bims-ginsta Biomed News
on Genome instability
Issue of 2024–12–08
23 papers selected by
Jinrong Hu, National University of Singapore
  1. Ageing limits stemness and tumorigenesis by reprogramming iron homeostasis.
  2. Intracellular polarization of RNAs and proteins in the human small intestinal epithelium.
  3. Origin, fate and function of extraembryonic tissues during mammalian development.
  4. RANK drives structured intestinal epithelial expansion during pregnancy.
  5. Long-range regulation of transcription scales with genomic distance in a gene-specific manner.
  6. Tracking transcription-translation coupling in real time.
  7. Myosin 1b regulates intestinal epithelial morphogenesis via interaction with UNC45A.
  8. Spatial Transcriptome and Single Nucleus Transcriptome Sequencing Reveals Tetrahydroxy Stilbene Glucoside Promotes Ovarian Organoids Development Through the Vegfa-Ephb2 Pair.
  9. Parallel measurement of transcriptomes and proteomes from same single cells using nanodroplet splitting.
  10. Long-term in vitro expansion of a human fetal pancreas stem cell that generates all three pancreatic cell lineages.
  11. Generation and long-term culture of human cerebellar organoids from pluripotent stem cells.
  12. The kinetochore protein KNL-1 regulates the actin cytoskeleton to control dendrite branching.
  13. Synthetic GPCRs for programmable sensing and control of cell behaviour.
  14. Roles of intrinsically disordered protein regions in transcriptional regulation and genome organization.
  15. Kinesin-like motor protein KIF23 maintains neural stem and progenitor cell pools in the developing cortex.
  16. Fate specification triggers a positive feedback loop of TEAD-YAP and NANOG to promote epiblast formation in preimplantation embryos.
  17. β-hydroxybutyrate is a metabolic regulator of proteostasis in the aged and Alzheimer disease brain.
  18. Cell polarity proteins promote macropinocytosis in response to metabolic stress.
  19. Histone methyltransferases MLL2 and SETD1A/B play distinct roles in H3K4me3 deposition during the transition from totipotency to pluripotency.
  20. Discovering geroprotectors through the explainable artificial intelligence-based platform AgeXtend.
  21. An integrated picture of the structural pathways controlling the heart performance.
  22. Investigating The Role of Elastin and Extracellular Matrix Damage in Cardiovascular Calcification.
  23. Novel imaging and biophysical approaches to study tissue hydraulics in mammalian folliculogenesis.
  1. Nature. 2024 Dec 04.
    Ageing limits stemness and tumorigenesis by reprogramming iron homeostasis.
    Xueqian Zhuang, Qing Wang, Simon Joost, Alexander Ferrena, David T Humphreys, Zhuxuan Li, Melissa Blum, Klavdija Krause, Selena Ding, Yuna Landais, Yingqian Zhan, Yang Zhao, Ronan Chaligne, Joo-Hyeon Lee, Sebastian E Carrasco, Umeshkumar K Bhanot, Richard P Koche, Matthew J Bott, Pekka Katajisto, Yadira M Soto-Feliciano, Thomas Pisanic, Tiffany Thomas, Deyou Zheng, Emily S Wong, Tuomas Tammela.
      Ageing is associated with a decline in the number and fitness of adult stem cells1,2. Ageing-associated loss of stemness is posited to suppress tumorigenesis3,4, but this hypothesis has not been tested in vivo. Here we use physiologically aged autochthonous genetically engineered5,6 mouse models and primary cells5,6 to demonstrate that ageing suppresses lung cancer initiation and progression by degrading the stemness of the alveolar cell of origin. This phenotype is underpinned by the ageing-associated induction of the transcription factor NUPR1 and its downstream target lipocalin-2 in the cell of origin in mice and humans, which leads to functional iron insufficiency in the aged cells. Genetic inactivation of the NUPR1-lipocalin-2 axis or iron supplementation rescues stemness and promotes the tumorigenic potential of aged alveolar cells. Conversely, targeting the NUPR1-lipocalin-2 axis is detrimental to young alveolar cells through ferroptosis induction. Ageing-associated DNA hypomethylation at specific enhancer sites is associated with increased NUPR1 expression, which is recapitulated in young alveolar cells through DNA methylation inhibition. We uncover that ageing drives functional iron insufficiency that leads to loss of stemness and tumorigenesis but promotes resistance to ferroptosis. These findings have implications for the therapeutic modulation of cellular iron homeostasis in regenerative medicine and in cancer prevention. Furthermore, our findings are consistent with a model whereby most human cancers initiate at a young age, thereby highlighting the importance of directing cancer prevention efforts towards young individuals.
    DOI:  https://doi.org/10.1038/s41586-024-08285-0
  2. PLoS Biol. 2024 Dec 02. 22(12): e3002942
    Intracellular polarization of RNAs and proteins in the human small intestinal epithelium.
    Roy Novoselsky, Yotam Harnik, Oran Yakubovsky, Corine Katina, Yishai Levin, Keren Bahar Halpern, Niv Pencovich, Ido Nachmany, Shalev Itzkovitz.
