bims-ginsta Biomed News
on Genome instability
Issue of 2024–06–16
25 papers selected by
Jinrong Hu, National University of Singapore
  1. Torques within and outside the human spindle balance twist at anaphase.
  2. Nucleolar organization and ribosomal DNA stability in response to DNA damage.
  3. Chromatin-associated cohesin turns over extensively and forms new cohesive linkages in Drosophila oocytes during meiotic prophase.
  4. Quantitative imaging of loop extruders rebuilding interphase genome architecture after mitosis.
  5. A temporal allocation of amino acid resources ensures fitness and body allometry in Drosophila.
  6. Single-cell proteomics reveals decreased abundance of proteostasis and meiosis proteins in advanced maternal age oocytes.
  7. Single-nucleus multi-omic profiling of polyploid heart nuclei identifies fusion-derived cardiomyocytes in the human heart.
  8. Proteolysis-free amoeboid migration of melanoma cells through crowded environments via bleb-driven worrying.
  9. Mechanochemical Principles of Epidermal Tissue Dynamics.
  10. Measuring and modeling the dynamics of mitotic error correction.
  11. The relationship between nanoscale genome organization and gene expression in mouse embryonic stem cells during pluripotency transition.
  12. DNA damage causes ATM-dependent heterochromatin loss leading to nuclear softening, blebbing, and rupture.
  13. Tissue-intrinsic beta-catenin signals antagonize Nodal-driven anterior visceral endoderm differentiation.
  14. Myosin II mediates Shh signals to shape dental epithelia via control of cell adhesion and movement.
  15. MTFP1 controls mitochondrial fusion to regulate inner membrane quality control and maintain mtDNA levels.
  16. TERRA transcripts localize at long telomeres to regulate telomerase access to chromosome ends.
  17. Dermal TRPV1 innervations engage a macrophage- and fibroblast-containing pathway to activate hair growth in mice.
  18. Ribosomal DNA copy number is associated with body mass in humans and other mammals.
  19. Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies.
  20. TRIM35 Monoubiquitinates H2B in Cardiac Cells, Implications for Heart Failure.
  21. Molecular mechanism of the ischemia-induced regulatory switch in mammalian complex I.
  22. A mechanical transition from tension to buckling underlies the jigsaw puzzle shape morphogenesis of histoblasts in the Drosophila epidermis.
  23. Metabolic inflexibility promotes mitochondrial health during liver regeneration.
  24. Generation of mouse and rat xenogeneic ovaries in vitro for production of mouse oocyte.
  25. Bioengineered human colon organoids with in vivo-like cellular complexity and function.
  1. J Cell Biol. 2024 Sep 02. pii: e202312046. [Epub ahead of print]223(9):
    Torques within and outside the human spindle balance twist at anaphase.
    Lila Neahring, Nathan H Cho, Yifei He, 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, 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 together 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.
    DOI:  https://doi.org/10.1083/jcb.202312046
  2. Curr Opin Cell Biol. 2024 Jun 10. pii: S0955-0674(24)00059-0. [Epub ahead of print]89 102380
    Nucleolar organization and ribosomal DNA stability in response to DNA damage.
    Stavroula Boukoura, Dorthe Helena Larsen.
      Eukaryotic nuclei are structured into sub-compartments orchestrating various cellular functions. The nucleolus is the largest nuclear organelle: a biomolecular condensate with an architecture composed of immiscible fluids facilitating ribosome biogenesis. The nucleolus forms upon the transcription of the repetitive ribosomal RNA genes (rDNA) that cluster in this compartment. rDNA is intrinsically unstable and prone to rearrangements and copy number variation. Upon DNA damage, a specialized nucleolar-DNA Damage Response (n-DDR) is activated: nucleolar transcription is inhibited, the architecture is rearranged, and rDNA is relocated to the nucleolar periphery. Recent data have highlighted how the composition of nucleoli, its structure, chemical and physical properties, contribute to rDNA stability. In this mini-review we focus on recent data that start to reveal how nucleolar composition and the n-DDR work together to ensure rDNA integrity.
    DOI:  https://doi.org/10.1016/j.ceb.2024.102380
  3. Curr Biol. 2024 Jun 06. pii: S0960-9822(24)00677-8. [Epub ahead of print]
    Chromatin-associated cohesin turns over extensively and forms new cohesive linkages in Drosophila oocytes during meiotic prophase.
    Muhammad A Haseeb, Katherine A Weng, Sharon E Bickel.
      In dividing cells, accurate chromosome segregation depends on sister chromatid cohesion, protein linkages that are established during DNA replication. Faithful chromosome segregation in oocytes requires that cohesion, first established in S phase, remain intact for days to decades, depending on the organism. Premature loss of meiotic cohesion in oocytes leads to the production of aneuploid gametes and contributes to the increased incidence of meiotic segregation errors as women age (maternal age effect). The prevailing model is that cohesive linkages do not turn over in mammalian oocytes. However, we have previously reported that cohesion-related defects arise in Drosophila oocytes when individual cohesin subunits or cohesin regulators are knocked down after meiotic S phase. Here, we use two strategies to express a tagged cohesin subunit exclusively during mid-prophase in Drosophila oocytes and demonstrate that newly expressed cohesin is used to form de novo linkages after meiotic S phase. Cohesin along the arms of oocyte chromosomes appears to completely turn over within a 2-day window during prophase, whereas replacement is less extensive at centromeres. Unlike S-phase cohesion establishment, the formation of new cohesive linkages during meiotic prophase does not require acetylation of conserved lysines within the Smc3 head. Our findings indicate that maintenance of cohesion between S phase and chromosome segregation in Drosophila oocytes requires an active cohesion rejuvenation program that generates new cohesive linkages during meiotic prophase.
