bims-ginsta 2024-02-11 papers

bims-ginsta

Biomed News

on Genome instability

Issue of 2024–02–11
29 papers selected by
Jinrong Hu, National University of Singapore

Maternal KLF17 controls zygotic genome activation by acting as a messenger for RNA Pol II recruitment in mouse embryos.
The nuclear factor ID3 endows macrophages with a potent anti-tumour activity.
Rac1 promotes kidney collecting duct repair by mechanically coupling cell morphology to mitotic entry.
Unraveling the mechanism of centromere inactivation in human aging.
Retrospective identification of cell-intrinsic factors that mark pluripotency potential in rare somatic cells.
Transcription elongation mechanisms of RNA polymerases I, II, and III and their therapeutic implications.
The cycling and aging mouse female reproductive tract at single-cell resolution.
Translation regulation in response to stress.
Mitochondrial outer membrane integrity regulates a ubiquitin-dependent and NF-κB-mediated inflammatory response.
WHAMM functions in kidney reabsorption and polymerizes actin to promote autophagosomal membrane closure and cargo sequestration.
Aneuploidy-induced cellular behaviors: Insights from Drosophila.
Determinants that enable disordered protein assembly into discrete condensed phases.
Senescent cells and macrophages cooperate through a multi-kinase signaling network to promote intestinal transformation in Drosophila.
Mitochondrial DNA replication stress triggers a pro-inflammatory endosomal pathway of nucleoid disposal.
Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites.
Transcriptional programming of translation by BCL6 controls skeletal muscle proteostasis.
Epithelial zonation along the mouse and human small intestine defines five discrete metabolic domains.
Lactic acid induces transcriptional repression of macrophage inflammatory response via histone acetylation.
Rearrangement of GUV-confined actin networks in response to micropipette aspiration.
The role of mitochondrial dynamics in oocyte and early embryo development.
The contribution of asymmetric cell division to phenotypic heterogeneity in cancer.
Cell cycle plasticity underlies fractional resistance to palbociclib in ER+/HER2- breast tumor cells.
LSD1 controls a nuclear checkpoint in Wnt/β-Catenin signaling to regulate muscle stem cell self-renewal.
Microglia maintain structural integrity during fetal brain morphogenesis.
Phosphoglycerate kinase 1 acts as a cargo adaptor to promote EGFR transport to the lysosome.
Puromycin reveals a distinct conformation of neuronal ribosomes.
Protein thermal sensing regulates physiological amyloid aggregation.
The alpha-1A adrenergic receptor regulates mitochondrial oxidative metabolism in the mouse heart.
Translation selectively destroys non-functional transcription complexes.

Dev Cell. 2024 Jan 31. pii: S1534-5807(24)00032-7. [Epub ahead of print]

Maternal KLF17 controls zygotic genome activation by acting as a messenger for RNA Pol II recruitment in mouse embryos.

Yue Hu, Yuxiang Wang, Yuanlin He, Maosheng Ye, Jie Yuan, Chao Ren, Xia Wang, Siqi Wang, Yueshuai Guo, Qiqi Cao, Shuai Zhou, Bing Wang, Anlan He, Jiongsong Hu, Xuejiang Guo, Wenjie Shu, Ran Huo.

  Initiation of timely and sufficient zygotic genome activation (ZGA) is crucial for the beginning of life, yet our knowledge of transcription factors (TFs) contributing to ZGA remains limited. Here, we screened the proteome of early mouse embryos after cycloheximide (CHX) treatment and identified maternally derived KLF17 as a potential TF for ZGA genes. Using a conditional knockout (cKO) mouse model, we further investigated the role of maternal KLF17 and found that it promotes embryonic development and full fertility. Mechanistically, KLF17 preferentially binds to promoters and recruits RNA polymerase II (RNA Pol II) in early 2-cell embryos, facilitating the expression of major ZGA genes. Maternal Klf17 knockout resulted in a downregulation of 9% of ZGA genes and aberrant RNA Pol II pre-configuration, which could be partially rescued by introducing exogenous KLF17. Overall, our study provides a strategy for screening essential ZGA factors and identifies KLF17 as a crucial TF in this process.

Keywords:  KLF17; RNA Pol II pre-configuration; early embryonic development; maternal transcription factor; zygotic genome activation

DOI:  https://doi.org/10.1016/j.devcel.2024.01.013
Nature. 2024 Feb 07.

The nuclear factor ID3 endows macrophages with a potent anti-tumour activity.

Zihou Deng, Pierre-Louis Loyher, Tomi Lazarov, Li Li, Zeyang Shen, Bhavneet Bhinder, Hairu Yang, Yi Zhong, Araitz Alberdi, Joan Massague, Joseph C Sun, Robert Benezra, Christopher K Glass, Olivier Elemento, Christine A Iacobuzio-Donahue, Frederic Geissmann.

Macrophage activation is controlled by a balance between activating and inhibitory receptors1-7, which protect normal tissues from excessive damage during infection8,9 but promote tumour growth and metastasis in cancer7,10. Here we report that the Kupffer cell lineage-determining factor ID3 controls this balance and selectively endows Kupffer cells with the ability to phagocytose live tumour cells and orchestrate the recruitment, proliferation and activation of natural killer and CD8 T lymphoid effector cells in the liver to restrict the growth of a variety of tumours. ID3 shifts the macrophage inhibitory/activating receptor balance to promote the phagocytic and lymphoid response, at least in part by buffering the binding of the transcription factors ELK1 and E2A at the SIRPA locus. Furthermore, loss- and gain-of-function experiments demonstrate that ID3 is sufficient to confer this potent anti-tumour activity to mouse bone-marrow-derived macrophages and human induced pluripotent stem-cell-derived macrophages. Expression of ID3 is therefore necessary and sufficient to endow macrophages with the ability to form an efficient anti-tumour niche, which could be harnessed for cell therapy in cancer.

