Integration of lipidomics and metabolomics for in-depth understanding of cellular mechanism and disease progression

Mass spectrometry(MS)-based omics technologies are now widely used to profile small molecules in multiple matrices to confer comprehensive snapshots of cellular metabolic phenotypes.The metabolomes of cells,tissues,and organisms comprise a variety of molecules including lipids,amino acids,sugars,organic acids,and so on.Metabolomics mainly focus on the hydrophilic classes,while lipidomics has emerged as an independent omics owing to the complexities of the organismal lipidomes.The potential roles of lipids and small metabolites in disease pathogenesis have been widely investigated in various human diseases,but system-level understanding is largely lacking,which could be partly attributed to the insufficiency in terms of metabolite coverage and quantitation accuracy in current analytical technologies.While scientists are continuously striving to develop high-coverage omics approaches,integration of metabolomics and lipidomics is becoming an emerging approach to mechanistic investigation.Integration of metabolome and lipidome offers a complete atlas of the metabolic landscape,enabling comprehensive network analysis to identify critical metabolic drivers in disease pathology,facilitating the study of interconnection between lipids and other metabolites in disease progression.In this review,we summarize omics-based findings on the roles of lipids and metabolites in the pathogenesis of selected major diseases threatening public health.We also discuss the advantages of integrating lipidomics and metabolomics for in-depth understanding of molecular mechanism in disease pathogenesis.     

Progress in gut microbiota-host interaction

<正>Recently, the gut microbiota has been recognized as a novel endocrine organ in the human body. It produces various bioactive metabolites and participates in metabolic processes. In addition, the gut microbiota is involved in the metabolism of drugs and natural components, which in turn influences the effects of various oral medications.     

The Chloroplast Outer Envelope Membrane： The Edge of Liaht and Excitement

The chloroplast is surrounded by a double-membrane envelope at which proteins, ions, and numerous metabolites including nucleotides, amino acids, fatty acids, and carbohydrates are exchanged between the two aqueous phases, the cytoplasm and the chloroplast stroma. The chloroplast envelope is also the location where the biosynthesis and accumulation of various lipids take place. By contrast to the inner membrane, which contains a number of specific transporters and acts as the permeability barrier, the chloroplast outer membrane has often been considered a passive compartment derived from the phagosomal membrane. However, the presence of galactoglycerolipids and β-barrel membrane proteins support the common origin of the outer membranes of the chloroplast envelope and extant cyanobacteria. Furthermore, recent progress in the field underlines that the chloroplast outer envelope plays important roles not only for translocation of various molecules, but also for regulation of metabolic activities and signaling processes. The chloroplast outer envelope membrane offers various interesting and challenging questions that are relevant to the understanding of organelle biogenesis, plant growth and development, and also membrane biology in general.     

Gut microbiota bridges the iron homeostasis and host health

The gut microbiota acts as a symbiotic microecosystem that plays an indispensable role in the regulation of a number of metabolic processes in the host by secreting secondary metabolites and impacting the physiology and pathophysiology of numerous organs and tissues through the circulatory system. This relationship, referred to as the “gut-X axis”, is associated with the development and progression of disorders, including obesity, fatty liver and Parkinson’s disease. Given its importance, the gu...     

Plant peroxisomal solute transporter proteins

Plant peroxisomes are unique subcellular organelles which play an indispensable role in several key metabolic pathways, including fatty acid b-oxidation,photorespiration, and degradation of reactive oxygen species. The compartmentalization of metabolic pathways into peroxisomes is a strategy for organizing the metabolic network and improving pathway efficiency. An important prerequisite, however, is the exchange of metabolites between peroxisomes and other cell compartments. Since the first studies in the 1970s scientists contributed to understanding how solutes enter or leave this organelle.This review gives an overview about our current knowledge of the solute permeability of peroxisomal membranes described in plants, yeast, mammals and other eukaryotes. In general, peroxisomes contain in their bilayer membrane specific transporters for hydrophobic fatty acids(ABC transporter) and large cofactor molecules(carrier for ATP, NAD and CoA). Smaller solutes with molecular masses below 300–400 Da, like the organic acids malate, oxaloacetate, and 2-oxoglutarate, are shuttled via non-selective channels across the peroxisomal membrane.In comparison to yeast, human, mammals and other eukaryotes, the function of these known peroxisomal transporters and channels in plants are discussed in this review.     

