Glycosylation is one of the most complex and important post-translational modifications in proteins,playing essential roles in cellular signaling,protein folding,and immune responses[1].Despite its biological sig-nifi...Glycosylation is one of the most complex and important post-translational modifications in proteins,playing essential roles in cellular signaling,protein folding,and immune responses[1].Despite its biological sig-nificance,low abundance and high heterogeneity of glycoproteins pose significant analytical challenges.In a recent study published in National Science Review,a team of scientists led by Prof.Haojie Lu from Fudan University developed a groundbreaking strategy to address these challenges,offering a robust and scalable method for the comprehensive profiling of protein glycosylation[2].展开更多
Targeting the PD-1/PD-L1 axis with small-molecular inhibitors is a promising approach for immunotherapy.Here,we identify a natural pentacyclic triterpenoid,Pygenic Acid A(PA),as a PD-1 signaling inhibitor.PA exerts an...Targeting the PD-1/PD-L1 axis with small-molecular inhibitors is a promising approach for immunotherapy.Here,we identify a natural pentacyclic triterpenoid,Pygenic Acid A(PA),as a PD-1 signaling inhibitor.PA exerts anti-tumor activity in hPD-1 knock-in C57BL/6 mice and enhances effector functions of T cells to promote immune responses by disrupting the PD-1 signaling transduction.Furthermore,we identify SHP-2 as the direct molecular target of PA for inhibiting the PD-1 signaling transduction.Subsequently,mechanistic studies suggest that PA binds to a new druggable site in the phosphorylated PD-1 ITSM recognition site of SHP-2,inhibiting the recruitment of SHP-2 by PD1.Taken together,our findings demonstrate that PA has a potential application in cancer immunotherapy and occupying the phosphorylated ITSM recognition site of SHP-2 may serve as an alternative strategy to develop PD-1 signaling inhibitors.In addition,our success in target recognition provides a paradigm of target identification and confirmation for natural products.展开更多
Accurate chromosome segregation in mitosis depends on kinetochores that connect centromeric chromatin to spindle microtubules.Centromeres are captured by individual microtubules via a kinetochore constitutive centrome...Accurate chromosome segregation in mitosis depends on kinetochores that connect centromeric chromatin to spindle microtubules.Centromeres are captured by individual microtubules via a kinetochore constitutive centromere-associated network(CCAN)during chromosome segregation.CCAN contains 16 subunits,including CENP-W and CENP-T.However,the molecular recognition and mitotic regulation of the CCAN assembly remain elusive.Here,we revealed that CENP-W binds to the histone fold domain and an uncharacterized N-terminal region of CENP-T.Aurora B phosphorylates CENP-W at threonine 60,which enhances the interaction between CENP-W and CENP-T to ensure robust metaphase chromosome alignment and accurate chromosome segregation in mitosis.These findings delineate a conserved signaling cascade that integrates protein phosphorylation with CCAN integrity for the maintenance of genomic stability.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
Faithful segregation of mitotic chromosomes requires bi-orientation of sister chromatids, which relies on the sensing of correct attachments between spindle microtubules and kinetochores. Although the mechanisms under...Faithful segregation of mitotic chromosomes requires bi-orientation of sister chromatids, which relies on the sensing of correct attachments between spindle microtubules and kinetochores. Although the mechanisms underlying PLK1 activation have been extensively studied, the regulatory mechanisms that couple PLK1 activity to accurate chromosome segregation are not well understood. In particular, PLK1 is implicated in stabilizing kinetochore–microtubule attachments, but how kinetochore PLK1 activity is regulated to avoid hyperstabilized kinetochore–microtubules in mitosis remains elusive. Here, we show that kinetochore PLK1 kinase activity is modulated by SET7/9 via lysine methylation during early mitosis. The SET7/9-elicited dimethylation occurs at the Lys191 of PLK1, which tunes down its activity by limiting ATP utilization. Overexpression of the non-methylatable PLK1 mutant or chemical inhibition of SET7/9 methyltransferase activity resulted in mitotic arrest due to destabilized kinetochore–microtubule attachments. These data suggest that kinetochore PLK1 is essential for stable kinetochore–microtubule attachments and methylation by SET7/9 promotes dynamic kinetochore–microtubule attachments for accurate error correction. Our findings define a novel homeostatic regulation at the kinetochore that integrates protein phosphorylation and methylation with accurate chromosome segregation for maintenance of genomic stability.展开更多
