1
|
Ilia K, Shakiba N, Bingham T, Jones RD, Kaminski MM, Aravera E, Bruno S, Palacios S, Weiss R, Collins JJ, Del Vecchio D, Schlaeger TM. Synthetic genetic circuits to uncover the OCT4 trajectories of successful reprogramming of human fibroblasts. Sci Adv 2023; 9:eadg8495. [PMID: 38019912 PMCID: PMC10686568 DOI: 10.1126/sciadv.adg8495] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023]
Abstract
Reprogramming human fibroblasts to induced pluripotent stem cells (iPSCs) is inefficient, with heterogeneity among transcription factor (TF) trajectories driving divergent cell states. Nevertheless, the impact of TF dynamics on reprogramming efficiency remains uncharted. We develop a system that accurately reports OCT4 protein levels in live cells and use it to reveal the trajectories of OCT4 in successful reprogramming. Our system comprises a synthetic genetic circuit that leverages noise to generate a wide range of OCT4 trajectories and a microRNA targeting endogenous OCT4 to set total cellular OCT4 protein levels. By fusing OCT4 to a fluorescent protein, we are able to track OCT4 trajectories with clonal resolution via live-cell imaging. We discover that a supraphysiological, stable OCT4 level is required, but not sufficient, for efficient iPSC colony formation. Our synthetic genetic circuit design and high-throughput live-imaging pipeline are generalizable for investigating TF dynamics for other cell fate programming applications.
Collapse
Affiliation(s)
- Katherine Ilia
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nika Shakiba
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3 Canada
| | - Trevor Bingham
- Stem Cell Program, Boston Children’s Hospital, Boston, MA 02115, USA
- Harvard University, Boston, MA 02115, USA
| | - Ross D. Jones
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3 Canada
| | - Michael M. Kaminski
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz-Association, Berlin 10115, Germany
- Department of Nephrology and Medical Intensive Care, Charité – Universitätsmedizin Berlin, Medizinische Klinik m.S. Nephrologie und Intensivmedizin, Berlin 10117, Germany
- Berlin Institute of Health, Berlin 13125, Germany
| | - Eliezer Aravera
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Simone Bruno
- Department of Mechanical Engineering, MIT, Cambridge, MA 02139, USA
| | - Sebastian Palacios
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Mechanical Engineering, MIT, Cambridge, MA 02139, USA
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA
| | - James J. Collins
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Domitilla Del Vecchio
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Mechanical Engineering, MIT, Cambridge, MA 02139, USA
| | | |
Collapse
|
2
|
Kang H, Hasselbeck S, Taškova K, Wang N, Oosten LNV, Mrowka R, Utikal J, Andrade-Navarro MA, Wang J, Wölfl S, Cheng X. Development of a next-generation endogenous OCT4 inducer and its anti-aging effect in vivo. Eur J Med Chem 2023; 257:115513. [PMID: 37253308 DOI: 10.1016/j.ejmech.2023.115513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/05/2023] [Accepted: 05/23/2023] [Indexed: 06/01/2023]
Abstract
The identification of small molecules capable of replacing transcription factors has been a longstanding challenge in the generation of human chemically induced pluripotent stem cells (iPSCs). Recent studies have shown that ectopic expression of OCT4, one of the master pluripotency regulators, compromised the developmental potential of resulting iPSCs, This highlights the importance of finding endogenous OCT4 inducers for the generation of clinical-grade human iPSCs. Through a cell-based high throughput screen, we have discovered several new OCT4-inducing compounds (O4Is). In this work, we prepared metabolically stable analogues, including O4I4, which activate endogenous OCT4 and associated signaling pathways in various cell lines. By combining these with a transcription factor cocktail consisting of SOX2, KLF4, MYC, and LIN28 (referred to as "CSKML") we achieved to reprogram human fibroblasts into a stable and authentic pluripotent state without the need for exogenous OCT4. In Caenorhabditis elegans and Drosophila, O4I4 extends lifespan, suggesting the potential application of OCT4-inducing compounds in regenerative medicine and rejuvenation therapy.
Collapse
Affiliation(s)
- Han Kang
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Germany
| | - Sebastian Hasselbeck
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt am Main, Germany
| | - Katerina Taškova
- Faculty of Biology, Johannes Gutenberg University Mainz, Germany
| | - Nessa Wang
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Germany
| | - Luuk N van Oosten
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Germany
| | - Ralf Mrowka
- Experimentelle Nephrologie, KIM III, Universitätsklinikum, Jena, Germany
| | - Jochen Utikal
- Skin Cancer Unit (G300), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Jichang Wang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Stefan Wölfl
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Germany
| | - Xinlai Cheng
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt am Main, Germany; Frankfurt Cancer Institute, Germany.
| |
Collapse
|
3
|
Ilia K, Shakiba N, Bingham T, Jones RD, Kaminski MM, Aravera E, Bruno S, Palacios S, Weiss R, Collins JJ, Del Vecchio D, Schlaeger TM. Synthetic genetic circuits to uncover and enforce the OCT4 trajectories of successful reprogramming of human fibroblasts. bioRxiv 2023:2023.01.25.525529. [PMID: 36747813 PMCID: PMC9900859 DOI: 10.1101/2023.01.25.525529] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Reprogramming human fibroblasts to induced pluripotent stem cells (iPSCs) is inefficient, with heterogeneity among transcription factor (TF) trajectories driving divergent cell states. Nevertheless, the impact of TF dynamics on reprogramming efficiency remains uncharted. Here, we identify the successful reprogramming trajectories of the core pluripotency TF, OCT4, and design a genetic controller that enforces such trajectories with high precision. By combining a genetic circuit that generates a wide range of OCT4 trajectories with live-cell imaging, we track OCT4 trajectories with clonal resolution and find that a distinct constant OCT4 trajectory is required for colony formation. We then develop a synthetic genetic circuit that yields a tight OCT4 distribution around the identified trajectory and outperforms in terms of reprogramming efficiency other circuits that less accurately regulate OCT4. Our synthetic biology approach is generalizable for identifying and enforcing TF dynamics for cell fate programming applications.
Collapse
Affiliation(s)
- Katherine Ilia
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Nika Shakiba
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, V6T 1Z3 Canada
| | - Trevor Bingham
- Boston Children’s Hospital Stem Cell Program, Boston Children’s Hospital, Boston, MA, 02115, USA
- Harvard University, Boston, MA, 02115, USA
| | - Ross D. Jones
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, V6T 1Z3 Canada
| | - Michael M. Kaminski
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Max Delbrück Center for Molecular Medicine, Berlin, 13125, Germany
| | - Eliezer Aravera
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- College of Engineering and Applied Sciences, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Simone Bruno
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sebastian Palacios
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - James J. Collins
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02139, USA
| | - Domitilla Del Vecchio
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Thorsten M. Schlaeger
- Boston Children’s Hospital Stem Cell Program, Boston Children’s Hospital, Boston, MA, 02115, USA
| |
Collapse
|
4
|
Ha J, Kim BS, Min B, Nam J, Lee JG, Lee M, Yoon BH, Choi YH, Im I, Park JS, Choi H, Baek A, Cho SM, Lee MO, Nam KH, Mun JY, Kim M, Kim SY, Son MY, Kang YK, Lee JS, Kim JK, Kim J. Intermediate cells of in vitro cellular reprogramming and in vivo tissue regeneration require desmoplakin. Sci Adv 2022; 8:eabk1239. [PMID: 36306352 PMCID: PMC9616504 DOI: 10.1126/sciadv.abk1239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Amphibians and fish show considerable regeneration potential via dedifferentiation of somatic cells into blastemal cells. In terms of dedifferentiation, in vitro cellular reprogramming has been proposed to share common processes with in vivo tissue regeneration, although the details are elusive. Here, we identified the cytoskeletal linker protein desmoplakin (Dsp) as a common factor mediating both reprogramming and regeneration. Our analysis revealed that Dsp expression is elevated in distinct intermediate cells during in vitro reprogramming. Knockdown of Dsp impedes in vitro reprogramming into induced pluripotent stem cells and induced neural stem/progenitor cells as well as in vivo regeneration of zebrafish fins. Notably, reduced Dsp expression impairs formation of the intermediate cells during cellular reprogramming and tissue regeneration. These findings suggest that there is a Dsp-mediated evolutionary link between cellular reprogramming in mammals and tissue regeneration in lower vertebrates and that the intermediate cells may provide alternative approaches for mammalian regenerative therapy.
Collapse
Affiliation(s)
- Jeongmin Ha
- Stem Cell Convergence Research Center, Korea Research Institute Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Bum Suk Kim
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu 42988, Republic of Korea
| | - Byungkuk Min
- Stem Cell Convergence Research Center, Korea Research Institute Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Juhyeon Nam
- Stem Cell Convergence Research Center, Korea Research Institute Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Jae-Geun Lee
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Republic of Korea
- Microbiome Convergence Research Center, KRIBB, Daejeon 34141, Republic of Korea
| | - Minhyung Lee
- Stem Cell Convergence Research Center, Korea Research Institute Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Byoung-Ha Yoon
- Korea Bioinformation Center, KRIBB, Daejeon 34141, Republic of Korea
| | - Yoon Ha Choi
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu 42988, Republic of Korea
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Ilkyun Im
- Bio-IT lab, NetTargets Inc., Daejeon 34141, Republic of Korea
| | - Jung Sun Park
- Development and Differentiation Research Center, KRIBB, Daejeon 34141, Republic of Korea
| | - Hyosun Choi
- Nanobioimaging Center, National Instrumentation Center for Environmental Management (NICEM), Seoul National University, Seoul, Republic of Korea
| | - Areum Baek
- Stem Cell Convergence Research Center, Korea Research Institute Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Sang Mi Cho
- Laboratory Animal Resource Center, KRIBB, Cheongju 28116, Republic of Korea
| | - Mi-Ok Lee
- Stem Cell Convergence Research Center, Korea Research Institute Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Ki-Hoan Nam
- Laboratory Animal Resource Center, KRIBB, Cheongju 28116, Republic of Korea
| | - Ji Young Mun
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Mirang Kim
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Republic of Korea
- Personalized Genomic Medicine Research Center, KRIBB, Daejeon 34141, Republic of Korea
| | - Seon-Young Kim
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Republic of Korea
- Korea Bioinformation Center, KRIBB, Daejeon 34141, Republic of Korea
- Personalized Genomic Medicine Research Center, KRIBB, Daejeon 34141, Republic of Korea
| | - Mi Young Son
- Stem Cell Convergence Research Center, Korea Research Institute Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Yong-Kook Kang
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Republic of Korea
- Development and Differentiation Research Center, KRIBB, Daejeon 34141, Republic of Korea
| | - Jeong-Soo Lee
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Republic of Korea
- Microbiome Convergence Research Center, KRIBB, Daejeon 34141, Republic of Korea
- Dementia DTC R&D Convergence Program, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Jong Kyoung Kim
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu 42988, Republic of Korea
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Janghwan Kim
- Stem Cell Convergence Research Center, Korea Research Institute Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Republic of Korea
- R&D Center, Regeners Inc., Daejeon 34141, Republic of Korea
| |
Collapse
|
5
|
Huyghe A, Furlan G, Schroeder J, Cascales E, Trajkova A, Ruel M, Stüder F, Larcombe M, Yang Sun YB, Mugnier F, De Matteo L, Baygin A, Wang J, Yu Y, Rama N, Gibert B, Kielbassa J, Tonon L, Wajda P, Gadot N, Brevet M, Siouda M, Mulligan P, Dante R, Liu P, Gronemeyer H, Mendoza-Parra M, Polo JM, Lavial F. Comparative roadmaps of reprogramming and oncogenic transformation identify Bcl11b and Atoh8 as broad regulators of cellular plasticity. Nat Cell Biol 2022. [PMID: 36075976 DOI: 10.1038/s41556-022-00986-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 07/27/2022] [Indexed: 12/22/2022]
Abstract
Coordinated changes of cellular plasticity and identity are critical for pluripotent reprogramming and oncogenic transformation. However, the sequences of events that orchestrate these intermingled modifications have never been comparatively dissected. Here, we deconvolute the cellular trajectories of reprogramming (via Oct4/Sox2/Klf4/c-Myc) and transformation (via Ras/c-Myc) at the single-cell resolution and reveal how the two processes intersect before they bifurcate. This approach led us to identify the transcription factor Bcl11b as a broad-range regulator of cell fate changes, as well as a pertinent marker to capture early cellular intermediates that emerge simultaneously during reprogramming and transformation. Multiomics characterization of these intermediates unveiled a c-Myc/Atoh8/Sfrp1 regulatory axis that constrains reprogramming, transformation and transdifferentiation. Mechanistically, we found that Atoh8 restrains cellular plasticity, independent of cellular identity, by binding a specific enhancer network. This study provides insights into the partitioned control of cellular plasticity and identity for both regenerative and cancer biology. Huyghe, Furlan et al. compare pluripotent reprogramming with oncogenic transformation and identify Bcl11b and Atoh8 as regulators of cellular plasticity in both processes, thus offering a unifying theory on the factors constraining cell fate changes.
Collapse
|
6
|
Molugu K, Battistini GA, Heaster TM, Rouw J, Guzman EC, Skala MC, Saha K. Label-Free Imaging to Track Reprogramming of Human Somatic Cells. GEN Biotechnol 2022; 1:176-191. [PMID: 35586336 PMCID: PMC9092522 DOI: 10.1089/genbio.2022.0001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/28/2022] [Indexed: 11/12/2022]
Abstract
The process of reprogramming patient samples to human-induced pluripotent stem cells (iPSCs) is stochastic, asynchronous, and inefficient, leading to a heterogeneous population of cells. In this study, we track the reprogramming status of patient-derived erythroid progenitor cells (EPCs) at the single-cell level during reprogramming with label-free live-cell imaging of cellular metabolism and nuclear morphometry to identify high-quality iPSCs. EPCs isolated from human peripheral blood of three donors were used for our proof-of-principle study. We found distinct patterns of autofluorescence lifetime for the reduced form of nicotinamide adenine dinucleotide (phosphate) and flavin adenine dinucleotide during reprogramming. Random forest models classified iPSCs with ∼95% accuracy, which enabled the successful isolation of iPSC lines from reprogramming cultures. Reprogramming trajectories resolved at the single-cell level indicated significant reprogramming heterogeneity along different branches of cell states. This combination of micropatterning, autofluorescence imaging, and machine learning provides a unique, real-time, and nondestructive method to assess the quality of iPSCs in a biomanufacturing process, which could have downstream impacts in regenerative medicine, cell/gene therapy, and disease modeling.
