bims-ginsta 2026-09-20 papers

bims-ginsta

Biomed News

on Genome instability

Issue of 2026–09–20
28 papers selected by
Jinrong Hu, National University of Singapore

α-Parvin regulation of cell rearrangement is critical for ureteric bud branching morphogenesis.
Chromatin decompaction within the nucleus increases plasma membrane tension promoting NETosis execution, independently of transcription.
Programmed ribosomal frameshifting triggers translational stress to promote viral replication.
The molecular landscape of hypertrophic cardiomyopathy across disease stages and genotypes.
Cohesin preservation across mitosis contributes to restart transcription via Cdk9-mediated activation of RNAPol2.
EPS8 dampens the growth dynamics and prolongs the lifetime of actin-based protrusions.
Hypoxia-activated scleraxis a mediates epicardial progenitor differentiation into a unique cardiac perivascular cell type.
Cysteine excess triggers a mitochondrial iron-dependent cell death.
Sarcomere dynamic instability and stochastic heterogeneity drive robust cardiomyocyte contraction.
Cohesin reshapes replication fork contacts to aid fork slowing and reversal.
Age-associated loss of lymphatic vessels promotes cardiac inflammation.
DFCP1-containing ER microdomains mediate lysosomal membrane repair.
Quantitative imaging of dynamic processes in intestinal organoids.
Quality control of glycogen through direct ubiquitylation by RNF213.
Two parallel neural ectoderm progenitors contribute to the developing brain.
GTPase cycle and ER membrane regulate cargo handover during cotranslational protein targeting.
Accelerating protein design by scaling experimental characterization.
Highly efficient base editing at PCSK9 and normal human embryo development.
ACTA2-directed actin filaments license STING trafficking and activation for antiviral immunity and autoimmune pathogenesis.
Dysregulated Ribonucleoprotein Granules Impair Mitochondrial Function in RBM20-Related Dilated Cardiomyopathy.
FAP53 facilitates formation of microtubule doublets.
Copper ion-induced MYH9 polymerization executes cuproptosis.
Encoded and non-genetic protein variants expand human functional proteome.
CK2α restriction of STING accumulation underlies systemic aging.
Cellular stress leading to epithelial cell dysfunction in Sjögren's syndrome.
Generation of eight-cell embryo-like cells from human pluripotent stem cells.
Self-organizing human dual neural organoids model regional disease defects and teratogenicity.
The Batten disease protein CLN8 is a stereospecific acyltransferase in bis(monoacylglycero)phosphate biosynthesis.

Sci Adv. 2026 Sep 18. 12(38): eaec9007

α-Parvin regulation of cell rearrangement is critical for ureteric bud branching morphogenesis.

Xinyu Dong, Fabian Bock, Ali Hashmi, Nada Bulus, Glenda Mernaugh, Gema Bolas, Shensen Li, Wanying Zhu, Meiling Melzer, Kyle Brown, Colton Miller, Olga Viquéz, Eloi Montañez, Ambra Pozzi, Sara A Wickström, Roy Zent.

All branched tubular structures, including the kidney collecting system, are formed by branching morphogenesis, a process that includes tip branching and trunk narrowing. Tight control of cell movement and rearrangement is a prerequisite for branching morphogenesis. The role of integrin-associated adhesion proteins in coordinating actin dynamics and cell rearrangement during branching morphogenesis is poorly understood. Here, we used three-dimensional live imaging of mouse ureteric bud branching to show that α-parvin, a component of the integrin binding ILK-PINCH-parvin complex, regulates tip branching and tubule thinning by inhibiting excessive cell adhesion and actin polymerization. Mechanistically, α-parvin promotes actin turnover by inhibiting activation of the small guanosine triphosphatases RhoA and Cdc42, which in turn enhances the severing function of the actin regulatory protein, cofilin. These results underscore the importance of adhesion protein-regulated actin dynamics in the critical process of cell rearrangement, which is required for branching morphogenesis.

DOI: https://doi.org/10.1126/sciadv.aec9007
Nat Commun. 2026 Aug 20. pii: 9938. [Epub ahead of print]17(1):

Chromatin decompaction within the nucleus increases plasma membrane tension promoting NETosis execution, independently of transcription.

Aidan T Cabral, Manasi Sawant, Minwoo Kang, Liangqi Xie, Hawa Racine Thiam.

Chromatin organizes DNA and regulates nuclear mechanics. However, whether and how chromatin regulates whole-cell mechanics and functions independently of transcription is largely unknown. Here, leveraging transcription-independent NETosis, we show that chromatin decompaction within the nucleus increases plasma membrane tension and cell volume. Mechanistically, we show that chromatin accessibility gradually increases and chromatin binding proteins (CBPs) H1, HP1α, and H3 differentially dissociate from chromatin as it decompacts during NETosis. We posit that dissociated CBPs become osmolytes that alter cellular osmolarity. Consistently, tuning extracellular osmolarity or disrupting regulators of membrane tension and cell volume (mTORC1/2, NHEs, or VRAC ion channels) alters plasma membrane rupture and NETosis execution. In non-NETing U2OS cells, decompacting chromatin increases membrane tension, independently of the cytoskeleton, indicating a causal relationship between chromatin organization and membrane tension. This work shows chromatin as a regulator of whole-cell mechanics, broadening our understanding of the non-genetic roles of chromatin in cell pathophysiology.

DOI: https://doi.org/10.1038/s41467-026-76578-1
Cell. 2026 Sep 14. pii: S0092-8674(26)01004-4. [Epub ahead of print]

Programmed ribosomal frameshifting triggers translational stress to promote viral replication.

Audrey Xavier, Melinda Kolling, Ashley M Bourke, Thorsten Mosler, Cristian Prieto-Garcia, Emil Karaulanov, Michaela Reissland, Michel Tassetto, Damian Kim, Katleen Klaassen, Katharina Grikscheit, Emma Torbica, Verena Dederer, Jonas Busam, Rubina Kazi, Ruth Olmer, Srinivas Reddy Pallerla, Sebastian Mathea, Markus E Diefenbacher, Kathi Zarnack, Denisa Bojkova, Marek Widera, Ranen Aviner, Raul Andino, Sandra Ciesek, Ivan Dikic.

  Programmed ribosomal frameshifting (PRF) is a conserved viral strategy for expressing polyproteins from compact genomes. Although PRF is traditionally viewed as a structural mechanism, here we show that it functions as a regulatory signal that rewires host translation in favor of viral replication. A minimal SARS-CoV-2 PRF element is sufficient to activate the GCN2 arm of the integrated stress response (ISR) independently of the canonical ISR sensor ZAKα. This activation serves as a temporal switch during early infection to shut off host translation and is required for viral propagation in cells and human airway organoids. Proteomic and genetic screens identify DRG1 and IGF2BP3 as key mediators of PRF-induced GCN2 activation. We further show that this PRF-GCN2 axis is conserved in human immunodeficiency virus (HIV)-1 and West Nile virus, highlighting its broad relevance across RNA viruses. These findings reveal a sophisticated mechanism of viral translational control, highlighting PRF as a stress-inducing module that enhances viral replication.

