bims-ginsta 2024-10-13 papers

bims-ginsta

Biomed News

on Genome instability

Issue of 2024–10–13
23 papers selected by
Jinrong Hu, National University of Singapore

YAP Overcomes Mechanical Barriers to Induce Mitotic Rounding and Adult Cardiomyocyte Division.
Actin-driven nanotopography promotes stable integrin adhesion formation in developing tissue.
Genome folding and zygotic genome activation in mammalian preimplantation embryos.
Nuclear and cytosolic fractions of SOX2 synergize as transcriptional and translational co-regulators of cell fate.
Structural basis of mRNA decay by the human exosome-ribosome supercomplex.
Temporal variability and cell mechanics control robustness in mammalian embryogenesis.
KaryoTap Enables Aneuploidy Detection in Thousands of Single Human Cells.
Jamming of nephron-forming niches in the developing mouse kidney creates cyclical mechanical stresses.
Advancing stem cell technologies for conservation of wildlife biodiversity.
Blood-generating heart-forming organoids recapitulate co-development of the human haematopoietic system and the embryonic heart.
Identifying specific functional roles for senescence across cell types.
RNA surveillance by the RNA helicase MTR4 determines volume of mouse oocytes.
scNanoSeq-CUT&Tag: a single-cell long-read CUT&Tag sequencing method for efficient chromatin modification profiling within individual cells.
Compensatory activity of the PC-ME1 metabolic axis underlies differential sensitivity to mitochondrial complex I inhibition.
Transgenic sensors reveal compartment-specific effects of aggregation-prone proteins on subcellular proteostasis during aging.
Cell-cycle-dependent mRNA localization in P-bodies.
Transcriptional inhibition after irradiation occurs preferentially at highly expressed genes in a manner dependent on cell cycle progression.
DELE1 maintains muscle proteostasis to promote growth and survival in mitochondrial myopathy.
Human embryonic stem cell-derived cardiovascular progenitor cells stimulate cardiomyocyte cell cycle activity via activating the PI3K/Akt pathway.
Waves of change: Dynamic actomyosin networks in embryonic development.
Single-nucleus multiomics reveals the gene-regulatory networks underlying sex determination of murine primordial germ cells.
Biomolecular condensates mediate bending and scission of endosome membranes.
Cell signaling facilitates apical constriction by basolaterally recruiting Arp2/3 via Rac and WAVE.

Circulation. 2024 Oct 11.

YAP Overcomes Mechanical Barriers to Induce Mitotic Rounding and Adult Cardiomyocyte Division.

Yuka Morikawa, Jong H Kim, Rich Gang Li, Lin Liu, Shijie Liu, Vaibhav Deshmukh, Matthew C Hill, James F Martin.

   BACKGROUND: Many specialized cells in adult organs acquire a state of cell cycle arrest and quiescence through unknown mechanisms. Our limited understanding of mammalian cell cycle arrest is derived primarily from cell culture models. Adult mammalian cardiomyocytes, a classic example of cell cycle arrested cells, exit the cell cycle postnatally and remain in an arrested state for the life of the organism. Cardiomyocytes can be induced to re-enter the cell cycle by YAP5SA, an active form of the Hippo signaling pathway effector YAP.
METHODS: We performed clonal analyses to determine the cell kinetics of YAP5SA cardiomyocytes. We also performed single-cell RNA sequencing, marker gene analysis, and functional studies to examine how YAP5SA cardiomyocytes progress through the cell cycle.
RESULTS: We discovered that YAP5SA-expressing cardiomyocytes divided efficiently, with >20% of YAP5SA cardiomyocyte clones containing ≥2 cardiomyocytes. YAP5SA cardiomyocytes re-entered cell cycle at the G1/S transition and had an S phase lasting ≈48 hours. Sarcomere disassembly is required for cardiomyocyte progression from S to G2 phase and the induction of mitotic rounding. Although oscillatory Cdk expression was induced in YAP5SA cardiomyocytes, these cells inefficiently progressed through G2 phase. This is improved by inhibiting P21 function, implicating checkpoint activity as an additional barrier to YAP5SA-induced cardiomyocyte division.
CONCLUSIONS: Our data reveal that YAP5SA overcomes the mechanically constrained myocardial microenvironment to induce mitotic rounding with cardiomyocyte division, thus providing new insights into the in vivo mechanisms that maintain cell cycle quiescence in adult mammals.

Keywords:  Hippo pathway; P21; YAP; cell cycle; mitotic rounding; myocyte proliferation; sarcomere disassembly

DOI:  https://doi.org/10.1161/CIRCULATIONAHA.123.066004
Nat Commun. 2024 Oct 07. 15(1): 8691

Actin-driven nanotopography promotes stable integrin adhesion formation in developing tissue.

Tianchi Chen, Cecilia H Fernández-Espartero, Abigail Illand, Ching-Ting Tsai, Yang Yang, Benjamin Klapholz, Pierre Jouchet, Mélanie Fabre, Olivier Rossier, Bianxiao Cui, Sandrine Lévêque-Fort, Nicholas H Brown, Grégory Giannone.

