bims-ginsta 2026-07-12 papers

bims-ginsta

Biomed News

on Genome instability

Issue of 2026–07–12
thirty-two papers selected by
Jinrong Hu, National University of Singapore

Embryo quality control via lineage-specific aneuploid cell elimination in embryos and stem cell-derived embryo models.
Mechanical constraints regulate embryonic stem cell mitosis in the developing brain.
Embryo models as experiments in self-organization: The logic of productive failure.
Modeling human embryo adhesion using a microfluidic platform.
Mechanosensing at the endoplasmic reticulum by IRE1.
Aneuploidy selects for the acquisition of driver genes in breast cancer.
Inorganic phosphate rapidly switches the stability of Arp2/3-induced actin branches.
PUMILIO proteins maintain lineage balance via post-transcriptional repression of germline fate and promotion of somatic differentiation.
CLASP-dependent microtubule stabilization generates microtubule-based protrusive forces during Drosophila epithelial morphogenesis.
Gata3 dosage governs primitive endoderm versus trophectoderm specification in embryonic stem cells.
Inhibition of lagging strand replication by G-rich telomeric DNA and the shelterin subunit POT1.
Dynamic integration of morphogen and juxtacrine signaling specifies cell fate at single-cell resolution.
Decoding stage-specific functions of PRC2 in early embryogenesis uncovers roles in preimplantation development and primordial germ cell fate.
Alterations in chromatin organization promote totipotent-like features in a DPPA2/DUX-dependent manner.
Molecular profiling of the single-cell proteome via gel electrophoresis and 3D single-molecule imaging.
CD44 restricts EGFR mobility to polarize cytoskeletal signalling modules driving bleb-based migration.
Cytoplasmic lattices store developmentally poised degradative and cytoskeletal complexes in mammalian eggs.
Intercellular mitochondrial transfer and trans-mitophagy in response to protein import dysfunction.
Hypoxia rescues complex 1-associated disease caused by proteostatic defects.
Spatial transcriptomic mapping of postnatal mouse uterine development.
ER-mitochondria contacts and mitochondrial fusion correlate with increased mitochondrial activity during vertebrate embryogenesis.
The Calcium-Calpain-ALIX Axis is the Major Link Between Gasdermin-D Membrane Pores and Terminal Membrane Damage in Pyroptosis.
The BRCA1-A complex restricts replication fork reversal-dependent DNA repair in ATM deficient cells.
The UFSP2-ODR4 complex spatially confines and dynamically controls UFM1 deconjugation to safeguard neuronal proteostasis.
Identifying critical lysines in mammalian histone H3 with high-throughput CRISPR prime editing.
The MEK inhibitor trametinib incurs mitochondrial injury and induces innate immune responses in the mouse heart.
Time-resolved proteolipidomics of the human aorta identifies stage-specific lipid-protein modules across development and aging.
An intrinsic cytoskeletal oscillator establishes neuronal polarity.
Evolutionarily conserved short linear motifs drive actin filament binding.
Topoisomerase IIIα resolves inter- and intra-molecular intertwines during DNA replication.
Mavacamten shows broad benefit in human and mouse models of MYBPC3-related hypertrophic cardiomyopathy.
AMPKγ2 Regulates Cardiac Hypertrophy and Arrhythmias via Interacting With Myosin.

Nat Commun. 2026 Jul 06.

Embryo quality control via lineage-specific aneuploid cell elimination in embryos and stem cell-derived embryo models.

Lisa K Iwamoto-Stohl, Laura Amaya, Pallavi Panda, Yuqi Wang, Ninadini Sharma, Catherine King, Magdalena Zernicka-Goetz.

Aneuploidy is frequent in human pre-implantation embryos and a leading cause of early pregnancy loss, yet is rarely observed at birth, implying robust embryonic surveillance. Here we define how this surveillance operates after implantation using an integrated, three-lineage stem cell-derived embryo model that recapitulates the epiblast (EPI), visceral endoderm (VE), and extraembryonic ectoderm (ExE). Seeding of aneuploid cells into each lineage independently reveals lineage-specific fates: aneuploid cells are selectively depleted from EPI and VE but persist within ExE. Live imaging captures their removal by apoptosis or physical extrusion. Single-cell RNA sequencing shows p53 activation and Myc repression in aneuploid cells, and pathway perturbations modulate their clearance, confirming causality. Together, these findings demonstrate a post-implantation, lineage-restricted quality-control program that eliminates aneuploid cells from the embryo proper while permitting extraembryonic tolerance. They also establish integrated embryo models as a tractable platform to dissect the molecular logic of developmental quality control.

DOI: https://doi.org/10.1038/s41467-026-75054-0
EMBO J. 2026 Jul 10.

Mechanical constraints regulate embryonic stem cell mitosis in the developing brain.

Véronique Marthiens, Lin Jawish, Margaux Malosse, Clara Basto, Denis Krndija, Anne-Sophie Macé, Elmar Laigna, Antonia Terrizzano, Corentin Peyret, Teng Pan, Olivier Zajac, Louisiane Perrin, Elsa Logarinho, Catherine Villard, Renata Basto.

Research on mitosis has predominantly examined cell-autonomous mechanisms, yet its regulation and consequences within the broader physiological context remain largely unexplored. It remains, therefore, unknown whether and how spindle assembly and chromosome segregation are influenced by tissue properties. We have investigated this question in the mammalian embryonic brain, using high-resolution microscopy combined with pharmacological perturbations and minimal cell systems to break down the contribution of tissue environment to mitotic fidelity. We found that cell density imposes biomechanical constraints upon the apical radial glial (aRG) cell population during their highly proliferative period, which enhances spindle pole microtubule polymerization rates and potentiates chromosome mis-segregation. Mechanistically, we show that cortical tension relying on branched actin organization at the cell cortex conveys mechanical stress exerted by cell density. We identified the microtubule depolymerase MCAK/Kif2C as a critical effector downstream of cortical actin, linking actin dynamics to spindle pole activity. Altogether, our findings demonstrate that aRG are mechanosensitive during their expansion phase, and that excessive biomechanical stress, imposed by high cell density in developing tissues, can disrupt mitotic fidelity.

DOI: https://doi.org/10.1038/s44318-026-00848-3
Dev Cell. 2026 Jul 08. pii: S1534-5807(26)00233-9. [Epub ahead of print]61(7): 1352-1362

Embryo models as experiments in self-organization: The logic of productive failure.

Magdalena Zernicka-Goetz, Sergio de la Rosa.

  Stem cell-derived embryo models help to transform inaccessible stages of mammalian development into experimentally tractable systems, revealing how development succeeds, stalls, or fails under defined conditions. Because natural embryos are shaped by stringent in vivo selection, they conceal many trajectories that embryo models bring into view. In mouse and human systems, embryo-like structures emerge through shared morphogenetic transitions-cell sorting, polarization, lumen formation, and symmetry breaking-with variable efficiency and along multiple routes. These alternative trajectories expose the rules and constraints of self-organization, the roles of extra-embryonic tissues, and the parameters that stabilize robust development. We propose that embryo models can be understood as experiments in productive failure, in which divergence from in vivo development becomes mechanistically informative. In doing so, embryo models reveal the hidden grammar of development, expose the fragilities that underlie pregnancy loss, and potentially reshape what is possible for regenerative biology and bioengineering.

