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Acanda De La Rocha AM, Berlow NE, Fader M, Coats ER, Saghira C, Espinal PS, Galano J, Khatib Z, Abdella H, Maher OM, Vorontsova Y, Andrade-Feraud CM, Daccache A, Jacome A, Reis V, Holcomb B, Ghurani Y, Rimblas L, Guilarte TR, Hu N, Salyakina D, Azzam DJ. Feasibility of functional precision medicine for guiding treatment of relapsed or refractory pediatric cancers. Nat Med 2024; 30:990-1000. [PMID: 38605166 PMCID: PMC11031400 DOI: 10.1038/s41591-024-02848-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 01/31/2024] [Indexed: 04/13/2024]
Abstract
Children with rare, relapsed or refractory cancers often face limited treatment options, and few predictive biomarkers are available that can enable personalized treatment recommendations. The implementation of functional precision medicine (FPM), which combines genomic profiling with drug sensitivity testing (DST) of patient-derived tumor cells, has potential to identify treatment options when standard-of-care is exhausted. The goal of this prospective observational study was to generate FPM data for pediatric patients with relapsed or refractory cancer. The primary objective was to determine the feasibility of returning FPM-based treatment recommendations in real time to the FPM tumor board (FPMTB) within a clinically actionable timeframe (<4 weeks). The secondary objective was to assess clinical outcomes from patients enrolled in the study. Twenty-five patients with relapsed or refractory solid and hematological cancers were enrolled; 21 patients underwent DST and 20 also completed genomic profiling. Median turnaround times for DST and genomics were within 10 days and 27 days, respectively. Treatment recommendations were made for 19 patients (76%), of whom 14 received therapeutic interventions. Six patients received subsequent FPM-guided treatments. Among these patients, five (83%) experienced a greater than 1.3-fold improvement in progression-free survival associated with their FPM-guided therapy relative to their previous therapy, and demonstrated a significant increase in progression-free survival and objective response rate compared to those of eight non-guided patients. The findings from our proof-of-principle study illustrate the potential for FPM to positively impact clinical care for pediatric and adolescent patients with relapsed or refractory cancers and warrant further validation in large prospective studies. ClinicalTrials.gov registration: NCT03860376 .
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Affiliation(s)
- Arlet M Acanda De La Rocha
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | | | - Maggie Fader
- Division of Pediatric Hematology Oncology, Department of Pediatrics, Nicklaus Children's Hospital, Miami, FL, USA
| | - Ebony R Coats
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Cima Saghira
- Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Paula S Espinal
- Center for Precision Medicine, Nicklaus Children's Hospital, Miami, FL, USA
| | - Jeanette Galano
- Center for Precision Medicine, Nicklaus Children's Hospital, Miami, FL, USA
| | - Ziad Khatib
- Division of Pediatric Hematology Oncology, Department of Pediatrics, Nicklaus Children's Hospital, Miami, FL, USA
| | - Haneen Abdella
- Division of Pediatric Hematology Oncology, Department of Pediatrics, Nicklaus Children's Hospital, Miami, FL, USA
| | - Ossama M Maher
- Division of Pediatric Hematology Oncology, Department of Pediatrics, Nicklaus Children's Hospital, Miami, FL, USA
| | - Yana Vorontsova
- Center for Precision Medicine, Nicklaus Children's Hospital, Miami, FL, USA
| | - Cristina M Andrade-Feraud
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Aimee Daccache
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Alexa Jacome
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Victoria Reis
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Baylee Holcomb
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Yasmin Ghurani
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Lilliam Rimblas
- Division of Pediatric Hematology Oncology, Department of Pediatrics, Nicklaus Children's Hospital, Miami, FL, USA
| | - Tomás R Guilarte
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Nan Hu
- Department of Biostatistics, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA
| | - Daria Salyakina
- Center for Precision Medicine, Nicklaus Children's Hospital, Miami, FL, USA
| | - Diana J Azzam
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, USA.
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2
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Grunewald TGP, Postel-Vinay S, Nakayama RT, Berlow NE, Bolzicco A, Cerullo V, Dermawan JK, Frezza AM, Italiano A, Jin JX, Loarer FL, Martin-Broto J, Pecora A, Perez-Martinez A, Tam YB, Tirode F, Trama A, Pasquali S, Vescia M, ortmann L, Wortmann M, Yoshida A, Webb K, Huang PH, Keller C, Antonescu CR. Translational Aspects of Epithelioid Sarcoma: Current Consensus. Clin Cancer Res 2024; 30:1079-1092. [PMID: 37916971 PMCID: PMC10947972 DOI: 10.1158/1078-0432.ccr-23-2174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/12/2023] [Accepted: 10/20/2023] [Indexed: 11/03/2023]
Abstract
Epithelioid sarcoma (EpS) is an ultra-rare malignant soft-tissue cancer mostly affecting adolescents and young adults. EpS often exhibits an unfavorable clinical course with fatal outcome in ∼50% of cases despite aggressive multimodal therapies combining surgery, chemotherapy, and irradiation. EpS is traditionally classified in a more common, less aggressive distal (classic) type and a rarer aggressive proximal type. Both subtypes are characterized by a loss of nuclear INI1 expression, most often following homozygous deletion of its encoding gene, SMARCB1-a core subunit of the SWI/SNF chromatin remodeling complex. In 2020, the EZH2 inhibitor tazemetostat was the first targeted therapy approved for EpS, raising new hopes. Still, the vast majority of patients did not benefit from this drug or relapsed rapidly. Further, other recent therapeutic modalities, including immunotherapy, are only effective in a fraction of patients. Thus, novel strategies, specifically targeted to EpS, are urgently needed. To accelerate translational research on EpS and eventually boost the discovery and development of new diagnostic tools and therapeutic options, a vibrant translational research community has formed in past years and held two international EpS digital expert meetings in 2021 and 2023. This review summarizes our current understanding of EpS from the translational research perspective and points to innovative research directions to address the most pressing questions in the field, as defined by expert consensus and patient advocacy groups.
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Affiliation(s)
- Thomas G. P. Grunewald
- Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
| | - Sophie Postel-Vinay
- Département d’Innovation Thérapeutique et d’Essais Précoces (DITEP), Gustave Roussy, Université Paris Saclay, Villejuif, France
- U981 INSERM, ERC StG team, Gustave Roussy, Villejuif, France
| | - Robert T. Nakayama
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Noah E. Berlow
- Children’s Cancer Therapy Development Institute, Hillsboro, Oregon
| | - Andrea Bolzicco
- Patients association ‘Orchestra per la vita’ Aps, Rome, Italy
- Patients association: ‘MC4 in corsa per la vita!’ ETS, Milan, Italy
| | - Vincenzo Cerullo
- Drug Research Program, University of Helsinki, Helsinki, Finland
| | - Josephine K. Dermawan
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Anna Maria Frezza
- Department of Medical Oncology 2, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Antoine Italiano
- Early Phase Trials and Sarcoma Units, Institut Bergonie, Bordeaux, France
- Faculty of Medicine, University of Bordeaux, Bordeaux, France
| | - Jia xiang Jin
- Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
| | - Francois Le Loarer
- Faculty of Medicine, University of Bordeaux, Bordeaux, France
- Department of Pathology, Institut Bergonie, Bordeaux, France
| | - Javier Martin-Broto
- Medical Oncology Department, Fundacion Jimenez Diaz University Hospital; University Hospital General de Villalba, and Instituto de Investigacion Sanitaria Fundacion Jimenez Diaz (IIS/FJD; UAM), Madrid, Spain
| | - Andrew Pecora
- John Theurer Cancer Center, Georgetown Lombardi Comprehensive Cancer Center, Washington, DC
| | - Antonio Perez-Martinez
- Patients association: ‘MC4 in corsa per la vita!’ ETS, Milan, Italy
- Department of Pediatric Hemato-Oncology, Autonomous University of Madrid, Institute for Health Research, IdiPAZ, La Paz University Hospital, Madrid, Spain
| | - Yuen Bun Tam
- Division of Molecular Pathology, Institute of Cancer Research, London, United Kingdom
| | - Franck Tirode
- Universite Claude Bernard, INSERM 1052, CNRS 5286, Cancer Research Center of Lyon, Centre Leon Berard, Lyon, France
| | - Annalisa Trama
- Department of Epidemiology and Data Science; Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Sandro Pasquali
- Molecular Pharmacology, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Lukas ortmann
- Patients association “Smarcb1” e.V., Bergisch Gladbach, Germany
| | | | - Akihiko Yoshida
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Kim Webb
- Patients association “Smarcb1” e.V., Bergisch Gladbach, Germany
| | - Paul H. Huang
- Division of Molecular Pathology, Institute of Cancer Research, London, United Kingdom
- Sarcoma Unit, Royal Marsden Hospital, Belmont, United Kingdom
| | - Charles Keller
- Children’s Cancer Therapy Development Institute, Hillsboro, Oregon
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3
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Rasmussen SV, Wozniak A, Lathara M, Goldenberg JM, Samudio BM, Bickford LR, Nagamori K, Wright H, Woods AD, Chauhan S, Lee CJ, Rudzinski ER, Swift MK, Kondo T, Fisher DE, Imyanitov E, Machado I, Llombart-Bosch A, Andrulis IL, Gokgoz N, Wunder J, Mirotaki H, Nakamura T, Srinivasa G, Thway K, Jones RL, Huang PH, Berlow NE, Schöffski P, Keller C. Functional genomics of human clear cell sarcoma: genomic, transcriptomic and chemical biology landscape for clear cell sarcoma. Br J Cancer 2023; 128:1941-1954. [PMID: 36959380 PMCID: PMC10147623 DOI: 10.1038/s41416-023-02222-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 02/14/2023] [Accepted: 02/24/2023] [Indexed: 03/25/2023] Open
Abstract
BACKGROUND Systemic therapy for metastatic clear cell sarcoma (CCS) bearing EWSR1-CREB1/ATF1 fusions remains an unmet clinical need in children, adolescents, and young adults. METHODS To identify key signaling pathway vulnerabilities in CCS, a multi-pronged approach was taken: (i) genomic and transcriptomic landscape analysis, (ii) integrated chemical biology interrogations, (iii) development of CREB1/ATF1 inhibitors, and (iv) antibody-drug conjugate testing (ADC). The first approach encompassed DNA exome and RNA deep sequencing of the largest human CCS cohort yet reported consisting of 47 patient tumor samples and 8 cell lines. RESULTS Sequencing revealed recurrent mutations in cell cycle checkpoint, DNA double-strand break repair or DNA mismatch repair genes, with a correspondingly low to intermediate tumor mutational burden. DNA multi-copy gains with corresponding high RNA expression were observed in CCS tumor subsets. CCS cell lines responded to the HER3 ADC patritumab deruxtecan in a dose-dependent manner in vitro, with impaired long term cell viability. CONCLUSION These studies of the genomic, transcriptomic and chemical biology landscape represent a resource 'atlas' for the field of CCS investigation and drug development. CHK inhibitors are identified as having potential relevance, CREB1 inhibitors non-dependence of CCS on CREB1 activity was established, and the potential utility of HER3 ADC being used in CCS is found.
