RNA binding proteins(RBPs) are a crucial class of proteins that interact with RNA and play a key role in various biological process.Deficiencies or abnormalities of RBPs are closely linked to the occurrence and progre...RNA binding proteins(RBPs) are a crucial class of proteins that interact with RNA and play a key role in various biological process.Deficiencies or abnormalities of RBPs are closely linked to the occurrence and progression of numerous diseases,making RBPs potential therapeutic targets.However,the limited tissue penetration of 254 nm UV irradiation makes it difficult to efficiently crosslink weak and dynamic RNA-protein interactions in mammal tissues.Additionally,RNA degradation in metal catalyzed click reaction further hinders the enrichment of RNA-protein complexes(RPCs).Due to these inherent limitations,globally profiling the RNA binding proteome in mammal organs has long been a challenge.Herein,we proposed a novel method,which utilized a dual crosslinking with formaldehyde and 254 nm UV irradiation,metabolic labeling and metal-free thiol-yne click reaction to enable large-scale enrichment and identification of RBPs in mouse liver,called FTYc_UV.In this method,formaldehyde is first used to crosslink the crude RNA-protein complexes(cRPCs) in situ to address the problem of poor tissue penetration of 254 nm UV irradiation.Furthermore,this method integrates metabolic labeling with a metal-free thiol-yne click reaction to achieve non-destructive RNA tagging.After specifically RNA-RBPs crosslinking by 254 nm UV irradiation in tissue lysates,formaldehyde decrosslinking is employed to remove non-specific proteins,leading to effective enrichment of RPCs from mouse liver and thereby overcoming the poor specificity of formaldehyde crosslinking.Application of FTYc_UV in mouse liver successfully identified over 1600 RBPs covering approximately 75 % of previously reported RBPs.Furthermore,420 candidate RBPs,including 151metabolic enzymes,were also obtained,demonstrating the sensitivity of FTYc_UV and the potential of this method for in-depth exploration of RNA-protein interactions in biological and clinical research.展开更多
Although many proteins have been found to exist as homooligomers in nature,the biological significance and mechanism for its occurring is far from clear.We have examined a variety of proteins,as represented by Hsp16.3...Although many proteins have been found to exist as homooligomers in nature,the biological significance and mechanism for its occurring is far from clear.We have examined a variety of proteins,as represented by Hsp16.3,IbpB,DegP,truncated hemoglobin,RbsD,and IdeR,that exhibit homooligomerization.Our data revealed that such a process of reversible protein-protein interaction can be utilized to effectively modulate the biological activities of various proteins,mostly in responding to fluctuations of environmental conditions.It appears that protein homo-oligomerization can be considered as the fourth general way(after allostery,covalent modification and proteolytic cleavage)through which protein activities can be effectively regulated in an immediate manner.展开更多
Radiological or nuclear accidents can lead to serious outcomes for individuals exposed to ionizing radiation,with health effects that are either acute or delayed,deterministic or stochastic,depending on the effective ...Radiological or nuclear accidents can lead to serious outcomes for individuals exposed to ionizing radiation,with health effects that are either acute or delayed,deterministic or stochastic,depending on the effective dose of exposure.Mechanistically,ionizing radiation can inflict damage either directly on DNA or through oxidative stress,which may trigger a cascade of damages to tissues and organs.The development of effective radiation medical countermeasures is an unmet need and should be a top priority in preparing for radiation emergencies.This paper aims to address the critical questions of whether current countermeasures are available,what additional measures are needed,and what actions can be taken to enhance the development of radiation medical countermeasures from a systematic perspective.展开更多
The cell surface membrane proteome is a class of proteins encoded by ~25% of all protein-coding genes in living organisms and plays a key role in mediating communication between the cells and their surrounding environ...The cell surface membrane proteome is a class of proteins encoded by ~25% of all protein-coding genes in living organisms and plays a key role in mediating communication between the cells and their surrounding environment. However, most cell surface membrane proteins(CSMPs) are naturally expressed at very low levels compared with intracellular proteins. The difficulties in their purification with high specificity further hinder the understanding of their structure and function. In this study, we developed a new photolabeling probe to achieve efficient tagging and facile enrichment of the CSMPs. The probe is composed of a lipid tail for cell surface localization, a polyethylene glycol(PEG) spacer for increased water solubility, two 4-(N-maleimido)benzophenone(MBP) groups for UV-active tagging of the CSMPs, and a biotin tag for subsequent isolation. Application of this photolabeling probe resulted in the successful enrichment and identification of 3098 annotated CSMPs in HT22 cells with close to 70% selectivity. The proposed photolabeling probe and enrichment strategy were demonstrated to be a powerful method for deep cell surface proteome profiling, representing one of the largest groups of current drug targets.展开更多
Three-dimensional(3 D)reconstruction of icosahedral viruses has played a crucial role in the development of cryoelectron microscopy single-particle reconstruction,with many cryo-electron microscopy techniques first es...Three-dimensional(3 D)reconstruction of icosahedral viruses has played a crucial role in the development of cryoelectron microscopy single-particle reconstruction,with many cryo-electron microscopy techniques first established for structural studies of icosahedral viruses,owing to their high symmetry and large mass.This review summarizes the computational methods for icosahedral and symmetry-mismatch reconstruction of viruses,as well as the likely challenges and bottlenecks in virus reconstruction,such as symmetry mismatch reconstruction,contrast transformation function(CTF)correction,and particle distortion.展开更多
Objective:To elucidate the biological basis of the heart qi deficiency(HQD)pattern,an in-depth understanding of which is essential for improving clinical herbal therapy.Methods: We predicted and characterized HQD patt...Objective:To elucidate the biological basis of the heart qi deficiency(HQD)pattern,an in-depth understanding of which is essential for improving clinical herbal therapy.Methods: We predicted and characterized HQD pattern genes using the new strategy,TCM-HIN2Vec,which involves heterogeneous network embedding and transcriptomic experiments.First,a heterogeneous network of traditional Chinese medicine(TCM)patterns was constructed using public databases.Next,we predicted HQD pattern genes using a heterogeneous network-embedding algorithm.We then analyzed the functional characteristics of HQD pattern genes using gene enrichment analysis and examined gene expression levels using RNA-seq.Finally,we identified TCM herbs that demonstrated enriched interactions with HQD pattern genes via herbal enrichment analysis.Results: Our TCM-HIN2Vec strategy revealed that candidate genes associated with HQD pattern were significantly enriched in energy metabolism,signal transduction pathways,and immune processes.Moreover,we found that these candidate genes were significantly differentially expressed in the transcriptional profile of mice model with heart failure with a qi deficiency pattern.Furthermore,herbal enrichment analysis identified TCM herbs that demonstrated enriched interactions with the top 10 candidate genes and could potentially serve as drug candidates for treating HQD.Conclusion: Our results suggested that TCM-HIN2Vec is capable of not only accurately identifying HQD pattern genes,but also deciphering the basis of HQD pattern.Furthermore our finding indicated that TCM-HIN2Vec may be further expanded to develop other patterns,leading to a new approach aimed at elucidating general TCM patterns and developing precision medicine.展开更多
