Deduced probable HLA-B*40:01:35-associated HLA haplotype (A*24-B*40:01:35-DRB1*11) found in a Taiwanese unrelated hematopoietic bone marrow stem cell donor

AbstractObjectiveHuman leukocyte antigen (HLA)-B*40:01:35 is a low incidence allele in the HLA-B locus. The objective of this study is to report the ethnicity of B*40:01:35 and its deduced probable HLA associated haplotype in a Taiwanese unrelated bone marrow hematopoietic stem cell donor.Materials and methodsA sequence-based typing method was employed to confirm the low incidence allele B*40:01:35. Polymerase chain reaction was performed to amplify exons 2 and 3 of the HLA-A and HLA-B loci and exon 2 of the HLA-DRB1 locus using group-specific primer sets. The amplicons were sequenced using the BigDye Terminator Cycle Sequencing Ready Reaction kit in both directions according to the manufacturer's protocols.ResultsThe DNA sequence of B*40:01:35 is identical to B*40:01:01 in exons 2 and 3, except for residue 324 where C is changed to T (codon 84, TAC→TAT). The nucleotide exchange does not cause amino acid alteration to the protein sequence of B*40:01:01 due to the silent mutation. We deduced the probable HLA haplotype in association with B*40:01:35 in Taiwanese to be A*24-B*40:01:35-DRB1*11.ConclusionInformation on the deduced probable HLA haplotype in association with the low incidence B*40:01:35 allele that we report here is of value for HLA testing laboratories for reference purposes. In addition, it can be used by stem cell transplantation donor search coordinators to determine a strategy for finding compatible donors in unrelated bone marrow donor registries when a patient has this uncommon HLA allele

Combining functional and linkage disequilibrium information in the selection of tag SNPs

Summary: We have developed an online program, WCLUSTAG, for tag SNP selection that allows the user to specify variable tagging thresholds for different SNPs. Tag SNPs are selected such that a SNP with user-specified tagging threshold C will have a minimum R2 of C with at least one tag SNP. This flexible feature is useful for researchers who wish to prioritize genomic regions or SNPs in an association study. © 2007 Oxford University Press.postprin

Algorithmes mémétiques de détection de communautés dans les réseaux complexes (techniques palliatives de la limite de résolution)

Les réseaux complexes, issus de relevés de terrain d origines trèsvariées, en biologie, science de l information ou sociologie,présentent une caractéristique remarquable dénommée structurecommunautaire. Des groupes, ou communautés, à l intérieur duréseau, ont une cohésion interne forte et des liens entre eux plusfaibles. Sans connaissance a priori du nombre de communautés, ladifficulté réside dans la caractérisation d un bon partitionnement encommunautés. La modularité est une mesure globale de qualité departitionnement très utilisée qui capture les contraintes de cohésioninterne forte et de liens externes faibles. Elle transforme le problèmede détection de communautés en problème d optimisationNP-difficile. Elle souffre d un défaut, la limite de résolution, qui tendà rendre indétectables les très petites communautés d autant plusque le réseau est grand. L algorithme le plus efficace pour optimiserla modularité, dit de Louvain, procède par fusion de communautés.Cette thèse s attache à modifier cet algorithme pour qu il réalisemajoritairement des fusions pertinentes, qui n aggravent pas lalimite de résolution, en utilisant une condition de fusion. De plus, enl associant à un algorithme mémétique, les partitions proposéessont très proches des partitions attendues pour des graphesgénérés par un modèle qui reproduit les caractéristiques desréseaux complexes. Enfin, cet algorithme mémétique réduitfortement l inconsistance de solution, défaut de la modularité selonlequel deux partitions trouvées à partir d un examen des noeudsdans un ordre aléatoire, pour le même graphe, peuvent êtrestructurellement très différentes, rendant leur interprétation délicate.From various applications, in sociology or biology for instance,complex networks exhib the remarquable property of communitystructure. Groups, sometimes called communities, has a stronginternal cohesion and poor links between them. Whithout priorknowledge of the number of communities, the difficulty lies in thecharacterization of a good clustering. Modularity is an overallmeasure of clustering quality widely used to capture the doubleconstraint, internal and external, of well formed communities. Theproblem became a NP-hard optimization problem. The main weakof modularity is the resolution limit, which tends to makeundetectable very small communities especially as the network islarge. The algorithm of Louvain, one of the most efficient one tooptimize modularity, proceeds by merging communities. This thesisattempts to modify the algorithm so that it mainly produces relevantmerges that do not make worse the effects of resolution limit, usinga merge condition. In addition, by combining it with a memeticalgorithm, proposed clusterings are very close to the expected onesfor graphs generated by a model that reproduces the characteristicsof complex networks. Finally, the memetic algorithm greatly reducesthe inconsistency of solution, another weakness of modularity suchthat, for the same graph, two partitions found from an exploration ofnodes in a random order can be structurally very different, makingthem difficult to interpret.LE MANS-BU Sciences (721812109) / SudocSudocFranceF

