bims-ginsta 2024-11-10 papers

bims-ginsta

Biomed News

on Genome instability

Issue of 2024–11–10
24 papers selected by
Jinrong Hu, National University of Singapore

Spatiotemporal coordination of actin regulators generates invasive protrusions in cell-cell fusion.
Coordinated inheritance of extrachromosomal DNAs in cancer cells.
Redundant pathways for removal of defective RNA polymerase II complexes at a promoter-proximal pause checkpoint.
Cell tumbling enhances stem cell differentiation in hydrogels via nuclear mechanotransduction.
Cellular ATP demand creates metabolically distinct subpopulations of mitochondria.
Single-cell morphometrics reveals T-box gene-dependent patterns of epithelial tension in the Second Heart field.
Polyclonal regeneration of mouse bone marrow endothelial cells after irradiative conditioning.
Developing a soft micropatterned substrate to enhance maturation of human induced pluripotent stem cell-derived cardiomyocytes.
A cellular basis for mapping behavioural structure.
Microglia depletion reduces human neuronal APOE4-related pathologies in a chimeric Alzheimer's disease model.
Blastocoel expansion and AMOT degradation cooperatively promote YAP nuclear localization during epiblast formation.
Increased DNA damage in full-grown oocytes is correlated with diminished autophagy activation.
Phenome-wide associations of human aging uncover sex-specific dynamics.
DNA-directed termination of mammalian RNA polymerase II.
Monitoring protein phosphorylation at the mitochondrial protein import machinery by PhosTag electrophoresis.
Dynamic rRNA modifications as a source of ribosome heterogeneity.
Transcriptomic profiling of day 3 human embryos of poor quality reveals molecular links to divergent developmental trajectories.
Organ-specific electrophile responsivity mapping in live C. elegans.
Enhancing transcription-replication conflict targets ecDNA-positive cancers.
Transfer of mitochondrial DNA into the nuclear genome during induced DNA breaks.
Dilated cardiomyopathy-associated skeletal muscle actin (ACTA1) mutation R256H disrupts actin structure and function and causes cardiomyocyte hypocontractility.
A multicellular developmental program in a close animal relative.
Type III interferons induce pyroptosis in gut epithelial cells and impair mucosal repair.
The effect of rapamycin treatment on mouse ovarian follicle development in dehydroepiandrosterone-induced polycystic ovary syndrome mouse model.

Nat Cell Biol. 2024 Nov 01.

Spatiotemporal coordination of actin regulators generates invasive protrusions in cell-cell fusion.

Yue Lu, Tezin Walji, Benjamin Ravaux, Pratima Pandey, Changsong Yang, Bing Li, Delgermaa Luvsanjav, Kevin H Lam, Ruihui Zhang, Zhou Luo, Chuanli Zhou, Christa W Habela, Scott B Snapper, Rong Li, David J Goldhamer, David W Schmidtke, Duojia Pan, Tatyana M Svitkina, Elizabeth H Chen.

Invasive membrane protrusions play a central role in a variety of cellular processes. Unlike filopodia, invasive protrusions are mechanically stiff and propelled by branched actin polymerization. However, how branched actin filaments are organized to create finger-like invasive protrusions is unclear. Here, by examining the mammalian fusogenic synapse, where invasive protrusions are generated to promote cell membrane juxtaposition and fusion, we have uncovered the mechanism underlying invasive protrusion formation. We show that two nucleation-promoting factors for the Arp2/3 complex, WAVE and N-WASP, exhibit different localization patterns in the protrusions. Whereas WAVE is closely associated with the plasma membrane at the leading edge of the protrusive structures, N-WASP is enriched with WIP along the actin bundles in the shafts of the protrusions. During protrusion initiation and growth, the Arp2/3 complex nucleates branched actin filaments to generate low-density actin clouds in which the large GTPase dynamin organizes the new branched actin filaments into bundles, followed by actin-bundle stabilization by WIP, the latter functioning as an actin-bundling protein. Disruption of any of these components results in defective protrusions and failed myoblast fusion in cultured cells and mouse embryos. Together, our study has revealed the intricate spatiotemporal coordination between two nucleation-promoting factors and two actin-bundling proteins in building invasive protrusions at the mammalian fusogenic synapse and has general implications in understanding invasive protrusion formation in cellular processes beyond cell-cell fusion.

DOI: https://doi.org/10.1038/s41556-024-01541-5
Nature. 2024 Nov;635(8037): 201-209

Coordinated inheritance of extrachromosomal DNAs in cancer cells.

