line we are able to successfully differentiate hematopoietic precursors and myeloid cells that contain a pathogenic SAMD9 mutation. Using our novel pediatric MDS model system, we demonstrate that in the presence of IFN, viability of HSPCs (CD34+) and differentiated myeloid cells (CD13+) is significantly decreased when the SAMD9 p.E1136Q mutation is present (CD34+; WT=16.7% vs Mut=11.5% (p=0.05), CD13+; WT=22.6% vs. Mut=3.5% (p&lt;0.0001)). Furthermore, we show that the genomically engineered SAMD9 locus of our iPSC-derived CD34+ and CD13+ cells remains robustly responsive to IFN stimulation. The basal level of SAMD9 expression is higher in differentiated myeloid cells than in HSPCs, a finding consistent with expression levels within normal hematopoiesis. These data suggest that we have a SAMD9 mutant pediatric MDS model system that provides a plentiful source of cells in which the effect of specific mutations on hematopoietic differentiation, proliferation, and viability may be investigated.
Citation Format: Jason R. Schwartz, Jon P. Connelly, Shondra M. Pruett-Miller, Jeffery M. Klco. Modeling a pathogenic SAMD9 mutation in human induced pluripotent stem cells [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 B49.
Abstract B52: Ewing sarcoma: A case study of clonal aneuploidy and DNA damage repair in pediatric cancer
Authors: Su Xiaofeng A. , Ma Duanduan , Parsons James V. , Replogle John M. , Amatruda James F. , Whittaker Charles A. , Stegmaier Kimberly , Amon Angelika 
Published: August 2020

Abstract
Many tumor types harbor specific chromosome gains or losses. In Ewing sarcoma (ES) chromosome 8 gain is extremely common, indicating that this trisomy drives tumorigenesis. However, in primary cells, whole chromosome gains and losses are universally detrimental. We hypothesize that gain of chromosome 8 suppresses cellular stresses associated with oncogenic transformation in ES. In this study, we induced expression of EWS-FLI1 fusion oncogene, which drives ES, in various primary human mesenchymal progenitor and fibroblast cells. We showed that expression of EWS-FLI1 results in a strong cell cycle-dependent replication stress in euploid mesenchymal progenitor cells and fibroblast cells. As a consequence, proliferation is impaired when EWS-FLI1 is expressed in these cells. However, primary fibroblast cells carrying an extra copy of chromosome 8 (trisomy 8) exhibit much less replication stress, and the impairment of proliferation was also not seen in these cells. The levels of replication-associated DNA damage are lower in the trisomy 8 cells than in the euploid cells in the presence of EWS-FLI1. Then, we applied weighted co-expression network analysis (WGCNA) to RNA sequencing data obtained from ES patient tumor tissues in combination of mouse synteny analysis. We identified multiple potential genes and regions on chromosome 8, which are beneficial to ES oncogenesis when gain of extra copies. Above all, we demonstrate that gain of chromosome 8 in Ewing sarcoma facilitates the primary mesenchymal-lineage cells to overcome certain oncogenic stresses and reduces DNA damage associated with tumorigenic processes, which is achieved by cooperative upregulation of multiple gene expression on chromosome 8.
Citation Format: Xiaofeng A. Su, Duanduan Ma, James V. Parsons, John M. Replogle, James F. Amatruda, Charles A. Whittaker, Kimberly Stegmaier, Angelika Amon. Ewing sarcoma: A case study of clonal aneuploidy and DNA damage repair in pediatric 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 B52.
