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Sun M, Chang L, He L, Wang L, Jiang Z, Si Y, Yu J, Ma Y. Combining single-cell profiling and functional analysis explores the role of pseudogenes in human early embryonic development. J Genet Genomics 2024:S1673-8527(24)00189-9. [PMID: 39032861 DOI: 10.1016/j.jgg.2024.07.013] [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: 03/25/2024] [Revised: 07/12/2024] [Accepted: 07/12/2024] [Indexed: 07/23/2024]
Abstract
More and more studies have demonstrated that pseudogenes possess coding ability, and the functions of their transcripts in the development of diseases have been partially revealed. However, the role of pseudogenes in maintenance of normal physiological states and life activities has long been neglected. Here we identify pseudogenes that are dynamically expressed during human early embryogenesis, showing different expression pattern from that of adult tissues. We explore the expression correlation between pseudogenes and the parent genes, part due to their shared gene regulatory elements or the potential regulation network between them. The essential role of three pseudogenes, PI4KAP1, TMED10P1, and FBXW4P1, in maintaining self-renewal of human embryonic stem cells is demonstrated. We further find that the three pseudogenes might perform their regulatory functions by binding to proteins or microRNAs. The pseudogene-related single-nucleotide polymorphisms are significantly associated with human congenital disease, further illustrating their importance during early embryonic development. Overall, this study is an excavation and exploration of functional pseudogenes during early human embryonic development, suggesting that pseudogenes are not only capable of being specifically activated in pathological states, but also play crucial functions in the maintenance of normal physiological states.
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Affiliation(s)
- Mengyao Sun
- State Key Laboratory of Common Mechanism Research for Major Diseases, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan 610052, China
| | - Le Chang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Liu He
- State Key Laboratory of Common Mechanism Research for Major Diseases, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Li Wang
- Department of Obstetrics, Haidian District Maternity and Child Health Hospital, Beijing 100080, China
| | - Zhengyang Jiang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Yanmin Si
- State Key Laboratory of Common Mechanism Research for Major Diseases, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Jia Yu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan 610052, China; Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China.
| | - Yanni Ma
- State Key Laboratory of Common Mechanism Research for Major Diseases, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, Sichuan 610052, China.
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Abstract
Stem cells self-renew and differentiate to generate all tissues and cells in the body. Stem cell health promotes adaptive responses to tissue damage or loss and is essential for tissue regeneration with age. In the past decade, the evolutionarily conserved transcription factors FOXO with known functions in promoting healthy aging have emerged as key regulators of stem cell homeostasis in various tissues, including blood, neural, and muscle stem cells. Aberrant FOXO functions have been implicated in a variety of disorders including neurodegenerative, blood, cancer, and diabetes some of which are fostered by abnormal stem cell function. As discussed in this chapter, at least in some stem cells FOXO regulatory mechanisms and applied functions follow a complex set of rules distinct from that operating in progenitor cell populations and in cultured cell lines. Elucidating the exact nature of FOXO properties in stem cells will be critical for identifying and targeting aberrant FOXO-mediated mechanisms that promote stem cell-derived disease specifically with age.
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Affiliation(s)
- Raymond Liang
- Icahn School of Medicine at Mount Sinai, New York, NY, United States; Developmental and Stem Cell Biology, Multidisciplinary Training Area, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Saghi Ghaffari
- Icahn School of Medicine at Mount Sinai, New York, NY, United States; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.
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Trib2 regulates the pluripotency of embryonic stem cells and enhances reprogramming efficiency. Exp Mol Med 2017; 49:e401. [PMID: 29170476 PMCID: PMC5704193 DOI: 10.1038/emm.2017.191] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 05/20/2017] [Accepted: 05/22/2017] [Indexed: 02/07/2023] Open
Abstract
Embryonic stem (ES) cells are pluripotent cells characterized by self-renewability and differentiation potential. Induced pluripotent stem (iPS) cells are ES cell-equivalent cells derived from somatic cells by the introduction of core reprogramming factors. ES and iPS cells are important sources for understanding basic biology and for generating therapeutic cells for clinical applications. Tribbles homolog 2 (Trib2) functions as a scaffold in signaling pathways. However, the relevance of Trib2 to the pluripotency of ES and iPS cells is unknown. In the present study, we elucidated the importance of Trib2 in maintaining pluripotency in mouse ES cells and in generating iPS cells from somatic cells through the reprogramming process. Trib2 expression decreased as ES cells differentiated, and Trib2 knockdown in ES cells changed their colony morphology while reducing the activity of alkaline phosphatase and the expression of the pluripotency marker genes Oct4, Sox2, Nanog and Klf4. Trib2 directly interacted with Oct4 and elevated Oct4 promoter activity. During the generation of iPS cells, Trib2 knockdown decreased the reprogramming efficiency of mouse embryonic fibroblasts, whereas Trib2 overexpression significantly increased their reprogramming efficiency. In summary, our results suggest that Trib2 is important for maintaining self-renewal in ES cells and for pluripotency induction during the reprogramming process.