Polymorphisms of CR1, CLU and PICALM confer susceptibility of Alzheimer's disease in a southern Chinese population

In this case-controlled study, we tested susceptible genetic variants for Alzheimer's disease (AD) in CR1, CLU and PICALM from genome-wide association studies (GWAS) in a southern Chinese population. Eight hundred twelve participants consisting of 462 late-onset Alzheimer's disease (LOAD) patients and 350 nondemented control subjects were recruited. We found by multivariate logistic regression analysis, that single nucleotide polymorphisms (SNPs) in CR1 (rs6656401 adjusted allelic p = 0.035; adjusted genotypic p = 0.043) and CLU (rs2279590 adjusted allelic p = 0.035; adjusted genotypic p = 0.006; rs11136000 adjusted allelic p = 0.038; adjusted genotypic p = 0.009) were significantly different between LOAD patients and nondemented controls. For PICALM, LOAD association was found only in the APOE ε4 (-) subgroup (rs3851179 adjusted allelic p = 0.028; adjusted genotypic p = 0.013). Our findings showed evidence of CR1, CLU, and PICALM and LOAD susceptibility in an independent southern Chinese population, which provides additional evidence for LOAD association apart from prior genome-wide association studies in Caucasian populations. © 2012 Elsevier Inc.postprin

M2Net: Multi-modal Multi-channel Network for Overall Survival Time Prediction of Brain Tumor Patients

Early and accurate prediction of overall survival (OS) time can help to obtain better treatment planning for brain tumor patients. Although many OS time prediction methods have been developed and obtain promising results, there are still several issues. First, conventional prediction methods rely on radiomic features at the local lesion area of a magnetic resonance (MR) volume, which may not represent the full image or model complex tumor patterns. Second, different types of scanners (i.e., multi-modal data) are sensitive to different brain regions, which makes it challenging to effectively exploit the complementary information across multiple modalities and also preserve the modality-specific properties. Third, existing methods focus on prediction models, ignoring complex data-to-label relationships. To address the above issues, we propose an end-to-end OS time prediction model; namely, Multi-modal Multi-channel Network (M2Net). Specifically, we first project the 3D MR volume onto 2D images in different directions, which reduces computational costs, while preserving important information and enabling pre-trained models to be transferred from other tasks. Then, we use a modality-specific network to extract implicit and high-level features from different MR scans. A multi-modal shared network is built to fuse these features using a bilinear pooling model, exploiting their correlations to provide complementary information. Finally, we integrate the outputs from each modality-specific network and the multi-modal shared network to generate the final prediction result. Experimental results demonstrate the superiority of our M2Net model over other methods.Comment: Accepted by MICCAI'2

Novel Quantitative Real-Time LCR for the Sensitive Detection of SNP Frequencies in Pooled DNA: Method Development, Evaluation and Application

