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Okamura D, Kohara A, Chigi Y, Katayama T, Sharif J, Wu J, Ito-Matsuoka Y, Matsui Y. p38 MAPK as a gatekeeper of reprogramming in mouse migratory primordial germ cells. Front Cell Dev Biol 2024; 12:1410177. [PMID: 38911025 PMCID: PMC11191381 DOI: 10.3389/fcell.2024.1410177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 05/06/2024] [Indexed: 06/25/2024] Open
Abstract
Mammalian germ cells are derived from primordial germ cells (PGCs) and ensure species continuity through generations. Unlike irreversible committed mature germ cells, migratory PGCs exhibit a latent pluripotency characterized by the ability to derive embryonic germ cells (EGCs) and form teratoma. Here, we show that inhibition of p38 mitogen-activated protein kinase (MAPK) by chemical compounds in mouse migratory PGCs enables derivation of chemically induced Embryonic Germ-like Cells (cEGLCs) that do not require conventional growth factors like LIF and FGF2/Activin-A, and possess unique naïve pluripotent-like characteristics with epiblast features and chimera formation potential. Furthermore, cEGLCs are regulated by a unique PI3K-Akt signaling pathway, distinct from conventional naïve pluripotent stem cells described previously. Consistent with this notion, we show by performing ex vivo analysis that inhibition of p38 MAPK in organ culture supports the survival and proliferation of PGCs and also potentially reprograms PGCs to acquire indefinite proliferative capabilities, marking these cells as putative teratoma-producing cells. These findings highlight the utility of our ex vivo model in mimicking in vivo teratoma formation, thereby providing valuable insights into the cellular mechanisms underlying tumorigenesis. Taken together, our research underscores a key role of p38 MAPK in germ cell development, maintaining proper cell fate by preventing unscheduled pluripotency and teratoma formation with a balance between proliferation and differentiation.
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Affiliation(s)
- Daiji Okamura
- Department of Advanced Bioscience, Faculty of Agriculture, Kindai University, Nara, Japan
| | - Aoi Kohara
- Department of Advanced Bioscience, Faculty of Agriculture, Kindai University, Nara, Japan
| | - Yuta Chigi
- Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Japan
| | - Tomoka Katayama
- Department of Advanced Bioscience, Faculty of Agriculture, Kindai University, Nara, Japan
| | - Jafar Sharif
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, United States
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Yumi Ito-Matsuoka
- Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Yasuhisa Matsui
- Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
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2
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Ferrai C, Schulte C. Mechanotransduction in stem cells. Eur J Cell Biol 2024; 103:151417. [PMID: 38729084 DOI: 10.1016/j.ejcb.2024.151417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 04/28/2024] [Accepted: 04/29/2024] [Indexed: 05/12/2024] Open
Abstract
Nowadays, it is an established concept that the capability to reach a specialised cell identity via differentiation, as in the case of multi- and pluripotent stem cells, is not only determined by biochemical factors, but that also physical aspects of the microenvironment play a key role; interpreted by the cell through a force-based signalling pathway called mechanotransduction. However, the intricate ties between the elements involved in mechanotransduction, such as the extracellular matrix, the glycocalyx, the cell membrane, Integrin adhesion complexes, Cadherin-mediated cell/cell adhesion, the cytoskeleton, and the nucleus, are still far from being understood in detail. Here we report what is currently known about these elements in general and their specific interplay in the context of multi- and pluripotent stem cells. We furthermore merge this overview to a more comprehensive picture, that aims to cover the whole mechanotransductive pathway from the cell/microenvironment interface to the regulation of the chromatin structure in the nucleus. Ultimately, with this review we outline the current picture of the interplay between mechanotransductive cues and epigenetic regulation and how these processes might contribute to stem cell dynamics and fate.
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Affiliation(s)
- Carmelo Ferrai
- Institute of Pathology, University Medical Centre Göttingen, Germany.
| | - Carsten Schulte
- Department of Biomedical and Clinical Sciences and Department of Physics "Aldo Pontremoli", University of Milan, Italy.
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Chowdhury MM, Zimmerman S, Leeson H, Nefzger CM, Mar JC, Laslett A, Polo JM, Wolvetang E, Cooper-White JJ. Superior Induced Pluripotent Stem Cell Generation through Phactr3-Driven Mechanomodulation of Both Early and Late Phases of Cell Reprogramming. Biomater Res 2024; 28:0025. [PMID: 38774128 PMCID: PMC11106629 DOI: 10.34133/bmr.0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/25/2024] [Indexed: 05/24/2024] Open
Abstract
Human cell reprogramming traditionally involves time-intensive, multistage, costly tissue culture polystyrene-based cell culture practices that ultimately produce low numbers of reprogrammed cells of variable quality. Previous studies have shown that very soft 2- and 3-dimensional hydrogel substrates/matrices (of stiffnesses ≤ 1 kPa) can drive ~2× improvements in human cell reprogramming outcomes. Unfortunately, these similarly complex multistage protocols lack intrinsic scalability, and, furthermore, the associated underlying molecular mechanisms remain to be fully elucidated, limiting the potential to further maximize reprogramming outcomes. In screening the largest range of polyacrylamide (pAAm) hydrogels of varying stiffness to date (1 kPa to 1.3 MPa), we have found that a medium stiffness gel (~100 kPa) increased the overall number of reprogrammed cells by up to 10-fold (10×), accelerated reprogramming kinetics, improved both early and late phases of reprogramming, and produced induced pluripotent stem cells (iPSCs) having more naïve characteristics and lower remnant transgene expression, compared to the gold standard tissue culture polystyrene practice. Functionalization of these pAAm hydrogels with poly-l-dopamine enabled, for the first-time, continuous, single-step reprogramming of fibroblasts to iPSCs on hydrogel substrates (noting that even the tissue culture polystyrene practice is a 2-stage process). Comparative RNA sequencing analyses coupled with experimental validation revealed that a novel reprogramming regulator, protein phosphatase and actin regulator 3, up-regulated under the gel condition at a very early time point, was responsible for the observed enhanced reprogramming outcomes. This study provides a novel culture protocol and substrate for continuous hydrogel-based cell reprogramming and previously unattained clarity of the underlying mechanisms via which substrate stiffness modulates reprogramming kinetics and iPSC quality outcomes.