Osteoarthritis(OA) is an age-related disorder that is strongly associated with chondrocyte senescence. The causal link between disruptive PTEN/Akt signaling and chondrocyte senescence and the underlying mechanism are ...Osteoarthritis(OA) is an age-related disorder that is strongly associated with chondrocyte senescence. The causal link between disruptive PTEN/Akt signaling and chondrocyte senescence and the underlying mechanism are unclear. In this study, we found activated Akt signaling in human OA cartilage as well as in a mouse OA model with surgical destabilization of the medial meniscus.Genetic mouse models mimicking sustained Akt signaling in articular chondrocytes via PTEN deficiency driven by either Col2a1-Cre or Col2a1-Cre^(ERT2) developed OA, whereas restriction of Akt signaling reversed the OA phenotypes in PTEN-deficient mice.Mechanistically, prolonged activation of Akt signaling caused an accumulation of reactive oxygen species and triggered chondrocyte senescence as well as a senescence-associated secretory phenotype, whereas chronic administration of the antioxidant N-acetylcysteine suppressed chondrocyte senescence and mitigated OA progression in PTEN-deficient mice. Therefore,inhibition of Akt signaling by PTEN is required for the maintenance of articular cartilage. Disrupted Akt signaling in articular chondrocytes triggers oxidative stress-induced chondrocyte senescence and causes OA.展开更多
Background:Toll-like receptor 5(TLR5)-mediated pathways play critical roles in regulating the hepatic immune response and show hepatoprotective effects in mouse models of hepatic diseases.However,the role of TLR5 in e...Background:Toll-like receptor 5(TLR5)-mediated pathways play critical roles in regulating the hepatic immune response and show hepatoprotective effects in mouse models of hepatic diseases.However,the role of TLR5 in experimental models of liver regeneration has not been reported.This study aimed to investigate the role of TLR5 in partial hepatectomy(PHx)-induced liver regeneration.Methods:We performed 2/3 PHx in wild-type(WT)mice,TLR5 knockout mice,or TLR5 agonist CBLB502 treated mice,as a model of liver regeneration.Bacterial flagellin content was measured with ELISA,and hepatic TLR5 expression was determined with quantitative PCR analyses and flow cytometry.To study the effects of TLR5 on hepatocyte proliferation,we analyzed bromodeoxyuridine(BrdU)incorporation and proliferating cell nuclear antigen(PCNA)expression with immunohistochemistry(IHC)staining.The effects of TLR5 during the priming phase of liver regeneration were examined with quantitative PCR analyses of immediate early gene mRNA levels,and with Western blotting analysis of hepatic NF-κB and STAT3 activation.Cytokine and growth factor production after PHx were detected with real-time PCR and cytometric bead array(CBA)assays.Oil Red O staining and hepatic lipid concentrations were analyzed to examine the effect of TLR5 on hepatic lipid accumulation after PHx.Results:The bacterial flagellin content in the serum and liver increased,and the hepatic TLR5 expression was significantly up-regulated in WT mice after PHx.TLR5-deficient mice exhibited diminished numbers of BrdU-and PCNA-positive cells,suppressed immediate early gene expression,and decreased cytokine and growth factor production.Moreover,PHx-induced hepatic NF-κB and STAT3 activation was inhibited in Tlr5–/–mice,as compared with WT mice.Consistently,the administration of CBLB502 significantly promoted PHx-mediated hepatocyte proliferation,which was correlated with enhanced production of proinflammatory cytokines and the recruitment of macrophages and neutrophils in the liver.Furthermore,Tlr5–/–mice displayed significantly lower hepatic lipid concentrations and smaller Oil Red O positive areas than those in control mice after PHx.Conclusions:We reveal that TLR5 activation contributes to the initial events of liver regeneration after PHx.Our findings demonstrate that TLR5 signaling positively regulates liver regeneration and suggest the potential of TLR5 agonist to promote liver regeneration.展开更多
The rapid development of genome editing technology has brought major breakthroughs in the fields of life science and medicine. In recent years, the clustered regularly interspaced short palindromic repeats(CRISPR)-bas...The rapid development of genome editing technology has brought major breakthroughs in the fields of life science and medicine. In recent years, the clustered regularly interspaced short palindromic repeats(CRISPR)-based genome editing toolbox has been greatly expanded, not only with emerging CRISPR-associated protein(Cas) nucleases, but also novel applications through combination with diverse effectors. Recently, transposon-associated programmable RNA-guided genome editing systems have been uncovered, adding myriads of potential new tools to the genome editing toolbox. CRISPR-based genome editing technology has also revolutionized cardiovascular research. Here we first summarize the advances involving newly identified Cas orthologs, engineered variants and novel genome editing systems, and then discuss the applications of the CRISPR-Cas systems in precise genome editing, such as base editing and prime editing. We also highlight recent progress in cardiovascular research using CRISPR-based genome editing technologies, including the generation of genetically modified in vitro and animal models of cardiovascular diseases(CVD) as well as the applications in treating different types of CVD. Finally, the current limitations and future prospects of genome editing technologies are discussed.展开更多
Posttranslational modifications of antibody products affect their stability,charge distribution,and drug activity and are thus a critical quality attribute.The comprehensive mapping of antibody modifications and diffe...Posttranslational modifications of antibody products affect their stability,charge distribution,and drug activity and are thus a critical quality attribute.The comprehensive mapping of antibody modifications and different charge isomers(CIs)is of utmost importance,but is challenging.We intended to quantitatively characterize the posttranslational modification status of CIs of antibody drugs and explore the impact of posttranslational modifications on charge heterogeneity.The CIs of antibodies were fractionated by strong cation exchange chromatography and verified by capillary isoelectric focusing-whole column imaging detection,followed by stepwise structural characterization at three levels.First,the differences between CIs were explored at the intact protein level using a top-down mass spectrometry approach;this showed differences in glycoforms and deamidation status.Second,at the peptide level,common modifications of oxidation,deamidation,and glycosylation were identified.Peptide mapping showed nonuniform deamidation and glycoform distribution among CIs.In total,10 N-glycoforms were detected by peptide mapping.Finally,an in-depth analysis of glycan variants of CIs was performed through the detection of enriched glycopeptides.Qualitative and quantitative analyses demonstrated the dynamics of 24 N-glycoforms.The results revealed that sialic acid modification is a critical factor accounting for charge heterogeneity,which is otherwise missed in peptide mapping and intact molecular weight analyses.This study demonstrated the importance of the comprehensive analyses of antibody CIs and provides a reference method for the quality control of biopharmaceutical analysis.展开更多
The Chinese Academy of Sciences held its 7th forum on frontiers of Science and Technology, April 12-13, 2012, in the academy hall of the Chinese Academy of Sciences. The Forum was organized by the Life Science and Med...The Chinese Academy of Sciences held its 7th forum on frontiers of Science and Technology, April 12-13, 2012, in the academy hall of the Chinese Academy of Sciences. The Forum was organized by the Life Science and Medicine Division and co-organized by Academy of Military Medical Sciences and Science China Press. The theme of the 7th Forum was ＂Lifeomics and Translational Medicine＂,展开更多
