bims-ginsta 2024-08-18 papers

bims-ginsta

Biomed News

on Genome instability

Issue of 2024‒08‒18
twenty-two papers selected by
Jinrong Hu, National University of Singapore

SKAP binding to microtubules reduces friction at the kinetochore-microtubule interface and increases attachment stability under force.
A nuclear jamming transition in vertebrate organogenesis.
Global transcription regulation revealed from dynamical correlations in time-resolved single-cell RNA sequencing.
Remodelling of the translatome controls diet and its impact on tumorigenesis.
Gata6 functions in zebrafish endoderm to regulate late differentiating arterial pole cardiogenesis.
The molecular architecture of the nuclear basket.
Polo-like kinase 1 prevents excess microtubule polymerization in C. elegans oocytes to ensure faithful meiosis.
Comparative single-cell analyses identify shared and divergent features of human and mouse kidney development.
Tight junctions control lumen morphology via hydrostatic pressure and junctional tension.
Substrates mimicking the blastocyst geometry revert pluripotent stem cell to naivety.
Guidelines for minimal information on cellular senescence experimentation in vivo.
DNA methylation in mammalian development and disease.
HMGA1 orchestrates chromatin compartmentalization and sequesters genes into 3D networks coordinating senescence heterogeneity.
Decreased glutathione synthesis in granulosa cells, but not oocytes, of growing follicles decreases fertility in mice.
Local photo-crosslinking of native tissue matrix regulates cell function.
Structural insights into the cooperative nucleosome recognition and chromatin opening by FOXA1 and GATA4.
An actomyosin network organizes niche morphology and responds to feedback from recruited stem cells.
Nuclear poly-glutamine aggregates rupture the nuclear envelope and hinder its repair.
De novo design of allosterically switchable protein assemblies.
Mitochondrial complex I promotes kidney cancer metastasis.
Amplification of autoimmune organ damage by NKp46-activated ILC1.
GLUD1 determines murine muscle stem cell fate by controlling mitochondrial glutamate levels.

bioRxiv. 2024 Aug 08. pii: 2024.08.08.607154. [Epub ahead of print]

SKAP binding to microtubules reduces friction at the kinetochore-microtubule interface and increases attachment stability under force.

Miquel Rosas-Salvans, Caleb Rux, Moumita Das, Sophie Dumont.

The kinetochore links chromosomes to spindle microtubules to drive chromosome segregation at cell division. We recently uncovered that the kinetochore complex Astrin-SKAP, which binds microtubules, reduces rather than increases friction at the mammalian kinetochore-microtubule interface. How it does so is not known. Astrin-SKAP could affect how other kinetochore complexes bind microtubules, reducing their friction along microtubules, or it could itself bind microtubules with similar affinity but lower friction than other attachment factors. Using SKAP mutants unable to bind microtubules, live imaging and laser ablation, we show that SKAP's microtubule binding is essential for sister kinetochore coordination, force dissipation at the interface and attachment responsiveness to force changes. Further, we show that SKAP's microtubule binding is essential to prevent chromosome detachment under both spindle forces and microneedle-generated forces. Together, our findings indicate that SKAP's microtubule binding reduces kinetochore friction and increases attachment responsiveness and stability under force. We propose that having complexes with both high and low sliding friction on microtubules, making a mechanically heterogeneous interface, is key to maintaining robust attachments under force and thus accurate segregation.

DOI: https://doi.org/10.1101/2024.08.08.607154
Nat Mater. 2024 Aug 12.

A nuclear jamming transition in vertebrate organogenesis.

Sangwoo Kim, Rana Amini, Shuo-Ting Yen, Petr Pospíšil, Arthur Boutillon, Ilker Ali Deniz, Otger Campàs.

Jamming of cell collectives and associated rigidity transitions have been shown to play a key role in tissue dynamics, structure and morphogenesis. Cellular jamming is controlled by cellular density and the mechanics of cell-cell contacts. However, the contribution of subcellular organelles to the physical state of the emergent tissue is unclear. Here we report a nuclear jamming transition in zebrafish retina and brain tissues, where physical interactions between highly packed nuclei restrict cellular movements and control tissue mechanics and architecture. Computational modelling suggests that the nuclear volume fraction and anisotropy of cells control the emerging tissue physical state. Analysis of tissue architecture, mechanics and nuclear movements during eye development show that retina tissues undergo a nuclear jamming transition as they form, with increasing nuclear packing leading to more ordered cellular arrangements, reminiscent of the crystalline cellular packings in the functional adult eye. Our results reveal an important role of the cell nucleus in tissue mechanics and architecture.

DOI: https://doi.org/10.1038/s41563-024-01972-3
Cell Syst. 2024 Aug 01. pii: S2405-4712(24)00201-1. [Epub ahead of print]

Global transcription regulation revealed from dynamical correlations in time-resolved single-cell RNA sequencing.

Dimitris Volteras, Vahid Shahrezaei, Philipp Thomas.

