title: Secretome analysis of Glioblastoma cell line--HNGC-2.
abstract: Glioblastoma multiforme (GBM) is the most common and aggressive type of primary malignant tumor of the central nervous system. We have carried out a deep analysis of the secretome of a rapidly proliferating and tumorigenic cell line HNGC-2, representing GBM, in an effort to identify proteins, which may be targeted in the plasma of GBM patients as markers for diagnosis and disease surveillance. Prefractionation of the proteins from the conditioned medium of HNGC-2 cells in SDS gels followed by LC-MS/MS analysis using an ESI-IT mass spectrometer (LTQ) led to a total of 996 protein identifications with ≥2 peptides each. Of them, 664 proteins were observed in the transcriptome of HNGC-2 cells. The dataset of 996 proteins was mapped to important functional groups, such as cellular assembly and organisation, DNA recombination and repair, and other classes. Actin cytoskeleton signalling, phosphatidyl inositol 3 kinase (PI3K/AKT) and integrin linked kinase (ILK) signalling pathways were seen as enriched pathways. Comparisons with the published secretome of cell lines from 12 different cancers, including GBM, revealed that 348 proteins shared a commonality with a secretome of at least one other cell line, 321 of which were found to contain signal sequences or transmembrane domains and 335 could be linked to a plasma membrane or extracellular localization. Through intergration of this data we arrived at a non-redundant list of 597 protein identifications with the potential for secretion either by classical secretory pathways or by non-secretory processes; 233 of them have been detected in cerebrospinal fluid or plasma as per the published literature, and 172 have been implicated in GBM or other cancers. The HNGC-2 secretome dataset could serve as a useful resource for designing a targeted investigation of GBM biomarkers in plasma.
authors.affiliation: Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Hyderabad, 500007, India.
authors.forename: Manoj Kumar
authors.initials: MK
authors.lastname: Gupta
authors.forename: Ravindra Varma
authors.initials: RV
authors.lastname: Polisetty
authors.forename: Kalidoss
authors.initials: K
authors.lastname: Ramamoorthy
authors.forename: Shivani
authors.initials: S
authors.lastname: Tiwary
authors.forename: Navjot
authors.initials: N
authors.lastname: Kaur
authors.forename: Megha S
authors.initials: MS
authors.lastname: Uppin
authors.forename: Anjali
authors.initials: A
authors.lastname: Shiras
authors.forename: Ravi
authors.initials: R
authors.lastname: Sirdeshmukh
mesh_terms: D008841:Actin Cytoskeleton / Q000378:metabolism; D045744:Cell Line, Tumor; D002853:Chromatography, Liquid; D020869:Gene Expression Profiling; D005909:Glioblastoma / Q000175:diagnosis / Q000378:metabolism*; D006801:Humans; D009363:Neoplasm Proteins / Q000032:analysis / Q000097:blood / Q000134:cerebrospinal fluid / Q000378:metabolism; D058539:Phosphatidylinositol 3-Kinase / Q000378:metabolism; D017346:Protein Serine-Threonine Kinases / Q000378:metabolism; D015398:Signal Transduction; D053719:Tandem Mass Spectrometry; D059467:Transcriptome; D000099200:Scaffold Protein ILK
chemical_list: D009363:Neoplasm Proteins; D058539:Phosphatidylinositol 3-Kinase; D017346:Protein Serine-Threonine Kinases; D000099200:Scaffold Protein ILK