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Affiliation(s)
| | - Agnieszka Wozniak
- University Hospitals Leuven, Department of General Medical Oncology, and Laboratory of Experimental Oncology, KU Leuven, Leuven Cancer Institute, Leuven, Belgium
| | | | | | | | | | - Kiyo Nagamori
- Children's Cancer Therapy Development Institute, Beaverton, OR, USA
| | | | - Andrew D Woods
- Children's Cancer Therapy Development Institute, Beaverton, OR, USA
| | - Shefali Chauhan
- Children's Cancer Therapy Development Institute, Beaverton, OR, USA
| | - Che-Jui Lee
- University Hospitals Leuven, Department of General Medical Oncology, and Laboratory of Experimental Oncology, KU Leuven, Leuven Cancer Institute, Leuven, Belgium
| | - Erin R Rudzinski
- Department of Pathology, Seattle Children's Hospital, Seattle, WA, USA
| | - Michael K Swift
- Children's Cancer Therapy Development Institute, Beaverton, OR, USA
| | - Tadashi Kondo
- Division of Rare Cancer Research, National Cancer Center Research Institute, Tokyo, Japan
| | - David E Fisher
- Department of Hematology/Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Evgeny Imyanitov
- N.N. Petrov National Medicine Research Center of Oncology, St. Petersburg, Russia
| | - Isidro Machado
- Pathology Department, Instituto Valenciano de Oncología and Patologika Laboratorio, Hospital QuironSalud, Valencia, Spain
| | | | - Irene L Andrulis
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Nalan Gokgoz
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Jay Wunder
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
- University Musculoskeletal Oncology Unit, Mount Sinai Hospital, Toronto, ON, Canada
- Division of Orthopaedic Surgery, Department of Surgery, University of Toronto, Toronto, Canada
| | | | - Takuro Nakamura
- The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | | | - Khin Thway
- Sarcoma Unit, Royal Marsden Hospital, Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | - Robin L Jones
- Sarcoma Unit, Royal Marsden Hospital, Division of Clinical Studies, Institute of Cancer Research, London, UK
| | - Paul H Huang
- Sarcoma Unit, Royal Marsden Hospital, Division of Molecular Pathology, Institute of Cancer Research, London, UK.
| | - Noah E Berlow
- Children's Cancer Therapy Development Institute, Beaverton, OR, USA.
| | - Patrick Schöffski
- University Hospitals Leuven, Department of General Medical Oncology, and Laboratory of Experimental Oncology, KU Leuven, Leuven Cancer Institute, Leuven, Belgium
| | - Charles Keller
- Children's Cancer Therapy Development Institute, Beaverton, OR, USA.
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4
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Frankel AO, Lathara M, Shaw CY, Wogmon O, Jackson JM, Clark MM, Eshraghi N, Keenen SE, Woods AD, Purohit R, Ishi Y, Moran N, Eguchi M, Ahmed FUA, Khan S, Ioannou M, Perivoliotis K, Li P, Zhou H, Alkhaledi A, Davis EJ, Galipeau D, Randall RL, Wozniak A, Schoffski P, Lee CJ, Huang PH, Jones RL, Rubin BP, Darrow M, Srinivasa G, Rudzinski ER, Chen S, Berlow NE, Keller C. Correction to: Machine learning for rhabdomyosarcoma histopathology. Mod Pathol 2022; 35:1496. [PMID: 35578013 DOI: 10.1038/s41379-022-01098-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Arthur O Frankel
- Children's Cancer Therapy Development Institute, Beaverton, OR, 97005, USA
| | | | - Celine Y Shaw
- Children's Cancer Therapy Development Institute, Beaverton, OR, 97005, USA
| | - Owen Wogmon
- Children's Cancer Therapy Development Institute, Beaverton, OR, 97005, USA
| | - Jacob M Jackson
- Children's Cancer Therapy Development Institute, Beaverton, OR, 97005, USA
| | - Mattie M Clark
- Children's Cancer Therapy Development Institute, Beaverton, OR, 97005, USA
| | - Navah Eshraghi
- Children's Cancer Therapy Development Institute, Beaverton, OR, 97005, USA
| | - Stephanie E Keenen
- Children's Cancer Therapy Development Institute, Beaverton, OR, 97005, USA
| | - Andrew D Woods
- Children's Cancer Therapy Development Institute, Beaverton, OR, 97005, USA
| | - Reshma Purohit
- Children's Cancer Therapy Development Institute, Beaverton, OR, 97005, USA
| | - Yukitomo Ishi
- Department of Neurosurgery, Hokkaido University School of Medicine, Sapporo, 060-8638, Japan
| | - Nirupama Moran
- Department of Otorhinolaryngology, Assam Medical College and Hospital, Assam, 786002, India
| | - Mariko Eguchi
- Department of Pediatrics, Ehime University Graduate School of Medicine, Ehime, 791-0295, Japan
| | - Farhat Ul Ain Ahmed
- Department of Obstetrics and Gynaecology, Fatima Memorial Hospital, Lahore, Pakistan
| | - Sara Khan
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, ON, M5G 1×8, Canada
| | - Maria Ioannou
- Department of Pathology, University of Thessaly, Biopolis Larisa, 41110, Greece
| | | | - Pin Li
- Department of Urology, Bayi Children's Hospital, 100700, Beijing, China
| | - Huixia Zhou
- Department of Urology, Bayi Children's Hospital, 100700, Beijing, China
| | - Ahmad Alkhaledi
- Department of Oncology, Damascus University Hospitals: Damascus, Damascus, Syria
| | | | - Danielle Galipeau
- OHSU Biolibrary, Oregon Health & Science University, Portland, OR, 97239, USA
| | - R L Randall
- Department of Orthopaedic Surgery, University of California Davis Health, Sacramento, CA, 95817, USA
| | - Agnieszka Wozniak
- Leuven Cancer Institute, University Hospitals Leuven, Department of Oncology & Research Unit Laboratory of Experimental Oncology, KU Leuven, Leuven, Belgium
| | - Patrick Schoffski
- Leuven Cancer Institute, University Hospitals Leuven, Department of Oncology & Research Unit Laboratory of Experimental Oncology, KU Leuven, Leuven, Belgium
| | - Che-Jui Lee
- Leuven Cancer Institute, University Hospitals Leuven, Department of Oncology & Research Unit Laboratory of Experimental Oncology, KU Leuven, Leuven, Belgium
| | - Paul H Huang
- Royal Marsden Hospital/Institute of Cancer Research, Fulham Road, London, SW3 6JJ, UK
| | - Robin L Jones
- Royal Marsden Hospital/Institute of Cancer Research, Fulham Road, London, SW3 6JJ, UK
| | - Brian P Rubin
- Pathology & Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Morgan Darrow
- Department of Pathology and Laboratory Medicine, University of California Davis Medical Center, Sacramento, CA, 95817, USA
| | | | | | - Sonja Chen
- Nationwide Children's Hospital, Columbus, OH, 43205, USA. .,Department of Pathology, Rhode Island Hospital, Providence, RI, 02903, USA.
| | - Noah E Berlow
- Children's Cancer Therapy Development Institute, Beaverton, OR, 97005, USA.
| | - Charles Keller
- Children's Cancer Therapy Development Institute, Beaverton, OR, 97005, USA.
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5
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Frankel AO, Lathara M, Shaw CY, Wogmon O, Jackson JM, Clark MM, Eshraghi N, Keenen SE, Woods AD, Purohit R, Ishi Y, Moran N, Eguchi M, Ahmed FUA, Khan S, Ioannou M, Perivoliotis K, Li P, Zhou H, Alkhaledi A, Davis EJ, Galipeau D, Randall RL, Wozniak A, Schoffski P, Lee CJ, Huang PH, Jones RL, Rubin BP, Darrow M, Srinivasa G, Rudzinski ER, Chen S, Berlow NE, Keller C. Machine learning for rhabdomyosarcoma histopathology. Mod Pathol 2022; 35:1193-1203. [PMID: 35449398 DOI: 10.1038/s41379-022-01075-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/16/2022] [Accepted: 03/19/2022] [Indexed: 02/07/2023]
Abstract
Correctly diagnosing a rare childhood cancer such as sarcoma can be critical to assigning the correct treatment regimen. With a finite number of pathologists worldwide specializing in pediatric/young adult sarcoma histopathology, access to expert differential diagnosis early in case assessment is limited for many global regions. The lack of highly-trained sarcoma pathologists is especially pronounced in low to middle-income countries, where pathology expertise may be limited despite a similar rate of sarcoma incidence. To address this issue in part, we developed a deep learning convolutional neural network (CNN)-based differential diagnosis system to act as a pre-pathologist screening tool that quantifies diagnosis likelihood amongst trained soft-tissue sarcoma subtypes based on whole histopathology tissue slides. The CNN model is trained on a cohort of 424 centrally-reviewed histopathology tissue slides of alveolar rhabdomyosarcoma, embryonal rhabdomyosarcoma and clear-cell sarcoma tumors, all initially diagnosed at the originating institution and subsequently validated by central review. This CNN model was able to accurately classify the withheld testing cohort with resulting receiver operating characteristic (ROC) area under curve (AUC) values above 0.889 for all tested sarcoma subtypes. We subsequently used the CNN model to classify an externally-sourced cohort of human alveolar and embryonal rhabdomyosarcoma samples and a cohort of 318 histopathology tissue sections from genetically engineered mouse models of rhabdomyosarcoma. Finally, we investigated the overall robustness of the trained CNN model with respect to histopathological variations such as anaplasia, and classification outcomes on histopathology slides from untrained disease models. Overall positive results from our validation studies coupled with the limited worldwide availability of sarcoma pathology expertise suggests the potential of machine learning to assist local pathologists in quickly narrowing the differential diagnosis of sarcoma subtype in children, adolescents, and young adults.