  Single-cell transcriptomics reveals significant variations in transcriptional activity across cells. Yet, it remains challenging to identify mechanisms of transcription dynamics from static snapshots. It is thus still unknown what drives global transcription dynamics in single cells. We present a stochastic model of gene expression with cell size- and cell cycle-dependent rates in growing and dividing cells that harnesses temporal dimensions of single-cell RNA sequencing through metabolic labeling protocols and cel lcycle reporters. We develop a parallel and highly scalable approximate Bayesian computation method that corrects for technical variation and accurately quantifies absolute burst frequency, burst size, and degradation rate along the cell cycle at a transcriptome-wide scale. Using Bayesian model selection, we reveal scaling between transcription rates and cell size and unveil waves of gene regulation across the cell cycle-dependent transcriptome. Our study shows that stochastic modeling of dynamical correlations identifies global mechanisms of transcription regulation. A record of this paper's transparent peer review process is included in the supplemental information.

Keywords:  approximate Bayesian computation; cell cycle; gene expression noise; genomics; modeling; single-cell transcriptomics; statistical inference; time-resolved; transcription dynamics; transcriptional bursting

DOI:  https://doi.org/10.1016/j.cels.2024.07.002
Nature. 2024 Aug 14.

Remodelling of the translatome controls diet and its impact on tumorigenesis.

Haojun Yang, Vincenzo Andrea Zingaro, James Lincoff, Harrison Tom, Satoshi Oikawa, Juan A Oses-Prieto, Quinn Edmondson, Ian Seiple, Hardik Shah, Shingo Kajimura, Alma L Burlingame, Michael Grabe, Davide Ruggero.

Fasting is associated with a range of health benefits1-6. How fasting signals elicit changes in the proteome to establish metabolic programmes remains poorly understood. Here we show that hepatocytes selectively remodel the translatome while global translation is paradoxically downregulated during fasting7,8. We discover that phosphorylation of eukaryotic translation initiation factor 4E (P-eIF4E) is induced during fasting. We show that P-eIF4E is responsible for controlling the translation of genes involved in lipid catabolism and the production of ketone bodies. Inhibiting P-eIF4E impairs ketogenesis in response to fasting and a ketogenic diet. P-eIF4E regulates those messenger RNAs through a specific translation regulatory element within their 5' untranslated regions (5' UTRs). Our findings reveal a new signalling property of fatty acids, which are elevated during fasting. We found that fatty acids bind and induce AMP-activated protein kinase (AMPK) kinase activity that in turn enhances the phosphorylation of MAP kinase-interacting protein kinase (MNK), the kinase that phosphorylates eIF4E. The AMPK-MNK-eIF4E axis controls ketogenesis, revealing a new lipid-mediated kinase signalling pathway that links ketogenesis to translation control. Certain types of cancer use ketone bodies as an energy source9,10 that may rely on P-eIF4E. Our findings reveal that on a ketogenic diet, treatment with eFT508 (also known as tomivosertib; a P-eIF4E inhibitor) restrains pancreatic tumour growth. Thus, our findings unveil a new fatty acid-induced signalling pathway that activates selective translation, which underlies ketogenesis and provides a tailored diet intervention therapy for cancer.

DOI: https://doi.org/10.1038/s41586-024-07781-7
Development. 2024 Aug 12. pii: dev.202895. [Epub ahead of print]

Gata6 functions in zebrafish endoderm to regulate late differentiating arterial pole cardiogenesis.

Jessica Sam, Ingrid Torregroza, Todd Evans.

  Mutations in GATA6 are associated with congenital heart disease, most notably conotruncal structural defects. However, how GATA6 regulates cardiac morphology during embryogenesis is undefined. We used knockout and conditional mutant zebrafish alleles to investigate the spatiotemporal role of gata6 during cardiogenesis. Loss of gata6 specifically impacts atrioventricular valve formation and recruitment of epicardium, with a prominent loss of arterial pole cardiac cells including for the ventricle and outflow tract. However, there are no obvious defects in cardiac progenitor cell specification, proliferation, or death. Conditional loss of gata6 starting at 24 hr is sufficient to disrupt the addition of late differentiating cardiomyocytes at the arterial pole with decreased expression levels of anterior second heart field (aSHF) markers spry4 and mef2cb. Conditional loss of gata6 in the endoderm is sufficient to phenocopy the straight knockout resulting in a significant loss of ventricular and outflow tract tissue. Exposure to a Dusp6 inhibitor largely rescues the loss of ventricular cells in gata6-/- larvae. Thus, gata6 functions in endoderm mediated by FGF signaling to regulate the addition of anterior SHF progenitor derivatives during heart formation.

Keywords:  Congenital heart disease; FGF signaling; Heart development; Morphogenesis; Second heart field

DOI:  https://doi.org/10.1242/dev.202895
Cell. 2024 Aug 05. pii: S0092-8674(24)00780-3. [Epub ahead of print]

The molecular architecture of the nuclear basket.