Abstract B54: Enhancer reprogramming by ASPSCR1-TFE3 in alveolar soft part sarcoma
Authors: Tanaka Miwa , Nakamura Takuro 
Published: August 2020

Abstract
Alveolar soft part sarcoma (ASPS) predominantly affects 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 frequent hematogenous metastasis. As for gene abnormality, the ASPSCR1-TFE3 (AT3) fusion is invariably observed in all ASPS cases with low genetic mutational burdens. To understand the functional roles of AT3 in ASPS development, we have generated an ex vivo mouse model for ASPS that well recapitulates its phenotypes. TFE3 belongs to the MiT/TFE (TFE3/TFEB/TFEC/MITF) gene family encoding bHLH/leucine zipper transcription factors, all of which share common DNA-binding domains and consensus DNA-binding motifs. Mutations or overexpression of MiT/TFE family genes trigger human malignancies including ASPS, renal cell carcinoma (RCC), and malignant melanoma (MM). To address whether AT3 possesses a specific potency to induce ASPS, we have generated artificial chimeras between ASPSCR1 and MiT/TFE family genes and have revealed that only TFE3 and TFEB could induce ASPS in vivo whereas the others could not. To get insights into the role of AT3 in enhancer reprogramming that affects tumor phenotypes, we investigated the epigenetic landscape of ASPS. ChIP-seq analyses of human and mouse ASPS showed frequent overlapping of AT3 DNA-binding with histone H3K27ac and H3K4me3 at target loci, indicating that AT3 frequently binds to active enhancers. Among them, canonical MiT/TFE target genes involved in the autophagy, lysosome/endosome and vesicle/protein transport, and mTOR signaling pathways were significantly enriched. Analysis of dataset from GEO revealed that these loci were common targets of MiT/TFE transcription factors activated in human ASPS, RCC, and MM. To identify the AT3-specific and/or AT3-dependent enhancer reprograming mechanism, we focused on super-enhancers (SEs) that determine the cell identity and characteristic phenotypes of ASPS, and examined its modification by AT3. Frequent association of SEs with genes for vasculogenesis and apoptosis were observed in ASPS but not in MM, and AT3 depletion in ASPS resulted in disappearance of these SEs, suggesting that AT3 contributes to chromatin remodeling to promote vasculogenesis required for its alveolar structure and growth expansion. Taken together, our study provides novel aspects on common oncogenic pathways regulated by MiT/TFE family tumor in ASPS, RCC, and MM as well as AT3-specific regulatory mechanism in ASPS, which will offer potential therapeutic targets and biomarkers.
Citation Format: Miwa Tanaka, Takuro Nakamura. Enhancer reprogramming by ASPSCR1-TFE3 in alveolar soft part 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 B54.
Abstract B61: Improvement of physical activity training in childhood acute lymphoblastic leukemia survivors: New specific equation to predict the peak oxygen uptake from the six-minute walk test
Authors: Caru Maxime , Labonté Jennifer , Lemay Valérie , Drouin Simon , Bertout Laurence , Andelfinger Gregor , Alos Nathalie , Krajinovic Maja , Laverdière Caroline , Sinnett Daniel , Curnier Daniel 
Published: August 2020

Abstract
Purpose: The six-minute walk test (6MWT) is the most widely used test to assess the functional capacity of cancer patients. However, it is reported that the actual equations cannot accurately predict oxygen uptake (VO2 value) or walk distance (6MWD) in cancer survivors. Because of the importance for clinicians and physiologists to have a validated VO2 or 6MWD equation from the 6MWT to observe the predicted survivors’ value, we focused on the validation of a standard and specific equation to predict VO2 peak and 6MWD.
Methods: A total of 200 survivors were enrolled in this study, among whom 168 participants underwent a cardiopulmonary exercise test and a 6MWT. They also completed a physical activity questionnaire. Participants were randomly divided in two groups to predict the equations (n=118 (70%)) and to validate them (n=50 (30%)). Multiple linear regression analyses were used to determine a new prediction equation for VO2 peak and 6MWD from 6MWT. Bland and Altman methods were used to assess the accuracy.
Results: Our findings showed that without specific variables in the VO2 peak equation, the mean bias was of 2.67 mL.kg-1.min-1 and of 2.51 mL.kg-1.min-1 with specific variables. We observed a better accuracy compared to previously published equations, which reported a mean bias of 12.09 mL.kg-1.min-1. The same results were observed for the 6MWD.
Conclusion: This was the first study to predict VO2 peak and 6MWD using clinical and specific variables related to the disease. Every health care professional and exercise physiologist should use both our validated equations to provide a better adapted physical training. Our findings strengthen the need to evaluate survivors’ cardiorespiratory fitness in the care process.
