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Transcriptomics and proteomics in stem cell research

null

《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    

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    

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    

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    

Multi-omics joint analysis revealed the metabolic profile of retroperitoneal liposarcoma

《医学前沿(英文)》 doi: 10.1007/s11684-023-1020-z

摘要: Retroperitoneal liposarcoma (RLPS) is the main subtype of retroperitoneal soft sarcoma (RSTS) and has a poor prognosis and few treatment options, except for surgery. The proteomic and metabolic profiles of RLPS have remained unclear. The aim of our study was to reveal the metabolic profile of RLPS. Here, we performed proteomic analysis (n = 10), metabolomic analysis (n = 51), and lipidomic analysis (n = 50) of retroperitoneal dedifferentiated liposarcoma (RDDLPS) and retroperitoneal well-differentiated liposarcoma (RWDLPS) tissue and paired adjacent adipose tissue obtained during surgery. Data analysis mainly revealed that glycolysis, purine metabolism, pyrimidine metabolism and phospholipid formation were upregulated in both RDDLPS and RWDLPS tissue compared with the adjacent adipose tissue, whereas the tricarboxylic acid (TCA) cycle, lipid absorption and synthesis, fatty acid degradation and biosynthesis, as well as glycine, serine, and threonine metabolism were downregulated. Of particular importance, the glycolytic inhibitor 2-deoxy-D-glucose and pentose phosphate pathway (PPP) inhibitor RRX-001 significantly promoted the antitumor effects of the MDM2 inhibitor RG7112 and CDK4 inhibitor abemaciclib. Our study not only describes the metabolic profiles of RDDLPS and RWDLPS, but also offers potential therapeutic targets and strategies for RLPS.

关键词: RLPS     proteomics     metabolomics     lipidomics     metabolism    

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    

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    

Cross-sectional network analysis of plasma proteins/metabolites correlated with pathogenesis and therapeutic response in acute promyelocytic leukemia

《医学前沿(英文)》 doi: 10.1007/s11684-023-1022-x

摘要: The treatment of PML/RARA+ acute promyelocytic leukemia (APL) with all-trans-retinoic acid and arsenic trioxide (ATRA/ATO) has been recognized as a model for translational medicine research. Though an altered microenvironment is a general cancer hallmark, how APL blasts shape their plasma composition is poorly understood. Here, we reported a cross-sectional correlation network to interpret multilayered datasets on clinical parameters, proteomes, and metabolomes of paired plasma samples from patients with APL before or after ATRA/ATO induction therapy. Our study revealed the two prominent features of the APL plasma, suggesting a possible involvement of APL blasts in modulating plasma composition. One was characterized by altered secretory protein and metabolite profiles correlating with heightened proliferation and energy consumption in APL blasts, and the other featured APL plasma-enriched proteins or enzymes catalyzing plasma-altered metabolites that were potential trans-regulatory targets of PML/RARA. Furthermore, results indicated heightened interferon-gamma signaling characterizing a tumor-suppressing function of the immune system at the first hematological complete remission stage, which likely resulted from therapy-induced cell death or senescence and ensuing supraphysiological levels of intracellular proteins. Overall, our work sheds new light on the pathophysiology and treatment of APL and provides an information-rich reference data cohort for the exploratory and translational study of leukemia microenvironment.

关键词: acute promyelocytic leukemia     plasma proteomics     plasma metabolomics     cross-sectional correlation network     pathogenesis     treatment    

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    

标题 作者 时间 类型 操作

Transcriptomics and proteomics in stem cell research

null

期刊论文

Application of proteomics in environmental science

Xiaona CHU, Jiangyong HU, Say Leong ONG,

期刊论文

Quantitative proteomics revealed extensive microenvironmental changes after stem cell transplantation

期刊论文

Sepsis biomarkers: an omics perspective

null

期刊论文

Multi-omics joint analysis revealed the metabolic profile of retroperitoneal liposarcoma

期刊论文

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

期刊论文

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

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

期刊论文

Cross-sectional network analysis of plasma proteins/metabolites correlated with pathogenesis and therapeutic response in acute promyelocytic leukemia

期刊论文

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

期刊论文