Heat shock proteins(Hsps)are a family of abundantly expressed ATP-dependent chaperone proteins.Hsp90 is an eminent member of Hsp family.Thus far,two primary functions have been described for Hsp90:first,as a regulator...Heat shock proteins(Hsps)are a family of abundantly expressed ATP-dependent chaperone proteins.Hsp90 is an eminent member of Hsp family.Thus far,two primary functions have been described for Hsp90:first,as a regulator of conformational change of some protein kinases and nuclear hormone receptors,and the other as an indispensable factor in cellular stress response.Hsp90 has an essential number of interaction proteins since it participates in almost every biological process and its importance is self-evident.Hsp90 has an inextricable relationship in the pathogenesis of cancer,especially in the proliferation and irradiation of cancer cells,thus being a notable cancer target.Since the discovery of geldanamycin,the first inhibitor of Hsp90,from the bacterial species Streptomyces hygroscopicus,even more attention has been focused toward Hsp90.Many structure-based inhibitors of Hsp90 have been designed to develop an innovative method to defeat cancer.However,already designed inhibitors have various deficiencies,such as hepatotoxicity,poor aqueous solubility,instability,and non-ideal oral bioavailability.Based on the aforementioned reasons and to achieve an optimal performance and fewer side effects,we designed a novel inhibitor of Hsp90,called FS5,and resolved the crystal structure of the Hsp90^N-FS5 complex(1.65 A°,PDB code 5XRB).Furthermore,we compared the complexes Hsp90^N,Hsp90^N-GDM,and Hsp90^N-ATP and suggest that the inhibitor FS5 may compete with ATP for binding to Hsp90,which can be regarded as a potential strategy for the development of novel cancer drugs in the future.展开更多
DEAR EDITOR,Extracellular vesicles(EVs)are important for the transport of biologically active materials and for intercellular communication.As an exposed mucosa,amphibian skin participates in many essential physiologi...DEAR EDITOR,Extracellular vesicles(EVs)are important for the transport of biologically active materials and for intercellular communication.As an exposed mucosa,amphibian skin participates in many essential physiological processes.To date,however,little is known about EVs in amphibian skin.Here,we successfully isolated EVs from the skin secretions of Bombina maxima,and characterized the EVs using nanoparticle tracking,western blotting,and electron microscopy.展开更多
Diagnosis of mitochondrial DNA（mt DNA）disorders has traditionally been focused on the presence of point mutations and large deletions.However,deviations in mitochondrial abundance or mt DNA copy number can also be a...Diagnosis of mitochondrial DNA（mt DNA）disorders has traditionally been focused on the presence of point mutations and large deletions.However,deviations in mitochondrial abundance or mt DNA copy number can also be associated with many physiological and pathological conditions（Bai and Wong,2005）.展开更多
DEAR EDITOR,Pore-forming proteins(PFPs)are widely distributed among all kingdoms of life and can oligomerize to form pores/channels in membrane systems.Extracellular vesicles(EVs)circulate in all biological fluids and...DEAR EDITOR,Pore-forming proteins(PFPs)are widely distributed among all kingdoms of life and can oligomerize to form pores/channels in membrane systems.Extracellular vesicles(EVs)circulate in all biological fluids and can trigger biological responses at a distance,thus emerging as an additional means of intercellular communication through the release of cellular cargo,such as lipids,nucleic acids,metabolites,and proteins.To date,however,the mechanism by which EV contents are released into extracellular space remains unclear.In our previous study on toads(Bombina maxima),we identified a PFP and trefoil factor complexβγ-CAT(βγ-crystallin fused aerolysin-like protein(α-subunit)and trefoil factor(β-subunit)complex,hence namedβγ-CAT),which assembled under strict regulation in response to environmental cues.Here,we observed that the PFPβγ-CAT colocalized with EVs in the skin of B.maxima in vivo.Using small EVs(sEVs)isolated from B.maxima dermal fibroblast cells and murine fibroblast cells,we found thatβγ-CAT could specifically target and oligomerize on purified EVs,rather than disrupt membrane integrity,and promote the release of different metabolites.Our analysis revealed that a secretory PFP drove metabolite release from EVs through channel formation,providing novel clues for the delivery of EV content into extracellular space.展开更多
