An Integrative Meta-analysis of MicroRNAs in Hepatocellular Carcinoma

We aimed to shed new light on the roles of microRNAs （miRNAs） in liver cancer using an integrative in silico bioinformatics analysis. A new protocol for target prediction and functional analysis is presented and applied to the 26 highly differentially deregulated miRNAs in hepatocellular carcinoma. This framework comprises： （1） the overlap of prediction results by four out of five target prediction tools, including TargetScan, PicTar, miRanda, DIANA-microT and miRDB （combining machine-learning, alignment, interaction energy and statistical tests in order to minimize false positives）, （2） evidence from previous microarray analysis on the expression of these targets, （3） gene ontology （GO） and pathway enrichment analysis of the miRNA targets and their pathways and （4） linking these results to oncogenesis and cancer hallmarks. This yielded new insights into the roles of miRNAs in cancer hallmarks. Here we presented several key targets and hundreds of new targets that are significantly enriched in many new cancer-related hallmarks. In addition, we also revealed some known and new oncogenic pathways for liver cancer. These included the famous MAPK, TGFβ and cell cycle pathways. New insights were also provided into Wnt signaling, prostate cancer, axon guidance and oocyte meiosis pathways. These signaling and developmental pathways crosstalk to regulate stem cell transformation and implicate a role of miRNAs in hepatic stem cell deregulation and cancer development. By analyzing their complete interactome, we proposed new categorization for some of these miRNAs as either tumor-suppressors or oncomiRs with dual roles. Therefore some of these miRNAs may be addressed as therapeutic targets or used as therapeutic agents. Such dual roles thus expand the view of miRNAs as active maintainers of cellular homeostasis.     

The origin and functions of the insect peritrophic membrane and peritrophic gel

There is a a fluid (peritrophic gel) or membranous (peritrophic membrane, PM) film surrounding the food bolus in most insects. The PM is composed of chitin and proteins, of which peritrophins are the most important. It is proposed here that, during evolution, midgut cells initially synthesized chitin and peritrophins derived from mucins by acquiring chitin-binding domains, thus permitting the formation of PM. Since PM compartmentalizes the midgut, new physiological roles were added to those of the ancestral mucus (protection against abrasion and microorganism invasion). These new roles are reviewed in the light of data on PM permeability and on enzyme compartmentalization, fluid fluxes, and ultrastructure of the midgut. The importance of the new roles in relation to those of protection is evaluated from data obtained with insects having disrupted PM. Finally, there is growing evidence suggesting that a peritrophic gel occurs when a highly permeable peritrophic structure is necessary or when chitin-binding molecules or chitinase are present in food.     

Embryonic stem cells shed new light on the developmental roles of p53

The viability and subtle developmental defects of p53 knockout mice suggest that p53 does not play major role in development. However, contradictory evidence also exists. This discrepancy mainly results from the lack of molecular and cellular mechanisms and the general fact that p53 activation requires stresses. Recent studies of p53 in mouse and human ES cells and induced pluripotent stem (iPS) cells shed new light on the mechanisms of the developmental roles of p53. This review summarizes these new studies that support the developmental roles of p53, highlights the possible underlying molecular mechanisms, and discusses the potential relationship between the developmental roles and the tumor suppressive function of p53. In summary, the molecular mechanisms underlying the developmental roles of p53 are emerging, and the developmental roles and tumor suppressive function of p53 may be closely related.     

Design, synthesis and bioactions of novel stable mimetics of lipoxins and aspirin-triggered lipoxins

The lipoxins (LX) are a class of potent endogenous oxygenated products that are enzymatically generated from arachidonic acid and have novel anti-inflammatory properties and promote resolution. Elucidation of the biochemical pathways involved in the metabolic inactivation of LX and the discovery of the aspirin-triggered lipoxins (ATL) provided the basis for the design and synthesis of stable analogs of LX and ATL. This special issue review describes the efforts that led to the design and synthesis of stable LX/ATL mimetics, which permitted the detailed elucidation of their novel biological roles, leading to the development of new anti-inflammatory agents that mimic their actions. These synthetic molecules provided the means to uncover the physiologic roles of both the LX and the ATL biosynthetic pathways which led to several unexpected discoveries. Among these findings is the involvement of polyisoprenyl phosphates (PIPP) in intracellular signaling mediated by presqualene diphosphate (PSDP), and the recognition of the novel roles of these lipid mediators in regulating cell trafficking during inflammation as well as in promoting resolution of inflammatory processes. These efforts also provided the basis for examining the potential therapeutic role of LX/ATL stable mimetics and led to the development of new analogs with improved pharmacokinetics that opened the way to potentially new approaches to treating human diseases.     

