The Antigen Receptor as a Driver of B-Cell Lymphoma Development and Evolution

The expression of a functional antigen receptor is necessary for cell survival of normal B lymphocytes and most B-cell neoplasms alike. When the genetic modifications of the B-cell receptor locus fail to produce a functional antigen receptor or result in deleterious mutations of a previously expressed receptor, the affected B cell will undergo apoptosis. The three physiological mechanisms that generate the B-cell receptor, VDJ recombination, somatic hypermutation, and class switch recombination, can induce double-strand DNA breaks and can specifically contribute to lymphomagenesis. On the other hand, the B-cell receptor activation and signaling pathways, which provide strong survival and proliferation signals to normal B cells, can support the growth and evolution of malignant lymphocytes. As a result, an otherwise structurally normal B-cell receptor can behave, from the functional perspective, as a true oncogene. In this chapter, we provide an in-depth discussion of the most recently discovered recurrent mechanisms involving the B-cell receptor in lymphoma pathogenesis. The discussion is structured around two major topics: (1) the genetic mechanisms that create a functional antigen receptor and their errors leading to oncogenic events, and (2) the pathogenic activation of the B-cell receptor signaling cascade. Finally, we will briefly comment on novel emerging therapies targeting the B-cell receptor at different levels

Molecular phylogeny, diagnostics, and diversity of plant-parasitic nematodes of the genus Hemicycliophora (Nematoda: Hemicycliophoridae)

The genus Hemicycliophora (Nematoda: Hemicycliophoridae) contains 132 valid species of plant-parasitic nematodes, collectively known as ‘sheath nematodes’. Hemicycliophora spp. are characterized morphologically by a long stylet with rounded basal knobs and a cuticular sheath, present in juvenile and adult stages. Populations of 20 valid and 14 putative species of Hemicycliophora and Loofia from several countries were characterized morphologically using light (LM) and scanning electron microscopy (SEM) and molecularly using the D2-D3 segments of 28S rRNA and internal transcribed spacer (ITS) rRNA gene sequences. LM and SEM observations provided new details on the morphology of these species. PCR-restriction fragment length polymorphisms (PCR-RFLPs) of the D2-D3 of 28S rDNA were proposed for identification of the species. Phylogenetic relationships within populations of 36 species of the genus Hemicycliophora using 102 D2-D3 of 28S rDNA and 97 ITS rRNA gene sequences as inferred from Bayesian analysis are reconstructed and discussed. Ancestral state reconstructions of diagnostic characters (body and stylet length, number of body annuli, shape of vulval lip and tail), using maximum parsimony and Bayesian inference, revealed that none of the traits are individually reliable characters for classifying the studied sheath nematode. The Shimodaira–Hasegawa test rejected the validity of the genus Loofia. This is the most complete phylogenetic analysis of Hemicycliophora species conducted so far.Fil: Subbotin, Sergei A.. California Department of Food and Agriculture; Estados Unidos. Institute of Ecology and Evolution of the Russian Academy of Sciences; RusiaFil: Chitambar, John J.. California Department of Food and Agriculture; Estados UnidosFil: Chizhov, Vladimir N.. Institute of Ecology and Evolution of the Russian Academy of Sciences; RusiaFil: Stanley, Jason D.. Florida Department of Agriculture and Consumer Services; Estados UnidosFil: Inserra, Renato N.. Florida Department of Agriculture and Consumer Services; Estados UnidosFil: Doucet, Marcelo Edmundo. Universidad Nacional de Cordoba. Facultad de Cs.exactas Fisicas y Naturales. Centro de Zoologia Aplicada; Argentina. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Cordoba. Instituto de Diversidad y Ecologia Animal; ArgentinaFil: Mcclure, Michael. University Of Arizona; Estados UnidosFil: Ye, Weimin. North Carolina Department of Agriculture & Consumer Services; Estados UnidosFil: Yeates, George.Fil: Mollov, Dimitre S.. University Of Minnesota; Estados UnidosFil: Cantalapiedra Navarrete, Carolina. Consejo Superior de Investigaciones Científicas. Instituto de Agricultura Sostenible; EspañaFil: Vovlas, Nicola. Istituto per la Protezione delle Piante; ItaliaFil: Van Den Berg, Esther. ARC-Plant Protection Research Institute; SudáfricaFil: Castillo, Pablo. Consejo Superior de Investigaciones Científicas. Instituto de Agricultura Sostenible; Españ

Structural and mechanistic insights into the catalytic-domain-mediated short-range glycosylation preferences of GalNAc-T4

