bims-ginsta Biomed News
on Genome instability
Issue of 2024–11–17
48 papers selected by
Jinrong Hu, National University of Singapore
  1. Force-transducing molecular ensembles at growing microtubule tips control mitotic spindle size.
  2. Microtubule poleward flux as a target for modifying chromosome segregation errors.
  3. Cell state transitions are decoupled from cell division during early embryo development.
  4. The chromosome folding problem and how cells solve it.
  5. Protocol for quantifying murine cardiomyocyte cell division by single-cell suspension.
  6. Deep learning-based models for preimplantation mouse and human embryos based on single-cell RNA sequencing.
  7. Harnessing the regenerative potential of interleukin11 to enhance heart repair.
  8. Chromatin remodelling in damaged intestinal crypts orchestrates redundant TGFβ and Hippo signalling to drive regeneration.
  9. How to build a human: Piecing together the body's cellular puzzle.
  10. HURP facilitates spindle assembly by stabilizing microtubules and working synergistically with TPX2.
  11. Clearance of p21 highly expressing senescent cells accelerates cutaneous wound healing.
  12. A comprehensive human embryo reference tool using single-cell RNA-sequencing data.
  13. The Drosophila adult midgut progenitor cells arise from asymmetric divisions of neuroblast-like cells.
  14. Cryo-electron tomography reveals how COPII assembles on cargo-containing membranes.
  15. Transcriptome-scale RNA-targeting CRISPR screens reveal essential lncRNAs in human cells.
  16. Netrin1 patterns the dorsal spinal cord through modulation of Bmp signaling.
  17. STK19 positions TFIIH for cell-free transcription-coupled DNA repair.
  18. How human brains got so big: our cells learned to handle the stress that comes with size.
  19. Tunneling nanotubes enable intercellular transfer in zebrafish embryos.
  20. Nuclear IMPDH2 controls the DNA damage response by modulating PARP1 activity.
  21. A comparative analysis of blastoid models through single-cell transcriptomics.
  22. Opposing roles for AMPK in regulating distinct mitophagy pathways.
  23. Autophagy-dependent splicing control directs translation toward inflammation during senescence.
  24. Klf9 is essential for cardiac mitochondrial homeostasis.
  25. Age-associated metabolic and epigenetic barriers during direct reprogramming of mouse fibroblasts into induced cardiomyocytes.
  26. Structural response of microtubule and actin cytoskeletons to direct intracellular load.
  27. Differential vegfc expression dictates lymphatic response during zebrafish heart development and regeneration.
  28. Shear stress-stimulated AMPK couples endothelial cell mechanics, metabolism, and vasodilation.
  29. A β-hydroxybutyrate shunt pathway generates anti-obesity ketone metabolites.
  30. Spatiotemporal modeling of molecular holograms.
  31. HIRA and dPCIF1 coordinately establish totipotent chromatin and control orderly ZGA in Drosophila embryos.
  32. Errors in cell division stopped by an atypical cyclin-dependent kinase.
  33. Brca1 haploinsufficiency promotes early tumor onset and epigenetic alterations in a mouse model of hereditary breast cancer.
  34. Charting and probing the activity of ADARs in human development and cell-fate specification.
  35. CRISPRi/a screens in human iPSC-cardiomyocytes identify glycolytic activation as a druggable target for doxorubicin-induced cardiotoxicity.
  36. Depolarization induces calcium-dependent BMP4 release from mouse embryonic palate mesenchymal cells.
  37. Regulated N-glycosylation controls chaperone function and receptor trafficking.
  38. Low-affinity ligands of the epidermal growth factor receptor are long-range signal transmitters in collective cell migration of epithelial cells.
  39. A non-canonical role of somatic Cyclin D/CYD-1 in oogenesis and in maintenance of reproductive fidelity, dependent on the FOXO/DAF-16 activation state.
  40. Clinical functional proteomics of intercellular signalling in pancreatic cancer.
  41. Spermidine limits diabetes by modulating RIPK1-mediated cell death and inflammation.
  42. Mechano-gradients drive morphogen-noise correction to ensure robust patterning.
  43. MDM4 exon skipping upon dysfunctional ribosome assembly.
  44. Cardiac regeneration leads to altered Purkinje fiber network and ventricular conduction.
  45. Pathogenic proteotoxicity of cryptic splicing is alleviated by ubiquitination and ER-phagy.
  46. NK2R control of energy expenditure and feeding to treat metabolic diseases.
  47. Nicotinamide and pyridoxine stimulate muscle stem cell expansion and enhance regenerative capacity during aging.
  48. Hepatocellular senescence induces multi-organ senescence and dysfunction via TGFβ.
  1. Nat Commun. 2024 Nov 14. 15(1): 9865
    Force-transducing molecular ensembles at growing microtubule tips control mitotic spindle size.
    Lee-Ya Chu, Daniel Stedman, Julian Gannon, Susan Cox, Georgii Pobegalov, Maxim I Molodtsov.
      Correct mitotic spindle size is required for accurate chromosome segregation during cell division. It is controlled by mechanical forces generated by molecular motors and non-motor proteins acting on spindle microtubules. However, how forces generated by individual proteins enable bipolar spindle organization is not well understood. Here, we develop tools to measure contributions of individual molecules to this force balance. We show that microtubule plus-end binding proteins act at microtubule tips synergistically with minus-end directed motors to produce a system that can generate both pushing and pulling forces. To generate pushing force, the system harnesses forces generated by the growing tips of microtubules providing unique contribution to the force balance distinct from all other motors that act in the mitotic spindle. Our results reveal that microtubules are essential force generators for establishing spindle size and pave the way for understanding how mechanical forces can be fine-tuned to control the fidelity of chromosome segregation.
    DOI:  https://doi.org/10.1038/s41467-024-54123-2
  2. Proc Natl Acad Sci U S A. 2024 Nov 19. 121(47): e2405015121
    Microtubule poleward flux as a target for modifying chromosome segregation errors.
    Patrik Risteski, Jelena Martinčić, Mihaela Jagrić, Erna Tintor, Ana Petelinec, Iva M Tolić.
      Cancer cells often display errors in chromosome segregation, some of which result from improper chromosome alignment at the spindle midplane. Chromosome alignment is facilitated by different rates of microtubule poleward flux between sister kinetochore fibers. However, the role of the poleward flux in supporting mitotic fidelity remains unknown. Here, we introduce the hypothesis that the finely tuned poleward flux safeguards against lagging chromosomes and micronuclei at mitotic exit by promoting chromosome alignment in metaphase. We used human untransformed RPE-1 cells depleted of KIF18A/kinesin-8 as a system with reduced mitotic fidelity, which we rescued by three mechanistically independent treatments, comprising low-dose taxol or codepletion of the spindle proteins HAUS8 or NuMA. The rescue of mitotic errors was due to shortening of the excessively long overlaps of antiparallel microtubules, serving as a platform for motor proteins that drive the flux, which in turn slowed down the overly fast flux and improved chromosome alignment. In contrast to the prevailing view, the rescue was not accompanied by reduction of overall microtubule growth rates. Instead, speckle microscopy revealed that the improved chromosome alignment in the rescue treatments was associated with slower growth and flux of kinetochore microtubules. In a similar manner, a low-dose taxol treatment rescued mitotic errors in a high-grade serous ovarian carcinoma cell line OVKATE. Collectively, our results highlight the potential of targeting microtubule poleward flux to modify chromosome instability and provide insight into the mechanism through which low doses of taxol rescue certain mitotic errors in cancer cells.
    Keywords:  chromosome alignment; chromosome instability; chromosome segregation; microtubule poleward flux; mitosis
    DOI:  https://doi.org/10.1073/pnas.2405015121
  3. Nat Cell Biol. 2024 Nov 08.
    Cell state transitions are decoupled from cell division during early embryo development.
    Kalki Kukreja, Bill Z Jia, Sean E McGeary, Nikit Patel, Sean G Megason, Allon M Klein.
      As tissues develop, cells divide and differentiate concurrently. Conflicting evidence shows that cell division is either dispensable or required for formation of cell types. Here, to determine the role of cell division in differentiation, we arrested the cell cycle in zebrafish embryos using two independent approaches and profiled them at single-cell resolution. We show that cell division is dispensable for differentiation of all embryonic tissues from early gastrulation to the end of segmentation. However, arresting cell division does slow down differentiation in some cell types, and it induces global stress responses. While differentiation is robust to blocking cell division, the proportions of cells across cell states are not, but show evidence of partial compensation. This work clarifies our understanding of the role of cell division in development and showcases the utility of combining embryo-wide perturbations with single-cell RNA sequencing to uncover the role of common biological processes across multiple tissues.
    DOI:  https://doi.org/10.1038/s41556-024-01546-0
  4. Cell. 2024 Nov 14. pii: S0092-8674(24)01208-X. [Epub ahead of print]187(23): 6424-6450
    The chromosome folding problem and how cells solve it.
    Job Dekker, Leonid A Mirny.
      Every cell must solve the problem of how to fold its genome. We describe how the folded state of chromosomes is the result of the combined activity of multiple conserved mechanisms. Homotypic affinity-driven interactions lead to spatial partitioning of active and inactive loci. Molecular motors fold chromosomes through loop extrusion. Topological features such as supercoiling and entanglements contribute to chromosome folding and its dynamics, and tethering loci to sub-nuclear structures adds additional constraints. Dramatically diverse chromosome conformations observed throughout the cell cycle and across the tree of life can be explained through differential regulation and implementation of these basic mechanisms. We propose that the first functions of chromosome folding are to mediate genome replication, compaction, and segregation and that mechanisms of folding have subsequently been co-opted for other roles, including long-range gene regulation, in different conditions, cell types, and species.