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Affiliation(s)
- Mohammad Mahfuz Chowdhury
- Australian Institute of Bioengineering and Nanotechnology (AIBN),
The University of Queensland, St. Lucia, QLD 4072, Australia
| | | | - Hannah Leeson
- Australian Institute of Bioengineering and Nanotechnology (AIBN),
The University of Queensland, St. Lucia, QLD 4072, Australia
| | | | - Jessica Cara Mar
- Australian Institute of Bioengineering and Nanotechnology (AIBN),
The University of Queensland, St. Lucia, QLD 4072, Australia
- Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Andrew Laslett
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Jose Maria Polo
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute and the Australian Regenerative Medicine Institute,
Monash University, Clayton, VIC 3800, Australia
- Adelaide Centre for Epigenetics and the South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences,
The University of Adelaide, Adelaide, SA 5005, Australia
| | - Ernst Wolvetang
- Australian Institute of Bioengineering and Nanotechnology (AIBN),
The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Justin John Cooper-White
- Australian Institute of Bioengineering and Nanotechnology (AIBN),
The University of Queensland, St. Lucia, QLD 4072, Australia
- School of Chemical Engineering, Andrew N. Liveris Building,
The University of Queensland, St. Lucia, QLD 4072, Australia
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4
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He Q, Sze SK, Ng KS, Koh CG. Paxillin interactome identified by SILAC and label-free approaches coupled to TurboID sheds light on the compositions of focal adhesions in mouse embryonic stem cells. Biochem Biophys Res Commun 2023; 680:73-85. [PMID: 37725837 DOI: 10.1016/j.bbrc.2023.09.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 08/25/2023] [Accepted: 09/08/2023] [Indexed: 09/21/2023]
Abstract
Self-renewal and differentiation of mouse embryonic stem cells (mESCs) are greatly affected by the extracellular matrix (ECM) environment; the composition and stiffness of which are sensed by the cells via integrin-associated focal adhesions (FAs) which link the cells to the ECM. Although FAs have been studied extensively in differentiated cells, their composition and function in mESCs are not as well elucidated. To gain more detailed knowledge of the molecular compositions of FAs in mESCs, we adopted the proximity-dependent biotinylation (BioID) proteomics approach. Paxillin, a known FA protein (FAP), is fused to the promiscuous biotin ligase TurboID as bait. We employed both SILAC- and label-free (LF)-based quantitative proteomics to strengthen as well as complement individual approach. The mass spectrometry data derived from SILAC and LF identified 38 and 443 proteins, respectively, with 35 overlapping candidates. Fifteen of these shared proteins are known FAPs based on literature-curated adhesome and 7 others are among the reported "meta-adhesome", suggesting the components of FAs are largely conserved between mESCs and differentiated cells. Furthermore, the LF data set contained an additional 18 literature-curated FAPs. Notably, the overlapped proteomics data failed to detect LIM-domain proteins such as zyxin family proteins, which suggests that FAs in mESCs are less mature than differentiated cells. Using the LF approach, we are able to identify PDLIM7, a LIM-domain protein, as a FAP in mESCs. This study illustrates the effectiveness of TurboID in mESCs. Importantly, we found that application of both SILAC and LF methods in combination allowed us to analyze the TurboID proteomics data in an unbiased, stringent and yet comprehensive manner.
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Affiliation(s)
- Qianqian He
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Kai Soon Ng
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Cheng-Gee Koh
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
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Guidotti G, Duelen R, Bloise N, Soccio M, Gazzano M, Aluigi A, Visai L, Sampaolesi M, Lotti N. The ad hoc chemical design of random PBS-based copolymers influences the activation of cardiac differentiation while altering the HYPPO pathway target genes in hiPSCs. BIOMATERIALS ADVANCES 2023; 154:213583. [PMID: 37604040 DOI: 10.1016/j.bioadv.2023.213583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 07/23/2023] [Accepted: 08/07/2023] [Indexed: 08/23/2023]
Abstract
Cardiac tissue engineering is a cutting-edge technology aiming to replace irreversibly damaged cardiac tissue and restore contractile functionality. However, cardiac tissue engineering porous and perfusable scaffolds to enable oxygen supply in vitro and eventually promote angiogenesis in vivo are still desirable. Two fully-aliphatic random copolymers of poly(butylene succinate) (PBS), poly(butylene succinate/Pripol), P(BSBPripol), and poly(butylene/neopentyl glycol succinate), P(BSNS), containing two different subunits, neopentyl glycol and Pripol 1009, were successfully synthesized and then electrospun in tridimentional fibrous mats. The copolymers show different thermal and mechanical behaviours as result of their chemical structure. In particular, copolymerization led to a reduction in crystallinity and consequently PBS stiffness, reaching values of elastic modulus very close to those of soft tissues. Then, to check the biological suitability, human induced Pluripotent Stem Cells (hiPSCs) were directly seeded on both PBS-based copolymeric scaffolds. The results confirmed the ability of both the scaffolds to sustain cell viability and to maintain their stemness during cell expansion. Furthermore, gene expression and immunofluorescence analysis showed that P(BSBPripol) scaffold promoted an upregulation of the early cardiac progenitor and later-stage markers with a simultaneously upregulation of HYPPO pathway gene expression, crucial for mechanosensing of cardiac progenitor cells. These results suggest that the correct ad-hoc chemical design and, in turn, the mechanical properties of the matrix, such as substrate stiffness, together with surface porosity, play a critical role in regulating the behaviour of cardiac progenitors, which ultimately offers valuable insights into the development of novel bio-inspired scaffolds for cardiac tissue regeneration.
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Affiliation(s)
- Giulia Guidotti
- Department of Civil, Chemical, Environmental and Materials Engineering, University of Bologna, Via Terracini 28, 40131 Bologna, Italy
| | - Robin Duelen
- Translational Cardiomyology Laboratory, Stem Cell Biology and Embryology, Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Nora Bloise
- Department of Molecular Medicine, Centre for Health Technologies (CHT), INSTM UdR of Pavia, University of Pavia, Viale Taramelli 3/B, 27100 Pavia, Italy; Medicina Clinica-Specialistica, UOR5 Laboratorio di Nanotecnologie, ICS Maugeri, IRCCS, Via Salvatore Maugeri 4, 27100 Pavia, Italy
| | - Michelina Soccio
- Department of Civil, Chemical, Environmental and Materials Engineering, University of Bologna, Via Terracini 28, 40131 Bologna, Italy
| | - Massimo Gazzano
- Organic Synthesis and Photoreactivity Institute, CNR, Via Gobetti 101, 40129 Bologna, Italy
| | - Annalisa Aluigi
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Piazza del Rinascimento, 6, 61029 Urbino, (PU), Italy
| | - Livia Visai
- Department of Molecular Medicine, Centre for Health Technologies (CHT), INSTM UdR of Pavia, University of Pavia, Viale Taramelli 3/B, 27100 Pavia, Italy; Medicina Clinica-Specialistica, UOR5 Laboratorio di Nanotecnologie, ICS Maugeri, IRCCS, Via Salvatore Maugeri 4, 27100 Pavia, Italy
| | - Maurilio Sampaolesi
- Translational Cardiomyology Laboratory, Stem Cell Biology and Embryology, Department of Development and Regeneration, KU Leuven, Leuven, Belgium; Histology and Medical Embryology Unit, Department of Anatomy, Histology, Forensic Medicine and Orthopedics, Sapienza University of Rome, Rome, Italy.
| | - Nadia Lotti
- Department of Civil, Chemical, Environmental and Materials Engineering, University of Bologna, Via Terracini 28, 40131 Bologna, Italy.
