bims-ginsta Biomed News
on Genome instability
Issue of 2024–12–01
39 papers selected by
Jinrong Hu, National University of Singapore
  1. The enhancer module of Integrator controls cell identity and early neural fate commitment.
  2. Comprehensive single-cell aging atlas of healthy mammary tissues reveals shared epigenomic and transcriptomic signatures of aging and cancer.
  3. Mechano-dependent sorbitol accumulation supports biomolecular condensate.
  4. On the origin of mitosis-derived human embryo aneuploidy.
  5. The ribotoxic stress response drives acute inflammation, cell death, and epidermal thickening in UV-irradiated skin in vivo.
  6. A mortality timer based on nucleolar size triggers nucleolar integrity loss and catastrophic genomic instability.
  7. Gastruloids are competent to specify both cardiac and skeletal muscle lineages.
  8. tRNA methylation drives early postnatal cardiomyocyte maturation.
  9. Copy number alterations in normal breast tissues revealed by single-cell whole-genome sequencing.
  10. Proteolethargy is a pathogenic mechanism in chronic disease.
  11. In vitro modelling of anterior primitive streak patterning with human pluripotent stem cells identifies the path to notochord progenitors.
  12. flt1 inactivation promotes zebrafish cardiac regeneration by enhancing endothelial activity and limiting the fibrotic response.
  13. Transposable element 5mC methylation state of blood cells predicts age and disease.
  14. 'Dark proteome' survey reveals thousands of new human genes.
  15. The maternal-to-zygotic transition: reprogramming of the cytoplasm and nucleus.
  16. Interplay between Notch signaling and mechanical forces during developmental patterning processes.
  17. Isolated Mouse Adult Cardiomyocytes Display Minimal Mitochondrial ATP Demand and Maximal Reliance on Glycolysis.
  18. Anillin tunes contractility and regulates barrier function during Rho flare-mediated tight junction remodeling.
  19. The vertebrate segmentation clock drives segmentation by stabilizing Dusp phosphatases in zebrafish.
  20. Multiple mechanisms for licensing human replication origins.
  21. A platform for multimodal in vivo pooled genetic screens reveals regulators of liver function.
  22. Single-cell genomics breaks new ground in cell cycle detection.
  23. The phosphatase PP1 sustains global transcription by promoting RNA polymerase II pause release.
  24. A panoramic view of cell population dynamics in mammalian aging.
  25. Stereochemistry in the disorder-order continuum of protein interactions.
  26. Multiple allelic configurations govern long-range Shh enhancer-promoter communication in the embryonic forebrain.
  27. Integration of Imaging-based and Sequencing-based Spatial Omics Mapping on the Same Tissue Section via DBiTplus.
  28. Age-related decline in CD8+ tissue resident memory T cells compromises antitumor immunity.
  29. High-density sampling reveals volume growth in human tumours.
  30. Restoration of hair follicle inductive properties by depletion of senescent cells.
  31. Tubulin glutamylation regulates axon guidance via the selective tuning of microtubule-severing enzymes.
  32. Endothelial Rho kinase controls blood vessel integrity and angiogenesis.
  33. Dynamic remodelling of the endoplasmic reticulum for mitosis.
  34. How proteins sense their cellular environment.
  35. Elevated type I interferon signaling defines the proliferative advantage of ARF and p53 mutant tumor cells.
  36. NR4A1 and NR4A2 orphan nuclear receptors regulate endothelial-to-hematopoietic transition in mouse hematopoietic stem cell specification.
  37. AMPK regulates Bcl2-L-13-mediated mitophagy induction for cardioprotection.
  38. EB3-informed dynamics of the microtubule stabilizing cap during stalled growth.
  39. Old Cells Need New Rules: New Guidelines for Senescent Cell Experimentation In Vivo.
  1. Nat Cell Biol. 2024 Nov 26.
    The enhancer module of Integrator controls cell identity and early neural fate commitment.
    Yingjie Zhang, Connor M Hill, Kelsey A Leach, Luca Grillini, Sandra Deliard, Sarah R Offley, Martina Gatto, Francis Picone, Avery Zucco, Alessandro Gardini.
      Lineage-specific transcription factors operate as master orchestrators of developmental processes by activating select cis-regulatory enhancers and proximal promoters. Direct DNA binding of transcription factors ultimately drives context-specific recruitment of the basal transcriptional machinery that comprises RNA polymerase II (RNAPII) and a host of polymerase-associated multiprotein complexes, including the metazoan-specific Integrator complex. Integrator is primarily known to modulate RNAPII processivity and to surveil RNA integrity across coding genes. Here we describe an enhancer module of Integrator that directs cell fate specification by promoting epigenetic changes and transcription factor binding at neural enhancers. Depletion of Integrator's INTS10 subunit upends neural traits and derails cells towards mesenchymal identity. Commissioning of neural enhancers relies on Integrator's enhancer module, which stabilizes SOX2 binding at chromatin upon exit from pluripotency. We propose that Integrator is a functional bridge between enhancers and promoters and a main driver of early development, providing new insight into a growing family of neurodevelopmental syndromes.
    DOI:  https://doi.org/10.1038/s41556-024-01556-y
  2. Nat Aging. 2024 Nov 25.
    Comprehensive single-cell aging atlas of healthy mammary tissues reveals shared epigenomic and transcriptomic signatures of aging and cancer.
    Brittany L Angarola, Siddhartha Sharma, Neerja Katiyar, Hyeon Gu Kang, Djamel Nehar-Belaid, SungHee Park, Rachel Gott, Giray N Eryilmaz, Mark A LaBarge, Karolina Palucka, Jeffrey H Chuang, Ron Korstanje, Duygu Ucar, Olga Anczukόw.
      Aging is the greatest risk factor for breast cancer; however, how age-related cellular and molecular events impact cancer initiation is unknown. In this study, we investigated how aging rewires transcriptomic and epigenomic programs of mouse mammary glands at single-cell resolution, yielding a comprehensive resource for aging and cancer biology. Aged epithelial cells exhibit epigenetic and transcriptional changes in metabolic, pro-inflammatory and cancer-associated genes. Aged stromal cells downregulate fibroblast marker genes and upregulate markers of senescence and cancer-associated fibroblasts. Among immune cells, distinct T cell subsets (Gzmk+, memory CD4+, γδ) and M2-like macrophages expand with age. Spatial transcriptomics reveals co-localization of aged immune and epithelial cells in situ. Lastly, we found transcriptional signatures of aging mammary cells in human breast tumors, suggesting possible links between aging and cancer. Together, these data uncover that epithelial, immune and stromal cells shift in proportions and cell identity, potentially impacting cell plasticity, aged microenvironment and neoplasia risk.
    DOI:  https://doi.org/10.1038/s43587-024-00751-8
  3. Cell. 2024 Nov 16. pii: S0092-8674(24)01271-6. [Epub ahead of print]
    Mechano-dependent sorbitol accumulation supports biomolecular condensate.
