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

Sent on Tuesday, 2014 June 17
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

Items 1 - 4 of 4

1.	Nature. 2014 May 1;509(7498):S14-5. doi: 10.1038/509S14a. Diagnostics: Detection drives defence. Kanthor R.
	PMID: 24784424 [PubMed - indexed for MEDLINE]
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2.	Nature. 2014 May 1;509(7498):105-9. doi: 10.1038/nature13148. Epub 2014 Mar 30. Quantitative proteomics identifies NCOA4 as the cargo receptor mediating ferritinophagy. Mancias JD1, Wang X2, Gygi SP3, Harper JW3, Kimmelman AC2. Author information: 11] Division of Genomic Stability and DNA Repair, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA [3] Harvard Radiation Oncology Program, Boston, Massachusetts 02115, USA [4] Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA. 2Division of Genomic Stability and DNA Repair, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA. 3Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA. Abstract Autophagy, the process by which proteins and organelles are sequestered in double-membrane structures called autophagosomes and delivered to lysosomes for degradation, is critical in diseases such as cancer and neurodegeneration. Much of our understanding of this process has emerged from analysis of bulk cytoplasmic autophagy, but our understanding of how specific cargo, including organelles, proteins or intracellular pathogens, are targeted for selective autophagy is limited. Here we use quantitative proteomics to identify a cohort of novel and known autophagosome-enriched proteins in human cells, including cargo receptors. Like known cargo receptors, nuclear receptor coactivator 4 (NCOA4) was highly enriched in autophagosomes, and associated with ATG8 proteins that recruit cargo-receptor complexes into autophagosomes. Unbiased identification of NCOA4-associated proteins revealed ferritin heavy and light chains, components of an iron-filled cage structure that protects cells from reactive iron species but is degraded via autophagy to release iron through an unknown mechanism. We found that delivery of ferritin to lysosomes required NCOA4, and an inability of NCOA4-deficient cells to degrade ferritin led to decreased bioavailable intracellular iron. This work identifies NCOA4 as a selective cargo receptor for autophagic turnover of ferritin (ferritinophagy), which is critical for iron homeostasis, and provides a resource for further dissection of autophagosomal cargo-receptor connectivity.
	PMID: 24695223 [PubMed - indexed for MEDLINE]
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3.	Nat Genet. 2014 May;46(5):492-7. doi: 10.1038/ng.2939. Epub 2014 Mar 30. Low copy number of the salivary amylase gene predisposes to obesity. Falchi M1, El-Sayed Moustafa JS2, Takousis P3, Pesce F4, Bonnefond A5, Andersson-Assarsson JC6, Sudmant PH7, Dorajoo R8, Al-Shafai MN9, Bottolo L10, Ozdemir E3, So HC11, Davies RW12, Patrice A13, Dent R14, Mangino M15, Hysi PG15, Dechaume A16, Huyvaert M16, Skinner J17, Pigeyre M18, Caiazzo R18, Raverdy V13, Vaillant E16, Field S19, Balkau B20, Marre M21, Visvikis-Siest S22, Weill J23, Poulain-Godefroy O16, Jacobson P24, Sjostrom L24, Hammond CJ15, Deloukas P25, Sham PC11, McPherson R26, Lee J27, Tai ES28, Sladek R29, Carlsson LM24, Walley A30, Eichler EE31, Pattou F18, Spector TD32, Froguel P33. Author information: 11] Department of Genomics of Common Disease, Imperial College London, London, UK. [2] [3] [4]. 21] Department of Genomics of Common Disease, Imperial College London, London, UK. [2]. 3Department of Genomics of Common Disease, Imperial College London, London, UK. 41] Department of Genomics of Common Disease, Imperial College London, London, UK. [2] Renal, Dialysis and Transplant Unit, Department of Emergency and Organ Transplantation (D.E.T.O.), University of Bari "Aldo Moro", Bari, Italy. 51] CNRS UMR 8199, Lille Pasteur Institute, Lille, France. [2] Lille 2 University, Lille, France. [3] Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Doha, Qatar. [4] European Genomic Institute for Diabetes (EGID), Lille, France. 61] Department of Genomics of Common Disease, Imperial College London, London, UK. [2] Department of Molecular and Clinical Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden. [3] Center for Cardiovascular and Metabolic Research, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden. 7Department of Genome Sciences, University of Washington, Seattle, Washington, USA. 81] Department of Genomics of Common Disease, Imperial College London, London, UK. [2] Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore. 91] Department of Genomics of Common Disease, Imperial College London, London, UK. [2] Research Division, Qatar Foundation, Doha, Qatar. 10Department of Mathematics, Imperial College London, London, UK. 11Department of Psychiatry, University of Hong Kong, Hong Kong, China. 