Drug discovery is a crucial part of human healthcare and has dramatically benefited human lifespan and life quality in recent centuries, however, it is usually time-and effort-consuming. Structural biology has been de...Drug discovery is a crucial part of human healthcare and has dramatically benefited human lifespan and life quality in recent centuries, however, it is usually time-and effort-consuming. Structural biology has been demonstrated as a powerful tool to accelerate drug development. Among different techniques, cryo-electron microscopy(cryo-EM) is emerging as the mainstream of structure determination of biomacromolecules in the past decade and has received increasing attention from the pharmaceutical industry. Although cryo-EM still has limitations in resolution, speed and throughput, a growing number of innovative drugs are being developed with the help of cryo-EM. Here, we aim to provide an overview of how cryo-EM techniques are applied to facilitate drug discovery. The development and typical workflow of cryo-EM technique will be briefly introduced, followed by its specific applications in structure-based drug design, fragment-based drug discovery, proteolysis targeting chimeras, antibody drug development and drug repurposing. Besides cryo-EM, drug discovery innovation usually involves other state-of-the-art techniques such as artificial intelligence(AI), which is increasingly active in diverse areas. The combination of cryo-EM and AI provides an opportunity to minimize limitations of cryo-EM such as automation, throughput and interpretation of mediumresolution maps, and tends to be the new direction of future development of cryo-EM. The rapid development of cryo-EM will make it as an indispensable part of modern drug discovery.展开更多
The advent of gene editing represents one of the most transformative breakthroughs in life science,making genome manipulation more accessible than ever before.While traditional CRISPR/Cas-based gene editing,which invo...The advent of gene editing represents one of the most transformative breakthroughs in life science,making genome manipulation more accessible than ever before.While traditional CRISPR/Cas-based gene editing,which involves double-strand DNA breaks(DSBs),excels at gene disruption,it is less effective for accurate gene modification.The limitation arises because DSBs are primarily repaired via non-homologous end joining(NHEJ),which tends to introduce indels at the break site.While homology directed repair(HDR)can achieve precise editing when a donor DNA template is provided,the reliance on DSBs often results in unintended genome damage.HDR is restricted to specific cell cycle phases,limiting its application.Currently,gene editing has evolved to unprecedented levels of precision without relying on DSB and HDR.The development of innovative systems,such as base editing,prime editing,and CRISPR-associated transposases(CASTs),now allow for precise editing ranging from single nucleotides to large DNA fragments.Base editors(BEs)enable the direct conversion of one nucleotide to another,and prime editors(PEs)further expand gene editing capabilities by allowing for the insertion,deletion,or alteration of small DNA fragments.The CAST system,a recent innovation,allows for the precise insertion of large DNA fragments at specific genomic locations.In recent years,the optimization of these precise gene editing tools has led to significant improvements in editing efficiency,specificity,and versatility,with advancements such as the creation of base editors for nucleotide transversions,enhanced prime editing systems for more efficient and precise modifications,and refined CAST systems for targeted large DNA insertions,expanding the range of applications for these tools.Concurrently,these advances are complemented by significant improvements in in vivo delivery methods,which have paved the way for therapeutic application of precise gene editing tools.Effective delivery systems are critical for the success of gene therapies,and recent developments in both viral and non-viral vectors have improved the efficiency and safety of gene editing.For instance,adeno-associated viruses(AAVs)are widely used due to their high transfection efficiency and low immunogenicity,though challenges such as limited cargo capacity and potential for immune responses remain.Non-viral delivery systems,including lipid nanoparticles(LNPs),offer an alternative with lower immunogenicity and higher payload capacity,although their transfection efficiency can be lower.The therapeutic potential of these precise gene editing technologies is vast,particularly in treating genetic disorders.Preclinical studies have demonstrated the effectiveness of base editing in correcting genetic mutations responsible for diseases such as cardiomyopathy,liver disease,and hereditary hearing loss.These technologies promise to treat symptoms and potentially cure the underlying genetic causes of these conditions.Meanwhile,challenges remain,such as optimizing the safety and specificity of gene editing tools,improving delivery systems,and overcoming off-target effects,all of which are critical for their successful application in clinical settings.In summary,the continuous evolution of precise gene editing technologies,combined with advancements in delivery systems,is driving the field toward new therapeutic applications that can potentially transform the treatment of genetic disorders by targeting their root causes.展开更多
Elongation factor 4（EF4） is one of the highly conserved translational GTPases, whose functions are largely unknown. Structures of EF4 bound ribosomal PRE-translocation and POST-translocation complexes have both been...Elongation factor 4（EF4） is one of the highly conserved translational GTPases, whose functions are largely unknown. Structures of EF4 bound ribosomal PRE-translocation and POST-translocation complexes have both been visualized. On top of cellular, structural, and biochemical studies, several controversial models have been raised to rationalize functions of EF4. However, how EF4 modulates elongation through its interactions with ribosomes has not been revealed. Here, using single-molecule fluorescence resonance energy transfer assays, we directly captured short-lived EF4·GTP bound ribosomal PRE and POST translocation complexes, which may adopt slightly different conformations from structures prepared using GDP, GDPNP, or GDPCP. Furthermore, we revealed that EF4·GTP severely impairs delivery of aminoacyl-tRNA into the A-site of the ribosome and moderately accelerates translocation. We proposed that functions of EF4 are to slow overall elongation and to stall majority of ribosomes in POST states under stress conditions.展开更多
Endothelial cells(ECs)form a single cell layer that lines the inner surface of all blood and lymphatic vessels,acting as the barrier between vessels and underlying tissues.ECs are not only responsible for the flow of ...Endothelial cells(ECs)form a single cell layer that lines the inner surface of all blood and lymphatic vessels,acting as the barrier between vessels and underlying tissues.ECs are not only responsible for the flow of substances and fluid into and out of tissues but are also involved in many processes,such as coagulation,fibrinolysis,and regulation of vascular tone and inflammation.展开更多
After decades of development,protein and peptide drugs have now grown into a major drug class in the marketplace.Target identification and validation are crucial for the discovery of protein and peptide drugs,and bioi...After decades of development,protein and peptide drugs have now grown into a major drug class in the marketplace.Target identification and validation are crucial for the discovery of protein and peptide drugs,and bioinformatics prediction of targets based on the characteristics of known target proteins will help improve the efficiency and success rate of target selection.However,owing to the developmental history in the pharmaceutical industry,previous systematic exploration of the target spaces has mainly focused on traditional small-molecule drugs,while studies related to protein and peptide drugs are lacking.Here,we systematically explore the target spaces in the human genome specifically for protein and peptide drugs.Compared with other proteins,both successful protein and peptide drug targets have many special characteristics,and are also significantly different from those of small-molecule drugs in many aspects.Based on these features,we develop separate effective genome-wide target prediction models for protein and peptide drugs.Finally,a user-friendly web server,Predictor Of Protein and Pept Ide drugs’therapeutic Targets(POPPIT)(http://poppit.ncpsb.org.cn/),is established,which provides not only target prediction specifically for protein and peptide drugs but also abundant annotations for predicted targets.展开更多