    Stephanie Torrino, William M Oldham, Andrés R Tejedor, Ignacio S Burgos, Lara Nasr, Nesrine Rachedi, Kéren Fraissard, Caroline Chauvet, Chaima Sbai, Brendan P O'Hara, Sophie Abélanet, Frederic Brau, Cyril Favard, Stephan Clavel, Rosana Collepardo-Guevara, Jorge R Espinosa, Issam Ben-Sahra, Thomas Bertero.
      Condensed droplets of protein regulate many cellular functions, yet the physiological conditions regulating their formation remain largely unexplored. Increasing our understanding of these mechanisms is paramount, as failure to control condensate formation and dynamics can lead to many diseases. Here, we provide evidence that matrix stiffening promotes biomolecular condensation in vivo. We demonstrate that the extracellular matrix links mechanical cues with the control of glucose metabolism to sorbitol. In turn, sorbitol acts as a natural crowding agent to promote biomolecular condensation. Using in silico simulations and in vitro assays, we establish that variations in the physiological range of sorbitol concentrations, but not glucose concentrations, are sufficient to regulate biomolecular condensates. Accordingly, pharmacological and genetic manipulation of intracellular sorbitol concentration modulates biomolecular condensates in breast cancer-a mechano-dependent disease. We propose that sorbitol is a mechanosensitive metabolite enabling protein condensation to control mechano-regulated cellular functions.
    Keywords:  LLPS; biomolecular condensate; breast cancer; cell metabolism; glucose metabolism; mechanobiology; phase transition; sorbitol
    DOI:  https://doi.org/10.1016/j.cell.2024.10.048
  4. Nat Commun. 2024 Nov 29. 15(1): 10391
    On the origin of mitosis-derived human embryo aneuploidy.
    Jiyeon Leem, Madison Gowett, Sarah Bolarinwa, Binyam Mogessie.
      
    DOI:  https://doi.org/10.1038/s41467-024-54953-0
  5. Mol Cell. 2024 Nov 19. pii: S1097-2765(24)00884-0. [Epub ahead of print]
    The ribotoxic stress response drives acute inflammation, cell death, and epidermal thickening in UV-irradiated skin in vivo.
    Anna Constance Vind, Zhenzhen Wu, Muhammad Jasrie Firdaus, Goda Snieckute, Gee Ann Toh, Malin Jessen, José Francisco Martínez, Peter Haahr, Thomas Levin Andersen, Melanie Blasius, Li Fang Koh, Nina Loeth Maartensson, John E A Common, Mads Gyrd-Hansen, Franklin L Zhong, Simon Bekker-Jensen.
      Solar UVB light causes damage to the outermost layer of skin. This insult induces rapid local responses, such as dermal inflammation, keratinocyte cell death, and epidermal thickening, all of which have traditionally been associated with DNA damage response signaling. Another stress response that is activated by UVB light is the ribotoxic stress response (RSR), which depends on the ribosome-associated mitogen-activated protein 3 kinases (MAP3K) ZAKα and culminates in p38 and JNK activation. Using ZAK knockout mice, we here show that it is the RSR that is responsible for the early manifestation of UVB-induced skin inflammation and keratinocyte death and subsequent proliferation in vivo. We also show that the RSR controls both p38-mediated pyroptotic and JNK-mediated apoptotic programmed cell death of human keratinocytes in vitro. In sum, our work highlights that skin cells rely on a cytoplasmic and ribosomal stress signal rather than a nuclear and DNA-templated signal for rapid inflammatory responses to UV exposure.
    Keywords:  JNK; UV; ZAK-alpha; apoptosis; inflammation; p38; pyroptosis; ribotoxic stress response; skin
    DOI:  https://doi.org/10.1016/j.molcel.2024.10.044
  6. Nat Aging. 2024 Nov 25.
    A mortality timer based on nucleolar size triggers nucleolar integrity loss and catastrophic genomic instability.
    J Ignacio Gutierrez, Jessica K Tyler.
      Genome instability is a hallmark of aging, with the highly repetitive ribosomal DNA (rDNA) within the nucleolus being particularly prone to genome instability. Nucleolar enlargement accompanies aging in organisms ranging from yeast to mammals, and treatment with many antiaging interventions results in small nucleoli. Here, we report that an engineered system to reduce nucleolar size robustly extends budding yeast replicative lifespan in a manner independent of protein synthesis rate or rDNA silencing. Instead, when nucleoli expand beyond a size threshold, their biophysical properties change, allowing entry of proteins normally excluded from the nucleolus, including the homologous recombinational repair protein Rad52. This triggers rDNA instability due to aberrant recombination, catastrophic genome instability and imminent death. These results establish that nucleolar expansion is sufficient to drive aging. Moreover, nucleolar expansion beyond a specific size threshold is a mortality timer, as the accompanying disruption of the nucleolar condensate boundary results in catastrophic genome instability that ends replicative lifespan.
    DOI:  https://doi.org/10.1038/s43587-024-00754-5
  7. Nat Commun. 2024 Nov 23. 15(1): 10172
    Gastruloids are competent to specify both cardiac and skeletal muscle lineages.
    Laurent Argiro, Céline Chevalier, Caroline Choquet, Nitya Nandkishore, Adeline Ghata, Anaïs Baudot, Stéphane Zaffran, Fabienne Lescroart.
      Cardiopharyngeal mesoderm contributes to the formation of the heart and head muscles. However, the mechanisms governing cardiopharyngeal mesoderm specification remain unclear. Here, we reproduce cardiopharyngeal mesoderm specification towards cardiac and skeletal muscle lineages with gastruloids from mouse embryonic stem cells. By conducting a comprehensive temporal analysis of cardiopharyngeal mesoderm development and differentiation in gastruloids compared to mouse embryos, we present the evidence for skeletal myogenesis in gastruloids. We identify different subpopulations of cardiomyocytes and skeletal muscles, the latter of which most likely correspond to different states of myogenesis with "head-like" and "trunk-like" skeletal myoblasts. In this work, we unveil the potential of gastruloids to undergo specification into both cardiac and skeletal muscle lineages, allowing the investigation of the mechanisms of cardiopharyngeal mesoderm differentiation in development and how this could be affected in congenital diseases.
    DOI:  https://doi.org/10.1038/s41467-024-54466-w
  8. Nat Cardiovasc Res. 2024 Nov 25.
    tRNA methylation drives early postnatal cardiomyocyte maturation.
    Pilar Ruiz-Lozano, Mark Mercola.
      
    DOI:  https://doi.org/10.1038/s44161-024-00572-3
  9. Nat Genet. 2024 Nov 26.
    Copy number alterations in normal breast tissues revealed by single-cell whole-genome sequencing.
      
    DOI:  https://doi.org/10.1038/s41588-024-02018-9
  10. Cell. 2024 Nov 25. pii: S0092-8674(24)01274-1. [Epub ahead of print]
    Proteolethargy is a pathogenic mechanism in chronic disease.
    Alessandra Dall'Agnese, Ming M Zheng, Shannon Moreno, Jesse M Platt, An T Hoang, Deepti Kannan, Giuseppe Dall'Agnese, Kalon J Overholt, Ido Sagi, Nancy M Hannett, Hailey Erb, Olivia Corradin, Arup K Chakraborty, Tong Ihn Lee, Richard A Young.
