Aberrations in protein glycosylation and polysaccharides play a pivotal role in pancreatic tumorigenesis, influencing cancer progression, metastasis, immunoresponse and chemoresistance. Abnormal expression in sugar mo...Aberrations in protein glycosylation and polysaccharides play a pivotal role in pancreatic tumorigenesis, influencing cancer progression, metastasis, immunoresponse and chemoresistance. Abnormal expression in sugar moieties can impact the function of various glycoproteins, including mucins, surface receptors, adhesive proteins, proteoglycans, as well as their effectors and binding ligands, resulting in an increase in pancreatic cancer invasiveness and a cancerfavored microenvironment. Recent advance in glycoproteomics, glycomics and other chemical biology techniques have been employed to better understand the complex mechanism of glycosylation events and how they orchestrate molecular activities in genomics, proteomics and metabolomics implicated in pancreatic adenocarcinoma. A variety of strategies have been demonstrated targeting protein glycosylation and polysaccharides for diagnostic and therapeutic development.展开更多
Identification evaluation and result dissemination are essential components in mass spectrometry-based proteomics analysis.The visualization of fragment ions in mass spectrum provides strong evidence for peptide ident...Identification evaluation and result dissemination are essential components in mass spectrometry-based proteomics analysis.The visualization of fragment ions in mass spectrum provides strong evidence for peptide identification and modification localization.Here,we present an easy-to-use tool,named GP-Plotter,for ion annotation of tandem mass spectra and corresponding image output.Identification result files of common searching tools in the community and user-customized files are supported as input of GP-Plotter.Multiple display modes and parameter customization can be achieved in GP-Plotter to present annotated spectra of interest.Different image formats,especially vector graphic formats,are available for image generation which is favorable for data publication.Notably,GP-Plotter is also well-suited for the visualization and evaluation of glycopeptide spectrum assignments with comprehensive annotation of glycan fragment ions.With a user-friendly graphical interface,GP-Plotter is expected to be a universal visualization tool for the community.GP-Plotter has been implemented in the latest version of Glyco-Decipher(v1.0.4)and the standalone GP-Plotter software is also freely available at https://github.com/DICP-1809.展开更多
Glycoproteins are complex biological macromolecules composed of proteins and glycans,playing a crucial role in various biological processes and being closely related to human health and diseases.However,the intricate ...Glycoproteins are complex biological macromolecules composed of proteins and glycans,playing a crucial role in various biological processes and being closely related to human health and diseases.However,the intricate structure and function of glycoproteins gives them with a vast capacity for information,which cannot be simply deduced from the genetic code(Di Marco et al.2023).展开更多
The first corona-pandemic,coronavirus disease 2019(COVID-19)caused a huge health crisis and incalculable damage worldwide.Knowledge of how to cure the disease is urgently needed.Emerging immune escaping mutants of the...The first corona-pandemic,coronavirus disease 2019(COVID-19)caused a huge health crisis and incalculable damage worldwide.Knowledge of how to cure the disease is urgently needed.Emerging immune escaping mutants of the virus suggested that it may be potentially persistent in human society as a regular health threat as the flu virus.Therefore,it is imperative to identify appropriate biomarkers to indicate pathological and physiological states,and more importantly,clinic outcomes.Proteins are the performers of life functions,and their abundance and modification status can directly reflect the immune status.Protein glycosylation serves a great impact in modulating protein function.The use of both unmodified and glycosylated proteins as biomarkers has also been proved feasible in the studies of SARS,Zika virus,influenza,etc.In recent years,mass spectrometry-based glycoproteomics,as well as proteomics approaches,advanced significantly due to the evolution of mass spectrometry.We focus on the current development of the mass spectrometry-based strategy for COVID-19 biomarkers’investigation.Potential application of glycoproteomics approaches and challenges in biomarkers identification are also discussed.展开更多
In order to establish the novel high throughput, high efficiency and low cost technological platform for the research of N-glycoproteomics, to resolve the significance of characteristic expression profile of glycoprot...In order to establish the novel high throughput, high efficiency and low cost technological platform for the research of N-glycoproteomics, to resolve the significance of characteristic expression profile of glycoprotein and to find the proteins with biological functional importance, the glycoproteins with high-mannose core and the two antennary types were purified and enriched by the Con A affinity chromatography. Con A affinity protein expression profiles of normal human liver tissue were gener- ated by using SDS-PAGE, two-dimensional electrophoresis (2-DE) followed by fast fluorescence stain- ing based on multiplexed proteomics (MP) technology. 301 visible protein spots on the gel were de- tected and 85 of glycoproteins were further successfully identified via peptide mass fingerprinting (PMF) by a matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF- MS/MS) and annotated to IPI databases. Identified glycoproteins definitely take part in the regulation of cell cycle and metabolic processes. The glycosylation sites were predicted with NetNGlyc 1.0 and NetOGlyc 3.1 software, meanwhile they were classified according to the geneontology methods. The construction of Con A affinity glycoprotein database of normal human liver tissue would contribute to the subsequent research.展开更多