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Forrester-Gauntlett B, Peters L, Oback B. Grainyhead-like 2 is required for morphological integrity of mouse embryonic stem cells and orderly formation of inner ear-like organoids. Front Cell Dev Biol 2023; 11:1112069. [PMID: 37745294 PMCID: PMC10513505 DOI: 10.3389/fcell.2023.1112069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 08/21/2023] [Indexed: 09/26/2023] Open
Abstract
Mutations in the transcription factor gene grainyhead-like 2 (GRHL2) are associated with progressive non-syndromic sensorineural deafness autosomal dominant type 28 (DFNA28) in humans. Since complete loss of Grhl2 is lethal in mouse embryos, we studied its role during inner ear pathology and hearing loss in vitro. To this end, we generated different homozygous deletions to knockout Grhl2 in mouse embryonic stem cells (Grhl2-KO ESCs), including some mimicking naturally occurring truncations in the dimerisation domain related to human DFNA28. Under naïve culture conditions, Grhl2-KO cells in suspension were more heterogenous in size and larger than wild-type controls. Adherent Grhl2-KO cells were also larger, with a less uniform shape, flattened, less circular morphology, forming loose monolayer colonies with poorly defined edges. These changes correlated with lower expression of epithelial cadherin Cdh1 but no changes in tight junction markers (Ocln, Tjp2) or other Grhl isoforms (Grhl1, Grhl3). Clonogenicity from single cells, proliferation rates of cell populations and proliferation markers were reduced in Grhl2-KO ESCs. We next induced stepwise directed differentiation of Grhl2-KO ESCs along an otic pathway, giving rise to three-dimensional inner ear-like organoids (IELOs). Quantitative morphometry revealed that Grhl2-KO cells initially formed larger IELOs with a less compacted structure, more eccentric shape and increased surface area. These morphological changes persisted for up to one week. They were partially rescued by forced cell aggregation and fully restored by stably overexpressing exogenous Grhl2 in Grhl2-KO ESCs, indicating that Grhl2 alters cell-cell interactions. On day 8, aggregates were transferred into minimal maturation medium to allow self-guided organogenesis for another two weeks. During this period, Grhl2-KO cells and wild-type controls developed similarly, expressing neural, neuronal and sensory hair cell markers, while maintaining their initial differences in size and shape. In summary, Grhl2 is required for morphological maintenance of ESCs and orderly formation of IELOs, consistent with an essential role in organising epithelial integrity during inner ear development. Our findings validate quantitative morphometry as a useful, non-invasive screening method for molecular phenotyping of candidate mutations during organoid development.
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Affiliation(s)
- Blaise Forrester-Gauntlett
- Animal Biotech, AgResearch, Hamilton, New Zealand
- School of Science, University of Waikato, Hamilton, New Zealand
| | - Linda Peters
- School of Science, University of Waikato, Hamilton, New Zealand
| | - Björn Oback
- Animal Biotech, AgResearch, Hamilton, New Zealand
- School of Science, University of Waikato, Hamilton, New Zealand
- School of Medical Sciences, University of Auckland, Auckland, New Zealand
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7
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Takeda Y, Matsuguchi S, Nozaki S, Mihara T, Abe J, Hirai Y. Suppression of P-cadherin expression as a key regulatory element for embryonic stem cell stemness. Cell Struct Funct 2023; 48:49-57. [PMID: 36575041 PMCID: PMC10721948 DOI: 10.1247/csf.22060] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/13/2022] [Indexed: 12/28/2022] Open
Abstract
In embryonic stem (ES) cell colonies, a small subpopulation that changes cell shape and loses pluripotency often appears in two-dimensional (2D) cultures, even in the presence of a stemness factor. We have previously shown that membrane translocation of the syntaxin4, t-SNARE protein contributes to this phenomenon. Here, we show that ES cells in three-dimensional (3D) aggregates do not succumb to extruded syntaxin4 owing to suppressed expression of P-cadherin protein. While extracellular expression of syntaxin4 led to the striking upregulation of P-cadherin mRNA in both 2D and 3D-ES cells, morphological changes and appreciable expression of P-cadherin protein were detected only in 2D-ES cells. Importantly, the introduction of an expression cassette for P-cadherin practically reproduced the effects induced by extracellular syntaxin4, where the transgene product was clearly detected in 2D-, but not 3D-ES cells. An expression construct for P-cadherin-Venus harboring an in-frame insertion of the P2A sequence at the joint region gave fluorescent signals only in the cytoplasm of 2D-ES cells, demonstrating translational regulation of P-cadherin. These results provide the mechanistic insight into the uncontrollable differentiation in 2D-ES cells and shed light on the validity of the "embryoid body protocol commonly used for ES cell handling" for directional differentiation.Key words: differentiation, embryoid body, ES cells, P-cadherin, syntaxin4.
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Affiliation(s)
- Yuka Takeda
- Department of Biomedical Sciences, Graduate School of Science and Technology, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, 669-1330, Japan
| | - Shuji Matsuguchi
- Department of Biomedical Sciences, Graduate School of Science and Technology, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, 669-1330, Japan
| | - Sae Nozaki
- Department of Biomedical Sciences, Graduate School of Science and Technology, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, 669-1330, Japan
| | - Taisei Mihara
- Department of Biomedical Sciences, Graduate School of Science and Technology, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, 669-1330, Japan
| | - Junya Abe
- Department of Biomedical Sciences, Graduate School of Science and Technology, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, 669-1330, Japan
| | - Yohei Hirai
- Department of Biomedical Sciences, Graduate School of Science and Technology, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, 669-1330, Japan
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8
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BMP4 signaling plays critical roles in self-renewal of R2i mouse embryonic stem cells. Biochem Biophys Res Commun 2022; 617:8-15. [DOI: 10.1016/j.bbrc.2022.05.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 05/11/2022] [Indexed: 11/23/2022]
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9
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Liu S, Kanchanawong P. Emerging interplay of cytoskeletal architecture, cytomechanics and pluripotency. J Cell Sci 2022; 135:275761. [PMID: 35726598 DOI: 10.1242/jcs.259379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Pluripotent stem cells (PSCs) are capable of differentiating into all three germ layers and trophoblasts, whereas tissue-specific adult stem cells have a more limited lineage potency. Although the importance of the cytoskeletal architecture and cytomechanical properties in adult stem cell differentiation have been widely appreciated, how they contribute to mechanotransduction in PSCs is less well understood. Here, we discuss recent insights into the interplay of cellular architecture, cell mechanics and the pluripotent states of PSCs. Notably, the distinctive cytomechanical and morphodynamic profiles of PSCs are accompanied by a number of unique molecular mechanisms. The extent to which such mechanobiological signatures are intertwined with pluripotency regulation remains an open question that may have important implications in developmental morphogenesis and regenerative medicine.