    DOI:  https://doi.org/10.1016/j.cell.2024.10.026
  5. STAR Protoc. 2024 Nov 08. pii: S2666-1667(24)00617-8. [Epub ahead of print]5(4): 103452
    Protocol for quantifying murine cardiomyocyte cell division by single-cell suspension.
    Samantha K Swift, Alexandra L Purdy, Michaela Patterson.
      The cardiac regeneration and development fields lack low-barrier-to-entry techniques that distinguish cardiomyocyte division from alternative outcomes in vivo. Here, we present a protocol in rodents to determine if cardiomyocyte cell division has occurred. We describe thymidine analog administration, Langendorff procedure, immunofluorescent labeling, microscopy, and analysis of fluorescent images to assess ploidy, thereby allowing an investigator to retrospectively claim cell division. Finally, we provide instructions for additional metrics including quantification of total cardiomyocytes, total cycling cardiomyocytes, and cellular dimensions. For complete details on the use and execution of this protocol, please refer to Swift et al.1.
    Keywords:  Cell Biology; Developmental biology; Microscopy
    DOI:  https://doi.org/10.1016/j.xpro.2024.103452
  6. Nat Methods. 2024 Nov 14.
    Deep learning-based models for preimplantation mouse and human embryos based on single-cell RNA sequencing.
    Martin Proks, Nazmus Salehin, Joshua M Brickman.
      The rapid growth of single-cell transcriptomic technology has produced an increasing number of datasets for both embryonic development and in vitro pluripotent stem cell-derived models. This avalanche of data surrounding pluripotency and the process of lineage specification has meant it has become increasingly difficult to define specific cell types or states in vivo, and compare these with in vitro differentiation. Here we utilize a set of deep learning tools to integrate and classify multiple datasets. This allows the definition of both mouse and human embryo cell types, lineages and states, thereby maximizing the information one can garner from these precious experimental resources. Our approaches are built on recent initiatives for large-scale human organ atlases, but here we focus on material that is difficult to obtain and process, spanning early mouse and human development. Using publicly available data for these stages, we test different deep learning approaches and develop a model to classify cell types in an unbiased fashion at the same time as defining the set of genes used by the model to identify lineages, cell types and states. We used our models trained on in vivo development to classify pluripotent stem cell models for both mouse and human development, showcasing the importance of this resource as a dynamic reference for early embryogenesis.
    DOI:  https://doi.org/10.1038/s41592-024-02511-3
  7. Nat Commun. 2024 Nov 08. 15(1): 9666
    Harnessing the regenerative potential of interleukin11 to enhance heart repair.
    Kwangdeok Shin, Anjelica Rodriguez-Parks, Chanul Kim, Isabella M Silaban, Yu Xia, Jisheng Sun, Chenyang Dong, Sunduz Keles, Jinhu Wang, Jingli Cao, Junsu Kang.
      Balancing between regenerative processes and fibrosis is crucial for heart repair, yet strategies regulating this balance remain a barrier to developing therapies. The role of Interleukin 11 (IL11) in heart regeneration remains controversial, as both regenerative and fibrotic functions have been reported. We uncovered that il11a, an Il11 homolog in zebrafish, can trigger robust regenerative programs in zebrafish hearts, including cardiomyocytes proliferation and coronary expansion, even in the absence of injury. Notably, il11a induction in uninjured hearts also activates the quiescent epicardium to produce epicardial progenitor cells, which later differentiate into cardiac fibroblasts. Consequently, prolonged il11a induction indirectly leads to persistent fibroblast emergence, resulting in cardiac fibrosis. While deciphering the regenerative and fibrotic effects of il11a, we found that il11-dependent fibrosis, but not regeneration, is mediated through ERK activity, suggesting to potentially uncouple il11a dual effects on regeneration and fibrosis. To harness the il11a's regenerative ability, we devised a combinatorial treatment through il11a induction with ERK inhibition. This approach enhances cardiomyocyte proliferation with mitigated fibrosis, achieving a balance between regenerative processes and fibrosis. Thus, we unveil the mechanistic insights into regenerative il11 roles, offering therapeutic avenues to foster cardiac repair without exacerbating fibrosis.
    DOI:  https://doi.org/10.1038/s41467-024-54060-0
  8. Nat Cell Biol. 2024 Nov 15.
    Chromatin remodelling in damaged intestinal crypts orchestrates redundant TGFβ and Hippo signalling to drive regeneration.
    Mardi Fink, Kizito Njah, Shyam J Patel, David P Cook, Vanessa Man, Francesco Ruso, Arsheen Rajan, Masahiro Narimatsu, Andreea Obersterescu, Melanie J Pye, Daniel Trcka, Kin Chan, Arshad Ayyaz, Jeffrey L Wrana.
      Cell state dynamics underlying successful tissue regeneration are undercharacterized. In the intestine, damage prompts epithelial reprogramming into revival stem cells (revSCs) that reconstitute Lgr5+ intestinal stem cells (ISCs). Here single-nuclear multi-omics of mouse crypts regenerating from irradiation shows revSC chromatin accessibility overlaps with ISCs and differentiated lineages. While revSC genes themselves are accessible throughout homeostatic epithelia, damage-induced remodelling of chromatin in the crypt converges on Hippo and the transforming growth factor-beta (TGFβ) signalling pathway, which we show is transiently activated and directly induces functional revSCs. Combinatorial gene expression analysis further suggests multiple sources of revSCs, and we demonstrate TGFβ can reprogramme enterocytes, goblet and paneth cells into revSCs and show individual revSCs form organoids. Despite this, loss of TGFβ signalling yields mild regenerative defects, whereas interference in both Hippo and TGFβ leads to profound defects and death. Intestinal regeneration is thus poised for activation by a compensatory system of crypt-localized, transient morphogen cues that support epithelial reprogramming and robust intestinal repair.
    DOI:  https://doi.org/10.1038/s41556-024-01550-4
  9. Science. 2024 Nov 15. 386(6723): 739
    How to build a human: Piecing together the body's cellular puzzle.
    Jarrod Shilts.
      Piecing together the body's cellular puzzle.
    DOI:  https://doi.org/10.1126/science.adt9012
  10. Nat Commun. 2024 Nov 08. 15(1): 9689
    HURP facilitates spindle assembly by stabilizing microtubules and working synergistically with TPX2.
    Venecia Alexandria Valdez, Meisheng Ma, Bernardo Gouveia, Rui Zhang, Sabine Petry.
      In vertebrate spindles, most microtubules are formed via branching microtubule nucleation, whereby microtubules nucleate along the side of pre-existing microtubules. Hepatoma up-regulated protein (HURP) is a microtubule-associated protein that has been implicated in spindle assembly, but its mode of action is yet to be defined. In this study, we show that HURP is necessary for RanGTP-induced branching microtubule nucleation in Xenopus egg extract. Specifically, HURP stabilizes the microtubule lattice to promote microtubule formation from γ-TuRC. This function is shifted to promote branching microtubule nucleation through enhanced localization to TPX2 condensates, which form the core of the branch site on microtubules. Lastly, we provide a high-resolution cryo-EM structure of HURP on the microtubule, revealing how HURP binding stabilizes the microtubule lattice. We propose a model in which HURP stabilizes microtubules during their formation, and TPX2 preferentially enriches HURP to microtubules to promote branching microtubule nucleation and thus spindle assembly.
    DOI:  https://doi.org/10.1038/s41467-024-53630-6
  11. Nat Aging. 2024 Nov 13.
    Clearance of p21 highly expressing senescent cells accelerates cutaneous wound healing.
    Nathan S Gasek, Pengyi Yan, Junyu Zhu, K-Raman Purushothaman, Taewan Kim, Lichao Wang, Binsheng Wang, William F Flynn, Mingda Sun, Chun Guo, Billy Huggins, Roshanak Sharafieh, Yueying Zhou, Vojtech Parizek, Tamar Tchkonia, James L Kirkland, Saranya P Wyles, Ming Xu.
      While senescent cells have detrimental roles in several contexts, they are highly heterogeneous. p16 highly expressing senescent cells have been reported to exert beneficial functions in wound healing. Here we use Xenium spatial transcriptomics to identify a distinct p21 highly expressing senescent population induced on wounding, with a pro-inflammatory profile. We find that clearing p21 highly expressing cells expedites wound closure and is partially mediated by NF-κB inhibition, thus enhancing our understanding of the multifaceted functions of senescence in tissue remodeling.
    DOI:  https://doi.org/10.1038/s43587-024-00755-4
  12. Nat Methods. 2024 Nov 14.
    A comprehensive human embryo reference tool using single-cell RNA-sequencing data.
    Cheng Zhao, Alvaro Plaza Reyes, John Paul Schell, Jere Weltner, Nicolás M Ortega, Yi Zheng, Åsa K Björklund, Laura Baqué-Vidal, Joonas Sokka, Ras Torokovic, Brian Cox, Janet Rossant, Jianping Fu, Sophie Petropoulos, Fredrik Lanner.