NEMO/IKKβcomplex is a central regulator of NF-κB signaling pathway,its dissociation has been considered to be an attractive therapeutic target.Herein,using a combined strategy of molecular pharmacological phenotypin...NEMO/IKKβcomplex is a central regulator of NF-κB signaling pathway,its dissociation has been considered to be an attractive therapeutic target.Herein,using a combined strategy of molecular pharmacological phenotyping,proteomics and bioinformatics analysis,Shikonin(SHK)is identified as a potential inhibitor of the IKKβ/NEMO complex.It destabilizes IKKβ/NEMO complex with IC_(50) of 174 nM,thereby significantly impairing the proliferation of colorectal cancer cells by suppressing the NF-κB pathway in vitro and in vivo.In addition,we also elucidated the potential target sites of SHK in the NEMO/IKKβcomplex.Our study provides some new insights for the development of potent small-molecule PPI inhibitors.展开更多
Prostate cancer(PCa)is the second most prevalent malignancy in males across the world.A greater knowledge of the relationship between protein abundance and drug responses would benefit precision treatment for PCa.Here...Prostate cancer(PCa)is the second most prevalent malignancy in males across the world.A greater knowledge of the relationship between protein abundance and drug responses would benefit precision treatment for PCa.Herein,we establish 35 Chinese PCa primary cell models to capture specific characteristics among PCa patients,including gene mutations,mRNA/protein/surface protein distributions,and pharmaceutical responses.The multi-omics analyses identify Anterior Gradient 2(AGR2)as a pre-operative prognostic biomarker in PCa.Through the drug library screening,we describe crizotinib as a selective compound for malignant PCa primary cells.We further perform the pharmacoproteome analysis and identify 14,372 significant protein-drug correlations.Surprisingly,the diminished AGR2 enhances the inhibition activity of crizotinib via ALK/c-MET-AKT axis activation which is validated by PC3 and xenograft model.Our integrated multi-omics approach yields a comprehensive understanding of PCa biomarkers and pharmacological responses,allowing for more precise diagnosis and therapies.展开更多
The human serum proteome is closely associated with the state of the body.Endogenous peptides derived from proteolytic enzymes cleaving on serum proteins are widely studied due to their potential application in diseas...The human serum proteome is closely associated with the state of the body.Endogenous peptides derived from proteolytic enzymes cleaving on serum proteins are widely studied due to their potential application in disease-specific marker discovery.However,the reproducibility of peptidome analysis of endogenous peptides is significantly influenced by the proteolytic enzymes within body fluids,thereby limiting the clinical use of the endogenous peptides.We comprehensively investigated the N and C terminus of endogenous peptides using peptidomics.The cleavage site patterns of the N and C terminus and adjacent sites from all the identified endogenous peptides were highly conserved under different sample preparation conditions,including long-term incubation at 37℃ and pretreatment with repeated freeze-thaw cycles.Furthermore,a distinguishable cleavage site pattern was obtained when a different disease serum was analyzed.The conserved cleavage site pattern derived from proteolytic enzymes holds potential in highly specific disease diagnosis.展开更多
In the process of collating the raw data,the authors noticed an inadvertent mistake occurred in Fig.3b that needs to be corrected after online publication of the article.In Fig.3b,as a result of an error in the graphi...In the process of collating the raw data,the authors noticed an inadvertent mistake occurred in Fig.3b that needs to be corrected after online publication of the article.In Fig.3b,as a result of an error in the graphics panel arrangement process,the band of NEMO was repeatedly inserted asβ-actin by mistake.The correct band is shown as below and in the updated Fig.3b.The correction did not affect any of our results or discussion as present in the original publication.We regret any inconvenience this has caused.展开更多
文摘Glycosylation is one of the most complex and important post-translational modifications in proteins,playing essential roles in cellular signaling,protein folding,and immune responses[1].Despite its biological sig-nificance,low abundance and high heterogeneity of glycoproteins pose significant analytical challenges.In a recent study published in National Science Review,a team of scientists led by Prof.Haojie Lu from Fudan University developed a groundbreaking strategy to address these challenges,offering a robust and scalable method for the comprehensive profiling of protein glycosylation[2].
