In-depth analysis of secretome and N-glycosecretome of human hepatocellular carcinoma metastatic cell lines shed light on metastasis correlated proteins

Li, Xianyu; Jiang, Jing; Zhao, Xinyuan; Zhao, Yan; Cao, Qin; Zhao, Qing; Han, Huanhuan; Wang, Jifeng; Yu, Zixiang; Peng, Bo; Ying, Wantao; Qian, Xiaohong

doi:10.18632/oncotarget.8247

Cited by 19 publications

(11 citation statements)

References 74 publications

(104 reference statements)

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“…Protocadherin Fat1 is a transmembrane protein belonging to Cadherin superfamily. The FAT1 N‐glycosylated peptide has been reported to be involved in the establishment of a proper epithelial cell polarity that requires glycosylation and association of the protein with detergent‐resistant membranes …”

Section: Discussionmentioning

confidence: 99%

Urinary Glycopeptide Analysis for the Investigation of Novel Biomarkers

Belczacka

Pejchinovski

Krochmal

et al. 2018

Proteomics Clinical Apps

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Purpose: Urine is a rich source of potential biomarkers, including glycoproteins. Glycoproteomic analysis remains difficult due to the high heterogeneity of glycans. Nevertheless, recent advances in glycoproteomics software solutions facilitate glycopeptide identification and characterization. The aim is to investigate intact glycopeptides in the urinary peptide profiles of normal subjects using a novel PTM-centric software-Byonic. Experimental design: The urinary peptide profiles of 238 normal subjects, previously analyzed using CE-MS and CE-MS/MS and/or LC-MS/MS, are subjected to glycopeptide analysis. Additionally, glycopeptide distribution is assessed in a set of 969 patients with five different cancer types: bladder, prostate and pancreatic cancer, cholangiocarcinoma, and renal cell carcinoma. Results: A total of 37 intact O-glycopeptides and 23 intact N-glycopeptides are identified in the urinary profiles of 238 normal subjects. Among the most commonly identified O-glycoproteins are Apolipoprotein C-III and insulin-like growth factor II, while titin among the N-glycoproteins. Further statistical analysis reveals that three O-glycopeptides and five N-glycopeptides differed significantly in their abundance among the different cancer types, comparing to normal subjects. Conclusions and clinical relevance: Through the established glycoproteomics workflow, intact O-and N-glycopeptides in human urine are identified and characterized, providing novel insights for further exploration of the glycoproteome with respect to specific diseases.

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Section: Discussionmentioning

confidence: 99%

Urinary Glycopeptide Analysis for the Investigation of Novel Biomarkers

Belczacka

Pejchinovski

Krochmal

et al. 2018

Proteomics Clinical Apps

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“…Single-cell-seq, metabolomics, and genomics: characterization of the metastatic nodes at multiple granularities and scale can reveal the evolution of secondary node formation (Enokida et al, 2005;Goldsmith et al, 2019) 3. Single-cell secretome: identifying the molecular communication between neighboring cells and metastatic cancer cells (Blanco et al, 2012;Li et al, 2016a) 4. MRS and PET: functional imaging can reveal environmental factors correlating with metastasis (Herzog et al, 2013;Koush et al, 2019) Dormancy and senescence 1.…”

Section: Mechanistic Models Of Metastasis--toward Linking Mechanisms mentioning

confidence: 99%

Systems Biology of Cancer Metastasis

et al. 2019

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Cancer metastasis is no longer viewed as a linear cascade of events but rather as a series of concurrent, partially overlapping processes, as successfully metastasizing cells assume new phenotypes while jettisoning older behaviors. The lack of a systemic understanding of this complex phenomenon has limited progress in developing treatments for metastatic disease. Because metastasis has traditionally been investigated in distinct physiological compartments, the integration of these complex and interlinked aspects remains a challenge for both systems-level experimental and computational modeling of metastasis. Here, we present some of the current perspectives on the complexity of cancer metastasis, the multiscale nature of its progression, and a systems-level view of the processes underlying the invasive spread of cancer cells. We also highlight the gaps in our current understanding of cancer metastasis as well as insights emerging from interdisciplinary systems biology approaches to understand this complex phenomenon.

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“…The label-free quantitative analyses of the hippocampus proteome proteins were estimated by the peak area method, and in-house data filtering and deconvolution were performed as described [ 64 ]. Briefly, precursor ions areas were extracted using Proteome Discoverer 1.4 (Thermo Fisher Scientific, Waltham, MA, USA) with 10 ppm mass precision (the experimental m / z and retention times were recorded for precursor area quantification).…”

Section: Methodsmentioning

confidence: 99%

In-Depth Proteomic Analysis of the Hippocampus in a Rat Model after Cerebral Ischaemic Injury and Repair by Danhong Injection (DHI)

Cui

Liu

et al. 2017

IJMS

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Stroke is the second most common cause of death worldwide. A systematic description and characterization of the strokes and the effects induced in the hippocampus have not been performed so far. Here, we analysed the protein expression in the hippocampus 24 h after cerebral ischaemic injury and repair. Drug intervention using Danhong injection (DHI), which has been reported to have good therapeutic effects in a clinical setting, was selected for our study of cerebral ischaemia repair in rat models. A larger proteome dataset and total 4091 unique proteins were confidently identified in three biological replicates by combining tissue extraction for rat hippocampus and LC-MS/MS analysis. A label-free approach was then used to quantify the differences among the four experimental groups (Naive, Sham, middle cerebral artery occlusion (MCAO) and MCAO + DHI groups) and showed that about 2500 proteins on average were quantified in each of the experiment group. Bioinformatics analysis revealed that in total 280 unique proteins identified above were differentially expressed (P < 0.05). By combining the subcellular localization, hierarchical clustering and pathway information with the results from injury and repair phase, 12 significant expressed proteins were chosen and verified with respect to their potential as candidates for cerebral ischaemic injury by Western blot. The primary three signalling pathways of the candidates related may be involved in molecular mechanisms related to cerebral ischaemic injury. In addition, a glycogen synthase kinase-3β (Gsk-3β) inhibitor of the candidates with the best corresponding expression trends between western blotting (WB) and label-free quantitative results were chosen for further validation. The results of Western blot analysis of protein expression and 2,3,5- chloride three phenyl tetrazole (TTC) staining of rat brains showed that DHI treatment and Gsk-3β inhibitor are both able to confer protection against ischaemic injury in rat MCAO model. The observations of the present study provide a novel understanding regarding the regulatory mechanism of cerebral ischaemic injury.

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In-depth analysis of secretome and N-glycosecretome of human hepatocellular carcinoma metastatic cell lines shed light on metastasis correlated proteins

Cited by 19 publications

References 74 publications

Urinary Glycopeptide Analysis for the Investigation of Novel Biomarkers

Urinary Glycopeptide Analysis for the Investigation of Novel Biomarkers

Systems Biology of Cancer Metastasis

In-Depth Proteomic Analysis of the Hippocampus in a Rat Model after Cerebral Ischaemic Injury and Repair by Danhong Injection (DHI)

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