Friday, 29 October 2010

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PubMed Results
Items 1 - 3 of 3

1. Lancet. 2010 Oct 16;376(9749):1320-8.

Effect of CYP2C19 and ABCB1 single nucleotide polymorphisms on outcomes of treatment with ticagrelor versus clopidogrel for acute coronary syndromes: a genetic substudy of the PLATO trial.

Wallentin L, James S, Storey RF, Armstrong M, Barratt BJ, Horrow J, Husted S, Katus H, Steg PG, Shah SH, Becker RC; PLATO investigators.

Uppsala Clinical Research Centre, Uppsala University, Uppsala, Sweden. lars.wallentin@ucr.uu.se

Comment in:

Abstract

BACKGROUND: In the PLATO trial of ticagrelor versus clopidogrel for treatment of acute coronary syndromes, ticagrelor reduced the composite outcome of cardiovascular death, myocardial infarction, and stroke, but increased events of major bleeding related to non-coronary artery bypass graft (CABG). CYP2C19 and ABCB1 genotypes are known to influence the effects of clopidogrel. In this substudy, we investigated the effects of these genotypes on outcomes between and within treatment groups.

METHODS: DNA samples obtained from patients in the PLATO trial were genotyped for CYP2C19 loss-of-function alleles (*2, *3, *4, *5, *6, *7, and *8), the CYP2C19 gain-of-function allele *17, and the ABCB1 single nucleotide polymorphism 3435C→T. For the CYP2C19 genotype, patients were stratified by the presence or absence of any loss-of-function allele, and for the ABCB1 genotype, patients were stratified by predicted gene expression (high, intermediate, or low). The primary efficacy endpoint was the composite of cardiovascular death, myocardial infarction, or stroke after up to 12 months' treatment with ticagrelor or clopidogrel.

FINDINGS: 10 285 patients provided samples for genetic analysis. The primary outcome occurred less often with ticagrelor versus clopidogrel, irrespective of CYP2C19 genotype: 8·6% versus 11·2% (hazard ratio 0·77, 95% CI 0·60-0·99, p=0·0380) in patients with any loss-of-function allele; and 8·8% versus 10·0% (0·86, 0·74-1·01, p=0·0608) in those without any loss-of-function allele (interaction p=0·46). For the ABCB1 genotype, event rates for the primary outcome were also consistently lower in the ticagrelor than in the clopidogrel group for all genotype groups (interaction p=0·39; 8·8%vs 11·9%; 0·71, 0·55-0·92 for the high-expression genotype). In the clopidogrel group, the event rate at 30 days was higher in patients with than in those without any loss-of-function CYP2C19 alleles (5·7%vs 3·8%, p=0·028), leading to earlier separation of event rates between treatment groups in patients with loss-of-function alleles. Patients on clopidogrel who had any gain-of-function CYP2C19 allele had a higher frequency of major bleeding (11·9%) than did those without any gain-of-function or loss-of-function alleles (9·5%; p=0·022), but interaction between treatment and genotype groups was not significant for any type of major bleeding.

INTERPRETATION: Ticagrelor is a more efficacious treatment for acute coronary syndromes than is clopidogrel, irrespective of CYP2C19 and ABCB1 polymorphisms. Use of ticagrelor instead of clopidogrel eliminates the need for presently recommended genetic testing before dual antiplatelet treatment.

FUNDING: AstraZeneca.

Copyright © 2010 Elsevier Ltd. All rights reserved.
PMID: 20801498 [PubMed - indexed for MEDLINE]
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2. Lancet. 2010 Oct 16;376(9749):1278-81.

Response to antiplatelet treatment: from genes to outcome.

Giusti B, Abbate R.

Department of Medical and Surgical Critical Care, University of Florence-Atherothrombotic Diseases Centre, Careggi Hospital, 50134 Florence, Italy. betti.giusti@unifi .it

Comment on:

PMID: 20801497 [PubMed - indexed for MEDLINE]
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3. Lancet. 2010 Oct 16;376(9749):1312-9.