DOI: https://doi.org/10.1038/s41586-023-06950-4
Sci Adv. 2024 Feb 09. 10(6): eadi7840

Rac1 promotes kidney collecting duct repair by mechanically coupling cell morphology to mitotic entry.

Fabian Bock, Xinyu Dong, Shensen Li, Olga M Viquez, Eric Sha, Matthew Tantengco, Elizabeth M Hennen, Erin Plosa, Alireza Ramezani, Kyle L Brown, Young Mi Whang, Andrew S Terker, Juan Pablo Arroyo, David G Harrison, Agnes Fogo, Cord H Brakebusch, Ambra Pozzi, Roy Zent.

Prolonged obstruction of the ureter, which leads to injury of the kidney collecting ducts, results in permanent structural damage, while early reversal allows for repair. Cell structure is defined by the actin cytoskeleton, which is dynamically organized by small Rho guanosine triphosphatases (GTPases). In this study, we identified the Rho GTPase, Rac1, as a driver of postobstructive kidney collecting duct repair. After the relief of ureteric obstruction, Rac1 promoted actin cytoskeletal reconstitution, which was required to maintain normal mitotic morphology allowing for successful cell division. Mechanistically, Rac1 restricted excessive actomyosin activity that stabilized the negative mitotic entry kinase Wee1. This mechanism ensured mechanical G2-M checkpoint stability and prevented premature mitotic entry. The repair defects following injury could be rescued by direct myosin inhibition. Thus, Rac1-dependent control of the actin cytoskeleton integrates with the cell cycle to mediate kidney tubular repair by preventing dysmorphic cells from entering cell division.

DOI: https://doi.org/10.1126/sciadv.adi7840
bioRxiv. 2023 Dec 30. pii: 2023.12.30.573721. [Epub ahead of print]

Unraveling the mechanism of centromere inactivation in human aging.

Sweta Sikder, Songjoon Baek, Truman McNeil, Yamini Dalal.

Aging involves a range of genetic, epigenetic, and physiological alterations. A key characteristic of aged cells is the loss of global heterochromatin, accompanied by a reduction in canonical histone levels. In this study, we track the fate of centromeres during aging in human cells. Our findings reveal that the centromeric histone H3 variant CENP-A is downregulated in aged cells, in a p53-dependent manner. We observe repression of centromeric noncoding transcription through an epigenetic mechanism via recruitment of a lysine-specific demethylase 1 (LSD1/KDM1A) to centromeres. This suppression results in defective de novo CENP-A loading at aging centromeres. By dual inhibition of p53 and LSD1/KDM1A in aged cells, we mitigate the reduction in centromeric proteins and centromeric transcripts, leading to mitotic rejuvenation of these cells. These results offer insights into a novel mechanism for centromeric inactivation during aging and provide potential strategies to reactivate centromeres.

DOI: https://doi.org/10.1101/2023.12.30.573721
Cell Syst. 2024 Jan 30. pii: S2405-4712(24)00022-X. [Epub ahead of print]

Retrospective identification of cell-intrinsic factors that mark pluripotency potential in rare somatic cells.

Naveen Jain, Yogesh Goyal, Margaret C Dunagin, Christopher J Cote, Ian A Mellis, Benjamin Emert, Connie L Jiang, Ian P Dardani, Sam Reffsin, Miles Arnett, Wenli Yang, Arjun Raj.

  Pluripotency can be induced in somatic cells by the expression of OCT4, KLF4, SOX2, and MYC. Usually only a rare subset of cells reprogram, and the molecular characteristics of this subset remain unknown. We apply retrospective clone tracing to identify and characterize the rare human fibroblasts primed for reprogramming. These fibroblasts showed markers of increased cell cycle speed and decreased fibroblast activation. Knockdown of a fibroblast activation factor identified by our analysis increased the reprogramming efficiency. We provide evidence for a unified model in which cells can move into and out of the primed state over time, explaining how reprogramming appears deterministic at short timescales and stochastic at long timescales. Furthermore, inhibiting the activity of LSD1 enlarged the pool of cells that were primed for reprogramming. Thus, even homogeneous cell populations can exhibit heritable molecular variability that can dictate whether individual rare cells will reprogram or not.

Keywords:  cellular barcoding; iPSC reprogramming; lineage tracing; systems biology

DOI:  https://doi.org/10.1016/j.cels.2024.01.001
J Biol Chem. 2024 Feb 07. pii: S0021-9258(24)00113-3. [Epub ahead of print] 105737

Transcription elongation mechanisms of RNA polymerases I, II, and III and their therapeutic implications.

Ruth Q Jacobs, David A Schneider.

  Transcription is a tightly regulated, complex, and essential cellular process in all living organisms. Transcription is comprised of three steps, transcription initiation, elongation, and termination. The distinct transcription initiation and termination mechanisms of eukaryotic RNA polymerases I, II, and III (Pols I, II, and III) have long been appreciated. Recent methodological advances have empowered high-resolution investigations of the Pols' transcription elongation mechanisms. Here, we review the kinetic similarities and differences in the individual steps of Pol I-, II-, and III-catalyzed transcription elongation, including NTP binding, bond formation, pyrophosphate release, and translocation. This review serves as an important summation of Saccharomyces cerevisiae (yeast) Pol I, II, and III kinetic investigations which reveal that transcription elongation by the Pols is governed by distinct mechanisms. Further, these studies illustrate how basic, biochemical investigations of the Pols can empower the development of chemotherapeutic compounds.

Keywords:  BMH-21; RNA polymerase I; RNA polymerase II; RNA polymerase III; kinetics; transcription elongation

DOI:  https://doi.org/10.1016/j.jbc.2024.105737
Cell. 2024 Jan 31. pii: S0092-8674(24)00058-8. [Epub ahead of print]

The cycling and aging mouse female reproductive tract at single-cell resolution.

Ivana Winkler, Alexander Tolkachov, Fritjof Lammers, Perrine Lacour, Klaudija Daugelaite, Nina Schneider, Marie-Luise Koch, Jasper Panten, Florian Grünschläger, Tanja Poth, Bianca Machado de Ávila, Augusto Schneider, Simon Haas, Duncan T Odom, Ângela Gonçalves.