Citation Format: Maxime Caru, Jennifer Labonté, Valérie Lemay, Simon Drouin, Laurence Bertout, Gregor Andelfinger, Nathalie Alos, Maja Krajinovic, Caroline Laverdière, Daniel Sinnett, Daniel Curnier. Improvement of physical activity training in childhood acute lymphoblastic leukemia survivors: New specific equation to predict the peak oxygen uptake from the six-minute walk test [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 B61.
Abstract B62: The need to improve exercise prescriptions to support care in pediatric oncology
Authors: Caru Maxime , Petrykey Kateryna , Samoilenko Mariia , Drouin Simon , Lemay Valérie , Kern Laurence , Romo Lucia , Beaulieu Patrick , St-Onge Pascal , Bertout Laurence , Lefebvre Geneviéve , Andelfinger Gregor , Krajinovic Maja , Laverdière Caroline , Sinnett Daniel , Curnier Daniel 
Published: August 2020

Abstract
Purpose: Cancer survivors’ exposure to chemotherapeutic agents leads to multiple long-term side effects with a decrease in their cardiorespiratory fitness. The first aim was to determine whether cardiorespiratory fitness and physical activity levels were lower among survivors than healthy Canadians, while the second aim was to report associations between genetic variants and cardiorespiratory fitness in survivors.
Methods: Cardiorespiratory fitness (VO2peak) and moderate to vigorous physical activity (MVPA) were compared between childhood ALL survivors (N=221) and healthy Canadians (N=825). We performed whole-exome sequencing in survivors. Germline variants (both common and rare) in a selected set of trainability genes were analyzed for an association with cardiorespiratory fitness.
Results: Survivors’ VO2 peak was found to be 22% lower than healthy Canadians. The cardiorespiratory fitness level was different between survivors and healthy Canadians despite a clinically equivalent level of MVPA. Positive associations between the cardiorespiratory fitness level and trainability genes (TTN, LEPR, IGFBPI, and ENO3 genes) were reported, especially in female survivors with a low cardiorespiratory fitness level.
Conclusion: The cardiorespiratory fitness was significantly lower in survivors, which can be associated with variants in genes related to subjects’ trainability. At this time, it appears that more physical activity would be beneficial to survivors to achieve the same benefits as the healthy population. However, the optimal amount of physical activity needed to reach these benefits is not yet clear. The survivors’ responder or nonresponder status several years after the end of the treatments is unknown. This study has important implications for the field of exercise in oncology.
Citation Format: Maxime Caru, Kateryna Petrykey, Mariia Samoilenko, Simon Drouin, Valérie Lemay, Laurence Kern, Lucia Romo, Patrick Beaulieu, Pascal St-Onge, Laurence Bertout, Geneviéve Lefebvre, Gregor Andelfinger, Maja Krajinovic, Caroline Laverdière, Daniel Sinnett, Daniel Curnier. The need to improve exercise prescriptions to support care in pediatric oncology [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 B62.
Abstract B69: Epigenomics and single-cell sequencing define a developmental hierarchy in Langerhans cell histiocytosis
Authors: Halbritter Florian , Farlik Matthias , Schwentner Raphaela , Jug Gunhild , Fortelny Nikolaus , Simonitsch-Klupp Ingrid , Bauer Wolfgang , Bock Christoph , Hutter Caroline 
Published: August 2020

Abstract
Langerhans cell histiocytosis (LCH) is a rare neoplasm predominantly affecting children. It occupies a characteristic hybrid position between cancer and inflammatory disease, which makes it an attractive model for studying cancer development. Constitutive activation of the ERK signaling pathway is a common feature of LCH, but its pathogenesis remains unclear. To explore the molecular mechanisms underlying the pathophysiology of LCH and the mechanisms that might cause the characteristic clinical heterogeneity of this disease, we investigated cellular heterogeneity in primary LCH lesions. We used a multilayered approach employing immunohistochemistry, flow cytometry, single-cell RNA-sequencing, and ATAC-sequencing of biopsies obtained from different patients with LCH. Based on the single-cell RNA expression data, we identified different LCH cell populations within LCH lesions that display distinct pathway signatures, including a stem cell-like, proliferative state and different subsets with a more differentiated phenotype, including subsets similar to maturing antigen-presenting cells and a subset that could contribute to tissue destruction in LCH. Computational analysis discovered a hierarchy between these cells that suggests a directed developmental program in each tumor. We confirmed the presence of these distinct subsets using immunohistochemical analysis of different biopsies. Furthermore, using chromatin accessibility profiling in prospectively purified LCH cell subsets in combination with single-cell RNA-seq data and integrative bioinformatic analysis, we analyzed the transcription factors and gene regulatory networks that may underlie the observed developmental hierarchy in LCH lesions. This analysis reveals an intricate interplay of immune-regulatory (including JAK-STAT, AP-1, and NF-κB signaling) and developmental regulators (including epigenetic modifiers such as EP300 or KDMs) that may shape LCH cell development. Together, this study sketches a molecular portrait of LCH lesions and enables new, unprecedented insight into this disease. Moreover, it demonstrates the power of combining single-cell RNA-sequencing and epigenome profiling for dissecting complex developmental hierarchies and their regulatory underpinnings, and thus can serve as a template for the analysis of tumorigenesis beyond LCH.
