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Williamson D, Schwalbe EC, Hicks D, Aldinger KA, Lindsey JC, Crosier S, Richardson S, Goddard J, Hill RM, Castle J, Grabovska Y, Hacking J, Pizer B, Wharton SB, Jacques TS, Joshi A, Bailey S, Clifford SC. Medulloblastoma group 3 and 4 tumors comprise a clinically and biologically significant expression continuum reflecting human cerebellar development. Cell Rep 2022; 40:111162. [PMID: 35926460 PMCID: PMC9638015 DOI: 10.1016/j.celrep.2022.111162] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 05/26/2022] [Accepted: 07/13/2022] [Indexed: 01/29/2023] Open
Abstract
Medulloblastoma is currently subclassified into distinct DNA methylation subgroups/subtypes with particular clinico-molecular features. Using RNA sequencing (RNA-seq) in large, well-annotated cohorts of medulloblastoma, we show that transcriptionally group 3 and group 4 medulloblastomas exist as intermediates on a bipolar continuum between archetypal group 3 and group 4 entities. Continuum position is prognostic, reflecting a propensity for specific DNA copy-number changes, and specific switches in isoform/enhancer usage and RNA editing. Examining single-cell RNA-seq (scRNA-seq) profiles, we show that intratumoral transcriptional heterogeneity along the continuum is limited in a subtype-dependent manner. By integrating with a human scRNA-seq reference atlas, we show that this continuum is mirrored by an equivalent continuum of transcriptional cell types in early fetal cerebellar development. We identify distinct developmental niches for all four major subgroups and link each to a common developmental antecedent. Our findings show a transcriptional continuum arising from oncogenic disruption of highly specific fetal cerebellar cell types, linked to almost every aspect of group 3/group 4 molecular biology and clinico-pathology.
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Affiliation(s)
- Daniel Williamson
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, UK.
| | - Edward C. Schwalbe
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, UK,Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Debbie Hicks
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, UK
| | - Kimberly A. Aldinger
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Janet C. Lindsey
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, UK
| | - Stephen Crosier
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, UK
| | - Stacey Richardson
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, UK
| | - Jack Goddard
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, UK
| | - Rebecca M. Hill
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, UK
| | - Jemma Castle
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, UK
| | - Yura Grabovska
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, UK,Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | - James Hacking
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, UK
| | - Barry Pizer
- Institute of Translational Research, University of Liverpool, Liverpool, UK
| | - Stephen B. Wharton
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Thomas S. Jacques
- Developmental Biology and Cancer Programme, UCL GOS Institute of Child Health, London, and Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Abhijit Joshi
- Department of Neuropathology, Royal Victoria Infirmary (RVI), Newcastle University Teaching Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Simon Bailey
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, UK
| | - Steven C. Clifford
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, UK,Corresponding author
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3
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Wassman ER, Ho KS, Bertrand D, Davis KW, Martin MM, Page S, Peiffer A, Prasad A, Serrano MA, Twede H, Vanzo R, Scherer SW, Uddin M, Hensel CH. Critical exon indexing improves clinical interpretation of copy number variants in neurodevelopmental disorders. NEUROLOGY-GENETICS 2019; 5:e378. [PMID: 32042908 PMCID: PMC6927359 DOI: 10.1212/nxg.0000000000000378] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Accepted: 10/11/2019] [Indexed: 11/15/2022]
Abstract
Objective To evaluate a new tool to aid interpretation of copy number variants (CNVs) in individuals with neurodevelopmental disabilities. Methods Critical exon indexing (CEI) was used to identify genes with critical exons (CEGs) from clinically reported CNVs, which may contribute to neurodevelopmental disorders (NDDs). The 742 pathogenic CNVs and 1,363 variants of unknown significance (VUS) identified by chromosomal microarray analysis in 5,487 individuals with NDDs were subjected to CEI to identify CEGs. CEGs identified in a subsequent random series of VUS were evaluated for relevance to CNV interpretation. Results CEI identified a total of 2,492 unique CEGs in pathogenic CNVs and 953 in VUS compared with 259 CEGs in 6,965 CNVs from 873 controls. These differences are highly significant (p < 0.00001) whether compared as frequency, average, or normalized by CNV size. Twenty-one percent of VUS CEGs were not represented in Online Mendelian Inheritance in Man, highlighting limitations of existing resources for identifying potentially impactful genes within CNVs. CEGs were highly correlated with other indices and known pathways of relevance. Separately, 136 random VUS reports were reevaluated, and 76% of CEGs had not been commented on. In multiple cases, further investigation yielded additional relevant literature aiding interpretation. As one specific example, we discuss GTF2I as a CEG, which likely alters interpretation of several reported duplication VUS in the Williams-Beuren region. Conclusions Application of CEI to CNVs in individuals with NDDs can identify genes of potential clinical relevance, aid laboratories in effectively searching the clinical literature, and support the clinical reporting of poorly annotated VUS.
