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Item Open Access Published version Peer-reviewed A Bayesian Approach to the Overlap Analysis of Epidemiologically Linked Traits.(Wiley, 2015-12) Asimit, Jennifer L; Panoutsopoulou, Kalliope; Wheeler, Eleanor; Berndt, Sonja I; GIANT consortium, the arcOGEN consortium; Cordell, Heather J; Morris, Andrew P; Zeggini, Eleftheria; Barroso, Inês; Asimit, Jennifer [0000-0002-4857-2249]; Wheeler, Eleanor [0000-0002-8616-6444]; Barroso, Ines [0000-0001-5800-4520]Diseases often cooccur in individuals more often than expected by chance, and may be explained by shared underlying genetic etiology. A common approach to genetic overlap analyses is to use summary genome-wide association study data to identify single-nucleotide polymorphisms (SNPs) that are associated with multiple traits at a selected P-value threshold. However, P-values do not account for differences in power, whereas Bayes' factors (BFs) do, and may be approximated using summary statistics. We use simulation studies to compare the power of frequentist and Bayesian approaches with overlap analyses, and to decide on appropriate thresholds for comparison between the two methods. It is empirically illustrated that BFs have the advantage over P-values of a decreasing type I error rate as study size increases for single-disease associations. Consequently, the overlap analysis of traits from different-sized studies encounters issues in fair P-value threshold selection, whereas BFs are adjusted automatically. Extensive simulations show that Bayesian overlap analyses tend to have higher power than those that assess association strength with P-values, particularly in low-power scenarios. Calibration tables between BFs and P-values are provided for a range of sample sizes, as well as an approximation approach for sample sizes that are not in the calibration table. Although P-values are sometimes thought more intuitive, these tables assist in removing the opaqueness of Bayesian thresholds and may also be used in the selection of a BF threshold to meet a certain type I error rate. An application of our methods is used to identify variants associated with both obesity and osteoarthritis.Item Open Access Published version Peer-reviewed A two-stage inter-rater approach for enrichment testing of variants associated with multiple traits.(Springer Science and Business Media LLC, 2017-02) Asimit, Jennifer L; Payne, Felicity; Morris, Andrew P; Cordell, Heather J; Barroso, Inês; Asimit, Jennifer L [0000-0002-4857-2249]Shared genetic aetiology may explain the co-occurrence of diseases in individuals more often than expected by chance. On identifying associated variants shared between two traits, one objective is to determine whether such overlap may be explained by specific genomic characteristics (eg, functional annotation). In clinical studies, inter-rater agreement approaches assess concordance among expert opinions on the presence/absence of a complex disease for each subject. We adapt a two-stage inter-rater agreement model to the genetic association setting to identify features predictive of overlap variants, while accounting for their marginal trait associations. The resulting corrected overlap and marginal enrichment test (COMET) also assesses enrichment at the individual trait level. Multiple categories may be tested simultaneously and the method is computationally efficient, not requiring permutations to assess significance. In an extensive simulation study, COMET identifies features predictive of enrichment with high power and has well-calibrated type I error. In contrast, testing for overlap with a single-trait enrichment test has inflated type I error. COMET is applied to three glycaemic traits using a set of functional annotation categories as predictors, followed by further analyses that focus on tissue-specific regulatory variants. The results support previous findings that regulatory variants in pancreatic islets are enriched for fasting glucose-associated variants, and give insight into differences/similarities between characteristics of variants associated with glycaemic traits. Also, despite regulatory variants in pancreatic islets being enriched for variants that are marginally associated with fasting glucose and fasting insulin, there is no enrichment of shared variants between the traits.Item Open Access Published version Peer-reviewed No metabolic effects of mustard allyl-isothiocyanate compared with placebo in men.(Elsevier BV, 2017-11) Langeveld, Mirjam; Tan, Chong Yew; Soeters, Maarten R; Virtue, Samuel; Watson, Laura Pe; Murgatroyd, Peter R; Ambler, Graeme K; Vidal-Puig, Santiago; Chatterjee, Krishna V; Vidal-Puig, Antonio; Chatterjee, Krishna [0000-0002-2654-8854]; Vidal-Puig, Antonio [0000-0003-4220-9577]Background: Induction of nonshivering thermogenesis can be used to influence energy balance to prevent or even treat obesity. The pungent component of mustard, allyl-isothiocyanate (AITC), activates the extreme cold receptor transient receptor potential channel, subfamily A, member 1 and may thus induce energy expenditure and metabolic changes.Objective: The objective of our study was to evaluate the potential of mustard AITC to induce thermogenesis (primary outcome) and alter body temperature, cold and hunger sensations, plasma metabolic parameters, and energy intake (secondary outcomes).Design: Energy expenditure in mice was measured after subcutaneous injection with vehicle, 1 mg norepinephrine/kg, or 5 mg AITC/kg. In our human crossover study, 11 healthy subjects were studied under temperature-controlled conditions after an overnight fast. After ingestion of 10 g of capsulated mustard or uncapsulated mustard or a capsulated placebo mixture, measurements of energy expenditure, substrate oxidation, core temperature, cold and hunger scores, and plasma parameters were repeated every 30 min during a 150-min period. Subjects were randomly selected for the placebo and capsulated mustard intervention; 9 of 11 subjects received the uncapsulated mustard as the final intervention because this could not be blinded. After the experiments, energy intake was measured with the universal eating monitor in a test meal.Results: In mice, AITC administration induced a 32% increase in energy expenditure compared with vehicle (17.5 ± 4.9 J · min-1 · mouse-1 compared with 12.5 ± 1.2 J · min-1 · mouse-1, P = 0.03). Of the 11 randomly selected participants, 1 was excluded because of intercurrent illness after the first visit and 1 withdrew after the second visit. Energy expenditure did not increase after ingestion of capsulated or uncapsulated mustard compared with placebo. No differences in substrate oxidation, core temperature, cold and hunger scores, or plasma parameters were found, nor was the energy intake at the end of the experiment different between the 3 conditions.Conclusion: The highest tolerable dose of mustard we were able to use did not elicit a relevant thermogenic response in humans. This trial was