Collapse
Affiliation(s)
- Kaivalya Molugu
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin, USA; Madison, Wisconsin, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA; Madison, Wisconsin, USA
| | - Giovanni A. Battistini
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA; Madison, Wisconsin, USA
| | - Tiffany M. Heaster
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA; and Madison, Wisconsin, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Jacob Rouw
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA; Madison, Wisconsin, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA; and Madison, Wisconsin, USA
| | | | - Melissa C. Skala
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA; and Madison, Wisconsin, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Krishanu Saha
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA; Madison, Wisconsin, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA; and Madison, Wisconsin, USA
| |
Collapse
|
7
|
Zhang W, Li Y, Chen S, Zhang C, Chen L, Peng G. nr0b1 (DAX1) loss of function in zebrafish causes hypothalamic defects via abnormal progenitor proliferation and differentiation. J Genet Genomics 2021:S1673-8527(21)00318-0. [PMID: 34606992 DOI: 10.1016/j.jgg.2021.08.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/25/2021] [Accepted: 08/27/2021] [Indexed: 11/23/2022]
Abstract
The nuclear receptor DAX-1 (encoded by the NR0B1 gene) is presented in the hypothalamic tissues in humans and other vertebrates. Human patients with NR0B1 mutations often have hypothalamic-pituitary defects, but the involvement of NR0B1 in hypothalamic development and function is not well understood. Here, we report the disruption of the nr0b1 gene in zebrafish causes abnormal expression of gonadotropins, a reduction in fertilization rate, and an increase in post-fasting food intake, which is indicative of abnormal hypothalamic functions. We find that loss of nr0b1 increases the number of prodynorphin (pdyn)-expressing neurons but decreases the number of pro-opiomelanocortin (pomcb)-expressing neurons in the zebrafish hypothalamic arcuate region (ARC). Further examination reveals that the proliferation of progenitor cells is reduced in the hypothalamus of nr0b1 mutant embryos accompanying with the decreased expression of genes in the Notch signaling pathway. Additionally, the inhibition of Notch signaling in wild-type embryos increases the number of pdyn neurons, mimicking the nr0b1 mutant phenotype. In contrast, ectopic activation of Notch signaling in nr0b1 mutant embryos decreases the number of pdyn neurons. Taken together, our results suggest that nr0b1 regulates neural progenitor proliferation and maintenance to ensure normal hypothalamic neuron development.
Collapse
|
8
|
He J, Cheng Y, Ruan Y, Wang J, Tian Y, Wang J, Wang F, Zhang C, Xu Y, Liu L, Yu M, Wang J, Zhao B, Zhang Y, Yang Y, Liu G, Wu W, He P, Xiong J, Huang H, Zhang J, Jian R. Pluripotency-State-Dependent Role of Dax1 in Embryonic Stem Cells Self-Renewal. Stem Cells Int 2021; 2021:5522723. [PMID: 34335791 DOI: 10.1155/2021/5522723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/18/2021] [Accepted: 06/14/2021] [Indexed: 11/24/2022] Open
Abstract
Dax1(also known as Nr0b1) is regarded as an important component of the transcription factor network in mouse embryonic stem cells (ESCs). However, the role and the molecular mechanism of Dax1 in the maintenance of different pluripotency states are poorly understood. Here, we constructed a stable Dax1 knockout (KO) cell line using the CRISPR/Cas9 system to analyze the precise function of Dax1. We reported that 2i/LIF-ESCs had significantly lower Dax1 expression than LIF/serum-ESCs. Dax1KO ES cell lines could be established in 2i/LIF and their pluripotency was confirmed. In contrast, Dax1-null ESCs could not be continuously passaged in LIF/serum due to severe differentiation and apoptosis. In LIF/serum, the activities of the Core module and Myc module were significantly reduced, while the PRC2 module was activated after Dax1KO. The expression of most proapoptotic genes and lineage-commitment genes were drastically increased, while the downregulated expression of antiapoptotic genes and many pluripotency genes was observed. Our research on the pluripotent state-dependent role of Dax1 provides clues to understand the molecular regulation mechanism at different stages of early embryonic development.
Collapse
|
9
|
Ibrahim MR, Medhat W, El-Fakahany H, Abdel-Raouf H, Snyder EY. The Developmental & Molecular Requirements for Ensuring that Human Pluripotent Stem Cell-Derived Hair Follicle Bulge Stem Cells Have Acquired Competence for Hair Follicle Generation Following Transplantation. Cell Transplant 2021; 30:9636897211014820. [PMID: 34053245 PMCID: PMC8182633 DOI: 10.1177/09636897211014820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
When using human induced pluripotent stem cells (hiPSCs) to achieve hair follicle (HF) replacement, we found it best to emulate the earliest fundamental developmental processes of gastrulation, ectodermal lineage commitment, and dermogenesis. Viewing hiPSCs as a model of the epiblast, we exploited insights from mapping the dynamic up- and down-regulation of the developmental molecules that determine HF lineage in order to ascertain the precise differentiation stage and molecular requirements for grafting HF-generating progenitors. To yield an integrin-dependent lineage like the HF in vivo, we show that hiPSC derivatives should co-express, just prior to transplantation, the following combination of markers: integrins α6 and β1 and the glycoprotein CD200 on their surface; and, intracellularly, the epithelial marker keratin 18 and the hair follicle bulge stem cell (HFBSC)-defining molecules transcription factor P63 and the keratins 15 and 19. If the degree of trichogenic responsiveness indicated by the presence of these molecules is not achieved (they peak on Days 11-18 of the protocol), HF generation is not possible. Conversely, if differentiation of the cells is allowed to proceed beyond the transient intermediate progenitor state represented by the HFBSC, and instead cascades to their becoming keratin 14+ keratin 5+ CD200– keratinocytes (Day 25), HF generation is equally impossible. We make the developmental case for transplanting at Day 16-18 of differentiation—the point at which the hiPSCs have lost pluripotency, have attained optimal expression of HFBSC markers, have not yet experienced downregulation of key integrins and surface glycoproteins, have not yet started expressing keratinocyte-associated molecules, and have sufficient proliferative capacity to allow a well-populated graft. This panel of markers may be used for isolating (by cytometry) HF-generating derivatives away from cell types unsuited for this therapy as well as for identifying trichogenic drugs.
Collapse
Affiliation(s)
- Michel R Ibrahim
- Department of Dermatology, STD's and Andrology, Faculty of Medicine, Minia University, Al-Minya, Egypt.,Center for Stem Cells & Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.,Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
| | - Walid Medhat
- Department of Dermatology, STD's and Andrology, Faculty of Medicine, Minia University, Al-Minya, Egypt
| | - Hasan El-Fakahany
- Department of Dermatology, STD's and Andrology, Faculty of Medicine, Minia University, Al-Minya, Egypt
| | - Hamza Abdel-Raouf
- Department of Dermatology, STD's and Andrology, Faculty of Medicine, Minia University, Al-Minya, Egypt
| | - Evan Y Snyder
- Center for Stem Cells & Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.,Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA.,Department of Pediatrics, University of California-San Diego, La Jolla, CA, USA
| |
Collapse
|
10
|
Lv Y, Qin X, Hu K, Huang Y, Zhao S. Hybrid MoS 2/g-C 3N 4-assisted LDI mass spectrometry for rapid detection of small molecules and polyethylene glycols and direct determination of uric acid in complicated biological samples. Mikrochim Acta 2021; 188:5. [PMID: 33389155 DOI: 10.1007/s00604-020-04675-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/30/2020] [Indexed: 10/22/2022]
Abstract
A novel matrix-assisted laser desorption/ionization time-of-flight mass spectrometric method (MALDI-TOF MS) for determination of highly sensitive small molecular compounds was developed based on molybdenum disulfide nanosheets hybridized with ultrathin graphitic carbon nitride (MoS2/g-C3N4) as the matrix. With this approach, the synergistic effects of MoS2 and g-C3N4 enhance the UV absorption of MoS2/g-C3N4, increase both desorption and ionization efficiency in LDI MS, and induce higher signal-to-noise ratio of analytes when compared with the bare MoS2 and g-C3N4 matrix in the determination of amino acids, antibiotics, neutral oligosaccharides, uric acid, and polyethylene glycols (PEGs). The detection limits of these small molecular compounds are in the ranges 0.1 to 10 μg mL-1, 1*10-3 to 1.0 μg mL-1, 1.0 to 10 μg mL-1, and 2*10-4 μg mL-1, respectively, and the polydispersity index of these PEGs is less than 1.02. Moreover, high salt tolera`nce and homogeneous deposition on the spot results in good reproducibility. The relative standard deviations (RSDs) of shot-to-shot and spot-to-spot (n = 15) of these compounds are less than 10.1% and 12.5%, respectively. With MoS2/g-C3N4, the uric acid in complicated biological samples can be directly determined in combination with LDI-TOF MS. We synthesized MoS2/g-C3N4 nanohybrid as an efficient matrix for MALDI-TOF MS analysis of small molecules as well as quantitative detection of uric acid in human urine.
Collapse
Affiliation(s)
- Yuanxia Lv
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, People's Republic of China
| | - Xiaohuan Qin
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, People's Republic of China
| | - Kun Hu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, People's Republic of China.
| | - Yong Huang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, People's Republic of China
| | - Shulin Zhao
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, People's Republic of China
| |
Collapse
|
11
|
Zhu K, Liu Y, Fan C, Zhang M, Cao H, He X, Li N, Chu D, Li F, Zou M, Hua J, Wang H, Wang Y, Fan G, Zhang S. Etv5 safeguards trophoblast stem cells differentiation from mouse EPSCs by regulating fibroblast growth factor receptor 2. Mol Biol Rep 2020; 47:9259-9269. [PMID: 33159233 DOI: 10.1007/s11033-020-05969-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/29/2020] [Accepted: 10/31/2020] [Indexed: 11/26/2022]
Abstract
Previous studies have demonstrated that transcription factor Etv5 plays an important role in the segregation between epiblast and primitive endoderm at the second fate decision of early embryo. However, it remains elusive whether Etv5 functions in the segregation between inner cell mass and trophectoderm at the first cell fate decision. In this study, we firstly generated Etv5 knockout mouse embryonic stem cells (mESCs) by CRISPR/Cas9, then converted them into extended potential stem cells (EPSCs) by culturing the cells in small molecule cocktail medium LCDM (LIF, CHIR99021, (S)-(+)-dimethindene maleate, minocycline hydrochloride), and finally investigated their differentiation efficiency of trophoblast stem cells (TSCs). The results showed that Etv5 knockout significantly decreased the efficiency of TSCs (CDX2+) differentiated from EPSCs. In addition, Etv5 knockout resulted in higher incidence of the differentiated cells with tetraploid and octoploid than that from wild type. Mechanistically, Etv5 was activated by extracellular-signal-regulated kinase (ERK) signaling pathway; in turn, Etv5 had a positive feedback on the expression of fibroblast growth factor receptor 2 (FGFR2) which lies upstream of ERK. Etv5 knockout decreased the expression of FGFR2, whose binding with fibroblast growth factor 4 was essentially needed for TSCs differentiation. Collectively, the findings in this study suggest that Etv5 is required to safeguard the TSCs differentiation by regulating FGFR2 and provide new clues to understand the specification of trophectoderm in vivo.
Collapse
Affiliation(s)
- Kui Zhu
- College of Veterinary Medicine, Shaanxi Center of Stem Cells Engineering and Technology, Northwest A&F University, 712100, Yangling, China
| | - Yuan Liu
- College of Veterinary Medicine, Shaanxi Center of Stem Cells Engineering and Technology, Northwest A&F University, 712100, Yangling, China
| | - Chen Fan
- College of Veterinary Medicine, Shaanxi Center of Stem Cells Engineering and Technology, Northwest A&F University, 712100, Yangling, China
| | - Mengyao Zhang
- College of Veterinary Medicine, Shaanxi Center of Stem Cells Engineering and Technology, Northwest A&F University, 712100, Yangling, China
| | - Hongxia Cao
- College of Veterinary Medicine, Shaanxi Center of Stem Cells Engineering and Technology, Northwest A&F University, 712100, Yangling, China
| | - Xin He
- College of Veterinary Medicine, Shaanxi Center of Stem Cells Engineering and Technology, Northwest A&F University, 712100, Yangling, China
| | - Na Li
- College of Veterinary Medicine, Shaanxi Center of Stem Cells Engineering and Technology, Northwest A&F University, 712100, Yangling, China
| | - Dianfeng Chu
- State Key Laboratory of Genetically Engineered Veterinary Vaccines, Yebio Bioengineering Co.Ltd of Qingdao, Qingdao, China
| | - Fang Li
- State Key Laboratory of Genetically Engineered Veterinary Vaccines, Yebio Bioengineering Co.Ltd of Qingdao, Qingdao, China
| | - Min Zou
- State Key Laboratory of Genetically Engineered Veterinary Vaccines, Yebio Bioengineering Co.Ltd of Qingdao, Qingdao, China
| | - Jinlian Hua
- College of Veterinary Medicine, Shaanxi Center of Stem Cells Engineering and Technology, Northwest A&F University, 712100, Yangling, China
| | - Huayan Wang
- College of Veterinary Medicine, Shaanxi Center of Stem Cells Engineering and Technology, Northwest A&F University, 712100, Yangling, China
| | - Yan Wang
- College of Veterinary Medicine, Shaanxi Center of Stem Cells Engineering and Technology, Northwest A&F University, 712100, Yangling, China
| | - Gencheng Fan
- State Key Laboratory of Genetically Engineered Veterinary Vaccines, Yebio Bioengineering Co.Ltd of Qingdao, Qingdao, China.
| | - Shiqiang Zhang
- College of Veterinary Medicine, Shaanxi Center of Stem Cells Engineering and Technology, Northwest A&F University, 712100, Yangling, China.
| |
Collapse
|
12
|
Hu X, Wu Q, Zhang J, Kim J, Chen X, Hartman AA, Eastman AE, Park IH, Guo S. Reprogramming progressive cells display low CAG promoter activity. Stem Cells 2020; 39:43-54. [PMID: 33075202 PMCID: PMC7821215 DOI: 10.1002/stem.3295] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 10/06/2020] [Indexed: 12/29/2022]
Abstract
There is wide variability in the propensity of somatic cells to reprogram into pluripotency in response to the Yamanaka factors. How to segregate these variabilities to enrich for cells of specific traits that reprogram efficiently remains challenging. Here we report that the variability in reprogramming propensity is associated with the activity of the MKL1/SRF transcription factor and concurs with small cell size as well as rapid cell cycle. Reprogramming progressive cells can be prospectively identified by their low activity of a widely used synthetic promoter, CAG. CAGlow cells arise and expand during cell cycle acceleration in the early reprogramming culture of both mouse and human fibroblasts. Our work illustrates a molecular scenario underlying the distinct reprogramming propensities and demonstrates a convenient practical approach for their enrichment.
Collapse
Affiliation(s)
- Xiao Hu
- Department of Cell Biology, Yale University, New Haven, Connecticut, USA.,Yale Stem Cell Center, Yale University, New Haven, Connecticut, USA
| | - Qiao Wu
- Department of Cell Biology, Yale University, New Haven, Connecticut, USA.,Yale Stem Cell Center, Yale University, New Haven, Connecticut, USA
| | - Jian Zhang
- Department of Cell Biology, Yale University, New Haven, Connecticut, USA.,Yale Stem Cell Center, Yale University, New Haven, Connecticut, USA
| | - Jonghun Kim
- Yale Stem Cell Center, Yale University, New Haven, Connecticut, USA.,Department of Genetics, Yale University, New Haven, Connecticut, USA
| | - Xinyue Chen
- Department of Cell Biology, Yale University, New Haven, Connecticut, USA.,Yale Stem Cell Center, Yale University, New Haven, Connecticut, USA
| | - Amaleah A Hartman
- Department of Cell Biology, Yale University, New Haven, Connecticut, USA.,Yale Stem Cell Center, Yale University, New Haven, Connecticut, USA
| | - Anna E Eastman
- Department of Cell Biology, Yale University, New Haven, Connecticut, USA.,Yale Stem Cell Center, Yale University, New Haven, Connecticut, USA
| | - In-Hyun Park
- Yale Stem Cell Center, Yale University, New Haven, Connecticut, USA.,Department of Genetics, Yale University, New Haven, Connecticut, USA
| | - Shangqin Guo
- Department of Cell Biology, Yale University, New Haven, Connecticut, USA.,Yale Stem Cell Center, Yale University, New Haven, Connecticut, USA
| |
Collapse
|
13
|
Lee J, Armenta Ochoa M, Maceda P, Yoon E, Samarneh L, Wong M, Baker AB. A high throughput screening system for studying the effects of applied mechanical forces on reprogramming factor expression. Sci Rep 2020; 10:15469. [PMID: 32963285 PMCID: PMC7508814 DOI: 10.1038/s41598-020-72158-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 08/20/2020] [Indexed: 12/12/2022] Open
Abstract
Mechanical forces are important in the regulation of physiological homeostasis and the development of disease. The application of mechanical forces to cultured cells is often performed using specialized systems that lack the flexibility and throughput of other biological techniques. In this study, we developed a high throughput platform for applying complex dynamic mechanical forces to cultured cells. We validated the system for its ability to accurately apply parallel mechanical stretch in a 96 well plate format in 576 well simultaneously. Using this system, we screened for optimized conditions to stimulate increases in Oct-4 and other transcription factor expression in mouse fibroblasts. Using high throughput mechanobiological screening assays, we identified small molecules that can synergistically enhance the increase in reprograming-related gene expression in mouse fibroblasts when combined with mechanical loading. Taken together, our findings demonstrate a new powerful tool for investigating the mechanobiological mechanisms of disease and performing drug screening in the presence of applied mechanical load.
