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Revisiting Clonal Evolution Through the Light of Retrotransposons. 从反转录转座子的角度回顾克隆进化。
IF 2.7 3区 生物学
BioEssays Pub Date : 2025-10-09 DOI: 10.1002/bies.70078
Anaïs Lamoureux, Emilie Elvira-Matelot, Françoise Porteu, Lucie Laplane
{"title":"Revisiting Clonal Evolution Through the Light of Retrotransposons.","authors":"Anaïs Lamoureux, Emilie Elvira-Matelot, Françoise Porteu, Lucie Laplane","doi":"10.1002/bies.70078","DOIUrl":"https://doi.org/10.1002/bies.70078","url":null,"abstract":"<p><p>The clonal evolution model provides a framework for understanding the evolution of cancer cells. According to this model, cancer cells accumulate genetic mutations over time, and these mutations are passed down to their descendants, leading to genetic diversity within the tumor. Some of these mutations confer selective advantages, causing certain lineages of cancer cells (clones) to dominate and expand. However, this model is rooted in certain conceptual assumptions, which we propose to revisit by considering the potential involvement of retrotransposons in cancer initiation and progression. In recent years, it has become evident that transposable elements, particularly retrotransposons, play a significant role in driving cancer transformation and progression. We first review how current knowledge about retrotransposon activity aligns with the clonal evolution model by highlighting its ability to modulate cancer cell fitness. We then take a forward-looking perspective to explore additional ways retrotransposons may also influence clonal dynamics beyond the current model.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":" ","pages":"e70078"},"PeriodicalIF":2.7,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145249852","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
Direct Protein Degradation: Emerging Tools to Probe Biological Complexity in Mammalian Systems. 直接蛋白质降解：探索哺乳动物系统生物复杂性的新兴工具。
IF 2.7 3区 生物学
BioEssays Pub Date : 2025-10-05 DOI: 10.1002/bies.70075
Sailasree Rajalekshmi, Kizhakke Mattada Sathyan
{"title":"Direct Protein Degradation: Emerging Tools to Probe Biological Complexity in Mammalian Systems.","authors":"Sailasree Rajalekshmi, Kizhakke Mattada Sathyan","doi":"10.1002/bies.70075","DOIUrl":"https://doi.org/10.1002/bies.70075","url":null,"abstract":"<p><p>Conditional degron approaches for acute and reversible protein depletion have become standard tools for studying gene function in cells and model organisms. Traditional gene perturbation methods have advanced gene function studies but are limited by slow kinetics, potential irreversibility, and lethality when targeting essential genes. To overcome these limitations, tag-based and antibody-based direct protein degradation technologies have been developed. These direct protein degradation systems utilize endogenous protein degradation pathways to achieve rapid and reversible protein depletion. When combined with genome editing, these systems provide precise temporal-and in some cases, spatial-control over endogenous protein expression. In this review, we will discuss the current status of tag-based and antibody-based direct protein degron technologies. We aim to provide a comprehensive guide for selecting these tools, highlighting their context-dependent applications and potential improvements to enhance efficiency and reliability.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":" ","pages":"e70075"},"PeriodicalIF":2.7,"publicationDate":"2025-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145231568","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
Integrating Astrocytes in the Sleep-Wake Cycle: The Time Is Now. 星形胶质细胞在睡眠-觉醒周期中的整合：时机就是现在。
IF 2.7 3区 生物学
BioEssays Pub Date : 2025-09-30 DOI: 10.1002/bies.70077
Marco Brancaccio
{"title":"Integrating Astrocytes in the Sleep-Wake Cycle: The Time Is Now.","authors":"Marco Brancaccio","doi":"10.1002/bies.70077","DOIUrl":"https://doi.org/10.1002/bies.70077","url":null,"abstract":"<p><p>Astrocytes are emerging as critical regulators of the sleep-wake cycle, actively contributing to both sleep homeostasis and circadian rheostasis. This dual role challenges neuron-centric frameworks that have dominated sleep and circadian biology and highlights astrocytes as potential integrators of internal temporal information. Experimental evidence shows that astrocytic calcium dynamics correlate with sleep state and that manipulating astrocytes can alter sleep architecture and homeostasis. In parallel, key aspects of circadian timekeeping can be autonomously driven by astrocytic clocks, with pulses of rhythmic GABA and glutamate able to synchronize circadian circuits and support circadian patterns of behavior. These findings are coherent with the idea that astrocytes can act as context-dependent integrators to convey environmental cues and internal states to neuronal circuitries and promote adaptive behavior. Incorporating astrocytes into conceptual models of the sleep-wake cycle may help reconcile contradictory findings and offer new frameworks to better understand how salient internal temporal representations are encoded within the brain.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":" ","pages":"e70077"},"PeriodicalIF":2.7,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145191139","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