registered at www.controlled-trials.com as ISRCTN19147515.Item Open Access Published version Peer-reviewed Poor maternal nutrition and accelerated postnatal growth induces an accelerated aging phenotype and oxidative stress in skeletal muscle of male rats(Company of Biologists, 2016-10-01) Tarry-Adkins, Jane L; Fernandez-Twinn, Denise S; Chen, Jian Hua; Hargreaves, Iain P; Neergheen, Viruna; Aiken, Catherine E; Ozanne, Susan E; Twinn, Denise [0000-0003-2610-277X]; Aiken, Catherine [0000-0002-6510-5626]; Ozanne, Susan [0000-0001-8753-5144]'Developmental programming', which occurs as a consequence of suboptimal in utero and early environments, can be associated with metabolic dysfunction in later life, including an increased incidence of cardiovascular disease and type 2 diabetes, and predisposition of older men to sarcopenia. However, the molecular mechanisms underpinning these associations are poorly understood. Many conditions associated with developmental programming are also known to be associated with the aging process. We therefore utilized our well-established rat model of low birth weight and accelerated postnatal catch-up growth (termed 'recuperated') in this study to establish the effects of suboptimal maternal nutrition on age-associated factors in skeletal muscle. We demonstrated accelerated telomere shortening (a robust marker of cellular aging) as evidenced by a reduced frequency of long telomeres (48.5-8.6 kb) and an increased frequency of short telomeres (4.2-1.3 kb) in vastus lateralis muscle from aged recuperated offspring compared to controls. This was associated with increased protein expression of the DNA-damage-repair marker 8-oxoguanine-glycosylase (OGG1) in recuperated offspring. Recuperated animals also demonstrated an oxidative stress phenotype, with decreased citrate synthase activity, increased electron-transport-complex activities of complex I, complex II-III and complex IV (all markers of functional mitochondria), and increased xanthine oxidase (XO), p67phoxand nuclear-factor kappa-light-chain-enhancer of activated B-cells (NF-κB). Recuperated offspring also demonstrated increased antioxidant defense capacity, with increased protein expression of manganese superoxide dismutase (MnSOD), copper-zinc superoxide dismutase (CuZnSOD), catalase and heme oxygenase-1 (HO1), all of which are known targets of NF-κB and can be upregulated as a consequence of oxidative stress. Recuperated offspring also had a pro-inflammatory phenotype, as evidenced by increased tumor necrosis factor-α (TNFα) and interleukin-1β (IL1β) protein levels. Taken together, we demonstrate, for the first time to our knowledge, an accelerated aging phenotype in skeletal muscle in the context of developmental programming. These findings may pave the way for suitable interventions in at-risk populations.Item Open Access Accepted version Peer-reviewed Neuropeptides in obesity and metabolic disease(American Association for Clinical Chemistry, 2018-01-02) van der Klaauw, AA; van der Klaauw, Agatha [0000-0001-6971-8828]Background: The global rise in the prevalence of obesity and associated co-morbidities such as type 2 diabetes, cardiovascular disease, and cancer represents a major public health concern. Content: Studies in rodents using global and targeted gene disruption, and mapping of neurocircuitry using optogenetics and DREADDs (Designer Receptors Exclusively Activated by Designer Drugs) have greatly advanced our understanding of the neural control of body weight. In conjunction with analytical chemistry techniques involving classical immunoassays and mass spectrometry, many neuropeptides that are key to energy homeostasis have been identified. The actions of neuropeptides are diverse, from paracrine modulation of local neurotransmission to hormonal control of distant target organs. Summary: Multiple hormones such as the adipocyte-derived leptin, insulin and gut hormones as well as nutrients signal peripheral energy state to the central nervous system. Neurons in distinct areas of the hypothalamus and brainstem integrate this information and translate this information by both direct inhibitory/ excitatory projections as well as anorexigenic or orexigenic neuropeptides into actions on food intake and energy expenditure. The importance of these neuropeptides in human energy balance is most powerfully illustrated by genetic forms of obesity that involve neuropeptides such as melanocortin-4-receptor (MC4R) deficiency. Drugs that mimic the actions of neuropeptides are being tested for the treatment of obesity. Successful therapeutic strategies in obesity will require in depth knowledge of the neuronal circuits they are working in, the downstream targets, and potential compensatory mechanisms.Item Open Access Published version Peer-reviewed Erratum: Large meta-analysis of genome-wide association studies identifies five loci for lean body mass(Springer Nature, 2017-11-07) Zillikens, M Carola; Demissie, Serkalem; Hsu, Yi-Hsiang; Yerges-Armstrong, Laura M; Chou, Wen-Chi; Stolk, Lisette; Livshits, Gregory; Broer, Linda; Johnson, Toby; Koller, Daniel L; Kutalik, Zoltán; Luan, Jian'an; Malkin, Ida; Ried, Janina S; Smith, Albert V; Thorleifsson, Gudmar; Vandenput, Liesbeth; Hua Zhao, Jing; Zhang, Weihua; Aghdassi, Ali; Åkesson, Kristina; Amin, Najaf; Baier, Leslie J; Barroso, Inês; Bennett, David A; Bertram, Lars; Biffar, Rainer; Bochud, Murielle; Boehnke, Michael; Borecki, Ingrid B; Buchman, Aron S; Byberg, Liisa; Campbell, Harry; Campos Obanda, Natalia; Cauley, Jane A; Cawthon, Peggy M; Cederberg, Henna; Chen, Zhao; Cho, Nam H; Jin Choi, Hyung; Claussnitzer, Melina; Collins, Francis; Cummings, Steven R; De Jager, Philip L; Demuth, Ilja; Dhonukshe-Rutten, Rosalie AM; Diatchenko, Luda; Eiriksdottir, Gudny; Enneman, Anke W; Erdos, Mike; Eriksson, Johan G; Eriksson, Joel; Estrada, Karol; Evans, Daniel S; Feitosa, Mary F; Fu, Mao; Garcia, Melissa; Gieger, Christian; Girke, Thomas; Glazer, Nicole L; Grallert, Harald; Grewal, Jagvir; Han, Bok-Ghee; Hanson, Robert L; Hayward, Caroline; Hofman, Albert; Hoffman, Eric P; Homuth, Georg; Hsueh, Wen-Chi; Hubal, Monica J; Hubbard, Alan; Huffman, Kim M; Husted, Lise B; Illig, Thomas; Ingelsson, Erik; Ittermann, Till; Jansson, John-Olov; Jordan, Joanne M; Jula, Antti; Karlsson, Magnus; Khaw, Kay-Tee; Kilpeläinen, Tuomas O; Klopp, Norman; Kloth, Jacqueline SL; Koistinen, Heikki A; Kraus, William E; Kritchevsky, Stephen; Kuulasmaa, Teemu; Kuusisto, Johanna; Laakso, Markku; Lahti, Jari; Lang, Thomas; Langdahl, Bente L; Launer, Lenore J; Lee, Jong-Young; Lerch, Markus M; Lewis, Joshua R; Lind, Lars; Lindgren, Cecilia; Liu, Yongmei; Liu, Tian; Liu, Youfang; Ljunggren, Östen; Lorentzon, Mattias; Luben, Robert N; Maixner, William; McGuigan, Fiona E; Medina-Gomez, Carolina; Meitinger, Thomas; Melhus, Håkan; Mellström, Dan; Melov, Simon; Michaëlsson, Karl; Mitchell, Braxton D; Morris, Andrew P; Mosekilde, Leif; Newman, Anne; Nielson, Carrie M; O'Connell, Jeffrey R; Oostra, Ben A; Orwoll, Eric