Keywords:  RNA virus; cellular stress; host-pathogen interactions; integrated stress response; programmed ribosomal frameshifting; ribosome collision; translation; virology

DOI:  https://doi.org/10.1016/j.cell.2026.08.031
Sci Transl Med. 2026 Sep 16. 18(867): eaea2747

The molecular landscape of hypertrophic cardiomyopathy across disease stages and genotypes.

Eleonora Adami, Yuri Kim, Sean L Zheng, Nikolay Shvetsov, Corinna Losert, Henrike Maatz, Syndi Barish, Gabriela Venturini, Natalia López Anguita, Qi Shi, Meraj Neyazi, Martin Beyer, Eric Q Wei, Amanda Adam, Abhilash Suresh, Daniel Reichart, Eric Lindberg, Kemar J Brown, Viktoria Strohmenger, David Saul, Anna Gärtner, Michael Lee, Lukas Mach, Jan Lukas Robertus, Joshua M Gorham, Jan Haas, Laura A Liebig, Christoph Lippert, Benjamin Meder, Anna Myronova, Giannino Patone, Sam N Barnett, James S Ware, Fabio de Robertis, Antonis Pantazis, Jan Gummert, Anissa Viveiros, Huachen Chen, Jorge Ruiz-Orera, Norbert Frey, Barbara A McDonough, Richard N Mitchell, Robert F Padera, Sharlene M Day, Carolyn Y Ho, Neal K Lakdawala, Hendrik Milting, Matthias Heinig, Gavin Y Oudit, Michela Noseda, Jonathan G Seidman, Norbert Hübner, Christine E Seidman.

Hypertrophic cardiomyopathy (HCM) is marked by asymmetric cardiac wall thickening, hypercontractility, diastolic dysfunction, and fibrosis. Pathogenic sarcomere gene variants cause HCM, but comparable abnormalities occur in patients with unexplained disease, albeit with fewer adverse events. To investigate stage- and genotype-specific disease mechanisms, we performed single-nucleus RNA sequencing of cardiac tissues from 47 patients with HCM, spanning obstructive HCM with preserved systolic function and end-stage HCM, and compared them with nonfailing donor and dilated cardiomyopathy hearts. We identified transcriptional programs associated with cardiomyocyte hypertrophy, fibrosis, and vascular remodeling. Pathogenic variant-positive early-stage HCM samples showed reduced cardiomyocyte abundance and expansion of a proarrhythmogenic cardiomyocyte state. We identified proline-rich 16 (PRR16) as a cardiomyocyte growth-associated gene in HCM and validated its increased expression by RNA in situ hybridization and in a human induced pluripotent stem cell-derived cardiomyocyte HCM model. In HCM samples, fibroblast compositional shifts were associated with profibrotic activation and adverse extracellular matrix remodeling, accompanied by reduced collagen IV (COL4A1/COL4A2) expression and ultrastructural basement membrane abnormalities. HCM samples also exhibited extensive vascular alterations, including shifts in endothelial cell subpopulations, reduced pericyte abundance suggestive of microvascular dysfunction, and increased lymphangiogenic vascular endothelial growth factor C signaling. Unsupervised and supervised machine learning approaches distinguished HCM from dilated cardiomyopathy and accurately predicted genotype status in early-stage HCM from cell type-resolved transcriptional profiles, revealing widespread genotype-driven remodeling. Together, our findings uncover multicellular, genotype-associated remodeling programs in HCM, providing insight into mechanisms underlying arrhythmia, fibrosis, microvascular dysfunction, and heart failure progression.

DOI: https://doi.org/10.1126/scitranslmed.aea2747
Mol Cell. 2026 Sep 16. pii: S1097-2765(26)00590-3. [Epub ahead of print]

Cohesin preservation across mitosis contributes to restart transcription via Cdk9-mediated activation of RNAPol2.

Aida Contreras-Pérez, Héctor Espinosa, Estrella Isabel Sayago, Avik Basu, Andrew Emili, Michael D Blower, Carlos Perea-Resa.

  Cohesin organizes 3D genome architecture yet its acute depletion in vitro minimally affects transcription, leaving its regulatory role puzzling. We hypothesized that cohesin function is relevant when first encounters chromatin after mitosis. Using in vivo labeling and cell-cycle synchronization in human cells, we demonstrate that cohesin complexes persist through mitosis. This inherited pool dominates over newly translated cohesin during telophase-G1, highlighting the relevance of such transmission. Acute depletion of cohesin Rad21 at mitotic exit impairs the expression of hundreds of genes, mostly downregulated, enriched on functions related to tissue growth and development. Rad21 binds the promoter of this group of genes. Remarkably, we uncover a direct interaction during the M-G1 transition between Rad21 and Cdk9, the kinase component of transcription elongation factor b (pTEFb) complex. Rad21 loss impairs Cdk9 chromatin association, reducing active-elongating RNAPol2 at down-regulated genes. Overall, preserving cohesin across mitosis enables post-mitotic transcriptional reactivation via Cdk9, establishing tissue-specific expression programs.

Keywords:  RNA polymerase 2; cell cycle; cohesin; gene expression; mitosis; transcription

DOI:  https://doi.org/10.1016/j.molcel.2026.08.021
J Biol Chem. 2026 Sep 16. pii: S0021-9258(26)02435-X. [Epub ahead of print] 113563

EPS8 dampens the growth dynamics and prolongs the lifetime of actin-based protrusions.

Alexandra G Mulligan, Zachary J Lehmann, Kianna L Robinson, Matthew J Tyska.

  Actin-based membrane protrusions such as filopodia, microvilli, and stereocilia support a range of cell functions, from nutrient absorption to mechanosensation. In each case, membrane deformation is supported by a core bundle of actin filaments, organized in a unipolar 'barbed-end out' manner. Although their structures and proteomes are well characterized, mechanisms governing the growth and stability of these protrusions remain less clear. Factors that localize to the distal tips of these structures are of particular interest, as they are well positioned to control actin assembly at filament barbed ends. One such factor, EPS8, localizes to distal tip puncta in multiple protrusion types. While early biochemical studies suggested a role in filament capping, loss of EPS8 in multiple models shortened microvilli and stereocilia, suggesting roles in elongation. More recent studies in differentiating epithelial cells suggested that EPS8 promotes protrusion growth and stability. To clarify EPS8's function in the distal tip compartment, we leveraged acute loss-of-function experiments and titrated gain-of-function approaches in combination with live imaging. Acute sequestration of exogenous EPS8 led to rapid depletion of filopodia. Conversely, increasing cellular EPS8 levels elevated the amount of EPS8 per distal tip punctum, increased F-actin content within filopodia, reduced elongation rates, increased protrusion lifetimes, and protected filopodia against cytochalasin D-induced collapse. These findings suggest that EPS8 binds filament barbed ends as a 'leaky capper,' slowing monomer addition while stabilizing bundles and preventing collapse. These activities are likely critical for building and maintaining the large arrays of protrusions that are assembled by diverse epithelial cell types.