Keywords:  developmental robustness; embryo models; extra-embryonic tissues; gastruloids; lineage specification; mammalian embryogenesis; morphogenesis; self-organization; stem cell-derived embryos; symmetry breaking

DOI:  https://doi.org/10.1016/j.devcel.2026.06.009
Sci Adv. 2026 Jul 10. 12(28): eadz2249

Modeling human embryo adhesion using a microfluidic platform.

Sofía Zaragozano, María Pardo-Figuerez, Ana Monteagudo-Sanchez, Anna Quirant, Javier Moncayo-Arlandi, Javier Gonzalez-Fernandez, Jaime Llera-Oyola, Petr Volkov, Sara Maggi, Luis Quintero, Francisco Raga, Pablo Grases, Xavier Santamaria, Inmaculada Moreno, Nicolas Plachta, Carlos Simon, Felipe Vilella.

Embryo adhesion represents a critical step of implantation, yet understanding this process has been hindered by the lack of human in vitro platforms that replicate endometrial physiology. Here, we present a dual-channel microfluidic platform containing organoid-derived endometrial epithelium and primary stromal cells. Our model recapitulates important endometrial hallmarks including epithelial polarization, stromal decidualization, extracellular vesicle release, and hormone-induced receptivity. We validated the model using mouse embryos and human blastocysts, where we showed that embryos displayed features of initial adhesion. These included establishment of embryo-epithelial contacts initiated via the polar trophectoderm, inner cell mass repositioning, and lineage reorganization. Moreover, human embryos secreted βhCG indicating a functional trophoblast. Thus, this work provides a platform to study key features of embryo adhesion and endometrial receptivity and disorders affecting embryo-endometrium interactions.

DOI: https://doi.org/10.1126/sciadv.adz2249
Res Sq. 2026 Jul 01. pii: rs.3.rs-10144286. [Epub ahead of print]

Mechanosensing at the endoplasmic reticulum by IRE1.

Hesso Farhan, Michaela Mayr, Luiz Garcia-Souza, Murphy McDermott, Utku Horzum, Yannick Frey, Margot Haun, Stephan Geley, Chao Jiang, Mattias Luber, Anush Bakunts, Camilla Pirolo, Alesia Yakimchyk, Klaus Liedl, Wylie Stroberg, Timo Betz, Liam Holt.

Sensing and integration of mechanical forces in eukaryotic cells have largely been attributed to the plasma membrane and the nucleus. Here, we identify the endoplasmic reticulum (ER) as an autonomous mechanosensitive organelle and uncover IRE1 as an ER-resident mechanosensor. We show that applying mechanical forces to ER membranes increases lateral tension, which is sensed by the transmembrane domain of IRE1. Mechano-activation of IRE1 was unrelated to its canonical role in the unfolded protein response and occurred independently of nuclear mechanosensing. Instead, mechanically activated IRE1 triggered JNK signaling and increased global protein synthesis independently of XBP1 splicing. In engineered skeletal muscle tissue, both electrical stimulation and passive stretch similarly activated IRE1, increased translation, and contributed to training-induced increases in contractile force. Collectively, our results uncover a non-canonical role for IRE1 as an ER-based mechanosensor that couples mechanical forces to the regulation of protein translation.

DOI: https://doi.org/10.21203/rs.3.rs-10144286/v1
Nature. 2026 Jul 08.

Aneuploidy selects for the acquisition of driver genes in breast cancer.

Khalid N Al-Zahrani, Ellen R Langille, Jocelyn Nurtanto, Andreea Obersterescu, Katie Teng, Christopher Lowden, Julien Dessapt, Cynthia H Chiu, Lauren V Caldwell, David P Cook, Miguel A Pérez-Castro, Jacob M Berman, Ricky Tsai, Alexander T Bahcheli, Geraldine Mbamalu, Shifei Wu, Masahiro Narimatsu, Adele G Lopes, Iosifina Fotiadou, Kin Chan, Linkang Zhang, K W Annie Bang, Michael J Parsons, Larissa Mourao, E Idil Temel, Liddy McCulla, Palavalasa Sravya, Li Zhang, Peter Sajjakulnukit, Costas A Lyssiotis, Alexander D Borowsky, Colinda L G J Scheele, Daniel R Wahl, Hartland W Jackson, Katherine S Stewart, Elaine Fuchs, Sean E Egan, Miguel Angel Pujana, Jüri Reimand, Jeffrey L Wrana, Daniel Schramek.

Chromosome instability is highly prevalent in cancer and drives large-scale chromosomal imbalances, known as aneuploidies1-4. How aneuploidy contributes to tumorigenesis remains difficult to study due to the vast numbers of genes affected. Here we established a CRISPR knockout- and activation-linked assay (CRISPR-KOALA), enabling high-throughput bidirectional genetic screens in immunocompetent mouse models of cancer. We developed a compendium of the ten most frequent human chromosome-arm-level alterations in basal-like breast cancer (BLBC), a disease type that is driven by large copy-number alterations (CNAs)5-8. Using CRISPR-KOALA, we screened the mouse orthologues of 3,752 genes on these arms and identified 90 cancer driver genes, the function of the vast majority of which is unknown. These genes drive distinct signalling pathways including MAPK, HIPPO and WNT, reflecting the high degree of BLBC heterogeneity. Manipulating the identified cancer driver genes overcomes the need for CNAs in Trp53-mutant BLBC mouse models. Mechanistically, we identify that PLGRKT is a potent oncogene that lies on chromosome 9p and show that its tumour-promoting activity is associated with highly stress-resistant mitochondria and an increased ability to detoxify reactive oxygen species. Together, our findings reveal that arm-level CNAs can function to select specific driver genes to promote heterogeneous biological processes.

DOI: https://doi.org/10.1038/s41586-026-10752-9
J Cell Biol. 2026 Sep 07. pii: e202605018. [Epub ahead of print]225(9):

Inorganic phosphate rapidly switches the stability of Arp2/3-induced actin branches.

Jiu Xiao, Foad Ghasemi, Adrien Schahl, Miroslav Mladenov, Rebecca Pagès, Matthieu Chavent, Michael Way, Luyan Cao, Guillaume Romet-Lemonne, Antoine Jégou.

Actin filaments often appear as branches, nucleated by the Arp2/3 complex. Arp2 and Arp3 are ATPases, which adopt different nucleotide-dependent conformations. We investigated how the nucleotide state of mammalian Arp2/3 complexes affects branch stability, by applying mechanical load. Branch junctions are 30-fold more stable when Arp2/3 is in the ADP-inorganic phosphate (Pi) rather than the ADP state. Pi is in rapid equilibrium with the ADP-Arp2/3 complex at the branch junction (release rate 0.2 s-1). Upon branch dissociation, Arp2/3 complexes remaining attached to the mother filament in the ADP-Pi state are 100-fold more stable, release their phosphate slowly (0.05 s-1), and can regrow branches without reloading ATP. Glia maturation factor (GMF) accelerates the dissociation of surviving ADP-Arp2/3 complexes, but does not prevent branch regrowth at physiological ATP concentration. Cortactin stabilizes branches and enhances renucleation. Neither GMF nor cortactin affects branch stability and renucleation of ADP-Pi-Arp2/3. Overall, these results identify Pi in the Arp2/3 complex as a critical regulator of branched actin network stability.

DOI: https://doi.org/10.1083/jcb.202605018
Cell Rep. 2026 Jul 09. pii: S2211-1247(26)00760-6. [Epub ahead of print]45(7): 117682

PUMILIO proteins maintain lineage balance via post-transcriptional repression of germline fate and promotion of somatic differentiation.