  The female reproductive tract (FRT) undergoes extensive remodeling during reproductive cycling. This recurrent remodeling and how it shapes organ-specific aging remains poorly explored. Using single-cell and spatial transcriptomics, we systematically characterized morphological and gene expression changes occurring in ovary, oviduct, uterus, cervix, and vagina at each phase of the mouse estrous cycle, during decidualization, and into aging. These analyses reveal that fibroblasts play central-and highly organ-specific-roles in FRT remodeling by orchestrating extracellular matrix (ECM) reorganization and inflammation. Our results suggest a model wherein recurrent FRT remodeling over reproductive lifespan drives the gradual, age-related development of fibrosis and chronic inflammation. This hypothesis was directly tested using chemical ablation of cycling, which reduced fibrotic accumulation during aging. Our atlas provides extensive detail into how estrus, pregnancy, and aging shape the organs of the female reproductive tract and reveals the unexpected cost of the recurrent remodeling required for reproduction.

Keywords:  aging; cervix; fibrosis; inflammation; ovary; oviduct; single cell; spatial; uterus; vagina

DOI:  https://doi.org/10.1016/j.cell.2024.01.021
FEBS J. 2024 Feb 03.

Translation regulation in response to stress.

Thomas D Williams, Adrien Rousseau.

  Cell stresses occur in a wide variety of settings: in disease, during industrial processes, and as part of normal day-to-day rhythms. Adaptation to these stresses requires cells to alter their proteome. Cells modify the proteins they synthesize to aid proteome adaptation. Changes in both mRNA transcription and translation contribute to altered protein synthesis. Here, we discuss the changes in translational mechanisms that occur following the onset of stress, and the impact these have on stress adaptation.

Keywords:  mRNA; proteostasis; signalling; stress; translation

DOI:  https://doi.org/10.1111/febs.17076
EMBO J. 2024 Feb 09.

Mitochondrial outer membrane integrity regulates a ubiquitin-dependent and NF-κB-mediated inflammatory response.

Esmee Vringer, Rosalie Heilig, Joel S Riley, Annabel Black, Catherine Cloix, George Skalka, Alfredo E Montes-Gómez, Aurore Aguado, Sergio Lilla, Henning Walczak, Mads Gyrd-Hansen, Daniel J Murphy, Danny T Huang, Sara Zanivan, Stephen Wg Tait.

  Mitochondrial outer membrane permeabilisation (MOMP) is often essential for apoptosis, by enabling cytochrome c release that leads to caspase activation and rapid cell death. Recently, MOMP has been shown to be inherently pro-inflammatory with emerging cellular roles, including its ability to elicit anti-tumour immunity. Nonetheless, how MOMP triggers inflammation and how the cell regulates this remains poorly defined. We find that upon MOMP, many proteins localised either to inner or outer mitochondrial membranes are ubiquitylated in a promiscuous manner. This extensive ubiquitylation serves to recruit the essential adaptor molecule NEMO, leading to the activation of pro-inflammatory NF-κB signalling. We show that disruption of mitochondrial outer membrane integrity through different means leads to the engagement of a similar pro-inflammatory signalling platform. Therefore, mitochondrial integrity directly controls inflammation, such that permeabilised mitochondria initiate NF-κB signalling.

Keywords:  Cell Death; Inflammation; Mitochondria; NF-κB; Ubiquitin

DOI:  https://doi.org/10.1038/s44318-024-00044-1
bioRxiv. 2024 Jan 23. pii: 2024.01.22.576497. [Epub ahead of print]

WHAMM functions in kidney reabsorption and polymerizes actin to promote autophagosomal membrane closure and cargo sequestration.

Alyssa M Coulter, Valerie Cortés, Corey J Theodore, Rachel E Cianciolo, Ron Korstanje, Kenneth G Campellone.

The actin cytoskeleton is essential for many functions of eukaryotic cells, but the factors that nucleate actin assembly are not well understood at the organismal level or in the context of disease. To explore the function of the actin nucleation factor WHAMM in mice, we examined how Whamm inactivation impacts kidney physiology and cellular proteostasis. We show that male WHAMM knockout mice excrete elevated levels of albumin, glucose, phosphate, and amino acids, and display abnormalities of the kidney proximal tubule, suggesting that WHAMM activity is important for nutrient reabsorption. In kidney tissue, the loss of WHAMM results in the accumulation of the lipidated autophagosomal membrane protein LC3, indicating an alteration in autophagy. In mouse fibroblasts and human proximal tubule cells, WHAMM and its binding partner the Arp2/3 complex control autophagic membrane closure and cargo receptor recruitment. These results reveal a role for WHAMM-mediated actin assembly in maintaining kidney function and promoting proper autophagosome membrane remodeling.

DOI: https://doi.org/10.1101/2024.01.22.576497
Dev Cell. 2024 Feb 05. pii: S1534-5807(23)00689-5. [Epub ahead of print]59(3): 295-307

Aneuploidy-induced cellular behaviors: Insights from Drosophila.

Jery Joy, Elena Fusari, Marco Milán.

  A balanced gene complement is crucial for proper cell function. Aneuploidy, the condition of having an imbalanced chromosome set, alters the stoichiometry of gene copy numbers and protein complexes and has dramatic consequences at the cellular and organismal levels. In humans, aneuploidy is associated with different pathological conditions including cancer, microcephaly, mental retardation, miscarriages, and aging. Over the last century, Drosophila has provided a valuable system for studying the consequences of systemic aneuploidies. More recently, it has contributed to the identification and molecular dissection of aneuploidy-induced cellular behaviors and their impact at the tissue and organismal levels. In this perspective, we review this active field of research, first by comparing knowledge from yeast, mouse, and human cells, then by highlighting the contributions of Drosophila. The aim of these discussions was to further our understanding of the functional interplay between aneuploidy, cell physiology, and tissue homeostasis in human development and disease.