Pancreatic cancer is among the most malignant cancers,and thus early intervention is the key to better survival outcomes.However,no methods have been derived that can reliably identify early precursors of development ...Pancreatic cancer is among the most malignant cancers,and thus early intervention is the key to better survival outcomes.However,no methods have been derived that can reliably identify early precursors of development into malignancy.Therefore,it is urgent to discover early molecular changes during pancreatic tumorigenesis.As aberrant glycosylation is closely associated with cancer progression,numerous efforts have been made to mine glycosylation changes as biomarkers for diagnosis;however,detailed glycoproteomic information,especially site-specific N-glycosylation changes in pancreatic cancer with and without drug treatment,needs to be further explored.Herein,we used comprehensive solid-phase chemoenzymatic glycoproteomics to analyze glycans,glycosites,and intact glycopeptides in pancreatic cancer cells and patient sera.The profiling of N-glycans in cancer cells revealed an increase in the secreted glycoproteins from the primary tumor of MIA PaCa-2 cells,whereas human sera,which contain many secreted glycoproteins,had significant changes of glycans at their specific glycosites.These results indicated the potential role for tumor-specific glycosylation as disease biomarkers.We also found that AMG-510,a small molecule inhibitor against Kirsten rat sarcoma viral oncogene homolog(KRAS)G12C mutation,profoundly reduced the glycosylation level in MIA PaCa-2 cells,suggesting that KRAS plays a role in the cellular glycosylation process,and thus glycosylation inhibition contributes to the anti-tumor effect of AMG-510.展开更多
Protein glycosylation is a critical post-translational modification that influences protein folding,localization,stability,and functional interactions by attaching glycans to specific sites.This process is crucial for...Protein glycosylation is a critical post-translational modification that influences protein folding,localization,stability,and functional interactions by attaching glycans to specific sites.This process is crucial for biological functions of glycoproteins,and aberrant glycosylation can lead to genetic disorders,immune system issues,and multi-organ pathologies.Recent advancements in glycoproteomic technologies have made the study of protein glycosylation a key focus for understanding the pathogenesis of kidney diseases.This review provides a comprehensive overview of protein glycosylation mechanisms,its biological roles,molecular pathways,and significant functions in renal physiology and pathology.It specifically highlights the dynamic changes and regulatory networks associated with aberrant glycosylation in kidney diseases such as immunoglobulin A nephropathy,diabetic kidney disease,autosomal dominant polycystic kidney disease,renal cell carcinoma,and acute kidney injury.It also evaluates the clinical applications of related technologies and biomarkers.Additionally,it discusses the challenges in developing glycosylation-targeted therapeutic strategies.Future research should focus on clarifying cell-specific glycosylation regulatory networks in the kidney,integrating glycobiology with multi-omics approaches,and improving precision diagnostics and treatment for kidney diseases.展开更多
The structure of N-glycans on specific proteins can regulate innate and adaptive immunity via sensing environmental signals.Meanwhile,the structural diversity of N-glycans poses analytical challenges that limit the ex...The structure of N-glycans on specific proteins can regulate innate and adaptive immunity via sensing environmental signals.Meanwhile,the structural diversity of N-glycans poses analytical challenges that limit the exploration of specific glycosylation functions.In this work,we used THP-1-derived macrophages as examples to show the vast potential of a N-glycan structural interpretation tool StrucGP in N-glycoproteomic analysis.The intact glycopeptides of macrophages were enriched and analyzed using mass spectrometry(MS)-based glycoproteomic approaches,followed by the large-scale mapping of site-specific glycan structures via StrucGP.Results revealed that bisected GlcNAc,core fucosylated,and sialylated glycans(e.g.,HexNAc4Hex5Fuc1Neu5Ac1,N4H5F1S1)were increased in M1 and M2 macrophages,especially in the latter.The findings indicated that these structures may be closely related to macrophage polarization.In addition,a high level of glycosylated PD-L1 was observed in M1 macrophages,and the LacNAc moiety was detected at Asn-192 and Asn-200 of PD-L1,and Asn-200 contained Lewis epitopes.The precision structural interpretation of site-specific glycans and subsequent intervention of target glycoproteins and related glycosyltransferases are of great value for the development of new diagnostic and therapeutic approaches for different diseases.展开更多
文摘Aberrations in protein glycosylation and polysaccharides play a pivotal role in pancreatic tumorigenesis, influencing cancer progression, metastasis, immunoresponse and chemoresistance. Abnormal expression in sugar moieties can impact the function of various glycoproteins, including mucins, surface receptors, adhesive proteins, proteoglycans, as well as their effectors and binding ligands, resulting in an increase in pancreatic cancer invasiveness and a cancerfavored microenvironment. Recent advance in glycoproteomics, glycomics and other chemical biology techniques have been employed to better understand the complex mechanism of glycosylation events and how they orchestrate molecular activities in genomics, proteomics and metabolomics implicated in pancreatic adenocarcinoma. A variety of strategies have been demonstrated targeting protein glycosylation and polysaccharides for diagnostic and therapeutic development.
