A selection of recent stem cell papers from members of the Center for Stem Cell Biology is provided below:

Li J, D Ankun, Saydaminova K, Chang H, Wang G, Ochiai H, Yamamoto T, Pertsinidis A. Single-Molecule Nanoscopy Elucidates RNA Polymerase II Transcription at Single Genes in Live Cells. Cell. 2019 May 27. pii: S0092-8674(19)30557-4. doi: 10.1016/j.cell.2019.05.029. [Epub ahead of print].

Li QV, Dixon G, Verma N, Rosen BP, Gordillo M, Luo R, Xu C, Wang Q, Soh CL, Yang D, Crespo M, Shukla A, Xiang Q, Dündar F, Zumbo P, Witkin M, Koche R, Betel D, Chen S, Massagué J, Garippa R, Evans T, Beer MA, Huangfu D. Genome-scale screens identify JNK-JUN signaling as a barrier for pluripotency exit and endoderm differentiation. Nat Genet. 2019 May 20. doi: 10.1038/s41588-019-0408-9. [Epub ahead of print].

Nowotschin S, Setty M, Kuo YY, Liu V, Garg V, Sharma R, Simon CS, Saiz N, Gardner R, Boutet SC, Church DM, Hoodless PA, Hadjantonakis AK, Pe’er D. The emergent landscape of the mouse gut endoderm at single-cell resolution. Nature. 2019 Apr 8. doi: 10.1038/s41586-019-1127-1. [Epub ahead of print].

Tchieu J, Calder EL, Guttikonda SR, Gutzwiller EM, Aromolaran KA, Steinbeck JA, Goldstein PA, Studer L. NFIA is a gliogenic switch enabling rapid derivation of functional human astrocytes from pluripotent stem cells. Nat Biotechnol. 2019 Mar;37(3):267-275. doi: 10.1038/s41587-019-0035-0. Epub 2019 Feb 25. DOI: 10.1038/s41587-019-0035-0

Park SM, Cho H, Thornton AM, Barlowe TS, Chou T, Chhangawala S, Fairchild L, Taggart J, Chow A, Schurer A, Gruet A, Witkin MD, Kim JH, Shevach EM, Krivtsov A, Armstrong SA, Leslie C, Kharas MG. IKZF2 Drives Leukemia Stem Cell Self-Renewal and Inhibits Myeloid Differentiation. Cell Stem Cell. 2019 Jan 3;24(1):153-165.e7. doi: 10.1016/j.stem.2018.10.016.

Smith, RC, Tabar, V. Constructing and Deconstructing Cancers using Human Pluripotent Stem Cells and Organoids. Cell Stem Cell. 2019 Jan 3;24(1):12-24. doi: 10.1016/j.stem.2018.11.012.

Finley LWS, Vardhana SA, Carey BW, Alonso-Curbelo D, Koche R, Chen Y, Wen D, King B, Radler MR, Rafii S, Lowe SW, Allis CD, Thompson CB. Pluripotency transcription factors and Tet1/2 maintain Brd4-independent stem cell identity. Nat Cell Biol. 2018 May;20(5):565-574. doi: 10.1038/s41556-018-0086-3.

Morgani SM, Metzger JJ, Nichols J, Siggia ED, Hadjantonakis AK. Micropattern differentiation of mouse pluripotent stem cells recapitulates embryo regionalized cell fate patterning. Elife. 2018 Feb 7;7. pii: e32839. doi: 10.7554/eLife.32839.

Verma N, Pan H, Doré LC, Shukla A, Li QV, Pelham-Webb B, Teijeiro V, González F, Krivtsov A, Chang CJ, Papapetrou EP, He C, Elemento O, Huangfu D. TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells. Nat Genet. 2018 Jan;50(1):83-95. doi: 10.1038/s41588-017-0002-y.

Vu LP, Pickering BF, Cheng Y, Zaccara S, Nguyen D, Minuesa G, Chou T, Chow A, Saletore Y, MacKay M, Schulman J, Famulare C, Patel M, Klimek VM, Garrett-Bakelman FE, Melnick A, Carroll M, Mason CE, Jaffrey SR, Kharas MG. The N₆-methyladenosine (m₆A)-forming enzyme METTL3 controls myeloid differentiation of normal hematopoietic and leukemia cells. Nat Med. 2017 Nov;23(11):1369-1376. doi: 10.1038/nm.4416.

