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Luo H, Tang L, Zeng M, Yin R, Ding P, Luo L, Li M. BertSNR: an interpretable deep learning framework for single-nucleotide resolution identification of transcription factor binding sites based on DNA language model. Bioinformatics 2024; 40:btae461. [PMID: 39107889 PMCID: PMC11310455 DOI: 10.1093/bioinformatics/btae461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 06/07/2024] [Indexed: 08/10/2024] Open
Abstract
MOTIVATION Transcription factors are pivotal in the regulation of gene expression, and accurate identification of transcription factor binding sites (TFBSs) at high resolution is crucial for understanding the mechanisms underlying gene regulation. The task of identifying TFBSs from DNA sequences is a significant challenge in the field of computational biology today. To address this challenge, a variety of computational approaches have been developed. However, these methods face limitations in their ability to achieve high-resolution identification and often lack interpretability. RESULTS We propose BertSNR, an interpretable deep learning framework for identifying TFBSs at single-nucleotide resolution. BertSNR integrates sequence-level and token-level information by multi-task learning based on pre-trained DNA language models. Benchmarking comparisons show that our BertSNR outperforms the existing state-of-the-art methods in TFBS predictions. Importantly, we enhanced the interpretability of the model through attentional weight visualization and motif analysis, and discovered the subtle relationship between attention weight and motif. Moreover, BertSNR effectively identifies TFBSs in promoter regions, facilitating the study of intricate gene regulation. AVAILABILITY AND IMPLEMENTATION The BertSNR source code can be found at https://github.com/lhy0322/BertSNR.
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Affiliation(s)
- Hanyu Luo
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, China
- School of Computer Science, University of South China, Hengyang, Hunan 421001, China
| | - Li Tang
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, China
| | - Min Zeng
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, China
| | - Rui Yin
- Department of Health Outcome and Biomedical Informatics, University of Florida, Gainesville, FL 32611, United States
| | - Pingjian Ding
- Center for Artificial Intelligence in Drug Discovery, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, United States
| | - Lingyun Luo
- School of Computer Science, University of South China, Hengyang, Hunan 421001, China
| | - Min Li
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, China
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2
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Chen HF, Wu KJ. LncRNAs and asymmetric cell division: the epigenetic mechanisms. Biomed J 2024:100774. [PMID: 39059582 DOI: 10.1016/j.bj.2024.100774] [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: 04/23/2024] [Revised: 07/16/2024] [Accepted: 07/24/2024] [Indexed: 07/28/2024] Open
Abstract
Asymmetric cell division (ACD) plays a pivotal role in development, tissue homeostasis, and stem cell maintenance. Emerging evidence suggests that long non-coding RNAs (lncRNAs) are key regulators of ACD, orchestrating the intricate molecular machinery that governs cell fate determination. This review summarizes current literature to elucidate the diverse roles of lncRNAs in modulating ACD across various biological contexts. The regulatory mechanisms of asymmetric cell division mediated by lncRNAs, including their interactions with protein effectors, epigenetic regulation, and subcellular localization are explored. Additionally, we discuss the implications of dysregulated lncRNAs in mediating ACD that lead to tumorigenesis. By integrating findings from diverse experimental models and cell types, this review provides insights into the multifaceted roles of lncRNAs in governing asymmetric cell division, shedding light on fundamental biological processes. Further research in this area may lead to the development of novel therapies targeting dysregulated lncRNAs to restore proper cell division and function. The knowledge of lncRNAs regulating ACD could potentially revolutionize the field of regenerative medicine and cancer therapy by targeting specific lncRNAs involved in ACD. By unraveling the complex interactions between lncRNAs and cellular processes, the potential novel opportunities for precision medicine approaches may be uncovered.
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Affiliation(s)
- Hsiao-Fan Chen
- Graduate Institutes of Biomedical Sciences, China Medical University, Taichung 404, Taiwan; Graduate Institutes of Cell Biology, China Medical University, Taichung 404, Taiwan.
| | - Kou-Juey Wu
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, Gueishan Dist., Taoyuan 333, Taiwan.
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3
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Wu J, Fu J. Toward developing human organs via embryo models and chimeras. Cell 2024; 187:3194-3219. [PMID: 38906095 PMCID: PMC11239105 DOI: 10.1016/j.cell.2024.05.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 02/02/2024] [Accepted: 05/14/2024] [Indexed: 06/23/2024]
Abstract
Developing functional organs from stem cells remains a challenging goal in regenerative medicine. Existing methodologies, such as tissue engineering, bioprinting, and organoids, only offer partial solutions. This perspective focuses on two promising approaches emerging for engineering human organs from stem cells: stem cell-based embryo models and interspecies organogenesis. Both approaches exploit the premise of guiding stem cells to mimic natural development. We begin by summarizing what is known about early human development as a blueprint for recapitulating organogenesis in both embryo models and interspecies chimeras. The latest advances in both fields are discussed before highlighting the technological and knowledge gaps to be addressed before the goal of developing human organs could be achieved using the two approaches. We conclude by discussing challenges facing embryo modeling and interspecies organogenesis and outlining future prospects for advancing both fields toward the generation of human tissues and organs for basic research and translational applications.
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Affiliation(s)
- Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Jianping Fu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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4
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Li S, Yang M, Shen H, Ding L, Lyu X, Lin K, Ong J, Du P. Capturing totipotency in human cells through spliceosomal repression. Cell 2024; 187:3284-3302.e23. [PMID: 38843832 DOI: 10.1016/j.cell.2024.05.010] [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: 06/19/2022] [Revised: 09/01/2023] [Accepted: 05/03/2024] [Indexed: 06/23/2024]
Abstract
The cleavage of zygotes generates totipotent blastomeres. In human 8-cell blastomeres, zygotic genome activation (ZGA) occurs to initiate the ontogenesis program. However, capturing and maintaining totipotency in human cells pose significant challenges. Here, we realize culturing human totipotent blastomere-like cells (hTBLCs). We find that splicing inhibition can transiently reprogram human pluripotent stem cells into ZGA-like cells (ZLCs), which subsequently transition into stable hTBLCs after long-term passaging. Distinct from reported 8-cell-like cells (8CLCs), both ZLCs and hTBLCs widely silence pluripotent genes. Interestingly, ZLCs activate a particular group of ZGA-specific genes, and hTBLCs are enriched with pre-ZGA-specific genes. During spontaneous differentiation, hTBLCs re-enter the intermediate ZLC stage and further generate epiblast (EPI)-, primitive endoderm (PrE)-, and trophectoderm (TE)-like lineages, effectively recapitulating human pre-implantation development. Possessing both embryonic and extraembryonic developmental potency, hTBLCs can autonomously generate blastocyst-like structures in vitro without external cell signaling. In summary, our study provides key criteria and insights into human cell totipotency.
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Affiliation(s)
- Shiyu Li
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Min Yang
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Hui Shen
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Li Ding
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xuehui Lyu
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Kexin Lin
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jennie Ong
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Peng Du
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; Beijing Advanced Center of RNA Biology, Peking University, Beijing 100871, China.
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5
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Onfray C, Chevolleau S, Moinard E, Girard O, Mahadik K, Allsop R, Georgolopoulos G, Lavigne R, Renoult O, Aksoy I, Lemaitre E, Hulin P, Ouimette JF, Fréour T, Pecqueur C, Pineau C, Pasque V, Rougeulle C, David L. Unraveling hallmark suitability for staging pre- and post-implantation stem cell models. Cell Rep 2024; 43:114232. [PMID: 38761378 DOI: 10.1016/j.celrep.2024.114232] [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: 07/11/2023] [Revised: 02/02/2024] [Accepted: 04/26/2024] [Indexed: 05/20/2024] Open
Abstract
The advent of novel 2D and 3D models for human development, including trophoblast stem cells and blastoids, has expanded opportunities for investigating early developmental events, gradually illuminating the enigmatic realm of human development. While these innovations have ushered in new prospects, it has become essential to establish well-defined benchmarks for the cell sources of these models. We aimed to propose a comprehensive characterization of pluripotent and trophoblastic stem cell models by employing a combination of transcriptomic, proteomic, epigenetic, and metabolic approaches. Our findings reveal that extended pluripotent stem cells share many characteristics with primed pluripotent stem cells, with the exception of metabolic activity. Furthermore, our research demonstrates that DNA hypomethylation and high metabolic activity define trophoblast stem cells. These results underscore the necessity of considering multiple hallmarks of pluripotency rather than relying on a single criterion. Multiplying hallmarks alleviate stage-matching bias.
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Affiliation(s)
- Constance Onfray
- Nantes Université, CHU Nantes, Inserm, CR2TI, 44000 Nantes, France
| | - Simon Chevolleau
- Nantes Université, CHU Nantes, Inserm, CR2TI, 44000 Nantes, France
| | - Eva Moinard
- Nantes Université, CHU Nantes, Inserm, CR2TI, 44000 Nantes, France
| | - Océane Girard
- Nantes Université, CHU Nantes, Inserm, CR2TI, 44000 Nantes, France
| | - Kasturi Mahadik
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, 75013 Paris, France
| | - Ryan Allsop
- KU Leuven - University of Leuven, Department of Development and Regeneration, Leuven Institute for Single Cell Omics and Leuven Stem Cell Institute, Herestraat 49, 3000 Leuven, Belgium
| | - Grigorios Georgolopoulos
- KU Leuven - University of Leuven, Department of Development and Regeneration, Leuven Institute for Single Cell Omics and Leuven Stem Cell Institute, Herestraat 49, 3000 Leuven, Belgium
| | - Régis Lavigne
- University Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, 35000 Rennes, France; University Rennes, CNRS, Inserm, Biosit UAR 3480 US_S 018, Protim Core Facility, 35000 Rennes, France
| | - Ophélie Renoult
- Nantes Université, CNRS, Inserm, CRCI2NA, 44000 Nantes, France
| | - Irene Aksoy
- University Lyon, Université Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Elsa Lemaitre
- Nantes Université, CHU Nantes, Inserm, CNRS, BioCore, SFR Bonamy, 44000 Nantes, France
| | - Philippe Hulin
- Nantes Université, CHU Nantes, Inserm, CNRS, BioCore, SFR Bonamy, 44000 Nantes, France
| | | | - Thomas Fréour
- Nantes Université, CHU Nantes, Inserm, CR2TI, 44000 Nantes, France; Department of Obstetrics, Gynecology and Reproductive Medicine, Dexeus University Hospital, 08028 Barcelona, Spain; CHU Nantes, Service de Biologie de la Reproduction, 44000 Nantes, France
| | - Claire Pecqueur
- Nantes Université, CNRS, Inserm, CRCI2NA, 44000 Nantes, France
| | - Charles Pineau
- University Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, 35000 Rennes, France; University Rennes, CNRS, Inserm, Biosit UAR 3480 US_S 018, Protim Core Facility, 35000 Rennes, France
| | - Vincent Pasque
- KU Leuven - University of Leuven, Department of Development and Regeneration, Leuven Institute for Single Cell Omics and Leuven Stem Cell Institute, Herestraat 49, 3000 Leuven, Belgium
| | - Claire Rougeulle
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, 75013 Paris, France
| | - Laurent David
- Nantes Université, CHU Nantes, Inserm, CR2TI, 44000 Nantes, France; Nantes Université, CHU Nantes, Inserm, CNRS, BioCore, SFR Bonamy, 44000 Nantes, France.
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6
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Shen Z, Wu Y, Manna A, Yi C, Cairns BR, Evason KJ, Chandrasekharan MB, Tantin D. Oct4 redox sensitivity potentiates reprogramming and differentiation. Genes Dev 2024; 38:308-321. [PMID: 38719541 PMCID: PMC11146590 DOI: 10.1101/gad.351411.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 04/17/2024] [Indexed: 05/21/2024]
Abstract
The transcription factor Oct4/Pou5f1 is a component of the regulatory circuitry governing pluripotency and is widely used to induce pluripotency from somatic cells. Here we used domain swapping and mutagenesis to study Oct4's reprogramming ability, identifying a redox-sensitive DNA binding domain, cysteine residue (Cys48), as a key determinant of reprogramming and differentiation. Oct4 Cys48 sensitizes the protein to oxidative inhibition of DNA binding activity and promotes oxidation-mediated protein ubiquitylation. Pou5f1 C48S point mutation has little effect on undifferentiated embryonic stem cells (ESCs) but upon retinoic acid (RA) treatment causes retention of Oct4 expression, deregulated gene expression, and aberrant differentiation. Pou5f1 C48S ESCs also form less differentiated teratomas and contribute poorly to adult somatic tissues. Finally, we describe Pou5f1 C48S (Janky) mice, which in the homozygous condition are severely developmentally restricted after E4.5. Rare animals bypassing this restriction appear normal at birth but are sterile. Collectively, these findings uncover a novel Oct4 redox mechanism involved in both entry into and exit from pluripotency.