Collapse
Affiliation(s)
- Jason Lee
- Department of Biomedical Engineering, University of Texas at Austin, 1 University Station, BME 5.202D, C0800, Austin, TX, 78712, USA
| | - Miguel Armenta Ochoa
- Department of Biomedical Engineering, University of Texas at Austin, 1 University Station, BME 5.202D, C0800, Austin, TX, 78712, USA
| | - Pablo Maceda
- Department of Biomedical Engineering, University of Texas at Austin, 1 University Station, BME 5.202D, C0800, Austin, TX, 78712, USA
| | - Eun Yoon
- Department of Biomedical Engineering, University of Texas at Austin, 1 University Station, BME 5.202D, C0800, Austin, TX, 78712, USA
| | - Lara Samarneh
- Department of Biomedical Engineering, University of Texas at Austin, 1 University Station, BME 5.202D, C0800, Austin, TX, 78712, USA
| | - Mitchell Wong
- Department of Biomedical Engineering, University of Texas at Austin, 1 University Station, BME 5.202D, C0800, Austin, TX, 78712, USA
| | - Aaron B Baker
- Department of Biomedical Engineering, University of Texas at Austin, 1 University Station, BME 5.202D, C0800, Austin, TX, 78712, USA. .,Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA. .,The Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, TX, USA. .,Institute for Biomaterials, Drug Delivery and Regenerative Medicine, University of Texas at Austin, Austin, TX, USA.
| |
Collapse
|
14
|
Tran KA, Pietrzak SJ, Zaidan NZ, Siahpirani AF, McCalla SG, Zhou AS, Iyer G, Roy S, Sridharan R. Defining Reprogramming Checkpoints from Single-Cell Analyses of Induced Pluripotency. Cell Rep 2019; 27:1726-1741.e5. [PMID: 31067459 DOI: 10.1016/j.celrep.2019.04.056] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 03/04/2019] [Accepted: 04/10/2019] [Indexed: 12/14/2022] Open
Abstract
Elucidating the mechanism of reprogramming is confounded by heterogeneity due to the low efficiency and differential kinetics of obtaining induced pluripotent stem cells (iPSCs) from somatic cells. Therefore, we increased the efficiency with a combination of epigenomic modifiers and signaling molecules and profiled the transcriptomes of individual reprogramming cells. Contrary to the established temporal order, somatic gene inactivation and upregulation of cell cycle, epithelial, and early pluripotency genes can be triggered independently such that any combination of these events can occur in single cells. Sustained co-expression of Epcam, Nanog, and Sox2 with other genes is required to progress toward iPSCs. Ehf, Phlda2, and translation initiation factor Eif4a1 play functional roles in robust iPSC generation. Using regulatory network analysis, we identify a critical role for signaling inhibition by 2i in repressing somatic expression and synergy between the epigenomic modifiers ascorbic acid and a Dot1L inhibitor for pluripotency gene activation.
Collapse
|
15
|
O'Huallachain M, Bava FA, Shen M, Dallett C, Paladugu S, Samusik N, Yu S, Hussein R, Hillman GR, Higgins S, Lou M, Trejo A, Qin L, Tai YC, Kinoshita SM, Jager A, Lashkari D, Goltsev Y, Ozturk S, Nolan GP. Ultra-high throughput single-cell analysis of proteins and RNAs by split-pool synthesis. Commun Biol 2020; 3:213. [PMID: 32382044 DOI: 10.1038/s42003-020-0896-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 03/04/2020] [Indexed: 12/11/2022] Open
Abstract
Single-cell omics provide insight into cellular heterogeneity and function. Recent technological advances have accelerated single-cell analyses, but workflows remain expensive and complex. We present a method enabling simultaneous, ultra-high throughput single-cell barcoding of millions of cells for targeted analysis of proteins and RNAs. Quantum barcoding (QBC) avoids isolation of single cells by building cell-specific oligo barcodes dynamically within each cell. With minimal instrumentation (four 96-well plates and a multichannel pipette), cell-specific codes are added to each tagged molecule within cells through sequential rounds of classical split-pool synthesis. Here we show the utility of this technology in mouse and human model systems for as many as 50 antibodies to targeted proteins and, separately, >70 targeted RNA regions. We demonstrate that this method can be applied to multi-modal protein and RNA analyses. It can be scaled by expansion of the split-pool process and effectively renders sequencing instruments as versatile multi-parameter flow cytometers. Maeve O’Huallachain et al. report a method that enables simultaneous, ultra-high throughput single-cell barcoding for targeted single-cell protein and RNA analysis. They show the utility of their method in analyses of mRNA and protein expression in human and mouse cells.
Collapse
|
16
|
Abstract
Here we report a semiconductor-assisted laser desorption/ionization mass spectrometry (SA-LDI MS) platform to monitor photocatalytic reactions online and apply it for ultrafast reaction screening. In this method, we use photocatalytic nanomaterials as the substrate for LDI and then initiate and monitor the reactions simultaneously. The features of our method include the following: (i) It has a reaction acceleration effect: only seconds are needed in our interfacial reactions vs hours in conventional bulk phase. (ii) The reaction trend in our system agrees with that in bulk phase. (iii) By adding a stable analogue of reactant as internal standard, a quantification of the reaction can be achieved. (iv) The sensitivity is high: for 500 amol of reactant, the photocatalytic reaction can still be initiated and detected. This platform has advantages in ultrafast reaction screening (e.g., screening of nine catalysts requires 24 h by the UPLC-MS system but only 10 min by SA-LDI MS). Furthermore, the high specificity of MS enables the screening of catalytic selectivity of A-TiO2 nanoparticles for a methyl red (MR) and acid yellow (AY) mixture, whose absorption wavelengths are overlapped and thus cannot be discriminated by conventional optical methods. Furthermore, by using SA-LDI MS, we also monitored reductive debrominations during the degradation process of polybrominated diphenyl ethers (PBDEs), which is a type of important pollutant that is difficult to degrade and detect in liquid phase, and the photocatalytic reduction of CO2. Overall, SA-LDI MS realizes ultrafast photocatalytic reaction screening for the first time and provides practical analytical value in the field of catalyst screening.
Collapse
Affiliation(s)
- Jie Sun
- Beijing National Laboratory for Molecular Sciences, Key Laboratory for Analytical Chemistry for Living Biosystems, Institute of Chemistry, the Chinese Academy of Sciences, Beijing 100190, China.,University of CAS, Beijing 100049, China
| | - Yuming Jiang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory for Analytical Chemistry for Living Biosystems, Institute of Chemistry, the Chinese Academy of Sciences, Beijing 100190, China.,University of CAS, Beijing 100049, China
| | - Huihui Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory for Analytical Chemistry for Living Biosystems, Institute of Chemistry, the Chinese Academy of Sciences, Beijing 100190, China
| | - Xi Huang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory for Analytical Chemistry for Living Biosystems, Institute of Chemistry, the Chinese Academy of Sciences, Beijing 100190, China.,University of CAS, Beijing 100049, China
| | - Caiqiao Xiong
- Beijing National Laboratory for Molecular Sciences, Key Laboratory for Analytical Chemistry for Living Biosystems, Institute of Chemistry, the Chinese Academy of Sciences, Beijing 100190, China
| | - Zongxiu Nie
- Beijing National Laboratory for Molecular Sciences, Key Laboratory for Analytical Chemistry for Living Biosystems, Institute of Chemistry, the Chinese Academy of Sciences, Beijing 100190, China.,University of CAS, Beijing 100049, China
| |
Collapse
|
17
|
Ko ME, Williams CM, Fread KI, Goggin SM, Rustagi RS, Fragiadakis GK, Nolan GP, Zunder ER. FLOW-MAP: a graph-based, force-directed layout algorithm for trajectory mapping in single-cell time course datasets. Nat Protoc 2020; 15:398-420. [PMID: 31932774 DOI: 10.1038/s41596-019-0246-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 08/29/2019] [Indexed: 12/12/2022]
Abstract
High-dimensional single-cell technologies present new opportunities for biological discovery, but the complex nature of the resulting datasets makes it challenging to perform comprehensive analysis. One particular challenge is the analysis of single-cell time course datasets: how to identify unique cell populations and track how they change across time points. To facilitate this analysis, we developed FLOW-MAP, a graphical user interface (GUI)-based software tool that uses graph layout analysis with sequential time ordering to visualize cellular trajectories in high-dimensional single-cell datasets obtained from flow cytometry, mass cytometry or single-cell RNA sequencing (scRNAseq) experiments. Here we provide a detailed description of the FLOW-MAP algorithm and how to use the open-source R package FLOWMAPR via its GUI or with text-based commands. This approach can be applied to many dynamic processes, including in vitro stem cell differentiation, in vivo development, oncogenesis, the emergence of drug resistance and cell signaling dynamics. To demonstrate our approach, we perform a step-by-step analysis of a single-cell mass cytometry time course dataset from mouse embryonic stem cells differentiating into the three germ layers: endoderm, mesoderm and ectoderm. In addition, we demonstrate FLOW-MAP analysis of a previously published scRNAseq dataset. Using both synthetic and experimental datasets for comparison, we perform FLOW-MAP analysis side by side with other single-cell analysis methods, to illustrate when it is advantageous to use the FLOW-MAP approach. The protocol takes between 30 min and 1.5 h to complete.
Collapse
Affiliation(s)
- Melissa E Ko
- Cancer Biology Program, Stanford School of Medicine, Stanford, CA, USA
| | - Corey M Williams
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA.,Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, USA
| | - Kristen I Fread
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Sarah M Goggin
- Neuroscience Graduate Program, University of Virginia, Charlottesville, VA, USA
| | - Rohit S Rustagi
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | | | - Garry P Nolan
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Eli R Zunder
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA.
| |
Collapse
|
18
|
Im I, Son YS, Jung KB, Kang I, Teh BE, Lee KB, Son MY, Kim J. Mass cytometry-based single-cell analysis of human stem cell reprogramming uncovers differential regulation of specific pluripotency markers. J Biol Chem 2019; 294:18547-18556. [PMID: 31570522 DOI: 10.1074/jbc.ra119.009061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 09/25/2019] [Indexed: 12/22/2022] Open
Abstract
Human induced pluripotent stem cells (hiPSCs) are reprogrammed from somatic cells and are regarded as promising sources for regenerative medicine and disease research. Recently, techniques for analyses of individual cells, such as single-cell RNA-Seq and mass cytometry, have been used to understand the stem cell reprogramming process in the mouse. However, the reprogramming process in hiPSCs remains poorly understood. Here we used mass cytometry to analyze the expression of pluripotency and cell cycle markers in the reprogramming of human stem cells. We confirmed that, during reprogramming, the main cell population was shifted to an intermediate population consisting of neither fibroblasts nor hiPSCs. Detailed population analyses using computational approaches, including dimensional reduction by spanning-tree progression analysis of density-normalized events, PhenoGraph, and diffusion mapping, revealed several distinct cell clusters representing the cells along the reprogramming route. Interestingly, correlation analysis of various markers in hiPSCs revealed that the pluripotency marker TRA-1-60 behaves in a pattern that is different from other pluripotency markers. Furthermore, we found that the expression pattern of another pluripotency marker, octamer-binding protein 4 (OCT4), was distinctive in the pHistone-H3high population (M phase) of the cell cycle. To the best of our knowledge, this is the first mass cytometry-based investigation of human reprogramming and pluripotency. Our analysis elucidates several aspects of hiPSC reprogramming, including several intermediate cell clusters active during the process of reprogramming and distinctive marker expression patterns in hiPSCs.
Collapse
Affiliation(s)
- Ilkyun Im
- Stem Cell Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahag-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Ye Seul Son
- Stem Cell Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahag-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Functional Genomics, Korea Research Institute of Bioscience and Biotechnology School of Bioscience, Korea University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Kwang Bo Jung
- Stem Cell Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahag-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Functional Genomics, Korea Research Institute of Bioscience and Biotechnology School of Bioscience, Korea University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Insoo Kang
- Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut 06520; Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520; Department of Orthopedics and Rehabilitation, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Boon-Eng Teh
- Fluidigm Corporation, South San Francisco, California 94080-7603
| | - Kyung-Bok Lee
- Center for Research Equipment, Korea Basic Science Institute, 162 Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju 28119, Republic of Korea
| | - Mi-Young Son
- Stem Cell Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahag-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Functional Genomics, Korea Research Institute of Bioscience and Biotechnology School of Bioscience, Korea University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea.
| | - Janghwan Kim
- Stem Cell Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahag-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Functional Genomics, Korea Research Institute of Bioscience and Biotechnology School of Bioscience, Korea University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea.
| |
Collapse
|
19
|
Abstract
Single-cell analysis provides insights into cellular heterogeneity and dynamics of individual cells. This Feature highlights recent developments in key analytical techniques suited for single-cell metabolic analysis with a special focus on mass spectrometry-based analytical platforms and RNA-seq as well as imaging techniques that reveal stochasticity in metabolism.
Collapse
Affiliation(s)
- Tom MJ Evers
- Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Mathematics and Natural Sciences, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Mazène Hochane
- Leiden Institute of Physics, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Sander J Tans
- AMOLF Institute, Science Park 104 1098 XG Amsterdam, The Netherlands
| | - Ron MA Heeren
- The Maastricht MultiModal Molecular Imaging Institute (M4I), Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| | - Stefan Semrau
- Leiden Institute of Physics, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Peter Nemes
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Alireza Mashaghi
- Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Mathematics and Natural Sciences, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| |
Collapse
|
20
|
Molugu K, Harkness T, Carlson-Stevermer J, Prestil R, Piscopo NJ, Seymour SK, Knight GT, Ashton RS, Saha K. Tracking and Predicting Human Somatic Cell Reprogramming Using Nuclear Characteristics. Biophys J 2019; 118:2086-2102. [PMID: 31699335 DOI: 10.1016/j.bpj.2019.10.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 10/11/2019] [Accepted: 10/15/2019] [Indexed: 02/06/2023] Open
Abstract
Reprogramming of human somatic cells to induced pluripotent stem cells (iPSCs) generates valuable resources for disease modeling, toxicology, cell therapy, and regenerative medicine. However, the reprogramming process can be stochastic and inefficient, creating many partially reprogrammed intermediates and non-reprogrammed cells in addition to fully reprogrammed iPSCs. Much of the work to identify, evaluate, and enrich for iPSCs during reprogramming relies on methods that fix, destroy, or singularize cell cultures, thereby disrupting each cell's microenvironment. Here, we develop a micropatterned substrate that allows for dynamic live-cell microscopy of hundreds of cell subpopulations undergoing reprogramming while preserving many of the biophysical and biochemical cues within the cells' microenvironment. On this substrate, we were able to both watch and physically confine cells into discrete islands during the reprogramming of human somatic cells from skin biopsies and blood draws obtained from healthy donors. Using high-content analysis, we identified a combination of eight nuclear characteristics that can be used to generate a computational model to predict the progression of reprogramming and distinguish partially reprogrammed cells from those that are fully reprogrammed. This approach to track reprogramming in situ using micropatterned substrates could aid in biomanufacturing of therapeutically relevant iPSCs and be used to elucidate multiscale cellular changes (cell-cell interactions as well as subcellular changes) that accompany human cell fate transitions.
Collapse
Affiliation(s)
- Kaivalya Molugu
- Graduate Program in Biophysics, University of Wisconsin-Madison, Madison, Wisconsin; Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin; Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin
| | - Ty Harkness
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin; Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin
| | - Jared Carlson-Stevermer
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin; Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin
| | - Ryan Prestil
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin; Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin
| | - Nicole J Piscopo
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin; Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin
| | - Stephanie K Seymour
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin; Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin
| | - Gavin T Knight
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin; Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin
| | - Randolph S Ashton
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin; Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin
| | - Krishanu Saha
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin; Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin.
| |
Collapse
|
21
|
Fortunel NO, Chadli L, Coutier J, Lemaître G, Auvré F, Domingues S, Bouissou-Cadio E, Vaigot P, Cavallero S, Deleuze JF, Roméo PH, Martin MT. KLF4 inhibition promotes the expansion of keratinocyte precursors from adult human skin and of embryonic-stem-cell-derived keratinocytes. Nat Biomed Eng 2019; 3:985-997. [PMID: 31636412 DOI: 10.1038/s41551-019-0464-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 09/13/2019] [Indexed: 01/01/2023]
Abstract
Expanded autologous skin keratinocytes are currently used in cutaneous cell therapy, and embryonic-stem-cell-derived keratinocytes could become a complementary alternative. Regardless of keratinocyte provenance, for efficient therapy it is necessary to preserve immature keratinocyte precursors during cell expansion and graft processing. Here, we show that stable and transient downregulation of the transcription factor Krüppel-like factor 4 (KLF4) in keratinocyte precursors from adult skin, using anti-KLF4 RNA interference or kenpaullone, promotes keratinocyte immaturity and keratinocyte self-renewal in vitro, and enhances the capacity for epidermal regeneration in mice. Both stable and transient KLF4 downregulation had no impact on the genomic integrity of adult keratinocytes. Moreover, transient KLF4 downregulation in human-embryonic-stem-cell-derived keratinocytes increased the efficiency of skin-orientated differentiation and of keratinocyte immaturity, and was associated with improved generation of epidermis. As a regulator of the cell fate of keratinocyte precursors, KLF4 could be used for promoting the ex vivo expansion and maintenance of functional immature keratinocyte precursors.
Collapse
Affiliation(s)
- Nicolas O Fortunel
- Laboratoire de Génomique et Radiobiologie de la Kératinopoïèse, CEA/DRF/IBFJ/IRCM, Evry, France. .,INSERM U967, Université Paris-Diderot, Paris, France. .,Université Paris-Saclay, Paris, France.
| | - Loubna Chadli
- Laboratoire de Génomique et Radiobiologie de la Kératinopoïèse, CEA/DRF/IBFJ/IRCM, Evry, France.,INSERM U967, Université Paris-Diderot, Paris, France.,Université Paris-Saclay, Paris, France
| | - Julien Coutier
- Laboratoire de Génomique et Radiobiologie de la Kératinopoïèse, CEA/DRF/IBFJ/IRCM, Evry, France.,INSERM U967, Université Paris-Diderot, Paris, France.,Université Paris-Saclay, Paris, France
| | - Gilles Lemaître
- Université d'Evry Val d'Essonne, Université Paris-Saclay, INSERM U861, Institut des Cellules Souches pour le Traitement et l'Etude des Maladies Monogéniques, Corbeil Essonne, France
| | - Frédéric Auvré
- Laboratoire de Génomique et Radiobiologie de la Kératinopoïèse, CEA/DRF/IBFJ/IRCM, Evry, France.,INSERM U967, Université Paris-Diderot, Paris, France.,Université Paris-Saclay, Paris, France
| | - Sophie Domingues
- Centre d'Etude des Cellules Souches, Institut des Cellules Souches pour le Traitement et l'Etude des Maladies Monogéniques, Corbeil Essonne, France
| | - Emmanuelle Bouissou-Cadio
- Laboratoire de Génomique et Radiobiologie de la Kératinopoïèse, CEA/DRF/IBFJ/IRCM, Evry, France.,INSERM U967, Université Paris-Diderot, Paris, France.,Université Paris-Saclay, Paris, France
| | - Pierre Vaigot
- Laboratoire de Génomique et Radiobiologie de la Kératinopoïèse, CEA/DRF/IBFJ/IRCM, Evry, France.,INSERM U967, Université Paris-Diderot, Paris, France.,Université Paris-Saclay, Paris, France
| | - Sophie Cavallero
- Laboratoire de Génomique et Radiobiologie de la Kératinopoïèse, CEA/DRF/IBFJ/IRCM, Evry, France.,INSERM U967, Université Paris-Diderot, Paris, France.,Université Paris-Saclay, Paris, France
| | | | - Paul-Henri Roméo
- INSERM U967, Université Paris-Diderot, Paris, France.,Université Paris-Saclay, Paris, France.,Laboratoire de Recherche sur la Réparation et la Transcription dans les Cellules Souches, CEA/DRF/IBFJ/IRCM, Fontenay-aux-Roses, France
| | - Michèle T Martin
- Laboratoire de Génomique et Radiobiologie de la Kératinopoïèse, CEA/DRF/IBFJ/IRCM, Evry, France. .,INSERM U967, Université Paris-Diderot, Paris, France. .,Université Paris-Saclay, Paris, France.
| |
Collapse
|
22
|
Jen HI, Hill MC, Tao L, Sheng K, Cao W, Zhang H, Yu HV, Llamas J, Zong C, Martin JF, Segil N, Groves AK. Transcriptomic and epigenetic regulation of hair cell regeneration in the mouse utricle and its potentiation by Atoh1. eLife 2019; 8:e44328. [PMID: 31033441 PMCID: PMC6504235 DOI: 10.7554/elife.44328] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 04/28/2019] [Indexed: 12/30/2022] Open
Abstract
The mammalian cochlea loses its ability to regenerate new hair cells prior to the onset of hearing. In contrast, the adult vestibular system can produce new hair cells in response to damage, or by reprogramming of supporting cells with the hair cell transcription factor Atoh1. We used RNA-seq and ATAC-seq to probe the transcriptional and epigenetic responses of utricle supporting cells to damage and Atoh1 transduction. We show that the regenerative response of the utricle correlates with a more accessible chromatin structure in utricle supporting cells compared to their cochlear counterparts. We also provide evidence that Atoh1 transduction of supporting cells is able to promote increased transcriptional accessibility of some hair cell genes. Our study offers a possible explanation for regenerative differences between sensory organs of the inner ear, but shows that additional factors to Atoh1 may be required for optimal reprogramming of hair cell fate.
Collapse
Affiliation(s)
- Hsin-I Jen
- Program in Developmental BiologyBaylor College of MedicineHoustonUnited States
| | - Matthew C Hill
- Program in Developmental BiologyBaylor College of MedicineHoustonUnited States
| | - Litao Tao
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUnited States
- Caruso Department of Otolaryngology - Head and Neck Surgery, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUnited States
| | - Kuanwei Sheng
- Program in Integrative Molecular and Biomedical SciencesBaylor College of MedicineHoustonUnited States
| | - Wenjian Cao
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUnited States
| | - Hongyuan Zhang
- Department of NeuroscienceBaylor College of MedicineHoustonUnited States
| | - Haoze V Yu
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUnited States
- Caruso Department of Otolaryngology - Head and Neck Surgery, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUnited States
| | - Juan Llamas
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUnited States
- Caruso Department of Otolaryngology - Head and Neck Surgery, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUnited States
| | - Chenghang Zong
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUnited States
| | - James F Martin
- Program in Developmental BiologyBaylor College of MedicineHoustonUnited States
- Department of Molecular Physiology and BiophysicsBaylor College of MedicineHoustonUnited States
- The Texas Heart InstituteHoustonUnited States
| | - Neil Segil
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUnited States
- Caruso Department of Otolaryngology - Head and Neck Surgery, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUnited States
| | - Andrew K Groves
- Program in Developmental BiologyBaylor College of MedicineHoustonUnited States
- Department of NeuroscienceBaylor College of MedicineHoustonUnited States
| |
Collapse
|
23
|
Abstract
Advances in single-cell mass cytometry have increasingly improved highly multidimensional characterization of immune cell heterogeneity. The immunoassay multiplexing capacity relies on monoclonal antibodies labeled with stable heavy-metal isotopes. To date, a variety of rare-earth elements and noble and post-transition metal isotopes have been used in mass cytometry; nevertheless, the methods used for antibody conjugation differ because of the individual metal coordination chemistries and distinct stabilities of various metal cations. Herein, we provide three optimized protocols for conjugating monoclonal IgG antibodies with 48 high-purity heavy-metal isotopes: (i) 38 isotopes of lanthanides, 2 isotopes of indium, and 1 isotope of yttrium; (ii) 6 isotopes of palladium; and (iii) 1 isotope of bismuth. Bifunctional chelating agents containing coordinative ligands of monomeric DOTA (1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid) or polymeric pentetic acid (DTPA) were used to stably sequester isotopic cations in aqueous solutions and were subsequently coupled to IgG antibodies using site-specific biorthogonal reactions. Furthermore, quantification methods based on antibody inherent absorption at 280 nm and on extrinsic absorption at 562 nm after staining with bicinchoninic acid (BCA) are reported to determine metal-isotope-tagged antibodies. In addition, a freeze-drying procedure to prepare palladium isotopic mass tags is described. To demonstrate the utility, experiments using six palladium-tagged CD45 antibodies for barcoding assays of live immune cells in cytometry by time-of-flight (CyTOF) are described. Conjugation of pure isotopes of lanthanides, indium, or yttrium takes ~3.5 h. Conjugation of bismuth takes ~4 h. Preparation of palladium mass tags takes ~8 h. Conjugation of pure isotopes of palladium takes ~2.5 h. Antibody titration takes ~4 h.
Collapse
|
24
|
Guo L, Lin L, Wang X, Gao M, Cao S, Mai Y, Wu F, Kuang J, Liu H, Yang J, Chu S, Song H, Li D, Liu Y, Wu K, Liu J, Wang J, Pan G, Hutchins AP, Liu J, Pei D, Chen J. Resolving Cell Fate Decisions during Somatic Cell Reprogramming by Single-Cell RNA-Seq. Mol Cell 2019; 73:815-829.e7. [DOI: 10.1016/j.molcel.2019.01.042] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/25/2018] [Accepted: 01/29/2019] [Indexed: 01/07/2023]
|
25
|
Hu X, Qin S, Huang X, Yuan Y, Tan Z, Gu Y, Cheng X, Wang D, Lian XF, He C, Su Z. Region-Restrict Astrocytes Exhibit Heterogeneous Susceptibility to Neuronal Reprogramming. Stem Cell Reports 2019; 12:290-304. [PMID: 30713039 PMCID: PMC6373495 DOI: 10.1016/j.stemcr.2018.12.017] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 12/26/2018] [Accepted: 12/28/2018] [Indexed: 12/21/2022] Open
Abstract
The adult CNS has poor ability to replace degenerated neurons following injury or disease. Recently, direct reprogramming of astrocytes into induced neurons has been proposed as an innovative strategy toward CNS repair. As a cell population that shows high diversity on physiological properties and functions depending on their spatiotemporal distribution, however, whether the astrocyte heterogeneity affect neuronal reprogramming is not clear. Here, we show that astrocytes derived from cortex, cerebellum, and spinal cord exhibit biological heterogeneity and possess distinct susceptibility to transcription factor-induced neuronal reprogramming. The heterogeneous expression level of NOTCH1 signaling in the different CNS regions-derived astrocytes is shown to be responsible for the neuronal reprogramming diversity. Taken together, our findings demonstrate that region-restricted astrocytes reveal different intrinsic limitation of the response to neuronal reprogramming. Region-restrict astrocytes (ACs) exhibit obvious heterogeneity Region-restrict ACs show distinct susceptibility to neuronal reprogramming AC heterogeneity does not affect the maturation of induced neurons Notch1 is involved in the neuronal reprogramming diversity of region-restrict ACs
Collapse
Affiliation(s)
- Xin Hu
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Second Military Medical University, Shanghai 200433, China; Department of Neurological Surgery, Xixi Hospital of Hangzhou, Hangzhou 200233 China
| | - Shangyao Qin
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Second Military Medical University, Shanghai 200433, China
| | - Xiao Huang
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Second Military Medical University, Shanghai 200433, China
| | - Yimin Yuan
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Second Military Medical University, Shanghai 200433, China
| | - Zijian Tan
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Second Military Medical University, Shanghai 200433, China
| | - Yakun Gu
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Second Military Medical University, Shanghai 200433, China
| | - Xueyan Cheng
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Second Military Medical University, Shanghai 200433, China
| | - Dan Wang
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Second Military Medical University, Shanghai 200433, China
| | - Xiao-Feng Lian
- Department of Orthopedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 310009, China
| | - Cheng He
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Second Military Medical University, Shanghai 200433, China.
| | - Zhida Su
- Institute of Neuroscience, Key Laboratory of Molecular Neurobiology of Ministry of Education and the Collaborative Innovation Center for Brain Science, Second Military Medical University, Shanghai 200433, China.
| |
Collapse
|
26
|
Kagawa H, Shimamoto R, Kim SI, Oceguera-Yanez F, Yamamoto T, Schroeder T, Woltjen K. OVOL1 Influences the Determination and Expansion of iPSC Reprogramming Intermediates. Stem Cell Reports 2019; 12:319-32. [PMID: 30639212 DOI: 10.1016/j.stemcr.2018.12.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 12/11/2018] [Accepted: 12/12/2018] [Indexed: 01/24/2023] Open
Abstract
During somatic cell reprogramming to induced pluripotent stem cells (iPSCs), fibroblasts undergo dynamic molecular changes, including a mesenchymal-to-epithelial transition (MET) and gain of pluripotency; processes that are influenced by Yamanaka factor stoichiometry. For example, in early reprogramming, high KLF4 levels are correlated with the induction of functionally undefined, transiently expressed MET genes. Here, we identified the cell-surface protein TROP2 as a marker for cells with transient MET induction in the high-KLF4 condition. We observed the emergence of cells expressing the pluripotency marker SSEA-1+ mainly from within the TROP2+ fraction. Using TROP2 as a marker in CRISPR/Cas9-mediated candidate screening of MET genes, we identified the transcription factor OVOL1 as a potential regulator of an alternative epithelial cell fate characterized by the expression of non-iPSC MET genes and low cell proliferation. Our study sheds light on how reprogramming factor stoichiometry alters the spectrum of intermediate cell fates, ultimately influencing reprogramming outcomes. High KLF4 activates transient MET genes early in reprogramming The cell-surface protein TROP2 marks a transient epithelial population TROP2 is followed by SSEA-1 presentation in cells efficient at reprogramming Suppression of partially reprogrammed cells improves the purity of reprogramming
Collapse
|
27
|
Abstract
Human induced pluripotent stem cells (iPSCs) provide a renewable supply of patient-specific and tissue-specific cells for cellular and molecular studies of disease mechanisms. Combined with advances in various omics technologies, iPSC models can be used to profile the expression of genes, transcripts, proteins, and metabolites in relevant tissues. In the past 2 years, large panels of iPSC lines have been derived from hundreds of genetically heterogeneous individuals, further enabling genome-wide mapping to identify coexpression networks and elucidate gene regulatory networks. Here, we review recent developments in omics profiling of various molecular phenotypes and the emergence of human iPSCs as a systems biology model of human diseases.