基金supported in part by the National Natural Science Foundation of China (81825020, 82150208, 82260682)the National Key R&D Program of China (2022YFC3400501, 2022YFC3400504)+3 种基金the Shanghai Science and Technology Commission Biomedical Science and Technology Support Special Project (21S11907900, 20S11901000)Project of Yunnan Characteristic Plant Screening and R&D Service CXO Platform (2022YKZY001)sponsored by the National Program for Special Supports of Eminent ProfessionalsNational Program for Support of Top-notch Young Professionals
文摘Targeting the PD-1/PD-L1 axis with small-molecular inhibitors is a promising approach for immunotherapy.Here,we identify a natural pentacyclic triterpenoid,Pygenic Acid A(PA),as a PD-1 signaling inhibitor.PA exerts anti-tumor activity in hPD-1 knock-in C57BL/6 mice and enhances effector functions of T cells to promote immune responses by disrupting the PD-1 signaling transduction.Furthermore,we identify SHP-2 as the direct molecular target of PA for inhibiting the PD-1 signaling transduction.Subsequently,mechanistic studies suggest that PA binds to a new druggable site in the phosphorylated PD-1 ITSM recognition site of SHP-2,inhibiting the recruitment of SHP-2 by PD1.Taken together,our findings demonstrate that PA has a potential application in cancer immunotherapy and occupying the phosphorylated ITSM recognition site of SHP-2 may serve as an alternative strategy to develop PD-1 signaling inhibitors.In addition,our success in target recognition provides a paradigm of target identification and confirmation for natural products.
基金supported by the National Key Research and Development Program of China(2022YFA1303100,2022YFA0806800,2022YFA1302700,and 2017YFA0503600)the National Natural Science Foundation of China(32090040,92254302,92153302,92253301,22137007,32170733,and 31871359)+3 种基金the Ministry of Education(IRT_17R102)the Plans for Major Provincial Science&Technology Projects of Anhui Province(202303a0702003)the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB19040000)the Fundamental Research Funds for the Central Universities(WK2070000066 and WK2070000194).
文摘Accurate chromosome segregation in mitosis depends on kinetochores that connect centromeric chromatin to spindle microtubules.Centromeres are captured by individual microtubules via a kinetochore constitutive centromere-associated network(CCAN)during chromosome segregation.CCAN contains 16 subunits,including CENP-W and CENP-T.However,the molecular recognition and mitotic regulation of the CCAN assembly remain elusive.Here,we revealed that CENP-W binds to the histone fold domain and an uncharacterized N-terminal region of CENP-T.Aurora B phosphorylates CENP-W at threonine 60,which enhances the interaction between CENP-W and CENP-T to ensure robust metaphase chromosome alignment and accurate chromosome segregation in mitosis.These findings delineate a conserved signaling cascade that integrates protein phosphorylation with CCAN integrity for the maintenance of genomic stability.
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.
基金This work was supported in part by the National Natural Science Foundation of China(31430054,31320103904,31621002,31671405,91854203,91853115,21922706,31671407,31871359,31601097,and 21672201)the National Key Research and Development Program of China(2017YFA0503600 and 2016YFA0100500)+2 种基金Strategic Priority Research Program of the Chinese Academy of Sciences(XDB19000000)Chinese Academy of Sciences Center for Excellence in Molecular Cell Science(2015HSC-UE010)MOE Innovative Team(IRT_17R102),and the US National Institutes of Health(CA164133and DK26929).
文摘Faithful segregation of mitotic chromosomes requires bi-orientation of sister chromatids, which relies on the sensing of correct attachments between spindle microtubules and kinetochores. Although the mechanisms underlying PLK1 activation have been extensively studied, the regulatory mechanisms that couple PLK1 activity to accurate chromosome segregation are not well understood. In particular, PLK1 is implicated in stabilizing kinetochore–microtubule attachments, but how kinetochore PLK1 activity is regulated to avoid hyperstabilized kinetochore–microtubules in mitosis remains elusive. Here, we show that kinetochore PLK1 kinase activity is modulated by SET7/9 via lysine methylation during early mitosis. The SET7/9-elicited dimethylation occurs at the Lys191 of PLK1, which tunes down its activity by limiting ATP utilization. Overexpression of the non-methylatable PLK1 mutant or chemical inhibition of SET7/9 methyltransferase activity resulted in mitotic arrest due to destabilized kinetochore–microtubule attachments. These data suggest that kinetochore PLK1 is essential for stable kinetochore–microtubule attachments and methylation by SET7/9 promotes dynamic kinetochore–microtubule attachments for accurate error correction. Our findings define a novel homeostatic regulation at the kinetochore that integrates protein phosphorylation and methylation with accurate chromosome segregation for maintenance of genomic stability.