      The intestinal epithelium is a polarized monolayer of cells, with an apical side facing the lumen and a basal side facing the blood stream. In mice, both proteins and mRNAs have been shown to exhibit global basal-apical polarization; however, polarization in the human intestine has not been systematically explored. Here, we employed laser-capture microdissection to isolate apical and basal epithelial segments from intestinal tissues of 8 individuals and performed RNA sequencing and mass-spectrometry proteomics. We find a substantial polarization of mRNA molecules that largely overlaps polarization patterns observed in mice. This mRNA polarization remains consistent across different zones of the intestinal villi and is generally correlated with the polarization of proteins. Our protein analysis exposes streamlined intracellular nutrient transport and processing and reveals that mitochondria and ribosomes are less polarized in humans compared to mice. Our study provides a resource for understanding human intestinal epithelial biology.
    DOI:  https://doi.org/10.1371/journal.pbio.3002942
  3. Nat Rev Mol Cell Biol. 2024 Dec 03.
    Origin, fate and function of extraembryonic tissues during mammalian development.
    Shifaan Thowfeequ, Courtney W Hanna, Shankar Srinivas.
      Extraembryonic tissues have pivotal roles in morphogenesis and patterning of the early mammalian embryo. Developmental programmes mediated through signalling pathways and gene regulatory networks determine the sequence in which fate determination and lineage commitment of extraembryonic tissues take place, and epigenetic processes allow the memory of cell identity and state to be sustained throughout and beyond embryo development, even extending across generations. In this Review, we discuss the molecular and cellular mechanisms necessary for the different extraembryonic tissues to develop and function, from their initial specification up until the end of gastrulation, when the body plan of the embryo and the anatomical organization of its supporting extraembryonic structures are established. We examine the interaction between extraembryonic and embryonic tissues during early patterning and morphogenesis, and outline how epigenetic memory supports extraembryonic tissue development.
    DOI:  https://doi.org/10.1038/s41580-024-00809-w
  4. Nature. 2024 Dec 04.
    RANK drives structured intestinal epithelial expansion during pregnancy.
    Masahiro Onji, Verena Sigl, Thomas Lendl, Maria Novatchkova, Asier Ullate-Agote, Amanda Andersson-Rolf, Ivona Kozieradzki, Rubina Koglgruber, Tsung-Pin Pai, Dominic Lichtscheidl, Komal Nayak, Matthias Zilbauer, Natalia A Carranza García, Laura Katharina Sievers, Maren Falk-Paulsen, Shane J F Cronin, Astrid Hagelkruys, Shinichiro Sawa, Lisa C Osborne, Philip Rosenstiel, Manolis Pasparakis, Jürgen Ruland, Hiroshi Takayanagi, Hans Clevers, Bon-Kyoung Koo, Josef M Penninger.
      During reproduction, multiple species such as insects and all mammals undergo extensive physiological and morphological adaptions to ensure health and survival of the mother and optimal development of the offspring. Here we report that the intestinal epithelium undergoes expansion during pregnancy and lactation in mammals. This enlargement of the intestinal surface area results in a novel geometry of expanded villi. Receptor activator of nuclear factor-κΒ (RANK, encoded by TNFRSF11A) and its ligand RANKL were identified as a molecular pathway involved in this villous expansion of the small intestine in vivo in mice and in intestinal mouse and human organoids. Mechanistically, RANK-RANKL protects gut epithelial cells from cell death and controls the intestinal stem cell niche through BMP receptor signalling, resulting in the elongation of villi and a prominent increase in the intestinal surface. As a transgenerational consequence, babies born to female mice that lack Rank in the intestinal epithelium show reduced weight and develop glucose intolerance after metabolic stress. Whereas gut epithelial remodelling in pregnancy/lactation is reversible, constitutive expression of an active form of RANK is sufficient to drive intestinal expansion followed by loss of villi and stem cells, and prevents the formation of Apcmin-driven small intestinal stem cell tumours. These data identify RANK-RANKL as a pathway that drives intestinal epithelial expansion in pregnancy/lactation, one of the most elusive and fundamental tissue remodelling events in mammalian life history and evolution.
    DOI:  https://doi.org/10.1038/s41586-024-08284-1
  5. Mol Cell. 2024 Nov 19. pii: S1097-2765(24)00861-X. [Epub ahead of print]
    Long-range regulation of transcription scales with genomic distance in a gene-specific manner.
    Christina L Jensen, Liang-Fu Chen, Tomek Swigut, Olivia J Crocker, David Yao, Mike C Bassik, James E Ferrell, Alistair N Boettiger, Joanna Wysocka.