Tchieu J, Zimmer B, Fattahi F, Amin S, Zeltner N, Chen S, Studer L. A Modular Platform for Differentiation of Human PSCs into All Major Ectodermal Lineages. Cell Stem Cell. 2017 Sep 7;21(3):399-410.e7. doi: 10.1016/j.stem.2017.08.015.

Wojcinski A, Lawton AK, Bayin NS, Lao Z, Stephen DN, Joyner AL. Cerebellar granule cell replenishment postinjury by adaptive reprogramming of Nestin₊ progenitors. Nat Neurosci. 2017 Oct;20(10):1361-1370. doi: 10.1038/nn.4621.

Zhou T, Tan L, Cederquist GY, Fan Y, Hartley BJ, Mukherjee S, Tomishima M, Brennand KJ, Zhang Q, Schwartz RE, Evans T, Studer L, Chen S. High-Content Screening in hPSC-Neural Progenitors Identifies Drug Candidates that Inhibit Zika Virus Infection in Fetal-like Organoids and Adult Brain. Cell Stem Cell. 2017 Jul 19. pii: S1934-5909(17)30279-5. doi: 10.1016/j.stem.2017.06.017

Vu LP, Prieto C, Amin EM, Chhangawala S, Krivtsov A, Calvo-Vidal MN, Chou T, Chow A, Minuesa G, Park SM, Barlowe TS, Taggart J, Tivnan P, Deering RP, Chu LP, Kwon JA, Meydan C, Perales-Paton J, Arshi A, Gönen M, Famulare C, Patel M, Paietta E, Tallman MS, Lu Y, Glass J, Garret-Bakelman FE, Melnick A, Levine R, Al-Shahrour F, Järås M, Hacohen N, Hwang A, Garippa R, Lengner CJ, Armstrong SA, Cerchietti L, Cowley GS, Root D, Doench J, Leslie C, Ebert BL, Kharas MG. Functional screen of MSI2 interactors identifies an essential role for SYNCRIP in myeloid leukemia stem cells. Nat Genet. 2017 Jun;49(6):866-875. doi: 10.1038/ng.3854.

Kang M, Garg V, Hadjantonakis AK. Lineage Establishment and Progression within the Inner Cell Mass of the Mouse Blastocyst Requires FGFR1 and FGFR2. Dev Cell. 2017 Jun 5;41(5):496-510.e5. doi: 10.1016/j.devcel.2017.05.003.

Shi ZD, Lee K, Yang D, Amin S, Verma N, Li QV, Zhu Z, Soh CL, Kumar R, Evans T, Chen S, Huangfu D. Genome Editing in hPSCs Reveals GATA6 Haploinsufficiency and a Genetic Interaction with GATA4 in Human Pancreatic Development. Cell Stem Cell. 2017 May 4;20(5):675-688.e6. doi: 10.1016/j.stem.2017.01.001.

Qi Y, Zhang XJ, Renier N, Wu Z, Atkin T, Sun Z, Ozair MZ, Tchieu J, Zimmer B, Fattahi F, Ganat Y, Azevedo R, Zeltner N, Brivanlou AH, Karayiorgou M, Gogos J, Tomishima M, Tessier-Lavigne M, Shi SH, Studer L. Combined small-molecule inhibition accelerates the derivation of functional cortical neurons from human pluripotent stem cells. Nat Biotechnol. 2017 Jan 23. doi: 10.1038/nbt.3777

Wang Q, Zou Y, Nowotschin S, Kim SY, Li QV, Soh CL, Su J, Zhang C, Shu W, Xi Q, Huangfu D, Hadjantonakis AK, Massagué J. The p53 Family Coordinates Wnt and Nodal Inputs in Mesendodermal Differentiation of Embryonic Stem Cells. Cell Stem Cell. 2016 Nov 9. pii: S1934-5909(16)30342-3. doi: 10.1016/j.stem.2016.10.002

Zeltner N, Fattahi F, Dubois NC, Saurat N, Lafaille F, Shang L, Zimmer B, Tchieu J, Soliman MA, Lee G, Casanova JL, Studer L. Capturing the biology of disease severity in a PSC-based model of familial dysautonomia. Nat Med. 2016 Nov 14. doi: 10.1038/nm.4220.