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Affiliation(s)
- Zuolian Shen
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Yifan Wu
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Asit Manna
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Chongil Yi
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Bradley R Cairns
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
- Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Kimberley J Evason
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Mahesh B Chandrasekharan
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Dean Tantin
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA;
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
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7
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Shen Z, Wu Y, Mana A, Yi C, Cairns B, Evason KJ, Chandrasekharan MB, Tantin D. Oct4 redox sensitivity potentiates reprogramming and differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.02.21.529404. [PMID: 36865286 PMCID: PMC9980064 DOI: 10.1101/2023.02.21.529404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
The transcription factor Oct4/Pou5f1 is a component of the regulatory circuitry governing pluripotency and is widely used to induce pluripotency from somatic cells. Here we use domain swapping and mutagenesis to study Oct4s reprogramming ability, identifying a redox-sensitive DNA binding domain cysteine residue (Cys48) as a key determinant of reprogramming and differentiation. Oct4 Cys48 sensitizes the protein to oxidative inhibition of DNA binding activity and promotes oxidation-mediated protein ubiquitylation. Pou5f1C48S point mutation has little effect on undifferentiated embryonic stem cells (ESCs), but upon retinoic acid (RA) treatment causes retention of Oct4 expression, deregulated gene expression and aberrant differentiation. Pou5f1C48S ESCs also form less differentiated teratomas and contribute poorly to adult somatic tissues. Finally, we describe Pou5f1C48S (Janky) mice, which in the homozygous condition are severely developmentally restricted after E4.5. Rare animals bypassing this restriction appear normal at birth but are sterile. Collectively, these findings uncover a novel Oct4 redox mechanism involved in both entry into and exit from pluripotency.
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8
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Wu Y, Wang C, Fan X, Ma Y, Liu Z, Ye X, Shen C, Wu C. The impact of induced pluripotent stem cells in animal conservation. Vet Res Commun 2024; 48:649-663. [PMID: 38228922 DOI: 10.1007/s11259-024-10294-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/04/2024] [Indexed: 01/18/2024]
Abstract
It is widely acknowledged that we are currently facing a critical tipping point with regards to global extinction, with human activities driving us perilously close to the brink of a devastating sixth mass extinction. As a promising option for safeguarding endangered species, induced pluripotent stem cells (iPSCs) hold great potential to aid in the preservation of threatened animal populations. For endangered species, such as the northern white rhinoceros (Ceratotherium simum cottoni), supply of embryos is often limited. After the death of the last male in 2019, only two females remained in the world. IPSC technology offers novel approaches and techniques for obtaining pluripotent stem cells (PSCs) from rare and endangered animal species. Successful generation of iPSCs circumvents several bottlenecks that impede the development of PSCs, including the challenges associated with establishing embryonic stem cells, limited embryo sources and immune rejection following embryo transfer. To provide more opportunities and room for growth in our work on animal welfare, in this paper we will focus on the progress made with iPSC lines derived from endangered and extinct species, exploring their potential applications and limitations in animal welfare research.
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Affiliation(s)
- Yurou Wu
- School of Pharmacy/School of Modem Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, People's Republic of China
| | - Chengwei Wang
- School of Pharmacy/School of Modem Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, People's Republic of China
| | - Xinyun Fan
- School of Pharmacy/School of Modem Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, People's Republic of China
| | - Yuxiao Ma
- Department of Biology, New York University, New York, NY, USA
| | - Zibo Liu
- School of Pharmacy/School of Modem Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, People's Republic of China
| | - Xun Ye
- School of Pharmacy/School of Modem Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, People's Republic of China
| | - Chongyang Shen
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, People's Republic of China.
| | - Chunjie Wu
- Innovative Institute of Chinese Medicine and Pharmacy/Academy for Interdiscipline, Chengdu Univesity of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, People's Republic of China.
- Sichuan Engineering Research Center for Endangered Medicinal Animals, Chengdu, China.
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Dai X, Yuan M, Yang Y, Dang M, Yang J, Shi J, Liu D, Li M, Yao H, Fei W. Dual cross-linked COL1/HAp bionic gradient scaffolds containing human amniotic mesenchymal stem cells promote rotator cuff tendon-bone interface healing. BIOMATERIALS ADVANCES 2024; 158:213799. [PMID: 38364326 DOI: 10.1016/j.bioadv.2024.213799] [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: 09/06/2023] [Revised: 01/17/2024] [Accepted: 02/08/2024] [Indexed: 02/18/2024]
Abstract
The tendon-bone interface heals through scar tissue, while the lack of a natural interface gradient structure and collagen fibre alignment leads to the occurrence of retearing. Therefore, the promotion of tendon healing has become the focus of regenerative medicine. The purpose of this study was to develop a gradient COL1/ hydroxyapatite (HAp) biomaterial loaded with human amniotic mesenchymal stem cells (hAMSCs). The performance of common cross-linking agents, Genipin, 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide/N-hydroxysuccinimide (EDC/NHS), and dual cross-linked materials were compared to select the best cross-linking mechanism to optimize the biological and mechanical properties of the scaffold. The optimal COL1/HAp-loaded with hAMSCs were implanted into the tendon-bone rotator cuff interfaces in rats and the effect on the tendon-bone healing was assessed by micro-CT, histological analysis, and biomechanical properties. The results showed that Genipin and EDC/NHS dual cross-linked COL1/HAp had good biological activity and mechanical properties and promoted the proliferation and differentiation of hAMSCs. Animal experiments showed that the group using a scaffold loaded with hAMSCs had excellent continuity and orientation of collagen fibers, increased fibrocartilage and bone formation, and significantly higher biomechanical functions than the control group at the interface at 12 weeks post operation. This study demonstrated that dual cross-linked gradient COL1/HAp-loaded hAMSCs could promote interface healing, thereby providing a feasible strategy for tendon-bone interface regeneration.
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Affiliation(s)
- Xiaomei Dai
- School of Nursing and School of Public Health, Yangzhou University, Yangzhou 225001, PR China; Department of Orthopedics and Sports Medicine, Northern Jiangsu People's Hospital, Affiliated to Yangzhou University, Yangzhou 225001, PR China
| | - Meijuan Yuan
- School of Nursing and School of Public Health, Yangzhou University, Yangzhou 225001, PR China; Department of Orthopedics and Sports Medicine, Northern Jiangsu People's Hospital, Affiliated to Yangzhou University, Yangzhou 225001, PR China
| | - Yuxia Yang
- Department of Orthopedics and Sports Medicine, Northern Jiangsu People's Hospital, Affiliated to Yangzhou University, Yangzhou 225001, PR China; Medical College, Yangzhou University, Yangzhou 225001, PR China
| | - Mengbo Dang
- Department of Orthopedics and Sports Medicine, Northern Jiangsu People's Hospital, Affiliated to Yangzhou University, Yangzhou 225001, PR China; Dalian Medical University, Dalian 116044, PR China
| | - Jian Yang
- Department of Orthopedics and Sports Medicine, Northern Jiangsu People's Hospital, Affiliated to Yangzhou University, Yangzhou 225001, PR China; Medical College, Yangzhou University, Yangzhou 225001, PR China
| | - Junli Shi
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225009, PR China
| | - Dianwei Liu
- Department of Orthopedics and Sports Medicine, Northern Jiangsu People's Hospital, Affiliated to Yangzhou University, Yangzhou 225001, PR China; Dalian Medical University, Dalian 116044, PR China
| | - Mingjun Li
- Department of Orthopedics and Sports Medicine, Northern Jiangsu People's Hospital, Affiliated to Yangzhou University, Yangzhou 225001, PR China; Dalian Medical University, Dalian 116044, PR China
| | - Hang Yao
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225009, PR China.
| | - Wenyong Fei
- Department of Orthopedics and Sports Medicine, Northern Jiangsu People's Hospital, Affiliated to Yangzhou University, Yangzhou 225001, PR China.
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Du P, Wu J. Hallmarks of totipotent and pluripotent stem cell states. Cell Stem Cell 2024; 31:312-333. [PMID: 38382531 PMCID: PMC10939785 DOI: 10.1016/j.stem.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/18/2024] [Accepted: 01/26/2024] [Indexed: 02/23/2024]
Abstract
Though totipotency and pluripotency are transient during early embryogenesis, they establish the foundation for the development of all mammals. Studying these in vivo has been challenging due to limited access and ethical constraints, particularly in humans. Recent progress has led to diverse culture adaptations of epiblast cells in vitro in the form of totipotent and pluripotent stem cells, which not only deepen our understanding of embryonic development but also serve as invaluable resources for animal reproduction and regenerative medicine. This review delves into the hallmarks of totipotent and pluripotent stem cells, shedding light on their key molecular and functional features.
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Affiliation(s)
- Peng Du
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.
| | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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11
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Liu J, Chu M, Zhang J, He J, Yang Q, Tao L, Wang Z, Yao F, Zhao W, Ouyang S, Chen L, Zhang S, Gao S, Tian J, Ren L, An L. Glutathione safeguards TET-dependent DNA demethylation and is critical for the acquisition of totipotency and pluripotency during preimplantation development. FASEB J 2024; 38:e23453. [PMID: 38318639 DOI: 10.1096/fj.202301220r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 12/21/2023] [Accepted: 01/16/2024] [Indexed: 02/07/2024]
Abstract
During early development, both genome-wide epigenetic reprogramming and metabolic remodeling are hallmark changes of normal embryogenesis. However, little is known about their relationship and developmental functions during the preimplantation window, which is essential for the acquisition of totipotency and pluripotency. Herein, we reported that glutathione (GSH), a ubiquitous intracellular protective antioxidant that maintains mitochondrial function and redox homeostasis, plays a critical role in safeguarding postfertilization DNA demethylation and is essential for establishing developmental potential in preimplantation embryos. By profiling mitochondria-related transcriptome that coupled with different pluripotency, we found GSH is a potential marker that is tightly correlated with full pluripotency, and its beneficial effect on prompting developmental potential was functionally conformed using in vitro fertilized mouse and bovine embryos as the model. Mechanistic study based on preimplantation embryos and embryonic stem cells further revealed that GSH prompts the acquisition of totipotency and pluripotency by facilitating ten-eleven-translocation (TET)-dependent DNA demethylation, and ascorbic acid (AsA)-GSH cycle is implicated in the process. In addition, we also reported that GSH serves as an oviductal paracrine factor that supports development potential of preimplantation embryos. Thus, our results not only advance the current knowledge of functional links between epigenetic reprogramming and metabolic remodeling during preimplantation development but also provided a promising approach for improving current in vitro culture system for assisted reproductive technology.
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Affiliation(s)
- Juan Liu
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Changsha, China
| | - Meiqiang Chu
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
- College of Agriculture and Forestry Science, Linyi University, Linyi, Shandong, China
| | - Jingyu Zhang
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jiale He
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qianying Yang
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Li Tao
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhaochen Wang
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Fusheng Yao
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Wei Zhao
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Si Ouyang
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lei Chen
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shuai Zhang
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shuai Gao
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jianhui Tian
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Likun Ren
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Lei An
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
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12
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Chen L, Tang B, Xie G, Yang R, Zhang B, Wang Y, Zhang Y, Jiang D, Zhang X. Bovine Pluripotent Stem Cells: Current Status and Prospects. Int J Mol Sci 2024; 25:2120. [PMID: 38396797 PMCID: PMC10889747 DOI: 10.3390/ijms25042120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/01/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Pluripotent stem cells (PSCs) can differentiate into three germ layers and diverse autologous cell lines. Since cattle are the most commonly used large domesticated animals, an important food source, and bioreactors, great efforts have been made to establish bovine PSCs (bPSCs). bPSCs have great potential in bovine breeding and reproduction, modeling in vitro differentiation, imitating cancer development, and modeling diseases. Currently, bPSCs mainly include bovine embryonic stem cells (bESCs), bovine induced pluripotent stem cells (biPSCs), and bovine expanded potential stem cells (bEPSCs). Establishing stable bPSCs in vitro is a critical scientific challenge, and researchers have made numerous efforts to this end. In this review, the category of PSC pluripotency; the establishment of bESCs, biPSCs, and bEPSCs and its challenges; and the application outlook of bPSCs are discussed, aiming to provide references for future research.