      Although critical for tuning the timing and level of transcription, enhancer communication with distal promoters is not well understood. Here, we bypass the need for sequence-specific transcription factors (TFs) and recruit activators directly using a chimeric array of gRNA oligos to target dCas9 fused to the activator VP64-p65-Rta (CARGO-VPR). We show that this approach achieves effective activator recruitment to arbitrary genomic sites, even those inaccessible when targeted with a single guide. We utilize CARGO-VPR across the Prdm8-Fgf5 locus in mouse embryonic stem cells (mESCs), where neither gene is expressed. Although activator recruitment to any tested region results in the transcriptional induction of at least one gene, the expression level strongly depends on the genomic distance between the promoter and activator recruitment site. However, the expression-distance relationship for each gene scales distinctly in a manner not attributable to differences in 3D contact frequency, promoter DNA sequence, or the presence of repressive chromatin marks at the locus.
    Keywords:  CRISPR activation; dCas9; enhancer; gene regulation; genomic distance; promoter
    DOI:  https://doi.org/10.1016/j.molcel.2024.10.021
  6. Nature. 2024 Dec 04.
    Tracking transcription-translation coupling in real time.
    Nusrat Shahin Qureshi, Olivier Duss.
      A central question in biology is how macromolecular machines function cooperatively. In bacteria, transcription and translation occur in the same cellular compartment, and can be physically and functionally coupled1-4. Although high-resolution structures of the ribosome-RNA polymerase (RNAP) complex have provided initial mechanistic insights into the coupling process5-10, we lack knowledge of how these structural snapshots are placed along a dynamic reaction trajectory. Here we reconstitute a complete and active transcription-translation system and develop multi-colour single-molecule fluorescence microscopy experiments to directly and simultaneously track transcription elongation, translation elongation and the physical and functional coupling between the ribosome and the RNAP in real time. Our data show that physical coupling between ribosome and RNAP can occur over hundreds of nucleotides of intervening mRNA by mRNA looping, a process facilitated by NusG. We detect active transcription elongation during mRNA looping and show that NusA-paused RNAPs can be activated by the ribosome by long-range physical coupling. Conversely, the ribosome slows down while colliding with the RNAP. We hereby provide an alternative explanation for how the ribosome can efficiently rescue RNAP from frequent pausing without requiring collisions by a closely trailing ribosome. Overall, our dynamic data mechanistically highlight an example of how two central macromolecular machineries, the ribosome and RNAP, can physically and functionally cooperate to optimize gene expression.
    DOI:  https://doi.org/10.1038/s41586-024-08308-w
  7. Cell Rep. 2024 Dec 03. pii: S2211-1247(24)01292-0. [Epub ahead of print]43(12): 114941
    Myosin 1b regulates intestinal epithelial morphogenesis via interaction with UNC45A.
    Céline Revenu, Corinne Lebreton, Magda Cannata Serio, Marion Rosello, Rémi Duclaux-Loras, Karine Duroure, Ophélie Nicolle, Fanny Eggeler, Marie-Thérèse Prospéri, Julie Stoufflet, Juliette Vougny, Priscilla Lépine, Grégoire Michaux, Nadine Cerf-Bensussan, Evelyne Coudrier, Franck Perez, Marianna Parlato, Filippo Del Bene.
      Vesicle trafficking and the establishment of apicobasal polarity are essential processes in epithelial morphogenesis. UNC45A deficiency has been reported in a multi-organ syndrome presenting with severe diarrhea associated with enterocyte polarity defects. Myosin 1b, an actin motor able to bind membranes, regulates membrane shaping and vesicle trafficking. Here, we show that MYO1B is part of the UNC45A interactome. In the absence of UNC45A, myosin 1b is degraded and forms aggregates when proteasome activity is inhibited. In 3D Caco-2 cells, lumen formation is impaired in the absence of myosin 1b, associated with spindle orientation defects, Golgi apparatus fragmentation, and trafficking impairment. In zebrafish larvae, loss of myo1b results in intestinal bulb epithelium folding defects associated with terminal web disorganization and vesicle accumulation, reminiscent of villous atrophy. In conclusion, we show that myosin 1b plays an unexpected role in the development of the intestinal epithelium downstream of UNC45A, establishing its contribution in the gut defects reported in UNC45A patients.
    Keywords:  CP: Cell biology; CP: Developmental biology; Intestinal epithelium; MYO1B; MYO5B; UNC45A; lumenogenesis; zebrafish
    DOI:  https://doi.org/10.1016/j.celrep.2024.114941
  8. Adv Sci (Weinh). 2024 Dec 04. e2410098
    Spatial Transcriptome and Single Nucleus Transcriptome Sequencing Reveals Tetrahydroxy Stilbene Glucoside Promotes Ovarian Organoids Development Through the Vegfa-Ephb2 Pair.
    Chunlan Mu, Xiaoyong Li, Jiamei Yang, Geng G Tian, Hepeng Bai, Wenhui Lin, Linhui Wang, Ji Wu.