    Keywords:  Drosophila; Smc1 tag-switch; cohesin; meiosis; oocyte; sister chromatid cohesion; synaptonemal complex
    DOI:  https://doi.org/10.1016/j.cub.2024.05.034
  4. bioRxiv. 2024 May 30. pii: 2024.05.29.596439. [Epub ahead of print]
    Quantitative imaging of loop extruders rebuilding interphase genome architecture after mitosis.
    Andreas Brunner, Natalia Rosalia Morero, Wanlu Zhang, M Julius Hossain, Marko Lampe, Hannah Pflaumer, Aliaksandr Halavatyi, Jan-Michael Peters, Kai S Beckwith, Jan Ellenberg.
      How cells establish the interphase genome organization after mitosis is incompletely understood. Using quantitative and super-resolution microscopy, we show that the transition from a Condensin to a Cohesin-based genome organization occurs dynamically over two hours. While a significant fraction of Condensins remains chromatin-bound until early Gl, Cohesin-STAGl and its boundary factor CTCF are rapidly imported into daughter nuclei in telophase, immediately bind chromosomes as individual complexes and are sufficient to build the first interphase TAD structures. By contrast, the more abundant Cohesin-STAG2 accumulates on chromosomes only gradually later in Gl, is responsible for compaction inside TAD structures and forms paired complexes upon completed nuclear import. 0ur quantitative time-resolved mapping of mitotic and interphase loop extruders in single cells reveals that the nested loop architecture formed by sequential action of two Condensins in mitosis is seamlessly replaced by a less compact, but conceptually similar hierarchically nested loop architecture driven by sequential action of two Cohesins.
    DOI:  https://doi.org/10.1101/2024.05.29.596439
  5. Dev Cell. 2024 Jun 02. pii: S1534-5807(24)00336-8. [Epub ahead of print]
    A temporal allocation of amino acid resources ensures fitness and body allometry in Drosophila.
    Luca Valzania, Aya Alami, Pierre Léopold.
      Organisms have evolved strategies to store resources and overcome periods of low or no nutrient access, including transient shortages or longer non-feeding developmental transitions. Holometabolous insects like Drosophila represent an attractive model to study resource allocation during development because they alternate feeding and non-feeding periods. Amino acids are essential components for tissue growth and renewal, but the strategies used for their storage remain largely unexplored. Here, we characterize the molecular mechanisms for the temporal production, accumulation, and use of specific storage proteins called hexamerins, and demonstrate their role in ensuring tissue formation and adult fitness. Moreover, we show that preventing hexamerin stores enhances the growth of early-developing organs while compromising the emergence of late-forming ones, consequently altering body allometry.
    Keywords:  Drosophila; allometry; growth; hexamerin; nutrition
    DOI:  https://doi.org/10.1016/j.devcel.2024.05.018
  6. Mol Hum Reprod. 2024 Jun 13. pii: gaae023. [Epub ahead of print]
    Single-cell proteomics reveals decreased abundance of proteostasis and meiosis proteins in advanced maternal age oocytes.
    Styliani Galatidou, Aleksandra A Petelski, Aïda Pujol, Karinna Lattes, Lais B Latorraca, Trudee Fair, Mina Popovic, Rita Vassena, Nikolai Slavov, Montserrat Barragán.
      Advanced maternal age is associated with a decline in oocyte quality, which often leads to reproductive failure in humans. However, the mechanisms behind this age-related decline remain unclear. To gain insights into this phenomenon, we applied plexDIA, a multiplexed data-independent acquisition, single-cell mass spectrometry method, to analyze the proteome of oocytes from both young women and women of advanced maternal age. Our findings primarily revealed distinct proteomic profiles between immature fully grown germinal vesicle and mature metaphase II oocytes. Importantly, we further show that a woman's age is associated with changes in her oocyte proteome. Specifically, when compared to oocytes obtained from young women, advanced maternal age oocytes exhibited lower levels of the proteasome and TRiC complex, as well as other key regulators of proteostasis and meiosis. This suggests that aging adversely affects the proteostasis and meiosis networks in human oocytes. The proteins identified in this study hold potential as targets for improving oocyte quality and may guide future studies into the molecular processes underlying oocyte aging.
    Keywords:  advanced maternal age; aging; human oocytes; meiosis; oocyte quality; proteostasis; single-cell proteomics
    DOI:  https://doi.org/10.1093/molehr/gaae023
  7. Res Sq. 2024 May 30. pii: rs.3.rs-4414468. [Epub ahead of print]
    Single-nucleus multi-omic profiling of polyploid heart nuclei identifies fusion-derived cardiomyocytes in the human heart.
