The significance of telomeric aggregates in the interphase nuclei of tumor cells

Telomeres are TTAGGG repetitive motifs found at the ends of vertebrate chromosomes. In humans, telomeres are protected by shelterin, a complex of six proteins (de Lange [2005] Genes Dev. 19: 2100-2110). Since (Müller [1938] Collecting Net. 13: 181-198; McClintock [1941] Genetics 26: 234-282), their function in maintaining chromosome stability has been intensively studied. This interest, especially in cancer biology, stems from the fact that telomere dysfunction is linked to genomic instability and tumorigenesis (Gisselsson et al. [2001] Proc. Natl. Acad. Sci. USA 98: 12683-12688; Deng et al. [2003] Genes Chromosomes Cancer 37: 92-97; DePinho and Polyak [2004] Nat. Genetics 36: 932-934; Meeker et al. [2004] Clin. Cancer Res. 10: 3317-3326). In the present overview, we will discuss the role of telomeres in genome stability, recent findings on three-dimensional (3D) changes of telomeres in tumor interphase nuclei, and outline future avenues of research.     

Beyond the cell cycle: a new role for Cdk6 in differentiation

Over 10 years ago, cdk6 was identified as a new member in a family of vertebrate cdc-2 related kinases. This novel kinase was found to partner with the D-type cyclins and to possess pRb kinase activity in vitro and has since been understood to function solely as a pRb kinase in the regulation of the G(1) phase of the cell cycle. In the past 2 years, several independent studies in multiple cell types have indicated a novel role for cdk6 in differentiation. For example, cdk6 expression must be reduced to allow proper osteoblast and osteoclast differentiation, forced cdk6 expression blocked differentiation of mouse erythroid leukemia cells and cdk6 expression in primary astrocytes favors the expression of progenitor cell markers. Since exit from the cell cycle is a necessary step in terminal differentiation, down-regulation of a mitogenic factor may be expected in this process, however it is surprising that this association has not been previously uncovered and that it is apparently not shared with cdk4, long understood to be a functional homolog of cdk6. The mechanism of cdk6 function in differentiation is not understood, but it may extend beyond the established role of cdk6 as a pRb kinase. As this story unfolds it will be important to discover if the function of cdk6 in differentiation is pRb-dependent or pRb-independent, since pRb has long been established as a key factor in initiating and maintaining cell cycle exit during differentiation.     

The germ cell nuclear factor (GCNF)

The germ cell nuclear factor (GCNF), which is also known as RTR (retinoid receptor-related testis-associated receptor) is a member of the nuclear receptor superfamily. As a natural ligand remains to be discovered, GCNF is referred to as an orphan receptor. Owing to GCNF's unique features and its distant relation to any other known nuclear receptor it has been classified as the only member of the subgroup six and designated NR6A1 by the Receptor Nomenclature Committee (Duarte et al., 2002: Nucleic Acids Res 30: 364-368). To date, GCNF has been cloned from distinct vertebrate species, including zebrafish, Xenopus laevis, mouse, rat, and human. Cloning and characterization of the gene, domain organization and DNA binding properties of the protein, as well as the differential expression of mRNA splice variants or the protein during development and in the adult animal have been comprehensively reviewed by others (Greschik and Schüle, 1998: J Mol Med 76:800-810; Cooney et al., 1999: Am Zool 39:796-806). In this minireview I focus on the pleiotropic function of GCNF in embryogenesis and germ cell differentiation, and discuss novel concepts about its putative role in neurogenesis.     

Predicting genotoxicity of aromatic and heteroaromatic amines using electrotopological state indices

