Combined effects of tamoxifen and a chimeric humanized single chain antibody against the type I IGF receptor on breast tumor growth in vivo.

Proliferative and anti-apoptotic actions of IGFs are mediated by the IGF-I receptor (IGF-IR), to which both IGF-I and -II bind with high affinity. We previously reported that alphaIGF-IR scFv-Fc (scFv-Fc) consisting of the alphaIGF-IR scFv and human IgG (1) Fc domain retained general characteristics of the parental 1H7 monoclonal antibody, and significantly suppressed MCF-7 tumor growth. We proposed IGF-IR down-regulation as a possible mechanism for inhibition of MCF-7 tumor growth. To further determine the therapeutic potentials of this approach, in vivo effects of this antibody on breast tumor growth were evaluated in the absence or presence of tamoxifen (Tam) using a T61 human breast tumor model. T61 xenograft growth in athymic mice was compared under five conditions, PBS, scFv-Fc, Tam, scFv-Fc+Tam, and control antibody. While treatment with PBS and control antibody did not affect T61 tumor growth, scFv-Fc, Tam, and scFv-Fc+Tam treatments significantly suppressed the tumor growth during the first two weeks of treatment. Although the growth inhibitory effect of scFv-Fc during the first two weeks was significant, the tumor grew as rapidly as PBS-treated tumors thereafter. This rapid tumor growth was suppressed when scFv-Fc was combined with Tam. Throughout four weeks, the combined Tam+scFv-Fc treatment was more effective in inhibiting the T61 tumor growth than scFv-Fc or Tam treatment alone. scFv-Fc treatment down-regulated IGF-IR which appears to contribute to tumor growth inhibition. This study provides evidence that simultaneous targeting of IGF-IR and the estrogen receptor may enhance the therapeutic effect.     

Assessing the exceptionality of network motifs.

Getting and analyzing biological interaction networks is at the core of systems biology. To help understanding these complex networks, many recent works have suggested to focus on motifs which occur more frequently than expected in random. To identify such exceptional motifs in a given network, we propose a statistical and analytical method which does not require any simulation. For this, we first provide an analytical expression of the mean and variance of the count under any exchangeable random graph model. Then we approximate the motif count distribution by a compound Poisson distribution whose parameters are derived from the mean and variance of the count. Thanks to simulations, we show that the compound Poisson approximation outperforms the Gaussian approximation. The compound Poisson distribution can then be used to get an approximate p-value and to decide if an observed count is significantly high or not. Our methodology is applied on protein-protein interaction (PPI) networks, and statistical issues related to exceptional motif detection are discussed.     

New biological indicators to evaluate and monitor radiation-induced damage: an accident case report

The aim of this work was to use several new biological indicators to evaluate damage to the main physiological systems in a victim exposed accidentally to ionizing radiation. Blood samples were used for biological dosimetry and for measurement of the plasma concentrations of several molecules: Flt3 ligand to assess the hematopoietic system, citrulline as an indicator of the digestive tract, and several oxysterols as lipid metabolism and vascular markers. The cytogenetic evaluation estimated the dose to the victim to be between 4.2 and 4.8 Gy, depending on the methodology used. Monitoring the Flt3 ligand demonstrated the severity of bone marrow aplasia. In contrast, the citrulline concentration showed the absence of gastrointestinal damage. Variations in oxysterol concentrations suggested radiation-induced damage to the liver and the cardiovascular system. These results were correlated with those from classic biochemical markers, which demonstrated severe damage to the hematopoietic system and suggested the appearance of subclinical damage to the liver and cardiovascular system. These results demonstrate for the first time the importance of a multiparameter biological approach in the evaluation of radiation damage after accidental irradiation.     