Digvijay Singh, Neelesh Soni, Joshua Hutchings, Ignacia Echeverria, Farhaz Shaikh, Madeleine Duquette, Sergey Suslov, Zhixun Li, Trevor van Eeuwen, Kelly Molloy, Yi Shi, Junjie Wang, Qiang Guo, Brian T Chait, Javier Fernandez-Martinez, Michael P Rout, Andrej Sali, Elizabeth Villa.

  The nuclear pore complex (NPC) is the sole mediator of nucleocytoplasmic transport. Despite great advances in understanding its conserved core architecture, the peripheral regions can exhibit considerable variation within and between species. One such structure is the cage-like nuclear basket. Despite its crucial roles in mRNA surveillance and chromatin organization, an architectural understanding has remained elusive. Using in-cell cryo-electron tomography and subtomogram analysis, we explored the NPC's structural variations and the nuclear basket across fungi (yeast; S. cerevisiae), mammals (mouse; M. musculus), and protozoa (T. gondii). Using integrative structural modeling, we computed a model of the basket in yeast and mammals that revealed how a hub of nucleoporins (Nups) in the nuclear ring binds to basket-forming Mlp/Tpr proteins: the coiled-coil domains of Mlp/Tpr form the struts of the basket, while their unstructured termini constitute the basket distal densities, which potentially serve as a docking site for mRNA preprocessing before nucleocytoplasmic transport.

Keywords:  NPC; chromatin organization; cross-linking mass spectrometry; cryo-electron tomography; cryo-focused-ion-beam milling; in-cell structural biology; integrative modeling; mRNA transport; nuclear basket; nuclear pore complex; subtomogram analysis

DOI:  https://doi.org/10.1016/j.cell.2024.07.020
bioRxiv. 2024 Aug 04. pii: 2024.08.03.606476. [Epub ahead of print]

Polo-like kinase 1 prevents excess microtubule polymerization in C. elegans oocytes to ensure faithful meiosis.

Juhi G Narula, Sarah M Wignall.

Sexual reproduction relies on meiosis, a specialized cell division program that produces haploid gametes. Oocytes of most organisms lack centrosomes, and therefore chromosome segregation is mediated by acentrosomal spindles. Here, we explore the role of Polo-like kinase 1 (PLK-1) in C. elegans oocytes, revealing mechanisms that ensure the fidelity of this unique form of cell division. Previously, PLK-1 was shown to be required for nuclear envelope breakdown and chromosome segregation in oocytes. We now find that PLK-1 is also required for establishing and maintaining acentrosomal spindle organization and for preventing excess microtubule polymerization in these cells. Additionally, our studies revealed an unexpected new role for this essential kinase. While PLK-1 is known to be required for centrosome maturation during mitosis, we found that removal of this kinase from oocytes caused premature recruitment of pericentriolar material to the sperm-provided centrioles following fertilization. Thus, PLK-1 suppresses centrosome maturation during oocyte meiosis, which is opposite to its role in mitosis. Taken together, our work reveals multiple new roles for PLK-1 in oocytes, identifying PLK-1 as a key player that promotes faithful acentrosomal meiosis.

DOI: https://doi.org/10.1101/2024.08.03.606476
Dev Cell. 2024 Aug 07. pii: S1534-5807(24)00450-7. [Epub ahead of print]

Comparative single-cell analyses identify shared and divergent features of human and mouse kidney development.

Sunghyun Kim, Kari Koppitch, Riana K Parvez, Jinjin Guo, MaryAnne Achieng, Jack Schnell, Nils O Lindström, Andrew P McMahon.

  The mammalian kidney maintains fluid homeostasis through diverse epithelial cell types generated from nephron and ureteric progenitor cells. To extend a developmental understanding of the kidney's epithelial networks, we compared chromatin organization (single-nuclear assay for transposase-accessible chromatin sequencing [ATAC-seq]; 112,864 nuclei) and gene expression (single-cell/nuclear RNA sequencing [RNA-seq]; 109,477 cells/nuclei) in the developing human (10.6-17.6 weeks; n = 10) and mouse (post-natal day [P]0; n = 10) kidney, supplementing analysis with published mouse datasets from earlier stages. Single-cell/nuclear datasets were analyzed at a species level, and then nephron and ureteric cellular lineages were extracted and integrated into a common, cross-species, multimodal dataset. Comparative computational analyses identified conserved and divergent features of chromatin organization and linked gene activity, identifying species-specific and cell-type-specific regulatory programs. In situ validation of human-enriched gene activity points to human-specific signaling interactions in kidney development. Further, human-specific enhancer regions were linked to kidney diseases through genome-wide association studies (GWASs), highlighting the potential for clinical insight from developmental modeling.

Keywords:  ATAC-seq; RNA-seq; enhancers; human; kidney development; mouse; multiomic; single cell; species specific

DOI:  https://doi.org/10.1016/j.devcel.2024.07.013
Dev Cell. 2024 Aug 08. pii: S1534-5807(24)00456-8. [Epub ahead of print]

Tight junctions control lumen morphology via hydrostatic pressure and junctional tension.

