Integrated Proteomic and Transcriptomic-Based Approaches to Identifying Signature Biomarkers and Pathways for Elucidation of Daoy and UW228 Subtypes
Medulloblastoma (MB) is the most common malignant pediatric brain tumor. Patient survival has remained largely the same for the past 20 years, with therapies causing significant health, cognitive, behavioral and developmental complications for those who survive the tumor. In this study, we profiled...
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doaj-98c76ada1e1f48e199ff1afa975ddbf02020-11-24T22:34:56ZengMDPI AGProteomes2227-73822017-02-0151510.3390/proteomes5010005proteomes5010005Integrated Proteomic and Transcriptomic-Based Approaches to Identifying Signature Biomarkers and Pathways for Elucidation of Daoy and UW228 SubtypesRoger Higdon0Jessie Kala1Devan Wilkins2Julia Fangfei Yan3Manveen K. Sethi4Liang Lin5Siqi Liu6Elizabeth Montague7Imre Janko8John Choiniere9Natali Kolker10William S. Hancock11Eugene Kolker12Susan Fanayan13Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children’s Research Institute, Seattle, WA 98101, USADepartment of Chemistry and Biological Sciences, Macquarie University, Sydney 2109, AustraliaDepartment of Chemistry and Biological Sciences, Macquarie University, Sydney 2109, AustraliaDepartment of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USADepartment of Chemistry and Biological Sciences, Macquarie University, Sydney 2109, AustraliaBeijing Genomics Institute, Shenzhen 518083, Guangdong, ChinaBeijing Genomics Institute, Shenzhen 518083, Guangdong, ChinaBioinformatics and High-Throughput Analysis Laboratory, Seattle Children’s Research Institute, Seattle, WA 98101, USAData and Analytics, Seattle Children’s Hospital, Seattle, WA 98101, USABioinformatics and High-Throughput Analysis Laboratory, Seattle Children’s Research Institute, Seattle, WA 98101, USAData and Analytics, Seattle Children’s Hospital, Seattle, WA 98101, USADepartment of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USABioinformatics and High-Throughput Analysis Laboratory, Seattle Children’s Research Institute, Seattle, WA 98101, USADepartment of Biomedical Sciences, Macquarie University, Sydney NSW 2109, AustraliaMedulloblastoma (MB) is the most common malignant pediatric brain tumor. Patient survival has remained largely the same for the past 20 years, with therapies causing significant health, cognitive, behavioral and developmental complications for those who survive the tumor. In this study, we profiled the total transcriptome and proteome of two established MB cell lines, Daoy and UW228, using high-throughput RNA sequencing (RNA-Seq) and label-free nano-LC-MS/MS-based quantitative proteomics, coupled with advanced pathway analysis. While Daoy has been suggested to belong to the sonic hedgehog (SHH) subtype, the exact UW228 subtype is not yet clearly established. Thus, a goal of this study was to identify protein markers and pathways that would help elucidate their subtype classification. A number of differentially expressed genes and proteins, including a number of adhesion, cytoskeletal and signaling molecules, were observed between the two cell lines. While several cancer-associated genes/proteins exhibited similar expression across the two cell lines, upregulation of a number of signature proteins and enrichment of key components of SHH and WNT signaling pathways were uniquely observed in Daoy and UW228, respectively. The novel information on differentially expressed genes/proteins and enriched pathways provide insights into the biology of MB, which could help elucidate their subtype classification.http://www.mdpi.com/2227-7382/5/1/5medulloblastomaDaoyUW228SHH subtypeWNT subtypetranscriptomeproteome |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Roger Higdon Jessie Kala Devan Wilkins Julia Fangfei Yan Manveen K. Sethi Liang Lin Siqi Liu Elizabeth Montague Imre Janko John Choiniere Natali Kolker William S. Hancock Eugene Kolker Susan Fanayan |
spellingShingle |
Roger Higdon Jessie Kala Devan Wilkins Julia Fangfei Yan Manveen K. Sethi Liang Lin Siqi Liu Elizabeth Montague Imre Janko John Choiniere Natali Kolker William S. Hancock Eugene Kolker Susan Fanayan Integrated Proteomic and Transcriptomic-Based Approaches to Identifying Signature Biomarkers and Pathways for Elucidation of Daoy and UW228 Subtypes Proteomes medulloblastoma Daoy UW228 SHH subtype WNT subtype transcriptome proteome |
author_facet |
Roger Higdon Jessie Kala Devan Wilkins Julia Fangfei Yan Manveen K. Sethi Liang Lin Siqi Liu Elizabeth Montague Imre Janko John Choiniere Natali Kolker William S. Hancock Eugene Kolker Susan Fanayan |
author_sort |
Roger Higdon |
title |
Integrated Proteomic and Transcriptomic-Based Approaches to Identifying Signature Biomarkers and Pathways for Elucidation of Daoy and UW228 Subtypes |
title_short |
Integrated Proteomic and Transcriptomic-Based Approaches to Identifying Signature Biomarkers and Pathways for Elucidation of Daoy and UW228 Subtypes |
title_full |
Integrated Proteomic and Transcriptomic-Based Approaches to Identifying Signature Biomarkers and Pathways for Elucidation of Daoy and UW228 Subtypes |
title_fullStr |
Integrated Proteomic and Transcriptomic-Based Approaches to Identifying Signature Biomarkers and Pathways for Elucidation of Daoy and UW228 Subtypes |
title_full_unstemmed |
Integrated Proteomic and Transcriptomic-Based Approaches to Identifying Signature Biomarkers and Pathways for Elucidation of Daoy and UW228 Subtypes |
title_sort |
integrated proteomic and transcriptomic-based approaches to identifying signature biomarkers and pathways for elucidation of daoy and uw228 subtypes |
publisher |
MDPI AG |
series |
Proteomes |
issn |
2227-7382 |
publishDate |
2017-02-01 |
description |
Medulloblastoma (MB) is the most common malignant pediatric brain tumor. Patient survival has remained largely the same for the past 20 years, with therapies causing significant health, cognitive, behavioral and developmental complications for those who survive the tumor. In this study, we profiled the total transcriptome and proteome of two established MB cell lines, Daoy and UW228, using high-throughput RNA sequencing (RNA-Seq) and label-free nano-LC-MS/MS-based quantitative proteomics, coupled with advanced pathway analysis. While Daoy has been suggested to belong to the sonic hedgehog (SHH) subtype, the exact UW228 subtype is not yet clearly established. Thus, a goal of this study was to identify protein markers and pathways that would help elucidate their subtype classification. A number of differentially expressed genes and proteins, including a number of adhesion, cytoskeletal and signaling molecules, were observed between the two cell lines. While several cancer-associated genes/proteins exhibited similar expression across the two cell lines, upregulation of a number of signature proteins and enrichment of key components of SHH and WNT signaling pathways were uniquely observed in Daoy and UW228, respectively. The novel information on differentially expressed genes/proteins and enriched pathways provide insights into the biology of MB, which could help elucidate their subtype classification. |
topic |
medulloblastoma Daoy UW228 SHH subtype WNT subtype transcriptome proteome |
url |
http://www.mdpi.com/2227-7382/5/1/5 |
work_keys_str_mv |
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