Copper ions can promote amyloid diseases that are associated with amyloid peptides, such as type 2 diabetes(T2D),Alzheimer's disease(AD), Parkinson's disease(PD), and amyotrophic lateral sclerosis(ALS). Howeve...Copper ions can promote amyloid diseases that are associated with amyloid peptides, such as type 2 diabetes(T2D),Alzheimer's disease(AD), Parkinson's disease(PD), and amyotrophic lateral sclerosis(ALS). However, the underlying molecular mechanism remains obscure. Here we present that Cu^(2+)is able to specifically bind to the backbone of T2D related human islet amyloid polypeptide(hIAPP) by forming a ring structure, which causes the reduction of Cu^(2+)to Cu^(+) to produce reactive oxygen species(ROS) and the modulation of hIAPP aggregation. Nuclear magnetic resonance spectroscopy showed that Cu^(2+)bound to the backbone of a turn region, His18-Ser21, which is critical for hIAPP aggregation.Ab initio calculations and x-ray absorption fine structure analyses revealed that Cu^(2+)simultaneously bound with both the amide nitrogen and carbonyl oxygen on the peptide backbone, resulting in a ring structure, and causing the reduction of Cu^(2+)to Cu^(+) to form a hIAPP-Cu^(+) complex. 2′,7′-dichlorodihydrofluorescin diacetate fluorescence measurements further indicated that this complex led to enhanced ROS levels in rat insulinoma cells. Additionally, thioflavin T fluorescence and atomic force microscopy measurements denoted that the backbone-Cu ring structure largely modulated hIAPP aggregation,including the inhibition of hIAPP fibrillation and the promotion of peptide oligomerization. These findings shed new light on the molecular mechanism of Cu^(2+)-induced amyloid toxicity involving both the enhancement of ROS and the modulation of hIAPP aggregation.展开更多
Stroke is one of the top causes of death and disability worldwide,and its pathogenesis and mechanism have not been fully elucidated.Several agents have shown protective effects against stroke in animal models;however,...Stroke is one of the top causes of death and disability worldwide,and its pathogenesis and mechanism have not been fully elucidated.Several agents have shown protective effects against stroke in animal models;however,few studies have shown obvious effects in clinical practice.This might be due to differences in brain structure and physiological function between humans and rodents.In this study,we established a hypoxic stroke model in human-induced pluripotent stem cell(hiPSC)-derived brain organoids to simulate the hypoxic stroke caused by ischemia.Then,by combining proteomics,single-cell transcriptome analysis,and histopathological analysis,a significant increase of three types of astrocytes was identified and they showed different responses to hypoxic environments;also the main type of astrocyte that cause brain tissue hyperplasia in ischemia brains was iden-tified.In addition,the cortical excitatory neurons had signs of apoptosis and aging after hypoxia both in vivo and in vitro.Most importantly,we identified a possible role of a traditional Chinese medicine formula called DengZhanShengMai capsule in ischemic and hypoxic stroke treatment through regulation of lipid metabolism related biological functions.These results indicate that the combination of brain organoids and multiomics method is helpful for developing a new strategy to direct study stroke,and could provide a promising platform for drug screening of stroke in the future.展开更多
Laser shaping was introduced to maskless projection soft lithography by using digital micro-mirror device (DMD). The predesigned intensity pattern was imprinted onto the DMD and the input laser beam with a Gaussian or...Laser shaping was introduced to maskless projection soft lithography by using digital micro-mirror device (DMD). The predesigned intensity pattern was imprinted onto the DMD and the input laser beam with a Gaussian or quasi-Gaussian distribution will carry the pattern on DMD to etch the resin. It provides a method of precise control of laser beam shapes and?photon-induced curing behavior of resin. This technology provides an accurate micro-fabrication of microstructures used for micro-systems. As a virtual mask generator and a binary-amplitude spatial light modulator, DMD is equivalent to the masks in the conventional exposure system. As the virtual masks and shaped laser beam can be achieved flexibly, it is a good method of precision soft lithography for 2D/3D microstructures.展开更多
Salivary proteins serve multifaceted roles in maintaining oral health and hold significant potential for diagnosing and monitoring diseases due to the non-invasive nature of saliva sampling.However,the clinical utilit...Salivary proteins serve multifaceted roles in maintaining oral health and hold significant potential for diagnosing and monitoring diseases due to the non-invasive nature of saliva sampling.However,the clinical utility of current saliva biomarker studies is limited by the lack of reference intervals(RIs)to correctly interpret the testing result.Here,we developed a rapid and robust saliva proteome profiling workflow,obtaining coverage of>1,200 proteins from a 50-μL unstimulated salivary flow with 30 min gradients.With the workflow,we investigated protein variation in a cohort of 1,743 healthy individuals.The significant differences in non-linear saliva proteomes among age groups resulted in the establishment of age-related RIs covering 1,123 salivary protein variations.We then utilized a cohort of 30 epilepsy patients as a case study to illustrate the practical application of RIs in identifying disease-enriched outlier proteins,elucidating their cellular origins,determining disease diagnosis,and visualizing outlier proteins in each epilepsy patient.Our study showed the classification model based on the RI achieved PR-AUC of 0.815(95%CI:0.813–0.826).Additionally,we validated these results in an independent test set.Furthermore,the epilepsy cohort could be further stratified into 2 major subtypes,with one subtype characterized by disrupted metabolic proteins and containing mostly Focal Cortical Dysplasia(FCD)type III epilepsy patients.Overall,our study provided a proof-of-principle workflow for the use of salivary proteome for health monitoring,epilepsy diagnosis and subtyping.展开更多
基金financial support from the National Key R&D Program of China (No.2021YFA1302604)Scientific and technological innovation project of China Academy of Chinese Medical Sciences (No.CI2021B017)China Postdoctoral Science Foundation (No.2023T160727)。
文摘RNA binding proteins(RBPs) are a crucial class of proteins that interact with RNA and play a key role in various biological process.Deficiencies or abnormalities of RBPs are closely linked to the occurrence and progression of numerous diseases,making RBPs potential therapeutic targets.However,the limited tissue penetration of 254 nm UV irradiation makes it difficult to efficiently crosslink weak and dynamic RNA-protein interactions in mammal tissues.Additionally,RNA degradation in metal catalyzed click reaction further hinders the enrichment of RNA-protein complexes(RPCs).Due to these inherent limitations,globally profiling the RNA binding proteome in mammal organs has long been a challenge.Herein,we proposed a novel method,which utilized a dual crosslinking with formaldehyde and 254 nm UV irradiation,metabolic labeling and metal-free thiol-yne click reaction to enable large-scale enrichment and identification of RBPs in mouse liver,called FTYc_UV.In this method,formaldehyde is first used to crosslink the crude RNA-protein complexes(cRPCs) in situ to address the problem of poor tissue penetration of 254 nm UV irradiation.Furthermore,this method integrates metabolic labeling with a metal-free thiol-yne click reaction to achieve non-destructive RNA tagging.After specifically RNA-RBPs crosslinking by 254 nm UV irradiation in tissue lysates,formaldehyde decrosslinking is employed to remove non-specific proteins,leading to effective enrichment of RPCs from mouse liver and thereby overcoming the poor specificity of formaldehyde crosslinking.Application of FTYc_UV in mouse liver successfully identified over 1600 RBPs covering approximately 75 % of previously reported RBPs.Furthermore,420 candidate RBPs,including 151metabolic enzymes,were also obtained,demonstrating the sensitivity of FTYc_UV and the potential of this method for in-depth exploration of RNA-protein interactions in biological and clinical research.
