bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract A14: Exploiting DNA damage repair defects to enhance PD-L1 expression in Ewing sarcoma
Authors: Maurer Lisa M. , Venier Rose M. , Julian Claire , Bailey Kelly M. 
Published: August 2020

Abstract
Objective: The purpose of this work is to determine whether PD-L1 expression can be upregulated by PARP inhibitor treatment in Ewing tumor cells harboring DNA damage repair defects. Further, we aimed to determine whether enhanced PD-L1 expression renders Ewing cells more susceptible to T-cell mediated apoptosis following PD-1 inhibition.
Experimental Procedures: Patient-derived tumor organoids and monolayers (named PSaRC-318) were established from a viably cryofrozen metastatic lung lesion from a patient with Ewing sarcoma and a paternally inherited germline BARD1 mutation. A673, CHLA9, and CHLA10 Ewing tumor cell lines were also employed. Sensitivity of PSaRC-318 to the PARP inhibitors olaparib and talazoparib was established by performing IncuCyte apoptosis assays. PD-L1 expression was examined using RT-PCR, Western blot, and flow cytometry. BARD1, BRCA, and RAD51D siRNA were also utilized to test the role of specific DNA damage repair proteins on this effect. T-cell/tumor cell cocultures and tumor-primed T-cells were established. T cell-induced tumor cell apoptosis was monitored in real-time using IncuCyte caspase and annexin assays.
Results: PSaRC-318 organoids demonstrate exquisite sensitivity to PARP inhibitors, with an IC50 for talazoparib of 3.54nM. Treatment of PARP inhibitor-resistant Ewing cell lines, such as CHLA10, with BARD1 siRNA rendered cells sensitive to PARP inhibition. Ewing tumor cells were found to upregulate tumor cell surface expression of the checkpoint protein PD-L1 in response to treatment with PARP inhibitors. The impact of BARD1, BRCA1, and RAD51D on PD-L1 expression in Ewing tumor cells was also determined. Next, Ewing tumor cells were pretreated with PARP inhibitors and then cocultured with tumor-primed T-cells. T cell-mediated tumor cell apoptosis was monitored in real time using caspase IncuCyte assays. PD-1 blocking antibody added to T-cell/tumor cell cocultures resulted in an increase in early tumor cell death compared to IgG controls.
Conclusion: Single-agent PARP inhibitors have not demonstrated significant clinical benefit in relapsed Ewing sarcoma to date, suggesting that combinatorial therapy with PARP inhibitors may be a more effective approach. Here, we have shown that Ewing tumor cells with germline mutations in DNA-damage repair proteins, such as BARD1, can upregulate PD-L1 expression following treatment with PARP inhibitors. Thus, PARP inhibitor/anti-PD-1 therapy may be a logical combination for the treatment of relapsed Ewing sarcoma. Ongoing preclinical studies are continuing to examine this combination.
Citation Format: Lisa M. Maurer, Rose M. Venier, Claire Julian, Kelly M. Bailey. Exploiting DNA damage repair defects to enhance PD-L1 expression 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 A14.