基金the National Natural Science Foundation of China(81930112 and 82004089)National Key Research and Development Program of China(No.2018YFC1705900 and 2020YFE0202200)+1 种基金Distinguished professor of Liaoning Province(XLYC2002008)Dalian Science and Technology Leading Talents Project(2019RD15)for financial support.
文摘NEMO/IKKβcomplex is a central regulator of NF-κB signaling pathway,its dissociation has been considered to be an attractive therapeutic target.Herein,using a combined strategy of molecular pharmacological phenotyping,proteomics and bioinformatics analysis,Shikonin(SHK)is identified as a potential inhibitor of the IKKβ/NEMO complex.It destabilizes IKKβ/NEMO complex with IC_(50) of 174 nM,thereby significantly impairing the proliferation of colorectal cancer cells by suppressing the NF-κB pathway in vitro and in vivo.In addition,we also elucidated the potential target sites of SHK in the NEMO/IKKβcomplex.Our study provides some new insights for the development of potent small-molecule PPI inhibitors.
基金supported by National Natural Science Foundation of China(22137002[Y.D.],32071432[M.T.],81872102[H.J.])University Innovation Research Group Project of Chongqing(CXQT21016[Y.D.])+3 种基金High-Level Innovation Platform Project of Chongqing[Y.D.]Talent Program of Chongqing(CQYC202003053[Y.D.])The collaborative project of Chinese Academy of Sciences institutions and universities in Chongqing(HZ2021006[Y.D.])Innovative Research Team of High-Level Local Universities in Shanghai(SSMU-ZDCX20181202[M.T.]).
文摘Prostate cancer(PCa)is the second most prevalent malignancy in males across the world.A greater knowledge of the relationship between protein abundance and drug responses would benefit precision treatment for PCa.Herein,we establish 35 Chinese PCa primary cell models to capture specific characteristics among PCa patients,including gene mutations,mRNA/protein/surface protein distributions,and pharmaceutical responses.The multi-omics analyses identify Anterior Gradient 2(AGR2)as a pre-operative prognostic biomarker in PCa.Through the drug library screening,we describe crizotinib as a selective compound for malignant PCa primary cells.We further perform the pharmacoproteome analysis and identify 14,372 significant protein-drug correlations.Surprisingly,the diminished AGR2 enhances the inhibition activity of crizotinib via ALK/c-MET-AKT axis activation which is validated by PC3 and xenograft model.Our integrated multi-omics approach yields a comprehensive understanding of PCa biomarkers and pharmacological responses,allowing for more precise diagnosis and therapies.
基金supported by the Creative Research Group Project of National Natural Science Foundation of China(Grant No.21021004)the National Basic Research Program(973 Program)(Nos.2012CB910601,2012CB910101)the Analytical Method Innovation Program of MOST(No.2010IM030500)(H.Z.)。
文摘The human serum proteome is closely associated with the state of the body.Endogenous peptides derived from proteolytic enzymes cleaving on serum proteins are widely studied due to their potential application in disease-specific marker discovery.However,the reproducibility of peptidome analysis of endogenous peptides is significantly influenced by the proteolytic enzymes within body fluids,thereby limiting the clinical use of the endogenous peptides.We comprehensively investigated the N and C terminus of endogenous peptides using peptidomics.The cleavage site patterns of the N and C terminus and adjacent sites from all the identified endogenous peptides were highly conserved under different sample preparation conditions,including long-term incubation at 37℃ and pretreatment with repeated freeze-thaw cycles.Furthermore,a distinguishable cleavage site pattern was obtained when a different disease serum was analyzed.The conserved cleavage site pattern derived from proteolytic enzymes holds potential in highly specific disease diagnosis.
文摘In the process of collating the raw data,the authors noticed an inadvertent mistake occurred in Fig.3b that needs to be corrected after online publication of the article.In Fig.3b,as a result of an error in the graphics panel arrangement process,the band of NEMO was repeatedly inserted asβ-actin by mistake.The correct band is shown as below and in the updated Fig.3b.The correction did not affect any of our results or discussion as present in the original publication.We regret any inconvenience this has caused.
