BioEssays最新文献

{"title":"Mouse embryos, chimeras, and embryonal carcinoma stem cells—Reflections on the winding road to gene manipulation","authors":"Virginia E. Papaioannou","doi":"10.1002/bies.202400061","DOIUrl":"10.1002/bies.202400061","url":null,"abstract":"<p>The relationship of embryonal carcinoma (EC) cells, the stem cells of germ cell- or embryo-derived teratocarcinoma tumors, to early embryonic cells came under intense scrutiny in the early 1970s when mouse chimeras were produced between EC cells and embryos. These chimeras raised tantalizing possibilities and high hopes for different areas of research. The normalization of EC cells by the embryo lent validity to their use as in vitro models for embryogenesis and indicated that they might reveal information about the relationship between malignancy and differentiation. Chimeras also showed the way for the potential introduction of genes, selected in EC cells in vitro, into the germ line of mice. Although EC cells provided material for the elucidation of early embryonic events and stimulated many studies of early molecular differentiation, after years of intense scrutiny, they fell short as the means of genetic manipulation of the germ line, although arguably they pointed the way to the development of embryonic stem (ES) cells that eventually fulfilled this goal.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"46 12","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141330398","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}

{"title":"Pioneer factors for DNA replication initiation in metazoans","authors":"Yue Wang,&nbsp;Jing Liang","doi":"10.1002/bies.202400002","DOIUrl":"10.1002/bies.202400002","url":null,"abstract":"<p>Precise DNA replication is fundamental for genetic inheritance. In eukaryotes, replication initiates at multiple origins that are first “licensed” and subsequently “fired” to activate DNA synthesis. Despite the success in identifying origins with specific DNA motifs in <i>Saccharomyces cerevisiae</i>, no consensus sequence or sequences with a predictive value of replication origins have been recognized in metazoan genomes. Rather, epigenetic rules and chromatin structures are believed to play important roles in governing the selection and activation of replication origins. We propose that replication initiation is facilitated by a group of sequence-specific “replication pioneer factors,” which function to increase chromatin accessibility and foster a chromatin environment that is conducive to the loading of the prereplication complex. Dysregulation of the function of these factors may lead to gene duplication, genomic instability, and ultimately the occurrence of pathological conditions such as cancer.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"46 9","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141330399","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}

{"title":"Interplay between altered metabolism and DNA damage and repair in ovarian cancer","authors":"Apoorva Uboveja,&nbsp;Katherine M. Aird","doi":"10.1002/bies.202300166","DOIUrl":"10.1002/bies.202300166","url":null,"abstract":"<p>Ovarian cancer is the most lethal gynecological malignancy and is often associated with both DNA repair deficiency and extensive metabolic reprogramming. While still emerging, the interplay between these pathways can affect ovarian cancer phenotypes, including therapeutic resistance to the DNA damaging agents that are standard-of-care for this tumor type. In this review, we will discuss what is currently known about cellular metabolic rewiring in ovarian cancer that may impact DNA damage and repair in addition to highlighting how specific DNA repair proteins also promote metabolic changes. We will also discuss relevant data from other cancers that could be used to inform ovarian cancer therapeutic strategies. Changes in the choice of DNA repair mechanism adopted by ovarian cancer are a major factor in promoting therapeutic resistance. Therefore, the impact of metabolic reprogramming on DNA repair mechanisms in ovarian cancer has major clinical implications for targeted combination therapies for the treatment of this devastating disease.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"46 8","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bies.202300166","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141316740","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}