Keywords:  CIN; aneuploidy; gene dosage imbalance; homeostasis; senescence; tumorigenesis

DOI:  https://doi.org/10.1016/j.devcel.2023.12.009
Nat Chem. 2024 Feb 05.

Determinants that enable disordered protein assembly into discrete condensed phases.

Rachel M Welles, Kandarp A Sojitra, Mikael V Garabedian, Boao Xia, Wentao Wang, Muyang Guan, Roshan M Regy, Elizabeth R Gallagher, Daniel A Hammer, Jeetain Mittal, Matthew C Good.

Cells harbour numerous mesoscale membraneless compartments that house specific biochemical processes and perform distinct cellular functions. These protein- and RNA-rich bodies are thought to form through multivalent interactions among proteins and nucleic acids, resulting in demixing via liquid-liquid phase separation. Proteins harbouring intrinsically disordered regions (IDRs) predominate in membraneless organelles. However, it is not known whether IDR sequence alone can dictate the formation of distinct condensed phases. We identified a pair of IDRs capable of forming spatially distinct condensates when expressed in cells. When reconstituted in vitro, these model proteins do not co-partition, suggesting condensation specificity is encoded directly in the polypeptide sequences. Through computational modelling and mutagenesis, we identified the amino acids and chain properties governing homotypic and heterotypic interactions that direct selective condensation. These results form the basis of physicochemical principles that may direct subcellular organization of IDRs into specific condensates and reveal an IDR code that can guide construction of orthogonal membraneless compartments.

DOI: https://doi.org/10.1038/s41557-023-01423-7
Dev Cell. 2024 Jan 31. pii: S1534-5807(24)00029-7. [Epub ahead of print]

Senescent cells and macrophages cooperate through a multi-kinase signaling network to promote intestinal transformation in Drosophila.

Ishwaree Datta, Erdem Bangi.

  Cellular senescence is a conserved biological process that plays a crucial and context-dependent role in cancer. The highly heterogeneous and dynamic nature of senescent cells and their small numbers in tissues make in vivo mechanistic studies of senescence challenging. As a result, how multiple senescence-inducing signals are integrated in vivo to drive senescence in only a small number of cells is unclear. Here, we identify cells that exhibit multiple features of senescence in a Drosophila model of intestinal transformation, which emerge in response to concurrent activation of AKT, JNK, and DNA damage signaling within transformed tissue. Eliminating senescent cells, genetically or by treatment with senolytic compounds, reduces overgrowth and improves survival. We find that senescent cells promote tumorigenesis by recruiting Drosophila macrophages to the transformed tissue, which results in non-autonomous activation of JNK signaling. These findings identify senescent cell-macrophage interactions as an important driver of epithelial transformation.

Keywords:  Drosophila; cell signaling; colon cancer; hemocyte; macrophage; senescence

DOI:  https://doi.org/10.1016/j.devcel.2024.01.009
Nat Cell Biol. 2024 Feb 08.

Mitochondrial DNA replication stress triggers a pro-inflammatory endosomal pathway of nucleoid disposal.

Laura E Newman, Sammy Weiser Novak, Gladys R Rojas, Nimesha Tadepalle, Cara R Schiavon, Danielle A Grotjahn, Christina G Towers, Marie-Ève Tremblay, Matthew P Donnelly, Sagnika Ghosh, Michaela Medina, Sienna Rocha, Ricardo Rodriguez-Enriquez, Joshua A Chevez, Ian Lemersal, Uri Manor, Gerald S Shadel.

Mitochondrial DNA (mtDNA) encodes essential subunits of the oxidative phosphorylation system, but is also a major damage-associated molecular pattern (DAMP) that engages innate immune sensors when released into the cytoplasm, outside of cells or into circulation. As a DAMP, mtDNA not only contributes to anti-viral resistance, but also causes pathogenic inflammation in many disease contexts. Cells experiencing mtDNA stress caused by depletion of the mtDNA-packaging protein, transcription factor A, mitochondrial (TFAM) or during herpes simplex virus-1 infection exhibit elongated mitochondria, enlargement of nucleoids (mtDNA-protein complexes) and activation of cGAS-STING innate immune signalling via mtDNA released into the cytoplasm. However, the relationship among aberrant mitochondria and nucleoid dynamics, mtDNA release and cGAS-STING activation remains unclear. Here we show that, under a variety of mtDNA replication stress conditions and during herpes simplex virus-1 infection, enlarged nucleoids that remain bound to TFAM exit mitochondria. Enlarged nucleoids arise from mtDNA experiencing replication stress, which causes nucleoid clustering via a block in mitochondrial fission at a stage when endoplasmic reticulum actin polymerization would normally commence, defining a fission checkpoint that ensures mtDNA has completed replication and is competent for segregation into daughter mitochondria. Chronic engagement of this checkpoint results in enlarged nucleoids trafficking into early and then late endosomes for disposal. Endosomal rupture during transit through this endosomal pathway ultimately causes mtDNA-mediated cGAS-STING activation. Thus, we propose that replication-incompetent nucleoids are selectively eliminated by an adaptive mitochondria-endosomal quality control pathway that is prone to innate immune system activation, which might represent a therapeutic target to prevent mtDNA-mediated inflammation during viral infection and other pathogenic states.

DOI: https://doi.org/10.1038/s41556-023-01343-1
Proc Natl Acad Sci U S A. 2024 Feb 13. 121(7): e2220075121

Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites.

Samo Curk, Johannes Krausser, Georg Meisl, Daan Frenkel, Sara Linse, Thomas C T Michaels, Tuomas P J Knowles, Anđela Šarić.