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Affiliation(s)
- Lanxin Chen
- State Key Laboratory for Zoonotic Diseases, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Bo Tang
- State Key Laboratory for Zoonotic Diseases, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Guanghong Xie
- State Key Laboratory for Zoonotic Diseases, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Rui Yang
- State Key Laboratory for Zoonotic Diseases, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Boyang Zhang
- State Key Laboratory for Zoonotic Diseases, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Yueqi Wang
- State Key Laboratory for Zoonotic Diseases, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Yan Zhang
- State Key Laboratory for Zoonotic Diseases, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Daozhen Jiang
- State Key Laboratory for Zoonotic Diseases, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Xueming Zhang
- State Key Laboratory for Zoonotic Diseases, College of Veterinary Medicine, Jilin University, Changchun 130062, China
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13
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Wu B, Wang Y, Wei X, Zhang J, Wu J, Cao G, Zhang Y, Liu J, Li X, Bao S. NELFA and BCL2 induce the 2C-like state in mouse embryonic stem cells in a chemically defined medium. Cell Prolif 2024; 57:e13534. [PMID: 37592709 PMCID: PMC10849787 DOI: 10.1111/cpr.13534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 08/19/2023] Open
Abstract
A minority of mouse embryonic stem cells (ESCs) display totipotent features resembling 2-cell stage embryos and are known as 2-cell-like (2C-like) cells. However, how ESCs transit into this 2C-like state remains largely unknown. Here, we report that the overexpression of negative elongation factor A (Nelfa), a maternally provided factor, enhances the conversion of ESCs into 2C-like cells in chemically defined conditions, while the deletion of endogenous Nelfa does not block this transition. We also demonstrate that Nelfa overexpression significantly enhances somatic cell reprogramming efficiency. Interestingly, we found that the co-overexpression of Nelfa and Bcl2 robustly activates the 2C-like state in ESCs and endows the cells with dual cell fate potential. We further demonstrate that Bcl2 overexpression upregulates endogenous Nelfa expression and can induce the 2C-like state in ESCs even in the absence of Nelfa. Our findings highlight the importance of BCL2 in the regulation of the 2C-like state and provide insights into the mechanism underlying the roles of Nelfa and Bcl2 in the establishment and regulation of the totipotent state in mouse ESCs.
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Affiliation(s)
- Baojiang Wu
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland LivestockInner Mongolia UniversityHohhotChina
- Research Centre for Animal Genetic Resources of Mongolia Plateau, College of Life SciencesInner Mongolia UniversityHohhotChina
| | - Yanqiu Wang
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland LivestockInner Mongolia UniversityHohhotChina
- Research Centre for Animal Genetic Resources of Mongolia Plateau, College of Life SciencesInner Mongolia UniversityHohhotChina
| | - Xinhua Wei
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland LivestockInner Mongolia UniversityHohhotChina
- Research Centre for Animal Genetic Resources of Mongolia Plateau, College of Life SciencesInner Mongolia UniversityHohhotChina
| | - Jingcheng Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, College of Veterinary MedicineNorthwest A&F UniversityYanglingChina
| | - Jiahui Wu
- School of Veterinary MedicineInner Mongolia Agricultural UniversityHohhotChina
| | - Guifang Cao
- School of Veterinary MedicineInner Mongolia Agricultural UniversityHohhotChina
- Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic AnimalHohhotChina
| | - Yong Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, College of Veterinary MedicineNorthwest A&F UniversityYanglingChina
| | - Jun Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture and Rural Affairs, College of Veterinary MedicineNorthwest A&F UniversityYanglingChina
| | - Xihe Li
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland LivestockInner Mongolia UniversityHohhotChina
- Research Centre for Animal Genetic Resources of Mongolia Plateau, College of Life SciencesInner Mongolia UniversityHohhotChina
- Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic AnimalHohhotChina
| | - Siqin Bao
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland LivestockInner Mongolia UniversityHohhotChina
- Research Centre for Animal Genetic Resources of Mongolia Plateau, College of Life SciencesInner Mongolia UniversityHohhotChina
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14
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Jiang N, Tian X, Wang Q, Hao J, Jiang J, Wang H. Regulation Mechanisms and Maintenance Strategies of Stemness in Mesenchymal Stem Cells. Stem Cell Rev Rep 2024; 20:455-483. [PMID: 38010581 DOI: 10.1007/s12015-023-10658-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2023] [Indexed: 11/29/2023]
Abstract
Stemness pertains to the intrinsic ability of mesenchymal stem cells (MSCs) to undergo self-renewal and differentiate into multiple lineages, while simultaneously impeding their differentiation and preserving crucial differentiating genes in a state of quiescence and equilibrium. Owing to their favorable attributes, including uncomplicated isolation protocols, ethical compliance, and ease of procurement, MSCs have become a focal point of inquiry in the domains of regenerative medicine and tissue engineering. As age increases or ex vivo cultivation is prolonged, the functionality of MSCs decreases and their stemness gradually diminishes, thereby limiting their potential therapeutic applications. Despite the existence of several uncertainties surrounding the comprehension of MSC stemness, considerable advancements have been achieved in the clarification of the potential mechanisms that lead to stemness loss, as well as the associated strategies for stemness maintenance. This comprehensive review provides a systematic overview of the factors influencing the preservation of MSC stemness, the molecular mechanisms governing it, the strategies for its maintenance, and the therapeutic potential associated with stemness. Finally, we underscore the obstacles and prospective avenues in present investigations, providing innovative perspectives and opportunities for the preservation and therapeutic utilization of MSC stemness.
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Affiliation(s)
- Nizhou Jiang
- Central Hospital of Dalian University of Technology Department of Spine Surgery, Dalian, China
- The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Xiliang Tian
- The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Quanxiang Wang
- Hongqi Hospital Affiliated to Mudanjiang Medical University, Mudanjiang, China
| | - Jiayu Hao
- Central Hospital of Dalian University of Technology Department of Spine Surgery, Dalian, China
| | - Jian Jiang
- Central Hospital of Dalian University of Technology Department of Spine Surgery, Dalian, China.
| | - Hong Wang
- Central Hospital of Dalian University of Technology Department of Spine Surgery, Dalian, China.
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15
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Hu S, Zhang J, Ji Q, Xie S, Jiang J, Ni H, He X, Yang Y, Wu M. Exosomes derived from uMSCs promote hair regrowth in alopecia areata through accelerating human hair follicular keratinocyte proliferation and migration. Cell Biol Int 2024; 48:154-161. [PMID: 37920124 DOI: 10.1002/cbin.12099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/14/2023] [Accepted: 09/22/2023] [Indexed: 11/04/2023]
Abstract
Alopecia areata (AA) is a complex genetic disease that results in hair loss due to an autoimmune-mediated attack on the hair follicle. Mesenchymal stem cells (MSCs) have great potential to induce hair regeneration due to their strong secretion ability and multidirectional differentiation. Recent studies have revealed that the therapeutic potential of MSCs comes from their secretion ability, which can produce large amounts of bioactive substances and regulate the key physiological functions of subjects. The secretion products of MSCs, such as vesicles, exosomes, and conditioned media, have significant advantages in preparing of biological products derived from stem cells. Human umbilical cord mesenchymal stem cells (uMSCs) are the best choice for exosome production. uMSCs are obtained from the human umbilical cord. The umbilical cord is easy to obtain, and the efficiency of uMSCs isolation and culture higher than that of obtaining MSCs from bone marrow or adipose tissue. In this study, we investigated the effects of exosomes released from uMSCs in AA mice. In summary, due to easy isolation and cultivation, simple preparation, and convenient storage, it is possible to obtain uMSCs, or uMSCs exosomes for research and clinical treatment.
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Affiliation(s)
- Shouyi Hu
- Brigade Three Team, Basic Medical College, Naval Medical University, Shanghai, China
| | - Jiayi Zhang
- Brigade Three Team, Basic Medical College, Naval Medical University, Shanghai, China
| | - Qingqing Ji
- Department of Anesthesiology, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Sujie Xie
- Brigade Three Team, Basic Medical College, Naval Medical University, Shanghai, China
| | - Jingnuo Jiang
- Brigade Three Team, Basic Medical College, Naval Medical University, Shanghai, China
| | - Haitao Ni
- Department of Traditional Chinese Medicine, Naval Medical University, Shanghai, China
| | - Xingying He
- Department of Anesthesiology, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Yanlong Yang
- Department of Traditional Chinese Medicine, Naval Medical University, Shanghai, China
| | - Minjuan Wu
- Department of Histology and Embryology, Naval Medical University, Shanghai, China
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16
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Ghosh A, Som A. Network analysis of transcriptomic data uncovers molecular signatures and the interplay of mRNAs, lncRNAs, and miRNAs in human embryonic stem cells. Differentiation 2024; 135:100738. [PMID: 38008592 DOI: 10.1016/j.diff.2023.11.001] [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: 08/21/2023] [Revised: 10/30/2023] [Accepted: 11/09/2023] [Indexed: 11/28/2023]
Abstract
Growing evidence has shown that besides the protein coding genes, the non-coding elements of the genome are indispensable for maintaining the property of self-renewal in human embryonic stem cells and in cell fate determination. However, the regulatory mechanisms and the landscape of interactions between the coding and non-coding elements is poorly understood. In this work, we used weighted gene co-expression network analysis (WGCNA) on transcriptomic data retrieved from RNA-seq and small RNA-seq experiments and reconstructed the core human pluripotency network (called PluriMLMiNet) consisting of 375 mRNA, 57 lncRNA and 207 miRNAs. Furthermore, we derived networks specific to the naïve and primed states of human pluripotency (called NaiveMLMiNet and PrimedMLMiNet respectively) that revealed a set of molecular markers (RPS6KA1, ZYG11A, ZNF695, ZNF273, and NLRP2 for naive state, and RAB34, TMEM178B, PTPRZ1, USP44, KIF1A and LRRN1 for primed state) which can be used to distinguish the pluripotent state from the non-pluripotent state and also to identify the intra-pluripotency states (i.e., naïve and primed state). The lncRNA DANT1 was found to be a crucial as it formed a bridge between the naive and primed state-specific networks. Analysis of the genes neighbouring DANT1 suggested its possible role as a competing endogenous RNA (ceRNA) for the induction and maintenance of human pluripotency. This was computationally validated by predicting the missing DANT1-miRNA interactions to complete the ceRNA circuit. Here we first report that DANT1 might harbour binding sites for miRNAs hsa-miR-30c-2-3p, hsa-miR-210-3p and hsa-let-7b-5p which may influence pluripotency.
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Affiliation(s)
- Arindam Ghosh
- Centre of Bioinformatics, Institute of Interdisciplinary Studies, University of Allahabad, Prayagraj, 211002, India; Institute of Biomedicine, University of Eastern Finland, FI-70210, Kuopio, Finland.
| | - Anup Som
- Centre of Bioinformatics, Institute of Interdisciplinary Studies, University of Allahabad, Prayagraj, 211002, India.
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17
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Teague S, Yao L, Heemskerk I. The many dimensions of germline competence. Curr Opin Cell Biol 2023; 85:102259. [PMID: 37852152 PMCID: PMC11123554 DOI: 10.1016/j.ceb.2023.102259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/15/2023] [Accepted: 09/17/2023] [Indexed: 10/20/2023]
Abstract
Primordial germ cell (PGC) specification is the first step in the development of the germline. Recent work has elucidated human-mouse differences in PGC differentiation and identified cell states with enhanced competency for PGC-like cell (PGCLC) differentiation in vitro in both species. However, it remains a subject of debate how different PGC competent states in vitro relate to each other, to embryonic development, and to the origin of PGCs in vivo. Here we review recent literature on human PGCLC differentiation in the context of mouse and non-human primate models. In contrast to what was previously thought, recent work suggests human pluripotent stem cells (hPSCs) are highly germline competent. We argue that paradoxical observations regarding the origin and signaling requirements of hPGCLCs may be due to local cell interactions. These confound assays of competence by generating endogenous signaling gradients and spatially modulating the ability to receive exogenous inductive signals. Furthermore, combinatorial signaling suggests that there is no unique germline competent state: rather than a one-dimensional spectrum of developmental progression, competence should be considered in a higher dimensional landscape of cell states.
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Affiliation(s)
- Seth Teague
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - LiAng Yao
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Idse Heemskerk
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA; Center for Cell Plasticity and Organ Design, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Physics, University of Michigan, Ann Arbor, MI, USA.
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18
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Sarel-Gallily R, Keshet G, Kinreich S, Haim-Abadi G, Benvenisty N. EpiTyping: analysis of epigenetic aberrations in parental imprinting and X-chromosome inactivation using RNA-seq. Nat Protoc 2023; 18:3881-3917. [PMID: 37914783 DOI: 10.1038/s41596-023-00898-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/28/2023] [Indexed: 11/03/2023]
Abstract
Human pluripotent stem cells (hPSCs) hold a central role in studying human development, in disease modeling and in regenerative medicine. These cells not only acquire genetic modifications when kept in culture, but they may also harbor epigenetic aberrations, mainly involving parental imprinting and X-chromosome inactivation. Here we present a detailed bioinformatic protocol for detecting such aberrations using RNA sequencing data. We provide a pipeline designed to process and analyze RNA sequencing data for the identification of abnormal biallelic expression of imprinted genes, and thus detect loss of imprinting. Furthermore, we show how to differentiate among X-chromosome inactivation, full activation and aberrant erosion of X chromosome in female hPSCs. In addition to providing bioinformatic tools, we discuss the impact of such epigenetic variations in hPSCs on their utility for various purposes. This pipeline can be used by any user with basic understanding of the Linux command line. It is available on GitHub as a software container ( https://github.com/Gal-Keshet/EpiTyping ) and produces reliable results in 1-4 d.
