Fatty Acid Metabolism Mediated by 12/15-Lipoxygenase is a Novel Regulator of Hematopoietic Stem Cell Function and Myelopoiesis

Fatty acid metabolism governs critical cellular processes in multiple cell types. The goal of my dissertation was to investigate the intersection between fatty acid metabolism and hematopoiesis. Although fatty acid metabolism has been extensively studied in mature hematopoietic subsets during inflammation, in developing hematopoietic cells the role of fatty acid metabolism, in particular by 12/15-Lipoxygenase (12/15-LOX), was unknown. The observation that 12/15-LOX-deficient (Alox15) mice developed a myeloid leukemia instigated my studies since leukemias are often a consequence of dysregulated hematopoiesis. This observation lead to the central hypothesis of this dissertation which is that polyunsaturated fatty acid metabolism mediated by 12/15-LOX participates in hematopoietic development. Using genetic mouse models and in vitro and in vivo cell development assays, I found that 12/15-LOX indeed regulates multiple stages of hematopoiesis including the function of hematopoietic stem cells (HSC) and the differentiation of B cells, T cells, basophils, granulocytes and monocytes. Within hematopoietic development, I concentrated on the mechanisms that underlie the defects in HSC function and monocyte development since these defects likely contribute to the myeloid leukemogenesis in Alox15 mice. Interestingly, I determined that 12/15-LOX promotes HSC self-renewal and quiescence, which is associated with the activation of canonical Wnt signaling. Moreover, my studies demonstrate that 12/15-LOX-mediated redox signaling of SHP-2 and the transcription factor ICSBP/IRF-8 promotes monocyte development while inhibiting granulocyte development. This pathway is also conserved in IL-12p40 expression in macrophages. Therefore, I establish 12/15- LOX as a critical regulator of hematopoiesis and provide insight into novel mechanisms whereby HSC function and monocyte cell fate decisions are regulated. These findings have implications for leukemogenesis and immunity

How do specialist trainee doctors acquire skills to practice patient-centred care? A qualitative exploration

Objectives: The importance of patient centred care (PCC) has been increasingly recognised. However, there is limited work exploring what doctors actually understand by PCC, and how they perceive they acquire PCC skills in the workplace. The objectives of our study were to explore (1) what UK doctors, in specialist training, perceive to be the essential components of PCC, and (2) if/how they acquire these skills; (3) any facilitators/barriers for engaging in PCC; and (4) views on their PCC training. Design: Qualitative study using in-depth individual semi-structured interviews with UK specialist trainees. Interview transcripts were thematically analysed.Setting and Participants: Thirty-one specialist trainee doctors, with at least 4 years postgraduate experience, were interviewed. Participants worked in various medical specialities within the Medical Directorate of an acute hospital in the East Midlands of England (UK). Results: Interview data were transcribed verbatim and categorised into three main themes. The first theme was ‘Understanding PCC’ where the doctors gave varied perspectives on what they understood by PCC. Although many were able to highlight key components of PCC there were also some accounts which demonstrated a lack of understanding. The second theme was ‘Learning PCC skills: A work in progress’. Learning to be patient-centred was perceived to be an on-going process. Within this, trainee doctors reported ‘on-the-job’ learning as the main means of acquiring PCC skills, but they also saw a place for formal training (e.g., educational sessions focussing on PCC, clinical scenarios/role play). ‘Delivering PCC: Beyond the physician’ referred to the many influences the doctors reported in learning and delivering PCC including patients, the organisation and colleagues. Observing consultants taking a patient-centred approach was cited as an important learning tool. Conclusions: Our findings may assist clinical educators in understanding how trainee doctors perceive PCC, and the factors that influence their learning; thereby, helping them shape PCC skills training

The TNF-Family Receptor DR3 is Essential for Diverse T Cell-Mediated Inflammatory Diseases