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Affiliation(s)
- Shiying Liu
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Republic of Singapore
| | - Pakorn Kanchanawong
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Republic of Singapore.,Department of Biomedical Engineering, National University of Singapore, Singapore 117411, Republic of Singapore
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10
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Liu S, Wei R, Liu H, Liu R, Li P, Zhang X, Wei W, Zhao X, Li X, Yang Y, Fu X, Zou K. Analysis of chromatin accessibility in p53 deficient spermatogonial stem cells for high frequency transformation into pluripotent state. Cell Prolif 2022; 55:e13195. [PMID: 35119145 PMCID: PMC8891552 DOI: 10.1111/cpr.13195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/03/2022] [Accepted: 01/18/2022] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES Spermatogonial stem cells (SSCs), the germline stem cells (GSCs) committed to spermatogenesis in niche, can transform into pluripotent state in long-term culture without introduction of exogenous factors, typically in p53 deficiency condition. As the guardian for genomic stability, p53 is associated with epigenetic alterations during SSCs transformation. However, the mechanism is still unknown, since complicated roles of p53 baffle our understanding of the regulating process. MATERIALS AND METHODS The chromatin accessibility and differentially expressed genes (DEGs) were analysed in p53+/+ and p53-/- SSCs using the Assay for Transposase-Accessible Chromatin with high-throughput Sequencing (ATAC-seq) and RNA-sequencing (RNA-seq), to explore the connection of p53 and cell fate at chromosomal level. RESULTS Several transcription factors (TFs), such as CTCF, SMAD3 and SOX2, were predicted as important factors mediating the transformation. Molecular evidence suggested that SMAD3 efficiently promoted pluripotency-associated gene expression both in fresh and long-term cultured SSCs. However, p53 knockout (KO) is insufficient to induce SMAD3 expression in SSCs. CONCLUSIONS These observations indicate that SMAD3 is a key factor for SSCs transformation, and an unknown event is required to activate SMAD3 as the prerequisite for SSCs reprogramming, which may occur in the long-term culture of SSCs. This study demonstrates the connection of p53 and pluripotency-associated factors, providing new insight for understanding the mechanisms of SSCs reprogramming and germline tumorigenesis.
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Affiliation(s)
- Sitong Liu
- College of Life SciencesJilin UniversityChangchunChina
| | - Rui Wei
- Germline Stem Cells and Microenvironment LabCollege of Animal Science and TechnologyNanjing Agricultural UniversityNanjingChina
| | - Hongyang Liu
- Germline Stem Cells and Microenvironment LabCollege of Animal Science and TechnologyNanjing Agricultural UniversityNanjingChina
| | - Ruiqi Liu
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Center for Systems Bio‐medicineShanghai Jiao Tong UniversityShanghaiChina
| | - Pengxiao Li
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Center for Systems Bio‐medicineShanghai Jiao Tong UniversityShanghaiChina
| | - Xiaoyu Zhang
- Germline Stem Cells and Microenvironment LabCollege of Animal Science and TechnologyNanjing Agricultural UniversityNanjingChina
| | - Wei Wei
- The Key Laboratory of Molecular Epigenetics of MOEInstitute of Genetics and CytologyNortheast Normal UniversityChangchunChina
| | - Xiaodong Zhao
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Center for Systems Bio‐medicineShanghai Jiao Tong UniversityShanghaiChina
| | - Xiaomeng Li
- The Key Laboratory of Molecular Epigenetics of MOEInstitute of Genetics and CytologyNortheast Normal UniversityChangchunChina
| | - Yang Yang
- State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjingChina
| | - Xueqi Fu
- College of Life SciencesJilin UniversityChangchunChina
| | - Kang Zou
- Germline Stem Cells and Microenvironment LabCollege of Animal Science and TechnologyNanjing Agricultural UniversityNanjingChina
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11
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Lin J, Zeng J, Sun W, Liu K, Enkhbat M, Yi D, Harati J, Liu J, Kingshott P, Chen B, Ma F, Wang PY. Colloidal Self-Assembled Patterns Maintain the Pluripotency and Promote the Hemopoietic Potential of Human Embryonic Stem Cells. Front Cell Dev Biol 2021; 9:771773. [PMID: 34869369 PMCID: PMC8636751 DOI: 10.3389/fcell.2021.771773] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/26/2021] [Indexed: 11/30/2022] Open
Abstract
The generation of blood cells in a significant amount for clinical uses is still challenging. Human pluripotent stem cells-derived hemopoietic cells (hPSC-HCs) are a promising cell source to generate blood cells. Previously, it has been shown that the attached substrates are crucial in the maintenance or differentiation of hPSCs. In this study, a new family of artificial extracellular matrix (ECM) called colloidal self-assembled patterns (cSAPs: #1-#5) was used for the expansion of mouse and human PSCs. The optimized cSAP (i.e., #4 and #5) was selected for subsequent hemopoietic differentiation of human embryonic stem cells (hESCs). Results showed that the hematopoietic potential of hESCs was enhanced approx 3-4 folds on cSAP #5 compared to the flat control. The cell population of hematopoietic progenitors (i.e., CD34+CD43+ cells) and erythroid progenitors (i.e., CD71+GPA+ cells) were enhanced 4 folds at day 8 and 3 folds at day 14. RNA sequencing analysis of cSAP-derived hESCs showed that there were 300 genes up-regulated and 627 genes down-regulated compared to the flat control. The enriched signaling pathways, including up-regulation (i.e., Toll-like receptor, HIF-1a, and Notch) or down-regulation (i.e., FAs, MAPK, JAK/STAT, and TGF-β) were classic in the maintenance of hESC phenotype Real time PCR confirmed that the expression of focal adhesion (PTK2, VCL, and CXCL14) and MAPK signaling (CAV1) related genes was down-regulated 2-3 folds compared to the flat control. Altogether, cSAP enhances the pluripotency and the hematopoietic potential of hESCs that subsequently generates more blood-like cells. This study reveals the potential of cSAPs on the expansion and early-stage blood cell lineage differentiation of hPSCs.
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Affiliation(s)
- Jiao Lin
- Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jiahui Zeng
- Stem Cell Center, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS and PUMC), Chengdu, China
| | - Wencui Sun
- Stem Cell Center, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS and PUMC), Chengdu, China
| | - Kun Liu
- Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Myagmartsend Enkhbat
- Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Danying Yi
- Stem Cell Center, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS and PUMC), Chengdu, China
| | - Javad Harati
- Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jiaxin Liu
- Stem Cell Center, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS and PUMC), Chengdu, China
| | - Peter Kingshott
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Hawthorn, VIC, Australia
| | - Bo Chen
- Stem Cell Center, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS and PUMC), Chengdu, China
| | - Feng Ma
- Stem Cell Center, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS and PUMC), Chengdu, China
| | - Peng-Yuan Wang
- Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Hawthorn, VIC, Australia
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12
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Bertels S, Jaggy M, Richter B, Keppler S, Weber K, Genthner E, Fischer AC, Thiel M, Wegener M, Greiner AM, Autenrieth TJ, Bastmeyer M. Geometrically defined environments direct cell division rate and subcellular YAP localization in single mouse embryonic stem cells. Sci Rep 2021; 11:9269. [PMID: 33927254 PMCID: PMC8084931 DOI: 10.1038/s41598-021-88336-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 04/01/2021] [Indexed: 01/09/2023] Open
Abstract
Mechanotransduction via yes-associated protein (YAP) is a central mechanism for decision-making in mouse embryonic stem cells (mESCs). Nuclear localization of YAP is tightly connected to pluripotency and increases the cell division rate (CDR). How the geometry of the extracellular environment influences mechanotransduction, thereby YAP localization, and decision-making of single isolated mESCs is largely unknown. To investigate this relation, we produced well-defined 2D and 2.5D microenvironments and monitored CDR and subcellular YAP localization in single mESCs hence excluding cell–cell interactions. By systematically varying size and shape of the 2D and 2.5D substrates we observed that the geometry of the growth environment affects the CDR. Whereas CDR increases with increasing adhesive area in 2D, CDR is highest in small 2.5D micro-wells. Here, mESCs attach to all four walls and exhibit a cross-shaped cell and nuclear morphology. This observation indicates that changes in cell shape are linked to a high CDR. Inhibition of actomyosin activity abrogate these effects. Correspondingly, nuclear YAP localization decreases in inhibitor treated cells, suggesting a relation between cell shape, intracellular forces, and cell division rate. The simplicity of our system guarantees high standardization and reproducibility for monitoring stem cell reactions and allows addressing a variety of fundamental biological questions on a single cell level.