      Stem cell-based embryo models offer unprecedented experimental tools for studying early human development. The usefulness of embryo models hinges on their molecular, cellular and structural fidelities to their in vivo counterparts. To authenticate human embryo models, single-cell RNA sequencing has been utilized for unbiased transcriptional profiling. However, an organized and integrated human single-cell RNA-sequencing dataset, serving as a universal reference for benchmarking human embryo models, remains unavailable. Here we developed such a reference through the integration of six published human datasets covering development from the zygote to the gastrula. Lineage annotations are contrasted and validated with available human and nonhuman primate datasets. Using stabilized Uniform Manifold Approximation and Projection, we constructed an early embryogenesis prediction tool, where query datasets can be projected on the reference and annotated with predicted cell identities. Using this reference tool, we examined published human embryo models, highlighting the risk of misannotation when relevant references are not utilized for benchmarking and authentication.
    DOI:  https://doi.org/10.1038/s41592-024-02493-2
  13. Dev Cell. 2024 Nov 05. pii: S1534-5807(24)00630-0. [Epub ahead of print]
    The Drosophila adult midgut progenitor cells arise from asymmetric divisions of neuroblast-like cells.
    Andrew T Plygawko, Camille Stephan-Otto Attolini, Ioanna Pitsidianaki, David P Cook, Alistair C Darby, Kyra Campbell.
      The Drosophila adult midgut progenitor cells (AMPs) give rise to all cells in the adult midgut epithelium, including the intestinal stem cells (ISCs). While they share many characteristics with the ISCs, it remains unclear how they are generated in the early embryo. Here, we show that they arise from a population of endoderm cells, which exhibit multiple similarities with Drosophila neuroblasts. These cells, which we have termed endoblasts, are patterned by homothorax (Hth) and undergo asymmetric divisions using the same molecular machinery as neuroblasts. We also show that the conservation of this molecular machinery extends to the generation of the enteroendocrine lineages. Parallels have previously been drawn between the pupal ISCs and larval neuroblasts. Our results suggest that these commonalities exist from the earliest stages of specification of progenitor cells of the intestinal and nervous systems and may represent an ancestral pathway for multipotent progenitor cell specification.
    Keywords:  Drosophila; adult progenitor cells; asymmetric division; endoderm; enteroendocrine cells; midgut; morphogenesis; scRNA-seq; stem cells
    DOI:  https://doi.org/10.1016/j.devcel.2024.10.011
  14. Nat Struct Mol Biol. 2024 Nov 07.
    Cryo-electron tomography reveals how COPII assembles on cargo-containing membranes.
    Euan Pyle, Elizabeth A Miller, Giulia Zanetti.
      Proteins traverse the eukaryotic secretory pathway through membrane trafficking between organelles. The coat protein complex II (COPII) mediates the anterograde transport of newly synthesized proteins from the endoplasmic reticulum, engaging cargoes with a wide range of size and biophysical properties. The native architecture of the COPII coat and how cargo might influence COPII carrier morphology remain poorly understood. Here we reconstituted COPII-coated membrane carriers using purified Saccharomyces cerevisiae proteins and cell-derived microsomes as a native membrane source. Using cryo-electron tomography with subtomogram averaging, we demonstrate that the COPII coat binds cargo and forms largely spherical vesicles from native membranes. We reveal the architecture of the inner and outer coat layers and shed light on how spherical carriers are formed. Our results provide insights into the architecture and regulation of the COPII coat and advance our current understanding of how membrane curvature is generated.
    DOI:  https://doi.org/10.1038/s41594-024-01413-4
  15. Cell. 2024 Nov 11. pii: S0092-8674(24)01203-0. [Epub ahead of print]
    Transcriptome-scale RNA-targeting CRISPR screens reveal essential lncRNAs in human cells.
    Wen-Wei Liang, Simon Müller, Sydney K Hart, Hans-Hermann Wessels, Alejandro Méndez-Mancilla, Akash Sookdeo, Olivia Choi, Christina M Caragine, Alba Corman, Lu Lu, Olena Kolumba, Breanna Williams, Neville E Sanjana.
      Mammalian genomes host a diverse array of RNA that includes protein-coding and noncoding transcripts. However, the functional roles of most long noncoding RNAs (lncRNAs) remain elusive. Using RNA-targeting CRISPR-Cas13 screens, we probed how the loss of ∼6,200 lncRNAs impacts cell fitness across five human cell lines and identified 778 lncRNAs with context-specific or broad essentiality. We confirm their essentiality with individual perturbations and find that the majority of essential lncRNAs operate independently of their nearest protein-coding genes. Using transcriptome profiling in single cells, we discover that the loss of essential lncRNAs impairs cell-cycle progression and drives apoptosis. Many essential lncRNAs demonstrate dynamic expression across tissues during development. Using ∼9,000 primary tumors, we pinpoint those lncRNAs whose expression in tumors correlates with survival, yielding new biomarkers and potential therapeutic targets. This transcriptome-wide survey of functional lncRNAs advances our understanding of noncoding transcripts and demonstrates the potential of transcriptome-scale noncoding screens with Cas13.
    Keywords:  CRISPR-Cas13; MALAT1; MIR17HG; RNA targeting; SLC16A1-AS1; essential genes; human development; lncRNA; noncoding RNA; transcriptome scale; tumor biomarkers
    DOI:  https://doi.org/10.1016/j.cell.2024.10.021
  16. Cell Rep. 2024 Nov 07. pii: S2211-1247(24)01305-6. [Epub ahead of print] 114954
    Netrin1 patterns the dorsal spinal cord through modulation of Bmp signaling.
    Sandy Alvarez, Sandeep Gupta, Yesica Mercado-Ayon, Kaitlyn Honeychurch, Cristian Rodriguez, Riki Kawaguchi, Samantha J Butler.
      We have identified an unexpected role for netrin1, a canonical axonal guidance cue, as a suppressor of bone morphogenetic protein (Bmp) signaling in the developing dorsal spinal cord. Using a combination of gain- and loss-of-function approaches in chicken and mouse embryonic models, as well as mouse embryonic stem cells (mESCs), we have observed that manipulating the level of netrin1 specifically alters the patterning of the Bmp-dependent dorsal interneurons (dIs), dI1-dI3. Altered netrin1 levels also change Bmp signaling activity, as assessed using bioinformatic approaches, as well as monitoring phosophoSmad1/5/8 activation, the canonical intermediate of Bmp signaling, and Id levels, a known Bmp target. Together, these studies support the hypothesis that netrin1 acts from the intermediate spinal cord to regionally confine Bmp signaling to the dorsal spinal cord. Thus, netrin1 has reiterative activities shaping dorsal spinal circuits, first by regulating cell fate decisions and then acting as a guidance cue to direct axon extension.
    Keywords:  Bmp; Bmp inhibition; CP: Developmental biology; CP: Neuroscience; cell fate; dorsal interneurons; interneuron differentiation; netrin1; neural development; patterning; spinal cord
    DOI:  https://doi.org/10.1016/j.celrep.2024.114954
  17. Cell. 2024 Nov 12. pii: S0092-8674(24)01202-9. [Epub ahead of print]
    STK19 positions TFIIH for cell-free transcription-coupled DNA repair.
    Tycho E T Mevissen, Maximilian Kümmecke, Ernst W Schmid, Lucas Farnung, Johannes C Walter.
      In transcription-coupled nucleotide excision repair (TC-NER), stalled RNA polymerase II (RNA Pol II) binds CSB and CRL4CSA, which cooperate with UVSSA and ELOF1 to recruit TFIIH. To explore the mechanism of TC-NER, we recapitulated this reaction in vitro. When a plasmid containing a site-specific lesion is transcribed in frog egg extract, error-free repair is observed that depends on CSB, CRL4CSA, UVSSA, and ELOF1. Repair also requires STK19, a factor previously implicated in transcription recovery after UV exposure. A 1.9-Å cryo-electron microscopy structure shows that STK19 binds the TC-NER complex through CSA and the RPB1 subunit of RNA Pol II. Furthermore, AlphaFold predicts that STK19 interacts with the XPD subunit of TFIIH, and disrupting this interface impairs cell-free repair. Molecular modeling suggests that STK19 positions TFIIH ahead of RNA Pol II for lesion verification. Our analysis of cell-free TC-NER suggests that STK19 couples RNA Pol II stalling to downstream repair events.
    Keywords:  AlphaFold; NER; STK19; TFIIH; cryo-EM; nucleotide excision repair; transcription; transcription-coupled DNA repair
    DOI:  https://doi.org/10.1016/j.cell.2024.10.020
  18. Nature. 2024 Nov 15.
    How human brains got so big: our cells learned to handle the stress that comes with size.
    Miryam Naddaf.
      
    Keywords:  Brain; Evolution
    DOI:  https://doi.org/10.1038/d41586-024-03716-4
  19. Dev Cell. 2024 Nov 08. pii: S1534-5807(24)00635-X. [Epub ahead of print]
    Tunneling nanotubes enable intercellular transfer in zebrafish embryos.
    Olga Korenkova, Shiyu Liu, Inès Prlesi, Anna Pepe, Shahad Albadri, Filippo Del Bene, Chiara Zurzolo.