S; Palotie, Aarno; Parker, Stephen CJ; Peacock, Munro; Perola, Markus; Peters, Annette; Polasek, Ozren; Prince, Richard L; Räikkönen, Katri; Ralston, Stuart H; Ripatti, Samuli; Robbins, John A; Rotter, Jerome I; Rudan, Igor; Salomaa, Veikko; Satterfield, Suzanne; Schadt, Eric E; Schipf, Sabine; Scott, Laura; Sehmi, Joban; Shen, Jian; Soo Shin, Chan; Sigurdsson, Gunnar; Smith, Shad; Soranzo, Nicole; Stančáková, Alena; Steinhagen-Thiessen, Elisabeth; Streeten, Elizabeth A; Styrkarsdottir, Unnur; Swart, Karin MA; Tan, Sian-Tsung; Tarnopolsky, Mark A; Thompson, Patricia; Thomson, Cynthia A; Thorsteinsdottir, Unnur; Tikkanen, Emmi; Tranah, Gregory J; Tuomilehto, Jaakko; van Schoor, Natasja M; Verma, Arjun; Vollenweider, Peter; Völzke, Henry; Wactawski-Wende, Jean; Walker, Mark; Weedon, Michael N; Welch, Ryan; Wichmann, H-Erich; Widen, Elisabeth; Williams, Frances MK; Wilson, James F; Wright, Nicole C; Xie, Weijia; Yu, Lei; Zhou, Yanhua; Chambers, John C; Döring, Angela; van Duijn, Cornelia M; Econs, Michael J; Gudnason, Vilmundur; Kooner, Jaspal S; Psaty, Bruce M; Spector, Timothy D; Stefansson, Kari; Rivadeneira, Fernando; Uitterlinden, André G; Wareham, Nicholas J; Ossowski, Vicky; Waterworth, Dawn; Loos, Ruth JF; Karasik, David; Harris, Tamara B; Ohlsson, Claes; Kiel, Douglas P; Luan, Jian'an [0000-0003-3137-6337]; Barroso, Ines [0000-0001-5800-4520]; Khaw, Kay-Tee [0000-0002-8802-2903]; Luben, Robert [0000-0002-5088-6343]; Soranzo, Nicole [0000-0003-1095-3852]; Wareham, Nicholas [0000-0003-1422-2993]A correction to this article has been published and is linked from the HTML version of this article.Item Open Access Accepted version Peer-reviewed Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci.(Nature Research, 2015-12) Gaulton, Kyle J; Ferreira, Teresa; Lee, Yeji; Raimondo, Anne; Mägi, Reedik; Reschen, Michael E; Mahajan, Anubha; Locke, Adam; Rayner, N William; Robertson, Neil; Scott, Robert A; Prokopenko, Inga; Scott, Laura J; Green, Todd; Sparso, Thomas; Thuillier, Dorothee; Yengo, Loic; Grallert, Harald; Wahl, Simone; Frånberg, Mattias; Strawbridge, Rona J; Kestler, Hans; Chheda, Himanshu; Eisele, Lewin; Gustafsson, Stefan; Steinthorsdottir, Valgerdur; Thorleifsson, Gudmar; Qi, Lu; Karssen, Lennart C; van Leeuwen, Elisabeth M; Willems, Sara M; Li, Man; Chen, Han; Fuchsberger, Christian; Kwan, Phoenix; Ma, Clement; Linderman, Michael; Lu, Yingchang; Thomsen, Soren K; Rundle, Jana K; Beer, Nicola L; van de Bunt, Martijn; Chalisey, Anil; Kang, Hyun Min; Voight, Benjamin F; Abecasis, Gonçalo R; Almgren, Peter; Baldassarre, Damiano; Balkau, Beverley; Benediktsson, Rafn; Blüher, Matthias; Boeing, Heiner; Bonnycastle, Lori L; Bottinger, Erwin P; Burtt, Noël P; Carey, Jason; Charpentier, Guillaume; Chines, Peter S; Cornelis, Marilyn C; Couper, David J; Crenshaw, Andrew T; van Dam, Rob M; Doney, Alex SF; Dorkhan, Mozhgan; Edkins, Sarah; Eriksson, Johan G; Esko, Tonu; Eury, Elodie; Fadista, João; Flannick, Jason; Fontanillas, Pierre; Fox, Caroline; Franks, Paul W; Gertow, Karl; Gieger, Christian; Gigante, Bruna; Gottesman, Omri; Grant, George B; Grarup, Niels; Groves, Christopher J; Hassinen, Maija; Have, Christian T; Herder, Christian; Holmen, Oddgeir L; Hreidarsson, Astradur B; Humphries, Steve E; Hunter, David J; Jackson, Anne U; Jonsson, Anna; Jørgensen, Marit E; Jørgensen, Torben; Kao, Wen-Hong L; Kerrison, Nicola D; Kinnunen, Leena; Klopp, Norman; Kong, Augustine; Kovacs, Peter; Kraft, Peter; Kravic, Jasmina; Langford, Cordelia; Leander, Karin; Liang, Liming; Lichtner, Peter; Lindgren, Cecilia M; Lindholm, Eero; Linneberg, Allan; Liu, Ching-Ti; Lobbens, Stéphane; Luan, Jian'an; Lyssenko, Valeriya; Männistö, Satu; McLeod, Olga; Meyer, Julia; Mihailov, Evelin; Mirza, Ghazala; Mühleisen, Thomas W; Müller-Nurasyid, Martina; Navarro, Carmen; Nöthen, Markus M; Oskolkov, Nikolay N; Owen, Katharine R; Palli, Domenico; Pechlivanis, Sonali; Peltonen, Leena; Perry, John RB; Platou, Carl GP; Roden, Michael; Ruderfer, Douglas; Rybin, Denis; van der Schouw, Yvonne T; Sennblad, Bengt; Sigurðsson, Gunnar; Stančáková, Alena; Steinbach, Gerald; Storm, Petter; Strauch, Konstantin; Stringham, Heather M; Sun, Qi; Thorand, Barbara; Tikkanen, Emmi; Tonjes, Anke; Trakalo, Joseph; Tremoli, Elena; Tuomi, Tiinamaija; Wennauer, Roman; Wiltshire, Steven; Wood, Andrew R; Zeggini, Eleftheria; Dunham, Ian; Birney, Ewan; Pasquali, Lorenzo; Ferrer, Jorge; Loos, Ruth JF; Dupuis, Josée; Florez, Jose C; Boerwinkle, Eric; Pankow, James S; van Duijn, Cornelia; Sijbrands, Eric; Meigs, James B; Hu, Frank B; Thorsteinsdottir, Unnur; Stefansson, Kari; Lakka, Timo A; Rauramaa, Rainer; Stumvoll, Michael; Pedersen, Nancy L; Lind, Lars; Keinanen-Kiukaanniemi, Sirkka M; Korpi-Hyövälti, Eeva; Saaristo, Timo E; Saltevo, Juha; Kuusisto, Johanna; Laakso, Markku; Metspalu, Andres; Erbel, Raimund; Jöcke, Karl-Heinz; Moebus, Susanne; Ripatti, Samuli; Salomaa, Veikko; Ingelsson, Erik; Boehm, Bernhard O; Bergman, Richard N; Collins, Francis S; Mohlke, Karen L; Koistinen, Heikki; Tuomilehto, Jaakko; Hveem, Kristian; Njølstad, Inger; Deloukas, Panagiotis; Donnelly, Peter J; Frayling, Timothy M; Hattersley, Andrew T; de Faire, Ulf; Hamsten, Anders; Illig, Thomas; Peters, Annette; Cauchi, Stephane; Sladek, Rob; Froguel, Philippe; Hansen, Torben; Pedersen, Oluf; Morris, Andrew D; Palmer, Collin NA; Kathiresan, Sekar; Melander, Olle; Nilsson, Peter M; Groop, Leif C; Barroso, Inês; Langenberg, Claudia; Wareham, Nicholas J; O'Callaghan, Christopher A; Gloyn, Anna L; Altshuler, David; Boehnke, Michael; Teslovich, Tanya M; McCarthy, Mark I; Morris, Andrew P; DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium; Luan, Jian'an [0000-0003-3137-6337]; Perry, John [0000-0001-6483-3771]; Barroso, Ines [0000-0001-5800-4520]; Langenberg, Claudia [0000-0002-5017-7344]; Wareham, Nicholas [0000-0003-1422-2993]We performed fine mapping of 39 established type 2 diabetes (T2D) loci in 27,206 cases and 57,574 controls of European ancestry. We identified 49 distinct association signals at these loci, including five mapping in or near KCNQ1. 'Credible sets' of the variants most likely to drive each distinct signal mapped predominantly to noncoding sequence, implying that association with T2D is mediated through gene regulation. Credible set variants were enriched for overlap with FOXA2 chromatin immunoprecipitation binding sites in human islet and liver cells, including at MTNR1B, where fine mapping implicated rs10830963 as driving T2D association. We confirmed that the T2D risk allele for this SNP increases FOXA2-bound enhancer activity in islet- and liver-derived cells. We observed allele-specific differences in NEUROD1 binding in islet-derived cells, consistent with evidence that the T2D risk allele increases islet MTNR1B expression. Our study demonstrates how integration of genetic and genomic information can define molecular mechanisms through which variants underlying association signals exert their effects on disease.Item Open Access Published version Peer-reviewed No interactions between previously associated 2-hour glucose gene variants and physical activity or BMI on 2-hour glucose levels.