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Affiliation(s)
- Sarah Bertels
- Zoological Institute, Cell- and Neurobiology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany.,Institute of Functional Interfaces, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.,3DMM2O - Cluster of Excellence (EXC-2082/1 - 390761711), Karlsruhe, Germany
| | - Mona Jaggy
- Zoological Institute, Cell- and Neurobiology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany.,Institute of Functional Interfaces, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Benjamin Richter
- Zoological Institute, Cell- and Neurobiology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany
| | - Stephan Keppler
- Zoological Institute, Cell- and Neurobiology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany.,3DMM2O - Cluster of Excellence (EXC-2082/1 - 390761711), Karlsruhe, Germany
| | - Kerstin Weber
- Zoological Institute, Cell- and Neurobiology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany
| | - Elisa Genthner
- Zoological Institute, Cell- and Neurobiology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany.,3DMM2O - Cluster of Excellence (EXC-2082/1 - 390761711), Karlsruhe, Germany
| | - Andrea C Fischer
- Zoological Institute, Cell- and Neurobiology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany.,Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Straße 1, 76131, Karlsruhe, Germany
| | - Michael Thiel
- Nanoscribe GmbH, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Martin Wegener
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Straße 1, 76131, Karlsruhe, Germany.,Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.,3DMM2O - Cluster of Excellence (EXC-2082/1 - 390761711), Karlsruhe, Germany
| | - Alexandra M Greiner
- Zoological Institute, Cell- and Neurobiology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany
| | - Tatjana J Autenrieth
- Zoological Institute, Cell- and Neurobiology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany.,Institute of Functional Interfaces, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Martin Bastmeyer
- Zoological Institute, Cell- and Neurobiology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany. .,Institute of Functional Interfaces, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany. .,3DMM2O - Cluster of Excellence (EXC-2082/1 - 390761711), Karlsruhe, Germany. .,Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.
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13
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Babaie A, Lumicisi J, Thissen H, Wang PY, Sumer H, Kingshott P. Binary Colloidal Crystal (BCC) Substrates for Controlling the Fate of Mouse Embryonic Stem Cells. Colloids Surf B Biointerfaces 2020; 194:111133. [PMID: 32554259 DOI: 10.1016/j.colsurfb.2020.111133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 04/20/2020] [Accepted: 05/11/2020] [Indexed: 11/28/2022]
Abstract
Understanding the interactions of stem cells with surface topography can give us an invaluable tool in controlling stemness and fate of stem cells for further use in biomedical applications. In this study, we have fabricated topographical features using a class of cell culture substrates called binary colloidal crystals (BCCs), that are made by self-assembly of mixtures of spherical micron sized silica (Si) and nanometer sized polystyrene (PS) or poly (methyl methacrylate) (PMMA) particles. The substrates formed are arrays of ordered, hexagonally packed large Si particles inter-dispersed with the PS particles that are stabilized by gentle heating, which melts the PS or PMMA forming substrates suitable for cell culture. BCC substrates were used for culture of mouse embryonic stem cells (mESCs). Compared to tissue culture plates, COM1 (Si5-PMMA0.4), COM2 (Si5-PS0.4) and COM4 (Si2-PSC0.22) have shown to provide a better support for mESC proliferation in the presence of the cytokine leukemia inhibitory factor (LIF). The behavior of mESCs with the BCCs in presence and absence of LIF, was further explored and it was found that interaction of mESCs with the culture substrate can be controlled by tuning surface topography and roughness, which is determined by the size and type of particles used in making BCCs. Furthermore, it was shown that limiting cell-surface interactions and controlling colony shape can promote stemness maintenance on COM1 and COM2 substrates as indicated by better proliferation and higher expression of pluripotency genes including Nanog both in presence and in absence of LIF. Together with higher expression of GATA6 gene, it can be stated that these surfaces can be used for endodermic priming of mESCs. Therefore, we believe that these surfaces, especially COM1 and COM2 surfaces can be beneficial as stem cell culture systems for further use in biomedical research.
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Affiliation(s)
- Ali Babaie
- Department of Chemistry and Biotechnology, School of Science, Swinburne University of Technology, Hawthorn, Victoria 3122, Australia; CSIRO Manufacturing, Research Way, Clayton, Victoria 3168, Australia
| | - James Lumicisi
- Department of Chemistry and Biotechnology, School of Science, Swinburne University of Technology, Hawthorn, Victoria 3122, Australia
| | - Helmut Thissen
- CSIRO Manufacturing, Research Way, Clayton, Victoria 3168, Australia
| | - Peng-Yuan Wang
- Department of Chemistry and Biotechnology, School of Science, Swinburne University of Technology, Hawthorn, Victoria 3122, Australia; Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
| | - Huseyin Sumer
- Department of Chemistry and Biotechnology, School of Science, Swinburne University of Technology, Hawthorn, Victoria 3122, Australia.
| | - Peter Kingshott
- Department of Chemistry and Biotechnology, School of Science, Swinburne University of Technology, Hawthorn, Victoria 3122, Australia
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14
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Miller AE, Hu P, Barker TH. Feeling Things Out: Bidirectional Signaling of the Cell-ECM Interface, Implications in the Mechanobiology of Cell Spreading, Migration, Proliferation, and Differentiation. Adv Healthc Mater 2020; 9:e1901445. [PMID: 32037719 PMCID: PMC7274903 DOI: 10.1002/adhm.201901445] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/10/2020] [Indexed: 12/16/2022]
Abstract
Biophysical cues stemming from the extracellular environment are rapidly transduced into discernible chemical messages (mechanotransduction) that direct cellular activities-placing the extracellular matrix (ECM) as a potent regulator of cell behavior. Dynamic reciprocity between the cell and its associated matrix is essential to the maintenance of tissue homeostasis and dysregulation of both ECM mechanical signaling, via pathological ECM turnover, and internal mechanotransduction pathways contribute to disease progression. This review covers the current understandings of the key modes of signaling used by both the cell and ECM to coregulate one another. By taking an outside-in approach, the inherent complexities and regulatory processes at each level of signaling (ECM, plasma membrane, focal adhesion, and cytoplasm) are captured to give a comprehensive picture of the internal and external mechanoregulatory environment. Specific emphasis is placed on the focal adhesion complex which acts as a central hub of mechanical signaling, regulating cell spreading, migration, proliferation, and differentiation. In addition, a wealth of available knowledge on mechanotransduction is curated to generate an integrated signaling network encompassing the central components of the focal adhesion, cytoplasm and nucleus that act in concert to promote durotaxis, proliferation, and differentiation in a stiffness-dependent manner.