Collapse
Affiliation(s)
- Edward Lau
- Stanford Cardiovascular Institute, and Department of Medicine, Division of Cardiology, Stanford University, Stanford, California 94305, USA;
| | - David T Paik
- Stanford Cardiovascular Institute, and Department of Medicine, Division of Cardiology, Stanford University, Stanford, California 94305, USA;
| | - Joseph C Wu
- Stanford Cardiovascular Institute, and Department of Medicine, Division of Cardiology, Stanford University, Stanford, California 94305, USA; .,Department of Radiology, Stanford University, Stanford, California 94305, USA
| |
Collapse
|
28
|
Yuan CW, Wang ZC, Liu K, Liu DJ. Incomplete radiofrequency ablation promotes the development of CD133(+) cancer stem cells in hepatocellular carcinoma cell line HepG2 via inducing SOX9 expression. Hepatobiliary Pancreat Dis Int 2018; 17:416-22. [PMID: 30262419 DOI: 10.1016/j.hbpd.2018.09.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 08/28/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND Cancer stem cells (CSCs) accelerate the growth of hepatocellular carcinoma (HCC) residual after incomplete radiofrequency ablation (In-RFA). The present study aimed to detect the effects of In-RFA on stemness transcription factors (STFs) expression which are important for the production and function of CSCs, and to find which STFs promote HCC stemness after In-RFA. METHODS HepG2 cells were used for in vitro and in vivo studies. Flow cytometry and sphere-formation assays were used to detect the level and function of CD133+CSCs in the models. PCR array and ELISA were applied to analyze the altered expression of 84 STFs in CD133+CSCs in two models. Specific lentiviral shRNA was used to knockdown STFs expression, followed by detecting In-RFA's effects on the levels and function of CD133+CSCs. RESULTS In-RFA was identified to induce CD133+CSCs and increase their tumorigenesis ability in vitro and in vivo. The mRNA levels of 84 STFs in CD133+CSCs were detected by PCR array, showing that 15 and 22 STFs were up-regulated in two models, respectively. Meanwhile, the mRNA levels of seven common STFs were up-regulated in both models. ELISA assay demonstrated that only the protein of sex determining region Y-box 9 (SOX9) was up-regulated in both models, the protein levels of the other 6 common STFs did not increase in both models. Finally, SOX9 was identified to play an important role in inducing, maintaining stemness and promoting tumorigenesis ability of CD133+CSCs in both models. CONCLUSION In-RFA-induced SOX9 stimulates CD133+CSCs proliferation and increases their tumorigenesis ability, suggesting that SOX9 may be a good target for HCC treatment.
Collapse
|
29
|
Guo L, Karoubi G, Duchesneau P, Aoki FG, Shutova MV, Rogers I, Nagy A, Waddell TK. Interrupted reprogramming of alveolar type II cells induces progenitor-like cells that ameliorate pulmonary fibrosis. NPJ Regen Med 2018; 3:14. [PMID: 30210809 PMCID: PMC6123410 DOI: 10.1038/s41536-018-0052-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 06/04/2018] [Accepted: 06/18/2018] [Indexed: 02/04/2023] Open
Abstract
We describe here an interrupted reprogramming strategy to generate “induced progenitor-like (iPL) cells” from alveolar epithelial type II (AEC-II) cells. A carefully defined period of transient expression of reprogramming factors (Oct4, Sox2, Klf4, and c-Myc (OSKM)) is able to rescue the limited in vitro clonogenic capacity of AEC-II cells, potentially by activation of a bipotential progenitor-like state. Importantly, our results demonstrate that interrupted reprogramming results in controlled expansion of cell numbers yet preservation of the differentiation pathway to the alveolar epithelial lineage. When transplanted to the injured lungs, AEC-II-iPL cells are retained in the lung and ameliorate bleomycin-induced pulmonary fibrosis. Interrupted reprogramming can be used as an alternative approach to produce highly specified functional therapeutic cell populations and may lead to significant advances in regenerative medicine. A modified reprogramming strategy helps expand populations of surfactant-producing lung cells in a dish without altering their cellular function. A team led by Thomas Waddell and Andras Nagy from the University of Toronto, Canada isolated alveolar type II cells from the lungs of mice. They transiently induced expression of four reprogramming factors in these cells for a defined period of time. Before this “interrupted” reprogramming, the lung cells had limited ability to continue replicating themselves. Afterwards, the cells could expand their numbers dramatically without entering a pluripotent state. Rather, the cells maintained their original function while also expressing genes associated with lung precursor cells, which could explain their proliferative ability. The cells, when transplanted into the injured lungs, helped ameliorate pulmonary fibrosis in a mouse model, suggesting that a similar cell-based therapy may be useful in people.
Collapse
Affiliation(s)
- Li Guo
- 1Division of Thoracic Surgery, Toronto General Hospital Research Institute, University Health Network, University of Toronto, Toronto, ON Canada
| | - Golnaz Karoubi
- 1Division of Thoracic Surgery, Toronto General Hospital Research Institute, University Health Network, University of Toronto, Toronto, ON Canada
| | - Pascal Duchesneau
- 1Division of Thoracic Surgery, Toronto General Hospital Research Institute, University Health Network, University of Toronto, Toronto, ON Canada
| | - Fabio Gava Aoki
- 1Division of Thoracic Surgery, Toronto General Hospital Research Institute, University Health Network, University of Toronto, Toronto, ON Canada
| | - Maria V Shutova
- Lunenfeld Tanenbaum Research Institute, Sinai Health System, Toronto, ON Canada
| | - Ian Rogers
- Lunenfeld Tanenbaum Research Institute, Sinai Health System, Toronto, ON Canada.,3Department of Physiology, University of Toronto, Toronto, ON Canada.,4Department of Obstetrics & Gynecology, University of Toronto, Toronto, ON Canada
| | - Andras Nagy
- Lunenfeld Tanenbaum Research Institute, Sinai Health System, Toronto, ON Canada.,4Department of Obstetrics & Gynecology, University of Toronto, Toronto, ON Canada.,5Institute of Medical Science, University of Toronto, Toronto, ON Canada.,6Monash University, Melbourne, VIC Australia
| | - Thomas K Waddell
- 1Division of Thoracic Surgery, Toronto General Hospital Research Institute, University Health Network, University of Toronto, Toronto, ON Canada.,5Institute of Medical Science, University of Toronto, Toronto, ON Canada
| |
Collapse
|
30
|
Mor N, Rais Y, Sheban D, Peles S, Aguilera-Castrejon A, Zviran A, Elinger D, Viukov S, Geula S, Krupalnik V, Zerbib M, Chomsky E, Lasman L, Shani T, Bayerl J, Gafni O, Hanna S, Buenrostro JD, Hagai T, Masika H, Vainorius G, Bergman Y, Greenleaf WJ, Esteban MA, Elling U, Levin Y, Massarwa R, Merbl Y, Novershtern N, Hanna JH. Neutralizing Gatad2a-Chd4-Mbd3/NuRD Complex Facilitates Deterministic Induction of Naive Pluripotency. Cell Stem Cell 2018; 23:412-425.e10. [PMID: 30122475 DOI: 10.1016/j.stem.2018.07.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 06/19/2018] [Accepted: 07/10/2018] [Indexed: 01/08/2023]
Abstract
Mbd3, a member of nucleosome remodeling and deacetylase (NuRD) co-repressor complex, was previously identified as an inhibitor for deterministic induced pluripotent stem cell (iPSC) reprogramming, where up to 100% of donor cells successfully complete the process. NuRD can assume multiple mutually exclusive conformations, and it remains unclear whether this deterministic phenotype can be attributed to a specific Mbd3/NuRD subcomplex. Moreover, since complete ablation of Mbd3 blocks somatic cell proliferation, we aimed to explore functionally relevant alternative ways to neutralize Mbd3-dependent NuRD activity. We identify Gatad2a, a NuRD-specific subunit, whose complete deletion specifically disrupts Mbd3/NuRD repressive activity on the pluripotency circuitry during iPSC differentiation and reprogramming without ablating somatic cell proliferation. Inhibition of Gatad2a facilitates deterministic murine iPSC reprogramming within 8 days. We validate a distinct molecular axis, Gatad2a-Chd4-Mbd3, within Mbd3/NuRD as being critical for blocking reestablishment of naive pluripotency and further highlight signaling-dependent and post-translational modifications of Mbd3/NuRD that influence its interactions and assembly.
Collapse
Affiliation(s)
- Nofar Mor
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel
| | - Yoach Rais
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel.
| | - Daoud Sheban
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel; Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Shani Peles
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel
| | | | - Asaf Zviran
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel; New York Genome Center, New York, NY, USA
| | - Dalia Elinger
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Sergey Viukov
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel
| | - Shay Geula
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel
| | - Vladislav Krupalnik
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel
| | - Mirie Zerbib
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel
| | - Elad Chomsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Lior Lasman
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel
| | - Tom Shani
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel
| | - Jonathan Bayerl
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel
| | - Ohad Gafni
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel
| | - Suhair Hanna
- Department of Pediatrics, Rambam Health Care Campus, Haifa, Israel
| | - Jason D Buenrostro
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Society of Fellows, Harvard University, Cambridge, MA, USA
| | - Tzachi Hagai
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Hagit Masika
- Department of Developmental Biology and Cancer Research, Hebrew University, Jerusalem, Israel
| | | | - Yehudit Bergman
- Department of Developmental Biology and Cancer Research, Hebrew University, Jerusalem, Israel
| | - William J Greenleaf
- Department of Genetics, Stanford University, Palo Alto, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Miguel A Esteban
- Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Ulrich Elling
- Institute of Molecular Biotechnology (IMBA), Vienna, Austria
| | - Yishai Levin
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Rada Massarwa
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel
| | - Yifat Merbl
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Novershtern
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel.
| | - Jacob H Hanna
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel.
| |
Collapse
|
31
|
Silva PGC, Moura MT, Silva RLO, Nascimento PS, Silva JB, Ferreira-Silva JC, Cantanhêde LF, Chaves MS, Benko-Iseppon AM, Oliveira MAL. Temporal expression of pluripotency-associated transcription factors in sheep and cattle preimplantation embryos. ZYGOTE 2018; 26:270-8. [PMID: 30033902 DOI: 10.1017/S0967199418000175] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
SummaryPluripotency-associated transcription factors (PATFs) modulate gene expression during early mammalian embryogenesis. Despite a strong understanding of PATFs during mouse embryogenesis, limited progress has been made in ruminants. This work aimed to describe the temporal expression of eight PATFs during both sheep and cattle preimplantation development. Transcript availability of PATFs was evaluated by reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) in eggs, cleavage-stage embryos, morulae, and blastocysts. Transcripts of five genes were detected in all developmental stages of both species (KLF5, OCT4, RONIN, ZFP281, and ZFX). Furthermore, CMYC was detected in all cattle samples but was found from cleavage-stage onwards in sheep. In contrast, NR0B1 was detected in all sheep samples but was not detected in cattle morulae. GLIS1 displayed the most significant variation in temporal expression between species, as this PATF was only detected in cattle eggs and sheep cleavage-stage embryos and blastocysts. In silico analysis suggested that cattle and sheep PATFs share similar size, isometric point and molecular weight. A phenetic analysis showed two patterns of PATF clustering between cattle and sheep, among several mammalian species. In conclusion, the temporal expression of pluripotency-associated transcription factors differs between sheep and cattle, suggesting species-specific regulation during preimplantation development.
Collapse
|
32
|
Schwarz BA, Cetinbas M, Clement K, Walsh RM, Cheloufi S, Gu H, Langkabel J, Kamiya A, Schorle H, Meissner A, Sadreyev RI, Hochedlinger K. Prospective Isolation of Poised iPSC Intermediates Reveals Principles of Cellular Reprogramming. Cell Stem Cell 2018; 23:289-305.e5. [PMID: 30017590 DOI: 10.1016/j.stem.2018.06.013] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 03/29/2018] [Accepted: 06/15/2018] [Indexed: 12/31/2022]
Abstract
Cellular reprogramming converts differentiated cells into induced pluripotent stem cells (iPSCs). However, this process is typically very inefficient, complicating mechanistic studies. We identified and molecularly characterized rare, early intermediates poised to reprogram with up to 95% efficiency, without perturbing additional genes or pathways, during iPSC generation from mouse embryonic fibroblasts. Analysis of these cells uncovered transcription factors (e.g., Tfap2c and Bex2) that are important for reprogramming but dispensable for pluripotency maintenance. Additionally, we observed striking patterns of chromatin hyperaccessibility at pluripotency loci, which preceded gene expression in poised intermediates. Finally, inspection of these hyperaccessible regions revealed an early wave of DNA demethylation that is uncoupled from de novo methylation of somatic regions late in reprogramming. Our study underscores the importance of investigating rare intermediates poised to produce iPSCs, provides insights into reprogramming mechanisms, and offers a valuable resource for the dissection of transcriptional and epigenetic dynamics intrinsic to cell fate change.
Collapse
Affiliation(s)
- Benjamin A Schwarz
- Department of Molecular Biology, Cancer Center, and Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Pathology, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA
| | - Murat Cetinbas
- Department of Molecular Biology, Cancer Center, and Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Kendell Clement
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ryan M Walsh
- Department of Molecular Biology, Cancer Center, and Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sihem Cheloufi
- Department of Molecular Biology, Cancer Center, and Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Hongcang Gu
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jan Langkabel
- University of Bonn Medical School, Institute of Pathology, Department of Developmental Pathology, Bonn, Germany
| | - Akihide Kamiya
- Department of Molecular Life Sciences, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, Japan
| | - Hubert Schorle
- University of Bonn Medical School, Institute of Pathology, Department of Developmental Pathology, Bonn, Germany
| | - Alexander Meissner
- Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Cancer Center, and Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Department of Pathology, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA
| | - Konrad Hochedlinger
- Department of Molecular Biology, Cancer Center, and Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
| |
Collapse
|
33
|
Apostolou E, Stadtfeld M. Cellular trajectories and molecular mechanisms of iPSC reprogramming. Curr Opin Genet Dev 2018; 52:77-85. [PMID: 29925040 DOI: 10.1016/j.gde.2018.06.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 04/24/2018] [Accepted: 06/04/2018] [Indexed: 12/30/2022]
Abstract
The discovery of induced pluripotent stem cells (iPSCs) has solidified the concept of transcription factors as major players in controlling cell identity and provided a tractable tool to study how somatic cell identity can be dismantled and pluripotency established. A number of landmark studies have established hallmarks and roadmaps of iPSC formation by describing relative kinetics of transcriptional, protein and epigenetic changes, including alterations in DNA methylation and histone modifications. Recently, technological advancements such as single-cell analyses, high-resolution genome-wide chromatin assays and more efficient reprogramming systems have been used to challenge and refine our understanding of the reprogramming process. Here, we will outline novel insights into the molecular mechanisms underlying iPSC formation, focusing on how the core reprogramming factors OCT4, KLF4, SOX2 and MYC (OKSM) drive changes in gene expression, chromatin state and 3D genome topology. In addition, we will discuss unexpected consequences of reprogramming factor expression in in vitro and in vivo systems that may point towards new applications of iPSC technology.
