1
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Chen W, Jiang S, Li S, Li C, Xu R. OSMR is a potential driver of inflammation in amyotrophic lateral sclerosis. Neural Regen Res 2024; 19:2513-2521. [PMID: 38526287 PMCID: PMC11090450 DOI: 10.4103/1673-5374.391309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/06/2023] [Accepted: 10/31/2023] [Indexed: 03/26/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202419110-00031/figure1/v/2024-03-08T184507Z/r/image-tiff Amyotrophic lateral sclerosis is a neurodegenerative disease, and the molecular mechanism underlying its pathology remains poorly understood. However, inflammation is known to play an important role in the development of this condition. To identify driver genes that affect the inflammatory response in amyotrophic lateral sclerosis, as well as potential treatment targets, it is crucial to analyze brain tissue samples from patients with both sporadic amyotrophic lateral sclerosis and C9orf72-related amyotrophic lateral sclerosis. Therefore, in this study we used a network-driven gene analysis tool, NetBID2.0, which is based on SJARACNe, a scalable algorithm for the reconstruction of accurate cellular networks, to experimentally analyze sequencing data from patients with sporadic amyotrophic lateral sclerosis. The results showed that the OSMR gene is pathogenic in amyotrophic lateral sclerosis and participates in the progression of amyotrophic lateral sclerosis by mediating the neuroinflammatory response. Furthermore, there were differences in OSMR activity and expression between patients with sporadic amyotrophic lateral sclerosis and those with C9orf72-related amyotrophic lateral sclerosis. These findings suggest that OSMR may be a diagnostic and prognostic marker for amyotrophic lateral sclerosis.
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Affiliation(s)
- Wenzhi Chen
- Department of Neurology, Jiangxi Provincial People’s Hospital, Xiangya Hospital Jiangxi Hospital of Central South University, The Clinical College of Nanchang Medical College, The First Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi Province, China
| | - Shishi Jiang
- Department of Neurology, Jiangxi Provincial People’s Hospital, Xiangya Hospital Jiangxi Hospital of Central South University, The Clinical College of Nanchang Medical College, The First Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi Province, China
| | - Shu Li
- Department of Neurology, Jiangxi Provincial People’s Hospital, Xiangya Hospital Jiangxi Hospital of Central South University, The Clinical College of Nanchang Medical College, The First Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi Province, China
| | - Cheng Li
- Department of Neurology, Jiangxi Provincial People’s Hospital, Xiangya Hospital Jiangxi Hospital of Central South University, The Clinical College of Nanchang Medical College, The First Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi Province, China
| | - Renshi Xu
- Department of Neurology, Jiangxi Provincial People’s Hospital, Xiangya Hospital Jiangxi Hospital of Central South University, The Clinical College of Nanchang Medical College, The First Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi Province, China
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2
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Morel VJ, Rössler J, Bernasconi M. Targeted immunotherapy and nanomedicine for rhabdomyosarcoma: The way of the future. Med Res Rev 2024. [PMID: 38885148 DOI: 10.1002/med.22059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 04/17/2024] [Accepted: 05/20/2024] [Indexed: 06/20/2024]
Abstract
Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma of childhood. Histology separates two main subtypes: embryonal RMS (eRMS; 60%-70%) and alveolar RMS (aRMS; 20%-30%). The aggressive aRMS carry one of two characteristic chromosomal translocations that result in the expression of a PAX3::FOXO1 or PAX7::FOXO1 fusion transcription factor; therefore, aRMS are now classified as fusion-positive (FP) RMS. Embryonal RMS have a better prognosis and are clinically indistinguishable from fusion-negative (FN) RMS. Next to histology and molecular characteristics, RMS risk groupings are now available defining low risk tumors with excellent outcomes and advanced stage disease with poor prognosis, with an overall survival of about only 20% despite intensified multimodal treatment. Therefore, development of novel effective targeted strategies to increase survival and to decrease long-term side effects is urgently needed. Recently, immunotherapies and nanomedicine have been emerging for potent and effective tumor treatments with minimal side effects, raising hopes for effective and safe cures for RMS patients. This review aims to describe the most relevant preclinical and clinical studies in immunotherapy and targeted nanomedicine performed so far in RMS and to provide an insight in future developments.
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Affiliation(s)
- Victoria Judith Morel
- Department of Pediatric Hematology and Oncology, Inselspital, Bern University Hospital, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Jochen Rössler
- Department of Pediatric Hematology and Oncology, Inselspital, Bern University Hospital, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Michele Bernasconi
- Department of Pediatric Hematology and Oncology, Inselspital, Bern University Hospital, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
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3
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Zhang W, Maeser D, Lee A, Huang Y, Gruener RF, Abdelbar IG, Jena S, Patel AG, Huang RS. Integration of Pan-Cancer Cell Line and Single-Cell Transcriptomic Profiles Enables Inference of Therapeutic Vulnerabilities in Heterogeneous Tumors. Cancer Res 2024; 84:2021-2033. [PMID: 38581448 PMCID: PMC11178452 DOI: 10.1158/0008-5472.can-23-3005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/18/2023] [Accepted: 04/01/2024] [Indexed: 04/08/2024]
Abstract
Single-cell RNA sequencing (scRNA-seq) greatly advanced the understanding of intratumoral heterogeneity by identifying distinct cancer cell subpopulations. However, translating biological differences into treatment strategies is challenging due to a lack of tools to facilitate efficient drug discovery that tackles heterogeneous tumors. Developing such approaches requires accurate prediction of drug response at the single-cell level to offer therapeutic options to specific cell subpopulations. Here, we developed a transparent computational framework (nicknamed scIDUC) to predict therapeutic efficacies on an individual cell basis by integrating single-cell transcriptomic profiles with large, data-rich pan-cancer cell line screening data sets. This method achieved high accuracy in separating cells into their correct cellular drug response statuses. In three distinct prospective tests covering different diseases (rhabdomyosarcoma, pancreatic ductal adenocarcinoma, and castration-resistant prostate cancer), the predicted results using scIDUC were accurate and mirrored biological expectations. In the first two tests, the framework identified drugs for cell subpopulations that were resistant to standard-of-care (SOC) therapies due to intrinsic resistance or tumor microenvironmental effects, and the results showed high consistency with experimental findings from the original studies. In the third test using newly generated SOC therapy-resistant cell lines, scIDUC identified efficacious drugs for the resistant line, and the predictions were validated with in vitro experiments. Together, this study demonstrates the potential of scIDUC to quickly translate scRNA-seq data into drug responses for individual cells, displaying the potential as a tool to improve the treatment of heterogenous tumors. SIGNIFICANCE A versatile method that infers cell-level drug response in scRNA-seq data facilitates the development of therapeutic strategies to target heterogeneous subpopulations within a tumor and address issues such as treatment failure and resistance.
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Affiliation(s)
- Weijie Zhang
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN 55455
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455
| | - Danielle Maeser
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN 55455
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455
| | - Adam Lee
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455
| | - Yingbo Huang
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455
| | - Robert F. Gruener
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455
| | - Israa G. Abdelbar
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455
- Clinical Pharmacy Practice Department, The British University in Egypt, El Sherouk, 11837, Egypt
| | - Sampreeti Jena
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455
| | - Anand G. Patel
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - R. Stephanie Huang
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN 55455
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455
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4
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Danielli SG, Wurth J, Morice S, Kisele S, Surdez D, Delattre O, Bode PK, Wachtel M, Schäfer BW. Evaluation of the Role of AXL in Fusion-positive Pediatric Rhabdomyosarcoma Identifies the Small-molecule Inhibitor Bemcentinib (BGB324) as Potent Chemosensitizer. Mol Cancer Ther 2024; 23:864-876. [PMID: 38471796 PMCID: PMC11148551 DOI: 10.1158/1535-7163.mct-23-0285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 12/16/2023] [Accepted: 03/08/2024] [Indexed: 03/14/2024]
Abstract
Rhabdomyosarcoma (RMS) is a highly aggressive pediatric cancer with features of skeletal muscle differentiation. More than 80% of the high-risk patients ultimately fail to respond to chemotherapy treatment, leading to limited therapeutic options and dismal prognostic rates. The lack of response and subsequent tumor recurrence is driven in part by stem cell-like cells, the tumor subpopulation that is enriched after treatment, and characterized by expression of the AXL receptor tyrosine kinase (AXL). AXL mediates survival, migration, and therapy resistance in several cancer types; however, its function in RMS remains unclear. In this study, we investigated the role of AXL in RMS tumorigenesis, migration, and chemotherapy response, and whether targeting of AXL with small-molecule inhibitors could potentiate the efficacy of chemotherapy. We show that AXL is expressed in a heterogeneous manner in patient-derived xenografts (PDX), primary cultures and cell line models of RMS, consistent with its stem cell-state selectivity. By generating a CRISPR/Cas9 AXL knock-out and overexpressing models, we show that AXL contributes to the migratory phenotype of RMS, but not to chemotherapy resistance. Instead, pharmacologic blockade with the AXL inhibitors bemcentinib (BGB324), cabozantinib and NPS-1034 rapidly killed RMS cells in an AXL-independent manner and augmented the efficacy of the chemotherapeutics vincristine and cyclophosphamide. In vivo administration of the combination of bemcentinib and vincristine exerted strong antitumoral activity in a rapidly progressing PDX mouse model, significantly reducing tumor burden compared with single-agent treatment. Collectively, our data identify bemcentinib as a promising drug to improve chemotherapy efficacy in patients with RMS.