King L Hung, Matthew G Jones, Ivy Tsz-Lo Wong, Ellis J Curtis, Joshua T Lange, Britney Jiayu He, Jens Luebeck, Rachel Schmargon, Elisa Scanu, Lotte Brückner, Xiaowei Yan, Rui Li, Aditi Gnanasekar, Rocío Chamorro González, Julia A Belk, Zhonglin Liu, Bruno Melillo, Vineet Bafna, Jan R Dörr, Benjamin Werner, Weini Huang, Benjamin F Cravatt, Anton G Henssen, Paul S Mischel, Howard Y Chang.

The chromosomal theory of inheritance dictates that genes on the same chromosome segregate together while genes on different chromosomes assort independently1. Extrachromosomal DNAs (ecDNAs) are common in cancer and drive oncogene amplification, dysregulated gene expression and intratumoural heterogeneity through random segregation during cell division2,3. Distinct ecDNA sequences, termed ecDNA species, can co-exist to facilitate intermolecular cooperation in cancer cells4. How multiple ecDNA species within a tumour cell are assorted and maintained across somatic cell generations is unclear. Here we show that cooperative ecDNA species are coordinately inherited through mitotic co-segregation. Imaging and single-cell analyses show that multiple ecDNAs encoding distinct oncogenes co-occur and are correlated in copy number in human cancer cells. ecDNA species are coordinately segregated asymmetrically during mitosis, resulting in daughter cells with simultaneous copy-number gains in multiple ecDNA species before any selection. Intermolecular proximity and active transcription at the start of mitosis facilitate the coordinated segregation of ecDNA species, and transcription inhibition reduces co-segregation. Computational modelling reveals the quantitative principles of ecDNA co-segregation and co-selection, predicting their observed distributions in cancer cells. Coordinated inheritance of ecDNAs enables co-amplification of specialized ecDNAs containing only enhancer elements and guides therapeutic strategies to jointly deplete cooperating ecDNA oncogenes. Coordinated inheritance of ecDNAs confers stability to oncogene cooperation and novel gene regulatory circuits, allowing winning combinations of epigenetic states to be transmitted across cell generations.

DOI: https://doi.org/10.1038/s41586-024-07861-8
Mol Cell. 2024 Oct 30. pii: S1097-2765(24)00835-9. [Epub ahead of print]

Redundant pathways for removal of defective RNA polymerase II complexes at a promoter-proximal pause checkpoint.

Daniel Blears, Jiangman Lou, Nova Fong, Richard Mitter, Ryan M Sheridan, Dandan He, A Barbara Dirac-Svejstrup, David Bentley, Jesper Q Svejstrup.

  The biological purpose of Integrator and RNA polymerase II (RNAPII) promoter-proximal pausing remains uncertain. Here, we show that loss of INTS6 in human cells results in increased interaction of RNAPII with proteins that can mediate its dissociation from the DNA template, including the CRL3ARMC5 E3 ligase, which ubiquitylates CTD serine5-phosphorylated RPB1 for degradation. ARMC5-dependent RNAPII ubiquitylation is activated by defects in factors acting at the promoter-proximal pause, including Integrator, DSIF, and capping enzyme. This ARMC5 checkpoint normally curtails a sizeable fraction of RNAPII transcription, and ARMC5 knockout cells produce more uncapped transcripts. When both the Integrator and CRL3ARMC5 turnover mechanisms are compromised, cell growth ceases and RNAPII with high pausing propensity disperses from the promoter-proximal pause site into the gene body. These data support a model in which CRL3ARMC5 functions alongside Integrator in a checkpoint mechanism that removes faulty RNAPII complexes at promoter-proximal pause sites to safeguard transcription integrity.

Keywords:  ARMC5; CTD phosphorylation; CUL3; DRB; DSIF; INTS6; Integrator; NELF; RNA polymerase II; RNGTT; RPB1; TFIIH kinase; TFIIS; TT-seq; eNET-seq; mRNA capping; nascent transcription; pTEFb kinase; promoter-proximal pausing; protein phosphatase 2A; senataxin

DOI:  https://doi.org/10.1016/j.molcel.2024.10.012
Nat Mater. 2024 Nov 01.

Cell tumbling enhances stem cell differentiation in hydrogels via nuclear mechanotransduction.

Manish Ayushman, Georgios Mikos, Xinming Tong, Sauradeep Sinha, Eunice Lopez-Fuentes, Sarah Jones, Pamela C Cai, Hung-Pang Lee, Ashby J Morrison, Andrew Spakowitz, Sarah C Heilshorn, Alejandro Sweet-Cordero, Fan Yang.

