Literature DB >> 28945704

Comprehensive characterization of distinct states of human naive pluripotency generated by reprogramming.

Xiaodong Liu1,2,3, Christian M Nefzger1,2,3, Fernando J Rossello1,2,3, Joseph Chen1,2,3, Anja S Knaupp1,2,3, Jaber Firas1,2,3, Ethan Ford4,5, Jahnvi Pflueger4,5, Jacob M Paynter1,2,3, Hun S Chy3,6, Carmel M O'Brien3,6, Cheng Huang7, Ketan Mishra1,2,3, Margeaux Hodgson-Garms1,2,3, Natasha Jansz8,9, Sarah M Williams1,2,3,10, Marnie E Blewitt8,9, Susan K Nilsson3,6, Ralf B Schittenhelm7, Andrew L Laslett3,6, Ryan Lister4,5, Jose M Polo1,2,3.   

Abstract

Recent reports on the characteristics of naive human pluripotent stem cells (hPSCs) obtained using independent methods differ. Naive hPSCs have been mainly derived by conversion from primed hPSCs or by direct derivation from human embryos rather than by somatic cell reprogramming. To provide an unbiased molecular and functional reference, we derived genetically matched naive hPSCs by direct reprogramming of fibroblasts and by primed-to-naive conversion using different naive conditions (NHSM, RSeT, 5iLAF and t2iLGöY). Our results show that hPSCs obtained in these different conditions display a spectrum of naive characteristics. Furthermore, our characterization identifies KLF4 as sufficient for conversion of primed hPSCs into naive t2iLGöY hPSCs, underscoring the role that reprogramming factors can play for the derivation of bona fide naive hPSCs.

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Year:  2017        PMID: 28945704     DOI: 10.1038/nmeth.4436

Source DB:  PubMed          Journal:  Nat Methods        ISSN: 1548-7091            Impact factor:   28.547


  50 in total

1.  Derivation of naive human embryonic stem cells.

Authors:  Carol B Ware; Angelique M Nelson; Brigham Mecham; Jennifer Hesson; Wenyu Zhou; Erica C Jonlin; Antonio J Jimenez-Caliani; Xinxian Deng; Christopher Cavanaugh; Savannah Cook; Paul J Tesar; Jeffrey Okada; Lilyana Margaretha; Henrik Sperber; Michael Choi; C Anthony Blau; Piper M Treuting; R David Hawkins; Vincenzo Cirulli; Hannele Ruohola-Baker
Journal:  Proc Natl Acad Sci U S A       Date:  2014-03-12       Impact factor: 11.205

2.  Human Naive Pluripotent Stem Cells Model X Chromosome Dampening and X Inactivation.

Authors:  Anna Sahakyan; Rachel Kim; Constantinos Chronis; Shan Sabri; Giancarlo Bonora; Thorold W Theunissen; Edward Kuoy; Justin Langerman; Amander T Clark; Rudolf Jaenisch; Kathrin Plath
Journal:  Cell Stem Cell       Date:  2016-12-15       Impact factor: 25.269

3.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.

Authors:  Bo Li; Colin N Dewey
Journal:  BMC Bioinformatics       Date:  2011-08-04       Impact factor: 3.307

4.  Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE.

Authors:  Peng Qiu; Erin F Simonds; Sean C Bendall; Kenneth D Gibbs; Robert V Bruggner; Michael D Linderman; Karen Sachs; Garry P Nolan; Sylvia K Plevritis
Journal:  Nat Biotechnol       Date:  2011-10-02       Impact factor: 54.908

5.  ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap.

Authors:  Tauno Metsalu; Jaak Vilo
Journal:  Nucleic Acids Res       Date:  2015-05-12       Impact factor: 16.971

6.  voom: Precision weights unlock linear model analysis tools for RNA-seq read counts.

Authors:  Charity W Law; Yunshun Chen; Wei Shi; Gordon K Smyth
Journal:  Genome Biol       Date:  2014-02-03       Impact factor: 13.583

7.  A Versatile Strategy for Isolating a Highly Enriched Population of Intestinal Stem Cells.

Authors:  Christian M Nefzger; Thierry Jardé; Fernando J Rossello; Katja Horvay; Anja S Knaupp; David R Powell; Joseph Chen; Helen E Abud; Jose M Polo
Journal:  Stem Cell Reports       Date:  2016-02-25       Impact factor: 7.765

8.  Systematic identification of culture conditions for induction and maintenance of naive human pluripotency.

Authors:  Thorold W Theunissen; Benjamin E Powell; Haoyi Wang; Maya Mitalipova; Dina A Faddah; Jessica Reddy; Zi Peng Fan; Dorothea Maetzel; Kibibi Ganz; Linyu Shi; Tenzin Lungjangwa; Sumeth Imsoonthornruksa; Yonatan Stelzer; Sudharshan Rangarajan; Ana D'Alessio; Jianming Zhang; Qing Gao; Meelad M Dawlaty; Richard A Young; Nathanael S Gray; Rudolf Jaenisch
Journal:  Cell Stem Cell       Date:  2014-07-24       Impact factor: 24.633

9.  Naive Pluripotent Stem Cells Derived Directly from Isolated Cells of the Human Inner Cell Mass.

Authors:  Ge Guo; Ferdinand von Meyenn; Fatima Santos; Yaoyao Chen; Wolf Reik; Paul Bertone; Austin Smith; Jennifer Nichols
Journal:  Stem Cell Reports       Date:  2016-03-03       Impact factor: 7.765