(American Diabetes Association, 2012-05) Scott, Robert A; Chu, Audrey Y; Grarup, Niels; Manning, Alisa K; Hivert, Marie-France; Shungin, Dmitry; Tönjes, Anke; Yesupriya, Ajay; Barnes, Daniel; Bouatia-Naji, Nabila; Glazer, Nicole L; Jackson, Anne U; Kutalik, Zoltán; Lagou, Vasiliki; Marek, Diana; Rasmussen-Torvik, Laura J; Stringham, Heather M; Tanaka, Toshiko; Aadahl, Mette; Arking, Dan E; Bergmann, Sven; Boerwinkle, Eric; Bonnycastle, Lori L; Bornstein, Stefan R; Brunner, Eric; Bumpstead, Suzannah J; Brage, Soren; Carlson, Olga D; Chen, Han; Chen, Yii-Der Ida; Chines, Peter S; Collins, Francis S; Couper, David J; Dennison, Elaine M; Dowling, Nicole F; Egan, Josephine S; Ekelund, Ulf; Erdos, Michael R; Forouhi, Nita G; Fox, Caroline S; Goodarzi, Mark O; Grässler, Jürgen; Gustafsson, Stefan; Hallmans, Göran; Hansen, Torben; Hingorani, Aroon; Holloway, John W; Hu, Frank B; Isomaa, Bo; Jameson, Karen A; Johansson, Ingegerd; Jonsson, Anna; Jørgensen, Torben; Kivimaki, Mika; Kovacs, Peter; Kumari, Meena; Kuusisto, Johanna; Laakso, Markku; Lecoeur, Cécile; Lévy-Marchal, Claire; Li, Guo; Loos, Ruth JF; Lyssenko, Valeri; Marmot, Michael; Marques-Vidal, Pedro; Morken, Mario A; Müller, Gabriele; North, Kari E; Pankow, James S; Payne, Felicity; Prokopenko, Inga; Psaty, Bruce M; Renström, Frida; Rice, Ken; Rotter, Jerome I; Rybin, Denis; Sandholt, Camilla H; Sayer, Avan A; Shrader, Peter; Schwarz, Peter EH; Siscovick, David S; Stancáková, Alena; Stumvoll, Michael; Teslovich, Tanya M; Waeber, Gérard; Williams, Gordon H; Witte, Daniel R; Wood, Andrew R; Xie, Weijia; Boehnke, Michael; Cooper, Cyrus; Ferrucci, Luigi; Froguel, Philippe; Groop, Leif; Kao, WH Linda; Vollenweider, Peter; Walker, Mark; Watanabe, Richard M; Pedersen, Oluf; Meigs, James B; Ingelsson, Erik; Barroso, Inês; Florez, Jose C; Franks, Paul W; Dupuis, Josée; Wareham, Nicholas J; Langenberg, Claudia; Barnes, Daniel [0000-0002-3781-7570]; Brage, Soren [0000-0002-1265-7355]; Forouhi, Nita [0000-0002-5041-248X]; Barroso, Ines [0000-0001-5800-4520]; Wareham, Nicholas [0000-0003-1422-2993]; Langenberg, Claudia [0000-0002-5017-7344]Gene-lifestyle interactions have been suggested to contribute to the development of type 2 diabetes. Glucose levels 2 h after a standard 75-g glucose challenge are used to diagnose diabetes and are associated with both genetic and lifestyle factors. However, whether these factors interact to determine 2-h glucose levels is unknown. We meta-analyzed single nucleotide polymorphism (SNP) × BMI and SNP × physical activity (PA) interaction regression models for five SNPs previously associated with 2-h glucose levels from up to 22 studies comprising 54,884 individuals without diabetes. PA levels were dichotomized, with individuals below the first quintile classified as inactive (20%) and the remainder as active (80%). BMI was considered a continuous trait. Inactive individuals had higher 2-h glucose levels than active individuals (β = 0.22 mmol/L [95% CI 0.13-0.31], P = 1.63 × 10(-6)). All SNPs were associated with 2-h glucose (β = 0.06-0.12 mmol/allele, P ≤ 1.53 × 10(-7)), but no significant interactions were found with PA (P > 0.18) or BMI (P ≥ 0.04). In this large study of gene-lifestyle interaction, we observed no interactions between genetic and lifestyle factors, both of which were associated with 2-h glucose. It is perhaps unlikely that top loci from genome-wide association studies will exhibit strong subgroup-specific effects, and may not, therefore, make the best candidates for the study of interactions.Item Open Access Published version Peer-reviewed Large meta-analysis of genome-wide association studies identifies five loci for lean body mass.(Springer Science and Business Media LLC, 2017-07-19) Zillikens, M Carola; Demissie, Serkalem; Hsu, Yi-Hsiang; Yerges-Armstrong, Laura M; Chou, Wen-Chi; Stolk, Lisette; Livshits, Gregory; Broer, Linda; Johnson, Toby; Koller, Daniel L; Kutalik, Zoltán; Luan, Jian'an; Malkin, Ida; Ried, Janina S; Smith, Albert V; Thorleifsson, Gudmar; Vandenput, Liesbeth; Hua Zhao, Jing; Zhang, Weihua; Aghdassi, Ali; Åkesson, Kristina; Amin, Najaf; Baier, Leslie J; Barroso, Inês; Bennett, David A; Bertram, Lars; Biffar, Rainer; Bochud, Murielle; Boehnke, Michael; Borecki, Ingrid B; Buchman, Aron S; Byberg, Liisa; Campbell, Harry; Campos Obanda, Natalia; Cauley, Jane A; Cawthon, Peggy M; Cederberg, Henna; Chen, Zhao; Cho, Nam H; Jin Choi, Hyung; Claussnitzer, Melina; Collins, Francis; Cummings, Steven R; De Jager, Philip L; Demuth, Ilja; Dhonukshe-Rutten, Rosalie AM; Diatchenko, Luda; Eiriksdottir, Gudny; Enneman, Anke W; Erdos, Mike; Eriksson, Johan G; Eriksson, Joel; Estrada, Karol; Evans, Daniel S; Feitosa, Mary F; Fu, Mao; Garcia, Melissa; Gieger, Christian; Girke, Thomas; Glazer, Nicole L; Grallert, Harald; Grewal, Jagvir; Han, Bok-Ghee; Hanson, Robert L; Hayward, Caroline; Hofman, Albert; Hoffman, Eric P; Homuth, Georg; Hsueh, Wen-Chi; Hubal, Monica J; Hubbard, Alan; Huffman, Kim M; Husted, Lise B; Illig, Thomas; Ingelsson, Erik; Ittermann, Till; Jansson, John-Olov; Jordan, Joanne M; Jula, Antti; Karlsson, Magnus; Khaw, Kay-Tee; Kilpeläinen, Tuomas O; Klopp, Norman; Kloth, Jacqueline SL; Koistinen, Heikki A; Kraus, William E; Kritchevsky, Stephen; Kuulasmaa, Teemu; Kuusisto, Johanna; Laakso, Markku; Lahti, Jari; Lang, Thomas; Langdahl, Bente L; Launer, Lenore J; Lee, Jong-Young; Lerch, Markus M; Lewis, Joshua R; Lind, Lars; Lindgren, Cecilia; Liu, Yongmei; Liu, Tian; Liu, Youfang; Ljunggren, Östen; Lorentzon, Mattias; Luben, Robert N; Maixner, William; McGuigan, Fiona E; Medina-Gomez, Carolina; Meitinger, Thomas; Melhus, Håkan; Mellström, Dan; Melov, Simon; Michaëlsson, Karl; Mitchell, Braxton D; Morris, Andrew P; Mosekilde, Leif; Newman, Anne; Nielson, Carrie M; O'Connell, Jeffrey R; Oostra, Ben A; Orwoll, Eric S; Palotie, Aarno; Parker, Stephen CJ; Peacock, Munro; Perola, Markus; Peters, Annette; Polasek, Ozren; Prince, Richard L; Räikkönen, Katri; Ralston, Stuart H; Ripatti, Samuli; Robbins, John A; Rotter, Jerome I; Rudan, Igor; Salomaa, Veikko; Satterfield, Suzanne; Schadt, Eric E; Schipf, Sabine; Scott, Laura; Sehmi, Joban; Shen, Jian; Soo Shin, Chan; Sigurdsson, Gunnar; Smith, Shad; Soranzo, Nicole; Stančáková, Alena; Steinhagen-Thiessen, Elisabeth; Streeten, Elizabeth A; Styrkarsdottir, Unnur; Swart, Karin MA; Tan, Sian-Tsung; Tarnopolsky, Mark A; Thompson, Patricia; Thomson, Cynthia A; Thorsteinsdottir, Unnur; Tikkanen, Emmi; Tranah, Gregory J; Tuomilehto, Jaakko; van Schoor, Natasja M; Verma, Arjun; Vollenweider, Peter; Völzke, Henry; Wactawski-Wende, Jean; Walker, Mark; Weedon, Michael N; Welch, Ryan; Wichmann, H-Erich; Widen, Elisabeth; Williams, Frances MK; Wilson, James F; Wright, Nicole C; Xie, Weijia; Yu, Lei; Zhou, Yanhua; Chambers, John C; Döring, Angela; van Duijn, Cornelia M; Econs, Michael J; Gudnason, Vilmundur; Kooner, Jaspal S; Psaty, Bruce M; Spector, Timothy