Publications by Tissue Repair PhD students

List of peer reviewed publications by Tissue Repair PhD students

(Authors in bold: contributions of students while studying on the Wellcome Trust Tissue Repair PhD programme)

Aleksieva N, Forbes SJ. (2019) Biliary-derived hepatocytes in chronic liver injury: Bringing new troops to the battlefield? J Hepatol 70(6):1051-1053.

Almeida RG, Pan S, Cole KLH, Williamson JM, Early JJ, Czopka T, Klingseisen A, Chan JR, Lyons DA. (2018) Myelination of Neuronal Cell Bodies when Myelin Supply Exceeds Axonal Demand. Curr Biol 28(8):1296-1305.e5.

Aloia L, McKie MA, Vernaz G, Cordero-Espinoza L, Aleksieva N, van den Ameele J, Antonica F, Font-Cunill B, Raven A, Aiese Cigliano R, Belenguer G, Mort RL, Brand AH, Zernicka-Goetz M, Forbes SJ, Miska EA, Huch M. (2019) Epigenetic remodelling licences adult cholangiocytes for organoid formation and liver regeneration. Nature Cell Biology 21:1321–1333.

Amor S, McNamara NB, Gerrits E, Marzin MC, Kooistra SM, Miron VE, Nutma E. (2022) White matter microglia heterogeneity in the CNS. Acta Neuropathol. 143(2):125-141. doi: 10.1007/s00401-021-02389-x.

Bain CC, Gibson DA, Steers NJ, Boufea K, Louwe PA, Doherty C, Gonzalez-Huici V, Gentek R, Mahalhaes-Pinto M, Shaw T, Bajenoff M, Benezech C, Walmsley SR, Dockrell DH, Saunders PTK, Batada NN, Jenkins SJ. (2020) Rate of replenishment and microenvironment contribute to the sexually dimorphic phenotype and function of peritoneal macrophages. Sci Immunol 5(48):eabc4466.

Bain CC, Louwe PA, Steers NJ, Bravo-Blas A, Hegarty LM, Pridans C, Milling SWF, MacDonald AS, Rückerl D, Jenkins SJ. (2022) CD11c identifies microbiota and EGR2-dependent MHCII⁺ serous cavity macrophages with sexually dimorphic fate in mice. Eur J Immunol. 52(8):1243-1257.

Barth ND, Subiros-Funosas R, Mendive-Tapia L, Duffin R, Shields MA, Cartwright JA, Henriques ST, Sot J, Goñi FM, Lavilla R, Marwick JA, Vermeren S, Rossi AG, Egeblad M, Dransfield I, Vendrell M. (2020) A fluorogenic cyclic peptide for imaging and quantification of drug-induced apoptosis. Nat Commun 11(1):4027.

Becker LM, Chen SH, Rodor J, de Rooij LPMH, Baker AH, Carmeliet P. (2022) ‘Deciphering endothelial heterogeneity in health and disease at single-cell resolution: progress and perspectives’. Cardiovascular Research Feb 18:cvac018

Blin G, Wisniewski D, Picart C, Thery M, Puceat M, Lowell S. (2018) Geometrical confinement controls the asymmetric patterning of brachyury in cultures of pluripotent cells. Development 145(18). pii: dev166025.

Bruton FA, Kaveh A, Ross-Stewart KM, Matrone G, Oremek MEM, Solomonidis EG, Tucker CS, Mullins JJ, Lucas CD, Brittan M, Taylor JM, Rossi AG, Denvir MA. (2022) Macrophages trigger cardiomyocyte proliferation by increasing epicardial vegfaa expression during larval zebrafish heart regeneration. Dev Cell. 57(12):1512-1528.e5.

Campbell RA, Docherty MH, Ferenbach1 DA, Mylonas KJ (2021) The role of ageing and parenchymal senescence on macrophage function and fibrosis. Front Immunol. 12:700790.

Cartwright JA, Lucas CD, Rossi AG. (2019) Inflammation resolution and the induction of granulocyte apoptosis by cyclin-dependent kinase inhibitor drugs. Front Pharmacol 10:55.

Cartwright JA, Simpson JP, Homer NZM, Rossi AG. (2023) Analysis of AT7519 as a pro-resolution compound in an acetaminophen-induced mouse model of acute inflammation by UPLC-MS/MS. J Inflamm (Lond). 20(1):20.