Morphogenesis requires building stable macromolecular structures from highly dynamic proteins. Muscles are anchored by long-lasting integrin adhesions to resist contractile force. However, the mechanisms governing integrin diffusion, immobilization, and activation within developing tissues remain elusive. Here, we show that actin polymerization-driven membrane protrusions form nanotopographies that enable strong adhesion at Drosophila muscle attachment sites (MASs). Super-resolution microscopy reveals that integrins assemble adhesive belts around Arp2/3-dependent actin protrusions, forming invadosome-like structures with membrane nanotopographies. Single protein tracking shows that, during MAS development, integrins become immobile and confined within diffusion traps formed by the membrane nanotopographies. Actin filaments also display restricted motion and confinement, indicating strong mechanical connection with integrins. Using isolated muscle cells, we show that substrate nanotopography, rather than rigidity, drives adhesion maturation by regulating actin protrusion, integrin diffusion and immobilization. These results thus demonstrate that actin-polymerization-driven membrane protrusions are essential for the formation of strong integrin adhesions sites in the developing embryo, and highlight the important contribution of geometry to morphogenesis.

DOI: https://doi.org/10.1038/s41467-024-52899-x
Curr Opin Genet Dev. 2024 Oct 08. pii: S0959-437X(24)00117-5. [Epub ahead of print]89 102268

Genome folding and zygotic genome activation in mammalian preimplantation embryos.

Anastasiia Bondarieva, Kikuë Tachibana.

The totipotent one-cell embryo, or zygote, gives rise to all germ layers and extraembryonic tissues that culminate in the development of a new organism. A zygote is produced at fertilisation by the fusion of differentiated germ cells, egg and sperm. The chromatin of parental genomes is reprogrammed and spatially reorganised in the early embryo. The 3D chromatin organisation is established de novo after fertilisation by a cohesin-dependent mechanism of loop extrusion that forms chromatin loops and topologically associating domains (TADs). Strengthening of TAD insulation is concomitant with the transcriptional 'awakening' of the embryo known as zygotic genome activation (ZGA). Whether and how these processes are causally linked remains poorly understood. In this review, we discuss recent findings of 3D chromatin organisation in mammalian gametes and embryos and how these are potentially related to ZGA.

DOI: https://doi.org/10.1016/j.gde.2024.102268
Cell Rep. 2024 Oct 03. pii: S2211-1247(24)01158-6. [Epub ahead of print]43(10): 114807

Nuclear and cytosolic fractions of SOX2 synergize as transcriptional and translational co-regulators of cell fate.

Thorsten Schaefer, Nitish Mittal, Hui Wang, Meric Ataman, Silvia Candido, Jonas Lötscher, Sergiy Velychko, Lionel Tintignac, Thomas Bock, Anastasiya Börsch, Jochen Baßler, Tata Nageswara Rao, Jakub Zmajkovic, Sarah Roffeis, Jordan Löliger, Francis Jacob, Alain Dumlin, Christoph Schürch, Alexander Schmidt, Radek C Skoda, Matthias P Wymann, Christoph Hess, Hans R Schöler, Holm Zaehres, Ed Hurt, Mihaela Zavolan, Claudia Lengerke.

  Stemness and pluripotency are mediated by transcriptional master regulators that promote self-renewal and repress cell differentiation, among which is the high-mobility group (HMG) box transcription factor SOX2. Dysregulated SOX2 expression, by contrast, leads to transcriptional aberrations relevant to oncogenic transformation, cancer progression, metastasis, therapy resistance, and relapse. Here, we report a post-transcriptional mechanism by which the cytosolic pool of SOX2 contributes to these events in an unsuspected manner. Specifically, a low-complexity region within SOX2's C-terminal segment connects to the ribosome to modulate the expression of cognate downstream factors. Independent of nuclear structures or DNA, this C-terminal functionality alone changes metabolic properties and induces non-adhesive growth when expressed in the cytosol of SOX2 knockout cells. We thus propose a revised model of SOX2 action where nuclear and cytosolic fractions cooperate to impose cell fate decisions via both transcriptional and translational mechanisms.

Keywords:  CP: Developmental biology; CP: Molecular biology; SOX2; cancer; differentiation; ribosome; stem cell; translation

DOI:  https://doi.org/10.1016/j.celrep.2024.114807
Nature. 2024 Oct 09.

Structural basis of mRNA decay by the human exosome-ribosome supercomplex.

Alexander Kögel, Achim Keidel, Matina-Jasemi Loukeri, Christopher C Kuhn, Lukas M Langer, Ingmar B Schäfer, Elena Conti.

The interplay between translation and mRNA decay is widespread in human cells1-3. In quality-control pathways, exonucleolytic degradation of mRNA associated with translating ribosomes is mediated largely by the cytoplasmic exosome4-9, which includes the exoribonuclease complex EXO10 and the helicase complex SKI238 (refs. 10-16). The helicase can extract mRNA from the ribosome and is expected to transfer it to the exoribonuclease core through a bridging factor, HBS1L3 (also known as SKI7), but the mechanisms of this molecular handover remain unclear7,17,18. Here we reveal how human EXO10 is recruited by HBS1L3 (SKI7) to an active ribosome-bound SKI238 complex. We show that rather than a sequential handover, a direct physical coupling mechanism takes place, which culminates in the formation of a cytoplasmic exosome-ribosome supercomplex. Capturing the structure during active decay reveals a continuous path in which an RNA substrate threads from the 80S ribosome through the SKI2 helicase into the exoribonuclease active site of the cytoplasmic exosome complex. The SKI3 subunit of the complex directly binds to HBS1L3 (SKI7) and also engages a surface of the 40S subunit, establishing a recognition platform in collided disomes. Exosome and ribosome thus work together as a single structural and functional unit in co-translational mRNA decay, coordinating their activities in a transient supercomplex.