Collapse
Affiliation(s)
- Effie Apostolou
- Edward and Sandra Meyer Cancer Center and Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA.
| | - Matthias Stadtfeld
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology and Helen L. and Martin S. Kimmel Center for Biology and Medicine, NYU School of Medicine, New York, NY 10016, USA.
| |
Collapse
|
34
|
Pijuan-Sala B, Guibentif C, Göttgens B. Single-cell transcriptional profiling: a window into embryonic cell-type specification. Nat Rev Mol Cell Biol 2018; 19:399-412. [DOI: 10.1038/s41580-018-0002-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
|
35
|
Li M, Izpisua Belmonte JC. Deconstructing the pluripotency gene regulatory network. Nat Cell Biol. 2018;20:382-392. [PMID: 29593328 DOI: 10.1038/s41556-018-0067-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 02/16/2018] [Indexed: 12/22/2022]
Abstract
Pluripotent stem cells can be isolated from embryos or derived by reprogramming. Pluripotency is stabilized by an interconnected network of pluripotency genes that cooperatively regulate gene expression. Here we describe the molecular principles of pluripotency gene function and highlight post-transcriptional controls, particularly those induced by RNA-binding proteins and alternative splicing, as an important regulatory layer of pluripotency. We also discuss heterogeneity in pluripotency regulation, alternative pluripotency states and future directions of pluripotent stem cell research.
Collapse
|
36
|
Zhang J, Cao H, Xie J, Fan C, Xie Y, He X, Liao M, Zhang S, Wang H. The oncogene Etv5 promotes MET in somatic reprogramming and orchestrates epiblast/primitive endoderm specification during mESCs differentiation. Cell Death Dis 2018; 9:224. [PMID: 29445086 PMCID: PMC5833841 DOI: 10.1038/s41419-018-0335-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/10/2018] [Accepted: 01/18/2018] [Indexed: 01/10/2023]
Abstract
Unipotent spermatogonial stem cells (SSCs) can be efficiently reprogrammed into pluripotent stem cells only by manipulating the culture condition, without introducing exogenous reprogramming factors. This phenotype raises the hypothesis that the endogenous transcription factors (TFs) in SSCs may facilitate reprogramming to acquire pluripotency. In this study, we screened a pool of SSCs TFs (Bcl6b, Lhx1, Foxo1, Plzf, Id4, Taf4b, and Etv5), and found that oncogene Etv5 could dramatically increase the efficiency of induced pluripotent stem cells (iPSCs) generation when combined with Yamanaka factors. We also demonstrated that Etv5 could promote mesenchymal-epithelial transition (MET) at the early stage of reprogramming by regulating Tet2-miR200s-Zeb1 axis. In addition, Etv5 knockdown in mouse embryonic stem cells (mESCs) could decrease the genomic 5hmC level by downregulating Tet2. Furthermore, the embryoid body assay revealed that Etv5 could positively regulate primitive endoderm specification through regulating Gata6 and negatively regulate epiblast specification by inhibiting Fgf5 expression. In summary, our findings provide insights into understanding the regulation mechanisms of Etv5 under the context of somatic reprogramming, mESCs maintenance, and differentiation.
Collapse
Affiliation(s)
- Jinglong Zhang
- College of Veterinary Medicine, Shaanxi Center of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Hongxia Cao
- College of Veterinary Medicine, Shaanxi Center of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jing Xie
- College of Veterinary Medicine, Shaanxi Center of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chen Fan
- College of Veterinary Medicine, Shaanxi Center of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Youlong Xie
- College of Veterinary Medicine, Shaanxi Center of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xin He
- College of Veterinary Medicine, Shaanxi Center of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Mingzhi Liao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Shiqiang Zhang
- College of Veterinary Medicine, Shaanxi Center of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Huayan Wang
- College of Veterinary Medicine, Shaanxi Center of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| |
Collapse
|
37
|
Slamecka J, McClellan S, Wilk A, Laurini J, Manci E, Hoerstrup SP, Weber B, Owen L. Induced pluripotent stem cells derived from human amnion in chemically defined conditions. Cell Cycle 2018; 17:330-347. [PMID: 29143560 DOI: 10.1080/15384101.2017.1403690] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Fetal stem cells are a unique type of adult stem cells that have been suggested to be broadly multipotent with some features of pluripotency. Their clinical potential has been documented but their upgrade to full pluripotency could open up a wide range of cell-based therapies particularly suited for pediatric tissue engineering, longitudinal studies or disease modeling. Here we describe episomal reprogramming of mesenchymal stem cells from the human amnion to pluripotency (AM-iPSC) in chemically defined conditions. The AM-iPSC expressed markers of embryonic stem cells, readily formed teratomas with tissues of all three germ layers present and had a normal karyotype after around 40 passages in culture. We employed novel computational methods to determine the degree of pluripotency from microarray and RNA sequencing data in these novel lines alongside an iPSC and ESC control and found that all lines were deemed pluripotent, however, with variable scores. Differential expression analysis then identified several groups of genes that potentially regulate this variability in lines within the boundaries of pluripotency, including metallothionein proteins. By further studying this variability, characteristics relevant to cell-based therapies, like differentiation propensity, could be uncovered and predicted in the pluripotent stage.
Collapse
Affiliation(s)
| | | | - Anna Wilk
- a Mitchell Cancer Institute, University of South Alabama , USA
| | - Javier Laurini
- c College of Medicine, University of South Alabama , Mobile , AL , USA
| | - Elizabeth Manci
- d College of Medicine, University of South Alabama , Mobile , AL , USA
| | - Simon P Hoerstrup
- b Institute for Regenerative Medicine, University of Zurich , Switzerland.,f Center for Applied Biotechnology and Molecular Medicine (CABMM) , University of Zurich - Irchel Campus , Zurich , Switzerland
| | - Benedikt Weber
- b Institute for Regenerative Medicine, University of Zurich , Switzerland.,e Department of Dermatology , University Hospital Zurich , Switzerland.,f Center for Applied Biotechnology and Molecular Medicine (CABMM) , University of Zurich - Irchel Campus , Zurich , Switzerland
| | - Laurie Owen
- g University of California San Diego , La Jolla , CA , USA
| |
Collapse
|
38
|
Abstract
The inherent heterogeneity in cell populations has become of great interest and importance as analytical techniques have improved over the past decades. With the advent of personalized medicine, understanding the impact of this heterogeneity has become an important challenge for the research community. Many different microfluidic approaches with varying levels of throughput and resolution exist to study single cell activity. In this review, we take a broad view of the recent microfluidic developments in single cell analysis based on microwell, microchamber, and droplet platforms. We cover physical, chemical, and molecular biology approaches for cellular and molecular analysis including newly emerging genome-wide analysis.
Collapse
Affiliation(s)
- Travis W Murphy
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA.
| | | | | | | | | |
Collapse
|
39
|
Nefzger CM, Rossello FJ, Chen J, Liu X, Knaupp AS, Firas J, Paynter JM, Pflueger J, Buckberry S, Lim SM, Williams B, Alaei S, Faye-chauhan K, Petretto E, Nilsson SK, Lister R, Ramialison M, Powell DR, Rackham OJ, Polo JM. Cell Type of Origin Dictates the Route to Pluripotency. Cell Rep 2017; 21:2649-60. [DOI: 10.1016/j.celrep.2017.11.029] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 10/02/2017] [Accepted: 11/08/2017] [Indexed: 11/23/2022] Open
|
40
|
Guo L, Karoubi G, Duchesneau P, Shutova MV, Sung HK, Tonge P, Bear C, Rogers I, Nagy A, Waddell TK. Generation of Induced Progenitor-like Cells from Mature Epithelial Cells Using Interrupted Reprogramming. Stem Cell Reports 2017; 9:1780-95. [PMID: 29198829 DOI: 10.1016/j.stemcr.2017.10.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 10/26/2017] [Accepted: 10/27/2017] [Indexed: 01/17/2023] Open
Abstract
A suitable source of progenitor cells is required to attenuate disease or affect cure. We present an "interrupted reprogramming" strategy to generate "induced progenitor-like (iPL) cells" using carefully timed expression of induced pluripotent stem cell reprogramming factors (Oct4, Sox2, Klf4, and c-Myc; OSKM) from non-proliferative Club cells. Interrupted reprogramming allowed controlled expansion yet preservation of lineage commitment. Under clonogenic conditions, iPL cells expanded and functioned as a bronchiolar progenitor-like population to generate mature Club cells, mucin-producing goblet cells, and cystic fibrosis transmembrane conductance regulator (CFTR)-expressing ciliated epithelium. In vivo, iPL cells can repopulate CFTR-deficient epithelium. This interrupted reprogramming process could be metronomically applied to achieve controlled progenitor-like proliferation. By carefully controlling the duration of expression of OSKM, iPL cells do not become pluripotent, and they maintain their memory of origin and retain their ability to efficiently return to their original phenotype. A generic technique to produce highly specified populations may have significant implications for regenerative medicine.
Collapse
|
41
|
Ruetz T, Pfisterer U, Di Stefano B, Ashmore J, Beniazza M, Tian TV, Kaemena DF, Tosti L, Tan W, Manning JR, Chantzoura E, Ottosson DR, Collombet S, Johnsson A, Cohen E, Yusa K, Linnarsson S, Graf T, Parmar M, Kaji K. Constitutively Active SMAD2/3 Are Broad-Scope Potentiators of Transcription-Factor-Mediated Cellular Reprogramming. Cell Stem Cell 2017; 21:791-805.e9. [PMID: 29174331 PMCID: PMC5732323 DOI: 10.1016/j.stem.2017.10.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 07/17/2017] [Accepted: 10/25/2017] [Indexed: 02/06/2023]
Abstract
Reprogramming of cellular identity using exogenous expression of transcription factors (TFs) is a powerful and exciting tool for tissue engineering, disease modeling, and regenerative medicine. However, generation of desired cell types using this approach is often plagued by inefficiency, slow conversion, and an inability to produce mature functional cells. Here, we show that expression of constitutively active SMAD2/3 significantly improves the efficiency of induced pluripotent stem cell (iPSC) generation by the Yamanaka factors. Mechanistically, SMAD3 interacts with reprogramming factors and co-activators and co-occupies OCT4 target loci during reprogramming. Unexpectedly, active SMAD2/3 also markedly enhances three other TF-mediated direct reprogramming conversions, from B cells to macrophages, myoblasts to adipocytes, and human fibroblasts to neurons, highlighting broad and general roles for SMAD2/3 as cell-reprogramming potentiators. Our results suggest that co-expression of active SMAD2/3 could enhance multiple types of TF-based cell identity conversion and therefore be a powerful tool for cellular engineering.
Collapse
Affiliation(s)
- Tyson Ruetz
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh BioQuarter, 5 Little France Drive, Edinburgh EH16 4UU, Scotland, UK
| | - Ulrich Pfisterer
- Department of Experimental Medical Science, Developmental and Regenerative Neurobiology, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, 22184 Lund, Sweden
| | - Bruno Di Stefano
- Centre for Genomic Regulation, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain
| | - James Ashmore
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh BioQuarter, 5 Little France Drive, Edinburgh EH16 4UU, Scotland, UK
| | - Meryam Beniazza
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh BioQuarter, 5 Little France Drive, Edinburgh EH16 4UU, Scotland, UK
| | - Tian V Tian
- Centre for Genomic Regulation, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain
| | - Daniel F Kaemena
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh BioQuarter, 5 Little France Drive, Edinburgh EH16 4UU, Scotland, UK
| | - Luca Tosti
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh BioQuarter, 5 Little France Drive, Edinburgh EH16 4UU, Scotland, UK
| | - Wenfang Tan
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh BioQuarter, 5 Little France Drive, Edinburgh EH16 4UU, Scotland, UK
| | - Jonathan R Manning
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh BioQuarter, 5 Little France Drive, Edinburgh EH16 4UU, Scotland, UK
| | - Eleni Chantzoura
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh BioQuarter, 5 Little France Drive, Edinburgh EH16 4UU, Scotland, UK
| | - Daniella Rylander Ottosson
- Department of Experimental Medical Science, Developmental and Regenerative Neurobiology, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, 22184 Lund, Sweden
| | - Samuel Collombet
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, 75005 Paris, France
| | - Anna Johnsson
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Scheeles väg 1, SE-171 77 Stockholm, Sweden
| | - Erez Cohen
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh BioQuarter, 5 Little France Drive, Edinburgh EH16 4UU, Scotland, UK
| | - Kosuke Yusa
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Sten Linnarsson
- Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Scheeles väg 1, SE-171 77 Stockholm, Sweden
| | - Thomas Graf
- Centre for Genomic Regulation, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain; The Barcelona Institute of Science and Technology, Carrer del Comte d'Urgell 187, Building 12 (BIST), 08036 Barcelona, Spain
| | - Malin Parmar
- Department of Experimental Medical Science, Developmental and Regenerative Neurobiology, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lund University, 22184 Lund, Sweden
| | - Keisuke Kaji
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh BioQuarter, 5 Little France Drive, Edinburgh EH16 4UU, Scotland, UK.
| |
Collapse
|
42
|
Miller ND, Kelsoe JR. Unraveling the biology of bipolar disorder using induced pluripotent stem-derived neurons. Bipolar Disord 2017; 19:544-551. [PMID: 29116664 PMCID: PMC6433126 DOI: 10.1111/bdi.12535] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 07/20/2017] [Indexed: 12/18/2022]
Abstract
OBJECTIVES Bipolar disorder has been studied from numerous angles, from pathological studies to large-scale genomic studies, overall making moderate gains toward an understanding of the disorder. With the advancement of induced pluripotent stem (iPS) cell technology, in vitro models based on patient samples are now available that inherently incorporate the complex genetic variants that largely are the basis for this disorder. A number of groups are starting to apply iPS technology to the study of bipolar disorder. METHODS We selectively reviewed the literature related to understanding bipolar disorder based on using neurons derived from iPS cells. RESULTS So far, most work has used the prototypical iPS cells. However, others have been able to transdifferentiate fibroblasts directly to neurons. Others still have utilized olfactory epithelium tissue as a source of neural-like cells that do not need reprogramming. In general, iPS and related cells can be used for studies of disease pathology, drug discovery, or stem cell therapy. CONCLUSIONS Published studies have primarily focused on understanding bipolar disorder pathology, but initial work is also being done to use iPS technology for drug discovery. In terms of disease pathology, some evidence is pointing toward a differentiation defect with more ventral cell types being prominent. Additionally, there is evidence for a calcium signaling defect, a finding that builds on the genome-wide association study results. Continued work with iPS cells will certainly help us understand bipolar disorder and provide a way forward for improved treatments.
