Comparative multidimensional molecular analyses of pediatric diffuse intrinsic pontine glioma reveals distinct molecular subtypes

Amanda M. Saratsis; Madhuri Kambhampati; Kendall Snyder; Sridevi Yadavilli; Joseph M. Devaney; Brennan Harmon; Jordan Hall; Eric H. Raabe; Ping An; Melanie Weingart; Brian R. Rood; Suresh N. Magge; Tobey J. MacDonald; Roger J. Packer; Javad Nazarian

doi:10.1007/s00401-013-1218-2

Comparative multidimensional molecular analyses of pediatric diffuse intrinsic pontine glioma reveals distinct molecular subtypes

Amanda M. Saratsis, Madhuri Kambhampati, Kendall Snyder, Sridevi Yadavilli, Joseph M. Devaney, Brennan Harmon, Jordan Hall, Eric H. Raabe, Ping An, Melanie Weingart, Brian R. Rood, Suresh N. Magge, Tobey J. MacDonald, Roger J. Packer, Javad Nazarian^*

^*Corresponding author for this work

Neurological Surgery

Research output: Contribution to journal › Article › peer-review

78 Scopus citations

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.

Original language	English (US)
Pages (from-to)	881-895
Number of pages	15
Journal	Acta Neuropathologica
Volume	127
Issue number	6
DOIs	https://doi.org/10.1007/s00401-013-1218-2
State	Published - Jun 2014

Funding

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).

Keywords

Brainstem glioma
Diffuse intrinsic pontine glioma (DIPG)
Hedgehog
Histone H3
Myc oncogene
Proteomics

ASJC Scopus subject areas

Clinical Neurology
Cellular and Molecular Neuroscience
Pathology and Forensic Medicine

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10.1007/s00401-013-1218-2

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Saratsis, A. M., Kambhampati, M., Snyder, K., Yadavilli, S., Devaney, J. M., Harmon, B., Hall, J., Raabe, E. H., An, P., Weingart, M., Rood, B. R., Magge, S. N., MacDonald, T. J., Packer, R. J., & Nazarian, J. (2014). Comparative multidimensional molecular analyses of pediatric diffuse intrinsic pontine glioma reveals distinct molecular subtypes. Acta Neuropathologica, 127(6), 881-895. https://doi.org/10.1007/s00401-013-1218-2

@article{54d1028b34ff4ccc99cca3b2d0b17189,

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.",

keywords = "Brainstem glioma, Diffuse intrinsic pontine glioma (DIPG), Hedgehog, Histone H3, Myc oncogene, Proteomics",

author = "Saratsis, {Amanda M.} and Madhuri Kambhampati and Kendall Snyder and Sridevi Yadavilli and Devaney, {Joseph M.} and Brennan Harmon and Jordan Hall and Raabe, {Eric H.} and Ping An and Melanie Weingart and Rood, {Brian R.} and Magge, {Suresh N.} and MacDonald, {Tobey J.} and Packer, {Roger J.} and Javad Nazarian",

note = "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).",

year = "2014",

month = jun,

doi = "10.1007/s00401-013-1218-2",

language = "English (US)",

volume = "127",

pages = "881--895",

journal = "Acta Neuropathologica",

issn = "0001-6322",

publisher = "Springer Science and Business Media Deutschland GmbH",

number = "6",

}

Saratsis, AM, Kambhampati, M, Snyder, K, Yadavilli, S, Devaney, JM, Harmon, B, Hall, J, Raabe, EH, An, P, Weingart, M, Rood, BR, Magge, SN, MacDonald, TJ, Packer, RJ & Nazarian, J 2014, 'Comparative multidimensional molecular analyses of pediatric diffuse intrinsic pontine glioma reveals distinct molecular subtypes', Acta Neuropathologica, vol. 127, no. 6, pp. 881-895. https://doi.org/10.1007/s00401-013-1218-2

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

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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 -

Comparative multidimensional molecular analyses of pediatric diffuse intrinsic pontine glioma reveals distinct molecular subtypes

Abstract

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Keywords

ASJC Scopus subject areas

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