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Xing Y, Su TT, Ruohola-Baker H. Tie-mediated signal from apoptotic cells protects stem cells in Drosophila melanogaster. Nat Commun 2015; 6:7058. [PMID: 25959206 DOI: 10.1038/ncomms8058] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 03/26/2015] [Indexed: 12/19/2022] Open
Abstract
Many types of normal and cancer stem cells are resistant to killing by genotoxins, but the mechanism for this resistance is poorly understood. Here we show that adult stem cells in Drosophila melanogaster germline and midgut are resistant to ionizing radiation (IR) or chemically induced apoptosis and dissect the mechanism for this protection. We find that upon IR the receptor tyrosine kinase Tie/Tie-2 is activated, leading to the upregulation of microRNA bantam that represses FOXO-mediated transcription of pro-apoptotic Smac/DIABLO orthologue, Hid in germline stem cells. Knockdown of the IR-induced putative Tie ligand, Pvf1, a functional homologue of human Angiopoietin, in differentiating daughter cells renders germline stem cells sensitive to IR, suggesting that the dying daughters send a survival signal to protect their stem cells for future repopulation of the tissue. If conserved in cancer stem cells, this mechanism may provide therapeutic options for the eradication of cancer.
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Affiliation(s)
- Yalan Xing
- Department of Biochemistry, Institute for Stem Cell &Regenerative Medicine, University of Washington, Seattle Washington 98109, USA
| | - Tin Tin Su
- Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309-0347, USA
| | - Hannele Ruohola-Baker
- 1] Department of Biochemistry, Institute for Stem Cell &Regenerative Medicine, University of Washington, Seattle Washington 98109, USA [2] Departments of Biology, Genome Sciences and Bioengineering, University of Washington, Seattle Washington 98109, USA
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Wang K, Zhang T, Dong Q, Nice EC, Huang C, Wei Y. Redox homeostasis: the linchpin in stem cell self-renewal and differentiation. Cell Death Dis 2013; 4:e537. [PMID: 23492768 PMCID: PMC3613828 DOI: 10.1038/cddis.2013.50] [Citation(s) in RCA: 204] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Stem cells are characterized by their unique ability of self-renewal to maintain the so-called stem cell pool. Over the past decades, reactive oxygen species (ROS) have been recognized as toxic aerobic metabolism byproducts that are harmful to stem cells, leading to DNA damage, senescence or cell death. Recently, a growing body of literature has shown that stem cells reside in redox niches with low ROS levels. The balance of Redox homeostasis facilitates stem cell self-renewal by an intricate network. Thus, to fully decipher the underlying molecular mechanisms involved in the maintenance of stem cell self-renewal, it is critical to address the important role of redox homeostasis in the regulation of self-renewal and differentiation of stem cells. In this regard, we will discuss the regulatory mechanisms involved in the subtly orchestrated balance of redox status in stem cells by scavenger antioxidant enzyme systems that are well monitored by the hypoxia niches and crucial redox regulators including forkhead homeobox type O family (FoxOs), apurinic/apyrimidinic (AP) endonuclease1/redox factor-1 (APE1/Ref-1), nuclear factor erythroid-2-related factor 2 (Nrf2) and ataxia telangiectasia mutated (ATM). We will also introduce several pivotal ROS-sensitive molecules, such as hypoxia-inducible factors, p38 mitogen-activated protein kinase (p38) and p53, involved in the redox-regulated stem cell self-renewal. Specifically, all the aforementioned molecules can act as ‘redox sensors' by virtue of redox modifications of their cysteine residues, which are critically important in the control of protein function. Given the importance of redox homeostasis in the regulation of stem cell self-renewal, understanding the underlying molecular mechanisms involved will provide important new insights into stem cell biology.
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Affiliation(s)
- Kui Wang
- The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, People's Republic of China
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