Conquering the complex world of human septins: implications for health and disease

Peterson EA and Petty EM. Conquering the complex world of human septins: implications for health and disease. Septins are highly conserved filamentous proteins first characterized in budding yeast and subsequently identified in must eukaryotes. Septins can bind and hydrolyze GTP, which is intrinsically related to their formation of septin hexamers and functional protein interactions. The human septin family is composed of 14 loci, SEPT1‐SEPT14, which encode dozens of different septin proteins. Their central GTPase and polybasic domain regions are highly conserved but they diverge in their N‐terminus and/or C‐terminus. The mechanism by which the different isoforms are generated is not yet well understood, but one can hypothesize that the use of different promoters and/or alternative splicing could give rise to these variants. Septins perform diverse cellular functions according to tissue expression and their interacting partners. Functions identified to date include cell division, chromosome segregation, protein scaffolding, cellular polarity, motility, membrane dynamics, vesicle trafficking, exocytosis, apoptosis, and DNA damage response. Their expression is tightly regulated to maintain proper filament assembly and normal cellular functions. Alterations of these proteins, by mutation or expression changes, have been associated with a variety of cancers and neurological diseases. The association of septins with cancer results from alterations of expression in solid tumors or translocations in leukemias [mixed lineage leukemia (MLL)]. Expression changes in septins have also been associated with neurological conditions such as Alzheimer's and Parkinson's disease, as well as retinopathies, hepatitis C, spermatogenesis and Listeria infection. Pathogenic mutations of SEPT9 were identified in the autosomal dominant neurological disorder hereditary neuralgic amyotrophy (HNA). Human septin research over the past decade has established their importance in cell biology and human disease. Further functional characterization of septins is crucial to our understanding of their possible diagnostic, prognostic, and therapeutic applications.     

The pathobiology of the septin gene family

Septins are an evolutionarily conserved group of GTP-binding and filament-forming proteins that belong to the large superclass of P-loop GTPases. While originally discovered in yeast as cell division cycle mutants with cytokinesis defects, they are now known to have diverse cellular roles which include polarity determination, cytoskeletal reorganization, membrane dynamics, vesicle trafficking, and exocytosis. Septin proteins form homo- and hetero-oligomeric polymers which can assemble into higher-order filaments. They are also known to interact with components of the cytoskeleton, ie actin and tubulin. The precise role of GTP binding is not clear but a current model suggests that it is associated with conformational changes which alter binding to other proteins. There are at least 12 human septin genes, and although information on expression patterns is limited, most undergo complex alternative splicing with some degree of tissue specificity. Nevertheless, an increasing body of data implicates the septin family in the pathogenesis of diverse disease states including neoplasia, neurodegenerative conditions, and infections. Here the known biochemical properties of mammalian septins are reviewed in the light of the data from yeast and other model organisms. The data implicating septins in human disease are considered and a model linking these data is proposed. It is posited that septins can act as regulatable scaffolds where the stoichiometry of septin associations, modifications, GTP status, and the interactions with other proteins allow the regulation of key cellular processes including polarity determination. Derangements of such septin scaffolds thus explain the role of septins in disease states.     

Expression profiling the human septin gene family

The septins are an evolutionarily conserved family of GTP-binding proteins involved in diverse processes including vesicle trafficking, apoptosis, remodelling of the cytoskeleton, infection, neurodegeneration, and neoplasia. The present paper reports a comprehensive study of septin gene expression by DNA microarray methods in 10 360 samples of normal, diseased, and tumour tissues. A novel septin, SEPT13, has been identified and is shown to be related to SEPT7. It is shown that SEPT13 and the other known human septins are expressed in all tissue types but some show high expression in lymphoid (SEPT1, 6, 9, and 12) or brain tissues (SEPT2, 3, 4, 5, 7, 8, and 11). For a given septin, some isoforms are highly expressed in the brain and others are not. For example, SEPT8_v2 and v1, 1* and 3 are highly expressed in the brain and cluster with SEPT2, 3, 4, 5, 7, and 11. However, a probe set specific for SEPT8_v1 with low brain expression clusters away from this set. Similarly, SEPT4 has lymphoid and non-lymphoid forms; SEPT2 has lymphoid and central nervous system (CNS) forms; and SEPT6 and SEPT9 are elevated in lymphoid tissues but both have forms that cluster away from the lymphoid forms. Perturbation of septin expression was widespread in disease and tumours of the various tissues examined, particularly for conditions of the CNS, where alterations in all 13 septin genes were identified. This analysis provides a comprehensive catalogue of the septin family in health and disease. It is a key step in understanding the role of septins in physiological and pathological states and provides insight into the complexity of septin biology.     