      Tunneling nanotubes (TNTs) are thin intercellular connections that facilitate the transport of diverse cargoes, ranging from ions to organelles. While TNT studies have predominantly been conducted in cell cultures, the existence of open-ended TNTs within live organisms remains unverified. Despite the observation of intercellular connections during embryonic development across various species, their functional role in facilitating material transfer between connected cells has not been confirmed. In this study, we performed mosaic labeling of gastrula cells in zebrafish embryos to demonstrate the coexistence of TNT-like structures alongside other cellular protrusions. These embryonic TNT-like connections exhibited a morphology similar to that of TNTs described in cell culture, appeared to have similar formation mechanisms, and could be induced by Eps8 overexpression and CK666 treatment. Most notably, we demonstrated their capability to transfer both soluble cargoes and organelles, thus confirming their open-endedness. This study demonstrates the existence of functional, open-ended TNTs in a living embryo.
    Keywords:  TNT-like structures; TNTs; cytokinetic bridges; cytonemes; intercellular communication; intercellular connections; organelle transfer; tunneling nanotubes; zebrafish embryo; zebrafish gastrula
    DOI:  https://doi.org/10.1016/j.devcel.2024.10.016
  20. Nat Commun. 2024 Nov 12. 15(1): 9515
    Nuclear IMPDH2 controls the DNA damage response by modulating PARP1 activity.
    Lorena Espinar, Marta Garcia-Cao, Alisa Schmidt, Savvas Kourtis, Antoni Gañez Zapater, Carla Aranda-Vallejo, Ritobrata Ghose, Laura Garcia-Lopez, Ilir Sheraj, Natalia Pardo-Lorente, Marina Bantulà, Laura Pascual-Reguant, Evangelia Darai, Maria Guirola, Joan Montero, Sara Sdelci.
      Nuclear metabolism and DNA damage response are intertwined processes, but the precise molecular links remain elusive. Here, we explore this crosstalk using triple-negative breast cancer (TNBC) as a model, a subtype often prone to DNA damage accumulation. We show that the de novo purine synthesis enzyme IMPDH2 is enriched on chromatin in TNBC compared to other subtypes. IMPDH2 chromatin localization is DNA damage dependent, and IMPDH2 repression leads to DNA damage accumulation. On chromatin, IMPDH2 interacts with and modulates PARP1 activity by controlling the nuclear availability of NAD+ to fine-tune the DNA damage response. However, when IMPDH2 is restricted to the nucleus, it depletes nuclear NAD+, leading to PARP1 cleavage and cell death. Our study identifies a non-canonical nuclear role for IMPDH2, acting as a convergence point of nuclear metabolism and DNA damage response.
    DOI:  https://doi.org/10.1038/s41467-024-53877-z
  21. iScience. 2024 Nov 15. 27(11): 111122
    A comparative analysis of blastoid models through single-cell transcriptomics.
    Ali Balubaid, Samhan Alsolami, Narsis A Kiani, David Gomez-Cabrero, Mo Li, Jesper Tegner.
      Pluripotent-stem-cell-derived blastocyst-like structures (blastoids) offer insights into early human embryogenesis (5-10 days post-fertilization). The similarity between blastoids and human blastocysts remains uncertain. To investigate, we evaluated single-cell RNA sequencing (scRNAseq) data from seven blastoid models, comparing them to peri-implantation blastocysts. We quantified cell-type composition, transcriptomic overlap, lineage profiles, and developmental propensities for primary (epiblast, primitive endoderm, trophectoderm) and potential lineages (amnion, extravillous cytotrophoblasts, syncytial trophoblasts). Blastoids from extended pluripotent stem cells (EPSCs) are distinct from those from naive pluripotent stem cells (nPSCs), which cluster closer to natural blastocysts. EPSC-blastoids show a higher composition of primitive endoderm cells and ambiguous cells with notable endoderm signatures. Starting cell lines' scRNAseq analysis reveals higher heterogeneity in nPSCs and prevalent amnionic signatures in EPSCs. These findings suggest gene expression heterogeneity in founding cells influences blastoid lineage differentiation, aiding protocol optimization for better human embryogenesis models.
    Keywords:  Developmental biology; Stem cells research; Transcriptomics
    DOI:  https://doi.org/10.1016/j.isci.2024.111122
  22. Mol Cell. 2024 Nov 05. pii: S1097-2765(24)00865-7. [Epub ahead of print]
    Opposing roles for AMPK in regulating distinct mitophagy pathways.
    Marianna Longo, Aniketh Bishnu, Pierpaolo Risiglione, Lambert Montava-Garriga, Joyceline Cuenco, Kei Sakamoto, Carol MacKintosh, Ian G Ganley.
      Mitophagy degrades damaged mitochondria, but we show here that it can also target functional mitochondria. This latter scenario occurs during programmed mitophagy and involves the mitophagy receptors NIX and BNIP3. Although AMP-activated protein kinase (AMPK), the energy-sensing protein kinase, can influence damaged-induced mitophagy, its role in programmed mitophagy is unclear. We found that AMPK directly inhibits NIX-dependent mitophagy by triggering 14-3-3-mediated sequestration of ULK1, via ULK1 phosphorylation at two sites: Ser556 and an additional identified site, Ser694. By contrast, AMPK activation increases Parkin phosphorylation and enhances the rate of depolarization-induced mitophagy, independently of ULK1. We show that this happens both in cultured cells and tissues in vivo, using the mito-QC mouse model. Our work unveils a mechanism whereby AMPK activation downregulates mitophagy of functional mitochondria but enhances that of dysfunctional/damaged ones.
    Keywords:  14-3-3; AMPK; NIX; Parkin; ULK1; autophagy; liver; mito-QC; mitophagy; skeletal muscle
    DOI:  https://doi.org/10.1016/j.molcel.2024.10.025
  23. Dev Cell. 2024 Nov 01. pii: S1534-5807(24)00627-0. [Epub ahead of print]
    Autophagy-dependent splicing control directs translation toward inflammation during senescence.
    Jaejin Kim, Yeonghyeon Lee, Taerang Jeon, Seonmin Ju, Jong-Seo Kim, Mi-Sung Kim, Chanhee Kang.
      The cellular proteome determines the functional state of cells and is often skewed to direct pathological conditions. Autophagy shapes cellular proteomes primarily through lysosomal degradation of either damaged or unnecessary proteins. Here, we show that autophagy directs the senescence-specific translatome to fuel inflammation by coupling selective protein degradation with alternative splicing. RNA splicing is significantly altered during senescence, some of which surprisingly depend on autophagy, including exon 5 skipping of the translation regulator EIF4H. Systematic translatome profiling indicates that this event is key to the translational bias toward inflammation in senescence. Autophagy promotes these changes by selectively degrading the splicing regulator splicing factor proline and glutamine rich (SFPQ) via the autophagy receptor NBR1. These autophagy-centric inflammatory controls appear to be conserved during human tissue aging and cancer. Our work highlights the role of autophagy in the on-demand functional remodeling of cellular proteomes as well as the crosstalk between autophagy, alternative splicing, and inflammatory translation.
    Keywords:  RNA homeostasis; aging; alternative splicing; autophagy; cancer; cellular senescence; inflammation; protein translation; selective autophagy
    DOI:  https://doi.org/10.1016/j.devcel.2024.10.008
  24. Nat Cardiovasc Res. 2024 Nov;3(11): 1318-1336
    Klf9 is essential for cardiac mitochondrial homeostasis.
    Lei Zhang, Menglin Zhang, Jinlong Huang, Jincan Huang, Yujie Zhang, Yinliang Zhang, Houzao Chen, Cuizhe Wang, Xiangwen Xi, Heng Fan, Jikui Wang, Dingsheng Jiang, Jinwei Tian, Jun Zhang, Yongsheng Chang.
      Mitochondrial dynamics and mitophagy are intimately linked physiological processes that are essential for cardiac homeostasis. Here we show that cardiac Krüppel-like factor 9 (Klf9) is dysregulated in human and rodent cardiomyopathy. Both global and cardiac-specific Klf9-deficient mice displayed hypertrophic cardiomyopathy. Klf9 knockout led to mitochondrial disarray and fragmentation, impairing mitochondrial respiratory function in cardiomyocytes. Furthermore, cardiac Klf9 deficiency inhibited mitophagy, thereby causing accumulation of dysfunctional mitochondria and acceleration of heart failure in response to angiotensin II treatment. In contrast, cardiac-specific Klf9 transgene improved cardiac systolic function. Mechanistically, Klf9 knockout decreased the expression of PGC-1α and its target genes involved in mitochondrial energy metabolism. Moreover, Klf9 controlled the expression of Mfn2, thereby regulating mitochondrial dynamics and mitophagy. Finally, adeno-associated virus-mediated Mfn2 rescue in Klf9-CKO hearts improved cardiac mitochondrial and systolic function. Thus, Klf9 integrates cardiac energy metabolism, mitochondrial dynamics and mitophagy. Modulating Klf9 activity may have therapeutic potential in the treatment of heart failure.
    DOI:  https://doi.org/10.1038/s44161-024-00561-6
  25. Aging Cell. 2024 Nov 14. e14371
    Age-associated metabolic and epigenetic barriers during direct reprogramming of mouse fibroblasts into induced cardiomyocytes.
    Francisco Santos, Magda Correia, Rafaela Dias, Bárbara Bola, Roberta Noberini, Rita S Ferreira, Diogo Trigo, Pedro Domingues, José Teixeira, Tiziana Bonaldi, Paulo J Oliveira, Christian Bär, Bruno Bernardes de Jesus, Sandrina Nóbrega-Pereira.