DOI: https://doi.org/10.1038/s41586-024-08015-6
Science. 2024 Oct 11. 386(6718): eadh1145

Temporal variability and cell mechanics control robustness in mammalian embryogenesis.

Dimitri Fabrèges, Bernat Corominas-Murtra, Prachiti Moghe, Alison Kickuth, Takafumi Ichikawa, Chizuru Iwatani, Tomoyuki Tsukiyama, Nathalie Daniel, Julie Gering, Anniek Stokkermans, Adrian Wolny, Anna Kreshuk, Véronique Duranthon, Virginie Uhlman, Edouard Hannezo, Takashi Hiiragi.

How living systems achieve precision in form and function despite their intrinsic stochasticity is a fundamental yet ongoing question in biology. We generated morphomaps of preimplantation embryogenesis in mouse, rabbit, and monkey embryos, and these morphomaps revealed that although blastomere divisions desynchronized passively, 8-cell embryos converged toward robust three-dimensional shapes. Using topological analysis and genetic perturbations, we found that embryos progressively changed their cellular connectivity to a preferred topology, which could be predicted by a physical model in which actomyosin contractility and noise facilitate topological transitions, lowering surface energy. This mechanism favored regular embryo packing and promoted a higher number of inner cells in the 16-cell embryo. Synchronized division reduced embryo packing and generated substantially more misallocated cells and fewer inner-cell-mass cells. These findings suggest that stochasticity in division timing contributes to robust patterning.

DOI: https://doi.org/10.1126/science.adh1145
bioRxiv. 2024 Sep 29. pii: 2023.09.08.555746. [Epub ahead of print]

KaryoTap Enables Aneuploidy Detection in Thousands of Single Human Cells.

Joseph C Mays, Sally Mei, Manjunatha Kogenaru, Helberth M Quysbertf, Nazario Bosco, Xin Zhao, Joy J Bianchi, Aleah Goldberg, Gururaj Rao Kidiyoor, Liam J Holt, David Fenyö, Teresa Davoli.

Investigating chromosomal instability and aneuploidy within tumors is essential for understanding tumorigenesis and developing diagnostic and therapeutic strategies. Single-cell DNA sequencing technologies have enabled such analyses, revealing aneuploidies specific to individual cells within the same tumor. However, it has been difficult to scale the throughput of these methods to detect rare aneuploidies while maintaining high sensitivity. To overcome this deficit, we developed KaryoTap, a method combining custom targeted DNA sequencing panels for the Tapestri platform with a computational framework to enable detection of chromosome- and chromosome arm-scale aneuploidy (gains or losses) and copy number neutral loss of heterozygosity in all human chromosomes across thousands of single cells simultaneously. KaryoTap allows detecting gains and losses with an average accuracy of 83% for arm events and 91% for chromosome events. Importantly, together with chromosomal copy number, our system allows us to detect barcodes and gRNAs integrated into the cells' genome, thus enabling pooled CRISPR- or ORF-based functional screens in single cells. As a proof of principle, we performed a small screen to expand the chromosomes that can be targeted by our recently described CRISPR-based KaryoCreate system for engineering aneuploidy in human cells. KaryoTap will prove a powerful and flexible approach for the study of aneuploidy and chromosomal instability in both tumors and normal tissues.

DOI: https://doi.org/10.1101/2023.09.08.555746
Nat Mater. 2024 Oct 09.

Jamming of nephron-forming niches in the developing mouse kidney creates cyclical mechanical stresses.

Louis S Prahl, Jiageng Liu, John M Viola, Aria Zheyuan Huang, Trevor J Chan, Gabriela Hayward-Lara, Catherine M Porter, Chenjun Shi, Jitao Zhang, Alex J Hughes.

Urinary collecting tubules form during kidney embryogenesis through the branching of the ureteric bud epithelium. A travelling mesenchyme niche of nephron progenitor cells caps each branching ureteric bud tip. These 'tip domain' niches pack more closely over developmental time and their number relates to nephron endowment at birth. Yet, how the crowded tissue environment impacts niche number and cell decision-making remains unclear. Here, through experiments and mathematical modelling, we show that niche packing conforms to physical limitations imposed by kidney curvature. We relate packing geometries to rigidity theory to predict a stiffening transition starting at embryonic day 15 in the mouse, validated by micromechanical analysis. Using a method to estimate tip domain 'ages' relative to their most recent branch events, we find that new niches overcome mechanical resistance as they branch and displace neighbours. This creates rhythmic mechanical stress in the niche. These findings expand our understanding of kidney development and inform engineering strategies for synthetic regenerative tissues.