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Affiliation(s)
- Sara G Danielli
- Department of Oncology and Children's Research Center, University Children's Hospital of Zürich, Zürich, Switzerland
| | - Jakob Wurth
- Department of Oncology and Children's Research Center, University Children's Hospital of Zürich, Zürich, Switzerland
| | - Sarah Morice
- Balgrist University Hospital, Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Samanta Kisele
- Department of Oncology and Children's Research Center, University Children's Hospital of Zürich, Zürich, Switzerland
| | - Didier Surdez
- Balgrist University Hospital, Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Laboratory, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Olivier Delattre
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Laboratory, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Peter K Bode
- Department of Pathology, University Hospital Zürich, Zürich, Switzerland
| | - Marco Wachtel
- Department of Oncology and Children's Research Center, University Children's Hospital of Zürich, Zürich, Switzerland
| | - Beat W Schäfer
- Department of Oncology and Children's Research Center, University Children's Hospital of Zürich, Zürich, Switzerland
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5
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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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6
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Kucinski JP, Calderon D, Kendall GC. Biological and therapeutic insights from animal modeling of fusion-driven pediatric soft tissue sarcomas. Dis Model Mech 2024; 17:dmm050704. [PMID: 38916046 DOI: 10.1242/dmm.050704] [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] [Indexed: 06/26/2024] Open
Abstract
Survival for children with cancer has primarily improved over the past decades due to refinements in surgery, radiation and chemotherapy. Although these general therapies are sometimes curative, the cancer often recurs, resulting in poor outcomes for patients. Fusion-driven pediatric soft tissue sarcomas are genetically defined by chromosomal translocations that create a chimeric oncogene. This distinctive, almost 'monogenic', genetic feature supports the generation of animal models to study the respective diseases in vivo. This Review focuses on a subset of fusion-driven pediatric soft tissue sarcomas that have transgenic animal tumor models, which includes fusion-positive and infantile rhabdomyosarcoma, synovial sarcoma, undifferentiated small round cell sarcoma, alveolar soft part sarcoma and clear cell sarcoma. Studies using the animal models of these sarcomas have highlighted that pediatric cancers require a specific cellular state or developmental stage to drive tumorigenesis, as the fusion oncogenes cause different outcomes depending on their lineage and timing of expression. Therefore, understanding these context-specific activities could identify targetable activities and mechanisms critical for tumorigenesis. Broadly, these cancers show dependencies on chromatin regulators to support oncogenic gene expression and co-opting of developmental pathways. Comparative analyses across lineages and tumor models will further provide biological and therapeutic insights to improve outcomes for these children.
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Affiliation(s)
- Jack P Kucinski
- Center for Childhood Cancer Research, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH 43215, USA
- Molecular, Cellular, and Developmental Biology PhD Program, The Ohio State University, Columbus, OH 43210, USA
| | - Delia Calderon
- Center for Childhood Cancer Research, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH 43215, USA
- Molecular, Cellular, and Developmental Biology PhD Program, The Ohio State University, Columbus, OH 43210, USA
| | - Genevieve C Kendall
- Center for Childhood Cancer Research, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH 43215, USA
- Molecular, Cellular, and Developmental Biology PhD Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43215, USA
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7
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Patton A, Dermawan JK. Current updates in sarcoma biomarker discovery: emphasis on next-generation sequencing-based methods. Pathology 2024; 56:274-282. [PMID: 38185613 DOI: 10.1016/j.pathol.2023.10.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/25/2023] [Accepted: 10/29/2023] [Indexed: 01/09/2024]
Abstract
Soft tissue sarcomas comprise a heterogeneous group of neoplasms. Although soft tissue malignancies make up only 2% of adult cancers, classification based on histomorphology presents a diagnostic challenge. Characterisation of soft tissue sarcomas by molecular analysis is rapidly evolving to improve diagnostic accuracy and develop targeted therapies. This review highlights the advances in molecular techniques, including current next-generation sequencing-based assays (fusion detection by RNA sequencing, targeted/whole exome sequencing, microRNA profiling), as well as emerging methods (liquid biopsies, DNA methylation profiling, single-cell molecular profiling and next-generation immunohistochemistry) for future clinical applications.
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Affiliation(s)
- Ashley Patton
- Department of Pathology & Laboratory Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Josephine K Dermawan
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA.
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8
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Kim YY, Gryder BE, Sinniah R, Peach ML, Shern JF, Abdelmaksoud A, Pomella S, Woldemichael GM, Stanton BZ, Milewski D, Barchi JJ, Schneekloth JS, Chari R, Kowalczyk JT, Shenoy SR, Evans JR, Song YK, Wang C, Wen X, Chou HC, Gangalapudi V, Esposito D, Jones J, Procter L, O'Neill M, Jenkins LM, Tarasova NI, Wei JS, McMahon JB, O'Keefe BR, Hawley RG, Khan J. KDM3B inhibitors disrupt the oncogenic activity of PAX3-FOXO1 in fusion-positive rhabdomyosarcoma. Nat Commun 2024; 15:1703. [PMID: 38402212 PMCID: PMC10894237 DOI: 10.1038/s41467-024-45902-y] [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: 11/21/2022] [Accepted: 02/07/2024] [Indexed: 02/26/2024] Open
Abstract
Fusion-positive rhabdomyosarcoma (FP-RMS) is an aggressive pediatric sarcoma driven primarily by the PAX3-FOXO1 fusion oncogene, for which therapies targeting PAX3-FOXO1 are lacking. Here, we screen 62,643 compounds using an engineered cell line that monitors PAX3-FOXO1 transcriptional activity identifying a hitherto uncharacterized compound, P3FI-63. RNA-seq, ATAC-seq, and docking analyses implicate histone lysine demethylases (KDMs) as its targets. Enzymatic assays confirm the inhibition of multiple KDMs with the highest selectivity for KDM3B. Structural similarity search of P3FI-63 identifies P3FI-90 with improved solubility and potency. Biophysical binding of P3FI-90 to KDM3B is demonstrated using NMR and SPR. P3FI-90 suppresses the growth of FP-RMS in vitro and in vivo through downregulating PAX3-FOXO1 activity, and combined knockdown of KDM3B and KDM1A phenocopies P3FI-90 effects. Thus, we report KDM inhibitors P3FI-63 and P3FI-90 with the highest specificity for KDM3B. Their potent suppression of PAX3-FOXO1 activity indicates a possible therapeutic approach for FP-RMS and other transcriptionally addicted cancers.