      Heart disease is the leading cause of mortality in developed countries, and novel regenerative procedures are warranted. Direct cardiac conversion (DCC) of adult fibroblasts can create induced cardiomyocytes (iCMs) for gene and cell-based heart therapy, and in addition to holding great promise, still lacks effectiveness as metabolic and age-associated barriers remain elusive. Here, by employing MGT (Mef2c, Gata4, Tbx5) transduction of mouse embryonic fibroblasts (MEFs) and adult (dermal and cardiac) fibroblasts from animals of different ages, we provide evidence that the direct reprogramming of fibroblasts into iCMs decreases with age. Analyses of histone posttranslational modifications and ChIP-qPCR revealed age-dependent alterations in the epigenetic landscape of DCC. Moreover, DCC is accompanied by profound mitochondrial metabolic adaptations, including a lower abundance of anabolic metabolites, network remodeling, and reliance on mitochondrial respiration. In vitro metabolic modulation and dietary manipulation in vivo improve DCC efficiency and are accompanied by significant alterations in histone marks and mitochondrial homeostasis. Importantly, adult-derived iCMs exhibit increased accumulation of oxidative stress in the mitochondria and activation of mitophagy or dietary lipids; they improve DCC and revert mitochondrial oxidative damage. Our study provides evidence that metaboloepigenetics plays a direct role in cell fate transitions driving DCC, highlighting the potential use of metabolic modulation to improve cardiac regenerative strategies.
    Keywords:  aging; cardiomyocytes; direct reprogramming; epigenetic; fibroblasts; metabolism; mitochondria; regenerative biology
    DOI:  https://doi.org/10.1111/acel.14371
  26. J Cell Biol. 2025 Feb 03. pii: e202403136. [Epub ahead of print]224(2):
    Structural response of microtubule and actin cytoskeletons to direct intracellular load.
    Ryota Orii, Hirokazu Tanimoto.
      Microtubule and actin are the two major cytoskeletal polymers that form organized functional structures in the interior of eukaryotic cells. Although the structural mechanics of the cytoskeleton has been extensively studied by direct manipulations in in vitro reconstitution systems, such unambiguous characterizations inside the living cell are sparse. Here, we report a comprehensive analysis of how the microtubule and actin cytoskeletons structurally respond to direct intracellular load. Ferrofluid-based intracellular magnetic tweezers reveal rheological properties of the microtubule complex primarily determined by filamentous actin. The strain fields of the microtubule complex and actin meshwork follow the same scaling, suggesting that the two cytoskeletal systems behave as an integrated elastic body. The structural responses of single microtubules to contact and remote forces further evidence that the individual microtubules are enclosed by the elastic medium of actin. These results, directly characterizing the microtubule and actin cytoskeletons as an interacting continuum throughout the cytoplasm, serve as a cornerstone for the physical understanding of intracellular organization.
    DOI:  https://doi.org/10.1083/jcb.202403136
  27. Development. 2024 Nov 08. pii: dev.202947. [Epub ahead of print]
    Differential vegfc expression dictates lymphatic response during zebrafish heart development and regeneration.
    Sierra Duca, Yu Xia, Laila Abd Elmagid, Isaac Bakis, Miaoyan Qiu, Yingxi Cao, Ylan Guo, James V Eichenbaum, Megan L McCain, Junsu Kang, Michael R M Harrison, Jingli Cao.
      Vascular endothelial growth factor C (Vegfc) is crucial for lymphatic and blood vessel development, yet its cellular sources and specific functions in heart development remain unclear. To address this, we created a vegfc reporter and an inducible overexpression line in zebrafish. We found vegfc expression in large coronary arteries, circulating thrombocytes, cardiac adipocytes, and outflow tract smooth muscle cells. Notably, while coronary lymphangiogenesis aligns with Vegfc-expressing arteries in juveniles, it occurs only after coronary artery formation. Vegfc overexpression induced ectopic lymphatics on the ventricular surface prior to arterial formation, indicating that Vegfc abundance, rather than arterial presence, drives lymphatic development. However, this overexpression did not affect coronary artery coverage, suggesting a specific role for Vegfc in lymphatic, rather than arterial, development. Thrombocytes emerged as the initial Vegfc source during inflammation following heart injuries, transitioning to endocardial and myocardial expression during regeneration. Lower Vegfc levels in the amputation model corresponded with a lack of lymphatic expansion. Importantly, Vegfc overexpression enhanced lymphatic expansion and promoted scar resolution without affecting cardiomyocyte proliferation, highlighting its role in regulating lymphangiogenesis and promoting heart regeneration.
    Keywords:  Coronary artery; Heart regeneration; Lymphatic vessel; Thrombocytes; Vegfc; Zebrafish
    DOI:  https://doi.org/10.1242/dev.202947
  28. J Cell Sci. 2024 Nov 08. pii: jcs.262232. [Epub ahead of print]
    Shear stress-stimulated AMPK couples endothelial cell mechanics, metabolism, and vasodilation.
    Nicholas M Cronin, Logan W Dawson, Kris A DeMali.
      Endothelial cells respond to mechanical force by stimulating cellular signaling, but how these pathways are linked to elevations in cell metabolism and whether metabolism supports the mechanical response remains poorly understood. Here, we show that the application of force to endothelial cells stimulates VE-cadherin to activate liver kinase B1 (LKB1) and AMP-activated protein kinase (AMPK), a master regulator of energy homeostasis. VE-cadherin stimulated AMPK increases eNOS activity and localization to the plasma membrane, reinforcement of the actin cytoskeleton and cadherin adhesion complex, and glucose uptake. We present evidence for the increase in metabolism being necessary to fortify the adhesion complex, actin cytoskeleton, and cellular alignment. Together these data extend the paradigm for how mechanotransduction and metabolism are linked to include a connection to vasodilation, thereby providing new insight into how diseases involving contractile, metabolic, and vasodilatory disturbances arise.
    Keywords:  Cell-Cell Adhesion; Mechanotransduction; VE-Cadherin
    DOI:  https://doi.org/10.1242/jcs.262232
  29. Cell. 2024 Nov 07. pii: S0092-8674(24)01214-5. [Epub ahead of print]
    A β-hydroxybutyrate shunt pathway generates anti-obesity ketone metabolites.
    Maria Dolores Moya-Garzon, Mengjie Wang, Veronica L Li, Xuchao Lyu, Wei Wei, Alan Sheng-Hwa Tung, Steffen H Raun, Meng Zhao, Laetitia Coassolo, Hashim Islam, Barbara Oliveira, Yuqin Dai, Jan Spaas, Antonio Delgado-Gonzalez, Kenyi Donoso, Aurora Alvarez-Buylla, Francisco Franco-Montalban, Anudari Letian, Catherine P Ward, Lichao Liu, Katrin J Svensson, Emily L Goldberg, Christopher D Gardner, Jonathan P Little, Steven M Banik, Yong Xu, Jonathan Z Long.
      β-Hydroxybutyrate (BHB) is an abundant ketone body. To date, all known pathways of BHB metabolism involve the interconversion of BHB and primary energy intermediates. Here, we identify a previously undescribed BHB secondary metabolic pathway via CNDP2-dependent enzymatic conjugation of BHB and free amino acids. This BHB shunt pathway generates a family of anti-obesity ketone metabolites, the BHB-amino acids. Genetic ablation of CNDP2 in mice eliminates tissue amino acid BHB-ylation activity and reduces BHB-amino acid levels. The most abundant BHB-amino acid, BHB-Phe, is a ketosis-inducible congener of Lac-Phe that activates hypothalamic and brainstem neurons and suppresses feeding. Conversely, CNDP2-KO mice exhibit increased food intake and body weight following exogenous ketone ester supplementation or a ketogenic diet. CNDP2-dependent amino acid BHB-ylation and BHB-amino acid metabolites are also conserved in humans. Therefore, enzymatic amino acid BHB-ylation defines a ketone shunt pathway and bioactive ketone metabolites linked to energy balance.
    Keywords:  BHB; enzyme; ketone; metabolite; metabolomics; obesity
    DOI:  https://doi.org/10.1016/j.cell.2024.10.032
  30. Cell. 2024 Nov 11. pii: S0092-8674(24)01159-0. [Epub ahead of print]
    Spatiotemporal modeling of molecular holograms.
    Xiaojie Qiu, Daniel Y Zhu, Yifan Lu, Jiajun Yao, Zehua Jing, Kyung Hoi Min, Mengnan Cheng, Hailin Pan, Lulu Zuo, Samuel King, Qi Fang, Huiwen Zheng, Mingyue Wang, Shuai Wang, Qingquan Zhang, Sichao Yu, Sha Liao, Chao Liu, Xinchao Wu, Yiwei Lai, Shijie Hao, Zhewei Zhang, Liang Wu, Yong Zhang, Mei Li, Zhencheng Tu, Jinpei Lin, Zhuoxuan Yang, Yuxiang Li, Ying Gu, David Ellison, Ao Chen, Longqi Liu, Jonathan S Weissman, Jiayi Ma, Xun Xu, Shiping Liu, Yinqi Bai.