基金supported in part by funds from the National Key R&D Program of China(Grant Nos.2022YFC3400801 and 2021YFA1302601)the National Natural Science Foundation of China(Grant Nos.22034007,22274014,92153302,22304174)+3 种基金the innovation program of science and research from the Dalian Institute of Chemical Physics(DICP)Chinese Academy of Sciences(CAS)(Grant No.DMU-2&DICP UN202303)the Youth Innovation Promotion Association of CAS(Grant No.Y2022059)the China Postdoctoral Science Foundation(Grant No.2023M743424).
文摘Identification evaluation and result dissemination are essential components in mass spectrometry-based proteomics analysis.The visualization of fragment ions in mass spectrum provides strong evidence for peptide identification and modification localization.Here,we present an easy-to-use tool,named GP-Plotter,for ion annotation of tandem mass spectra and corresponding image output.Identification result files of common searching tools in the community and user-customized files are supported as input of GP-Plotter.Multiple display modes and parameter customization can be achieved in GP-Plotter to present annotated spectra of interest.Different image formats,especially vector graphic formats,are available for image generation which is favorable for data publication.Notably,GP-Plotter is also well-suited for the visualization and evaluation of glycopeptide spectrum assignments with comprehensive annotation of glycan fragment ions.With a user-friendly graphical interface,GP-Plotter is expected to be a universal visualization tool for the community.GP-Plotter has been implemented in the latest version of Glyco-Decipher(v1.0.4)and the standalone GP-Plotter software is also freely available at https://github.com/DICP-1809.
文摘Glycoproteins are complex biological macromolecules composed of proteins and glycans,playing a crucial role in various biological processes and being closely related to human health and diseases.However,the intricate structure and function of glycoproteins gives them with a vast capacity for information,which cannot be simply deduced from the genetic code(Di Marco et al.2023).
基金funded by SZSTC(SGDX20190816230207535)obtained a donation from Kwok Chung Bo Fun Charitable Fund,which commemorates the establishment of the Kwok Yat Wai Endowed Chair of Environmental and Biological Analysis。
文摘The first corona-pandemic,coronavirus disease 2019(COVID-19)caused a huge health crisis and incalculable damage worldwide.Knowledge of how to cure the disease is urgently needed.Emerging immune escaping mutants of the virus suggested that it may be potentially persistent in human society as a regular health threat as the flu virus.Therefore,it is imperative to identify appropriate biomarkers to indicate pathological and physiological states,and more importantly,clinic outcomes.Proteins are the performers of life functions,and their abundance and modification status can directly reflect the immune status.Protein glycosylation serves a great impact in modulating protein function.The use of both unmodified and glycosylated proteins as biomarkers has also been proved feasible in the studies of SARS,Zika virus,influenza,etc.In recent years,mass spectrometry-based glycoproteomics,as well as proteomics approaches,advanced significantly due to the evolution of mass spectrometry.We focus on the current development of the mass spectrometry-based strategy for COVID-19 biomarkers’investigation.Potential application of glycoproteomics approaches and challenges in biomarkers identification are also discussed.
基金the National Basic Research Program of China (973)(Grant No. 2004CB520802)
文摘In order to establish the novel high throughput, high efficiency and low cost technological platform for the research of N-glycoproteomics, to resolve the significance of characteristic expression profile of glycoprotein and to find the proteins with biological functional importance, the glycoproteins with high-mannose core and the two antennary types were purified and enriched by the Con A affinity chromatography. Con A affinity protein expression profiles of normal human liver tissue were gener- ated by using SDS-PAGE, two-dimensional electrophoresis (2-DE) followed by fast fluorescence stain- ing based on multiplexed proteomics (MP) technology. 301 visible protein spots on the gel were de- tected and 85 of glycoproteins were further successfully identified via peptide mass fingerprinting (PMF) by a matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF- MS/MS) and annotated to IPI databases. Identified glycoproteins definitely take part in the regulation of cell cycle and metabolic processes. The glycosylation sites were predicted with NetNGlyc 1.0 and NetOGlyc 3.1 software, meanwhile they were classified according to the geneontology methods. The construction of Con A affinity glycoprotein database of normal human liver tissue would contribute to the subsequent research.