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Affiliation(s)
- E Robert Wassman
- Lineagen Inc. (E.R.W., K.S.H., D.B., K.W.D., M.M.M., S.P., A. Peiffer, A. Prasad, M.A.S., H.T., R.V., C.H.H.); Life Designs Ventures (E.R.W.), Park City, UT; Department of Pediatrics (K.S.H., A. Peiffer), University of Utah; The Centre for Applied Genomics (S.W.S., M.U.), The Hospital for Sick Children, Toronto, Ontario, Canada; Program in Genetics and Genome Biology (S.W.S), The Hospital for Sick Children; McLaughlin Centre (S.W.S), University of Toronto, Toronto, Ontario, Canada; and Department of Molecular Genetics (S.W.S), University of Toronto, Toronto, Ontario, Canada
| | - Karen S Ho
- Lineagen Inc. (E.R.W., K.S.H., D.B., K.W.D., M.M.M., S.P., A. Peiffer, A. Prasad, M.A.S., H.T., R.V., C.H.H.); Life Designs Ventures (E.R.W.), Park City, UT; Department of Pediatrics (K.S.H., A. Peiffer), University of Utah; The Centre for Applied Genomics (S.W.S., M.U.), The Hospital for Sick Children, Toronto, Ontario, Canada; Program in Genetics and Genome Biology (S.W.S), The Hospital for Sick Children; McLaughlin Centre (S.W.S), University of Toronto, Toronto, Ontario, Canada; and Department of Molecular Genetics (S.W.S), University of Toronto, Toronto, Ontario, Canada
| | - Diana Bertrand
- Lineagen Inc. (E.R.W., K.S.H., D.B., K.W.D., M.M.M., S.P., A. Peiffer, A. Prasad, M.A.S., H.T., R.V., C.H.H.); Life Designs Ventures (E.R.W.), Park City, UT; Department of Pediatrics (K.S.H., A. Peiffer), University of Utah; The Centre for Applied Genomics (S.W.S., M.U.), The Hospital for Sick Children, Toronto, Ontario, Canada; Program in Genetics and Genome Biology (S.W.S), The Hospital for Sick Children; McLaughlin Centre (S.W.S), University of Toronto, Toronto, Ontario, Canada; and Department of Molecular Genetics (S.W.S), University of Toronto, Toronto, Ontario, Canada
| | - Kyle W Davis
- Lineagen Inc. (E.R.W., K.S.H., D.B., K.W.D., M.M.M., S.P., A. Peiffer, A. Prasad, M.A.S., H.T., R.V., C.H.H.); Life Designs Ventures (E.R.W.), Park City, UT; Department of Pediatrics (K.S.H., A. Peiffer), University of Utah; The Centre for Applied Genomics (S.W.S., M.U.), The Hospital for Sick Children, Toronto, Ontario, Canada; Program in Genetics and Genome Biology (S.W.S), The Hospital for Sick Children; McLaughlin Centre (S.W.S), University of Toronto, Toronto, Ontario, Canada; and Department of Molecular Genetics (S.W.S), University of Toronto, Toronto, Ontario, Canada
| | - Megan M Martin
- Lineagen Inc. (E.R.W., K.S.H., D.B., K.W.D., M.M.M., S.P., A. Peiffer, A. Prasad, M.A.S., H.T., R.V., C.H.H.); Life Designs Ventures (E.R.W.), Park City, UT; Department of Pediatrics (K.S.H., A. Peiffer), University of Utah; The Centre for Applied Genomics (S.W.S., M.U.), The Hospital for Sick Children, Toronto, Ontario, Canada; Program in Genetics and Genome Biology (S.W.S), The Hospital for Sick Children; McLaughlin Centre (S.W.S), University of Toronto, Toronto, Ontario, Canada; and Department of Molecular Genetics (S.W.S), University of Toronto, Toronto, Ontario, Canada