      Quantifying spatiotemporal dynamics during embryogenesis is crucial for understanding congenital diseases. We developed Spateo (https://github.com/aristoteo/spateo-release), a 3D spatiotemporal modeling framework, and applied it to a 3D mouse embryogenesis atlas at E9.5 and E11.5, capturing eight million cells. Spateo enables scalable, partial, non-rigid alignment, multi-slice refinement, and mesh correction to create molecular holograms of whole embryos. It introduces digitization methods to uncover multi-level biology from subcellular to whole organ, identifying expression gradients along orthogonal axes of emergent 3D structures, e.g., secondary organizers such as midbrain-hindbrain boundary (MHB). Spateo further jointly models intercellular and intracellular interaction to dissect signaling landscapes in 3D structures, including the zona limitans intrathalamica (ZLI). Lastly, Spateo introduces "morphometric vector fields" of cell migration and integrates spatial differential geometry to unveil molecular programs underlying asymmetrical murine heart organogenesis and others, bridging macroscopic changes with molecular dynamics. Thus, Spateo enables the study of organ ecology at a molecular level in 3D space over time.
    Keywords:  3D reconstruction; Spateo; Stereo-seq; intercellular and intracellular interactions; ligand-receptor interactions, cell-cell interactions; morphometric vector field; spatial differential geometry analyses; spatial domain digitization; whole-embryo 3D spatial transcriptomics
    DOI:  https://doi.org/10.1016/j.cell.2024.10.011
  31. Proc Natl Acad Sci U S A. 2024 Nov 19. 121(47): e2410261121
    HIRA and dPCIF1 coordinately establish totipotent chromatin and control orderly ZGA in Drosophila embryos.
    Guoqiang Zhang, Yaqi Miao, Yuan Song, Liangliang Wang, Yawei Li, Yuanxiang Zhu, Wenxin Zhang, Qinmiao Sun, Dahua Chen.
      Early embryos undergo profound changes in their genomic architecture to establish the totipotent state, enabling pioneer factors to access chromatin and drive zygotic genome activation (ZGA). However, the mechanisms by which the totipotent state is established and properly interpreted by pioneer factors to allow orderly ZGA remain unknown. Here, we identify the H3.3-specific chaperone HIRA as a factor involving establishing totipotent-state chromatin in Drosophila early embryos. Through cophase separation with HIRA, the pioneer factor GAGA factor (GAF) efficiently binds to H3.3-marked nucleosomes to activate major-wave zygotic genes. Importantly, dPCIF1, a chromatin-associated protein, antagonized the GAF-HIRA interaction by competitively binding to HIRA, thereby restricting GAF on earlier chromatin and avoiding premature ZGA. Hence, the coordinated action of HIRA and dPCIF1 ensures sequential ZGA from the minor to major wave in early embryos. This study provides insights into understanding how a totipotent state is established and properly controlled during ZGA.
    Keywords:  Drosophila; early embryo; pioneer factor; zygotic genome activation
    DOI:  https://doi.org/10.1073/pnas.2410261121
  32. Nature. 2024 Nov 13.
    Errors in cell division stopped by an atypical cyclin-dependent kinase.
      
    Keywords:  Cell biology; Chemical biology; Genetics
    DOI:  https://doi.org/10.1038/d41586-024-03691-w
  33. Nat Genet. 2024 Nov 11.
    Brca1 haploinsufficiency promotes early tumor onset and epigenetic alterations in a mouse model of hereditary breast cancer.
    Carman Man-Chung Li, Alyssa Cordes, Michael U J Oliphant, S Aidan Quinn, Mayura Thomas, Laura M Selfors, Francesca Silvestri, Nomeda Girnius, Gianmarco Rinaldi, Jason J Zoeller, Hana Shapiro, Christina Tsiobikas, Kushali P Gupta, Shailja Pathania, Aviv Regev, S Cigall Kadoch, Senthil K Muthuswamy, Joan S Brugge.
      Germline BRCA1 mutation carriers face a high breast cancer risk; however, the underlying mechanisms for this risk are not completely understood. Using a new genetically engineered mouse model of germline Brca1 heterozygosity, we demonstrate that early tumor onset in a Brca1 heterozygous background cannot be fully explained by the conventional 'two-hit' hypothesis, suggesting the existence of inherent tumor-promoting alterations in the Brca1 heterozygous state. Single-cell RNA sequencing and assay for transposase-accessible chromatin with sequencing analyses uncover a unique set of differentially accessible chromatin regions in ostensibly normal Brca1 heterozygous mammary epithelial cells, distinct from wild-type cells and partially mimicking the chromatin and RNA-level changes in tumor cells. Transcription factor analyses identify loss of ELF5 and gain of AP-1 sites in these epigenetically primed regions; in vivo experiments further implicate AP-1 and Wnt10a as strong promoters of Brca1-related breast cancer. These findings reveal a previously unappreciated epigenetic effect of Brca1 haploinsufficiency in accelerating tumorigenesis, advancing our mechanistic understanding and informing potential therapeutic strategies.
    DOI:  https://doi.org/10.1038/s41588-024-01958-6
  34. Nat Commun. 2024 Nov 13. 15(1): 9818
    Charting and probing the activity of ADARs in human development and cell-fate specification.
    Amir Dailamy, Weiqi Lyu, Sami Nourreddine, Michael Tong, Joseph Rainaldi, Daniella McDonald, Rebecca Panwala, Alysson Muotri, Michael S Breen, Kun Zhang, Prashant Mali.
      Adenosine deaminases acting on RNA (ADARs) impact diverse cellular processes and pathological conditions, but their functions in early cell-fate specification remain less understood. To gain insights here, we began by charting time-course RNA editing profiles in human organs from fetal to adult stages. Next, we utilized hPSC differentiation to experimentally probe ADARs, harnessing brain organoids as neural specific, and teratomas as pan-tissue developmental models. We show that time-series teratomas faithfully recapitulate fetal developmental trends, and motivated by this, conducted pan-tissue, single-cell CRISPR-KO screens of ADARs in teratomas. Knocking out ADAR leads to a global decrease in RNA editing across all germ-layers. Intriguingly, knocking out ADAR leads to an enrichment of adipogenic cells, revealing a role for ADAR in human adipogenesis. Collectively, we present a multi-pronged framework charting time-resolved RNA editing profiles and coupled ADAR perturbations in developmental models, thereby shedding light on the role of ADARs in cell-fate specification.
    DOI:  https://doi.org/10.1038/s41467-024-53973-0
  35. Cell Stem Cell. 2024 Nov 05. pii: S1934-5909(24)00369-2. [Epub ahead of print]
    CRISPRi/a screens in human iPSC-cardiomyocytes identify glycolytic activation as a druggable target for doxorubicin-induced cardiotoxicity.
    Chun Liu, Mengcheng Shen, Yanxia Liu, Amit Manhas, Shane Rui Zhao, Mao Zhang, Nadjet Belbachir, Lu Ren, Joe Z Zhang, Arianne Caudal, Masataka Nishiga, Dilip Thomas, Angela Zhang, Huaxiao Yang, Yang Zhou, Mohamed Ameen, Nazish Sayed, June-Wha Rhee, Lei S Qi, Joseph C Wu.
      Doxorubicin is limited in its therapeutic utility due to its life-threatening cardiovascular side effects. Here, we present an integrated drug discovery pipeline combining human induced pluripotent stem cell (iPSC)-derived cardiomyocytes (iCMs), CRISPR interference and activation (CRISPRi/a) bidirectional pooled screens, and a small-molecule screening to identify therapeutic targets mitigating doxorubicin-induced cardiotoxicity (DIC) without compromising its oncological effects. The screens revealed several previously unreported candidate genes contributing to DIC, including carbonic anhydrase 12 (CA12). Genetic inhibition of CA12 protected iCMs against DIC by improving cell survival, sarcomere structural integrity, contractile function, and calcium handling. Indisulam, a CA12 antagonist, can effectively attenuate DIC in iCMs, engineered heart tissue, and animal models. Mechanistically, doxorubicin-induced CA12 potentiated a glycolytic activation in cardiomyocytes, contributing to DIC by interfering with cellular metabolism and functions. Collectively, our study provides a roadmap for future drug discovery efforts, potentially leading to more targeted therapies with minimal off-target toxicity.
    Keywords:  CRISPR screen; carbonic anhydrase; cardio-oncology; cardiomyoctye; doxorubicin; glycolysis; iPSC
    DOI:  https://doi.org/10.1016/j.stem.2024.10.007
  36. Nat Commun. 2024 Nov 12. 15(1): 9806
    Depolarization induces calcium-dependent BMP4 release from mouse embryonic palate mesenchymal cells.
    Mikaela L Follmer, Trevor J Isner, Yunus H Ozekin, Claire H Levitt, Carolyn L Burek, Richard K P Benninger, Emily Anne Bates.
      Bone Morphogenetic Protein (BMP) signaling is essential for craniofacial development, though little is known about the mechanisms that govern BMP secretion. We show that depolarization induces calcium-dependent BMP4 release from mouse embryonic palate mesenchyme. We show endogenous transient changes in intracellular calcium occur in cranial neural crest cells, the cells from which embryonic palate mesenchyme derives. Waves of transient changes in intracellular calcium suggest that these cells are electrically coupled and may temporally coordinate BMP release. These transient changes in intracellular calcium persist in palate mesenchyme cells from embryonic day 9.5 to 13.5 mice. Disruption of a potassium channel called Kcnj2 significantly decreases the amplitude of calcium transients and the ability of cells to secrete BMP. Kcnj2 knockout mice have cleft palate and reduced BMP signaling. Our data suggest that temporal control of developmental cues is regulated by ion channels, depolarization, and intracellular calcium for mammalian craniofacial morphogenesis.