Genetic variants in ABCB1 and CYP2C19 and cardiovascular outcomes after treatment with clopidogrel and p rasugrel in the TRITON-TIMI 38 trial: a pharmacogenetic analysis.

Mega JL, Close SL, Wiviott SD, Shen L, Walker JR, Simon T, Antman EM, Braunwald E, Sabatine MS.

TIMI Study Group, Cardiovascular Division, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA. jmega@partners.org

Comment in:

Abstract

BACKGROUND: Clopidogrel and prasugrel are subject to efflux via P-glycoprotein (encoded by ABCB1, also known as MDR1). ABCB1 polymorphisms, particularly 3435C→T, may affect drug transport and efficacy. We aimed to assess the effect of this polymorphism by itself and alongside variants in CYP2C19 on cardiovascular outcomes in patients treated with clopidogrel or prasugrel in TRITON-TIMI 38. We also assessed the effect of genotype on the pharmacodynamic and pharmacokinetic properties of these drugs in healthy individuals.

METHODS: We genotyped ABCB1 in 2932 patients with acute coronary syndromes undergoing percutaneous intervention who were treated with clopidogrel (n=1471) or prasugrel (n=1461) in the TRITON-TIMI 38 trial. We evaluated the association between ABCB1 3435C→T and rates of the primary efficacy endpoint (cardiovascular death, myocardial infarction, or stroke) until 15 months. We then assessed the combined effect of ABCB1 3435C→T genotype and reduced-function alleles of CYP2C19. 321 healthy individuals were also genotyped, and we tested the association of genetic variants with reduction in maximum platelet aggregation and plasma concentrations of active drug metabolites.

FINDINGS: In patients treated with clopidogrel, ABCB1 3435C→T genotype was significantly associated with the risk of cardiovascular death, myocardial infarction, or stroke (p=0·0064). TT homozygotes had a 72% increased risk of the primary endpoint compared with CT/CC individuals (Kaplan-Meier event rates 12·9% [52 of 414] vs 7·8% [80 of 1057 participants]; HR 1·72, 95% CI 1·22-2·44, p=0·002). ABCB1 3435C→T and CYP2C19 genotypes were significant, independent predictors of the primary endpoint, and 681 (47%) of the 1454 genotyped patients taking clopidogrel who were either CYP2C19 reduced-function allele carriers, ABCB1 3435 TT homozygotes, or both were at increased risk of the primary endpoint (HR 1·97, 95% CI 1·38-2·82, p=0·0002). In healthy participants, 3435 TT homozygotes had an absolute reduction in maximum platelet aggregation with clopidogrel that was 7·3 percentage points less than for CT/CC individuals (p=0·0127). ABCB1 genotypes were not significantly associated with clinical or pharmacological outcomes in patients with an acute coronary syndrome or healthy individuals treated with prasugrel, respectively.

INTERPRETATION: Individuals with the ABCB1 3435 TT genotype have reduced platelet inhibition and are at increased risk of recurrent ischaemic events during clopidogrel treatment. In patients with acute coronary syndromes who have undergone percutaneous intervention, when both ABCB1 and CYP2C19 are taken into account, nearly half of the population carries a genotype associated with increased risk of major adverse cardiovascular events while on standard doses of clopidogrel.

FUNDING: Daiichi Sankyo Company Ltd and Eli Lilly and Company.

Copyright © 2010 Elsevier Ltd. All rights reserved.
PMID: 20801494 [PubMed - indexed for MEDLINE]
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Thursday, 28 October 2010

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PubMed Results
Items 1 - 3 of 3

1. Nat Med. 2010 Sep;16(9):953-5.

Personalized investigation.

Dolgin E.
PMID: 20823867 [PubMed - indexed for MEDLINE]
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2. Nat Med. 2010 Sep;16(9):943.

Selling point: David Goodsell.

Söderqvist T.