{"title":"Let's talk about sex","authors":"Dave Speijer","doi":"10.1002/bies.202400134","DOIUrl":"10.1002/bies.202400134","url":null,"abstract":"&lt;p&gt;Most people know that using the word “sex” in a title will get you many more “clicks.” So, now that you are here, how do I hold your attention? By doing two things: (i) tell you about one of the most beautiful scientific articles I ever encountered, and (ii) explain how the process of &lt;i&gt;eukaryotic&lt;/i&gt; “meiotic” sex illustrates exquisitely that biology can only be understood as the interplay of historical accident and physio-chemical constraints. I will start with (ii). Though the studies about meiotic sex fill libraries, most researchers focus on just a few basic, interrelated, questions: Why settle for only giving half your genome to a new generation (if lucky enough to be able to) instead of just cloning yourself?; How did this elaborate, complex, process evolve and under which selective pressures?; How do selective forces during its origins relate to present-day advantages (if any)?&lt;/p&gt;&lt;p&gt;Thus, simply put: Meiotic sex, what is it good for? To present just a few answers: (i) The Red Queen “arms race” model, stating that as species (constituting prey, predator, host, and pathogen) are constantly pitted against other rapidly evolving opposing species, they have to change quickly, and only sex enables this&lt;sup&gt;[&lt;/sup&gt;&lt;span&gt;&lt;sup&gt;1&lt;/sup&gt;&lt;/span&gt;&lt;sup&gt;]&lt;/sup&gt;; (ii) The first model can be seen as a specific instance of a more general framework: recombination, implicit in meiotic sex, allows a &lt;i&gt;much faster&lt;/i&gt; probing of the space of combinatorial possibilities: selecting winners and weeding out losers&lt;sup&gt;[&lt;/sup&gt;&lt;span&gt;&lt;sup&gt;2&lt;/sup&gt;&lt;/span&gt;&lt;sup&gt;]&lt;/sup&gt;; (iii) Overcoming the limitations imposed by Muller's Ratchet: the process leading to accumulated, irreversible, deleterious mutations. Absent purifying sexual recombination, only organisms combining small genomes and low mutational loads can survive. Thus, without meiotic sex, the larger genomes of eukaryotes would be unsustainable.&lt;/p&gt;&lt;p&gt;Here we come to the crucial insight illustrating the interaction of historical accidents and nature's laws in biology. All the hypotheses mentioned explain the possible advantages, but as &lt;i&gt;evolution has no foresight&lt;/i&gt;, only the last framework can be used to explain the emergence of meiotic sex and its presence in the last eukaryotic common ancestor, because it invokes direct adaptation to actual selection forces, instead of &lt;i&gt;later&lt;/i&gt; advantages. Many researchers now accept that eukaryotes emerged from the merger of an (Asgard) archaeon and an alpha-proteobacterial endosymbiont, capable of oxidative respiration, which would become the mitochondrion.&lt;sup&gt;[&lt;/sup&gt;&lt;span&gt;&lt;sup&gt;3&lt;/sup&gt;&lt;/span&gt;&lt;sup&gt;]&lt;/sup&gt; Thus, the evolving organism would have had to contend with an initial genome doubling in size and (much) higher mutation rates because of &lt;i&gt;internal&lt;/i&gt; reactive oxygen species (ROS) formation. Considering Muller's Ratchet: a deadly combination. Archaeal genome repair mechanisms evolved into full blown meiotic sex next.&lt;sup&gt;[&lt;/sup&gt;&lt;span&gt;&lt;sup&gt;4&lt;/sup&gt;&lt;/span&gt;&lt;sup&gt;]&lt;/sup","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"46 8","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bies.202400134","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141316741","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}

{"title":"C2H2 proteins: Evolutionary aspects of domain architecture and diversification","authors":"Artem N. Bonchuk,&nbsp;Pavel G. Georgiev","doi":"10.1002/bies.202400052","DOIUrl":"10.1002/bies.202400052","url":null,"abstract":"<p>The largest group of transcription factors in higher eukaryotes are C2H2 proteins, which contain C2H2-type zinc finger domains that specifically bind to DNA. Few well-studied C2H2 proteins, however, demonstrate their key role in the control of gene expression and chromosome architecture. Here we review the features of the domain architecture of C2H2 proteins and the likely origin of C2H2 zinc fingers. A comprehensive investigation of proteomes for the presence of proteins with multiple clustered C2H2 domains has revealed a key difference between groups of organisms. Unlike plants, transcription factors in metazoans contain clusters of C2H2 domains typically separated by a linker with the TGEKP consensus sequence. The average size of C2H2 clusters varies substantially, even between genomes of higher metazoans, and with a tendency to increase in combination with SCAN, and especially KRAB domains, reflecting the increasing complexity of gene regulatory networks.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"46 8","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141316738","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}

