Showing papers by "Ajit Varki published in 2006"

Siglecs--the major subfamily of I-type lectins.

Abstract: Animal glycan-recognizing proteins can be broadly classified into two groups-lectins (which typically contain an evolutionarily conserved carbohydrate-recognition domain [CRD]) and sulfated glycosaminoglycan (SGAG)-binding proteins (which appear to have evolved by convergent evolution). Proteins other than antibodies and T-cell receptors that mediate glycan recognition via immunoglobulin (Ig)-like domains are called "I-type lectins." The major homologous subfamily of I-type lectins with sialic acid (Sia)-binding properties and characteristic amino-terminal structural features are called the "Siglecs" (Sia-recognizing Ig-superfamily lectins). The Siglecs can be divided into two groups: an evolutionarily conserved subgroup (Siglecs-1, -2, and -4) and a CD33/Siglec-3-related subgroup (Siglecs-3 and -5-13 in primates), which appear to be rapidly evolving. This article provides an overview of historical and current information about the Siglecs.

Loss of Siglec expression on T lymphocytes during human evolution

Abstract: We report here that human T cells give much stronger proliferative responses to specific activation via the T cell receptor (TCR) than those from chimpanzees, our closest evolutionary relatives. Nonspecific activation using phytohemagglutinin was robust in chimpanzee T cells, indicating that the much lower response to TCR simulation is not due to any intrinsic inability to respond to an activating stimulus. CD33-related Siglecs are inhibitory signaling molecules expressed on most immune cells and are thought to down-regulate cellular activation pathways via cytosolic immunoreceptor tyrosine-based inhibitory motifs. Among human immune cells, T lymphocytes are a striking exception, expressing little to none of these molecules. In stark contrast, we find that T lymphocytes from chimpanzees as well as the other closely related “great apes” (bonobos, gorillas, and orangutans) express several CD33-related Siglecs on their surfaces. Thus, human-specific loss of T cell Siglec expression occurred after our last common ancestor with great apes, potentially resulting in an evolutionary difference with regard to inhibitory signaling. We confirmed this by studying Siglec-5, which is prominently expressed on chimpanzee lymphocytes, including CD4 T cells. Ab-mediated clearance of Siglec-5 from chimpanzee T cells enhanced TCR-mediated activation. Conversely, primary human T cells and Jurkat cells transfected with Siglec-5 become less responsive; i.e., they behave more like chimpanzee T cells. This human-specific loss of T cell Siglec expression associated with T cell hyperactivity may help explain the strikingly disparate prevalence and severity of T cell-mediated diseases such as AIDS and chronic active hepatitis between humans and chimpanzees.

Discovery of Siglec-14, a novel sialic acid receptor undergoing concerted evolution with Siglec-5 in primates

Abstract: Immune receptors that show high mutual sequence similarity and have antagonizing signaling properties are called paired receptors, and are believed to fine-tune immune responses. Siglecs are sialic acid-recognizing receptors of the immunoglobulin (Ig) superfamily expressed on immune cells. Human Siglec-5, encoded by SIGLEC5 gene, has four extracellular Ig-like domains and a cytosolic inhibitory motif. We discovered human Siglec-14 with three Ig-like domains, encoded by the SIGLEC14 gene, adjacent to SIGLEC5. Human Siglec-14 has almost complete sequence identity with human Siglec-5 at the first two Ig-like domains, shows a glycan binding preference similar to that of human Siglec-5, and associates with the activating adapter protein DAP12. Thus, Siglec-14 and Siglec-5 appear to be the first glycan binding paired receptors. Near-complete sequence identity of the amino-terminal part of human Siglec-14 and Siglec-5 indicates partial gene conversion between SIGLEC14 and SIGLEC5. Remarkably, SIGLEC14 and SIGLEC5 in other primates also show evidence of gene conversions within each lineage. Evidently, balancing the interactions between Siglec-14, Siglec-5 and their common ligand(s) had selective advantage during the course of evolution. The "essential arginine" critical for sialic acid recognition in both Siglec-14 and Siglec-5 is present in humans but mutated in almost all great ape alleles.

L-selectin facilitation of metastasis involves temporal induction of Fut7-dependent ligands at sites of tumor cell arrest.