文摘Although many proteins have been found to exist as homooligomers in nature,the biological significance and mechanism for its occurring is far from clear.We have examined a variety of proteins,as represented by Hsp16.3,IbpB,DegP,truncated hemoglobin,RbsD,and IdeR,that exhibit homooligomerization.Our data revealed that such a process of reversible protein-protein interaction can be utilized to effectively modulate the biological activities of various proteins,mostly in responding to fluctuations of environmental conditions.It appears that protein homo-oligomerization can be considered as the fourth general way(after allostery,covalent modification and proteolytic cleavage)through which protein activities can be effectively regulated in an immediate manner.
基金Beijing Nova Program,Grant/Award Number:20220484086。
文摘Radiological or nuclear accidents can lead to serious outcomes for individuals exposed to ionizing radiation,with health effects that are either acute or delayed,deterministic or stochastic,depending on the effective dose of exposure.Mechanistically,ionizing radiation can inflict damage either directly on DNA or through oxidative stress,which may trigger a cascade of damages to tissues and organs.The development of effective radiation medical countermeasures is an unmet need and should be a top priority in preparing for radiation emergencies.This paper aims to address the critical questions of whether current countermeasures are available,what additional measures are needed,and what actions can be taken to enhance the development of radiation medical countermeasures from a systematic perspective.
基金supported by National Natural Science Foundation of China (Nos. 32088101, 22074158, 21904008)National Key R&D Program of China (Nos. 2021YFA1302604, 2021YFA1301601, 2017YFA0505002)National Key Laboratory of Proteomics (Nos. SKLP-K201706, 2021-NCPSB-003)。
文摘The cell surface membrane proteome is a class of proteins encoded by ~25% of all protein-coding genes in living organisms and plays a key role in mediating communication between the cells and their surrounding environment. However, most cell surface membrane proteins(CSMPs) are naturally expressed at very low levels compared with intracellular proteins. The difficulties in their purification with high specificity further hinder the understanding of their structure and function. In this study, we developed a new photolabeling probe to achieve efficient tagging and facile enrichment of the CSMPs. The probe is composed of a lipid tail for cell surface localization, a polyethylene glycol(PEG) spacer for increased water solubility, two 4-(N-maleimido)benzophenone(MBP) groups for UV-active tagging of the CSMPs, and a biotin tag for subsequent isolation. Application of this photolabeling probe resulted in the successful enrichment and identification of 3098 annotated CSMPs in HT22 cells with close to 70% selectivity. The proposed photolabeling probe and enrichment strategy were demonstrated to be a powerful method for deep cell surface proteome profiling, representing one of the largest groups of current drug targets.
基金Project supported by the National Key R&D Program of China(Grant No.2016YFA0501100)the National Natural Science Foundation of China(Grant Nos.91530321,31570742,and 31570727)Science and Technology Planning Project of Hunan Province,China(Grant No.2017RS3033)
文摘Three-dimensional(3 D)reconstruction of icosahedral viruses has played a crucial role in the development of cryoelectron microscopy single-particle reconstruction,with many cryo-electron microscopy techniques first established for structural studies of icosahedral viruses,owing to their high symmetry and large mass.This review summarizes the computational methods for icosahedral and symmetry-mismatch reconstruction of viruses,as well as the likely challenges and bottlenecks in virus reconstruction,such as symmetry mismatch reconstruction,contrast transformation function(CTF)correction,and particle distortion.
基金supported by the National Natural Science Foundation of China(32088101)National key Research and Development Program of China(2017YFC1700105,2021YFA1301603).
文摘Objective:To elucidate the biological basis of the heart qi deficiency(HQD)pattern,an in-depth understanding of which is essential for improving clinical herbal therapy.Methods: We predicted and characterized HQD pattern genes using the new strategy,TCM-HIN2Vec,which involves heterogeneous network embedding and transcriptomic experiments.First,a heterogeneous network of traditional Chinese medicine(TCM)patterns was constructed using public databases.Next,we predicted HQD pattern genes using a heterogeneous network-embedding algorithm.We then analyzed the functional characteristics of HQD pattern genes using gene enrichment analysis and examined gene expression levels using RNA-seq.Finally,we identified TCM herbs that demonstrated enriched interactions with HQD pattern genes via herbal enrichment analysis.Results: Our TCM-HIN2Vec strategy revealed that candidate genes associated with HQD pattern were significantly enriched in energy metabolism,signal transduction pathways,and immune processes.Moreover,we found that these candidate genes were significantly differentially expressed in the transcriptional profile of mice model with heart failure with a qi deficiency pattern.Furthermore,herbal enrichment analysis identified TCM herbs that demonstrated enriched interactions with the top 10 candidate genes and could potentially serve as drug candidates for treating HQD.Conclusion: Our results suggested that TCM-HIN2Vec is capable of not only accurately identifying HQD pattern genes,but also deciphering the basis of HQD pattern.Furthermore our finding indicated that TCM-HIN2Vec may be further expanded to develop other patterns,leading to a new approach aimed at elucidating general TCM patterns and developing precision medicine.