{"title":"Culture-acquired genetic variation in human pluripotent stem cells: Twenty years on","authors":"John P. Vales,&nbsp;Ivana Barbaric","doi":"10.1002/bies.202400062","DOIUrl":"10.1002/bies.202400062","url":null,"abstract":"<p>Genetic changes arising in human pluripotent stem cells (hPSC) upon culture may bestow unwanted or detrimental phenotypes to cells, thus potentially impacting on the applications of hPSCs for clinical use and basic research. In the 20 years since the first report of culture-acquired genetic aberrations in hPSCs, a characteristic spectrum of recurrent aberrations has emerged. The preponderance of such aberrations implies that they provide a selective growth advantage to hPSCs upon expansion. However, understanding the consequences of culture-acquired variants for specific applications in cell therapy or research has been more elusive. The rapid progress of hPSC-based therapies to clinics is galvanizing the field to address this uncertainty and provide definitive ways both for risk assessment of variants and reducing their prevalence in culture. Here, we aim to provide a timely update on almost 20 years of research on this fascinating, but a still unresolved and concerning, phenomenon.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"46 12","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bies.202400062","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141316739","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}

{"title":"Crosstalk between co-assembling filamentous enzymes","authors":"Nancy Horton","doi":"10.1002/bies.202400129","DOIUrl":"10.1002/bies.202400129","url":null,"abstract":"","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"46 8","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141293164","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}

{"title":"Heart and vessels from stem cells: A short history of serendipity and good luck","authors":"Christine Mummery","doi":"10.1002/bies.202400078","DOIUrl":"10.1002/bies.202400078","url":null,"abstract":"<p>Stem cell research is the product of cumulative, integrated effort between and within laboratories and disciplines. The many collaborative steps that lead to that special “Eureka moment”, when something that has been a puzzle perhaps for years suddenly become clear, is among the greatest pleasures of a scientific career. In this essay, the serendipitous pathway from first acquaintance with pluripotent stem cells to advanced cardiovascular models that emerged from studying development and disease will be described. Perhaps inspiration for later generations of stem cell researchers simply to follow whatever they find interesting.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"46 12","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bies.202400078","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141258729","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}

{"title":"Oxidative status: A general but overlooked indicator of welfare across animal species?","authors":"Michaël Beaulieu","doi":"10.1002/bies.202300205","DOIUrl":"10.1002/bies.202300205","url":null,"abstract":"<p>Because of their ubiquity, plasticity, and direct effects on the nervous system, markers of oxidative status may be of great value to assess animal welfare across species and conditions in the wild. However, welfare biologists have not yet seized this opportunity, possibly because the validity of these markers as welfare indicators remains questionable. A validation process was, therefore, performed here using a meta-analytical approach considering three conditions assumed to impair the welfare of animals. With very few exceptions, two of the four considered markers consistently varied across these negatively-valenced conditions. By highlighting the current underrepresentation of markers of oxidative status in animal welfare studies, and by concretely illustrating that some of these markers can consistently reflect negative affective states, this article aims to encourage biologists to include these physiological markers in their toolbox to better measure, monitor, and perhaps also improve the welfare of animals in their natural habitat.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"46 8","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bies.202300205","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141258964","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}

{"title":"T-Rex escaped from the cytosolic park: Re-thinking the impact of TREX1 exonuclease deficiencies on genomic stability","authors":"Hervé Técher","doi":"10.1002/bies.202400066","DOIUrl":"10.1002/bies.202400066","url":null,"abstract":"<p>The Three Prime Repair Exonuclease 1 (TREX1) has been implicated in several pathologies characterized by chronic and inborn inflammation. Aberrant innate immunity caused by DNA sensing through the cGAS-STING pathway has been proposed to play a major role in the etiology of these interferonopathies. However, the molecular source of this DNA sensing and the possible involvement of TREX1 in genome (in)stability remains poorly understood. Recent findings reignite the debate about the cellular functions performed by TREX1 nuclease, notably in chromosome biology and stability. Here I put into perspective recent findings that suggest that TREX1 is at the crossroads of DNA damage response and inflammation in different pathological contexts.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"46 8","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bies.202400066","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141258721","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}