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Affiliation(s)
- Roni Sarel-Gallily
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gal Keshet
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Shay Kinreich
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Guy Haim-Abadi
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nissim Benvenisty
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
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19
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Zhu P, Zhang B, Sun R, Wang J, Liu Z, Liu X, Yan M, Cui Y, Sha J, Yuan Y. Derivation of new pluripotent stem cells from human extended pluripotent stem cells with formative features and trophectoderm potential. Cell Prolif 2023; 56:e13480. [PMID: 37052060 PMCID: PMC10623941 DOI: 10.1111/cpr.13480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 03/28/2023] [Accepted: 04/04/2023] [Indexed: 04/14/2023] Open
Abstract
Previous studies have demonstrated the existence of intermediate stem cells, which have been successfully obtained from human naive pluripotent stem cells (PSCs) and peri-implantation embryos. However, it is not known whether human extended pluripotent stem cells (hEPSCs) can be directly induced into intermediate stem cells. Moreover, the ability of extra-embryonic lineage differentiation in intermediate stem cells has not been verified. In this issue, we transformed hEPSCs into a kind of novel intermediate pluripotent stem cell resembling embryonic days 8-9 (E8-E9) epiblasts and proved its feature of formative epiblasts. We engineered hEPSCs from primed hPSCs under N2B27-LCDM (N2B27 plus Lif, CHIR, DiH and MiH) conditions. Then, we added Activin A, FGF and XAV939 to modulate signalling pathways related to early humans' embryogenesis. We performed RNA-seq and CUT&Tag analysis to compare with AF9-hPSCs from different pluripotency stages of hPSCs. Trophectoderm (TE), primordial germ cells-like cells (PGCLC) and endoderm, mesoderm, and neural ectoderm induction were conducted by specific small molecules and proteins. AF9-hPSCs transcription resembled that of E8-E9 peri-implantation epiblasts. Signalling pathway responsiveness and histone methylation further revealed their formative pluripotency. Additionally, AF9-hPSCs responded directly to primordial germ cells (PGCs) specification and three germ layer differentiation signals in vitro. Moreover, AF9-hPSCs could differentiate into the TE lineage. Therefore, AF9-hPSCs represented an E8-E9 formative pluripotency state between naïve and primed pluripotency, opening new avenues for studying human pluripotency development during embryogenesis.
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Affiliation(s)
- Pinmou Zhu
- State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjingChina
| | - Bohang Zhang
- State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjingChina
| | - Ruiqi Sun
- State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjingChina
| | - Jiachen Wang
- State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjingChina
| | - Zhaode Liu
- State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjingChina
| | - Xiaorui Liu
- State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjingChina
| | - Min Yan
- State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjingChina
| | - Yiqiang Cui
- State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjingChina
| | - Jiahao Sha
- State Key Laboratory of Reproductive MedicineWomen's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical UniversityNanjingChina
| | - Yan Yuan
- State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjingChina
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20
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Liu F, Wang J, Yue Y, Li C, Zhang X, Xiang J, Wang H, Li X. Derivation of Arbas Cashmere Goat Induced Pluripotent Stem Cells in LCDM with Trophectoderm Lineage Differentiation and Interspecies Chimeric Abilities. Int J Mol Sci 2023; 24:14728. [PMID: 37834175 PMCID: PMC10572416 DOI: 10.3390/ijms241914728] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/22/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
The Arbas cashmere goat is a unique biological resource that plays a vital role in livestock husbandry in China. LCDM is a medium with special small molecules (consisting of human LIF, CHIR99021, (S)-(+)-dimethindene maleate, and minocycline hydrochloride) for generation pluripotent stem cells (PSCs) with bidirectional developmental potential in mice, humans, pigs, and bovines. However, there is no report on whether LCDM can support for generation of PSCs with the same ability in Arbas cashmere goats. In this study, we applied LCDM to generate goat induced PSCs (giPSCs) from goat fetal fibroblasts (GFFs) by reprogramming. The derived giPSCs exhibited stem cell morphology, expressing pluripotent markers, and could differentiate into three germ layers. Moreover, the giPSCs differentiated into the trophectoderm lineage by spontaneous and directed differentiation in vitro. The giPSCs contributed to embryonic and extraembryonic tissue in preimplantation blastocysts and postimplantation chimeric embryos. RNA-sequencing analysis showed that the giPSCs were very close to goat embryos at the blastocyst stage and giPSCs have similar properties to typical extended PSCs (EPSCs). The establishment of giPSCs with LCDM provides a new way to generate PSCs from domestic animals and lays the foundation for basic and applied research in biology and agriculture.
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Affiliation(s)
- Fang Liu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Jing Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Yongli Yue
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Chen Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Xuemin Zhang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Jinzhu Xiang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Hanning Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Xueling Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
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21
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Iwatsuki K, Oikawa M, Kobayashi H, Penfold CA, Sanbo M, Yamamoto T, Hochi S, Kurimoto K, Hirabayashi M, Kobayashi T. Rat post-implantation epiblast-derived pluripotent stem cells produce functional germ cells. CELL REPORTS METHODS 2023; 3:100542. [PMID: 37671016 PMCID: PMC10475792 DOI: 10.1016/j.crmeth.2023.100542] [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: 01/11/2023] [Revised: 05/10/2023] [Accepted: 07/03/2023] [Indexed: 09/07/2023]
Abstract
In mammals, pluripotent cells transit through a continuum of distinct molecular and functional states en route to initiating lineage specification. Capturing pluripotent stem cells (PSCs) mirroring in vivo pluripotent states provides accessible in vitro models to study the pluripotency program and mechanisms underlying lineage restriction. Here, we develop optimal culture conditions to derive and propagate post-implantation epiblast-derived PSCs (EpiSCs) in rats, a valuable model for biomedical research. We show that rat EpiSCs (rEpiSCs) can be reset toward the naive pluripotent state with exogenous Klf4, albeit not with the other five candidate genes (Nanog, Klf2, Esrrb, Tfcp2l1, and Tbx3) effective in mice. Finally, we demonstrate that rat EpiSCs retain competency to produce authentic primordial germ cell-like cells that undergo functional gametogenesis leading to the birth of viable offspring. Our findings in the rat model uncover principles underpinning pluripotency and germline competency across species.
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Affiliation(s)
- Kenyu Iwatsuki
- Division of Mammalian Embryology, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
- Graduate School of Medicine, Science and Technology, Shinshu University, Nagano 386-8567, Japan
| | - Mami Oikawa
- Division of Mammalian Embryology, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
- Laboratory of Regenerative Medicine, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan
| | - Hisato Kobayashi
- Department of Embryology, Nara Medical University, Nara 634-0813, Japan
| | - Christopher A. Penfold
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Site, Cambridge CB2 3EG, UK
- Centre for Trophoblast Research, University of Cambridge, Downing Site, Cambridge CB2 3EG, UK
- Wellcome Trust – Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Makoto Sanbo
- Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Aichi 444-8787, Japan
| | - Takuya Yamamoto
- Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8501, Japan
- Medical-risk Avoidance Based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project, Kyoto 606-8501, Japan
| | - Shinichi Hochi
- Graduate School of Medicine, Science and Technology, Shinshu University, Nagano 386-8567, Japan
- Faculty of Textile Science and Technology, Shinshu University, Nagano 386-8567, Japan
| | - Kazuki Kurimoto
- Department of Embryology, Nara Medical University, Nara 634-0813, Japan
| | - Masumi Hirabayashi
- Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Aichi 444-8787, Japan
- The Graduate University of Advanced Studies, Aichi 444-8787, Japan
| | - Toshihiro Kobayashi
- Division of Mammalian Embryology, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
- Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Aichi 444-8787, Japan
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22
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Abel A, Sozen B. Shifting early embryology paradigms: Applications of stem cell-based embryo models in bioengineering. Curr Opin Genet Dev 2023; 81:102069. [PMID: 37392541 PMCID: PMC10530566 DOI: 10.1016/j.gde.2023.102069] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/16/2023] [Accepted: 05/30/2023] [Indexed: 07/03/2023]
Abstract
Technologies to reproduce specific aspects of early mammalian embryogenesis in vitro using stem cells have skyrocketed over the last several years. With these advances, we have gained new perspectives on how embryonic and extraembryonic cells self-organize to form the embryo. These reductionist approaches hold promise for the future implementation of precise environmental and genetic controls to understand variables affecting embryo development. Our review discusses recent progress in cellular models of early mammalian embryo development and bioengineering advancements that can be leveraged to study the embryo-maternal interface. We summarize current gaps in the field, emphasizing the importance of understanding how intercellular interactions at this interface contribute to reproductive and developmental health.
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Affiliation(s)
- Ashley Abel
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT 06520, USA. https://twitter.com/@caitrionacunn
| | - Berna Sozen
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT 06520, USA; Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, Yale University, New Haven, CT 06520, USA.
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23
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Li C, Han X, Wang J, Liu F, Zhang Y, Li Z, Lu Z, Yue Y, Xiang J, Li X. Mixed-Lineage Leukemia 1 Inhibition Enhances the Differentiation Potential of Bovine Embryonic Stem Cells by Increasing H3K4 Mono-Methylation at Active Promoters. Int J Mol Sci 2023; 24:11901. [PMID: 37569280 PMCID: PMC10418322 DOI: 10.3390/ijms241511901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/08/2023] [Accepted: 07/18/2023] [Indexed: 08/13/2023] Open
Abstract
Mixed-lineage leukemia 1 (MLL1) introduces 1-, 2- and 3-methylation into histone H3K4 through the evolutionarily conserved set domain. In this study, bovine embryonic stem cells (bESCs, known as bESCs-F7) were established from in vitro-fertilized (IVF) embryos via Wnt signaling inhibition; however, their contribution to the endoderm in vivo is limited. To improve the quality of bESCs, MM-102, an inhibitor of MLL1, was applied to the culture. The results showed that MLL1 inhibition along with GSK3 and MAP2K inhibition (3i) at the embryonic stage did not affect bESCs' establishment and pluripotency. MLL1 inhibition improved the pluripotency and differentiation potential of bESCs via the up-regulation of stem cell signaling pathways such as PI3K-Akt and WNT. MLL1 inhibition decreased H3K4me1 modification at the promoters and altered the distribution of DNA methylation in bESCs. In summary, MLL1 inhibition gives bESCs better pluripotency, and its application may provide high-quality pluripotent stem cells for domestic animals.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Xueling Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestocks, Inner Mongolia University, Hohhot 010070, China; (C.L.); (X.H.); (J.W.); (F.L.); (Y.Z.); (Z.L.); (Z.L.); (Y.Y.); (J.X.)
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24
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Guo Z, Zhu J, Qin G, Jia Y, Liu Z, Yang N, Guo R. Static Magnetic Fields Promote Generation of Muscle Lineage Cells from Pluripotent Stem Cells and Myoblasts. Stem Cell Rev Rep 2023; 19:1402-1414. [PMID: 37000377 DOI: 10.1007/s12015-023-10535-z] [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] [Accepted: 03/21/2023] [Indexed: 04/01/2023]
Abstract
Static magnetic fields (SMFs) exhibit numerous biological effects and regulate the proliferation and differentiation of several adult stem cells. However, the role of SMFs in the self-renewal maintenance and developmental potential of pluripotent embryonic stem cells (ESCs) remains largely uninvestigated. Here, we show that SMFs promote the expression of the core pluripotent markers Sox2 and SSEA-1. Furthermore, SMFs facilitate the differentiation of ESCs into cardiomyocytes and skeletal muscle cells. Consistently, transcriptome analysis reveals that muscle lineage differentiation and skeletal system specification of ESCs are remarkably strengthened by SMF stimuli. Additionally, when treated with SMFs, C2C12 myoblasts exhibit an increased proliferation rate, improved expression of skeletal muscle markers and elevated myogenic differentiation capacity compared with control cells. Together, our data show that SMFs effectively promote muscle cell generation from pluripotent stem cells and myoblasts. The noninvasive and convenient physical stimuli can be used to increase the production of muscle cells in regenerative medicine and the manufacture of cultured meat in cellular agriculture.
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Affiliation(s)
- Zhaoyuan Guo
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiahao Zhu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guanyu Qin
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yumei Jia
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zheng Liu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Na Yang
- School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
- INDUC Scientific Co., Ltd, No. 28-132 Jinshan North Photoelectric Science and Technology Park, Wuxi, 214000, China
| | - Renpeng Guo
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
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25
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Tian C, Wang J, Ye X, Chen J, Zheng R, Yu H, Li J, Yin G, Liu L, Zhao N, Feng G, Zhu Z, Wang J, Fan G, Liu L. Culture conditions of mouse ESCs impact the tumor appearance in vivo. Cell Rep 2023; 42:112645. [PMID: 37314926 DOI: 10.1016/j.celrep.2023.112645] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/22/2023] [Accepted: 05/27/2023] [Indexed: 06/16/2023] Open
Abstract
Various culture conditions by small molecules have been explored to extend pluripotency of stem cells, but their impacts on cell fate in vivo remain elusive. We systematically compared the effects of various culture conditions on the pluripotency and cell fate in vivo of mouse embryonic stem cells (ESCs) by tetraploid embryo complementation assay. Conventional ESC cultures in serum/LIF-based condition produced complete ESC mice and also the survival to adulthood at the highest rates of all other chemical-based cultures. Moreover, long-term examination of the survived ESC mice demonstrated that conventional ESC cultures did not lead to visible abnormality for up to 1.5-2 years, whereas the prolonged chemical-based cultures developed retroperitoneal atypical teratomas or leiomyomas. The chemical-based cultures exhibited transcriptomes and epigenomes that typically differed from those of conventional ESC cultures. Our results warrant further refinement of culture conditions in promoting the pluripotency and safety of ESCs in future applications.