BACKGROUND: Single nucleotide polymorphisms (SNP) have proven to be powerful genetic markers for genetic applications in medicine, life science and agriculture. A variety of methods exist for SNP detection but few can quantify SNP frequencies when the mutated DNA molecules correspond to a small fraction of the wild-type DNA. Furthermore, there is no generally accepted gold standard for SNP quantification, and, in general, currently applied methods give inconsistent results in selected cohorts. In the present study we sought to develop a novel method for accurate detection and quantification of SNP in DNA pooled samples. METHODS: The development and evaluation of a novel Ligase Chain Reaction (LCR) protocol that uses a DNA-specific fluorescent dye to allow quantitative real-time analysis is described. Different reaction components and thermocycling parameters affecting the efficiency and specificity of LCR were examined. Several protocols, including gap-LCR modifications, were evaluated using plasmid standard and genomic DNA pools. A protocol of choice was identified and applied for the quantification of a polymorphism at codon 136 of the ovine PRNP gene that is associated with susceptibility to a transmissible spongiform encephalopathy in sheep. CONCLUSIONS: The real-time LCR protocol developed in the present study showed high sensitivity, accuracy, reproducibility and a wide dynamic range of SNP quantification in different DNA pools. The limits of detection and quantification of SNP frequencies were 0.085% and 0.35%, respectively. SIGNIFICANCE: The proposed real-time LCR protocol is applicable when sensitive detection and accurate quantification of low copy number mutations in DNA pools is needed. Examples include oncogenes and tumour suppressor genes, infectious diseases, pathogenic bacteria, fungal species, viral mutants, drug resistance resulting from point mutations, and genetically modified organisms in food

Synthetic RGDS peptide attenuates lipopolysaccharide-induced pulmonary inflammation by inhibiting integrin signaled MAP kinase pathways

<p>Abstract</p> <p>Background</p> <p>Synthetic peptides containing the RGD sequence inhibit integrin-related functions in different cell systems. Here, we investigated the effects of synthetic Arg-Gly-Asp-Ser (RGDS) peptide on key inflammatory responses to intratracheal (<it>i.t.</it>) lipopolysaccharide (LPS) treatment and on the integrin signaled mitogen-activated protein (MAP) kinase pathway during the development of acute lung injury.</p> <p>Methods</p> <p>Saline or LPS (1.5 mg/kg) was administered <it>i.t. </it>with or without a single dose of RGDS (1, 2.5, or 5 mg/kg, i.p.), anti-α_vor anti-β₃mAb (5 mg/kg, i.p.). Mice were sacrificed 4 or 24 h post-LPS.</p> <p>Results</p> <p>A pretreatment with RGDS inhibited LPS-induced increases in neutrophil and macrophage numbers, total protein levels and TNF-α and MIP-2 levels, and matrix metalloproteinase-9 activity in bronchoalveolar lavage (BAL) fluid at 4 or 24 h post-LPS treatment. RGDS inhibited LPS-induced phosphorylation of focal adhesion kinase and MAP kinases, including ERK, JNK, and p38 MAP kinase, in lung tissue. Importantly, the inhibition of the inflammatory responses and the kinase pathways were still evident when this peptide was administered 2 h after LPS treatment. Similarly, a blocking antibody against integrin α_vsignificantly inhibited LPS-induced inflammatory cell migration into the lung, protein accumulation and proinflammatory mediator production in BAL fluid, at 4 or 24 h post-LPS. Anti-β₃also inhibited all LPS-induced inflammatory responses, except the accumulation of BAL protein at 24 h post-LPS.</p> <p>Conclusion</p> <p>These results suggest that RGDS with high specificity for α_vintegrins attenuates inflammatory cascade during LPS-induced development of acute lung injury.</p

Endothelial-Mesenchymal Transition of Brain Endothelial Cells: Possible Role during Metastatic Extravasation