  Self-replication of amyloid fibrils via secondary nucleation is an intriguing physicochemical phenomenon in which existing fibrils catalyze the formation of their own copies. The molecular events behind this fibril surface-mediated process remain largely inaccessible to current structural and imaging techniques. Using statistical mechanics, computer modeling, and chemical kinetics, we show that the catalytic structure of the fibril surface can be inferred from the aggregation behavior in the presence and absence of a fibril-binding inhibitor. We apply our approach to the case of Alzheimer's A[Formula: see text] amyloid fibrils formed in the presence of proSP-C Brichos inhibitors. We find that self-replication of A[Formula: see text] fibrils occurs on small catalytic sites on the fibril surface, which are far apart from each other, and each of which can be covered by a single Brichos inhibitor.

Keywords:  amyloid aggregation; auto-catalysis; inhibition mechanism; secondary nucleation; self-replication

DOI:  https://doi.org/10.1073/pnas.2220075121
Nat Metab. 2024 Feb 09.

Transcriptional programming of translation by BCL6 controls skeletal muscle proteostasis.

Krithika Ramachandran, Christopher R Futtner, Meredith A Sommars, Mattia Quattrocelli, Yasuhiro Omura, Ellen Fruzyna, Janice C Wang, Nathan J Waldeck, Madhavi D Senagolage, Carmen G Telles, Alexis R Demonbreun, Erin Prendergast, Nicola Lai, Daniel Arango, Ilya R Bederman, Elizabeth M McNally, Grant D Barish.

Skeletal muscle is dynamically controlled by the balance of protein synthesis and degradation. Here we discover an unexpected function for the transcriptional repressor B cell lymphoma 6 (BCL6) in muscle proteostasis and strength in mice. Skeletal muscle-specific Bcl6 ablation in utero or in adult mice results in over 30% decreased muscle mass and force production due to reduced protein synthesis and increased autophagy, while it promotes a shift to a slower myosin heavy chain fibre profile. Ribosome profiling reveals reduced overall translation efficiency in Bcl6-ablated muscles. Mechanistically, tandem chromatin immunoprecipitation, transcriptomic and translational analyses identify direct BCL6 repression of eukaryotic translation initiation factor 4E-binding protein 1 (Eif4ebp1) and activation of insulin-like growth factor 1 (Igf1) and androgen receptor (Ar). Together, these results uncover a bifunctional role for BCL6 in the transcriptional and translational control of muscle proteostasis.

DOI: https://doi.org/10.1038/s42255-024-00983-3
Nat Cell Biol. 2024 Feb 06.

Epithelial zonation along the mouse and human small intestine defines five discrete metabolic domains.

Rachel K Zwick, Petr Kasparek, Brisa Palikuqi, Sara Viragova, Laura Weichselbaum, Christopher S McGinnis, Kara L McKinley, Asoka Rathnayake, Dedeepya Vaka, Vinh Nguyen, Coralie Trentesaux, Efren Reyes, Alexander R Gupta, Zev J Gartner, Richard M Locksley, James M Gardner, Shalev Itzkovitz, Dario Boffelli, Ophir D Klein.

A key aspect of nutrient absorption is the exquisite division of labour across the length of the small intestine, with individual nutrients taken up at different proximal:distal positions. For millennia, the small intestine was thought to comprise three segments with indefinite borders: the duodenum, jejunum and ileum. By examining the fine-scale longitudinal transcriptional patterns that span the mouse and human small intestine, we instead identified five domains of nutrient absorption that mount distinct responses to dietary changes, and three regional stem cell populations. Molecular domain identity can be detected with machine learning, which provides a systematic method to computationally identify intestinal domains in mice. We generated a predictive model of transcriptional control of domain identity and validated the roles of Ppar-δ and Cdx1 in patterning lipid metabolism-associated genes. These findings represent a foundational framework for the zonation of absorption across the mammalian small intestine.

DOI: https://doi.org/10.1038/s41556-023-01337-z
Cell Rep. 2024 Feb 07. pii: S2211-1247(24)00074-3. [Epub ahead of print]43(2): 113746

Lactic acid induces transcriptional repression of macrophage inflammatory response via histone acetylation.

Weiwei Shi, Tiffany J Cassmann, Aditya Vijay Bhagwate, Taro Hitosugi, W K Eddie Ip.

  Lactic acid has emerged as an important modulator of immune cell function. It can be produced by both gut microbiota and the host metabolism at homeostasis and during disease states. The production of lactic acid in the gut microenvironment is vital for tissue homeostasis. In the present study, we examined how lactic acid integrates cellular metabolism to shape the epigenome of macrophages during pro-inflammatory response. We found that lactic acid serves as a primary fuel source to promote histone H3K27 acetylation, which allows the expression of immunosuppressive gene program including Nr4a1. Consequently, macrophage pro-inflammatory function was transcriptionally repressed. Furthermore, the histone acetylation induced by lactic acid promotes a form of long-term immunosuppression ("trained immunosuppression"). Pre-exposure to lactic acid induces lipopolysaccharide tolerance. These findings thus indicate that lactic acid sensing and its effect on chromatin remodeling in macrophages represent a key homeostatic mechanism that can provide a tolerogenic tissue microenvironment.

Keywords:  CP: Immunology; CP: Metabolism; epigenetic reprogramming; histone acetylation; immunosuppression; inflammation; inflammatory bowel disease; lactic acid; macrophage; metabolism; metabolite sensing; tissue microenvironment

DOI:  https://doi.org/10.1016/j.celrep.2024.113746
Cytoskeleton (Hoboken). 2024 Feb 07.

Rearrangement of GUV-confined actin networks in response to micropipette aspiration.

Nadab H Wubshet, Cole J Young, Allen P Liu.

  Although diverse actin network architectures found inside the cell have been individually reconstituted outside of the cell, how different types of actin architectures reorganize under applied forces is not entirely understood. Recently, bottom-up reconstitution has enabled studies where dynamic and phenotypic characteristics of various actin networks can be recreated in an isolated cell-like environment. Here, by creating a giant unilamellar vesicle (GUV)-based cell model encapsulating actin networks, we investigate how actin networks rearrange in response to localized stresses applied by micropipette aspiration. We reconstitute actin bundles and branched bundles in GUVs separately and mechanically perturb them. Interestingly, we find that, when aspirated, protrusive actin bundles that are otherwise randomly oriented in the GUV lumen collapse and align along the axis of the micropipette. However, when branched bundles are aspirated, the network remains intact and outside of the pipette while the GUV membrane is aspirated into the micropipette. These results reveal distinct responses in the rearrangement of actin networks in a network architecture-dependent manner when subjected to physical forces.

