Dataset Information

Dysregulation of phosphoproteins in hepatocellular carcinoma revealed via quantitative analysis of the phosphoproteome.

ABSTRACT: Hepatocellular carcinoma (HCC) is one of the most frequently diagnosed types of cancer in the world. Post-translational modifications, such as phosphorylation, serve an essential role during cancer development. To identify aberrant phosphorylation in HCC, a multiplexed tandem mass tag approach combined with liquid chromatography tandem-mass spectrometry was used in the present study. The results are available via ProteomeXchange (identifier no. PXD013934). A total of 4,780 phosphorylated sites distributed on 2,209 proteins were identified and quantified, including 74 and 459 phosphorylated upregulated and downregulated proteins, respectively. Bioinformatic analysis revealed differences and similarities between HCC and normal tissues. Gene Ontology enrichment analysis provided information on biological processes, molecular functions, cellular components and sub-cellular localizations. Protein domains enrichment of differentially expressed proteins was analyzed using InterPro database. Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed pathways that may potentially be involved in HCC. Integrative analysis of the functions, pathways, motifs of phosphorylated peptides, protein domains and protein interactions established a profile of the phosphoproteome of HCC, which may contribute to identify novel biomarkers for the diagnosis and prognosis of HCC, as well as novel therapeutic targets for HCC treatment.

SUBMITTER: Liu Y

PROVIDER: S-EPMC7779902 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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Dysregulation of phosphoproteins in hepatocellular carcinoma revealed via quantitative analysis of the phosphoproteome.

Liu Yixian Y Zhao Qianwei Q Xu Fang F Wang Kaijuan K Zhao Ying Y Chen Huiping H He Wei W Wang Weidong W Zhang Jianying J Zhang Jintao J

Oncology letters 20201215 2

Hepatocellular carcinoma (HCC) is one of the most frequently diagnosed types of cancer in the world. Post-translational modifications, such as phosphorylation, serve an essential role during cancer development. To identify aberrant phosphorylation in HCC, a multiplexed tandem mass tag approach combined with liquid chromatography tandem-mass spectrometry was used in the present study. The results are available via ProteomeXchange (identifier no. PXD013934). A total of 4,780 phosphorylated sites d ...[more]

PMID: 33408763

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Project description:Hepatocellular carcinoma is one of the most frequently diagnosed cancers in the world. Post-translational modifications (PTMs) play an essential role during cancer development. Phosphorylation is an important PTMs. To identify the modifications of phosphorylation in HCC, a multiplexed tandem mass tag (TMT) approach combined with LC−MS/MS was used. A total of 4,780 phosphorylated sites distributed on 2,209 proteins were identified and quantified, including 74 and 459 phosphorylated up-regulated and down-regulated proteins, respectively. Bio-informatic analysis revealed the differences and commonalities between HCC and normal tissues. Gene ontology enrichment analysis provided the information on biological processes, molecular functions, cellular components, and sub-cellular localizations. Protein domains enrichment of differentially expressed proteins were analyzed by InterPro database. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed the pathways that could potentially be involved in HCC. Integrative analysis of the functions, pathways, motifs of phosphorylated peptides, protein domains and protein interactions could establish a profile of phosphoproteome of HCC, which may contribute to identify new biomarkers for diagnosis and prognosis for HCC and novel therapeutic targets for HCC treatment.Hepatocellular carcinoma is one of the most frequently diagnosed cancers in the world. Post-translational modifications (PTMs) play an essential role during cancer development. Phosphorylation is an important PTMs. To identify the modifications of phosphorylation in HCC, a multiplexed tandem mass tag (TMT) approach combined with LC−MS/MS was used. A total of 4,780 phosphorylated sites distributed on 2,209 proteins were identified and quantified, including 74 and 459 phosphorylated up-regulated and down-regulated proteins, respectively. Bio-informatic analysis revealed the differences and commonalities between HCC and normal tissues. Gene ontology enrichment analysis provided the information on biological processes, molecular functions, cellular components, and sub-cellular localizations. Protein domains enrichment of differentially expressed proteins were analyzed by InterPro database. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed the pathways that could potentially be involved in HCC. Integrative analysis of the functions, pathways, motifs of phosphorylated peptides, protein domains and protein interactions could establish a profile of phosphoproteome of HCC, which may contribute to identify new biomarkers for diagnosis and prognosis for HCC and novel therapeutic targets for HCC treatment.

