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Three-dimensional stem cell models of mammalian gastrulation 哺乳动物胃形成的三维干细胞模型。
IF 3.2 3区 生物学
BioEssays Pub Date : 2024-08-28 DOI: 10.1002/bies.202400123
David A. Turner, Alfonso Martinez Arias
{"title":"Three-dimensional stem cell models of mammalian gastrulation","authors":"David A. Turner,&nbsp;Alfonso Martinez Arias","doi":"10.1002/bies.202400123","DOIUrl":"10.1002/bies.202400123","url":null,"abstract":"<p>Gastrulation is a key milestone in the development of an organism. It is a period of cell proliferation and coordinated cellular rearrangement, that creates an outline of the body plan. Our current understanding of mammalian gastrulation has been improved by embryo culture, but there are still many open questions that are difficult to address because of the intrauterine development of the embryos and the low number of specimens. In the case of humans, there are additional difficulties associated with technical and ethical challenges. Over the last few years, pluripotent stem cell models are being developed that have the potential to become useful tools to understand the mammalian gastrulation. Here we review these models with a special emphasis on gastruloids and provide a survey of the methods to produce them robustly, their uses, relationship to embryos, and their prospects as well as their limitations.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"46 12","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bies.202400123","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142079212","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Propagating pluripotency – The conundrum of self-renewal 繁殖多能性--自我更新的难题。
IF 3.2 3区 生物学
BioEssays Pub Date : 2024-08-23 DOI: 10.1002/bies.202400108
Austin Smith
{"title":"Propagating pluripotency – The conundrum of self-renewal","authors":"Austin Smith","doi":"10.1002/bies.202400108","DOIUrl":"10.1002/bies.202400108","url":null,"abstract":"<p>The discovery of mouse embryonic stem cells in 1981 transformed research in mammalian developmental biology and functional genomics. The subsequent generation of human pluripotent stem cells (PSCs) and the development of molecular reprogramming have opened unheralded avenues for drug discovery and cell replacement therapy. Here, I review the history of PSCs from the perspective that long-term self-renewal is a product of the in vitro signaling environment, rather than an intrinsic feature of embryos. I discuss the relationship between pluripotent states captured in vitro to stages of epiblast in the embryo and suggest key considerations for evaluation of PSCs. A remaining fundamental challenge is to determine whether naïve pluripotency can be propagated from the broad range of mammals by exploiting common principles in gene regulatory architecture.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"46 12","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bies.202400108","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142046395","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
An "R-spondin code" for multimodal signaling ON-OFF states 多模式信号开-关状态的 "R-spondin 代码"。
IF 3.2 3区 生物学
BioEssays Pub Date : 2024-08-23 DOI: 10.1002/bies.202400144
Christof Niehrs, Carina Seidl, Hyeyoon Lee
{"title":"An \"R-spondin code\" for multimodal signaling ON-OFF states","authors":"Christof Niehrs,&nbsp;Carina Seidl,&nbsp;Hyeyoon Lee","doi":"10.1002/bies.202400144","DOIUrl":"10.1002/bies.202400144","url":null,"abstract":"<p>R-spondins (RSPOs) are a family of secreted proteins and stem cell growth factors that are potent co-activators of Wnt signaling. Recently, RSPO2 and RSPO3 were shown to be multifunctional, not only amplifying Wnt- but also binding BMP- and FGF receptors to downregulate signaling. The common mechanism underlying these diverse functions is that RSPO2 and RSPO3 act as “endocytosers” that link transmembrane proteins to ZNRF3/RNF43 E3 ligases and trigger target internalization. Thus, RSPOs are natural protein targeting chimeras for cell surface proteins. Conducting data mining and cell surface binding assays we report additional candidate RSPO targets, including SMO, PTC1,2, LGI1, ROBO4, and PTPR(F/S). We propose that there is an “R-spondin code” that imparts combinatorial signaling ON-OFF states of multiple growth factors. This code involves the modular RSPO domains, notably distinct motifs in the divergent RSPO-TSP1 domains to mediate target interaction and internalization. The RSPO code offers a novel framework for the understanding how diverse signaling pathways may be coordinately regulated in development and disease.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"46 10","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bies.202400144","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142046363","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Pushing the TAD boundary: Decoding insulator codes of clustered CTCF sites in 3D genomes 突破 TAD 边界：解码三维基因组中集群 CTCF 位点的绝缘体代码。
IF 3.2 3区 生物学
BioEssays Pub Date : 2024-08-21 DOI: 10.1002/bies.202400121
Haiyan Huang, Qiang Wu