A quantitative structure-activity relationship (QSAR) model relating electrotopological state (E-state) indices and mutagenic potency was previously described by Cash [Mutat. Res. 491 (2001) 31-37] using a data set of 95 aromatic amines published by Debnath et al. [Environ. Mol. Mutagen. 19 (1992) 37-52]. Mutagenic potency was expressed as the number of Salmonella typhimurium TA98 revertants per nmol (LogR). Earlier work on the development of QSARs for the prediction of genotoxicity indicated that numerous methods could be effectively employed to model the same aromatic amines data set, namely, Debnath et al.; Maran et al. [Quant. Struct.-Act. Relat. 18 (1999) 3-10]; Basak et al. [J. Chem. Inf. Comput. Sci. 41 (2001) 671-678]; Gramatica et al. [SAR QSAR Environ. Res. 14 (2003) 237-250]. However, results obtained from external validations of those models revealed that the effective predictivity of the QSARs was well below the potential indicated by internal validation statistics (Debnath et al., Gramatica et al.). The purpose of the current research is to externally validate the model published by Cash using a data set of 29 aromatic amines reported by Glende et al. [Mutat. Res. 498 (2001) 19-37; Mutat. Res. 515 (2002) 15-38] and to further explore the potential utility of using E-state sums for the prediction of mutagenic potency of aromatic amines.     

Novel biochemical pathways of endoglin in vascular cell physiology

The broad role of the transforming growth factor beta (TGFbeta) signaling pathway in vascular development, homeostasis, and repair is well appreciated. Endoglin is emerging as a novel, complex, and poorly understood regulatory component of the TGFbeta receptor complex, whose importance is underscored by its recognition as the site of mutations causing hereditary hemorrhagic telangiectasia (HHT) [McAllister et al., 1994]. Extensive analyses of endoglin function in normal developmental mouse models [Bourdeau et al., 1999; Li et al., 1999; Arthur et al., 2000] and in HHT animal models [Bourdeau et al., 2000; Torsney et al., 2003] exemplify the importance of understanding endoglin's biochemical functions. However, novel mechanisms underlying the regulation of these pathways continue to emerge. These mechanisms include modification of TGFbeta receptor signaling at the ligand and receptor activation level, direct effects of endoglin on cell adhesion and migration, and emerging roles for endoglin in the determination of stem cell fate and tissue patterning. The purpose of this review is to highlight the cellular and molecular studies that underscore the central role of endoglin in vascular development and disease.     

Evaluating CK2 activity with the antibody specific for the CK2-phosphorylated form of a kinase-targeting cochaperone Cdc37

CK2-dependent phosphorylation of a kinase-specific Hsp90 co-chaperone Cdc37 on a conserved serine residue (Ser13) is essential for the function of Cdc37 [Bandhakavi S. et al. J. Biol. Chem. 278:2829-2836, 2003; Shao J. et al. J. Biol. Chem. 278:38117-38220, 2003; Miyata Y., & Nishida E. Mol. Cell. Biol. 24:4065-4074, 2004]. We have recently produced an anti-[pSer13]-Cdc37 antibody which specifically recognizes Cdc37 that is phosphorylated on Ser 13 [Miyata Y. & Nishida E. FEBS J. 274:5690-5703, 2007]. Here we investigated CK2 activity both in vitro and in cultured cells by using anti-[pSer13]-Cdc37 antibody. Immunoblotting with this antibody showed that heparin and 4,5,6,7-tetrabromobenzotriazole (TBB), known CK2 inhibitors, inhibited in vitro phosphorylation of Cdc37 on Ser13 by CK2 holoenzyme or CK2alpha, confirming the specificity of the antibody to detect CK2 activity. Treatment of cells with TBB resulted in the decrease in the phosphorylation level of endogenous Cdc37 on Ser13, as revealed by anti-[pSer13]-Cdc37, and overexpression of either CK2alpha or CK2beta subunit enhanced the Cdc37 phosphorylation level. While CK2 is suggested to be involved in cell proliferation, mitogenic stimulation of starved cells by fresh serum or insulin-like growth factor-I did not enhance phosphorylation of Cdc37 on Ser13. CK2 inhibitors are known to induce cell apoptosis, suggesting a reverse correlation between cell apoptosis and CK2 activity. However, cellular apoptotic stresses, such as anisomycin treatment and UV irradiation, were found to rather modestly increase phosphorylation of Cdc37 on Ser13. These results show that the anti-[pSer13]-Cdc37 antibody can be a promising new tool to evaluate in vivo CK2 activity.     