The roles of cytoplasmic poly(A)-binding proteins in regulating gene expression: a developmental perspective.

Poly(A)-binding proteins (PABPs) are central to the regulation of messenger RNA (mRNA) translation and stability; however, the roles and contributions of different PABP family members in controlling gene expression are not yet fully understood. In this paper, the current state of knowledge of the different cytoplasmic PABP proteins and their function in animal cells will be summarised, with particular reference to their roles in development. Possible regulatory mechanisms and potential new roles for these proteins in the control of specific mRNAs are also highlighted.     

Regulatory roles of cyclin dependent kinase phosphorylation in cell cycle control

Cyclins and cyclin-dependent kinases (Cdks) are universal regulators of cell cycle progression in eukaryotic cells. Cdk activity is controlled by phosphorylation at three conserved sites, and many of the enzymes that act on these sites have now been identified. Although the biochemistry of CdK phosphorylation is relatively well understood, the regulatory roles of such phosphorylation are, in many cases, obscure. Recent studies have uncovered new and unexpected potential roles, and prompted re-examination of previously assumed roles, of Cdk phosphorylation.     

二氧化硫生物学研究进展:从毒理学到生理学

本文以作者20余年的系列研究为基础,对二氧化硫(SO2)生物学研究进展进行了综述.首先,总结近年来SO2的毒理学作用及其机制的研究;其次,评述SO2作为一种新型气体信号分子的生理学作用及SO2供体方面的最新研究进展;最后介绍SO2的病理生理学作用的研究进展.     

Functional lipidomics: the roles of specialized lipids and lipid-protein interactions in modulating neuronal function

Lipids fulfill multiple specialized roles in neuronal function. In brain, the conduction of electrical impulses, synaptic function, and complex signaling pathways depend on the temporally and spatially coordinated interactions of specialized lipids (e.g., arachidonic acid and plasmalogens), proteins (e.g., ion channels, phospholipases and cyclooxygenases) and integrative lipid-protein interactions. Recent technical advances in mass spectrometry have allowed unparalled insight into the roles of lipids in neuronal function. Through shotgun lipidomics and multidimensional mass spectrometry, in conjunction with the identification of new classes of phospholipases (e.g., calcium dependent and calcium independent intracellular phospholipases), new roles for lipids in cerebral function have been accrued. This review summarizes the advances in our understanding of the types of lipids and phospholipases in the brain and the role of functional lipidomics in increasing our chemical understanding of complex neuronal processes.     

The Role of ATP Receptors in Pain Signaling

Neurochemical Research - Since new roles of nucleotides as neurotransmitters were proposed by Geoffrey Burnstock, the roles of ATP and P2 receptors (P2Rs) have been extensively studied in pain...     

Fibroblasts: The arbiters of extracellular matrix remodeling

Extracellular matrix (ECM) is the foundation on which all cells and organs converge to orchestrate normal physiological functions. In the setting of pathology, the ECM is modified to incorporate additional roles, with modifications including turnover of existing ECM and deposition of new ECM. The fibroblast is center stage in coordinating both normal tissue homeostasis and response to disease. Understanding how fibroblasts work under normal conditions and are activated in response to injury or stress will provide mechanistic insight that triggers discovery of new therapeutic treatments for a wide range of disease. We highlight here fibroblast roles in the cancer, lung, and heart as example systems where fibroblasts are major contributors to homeostasis and pathology.     

Perspective: genetic and hormonal roles in bone disorders: insights of an updated bone physiology

