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Yin H, Zhu J. Methods for quantification of glycopeptides by liquid separation and mass spectrometry. MASS SPECTROMETRY REVIEWS 2023; 42:887-917. [PMID: 35099083 PMCID: PMC9339036 DOI: 10.1002/mas.21771] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 11/14/2021] [Accepted: 01/13/2022] [Indexed: 05/05/2023]
Abstract
Recent advances in analytical techniques provide the opportunity to quantify even low-abundance glycopeptides derived from complex biological mixtures, allowing for the identification of glycosylation differences between healthy samples and those derived from disease states. Herein, we discuss the sample preparation procedures and the mass spectrometry (MS) strategies that have facilitated glycopeptide quantification, as well as the standards used for glycopeptide quantification. For sample preparation, various glycopeptide enrichment methods are summarized including the columns used for glycopeptide separation in liquid chromatography separation. For MS analysis strategies, MS1 level-based quantification and MS2 level-based quantification are described, either with or without labeling, where we have covered isotope labeling, TMT/iTRAQ labeling, data dependent acquisition, data independent acquisition, multiple reaction monitoring, and parallel reaction monitoring. The strengths and weaknesses of these methods are compared, particularly those associated with the figures of merit that are important for clinical biomarker studies and the pathological and functional studies of glycoproteins in various diseases. Possible future developments for glycopeptide quantification are discussed.
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Affiliation(s)
- Haidi Yin
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518132, China
- Correspondence to: Haidi Yin, Shenzhen Bay Laboratory, A1201, Shenzhen, Guangdong, 518132, China. Phone: 0755-26849276. , Jianhui Zhu, Department of Surgery, University of Michigan, 1150 West Medical Center Drive, Building MSRB1, Rm A500, Ann Arbor, MI 48109-0656, USA. Tel: 734-615-2567. Fax: 734-615-2088.
| | - Jianhui Zhu
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109, USA
- Correspondence to: Haidi Yin, Shenzhen Bay Laboratory, A1201, Shenzhen, Guangdong, 518132, China. Phone: 0755-26849276. , Jianhui Zhu, Department of Surgery, University of Michigan, 1150 West Medical Center Drive, Building MSRB1, Rm A500, Ann Arbor, MI 48109-0656, USA. Tel: 734-615-2567. Fax: 734-615-2088.
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Cao X, Shao Y, Meng P, Cao Z, Yan G, Yao J, Zhou X, Liu C, Zhang L, Shu H, Lu H. Nascent Proteome and Glycoproteome Reveal the Inhibition Role of ALG1 in Hepatocellular Carcinoma Cell Migration. PHENOMICS (CHAM, SWITZERLAND) 2022; 2:230-241. [PMID: 36939752 PMCID: PMC9590484 DOI: 10.1007/s43657-022-00050-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 03/14/2022] [Accepted: 03/20/2022] [Indexed: 12/09/2022]
Abstract
Asparagine-linked glycosylation protein 1 homolog (ALG1) participates in the initial stage of protein N-glycosylation and N-glycosylation has been implicated in the process of hepatocellular carcinoma (HCC) progression. However, whether ALG1 plays a role in human HCC remains unknown. In this study, the expression profile of ALG1 in tumorous and corresponding adjacent non-tumor tissues was analyzed. The relationship of ALG1 expression with clinical features and prognosis of HCC patients was also evaluated using immuno-histochemical method. Here we found ALG1 decreased in HCC tissues compared with adjacent normal liver tissues, which predicted an unfavorable prognosis. Combined with RNA interference, nascent proteome and glycoproteome were determined systematically in Huh7 cell line. Bioinformatics analysis indicated that the differentially expressed proteins participating in the response of ALG1 knockdown were most significantly associated with cell-cell adhesion. Functional studies confirmed that knockdown of ALG1 reduced cell adhesion capacity, and promoted cell migration. Furthermore, down-regulation of H8N2 (on N-glycosite N651) and H5N4S2F1 (on N-glycosite N692) from N-cadherin was identified as a feature of ALG1 knockdown. Our findings revealed that ALG1 controlled the expression of glycosylated N-cadherin and played a role in HCC migration, with implications for prognosis. Graphical Abstract Supplementary Information The online version contains supplementary material available at 10.1007/s43657-022-00050-5.