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Affiliation(s)
| | - Berkley E Gryder
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | | | - Megan L Peach
- Basic Science Program, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD, USA
| | - Jack F Shern
- Pediatric Oncology Branch, NCI, NIH, Bethesda, MD, USA
| | | | - Silvia Pomella
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
- Department of Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Girma M Woldemichael
- Leidos Biomed Res Inc, FNLCR, Basic Sci Program, Frederick, MD, USA
- Molecular Targets Program, NCI, NIH, Frederick, MD, USA
| | - Benjamin Z Stanton
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
- Nationwide Children's Hospital, Center for Childhood Cancer Research, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
- Department of Biological Chemistry & Pharmacology, The Ohio State University College of Medicine, Columbus, OH, USA
| | | | | | | | - Raj Chari
- Genome Modification Core, Laboratory Animal Sciences Program, FNLCR, Frederick, MD, USA
| | | | - Shilpa R Shenoy
- Leidos Biomed Res Inc, FNLCR, Basic Sci Program, Frederick, MD, USA
- Molecular Targets Program, NCI, NIH, Frederick, MD, USA
| | - Jason R Evans
- Natural Products Branch, NCI, NIH, Frederick, MD, USA
| | | | - Chaoyu Wang
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
| | - Xinyu Wen
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
| | | | | | | | - Jane Jones
- Protein Expression Laboratory, FNLCR, NIH, Frederick, MD, USA
| | - Lauren Procter
- Protein Expression Laboratory, FNLCR, NIH, Frederick, MD, USA
| | - Maura O'Neill
- Protein Characterization Laboratory, FNLCR, NIH, Frederick, MD, USA
| | | | | | - Jun S Wei
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
| | | | - Barry R O'Keefe
- Molecular Targets Program, NCI, NIH, Frederick, MD, USA
- Natural Products Branch, NCI, NIH, Frederick, MD, USA
| | - Robert G Hawley
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
- Department of Anatomy and Cell Biology, George Washington University, Washington, DC, USA
| | - Javed Khan
- Genetics Branch, NCI, NIH, Bethesda, MD, USA.
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9
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Patel AG, Ashenberg O, Collins NB, Segerstolpe Å, Jiang S, Slyper M, Huang X, Caraccio C, Jin H, Sheppard H, Xu K, Chang TC, Orr BA, Shirinifard A, Chapple RH, Shen A, Clay MR, Tatevossian RG, Reilly C, Patel J, Lupo M, Cline C, Dionne D, Porter CBM, Waldman J, Bai Y, Zhu B, Barrera I, Murray E, Vigneau S, Napolitano S, Wakiro I, Wu J, Grimaldi G, Dellostritto L, Helvie K, Rotem A, Lako A, Cullen N, Pfaff KL, Karlström Å, Jané-Valbuena J, Todres E, Thorner A, Geeleher P, Rodig SJ, Zhou X, Stewart E, Johnson BE, Wu G, Chen F, Yu J, Goltsev Y, Nolan GP, Rozenblatt-Rosen O, Regev A, Dyer MA. A spatial cell atlas of neuroblastoma reveals developmental, epigenetic and spatial axis of tumor heterogeneity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.07.574538. [PMID: 38260392 PMCID: PMC10802404 DOI: 10.1101/2024.01.07.574538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Neuroblastoma is a pediatric cancer arising from the developing sympathoadrenal lineage with complex inter- and intra-tumoral heterogeneity. To chart this complexity, we generated a comprehensive cell atlas of 55 neuroblastoma patient tumors, collected from two pediatric cancer institutions, spanning a range of clinical, genetic, and histologic features. Our atlas combines single-cell/nucleus RNA-seq (sc/scRNA-seq), bulk RNA-seq, whole exome sequencing, DNA methylation profiling, spatial transcriptomics, and two spatial proteomic methods. Sc/snRNA-seq revealed three malignant cell states with features of sympathoadrenal lineage development. All of the neuroblastomas had malignant cells that resembled sympathoblasts and the more differentiated adrenergic cells. A subset of tumors had malignant cells in a mesenchymal cell state with molecular features of Schwann cell precursors. DNA methylation profiles defined four groupings of patients, which differ in the degree of malignant cell heterogeneity and clinical outcomes. Using spatial proteomics, we found that neuroblastomas are spatially compartmentalized, with malignant tumor cells sequestered away from immune cells. Finally, we identify spatially restricted signaling patterns in immune cells from spatial transcriptomics. To facilitate the visualization and analysis of our atlas as a resource for further research in neuroblastoma, single cell, and spatial-omics, all data are shared through the Human Tumor Atlas Network Data Commons at www.humantumoratlas.org.
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Affiliation(s)
- Anand G Patel
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
- These authors contributed equally
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- These authors contributed equally
| | - Natalie B Collins
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, USA
- These authors contributed equally
| | - Åsa Segerstolpe
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sizun Jiang
- Department of Pathology, Stanford University, Stanford, CA, USA
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Michal Slyper
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xin Huang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Chiara Caraccio
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Hongjian Jin
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Heather Sheppard
- Comparative Pathology Core, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ke Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ti-Cheng Chang
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Brent A Orr
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Abbas Shirinifard
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Richard H Chapple
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Amber Shen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael R Clay
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Ruth G Tatevossian
- Cancer Biomarkers Laboratory, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Colleen Reilly
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jaimin Patel
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Marybeth Lupo
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cynthia Cline
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Danielle Dionne
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Caroline B M Porter
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julia Waldman
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yunhao Bai
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Bokai Zhu
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Evan Murray
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sébastien Vigneau
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sara Napolitano
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Isaac Wakiro
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jingyi Wu
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Grace Grimaldi
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Laura Dellostritto
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Karla Helvie
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Asaf Rotem
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ana Lako
- Center for Immuno-Oncology (CIO), Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nicole Cullen
- Center for Immuno-Oncology (CIO), Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kathleen L Pfaff
- Center for Immuno-Oncology (CIO), Dana-Farber Cancer Institute, Boston, MA, USA
| | - Åsa Karlström
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Judit Jané-Valbuena
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ellen Todres
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aaron Thorner
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Paul Geeleher
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Scott J Rodig
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Elizabeth Stewart
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Bruce E Johnson
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gang Wu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Fei Chen
- Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Jiyang Yu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yury Goltsev
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Current address: Research and Early Development, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Current address: Research and Early Development, Genentech Inc., South San Francisco, CA, 94080, USA
- Lead contacts
| | - Michael A Dyer
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Lead contacts
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10
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Savary C, Luciana L, Huchedé P, Tourbez A, Coquet C, Broustal M, Lopez Gonzalez A, Deligne C, Diot T, Naret O, Costa M, Meynard N, Barbet V, Müller K, Tonon L, Gadot N, Degletagne C, Attignon V, Léon S, Vanbelle C, Bomane A, Rochet I, Mournetas V, Oliveira L, Rinaudo P, Bergeron C, Dutour A, Cordier-Bussat M, Roch A, Brandenberg N, El Zein S, Watson S, Orbach D, Delattre O, Dijoud F, Corradini N, Picard C, Maucort-Boulch D, Le Grand M, Pasquier E, Blay JY, Castets M, Broutier L. Fusion-negative rhabdomyosarcoma 3D organoids to predict effective drug combinations: A proof-of-concept on cell death inducers. Cell Rep Med 2023; 4:101339. [PMID: 38118405 PMCID: PMC10772578 DOI: 10.1016/j.xcrm.2023.101339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 09/29/2023] [Accepted: 11/22/2023] [Indexed: 12/22/2023]
Abstract
Rhabdomyosarcoma (RMS) is the main form of pediatric soft-tissue sarcoma. Its cure rate has not notably improved in the last 20 years following relapse, and the lack of reliable preclinical models has hampered the design of new therapies. This is particularly true for highly heterogeneous fusion-negative RMS (FNRMS). Although methods have been proposed to establish FNRMS organoids, their efficiency remains limited to date, both in terms of derivation rate and ability to accurately mimic the original tumor. Here, we present the development of a next-generation 3D organoid model derived from relapsed adult and pediatric FNRMS. This model preserves the molecular features of the patients' tumors and is expandable for several months in 3D, reinforcing its interest to drug combination screening with longitudinal efficacy monitoring. As a proof-of-concept, we demonstrate its preclinical relevance by reevaluating the therapeutic opportunities of targeting apoptosis in FNRMS from a streamlined approach based on transcriptomic data exploitation.