Abstract A31: Podxl as therapeutic target for metastasis
Authors: Dhez Anne-Chloe , Paassen Irene , Sorensen Poul 
Published: August 2020

Abstract
Osteosarcoma (OS) is the most common bone tumor in pediatric patients. Metastasis is a major cause of mortality and morbidity. The rarity of this disease coupled with the challenges of drug development for metastatic cancers have slowed the delivery of improvements in long-term outcomes for these patients. Recently, we found that high podocalyxin (gene name PODXL, protein name Podxl) expression is associated with high metastatic profile in OS cell lines. Consistent with this data, we found a significant association between high Podxl expression and poor outcome in pediatric OS patients. Podxl is a cell surface transmembrane glycoprotein belonging to the CD34 family. The functional role of Podxl in tumorigenesis is largely unknown, but it has been demonstrated to promote cancer cell invasion and migration and to enhance metastatic potential. Podxl is upregulated on a variety of human tumors, facilitates disease progression, and is a promising target for immunotherapy as an approach to blocking metastatic disease. Accordingly, in collaboration for the Centre for Drug Research and Development, Kelly McNagny and his collaborators have developed a novel panel of monoclonal antibodies to human Podxl and have explored their utility in suppressing tumor cell growth in vitro and in vivo. To define the relevance of Podxl in the biology of metastasis, we examined Podxl expression in different OS cell lines with different metastatic profiles. Then, we studied the importance of Podxl in migration and invasion processes and in in vitro 3D cell system formation. To assess Podxl’s role in metastatic progression we performed the Pulmonary Metastasis Assay (PuMA). PuMA is an ex vivo lung explant and closed cell culture system that permits to study the biology of lung colonization by fluorescence microscopy. With PuMA model, we assessed the effects of antimetastatic therapeutics over time. In the present study, we found that suppression of Podxl profoundly impairs cell proliferation, migration, invasion properties, and tumorsphere formation in OS cells in vitro. With PuMA model, we found that Podxl is required for the progression of metastasis disease. These data tend to validate podocalyxin as a regulator of tumor progression and a novel therapeutic target in OS. It is necessary to perform in vivo experiments to further explore the functions of Podxl and the effect of the podocalyxin-specific monoclonal antibody (coupled or not to a toxic payload) to suppress the metastasis progression in our model.
Citation Format: Anne-Chloe Dhez, Irene Paassen, Poul Sorensen. Podxl as therapeutic target for metastasis [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 A31.
Abstract A36: Targeting anaplastic lymphoma kinase in neuroblastoma
Authors: Guan Jikui , Cervantes-Madrid Diana , Siaw Joachim , Alam Wasi , Umapathy Ganesh , Borenäs Marcus , Lind Dan , Szydzik Joanna , Pfeifer Kathrin , Mendoza-Garcia Patricia , Palmer Ruth , Hallberg Bengt 
Published: August 2020

Abstract
Over the last decade Anaplastic Lymphoma Kinase (ALK), a receptor tyrosine kinase (RTK), has been identified as a fusion partner in a diverse variety of translocation events resulting in oncogenic signaling in many different cancer types. In tumors where full-length ALK RTK itself is mutated, such as neuroblastoma, the picture regarding the role of ALK as an oncogenic driver is less clear. Neuroblastoma is a complex and heterogeneous tumor that arises from the neural crest-derived peripheral nervous system. Although high-risk neuroblastoma is rare, it often relapses and becomes refractory to treatment. Thus, neuroblastoma accounts for 10-15% of all childhood cancer deaths. Since most cases are in children under the age of two, understanding the role and regulation of ALK during neural crest development is an important goal in addressing neuroblastoma tumorigenesis. An impressive array of tyrosine kinase inhibitors (TKIs) that act to inhibit ALK have been FDA approved for using in ALK-driven cancers. ALK TKIs bind differently within the ATP-binding pocket of the ALK kinase domain and have been associated with different resistance mutations within ALK itself that arise in response to therapeutic use, particularly in ALK fusion-positive NSCLC. This patient population has highlighted the importance of considering the relevant ALK TKI to be used for a given ALK mutant variant. In this poster we discuss ALK in neuroblastoma, as well as the use of ALK TKIs and other strategies to inhibit tumor growth. Current efforts combining novel approaches and increasing our understanding of the oncogenic role of ALK in neuroblastoma are aimed at improving efficacy of ALK TKIs as precision medicine options in the clinic.
Citation Format: Jikui Guan, Diana Cervantes-Madrid, Joachim Siaw, Wasi Alam, Ganesh Umapathy, Marcus Borenäs, Dan Lind, Joanna Szydzik, Kathrin Pfeifer, Patricia Mendoza-Garcia, Ruth Palmer, Bengt Hallberg. Targeting anaplastic lymphoma kinase in neuroblastoma [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 A36.
Abstract A40: Integration of high-throughput drug screening on patient-derived organdies into pediatric precision medicine programs: The future is now!