Cells can deform their local niche in three dimensions via whole-cell movements such as spreading, migration or volume expansion. These behaviours, occurring over hours to days, influence long-term cell fates including differentiation. Here we report a whole-cell movement that occurs in sliding hydrogels at the minutes timescale, termed cell tumbling, characterized by three-dimensional cell dynamics and hydrogel deformation elicited by heightened seconds-to-minutes-scale cytoskeletal and nuclear activity. Studies inhibiting or promoting the cell tumbling of mesenchymal stem cells show that this behaviour enhances differentiation into chondrocytes. Further, it is associated with a decrease in global chromatin accessibility, which is required for enhanced differentiation. Cell tumbling also occurs during differentiation into other lineages and its differentiation-enhancing effects are validated in various hydrogel platforms. Our results establish that cell tumbling is an additional regulator of stem cell differentiation, mediated by rapid niche deformation and nuclear mechanotransduction.

DOI: https://doi.org/10.1038/s41563-024-02038-0
Nature. 2024 Nov 06.

Cellular ATP demand creates metabolically distinct subpopulations of mitochondria.

Keun Woo Ryu, Tak Shun Fung, Daphne C Baker, Michelle Saoi, Jinsung Park, Christopher A Febres-Aldana, Rania G Aly, Ruobing Cui, Anurag Sharma, Yi Fu, Olivia L Jones, Xin Cai, H Amalia Pasolli, Justin R Cross, Charles M Rudin, Craig B Thompson.

Mitochondria serve a crucial role in cell growth and proliferation by supporting both ATP synthesis and the production of macromolecular precursors. Whereas oxidative phosphorylation (OXPHOS) depends mainly on the oxidation of intermediates from the tricarboxylic acid cycle, the mitochondrial production of proline and ornithine relies on reductive synthesis1. How these competing metabolic pathways take place in the same organelle is not clear. Here we show that when cellular dependence on OXPHOS increases, pyrroline-5-carboxylate synthase (P5CS)-the rate-limiting enzyme in the reductive synthesis of proline and ornithine-becomes sequestered in a subset of mitochondria that lack cristae and ATP synthase. This sequestration is driven by both the intrinsic ability of P5CS to form filaments and the mitochondrial fusion and fission cycle. Disruption of mitochondrial dynamics, by impeding mitofusin-mediated fusion or dynamin-like-protein-1-mediated fission, impairs the separation of P5CS-containing mitochondria from mitochondria that are enriched in cristae and ATP synthase. Failure to segregate these metabolic pathways through mitochondrial fusion and fission results in cells either sacrificing the capacity for OXPHOS while sustaining the reductive synthesis of proline, or foregoing proline synthesis while preserving adaptive OXPHOS. These findings provide evidence of the key role of mitochondrial fission and fusion in maintaining both oxidative and reductive biosyntheses in response to changing nutrient availability and bioenergetic demand.

DOI: https://doi.org/10.1038/s41586-024-08146-w
Nat Commun. 2024 Nov 04. 15(1): 9512

Single-cell morphometrics reveals T-box gene-dependent patterns of epithelial tension in the Second Heart field.

Clara Guijarro, Solène Song, Benoit Aigouy, Raphaël Clément, Paul Villoutreix, Robert G Kelly.

The vertebrate heart tube extends by progressive addition of epithelial second heart field (SHF) progenitor cells from the dorsal pericardial wall. The interplay between epithelial mechanics and genetic mechanisms during SHF deployment is unknown. Here, we present a quantitative single-cell morphometric analysis of SHF cells during heart tube extension, including force inference analysis of epithelial stress. Joint spatial Principal Component Analysis reveals that cell orientation and stress direction are the main parameters defining apical cell morphology and distinguishes cells adjacent to the arterial and venous poles. Cell shape and mechanical forces display a dynamic relationship during heart tube formation. Moreover, while the T-box transcription factor Tbx1 is necessary for cell orientation towards the arterial pole, activation of Tbx5 in the posterior SHF correlates with the establishment of epithelial stress and SHF deletion of Tbx5 relaxes the progenitor epithelium. Integrating findings from cell-scale feature patterning and mechanical stress provides new insights into cardiac morphogenesis.

DOI: https://doi.org/10.1038/s41467-024-53612-8
Cell Rep. 2024 Oct 25. pii: S2211-1247(24)01130-6. [Epub ahead of print]43(11): 114779

Polyclonal regeneration of mouse bone marrow endothelial cells after irradiative conditioning.

Izabella Skulimowska, Jan Morys, Justyna Sosniak, Monika Gonka, Gunsagar Gulati, Rahul Sinha, Kacper Kowalski, Sylwester Mosiolek, Irving L Weissman, Alicja Jozkowicz, Agata Szade, Krzysztof Szade.