Sultan KT, Han Z, Zhang XJ, Xianyu A, Li Z, Huang K, Shi SH. Clonally Related GABAergic Interneurons Do Not Randomly Disperse but Frequently Form Local Clusters in the Forebrain. Neuron. 2016 Oct 5;92(1):31-44. doi: 10.1016/j.neuron.2016.09.033

Policy: Global standards for stem-cell research. Kimmelman J, Hyun I, Benvenisty N, Caulfield T, Heslop HE, Murry CE, Sipp D, Studer L, Sugarman J, Daley GQ. Nature. 2016 May 12;533(7603):311-3. doi: 10.1038/533311a. No abstract available.  

Genome Editing of Lineage Determinants in Human Pluripotent Stem Cells Reveals Mechanisms of Pancreatic Development and Diabetes. Zhu Z, Li QV, Lee K, Rosen BP, González F, Soh CL, Huangfu D. Cell Stem Cell. 2016 Apr 27. pii: S1934-5909(16)30002-9. doi: 10.1016/j.stem.2016.03.015. [Epub ahead of print]

Tan X, Liu WA, Zhang XJ, Shi W, Ren SQ, Li Z, Brown KN, Shi SH. Vascular Influence on Ventral Telencephalic Progenitors and Neocortical Interneuron Production. Dev Cell. 2016 Mar 21;36(6):624-38. doi: 10.1016/j.devcel.2016.02.023.

Deriving human ENS lineages for cell therapy and drug discovery in Hirschsprung disease. Fattahi F, Steinbeck JA, Kriks S, Tchieu J, Zimmer B, Kishinevsky S, Zeltner N, Mica Y, El-Nachef W Zhao H de Stanchina E Gershon MD, Grikscheit TC, Chen S, Studer L. Nature. 2016 Feb 10. doi: 10.1038/nature16951.

Programming and Reprogramming Cellular Age in the Era of Induced Pluripotency. Studer L, Vera E, Cornacchia D. Cell Stem Cell. 2015 Jun 4;16(6):591-600. doi: 10.1016/j.stem.2015.05.004. Review.

Inside-Out Radial Migration Facilitates Lineage-Dependent Neocortical Microcircuit Assembly. He S, Li Z, Ge S, Yu YC, Shi SH. Neuron. 2015 Jun 3;86(5):1159-1166. doi: 10.1016/j.neuron.2015.05.002.

Moving Stem Cells to the Clinic: Potential and Limitations for Brain Repair. Steinbeck JA, Studer L. Neuron. 2015 Apr 8;86(1):187-206. doi: 10.1016/j.neuron.2015.03.002.

New Cell Sources for T Cell Engineering and Adoptive Immunotherapy. Themeli M, Rivière I, Sadelain M. Cell Stem Cell. 2015 Apr 2;16(4):357-366. doi: 10.1016/j.stem.2015.03.011.

Human Embryonic Stem Cell-Derived Oligodendrocyte Progenitors Remyelinate the Brain and Rescue Behavioral Deficits following Radiation. Piao J, Major T, Auyeung G, Policarpio E, Menon J, Droms L, Gutin P, Uryu K, Tchieu J, Soulet D, Tabar V. Cell Stem Cell. 2015 Feb 5;16(2):198-210. doi: 10.1016/j.stem.2015.01.004.

Lineage specificity of primary cilia in the mouse embryo. Bangs FK, Schrode N, Hadjantonakis AK, Anderson KV. Nat Cell Biol. 2015 Jan 19. doi: 10.1038/ncb3091.

Optogenetics enables functional analysis of human embryonic stem cell–derived grafts in a Parkinson’s disease model. Steinbeck, JA, Choi SJ, Mrejeru A, Ganat Y, Deisseroth K, Sulzer D, Mosharov EV, Studer L. Nature Biotechnology (2015) doi:10.1038/nbt.3124

Deterministic progenitor behavior and unitary production of neurons in the neocortex. Gao P, Postiglione MP, Krieger TG, Hernandez L, Wang C, Han Z, Streicher C, Papusheva E, Insolera R, Chugh K, Kodish O, Huang K, Simons BD, Luo L8, Hippenmeyer S, Shi SH. Cell. 2014 Nov 6;159(4):775-88. doi: 10.1016/j.cell.2014.10.027.

Use of human embryonic stem cells to model pediatric gliomas with H3.3K27M histone mutation. Funato K, Major, T, Lewis PW, Allis CD and Tabar, V. Science DOI: 10.1126/science.1253799.

Cortical neurogenesis in the absence of centrioles. Insolera R, Bazzi H, Shao W, Anderson KV, Shi SH. Nat Neurosci. 2014 Nov;17(11):1528-35. doi: 10.1038/nn.3831. Epub 2014 Oct 5.