    Sangita Choudhury, Indu Sivankutty, Youngsook Jung, August Huang, Sarah Araten, Connor Kenny, Zheming An, Ryan Doan, Floris Foijer, Erica Matsu, Ila Rosen, Jack Marciano, Asish Jain, Liang Sun, Nazia Hilal, Eunjung Lee, Christopher Walsh, Ming Chen.
      Understanding the mechanisms of polyploidization in cardiomyocytes is crucial for advancing strategies to stimulate myocardial regeneration. Although endoreplication has long been considered the primary source of polyploid human cardiomyocytes, recent animal work suggests the potential for cardiomyocyte fusion. Moreover, the effects of polyploidization on the genomic-transcriptomic repertoire of human cardiomyocytes have not been studied previously. We applied single-nuclei whole genome sequencing, single nuclei RNA sequencing, and multiome ATAC + gene expression (from the same nuclei) techniques to nuclei isolated from 11 healthy hearts. Utilizing post-zygotic non-inherited somatic mutations occurring during development as "endogenous barcodes," to reconstruct lineage relationships of polyploid cardiomyocytes. Of 482 cardiomyocytes from multiple healthy donor hearts 75.7% can be sorted into several developmental clades marked by one or more somatic single-nucleotide variants (SNVs). At least ~10% of tetraploid cardiomyocytes contain cells from distinct clades, indicating fusion of lineally distinct cells, whereas 60% of higher-ploidy cardiomyocytes contain fused cells from distinct clades. Combined snRNA-seq and snATAC-seq revealed transcriptome and chromatin landscapes of polyploid cardiomyocytes distinct from diploid cardiomyocytes, and show some higher-ploidy cardiomyocytes with transcriptional signatures suggesting fusion between cardiomyocytes and endothelial and fibroblast cells. These observations provide the first evidence for cell and nuclear fusion of human cardiomyocytes, raising the possibility that cell fusion may contribute to developing or maintaining polyploid cardiomyocytes in the human heart.
    DOI:  https://doi.org/10.21203/rs.3.rs-4414468/v1
  8. Dev Cell. 2024 Jun 05. pii: S1534-5807(24)00342-3. [Epub ahead of print]
    Proteolysis-free amoeboid migration of melanoma cells through crowded environments via bleb-driven worrying.
    Meghan K Driscoll, Erik S Welf, Andrew Weems, Etai Sapoznik, Felix Zhou, Vasanth S Murali, Juan Manuel García-Arcos, Minna Roh-Johnson, Matthieu Piel, Kevin M Dean, Reto Fiolka, Gaudenz Danuser.
      In crowded microenvironments, migrating cells must find or make a path. Amoeboid cells are thought to find a path by deforming their bodies to squeeze through tight spaces. Yet, some amoeboid cells seem to maintain a near-spherical morphology as they move. To examine how they do so, we visualized amoeboid human melanoma cells in dense environments and found that they carve tunnels via bleb-driven degradation of extracellular matrix components without the need for proteolytic degradation. Interactions between adhesions and collagen at the cell front induce a signaling cascade that promotes bleb enlargement via branched actin polymerization. Large blebs abrade collagen, creating feedback between extracellular matrix structure, cell morphology, and polarization that enables both path generation and persistent movement.
    Keywords:  amoeboid; blebbing; cell migration; computer vision; extracellular matrix remodeling; fluorescence microscopy; light-sheet microscopy; macropinocytosis; melanoma
    DOI:  https://doi.org/10.1016/j.devcel.2024.05.024
  9. Cold Spring Harb Perspect Biol. 2024 Jun 10. pii: a041518. [Epub ahead of print]
    Mechanochemical Principles of Epidermal Tissue Dynamics.
    Carien M Niessen, M Lisa Manning, Sara A Wickström.
      How tissue architecture and function emerge during development and what facilitates their resilience and homeostatic dynamics during adulthood is a fundamental question in biology. Biological tissue barriers such as the skin epidermis have evolved strategies that integrate dynamic cellular turnover with high resilience against mechanical and chemical stresses. Interestingly, both dynamic and resilient functions are generated by a defined set of molecular and cell-scale processes, including adhesion and cytoskeletal remodeling, cell shape changes, cell division, and cell movement. These traits are coordinated in space and time with dynamic changes in cell fates and cell mechanics that are generated by contractile and adhesive forces. In this review, we discuss how studies on epidermal morphogenesis and homeostasis have contributed to our understanding of the dynamic interplay between biochemical and mechanical signals during tissue morphogenesis and homeostasis, and how the material properties of tissues dictate how cells respond to these active stresses, thereby linking cell-scale behaviors to tissue- and organismal-scale changes.
    DOI:  https://doi.org/10.1101/cshperspect.a041518
  10. Proc Natl Acad Sci U S A. 2024 Jun 18. 121(25): e2323009121
    Measuring and modeling the dynamics of mitotic error correction.
    Gloria Ha, Paul Dieterle, Hao Shen, Ariel Amir, Daniel J Needleman.
      Error correction is central to many biological systems and is critical for protein function and cell health. During mitosis, error correction is required for the faithful inheritance of genetic material. When functioning properly, the mitotic spindle segregates an equal number of chromosomes to daughter cells with high fidelity. Over the course of spindle assembly, many initially erroneous attachments between kinetochores and microtubules are fixed through the process of error correction. Despite the importance of chromosome segregation errors in cancer and other diseases, there is a lack of methods to characterize the dynamics of error correction and how it can go wrong. Here, we present an experimental method and analysis framework to quantify chromosome segregation error correction in human tissue culture cells with live cell confocal imaging, timed premature anaphase, and automated counting of kinetochores after cell division. We find that errors decrease exponentially over time during spindle assembly. A coarse-grained model, in which errors are corrected in a chromosome-autonomous manner at a constant rate, can quantitatively explain both the measured error correction dynamics and the distribution of anaphase onset times. We further validated our model using perturbations that destabilized microtubules and changed the initial configuration of chromosomal attachments. Taken together, this work provides a quantitative framework for understanding the dynamics of mitotic error correction.
    Keywords:  anaphase timing; chromosome segregation; coarse-grained modeling; error correction; mitosis
    DOI:  https://doi.org/10.1073/pnas.2323009121
  11. Nucleic Acids Res. 2024 Jun 08. pii: gkae476. [Epub ahead of print]
    The relationship between nanoscale genome organization and gene expression in mouse embryonic stem cells during pluripotency transition.
    Ximena Garate, Pablo Aurelio Gómez-García, Manuel Fernández Merino, Marta Cadevall Angles, Chenggan Zhu, Alvaro Castells-García, Ilyas Ed-Daoui, Laura Martin, Hiroshi Ochiai, Maria Victoria Neguembor, Maria Pia Cosma.
      During early development, gene expression is tightly regulated. However, how genome organization controls gene expression during the transition from naïve embryonic stem cells to epiblast stem cells is still poorly understood. Using single-molecule microscopy approaches to reach nanoscale resolution, we show that genome remodeling affects gene transcription during pluripotency transition. Specifically, after exit from the naïve pluripotency state, chromatin becomes less compacted, and the OCT4 transcription factor has lower mobility and is more bound to its cognate sites. In epiblast cells, the active transcription hallmark, H3K9ac, decreases within the Oct4 locus, correlating with reduced accessibility of OCT4 and, in turn, with reduced expression of Oct4 nascent RNAs. Despite the high variability in the distances between active pluripotency genes, distances between Nodal and Oct4 decrease during epiblast specification. In particular, highly expressed Oct4 alleles are closer to nuclear speckles during all stages of the pluripotency transition, while only a distinct group of highly expressed Nodal alleles are in close proximity to Oct4 when associated with a nuclear speckle in epiblast cells. Overall, our results provide new insights into the role of the spatiotemporal genome remodeling during mouse pluripotency transition and its correlation with the expression of key pluripotency genes.
    DOI:  https://doi.org/10.1093/nar/gkae476
  12. bioRxiv. 2024 May 29. pii: 2024.05.24.595790. [Epub ahead of print]
    DNA damage causes ATM-dependent heterochromatin loss leading to nuclear softening, blebbing, and rupture.
    Nebiyat Eskndir, Manseeb Hossain, Marilena L Currey, Mai Pho, Yasmin Berrada, Andrew D Stephens.
      The nucleus must maintain stiffness to protect the shape and integrity of the nucleus to ensure proper function. Defects in nuclear stiffness caused from chromatin and lamin perturbations produce abnormal nuclear shapes common in aging, heart disease, and cancer. Loss of nuclear shape via protrusions called blebs leads to nuclear rupture that is well-established to cause nuclear dysfunction, including DNA damage. However, it remains unknown how increased DNA damage affects nuclear stiffness, shape, and ruptures, which could create a negative feedback loop. To determine if increased DNA damage alters nuclear physical properties, we treated MEF cells with DNA damage drugs cisplatin and bleomycin. DNA damage drugs caused increased nuclear blebbing and rupture in interphase nuclei within a few hours and independent of mitosis. Micromanipulation force measurements reveal that DNA damage decreased chromatin-based nuclear mechanics but did not change lamin-based strain stiffening at long extensions relative to wild type. Immunofluorescence measurements of DNA damage treatments reveal the mechanism is an ATM-dependent decrease in heterochromatin leading to nuclear weaken, blebbing, and rupture which can be rescued upon ATM inhibition treatment. Thus, DNA damage drugs cause ATM-dependent heterochromatin loss resulting in nuclear softening, blebbing, and rupture.
    DOI:  https://doi.org/10.1101/2024.05.24.595790
  13. Nat Commun. 2024 Jun 13. 15(1): 5055
    Tissue-intrinsic beta-catenin signals antagonize Nodal-driven anterior visceral endoderm differentiation.
    Sina Schumacher, Max Fernkorn, Michelle Marten, Rui Chen, Yung Su Kim, Ivan Bedzhov, Christian Schröter.