SummaryDR3 (TRAMP, LARD, WSL-1, TNFRSF25) is a death-domain-containing tumor necrosis factor (TNF)-family receptor primarily expressed on T cells. TL1A, the TNF-family ligand for DR3, can costimulate T cells, but the physiological function of TL1A-DR3 interactions in immune responses is not known. Using DR3-deficient mice, we identified DR3 as the receptor responsible for TL1A-induced T cell costimulation and dendritic cells as the likely source for TL1A during T cell activation. Despite its role in costimulation, DR3 was not required for in vivo T cell priming, for polarization into T helper 1 (Th1), Th2, or Th17 effector cell subtypes, or for effective control of infection with Toxoplasma gondii. Instead, DR3 expression was required on T cells for immunopathology, local T cell accumulation, and cytokine production in Experimental Autoimmune Encephalomyelitis (EAE) and allergic lung inflammation, disease models that depend on distinct effector T cell subsets. DR3 could be an attractive therapeutic target for T cell-mediated autoimmune and allergic diseases

A framework for human microbiome research

A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies

Structure, function and diversity of the healthy human microbiome

Author Posting. © The Authors, 2012. This article is posted here by permission of Nature Publishing Group. The definitive version was published in Nature 486 (2012): 207-214, doi:10.1038/nature11234.Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.This research was supported in part by National Institutes of Health grants U54HG004969 to B.W.B.; U54HG003273 to R.A.G.; U54HG004973 to R.A.G., S.K.H. and J.F.P.; U54HG003067 to E.S.Lander; U54AI084844 to K.E.N.; N01AI30071 to R.L.Strausberg; U54HG004968 to G.M.W.; U01HG004866 to O.R.W.; U54HG003079 to R.K.W.; R01HG005969 to C.H.; R01HG004872 to R.K.; R01HG004885 to M.P.; R01HG005975 to P.D.S.; R01HG004908 to Y.Y.; R01HG004900 to M.K.Cho and P. Sankar; R01HG005171 to D.E.H.; R01HG004853 to A.L.M.; R01HG004856 to R.R.; R01HG004877 to R.R.S. and R.F.; R01HG005172 to P. Spicer.; R01HG004857 to M.P.; R01HG004906 to T.M.S.; R21HG005811 to E.A.V.; M.J.B. was supported by UH2AR057506; G.A.B. was supported by UH2AI083263 and UH3AI083263 (G.A.B., C. N. Cornelissen, L. K. Eaves and J. F. Strauss); S.M.H. was supported by UH3DK083993 (V. B. Young, E. B. Chang, F. Meyer, T. M. S., M. L. Sogin, J. M. Tiedje); K.P.R. was supported by UH2DK083990 (J. V.); J.A.S. and H.H.K. were supported by UH2AR057504 and UH3AR057504 (J.A.S.); DP2OD001500 to K.M.A.; N01HG62088 to the Coriell Institute for Medical Research; U01DE016937 to F.E.D.; S.K.H. was supported by RC1DE0202098 and R01DE021574 (S.K.H. and H. Li); J.I. was supported by R21CA139193 (J.I. and D. S. Michaud); K.P.L. was supported by P30DE020751 (D. J. Smith); Army Research Office grant W911NF-11-1-0473 to C.H.; National Science Foundation grants NSF DBI-1053486 to C.H. and NSF IIS-0812111 to M.P.; The Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231 for P.S. C.; LANL Laboratory-Directed Research and Development grant 20100034DR and the US Defense Threat Reduction Agency grants B104153I and B084531I to P.S.C.; Research Foundation - Flanders (FWO) grant to K.F. and J.Raes; R.K. is an HHMI Early Career Scientist; Gordon&BettyMoore Foundation funding and institutional funding fromthe J. David Gladstone Institutes to K.S.P.; A.M.S. was supported by fellowships provided by the Rackham Graduate School and the NIH Molecular Mechanisms in Microbial Pathogenesis Training Grant T32AI007528; a Crohn’s and Colitis Foundation of Canada Grant in Aid of Research to E.A.V.; 2010 IBM Faculty Award to K.C.W.; analysis of the HMPdata was performed using National Energy Research Scientific Computing resources, the BluBioU Computational Resource at Rice University

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio