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Acta Neuropathologica

, Volume 136, Issue 2, pp 227–237 | Cite as

Heterogeneity within the PF-EPN-B ependymoma subgroup

  • Florence M. G. Cavalli
  • Jens-Martin Hübner
  • Tanvi Sharma
  • Betty Luu
  • Martin Sill
  • Michal Zapotocky
  • Stephen C. Mack
  • Hendrik Witt
  • Tong Lin
  • David J. H. Shih
  • Ben Ho
  • Mariarita Santi
  • Lyndsey Emery
  • Juliette Hukin
  • Christopher Dunham
  • Roger E. McLendon
  • Eric S. Lipp
  • Sridharan Gururangan
  • Andrew Grossbach
  • Pim French
  • Johan M. Kros
  • Marie-Lise C. van Veelen
  • Amulya A. Nageswara Rao
  • Caterina Giannini
  • Sarah Leary
  • Shin Jung
  • Claudia C. Faria
  • Jaume Mora
  • Ulrich Schüller
  • Marta M. Alonso
  • Jennifer A. Chan
  • Almos Klekner
  • Lola B. Chambless
  • Eugene I. Hwang
  • Maura Massimino
  • Charles G. Eberhart
  • Matthias A. Karajannis
  • Benjamin Lu
  • Linda M. Liau
  • Massimo Zollo
  • Veronica Ferrucci
  • Carlos Carlotti
  • Daniela P. C. Tirapelli
  • Uri Tabori
  • Eric Bouffet
  • Marina Ryzhova
  • David W. Ellison
  • Thomas E. Merchant
  • Mark R. Gilbert
  • Terri S. Armstrong
  • Andrey Korshunov
  • Stefan M. Pfister
  • Michael D. Taylor
  • Kenneth Aldape
  • Kristian W. Pajtler
  • Marcel Kool
  • Vijay Ramaswamy
Original Paper

Abstract

Posterior fossa ependymoma comprise three distinct molecular variants, termed PF-EPN-A (PFA), PF-EPN-B (PFB), and PF-EPN-SE (subependymoma). Clinically, they are very disparate and PFB tumors are currently being considered for a trial of radiation avoidance. However, to move forward, unraveling the heterogeneity within PFB would be highly desirable. To discern the molecular heterogeneity within PFB, we performed an integrated analysis consisting of DNA methylation profiling, copy-number profiling, gene expression profiling, and clinical correlation across a cohort of 212 primary posterior fossa PFB tumors. Unsupervised spectral clustering and t-SNE analysis of genome-wide methylation data revealed five distinct subtypes of PFB tumors, termed PFB1-5, with distinct demographics, copy-number alterations, and gene expression profiles. All PFB subtypes were distinct from PFA and posterior fossa subependymomas. Of the five subtypes, PFB4 and PFB5 are more discrete, consisting of younger and older patients, respectively, with a strong female-gender enrichment in PFB5 (age: p = 0.011, gender: p = 0.04). Broad copy-number aberrations were common; however, many events such as chromosome 2 loss, 5 gain, and 17 loss were enriched in specific subtypes and 1q gain was enriched in PFB1. Late relapses were common across all five subtypes, but deaths were uncommon and present in only two subtypes (PFB1 and PFB3). Unlike the case in PFA ependymoma, 1q gain was not a robust marker of poor progression-free survival; however, chromosome 13q loss may represent a novel marker for risk stratification across the spectrum of PFB subtypes. Similar to PFA ependymoma, there exists a significant intertumoral heterogeneity within PFB, with distinct molecular subtypes identified. Even when accounting for this heterogeneity, extent of resection remains the strongest predictor of poor outcome. However, this biological heterogeneity must be accounted for in future preclinical modeling and personalized therapies.