      The anterior-posterior axis of the mammalian embryo is laid down by the anterior visceral endoderm (AVE), an extraembryonic signaling center that is specified within the visceral endoderm. Current models posit that AVE differentiation is promoted globally by epiblast-derived Nodal signals, and spatially restricted by a BMP gradient established by the extraembryonic ectoderm. Here, we report spatially restricted AVE differentiation in bilayered embryo-like aggregates made from mouse embryonic stem cells that lack an extraembryonic ectoderm. Notably, clusters of AVE cells also form in pure visceral endoderm cultures upon activation of Nodal signaling, indicating that tissue-intrinsic factors can restrict AVE differentiation. We identify β-catenin activity as a tissue-intrinsic factor that antagonizes AVE-inducing Nodal signals. Together, our results show how an AVE-like population can arise through interactions between epiblast and visceral endoderm alone. This mechanism may be a flexible solution for axis patterning in a wide range of embryo geometries, and provide robustness to axis patterning when coupled with signal gradients.
    DOI:  https://doi.org/10.1038/s41467-024-49380-0
  14. PLoS Genet. 2024 Jun 10. 20(6): e1011326
    Myosin II mediates Shh signals to shape dental epithelia via control of cell adhesion and movement.
    Wei Du, Adya Verma, Qianlin Ye, Wen Du, Sandy Lin, Atsushi Yamanaka, Ophir D Klein, Jimmy K Hu.
      The development of ectodermal organs begins with the formation of a stratified epithelial placode that progressively invaginates into the underlying mesenchyme as the organ takes its shape. Signaling by secreted molecules is critical for epithelial morphogenesis, but how that information leads to cell rearrangement and tissue shape changes remains an open question. Using the mouse dentition as a model, we first establish that non-muscle myosin II is essential for dental epithelial invagination and show that it functions by promoting cell-cell adhesion and persistent convergent cell movements in the suprabasal layer. Shh signaling controls these processes by inducing myosin II activation via AKT. Pharmacological induction of AKT and myosin II can also rescue defects caused by the inhibition of Shh. Together, our results support a model in which the Shh signal is transmitted through myosin II to power effective cellular rearrangement for proper dental epithelial invagination.
    DOI:  https://doi.org/10.1371/journal.pgen.1011326
  15. Cell. 2024 Jun 05. pii: S0092-8674(24)00526-9. [Epub ahead of print]
    MTFP1 controls mitochondrial fusion to regulate inner membrane quality control and maintain mtDNA levels.
    Luis Carlos Tábara, Stephen P Burr, Michele Frison, Suvagata R Chowdhury, Vincent Paupe, Yu Nie, Mark Johnson, Jara Villar-Azpillaga, Filipa Viegas, Mayuko Segawa, Hanish Anand, Kasparas Petkevicius, Patrick F Chinnery, Julien Prudent.
      Mitochondrial dynamics play a critical role in cell fate decisions and in controlling mtDNA levels and distribution. However, the molecular mechanisms linking mitochondrial membrane remodeling and quality control to mtDNA copy number (CN) regulation remain elusive. Here, we demonstrate that the inner mitochondrial membrane (IMM) protein mitochondrial fission process 1 (MTFP1) negatively regulates IMM fusion. Moreover, manipulation of mitochondrial fusion through the regulation of MTFP1 levels results in mtDNA CN modulation. Mechanistically, we found that MTFP1 inhibits mitochondrial fusion to isolate and exclude damaged IMM subdomains from the rest of the network. Subsequently, peripheral fission ensures their segregation into small MTFP1-enriched mitochondria (SMEM) that are targeted for degradation in an autophagic-dependent manner. Remarkably, MTFP1-dependent IMM quality control is essential for basal nucleoid recycling and therefore to maintain adequate mtDNA levels within the cell.
    Keywords:  IMM quality control; IMM remodeling; MTFP1; autophagy; fission and fusion; mitochondria; mitochondrial dynamics; mitophagy; mtDNA
    DOI:  https://doi.org/10.1016/j.cell.2024.05.017
  16. Sci Adv. 2024 Jun 14. 10(24): eadk4387
    TERRA transcripts localize at long telomeres to regulate telomerase access to chromosome ends.
    Nicole Bettin, Emmanuelle Querido, Irene Gialdini, Glenda Paola Grupelli, Elena Goretti, Marta Cantarelli, Marta Andolfato, Eslam Soror, Alessandra Sontacchi, Katarina Jurikova, Pascal Chartrand, Emilio Cusanelli.
      The function of TERRA in the regulation of telomerase in human cells is still debated. While TERRA interacts with telomerase, how it regulates telomerase function remains unknown. Here, we show that TERRA colocalizes with the telomerase RNA subunit hTR in the nucleoplasm and at telomeres during different phases of the cell cycle. We report that TERRA transcripts relocate away from chromosome ends during telomere lengthening, leading to a reduced number of telomeric TERRA-hTR molecules and consequent increase in "TERRA-free" telomerase molecules at telomeres. Using live-cell imaging and super-resolution microscopy, we show that upon transcription, TERRA relocates from its telomere of origin to long chromosome ends. Furthermore, TERRA depletion by antisense oligonucleotides promoted hTR localization to telomeres, leading to increased residence time and extended half-life of hTR molecules at telomeres. Overall, our findings indicate that telomeric TERRA transcripts inhibit telomere elongation by telomerase acting in trans, impairing telomerase access to telomeres that are different from their chromosome end of origin.
