Merkle Labs

Publications & pre-prints

Photo of a line of journal covers including Cell, Nature Neuroscience and Sciene

Recent highlights and links are below, and a full list of publications can be found here.  Please don’t hesitate to contact us!

  1. Chen H-J C*, Yang A*, Mazzaferro S, Mali I, Cahn O, Kentistou K, Rowley C, Stewart N, Seah JWE,  Pisupati V, Kirwan P, Aggarwal S, Toyohara T, Mary H.C. Florido MHC, Cowan C, Quambusch L, Hyvönen M, Livesey MR, Perry JRB, Marioni JC, Merkle FT§. Profiling human hypothalamic neurons reveals a candidate combination drug therapy for weight loss. BioRxiv. July 2023. doi:10.1101/2023.07.18.549357.
  2. Harding EC, Chen H-J C, Schwiening A, AggarwalS, Rowley C, Swinden D, Mallucci G, Merkle FT§. Metformin may reduce dementia risk through neuroprotection not mitigation of diabetes. BioRxiv. July 2023. doi:10.1101/2023.07.18.549549.
  3. Yajie Zhao, Maria Chukanova, Katherine A Kentistou, … Florian T. Merkle, Nick J Wareham, Slave Petrovski, Steve O’Rahilly, Ken K Ong, Giles SH Yeo, John RB Perry. Protein-truncating variants in BSN are associated with severe adult-onset obesity, type 2 diabetes and fatty liver disease. medRxiv, 2023, doi: 10.1101/2023.06.14.23291368
  4. Sara KM Jorgensen, Alena Karnosova, Simone Mazzaferro, Hsiao-Jou Cortina Chen, Sarah J Robbins, Sarah Christofides, Florian T Merkle, Lenka Maletinska, David Petrik. An analogue of the Prolactin Releasing Peptide reduces obesity and promotes adult neurogenesis. BioRxiv, 2023, https://doi.org/10.1101/2023.02.28.528936
  5. Chen HC, Mazzaferro S, Tian T, Mali I, Merkle FT§. Differentiation, Transcriptomic Profiling, and Calcium Imaging of Human Hypothalamic Neurons. Curr Protoc. 2023 Jun;3(6):e786. doi: 10.1002/cpz1.786. PMID: 37272700.
  6. Macarelli V, Leventea E, Merkle FT§. Regulation of the length of neuronal primary cilia and its potential effects on signalling. Trends Cell Biol. 2023 Jun 9:S0962-8924(23)00088-0. doi: 10.1016/j.tcb.2023.05.005. Epub ahead of print. PMID: 37302961.
  7. Pantazis CB, Yang A, Lara E, McDonough JA, Blauwendraat C, Peng L, Oguro H, Kanaujiya J, Zou J, Sebesta D, Pratt G, Cross E, Blockwick J, Buxton P, Kinner-Bibeau L, Medura C, Tompkins C, Hughes S, Santiana M, Faghri F, Nalls MA, Vitale D, Ballard S, Qi YA, Ramos DM, Anderson KM, Stadler J, Narayan P, Papademetriou J, Reilly L, Nelson MP, Aggarwal S, Rosen LU, Kirwan P, Pisupati V, Coon SL, Scholz SW, Priebe T, Öttl M, Dong J, Meijer M, Janssen LJM, Lourenco VS, van der Kant R, Crusius D, Paquet D, Raulin AC, Bu G, Held A, Wainger BJ, Gabriele RMC, Casey JM, Wray S, Abu-Bonsrah D, Parish CL, Beccari MS, Cleveland DW, Li E, Rose IVL, Kampmann M, Calatayud Aristoy C, Verstreken P, Heinrich L, Chen MY, Schüle B, Dou D, Holzbaur ELF, Zanellati MC, Basundra R, Deshmukh M, Cohen S, Khanna R, Raman M, Nevin ZS, Matia M, Van Lent J, Timmerman V, Conklin BR, Johnson Chase K, Zhang K, Funes S, Bosco DA, Erlebach L, Welzer M, Kronenberg-Versteeg D, Lyu G, Arenas E, Coccia E, Sarrafha L, Ahfeldt T, Marioni JC, Skarnes WC§, Cookson MR§, Ward ME§, Merkle FT§. A reference human induced pluripotent stem cell line for large-scale collaborative studies. Cell Stem Cell. 2022 Dec 1;29(12):1685-1702.e22. doi: 10.1016/j.stem.2022.11.004. PMID: 36459969; PMCID: PMC9782786.
