bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract B41: Genomic landscape of somatic mutations in osteosarcomas
Authors: Pires Sara F. , Costa Silvia S. , Vidal Daniel O. , Lengert André van Helvoort , Boldrini Érica , da Silva Sandra R.M. , Rosenberg Carla , Lopes Luiz F. , Maschietto Mariana , Krepischi Ana 
Published: August 2020

Abstract
Pediatric cancers are among the leading causes of childhood mortality, with osteosarcomas being the most prevalent bone tumors, characterized by an aggressive clinical course. However, knowledge about the molecular basis of osteosarcomas is still limited, hampering advances in diagnosis and treatment. In this context, we characterized the genomic landscape of somatic mutations in 28 osteosarcomas (24 pediatric patients and 4 adults) aiming to delineate the panel of prevalent mutations in Brazilian patients. Genomic libraries of these osteosarcoma samples were constructed using the TruSight One panel (Illumina), covering 4,813 clinically relevant genes, including known cancer genes. Generated data at high coverage (median &gt;100x depth coverage) were annotated based on public databases containing population variant frequencies (including the Brazilian ABRAOM), as well as clinical information. For further analysis, we filtered only coding nonsynonymous variants absent from both population databases and an additional pool of 20 nonrelated germline samples. In total, 728 variants were identified mapping in 606 genes, with an average rate of 41 mutations per tumor. The panel of detected variants was composed by 93 loss-of-function mutations (38 frameshift, 25 splicing, and 30 premature stop codon) and 635 missense (43 inframe insertions/deletions and 592 single-nucleotide variations), some of them already reported in cancer databases (27 in COSMIC and 39 in ICGC). From 606 genes, 25 were previously associated with osteosarcomas, and they are related to apoptosis, cell growth and differentiation, DNA repair, transcriptional regulation, and tumor-suppression mechanisms. The most frequent mutations were detected in RB1 and TP53; other recurrently mutated genes were mostly linked to biologic pathways potentially related to the disease onset, such as hormonal response (AR), transcriptional regulation and muscle differentiation (FRG1), DNA repair (HERC2), cell signaling (KIR2DL4), and cell proliferation/differentiation (PTPRQ). Additionally, the tumors presented a highly complex pattern of copy number alterations, some of them resembling chromothripsis. This is the first assessment of a Brazilian cohort of osteosarcomas, and functional studies will be further applied to better understand the role of the disclosed mutations for tumor biology.
Citation Format: Sara F. Pires, Silvia S. Costa, Daniel O. Vidal, André van Helvoort Lengert, Érica Boldrini, Sandra R.M. da Silva, Carla Rosenberg, Luiz F. Lopes, Mariana Maschietto, Ana Krepischi. Genomic landscape of somatic mutations in osteosarcomas [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 B41.
Abstract B45: Therapeutic potential of splicing in RMS: SRSF2 binding modulation controls MDM2 alternative splicing
Authors: Montes Matias I. , Comiskey Daniel F. , Khurshid Safiya , Chandler Dawn S. 
Published: August 2020