  Bone marrow endothelial cells (BM-ECs) are the essential components of the BM niche and support the function of hematopoietic stem cells (HSCs). However, conditioning for HSC transplantation causes damage to the recipients' BM-ECs and may lead to transplantation-related morbidity. Here, we investigated the cellular and clonal mechanisms of BM-EC regeneration after irradiative conditioning. Using single-cell RNA sequencing, imaging, and flow cytometry, we revealed how the heterogeneous pool of BM-ECs changes during regeneration from irradiation stress. Next, we developed a single-cell in vitro clonogenic assay and demonstrated that all EC fractions hold a high potential to reenter the cell cycle and form vessel-like structures. Finally, we used Rainbow mice and a machine-learning-based model to show that the regeneration of BM-ECs after irradiation is mostly polyclonal and driven by the broad fraction of BM-ECs; however, the cell output among clones varies at later stages of regeneration.

Keywords:  CP: Stem cell research; bone marrow endothelial cells; bone marrow niche; bone marrow regeneration; conditioning; hematopoietic stem cells; irradiation; sinusoids; transplantation

DOI:  https://doi.org/10.1016/j.celrep.2024.114779
Acta Biomater. 2024 Oct 26. pii: S1742-7061(24)00621-4. [Epub ahead of print]

Developing a soft micropatterned substrate to enhance maturation of human induced pluripotent stem cell-derived cardiomyocytes.

Yasaman Maaref, Shayan Jannati, Farah Jayousi, Philipp Lange, Mohsen Akbari, Mu Chiao, Glen F Tibbits.

  Human induced pluripotent stem cell-derived cardiomyocytes (hiPSCCMs) offer numerous advantages as a biological model, yet their inherent immaturity compared to adult cardiomyocytes poses significant limitations. This study addresses hiPSCCM immaturity by introducing a physiologically relevant micropatterned substrate for long-term culture and maturation. An innovative microfabrication methodology combining laser etching and casting creates a micropatterned polydimethylsiloxane (PDMS) substrate with varying stiffness, from 2 to 50 kPa, mimicking healthy and fibrotic cardiac tissue. Platinum electrodes were integrated into the cell culture chamber enable pacing of cells at various frequencies. Subsequently, cells were transferred to the incubator for time-course analysis, ensuring contamination-free conditions. Cell contractility, cytosolic Ca2+ transient, sarcomere orientation, and nucleus aspect ratio were analyzed in a 2D hiPSCCM monolayer up to 90 days post-replating in relation to substrate micropattern dimensions. Culturing hiPSCCMs for three weeks on a micropatterned PDMS substrate (2.5-5 µm deep, 20 µm center-to-center spacing of grooves, 2-5 kPa stiffness) emerges as optimal for cardiomyocyte alignment, contractility, and cytosolic Ca2+ transient. The study provides insights into substrate stiffness effects on hiPSCCM contractility and Ca2+ transient at immature and mature states. Maximum contractility and fastest Ca2+transient kinetics occur in mature hiPSCCMs cultured for two to four weeks, with the optimum at three weeks, on a soft micropatterned PDMS substrate. MS proteomic analysis further revealed that hiPSCCMs cultured on soft micropatterned substrates exhibit advanced maturation, marked by significant upregulation of key structural, electrophysiological, and metabolic proteins. This new substrate offers a promising platform for disease modeling and therapeutic interventions. STATEMENT OF SIGNIFICANCE: Human induced pluripotent stem cell derived cardiomyocytes (hiPSCCMs) have been transformative to disease-in-a-dish modeling, drug discovery and testing, and autologous regeneration for human hearts and their role will continue to expand dramatically. However, one of the major limitations of hiPSCCMs is that without intervention, the cells are immature and represent those in the fetal heart. We developed protocols for the fabrication of the PDMS matrices that includes variations in its stiffness and micropatterning. Growing our hiPSCCMs on matrices of comparable stiffness to a healthy heart (5 kPa) and grooves of 20 μm, generate heart cells typical of the healthy adult human heart.

Keywords:  Contractility; HiPSC-CMs; Long-term culture; Maturation; Micropatterned substrate; PDMS

DOI:  https://doi.org/10.1016/j.actbio.2024.10.029
Nature. 2024 Nov 06.

A cellular basis for mapping behavioural structure.

Mohamady El-Gaby, Adam Loyd Harris, James C R Whittington, William Dorrell, Arya Bhomick, Mark E Walton, Thomas Akam, Timothy E J Behrens.