Ting Lu, Yiying Yang, Xiajun Li, Shuo Shi.

  Loss of the RNA-binding proteins PUM1 and PUM2 leads to gastrulation failure and embryonic lethality, but the mechanisms underlying this phenotype remain unclear. Using embryoid bodies as an in vitro model of early embryogenesis, we show that PUM proteins maintain lineage balance by post-transcriptionally repressing germline fate, silencing pluripotency networks, and promoting somatic differentiation. They directly inhibit Prdm1 to prevent premature germline specification and activate Wnt signaling to support germ layer formation. PUM-deficient cells exhibit impaired patterning along both the anterior-posterior and dorsoventral axes, along with defective neural differentiation. RIP-seq analyses identify key developmental mRNAs directly regulated by PUM1 and PUM2, linking these proteins to multiple regulatory modules. These findings establish PUM proteins as essential post-transcriptional regulators of early embryogenesis, demonstrating how RNA-binding proteins coordinate cell fate and patterning.

Keywords:  CP: developmental biology; CP: molecular biology; PUMILIO proteins; Prdm1; RNA-binding proteins; embryonic stem cells; germline specification; lineage specification; post-transcriptional regulation; somatic differentiation

DOI:  https://doi.org/10.1016/j.celrep.2026.117682
Curr Biol. 2026 Jul 06. pii: S0960-9822(26)00746-3. [Epub ahead of print]

CLASP-dependent microtubule stabilization generates microtubule-based protrusive forces during Drosophila epithelial morphogenesis.

Sayani Sarkar, Anna Pawluchin, Anastasiia Sokolova, Andrea Ricker, Harald Nüsse, Jürgen Klingauf, Milos Galic, Maja Matis.

  Tissue morphogenesis requires tight coordination between biochemical signaling and mechanical forces that sculpt cells and tissues. While actomyosin networks are well-established force generators, microtubule-based mechanics have recently emerged as crucial contributors to tissue remodeling. Yet, how dynamic microtubules, whose plus ends undergo compression-induced catastrophes that limit their load-bearing capacity, generate forces in vivo remains unclear. Here, we identify Orbit, the Drosophila cytoplasmic linker-associated protein (CLASP) homolog, as a key factor that stabilizes non-centrosomal microtubule plus ends in vivo, enabling them to sustain mechanical loads. In the pupal wing epithelium, these Orbit-stabilized, planar-polarized microtubules are consistent with a role in counteracting actomyosin contractility and promoting tissue elongation. Loss of Orbit increases catastrophe frequency and disrupts epithelial elongation, whereas Orbit overexpression enhances microtubule rescues by suppressing catastrophes, thereby promoting cell anisotropy and tissue extension. Moreover, Orbit-mediated stabilization is sufficient to induce microtubule-dependent, filopodia-like protrusions independent of actin. Together, these findings establish CLASP-dependent microtubule stabilization as a key mechanism linking polymerization dynamics to epithelial morphogenesis.

Keywords:  CLASP/Orbit; Drosophila; cell anisotropy; epithelial mechanics; epithelial morphogenesis; force generation; microtubule dynamics; non-centrosomal microtubules; tissue elongation

DOI:  https://doi.org/10.1016/j.cub.2026.06.035
EMBO Rep. 2026 Jul 06.

Gata3 dosage governs primitive endoderm versus trophectoderm specification in embryonic stem cells.

Yeejin Jang, Mijeong Kim, Joonhyuk Choi, Jonghwan Kim.

Transcription factor (TF) dosage represents an overlooked aspect of developmental regulation. While Gata3 has traditionally been viewed as a determinant of trophectoderm (TE), its potential role in primitive endoderm (PE) has remained unclear. Here, we demonstrate that Gata3 functions as a dosage-sensitive regulator directing mutually exclusive lineage programs in mouse embryonic stem (ES) cells. Low levels of Gata3 (Gata3-L) promote PE-like transcriptional states, while high levels (Gata3-H) drive TE identity by rapidly repressing pluripotency and inducing TE markers. Genome-wide binding analysis reveals a dose-dependent redistribution of Gata3 across enhancers, with chromatin engagement consistent with pioneer factor-like activity. Functional 3D blastoid assays combined with single-cell transcriptomics further establish that Gata3 dosage alone is sufficient to instruct the spatial segregation of PE- versus TE-like compartments. These findings redefine Gata3 not merely as a TE determinant but as a central dosage-sensitive switch in lineage specification. More broadly, our results position TF dosage as a fundamental regulatory parameter that integrates enhancer selection, chromatin engagement, and spatial patterning, providing new opportunities to refine stem cell-based models and engineer developmental outcomes.

DOI: https://doi.org/10.1038/s44319-026-00860-y
EMBO J. 2026 Jul 09.

Inhibition of lagging strand replication by G-rich telomeric DNA and the shelterin subunit POT1.

Ciara Leonard-Booker, Giulia Mazzucco, Charlotte E L Fisher, Karim Hussain, Tom D Deegan, Ylli Doksani, Max E Douglas.

Telomeres preserve stable eukaryotic chromosomes by protecting the natural chromosome ends from DNA repair but pose a persistent challenge to the replication machinery and an endogenous source of replication stress. Different features have been implicated in causing this effect but how the canonical replication process is altered at telomeres remains poorly understood. To address this question, we have reconstituted telomere replication with purified human proteins. Our system reveals that G-rich telomeric DNA can directly and specifically block lagging strand replication in a manner counteracted by BLM helicase. Unexpectedly, we also identify shelterin as inhibitory for the lagging strand. Biochemical experiments and electron microscopy imaging show that POT1-containing shelterin complexes induce Okazaki fragment skipping by binding the lagging strand template, generating large single-stranded gaps that are left behind on otherwise fully replicated molecules. Our study defines how the core components of telomeres interfere with the canonical replication process, identifying multiple potential sources of replication stress.

DOI: https://doi.org/10.1038/s44318-026-00844-7
Curr Biol. 2026 Jul 10. pii: S0960-9822(26)00735-9. [Epub ahead of print]

Dynamic integration of morphogen and juxtacrine signaling specifies cell fate at single-cell resolution.

Alicia Donoghue, Lewis S Mosby, Inês Lago-Baldaia, Tamara Hodgetts, Evelina Ursu, Zeynep Erten, Zena Hadjivasiliou, Vilaiwan M Fernandes.

  Morphogen gradients guide tissue patterning but do not act in isolation. To address how they integrate with other signaling modalities and how such integrations influence pattern resolution and robustness, we focused on the Drosophila lamina, where columns of precursors are patterned with single-cell resolution into distinct motion-processing neurons. Although a photoreceptor-derived Hedgehog gradient diversifies cell fates, it cannot account for all fates specified. Combining experiments and theory, we show that glial-induced extracellular signal-regulated kinase (ERK) activity drives Delta expression in lamina precursors, generating graded Notch activity. This subdivides Hedgehog-responsive domains into subdomains that map to distinct fates. We identify a Hedgehog morphogen relay between photoreceptors and the lamina and show that Notch restricts this relay, enhancing positional information. Glia act as timekeepers, scheduling ERK-driven differentiation to coincide with stable Hedgehog and Notch activity patterns. Thus, Notch and ERK dynamically integrate with Hedgehog to encode positional information, enabling precise and reproducible cell fate patterning.