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Affiliation(s)
- Arthur O Frankel
- Children's Cancer Therapy Development Institute, Beaverton, OR, 97005, USA
| | | | - Celine Y Shaw
- Children's Cancer Therapy Development Institute, Beaverton, OR, 97005, USA
| | - Owen Wogmon
- Children's Cancer Therapy Development Institute, Beaverton, OR, 97005, USA
| | - Jacob M Jackson
- Children's Cancer Therapy Development Institute, Beaverton, OR, 97005, USA
| | - Mattie M Clark
- Children's Cancer Therapy Development Institute, Beaverton, OR, 97005, USA
| | - Navah Eshraghi
- Children's Cancer Therapy Development Institute, Beaverton, OR, 97005, USA
| | - Stephanie E Keenen
- Children's Cancer Therapy Development Institute, Beaverton, OR, 97005, USA
| | - Andrew D Woods
- Children's Cancer Therapy Development Institute, Beaverton, OR, 97005, USA
| | - Reshma Purohit
- Children's Cancer Therapy Development Institute, Beaverton, OR, 97005, USA
| | - Yukitomo Ishi
- Department of Neurosurgery, Hokkaido University School of Medicine, Sapporo, 060-8638, Japan
| | - Nirupama Moran
- Department of Otorhinolaryngology, Assam Medical College and Hospital, Assam, 786002, India
| | - Mariko Eguchi
- Department of Pediatrics, Ehime University Graduate School of Medicine, Ehime, 791-0295, Japan
| | - Farhat Ul Ain Ahmed
- Department of Obstetrics and Gynaecology, Fatima Memorial Hospital, Lahore, Pakistan
| | - Sara Khan
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, ON, M5G 1×8, Canada
| | - Maria Ioannou
- Department of Pathology, University of Thessaly, Biopolis Larisa, 41110, Greece
| | | | - Pin Li
- Department of Urology, Bayi Children's Hospital, Beijing, 100700, China
| | - Huixia Zhou
- Department of Urology, Bayi Children's Hospital, Beijing, 100700, China
| | - Ahmad Alkhaledi
- Department of Oncology, Damascus University Hospitals: Damascus, Damascus, Syria
| | | | - Danielle Galipeau
- OHSU Biolibrary, Oregon Health & Science University, Portland, OR, 97239, USA
| | - R L Randall
- Department of Orthopaedic Surgery, University of California Davis Health, Sacramento, CA, 95817, USA
| | - Agnieszka Wozniak
- Leuven Cancer Institute, University Hospitals Leuven, Department of Oncology & Research Unit Laboratory of Experimental Oncology, KU Leuven, Leuven, Belgium
| | - Patrick Schoffski
- Leuven Cancer Institute, University Hospitals Leuven, Department of Oncology & Research Unit Laboratory of Experimental Oncology, KU Leuven, Leuven, Belgium
| | - Che-Jui Lee
- Leuven Cancer Institute, University Hospitals Leuven, Department of Oncology & Research Unit Laboratory of Experimental Oncology, KU Leuven, Leuven, Belgium
| | - Paul H Huang
- Royal Marsden Hospital/Institute of Cancer Research, Fulham Road, London, SW3 6JJ, UK
| | - Robin L Jones
- Royal Marsden Hospital/Institute of Cancer Research, Fulham Road, London, SW3 6JJ, UK
| | - Brian P Rubin
- Pathology & Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Morgan Darrow
- Department of Pathology and Laboratory Medicine, University of California Davis Medical Center, Sacramento, CA, 95817, USA
| | | | | | - Sonja Chen
- Nationwide Children's Hospital, Columbus, OH, 43205, USA. .,Department of Pathology, Rhode Island Hospital, Providence, RI, 02903, USA.
| | - Noah E Berlow
- Children's Cancer Therapy Development Institute, Beaverton, OR, 97005, USA.
| | - Charles Keller
- Children's Cancer Therapy Development Institute, Beaverton, OR, 97005, USA.
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6
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Kim JA, Berlow NE, Lathara M, Bharathy N, Martin LR, Purohit R, Cleary MM, Liu Q, Michalek JE, Srinivasa G, Cole BL, Chen SD, Keller C. Sensitization of osteosarcoma to irradiation by targeting nuclear FGFR1. Biochem Biophys Res Commun 2022; 621:101-108. [DOI: 10.1016/j.bbrc.2022.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 06/22/2022] [Accepted: 07/01/2022] [Indexed: 11/30/2022]
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7
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Rasmussen SV, Jin JX, Bickford LR, Woods AD, Sahm F, Crawford KA, Nagamori K, Goto H, Torres KE, Sidoni A, Rudzinski ER, Thway K, Jones RL, Ciulli A, Wright H, Lathara M, Srinivasa G, Kannan K, Huang PH, Grünewald TGP, Berlow NE, Keller C. Functional genomic analysis of epithelioid sarcoma reveals distinct proximal and distal subtype biology. Clin Transl Med 2022; 12:e961. [PMID: 35839307 PMCID: PMC9286527 DOI: 10.1002/ctm2.961] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/13/2022] [Accepted: 06/17/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Metastatic epithelioid sarcoma (EPS) remains a largely unmet clinical need in children, adolescents and young adults despite the advent of EZH2 inhibitor tazemetostat. METHODS In order to realise consistently effective drug therapies, a functional genomics approach was used to identify key signalling pathway vulnerabilities in a spectrum of EPS patient samples. EPS biopsies/surgical resections and cell lines were studied by next-generation DNA exome and RNA deep sequencing, then EPS cell cultures were tested against a panel of chemical probes to discover signalling pathway targets with the most significant contributions to EPS tumour cell maintenance. RESULTS Other biologically inspired functional interrogations of EPS cultures using gene knockdown or chemical probes demonstrated only limited to modest efficacy in vitro. However, our molecular studies uncovered distinguishing features (including retained dysfunctional SMARCB1 expression and elevated GLI3, FYN and CXCL12 expression) of distal, paediatric/young adult-associated EPS versus proximal, adult-associated EPS. CONCLUSIONS Overall results highlight the complexity of the disease and a limited chemical space for therapeutic advancement. However, subtle differences between the two EPS subtypes highlight the biological disparities between younger and older EPS patients and emphasise the need to approach the two subtypes as molecularly and clinically distinct diseases.
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Affiliation(s)
| | - Jia Xiang Jin
- Division of Translational Pediatric Sarcoma Research, Hopp Children's Cancer Center (KiTZ), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | | | - Andrew D Woods
- Children's Cancer Therapy Development Institute, Beaverton, Oregon, USA
| | - Felix Sahm
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | | | - Kiyo Nagamori
- Children's Cancer Therapy Development Institute, Beaverton, Oregon, USA
| | - Hiroaki Goto
- Division of Hematology/Oncology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Keila E Torres
- Sarcoma Surgical Oncology, MD Anderson Cancer Center, Houston, Texas, USA
| | - Angelo Sidoni
- Section of Pathology, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Erin R Rudzinski
- Department of Pathology, Seattle Children's Hospital, Seattle, Washington, USA
| | - Khin Thway
- Sarcoma Unit, Royal Marsden Hospital, Belmont, UK.,Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | - Robin L Jones
- Sarcoma Unit, Royal Marsden Hospital, Belmont, UK.,Division of Clinical Studies, Institute of Cancer Research, London, UK
| | - Alessio Ciulli
- School of Life Sciences, University of Dundee, Dundee, UK
| | | | | | | | | | - Paul H Huang
- Sarcoma Unit, Royal Marsden Hospital, Belmont, UK.,Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | - Thomas G P Grünewald
- Division of Translational Pediatric Sarcoma Research, Hopp Children's Cancer Center (KiTZ), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Noah E Berlow
- Children's Cancer Therapy Development Institute, Beaverton, Oregon, USA
| | - Charles Keller
- Children's Cancer Therapy Development Institute, Beaverton, Oregon, USA
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8
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Woods AD, Berlow NE, Ortiz MV, Cruz FD, Siddiquee A, Coutinho DF, Purohit R, Freier KET, Michalek JE, Lathara M, Matlock K, Srivivasa G, Royer-Pokora B, Veselska R, Kung AL, Keller C. Bromodomain 4 inhibition leads to MYCN downregulation in Wilms tumor. Pediatr Blood Cancer 2022; 69:e29401. [PMID: 34693628 PMCID: PMC9450910 DOI: 10.1002/pbc.29401] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 09/17/2021] [Accepted: 09/22/2021] [Indexed: 02/03/2023]
Abstract
BACKGROUND Wilms tumor is the most common childhood kidney cancer. Two distinct histological subtypes of Wilms tumor have been described: tumors lacking anaplasia (the favorable subtype) and tumors displaying anaplastic features (the unfavorable subtype). Children with favorable disease generally have a very good prognosis, whereas those with anaplasia are oftentimes refractory to standard treatments and suffer poor outcomes, leading to an unmet clinical need. MYCN dysregulation has been associated with a number of pediatric cancers including Wilms tumor. PROCEDURES In this context, we undertook a functional genomics approach to uncover novel therapeutic strategies for those patients with anaplastic Wilms tumor. Genomic analysis and in vitro experimentation demonstrate that cell growth can be reduced by modulating MYCN overexpression via bromodomain 4 (BRD4) inhibition in both anaplastic and nonanaplastic Wilms tumor models. RESULTS We observed a time-dependent reduction of MYCN and MYCC protein levels upon BRD4 inhibition in Wilms tumor cell lines, which led to cell death and proliferation suppression. BRD4 inhibition significantly reduced tumor volumes in Wilms tumor patient-derived xenograft (PDX) mouse models. CONCLUSIONS We suggest that AZD5153, a novel dual-BRD4 inhibitor, can reduce MYCN levels in both anaplastic and nonanaplastic Wilms tumor cell lines, reduces tumor volume in Wilms tumor PDXs, and should be further explored for its therapeutic potential.