The mitochondrial organelle is crucial to the energy metabolism of the eukaryotic cell. Defects in mitochondrial function lie at the core of a wide range of disorders, including both rare primary mitochondrial disorde...The mitochondrial organelle is crucial to the energy metabolism of the eukaryotic cell. Defects in mitochondrial function lie at the core of a wide range of disorders, including both rare primary mitochondrial disorders and more common conditions such as Parkinson＇s disease and diabetes. Inherited defects in mitochondrial function can be found in both the nuclear genome and the mitochondrial genome, with the latter creating unique challenges in the treatment and understanding of disease passed on through the mitochondrial genome. In this review, we will describe the limited treatment regimens currently used to alleviate primary mitochondrial disorders, as well as the potential for emerging technologies（in particular, those involving direct manipulation of the mitochondrial genome） to more decisively treat this class of disease. We will also emphasize the critical parallels between primary mitochondrial disorders and more common ailments such as cancer and diabetes.展开更多
More than 90%of disease-and trait-associated human variants are noncoding.By systematically screening multiple large-scale studies,we compiled REVA,a manually curated database for over 11.8 million experimentally test...More than 90%of disease-and trait-associated human variants are noncoding.By systematically screening multiple large-scale studies,we compiled REVA,a manually curated database for over 11.8 million experimentally tested noncoding variants with expression-modulating potentials.We provided 2424 functional annotations that could be used to pinpoint the plausible regulatory mechanism of these variants.We further benchmarked multiple state-of-the-art computational tools and found that their limited sensitivity remains a serious challenge for effective large-scale analysis.REVA provides high-quality experimentally tested expression-modulating variants with extensive functional annotations,which will be useful for users in the noncoding variant community.REVA is freely available at http://reva.gao-lab.org.展开更多
Aging is characterized by a progressive deterioration of physiological integrity,leading to impaired functional ability and ultimately increased susceptibility to death.It is a major risk factor for chronic human dise...Aging is characterized by a progressive deterioration of physiological integrity,leading to impaired functional ability and ultimately increased susceptibility to death.It is a major risk factor for chronic human diseases,including cardiovascular disease,diabetes,neurological degeneration,and cancer.Therefore,the growing emphasis on “healthy aging” raises a series of important questions in life and social sciences.In recent years,there has been unprecedented progress in aging research,particularly the discovery that the rate of aging is at least partly controlled by evolutionarily conserved genetic pathways and biological processes.In an attempt to bring full-fledged understanding to both the aging process and age-associated diseases,we review the descriptive,conceptual,and interventive aspects of the landscape of aging composed of a number of layers at the cellular,tissue,organ,organ system,and organismal levels.展开更多
Angiogenic factor with G-patch and FHA domains 1(AGGF1) exhibits a dynamic distribution from the nucleus to the cytoplasm in endothelial cells during angiogenesis, but the biological significance and underlying mechan...Angiogenic factor with G-patch and FHA domains 1(AGGF1) exhibits a dynamic distribution from the nucleus to the cytoplasm in endothelial cells during angiogenesis, but the biological significance and underlying mechanism of this nucleocytoplasmic transport remains unknown. Here, we demonstrate that the dynamic distribution is essential for AGGF1 to execute its angiogenic function. To search the structural bases for this nucleocytoplasmic transport, we characterized three potential nuclear localization regions, one potential nuclear export region, forkhead-associated(FHA), and G-patch domains to determine their effects on nucleocytoplasmic transport and angiogenesis, and we show that AGGF1 remains intact during the dynamic subcellular distribution and the region from 260 to 288 amino acids acts as a signal for its nuclear localization. The distribution of AGGF1 in cytoplasm needs both FHA domain and 14-3-3α/β. Binding of AGGF1 via FHA domain to 14-3-3α/β is required to complete the transport. Thus, we for the first time established structural bases for the nucleocytoplasmic transport of AGGF1 and revealed that the FHA domain of AGGF1 is essential for its nucleocytoplasmic transport and angiogenesis.展开更多
