BioEssaysPub Date : 2026-03-25DOI: 10.1002/bies.70132
{"title":"BioEssays 3/2026","authors":"","doi":"10.1002/bies.70132","DOIUrl":"https://doi.org/10.1002/bies.70132","url":null,"abstract":"<p>The cover image is based on the article Vimentin Intermediate Filaments: A Paradigm Shift From Static Structure to Dynamic Cytoplasmic Network by Bhuvanasundar Renganathan et al., 70125.\u0000\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure>\u0000 </p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"48 3","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bies.70132","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147579805","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}
BioEssaysPub Date : 2026-03-25DOI: 10.1002/bies.70129
Yuzhen Li, Richard D. Wood
{"title":"Beyond Short Microhomologies: Mismatch-Compatible Pol θ-Mediated DNA Damage Repair","authors":"Yuzhen Li, Richard D. Wood","doi":"10.1002/bies.70129","DOIUrl":"10.1002/bies.70129","url":null,"abstract":"<p>DNA polymerase θ (Pol θ)-mediated end-joining (TMEJ), one of several pathways for repairing DNA double-strand breaks, is traditionally thought to initiate via anchoring at short, consecutive, and perfectly matched microhomologies (MHs). Emerging evidence indicates that Pol θ can utilize MHs containing mismatches both in vitro and in vivo. This revised definition of MH provides a mechanistic explanation for a broader spectrum of Pol θ-dependent repair outcomes. Here, we summarize recent findings on the revised definition of MHs utilized by Pol θ, assess the applicability of this concept across species, and compare TMEJ with other (micro)hom(e)ology-mediated repair pathways. We explore how mismatch-containing MHs expand Pol θ-associated mutational signatures and provide a framework for future studies on Pol θ’s role in DNA repair and cancer biology.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"48 3","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13015775/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147509312","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}
BioEssaysPub Date : 2026-03-25DOI: 10.1002/bies.70123
Alexios-Fotios A. Mentis, Athanasios Kossyvakis, Dimitrios Chatzidimitriou
{"title":"Host Genetic Regulation of Stem Cell–Virus Interactions in Human Health","authors":"Alexios-Fotios A. Mentis, Athanasios Kossyvakis, Dimitrios Chatzidimitriou","doi":"10.1002/bies.70123","DOIUrl":"10.1002/bies.70123","url":null,"abstract":"<div>\u0000 \u0000 <p>The interactions between human viruses and human stem cells may differ from those with differentiated cells. These differences may arise through heterogeneous intercellular mechanisms and responses to specific infectious agents, resulting in different phenotypes that affect human pathophysiology. Understanding and exploiting such differences could have clinical and translational potential. Here, we discuss the various mechanistic interactions between stem cells and viruses related to entry mechanisms, replication dynamics, and immunomodulation. In doing so, we critically assess proposed models and hypotheses about how viruses manipulate stem cell biology, while also providing new paradigms for stem cell biology and therapeutic interventions. We highlight recent discoveries on the dual role of viruses in oncogenesis and oncolysis. In parallel, we explore similarities between stem cells and complex viruses—such as giant viruses and jumbo phages—to propose novel perspectives on viral adaptability and pathogenesis. We examine both established mechanisms and emerging viral phenomena to encourage further research and debate on the clinical implications of viral interactions with stem cells.</p>\u0000 </div>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"48 3","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147509568","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}
BioEssaysPub Date : 2026-03-25DOI: 10.1002/bies.70126
Bassant Eldaly, Brian M. Baker
