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Systems-Based interactome Analysis for Hematopoiesis Effect of Angelicae sinensis Radix: Regulated Network of Cell Proliferation towards Hemopoiesis

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Chinese Journal of Integrative Medicine 2019年第12期25卷 939-947页

作者： ZHENG Guang ZHANG He YANG Yun SUN Ying-li ZHANG Yan-jing CHEN Ju-ping HAO Ting LU Cheng GUO Hong-tao ZHANG Ge FAN Dan-ping HE Xiao-juan LU Ai-ping Information Science and Engineering School Lanzhou UniversityLanzhou(730000)China School of Biology Lanzhou UniversityLanzhou(730000)China Institute of Basic Research in Chinese Medicine China Academy of Chinese Medical SciencesBeijing(100700)China Department of Rheumatism the First Affiliated Hospital of Henan University of Traditional Chinese MedicineZhengzhou(450000)China School of Chinese Medicine Hong Kong Baptist UniversityKowloon TongKowloonHong Kong SARChina

Objective: To explore the molecular-level mechanism on the hematopoiesis effect of Angelicae sinensis Radix(ASR) with systems-based interactome analysis. Methods: This systems-based interactome analysis was designed to enforce the workflow of "ASR(herb)→compound→target protein→internal protein actions→ending regulated protein for hematopoiesis". This workflow was deployed with restrictions on regulated proteins expresses in bone marrow and anemia disease and futher validated with experiments. Results: The hematopoiesis mechanism of ASR might be accomplished through regulating pathways of cell proliferation towards hemopoiesis with cross-talking agents of spleen tyrosine kinase(SYK), Janus kinase 2(JAK2), and interleukin-2-inducible T-cell kinase(ITK). The hematopoietic function of ASR was also validated by colonyforming assay performed on mice bone marrow cells. As a result, SYK, JAK2 and ITK were activated. Conclusion: This study provides a new approach to systematically study and predict the therapeutic mechanism for ASR based on interactome analysis towards biological process with experimental validations.

关键词： Angelicae sinensis Radix interactome cell proliferation hemopoiesis regulation cross-talking agents

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Elucidating cellular interactome of chikungunya virus identifies host dependency factors

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Virologica Sinica 2023年第4期38卷 497-507页

作者： Peiqi Yin Xia Jian Yihan Liu Yuwen Liu Lu Lv Haoran Cui Leiliang Zhang Department of Clinical Laboratory Medicine The First Affiliated Hospital of Shandong First Medical University&Shandong Provincial Qianfoshan HospitalJinan250013China NHC Key Laboratory of Systems Biology of Pathogens Institute of Pathogen BiologyChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100176China Department of Pathogen Biology School of Clinical and Basic Medical SciencesShandong First Medical University&Shandong Academy of Medical SciencesJinan250117China Medical Science and Technology Innovation Center Shandong First Medical University&Shandong Academy of Medical SciencesJinan250117China

Chikungunya virus(CHIKV)is a re-emerging mosquito-transmitted RNA virus causing joint and muscle pain.To better understand how CHIKV rewires the host cell and usurps host cell functions,we generated a systematic CHIKV-human protein-protein interaction map and revealed several novel connections that will inform further mechanistic studies.One of these novel interactions,between the viral protein E1 and STIP1 homology and U-box containing protein 1(STUB1),was found to mediate ubiquitination of E1 and degrade E1 through the proteasome.Capsid associated with G3BP1,G3BP2 and AAAþATPase valosin-containing protein(VCP).Furthermore,VCP inhibitors blocked CHIKV infection,suggesting VCP could serve as a therapeutic target.Further work is required to fully understand the functional consequences of these interactions.Given that CHIKV proteins are conserved across alphaviruses,many virus-host protein-protein interactions identified in this study might also exist in other alphaviruses.Construction of interactome of CHIKV provides the basis for further studying the function of alphavirus biology.