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Affiliation(s)
- Xinyi Cao
- Institutes of Biomedical Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200032 China
| | - Yuyin Shao
- Institutes of Biomedical Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200032 China
| | - Peiyi Meng
- Department of Chemistry and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, 200433 China
| | - Zhao Cao
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning, 530021 China
| | - Guoquan Yan
- Institutes of Biomedical Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200032 China
| | - Jun Yao
- Institutes of Biomedical Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200032 China
| | - Xinwen Zhou
- Institutes of Biomedical Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200032 China
| | - Chao Liu
- Beijing Advanced Innovation Center for Precision Medicine, Beihang University, Beijing, 100083 China
| | - Lei Zhang
- Institutes of Biomedical Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200032 China
| | - Hong Shu
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital, Nanning, 530021 China
| | - Haojie Lu
- Institutes of Biomedical Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200032 China
- Department of Chemistry and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, 200433 China
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Cao X, Meng P, Shao Y, Yan G, Yao J, Zhou X, Liu C, Zhang L, Shu H, Lu H. Nascent Glycoproteome Reveals That N-Linked Glycosylation Inhibitor-1 Suppresses Expression of Glycosylated Lysosome-Associated Membrane Protein-2. Front Mol Biosci 2022; 9:899192. [PMID: 35573732 PMCID: PMC9092021 DOI: 10.3389/fmolb.2022.899192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 04/12/2022] [Indexed: 11/15/2022] Open
Abstract
Glycosylation inhibition has great potential in cancer treatment. However, the corresponding cellular response, protein expression and glycosylation changes remain unclear. As a cell-permeable small-molecule inhibitor with reduced cellular toxicity, N-linked glycosylation inhibitor-1 (NGI-1) has become a great approach to regulate glycosylation in mammalian cells. Here for the first time, we applied a nascent proteomic method to investigate the effect of NGI-1 in hepatocellular carcinoma (HCC) cell line. Besides, hydrophilic interaction liquid chromatography (HILIC) was adopted for the enrichment of glycosylated peptides. Glycoproteomic analysis revealed the abundance of glycopeptides from LAMP2, NICA, and CEIP2 was significantly changed during NGI-1 treatment. Moreover, the alterations of LAMP2 site-specific intact N-glycopeptides were comprehensively assessed. NGI-1 treatment also led to the inhibition of Cathepsin D maturation and the induction of autophagy. In summary, we provided evidence that NGI-1 repressed the expression of glycosylated LAMP2 accompanied with the occurrence of lysosomal defects and autophagy.
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Affiliation(s)
- Xinyi Cao
- Institutes of Biomedical Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Peiyi Meng
- Department of Chemistry, Fudan University, Shanghai, China
| | - Yuyin Shao
- Institutes of Biomedical Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Guoquan Yan
- Institutes of Biomedical Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jun Yao
- Institutes of Biomedical Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Xinwen Zhou
- Institutes of Biomedical Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Chao Liu
- Beijing Advanced Innovation Center for Precision Medicine, Beihang University, Beijing, China
| | - Lei Zhang
- Institutes of Biomedical Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Hong Shu
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital, Nanning, China
- *Correspondence: Hong Shu, ; Haojie Lu,
| | - Haojie Lu
- Institutes of Biomedical Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
- Department of Chemistry, Fudan University, Shanghai, China
- NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China
- *Correspondence: Hong Shu, ; Haojie Lu,
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Huo J, Fan X, Qi B, Sun P. A Five-Gene Signature Associated With DNA Damage Repair Molecular Subtype Predict Overall Survival for Hepatocellular Carcinoma. Front Genet 2022; 13:771819. [PMID: 35126478 PMCID: PMC8811360 DOI: 10.3389/fgene.2022.771819] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/03/2022] [Indexed: 01/02/2023] Open
Abstract