Abstract: Hematogenous carcinoma metastasis is supported by aggregated platelets and leukocytes, forming tumor cell emboli. Early tumor cell-platelet interactions can be mediated by P-selectin binding to tumor cell surface ligands and this process is blocked by heparin. We previously showed that L-selectin deficiency also attenuates experimental metastasis. However, the mechanisms and timing of L-selectin action remained unknown. Here, we study how L-selectin facilitates establishment of pulmonary metastatic foci in syngeneic mice by using experimental metastasis to time events following entry of tumor cells into the bloodstream. Although L-selectin deficiency did not affect platelet aggregation or initial tumor cell embolization, the association of leukocytes with tumor cells was reduced and tumor cell survival was diminished 24 hours later. Temporal inhibition of L-selectin by a function-blocking antibody reduced metastasis. Moreover, although selectin blockade by heparin 6 to 18 hours after tumor cell injection was synergistic with P-selectin deficiency in reducing metastasis, there was no further effect in L-selectin-deficient animals. Thus, heparin apparently works at these time points primarily by blocking L-selectin. Endogenous L-selectin ligands were concomitantly induced adjacent to established intravascular tumor cell emboli in a similar time window when leukocytes were also present. Metastasis was attenuated in mice missing these induced endogenous L-selectin ligands due to fucosyltransferase-7 deficiency. Thus, L-selectin facilitation of metastasis progression involves leukocyte-endothelial interactions at sites of intravascular arrest supported by local induction of L-selectin ligands via fucosyltransferase-7. These data provide the first explanation for how leukocyte L-selectin facilitates tumor metastasis.

17 Comparing the Human and Chimpanzee Genomes: Searching for Needles in a Haystack

Abstract: Humans ( Homo sapiens ) and chimpanzees ( Pan troglodytes ) last shared a common ancestor ~5–7 million years ago (Mya) (Chen and Li 2001; Brunet et al. 2002). What makes humans different from their closest evolutionary relatives, and how, why, and when did these changes occur? These are fascinating questions, and a major challenge is to explain how genomic differences contributed to this process (Goodman 1999; Gagneux and Varki 2001; Klein and Takahata 2002; Carroll 2003; Olson and Varki 2003; Enard and Paabo 2004; Gagneux 2004; Ruvolo 2004; Goodman et al. 2005; Li and Saunders 2005; McConkey and Varki 2005). Most genome projects focus on elucidating the sequence and structure of a species’ genome and then identifying conserved functionally important genes and genomic elements. The finished human genome (International Human Genome Sequencing Consortium 2004) provides such a catalog of genomic features that ultimately interact with the environment to determine our biology, physiology, and disease susceptibility. Completion of the draft chimpanzee genome sequence (The Chimpanzee Sequencing and Analysis Consortium 2005) provides a genome-wide comparative catalog that can be used to identify genes or genomic regions underlying the many features that distinguish humans and chimpanzees. As humans, we have an inherent interest in understanding and improving the human condition. We also believe that we have many characteristics that are uniquely human. Table 1 lists some of the definite and possible phenotypic traits that appear to differentiate us from chimpanzees and other “great apes.”1 For the most part, we do not know which genetic features...

Fixation of the human-specific CMP-N-acetylneuraminic acid hydroxylase pseudogene and implications of haplotype diversity for human evolution.

Abstract: The human CMP-N-acetylneuraminic acid hydroxylase gene (CMAH) suffered deletion of an exon that encodes an active center for the enzyme ∼3.2 million years ago (MYA). We analyzed a 7.3-kb intronic region of 132 CMAH genes to explore the fixation process of this pseudogene and the demographic implication of its haplotype diversity. Fifty-six variable sites were sorted into 18 different haplotypes with significant linkage disequilibrium. Despite the rather low nucleotide diversity, the most recent common ancestor at CMAH dates to 2.9 MYA. This deep genealogy follows shortly after the original exon deletion, indicating that the deletion has fixed in the population, although whether this fixation was facilitated by natural selection remains to be resolved. Remarkable features are exceptionally long persistence of two lineages and the confinement of one lineage in Africa, implying that some African local populations were in relative isolation while others were directly involved in multiple African exoduses of the genus Homo. Importantly, haplotypes found in Eurasia suggest interbreeding between then-contemporaneous human species. Although population structure within Africa complicates the interpretation of phylogeographic information of haplotypes, the data support a single origin of modern humans, but not with complete replacement of archaic inhabitants by modern humans.