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Affiliation(s)
- Clara Savary
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Léa Luciana
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Paul Huchedé
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Arthur Tourbez
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Claire Coquet
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Maëlle Broustal
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Alejandro Lopez Gonzalez
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Clémence Deligne
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Thomas Diot
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Olivier Naret
- DOPPL, EPFL Innovation Park, Building L, Ch. de la Dent d'Oche 1, 1024 Ecublens, Switzerland
| | - Mariana Costa
- DOPPL, EPFL Innovation Park, Building L, Ch. de la Dent d'Oche 1, 1024 Ecublens, Switzerland
| | - Nina Meynard
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Virginie Barbet
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Kevin Müller
- Université Aix-Marseille, CNRS 7258, INSERM 1068, Institute Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), 13009 Marseille, France
| | - Laurie Tonon
- Synergie Lyon Cancer, Gilles Thomas' Bioinformatics Platform, Centre Léon Bérard, 69008 Lyon, France
| | - Nicolas Gadot
- Anatomopathology Research Platform, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Cyril Degletagne
- Cancer Genomics Platform, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Valéry Attignon
- Cancer Genomics Platform, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Sophie Léon
- EX-VIVO Platform, Centre de recherche en cancérologie de Lyon (CRCL), Centre Léon Bérard, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Christophe Vanbelle
- Plateforme d'Imagerie cellulaire, Centre de recherche en cancérologie de Lyon (CRCL), Centre Léon Bérard, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Alexandra Bomane
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Isabelle Rochet
- Multisite Institute of Pathology, Groupement Hospitalier Est du CHU de Lyon, Hôpital Femme-Mère-Enfant, 69677 Bron, France; Department of Pediatric Oncology, Institut d'Hématologie et d'Oncologie Pédiatrique, Centre Léon Bérard, 69008 Lyon, France
| | | | | | | | - Christophe Bergeron
- Department of Pediatric Oncology, Institut d'Hématologie et d'Oncologie Pédiatrique, Centre Léon Bérard, 69008 Lyon, France
| | - Aurélie Dutour
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Martine Cordier-Bussat
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France
| | - Aline Roch
- DOPPL, EPFL Innovation Park, Building L, Ch. de la Dent d'Oche 1, 1024 Ecublens, Switzerland
| | - Nathalie Brandenberg
- DOPPL, EPFL Innovation Park, Building L, Ch. de la Dent d'Oche 1, 1024 Ecublens, Switzerland
| | - Sophie El Zein
- Department of Biopathology, Institut Curie, Paris, France
| | - Sarah Watson
- SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), Institut Curie, PSL Research University, Paris, France; INSERM U830, Diversity and Plasticity of Childhood Tumors Lab, Institut Curie, PSL Research University, Paris, France; Medical Oncology Department, Institut Curie, PSL Research University, Paris, France
| | - Daniel Orbach
- SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), Institut Curie, PSL Research University, Paris, France
| | - Olivier Delattre
- SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), Institut Curie, PSL Research University, Paris, France; INSERM U830, Diversity and Plasticity of Childhood Tumors Lab, Institut Curie, PSL Research University, Paris, France
| | - Frédérique Dijoud
- Multisite Institute of Pathology, Groupement Hospitalier Est du CHU de Lyon, Hôpital Femme-Mère-Enfant, 69677 Bron, France
| | - Nadège Corradini
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France; Department of Pediatric Oncology, Institut d'Hématologie et d'Oncologie Pédiatrique, Centre Léon Bérard, 69008 Lyon, France; Department of Translational Research in Pediatric Oncology PROSPECT, Centre Léon Bérard, 69008 Lyon, France
| | - Cécile Picard
- Multisite Institute of Pathology, Groupement Hospitalier Est du CHU de Lyon, Hôpital Femme-Mère-Enfant, 69677 Bron, France
| | - Delphine Maucort-Boulch
- Université Lyon 1, 69100 Villeurbanne, France; Hospices Civils de Lyon, Pôle Santé Publique, Service de Biostatistique et Bioinformatique, 69003 Lyon, France; CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Évolutive, Équipe Biostatistique-Santé, 69100 Villeurbanne, France
| | - Marion Le Grand
- Université Aix-Marseille, CNRS 7258, INSERM 1068, Institute Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), 13009 Marseille, France
| | - Eddy Pasquier
- Université Aix-Marseille, CNRS 7258, INSERM 1068, Institute Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), 13009 Marseille, France
| | - Jean-Yves Blay
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France; Department of Translational Research in Pediatric Oncology PROSPECT, Centre Léon Bérard, 69008 Lyon, France
| | - Marie Castets
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France; Department of Translational Research in Pediatric Oncology PROSPECT, Centre Léon Bérard, 69008 Lyon, France.
| | - Laura Broutier
- Childhood Cancer & Cell Death Team (C3 Team), LabEx DEVweCAN, Institut Convergence Plascan, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008 Lyon, France; Department of Translational Research in Pediatric Oncology PROSPECT, Centre Léon Bérard, 69008 Lyon, France.
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11
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Searcy MB, Larsen RK, Stevens BT, Zhang Y, Jin H, Drummond CJ, Langdon CG, Gadek KE, Vuong K, Reed KB, Garcia MR, Xu B, Kimbrough DW, Adkins GE, Djekidel N, Porter SN, Schreiner PA, Pruett-Miller SM, Abraham BJ, Rehg JE, Hatley ME. PAX3-FOXO1 dictates myogenic reprogramming and rhabdomyosarcoma identity in endothelial progenitors. Nat Commun 2023; 14:7291. [PMID: 37968277 PMCID: PMC10651858 DOI: 10.1038/s41467-023-43044-1] [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: 12/12/2022] [Accepted: 10/27/2023] [Indexed: 11/17/2023] Open
Abstract
Fusion-positive rhabdomyosarcoma (FP-RMS) driven by the expression of the PAX3-FOXO1 (P3F) fusion oncoprotein is an aggressive subtype of pediatric rhabdomyosarcoma. FP-RMS histologically resembles developing muscle yet occurs throughout the body in areas devoid of skeletal muscle highlighting that FP-RMS is not derived from an exclusively myogenic cell of origin. Here we demonstrate that P3F reprograms mouse and human endothelial progenitors to FP-RMS. We show that P3F expression in aP2-Cre expressing cells reprograms endothelial progenitors to functional myogenic stem cells capable of regenerating injured muscle fibers. Further, we describe a FP-RMS mouse model driven by P3F expression and Cdkn2a loss in endothelial cells. Additionally, we show that P3F expression in TP53-null human iPSCs blocks endothelial-directed differentiation and guides cells to become myogenic cells that form FP-RMS tumors in immunocompromised mice. Together these findings demonstrate that FP-RMS can originate from aberrant development of non-myogenic cells driven by P3F.
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Affiliation(s)
- Madeline B Searcy
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- St. Jude Graduate School of Biomedical Sciences, Memphis, TN, 38105, USA
| | - Randolph K Larsen
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- St. Jude Graduate School of Biomedical Sciences, Memphis, TN, 38105, USA
| | - Bradley T Stevens
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- St. Jude Graduate School of Biomedical Sciences, Memphis, TN, 38105, USA
| | - Yang Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Hongjian Jin
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Catherine J Drummond
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Casey G Langdon
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Katherine E Gadek
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Kyna Vuong
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Kristin B Reed
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Matthew R Garcia
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Darden W Kimbrough
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Rhodes College, Memphis, TN, 38112, USA
| | - Grace E Adkins
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- St. Jude Graduate School of Biomedical Sciences, Memphis, TN, 38105, USA
| | - Nadhir Djekidel
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Shaina N Porter
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Patrick A Schreiner
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Brian J Abraham
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jerold E Rehg
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Mark E Hatley
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
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12
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Zhang W, Maeser D, Lee A, Huang Y, Gruener RF, Abdelbar IG, Jena S, Patel AG, Huang RS. Inferring therapeutic vulnerability within tumors through integration of pan-cancer cell line and single-cell transcriptomic profiles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.29.564598. [PMID: 37961545 PMCID: PMC10634928 DOI: 10.1101/2023.10.29.564598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Single-cell RNA sequencing greatly advanced our understanding of intratumoral heterogeneity through identifying tumor subpopulations with distinct biologies. However, translating biological differences into treatment strategies is challenging, as we still lack tools to facilitate efficient drug discovery that tackles heterogeneous tumors. One key component of such approaches tackles accurate prediction of drug response at the single-cell level to offer therapeutic options to specific cell subpopulations. Here, we present a transparent computational framework (nicknamed scIDUC) to predict therapeutic efficacies on an individual-cell basis by integrating single-cell transcriptomic profiles with large, data-rich pan-cancer cell line screening datasets. Our method achieves high accuracy, with predicted sensitivities easily able to separate cells into their true cellular drug resistance status as measured by effect size (Cohen's d > 1.0). More importantly, we examine our method's utility with three distinct prospective tests covering different diseases (rhabdomyosarcoma, pancreatic ductal adenocarcinoma, and castration-resistant prostate cancer), and in each our predicted results are accurate and mirrored biological expectations. In the first two, we identified drugs for cell subpopulations that are resistant to standard-of-care (SOC) therapies due to intrinsic resistance or effects of tumor microenvironments. Our results showed high consistency with experimental findings from the original studies. In the third test, we generated SOC therapy resistant cell lines, used scIDUC to identify efficacious drugs for the resistant line, and validated the predictions with in-vitro experiments. Together, scIDUC quickly translates scRNA-seq data into drug response for individual cells, displaying the potential as a first-line tool for nuanced and heterogeneity-aware drug discovery.