Almost everyone is susceptible to the severe acute respiratorysyndrome coronavirus 2(SARS-CoV-2),an RNA virus,which cancause many symptoms and even death among high-risk individu-als[1,2].The main protease(M^(Pro),als...Almost everyone is susceptible to the severe acute respiratorysyndrome coronavirus 2(SARS-CoV-2),an RNA virus,which cancause many symptoms and even death among high-risk individu-als[1,2].The main protease(M^(Pro),also known as 3CL^(Pro))is a cys-teine protease essential for producing infectious virions and thusan attractive target for drug development.Up to now,many studiesusing either in silico ligand docking or drug discovery based onavailable structures have been performed to discover new MPTO.inhibiting agents[3.4].展开更多
Large-scale genome-wide association studies(GWAS)and expression quantitative trait locus(eQTL)studies have identified multiple non-coding variants associated with genetic diseases by affecting gene expression.However,...Large-scale genome-wide association studies(GWAS)and expression quantitative trait locus(eQTL)studies have identified multiple non-coding variants associated with genetic diseases by affecting gene expression.However,pinpointing causal variants effectively and efficiently remains a serious challenge.Here,we developed CARMEN,a novel algorithm to identify functional non-coding expression-modulating variants.Multiple evaluations demonstrated CARMEN’s superior performance over state-of-the-art tools.Applying CARMEN to GWAS and eQTL datasets further pinpointed several causal variants other than the reported lead single-nucleotide polymorphisms(SNPs).CARMEN scales well with the massive datasets,and is available online as a web server at http://carmen.gao-lab.org.展开更多
基金supported by the Open Project of Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases,Ministry of Education(No.XN201904)Gannan Medical University(No.QD201910)+1 种基金the National Natural Science Foundation of China(Nos.31770795 and 31971043)the Jiangxi Province Natural Science Foundation(No.20181ACB20014)
文摘Heat shock proteins(Hsps)are a family of abundantly expressed ATP-dependent chaperone proteins.Hsp90 is an eminent member of Hsp family.Thus far,two primary functions have been described for Hsp90:first,as a regulator of conformational change of some protein kinases and nuclear hormone receptors,and the other as an indispensable factor in cellular stress response.Hsp90 has an essential number of interaction proteins since it participates in almost every biological process and its importance is self-evident.Hsp90 has an inextricable relationship in the pathogenesis of cancer,especially in the proliferation and irradiation of cancer cells,thus being a notable cancer target.Since the discovery of geldanamycin,the first inhibitor of Hsp90,from the bacterial species Streptomyces hygroscopicus,even more attention has been focused toward Hsp90.Many structure-based inhibitors of Hsp90 have been designed to develop an innovative method to defeat cancer.However,already designed inhibitors have various deficiencies,such as hepatotoxicity,poor aqueous solubility,instability,and non-ideal oral bioavailability.Based on the aforementioned reasons and to achieve an optimal performance and fewer side effects,we designed a novel inhibitor of Hsp90,called FS5,and resolved the crystal structure of the Hsp90^N-FS5 complex(1.65 A°,PDB code 5XRB).Furthermore,we compared the complexes Hsp90^N,Hsp90^N-GDM,and Hsp90^N-ATP and suggest that the inhibitor FS5 may compete with ATP for binding to Hsp90,which can be regarded as a potential strategy for the development of novel cancer drugs in the future.
基金supported by the National Natural Science Foundation of China(31572268,U1602225,31872226)Yunling Scholar Program to Y.Z.,and the Basic Research of Yunnan Province(202101AT070292)to X.L.G.
文摘DEAR EDITOR,Extracellular vesicles(EVs)are important for the transport of biologically active materials and for intercellular communication.As an exposed mucosa,amphibian skin participates in many essential physiological processes.To date,however,little is known about EVs in amphibian skin.Here,we successfully isolated EVs from the skin secretions of Bombina maxima,and characterized the EVs using nanoparticle tracking,western blotting,and electron microscopy.
文摘Diagnosis of mitochondrial DNA（mt DNA）disorders has traditionally been focused on the presence of point mutations and large deletions.However,deviations in mitochondrial abundance or mt DNA copy number can also be associated with many physiological and pathological conditions（Bai and Wong,2005）.
基金supported by the National Natural Science Foundation of China (31572268, U1602225, 31872226)Yunling Scholar Program to Y.Z.Basic Research of Yunnan Province(202101AT070292) to X.L.G.