DOI: https://doi.org/10.1038/s41563-024-02019-3
Development. 2024 Oct 15. pii: dev203116. [Epub ahead of print]151(20):

Advancing stem cell technologies for conservation of wildlife biodiversity.

Ashlee M Hutchinson, Ruth Appeltant, Tom Burdon, Qiuye Bao, Rhishikesh Bargaje, Andrea Bodnar, Stuart Chambers, Pierre Comizzoli, Laura Cook, Yoshinori Endo, Bob Harman, Katsuhiko Hayashi, Thomas Hildebrandt, Marisa L Korody, Uma Lakshmipathy, Jeanne F Loring, Clara Munger, Alex H M Ng, Ben Novak, Manabu Onuma, Sara Ord, Monique Paris, Andrew J Pask, Francisco Pelegri, Martin Pera, Ryan Phelan, Benyamin Rosental, Oliver A Ryder, Woranop Sukparangsi, Gareth Sullivan, Nicole Liling Tay, Nikki Traylor-Knowles, Shawn Walker, Antonia Weberling, Deanne J Whitworth, Suzannah A Williams, Jessye Wojtusik, Jun Wu, Qi-Long Ying, Thomas P Zwaka, Timo N Kohler.

  Wildlife biodiversity is essential for healthy, resilient and sustainable ecosystems. For biologists, this diversity also represents a treasure trove of genetic, molecular and developmental mechanisms that deepen our understanding of the origins and rules of life. However, the rapid decline in biodiversity reported recently foreshadows a potentially catastrophic collapse of many important ecosystems and the associated irreversible loss of many forms of life on our planet. Immediate action by conservationists of all stripes is required to avert this disaster. In this Spotlight, we draw together insights and proposals discussed at a recent workshop hosted by Revive & Restore, which gathered experts to discuss how stem cell technologies can support traditional conservation techniques and help protect animal biodiversity. We discuss reprogramming, in vitro gametogenesis, disease modelling and embryo modelling, and we highlight the prospects for leveraging stem cell technologies beyond mammalian species.

Keywords:   In vitro gametogenesis; Biodiversity; Conservation; Disease modelling; IPSC; Stem cells

DOI:  https://doi.org/10.1242/dev.203116
Nat Cell Biol. 2024 Oct 08.

Blood-generating heart-forming organoids recapitulate co-development of the human haematopoietic system and the embryonic heart.

Miriana Dardano, Felix Kleemiß, Maike Kosanke, Dorina Lang, Liam Wilson, Annika Franke, Jana Teske, Akshatha Shivaraj, Jeanne de la Roche, Martin Fischer, Lucas Lange, Axel Schambach, Lika Drakhlis, Robert Zweigerdt.

Despite the biomedical importance of haematopoietic stem cells and haematopoietic progenitor cells, their in vitro stabilization in a developmental context has not been achieved due to limited knowledge of signals and markers specifying the multiple haematopoietic waves as well as ethically restricted access to the human embryo. Thus, an in vitro approach resembling aspects of haematopoietic development in the context of neighbouring tissues is of interest. Our established human pluripotent stem cell-derived heart-forming organoids (HFOs) recapitulate aspects of heart, vasculature and foregut co-development. Modulating HFO differentiation, we here report the generation of blood-generating HFOs. While maintaining a functional ventricular-like heart anlagen, blood-generating HFOs comprise a mesenchyme-embedded haemogenic endothelial layer encompassing multiple haematopoietic derivatives and haematopoietic progenitor cells with erythro-myeloid and lymphoid potential, reflecting aspects of primitive and definitive haematopoiesis. The model enables the morphologically structured co-development of cardiac, endothelial and multipotent haematopoietic tissues equivalent to the intra-embryonic haematopoietic region in vivo, promoting research on haematopoiesis in vitro.

DOI: https://doi.org/10.1038/s41556-024-01526-4
Cell. 2024 Oct 01. pii: S0092-8674(24)01069-9. [Epub ahead of print]

Identifying specific functional roles for senescence across cell types.

Huan Zhao, Zixin Liu, Hui Chen, Maoying Han, Mingjun Zhang, Kuo Liu, Hengwei Jin, Xiuxiu Liu, Mengyang Shi, Wenjuan Pu, Markus Werner, Michael Meister, Stefan G Kauschke, Ruilin Sun, Jinjin Wang, Ruling Shen, Qing-Dong Wang, Xin Ma, Jan S Tchorz, Bin Zhou.

  Cellular senescence plays critical roles in aging, regeneration, and disease; yet, the ability to discern its contributions across various cell types to these biological processes remains limited. In this study, we generated an in vivo genetic toolbox consisting of three p16Ink4a-related intersectional genetic systems, enabling pulse-chase tracing (Sn-pTracer), Cre-based tracing and ablation (Sn-cTracer), and gene manipulation combined with tracing (Sn-gTracer) of defined p16Ink4a+ cell types. Using liver injury and repair as an example, we found that macrophages and endothelial cells (ECs) represent distinct senescent cell populations with different fates and functions during liver fibrosis and repair. Notably, clearance of p16Ink4a+ macrophages significantly mitigates hepatocellular damage, whereas eliminating p16Ink4a+ ECs aggravates liver injury. Additionally, targeted reprogramming of p16Ink4a+ ECs through Kdr overexpression markedly reduces liver fibrosis. This study illuminates the functional diversity of p16Ink4a+ cells and offers insights for developing cell-type-specific senolytic therapies in the future.