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Affiliation(s)
- Weijie Zhang
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN 55455
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN 55455
| | - Danielle Maeser
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN 55455
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN 55455
| | - Adam Lee
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN 55455
| | - Yingbo Huang
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN 55455
| | - Robert F Gruener
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN 55455
| | - Israa G Abdelbar
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN 55455
- Clinical Pharmacy Practice Department, The British University in Egypt, El Sherouk, 11837, Egypt
| | - Sampreeti Jena
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN 55455
| | - Anand G Patel
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - R Stephanie Huang
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN 55455
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN 55455
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13
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Hüttner SS, Henze H, Elster D, Koch P, Anderer U, von Eyss B, von Maltzahn J. A dysfunctional miR-1-TRPS1-MYOG axis drives ERMS by suppressing terminal myogenic differentiation. Mol Ther 2023; 31:2612-2632. [PMID: 37452493 PMCID: PMC10492030 DOI: 10.1016/j.ymthe.2023.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 05/12/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023] Open
Abstract
Rhabdomyosarcoma is the most common pediatric soft tissue tumor, comprising two major subtypes: the PAX3/7-FOXO1 fusion-negative embryonal and the PAX3/7-FOXO1 fusion-positive alveolar subtype. Here, we demonstrate that the expression levels of the transcriptional repressor TRPS1 are specifically enhanced in the embryonal subtype, resulting in impaired terminal myogenic differentiation and tumor growth. During normal myogenesis, expression levels of TRPS1 have to decrease to allow myogenic progression, as demonstrated by overexpression of TRPS1 in myoblasts impairing myotube formation. Consequentially, myogenic differentiation in embryonal rhabdomyosarcoma in vitro as well as in vivo can be achieved by reducing TRPS1 levels. Furthermore, we show that TRPS1 levels in RD cells, the bona fide model cell line for embryonal rhabdomyosarcoma, are regulated by miR-1 and that TRPS1 and MYOD1 share common genomic binding sites. The myogenin (MYOG) promoter is one of the critical targets of TRPS1 and MYOD1; we demonstrate that TRPS1 restricts MYOG expression and thereby inhibits terminal myogenic differentiation. Therefore, reduction of TRPS1 levels in embryonal rhabdomyosarcoma might be a therapeutic approach to drive embryonal rhabdomyosarcoma cells into myogenic differentiation, thereby generating postmitotic myotubes.
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Affiliation(s)
- Sören S Hüttner
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstrasse 11, 07745 Jena, Germany
| | - Henriette Henze
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstrasse 11, 07745 Jena, Germany
| | - Dana Elster
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstrasse 11, 07745 Jena, Germany
| | - Philipp Koch
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstrasse 11, 07745 Jena, Germany
| | - Ursula Anderer
- Department of Cell Biology and Tissue Engineering, Brandenburg University of Technology Cottbus-Senftenberg, Universitätsplatz 1, 01968 Senftenberg, Germany
| | - Björn von Eyss
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstrasse 11, 07745 Jena, Germany
| | - Julia von Maltzahn
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstrasse 11, 07745 Jena, Germany; Faculty of Health Sciences Brandenburg, Brandenburg University of Technology Cottbus-Senftenberg, Universitätsplatz 1, 01968 Senftenberg, Germany.
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14
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Chory EJ, Wang M, Ceribelli M, Michalowska AM, Golas S, Beck E, Klumpp-Thomas C, Chen L, McKnight C, Itkin Z, Wilson KM, Holland D, Divakaran S, Bradner J, Khan J, Gryder BE, Thomas CJ, Stanton BZ. High-throughput approaches to uncover synergistic drug combinations in leukemia. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2023; 28:193-201. [PMID: 37121274 PMCID: PMC10449086 DOI: 10.1016/j.slasd.2023.04.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 03/30/2023] [Accepted: 04/26/2023] [Indexed: 05/02/2023]
Abstract
We report a comprehensive drug synergy study in acute myeloid leukemia (AML). In this work, we investigate a panel of cell lines spanning both MLL-rearranged and non-rearranged subtypes. The work comprises a resource for the community, with many synergistic drug combinations that could not have been predicted a priori, and open source code for automation and analyses. We base our definitions of drug synergy on the Chou-Talalay method, which is useful for visualizations of synergy experiments in isobolograms, and median-effects plots, among other representations. Our key findings include drug synergies affecting the chromatin state, specifically in the context of regulation of the modification state of histone H3 lysine-27. We report open source high throughput methodology such that multidimensional drug screening can be accomplished with equipment that is accessible to most laboratories. This study will enable preclinical investigation of new drug combinations in a lethal blood cancer, with data analysis and automation workflows freely available to the community.
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Affiliation(s)
- Emma J Chory
- Media Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.; Broad Institute of MIT and Harvard, Cambridge, MA, USA..
| | - Meng Wang
- Nationwide Children's Hospital, Center for Childhood Cancer and Blood Diseases, Columbus, OH, USA
| | - Michele Ceribelli
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville MD 20850, USA
| | - Aleksandra M Michalowska
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville MD 20850, USA
| | - Stefan Golas
- Media Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Erin Beck
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville MD 20850, USA
| | - Carleen Klumpp-Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville MD 20850, USA
| | - Lu Chen
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville MD 20850, USA
| | - Crystal McKnight
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville MD 20850, USA
| | - Zina Itkin
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville MD 20850, USA
| | - Kelli M Wilson
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville MD 20850, USA
| | - David Holland
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville MD 20850, USA
| | - Sanjay Divakaran
- Cardio-Oncology Program, Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - James Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Javed Khan
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Berkley E Gryder
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.; Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Case Comprehensive Cancer Center, Cleveland, Ohio 44106, United States
| | - Craig J Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville MD 20850, USA.; Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Benjamin Z Stanton
- Nationwide Children's Hospital, Center for Childhood Cancer and Blood Diseases, Columbus, OH, USA.; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA; Department of Biological Chemistry & Pharmacology, The Ohio State University College of Medicine, Columbus, OH, USA..
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15
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DeMartino J, Meister MT, Visser LL, Brok M, Groot Koerkamp MJA, Wezenaar AKL, Hiemcke-Jiwa LS, de Souza T, Merks JHM, Rios AC, Holstege FCP, Margaritis T, Drost J. Single-cell transcriptomics reveals immune suppression and cell states predictive of patient outcomes in rhabdomyosarcoma. Nat Commun 2023; 14:3074. [PMID: 37244912 DOI: 10.1038/s41467-023-38886-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 05/19/2023] [Indexed: 05/29/2023] Open
Abstract
Paediatric rhabdomyosarcoma (RMS) is a soft tissue malignancy of mesenchymal origin that is thought to arise as a consequence of derailed myogenic differentiation. Despite intensive treatment regimens, the prognosis for high-risk patients remains dismal. The cellular differentiation states underlying RMS and how these relate to patient outcomes remain largely elusive. Here, we use single-cell mRNA sequencing to generate a transcriptomic atlas of RMS. Analysis of the RMS tumour niche reveals evidence of an immunosuppressive microenvironment. We also identify a putative interaction between NECTIN3 and TIGIT, specific to the more aggressive fusion-positive (FP) RMS subtype, as a potential cause of tumour-induced T-cell dysfunction. In malignant RMS cells, we define transcriptional programs reflective of normal myogenic differentiation and show that these cellular differentiation states are predictive of patient outcomes in both FP RMS and the less aggressive fusion-negative subtype. Our study reveals the potential of therapies targeting the immune microenvironment of RMS and suggests that assessing tumour differentiation states may enable a more refined risk stratification.