Septins: a ring to part mother and daughter

The septins are well conserved GTPases found in animals and fungi. In yeast, they are required for the formation of 10-nm filaments, with which they co-localize at the bud neck. Therefore, septins have been proposed to be components of the neck filaments and to have polymerization properties. In support of this hypothesis, septin complexes purified from yeast and flies form filaments in vitro. However, recent studies have questioned the relevance of septin filament formation for septin function. Particularly, septin polymerization may not be required for their function in cytokinesis. New septin functions have also been recently uncovered: in budding yeast, the septin ring is required for the maintenance of cell polarity. It forms a cortical barrier that prevents lateral diffusion of membrane-associated proteins through the bud neck. Here, we review the most recent functional and biochemical data, to discuss whether there is a link between septin polymerization properties and septin function.     

Localization of septin 8 in murine retina, and spatiotemporal expression of septin 8 in a murine model of photoreceptor cell degeneration

The septins, which form a conserved family of cytoskeletal GTP-binding proteins in mammals, comprise stable heteromeric complexes and have diverse roles in protein scaffolding, cytokinesis, vesicle trafficking and plasma membrane integrity following cell division. The goal of this study was to determine the localization of septin 8 in murine adult retina, and analyze the spatiotemporal expression of septin 8 in a murine model of photoreceptor cell degeneration. Expression of septin 8 in the normal retina of mouse and rat was observed by using immunohistochemistry and Western blotting. Furthermore, time course of the expression of septin 8 in mouse photoreceptor cell degeneration were examined by immunohistochemistry combined with hematoxylin and eosin staining, and in situ DNA fragment labeling method. In normal mouse and rat retina, localization of septin 8 is restricted in nuclei of photoreceptor cells. 96 h after intravitreal injection of cobalt chloride most photoreceptor cells lost septin 8 immunostaining at the same time as nuclear DNA fragmentation. The results of this study show that septin 8 protein is present in the specific location within the retina. Furthermore, the disappearance of septin 8 in the nuclei of photoreceptor cells is concomitant with nuclear DNA fragmentation. This suggests that loss of septin 8 could be a useful prognostic indicator for photoreceptor cell degeneration.     

Microtubule capture by the cleavage apparatus is required for proper spindle positioning in yeast

Cell division is the result of two major cytoskeletal events: partition of the chromatids by the mitotic spindle and cleavage of the cell by the cytokinetic apparatus. Spatial coordination of these events ensures that each daughter cell inherits a nucleus. Here we show that, in budding yeast, capture and shrinkage of astral microtubules at the bud neck is required to position the spindle relative to the cleavage apparatus. Capture required the septins and the microtubule-associated protein Kar9. Like Kar9-defective cells, cells lacking the septin ring failed to position their spindle correctly and showed an increased frequency of nuclear missegregation. Microtubule attachment at the bud neck was followed by shrinkage and a pulling action on the spindle. Enhancement of microtubule shrinkage at the bud neck required the Par-1-related, septin-dependent kinases (SDK) Hsl1 and Gin4. Neither the formin Bnr1 nor the actomyosin contractile ring was required for either microtubule capture or microtubule shrinkage. Together, our results indicate that septins and septin-dependent kinases may coordinate microtubule and actin functions in cell division.     

The septin CDCrel-1 binds syntaxin and inhibits exocytosis.