Cousins FL, Kirkwood PM, Saunders PT, Gibson DA. (2016) Evidence for a dynamic role for mononuclear phagocytes during endometrial repair and remodelling. Sci Rep 6:36748. 

Cousins FL, Kirkwood PM, Murray AA, Collins F, Gibson DA, Saunders PT (2016) Androgens regulate scarless repair of the endometrial "wound" in a mouse model of menstruation. FASEB J 30(8):2802-11. 

Curley M, Milne L, Smith S, Atanassova N, Rebourcet D, Darbey A, Hadoke PWF, Wells S, Smith LB. (2018) Leukemia Inhibitory Factor-Receptor is Dispensable for Prenatal Testis Development but is Required in Sertoli cells for Normal Spermatogenesis in Mice. Sci Rep 1;8(1):11532.

Darbey A, Smith LB. (2018) Deliverable transgenics & gene therapy possibilities for the testes. Mol Cell Endocrinol 15;468:81-94.

Early JJ, Cole KL, Williamson JM, Swire M, Kamadurai H, Muskavitch M, Lyons DA. (2018) An automated high-resolution in vivo screen in zebrafish to identify chemical regulators of myelination. Elife 7. pii: e35136.

Elder SS, Emmerson E. (2020) Senescent cells and macrophages: key players for regeneration? Open Biol. 10(12):200309.

Elder S, Cholewa-Waclaw J, Emmerson E. (2021) Interrogating Cell-Cell Interactions in the Salivary Gland via Ex Vivo Live Cell Imaging. J Vis Exp. Nov 17;(201).

Felton JM, Dorward DA, Cartwright JA, Potey PM, Robb CT, Gui J, Craig RW, Schwarze J, Haslett C, Duffin R, Dransfield I, Lucas CD, Rossi AG. (2020) Mcl-1 protects eosinophils from apoptosis and exacerbates allergic airway inflammation. Thorax. 75(7):600-605.

Ferrari Bardile C, Garcia-Miralles M, Caron NS, Rayan NA, Langley SR, Harmston N, Rondelli AM, Teo RTY, Waltl S, Anderson LM, Bae HG, Jung S, Williams A, Prabhakar S, Petretto E, Hayden MR, Pouladi MA. (2019) Intrinsic mutant HTT-mediated defects in oligodendroglia cause myelination deficits and behavioral abnormalities in Huntington disease. Proc Natl Acad Sci U S A 116(19):9622-9627.

Ferreira-Gonzalez S, Man TY, …, Dwyer B, Aleksieva N, Boulter L, …, Forbes SJ. Senolytic treatment preserves biliary regenerative capacity lost through cellular senescence during cold storage. (2022) Sci Transl Med. 14(674):eabj4375.

Gadd VL, Aleksieva N, Forbes SJ (2020) Epithelial plasticity during liver injury and regeneration. Cell Stem Cell 27(4):557-573

Haideri SS, McKinnon AC, Taylor AH, Kirkwood P, Starkey Lewis PJ, O'Duibhir E, Vernay B, Forbes S, Forrester LM. (2017) Injection of embryonic stem cell derived macrophages ameliorates fibrosis in a murine model of liver injury. NPJ Regen Med 23;2:14.

Hawley CA, Rojo R, Raper A, Sauter KA, Lisowski ZM, Grabert K, Bain CC, Davis GM, Louwe PA, Ostrowski MC, Hume DA, Pridans C, Jenkins SJ. (2018) Csf1r-mApple transgene expression and ligand binding in vivo reveal dynamics of CSF1R expression within the mononuclear phagocyte system. J Immunol 200(6):2209-2223.

Hegarty LM, Jones GR, Bain CC. (2023) Macrophages in intestinal homeostasis and inflammatory bowel disease. Nat Rev Gastroenterol Hepatol. doi: 10.1038/s41575-023-00769-0.

Heideveld E, Horcas-Lopez M, Lopez-Yrigoyen M, Forrester LM, Cassetta L, Pollard JW. (2020) Methods for macrophage differentiation and in vitro generation of human tumor associated-like macrophages. Methods Enzymol 632:113-131.