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Affiliation(s)
- Andrew D. Woods
- Children’s Cancer Therapy Development Institute, Beaverton, OR USA,correspondence to: Charles Keller MD, 12655 SW Beaverdam Rd W, Beaverton OR 97005 USA, tel: 801-232-8038, fax: 270-675-3313,
| | - Noah E. Berlow
- Children’s Cancer Therapy Development Institute, Beaverton, OR USA
| | - Michael V. Ortiz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York USA
| | - Filemon Dela Cruz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York USA
| | - Armaan Siddiquee
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York USA
| | - Diego F. Coutinho
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York USA
| | - Reshma Purohit
- Children’s Cancer Therapy Development Institute, Beaverton, OR USA
| | | | - Joel E. Michalek
- Department of Population Health Sciences, Joe R. & Teresa Lozano Long School of Medicine, University of Texas Health Science Center, San Antonio, TX USA
| | | | | | | | - Brigitte Royer-Pokora
- Institute of Human Genetics, Medical Faculty, Heinrich-Heine-University Duesseldorf, Germany
| | - Renata Veselska
- Department of Experimental Biology, Faculty of Science, Masaryk University Brno, Czech Republic
| | - Andrew L. Kung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York USA
| | - Charles Keller
- Children’s Cancer Therapy Development Institute, Beaverton, OR USA,correspondence to: Charles Keller MD, 12655 SW Beaverdam Rd W, Beaverton OR 97005 USA, tel: 801-232-8038, fax: 270-675-3313,
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9
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Rasmussen SV, Berlow NE, Price LH, Mansoor A, Cairo S, Rugonyi S, Keller C. Preclinical therapeutics ex ovo quail eggs as a biomimetic automation-ready xenograft platform. Sci Rep 2021; 11:23302. [PMID: 34857796 PMCID: PMC8639741 DOI: 10.1038/s41598-021-02509-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 11/10/2021] [Indexed: 01/10/2023] Open
Abstract
Preclinical cancer research ranges from in vitro studies that are inexpensive and not necessarily reflective of the tumor microenvironment to mouse studies that are better models but prohibitively expensive at scale. Chorioallantoic membrane (CAM) assays utilizing Japanese quail (Coturnix japonica) are a cost-effective screening method to precede and minimize the scope of murine studies for anti-cancer efficacy and drug toxicity. To increase the throughput of CAM assays we have built and optimized an 11-day platform for processing up to 200 quail eggs per screening to evaluate drug efficacy and drug toxicity caused by a therapeutic. We demonstrate ex ovo concordance with murine in vivo studies, even when the in vitro and in vivo studies diverge, suggesting a role for this quail shell-free CAM xenograft assay in the validation of new anti-cancer agents.
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Affiliation(s)
- Samuel V Rasmussen
- Children's Cancer Therapy Development Institute, 12655 SW Beaverdam Rd West, Beaverton, OR, 97005, USA
| | - Noah E Berlow
- Children's Cancer Therapy Development Institute, 12655 SW Beaverdam Rd West, Beaverton, OR, 97005, USA
| | - Lisa Hudson Price
- Children's Cancer Therapy Development Institute, 12655 SW Beaverdam Rd West, Beaverton, OR, 97005, USA
| | - Atiya Mansoor
- Children's Cancer Therapy Development Institute, 12655 SW Beaverdam Rd West, Beaverton, OR, 97005, USA
| | - Stefano Cairo
- Children's Cancer Therapy Development Institute, 12655 SW Beaverdam Rd West, Beaverton, OR, 97005, USA.,Xentech, Evry, France
| | - Sandra Rugonyi
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Charles Keller
- Children's Cancer Therapy Development Institute, 12655 SW Beaverdam Rd West, Beaverton, OR, 97005, USA.
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10
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Abstract
As high-throughput sequencing experiments become more widely used in pre-clinical and clinical settings, pharmacogenetic and pharmacogenomic biomarker development plays an increasingly important role in oncology drug development pipelines and programs. Consequently, computer-based learning approaches have entered into use at multiple stages in pre-clinical and clinical pipelines. However, few approaches are available to identify interpretable and implementable biomarkers of response early in the drug development process when only small pre-clinical data packages are available. To address the need for early-stage biomarker development using pre-clinical tumor models, we have adapted the previously published Probabilistic Target Inhibitor Map (PTIM) platform to the challenge of biomarker hypothesis development, and denoted this approach the Probabilistic Target Map-Biomarker (PTM-Biomarker). In this article, we detail the history and design philosophy of PTM-Biomarker, and present two case studies using the biomarker discovery tool to illustrate its utility in guiding cancer drug development. © 2021 Wiley Periodicals LLC.
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11
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Lian X, Kats D, Rasmussen S, Martin LR, Karki A, Keller C, Berlow NE. Correction to: Design considerations of an IL13Rα2 antibody-drug conjugate for difuse intrinsic pontine glioma. Acta Neuropathol Commun 2021; 9:114. [PMID: 34172087 PMCID: PMC8235579 DOI: 10.1186/s40478-021-01210-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
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12
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Lian X, Kats D, Rasmussen S, Martin LR, Karki A, Keller C, Berlow NE. Design considerations of an IL13Rα2 antibody-drug conjugate for diffuse intrinsic pontine glioma. Acta Neuropathol Commun 2021; 9:88. [PMID: 34001278 PMCID: PMC8127302 DOI: 10.1186/s40478-021-01184-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/18/2021] [Indexed: 11/10/2022] Open
Abstract
Diffuse intrinsic pontine glioma (DIPG), a rare pediatric brain tumor, afflicts approximately 350 new patients each year in the United States. DIPG is noted for its lethality, as fewer than 1% of patients survive to five years. Multiple clinical trials involving chemotherapy, radiotherapy, and/or targeted therapy have all failed to improve clinical outcomes. Recently, high-throughput sequencing of a cohort of DIPG samples identified potential therapeutic targets, including interleukin 13 receptor subunit alpha 2 (IL13Rα2) which was expressed in multiple tumor samples and comparably absent in normal brain tissue, identifying IL13Rα2 as a potential therapeutic target in DIPG. In this work, we investigated the role of IL13Rα2 signaling in progression and invasion of DIPG and viability of IL13Rα2 as a therapeutic target through the use of immunoconjugate agents. We discovered that IL13Rα2 stimulation via canonical ligands demonstrates minimal impact on both the cellular proliferation and cellular invasion of DIPG cells, suggesting IL13Rα2 signaling is non-essential for DIPG progression in vitro. However, exposure to an anti-IL13Rα2 antibody-drug conjugate demonstrated potent pharmacological response in DIPG cell models both in vitro and ex ovo in a manner strongly associated with IL13Rα2 expression, supporting the potential use of targeting IL13Rα2 as a DIPG therapy. However, the tested ADC was effective in most but not all cell models, thus selection of the optimal payload will be essential for clinical translation of an anti-IL13Rα2 ADC for DIPG.
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Affiliation(s)
- Xiaolei Lian
- Children's Cancer Therapy Development Institute, 12655 SW Beaverdam Road-West, Beaverton, OR, 97005, USA
| | - Dina Kats
- Children's Cancer Therapy Development Institute, 12655 SW Beaverdam Road-West, Beaverton, OR, 97005, USA
| | - Samuel Rasmussen
- Children's Cancer Therapy Development Institute, 12655 SW Beaverdam Road-West, Beaverton, OR, 97005, USA
| | - Leah R Martin
- Children's Cancer Therapy Development Institute, 12655 SW Beaverdam Road-West, Beaverton, OR, 97005, USA
| | - Anju Karki
- Children's Cancer Therapy Development Institute, 12655 SW Beaverdam Road-West, Beaverton, OR, 97005, USA
| | - Charles Keller
- Children's Cancer Therapy Development Institute, 12655 SW Beaverdam Road-West, Beaverton, OR, 97005, USA.
| | - Noah E Berlow
- Children's Cancer Therapy Development Institute, 12655 SW Beaverdam Road-West, Beaverton, OR, 97005, USA.
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13
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Berlow NE, Crawford KA, Bult CJ, Noakes C, Sloma I, Rudzinski ER, Keller C. Functional impact of a germline RET mutation in alveolar rhabdomyosarcoma. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a006049. [PMID: 33722797 PMCID: PMC8208040 DOI: 10.1101/mcs.a006049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 03/01/2021] [Indexed: 11/24/2022] Open
Abstract
Specific mutations in the RET proto-oncogene are associated with multiple endocrine neoplasia type 2A, a hereditary syndrome characterized by tumorigenesis in multiple glandular elements. In rare instances, MEN2A-associated germline RET mutations have also occurred with non-MEN2A associated cancers. One such germline mutant RET mutation occurred concomitantly in a young adult diagnosed with alveolar rhabdomyosarcoma, a pediatric and young adult soft-tissue cancer with a generally poor prognosis. Although tumor tissue samples were initially unable to provide a viable cell culture for study, tumor tissues were sequenced for molecular characteristics. Through a hierarchical clustering approach, the index case sample was matched to several genetically similar cell models, which were transformed to express the same mutant RET as the index case and used to explore potential therapeutic options for mutant RET-bearing alveolar rhabdomyosarcoma. We also determined whether the RET mutation associated with the index case caused synthetic lethality to select clinical agents. From our investigation, we did not identify synthetic lethality associated with the expression of that patient's RET variant, and overall we did not find experimental evidence for the role of RET in rhabdomyosarcoma progression.
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Affiliation(s)
- Noah E Berlow
- Children's Cancer Therapy Development Institute, Beaverton, Oregon 97005, USA
| | - Kenneth A Crawford
- Children's Cancer Therapy Development Institute, Beaverton, Oregon 97005, USA
| | - Carol J Bult
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | | | - Ido Sloma
- Champions Oncology, Hackensack, New Jersey 07601, USA
| | | | - Charles Keller
- Children's Cancer Therapy Development Institute, Beaverton, Oregon 97005, USA
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14
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Karki A, Berlow NE, Kim JA, Hulleman E, Liu Q, Michalek JE, Keller C. Receptor-driven invasion profiles in diffuse intrinsic pontine glioma. Neurooncol Adv 2021; 3:vdab039. [PMID: 34013206 PMCID: PMC8117434 DOI: 10.1093/noajnl/vdab039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Background Diffuse intrinsic pontine glioma (DIPG) is a devastating pediatric cancer with unmet clinical need. DIPG is invasive in nature, where tumor cells interweave into the fiber nerve tracts of the pons making the tumor unresectable. Accordingly, novel approaches in combating the disease are of utmost importance and receptor-driven cell invasion in the context of DIPG is under-researched area. Here, we investigated the impact on cell invasion mediated by PLEXINB1, PLEXINB2, platelet growth factor receptor (PDGFR)α, PDGFRβ, epithelial growth factor receptor (EGFR), activin receptor 1 (ACVR1), chemokine receptor 4 (CXCR4), and NOTCH1. Methods We used previously published RNA-sequencing data to measure gene expression of selected receptors in DIPG tumor tissue versus matched normal tissue controls (n = 18). We assessed protein expression of the corresponding genes using DIPG cell culture models. Then, we performed cell viability and cell invasion assays of DIPG cells stimulated with chemoattractants/ligands. Results RNA-sequencing data showed increased gene expression of receptor genes such as PLEXINB2, PDGFRα, EGFR, ACVR1, CXCR4, and NOTCH1 in DIPG tumors compared to the control tissues. Representative DIPG cell lines demonstrated correspondingly increased protein expression levels of these genes. Cell viability assays showed minimal effects of growth factors/chemokines on tumor cell growth in most instances. Recombinant SEMA4C, SEM4D, PDGF-AA, PDGF-BB, ACVA, CXCL12, and DLL4 ligand stimulation altered invasion in DIPG cells. Conclusions We show that no single growth factor-ligand pair universally induces DIPG cell invasion. However, our results reveal a potential to create a composite of cytokines or anti-cytokines to modulate DIPG cell invasion.
