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Fu R, Norris GA, Willard N, Griesinger AM, Riemondy KA, Amani V, Grimaldo E, Harris F, Hankinson TC, Mitra S, Ritzmann TA, Grundy RR, Foreman NK, Donson AM. Spatial transcriptomic analysis delineates epithelial and mesenchymal subpopulations and transition stages in childhood ependymoma. Neuro Oncol 2023; 25:786-798. [PMID: 36215273 PMCID: PMC10076949 DOI: 10.1093/neuonc/noac219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The diverse cellular constituents of childhood brain tumor ependymoma, recently revealed by single cell RNA-sequencing, may underly therapeutic resistance. Here we use spatial transcriptomics to further advance our understanding of the tumor microenvironment, mapping cellular subpopulations to the tumor architecture of ependymoma posterior fossa subgroup A (PFA), the commonest and most deadly childhood ependymoma variant. METHODS Spatial transcriptomics data from intact PFA sections was deconvoluted to resolve the histological arrangement of neoplastic and non-neoplastic cell types. Key findings were validated using immunohistochemistry, in vitro functional assays and outcome analysis in clinically-annotated PFA bulk transcriptomic data. RESULTS PFA are comprised of epithelial and mesenchymal histological zones containing a diversity of cellular states, each zone including co-existing and spatially distinct undifferentiated progenitor-like cells; a quiescent mesenchymal zone population, and a second highly mitotic progenitor population that is restricted to hypercellular epithelial zones and that is more abundant in progressive tumors. We show that myeloid cell interaction is the leading cause of mesenchymal transition in PFA, occurring in zones spatially distinct from hypoxia-induced mesenchymal transition, and these distinct EMT-initiating processes were replicated using in vitro models of PFA. CONCLUSIONS These insights demonstrate the utility of spatial transcriptomics to advance our understanding of ependymoma biology, revealing a clearer picture of the cellular constituents of PFA, their interactions and influence on tumor progression.
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Affiliation(s)
- Rui Fu
- RNA Biosciences Initiative, University of Colorado Denver, Aurora, Colorado, USA
| | - Gregory A Norris
- Department of Pediatrics, University of Colorado Denver, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Nicholas Willard
- Department of Pathology, University of Colorado Denver, Aurora, Colorado, USA
| | - Andrea M Griesinger
- Department of Pediatrics, University of Colorado Denver, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Kent A Riemondy
- RNA Biosciences Initiative, University of Colorado Denver, Aurora, Colorado, USA
| | - Vladimir Amani
- Department of Pediatrics, University of Colorado Denver, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Enrique Grimaldo
- Department of Pediatrics, University of Colorado Denver, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Faith Harris
- Department of Pediatrics, University of Colorado Denver, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Todd C Hankinson
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
- Department of Neurosurgery, University of Colorado Denver, Aurora, Colorado, USA
| | - Siddhartha Mitra
- Department of Pediatrics, University of Colorado Denver, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Timothy A Ritzmann
- Children’s Brain Tumor Research Centre, School of Medicine, University of Nottingham, Nottingham, UK
| | - Richard R Grundy
- Children’s Brain Tumor Research Centre, School of Medicine, University of Nottingham, Nottingham, UK
| | - Nicholas K Foreman
- Department of Pediatrics, University of Colorado Denver, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Andrew M Donson
- Department of Pediatrics, University of Colorado Denver, Aurora, Colorado, USA
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children’s Hospital Colorado, Aurora, Colorado, USA
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Rao S, Han AL, Zukowski A, Kopin E, Sartorius CA, Kabos P, Ramachandran S. Transcription factor-nucleosome dynamics from plasma cfDNA identifies ER-driven states in breast cancer. Sci Adv 2022; 8:eabm4358. [PMID: 36001652 PMCID: PMC9401618 DOI: 10.1126/sciadv.abm4358] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 07/12/2022] [Indexed: 06/09/2023]
Abstract
Genome-wide binding profiles of estrogen receptor (ER) and FOXA1 reflect cancer state in ER+ breast cancer. However, routine profiling of tumor transcription factor (TF) binding is impractical in the clinic. Here, we show that plasma cell-free DNA (cfDNA) contains high-resolution ER and FOXA1 tumor binding profiles for breast cancer. Enrichment of TF footprints in plasma reflects the binding strength of the TF in originating tissue. We defined pure in vivo tumor TF signatures in plasma using ER+ breast cancer xenografts, which can distinguish xenografts with distinct ER states. Furthermore, state-specific ER-binding signatures can partition human breast tumors into groups with significantly different ER expression and mortality. Last, TF footprints in human plasma samples can identify the presence of ER+ breast cancer. Thus, plasma TF footprints enable minimally invasive mapping of the regulatory landscape of breast cancer in humans and open vast possibilities for clinical applications across multiple tumor types.
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Affiliation(s)
- Satyanarayan Rao
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
| | - Amy L. Han
- Department of Medicine/Division of Medical Oncology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Alexis Zukowski
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
| | - Etana Kopin
- Department of Medicine/Division of Medical Oncology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Carol A. Sartorius
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Peter Kabos
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
- Department of Medicine/Division of Medical Oncology, University of Colorado School of Medicine, Aurora, CO, USA
- University of Colorado Cancer Center, Aurora, CO, USA
| | - Srinivas Ramachandran
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
- University of Colorado Cancer Center, Aurora, CO, USA
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