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Affiliation(s)
- Chenglei Tian
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China; Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jing Wang
- Department of Human Genetics and Broad Stem Cell Research Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Xiaoying Ye
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China; Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jiyu Chen
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China; Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Rongyan Zheng
- Key Laboratory for Stem Cells and Tissue Engineering, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Hanwen Yu
- Key Laboratory for Stem Cells and Tissue Engineering, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Jie Li
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China; Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Guoxing Yin
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China; Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Linlin Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China; Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Nannan Zhao
- Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Guofeng Feng
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China; Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zhengmao Zhu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China; Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jichang Wang
- Key Laboratory for Stem Cells and Tissue Engineering, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.
| | - Guoping Fan
- Department of Human Genetics and Broad Stem Cell Research Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China.
| | - Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China; Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China; Institute of Translational Medicine, Tianjin Union Medical Center, Nankai University, Tianjin 300071, China.
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26
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Sato S, Hishida T, Kinouchi K, Hatanaka F, Li Y, Nguyen Q, Chen Y, Wang PH, Kessenbrock K, Li W, Izpisua Belmonte JC, Sassone-Corsi P. The circadian clock CRY1 regulates pluripotent stem cell identity and somatic cell reprogramming. Cell Rep 2023; 42:112590. [PMID: 37261952 DOI: 10.1016/j.celrep.2023.112590] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 03/28/2023] [Accepted: 05/16/2023] [Indexed: 06/03/2023] Open
Abstract
Distinct metabolic conditions rewire circadian-clock-controlled signaling pathways leading to the de novo construction of signal transduction networks. However, it remains unclear whether metabolic hallmarks unique to pluripotent stem cells (PSCs) are connected to clock functions. Reprogramming somatic cells to a pluripotent state, here we highlighted non-canonical functions of the circadian repressor CRY1 specific to PSCs. Metabolic reprogramming, including AMPK inactivation and SREBP1 activation, was coupled with the accumulation of CRY1 in PSCs. Functional assays verified that CRY1 is required for the maintenance of self-renewal capacity, colony organization, and metabolic signatures. Genome-wide occupancy of CRY1 identified CRY1-regulatory genes enriched in development and differentiation in PSCs, albeit not somatic cells. Last, cells lacking CRY1 exhibit differential gene expression profiles during induced PSC (iPSC) reprogramming, resulting in impaired iPSC reprogramming efficiency. Collectively, these results suggest the functional implication of CRY1 in pluripotent reprogramming and ontogenesis, thereby dictating PSC identity.
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Affiliation(s)
- Shogo Sato
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA; Center for Biological Clocks Research, Department of Biology, Texas A&M University, College Station, TX, USA.
| | - Tomoaki Hishida
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA; Laboratory of Biological Chemistry, School of Pharmaceutical Sciences, Wakayama Medical University, Wakayama, Japan
| | - Kenichiro Kinouchi
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Fumiaki Hatanaka
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA; Altos Labs, San Diego, CA, USA
| | - Yumei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Quy Nguyen
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Yumay Chen
- UC Irvine Diabetes Center, Sue and Bill Gross Stem Cell Research Center, Department of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Ping H Wang
- UC Irvine Diabetes Center, Sue and Bill Gross Stem Cell Research Center, Department of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Kai Kessenbrock
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Wei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Juan Carlos Izpisua Belmonte
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA; Altos Labs, San Diego, CA, USA.
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
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27
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Zaghi M, Banfi F, Massimino L, Volpin M, Bellini E, Brusco S, Merelli I, Barone C, Bruni M, Bossini L, Lamparelli LA, Pintado L, D'Aliberti D, Spinelli S, Mologni L, Colasante G, Ungaro F, Cioni JM, Azzoni E, Piazza R, Montini E, Broccoli V, Sessa A. Balanced SET levels favor the correct enhancer repertoire during cell fate acquisition. Nat Commun 2023; 14:3212. [PMID: 37270547 DOI: 10.1038/s41467-023-39043-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 05/23/2023] [Indexed: 06/05/2023] Open
Abstract
Within the chromatin, distal elements interact with promoters to regulate specific transcriptional programs. Histone acetylation, interfering with the net charges of the nucleosomes, is a key player in this regulation. Here, we report that the oncoprotein SET is a critical determinant for the levels of histone acetylation within enhancers. We disclose that a condition in which SET is accumulated, the severe Schinzel-Giedion Syndrome (SGS), is characterized by a failure in the usage of the distal regulatory regions typically employed during fate commitment. This is accompanied by the usage of alternative enhancers leading to a massive rewiring of the distal control of the gene transcription. This represents a (mal)adaptive mechanism that, on one side, allows to achieve a certain degree of differentiation, while on the other affects the fine and corrected maturation of the cells. Thus, we propose the differential in cis-regulation as a contributing factor to the pathological basis of SGS and possibly other the SET-related disorders in humans.
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Affiliation(s)
- Mattia Zaghi
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Federica Banfi
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
- CNR Institute of Neuroscience, 20129, Milan, Italy
| | - Luca Massimino
- Esperimental Gastroenterology Unit, Division of Immunology, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Monica Volpin
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget); IRCCS, San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Edoardo Bellini
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Simone Brusco
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
- CNR Institute of Neuroscience, 20129, Milan, Italy
| | - Ivan Merelli
- CNR Institute of Biomedical Technologies, 20090, Segrate, Italy
| | - Cristiana Barone
- School of Medicine and Surgery, University of Milano-Bicocca, 20900, Monza, Italy
| | - Michela Bruni
- RNA biology of the Neuron Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Linda Bossini
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Luigi Antonio Lamparelli
- Esperimental Gastroenterology Unit, Division of Immunology, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Laura Pintado
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Deborah D'Aliberti
- School of Medicine and Surgery, University of Milano-Bicocca, 20900, Monza, Italy
| | - Silvia Spinelli
- School of Medicine and Surgery, University of Milano-Bicocca, 20900, Monza, Italy
| | - Luca Mologni
- School of Medicine and Surgery, University of Milano-Bicocca, 20900, Monza, Italy
| | - Gaia Colasante
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Federica Ungaro
- Esperimental Gastroenterology Unit, Division of Immunology, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Jean-Michel Cioni
- RNA biology of the Neuron Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Emanuele Azzoni
- School of Medicine and Surgery, University of Milano-Bicocca, 20900, Monza, Italy
| | - Rocco Piazza
- School of Medicine and Surgery, University of Milano-Bicocca, 20900, Monza, Italy
| | - Eugenio Montini
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget); IRCCS, San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Vania Broccoli
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
- CNR Institute of Neuroscience, 20129, Milan, Italy
| | - Alessandro Sessa
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy.
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28
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Meharwade T, Joumier L, Parisotto M, Huynh V, Lummertz da Rocha E, Malleshaiah M. Cross-activation of FGF, NODAL, and WNT pathways constrains BMP-signaling-mediated induction of the totipotent state in mouse embryonic stem cells. Cell Rep 2023; 42:112438. [PMID: 37126449 DOI: 10.1016/j.celrep.2023.112438] [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: 05/03/2022] [Revised: 11/11/2022] [Accepted: 04/11/2023] [Indexed: 05/02/2023] Open
Abstract
Embryonic stem cells (ESCs) are an attractive model to study the relationship between signaling and cell fates. Cultured mouse ESCs can exist in multiple states resembling distinct stages of early embryogenesis, such as totipotent, pluripotent, primed, and primitive endoderm. The signaling mechanisms regulating the totipotent state and coexistence of these states are poorly understood. Here we identify bone morphogenetic protein (BMP) signaling as an inducer of the totipotent state. However, we discover that BMP's role is constrained by the cross-activation of FGF, NODAL, and WNT pathways. We exploit this finding to enhance the proportion of totipotent cells by rationally inhibiting the cross-activated pathways. Single-cell mRNA sequencing reveals that induction of the totipotent state is accompanied by suppression of primed and primitive endoderm states. Furthermore, reprogrammed totipotent cells we generate in culture resemble totipotent cells of preimplantation embryo. Our findings reveal a BMP signaling mechanism regulating both the totipotent state and heterogeneity of ESCs.
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Affiliation(s)
- Thulaj Meharwade
- Montreal Clinical Research Institute (IRCM), 110 Pine Avenue West, Montreal, QC H2W 1R7, Canada; Department of Biochemistry and Molecular Medicine, University of Montreal, C.P. 6128, Succursale Centre-ville, Montreal, QC H3C 3J7, Canada
| | - Loïck Joumier
- Montreal Clinical Research Institute (IRCM), 110 Pine Avenue West, Montreal, QC H2W 1R7, Canada; Department of Biochemistry and Molecular Medicine, University of Montreal, C.P. 6128, Succursale Centre-ville, Montreal, QC H3C 3J7, Canada
| | - Maxime Parisotto
- Montreal Clinical Research Institute (IRCM), 110 Pine Avenue West, Montreal, QC H2W 1R7, Canada
| | - Vivian Huynh
- Montreal Clinical Research Institute (IRCM), 110 Pine Avenue West, Montreal, QC H2W 1R7, Canada; Molecular Biology Program, University of Montreal, C.P. 6128, Succursale Centre-ville, Montreal, QC H3C 3J7, Canada
| | - Edroaldo Lummertz da Rocha
- Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Mohan Malleshaiah
- Montreal Clinical Research Institute (IRCM), 110 Pine Avenue West, Montreal, QC H2W 1R7, Canada; Department of Biochemistry and Molecular Medicine, University of Montreal, C.P. 6128, Succursale Centre-ville, Montreal, QC H3C 3J7, Canada; Molecular Biology Program, University of Montreal, C.P. 6128, Succursale Centre-ville, Montreal, QC H3C 3J7, Canada; The Division of Experimental Medicine, McGill University, 1001 Decarie Boulevard, Montreal, QC H4A 3J1, Canada; McGill Regenerative Medicine Network, 1160 Pine Avenue West, Montreal, QC H3A 1A3, Canada.
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29
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Candiello E, Reato G, Verginelli F, Gambardella G, D Ambrosio A, Calandra N, Orzan F, Iuliano A, Albano R, Sassi F, Luraghi P, Comoglio PM, Bertotti A, Trusolino L, Boccaccio C. MicroRNA 483-3p overexpression unleashes invasive growth of metastatic colorectal cancer via NDRG1 downregulation and ensuing activation of the ERBB3/AKT axis. Mol Oncol 2023. [PMID: 36862005 DOI: 10.1002/1878-0261.13408] [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: 11/04/2022] [Revised: 02/07/2023] [Accepted: 02/27/2023] [Indexed: 03/03/2023] Open
Abstract
In colorectal cancer, the mechanisms underlying tumor aggressiveness require further elucidation. Taking advantage of a large panel of human metastatic colorectal cancer xenografts and matched stem-like cell cultures (m-colospheres), here we show that the overexpression of microRNA 483-3p (miRNA-483-3p; also known as MIR-483-3p), encoded by a frequently amplified gene locus, confers an aggressive phenotype. In m-colospheres, endogenous or ectopic miRNA-483-3p overexpression increased proliferative response, invasiveness, stem cell frequency, and resistance to differentiation. Transcriptomic analyses and functional validation found that miRNA-483-3p directly targets NDRG1, known as a metastasis suppressor involved in EGFR family downregulation. Mechanistically, miRNA-483-3p overexpression induced the signaling pathway triggered by ERBB3, including AKT and GSK3β, and led to the activation of transcription factors regulating epithelial-mesenchymal transition (EMT). Consistently, treatment with selective anti-ERBB3 antibodies counteracted the invasive growth of miRNA-483-3p-overexpressing m-colospheres. In human colorectal tumors, miRNA-483-3p expression inversely correlated with NDRG1 and directly correlated with EMT transcription factor expression and poor prognosis. These results unveil a previously unrecognized link between miRNA-483-3p, NDRG1, and ERBB3-AKT signaling that can directly support colorectal cancer invasion and is amenable to therapeutic targeting.