Abstract
MDM2 undergoes complex alternative splicing and one of its spliced isoforms, MDM2-ALT1, comprised of coding exons 3 and 12, is highly expressed in pediatric rhabdomyosarcoma, and its expression correlates with a poor disease prognosis. MDM2-ALT1 expression is also upregulated under conditions of cellular genotoxic stress, and this alternative splicing is conserved in the mouse Mdm2 gene. Furthermore, previous research from our lab has reported that the splicing factors SRSF1, FUBP1, and PTBP1 are involved in this regulation; nevertheless, the way that MDM2 splicing is controlled is not entirely understood. In this work, we explore the role of the splicing factor SRSF2/SC35 in the alternative splicing of MDM2, hypothesizing that this factor acts as a positive regulator, in both human and mouse, facilitating the production of the full-length MDM2 mature transcript. This splicing factor has been reported to be mutated in several cancers, including myelodysplastic syndromes and rhabdomyosarcoma. Moreover, using a minigene system that mimics the endogenous Mdm2 splicing in response to UV and cisplatinum-induced DNA damage and the CRISPR-Cas9 technology, we show that mutations in SRSF2 predicted binding sites alter Mdm2 alternative splicing. The CRISPR-engineered mutant cells that express this splice isoform show increased proliferation in an Arf/p19 null context. On the other hand, we show that by using antisense oligonucleotides working as splice-switching molecules that target the SRSF2 binding sites in the MDM2 pre-mRNA, we are able to shift the expression of the MDM2 splice isoforms to drive p53 target gene expression in p53 wild-type cells. Furthermore, in an effort to understand better the effect of the MDM2-ALT1 isoform in carcinogenesis, we performed the CRISPR-Cas9 technique to generate a mouse model expressing the cancer-associated spliced isoform. We expect the mouse to be a cancer-sensitized model that will give rise to RMS tumors and provide a preclinical model for testing splice-switching oligonucleotide therapies.
Citation Format: Matias I. Montes, Daniel F. Comiskey, Safiya Khurshid, Dawn S. Chandler. Therapeutic potential of splicing in RMS: SRSF2 binding modulation controls MDM2 alternative splicing [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 B45.
Abstract B56: A CRISPR/Cas9 domain screen identifies a small motif in the PAX3-FOXO1 transactivation domain relevant for tumor maintenance in alveolar rhabdomyosarcoma
Authors: Wachtel Marco , Benischke Katharina , Schäfer Beat W. 
Published: August 2020

Abstract
Fusion transcription factors are the main drivers of tumorigenesis in many pediatric leukemias and sarcomas. One example is PAX3-FOXO1 (P3F), the pathognomonic marker of alveolar rhabdomyosarcoma (aRMS). Since these tumors are often also characterized by a quiet mutational landscape and a paucity of druggable oncogenes, the fusion proteins often remain as the only relevant drug target. However, transcription factors are challenging targets for small-molecule inhibitors, since they lack an enzymatic activity and, apart from the DNA binding domains, are usually intrinsically disordered. Identification of druggable structures in such proteins is therefore of great clinical interest. Our goal of this study was to identify new elements important for P3F activity. Towards this aim, we made use of the CRISPR/Cas9 technology and performed a saturated screen for identification of important functional domains in P3F in the endogenous context. This revealed that both DNA binding domains are indispensable, as expected for a transcription factor. Importantly, however, the screen also identified a 40-amino-acid-long domain at the C-terminus of the FOXO1 part to be strictly required for the function of the protein. Using a series of mutations in this domain in reporter assays, we identified a single cysteine whose mutation leads to more than 50% reduction in transcriptional activity. In addition, cells efficiently differentiated and stopped proliferating when this Cys was mutated in aRMS cells. These results suggest that functional interference with this domain could be a promising approach for aRMS therapy.
Citation Format: Marco Wachtel, Katharina Benischke, Beat W. Schäfer. A CRISPR/Cas9 domain screen identifies a small motif in the PAX3-FOXO1 transactivation domain relevant for tumor maintenance in alveolar 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 B56.
Abstract B57: A combination of IL7Rα and NRAS mutations sheds light on the oncogenesis of T-cell acute lymphoblastic leukemia in a murine model
Authors: Winer Hila , Rodrigues Gisele , Li Wenqing , Hixon Julie , Durum Scott 
Published: August 2020