关键词： Chikungunya virus(CHIKV) interactome STIP1 homology and U-box containing protein 1(STUB1) Valosin-containing protein(VCP) Capsid

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Integrated interactome and transcriptome analysis reveals key host factors critical for SARS-CoV-2 infection

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Virologica Sinica 2023年第4期38卷 508-519页

作者： Jie Sheng Lili Li Xueying Lv Meiling Gao Ziyi Chen Zhuo Zhou Jingfeng Wang Aiping Wu Taijiao Jiang Institute of Systems Medicine Chinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing100005China Suzhou Institute of Systems Medicine Suzhou215123China Institute of Basic Medical Sciences Chinese Academy of Medical SciencesSchool of Basic MedicinePeking Union Medical CollegeBeijing100005China Department of Microbiology and Parasitology College of Basic Medical SciencesChina Medical UniversityShenyang110122China Guangzhou Laboratory Guangzhou510005China State Key Laboratory of Respiratory Disease the First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou Medical UniversityGuangzhou510120China

The coronavirus disease 2019(COVID-19)pandemic,caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),has seriously threatened global public health and caused huge economic losses.Omics studies of SARS-CoV-2 can help understand the interaction between the virus and host,thereby providing a new perspective in guiding the intervention and treatment of the SARS-CoV-2 infection.Since large amount of SARS-CoV-2 omics data have been accumulated in public databases,this study aimed to identify key host factors involved in SARSCoV-2 infection through systematic integration of transcriptome and interactome data.By manually curating published studies,we obtained a comprehensive SARS-CoV-2-human protein-protein interactions(PPIs)network,comprising 3591 human proteins interacting with 31 SARS-CoV-2 viral proteins.Using the RobustRankAggregation method,we identified 123 multiple cell line common genes(CLCGs),of which 115 up-regulated CLCGs showed host enhanced innate immunity and chemotactic response signatures.Combined with network analysis,co-expression and functional enrichment analysis,we discovered four key host factors involved in SARS-CoV-2 infection:IFITM1,SERPINE1,DDX60,and TNFAIP2.Furthermore,SERPINE1 was found to facilitate SARSCoV-2 replication,and can alleviate the endoplasmic reticulum(ER)stress induced by ORF8 protein through interaction with ORF8.Our findings highlight the importance of systematic integration analysis in understanding SARS-CoV-2-human interactions and provide valuable insights for future research on potential therapeutic targets against SARS-CoV-2 infection.

关键词： SARS-CoV-2 interactome Transcriptome Integration analysis ER stress

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The interactome of ppGalNAc-T18 in ER plays a role in its ER retention

The interactome of ppGalNAc-T18 in ER plays a role in its ER...

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2020年糖科学青年科技论坛

作者：贾文娟许之珏单爱东张延 Key Laboratory of Systems Biomedicine (Ministry of Education) Shanghai Center for Systems BiomedicineShanghai Jiao Tong University

Mucin type O-glycosylation is a post-translational modification(PTM) which begins with the transfer of GalNAc moiety from UDP-GalNAc onto Ser or Thr residues of their protein substrates.This modification is initiated by UDP-GalNAc:polypeptide N-α-acetylgalactosaminyl-transferases(ppGalNAc-T’s),a family consists 20 members in human and most of them localize in Golgi apparatus.However,we have identified that ppGalNAc-T18(T18) localizes in the endoplasmic reticulum(ER) rather than the Golgi apparatus in lung carcinoma cells and it only exists in vertebrates.Intriguingly,ppGalNAc-T18 silencing in cells decreases the overall O-glycosylation level,activates ER stress and induces apoptosis via a non-catalytic mechanism.However,the ER retention mechanisms for ppGalNAc-T18 is still unknown.Recently we have shown that the full-length T18 and recombinant T18 with a truncated N-terminal(re T18) localized in ER.In this study,we determined that the cytoplasmic and transmembrane domains of ppGalNAc-T18,was similar with other members of ppGalNAc-Ts family,contains ER exporting signals and localizes in Golgi apparatus.To gain deep insight into the molecular and cellular mechanisms of T18 localization,we performed immunoprecipitation-mass spectrometry(IP-MS) analysis and detected the potential interactome of T18 by anti-Flag pull down in HEK293 T cells expressing c-Flag-tagged T18.Proteomics analysis identified the ER localized proteins,such as LPCAT1,PLOD3 and UGGT1 as potential interaction proteins of T18.Co-immunoprecipitation(Co-IP) and fluorescence staining were used to confirm the interaction and localization.Those data showed that the interactome of ppGalNAc-T18 in ER may be important in its localization.In addition,the N-glycosylation is unnecessary for the ER localization of ppGalNAc-T18 and its interaction with UGGT1.