Keywords

Ependymoma Posterior fossa Subgrouping PFB PFA Clustering 

Notes

Acknowledgements

VR is supported by operating funds from the Canadian Institutes of Health Research, American Brain Tumor Association, the Garron Family Cancer Center, Meagan’s Walk, b.r.a.i.n.child, the Brain Tumor Foundation of Canada and a Collaborative Ependymoma Research Network (CERN) basic science fellowship. FMGC is supported by the Stephen Buttrum Brain Tumor Research Fellowship, granted by Brain Tumor Foundation of Canada. MZ is supported by Garron Family Cancer Center Fellowship, Meagan’s Walk Neuro-Oncology Fellowship and Restracomp from Research Training Center at The Hospital for Sick Children. MDT is supported by funds from the Garron Family Chair in Childhood Cancer Research at The Hospital for Sick Children and The University of Toronto, and operating funds from the National Institutes of Health (R01CA159859 and R01CA148699), and the Pediatric Brain Tumor Foundation. EB is supported by funds from the Garron Family Chair in Childhood Cancer Research at The Hospital for Sick Children and The University of Toronto. This research was funded in part through the NIH/NCI Cancer Center Support Grant P30 CA008748 to Memorial Sloan Kettering Cancer Center. KWP is supported by a CERN Research Fellowship.