Markus Mukenhirn, Chen-Ho Wang, Tristan Guyomar, Matthew J Bovyn, Michael F Staddon, Rozemarijn E van der Veen, Riccardo Maraspini, Linjie Lu, Cecilie Martin-Lemaitre, Masaki Sano, Martin Lehmann, Tetsuya Hiraiwa, Daniel Riveline, Alf Honigmann.

  Formation of fluid-filled lumina by epithelial tissues is essential for organ development. How cells control the hydraulic and cortical forces to control lumen morphology is not well understood. Here, we quantified the mechanical role of tight junctions in lumen formation using MDCK-II cysts. We found that the paracellular ion barrier formed by claudin receptors is not required for the hydraulic inflation of a lumen. However, the depletion of the zonula occludens scaffold resulted in lumen collapse and folding of apical membranes. Combining quantitative measurements of hydrostatic lumen pressure and junctional tension with modeling enabled us to explain lumen morphologies from the pressure-tension force balance. Tight junctions promote lumen inflation by decreasing cortical tension via the inhibition of myosin. In addition, our results suggest that excess apical area contributes to lumen opening. Overall, we provide a mechanical understanding of how epithelial cells use tight junctions to modulate tissue and lumen shape.

Keywords:  biological physics; lumen morphogenesis; lumen pressure; mechano-biology; myosin contractility; tight junction; tissue hydraulics

DOI:  https://doi.org/10.1016/j.devcel.2024.07.016
Nat Mater. 2024 Aug 12.

Substrates mimicking the blastocyst geometry revert pluripotent stem cell to naivety.

Xun Xu, Weiwei Wang, Yue Liu, Johan Bäckemo, Matthias Heuchel, Wei Wang, Yan Nie, Imran Iqbal, Karl Kratz, Andreas Lendlein, Nan Ma.

Naive pluripotent stem cells have the highest developmental potential but their in vivo existence in the blastocyst is transient. Here we report a blastocyst motif substrate for the in vitro reversion of mouse and human pluripotent stem cells to a naive state. The substrate features randomly varied microstructures, which we call motifs, mimicking the geometry of the blastocyst. Motifs representing mouse-blastocyst-scaled curvature ranging between 15 and 62 mm-1 were the most efficient in promoting reversion to naivety, as determined by time-resolved correlative analysis. In these substrates, apical constriction enhances E-cadherin/RAC1 signalling and activates the mechanosensitive nuclear transducer YAP, promoting the histone modification of pluripotency genes. This results in enhanced levels of pluripotency transcription factor NANOG, which persist even after cells are removed from the substrate. Pluripotent stem cells cultured in blastocyst motif substrates display a higher development potential in generating embryoid bodies and teratomas. These findings shed light on naivety-promoting substrate design and their large-scale implementation.

DOI: https://doi.org/10.1038/s41563-024-01971-4
Cell. 2024 Aug 08. pii: S0092-8674(24)00640-8. [Epub ahead of print]187(16): 4150-4175

Guidelines for minimal information on cellular senescence experimentation in vivo.

Mikolaj Ogrodnik, Juan Carlos Acosta, Peter D Adams, Fabrizio d'Adda di Fagagna, Darren J Baker, Cleo L Bishop, Tamir Chandra, Manuel Collado, Jesus Gil, Vassilis Gorgoulis, Florian Gruber, Eiji Hara, Pidder Jansen-Dürr, Diana Jurk, Sundeep Khosla, James L Kirkland, Valery Krizhanovsky, Tohru Minamino, Laura J Niedernhofer, João F Passos, Nadja A R Ring, Heinz Redl, Paul D Robbins, Francis Rodier, Karin Scharffetter-Kochanek, John M Sedivy, Ewa Sikora, Kenneth Witwer, Thomas von Zglinicki, Maximina H Yun, Johannes Grillari, Marco Demaria.

  Cellular senescence is a cell fate triggered in response to stress and is characterized by stable cell-cycle arrest and a hypersecretory state. It has diverse biological roles, ranging from tissue repair to chronic disease. The development of new tools to study senescence in vivo has paved the way for uncovering its physiological and pathological roles and testing senescent cells as a therapeutic target. However, the lack of specific and broadly applicable markers makes it difficult to identify and characterize senescent cells in tissues and living organisms. To address this, we provide practical guidelines called "minimum information for cellular senescence experimentation in vivo" (MICSE). It presents an overview of senescence markers in rodent tissues, transgenic models, non-mammalian systems, human tissues, and tumors and their use in the identification and specification of senescent cells. These guidelines provide a uniform, state-of-the-art, and accessible toolset to improve our understanding of cellular senescence in vivo.

Keywords:  aging; humans; in vivo; mouse; senescence; senotherapy

DOI:  https://doi.org/10.1016/j.cell.2024.05.059
Nat Rev Genet. 2024 Aug 12.

DNA methylation in mammalian development and disease.

