bims-ginsta 2024-03-03 papers

bims-ginsta

Biomed News

on Genome instability

Issue of 2024–03–03
48 papers selected by
Jinrong Hu, National University of Singapore

Rewiring of the phosphoproteome executes two meiotic divisions in budding yeast.
Distinct negative elongation factor conformations regulate RNA polymerase II promoter-proximal pausing.
A Patterned Human Neural Tube Model Using Microfluidic Gradients.
Triaging of α-helical proteins to the mitochondrial outer membrane by distinct chaperone machinery based on substrate topology.
Torques within and outside the human spindle balance twist at anaphase.
Cellular reprogramming in vivo initiated by SOX4 pioneer factor activity.
Human kinesin-5 KIF11 drives the helical motion of anti-parallel and parallel microtubules around each other.
CKAP5 stabilizes CENP-E at kinetochores by regulating microtubule-chromosome attachments.
Liquid-like VASP condensates drive actin polymerization and dynamic bundling.
Atypical cofilin signaling drives dendritic cell migration through the extracellular matrix via nuclear deformation.
What fraction of cellular DNA turnover becomes cfDNA?
Myosin-I Synergizes with Arp2/3 Complex to Enhance Pushing Forces of Branched Actin Networks.
Expansion of human centromeric arrays in cells undergoing break-induced replication.
Oct4 is a gatekeeper of epithelial identity by regulating cytoskeletal organization in skin keratinocytes.
Nucleosome-bound NR5A2 structure reveals pioneer factor mechanism by DNA minor groove anchor competition.
Functional consequences of somatic polyploidy in development.
Dynamic PRC1-CBX8 stabilizes a porous structure of chromatin condensates.
The apparent loss of PRC2 chromatin occupancy as an artifact of RNA depletion.
Mediator complex subunit 1 architects a tumorigenic Treg cell program independent of inflammation.
A common cellular response to broad splicing perturbations is characterized by metabolic transcript downregulation driven by the Mdm2-p53 axis.
RNA-mediated ribonucleoprotein assembly controls TDP-43 nuclear retention.
A Specialized Centrosome-Proteasome Axis Mediates Proteostasis and Influences Cardiac Stress through Txlnb.
SnapShot: Eukaryotic ribosome biogenesis II.
Deficiency of factor-inhibiting HIF creates a tumor-promoting immune microenvironment.
DNA methylation-dependent and -independent binding of CDX2 directs activation of distinct developmental and homeostatic genes.
Region-specific cellular and molecular basis of liver regeneration after acute pericentral injury.
Scalable and Efficient Generation of Mouse Primordial Germ Cell-like Cells.
An immunosuppressive vascular niche drives macrophage polarization and immunotherapy resistance in glioblastoma.
Proteins shaping global chromatin accessibility.
Mechanical complexity of living cells can be mapped onto simple homogeneous equivalents.
BRG1 establishes the neuroectodermal chromatin landscape to restrict dorsal cell fates.
A transcription factor atlas of stem cell fate in planarians.
Changes in cell-cycle rate drive diverging cell fates.
CD38 promotes hematopoietic stem cell dormancy.
Mouse SAS‑6 is required for centriole formation in embryos and integrity in embryonic stem cells.
The CRL5-SPSB3 ubiquitin ligase targets nuclear cGAS for degradation.
Aging STINGs: mitophagy at the crossroads of neuroinflammation.
Targeting HDAC6 to treat heart failure with preserved ejection fraction in mice.
Stromal Pbrm1 mediates chromatin remodeling necessary for embryo implantation in the mouse uterus.
Single-cell analysis reveals insights into epithelial abnormalities in ovarian endometriosis.
Moonwalking molecular machines: Unraveling the choreography of myosin filament assembly.
Genetic and bioinformatic analyses reveal transcriptional networks underlying dual genomic coordination of mitochondrial biogenesis.
Enhanced branched-chain amino acid metabolism improves age-related reproduction in C. elegans.
Human surface ectoderm and amniotic ectoderm are sequentially specified according to cellular density.
Translation is an emerging constraint on protein homeostasis in ageing.
Editorial overview: Functional specialization of the cytoskeleton in diverse cell types.
Reducing the metabolic burden of rRNA synthesis promotes healthy longevity in Caenorhabditis elegans.
HER2 phosphorylation induced by TGF-β promotes mammary morphogenesis and breast cancer progression.

EMBO J. 2024 Feb 27.

Rewiring of the phosphoproteome executes two meiotic divisions in budding yeast.

Lori B Koch, Christos Spanos, Van Kelly, Tony Ly, Adele L Marston.

  The cell cycle is ordered by a controlled network of kinases and phosphatases. To generate gametes via meiosis, two distinct and sequential chromosome segregation events occur without an intervening S phase. How canonical cell cycle controls are modified for meiosis is not well understood. Here, using highly synchronous budding yeast populations, we reveal how the global proteome and phosphoproteome change during the meiotic divisions. While protein abundance changes are limited to key cell cycle regulators, dynamic phosphorylation changes are pervasive. Our data indicate that two waves of cyclin-dependent kinase (Cdc28Cdk1) and Polo (Cdc5Polo) kinase activity drive successive meiotic divisions. These two distinct phases of phosphorylation are ensured by the meiosis-specific Spo13 protein, which rewires the phosphoproteome. Spo13 binds to Cdc5Polo to promote phosphorylation in meiosis I, particularly of substrates containing a variant of the canonical Cdc5Polo motif. Overall, our findings reveal that a master regulator of meiosis directs the activity of a kinase to change the phosphorylation landscape and elicit a developmental cascade.

Keywords:  Cell Cycle; Kinases; Meiosis; Phosphorylation; Proteomics

DOI:  https://doi.org/10.1038/s44318-024-00059-8
Mol Cell. 2024 Feb 10. pii: S1097-2765(24)00090-X. [Epub ahead of print]

Distinct negative elongation factor conformations regulate RNA polymerase II promoter-proximal pausing.

Bonnie G Su, Seychelle M Vos.

  Metazoan gene expression regulation involves pausing of RNA polymerase (Pol II) in the promoter-proximal region of genes and is stabilized by DSIF and NELF. Upon depletion of elongation factors, NELF appears to accompany elongating Pol II past pause sites; however, prior work indicates that NELF prevents Pol II elongation. Here, we report cryoelectron microscopy structures of Pol II-DSIF-NELF complexes with NELF in two distinct conformations corresponding to paused and poised states. The paused NELF state supports Pol II stalling, whereas the poised NELF state enables transcription elongation as it does not support a tilted RNA-DNA hybrid. Further, the poised NELF state can accommodate TFIIS binding to Pol II, allowing for Pol II reactivation at paused or backtracking sites. Finally, we observe that the NELF-A tentacle interacts with the RPB2 protrusion and is necessary for pausing. Our results define how NELF can support pausing, reactivation, and elongation by Pol II.

Keywords:  DSIF; NELF; RNA polymerase II; TFIIS; promoter proximal pausing; transcription

DOI:  https://doi.org/10.1016/j.molcel.2024.01.023
Nature. 2024 Feb 26.

A Patterned Human Neural Tube Model Using Microfluidic Gradients.

Xufeng Xue, Yung Su Kim, Alfredo-Isaac Ponce-Arias, Richard O'Laughlin, Robin Zhexuan Yan, Norio Kobayashi, Rami Yair Tshuva, Yu-Hwai Tsai, Shiyu Sun, Yi Zheng, Yue Liu, Frederick C K Wong, Azim Surani, Jason R Spence, Hongjun Song, Guo-Li Ming, Orly Reiner, Jianping Fu.

Human nervous system is arguably the most complex but highly organized organ. Foundation of its complexity and organization is laid down during regional patterning of neural tube (NT), the embryonic precursor to human nervous system. Historically, studies of NT patterning have relied on animal models to uncover underlying principles. Recently, human pluripotent stem cell (hPSC)-based models of neurodevelopment, including neural organoids1-5 and bioengineered NT development models6-10, are emerging. However, existing hPSC-based models fail to recapitulate neural patterning along both rostral-caudal (R-C) and dorsal-ventral (D-V) axes in a three-dimensional (3D) tubular geometry, a hallmark of NT development. Herein we report a hPSC-based, microfluidic NT-like structure (or μNTLS), whose development recapitulates some critical aspects of neural patterning in both brain and spinal cord (SC) regions and along both R-C and D-V axes. The μNTLS was utilized for studying neuronal lineage development, revealing prepatterning of axial identities of neural crest (NC) progenitors and functional roles of neuromesodermal progenitors (NMPs) and caudal gene CDX2 in SC and trunk NC development. We further developed D-V patterned, microfluidic forebrain-like structures (μFBLS) with spatially segregated dorsal and ventral regions and layered apicobasal cellular organizations that mimic human forebrain pallium and subpallium developments, respectively. Together, both μNTLS and μFBLS offer 3D lumenal tissue architectures with an in vivo-like spatiotemporal cell differentiation and organization, promising for studying human neurodevelopment and disease.

DOI: https://doi.org/10.1038/s41586-024-07204-7
Mol Cell. 2024 Feb 27. pii: S1097-2765(24)00095-9. [Epub ahead of print]

Triaging of α-helical proteins to the mitochondrial outer membrane by distinct chaperone machinery based on substrate topology.