Keywords:  Cdkn2a; aging; cellular senescence; dual recombinases; endothelial cell; lineage tracing; liver fibrosis; liver repair; macrophage; p16(Ink4a)

DOI:  https://doi.org/10.1016/j.cell.2024.09.021
Dev Cell. 2024 Oct 04. pii: S1534-5807(24)00537-9. [Epub ahead of print]

RNA surveillance by the RNA helicase MTR4 determines volume of mouse oocytes.

Yun-Wen Wu, Zuo-Qi Deng, Yan Rong, Guo-Wei Bu, Yu-Ke Wu, Xuan Wu, Hong Cheng, Heng-Yu Fan.

  Oocytes are the largest cell type in multicellular animals. Here, we show that mRNA transporter 4 (MTR4) is indispensable for oocyte growth and functions as part of the RNA surveillance mechanism, which is responsible for nuclear waste RNA clearance. MTR4 ensures the normal post-transcriptional processing of maternal RNAs, their nuclear export to the cytoplasm, and the accumulation of properly processed transcripts. Oocytes with Mtr4 knockout fail to accumulate sufficient and normal transcripts in the cytoplasm and cannot grow to normal sizes. MTR4-dependent RNA surveillance has a previously unrecognized function in maintaining a stable nuclear environment for the establishment of non-canonical histone H3 lysine-4 trimethylation and chromatin reorganization, which is necessary to form a nucleolus-like structure in oocytes. In conclusion, MTR4-dependent RNA surveillance activity is a checkpoint that allows oocytes to grow to a normal size, undergo nuclear and cytoplasmic maturation, and acquire developmental competence.

Keywords:  RNA exosome; RNA surveillance; chromatin configuration; germ cell; histone modification; post-transcriptional regulation

DOI:  https://doi.org/10.1016/j.devcel.2024.09.009
Nat Methods. 2024 Oct 07.

scNanoSeq-CUT&Tag: a single-cell long-read CUT&Tag sequencing method for efficient chromatin modification profiling within individual cells.

Qingqing Li, Yuqing Guo, Zixin Wu, Xueqiang Xu, Zhenhuan Jiang, Shuyue Qi, Zhenyu Liu, Lu Wen, Fuchou Tang.

Chromatin modifications are fundamental epigenetic marks that determine genome functions, but it remains challenging to profile those of repetitive elements and complex genomic regions. Here, we develop scNanoSeq-CUT&Tag, a streamlined method, by adapting modified cleavage under targets and tagmentation (CUT&Tag) to the nanopore sequencing platform for genome-wide chromatin modification profiling within individual cells. We show that scNanoSeq-CUT&Tag can accurately profile histone marks and transcription factor occupancy patterns at single-cell resolution as well as distinguish different cell types. scNanoSeq-CUT&Tag efficiently maps the allele-specific chromatin modifications and allows analysis of their neighboring region co-occupancy patterns within individual cells. Moreover, scNanoSeq-CUT&Tag can accurately detect chromatin modifications for individual copies of repetitive elements in both human and mouse genomes. Overall, we prove that scNanoSeq-CUT&Tag is a valuable single-cell tool for efficiently profiling histone marks and transcription factor occupancies, especially for previously poorly studied complex genomic regions and blacklist genomic regions.

DOI: https://doi.org/10.1038/s41592-024-02453-w
Nat Commun. 2024 Oct 07. 15(1): 8682

Compensatory activity of the PC-ME1 metabolic axis underlies differential sensitivity to mitochondrial complex I inhibition.

Lucia Del Prado, Myriam Jaraíz-Rodríguez, Mauro Agro, Marcos Zamora-Dorta, Natalia Azpiazu, Manuel Calleja, Mario Lopez-Manzaneda, Jaime de Juan-Sanz, Alba Fernández-Rodrigo, José A Esteban, Mònica Girona, Albert Quintana, Eduardo Balsa.

Deficiencies in the electron transport chain (ETC) lead to mitochondrial diseases. While mutations are distributed across the organism, cell and tissue sensitivity to ETC disruption varies, and the molecular mechanisms underlying this variability remain poorly understood. Here we show that, upon ETC inhibition, a non-canonical tricarboxylic acid (TCA) cycle upregulates to maintain malate levels and concomitant production of NADPH. Our findings indicate that the adverse effects observed upon CI inhibition primarily stem from reduced NADPH levels, rather than ATP depletion. Furthermore, we find that Pyruvate carboxylase (PC) and ME1, the key mediators orchestrating this metabolic reprogramming, are selectively expressed in astrocytes compared to neurons and underlie their differential sensitivity to ETC inhibition. Augmenting ME1 levels in the brain alleviates neuroinflammation and corrects motor function and coordination in a preclinical mouse model of CI deficiency. These studies may explain why different brain cells vary in their sensitivity to ETC inhibition, which could impact mitochondrial disease management.