Keywords:  Drosophila visual system; ERK signaling; Hedgehog signaling; Notch signaling; cell fate specification; developmental patterning; developmental robustness; morphogen gradient; morphogen relay; neuronal diversity

DOI:  https://doi.org/10.1016/j.cub.2026.06.024
Nat Cell Biol. 2026 Jul 10.

Decoding stage-specific functions of PRC2 in early embryogenesis uncovers roles in preimplantation development and primordial germ cell fate.

Chengjie Zhou, Meng Wang, Zhiyuan Chen, Yi Zhang.

Early embryogenesis is accompanied by dynamic epigenetic modifications. Although such dynamics are important in cell intrinsic regulation of gene expression, their extrinsic roles in mediating intercellular communication during early embryogenesis are less understood. Here, using the dTAG system, we reveal previously underappreciated stage-specific functions of PRC2 in regulating preimplantation and primordial germ cell (PGC) development. We demonstrate that PRC2 plays important roles in regulating maternal-to-zygotic transition and epiblast formation. By systematically analysing H3K27me3 and H3K4me3 dynamics, we redefine the timing of bivalency establishment and uncover a stepwise mechanism governing bivalency acquisition in early embryogenesis. Moreover, PRC2 regulates proper PGC numbers in the epiblast by controlling Esrrb expression in the extraembryonic ectoderm. Thus, our study uncovers a previously unknown cell-autonomous function of PRC2 in preimplantation development and its non-cell-autonomous impact in PGC number regulation, both through interplays between epigenetic-epigenetic and epigenetic-transcription factors networks.

DOI: https://doi.org/10.1038/s41556-026-02002-x
EMBO J. 2026 Jul 09.

Alterations in chromatin organization promote totipotent-like features in a DPPA2/DUX-dependent manner.

Grace I Carey, Maria Vega-Sendino, Desiree Tillo, Sarah C Hoelscher, Amir Khan, Ian Taukulis, Teresa Olbrich, Bechara Saykali, Andy D Tran, Bhavya Soni, Anna Lee Fong, Melissa Mikolaj, Adam Harned, Kedar Narayan, Michael J Kruhlak, Michael Kelly, Ning Qing Liu, Elzo de Wit, Sergio Ruiz.

2-cell like cells (2CLC) are a transiently cycling population of cells with totipotent-associated features. Although CTCF depletion induces 2CLC conversion in mouse ESC, whether this reprogramming is a consequence of disrupted higher-order chromatin organization or of CTCF-specific functions remained unclear. Here, we show that depletion of the cohesin release factor WAPL in ESC also promotes 2CLC reprogramming, which is increased by CTCF co-depletion. Single-cell RNA-seq/ATAC-seq analyses in CTCF/WAPL-depleted ESC revealed that chromatin accessibility precedes 2C-associated gene expression. Moreover, we identified ARID3A as a transcription factor that regulates the extent of 2CLC conversion following WAPL/CTCF depletion. Although WAPL or CTCF depletion induces distinct transcriptional changes in human ESC, these do not resemble transcriptional programs of early human embryogenesis, suggesting limited evolutionary conservation. Finally, we demonstrate that 2CLC conversion mediated by alterations in chromatin organization depends on the DPPA2/DUX axis and correlates with nucleolar integrity. Together, these findings establish a mechanistic link between higher-order chromatin organization and totipotency-like cell identity in mice.

DOI: https://doi.org/10.1038/s44318-026-00853-6
Nat Commun. 2026 Jul 08. pii: 5727. [Epub ahead of print]17(1):

Molecular profiling of the single-cell proteome via gel electrophoresis and 3D single-molecule imaging.

Latiefa Kamarulzaman, Sooyeon Kim, Takuya Hidaka, Misaki Tsuchida, Yuichi Taniguchi.

Recent advances in shotgun proteomics and immunoassays have yielded powerful single-cell proteomics technologies. However, current methods lack the sensitivity required to comprehensively quantify protein abundances in individual cells. Here, we present single-cell PAGE-PISA, an ultra-sensitive proteome profiling strategy that combines gel electrophoresis with 3D single-molecule fluorescence imaging. Our approach labels all proteins in single cells with fluorescent dyes, separates them by electrophoresis, and counts with single-molecule resolution. This technique quantified over 107 protein copies from a single mammalian cell with the sensitivity to detect low-abundance proteins down to 105 copies per species. Single-cell PAGE-PISA successfully classified cells into distinct cell types based on their proteomic profiles. Furthermore, our single-cell proteome data strongly correlated with predicted developmental states during cardiomyocyte differentiation, providing complementary information to single-cell transcriptome data. Together, single-cell PAGE-PISA enables highly sensitive and quantitative proteome profiling at the single-cell level, capturing subtle proteomic differences that distinguish diverse cellular states.

DOI: https://doi.org/10.1038/s41467-026-74840-0
Nat Cell Biol. 2026 Jul 06.

CD44 restricts EGFR mobility to polarize cytoskeletal signalling modules driving bleb-based migration.

Ankita Jha, Ankit Chandra, Payam E Farahani, Jared E Toettcher, Ana M Pasapera, Jason M Haugh, Clare M Waterman.

Cells under high confinement migrate efficiently in low-adhesion environments by forming stable, polarized, hydrostatic pressure-driven leader blebs. Here we investigated the basis of polarized bleb morphology in metastatic melanoma cells migrating under low-adhesive and highly confined microenvironments. Using high-resolution live imaging, molecular perturbations and biosensors, we show that EGF signalling through PI3K stabilizes and maintains polarized leader blebs. EGFR and PI3K activities form a gradient within leader blebs that decreases from rear to front, promoting phosphatidylinositol 3,4,5-trisphosphate and Rac1-GTP accumulation at the bleb rear, whereas phosphatidylinositol 4,5-bisphosphate and RhoA-GTP concentrate at the bleb tip, the inverse of the organization observed in integrin-dependent mesenchymal migration. Optogenetic disruption of this gradient triggers bleb retraction, underscoring its functional importance. Mathematical modelling and experiments identified a mechanism whereby during bleb initiation, CD44 and ERM proteins restrict EGFR mobility within a membrane-apposed cortical actin meshwork at the bleb rear, establishing the EGFR-PI3K-Rac gradient. Together, these findings define the biophysical and molecular mechanisms that underlie polarity in bleb-based migration and highlight how alternative spatial organization of signalling modules supports distinct migration modes in different microenvironments.

DOI: https://doi.org/10.1038/s41556-026-01981-1
Nat Struct Mol Biol. 2026 Jul 09.

Cytoplasmic lattices store developmentally poised degradative and cytoskeletal complexes in mammalian eggs.

Yujie Li, Wei Zheng, Jiyeon Leem, Chunxiang Wu, Shaogeng Tang, Binyam Mogessie, Yong Xiong.

The cytoplasmic lattice (CPL) in mammalian eggs is essential for early embryonic development but its molecular components, structural organization and functional capacity have remained elusive. Here, using cryo-electron microscopy, we show that the CPL filament in mouse metaphase II eggs contains repeating units with a periodicity of ~37 nm and determine its high-resolution, native structure and complete subunit composition. The CPL architecture organizes maternal-effect proteins, ubiquitination machinery and tubulin into a highly structured reservoir. Maternal-effect proteins form the scaffold of the CPL to sequester a UHRF1-UBE2D3 E3-E2 ubiquitination module and three distinct FBXW-SKP1 E3 ubiquitin ligase components, notably all in activity-excluded states. The CPL further contains αβ-tubulin heterodimers in a GTP-bound state, indicating microtubule-assembly-competent tubulin held in reserve. CPL filaments are capped by a terminal unit that lacks a PADI6 dimer, a scaffold component, suggesting a structural mechanism that prevents further oligomerization. Interactions between neighboring CPL filaments promote the assembly of a three-dimensional network in the egg cytoplasm. Taken together, our work defines how CPL assembly and architecture prime mammalian eggs for ubiquitin-mediated protein degradation and cytoskeletal remodeling during the egg-to-embryo transition.