17 pags, 4 figs, 2 tabsMucin-type O-glycosylation is initiated by a family of polypeptide GalNAc-transferases (GalNAc-Ts) which are type-II transmembrane proteins that contain Golgi luminal catalytic and lectin domains that are connected by a flexible linker. Several GalNAc-Ts, including GalNAc-T4, show both long-range and short-range prior glycosylation specificity, governed by their lectin and catalytic domains, respectively. While the mechanism of the lectin-domain-dependent glycosylation is well-known, the molecular basis for the catalytic-domain-dependent glycosylation of glycopeptides is unclear. Herein, we report the crystal structure of GalNAc-T4 bound to the diglycopeptide GAT GAGAGAGT TPGPG (containing two α-GalNAc glycosylated Thr (T ), the PXP motif and a "naked" Thr acceptor site) that describes its catalytic domain glycopeptide GalNAc binding site. Kinetic studies of wild-type and GalNAc binding site mutant enzymes show the lectin domain GalNAc binding activity dominates over the catalytic domain GalNAc binding activity and that these activities can be independently eliminated. Surprisingly, a flexible loop protruding from the lectin domain was found essential for the optimal activity of the catalytic domain. This work provides the first structural basis for the short-range glycosylation preferences of a GalNAc-T.We thank synchrotron radiation sources DLS (Oxford) and in particular beamline I03 (experiment number MX10121-15). We thank ARAID, MEC (CTQ2013-44367-C2-2-P, BFU2016-75633-P, CTQ2015-67727-R, CTQ2015-70524-R, and CTQ2017-85496-P), AGAUR (SGR2017-1189), the National Institutes of Health (R01-GM113534, and instrument Grant GM113534-01S to T. A. Gerken), the Danish National Research Foundation (DNRF107), the FCT-Portugal [UID/Multi/04378/2013 cofinanced by the FEDER (POCI- 01-0145-FEDER-007728)], and the DGA (E34_R17) for financial support. I. Compañón thanks Universidad de La Rioja for the FPI grant. F. Marcelo thanks FCT-Portugal for IF Investigator grant (IF/00780/2015) and PTNMR supported by Project 022161. E. Lira-Navarrete acknowledges her postdoctoral EMBO fellowship ALTF 1553-2015 cofunded by the European Commission (LTFCOFUND2013, GA-2013-609409) and Marie Curie Actions. H. Coelho and J. Jiménez-Barbero thank EU for the TOLLerant project. The research leading to these results has also received funding from the FP7 (2007−2013) under BioStruct-X (Grant agreement 283570 and BIOSTRUCTX_5186). We would also like to acknowledge the assistance of Juwan Lee in obtaining the GalNAc-T4 random peptide motif

The interdomain flexible linker of the polypeptide GalNAc transferases dictates their long-range glycosylation preferences

11 pags, 3 figs, 2 tabsThe polypeptide GalNAc-transferases (GalNAc-Ts), that initiate mucin-type O-glycosylation, consist of a catalytic and a lectin domain connected by a flexible linker. In addition to recognizing polypeptide sequence, the GalNAc-Ts exhibit unique long-range N- A nd/or C-terminal prior glycosylation (GalNAc-O-Ser/Thr) preferences modulated by the lectin domain. Here we report studies on GalNAc-T4 that reveal the origins of its unique N-terminal long-range glycopeptide specificity, which is the opposite of GalNAc-T2. The GalNAc-T4 structure bound to a monoglycopeptide shows that the GalNAc-binding site of its lectin domain is rotated relative to the homologous GalNAc-T2 structure, explaining their different long-range preferences. Kinetics and molecular dynamics simulations on several GalNAc-T2 flexible linker constructs show altered remote prior glycosylation preferences, confirming that the flexible linker dictates the rotation of the lectin domain, thus modulating the GalNAc-Ts' long-range preferences. This work for the first time provides the structural basis for the different remote prior glycosylation preferences of the GalNAc-Ts.We thank synchrotron radiation sources DLS (Oxford) and in particular beamline I03 (experiment number MX10121-7). We thank ARAID, MEC (CTQ2013-44367-C2-2-P, BFU2016-75633-P, CTQ2015-67727-R, CTQ2015-70524-R, and RYC-2013-14706), the National Institutes of Health (GM113534, and instrument grant GM113534-01S), the Danish National Research Foundation (DNRF107), the FCT-Portugal (UID/Multi/04378/2013 and PTNMR Project No 022161), and the DGA (B89) for the financial support. I.C. thanks Universidad de La Rioja for the FPI grant. F.M. thanks FCT-Portugal for IF Investigator. E.L.-N. acknowledges her postdoctoral EMBO fellowship ALTF 1553-2015 co-funded by the European Commission (LTFCOFUND2013, GA-2013-609409) and Marie Curie Actions. H.C. and J.J.-B. thank EU for the TOLLerant project. The research leading to these results has also received funding from the FP7 (2007-2013) under BioStruct-X (grant agreement No. 283570 and BIOSTRUCTX_5186). We also thank BIFI (Memento cluster) and CESGA for computer support.Peer reviewe