Gayathri Muthukumar, Taylor A Stevens, Alison J Inglis, Theodore K Esantsi, Reuben A Saunders, Fabian Schulte, Rebecca M Voorhees, Alina Guna, Jonathan S Weissman.

  Mitochondrial outer membrane ⍺-helical proteins play critical roles in mitochondrial-cytoplasmic communication, but the rules governing the targeting and insertion of these biophysically diverse proteins remain unknown. Here, we first defined the complement of required mammalian biogenesis machinery through genome-wide CRISPRi screens using topologically distinct membrane proteins. Systematic analysis of nine identified factors across 21 diverse ⍺-helical substrates reveals that these components are organized into distinct targeting pathways that act on substrates based on their topology. NAC is required for the efficient targeting of polytopic proteins, whereas signal-anchored proteins require TTC1, a cytosolic chaperone that physically engages substrates. Biochemical and mutational studies reveal that TTC1 employs a conserved TPR domain and a hydrophobic groove in its C-terminal domain to support substrate solubilization and insertion into mitochondria. Thus, the targeting of diverse mitochondrial membrane proteins is achieved through topological triaging in the cytosol using principles with similarities to ER membrane protein biogenesis systems.

Keywords:  CRISPR; NAC; TTC1; cell biology; cytosolic targeting; genetic screens; membrane protein insertion; mitochondrial outer membrane; topology

DOI:  https://doi.org/10.1016/j.molcel.2024.01.028
bioRxiv. 2023 Dec 10. pii: 2023.12.10.570990. [Epub ahead of print]

Torques within and outside the human spindle balance twist at anaphase.

Lila Neahring, Yifei He, Nathan H Cho, Gaoxiang Liu, Jonathan Fernandes, Caleb J Rux, Konstantinos Nakos, Radhika Subramanian, Srigokul Upadhyayula, Ahmet Yildiz, Sophie Dumont.

  At each cell division, nanometer-scale motors and microtubules give rise to the micron-scale spindle. Many mitotic motors step helically around microtubules in vitro, and most are predicted to twist the spindle in a left-handed direction. However, the human spindle exhibits only slight global twist, raising the question of how these molecular torques are balanced. Here, using lattice light sheet microscopy, we find that anaphase spindles in the epithelial cell line MCF10A have a high baseline twist, and we identify factors that both increase and decrease this twist. The midzone motors KIF4A and MKLP1 are redundantly required for left-handed twist at anaphase, and we show that KIF4A generates left-handed torque in vitro. The actin cytoskeleton also contributes to left-handed twist, but dynein and its cortical recruitment factor LGN counteract it. Together, our work demonstrates that force generators regulate twist in opposite directions from both within and outside the spindle, preventing strong spindle twist during chromosome segregation.

Keywords:  chirality; cortex; dynein; lattice light sheet microscopy; mitosis; motors; spindle; torque; twist

DOI:  https://doi.org/10.1101/2023.12.10.570990
Nat Commun. 2024 Feb 26. 15(1): 1761

Cellular reprogramming in vivo initiated by SOX4 pioneer factor activity.

Takeshi Katsuda, Jonathan H Sussman, Kenji Ito, Andrew Katznelson, Salina Yuan, Naomi Takenaka, Jinyang Li, Allyson J Merrell, Hector Cure, Qinglan Li, Reyaz Ur Rasool, Irfan A Asangani, Kenneth S Zaret, Ben Z Stanger.

Tissue damage elicits cell fate switching through a process called metaplasia, but how the starting cell fate is silenced and the new cell fate is activated has not been investigated in animals. In cell culture, pioneer transcription factors mediate "reprogramming" by opening new chromatin sites for expression that can attract transcription factors from the starting cell's enhancers. Here we report that SOX4 is sufficient to initiate hepatobiliary metaplasia in the adult mouse liver, closely mimicking metaplasia initiated by toxic damage to the liver. In lineage-traced cells, we assessed the timing of SOX4-mediated opening of enhancer chromatin versus enhancer decommissioning. Initially, SOX4 directly binds to and closes hepatocyte regulatory sequences via an overlapping motif with HNF4A, a hepatocyte master regulatory transcription factor. Subsequently, SOX4 exerts pioneer factor activity to open biliary regulatory sequences. The results delineate a hierarchy by which gene networks become reprogrammed under physiological conditions, providing deeper insight into the basis for cell fate transitions in animals.

DOI: https://doi.org/10.1038/s41467-024-45939-z
EMBO J. 2024 Feb 29.

Human kinesin-5 KIF11 drives the helical motion of anti-parallel and parallel microtubules around each other.

Laura Meißner, Lukas Niese, Irene Schüring, Aniruddha Mitra, Stefan Diez.

  During mitosis, motor proteins and microtubule-associated protein organize the spindle apparatus by cross-linking and sliding microtubules. Kinesin-5 plays a vital role in spindle formation and maintenance, potentially inducing twist in the spindle fibers. The off-axis power stroke of kinesin-5 could generate this twist, but its implications in microtubule organization remain unclear. Here, we investigate 3D microtubule-microtubule sliding mediated by the human kinesin-5, KIF11, and found that the motor caused right-handed helical motion of anti-parallel microtubules around each other. The sidestepping ratio increased with reduced ATP concentration, indicating that forward and sideways stepping of the motor are not strictly coupled. Further, the microtubule-microtubule distance (motor extension) during sliding decreased with increasing sliding velocity. Intriguingly, parallel microtubules cross-linked by KIF11 orbited without forward motion, with nearly full motor extension. Altering the length of the neck linker increased the forward velocity and pitch of microtubules in anti-parallel overlaps. Taken together, we suggest that helical motion and orbiting of microtubules, driven by KIF11, contributes to flexible and context-dependent filament organization, as well as torque regulation within the mitotic spindle.

Keywords:  Helical Motion; Kinesin; Spindle; Torque

DOI:  https://doi.org/10.1038/s44318-024-00048-x
EMBO Rep. 2024 Feb 29.

CKAP5 stabilizes CENP-E at kinetochores by regulating microtubule-chromosome attachments.

R Bhagya Lakshmi, Pinaki Nayak, Linoy Raz, Apurba Sarkar, Akshay Saroha, Pratibha Kumari, Vishnu M Nair, Delvin P Kombarakkaran, S Sajana, Sanusha M G, Sarit S Agasti, Raja Paul, Uri Ben-David, Tapas K Manna.

  Stabilization of microtubule plus end-directed kinesin CENP-E at the metaphase kinetochores is important for chromosome alignment, but its mechanism remains unclear. Here, we show that CKAP5, a conserved microtubule plus tip protein, regulates CENP-E at kinetochores in human cells. Depletion of CKAP5 impairs CENP-E localization at kinetochores at the metaphase plate and results in increased kinetochore-microtubule stability and attachment errors. Erroneous attachments are also supported by computational modeling. Analysis of CKAP5 knockout cancer cells of multiple tissue origins shows that CKAP5 is preferentially essential in aneuploid, chromosomally unstable cells, and the sensitivity to CKAP5 depletion is correlated to that of CENP-E depletion. CKAP5 depletion leads to reduction in CENP-E-BubR1 interaction and the interaction is rescued by TOG4-TOG5 domain of CKAP5. The same domain can rescue CKAP5 depletion-induced CENP-E removal from the kinetochores. Interestingly, CKAP5 depletion facilitates recruitment of PP1 to the kinetochores and furthermore, a PP1 target site-specific CENP-E phospho-mimicking mutant gets stabilized at kinetochores in the CKAP5-depleted cells. Together, the results support a model in which CKAP5 controls mitotic chromosome attachment errors by stabilizing CENP-E at kinetochores and by regulating stability of the kinetochore-attached microtubules.

Keywords:  CENP-E; CKAP5; Kinetochore; Microtubule; PP1

DOI:  https://doi.org/10.1038/s44319-024-00106-9
Nat Phys. 2023 Apr;19(4): 574-585

Liquid-like VASP condensates drive actin polymerization and dynamic bundling.

Kristin Graham, Aravind Chandrasekaran, Liping Wang, Aly Ladak, Eileen M Lafer, Padmini Rangamani, Jeanne C Stachowiak.

The organization of actin filaments into bundles is required for cellular processes such as motility, morphogenesis, and cell division. Filament bundling is controlled by a network of actin-binding proteins. Recently, several proteins that comprise this network have been found to undergo liquid-liquid phase separation. How might liquid-like condensates contribute to filament bundling? Here, we show that the processive actin polymerase and bundling protein, VASP, forms liquid-like droplets under physiological conditions. As actin polymerizes within VASP droplets, elongating filaments partition to the edges of the droplet to minimize filament curvature, forming an actin-rich ring within the droplet. The rigidity of this ring is balanced by the droplet's surface tension, as predicted by a continuum-scale computational model. However, as actin polymerizes and the ring grows thicker, its rigidity increases and eventually overcomes the surface tension of the droplet, deforming into a linear bundle. The resulting bundles contain long, parallel actin filaments that grow from their tips. Significantly, the fluid nature of the droplets is critical for bundling, as more solid droplets resist deformation, preventing filaments from rearranging to form bundles. Once the parallel arrangement of filaments is created within a VASP droplet, it propagates through the addition of new actin monomers to achieve a length that is many times greater than the initial droplet. This droplet-based mechanism of bundling may be relevant to the assembly of cellular architectures rich in parallel actin filaments, such as filopodia, stress fibers, and focal adhesions.