      Ovarian dysfunction is a major factor leading to female infertility. Understanding how to improve or reshape ovarian function has become an important entry point for preventing and treating female infertility caused by ovarian dysfunction. Here, plant-derived compounds are screened for in vitro activity upon ovarian organoids derived from feeder-free female germline stem cells. Tetrahydroxy stilbene glucoside (TSG) is found to promote the development of ovarian organoids. Single nucleus transcriptome sequencing and spatial transcriptome sequencing are used to establish a comprehensive spatiotemporal map to elucidate the role of TSG in ovarian organoid development, encompassing cell types and subtypes, transcription factors, pseudo-time sequence, and cell communication dynamics. This analysis indicates that TSG promotes ovarian organoid development through the vascular endothelial growth factor A-Eph receptor B2 ligand-receptor pair between granulosa cells and oocytes. This study has enhanced the understanding of the mechanisms of ovarian organoid development, establishes a technical platform for screening compounds for treating infertility and related diseases, and lays a foundation for clinically applying plant-derived compounds.
    Keywords:  ligand‐receptor pairs; ovarian organoids; plant‐derived compounds; single nucleus transcriptome sequencing; spatial transcriptome sequencing
    DOI:  https://doi.org/10.1002/advs.202410098
  9. Nat Commun. 2024 Dec 05. 15(1): 10614
    Parallel measurement of transcriptomes and proteomes from same single cells using nanodroplet splitting.
    James M Fulcher, Lye Meng Markillie, Hugh D Mitchell, Sarah M Williams, Kristin M Engbrecht, David J Degnan, Lisa M Bramer, Ronald J Moore, William B Chrisler, Joshua Cantlon-Bruce, Johannes W Bagnoli, Wei-Jun Qian, Anjali Seth, Ljiljana Paša-Tolić, Ying Zhu.
      Single-cell multiomics provides comprehensive insights into gene regulatory networks, cellular diversity, and temporal dynamics. Here, we introduce nanoSPLITS (nanodroplet SPlitting for Linked-multimodal Investigations of Trace Samples), an integrated platform that enables global profiling of the transcriptome and proteome from same single cells via RNA sequencing and mass spectrometry-based proteomics, respectively. Benchmarking of nanoSPLITS demonstrates high measurement precision with deep proteomic and transcriptomic profiling of single-cells. We apply nanoSPLITS to cyclin-dependent kinase 1 inhibited cells and found phospho-signaling events could be quantified alongside global protein and mRNA measurements, providing insights into cell cycle regulation. We extend nanoSPLITS to primary cells isolated from human pancreatic islets, introducing an efficient approach for facile identification of unknown cell types and their protein markers by mapping transcriptomic data to existing large-scale single-cell RNA sequencing reference databases. Accordingly, we establish nanoSPLITS as a multiomic technology incorporating global proteomics and anticipate the approach will be critical to furthering our understanding of biological systems.
    DOI:  https://doi.org/10.1038/s41467-024-54099-z
  10. Cell. 2024 Dec 02. pii: S0092-8674(24)01254-6. [Epub ahead of print]
    Long-term in vitro expansion of a human fetal pancreas stem cell that generates all three pancreatic cell lineages.
    Amanda Andersson-Rolf, Kelvin Groot, Jeroen Korving, Harry Begthel, Maaike A J Hanegraaf, Michael VanInsberghe, Fredrik Salmén, Stieneke van den Brink, Carmen Lopez-Iglesias, Peter J Peters, Daniel Krueger, Joep Beumer, Maarten H Geurts, Anna Alemany, Helmuth Gehart, Françoise Carlotti, Eelco J P de Koning, Susana M Chuva de Sousa Lopes, Alexander van Oudenaarden, Johan H van Es, Hans Clevers.
      The mammalian pancreas consists of three epithelial compartments: the acini and ducts of the exocrine pancreas and the endocrine islets of Langerhans. Murine studies indicate that these three compartments derive from a transient, common pancreatic progenitor. Here, we report derivation of 18 human fetal pancreas organoid (hfPO) lines from gestational weeks 8-17 (8-17 GWs) fetal pancreas samples. Four of these lines, derived from 15 to 16 GWs samples, generate acinar-, ductal-, and endocrine-lineage cells while expanding exponentially for >2 years under optimized culture conditions. Single-cell RNA sequencing identifies rare LGR5+ cells in fetal pancreas and in hfPOs as the root of the developmental hierarchy. These LGR5+ cells share multiple markers with adult gastrointestinal tract stem cells. Organoids derived from single LGR5+ organoid-derived cells recapitulate this tripotency in vitro. We describe a human fetal tripotent stem/progenitor cell capable of long-term expansion in vitro and of generating all three pancreatic cell lineages.
    Keywords:  LGR5; acinar cells; development; endocrine cells; fetal pancreas; human organoids; organoids; pancreas; stem cell; tripotent stem cell
    DOI:  https://doi.org/10.1016/j.cell.2024.10.044
  11. Nat Protoc. 2024 Dec 02.
    Generation and long-term culture of human cerebellar organoids from pluripotent stem cells.
    Alexander Atamian, Marcella Birtele, Negar Hosseini, Giorgia Quadrato.
