Biology & Life Sciences

Editor’s Picks: Stem Cell Research

Published May 25, 2018 Curated Collections

Stem cell research covers a broad range of topics, from disease modelling to cellular plasticity and reprogramming. This diversity is highlighted in the program for the Annual Meeting for the International Society for Stem Cell Research (ISSCR). Below, PLOS staff editors Eric Martens, Ines Alvarez-Garcia, and Jenna Wilson share recent PLOS articles highlighting many facets of stem cell research. PLOS welcomes submissions in these fields.

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The Pluripotent State
Disease Modeling and Drug Screening
Stem Cell Differentiation
Computational Modeling Approaches
Stem Cell Heterogeneity

The Pluripotent State

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10.1371/journal.pone.0154770

PLOS ONE PI3K/AKT Signaling Pathway Is Essential for Survival of Induced Pluripotent Stem Cells
May 3, 2016 Amir M. Hossini, Annika S. Quast, Michael Plötz, Katharina Grauel, Tarik Exner, Judit Küchler, Harald Stachelscheid, Jürgen Eberle, Anja Rabien, Evgenia Makrantonaki, Christos C. Zouboulis
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10.1371/journal.pgen.1005932

PLOS Genetics Mutational History of a Human Cell Lineage from Somatic to Induced Pluripotent Stem Cells
April 7, 2016 Foad J. Rouhani, Serena Nik-Zainal, Arthur Wuster, Yilong Li, Nathalie Conte, Hiroko Koike-Yusa, Natsuhiko Kumasaka, Ludovic Vallier, Kosuke Yusa, Allan Bradley
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10.1371/journal.pgen.1005897

PLOS Genetics Maintenance of Tissue Pluripotency by Epigenetic Factors Acting at Multiple Levels
February 29, 2016 Devendran A. Sadasivam, Der-Hwa Huang
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10.1371/journal.pone.0143235

PLOS ONE Embryonic Stem Cells Exhibit mRNA Isoform Specific Translational Regulation
January 22, 2016 Queenie Wing-Lei Wong, Candida Vaz, Qian Yi Lee, Tian Yun Zhao, Raymond Luo, Stuart K. Archer, Thomas Preiss, Vivek Tanavde, Leah A. Vardy
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10.1371/journal.pone.0126338

PLOS ONE Evaluation of Changes in Morphology and Function of Human Induced Pluripotent Stem Cell Derived Cardiomyocytes (HiPSC-CMs) Cultured on an Aligned-Nanofiber Cardiac Patch
May 19, 2015 Mahmood Khan, Yanyi Xu, Serena Hua, Jed Johnson, Andriy Belevych, Paul M. L. Janssen, Sandor Gyorke, Jianjun Guan, Mark G. Angelos
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10.1371/journal.pone.0114485

PLOS ONE CRISPR Reveals a Distal Super-Enhancer Required for Sox2 Expression in Mouse Embryonic Stem Cells
December 8, 2014 Yan Li, Chloe M. Rivera, Haruhiko Ishii, Fulai Jin, Siddarth Selvaraj, Ah Young Lee, Jesse R. Dixon, Bing Ren
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10.1371/journal.pcbi.1003734

PLOS Computational Biology Epigenetic Landscapes Explain Partially Reprogrammed Cells and Identify Key Reprogramming Genes
August 14, 2014 Alex H. Lang, Hu Li, James J. Collins, Pankaj Mehta

Disease Modeling and Drug Screening

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10.1371/journal.pone.0161969

PLOS ONE Self-Organizing 3D Human Neural Tissue Derived from Induced Pluripotent Stem Cells Recapitulate Alzheimer’s Disease Phenotypes
September 13, 2016 Waseem K. Raja, Alison E. Mungenast, Yuan-Ta Lin, Tak Ko, Fatema Abdurrob, Jinsoo Seo, Li-Huei Tsai
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10.1371/journal.ppat.1005544

PLOS Pathogens Influenza Virus Infects Epithelial Stem/Progenitor Cells of the Distal Lung: Impact on Fgfr2b-Driven Epithelial Repair
June 20, 2016 Jennifer Quantius, Carole Schmoldt, Ana I. Vazquez-Armendariz, Christin Becker, Elie El Agha, Jochen Wilhelm, Rory E. Morty, István Vadász, Konstantin Mayer, Stefan Gattenloehner, Ludger Fink, Mikhail Matrosovich, Xiaokun Li, Werner Seeger, Juergen Lohmeyer, Saverio Bellusci, Susanne Herold
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10.1371/journal.pone.0156161

