Epigenome-wide association study on the plasma metabolome suggests self-regulation of the glycine and serine pathway through DNA methylation

Autor: Jiafei Wu, Victoria Palasantzas, Sergio Andreu-Sánchez, Torsten Plösch, Sam Leonard, Shuang Li, Marc Jan Bonder, Harm-Jan Westra, Joyce van Meurs, Mohsen Ghanbari, Lude Franke, Alexandra Zhernakova, Jingyuan Fu, Joanne A. Hoogerland, Daria V. Zhernakova

Publikováno v: Clinical Epigenetics, Vol 16, Iss 1, Pp 1-16 (2024)

Abstract Background The plasma metabolome reflects the physiological state of various biological processes and can serve as a proxy for disease risk. Plasma metabolite variation, influenced by genetic and epigenetic mechanisms, can also affect the ce

Externí odkaz: https://doaj.org/article/9ba2686e25cc4689806e48f764522f07

NMR metabolomics-guided DNA methylation mortality predictorsResearch in context

Autor: Daniele Bizzarri, Marcel J.T. Reinders, Lieke Kuiper, Marian Beekman, Joris Deelen, Joyce B.J. van Meurs, Jenny van Dongen, René Pool, Dorret I. Boomsma, Mohsen Ghanbari, Lude Franke, Pieternella E. Slagboom, Erik B. van den Akker, J.M. Geleijnse, E. Boersma, W.E. van Spil, M.M.J. van Greevenbroek, C.D.A. Stehouwer, C.J.H. van der Kallen, I.C.W. Arts, F. Rutters, J.W.J. Beulens, M. Muilwijk, P.J.M. Elders, L.M. 't Hart, M. Ghanbari, M.A. Ikram, M.G. Netea, M. Kloppenburg, Y.F.M. Ramos, N. Bomer, I. Meulenbelt, K. Stronks, M.B. Snijder, A.H. Zwinderman, B.T. Heijmans, L.H. Lumey, C. Wijmenga, J. Fu, A. Zhernakova, J. Deelen, S.P. Mooijaart, M. Beekman, P.E. Slagboom, G.L.J. Onderwater, A.M.J.M. van den Maagdenberg, G.M. Terwindt, C. Thesing, M. Bot, B.W.J.H. Penninx, S. Trompet, J.W. Jukema, N. Sattar, I.C.C. van der Horst, P. van der Harst, C. So-Osman, J.A. van Hilten, R.G.H.H. Nelissen, I.E. Höfer, F.W. Asselbergs, P. Scheltens, C.E. Teunissen, W.M. van der Flier, J. van Dongen, R. Pool, A.H.M. Willemsen, D.I. Boomsma, H.E.D. Suchiman, J.J.H. Barkey Wolf, D. Cats, H. Mei, M. Slofstra, M. Swertz, M.J.T. Reinders, E.B. van den Akker

Publikováno v: EBioMedicine, Vol 107, Iss , Pp 105279- (2024)

Summary: Background: 1H-NMR metabolomics and DNA methylation in blood are widely known biomarkers predicting age-related physiological decline and mortality yet exert mutually independent mortality and frailty signals. Methods: Leveraging multi-omics

Externí odkaz: https://doaj.org/article/dd2f1125885a4ef2be328f0b36ea785b

An iPSC-derived small intestine-on-chip with self-organizing epithelial, mesenchymal, and neural cells

Autor: Renée Moerkens, Joram Mooiweer, Aarón D. Ramírez-Sánchez, Roy Oelen, Lude Franke, Cisca Wijmenga, Robert J. Barrett, Iris H. Jonkers, Sebo Withoff

Publikováno v: Cell Reports, Vol 43, Iss 7, Pp 114247- (2024)

Summary: Human induced pluripotent stem cell (hiPSC)-derived intestinal organoids are valuable tools for researching developmental biology and personalized therapies, but their closed topology and relative immature state limit applications. Here, we

Externí odkaz: https://doaj.org/article/cd45fee274a64df99505faa880e9eee4

PICALO: principal interaction component analysis for the identification of discrete technical, cell-type, and environmental factors that mediate eQTLs

Autor: Martijn Vochteloo, Patrick Deelen, Britt Vink, BIOS Consortium, Ellen A. Tsai, Heiko Runz, Sergio Andreu-Sánchez, Jingyuan Fu, Alexandra Zhernakova, Harm-Jan Westra, Lude Franke

Publikováno v: Genome Biology, Vol 25, Iss 1, Pp 1-26 (2024)

Abstract Expression quantitative trait loci (eQTL) offer insights into the regulatory mechanisms of trait-associated variants, but their effects often rely on contexts that are unknown or unmeasured. We introduce PICALO, a method for hidden variable

Externí odkaz: https://doaj.org/article/1bb030c23f7a471a97ee8771da5fe1e3

Comprehensive evaluation of smoking exposures and their interactions on DNA methylationResearch in context

Autor: Thanh T. Hoang, Yunsung Lee, Daniel L. McCartney, Elin T.G. Kersten, Christian M. Page, Paige M. Hulls, Mikyeong Lee, Rosie M. Walker, Charles E. Breeze, Brian D. Bennett, Adam B. Burkholder, James Ward, Anne Lise Brantsæter, Ida H. Caspersen, Alison A. Motsinger-Reif, Marie Richards, Julie D. White, Shanshan Zhao, Rebecca C. Richmond, Maria C. Magnus, Gerard H. Koppelman, Kathryn L. Evans, Riccardo E. Marioni, Siri E. Håberg, Stephanie J. London, Bastiaan Heijmans, Peter ’t Hoen, Joyce van Meurs, Rick Jansen, Lude Franke, Dorret Boomsma, René Pool, Jenny van Dongen, Jouke Hottenga, Marleen van Greevenbroek, Coen Stehouwer, Carla van der Kallen, Casper Schalkwijk, Cisca Wijmenga, Sasha Zhernakova, Ettje Tigchelaar, P. Eline Slagboom, Marian Beekman, Joris Deelen, Diana Van Heemst, Jan Veldink, Leonard van den Berg, Cornelia van Duijn, Bert Hofman, Aaron Isaacs, André Uitterlinden, P. Mila Jhamai, Michael Verbiest, H. Eka Suchiman, Marijn Verkerk, Ruud van der Breggen, Jeroen van Rooij, Nico Lakenberg, Hailiang Mei, Maarten van Iterson, Michiel van Galen, Jan Bot, Dasha Zhernakova, Peter van ‘t Hof, Patrick Deelen, Irene Nooren, Matthijs Moed, Martijn Vermaat, René Luijk, Marc Bonder, Freerk van Dijk, Wibowo Arindrarto, Szymon Kielbasa, Morris Swertz, Erik van Zwet

Publikováno v: EBioMedicine, Vol 100, Iss , Pp 104956- (2024)

Summary: Background: Smoking impacts DNA methylation, but data are lacking on smoking-related differential methylation by sex or dietary intake, recent smoking cessation (

Externí odkaz: https://doaj.org/article/3985b627485b4ff999b2ec073dfaf4e4