D; Stefansson, Kari; Rivadeneira, Fernando; Uitterlinden, André G; Wareham, Nicholas J; Ossowski, Vicky; Waterworth, Dawn; Loos, Ruth JF; Karasik, David; Harris, Tamara B; Ohlsson, Claes; Kiel, Douglas P; Luan, Jian'an [0000-0003-3137-6337]; Barroso, Ines [0000-0001-5800-4520]; Khaw, Kay-Tee [0000-0002-8802-2903]; Luben, Robert [0000-0002-5088-6343]; Soranzo, Nicole [0000-0003-1095-3852]; Wareham, Nicholas [0000-0003-1422-2993]Lean body mass, consisting mostly of skeletal muscle, is important for healthy aging. We performed a genome-wide association study for whole body (20 cohorts of European ancestry with n = 38,292) and appendicular (arms and legs) lean body mass (n = 28,330) measured using dual energy X-ray absorptiometry or bioelectrical impedance analysis, adjusted for sex, age, height, and fat mass. Twenty-one single-nucleotide polymorphisms were significantly associated with lean body mass either genome wide (p < 5 × 10-8) or suggestively genome wide (p < 2.3 × 10-6). Replication in 63,475 (47,227 of European ancestry) individuals from 33 cohorts for whole body lean body mass and in 45,090 (42,360 of European ancestry) subjects from 25 cohorts for appendicular lean body mass was successful for five single-nucleotide polymorphisms in/near HSD17B11, VCAN, ADAMTSL3, IRS1, and FTO for total lean body mass and for three single-nucleotide polymorphisms in/near VCAN, ADAMTSL3, and IRS1 for appendicular lean body mass. Our findings provide new insight into the genetics of lean body mass.Lean body mass is a highly heritable trait and is associated with various health conditions. Here, Kiel and colleagues perform a meta-analysis of genome-wide association studies for whole body lean body mass and find five novel genetic loci to be significantly associated.Item Open Access Accepted version Peer-reviewed An Investigation Into the Differences in Bone Density and Body Composition Measurements Between 2 GE Lunar Densitometers and Their Comparison to a 4-Component Model(Elsevier, 2017-10) Watson, LPE; Venables, M; Murgatroyd, PR; Watson, Laura [0000-0002-2120-3531]; Venables, Michelle [0000-0002-9380-0060]We describe a study to assess the precision of the GE Lunar iDXA and the agreement between the iDXA and GE Lunar Prodigy densitometers for the measurement of regional- and total-body bone and body composition in normal to obese healthy adults. We compare the whole-body fat mass by dual-energy X-ray absorptiometry (DXA) to measurements by a 4-component (4-C) model. Sixty-nine participants, aged 37 ± 12 yr, with a body mass index of 26.2 ± 5.1 kg/cm2, were measured once on the Prodigy and twice on the iDXA. The 4-C model estimated fat mass from body mass, total body water by deuterium dilution, body volume by air displacement plethysmography, and bone mass by DXA. Agreements between measurements made on the 2 instruments and by the 4-C model were analyzed by Bland-Altman and linear regression analyses. Where appropriate, translational cross-calibration equations were derived. Differences between DXA software versions were investigated. iDXA precision was less than 2% of the measured value for all regional- and whole-body bone and body composition measurements with the exception of arm fat mass (2.28%). We found significant differences between iDXA and Prodigy (p < 0.05) whole-body and regional bone, fat mass (FM), and lean mass, with the exception of hip bone mass, area and density, and spine area. Compared to iDXA, Prodigy overestimated FM and underestimated lean mass. However, compared to 4-C, iDXA showed a smaller bias and narrower limits of agreement than Prodigy. No significant differences between software versions in FM estimations existed. Our results demonstrate excellent iDXA precision. However, significant differences exist between the 2 GE Lunar instruments, Prodigy and iDXA measurement values. A divergence from the reference 4-C observations remains in FM estimations made by DXA even following the recent advances in technology. Further studies are particularly warranted in individuals with large FM contents.Item Open Access Accepted version Peer-reviewed Serine peptidase inhibitor Kazal type 1 (SPINK1) as novel downstream effector of the cadherin-17/beta-catenin axis in hepatocellular carcinoma(Springer, 2017-10-01) Skec, FHS; Lou, R; Lam, YHB; Sung, WKS; Lam, T-W; Luk, JM; Leung, MS; Chan, KT; Poon, RT; Lee, NP; Lam, Brian [0000-0002-3638-9025]Background: Hepatocellular carcinoma (HCC) is the most common type of liver cancer worldwide. Previously, we reported that cadherin-17 (CDH17) and its related CDH17/-catenin axis may be responsible for inducing HCC in a subset of patients exhibiting CDH17 over-expression. Here we aimed at obtaining a better understanding of the CDH17-related HCC biology and to obtain further indications for the design of targeted therapies in CDH17 over-expressing HCC patients. Results: We found that SPINK1 acts as a downstream effector of the CDH17/-catenin axis in HCC. In addition, we found that SPINK1 expression exhibited a positive correlation with CDH17 expression in human HCCs and was over-expressed in up to 70% of the tumors. We identified SPINK1 as a downstream effector of the CDH17/-catenin axis using a spectrum of in vitro assays, including gene expression modulation and inhibitor assays, bioinformatics analyses and luciferase reporter assays. These in vitro results were validated in primary human HCCs, including the observation that alteration in -catenin expression (a core component of the CDH17/-catenin axis) in tumors affects SPINK1 serum levels in HCC patients. Similar to CDH17, SPINK1 expression in HCC cells was found to be associated with specific tumor-related properties via activating the c-Raf/MEK/ERK pathway. Conclusions: Our current data substantiate our knowledge on the role of CDH17 in the biology of HCC and suggest that components of the CDH17/-catenin axis may serve as therapeutic targets in CDH17 over-expressing HCC patients.Item Open Access Accepted version Peer-reviewed An Expanded Genome-Wide Association Study of Type 2 Diabetes in Europeans.