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Chen X, Yang W, Roberts CWM, Zhang J. Developmental origins shape the paediatric cancer genome. Nat Rev Cancer 2024; 24:382-398. [PMID: 38698126 DOI: 10.1038/s41568-024-00684-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/18/2024] [Indexed: 05/05/2024]
Abstract
In the past two decades, technological advances have brought unprecedented insights into the paediatric cancer genome revealing characteristics distinct from those of adult cancer. Originating from developing tissues, paediatric cancers generally have low mutation burden and are driven by variants that disrupt the transcriptional activity, chromatin state, non-coding cis-regulatory regions and other biological functions. Within each tumour, there are multiple populations of cells with varying states, and the lineages of some can be tracked to their fetal origins. Genome-wide genetic screening has identified vulnerabilities associated with both the cell of origin and transcription deregulation in paediatric cancer, which have become a valuable resource for designing new therapeutic approaches including those for small molecules, immunotherapy and targeted protein degradation. In this Review, we present recent findings on these facets of paediatric cancer from a pan-cancer perspective and provide an outlook on future investigations.
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Affiliation(s)
- Xiaolong Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wentao Yang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles W M Roberts
- Comprehensive Cancer Center, St Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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2
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Hendrickson PG, Oristian KM, Browne MR, Luo L, Ma Y, Cardona DM, Nash JO, Ballester PL, Davidson S, Shlien A, Linardic CM, Kirsch DG. Spontaneous expression of the CIC::DUX4 fusion oncoprotein from a conditional allele potently drives sarcoma formation in genetically engineered mice. Oncogene 2024; 43:1223-1230. [PMID: 38413794 PMCID: PMC11027086 DOI: 10.1038/s41388-024-02984-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 02/07/2024] [Accepted: 02/14/2024] [Indexed: 02/29/2024]
Abstract
CIC::DUX4 sarcoma (CDS) is a rare but highly aggressive undifferentiated small round cell sarcoma driven by a fusion between the tumor suppressor Capicua (CIC) and DUX4. Currently, there are no effective treatments and efforts to identify and translate better therapies are limited by the scarcity of patient tumor samples and cell lines. To address this limitation, we generated three genetically engineered mouse models of CDS (Ch7CDS, Ai9CDS, and TOPCDS). Remarkably, chimeric mice from all three conditional models developed spontaneous soft tissue tumors and disseminated disease in the absence of Cre-recombinase. The penetrance of spontaneous (Cre-independent) tumor formation was complete irrespective of bi-allelic Cic function and the distance between adjacent loxP sites. Characterization of soft tissue and presumed metastatic tumors showed that they consistently expressed the CIC::DUX4 fusion protein and many downstream markers of the disease credentialing the models as CDS. In addition, tumor-derived cell lines were generated and ChIP-seq was preformed to map fusion-gene specific binding using an N-terminal HA epitope tag. These datasets, along with paired H3K27ac ChIP-sequencing maps, validate CIC::DUX4 as a neomorphic transcriptional activator. Moreover, they are consistent with a model where ETS family transcription factors are cooperative and redundant drivers of the core regulatory circuitry in CDS.
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Affiliation(s)
- Peter G Hendrickson
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | | | - MaKenna R Browne
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
- Developmental and Stem Cell Biology Program, Duke University Medical Center, Durham, NC, USA
| | - Lixia Luo
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - Yan Ma
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - Diana M Cardona
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Joshua O Nash
- Program in Genetics and Genome Biology, The Hospital for Sick Children (SickKids), University of Toronto, Toronto, ON, Canada
- Laboratory of Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Pedro L Ballester
- Laboratory of Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Scott Davidson
- Laboratory of Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Adam Shlien
- Program in Genetics and Genome Biology, The Hospital for Sick Children (SickKids), University of Toronto, Toronto, ON, Canada
- Laboratory of Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Corinne M Linardic
- Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
| | - David G Kirsch
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA.
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA.
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
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3
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Luo W, Hoang H, Liao Y, Pan J, Ayello J, Cairo MS. A humanized orthotopic mouse model for preclinical evaluation of immunotherapy in Ewing sarcoma. Front Immunol 2023; 14:1277987. [PMID: 37868989 PMCID: PMC10587429 DOI: 10.3389/fimmu.2023.1277987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 09/19/2023] [Indexed: 10/24/2023] Open
Abstract
The advent of novel cancer immunotherapy approaches is revolutionizing the treatment for cancer. Current small animal models for most cancers are syngeneic or genetically engineered mouse models or xenograft models based on immunodeficient mouse strains. These models have been limited in evaluating immunotherapy regimens due to the lack of functional human immune system. Development of animal models for bone cancer faces another challenge in the accessibility of tumor engraftment sites. Here, we describe a protocol to develop an orthotopic humanized mouse model for a bone and soft tissue sarcoma, Ewing sarcoma, by transplanting fresh human cord blood CD34+ hematopoietic stem cells into young NSG-SGM3 mice combined with subsequent Ewing sarcoma patient derived cell engraftment in the tibia of the humanized mice. We demonstrated early and robust reconstitution of human CD45+ leukocytes including T cells, B cells, natural killer cells and monocytes. Ewing sarcoma xenograft tumors successfully orthotopically engrafted in the humanized mice with minimal invasive procedures. We validated the translational utility of this orthotopic humanized model by evaluating the safety and efficacy of an immunotherapy antibody, magrolimab. Treatment with magrolimab induces CD47 blockade resulting in significantly decreased primary tumor growth, decreased lung metastasis and prolonged animal survival in the established humanized model. Furthermore, the humanized model recapitulated the dose dependent toxicity associated with the CD47 blockade as observed in patients in clinical trials. In conclusion, this orthotopic humanized mouse model of Ewing sarcoma represents an improved platform for evaluating immunotherapy in bone and soft tissue sarcoma, such as Ewing sarcoma. With careful design and optimization, this model is generalizable for other bone malignancies.