Cancer progression towards metastasis follows a defined sequence of events described as the metastatic cascade. For extravasation and transendothelial migration metastatic cells interact first with endothelial cells. Yet the role of endothelial cells during the process of metastasis formation and extravasation is still unclear, and the interaction between metastatic and endothelial cells during transendothelial migration is poorly understood. Since tumor cells are well known to express TGF-beta, and the compact endothelial layer undergoes a series of changes during metastatic extravasation (cell contact disruption, cytoskeletal reorganization, enhanced contractility), we hypothesized that an EndMT may be necessary for metastatic extravasation. We demonstrate that primary cultured rat brain endothelial cells (BEC) undergo EndMT upon TGF-beta 1 treatment, characterized by the loss of tight and adherens junction proteins, expression of fibronectin, beta 1-integrin, calponin and a-smooth muscle actin (SMA). B16/F10 cell line conditioned and activated medium (ACM) had similar effects: claudin-5 down-regulation, fibronectin and SMA expression. Inhibition of TGF-beta signaling during B16/F10 ACM stimulation using SB-431542 maintained claudin-5 levels and mitigated fibronectin and SMA expression. B16/F10 ACM stimulation of BECs led to phosphorylation of Smad2 and Smad3. SB-431542 prevented SMA up-regulation upon stimulation of BECs with A2058, MCF-7 and MDA-MB231 ACM as well. Moreover, B16/F10 ACM caused a reduction in trans-endothelial electrical resistance, enhanced the number of melanoma cells adhering to and transmigrating through the endothelial layer, in a TGF-beta-dependent manner. These effects were not confined to BECs: HUVECs showed TGF-beta-dependent SMA expression when stimulated with breast cancer cell line ACM. Our results indicate that an EndMT may be necessary for metastatic transendothelial migration, and this transition may be one of the potential mechanisms occurring during the complex phenomenon known as metastatic extravasation

Helicobacter pylori Impairs Murine Dendritic Cell Responses to Infection

International audienceBACKGROUND: Helicobacter pylori, a human pathogen associated with chronic gastritis, peptic ulcer and gastric malignancies, is generally viewed as an extracellular microorganism. Here, we show that H. pylori replicates in murine bone marrow derived-dendritic cells (BMDCs) within autophagosomes. METHODOLOGY/PRINCIPAL FINDINGS: A 10-fold increase of CFU is found between 2 h and 6 h p.i. in H. pylori-infected BMDCs. Autophagy is induced around the bacterium and participates at late time points of infection for the clearance of intracellular H. pylori. As a consequence of infection, LC3, LAMP1 and MHC class II molecules are retained within the H. pylori-containing vacuoles and export of MHC class II molecules to cell surface is blocked. However, formalin-fixed H. pylori still maintain this inhibitory activity in BMDC derived from wild type mice, but not in from either TLR4 or TLR2-deficient mice, suggesting the involvement of H. pylori-LPS in this process. TNF-alpha, IL-6 and IL-10 expression was also modulated upon infection showing a TLR2-specific dependent IL-10 secretion. No IL-12 was detected favoring the hypothesis of a down modulation of DC functions during H. pylori infection. Furthermore, antigen-specific T cells proliferation was also impaired upon infection. CONCLUSIONS/SIGNIFICANCE: H. pylori can infect and replicate in BMDCs and thereby affects DC-mediated immune responses. The implication of this new finding is discussed for the biological life cycle of H. pylori in the host

Inflammatory Monocytes and Neutrophils Are Licensed to Kill during Memory Responses In Vivo

Immunological memory is a hallmark of B and T lymphocytes that have undergone a previous encounter with a given antigen. It is assumed that memory cells mediate better protection of the host upon re-infection because of improved effector functions such as antibody production, cytotoxic activity and cytokine secretion. In contrast to cells of the adaptive immune system, innate immune cells are believed to exhibit a comparable functional effector response each time the same pathogen is encountered. Here, using mice infected by the intracellular bacterium Listeria monocytogenes, we show that during a recall bacterial infection, the chemokine CCL3 secreted by memory CD8+ T cells drives drastic modifications of the functional properties of several populations of phagocytes. We found that inflammatory ly6C+ monocytes and neutrophils largely mediated memory CD8+ T cell bacteriocidal activity by producing increased levels of reactive oxygen species (ROS), augmenting the pH of their phagosomes and inducing antimicrobial autophagy. These events allowed an extremely rapid control of bacterial growth in vivo and accounted for protective immunity. Therefore, our results provide evidence that cytotoxic memory CD8+ T cells can license distinct antimicrobial effector mechanisms of innate cells to efficiently clear pathogens