Abstract:Membrane-less and membrane-bound organelles provide sites for many crucial biological processes to take place within eukaryotic cells. Signalling and exchange of materials occurring at membrane contact sites (MCSs) among membrane-bound organelles are also vital for cell homeostasis. Proteomic mapping of molecular machineries within membrane-less organelles or MCSs are essential for the understanding all those events within such sites, as well as for the study of organelle interactions. However， the attempts to dissect molecular determinants in these sites using traditional biochemical techniques were far from fruitful. Recent advances in proximity labelling techniques provide an ideal solution for this challenge. Mostly by utilizing different type of biotin ligases which fused to target proteins， proteomes surrounding the target protein (within tens of nanometers) could be tagged (often with biotin or its derivatives). These covalently labelled proteins could then be enriched and identified with mass spectrometry.Here，we reviewed most recent advances in proximity labeling approaches， hoping to provide a general guide for researches focusing on proteomic mapping of molecular machineries within organelles or MCSs.

Abstract:Cancer stem cells(CSCs) are a small group of special undifferentiated cells in tumor tissues. Because of the drug tolerance and tumorigenic potential, CSCs are considered to be the source of tumor occurrence, recurrence and metastasis. Therefore, it is very significant to understand the characteristics of CSCs in augmenting clinical therapeutic efficiency. In tumor microenvironment the complex crosstalk between immune cells and CSCs sustains the stemness and self-renewal ability of CSCs. The effect of immune microenvironment on CSCs, the role of CSCs in shaping immune microenvironment, and the targeted therapy of CSCs or immune microenvironment are hot topics in this field. In this review, the effects of immune microenvironment on the characteristics of CSCs and the research progress of targeting CSCs and microenvironment are summarized.

Abstract:Cancer is a serious disease that endangers human health. Solid tumors are surrounded by extracellular matrix, infiltrated immune cells, and the secretum of surrounding mesenchymal cells. The tumor microenvironment plays a key role in tumorigenesis, tumor growth, and resistance to antineoplastic therapy. Plasminogen activator inhibitor-1 (PAI-1) is an important regulatory factor in tumor microenvironment. PAI-1 not only functions as a key constitution with tissue-type plasminogen activators (tPA) in regulating fibrinolytic activity, but also participates in invasion, infiltration and migration of tumor. In this paper, the structure and function of PAI-1 and its significance in tumor microenvironment in recent years are reviewed. It is considered that PAI-1 may be an important target for anti-cancer therapy. At the same time, the latest research results of PAI-1 inhibitors in the field of anticancer were analyzed, and the potential application value of PAI-1 inhibitors was demonstrated.

Abstract:Long noncoding RNA(lncRNA) is the most important transcript in the transcriptomes of many complex organisms. LncRNA has low conservation and expression level among various organisms. Compared with coding genes, lncRNAs have similar promoter regions and splicing sites, and have better cellular and tissue-specific distribution, especially in the nervous system. The rich expression of lncRNAs suggests that they play an important role in the nervous system. Based on the latest research results of lncRNAs in the neural system in recent years, this review summarizes the regulatory roles and mechanisms of lncRNAs in the development of central and peripheral nervous system and the function of nervous system. At the same time, the new ideas and technologies of lncRNA research are prospected, which will promote the future research of neuroscience.

Abstract:DNA methylation abnormalities are frequent events in early tumors. Additionally, DNA methylation is relatively stable over time and can be non-invasively detected in blood. Therefore, DNA methylation has a great potential to become an early diagnostic biomarker of cancers. In order to find potential diagnostic markers for lung squamous cell carcinoma (LUSC), a method for identifying LUSC-specific candidate diagnostic markers was proposed. We screened 6 LUSC-specific CpGs by comparing the methylation profiles of 172 samples from LUSC patients, 42 normal lung samples, 184 normal blood samples, and 1 306 samples from patients with other cancers which was collected from TCGA (The Cancer GenomeAtlas) database. A supportvector machine model was constructed to distinguish LUSC patients from normal controls. The combination of six sites achieved 93%-99% sensitivity in predicting LUSC, 100% specificity in excluding all normal samples, and ~ 99% specificity in excluding other cancers. Overall, our study provides promising biomarkers for the diagnosis of LUSC.