Eukaryogenesis From FECA to LECA: Radical Steps Along the Way. 真核发生从FECA到LECA：沿途的激进步骤。
IF 2.7 3区 生物学
BioEssays Pub Date : 2025-09-29 DOI: 10.1002/bies.70063
Dave Speijer
{"title":"Eukaryogenesis From FECA to LECA: Radical Steps Along the Way.","authors":"Dave Speijer","doi":"10.1002/bies.70063","DOIUrl":"https://doi.org/10.1002/bies.70063","url":null,"abstract":"<p><p>The characteristics of the last eukaryotic common ancestor (LECA) population and the root of the eukaryotic tree have been coming into focus lately. However, the trajectory taking the host, related to present-day Asgard archaea and the endosymbiont, related to present-day alphaproteobacteria, toward such fully integrated and complex organisms is still unclear. Here I marshal recent evidence supporting the early arrival of the \"mitochondrion-to-be\", setting up the evolutionary dynamic for a series of mutual adaptations leading to eukaryotes. Upon critical analysis of some presuppositions in phylogenomic reconstructions of eukaryogenesis, I again propose that pre-symbiosis, efficient ATP generation, internal reactive oxygen species (ROS) formation and enhanced retention of genes supplied by horizontal gene transfer (HGT) interdependently allowed this unique transformation to occur.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":" ","pages":"e70063"},"PeriodicalIF":2.7,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145191163","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
Cytosolic fMet-Protein Synthesis as Source of Endogenous Ligands for Formyl Peptide Receptors. 酰基肽受体内源性配体来源的胞浆fmet蛋白合成。
IF 2.7 3区 生物学
BioEssays Pub Date : 2025-09-28 DOI: 10.1002/bies.70074
Chang-Seok Lee, Cheol-Sang Hwang
{"title":"Cytosolic fMet-Protein Synthesis as Source of Endogenous Ligands for Formyl Peptide Receptors.","authors":"Chang-Seok Lee, Cheol-Sang Hwang","doi":"10.1002/bies.70074","DOIUrl":"https://doi.org/10.1002/bies.70074","url":null,"abstract":"<p><p>Formyl peptides, exemplified by the synthetic tripeptide formyl-Met-Leu-Phe (fMLF), are well-established ligands for formyl peptide receptors (FPRs), central to neutrophil chemotaxis, and innate immune signaling. Traditionally attributed to bacterial and mitochondrial origins, these peptides are now proposed to arise from an additional, stress-inducible source within the eukaryotic cytosol. Recent findings suggest that under specific stress conditions, eukaryotic translation can initiate with formylmethionine (fMet), producing fMet-bearing nascent chains that are processed by the fMet/N-degron and fMet-mediated ribosome quality control (fMet-RQC) pathways. These proteostatic mechanisms may generate short, structurally diverse formyl peptides with the potential to function as endogenous FPR ligands. By introducing cytosolic proteostasis as a hypothetical source of formyl peptides, this perspective expands the landscape of formyl peptide biology and opens new directions for investigating their roles in immune regulation under stress and disease.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":" ","pages":"e70074"},"PeriodicalIF":2.7,"publicationDate":"2025-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145184526","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
Cancer Metabolism Meets DNA Repair: The Hidden Link to Therapy Resistance. 癌症代谢与DNA修复：治疗抵抗的隐藏联系。
IF 2.7 3区 生物学
BioEssays Pub Date : 2025-09-28 DOI: 10.1002/bies.70073
Chunzhang Yang
{"title":"Cancer Metabolism Meets DNA Repair: The Hidden Link to Therapy Resistance.","authors":"Chunzhang Yang","doi":"10.1002/bies.70073","DOIUrl":"https://doi.org/10.1002/bies.70073","url":null,"abstract":"<p><p>Cancer cells exhibit reprogrammed metabolic pathways to sustain aggressive phenotypes, including continuous cell division, stemness, invasion, and metastasis. Emerging evidence suggests that these metabolic adaptations profoundly impact DNA repair pathways, which contribute to the responses to therapy and influence overall outcomes. Metabolic processes such as the Warburg effect, nicotinamide adenine dinucleotide (NAD) metabolism, glutamine metabolism, and one-carbon metabolism support DNA repair by expanding the metabolite pool and facilitating post-translational modifications. Conversely, oncometabolites impair DNA repair pathways through epigenetic reprogramming, thereby promoting genomic instability. This review highlights recent discoveries that elucidate the intricate connections between metabolic hallmarks in cancer cells and DNA repair mechanisms, offering insights into potential therapeutic targets for future cancer treatments.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":" ","pages":"e70073"},"PeriodicalIF":2.7,"publicationDate":"2025-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145184598","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