DOI: https://doi.org/10.1038/s41567-022-01924-1
Cell Rep. 2024 Feb 27. pii: S2211-1247(24)00194-3. [Epub ahead of print]43(3): 113866

Atypical cofilin signaling drives dendritic cell migration through the extracellular matrix via nuclear deformation.

Harry Warner, Giulia Franciosa, Guus van der Borg, Britt Coenen, Felix Faas, Claire Koenig, Rinse de Boer, René Classens, Sjors Maassen, Maksim V Baranov, Shweta Mahajan, Deepti Dabral, Frans Bianchi, Niek van Hilten, Herre Jelger Risselada, Wouter H Roos, Jesper Velgaard Olsen, Laia Querol Cano, Geert van den Bogaart.

  To mount an adaptive immune response, dendritic cells must migrate to lymph nodes to present antigens to T cells. Critical to 3D migration is the nucleus, which is the size-limiting barrier for migration through the extracellular matrix. Here, we show that inflammatory activation of dendritic cells leads to the nucleus becoming spherically deformed and enables dendritic cells to overcome the typical 2- to 3-μm diameter limit for 3D migration through gaps in the extracellular matrix. We show that the nuclear shape change is partially attained through reduced cell adhesion, whereas improved 3D migration is achieved through reprogramming of the actin cytoskeleton. Specifically, our data point to a model whereby the phosphorylation of cofilin-1 at serine 41 drives the assembly of a cofilin-actomyosin ring proximal to the nucleus and enhances migration through 3D collagen gels. In summary, these data describe signaling events through which dendritic cells deform their nucleus and enhance their migratory capacity.

Keywords:  CP: Cell biology; cofilin; dendritic cell; mechanosensing; nucleus; phosphoproteomics

DOI:  https://doi.org/10.1016/j.celrep.2024.113866
Elife. 2024 Feb 26. pii: RP89321. [Epub ahead of print]12

What fraction of cellular DNA turnover becomes cfDNA?

Ron Sender, Elad Noor, Ron Milo, Yuval Dor.

  Cell-free DNA (cfDNA) tests use small amounts of DNA in the bloodstream as biomarkers. While it is thought that cfDNA is largely released by dying cells, the proportion of dying cells' DNA that reaches the bloodstream is unknown. Here, we integrate estimates of cellular turnover rates to calculate the expected amount of cfDNA. By comparing this to the actual amount of cell type-specific cfDNA, we estimate the proportion of DNA reaching plasma as cfDNA. We demonstrate that <10% of the DNA from dying cells is detectable in plasma, and the ratios of measured to expected cfDNA levels vary a thousand-fold among cell types, often reaching well below 0.1%. The analysis suggests that local clearance, presumably via phagocytosis, takes up most of the dying cells' DNA. Insights into the underlying mechanism may help to understand the physiological significance of cfDNA and improve the sensitivity of liquid biopsies.

Keywords:  cellular turnover; cfDNA; clearance mechanisms; computational biology; human; liquid biopsy; systems biology

DOI:  https://doi.org/10.7554/eLife.89321
bioRxiv. 2024 Feb 12. pii: 2024.02.09.579714. [Epub ahead of print]

Myosin-I Synergizes with Arp2/3 Complex to Enhance Pushing Forces of Branched Actin Networks.

Mengqi Xu, David M Rutkowski, Grzegorz Rebowski, Malgorzata Boczkowska, Luther W Pollard, Roberto Dominguez, Dimitrios Vavylonis, E Michael Ostap.

Myosin-Is colocalize with Arp2/3 complex-nucleated actin networks at sites of membrane protrusion and invagination, but the mechanisms by which myosin-I motor activity coordinates with branched actin assembly to generate force are unknown. We mimicked the interplay of these proteins using the "comet tail" bead motility assay, where branched actin networks are nucleated by Arp2/3 complex on the surface of beads coated with myosin-I and the WCA domain of N-WASP. We observed that myosin-I increased bead movement efficiency by thinning actin networks without affecting growth rates. Remarkably, myosin-I triggered symmetry breaking and comet-tail formation in dense networks resistant to spontaneous fracturing. Even with arrested actin assembly, myosin-I alone could break the network. Computational modeling recapitulated these observations suggesting myosin-I acts as a repulsive force shaping the network's architecture and boosting its force-generating capacity. We propose that myosin-I leverages its power stroke to amplify the forces generated by Arp2/3 complex-nucleated actin networks.

DOI: https://doi.org/10.1101/2024.02.09.579714
Cell Rep. 2024 Feb 29. pii: S2211-1247(24)00179-7. [Epub ahead of print]43(3): 113851

Expansion of human centromeric arrays in cells undergoing break-induced replication.

Soyeon Showman, Paul B Talbert, Yiling Xu, Richard O Adeyemi, Steven Henikoff.

  Human centromeres are located within α-satellite arrays and evolve rapidly, which can lead to individual variation in array length. Proposed mechanisms for such alterations in length are unequal crossover between sister chromatids, gene conversion, and break-induced replication. However, the underlying molecular mechanisms responsible for the massive, complex, and homogeneous organization of centromeric arrays have not been experimentally validated. Here, we use droplet digital PCR assays to demonstrate that centromeric arrays can expand and contract within ∼20 somatic cell divisions of an alternative lengthening of telomere (ALT)-positive cell line. We find that the frequency of array variation among single-cell-derived subclones ranges from a minimum of ∼7% to a maximum of ∼100%. Further clonal evolution revealed that centromere expansion is favored over contraction. We find that the homologous recombination protein RAD52 and the helicase PIF1 are required for extensive array change, suggesting that centromere sequence evolution can occur via break-induced replication.

Keywords:  BIR; CP: Molecular biology; PIF1; RAD52; centromere; tandem repeats; α-satellite

DOI:  https://doi.org/10.1016/j.celrep.2024.113851
Cell Rep. 2024 Feb 28. pii: S2211-1247(24)00187-6. [Epub ahead of print]43(3): 113859

Oct4 is a gatekeeper of epithelial identity by regulating cytoskeletal organization in skin keratinocytes.

Elena D Christofidou, Marios Tomazou, Chrysovalantis Voutouri, Christina Michael, Triantafyllos Stylianopoulos, George M Spyrou, Katerina Strati.

  Oct4 is a pioneer transcription factor regulating pluripotency. However, it is not well known whether Oct4 has an impact on epidermal cells. We generated OCT4 knockout clonal cell lines using immortalized human skin keratinocytes to identify a functional role for the protein. Here, we report that Oct4-deficient cells transitioned into a mesenchymal-like phenotype with enlarged size and shape, exhibited accelerated migratory behavior, decreased adhesion, and appeared arrested at the G2/M cell cycle checkpoint. Oct4 absence had a profound impact on cortical actin organization, with loss of microfilaments from the cell membrane, increased puncta deposition in the cytoplasm, and stress fiber formation. E-cadherin, β-catenin, and ZO1 were almost absent from cell-cell contacts, while fibronectin deposition was markedly increased in the extracellular matrix (ECM). Mapping of the transcriptional and chromatin profiles of Oct4-deficient cells revealed that Oct4 controls the levels of cytoskeletal, ECM, and differentiation-related genes, whereas epithelial identity is preserved through transcriptional and non-transcriptional mechanisms.

Keywords:  CP: Cell biology; Oct4; actin; adherens junctions; chromatin; cytoskeleton; extracellular matrix; skin keratinocytes; tight junctions

DOI:  https://doi.org/10.1016/j.celrep.2024.113859
Nat Struct Mol Biol. 2024 Feb 26.

Nucleosome-bound NR5A2 structure reveals pioneer factor mechanism by DNA minor groove anchor competition.

Wataru Kobayashi, Anna H Sappler, Daniel Bollschweiler, Maximilian Kümmecke, Jérôme Basquin, Eda Nur Arslantas, Siwat Ruangroengkulrith, Renate Hornberger, Karl Duderstadt, Kikuë Tachibana.

Gene expression during natural and induced reprogramming is controlled by pioneer transcription factors that initiate transcription from closed chromatin. Nr5a2 is a key pioneer factor that regulates zygotic genome activation in totipotent embryos, pluripotency in embryonic stem cells and metabolism in adult tissues, but the mechanism of its pioneer activity remains poorly understood. Here, we present a cryo-electron microscopy structure of human NR5A2 bound to a nucleosome. The structure shows that the conserved carboxy-terminal extension (CTE) loop of the NR5A2 DNA-binding domain competes with a DNA minor groove anchor of the nucleosome and releases entry-exit site DNA. Mutational analysis showed that NR5A2 D159 of the CTE is dispensable for DNA binding but required for stable nucleosome association and persistent DNA 'unwrapping'. These findings suggest that NR5A2 belongs to an emerging class of pioneer factors that can use DNA minor groove anchor competition to destabilize nucleosomes and facilitate gene expression during reprogramming.

DOI: https://doi.org/10.1038/s41594-024-01239-0
Development. 2024 Mar 01. pii: dev202392. [Epub ahead of print]151(5):

Functional consequences of somatic polyploidy in development.