      The pathogenic mechanisms of many diseases are well understood at the molecular level, but there are prevalent syndromes associated with pathogenic signaling, such as diabetes and chronic inflammation, where our understanding is more limited. Here, we report that pathogenic signaling suppresses the mobility of a spectrum of proteins that play essential roles in cellular functions known to be dysregulated in these chronic diseases. The reduced protein mobility, which we call proteolethargy, was linked to cysteine residues in the affected proteins and signaling-related increases in excess reactive oxygen species. Diverse pathogenic stimuli, including hyperglycemia, dyslipidemia, and inflammation, produce similar reduced protein mobility phenotypes. We propose that proteolethargy is an overlooked cellular mechanism that may account for various pathogenic features of diverse chronic diseases.
    Keywords:  chronic disease; cysteine; protein mobility; proteolethargy; reactive oxygen species; signaling
    DOI:  https://doi.org/10.1016/j.cell.2024.10.051
  11. Development. 2024 Nov 25. pii: dev.202983. [Epub ahead of print]
    In vitro modelling of anterior primitive streak patterning with human pluripotent stem cells identifies the path to notochord progenitors.
    M Robles-Garcia, C Thimonier, K Angoura, E Ozga, H MacPherson, G Blin.
      Notochord progenitors (NotoPs) represent a scarce yet crucial embryonic cell population, playing important roles in embryo patterning and eventually giving rise to the cells that form and maintain intervertebral discs. The mechanisms regulating NotoPs emergence are unclear. This knowledge gap persists due to the inherent complexity of cell fate patterning during gastrulation, particularly within the anterior primitive streak (APS), where NotoPs first arise alongside neuro-mesoderm and endoderm. To gain insights into this process, we use micropatterning together with FGF and the WNT pathway activator CHIR9901, to guide the development of human embryonic stem cells into reproducible patterns of APS cell fates. We show that CHIR9901 dosage dictates the downstream dynamics of endogenous TGFbeta signalling which in turn controls cell fate decisions. While sustained NODAL signalling defines endoderm and NODAL inhibition is imperative for neuro-mesoderm emergence, timely inhibition of NODAL signalling with spatial confinement potentiates WNT activity and enables us to generate NotoPs efficiently. Our work elucidates the signalling regimes underpinning NotoPs emergence and provides novel insights into the regulatory mechanisms controlling the balance of APS cell fates during gastrulation.
    Keywords:  Gastrulation; Human; Micropatterns; Notochord; Pluripotent stem cells
    DOI:  https://doi.org/10.1242/dev.202983
  12. Development. 2024 Dec 01. pii: dev203028. [Epub ahead of print]151(23):
    flt1 inactivation promotes zebrafish cardiac regeneration by enhancing endothelial activity and limiting the fibrotic response.
    Zhen-Yu Wang, Armaan Mehra, Qian-Chen Wang, Savita Gupta, Agatha Ribeiro da Silva, Thomas Juan, Stefan Günther, Mario Looso, Jan Detleffsen, Didier Y R Stainier, Rubén Marín-Juez.
      VEGFA administration has been explored as a pro-angiogenic therapy for cardiovascular diseases including heart failure for several years, but with little success. Here, we investigate a different approach to augment VEGFA bioavailability: by deleting the VEGFA decoy receptor VEGFR1 (also known as FLT1), one can achieve more physiological VEGFA concentrations. We find that after cryoinjury, zebrafish flt1 mutant hearts display enhanced coronary revascularization and endocardial expansion, increased cardiomyocyte dedifferentiation and proliferation, and decreased scarring. Suppressing Vegfa signaling in flt1 mutants abrogates these beneficial effects of flt1 deletion. Transcriptomic analyses of cryoinjured flt1 mutant hearts reveal enhanced endothelial MAPK/ERK signaling and downregulation of the transcription factor gene egr3. Using newly generated genetic tools, we observe egr3 upregulation in the regenerating endocardium, and find that Egr3 promotes myofibroblast differentiation. These data indicate that with enhanced Vegfa bioavailability, the endocardium limits myofibroblast differentiation via egr3 downregulation, thereby providing a more permissive microenvironment for cardiomyocyte replenishment after injury.
    Keywords:  Cardiac regeneration; Egr3; Flt1; Vegfa; Zebrafish
    DOI:  https://doi.org/10.1242/dev.203028
  13. Nat Aging. 2024 Nov 27.
    Transposable element 5mC methylation state of blood cells predicts age and disease.
    Francesco Morandini, Jinlong Y Lu, Cheyenne Rechsteiner, Aladdin H Shadyab, Ramon Casanova, Beverly M Snively, Andrei Seluanov, Vera Gorbunova.
      Transposable elements (TEs) are DNA sequences that expand selfishly in the genome, possibly causing severe cellular damage. While normally silenced, TEs have been shown to activate during aging. DNA 5-methylcytosine (5mC) is one of the main epigenetic modifications by which TEs are silenced and has been used to train highly accurate age predictors. Yet, one common criticism of such predictors is that they lack interpretability. In this study, we investigate the changes in TE 5mC methylation that occur during aging in human blood using published methylation array data. We find that evolutionarily young long interspersed nuclear elements 1 (L1s), the only known TEs capable of autonomous transposition in humans, undergo the fastest loss of 5mC methylation, suggesting an active mechanism of de-repression. The same young L1s also showed preferential gain in chromatin accessibility but not expression. The long terminal repeat retrotransposons THE1A and THE1C also showed very rapid 5mC loss. We then show that accurate age predictors can be trained on both 5mC methylation of individual TE copies and average methylation of TE families genome wide. Lastly, we show that while old L1s gradually lose 5mC during the entire lifespan, demethylation of young L1s only happens late in life and is associated with cancer.
    DOI:  https://doi.org/10.1038/s43587-024-00757-2
  14. Science. 2024 Nov 29. 386(6725): 951-952
    'Dark proteome' survey reveals thousands of new human genes.
    Elizabeth Pennisi.
      Database confirms that overlooked segments of the genome code for a multitude of tiny proteins.
    DOI:  https://doi.org/10.1126/science.adu8277
  15. Nat Rev Genet. 2024 Nov 25.
    The maternal-to-zygotic transition: reprogramming of the cytoplasm and nucleus.
    Mina L Kojima, Caroline Hoppe, Antonio J Giraldez.
      A fertilized egg is initially transcriptionally silent and relies on maternally provided factors to initiate development. For embryonic development to proceed, the oocyte-inherited cytoplasm and the nuclear chromatin need to be reprogrammed to create a permissive environment for zygotic genome activation (ZGA). During this maternal-to-zygotic transition (MZT), which is conserved in metazoans, transient totipotency is induced and zygotic transcription is initiated to form the blueprint for future development. Recent technological advances have enhanced our understanding of MZT regulation, revealing common themes across species and leading to new fundamental insights about transcription, mRNA decay and translation.
    DOI:  https://doi.org/10.1038/s41576-024-00792-0
  16. Curr Opin Cell Biol. 2024 Nov 27. pii: S0955-0674(24)00123-6. [Epub ahead of print]91 102444
    Interplay between Notch signaling and mechanical forces during developmental patterning processes.
    Shahar Kasirer, David Sprinzak.