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Affiliation(s)
- Ermes Candiello
- Laboratory of Cancer Stem Cell Research, Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
| | - Gigliola Reato
- Laboratory of Cancer Stem Cell Research, Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy.,Department of Oncology, University of Turin Medical School, Italy
| | - Federica Verginelli
- Laboratory of Cancer Stem Cell Research, Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
| | - Gennaro Gambardella
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy.,Department of Chemical Materials and Industrial Engineering, University of Naples Federico II, Italy
| | - Antonio D Ambrosio
- Laboratory of Cancer Stem Cell Research, Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
| | - Noemi Calandra
- Laboratory of Cancer Stem Cell Research, Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy.,Department of Oncology, University of Turin Medical School, Italy
| | - Francesca Orzan
- Laboratory of Cancer Stem Cell Research, Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
| | | | - Raffaella Albano
- Laboratory of Cancer Stem Cell Research, Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
| | - Francesco Sassi
- Translational Cancer Medicine, Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
| | - Paolo Luraghi
- Laboratory of Cancer Stem Cell Research, Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
| | | | - Andrea Bertotti
- Department of Oncology, University of Turin Medical School, Italy.,Translational Cancer Medicine, Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
| | - Livio Trusolino
- Department of Oncology, University of Turin Medical School, Italy.,Translational Cancer Medicine, Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
| | - Carla Boccaccio
- Laboratory of Cancer Stem Cell Research, Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy.,Department of Oncology, University of Turin Medical School, Italy
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30
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Zhai N, Pan X, Zeng M, Xu L. Developmental trajectory of pluripotent stem cell establishment in Arabidopsis callus guided by a quiescent center-related gene network. Development 2023; 150:286991. [PMID: 36762604 DOI: 10.1242/dev.200879] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023]
Abstract
In plant tissue culture, callus formation is induced by a high auxin concentration. Among the three cell layers (the outer, middle and inner cell layers) of the callus, pluripotency acquisition in the middle cell layer is required for the potential ability of the callus to regenerate organs. Here, we reveal the developmental trajectory of middle cell layer initiation and maintenance in callus tissue originating from Arabidopsis thaliana hypocotyls. The S phase of the cell cycle is essential for the expression of quiescent center-related SCARECROW (SCR), PLETHORA1 (PLT1) and WUSCHEL-RELATED HOMEOBOX5 (WOX5) genes during the division of callus founder cells to initiate the callus primordium. After callus initiation, SHOOT-ROOT (SHR) proteins move from the inner to the middle cell layer and act together with SCR to promote the expression of PLT1 and WOX5. WOX5 represses the expression of VASCULAR-RELATED NAC-DOMAIN (VND) genes, thereby preventing callus tissue from differentiating into xylem cells. PLT1 and PLT2 directly activate JACKDAW (JKD), which is necessary for pluripotency acquisition in the middle cell layer. We hypothesize that the middle cell layer could have pluripotent stem cell activity and its establishment requires the quiescent center-related SCR-SHR-WOX5-PLT1/2-JKD gene network.
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Affiliation(s)
- Ning Zhai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Xuan Pan
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Minhuan Zeng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
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31
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Hao Y, Li X, Qin K, Shi Y, He Y, Zhang C, Cheng B, Zhang X, Hu G, Liang S, Tang Q, Chen X. Chemoproteomic and Transcriptomic Analysis Reveals that O-GlcNAc Regulates Mouse Embryonic Stem Cell Fate through the Pluripotency Network. Angew Chem Int Ed Engl 2023; 62:e202300500. [PMID: 36852467 DOI: 10.1002/anie.202300500] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/22/2023] [Accepted: 02/27/2023] [Indexed: 03/01/2023]
Abstract
Self-renewal and differentiation of embryonic stem cells (ESCs) are influenced by protein O-linked β-N-acetylglucosamine (O-GlcNAc) modification, but the underlying mechanism remains incompletely understood. Herein, we report the identification of 979 O-GlcNAcylated proteins and 1340 modification sites in mouse ESCs (mESCs) by using a chemoproteomics method. In addition to OCT4 and SOX2, the third core pluripotency transcription factor (PTF) NANOG was found to be modified and functionally regulated by O-GlcNAc. Upon differentiation along the neuronal lineage, the O-GlcNAc stoichiometry at 123 sites of 83 proteins-several of which were PTFs-was found to decline. Transcriptomic profiling reveals 2456 differentially expressed genes responsive to OGT inhibition during differentiation, of which 901 are target genes of core PTFs. By acting on the core PTF network, suppression of O-GlcNAcylation upregulates neuron-related genes, thus contributing to mESC fate determination.
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Affiliation(s)
- Yi Hao
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Xiang Li
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Ke Qin
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Yujie Shi
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Yanwen He
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Che Zhang
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Bo Cheng
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Xiwen Zhang
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Guangyu Hu
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Shuyu Liang
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Qi Tang
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Xing Chen
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
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32
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Durand S, Bruelle M, Bourdelais F, Bennychen B, Blin-Gonthier J, Isaac C, Huyghe A, Martel S, Seyve A, Vanbelle C, Adrait A, Couté Y, Meyronet D, Catez F, Diaz JJ, Lavial F, Ricci EP, Ducray F, Gabut M. RSL24D1 sustains steady-state ribosome biogenesis and pluripotency translational programs in embryonic stem cells. Nat Commun 2023; 14:356. [PMID: 36690642 PMCID: PMC9870888 DOI: 10.1038/s41467-023-36037-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 01/13/2023] [Indexed: 01/24/2023] Open
Abstract
Embryonic stem cell (ESC) fate decisions are regulated by a complex circuitry that coordinates gene expression at multiple levels from chromatin to mRNA processing. Recently, ribosome biogenesis and translation have emerged as key pathways that efficiently control stem cell homeostasis, yet the underlying molecular mechanisms remain largely unknown. Here, we identified RSL24D1 as highly expressed in both mouse and human pluripotent stem cells. RSL24D1 is associated with nuclear pre-ribosomes and is required for the biogenesis of 60S subunits in mouse ESCs. Interestingly, RSL24D1 depletion significantly impairs global translation, particularly of key pluripotency factors and of components from the Polycomb Repressive Complex 2 (PRC2). While having a moderate impact on differentiation, RSL24D1 depletion significantly alters ESC self-renewal and lineage commitment choices. Altogether, these results demonstrate that RSL24D1-dependant ribosome biogenesis is both required to sustain the expression of pluripotent transcriptional programs and to silence PRC2-regulated developmental programs, which concertedly dictate ESC homeostasis.
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Affiliation(s)
- Sébastien Durand
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Labex Dev2Can, Lyon, France
| | - Marion Bruelle
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
| | - Fleur Bourdelais
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Labex Dev2Can, Lyon, France
- Inovarion, 75005, Paris, France
| | - Bigitha Bennychen
- Dept. of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, K1A 0R6, Canada
| | - Juliana Blin-Gonthier
- Laboratoire de Biologie et de Modélisation de la Cellule, ENS de Lyon, CNRS UMR 5239, Inserm U1293, Lyon, France
| | - Caroline Isaac
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Labex Dev2Can, Lyon, France
| | - Aurélia Huyghe
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Labex Dev2Can, Lyon, France
- Equipe labellisée la Ligue contre le cancer, Lyon, France
| | - Sylvie Martel
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
| | - Antoine Seyve
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Neuro-oncology department, Hospices Civils de Lyon, Lyon, France
| | - Christophe Vanbelle
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
| | - Annie Adrait
- University Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, CEA, FR2048, 38000, Grenoble, France
| | - Yohann Couté
- University Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, CEA, FR2048, 38000, Grenoble, France
| | - David Meyronet
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Institut de Pathologie Est, Hospices Civils de Lyon, Lyon, France
| | - Frédéric Catez
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Labex Dev2Can, Lyon, France
| | - Jean-Jacques Diaz
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Labex Dev2Can, Lyon, France
| | - Fabrice Lavial
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Labex Dev2Can, Lyon, France
- Equipe labellisée la Ligue contre le cancer, Lyon, France
| | - Emiliano P Ricci
- Laboratoire de Biologie et de Modélisation de la Cellule, ENS de Lyon, CNRS UMR 5239, Inserm U1293, Lyon, France
| | - François Ducray
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Neuro-oncology department, Hospices Civils de Lyon, Lyon, France
| | - Mathieu Gabut
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France.
- Institut Convergence Plascan, Lyon, France.
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33
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Lee YJ, Wang JK, Pai YM, Frost A, Viprakasit V, Ekwattanakit S, Chin HC, Liu JY. Culture of leukocyte-derived cells from human peripheral blood: Increased expression of pluripotent genes OCT4, NANOG, SOX2, self-renewal gene TERT and plasticity. Medicine (Baltimore) 2023; 102:e32746. [PMID: 36701726 PMCID: PMC9857475 DOI: 10.1097/md.0000000000032746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
There are few stem cells in human peripheral blood (PB). Increasing the population and plasticity of stem cells in PB and applying it to regenerative medicine require suitable culture methods. In this study, leukocyte populations 250 mL of PB were collected using a blood separator before that were cultured in optimal cell culture medium for 4 to 7 days. After culturing, stemness characteristics were analyzed, and red blood cells were removed from the cultured cells. In our results, stemness markers of the leukocyte populations Sca-1+ CD45+, CD117+ CD45+, and very small embryonic-like stem cells CD34+ Lin- CD45- and CXCR4+ Lin- CD45- were significantly increased. Furthermore, the expression of stem cell genes OCT4 (POU5F1), NANOG, SOX2, and the self-renewal gene TERT was analyzed by quantitative real-time polymerase chain reaction in these cells, and it showed a significant increase. These cells could be candidates for multi-potential cells and were further induced using trans-differentiation culture methods. These cells showed multiple differentiation potentials for osteocytes, nerve cells, cardiomyocytes, and hepatocytes. These results indicate that appropriate culture methods can be applied to increase expression of pluripotent genes and plasticity. Leukocytes of human PB can be induced to trans-differentiate into pluripotent potential cells, which will be an important breakthrough in regenerative medicine.
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Affiliation(s)
- Yi-Jen Lee
- Department of Biochemistry, National Defense Medical Center, Taipei, Taiwan
| | - Jehng-Kang Wang
- Department of Biochemistry, National Defense Medical Center, Taipei, Taiwan
| | - Yu-Ming Pai
- Autologous Stem Cell Technology Pty Ltd, Brisbane, Australia
| | - Alan Frost
- School of Veterinary Science, University of Queensland, Australia
| | - Vip Viprakasit
- Department of Pediatrics and Thalassemia Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Supachai Ekwattanakit
- Thalassemia Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Hui-Chieh Chin
- Autologous Stem Cell Technology Pty Ltd, Brisbane, Australia
| | - Jah-Yao Liu
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
- * Correspondence: Jah-Yao Liu, Department of Obstetrics and Gynecology, Tri-Service General Hospital, National Defense Medical Center, 325, Section 2, Cheng-Kong Road, Taipei 11490, Taiwan (ROC) (e-mail: )
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34
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Jia Y, Guo Z, Zhu J, Qin G, Sun W, Yin Y, Wang H, Guo R. Snap29 Is Dispensable for Self-Renewal Maintenance but Required for Proper Differentiation of Mouse Embryonic Stem Cells. Int J Mol Sci 2023; 24:ijms24010750. [PMID: 36614195 PMCID: PMC9821219 DOI: 10.3390/ijms24010750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/04/2023] Open
Abstract
Pluripotent embryonic stem cells (ESCs) can self-renew indefinitely and are able to differentiate into all three embryonic germ layers. Synaptosomal-associated protein 29 (Snap29) is implicated in numerous intracellular membrane trafficking pathways, including autophagy, which is involved in the maintenance of ESC pluripotency. However, the function of Snap29 in the self-renewal and differentiation of ESCs remains elusive. Here, we show that Snap29 depletion via CRISPR/Cas does not impair the self-renewal and expression of pluripotency-associated factors in mouse ESCs. However, Snap29 deficiency enhances the differentiation of ESCs into cardiomyocytes, as indicated by heart-like beating cells. Furthermore, transcriptome analysis reveals that Snap29 depletion significantly decreased the expression of numerous genes required for germ layer differentiation. Interestingly, Snap29 deficiency does not cause autophagy blockage in ESCs, which might be rescued by the SNAP family member Snap47. Our data show that Snap29 is dispensable for self-renewal maintenance, but required for the proper differentiation of mouse ESCs.
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Affiliation(s)
- Yumei Jia
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhaoyuan Guo
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiahao Zhu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Guanyu Qin
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenwen Sun
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yu Yin
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
| | - Haiying Wang
- State Key Laboratory of Medicinal Chemical Biology, Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Renpeng Guo
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence:
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35
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Corridon PR. Still finding ways to augment the existing management of acute and chronic kidney diseases with targeted gene and cell therapies: Opportunities and hurdles. Front Med (Lausanne) 2023; 10:1143028. [PMID: 36960337 PMCID: PMC10028138 DOI: 10.3389/fmed.2023.1143028] [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: 01/12/2023] [Accepted: 02/17/2023] [Indexed: 03/09/2023] Open
Abstract
The rising global incidence of acute and chronic kidney diseases has increased the demand for renal replacement therapy. This issue, compounded with the limited availability of viable kidneys for transplantation, has propelled the search for alternative strategies to address the growing health and economic burdens associated with these conditions. In the search for such alternatives, significant efforts have been devised to augment the current and primarily supportive management of renal injury with novel regenerative strategies. For example, gene- and cell-based approaches that utilize recombinant peptides/proteins, gene, cell, organoid, and RNAi technologies have shown promising outcomes primarily in experimental models. Supporting research has also been conducted to improve our understanding of the critical aspects that facilitate the development of efficient gene- and cell-based techniques that the complex structure of the kidney has traditionally limited. This manuscript is intended to communicate efforts that have driven the development of such therapies by identifying the vectors and delivery routes needed to drive exogenous transgene incorporation that may support the treatment of acute and chronic kidney diseases.