Keywords:  actin; bundle; cell biology; cytoskeleton; membrane; microscopy; protrusion

DOI:  https://doi.org/10.1016/j.jbc.2026.113563
Nat Commun. 2026 Aug 20. pii: 9953. [Epub ahead of print]17(1):

Hypoxia-activated scleraxis a mediates epicardial progenitor differentiation into a unique cardiac perivascular cell type.

Björn Perder, Yu Xia, Jun Yao, Ignace Van der Wee, Miaoyan Qiu, Alvin Gea Chen Yao, Muhammad Naeem, Paul Zumbo, Avi Yakubov, Stephanie L Tsai, Kazu Kikuchi, Jenna L Galloway, Doron Betel, Todd Evans, Michael R M Harrison, Jingli Cao.

The epicardium provides progenitor cells and paracrine signals essential for heart development and regeneration, yet the mechanisms regulating epicardial cell fate remain poorly understood. Here, we identify the transcription factor Scleraxis a (scxa) as a key regulator of epicardial progenitor differentiation in zebrafish. Single-cell transcriptomics, genetic lineage tracing, and cardiac injury models reveal transient scxa expression in activated epicardial progenitor cells (aEPCs) during developmental coronary angiogenesis and heart regeneration. scxa+ epicardial cells predominantly differentiate into a previously uncharacterized col18a1a+ perivascular population, termed epicardial-derived perivascular mesenchymal cells (Epi-PMCs), which is distinct from pericytes, vascular smooth muscle cells, and mammalian adventitial fibroblasts. Epi-PMCs closely associate with coronary vessels and may contribute to vascular stabilization and remodeling, potentially through collagen XVIII. Loss of scxa increases coronary vessel density. Hypoxia and Hif signaling induce scxa expression, identifying a hypoxia-responsive mechanism that promotes epicardial differentiation toward a vascular-supportive fate during heart development and regeneration.

DOI: https://doi.org/10.1038/s41467-026-77008-y
Nat Metab. 2026 Sep 15.

Cysteine excess triggers a mitochondrial iron-dependent cell death.

Toshitaka Nakamura, Ayaka Inoki, Nupur K Das, Brandon Chen, Artem Khan, Yuyang Liu, Beste Uygur, Frederick S Yen, Gokhan Unlu, Yatrik M Shah, Kıvanç Birsoy.

Thiol-containing metabolites are central to cellular redox homeostasis1. Among these, cysteine functions as a proteogenic amino acid, supports redox balance and iron-sulfur cluster biogenesis, and, when depleted, triggers ferroptosis2. Cells nevertheless maintain cysteine at low levels, reflecting its intrinsic toxicity, but the mechanisms by which excess cysteine causes cell death remain unclear3. Here we performed a genome-wide CRISPR screen and identified mitochondrial iron transporters as essential mediators of cysteine toxicity. Limiting mitochondrial iron availability suppresses cysteine-induced cell death and prevents impairment of iron-sulfur cluster proteins and respiration. Mechanistically, cysteine mobilizes iron from ferritin, expands the cytosolic iron pool and drives mitochondrial iron accumulation. Enhancing glutathione reductase activity specifically within mitochondria restores redox balance downstream of iron accumulation and protects cells by maintaining iron-sulfur cluster integrity. Our findings suggest that maintaining low cysteine levels safeguards mitochondrial iron homeostasis, and that excess cysteine triggers a distinct mitochondrial iron-dependent cell death under conditions of thiol imbalance.

DOI: https://doi.org/10.1038/s42255-026-01616-7
Elife. 2026 Sep 14. pii: RP97321. [Epub ahead of print]13

Sarcomere dynamic instability and stochastic heterogeneity drive robust cardiomyocyte contraction.

Daniel Haertter, Lara Hauke, Til Driehorst, Kengo Nishi, Wolfram H Zimmermann, Christoph F Schmidt.

  Cardiac contraction is driven by the collective action of cardiomyocytes (CMs) that contain parallel bundles of myofibrils consisting of linear chains of sarcomeres, the basic force-generating units. The dynamics of individual sarcomeres within intact CMs remain incompletely understood. While most models assume uniform, synchronized contractions, recent studies hint at unexpected heterogeneity, whose origins and significance are not yet clear. By combining the culture of fluorescent sarcomere-reporter human induced pluripotent stem cell-derived CMs on micropatterned soft gels of different stiffness (5-85 kPa) with AI-based tracking of sarcomere motion, we found that increasingly stiff substrates inhibited overall CM contraction, but, surprisingly, did not diminish individual sarcomere dynamics. Instead, sarcomeres competed in a tug-of-war, causing increasing heterogeneity, including rapid length oscillations and overextensions (popping). Statistical analysis showed that the heterogeneous dynamics were not caused by static structural differences but were largely stochastic. Stochastic heterogeneity is thus an intrinsic property of cardiac sarcomeres and likely mediates the adaptation of CM contractility to mechanical constraints. A mesoscopic model of coupled sarcomeres shows that these phenomena can be explained by a non-monotonic force-velocity relationship and stochastic fluctuations, where dynamic instability at a critical yielding force creates heterogeneity. Stochastic heterogeneity compensates for structural disorder by randomizing yield events beat-to-beat, preventing damage to specific sarcomeres. Our findings recast cardiac sarcomeres as active, dynamically unstable, and stochastic units engaged in a stochastic tug-of-war, where transient, velocity-dependent forces dominate. We propose that pathological disorder in cardiomyopathy drives a transition from protective stochastic fluctuations to more deterministic, persistently overloaded sarcomeres.

Keywords:  cardiomyocytes; cell biology; dynamic instability; force–velocity relationship; human; physics of living systems; sarcomere popping; stochastic heterogeneity; tug-of-war

DOI:  https://doi.org/10.7554/eLife.97321
Nature. 2026 Sep 16.

Cohesin reshapes replication fork contacts to aid fork slowing and reversal.

Daniel González-Acosta, Daniel Giménez-Llorente, Melani Rodrigues, Moses Aouami, Orhi Barroso-Gomila, Javier Muñoz, Ana Cuadrado, Ana Losada, Massimo Lopes.