DOI: https://doi.org/10.1038/s41594-026-01843-2
J Cell Biol. 2026 Sep 07. pii: e202511211. [Epub ahead of print]225(9):

Intercellular mitochondrial transfer and trans-mitophagy in response to protein import dysfunction.

Emily Glover, Beth Wiseman, Celyn Dugdale, Charlie Humphery, Lorena Sueiro Ballesteros, Lorna Hodgson, Kevin Wilkinson, Ian Collinson.

Mitochondrial protein import is critical for organelle biogenesis, maintenance, and regeneration-essential for cellular homeostasis. Import dysfunction compromises cellular energy supplies, which is damaging to cells, particularly those with high energetic demands like neurons. Previously, we have shown that import failure is rescued by intercellular mitochondrial transfer (IMT) via tunnelling nanotubes (TNTs) however, the fate of the transferred mitochondria and the mechanistic basis for rescue were unresolved. Here, we show that bidirectional mitochondrial trafficking between cells harboring import-defective and import-competent mitochondria is distinct in terms of their regulation and ensuing consequences. Transferred import-defective mitochondria are highly fragmented and destined for canonical lysosomal degradation. In contrast, reactive oxygen species (ROS)-producing mitochondria at the periphery of cells with import-competent mitochondria are transferred into neighboring cells undergoing import failure. These new arrivals then accumulate within previously uncharacterized "mitochondrial degradation bodies" (MDBs). We speculate that the cooperation of these distinct cases of TNT-mediated conventional and noncanonical "trans-mitophagy" instigates mitochondrial regeneration, and thereby rescues mitochondrial function.

DOI: https://doi.org/10.1083/jcb.202511211
Nat Metab. 2026 Jul 08.

Hypoxia rescues complex 1-associated disease caused by proteostatic defects.

Ankur Garg, Brandon R Desousa, Raju Roy, Amy Flis, Skyler Y Blume, Yohei Abe, Arthur A Melo, Ryan R Cupo, Gabriela Grigorean, Daniel R Southworth, James Shorter, Isha H Jain.

Impaired mitochondrial proteostasis underlies a broad spectrum of diseases, yet effective therapies remain limited. Here we show that deficiency of HTRA2, a mitochondrial intermembrane space protease, can be rescued by hypoxia therapy. Using an Htra2 mutant mouse model that displays severe neurodegeneration and early lethality, we find that continuous hypoxia rescues striatal degeneration and extends lifespan. Mechanistically, we demonstrate that HTRA2 forms a functional complex with the disaggregase CLPB. Loss of function of either protein drives aggregation of intermembrane space-facing subunits of complex I of the electron transport chain, resulting in secondary complex I dysfunction. These changes impair tissue oxygen consumption and probably cause pathological hyperoxia, which is corrected by hypoxia. Together, these findings define a proteostasis pathway linking intermembrane space quality control to complex I function and expand the potential of hypoxia therapy to secondary complex I disease.

DOI: https://doi.org/10.1038/s42255-026-01566-0
Proc Natl Acad Sci U S A. 2026 Jul 14. 123(28): e2600524123

Spatial transcriptomic mapping of postnatal mouse uterine development.

M Fairuz B Jamaluddin, Shafiq M Syed, Riazuddin Mohammed, Jyoti Goad, Mehedi Hasan, Manish Kumar, Isabella Moore, Prathima B Nagendra, Naga Veera Srikanth Vallabani, Florence Bartlett, Vimala Anthonydhason, Pradeep S Tanwar.

  Postnatal uterine development requires precise coordination of epithelial differentiation, gland formation, and stromal organization, yet how transcriptional programs are spatially integrated during this process remains poorly understood. Here, we generated a spatially resolved transcriptomic map of the mouse uterus across key postnatal stages from day 3 to day 21 by combining high resolution in situ transcriptomics with histology, proteomics, genetic models, and functional assays. This approach defines the temporal emergence and spatial arrangement of all major uterine cell types and demonstrates that endometrial glands arise from luminal epithelium through progressive transcriptional reprogramming rather than from a prespecified progenitor population. Spatial analysis reveals marked compartmentalization of signaling pathways during adenogenesis. Luminal epithelium is enriched for Wnt ligands and hormone receptors, whereas glandular epithelium engages inhibitory and negative feedback programs that constrain Wnt activity while supporting proliferation and differentiation. Functional genetic studies establish that epithelial canonical Wnt signaling is essential for prepubertal gland establishment and long-term epithelial maintenance but is dispensable for postpartum gland regeneration. Retinoic acid synthesis becomes increasingly concentrated within glands, while hedgehog signaling polarizes into an epithelial to stromal axis during gland morphogenesis. Additional pathways including RTK, Notch, TGFβ, BMP, hypoxia, Hippo, and PI3K-mTOR exhibit distinct spatial biases that collectively shape epithelial identity and tissue maturation. Together, these findings provide a comprehensive spatial framework for uterine gland development and reveal how compartment specific signaling networks coordinate postnatal uterine morphogenesis.

Keywords:  endometrium; female fertility; organoids; spatial; uterus

DOI:  https://doi.org/10.1073/pnas.2600524123
Cell Rep. 2026 Jul 09. pii: S2211-1247(26)00693-5. [Epub ahead of print]45(7): 117615

ER-mitochondria contacts and mitochondrial fusion correlate with increased mitochondrial activity during vertebrate embryogenesis.

Anastasia Chugunova, Isabelle Schütz, Hannah Keresztes, Roksolana Kobylinska, Maria Novatchkova, Thomas Lendl, Marcus Strobl, Jörg Fallmann, David Márquez Oller, Michael Schutzbier, Gerhard Dürnberger, Richard Imre, Elisabeth Roitinger, Phylicia Kidd, Pawel Pasierbek, Alberto Moreno Cencerrado, Marlene Brandstetter, Thomas Köcher, Benedikt Agerer, Jakob-Wendelin Genger, Andreas Bergthaler, Andrea Pauli.

  Increased mitochondrial activity is essential for embryo development. Although conserved across organisms, the molecular basis of this increase is unknown, as detailed biochemical analysis in vertebrates is hampered by the limited availability of material. Using zebrafish as a model for vertebrate development, we comprehensively profile mitochondrial activity, morphology, metabolome, proteome, and phospho-proteome, as well as respiratory chain activity. Our data show that the mitochondrial proteome undergoes major changes during embryogenesis. While respiratory chain complex levels remain largely constant, we identify a marked increase in mitochondrial-ER association during early embryogenesis. Moreover, time-lapse imaging of mitochondrial dynamics reveals a transition from fragmented to elongated mitochondria starting during somitogenesis. Overall, our systematic profiling of the molecular and morphological changes of mitochondria during embryogenesis provides a valuable resource for further investigation of mitochondrial function. Our study reveals that increased mitochondrial-ER interaction and changes in mitochondrial morphology may contribute to its regulation during vertebrate development.