Gabriella S Darmasaputra, Lotte M van Rijnberk, Matilde Galli.

  Polyploid cells contain multiple genome copies and arise in many animal tissues as a regulated part of development. However, polyploid cells can also arise due to cell division failure, DNA damage or tissue damage. Although polyploidization is crucial for the integrity and function of many tissues, the cellular and tissue-wide consequences of polyploidy can be very diverse. Nonetheless, many polyploid cell types and tissues share a remarkable similarity in function, providing important information about the possible contribution of polyploidy to cell and tissue function. Here, we review studies on polyploid cells in development, underlining parallel functions between different polyploid cell types, as well as differences between developmentally-programmed and stress-induced polyploidy.

Keywords:  Cancer; Cell size; Gene expression; Polyploidy

DOI:  https://doi.org/10.1242/dev.202392
bioRxiv. 2024 Feb 12. pii: 2023.05.08.539931. [Epub ahead of print]

Dynamic PRC1-CBX8 stabilizes a porous structure of chromatin condensates.

Michael Uckelmann, Vita Levina, Cyntia Taveneau, Xiao Han Ng, Varun Pandey, Jasmine Martinez, Shweta Mendiratta, Justin Houx, Marion Boudes, Hari Venugopal, Sylvain Trépout, Qi Zhang, Sarena Flanigan, Minrui Li, Emma Sierecki, Yann Gambin, Partha Pratim Das, Oliver Bell, Alex de Marco, Chen Davidovich.

The compaction of chromatin is a prevalent paradigm in gene repression. Chromatin compaction is commonly thought to repress transcription by restricting chromatin accessibility. However, the spatial organisation and dynamics of chromatin compacted by gene-repressing factors are unknown. Using cryo-electron tomography, we solved the threedimensional structure of chromatin condensed by the Polycomb Repressive Complex 1 (PRC1) in a complex with CBX8. PRC1-condensed chromatin is porous and stabilised through multivalent dynamic interactions of PRC1 with chromatin. Mechanistically, positively charged residues on the internally disordered regions (IDRs) of CBX8 mask negative charges on the DNA to stabilize the condensed state of chromatin. Within condensates, PRC1 remains dynamic while maintaining a static chromatin structure. In differentiated mouse embryonic stem cells, CBX8-bound chromatin remains accessible. These findings challenge the idea of rigidly compacted polycomb domains and instead provides a mechanistic framework for dynamic and accessible PRC1-chromatin condensates.

DOI: https://doi.org/10.1101/2023.05.08.539931
Cell Rep. 2024 Feb 27. pii: S2211-1247(24)00186-4. [Epub ahead of print]43(3): 113858

The apparent loss of PRC2 chromatin occupancy as an artifact of RNA depletion.

Evan Healy, Qi Zhang, Emma H Gail, Samuel C Agius, Guizhi Sun, Michael Bullen, Varun Pandey, Partha Pratim Das, Jose M Polo, Chen Davidovich.

  RNA has been implicated in the recruitment of chromatin modifiers, and previous studies have provided evidence in favor and against this idea. RNase treatment of chromatin is commonly used to study RNA-mediated regulation of chromatin modifiers, but the limitations of this approach remain unclear. RNase A treatment during chromatin immunoprecipitation (ChIP) reduces chromatin occupancy of the H3K27me3 methyltransferase Polycomb repressive complex 2 (PRC2). This led to suggestions of an "RNA bridge" between PRC2 and chromatin. Here, we show that RNase A treatment during ChIP causes the apparent loss of all facultative heterochromatin, including both PRC2 and H3K27me3 genome-wide. We track this observation to a gain of DNA from non-targeted chromatin, sequenced at the expense of DNA from facultative heterochromatin, which reduces ChIP signals. Our results emphasize substantial limitations in using RNase A treatment for mapping RNA-dependent chromatin occupancy and invalidate conclusions that were previously established for PRC2 based on this assay.

Keywords:  CP: Molecular biology; ChIP-seq; EZH2; H3K27me3; PRC2; RNA; RNase; RNase-ChIP; chromatin; rChIP

DOI:  https://doi.org/10.1016/j.celrep.2024.113858
Cell Rep Med. 2024 Feb 22. pii: S2666-3791(24)00064-8. [Epub ahead of print] 101441

Mediator complex subunit 1 architects a tumorigenic Treg cell program independent of inflammation.

Shuvam M Chaudhuri, Samuel E Weinberg, Dongmei Wang, Lenore K Yalom, Elena Montauti, Radhika Iyer, Amy Y Tang, Manuel A Torres Acosta, Jian Shen, Nikita L Mani, Shengnan Wang, Kun Liu, Weiyuan Lu, Triet M Bui, Laura D Manzanares, Zeinab Dehghani, Ching Man Wai, Beixue Gao, Juncheng Wei, Feng Yue, Weiguo Cui, Benjamin D Singer, Ronen Sumagin, Yana Zhang, Deyu Fang.

  While immunotherapy has revolutionized cancer treatment, its safety has been hampered by immunotherapy-related adverse events. Unexpectedly, we show that Mediator complex subunit 1 (MED1) is required for T regulatory (Treg) cell function specifically in the tumor microenvironment. Treg cell-specific MED1 deletion does not predispose mice to autoimmunity or excessive inflammation. In contrast, MED1 is required for Treg cell promotion of tumor growth because MED1 is required for the terminal differentiation of effector Treg cells in the tumor. Suppression of these terminally differentiated Treg cells is sufficient for eliciting antitumor immunity. Both human and murine Treg cells experience divergent paths of differentiation in tumors and matched tissues with non-malignant inflammation. Collectively, we identify a pathway promoting the differentiation of a Treg cell effector subset specific to tumors and demonstrate that suppression of a subset of Treg cells is sufficient for promoting antitumor immunity in the absence of autoimmune consequences.

Keywords:  ATAC-seq; FOXP3; MED1; autoimmunity; differentiation; scRNA-seq; tumor T regulatory cell; tumor immunology

DOI:  https://doi.org/10.1016/j.xcrm.2024.101441
Dis Model Mech. 2024 Feb 01. pii: dmm050356. [Epub ahead of print]17(2):

A common cellular response to broad splicing perturbations is characterized by metabolic transcript downregulation driven by the Mdm2-p53 axis.

Jade E Varineau, Eliezer Calo.

  Disruptions in core cellular processes elicit stress responses that drive cell-state changes leading to organismal phenotypes. Perturbations in the splicing machinery cause widespread mis-splicing, resulting in p53-dependent cell-state changes that give rise to cell-type-specific phenotypes and disease. However, a unified framework for how cells respond to splicing perturbations, and how this response manifests itself in nuanced disease phenotypes, has yet to be established. Here, we show that a p53-stabilizing Mdm2 alternative splicing event and the resulting widespread downregulation of metabolic transcripts are common events that arise in response to various splicing perturbations in both cellular and organismal models. Together, our results classify a common cellular response to splicing perturbations, put forth a new mechanism behind the cell-type-specific phenotypes that arise when splicing is broadly disrupted, and lend insight into the pleiotropic nature of the effects of p53 stabilization in disease.

Keywords:  Craniofacial disorders; P53; Splicing

DOI:  https://doi.org/10.1242/dmm.050356
PLoS Biol. 2024 Feb 29. 22(2): e3002527

RNA-mediated ribonucleoprotein assembly controls TDP-43 nuclear retention.

Patricia M Dos Passos, Erandika H Hemamali, Lohany D Mamede, Lindsey R Hayes, Yuna M Ayala.

TDP-43 is an essential RNA-binding protein strongly implicated in the pathogenesis of neurodegenerative disorders characterized by cytoplasmic aggregates and loss of nuclear TDP-43. The protein shuttles between nucleus and cytoplasm, yet maintaining predominantly nuclear TDP-43 localization is important for TDP-43 function and for inhibiting cytoplasmic aggregation. We previously demonstrated that specific RNA binding mediates TDP-43 self-assembly and biomolecular condensation, requiring multivalent interactions via N- and C-terminal domains. Here, we show that these complexes play a key role in TDP-43 nuclear retention. TDP-43 forms macromolecular complexes with a wide range of size distribution in cells and we find that defects in RNA binding or inter-domain interactions, including phase separation, impair the assembly of the largest species. Our findings suggest that recruitment into these macromolecular complexes prevents cytoplasmic egress of TDP-43 in a size-dependent manner. Our observations uncover fundamental mechanisms controlling TDP-43 cellular homeostasis, whereby regulation of RNA-mediated self-assembly modulates TDP-43 nucleocytoplasmic distribution. Moreover, these findings highlight pathways that may be implicated in TDP-43 proteinopathies and identify potential therapeutic targets.

DOI: https://doi.org/10.1371/journal.pbio.3002527
bioRxiv. 2024 Feb 14. pii: 2024.02.12.580020. [Epub ahead of print]

A Specialized Centrosome-Proteasome Axis Mediates Proteostasis and Influences Cardiac Stress through Txlnb.

Jared M McLendon, Xiaoming Zhang, Colleen S Stein, Leslie M Baehr, Sue C Bodine, Ryan L Boudreau.