Medical Museion, University of Copenhagen.

PMID: 20823862 [PubMed - indexed for MEDLINE]
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3. Nat Med. 2010 Sep;16(9):1042-7. Epub 2010 Aug 29.

Clinical microfluidics for neutrophil genomics and proteomics.

Kotz KT, Xiao W, Miller-Graziano C, Qian WJ, Russom A, Warner EA, Moldawer LL, De A, Bankey PE, Petritis BO, Camp DG 2nd, Rosenbach AE, Goverman J, Fagan SP, Brownstein BH, Irimia D, Xu W, Wilhelmy J, Mindrinos MN, Smith RD, Davis RW, Tompkins RG, Toner M; Inflammation and the Host Response to Injury Collaborative Research Program.

Collaborators: Baker HV, Balis UG, Billiar TR, Calvano SE, Cobb JP, Cuschieri J, Finnerty CC, Gamelli RL, Gibran NS, Harbrecth BG, Hayden DL, Hennessy L, Herndon DN, Jeschke MG, Johnson JL, Klein MB, Lowry SF, Maier RV, Mason PH, McDonald-Smith GP, Minei JP, Moore EE, Nathens AB, O'Keefe GE, Rahme LG, Remick DG, Schoenfeld DA, Shapiro MB, Sperry J, Storey JD, Tibshirani R, Warren HS, West MA, Wispelwey B, Wong WH.

Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA. kkotz@partners.org

Abstract

Neutrophils have key roles in modulating the immune response. We present a robust methodology for rapidly isolating neutrophils directly from whole blood with 'on-chip' processing for mRNA and protein isolation for genomics and proteomics. We validate this device with an ex vivo stimulation experiment and by comparison with standard bulk isolation methodologies. Last, we implement this tool as part of a near-patient blood processing system within a multi-center clinical study of the immune response to severe trauma and burn injury. The preliminary results from a small cohort of subjects in our study and healthy controls show a unique time-dependent gene expression pattern clearly demonstrating the ability of this tool to discriminate temporal transcriptional events of neutrophils within a clinical setting.

PMID: 20802500 [PubMed - indexed for MEDLINE]
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Saturday, 23 October 2010

What's new for 'JKB_daily1' in PubMed

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PubMed Results
Items 1 - 3 of 3

1. Nature. 2010 Sep 23;467(7314):401.

Disclose all data in publications.

Baggerly K.
PMID: 20864982 [PubMed - indexed for MEDLINE]
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2. Nature. 2010 Sep 23;467(7314):380.

China pushes for the proteome.

Cyranoski D.
PMID: 20864967 [PubMed - indexed for MEDLINE]
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3. Nature. 2010 Sep 23;467(7314):460-4. Epub 2010 Sep 8.

A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk.

Heinig M, Petretto E, Wallace C, Bottolo L, Rotival M, Lu H, Li Y, Sarwar R, Langley SR, Bauerfeind A, Hummel O, Lee YA, Paskas S, Rintisch C, Saar K, Cooper J, Buchan R, Gray EE, Cyster JG; Cardiogenics Consortium, Erdmann J, Hengstenberg C, Maouche S, Ouwehand WH, Rice CM, Samani NJ, Schunkert H, Goodall AH, Schulz H, Roider HG, Vingron M, Blankenberg S, Münzel T, Zeller T, Szymczak S, Ziegler A, Tiret L, Smyth DJ, Pravenec M, Aitman TJ, Cambien F, Clayton D, Todd JA, Hubner N, Cook SA.

Collaborators: Braund P, Gracey J, Krishnan U, Moore JS, Nelson CP, Pollard H, Attwood T, Crisp-Hihn A, Foad N, Jolley J, Lloyd-Jones H, Muir D, Murray E, O'Leary K, Rankin A, Sambrook J, Godfroy T, Brocheton J, Proust C, Schmitz G, Heimerl S, Lugauer I, Belz S, Gulde S, Linsel-Nitschke P, Sager H, Schroeder L, Lundmark P, Syvannen AC, Neudert J, Scholz M, Deloukas P, Gray E, Gwilliams R, Niblett D.

Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany.

Abstract

Combined analyses of gene networks and DNA sequence variation can provide new insights into the aetiology of common diseases that may not be apparent from genome-wide association studies alone. Recent advances in rat genomics are facilitating systems-genetics approaches. Here we report the use of integrated genome-wide approaches across seven rat tissues to identify gene networks and the loci underlying their regulation. We defined an interferon regulatory factor 7 (IRF7)-driven inflammatory network (IDIN) enriched for viral response genes, which represents a molecular biomarker for macrophages and which was regulated in multiple tissues by a locus on rat chromosome 15q25. We show that Epstein-Barr virus induced gene 2 (Ebi2, also known as Gpr183), which lies at this locus and controls B lymphocyte migration, is expressed in macrophages and regulates the IDIN. The human orthologous locus on chromosome 13q32 controlled the human equivalent of the IDIN, which was conserved in monocytes. IDIN genes were more likely to associate with susceptibility to type 1 diabetes (T1D)-a macrophage-associated autoimmune disease-than randomly selected immune response genes (P = 8.85 × 10(-6)). The human locus controlling the IDIN was associated with the risk of T1D at single nucleotide polymorphism rs9585056 (P = 7.0 × 10(-10); odds ratio, 1.15), which was one of five single nucleotide polymorphisms in this region associated with EBI2 (GPR183) expression. These data implicate IRF7 network genes and their regulatory locus in the pathogenesis of T1D.

PMID: 20827270 [PubMed - indexed for MEDLINE]
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Friday, 22 October 2010

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PubMed Results
Item 1 of 1

1. N Engl J Med. 2010 Oct 14;363(16):1551-8.

Ancestry and disease in the age of genomic medicine.

Rotimi CN, Jorde LB.

Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20851-5635, USA. rotimic@mail.nih.gov

PMID: 20942671 [PubMed - indexed for MEDLINE]
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Thursday, 21 October 2010

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PubMed Results
Items 1 - 5 of 5

1. Science. 2010 Oct 1;330(6000):86-8.

Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics.

Arensburger P, Megy K, Waterhouse RM, Abrudan J, Amedeo P, Antelo B, Bartholomay L, Bidwell S, Caler E, Camara F, Campbell CL, Campbell KS, Casola C, Castro MT, Chandramouliswaran I, Chapman SB, Christley S, Costas J, Eisenstadt E, Feschotte C, Fraser-Liggett C, Guigo R, Haas B, Hammond M, Hansson BS, Hemingway J, Hill SR, Howarth C, Ignell R, Kennedy RC, Kodira CD, Lobo NF, Mao C, Mayhew G, Michel K, Mori A, Liu N, Naveira H, Nene V, Nguyen N, Pearson MD, Pritham EJ, Puiu D, Qi Y, Ranson H, Ribeiro JM, Roberston HM, Severson DW, Shumway M, Stanke M, Strausberg RL, Sun C, Sutton G, Tu ZJ, Tubio JM, Unger MF, Vanlandingham DL, Vilella AJ, White O, White JR, Wondji CS, Wortman J, Zdobnov EM, Birren B, Christensen BM, Collins FH, Cornel A, Dimopoulos G, Hannick LI, Higgs S, Lanzaro GC, Lawson D, Lee NH, Muskavitch MA, Raikhel AS, Atkinson PW.