Ho GT, Cartwright JA, Thompson EJ, Bain CC, Rossi AG. (2020) Resolution of inflammation and gut repair in IBD: translational steps towards complete mucosal healing. Inflamm Bowel Dis. 26(8):1131-1143.

Jarman EJ, Horcas-Lopez M, Waddell SH, MacMaster S, Gournopanos K, Soong DYH, Musialik KI, Tsokkou P, Ng ME, Cambridge WA, Wilson DH, Kagey MH, Newman W, Pollard JW, Boulter L. (2022) DKK1 drives immune suppressive phenotypes in intrahepatic cholangiocarcinoma and can be targeted with anti-DKK1 therapeutic DKN-01. Liver Int. 43(1):208-220.

Kauts ML, De Leo B, Rodríguez-Seoane C, Ronn R, Glykofrydis F, Maglitto A, Kaimakis P, Basi M, Taylor H, Forrester L, Wilkinson AC, Göttgens B, Saunders P, Dzierzak E. (2018) Rapid mast cell generation from Gata2 reporter pluripotent stem cells. Stem Cell Reports 11(4):1009-1020.

Kapeni C, Nitsche L, Kilpatrick AM, Wilson NK, Xia K, Mirshekar-Syahkal B, Chandrakanthan V, Malouf C, Pimanda JE, Göttgens B, Kirschner K, Tomlinson SR, Ottersbach K. (2022) p57Kip2 regulates embryonic blood stem cells by controlling sympathoadrenal progenitor expansion. Blood 140(5):464-477.

Klingseisen A, Ristoiu AM, Kegel L, Sherman DL, Rubio-Brotons M, Almeida RG, Koudelka S, Benito-Kwiecinski SK, Poole RJ, Brophy PJ, Lyons DA. (2019) Oligodendrocyte Neurofascin independently regulates both myelin targeting and sheath growth in the CNS. Dev Cell 51(6):730-744.e6.

Li Z, Solomonidis EG, Meloni M, Taylor RS, Duffin R, Dobie R, Magalhaes MS, Henderson BEP, Louwe PA, D'Amico G, Hodivala-Dilke KM, Shah AM, Mills NL, Simons BD, Gray GA, Henderson NC, Baker AH, Brittan M. (2019) Single-cell transcriptome analyses reveal novel targets modulating cardiac neovascularization by resident endothelial cells following myocardial infarction. Eur Heart J. 40(30):2507-2520

Li Z, Ross Stewart KM, Bruton FA, Denvir MA, Brittan M. (2022) Isolation of Cardiac Endothelial Cells for Transcriptomic Analysis of the Zebrafish and Mouse Heart. Methods Mol Biol. 2441:297-309.

Lopez-Yrigoyen M, Fidanza A, Cassetta L, Axton RA, Taylor AH, Meseguer-Ripolles J, Tsakiridis A, Wilson V, Hay DC, Pollard JW, Forrester LM. (2018) A human iPSC line capable of differentiating into functional macrophages expressing ZsGreen: a tool for the study and in vivo tracking of therapeutic cells. Royal Society 373(1750). pii: 20170219.

Lopez-Yrigoyen M, May A, Ventura T, Taylor H, Fidanza A, Cassetta L, Pollard JW, Forrester LM. (2020) Production and characterization of human macrophages from pluripotent stem cells. J Vis Exp Apr 16;158.

Louwe PA, Badiola Gomez L, Webster H, Perona-Wright G, Bain CC, Forbes SJ, Jenkins SJ. (2021) Recruited macrophages that colonize the post-inflammatory peritoneal niche convert into functionally divergent resident cells. Nat Commun. 12(1):1770.

Louwe PA, Forbes SJ, Benezech C, Pridans C, Jenkins SJ. (2022) Cell origin and niche availability dictate the capacity of peritoneal macrophages to colonize the cavity and omentum. Immunology. 166(4):458-474.

Lucendo-Villarin B, Filis P, Swortwood MJ, Huestis MA, Meseguer-Ripolles J, Cameron K, Iredale JP, O'Shaughnessy PJ, Fowler PA, Hay DC. (2017) Modelling foetal exposure to maternal smoking using hepatoblasts from pluripotent stem cells. Archives of Toxicology 91;11:3633–3643.