Multiple Hepatic Receptors Cooperate to Eliminate Secretory Mucins Aberrantly Entering the Bloodstream: Are Circulating Cancer Mucins the “Tip of the Iceberg”?

Abstract: Hollow organs lined by columnar epithelial cells normally secrete mucins and their proteolytic fragments vectorially into the lumen. These heterogeneously O-glycosylated molecules are known to aberrantly enter the bloodstream in the setting of epithelial carcinomas and possibly during injury or inflammation. We have recently shown that carcinoma mucin fragments can trigger the rapid formation of platelet-rich microthrombi in vivo . Thus, mechanisms to clear such aberrantly secreted mucins must exist. Indeed, we found that i.v. injected carcinoma mucin fragments had an ∼1 minute half-life in mice, which was primarily due to rapid clearance by hepatic reticuloendothelial cells. Inhibition of known glycan-recognizing hepatic clearance receptors showed involvement of multiple partially overlapping clearance systems. Studies of genetically deficient mice and incomplete competition between different mucins confirmed this result. Thus, multiple hepatic clearance receptors cooperate to eliminate secretory mucins entering the circulation, limiting potential pathology. This may also explain why mucin-type clustered O-glycosylation is rare on plasma proteins. Notably, small subsets of injected carcinoma mucins remained unrecognized by clearance systems, had a much longer half-life, and carried highly sialylated O-glycans. Similar circulating mucins were found in tumor-bearing mice despite lack of saturation of hepatic clearance mechanisms. Thus, circulating cancer mucins currently used as clinical diagnostic markers likely represent only the clearance-resistant “tip of the iceberg.” Such aberrantly circulating mucins could play pathologic roles not only in cancer but also during injury or inflammation of hollow organs and in liver disease. (Cancer Res 2006; 66(4): 2433-41)

REVIEW Siglecs—the major subfamily of I-type lectins

Abstract: Animal glycan-recognizing proteins can be broadly classified into two groups-lectins (which typically contain an evolutionarily conserved carbohydrate-recognition domain [CRD]) and sulfated glycosaminoglycan (SGAG)-binding proteins (which appear to have evolved by convergent evolution). Proteins other than antibodies and T-cell receptors that mediate glycan recognition via immunoglobulin (Ig)-like domains are called "I-type lectins." The major homologous subfamily of I-type lectins with sialic acid (Sia)-binding properties and characteristic amino-terminal structural features are called the "Siglecs" (Sia-recognizing Ig-superfamily lectins). The Siglecs can be divided into two groups: an evolutionarily conserved subgroup (Siglecs-1, -2, and -4) and a CD33/Siglec-3-related subgroup (Siglecs-3 and -5-13 in primates), which appear to be rapidly evolving. This article provides an overview of historical and current information about the Siglecs.

Heparin Compositions and Selectin Inhibition

Abstract: The disclosure provides in vitro and in vivo methods for identifying Heparins and Heparinoids that modulate the activity of selectins. The disclosure also provides Heparins and Heparinoids that modulate the activity of selectins. The identification and isolation of these heparin formulations has the potential to mediate a wide variety of pathologies mediated by P- and/or L-selectin, including hematogenous metastasis, diseases associated with inflammation (e.g., asthma, arthritis, allergic dermatitis), ischemia-reperfusion injury, or other pathologies such as sickle cell anemia. Selectin inhibition can be achieved at plasma concentrations lower than those that cause excessive anticoagulation or unwanted bleeding in a human subject.

Elimination of n-glycolylneuraminic acid from mammalian products for human use

Abstract: This application is in the field of sialic acid chemistry, metabolism, antigenicity, and the production of transgenic non-human mammals with altered sialic acid production. More particularly, this application relates to N-glycolylneuraminic acid (Neu5Gc) being an immunogen in humans, and the production of Neu5Gc-free mammalian products for laboratory and human use.