关键词： ppGalNAc-T18 localization interactome

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Layered and annotation grouped interactome demonstrates enhanced autophagy activity in a recurrent experimental autoimmune uveitis T cell line

Layered and annotation grouped interactome demonstrates enha...

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第八届全国免疫学学术大会

作者：贾秀志任欢哈尔滨医科大学

Background:Autoimmune uveitis is usually a recurrent-remitting disease and seldom monophasic.However, the mechanism is not well understood.Methods:Publicly available gene expression data of recurrent and monophasic T cell lines were linked with the Fun Coup(functional coupling between proteins) database to construct a global interactome.Cytoscape and the Cerebral(Cell Region-Based Rendering And Layout) plugin were then used to establish layered interactome based upon information of subcellular protein localizations that was retrieved from the Human Protein Reference Database(HP RD).After the layered interactomes were individually annotated according to gene ontology(GO) and Kyoto Encyclopedia of Genes and Genomes database(KEGG), the Clue GO plugin was applied to group these functional annotations in order to decipher cellular events at the organelle level in the 3 different layers.Results:The global functional protein interactome was constructed and divided into 3 layers:the plasma membrane, the cytoplasm, and the nucleus.Clue GO analysis showed that 9 groups of annotations were obtained characterizing over-represented biological processes in the 3 different layers.Of the 5 groups annotated in the cytoplasm layer, "autophagosome formation"(correlated, p=0.025) was directly annotated, the otherannotated processes also showed clear association with autophagy.Moreover, the grouped annotations in the plasma membrane and the nucleus signified active processes that highly linked with T cell activation and autoimmunity.Conclusions:This study shows that layered and annotation grouped analysis provides great insights, especially at the organelle level, into the mechanism of recurrent uveitis.The recurrent T cell line showed increased autophagy activity.

关键词： recurrent monophasic uveitis interactome autophagy

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The sperm-interacting proteome in the bovine isthmus and ampulla during the periovulatory period

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Journal of Animal Science and Biotechnology 2023年第3期14卷 980-1000页

作者： Coline Mahe Regis Lavigne Emmanuelle Com Charles Pineau Aleksandra Maria Zlotkowska Guillaume Tsikis Pascal Mermillod Jennifer Schoen Marie Saint-Dizier CNRS IFCEINRAEUniversite de ToursPRC37380 NouzillyFrance Univ Rennes InsermEHESPIrset(Institut de Recherche en SanteEnvironnement Et Travail)-UMR-S 1085F‑35000 RennesFrance Univ Rennes CNRSInsermBiosit UAR 3480 US_S 018Protim Core Facility35000 RennesFrance Institute of Reproductive Biology Leibniz Institute for Farm Animal BiologyFBNDummerstorfGermany Present Address:Department of Reproduction Biology Leibniz Institute for Zoo and Wildlife Research(IZW)BerlinGermany