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Affiliation(s)
- Anju Karki
- Children's Cancer Therapy Development Institute, Beaverton, Oregon, USA
| | - Noah E Berlow
- Children's Cancer Therapy Development Institute, Beaverton, Oregon, USA
| | - Jin-Ah Kim
- Children's Cancer Therapy Development Institute, Beaverton, Oregon, USA
| | - Esther Hulleman
- Department of Pediatric Oncology/Hematology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, the Netherlands.,Princess Máxima Center for Pediatric Oncology, Utrecht,The Netherlands
| | - Qianqian Liu
- Department of Epidemiology and Biostatistics, University of Texas Health Science Center, San Antonio, Texas, USA
| | - Joel E Michalek
- Department of Epidemiology and Biostatistics, University of Texas Health Science Center, San Antonio, Texas, USA
| | - Charles Keller
- Children's Cancer Therapy Development Institute, Beaverton, Oregon, USA
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15
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Lian X, Bond JS, Bharathy N, Boudko SP, Pokidysheva E, Shern JF, Lathara M, Sasaki T, Settelmeyer T, Cleary MM, Bajwa A, Srinivasa G, Hartley CP, Bächinger HP, Mansoor A, Gultekin SH, Berlow NE, Keller C. Defining the Extracellular Matrix of Rhabdomyosarcoma. Front Oncol 2021; 11:601957. [PMID: 33708626 PMCID: PMC7942227 DOI: 10.3389/fonc.2021.601957] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 01/05/2021] [Indexed: 01/20/2023] Open
Abstract
Rhabdomyosarcoma (RMS) is the most common soft-tissue sarcoma of childhood with a propensity to metastasize. Current treatment for patients with RMS includes conventional systemic chemotherapy, radiation therapy, and surgical resection; nevertheless, little to no improvement in long term survival has been achieved in decades-underlining the need for target discovery and new therapeutic approaches to targeting tumor cells or the tumor microenvironment. To evaluate cross-species sarcoma extracellular matrix production, we have used murine models which feature knowledge of the myogenic cell-of-origin. With focus on the RMS/undifferentiated pleomorphic sarcoma (UPS) continuum, we have constructed tissue microarrays of 48 murine and four human sarcomas to analyze expression of seven different collagens, fibrillins, and collagen-modifying proteins, with cross-correlation to RNA deep sequencing. We have uncovered that RMS produces increased expression of type XVIII collagen alpha 1 (COL18A1), which is clinically associated with decreased long-term survival. We have also identified significantly increased RNA expression of COL4A1, FBN2, PLOD1, and PLOD2 in human RMS relative to normal skeletal muscle. These results complement recent studies investigating whether soft tissue sarcomas utilize collagens, fibrillins, and collagen-modifying enzymes to alter the structural integrity of surrounding host extracellular matrix/collagen quaternary structure resulting in improved ability to improve the ability to invade regionally and metastasize, for which therapeutic targeting is possible.
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Affiliation(s)
- Xiaolei Lian
- Pediatric Cancer Biology, Children’s Cancer Therapy Development Institute, Beaverton, OR, United States
| | - J. Steffan Bond
- Department of Pathology, Oregon Health & Science University, Portland, OR, United States
| | - Narendra Bharathy
- Pediatric Cancer Biology, Children’s Cancer Therapy Development Institute, Beaverton, OR, United States
| | - Sergei P. Boudko
- Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Elena Pokidysheva
- Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Jack F. Shern
- Pediatric Oncology Branch, Center for Cancer Research, National Institutes of Health, Bethesda, MD, United States
| | - Melvin Lathara
- Bioinformatics, Omics Data Automation, Beaverton, OR, United States
| | - Takako Sasaki
- Department of Matrix Medicine, Oita University, Oita, Japan
| | - Teagan Settelmeyer
- Pediatric Cancer Biology, Children’s Cancer Therapy Development Institute, Beaverton, OR, United States
| | - Megan M. Cleary
- Pediatric Cancer Biology, Children’s Cancer Therapy Development Institute, Beaverton, OR, United States
| | - Ayeza Bajwa
- Pediatric Cancer Biology, Children’s Cancer Therapy Development Institute, Beaverton, OR, United States
| | | | | | - Hans Peter Bächinger
- Department of Biochemistry and Molecular Biology, Shriners Hospital for Children, Portland, OR, United States
| | - Atiya Mansoor
- Department of Pathology, Oregon Health & Science University, Portland, OR, United States
| | - Sakir H. Gultekin
- Department of Pathology, Oregon Health & Science University, Portland, OR, United States
| | - Noah E. Berlow
- Pediatric Cancer Biology, Children’s Cancer Therapy Development Institute, Beaverton, OR, United States
| | - Charles Keller
- Pediatric Cancer Biology, Children’s Cancer Therapy Development Institute, Beaverton, OR, United States
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16
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Ricker CA, Woods AD, Simonson W, Lathara M, Srinivasa G, Rudzinski ER, Mansoor A, Irwin RG, Keller C, Berlow NE. Refractory alveolar rhabdomyosarcoma in an 11-year-old male. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a005983. [PMID: 33436392 PMCID: PMC7903883 DOI: 10.1101/mcs.a005983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 02/11/2021] [Indexed: 12/29/2022] Open
Abstract
Rhabdomyosarcoma (RMS) is a mesenchymal malignancy phenocopying muscle and is among the leading causes of death from childhood cancer. Metastatic alveolar rhabdomyosarcoma is the most aggressive subtype with an 8% 5-yr disease-free survival rate when a chromosomal fusion is present and a 29% 5-yr disease-free survival rate when negative for a fusion event. The underlying biology of PAX-fusion-negative alveolar rhabdomyosarcoma remains largely unexplored and is exceedingly rare in Li–Fraumeni syndrome patients. Here, we present the case of an 11-yr-old male with fusion-negative alveolar rhabdomyosarcoma studied at end of life with a comprehensive functional genomics characterization, resulting in identification of potential therapeutic targets for broader investigation.
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Affiliation(s)
- Cora A Ricker
- Children's Cancer Therapy Development Institute, Beaverton, Oregon 97005, USA
| | - Andrew D Woods
- Children's Cancer Therapy Development Institute, Beaverton, Oregon 97005, USA
| | | | | | | | - Erin R Rudzinski
- Department of Laboratories, Seattle Children's Hospital, Seattle, Washington 98105, USA
| | - Atiya Mansoor
- Children's Cancer Therapy Development Institute, Beaverton, Oregon 97005, USA
| | | | - Charles Keller
- Children's Cancer Therapy Development Institute, Beaverton, Oregon 97005, USA
| | - Noah E Berlow
- Children's Cancer Therapy Development Institute, Beaverton, Oregon 97005, USA
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17
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Crawford KA, Berlow NE, Tsay J, Lazich M, Mancini M, Noakes C, Huang T, Keller C. Case report for an adolescent with germline RET mutation and alveolar rhabdomyosarcoma. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a004853. [PMID: 32532875 PMCID: PMC7304354 DOI: 10.1101/mcs.a004853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 04/13/2020] [Indexed: 11/25/2022] Open
Abstract
In this case report we evaluate the genetics of and scientific basis of therapeutic options for a 14-yr-old male patient diagnosed with metastatic PAX3–FOXO1 fusion positive alveolar rhabdomyosarcoma. A distinguishing genetic feature of this patient was a germline RET C634F mutation, which is a known driver of multiple endocrine neoplasia type 2A (MEN2A) cancer. Through sequential DNA and RNA sequencing analyses over the patient's clinical course, a set of gene mutations, amplifications, and overexpressed genes were identified and biological hypotheses generated to explore the biology of RET and coexisting signaling pathways in rhabdomyosarcoma. Somatic genetic abnormalities identified include CDK4 amplification and FGFR4 G388R polymorphism. Because of the initial lack of patient-derived primary cell cultures, these hypotheses were evaluated using several approaches including western blot analysis and pharmacological evaluation with molecularly similar alveolar rhabdomyosarcoma cell lines. Once a primary cell culture became available, the RET inhibitor cabozantinib was tested but showed no appreciable efficacy in vitro, affirming with the western blot negative for RET protein expression that RET germline mutation could be only incidental. In parallel, the patient was treated with cabozantinib without definitive clinical benefit. Parallel chemical screens identified PI3K and HSP90 as potential tumor-specific biological features. Inhibitors of PI3K and HSP90 were further validated in drug combination synergy experiments and shown to be synergistic in the patient-derived culture. We also evaluated the use of JAK/STAT pathway inhibitors in the context of rhabdomyosarcomas bearing the FGFR4 G388R coding variant. Although the patient succumbed to his disease, study of the patient's tumor has generated insights into the biology of RET and other targets in rhabdomyosarcoma.
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Affiliation(s)
- Kenneth A Crawford
- Children's Cancer Therapy Development Institute, Beaverton, Oregon 97005, USA
| | - Noah E Berlow
- Children's Cancer Therapy Development Institute, Beaverton, Oregon 97005, USA
| | - Jennifer Tsay
- 2016 Pediatric Cancer Nanocourse, Children's Cancer Therapy Development Institute, Beaverton, Oregon 97005, USA
| | - Michael Lazich
- 2016 Pediatric Cancer Nanocourse, Children's Cancer Therapy Development Institute, Beaverton, Oregon 97005, USA
| | - Maria Mancini
- Champions Oncology, Hackensack, New Jersey 07601, USA
| | | | - Tannie Huang
- Kaiser Permanente Santa Clara Medical Center, Santa Clara, California 95051, USA
| | - Charles Keller
- Children's Cancer Therapy Development Institute, Beaverton, Oregon 97005, USA
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18
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Ricker CA, Crawford K, Matlock K, Lathara M, Seguin B, Rudzinski ER, Berlow NE, Keller C. Defining an embryonal rhabdomyosarcoma endotype. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a005066. [PMID: 32238403 PMCID: PMC7133750 DOI: 10.1101/mcs.a005066] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/13/2020] [Indexed: 02/06/2023] Open
Abstract
Rhabdomyosarcoma (RMS) is the most common childhood soft-tissue sarcoma. The largest subtype of RMS is embryonal rhabdomyosarcoma (ERMS) and accounts for 53% of all RMS. ERMS typically occurs in the head and neck region, bladder, or reproductive organs and portends a promising prognosis when localized; however, when metastatic the 5-yr overall survival rate is ∼43%. The genomic landscape of ERMS demonstrates a range of putative driver mutations, and thus the recognition of the pathological mechanisms driving tumor maintenance should be critical for identifying effective targeted treatments at the level of the individual patients. Here, we report genomic, phenotypic, and bioinformatic analyses for a case of a 3-yr-old male who presented with bladder ERMS. Additionally, we use an unsupervised agglomerative clustering analysis of RNA and whole-exome sequencing data across ERMS and undifferentiated pleomorphic sarcoma (UPS) tumor samples to determine several major endotypes inferring potential targeted treatments for a spectrum of pediatric ERMS patient cases.