Distinct lineage-dependent structural and functional organization of the hippocampus. Xu HT, Han Z, Gao P, He S, Li Z, Shi W, Kodish O, Shao W, Brown KN, Huang K, Shi SH. Cell. 2014 Jun 19;157(7):1552-64. doi: 10.1016/j.cell.2014.03.067.

An iCRISPR Platform for Rapid, Multiplexable, and Inducible Genome Editing in Human Pluripotent Stem Cells.González F, Zhu Z, Shi ZD, Lelli K, Verma N, Li QV, Huangfu D. Cell Stem Cell. 2014 Jun 11. pii: S1934-5909(14)00205-7. doi: 10.1016/j.stem.2014.05.018. [Epub ahead of print]

Metastatic Stem Cells: Sources, Niches, and Vital Pathways. Oskarsson T, Batlle E, Massagué J. Cell Stem Cell. 2014 Mar 6;14(3):306-321. doi: 10.1016/j.stem.2014.02.002. Review.

Serpins promote cancer cell survival and vascular co-option in brain metastasis. Valiente M, Obenauf AC, Jin X, Chen Q, Zhang XH, Lee DJ, Chaft JE, Kris MG, Huse JT, Brogi E, Massagué J. Cell. 2014 Feb 27;156(5):1002-16. doi: 10.1016/j.cell.2014.01.040.

Pluripotent stem cells in regenerative medicine: challenges and recent progress. Tabar V, Studer L. Nat Rev Genet. 2014 Jan 17;15(2):82-92. doi: 10.1038/nrg3563.

Human iPSC-Based Modeling of Late-Onset Disease via Progerin-Induced Aging.  Miller JD, Ganat YM, Kishinevsky S, Bowman RL, Liu B, Tu ET, Mandal PJ, Vera E, Shim J-w, Kriks S, Taldone T, Fusaki N, Tomishima MJ, Krainc D, Milner TA, Rossi DJ, Studer L. Cell Stem Cell, Volume 13, Issue 6, 691-705, 5 December 2013. Copyright  2013 Elsevier Inc. All rights reserved. 10.1016/j.stem.2013.11.006

Specification of Functional Cranial Placode Derivatives from Human Pluripotent Stem Cells.  Dincer Z, Piao J, Niu L, Ganat Y, Kriks S, Zimmer B, Shi SH, Tabar V, Studer L. Cell Rep. 2013 Nov 25. pii: S2211-1247(13)00647-5. doi: 10.1016/j.celrep.2013.10.048. [Epub ahead of print]

Generation of tumor-targeted human T lymphocytes from induced pluripotent stem cells for cancer therapy. Themeli M, Kloss CC, Ciriello G, Fedorov VD, Perna F, Gonen M, Sadelain M.  Nat Biotechnol. 2013 Aug 11. doi: 10.1038/nbt.2678. [Epub ahead of print]

Directed differentiation and functional maturation of cortical interneurons from human embryonic stem cells. Maroof AM, Keros S, Tyson JA, Ying SW, Ganat YM, Merkle FT, Liu B, Goulburn A, Stanley EG, Elefanty AG, Widmer HR, Eggan K, Goldstein PA, Anderson SA, Studer L. Cell Stem Cell. 2013 May 2;12(5):559-72. doi: 10.1016/j.stem.2013.04.008.

Nrf2 regulates haematopoietic stem cell function. Tsai JJ, Dudakov JA, Takahashi K, Shieh JH, Velardi E, Holland AM, Singer NV, West ML, Smith OM, Young LF, Shono Y, Ghosh A, Hanash AM, Tran HT, Moore MA, van den Brink MR. Nat Cell Biol. 2013 Mar;15(3):309-16. doi: 10.1038/ncb2699. Epub 2013 Feb 24.

Homologous recombination DNA repair genes play a critical role in reprogramming to a pluripotent state. González F, Georgieva D, Vanoli F, Shi ZD, Stadtfeld M, Ludwig T, Jasin M, Huangfu D. Cell Rep. 2013 Mar 28;3(3):651-60. doi: 10.1016/j.celrep.2013.02.005. Epub 2013 Mar 7.

Human pluripotent stem cells: an emerging model in developmental biology. Zhu Z, Huangfu D. Development. 2013 Feb;140(4):705-17. doi: 10.1242/dev.086165.