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Transcriptomics and proteomics in stem cell research

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《医学前沿（英文）》 2014年第8卷第4期页码 433-444 doi: 10.1007/s11684-014-0336-0

摘要：

Stem cells are capable of self-renewal and differentiation, and the processes regulating these events are among the most comprehensively investigated topics in life sciences. In particular, the molecular mechanisms of the self-renewal, proliferation, and differentiation of stem cells have been extensively examined. Multi-omics integrative analysis, such as transcriptomics combined with proteomics, is one of the most promising approaches to the systemic investigation of stem cell biology. We reviewed the available information on stem cells by examining published results using transcriptomic and proteomic characterization of the different stem cell processes. Comprehensive understanding of these important processes can only be achieved using a systemic methodology, and employing such method will strengthen the study on stem cell biology and promote the clinical applications of stem cells.

关键词： embryonic stem cells transcriptomics proteomics

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Application of proteomics in environmental science

Xiaona CHU, Jiangyong HU, Say Leong ONG,

《环境科学与工程前沿（英文）》 2009年第3卷第4期页码 393-403 doi: 10.1007/s11783-009-0145-x

摘要： Proteomics involves the separation of proteins, identification of the amino acid sequence of the interested or target proteins, study of the function of the proteins, modification, structure and ultimate assignments to functional pathways in the cell. The proteomic investigations have contributed greatly to human diseases studies, new drugs discovery researches, and environmental science in recent years. This article provides a review on the development of the main proteomic technologies, including both the gel based and non-gel based technologies, and their applications in environmental science. Proteomic technologies have been utilized in the environmental stresses studies to analyze the induction or reduction of proteins at expression level and identify the target proteins to investigate their function in response to environmental stresses, such as high or low pH, oxidation stress, and toxic chemicals. Such protein responses are also helpful to understand the mechanisms of some cellular activities and the functions of some proteins.

关键词： proteomics environmental stress two dimensional (2D) gel electrophoresis mass spectrometry

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Quantitative proteomics revealed extensive microenvironmental changes after stem cell transplantation

《医学前沿（英文）》 2022年第16卷第3期页码 429-441 doi: 10.1007/s11684-021-0842-9

摘要： The local microenvironment is essential to stem cell-based therapy for ischemic stroke, and spatiotemporal changes of the microenvironment in the pathological process provide vital clues for understanding the therapeutic mechanisms. However, relevant studies on microenvironmental changes were mainly confined in the acute phase of stroke, and long-term changes remain unclear. This study aimed to investigate the microenvironmental changes in the subacute and chronic phases of ischemic stroke after stem cell transplantation. Herein, induced pluripotent stem cells (iPSCs) and neural stem cells (NSCs) were transplanted into the ischemic brain established by middle cerebral artery occlusion surgery. Positron emission tomography imaging and neurological tests were applied to evaluate the metabolic and neurofunctional alterations of rats transplanted with stem cells. Quantitative proteomics was employed to investigate the protein expression profiles in iPSCs-transplanted brain in the subacute and chronic phases of stroke. Compared with NSCs-transplanted rats, significantly increased glucose metabolism and neurofunctional scores were observed in iPSCs-transplanted rats. Subsequent proteomic data of iPSCs-transplanted rats identified a total of 39 differentially expressed proteins in the subacute and chronic phases, which are involved in various ischemic stroke-related biological processes, including neuronal survival, axonal remodeling, antioxidative stress, and mitochondrial function restoration. Taken together, our study indicated that iPSCs have a positive therapeutic effect in ischemic stroke and emphasized the wide-ranging microenvironmental changes in the subacute and chronic phases.

关键词： ischemic stroke microenvironment induced pluripotent stem cells (iPSCs) positron emission tomography (PET) quantitative proteomics

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Sepsis biomarkers: an omics perspective

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《医学前沿（英文）》 2014年第8卷第1期页码 58-67 doi: 10.1007/s11684-014-0318-2

摘要：

Sepsis is a common cause of death in hospitalized patients worldwide. The early detection of sepsis remains a great challenge for clinicians, and delayed diagnosis frequently undermines treatment efforts, thereby contributing to high mortality. Omics technologies allow high-throughput screening of sepsis biomarkers. This review describes currently available and novel sepsis biomarkers in the context of genomics, transcriptomics, proteomics, and metabolomics. The combination of these technologies can help refine the diagnosis of sepsis. This review paper serves as a reference for future studies that employ an integrated, multi-omics approach to disease identification.