DNA replication forks can be challenged by cancer chemotherapeutic treatments, leading to accumulation of single-stranded DNA and slowdown of DNA synthesis. The marked plasticity of replication forks under replication stress ensures fork stability, damage tolerance and complete genome duplication1. Initiation and progression of replication forks occur in a three-dimensionally organized genome. DNA loop extrusion by the cohesin complex organizes the genome2 and regulates the initiation and positioning of DNA replication origins3,4. Although transient interaction of sister forks was recently reported during unperturbed replication5, the functional relevance of fork contacts during replication stress and the role of cohesin in this context remain unknown. Here we show that cohesin-mediated loop extrusion rearranges nascent DNA contacts at stressed replication forks to promote genome stability. Using auxin-inducible degron6, separation-of-function mutants7-9 and a newly developed Micro-C-based technique to capture chromatin contacts at nascent DNA (Repli-C), we found that loop-extruding cohesin accumulates at stalled replication forks, limiting sister-fork coupling in favour of inter-replicon contacts. This process promotes active fork slowing and reversal by preventing PRIMPOL action on single-stranded DNA1. These findings show that the replication stress response is not merely an accumulation of individual regulatory events, but is topologically integrated across the genome through cohesin loop extrusion. While providing a new function for loop-extruding cohesin, our results indicate the potential impact on cancer therapy of frequent cohesin mutations in tumours10.

DOI: https://doi.org/10.1038/s41586-026-11034-0
Nat Cardiovasc Res. 2026 Sep 15.

Age-associated loss of lymphatic vessels promotes cardiac inflammation.

Julian U G Wagner, Hamza Gulshan, Ibrahim Sultan, Salli Antila, Laia-Canes Esteve, David Rodriguez Morales, Mariano Ruz Jurado, David John, Emmanouil G Solomonidis, Katja Schmitz, Josefine Panthel, Haris Kujundzic, Susanne Hille, Oliver J Müller, Christoph Kugler, Haider Sami, Manfred Ogris, Simone-Franziska Glaser, Wesley T Abplanalp, Tara Procida-Kowalski, Marek Bartkuhn, Evelyn Ullrich, Marion Muhly-Reinholz, Sarmad Ahmad Khan, Tarik Bozoglu, Christian Kupatt, Florian Buettner, Jochen Pöling, Thomas Braun, Kari Alitalo, Stefanie Dimmeler.

Aging is a major risk factor for cardiovascular disease, but the role of the cardiac lymphatic vasculature in this process remains poorly understood. Here we show that aging reduces cardiac lymphatic vessel density in humans and mice and induces structural remodeling characterized by tighter, zipper-like endothelial junctions. These changes are associated with immune cell infiltration, fibrinogen and amyloid accumulation, and myocardial edema. Selective reduction of cardiac lymphatics in young mice, through Flt4 (VEGFR3) depletion or soluble Flt4 overexpression, recapitulates key features of cardiac aging, including inflammation and impaired lymphatic integrity. Mechanistically, aging induces selective upregulation of nuclear interleukin-33 (IL-33) in lymphatic endothelial cells. Unlike extracellular IL-33, nuclear IL-33 promotes lymphatic endothelial cell death and junctional remodeling. We identify VEGFC as an age-sensitive regulator that declines with aging and suppresses IL-33. Cardiac Vegfc overexpression or Il33 silencing restores lymphatic density and tissue homeostasis in aged hearts, identifying a potential therapeutic target for age-related cardiac dysfunction.

DOI: https://doi.org/10.1038/s44161-026-00870-y
Nat Cell Biol. 2026 Sep 15.

DFCP1-containing ER microdomains mediate lysosomal membrane repair.

Maja Radulovic, Sascha Pust, Athanasios Kournoutis, Di Chen, M Isabel Giner, Qijian Liang, Santosh Phuyal, Thomas J Böddeker, Katy McCarron, Eric Herrmann, Kevin Rose, Sebastian W Schultz, Andreas Brech, James H Hurley, Claudio Bussi, Luis Bonet-Ponce, Maximiliano G Gutierrez, Camilla Raiborg, Harald Stenmark.

Lysosomal membrane integrity is essential for preserving cellular homeostasis in response to different stressors. Upon lysosomal membrane permeabilization, cells activate several mechanisms for lysosomal membrane repair, including ESCRT proteins, phosphatidylinositol 4-phosphate (PI4P)-dependent lipid transfer from the endoplasmic reticulum (ER) and conjugation of ATG8 family proteins to single membranes (CASM). The interplay between these pathways and the regulation of the lipid transfer machinery remain incompletely understood. Here we show that phosphatidylinositol 3-phosphate (PI3P)-containing ER domains play a major role in lysosomal membrane repair. PI3P is formed on lysosome-proximal ER domains by the phosphatidylinositol 3-kinase PIK3C3/VPS34 in response to membrane damage, and inhibition or depletion of PIK3C3 inhibits lysosome repair. Mechanistically, the ATPase DFCP1/ZFYVE1 accumulates on lysosome-proximal ER domains by its PI3P binding, triggered by Ca2+ efflux from lysosomes and requiring the ULK1 kinase complex and ER proteins of the VAP family. Downstream of CASM, PI4P, ESCRTs and PI3P, DFCP1 promotes focal accumulation of the lipid channel VPS13C on ER domains proximal to damaged lysosomes to promote their repair. The function and dynamics of DFCP1 depend on its ability to bind and hydrolyse ATP, and absence of DFCP1 compromises cellular resistance to vacuolar damage induced by Listeria monocytogenes. We conclude that DFCP1 mediates concentration of the ER-associated lipid transport machinery at damaged lysosomes to promote their sealing in response to Ca2+ flux and PIK3C3 activation.

DOI: https://doi.org/10.1038/s41556-026-02062-z
Nat Protoc. 2026 Sep 15.

Quantitative imaging of dynamic processes in intestinal organoids.

Willem Kasper Spoelstra, Xuan Zheng, Rutger N U Kok, Guizela Huelsz-Prince, Max Betjes, Pascal Ender, Yvonne Goos, Kim A Kuentzelmann, Heidi E Klumpe, Daniel Krueger, Daisong Wang, Hans Clevers, Sander J Tans, Jeroen S van Zon.

Organoids are powerful models for studying tissue dynamics across multiple cellular generations and offer key insights into organ homeostasis, cellular differentiation and disease. Live imaging of organoids is an essential tool for understanding dynamic processes on the cell level, while still in the tissue context. It allows for simultaneous quantification of gene expression and reconstruction of lineage trees, while tracking cells over space and time. Here, we present protocols for long-term imaging and quantitative analysis of intestinal organoids. Our workflow consists of sample preparation, experimental manipulations (such as drug treatments, laser ablations and fluorescence recovery after photobleaching), long-term live imaging (120 h), in situ fixation and permeabilization, multiplexed antibody staining and single-cell tracking with lineage reconstruction. The workflow is broadly applicable to studying dynamic cellular processes in both 2D and 3D organoids, at timescales from minutes to days. We outline strategies for optimizing organoid health, imaging conditions and experimental interventions to ensure efficient downstream analysis. In addition, we describe how this workflow enables real-time quantification of gene expression using fluorescent reporters and inferring cell type changes by combining multiplexed antibody staining with cell-tracking data. The skills required for following these protocols are organoid culturing and standard live-cell confocal microscopy, and the full experimental protocol takes ~2 weeks. Together, these protocols provide a comprehensive approach for studying cellular behavior, lineage trees, expression dynamics and cell-cell interactions in organoids.

DOI: https://doi.org/10.1038/s41596-026-01432-z
Nature. 2026 Sep 15.