    DOI:  https://doi.org/10.1126/sciadv.adk4387
  17. Dev Cell. 2024 Jun 04. pii: S1534-5807(24)00337-X. [Epub ahead of print]
    Dermal TRPV1 innervations engage a macrophage- and fibroblast-containing pathway to activate hair growth in mice.
    Tamar L Ben-Shaanan, Konrad Knöpper, Lihui Duan, Ruiqi Liu, Hanna Taglinao, Ying Xu, Jinping An, Maksim V Plikus, Jason G Cyster.
      Pain, detected by nociceptors, is an integral part of injury, yet whether and how it can impact tissue physiology and recovery remain understudied. Here, we applied chemogenetics in mice to locally activate dermal TRPV1 innervations in naive skin and found that it triggered new regenerative cycling by dormant hair follicles (HFs). This was preceded by rapid apoptosis of dermal macrophages, mediated by the neuropeptide calcitonin gene-related peptide (CGRP). TRPV1 activation also triggered a macrophage-dependent induction of osteopontin (Spp1)-expressing dermal fibroblasts. The neuropeptide CGRP and the extracellular matrix protein Spp1 were required for the nociceptor-triggered hair growth. Finally, we showed that epidermal abrasion injury induced Spp1-expressing dermal fibroblasts and hair growth via a TRPV1 neuron and CGRP-dependent mechanism. Collectively, these data demonstrated a role for TRPV1 nociceptors in orchestrating a macrophage and fibroblast-supported mechanism to promote hair growth and enabling the efficient restoration of this mechano- and thermo-protective barrier after wounding.
    Keywords:  CGRP; Spp1; TRPV1; fibroblasts; hair; injury; macrophages; neurons; pain; skin
    DOI:  https://doi.org/10.1016/j.devcel.2024.05.019
  18. Nat Commun. 2024 Jun 12. 15(1): 5006
    Ribosomal DNA copy number is associated with body mass in humans and other mammals.
    Pui Pik Law, Liudmila A Mikheeva, Francisco Rodriguez-Algarra, Fredrika Asenius, Maria Gregori, Robert A E Seaborne, Selin Yildizoglu, James R C Miller, Hemanth Tummala, Robin Mesnage, Michael N Antoniou, Weilong Li, Qihua Tan, Sara L Hillman, Vardhman K Rakyan, David J Williams, Michelle L Holland.
      Body mass results from a complex interplay between genetics and environment. Previous studies of the genetic contribution to body mass have excluded repetitive regions due to the technical limitations of platforms used for population scale studies. Here we apply genome-wide approaches, identifying an association between adult body mass and the copy number (CN) of 47S-ribosomal DNA (rDNA). rDNA codes for the 18 S, 5.8 S and 28 S ribosomal RNA (rRNA) components of the ribosome. In mammals, there are hundreds of copies of these genes. Inter-individual variation in the rDNA CN has not previously been associated with a mammalian phenotype. Here, we show that rDNA CN variation associates with post-pubertal growth rate in rats and body mass index in adult humans. rDNA CN is not associated with rRNA transcription rates in adult tissues, suggesting the mechanistic link occurs earlier in development. This aligns with the observation that the association emerges by early adulthood.
    DOI:  https://doi.org/10.1038/s41467-024-49397-5
  19. Cell. 2024 Jun 07. pii: S0092-8674(24)00534-8. [Epub ahead of print]
    Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies.
    Natasha I Edman, Ashish Phal, Rachel L Redler, Thomas Schlichthaerle, Sanjay R Srivatsan, Devon Duron Ehnes, Ali Etemadi, Seong J An, Andrew Favor, Zhe Li, Florian Praetorius, Max Gordon, Thomas Vincent, Silvia Marchiano, Leslie Blakely, Chuwei Lin, Wei Yang, Brian Coventry, Derrick R Hicks, Longxing Cao, Neville Bethel, Piper Heine, Analisa Murray, Stacey Gerben, Lauren Carter, Marcos Miranda, Babak Negahdari, Sangwon Lee, Cole Trapnell, Ying Zheng, Charles E Murry, Devin K Schweppe, Benjamin S Freedman, Lance Stewart, Damian C Ekiert, Joseph Schlessinger, Jay Shendure, Gira Bhabha, Hannele Ruohola-Baker, David Baker.
      Many growth factors and cytokines signal by binding to the extracellular domains of their receptors and driving association and transphosphorylation of the receptor intracellular tyrosine kinase domains, initiating downstream signaling cascades. To enable systematic exploration of how receptor valency and geometry affect signaling outcomes, we designed cyclic homo-oligomers with up to 8 subunits using repeat protein building blocks that can be modularly extended. By incorporating a de novo-designed fibroblast growth factor receptor (FGFR)-binding module into these scaffolds, we generated a series of synthetic signaling ligands that exhibit potent valency- and geometry-dependent Ca2+ release and mitogen-activated protein kinase (MAPK) pathway activation. The high specificity of the designed agonists reveals distinct roles for two FGFR splice variants in driving arterial endothelium and perivascular cell fates during early vascular development. Our designed modular assemblies should be broadly useful for unraveling the complexities of signaling in key developmental transitions and for developing future therapeutic applications.
