Systems biology of the secretory pathway: What have we learned so far?

Several RNAi screens were performed in search for regulators of the secretory pathway. These screens were performed in different organisms and cell lines and relied on different readouts. Therefore, they have only little overlap among their hits, leading to the question of what we have learned from this approach so far and how these screens contributed towards an integrative understanding of the endomembrane system. The aim of this review is to revisit these screens and discuss their strengths and weaknesses as well as potential reasons for their failure to overlap with each other. As with secretory trafficking, RNAi screens were also performed on other cellular processes such as cell migration and autophagy, both of which were shown to be intimately linked to secretion. Another aim of this review is to compare the outcome of the RNAi screens on secretion, autophagy and cell migration and ask whether the functional genomic approaches have uncovered potential mechanistic insights into the links between these processes.     

Role of glycoproteins in neuronal differentiation : Inhibition of neurite outgrowth and the major cell surface glycoprotein of murine neuroblastoma cells by a purified tunicamycin homologue

Mouse neuroblastoma cells in culture can be induced to differentiate morphologically by serum deprivation or by dibutyryl cyclic AMP (db-cAMP), e.g. they appear flattened, adhere more firmly to the culture substratum and extend long neuritic processes, and thus represent a widely used model system for neuronal cells. This differentiation is accompanied by modulation of cell surface components, such as the induction of a high molecular weight (HMW) glycoprotein (200 kD). We have studied the role of glycoproteins in the process of neuronal differentiation, using a purified homologue of the antibiotic tunicamycin (Al-tunicamycin) and neuroblastoma N115 cells grown in culture. Al-tunicamycin markedly inhibited (up to 60–75%) the incorporation of radioactively labelled sugars into cellular proteins of differentiating neuroblastoma cells. Concomitantly, the cells altered their morphology, they became rounded and less adhesive and retracted their neurites. Changes in the appearance, glycosylation and electrophoretic mobility of several cellular and secreted glycoproteins were observed, when cells were incubated in the presence of Al-tunicamycin. The most striking effect of Al-tunicamycin on the composition of cellular glycoproteins was the marked reduction in appearance of the 200 kD glycoprotein. The findings suggest that glycoproteins and in particular the neuron-specific 200 kD glycoprotein, are related to morphological differentiation processes, mainly to cellular adhesion and neurite outgrowth.     

Targeting the sphingosine kinase/sphingosine 1-phosphate pathway in disease: Review of sphingosine kinase inhibitors

Sphingosine 1-phosphate (S1P) is an important bioactive sphingolipid metabolite that has been implicated in numerous physiological and cellular processes. Not only does S1P play a structural role in cells by defining the components of the plasma membrane, but in the last 20 years it has been implicated in various significant cell signaling pathways and physiological processes: for example, cell migration, survival and proliferation, cellular architecture, cell–cell contacts and adhesions, vascular development, atherosclerosis, acute pulmonary injury and respiratory distress, inflammation and immunity, and tumorogenesis and metastasis [ and ]. Given the wide variety of cellular and physiological processes in which S1P is involved, it is immediately obvious why the mechanisms governing S1P synthesis and degradation, and the manner in which these processes are regulated, are necessary to understand. In gaining more knowledge about regulation of the sphingosine kinase (SK)/S1P pathway, many potential therapeutic targets may be revealed. This review explores the roles of the SK/S1P pathway in disease, summarizes available SK enzyme inhibitors and examines their potential as therapeutic agents. This article is part of a Special Issue entitled Advances in Lysophospholipid Research.     

Synthesis and structure-activity relationship of histone deacetylase (HDAC) inhibitors with triazole-linked cap group

Histone deacetylase (HDAC) inhibition is a recent, clinically validated therapeutic strategy for cancer treatment. Small molecule HDAC inhibitors identified so far fall in to three distinct structural motifs: the zinc-binding group (ZBG), a hydrophobic linker, and a recognition cap group. Here we report the suitability of a 1,2,3-triazole ring as a surface recognition cap group-linking moiety in suberoylanilide hydroxamic acid-like (SAHA-like) HDAC inhibitors. Using “click” chemistry (Huisgen cycloaddition reaction), several triazole-linked SAHA-like hydroxamates were synthesized. Structure–activity relationship revealed that the position of the triazole moiety as well as the identity of the cap group markedly affected the in vitro HDAC inhibition and cell growth inhibitory activities of this class of compounds.     