Supplementary material

401_2018_1888_MOESM1_ESM.eps (37.7 mb)
Supplemental Fig. 1A–F: Spectral clustering of PFB at k = 2–7. Heatmap of the similarity matrix obtained by methylation data on the 212 primary PFB samples. Yellow represents more similar and red represents dissimilar. Color bar at the top represents the final PFB1–5 cluster assignation of the samples (EPS 38612 kb)
401_2018_1888_MOESM2_ESM.eps (2.1 mb)
Supplemental Fig. 2: Genomic comparison of PFB subtypes. A) Comparison of subtype assignments between spectral clustering and t-SNE analysis. Relationships (indicated by the grey bars between columns) between the groups of samples obtained by t-SNE analysis (3 to 5 clusters) and the groups obtained by spectral clustering (SpC, 2–5 clusters). B) Density plot of overall promoter methylation levels across the five PFB subtypes (EPS 2173 kb)
401_2018_1888_MOESM3_ESM.eps (1.8 mb)
Supplemental Fig. 3: List of differentially regulated pathways across PFB subtypes. Enrichment of specific pathways within the PFB subtypes using significantly differentially expressed genes (adjusted p < 0.05). No pathway were identified for PFB2 and 3, since those two subtypes had a low number of significantly expressed genes (EPS 1839 kb)
401_2018_1888_MOESM4_ESM.eps (30.8 mb)
Supplemental Fig. 4: Unsupervised clustering of broad copy-number events across PFB subtypes. A) t-SNE analysis of broad copy-number profiles across 212 PFB ependymomas with corresponding methylation t-SNE subtype assigned. B) Unsupervised consensus clustering of broad copy-number events using negative matrix factorization (NMF) from k = 2 to k = 6 and a plot of the cophenetic coefficient (EPS 31557 kb)
401_2018_1888_MOESM5_ESM.eps (1.4 mb)
Supplemental Fig. 5: Arm-level cytogenetic events at k = 4 PFB subtypes from t-SNE analysis. A) Frequency and significance of arm-level gains and losses across the 4 PFB subtypes. Darker bars show significant arm-level events (q value ≤ 0.1, Chi-squared test). B) Frequency and significance of whole chromosome gain and losses across the four PFB subtypes. Darker bars show significant arm-level events (q value ≤ 0.1, Chi-squared test) (EPS 1472 kb)
401_2018_1888_MOESM6_ESM.eps (2.4 mb)
Supplemental Fig. 6: Clinical characteristics of PFB subtypes. A) Progression-free and B) overall survival across PFB subtypes. P values determined using the log-rank test. C) Pie chart of the administration of upfront radiation across PFB subtypes and D) Pie chart of the incidence of gross total resection across PFB subtypes. P values determined using the Fisher’s exact test. Overall survival stratified by E) 1q gain and F) 13q status. p values determined using the log-rank test (EPS 2421 kb)
401_2018_1888_MOESM7_ESM.xlsx (55 kb)
Supplementary material 7 (XLSX 55 kb)
401_2018_1888_MOESM8_ESM.docx (58 kb)
Supplementary material 8 (DOCX 58 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Florence M. G. Cavalli
    • 1
  • Jens-Martin Hübner
    • 2
    • 3
    • 4
  • Tanvi Sharma
    • 2
    • 3
    • 4
  • Betty Luu
    • 1
  • Martin Sill
    • 3
  • Michal Zapotocky
    • 5
  • Stephen C. Mack
    • 6
  • Hendrik Witt
    • 2
    • 3
    • 41
  • Tong Lin
    • 7
  • David J. H. Shih
    • 8
  • Ben Ho
    • 5
  • Mariarita Santi
    • 9
  • Lyndsey Emery
    • 10
  • Juliette Hukin
    • 11
  • Christopher Dunham
    • 12
  • Roger E. McLendon
    • 13
  • Eric S. Lipp
    • 13
  • Sridharan Gururangan
    • 14
  • Andrew Grossbach
    • 15
  • Pim French
    • 16
  • Johan M. Kros
    • 16
  • Marie-Lise C. van Veelen
    • 16
  • Amulya A. Nageswara Rao
    • 17
  • Caterina Giannini
    • 18
  • Sarah Leary
    • 19
  • Shin Jung
    • 20
  • Claudia C. Faria
    • 21
  • Jaume Mora
    • 22
  • Ulrich Schüller
    • 23
  • Marta M. Alonso
    • 24
  • Jennifer A. Chan
    • 25
  • Almos Klekner
    • 26
  • Lola B. Chambless
    • 27
  • Eugene I. Hwang
    • 28
  • Maura Massimino
    • 29
  • Charles G. Eberhart
    • 30
  • Matthias A. Karajannis
    • 31
  • Benjamin Lu
    • 32
  • Linda M. Liau
    • 33
  • Massimo Zollo
    • 34
  • Veronica Ferrucci
    • 34
  • Carlos Carlotti
    • 35
  • Daniela P. C. Tirapelli
    • 35
  • Uri Tabori
    • 5
  • Eric Bouffet
    • 5
  • Marina Ryzhova
    • 36
  • David W. Ellison
    • 37
  • Thomas E. Merchant
    • 38
  • Mark R. Gilbert
    • 39
  • Terri S. Armstrong
    • 39
  • Andrey Korshunov
    • 40
  • Stefan M. Pfister
    • 2
    • 3