Abstract
Acute lymphoblastic leukemia (ALL) is the most common cancer in children. While most cases of ALL arise from B-cell precursors, 15% originate from T cells in the thymus (T-ALL). With current treatments, survival rate is high, but relapse occurs in 15-20% of children. In addition, most treatments are highly toxic, with severe side effects. Approximately 10% of T-ALL patients have somatic gain-of-function mutations in IL7Rα gene, and 15-22% of ALL patients have mutations in NRAS or KRAS. Furthermore, Ras pathway mutations are responsible for 30%-50% of ALL relapse. Recently, our lab showed that mutations in human IL7Rα alone (c.731_732insTTGTCCCAC) or human NRAS alone (G13D) are not sufficient to induce T-ALL from primary cells. However, a combination of both causes severe T-ALL in mice. Treatment with inhibitors against IL7Rα and NRAS signaling led to prolonged survival in these mice. Our new data indicate that the correct ratio between IL7Rα and NRAS expression is necessary to generate T-ALL in mice. Using RAG-/- mice injected with primary thymocytes transduced with mutated IL7Rα and NRAS in the optimal sequence in a polycistronic vector led to fatal disease 3 weeks after injection. These mice showed a 30-fold increase of leukocytes in the blood, spleen, and thymus, 80-fold increase in the lymph nodes, and a 5-fold increase in spleen weight, all indications of severe T-ALL. There was no indication of disease progression in mice injected with either empty vector or wild-type IL7Rα and mutated NRAS. To identify the pathways involved in T-ALL by these mutations, we used mass spectrometry and RNA sequencing. Our analysis showed significant increases in the well-known antiapoptotic, B-cell lymphoma 2 (BCL-2), mRNA, and protein levels and a major decrease in the proapoptotic BCL-2 antagonist/killer 1 (BAK-1) protein levels. In this manner, combination of both IL7Rα and NRAS mutations resulted in high Bcl-2:Bak-1 ratio, supported also by Western blot analysis. In addition, we observed a significant increase in the protein cytokinesis midbody regulator citron kinase (Cit), potentially leading to increased thymocytes proliferation and driving T-ALL formation. Taken together, our lab developed a strong model to study T-ALL in mice, shedding light on novel pathways of oncogenesis and targets for better therapeutic development.
Citation Format: Hila Winer, Gisele Rodrigues, Wenqing Li, Julie Hixon, Scott Durum. A combination of IL7Rα and NRAS mutations sheds light on the oncogenesis of T-cell acute lymphoblastic leukemia in a murine model [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 B57.
Abstract IA04: New approaches to study cancer predisposition syndromes
Authors: Kratz Christian P. 
Published: August 2020

Abstract
The diagnosis of a cancer predisposition syndrome (CPS) in a child diagnosed with cancer influences medical care; however, many open questions remain in the areas of counseling, psychosocial support, cancer prevention, surveillance, and therapy. To address such issues, a CPS-registry was launched: www.cancer-predisposition.org. The CPS-registry (1) provides detailed information for affected families and health care professionals, (2) collects biospecimens for translational research, (3) assembles both retrospective and annual prospective data on cancer diagnoses and surveillance measures in individuals with approximately 60 different CPS, (4) makes mutation data publicly available through accessible databases, (5) shares data internationally, (6) links data with trial groups and cancer registries, and (7) provides expert opinion for individual treatment decisions. Due to hidden clinical signs, CPS are often overlooked; however, various clinical tools have been developed to increase the percentage of families that are being offered counseling and testing. Moreover, CPS diagnosis is dramatically facilitated by the increasing use of agnostic next-generation sequencing in pediatric oncology, supporting the notion that 10% of children with cancer harbor mutations in cancer predisposition genes, often in the absence of clinical signs. CPS diagnosis yet remains a challenge prior to a first cancer diagnosis; however, a more systematic diagnostic approach is required to offer prevention and surveillance measures to these individuals. Strong family support organizations such as LFSA and FARF have dramatically improved collaborative research in the CPS field. In the future, clinical protocols for CPS individuals will pave the way for better prevention, surveillance, and cancer treatment strategies.
Citation Format: Christian P. Kratz. New approaches to study cancer predisposition syndromes [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 IA04.
Abstract IA05: Circulating tumor DNA as a tool for prognostication, translational discovery, and early cancer detection
Authors: Crompton Brian 
Published: August 2020