Project description:Streptomycetes are multicellular bacteria with complex developmental cycles. They are of biotechnological importance as they produce most bioactive compounds used in biomedicine, e.g. antibiotic, antitumoral and immunosupressor compounds. Streptomyces genomes encode many Ser/Thr/Tyr kinases, making this genus an outstanding model for the study of bacterial protein phosphorylation events. We used mass spectrometry based quantitative proteomics and phosphoproteomics to characterize bacterial differentiation and activation of secondary metabolism of Streptomyces coelicolor We identified and quantified 3461 proteins corresponding to 44.3% of the S. coelicolor proteome across three developmental stages: vegetative hypha (first mycelium); secondary metabolite producing hyphae (second mycelium); and sporulating hyphae. A total of 1350 proteins exhibited more than 2-fold expression changes during the bacterial differentiation process. These proteins include 136 regulators (transcriptional regulators, transducers, Ser/Thr/Tyr kinases, signaling proteins), as well as 542 putative proteins with no clear homology to known proteins which are likely to play a role in differentiation and secondary metabolism. Phosphoproteomics revealed 85 unique protein phosphorylation sites, 58 of them differentially phosphorylated during differentiation. Computational analysis suggested that these regulated protein phosphorylation events are implicated in important cellular processes, including cell division, differentiation, regulation of secondary metabolism, transcription, protein synthesis, protein folding and stress responses. We discovered a novel regulated phosphorylation site in the key bacterial cell division protein FtsZ (pSer319) that modulates sporulation and regulates actinorhodin antibiotic production. We conclude that manipulation of distinct protein phosphorylation events may improve secondary metabolite production in industrial streptomycetes, including the activation of cryptic pathways during the screening for new secondary metabolites from streptomycetes.

Project description:Background:Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide. However, the molecular mechanisms involved in HCC remain unclear and are in urgent need of elucidation. Therefore, we sought to identify biomarkers in the prognosis of HCC through an integrated bioinformatics analysis. Methods:Messenger RNA (mRNA) expression profiles were obtained from the Gene Expression Omnibus database and The Cancer Genome Atlas-Liver Hepatocellular Carcinoma (TCGA-LIHC) for the screening of common differentially expressed genes (DEGs). Function and pathway enrichment analysis, protein-protein interaction network construction and key gene identification were performed. The significance of key genes in HCC was validated by overall survival analysis and immunohistochemistry. Meanwhile, based on TCGA data, prognostic microRNAs (miRNAs) were decoded using univariable and multivariable Cox regression analysis, and their target genes were predicted by miRWalk. Results:Eleven hub genes (upregulated ASPM, AURKA, CCNB2, CDC20, PRC1 and TOP2A and downregulated AOX1, CAT, CYP2E1, CYP3A4 and HP) with the most interactions were considered as potential biomarkers in HCC and confirmed by overall survival analysis. Moreover, AURKA, PRC1, TOP2A, AOX1, CYP2E1, and CYP3A4 were considered candidate liver-biopsy markers for high risk of developing HCC and poor prognosis in HCC. Upregulation of hsa-mir-1269b, hsa-mir-518d, hsa-mir-548aq, hsa-mir-548f-1, and hsa-mir-6728, and downregulation of hsa-mir-139 and hsa-mir-4800 were determined to be risk factors of poor prognosis, and most of these miRNAs have strong potential to help regulate the expression of key genes. Conclusions:This study undertook the first large-scale integrated bioinformatics analysis of the data from Illumina BeadArray platforms and the TCGA database. With a comprehensive analysis of transcriptional alterations, including mRNAs and miRNAs, in HCC, our study presented candidate biomarkers for the surveillance and prognosis of the disease, and also identified novel therapeutic targets at the molecular and pathway levels.

Dataset Information

Dysregulation of phosphoproteins in hepatocellular carcinoma revealed via quantitative analysis of the phosphoproteome.

Publications

Dysregulation of phosphoproteins in hepatocellular carcinoma revealed via quantitative analysis of the phosphoproteome.

Similar Datasets

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