Septins are GTPases required for the completion of cytokinesis in diverse organisms, yet their roles in cytokinesis or other cellular processes remain unknown. Here we describe studies of a newly identified septin, CDCrel-1, which is predominantly expressed in the nervous system. This protein was associated with membrane fractions, and a significant fraction of the protein copurified and coprecipitated with synaptic vesicles. In detergent extracts, CDCrel-1 and another septin, Nedd5, immunoprecipitated with the SNARE protein syntaxin by directly binding to syntaxin via the SNARE interaction domain. Transfection of HIT-T15 cells with wild-type CDCrel-1 inhibited secretion, whereas GTPase dominant-negative mutants enhanced secretion. These data suggest that septins may regulate vesicle dynamics through interactions with syntaxin.     

Novel cell-scaffold interactions encountered in tissue engineering: contractile behavior of musculoskeletal connective tissue cells

Methods employed in the course of tissue engineering often offer unique opportunities to observe cell-matrix interactions that cannot otherwise be viewed. These observations may provide insights into cell behavior than can contribute important new knowledge about cell biology. One such set of observations led to the discoveries that musculoskeletal connective tissue cells express a contractile muscle actin isoform, alpha-smooth muscle actin, and can contract. This knowledge may help to explain how these cells generate forces required for certain physiological and pathological functions, and this information may inform future approaches to regulate this function to advance tissue engineering. Tissue engineering science is thus emerging as an importance force that can both contribute to cell and molecular biology and add to the fund of knowledge supporting the production of tissue in vitro or in vivo to improve the management of a wide variety of disorders.     

Human NK cells,their receptors and function

NK cells are cytotoxic components of innate lymphoid cells (ILC) that provide a first line of defense against viral infections and contribute to control tumor growth and metastasis. Their function is finely regulated by an array of HLA-specific and non-HLA-specific inhibitory and activating receptors which allow to discriminate between healthy and altered cells. Human NK cells gained a major attention in recent years because of the important progresses in understanding their biology and of some promising data in tumor therapy. In this review, we will outline well-established issues of human NK cells and discuss some of the open questions, debates, and recent advances regarding their origin, differentiation, and tissue distribution. Newly defined NK cell specializations, including the impact of inhibitory checkpoints on their function, their crosstalk with other cell types, and the remarkable adaptive features acquired in response to certain virus infections will also be discussed.     

The role of septins in infections with vacuole-dwelling intracellular bacteria

Septins are a relatively little understood group of GTPases that form large assemblies in cells from all eukaryotes other than plants. Septins were first identified in cell division but have also been implicated in microbial infections. Septins often associate with cytoskeletal proteins − most often described for filamentous (F-) actin − and are considered cytoskeletal components themselves. Septins have increasingly been found to partake in processes that are linked to intracellular membranes, from mitochondria to phagosomes, and evidence is accumulating that septins specifically bind to membranes. Since a number of microorganisms have specialized to live and grow inside membranous vacuoles in the cytosol of mammalian cells, this membrane-association of septins suggests that septins may also be involved in the membranous, vacuolar structures that develop around these microbes. However, data are limited on this issue: septins have been identified by proteome analysis on some microbe-bearing vacuoles, but more extensive experimental data are only available for infections with the obligate intracellular bacterium Chlamydia trachomatis. In this review article I will discuss the available data and speculate about the mechanisms of recruitment and potential functions of septins for vacuole-dwelling microorganisms, which may be peculiar to Chlamydia or may pertain more generally to this class of microbes.     