(American Diabetes Association, 2017-11-01) Scott, Robert A; Scott, Laura J; Mägi, Reedik; Marullo, Letizia; Gaulton, Kyle J; Kaakinen, Marika; Pervjakova, Natalia; Pers, Tune H; Johnson, Andrew D; Eicher, John D; Jackson, Anne U; Ferreira, Teresa; Lee, Yeji; Ma, Clement; Steinthorsdottir, Valgerdur; Thorleifsson, Gudmar; Qi, Lu; Van Zuydam, Natalie R; Mahajan, Anubha; Chen, Han; Almgren, Peter; Voight, Ben F; Grallert, Harald; Müller-Nurasyid, Martina; Ried, Janina S; Rayner, Nigel W; Robertson, Neil; Karssen, Lennart C; van Leeuwen, Elisabeth M; Willems, Sara M; Fuchsberger, Christian; Kwan, Phoenix; Teslovich, Tanya M; Chanda, Pritam; Li, Man; Lu, Yingchang; Dina, Christian; Thuillier, Dorothee; Yengo, Loic; Jiang, Longda; Sparso, Thomas; Kestler, Hans A; Chheda, Himanshu; Eisele, Lewin; Gustafsson, Stefan; Frånberg, Mattias; Strawbridge, Rona J; Benediktsson, Rafn; Hreidarsson, Astradur B; Kong, Augustine; Sigurðsson, Gunnar; Kerrison, Nicola D; Luan, Jian'an; Liang, Liming; Meitinger, Thomas; Roden, Michael; Thorand, Barbara; Esko, Tõnu; Mihailov, Evelin; Fox, Caroline; Liu, Ching-Ti; Rybin, Denis; Isomaa, Bo; Lyssenko, Valeriya; Tuomi, Tiinamaija; Couper, David J; Pankow, James S; Grarup, Niels; Have, Christian T; Jørgensen, Marit E; Jørgensen, Torben; Linneberg, Allan; Cornelis, Marilyn C; van Dam, Rob M; Hunter, David J; Kraft, Peter; Sun, Qi; Edkins, Sarah; Owen, Katharine R; Perry, John RB; Wood, Andrew R; Zeggini, Eleftheria; Tajes-Fernandes, Juan; Abecasis, Goncalo R; Bonnycastle, Lori L; Chines, Peter S; Stringham, Heather M; Koistinen, Heikki A; Kinnunen, Leena; Sennblad, Bengt; Mühleisen, Thomas W; Nöthen, Markus M; Pechlivanis, Sonali; Baldassarre, Damiano; Gertow, Karl; Humphries, Steve E; Tremoli, Elena; Klopp, Norman; Meyer, Julia; Steinbach, Gerald; Wennauer, Roman; Eriksson, Johan G; Mӓnnistö, Satu; Peltonen, Leena; Tikkanen, Emmi; Charpentier, Guillaume; Eury, Elodie; Lobbens, Stéphane; Gigante, Bruna; Leander, Karin; McLeod, Olga; Bottinger, Erwin P; Gottesman, Omri; Ruderfer, Douglas; Blüher, Matthias; Kovacs, Peter; Tonjes, Anke; Maruthur, Nisa M; Scapoli, Chiara; Erbel, Raimund; Jöckel, Karl-Heinz; Moebus, Susanne; de Faire, Ulf; Hamsten, Anders; Stumvoll, Michael; Deloukas, Panagiotis; Donnelly, Peter J; Frayling, Timothy M; Hattersley, Andrew T; Ripatti, Samuli; Salomaa, Veikko; Pedersen, Nancy L; Boehm, Bernhard O; Bergman, Richard N; Collins, Francis S; Mohlke, Karen L; Tuomilehto, Jaakko; Hansen, Torben; Pedersen, Oluf; Barroso, Inês; Lannfelt, Lars; Ingelsson, Erik; Lind, Lars; Lindgren, Cecilia M; Cauchi, Stephane; Froguel, Philippe; Loos, Ruth JF; Balkau, Beverley; Boeing, Heiner; Franks, Paul W; Barricarte Gurrea, Aurelio; Palli, Domenico; van der Schouw, Yvonne T; Altshuler, David; Groop, Leif C; Langenberg, Claudia; Wareham, Nicholas J; Sijbrands, Eric; van Duijn, Cornelia M; Florez, Jose C; Meigs, James B; Boerwinkle, Eric; Gieger, Christian; Strauch, Konstantin; Metspalu, Andres; Morris, Andrew D; Palmer, Colin NA; Hu, Frank B; Thorsteinsdottir, Unnur; Stefansson, Kari; Dupuis, Josée; Morris, Andrew P; Boehnke, Michael; McCarthy, Mark I; Prokopenko, Inga; DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium; Luan, Jian'an [0000-0003-3137-6337]; Perry, John [0000-0001-6483-3771]; Barroso, Ines [0000-0001-5800-4520]; Langenberg, Claudia [0000-0002-5017-7344]; Wareham, Nicholas [0000-0003-1422-2993]To characterize type 2 diabetes (T2D)-associated variation across the allele frequency spectrum, we conducted a meta-analysis of genome-wide association data from 26,676 T2D case and 132,532 control subjects of European ancestry after imputation using the 1000 Genomes multiethnic reference panel. Promising association signals were followed up in additional data sets (of 14,545 or 7,397 T2D case and 38,994 or 71,604 control subjects). We identified 13 novel T2D-associated loci (P < 5 × 10(-8)), including variants near the GLP2R, GIP, and HLA-DQA1 genes. Our analysis brought the total number of independent T2D associations to 128 distinct signals at 113 loci. Despite substantially increased sample size and more complete coverage of low-frequency variation, all novel associations were driven by common single nucleotide variants. Credible sets of potentially causal variants were generally larger than those based on imputation with earlier reference panels, consistent with resolution of causal signals to common risk haplotypes. Stratification of T2D-associated loci based on T2D-related quantitative trait associations revealed tissue-specific enrichment of regulatory annotations in pancreatic islet enhancers for loci influencing insulin secretion and in adipocytes, monocytes, and hepatocytes for insulin action-associated loci. These findings highlight the predominant role played by common variants of modest effect and the diversity of biological mechanisms influencing T2D pathophysiology.Item Open Access Published version Peer-reviewed Short-chain fatty acids stimulate glucagon-like peptide-1 secretion via the G-protein-coupled receptor FFAR2.(American Diabetes Association, 2012-02) Tolhurst, Gwen; Heffron, Helen; Lam, Yu Shan; Parker, Helen E; Habib, Abdella M; Diakogiannaki, Eleftheria; Cameron, Jennifer; Grosse, Johannes; Reimann, Frank; Gribble, Fiona M; Reimann, Frank [0000-0001-9399-6377]; Gribble, Fiona [0000-0002-4232-2898]Interest in how the gut microbiome can influence the metabolic state of the host has recently heightened. One postulated link is bacterial fermentation of "indigestible" prebiotics to short-chain fatty acids (SCFAs), which in turn modulate the release of gut hormones controlling insulin release and appetite. We show here that SCFAs trigger secretion of the incretin hormone glucagon-like peptide (GLP)-1 from mixed colonic cultures in vitro. Quantitative PCR revealed enriched expression of the SCFA receptors ffar2 (grp43) and ffar3 (gpr41) in GLP-1-secreting L cells, and consistent with the reported coupling of GPR43 to Gq signaling pathways, SCFAs raised cytosolic Ca2+ in L cells in primary culture. Mice lacking ffar2 or ffar3 exhibited reduced SCFA-triggered GLP-1 secretion in vitro and in vivo and a parallel impairment of glucose tolerance. These results highlight SCFAs and their receptors as potential targets for the treatment of diabetes.Item Open Access Published version Peer-reviewed AKR1C3-mediated adipose androgen generation drives lipotoxicity in women with polycystic ovary syndrome(Oxford University Press, 2017-09-01) O'Reilly, MW; Kempegowda, P; Walsh, M; Taylor, AE; Manolopoulos, K; Allwood, JW; Semple, RK; Hebenstreit, D; Dunn, WB; Tomlinson, JW; Arlt, W; Semple, Robert [0000-0001-6539-3069]Context: Polycystic ovary syndrome (PCOS) is a prevalent metabolic disorder, occurring in up to 10% of women of reproductive age. PCOS is associated with insulin resistance and cardiovascular risk. Androgen excess is a defining feature of PCOS and has been suggested as causally associated with insulin resistance; however, mechanistic evidence linking both is lacking. We hypothesized that adipose tissue is an important site linking androgen activation and metabolic dysfunction in PCOS. Methods We performed a human deep metabolic in vivo phenotyping study, examining the systemic and intra-adipose effects of acute and chronic androgen exposure in ten PCOS women, in comparison to ten body mass index-matched healthy controls, complemented by in vitro experiments. Results: PCOS women had increased intra-adipose concentrations of testosterone (p=0.0006) and dihydrotestosterone (p=0.01), with increased expression of the androgen-activating enzyme aldoketoreductase type 1 C3 (AKR1C3, p=0.04) in subcutaneous adipose tissue. Adipose glycerol levels in subcutaneous adipose tissue microdialysate supported in vivo suppression of lipolysis after acute androgen exposure in PCOS (p=0.04). Mirroring this, non-targeted serum metabolomics revealed pro-lipogenic effects of androgens