Lucendo-Villarin B, Rashidi H, Alhaque S, Fischer L, Meseguer-Ripolles J, Wang Y, O'Farrelly C, Themis M, Hay DC. (2019) Serum free production of three-dimensional human hepatospheres from pluripotent stem cells. J Vis Exp. 2019 Jul 20;(149).

Lyall MJ, Cartier J, Thomson JP, Cameron K, Meseguer-Ripolles J, O'Duibhir E, Szkolnicka D, Villarin BL, Wang Y, Blanco GR, Dunn WB, Meehan RR, Hay DC, Drake AJ. (2018) Modelling non-alcoholic fatty liver disease in human hepatocyte-like cells. Royal Society 373(1750). pii: 20170362.

Malaguti M, Portero Migueles R, Annoh J, Sadurska D, Blin G, Lowell S. (2022) SyNPL: Synthetic Notch pluripotent cell lines to monitor and manipulate cell interactions in vitro and in vivo. Development. 149(12):dev200226.

Mapperley C, van de Lagemaat LN, Lawson H, Tavosanis A, Paris J, Campos J, Wotherspoon D, Durko J, Sarapuu A, Choe J, Ivanova I, Krause DS, von Kriegsheim A, Much C, Morgan M, Gregory RI, Mead AJ, O'Carroll D, Kranc KR. (2021) The mRNA m6A reader YTHDF2 suppresses proinflammatory pathways and sustains hematopoietic stem cell function. J Exp Med 218(3):e20200829.

Markose D, Kirkland P, Ramachandran P, Henderson NC. (2018) Immune cell regulation of liver regeneration and repair. J Immunology and Regenerative Medicine Volume 2:1-10.

May A, Forrester LM.  (2020) The erythroblastic island niche: modeling in health, stress, and disease. Exp Hematol. Sep 7:S0301-472X(20)30547-6.

May A, Ventura T, Fidanza A, ..., Bieker JJ, Forrester LM. (2023) Modelling the erythroblastic island niche of dyserythropoietic anaemia type IV patients using induced pluripotent stem cells. Front Cell Dev Biol. 11:1148013.

McCowan J, Fercoq F, Kirkwood PM, T'Jonck W, Hegarty LM, Mawer CM, ... Walmsley SR, Dockrell DH, Saunders PTK, Carlin LM, Bain CC. (2021) The transcription factor EGR2 is indispensable for tissue-specific imprinting of alveolar macrophages in health and tissue repair. Sci Immunol 19;6(65):eabj2132.

McHugh BJ, Stephen J, Robb CT, Fox S, Kipari T, Cartwright JA, Haslett C, Duffin R, Lucas CD and Rossi AG. (2022) Inhibition of Cyclin-Dependent Kinase 9 downregulates cytokine production without detrimentally affecting human monocyte-derived macrophage viability. Front. Cell Dev. Biol., 26.

McKendrick JG, Jones GR, Elder SS, Watson E, T'Jonck W, Mercer E, Magalhaes MS, Rocchi C, Hegarty LM, Johnson AL, ... Gentek R, Bain CC, Emmerson E. (2023) CSF1R-dependent macrophages in the salivary gland are essential for epithelial regeneration after radiation-induced injury. 8(89):eadd4374

McNamara NB, Munro DAD, B, … Williams A, Priller J, Miron VE. (2023) Microglia regulate central nervous system myelin growth and integrity. Nature. 613(7942):120-129.

McNamara NB, Miron VE. (2021) Replenishing our mind orchards: Enhancing myelin renewal to rescue cognition in Alzheimer's disease. Neuron 109(14):2204-2206.

McNamara NB, Miron VE. (2020) Microglia in developing white matter and perinatal brain injury. Neuroscience Letters 714:134539.

Meseguer-Ripolles J, Khetani SR, Blanco JG, Iredale M, Hay DC. (2017) Pluripotent stem cell-derived human tissue: Platforms to evaluate drug metabolism and safety. AAPS J 20(1):20.

Meseguer-Ripolles J, Lucendo-Villarin B, Wang Y, Hay DC. (2018) Semi-automated production of hepatocyte like cells from pluripotent stem cells. J Vis Exp (137) e57995, doi:10.3791/57995.