    Keywords:  FGF signaling; binder design; cryo-EM; de novo protein design; endothelial cell differentiation; iPSCs; oligomeric scaffolds; vascular development
    DOI:  https://doi.org/10.1016/j.cell.2024.05.025
  20. Circ Res. 2024 Jun 11.
    TRIM35 Monoubiquitinates H2B in Cardiac Cells, Implications for Heart Failure.
    Maria Areli Lorenzana-Carrillo, Saymon Tejay, Joseph Nanoa, Guocheng Huang, Yongsheng Liu, Alois Haromy, Yuan Yuan Zhao, Michelle Mendiola Pla, Dawn E Bowles, Adam Kinnaird, Evangelos D Michelakis, Gopinath Sutendra.
       BACKGROUND: The tumor suppressor and proapoptotic transcription factor P53 is induced (and activated) in several forms of heart failure, including cardiotoxicity and dilated cardiomyopathy; however, the precise mechanism that coordinates its induction with accessibility to its transcriptional promoter sites remains unresolved, especially in the setting of mature terminally differentiated (nonreplicative) cardiomyocytes.
    METHODS: Male and female control or TRIM35 (tripartite motif containing 35) overexpression adolescent (aged 1-3 years months) and adult (aged 4-6 years months) transgenic mice were used for all in vivo experiments. Primary adolescent or adult mouse cardiomyocytes were isolated from control or TRIM35 overexpression transgenic mice for all in vitro experiments. Adenovirus or small-interfering RNA was used for all molecular experiments to overexpress or knockdown, respectively, target genes in primary mouse cardiomyocytes. Patient dilated cardiomyopathy or nonfailing left ventricle samples were used for translational and mechanistic insight in human samples. Chromatin immunoprecipitation was used to assess P53 binding to its transcriptional promoter targets, and RNA sequencing was used to identify disease-specific signaling pathways.
    RESULTS: Here, we show that E3-ubiquitin ligase TRIM35 can directly monoubiquitinate lysine-120 (K120) on histone 2B in postnatal mature cardiomyocytes. This epigenetic modification was sufficient to promote chromatin remodeling, accessibility of P53 to its transcriptional targets, and elongation of its transcribed mRNA. We found that increased P53 transcriptional activity (in cardiomyocyte-specific Trim35 overexpression transgenic mice) was sufficient to initiate heart failure and these molecular findings were recapitulated in nonischemic human LV dilated cardiomyopathy samples.
    CONCLUSIONS: These findings suggest that TRIM35 and the K120Ub-histone 2B epigenetic modification are molecular features of cardiomyocytes that can collectively predict dilated cardiomyopathy pathogenesis.
    Keywords:  chromatin and epigenetics; fibrosis; heart failure; histones; monoubiquitination
    DOI:  https://doi.org/10.1161/CIRCRESAHA.123.324202
  21. Science. 2024 Jun 14. 384(6701): 1247-1253
    Molecular mechanism of the ischemia-induced regulatory switch in mammalian complex I.
    Daniel N Grba, John J Wright, Zhan Yin, William Fisher, Judy Hirst.
      Respiratory complex I is an efficient driver for oxidative phosphorylation in mammalian mitochondria, but its uncontrolled catalysis under challenging conditions leads to oxidative stress and cellular damage. Ischemic conditions switch complex I from rapid, reversible catalysis into a dormant state that protects upon reoxygenation, but the molecular basis for the switch is unknown. We combined precise biochemical definition of complex I catalysis with high-resolution cryo-electron microscopy structures in the phospholipid bilayer of coupled vesicles to reveal the mechanism of the transition into the dormant state, modulated by membrane interactions. By implementing a versatile membrane system to unite structure and function, attributing catalytic and regulatory properties to specific structural states, we define how a conformational switch in complex I controls its physiological roles.
    DOI:  https://doi.org/10.1126/science.ado2075
  22. PLoS Biol. 2024 Jun;22(6): e3002662
    A mechanical transition from tension to buckling underlies the jigsaw puzzle shape morphogenesis of histoblasts in the Drosophila epidermis.
    Annafrancesca Rigato, Huicheng Meng, Claire Chardes, Adam Runions, Faris Abouakil, Richard S Smith, Loïc LeGoff.
      The polygonal shape of cells in proliferating epithelia is a result of the tensile forces of the cytoskeletal cortex and packing geometry set by the cell cycle. In the larval Drosophila epidermis, two cell populations, histoblasts and larval epithelial cells, compete for space as they grow on a limited body surface. They do so in the absence of cell divisions. We report a striking morphological transition of histoblasts during larval development, where they change from a tensed network configuration with straight cell outlines at the level of adherens junctions to a highly folded morphology. The apical surface of histoblasts shrinks while their growing adherens junctions fold, forming deep lobules. Volume increase of growing histoblasts is accommodated basally, compensating for the shrinking apical area. The folded geometry of apical junctions resembles elastic buckling, and we show that the imbalance between the shrinkage of the apical domain of histoblasts and the continuous growth of junctions triggers buckling. Our model is supported by laser dissections and optical tweezer experiments together with computer simulations. Our analysis pinpoints the ability of histoblasts to store mechanical energy to a much greater extent than most other epithelial cell types investigated so far, while retaining the ability to dissipate stress on the hours time scale. Finally, we propose a possible mechanism for size regulation of histoblast apical size through the lateral pressure of the epidermis, driven by the growth of cells on a limited surface. Buckling effectively compacts histoblasts at their apical plane and may serve to avoid physical harm to these adult epidermis precursors during larval life. Our work indicates that in growing nondividing cells, compressive forces, instead of tension, may drive cell morphology.