Colocalization of APC and DLG at the tips of cellular protrusions in cultured epithelial cells and its dependency on cytoskeletons

Adenomatous polyposis coli gene product (APC) is a tumor suppressor linked to familial adenomatous polyposis and is thought to be involved in cellular polarization and migration in moving epithelial cells. APC interacts with the mammalian homolog of Discs large (DLG). DLG is a member of the membrane-associated guanylate kinase superfamily and is thought to function as a scaffolding protein that coordinates the assembly of a lateral plasma membrane-localized protein complex in epithelial cells. We confirmed the suitability of several anti-APC antibodies for immunocytochemical analysis. Using these antibodies, we showed that APC clusters were colocalized with DLG protein at cellular protrusions of subconfluent MDCK cells. A portion of the clusters was found at the tips of microtubules extending into the cellular protrusions. In addition, actin stress fibers converged near the clusters. When microtubules were disrupted by nocodazole, the colocalization of APC and DLG was lost due to the disappearance of APC clusters. However, the coclusters remained after depolymerization of actin filaments with latrunculin A. This is the first report showing colocalization of APC and DLG in non-polarized epithelial cells. This colocalization suggests that DLG functions not only at the lateral cell–cell contact sites of polarized epithelial cells but also at the protrusions of non-polarized epithelial cells through the interaction with APC protein.     

Bacterial FHA domains: neglected players in the phospho-threonine signalling game?

Forkhead-associated (FHA) domains bind phospho-threonine peptides and are known to mediate phosphorylation-dependent protein–protein interactions in a variety of eukaryotic settings. However, their role in bacterial physiology and signalling has been largely neglected. We have surveyed bacterial FHA domains and discovered that they are implicated in many bacterial processes, including regulation of cell shape, type III secretion, sporulation, pathogenic and symbiotic host–bacterium interactions, carbohydrate storage and transport, signal transduction and ethambutol resistance. The way is now open to identify the targets of each FHA domain, and their roles in cellular physiology, and perhaps even to develop novel FHA-blocking antibacterial agents.     

High Immunogenicity of the Human Leukocyte Antigen Peptidomes of Melanoma Tumor Cells

Human leukocyte antigens (HLA) bind peptides generated by limited proteolysis in cells and present them at the cell surfaces for recognition by T cells. Through this antigen presentation function they control the specificity of T cell responses and thereby adaptive immune responses. Knowledge of HLA-bound peptides is thus key to understanding adaptive immunity and to the development of vaccines and other specific immune intervention strategies. To gain insight into the antigenicity of melanomas, peptides were extracted from HLA isolated from the tumor cells, separated by two-dimensional HPLC, and sequenced by mass spectrometry. The spectra were analyzed by database-dependent MASCOT searches and database-independent de novo sequencing and, where required, confirmed with synthetic peptides, which were also used to determine their immunogenicity. Comparing four different melanoma cell lines, little overlap of the HLA-bound peptides was found, suggesting a high degree of individualization of the HLA peptidomes. This notwithstanding, the peptidomes were highly immunogenic in the patients from whom the tumor cells had been established and in unrelated patients. This broad cross-patient immunogenicity was only exceptionally related to individual peptides. The majority of the identified epitopes were derived from low to medium abundance proteins, mostly involved in sensitive cellular processes such as cell cycle control, DNA replication, control of gene expression, tumor suppressor function, and protein metabolism. The peptidomes thus provide insights into processes potentially related to tumorigenesis. Furthermore, analyses of the peptide sequences yield information on the specificity of peptide selection by HLA applicable to the developing prediction algorithms for T cell epitopes.     

The blood cells of the Antarctic icefish Chaenocephalus aceratus Lönnberg: light and electron microscopic observations

Peripheral blood and haemopoietic tissues of spleen and kidney of the icefish, Chaenocephalus aceratus were examined using LM and EM techniques. The peripheral blood contained cellular elements from all the recognized cell lines usually seen in other teleost groups. Erythrocytes were very rare; when found, they were mature or senile and fragile. Thrombocytes of two morphologies, several cell types considered to be part of the lymphoid series and monocytes/macrophages were present. Two distinctive types of granulocytes also were found; their morphologies and granulation were so different from teleost granulocytes hitherto described that their identification was impossible.     