DOI: https://doi.org/10.1038/s41467-024-52968-1
Cell Rep Methods. 2024 Oct 03. pii: S2667-2375(24)00258-3. [Epub ahead of print] 100875

Transgenic sensors reveal compartment-specific effects of aggregation-prone proteins on subcellular proteostasis during aging.

Michelle Curley, Mamta Rai, Chia-Lung Chuang, Vishwajeeth Pagala, Anna Stephan, Zane Coleman, Maricela Robles-Murguia, Yong-Dong Wang, Junmin Peng, Fabio Demontis.

  Loss of proteostasis is a hallmark of aging that underlies many age-related diseases. Different cell compartments experience distinctive challenges in maintaining protein quality control, but how aging regulates subcellular proteostasis remains underexplored. Here, by targeting the misfolding-prone FlucDM luciferase to the cytoplasm, mitochondria, and nucleus, we established transgenic sensors to examine subcellular proteostasis in Drosophila. Analysis of detergent-insoluble and -soluble levels of compartment-targeted FlucDM variants indicates that thermal stress, cold shock, and pro-longevity inter-organ signaling differentially affect subcellular proteostasis during aging. Moreover, aggregation-prone proteins that cause different neurodegenerative diseases induce a diverse range of outcomes on FlucDM insolubility, suggesting that subcellular proteostasis is impaired in a disease-specific manner. Further analyses with FlucDM and mass spectrometry indicate that pathogenic tauV337M produces an unexpectedly complex regulation of solubility for different FlucDM variants and protein subsets. Altogether, compartment-targeted FlucDM sensors pinpoint a diverse modulation of subcellular proteostasis by aging regulators.

Keywords:  CP: cell biology; CP: molecular biology; cell compartments; inter-tissue signaling; myokines; organelles; protein quality control; subcellular proteostasis; tools for aging research

DOI:  https://doi.org/10.1016/j.crmeth.2024.100875
Mol Cell. 2024 Sep 28. pii: S1097-2765(24)00744-5. [Epub ahead of print]

Cell-cycle-dependent mRNA localization in P-bodies.

Adham Safieddine, Marie-Noëlle Benassy, Thomas Bonte, Floric Slimani, Oriane Pourcelot, Michel Kress, Michèle Ernoult-Lange, Maïté Courel, Emeline Coleno, Arthur Imbert, Antoine Laine, Annie Munier Godebert, Angelique Vinit, Corinne Blugeon, Guillaume Chevreux, Daniel Gautheret, Thomas Walter, Edouard Bertrand, Marianne Bénard, Dominique Weil.

  Understanding the dynamics of RNA targeting to membraneless organelles is essential to disentangle their functions. Here, we investigate how P-bodies (PBs) evolve during cell-cycle progression in HEK293 cells. PB purification across the cell cycle uncovers widespread changes in their RNA content, partly uncoupled from cell-cycle-dependent changes in RNA expression. Single-molecule fluorescence in situ hybridization (FISH) shows various mRNA localization patterns in PBs peaking in G1, S, or G2, with examples illustrating the timely capture of mRNAs in PBs when their encoded protein becomes dispensable. Rather than directly reflecting absence of translation, cyclic mRNA localization in PBs can be controlled by RBPs, such as HuR in G2, and by RNA features. Indeed, while PB mRNAs are AU rich at all cell-cycle phases, they are specifically longer in G1, possibly related to post-mitotic PB reassembly. Altogether, our study supports a model where PBs are more than a default location for excess untranslated mRNAs.

Keywords:  P-bodies; RNA imaging; RNA localization; cell cycle; membraneless organelles

DOI:  https://doi.org/10.1016/j.molcel.2024.09.011
Elife. 2024 Oct 11. pii: RP94001. [Epub ahead of print]13

Transcriptional inhibition after irradiation occurs preferentially at highly expressed genes in a manner dependent on cell cycle progression.

Zulong Chen, Xin Wang, Xinlei Gao, Nina Arslanovic, Kaifu Chen, Jessica K Tyler.

  In response to DNA double-strand damage, ongoing transcription is inhibited to facilitate accurate DNA repair while transcriptional recovery occurs after DNA repair is complete. However, the mechanisms at play and the identity of the transcripts being regulated in this manner are unclear. In contrast to the situation following UV damage, we found that transcriptional recovery after ionizing radiation (IR) occurs in a manner independent of the HIRA histone chaperone. Sequencing of the nascent transcripts identified a programmed transcriptional response, where certain transcripts and pathways are rapidly downregulated after IR, while other transcripts and pathways are upregulated. Specifically, most of the loss of nascent transcripts occurring after IR is due to inhibition of transcriptional initiation of the highly transcribed histone genes and the rDNA. To identify factors responsible for transcriptional inhibition after IR in an unbiased manner, we performed a whole genome gRNA library CRISPR/Cas9 screen. Many of the top hits on our screen were factors required for protein neddylation. However, at short times after inhibition of neddylation, transcriptional inhibition still occurred after IR, even though neddylation was effectively inhibited. Persistent inhibition of neddylation blocked transcriptional inhibition after IR, and it also leads to cell cycle arrest. Indeed, we uncovered that many inhibitors and conditions that lead to cell cycle arrest in G1 or G2 phase also prevent transcriptional inhibition after IR. As such, it appears that transcriptional inhibition after IR occurs preferentially at highly expressed genes in cycling cells.