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Affiliation(s)
- Andrew E Miller
- Department of Biomedical Engineering, University of Virginia, 415 Lane Rd. MR5 1225, Charlottesville, VA, 22903, USA
| | - Ping Hu
- Department of Biomedical Engineering, University of Virginia, 415 Lane Rd. MR5 1225, Charlottesville, VA, 22903, USA
| | - Thomas H Barker
- Department of Biomedical Engineering, University of Virginia, 415 Lane Rd. MR5 1225, Charlottesville, VA, 22903, USA
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15
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Farzaneh M, Derakhshan Z, Hallajzadeh J, Sarani NH, Nejabatdoust A, Khoshnam SE. Suppression of TGF-β and ERK Signaling Pathways as a New Strategy to Provide Rodent and Non-Rodent Pluripotent Stem Cells. Curr Stem Cell Res Ther 2020; 14:466-473. [PMID: 30868962 DOI: 10.2174/1871527318666190314110529] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 02/02/2019] [Accepted: 02/21/2019] [Indexed: 01/07/2023]
Abstract
Stem cells are unspecialized cells and excellent model in developmental biology and a promising approach to the treatment of disease and injury. In the last 30 years, pluripotent embryonic stem (ES) cells were established from murine and primate sources, and display indefinite replicative potential and the ability to differentiate to all three embryonic germ layers. Despite large efforts in many aspects of rodent and non-rodent pluripotent stem cell culture, a number of diverse challenges remain. Natural and synthetic small molecules (SMs) strategy has the potential to overcome these hurdles. Small molecules are typically fast and reversible that target specific signaling pathways, epigenetic processes and other cellular processes. Inhibition of the transforming growth factor-β (TGF-β/Smad) and fibroblast growth factor 4 (FGF4)/ERK signaling pathways by SB431542 and PD0325901 small molecules, respectively, known as R2i, enhances the efficiency of mouse, rat, and chicken pluripotent stem cells passaging from different genetic backgrounds. Therefore, the application of SM inhibitors of TGF-β and ERK1/2 with leukemia inhibitory factor (LIF) allows the cultivation of pluripotent stem cells in a chemically defined condition. In this review, we discuss recently emerging evidence that dual inhibition of TGF-β and FGF signaling pathways plays an important role in regulating pluripotency in both rodent and non-rodent pluripotent stem cells.
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Affiliation(s)
- Maryam Farzaneh
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Zahra Derakhshan
- Department of Reproductive Biology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Jamal Hallajzadeh
- Department of Biochemistry and Toxicology, Maraghe University of Medical Science, Maraghe, Iran
| | | | - Armin Nejabatdoust
- Department of Biology, Rasht Branch, Islamic Azad University, Rasht, Iran
| | - Seyed Esmaeil Khoshnam
- Physiology Research Center, Department of Physiology, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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16
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Yousefi M, Marashi SA, Sharifi-Zarchi A, Taleahmad S. The metabolic network model of primed/naive human embryonic stem cells underlines the importance of oxidation-reduction potential and tryptophan metabolism in primed pluripotency. Cell Biosci 2019; 9:71. [PMID: 31485322 PMCID: PMC6716874 DOI: 10.1186/s13578-019-0334-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 08/19/2019] [Indexed: 01/01/2023] Open
Abstract
Background Pluripotency is proposed to exist in two different stages: Naive and Primed. Conventional human pluripotent cells are essentially in the primed stage. In recent years, several protocols have claimed to generate naive human embryonic stem cells (hESCs). To the best of our knowledge, none of these protocols is currently recognized as the gold standard method. Furthermore, the consistency of the resulting cells from these diverse protocols at the molecular level is yet to be shown. Additionally, little is known about the principles that govern the metabolic differences between naive and primed pluripotency. In this work, using a computational approach, we tried to shed light on these basic issues. Results We showed that, after batch effect removal, the transcriptome data of eight different protocols which supposedly produce naive hESCs are clustered consistently when compared to the primed ones. Next, by integrating transcriptomes of all hESCs obtained by these protocols, we reconstructed p-hESCNet and n-hESCNet, the first metabolic network models representing hESCs. By exploiting reporter metabolite analysis we showed that the status of NAD\documentclass[12pt]{minimal}
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\begin{document}$$^{+}$$\end{document}+ and the metabolites involved in the TCA cycle are significantly altered between naive and primed hESCs. Furthermore, using flux variability analysis (FVA), the models showed that the kynurenine-mediated metabolism of tryptophan is remarkably downregulated in naive human pluripotent cells. Conclusion The aim of the present paper is twofold. Firstly, our findings confirm the applicability of all these protocols for generating naive hESCs, due to their consistency at the transcriptome level. Secondly, we showed that in silico metabolic models of hESCs can be used to simulate the metabolic states of naive and primed pluripotency. Our models confirmed the OXPHOS activation in naive cells and showed that oxidation-reduction potential vary between naive and primed cells. Tryptophan metabolism is also outlined as a key pathway in primed pluripotency and the models suggest that decrements in the activity of this pathway might be an appropriate marker for naive pluripotency.
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Affiliation(s)
- Meisam Yousefi
- 1Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran.,2Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Sayed-Amir Marashi
- 1Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Ali Sharifi-Zarchi
- 3Department of Computer Engineering, Sharif University of Technology, Tehran, Iran
| | - Sara Taleahmad
- 2Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
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17
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Meyfour A, Hosseini M, Sobhanian H, Pahlavan S. Iran's Contribution to Human Proteomic Research. CELL JOURNAL 2019; 21:229-235. [PMID: 31210427 PMCID: PMC6582420 DOI: 10.22074/cellj.2019.6303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 11/17/2018] [Indexed: 11/04/2022]
Abstract
Proteomics is a powerful approach to study the whole set of proteins expressed in an organism, organ, tissue or cell resulting in valuable information on physiological or pathological state of a biological system. High throughput proteomic data facilitated the understanding of various biological systems with respect to normal and pathological conditions particularly in the instances of human clinical manifestations. The important role of proteins as the functional gene products encouraged scientists to apply this technology to gain a better understanding of extremely complex biological systems. In last two decades, several proteomics teams have been gradually formed in Iran. In this review, we highlight the most important findings of proteomic research groups in Iran at various areas of stem cells, Y chromosome, infertility, infectious disease and biomarker discovery.