Issue Information: BioEssays 10/2025 期刊信息：BioEssays 10/2025
IF 2.7 3区 生物学
BioEssays Pub Date : 2025-09-23 DOI: 10.1002/bies.70067
{"title":"Issue Information: BioEssays 10/2025","authors":"","doi":"10.1002/bies.70067","DOIUrl":"10.1002/bies.70067","url":null,"abstract":"","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"47 10","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bies.70067","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145135517","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
Multimodal Breathing Control: Pontomedullary Mechanisms and Current Perspectives. 多模式呼吸控制：桥髓机制和当前的观点。
IF 2.7 3区 生物学
BioEssays Pub Date : 2025-09-22 DOI: 10.1002/bies.70072
Nathan A Baertsch, Elora Reily, Jonathan Sedano, Ryan S Phillips, Joseph W Arthurs
{"title":"Multimodal Breathing Control: Pontomedullary Mechanisms and Current Perspectives.","authors":"Nathan A Baertsch, Elora Reily, Jonathan Sedano, Ryan S Phillips, Joseph W Arthurs","doi":"10.1002/bies.70072","DOIUrl":"https://doi.org/10.1002/bies.70072","url":null,"abstract":"<p><p>Breathing is a vital, continuous behavior that maintains physiological homeostasis, yet it is also remarkably flexible-modulated by volitional, emotional, and behavioral states. This review highlights recent advances in understanding how distributed neural circuits, particularly in the ventrolateral medulla and dorsolateral pons, integrate both homeostatic and non-homeostatic influences on respiratory control. We examine how higher-order brain regions interact with brainstem rhythm generators such as the preBötzinger complex, emphasizing a dynamic, state-dependent framework for respiratory regulation. Once considered a reflexive brainstem function, breathing is now recognized as the emergent output of interconnected networks that flexibly adapt rhythm and pattern based on internal state, behavior, and environmental context. Grasping this complexity is critical for understanding both the normal versatility and pathological vulnerability of respiratory control.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":" ","pages":"e70072"},"PeriodicalIF":2.7,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145111959","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
Equality, Diversity and Inclusivity (EDI) Sandpit: Views on Research Paradigms and the Future of Academia. 平等、多元和包容（EDI）沙坑：对研究范式和学术界未来的看法。
IF 2.7 3区 生物学
BioEssays Pub Date : 2025-09-14 DOI: 10.1002/bies.70070
Riaz Akhtar, Eric Hill, Paul Gilbert, Massimo Vassalli, Elizabeth G Canty-Laird, Lisa J White
{"title":"Equality, Diversity and Inclusivity (EDI) Sandpit: Views on Research Paradigms and the Future of Academia.","authors":"Riaz Akhtar, Eric Hill, Paul Gilbert, Massimo Vassalli, Elizabeth G Canty-Laird, Lisa J White","doi":"10.1002/bies.70070","DOIUrl":"https://doi.org/10.1002/bies.70070","url":null,"abstract":"<p><p>In this report, we summarize the outcome of a consultation session held in January 2024 appraising adopted attitudes within scientific research. This Equality, Diversity & Inclusion (EDI) Sandpit was a collaboration between interdisciplinary researchers from the ECMage (Extracellular Matrix [ECM] ageing across the life course interdisciplinary research network) and BLAST (Building Links in Ageing Science & Translation) networks, both part of the UK Ageing Networks, and the lifETIME (Engineered Tissues for Discovery, Industry and Medicine) Centre for Doctoral Training. Statements representing previously prevalent patterns of thinking that could influence research practice were put to delegate teams to discuss in relation to social and cultural behaviors that have been adopted over the years. Discussions focused on five themes across two main categories, aiming to identify and understand areas where change is needed, as well as to offer suggestions on how best to concentrate efforts to make the most impact.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":" ","pages":"e70070"},"PeriodicalIF":2.7,"publicationDate":"2025-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145063388","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
The Dark Side of Flow: Shear Stress as a Trigger for Thromboinflammatory NETs. 血流的阴暗面：剪切应力作为血栓炎性NETs的触发因素。
IF 2.7 3区 生物学
BioEssays Pub Date : 2025-09-14 DOI: 10.1002/bies.70071
Minoru Inoue
{"title":"The Dark Side of Flow: Shear Stress as a Trigger for Thromboinflammatory NETs.","authors":"Minoru Inoue","doi":"10.1002/bies.70071","DOIUrl":"https://doi.org/10.1002/bies.70071","url":null,"abstract":"","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":" ","pages":"e70071"},"PeriodicalIF":2.7,"publicationDate":"2025-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145063391","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
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