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Affiliation(s)
- Jeff DeMartino
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
- Oncode Institute, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Michael T Meister
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
- Oncode Institute, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Lindy L Visser
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Mariël Brok
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
- Oncode Institute, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Marian J A Groot Koerkamp
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
- Oncode Institute, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Amber K L Wezenaar
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
- Oncode Institute, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Laura S Hiemcke-Jiwa
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Terezinha de Souza
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
- Oncode Institute, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Johannes H M Merks
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Anne C Rios
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
- Oncode Institute, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Frank C P Holstege
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
- Center for Molecular Medicine, UMC Utrecht and Utrecht University, Universiteitsweg 100, 3584 CG, Utrecht, the Netherlands
| | - Thanasis Margaritis
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands.
| | - Jarno Drost
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands.
- Oncode Institute, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands.
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16
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Pomella S, Danielli SG, Alaggio R, Breunis WB, Hamed E, Selfe J, Wachtel M, Walters ZS, Schäfer BW, Rota R, Shipley JM, Hettmer S. Genomic and Epigenetic Changes Drive Aberrant Skeletal Muscle Differentiation in Rhabdomyosarcoma. Cancers (Basel) 2023; 15:2823. [PMID: 37345159 DOI: 10.3390/cancers15102823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 05/14/2023] [Accepted: 05/16/2023] [Indexed: 06/23/2023] Open
Abstract
Rhabdomyosarcoma (RMS), the most common soft-tissue sarcoma in children and adolescents, represents an aberrant form of skeletal muscle differentiation. Both skeletal muscle development, as well as regeneration of adult skeletal muscle are governed by members of the myogenic family of regulatory transcription factors (MRFs), which are deployed in a highly controlled, multi-step, bidirectional process. Many aspects of this complex process are deregulated in RMS and contribute to tumorigenesis. Interconnected loops of super-enhancers, called core regulatory circuitries (CRCs), define aberrant muscle differentiation in RMS cells. The transcriptional regulation of MRF expression/activity takes a central role in the CRCs active in skeletal muscle and RMS. In PAX3::FOXO1 fusion-positive (PF+) RMS, CRCs maintain expression of the disease-driving fusion oncogene. Recent single-cell studies have revealed hierarchically organized subsets of cells within the RMS cell pool, which recapitulate developmental myogenesis and appear to drive malignancy. There is a large interest in exploiting the causes of aberrant muscle development in RMS to allow for terminal differentiation as a therapeutic strategy, for example, by interrupting MEK/ERK signaling or by interfering with the epigenetic machinery controlling CRCs. In this review, we provide an overview of the genetic and epigenetic framework of abnormal muscle differentiation in RMS, as it provides insights into fundamental mechanisms of RMS malignancy, its remarkable phenotypic diversity and, ultimately, opportunities for therapeutic intervention.
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Affiliation(s)
- Silvia Pomella
- Department of Hematology/Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS Istituto Ospedale Pediatrico Bambino Gesu, Viale San Paolo 15, 00146 Rome, Italy
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Sara G Danielli
- Department of Oncology and Children's Research Center, University Children's Hospital of Zurich, 8032 Zürich, Switzerland
| | - Rita Alaggio
- Department of Pathology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Viale San Paolo 15, 00146 Rome, Italy
| | - Willemijn B Breunis
- Department of Oncology and Children's Research Center, University Children's Hospital of Zurich, 8032 Zürich, Switzerland
| | - Ebrahem Hamed
- Division of Pediatric Hematology and Oncology, Department of Pediatric and Adolescent Medicine, University Medical Center Freiburg, University of Freiburg, 79106 Freiburg, Germany
| | - Joanna Selfe
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London SM2 FNG, UK
| | - Marco Wachtel
- Department of Oncology and Children's Research Center, University Children's Hospital of Zurich, 8032 Zürich, Switzerland
| | - Zoe S Walters
- Translational Epigenomics Team, Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK
| | - Beat W Schäfer
- Department of Oncology and Children's Research Center, University Children's Hospital of Zurich, 8032 Zürich, Switzerland
| | - Rossella Rota
- Department of Hematology/Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS Istituto Ospedale Pediatrico Bambino Gesu, Viale San Paolo 15, 00146 Rome, Italy
| | - Janet M Shipley
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London SM2 FNG, UK
| | - Simone Hettmer
- Division of Pediatric Hematology and Oncology, Department of Pediatric and Adolescent Medicine, University Medical Center Freiburg, University of Freiburg, 79106 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), 79104 Freiburg, Germany
- Comprehensive Cancer Centre Freiburg (CCCF), University Medical Center Freiburg, 790106 Freiburg, Germany
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17
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Fritzke M, Chen K, Tang W, Stinson S, Pham T, Wang Y, Xu L, Chen EY. The MYC-YBX1 Circuit in Maintaining Stem-like Vincristine-Resistant Cells in Rhabdomyosarcoma. Cancers (Basel) 2023; 15:2788. [PMID: 37345125 DOI: 10.3390/cancers15102788] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/03/2023] [Accepted: 05/09/2023] [Indexed: 06/23/2023] Open
Abstract
Rhabdomyosarcoma (RMS) is a pediatric soft tissue sarcoma that causes significant devastation, with no effective therapy for relapsed disease. The mechanisms behind treatment failures are poorly understood. Our study showed that treatment of RMS cells with vincristine led to an increase in CD133-positive stem-like resistant cells. Single cell RNAseq analysis revealed that MYC and YBX1 were among the top-scoring transcription factors in CD133-high expressing cells. Targeting MYC and YBX1 using CRISPR/Cas9 reduced stem-like characteristics and viability of the vincristine-resistant cells. MYC and YBX1 showed mutual regulation, with MYC binding to the YBX1 promoter and YBX1 binding to MYC mRNA. The MYC inhibitor MYC361i synergized with vincristine to reduce tumor growth and stem-like cells in a zebrafish model of RMS. MYC and YBX expression showed a positive correlation in RMS patients, and high MYC expression correlated with poor survival. Targeting the MYC-YBX1 axis holds promise for improving survival in RMS patients.
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Affiliation(s)
- Madeline Fritzke
- Department of Laboratory Pathology and Medicine, University of Washington, Seattle, WA 98195, USA
| | - Kenian Chen
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Weiliang Tang
- Department of Laboratory Pathology and Medicine, University of Washington, Seattle, WA 98195, USA
| | - Spencer Stinson
- Department of Laboratory Pathology and Medicine, University of Washington, Seattle, WA 98195, USA
| | - Thao Pham
- Department of Laboratory Pathology and Medicine, University of Washington, Seattle, WA 98195, USA
- Astellas US Technologies, Universal Cells, Inc., Seattle, WA 98121, USA
| | - Yadong Wang
- Department of Laboratory Pathology and Medicine, University of Washington, Seattle, WA 98195, USA
| | - Lin Xu
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Eleanor Y Chen
- Department of Laboratory Pathology and Medicine, University of Washington, Seattle, WA 98195, USA
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18
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Shah AM, Guo L, Morales MG, Jaichander P, Chen K, Huang H, Cano Hernandez K, Xu L, Bassel-Duby R, Olson EN, Liu N. TWIST2-mediated chromatin remodeling promotes fusion-negative rhabdomyosarcoma. SCIENCE ADVANCES 2023; 9:eade8184. [PMID: 37115930 PMCID: PMC10146891 DOI: 10.1126/sciadv.ade8184] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 03/27/2023] [Indexed: 05/03/2023]
Abstract
Rhabdomyosarcoma (RMS) is a common soft tissue sarcoma in children that resembles developing skeletal muscle. Unlike normal muscle cells, RMS cells fail to differentiate despite expression of the myogenic determination protein MYOD. The TWIST2 transcription factor is frequently overexpressed in fusion-negative RMS (FN-RMS). TWIST2 blocks differentiation by inhibiting MYOD activity in myoblasts, but its role in FN-RMS pathogenesis is incompletely understood. Here, we show that knockdown of TWIST2 enables FN-RMS cells to exit the cell cycle and undergo terminal myogenesis. TWIST2 knockdown also substantially reduces tumor growth in a mouse xenograft model of FN-RMS. Mechanistically, TWIST2 controls H3K27 acetylation at distal enhancers by interacting with the chromatin remodelers SMARCA4 and CHD3 to activate growth-related target genes and repress myogenesis-related target genes. These findings provide insights into the role of TWIST2 in maintaining an undifferentiated and tumorigenic state of FN-RMS and highlight the potential of suppressing TWIST2-regulated pathways to treat FN-RMS.
