With the maturation of proteomics technologies in recent years, proteomics has made significant achievements in early detection of major diseases, disease classification, drug target discovery, and other fields. To explore the important role of proteomics, especially proteomics-based cutting-edge lifeomics technologies, in promoting the development of precision laboratory medicine and to discuss the opportunities and challenges faced during the clinical translation of innovative outcomes, the National Center for Protein Sciences-Beijing invited renowned experts and scholars in laboratory medicine, lifeomics, and precision medicine. The discussions revolved around the collaborative development of laboratory medicine and lifeomics, the future trends of new technologies in clinical laboratory testing, the innovation and development of lifeomics in laboratory medicine, the translational application of proteomics technologies in laboratory medicine, and the opportunities and challenges in the industrialization of proteomics achievements. All participants agreed that proteomics provides new directions and opportunities for precision diagnosis and treatment of diseases. However, close collaboration between academia, hospitals and industry is required. Additionally, challenges such as clinical applicability of equipment, standardization of detection methods and data, cost and quality control, talent cultivation, and the industrialization pathway need to be addressed.

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 suc-cessful 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 Peptide 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.

Genome-wide physical protein-protein interaction(PPI)mapping remains a major chal-lenge for current technologies.Here,we reported a high-efficiency BiFC-seq method,yeast-enhanced green fluorescent protein-based bimolecular fluorescence complementation(yEGFP-BiFC)coupled with next-generation DNA sequencing,for interactome mapping.We first applied yEGFP-BiFC method to systematically investigate an intraviral network of the Ebola virus.Two-thirds(9/14)of known interactions of EBOV were recaptured,and five novel interactions were discovered.Next,we used the BiFC-seq method to map the interactome of the tumor protein p53.We identified 97 interactors of p53,more than three-quarters of which were novel.Furthermore,in a more complex background,we screened potential interactors by pooling two BiFC libraries together and revealed a network of 229 interactions among 205 proteins.These results show that BiFC-seq is a highly sensitive,rapid,and economical method for genome-wide interactome map-ping.

Cancers have been widely recognized as highly heterogeneous diseases, and early diagnosis and prognosis of cancer types have become the focus of cancer research. In the era of big data, efficient mining of massive biomedical data has become a grand challenge for bioinformatics research. As a typical neural network model, the autoencoder is able to efficiently learn the features of input data by unsupervised training method and further help integrate and mine the biological data. In this article, the primary structure and workflow of the autoencoder model are introduced, followed by summarizing the advances of the autoencoder model in cancer informatics using various types of biomedical data. Finally, the challenges and perspectives of the autoencoder model are discussed.
Algorithms ; Humans ; Informatics ; Neoplasms/diagnosis* ; Neural Networks, Computer

The liver is the metabolic center of mammalian body. Systematic study on liver's proteome expression under different physiological and pathological conditions helps us understand the functional mechanisms of the liver. With the rapid development of liquid chromatography tandem mass spectrometry technique, numerous studies on liver physiology and pathology features produced a large number of proteomics data. In this paper, 834 proteomics experiments of mouse liver were systematically collected and the mouse liver proteome database (Mouse Liver Portal, http://mouseliver.com) was established. The Mouse Liver Portal contains the liver's proteomics data under different physiology and pathology conditions, such as different gender, age, circadian rhythm, cell type and different phase of partial hepatectomy, non-alcoholic fatty liver. This portal provides the changes in proteins' expression in different conditions of the liver, differently expressed proteins and the biological processes which they are involved in, potential signal transduction and regulatory networks. As the most comprehensive mouse liver proteome database, it can provide important resources and clues for liver biology research.
Animals ; Chromatography, Liquid ; Databases, Factual ; Liver ; Mice ; Proteome ; Proteomics

Objective To establish neoplasm transplantation models of breast cancer cells in BALB /c nude mice and to isolate tumor infiltrating myeloid cells.Methods pHAGE-EF-ZsG-DEST plasmid,pMD2.G plasmid and psPAX2 were transfected into BT474 using the method of calcium phosphate transfection .The positive cells were selected by flow cytometry and implanted in the fat pad of nude mice .A tumor model of breast cancer cells implanted in nude mice was constructed, and the tumor infiltrating myeloid cells were isolated .Conclusion Tumor infiltrating myeloid cells are successfully isolated, which will contribute to the study of the functions of tumor infiltrating myeloid cells .