Heparan sulfate proteoglycan specificity during axon pathway formation in the Drosophila embryo

Axon guidance is influenced by the presence of heparan sulfate (HS) proteoglycans (HSPGs) on the surface of axons and growth cones (Hu, [2001]: Nat Neurosci 4:695-701; Irie et al. [2002]: Development 129:61-70; Inatani et al. [2003]: Science 302:1044-1046; Johnson et al. [2004]: Curr Biol 14:499-504; Steigemann et al. [2004]: Curr Biol 14:225-230). Multiple HSPGs, including Syndecans, Glypicans and Perlecans, carry the same carbohydrate polymer backbones, raising the question of how these molecules display functional specificity during nervous system development. Here we use the Drosophila central nervous system (CNS) as a model to compare the impact of eliminating Syndecan (Sdc) and/or the Glypican Dally-like (Dlp). We show that Dlp and Sdc share a role in promoting accurate patterns of axon fasciculation in the lateral longitudinal neuropil; however, unlike mutations in sdc, which disrupt the ability of the secreted repellent Slit to prevent inappropriate passage of axons across the midline, mutations in dlp show neither midline defects nor genetic interactions with Slit and its Roundabout (Robo) receptors at the midline. Dlp mutants do show genetic interactions with Slit and Robo in lateral fascicle formation. In addition, simultaneous loss of Dlp and Sdc demonstrates an important role for Dlp in midline repulsion, reminiscent of the functional overlap between Robo receptors. A comparison of HSPG distribution reveals a pattern that leaves midline proximal axons with relatively little Dlp. Finally, the loss of Dlp alters Slit distribution distal but not proximal to the midline, suggesting that distinct yet overlapping pattern of HSPG expression provides a spatial system that regulates axon guidance decisions.     

Membrane guanylate cyclase is a beautiful signal transduction machine: overview

This article is a sequel to the four earlier comprehensive reviews which covered the field of membrane guanylate cyclase from its origin to the year 2002 (Sharma in Mol Cell Biochem 230:3–30, 2002) and then to the year 2004 (Duda et al. in Peptides 26:969–984, 2005); and of the Ca²⁺-modulated membrane guanylate cyclase to the year 1997 (Pugh et al. in Biosci Rep 17:429–473, 1997) and then to 2004 (Sharma et al. in Curr Top Biochem Res 6:111–144, 2004). This article contains three parts. The first part is “Historical”; it is brief, general, and freely borrowed from the earlier reviews, covering the field from its origin to the year 2004 (Sharma in Mol Cell Biochem, 230:3–30, 2002; Duda et al. in Peptides 26:969–984, 2005). The second part focuses on the “Ca²⁺-modulated ROS-GC membrane guanylate cyclase subfamily”. It is divided into two sections. Section “Historical” and covers the area from its inception to the year 2004. It is also freely borrowed from an earlier review (Sharma et al. in Curr Top Biochem Res 6:111–144, 2004). Section “Ca²⁺-modulated ROS-GC membrane guanylate cyclase subfamily” covers the area from the year 2004 to May 2009. The objective is to focus on the chronological development, recognize major contributions of the original investigators, correct misplaced facts, and project on the future trend of the field of mammalian membrane guanylate cyclase. The third portion covers the present status and concludes with future directions in the field.     

Hypoxia-induced dedifferentiation of tumor cells--a mechanism behind heterogeneity and aggressiveness of solid tumors