PLOS ONE Comparison between Stromal Vascular Fraction and Adipose Mesenchymal Stem Cells in Remodeling Hypertrophic Scars
May 26, 2016 Sophie Domergue, Claire Bony, Marie Maumus, Karine Toupet, Eric Frouin, Valérie Rigau, Marie-Catherine Vozenin, Guy Magalon, Christian Jorgensen, Danièle Noël
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10.1371/journal.pone.0147184

PLOS ONE A Silk Fibroin/Collagen Nerve Scaffold Seeded with a Co-Culture of Schwann Cells and Adipose-Derived Stem Cells for Sciatic Nerve Regeneration
January 22, 2016 Yunqiang Xu, Zhenhui Zhang, Xuyi Chen, Ruixin Li, Dong Li, Shiqing Feng
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10.1371/journal.pone.0144523

PLOS ONE Widespread Myocardial Delivery of Heart-Derived Stem Cells by Nonocclusive Triple-Vessel Intracoronary Infusion in Porcine Ischemic Cardiomyopathy: Superior Attenuation of Adverse Remodeling Documented by Magnetic Resonance Imaging and Histology
January 19, 2016 Eleni Tseliou, Hideaki Kanazawa, James Dawkins, Romain Gallet, Michelle Kreke, Rachel Smith, Ryan Middleton, Jackelyn Valle, Linda Marbán, Saibal Kar, Rajendra Makkar, Eduardo Marbán
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10.1371/journal.pone.0146697

PLOS ONE Human Engineered Cardiac Tissues Created Using Induced Pluripotent Stem Cells Reveal Functional Characteristics of BRAF-Mediated Hypertrophic Cardiomyopathy
January 19, 2016 Timothy J. Cashman, Rebecca Josowitz, Bryce V. Johnson, Bruce D. Gelb, Kevin D. Costa
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10.1371/journal.pone.0132387

PLOS ONE MicroRNA Profiling of Neurons Generated Using Induced Pluripotent Stem Cells Derived from Patients with Schizophrenia and Schizoaffective Disorder, and 22q11.2 Del
July 14, 2015 Dejian Zhao, Mingyan Lin, Jian Chen, Erika Pedrosa, Anastasia Hrabovsky, H. Matthew Fourcade, Deyou Zheng, Herbert M. Lachman
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10.1371/journal.pone.0118020

PLOS ONE Modeling Chemotherapeutic Neurotoxicity with Human Induced Pluripotent Stem Cell-Derived Neuronal Cells
February 17, 2015 Heather E. Wheeler, Claudia Wing, Shannon M. Delaney, Masaaki Komatsu, M. Eileen Dolan
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10.1371/journal.pone.0102796

PLOS ONE Directed Differentiation of Patient-Specific Induced Pluripotent Stem Cells Identifies the Transcriptional Repression and Epigenetic Modification of NKX2-5, HAND1, and NOTCH1 in Hypoplastic Left Heart Syndrome
July 22, 2014 Junko Kobayashi, Masashi Yoshida, Suguru Tarui, Masataka Hirata, Yusuke Nagai, Shingo Kasahara, Keiji Naruse, Hiroshi Ito, Shunji Sano, Hidemasa Oh

Stem Cell Differentiation

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10.1371/journal.pone.0167807

PLOS ONE Angiogenic Capacity of Periodontal Ligament Stem Cells Pretreated with Deferoxamine and/or Fibroblast Growth Factor-2
December 9, 2016 Jessica Ratajczak, Petra Hilkens, Pascal Gervois, Esther Wolfs, Reinhilde Jacobs, Ivo Lambrichts, Annelies Bronckaers
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10.1371/journal.pone.0158282

PLOS ONE Differentiation/Purification Protocol for Retinal Pigment Epithelium from Mouse Induced Pluripotent Stem Cells as a Research Tool
July 6, 2016 Yuko Iwasaki, Sunao Sugita, Michiko Mandai, Shigenobu Yonemura, Akishi Onishi, Shin-ichiro Ito, Manabu Mochizuki, Kyoko Ohno-Matsui, Masayo Takahashi
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10.1371/journal.pgen.1006109

PLOS Genetics NF-YB Regulates Spermatogonial Stem Cell Self-Renewal and Proliferation in the Planarian Schmidtea mediterranea
June 15, 2016 Harini Iyer, James J. Collins III, Phillip A. Newmark
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10.1371/journal.pbio.1002457

