Integrative Network Analysis Combined with Quantitative Phosphoproteomics Reveals Transforming Growth Factor-beta Receptor type-2 (TGFBR2) as a Novel Regulator of Glioblastoma Stem Cell Properties

Narushima, Yuta; Kozuka‐Hata, Hiroko; Koyama‐Nasu, Ryo; Tsumoto, Kouhei; Inoue, Jun‐ichiro; Akiyama, Tetsu; Oyama, Masaaki

doi:10.1074/mcp.m115.049999

Cited by 17 publications

(17 citation statements)

References 51 publications

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“… (A) The protein extracts from the three exocrine glands separated according to division of labor; nPcGs, fPcGs, nTGs, fTGs, nMGs, and fMGs, were in-solution digested and subjected to shotgun LC-MS/MS [ 67 ]. (B) The number of proteins identified according to the criteria described in the Methods section and the total number of spectral counts detected in each gland (nPcG, fPcG, nTG, fTG, nMG, and fMG) are shown.…”

Section: Resultsmentioning

confidence: 99%

“…The protein extracts (10 μg/sample) were subjected to shotgun proteomics using a direct nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) system, as described previously [ 67 ]. Briefly, the extracts were digested with 25 pmol of trypsin, desalted using ZipTip C 18 (Millipore, Billerica, MA), concentrated, and injected into a direct nanoflow liquid chromatography system (DiNa-2A, KYA Technologies, Tokyo, Japan) coupled to the LTQ-Orbitrap Velos mass spectrometer (Thermo Fisher Scientific, Bremen, Germany), as described previously [ 67 ]. After applying the peptide mixture to a C 18 column (800 μm inner diameter x 3 mm long), reversed-phase separation of the captured peptides was performed using a column (150 μm inner diameter x 150 mm long) filled with HiQ sil C 18 (3 μm particles, 120Å pore; KYA Technologies, Tokyo, Japan).…”

Section: Methodsmentioning

confidence: 99%

“…The acquired MS/MS signals were processed with Proteome Discoverer (version 1.3, Thermo Fisher Scientific) and searched against a dataset of honeybee RefSeqs using the Mascot algorithm (version 2.4.1, Matrix Science) with the following parameters; fixed modifications: carbamidomethylation (cysteine); variable modifications: oxidation (methionine), acetylation (protein N-term), and pyro-glutamination (N-terminal glutamine); maximum missed cleavages: 2; peptide mass tolerance: 3 ppm; and MS/MS tolerance: 0.8 Da; as described by Narushima et al . [ 67 ]. For peptide identification, we conducted decoy database searches using Mascot and applied a filter to satisfy a false positive rate of less than 1% [ 68 ].…”

Section: Methodsmentioning

confidence: 99%

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Shotgun proteomics deciphered age/division of labor-related functional specification of three honeybee (Apis mellifera L.) exocrine glands

et al. 2018

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The honeybee (Apis mellifera L.) uses various chemical signals produced by the worker exocrine glands to maintain the functioning of its colony. The roles of worker postcerebral glands (PcGs), thoracic glands (TGs), and mandibular glands (MGs) and the functional changes they undergo according to the division of labor from nursing to foraging are not as well studied. To comprehensively characterize the molecular roles of these glands in workers and their changes according to the division of labor of workers, we analyzed the proteomes of PcGs, TGs, and MGs from nurse bees and foragers using shotgun proteomics technology. We identified approximately 2000 proteins from each of the nurse bee or forager glands and highlighted the features of these glands at the molecular level by semiquantitative enrichment analyses of frequently detected, gland-selective, and labor-selective proteins. First, we found the high potential to produce lipids in PcGs and MGs, suggesting their relation to pheromone production. Second, we also found the proton pumps abundant in TGs and propose some transporters possibly related to the saliva production. Finally, our data unveiled candidate enzymes involved in labor-dependent acid production in MGs.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Shotgun proteomics deciphered age/division of labor-related functional specification of three honeybee (Apis mellifera L.) exocrine glands

et al. 2018

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“…TGFBR2 is a key receptor in mediating the tumour growth factor‐beta signal propagation, and knockdown of TGFBR2 was effective in suppressing GBM invasion via a tumour growth factor‐beta‐dependent manner 28 . In addition, TGFBR2 has also been identified as a novel regulator of GBM stemness, 29 which may be related to the platelet‐derived growth factor receptor inhibitor resistance in GBM treatment 30 . TGFBR2 exerted the tumour‐enhancing effects via targeting different downstream mediators such as inhibitor of DNA binding, 31 Smad2/3 32 and p53 33 in other types of cancers.…”

Section: Discussionmentioning

confidence: 99%

LncRNA MIR4435‐2HG potentiates the proliferation and invasion of glioblastoma cells via modulating miR‐1224‐5p/TGFBR2 axis