    DOI:  https://doi.org/10.1038/s41467-024-53642-2
  37. Science. 2024 Nov 08. 386(6722): 667-672
    Regulated N-glycosylation controls chaperone function and receptor trafficking.
    Mengxiao Ma, Ramin Dubey, Annie Jen, Ganesh V Pusapati, Bharti Singal, Evgenia Shishkova, Katherine A Overmyer, Valérie Cormier-Daire, Juliette Fedry, L Aravind, Joshua J Coon, Rajat Rohatgi.
      One-fifth of human proteins are N-glycosylated in the endoplasmic reticulum (ER) by two oligosaccharyltransferases, OST-A and OST-B. Contrary to the prevailing view of N-glycosylation as a housekeeping function, we identified an ER pathway that modulates the activity of OST-A. Genetic analyses linked OST-A to HSP90B1, an ER chaperone for membrane receptors, and CCDC134, an ER luminal protein. During its translocation into the ER, an N-terminal peptide in HSP90B1 templates the assembly of a translocon complex containing CCDC134 and OST-A that protects HSP90B1 during folding, preventing its hyperglycosylation and degradation. Disruption of this pathway impairs WNT and IGF1R signaling and causes the bone developmental disorder osteogenesis imperfecta. Thus, N-glycosylation can be regulated by specificity factors in the ER to control cell surface receptor signaling and tissue development.
    DOI:  https://doi.org/10.1126/science.adp7201
  38. Cell Rep. 2024 Nov 14. pii: S2211-1247(24)01337-8. [Epub ahead of print]43(11): 114986
    Low-affinity ligands of the epidermal growth factor receptor are long-range signal transmitters in collective cell migration of epithelial cells.
    Eriko Deguchi, Shuhao Lin, Daiki Hirayama, Kimiya Matsuda, Akira Tanave, Kenta Sumiyama, Shinya Tsukiji, Tetsuhisa Otani, Mikio Furuse, Alexander Sorkin, Michiyuki Matsuda, Kenta Terai.
      Canonical epidermal growth factor (EGF) receptor (EGFR) activation involves the binding of seven EGFR ligands (EGFRLs); however, their extracellular dynamics remain elusive. Here, employing fluorescent probes and a tool for triggering ectodomain shedding, we show that epiregulin (EREG), a low-affinity EGFRL, rapidly and efficiently activates EGFR in Madin-Darby canine kidney (MDCK) epithelial cells and mouse epidermis. During collective cell migration, EGFR and extracellular signal-regulated kinase (ERK) activation waves propagate in an a disintegrin and metalloprotease 17 (ADAM17) sheddase- and EGFRL-dependent manner. Upon induced EGFRL shedding, low-affinity ligands EREG and amphiregulin (AREG) mediate faster and broader ERK waves than high-affinity ligands. Tight/adherens junction integrity is essential for ERK activation propagation, suggesting that tight intercellular spaces prefer the low-affinity EGFRLs for efficient signal transmission. In EREG-deficient mice, ERK wave propagation and cell migration were impaired during skin wound repair. We additionally show that heparin-binding EGF-like growth factor (HBEGF) primarily promotes surrounding cell motility. Our findings underscore the pivotal role of low-affinity EGFRLs in rapid intercellular signal transmission.
    Keywords:  ADAM17; CP: Cell biology; EGFR ligand; EREG; ERK activation wave; FRET; chemogenetics; collective cell migration; transgenic mice
    DOI:  https://doi.org/10.1016/j.celrep.2024.114986
  39. PLoS Genet. 2024 Nov 15. 20(11): e1011453
    A non-canonical role of somatic Cyclin D/CYD-1 in oogenesis and in maintenance of reproductive fidelity, dependent on the FOXO/DAF-16 activation state.
    Umanshi Rautela, Gautam Chandra Sarkar, Ayushi Chaudhary, Debalina Chatterjee, Mohtashim Rosh, Aneeshkumar G Arimbasseri, Arnab Mukhopadhyay.
      For the optimal survival of a species, an organism coordinates its reproductive decisions with the nutrient availability of its niche. Thus, nutrient-sensing pathways like insulin-IGF-1 signaling (IIS) play an important role in modulating cell division, oogenesis, and reproductive aging. Lowering of the IIS leads to the activation of the downstream FOXO transcription factor (TF) DAF-16 in Caenorhabditis elegans which promotes oocyte quality and delays reproductive aging. However, less is known about how the IIS axis responds to changes in cell cycle proteins, particularly in the somatic tissues. Here, we show a new aspect of the regulation of the germline by this nutrient-sensing axis. First, we show that the canonical G1-S cyclin, Cyclin D/CYD-1, regulates reproductive fidelity from the uterine tissue of wild-type worms. Then, we show that knocking down cyd-1 in the uterine tissue of an IIS receptor mutant arrests oogenesis at the pachytene stage of meiosis-1 in a DAF-16-dependent manner. We observe activated DAF-16-dependent deterioration of the somatic gonadal tissues like the sheath cells, and transcriptional de-regulation of the sperm-to-oocyte switch genes which may be the underlying reason for the absence of oogenesis. Deleting DAF-16 releases the arrest and leads to restoration of the somatic gonad but poor-quality oocytes are produced. Together, our study reveals the unrecognized cell non-autonomous interaction of Cyclin D/CYD-1 and FOXO/DAF-16 in the regulation of oogenesis and reproductive fidelity.
    DOI:  https://doi.org/10.1371/journal.pgen.1011453
  40. Nature. 2024 Nov 13.
    Clinical functional proteomics of intercellular signalling in pancreatic cancer.
    Peiwu Huang, Weina Gao, Changying Fu, Min Wang, Yunguang Li, Bizhu Chu, An He, Yuan Li, Xiaomei Deng, Yehan Zhang, Qian Kong, Jingxiong Yuan, Hebin Wang, Yu Shi, Dong Gao, Renyi Qin, Tony Hunter, Ruijun Tian.
      Pancreatic ductal adenocarcinoma (PDAC) has an atypical, highly stromal tumour microenvironment (TME) that profoundly contributes to its poor prognosis1. Here, to better understand the intercellular signalling between cancer and stromal cells directly in PDAC tumours, we developed a multidimensional proteomic strategy called TMEPro. We applied TMEPro to profile the glycosylated secreted and plasma membrane proteome of 100 human pancreatic tissue samples to a great depth, define cell type origins and identify potential paracrine cross-talk, especially that mediated through tyrosine phosphorylation. Temporal dynamics during pancreatic tumour progression were investigated in a genetically engineered PDAC mouse model. Functionally, we revealed reciprocal signalling between stromal cells and cancer cells mediated by the stromal PDGFR-PTPN11-FOS signalling axis. Furthermore, we examined the generic shedding mechanism of plasma membrane proteins in PDAC tumours and revealed that matrix-metalloprotease-mediated shedding of the AXL receptor tyrosine kinase ectodomain provides an additional dimension of intercellular signalling regulation in the PDAC TME. Importantly, the level of shed AXL has a potential correlation with lymph node metastasis, and inhibition of AXL shedding and its kinase activity showed a substantial synergistic effect in inhibiting cancer cell growth. In summary, we provide TMEPro, a generically applicable clinical functional proteomic strategy, and a comprehensive resource for better understanding the PDAC TME and facilitating the discovery of new diagnostic and therapeutic targets.
    DOI:  https://doi.org/10.1038/s41586-024-08225-y
  41. Nat Cell Biol. 2024 Nov 07.
    Spermidine limits diabetes by modulating RIPK1-mediated cell death and inflammation.
      
    DOI:  https://doi.org/10.1038/s41556-024-01542-4
  42. Sci Adv. 2024 Nov 15. 10(46): eadp2357
    Mechano-gradients drive morphogen-noise correction to ensure robust patterning.
    Kana Aoki, Taiki Higuchi, Yuki Akieda, Kotone Matsubara, Yasuyuki Ohkawa, Tohru Ishitani.
      Morphogen gradients instruct cells to pattern tissues. Although the mechanisms by which morphogens transduce chemical signals have been extensively studied, the roles and regulation of the physical communication between morphogen-receiver cells remain unclear. Here, we show that the Wnt/β-catenin-morphogen gradient, which patterns the embryonic anterior-posterior (AP) axis, generates intercellular tension gradients along the AP axis by controlling membrane cadherin levels in zebrafish embryos. This "mechano-gradient" is used for the cell competition-driven correction of noisy morphogen gradients. Naturally and artificially generated unfit cells, producing noisy Wnt/β-catenin gradients, induce local deformation of the mechano-gradients that activate mechanosensitive calcium channels in the neighboring fit cells, which then secrete annexin A1a to kill unfit cells. Thus, chemo-mechanical interconversion-mediated competitive communication between the morphogen-receiver cells ensures precise tissue patterning.
    DOI:  https://doi.org/10.1126/sciadv.adp2357
  43. Trends Cell Biol. 2024 Nov 07. pii: S0962-8924(24)00212-5. [Epub ahead of print]
    MDM4 exon skipping upon dysfunctional ribosome assembly.
    Jennifer Jansen, Matthias Dobbelstein.
      Recent studies revealed how nucleolar stress enhances MDM4 exon skipping and activates p53 via the ribosomal protein L22 (RPL22; eL22). Tumor-associated L22 mutations lead to full-length MDM4 synthesis, overcoming tumor suppression by p53. This forum article explores how MDM4 splicing patterns integrate stress signaling to take p53-dependent cell fate decisions.