文摘DEAR EDITOR,Pore-forming proteins(PFPs)are widely distributed among all kingdoms of life and can oligomerize to form pores/channels in membrane systems.Extracellular vesicles(EVs)circulate in all biological fluids and can trigger biological responses at a distance,thus emerging as an additional means of intercellular communication through the release of cellular cargo,such as lipids,nucleic acids,metabolites,and proteins.To date,however,the mechanism by which EV contents are released into extracellular space remains unclear.In our previous study on toads(Bombina maxima),we identified a PFP and trefoil factor complexβγ-CAT(βγ-crystallin fused aerolysin-like protein(α-subunit)and trefoil factor(β-subunit)complex,hence namedβγ-CAT),which assembled under strict regulation in response to environmental cues.Here,we observed that the PFPβγ-CAT colocalized with EVs in the skin of B.maxima in vivo.Using small EVs(sEVs)isolated from B.maxima dermal fibroblast cells and murine fibroblast cells,we found thatβγ-CAT could specifically target and oligomerize on purified EVs,rather than disrupt membrane integrity,and promote the release of different metabolites.Our analysis revealed that a secretory PFP drove metabolite release from EVs through channel formation,providing novel clues for the delivery of EV content into extracellular space.
文摘The mitochondrial organelle is crucial to the energy metabolism of the eukaryotic cell. Defects in mitochondrial function lie at the core of a wide range of disorders, including both rare primary mitochondrial disorders and more common conditions such as Parkinson＇s disease and diabetes. Inherited defects in mitochondrial function can be found in both the nuclear genome and the mitochondrial genome, with the latter creating unique challenges in the treatment and understanding of disease passed on through the mitochondrial genome. In this review, we will describe the limited treatment regimens currently used to alleviate primary mitochondrial disorders, as well as the potential for emerging technologies（in particular, those involving direct manipulation of the mitochondrial genome） to more decisively treat this class of disease. We will also emphasize the critical parallels between primary mitochondrial disorders and more common ailments such as cancer and diabetes.
基金supported by funds from the National Key R&D Program of China(Grant No.2016YFC0901603)the National High Technology Research and Development Program of China(Grant No.2015AA020108)+2 种基金the State Key Laboratory of Protein and Plant Gene Research and the Beijing Advanced Innovation Center for Genomics(ICG)at Peking University,Chinasupported in part by the National Program for Support of Top-notch Young Professionalssupported by the High-performance Computing Platform of Peking University。
文摘More than 90%of disease-and trait-associated human variants are noncoding.By systematically screening multiple large-scale studies,we compiled REVA,a manually curated database for over 11.8 million experimentally tested noncoding variants with expression-modulating potentials.We provided 2424 functional annotations that could be used to pinpoint the plausible regulatory mechanism of these variants.We further benchmarked multiple state-of-the-art computational tools and found that their limited sensitivity remains a serious challenge for effective large-scale analysis.REVA provides high-quality experimentally tested expression-modulating variants with extensive functional annotations,which will be useful for users in the noncoding variant community.REVA is freely available at http://reva.gao-lab.org.
基金supported by the National Natural Science Foundation of China(31871380,32000500,32070730,32170756,32170804,81330008,81671377,81725010,81725010,81872874,81921006,81922027,81971312,81991512,82030041,82103167,82122024,82125009,82125011,82130044,91749126,91949101,91949207,92049302)the National Key Research and Development Program of China(2017YFA0506400,2018YFA0800200,2018YFA0800700,2018YFA0900200,2018YFC2000100,2018YFC2000400,2018YFE-0203700,20192ACB70002,2019YFA0802202,2020YFA0113400,2020YFA0803401,2020YFA0804000,2020YFC2002800,2020YFC-2002900,2021ZD0202401)+11 种基金the Strategic Priority Research Program of the Chinese Academy of Sciences(XDA16010100,XDA16010603,XDA16020400,XDB29020000,XDB39000000,XDB39000000,XDB39030300)the China Association for Science and Technology(2021QNRC001)the Beijing Municipal Science and Technology Commission(Z200022)the Natural Science Foundation of Shanghai(21JC1406400)the Key Programs of the Jiangxi ProvinceChina(20192ACB70002)the“Shu Guang”Project supported by the Shanghai Municipal Education Commission and Shanghai Education Development Foundation(19SG18)the Shanghai Sailing Program(22YF1434300)the Research Project of Joint Laboratory of University of Science and Technology of China and Anhui Mental Health Center(2019LH03)the Fundamental Research Funds for the Central Universities(WK2070210004)the Young Elite Scientists Sponsorship Program by China Association for Science and Technology(YESS20210002)the Youth Innovation Promotion Association of Chinese Academy of Sciences(2022083)。
文摘Aging is characterized by a progressive deterioration of physiological integrity,leading to impaired functional ability and ultimately increased susceptibility to death.It is a major risk factor for chronic human diseases,including cardiovascular disease,diabetes,neurological degeneration,and cancer.Therefore,the growing emphasis on “healthy aging” raises a series of important questions in life and social sciences.In recent years,there has been unprecedented progress in aging research,particularly the discovery that the rate of aging is at least partly controlled by evolutionarily conserved genetic pathways and biological processes.In an attempt to bring full-fledged understanding to both the aging process and age-associated diseases,we review the descriptive,conceptual,and interventive aspects of the landscape of aging composed of a number of layers at the cellular,tissue,organ,organ system,and organismal levels.