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Affiliation(s)
- Cora A Ricker
- Children's Cancer Therapy Development Institute, Beaverton, Oregon 97005, USA
| | - Kenneth Crawford
- Children's Cancer Therapy Development Institute, Beaverton, Oregon 97005, USA
| | | | | | - Bernard Seguin
- Flint Animal Cancer Center, Colorado State University, Fort Collins, Colorado 80525, USA
| | | | - Noah E Berlow
- Children's Cancer Therapy Development Institute, Beaverton, Oregon 97005, USA
| | - Charles Keller
- Children's Cancer Therapy Development Institute, Beaverton, Oregon 97005, USA
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19
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Ricker CA, Berlow NE, Crawford KA, Georgopapadakos T, Huelskamp AN, Woods AD, Dhimolea E, Ramkissoon SH, Spunt SL, Rudzinski ER, Keller C. Undifferentiated small round cell sarcoma in a young male: a case report. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a004812. [PMID: 32014859 PMCID: PMC6996518 DOI: 10.1101/mcs.a004812] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 12/09/2019] [Indexed: 12/12/2022] Open
Abstract
CIC-rearranged sarcomas (CRSs) have recently been characterized as a distinct sarcoma subgroup with a less favorable prognosis compared to other small round cell sarcomas. CRSs share morphologic features with Ewing's sarcoma and prior to 2013 were grouped under undifferentiated sarcomas with round cell phenotype by the WHO classification. In this report, whole-genome sequencing and RNA sequencing were performed for an adolescent male patient with CRS who was diagnosed with undifferentiated pleomorphic sarcoma (UPS) by three contemporary institutions. Somatic mutation analysis identified mutations in IQGAP1, CCNC, and ATXN1L in pre- and post-treatment tissue samples, as well as a CIC–DUX4 fusion that was confirmed by qPCR and DUX4 immunohistochemistry. Of particular interest was the overexpression of the translation factor eEF1A1, which has oncogenic properties and has recently been identified as a target of the investigational agent plitidepsin. This case may provide a valuable waypoint in the understanding and classification of CRSs and may provide a rationale for targeting eEF1A1 in similar soft tissue sarcoma cases.
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Affiliation(s)
- Cora A Ricker
- Children's Cancer Therapy Development Institute, Beaverton, Oregon 97005, USA
| | - Noah E Berlow
- Children's Cancer Therapy Development Institute, Beaverton, Oregon 97005, USA
| | - Kenneth A Crawford
- Children's Cancer Therapy Development Institute, Beaverton, Oregon 97005, USA
| | | | - Audrey N Huelskamp
- Children's Cancer Therapy Development Institute, Beaverton, Oregon 97005, USA
| | - Andrew D Woods
- Children's Cancer Therapy Development Institute, Beaverton, Oregon 97005, USA
| | - Eugen Dhimolea
- Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | | | - Sheri L Spunt
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, California 94304, USA
| | | | - Charles Keller
- Children's Cancer Therapy Development Institute, Beaverton, Oregon 97005, USA
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20
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Harrold AP, Cleary MM, Bharathy N, Lathara M, Berlow NE, Foreman NK, Donson AM, Amani V, Zuercher WJ, Keller C. In vitro benchmarking of NF-κB inhibitors. Eur J Pharmacol 2020; 873:172981. [PMID: 32014486 DOI: 10.1016/j.ejphar.2020.172981] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 01/30/2020] [Accepted: 01/30/2020] [Indexed: 11/27/2022]
Abstract
Dysregulated activity of the transcription factors of the nuclear factor κb (NF-κB) family has been implicated in numerous cancer types, inflammatory diseases, autoimmune disease, and other disorders. As such, selective NF-κB pathway inhibition is an attractive target to researchers for preclinical and clinical drug development. A plethora of commercially and clinically available inhibitors claim to be NF-κB specific; however, such claims of specificity are rarely quantitative or benchmarked, making the biomedical literature difficult to contextualize. This imprecision is worsened because some NF-κB reporter systems have low signal-to-noise ratios. Herein, we use a robust, defined, commercially available reporter system to benchmark NF-κB agonists and antagonists for the field. We also functionally characterize a RELA fusion-positive ependymoma cell culture with validated NF-κB inhibitor compounds.
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Affiliation(s)
| | - Megan M Cleary
- Children's Cancer Therapy Development Institute, Beaverton, OR, 97005, USA
| | - Narendra Bharathy
- Children's Cancer Therapy Development Institute, Beaverton, OR, 97005, USA
| | | | - Noah E Berlow
- Children's Cancer Therapy Development Institute, Beaverton, OR, 97005, USA
| | - Nicholas K Foreman
- Department of Pediatrics, University of Colorado Denver, Aurora, CO, 80045, USA
| | - Andrew M Donson
- Department of Pediatrics, University of Colorado Denver, Aurora, CO, 80045, USA
| | - Vladimir Amani
- Department of Pediatrics, University of Colorado Denver, Aurora, CO, 80045, USA
| | - William J Zuercher
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, SGC Center for Chemical Biology, Chapel Hill, NC, 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Charles Keller
- Children's Cancer Therapy Development Institute, Beaverton, OR, 97005, USA.
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21
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Bharathy N, Berlow NE, Wang E, Abraham J, Settelmeyer TP, Hooper JE, Svalina MN, Bajwa Z, Goros MW, Hernandez BS, Wolff JE, Pal R, Davies AM, Ashok A, Bushby D, Mancini M, Noakes C, Goodwin NC, Ordentlich P, Keck J, Hawkins DS, Rudzinski ER, Mansoor A, Perkins TJ, Vakoc CR, Michalek JE, Keller C. Preclinical rationale for entinostat in embryonal rhabdomyosarcoma. Skelet Muscle 2019; 9:12. [PMID: 31113472 PMCID: PMC6528217 DOI: 10.1186/s13395-019-0198-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 04/17/2019] [Indexed: 11/10/2022] Open
Abstract
Background Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in the pediatric cancer population. Survival among metastatic RMS patients has remained dismal yet unimproved for years. We previously identified the class I-specific histone deacetylase inhibitor, entinostat (ENT), as a pharmacological agent that transcriptionally suppresses the PAX3:FOXO1 tumor-initiating fusion gene found in alveolar rhabdomyosarcoma (aRMS), and we further investigated the mechanism by which ENT suppresses PAX3:FOXO1 oncogene and demonstrated the preclinical efficacy of ENT in RMS orthotopic allograft and patient-derived xenograft (PDX) models. In this study, we investigated whether ENT also has antitumor activity in fusion-negative eRMS orthotopic allografts and PDX models either as a single agent or in combination with vincristine (VCR). Methods We tested the efficacy of ENT and VCR as single agents and in combination in orthotopic allograft and PDX mouse models of eRMS. We then performed CRISPR screening to identify which HDAC among the class I HDACs is responsible for tumor growth inhibition in eRMS. To analyze whether ENT treatment as a single agent or in combination with VCR induces myogenic differentiation, we performed hematoxylin and eosin (H&E) staining in tumors. Results ENT in combination with the chemotherapy VCR has synergistic antitumor activity in a subset of fusion-negative eRMS in orthotopic “allografts,” although PDX mouse models were too hypersensitive to the VCR dose used to detect synergy. Mechanistic studies involving CRISPR suggest that HDAC3 inhibition is the primary mechanism of cell-autonomous cytoreduction in eRMS. Following cytoreduction in vivo, residual tumor cells in the allograft models treated with chemotherapy undergo a dramatic, entinostat-induced (70–100%) conversion to non-proliferative rhabdomyoblasts. Conclusion Our results suggest that the targeting class I HDACs may provide a therapeutic benefit for selected patients with eRMS. ENT’s preclinical in vivo efficacy makes ENT a rational drug candidate in a phase II clinical trial for eRMS. Electronic supplementary material The online version of this article (10.1186/s13395-019-0198-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Narendra Bharathy
- Children's Cancer Therapy Development Institute, 12655 Sw Beaverdam Rd. W, Beaverton, OR, 97005, USA.
| | - Noah E Berlow
- Children's Cancer Therapy Development Institute, 12655 Sw Beaverdam Rd. W, Beaverton, OR, 97005, USA
| | - Eric Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Jinu Abraham
- Department of Pediatrics, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Teagan P Settelmeyer
- Children's Cancer Therapy Development Institute, 12655 Sw Beaverdam Rd. W, Beaverton, OR, 97005, USA
| | - Jody E Hooper
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Matthew N Svalina
- Children's Cancer Therapy Development Institute, 12655 Sw Beaverdam Rd. W, Beaverton, OR, 97005, USA
| | - Zia Bajwa
- Children's Cancer Therapy Development Institute, 12655 Sw Beaverdam Rd. W, Beaverton, OR, 97005, USA.,Department of Pathology, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Martin W Goros
- Department of Epidemiology and Biostatistics, University of Texas Health Science Center, San Antonio, TX, 78229, USA
| | - Brian S Hernandez
- Department of Epidemiology and Biostatistics, University of Texas Health Science Center, San Antonio, TX, 78229, USA
| | - Johannes E Wolff
- Department of Pediatric Hematology Oncology and Blood and Marrow Transplantation, Cleveland Clinic Children's, Cleveland, OH, 44195, USA.,Present Address: AbbVie, North Chicago, IL, 60064, USA
| | - Ranadip Pal
- Electrical and Computer Engineering, Texas Tech University, Lubbock, TX, 79409, USA
| | | | - Arya Ashok
- Champions Oncology, Rockville, MD, 20850, USA
| | | | | | | | | | | | - James Keck
- The Jackson Laboratory, Sacramento, CA, 95838, USA
| | | | | | - Atiya Mansoor
- Department of Pathology, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Theodore J Perkins
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, K1H 8L6, Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, K1H 8M5, Canada
| | | | - Joel E Michalek
- Department of Epidemiology and Biostatistics, University of Texas Health Science Center, San Antonio, TX, 78229, USA
| | - Charles Keller
- Children's Cancer Therapy Development Institute, 12655 Sw Beaverdam Rd. W, Beaverton, OR, 97005, USA.
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22
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Wei Q, Ramsey SA, Larson MK, Berlow NE, Ochola D, Shiprack C, Kashyap A, Séguin B, Keller C, Löhr CV. Elucidating the transcriptional program of feline injection-site sarcoma using a cross-species mRNA-sequencing approach. BMC Cancer 2019; 19:311. [PMID: 30947707 PMCID: PMC6449919 DOI: 10.1186/s12885-019-5501-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 03/20/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Feline injection-site sarcoma (FISS), an aggressive iatrogenic subcutaneous malignancy, is challenging to manage clinically and little is known about the molecular basis of its pathogenesis. Tumor transcriptome profiling has proved valuable for gaining insights into the molecular basis of cancers and for identifying new therapeutic targets. Here, we report the first study of the FISS transcriptome and the first cross-species comparison of the FISS transcriptome with those of anatomically similar soft-tissue sarcomas in dogs and humans. METHODS Using high-throughput short-read paired-end sequencing, we comparatively profiled FISS tumors vs. normal tissue samples as well as cultured FISS-derived cell lines vs. skin-derived fibroblasts. We analyzed the mRNA-seq data to compare cancer/normal gene expression level, identify biological processes and molecular pathways that are associated with the pathogenesis of FISS, and identify multimegabase genomic regions of potential somatic copy number alteration (SCNA) in FISS. We additionally conducted cross-species analyses to compare the transcriptome of FISS to those of soft-tissue sarcomas in dogs and humans, at the level of cancer/normal gene expression ratios. RESULTS We found: (1) substantial differential expression biases in feline orthologs of human oncogenes and tumor suppressor genes suggesting conserved functions in FISS; (2) a genomic region with recurrent SCNA in human sarcomas that is syntenic to a feline genomic region of probable SCNA in FISS; and (3) significant overlap of the pattern of transcriptional alterations in FISS with the patterns of transcriptional alterations in soft-tissue sarcomas in humans and in dogs. We demonstrated that a protein, BarH-like homeobox 1 (BARX1), has increased expression in FISS cells at the protein level. We identified 11 drugs and four target proteins as potential new therapies for FISS, and validated that one of them (GSK-1059615) inhibits growth of FISS-derived cells in vitro. CONCLUSIONS (1) Window-based analysis of mRNA-seq data can uncover SCNAs. (2) The transcriptome of FISS-derived cells is highly consistent with that of FISS tumors. (3) FISS is highly similar to soft-tissue sarcomas in dogs and humans, at the level of gene expression. This work underscores the potential utility of comparative oncology in improving understanding and treatment of FISS.
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Affiliation(s)
- Qi Wei
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR, USA
| | - Stephen A Ramsey
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR, USA.
| | - Maureen K Larson
- Department of Clinical Sciences, Oregon State University, Corvallis, OR, USA
| | - Noah E Berlow
- Children's Cancer Therapy Development Institute, Beaverton, OR, USA
| | - Donasian Ochola
- Flint Animal Cancer Center, Colorado State University, Fort Collins, CO, USA
| | | | - Amita Kashyap
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR, USA
| | - Bernard Séguin
- Flint Animal Cancer Center, Colorado State University, Fort Collins, CO, USA
| | - Charles Keller
- Children's Cancer Therapy Development Institute, Beaverton, OR, USA
| | - Christiane V Löhr
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR, USA.
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23
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Bharathy N, Berlow NE, Wang E, Abraham J, Settelmeyer TP, Hooper JE, Svalina MN, Ishikawa Y, Zientek K, Bajwa Z, Goros MW, Hernandez BS, Wolff JE, Rudek MA, Xu L, Anders NM, Pal R, Harrold AP, Davies AM, Ashok A, Bushby D, Mancini M, Noakes C, Goodwin NC, Ordentlich P, Keck J, Hawkins DS, Rudzinski ER, Chatterjee B, Bächinger HP, Barr FG, Liddle J, Garcia BA, Mansoor A, Perkins TJ, Vakoc CR, Michalek JE, Keller C. The HDAC3-SMARCA4-miR-27a axis promotes expression of the PAX3:FOXO1 fusion oncogene in rhabdomyosarcoma. Sci Signal 2018; 11:11/557/eaau7632. [PMID: 30459282 DOI: 10.1126/scisignal.aau7632] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma of childhood with an unmet clinical need for decades. A single oncogenic fusion gene is associated with treatment resistance and a 40 to 45% decrease in overall survival. We previously showed that expression of this PAX3:FOXO1 fusion oncogene in alveolar RMS (aRMS) mediates tolerance to chemotherapy and radiotherapy and that the class I-specific histone deacetylase (HDAC) inhibitor entinostat reduces PAX3:FOXO1 protein abundance. Here, we established the antitumor efficacy of entinostat with chemotherapy in various preclinical cell and mouse models and found that HDAC3 inhibition was the primary mechanism of entinostat-induced suppression of PAX3:FOXO1 abundance. HDAC3 inhibition by entinostat decreased the activity of the chromatin remodeling enzyme SMARCA4, which, in turn, derepressed the microRNA miR-27a. This reexpression of miR-27a led to PAX3:FOXO1 mRNA destabilization and chemotherapy sensitization in aRMS cells in culture and in vivo. Furthermore, a phase 1 clinical trial (ADVL1513) has shown that entinostat is tolerable in children with relapsed or refractory solid tumors and is planned for phase 1B cohort expansion or phase 2 clinical trials. Together, these results implicate an HDAC3-SMARCA4-miR-27a-PAX3:FOXO1 circuit as a driver of chemoresistant aRMS and suggest that targeting this pathway with entinostat may be therapeutically effective in patients.
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Affiliation(s)
- Narendra Bharathy
- Children's Cancer Therapy Development Institute, Beaverton, OR 97005, USA
| | - Noah E Berlow
- Children's Cancer Therapy Development Institute, Beaverton, OR 97005, USA
| | - Eric Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Jinu Abraham
- Department of Pediatrics, Oregon Health & Science University, Portland, OR 97239, USA
| | | | - Jody E Hooper
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Matthew N Svalina
- Children's Cancer Therapy Development Institute, Beaverton, OR 97005, USA
| | - Yoshihiro Ishikawa
- Research Center, Shriners Hospital for Children, Portland, OR 97239, USA
| | - Keith Zientek
- Research Center, Shriners Hospital for Children, Portland, OR 97239, USA
| | - Zia Bajwa
- Children's Cancer Therapy Development Institute, Beaverton, OR 97005, USA.,Department of Pathology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Martin W Goros
- Department of Epidemiology and Biostatistics, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Brian S Hernandez
- Department of Epidemiology and Biostatistics, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Johannes E Wolff
- Department of Pediatric Hematology Oncology and Blood and Marrow Transplantation, Cleveland Clinic Children's, Cleveland, OH 44195, USA
| | - Michelle A Rudek
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD 21231, USA.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD 21224, USA.,Division of Clinical Pharmacology, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Linping Xu
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD 21231, USA.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD 21224, USA
| | - Nicole M Anders
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD 21231, USA.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD 21224, USA
| | - Ranadip Pal
- Electrical and Computer Engineering, Texas Tech University, Lubbock, TX 79409, USA
| | | | | | - Arya Ashok
- Champions Oncology, Rockville, MD 20850, USA
| | | | | | | | | | | | - James Keck
- The Jackson Laboratory, Sacramento, CA 95838, USA
| | | | | | - Bishwanath Chatterjee
- Cancer Molecular Pathology Section, Laboratory of Pathology, National Cancer Institute, Bethesda, MD 20892-1500, USA
| | - Hans Peter Bächinger
- Research Center, Shriners Hospital for Children, Portland, OR 97239, USA.,Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Frederic G Barr
- Cancer Molecular Pathology Section, Laboratory of Pathology, National Cancer Institute, Bethesda, MD 20892-1500, USA
| | - Jennifer Liddle
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Atiya Mansoor
- Department of Pathology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Theodore J Perkins
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa K1H 8L6, Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa K1H 8M5, Canada
| | | | - Joel E Michalek
- Department of Epidemiology and Biostatistics, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Charles Keller
- Children's Cancer Therapy Development Institute, Beaverton, OR 97005, USA.
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24
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Berlow NE, Svalina MN, Quist MJ, Settelmeyer TP, Zherebitskiy V, Kogiso M, Qi L, Du Y, Hawkins CE, Hulleman E, Li XN, Gultekin SH, Keller C. IL-13 receptors as possible therapeutic targets in diffuse intrinsic pontine glioma. PLoS One 2018; 13:e0193565. [PMID: 29621254 PMCID: PMC5886401 DOI: 10.1371/journal.pone.0193565] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Accepted: 02/14/2018] [Indexed: 11/19/2022] Open
Abstract
Diffuse intrinsic pontine glioma (DIPG) is a universally fatal childhood cancer of the brain. Despite the introduction of conventional chemotherapy and radiotherapy, improvements in survival have been marginal and long-term survivorship is uncommon. Thus, new targets for therapeutics are critically needed. Early phase clinical trials exploring molecularly-targeted therapies against the epidermal growth factor receptor (EGFR) and novel immunotherapies targeting interleukin receptor-13α2 (IL-13Rα2) have demonstrated activity in this disease. To identify additional therapeutic markers for cell surface receptors, we performed exome sequencing (16 new samples, 22 previously published samples, total 38 with 26 matched normal DNA samples), RNA deep sequencing (17 new samples, 11 previously published samples, total 28 with 18 matched normal RNA samples), and immunohistochemistry (17 DIPG tissue samples) to examine the expression of the interleukin-4 (IL-4) signaling axis components (IL-4, interleukin 13 (IL-13), and their respective receptors IL-4Rα, IL-13Rα1, and IL-13Rα2). In addition, we correlated cytokine and receptor expression with expression of the oncogenes EGFR and c-MET. In DIPG tissues, transcript-level analysis found significant expression of IL-4, IL-13, and IL-13Rα1/2, with strong differential expression of IL-13Rα1/2 in tumor versus normal brain. At the protein level, immunohistochemical studies revealed high content of IL-4 and IL-13Rα1/2 but notably low expression of IL-13. Additionally, a strong positive correlation was observed between c-Met and IL-4Rα. The genomic and transcriptional landscape across all samples was also summarized. These data create a foundation for the design of potential new immunotherapies targeting IL-13 cell surface receptors in DIPG.