    • 41
  • Michael D. Taylor
    • 1
    • 42
  • Kenneth Aldape
    • 43
  • Kristian W. Pajtler
    • 2
    • 3
    • 41
  • Marcel Kool
    • 2
    • 3
  • Vijay Ramaswamy
    • 1
    • 5
  1. 1.Programme in Developmental and Stem Cell BiologyThe Hospital for Sick ChildrenTorontoCanada
  2. 2.Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ)HeidelbergGermany
  3. 3.Division of Pediatric NeurooncologyGerman Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK)HeidelbergGermany
  4. 4.Faculty of BiosciencesHeidelberg UniversityHeidelbergGermany
  5. 5.Division of Haematology/Oncology, Department of PediatricsThe Hospital for Sick ChildrenTorontoCanada
  6. 6.Department of PediatricsBaylor College of MedicineHoustonUSA
  7. 7.Department of BiostatisticsSt. Jude Children’s Research HospitalMemphisUSA
  8. 8.Department of Biostatistics and Computational Biology, Dana Farber Cancer CenterHarvard Medical SchoolBostonUSA
  9. 9.Department of PathologyChildren’s Hospital of PhiladelphiaPhiladelphiaUSA
  10. 10.Pathology and Laboratory MedicineHospital of the University of PennsylvaniaPhiladelphiaUSA
  11. 11.Division of Oncology and NeurologyBritish Columbia Children’s HospitalVancouverCanada
  12. 12.Department of PathologyBritish Columbia Children’s HospitalVancouverCanada
  13. 13.The Preston Robert Tisch Brain Tumor CenterDuke UniversityDurhamUSA
  14. 14.Department of Neurosurgery, Preston A. Wells Center for Brain Tumor Therapy, McKnight Brain InstituteUniversity of FloridaGainsvilleUSA
  15. 15.Department of NeurosurgeryUniversity of Iowa Hospitals and ClinicsIowa CityUSA
  16. 16.Erasmus University Medical CenterRotterdamThe Netherlands
  17. 17.Division of Pediatric Hematology/OncologyMayo ClinicRochesterUSA
  18. 18.Department of Laboratory Medicine and PathologyMayo ClinicRochesterUSA
  19. 19.Cancer and Blood Disorders CenterSeattle Children’s HospitalSeattleUSA
  20. 20.Department of NeurosurgeryChonnam National University Research Institute of Medical Sciences, Chonnam National University Hwasun Hospital and Medical SchoolChonnamSouth Korea
  21. 21.Division of Neurosurgery, Centro Hospitalar Lisboa NorteHospital de Santa MariaLisbonPortugal
  22. 22.Developmental Tumor Biology LaboratoryHospital Sant Joan de DéuBarcelonaSpain
  23. 23.Pediatric Hematology and OncologyInstitute of Neuropathology, University Medical Center, Research Institute Children’s Cancer CenterHamburg-EppendorfGermany
  24. 24.Program in Solid Tumors and Biomarkers, Department of Pediatrics, The Health Research Institute of Navarra (IDISNA), Foundation for the Applied Medical ResearchClínica Universidad de Navarra, University of NavarraPamplonaSpain
  25. 25.Department of Pathology and Laboratory MedicineUniversity of CalgaryCalgaryCanada
  26. 26.Department of Neurosurgery, Medical and Health Science CentreUniversity of DebrecenDebrecenHungary
  27. 27.Department of Neurological SurgeryVanderbilt Medical CenterNashvilleUSA
  28. 28.Center for Cancer and Blood Disorders, Children’s National Medical CenterWashington DCUSA
  29. 29.Fondazione IRCCS Istituto Nazionale TumoriMilanItaly
  30. 30.Departments of Pathology, Ophthalmology and OncologyJohn Hopkins University School of MedicineBaltimoreUSA
  31. 31.Department of PediatricsMemorial Sloan Kettering Cancer CenterNew YorkUSA
  32. 32.Division of Pediatric Hematology/OncologyNYU Langone Medical CenterNew YorkUSA
  33. 33.Department of NeurosurgeryDavid Geffen School of Medicine at UCLALos AngelesUSA
  34. 34.Dipartimento di Biochimica e Biotecnologie MedicheUniversity of NaplesNaplesItaly
  35. 35.Department of Surgery and Anatomy, Faculty of Medicine of Ribeirão PretoUniversity of Sao PauloSão PauloBrazil
  36. 36.Department of NeuropathologyNN Burdenko Neurosurgical InstituteMoscowRussia
  37. 37.Department of PathologySt. Jude Children’s Research HospitalMemphisUSA
  38. 38.Department of Radiation OncologySt. Jude Children’s Research HospitalMemphisUSA
  39. 39.Neuro-Oncology BranchNational Cancer InstituteBethesdaUSA
  40. 40.Clinical Cooperation Unit NeuropathologyGerman Cancer Research Center (DKFZ)HeidelbergGermany
  41. 41.Department of Pediatric Hematology and OncologyUniversity Hospital HeidelbergHeidelbergGermany
  42. 42.Department of Laboratory Medicine and PathobiologyUniversity of TorontoTorontoCanada
  43. 43.Center for Cancer ResearchNational Cancer InstituteBethesdaUSA

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