Collapse
Affiliation(s)
- Nathaniel D. Miller
- Department of Psychiatry, University of California San Diego, La Jolla, CA,Department of Psychiatry, VA Healthcare Systems, La Jolla, CA
| | - John R. Kelsoe
- Department of Psychiatry, University of California San Diego, La Jolla, CA,Department of Psychiatry, VA Healthcare Systems, La Jolla, CA,Institute for Genomic Medicine, University of California San Diego, La Jolla, CA
| |
Collapse
|
43
|
Jaber M, Sebban S, Buganim Y. Acquisition of the pluripotent and trophectoderm states in the embryo and during somatic nuclear reprogramming. Curr Opin Genet Dev 2017; 46:37-43. [DOI: 10.1016/j.gde.2017.06.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 05/08/2017] [Accepted: 06/08/2017] [Indexed: 10/19/2022]
|
44
|
Natarajan KN, Teichmann SA, Kolodziejczyk AA. Single cell transcriptomics of pluripotent stem cells: reprogramming and differentiation. Curr Opin Genet Dev 2017; 46:66-76. [DOI: 10.1016/j.gde.2017.06.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 05/08/2017] [Accepted: 06/10/2017] [Indexed: 12/20/2022]
|
45
|
Cossarizza A, Chang HD, Radbruch A, Akdis M, Andrä I, Annunziato F, Bacher P, Barnaba V, Battistini L, Bauer WM, Baumgart S, Becher B, Beisker W, Berek C, Blanco A, Borsellino G, Boulais PE, Brinkman RR, Büscher M, Busch DH, Bushnell TP, Cao X, Cavani A, Chattopadhyay PK, Cheng Q, Chow S, Clerici M, Cooke A, Cosma A, Cosmi L, Cumano A, Dang VD, Davies D, De Biasi S, Del Zotto G, Della Bella S, Dellabona P, Deniz G, Dessing M, Diefenbach A, Di Santo J, Dieli F, Dolf A, Donnenberg VS, Dörner T, Ehrhardt GRA, Endl E, Engel P, Engelhardt B, Esser C, Everts B, Dreher A, Falk CS, Fehniger TA, Filby A, Fillatreau S, Follo M, Förster I, Foster J, Foulds GA, Frenette PS, Galbraith D, Garbi N, García-Godoy MD, Geginat J, Ghoreschi K, Gibellini L, Goettlinger C, Goodyear CS, Gori A, Grogan J, Gross M, Grützkau A, Grummitt D, Hahn J, Hammer Q, Hauser AE, Haviland DL, Hedley D, Herrera G, Herrmann M, Hiepe F, Holland T, Hombrink P, Houston JP, Hoyer BF, Huang B, Hunter CA, Iannone A, Jäck HM, Jávega B, Jonjic S, Juelke K, Jung S, Kaiser T, Kalina T, Keller B, Khan S, Kienhöfer D, Kroneis T, Kunkel D, Kurts C, Kvistborg P, Lannigan J, Lantz O, Larbi A, LeibundGut-Landmann S, Leipold MD, Levings MK, Litwin V, Liu Y, Lohoff M, Lombardi G, Lopez L, Lovett-Racke A, Lubberts E, Ludewig B, Lugli E, Maecker HT, Martrus G, Matarese G, Maueröder C, McGrath M, McInnes I, Mei HE, Melchers F, Melzer S, Mielenz D, Mills K, Mirrer D, Mjösberg J, Moore J, Moran B, Moretta A, Moretta L, Mosmann TR, Müller S, Müller W, Münz C, Multhoff G, Munoz LE, Murphy KM, Nakayama T, Nasi M, Neudörfl C, Nolan J, Nourshargh S, O'Connor JE, Ouyang W, Oxenius A, Palankar R, Panse I, Peterson P, Peth C, Petriz J, Philips D, Pickl W, Piconese S, Pinti M, Pockley AG, Podolska MJ, Pucillo C, Quataert SA, Radstake TRDJ, Rajwa B, Rebhahn JA, Recktenwald D, Remmerswaal EBM, Rezvani K, Rico LG, Robinson JP, Romagnani C, Rubartelli A, Ruckert B, Ruland J, Sakaguchi S, Sala-de-Oyanguren F, Samstag Y, Sanderson S, Sawitzki B, Scheffold A, Schiemann M, Schildberg F, Schimisky E, Schmid SA, Schmitt S, Schober K, Schüler T, Schulz AR, Schumacher T, Scotta C, Shankey TV, Shemer A, Simon AK, Spidlen J, Stall AM, Stark R, Stehle C, Stein M, Steinmetz T, Stockinger H, Takahama Y, Tarnok A, Tian Z, Toldi G, Tornack J, Traggiai E, Trotter J, Ulrich H, van der Braber M, van Lier RAW, Veldhoen M, Vento-Asturias S, Vieira P, Voehringer D, Volk HD, von Volkmann K, Waisman A, Walker R, Ward MD, Warnatz K, Warth S, Watson JV, Watzl C, Wegener L, Wiedemann A, Wienands J, Willimsky G, Wing J, Wurst P, Yu L, Yue A, Zhang Q, Zhao Y, Ziegler S, Zimmermann J. Guidelines for the use of flow cytometry and cell sorting in immunological studies. Eur J Immunol 2017; 47:1584-1797. [PMID: 29023707 PMCID: PMC9165548 DOI: 10.1002/eji.201646632] [Citation(s) in RCA: 381] [Impact Index Per Article: 54.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Andrea Cossarizza
- Department of Medical and Surgical Sciences for Children and Adults, Univ. of Modena and Reggio Emilia School of Medicine, Modena, Italy
| | - Hyun-Dong Chang
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Andreas Radbruch
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Mübeccel Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University Zurich, Davos, Switzerland
| | - Immanuel Andrä
- Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, Technische Universität München, Munich, Germany
| | | | | | - Vincenzo Barnaba
- Dipartimento di Medicina Interna e Specialità Mediche, Sapienza Università di Roma, Via Regina Elena 324, 00161 Rome, Italy
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
| | - Luca Battistini
- Neuroimmunology and Flow Cytometry Units, Santa Lucia Foundation, Rome, Italy
| | - Wolfgang M Bauer
- Division of Immunology, Allergy and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Sabine Baumgart
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Burkhard Becher
- University of Zurich, Institute of Experimental Immunology, Zürich, Switzerland
| | - Wolfgang Beisker
- Flow Cytometry Laboratory, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München, German Research Center for Environmental Health
| | - Claudia Berek
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Alfonso Blanco
- Flow Cytometry Core Technologies, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Giovanna Borsellino
- Neuroimmunology and Flow Cytometry Units, Santa Lucia Foundation, Rome, Italy
| | - Philip E Boulais
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, USA
- The Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Bronx, New York, USA
| | - Ryan R Brinkman
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Martin Büscher
- Biopyhsics, R&D Engineering, Miltenyi Biotec GmbH, Bergisch Gladbach, Germany
| | - Dirk H Busch
- Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, Technische Universität München, Munich, Germany
- DZIF - National Centre for Infection Research, Munich, Germany
- Focus Group ''Clinical Cell Processing and Purification", Institute for Advanced Study, Technische Universität München, Munich, Germany
| | - Timothy P Bushnell
- Department of Pediatrics and Shared Resource Laboratories, University of Rochester Medical Center, Rochester NY, United States of America
| | - Xuetao Cao
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China
- National Key Laboratory of Medical Immunology & Institute of Immunology, Second Military Medical University, Shanghai 200433, China
- Department of Immunology & Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China
| | | | | | - Qingyu Cheng
- Medizinische Klinik mit Schwerpunkt Rheumatologie und Medizinische Immunolologie Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Sue Chow
- Divsion of Medical Oncology and Hematology, Princess Margaret Hospital, Toronto, Ontario, Canada
| | - Mario Clerici
- University of Milano and Don C Gnocchi Foundation IRCCS, Milano, Italy
| | - Anne Cooke
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Antonio Cosma
- CEA - Université Paris Sud - INSERM U, Immunology of viral infections and autoimmune diseases, France
| | - Lorenzo Cosmi
- Department of Experimental and Clinical Medicine, University of Firenze, Firenze, Italia
| | - Ana Cumano
- Lymphopoiesis Unit, Immunology Department Pasteur Institute, Paris, France
| | - Van Duc Dang
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Derek Davies
- Flow Cytometry Facility, The Francis Crick Institute, London, United Kingdom
| | - Sara De Biasi
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, Univ. of Modena and Reggio Emilia, Modena, Italy
| | | | - Silvia Della Bella
- University of Milan, Department of Medical Biotechnologies and Translational Medicine
- Humanitas Clinical and Research Center, Lab of Clinical and Experimental Immunology, Rozzano, Milan, Italy
| | - Paolo Dellabona
- Experimental Immunology Unit, Head, Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milano, Italy
| | - Günnur Deniz
- Istanbul University, Aziz Sancar Institute of Experimental Medicine, Department of Immunology, Istanbul, Turkey
| | | | | | | | - Francesco Dieli
- University of Palermo, Department of Biopathology, Palermo, Italy
| | - Andreas Dolf
- Institute of Experimental Immunology, University Bonn, Bonn, Germany
| | - Vera S Donnenberg
- Department of Cardiothoracic Surgery, School of Medicine, University of Pittsburgh, PA
| | - Thomas Dörner
- Department of Medicine/Rheumatology and Clinical Immunology, Charite Universitätsmedizin Berlin, Germany
| | | | - Elmar Endl
- Department of Molecular Medicine and Experimental Immunology, (Core Facility Flow Cytometry) University of Bonn, Germany
| | - Pablo Engel
- Department of Biomedical Sciences, University of Barcelona, Barcelona, Spain
| | - Britta Engelhardt
- Professor for Immunobiology, Director, Theodor Kocher Institute, University of Bern, Bern, Switzerland
| | - Charlotte Esser
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - Bart Everts
- Leiden University Medical Center, Department of Parasitology, Leiden, The Netherlands
| | - Anita Dreher
- Swiss Institute of Allergy and Asthma Research (SIAF), University Zurich, Davos, Switzerland
| | - Christine S Falk
- Institute of Transplant Immunology, IFB-Tx, MHH Hannover Medical School, Hannover, Germany
- German Center for Infectious diseases (DZIF), TTU-IICH, Hannover, Germany
| | - Todd A Fehniger
- Divisions of Hematology & Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO
| | - Andrew Filby
- The Flow Cytometry Core Facility, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Simon Fillatreau
- Institut Necker-Enfants Malades (INEM), INSERM U-CNRS UMR, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France
- Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpital Necker Enfants Malades, Paris, France
| | - Marie Follo
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Irmgard Förster
- Immunology and Environment, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | | | - Gemma A Foulds
- John van Geest Cancer Research Centre, Nottingham Trent University, Nottingham, UK
| | - Paul S Frenette
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | - David Galbraith
- University of Arizona, Bio Institute, School of Plant Sciences and Arizona Cancer Center, Tucson, Arizona, USA
| | - Natalio Garbi
- Institute of Experimental Immunology, University Bonn, Bonn, Germany
- Department of Molecular Immunology, Institute of Experimental Immunology, Bonn, Germany
| | | | - Jens Geginat
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Kamran Ghoreschi
- Flow Cytometry Core Facility, Department of Dermatology, University Medical Center, Eberhard Karls University Tübingen, Germany
| | - Lara Gibellini
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, Univ. of Modena and Reggio Emilia, Modena, Italy
| | | | - Carl S Goodyear
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow
| | - Andrea Gori
- Clinic of Infectious Diseases, "San Gerardo" Hospital - ASST Monza, University Milano-Bicocca, Monza, Italy
| | - Jane Grogan
- Genentech, Department of Cancer Immunology, South San Francisco, California, USA
| | - Mor Gross
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Andreas Grützkau
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | | | - Jonas Hahn
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Internal Medicine, Rheumatology and Immunology, Universitätsklinikum Erlangen, Erlangen
| | - Quirin Hammer
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Anja E Hauser
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
- Immundynamics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - David Hedley
- Divsion of Medical Oncology and Hematology, Princess Margaret Hospital, Toronto, Ontario, Canada
| | - Guadalupe Herrera
- Cytometry Service, Incliva Foundation. Clinic Hospital and Faculty of Medicine, The University of Valencia. Av. Blasco Ibáñez, Valencia, Spain
| | - Martin Herrmann
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Internal Medicine, Rheumatology and Immunology, Universitätsklinikum Erlangen, Erlangen
| | - Falk Hiepe
- Medizinische Klinik mit Schwerpunkt Rheumatologie und Medizinische Immunolologie Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Tristan Holland
- Department of Molecular Immunology, Institute of Experimental Immunology, Bonn, Germany
| | - Pleun Hombrink
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam, The Netherlands
| | - Jessica P Houston
- Chemical and Materials Engineering, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Bimba F Hoyer
- Medizinische Klinik mit Schwerpunkt Rheumatologie und Medizinische Immunolologie Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Bo Huang
- Department of Biochemistry and Molecular Biology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Immunology, Institute of Basic Medical Sciences & State Key Laboratory of Medical Molecular Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Clinical Immunology Center, Chinese Academy of Medical Sciences, Beijing, China
| | - Christopher A Hunter
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anna Iannone
- Department of Diagnostic Medicine, Clinical and Public Health, Univ. of Modena and Reggio Emilia, Modena, Italy
| | - Hans-Martin Jäck
- Division of Molecular Immunology, Internal Medicine III, Nikolaus-Fiebiger-Center of MolecularMedicine, University Hospital Erlangen, Erlangen, Germany
| | - Beatriz Jávega
- Laboratory of Cytomics, Joint Research Unit CIPF-UVEG, Department of Biochemistry and Molecular Biology, The University of Valencia. Av. Blasco Ibáñez, Valencia, Spain
| | - Stipan Jonjic
- Faculty of Medicine, Center for Proteomics, University of Rijeka, Rijeka, Croatia
- Department for Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Kerstin Juelke
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Steffen Jung
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Toralf Kaiser
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Tomas Kalina
- Department of Paediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Baerbel Keller
- Center for Chronic Immunodeficiency (CCI), Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Srijit Khan
- Department of Immunology, University of Toronto, Toronto, Canada
| | - Deborah Kienhöfer
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Internal Medicine, Rheumatology and Immunology, Universitätsklinikum Erlangen, Erlangen
| | - Thomas Kroneis
- Medical University of Graz, Institute of Cell Biology, Histology & Embryology, Graz, Austria
| | - Désirée Kunkel
- BCRT Flow Cytometry Lab, Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin
| | - Christian Kurts
- Institute of Experimental Immunology, University Bonn, Bonn, Germany
| | - Pia Kvistborg
- Division of immunology, the Netherlands Cancer Institute, Amsterdam
| | - Joanne Lannigan
- University of Virginia School of Medicine, Flow Cytometry Shared Resource, Charlottesville, VA, USA
| | - Olivier Lantz
- INSERM U932, Institut Curie, Paris 75005, France
- Laboratoire d'immunologie clinique, Institut Curie, Paris 75005, France
- Centre d'investigation Clinique en Biothérapie Gustave-Roussy Institut Curie (CIC-BT1428), Institut Curie, Paris 75005, France
| | - Anis Larbi
- Singapore Immunology Network (SIgN), Principal Investigator, Biology of Aging Program
- Director Flow Cytomerty Platform, Immunomonitoring Platform, Agency for Science Technology and Research (A*STAR), Singapore
- Department of Medicine, University of Sherbrooke, Qc, Canada
- Faculty of Sciences, ElManar University, Tunis, Tunisia
| | | | - Michael D Leipold
- The Human Immune Monitoring Center (HIMC), Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, CA, USA
| | - Megan K Levings
- Department of Surgery, University of British Columbia & British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | | | - Yanling Liu
- Department of Immunology, University of Toronto, Toronto, Canada
| | - Michael Lohoff
- Institute for Medical Microbiology and Hospital Hygiene, University of Marburg, Marburg 35043, Germany
| | - Giovanna Lombardi
- MRC Centre for Transplantation, King's College London, Guy's Hospital, SE1 9RT London, UK
| | | | - Amy Lovett-Racke
- Department of Microbial Infection and Immunity, Ohio State University, Columbus, OH, USA
| | - Erik Lubberts
- Erasmus MC, University Medical Center, Department of Rheumatology, Rotterdam, The Netherlands
| | - Burkhard Ludewig
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Enrico Lugli
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center, Rozzano, Milan, Italy
- Humanitas Flow Cytometry Core, Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Holden T Maecker
- The Human Immune Monitoring Center (HIMC), Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, CA, USA
| | - Glòria Martrus
- Department of Virus Immunology, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Giuseppe Matarese
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Napoli, Italy and Istituto per l'Endocrinologia e l'Oncologia Sperimentale, Consiglio Nazionale delle Ricerche (IEOS-CNR), Napoli, Italy
| | - Christian Maueröder
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Internal Medicine, Rheumatology and Immunology, Universitätsklinikum Erlangen, Erlangen
| | - Mairi McGrath
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Iain McInnes