To flexibly adapt to new situations, our brains must understand the regularities in the world, as well as those in our own patterns of behaviour. A wealth of findings is beginning to reveal the algorithms that we use to map the outside world1-6. However, the biological algorithms that map the complex structured behaviours that we compose to reach our goals remain unknown. Here we reveal a neuronal implementation of an algorithm for mapping abstract behavioural structure and transferring it to new scenarios. We trained mice on many tasks that shared a common structure (organizing a sequence of goals) but differed in the specific goal locations. The mice discovered the underlying task structure, enabling zero-shot inferences on the first trial of new tasks. The activity of most neurons in the medial frontal cortex tiled progress to goal, akin to how place cells map physical space. These 'goal-progress cells' generalized, stretching and compressing their tiling to accommodate different goal distances. By contrast, progress along the overall sequence of goals was not encoded explicitly. Instead, a subset of goal-progress cells was further tuned such that individual neurons fired with a fixed task lag from a particular behavioural step. Together, these cells acted as task-structured memory buffers, implementing an algorithm that instantaneously encoded the entire sequence of future behavioural steps, and whose dynamics automatically computed the appropriate action at each step. These dynamics mirrored the abstract task structure both on-task and during offline sleep. Our findings suggest that schemata of complex behavioural structures can be generated by sculpting progress-to-goal tuning into task-structured buffers of individual behavioural steps.

DOI: https://doi.org/10.1038/s41586-024-08145-x
Cell Stem Cell. 2024 Oct 30. pii: S1934-5909(24)00367-9. [Epub ahead of print]

Microglia depletion reduces human neuronal APOE4-related pathologies in a chimeric Alzheimer's disease model.

Antara Rao, Nuo Chen, Min Joo Kim, Jessica Blumenfeld, Oscar Yip, Zherui Liang, David Shostak, Yanxia Hao, Maxine R Nelson, Nicole Koutsodendris, Brian Grone, Leo Ding, Seo Yeon Yoon, Patrick Arriola, Misha Zilberter, Yadong Huang.

  Despite strong evidence supporting the important roles of both apolipoprotein E4 (APOE4) and microglia in Alzheimer's disease (AD) pathogenesis, the effects of microglia on neuronal APOE4-related AD pathogenesis remain elusive. To examine such effects, we utilized microglial depletion in a chimeric model with induced pluripotent stem cell (iPSC)-derived human neurons in mouse hippocampus. Specifically, we transplanted homozygous APOE4, isogenic APOE3, and APOE-knockout (APOE-KO) iPSC-derived human neurons into the hippocampus of human APOE3 or APOE4 knockin mice and then depleted microglia in half of the chimeric mice. We found that both neuronal APOE and microglial presence were important for the formation of Aβ and tau pathologies in an APOE isoform-dependent manner (APOE4 > APOE3). Single-cell RNA sequencing analysis identified two pro-inflammatory microglial subtypes with elevated MHC-II gene expression enriched in chimeric mice with human APOE4 neuron transplants. These findings highlight the concerted roles of neuronal APOE, especially APOE4, and microglia in AD pathogenesis.

Keywords:  APOE4; Alzheimer’s disease; RNA-seq; amyloid; chimeric disease model; iPSC; microglia; tau; transplantation

DOI:  https://doi.org/10.1016/j.stem.2024.10.005
Dev Biol. 2024 Oct 30. pii: S0012-1606(24)00250-1. [Epub ahead of print]517 234-247

Blastocoel expansion and AMOT degradation cooperatively promote YAP nuclear localization during epiblast formation.

Hinako Maeda, Hiroshi Sasaki.

  The epiblast is a pluripotent cell population formed in the late blastocyst stage of preimplantation embryos. During the process of epiblast formation from the inner cell mass (ICM) of the early blastocyst, activation of the Hippo pathway transcription factor TEAD by the nuclear translocation of the coactivator protein YAP is required for the robust expression of pluripotency factors. However, the mechanisms that alter YAP localization during epiblast formation remain unknown. Here, we reveal two such mechanisms. Expansion of the blastocoel promotes nuclear YAP localization by increasing cytoplasmic F-actin and reducing YAP phosphorylation. Additionally, cell differentiation regulates YAP. Expression of the junctional Hippo component, AMOT, gradually decreases during epiblast formation through a tankyrase-mediated degradation. SOX2 expression in the ICM is necessary for the reduction of AMOT and YAP phosphorylation. These two mechanisms function in parallel. Thus, the blastocoel-F-actin and SOX2-AMOT axes cooperatively suppress YAP phosphorylation and promote YAP nuclear localization during epiblast formation. The cooperation of these two distinct mechanisms likely contributes to the robustness of epiblast cell differentiation.