Citation Format: Florian Halbritter, Matthias Farlik, Raphaela Schwentner, Gunhild Jug, Nikolaus Fortelny, Ingrid Simonitsch-Klupp, Wolfgang Bauer, Christoph Bock, Caroline Hutter. Epigenomics and single-cell sequencing define a developmental hierarchy in Langerhans cell histiocytosis [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 B69.
Abstract B76: Characterizing vascular invasion in hepatoblastoma
Authors: Woodfield Sarah E. , Patel Roma H. , Ibarra Aryana M. , Zorman Barry , Badachhape Andrew , Ghaghada Ketan B. , Lopez-Terrada Dolores , Sumazin Pavel , Vasudevan Sanjeev A. 
Published: August 2020

Abstract
Hepatoblastoma (HB) is the most common pediatric liver malignancy, and patients with high-risk, metastatic disease have a five-year overall survival (OS) of only about 40%. Of note, HB patients with vascular invasion (VI) have a much worse OS. Our hypothesis is that HB tumors with VI possess unique clones that invade the vasculature, resulting in dissemination of disease. We injected the aggressive HepT1 cell line with confirmed CTNNB1 and NFE2L2 mutations in the livers of immunocompromised NSG mice to generate intrahepatic tumors. After 4 weeks, we had 100% take of tumors in animals. Serum human α-fetoprotein (AFP) increased with the growth of tumors. At time of death, we saw clear presence of intrahepatic VI, vena caval tumor thrombus, extrahepatic disease including within periportal lymph nodes, and lung metastasis in animals with tumors. We grew adherent and nonadherent cell lines from tumor samples, including one cell line from intrahepatic VI and one from vena caval tumor thrombus. Cells derived from VI areas had obvious differences in phenotype from cells from the primary tumor (PT). To further pursue these provocative changes between PT and VI areas, we generated two unique patient-derived xenograft (PDX) models of HB with intrahepatic implantation of PT and VI tumor samples from a nonmetastatic pretreatment extent of disease (PRETEXT) stage 4 patient. Mice harboring the VI PDX showed serum elevation of human AFP and obvious tumor with MRI. PT and VI PDX tissues expressed established HB markers nuclear Beta-catenin, Glypican-3, and AFP, resembling the primary patient sample. We also developed a novel cell line with growth of cells from a VI tumor in vitro. With both the HepT1 and PDX models, gene set enrichment transcriptomic analyses of RNA sequencing data showed clear changes in expression in aggressive tissues that invaded vessels, including significant (p&lt;0.05) changes in pathways associated with liver damage, inflammation, and metabolism. Further exploration of these pathways and agents that target these pathways could improve outcomes for HB patients with invasive disease.
Citation Format: Sarah E. Woodfield, Roma H. Patel, Aryana M. Ibarra, Barry Zorman, Andrew Badachhape, Ketan B. Ghaghada, Dolores Lopez-Terrada, Pavel Sumazin, Sanjeev A. Vasudevan. Characterizing vascular invasion in hepatoblastoma [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 B76.