Keywords:  CP: cell biology; CP: developmental biology; ER-mitochondrial interaction; metabolism; mitochondria; mitochondrial activation; proteomics; vertebrate embryogenesis; zebrafish

DOI:  https://doi.org/10.1016/j.celrep.2026.117615
Res Sq. 2026 Jun 29. pii: rs.3.rs-10100112. [Epub ahead of print]

The Calcium-Calpain-ALIX Axis is the Major Link Between Gasdermin-D Membrane Pores and Terminal Membrane Damage in Pyroptosis.

Gergely Imre, Sylvia Otchere, Himesh Parmar, Kushagra Singh, Lauren Tereshisnki, Natalie Thiex, Adam Hoppe.

Pyroptosis is an inflammatory form of regulated cell death driven by gasdermin-mediated membrane pore formation. Although gasdermin D (GSDMD) pores are widely regarded as the executioners of pyroptosis, recent studies demonstrate that pore formation is not necessarily lethal because cells can actively repair membrane damage through the Endosomal Sorting Complex Required for Transport (ESCRT) machinery. The molecular mechanism that converts reversible GSDMD pore formation into irreversible membrane rupture and cell death remains unknown. Here, we identify a calcium-calpain-ALIX signaling axis that mechanistically links GSDMD pore formation to catastrophic membrane damage. Using primary macrophages, THP-1 monocytes, and HCT-116 epithelial cells, we show that depletion of the ESCRT adaptor ALG-2-interacting protein X (ALIX) abolishes membrane repair, promotes GSDMD accumulation, and markedly increases susceptibility to pyroptotic death. We further demonstrate that GSDMD pores trigger calcium influx, which induces proteolytic cleavage of ALIX. Preventing calcium influx or chelating intracellular calcium blocks ALIX cleavage, reduces GSDMD accumulation, and markedly improves cell survival. Mechanistically, we identify calpains as the calcium-dependent proteases responsible for ALIX cleavage and establish ALIX as a previously unrecognized calpain substrate. Pharmacologic inhibition or genetic depletion of calpains significantly reduces membrane permeabilization and pyroptotic cell death. Mapping of calpain cleavage sites localizes the major cleavage site within the ALIX V-domain. Importantly, calpain-mediated cleavage disrupts ALIX interaction with the ESCRT-III component CHMP4B, thereby preventing ESCRT assembly and membrane repair. In contrast, calcium depletion or calpain knock down restores CHMP4B recruitment and ESCRT activation Collectively, these findings reveal the first mechanistic pathway linking reversible membrane GSDMD pore formation to irreversible membrane rupture. We propose that GSDMD pore-induced Ca2+ influx activates calpains, disables ALIX-dependent ESCRT repair, and drives the transition from repairable membrane injury to terminal pyroptotic lysis. This pathway represents a potential therapeutic target for inflammatory diseases driven by excessive pyroptosis.

DOI: https://doi.org/10.21203/rs.3.rs-10100112/v1
Nat Commun. 2026 Jul 04.

The BRCA1-A complex restricts replication fork reversal-dependent DNA repair in ATM deficient cells.

Arindam Datta, Jessica Jackson, Yaroslav I Morozov, Jinghan Qiu, Alessandro Vindigni, Roger A Greenberg.

Ataxia Telangiectasia Mutated (ATM) kinase deficiency results in cancer susceptibility and drug hypersensitivity. Deficiency in either the BRCA1 interacting A complex or XRCC4/Ligase 4 confers resistance to Topoisomerase I or PARP1 inhibitors in ATM-deficient cells. This suggests that BRCA1-A directs toxicity to fork-damaging agents in ATM mutated cells via illegitimate end-joining. Here, we show that ATM inhibition triggers combined SUMO and ubiquitin mediated BRCA1-A damaged fork recognition to restrict end-resection and cause Topoisomerase I inhibitor hypersensitivity. BRCA1-A deficient cells display elevated chromatin accessibility and nuclease activity at damaged forks, coupled with restored resection and drug resistance. Electron microscopy evidence demonstrates that ATM inhibition prevents replication fork reversal, which is restored by BRCA1-A loss to generate substrates for end resection. These findings reveal that BRCA1-A enforces a restrictive chromatin state to suppress the genesis of resection substrates, implicating fork reversal as a key determinant of chemotherapy response in ATM deficient cells.

DOI: https://doi.org/10.1038/s41467-026-75271-7
Mol Cell. 2026 Jul 09. pii: S1097-2765(26)00415-6. [Epub ahead of print]

The UFSP2-ODR4 complex spatially confines and dynamically controls UFM1 deconjugation to safeguard neuronal proteostasis.

Gaoxin Mao, Sota Ito, Ryosuke Ishimura, Jun-Ichi Sakamaki, Ryohei Sasaki, Takefumi Uemura, Kei-Ichi Ishikawa, Satoko Komatsu-Hirota, Wado Akamatsu, Manabu Abe, Satoshi Waguri, Sunita Bijarnia-Mahay, Nobuo N Noda, Toshifumi Inada, Masaaki Komatsu.

  The ubiquitin-fold modifier 1 (UFM1) pathway is essential for endoplasmic-reticulum-associated ribosome quality control (ER-RQC) through UFMylation of the 60S ribosomal protein RPL26, but the regulation and physiological significance of UFM1 deconjugation remain poorly understood. Here, we identify the ER-anchored UFSP2-ODR4 complex as a spatially confined deUFMylation module critical for neuronal proteostasis. Structural modeling and biochemical analyses show that ODR4 recruits UFSP2 to the ER, enabling efficient deUFMylation of RPL26. Disruption of the UFSP2-ODR4 interaction causes the accumulation of UFMylated RPL26 and defective ER-RQC. Neural progenitor-specific knockin mice expressing a catalytically inactive UFSP2 mutant exhibit perinatal lethality, microcephaly, and neuronal apoptosis. We also identify a patient with biallelic UFC1 mutations that enhance UFL1 binding and induce hyper-UFMylation of RPL26 in patient-derived neurons. These findings establish spatially confined deUFMylation as a critical mechanism for safeguarding neuronal proteostasis.

Keywords:  ER-RQC; ODR4; UFC1; UFM1; UFSP2; endoplasmic-reticulum-ribosome quality control; neurodevelopmental disorders; neuronal proteostasis; ribosomal protein RPL26

DOI:  https://doi.org/10.1016/j.molcel.2026.06.026
Nat Genet. 2026 Jul 08.

Identifying critical lysines in mammalian histone H3 with high-throughput CRISPR prime editing.

Daniel Price, Grigory Zemlyanskiy, Watanya Trakarnphornsombat, Ignasi Forne, Nadezda Volkova, Louis Dubusse, Alexandra J Cooper, Axel Imhof, Aliaksandra Radzisheuskaya.

Histone post-translational modifications are fundamental to genome regulation, yet dissecting the functions of individual histone marks in mammals remains challenging due to the presence of multiple histone gene copies. Here we develop a high-throughput clustered regularly interspaced short palindromic repeats (CRISPR) prime editing platform enabling precise, reversible and combinatorial mutagenesis of canonical and noncanonical histone H3 genes within their native genomic context. Using systematic lysine-to-arginine substitutions benchmarked against synonymous controls, we identify key residues, including H3K4, H3K9, H3K14, H3K18 and H3K79, whose mutation compromises fitness in mouse embryonic stem cells. We further show that H3K56, linked to genome stability in yeast and Drosophila, has a conserved role in mammalian cells. Through analysis of selected double mutants, we uncover functional crosstalk across residues, with combinations such as H3K27R + H3K36R impairing stem cell self-renewal and altering transcription. Altogether, this study establishes a functional map of histone H3 lysines in mammals and provides a broadly applicable platform for systematic dissection of chromatin regulation.