European guidelines for quality assurance in cervical cancer screening: recommendations for clinical management of abnormal cervical cytology, part 1

The current paper presents the first part of Chapter 6 of the second edition of the European Guidelines for Quality Assurance in Cervical Cancer Screening. It provides guidance on how to manage women with abnormal cervical cytology. Throughout this article the Bethesda system is used for cervical cytology terminology, as the European guidelines have recommended that all systems should at least be translated into that terminology while cervical intraepithelial neoplasia (CIN) is used for histological biopsies (Cytopathology 2007; 18 :213–9). A woman with a high‐grade cytological lesion, a repeated low‐grade lesion or with an equivocal cytology result and a positive human papillomavirus (HPV) test should be referred for colposcopy. The role of the colposcopist is to identify the source of the abnormal cells and to make an informed decision as to whether or not any treatment is required. If a patient requires treatment the colposcopist will decide which is the most appropriate method of treatment for each individual woman. The colposcopist should also organize appropriate follow‐up for each woman seen. Reflex testing for high‐risk HPV types of women with atypical squamous cells (ASC) of undetermined significance with referral for colposcopy of women who test positive is a first option. Repeat cytology is a second possibility. Direct referral to a gynaecologist should be restricted to special circumstances. Follow‐up of low‐grade squamous intraepithelial lesion is more difficult because currently there is no evidence to support any method of management as being optimal; repeat cytology and colposcopy are options, but HPV testing is not sufficiently selective, unless for older women. Women with high‐grade squamous intraepithelial lesion (HSIL) or atypical squamous cells, cannot exclude HSIL (ASC‐H) should be referred without triage. Women with glandular lesions require particular attention. In a subsequent issue of Cytopathology, the second part of Chapter 6 will be presented, with recommendations for management and treatment of histologically confirmed intraepithelial neoplasia and guidance for follow‐up of special cases such as women who are pregnant, postmenopausal or immunocompromised.     

How do plant waxes cause flies to slide? Experimental tests of wax-based trapping mechanisms in three pitfall carnivorous plants

The waxy surfaces of three carnivorous plants, Nepenthes ventrata (Nepenthaceae), Brocchinia reducta and Catopsis berteroniana (Bromeliaceae), were compared using scanning electron microscopy (SEM). Their effects on attachment and locomotion of the fly Calliphora vomitoria were studied. The waxy surface of N. ventrata is comprised of a heterogeneous layer from which only platelet-shaped crystalloids could be detached by brushing. In the two bromeliads, the crystalloids are thread-shaped and form a homogenous dense network, which was entirely removable from the epidermis. Experimental data showed that none of the flies was able to walk across any of the waxy surfaces and only a few were able to take off from those surfaces. Both the absence of sites for claw anchorage, especially in N. ventrata, and the wax itself were shown to contribute to the trapping ability of the plants. Only half of the flies quickly recovered their locomotion ability on a glass surface after 20 min of being tested on waxy plant surfaces. SEM observations revealed that the wax of C. berteroniana formed a powder of broken crystals on the tenent setae of the flies' pulvilli. In contrast, the waxes of B. reducta and N. ventrata appeared to have lost their crystal structure in contact with the tenent setae and formed an amorphous substance that adhered setae together. We hypothesize that wax interacts with adhesive fluids secreted by the fly pad and thereby prevents the tenent setae from functioning effectively.     

Determination of the differentially expressed genes in microarray experiments using local FDR

Background  

Thousands of genes in a genomewide data set are tested against some null hypothesis, for detecting differentially expressed genes in microarray experiments. The expected proportion of false positive genes in a set of genes, called the False Discovery Rate (FDR), has been proposed to measure the statistical significance of this set. Various procedures exist for controlling the FDR. However the threshold (generally 5%) is arbitrary and a specific measure associated with each gene would be worthwhile.     