基金This work was supported by grants from the National Natural Science Foundation of China(30730047,81070262,81130003 and 81630034).
文摘Angiogenic factor with G-patch and FHA domains 1(AGGF1) exhibits a dynamic distribution from the nucleus to the cytoplasm in endothelial cells during angiogenesis, but the biological significance and underlying mechanism of this nucleocytoplasmic transport remains unknown. Here, we demonstrate that the dynamic distribution is essential for AGGF1 to execute its angiogenic function. To search the structural bases for this nucleocytoplasmic transport, we characterized three potential nuclear localization regions, one potential nuclear export region, forkhead-associated(FHA), and G-patch domains to determine their effects on nucleocytoplasmic transport and angiogenesis, and we show that AGGF1 remains intact during the dynamic subcellular distribution and the region from 260 to 288 amino acids acts as a signal for its nuclear localization. The distribution of AGGF1 in cytoplasm needs both FHA domain and 14-3-3α/β. Binding of AGGF1 via FHA domain to 14-3-3α/β is required to complete the transport. Thus, we for the first time established structural bases for the nucleocytoplasmic transport of AGGF1 and revealed that the FHA domain of AGGF1 is essential for its nucleocytoplasmic transport and angiogenesis.
基金supported by the Thousand Young Talents Program of Chinathe National Natural Science Foundation of China(31770795,81974514,21961003+8 种基金31971043)the Jiangxi Provincial Natural Science Foundation(20181ACB20014 and20192BAB205114)the Open Project of Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases,Ministry of Education(XN201904)Gannan Medical University(QD201910)Jiangxi"Double Thousand Plan"the Foreign Talent Project of Jiangxi ProvinceTalent Project of Jiangxi ProvinceShenzhen Fundamental Research ProgramGanzhou COVID-19 Emergency Research Project。
文摘Almost everyone is susceptible to the severe acute respiratorysyndrome coronavirus 2(SARS-CoV-2),an RNA virus,which cancause many symptoms and even death among high-risk individu-als[1,2].The main protease(M^(Pro),also known as 3CL^(Pro))is a cys-teine protease essential for producing infectious virions and thusan attractive target for drug development.Up to now,many studiesusing either in silico ligand docking or drug discovery based onavailable structures have been performed to discover new MPTO.inhibiting agents[3.4].
基金supported by funds from the National Key R&D Program of China(Grant No.2016YFC0901603)the National High-tech R&D Program of China(Grant No.2015AA020108)+1 种基金as well as the State Key Laboratory of Protein and Plant Gene Research and the Beijing Advanced Innovation Center for Genomics(ICG)at Peking Universitysupported in part by the National Program for Support of Top-notch Young Professionals。
文摘Large-scale genome-wide association studies(GWAS)and expression quantitative trait locus(eQTL)studies have identified multiple non-coding variants associated with genetic diseases by affecting gene expression.However,pinpointing causal variants effectively and efficiently remains a serious challenge.Here,we developed CARMEN,a novel algorithm to identify functional non-coding expression-modulating variants.Multiple evaluations demonstrated CARMEN’s superior performance over state-of-the-art tools.Applying CARMEN to GWAS and eQTL datasets further pinpointed several causal variants other than the reported lead single-nucleotide polymorphisms(SNPs).CARMEN scales well with the massive datasets,and is available online as a web server at http://carmen.gao-lab.org.