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Affiliation(s)
- Akansha M. Shah
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lei Guo
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Maria Gabriela Morales
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Priscilla Jaichander
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kenian Chen
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Huocong Huang
- Department of Surgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Karla Cano Hernandez
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lin Xu
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Rhonda Bassel-Duby
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Eric N. Olson
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ning Liu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
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19
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Danielli SG, Porpiglia E, De Micheli AJ, Navarro N, Zellinger MJ, Bechtold I, Kisele S, Volken L, Marques JG, Kasper S, Bode PK, Henssen AG, Gürgen D, Delattre O, Surdez D, Roma J, Bühlmann P, Blau HM, Wachtel M, Schäfer BW. Single-cell profiling of alveolar rhabdomyosarcoma reveals RAS pathway inhibitors as cell-fate hijackers with therapeutic relevance. SCIENCE ADVANCES 2023; 9:eade9238. [PMID: 36753540 PMCID: PMC9908029 DOI: 10.1126/sciadv.ade9238] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Rhabdomyosarcoma (RMS) is a group of pediatric cancers with features of developing skeletal muscle. The cellular hierarchy and mechanisms leading to developmental arrest remain elusive. Here, we combined single-cell RNA sequencing, mass cytometry, and high-content imaging to resolve intratumoral heterogeneity of patient-derived primary RMS cultures. We show that the aggressive alveolar RMS (aRMS) subtype contains plastic muscle stem-like cells and cycling progenitors that drive tumor growth, and a subpopulation of differentiated cells that lost its proliferative potential and correlates with better outcomes. While chemotherapy eliminates cycling progenitors, it enriches aRMS for muscle stem-like cells. We screened for drugs hijacking aRMS toward clinically favorable subpopulations and identified a combination of RAF and MEK inhibitors that potently induces myogenic differentiation and inhibits tumor growth. Overall, our work provides insights into the developmental states underlying aRMS aggressiveness, chemoresistance, and progression and identifies the RAS pathway as a promising therapeutic target.
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Affiliation(s)
- Sara G. Danielli
- Department of Oncology and Children’s Research Center, University Children’s Hospital of Zurich, Zürich 8032, Switzerland
| | - Ermelinda Porpiglia
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Biomedicine, Aarhus University, Aarhus C 8000, Denmark
- Corresponding author. (B.W.S.); (M.W.); (E.P.)
| | - Andrea J. De Micheli
- Department of Oncology and Children’s Research Center, University Children’s Hospital of Zurich, Zürich 8032, Switzerland
| | - Natalia Navarro
- Laboratory of Translational Research in Child and Adolescent Cancer, Vall d’Hebron Research Institute, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | | | - Ingrid Bechtold
- Department of Oncology and Children’s Research Center, University Children’s Hospital of Zurich, Zürich 8032, Switzerland
| | - Samanta Kisele
- Department of Oncology and Children’s Research Center, University Children’s Hospital of Zurich, Zürich 8032, Switzerland
| | - Larissa Volken
- Department of Oncology and Children’s Research Center, University Children’s Hospital of Zurich, Zürich 8032, Switzerland
| | - Joana G. Marques
- Department of Oncology and Children’s Research Center, University Children’s Hospital of Zurich, Zürich 8032, Switzerland
| | - Stephanie Kasper
- Department of Oncology and Children’s Research Center, University Children’s Hospital of Zurich, Zürich 8032, Switzerland
| | - Peter K. Bode
- Department of Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Anton G. Henssen
- Department of Pediatric Oncology/Hematology, Charité–Universitätsmedizin Berlin, Berlin 13353, Germany
| | - Dennis Gürgen
- EPO Experimental Pharmacology and Oncology Berlin-Buch GmbH Berlin 13125, Germany
| | - Olivier Delattre
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Laboratory, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris 75005, France
| | - Didier Surdez
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Laboratory, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris 75005, France
- Balgrist University Hospital, Faculty of Medicine, University of Zurich (UZH), Zurich, Switzerland
| | - Josep Roma
- Laboratory of Translational Research in Child and Adolescent Cancer, Vall d’Hebron Research Institute, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - Peter Bühlmann
- Seminar for Statistics, ETH Zürich, Zürich 8092, Switzerland
| | - Helen M. Blau
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marco Wachtel
- Department of Oncology and Children’s Research Center, University Children’s Hospital of Zurich, Zürich 8032, Switzerland
- Corresponding author. (B.W.S.); (M.W.); (E.P.)
| | - Beat W. Schäfer
- Department of Oncology and Children’s Research Center, University Children’s Hospital of Zurich, Zürich 8032, Switzerland
- Corresponding author. (B.W.S.); (M.W.); (E.P.)
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20
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Hensch NR, Bondra K, Wang L, Sreenivas P, Zhao XR, Modi P, Vaseva AV, Houghton PJ, Ignatius MS. Sensitization to Ionizing Radiation by MEK Inhibition Is Dependent on SNAI2 in Fusion-Negative Rhabdomyosarcoma. Mol Cancer Ther 2023; 22:123-134. [PMID: 36162055 PMCID: PMC10046682 DOI: 10.1158/1535-7163.mct-22-0310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 07/15/2022] [Accepted: 09/21/2022] [Indexed: 02/03/2023]
Abstract
In fusion-negative rhabdomyosarcoma (FN-RMS), a pediatric malignancy with skeletal muscle characteristics, >90% of high-risk patients have mutations that activate the RAS/MEK signaling pathway. We recently discovered that SNAI2, in addition to blocking myogenic differentiation downstream of MEK signaling in FN-RMS, represses proapoptotic BIM expression to protect RMS tumors from ionizing radiation (IR). As clinically relevant concentrations of the MEK inhibitor trametinib elicit poor responses in preclinical xenograft models, we investigated the utility of low-dose trametinib in combination with IR for the treatment of RAS-mutant FN-RMS. We hypothesized that trametinib would sensitize FN-RMS to IR through its downregulation of SNAI2 expression. While we observed little to no difference in myogenic differentiation or cell survival with trametinib treatment alone, robust differentiation and reduced survival were observed after IR. In addition, IR-induced apoptosis was significantly increased in FN-RMS cells treated concurrently with trametinib, as was increased BIM expression. SNAI2's role in these processes was established using overexpression rescue experiments, where overexpression of SNAI2 prevented IR-induced myogenic differentiation and apoptosis. Moreover, combining MEK inhibitor with IR resulted in complete tumor regression and a 2- to 4-week delay in event-free survival (EFS) in preclinical xenograft and patient-derived xenograft models. Our findings demonstrate that the combination of MEK inhibition and IR results in robust differentiation and apoptosis, due to the reduction of SNAI2, which leads to extended EFS in FN-RMS. SNAI2 thus is a potential biomarker of IR insensitivity and target for future therapies to sensitize aggressive sarcomas to IR.
