TY - JOUR
T1 - Comparative multidimensional molecular analyses of pediatric diffuse intrinsic pontine glioma reveals distinct molecular subtypes
AU - Saratsis, Amanda M.
AU - Kambhampati, Madhuri
AU - Snyder, Kendall
AU - Yadavilli, Sridevi
AU - Devaney, Joseph M.
AU - Harmon, Brennan
AU - Hall, Jordan
AU - Raabe, Eric H.
AU - An, Ping
AU - Weingart, Melanie
AU - Rood, Brian R.
AU - Magge, Suresh N.
AU - MacDonald, Tobey J.
AU - Packer, Roger J.
AU - Nazarian, Javad
N1 - Funding Information:
Acknowledgments We would like to thank Dr. Kristy J. Brown for her kind assistance in collection and processing of proteomic mass spectrometry samples. The authors would like to thank all of the patients and families for donating tissue for this research. Funding was provided by Childhood Brain Tumor Foundation, Isabella Kerr Molina Foundation, Zickler Family Foundation, Musella Foundation, Brain Tumor Foundation for Children, The Sheikh Zayed Institute for Pediatric Surgical Innovation rAC Award, Clinical and Translational Science Institute (CTSI) Award (1Ul1rr031988-01) and Intellectual and Developmental Disabilities research Center (NICHD 5P30HD040677).
PY - 2014/6
Y1 - 2014/6
N2 - 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.
AB - 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.
KW - Brainstem glioma
KW - Diffuse intrinsic pontine glioma (DIPG)
KW - Hedgehog
KW - Histone H3
KW - Myc oncogene
KW - Proteomics
UR - http://www.scopus.com/inward/record.url?scp=84901676138&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84901676138&partnerID=8YFLogxK
U2 - 10.1007/s00401-013-1218-2
DO - 10.1007/s00401-013-1218-2
M3 - Article
C2 - 24297113
AN - SCOPUS:84901676138
SN - 0001-6322
VL - 127
SP - 881
EP - 895
JO - Acta Neuropathologica
JF - Acta Neuropathologica
IS - 6
ER -