Twisted rhabdomeres in the compound eye of a tipulid fly (Diptera)

Summary The individual rhabdomeres of the outer retinular cells (R1–6) in the tipulid fly, Ptilogyna, twist about their long axes. Proximally, the rhabdoms become partitioned off by processes from the retinular cells, so that the basal region of each rhabdomere is enclosed in a pocket formed by its own cell (Fig. 2). This organisation of the rhabdom enables each rhabdomere to twist while supported within its own retinular cell, and while the cell itself maintains its orientation with respect to the entire ommatidium. Theory predicts that the rhabdomeral twisting should significantly reduce the polarisation sensitivity of R1–6, but have little effect on the efficiency with which unpolarised light is absorbed.     

Implications of the noncoding RNAs in rheumatoid arthritis pathogenesis

Epigenetics refers to a set of regulatory mechanisms that affect gene expression, while the original sequence of the DNA remains unchanged. Because the advance of noncoding RNAs (ncRNAs), the role of microRNAs (miRNAs) has been gradually highlighted in the regulation of numerous cellular processes. A bulk of studies has identified that ncRNAs might be divided into several subtypes. On the one hand, investigations have disclosed the role of these molecules in normal physiological conditions of the cells. On the other hand, there is sufficient evidence that ncRNAs participate in the pathogenesis of diseases. Through this review article, we attempted to gain a comprehensive understanding of the role of ncRNAs, long ncRNAs, miRNAs, and other subtypes in pathogenesis, diagnosis, and treatment of rheumatoid arthritis (RA). Research demonstrated aberrant expression of several miRNAs in various cell and tissue types of patients with RA in comparison to the healthy individuals as well as in animal studies. Furthermore, plausible molecular mechanisms of alterations in ncRNAs expression has been discussed in causing the disease state. These alterations seem promising to be used as biomarkers in RA diagnosis. Alternately, they might be targeted by drugs to interrupt inflammation and other disease complications to treat patients with RA.     

Determining to Divide: How Do Cells Decide?

A cell's decision to divide must be regulated with the highest fidelity. Otherwise, abnormalities occurring in the replication of genetic material and cytokinesis would be incompatible with life. It has been known for almost a century that cells comprising a population undergo cellular division at extremely variable rates, even though genetically identical cell clones have been examined. Studies with T lymphocytes at the single cell level have revealed that the rate of cellular division is determined by the accumulation of a critical number of ligand-triggered interleukin-2 (IL2) receptors at the cell surface throughout the G₁ phase of the cell cycle. Thus, the cell “counts” the number of triggered IL2 receptors, and only decides to divide when the critical number has been attained. This information is then transferred to the cellular interior via intracellular sensors comprised of D-type cyclins, which ultimately determine when the cell surpasses the “Restriction Point” in late G₁, and which commits the cell irrevocably to initiate DNA replication. Beyond the R-point, the cell assembles a definite number of macromolecular pre-replication complexes (Pre-RCs) comprised of at least 6 distinct proteins at sites of the origin of replication on DNA. Complete assembly of the Pre-RCs is a prerequisite for their subsequent disassembly, which must occur before the initiation of DNA strand replication, and which occurs asynchronously throughout the S-phase of the cell cycle and only terminates when the entire DNA has been duplicated. Thus, the fidelity of the decision to divide is exquisitely regulated by macromolecular mechanisms initiated at the cell surface and transferred to the cellular interior so that the cell can make the decision in a quantal (all-or-none) fashion. The question before us is how this quantal decision is made at the molecular level. The available data indicate that the assembly and disassembly of a definite number of large multicomponent macromolecular complexes make the quantal decisions. Here, it is postulated that all fundamental cellular decisions, i.e. survival, death, proliferation and differentiation, are regulated in this fashion. It remains to be determined how the cell counts the signals it receives, and what the molecular forces are that dictate the behavior of macromolecular complexes. Alexander Hamilton: “The best security for the fidelity of men, is to make interest coincide with duty.”     