Abstract
New sequencing technologies have facilitated the detection and profiling of circulating tumor DNA (ctDNA) in the blood of patients with cancer. Recent efforts have demonstrated that ctDNA can be detected in the blood of pediatric patients with solid malignancies, using assays specifically designed for the unique somatic profiles observed in these cancers. Once identified in a blood sample, ctDNA levels appear to correlate with outcome and can be tracked over time to measure response to therapy and detect recurrence. Deep profiling of ctDNA can identify subclonal somatic variants that are not detectable in single-tumor biopsy samples, enabling a broader understanding of tumor heterogeneity and the ability to discover novel patterns of tumor evolution and treatment resistance. Validation of the prognostic and translational value of these assays requires leveraging large prospective studies, and this work is ongoing. One obvious application of this new technology is the potential to detect the presence of cancer in pediatric patients with increased cancer risks, including cancer predisposition syndromes. Collaborative multi-institutional efforts are under way to collect samples and develop new ctDNA assays for early cancer detection.
Citation Format: Brian Crompton. Circulating tumor DNA as a tool for prognostication, translational discovery, and early cancer detection [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 IA05.
Abstract IA09: Immunotherapeutic approaches for pediatric solid tumors
Authors: Handgretinger Rupert 
Published: August 2020

Abstract
For patients with primary metastatic or recurrent soft tissue sarcomas, cytotoxic chemotherapy is currently the primary treatment modality. Despite intensive chemotherapy, the outcome is poor and additional new therapeutic strategies in combination with chemotherapy have to be investigated. Immunotherapy, which involves the patient’s own or a new allogeneic immune system, might have great potential to improve the outcome of affected patients. We have focused on the use of haploidentical transplantation as a form of intensive immunotherapy in order to utilize a graft-versus-solid tumor effect, which might be exerted by donor-derived alloreactive Natural Killer (NK) cells, but also by donor-derived T cells. In a first pilot trial, we have transplanted 26 patients with relapsed neuroblastoma from a haploidentical donor. The transplant-related mortality (TRM) was 0% and the overall survival (OS) was 20%. We then started a protocol using haploidentical transplantation in 68 patients followed post-transplant by 6-9 cycles of the monoclonal anti-GD2 antibody ch14.18CHO. The TRM was 5% and the 3-year OS is 58%. In addition to neuroblastoma, we also hope to apply similar strategies to other pediatric advanced solid tumors including Ewing’s sarcoma, rhabdomyosarcoma, and others. We conclude that haploidentical transplantation of patients with relapsed/refractory solid tumors is a platform on which further immunotherapeutic strategies can be developed, such as antibodies directed against other targets than GD2, such as CD276, or bispecific T-cell engagers (BiTEs), chimeric antigen receptor (CAR) T-cells or CAR NK cells, or antibody/cytokine fusion proteins, and these approaches will be discussed. The main goal of immunotherapy, however, must be to establish a long-term memory immune response against the tumor, and haploidentical transplantation might facilitate such a response.
Citation Format: Rupert Handgretinger. Immunotherapeutic approaches for 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 IA09.
Abstract IA17: From functional genomics to new targets in pediatric oncology
Authors: Stegmaier Kimberly 
Published: August 2020

Abstract
The sequencing of human genomes harkened a new era of pediatric cancer investigations. Indeed, genomic discoveries, such as the identification of ALK mutations in neuroblastoma, Philadelphia-like fusions in acute B-cell acute lymphoblastic leukemia (B-ALL), and NTRK fusions in infantile fibrosarcoma, have led to early successes in the application of genomically informed, targeted therapy for children with cancer. While these new drugs have become an important part of the pediatric cancer armamentarium, many children with cancer still lack targeted therapies. Thus, new therapeutic approaches are still needed. Approaches such as RNA interference and CRISPR-Cas9 have transformed the functionalizing of the genome and offer promise for identifying new cancer therapeutic targets. We have applied genome-scale CRISPR-CAS9 screening to identify novel therapeutic targets in pediatric malignancies through the development of a Pediatric Cancer Dependency Map. We screened the Broad Institute’s Avana library in over 100 pediatric cancer cell lines and compared their dependencies to over 600 nonpediatric cell lines. Novel targets emerging from these efforts will be discussed.
Citation Format: Kimberly Stegmaier. From functional genomics to new targets 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 IA17.
Abstract IA18: Clinically relevant mutational signatures in childhood cancer
Authors: Shlien Adam 
Published: August 2020