Authors: Langenberg Karin , Dolman Emmy , Molenaar Jan 
Published: August 2020

Abstract
Background/Objectives: The most promising option to improve outcomes for pediatric cancer patients with relapsed or refractory disease is through mutation-based targeted therapeutic strategies. However, only 50% of these tumors harbor actionable events. Therefore, compound screening on organoids grown from tumor tissue might reveal additional treatment options.
Design/Methods: The Dutch Childhood Oncology Group-individualized Therapies (DCOG-iTHER) clinical trial in collaboration with INFORM consists of whole-exome sequencing (WES), low-coverage whole-genome sequencing (WGS), RNA profiling using RNAseq and Affymetrix microarrays, and a methylation array. Data are analyzed using the Dutch R2 bioinformatic platform. In addition, tumor-derived organoids are cultured profiled through the same pipeline. Semi-high-throughput screening of a 170-compound library is performed, and effect on cell viability using the CellTiter-Glo® 3D cell viability assay is assessed.
Results: To date, 133 patients with relapsed/refractory pediatric malignancies have been enrolled and analysis has been completed in 80 study subjects. In 47 patients, a total of 128 molecular targets were identified and 29 patients harbored an actionable event with priority score ≥ moderate (46%). In 14% a matched targeted therapy was initiated, and one-third of these patients achieved complete remission. In addition, tumor organoids have been cultured of neuroblastoma tumors and molecular profiling was performed to confirm they reflect the patient’s tumor biology. High-throughput drug screen confirmed existing molecular targets such as ALK and c-kit and in addition revealed increased compound sensitivity to drugs not previously found through sequencing.
Conclusions: Our proof of concept of patient-specific drug testing on tumor organoids within our pediatric precision medicine program might reveal additional treatment options for children who currently have none. Clinical benefit will be evaluated in our upcoming clinical trial iTHER 2.0.
Citation Format: Karin Langenberg, Emmy Dolman, Jan Molenaar. Integration of high-throughput drug screening on patient-derived organdies into pediatric precision medicine programs: The future is now! [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 A40.
Abstract A44: Comparative gene expression analysis for identification and prioritization of therapeutic targets in a cohort of childhood cancers
Authors: Sanders Lauren M. , Lyle A. Geoffrey , Beale Holly C. , Kephart Ellen Towle , Learned Katrina , Peralez Jennifer , Lacayo Norman , Rangaswami Arun , Spunt Sheri L. , Bjork Isabel , Haussler David , Salama Sofie R. , Vaske Olena M. 
Published: August 2020

Abstract
Here we describe the utility of comparative RNA sequencing (RNA-seq) analysis in identifying cancer driver pathways and relevant therapeutics in childhood cancer, and we introduce a novel system for prioritizing gene targets based on analytical and published evidence. The purpose of our study was to evaluate the clinical utility of comparative N-of-1 gene expression analysis in identifying therapeutic options for pediatric patients with relapsed or recurrent cancers. The comparative analysis framework and large cancer background cohorts were developed at the Treehouse Childhood Cancer Initiative at UC Santa Cruz. We employed this analysis in a pilot study of 26 patients at the Lucile Packard Children’s Hospital. We analyzed RNA-seq data from 30 biopsied samples from 26 patient donors, including 16 sarcomas, 5 CNS tumors, 3 hematopoietic cancers, 1 liver, and 1 colon cancer. We compared gene expression from each child’s tumor biopsy to a background cohort of RNA-seq data from over 11,000 cancer patients, and also to a smaller cohort defined by molecular and histopathologic similarity to the child’s tumor biopsy. This comparison yielded outlier gene activations in the child’s biopsy compared to those in the background cohorts, reflecting cancer driver pathways in the child’s tumor that are actionable. We stratified each of the resulting therapeutic leads into 5 baskets: RTK activation, JAK/STAT signaling, PI3K/AKT/mTOR signaling, Cell Cycle activation, or Other. Because 27 of the 30 samples had more than one lead, we developed a novel scoring system to prioritize each sample’s therapeutic gene targets based on the analytical strength of the gene expression analysis result, and on published literature evidence for each gene as a biomarker indicative of drug response. We presented the results of our analysis in genomic consensus meetings at Stanford and surveyed the responses of clinicians and families on the utility of our analysis for treatment decisions. Here we report our experience with the method and highlight case studies in which this analysis informed treatment decisions.