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Affiliation(s)
- Anna Meyfour
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Mahya Hosseini
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | | | - Sara Pahlavan
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.Electronic Address:
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18
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Slc25a36 modulates pluripotency of mouse embryonic stem cells by regulating mitochondrial function and glutathione level. Biochem J 2019; 476:1585-1604. [PMID: 31036718 DOI: 10.1042/bcj20190057] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 04/09/2019] [Accepted: 04/29/2019] [Indexed: 01/01/2023]
Abstract
Mitochondria play a central role in the maintenance of the naive state of embryonic stem cells. Many details of the mechanism remain to be fully elucidated. Solute carrier family 25 member 36 (Slc25a36) might regulate mitochondrial function through transporting pyrimidine nucleotides for mtDNA/RNA synthesis. Its physical role in this process remains unknown; however, Slc25a36 was recently found to be highly expressed in naive mouse embryonic stem cells (mESCs). Here, the function of Slc25a36 was characterized as a maintenance factor of mESCs pluripotency. Slc25a36 deficiency (via knockdown) has been demonstrated to result in mitochondrial dysfunction, which induces the differentiation of mESCs. The expression of key pluripotency markers (Pou5f1, Sox2, Nanog, and Utf1) decreased, while that of key TE genes (Cdx2, Gata3, and Hand1) increased. Cdx2-positive cells emerged in Slc25a36-deficient colonies under trophoblast stem cell culture conditions. As a result of Slc25a36 deficiency, mtDNA of knockdown cells declined, leading to impaired mitochondria with swollen morphology, decreased mitochondrial membrane potential, and low numbers. The key transcription regulators of mitochondrial biogenesis also decreased. These results indicate that mitochondrial dysfunction leads to an inability to support the pluripotency maintenance. Moreover, down-regulated glutathione metabolism and up-regulated focal adhesion reinforced and stabilized the process of differentiation by separately enhancing OCT4 degradation and promoting cell spread. This study improves the understanding of the function of Slc25a36, as well as the relationship of mitochondrial function with naive pluripotency maintenance and stem cell fate decision.
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19
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The N-end rule pathway enzyme Naa10 supports epiblast specification in mouse embryonic stem cells by modulating FGF/MAPK. In Vitro Cell Dev Biol Anim 2019; 55:355-367. [PMID: 30993557 DOI: 10.1007/s11626-019-00341-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 03/11/2019] [Indexed: 10/27/2022]
Abstract
N-terminal acetylation (Nt-acetylation) refers to the acetylation of the free α-amino group at the N-terminus of a polypeptide. While the effects of Nt-acetylation are multifaceted, its most known function is in the acetylation-dependent N-end rule protein degradation pathway (Ac/N-end rule pathway), where Nt-acetylation is recognized as a degron by designated E3 ligases, eventually leading to target degradation by the ubiquitin-proteasome system. Naa10 is the catalytic subunit of the major Nt-acetylation enzyme NatA, which Nt-acetylates proteins whose second amino acid has a small side chain. In humans, NAA10 is the responsible mutated gene in Ogden syndrome and is thought to play important roles in development. However, it is unclear how the Ac/N-end rule pathway affects the differentiation ability of mouse embryonic stem cells (mESCs). We hypothesized that the balance of pluripotency factors may be maintained by the Ac/N-end rule pathway. Thus, we established Naa10 knockout mESCs to test this hypothesis. We found that Naa10 deficiency attenuated differentiation towards the epiblast lineage, deviating towards primitive endoderm. However, this was not caused by disturbing the balance of pluripotency factors, rather by augmenting FGF/MAPK signaling.
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20
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Sayago C, Martinez-Val A, Munoz J. Proteotyping pluripotency with mass spectrometry. Expert Rev Proteomics 2019; 16:391-400. [PMID: 30947573 DOI: 10.1080/14789450.2019.1604229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
INTRODUCTION Pluripotency emerges transiently during embryogenesis in two main forms with different developmental potential, termed naïve and primed states. Importantly, these pluripotent states can be recapitulated in vitro under specific culture conditions, representing a unique model to study the regulatory principles of development and cellular plasticity. Areas covered: A complex network of signaling pathways that senses intrinsic and extrinsic cues controls the fine balance between self-renewal and differentiation. Much of our knowledge on this tight regulation originates from epigenetic and transcriptomic approaches. However, the presence of post-transcriptional and post-translational mechanisms demands a direct assessment of the proteome in its multiple facets. Mass spectrometry-based proteomics is now a mature technique and has started to deliver new insights in the stem cell field. Expert opinion: Here, we review our current understanding on the mechanisms that dictate the spectrum of pluripotency levels. We put special emphasis on the emerging proteomic studies that focused on the molecular properties behind the naïve and primed states. In addition, we hypothesize on the impact that future developments in proteomic technologies can have to improve our view of pluripotency.
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Affiliation(s)
- Cristina Sayago
- a Proteomics Unit , Spanish National Cancer Research Centre (CNIO) , Madrid , Spain.,b ISCIII-ProteoRed , Spain
| | - Ana Martinez-Val
- a Proteomics Unit , Spanish National Cancer Research Centre (CNIO) , Madrid , Spain.,b ISCIII-ProteoRed , Spain
| | - Javier Munoz
- a Proteomics Unit , Spanish National Cancer Research Centre (CNIO) , Madrid , Spain.,b ISCIII-ProteoRed , Spain
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21
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Hassani SN, Moradi S, Taleahmad S, Braun T, Baharvand H. Transition of inner cell mass to embryonic stem cells: mechanisms, facts, and hypotheses. Cell Mol Life Sci 2019; 76:873-892. [PMID: 30420999 PMCID: PMC11105545 DOI: 10.1007/s00018-018-2965-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 11/01/2018] [Accepted: 11/02/2018] [Indexed: 12/28/2022]
Abstract
Embryonic stem cells (ESCs) are immortal stem cells that own multi-lineage differentiation potential. ESCs are commonly derived from the inner cell mass (ICM) of pre-implantation embryos. Due to their tremendous developmental capacity and unlimited self-renewal, ESCs have diverse biomedical applications. Different culture media have been developed to procure and maintain ESCs in a state of naïve pluripotency, and to preserve a stable genome and epigenome during serial passaging. Chromatin modifications such as DNA methylation and histone modifications along with microRNA activity and different signaling pathways dynamically contribute to the regulation of the ESC gene regulatory network (GRN). Such modifications undergo remarkable changes in different ESC media and determine the quality and developmental potential of ESCs. In this review, we discuss the current approaches for derivation and maintenance of ESCs, and examine how differences in culture media impact on the characteristics of pluripotency via modulation of GRN during the course of ICM outgrowth into ESCs. We also summarize the current hypotheses concerning the origin of ESCs and provide a perspective about the relationship of these cells to their in vivo counterparts (early embryonic cells around the time of implantation). Finally, we discuss generation of ESCs from human embryos and domesticated animals, and offer suggestions to further advance this fascinating field.
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Affiliation(s)
- Seyedeh-Nafiseh Hassani
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Sharif Moradi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Sara Taleahmad
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Thomas Braun
- Department of Cardiac Development and Remodelling, Max-Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
- Department of Developmental Biology, University of Science and Culture, Tehran, Iran.