Background: DNA damage repair (DDR) is an important mechanism for the occurrence and development of hepatocellular carcinoma (HCC), but its impact on prognosis has not been fully understood.Materials and methods: A total of 904 HCC patients were included in our study, TCGA (n = 370) and GSE14520 (n = 239) were merged into a large-sample training cohort (n = 609). The training cohort was clustered into C1 and C2 based on prognostic DDR-related genes, the differentially expressed genes (DEGs) between C1 and C2 were identified by the Wilcoxon signed-rank test referred to criteria (|log2FC|≥1 and FDR< 0.05). The univariate Cox analysis was used to screen the prognostic-related DEGs, and Lasso penalized Cox regression analysis was used to construct the risk score. The patients were clarified into high- and low-risk groups based on the median risk score. ICGC (n = 231) and GSE116174 (n = 64) cohorts were used for external validation of the risk score’s prognostic value.Results: The Kaplan–Meier survival analysis showed that the high-risk group had a significantly reduced overall survival (OS) compared to the low-risk group in the three independent cohorts, and the time-dependent ROC curve showed that the five-gene (STMN1, PON1, PLOD2, MARCKSL1, and SPP1) risk score with a high accuracy in predicting OS. The patients with AFP >300 ng/ml, tumor poor differentiation (grade 3–4), micro and macro vascular tumor invasion, advanced stage (AJCC III-IV, BCLC stage B-C, and CLIP score >2) exhibited a higher risk score. Subgroup survival analysis found that the risk score was applicable to patients with different clinical characteristics. GO and KEGG functional enrichment analysis revealed that cell cycle, p53 signaling, TNF signaling-related pathways were upregulated in the high-risk group. The higher infiltration level of activated CD4 T cell, CD56 bright natural killer cell, plasmacytoid dendritic cell, and type 2 T helper cells were found to lead an unfavorable impact on the OS of HCC patients, and these four kinds of immune cells exhibited a higher infiltration level in the high-risk group.Conclusion: The five-gene risk score proposed in the research may provide new insights into the individualized evaluation of HCC prognosis.
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Affiliation(s)
- Junyu Huo
- Liver Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xinyi Fan
- Department of Allergy, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Bingxin Qi
- School of Public Health, Qingdao University, Qingdao, China
| | - Peng Sun
- Department of Hepatobilary and Pancreatic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
- *Correspondence: Peng Sun,
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Xu D, Wang Y, Wu J, Lin S, Chen Y, Zheng J. Identification and clinical validation of EMT-associated prognostic features based on hepatocellular carcinoma. Cancer Cell Int 2021; 21:621. [PMID: 34819088 PMCID: PMC8613962 DOI: 10.1186/s12935-021-02326-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 11/10/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The aim of this study was to construct a model based on the prognostic features associated with epithelial-mesenchymal transition (EMT) to explore the various mechanisms and therapeutic strategies available for the treatment of metastasis and invasion by hepatocellular carcinoma (HCC) cells. METHODS EMT-associated genes were identified, and their molecular subtypes were determined by consistent clustering analysis. The differentially expressed genes (DEGs) among the molecular subtypes were ascertained using the limma package and they were subjected to functional enrichment analysis. The immune cell scores of the molecular subtypes were evaluated using ESTIMATE, MCPcounter, and GSCA packages of R. A multi-gene prognostic model was constructed using lasso regression, and the immunotherapeutic effects of the model were analyzed using the Imvigor210 cohort. In addition, immunohistochemical analysis was performed on a cohort of HCC tissue to validate gene expression. RESULTS Based on the 59 EMT-associated genes identified, the 365-liver hepatocellular carcinoma (LIHC) samples were divided into two subtypes, C1 and C2. The C1 subtype mostly showed poor prognosis, had higher immune scores compared to the C2 subtype, and showed greater correlation with pathways of tumor progression. A four-gene signature construct was fabricated based on the 1130 DEGs among the subtypes. The construct was highly robust and showed stable predictive efficacy when validated using datasets from different platforms (HCCDB18 and GSE14520). Additionally, compared to currently existing models, our model demonstrated better performance. The results of the immunotherapy cohort showed that patients in the low-risk group have a better immune response, leading to a better patient's prognosis. Immunohistochemical analysis revealed that the expression levels of the FTCD, PON1, and TMEM45A were significantly over-expressed in 41 normal samples compared to HCC samples, while that of the G6PD was significantly over-expressed in cancerous tissues. CONCLUSIONS The four-gene signature construct fabricated based on the EMT-associated genes provides valuable information to further study the pathogenesis and clinical management of HCC.
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Affiliation(s)
- Dafeng Xu
- Department of Hepatobiliary and Pancreatic Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Yu Wang
- Geriatric Medicine Center, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Jincai Wu
- Department of Hepatobiliary and Pancreatic Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Shixun Lin
- Department of Hepatobiliary and Pancreatic Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Yonghai Chen
- Department of Hepatobiliary and Pancreatic Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Jinfang Zheng
- Department of Hepatobiliary and Pancreatic Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China.
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