Nor1, a novel cytokine-responsive regulator of pancreatic β-cell mass and function mediated by disruption of mitochondrial networks

Type 2 diabetes(T2D)is a chronic metabolic disease characterized by insulin resistance and hyperglycemia,which is ultimately linked to the loss of pancreaticβ-cells and their function[1].Understanding the pathological mechanisms ofβ-cell dysfunction in T2D may lead to development of new therapeutic approaches.Recently,compelling evidence suggests that members of the nuclear receptor 4A(NR4A)subgroup play a pivotal role inβ-cell loss[2].Nor1,also known as NR4A3,belongs to the NR4A subfamily,which also includes Nur77(NR4A1)and Nurr1(NR4A2),and is defined as a true orphan nuclear receptor with an unknown endogenous ligand or ligand independent[3].As a regulator of gene expression located in the nucleus,Nor1 exhibits tissue-specific expression,which selectively controls diverse biological processes,including cell proliferation,apoptosis,differentiation,immune homeostasis,and fuel utilization[4].Thus far,it was reported that Nor1 is involved in numerous pathologies such as cancer,inflammatory diseases,and Parkinson’s disease[4].     

Chronic alcohol consumption potentiates the development of diabetes through pancreatic β-cell dysfunction

Chronic ethanol consumption is well established as a major risk factor for type-2 diabetes(T2D), which is evidenced by impaired glucose metabolism and insulin resistance. However, the relationships between alcoholconsumption and the development of T2 D remain controversial. In particular, the direct effects of ethanol consumption on proliferation of pancreatic β-cell and the exact mechanisms associated with ethanolmediated β-cell dysfunction and apoptosis remain elusive. Although alcoholism and alcohol consumption are prevalent and represent crucial public health problems worldwide, many people believe that low-tomoderate ethanol consumption may protect against T2 D and cardiovascular diseases. However, the J- or U-shaped curves obtained from cross-sectional and large prospective studies have not fully explained the relationship between alcohol consumption and T2 D. This review provides evidence for the harmful effects of chronic ethanol consumption on the progressive development of T2 D, particularly with respect to pancreatic β-cell mass and function in association with insulin synthesis and secretion. This review also discusses a conceptual framework for how ethanolproduced peroxynitrite contributes to pancreatic β-cell dysfunction and metabolic syndrome.     

Acetylation control of metabolic enzymes in cancer： an updated version

Metabolic reprogramming is one of the critical features in cancer. Tumor cells preferentially utilize glycolysis instead of oxidative phosphorylation in the presence of oxygen, namely ＇Warburg Effect＇. Recent studies have provided new insights into the Warburg effect, elucidating metabol- ic-dependent and independent mechanisms of metabolic enzymes regulated by post-translational modifications and providing further evidence for the critical role of these tricks in cancer metabolism and tumorigenesis. Of particu- lar interest, we summarized the latest advances in both the metabolic and the non-metabolic functions of metabolic enzymes via the acetylation regulation in the Warburg effect. In addition, their potential roles in cancer metabol- ism therapy will also be briefly discussed.     

Tyrosine metabolic enzymes from insects and mammals：A comparative perspective

Differences in the metabolism of tyrosine between insects and mammals present an interesting example of molecular evolution. Both insects and mammals possess finetuned systems of enzymes to meet their specific demands for tyrosine metabolites; however, more homologous enzymes involved in tyrosine metabolism have emerged in many insect species. Without knowledge of modem genomics, one might suppose that mammals, which are generally more complex than insects and require tyrosine as a precur sor for important catecholamine neurotransmitters and for melanin, should possess more enzymes to control tyrosine metabolism. Therefore, the question of why insects actually possess more tyrosine metabolic enzymes is quite interesting. It has long been known that insects rely heavily on tyrosine metabolism for cuticle hardening and for innate immune responses, and these evolutionary constraints are likely the key answers to this question. In terms of melanogenesis, mammals also possess a high level of regulation; yet mam malian systems possess more mechanisms for detoxification whereas insects accelerate pathways like melanogenesis and therefore must bear increased oxidative pressure. Our research group has had the opportunity to characterize the structure and function of many key proteins involved in tyrosine metabolism from both insects and mammals. In this mini review we will give a brief overview of our research on tyrosine metabolic enzymes in the scope of an evolutionary perspective of mammals in comparison to insects.     