PLOS Biology GPCRs Direct Germline Development and Somatic Gonad Function in Planarians
May 10, 2016 Amir Saberi, Ayana Jamal, Isabel Beets, Liliane Schoofs, Phillip A. Newmark
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10.1371/journal.pbio.1002450

PLOS Biology Neuronal Cell Fate Specification by the Convergence of Different Spatiotemporal Cues on a Common Terminal Selector Cascade
May 4, 2016 Hugo Gabilondo, Johannes Stratmann, Irene Rubio-Ferrera, Irene Millán-Crespo, Patricia Contero-García, Shahrzad Bahrampour, Stefan Thor, Jonathan Benito-Sipos
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10.1371/journal.pone.0153795

PLOS ONE In Vitro Polarization of Colonoids to Create an Intestinal Stem Cell Compartment
April 21, 2016 Peter J. Attayek, Asad A. Ahmad, Yuli Wang, Ian Williamson, Christopher E. Sims, Scott T. Magness, Nancy L. Allbritton
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10.1371/journal.pone.0153412

PLOS ONE Mesenchymal Stem Cell Seeding of Porcine Small Intestinal Submucosal Extracellular Matrix for Cardiovascular Applications
April 12, 2016 Chia Wei Chang, Tye Petrie, Alycia Clark, Xin Lin, Claus S. Sondergaard, Leigh G. Griffiths
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10.1371/journal.pone.0148225

PLOS ONE Odontogenic Differentiation of Human Dental Pulp Stem Cells on Hydrogel Scaffolds Derived from Decellularized Bone Extracellular Matrix and Collagen Type I
February 16, 2016 Francesco Paduano, Massimo Marrelli, Lisa J. White, Kevin M. Shakesheff, Marco Tatullo
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10.1371/journal.pcbi.1004453

PLOS Computational Biology Quantitative Live Imaging of Human Embryonic Stem Cell Derived Neural Rosettes Reveals Structure-Function Dynamics Coupled to Cortical Development
October 16, 2015 Omer Ziv, Assaf Zaritsky, Yakey Yaffe, Naresh Mutukula, Reuven Edri, Yechiel Elkabetz
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10.1371/journal.pbio.1002217

PLOS Biology Sustained Pax6 Expression Generates Primate-like Basal Radial Glia in Developing Mouse Neocortex
August 7, 2015 Fong Kuan Wong, Ji-Feng Fei, Felipe Mora-Bermúdez, Elena Taverna, Christiane Haffner, Jun Fu, Konstantinos Anastassiadis, A. Francis Stewart, Wieland B. Huttner
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10.1371/journal.pone.0126596

PLOS ONE Generation of Highly Purified Human Cardiomyocytes from Peripheral Blood Mononuclear Cell-Derived Induced Pluripotent Stem Cells
May 10, 2015 Maya Fuerstenau-Sharp, Martina E. Zimmermann, Klaus Stark, Nico Jentsch, Melanie Klingenstein, Marzena Drzymalski, Stefan Wagner, Lars S. Maier, Ute Hehr, Andrea Baessler, Marcus Fischer, Christian Hengstenberg
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10.1371/journal.pbio.1002111

PLOS Biology Cell Cycle–Dependent Differentiation Dynamics Balances Growth and Endocrine Differentiation in the Pancreas
March 18, 2015 Yung Hae Kim, Hjalte List Larsen, Pau Rué, Laurence A. Lemaire, Jorge Ferrer, Anne Grapin-Botton

Computational Modeling Approaches

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10.1371/journal.pcbi.1005391

PLOS Computational Biology Mathematical models of tissue stem and transit target cell divisions and the risk of radiation- or smoking-associated cancer
February 14, 2017 Mark P. Little, Jolyon H. Hendry
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10.1371/journal.pcbi.1005108

PLOS Computational Biology Immersed Boundary Models for Quantifying Flow-Induced Mechanical Stimuli on Stem Cells Seeded on 3D Scaffolds in Perfusion Bioreactors
September 22, 2016 Yann Guyot, Tim Odenthal, Ramesh Subramani, Frank P. Luyten, Herman Ramon, Ioannis Papantoniou, Liesbet Geris, Bart Smeets
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10.1371/journal.pcbi.1005014

PLOS Computational Biology Modeling Electrophysiological Coupling and Fusion between Human Mesenchymal Stem Cells and Cardiomyocytes
July 25, 2016 Joshua Mayourian, Ruben M. Savizky, Eric A. Sobie, Kevin D. Costa
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10.1371/journal.pcbi.1004990

PLOS Computational Biology Near Equilibrium Calculus of Stem Cells in Application to the Airway Epithelium Lineage
July 18, 2016 Zheng Sun, Maksim V. Plikus, Natalia L. Komarova
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10.1371/journal.pcbi.1004814