  8. Whole-genome analysis of human embryonic stem cells enables rational line selection based on genetic variation. Florian T Merkle§, Sulagna Ghosh, Giulio Genovese, Robert E Handsaker, Seva Kashin, Daniel Meyer, Konrad J Karczewski, Colm O’Dushlaine, Carlos Pato, Michele Pato, Daniel G MacArthur, Steven A McCarroll§, Kevin Eggan§. March 3, 2022 Cell Stem Cell volume 29(3), pages 472-486. e7 https://doi.org/10.1016/j.stem.2022.01.011
  9. The Genetic Architecture of DNA Replication Timing in Human Pluripotent Stem Cells. Qiliang Ding, Matthew M. Edwards, Michelle L. Hulke, Alexa N. Bracci, Ya Hu, Yao Tong, Xiang Zhu, Joyce Hsiao, Christine J. Charvet, Sulagna Ghosh, Robert E. Handsaker, Kevin Eggan, Florian T. Merkle, Jeannine Gerhardt, Dieter Egli, Andrew G. Clark, Amnon Koren. Nature Communications 2021 Nov 19 volume 12, Article number: 6746 https://www.nature.com/articles/s41467-021-27115-9
  10. POMC neurons functional heterogeneity relies on mTORC1 signaling. Nicolas Saucisse, Wilfrid Mazier, Vincent Simon, Elke Binder, Caterina Catania, Luigi Bellocchio, Roman A. Romanov, Isabelle Matias, Philippe Zizzari, Stephane Leon, Carmelo Quarta, Astrid Cannich, Kana Meece, Delphine Gonzales, Samantha Clark, Julia M. Becker, Giles S.H. Yeo, Florian T. Merkle, Sharon L. Wardlaw, Tibor Harkany, Federico Massa, Giovanni Marsicano, Daniela Cota. Cell Reports 2021 Oct 12;37(2):109800.doi: 10.1016/j.celrep.2021.109800. PMID: 34644574
  11. Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation. J Jerber, DD Seaton, ASE Cuomo, N Kumasaka, J Haldane, J Steer, M Patel, D Pearce, M Andersson, MJ Bonder, E Mountjoy, M Ghoussaini, MA Lancaster, HipSci Consortium, JC Marioni§, FT Merkle§,  DJ Gaffney§, O Stegle§. Nature Genetics volume 53, pages304–312(2021), https://www.nature.com/articles/s41588-021-00801-6
  12. Kirwan P, Kay RG, Brouwers B, Herranz-Pérez V, Jura M, Larraufie P, Jerber J, Pembroke J, Bartels T, White A, Gribble FM, Reimann F, Farooqi IS, O’Rahilly S, Merkle FT§. Quantitative mass spectrometry for human melanocortin peptides in vitro and in vivo suggests prominent roles for β-MSH and desacetyl α-MSH in energy homeostasis. Mol Metab. 2018 Nov;17:82-97. doi: 10.1016/j.molmet.2018.08.006. Epub 2018 Aug 21.
  13. Merkle FT, Ghosh S, Kamataki N, Mitchell J, Avior Y, Mello C, Kashin S, Mekhoubad S, Ilic D, Charlton M, Saphier G, Handsaker RE, Genovese G, Bar S, Benvenisty N, McCarroll S, Eggan K. Human pluripotent stem cells recurrently acquire and expand dominant negative P53 mutations. Nature, 2017 April 26. doi:10.1038/nature22312
  14. Merkle FT, Maroof A, Wataya T, Sasai Y, Studer L, Eggan KC, Schier AF. Generation of neuropeptidergic hypothalamic neurons from human pluripotent stem cells. Development. 2015 Feb 2;142 (4), 633-643.
  15. Merkle FT, Eggan K. Modeling human disease with pluripotent stem cells: from genome association to function. Cell Stem Cell. 2013 Jun 6;12(6):656-68. PMID: 23746975.
  16. Merkle FT, Mirzadeh Z, Alvarez-Buylla A. Mosaic organization of neural stem cells in the adult brain. Science. 2007 Jul 20;317(5836):381-4. PMID: 17615304.
  17. Merkle FT, Tramontin AD, Garcia-Verdugo JM, Alvarez-Buylla A. Radial glia give rise to adult neural stem cells in the subventricular zone. Proc Natl Acad Sci. 2004 Dec 14;101(50):17528-32. PMC536036.

§corresponding author