12Cardiovascular Research Methods Centre, University of Ottawa Heart Institute, Ottawa, Ontario, Canada. 131] European Genomic Institute for Diabetes (EGID), Lille, France. [2] INSERM UMR 859, Lille, France. [3] Centre Hospitalier Régional Universitaire (CHRU) Lille, Lille, France. 14Bariatric Program, Ottawa Hospital, Ottawa, Ontario, Canada. 15Department of Twin Research & Genetic Epidemiology, King's College London, St. Thomas' Hospital Campus, London, UK. 161] CNRS UMR 8199, Lille Pasteur Institute, Lille, France. [2] Lille 2 University, Lille, France. [3] European Genomic Institute for Diabetes (EGID), Lille, France. 17Norwich Medical School, University of East Anglia, Norwich, UK. 181] Lille 2 University, Lille, France. [2] European Genomic Institute for Diabetes (EGID), Lille, France. [3] INSERM UMR 859, Lille, France. [4] Centre Hospitalier Régional Universitaire (CHRU) Lille, Lille, France. 19Wellcome Trust Sanger Institute, Hinxton, UK. 201] Centre de Recherche en Epidémiologie et Santé des Populations, INSERM U1018, Epidemiology of Diabetes, Obesity and Chronic Kidney Disease over the Life Course, Villejuif, France. [2] Université Paris-Sud 11, UMRS 1018, Villejuif, France. 211] Department of Endocrinology, Diabetology and Nutrition, Bichat-Claude Bernard University Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France. [2] INSERM U695, Paris 7 University, Paris, France. 22INSERM UMR 1122 Interactions Géne-Environnement en Physiopathologie Cardio-Vasculaire, Université de Lorraine, Nancy, France. 23Paediatric Endocrine Unit, Lille Teaching Hospital, Lille, France. 241] Department of Molecular and Clinical Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden. [2] Center for Cardiovascular and Metabolic Research, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden. 251] Wellcome Trust Sanger Institute, Hinxton, UK. [2] William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK. [3] Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia. 261] Atherogenomics Laboratory, University of Ottawa Heart Institute, Ottawa, Ontario, Canada. [2] Division of Cardiology, University of Ottawa Heart Institute, Ottawa, Ontario, Canada. 27Saw Swee Hock School of Public Health, National University of Singapore, National University Hospital System, Singapore. 281] Saw Swee Hock School of Public Health, National University of Singapore, National University Hospital System, Singapore. [2] Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, National University Hospital System, Singapore. [3] Duke-National University of Singapore Graduate Medical School, Singapore. 291] Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada. [2] Department of Medicine, Faculty of Medicine, McGill University, Montreal, Quebec, Canada. [3] McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada. 301] Department of Genomics of Common Disease, Imperial College London, London, UK. [2] Section of Genomic Medicine, National Heart and Lung Institute, Imperial College London, London, UK. 311] Department of Genome Sciences, University of Washington, Seattle, Washington, USA. [2] Howard Hughes Medical Institute, Seattle, Washington, USA. 321] Department of Twin Research & Genetic Epidemiology, King's College London, St. Thomas' Hospital Campus, London, UK. [2]. 331] Department of Genomics of Common Disease, Imperial College London, London, UK. [2] CNRS UMR 8199, Lille Pasteur Institute, Lille, France. [3] Lille 2 University, Lille, France. [4] Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Doha, Qatar. [5] European Genomic Institute for Diabetes (EGID), Lille, France. [6] [7]. Abstract Common multi-allelic copy number variants (CNVs) appear enriched for phenotypic associations compared to their biallelic counterparts. Here we investigated the influence of gene dosage effects on adiposity through a CNV association study of gene expression levels in adipose tissue. We identified significant association of a multi-allelic CNV encompassing the salivary amylase gene (AMY1) with body mass index (BMI) and obesity, and we replicated this finding in 6,200 subjects. Increased AMY1 copy number was positively associated with both amylase gene expression (P = 2.31 × 10(-14)) and serum enzyme levels (P < 2.20 × 10(-16)), whereas reduced AMY1 copy number was associated with increased BMI (change in BMI per estimated copy = -0.15 (0.02) kg/m(2); P = 6.93 × 10(-10)) and obesity risk (odds ratio (OR) per estimated copy = 1.19, 95% confidence interval (CI) = 1.13-1.26; P = 1.46 × 10(-10)). The OR value of 1.19 per copy of AMY1 translates into about an eightfold difference in risk of obesity between subjects in the top (copy number > 9) and bottom (copy number < 4) 10% of the copy number distribution. Our study provides a first genetic link between carbohydrate metabolism and BMI and demonstrates the power of integrated genomic approaches beyond genome-wide association studies.