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Affiliation(s)
- Wen Luo
- Department of Pediatrics, New York Medical College, Valhalla, NY, United States
- Department of Pathology, Immunology and Microbiology, New York Medical College, Valhalla, NY, United States
| | - Hai Hoang
- Department of Pediatrics, New York Medical College, Valhalla, NY, United States
| | - Yanling Liao
- Department of Pediatrics, New York Medical College, Valhalla, NY, United States
| | - Jian Pan
- Department of Pediatrics, New York Medical College, Valhalla, NY, United States
| | - Janet Ayello
- Department of Pediatrics, New York Medical College, Valhalla, NY, United States
| | - Mitchell S. Cairo
- Department of Pediatrics, New York Medical College, Valhalla, NY, United States
- Department of Pathology, Immunology and Microbiology, New York Medical College, Valhalla, NY, United States
- Department of Medicine, New York Medical College, Valhalla, NY, United States
- Department of Cell Biology and Anatomy, New York Medical College, Valhalla, NY, United States
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4
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Hendrickson PG, Oristian KM, Browne MR, Lou L, Ma Y, Cardona DM, Linardic CM, Kirsch DG. Expression of the CIC-DUX4 fusion oncoprotein mimics human CIC-rearranged sarcoma in genetically engineered mouse models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.26.559519. [PMID: 37808628 PMCID: PMC10557731 DOI: 10.1101/2023.09.26.559519] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
CIC-DUX4 sarcoma (CDS) is a rare but highly aggressive undifferentiated small round cell sarcoma driven by a fusion between the tumor suppressor Capicua (CIC) and DUX4. Currently, there are no effective treatments and efforts to identify and translate better therapies are limited by the scarcity of tissues and patients. To address this limitation, we generated three genetically engineered mouse models of CDS (Ch7CDS, Ai9CDS, and TOPCDS). Remarkably, chimeric mice from all three conditional models developed spontaneous tumors and widespread metastasis in the absence of Cre-recombinase. The penetrance of spontaneous (Cre-independent) tumor formation was complete irrespective of bi-allelic CIC function and loxP site proximity. Characterization of primary and metastatic mouse tumors showed that they consistently expressed the CIC-DUX4 fusion protein as well as other downstream markers of the disease credentialing these models as CDS. In addition, tumor-derived cell lines were generated and ChIP-seq was preformed to map fusion-gene specific binding using an N-terminal HA epitope tag. These datasets, along with paired H3K27ac ChIP-seq maps, validate CIC-DUX4 as a neomorphic transcriptional activator. Moreover, they are consistent with a model where ETS family transcription factors are cooperative and redundant drivers of the core regulatory circuitry in CDS.
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Affiliation(s)
- Peter G. Hendrickson
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | | | - MaKenna R. Browne
- Developmental and Stem Cell Biology Program, Duke University Medical Center, Durham, NC, USA
| | - Lixia Lou
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - Yan Ma
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - Dianna M. Cardona
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Corinne M. Linardic
- Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
| | - David G. Kirsch
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
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5
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Zerella JR, Homan CC, Arts P, Brown AL, Scott HS, Hahn CN. Transcription factor genetics and biology in predisposition to bone marrow failure and hematological malignancy. Front Oncol 2023; 13:1183318. [PMID: 37377909 PMCID: PMC10291195 DOI: 10.3389/fonc.2023.1183318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
Transcription factors (TFs) play a critical role as key mediators of a multitude of developmental pathways, with highly regulated and tightly organized networks crucial for determining both the timing and pattern of tissue development. TFs can act as master regulators of both primitive and definitive hematopoiesis, tightly controlling the behavior of hematopoietic stem and progenitor cells (HSPCs). These networks control the functional regulation of HSPCs including self-renewal, proliferation, and differentiation dynamics, which are essential to normal hematopoiesis. Defining the key players and dynamics of these hematopoietic transcriptional networks is essential to understanding both normal hematopoiesis and how genetic aberrations in TFs and their networks can predispose to hematopoietic disease including bone marrow failure (BMF) and hematological malignancy (HM). Despite their multifaceted and complex involvement in hematological development, advances in genetic screening along with elegant multi-omics and model system studies are shedding light on how hematopoietic TFs interact and network to achieve normal cell fates and their role in disease etiology. This review focuses on TFs which predispose to BMF and HM, identifies potential novel candidate predisposing TF genes, and examines putative biological mechanisms leading to these phenotypes. A better understanding of the genetics and molecular biology of hematopoietic TFs, as well as identifying novel genes and genetic variants predisposing to BMF and HM, will accelerate the development of preventative strategies, improve clinical management and counseling, and help define targeted treatments for these diseases.
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Affiliation(s)
- Jiarna R. Zerella
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Claire C. Homan
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Peer Arts
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Anna L. Brown
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Hamish S. Scott
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
| | - Christopher N. Hahn
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, Australia
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Oncogenic role for an EWS-FLI1 suppressor. Nat Cell Biol 2023; 25:214-216. [PMID: 36658218 DOI: 10.1038/s41556-022-01067-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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