Zhang

Yang

et al. 2020

J Cellular Molecular Medi

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Glioblastoma (GBM) belongs to the high‐grade (IV) gliomas with extremely poor prognosis. Accumulating evidence uncovered the key roles of long non‐coding RNAs (lncRNAs) in GBM development. This study aimed to determine the biological actions and the clinical relevance of lncRNA MIR4435‐2 Host Gene (MIR4435‐2HG) in GBM. Data from GEPIA database showed that MIR4435‐2HG was up‐regulated in GBM tissues and high expression of MIR4435‐2HG correlated with shorter overall survival of GBM patients. Further experimental assays verified the up‐regulation of MIR4435‐2HG in GBM tissues and cell lines. In vitro cell studies and in vivo animal studies showed that knockdown of MIR4435‐2HG resulted in the inhibition of GBM cell proliferation and invasion and in vivo tumour growth, while MIR4435‐2HG overexpression driven GBM progression. Furthermore, MIR44435‐2HG was found to sponge miR‐1224‐5p and suppress miR‐1224‐5p expression; overexpression of miR‐1224‐5p attenuated the enhancement in GBM cell proliferation and invasion induced by MIR4435‐2HG overexpression. In a subsequent study, miR‐1224‐5p was found to target transforming growth factor‐beta receptor type 2 (TGFBR2) and repressed TGFBR2 expression, and in vitro assays showed that miR‐1224‐5p exerted tumour‐suppressive effects via targeting TGFBR2. More importantly, TGFRB2 knockdown antagonized hyper‐proliferation and invasion of GBM cells with MIR4435‐2HG overexpression. Clinically, the down‐regulation of miR‐1224‐5p and up‐regulation of TGFBR2 were verified in the GBM clinical samples. Taken together, the present study suggests the oncogenic role of MIR4435‐2HG in GBM and underlies the key function of MIR4435‐2HG‐driven GBM progression via targeting miR‐1224‐5p/TGFBR2 axis.

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“…The computational analysis for the statistical extraction of canonical pathways was performed using Ingenuity Pathway Analysis (IPA, QIAGEN, Redwood City, CA, USA) [16]. The proteins modified with the ubiquitination and/or acetylation were uploaded into the IPA software (version 2018-2019), and the top canonical pathways associated with the uploaded proteins were listed along with the p-values calculated using a right tailed Fisher's exact test [17].…”

Section: Pathway Analysismentioning

confidence: 99%

System-Wide Analysis of Protein Acetylation and Ubiquitination Reveals a Diversified Regulation in Human Cancer Cells

et al. 2020

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Post-translational modifications are known to be widely involved in the regulation of various biological processes, through the extensive diversification of each protein function at the cellular network level. In order to unveil the system-wide function of the protein lysine modification in cancer cell signaling, we performed global acetylation and ubiquitination proteome analyses of human cancer cells, based on high-resolution nanoflow liquid chromatography-tandem mass spectrometry, in combination with the efficient biochemical enrichment of target modified peptides. Our large-scale proteomic analysis enabled us to identify more than 5000 kinds of ubiquitinated sites and 1600 kinds of acetylated sites, from representative human cancer cell lines, leading to the identification of approximately 900 novel lysine modification sites in total. Very interestingly, 236 lysine residues derived from 141 proteins were found to be modified with both ubiquitination and acetylation. As a consequence of the subsequent motif extraction analyses, glutamic acid (E) was found to be highly enriched at the position (−1) for the lysine acetylation sites, whereas the same amino acid was relatively dispersed along the neighboring residues of the lysine ubiquitination sites. Our pathway analysis also indicated that the protein translational control pathways, such as the eukaryotic initiation factor 2 (EIF2) and the ubiquitin signaling pathways, were highly enriched in both of the acetylation and ubiquitination proteome data at the network level. This report provides the first integrative description of the protein acetylation and ubiquitination-oriented systematic regulation in human cancer cells.

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Integrative Network Analysis Combined with Quantitative Phosphoproteomics Reveals Transforming Growth Factor-beta Receptor type-2 (TGFBR2) as a Novel Regulator of Glioblastoma Stem Cell Properties

Cited by 17 publications

References 51 publications

Shotgun proteomics deciphered age/division of labor-related functional specification of three honeybee (Apis mellifera L.) exocrine glands

Shotgun proteomics deciphered age/division of labor-related functional specification of three honeybee (Apis mellifera L.) exocrine glands

LncRNA MIR4435‐2HG potentiates the proliferation and invasion of glioblastoma cells via modulating miR‐1224‐5p/TGFBR2 axis

System-Wide Analysis of Protein Acetylation and Ubiquitination Reveals a Diversified Regulation in Human Cancer Cells

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