{"title":"Pushing the TAD boundary: Decoding insulator codes of clustered CTCF sites in 3D genomes","authors":"Haiyan Huang,&nbsp;Qiang Wu","doi":"10.1002/bies.202400121","DOIUrl":"10.1002/bies.202400121","url":null,"abstract":"<p>Topologically associating domain (TAD) boundaries are the flanking edges of TADs, also known as insulated neighborhoods, within the 3D structure of genomes. A prominent feature of TAD boundaries in mammalian genomes is the enrichment of clustered CTCF sites often with mixed orientations, which can either block or facilitate enhancer–promoter (E-P) interactions within or across distinct TADs, respectively. We will discuss recent progress in the understanding of fundamental organizing principles of the clustered CTCF insulator codes at TAD boundaries. Specifically, both inward- and outward-oriented CTCF sites function as topological chromatin insulators by asymmetrically blocking improper TAD-boundary-crossing cohesin loop extrusion. In addition, boundary stacking and enhancer clustering facilitate long-distance E-P interactions across multiple TADs. Finally, we provide a unified mechanism for RNA-mediated TAD boundary function via R-loop formation for both insulation and facilitation. This mechanism of TAD boundary formation and insulation has interesting implications not only on how the 3D genome folds in the Euclidean nuclear space but also on how the specificity of E-P interactions is developmentally regulated.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"46 10","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bies.202400121","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142016435","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
In through the out door: A loop-binding-first model for topological cohesin loading 从外门进入：拓扑凝聚蛋白加载的环路结合优先模型
IF 3.2 3区 生物学
BioEssays Pub Date : 2024-08-19 DOI: 10.1002/bies.202400120
Nicholas Rhind
{"title":"In through the out door: A loop-binding-first model for topological cohesin loading","authors":"Nicholas Rhind","doi":"10.1002/bies.202400120","DOIUrl":"10.1002/bies.202400120","url":null,"abstract":"<p>Cohesin is a ring-shaped complex that is loaded on DNA in two different conformations. In one conformation, it forms loops to organize the interphase genome; in the other, it topologically encircles sibling chromosomes to facilitate homologous recombination and to establish the cohesion that is required for orderly segregation during mitosis. How, and even if, these two loading conformation are related is unclear. Here, I propose that loop binding is a required first step for topological binding. This loop-binding-first model integrates the known information about the two loading mechanisms, explains genetic requirements for the two and explains how topological loading evolved from loop binding.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"46 10","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142003679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
FAM210A: An emerging regulator of mitochondrial homeostasis FAM210A：线粒体平衡的新调节器
IF 3.2 3区 生物学
BioEssays Pub Date : 2024-08-19 DOI: 10.1002/bies.202400090
Yubo Wang, Feng Yue
{"title":"FAM210A: An emerging regulator of mitochondrial homeostasis","authors":"Yubo Wang,&nbsp;Feng Yue","doi":"10.1002/bies.202400090","DOIUrl":"10.1002/bies.202400090","url":null,"abstract":"<p>Mitochondrial homeostasis serves as a cornerstone of cellular function, orchestrating a delicate balance between energy production, redox status, and cellular signaling transduction. This equilibrium involves a myriad of interconnected processes, including mitochondrial dynamics, quality control mechanisms, and biogenesis and degradation. Perturbations in mitochondrial homeostasis have been implicated in a wide range of diseases, including neurodegenerative diseases, metabolic syndromes, and aging-related disorders. In the past decades, the discovery of numerous mitochondrial proteins and signaling has led to a more complete understanding of the intricate mechanisms underlying mitochondrial homeostasis. Recent studies have revealed that Family with sequence similarity 210 member A (FAM210A) is a novel nuclear-encoded mitochondrial protein involved in multiple aspects of mitochondrial homeostasis, including mitochondrial quality control, dynamics, cristae remodeling, metabolism, and proteostasis. Here, we review the function and physiological role of FAM210A in cellular and organismal health. This review discusses how FAM210A acts as a regulator on mitochondrial inner membrane to coordinate mitochondrial dynamics and metabolism.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"46 10","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142003678","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Balancing Plk1 activity levels: The secret of synchrony between the cell and the centrosome cycle 平衡 Plk1 的活性水平：细胞与中心体周期同步的秘密
IF 3.2 3区 生物学
BioEssays Pub Date : 2024-08-11 DOI: 10.1002/bies.202400048
Devashish Dwivedi, Patrick Meraldi
{"title":"Balancing Plk1 activity levels: The secret of synchrony between the cell and the centrosome cycle","authors":"Devashish Dwivedi,&nbsp;Patrick Meraldi","doi":"10.1002/bies.202400048","DOIUrl":"10.1002/bies.202400048","url":null,"abstract":"<p>The accuracy of cell division requires precise regulation of the cellular machinery governing DNA/genome duplication, ensuring its equal distribution among the daughter cells. The control of the centrosome cycle is crucial for the formation of a bipolar spindle, ensuring error-free segregation of the genome. The cell and centrosome cycles operate in close synchrony along similar principles. Both require a single duplication round in every cell cycle, and both are controlled by the activity of key protein kinases. Nevertheless, our comprehension of the precise cellular mechanisms and critical regulators synchronizing these two cycles remains poorly defined. Here, we present our hypothesis that the spatiotemporal regulation of a dynamic equilibrium of mitotic kinases activities forms a molecular clock that governs the synchronous progression of both the cell and the centrosome cycles.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"46 10","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bies.202400048","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141916114","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Germ cell tumors, cell surface markers, and the early search for human pluripotent stem cells 生殖细胞肿瘤、细胞表面标志物和人类多能干细胞的早期探索。
