Proteomic analysis of Medulloblastoma reveals functional biology with translational potential

Abstract

Genomic characterization has begun to redefine diagnostic classifications of cancers. However, it remains a challenge to infer disease phenotypes from genomic alterations alone. To help realize the promise of genomics, we have performed a quantitative proteomics investigation using Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) and 41 tissue samples spanning the 4 genomically based subgroups of medulloblastoma and control cerebellum. We have identified and quantitated thousands of proteins across these groups and find that we are able to recapitulate the genomic subgroups based upon subgroup restricted and differentially abundant proteins while also identifying subgroup specific protein isoforms. Integrating our proteomic measurements with genomic data, we calculate a poor correlation between mRNA and protein abundance. Using EPIC 850 k methylation array data on the same tissues, we also investigate the influence of copy number alterations and DNA methylation on the proteome in an attempt to characterize the impact of these genetic features on the proteome. Reciprocally, we are able to use the proteome to identify which genomic alterations result in altered protein abundance and thus are most likely to impact biology. Finally, we are able to assemble protein-based pathways yielding potential avenues for clinical intervention. From these, we validate the EIF4F cap-dependent translation pathway as a novel druggable pathway in medulloblastoma. Thus, quantitative proteomics complements genomic platforms to yield a more complete understanding of functional tumor biology and identify novel therapeutic targets for medulloblastoma.Electronic supplementary materialThe online version of this article (10.1186/s40478-018-0548-7) contains supplementary material, which is available to authorized users.

Genetic Abnormalities, Clonal Evolution, and Cancer Stem Cells of Brain Tumors

“…Recently, the results of a first proteomic analysis of medulloblastomas were reported, showing that the proteomic data at a large extent recapitulate the data observed at genomic level [188]. Interestingly, the expression of some proteins exhibits a MB group-specific pattern of expression: particularly, the most significant were isoforms of the genes CALD1 , HMGA1 , TMP4 , SPTAN1 , MCM3 , and EEF1D [188].…”

“…Recently, the results of a first proteomic analysis of medulloblastomas were reported, showing that the proteomic data at a large extent recapitulate the data observed at genomic level [188]. Interestingly, the expression of some proteins exhibits a MB group-specific pattern of expression: particularly, the most significant were isoforms of the genes CALD1 , HMGA1 , TMP4 , SPTAN1 , MCM3 , and EEF1D [188]. Caldesmon 1 ( CALD1 ) encodes a calmodulin- and actin-binding protein that plays an essential role in the regulation of smooth muscle contraction; some isoforms of CALD1 , such as WI-38 l-CALDI and WI38 l-CALDII in all MB groups, occurred at higher levels in MB SHH ; however, the HeLa-type CALD1 isoforms are detected only in the WNT group [188].…”

“…Interestingly, the expression of some proteins exhibits a MB group-specific pattern of expression: particularly, the most significant were isoforms of the genes CALD1 , HMGA1 , TMP4 , SPTAN1 , MCM3 , and EEF1D [188]. Caldesmon 1 ( CALD1 ) encodes a calmodulin- and actin-binding protein that plays an essential role in the regulation of smooth muscle contraction; some isoforms of CALD1 , such as WI-38 l-CALDI and WI38 l-CALDII in all MB groups, occurred at higher levels in MB SHH ; however, the HeLa-type CALD1 isoforms are detected only in the WNT group [188]. The HeLa-type CALD1 isoforms are localized in tumor vessels and could play a relevant role in promoting tumor angiogenesis, a phenomenon particularly pronounced in MB SHH .…”

Identification of hub genes and small-molecule compounds in medulloblastoma by integrated bioinformatic analyses

“…The GSE50161 data set was based on the GPL570 Platform (Affymetrix Human Genome U133 Plus 2.0 Array) and included 22 MB samples and 13 normal brain tissues (Griesinger et al, 2013). The GSE109401 data set was based on GPL16686 Platforms (Affymetrix Human Gene 2.0 ST Array (transcript (gene) version)) and included 19 medulloblastoma samples and five normal brain samples (Rivero-Hinojosa et al, 2018). We selected these four gene expression profiles for further integrated analyses to avoid racial differences and errors in individual experiments.…”

Origins and clinical relevance of proteoforms in pediatric malignancies

“…Proteogenomics studies can also provide in-depth resolution of mechanisms within a single type of cancer. A proteogenomic study on medulloblastoma, a major pediatric brain cancer, was performed using an adapted form of a labeled MS-based technique called stable isotope labeling by/with amino acids in cell culture (SILAC) [133]. A special atlas containing labeled proteins from eight medulloblastoma cell lines was developed for this study and used to comparatively analyze protein networks between the four genomic subgroups of medulloblastoma.…”