title: Comparative multidimensional molecular analyses of pediatric diffuse intrinsic pontine glioma reveals distinct molecular subtypes.
abstract: Diffuse intrinsic pontine glioma (DIPG) is a highly morbid form of pediatric brainstem glioma. Here, we present the first comprehensive protein, mRNA, and methylation profiles of fresh-frozen DIPG specimens (n = 14), normal brain tissue (n = 10), and other pediatric brain tumors (n = 17). Protein profiling identified 2,305 unique proteins indicating distinct DIPG protein expression patterns compared to other pediatric brain tumors. Western blot and immunohistochemistry validated upregulation of Clusterin (CLU), Elongation Factor 2 (EF2), and Talin-1 (TLN1) in DIPGs studied. Comparisons to mRNA expression profiles generated from tumor and adjacent normal brain tissue indicated two DIPG subgroups, characterized by upregulation of Myc (N-Myc) or Hedgehog (Hh) signaling. We validated upregulation of PTCH, a membrane receptor in the Hh signaling pathway, in a subgroup of DIPG specimens. DNA methylation analysis indicated global hypomethylation of DIPG compared to adjacent normal tissue specimens, with differential methylation of 24 genes involved in Hh and Myc pathways, correlating with protein and mRNA expression patterns. Sequencing analysis showed c.83A>T mutations in the H3F3A or HIST1H3B gene in 77 % of our DIPG cohort. Supervised analysis revealed a unique methylation pattern in mutated specimens compared to the wild-type DIPG samples. This study presents the first comprehensive multidimensional protein, mRNA, and methylation profiling of pediatric brain tumor specimens, detecting the presence of two subgroups within our DIPG cohort. This multidimensional analysis of DIPG provides increased analytical power to more fully explore molecular signatures of DIPGs, with implications for evaluating potential molecular subtypes and biomarker discovery for assessing response to therapy.
authors.affiliation: Division of Neurosurgery, Ann & Robert H. Lurie Children's Hospital of Chicago, 225 E. Chicago Avenue, Chicago, IL, 60611, USA.
authors.forename: Amanda M
authors.initials: AM
authors.lastname: Saratsis
authors.forename: Madhuri
authors.initials: M
authors.lastname: Kambhampati
authors.forename: Kendall
authors.initials: K
authors.lastname: Snyder
authors.forename: Sridevi
authors.initials: S
authors.lastname: Yadavilli
authors.forename: Joseph M
authors.initials: JM
authors.lastname: Devaney
authors.forename: Brennan
authors.initials: B
authors.lastname: Harmon
authors.forename: Jordan
authors.initials: J
authors.lastname: Hall
authors.forename: Eric H
authors.initials: EH
authors.lastname: Raabe
authors.forename: Ping
authors.initials: P
authors.lastname: An
authors.forename: Melanie
authors.initials: M
authors.lastname: Weingart
authors.forename: Brian R
authors.initials: BR
authors.lastname: Rood
authors.forename: Suresh N
authors.initials: SN
authors.lastname: Magge
authors.forename: Tobey J
authors.initials: TJ
authors.lastname: MacDonald
authors.forename: Roger J
authors.initials: RJ
authors.lastname: Packer
authors.forename: Javad
authors.initials: J
authors.lastname: Nazarian
mesh_terms: D000293:Adolescent; D000328:Adult; D015153:Blotting, Western; D001921:Brain / Q000378:metabolism*; D001932:Brain Neoplasms / Q000235:genetics / Q000378:metabolism; D020295:Brain Stem Neoplasms / Q000235:genetics / Q000378:metabolism*; D002648:Child; D002675:Child, Preschool; D015331:Cohort Studies; D019175:DNA Methylation; D005260:Female; D020869:Gene Expression Profiling; D005910:Glioma / Q000235:genetics / Q000378:metabolism*; D006657:Histones / Q000235:genetics / Q000378:metabolism; D006801:Humans; D007150:Immunohistochemistry; D008297:Male; D040901:Proteomics; D012333:RNA, Messenger / Q000378:metabolism; D055815:Young Adult
chemical_list: D006657:Histones; D012333:RNA, Messenger