Citation Format: Lauren M. Sanders, A. Geoffrey Lyle, Holly C. Beale, Ellen Towle Kephart, Katrina Learned, Jennifer Peralez, Norman Lacayo, Arun Rangaswami, Sheri L. Spunt, Isabel Bjork, David Haussler, Sofie R. Salama, Olena M. Vaske. Comparative gene expression analysis for identification and prioritization of therapeutic targets in a cohort of childhood cancers [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 A44.
Abstract A48: YB-1-based oncolytic virotherapy in combination with CDK4/6-inhibitors against Ewing sarcoma
Authors: Schober Sebastian J. , Thiel Uwe , Thiede Melanie , Ehrenfeld Maximilian , Nawroth Roman , Richter Guenther HS , Burdach Stefan E.G. , Holm Per Sonne 
Published: August 2020

Abstract
Oncolytic virotherapy is associated with immunogenic cell death and antitumor inflammatory immune responses. Thereby, a local as well as systemic immunosuppressive microenvironment might be abrogated, resulting in efficient phagocytic and antigen-presenting properties. Consecutively, priming of naive T cells against a multitude of de-repressed tumor and viral antigens is claimed to elicit strong antitumor immune responses accompanied by tumor-infiltrating T cells, especially in combination with immune checkpoint blockade. These features might be beneficial for patients with relapsed and metastatic Ewing sarcoma, who have poor prognosis and lack innovative therapy concepts, and whose tumor biopsies are characterized by low or absent T-cell infiltration. Here, we explore the efficacy of the oncolytic YB-1-selective adenovirus XVir-N-31 in combination with the CDK4/6-inhibitor abemaciclib (LY2835219) in established Ewing sarcoma cell lines. We demonstrate enhanced viral replication, particle formation, and oncolysis when combined with abemaciclib in vitro. Priming of tumor cells with abemaciclib before viral infection leads to cell cycle arrest in G1 phase, with consecutive decrease in Rb, pRb, and E2F1 protein levels. Interestingly, in the Rb-mutated hence CDK4/6-inhibitor-resistant cell line SK-N-MC, the combination with abemaciclib does not result in enhanced viral replication oor oncolysis. However, the same effects as for CDK4/6-inhibitor sensitive cell lines can be induced by siRNA-mediated E2F1 knockdown, indicating the crucial role of E2F1 as a repressor for initiation of viral replication. In summary, our results further support the hypothesis of E2F1 being a repressor of adenoviral replication (Holm et al., manuscript in preparation) and suggest the use of CDK4/6-inhibitors to boost oncolytic adenoviral efficacy. Further in vivo confirmation is planned in order to prepare a clinical phase I study of XVir-N-31 in combination with a CDK4/6-inhibitor and immune checkpoint blockade for treatment-refractory pediatric sarcoma patients.
Citation Format: Sebastian J. Schober, Uwe Thiel, Melanie Thiede, Maximilian Ehrenfeld, Roman Nawroth, Guenther HS Richter, Stefan E.G. Burdach, Per Sonne Holm. YB-1-based oncolytic virotherapy in combination with CDK4/6-inhibitors against 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 A48.