基金supported by grants from the State Key Program of National Natural Science of China (31630093)the National Natural Science Foundation of China (31571512, 31871476, and 81241062)+1 种基金the Beijing Nova Program (Z161100004916146)the National Basic Research Program of China (2012CB966904)
文摘Osteoarthritis(OA) is an age-related disorder that is strongly associated with chondrocyte senescence. The causal link between disruptive PTEN/Akt signaling and chondrocyte senescence and the underlying mechanism are unclear. In this study, we found activated Akt signaling in human OA cartilage as well as in a mouse OA model with surgical destabilization of the medial meniscus.Genetic mouse models mimicking sustained Akt signaling in articular chondrocytes via PTEN deficiency driven by either Col2a1-Cre or Col2a1-Cre^(ERT2) developed OA, whereas restriction of Akt signaling reversed the OA phenotypes in PTEN-deficient mice.Mechanistically, prolonged activation of Akt signaling caused an accumulation of reactive oxygen species and triggered chondrocyte senescence as well as a senescence-associated secretory phenotype, whereas chronic administration of the antioxidant N-acetylcysteine suppressed chondrocyte senescence and mitigated OA progression in PTEN-deficient mice. Therefore,inhibition of Akt signaling by PTEN is required for the maintenance of articular cartilage. Disrupted Akt signaling in articular chondrocytes triggers oxidative stress-induced chondrocyte senescence and causes OA.
基金the National Natural Science Foundation of China(81800561)the State Key Laboratory of Proteomics(SKLP-K201404).
文摘Background:Toll-like receptor 5(TLR5)-mediated pathways play critical roles in regulating the hepatic immune response and show hepatoprotective effects in mouse models of hepatic diseases.However,the role of TLR5 in experimental models of liver regeneration has not been reported.This study aimed to investigate the role of TLR5 in partial hepatectomy(PHx)-induced liver regeneration.Methods:We performed 2/3 PHx in wild-type(WT)mice,TLR5 knockout mice,or TLR5 agonist CBLB502 treated mice,as a model of liver regeneration.Bacterial flagellin content was measured with ELISA,and hepatic TLR5 expression was determined with quantitative PCR analyses and flow cytometry.To study the effects of TLR5 on hepatocyte proliferation,we analyzed bromodeoxyuridine(BrdU)incorporation and proliferating cell nuclear antigen(PCNA)expression with immunohistochemistry(IHC)staining.The effects of TLR5 during the priming phase of liver regeneration were examined with quantitative PCR analyses of immediate early gene mRNA levels,and with Western blotting analysis of hepatic NF-κB and STAT3 activation.Cytokine and growth factor production after PHx were detected with real-time PCR and cytometric bead array(CBA)assays.Oil Red O staining and hepatic lipid concentrations were analyzed to examine the effect of TLR5 on hepatic lipid accumulation after PHx.Results:The bacterial flagellin content in the serum and liver increased,and the hepatic TLR5 expression was significantly up-regulated in WT mice after PHx.TLR5-deficient mice exhibited diminished numbers of BrdU-and PCNA-positive cells,suppressed immediate early gene expression,and decreased cytokine and growth factor production.Moreover,PHx-induced hepatic NF-κB and STAT3 activation was inhibited in Tlr5–/–mice,as compared with WT mice.Consistently,the administration of CBLB502 significantly promoted PHx-mediated hepatocyte proliferation,which was correlated with enhanced production of proinflammatory cytokines and the recruitment of macrophages and neutrophils in the liver.Furthermore,Tlr5–/–mice displayed significantly lower hepatic lipid concentrations and smaller Oil Red O positive areas than those in control mice after PHx.Conclusions:We reveal that TLR5 activation contributes to the initial events of liver regeneration after PHx.Our findings demonstrate that TLR5 signaling positively regulates liver regeneration and suggest the potential of TLR5 agonist to promote liver regeneration.
基金supported by the National Natural Science Foundation of China (82270355, 82270354, 81970134, 82030011, 31630093)the National Key Research and Development Program of China (2019YFA0801601, 2021YFA1101801)。
文摘The rapid development of genome editing technology has brought major breakthroughs in the fields of life science and medicine. In recent years, the clustered regularly interspaced short palindromic repeats(CRISPR)-based genome editing toolbox has been greatly expanded, not only with emerging CRISPR-associated protein(Cas) nucleases, but also novel applications through combination with diverse effectors. Recently, transposon-associated programmable RNA-guided genome editing systems have been uncovered, adding myriads of potential new tools to the genome editing toolbox. CRISPR-based genome editing technology has also revolutionized cardiovascular research. Here we first summarize the advances involving newly identified Cas orthologs, engineered variants and novel genome editing systems, and then discuss the applications of the CRISPR-Cas systems in precise genome editing, such as base editing and prime editing. We also highlight recent progress in cardiovascular research using CRISPR-based genome editing technologies, including the generation of genetically modified in vitro and animal models of cardiovascular diseases(CVD) as well as the applications in treating different types of CVD. Finally, the current limitations and future prospects of genome editing technologies are discussed.
基金the financial support from the National Key Program for Basic Research of China(Grant Nos.:2018YFC0910302 and 2017YFF0205400)the National Natural Science Foundation of China(Grant No.:81530021)Innovation Foundation of Medicine(Grant Nos.:BWS14J052 and 16CXZ027)
文摘Posttranslational modifications of antibody products affect their stability,charge distribution,and drug activity and are thus a critical quality attribute.The comprehensive mapping of antibody modifications and different charge isomers(CIs)is of utmost importance,but is challenging.We intended to quantitatively characterize the posttranslational modification status of CIs of antibody drugs and explore the impact of posttranslational modifications on charge heterogeneity.The CIs of antibodies were fractionated by strong cation exchange chromatography and verified by capillary isoelectric focusing-whole column imaging detection,followed by stepwise structural characterization at three levels.First,the differences between CIs were explored at the intact protein level using a top-down mass spectrometry approach;this showed differences in glycoforms and deamidation status.Second,at the peptide level,common modifications of oxidation,deamidation,and glycosylation were identified.Peptide mapping showed nonuniform deamidation and glycoform distribution among CIs.In total,10 N-glycoforms were detected by peptide mapping.Finally,an in-depth analysis of glycan variants of CIs was performed through the detection of enriched glycopeptides.Qualitative and quantitative analyses demonstrated the dynamics of 24 N-glycoforms.The results revealed that sialic acid modification is a critical factor accounting for charge heterogeneity,which is otherwise missed in peptide mapping and intact molecular weight analyses.This study demonstrated the importance of the comprehensive analyses of antibody CIs and provides a reference method for the quality control of biopharmaceutical analysis.