Keywords:  actin network reconstitution; cell mechanics; giant unilamellar vesicle encapsulation

DOI:  https://doi.org/10.1002/cm.21836
Semin Cell Dev Biol. 2024 Feb 06. pii: S1084-9521(24)00019-3. [Epub ahead of print]159-160 52-61

The role of mitochondrial dynamics in oocyte and early embryo development.

Raziye Melike Yildirim, Emre Seli.

  Mitochondrial dysfunction is widely implicated in various human diseases, through mechanisms that go beyond mitochondria's well-established role in energy generation. These dynamic organelles exert vital control over numerous cellular processes, including calcium regulation, phospholipid synthesis, innate immunity, and apoptosis. While mitochondria's importance is acknowledged in all cell types, research has revealed the exceptionally dynamic nature of the mitochondrial network in oocytes and embryos, finely tuned to meet unique needs during gamete and pre-implantation embryo development. Within oocytes, both the quantity and morphology of mitochondria can significantly change during maturation and post-fertilization. These changes are orchestrated by fusion and fission processes (collectively known as mitochondrial dynamics), crucial for energy production, content exchange, and quality control as mitochondria adjust to the shifting energy demands of oocytes and embryos. The roles of proteins that regulate mitochondrial dynamics in reproductive processes have been primarily elucidated through targeted deletion studies in animal models. Notably, impaired mitochondrial dynamics have been linked to female reproductive health, affecting oocyte quality, fertilization, and embryo development. Dysfunctional mitochondria can lead to fertility problems and can have an impact on the success of pregnancy, particularly in older reproductive age women.

Keywords:  Mitochondrial dynamics; Mitochondrial dysfunction; Mitophagy; MtDNA

DOI:  https://doi.org/10.1016/j.semcdb.2024.01.007
J Cell Sci. 2024 Mar 01. pii: jcs261400. [Epub ahead of print]137(5):

The contribution of asymmetric cell division to phenotypic heterogeneity in cancer.

Julieti Huch Buss, Karine Rech Begnini, Guido Lenz.

  Cells have evolved intricate mechanisms for dividing their contents in the most symmetric way during mitosis. However, a small proportion of cell divisions results in asymmetric segregation of cellular components, which leads to differences in the characteristics of daughter cells. Although the classical function of asymmetric cell division (ACD) in the regulation of pluripotency is the generation of one differentiated daughter cell and one self-renewing stem cell, recent evidence suggests that ACD plays a role in other physiological processes. In cancer, tumor heterogeneity can result from the asymmetric segregation of genetic material and other cellular components, resulting in cell-to-cell differences in fitness and response to therapy. Defining the contribution of ACD in generating differences in key features relevant to cancer biology is crucial to advancing our understanding of the causes of tumor heterogeneity and developing strategies to mitigate or counteract it. In this Review, we delve into the occurrence of asymmetric mitosis in cancer cells and consider how ACD contributes to the variability of several phenotypes. By synthesizing the current literature, we explore the molecular mechanisms underlying ACD, the implications of phenotypic heterogeneity in cancer, and the complex interplay between these two phenomena.

Keywords:  Asymmetric cell division; Cancer heterogeneity; Cell division; Fitness; Sister cells

DOI:  https://doi.org/10.1242/jcs.261400
Proc Natl Acad Sci U S A. 2024 02 13. 121(7): e2309261121

Cell cycle plasticity underlies fractional resistance to palbociclib in ER+/HER2- breast tumor cells.

Tarek M Zikry, Samuel C Wolff, Jolene S Ranek, Harris M Davis, Ander Naugle, Namit Luthra, Austin A Whitman, Katarzyna M Kedziora, Wayne Stallaert, Michael R Kosorok, Philip M Spanheimer, Jeremy E Purvis.

  The CDK4/6 inhibitor palbociclib blocks cell cycle progression in Estrogen receptor-positive, human epidermal growth factor 2 receptor-negative (ER+/HER2-) breast tumor cells. Despite the drug's success in improving patient outcomes, a small percentage of tumor cells continues to divide in the presence of palbociclib-a phenomenon we refer to as fractional resistance. It is critical to understand the cellular mechanisms underlying fractional resistance because the precise percentage of resistant cells in patient tissue is a strong predictor of clinical outcomes. Here, we hypothesize that fractional resistance arises from cell-to-cell differences in core cell cycle regulators that allow a subset of cells to escape CDK4/6 inhibitor therapy. We used multiplex, single-cell imaging to identify fractionally resistant cells in both cultured and primary breast tumor samples resected from patients. Resistant cells showed premature accumulation of multiple G1 regulators including E2F1, retinoblastoma protein, and CDK2, as well as enhanced sensitivity to pharmacological inhibition of CDK2 activity. Using trajectory inference approaches, we show how plasticity among cell cycle regulators gives rise to alternate cell cycle "paths" that allow individual tumor cells to escape palbociclib treatment. Understanding drivers of cell cycle plasticity, and how to eliminate resistant cell cycle paths, could lead to improved cancer therapies targeting fractionally resistant cells to improve patient outcomes.

Keywords:  ER+/HER2− breast cancer; cell cycle arrest; fractional resistance; single-cell imaging; single-cell proteomics

DOI:  https://doi.org/10.1073/pnas.2309261121
Nucleic Acids Res. 2024 Feb 07. pii: gkae060. [Epub ahead of print]

LSD1 controls a nuclear checkpoint in Wnt/β-Catenin signaling to regulate muscle stem cell self-renewal.

Sandrine Mouradian, Delia Cicciarello, Nicolas Lacoste, Valérie Risson, Francesca Berretta, Fabien Le Grand, Nicolas Rose, Thomas Simonet, Laurent Schaeffer, Isabella Scionti.