Zachary D Smith, Sara Hetzel, Alexander Meissner.

The DNA methylation field has matured from a phase of discovery and genomic characterization to one seeking deeper functional understanding of how this modification contributes to development, ageing and disease. In particular, the past decade has seen many exciting mechanistic discoveries that have substantially expanded our appreciation for how this generic, evolutionarily ancient modification can be incorporated into robust epigenetic codes. Here, we summarize the current understanding of the distinct DNA methylation landscapes that emerge over the mammalian lifespan and discuss how they interact with other regulatory layers to support diverse genomic functions. We then review the rising interest in alternative patterns found during senescence and the somatic transition to cancer. Alongside advancements in single-cell and long-read sequencing technologies, the collective insights made across these fields offer new opportunities to connect the biochemical and genetic features of DNA methylation to cell physiology, developmental potential and phenotype.

DOI: https://doi.org/10.1038/s41576-024-00760-8
Nat Commun. 2024 Aug 12. 15(1): 6891

HMGA1 orchestrates chromatin compartmentalization and sequesters genes into 3D networks coordinating senescence heterogeneity.

Ioana Olan, Masami Ando-Kuri, Aled J Parry, Tetsuya Handa, Stefan Schoenfelder, Peter Fraser, Yasuyuki Ohkawa, Hiroshi Kimura, Masako Narita, Masashi Narita.

HMGA1 is an abundant non-histone chromatin protein that has been implicated in embryonic development, cancer, and cellular senescence, but its specific role remains elusive. Here, we combine functional genomics approaches with graph theory to investigate how HMGA1 genomic deposition controls high-order chromatin networks in an oncogene-induced senescence model. While the direct role of HMGA1 in gene activation has been described previously, we find little evidence to support this. Instead, we show that the heterogeneous linear distribution of HMGA1 drives a specific 3D chromatin organization. HMGA1-dense loci form highly interactive networks, similar to, but independent of, constitutive heterochromatic loci. This, coupled with the exclusion of HMGA1-poor chromatin regions, leads to coordinated gene regulation through the repositioning of genes. In the absence of HMGA1, the whole process is largely reversed, but many regulatory interactions also emerge, amplifying the inflammatory senescence-associated secretory phenotype. Such HMGA1-mediated fine-tuning of gene expression contributes to the heterogeneous nature of senescence at the single-cell level. A similar 'buffer' effect of HMGA1 on inflammatory signalling is also detected in lung cancer cells. Our study reveals a mechanism through which HMGA1 modulates chromatin compartmentalization and gene regulation in senescence and beyond.

DOI: https://doi.org/10.1038/s41467-024-51153-8
Biol Reprod. 2024 Aug 16. pii: ioae124. [Epub ahead of print]

Decreased glutathione synthesis in granulosa cells, but not oocytes, of growing follicles decreases fertility in mice.

Rachel Cinco, Kelli Malott, Jinhwan Lim, Laura Ortiz, Christine Pham, Angelica Rosario, Jennifer Welch, Ulrike Luderer.

  Prior studies showed that mice deficient in the modifier subunit of glutamate cysteine ligase (Gclm), the rate-limiting enzyme in synthesis of the thiol antioxidant glutathione (GSH), have decreased ovarian GSH concentrations, chronic ovarian oxidative stress, poor oocyte quality resulting in early preimplantation embryonic mortality and decreased litter size, and accelerated age-related decline in ovarian follicle numbers. Global deficiency of the catalytic subunit of this enzyme, Gclc, is embryonic lethal. We tested the hypothesis that granulosa cell- or oocyte-specific deletion of Gclc recapitulates the female reproductive phenotype of global Gclm deficiency. We deleted Gclc in granulosa cells or oocytes of growing follicles using Gclc floxed transgenic mice paired with Amhr2-Cre or Zp3-Cre alleles respectively. We discovered that granulosa cell-specific deletion of Gclc in Amhr2Cre;Gclc(f/-) mice recapitulates the decreased litter size observed in Gclm-/- mice, but does not recapitulate the accelerated age-related decline in ovarian follicles observed in Gclm-/- mice. In addition to having lower GSH concentrations in granulosa cells, Amhr2Cre;Gclc(f/-) mice also had decreased GSH concentrations in oocytes. By contrast, oocyte-specific deletion of Gclc in Zp3Cre;Gclc(f/-) mice did not affect litter size or accelerate the age-related decline in follicle numbers, and these mice did not have decreased oocyte GSH concentrations, consistent with transport of GSH between cells via gap junctions. The results suggest that GSH deficiency at earlier stages of follicle development may be required to generate the accelerated follicle depletion phenotype observed in global Gclm null mice.

Keywords:  Fertility; Glutamate cysteine ligase; Glutathione; Ovarian follicle; Ovary; Oxidative stress

DOI:  https://doi.org/10.1093/biolre/ioae124
bioRxiv. 2024 Aug 10. pii: 2024.08.10.607417. [Epub ahead of print]

Local photo-crosslinking of native tissue matrix regulates cell function.