文摘The Chinese Academy of Sciences held its 7th forum on frontiers of Science and Technology, April 12-13, 2012, in the academy hall of the Chinese Academy of Sciences. The Forum was organized by the Life Science and Medicine Division and co-organized by Academy of Military Medical Sciences and Science China Press. The theme of the 7th Forum was ＂Lifeomics and Translational Medicine＂,
基金funded by the National Natural Science Foundation of China (NSFC, 31900046, 81972085, 82172465 and 32161133022)the Guangdong Provincial Key Laboratory of Advanced Biomaterials (2022B1212010003)+7 种基金the National Science and Technology Innovation 2030 Major Program (2022ZD0211900)the Shenzhen Key Laboratory of Computer Aided Drug Discovery (ZDSYS20201230165400001)the Chinese Academy of Science President’s International Fellowship Initiative (PIFI)(2020FSB0003)the Guangdong Retired Expert (granted by Guangdong Province)the Shenzhen Pengcheng ScientistNSFC-SNSF Funding (32161133022)Alpha Mol&SIAT Joint LaboratoryShenzhen Government Top-talent Working Funding and Guangdong Province Academician Work Funding。
文摘Drug discovery is a crucial part of human healthcare and has dramatically benefited human lifespan and life quality in recent centuries, however, it is usually time-and effort-consuming. Structural biology has been demonstrated as a powerful tool to accelerate drug development. Among different techniques, cryo-electron microscopy(cryo-EM) is emerging as the mainstream of structure determination of biomacromolecules in the past decade and has received increasing attention from the pharmaceutical industry. Although cryo-EM still has limitations in resolution, speed and throughput, a growing number of innovative drugs are being developed with the help of cryo-EM. Here, we aim to provide an overview of how cryo-EM techniques are applied to facilitate drug discovery. The development and typical workflow of cryo-EM technique will be briefly introduced, followed by its specific applications in structure-based drug design, fragment-based drug discovery, proteolysis targeting chimeras, antibody drug development and drug repurposing. Besides cryo-EM, drug discovery innovation usually involves other state-of-the-art techniques such as artificial intelligence(AI), which is increasingly active in diverse areas. The combination of cryo-EM and AI provides an opportunity to minimize limitations of cryo-EM such as automation, throughput and interpretation of mediumresolution maps, and tends to be the new direction of future development of cryo-EM. The rapid development of cryo-EM will make it as an indispensable part of modern drug discovery.
文摘The advent of gene editing represents one of the most transformative breakthroughs in life science,making genome manipulation more accessible than ever before.While traditional CRISPR/Cas-based gene editing,which involves double-strand DNA breaks(DSBs),excels at gene disruption,it is less effective for accurate gene modification.The limitation arises because DSBs are primarily repaired via non-homologous end joining(NHEJ),which tends to introduce indels at the break site.While homology directed repair(HDR)can achieve precise editing when a donor DNA template is provided,the reliance on DSBs often results in unintended genome damage.HDR is restricted to specific cell cycle phases,limiting its application.Currently,gene editing has evolved to unprecedented levels of precision without relying on DSB and HDR.The development of innovative systems,such as base editing,prime editing,and CRISPR-associated transposases(CASTs),now allow for precise editing ranging from single nucleotides to large DNA fragments.Base editors(BEs)enable the direct conversion of one nucleotide to another,and prime editors(PEs)further expand gene editing capabilities by allowing for the insertion,deletion,or alteration of small DNA fragments.The CAST system,a recent innovation,allows for the precise insertion of large DNA fragments at specific genomic locations.In recent years,the optimization of these precise gene editing tools has led to significant improvements in editing efficiency,specificity,and versatility,with advancements such as the creation of base editors for nucleotide transversions,enhanced prime editing systems for more efficient and precise modifications,and refined CAST systems for targeted large DNA insertions,expanding the range of applications for these tools.Concurrently,these advances are complemented by significant improvements in in vivo delivery methods,which have paved the way for therapeutic application of precise gene editing tools.Effective delivery systems are critical for the success of gene therapies,and recent developments in both viral and non-viral vectors have improved the efficiency and safety of gene editing.For instance,adeno-associated viruses(AAVs)are widely used due to their high transfection efficiency and low immunogenicity,though challenges such as limited cargo capacity and potential for immune responses remain.Non-viral delivery systems,including lipid nanoparticles(LNPs),offer an alternative with lower immunogenicity and higher payload capacity,although their transfection efficiency can be lower.The therapeutic potential of these precise gene editing technologies is vast,particularly in treating genetic disorders.Preclinical studies have demonstrated the effectiveness of base editing in correcting genetic mutations responsible for diseases such as cardiomyopathy,liver disease,and hereditary hearing loss.These technologies promise to treat symptoms and potentially cure the underlying genetic causes of these conditions.Meanwhile,challenges remain,such as optimizing the safety and specificity of gene editing tools,improving delivery systems,and overcoming off-target effects,all of which are critical for their successful application in clinical settings.In summary,the continuous evolution of precise gene editing technologies,combined with advancements in delivery systems,is driving the field toward new therapeutic applications that can potentially transform the treatment of genetic disorders by targeting their root causes.
基金supported by funds from the National Natural Science Foundation of China (No. 31570754)Tsinghua-Peking Joint Center for Life Sciences and Beijing Advanced Innovation Center for Structural Biology to C. ChenLab Innovation Funding from Lab and Instrument Department, Tsinghua University to W. Wang
文摘Elongation factor 4（EF4） is one of the highly conserved translational GTPases, whose functions are largely unknown. Structures of EF4 bound ribosomal PRE-translocation and POST-translocation complexes have both been visualized. On top of cellular, structural, and biochemical studies, several controversial models have been raised to rationalize functions of EF4. However, how EF4 modulates elongation through its interactions with ribosomes has not been revealed. Here, using single-molecule fluorescence resonance energy transfer assays, we directly captured short-lived EF4·GTP bound ribosomal PRE and POST translocation complexes, which may adopt slightly different conformations from structures prepared using GDP, GDPNP, or GDPCP. Furthermore, we revealed that EF4·GTP severely impairs delivery of aminoacyl-tRNA into the A-site of the ribosome and moderately accelerates translocation. We proposed that functions of EF4 are to slow overall elongation and to stall majority of ribosomes in POST states under stress conditions.
基金This work was supported by the National Key Research and Development Program of China(2018YFA0801104 and 2021YFA1301604)the National Natural Science Foundation of China(82372721,31630093,and 82394443)Independent Research Program of the State Key Laboratory of Proteomics(SKLP-K202004).
文摘Endothelial cells(ECs)form a single cell layer that lines the inner surface of all blood and lymphatic vessels,acting as the barrier between vessels and underlying tissues.ECs are not only responsible for the flow of substances and fluid into and out of tissues but are also involved in many processes,such as coagulation,fibrinolysis,and regulation of vascular tone and inflammation.