The Wnt/β-Catenin pathway plays a key role in cell fate determination during development and in adult tissue regeneration by stem cells. These processes involve profound gene expression and epigenome remodeling and linking Wnt/β-Catenin signaling to chromatin modifications has been a challenge over the past decades. Functional studies of the lysine demethylase LSD1/KDM1A converge to indicate that this epigenetic regulator is a key regulator of cell fate, although the extracellular cues controlling LSD1 action remain largely unknown. Here we show that β-Catenin is a substrate of LSD1. Demethylation by LSD1 prevents β-Catenin degradation thereby maintaining its nuclear levels. Consistently, in absence of LSD1, β-Catenin transcriptional activity is reduced in both MuSCs and ESCs. Moreover, inactivation of LSD1 in mouse muscle stem cells and embryonic stem cells shows that LSD1 promotes mitotic spindle orientation via β-Catenin protein stabilization. Altogether, by inscribing LSD1 and β-Catenin in the same molecular cascade linking extracellular factors to gene expression, our results provide a mechanistic explanation to the similarity of action of canonical Wnt/β-Catenin signaling and LSD1 on stem cell fate.

DOI: https://doi.org/10.1093/nar/gkae060
Cell. 2024 Jan 31. pii: S0092-8674(24)00044-8. [Epub ahead of print]

Microglia maintain structural integrity during fetal brain morphogenesis.

Akindé René Lawrence, Alice Canzi, Cécile Bridlance, Nicolas Olivié, Claire Lansonneur, Clarissa Catale, Lara Pizzamiglio, Benoit Kloeckner, Aymeric Silvin, David A D Munro, Aurélien Fortoul, Davide Boido, Feriel Zehani, Hugues Cartonnet, Sarah Viguier, Guillaume Oller, Paola Squarzoni, Adrien Candat, Julie Helft, Cécile Allet, Francoise Watrin, Jean-Bernard Manent, Pierre Paoletti, Denis Thieffry, Laura Cantini, Clare Pridans, Josef Priller, Antoinette Gélot, Paolo Giacobini, Luisa Ciobanu, Florent Ginhoux, Morgane Sonia Thion, Ludmilla Lokmane, Sonia Garel.

  Microglia (MG), the brain-resident macrophages, play major roles in health and disease via a diversity of cellular states. While embryonic MG display a large heterogeneity of cellular distribution and transcriptomic states, their functions remain poorly characterized. Here, we uncovered a role for MG in the maintenance of structural integrity at two fetal cortical boundaries. At these boundaries between structures that grow in distinct directions, embryonic MG accumulate, display a state resembling post-natal axon-tract-associated microglia (ATM) and prevent the progression of microcavities into large cavitary lesions, in part via a mechanism involving the ATM-factor Spp1. MG and Spp1 furthermore contribute to the rapid repair of lesions, collectively highlighting protective functions that preserve the fetal brain from physiological morphogenetic stress and injury. Our study thus highlights key major roles for embryonic MG and Spp1 in maintaining structural integrity during morphogenesis, with major implications for our understanding of MG functions and brain development.

Keywords:  Spp1; amygdala; cavity; cerebral cortex; corpus callosum; development; microglia; microglial state; osteopontin; repair

DOI:  https://doi.org/10.1016/j.cell.2024.01.012
Nat Commun. 2024 Feb 03. 15(1): 1021

Phosphoglycerate kinase 1 acts as a cargo adaptor to promote EGFR transport to the lysosome.

Shao-Ling Chu, Jia-Rong Huang, Yu-Tzu Chang, Shu-Yun Yao, Jia-Shu Yang, Victor W Hsu, Jia-Wei Hsu.

The epidermal growth factor receptor (EGFR) plays important roles in multiple cellular events, including growth, differentiation, and motility. A major mechanism of downregulating EGFR function involves its endocytic transport to the lysosome. Sorting of proteins into intracellular pathways involves cargo adaptors recognizing sorting signals on cargo proteins. A dileucine-based sorting signal has been identified previously for the sorting of endosomal EGFR to the lysosome, but a cargo adaptor that recognizes this signal remains unknown. Here, we find that phosphoglycerate kinase 1 (PGK1) is recruited to endosomal membrane upon its phosphorylation, where it binds to the dileucine sorting signal in EGFR to promote the lysosomal transport of this receptor. We also elucidate two mechanisms that act in concert to promote PGK1 recruitment to endosomal membrane, a lipid-based mechanism that involves phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] and a protein-based mechanism that involves hepatocyte growth factor receptor substrate (Hrs). These findings reveal an unexpected function for a metabolic enzyme and advance the mechanistic understanding of how EGFR is transported to the lysosome.

DOI: https://doi.org/10.1038/s41467-024-45443-4
Proc Natl Acad Sci U S A. 2024 Feb 13. 121(7): e2306993121

Puromycin reveals a distinct conformation of neuronal ribosomes.

Mina N Anadolu, Jingyu Sun, Jewel T-Y Li, Tyson E Graber, Joaquin Ortega, Wayne S Sossin.

  Puromycin is covalently added to the nascent chain of proteins by the peptidyl transferase activity of the ribosome and the dissociation of the puromycylated peptide typically follows this event. It was postulated that blocking the translocation of the ribosome with emetine could retain the puromycylated peptide on the ribosome, but evidence against this has recently been published [Hobson et al., Elife 9, e60048 (2020); and Enam et al., Elife 9, e60303 (2020)]. In neurons, puromycylated nascent chains remain in the ribosome even in the absence of emetine, yet direct evidence for this has been lacking. Using biochemistry and cryoelectron microscopy, we show that the puromycylated peptides remain in the ribosome exit channel in the large subunit in a subset of neuronal ribosomes stalled in the hybrid state. These results validate previous experiments to localize stalled polysomes in neurons and provide insight into how neuronal ribosomes are stalled. Moreover, in these hybrid-state neuronal ribosomes, anisomycin, which usually blocks puromycylation, competes poorly with puromycin in the puromycylation reaction, allowing a simple assay to determine the proportion of nascent chains that are stalled in this state. In early hippocampal neuronal cultures, over 50% of all nascent peptides are found in these stalled polysomes. These results provide insights into the stalling mechanisms of neuronal ribosomes and suggest that puromycylated peptides can be used to reveal subcellular sites of hybrid-state stalled ribosomes in neurons.