      The coordination between biochemical signals and cell mechanics has emerged in recent years as a crucial mechanism driving developmental patterning processes across a variety of developing and homeostatic systems. An important class of such developmental processes relies on local communication between neighboring cells through Notch signaling. Here, we review how the coordination between Notch-mediated differentiation and cell mechanics can give rise to unique cellular patterns. We discuss how global and local mechanical cues can affect, and be affected by, cellular differentiation and reorganization controlled by Notch signaling. We compare recent studies of such developmental processes, including the mammalian inner ear, Drosophila ommatidia, intestinal organoids, and zebrafish myocardium, to draw shared general concepts and their broader implications in biology.
    DOI:  https://doi.org/10.1016/j.ceb.2024.102444
  17. bioRxiv. 2024 Nov 18. pii: 2024.11.17.623751. [Epub ahead of print]
    Isolated Mouse Adult Cardiomyocytes Display Minimal Mitochondrial ATP Demand and Maximal Reliance on Glycolysis.
    Ushodaya Mattam, Noble Kumar Talari, Ashish Rao Sathyanarayana, Sobuj Mia, James Frazier, Sam Slone, Konstantinos Drosatos, Karthickeyan Chella Krishnan.
      Mitochondrial maladaptation is a hallmark of heart failure, contributing to impaired energy production and contractile dysfunction. Understanding the bioenergetics of cardiomyocytes under healthy and pathological conditions is critical for characterizing mitochondrial maladaptation. While adult cardiomyocytes from rodents are a widely used model, recent studies have reported oligomycin insensitivity in these cells, a phenomenon often overlooked. This has led to incomplete assessments of key bioenergetic parameters, such as ATP-linked respiration and glycolytic capacity, focusing primarily on basal and maximal respiration. In this study, we performed a comprehensive characterization of bioenergetic and glycolytic profiles in three cardiomyocyte models: neonatal rat ventricular myocytes (NRVMs), human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs), and mouse adult cardiomyocytes (mouse ACMs). Our findings demonstrate distinct metabolic adaptations in mouse ACMs, revealing critical insights into mitochondrial function, ATP demand, and glycolytic reliance. These results underscore the importance of selecting appropriate cellular models for studying mitochondrial bioenergetics in cardiac physiology and pathology.
    DOI:  https://doi.org/10.1101/2024.11.17.623751
  18. bioRxiv. 2024 Nov 21. pii: 2024.11.20.624537. [Epub ahead of print]
    Anillin tunes contractility and regulates barrier function during Rho flare-mediated tight junction remodeling.
    Zie Craig, Torey R Arnold, Kelsey Walworth, Alexander Walkon, Ann L Miller.
      To preserve barrier function, cell-cell junctions must dynamically remodel during cell shape changes. We have previously described a rapid tight junction repair pathway characterized by local, transient activation of RhoA, termed 'Rho flares,' which repair leaks in tight junctions via promoting local actomyosin-mediated junction remodeling. In this pathway, junction elongation is a mechanical trigger that initiates RhoA activation through an influx of intracellular calcium and recruitment of p115RhoGEF. However, mechanisms that tune the level of RhoA activation and Myosin II contractility during the process remain uncharacterized. Here, we show that the scaffolding protein Anillin localizes to Rho flares and regulates RhoA activity and actomyosin contraction at flares. Knocking down Anillin results in Rho flares with increased intensity but shorter duration. These changes in active RhoA dynamics weaken downstream F-actin and Myosin II accumulation at the site of Rho flares, resulting in decreased junction contraction. Consequently, tight junction breaks are not reinforced following Rho flares. We show that Anillin-driven RhoA regulation is necessary for successfully repairing tight junction leaks and protecting junctions from repeated barrier damage. Together, these results uncover a novel regulatory role for Anillin during tight junction repair and barrier function maintenance.
    Significance Statement: Barrier function is critical for epithelial tissues. Epithelial cells maintain barrier function via tight junctions, which must be remodeled to allow for cell- and tissue-scale shape changes. How barrier function is maintained and remodeled as epithelial cells change shape remains unclear.The scaffolding protein Anillin is required for generating effective actomyosin contraction to reinforce damaged tight junctions; lack of reinforcement leads to repeated barrier leaks.These findings highlight a novel role for Anillin in tight junction remodeling and suggest that Anillin's ability to tune the level and duration of local Rho activation affects the contractile output.
    DOI:  https://doi.org/10.1101/2024.11.20.624537
  19. Dev Cell. 2024 Nov 19. pii: S1534-5807(24)00668-3. [Epub ahead of print]
    The vertebrate segmentation clock drives segmentation by stabilizing Dusp phosphatases in zebrafish.
    M Fethullah Simsek, Didar Saparov, Kemal Keseroglu, Oriana Zinani, Angad Singh Chandel, Bibek Dulal, Bal Krishan Sharma, Soling Zimik, Ertuğrul M Özbudak.
      Pulsatile activity of the extracellular signal-regulated kinase (ERK) controls several cellular, developmental, and regenerative programs. Sequential segmentation of somites along the vertebrate body axis, a key developmental program, is also controlled by ERK activity oscillation. The oscillatory expression of Her/Hes family transcription factors constitutes the segmentation clock, setting the period of segmentation. Although oscillation of ERK activity depends on Her/Hes proteins, the underlying molecular mechanism remained mysterious. Here, we show that Her/Hes proteins physically interact with and stabilize dual-specificity phosphatases (Dusp) of ERK, resulting in oscillations of Dusp4 and Dusp6 proteins. Pharmaceutical and genetic inhibition of Dusp activity disrupt ERK activity oscillation and somite segmentation in zebrafish. Our results demonstrate that post-translational interactions of Her/Hes transcription factors with Dusp phosphatases establish the fundamental vertebrate body plan. We anticipate that future studies will identify currently unnoticed post-translational control of ERK pulses in other systems.
    Keywords:  Dusp; ERK; clock; oscillation; pattern formation; post-translational; segmentation; somitogenesis; wave
    DOI:  https://doi.org/10.1016/j.devcel.2024.11.003
  20. Nature. 2024 Nov 27.
    Multiple mechanisms for licensing human replication origins.
    Ran Yang, Olivia Hunker, Marleigh Wise, Franziska Bleichert.
      Loading of replicative helicases is obligatory for the assembly of DNA replication machineries. The eukaryotic MCM2-7 replicative helicase motor is deposited onto DNA by the origin recognition complex (ORC) and co-loader proteins as a head-to-head double hexamer to license replication origins. Although extensively studied in budding yeast1-4, the mechanisms of origin licensing in multicellular eukaryotes remain poorly defined. Here we use biochemical reconstitution and electron microscopy to reconstruct the human MCM loading pathway. We find that unlike in yeast, the ORC6 subunit of the ORC is not essential for-but enhances-human MCM loading. Electron microscopy analyses identify several intermediates en route to MCM double hexamer formation in the presence and absence of ORC6, including a DNA-loaded, closed-ring MCM single hexamer intermediate that can mature into a head-to-head double hexamer through multiple mechanisms. ORC6 and ORC3 facilitate the recruitment of the ORC to the dimerization interface of the first hexamer into MCM-ORC (MO) complexes that are distinct from the yeast MO complex5,6 and may orient the ORC for second MCM hexamer loading. Additionally, MCM double hexamer formation can proceed through dimerization of independently loaded MCM single hexamers, promoted by a propensity of human MCM2-7 hexamers to self-dimerize. This flexibility in human MCM loading may provide resilience against cellular replication stress, and the reconstitution system will enable studies addressing outstanding questions regarding DNA replication initiation and replication-coupled events in the future.