      The advancement of research on human cerebellar development and diseases has been hindered by the lack of a cell-based system that mirrors the cellular diversity and functional characteristics of the human cerebellum. Here, we describe our protocol for a human pluripotent stem cell-derived human cerebellar organoid (hCerO) model, which successfully replicates the cellular diversity of the fetal cerebellum along with some of its distinct cytoarchitectural features. Our approach involves the patterning of human pluripotent stem cells, resulting in the generation of both cerebellar excitatory and inhibitory progenitor populations-specifically, the rhombic lip and ventricular zone progenitors, respectively. This patterning strategy leads to the reproducible differentiation of the major neurons of the cerebellum such as granule cells and Purkinje cells within just one month of culture. hCerOs serve as platforms for molecular, cellular and functional assays, including single-cell transcriptomics, immunohistochemistry and investigations into calcium dynamics and electrophysiological properties. Remarkably, the cultivation of hCerOs for up to 8 months enables the healthy survival and maturation of Purkinje cells, which exhibit molecular and electrophysiological features akin to their in vivo counterparts. Overall, our protocol generates and allows for the long-term culture of all major cell types within the cerebellum. Consequently, this significant advancement provides the developmental neurobiology field with a robust platform for exploring both cerebellar development and diseases within an all-human system. This protocol can be easily implemented by a technician with cell culture experience and takes 1-2 months to complete with an option for extended maturation over the course of several months.
    DOI:  https://doi.org/10.1038/s41596-024-01093-w
  12. J Cell Biol. 2025 Feb 03. pii: e202311147. [Epub ahead of print]224(2):
    The kinetochore protein KNL-1 regulates the actin cytoskeleton to control dendrite branching.
    Henrique Alves Domingos, Mattie Green, Vasileios R Ouzounidis, Cameron Finlayson, Bram Prevo, Dhanya K Cheerambathur.
      The function of the nervous system is intimately tied to its complex and highly interconnected architecture. Precise control of dendritic branching in individual neurons is central to building the complex structure of the nervous system. Here, we show that the kinetochore protein KNL-1 and its associated KMN (Knl1/Mis12/Ndc80 complex) network partners, typically known for their role in chromosome-microtubule coupling during mitosis, control dendrite branching in the Caenorhabditis elegans mechanosensory PVD neuron. KNL-1 restrains excess dendritic branching and promotes contact-dependent repulsion events, ensuring robust sensory behavior and preventing premature neurodegeneration. Unexpectedly, KNL-1 loss resulted in significant alterations of the actin cytoskeleton alongside changes in microtubule dynamics within dendrites. We show that KNL-1 modulates F-actin dynamics to generate proper dendrite architecture and that its N-terminus can initiate F-actin assembly. These findings reveal that the postmitotic neuronal KMN network acts to shape the developing nervous system by regulating the actin cytoskeleton and provide new insight into the mechanisms controlling dendrite architecture.
    DOI:  https://doi.org/10.1083/jcb.202311147
  13. Nature. 2024 Dec 04.
    Synthetic GPCRs for programmable sensing and control of cell behaviour.
    Nicholas A Kalogriopoulos, Reika Tei, Yuqi Yan, Peter M Klein, Matthew Ravalin, Bo Cai, Ivan Soltesz, Yulong Li, Alice Ting.
      Synthetic receptors that mediate antigen-dependent cell responses are transforming therapeutics, drug discovery and basic research1,2. However, established technologies such as chimeric antigen receptors3 can only detect immobilized antigens, have limited output scope and lack built-in drug control3-7. Here we engineer synthetic G-protein-coupled receptors (GPCRs) that are capable of driving a wide range of native or non-native cellular processes in response to a user-defined antigen. We achieve modular antigen gating by engineering and fusing a conditional auto-inhibitory domain onto GPCR scaffolds. Antigen binding to a fused nanobody relieves auto-inhibition and enables receptor activation by drug, thus generating programmable antigen-gated G-protein-coupled engineered receptors (PAGERs). We create PAGERs that are responsive to more than a dozen biologically and therapeutically important soluble and cell-surface antigens in a single step from corresponding nanobody binders. Different PAGER scaffolds allow antigen binding to drive transgene expression, real-time fluorescence or endogenous G-protein activation, enabling control of diverse cellular functions. We demonstrate multiple applications of PAGER, including induction of T cell migration along a soluble antigen gradient, control of macrophage differentiation, secretion of therapeutic antibodies and inhibition of neuronal activity in mouse brain slices. Owing to its modular design and generalizability, we expect PAGERs to have broad utility in discovery and translational science.
    DOI:  https://doi.org/10.1038/s41586-024-08282-3
  14. Curr Opin Genet Dev. 2024 Dec 03. pii: S0959-437X(24)00134-5. [Epub ahead of print]90 102285
    Roles of intrinsically disordered protein regions in transcriptional regulation and genome organization.
    Jiapei Miao, Shasha Chong.