Keywords:  DNA damage; chromosomes; gene expression; genome integrity; human

DOI:  https://doi.org/10.7554/eLife.94001
EMBO J. 2024 Oct 08.

DELE1 maintains muscle proteostasis to promote growth and survival in mitochondrial myopathy.

Hsin-Pin Lin, Jennifer D Petersen, Alexandra J Gilsrud, Angelo Madruga, Theresa M D'Silva, Xiaoping Huang, Mario K Shammas, Nicholas P Randolph, Kory R Johnson, Yan Li, Drew R Jones, Michael E Pacold, Derek P Narendra.

  Mitochondrial dysfunction causes devastating disorders, including mitochondrial myopathy, but how muscle senses and adapts to mitochondrial dysfunction is not well understood. Here, we used diverse mouse models of mitochondrial myopathy to show that the signal for mitochondrial dysfunction originates within mitochondria. The mitochondrial proteins OMA1 and DELE1 sensed disruption of the inner mitochondrial membrane and, in response, activated the mitochondrial integrated stress response (mt-ISR) to increase the building blocks for protein synthesis. In the absence of the mt-ISR, protein synthesis in muscle was dysregulated causing protein misfolding, and mice with early-onset mitochondrial myopathy failed to grow and survive. The mt-ISR was similar following disruptions in mtDNA maintenance (Tfam knockout) and mitochondrial protein misfolding (CHCHD10 G58R and S59L knockin) but heterogenous among mitochondria-rich tissues, with broad gene expression changes observed in heart and skeletal muscle and limited changes observed in liver and brown adipose tissue. Taken together, our findings identify that the DELE1 mt-ISR mediates a similar response to diverse forms of mitochondrial stress and is critical for maintaining growth and survival in early-onset mitochondrial myopathy.

Keywords:  Mitochondria Unfolded Protein Response (mt-UPR); Mitochondrial Disorders; Mitohormesis; Mitonuclear Communication; Mitophagy

DOI:  https://doi.org/10.1038/s44318-024-00242-x
J Mol Cell Cardiol. 2024 Oct 09. pii: S0022-2828(24)00163-9. [Epub ahead of print]

Human embryonic stem cell-derived cardiovascular progenitor cells stimulate cardiomyocyte cell cycle activity via activating the PI3K/Akt pathway.

Zhongyan Chen, Xiujian Yu, Minxia Ke, Hao Li, Yun Jiang, Peng Zhang, Jiliang Tan, Nan Cao, Huang-Tian Yang.

  Promoting endogenous cardiomyocyte proliferation is crucial for repairing infarcted hearts. Implantation of human pluripotent stem cell-derived cardiovascular progenitor cells (hCVPCs) promotes healing of infarcted hearts. However, little is known regarding their impact on host cardiomyocyte proliferation. Here, we revealed that hCVPC implantation into mouse infarcted hearts induced dedifferentiation and cell cycle re-entry of host cardiomyocytes, which was further confirmed in vitro by hCVPC-conditioned medium. Mechanistically, the PI3K/Akt signaling pathway mediated hCVPC-induced cardiomyocyte cell cycle re-entry. The findings reveal the novel function of hCVPCs in triggering cardiomyocyte dedifferentiation and cell cycle activation and highlight a strategy utilizing cells at early developmental stages to rejuvenate adult cardiomyocytes.

Keywords:  Cardiomyocyte dedifferentiation; Cardiomyocyte proliferation; Cardiovascular progenitor cells; Myocardial infarction; PI3K/Akt pathway

DOI:  https://doi.org/10.1016/j.yjmcc.2024.10.002
Curr Opin Cell Biol. 2024 Oct 07. pii: S0955-0674(24)00114-5. [Epub ahead of print]91 102435

Waves of change: Dynamic actomyosin networks in embryonic development.

Negar Balaghi, Rodrigo Fernandez-Gonzalez.

As animals develop, molecules, cells, and cell ensembles move in beautifully orchestrated choreographies. Movement at each of these scales requires generation of mechanical force. In eukaryotic cells, the actomyosin cytoskeleton generates mechanical forces. Continuous advances in in vivo microscopy have enabled visualization and quantitative assessment of actomyosin dynamics and force generation, within and across cells, in living embryos. Recent studies reveal that actomyosin networks can form periodic waves in vivo. Here, we highlight contributions of actomyosin waves to molecular transport, cell movement, and cell coordination in developing embryos.

DOI: https://doi.org/10.1016/j.ceb.2024.102435
bioRxiv. 2024 Sep 25. pii: 2024.02.19.581036. [Epub ahead of print]

Single-nucleus multiomics reveals the gene-regulatory networks underlying sex determination of murine primordial germ cells.

Adriana K Alexander, Karina F Rodriguez, Yu-Ying Chen, Ciro M Amato, Martin A Estermann, Barbara Nicol, Xin Xu, Humphrey Hung-Chang Yao.