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22
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van Mierlo G, Wester RA, Marks H. Quantitative subcellular proteomics using SILAC reveals enhanced metabolic buffering in the pluripotent ground state. Stem Cell Res 2018; 33:135-145. [PMID: 30352361 DOI: 10.1016/j.scr.2018.09.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 08/13/2018] [Accepted: 09/17/2018] [Indexed: 11/26/2022] Open
Abstract
The ground state of pluripotency is defined as a minimal unrestricted epigenetic state as present in the Inner Cell Mass. Mouse embryonic stem cells (ESCs) grown in a defined serum-free medium with two kinase inhibitors ("2i ESCs") have been postulated to reflect ground-state pluripotency, whereas ESCs grown in the presence of serum ("serum ESCs") share more similarities with post-implantation epiblast cells. Pluripotency results from an intricate interplay between cytoplasmic, nuclear and chromatin-associated proteins. Here, we perform quantitative subcellular proteomics to gain insight in the molecular mechanisms sustaining the pluripotent states reflected by 2i and serum ESCs. We describe a full SILAC workflow and quality controls for proteomic comparison of 2i and serum ESCs, allowing subcellular proteomics of the cytoplasm, nucleoplasm and chromatin. The obtained quantitative information revealed increased levels of naïve pluripotency factors on the chromatin of 2i ESCs. Surprisingly, the cytoplasmic proteome suggests that 2i and serum ESCs utilize distinct metabolic programs, which include upregulation of free radical buffering by the glutathione pathway in 2i ESCs. Through induction of intracellular radicals, we show that the altered metabolic environment renders 2i ESCs less sensitive to oxidative stress. Altogether, this work provides novel insights into the proteomic landscape underlying ground state pluripotency.
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Affiliation(s)
- Guido van Mierlo
- Department of Molecular Biology, Faculty of Science, Radboud University, Radboud Institute for Molecular Life Sciences (RIMLS), Geert Grooteplein 26/28, 6525GA Nijmegen, the Netherlands
| | - Roelof A Wester
- Department of Molecular Biology, Faculty of Science, Radboud University, Radboud Institute for Molecular Life Sciences (RIMLS), Geert Grooteplein 26/28, 6525GA Nijmegen, the Netherlands
| | - Hendrik Marks
- Department of Molecular Biology, Faculty of Science, Radboud University, Radboud Institute for Molecular Life Sciences (RIMLS), Geert Grooteplein 26/28, 6525GA Nijmegen, the Netherlands.
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Gholami D, Ghaffari SM, Shahverdi A, Sharafi M, Riazi G, Fathi R, Esmaeili V, Hezavehei M. Proteomic analysis and microtubule dynamicity of human sperm in electromagnetic cryopreservation. J Cell Biochem 2018; 119:9483-9497. [PMID: 30074256 DOI: 10.1002/jcb.27265] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 06/22/2018] [Indexed: 12/23/2022]
Abstract
The proteomic changes, microtubule dynamicity, and quality parameters of human sperm were investigated during cryopreservation in an extremely low electromagnetic field (ELEF) condition. Semen samples were obtained from 210 healthy individuals with normospermia and then were divided into three experimental groups: fresh control, frozen control, and frozen ELEF group. Shotgun proteomics was performed to assess the identification of microtubule proteins of the sperm in experimental groups. Microtubule dynamicity, secondary, and tertiary structure modifications of tubulins, characteristics of transmission electron microscopy of sperm as well as sperm quality parameters were evaluated. The expression ratios of α- and β-tubulins were significantly increased after cryopreservation compared with fresh control while this ratio was not significantly different in frozen ELEF group. The expression ratio of tubulin polymerization-promoting protein was significantly decreased after cryopreservation compared with fresh control. The length, width, and the activity of microtubule, secondary, and tertiary structures of tubulins, motility, and the viability of the sperm were decreased in frozen control as compared with fresh control. The microtubule activity, secondary, and tertiary structures of sperm tubulin in frozen ELEF group were higher than frozen control. Transmission electron microscopy of microtubules showed that the size of the width and length of the microtubules in frozen ELEF group were greater than frozen control. Motility, viability, and reactive oxygen species levels were improved in frozen ELEF group when compared with frozen control. While the microtubule dynamicity of the sperm was affected by the cryopreservation, this trait was improved during the electromagnetic cryopreservation resulted in better motility and viability.
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Affiliation(s)
- Dariush Gholami
- Department of Biochemistry, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Seyed Mahmood Ghaffari
- Department of Biochemistry, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Abdolhossein Shahverdi
- Department of Embryology, Reproduction Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACER, Tehran, Iran
| | - Mohsen Sharafi
- Department of Embryology, Reproduction Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACER, Tehran, Iran.,Department of Poultry Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Gholamhossein Riazi
- Department of Biochemistry, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Rouhollah Fathi
- Department of Embryology, Reproduction Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACER, Tehran, Iran
| | - Vahid Esmaeili
- Department of Embryology, Reproduction Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACER, Tehran, Iran
| | - Maryam Hezavehei
- Department of Embryology, Reproduction Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACER, Tehran, Iran
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24
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Taleahmad S, Hassani SN, Hosseini Salekdeh G, Baharvand H. Metabolic Signature of Pluripotent Stem Cells. CELL JOURNAL 2018; 20:388-395. [PMID: 29845793 PMCID: PMC6004998 DOI: 10.22074/cellj.2018.5514] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 11/25/2017] [Indexed: 01/12/2023]
Abstract
Objective Pluripotent stem cells (PSCs), with the capacity to self-renew and differentiate into all other cell types, are of benefit
in regenerative medicine applications. Tightly controlled gene expression networks and epigenetic factors regulate these
properties. In this study, we aim to evaluate the metabolic signature of pluripotency under 2i and R2i culture conditions versus
serum condition.
Materials and Methods In this experimental study, we investigated bioinformatics analysis of the shotgun proteomics
data for cells grown under 2i, R2i, and serum culture conditions. The findings were validated by cell cycle analysis and
gene expressions of the cells with flow cytometry and quantitative reverse transcription-polymerase chain reaction
(qRT-PCR), respectively.
Results Expressions of 163 proteins increased in 2i-grown cells and 181 proteins increased in R2i-grown cells versus
serum, which were mostly involved in glycolysis signaling pathway, oxidation-reduction, metabolic processes, amino
acid and lipid metabolism. Flow cytometry analysis showed significant accumulation of cells in S phase for 2i (70%)
and R2i (61%) grown cells.
Conclusion This study showed that under 2i and R2i conditions, glycolysis was highlighted for energy production
and used to maintain high levels of glycolytic intermediates to support cell proliferation. Cells grown under 2i and R2i
conditions showed rapid cell cycling in comparison with the cells grown under serum conditions.
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Affiliation(s)
- Sara Taleahmad
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.,Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Seyedeh Nafiseh Hassani
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.,Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Karaj, Iran.Electronic Address:
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.,Department of Developmental Biology, University of Science and Culture, ACECR, Tehran, Iran.Electronic Address:
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