Quality control of glycogen through direct ubiquitylation by RNF213.

Matthew C J Yip, Katerina Naydenova, Elsje G Otten, Alexander Heatley, Agnes Moe, Leonie Anton, Lucía de Los Reyes-Ramírez, Helen E Jolin, Frederic Langevin, Michal Wiacek, Catarina Franco, Anne Bertolotti, Wanda Kukulski, Andrew N J McKenzie, Felix Randow.

Quality control of biomolecules is vital for organismal health. While DNA repair and protein quality control are well understood, how cells monitor other important biomolecules such as glycogen remains ill-defined. The accumulation of aberrant, poorly branched glycogen into insoluble polyglucosan bodies causes severe disease1,2. Here, we discover autophagy of ubiquitylated aberrant glycogen as a previously unrecognized quality control mechanism safeguarding the brain from polyglucosan buildup. This mechanism depends on the E3 ubiquitin ligase RNF213. Mice lacking ligase activity in RNF213 accumulate polyglucosan in cerebellum, pons, and hippocampus. Using cells engineered to produce polyglucosan, we show that RNF213 selectively ubiquitylates abnormal glycogen. Cryo-EM analysis of RNF213 bound to glycogen-derived maltoheptaose revealed its CBM20 domain binds linear oligosaccharides. Disrupting carbohydrate binding results in gain of E3 ligase activity towards physiological glycogen, indicating the CBM20 domain limits RNF213 activity towards physiological glycogen. Epistasis analysis places RNF213 upstream of LUBAC, suggesting a hierarchical network of multiple E3 ligases surveying glycogen quality. Ubiquitylated polyglucosan recruits the autophagy receptors SQSTM1, TAX1BP1, and optineurin, thereby triggering uptake into autophagosomes. These findings identify RNF213 as a quality control factor preventing polyglucosan accumulation in astrocytes through direct ubiquitylation of polyglucosan, revealing an essential role for non-protein ubiquitylation in glycogen quality control.

DOI: https://doi.org/10.1038/s41586-026-11139-6
Nat Neurosci. 2026 Sep 18.

Two parallel neural ectoderm progenitors contribute to the developing brain.

Rayyan T Jokhai, Carolyn E Dundes, Hadia S Ahsan, Rachel S Kang, Rachel E A Salomon-Shulman, Arjun Rajan, Yoon Seok Kim, Liam J Stanton, Christine Xu, Stephanie Do, Brennan D McDonald, José Miguel Andrade López, Hugo A Urrutia, Hannah Greenfeld, Alicia Wong, Yimiao Qu, Andrew S Petkovic, Yi Miao, K Christopher Garcia, Michelle Monje, Daniel E Wagner, Marianne E Bronner, Christopher J Lowe, Kyle M Loh.

When and how different brain regions diversify from one another remains unresolved. Does a common neural ectoderm progenitor generate the entire brain? Or do multiple neural ectoderm progenitors exist, each restricted to form specific brain regions? Here our lineage tracing studies of mouse embryos support the latter model. Two parallel brain progenitors emerge simultaneously during gastrulation: anterior neural ectoderm (forebrain/midbrain progenitor) and posterior neural ectoderm (hindbrain progenitor). Differentiation of human pluripotent stem cells into anterior or posterior neural ectoderm-like cells revealed these were lineage committed to forebrain/midbrain versus hindbrain fates, respectively. They harbored diverging chromatin landscapes foreshadowing future forebrain/midbrain versus hindbrain identities. We further differentiated human pluripotent stem cells into hindbrain rhombomere 5/6-specific motor neurons, which were hitherto difficult to generate in vitro. Hence, we postulate the brain is a composite organ emanating from two lineage-restricted progenitors; these dual progenitors may be evolutionarily conserved across 550 million years from hemichordates to mammals.

DOI: https://doi.org/10.1038/s41593-026-02433-7
Sci Adv. 2026 Sep 18. 12(38): eaeh8258

GTPase cycle and ER membrane regulate cargo handover during cotranslational protein targeting.

Ruilin Qian, Radoslaw J Gora, SangYoon Chung, Jae Ho Lee, Sowmya Chandrasekar, Max Feng-Yu Wang, Shimon Weiss, Shu-Ou Shan.

Signal recognition particle (SRP), a universally conserved protein-targeting machine, cotranslationally recognizes signal sequences of nascent endomembrane proteins and engages the SRP receptor (SR) at the endoplasmic reticulum (ER) membrane to unload the translating ribosome. The mechanism of membrane-associated steps in this pathway remains unclear. Here, we address this question using pre-steady-state and single-molecule fluorescence measurements. SR induces release of the signal sequence from SRP and detachment of the SRP guanosine triphosphatase (GTPase) domain from the ribosome. Despite the dissolution of these contacts, SR acts as a tether to stabilize SRP association with the ribosome. Guanosine 5'-triphosphate (GTP) hydrolysis in the SRP-SR complex abolishes this stabilizing effect to facilitate ribosome-nascent chain complex (RNC) release from SRP. The ER membrane selectively promotes a prehandover conformation of the RNC-SRP-SR complex, in which delayed GTP hydrolysis optimizes the transition from targeting to translocation. Our findings provide a high-resolution model for key steps during cargo handover at the ER and highlight the critical role of fine-tuned GTPase activity in the SRP pathway.

DOI: https://doi.org/10.1126/sciadv.aeh8258
Nat Commun. 2026 Aug 20. pii: 9945. [Epub ahead of print]17(1):

Accelerating protein design by scaling experimental characterization.

Jason Qian, Lukas F Milles, Basile I M Wicky, Robert J Ragotte, Amir Motmaen, Andrew J Borst, Rebecca Skotheim, Sebastian Ols, Brian Coventry, Xinting Li, Ryan D Kibler, Inna Goreshnik, Marc Expòsit, Karin Loré, Lance Stewart, David Baker.

Recent advances in de novo protein design have greatly outpaced standard protein biochemistry workflows, making experimental validation a bottleneck. Here, we describe workflows to address the scale, speed and reproducibility of common in vitro protein testing methods, enabling at least an order of magnitude increase in throughput while reducing wetlab time. Semi-Automated Protein Production (SAPP) is a rapid, modular, scalable and cost-effective protocol, enabling up to milligram-scale protein production and standardized characterization - including yield, dispersity, and oligomeric state - of hundreds of designs per day, at the cost-equivalent of a few DNA oligos per construct. End-to-end protocol execution takes 48 hours, with ~6 hours spent benchside using standard laboratory equipment. We showcase the platform by rapidly screening redesigned fluorescent proteins, as well as identifying de novo binders that potently neutralize respiratory syncytial virus. We also developed a barcoding and demultiplexing protocol (DMX) to further reduce gene synthesis cost 5-fold by leveraging oligo pools as input DNA for the generation of thousands of sequence-verified arrayed clones. These protocols which combine optimized molecular biology, automated analysis, and optional open-source robotics should be widely adoptable, accelerating protein design.