Background Spermatozoa interact with oviduct secretions before fertilization in vivo but the molecular players of this dialog and underlying dynamics remain largely unknown.Our objectives were to identify an exhaustive list of sperm-interacting proteins(SIPs)in the bovine oviduct fluid and to evaluate the impact of the oviduct anatomical region(isthmus vs.ampulla)and time relative to ovulation(pre-ovulatory vs.post-ovulatory)on SIPs number and abundance.Methods Pools of oviduct fluid(OF)from the pre-ovulatory ampulla,pre-ovulatory isthmus,post-ovulatory ampulla,and post-ovulatory isthmus in the side of ovulation were collected from the slaughterhouse.Frozen-thawed bull sperm were incubated with OF or phosphate-buffered saline(control)for 60 min at 38.5℃.After protein extraction and digestion,sperm and OF samples were analyzed by nanoLC-MS/MS and label-free protein quantification.Results A quantitative comparison between proteins identified in sperm and OF samples(2333 and 2471 proteins,respectively)allowed for the identification of 245 SIPs.The highest number(187)were found in the pre-ovulatory isthmus,i.e.,time and place of the sperm reservoir.In total,41 SIPs(17%)were differentially abundant between stages in a given region or between regions at a given stage and 76 SIPs(31%)were identified in only one region×stage condition.Functional analysis of SIPs predicted roles in cell response to stress,regulation of cell motility,fertilization,and early embryo development.Conclusion This study provides a comprehensive list of SIPs in the bovine oviduct and evidences dynamic spatiotemporal changes in sperm-oviduct interactions around ovulation time.Moreover,these data provide protein candidates to improve sperm conservation and in vitro fertilization media.

关键词： Ampulla Fallopian tube interactome Isthmus Oviduct Ovulation Post-ovulatory Pre-ovulatory Proteomics Spermatozoa

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The protein-protein interaction landscape of transcription factors during gynoecium development in Arabidopsis

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Molecular Plant 2023年第1期16卷 260-278页

作者： Humberto Herrera-Ubaldo Sergio E.Campos Pablo López-Gómez Valentín Luna-García Víctor M.Zúñiga-Mayo Gerardo E.Armas-Caballero Karla L.González-Aguilera Alexander DeLuna Nayelli Marsch-Martínez Carlos Espinosa-Soto Stefan de Folter Unidad de Genómica Avanzada(UGA-LANGEBIO) Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional(CINVESTAV-IPN)IrapuatoGuanajuato 36824México Departamento de Biotecnología y Bioquímica Unidad IrapuatoCINVESTAV-IPNIrapuatoGuanajuato 36824México Instituto de Física Universidad de San Luis PotosíSan Luis PotosíSLP 78290México Present address:Department of Plant Sciences University of CambridgeCambridgeUK Present address:Department of Molecular and Cellular Biology University of California DavisDavisCAUSA Present address:CONACYT Instituto de FitosanidadColegio de PostgraduadosCampus MontecilloTexcocoMéxico

Flowers are composed of organs whose identity is defined by the combinatorial activity of transcription factors(TFs).The interactions between MADS-box TFs and protein complex formation have been schematized in the floral quartet model of flower development.The gynoecium is the flower’s female reproductive part,crucial for fruit and seed production and,hence,for reproductive success.After the establishment of carpel identity,many tissues arise to form a mature gynoecium.TFs have been described as regulators of gynoecium development,and some interactions and complexes have been identified.However,broad knowledge about the interactions among these TFs and their participation during development remains scarce.In this study,we used a systems biology approach to understand the formation of a complex reproductive unit—as the gynoecium—by mapping binary interactions between well-characterized TFs.We analyzed almost 4500 combinations and detected more than 250 protein-protein interactions(PPIs),resulting in a process-specific interaction map.Topological analyses suggest hidden functions and novel roles for many TFs.In addition,we observed a close relationship between TFs involved in auxin and cytokinin-signaling pathways and other TFs.Furthermore,we analyzed the network by combining PPI data,expression,and genetic data,which helped us to dissect it into several dynamic spatio-temporal subnetworks related to gynoecium development processes.Finally,we generated an extended PPI network that predicts new players in gynoecium development.Taken together,all these results serve as a valuable resource for the plant community.

关键词： interactome networks transcription factors gynoecium development

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Mass spectrometry-based protein-protein interaction techniques and their applications in studies of DNA damage repair

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2021年第1期22卷 1-20页

作者： Zhen CHEN Junjie CHEN Department of Experimental Radiation Oncology The University of Texas MD Anderson Cancer CenterHoustonTX77030USA