Abstract:The centrosome is the principal microtubule organizing center in most animal cells. It ensures orderly cell cycle progression with accurate chromosome segregation. We have previously reported that the centrosomal protein Centlein functions as a molecular linker between C-Nap1 and Cep68 to maintain centrosome cohesion. To explore novel function of Centlein, in this study, we generated Centlein knockout cell lines, and performed RNA-seq and data analysis on Centlein knock out and control cells, in parallel. Ablation of Centlein upregulated PLK1, CCNB1, CCNA2 and CDC20, and promoted cell cycle progression. PLK1 protein, found elevated in Centlein knock out cells, interacted with Centlein in vivo. We propose that centrosomal PLK1 exerting control over the cell cycle relies upon the interaction with Centlein.

Abstract:Derivatives of 4-hydroxy-6-methyl-2-pyrone（2-pyrone） are actively involved in plant resistance to insects and pathogens, and are considered as potential renewable chemical platforms for phloroglucinol and 1,3,5-triamino-2,4,6-trinitrobenzene. 2-Pyrone synthase (2PS), one of the type Ⅲ polyketide synthases (PKSs), is the key enzyme to produce 2-pyrone. In this study, a novel Pc2PS was isolated from Polygonum cuspidatum Sieb. et Zucc., a traditional Chinese herb used for the treatment of cough, suppurative conditions, and hypertension. The Pc2PS shared 54%–56% amino acid sequence identity with 2PSs of other species. Enzymatic activity analysis showed that Pc2PS could catalyze the condensation of one molecule of acetyl-CoA with two molecules of malonyl-CoA at almost the same efficiency as that of three molecules of malonyl-CoA alone for production of 4-hydroxy-6-methyl-2-pyrone. Thus, the presence or absence of acetyl-CoA in the reaction mixture did not affect catalytic efficiency. This catalytic property of Pc2PS differs from that of previously reported Gh2PSs, which catalyzed malonyl-CoA condensation to form the same products as Pc2PS but at a lower rate in the absence of acetyl-CoA. In addition, we determined the kinetics of Pc2PS with malonyl-CoA alone as the substrate for the first time. Pc2PS showed tissue-specific expression in P. cuspidatum; Pc2PS was predominantly expressed in the root, whereas few transcripts were detected in the leaf. This study enriches the known diversity of 2PS proteins, and provides a novel genetic resource for 2-pyrone biosynthesis.

Abstract:Tumor neoantigens are important targets for immunotherapy. Based on high-throughput tumor genomic analysis, each missense mutation can potentially give rise to multiple neopeptides, numerous false positive neoantigens will be produced, experimental verification would require immense time and experience. Specific identification of immunogenic candidate neoantigens is consequently a major challenge. Here we introduce a workflow to predict and filter neoantigens of breast cancer with proteogenomic methodology, which can be beneficial to high quality identification of neoantigens. We found that C2 (IFN-γdominant) immunophenotype possessed the most number of neoantigens. C2 immunophenotype shows the highest M1/M2 macrophage polarization, a strong CD8 signal and the greatest T cell receptor(TCR) diversity, which may lead to more neoantigen number than in other immunophenotypes of breast cancer. In addition, we also observed that there is a positive linear relationship between neoantigen number and tumor mutation burden. By further screening for predicted tumor mutant peptides using mass spectral data of breast cancer, we found that more than 20 000 predicted neoantigens were reduced to dozens of mutant peptides in protein expression level, the corresponding mutant genes could be further analyzed. Finally, in order to define which neoantigens were more likely to be immunogenic, TCR recognition probability was calculated using blastp method. In this study, proteomics data was used to further screen the predicted neoantigens, which improved the prediction accuracy of neoantigens, and could greatly reduce the validation scope of potential subsequent experiments. This workflow provides a new insight for tumor neoantigen prediction and screening.

Abstract:Restriction free cloning(RFC) is a simple and universal DNA cloning technology developed in recent years, which can accurately insert the target DNA sequence into any position of any plasmids. It is a novel DNA recombination method that is not limited by restriction endonuclease, efficiency of ligase, length of target DNA sequence or vector sequence. Compared with other cloning methods, RFC technology has irreplaceable advantages. On the basis of summarizing the researches of RFC at home and abroad, this manuscript systematically introduces the action principle, characteristics and research progress of RFC technology and discuss its application value in molecular biology and synthetic biology.