MicroRNAs在系统性硬化症纤维化中的作用及机制

微RNA（microRNAs,miRNAs）是在基因编码中起负性调控作用的内源性短链非编码RNA（non-coding RNAs,ncRNAs）,是生理和病理过程中基因表达必不可少的转录后调控物。miRNAs占人类基因组的1%～2%,通过与各自的mRNA结合并抑制其翻译,调节大于50%的人类基因及60%的哺乳动物蛋白质编码基因。系统性硬化症（systemic sclerosis,SSc）的发病机制由复杂的miRNAs网络调控。这些miRNAs位于与SSc纤维化相关的基因组区域,通过参与调节重要的细胞信号通路,如TGF-β、Wnt/β-catenin、TLR-4、IL和PDGF-β等,在SSc纤维化过程中发挥作用。同时,还与细胞信号转导、基质修复与重塑、成纤维细胞凋亡、胶原蛋白质合成和细胞外基质（extracellular matrix,ECM）沉积等相关。充分了解miRNAs在SSc纤维化中的重要性,有助于为SSc的诊断提供新的生物标记,为治疗提供新策略。本文综述了miRNAs在SSc纤维化过程中参与调节的这些复杂细胞信号通路的作用及机制,以期为SSc诊断、严重程度判断、预后评估,以及寻求潜在治疗靶点提供新思路。     

Changes in the electrical polarity of tobacco cells following the application of weak external currents

Weak externally applied electric currents changed the natural electrical pattern surrounding cells from tobacco (Nicotiana tabacum L.) suspension cultures. The artificial currents were applied transversely to short filaments of cells placed between a microelectrode lose to the filament surface and a large platinum electrode some distance away. The natural current patterns before and after electrical treatment were measured with a vibrating probe. Significant effects were confined to the cell adjacent to the microelectrode. Currents with densities of 100 A · cm^–2 at the cell surface applied for 10 min or 3 A · cm^–2 for several hours caused a localized increase in the natural current entering the part of the cell which had been nearest the positive electrode. There was no corresponding local increase in current leaving from the opposite side of the cell. Instead, the extra current appeared to leave over a relatively large area. The overall effect was a tendency for the cell to repolarize transversely with a greater proportion of its transcellular currents flowing in the direction of the current applied. The effect was measurable for several hours after the external current was discontinued and may be evidence for a natural mechanism by which neighbouring cells entrain one another's polarities during differentiation. The effect of external currents on cells growing in a 2,4-dichlorophenoxyacetic acid (2,4-D) medium (which suppresses differentiation) was qualitatively the same as on cells in an indole-3-acetic acid medium (which promotes differentiation). If anything, the response was greater in 2,4-D, implying that the disruptive effect of 2,4-D on cell and tissue polarization is not a consequence of it preventing cells sensing the transcellular currents of their neighbours.Abbreviation 2,4-D 2,4-dichlorophenoxyacetic acid The authors are indebted to the Agricultural and Food Research Council of the U.K. for financial support and to the Royal Society for the provision of the vibrating probe.     

Emerging links between the biological clock and the DNA damage response

For life forms to survive, they must adapt to their environmental conditions. One such factor that impacts on both prokaryotic and eukaryotic organisms is the light–dark cycle, a consequence of planetary rotation in relation to our sun. In mammals, the daily light cycle has affected the regulation of many cellular processes such as sleep–wake and calorific intake activities, hormone secretion, blood pressure and immune system responses. Such rhythmic behaviour is the consequence of circadian rhythm/biological clock (BC) systems which are controlled in a light stimulus-dependent manner by a master clock called the suprachiasmatic nucleus (SCN) situated within the anterior hypothalamus. Peripheral clocks located in other organs such as the liver and kidneys relay signals from the SCN, which ultimately leads to tightly controlled expression of several protein families that in turn act on a broad range of cellular functions. Work in lower organisms has demonstrated a link between aging processes and BC factors, and studies in both animal models and clinical trials have postulated a role for certain BC-associated proteins in tumourigenesis and cancer progression. Recent exciting data reported within the last year or so have now established a molecular link between specific BC proteins and factors that control the mammalian cell cycle and DNA damage checkpoints. This mini review will focus on these discoveries and emphasise how such BC proteins may be involved, through their interplay with cell cycle/DNA damage response pathways, in the development of human disease such as cancer.     

Identification and expression analysis of miRNAs during batch culture of HEK-293 cells

MicroRNAs (miRNAs) are small non-coding RNAs of about 20–24 nucleotides in length. They regulate gene expression negatively and have been implicated in a wide variety of biological processes. To identify potential miRNAs that may influence the growth and proliferation of mammalian cells cultured in bioreactors, we applied miRNA microarray expression profiling technology to batch cultures of HEK293 cells in protein free media. In our study, we identified miRNAs that were differentially expressed during the exponential and stationary phases, 13 of these showed distinct up regulation trends while 1 exhibited down regulation. These miRNAs have been implicated in cellular differentiation, growth arrest and apoptosis. Specifically, miR-16 and let-7b are potentially useful in the enhancement of bioreactor cell cultures.     