Apolipoprotein E and beta-amyloid (1-42) regulation of glycogen synthase kinase-3beta

Glycogen synthase kinase-3beta (GSK-3beta) is implicated in regulating apoptosis and tau protein hyperphosphorylation in Alzheimer's disease (AD). We investigated the effects of two key AD molecules, namely apoE (E3 and E4 isoforms) and beta-amyloid (Abeta) 1-42 on GSK-3beta and its major upstream regulators, intracellular calcium and protein kinases C and B (PKC and PKB) in human SH-SY5Y neuroblastoma cells. ApoE3 induced a mild, transient, Ca2+-independent and early activation of GSK-3beta. ApoE4 effects were biphasic, with an early strong GSK-3beta activation that was partially dependent on extracellular Ca2+, followed by a GSK-3beta inactivation. ApoE4 also activated PKC-alpha and PKB possibly giving the subsequent GSK-3beta inhibition. Abeta(1-42) effects were also biphasic with a strong activation dependent partially on extracellular Ca2+ followed by an inactivation. Abeta(1-42) induced an early and potent activation of PKC-alpha and a late decrease of PKB activity. ApoE4 and Abeta(1-42) were more toxic than apoE3 as shown by MTT reduction assays and generation of activated caspase-3. ApoE4 and Abeta(1-42)-induced early activation of GSK-3beta could lead to apoptosis and tau hyperphosphorylation. A late inhibition of GSK-3beta through activation of upstream kinases likely compensates the effects of apoE4 and Abeta(1-42) on GSK-3beta, the unbalanced regulation of which may contribute to AD pathology.     