Proteins are major functional units that are tightly connected to form complex and dynamic networks.These networks enable cells and organisms to operate properly and respond efficiently to environmental cues.Over the past decades,many biochemical methods have been developed to search for protein-binding partners in order to understand how protein networks are constructed and connected.At the same time,rapid development in proteomics and mass spectrometry(MS)techniques makes it possible to identify interacting proteins and build comprehensive protein-protein interaction networks.The resulting interactomes and networks have proven informative in the investigation of biological functions,such as in the field of DNA damage repair.In recent years,a number of proteins involved in DNA damage response and DNA repair pathways have been uncovered with MS-based protein-protein interaction studies.As the technologies for enriching associated proteins and MS become more sophisticated,the studies of protein-protein interactions are entering a new era.In this review,we summarize the strategies and recent developments for exploring protein-protein interaction.In addition,we discuss the application of these tools in the investigation of protein-protein interaction networks involved in DNA damage response and DNA repair.

关键词： Protein-protein interaction interactome Proteomics Mass spectrometry DNA repair DNA damage response

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Marking RNA:m^6A writers,readers,and functions in Arabidopsis

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Journal of Molecular Cell Biology 2019年第10期11卷 899-910页

作者： Marlene Reichel Tino Koster Dorothee Staiger RNA Biology and Molecular Physiology Faculty of BiologyBielefeld University33615 BielefeldGermany

N^6-methyladenosine(m^6A)emerges as an important modification in eukaryotic mRNAs.m^6A has first been reported in 1974,and its functional significance in mammalian gene regulation and importance for proper development have been well established.An arsenal of writer,eraser,and reader proteins accomplish deposition,removal,and interpretation of the m^6A mark,resulting in dynamic function.This led to the concept of an epitranscriptome,the compendium of RNA species with chemical modification ofthe nucleobases in the cell,in analogy to the epigenome.While m^6A has long been known to also exist in plant mRNAs,proteins involved in m^6A metabolism have only recently been detected by mutant analysis,homology search,and mRNA interactome capture in the reference plant Arabidopsis thaliana.Dysregulation ofthe m^6A modification causes severe developmental abnormalities of leaves and roots and altered timing of reproductive development.Furthermore,m^6A modification affects viral infection.Here,we discuss recent progress in identifying m^6A sites transcriptome-wide,in identifying the molecular players involved in writing,removing,and reading the mark,and in assigning functions to this RNA modification in 4.thaliana.We highlight similarities and differences to m^6A modification in mammals and provide an outlook on important questions that remain to be addressed.

关键词： Arabidopsis m^6A mRNA interactome posttranscriptional RNA-binding protein

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The mRNA Binding Proteome of Proliferating and Differentiated Muscle Cells

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Genomics, Proteomics & Bioinformatics 2020年第4期18卷 384-396页

作者： Monika Hiller Miriam Geissler George Janssen Peter van Veelen Annemieke Aartsma-Rus Pietro Spitali Department of Human Genetics Leiden University Medical CenterLeiden 2333 ZCthe Netherlands Center for Proteomics and Metabolomics Leiden University Medical CenterLeiden 2333 ZCthe Netherlands

Muscle formation is a coordinated process driven by extensive gene expression changes where single cells fuse together to form multinucleated muscle fibers. Newly synthesized m RNAs are then regulated by RNA binding proteins(RBPs), affecting post-transcriptional transcript metabolism. Here, we determined how large-scale gene expression changes affect the catalog of RBPs by studying proliferating and differentiated muscle cells in healthy and dystrophic conditions. Transcriptomic analysis showed that the expression of more than 7000 genes was affected during myogenesis. We identified 769 RBPs, of which 294 were muscle-specific and 49 were uniquely shared with cardiomyocytes. A subset of 32 RBPs(half of which were muscle-specific) was found to be preferentially associated with target mRNAs in either myoblasts(MBs) or myotubes(MTs). A large proportion of catalytic proteins were bound to mRNAs even though they lack classical RNA binding domains. Finally, we showed how the identification of cell-specific RBPs enabled the identification of biomarkers that can separate healthy individuals from dystrophic patients. Our data show how interactome data can shed light on new basic RNA biology as well as provide cell-specific data that can be used for diagnostic purposes.

关键词： RNA binding protein interactome Duchenne muscular dystrophy Proteomics Skeletal muscle

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