Histopathological examination of solid tumors frequently reveals pronounced tumor cell heterogeneity with regards to cell organization, cell morphology, cell size, nuclei morphology, etc. Analyses of gene expression patterns by immunohistochemistry or in situ hybridization techniques further strengthen the actual presence of phenotypic heterogeneity, often demonstrating substantial diversity within a given tumor. The molecular mechanisms underlying the phenotypic heterogeneity are very complex with genetic, epigenetic and environmental components. Hypoxia, shortage in oxygen, greatly influences cellular phenotypes by altering the expression of specific genes, and is an important contributor to intra- and inter-tumor cell diversity as revealed by the pronounced but non-uniform expression of hypoxia-driven genes in solid tumors (reviewed in [Semenza GL. Targeting HIF-1 for cancer therapy. Nat Rev Cancer 2003;3:721-32; Harris AL. Hypoxia--a key regulatory factor in tumour growth. Nat Rev Cancer 2002;2:38-47.]). The oxygen pressure in solid tumors is generally lower than in the surrounding non-malignant tissues, and tumors exhibiting extensive hypoxia have been shown to be more aggressive than corresponding tumors that are better oxygenized [Vaupel P. Oxygen transport in tumors: characteristics and clinical implications. Adv Exp Med Biol 1996;388:341-51; Vaupel P, Thews O, Hoeckel M. Treatment resistance of solid tumors: role of hypoxia and anemia. Med Oncol 2001;18:243-59.]. We recently observed that hypoxic neuroblastoma cells and breast cancer cells lose their differentiated gene expression patterns and develop stem cell-like phenotypes [J?gi A, ?ra I, Nilsson H, Lindeheim A, Makino Y, Poellinger L, et al. Hypoxia alters gene expression in human neuroblastoma cells toward an immature and neural crest-like phenotype. Proc Natl Acad Sci USA 2002;99:7021-6; Helczynska K, Kronblad A, J?gi A, Nilsson E, Beckman S, Landberg G, et al. Hypoxia promotes a dedifferentiated phenotype in ductal breast carcinoma in situ. Cancer Res 2003;63:1441-4.]. As low stage of differentiation in neuroblastoma and in breast cancer is linked to poor prognosis, hypoxia-induced dedifferentiation will not only contribute to tumor heterogeneity but could also be one mechanism behind increased aggressiveness of hypoxic tumors. The effect(s) of hypoxia on tumor cell differentiation status is the focus of this review.     

Hypoxic culture and in vivo inflammatory environments affect the assumption of pericyte characteristics by human adipose and bone marrow progenitor cells

Previous studies have shown that exposure to a hypoxic in vitro environment increases the secretion of pro-angiogenic growth factors by human adipose-derived stromal cells (hASCs) [Cao Y, et al., Biochem Biophys Res Commun 332: 370-379, 2005; Kokai LE, et al., Plast Reconstr Surg 116: 1453-1460, 2005; Park BS, et al., Biomed Res (Tokyo) 31: 27-34, 2010; Rasmussen JG, et al., Cytotherapy 13: 318-328, 2010; Rehman J, et al., Circulation 109: 1292-1298, 2004]. Previously, it has been demonstrated that hASCs can differentiate into pericytes and promote microvascular stability and maintenance during angiogenesis in vivo (Amos PJ, et al., Stem Cells 26: 2682-2690, 2008; Traktuev DO, et al., Circ Res 102: 77-85, 2008). In this study, we tested the hypotheses that angiogenic induction can be increased and pericyte differentiation decreased by pretreatment of hASCs with hypoxic culture and that hASCs are similar to human bone marrow-derived stromal cells (hBMSCs) in these regards. Our data confirms previous studies showing that hASCs: 1) secrete pro-angiogenic proteins, which are upregulated following culture in hypoxia, and 2) migrate up gradients of PDGF-BB in vitro, while showing for the first time that a rat mesenteric model of angiogenesis induced by 48/80 increases the propensity of both hASCs and hBMSCs to assume perivascular phenotypes following injection. Moreover, culture of both cell types in hypoxia before injection results in a biphasic vascular length density response in this model of inflammation-induced angiogenesis. The effects of hypoxia and inflammation on the phenotype of adult progenitor cells impacts both the therapeutic and the basic science applications of the cell types, as hypoxia and inflammation are common features of natural and pathological vascular compartments in vivo.     

Active sites in the carboxyl-terminal region of the laminin alpha chain in Drosophila neuronal cell spreading

An established Drosophila neuronal cell line (BG2-c6) proved to be useful to analyze laminin-mediated cell spreading and signal transduction [Takagi et al. (2000) Biochem Biophys Res Commun 270:482-487]. Here, we report, in addition to the whole molecule, the truncated alpha chain of Drosophila laminin (containing the entire carboxyl-terminal globular domain) and two dodecapeptides corresponding to the cell-binding sites identified in the alpha1 chain of mouse laminin were also active to stimulate BG2-c6 cell spreading. Our previous study [Takagi et al. (1996) J Biol Chem 271:18074-18081] revealed that these recombinant protein and synthetic peptides promoted neurite outgrowth in the primary cell culture system prepared from Drosophila embryo. Therefore, the similar effects by these proteins and peptides suggest the presence of a common mechanism of laminin and neuronal cell interaction working in both primary and established cells. One of the two active peptides contains the sequence SIKVGV. Its murine counterpart carries the sequence SIKVAV by which the interaction of laminin and cells is mediated. Furthermore, laminin-dependent BG2-c6 cell spreading was inhibited by heparin. This observation suggests that cell surface glycoproteins participate in the interaction of laminin and BG2-c6 cells.     