DOI: https://doi.org/10.1038/s41588-026-02675-y
Sci Adv. 2026 Jul 10. 12(28): eaeb2695

The MEK inhibitor trametinib incurs mitochondrial injury and induces innate immune responses in the mouse heart.

Kelsey H Fisher-Wellman, Richard D Lutze, Logan G Kirkland, Ju Youn Beak, Mansi Goyal, Raghu Nagalingam, Samantha M Morrissey, Peyton B Sandroni, Wei Huang, Julian D Bailon, Melissa A Schroder, Lars A Albrecht, Ethelyn Ofei, Andrew L Chin, Thomas D Green, Joseph M McClung, McLane M Montgomery, James T Hagen, Brett R Chrest, Edziu M Franczak, Polina Krassovkaia, Raphael T Aruleba, Jon S Zawistowski, Timothy J Stuhlmiller, Shawn M Gomez, Nanthip Prathumsap, Qing Zhang, Jing Zhang, Weiyi Xu, Lilei Zhang, Jeremy A Meier, Lisa A Carey, Jonathan C Schisler, Gary L Johnson, Brian C Jensen.

Trametinib (Trm) is a highly selective mitogen-activated protein kinase kinase (MEK) inhibitor that potently and persistently abrogates extracellular signal-regulated kinase 1/2 activation. Trm initially was used to treat BRAF Val600→Glu (V600E)-mutated melanoma, but its Food and Drug Administration-approved indications are expanding rapidly. Trm generally is well tolerated, but it can cause dose-limiting cardiomyopathy and heart failure. Here, we characterize a mouse model of Trm cardiotoxicity using complementary in vitro approaches to show that Trm induces mitochondrial dysfunction in cardiomyocytes and some cancer cell types. In vivo, Trm caused contractile dysfunction within 3 days and heart failure within 2 weeks. High-resolution respirometry using isolated cardiac mitochondria revealed that Trm compromises oxidative metabolism, in part, through blunted activity of electron transport system complexes. Trm-mediated mitochondrial injury led to the release of mitochondrial damage-associated molecular patterns including mitochondrial DNA in both mice and humans, triggering activation of canonical innate immune pathways including cGAS-STING. In multiple rodent and human cardiomyocyte platforms, Trm diminished mitochondrial respiratory capacity at nanomolar concentrations, but this lesion was reversed by expression of a phosphomimetic signal transducer and activator of transcription 3-S727 construct. We also found that Trm induced mitochondrial dysfunction in some but not all cancer cell lines, identifying a previously unrecognized effect that could contribute to Trm's anticancer efficacy.

DOI: https://doi.org/10.1126/sciadv.aeb2695
Cell Rep. 2026 Jul 08. pii: S2211-1247(26)00744-8. [Epub ahead of print]45(7): 117666

Time-resolved proteolipidomics of the human aorta identifies stage-specific lipid-protein modules across development and aging.

Hao Cui, Sin Man Lam, Yiqi Zhao, Yuan Chang, Mengda Xu, Jingkang Cui, Ningning Zhang, Yifan Wang, Dongxing Zhu, Xiumeng Hua, Xiao Chen, Qian Zhao, Han Mo, Guanghou Shui, Jiangping Song.

  An established vascular network is a prerequisite to ensuring an optimal supply of oxygen and nutrients for sustaining developmental events and systemic function. Herein, we construct a time-resolved proteolipidomic atlas of the aorta across the human life cycle. trans-omics integration reveals that postnatal ganglioside GM3 accumulation is functionally coregulated with calcium homeostasis mediated by plasma membrane calcium-transporting ATPases (PMCAs). We then verify mechanistically in senescence-induced primary vascular smooth muscle cells (VSMCs) that knockdown of GM3 synthase leads to diminished expressions of both PMCA1 and contractile phenotype marker protein. In aged aortas, defects in branched-chain amino acid catabolism emerge as key adult-to-fetal metabolic reversion, with synchronous reductions in serine-derived lipids, including GM3 and phosphatidylserines. Our work suggests that postnatal increases in aortic GM3s maintain PMCA-regulated calcium homeostasis that delays pathological phenotypic transitions of VSMCs. Reductions in aortic GM3s at old age might cause such adaptations to disintegrate and increase disease susceptibility.

Keywords:  CP: developmental biology; aging; aorta; calcification; ganglioside; vascular smooth muscle

DOI:  https://doi.org/10.1016/j.celrep.2026.117666
Nature. 2026 Jul 08.

An intrinsic cytoskeletal oscillator establishes neuronal polarity.

Tien-Chen Lin, Charlotte H Coles, Eissa Alfadil, Florian Fäßler, Andreas Husch, Sebastian Dupraz, Thorben Pietralla, Akihiro Narita, Max Schelski, Kevin C Flynn, Sina Stern, Christoph Möhl, Brett J Hilton, Franz Vauti, Hans-Henning Arnold, Florian K M Schur, Frank Bradke.

Neurons acquire polarity by specifying one neurite as the axon, whereas the others become dendrites. But how this fundamental asymmetry is established remains unclear1. Neuronal polarization has been thought to rely primarily on growth cones that sense external cues2. Here we show that growth cones alone do not direct this process and that the soma acts as a central organizer of neuronal polarization. Using live imaging and genetic loss-of-function approaches in vivo, combined with optogenetic control and local cytoskeletal perturbations in cultured neurons, we uncover a soma-initiated oscillatory program that primes axon selection. Periodic actin branching that depends on the actin-related protein 2/3 (ARP2/3) complex at the soma remodels a global actomyosin network, thereby generating an actin wave that retracts neurites before propagating into a single neurite tip. Exposure to this wave relaxes local actomyosin contractility, which drives a transient microtubule-based protrusion and biases this neurite towards axon fate. As the cell exits this oscillatory stage, this neurite can overcome global inhibition and extend independently of ARP2/3, whereas actomyosin activity suppresses axon formation in the remaining neurites so that they subsequently become dendrites. This soma-driven mechanism ensures the emergence of a single axon independent of environmental cues and underpins the unidirectional information flow in neuronal circuits.

DOI: https://doi.org/10.1038/s41586-026-10755-6
Nat Cell Biol. 2026 Jul 06.

Evolutionarily conserved short linear motifs drive actin filament binding.

Themistoklis Paraschiakos, Biao Yuan, Michael Hecht-Bucher, Kostiantyn Sopelniak, Pasquale Cervero, Lisa Simon, Ksenija Zonjic, Dominic Eggers, Franziska Selle, Jing Li, Ali Biabani, Stefan Linder, Thomas C Marlovits, Sabine Windhorst.

Regulation of the actin cytoskeleton by actin-binding proteins is essential for cellular homeostasis, and the mode of actin binding determines the activity of actin-binding proteins. Here we identify a 'short linear actin filament-binding motif' (SFM) based on the cryo-electron microscopy structure of the ITPKA-actin filament complex. Using the computational pipeline SLiMFold, we discovered 103 human proteins containing SFMs with diverse cellular roles. Phylogenetic analysis suggests that SFMs arose de novo and are conserved across eukaryotes, exhibiting actin filament-binding affinities of 2-12 µM. Critical residues mediating binding and modulating affinity were defined, and the cryo-electron microscopy structures of two SFM-actin filament complexes revealed that SFM binding decreases actin-filament stiffness. These findings indicate that SFMs regulate actin-filament conformation and serve as anchoring modules that connect actin dynamics to a broad variety of cellular functions, providing a framework for understanding the actin-associated roles of numerous proteins.