IF 3.2 3区 生物学
BioEssays Pub Date : 2024-08-08 DOI: 10.1002/bies.202400094
Peter W. Andrews
{"title":"Germ cell tumors, cell surface markers, and the early search for human pluripotent stem cells","authors":"Peter W. Andrews","doi":"10.1002/bies.202400094","DOIUrl":"10.1002/bies.202400094","url":null,"abstract":"<p>Many strands of research by different groups, starting from teratocarcinomas in the laboratory mouse, later moving the corresponding human tumors, contributed to the isolation and description of human pluripotent stem cells (PSCs). In this review, I highlight the contributions from my own research, particularly at the Wistar Institute during the 1980s, when with my colleagues we characterized one of the first clonal lines of pluripotent human embryonal carcinoma (EC) cells, the stem cells of teratocarcinomas, and identified key features including cell surface antigen markers that have since found a place in the study and exploitation of human PSC. Much of this research depended upon close teamwork with colleagues, many in other laboratories, who contributed different expertise and experience. It was also often driven by circumstance and chance rather than pursuit of a grand design.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"46 12","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bies.202400094","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141900930","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Pluripotent stem cell-derived organoids: A brief history of curiosity-led discoveries 多能干细胞衍生的器官组织：好奇心引领的发现简史。
IF 3.2 3区 生物学
BioEssays Pub Date : 2024-08-05 DOI: 10.1002/bies.202400105
Madeline A. Lancaster
{"title":"Pluripotent stem cell-derived organoids: A brief history of curiosity-led discoveries","authors":"Madeline A. Lancaster","doi":"10.1002/bies.202400105","DOIUrl":"10.1002/bies.202400105","url":null,"abstract":"<p>Organoids are quickly becoming an accepted model for understanding human biology and disease. Pluripotent stem cells (PSC) provide a starting point for many organs and enable modeling of the embryonic development and maturation of such organs. The foundation of PSC-derived organoids can be found in elegant developmental studies demonstrating the remarkable ability of immature cells to undergo histogenesis even when taken out of the embryo context. PSC-organoids are an evolution of earlier methods such as embryoid bodies, taken to a new level with finer control and in some cases going beyond tissue histogenesis to organ-like morphogenesis. But many of the discoveries that led to organoids were not necessarily planned, but rather the result of inquisitive minds with freedom to explore. Protecting such curiosity-led research through flexible funding will be important going forward if we are to see further ground-breaking discoveries.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"46 12","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bies.202400105","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141888496","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Permeable TAD boundaries and their impact on genome-associated functions 可渗透的 TAD 边界及其对基因组相关功能的影响
IF 3.2 3区 生物学
BioEssays Pub Date : 2024-08-02 DOI: 10.1002/bies.202400137
Li-Hsin Chang, Daan Noordermeer
{"title":"Permeable TAD boundaries and their impact on genome-associated functions","authors":"Li-Hsin Chang,&nbsp;Daan Noordermeer","doi":"10.1002/bies.202400137","DOIUrl":"10.1002/bies.202400137","url":null,"abstract":"<p>TAD boundaries are genomic elements that separate biological processes in neighboring domains by blocking DNA loops that are formed through Cohesin-mediated loop extrusion. Most TAD boundaries consist of arrays of binding sites for the CTCF protein, whose interaction with the Cohesin complex blocks loop extrusion. TAD boundaries are not fully impermeable though and allow a limited amount of inter-TAD loop formation. Based on the reanalysis of Nano-C data, a multicontact Chromosome Conformation Capture assay, we propose a model whereby clustered CTCF binding sites promote the successive stalling of Cohesin and subsequent dissociation from the chromatin. A fraction of Cohesin nonetheless achieves boundary read-through. Due to a constant rate of Cohesin dissociation elsewhere in the genome, the maximum length of inter-TAD loops is restricted though. We speculate that the DNA-encoded organization of stalling sites regulates TAD boundary permeability and discuss implications for enhancer–promoter loop formation and other genomic processes.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"46 10","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bies.202400137","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141874210","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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