Donia W Ahmed, Matthew L Tan, Jackson Gabbard, Yuchen Liu, Michael M Hu, Miriam Stevens, Firaol S Midekssa, Lin Han, Rachel L Zemans, Brendon M Baker, Claudia Loebel.

Within most tissues, the extracellular microenvironment provides mechanical cues that guide cell fate and function. Changes in the extracellular matrix such as aberrant deposition, densification and increased crosslinking are hallmarks of late-stage fibrotic diseases that often lead to organ dysfunction. Biomaterials have been widely used to mimic the mechanical properties of the fibrotic matrix and study cell function. However, the initiation of fibrosis has largely been overlooked, due to the challenges in recapitulating early fibrotic lesions within the native extracellular microenvironment. Using visible light mediated photochemistry, we induced local crosslinking and stiffening of extracellular matrix proteins within ex vivo murine and human tissue. In ex vivo lung tissue of epithelial cell lineage-traced mice, local matrix crosslinking mimicked early fibrotic lesions that increased alveolar epithelial cell spreading, differentiation and extracellular matrix remodeling. However, inhibition of cytoskeletal tension or integrin engagement reduced epithelial cell spreading and differentiation, resulting in alveolar epithelial cell dedifferentiation and reduced extracellular matrix deposition. Our findings emphasize the role of local extracellular matrix crosslinking and remodeling in early-stage tissue fibrosis and have implications for ex vivo disease modeling and applications to other tissues.

DOI: https://doi.org/10.1101/2024.08.10.607417
Mol Cell. 2024 Jul 31. pii: S1097-2765(24)00592-6. [Epub ahead of print]

Structural insights into the cooperative nucleosome recognition and chromatin opening by FOXA1 and GATA4.

Bing-Rui Zhou, Hanqiao Feng, Furong Huang, Iris Zhu, Stephanie Portillo-Ledesma, Dan Shi, Kenneth S Zaret, Tamar Schlick, David Landsman, Qianben Wang, Yawen Bai.

  Mouse FOXA1 and GATA4 are prototypes of pioneer factors, initiating liver cell development by binding to the N1 nucleosome in the enhancer of the ALB1 gene. Using cryoelectron microscopy (cryo-EM), we determined the structures of the free N1 nucleosome and its complexes with FOXA1 and GATA4, both individually and in combination. We found that the DNA-binding domains of FOXA1 and GATA4 mainly recognize the linker DNA and an internal site in the nucleosome, respectively, whereas their intrinsically disordered regions interact with the acidic patch on histone H2A-H2B. FOXA1 efficiently enhances GATA4 binding by repositioning the N1 nucleosome. In vivo DNA editing and bioinformatics analyses suggest that the co-binding mode of FOXA1 and GATA4 plays important roles in regulating genes involved in liver cell functions. Our results reveal the mechanism whereby FOXA1 and GATA4 cooperatively bind to the nucleosome through nucleosome repositioning, opening chromatin by bending linker DNA and obstructing nucleosome packing.

Keywords:  FOXA1; GATA4; N1 nucleosome; cell fate determination; chromatin; chromatosome; enhancer; nucleosome; nucleosome array; pioneer transcription factor

DOI:  https://doi.org/10.1016/j.molcel.2024.07.016
Curr Biol. 2024 Aug 06. pii: S0960-9822(24)00944-8. [Epub ahead of print]

An actomyosin network organizes niche morphology and responds to feedback from recruited stem cells.

Bailey N Warder, Kara A Nelson, Justin Sui, Lauren Anllo, Stephen DiNardo.

  Stem cells often rely on signals from a niche, which in many tissues adopts a precise morphology. What remains elusive is how niches are formed and how morphology impacts function. To address this, we leverage the Drosophila gonadal niche, which affords genetic tractability and live-imaging. We have previously shown mechanisms dictating niche cell migration to their appropriate position within the gonad and the resultant consequences on niche function. Here, we show that once positioned, niche cells robustly polarize filamentous actin (F-actin) and non-muscle myosin II (MyoII) toward neighboring germ cells. Actomyosin tension along the niche periphery generates a highly reproducible smoothened contour. Without contractility, niches are misshapen and exhibit defects in their ability to regulate germline stem cell behavior. We additionally show that germ cells aid in polarizing MyoII within niche cells and that extrinsic input is required for niche morphogenesis and function. Our work reveals a feedback mechanism where stem cells shape the niche that guides their behavior.

Keywords:  Drosophila; actomyosin contractility; feedback; morphogenesis; niche; stem cell; testis

DOI:  https://doi.org/10.1016/j.cub.2024.07.041
J Cell Biol. 2024 Nov 04. pii: e202307142. [Epub ahead of print]223(11):

Nuclear poly-glutamine aggregates rupture the nuclear envelope and hinder its repair.

Giel Korsten, Miriam Osinga, Robin A Pelle, Albert K Serweta, Baukje Hoogenberg, Harm H Kampinga, Lukas C Kapitein.