Complement targeting of nonhuman sialic acid does not mediate cell death of human embryonic stem cells

Abstract: Complement targeting of nonhuman sialic acid does not mediate cell death of human embryonic stem cells

Physician-scientists are needed now more than ever.

Abstract: SIR — Your Special Report “The costs of global warming” (Nature 439, 374–375; 2006) gives an unbalanced picture of the emissions scenarios developed by the Intergovernmental Panel on Climate Change (IPCC). In contrast to the claim that these scenarios are outdated, a recent peer-reviewed assessment has concluded that, with a few notable exceptions, they compare reasonably well to recent data and projections for gross domestic product, population and emissions (D.v.V. and B.O’N. Clim. Change, in the press. doi: 10.1007/s10584-005-9031-0; see www. iiasa.ac.at/Research/PCC/pubs/vanVuuren& ONeill2006_CC_uncorproof.pdf). Although we believe that progress on scenario development can and will be made, the elements of ‘up-to-date’ economic theory identified as overlooked — “how future societies will operate, how fast the population will grow, and how technological progress will change things” — are either too vague to be meaningful, or are issues the community has been dealing with for years. The Energy Modeling Forum has a 30-year history of model comparisons, exploring the implications for climate policy of a range of rates of economic growth and technological change (D. W. Gaskins and J. P. Weyant Am. Econ. Rev. 83, 318–323; 1993, and J. P. Weyant Energy Econ. 26, 501–515; 2004). It is not correct to imply that the scenarios only use market exchange rates, or that they all assume that “the economies of poor countries will quickly catch up with those of rich nations”. Some scenarios are also reported in terms of purchasing-power parity exchange rates in the original 2000 IPCC Special Report. The debate on the emissions impacts of alternative exchange rates in economic modelling is not conclusive, but such impacts are likely to be small compared with the influence of technology, lifestyle and climate policies. And in no scenario do developing countries become as affluent as industrialized ones. The assumed degree of catching up in the scenarios covers a wide range of possibilities. Focusing on a small number of most-likely futures ignores lessons from history: if the world always worked according to best-guess projections, we would now be living with nuclear power too cheap to meter and no ozone hole. Arnulf Grubler*†, Brian O’Neill*‡, Detlef van Vuuren§ *International Institute for Applied Systems Analysis, A-2361 Laxenburg, Austria †School of Forestry & Environmental Studies, Yale University, New Haven, Connecticut 06511, USA ‡Watson Institute for International Studies, Brown University, Providence, Rhode Island 02912, USA §Netherlands Environmental Assessment Agency, PO Box 303, 3720 BA Bilthoven, The Netherlands

Culturing human cells and tissues in an N-glycolylneuraminic acid-free environment

Abstract: This application is in the field of sialic acid chemistry, metabolism, antigenicity, and the production of transgenic non-human mammals with altered sialic acid production. More particularly, this application relates to N-glycolylneuraminic acid (Neu5Gc) being an immunogen in humans, and the production of Neu5Gc-free mammalian products for laboratory and human use.

Transgenic mouse with a homozygous mutation in the CMAH gene

Abstract: This application is in the field of sialic acid chemistry, metabolism, antigenicity, and the production of transgenic non-human mammals with altered sialic acid production. More particularly, this application relates to N-glycolylneuraminic acid (Neu5Gc) being an immunogen in humans, and the production of Neu5Gc-free mammalian products for laboratory and human use.

Compositions d'heparine inhibitrices de la selectine

Abstract: L'invention porte sur des methodes in vitro et in vivo d'identification d'heparines et d'heparinoides modulant l'activite des selectines et sur ces d'heparines et d'heparinoides. L'identification et l'isolement de ces preparations d'heparine permet de traiter une grande variete de pathologies mediees par la P-selectine et/ou la L-selectine dont les metastases hematogenes, les maladies associees a l'inflammation(par exemple l'asthme, l'arthrite, les dermatites allergiques), les lesions par reperfusion d'ischemies ou d'autres pathologies telle que l'anemie falciforme. L'inhibition de la selectine peut de faire pour des concentrations plasmatiques inferieures a celles qui entrainent une anticoagulation excessive ou des saignements indesires chez l'homme.