10.  Molecular Criteria for Defining the Naive Human Pluripotent State.

Authors:  Thorold W Theunissen; Marc Friedli; Yupeng He; Evarist Planet; Ryan C O'Neil; Styliani Markoulaki; Julien Pontis; Haoyi Wang; Alexandra Iouranova; Michaël Imbeault; Julien Duc; Malkiel A Cohen; Katherine J Wert; Rosa Castanon; Zhuzhu Zhang; Yanmei Huang; Joseph R Nery; Jesse Drotar; Tenzin Lungjangwa; Didier Trono; Joseph R Ecker; Rudolf Jaenisch
Journal:  Cell Stem Cell       Date:  2016-07-14       Impact factor: 25.269

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  51 in total

Review 1.  Mechanisms of gene regulation in human embryos and pluripotent stem cells.

Authors:  Thorold W Theunissen; Rudolf Jaenisch
Journal:  Development       Date:  2017-12-15       Impact factor: 6.868

2.  Modeling human embryo development with embryonic and extra-embryonic stem cells.

Authors:  Bailey A T Weatherbee; Tongtong Cui; Magdalena Zernicka-Goetz
Journal:  Dev Biol       Date:  2020-12-24       Impact factor: 3.582

3.  NANOS3 downregulation in Down syndrome hiPSCs during primordial germ cell-like cell differentiation.

Authors:  V K Abdyyev; N O Dashenkova; E B Dashinimaev; E A Vorotelyak; A V Vasiliev
Journal:  Histochem Cell Biol       Date:  2021-10-15       Impact factor: 4.304

4.  OCT4 cooperates with distinct ATP-dependent chromatin remodelers in naïve and primed pluripotent states in human.

Authors:  Xin Huang; Kyoung-Mi Park; Paul Gontarz; Bo Zhang; Joshua Pan; Zachary McKenzie; Laura A Fischer; Chen Dong; Sabine Dietmann; Xiaoyun Xing; Pavel V Shliaha; Jihong Yang; Dan Li; Junjun Ding; Tenzin Lungjangwa; Maya Mitalipova; Shafqat A Khan; Sumeth Imsoonthornruksa; Nick Jensen; Ting Wang; Cigall Kadoch; Rudolf Jaenisch; Jianlong Wang; Thorold W Theunissen
Journal:  Nat Commun       Date:  2021-08-26       Impact factor: 14.919

5.  AP-1 activity is a major barrier of human somatic cell reprogramming.

Authors:  Yuting Liu; Jiangping He; Ruhai Chen; He Liu; Jocelyn Chen; Yujian Liu; Bo Wang; Lin Guo; Duanqing Pei; Jie Wang; Jing Liu; Jiekai Chen
Journal:  Cell Mol Life Sci       Date:  2021-06-28       Impact factor: 9.261

6.  Chemical Reversion of Conventional Human Pluripotent Stem Cells to a Naïve-like State with Improved Multilineage Differentiation Potency.

Authors:  Tea Soon Park; Ludovic Zimmerlin; Rebecca Evans-Moses; Elias T Zambidis
Journal:  J Vis Exp       Date:  2018-06-10       Impact factor: 1.355

7.  Non-transmissible MV Vector with Segmented RNA Genome Establishes Different Types of iPSCs from Hematopoietic Cells.

Authors:  Takafumi Hiramoto; Maino Tahara; Jiyuan Liao; Yasushi Soda; Yoshie Miura; Ryo Kurita; Hiroshi Hamana; Kota Inoue; Hiroshi Kohara; Shohei Miyamoto; Yasuki Hijikata; Shinji Okano; Yoshiyuki Yamaguchi; Yoshinao Oda; Kenji Ichiyanagi; Hidehiro Toh; Hiroyuki Sasaki; Hiroyuki Kishi; Akihide Ryo; Atsushi Muraguchi; Makoto Takeda; Kenzaburo Tani
Journal:  Mol Ther       Date:  2019-09-12       Impact factor: 11.454

8.  Temporal activation of LRH-1 and RAR-γ in human pluripotent stem cells induces a functional naïve-like state.

Authors:  Adeleh Taei; Tahereh Kiani; Zeinab Taghizadeh; Sharif Moradi; Azam Samadian; Sepideh Mollamohammadi; Ali Sharifi-Zarchi; Stefan Guenther; Azimeh Akhlaghpour; Behrouz Asgari Abibeiglou; Mostafa Najar-Asl; Razieh Karamzadeh; Keynoosh Khalooghi; Thomas Braun; Seyedeh-Nafiseh Hassani; Hossein Baharvand
Journal:  EMBO Rep       Date:  2020-08-16       Impact factor: 8.807

9.  Induction of Human Naïve Pluripotent Stem Cells from Somatic Cells.

Authors:  Constance Onfray; Jia Ping Tan; Stéphanie Kilens; Xiaodong Liu; Jose Polo; Laurent David
Journal:  Methods Mol Biol       Date:  2022

10.  Probing the signaling requirements for naive human pluripotency by high-throughput chemical screening.

Authors:  Shafqat A Khan; Kyoung-Mi Park; Laura A Fischer; Chen Dong; Tenzin Lungjangwa; Marta Jimenez; Dominick Casalena; Brian Chew; Sabine Dietmann; Douglas S Auld; Rudolf Jaenisch; Thorold W Theunissen
Journal:  Cell Rep       Date:  2021-06-15       Impact factor: 9.995

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