Huntington's disease (HD) is caused by a polyglutamine expansion of the huntingtin protein, resulting in the formation of polyglutamine aggregates. The mechanisms of toxicity that result in the complex HD pathology remain only partially understood. Here, we show that nuclear polyglutamine aggregates induce nuclear envelope (NE) blebbing and ruptures that are often repaired incompletely. These ruptures coincide with disruptions of the nuclear lamina and lead to lamina scar formation. Expansion microscopy enabled resolving the ultrastructure of nuclear aggregates and revealed polyglutamine fibrils sticking into the cytosol at rupture sites, suggesting a mechanism for incomplete repair. Furthermore, we found that NE repair factors often accumulated near nuclear aggregates, consistent with stalled repair. These findings implicate nuclear polyQ aggregate-induced loss of NE integrity as a potential contributing factor to Huntington's disease and other polyglutamine diseases.

DOI: https://doi.org/10.1083/jcb.202307142
Nature. 2024 Aug 14.

De novo design of allosterically switchable protein assemblies.

Arvind Pillai, Abbas Idris, Annika Philomin, Connor Weidle, Rebecca Skotheim, Philip J Y Leung, Adam Broerman, Cullen Demakis, Andrew J Borst, Florian Praetorius, David Baker.

Allosteric modulation of protein function, wherein the binding of an effector to a protein triggers conformational changes at distant functional sites, plays a central part in the control of metabolism and cell signalling1-3. There has been considerable interest in designing allosteric systems, both to gain insight into the mechanisms underlying such 'action at a distance' modulation and to create synthetic proteins whose functions can be regulated by effectors4-7. However, emulating the subtle conformational changes distributed across many residues, characteristic of natural allosteric proteins, is a significant challenge8,9. Here, inspired by the classic Monod-Wyman-Changeux model of cooperativity10, we investigate the de novo design of allostery through rigid-body coupling of peptide-switchable hinge modules11 to protein interfaces12 that direct the formation of alternative oligomeric states. We find that this approach can be used to generate a wide variety of allosterically switchable systems, including cyclic rings that incorporate or eject subunits in response to peptide binding and dihedral cages that undergo effector-induced disassembly. Size-exclusion chromatography, mass photometry13 and electron microscopy reveal that these designed allosteric protein assemblies closely resemble the design models in both the presence and absence of peptide effectors and can have ligand-binding cooperativity comparable to classic natural systems such as haemoglobin14. Our results indicate that allostery can arise from global coupling of the energetics of protein substructures without optimized side-chain-side-chain allosteric communication pathways and provide a roadmap for generating allosterically triggerable delivery systems, protein nanomachines and cellular feedback control circuitry.

DOI: https://doi.org/10.1038/s41586-024-07813-2
Nature. 2024 Aug 14.

Mitochondrial complex I promotes kidney cancer metastasis.

Divya Bezwada, Luigi Perelli, Nicholas P Lesner, Ling Cai, Bailey Brooks, Zheng Wu, Hieu S Vu, Varun Sondhi, Daniel L Cassidy, Stacy Kasitinon, Sherwin Kelekar, Feng Cai, Arin B Aurora, McKenzie Patrick, Ashley Leach, Rashed Ghandour, Yuanyuan Zhang, Duyen Do, Phyllis McDaniel, Jessica Sudderth, Dennis Dumesnil, Sara House, Tracy Rosales, Alan M Poole, Yair Lotan, Solomon Woldu, Aditya Bagrodia, Xiaosong Meng, Jeffrey A Cadeddu, Prashant Mishra, Javier Garcia-Bermudez, Ivan Pedrosa, Payal Kapur, Kevin D Courtney, Craig R Malloy, Giannicola Genovese, Vitaly Margulis, Ralph J DeBerardinis.

Most kidney cancers are metabolically dysfunctional1-4, but how this dysfunction affects cancer progression in humans is unknown. We infused 13C-labelled nutrients in over 80 patients with kidney cancer during surgical tumour resection. Labelling from [U-13C]glucose varies across subtypes, indicating that the kidney environment alone cannot account for all tumour metabolic reprogramming. Compared with the adjacent kidney, clear cell renal cell carcinomas (ccRCCs) display suppressed labelling of tricarboxylic acid (TCA) cycle intermediates in vivo and in ex vivo organotypic cultures, indicating that suppressed labelling is tissue intrinsic. [1,2-13C]acetate and [U-13C]glutamine infusions in patients, coupled with measurements of respiration in isolated human kidney and tumour mitochondria, reveal lower electron transport chain activity in ccRCCs that contributes to decreased oxidative and enhanced reductive TCA cycle labelling. However, ccRCC metastases unexpectedly have enhanced TCA cycle labelling compared with that of primary ccRCCs, indicating a divergent metabolic program during metastasis in patients. In mice, stimulating respiration or NADH recycling in kidney cancer cells is sufficient to promote metastasis, whereas inhibiting electron transport chain complex I decreases metastasis. These findings in humans and mice indicate that metabolic properties and liabilities evolve during kidney cancer progression, and that mitochondrial function is limiting for metastasis but not growth at the original site.