Microtubule self-organisation by reaction-diffusion processes in miniature cell-sized containers and phospholipid vesicles

Under appropriate conditions, in vitro microtubule preparations self-organise over macroscopic distances by a process of reaction and diffusion. To investigate whether such self-organisation can also occur in objects as small as a cell or an embryo we carried out experiments in miniature containers of cellular dimension. When assembled under self-organising conditions in wells of 120–500 μm, microtubules developed organised structures. Self-organisation is strongly affected by shape, being highly favoured by elongated forms. In wells of more complex shape, geometrical factors may either oppose or strengthen one another and so inhibit or reinforce self-organisation. Microtubules were also assembled within phospholipid vesicles of 2–5 μm diameter. Under self-organising conditions, we observed large shape changes from spheroids to long tubes (50–100 μm) and intertwined coils. We conclude that self-organisation of microtubules by reaction–diffusion processes can occur in containers of cellular dimensions and is capable of strongly deforming the cellular membrane.     

Are type C viruses transforming agents?

Type C RNA viruses have been considered oncogenic because they are found associated with animal tumors and can induce cancers in several animal species. Those viruses that rapidly cause cancer appear to contain an oncogenic gene which resembles genetic sequences present in normal cells. This gene codes for a transforming protein which may be a normal cellular enzyme or a slightly altered cellular product. Its mechanism for transforming a cell is not yet known. Other oncogenic viruses, such as the chronic leukemia viruses, may not produce an oncogenic protein but may affect, by other means, specific target cells so they become malignant. Recent evidence now suggests that the majority of endogenous type C viruses are not transforming agents but inherited in the host to function in other biologic processes. These viruses do not contain transduced cellular genes which are responsible for cancer. Their role probably depends on their expression of other gene products which aid in normal development. These observations suggest that the ultimate control of human cancer may result from the identification of the oncogenic cellular-like genes transduced by some type C viruses even if a true human oncogenic virus is not isolated.     

Methionine supplementation stimulates mitochondrial respiration

Mitochondria play essential metabolic functions in eukaryotes. Although their major role is the generation of energy in the form of ATP, they are also involved in maintenance of cellular redox state, conversion and biosynthesis of metabolites and signal transduction. Most mitochondrial functions are conserved in eukaryotic systems and mitochondrial dysfunctions trigger several human diseases.By using multi-omics approach, we investigate the effect of methionine supplementation on yeast cellular metabolism, considering its role in the regulation of key cellular processes. Methionine supplementation induces an up-regulation of proteins related to mitochondrial functions such as TCA cycle, electron transport chain and respiration, combined with an enhancement of mitochondrial pyruvate uptake and TCA cycle activity. This metabolic signature is more noticeable in cells lacking Snf1/AMPK, the conserved signalling regulator of energy homeostasis. Remarkably, snf1Δ cells strongly depend on mitochondrial respiration and suppression of pyruvate transport is detrimental for this mutant in methionine condition, indicating that respiration mostly relies on pyruvate flux into mitochondrial pathways.These data provide new insights into the regulation of mitochondrial metabolism and extends our understanding on the role of methionine in regulating energy signalling pathways.     

Inhibitor of apoptosis proteins in Drosophila: gatekeepers of death

Regulation of apoptosis is crucial to ensure cellular viability, and failure to do so is linked to several human pathologies. The apoptotic cell death programme culminates in the activation of caspases, a family of highly specific cysteine proteases essential for the destruction of the cell. Although best known for their role in executing apoptosis, caspases also play important signalling roles in non-apoptotic processes, such as regulation of actin dynamics, innate immunity, cell proliferation, differentiation and survival. Under such conditions, caspases are activated without killing the cell. Caspase activation and activity is subject to complex regulation, and various cellular and viral inhibitors have been identified that control the activity of caspases in their apoptotic and non-apoptotic roles. Members of the Inhibitor of APoptosis (IAP) protein family ensure cell viability in Drosophila by directly binding to caspases and regulating their activities in a ubiquitin-dependent manner. The observation that IAPs are essential for cell survival in Drosophila, and are frequently deregulated in human cancer, contributing to tumourigenesis, chemoresistance, disease progression and poor patient survival, highlights the importance of this family of caspase regulators in health and disease. Here we summarise recent advances from Drosophila that start to elucidate how the cellular response to caspase activation is modulated by IAPs and their regulators.