Keywords:  AMOT; Blastocoel; Epiblast; Hippo signal; Preimplantation embryo; YAP

DOI:  https://doi.org/10.1016/j.ydbio.2024.10.007
Nat Commun. 2024 Nov 01. 15(1): 9463

Increased DNA damage in full-grown oocytes is correlated with diminished autophagy activation.

Fei Sun, Nourhan Nashat Ali, Daniela Londoño-Vásquez, Constantine A Simintiras, Huanyu Qiao, M Sofia Ortega, Yuksel Agca, Masashi Takahashi, Rocío M Rivera, Andrew M Kelleher, Peter Sutovsky, Amanda L Patterson, Ahmed Z Balboula.

Unlike mild DNA damage exposure, DNA damage repair (DDR) is reported to be ineffective in full-grown mammalian oocytes exposed to moderate or severe DNA damage. The underlying mechanisms of this weakened DDR are unknown. Here, we show that moderate DNA damage in full-grown oocytes leads to aneuploidy. Our data reveal that DNA-damaged oocytes have an altered, closed, chromatin state, and suggest that the failure to repair damaged DNA could be due to the inability of DDR proteins to access damaged loci. Our data also demonstrate that, unlike somatic cells, mouse and porcine oocytes fail to activate autophagy in response to DNA double-strand break-inducing treatment, which we suggest may be the cause of the altered chromatin conformation and inefficient DDR. Importantly, autophagy activity is further reduced in maternally aged oocytes (which harbor severe DNA damage), and its induction is correlated with reduced DNA damage in maternally aged oocytes. Our findings provide evidence that reduced autophagy activation contributes to weakened DDR in oocytes, especially in those from aged females, offering new possibilities to improve assisted reproductive therapy in women with compromised oocyte quality.

DOI: https://doi.org/10.1038/s41467-024-53559-w
Nat Aging. 2024 Nov 05.

Phenome-wide associations of human aging uncover sex-specific dynamics.

Lee Reicher, Noam Bar, Anastasia Godneva, Yotam Reisner, Liron Zahavi, Nir Shahaf, Raja Dhir, Adina Weinberger, Eran Segal.

Aging varies significantly among individuals of the same chronological age, indicating that biological age (BA), estimated from molecular and physiological biomarkers, may better reflect aging. Prior research has often ignored sex-specific differences in aging patterns and mainly focused on aging biomarkers from a single data modality. Here we analyze a deeply phenotyped longitudinal cohort (10K project, Israel) of 10,000 healthy individuals aged 40-70 years that includes clinical, physiological, behavioral, environmental and multiomic parameters. Follow-up visits are scheduled every 2 years for a total of 25 years. We devised machine learning models of chronological age and computed biological aging scores that represented diverse physiological systems, revealing different aging patterns among sexes. Higher BA scores were associated with a higher prevalence of age-related medical conditions, highlighting the clinical relevance of these scores. Our analysis revealed system-specific aging dynamics and the potential of deeply phenotyped cohorts to accelerate improvements in our understanding of chronic diseases. Our findings present a more holistic view of the aging process, and lay the foundation for personalized medical prevention strategies.

DOI: https://doi.org/10.1038/s43587-024-00734-9
Genes Dev. 2024 Nov 04.

DNA-directed termination of mammalian RNA polymerase II.

Lee Davidson, Jérôme O Rouvière, Rui Sousa-Luís, Takayuki Nojima, Nicholas J Proudfoot, Torben Heick Jensen, Steven West.

  The best-studied mechanism of eukaryotic RNA polymerase II (RNAPII) transcriptional termination involves polyadenylation site-directed cleavage of the nascent RNA. The RNAPII-associated cleavage product is then degraded by XRN2, dislodging RNAPII from the DNA template. In contrast, prokaryotic RNAP and eukaryotic RNAPIII often terminate directly at T-tracts in the coding DNA strand. Here, we demonstrate a similar and omnipresent capability for mammalian RNAPII. Importantly, this termination mechanism does not require upstream RNA cleavage. Accordingly, T-tract-dependent termination can take place when XRN2 cannot be engaged. We show that T-tracts can terminate snRNA transcription independently of RNA cleavage by the Integrator complex. Importantly, we found genome-wide termination at T-tracts in promoter-proximal regions but not within protein-coding gene bodies. XRN2-dependent termination dominates downstream from protein-coding genes, but the T-tract process is sometimes used. Overall, we demonstrate global DNA-directed attrition of RNAPII transcription, suggesting that RNAPs retain the potential to terminate over T-rich sequences throughout evolution.