in PCOS women only. In vitro studies showed that insulin increased adipose AKR1C3 expression and activity while androgen exposure increased adipocyte de novo lipid synthesis. Pharmacological AKR1C3 inhibition in vitro decreased de novo lipogenesis. Conclusions: These findings define a novel intra-adipose mechanism of androgen activation that contributes to adipose remodelling and a systemic lipotoxic metabolome, with intra-adipose androgens driving lipid accumulation and insulin resistance in PCOS. AKR1C3 represents a promising novel therapeutic target in PCOS.Item Open Access Accepted version Peer-reviewed Insulin delivery and nocturnal glucose control in children and adolescents with type 1 diabetes(Taylor & Francis, 2017-12) Hovorka, R; Tauschmann, M; Hovorka, Roman [0000-0003-2901-461X]; Tauschmann, Martin [0000-0002-2305-2490]$\textbf{Introduction:}$ Nocturnal glucose control remains challenging in children and adolescents with type 1 diabetes due to highly variable overnight insulin requirements. The issue may be addressed by glucose responsive insulin delivery based on real-time continuous glucose measurements. $\textbf{Areas covered:}$ This review outlines recent developments of glucose responsive insulin delivery systems from a paediatric perspective. We cover threshold-based suspend application, predictive low glucose suspend, and more advanced single hormone and dual-hormone closed-loop systems. Approaches are evaluated in relation to nocturnal glucose control particularly during outpatient randomised controlled trials. $\textbf{Expert opinion:}$ Significant progress translating research from controlled clinical centre settings to free-living unsupervised home studies have been achieved over the past decade. Nocturnal glycaemic control can be improved whilst reducing the risk of hypoglycaemia with closed-loop systems. Following the US regulatory approval of the first hybrid closed-loop system in non-paediatric population, large multinational closed-loop clinical trials and pivotal studies including paediatric populations are underway or in preparation to facilitate the use of closed-loop systems in clinical practice.Item Open Access Published version Peer-reviewed Investigation of a Cluster of Sequence Type 22 MethicillinResistant Staphylococcus aureus Transmission in a Community Setting(Oxford University Press, 2017-12-15) Toleman, MS; Blane, B; Harrison, E; Coll, F; Parkhill, J; Brown, N; Peacock, SJ; Harrison, Ewan [0000-0003-2720-0507]; Parkhill, Julian [0000-0002-7069-5958]; Peacock, Sharon [0000-0002-1718-2782]BACKGROUND: Whole-genome sequencing (WGS) has typically been used to confirm or refute hospital/ward outbreaks of methicillin-resistant Staphylococcus aureus (MRSA) identified through routine practice. However, appropriately targeted WGS strategies that identify routinely ‘undetectable’ transmission remains the ultimate aim. METHODS: WGS of MRSA isolates sent to a regional microbiological laboratory was performed as part of a 12-month prospective observational study. Phylogenetic analyses identified a genetically-related cluster of E-MRSA15 isolated from patients registered to the same General Practice (GP) surgery. This led to an investigation to identify epidemiological links, find additional cases and determine potential for on-going transmission. RESULTS: We identified 15 MRSA-positive individuals with 27 highly-related MRSA isolates who were linked to the GP surgery, two of whom died with MRSA bacteremia. Of the 13 cases who were further investigated, 11 had attended a leg ulcer/podiatry clinic. Cases lacked epidemiological links to hospitals, suggesting that transmission occurred elsewhere. Environmental and staff screening at the GP surgery did not identify an on-going source of infection. CONCLUSIONS: Surveillance in the United Kingdom shows that the proportion of MRSA bacteremias apportioned to hospitals is decreasing, suggesting the need for greater focus on the detection of MRSA outbreaks and transmission in the community. This case study confirms that the typically nosocomial lineage (E-MRSA15) can transmit within community settings. Our study exemplifies the continued importance of WGS in detecting outbreaks including those which may be missed by routine practice, and suggests that universal WGS of bacteremia isolates may help detect outbreaks in low-surveillance settings.Item Open Access Published version Peer-reviewed Human biallelic MFN2 mutations induce mitochondrial dysfunction, upper body adipose hyperplasia, and suppression of leptin expression(eLife Sciences Publications Ltd, 2017-04-17) Rocha, N; Bulger, DA; Frontini, A; Titheradge, H; Gribsholt, SB; Knox, R; Page, M; Harris, J; Payne, F; Adams, C; Sleigh, A; Crawford, J; Gjesing, AP; Bork-Jensen, J; Pedersen, O; Barroso, I; Hansen, T; Cox, H; Reilly, M; Rossor, A; Brown, RJ; Taylor, SI; McHale, D; Armstrong, M; Oral, EA; Saudek, V; O'Rahilly, S; Maher, ER; Richelsen, B; Savage, DB; Semple, RK; Adams, Claire [0000-0002-4445-4747]; Barroso, Ines [0000-0001-5800-4520]; O'Rahilly, Stephen [0000-0003-2199-4449]; Maher, Eamonn [0000-0002-6226-6918]; Savage, David [0000-0002-7857-7032]; Semple, Robert [0000-0001-6539-3069]MFN2 encodes mitofusin 2, a membrane-bound mediator of mitochondrial membrane fusion and inter-organelle communication. MFN2 mutations cause axonal neuropathy, with associated lipodystrophy only occasionally noted, however homozygosity for the p.Arg707Trp mutation was recently associated with upper body adipose overgrowth. We describe similar massive adipose overgrowth with suppressed leptin expression in four further patients with biallelic MFN2 mutations and at least one p.Arg707Trp allele. Overgrown tissue was composed of normal-sized, UCP1-negative unilocular adipocytes, with mitochondrial network fragmentation, disorganised cristae, and increased autophagosomes. There was strong transcriptional evidence of mitochondrial stress signalling, increased protein synthesis, and suppression of signatures of cell death in affected tissue, whereas mitochondrial morphology and gene expression were normal in skin fibroblasts. These findings suggest that specific MFN2 mutations cause tissue-selective mitochondrial dysfunction with increased adipocyte proliferation and survival, confirm a novel form of excess adiposity with paradoxical suppression of leptin expression, and suggest potential targeted therapies.Item Open Access Published version Peer-reviewed Refining genotype-phenotype correlation in Alström syndrome through study of primary human fibroblasts(Wiley, 2017-07) Chen, J-H; Geberhiwot, T; Barrett, TG; Paisey, R; Semple, RK; Semple, Robert [0000-0001-6539-3069]BACKGROUND: Alström syndrome (AS), featuring retinal dystrophy, neuronal deafness, cardiomyopathy, metabolic syndrome, and diffuse fibrosis, is caused by biallelic mutations in the centrosomal protein ALMS1. Genotype-phenotype correlation has been suggested without assessment of ALMS1 expression. METHODS: ALMS1 expression (real-time PCR and