Complement activation and kidney transplantation; a complex relationship

Although kidney transplantation is the best treatment for end stage kidney disease, the benefits are limited by factors such as the short fall in donor numbers, the burden of immunosuppression and graft failure. Although there have been improvements in one-year outcomes, the annual rate of graft loss beyond the first year has not significantly improved, despite better therapies to control the alloimmune response. There is therefore a need to develop alternative strategies to limit kidney injury at all stages along the transplant pathway and so improve graft survival. Complement is primarily part of the innate immune system, but is also known to enhance the adaptive immune response. There is increasing evidence that complement activation occurs at many stages during transplantation and can have deleterious effects on graft outcome. Complement activation begins in the donor and occurs again on reperfusion following a period of ischemia. Complement can contribute to the development of the alloimmune response and may directly contribute to graft injury during acute and chronic allograft rejection. The complexity of the relationship between complement activation and allograft outcome is further increased by the capacity of the allograft to synthesise complement proteins, the contribution complement makes to interstitial fibrosis and complement’s role in the development of recurrent disease. The better we understand the role played by complement in kidney transplant pathology the better placed we will be to intervene. This is particularly relevant with the rapid development of complement therapeutics which can now target different the different pathways of the complement system. Combining our basic understanding of complement biology with preclinical and observational data will allow the development and delivery of clinical trials which have best chance to identify any benefit of complement inhibition.     

Identification of structural domains involved in astrovirus capsid biology

Coat proteins of non-enveloped, icosahedral viruses must perform a variety of functions during their life cycle such as assembly of the coat protein subunits into a closed shell, specific encapsidation of the viral nucleic acid, maturation of the capsid, interaction with host receptors, and disassembly to deliver the genetic information into the newly infected cell. A thorough understanding of the multiple capsid properties at the molecular level is required in order to identify potential targets for antiviral therapy and the prevention of viral disease. The system we have chosen for study is the astrovirus, a family of icosahedral, single-stranded RNA viruses that cause disease in mammals and birds. Very little is known about what regions of the coat protein contribute to the diverse capsid functions. This review will present novel structural predictions for the coat protein sequence of different astrovirus family members. Based on these predictions, we hypothesize that the assembly and RNA packaging functions of the astrovirus coat protein constitutes an individual domain distinct from the determinants required for receptor binding and internalization. Information derived from these structural predictions will serve as an important tool in designing experiments to understand astrovirus biology.     

Mammalian septin Sept2 modulates the activity of GLAST, a glutamate transporter in astrocytes

Sept2 is a member of the septin family of GTPases. Septins form filaments in a GTP-form dependent manner, and are involved in cytokinesis from yeast to mammals; however, some mammalian septins, including Sept2, are expressed in the brain, a tissue in which almost all the cells are postmitotic. Recently, some functions of mammalian septin other than cytokinesis such as vesicle transport have been reported. However, mammalian septin's physiological functions are still unclear. The present study revealed that Sept2 co-localizes with the astrocyte glutamate transporter GLAST in the Bergmann glial processes facing axons and synapses. Biochemical analyses demonstrated that Sept2 bound directly to the carboxy-terminal region of GLAST in a GDP-form dependent manner. Expression of constitutive GDP-form Sept2 mutant reduced the glutamate uptake activity of GLAST via internalization of GLAST from cell surface. Thus Sept2 may regulate GLAST-mediated glutamate uptake by astrocytes, which is important for appropriate transmitter signalling in the cerebellum.     

The TNF family in T cell differentiation and function – Unanswered questions and future directions

Proteins in the TNF/TNFR superfamily are recognized as major regulators of the activity of conventional CD4 and CD8 T cells, and also of regulatory T cells (Treg). Stimulatory molecules such as OX40, CD27, GITR, DR3, CD30, 4-1BB, TACI, and TNFR2 can promote division and survival in T cells, enhance effector activity including cytokine production, and drive the generation of T cell memory. They also display the capacity to block the development of inducible Treg cells or inhibit suppressive activity in Treg cells. Additionally, molecules such as Fas, TNFR1, and TRAILR promote apoptotic death in T cells and generally limit T cell activity. Although our knowledge of these proteins is quite good at this point in time, there are still many unknowns regarding their function, their expression patterns, and the involvement of these different molecules at various stages of the T cell response that occurs in autoimmunity, cancer, infectious disease, and during vaccination. Importantly, it is still unresolved how similar or dissimilar each of these receptors are to one another, the extent to which cooperation occurs between family members, and whether alternate TNF–TNFR interactions induce qualitatively different cellular responses. All of the molecules are attractive targets for immunotherapy of human disease, but it is not yet clear how to differentiate between them and make an informed decision as to whether any one protein may be the preferred focus of clinical development for a given specific disease indication. This review will highlight unanswered questions related to these molecules and the biology of T cells, and describe possible future directions for research in this area. Expanding our knowledge of how the TNF/TNFR family control T cells will undoubtedly help fulfill the promise of these molecules for providing efficacious clinical therapy of immune system disease.     