基金approved by the Research Ethics Committees of Zhejiang Provincial People’s Hospital(No.QT2022387).
文摘Pancreatic cancer is among the most malignant cancers,and thus early intervention is the key to better survival outcomes.However,no methods have been derived that can reliably identify early precursors of development into malignancy.Therefore,it is urgent to discover early molecular changes during pancreatic tumorigenesis.As aberrant glycosylation is closely associated with cancer progression,numerous efforts have been made to mine glycosylation changes as biomarkers for diagnosis;however,detailed glycoproteomic information,especially site-specific N-glycosylation changes in pancreatic cancer with and without drug treatment,needs to be further explored.Herein,we used comprehensive solid-phase chemoenzymatic glycoproteomics to analyze glycans,glycosites,and intact glycopeptides in pancreatic cancer cells and patient sera.The profiling of N-glycans in cancer cells revealed an increase in the secreted glycoproteins from the primary tumor of MIA PaCa-2 cells,whereas human sera,which contain many secreted glycoproteins,had significant changes of glycans at their specific glycosites.These results indicated the potential role for tumor-specific glycosylation as disease biomarkers.We also found that AMG-510,a small molecule inhibitor against Kirsten rat sarcoma viral oncogene homolog(KRAS)G12C mutation,profoundly reduced the glycosylation level in MIA PaCa-2 cells,suggesting that KRAS plays a role in the cellular glycosylation process,and thus glycosylation inhibition contributes to the anti-tumor effect of AMG-510.
基金supported by the National Key Research and Development Program of China(grant Nos.2022YFF0608401,2022YFF0608404,2021YFF0702003-02)the National Natural Science Foundation of China(grant No.92478101).
文摘Protein glycosylation is a critical post-translational modification that influences protein folding,localization,stability,and functional interactions by attaching glycans to specific sites.This process is crucial for biological functions of glycoproteins,and aberrant glycosylation can lead to genetic disorders,immune system issues,and multi-organ pathologies.Recent advancements in glycoproteomic technologies have made the study of protein glycosylation a key focus for understanding the pathogenesis of kidney diseases.This review provides a comprehensive overview of protein glycosylation mechanisms,its biological roles,molecular pathways,and significant functions in renal physiology and pathology.It specifically highlights the dynamic changes and regulatory networks associated with aberrant glycosylation in kidney diseases such as immunoglobulin A nephropathy,diabetic kidney disease,autosomal dominant polycystic kidney disease,renal cell carcinoma,and acute kidney injury.It also evaluates the clinical applications of related technologies and biomarkers.Additionally,it discusses the challenges in developing glycosylation-targeted therapeutic strategies.Future research should focus on clarifying cell-specific glycosylation regulatory networks in the kidney,integrating glycobiology with multi-omics approaches,and improving precision diagnostics and treatment for kidney diseases.
基金supported by the National Key Research and Development Program of China(No.2019YFA0905200)the National Natural Science Foundation of China(Nos.91853123,81773180,and 21705127).
文摘The structure of N-glycans on specific proteins can regulate innate and adaptive immunity via sensing environmental signals.Meanwhile,the structural diversity of N-glycans poses analytical challenges that limit the exploration of specific glycosylation functions.In this work,we used THP-1-derived macrophages as examples to show the vast potential of a N-glycan structural interpretation tool StrucGP in N-glycoproteomic analysis.The intact glycopeptides of macrophages were enriched and analyzed using mass spectrometry(MS)-based glycoproteomic approaches,followed by the large-scale mapping of site-specific glycan structures via StrucGP.Results revealed that bisected GlcNAc,core fucosylated,and sialylated glycans(e.g.,HexNAc4Hex5Fuc1Neu5Ac1,N4H5F1S1)were increased in M1 and M2 macrophages,especially in the latter.The findings indicated that these structures may be closely related to macrophage polarization.In addition,a high level of glycosylated PD-L1 was observed in M1 macrophages,and the LacNAc moiety was detected at Asn-192 and Asn-200 of PD-L1,and Asn-200 contained Lewis epitopes.The precision structural interpretation of site-specific glycans and subsequent intervention of target glycoproteins and related glycosyltransferases are of great value for the development of new diagnostic and therapeutic approaches for different diseases.