Center for Disease Vector Research, University of California Riverside, Riverside, CA 92521, USA. arensburger@gmail.com

Abstract

Culex quinquefasciatus (the southern house mosquito) is an important mosquito vector of viruses such as West Nile virus and St. Louis encephalitis virus, as well as of nematodes that cause lymphatic filariasis. C. quinquefasciatus is one species within the Culex pipiens species complex and can be found throughout tropical and temperate climates of the world. The ability of C. quinquefasciatus to take blood meals from birds, livestock, and humans contributes to its ability to vector pathogens between species. Here, we describe the genomic sequence of C. quinquefasciatus: Its repertoire of 18,883 protein-coding genes is 22% larger than that of Aedes aegypti and 52% larger than that of Anopheles gambiae with multiple gene-family expansions, including olfactory and gustatory receptors, salivary gland genes, and genes associated with xenobiotic detoxification.

PMID: 20929810 [PubMed - indexed for MEDLINE]
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2. Science. 2010 Oct 1;330(6000):78-81.

Human adaptation and plant use in highland New Guinea 49,000 to 44,000 years ago.

Summerhayes GR, Leavesley M, Fairbairn A, Mandui H, Field J, Ford A, Fullagar R.

Department of Anthropology, Gender and Sociology, University of Otago, Post Office Box 56, Dunedin, New Zealand. Glenn.summerhayes@otago.ac.nz

Comment in:

Abstract

After their emergence by 200,000 years before the present in Africa, modern humans colonized the globe, reaching Australia and New Guinea by 40,000 to 50,000 years ago. Understanding how humans lived and adapted to the range of environments in these areas has been difficult because well-preserved settlements are scarce. Data from the New Guinea Highlands (at an elevation of ~2000 meters) demonstrate the exploitation of the endemic nut Pandanus and yams in archaeological sites dated to 49,000 to 36,000 years ago, which are among the oldest human sites in this region. The sites also contain stone tools thought to be used to remove trees, which suggests that the early inhabitants cleared forest patches to promote the growth of useful plants.

PMID: 20929808 [PubMed - indexed for MEDLINE]
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3. Science. 2010 Oct 1;330(6000):41-2.

Archaeology. When humans arrived in the New Guinea Highlands.

Gosden C.

Institute of Archaeology, Oxford University, 36 Beaumont Street, Oxford, OX1 2PG, UK. chris.gosden@arch.ox.ac.uk

Comment on:

PMID: 20929797 [PubMed - indexed for MEDLINE]
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4. Science. 2010 Oct 1;330(6000):28-9.

Archaeology. Archaeologists see big promise in going molecular.

Travis J.
PMID: 20929786 [PubMed - indexed for MEDLINE]
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5. Science. 2010 Oct 1;330(6000):11.

The future of Russian science.

Georgiev G, Sverdlov E. Free Article
PMID: 20929777 [PubMed - indexed for MEDLINE]
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Saturday, 16 October 2010

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PubMed Results
Item 1 of 1

1. N Engl J Med. 2010 Oct 7;363(15):1482-3; author reply 1483-4.

Hospital-acquired infections due to gram-negative bacteria.

de Oliveira JM, Lisboa Lde B.

Comment on:

PMID: 20931723 [PubMed - indexed for MEDLINE]

Wednesday, 13 October 2010

What's new for 'JKB_daily1' in PubMed

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PubMed Results
Items 1 - 2 of 2

1. N Engl J Med. 2010 Sep 30;363(14):1382-3.

Fatal Clostridium sordellii infections after medical abortions.

Meites E, Zane S, Gould C; C. sordellii Investigators.
PMID: 20879895 [PubMed - indexed for MEDLINE]
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2. Nature. 2010 Sep 9;467(7312):146-8.

Neuroscience: In their nu rture.

Buchen L.
PMID: 20829771 [PubMed - indexed for MEDLINE]
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Tuesday, 5 October 2010

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PubMed Results
Items 1 - 6 of 6

1. Science. 2010 Sep 17;329(5998):1530-4.

Bifurcation of Toll-like receptor 9 signaling by adaptor protein 3.

Sasai M, Linehan MM, Iwasaki A.

Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA.