Abstract
Mutagenic processes leave imprints on the genome in the form of mutations in a specific nucleotide context, forming a unique signature. The driving forces of rarer signatures, especially those seen in relapsed childhood cancers, are mostly unknown. In this talk, I will present data showing the contribution of intrinsic and extrinsic mutators to childhood cancer, and analyses using mutation signatures to accurately predict past mutagen exposure and inform therapeutic choice for ongoing patients.
Citation Format: Adam Shlien. Clinically relevant mutational signatures in 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 IA18.
Abstract IA27: Patient-derived organoids in pediatric cancer research
Authors: Calandrini Camilla , Schutgens Frans , Oka Rurika , Margaritis Thanasis , Candelli Tito , Mathijsen Luka , Ammerlaan Carola , van Ineveld Ravian , Derakhshan Sepideh , Custers Lars , Lijnzaad Philip , Begthel Harry , Kerstens Hinri , Rookmaker Maarten , Verhaar Marianne , Kemmeren Patrick , de Krijger Ronald , Pritchard-Jones Kathy , Rios Anne , van den Heuvel-Eibrink Marry , Holstege Frank , van Boxtel Ruben , Clevers Hans , Drost Jarno 
Published: August 2020

Abstract
Recent advances in in vitro culture technologies, such as adult stem cell-derived organoids, have opened up new avenues for the development of novel, more physiologic human cancer models. Such preclinical models are essential for efficient translation of basic cancer research into novel treatment regimens. We succeeded in growing organoids from a range of pediatric solid tumors, including Wilms’ tumors, renal cell carcinomas, and different types of rhabdoid tumors (i.e., AT/RT, MRT). Tumor organoids retain many characteristics of parental tumor tissue. For instance, Wilms’ tumor organoids retain the cellular heterogeneity of tumors, as they are composed of an intricate network of different cell types. Moreover, we demonstrate that tumor organoids are amenable to gene editing and high-throughput drug screens. In conclusion, our pediatric cancer organoids capture disease and tissue heterogeneity and provide a platform for basic cancer research, drug screening, and personalized medicine.
Citation Format: Camilla Calandrini, Frans Schutgens, Rurika Oka, Thanasis Margaritis, Tito Candelli, Luka Mathijsen, Carola Ammerlaan, Ravian van Ineveld, Sepideh Derakhshan, Lars Custers, Philip Lijnzaad, Harry Begthel, Hinri Kerstens, Maarten Rookmaker, Marianne Verhaar, Patrick Kemmeren, Ronald de Krijger, Kathy Pritchard-Jones, Anne Rios, Marry van den Heuvel-Eibrink, Frank Holstege, Ruben van Boxtel, Hans Clevers, Jarno Drost. Patient-derived organoids in pediatric cancer research [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 IA27.
Abstract IA29: Developmental and oncogenic programs in pediatric brain tumors dissected by single-cell RNA-sequencing
Authors: Filbin Mariella G. 
Published: August 2020

Abstract
During development, the multiple cell types of human brain arise from pluripotent stem cells via progressively more committed progenitor cells. Emerging data suggest that pediatric brain tumors arise from progenitors that have become developmentally stalled. In preliminary studies, our lab used single-cell RNA-seq to display the expression profiles of individual cells within pediatric midline and hemispheric high-grade gliomas. Our data show that these tumors are composed of (i) replicating cells that resemble glial and neural progenitors and (ii) maturing cells resembling astrocytes, oligodendrocytes, or mesenchymal cells. In this presentation I will address how single-cell RNA-sequencing has revolutionized our understanding of the developmental hierarchy and oncogenic programs in pediatric brain tumors. Our recent findings pointing towards potential cells of origin of midline and hemispheric pediatric high-grade gliomas as well as plasticity of different cancer cell states will be discussed.
Citation Format: Mariella G. Filbin. Developmental and oncogenic programs in pediatric brain tumors dissected by single-cell RNA-sequencing [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 IA29.