Keywords:  local translation; neuron; puromycin; puromycylation; stalled polysomes

DOI:  https://doi.org/10.1073/pnas.2306993121
Nat Commun. 2024 Feb 09. 15(1): 1222

Protein thermal sensing regulates physiological amyloid aggregation.

Dane Marijan, Evgenia A Momchilova, Daniel Burns, Sahil Chandhok, Richard Zapf, Holger Wille, Davit A Potoyan, Timothy E Audas.

To survive, cells must respond to changing environmental conditions. One way that eukaryotic cells react to harsh stimuli is by forming physiological, RNA-seeded subnuclear condensates, termed amyloid bodies (A-bodies). The molecular constituents of A-bodies induced by different stressors vary significantly, suggesting this pathway can tailor the cellular response by selectively aggregating a subset of proteins under a given condition. Here, we identify critical structural elements that regulate heat shock-specific amyloid aggregation. Our data demonstrates that manipulating structural pockets in constituent proteins can either induce or restrict their A-body targeting at elevated temperatures. We propose a model where selective aggregation within A-bodies is mediated by the thermal stability of a protein, with temperature-sensitive structural regions acting as an intrinsic form of post-translational regulation. This system would provide cells with a rapid and stress-specific response mechanism, to tightly control physiological amyloid aggregation or other cellular stress response pathways.

DOI: https://doi.org/10.1038/s41467-024-45536-0
J Mol Cell Cardiol. 2024 Feb;pii: S0022-2828(23)00197-9. [Epub ahead of print]187 101-117

The alpha-1A adrenergic receptor regulates mitochondrial oxidative metabolism in the mouse heart.

Peyton B Sandroni, Melissa A Schroder, Hunter T Hawkins, Julian D Bailon, Wei Huang, James T Hagen, McLane Montgomery, Seok J Hong, Andrew L Chin, Jiandong Zhang, Manoj C Rodrigo, Boa Kim, Paul C Simpson, Jonathan C Schisler, Jessica M Ellis, Kelsey H Fisher-Wellman, Brian C Jensen.

   AIMS: The sympathetic nervous system regulates numerous critical aspects of mitochondrial function in the heart through activation of adrenergic receptors (ARs) on cardiomyocytes. Mounting evidence suggests that α1-ARs, particularly the α1A subtype, are cardioprotective and may mitigate the deleterious effects of chronic β-AR activation by shared ligands. The mechanisms underlying these adaptive effects remain unclear. Here, we tested the hypothesis that α1A-ARs adaptively regulate cardiomyocyte oxidative metabolism in both the uninjured and infarcted heart.
METHODS: We used high resolution respirometry, fatty acid oxidation (FAO) enzyme assays, substrate-specific electron transport chain (ETC) enzyme assays, transmission electron microscopy (TEM) and proteomics to characterize mitochondrial function comprehensively in the uninjured hearts of wild type and α1A-AR knockout mice and defined the effects of chronic β-AR activation and myocardial infarction on selected mitochondrial functions.
RESULTS: We found that isolated cardiac mitochondria from α1A-KO mice had deficits in fatty acid-dependent respiration, FAO, and ETC enzyme activity. TEM revealed abnormalities of mitochondrial morphology characteristic of these functional deficits. The selective α1A-AR agonist A61603 enhanced fatty-acid dependent respiration, fatty acid oxidation, and ETC enzyme activity in isolated cardiac mitochondria. The β-AR agonist isoproterenol enhanced oxidative stress in vitro and this adverse effect was mitigated by A61603. A61603 enhanced ETC Complex I activity and protected contractile function following myocardial infarction.
CONCLUSIONS: Collectively, these novel findings position α1A-ARs as critical regulators of cardiomyocyte metabolism in the basal state and suggest that metabolic mechanisms may underlie the protective effects of α1A-AR activation in the failing heart.

Keywords:  Adrenergic; Alpha; Basal metabolism; Heart; Lipid metabolism; Mitochondria; Oxidative phosphorylation; Receptors

DOI:  https://doi.org/10.1016/j.yjmcc.2023.12.003
Nature. 2024 Feb 07.

Translation selectively destroys non-functional transcription complexes.

Jason Woodgate, Hamed Mosaei, Pavel Brazda, Flint Stevenson-Jones, Nikolay Zenkin.

Transcription elongation stalls at lesions in the DNA template1. For the DNA lesion to be repaired, the stalled transcription elongation complex (EC) has to be removed from the damaged site2. Here we show that translation, which is coupled to transcription in bacteria, actively dislodges stalled ECs from the damaged DNA template. By contrast, paused, but otherwise elongation-competent, ECs are not dislodged by the ribosome. Instead, they are helped back into processive elongation. We also show that the ribosome slows down when approaching paused, but not stalled, ECs. Our results indicate that coupled ribosomes functionally and kinetically discriminate between paused ECs and stalled ECs, ensuring the selective destruction of only the latter. This functional discrimination is controlled by the RNA polymerase's catalytic domain, the Trigger Loop. We show that the transcription-coupled DNA repair helicase UvrD, proposed to cause backtracking of stalled ECs3, does not interfere with ribosome-mediated dislodging. By contrast, the transcription-coupled DNA repair translocase Mfd4 acts synergistically with translation, and dislodges stalled ECs that were not destroyed by the ribosome. We also show that a coupled ribosome efficiently destroys misincorporated ECs that can cause conflicts with replication5. We propose that coupling to translation is an ancient and one of the main mechanisms of clearing non-functional ECs from the genome.

DOI: https://doi.org/10.1038/s41586-023-07014-3