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow
| | - Henrik E Mei
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Fritz Melchers
- Senior Group on Lymphocyte Development, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Susanne Melzer
- Clinical Trial Center Leipzig, University Leipzig, Leipzig, Germany
| | - Dirk Mielenz
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Dept. of Internal Medicine III, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Kingston Mills
- Trinity Biomedical Sciences Institute, Trinity College Dublin, the University of Dublin, Dublin, Ireland
| | - David Mirrer
- Swiss Institute of Allergy and Asthma Research (SIAF), University Zurich, Davos, Switzerland
| | - Jenny Mjösberg
- Center for Infectious Medicine, Department of Medicine, Karolinska Institute Stockholm, Sweden
- Department of Clinical and Experimental Medicine, Linköping University, Sweden
| | - Jonni Moore
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Barry Moran
- Trinity Biomedical Sciences Institute, Trinity College Dublin, the University of Dublin, Dublin, Ireland
| | - Alessandro Moretta
- Department of Experimental Medicine, University of Genova, Genova, Italy
- Centro di Eccellenza per la Ricerca Biomedica-CEBR, Genova, Italy
| | - Lorenzo Moretta
- Department of Immunology, IRCCS Bambino Gesu Children's Hospital, Rome, Italy
| | - Tim R Mosmann
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
| | - Susann Müller
- Centre for Environmental Research - UFZ, Department Environemntal Microbiology, Leipzig, Germany
| | - Werner Müller
- Bill Ford Chair in Cellular Immunology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Christian Münz
- University of Zurich, Institute of Experimental Immunology, Zürich, Switzerland
| | - Gabriele Multhoff
- Department of Radiation Oncology, Klinikum rechts der Isar, Technische Universität München (TUM), Munich, Germany
- Institute for Innovative Radiotherapy (iRT), Experimental Immune Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Luis Enrique Munoz
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Internal Medicine, Rheumatology and Immunology, Universitätsklinikum Erlangen, Erlangen
| | - Kenneth M Murphy
- Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Howard Hughes Medical Institute, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Toshinori Nakayama
- Department of Immunology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Milena Nasi
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, Univ. of Modena and Reggio Emilia, Modena, Italy
| | - Christine Neudörfl
- Institute of Transplant Immunology, IFB-Tx, MHH Hannover Medical School, Hannover, Germany
| | - John Nolan
- The Scintillon Institute, Nancy Ridge Drive, San Diego, CA, USA
| | - Sussan Nourshargh
- Centre for Microvascular Research, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - José-Enrique O'Connor
- Laboratory of Cytomics, Joint Research Unit CIPF-UVEG, Department of Biochemistry and Molecular Biology, The University of Valencia. Av. Blasco Ibáñez, Valencia, Spain
| | - Wenjun Ouyang
- Department of Inflammation and Oncology, Amgen Inc., South San Francisco, CA, USA
| | | | - Raghav Palankar
- Institute for Immunology and Transfusion Medicine, University Medicine Greifswald, Ferdinand-Sauerbruch-Straße, 17489, Greifswald, Germany
| | - Isabel Panse
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Pärt Peterson
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Christian Peth
- Biopyhsics, R&D Engineering, Miltenyi Biotec GmbH, Bergisch Gladbach, Germany
| | - Jordi Petriz
- Josep Carreras Leukemia Research Institute, Barcelona, Spain
| | - Daisy Philips
- Division of immunology, the Netherlands Cancer Institute, Amsterdam
| | - Winfried Pickl
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Silvia Piconese
- Dipartimento di Medicina Interna e Specialità Mediche, Sapienza Università di Roma, Via Regina Elena 324, 00161 Rome, Italy
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
| | - Marcello Pinti
- Department of Life Sciences, Univ. of Modena and Reggio Emilia, Modena, Italy
| | - A Graham Pockley
- John van Geest Cancer Research Centre, Nottingham Trent University, Nottingham, UK
- Chromocyte Limited, Electric Works, Sheffield, UK
| | - Malgorzata Justyna Podolska
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Internal Medicine, Rheumatology and Immunology, Universitätsklinikum Erlangen, Erlangen
| | - Carlo Pucillo
- Univeristy of Udine - Department of Medicine, Lab of Immunology, Udine, Italy
| | - Sally A Quataert
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
| | - Timothy R D J Radstake
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht, The Netherlands; Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bartek Rajwa
- Bindley Biosciences Center, Purdue University, West Lafayette, In, USA
| | - Jonathan A Rebhahn
- David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
| | | | - Ester B M Remmerswaal
- Department of Experimental Immunology and Renal Transplant Unit, Division of Internal Medicine, Academic Medical Centre, The Netherlands
| | - Katy Rezvani
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Laura G Rico
- Josep Carreras Leukemia Research Institute, Barcelona, Spain
| | - J Paul Robinson
- The SVM Professor of Cytomics & Professor of Biomedical Engineering, Purdue University Cytometry Laboratories, Purdue University, West Lafayette, IN, USA
| | - Chiara Romagnani
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | | | - Beate Ruckert
- Swiss Institute of Allergy and Asthma Research (SIAF), University Zurich, Davos, Switzerland
| | - Jürgen Ruland
- Institut für Klinische Chemie und Pathobiochemie, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Shimon Sakaguchi
- Laboratory of Experimental Immunology, WPI Immunology Frontier Research Center (IFReC), Osaka University, Suita 565-0871, Japan
- Department of Experimental Pathology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Francisco Sala-de-Oyanguren
- Laboratory of Cytomics, Joint Research Unit CIPF-UVEG, Department of Biochemistry and Molecular Biology, The University of Valencia. Av. Blasco Ibáñez, Valencia, Spain
| | - Yvonne Samstag
- Institute of Immunology, Section Molecular Immunology, Ruprecht-Karls-University, D-69120, Heidelberg, Germany
| | - Sharon Sanderson
- Translational Immunology Laboratory, NIHR BRC, University of Oxford, Kennedy Institute of Rheumatology,Oxford, United Kingdom
| | - Birgit Sawitzki
- Charité-Universitaetsmedizin Berlin, Corporate Member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin
- Berlin Institute of Health, Institute of Medical Immunology, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Alexander Scheffold
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Germany
| | - Matthias Schiemann
- Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, Technische Universität München, Munich, Germany
| | - Frank Schildberg
- Harvard Medical School, Department of Microbiology and Immunobiology, Boston, MA, USA
| | | | - Stephan A Schmid
- Klinik und Poliklinik für Innere Medizin I, Universitätsklinikum Regensburg, Regensburg, Germany
| | - Steffen Schmitt
- Imaging and Cytometry Core Facility, Flow Cytometry Unit, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Kilian Schober
- Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, Technische Universität München, Munich, Germany
| | - Thomas Schüler
- Institute of Molecular and Clinical Immunology, Otto-von-Guericke University, Magdeburg, Germany
| | - Axel Ronald Schulz
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Ton Schumacher
- Division of immunology, the Netherlands Cancer Institute, Amsterdam
| | - Cristiano Scotta
- MRC Centre for Transplantation, King's College London, Guy's Hospital, SE1 9RT London, UK
| | | | - Anat Shemer
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Josef Spidlen
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, Canada
| | | | - Regina Stark
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam, The Netherlands
| | - Christina Stehle
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, Berlin, Germany
| | - Merle Stein
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Dept. of Internal Medicine III, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Tobit Steinmetz
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Dept. of Internal Medicine III, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Hannes Stockinger
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Yousuke Takahama
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, University of Tokushima, Tokushima, Japan
| | - Attila Tarnok
- Departement for Therapy Validation, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
- Institute for Medical Informatics, IMISE, Leipzig, Germany
| | - ZhiGang Tian
- School of Life Sciences and Medical Center, Institute of Immunology, Key Laboratory of Innate Immunity and Chronic Disease of Chinese Academy of Science, University of Science and Technology of China, Hefei, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Gergely Toldi
- University of Birmingham, Institute of Immunology and Immunotherapy, Birmingham, UK
| | - Julia Tornack
- Senior Group on Lymphocyte Development, Max Planck Institute for Infection Biology, Berlin, Germany
| | | | | | - Henning Ulrich
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo
| | | | - René A W van Lier
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam, The Netherlands
| | | | | | - Paulo Vieira
- Unité Lymphopoiese, Institut Pasteur, Paris, France
| | - David Voehringer
- Department of Infection Biology, University Hospital Erlangen, Wasserturmstr. 3/5, 91054 Erlangen, Germany
| | | | | | - Ari Waisman
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg University of Mainz, Mainz, Germany
| | | | | | - Klaus Warnatz
- Center for Chronic Immunodeficiency (CCI), Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sarah Warth
- BCRT Flow Cytometry Lab, Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin
| | | | - Carsten Watzl
- Leibniz Research Centre for Working Environment and Human Factors at TU Dortmund, IfADo, Department of Immunology, Dortmund, Germany
| | - Leonie Wegener
- Biopyhsics, R&D Engineering, Miltenyi Biotec GmbH, Bergisch Gladbach, Germany
| | - Annika Wiedemann
- Department of Medicine/Rheumatology and Clinical Immunology, Charite Universitätsmedizin Berlin, Germany
| | - Jürgen Wienands
- Universitätsmedizin Göttingen, Georg-August-Universität, Abt. Zelluläre und Molekulare Immunologie, Humboldtallee 34, 37073 Göttingen, Germany
| | - Gerald Willimsky
- Cooperation Unit for Experimental and Translational Cancer Immunology, Institute of Immunology (Charité - Universitätsmedizin Berlin) and German Cancer Research Center (DKFZ), Berlin, Germany
| | - James Wing
- Laboratory of Experimental Immunology, WPI Immunology Frontier Research Center (IFReC), Osaka University, Suita 565-0871, Japan
- Department of Experimental Pathology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Peter Wurst
- Institute of Experimental Immunology, University Bonn, Bonn, Germany
| | | | - Alice Yue
- School of Computing Science, Simon Fraser University, Burnaby, Canada
| | | | - Yi Zhao
- Department of Rheumatology & Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Susanne Ziegler
- Department of Virus Immunology, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Jakob Zimmermann
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Murtenstrasse, Bern
| |
Collapse
|
46
|
Liu Z, Li X, Xiao G, Chen B, He M, Hu B. Application of inductively coupled plasma mass spectrometry in the quantitative analysis of biomolecules with exogenous tags: A review. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.05.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
47
|
Beagan JA, Gilgenast TG, Kim J, Plona Z, Norton HK, Hu G, Hsu SC, Shields EJ, Lyu X, Apostolou E, Hochedlinger K, Corces VG, Dekker J, Phillips-Cremins JE. Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming. Cell Stem Cell 2017; 18:611-24. [PMID: 27152443 DOI: 10.1016/j.stem.2016.04.004] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 12/31/2015] [Accepted: 04/15/2016] [Indexed: 10/21/2022]
Abstract
Pluripotent genomes are folded in a topological hierarchy that reorganizes during differentiation. The extent to which chromatin architecture is reconfigured during somatic cell reprogramming is poorly understood. Here we integrate fine-resolution architecture maps with epigenetic marks and gene expression in embryonic stem cells (ESCs), neural progenitor cells (NPCs), and NPC-derived induced pluripotent stem cells (iPSCs). We find that most pluripotency genes reconnect to target enhancers during reprogramming. Unexpectedly, some NPC interactions around pluripotency genes persist in our iPSC clone. Pluripotency genes engaged in both "fully-reprogrammed" and "persistent-NPC" interactions exhibit over/undershooting of target expression levels in iPSCs. Additionally, we identify a subset of "poorly reprogrammed" interactions that do not reconnect in iPSCs and display only partially recovered, ESC-specific CTCF occupancy. 2i/LIF can abrogate persistent-NPC interactions, recover poorly reprogrammed interactions, reinstate CTCF occupancy, and restore expression levels. Our results demonstrate that iPSC genomes can exhibit imperfectly rewired 3D-folding linked to inaccurately reprogrammed gene expression.
Collapse
Affiliation(s)
- Jonathan A Beagan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Thomas G Gilgenast
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jesi Kim
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zachary Plona
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Heidi K Norton
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gui Hu
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah C Hsu
- Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Emily J Shields
- Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xiaowen Lyu
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Effie Apostolou
- Massachusetts General Hospital Cancer Center and Center for Regenerative Medicine, Boston, MA 02114, USA
| | - Konrad Hochedlinger
- Massachusetts General Hospital Cancer Center and Center for Regenerative Medicine, Boston, MA 02114, USA
| | - Victor G Corces
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Job Dekker
- Howard Hughes Medical Institute, Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jennifer E Phillips-Cremins
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
48
|
Sone M, Morone N, Nakamura T, Tanaka A, Okita K, Woltjen K, Nakagawa M, Heuser JE, Yamada Y, Yamanaka S, Yamamoto T. Hybrid Cellular Metabolism Coordinated by Zic3 and Esrrb Synergistically Enhances Induction of Naive Pluripotency. Cell Metab 2017; 25:1103-1117.e6. [PMID: 28467928 DOI: 10.1016/j.cmet.2017.04.017] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 03/06/2017] [Accepted: 04/15/2017] [Indexed: 01/05/2023]
Abstract
Naive pluripotent stem cells (PSCs) utilize both glycolysis and oxidative phosphorylation (OXPHOS) to satisfy their metabolic demands. However, it is unclear how somatic cells acquire this hybrid energy metabolism during reprogramming toward naive pluripotency. Here, we show that when transduced with Oct4, Sox2, and Klf4 (OSK) into murine fibroblasts, Zic3 and Esrrb synergistically enhance the reprogramming efficiency by regulating cellular metabolic pathways. These two transcription factors (TFs) cooperatively activate glycolytic metabolism independently of hypoxia inducible factors (HIFs). In contrast, the regulatory modes of the TFs on OXPHOS are antagonistic: Zic3 represses OXPHOS, whereas Esrrb activates it. Therefore, when introduced with Zic3, Esrrb restores OXPHOS activity, which is essential for efficient reprogramming. In addition, Esrrb-mediated OXPHOS activation is critical for the conversion of primed PSCs into the naive state. Our study suggests that the combinatorial function of TFs achieves an appropriate balance of metabolic pathways to induce naive PSCs.
Collapse
Affiliation(s)
- Masamitsu Sone
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan; Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Nobuhiro Morone
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan; MRC Toxicology Unit, University of Leicester, Leicester, LE1 9HN, UK
| | - Tomonori Nakamura
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Akito Tanaka
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Keisuke Okita
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Knut Woltjen
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan; Hakubi Center for Advanced Research, Kyoto University, Kyoto 606-8501, Japan
| | - Masato Nakagawa
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - John E Heuser
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yasuhiro Yamada
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan; Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Shinya Yamanaka
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan; Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Takuya Yamamoto
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan; Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan; AMED-CREST, AMED 1-7-1 Otemach, Chiyodaku, Tokyo, 100-0004, Japan.
| |
Collapse
|
49
|
|
50
|
|