PLOS Computational Biology Feedback, Lineages and Self-Organizing Morphogenesis
March 18, 2016 Sameeran Kunche, Huaming Yan, Anne L. Calof, John S. Lowengrub, Arthur D. Lander
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10.1371/journal.pcbi.1004629

PLOS Computational Biology The Role of Symmetric Stem Cell Divisions in Tissue Homeostasis
December 23, 2015 Jienian Yang, Maksim V. Plikus, Natalia L. Komarova
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10.1371/journal.pone.0137392

PLOS ONE Proportional-Integral-Derivative (PID) Control of Secreted Factors for Blood Stem Cell Culture
September 8, 2015 Julia Caldwell, Weijia Wang, Peter W. Zandstra
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10.1371/journal.pcbi.1003969

PLOS Computational Biology Embryonic Stem Cell Specific “Master” Replication Origins at the Heart of the Loss of Pluripotency
February 6, 2015 Hanna Julienne, Alain Arneodo, Benjamin Audit
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10.1371/journal.pcbi.1003794

PLOS Computational Biology Stochastic Dynamics of Interacting Haematopoietic Stem Cell Niche Lineages
September 4, 2014 Tamás Székely Jr, Kevin Burrage, Marc Mangel, Michael B. Bonsall

Stem Cell Heterogeneity

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10.1371/journal.pbio.2000731

PLOS Biology Lung Basal Stem Cells Rapidly Repair DNA Damage Using the Error-Prone Nonhomologous End-Joining Pathway
January 26, 2017 Clare E. Weeden, Yunshun Chen, Stephen B. Ma, Yifang Hu, Georg Ramm, Kate D. Sutherland, Gordon K. Smyth, Marie-Liesse Asselin-Labat
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10.1371/journal.pbio.2000640

PLOS Biology Cell Fate Decision as High-Dimensional Critical State Transition
December 27, 2016 Mitra Mojtahedi, Alexander Skupin, Joseph Zhou, Ivan G. Castaño, Rebecca Y. Y. Leong-Quong, Hannah Chang, Kalliopi Trachana, Alessandro Giuliani, Sui Huang
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10.1371/journal.pbio.1002581

PLOS Biology SOX2 and PI3K Cooperate to Induce and Stabilize a Squamous-Committed Stem Cell Injury State during Lung Squamous Cell Carcinoma Pathogenesis
November 23, 2016 Bo Ram Kim, Emily Van de Laar, Michael Cabanero, Shintaro Tarumi, Stefan Hasenoeder, Dennis Wang, Carl Virtanen, Takaya Suzuki, Bizhan Bandarchi, Shingo Sakashita, Nhu An Pham, Sharon Lee, Shaf Keshavjee, Thomas K. Waddell, Ming-Sound Tsao, Nadeem Moghal
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10.1371/journal.pbio.1002491

PLOS Biology Paneth Cell-Rich Regions Separated by a Cluster of Lgr5+ Cells Initiate Crypt Fission in the Intestinal Stem Cell Niche
June 27, 2016 Alistair J. Langlands, Axel A. Almet, Paul L. Appleton, Ian P. Newton, James M. Osborne, Inke S. Näthke
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10.1371/journal.pgen.1005819

PLOS Genetics Strong Components of Epigenetic Memory in Cultured Human Fibroblasts Related to Site of Origin and Donor Age
February 25, 2016 Nikolay A. Ivanov, Ran Tao, Joshua G. Chenoweth, Anna Brandtjen, Michelle I. Mighdoll, John D. Genova, Ronald D. McKay, Yankai Jia, Daniel R. Weinberger, Joel E. Kleinman, Thomas M. Hyde, Andrew E. Jaffe
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10.1371/journal.pgen.1005793

PLOS Genetics Genetic Variation, Not Cell Type of Origin, Underlies the Majority of Identifiable Regulatory Differences in iPSCs
January 26, 2016 Courtney K. Burrows, Nicholas E. Banovich, Bryan J. Pavlovic, Kristen Patterson, Irene Gallego Romero, Jonathan K. Pritchard, Yoav Gilad
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10.1371/journal.pgen.1004432

PLOS Genetics Genetic Background Drives Transcriptional Variation in Human Induced Pluripotent Stem Cells
June 5, 2014 Foad Rouhani, Natsuhiko Kumasaka, Miguel Cardoso de Brito, Allan Bradley, Ludovic Vallier, Daniel Gaffney

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