Predictable Engineering of Signal-Dependent Cis-Regulatory Elements

Cornwall-Scoones J, Benzinger D, Yu T, Pezzotta A, Sagner A, Gerontogianni L, Bernadet S, Finnie E, Boezio GLM, Stuart HT, Melchionda M, Inge OCK, Dumitrascu B, Briscoe J, Delás MJ.

2025

doi:10.1101/2025.03.07.642002.

From naïve pluripotency to human neural organoids through a three-dimensional morphogenetic continuum

Laterza C, Cesare E, Stuart HT, D’Ercole M, Gesualdo A, La Barbera MG, Brignani S, Ribecco C, Polli R, Frison R, Angiolillo S, Maset A, Gagliano O, Cacchiarelli D, Briscoe J, Tanaka EM, Murgia A, Elvassore N.

2024

doi:10.1101/2024.11.14.623407.

Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition.

Krammer T, Stuart HT, Gromberg E, Ishihara K, Cislo D, Melchionda M, Becerril Perez F, Wang J, Costantini E, Lehr S, Arbanas L, Hörmann A, Neumüller RA, Elvassore N, Siggia E, Briscoe J, Kicheva A, Tanaka EM.

Dev Cell, 2024

doi:10.1016/j.devcel.2024.04.021.

In vitro generation of mouse morula-like cells.

Li H, Chang L, Wu J, Huang J, Guan W, Bates LE, Stuart HT, Guo M, Zhang P, Huang B, Chen C, Zhang M, Chen J, Min M, Wu G, Hutchins AP, Silva JCR.

Dev Cell, 2023

doi:10.1016/j.devcel.2023.09.013.

Cellular population dynamics shape the route to human pluripotency.

Panariello F, Gagliano O, Luni C, Grimaldi A, Angiolillo S, Qin W, Manfredi A, Annunziata P, Slovin S, Vaccaro L, Riccardo S, Bouche V, Dionisi M, Salvi M, Martewicz S, Hu M, Cui M, Stuart H, Laterza C, Baruzzo G, Schiebinger G, Di Camillo B, Cacchiarelli D, Elvassore N.

Nat Commun, 2023

doi:10.1038/s41467-023-37270-w.

Developmental cell fate choice in neural tube progenitors employs two distinct cis-regulatory strategies.

Delás MJ, Kalaitzis CM, Fawzi T, Demuth M, Zhang I, Stuart HT, Costantini E, Ivanovitch K, Tanaka EM, Briscoe J.

Dev Cell, 2022

doi:10.1016/j.devcel.2022.11.016.

3D ECM-rich environment sustains the identity of naive human iPSCs.

Cesare E, Urciuolo A, Stuart HT, Torchio E, Gesualdo A, Laterza C, Gagliano O, Martewicz S, Cui M, Manfredi A, Di Filippo L, Sabatelli P, Squarzoni S, Zorzan I, Betto RM, Martello G, Cacchiarelli D, Luni C, Elvassore N.

Cell Stem Cell, 2022

doi:10.1016/j.stem.2022.11.011.

Human Pluripotent Stem Cell-Derived Micropatterned Ectoderm Allows Cell Sorting of Meso-Endoderm Lineages.

Yang Y, Laterza C, Stuart HT, Michielin F, Gagliano O, Urciuolo A, Elvassore N.

Front Bioeng Biotechnol, 2022

doi:10.3389/fbioe.2022.907159.

SARS-CoV-2 infection and replication in human gastric organoids.

Giobbe GG, Bonfante F, Jones BC, Gagliano O, Luni C, Zambaiti E, Perin S, Laterza C, Busslinger G, Stuart H, Pagliari M, Bortolami A, Mazzetto E, Manfredi A, Colantuono C, Di Filippo L, Pellegata AF, Panzarin V, Thapar N, Li VSW, Eaton S, Cacchiarelli D, Clevers H, Elvassore N, De Coppi P.

Nat Commun, 2021

doi:10.1038/s41467-021-26762-2.

StemBond hydrogels control the mechanical microenvironment for pluripotent stem cells.

Labouesse C, Tan BX, Agley CC, Hofer M, Winkel AK, Stirparo GG, Stuart HT, Verstreken CM, Mulas C, Mansfield W, Bertone P, Franze K, Silva JCR, Chalut KJ.

Nat Commun, 2021

doi:10.1038/s41467-021-26236-5.

Sox2 modulation increases naïve pluripotency plasticity.

Tremble KC, Stirparo GG, Bates LE, Maskalenka K, Stuart HT, Jones K, Andersson-Rolf A, Radzisheuskaya A, Koo BK, Bertone P, Silva JCR.

iScience, 2021

doi:10.1016/j.isci.2021.102153.

OCT4 induces embryonic pluripotency via STAT3 signaling and metabolic mechanisms.

Stirparo GG, Kurowski A, Yanagida A, Bates LE, Strawbridge SE, Hladkou S, Stuart HT, Boroviak TE, Silva JCR, Nichols J.

Proc Natl Acad Sci U S A, 2021

doi:10.1073/pnas.2008890118.

Distinct Molecular Trajectories Converge to Induce Naive Pluripotency.

Stuart HT, Stirparo GG, Lohoff T, Bates LE, Kinoshita M, Lim CY, Sousa EJ, Maskalenka K, Radzisheuskaya A, Malcolm AA, Alves MRP, Lloyd RL, Nestorowa S, Humphreys P, Mansfield W, Reik W, Bertone P, Nichols J, Göttgens B, Silva JCR.

Cell Stem Cell, 2019

doi:10.1016/j.stem.2019.07.009.

Exit from Naive Pluripotency Induces a Transient X Chromosome Inactivation-like State in Males.

Sousa EJ, Stuart HT, Bates LE, Ghorbani M, Nichols J, Dietmann S, Silva JCR.

Cell Stem Cell, 2018

doi:10.1016/j.stem.2018.05.001.

NANOG amplifies STAT3 activation and they synergistically induce the naive pluripotent program.

Stuart HT, van Oosten AL, Radzisheuskaya A, Martello G, Miller A, Dietmann S, Nichols J, Silva JC.

Curr Biol, 2014

doi:10.1016/j.cub.2013.12.040.

Genome-wide chromatin interactions of the Nanog locus in pluripotency, differentiation, and reprogramming.

Apostolou E, Ferrari F, Walsh RM, Bar-Nur O, Stadtfeld M, Cheloufi S, Stuart HT, Polo JM, Ohsumi TK, Borowsky ML, Kharchenko PV, Park PJ, Hochedlinger K.

Cell Stem Cell, 2013

doi:10.1016/j.stem.2013.04.013.