Heterogeneous Nuclear Ribonucleoproteins and Their Interactors Are a Major Class of Deregulated Proteins in Anaplastic Astrocytoma: A Grade III Malignant Glioma

Abstract

Anaplastic astrocytoma is a high grade malignant glioma (WHO grade III) of the central nervous system which arises from a low grade II tumor and invariably progresses into lethal glioblastoma (WHO grade IV). We have studied differentially expressed proteins from the microsomal fraction of the clinical specimens of these tumors, using iTRAQ and high-resolution mass spectrometry followed by immunohistochemistry for representative proteins on tissue sections. A total of 2642 proteins were identified, 266 of them with minimum 2 peptide signatures and 2-fold change in expression. The major groups of proteins revealed to be differentially expressed were associated with key cellular processes such as post transcriptional processing, protein translation, and acute phase response signaling. A distinct inclusion among these important proteins is 10 heterogeneous nuclear ribonucleoproteins (hnRNPs) and their interacting partners which have regulatory functions in the cell. hnRNP-mediated post transcriptional events are known to play a major role in mRNA processing, stability, and distribution. Their altered levels have also been observed by us in lower (diffused astrocytoma) and higher (glioblastoma) grades of gliomas, and membrane localization of hnRNPs has also been documented in the literature. hnRNPs may thus be major factors underlying global gene expression changes observed in glial tumors while their differential presence in the microsomal fraction suggests yet additional and unknown roles in tumorigenesis.

Microsomal membrane proteome of low grade diffuse astrocytomas: Differentially expressed proteins and candidate surveillance biomarkers

“…Comparison of this subset (n = 81) with the proteins experimentally detected in blood plasma or cerebrospinal fluid leaves a filtered list of 43 proteins with secretory character 51 52 . We generated a similar list of proteins (n = 40) from our dataset on anaplastic astrocytoma (WHO grade III) 20 using the same criteria as above. Integration of the two resulted in a non-redundant list of 64 potential secretory proteins representing both grade II and III tumors ( Supplementary Table S6 ).…”

“…The average relative intensities of the two reporter ions for each of the unique peptide identifiers for a protein were used to determine relative quantity of a protein and percentage variability. Appropriate filters at the level of peptides/peptide spectral matches (PSMs) and then at the protein level were applied to the quantification values as described in earlier publication 20 . In brief, Only PSMs that are ‘unique’ for a protein were included for fold change calculation.…”

Insights from Chromosome-Centric Mapping of Disease-Associated Genes: Chromosome 12 Perspective

“…Chromosome-centric modules involving genes, pathways and processes in related clinical conditions would help in building of diseasome network that might provide a global view of molecular entities and clinical phenotypes and their linkages. 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 which were found to be differentially expressed in the proteomics experimental datasets generated in our lab 13,21 are shown in red. The other glioma-related genes are in green.…”

Altered transcriptional regulatory proteins in glioblastoma and YBX1 as a potential regulator of tumor invasion

“…The fragmentation was carried out using higher-energy collision dissociation (HCD) with 40% normalized collision energy. The ions selected for fragmentation were excluded for 30 sec 8 . The automatic gain control for full FT-MS was set to 1 million ions and for FT-MS/MS was set to 0.1 million ions with a maximum time of accumulation of 500 ms. For accurate mass measurements, the lock mass option was enabled.…”