Accurate specification of female and male germ cells during embryonic development is critical for sexual reproduction. Primordial germ cells (PGCs) are the bipotential precursors of mature gametes that commit to an oogenic or spermatogenic fate in response to sex-determining cues from the fetal gonad. The critical processes required for PGCs to integrate and respond to signals from the somatic environment in gonads are not understood. In this study, we developed the first single-nucleus multiomics map of chromatin accessibility and gene expression during murine PGC development in both XX and XY embryos. Profiling of cell-type specific transcriptomes and regions of open chromatin from the same cell captured the molecular signatures and gene networks underlying PGC sex determination. Joint RNA and ATAC data for single PGCs resolved previously unreported PGC subpopulations and cataloged a multimodal reference atlas of differentiating PGC clusters. We discovered that regulatory element accessibility precedes gene expression during PGC development, suggesting that changes in chromatin accessibility may prime PGC lineage commitment prior to differentiation. Similarly, we found that sexual dimorphism in chromatin accessibility and gene expression increased temporally in PGCs. Combining single-nucleus sequencing data, we computationally mapped the cohort of transcription factors that regulate the expression of sexually dimorphic genes in PGCs. For example, the gene regulatory networks of XX PGCs are enriched for the transcription factors, TFAP2c, TCFL5, GATA2, MGA, NR6A1, TBX4, and ZFX. Sex-specific enrichment of the forkhead-box and POU6 families of transcription factors was also observed in XY PGCs. Finally, we determined the temporal expression patterns of WNT, BMP, and RA signaling during PGC sex determination, and our discovery analyses identified potentially new cell communication pathways between supporting cells and PGCs. Our results illustrate the diversity of factors involved in programming PGCs towards a sex-specific fate.

DOI: https://doi.org/10.1101/2024.02.19.581036
Nature. 2024 Oct 09.

Biomolecular condensates mediate bending and scission of endosome membranes.

Yanning Wang, Shulin Li, Marcel Mokbel, Alexander I May, Zizhen Liang, Yonglun Zeng, Weiqi Wang, Honghong Zhang, Feifei Yu, Katharina Sporbeck, Liwen Jiang, Sebastian Aland, Jaime Agudo-Canalejo, Roland L Knorr, Xiaofeng Fang.

Multivesicular bodies are key endosomal compartments implicated in cellular quality control through their degradation of membrane-bound cargo proteins1-3. The ATP-consuming ESCRT protein machinery mediates the capture and engulfment of membrane-bound cargo proteins through invagination and scission of multivesicular-body membranes to form intraluminal vesicles4,5. Here we report that the plant ESCRT component FREE16 forms liquid-like condensates that associate with membranes to drive intraluminal vesicle formation. We use a minimal physical model, reconstitution experiments and in silico simulations to identify the dynamics of this process and describe intermediate morphologies of nascent intraluminal vesicles. Furthermore, we find that condensate-wetting-induced line tension forces and membrane asymmetries are sufficient to mediate scission of the membrane neck without the ESCRT protein machinery or ATP consumption. Genetic manipulation of the ESCRT pathway in several eukaryotes provides additional evidence for condensate-mediated membrane scission in vivo. We find that the interplay between condensate and machinery-mediated scission mechanisms is indispensable for osmotic stress tolerance in plants. We propose that condensate-mediated scission represents a previously undescribed scission mechanism that depends on the physicomolecular properties of the condensate and is involved in a range of trafficking processes. More generally, FREE1 condensate-mediated membrane scission in multivesicular-body biogenesis highlights the fundamental role of wetting in intracellular dynamics and organization.

DOI: https://doi.org/10.1038/s41586-024-07990-0
bioRxiv. 2024 Sep 23. pii: 2024.09.23.614059. [Epub ahead of print]

Cell signaling facilitates apical constriction by basolaterally recruiting Arp2/3 via Rac and WAVE.

Pu Zhang, Taylor N Medwig-Kinney, Eleanor A Breiner, Jadyn M Perez, April N Song, Bob Goldstein.

Apical constriction is a critical cell shape change that bends tissues. How precisely-localized actomyosin regulators drive apical constriction remains poorly understood. C. elegans gastrulation provides a valuable model to address this question. The Arp2/3 complex is essential in C. elegans gastrulation. To understand how Arp2/3 is locally regulated, we imaged embryos with endogenously-tagged Arp2/3 and its nucleation-promoting factors (NPFs). The three NPFs - WAVE, WASP, and WASH - colocalized with Arp2/3 and controlled Arp2/3 localization at distinct subcellular locations. We exploited this finding to study distinct populations of Arp2/3 and found that only WAVE depletion caused penetrant gastrulation defects. WAVE localized basolaterally with Arp2/3 at cell-cell contacts, dependent on CED-10/Rac. Establishing ectopic cell contacts recruited WAVE and Arp2/3, identifying contact as a symmetry-breaking cue for localization of these proteins. These results suggest that cell-cell signaling via Rac activates WAVE and Arp2/3 basolaterally, and that basolateral Arp2/3 is important for apical constriction.

DOI: https://doi.org/10.1101/2024.09.23.614059