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Affiliation(s)
- Peter R. Corridon
- Department of Immunology and Physiology, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
- Biomedical Engineering, Healthcare Engineering Innovation Center, Khalifa University, Abu Dhabi, United Arab Emirates
- Center for Biotechnology, Khalifa University, Abu Dhabi, United Arab Emirates
- *Correspondence: Peter R. Corridon,
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36
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Bruggeman JW, Koster J, van Pelt AMM, Speijer D, Hamer G. How germline genes promote malignancy in cancer cells. Bioessays 2023; 45:e2200112. [PMID: 36300921 DOI: 10.1002/bies.202200112] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/06/2022] [Accepted: 10/14/2022] [Indexed: 02/01/2023]
Abstract
Cancers often express hundreds of genes otherwise specific to germ cells, the germline/cancer (GC) genes. Here, we present and discuss the hypothesis that activation of a "germline program" promotes cancer cell malignancy. We do so by proposing four hallmark processes of the germline: meiosis, epigenetic plasticity, migration, and metabolic plasticity. Together, these hallmarks enable replicative immortality of germ cells as well as cancer cells. Especially meiotic genes are frequently expressed in cancer, implying that genes unique to meiosis may play a role in oncogenesis. Because GC genes are not expressed in healthy somatic tissues, they form an appealing source of specific treatment targets with limited side effects besides infertility. Although it is still unclear why germ cell specific genes are so abundantly expressed in cancer, from our hypothesis it follows that the germline's reproductive program is intrinsic to cancer development.
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Affiliation(s)
- Jan Willem Bruggeman
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands.,Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands
| | - Jan Koster
- Center for Experimental and Molecular Medicine, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
| | - Ans M M van Pelt
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands.,Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands
| | - Dave Speijer
- Medical Biochemistry, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
| | - Geert Hamer
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands.,Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands
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37
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CRISPR Manipulations in Stem Cell Lines. Methods Mol Biol 2022; 2560:249-256. [PMID: 36481901 DOI: 10.1007/978-1-0716-2651-1_23] [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: 12/13/2022]
Abstract
Insights into genome engineering in cells have allowed researchers to cultivate and modify cells as organoids that display structural and phenotypic features of human diseases or normal health status. The generation of targeted mutants is a crucial step toward studying the biomedical effect of genes of interest. Modified organoids derived from patients' tissue cells are used as models to study diseases and test novel drugs. CRISPR-Cas9 technology has contributed to an explosion of advances that have the ability to edit genomes for the study of monogenic diseases and cancers. The generation of such mutants in human induced pluripotent stem cells (iPSCs) is of utmost importance as these cells carry the potential to be differentiated into any cell lineage. We describe recent developments that are broadening our understanding and extend DNA specificity, product selectivity, and fundamental capabilities. Furthermore, fundamental capabilities and remarkable advancements in basic research, biotechnology, and therapeutics development in cell engineering are detailed within this chapter. Using the CRISPR/Cas9 nuclease system for induction of targeted double-strand breaks, gene editing of target loci in iPSCs can be achieved with high efficiency. This chapter includes detailed protocols for the preparation of reagents to target loci of interest and transfection to genotype single cell-derived iPSC clones. Furthermore, we provide a protocol for the convenient generation of ribonucleoprotein (RNP) delivered directly to cells.
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38
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Bigas A, Galán Palma L, Kartha GM, Giorgetti A. Using Pluripotent Stem Cells to Understand Normal and Leukemic Hematopoietic Development. Stem Cells Transl Med 2022; 11:1123-1134. [PMID: 36398586 PMCID: PMC9672852 DOI: 10.1093/stcltm/szac071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/29/2022] [Indexed: 12/02/2023] Open
Abstract
Several decades have passed since the generation of the first embryonic stem cell (ESC) lines both in mice and in humans. Since then, stem cell biologists have tried to understand their potential biological and clinical uses for their implementation in regenerative medicine. The hematopoietic field was a pioneer in establishing the potential use for the development of blood cell products and clinical applications; however, early expectations have been truncated by the difficulty in generating bonafide hematopoietic stem cells (HSCs). Despite some progress in understanding the origin of HSCs during embryonic development, the reproduction of this process in vitro is still not possible, but the knowledge acquired in the embryo is slowly being implemented for mouse and human pluripotent stem cells (PSCs). In contrast, ESC-derived hematopoietic cells may recapitulate some leukemic transformation processes when exposed to oncogenic drivers. This would be especially useful to model prenatal leukemia development or other leukemia-predisposing syndromes, which are difficult to study. In this review, we will review the state of the art of the use of PSCs as a model for hematopoietic and leukemia development.
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Affiliation(s)
- Anna Bigas
- Program in Cancer Research, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), CIBERONC, Barcelona, Spain
- Josep Carreras Leukemia Research Institute (IJC), Barcelona, Spain
| | - Luis Galán Palma
- Program in Cancer Research, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), CIBERONC, Barcelona, Spain
- Josep Carreras Leukemia Research Institute (IJC), Barcelona, Spain
| | - Gayathri M Kartha
- Program in Cancer Research, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), CIBERONC, Barcelona, Spain
- Josep Carreras Leukemia Research Institute (IJC), Barcelona, Spain
| | - Alessandra Giorgetti
- Regenerative Medicine Program, Institut d’Investigació Biomèdica de Bellvitge (IDIBELL), Barcelona, Spain
- Department of Pathology and Experimental Therapeutics, Faculty of Medicine and Health Sciences, Barcelona University, Barcelona, Spain
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39
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Xu Y, Yang X. Autophagy and pluripotency: self-eating your way to eternal youth. Trends Cell Biol 2022; 32:868-882. [PMID: 35490141 PMCID: PMC10433133 DOI: 10.1016/j.tcb.2022.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/30/2022] [Accepted: 04/01/2022] [Indexed: 01/18/2023]
Abstract
Pluripotent stem cells (PSCs) can self-renew indefinitely in culture while retaining the potential to differentiate into virtually all normal cell types in the adult animal. Due to these remarkable properties, PSCs not only provide a superb system to investigate mammalian development and model diseases, but also hold promise for regenerative therapies. Autophagy is a self-digestive process that targets proteins, organelles, and other cellular contents for lysosomal degradation. Here, we review recent literature on the mechanistic role of different types of autophagy in embryonic development, embryonic stem cells (ESCs), and induced PSCs (iPSCs), focusing on their remodeling functions on protein, metabolism, and epigenetics. We present a perspective on unsolved issues and propose that autophagy is a promising target to modulate acquisition, maintenance, and directed differentiation of PSCs.
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Affiliation(s)
- Yi Xu
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA; Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China.
| | - Xiaolu Yang
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.
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40
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Arez M, Eckersley-Maslin M, Klobučar T, von Gilsa Lopes J, Krueger F, Mupo A, Raposo AC, Oxley D, Mancino S, Gendrel AV, Bernardes de Jesus B, da Rocha ST. Imprinting fidelity in mouse iPSCs depends on sex of donor cell and medium formulation. Nat Commun 2022; 13:5432. [PMID: 36114205 PMCID: PMC9481624 DOI: 10.1038/s41467-022-33013-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 08/29/2022] [Indexed: 11/24/2022] Open
Abstract
Reprogramming of somatic cells into induced Pluripotent Stem Cells (iPSCs) is a major leap towards personalised approaches to disease modelling and cell-replacement therapies. However, we still lack the ability to fully control the epigenetic status of iPSCs, which is a major hurdle for their downstream applications. Epigenetic fidelity can be tracked by genomic imprinting, a phenomenon dependent on DNA methylation, which is frequently perturbed in iPSCs by yet unknown reasons. To try to understand the causes underlying these defects, we conducted a thorough imprinting analysis using IMPLICON, a high-throughput method measuring DNA methylation levels, in multiple female and male murine iPSC lines generated under different experimental conditions. Our results show that imprinting defects are remarkably common in iPSCs, but their nature depends on the sex of donor cells and their response to culture conditions. Imprints in female iPSCs resist the initial genome-wide DNA demethylation wave during reprogramming, but ultimately cells accumulate hypomethylation defects irrespective of culture medium formulations. In contrast, imprinting defects on male iPSCs depends on the experimental conditions and arise during reprogramming, being mitigated by the addition of vitamin C (VitC). Our findings are fundamental to further optimise reprogramming strategies and generate iPSCs with a stable epigenome.
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Affiliation(s)
- Maria Arez
- iBB - Institute for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Melanie Eckersley-Maslin
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, United Kingdom
- Peter MacCallum Cancer Centre, Melbourne, Victoria, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, 3010, Australia
- Department of Anatomy and Physiology, The University of Melbourne, Victoria, 3010, Australia
| | - Tajda Klobučar
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- National Institute of Chemistry, Ljubljana, Slovenia
| | - João von Gilsa Lopes
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- NOVA Medical School|Faculdade de Ciências Médicas, NMS|FCM, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Felix Krueger
- Bioinformatics Group, Babraham Institute, Cambridge, CB22 3AT, United Kingdom
- Altos Labs, Cambridge, United Kingdom
| | - Annalisa Mupo
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, United Kingdom
- Altos Labs, Cambridge, United Kingdom
| | - Ana Cláudia Raposo
- iBB - Institute for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - David Oxley
- Mass Spectrometry Facility, The Babraham Institute, Cambridge, United Kingdom
| | - Samantha Mancino
- iBB - Institute for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Anne-Valerie Gendrel
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Genetics and Developmental Biology Unit, Institut Curie, INSERM U934, CNRS UMR3215, PSL University, Paris, France
| | - Bruno Bernardes de Jesus
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Simão Teixeira da Rocha
- iBB - Institute for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.
- Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.
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41
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Steens J, Klein D. HOX genes in stem cells: Maintaining cellular identity and regulation of differentiation. Front Cell Dev Biol 2022; 10:1002909. [PMID: 36176275 PMCID: PMC9514042 DOI: 10.3389/fcell.2022.1002909] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
Stem cells display a unique cell type within the body that has the capacity to self-renew and differentiate into specialized cell types. Compared to pluripotent stem cells, adult stem cells (ASC) such as mesenchymal stem cells (MSCs) and hematopoietic stem cells (HSCs) exhibit restricted differentiation capabilities that are limited to cell types typically found in the tissue of origin, which implicates that there must be a certain code or priming determined by the tissue of origin. HOX genes, a subset of homeobox genes encoding transcription factors that are generally repressed in undifferentiated pluripotent stem cells, emerged here as master regulators of cell identity and cell fate during embryogenesis, and in maintaining this positional identity throughout life as well as specifying various regional properties of respective tissues. Concurrently, intricate molecular circuits regulated by diverse stem cell-typical signaling pathways, balance stem cell maintenance, proliferation and differentiation. However, it still needs to be unraveled how stem cell-related signaling pathways establish and regulate ASC-specific HOX expression pattern with different temporal-spatial topography, known as the HOX code. This comprehensive review therefore summarizes the current knowledge of specific ASC-related HOX expression patterns and how these were integrated into stem cell-related signaling pathways. Understanding the mechanism of HOX gene regulation in stem cells may provide new ways to manipulate stem cell fate and function leading to improved and new approaches in the field of regenerative medicine.
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42
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Cancer cells as a new source of induced pluripotent stem cells. Stem Cell Res Ther 2022; 13:459. [PMID: 36064437 PMCID: PMC9446809 DOI: 10.1186/s13287-022-03145-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 08/17/2022] [Indexed: 11/10/2022] Open
Abstract
Over the last 2 decades, induced pluripotent stem cells (iPSCs) have had various potential applications in various medical research areas, from personalized medicine to disease treatment. Different cellular resources are accessible for iPSC generation, such as keratinocytes, skin fibroblasts, and blood or urine cells. However, all these sources are somatic cells, and we must make several changes in a somatic cell's transcriptome and chromatin state to become a pluripotent cell. It has recently been revealed that cancer cells can be a new source of iPSCs production. Cancer cells show similarities with iPSCs in self-renewal capacity, reprogramming potency, and signaling pathways. Although genetic abnormalities and potential tumor formation in cancer cells pose a severe risk, reprogrammed cancer-induced pluripotent stem cells (cancer-iPSCs) indicate that pluripotency can transiently overcome the cancer phenotype. This review discusses whether cancer cells can be a preferable source to generate iPSCs.