    DOI:  https://doi.org/10.1038/s41586-024-08237-8
  21. bioRxiv. 2024 Nov 21. pii: 2024.11.18.624217. [Epub ahead of print]
    A platform for multimodal in vivo pooled genetic screens reveals regulators of liver function.
    Reuben A Saunders, William E Allen, Xingjie Pan, Jaspreet Sandhu, Jiaqi Lu, Thomas K Lau, Karina Smolyar, Zuri A Sullivan, Catherine Dulac, Jonathan S Weissman, Xiaowei Zhuang.
      Organ function requires coordinated activities of thousands of genes in distinct, spatially organized cell types. Understanding the basis of emergent tissue function requires approaches to dissect the genetic control of diverse cellular and tissue phenotypes in vivo . Here, we develop paired imaging and sequencing methods to construct large-scale, multi-modal genotype-phenotypes maps in tissue with pooled genetic perturbations. Using imaging, we identify genetic perturbations in individual cells while simultaneously measuring their gene expression and subcellular morphology. Using single-cell sequencing, we measure transcriptomic responses to the same genetic perturbations. We apply this approach to study hundreds of genetic perturbations in the mouse liver. Our study reveals regulators of hepatocyte zonation and liver unfolded protein response, as well as distinct pathways that cause hepatocyte steatosis. Our approach enables new ways of interrogating the genetic basis of complex cellular and organismal physiology and provides crucial training data for emerging machine-learning models of cellular function.
    DOI:  https://doi.org/10.1101/2024.11.18.624217
  22. Nat Genet. 2024 Nov 29.
    Single-cell genomics breaks new ground in cell cycle detection.
    Qian Du.
      
    DOI:  https://doi.org/10.1038/s41588-024-01987-1
  23. Mol Cell. 2024 Nov 20. pii: S1097-2765(24)00885-2. [Epub ahead of print]
    The phosphatase PP1 sustains global transcription by promoting RNA polymerase II pause release.
    Zhenning Wang, Aixia Song, Bolin Tao, Maojian Miao, Yi-Qing Luo, Jingwen Wang, Zhinang Yin, Ruijing Xiao, Xinwen Zhou, Xue-Ying Shang, Shibin Hu, Kaiwei Liang, Charles G Danko, Fei Xavier Chen.
      RNA polymerase II progression from initiation to elongation is driven in part by a cascade of protein kinases acting on the core transcription machinery. Conversely, the corresponding phosphatases, notably PP2A and PP1-the most abundant serine-threonine phosphatases in cells-are thought to mainly impede polymerase progression, respectively restraining pause release at promoters and elongation at terminators. Here, we reveal an unexpected role of PP1, within the phosphatase 1 nuclear targeting subunit (PNUTS)-PP1 complex, in sustaining global transcriptional activation in human cells. Acute disruption of PNUTS-PP1 leads to severe defects in the release of paused polymerase and subsequent downregulation for the majority of transcribed genes. PNUTS-PP1 promotes pause release by dephosphorylating multiple substrates, including the 7SK small nuclear ribonucleoprotein particle (snRNP) subunit MEPCE, a known pausing regulator. PNUTS-PP1 exhibits antagonistic functions compared with Integrator-PP2A (INTAC) phosphatase, which generally inhibits pause release. Our research thus highlights opposing roles of PP1 and PP2A in modulating genome-wide transcriptional pausing and gene expression.
    Keywords:  7SK snRNP; INTAC; PNUTS; PNUTS-PP1; PP1; PP2A; RNA polymerase II; pausing; phosphatase; transcription
    DOI:  https://doi.org/10.1016/j.molcel.2024.10.046
  24. Science. 2024 Nov 28. eadn3949
    A panoramic view of cell population dynamics in mammalian aging.
    Zehao Zhang, Chloe Schaefer, Weirong Jiang, Ziyu Lu, Jasper Lee, Andras Sziraki, Abdulraouf Abdulraouf, Brittney Wick, Maximilian Haeussler, Zhuoyan Li, Gesmira Molla, Rahul Satija, Wei Zhou, Junyue Cao.
      To elucidate aging-associated cellular population dynamics, we present PanSci, a single-cell transcriptome atlas profiling over 20 million cells from 623 mouse tissues across different life stages, sexes, and genotypes. This comprehensive dataset reveals more than 3,000 unique cellular states and over 200 aging-associated cell populations. Our panoramic analysis uncovered organ-, lineage-, and sex-specific shifts of cellular dynamics during lifespan progression. Moreover, we identify both systematic and organ-specific alterations in immune cell populations associated with aging. We further explored the regulatory roles of the immune system on aging and pinpointed specific age-related cell population expansions that are lymphocyte dependent. Our "cell-omics" strategy enhances comprehension of cellular aging and lays the groundwork for exploring the complex cellular regulatory networks in aging and aging-associated diseases.
    DOI:  https://doi.org/10.1126/science.adn3949
  25. Nature. 2024 Nov 27.
    Stereochemistry in the disorder-order continuum of protein interactions.
    Estella A Newcombe, Amanda D Due, Andrea Sottini, Steffie Elkjær, Frederik Friis Theisen, Catarina B Fernandes, Lasse Staby, Elise Delaforge, Christian R O Bartling, Inna Brakti, Katrine Bugge, Benjamin Schuler, Karen Skriver, Johan G Olsen, Birthe B Kragelund.
      Intrinsically disordered proteins can bind via the formation of highly disordered protein complexes without the formation of three-dimensional structure1. Most naturally occurring proteins are levorotatory (L)-that is, made up only of L-amino acids-imprinting molecular structure and communication with stereochemistry2. By contrast, their mirror-image dextrorotatory (D)-amino acids are rare in nature. Whether disordered protein complexes are truly independent of chiral constraints is not clear. Here, to investigate the chiral constraints of disordered protein-protein interactions, we chose as representative examples a set of five interacting protein pairs covering the disorder-order continuum. By observing the natural ligands and their stereochemical mirror images in free and bound states, we found that chirality was inconsequential in a fully disordered complex. However, if the interaction relied on the ligand undergoing extensive coupled folding and binding, correct stereochemistry was essential. Between these extremes, binding could be observed for the D-ligand with a strength that correlated with disorder in the final complex. These findings have important implications for our understanding of the molecular processes that lead to complex formation, the use of D-peptides in drug discovery and the chemistry of protein evolution of the first living entities on Earth.
    DOI:  https://doi.org/10.1038/s41586-024-08271-6
  26. Mol Cell. 2024 Nov 14. pii: S1097-2765(24)00882-7. [Epub ahead of print]
    Multiple allelic configurations govern long-range Shh enhancer-promoter communication in the embryonic forebrain.