Abstract

Endosomal Toll-like receptors (TLRs) 7 and 9 recognize viral pathogens and induce signals leading to the activation of nuclear factor κB (NF-κB)-dependent proinflammatory cytokines and interferon regulatory factor 7 (IRF7)-dependent type I interferons (IFNs). Recognition of viral nucleic acids by TLR9 requires its cleavage in the endolysosomal compartment. Here, we show that TLR9 signals leading to the activation of type I IFN, but not proinflammatory cytokine genes, require TLR9 trafficking from endosomes to a specialized lysosome-related organelle. Furthermore, we identify adapter protein-3 as the protein complex responsible for the trafficking of TLR9 to this subcellular compartment. Our results reveal an intracellular mechanism for bifurcation of TLR9 signals by selective receptor trafficking within the endosomal system.

PMID: 20847273 [PubMed - indexed for MEDLINE]
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2. Science. 2010 Sep 17;329(5998):1467; author reply 1467-8.

Archaeology augments Tibet's genetic history.

< a href="http://www.ncbi.nlm.nih.gov/pubmed?term=%22Brantingham%20PJ%22%5BAuthor%5D">Brantingham PJ, Rhode D, Madsen DB.

Comment on:

PMID: 20847252 [PubMed - indexed for MEDLINE]
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3. Nature. 2010 Aug 12;466(7308):817-8.

Which way for genetic-test regulation? Assign regulation appropriate to the level of risk.

Javitt G.

Berman Institute of Bioethics, Johns Hopkins University, USA. gjavitt1@jhu.edu

PMID: 20703288 [PubMed - indexed for MEDLINE]
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4. Nature. 2010 Aug 12;466(7308):816-7.

Which way for genetic-test regulation? Leave test interpretation to specialists.

Beaudet AL.

Department of Molecular and Human Genetics at Baylor College of Medicine, Houston, Texas 77030, USA. abeaudet@bcm.edu

Comment in:

PMID: 20703287 [PubMed - indexed for MEDLINE]
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5. Nature. 2010 Aug 12;466(7308):808-10.

Francis Collins: One year at the helm.

Wadman M.
PMID: 20703281 [PubMed - indexed for MEDLINE]
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6. Nature. 2010 Aug 12;466(7308):806.

Mountain mining damages streams.

Gilbert N.
PMID: 20703278 [PubMed - indexed for MEDLINE]
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Sunday, 3 October 2010

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Sender's message: Sepsis or genomics or altitude: JKB_daily1

Sent on Sunday, 2010 Oct 03
Search (sepsis[MeSH Terms] OR septic shock[MeSH Terms] OR altitude[MeSH Terms] OR genomics[MeSH Terms] OR genetics[MeSH Terms] OR retrotransposons[MeSH Terms] OR macrophage[MeSH Terms]) AND ("2009/8/8"[Publication Date] : "3000"[Publication Date]) AND (("Science"[Journal] OR "Nature"[Journal] OR "The New England journal of medicine"[Journal] OR "Lancet"[Journal] OR "Nature genetics"[Journal] OR "Nature medicine"[Journal]) OR (Hume DA[Author] OR Baillie JK[Author] OR Faulkner, Geoffrey J[Author]))
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PubMed Results
Item 1 of 1

1. J Leukoc Biol. 2010 Sep;88(3):475-81. Epub 2010 Jun 2.

CSF-1, IGF-1, and the control of postnatal growth and development.

Gow DJ, Sester DP, Hume DA.

The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian EH25 9PS, UK.

Abstract

Growth hormone controls somatic growth in mammals by regulating the production of IGF-1, which is predominantly made by the liver. The development of cells within the MPS is controlled by the lineage-specific growth factor M-CSF (CSF-1). In this review, we summarize the role of CSF-1-dependent macrophages in somatic growth and organogenesis. We propose that macrophages are the major extrahepatic source of IGF-1 and that a surge of CSF-1 production contributes to the control of postnatal growth and organ maturation. Accordingly, CSF-1 may be considered a part of the GH/IGF-1 axis.

PMID: 20519640 [PubMed - indexed for MEDLINE]
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