DOI: https://doi.org/10.1038/s41467-026-76740-9
Nature. 2026 Sep 09.

Highly efficient base editing at PCSK9 and normal human embryo development.

Stepan Jerabek, Chanju Jung, Michelle Kappy, Qiaojin Zhao, Julie Sung, Ning Wang, Euihyun Kim, Jimin Kim, Marcos Iuri Roos Kulmann, Madeleine Bliss King, Mitchell John McAndrew, Meng Li, Sakshi Bhatele, Melisa Isado, Hong-Su Jang, Michal Dolezal, Robert Prosser, Shuangyi Xu, Gue-Ho Hwang, Iva Pichova, Jia Xu, Diego Marin, Jae-Sung Woo, Sangsu Bae, Nathan Treff, Audrone Lapinaite, Dieter Egli.

Cas9-based tools enable programmable DNA lesions for studying repair outcomes, gene function, and genome correction. In human embryos, Cas9-induced DNA double-strand breaks are genotoxic, causing frequent aneuploidy and large deletions1,2. Here, we evaluate DNA repair outcomes at nicks and mismatches introduced by base editors at the PCSK9 and HBG loci in human embryos. Delivering ABE8e-V106W as a protein at fertilization achieved editing at all PCSK9 alleles, supporting development to the blastocyst stage and the derivation of homozygous edited stem cell lines. No insertions or deletions were detected, although rare on-target chromosome breakage and chromosomal abnormalities occurred. Nevertheless, editing at bystander and off-target sites was mosaic, and the introduction of the editor as mRNA caused frequent embryo arrest due to guide-independent deaminase activity. Thus, unlike Cas9-induced DNA breaks, base editor-induced lesions are efficiently repaired. However, undesirable consequences for the genome and development can occur, currently precluding clinical use in reproduction.

DOI: https://doi.org/10.1038/s41586-026-11118-x
Proc Natl Acad Sci U S A. 2026 Sep 22. 123(38): e2608171123

ACTA2-directed actin filaments license STING trafficking and activation for antiviral immunity and autoimmune pathogenesis.

Xianteng Hou, Qing Wu, Yangting Du, Changwan Wang, Junyan Zhu, Yingbo Jiang, She Chen, Lisha Zhou, Xiaoyu Wu, Hongyan Wang, Hui Yang, Fajian Hou.

  The cyclic GMP-AMP synthase-stimulator of interferon genes (STING) pathway is essential for antiviral immunity, and its dysregulation causes inflammatory disease. The mechanism underlying STING activation, including its essential endoplasmic reticulum-to-Golgi translocation, has remained elusive. Here, we identify a dedicated actin-based transport system licensed by the smooth muscle actin isoform ACTA2 via in vitro reconstitution. Superresolution live imaging reveals STING becomes punctate and activated while moving along ACTA2 filaments. This ACTA2-directed network is required for antiviral interferon responses against HSV-1. Strikingly, it also drives pathological interferon production and lethal autoimmunity in Trex1-/- mice, where its genetic or pharmacological disruption rescues disease. Furthermore, ACTA2 expression correlates with proinflammatory cytokine levels in peripheral blood mononuclear cells from systemic lupus erythematosus patients, and its downregulation ameliorates this inflammatory signature. Our work defines a specific cytoskeletal network that governs STING-dependent inflammatory responses to both foreign and self-DNA, thereby establishing stimulus-directed organelle trafficking as a central control point in innate immune signaling.

Keywords:  ACTA2; autoimmunity; cGAS-STING; innate immunity; microfilament

DOI:  https://doi.org/10.1073/pnas.2608171123
Circulation. 2026 Sep 15.

Dysregulated Ribonucleoprotein Granules Impair Mitochondrial Function in RBM20-Related Dilated Cardiomyopathy.

Julia Kornienko, Linda H Müller, Alexander Nickel, Michael Kohlhaas, Mandy Börmel, Carlos Alfonso-Gonzalez, Viola M J Oorschot, Michel Fungate, Susanne Lewey, Jacob Kees, Johanna Müller, Dominik Lindenhofer, Kai Fenzl, Laura Schraft, Sandra Clauder-Münster, Laura Konrad, Per Haberkant, Frank D M Montoya, Vita Dauksaite, Michael Gotthardt, Maarten M G van den Hoogenhof, Christoph Maack, Lars M Steinmetz.

   BACKGROUND: Pathogenic variants in RBM20 cause severe dilated cardiomyopathy. Loss-of-function variants disrupt splicing; neomorphic gain-of-function (GoF) variants also mislocalize RBM20 to cytoplasmic ribonucleoprotein granules and are associated with more aggressive disease. The mechanism by which RBM20 mislocalization drives cardiac dysfunction remains unknown.
METHODS: We investigated the effects of Rbm20 GoF and loss-of-function (LoF) variants using proteomic profiling, protein solubility assays, mitochondrial respiration and calcium flux analyses, and ultrastructural imaging in mouse models. Human induced pluripotent stem cell-derived cardioids were used to validate variant-specific phenotypes.
RESULTS: Rbm20 GoF, but not LoF, variants caused posttranscriptional downregulation of soluble mitochondrial proteins, including the calcium efflux regulator TMEM65 (transmembrane protein 65), and reduced solubility of mitochondrial membrane proteins. Electron microscopy revealed enlarged mitochondria with cristae disorganization. Functional assays confirmed impaired oxidative phosphorylation, reduced mitochondrial membrane potential, and abnormal calcium handling in Rbm20 GoF models. Human cardioids reproduced these findings, demonstrating that cytoplasmic mislocalization, rather than splicing deficiency, drives mitochondrial dysfunction.
CONCLUSIONS: Cytoplasmic mislocalization of RBM20 disrupts mitochondrial function by reducing mitochondrial protein abundance, leading to oxidative phosphorylation failure and abnormal mitochondrial calcium handling. This mechanism distinguishes RBM20 GoF from LoF variants and may explain the more severe heart failure phenotype observed in patients with RBM20 GoF variants. These insights advance the mechanistic understanding of RBM20-related cardiomyopathy and identify mitochondrial mRNA/protein regulation as a key node in cardiac energetics.

Keywords:  cardiomyopathy, dilated; metabolism; mitochondria, heart; mitochondrial diseases; precision medicine; ribonucleoproteins

DOI:  https://doi.org/10.1161/CIRCULATIONAHA.125.077061
Proc Natl Acad Sci U S A. 2026 Sep 22. 123(38): e2531822123

FAP53 facilitates formation of microtubule doublets.

Ming Li, Guanghan Chen, Zhe Chen, Zhengyang Guo, Zi Wang, Yongping Chai, Wei Li, Guangshuo Ou.