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Affiliation(s)
- Nicole R. Hensch
- Greehey Children's Cancer Research Institute (GCCRI), Department of Molecular Medicine, UT Health Sciences Center, San Antonio, Texas, USA
| | - Kathryn Bondra
- Greehey Children's Cancer Research Institute (GCCRI), Department of Molecular Medicine, UT Health Sciences Center, San Antonio, Texas, USA
| | - Long Wang
- Greehey Children's Cancer Research Institute (GCCRI), Department of Molecular Medicine, UT Health Sciences Center, San Antonio, Texas, USA
| | - Prethish Sreenivas
- Greehey Children's Cancer Research Institute (GCCRI), Department of Molecular Medicine, UT Health Sciences Center, San Antonio, Texas, USA
| | - Xiang R. Zhao
- Greehey Children's Cancer Research Institute (GCCRI), Department of Molecular Medicine, UT Health Sciences Center, San Antonio, Texas, USA
| | - Paulomi Modi
- Greehey Children's Cancer Research Institute (GCCRI), Department of Molecular Medicine, UT Health Sciences Center, San Antonio, Texas, USA
| | - Angelina V. Vaseva
- Greehey Children's Cancer Research Institute (GCCRI), Department of Molecular Medicine, UT Health Sciences Center, San Antonio, Texas, USA
| | - Peter J. Houghton
- Greehey Children's Cancer Research Institute (GCCRI), Department of Molecular Medicine, UT Health Sciences Center, San Antonio, Texas, USA
| | - Myron S. Ignatius
- Greehey Children's Cancer Research Institute (GCCRI), Department of Molecular Medicine, UT Health Sciences Center, San Antonio, Texas, USA
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21
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Zeineldin M, Patel AG, Dyer MA. Neuroblastoma: When differentiation goes awry. Neuron 2022; 110:2916-2928. [PMID: 35985323 PMCID: PMC9509448 DOI: 10.1016/j.neuron.2022.07.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 04/21/2022] [Accepted: 07/13/2022] [Indexed: 10/15/2022]
Abstract
Neuroblastoma is a leading cause of cancer-related death in children. Accumulated data suggest that differentiation arrest of the neural-crest-derived sympathoadrenal lineage contributes to neuroblastoma formation. The developmental arrest of these cell types explains many biological features of the disease, including its cellular heterogeneity, mutational spectrum, spontaneous regression, and response to drugs that induce tumor cell differentiation. In this review, we provide evidence that supports the notion that arrested neural-crest-derived progenitor cells give rise to neuroblastoma and discuss how this concept could be exploited for clinical management of the disease.
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Affiliation(s)
- Maged Zeineldin
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Anand G Patel
- Departments of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Michael A Dyer
- Department of Developmental Neurobiology, MS-323, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
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22
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Wei Y, Qin Q, Yan C, Hayes MN, Garcia SP, Xi H, Do D, Jin AH, Eng TC, McCarthy KM, Adhikari A, Onozato ML, Spentzos D, Neilsen GP, Iafrate AJ, Wexler LH, Pyle AD, Suvà ML, Dela Cruz F, Pinello L, Langenau DM. Single-cell analysis and functional characterization uncover the stem cell hierarchies and developmental origins of rhabdomyosarcoma. NATURE CANCER 2022; 3:961-975. [PMID: 35982179 PMCID: PMC10430812 DOI: 10.1038/s43018-022-00414-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 06/24/2022] [Indexed: 04/29/2023]
Abstract
Rhabdomyosarcoma (RMS) is a common childhood cancer that shares features with developing skeletal muscle. Yet, the conservation of cellular hierarchy with human muscle development and the identification of molecularly defined tumor-propagating cells has not been reported. Using single-cell RNA-sequencing, DNA-barcode cell fate mapping and functional stem cell assays, we uncovered shared tumor cell hierarchies in RMS and human muscle development. We also identified common developmental stages at which tumor cells become arrested. Fusion-negative RMS cells resemble early myogenic cells found in embryonic and fetal development, while fusion-positive RMS cells express a highly specific gene program found in muscle cells transiting from embryonic to fetal development at 7-7.75 weeks of age. Fusion-positive RMS cells also have neural pathway-enriched states, suggesting less-rigid adherence to muscle-lineage hierarchies. Finally, we identified a molecularly defined tumor-propagating subpopulation in fusion-negative RMS that shares remarkable similarity to bi-potent, muscle mesenchyme progenitors that can make both muscle and osteogenic cells.
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Affiliation(s)
- Yun Wei
- Molecular Pathology Unit, Massachusetts General Research Institute, Charlestown, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Qian Qin
- Molecular Pathology Unit, Massachusetts General Research Institute, Charlestown, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Chuan Yan
- Molecular Pathology Unit, Massachusetts General Research Institute, Charlestown, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Madeline N Hayes
- Molecular Pathology Unit, Massachusetts General Research Institute, Charlestown, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Sara P Garcia
- Molecular Pathology Unit, Massachusetts General Research Institute, Charlestown, MA, USA
| | - Haibin Xi
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA, USA
| | - Daniel Do
- Molecular Pathology Unit, Massachusetts General Research Institute, Charlestown, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Alexander H Jin
- Molecular Pathology Unit, Massachusetts General Research Institute, Charlestown, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Tiffany C Eng
- Molecular Pathology Unit, Massachusetts General Research Institute, Charlestown, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Karin M McCarthy
- Molecular Pathology Unit, Massachusetts General Research Institute, Charlestown, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Abhinav Adhikari
- Molecular Pathology Unit, Massachusetts General Research Institute, Charlestown, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Maristela L Onozato
- Molecular Pathology Unit, Massachusetts General Research Institute, Charlestown, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
| | - Dimitrios Spentzos
- Center for Sarcoma and Connective Tissue Oncology, Department of Orthopedic Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Gunnlaugur P Neilsen
- Center for Sarcoma and Connective Tissue Oncology, Department of Orthopedic Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - A John Iafrate
- Molecular Pathology Unit, Massachusetts General Research Institute, Charlestown, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
| | - Leonard H Wexler
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - April D Pyle
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA, USA
| | - Mario L Suvà
- Molecular Pathology Unit, Massachusetts General Research Institute, Charlestown, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Filemon Dela Cruz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Luca Pinello
- Molecular Pathology Unit, Massachusetts General Research Institute, Charlestown, MA, USA.
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA.
| | - David M Langenau
- Molecular Pathology Unit, Massachusetts General Research Institute, Charlestown, MA, USA.
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA.
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
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23
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Pediatric Sarcomas: The Next Generation of Molecular Studies. Cancers (Basel) 2022; 14:cancers14102515. [PMID: 35626119 PMCID: PMC9139929 DOI: 10.3390/cancers14102515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/13/2022] [Accepted: 05/13/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary There has been an incredible amount of discovery in pediatric sarcomas, but much remains to be accomplished. Clinical challenges include diagnostic heterogeneity and the poor outcome of patients with high risk, metastatic, and relapsed disease. The emergence of single cell sequencing has allowed the ability to document tumor cell heterogeneity in amazing detail, but it does not allow the ability to visualize spatial orientation. This problem has been solved by spatial multi-omics, which can be used to map tumors and visualize the distribution of critical transcripts, mutations, and proteins. However, these tools only offer observational data. High-throughput functional genomics provides a powerful way to highlight oncogenic drivers and potential therapy opportunities. Research has been hamstrung by a need for annotated specimens, particularly in post-therapy, relapsed, and metastatic disease, and initial biopsies offer only limited data opportunities. Data complexity, variability, and inconsistency present problems best approached with AI/machine learning. We stand on the threshold of a revolution in cancer cell biology that has the potential for translation into more effective and more directed therapies, particularly for previously recalcitrant diseases. Abstract Pediatric sarcomas constitute one of the largest groups of childhood cancers, following hematopoietic, neural, and renal lesions. Partly because of their diversity, they continue to offer challenges in diagnosis and treatment. In spite of the diagnostic, nosologic, and therapeutic gains made with genetic technology, newer means for investigation are needed. This article reviews emerging technology being used to study human neoplasia and how these methods might be applicable to pediatric sarcomas. Methods reviewed include single cell RNA sequencing (scRNAseq), spatial multi-omics, high-throughput functional genomics, and clustered regularly interspersed short palindromic sequence-Cas9 (CRISPR-Cas9) technology. In spite of these advances, the field continues to be challenged by a dearth of properly annotated materials, particularly from recurrences and metastases and pre- and post-treatment samples.
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