| | - Stephanie Page
- Lineagen Inc. (E.R.W., K.S.H., D.B., K.W.D., M.M.M., S.P., A. Peiffer, A. Prasad, M.A.S., H.T., R.V., C.H.H.); Life Designs Ventures (E.R.W.), Park City, UT; Department of Pediatrics (K.S.H., A. Peiffer), University of Utah; The Centre for Applied Genomics (S.W.S., M.U.), The Hospital for Sick Children, Toronto, Ontario, Canada; Program in Genetics and Genome Biology (S.W.S), The Hospital for Sick Children; McLaughlin Centre (S.W.S), University of Toronto, Toronto, Ontario, Canada; and Department of Molecular Genetics (S.W.S), University of Toronto, Toronto, Ontario, Canada
| | - Andreas Peiffer
- Lineagen Inc. (E.R.W., K.S.H., D.B., K.W.D., M.M.M., S.P., A. Peiffer, A. Prasad, M.A.S., H.T., R.V., C.H.H.); Life Designs Ventures (E.R.W.), Park City, UT; Department of Pediatrics (K.S.H., A. Peiffer), University of Utah; The Centre for Applied Genomics (S.W.S., M.U.), The Hospital for Sick Children, Toronto, Ontario, Canada; Program in Genetics and Genome Biology (S.W.S), The Hospital for Sick Children; McLaughlin Centre (S.W.S), University of Toronto, Toronto, Ontario, Canada; and Department of Molecular Genetics (S.W.S), University of Toronto, Toronto, Ontario, Canada
| | - Aparna Prasad
- Lineagen Inc. (E.R.W., K.S.H., D.B., K.W.D., M.M.M., S.P., A. Peiffer, A. Prasad, M.A.S., H.T., R.V., C.H.H.); Life Designs Ventures (E.R.W.), Park City, UT; Department of Pediatrics (K.S.H., A. Peiffer), University of Utah; The Centre for Applied Genomics (S.W.S., M.U.), The Hospital for Sick Children, Toronto, Ontario, Canada; Program in Genetics and Genome Biology (S.W.S), The Hospital for Sick Children; McLaughlin Centre (S.W.S), University of Toronto, Toronto, Ontario, Canada; and Department of Molecular Genetics (S.W.S), University of Toronto, Toronto, Ontario, Canada
| | - Moises A Serrano
- Lineagen Inc. (E.R.W., K.S.H., D.B., K.W.D., M.M.M., S.P., A. Peiffer, A. Prasad, M.A.S., H.T., R.V., C.H.H.); Life Designs Ventures (E.R.W.), Park City, UT; Department of Pediatrics (K.S.H., A. Peiffer), University of Utah; The Centre for Applied Genomics (S.W.S., M.U.), The Hospital for Sick Children, Toronto, Ontario, Canada; Program in Genetics and Genome Biology (S.W.S), The Hospital for Sick Children; McLaughlin Centre (S.W.S), University of Toronto, Toronto, Ontario, Canada; and Department of Molecular Genetics (S.W.S), University of Toronto, Toronto, Ontario, Canada
| | - Hope Twede