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43
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Guo X, Ma R, Wang M, Wui-Man Lau B, Chen X, Li Y. Novel perspectives on the therapeutic role of cryptotanshinone in the management of stem cell behaviors for high-incidence diseases. Front Pharmacol 2022; 13:971444. [PMID: 36046823 PMCID: PMC9420941 DOI: 10.3389/fphar.2022.971444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 07/18/2022] [Indexed: 11/22/2022] Open
Abstract
Cryptotanshinone (CTS), a diterpenoid quinone, is found mostly in Salvia miltiorrhiza Bunge (S. miltiorrhiza) and plays a crucial role in many cellular processes, such as cell proliferation/self-renewal, differentiation and apoptosis. In particular, CTS’s profound physiological impact on various stem cell populations and their maintenance and fate determination could improve the efficiency and accuracy of stem cell therapy for high-incidence disease. However, as much promise CTS holds, these CTS-mediated processes are complex and multifactorial and many of the underlying mechanisms as well as their clinical significance for high-incidence diseases are not yet fully understood. This review aims to shed light on the impact and mechanisms of CTS on the actions of diverse stem cells and the involvement of CTS in the many processes of stem cell behavior and provide new insights for the application of CTS and stem cell therapy in treating high-incidence diseases.
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Affiliation(s)
- Xiaomeng Guo
- State Key Laboratory of Component-Based Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Ruishuang Ma
- State Key Laboratory of Component-Based Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Meng Wang
- State Key Laboratory of Component-Based Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Benson Wui-Man Lau
- Department of Rehabilitation Sciences, The Hong Kong Polytechnic University, Hong Kong, Hong Kong SAR, China
| | - Xiaopeng Chen
- State Key Laboratory of Component-Based Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- *Correspondence: Xiaopeng Chen, ; Yue Li,
| | - Yue Li
- State Key Laboratory of Component-Based Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- *Correspondence: Xiaopeng Chen, ; Yue Li,
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44
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Guglielmo M, Marta B. Stem Cells and the Microenvironment: Reciprocity with Asymmetry in Regenerative Medicine. Acta Biotheor 2022; 70:24. [PMID: 35962861 DOI: 10.1007/s10441-022-09448-0] [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: 11/17/2021] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 11/29/2022]
Abstract
Much of the current research in regenerative medicine concentrates on stem-cell therapy that exploits the regenerative capacities of stem cells when injected into different types of human tissues. Although new therapeutic paths have been opened up by induced pluripotent cells and human mesenchymal cells, the rate of success is still low and mainly due to the difficulties of managing cell proliferation and differentiation, giving rise to non-controlled stem cell differentiation that ultimately leads to cancer. Despite being still far from becoming a reality, these studies highlight the role of physical and biological constraints (e.g., cues and morphogenetic fields) placed by tissue microenvironment on stem cell fate. This asks for a clarification of the coupling of stem cells and microenvironmental factors in regenerative medicine. We argue that extracellular matrix and stem cells have a causal reciprocal and asymmetric relationship in that the 3D organization and composition of the extracellular matrix establish a spatial, temporal, and mechanical control over the fate of stem cells, which enable them to interact and control (as well as be controlled by) the cellular components and soluble factors of microenvironment. Such an account clarifies the notions of stemness and stem cell regeneration consistently with that of microenvironment.
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Affiliation(s)
- Militello Guglielmo
- IAS-Research Centre, University of the Basque Country, San Sebastián, Spain.
| | - Bertolaso Marta
- University Campus Bio-Medico of Rome, Institute of Scientific and Technological Practice, Rome, Italy
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45
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Thompson JJ, Lee DJ, Mitra A, Frail S, Dale RK, Rocha PP. Extensive co-binding and rapid redistribution of NANOG and GATA6 during emergence of divergent lineages. Nat Commun 2022; 13:4257. [PMID: 35871075 PMCID: PMC9308780 DOI: 10.1038/s41467-022-31938-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 07/11/2022] [Indexed: 11/26/2022] Open
Abstract
Fate-determining transcription factors (TFs) can promote lineage-restricted transcriptional programs from common progenitor states. The inner cell mass (ICM) of mouse blastocysts co-expresses the TFs NANOG and GATA6, which drive the bifurcation of the ICM into either the epiblast (Epi) or the primitive endoderm (PrE), respectively. Here, we induce GATA6 in embryonic stem cells-that also express NANOG-to characterize how a state of co-expression of opposing TFs resolves into divergent lineages. Surprisingly, we find that GATA6 and NANOG co-bind at the vast majority of Epi and PrE enhancers, a phenomenon we also observe in blastocysts. The co-bound state is followed by eviction and repression of Epi TFs, and quick remodeling of chromatin and enhancer-promoter contacts thus establishing the PrE lineage while repressing the Epi fate. We propose that co-binding of GATA6 and NANOG at shared enhancers maintains ICM plasticity and promotes the rapid establishment of Epi- and PrE-specific transcriptional programs.
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Affiliation(s)
- Joyce J Thompson
- Unit on Genome Structure and Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Daniel J Lee
- Unit on Genome Structure and Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Apratim Mitra
- Bioinformatics and Scientific Programming Core, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sarah Frail
- Unit on Genome Structure and Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ryan K Dale
- Bioinformatics and Scientific Programming Core, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Pedro P Rocha
- Unit on Genome Structure and Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA.
- National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
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46
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Williams MR, Xiaokang Y, Hathaway NA, Kireev D. A simulation model of heterochromatin formation at submolecular detail. iScience 2022; 25:104590. [PMID: 35800764 PMCID: PMC9254115 DOI: 10.1016/j.isci.2022.104590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 11/16/2021] [Accepted: 06/08/2022] [Indexed: 11/15/2022] Open
Abstract
Heterochromatin is a physical state of the chromatin fiber that maintains gene repression during cell development. Although evidence exists on molecular mechanisms involved in heterochromatin formation, a detailed structural mechanism of heterochromatin formation needs a better understanding. We made use of a simple Monte Carlo simulation model with explicit representation of key molecular events to observe molecular self-organization leading to heterochromatin formation. Our simulations provide a structural interpretation of several important traits of the heterochromatinization process. In particular, this study provides a depiction of how small amounts of HP1 are able to induce a highly condensed chromatin state through HP1 dimerization and bridging of sequence-remote nucleosomes. It also elucidates structural roots of a yet poorly understood phenomenon of a nondeterministic nature of heterochromatin formation and subsequent gene repression. Experimental chromatin in vivo assay provides an unbiased estimate of time scale of repressive response to a heterochromatin-triggering event.
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Affiliation(s)
- Michael R. Williams
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina, Chapel Hill, NC 27513, USA
| | - Yan Xiaokang
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina, Chapel Hill, NC 27513, USA
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, Chapel Hill, NC 27599, USA
| | - Nathaniel A. Hathaway
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina, Chapel Hill, NC 27513, USA
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, Chapel Hill, NC 27599, USA
| | - Dmitri Kireev
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina, Chapel Hill, NC 27513, USA
- Department of Chemistry, University of Missouri, Columbia, MO 65211, USA
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47
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Epigenetics as "conductor" in "orchestra" of pluripotent states. Cell Tissue Res 2022; 390:141-172. [PMID: 35838826 DOI: 10.1007/s00441-022-03667-0] [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: 12/30/2021] [Accepted: 07/01/2022] [Indexed: 11/02/2022]
Abstract
Pluripotent character is described as the potency of cells to differentiate into all three germ layers. The best example to reinstate the term lies in the context of embryonic stem cells (ESCs). Pluripotent ESC describes the in vitro status of those cells that originate during the complex process of embryogenesis. Pre-implantation to post-implantation development of embryo embrace cells with different levels of stemness. Currently, four states of pluripotency have been recognized, in the progressing order of "naïve," "poised," "formative," and "primed." Epigenetics act as the "conductor" in this "orchestra" of transition in pluripotent states. With a distinguishable gene expression profile, these four states associate with different epigenetic signatures, sometimes distinct while otherwise overlapping. The present review focuses on how epigenetic factors, including DNA methylation, bivalent chromatin, chromatin remodelers, chromatin/nuclear architecture, and microRNA, could dictate pluripotent states and their transition among themselves.
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48
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Vitale E, Perveen S, Rossin D, Lo Iacono M, Rastaldo R, Giachino C. Role of Chaperone-Mediated Autophagy in Ageing Biology and Rejuvenation of Stem Cells. Front Cell Dev Biol 2022; 10:912470. [PMID: 35837330 PMCID: PMC9273769 DOI: 10.3389/fcell.2022.912470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/07/2022] [Indexed: 11/17/2022] Open
Abstract
What lies at the basis of the mechanisms that regulate the maintenance and self-renewal of pluripotent stem cells is still an open question. The control of stemness derives from a fine regulation between transcriptional and metabolic factors. In the last years, an emerging topic has concerned the involvement of Chaperone-Mediated Autophagy (CMA) as a key mechanism in stem cell pluripotency control acting as a bridge between epigenetic, transcriptional and differentiation regulation. This review aims to clarify this new and not yet well-explored horizon discussing the recent studies regarding the CMA impact on embryonic, mesenchymal, and haematopoietic stem cells. The review will discuss how CMA influences embryonic stem cell activity promoting self-renewal or differentiation, its involvement in maintaining haematopoietic stem cell function by increasing their functionality during the normal ageing process and its effects on mesenchymal stem cells, in which modulation of CMA regulates immunosuppressive and differentiation properties. Finally, the importance of these new discoveries and their relevance for regenerative medicine applications, from transplantation to cell rejuvenation, will be addressed.
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49
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A single-cell survey unveils cellular heterogeneity and sensitive responses in mouse cortices induced by oral exposure to triphenyl phosphate. Arch Toxicol 2022; 96:2545-2557. [PMID: 35752650 DOI: 10.1007/s00204-022-03301-6] [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: 02/17/2022] [Accepted: 04/07/2022] [Indexed: 11/02/2022]
Abstract
Triphenyl phosphate (TPhP) is a non-halogenated organophosphorus flame retardant, and there is a higher exposure risk in children. TPhP has been found to be neurotoxic upon developmental exposure, yet the specific mechanism remains unclear. To characterize the cellular responses underlying TPhP-induced developmental neurotoxicity, we administered TPhP (0.5, 5 or 50 mg/kg/day) to neonatal mice from postnatal day 10 (P10)-P70. A total of 17,229 cells and 26,338 genes were identified in cortical samples from control and low-dose (the internal doses of metabolite DPhP comparable to human exposure level) groups using single-cell RNA sequencing (scRNA-seq). TPhP exposure led to heterogeneous transcriptional alterations and intercellular crosstalk among neurons, neural stem/progenitor cells (NSPCs), endothelial cells, and immunocytes. Deprivation of NSPCs, loss of mature neurons, and concomitant neuroinflammation mediated by extrinsic and intrinsic immunocytes were found in TPhP-exposed cortices. In addition, we observed blood-brain barrier destruction prior to the anxiety/depression-like neurobehavioral changes. These results reveal the distinctive cellular processes in TPhP's neurodevelopmental toxicity and uncover that the impeded neurogenesis, disrupted vascular barrier, and concomitant neuroinflammation are the sensitive responses to TPhP exposure. Our study paves the way for the application of scRNA-seq in toxicity assessments for emerging neurotoxic pollutants.
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50
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Malaguti M, Portero Migueles R, Annoh J, Sadurska D, Blin G, Lowell S. SyNPL: Synthetic Notch pluripotent cell lines to monitor and manipulate cell interactions in vitro and in vivo. Development 2022; 149:275525. [PMID: 35616331 PMCID: PMC9270970 DOI: 10.1242/dev.200226] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 05/13/2022] [Indexed: 12/11/2022]
Abstract
Cell-cell interactions govern differentiation and cell competition in pluripotent cells during early development, but the investigation of such processes is hindered by a lack of efficient analysis tools. Here, we introduce SyNPL: clonal pluripotent stem cell lines that employ optimised Synthetic Notch (SynNotch) technology to report cell-cell interactions between engineered ‘sender’ and ‘receiver’ cells in cultured pluripotent cells and chimaeric mouse embryos. A modular design makes it straightforward to adapt the system for programming differentiation decisions non-cell-autonomously in receiver cells in response to direct contact with sender cells. We demonstrate the utility of this system by enforcing neuronal differentiation at the boundary between two cell populations. In summary, we provide a new adaptation of SynNotch technology that could be used to identify cell interactions and to profile changes in gene or protein expression that result from direct cell-cell contact with defined cell populations in culture and in early embryos, and that can be customised to generate synthetic patterning of cell fate decisions. Summary: Optimised Synthetic Notch circuitry in mouse pluripotent stem cells provides a modular tool with which to monitor cell-cell interactions and program synthetic patterning of cell fates in culture and in embryos.
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Affiliation(s)
- Mattias Malaguti
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Rosa Portero Migueles
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Jennifer Annoh
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Daina Sadurska
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Guillaume Blin
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Sally Lowell
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
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