Keywords:  Integrator; RNA polymerase II; Xrn2; exosome; histone; snRNA; transcription termination

DOI:  https://doi.org/10.1101/gad.351978.124
Methods Enzymol. 2024 ;pii: S0076-6879(24)00408-7. [Epub ahead of print]707 501-517

Monitoring protein phosphorylation at the mitochondrial protein import machinery by PhosTag electrophoresis.

Fatimah Lami Imam, Chris Meisinger, Adinarayana Marada.

  The mitochondrial import machinery is regulated by several protein kinases that phosphorylate key components. This allows an adjustment of the protein flux to changing cellular demands and allow a dynamic organellar proteome. PhosTag electrophoresis has been proven as highly valuably tool to study these signalling machanisms at the import machinery.

Keywords:  TOM complex; assembly; biogenesis; import machinery; precursor protein; protein kinase; reversible phosphorylation; signalling

DOI:  https://doi.org/10.1016/bs.mie.2024.07.063
Trends Cell Biol. 2024 Nov 04. pii: S0962-8924(24)00207-1. [Epub ahead of print]

Dynamic rRNA modifications as a source of ribosome heterogeneity.

Ivan Milenkovic, Eva Maria Novoa.

  Ribosomal RNAs (rRNA) are the most abundant RNA molecules in almost all cell types. The general consensus in the field is that rRNA modifications are largely species-specific, with most previous works and databases solely stratifying modifications by the species of origin, without taking other levels of complexity into account. However, new evidence has emerged suggesting dynamic rRNA modifications may have additional layers of complexity and might play an important role in development and disease. In this review article, we summarize recent evidence supporting heterogeneity and dynamics in rRNA modifications in diverse biological contexts, challenging the simplistic view of 'one-species-one-rRNA-modification-pattern'. Moreover, we highlight how rRNA modification dynamics have been studied to date and how long-read sequencing methods can significantly improve our understanding of this largely unexplored yet highly abundant RNA family, across tissues, developmental stages, and diseases.

Keywords:  development; disease; methylation; modification; pseudouridine; rRNA

DOI:  https://doi.org/10.1016/j.tcb.2024.10.001
Cell Rep. 2024 Oct 31. pii: S2211-1247(24)01239-7. [Epub ahead of print]43(11): 114888

Transcriptomic profiling of day 3 human embryos of poor quality reveals molecular links to divergent developmental trajectories.

Yan Li, Wencheng Zhu, Yuchen Qian, Haiyan Yang, Yonggen Wu, Juan Meng, Xuefeng Huang, Zhen Liu, Liangshan Mu.

  Poor-quality (PQ) embryos are commonly formed in assisted reproduction and often discarded, but emerging evidence suggests that some can develop into healthy children. Here, we performed single-embryo transcriptome profiling of day 3 human embryos of both good quality (GQ) and PQ. Our analyses revealed that day 3 PQ embryos can be categorized into two distinct subgroups: genuine PQ (gPQ) and morphological PQ (mPQ) embryos. This was further supported by additional transcriptomic data of GQ and PQ embryos donated by the same individuals. gPQ embryos showed greater impairments in both RNA decay and zygotic genome activation (ZGA) compared to mPQ embryos. Blastocysts that emerged from PQ embryos, more likely from mPQ embryos, demonstrated transcriptomic similarity to normal blastocysts. We also identified genes highly upregulated in day 3 gPQ embryos. These molecular insights may improve embryo selection and offer valuable clues for enhancing embryo quality in the future.

Keywords:  CP: Developmental biology

DOI:  https://doi.org/10.1016/j.celrep.2024.114888
Cell. 2024 Nov 02. pii: S0092-8674(24)01190-5. [Epub ahead of print]

Organ-specific electrophile responsivity mapping in live C. elegans.

Jinmin Liu, Amogh Kulkarni, Yong-Qi Gao, Daniel A Urul, Romain Hamelin, Balázs Á Novotny, Marcus J C Long, Yimon Aye.

  Proximity labeling technologies are limited to indexing localized protein residents. Such data-although valuable-cannot inform on small-molecule responsivity of local residents. We here bridge this gap by demonstrating in live C. elegans how electrophile-sensing propensity in specific organs can be quantitatively mapped and ranked. Using this method, >70% of tissue-specific responders exhibit electrophile responsivity, independent of tissue-specific abundance. One responder, cyp-33e1-for which both human and worm orthologs are electrophile responsive-marshals stress-dependent gut functions, despite manifesting uniform abundance across all tissues studied. Cyp-33e1's localized electrophile responsivity operates site specifically, triggering multifaceted responses: electrophile sensing through the catalytic-site cysteine results in partitioning between enzyme inhibition and localized production of a critical metabolite that governs global lipid availability, whereas rapid dual-cysteine site-specific sensing modulates gut homeostasis. Beyond pinpointing chemical actionability within local proteomes, organ-specific electrophile responsivity mapping illuminates otherwise intractable locale-specific metabolite signaling and stress response programs influencing organ-specific decision-making.