Autonomous B-cell receptor signaling and genetic aberrations in chronic lymphocytic leukemia-phenotype monoclonal B lymphocytosis in siblings of patients with chronic lymphocytic leukemia

Clonal expansion of CD5-expressing B cells, commonly designated as monoclonal B lymphocytosis (MBL), is a precursor condition for chronic lymphocytic leukemia (CLL). The mechanisms driving subclinical MBL B-cell expansion and progression to CLL, occurring in approximately 1% of affected individuals, are unknown. An autonomously signaling B-cell receptor (BCR) is essential for the pathogenesis of CLL. The objectives of this study were functional characterization of the BCR of MBL in siblings of CLL patients and a comparison of genetic variants in MBL-CLL sibling pairs. Screening of peripheral blood by flow cytometry detected 0.2-480 clonal CLL-phenotype cells per microliter (median: 37/μL) in 34 of 191 (17.8%) siblings of CLL patients. Clonal BCR isolated from highly purified CLL-phenotype cells induced robust calcium mobilization in BCR-deficient murine pre-B cells in the absence of external antigen and without experimental crosslinking. This autonomous BCR signal was less intense than the signal originating from the CLL BCR of their CLL siblings. According to genotyping by single nucleotide polymorphism array, whole exome, and targeted panel sequencing, CLL risk alleles were found with high and similar prevalence in CLL patients and MBL siblings, respectively. Likewise, the prevalence of recurrent CLL-associated genetic variants was similar between CLL and matched MBL samples. However, copy number variations and small variants were frequently subclonal in MBL cells, suggesting their acquisition during subclinical clonal expansion. These findings support a stepwise model of CLL pathogenesis, in which autonomous BCR signaling leads to a non-malignant (oligo)clonal expansion of CD5+ B cells, followed by malignant progression to CLL after acquisition of pathogenic genetic variants

The PREDICTS database: a global database of how local terrestrial biodiversity responds to human impacts

Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species’ threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project – and avert – future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups – including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems – www.predicts.org.uk). We make site-level summary data available alongside this article. The full database will be publicly available in 2015

The elusive tidal tails of the Milky Way globular cluster NGC 7099

We present results on the extra-tidal features of the Milky Way globular cluster NGC 7099, using deep gr photometry obtained with the Dark Energy Camera (DECam). We reached nearly 6 mag below the cluster's main sequence (MS) turnoff, so that we dealt with the most suitable candidates to trace any stellar structure located beyond the cluster tidal radius. From star-by-star reddening corrected color-magnitude diagrams (CMDs), we defined four adjacent strips along the MS, for which we built the respective stellar density maps, once the contamination by field stars was properly removed. The resulting, cleaned, field star stellar density maps show a short tidal tail and some scattered debris. Such extra-tidal features are hardly detected when much shallower Gaia DR2 data sets are used and the same CMD field star cleaning procedure is applied. Indeed, by using 2.5 mag below the MS turnoff of the cluster as the faintest limit (G < 20.5 mag), cluster members turned out to be distributed within the cluster's tidal radius, and some hints for field star density variations are found across a circle of radius 3.5° centered on the cluster and with similar CMD features as cluster stars. The proper motion distribution of these stars is distinguishable from that of the cluster, with some superposition, which resembles that of stars located beyond 3.5° from the cluster center.Fil: Piatti, Andres Eduardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Interdisciplinario de Ciencias Básicas. - Universidad Nacional de Cuyo. Instituto Interdisciplinario de Ciencias Básicas; ArgentinaFil: Carballo Bello, Julio A.. Universidad de Tarapacá; ChileFil: Mora, Marcelo D.. Pontificia Universidad Católica de Chile; ChileFil: Cenzano, Carolina. Pontificia Universidad Católica de Chile; ChileFil: Navarrete, Camila. European Southern Observatory Santiago; Chile. Instituto Milenio de Astrofísica; ChileFil: Catelan, Márcio. Universidad Católica de Chile; Chile. Instituto Milenio de Astrofísica; Chil