Rapid and specific isolation of intact mitochondria from Arabidopsis leaves

正Mitochondria carry out many essential metabolic processes, the dynamic of which impacts most aspects of cellular physiology(Balk and Leaver, 2001; Rose and Sheahan, 2012). Therefore, characterizing the real-time metabolism of mitochondria is of great biological significance. The major challenge for reliable and authentic measurement of mitochondrial metabolites is the pure and rapid isolation of mitochondria, which can avoid the contamination     

Proliferation and tenogenic differentiation of bone marrow mesenchymal stem cells in a porous collagen sponge scaffold

BACKGROUND Collagen is one of the most commonly used natural biomaterials for tendon tissue engineering.One of the possible practical ways to further enhance tendon repair is to combine a porous collagen sponge scaffold with a suitable growth factor or cytokine that has an inherent ability to promote the recruitment,proliferation,and tenogenic differentiation of cells.However,there is an incomplete understanding of which growth factors are sufficient and optimal for the tenogenic differentiation of rat bone marrow mesenchymal stem cells(BMSCs)in a collagen sponge-based 3D culture system.AIM To identify one or more ideal growth factors that benefit the proliferation and tenogenic differentiation of rat BMSCs in a porous collagen sponge scaffold.METHODS We constructed a 3D culture system based on a type I collagen sponge scaffold.The surface topography of the collagen sponge scaffold was observed by scanning electron microscopy.Primary BMSCs were isolated from Sprague-Dawley rats.Cell survival on the surfaces of the scaffolds with different growth factors was assessed by live/dead assay and CCK-8 assay.The mRNA and protein expression levels were confirmed by quantitative real-time polymerase chain reaction and Western blot,respectively.The deposited collagen was assessed by Sirius Red staining.RESULTS Transforming growth factorβ1(TGF-β1)showed great promise in the tenogenic differentiation of BMSCs compared to growth differentiation factor 7(GDF-7)and insulin-like growth factor 1(IGF-1)in both the 2D and 3D cultures,and the 3D culture enhanced the differentiation of BMSCs into tenocytes well beyond the level of induction in the 2D culture after TGF-β1 treatment.In the 2D culture,the proliferation of the BMSCs showed no significant changes compared to the control group after TGF-β1,IGF-1,or GDF-7 treatment.However,TGF-β1 and GDF-7 could increase the cell proliferation in the 3D culture.Strangely,we also found more dead cells in the BMSC-collagen sponge constructs that were treated with TGF-β1.Moreover,TGF-β1 promoted more collagen deposition in both the 2D and 3D cultures.CONCLUSION Collagen sponge-based 3D culture with TGF-β1 enhances the responsiveness of the proliferation and tenogenic differentiation of rat BMSCs.     

Plant water balance with tritiated water-tracing dynamical method

The conception of "metabolic pool" is introduced and an ecosystem model consisting of sand body metabolic pool, plant metabolic pool, atmospheric pool and their corresponding channels is established. In addition, the input and output terms of water balance including plant transpiration etc. are measured by tritiated water-tracing dynamical method, etc. and thus a water balance table is obtained. Finally, the plant water balance in the steppified desert environment of the Shapotou area at southeastern fringe of Tengger Desert in China is comprehensively analysed.     

Hydrogen Peroxide in Plants： a Versatile Molecule of the Reactive Oxygen Species Network

Plants often face the challenge of severe environmental conditions, which include various biotic and abiotic stresses that exert adverse effects on plant growth and development. During evolution, plants have evolved complex regulatory mechanisms to adapt to various environmental stressors. One of the consequences of stress is an increase in the cellular concentration of reactive oxygen species （ROS）, which are subsequently converted to hydrogen peroxide （H2O2）. Even under normal conditions, higher plants produce ROS during metabolic processes. Excess concentrations of ROS result in oxidative damage to or the apoptotic death of cells. Development of an antioxidant defense system in plants protects them against oxidative stress damage. These ROS and, more particularly, H2O2, play versatile roles in normal plant physiological processes and in resistance to stresses. Recently, H2O2 has been regarded as a signaling molecule and regulator of the expression of some genes in cells. This review describes various aspects of H2O2 function, generation and scavenging, gene regulation and cross-links with other physiological molecules during plant growth, development and resistance responses.     

Dynamic changes in butyrate levels regulate satellite cell homeostasis by preventing spontaneous activation during aging

The gut microbiota plays a pivotal role in systemic metabolic processes and in particular functions, such as developing and preserving the skeletal muscle system. However, the interplay between gut microbiota/metabolites and the regulation of satellite cell(SC) homeostasis,particularly during aging, remains elusive. We propose that gut microbiota and its metabolites modulate SC physiology and homeostasis throughout skeletal muscle development, regeneration, and aging process. Our investigation r...