{"title":"Dynamic Allostery in T Cell Receptor Specificity: A Role for Peptides and MHC Polymorphisms in Allosterically Tuning Immune Recognition","authors":"Bassant Eldaly, Brian M. Baker","doi":"10.1002/bies.70126","DOIUrl":"10.1002/bies.70126","url":null,"abstract":"<p>T cell receptor (TCR) recognition of peptide/MHC complexes is fundamental for adaptive immunity. Many studies have described the importance of peptide/MHC motion or dynamics in TCR recognition. A role for dynamics in recognition intersects with the concept of dynamic allostery, which describes how alterations to a protein's energy landscape and thus motions influence function, often in the absence of conformational changes. Tuning of MHC protein energy landscapes by different peptides has clearly been shown. Evidence is mounting, however, that MHC polymorphisms also alter the protein's energy landscape. Here, we address this concept, summarizing findings that suggest that, in addition to dictating peptide binding and selection, naturally occurring variations within MHC proteins promote differential peptide and protein dynamics, altering TCR recognition in an MHC allele-dependent manner. We hypothesize that MHC polymorphisms have been selected evolutionarily in part to tune the protein's dynamic response, altering immune specificity and further diversifying immune responses across populations.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"48 3","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13015781/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147509374","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}
BioEssaysPub Date : 2026-03-25DOI: 10.1002/bies.70127
Chuying Zhou, Mineko Kengaku
{"title":"Motor-Assisted Co-Migration of Intracellular Organelles and Microtubules as a Mechanism for Directed Cargo Transport","authors":"Chuying Zhou, Mineko Kengaku","doi":"10.1002/bies.70127","DOIUrl":"10.1002/bies.70127","url":null,"abstract":"<p>Intracellular cargo transport relies on a microtubule (MT) network and its molecular motors, dynein and kinesin. While conventional models emphasize motor-driven cargo movement along stationary MT tracks, emerging evidence suggests that dynamic movements of MTs also contribute to directional transport. We propose a model of cargo co-migration with moving MTs, exemplified by nuclear migration in developing neurons. This transport mode may operate across cell types, provided that cargo-MT tethering and directional MT movements are present. We hypothesize multiple complementary mechanisms, including motor catch-bond formation and clustering, as well as MT-associated protein-mediated anchorage. We further discuss how directional MT movements can be generated through motor-driven sliding, cortical gliding, actin-MT crosslinking, and dynamic MT instability. This coupled transport mechanism provides an additional layer of directional control that supplements motor-stepping-dependent transport. Potential experimental approaches to validate this hypothesis are discussed. Understanding MT-mediated cargo delivery could refine our current models of intracellular transport and reveal new insights into neurodevelopmental and neurodegenerative disorders.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"48 3","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13015778/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147509593","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}
BioEssaysPub Date : 2026-03-25DOI: 10.1002/bies.70130
Elvira Boršić-Mlinarič, Iva Hafner-Bratkovič
{"title":"Diverse Scaffolds Facilitate NLRP3 Clustering and Inflammasome Formation in Response to Perturbations in Cell Homeostasis","authors":"Elvira Boršić-Mlinarič, Iva Hafner-Bratkovič","doi":"10.1002/bies.70130","DOIUrl":"10.1002/bies.70130","url":null,"abstract":"<p>A central component of innate immunity, the NLRP3 inflammasome is a multiprotein complex formed in response to a chemically and morphologically diverse spectrum of stimuli. Despite extensive investigation, no single ligand or signal has emerged to account for this breadth of activation. Here, we review the landscape of NLRP3 activation across subcellular compartments and examine how this process is shaped by a network of interacting partners. Recent studies suggest that NLRP3 responds to cellular perturbations, such as changes in lipid membrane composition, protein localization, or organelle function. We propose that distinct upstream cues converge to generate diverse molecular scaffolds that recruit NLRP3. The NLRP3-scaffold interactions promote NLRP3 clustering, destabilize its autoinhibited conformation, and drive assembly of the inflammasome. NLRP3 is thus an adaptable sensor, equipped with versatile molecular interactions that allow it to integrate multiple danger signals into inflammasome activation.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"48 3","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13015780/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147509300","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}
BioEssaysPub Date : 2026-03-25DOI: 10.1002/bies.70128
Sergio P. Acebrón, Janina Hattemer, Tobias Rausch, Anchel De Jaime-Soguero