In 1997 Professor J. Gorski suggested endocrinology needed new paradigms (Endocrine News 1997; 22:4,12). 'Connecting the dots' between diverse facts and ideas drawn from many lines of inquiry, plus accumulating evidence and increasing inadequacies of earlier ideas and terminology, led to an updated bone physiology called the 'Utah paradigm' that reveals new genetic and hormonal potential roles in bone physiology and disorders. One way to find a bone disorder's cause(s) and treatment( s) could depend on understanding the underlying physiology well enough to design effective drugs for it. In early views cell-level effects on osteoblasts and osteoclasts could explain most endocrine and genetic roles in bone disorders. The updated bone physiology supplements those views with roles of bone's tissue-level 'nephron-equivalent' mechanisms (NEMs) and their functions (NEFs), including some roles of biomechanics, whole-bone strength and muscle strength. That updated physiology reveals at least 42 nexuses above the cell level, some of them extraosseous, where genetic and/or hormonal effects might cause or help to treat varied bone problems. That multifactorial physiology also suggests that in vivo skeletal phenomena usually depend on many interlocking, laddered and nested feedback systems. Due to lack of study, how genes and hormones affect those nexuses and feedback systems still remains nearly unknown. Because studies of bone physiology in in vitro systems seldom if ever correctly predicted the in vivo effects, further live-animal research should seek the in vivo effects. This article suggests why more of that kind of research is needed, and some directions it could take.     

Kisspeptin在女性生殖内分泌和辅助生殖技术中的研究进展

近年来研究显示,kisspeptin在大脑的性别分化、性激素正负反馈调节、青春期始动以及机体能量信号转导等生理过程中起到重要作用,表明kisspeptin可能是女性生殖功能成熟及调控的一个关键性信号因子。除下丘脑分泌的kisspeptin之外,生殖器官局部表达的kisspeptin在机体正常生殖过程中的作用也不断得到证实。研究表明,很多生殖内分泌疾病,如单纯性促性腺激素分泌不足的性腺机能减退症(isolated hypogonadotropic hypogonadism, IHH)、多囊卵巢综合征(polycystic ovary syndrome, PCOS)、卵巢早衰(premature ovarian failure, POF)、病理性高泌乳素血症等,都与kisspeptin的异常表达有关。通过给予外源性kisspeptin可解决辅助生殖技术应用中的一些问题。本文主要就kisspeptin在女性生殖内分泌尤其是在辅助生殖领域研究中所取得的进展进行论述。     

Endocytosis and sorting of glycosphingolipids in sphingolipid storage disease

Recent studies on the endocytic itinerary of glycosphingolipids (GSLs) in sphingolipid storage disease (SLSD) fibroblasts have yielded new insights into the mechanisms underlying the endocytosis and intracellular sorting of lipids in normal and disease cells. Here we highlight new data on clathrin-independent endocytosis of GSLs, the involvement of sphingolipid–cholesterol interactions in perturbation of endocytic trafficking, and potential roles for rab proteins in regulation of GSL transport in SLSDs.     

Disease causing mutations in the TNF and TNFR superfamilies: Focus on molecular mechanisms driving disease

The tumor necrosis factor (TNF) and TNF receptor (TNFR) superfamilies comprise multidomain proteins with diverse roles in cell activation, proliferation and cell death. These proteins play pivotal roles in the initiation, maintenance and termination of immune responses and have vital roles outside the immune system. The discovery and analysis of diseases associated with mutations in these families has revealed crucial mechanistic details of their normal functions. This review focuses on mutations causing four different diseases, which represent distinct pathological mechanisms that can exist within these superfamilies: autoimmune lymphoproliferative syndrome (ALPS; FAS mutations), common variable immunodeficiency (CVID; TACI mutations), tumor necrosis factor receptor associated periodic syndrome (TRAPS; TNFR1 mutations) and hypohidrotic ectodermal dysplasia (HED; EDA1/EDAR mutations). In particular, we highlight how mutations have revealed information about normal receptor-ligand function and how such studies might direct new therapeutic approaches.     

The cellular language of myo-inositol signaling

The simple polyol, myo-inositol, is used as a building block of a cellular language that plays various roles in signal transduction. This review describes the terminology used to denote myo-inositol-containing molecules, with an emphasis on how phosphate and fatty acids are added to create second messengers used in signaling. Work in model systems has delineated the genes and enzymes required for synthesis and metabolism of many myo-inositol-containing molecules, with genetic mutants and measurement of second messengers playing key roles in developing our understanding. There is increasing evidence that molecules such as myo- inositol(1,4,5)trisphosphate and phosphatidylinositol(4,5)bisphosphate are synthesized in response to various signals plants encounter. In particular, the controversial role of myo-inositol(1,4,5)trisphosphate is addressed, accompanied by a discussion of the multiple enzymes that act to regulate this molecule. We are also beginning to understand new connections of myo-inositol signaling in plants. These recent discoveries include the novel roles of inositol phosphates in binding to plant hormone receptors and that of phosphatidylinositol(3)phosphate binding to pathogen effectors.