    Keywords:  MDM2; MDM4; exon skipping; nucleolar stress; p53; ribosomal protein L22
    DOI:  https://doi.org/10.1016/j.tcb.2024.10.006
  44. Nat Cardiovasc Res. 2024 Nov;3(11): 1272-1273
    Cardiac regeneration leads to altered Purkinje fiber network and ventricular conduction.
      
    DOI:  https://doi.org/10.1038/s44161-024-00549-2
  45. Science. 2024 Nov 15. 386(6723): 768-776
    Pathogenic proteotoxicity of cryptic splicing is alleviated by ubiquitination and ER-phagy.
    Cristian Prieto-Garcia, Vigor Matkovic, Thorsten Mosler, Congxin Li, Jie Liang, James A Oo, Felix Haidle, Igor Mačinković, Alfredo Cabrera-Orefice, Rayene Berkane, Giulio Giuliani, Fenfen Xu, Anne-Claire Jacomin, Ines Tomaskovic, Marion Basoglu, Marina E Hoffmann, Rajeshwari Rathore, Ronay Cetin, Doha Boutguetait, Süleyman Bozkurt, María Clara Hernández Cañás, Mario Keller, Jonas Busam, Varun Jayeshkumar Shah, Ilka Wittig, Manuel Kaulich, Petra Beli, Wojciech P Galej, Ingo Ebersberger, Likun Wang, Christian Münch, Alexandra Stolz, Ralf P Brandes, William Ka Fai Tse, Stefan Eimer, Didier Y R Stainier, Stefan Legewie, Kathi Zarnack, Michaela Müller-McNicoll, Ivan Dikic.
      RNA splicing enables the functional adaptation of cells to changing contexts. Impaired splicing has been associated with diseases, including retinitis pigmentosa, but the underlying molecular mechanisms and cellular responses remain poorly understood. In this work, we report that deficiency of ubiquitin-specific protease 39 (USP39) in human cell lines, zebrafish larvae, and mice led to impaired spliceosome assembly and a cytotoxic splicing profile characterized by the use of cryptic 5' splice sites. Disruptive cryptic variants evaded messenger RNA (mRNA) surveillance pathways and were translated into misfolded proteins, which caused proteotoxic aggregates, endoplasmic reticulum (ER) stress, and, ultimately, cell death. The detrimental consequence of splicing-induced proteotoxicity could be mitigated by up-regulating the ubiquitin-proteasome system and selective autophagy. Our findings provide insight into the molecular pathogenesis of spliceosome-associated diseases.
    DOI:  https://doi.org/10.1126/science.adi5295
  46. Nature. 2024 Nov 13.
    NK2R control of energy expenditure and feeding to treat metabolic diseases.
    Frederike Sass, Tao Ma, Jeppe H Ekberg, Melissa Kirigiti, Mario G Ureña, Lucile Dollet, Jenny M Brown, Astrid L Basse, Warren T Yacawych, Hayley B Burm, Mette K Andersen, Thomas S Nielsen, Abigail J Tomlinson, Oksana Dmytiyeva, Dan P Christensen, Lindsay Bader, Camilla T Vo, Yaxu Wang, Dylan M Rausch, Cecilie K Kristensen, María Gestal-Mato, Wietse In Het Panhuis, Kim A Sjøberg, Stace Kernodle, Jacob E Petersen, Artem Pavlovskyi, Manbir Sandhu, Ida Moltke, Marit E Jørgensen, Anders Albrechtsen, Niels Grarup, M Madan Babu, Patrick C N Rensen, Sander Kooijman, Randy J Seeley, Anna Worthmann, Joerg Heeren, Tune H Pers, Torben Hansen, Magnus B F Gustafsson, Mads Tang-Christensen, Tuomas O Kilpeläinen, Martin G Myers, Paul Kievit, Thue W Schwartz, Jakob B Hansen, Zachary Gerhart-Hines.
      The combination of decreasing food intake and increasing energy expenditure represents a powerful strategy for counteracting cardiometabolic diseases such as obesity and type 2 diabetes1. Yet current pharmacological approaches require conjugation of multiple receptor agonists to achieve both effects2-4, and so far, no safe energy-expending option has reached the clinic. Here we show that activation of neurokinin 2 receptor (NK2R) is sufficient to suppress appetite centrally and increase energy expenditure peripherally. We focused on NK2R after revealing its genetic links to obesity and glucose control. However, therapeutically exploiting NK2R signalling has previously been unattainable because its endogenous ligand, neurokinin A, is short-lived and lacks receptor specificity5,6. Therefore, we developed selective, long-acting NK2R agonists with potential for once-weekly administration in humans. In mice, these agonists elicit weight loss by inducing energy expenditure and non-aversive appetite suppression that circumvents canonical leptin signalling. Additionally, a hyperinsulinaemic-euglycaemic clamp reveals that NK2R agonism acutely enhances insulin sensitization. In diabetic, obese macaques, NK2R activation significantly decreases body weight, blood glucose, triglycerides and cholesterol, and ameliorates insulin resistance. These findings identify a single receptor target that leverages both energy-expending and appetite-suppressing programmes to improve energy homeostasis and reverse cardiometabolic dysfunction across species.
    DOI:  https://doi.org/10.1038/s41586-024-08207-0
  47. J Clin Invest. 2024 Nov 12. pii: e163648. [Epub ahead of print]
    Nicotinamide and pyridoxine stimulate muscle stem cell expansion and enhance regenerative capacity during aging.
    Sara Ancel, Joris Michaud, Eugenia Migliavacca, Charline Jomard, Aurélie Fessard, Pauline Garcia, Sonia Karaz, Sruthi Raja, Guillaume E Jacot, Thibaut Desgeorges, José-Luis Sánchez-García, Loic Tauzin, Yann Ratinaud, Benjamin Brinon, Sylviane Métairon, Lucas Pinero, Denis Barron, Stephanie Blum, Leonidas G Karagounis, Ramin Heshmat, Afshin Ostovar, Farshad Farzadfar, Isabella Scionti, Rémi Mounier, Julien Gondin, Pascal Stuelsatz, Jerome N Feige.
      Skeletal muscle relies on resident muscle stem cells (MuSCs) for growth and repair. Aging and muscle diseases impair MuSC function, leading to stem cell exhaustion and regenerative decline that contribute to the progressive loss of skeletal muscle mass and strength. In the absence of clinically available nutritional solutions specifically targeting MuSCs, we used a human myogenic progenitor (hMP) high-content imaging screen of natural molecules from food to identify nicotinamide (NAM) and pyridoxine (PN) as bioactive nutrients that stimulate MuSCs and have history of safe human use. NAM and PN synergize via CK1-mediated cytoplasmic β-catenin activation and AKT signaling to promote amplification and differentiation of MuSCs. Oral treatment with a combination of NAM/PN accelerates muscle regeneration in vivo by stimulating MuSCs, increases muscle strength during recovery, and overcomes MuSC dysfunction and regenerative failure during aging. Levels of NAM and bioactive PN spontaneously decline during aging in model organisms and inter-independently associate with muscle mass and walking speed in a human cohort of 186 aged people. Collectively, our results establish NAM/PN as a new nutritional intervention that stimulates MuSCs, enhances muscle regeneration, and alleviates age-related muscle decline with a direct opportunity for clinical translation.
    Keywords:  Adult stem cells; Epidemiology; Muscle biology; Skeletal muscle; Stem cells
    DOI:  https://doi.org/10.1172/JCI163648
  48. Nat Cell Biol. 2024 Nov 13.
    Hepatocellular senescence induces multi-organ senescence and dysfunction via TGFβ.
    Christos Kiourtis, Maria Terradas-Terradas, Lucy M Gee, Stephanie May, Anastasia Georgakopoulou, Amy L Collins, Eoin D O'Sullivan, David P Baird, Mohsin Hassan, Robin Shaw, Ee Hong Tan, Miryam Müller, Cornelius Engelmann, Fausto Andreola, Ya-Ching Hsieh, Lee H Reed, Lee A Borthwick, Colin Nixon, William Clark, Peter S Hanson, David Sumpton, Gillian Mackay, Toshiyasu Suzuki, Arafath K Najumudeen, Gareth J Inman, Andrew Campbell, Simon T Barry, Alberto Quaglia, Christopher M Morris, Fiona E N LeBeau, Owen J Sansom, Kristina Kirschner, Rajiv Jalan, Fiona Oakley, Thomas G Bird.
      Cellular senescence is not only associated with ageing but also impacts physiological and pathological processes, such as embryonic development and wound healing. Factors secreted by senescent cells affect their microenvironment and can induce spreading of senescence locally. Acute severe liver disease is associated with hepatocyte senescence and frequently progresses to multi-organ failure. Why the latter occurs is poorly understood. Here we demonstrate senescence development in extrahepatic organs and associated organ dysfunction in response to liver senescence using liver injury models and genetic models of hepatocyte-specific senescence. In patients with severe acute liver failure, we show that the extent of hepatocellular senescence predicts disease outcome, the need for liver transplantation and the occurrence of extrahepatic organ failure. We identify the TGFβ pathway as a critical mediator of systemic spread of senescence and demonstrate that TGFβ inhibition in vivo blocks senescence transmission to other organs, preventing liver senescence induced renal dysfunction. Our results highlight the systemic consequences of organ-specific senescence, which, independent of ageing, contributes to multi-organ dysfunction.
    DOI:  https://doi.org/10.1038/s41556-024-01543-3
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