{"title":"Morphogen Gradients as Drivers of Mosaicism During Early Human Development","authors":"Sergio P. Acebrón, Janina Hattemer, Tobias Rausch, Anchel De Jaime-Soguero","doi":"10.1002/bies.70128","DOIUrl":"10.1002/bies.70128","url":null,"abstract":"<p>WNT, BMP, FGF, and Nodal signalling gradients drive naive to primed epiblast transitions and primitive endoderm specification, as well as subsequent gastrulation of the implanted embryo. Recently, these pathways were shown to control a signalling rheostat that modulates chromosome replication and segregation fidelity in human pluripotent stem cells. In particular, WNT and BMP antagonists associated with embryo anteriorization during gastrulation (DKK1, Cerberus, LEFTY2, Noggin, and Chordin) induce DNA replication stress and damage in S-phase leading to ultra-fine-bridges and whole-chromosome mis segregation in the subsequent mitosis. Of note, aneuploidy in pre- and early post-implantation embryos is the first cause of miscarriage in humans, and has also been associated with neurodevelopmental disorders. Here, we hypothesize that the antero-posterior (A–P) signalling gradient generates overlapping patterns of genome and chromosomal mosaicism in human embryos, with potential links to human infertility and lineage-specific developmental disorders.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"48 3","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13015771/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147509586","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}
BioEssaysPub Date : 2026-03-15DOI: 10.1002/bies.70125
Bhuvanasundar Renganathan, Stephen A. Adam, Vladimir I. Gelfand
{"title":"Vimentin Intermediate Filaments: A Paradigm Shift From Static Structure to Dynamic Cytoplasmic Network","authors":"Bhuvanasundar Renganathan, Stephen A. Adam, Vladimir I. Gelfand","doi":"10.1002/bies.70125","DOIUrl":"10.1002/bies.70125","url":null,"abstract":"<p>Recent advances in live-cell imaging, super-resolution microscopy, labeling techniques and cryo-electron microscopy reveal vimentin intermediate filaments (VIFs) as adaptable polymers that couple mechanical stability with rapid remodeling. In this review, we highlight recent findings and discuss how VIFs function as dynamic, interpenetrating networks with actin microfilaments and microtubules, coordinating cytoskeletal architecture while simultaneously facilitating organelle positioning and influencing cellular behavior. We also propose a hybrid transport model to capture the diverse modes of VIF cellular interactions. This emerging framework positions VIFs as dynamic integrators of cytoskeletal organization and intracellular logistics, with broad implications for understanding cell mechanics, migration, and disease.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"48 3","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12989643/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147462623","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}
BioEssaysPub Date : 2026-03-14DOI: 10.1002/bies.70124
Stefan Linquist, Tyler A. Elliott, Stefan C. Kremer, T. Ryan Gregory, Brent Saylor, Karl Cottenie
{"title":"Transposon Ecology and the Octopus Genome","authors":"Stefan Linquist, Tyler A. Elliott, Stefan C. Kremer, T. Ryan Gregory, Brent Saylor, Karl Cottenie","doi":"10.1002/bies.70124","DOIUrl":"10.1002/bies.70124","url":null,"abstract":"<p>Recent discoveries of transposable element (TE) activity in the octopus genome suggest, to some, that these “jumping genes” facilitated the evolution of cephalopod brains and possibly contribute to cognitive flexibility in these animals. In contrast, TEs are often regarded as genomic parasites with net deleterious effects on host fitness. The octopus genome provides an opportunity to compare these proposals to a genome-ecological alternative. We review evidence of TE accumulation and somatic activity, showing compatibility with both organism-beneficial and selfish-DNA interpretations. To resolve this, we apply ecological thinking within the genome to generate novel predictions. If TEs are adapted to a “requirement niche” typically found in germline cells, then TE-population growth rates (replication rates) should be nonnegative under similar “environmental” conditions (e.g., similar gene expression patterns to testes). This invites a comparison of expression levels across tissues. It is reasonable to infer some organism-beneficial function only when TE expression levels deviate from those predicted by the degree of niche-overlap with germline cells.</p>","PeriodicalId":9264,"journal":{"name":"BioEssays","volume":"48 3","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12988792/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147455599","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}