Meseguer-Ripolles J, Wang Y, Sorteberg A, Sharma A, Ding NL, Lucendo-Villarin B, Kramer P, Segeritz CP, Hay DC. (2020) Hepatic progenitor specification from pluripotent stem cells using a defined differentiation system. Journal of Visualized Experiments : Jove 10 May;159.

Minnis-Lyons SE, Ferreira-González S, Aleksieva N, Man TY, Gadd VL, Williams MJ, Guest RV, Lu WY, Dwyer BJ, Jamieson T, Nixon C, Van Hul N, Lemaigre FP, McCafferty J, Leclercq IA, Sansom OJ, Boulter L, Forbes SJ. (2021) Notch-IGF1 signaling during liver regeneration drives biliary epithelial cell expansion and inhibits hepatocyte differentiation. Sci Signal 14(688):eaay9185.

Monteiro JP, Rodor J, …. , Chen S-H, Brandes RP, Baker A. (2021) MIR503HG loss promotes endothelial-to-mesenchymal transition in vascular disease. Circ Res 128;8.

Mylonas KJ, O'Sullivan ED, Humphries D, Baird DP, Docherty MH, Neely SA, Krimpenfort PJ, Melk A, Schmitt R, Ferreira-Gonzalez S, Forbes SJ, Hughes J, Ferenbach DA. (2021) Cellular senescence inhibits renal regeneration after injury in mice, with senolytic treatment promoting repair. Sci Transl Med 19;13(594):eabb0203.

Neely SA, Lyons DA. (2021) Insights Into Central Nervous System Glial Cell Formation and Function From Zebrafish. Front Cell Dev Biol. 9:754606.

Neely SA, Williamson JM, Klingseisen A, Zoupi L, Early JJ, Williams A, Lyons DA. (2022) New oligodendrocytes exhibit more abundant and accurate myelin regeneration than those that survive demyelination. Nat Neurosci. 25(4):415-420.

O'Sullivan ED, Mylonas KJ, Xin C, Baird DP, Carvalho C, Docherty MH, Campbell R, …, Ferenbach DA. (2023) Indian Hedgehog release from TNF-activated renal epithelia drives local and remote organ fibrosis. Sci Transl Med. 15(698):eabn0736.

Paris J, Morgan M, Campos J, Spencer GJ, Shmakova A, Ivanova I, Mapperley C, Lawson H, Wotherspoon DA, …, O'Carroll D, Kranc KR. (2019) Targeting the RNA m6A reader YTHDF2 selectively compromises cancer stem cells in acute myeloid leukemia. Cell Stem Cell pii: S1934-5909(19)30120-1.

Pastore N, Huynh T, ..., Mutarelli M, Aleksieva N, ..., Forbes SJ, Ballabio A (2020). TFEB regulates murine liver cell fate during development and regeneration. Nat Commun 11(1):2461.

Patel SH, O'Hara L, Atanassova N, Smith SE, Curley MK, Rebourcet D, Darbey AL, Gannon AL, Sharpe RM, Smith LB. (2017) Low-dose tamoxifen treatment in juvenile males has long-term adverse effects on the reproductive system: implications for inducible transgenics. Sci Rep 21;7(1):8991.

Popravko A, Mackintosh L, Dzierzak E. (2024) A life-time of hematopoietic cell function: ascent, stability, and decline. FEBS Lett. Mar 5. doi: 10.1002/1873-3468.14843.

Quick S, Moss J, Rajani RM, Williams A. (2020) A vessel for change: endothelial dysfunction in cerebral small vessel disease. Trends Neurosci S0166-2236(20)30266-6

Rajani RM, Quick S, Ruigrok SR, Graham D, Harris SE, Verhaaren BFJ, Fornage M, Seshadri S, Atanur SS, Dominiczak AF, Smith C, Wardlaw JM, Williams A. (2018) Reversal of endothelial dysfunction reduces white matter vulnerability in cerebral small vessel disease in rats. Sci Transl Med 10(448) pii: eaam9507.

Rao C, Malaguti M, Mason JO, Lowell S. (2020) The transcription factor E2A drives neural differentiation in pluripotent cells. Development 22;147(12):dev184093.

Rebourcet D, Darbey A, Monteiro A, Soffientini U, Tsai YT, Handel I, Pitetti JL, Nef S, Smith LB, O'Shaughnessy PJ.  (2017) Sertoli cell number defines and predicts germ and leydig cell population sizes in the adult mouse testis. Endocrinology 1;158(9):2955-2969.