Background: Centrosomes localize to perinuclear foci where they serve multifunctional roles, arranging the microtubule organizing center (MTOC) and anchoring ubiquitin-proteasome system (UPS) machinery. In mature cardiomyocytes, centrosomal proteins redistribute into a specialized perinuclear cage-like structure, and a potential centrosome-UPS interface has not been studied. Taxilin-beta (Txlnb), a cardiomyocyte-enriched protein, belongs to a family of centrosome adapter proteins implicated in protein quality control. We hypothesize that Txlnb plays a key role in centrosomal-proteasomal crosstalk in cardiomyocytes.
Methods: Integrative bioinformatics assessed centrosomal gene dysregulation in failing hearts. Txlnb gain/loss-of-function studies were conducted in cultured cardiomyocytes and mice. Txlnb's role in cardiac proteotoxicity and hypertrophy was examined using CryAB-R120G mice and transverse aortic constriction (TAC), respectively. Molecular modeling investigated Txlnb structure/function.
Results: Human failing hearts show consistent dysregulation of many centrosome-associated genes, alongside UPS-related genes. Txlnb emerged as a candidate regulator of cardiomyocyte proteostasis that localizes to the perinuclear centrosomal compartment. Txlnb's interactome strongly supports its involvement in cytoskeletal, microtubule, and UPS processes, particularly centrosome-related functions. Overexpressing Txlnb in cardiomyocytes reduced ubiquitinated protein accumulation and enhanced proteasome activity during hypertrophy. Txlnb-knockout (KO) mouse hearts exhibit proteasomal insufficiency and altered cardiac growth, evidenced by ubiquitinated protein accumulation, decreased 26Sβ5 proteasome activity, and lower mass with age. In Cryab-R120G mice, Txlnb loss worsened heart failure, causing lower ejection fractions. After TAC, Txlnb-KO mice also showed reduced ejection fraction, increased heart mass, and elevated ubiquitinated protein accumulation. Investigations into the molecular mechanisms revealed that Txlnb-KO did not affect proteasomal subunit expression but led to the upregulation of Txlna and several centrosomal proteins (Cep63, Ofd1, and Tubg) suggesting altered centrosomal dynamics. Structural predictions support Txlnb's role as a specialized centrosomal-adapter protein bridging centrosomes with proteasomes, confirmed by microtubule-dependent perinuclear localization.
Conclusions: Together, these data provide initial evidence connecting Txlnb to cardiac proteostasis, hinting at the potential importance of functional bridging between specialized centrosomes and UPS in cardiomyocytes.

DOI: https://doi.org/10.1101/2024.02.12.580020
Cell. 2024 Feb 29. pii: S0092-8674(24)00112-0. [Epub ahead of print]187(5): 1314-1314.e1

SnapShot: Eukaryotic ribosome biogenesis II.

Ed Hurt, Janet Iwasa, Roland Beckmann.

Ribosome production is essential for cell growth. Approximately 200 assembly factors drive this complicated pathway that starts in the nucleolus and ends in the cytoplasm. A large number of structural snapshots of the pre-60S pathway have revealed the principles behind large subunit synthesis. To view this SnapShot, open or download the PDF.

DOI: https://doi.org/10.1016/j.cell.2024.01.043
Proc Natl Acad Sci U S A. 2024 Mar 05. 121(10): e2309957121

Deficiency of factor-inhibiting HIF creates a tumor-promoting immune microenvironment.

Jingyi Ma, Khatoun Al Moussawi, Hantao Lou, Hok Fung Chan, Yihua Wang, Joseph Chadwick, Chansavath Phetsouphanh, Elizabeth A Slee, Shan Zhong, Thomas M Leissing, Andrew Roth, Xiao Qin, Shuo Chen, Jie Yin, Indrika Ratnayaka, Yang Hu, Pakavarin Louphrasitthiphol, Lewis Taylor, Paulo J G Bettencourt, Mary Muers, David R Greaves, Helen McShane, Robert Goldin, Elizabeth J Soilleux, Mathew L Coleman, Peter J Ratcliffe, Xin Lu.

  Hypoxia signaling influences tumor development through both cell-intrinsic and -extrinsic pathways. Inhibiting hypoxia-inducible factor (HIF) function has recently been approved as a cancer treatment strategy. Hence, it is important to understand how regulators of HIF may affect tumor growth under physiological conditions. Here we report that in aging mice factor-inhibiting HIF (FIH), one of the most studied negative regulators of HIF, is a haploinsufficient suppressor of spontaneous B cell lymphomas, particular pulmonary B cell lymphomas. FIH deficiency alters immune composition in aged mice and creates a tumor-supportive immune environment demonstrated in syngeneic mouse tumor models. Mechanistically, FIH-defective myeloid cells acquire tumor-supportive properties in response to signals secreted by cancer cells or produced in the tumor microenvironment with enhanced arginase expression and cytokine-directed migration. Together, these data demonstrate that under physiological conditions, FIH plays a key role in maintaining immune homeostasis and can suppress tumorigenesis through a cell-extrinsic pathway.

Keywords:  B cell lymphoma; factor-inhibiting HIF; hypoxia-inducible factor; tumor microenvironment; tumor suppression

DOI:  https://doi.org/10.1073/pnas.2309957121
bioRxiv. 2024 Feb 17. pii: 2024.02.11.579850. [Epub ahead of print]

DNA methylation-dependent and -independent binding of CDX2 directs activation of distinct developmental and homeostatic genes.

Alireza Lorzadeh, George Ye, Sweta Sharma, Unmesh Jadhav.

Precise spatiotemporal and cell type-specific gene expression is essential for proper tissue development and function. Transcription factors (TFs) guide this process by binding to developmental stage-specific targets and establishing an appropriate enhancer landscape. In turn, DNA and chromatin modifications direct the genomic binding of TFs. However, how TFs navigate various chromatin features and selectively bind a small portion of the millions of possible genomic target loci is still not well understood. Here we show that Cdx2 - a pioneer TF that binds distinct targets in developing versus adult intestinal epithelial cells - has a preferential affinity for a non-canonical CpG-containing motif in vivo. A higher frequency of this motif at embryonic and fetal Cdx2 target loci and the specifically methylated state of the CpG during development allows selective Cdx2 binding and activation of developmental enhancers and linked genes. Conversely, demethylation at these enhancers prohibits ectopic Cdx2 binding in adult cells, where Cdx2 binds its canonical motif without a CpG. This differential Cdx2 binding allows for corecruitment of Ctcf and Hnf4, facilitating the establishment of intestinal superenhancers during development and enhancers mediating adult homeostatic functions, respectively. Induced gain of DNA methylation in the adult mouse epithelium or cultured cells causes ectopic recruitment of Cdx2 to the developmental target loci and facilitates cobinding of the partner TFs. Together, our results demonstrate that the differential CpG motif requirements for Cdx2 binding to developmental versus adult target sites allow it to navigate different DNA methylation profiles and activate cell type-specific genes at appropriate times.

DOI: https://doi.org/10.1101/2024.02.11.579850
Cell Stem Cell. 2024 Feb 21. pii: S1934-5909(24)00043-2. [Epub ahead of print]

Region-specific cellular and molecular basis of liver regeneration after acute pericentral injury.

Shuyong Wang, Xuan Wang, Yiran Shan, Zuolong Tan, Yuxin Su, Yannan Cao, Shuang Wang, Jiahong Dong, Jin Gu, Yunfang Wang.

  Liver injuries often occur in a zonated manner. However, detailed regenerative responses to such zonal injuries at cellular and molecular levels remain largely elusive. By using a fate-mapping strain, Cyp2e1-DreER, to elucidate liver regeneration after acute pericentral injury, we found that pericentral regeneration is primarily compensated by the expansion of remaining pericentral hepatocytes, and secondarily by expansion of periportal hepatocytes. Employing single-cell RNA sequencing, spatial transcriptomics, immunostaining, and in vivo functional assays, we demonstrated that the upregulated expression of the mTOR/4E-BP1 axis and lactate dehydrogenase A in hepatocytes contributes to pericentral regeneration, while activation of transforming growth factor β (TGF-β1) signaling in the damaged area mediates fibrotic responses and inhibits hepatocyte proliferation. Inhibiting the pericentral accumulation of monocytes and monocyte-derived macrophages through an Arg-Gly-Asp (RGD) peptide-based strategy attenuates these cell-derived TGF-β1 signalings, thus improving pericentral regeneration. Our study provides integrated and high-resolution spatiotemporal insights into the cellular and molecular basis of pericentral regeneration.

Keywords:  Cyp2e1+ hepatocytes; RGD; lineage tracing; liver regeneration; pericentral injury; spatial transcriptome; spatiotemporal dynamics

DOI:  https://doi.org/10.1016/j.stem.2024.01.013
bioRxiv. 2024 Feb 15. pii: 2024.02.15.580543. [Epub ahead of print]

Scalable and Efficient Generation of Mouse Primordial Germ Cell-like Cells.

Xinbao Ding, Liangdao Li, Jingyi Gao, Dain Yi, John C Schimenti.