      Eukaryotic transcription is a complex process regulated by transcription factors (TFs), coactivators, and RNA polymerase machineries, many of which contain sizable intrinsically disordered regions (IDRs). Many TFs activate transcription through multivalent IDR-IDR interactions. Optimal levels of such multivalent interactions associated with appropriate IDR concentrations, interaction strengths, or interaction valencies are required for effective transcriptional activation. The interaction selectivity of IDRs is crucial for the precise regulation of transcription, and this selectivity is dependent on the IDR sequences. Furthermore, IDRs modulate gene expression by bringing chromatin sites together to form transcriptionally active chromatin hubs. Mutations in IDRs may cause dysregulation of their multivalent interactions, contributing to diseases, including cancers and neurodegenerative disorders. Understanding the effects of IDR-related mutations on transcription control and genome organization opens new opportunities for developing targeted therapeutic strategies. In this review, we discuss recent reports documenting important functions of IDRs in transcriptional regulation and their implications for human health and disease.
    DOI:  https://doi.org/10.1016/j.gde.2024.102285
  15. EMBO J. 2024 Dec 04.
    Kinesin-like motor protein KIF23 maintains neural stem and progenitor cell pools in the developing cortex.
    Sharmin Naher, Kenji Iemura, Satoshi Miyashita, Mikio Hoshino, Kozo Tanaka, Shinsuke Niwa, Jin-Wu Tsai, Takako Kikkawa, Noriko Osumi.
      Accurate mitotic division of neural stem and progenitor cells (NSPCs) is crucial for the coordinated generation of progenitors and mature neurons, which determines cortical size and structure. While mutations in the kinesin-like motor protein KIF23 gene have been recently linked to microcephaly in humans, the underlying mechanisms remain elusive. Here, we explore the pivotal role of KIF23 in embryonic cortical development. We characterize the dynamic expression of KIF23 in the cortical NSPCs of mice, ferrets, and humans during embryonic neurogenesis. Knockdown of Kif23 in mice results in precocious neurogenesis and neuronal apoptosis, attributed to an accelerated cell cycle exit, likely resulting from disrupted mitotic spindle orientation and impaired cytokinesis. Additionally, KIF23 depletion perturbs the apical surface structure of NSPCs by affecting the localization of apical junction proteins. We further demonstrate that the phenotypes induced by Kif23 knockdown are rescued by introducing wild-type human KIF23, but not by a microcephaly-associated variant. Our findings unveil a previously unexplored role of KIF23 in neural stem and progenitor cell maintenance via regulating spindle orientation and apical structure in addition to cytokinesis, shedding light on microcephaly pathogenesis.
    Keywords:  Apoptosis; Cytokinesis; Kinesin Motor Proteins; Microcephaly; Neurogenesis
    DOI:  https://doi.org/10.1038/s44318-024-00327-7
  16. Development. 2024 Dec 04. pii: dev.203091. [Epub ahead of print]
    Fate specification triggers a positive feedback loop of TEAD-YAP and NANOG to promote epiblast formation in preimplantation embryos.
    Naoki Hirono, Masakazu Hashimoto, Hiromi Shimojo, Hiroshi Sasaki.
      In preimplantation embryos, epiblast (EPI) fate specification from the inner cell mass is controlled by the segregation of NANOG and GATA6 expression. TEAD-YAP interaction is activated during EPI formation, and is required for pluripotency factor expression. These events occur asynchronously with similar timing during EPI formation, and their relationship remains elusive. Here, we examined the relationship between NANOG-GATA6 and TEAD-YAP. The nuclear accumulation of YAP takes place only in EPI-specified cells, and a positive feedback loop operates between NANOG and TEAD-YAP. The effects of TEAD-YAP on SOX2 upregulation in EPI-specified cells are likely indirect. EPI fate specification also alters the response of Nanog, Sox2 and Cdx2 to TEAD-YAP. These results suggest that EPI-fate specification alters the transcriptional network from the morula-like to the EPI-specified state and activates TEAD-YAP to trigger a positive feedback loop with NANOG, which stabilizes the EPI fate. The coordinated occurrence of these processes in individual cells likely supports proper EPI formation under the condition of asynchronous EPI-fate specification.
    Keywords:  Epiblast; NANOG; Preimplantation embryo; TEAD; YAP
    DOI:  https://doi.org/10.1242/dev.203091
  17. Cell Chem Biol. 2024 Nov 25. pii: S2451-9456(24)00459-8. [Epub ahead of print]
    β-hydroxybutyrate is a metabolic regulator of proteostasis in the aged and Alzheimer disease brain.
    Sidharth S Madhavan, Stephanie Roa Diaz, Sawyer Peralta, Mitsunori Nomura, Christina D King, Kaya E Ceyhan, Anwen Lin, Dipa Bhaumik, Anna C Foulger, Samah Shah, Thanh Blade, Wyatt Gray, Manish Chamoli, Brenda Eap, Oishika Panda, Diego Diaz, Thelma Y Garcia, Brianna J Stubbs, Scott M Ulrich, Gordon J Lithgow, Birgit Schilling, Eric Verdin, Asish R Chaudhuri, John C Newman.