Annexin-1 regulated by HAUSP is essential for UV-induced damage response

DNA damage can occur through diverse stimulations such as toxins, drugs, and environmental factors. To respond to DNA damage, mammalian cells induce DNA damage response (DDR). DDR signal activates a rapid signal transduction pathway, regulating the cell fate based on the damaged cell condition. Moreover, serious damaged cells have to be eliminated by the macrophage to maintain homeostasis. Because the DDR induces genomic instability followed by tumor formation, targeting the DDR signaling can be applied for the cancer therapy. Herpes virus-associated ubiquitin-specific protease (HAUSP/USP7) is one of the well-known deubiquitinating enzymes (DUBs) owing to its relevance with Mdm2-p53 complex. The involvement of HAUSP in DDR through p53 led us to investigate novel substrates for HAUSP, which is related to DDR or apoptosis. As a result, we identified annexin-1 (ANXA1) as one of the putative substrates for HAUSP. ANXA1 has numerous roles in cellular systems including anti-inflammation, damage response, and apoptosis. Several studies have demonstrated that ANXA1 can be modified in a post-translational manner by processes such as phosphorylation, SUMOylation, and ubiquitination. In addition, DNA damage gives various functions to ANXA1 such as stress response or cleavage-mediated apoptotic cell clearance. In the current study, our proteomic analysis using two-dimensional electrophoresis, matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF-MS) and nano LC-MS/MS, and immunoprecipitation revealed that ANXA1 binds to HAUSP through its HAUSP-binding motif (P/AXXS), and the cleavage and damage-responsive functions of ANXA1 upon UV-induced DNA damage may be followed by HAUSP-mediated deubiquitination of ANXA1. Intriguingly, the UV-induced damage responses via HAUSP-ANXA1 interaction in HeLa cells were different from the responses shown in the Jurkat cells, suggesting that their change of roles may depend on the cell types.Most proteins follow the ubiquitin-proteasome pathway (UPP) to degradation; this involves successive enzymatic activities of the E1, E2, and E3 enzymes. In addition to proteasomal degradation, the proteins obtain or alter their functions through mono- or polyubiquitination.¹ Thus, the ‘ubiquitin tag'' is considered as an important feature for intracellular homeostasis. Deubiquitination is a reversible process against ubiquitination that detaches ubiquitin molecules from ubiquitinated proteins, and the process of deubiquitination is mediated by specific enzymes called deubiquitinating enzymes (DUBs). To date, almost ~100 DUBs have been identified, and they are involved in various cellular functions through their capability by which they deubiquitinate and thereby stabilize or alter the functions of their target proteins.² DUBs are composed of at least six subfamilies: ubiquitin-specific proteases (USPs), ubiquitin C-terminal hydrolases (UCHs), ovarian tumor (OTU), Machado-Josephin domain papain-like cysteine proteases (MJDs), JAB1/MPN/Mov34 metalloenzyme (JAMM) domain zinc-dependent metalloprotease family, and monocyte chemotactic protein-induced proteases (MCPIPs).³ In addition, DUBs share specific regions including Cys, Asp/Asn, and His boxes for their deubiquitinating activities.⁴ The USP family has the most number among DUBs (~58 USPs),⁵ and many studies have demonstrated that human USPs have important roles in a broad range of cellular systems.⁶ In particular, their involvement in cell proliferation, signal transduction, and apoptosis emphasizes that abnormal or deregulated functions of USPs can be related to severe diseases including immune disorders and cancers.^{2, 6, 7} Accordingly, USPs have been widely targeted for the therapy of several diseases; however, a clear understanding of the molecular details underlining USPs and other DUBs has not yet been obtained.HAUSP, also known as USP7, is a member of the USP family of DUBs. The importance of HAUSP in cells was demonstrated by its ability to specifically recognize and deubiquitinate both the tumor suppressor p53 and Mdm2, a p53-specific E3 ligase. In the normal state, HAUSP specifically binds to and deubiquitinates Mdm2, thereby stabilizing Mdm2 and subsequently inducing the proteasomal degradation of p53 through Mdm2 activity. Upon DNA damage, HAUSP is dephosphorylated by PPM1G. In this state, the deubiquitinating activity of HAUSP for Mdm2 decreases and HAUSP prefers p53 for its substrate instead of Mdm2. Such altered affinity of HAUSP to p53 leads to DNA repair and tumor-suppressive functions of p53.^{8, 9, 10} In addition to Mdm2 and p53, further studies have revealed that HAUSP can regulate various substrates, including ataxin-1, Chfr, claspin, Daxx, FOXO4, histone H2B, PTEN, NF-κB, Tip60, UbE2E1, and UVSSA.² These findings suggest that HAUSP has diverse roles in the cell through the regulation of different substrates and other additional proteins. In a present study, we performed two-dimensional gel electrophoresis (2-DE) and other proteomics-based experiments using HeLa cells to identify putative substrates regulated by HAUSP. We found several putative substrates, some of which are known to be involved in apoptosis or DNA damage response (DDR). Annexin a1, also known as ANXA1 and lipocortin 1, was also found as a putative binding partner for HAUSP, suggesting that ANXA1 may possibly be regulated by HAUSP-mediated deubiquitination.Annexins consist of 13 annexin members and have four conserved repeated domains, which are responsible for Ca²⁺ and phospholipid binding. In most annexins, the conserved annexin domains enable them to bind the phospholipid of the membranes in a Ca²⁺-dependent manner, resulting in subsequent activities such as membrane trafficking, signal transduction, and exocytosis.¹¹ However, major differences of annexins derive from their unique N-terminal regions. The N-terminus of each annexin member, which is responsible for specific functions, varies.¹² ANXA1, the first member of the annexin superfamily, is a 37-kDa protein abundant in cells. Like other annexin proteins, ANXA1 binds to phospholipid in the presence of Ca²⁺.¹³ The biological functions of ANXA1 are extensively studied: anti-inflammatory mediator,^{14, 15} relationship with tumorigenesis,¹⁶ DDR,^{17, 18} and involvement in apoptosis and apoptotic cell clearance.^{19, 20} Another important feature of ANXA1 activity is the cleavage of the N-terminal region of ANXA1. When DNA damage or stress occurs, ANXA1 is cleaved by several proteases, resulting in the generation of the N-terminal fragment (Ac2-26) and cleaved form of ANXA1 (33 kDa). Importantly, both the full-length ANXA1 and Ac2-26 can be translocated to the cell membrane and induce apoptotic cell clearance by recruiting monocytes via chemoattraction.²⁰ Thus, the ANXA1 cleavage process is considered essential for cell phagocytosis, as also revealed in neutrophil apoptosis and phagocytosis during inflammation.¹⁴ Otherwise, in response to cell damage, ANXA1 functions as a stress protein or a protective protein for DNA damage, resulting in nuclear localization of ANXA1.^{18, 21, 22} Overall, it is evident that ANXA1 participates in various cellular responses.In the current study, we have identified ANXA1 as a novel substrate for HAUSP. HAUSP can bind to, deubiquitinate, and co-localize with ANXA1. Surprisingly, upon UV-induced DNA damage, the binding and the deubiquitinating activity of HAUSP to ANXA1 are increased. In addition, ANXA1 in HAUSP-deficient cells showed different localization and altered expression level and cleavage. Moreover, HAUSP-mediated regulation of ANXA1 shown in HeLa cells was different from the one in Jurkat cells. We found that apoptosis and transmigrative ratio of monocytes in HAUSP-depleted Jurkat cells coincides with the regulation of ANXA1 protein level and cleavage. Taken together, we suggest that ANXA1 functions of UV-induced DDR are regulated by the deubiquitinating activity of HAUSP.     