DOI: https://doi.org/10.1038/s41556-026-01979-9
bioRxiv. 2026 Jul 01. pii: 2026.06.30.735647. [Epub ahead of print]

Topoisomerase IIIα resolves inter- and intra-molecular intertwines during DNA replication.

Sabrina X Van Ravenstein, Lillian V Campos, Gabor M Harami, Darren R Heintzman, Steven N Dahmen, William G Dunphy, Keir C Neuman, James M Dewar.

Resolution of topological stress is crucial for genome integrity. Vertebrate topoisomerase IIα (TOP2α) resolves catenanes to relieve topological stress and unlink daughter molecules during DNA replication. Topoisomerase IIIα (TOP3α) can also resolve catenanes, but its direct role during DNA replication, substrate specificity, and relevant binding partners remain unclear. Here we show that TOP3α becomes crucial when TOP2α function is compromised. We find that in Xenopus egg extracts, TOP3α promotes replication fork progression and daughter strand unlinking specifically during replication termination. TOP3α can carry out this role independently of its binding partners RMI1-RMI2 and the BLM helicase by acting on lagging-strand single-stranded DNA (ssDNA). Strikingly, elevated lagging-strand ssDNA drives formation of intramolecular ssDNA intertwines, which are ordinarily resolved by TOP3α. Thus, TOP3α resolves intermolecular linkages to promote fork progression during termination and resolves intramolecular linkages that arise when high levels of ssDNA are present during DNA replication.

DOI: https://doi.org/10.64898/2026.06.30.735647
Nat Cardiovasc Res. 2026 Jul 07.

Mavacamten shows broad benefit in human and mouse models of MYBPC3-related hypertrophic cardiomyopathy.

Laura Sen-Martín, Ángel Fernández-Trasancos, Miguel Á López-Unzu, Agata Bak, Magdalena Zafra-Castellano, Rajiven Srikantharajah, Divya Pathak, Annika Klotz, Michel N Kuehn, Alessia Ferrarini, Verónica Labrador-Cantarero, David Sánchez-Ortiz, María Rosaria Pricolo, Natalia Vicente, Diana Velázquez-Carreras, Lucía Sánchez-García, Jon Sicilia, José Ángel Nicolás-Ávila, María Sánchez-Díaz, Saskia Schlossarek, Lorena Cussó, Manuel Desco, María Villalba-Orero, Gabriela Guzmán-Martínez, Enrique Calvo, Roberto Barriales-Villa, Jesús Vázquez, Fátima Sánchez-Cabo, Andrés Hidalgo, Pieter P de Tombe, Lucie Carrier, James A Spudich, Kathleen M Ruppel, Florian Weinberger, Olivier Cazorla, Anthony L Hessel, Jorge Alegre-Cebollada.

Mavacamten is a targeted treatment for hypertrophic cardiomyopathy, a disease caused by genetic variants affecting mainly sarcomeric myosin and its regulator cardiac myosin-binding protein C (cMyBP-C, encoded by MYBPC3). Here we generate knock-in mice including missense pathogenic variant cMyBP-C p.R502W, which unlike carriers of cMyBP-C truncations, develop pathogenic myocardial remodeling with preserved cMyBP-C levels and localization. Mechanistically, R502W reduces cMyBP-C-myosin affinity and generates sarcomere hypercontractility due to increased Ca2+ sensitivity and a favored ON structural state of myosin. Even though these pathomechanisms do not overlap with those triggered by truncating MYBPC3 variants, mavacamten blunts myocardial remodeling both in R502W and cMyBP-C-deficient hearts, correlating with the drug's ability to restore OFF myosin in R502W sarcomeres. In R502W human engineered heart tissues, mavacamten also opposes hypercontractility. Hence, our results indicate that mavacamten is effective in treating hypertrophic cardiomyopathy caused by both truncating and missense MYBPC3 variants regardless of their primary pathomechanisms.

DOI: https://doi.org/10.1038/s44161-026-00833-3
Circ Res. 2026 Jul 09.

AMPKγ2 Regulates Cardiac Hypertrophy and Arrhythmias via Interacting With Myosin.

Qianyun Ge, Kusumika Saha, Micah L Burch, Willow H Battista, Ashmita Kc, Max Homilius, Rachelle A Victorio, Dajun Quan, Hsiang-Ling Huang, Joseph M Hazel, Alex Williams, Emily Pan, Krishna Chinthalapudi, Sarah M Heissler, Calum A MacRae, Wandi Zhu.

   BACKGROUND: Variants in PRKAG2 cause hypertrophic cardiomyopathy and conduction disturbances. Although prior studies associated PRKAG2-related hypertrophy with increased glycogen storage, many hypertrophic cardiomyopathy phenotypes remain unexplained. We aimed to uncover how PRKAG2 variants induce myocyte hypertrophy and electrical changes during early cardiac development.
METHODS: We generated transgenic zebrafish expressing wild-type or pathogenic variant Prkag2 cDNA (TgR299Q) under a myocardium-specific promoter, and examined cardiac electrophysiology, contractile function, and cytoarchitecture during cardiogenesis and in adult hearts.
RESULTS: TgR299Q fish showed hypertrophic cardiomyocytes and progressive contractile abnormalities, recapitulating human hypertrophic cardiomyopathy phenotypes. Cardiomyocyte glycogen was elevated in adult but not embryonic hearts. Despite the absence of glycogen accumulation at 6 days postfertilization, TgR299Q hearts showed electrical abnormalities, including reduced conduction velocity and prolonged action potential and Ca2+ transient durations. We observed decreased AMPK (AMP-activated protein kinase) phosphorylation in the TgR299Q hearts. However, AMPK activation did not rescue the electrophysiological abnormalities in TgR299Q. Proximity ligation assays and coimmunoprecipitation identified a physical interaction between AMPKγ2 and myosin, enhanced by the R299Q variant and accompanied by increased AMPKγ2 localization to the myofilament. NCX (Na+/Ca2+ exchanger) inhibition increased Ca2+ duration and diastolic Ca2+ in transgenic zebrafish expressing wild-type Prkag2 cDNA but not TgR299Q hearts, indicating reduced free cytosolic Ca2+ for NCX-mediated extrusion in TgR299Q. These findings suggest that enhanced AMPKγ2-myosin interaction may promote myofilament Ca2+ retention, thereby prolonging Ca2+ transient duration and action potential duration in the mutant. Notably, the myosin inhibitor mavacamten reduced AMPKγ2-myosin interaction in TgR299Q hearts, and both mavacamten and vmhcl knockdown rescued the early electrophysiological abnormalities.
CONCLUSIONS: The PRKAG2 variant altered cardiac excitability, contractility, and Ca2+ handling during cardiogenesis, independent of glycogen accumulation. Enhanced interactions between AMPKγ2 and myosin contributed to these early changes. Our study revealed a novel link between cellular energy sensing and contractile machinery, with therapeutic potential for modulating contractile function in cardiomyopathies.

Keywords:  cardiomyopathy, hypertrophic; glycogen; hypertrophy; myocytes, cardiac; myosins

DOI:  https://doi.org/10.1161/CIRCRESAHA.126.328910