Primordial germ cells (PGCs) are the founder cells of the germline. The ability to generate PGC-like cells (PGCLCs) from pluripotent stem cells has advanced our knowledge of gametogenesis and holds promise for developing infertility treatments. However, generating an ample supply of PGCLCs for demanding applications such as high-throughput genetic screens has been a limitation. Here, we demonstrated that simultaneous overexpressing 4 transcriptional factors - Nanog and three PGC master regulators Prdm1, Prdm14 and Tfap2c - in suspended mouse epiblast like cells (EpiLCs) and formative embryonic stem cells (ESCs) results in efficient and cost-effective production of PGCLCs. The overexpression of Nanog enhances the PGC regulatory network and suppresses differentiation of somatic lineages, enabling a significant improvement in the efficiency of PGCLC production. Transcriptomic analysis reveals that differentiated PGCLCs exhibit similarities to in vivo PGCs and are more advanced compared to cytokine-induced PGCLCs. These differentiated PGCLCs could be sustained over prolonged periods of culture and could differentiate into spermatogonia-like cells in vitro. Importantly, the ability to produce PGCLCs at scale, without using costly cytokines, enables biochemical and functional genomic screens to dissect mechanisms of germ cell development and infertility.

DOI: https://doi.org/10.1101/2024.02.15.580543
Sci Adv. 2024 Mar;10(9): eadj4678

An immunosuppressive vascular niche drives macrophage polarization and immunotherapy resistance in glioblastoma.

Fan Yang, Md Naushad Akhtar, Duo Zhang, Rakan El-Mayta, Junyoung Shin, Jay F Dorsey, Lin Zhang, Xiaowei Xu, Wei Guo, Stephen J Bagley, Serge Y Fuchs, Constantinos Koumenis, Justin D Lathia, Michael J Mitchell, Yanqing Gong, Yi Fan.

Cancer immunity is subjected to spatiotemporal regulation by leukocyte interaction with neoplastic and stromal cells, contributing to immune evasion and immunotherapy resistance. Here, we identify a distinct mesenchymal-like population of endothelial cells (ECs) that form an immunosuppressive vascular niche in glioblastoma (GBM). We reveal a spatially restricted, Twist1/SATB1-mediated sequential transcriptional activation mechanism, through which tumor ECs produce osteopontin to promote immunosuppressive macrophage (Mφ) phenotypes. Genetic or pharmacological ablation of Twist1 reverses Mφ-mediated immunosuppression and enhances T cell infiltration and activation, leading to reduced GBM growth and extended mouse survival, and sensitizing tumor to chimeric antigen receptor T immunotherapy. Thus, these findings uncover a spatially restricted mechanism controlling tumor immunity and suggest that targeting endothelial Twist1 may offer attractive opportunities for optimizing cancer immunotherapy.

DOI: https://doi.org/10.1126/sciadv.adj4678
Nat Genet. 2024 Feb 28.

Proteins shaping global chromatin accessibility.

DOI: https://doi.org/10.1038/s41588-024-01667-0
Biomech Model Mechanobiol. 2024 Feb 27.

Mechanical complexity of living cells can be mapped onto simple homogeneous equivalents.

Sebastian Wohlrab, Sebastian Mueller, Stephan Gekle.

  Biological cells are built up from different constituents of varying size and stiffness which all contribute to the cell's mechanical properties. Despite this heterogeneity, in the analysis of experimental measurements one often assumes a strongly simplified homogeneous cell and thus a single elastic modulus is assigned to the entire cell. This ad-hoc simplification has so far mostly been used without proper justification. Here, we use computer simulations to show that indeed a mechanically heterogeneous cell can effectively be replaced by a homogeneous equivalent cell with a volume averaged elastic modulus. To demonstrate the validity of this approach, we investigate a hyperelastic cell with a heterogeneous interior under compression and in shear/channel flow mimicking atomic force and microfluidic measurements, respectively. We find that the homogeneous equivalent cell reproduces quantitatively the behavior of its heterogeneous counterpart, and that this equality is largely independent of the stiffness or spatial distribution of the heterogeneity.

Keywords:  Atomic force microscopy; Cell elasticity; Cell mechanics; Cell nucleus; Shear flow

DOI:  https://doi.org/10.1007/s10237-024-01823-9
Sci Adv. 2024 Mar;10(9): eadj5107

BRG1 establishes the neuroectodermal chromatin landscape to restrict dorsal cell fates.

Jackson A Hoffman, Ginger W Muse, Lee F Langer, A Isabella Patterson, Isabella Gandara, James M Ward, Trevor K Archer.

Cell fate decisions are achieved with gene expression changes driven by lineage-specific transcription factors (TFs). These TFs depend on chromatin remodelers including the Brahma-related gene 1 (BRG1)-associated factor (BAF) complex to activate target genes. BAF complex subunits are essential for development and frequently mutated in cancer. Thus, interrogating how BAF complexes contribute to cell fate decisions is critical for human health. We examined the requirement for the catalytic BAF subunit BRG1 in neural progenitor cell (NPC) specification from human embryonic stem cells. During the earliest stages of differentiation, BRG1 was required to establish chromatin accessibility at neuroectoderm-specific enhancers. Depletion of BRG1 dorsalized NPCs and promoted precocious neural crest specification and enhanced neuronal differentiation. These findings demonstrate that BRG1 mediates NPC specification by ensuring proper expression of lineage-specific TFs and appropriate activation of their transcriptional programs.

DOI: https://doi.org/10.1126/sciadv.adj5107
Cell Rep. 2024 Feb 23. pii: S2211-1247(24)00171-2. [Epub ahead of print]43(3): 113843

A transcription factor atlas of stem cell fate in planarians.

Hunter O King, Kwadwo E Owusu-Boaitey, Christopher T Fincher, Peter W Reddien.

  Whole-body regeneration requires the ability to produce the full repertoire of adult cell types. The planarian Schmidtea mediterranea contains over 125 cell types, which can be regenerated from a stem cell population called neoblasts. Neoblast fate choice can be regulated by the expression of fate-specific transcription factors (FSTFs). How fate choices are made and distributed across neoblasts versus their post-mitotic progeny remains unclear. We used single-cell RNA sequencing to systematically map fate choices made in S/G2/M neoblasts and, separately, in their post-mitotic progeny that serve as progenitors for all adult cell types. We defined transcription factor expression signatures associated with all detected fates, identifying numerous new progenitor classes and FSTFs that regulate them. Our work generates an atlas of stem cell fates with associated transcription factor signatures for most cell types in a complete adult organism.

Keywords:  CP: Stem cell research; cell fate; neoblasts; planarians; progenitor; regeneration; stem cells; transcription factor

DOI:  https://doi.org/10.1016/j.celrep.2024.113843
Nat Rev Genet. 2024 Mar 01.

Changes in cell-cycle rate drive diverging cell fates.

Kate E Galloway.

DOI: https://doi.org/10.1038/s41576-024-00714-0
PLoS Biol. 2024 Feb 29. 22(2): e3002517

CD38 promotes hematopoietic stem cell dormancy.

Liliia Ibneeva, Sumeet Pal Singh, Anupam Sinha, Sema Elif Eski, Rebekka Wehner, Luise Rupp, Iryna Kovtun, Juan Alberto Pérez-Valencia, Alexander Gerbaulet, Susanne Reinhardt, Manja Wobus, Malte von Bonin, Jaime Sancho, Frances Lund, Andreas Dahl, Marc Schmitz, Martin Bornhäuser, Triantafyllos Chavakis, Ben Wielockx, Tatyana Grinenko.

A subpopulation of deeply quiescent, so-called dormant hematopoietic stem cells (dHSCs) resides at the top of the hematopoietic hierarchy and serves as a reserve pool for HSCs. The state of dormancy protects the HSC pool from exhaustion throughout life; however, excessive dormancy may prevent an efficient response to hematological stresses. Despite the significance of dHSCs, the mechanisms maintaining their dormancy remain elusive. Here, we identify CD38 as a novel and broadly applicable surface marker for the enrichment of murine dHSCs. We demonstrate that cyclic adenosine diphosphate ribose (cADPR), the product of CD38 cyclase activity, regulates the expression of the transcription factor c-Fos by increasing the release of Ca2+ from the endoplasmic reticulum (ER). Subsequently, we uncover that c-Fos induces the expression of the cell cycle inhibitor p57Kip2 to drive HSC dormancy. Moreover, we found that CD38 ecto-enzymatic activity at the neighboring CD38-positive cells can promote human HSC quiescence. Together, CD38/cADPR/Ca2+/c-Fos/p57Kip2 axis maintains HSC dormancy. Pharmacological manipulations of this pathway can provide new strategies to improve the success of stem cell transplantation and blood regeneration after injury or disease.

DOI: https://doi.org/10.1371/journal.pbio.3002517
Elife. 2024 Feb 26. pii: e94694. [Epub ahead of print]13

Mouse SAS‑6 is required for centriole formation in embryos and integrity in embryonic stem cells.

Marta Grzonka, Hisham Bazzi.

  SAS‑6 (SASS6) is essential for centriole formation in human cells and other organisms but its function in mouse is unclear. Here, we report that Sass6‑mutant mouse embryos lack centrioles, activate the mitotic surveillance cell death pathway and arrest at mid‑gestation. In contrast, SAS‑6 is not required for centriole formation in mouse embryonic stem cells (mESCs), but is essential to maintain centriole architecture. Of note, centrioles appeared after just one day of culture of Sass6‑mutant blastocysts, from which mESCs are derived. Conversely, the number of cells with centrosomes is drastically decreased upon the exit from a mESC pluripotent state. At the mechanistic level, the activity of the master kinase in centriole formation, PLK4, associated with increased centriolar and centrosomal protein levels, endow mESCs with the robustness in using SAS‑6‑independent centriole-duplication pathways. Collectively, our data suggest a differential requirement for mouse SAS‑6 in centriole formation or integrity depending on PLK4 and centrosome composition.