    Jailynn Harke, Jeewon R Lee, Son C Nguyen, Arian Arab, Staci M Rakowiecki, Siewert Hugelier, Christina Paliou, Antonella Rauseo, Rebecca Yunker, Kellen Xu, Yao Yao, Melike Lakadamyali, Guillaume Andrey, Douglas J Epstein, Eric F Joyce.
      Developmental gene regulation requires input from enhancers spread over large genomic distances. Our understanding of long-range enhancer-promoter (E-P) communication, characterized as loops, remains incomplete without addressing the role of intervening chromatin. Here, we examine the topology of the entire Sonic hedgehog (Shh) regulatory domain in individual alleles from the mouse embryonic forebrain. Through sequential Oligopaint labeling and super-resolution microscopy, we find that the Shh locus maintains a compact structure that adopts several diverse configurations independent of Shh expression. The most frequent configuration contained distal E-P contacts at the expense of those more proximal to Shh, consistent with an interconnected loop. Genetic perturbations demonstrate that this long-range E-P communication operates by Shh-expression-independent and dependent mechanisms, involving CTCF binding sites and active enhancers, respectively. We propose a model whereby gene regulatory elements secure long-range E-P interactions amid an inherent architectural framework to coordinate spatiotemporal patterns of gene expression.
    Keywords:  3D genome organization; CTCF; E-P; Shh; allelic configurations; developmental gene regulation; enhancer activity; enhancer-promoter communication; sequential DNA-FISH; super-resolution microscopy
    DOI:  https://doi.org/10.1016/j.molcel.2024.10.042
  27. bioRxiv. 2024 Nov 11. pii: 2024.11.07.622523. [Epub ahead of print]
    Integration of Imaging-based and Sequencing-based Spatial Omics Mapping on the Same Tissue Section via DBiTplus.
    Archibald Enninful, Zhaojun Zhang, Dmytro Klymyshyn, Hailing Zong, Zhiliang Bai, Negin Farzad, Graham Su, Alev Baysoy, Jungmin Nam, Mingyu Yang, Yao Lu, Nancy Zhang, Oliver Braubach, Mina L Xu, Zongming Ma, Rong Fan.
      Spatially mapping the transcriptome and proteome in the same tissue section can significantly advance our understanding of heterogeneous cellular processes and connect cell type to function. Here, we present Deterministic Barcoding in Tissue sequencing plus (DBiTplus), an integrative multi-modality spatial omics approach that combines sequencing-based spatial transcriptomics and image-based spatial protein profiling on the same tissue section to enable both single-cell resolution cell typing and genome-scale interrogation of biological pathways. DBiTplus begins with in situ reverse transcription for cDNA synthesis, microfluidic delivery of DNA oligos for spatial barcoding, retrieval of barcoded cDNA using RNaseH, an enzyme that selectively degrades RNA in an RNA-DNA hybrid, preserving the intact tissue section for high-plex protein imaging with CODEX. We developed computational pipelines to register data from two distinct modalities. Performing both DBiT-seq and CODEX on the same tissue slide enables accurate cell typing in each spatial transcriptome spot and subsequently image-guided decomposition to generate single-cell resolved spatial transcriptome atlases. DBiTplus was applied to mouse embryos with limited protein markers but still demonstrated excellent integration for single-cell transcriptome decomposition, to normal human lymph nodes with high-plex protein profiling to yield a single-cell spatial transcriptome map, and to human lymphoma FFPE tissue to explore the mechanisms of lymphomagenesis and progression. DBiTplusCODEX is a unified workflow including integrative experimental procedure and computational innovation for spatially resolved single-cell atlasing and exploration of biological pathways cell-by-cell at genome-scale.
    DOI:  https://doi.org/10.1101/2024.11.07.622523
  28. Nat Aging. 2024 Nov 26.
    Age-related decline in CD8+ tissue resident memory T cells compromises antitumor immunity.
    Siyu Pei, Xiuyu Deng, Ruirui Yang, Hui Wang, Jian-Hong Shi, Xueqing Wang, Jia Huang, Yu Tian, Rongjing Wang, Sulin Zhang, Hui Hou, Jing Xu, Qingcheng Zhu, Huan Huang, Jialing Ye, Cong-Yi Wang, Wei Lu, Qingquan Luo, Zhi-Yu Ni, Mingyue Zheng, Yichuan Xiao.
      Aging compromises antitumor immunity, but the underlying mechanisms remain elusive. Here, we report that aging impairs the generation of CD8+ tissue resident memory T (TRM) cells in nonlymphoid tissues in mice, thus compromising the antitumor activity of aged CD8+ T cells, which we also observed in human lung adenocarcinoma. We further identified that the apoptosis regulator BFAR was highly enriched in aged CD8+ T cells, in which BFAR suppressed cytokine-induced JAK2 signaling by activating JAK2 deubiquitination, thereby limiting downstream STAT1-mediated TRM reprogramming. Targeting BFAR either through Bfar knockout or treatment with our developed BFAR inhibitor, iBFAR2, rescued the antitumor activity of aged CD8+ T cells by restoring TRM generation in the tumor microenvironment, thus efficiently inhibiting tumor growth in aged CD8+ T cell transfer and anti-programmed cell death protein 1 (PD-1)-resistant mouse tumor models. Together, our findings establish BFAR-induced TRM restriction as a key mechanism causing aged CD8+ T cell dysfunction and highlight the translational potential of iBFAR2 in restoring antitumor activity in aged individuals or patients resistant to anti-PD-1 therapy.
    DOI:  https://doi.org/10.1038/s43587-024-00746-5
  29. Elife. 2024 Nov 26. pii: RP95338. [Epub ahead of print]13
    High-density sampling reveals volume growth in human tumours.
    Arman Angaji, Michel Owusu, Christoph Velling, Nicola Dick, Donate Weghorn, Johannes Berg.
      In growing cell populations such as tumours, mutations can serve as markers that allow tracking the past evolution from current samples. The genomic analyses of bulk samples and samples from multiple regions have shed light on the evolutionary forces acting on tumours. However, little is known empirically on the spatio-temporal dynamics of tumour evolution. Here, we leverage published data from resected hepatocellular carcinomas, each with several hundred samples taken in two and three dimensions. Using spatial metrics of evolution, we find that tumour cells grow predominantly uniformly within the tumour volume instead of at the surface. We determine how mutations and cells are dispersed throughout the tumour and how cell death contributes to the overall tumour growth. Our methods shed light on the early evolution of tumours in vivo and can be applied to high-resolution data in the emerging field of spatial biology.
    Keywords:  cancer biology; evolutionary biology; human; multi-region tumour samples; spatial genomics; tumour samples
    DOI:  https://doi.org/10.7554/eLife.95338
  30. Aging Cell. 2024 Nov 29. e14353
    Restoration of hair follicle inductive properties by depletion of senescent cells.
    Alberto Pappalardo, Jin Yong Kim, Hasan Erbil Abaci, Angela M Christiano.