Rebourcet D, Darbey A, Curley M, O'Shaughnessy P, Smith LB. (2018) Testicular cell selective ablation using diphtheria toxin receptor transgenic mice. Methods Mol Biol 1748:203-228.

Riley SE, Feng Y, Hansen CG. (2022)  Hippo-Yap/Taz signalling in zebrafish regeneration. NPJ Regen Med. 7(1):9.

Rodor J, Chen SH, Scanlon JP, Monteiro JP, Caudrillier A, Sweta S, Stewart KR, …,  Brittan M, Baker AH. (2021) Single-cell RNA-seq profiling of mouse endothelial cells in response to pulmonary arterial hypertension. Cardiovasc Res. 118(11): 2519–2534.

Ross Stewart KM, Walker SL, Baker AH, Riley PR, Brittan M. (2022) Hooked on heart regeneration: the zebrafish guide to recovery. Cardiovasc Res. 118(7):1667-1679.

Seeker LA, Bestard-Cuche N, Jäkel S, Kazakou NL, …. Williams A. (2023) Brain matters: unveiling the distinct contributions of region, age, and sex to glia diversity and CNS function. Acta Neuropathol Commun. 11(1):84.

Shaw I, Rider S, Mullins J, Hughes J, Péault B. (2018) Pericytes in the renal vasculature: roles in health and disease. Nat Rev Nephrol 14(8):521-534.

Starkey Lewis P, Campana L, Aleksieva N, Cartwright JA, Mackinnon A, O'Duibhir E, Kendall T, Vermeren M, Thomson A, Gadd V, Dwyer B, Aird R, Man TY, Rossi AG, Forrester L, Park BK, Forbes SJ. (2020) Alternatively activated macrophages promote resolution of necrosis following acute liver injury. J Hepatol. Mar 10. pii: S0168-8278(20)30133-1.

Stefanska A, Kenyon C, Christian HC, Buckley C, Shaw I, Mullins JJ, Péault B. (2016) Human kidney pericytes produce renin. Kidney Int 90(6):1251-1261.

Vezzani B, Shaw I, Lesme H, Yong L, Khan N, Tremolada C, Péault B. (2018) Higher pericyte content and secretory activity of microfragmented human adipose tissue compared to enzymatically derived stromal vascular fraction. Stem Cells Transl Med 7(12):876-886.

Vink CS, Popravko A, Dzierzak E. (2023) De novo hematopoietic (stem) cell generation - A differentiation or stochastic process? Curr Opin Cell Biol. 85:102255.

Wang Y, Alhaque S, Cameron K, Meseguer-Ripolles J, Lucendo-Villarin B, Rashidi H, Hay DC. (2017) Defined and scalable generation of hepatocyte-like cells from human pluripotent stem cells. J Vis Exp (121), e55355, doi:10.3791/55355.

Wang Y, Tatham MH, Schmidt-Heck W, Swann C, Singh-Dolt K, Meseguer-Ripolles J, Lucendo-Villarin B,  Kunath T, Rudd TR, Smith AJH, Hengstler JG, Godoy P, Hay RT, Hay DC. (2019) Multiomics analyses of HNF4α protein domain function during human pluripotent stem cell differentiation. iScience 16:206-217. doi: 10.1016/j.isci.2019.05.028.

Williamson JM, Lyons DA. (2018) Myelin dynamics throughout life: An ever-changing landscape? Front Cell Neurosci 12:424. 

Williamson JM, Lyons DA, Almeida RG. (2019) Manipulating neuronal activity in the developing zebrafish spinal cord to investigate adaptive myelination. Methods Mol Biol 1936:211-225.

Wisniewski D, Lowell S, Blin G. (2019) Mapping the emergent spatial organization of mammalian cells using micropatterns and quantitative imaging. J Vis Exp (146) e59634, doi:10.3791/59634.

Zaidan N, Nitsche L, Diamanti E, Hannah R, Fidanza A, Wilson NK, Forrester LM, Göttgens B, Ottersbach K. (2022) Endothelial-specific Gata3 expression is required for hematopoietic stem cell generation. Stem Cell Reports. 2022;17(8):1788-1798.