关键词： sepsis biomarker genomics transcriptomics proteomics metabolomics

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Identification of transporter proteins for PQQ-secretion pathways by transcriptomics and proteomics analysis

Hui Wan,Yu Xia,Jianghua Li,Zhen Kang,Jingwen Zhou

《化学科学与工程前沿（英文）》 2017年第11卷第1期页码 72-88 doi: 10.1007/s11705-016-1580-4

摘要： Pyrroloquinoline quinone (PQQ) plays a significant role as a redox cofactor in combination with dehydrogenases in bacteria. These dehydrogenases play key roles in the oxidation of important substrates for the biotechnology industry, such as vitamin C production. While biosynthesis of PQQ genes has been widely studied, PQQ-transport mechanisms remain unclear. Herein, we used both two-dimensional fluorescence-difference gel electrophoresis tandem mass spectrometry and RNA sequencing to investigate the effects of overexpression in an industrial strain of WSH-003. We have identified 73 differentially expressed proteins and 99 differentially expressed genes, a majority of which are related to oxidation-reduction and transport processes by gene ontology analysis. We also described several putative candidate effectors that responded to increased PQQ levels resulting from overexpression. Furthermore, quantitative PCR was used to verify five putative PQQ-transport genes among different PQQ producing strains, and the results showed that , and were upregulated in all conditions. Then the three genes were over-expressed in WSH-003 and PQQ production were detected. The results showed that extracellular PQQ of B932_1930 (a transporter) and B932_2186 (an ABC transporter permease) overexpression strains were enhanced by 1.77-fold and 1.67-fold, respectively. The results suggest that the proteins encoded by PqqB, B932_1930 and B932_2186 might enhance the PQQ secretion process.

关键词： 2D-DIGE pqqB pyrroloquinoline quinone RNA-Seq Vitamin C

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Proteomics study of Mycoplasma pneumoniae pneumonia reveals the Fc fragment of the IgG-binding protein

《医学前沿（英文）》 2022年第16卷第3期页码 378-388 doi: 10.1007/s11684-021-0840-y

摘要： Macrolide and corticosteroid resistance has been reported in patients with Mycoplasma pneumoniae (MP) pneumonia (MPP). MP clearance is difficult to achieve through antibiotic treatment in sensitive patients with severe MPP (SMPP). SMPP in children might progress to airway remodeling and even bronchiolitis/bronchitis obliterans. Therefore, identifying serum biomarkers that indicate MPP progression and exploring new targeted drugs for SMPP treatment require urgency. In this study, serum samples were collected from patients with general MPP (GMPP) and SMPP to conduct proteomics profiling. The Fc fragment of the IgG-binding protein (FCGBP) was identified as the most promising indicator of SMPP. Biological enrichment analysis indicated uncontrolled inflammation in SMPP. ELISA results proved that the FCGBP level in patients with SMPP was substantially higher than that in patients with GMPP. Furthermore, the FCGBP levels showed a decreasing trend in patients with GMPP but the opposite trend in patients with SMPP during disease progression. Connectivity map analyses identified 25 possible targeted drugs for SMPP treatment. Among them, a mechanistic target of rapamycin kinase (mTOR) inhibitor, which is a macrolide compound and a cell proliferation inhibitor, was the most promising candidate for targeting SMPP. To our knowledge, this study was the first proteomics-based characterization of patients with SMPP and GMPP.

关键词： severe Mycoplasma pneumoniae pneumonia children proteomics Fc fragment of the IgG-binding protein mechanistic target of rapamycin kinase inhibitor

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Transmembrane transport of polycyclic aromatic hydrocarbons by bacteria and functional regulation of membrane proteins

Hongqi Wang, Ruhan Jiang, Dekang Kong, Zili Liu, Xiaoxiong Wu, Jie Xu, Yi Li

《环境科学与工程前沿（英文）》 2020年第14卷第1期 doi: 10.1007/s11783-019-1188-2

摘要： Explaintheadsorption, uptake and transmembrane transport of PAHs by bacteria. Analyze functional regulation of membrane proteins inthe transmembrane transport. Proteomics technology such as iTRAQ labeling was used to access expressed proteins. Single cell analysis technology wereused to study the morphological structure. In recent years, increasing research has been conducted on transmembrane transport processes and the mechanisms behind the microbial breakdown of polycyclic aromatic hydrocarbons (PAHs), including the role of membrane proteins in transmembrane transport and the mode of transmission. This article explains the adsorption, uptake and transmembrane transport of PAHs by bacteria, the regulation of membrane protein function during the transmembrane transport. There are three different regulation mechanisms for uptake, depending on the state and size of the oil droplets relative to the size of the microbial cells, which are (i) direct adhesion, (ii) emulsification and pseudosolubilization, and (iii) interfacial uptake. Furthermore, two main transmembrane transport modes are introduced, which are (i) active transport and (ii) passive uptake and active efflux mechanism. Meanwhile, introduce the proteomics and single cell analysis technology used to address these areas of research, such as Isobaric tags for relative and absolute quantitation (iTRAQ) technology and Nano Secondary ion mass spectrometry (Nano-SIMS). Additionally, analyze the changes in morphology and structure and the characteristics of microbial cell membranes in the process of transmembrane transport. Finally, recognize the microscopic mechanism of PAHs biodegradation in terms of cell and membrane proteins are of great theoretical and practical significance for understanding the factors that influence the efficient degradation of PAHs contaminants in soil and for remediating the PAHs contamination in this area with biotechnology.

关键词： Polycyclic aromatic hydrocarbons Transmembrane transport Adsorption and uptake of hydrocarbons Proteomics Functional regulation of membrane protein Single cell analysis technology