Enhancement of G2 checkpoint function by gelsolin transfection in human cancer cells.

We have previously reported that human gastric (TMK1) and urinary bladder (UMUC2) cancer cell lines show markedly reduced expression of an actin-regulatory protein, gelsolin [S. Moriya et al., (1994), Int. J. Oncol. 5, 1347-1351, M. Tanaka et al. (1995), Cancer Res. 55, 3228-3232]. When gelsolin expression is restored by transfection, cancer cells lost tumorigenicity in vivo [M. Tanaka et al. (1995), Cancer Res. 55, 3228-3232]. Here, we show that gelsolin-overexpressing TMK1 and UMUC2 cells are more resistant to UVC irradiation. Increased resistance is associated with increases in the proportion of cells in the G2 phase of the cell cycle compared to similarly treated control neotransfectants. After UVC irradiation, synchronized gelsolin-overexpressing UMUC2 cells had a prolonged S phase followed by delayed G2 accumulation compared to neotransfected UMUC2 cells as determined by cell cycle analysis. The levels of cyclin B1 and cdk1 histone H1 kinase activity in gelsolin transfectants remained low during S and early G2 phase and the production of diacylglycerol induced by UVC was reduced in gelsolin transfectants compared to neotransfectants. These observations suggest that gelsolin enhances G2 checkpoint function of cells through lipid metabolism, leading to UVC resistance. Considered together with recent evidence that radiation clastogenesis and chemical carcinogenesis are cell-cycle-dependent, down regulation of gelsolin may lead to the malignant transformation of human gastric or urinary bladder cancers by attenuating G2 checkpoint function.     

Grape seed procyanidins inhibit the expression of metallothione in genes in human HepG2 cells

Procyanidins are the most abundant polyphenols in red wine and are also found in cereals, fruits, chocolate and tea. They exert many beneficial health effects, especially on the cardiovascular system (Bagchi et al. in Mutat Res 523-524:87-97, 2003; Williams et al. in Free Radic Biol Med 36:838-849, 2004; Dell'Agli et al. in Cardiovasc Res 63(4):593-602, 2004; Del Bas et al. FASEB J 19:479-480, 2005). Here, we show that oral administration of a grape seed procyanidins extract (GSPE) to healthy rats results, 5 h after treatment, in a 70% inhibition of metallothionein (MT) gene expression in the liver, as determined by oligonucleotide microarray hybridization. Similarly, in cultured human hepatocytes HepG2, GSPE downregulate the expression of MT genes at the mRNA level, as evaluated by quantitative RTPCR. Thus, mRNA levels of six functional MT genes, MT1A, 1E, 1F, 1G, 1X and MT2A, are diminished between 50 and 80% when HepG2 cells are treated during 12 h with GSPE. Only the expression of two human MT genes, MT1G and MT1E, is transiently increased during the first 2 h of treatment. GSPE-induced inhibition of MT genes expression is dose dependent, at concentrations that are not toxic for the cells. Our findings demonstrate that metallothionein genes are direct targets of procyanidins action, both in vivo and in vitro, in hepatic cells. Thus, this study will help to elucidate the mechanisms by which procyanidin exert their beneficial actions.     