      Loss of proteostasis is a hallmark of aging and Alzheimer disease (AD). We identify β-hydroxybutyrate (βHB), a ketone body, as a regulator of protein solubility. βHB primarily provides ATP substrate during periods of reduced glucose availability, and regulates other cellular processes through protein interactions. We demonstrate βHB-induced protein insolubility is not dependent on covalent protein modification, pH, or solute load, and is observable in mouse brain in vivo after delivery of a ketone ester. This mechanism is selective for pathological proteins such as amyloid-β, and exogenous βHB ameliorates pathology in nematode models of amyloid-β aggregation toxicity. We generate libraries of the βHB-induced protein insolublome using mass spectrometry proteomics, and identify common protein domains and upstream regulators. We show enrichment of neurodegeneration-related proteins among βHB targets and the clearance of these targets from mouse brain. These data indicate a metabolically regulated mechanism of proteostasis relevant to aging and AD.
    Keywords:  Alzheimer disease; aging; ketone body; neurodegenerative disease; proteostasis
    DOI:  https://doi.org/10.1016/j.chembiol.2024.11.001
  18. Nat Commun. 2024 Dec 03. 15(1): 10541
    Cell polarity proteins promote macropinocytosis in response to metabolic stress.
    Guillem Lambies, Szu-Wei Lee, Karen Duong-Polk, Pedro Aza-Blanc, Swetha Maganti, Cheska M Galapate, Anagha Deshpande, Aniruddha J Deshpande, David A Scott, David W Dawson, Cosimo Commisso.
      Macropinocytosis has emerged as a scavenging pathway that cancer cells exploit to survive in a nutrient-deprived microenvironment. Tumor cells are especially reliant on glutamine for their survival, and in pancreatic ductal adenocarcinoma (PDAC) cells, glutamine deficiency can enhance the stimulation of macropinocytosis. Here, we identify the atypical protein kinase C (aPKC) enzymes, PKCζ and PKCι, as regulators of macropinocytosis. In normal epithelial cells, aPKCs associate with the scaffold proteins Par3 and Par6 to regulate cell polarity, affecting several targets, including the Par1 kinases and we find that each of these proteins is required for macropinocytosis. Mechanistically, aPKCs are regulated by EGFR signaling or by the transcription factor CREM to promote the Par3 relocation to microtubules, facilitating macropinocytosis in a dynein-dependent manner. Importantly, cell fitness impairment caused by aPKC depletion is rescued by the restoration of macropinocytosis and aPKCs support PDAC growth in vivo. Our findings enhance our understanding of the mechanistic underpinnings that control macropinocytic uptake in the context of metabolic stress.
    DOI:  https://doi.org/10.1038/s41467-024-54788-9
  19. EMBO J. 2024 Dec 05.
    Histone methyltransferases MLL2 and SETD1A/B play distinct roles in H3K4me3 deposition during the transition from totipotency to pluripotency.
    Jingjing Zhang, Qiaoran Sun, Liang Liu, Shichun Yang, Xia Zhang, Yi-Liang Miao, Xin Liu.
      In early mammalian embryogenesis, a shift from non-canonical histone H3 lysine 4 trimethylation (H3K4me3) linked to transcriptional repression to canonical H3K4me3 indicating active promoters occurs during zygotic genome activation (ZGA). However, the mechanisms and roles of these H3K4me3 states in embryogenesis remain poorly understood. Our research reveals that the histone methyltransferase MLL2 is responsible for installing H3K4me3 (both non-canonical and canonical) in totipotent embryos, while a transition to SETD1A/B-deposited H3K4me3 occurs in pluripotent embryos. Interestingly, MLL2-mediated H3K4me3 operates independently of transcription, fostering a relaxed chromatin state conducive to totipotency rather than directly influencing transcription. Conversely, SETD1A/B-mediated H3K4me3, which depends on transcription, is crucial for facilitating expression of genes essential for pluripotency and pre-implantation development. Our findings highlight the role of the H3K4me3 transition, mediated by an MLL2-to-SETD1A/B relay mechanism, in the regulation of transition from totipotency to pluripotency during early embryogenesis.
    Keywords:  First Lineage Segregation; H3K4me3; MLL2; SETD1A/B; Zygotic Genome Activation
    DOI:  https://doi.org/10.1038/s44318-024-00329-5
  20. Nat Aging. 2024 Dec 03.
    Discovering geroprotectors through the explainable artificial intelligence-based platform AgeXtend.
    Sakshi Arora, Aayushi Mittal, Subhadeep Duari, Sonam Chauhan, Nilesh Kumar Dixit, Sanjay Kumar Mohanty, Arushi Sharma, Saveena Solanki, Anmol Kumar Sharma, Vishakha Gautam, Pushpendra Singh Gahlot, Shiva Satija, Jeet Nanshi, Nikita Kapoor, Lavanya Cb, Debarka Sengupta, Parul Mehrotra, Tarini Shankar Ghosh, Gaurav Ahuja.