immunocytochemistry) and cilia formation (immunocytochemistry) were assessed in fibroblasts from deeply phenotyped volunteers diagnosed with AS recruited from a dedicated AS Service. Exome sequencing was used in two participants without convincing biallelic ALMS1 mutations, and BBS2 (Bardet-Biedl syndrome 2) protein expression was assessed in one patient with biallelic BBS2 mutations. Hedgehog-induced GLI1 expression and PDGFA signaling was assessed using quantitative real-time PCR, immunoblotting, or immunostaining of fixed cells after stimulation. RESULTS: In 16 of the patient cell lines examined, ALMS1 protein was undetectable (14 with biallelic loss-of-function (LoF) mutations), and in two, ALMS1 staining was equivocal (one with biallelic LoF mutations). In five lines, ALMS1 expression was normal using at least one fixation method (one with biallelic LoF mutations). These differences were not accounted for by major differences in ALMS1 mRNA expression. Exome sequencing of two participants with normal ALMS1 expression identified biallelic LoF BBS2 mutations in one. No second, known ciliopathy mutation was found in the other patient, who had one LoF ALMS1 mutation. Phenotypes were milder or atypical in participants with preserved ALMS1 immunostaining, even when two with likely alternative genetic diagnoses were excluded. All cells studied developed normal cilia, ALMS1 and BBS2 mutant cells showed normal Hedgehog-induced upregulation of GLI1 expression, and PDGFA signaling was normal in ALMS1-deficient cells. CONCLUSION: Milder or atypical presentations of AS should prompt genetic evaluation for alternative, clinically overlapping ciliopathies. A subgroup of patients with bona fide ALMS1 defects have milder phenotypes due to residual ALMS1 expression, which may be more important than mutation site.Item Open Access Published version Peer-reviewed Rare Variant Analysis of Human and Rodent Obesity Genes in Individuals with Severe Childhood Obesity(Nature Publishing Group, 2017-06-29) Hendricks, AE; Bochukova, EG; Marenne, G; Keogh, JM; Atanassova, N; Bounds, R; Wheeler, E; Mistry, V; Henning, E; Körner, A; Muddyman, D; McCarthy, S; Hinney, A; Hebebrand, J; Scott, RA; Langenberg, C; Wareham, NJ; Surendran, P; Howson, JM; Butterworth, AS; Danesh, J; Nordestgaard, BG; Nielsen, SF; Afzal, S; Papadia, S; Ashford, S; Garg, S; Millhauser, GL; Palomino, RI; Kwasniewska, A; Tachmazidou, I; O'Rahilly, S; Zeggini, E; Barroso, I; Farooqi, IS; Understanding Society Scientific Group; EPIC-CVD Consortium; UK10K Consortium; Keogh, Julia [0000-0002-0399-4114]; Wheeler, Eleanor [0000-0002-8616-6444]; Henning, Elana [0000-0002-0399-4114]; McCarthy, Shane [0000-0002-2715-4187]; Langenberg, Claudia [0000-0002-5017-7344]; Wareham, Nicholas [0000-0003-1422-2993]; Surendran, Praveen [0000-0002-4911-6077]; Howson, Joanna [0000-0001-7618-0050]; Butterworth, Adam [0000-0002-6915-9015]; Danesh, John [0000-0003-1158-6791]; Papadia, Sofia [0000-0002-9222-3812]; O'Rahilly, Stephen [0000-0003-2199-4449]; Barroso, Ines [0000-0001-5800-4520]; Farooqi, Ismaa [0000-0001-7609-3504]Obesity is a genetically heterogeneous disorder. Using targeted and whole-exome sequencing, we studied 32 human and 87 rodent obesity genes in 2,548 severely obese children and 1,117 controls. We identified 52 variants contributing to obesity in 2% of cases including multiple novel variants in GNAS, which were sometimes found with accelerated growth rather than short stature as described previously. Nominally significant associations were found for rare functional variants in BBS1, BBS9, GNAS, MKKS, CLOCK and ANGPTL6. The p.S284X variant in ANGPTL6 drives the association signal (rs201622589, MAF~0.1%, odds ratio = 10.13, p-value = 0.042) and results in complete loss of secretion in cells. Further analysis including additional case-control studies and population controls (N = 260,642) did not support association of this variant with obesity (odds ratio = 2.34, p-value = 2.59 × 10(-3)), highlighting the challenges of testing rare variant associations and the need for very large sample sizes. Further validation in cohorts with severe obesity and engineering the variants in model organisms will be needed to explore whether human variants in ANGPTL6 and other genes that lead to obesity when deleted in mice, do contribute to obesity. Such studies may yield druggable targets for weight loss therapies.Item Open Access Accepted version Peer-reviewed Hypoinsulinaemic, hypoketotic hypoglycaemia due to mosaic genetic activation of PI3-kinase.(Oxford University Press (OUP), 2017-08) Leiter, Sarah M; Parker, Victoria ER; Welters, Alena; Knox, Rachel; Rocha, Nuno; Clark, Graeme; Payne, Felicity; Lotta, Luca; Harris, Julie; Guerrero-Fernández, Julio; González-Casado, Isabel; García-Miñaur, Sixto; Gordo, Gema; Wareham, Nick; Martínez-Glez, Víctor; Allison, Michael; O'Rahilly, Stephen; Barroso, Inês; Meissner, Thomas; Davies, Susan; Hussain, Khalid; Temple, Karen; Barreda-Bonis, Ana-Coral; Kummer, Sebastian; Semple, Robert K; Wareham, Nicholas [0000-0003-1422-2993]; O'Rahilly, Stephen [0000-0003-2199-4449]; Barroso, Ines [0000-0001-5800-4520]; Semple, Robert [0000-0001-6539-3069]OBJECTIVE: Genetic activation of the insulin signal-transducing kinase AKT2 causes syndromic hypoketotic hypoglycaemia without elevated insulin. Mosaic activating mutations in class 1A phospatidylinositol-3-kinase (PI3K), upstream from AKT2 in insulin signalling, are known to cause segmental overgrowth, but the metabolic consequences have not been systematically reported. We assess the metabolic phenotype of 22 patients with mosaic activating mutations affecting PI3K, thereby providing new insight into the metabolic function of this complex node in insulin signal transduction. METHODS: Three patients with megalencephaly, diffuse asymmetric overgrowth, hypoketotic, hypoinsulinaemic hypoglycaemia and no AKT2 mutation underwent further genetic, clinical and metabolic investigation. Signalling in dermal fibroblasts from one patient and efficacy of the mTOR inhibitor Sirolimus on pathway activation were examined. Finally, the metabolic profile of a cohort of 19 further patients with mosaic activating mutations in PI3K was assessed. RESULTS: In the first three patients, mosaic mutations in PIK3CA (p.Gly118Asp or p.Glu726Lys) or PIK3R2 (p.Gly373Arg) were found. In different tissue samples available from one patient, the PIK3CA p.Glu726Lys mutation was present at burdens from 24% to 42%, with the highest level in the liver. Dermal fibroblasts showed increased basal AKT phosphorylation which was potently suppressed by Sirolimus. Nineteen further patients with mosaic mutations in PIK3CA had neither clinical nor biochemical evidence of hypoglycaemia. CONCLUSIONS: Mosaic mutations activating class 1A PI3K cause severe non-ketotic hypoglycaemia in a subset of patients, with the metabolic phenotype presumably related to the extent of mosaicism within the liver. mTOR or PI3K inhibitors offer the prospect for future therapy.