  The formation of microtubule doublets (MTDs) is a foundational step in cilia biogenesis, yet how B-tubule nucleation is initiated at the molecular level remains elusive. Here, we identify FAP53 as a factor that facilitates B-tubule assembly in a scaffold-dependent manner. In vitro reconstitution demonstrated that recombinant FAP53 enhances MTD formation in the presence of preassembled microtubule scaffolds, but is insufficient to drive de novo assembly from free tubulin alone. In cultured HeLa cells, coexpression of CFAP53 and CFAP20-an inner junction protein-induced ectopic MTD-like structures in the cytoplasm. Furthermore, we identified a structurally homologous protein in Caenorhabditis elegans, WFAP-53, which localized to sensory cilia. Loss of wfap-53 does not abolish MTD formation in vivo, but its overexpression triggered ectopic MTD formation in neuronal dendrites and concomitantly led to sensory cilia disassembly. Molecular dynamics simulations suggested that FAP53 could stabilize B-tubule docking at the A-tubule surface. These findings uncover a conserved mechanism of B-tubule initiation and underscore the necessity for spatially restricted expression of MTD assembly factors during ciliogenesis.

Keywords:  FAP53; microtubule doublets; reconstitution

DOI:  https://doi.org/10.1073/pnas.2531822123
Cell. 2026 Sep 14. pii: S0092-8674(26)01003-2. [Epub ahead of print]

Copper ion-induced MYH9 polymerization executes cuproptosis.

Liu-Zheng Wu, Xiang-Yu Mi, Zai-Jun Liu, Yang Ding, Wen-Bin Hong, Chen-Xi Cai, Hai-Jing Hu, Yuan-Li Ai, Bi-Xing Zhao, Duo-Duo Qiu, Jing-Song Ma, Xue-Qin Chen, Han You, Tianwei Lin, Fu-Nan Li, Xue-Hui Hong, Hang-Zi Chen, Qiao Wu.

  Cuproptosis is a recently identified form of copper-dependent cell death implicated in various physiological and pathological processes. However, the executive proteins involved and the role of physiological intracellular copper in cuproptosis remain unclear. Herein, we identified myosin heavy-chain 9 (MYH9) as a cuproptosis executioner. Copper binding induced MYH9 polymerization, which disrupted the actin cytoskeleton and led to cuproptotic cell death. Hexyl 2-(3,4,5-trihydroxy-phenyl) acetate (HThPA) was shown to induce cuproptosis by binding to the nuclear receptor Nur77, leading to depletion of copper chelate glutathione (GSH) and release of free copper from intracellular copper stores. Acetylation of MYH9 by acetyltransferase dihydrolipoamide S-acetyltransferase (DLAT) facilitated copper binding, regardless of its extracellular or intracellular origin. Physiological copper levels were higher in drug-resistant tumor cells and clinical samples, which increased the likelihood of HThPA-induced cuproptosis. These results elucidate the mechanisms underlying cuproptosis, establish MYH9 as an executioner, and propose a treatment strategy for drug-resistant tumors.

Keywords:  MYH9 polymerization; compound HThPA; cuproptosis; extracellular and intracellular copper; hexyl 2-(3,4,5-trihydroxy-phenyl) acetate

DOI:  https://doi.org/10.1016/j.cell.2026.08.030
Nature. 2026 Sep 14.

Encoded and non-genetic protein variants expand human functional proteome.

Vyacheslav Tretyachenko, Tehila Leiman, David Morgenstern, Yishai Levin, Omer Asraf, Orna Dahan, Dvir Dahary, Yitzhak Pilpel.

Each stage of the Central Dogma contributes to proteome diversity through mechanisms such as heterozygosity, somatic mutations, transcriptional errors, and translational errors. As a result, a diverse array of protein variants can coexist within a single proteome, such as that of humans. However, until now, methods to detect, quantify, and evaluate the functional consequences of these variants have been lacking. Here we examined a large-scale proteogenomic dataset from 29 healthy human tissues and uncovered 13,910 confidently localized variants representing 7,215 unique single amino acid substitutions co-existing alongside their corresponding reference proteoforms 1.We found that the abundance of both genetic (SNP's, somatic mutations) and mistranslated protein variants mirrors their allele frequencies in the human population. Moreover, we show that non-genetic substitutions may provide a distinct route for exploring protein sequence space, circumventing the mutational constraints imposed by the genetic code. In addition, we provide experimental validation of non-genetic substitution on selected purified proteins. We demonstrate specific and recurring non-genetic variation patterns upon amino acid starvation in proteome-wide analyses of cancer-derived cell lines and identify hundreds of substituted non-genetic proteoforms that recur consistently in multiple healthy individuals or map to annotated protein functional sites. We propose that these substitutions constitute a novel class of functional protein phenotypic variants. Collectively, our findings indicate that non-genetic amino acid substitutions in human proteins provide an abundant source to expanding the functional proteome.

DOI: https://doi.org/10.1038/s41586-026-11124-z
Nat Commun. 2026 08 19. pii: 9901. [Epub ahead of print]17(1):

CK2α restriction of STING accumulation underlies systemic aging.

Jie Zhang, Meiling Jin, Dan Rao, Ming Wang, Jing Wang, Canjie Ma, Lanlan Rao, Yanzhen Mo, Baohua Liu, Zimei Wang, Ying Ao.

Chronic activation of the cGAS-STING pathway drives inflammaging and cellular senescence. Although nuclear envelope (NE) barrier failure leading to cytoplasmic chromatin leakage is a key trigger, the molecular mechanisms governing STING activity at the NE during aging remain poorly understood. Here, we identify lamin A/C (LMNA) as a critical NE scaffold that orchestrates STING regulation by recruiting both STING and Casein Kinase 2 (CK2α). We demonstrate that LMNA facilitates the phosphorylation of STING at Ser366 by CK2α, which promotes STING turnover and restricts its accumulation, thereby attenuating pathway activation and mitigating senescence in myeloid cells as well as systemic aging. Strikingly, pharmacologic STING inhibition in vivo robustly rescues progeroid phenotypes-including loss of bone density and multi-tissue senescence-and extends lifespan in progeroid mouse models. Moreover, H-151 treatment also ameliorates the premature aging phenotypes induced by myeloid-specific CK2α ablation. In contrast, constitutive STING ablation yields limited survival benefits, revealing that controlled attenuation of STING signaling, rather than complete elimination, drives therapeutic efficacy. Our findings establish the LMNA-CK2-STING axis as a key biochemical mechanism that suppresses innate immune activation at the NE, offering a promising strategy for ameliorating aging and progeroid pathologies.

DOI: https://doi.org/10.1038/s41467-026-76351-4
Curr Opin Immunol. 2026 Sep 17. pii: S0952-7915(26)00115-9. [Epub ahead of print]103 102838

Cellular stress leading to epithelial cell dysfunction in Sjögren's syndrome.

María-José Barrera, Isabel Castro, María-Julieta González.