A segmentation/clustering model for the analysis of array CGH data

Microarray-CGH (comparative genomic hybridization) experiments are used to detect and map chromosomal imbalances. A CGH profile can be viewed as a succession of segments that represent homogeneous regions in the genome whose representative sequences share the same relative copy number on average. Segmentation methods constitute a natural framework for the analysis, but they do not provide a biological status for the detected segments. We propose a new model for this segmentation/clustering problem, combining a segmentation model with a mixture model. We present a new hybrid algorithm called dynamic programming-expectation maximization (DP-EM) to estimate the parameters of the model by maximum likelihood. This algorithm combines DP and the EM algorithm. We also propose a model selection heuristic to select the number of clusters and the number of segments. An example of our procedure is presented, based on publicly available data sets. We compare our method to segmentation methods and to hidden Markov models, and we show that the new segmentation/clustering model is a promising alternative that can be applied in the more general context of signal processing.     

Phosphorylated PP2A (tyrosine 307) is associated with Alzheimer neurofibrillary pathology

Down-regulation of protein phosphatase 2A (PP2A) is thought to play a critical role in tau hyperphosphorylation in Alzheimer's disease (AD). In vitro phosphorylation of PP2A catalytic subunit at Y307 efficiently inactivates PP2A. A specific antibody against phosphorylated (p) PP2A (Y307) (PP2Ac-Yp307) was used to investigate possible PP2A down-regulation by known pathophysiological changes associated with AD, such as Abeta accumulation and oestrogen deficiency. Immunohistochemistry and immunofluorescence confocal microscopy showed an aberrant accumulation of PP2Ac-Yp307 in neurons that bear pretangles or tangles in the susceptible brain regions, such as the entorhinal cortical cortex and the hippocampus. Experimentally, increased PP2Ac-Yp307 was observed in mouse N2a neuroblastoma cells that stably express the human amyloid precursor protein with Swedish mutation (APPswe) compared with wild-type, and in the brains of transgenic APPswe/ presenilin (PS1, A246E) mice, which corresponded to the increased tau phosphorylation. Treating N2a cells with Abeta25-35 mimicked the changes of PP2Ac-Yp307 and tau phosphorylation in N2a APPswe cells. Knockout of oestrogen receptor (ER) alpha or ERbeta gave similar changes of PP2Ac-Yp307 level and tau phosphorylation in the mouse brain. Taken together, these findings suggest that increased PP2A phosphorylation (Y307) can be mediated by Abeta deposition or oestrogen deficiency in the AD brain, and consequently compromise dephosphorylation of abnormally hyperphosphorylated tau, and lead to neurofibrillary tangle formation.