Keywords:  developmental biology; mouse

DOI:  https://doi.org/10.7554/eLife.94694
Nature. 2024 Feb 28.

The CRL5-SPSB3 ubiquitin ligase targets nuclear cGAS for degradation.

Pengbiao Xu, Ying Liu, Chong Liu, Baptiste Guey, Lingyun Li, Pauline Melenec, Jonathan Ricci, Andrea Ablasser.

Cyclic GMP-AMP synthase (cGAS) senses aberrant DNA during infection, cancer and inflammatory disease, and initiates potent innate immune responses through the synthesis of 2'3'-cyclic GMP-AMP (cGAMP)1-7. The indiscriminate activity of cGAS towards DNA demands tight regulatory mechanisms that are necessary to maintain cell and tissue homeostasis under normal conditions. Inside the cell nucleus, anchoring to nucleosomes and competition with chromatin architectural proteins jointly prohibit cGAS activation by genomic DNA8-15. However, the fate of nuclear cGAS and its role in cell physiology remains unclear. Here we show that the ubiquitin proteasomal system (UPS) degrades nuclear cGAS in cycling cells. We identify SPSB3 as the cGAS-targeting substrate receptor that associates with the cullin-RING ubiquitin ligase 5 (CRL5) complex to ligate ubiquitin onto nuclear cGAS. A cryo-electron microscopy structure of nucleosome-bound cGAS in a complex with SPSB3 reveals a highly conserved Asn-Asn (NN) minimal degron motif at the C terminus of cGAS that directs SPSB3 recruitment, ubiquitylation and cGAS protein stability. Interference with SPSB3-regulated nuclear cGAS degradation primes cells for type I interferon signalling, conferring heightened protection against infection by DNA viruses. Our research defines protein degradation as a determinant of cGAS regulation in the nucleus and provides structural insights into an element of cGAS that is amenable to therapeutic exploitation.

DOI: https://doi.org/10.1038/s41586-024-07112-w
Autophagy. 2024 Feb 27.

Aging STINGs: mitophagy at the crossroads of neuroinflammation.

Juan Ignacio Jiménez-Loygorri, Patricia Boya.

  Loss of proteostasis and dysregulated mitochondrial function are part of the traditional hallmarks of aging, and in their last revision impaired macroautophagy and chronic inflammation are also included. Mitophagy is at the intersection of all these processes but whether it undergoes age-associated perturbations was not known. In our recent work, we performed a systematic and systemic analysis of mitolysosome levels in mice and found that, despite the already-known decrease in non-selective macroautophagy, mitophagy remains stable or increases upon aging in all tissues analyzed and is mediated by the PINK1-PRKN-dependent pathway. Further analyses revealed a concomitant increase in mtDNA leakage into the cytosol and activation of the CGAS-STING1 inflammation axis. Notably, both phenomena are also observed in primary fibroblasts from aged human donors. We hypothesized that mitophagy might be selectively upregulated during aging to improve mitochondrial fitness and reduce mtDNA-induced inflammation. Treatment with the mitophagy inducer urolithin A alleviates age-associated neurological decline, including improved synaptic connectivity, cognitive memory and visual function. Supporting our initial hypothesis, urolithin A reduces the levels of cytosolic mtDNA, CGAS-STING1 activation and neuroinflammation. Finally, using an in vitro model of mitochondrial membrane permeabilization we validated that PINK1-PRKN-mediated mitophagy is essential to resolve cytosolic mtDNA-triggered inflammation. These findings open up an integrative approach to tackle aging and increase healthspan via mitophagy induction.

Keywords:  Inflammation; PINK1; Parkin; mitochondria; mtDNA; retina

DOI:  https://doi.org/10.1080/15548627.2024.2322421
Nat Commun. 2024 Feb 26. 15(1): 1352

Targeting HDAC6 to treat heart failure with preserved ejection fraction in mice.

Sara Ranjbarvaziri, Aliya Zeng, Iris Wu, Amara Greer-Short, Farshad Farshidfar, Ana Budan, Emma Xu, Reva Shenwai, Matthew Kozubov, Cindy Li, Melissa Van Pell, Francis Grafton, Charles E MacKay, Xiaomei Song, James R Priest, Gretchen Argast, Mohammad A Mandegar, Timothy Hoey, Jin Yang.

Heart failure with preserved ejection fraction (HFpEF) poses therapeutic challenges due to the limited treatment options. Building upon our previous research that demonstrates the efficacy of histone deacetylase 6 (HDAC6) inhibition in a genetic cardiomyopathy model, we investigate HDAC6's role in HFpEF due to their shared mechanisms of inflammation and metabolism. Here, we show that inhibiting HDAC6 with TYA-018 effectively reverses established heart failure and its associated symptoms in male HFpEF mouse models. Additionally, in male mice lacking Hdac6 gene, HFpEF progression is delayed and they are resistant to TYA-018's effects. The efficacy of TYA-018 is comparable to a sodium-glucose cotransporter 2 (SGLT2) inhibitor, and the combination shows enhanced effects. Mechanistically, TYA-018 restores gene expression related to hypertrophy, fibrosis, and mitochondrial energy production in HFpEF heart tissues. Furthermore, TYA-018 also inhibits activation of human cardiac fibroblasts and enhances mitochondrial respiratory capacity in cardiomyocytes. In this work, our findings show that HDAC6 impacts on heart pathophysiology and is a promising target for HFpEF treatment.

DOI: https://doi.org/10.1038/s41467-024-45440-7
J Clin Invest. 2024 Mar 01. pii: e174194. [Epub ahead of print]134(5):

Stromal Pbrm1 mediates chromatin remodeling necessary for embryo implantation in the mouse uterus.

Qiliang Xin, Iris Feng, Guoyun Yu, Jurrien Dean.

  Early gestational loss occurs in approximately 20% of all clinically recognized human pregnancies and is an important cause of morbidity. Either embryonic or maternal defects can cause loss, but a functioning and receptive uterine endometrium is crucial for embryo implantation. We report that the switch/sucrose nonfermentable (SWI/SNF) remodeling complex containing polybromo-1 (PBRM1) and Brahma-related gene 1 (BRG1) is essential for implantation of the embryonic blastocyst on the wall of the uterus in mice. Although preimplantation development is unaffected, conditional ablation of Pbrm1 in uterine stromal cells disrupts progesterone pathways and uterine receptivity. Heart and neural crest derivatives expressed 2 (Hand2) encodes a basic helix-loop-helix (bHLH) transcription factor required for embryo implantation. We identify an enhancer of the Hand2 gene in stromal cells that requires PBRM1 for epigenetic histone modifications/coactivator recruitment and looping with the promoter. In Pbrm1cKO mice, perturbation of chromatin assembly at the promoter and enhancer sites compromises Hand2 transcription, adversely affects fibroblast growth factor signaling pathways, prevents normal stromal-epithelial crosstalk, and disrupts embryo implantation. The mutant female mice are infertile and provide insight into potential causes of early pregnancy loss in humans.

Keywords:  Endocrinology; Epigenetics; Fertility; Reproductive biology; Sex hormones

DOI:  https://doi.org/10.1172/JCI174194
Cell Rep. 2024 Feb 26. pii: S2211-1247(24)00044-5. [Epub ahead of print]43(3): 113716

Single-cell analysis reveals insights into epithelial abnormalities in ovarian endometriosis.

Jia Yan, Ling Zhou, Mengya Liu, Honglan Zhu, Xin Zhang, E Cai, Xueqiang Xu, Tinghan Chen, Hongyan Cheng, Jun'e Liu, Shang Wang, Lin Dai, Xiaohong Chang, Fuchou Tang.

  Ovarian endometriosis is characterized by the growth of endometrial tissue within the ovary, causing infertility and chronic pain. However, its pathophysiology remains unclear. Utilizing high-precision single-cell RNA sequencing, we profile the normal, eutopic, and ectopic endometrium from 34 individuals across proliferative and secretory phases. We observe an increased proportion of ciliated cells in both eutopic and ectopic endometrium, characterized by a diminished expression of estrogen sulfotransferase, which likely confers apoptosis resistance. After translocating to ectopic lesions, endometrial epithelium upregulates nicotinamide N-methyltransferase expression that inhibits apoptosis by promoting deacetylation and subsequent nuclear exclusion of transcription factor forkhead box protein O1, thereby leading to the downregulation of the apoptotic gene BIM. Moreover, epithelial cells in ectopic lesions elevate HLA class II complex expression, which stimulates CD4+ T cells and consequently contributes to chronic inflammation. Altogether, our study provides a comprehensive atlas of ovarian endometriosis and highlights potential therapeutic targets for modulating apoptosis and inflammation.

Keywords:  CP: Developmental biology; FOXO1; HLA class II; NNMT; SULT1E1; apoptosis; ciliated cells; endometrium; inflammation; ovarian endometriosis; single-cell RNA sequencing

DOI:  https://doi.org/10.1016/j.celrep.2024.113716
J Cell Biol. 2024 Apr 01. pii: e202402093. [Epub ahead of print]223(4):

Moonwalking molecular machines: Unraveling the choreography of myosin filament assembly.