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Affiliation(s)
- Noah E. Berlow
- Children's Cancer Therapy Development Institute, Beaverton, OR, United States of America
| | - Matthew N. Svalina
- Children's Cancer Therapy Development Institute, Beaverton, OR, United States of America
| | - Michael J. Quist
- Children's Cancer Therapy Development Institute, Beaverton, OR, United States of America
| | - Teagan P. Settelmeyer
- Children's Cancer Therapy Development Institute, Beaverton, OR, United States of America
| | - Viktor Zherebitskiy
- Department of Pathology, Oregon Health & Science University, Portland, OR, United States of America
| | - Mari Kogiso
- Department of Pediatrics, Texas Children's Cancer Center, Houston, TX, United States of America
| | - Lin Qi
- Department of Pediatrics, Texas Children's Cancer Center, Houston, TX, United States of America
| | - Yuchen Du
- Department of Pediatrics, Texas Children's Cancer Center, Houston, TX, United States of America
| | - Cynthia E. Hawkins
- Division of Pathology, The Hospital for Sick Children, Toronto, ON, CANADA
| | - Esther Hulleman
- Neuro-Oncology Research Group, Cancer Center Amsterdam, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands
| | - Xiao-Nan Li
- Department of Pediatrics, Texas Children's Cancer Center, Houston, TX, United States of America
| | - Sakir H. Gultekin
- Department of Pathology, Oregon Health & Science University, Portland, OR, United States of America
| | - Charles Keller
- Children's Cancer Therapy Development Institute, Beaverton, OR, United States of America
- Department of Pediatrics, Oregon Health & Science University, Portland, OR, United States of America
- * E-mail:
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25
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Grasso CS, Tang Y, Truffaux N, Berlow NE, Liu L, Debily MA, Quist MJ, Davis LE, Huang EC, Woo PJ, Ponnuswami A, Chen S, Johung TB, Sun W, Kogiso M, Du Y, Qi L, Huang Y, Hütt-Cabezas M, Warren KE, Le Dret L, Meltzer PS, Mao H, Quezado M, van Vuurden DG, Abraham J, Fouladi M, Svalina MN, Wang N, Hawkins C, Nazarian J, Alonso MM, Raabe EH, Hulleman E, Spellman PT, Li XN, Keller C, Pal R, Grill J, Monje M. Functionally defined therapeutic targets in diffuse intrinsic pontine glioma. Nat Med 2015; 21:555-9. [PMID: 25939062 PMCID: PMC4862411 DOI: 10.1038/nm.3855] [Citation(s) in RCA: 378] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 04/10/2015] [Indexed: 12/16/2022]
Abstract
Diffuse Intrinsic Pontine Glioma (DIPG) is a fatal childhood cancer. We performed a chemical screen in patient-derived DIPG cultures along with RNAseq analyses and integrated computational modeling to identify potentially effective therapeutic strategies. The multi-histone deacetylase inhibitor panobinostat demonstrated efficacy in vitro and in DIPG orthotopic xenograft models. Combination testing of panobinostat with histone demethylase inhibitor GSKJ4 revealed synergy. Together, these data suggest a promising therapeutic strategy for DIPG.
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Affiliation(s)
- Catherine S Grasso
- Center for Spatial Systems Biomedicine, Department of Molecular and Medical Genetics, Oregon Health &Science University (OHSU), Portland, Oregon, USA
| | - Yujie Tang
- 1] Department of Neurology, Stanford University, Stanford, California, USA. [2] Department of Neurosurgery, Stanford University, Stanford, California, USA. [3] Department of Pediatrics, Stanford University, Stanford, California, USA. [4] Department of Pathology, Stanford University, Stanford, California, USA. [5] Present addresses: Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China (Y.T.) and Department of Neurosurgery, The First Affiliated Hospital of Suzhou University, Suzhou, China (Y.H.)
| | | | - Noah E Berlow
- Electrical and Computer Engineering, Texas Tech University, Lubbock, Texas, USA
| | - Lining Liu
- 1] Department of Neurology, Stanford University, Stanford, California, USA. [2] Department of Neurosurgery, Stanford University, Stanford, California, USA. [3] Department of Pediatrics, Stanford University, Stanford, California, USA. [4] Department of Pathology, Stanford University, Stanford, California, USA
| | - Marie-Anne Debily
- 1] CNRS, UMR 8203, Gustave Roussy, Université Paris-Sud, Villejuif, France. [2] Département de biologie, Université d'Evry-Val d'Essone, Evry, France
| | - Michael J Quist
- Center for Spatial Systems Biomedicine, Department of Molecular and Medical Genetics, Oregon Health &Science University (OHSU), Portland, Oregon, USA
| | - Lara E Davis
- Pediatric Cancer Biology Program, Papé Family Pediatric Research Institute, Department of Pediatrics, OHSU, Portland, Oregon, USA
| | - Elaine C Huang
- Pediatric Cancer Biology Program, Papé Family Pediatric Research Institute, Department of Pediatrics, OHSU, Portland, Oregon, USA
| | - Pamelyn J Woo
- 1] Department of Neurology, Stanford University, Stanford, California, USA. [2] Department of Neurosurgery, Stanford University, Stanford, California, USA. [3] Department of Pediatrics, Stanford University, Stanford, California, USA. [4] Department of Pathology, Stanford University, Stanford, California, USA
| | - Anitha Ponnuswami
- 1] Department of Neurology, Stanford University, Stanford, California, USA. [2] Department of Neurosurgery, Stanford University, Stanford, California, USA. [3] Department of Pediatrics, Stanford University, Stanford, California, USA. [4] Department of Pathology, Stanford University, Stanford, California, USA
| | - Spenser Chen
- 1] Department of Neurology, Stanford University, Stanford, California, USA. [2] Department of Neurosurgery, Stanford University, Stanford, California, USA. [3] Department of Pediatrics, Stanford University, Stanford, California, USA. [4] Department of Pathology, Stanford University, Stanford, California, USA
| | - Tessa B Johung
- 1] Department of Neurology, Stanford University, Stanford, California, USA. [2] Department of Neurosurgery, Stanford University, Stanford, California, USA. [3] Department of Pediatrics, Stanford University, Stanford, California, USA. [4] Department of Pathology, Stanford University, Stanford, California, USA
| | - Wenchao Sun
- Department of Neurology, Stanford University, Stanford, California, USA
| | - Mari Kogiso
- Laboratory of Molecular Neurooncology, Texas Children's Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Yuchen Du
- Laboratory of Molecular Neurooncology, Texas Children's Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Lin Qi
- Laboratory of Molecular Neurooncology, Texas Children's Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Yulun Huang
- 1] Laboratory of Molecular Neurooncology, Texas Children's Cancer Center, Baylor College of Medicine, Houston, Texas, USA. [2] Present addresses: Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China (Y.T.) and Department of Neurosurgery, The First Affiliated Hospital of Suzhou University, Suzhou, China (Y.H.)
| | - Marianne Hütt-Cabezas
- 1] Department of Oncology, Johns Hopkins University, Baltimore, Maryland, USA. [2] Department of Pathology, Johns Hopkins University, Baltimore, Maryland, USA
| | | | - Ludivine Le Dret
- CNRS, UMR 8203, Gustave Roussy, Université Paris-Sud, Villejuif, France
| | | | - Hua Mao
- Laboratory of Molecular Neurooncology, Texas Children's Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | | | - Dannis G van Vuurden
- 1] Department of Pediatric Oncology and Hematology, VU University Medical Center, Amsterdam, The Netherlands. [2] Neuro-Oncology Research Group Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Jinu Abraham
- Pediatric Cancer Biology Program, Papé Family Pediatric Research Institute, Department of Pediatrics, OHSU, Portland, Oregon, USA
| | - Maryam Fouladi
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Matthew N Svalina
- 1] Center for Spatial Systems Biomedicine, Department of Molecular and Medical Genetics, Oregon Health &Science University (OHSU), Portland, Oregon, USA. [2] Children's Cancer Therapy Development Institute, Fort Collins, Colorado, USA
| | - Nicholas Wang
- Center for Spatial Systems Biomedicine, Department of Molecular and Medical Genetics, Oregon Health &Science University (OHSU), Portland, Oregon, USA
| | - Cynthia Hawkins
- 1] Department of Pediatric Laboratory Medicine, University of Toronto, Toronto, Ontario, Canada. [2] Labatt Brain Tumor Research Centre, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Javad Nazarian
- Center for Research Institute, Children's National Health Systems, Washington, DC, USA
| | - Marta M Alonso
- Department of Oncology, University Hospital of Navarra, Pamplona, Spain
| | - Eric H Raabe
- 1] Department of Oncology, Johns Hopkins University, Baltimore, Maryland, USA. [2] Department of Pathology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Esther Hulleman
- 1] Department of Pediatric Oncology and Hematology, VU University Medical Center, Amsterdam, The Netherlands. [2] Neuro-Oncology Research Group Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Paul T Spellman
- Center for Spatial Systems Biomedicine, Department of Molecular and Medical Genetics, Oregon Health &Science University (OHSU), Portland, Oregon, USA
| | - Xiao-Nan Li
- Laboratory of Molecular Neurooncology, Texas Children's Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Charles Keller
- 1] Pediatric Cancer Biology Program, Papé Family Pediatric Research Institute, Department of Pediatrics, OHSU, Portland, Oregon, USA. [2] Children's Cancer Therapy Development Institute, Fort Collins, Colorado, USA
| | - Ranadip Pal
- Electrical and Computer Engineering, Texas Tech University, Lubbock, Texas, USA
| | - Jacques Grill
- 1] CNRS, UMR 8203, Gustave Roussy, Université Paris-Sud, Villejuif, France. [2] Departement de Cancerologie de l'Enfant et de l'Adolescent, Institut Gustave Roussy, Université Paris-Sud, Villejuif, France
| | - Michelle Monje
- 1] Department of Neurology, Stanford University, Stanford, California, USA. [2] Department of Neurosurgery, Stanford University, Stanford, California, USA. [3] Department of Pediatrics, Stanford University, Stanford, California, USA. [4] Department of Pathology, Stanford University, Stanford, California, USA
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