Hepatic Stellate Cells ; Humans ; Liver Cirrhosis

Objective To analyze the construction of mouse liver phosphoproteome and phosphorylated kinases to provide useful information for integrating mouse kinase phosphorylation regulatory networks.Methods A new method was established to identify phosphoproteome from the mouse liver.First of all, liver protein was digested with trypsin before the resulting peptides were subjected to a two-step phosphopeptide enrichment and separation procedure consisting of TiO2 chro-maphy enrichment combined with high pHHPLC separation.Samples were injected onto aNanolC-Ultra-2Dplus system cou-pled to an AB-Sciex 5600 Triple TOF mass spectrometer instrument.Then data analysis was performed to provide information of new identified phosphorylation sites of kinase.Results and Conclusion Using our efficient and high-throughput platform, we reported the identification of 5386 phosophorylation sites and 4553 phosphopeptides from 1533 proteins of the mouse liver.126 new phosphorylation sites were identified from 116 kinases, which provides valuable infor-mation for phosphorylation networks in the mouse liver.

Objective To elaborate the role of hepatic inherent macrophages and monocyte-derived macrophages in acute liver injury.Methods A model of acute liver injury in mice was induced via intraperitoneally injection of CCl 4 .Af-ter CCl4 injection, analysis of the expression of CD45, F4/80, Ly6C and CD11b on the hepatic macrophage surface was performed by flow cytometry at 24, 48 and 72 h before the hepatic inherent macrophages (CD45+F4/80hi) and monocyte-de-rived macrophages ( CD45+F4/80 lo ) were sorted at the same time .The relative expression of cytokines in the two popula-tions of macrophages was detected by qRT-PCR.Results Compared with control , the number of total F4/80 +cells in the liver was markedly increased after CCl 4 injection, especially at 72 h.The number of CD45+F4/80lo cells increased signifi-cantly after CCl4 injection 24 h.The mRNA levels of MCP-1, TNF-α, TGF-β1, matrix metalloproteinase(MMP)-12 and MMP-13 were elevated significantly both in F 4/80 hi and F4/80 lo macrophages .IL-12βand IL-6 mRNA levels increased significantly only in F4/80hi macrophages, while the level of MMP-9 mRNA increased markedly only in F4/80lo macropha-ges.When compared with F4/80lo macrophages, MCP-1 and MMP-12 mRNA levels were elevated significantly , while the level of TNF-αmRNA decreased significantly in F4/80hi macrophages.Conclusion In acute liver injury, hepatic inherent macrophages and monocyte-derived macrophages both express inflammatory cytokines , promoting inflammation response and leading to liver damage .The ability to recruit inflammatory monocytes into the liver is much stronger ,the expression of in-flammatory cytokines ( IL-12βand IL-6 ) and MMP-12 is higher , but the expression of inflammatory cytokines ( TNF-α) MMP-9 is lower in hepatic inherent macrophages than in monocyte-derived macrophages .

Microtubules play important roles in mitotic spindle assembly and chromosome segregation to maintain normal cell cycle progression. A number of microtubule-associated proteins have been identified in epithelial and neural cell cultures; however, their physiological significance is not well characterized due to the lack of appropriate in vivo animal models. Nucleolar spindle-associated protein (NuSAP) is a microtubule-binding protein and is reported to be involved in mitosis by cell culture studies. In this report, we identified the zebrafish homologue of human NuSAP and investigated its expression profile and functions. Using in situ hybridization, we demonstrated that transcripts of zebrafish nusap1 are specifically expressed in the retina, forebrain, hindbrain and neural crest. When the in vivo expression of nusap1 was knocked down through antisense oligonucleotide morpholino technology, the morphants of nusap1 showed impaired morphogenesis in the trunk and yolk extension, implying the involvement of Nusap1 in cell migration. Mechanistic studies revealed that nusap1 morphants have an altered expression pattern of neural crest markers crestin and sox9b, but normal expression of blood vessel and notochord markers gata1 and shh. In addition, nusap1 mRNA injection caused serious apoptosis in retina and hindbrain tissue, and these phenotypes can be rescued by co-injection of morpholino against nusap1. These observations not only suggest a role for Nusap1 in connecting apoptosis with cell migration, but also provide strong evidences that Nusap1 is potentially involved in morphogenesis in vertebrates.
Amino Acid Sequence ; Animals ; Animals, Genetically Modified ; Apoptosis ; genetics ; physiology ; Base Sequence ; Cell Movement ; genetics ; physiology ; Cloning, Molecular ; DNA Primers ; genetics ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Gene Knockdown Techniques ; Humans ; In Situ Hybridization ; Microtubule-Associated Proteins ; genetics ; physiology ; Molecular Sequence Data ; Neural Crest ; cytology ; embryology ; physiology ; Phylogeny ; Sequence Homology, Amino Acid ; Zebrafish ; embryology ; genetics ; Zebrafish Proteins ; genetics ; physiology