	PMID: 24686848 [PubMed - indexed for MEDLINE]
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4.	Nature. 2014 May 1;509(7498):91-5. doi: 10.1038/nature13176. Epub 2014 Mar 16. Identification of genomic alterations in oesophageal squamous cell cancer. Song Y1, Li L2, Ou Y3, Gao Z2, Li E4, Li X2, Zhang W5, Wang J6, Xu L7, Zhou Y6, Ma X5, Liu L5, Zhao Z5, Huang X6, Fan J5, Dong L5, Chen G6, Ma L5, Yang J6, Chen L6, He M6, Li M6, Zhuang X6, Huang K6, Qiu K6, Yin G6, Guo G6, Feng Q6, Chen P6, Wu Z8, Wu J9, Ma L5, Zhao J6, Luo L6, Fu M5, Xu B10, Chen B7, Li Y6, Tong T5, Wang M5, Liu Z5, Lin D5, Zhang X6, Yang H6, Wang J6, Zhan Q5. Author information: 11] State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China [2]. 21] BGI-Shenzhen, Shenzhen 518083, Guangdong 518083, China [2]. 31] State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China [2] Department of Neurosurgery, Chinese PLA General Hospital, Beijing 100853, China [3]. 41] Department of Biochemistry and Molecular Biology, The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, China [2]. 5State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China. 6BGI-Shenzhen, Shenzhen 518083, Guangdong 518083, China. 7Institute of Oncologic Pathology, Shantou University Medical College, Shantou 515041, Guangdong, China. 8Department of Tumor Surgery, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University, Shantou 515041, Guangdong, China. 9Department of Biochemistry and Molecular Biology, The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, China. 10Department of Neurosurgery, Chinese PLA General Hospital, Beijing 100853, China. Abstract Oesophageal cancer is one of the most aggressive cancers and is the sixth leading cause of cancer death worldwide. Approximately 70% of global oesophageal cancer cases occur in China, with oesophageal squamous cell carcinoma (ESCC) being the histopathological form in the vast majority of cases (>90%). Currently, there are limited clinical approaches for the early diagnosis and treatment of ESCC, resulting in a 10% five-year survival rate for patients. However, the full repertoire of genomic events leading to the pathogenesis of ESCC remains unclear. Here we describe a comprehensive genomic analysis of 158 ESCC cases, as part of the International Cancer Genome Consortium research project. We conducted whole-genome sequencing in 17 ESCC cases and whole-exome sequencing in 71 cases, of which 53 cases, plus an additional 70 ESCC cases not used in the whole-genome and whole-exome sequencing, were subjected to array comparative genomic hybridization analysis. We identified eight significantly mutated genes, of which six are well known tumour-associated genes (TP53, RB1, CDKN2A, PIK3CA, NOTCH1, NFE2L2), and two have not previously been described in ESCC (ADAM29 and FAM135B). Notably, FAM135B is identified as a novel cancer-implicated gene as assayed for its ability to promote malignancy of ESCC cells. Additionally, MIR548K, a microRNA encoded in the amplified 11q13.3-13.4 region, is characterized as a novel oncogene, and functional assays demonstrate that MIR548K enhances malignant phenotypes of ESCC cells. Moreover, we have found that several important histone regulator genes (MLL2 (also called KMT2D), ASH1L, MLL3 (KMT2C), SETD1B, CREBBP and EP300) are frequently altered in ESCC. Pathway assessment reveals that somatic aberrations are mainly involved in the Wnt, cell cycle and Notch pathways. Genomic analyses suggest that ESCC and head and neck squamous cell carcinoma share some common pathogenic mechanisms, and ESCC development is associated with alcohol drinking. This study has explored novel biological markers and tumorigenic pathways that would greatly improve therapeutic strategies for ESCC.
	PMID: 24670651 [PubMed - indexed for MEDLINE]
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