Abstract A56: Effect of chemotherapy on gut microbiota and microbiota-derived metabolites in children with cancer
Authors: Benmoussa Abderrahim , Bélanger Véronique , Levy Emile , Laverdière Caroline , Stintzi Alain , Sinnett Daniel , Marcil Valérie 
Published: August 2020

Abstract
Chemotherapy used to treat pediatric cancers often causes significant side effects including vomiting, diarrhea, and severe infections. Bacteria composing the intestinal microbiota play a major role in the health of individuals. The modification of the gut microbiota profile (by nutrition, antibiotics, or other chemical agents) can lead to beneficial or adverse effects on health status. It has been suggested that the gut microbiota may modulate response to treatment, including side effects from chemotherapy. However, studies in the field are lacking to prove this concept. We aim to examine whether the modifications of gut microbiota profiles are associated with negative sides effects of pediatric cancer treatment and lead to higher peripheral inflammation and oxidative stress. To explore this new line of research, we are studying the longitudinal changes in gut microbiota, bacterial-derived metabolites, and state of inflammation and oxidative stress during cancer treatment. A total of 38 children with acute lymphoblastic leukemia and non-Hodgkin lymphoma will be recruited at Sainte-Justine UHC in Montreal. We are collecting clinical data, blood, and fecal samples at different time points during treatment. Nutritional data are gathered with 24-hour recalls assessing diet prior to sample collection. Our methodology includes multiplexed massively parallel sequencing, ELISA, high-performance liquid chromatography, gas chromatography-mass spectrometry, and enzymatic techniques. Our findings will serve as a foundation for mechanistic studies and the development of biomarkers for therapeutic use, and contribute to a better understanding of individual responses to childhood cancer therapy.
Citation Format: Abderrahim Benmoussa, Véronique Bélanger, Emile Levy, Caroline Laverdière, Alain Stintzi, Daniel Sinnett, Valérie Marcil. Effect of chemotherapy on gut microbiota and microbiota-derived metabolites in children with 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 A56.
Abstract A60: Transcriptional profile of CD56negCD16pos Natural Killer cells within endemic Burkitt lymphoma
Authors: Forconi Catherine S. , Oduor Cliff , Ong’echa John M. , Bailey Jeff , Moormann Ann M. 
Published: August 2020

Abstract
Endemic Burkitt lymphoma (eBL), the most common pediatric cancer in equatorial Africa, has long been associated with two etiologic agents: Epstein-Barr virus (EBV) and Plasmodium falciparum malaria. On the other hand, Natural Killer (NK) cells are essential in the clearance of infected cells as well as play a critical role in tumor immunosurveillance. Despite chronic viral infections as HIV, HCV, which have been found to promote the expansion of a CD56 (negative) NK cell subset with impaired effector function, previous cancer studies have been limited to investigations of CD56dimCD16pos NK cells. We previously published that eBL children had significantly more CD56negCD16pos NK cells compared to age-matched healthy children from a low and high malaria transmission area. Here, we characterized this CD56negCD16pos NK subset using histology staining, multicolor flow cytometry, and RNA-sequencing. We found CD56negCD16pos NK cells to be morphologically similar to CD56dimCD16pos NK cells but had higher expression of FCGR3B (CD16b) (p=0.000008) and MPEG1 (Perforin 2) (p=0.0000007), and lower expression of KLRF1 (NKp80), IL18RAP and IL18R1 (IL18 receptor) (p=0.000003, p=0.000003 and p=0.00005, respectively). Phenotypically, CD56negCD16pos NK cells share characteristics of adaptive NK cells; however, they differ from “memory-like” NK cells, with consistent expression of NKG2C/CD57, lower expression of NKp46 and CD160, and higher expression of KIR3DL1 compared to CD56dimCD16pos NK cells. Finally, higher plasma levels of IL-12p70 and IL-2 (known to help NK cell activation and proliferation) and IL-6 and MIP1a were found in healthy compared to eBL children. Together, these findings suggest that the expansion of CD56negCD16pos NK cells could help explain diminished tumor immunosurveillance and might be a mechanism by which EBV-infected cells evades NK-cell mediated immunity.
Citation Format: Catherine S. Forconi, Cliff Oduor, John M. Ong’echa, Jeff Bailey, Ann M. Moormann. Transcriptional profile of CD56negCD16pos Natural Killer cells within endemic Burkitt lymphoma [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 A60.