      Senescent cells secrete a senescence-associated secretory phenotype (SASP), which can induce senescence in neighboring cells. Human dermal papilla (DP) cells lose their original hair inductive properties when expanded in vitro, and rapidly accumulate senescent cells in culture. Protein and RNA-seq analysis revealed an accumulation of DP-specific SASP factors including IL-6, IL-8, MCP-1, and TIMP-2. We found that combined senolytic treatment of dasatinib and quercetin depleted senescent cells, and reversed SASP accumulation and SASP-mediated repressive interactions in human DP culture, resulting in an increased Wnt-active cell population. In hair reconstitution assays, senolytic-depleted DP cells exhibited restored hair inductive properties by regenerating de novo hair follicles (HFs) compared to untreated DP cells. In 3D skin constructs, senolytic-depleted DP cells enhanced inductive potential and hair lineage specific differentiation of keratinocytes. These data revealed that senolytic treatment of cultured human DP cells markedly increased their inductive potency in HF regeneration, providing a new rationale for clinical applications of senolytic treatment in combination with cell-based therapies.
    Keywords:  cellular senescence; dasatinib; dermal papilla; hair follicle; quercetin; regeneration; senescence‐associated secretory phenotype; senolytic
    DOI:  https://doi.org/10.1111/acel.14353
  31. EMBO J. 2024 Nov 29.
    Tubulin glutamylation regulates axon guidance via the selective tuning of microtubule-severing enzymes.
    Daniel Ten Martin, Nicolas Jardin, Juliette Vougny, François Giudicelli, Laïla Gasmi, Naomi Berbée, Véronique Henriot, Laura Lebrun, Cécile Haumaître, Matthias Kneussel, Xavier Nicol, Carsten Janke, Maria M Magiera, Jamilé Hazan, Coralie Fassier.
      The microtubule cytoskeleton is a major driving force of neuronal circuit development. Fine-tuned remodelling of this network by selective activation of microtubule-regulating proteins, including microtubule-severing enzymes, has emerged as a central process in neuronal wiring. Tubulin posttranslational modifications control both microtubule properties and the activities of their interacting proteins. However, whether and how tubulin posttranslational modifications may contribute to neuronal connectivity has not yet been addressed. Here we show that the microtubule-severing proteins p60-katanin and spastin play specific roles in axon guidance during zebrafish embryogenesis and identify a key role for tubulin polyglutamylation in their functional specificity. Furthermore, our work reveals that polyglutamylases with undistinguishable activities in vitro, TTLL6 and TTLL11, play exclusive roles in motor circuit wiring by selectively tuning p60-katanin- and spastin-driven motor axon guidance. We confirm the selectivity of TTLL11 towards spastin regulation in mouse cortical neurons and establish its relevance in preventing axonal degeneration triggered by spastin haploinsufficiency. Our work thus provides mechanistic insight into the control of microtubule-driven neuronal development and homeostasis and opens new avenues for developing therapeutic strategies in spastin-associated hereditary spastic paraplegia.
    Keywords:  Axon Guidance; Hereditary Spastic Paraplegia; Katanin; Spastin; Tubulin Polyglutamylation
    DOI:  https://doi.org/10.1038/s44318-024-00307-x
  32. bioRxiv. 2024 Nov 19. pii: 2024.11.19.624343. [Epub ahead of print]
    Endothelial Rho kinase controls blood vessel integrity and angiogenesis.
    Martin Lange, Caitlin Francis, Jessica Furtado, Young-Bum Kim, James K Liao, Anne Eichmann.
       Background: The Rho kinases 1 and 2 (ROCK1/2) are serine-threonine specific protein kinases that control actin cytoskeleton dynamics. They are expressed in all cells throughout the body, including cardiomyocytes, smooth muscle cells and endothelial cells, and intimately involved in cardiovascular health and disease. Pharmacological ROCK inhibition is beneficial in mouse models of hypertension, atherosclerosis, and neointimal thickening that display overactivated ROCK. However, the consequences of endothelial ROCK signaling deficiency in vivo remain unknown. To address this issue, we analyzed endothelial cell (EC) specific ROCK1 and 2 deletions.
    Methods: We generated Cdh5-CreERT2 driven, tamoxifen inducible loss of function alleles of ROCK1 and ROCK2 and analyzed mouse survival and vascular defects through cellular, biochemical, and molecular biology approaches.
    Results: We observed that postnatal or adult loss of endothelial ROCK1 and 2 was lethal within a week. Mice succumbed to multi-organ hemorrhage that occurred because of loss of vascular integrity. ECs displayed deficient cytoskeletal actin polymerization that prevented focal adhesion formation and disrupted junctional integrity. Retinal sprouting angiogenesis was also perturbed, as sprouting vessels exhibited lack of polymerized actin and defective lumen formation. In a three-dimensional endothelial sprouting assay, combined knockdown of ROCK1/2 or knockdown or ROCK2 but not ROCK1 led to reduced sprouting, lumenization and cell polarization defects caused by defective actin and altered VE-cadherin dynamics. The isoform specific role of endothelial ROCK2 correlated with ROCK2 substrate specificity for FAK and LIMK. By analyzing single and three allele mutants we show that one intact allele of ROCK2 is sufficient to maintain vascular integrity in vivo .
    Conclusion: Endothelial ROCK1 and 2 maintain junctional integrity and ensure proper angiogenesis and lumen formation. The presence of one allele of ROCK2 is sufficient to maintain vascular growth and integrity. These data indicate the need of careful consideration for the use of ROCK inhibitors in disease settings.
    DOI:  https://doi.org/10.1101/2024.11.19.624343
  33. J Cell Sci. 2024 Nov 15. pii: jcs261444. [Epub ahead of print]137(22):
    Dynamic remodelling of the endoplasmic reticulum for mitosis.
    Suzan Kors, Anne-Lore Schlaitz.
      The endoplasmic reticulum (ER) is a dynamic and continuous membrane network with roles in many cellular processes. The importance and maintenance of ER structure and function have been extensively studied in interphase cells, yet recent findings also indicate crucial roles of the ER in mitosis. During mitosis, the ER is remodelled significantly with respect to composition and morphology but persists as a continuous network. The ER interacts with microtubules, actin and intermediate filaments, and concomitant with the mitotic restructuring of all cytoskeletal systems, ER dynamics and distribution change. The ER is a metabolic hub and several examples of altered ER functions during mitosis have been described. However, we lack an overall understanding of the ER metabolic pathways and functions that are active during mitosis. In this Review, we will discuss mitotic changes to the ER at different organizational levels to explore how the mitotic ER, with its distinct properties, might support cell division.
    Keywords:  Cell division; ER; ER dynamics and morphology; ER–cytoskeleton contacts; Endoplasmic reticulum; Membrane contact sites; Mitosis
    DOI:  https://doi.org/10.1242/jcs.261444
  34. Nat Rev Mol Cell Biol. 2024 Nov 28.
    How proteins sense their cellular environment.
    Monika Fuxreiter.
      
    DOI:  https://doi.org/10.1038/s41580-024-00812-1
  35. bioRxiv. 2024 Nov 11. pii: 2024.11.11.623046. [Epub ahead of print]
    Elevated type I interferon signaling defines the proliferative advantage of ARF and p53 mutant tumor cells.
    Alex Mabry, Catherine E Kuzmicki, Angelina O'Brien, Leonard B Maggi, Jason D Weber.