Noah J Gurley, Mark Peifer.

We have made tremendous progress in identifying the machines that shape the architecture of actin filaments. However, we know less about the mechanisms mediating myosin assembly at the supramolecular level. In this issue, Quintanilla et al. (https://doi.org/10.1083/jcb.202305023) provide important new insights into this process.

DOI: https://doi.org/10.1083/jcb.202402093
bioRxiv. 2024 Jan 29. pii: 2024.01.25.577217. [Epub ahead of print]

Genetic and bioinformatic analyses reveal transcriptional networks underlying dual genomic coordination of mitochondrial biogenesis.

Fan Zhang, Annie Lee, Anna Freitas, Jake Herb, Zongheng Wang, Snigdha Gupta, Zhe Chen, Hong Xu.

Mitochondrial genome encodes handful genes of respiratory chain complexes, whereas all the remaining mitochondrial proteins are encoded on the nuclear genome. However, the mechanisms coordinating these two genomes to control mitochondrial biogenesis remain largely unknown. To identify transcription circuits involved in these processes, we performed a candidate RNAi screen in developing eyes that had reduced mitochondrial DNA contents. We reasoned that impaired mitochondrial biogenesis would synergistically interact with mtDNA deficiency in disrupting tissue development. Over 638 transcription factors annotated in the fly genome, we identified 77 transcription factors that may be involved in mitochondrial genome maintenance and gene expression. Additional genetic and genomic analyses revealed that a novel transcription factor, CG1603, and its upstream factor YL-1 are essential for mitochondrial biogenesis. We constructed a regulator network among positive hits using the published CHIP-seq data. The network analysis revealed extensive connections, and complex hierarchical organization underlying the transcription regulation of mitochondrial biogenesis.

DOI: https://doi.org/10.1101/2024.01.25.577217
Nat Metab. 2024 Feb 28.

Enhanced branched-chain amino acid metabolism improves age-related reproduction in C. elegans.

Chen Lesnik, Rachel Kaletsky, Jasmine M Ashraf, Salman Sohrabi, Vanessa Cota, Titas Sengupta, William Keyes, Shijing Luo, Coleen T Murphy.

Reproductive ageing is one of the earliest human ageing phenotypes, and mitochondrial dysfunction has been linked to oocyte quality decline; however, it is not known which mitochondrial metabolic processes are critical for oocyte quality maintenance with age. To understand how mitochondrial processes contribute to Caenorhabditis elegans oocyte quality, we characterized the mitochondrial proteomes of young and aged wild-type and long-reproductive daf-2 mutants. Here we show that the mitochondrial proteomic profiles of young wild-type and daf-2 worms are similar and share upregulation of branched-chain amino acid (BCAA) metabolism pathway enzymes. Reduction of the BCAA catabolism enzyme BCAT-1 shortens reproduction, elevates mitochondrial reactive oxygen species levels, and shifts mitochondrial localization. Moreover, bcat-1 knockdown decreases oocyte quality in daf-2 worms and reduces reproductive capability, indicating the role of this pathway in the maintenance of oocyte quality with age. Notably, oocyte quality deterioration can be delayed, and reproduction can be extended in wild-type animals both by bcat-1 overexpression and by supplementing with vitamin B1, a cofactor needed for BCAA metabolism.

DOI: https://doi.org/10.1038/s42255-024-00996-y
Sci Adv. 2024 Mar;10(9): eadh7748

Human surface ectoderm and amniotic ectoderm are sequentially specified according to cellular density.

Shota Nakanoh, Kendig Sham, Sabitri Ghimire, Irina Mohorianu, Teresa Rayon, Ludovic Vallier.

Mechanisms specifying amniotic ectoderm and surface ectoderm are unresolved in humans due to their close similarities in expression patterns and signal requirements. This lack of knowledge hinders the development of protocols to accurately model human embryogenesis. Here, we developed a human pluripotent stem cell model to investigate the divergence between amniotic and surface ectoderms. In the established culture system, cells differentiated into functional amnioblast-like cells. Single-cell RNA sequencing analyses of amnioblast differentiation revealed an intermediate cell state with enhanced surface ectoderm gene expression. Furthermore, when the differentiation started at the confluent condition, cells retained the expression profile of surface ectoderm. Collectively, we propose that human amniotic ectoderm and surface ectoderm are specified along a common nonneural ectoderm trajectory based on cell density. Our culture system also generated extraembryonic mesoderm-like cells from the primed pluripotent state. Together, this study provides an integrative understanding of the human nonneural ectoderm development and a model for embryonic and extraembryonic human development around gastrulation.

DOI: https://doi.org/10.1126/sciadv.adh7748
Trends Cell Biol. 2024 Feb 28. pii: S0962-8924(24)00024-2. [Epub ahead of print]

Translation is an emerging constraint on protein homeostasis in ageing.

Jack Llewellyn, Simon J Hubbard, Joe Swift.

  Proteins are molecular machines that provide structure and perform vital transport, signalling and enzymatic roles. Proteins expressed by cells require tight regulation of their concentration, folding, localisation, and modifications; however, this state of protein homeostasis is continuously perturbed by tissue-level stresses. While cells in healthy tissues are able to buffer against these perturbations, for example, by expression of chaperone proteins, protein homeostasis is lost in ageing, and can lead to protein aggregation characteristic of protein folding diseases. Here, we review reports of a progressive disconnect between transcriptomic and proteomic regulation during cellular ageing. We discuss how age-associated changes to cellular responses to specific stressors in the tissue microenvironment are exacerbated by loss of ribosomal proteins, ribosomal pausing, and mistranslation.

Keywords:  cellular senescence; mistranslation; molecular chaperones; protein turnover; proteostasis network; ribosomal activity

DOI:  https://doi.org/10.1016/j.tcb.2024.02.001
Curr Opin Cell Biol. 2024 Feb 23. pii: S0955-0674(24)00022-X. [Epub ahead of print]87 102343

Editorial overview: Functional specialization of the cytoskeleton in diverse cell types.

Adele Marston, Matthew J Tyska.

DOI: https://doi.org/10.1016/j.ceb.2024.102343
Nat Commun. 2024 Feb 24. 15(1): 1702

Reducing the metabolic burden of rRNA synthesis promotes healthy longevity in Caenorhabditis elegans.

Samim Sharifi, Prerana Chaudhari, Asya Martirosyan, Alexander Otto Eberhardt, Finja Witt, André Gollowitzer, Lisa Lange, Yvonne Woitzat, Eberechukwu Maryann Okoli, Huahui Li, Norman Rahnis, Joanna Kirkpatrick, Oliver Werz, Alessandro Ori, Andreas Koeberle, Holger Bierhoff, Maria Ermolaeva.

Ribosome biogenesis is initiated by RNA polymerase I (Pol I)-mediated synthesis of pre-ribosomal RNA (pre-rRNA). Pol I activity was previously linked to longevity, but the underlying mechanisms were not studied beyond effects on nucleolar structure and protein translation. Here we use multi-omics and functional tests to show that curtailment of Pol I activity remodels the lipidome and preserves mitochondrial function to promote longevity in Caenorhabditis elegans. Reduced pre-rRNA synthesis improves energy homeostasis and metabolic plasticity also in human primary cells. Conversely, the enhancement of pre-rRNA synthesis boosts growth and neuromuscular performance of young nematodes at the cost of accelerated metabolic decline, mitochondrial stress and premature aging. Moreover, restriction of Pol I activity extends lifespan more potently than direct repression of protein synthesis, and confers geroprotection even when initiated late in life, showcasing this intervention as an effective longevity and metabolic health treatment not limited by aging.

DOI: https://doi.org/10.1038/s41467-024-46037-w
J Cell Biol. 2024 04 01. pii: e202307138. [Epub ahead of print]223(4):

HER2 phosphorylation induced by TGF-β promotes mammary morphogenesis and breast cancer progression.

Qiaoni Shi, Fei Huang, Yalong Wang, Huidong Liu, Haiteng Deng, Ye-Guang Chen.

Transforming growth factor β (TGF-β) and HER2 signaling collaborate to promote breast cancer progression. However, their molecular interplay is largely unclear. TGF-β can activate mitogen-activated protein kinase (MAPK) and AKT, but the underlying mechanism is not fully understood. In this study, we report that TGF-β enhances HER2 activation, leading to the activation of MAPK and AKT. This process depends on the TGF-β type I receptor TβRI kinase activity. TβRI phosphorylates HER2 at Ser779, promoting Y1248 phosphorylation and HER2 activation. Mice with HER2 S779A mutation display impaired mammary morphogenesis, reduced ductal elongation, and branching. Furthermore, wild-type HER2, but not S779A mutant, promotes TGF-β-induced epithelial-mesenchymal transition, cell migration, and lung metastasis of breast cells. Increased HER2 S779 phosphorylation is observed in human breast cancers and positively correlated with the activation of HER2, MAPK, and AKT. Our findings demonstrate the crucial role of TGF-β-induced S779 phosphorylation in HER2 activation, mammary gland development, and the pro-oncogenic function of TGF-β in breast cancer progression.

DOI: https://doi.org/10.1083/jcb.202307138