      Aging involves metabolic changes that lead to reduced cellular fitness, yet the role of many metabolites in aging is unclear. Understanding the mechanisms of known geroprotective molecules reveals insights into metabolic networks regulating aging and aids in identifying additional geroprotectors. Here we present AgeXtend, an artificial intelligence (AI)-based multimodal geroprotector prediction platform that leverages bioactivity data of known geroprotectors. AgeXtend encompasses modules that predict geroprotective potential, assess toxicity and identify target proteins and potential mechanisms. We found that AgeXtend accurately identified the pro-longevity effects of known geroprotectors excluded from training data, such as metformin and taurine. Using AgeXtend, we screened ~1.1 billion compounds and identified numerous potential geroprotectors, which we validated using yeast and Caenorhabditis elegans lifespan assays, as well as exploring microbiome-derived metabolites. Finally, we evaluated endogenous metabolites predicted as senomodulators using senescence assays in human fibroblasts, highlighting AgeXtend's potential to reveal unidentified geroprotectors and provide insights into aging mechanisms.
    DOI:  https://doi.org/10.1038/s43587-024-00763-4
  21. Proc Natl Acad Sci U S A. 2024 Dec 10. 121(50): e2410893121
    An integrated picture of the structural pathways controlling the heart performance.
    Ilaria Morotti, Marco Caremani, Matteo Marcello, Irene Pertici, Caterina Squarci, Pasquale Bianco, Theyencheri Narayanan, Gabriella Piazzesi, Massimo Reconditi, Vincenzo Lombardi, Marco Linari.
      The regulation of heart function is attributed to a dual filament mechanism: i) the Ca2+-dependent structural changes in the regulatory proteins of the thin, actin-containing filament making actin available for myosin motor attachment, and ii) the release of motors from their folded (OFF) state on the surface of the thick filament allowing them to attach and pull the actin filament. Thick filament mechanosensing is thought to control the number of motors switching ON in relation to the systolic performance, but its molecular basis is still controversial. Here, we use high spatial resolution X-ray diffraction data from electrically paced rat trabeculae and papillary muscles to provide a molecular explanation of the modulation of heart performance that calls for a revision of the mechanosensing hypothesis. We find that upon stimulation, titin-mediated structural changes in the thick filament switch motors ON throughout the filament within ~½ the maximum systolic force. These structural changes also drive Myosin Binding Protein-C (MyBP-C) to promote first motor attachments to actin from the central 1/3 of the half-thick filament. Progression of attachments toward the periphery of half-thick filament with increase in systolic force is carried on by near-neighbor cooperative thin filament activation by attached motors. The identification of the roles of MyBP-C, titin, thin and thick filaments in heart regulation enables their targeting for potential therapeutic interventions.
    Keywords:  actin; cardiac muscle regulation; myosin; myosin-binding protein C; titin
    DOI:  https://doi.org/10.1073/pnas.2410893121
  22. J Struct Biol. 2024 Dec 03. pii: S1047-8477(24)00080-7. [Epub ahead of print] 108140
    Investigating The Role of Elastin and Extracellular Matrix Damage in Cardiovascular Calcification.
    Elham Radvar, Khushbu Mehta, Alexander D'Ambrosio, Giulia Mastroianni, Maisoon Al-Jawad, Molly M Stevens, Alvaro Mata, Sherif Elsharkawy.
      Although calcification in the cardiovascular system is highly studied, the mechanisms behind it are not well understood. Current proposed mechanisms focus on cellular processes leading to, or controlling the unwanted mineralization in soft tissues. However, extracellular components such as collagen and elastin fundamentally regulate the mechanical properties of heart tissues. Here, we report on a toolkit to control the composition of tissues through the selective digestion of extracellular matrix (ECM) components, which can be used to design disease-specific in vitro models. Using this technique, we show that elastin as well as matrix tissue damage may play major role in cardiovascular calcification. This study highlights a novel approach to understand the role of proteins in soft tissue calcifications and may lead to the development of strategies to treat and prevent these unwanted pathological disorders.
    DOI:  https://doi.org/10.1016/j.jsb.2024.108140
  23. Biophys Rev. 2024 Oct;16(5): 625-637
    Novel imaging and biophysical approaches to study tissue hydraulics in mammalian folliculogenesis.
    Jake Turley, Kim Whye Leong, Chii Jou Chan.
      A key developmental stage in mammalian folliculogenesis is the formation of a fluid-filled lumen (antrum) prior to ovulation. While it has long been speculated that the follicular fluid is essential for oocyte maturation and ovulation, little is known about the morphogenesis and the mechanisms driving the antrum formation and ovulation, potentially due to challenges in imaging tissue dynamics in large tissues. Misregulation of such processes leads to anovulation, a hallmark of infertility in ageing and diseases such as the polycystic ovary syndrome (PCOS). In this review, we discuss recent advances in deep tissue imaging techniques, machine learning and theoretical approaches that have been applied to study development and diseases. We propose that an integrative approach combining these techniques is essential for understanding the physics of hydraulics in follicle development and ovarian functions.
    Keywords:  Biophotonics; Folliculogenesis; Machine learning; Ovary; Ovulation; Tissue mechanics
    DOI:  https://doi.org/10.1007/s12551-024-01231-4
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