基金supported by the National Key R&D Program of China(Grant Nos.2020YFE0202200 and 2017YFC1700105)the National Natural Science Foundation of China(Grant Nos.31601064,31871341,and 32088101)+1 种基金the Beijing Nova Program of China(Grant No.Z171100001117117)the State Key Laboratory of Proteomics of China(Grant No.SKLPO202010)。
文摘After decades of development,protein and peptide drugs have now grown into a major drug class in the marketplace.Target identification and validation are crucial for the discovery of protein and peptide drugs,and bioinformatics prediction of targets based on the characteristics of known target proteins will help improve the efficiency and success rate of target selection.However,owing to the developmental history in the pharmaceutical industry,previous systematic exploration of the target spaces has mainly focused on traditional small-molecule drugs,while studies related to protein and peptide drugs are lacking.Here,we systematically explore the target spaces in the human genome specifically for protein and peptide drugs.Compared with other proteins,both successful protein and peptide drug targets have many special characteristics,and are also significantly different from those of small-molecule drugs in many aspects.Based on these features,we develop separate effective genome-wide target prediction models for protein and peptide drugs.Finally,a user-friendly web server,Predictor Of Protein and Pept Ide drugs’therapeutic Targets(POPPIT)(http://poppit.ncpsb.org.cn/),is established,which provides not only target prediction specifically for protein and peptide drugs but also abundant annotations for predicted targets.
基金Project supported by the National Natural Science Foundation of China (Grant Nos. 12074208 and 11375256)the Natural Science Foundation of Jiangsu Province (Grant No. BK20200176)+2 种基金the Natural Science Foundation of Jiangsu Higher Education Institutions of China (Grant Nos. 20KJB140020 and 19KJB140005)Fundamental Research Project from Changzhou Science and Technology (Grant No. CJ20200029)the Jiangsu Province High-level Innovative and Entrepreneurial Talents Introduction Plan。
文摘Copper ions can promote amyloid diseases that are associated with amyloid peptides, such as type 2 diabetes(T2D),Alzheimer's disease(AD), Parkinson's disease(PD), and amyotrophic lateral sclerosis(ALS). However, the underlying molecular mechanism remains obscure. Here we present that Cu^(2+)is able to specifically bind to the backbone of T2D related human islet amyloid polypeptide(hIAPP) by forming a ring structure, which causes the reduction of Cu^(2+)to Cu^(+) to produce reactive oxygen species(ROS) and the modulation of hIAPP aggregation. Nuclear magnetic resonance spectroscopy showed that Cu^(2+)bound to the backbone of a turn region, His18-Ser21, which is critical for hIAPP aggregation.Ab initio calculations and x-ray absorption fine structure analyses revealed that Cu^(2+)simultaneously bound with both the amide nitrogen and carbonyl oxygen on the peptide backbone, resulting in a ring structure, and causing the reduction of Cu^(2+)to Cu^(+) to form a hIAPP-Cu^(+) complex. 2′,7′-dichlorodihydrofluorescin diacetate fluorescence measurements further indicated that this complex led to enhanced ROS levels in rat insulinoma cells. Additionally, thioflavin T fluorescence and atomic force microscopy measurements denoted that the backbone-Cu ring structure largely modulated hIAPP aggregation,including the inhibition of hIAPP fibrillation and the promotion of peptide oligomerization. These findings shed new light on the molecular mechanism of Cu^(2+)-induced amyloid toxicity involving both the enhancement of ROS and the modulation of hIAPP aggregation.
文摘Stroke is one of the top causes of death and disability worldwide,and its pathogenesis and mechanism have not been fully elucidated.Several agents have shown protective effects against stroke in animal models;however,few studies have shown obvious effects in clinical practice.This might be due to differences in brain structure and physiological function between humans and rodents.In this study,we established a hypoxic stroke model in human-induced pluripotent stem cell(hiPSC)-derived brain organoids to simulate the hypoxic stroke caused by ischemia.Then,by combining proteomics,single-cell transcriptome analysis,and histopathological analysis,a significant increase of three types of astrocytes was identified and they showed different responses to hypoxic environments;also the main type of astrocyte that cause brain tissue hyperplasia in ischemia brains was iden-tified.In addition,the cortical excitatory neurons had signs of apoptosis and aging after hypoxia both in vivo and in vitro.Most importantly,we identified a possible role of a traditional Chinese medicine formula called DengZhanShengMai capsule in ischemic and hypoxic stroke treatment through regulation of lipid metabolism related biological functions.These results indicate that the combination of brain organoids and multiomics method is helpful for developing a new strategy to direct study stroke,and could provide a promising platform for drug screening of stroke in the future.
文摘Laser shaping was introduced to maskless projection soft lithography by using digital micro-mirror device (DMD). The predesigned intensity pattern was imprinted onto the DMD and the input laser beam with a Gaussian or quasi-Gaussian distribution will carry the pattern on DMD to etch the resin. It provides a method of precise control of laser beam shapes and?photon-induced curing behavior of resin. This technology provides an accurate micro-fabrication of microstructures used for micro-systems. As a virtual mask generator and a binary-amplitude spatial light modulator, DMD is equivalent to the masks in the conventional exposure system. As the virtual masks and shaped laser beam can be achieved flexibly, it is a good method of precision soft lithography for 2D/3D microstructures.
基金supported by the National Natural Science Foundation of China(32088101,32271498)the National Key Research and Development Program of China(2022YFA1303200)+3 种基金State Key Laboratory of Proteomics(SKLP-K202002)State Key Laboratory of Dampness Syndrome of Chinese Medicine,The Second Affiliated Hospital of Guangzhou University of Chinese Medicine(SZ2021ZZ06,SZ2021ZZ3205)Key-Area Research and Development Program of Guangdong Province(2020B1111100009)Guangzhou Science and Technology Plan Project(202102010275,202201020499).
文摘Salivary proteins serve multifaceted roles in maintaining oral health and hold significant potential for diagnosing and monitoring diseases due to the non-invasive nature of saliva sampling.However,the clinical utility of current saliva biomarker studies is limited by the lack of reference intervals(RIs)to correctly interpret the testing result.Here,we developed a rapid and robust saliva proteome profiling workflow,obtaining coverage of>1,200 proteins from a 50-μL unstimulated salivary flow with 30 min gradients.With the workflow,we investigated protein variation in a cohort of 1,743 healthy individuals.The significant differences in non-linear saliva proteomes among age groups resulted in the establishment of age-related RIs covering 1,123 salivary protein variations.We then utilized a cohort of 30 epilepsy patients as a case study to illustrate the practical application of RIs in identifying disease-enriched outlier proteins,elucidating their cellular origins,determining disease diagnosis,and visualizing outlier proteins in each epilepsy patient.Our study showed the classification model based on the RI achieved PR-AUC of 0.815(95%CI:0.813–0.826).Additionally,we validated these results in an independent test set.Furthermore,the epilepsy cohort could be further stratified into 2 major subtypes,with one subtype characterized by disrupted metabolic proteins and containing mostly Focal Cortical Dysplasia(FCD)type III epilepsy patients.Overall,our study provided a proof-of-principle workflow for the use of salivary proteome for health monitoring,epilepsy diagnosis and subtyping.