    DOI:  https://doi.org/10.1371/journal.pbio.3002662
  23. Science. 2024 Jun 14. 384(6701): eadj4301
    Metabolic inflexibility promotes mitochondrial health during liver regeneration.
    Xun Wang, Cameron J Menezes, Yuemeng Jia, Yi Xiao, Siva Sai Krishna Venigalla, Feng Cai, Meng-Hsiung Hsieh, Wen Gu, Liming Du, Jessica Sudderth, Dohun Kim, Spencer D Shelton, Claire B Llamas, Yu-Hsuan Lin, Min Zhu, Salma Merchant, Divya Bezwada, Sherwin Kelekar, Lauren G Zacharias, Thomas P Mathews, Gerta Hoxhaj, R Max Wynn, Uttam K Tambar, Ralph J DeBerardinis, Hao Zhu, Prashant Mishra.
      Mitochondria are critical for proper organ function and mechanisms to promote mitochondrial health during regeneration would benefit tissue homeostasis. We report that during liver regeneration, proliferation is suppressed in electron transport chain (ETC)-dysfunctional hepatocytes due to an inability to generate acetyl-CoA from peripheral fatty acids through mitochondrial β-oxidation. Alternative modes for acetyl-CoA production from pyruvate or acetate are suppressed in the setting of ETC dysfunction. This metabolic inflexibility forces a dependence on ETC-functional mitochondria and restoring acetyl-CoA production from pyruvate is sufficient to allow ETC-dysfunctional hepatocytes to proliferate. We propose that metabolic inflexibility within hepatocytes can be advantageous by limiting the expansion of ETC-dysfunctional cells.
    DOI:  https://doi.org/10.1126/science.adj4301
  24. Anim Cells Syst (Seoul). 2024 ;28(1): 303-314
    Generation of mouse and rat xenogeneic ovaries in vitro for production of mouse oocyte.
    Si Won Jang, Ye Rim Kim, Jae Ho Han, Hoon Jang, Hyun Woo Choi.
      The system forming ovarian follicles is developed to investigate in vitro folliculogenesis in a confined environment to obtain functional oocytes. Several studies have reported the successful generation of fully functional oocytes using mouse-induced pluripotent stem cells (iPSCs) and mouse female germline stem cells (fGSCs) as sources of stem cells for in vitro gametogenesis models. In addition, human oogonia have been generated through heterologous co-culture of differentiated human primordial germ cell-like cells (hPGCLCs) with mouse germline somatic cells, although oocyte formation remains challenging. Thus, studies on in vitro ovarian formation in other species are utilized as an introductory approach for in vitro mammalian gametogenesis by understanding the differences in culture systems between species and underlying mechanisms. In this study, we optimized the method of the entire oogenesis process from rat embryonic gonads. We identified well-maturated MII oocytes from rat gonads using our constructed method. Moreover, we generated the first successful in vitro reconstitution of xenogeneic follicles from mouse primordial germ cells (PGCs) and rat somatic cells. We also established an appropriate culture medium and incubation period for xenogeneic follicles. This method will be helpful in studies of xenogeneic follicular development and oocyte generation.
    Keywords:  Xenogeneic; follicle; in vitro; mouse; oocyte; oogenesis; rat
    DOI:  https://doi.org/10.1080/19768354.2024.2363601
  25. Cell Stem Cell. 2024 Jun 09. pii: S1934-5909(24)00184-X. [Epub ahead of print]
    Bioengineered human colon organoids with in vivo-like cellular complexity and function.
    Olga Mitrofanova, Mikhail Nikolaev, Quan Xu, Nicolas Broguiere, Irineja Cubela, J Gray Camp, Michael Bscheider, Matthias P Lutolf.
      Organoids and organs-on-a-chip have emerged as powerful tools for modeling human gut physiology and disease in vitro. Although physiologically relevant, these systems often lack the environmental milieu, spatial organization, cell type diversity, and maturity necessary for mimicking human intestinal mucosa. To instead generate models closely resembling in vivo tissue, we herein integrated organoid and organ-on-a-chip technology to develop an advanced human organoid model, called "mini-colons." By employing an asymmetric stimulation with growth factors, we greatly enhanced tissue longevity and replicated in vivo-like diversity and patterning of proliferative and differentiated cell types. Mini-colons contain abundant mucus-producing goblet cells and, signifying mini-colon maturation, single-cell RNA sequencing reveals emerging mature and functional colonocytes. This methodology is expanded to generate microtissues from the small intestine and incorporate additional microenvironmental components. Finally, our bioengineered organoids provide a precise platform to systematically study human gut physiology and pathology, and a reliable preclinical model for drug safety assessment.
    Keywords:  bioengineering; colon; colonocyte; gastrointestinal drug toxicity; gut physiology; mucus; organ-on-chip; organoid; small intestine
    DOI:  https://doi.org/10.1016/j.stem.2024.05.007
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