- Lineagen Inc. (E.R.W., K.S.H., D.B., K.W.D., M.M.M., S.P., A. Peiffer, A. Prasad, M.A.S., H.T., R.V., C.H.H.); Life Designs Ventures (E.R.W.), Park City, UT; Department of Pediatrics (K.S.H., A. Peiffer), University of Utah; The Centre for Applied Genomics (S.W.S., M.U.), The Hospital for Sick Children, Toronto, Ontario, Canada; Program in Genetics and Genome Biology (S.W.S), The Hospital for Sick Children; McLaughlin Centre (S.W.S), University of Toronto, Toronto, Ontario, Canada; and Department of Molecular Genetics (S.W.S), University of Toronto, Toronto, Ontario, Canada
| | - Rena Vanzo
- Lineagen Inc. (E.R.W., K.S.H., D.B., K.W.D., M.M.M., S.P., A. Peiffer, A. Prasad, M.A.S., H.T., R.V., C.H.H.); Life Designs Ventures (E.R.W.), Park City, UT; Department of Pediatrics (K.S.H., A. Peiffer), University of Utah; The Centre for Applied Genomics (S.W.S., M.U.), The Hospital for Sick Children, Toronto, Ontario, Canada; Program in Genetics and Genome Biology (S.W.S), The Hospital for Sick Children; McLaughlin Centre (S.W.S), University of Toronto, Toronto, Ontario, Canada; and Department of Molecular Genetics (S.W.S), University of Toronto, Toronto, Ontario, Canada
| | - Stephen W Scherer
- Lineagen Inc. (E.R.W., K.S.H., D.B., K.W.D., M.M.M., S.P., A. Peiffer, A. Prasad, M.A.S., H.T., R.V., C.H.H.); Life Designs Ventures (E.R.W.), Park City, UT; Department of Pediatrics (K.S.H., A. Peiffer), University of Utah; The Centre for Applied Genomics (S.W.S., M.U.), The Hospital for Sick Children, Toronto, Ontario, Canada; Program in Genetics and Genome Biology (S.W.S), The Hospital for Sick Children; McLaughlin Centre (S.W.S), University of Toronto, Toronto, Ontario, Canada; and Department of Molecular Genetics (S.W.S), University of Toronto, Toronto, Ontario, Canada
| | - Mohammed Uddin
- Lineagen Inc. (E.R.W., K.S.H., D.B., K.W.D., M.M.M., S.P., A. Peiffer, A. Prasad, M.A.S., H.T., R.V., C.H.H.); Life Designs Ventures (E.R.W.), Park City, UT; Department of Pediatrics (K.S.H., A. Peiffer), University of Utah; The Centre for Applied Genomics (S.W.S., M.U.), The Hospital for Sick Children, Toronto, Ontario, Canada; Program in Genetics and Genome Biology (S.W.S), The Hospital for Sick Children; McLaughlin Centre (S.W.S), University of Toronto, Toronto, Ontario, Canada; and Department of Molecular Genetics (S.W.S), University of Toronto, Toronto, Ontario, Canada
| | - Charles H Hensel
- Lineagen Inc. (E.R.W., K.S.H., D.B., K.W.D., M.M.M., S.P., A. Peiffer, A. Prasad, M.A.S., H.T., R.V., C.H.H.); Life Designs Ventures (E.R.W.), Park City, UT; Department of Pediatrics (K.S.H., A. Peiffer), University of Utah; The Centre for Applied Genomics (S.W.S., M.U.), The Hospital for Sick Children, Toronto, Ontario, Canada; Program in Genetics and Genome Biology (S.W.S), The Hospital for Sick Children; McLaughlin Centre (S.W.S), University of Toronto, Toronto, Ontario, Canada; and Department of Molecular Genetics (S.W.S), University of Toronto, Toronto, Ontario, Canada
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