DOI: https://doi.org/10.1038/s41586-024-07812-3
Nature. 2024 Aug 13.

Amplification of autoimmune organ damage by NKp46-activated ILC1.

Stylianos-Iason Biniaris-Georgallis, Tom Aschman, Katerina Stergioula, Frauke Schreiber, Vajiheh Jafari, Anna Taranko, Tejal Karmalkar, Ana Kasapi, Tihana Lenac Rovis, Vedrana Jelencic, David A Bejarano, Lea Fabry, Michail Papacharalampous, Irene Mattiola, Martina Molgora, Jinchao Hou, Karolin W Hublitz, Frederik Heinrich, Gabriela Maria Guerra, Pawel Durek, Giannino Patone, Eric Lars-Helge Lindberg, Henrike Maatz, Oliver Hölsken, Gerhard Krönke, Arthur Mortha, Reinhard E Voll, Alexander J Clarke, Anja E Hauser, Marco Colonna, Kevin Thurley, Andreas Schlitzer, Christoph Schneider, Efstathios G Stamatiades, Mir-Farzin Mashreghi, Stipan Jonjic, Norbert Hübner, Andreas Diefenbach, Masatoshi Kanda, Antigoni Triantafyllopoulou.

In systemic lupus erythematosus (SLE) loss of immune tolerance, autoantibody production and immune complex deposition are required but not sufficient for organ damage1. How inflammatory signals are initiated and amplified in the setting of autoimmunity remains elusive. Here, we set out to dissect layers and hierarchies of autoimmune kidney inflammation in order to identify tissue-specific cellular hubs that amplify auto-inflammatory responses. Using high-resolution single-cell profiling of kidney immune and parenchymal cells, in combination with antibody blocking and genetic deficiency, we show that tissue-resident NKp46+ innate lymphoid cells (ILC) are crucial signal amplifiers of disease-associated macrophage expansion and epithelial cell injury in lupus nephritis, downstream of autoantibody production. NKp46 signaling in a distinct subset of ILC1 instructed an unconventional immune-regulatory transcriptional program, which included the expression of the myeloid cell growth factor CSF2. CSF2 production by NKp46+ ILC promoted the population expansion of monocyte-derived macrophages. Blockade of the NKp46 receptor (using the antibody mNCR1.152) or genetic deficiency of NKp46 abrogated epithelial cell injury. The same cellular and molecular patterns were operative in human lupus nephritis. Our data support that NKp46+ ILC1 promote parenchymal cell injury by granting monocyte-derived macrophages access to epithelial cell niches. NKp46 activation in ILC1 thus constitutes a previously unrecognized, critical tissue rheostat that amplifies organ damage in autoimmune hosts, with broad implications for inflammatory pathologies and therapies.

DOI: https://doi.org/10.1038/s41586-024-07907-x
Dev Cell. 2024 Aug 02. pii: S1534-5807(24)00455-6. [Epub ahead of print]

GLUD1 determines murine muscle stem cell fate by controlling mitochondrial glutamate levels.

Inés Soro-Arnáiz, Gillian Fitzgerald, Sarah Cherkaoui, Jing Zhang, Paola Gilardoni, Adhideb Ghosh, Ori Bar-Nur, Evi Masschelein, Pierre Maechler, Nicola Zamboni, Martin Poms, Alessio Cremonesi, Juan Carlos Garcia-Cañaveras, Katrien De Bock, Raphael Johannes Morscher.

  Muscle stem cells (MuSCs) enable muscle growth and regeneration after exercise or injury, but how metabolism controls their regenerative potential is poorly understood. We describe that primary metabolic changes can determine murine MuSC fate decisions. We found that glutamine anaplerosis into the tricarboxylic acid (TCA) cycle decreases during MuSC differentiation and coincides with decreased expression of the mitochondrial glutamate deaminase GLUD1. Deletion of Glud1 in proliferating MuSCs resulted in precocious differentiation and fusion, combined with loss of self-renewal in vitro and in vivo. Mechanistically, deleting Glud1 caused mitochondrial glutamate accumulation and inhibited the malate-aspartate shuttle (MAS). The resulting defect in transporting NADH-reducing equivalents into the mitochondria induced compartment-specific NAD+/NADH ratio shifts. MAS activity restoration or directly altering NAD+/NADH ratios normalized myogenesis. In conclusion, GLUD1 prevents deleterious mitochondrial glutamate accumulation and inactivation of the MAS in proliferating MuSCs. It thereby acts as a compartment-specific metabolic brake on MuSC differentiation.

Keywords:  GLUD1; glutamine metabolism; malate aspartate shuttle; metabolite compartmentalization; muscle stem cells; tricarboxylic acid cycle

DOI:  https://doi.org/10.1016/j.devcel.2024.07.015