WHISCY: What information does surface conservation yield? Application to data‐driven docking

Protein-protein interactions play a key role in biological processes. Identifying the interacting residues is a first step toward understanding these interactions at a structural level. In this study, the interface prediction program WHISCY is presented. It combines surface conservation and structural information to predict protein-protein interfaces. The accuracy of the predictions is more than three times higher than a random prediction. These predictions have been combined with another interface prediction program, ProMate [Neuvirth et al. J Mol Biol 2004;338:181-199], resulting in an even more accurate predictor. The usefulness of the predictions was tested using the data-driven docking program HADDOCK [Dominguez et al. J Am Chem Soc 2003;125:1731-1737] in an unbound docking experiment, with the goal of generating as many near-native structures as possible. Unrefined rigid body docking solutions within 10 A ligand RMSD from the true structure were generated for 22 out of 25 docked complexes. For 18 complexes, more than 100 of the 8000 generated models were correct. Our results demonstrates the potential of using interface predictions to drive protein-protein docking.     

From Cell Cycle to Differentiation: An Expanding Role for Cdk6

Over ten years ago, cdk6 was identified as a new member in a family of vertebrate cdc-2 related kinases. This novel kinase was found to partner with the D-type cyclins and to possess pRb kinase activity in vitro. 1 Recently, several independent studies in multiple cell types have indicated a novel role for cdk6 in differentiation. Since exit from the cell cycle is a necessary step in the process of differentiation, it may not seem surprising that down-regulation of a mitogenic factor may be required for this process. It is, however, surprising that this association has not been previously uncovered and that it is apparently not a shared with cdk4, long understood to be a functional homolog of cdk6. As this story unfolds it will be important to discover if the role of cdk6 in differentiation is pRb-dependent or pRb-independent, since pRb has long been established as a key factor in initiating and maintaining cell cycle exit during differentiation.     

Semi-parametric differential expression analysis via partial mixture estimation

We develop an approach for microarray differential expression analysis, i.e. identifying genes whose expression levels differ between two or more groups. Current approaches to inference rely either on full parametric assumptions or on permutation-based techniques for sampling under the null distribution. In some situations, however, a full parametric model cannot be justified, or the sample size per group is too small for permutation methods to be valid. We propose a semi-parametric framework based on partial mixture estimation which only requires a parametric assumption for the null (equally expressed) distribution and can handle small sample sizes where permutation methods break down. We develop two novel improvements of Scott's minimum integrated square error criterion for partial mixture estimation [Scott, 2004a,b]. As a side benefit, we obtain interpretable and closed-form estimates for the proportion of EE genes. Pseudo-Bayesian and frequentist procedures for controlling the false discovery rate are given. Results from simulations and real datasets indicate that our approach can provide substantial advantages for small sample sizes over the SAM method of Tusher et al. [2001], the empirical Bayes procedure of Efron and Tibshirani [2002], the mixture of normals of Pan et al. [2003] and a t-test with p-value adjustment [Dudoit et al., 2003] to control the FDR [Benjamini and Hochberg, 1995].     

3-D in vitro model of early skeletal muscle development

An understanding of the mechanical and mechano-molecular responses that occur during the differentiation of mouse C2C12 [corrected] myoblasts in 3-D culture is critical for understanding growth, which is important for progress towards producing a tissue-engineered muscle construct. We have established the main differences in force generation between skeletal myoblasts, dermal fibroblasts, and smooth muscle cells in a 3-D culture model in which cells contract a collagen gel construct. This model was developed to provide a reproducible 3-D muscle organoid in which differences in force generation could be measured, as the skeletal myoblasts fused to form myotubes within a collagen gel. Maintenance of the 3-D culture under sustained uni-axial tension, was found to promote fusion of myoblasts to form aligned multi-nucleate myotubes. Gene expression of both Insulin Like Growth Factor (IGF-1 Ea) and an isoform of IGF-1 Ea, Mechano-growth factor (IGF-1 Eb, also termed MGF), was monitored in this differentiating collagen construct over the time course of fusion and maturation (0-7 days). This identified a transient surge in both IGF-1 and MGF expression on day 3 of the developing construct. This peak of IGF-1 and MGF expression, just prior to differentiation, was consistent with the idea that IGF-1 stimulates differentiation through a Myogenin pathway [Florini et al., 1991: Mol. Endocrinol. 5:718-724]. MGF gene expression was increased 77-fold on day 3, compared to a 36-fold increase with IGF-1 on day 3. This indicates an important role for MGF in either differentiation or, more likely, a response to mechanical or tensional cues.