Candida albicans septin mutants are defective for invasive growth and virulence

Hyphal growth of Candida albicans is implicated as an important virulence factor for this opportunistic human pathogen. Septin proteins, a family of cytoskeletal elements that regulate membrane events and are important for proper morphogenesis of C. albicans, were examined for their role in tissue invasion and virulence in the mouse model of systemic infection. In vitro, septin mutants are only mildly defective for hyphal growth in liquid culture but display pronounced defects for invasive growth into agar. In vivo, the septin mutants were found to exhibit attenuated virulence. However, mice infected with the mutants displayed high fungal burdens in their kidneys without obvious symptoms of disease. Histological examination of infected kidneys revealed defects in organ invasion for the cdc10 Delta and cdc11 Delta deletion mutants, which displayed both reduced tissue penetration and noninvasive fungal masses. Thus, the septin proteins are necessary for invasive growth, which appears to be more important to the successful pathogenesis of C. albicans than hyphal growth alone.     

SEPT9 sequence alternations causing hereditary neuralgic amyotrophy are associated with altered interactions with SEPT4/SEPT11 and resistance to Rho/Rhotekin-signaling

SEPT9 is a member of the cytoskeleton-related septin family, which is highly expressed in glia cells in neuronal tissues. Sequence alterations in SEPT9 are known to cause hereditary neuralgic amyotrophy (HNA) but precise cellular consequences have yet to be determined. Since SEPT9 is thought to function through interaction with other septins and small GTPase Rho-mediated signaling, we analyzed the properties of HNA-associated SEPT9 missense variants, SEPT9F (c.278C>T/p.Ser93Phe in SEPT9_v3; NM_006640.3) and SEPT9W (c.262C>T/p.Arg88Trp in SEPT9_v3). We found both sequence variants, but not the wild type, to form filaments with SEPT4 along stress fibers in mesenchymal mouse mammary gland NMuMG cells. In the epithelial cells, the variants, but not the wild type, were colocalized with SEPT11 at cell-cell junctions. In addition, although septin filaments containing SEPT9_v3 were disrupted by Rho/Rhotekin signaling, this was not the case with SEPT9F and SEPT9W. Sequence variations in SEPT9 causing HNA are thus likely to alter modes of interaction with partner molecules in cells, and consequently contribute to the pathogenesis of HNA.     

Biomedical text mining and its applications in cancer research

Cancer is a malignant disease that has caused millions of human deaths. Its study has a long history of well over 100 years. There have been an enormous number of publications on cancer research. This integrated but unstructured biomedical text is of great value for cancer diagnostics, treatment, and prevention. The immense body and rapid growth of biomedical text on cancer has led to the appearance of a large number of text mining techniques aimed at extracting novel knowledge from scientific text. Biomedical text mining on cancer research is computationally automatic and high-throughput in nature. However, it is error-prone due to the complexity of natural language processing. In this review, we introduce the basic concepts underlying text mining and examine some frequently used algorithms, tools, and data sets, as well as assessing how much these algorithms have been utilized. We then discuss the current state-of-the-art text mining applications in cancer research and we also provide some resources for cancer text mining. With the development of systems biology, researchers tend to understand complex biomedical systems from a systems biology viewpoint. Thus, the full utilization of text mining to facilitate cancer systems biology research is fast becoming a major concern. To address this issue, we describe the general workflow of text mining in cancer systems biology and each phase of the workflow. We hope that this review can (i) provide a useful overview of the current work of this field; (ii) help researchers to choose text mining tools and datasets; and (iii) highlight how to apply text mining to assist cancer systems biology research.