      The tumor suppressors p53 and ARF collaborate to prevent unwarranted cell proliferation and as such are two of the most frequently mutated genes in human cancer. Concomitant loss of functional p53 and ARF leads to massive gains in cell proliferation and transformation and is often observed in some of the most aggressive human cancer subtypes. These phenotypic gains are preceded by increased type I interferon (IFN) signaling that involves canonical STAT1 activation and a subsequent IFN-stimulated gene (ISG) signature. Here, we show that cells lacking p53 and ARF require active JAK1 to phosphorylate STAT1 on Y701 to maintain their high rate of proliferation. In fact, the use of selective JAK1 inhibitors ruxolitinib or baricitinib inhibited the induction of ISG's and the proliferation of p53 and ARF deleted cells. We identify a group of solid human tumors that lack functional p53 and ARF, show an expression signature of the upregulated type I IFN response genes, and are sensitive to selective JAK1 inhibitors. These data suggest that the type I IFN response acts as a positive driver of proliferation in the absence of p53 and ARF and, as such, presents itself as a potential therapeutic target in aggressive solid tumors.
    DOI:  https://doi.org/10.1101/2024.11.11.623046
  36. Development. 2024 Nov 15. pii: dev201957. [Epub ahead of print]151(22):
    NR4A1 and NR4A2 orphan nuclear receptors regulate endothelial-to-hematopoietic transition in mouse hematopoietic stem cell specification.
    Diana Sá da Bandeira, Chris D Nevitt, Felipe Segato Dezem, Maycon Marção, Yutian Liu, Zakiya Kelley, Hannah DuBose, Ashley Chabot, Trent Hall, Claire Caprio, Victoria Okhomina, Guolian Kang, Jasmine Plummer, Shannon McKinney-Freeman, Wilson K Clements, Miguel Ganuza.
      Hematopoietic stem cells (HSCs) sustain life-long hematopoiesis and emerge during mid-gestation from hemogenic endothelial progenitors via an endothelial-to-hematopoietic transition (EHT). The full scope of molecular mechanisms governing this process remains unclear. The NR4A subfamily of orphan nuclear receptors act as tumor suppressors in myeloid leukemogenesis and have never been implicated in HSC specification. Here, we report that Nr4a1 and Nr4a2 expression is upregulated in hemogenic endothelium during EHT. Progressive genetic ablation of Nr4a gene dosage results in a gradual decrease in numbers of nascent c-Kit+ hematopoietic progenitors in developing embryos, c-Kit+ cell cluster size in the dorsal aorta, and a block in HSC maturation, revealed by an accumulation of pro-HSCs and pre-HSC-type I cells and decreased numbers of pre-HSC-type II cells. Consistent with these observations, cells isolated from embryonic day 11.5 Nr4a1-/-; Nr4a2-/- aorta-gonads-mesonephros are devoid of in vivo long-term hematopoietic repopulating potential. Molecularly, employing spatial transcriptomic analysis we determined that the genetic ablation of Nr4a1 and Nr4a2 prevents Notch signaling from being downregulated in intra-aortic clusters and thus for pro-HSCs to mature into HSCs. Interestingly, this defect is partially rescued by ex vivo culture of dissected aorta-gonads-mesonephros with SCF, IL3 and FLT3L, which may bypass Notch-dependent regulation. Overall, our data reveal a role for the NR4A family of orphan nuclear receptors in EHT.
    Keywords:  AGM; Developmental hematopoiesis; Endothelial to hematopoietic transition; HSC specification; Hematopoietic stem cells; NR4A
    DOI:  https://doi.org/10.1242/dev.201957
  37. Cell Rep. 2024 Nov 23. pii: S2211-1247(24)01352-4. [Epub ahead of print]43(12): 115001
    AMPK regulates Bcl2-L-13-mediated mitophagy induction for cardioprotection.
    Tomokazu Murakawa, Jumpei Ito, Mara-Camelia Rusu, Manabu Taneike, Shigemiki Omiya, Javier Moncayo-Arlandi, Chiaki Nakanishi, Ryuta Sugihara, Hiroki Nishida, Kentaro Mine, Roland Fleck, Min Zhang, Kazuhiko Nishida, Ajay M Shah, Osamu Yamaguchi, Yasushi Sakata, Kinya Otsu.
      The accumulation of damaged mitochondria in the heart is associated with heart failure. Mitophagy is an autophagic degradation system that specifically targets damaged mitochondria. We have reported previously that Bcl2-like protein 13 (Bcl2-L-13) mediates mitophagy and mitochondrial fission in mammalian cells. However, the in vivo function of Bcl2-L-13 remains unclear. Here, we demonstrate that Bcl2-L-13-deficient mice and knockin mice, in which the phosphorylation site (Ser272) on Bcl2-L-13 was changed to Ala, showed left ventricular dysfunction in response to pressure overload. Attenuation of mitochondrial fission and mitophagy led to impairment of ATP production in these mouse hearts. In addition, we identified AMPKα2 as the kinase responsible for the phosphorylation of Bcl2-L-13 at Ser272. These results indicate that Bcl2-L-13 and its phosphorylation play an important role in maintaining cardiac function. Furthermore, the amplitude of stress-stimulated mitophagic activity could be modulated by AMPKα2.
    Keywords:  Bcl2-L-13; CP: Cell biology; heart failure; mitochondria; mitophagy
    DOI:  https://doi.org/10.1016/j.celrep.2024.115001
  38. Biophys J. 2024 Nov 26. pii: S0006-3495(24)04053-0. [Epub ahead of print]
    EB3-informed dynamics of the microtubule stabilizing cap during stalled growth.
    Maurits Kok, Florian Huber, Svenja-Marei Kalisch, Marileen Dogterom.
      Microtubule stability is known to be governed by a stabilizing GTP/GDP-Pi cap, but the exact relation between growth velocity, GTP hydrolysis and catastrophes remains unclear. We investigate the dynamics of the stabilizing cap through in vitro reconstitution of microtubule dynamics in contact with micro-fabricated barriers, using the plus-end binding protein GFP-EB3 as a marker for the nucleotide state of the tip. The interaction of growing microtubules with steric objects is known to slow down microtubule growth and accelerate catastrophes. We show that the lifetime distributions of stalled microtubules, as well as the corresponding lifetime distributions of freely growing microtubules, can be fully described with a simple phenomenological 1D model based on noisy microtubule growth and a single EB3-dependent hydrolysis rate. This same model is furthermore capable of explaining both the previously reported mild catastrophe dependence on microtubule growth rates and the catastrophe statistics during tubulin washout experiments.
    DOI:  https://doi.org/10.1016/j.bpj.2024.11.3314
  39. J Invest Dermatol. 2024 Nov 27. pii: S0022-202X(24)02814-8. [Epub ahead of print]
    Old Cells Need New Rules: New Guidelines for Senescent Cell Experimentation In Vivo.
    Florian Gruber, Christopher Kremslehner.
      
    Keywords:  Aging; Cellular senescence; SASP; Senescence; Skin aging
    DOI:  https://doi.org/10.1016/j.jid.2024.10.590
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