Cells are highly compartmentalized entities composed of membranous and nonmembranous structures, where organelles such as the endoplasmic reticulum (ER), Golgi apparatus, nucleus, mitochondria, lysosomes, peroxisomes, endosomes, and plasma membrane are organized. The plasma membrane physically and functionally connects the cytoplasm to the extracellular matrix, thereby generating a microenvironment that allows for the development of all the metabolic demands necessary to maintain cellular homeostasis. Salivary gland epithelial cells (SGECs, acinar and ductal) from Sjögren's syndrome (SS) patients undergo structural changes leading to loss of cell polarity and disrupted barrier function, resulting in severe alterations in the architecture of acini and ducts, which are sensed by their subcellular organelles as a condition of stress. The cellular stress response is a defensive mechanism that occurs when a cell loses its homeostasis due to internal or external factors. This response is organized into three sequential components: sensors detect the damage, the signaling cascade transmits the alarm, and effectors execute the adaptive action. One of these adaptive mechanisms is the integrated stress response, which is activated by various stress-inducing factors to adjust protein biosynthetic rates and redirect resources to mitigate stress and restore cellular homeostasis. Another adaptive mechanism is the unfolded protein response, which is activated by the accumulation of unfolded/misfolded proteins to restore ER proteostasis. Altered lysosomes, the Golgi apparatus, and mitochondria can also trigger stress. This review briefly discusses some cellular stress response pathways activated in SGECs, highlighting the perpetuating loop between inflammation and cellular stress in SS.

DOI: https://doi.org/10.1016/j.coi.2026.102838
Nat Protoc. 2026 Sep 11.

Generation of eight-cell embryo-like cells from human pluripotent stem cells.

Md Abdul Mazid, Yunpan Li, Mindie Zhao, Lixin Fu, Hao Liu, Yu Jiang, Wenqi Jia, Junjian Lai, Jinxiu Li, Haiwei Li, Babangida Jabir Saeed, Amash Manzoor, Zhiwei Luo, Yiwei Lai, Liang Wu, Yi Zou, Chaiyaboot Ariyachet, Carl Ward, Chuanyu Liu, Longqi Liu, Miguel A Esteban, Wenjuan Li.

Mammalian embryonic development is a highly orchestrated process initiated by the fusion of the oocyte with sperm to generate the zygote. In humans, the zygote remains transcriptionally quiescent until the major wave of zygotic genome activation (ZGA) occurs around the eight-cell (8C) stage (day 3 after fertilization). These cells and the derived morula cells are totipotent: they have the capacity to form a whole individual. Our understanding of human totipotency is very limited because of ethical concerns using embryos and the scarcity of material available for research. Recently, we established a controllable transgene-free methodology to generate totipotent eight-cell embryo-like cells (8CLCs) from human pluripotent stem cells (PSCs) in vitro. These 8CLCs are produced using a novel medium, formulated by us, containing specific chemical compounds and cytokines. Here, we provide a detailed protocol for inducing, isolating and characterizing 8CLCs generated with this medium. The induction process can be done either in a stepwise manner (primed-naive-8CLC) that requires only 5 d starting from naive PSCs or directly from primed PSCs, which takes ~7 d. The resulting 8CLCs exhibit transcriptional and epigenetic features resembling those of human 8C embryo cells. On the basis of our experience, we expect that an individual with ~1 year of experience working with human PSC culture would be able to carry out this protocol. Our approach provides a valuable model for studying human early embryogenesis, particularly the molecular events surrounding ZGA.

DOI: https://doi.org/10.1038/s41596-026-01414-1
Dev Cell. 2026 Sep 18. pii: S1534-5807(26)00324-2. [Epub ahead of print]

Self-organizing human dual neural organoids model regional disease defects and teratogenicity.

Xiaoxiang Lu, Siyuan Chu, Jianfeng Wei, Jinkui Zhu, Wei Zhou, Yantong Liu, Xurui Feng, Xinrui Zhang, Mengqian Wang, Mingjuan Li, Jie Gao, Linlin Jiang, Wei Pang, Yao Yin, Ziling Chen, Yajing Cao, Qinzhi Zhang, Sisi Chen, Shaojie Ma, Yangfei Xiang.

  The human nervous system emerges during early embryogenesis through coordinated, self-organizing differentiation of peripheral and central lineages. A key event in this process is the emergence of neural crest from the dorsal neural tube, which gives rise to major peripheral nervous system (PNS) structures. However, current in vitro models face challenges in recapitulating this process, limiting mechanistic insights into human central-peripheral neurogenesis. Here, we report a method for generating human peripheral-central dual neural organoids (hPCOs), a self-organizing organoid system that recapitulates the co-development of peripheral sensory ganglia and dorsal spinal cord. Using hPCOs, we uncover an unexpected bidirectional role of Wnt signaling in orchestrating peripheral and central fate determination. Modeling with hPCOs reveals nociceptor defects in human congenital insensitivity to pain. Furthermore, integrating hPCOs with image analysis enables the visual assessment of teratogenic risks. Together, hPCOs provide a physiologically relevant platform for investigating human self-organized central nervous system (CNS)-PNS co-development, disease mechanisms, and drug discovery.

Keywords:  co-development; neural organoids; self-organization; sensory ganglion; spinal cord

DOI:  https://doi.org/10.1016/j.devcel.2026.08.013
Nat Cell Biol. 2026 Sep 15.

The Batten disease protein CLN8 is a stereospecific acyltransferase in bis(monoacylglycero)phosphate biosynthesis.

Pradeep K Sheokand, Denis Lacabanne, Andrew M James, Stefania Della Vecchia, Jonathan J Ruprecht, Joris van der Kleij, Keira Turner, Jessica Müller-Niva, Miia H Salo, Benjamin Jenkins, Susannah K Leese, Nidhi Juneja, Chak Shun Yu, Clarissa D Booth, Martin S King, Johanna Uusimaa, Jill M Weimer, Albert Koulman, Reetta Hinttala, Filippo M Santorelli, Maria Marchese, Michael P Murphy, Edmund R S Kunji, Kasparas Petkevicius.

Loss-of-function mutations in the endoplasmic reticulum membrane protein CLN8 cause Batten disease, a neurodegenerative lysosomal storage disorder. CLN8 acts with the lysosomal enzyme CLN5 to produce bis(monoacylglycero)phosphate (BMP), a signature lysosomal phospholipid with unique S,S stereochemistry. However, the role of CLN8 in this pathway has remained unclear. Here we establish that CLN8 is a glycerophosphoglycerol acyltransferase that catalyses the stereospecific acylation of S,S-glycerophosphoglycerol to generate S,S-lysophosphatidylglycerol, the CLN5 substrate in BMP synthesis. Cryo-electron microscopy structures define the CLN8 active site and support a ping-pong acyl transfer mechanism. Batten disease mutations impair CLN8 enzymatic activity and abolish BMP production in mice. Exogenous S,S-lysophosphatidylglycerol, but not the R,S stereoisomer, restores BMP synthesis in CLN8-deficient cells and mice and improves neurological phenotypes in cln8 mutant zebrafish. These findings define the function of CLN8, explain the biochemical basis of CLN8 Batten disease and establish BMP precursor supplementation as a proof-of-concept therapeutic strategy.

DOI: https://doi.org/10.1038/s41556-026-02061-0