Keywords:  4-hydroxynonenal; C. elegans; cytochrome P450; function-guided spatial mapping; organ-specific responsivity profiling; proximity labeling proteomics; reactive metabolite signaling; tissue-specific stress response

DOI:  https://doi.org/10.1016/j.cell.2024.10.014
Nature. 2024 Nov;635(8037): 210-218

Enhancing transcription-replication conflict targets ecDNA-positive cancers.

Jun Tang, Natasha E Weiser, Guiping Wang, Sudhir Chowdhry, Ellis J Curtis, Yanding Zhao, Ivy Tsz-Lo Wong, Georgi K Marinov, Rui Li, Philip Hanoian, Edison Tse, Salvador Garcia Mojica, Ryan Hansen, Joshua Plum, Auzon Steffy, Snezana Milutinovic, S Todd Meyer, Jens Luebeck, Yanbo Wang, Shu Zhang, Nicolas Altemose, Christina Curtis, William J Greenleaf, Vineet Bafna, Stephen J Benkovic, Anthony B Pinkerton, Shailaja Kasibhatla, Christian A Hassig, Paul S Mischel, Howard Y Chang.

Extrachromosomal DNA (ecDNA) presents a major challenge for cancer patients. ecDNA renders tumours treatment resistant by facilitating massive oncogene transcription and rapid genome evolution, contributing to poor patient survival1-7. At present, there are no ecDNA-specific treatments. Here we show that enhancing transcription-replication conflict enables targeted elimination of ecDNA-containing cancers. Stepwise analyses of ecDNA transcription reveal pervasive RNA transcription and associated single-stranded DNA, leading to excessive transcription-replication conflicts and replication stress compared with chromosomal loci. Nucleotide incorporation on ecDNA is markedly slower, and replication stress is significantly higher in ecDNA-containing tumours regardless of cancer type or oncogene cargo. pRPA2-S33, a mediator of DNA damage repair that binds single-stranded DNA, shows elevated localization on ecDNA in a transcription-dependent manner, along with increased DNA double strand breaks, and activation of the S-phase checkpoint kinase, CHK1. Genetic or pharmacological CHK1 inhibition causes extensive and preferential tumour cell death in ecDNA-containing tumours. We advance a highly selective, potent and bioavailable oral CHK1 inhibitor, BBI-2779, that preferentially kills ecDNA-containing tumour cells. In a gastric cancer model containing FGFR2 amplified on ecDNA, BBI-2779 suppresses tumour growth and prevents ecDNA-mediated acquired resistance to the pan-FGFR inhibitor infigratinib, resulting in potent and sustained tumour regression in mice. Transcription-replication conflict emerges as a target for ecDNA-directed therapy, exploiting a synthetic lethality of excess to treat cancer.

DOI: https://doi.org/10.1038/s41586-024-07802-5
Nat Commun. 2024 Nov 01. 15(1): 9438

Transfer of mitochondrial DNA into the nuclear genome during induced DNA breaks.

Jinchun Wu, Yang Liu, Liqiong Ou, Tingting Gan, Zhengrong Zhangding, Shaopeng Yuan, Xinyi Liu, Mengzhu Liu, Jiasheng Li, Jianhang Yin, Changchang Xin, Ye Tian, Jiazhi Hu.

Mitochondria serve as the cellular powerhouse, and their distinct DNA makes them a prospective target for gene editing to treat genetic disorders. However, the impact of genome editing on mitochondrial DNA (mtDNA) stability remains a mystery. Our study reveals previously unknown risks of genome editing that both nuclear and mitochondrial editing cause discernible transfer of mitochondrial DNA segments into the nuclear genome in various cell types including human cell lines, primary T cells, and mouse embryos. Furthermore, drug-induced mitochondrial stresses and mtDNA breaks exacerbate this transfer of mtDNA into the nuclear genome. Notably, we observe that mitochondrial editors, including mitoTALEN and recently developed base editor DdCBE, can also enhance crosstalk between mtDNA and the nuclear genome. Moreover, we provide a practical solution by co-expressing TREX1 or TREX2 exonucleases during DdCBE editing. These findings imply genome instability of mitochondria during induced DNA breaks and explain the origins of mitochondrial-nuclear DNA segments.

DOI: https://doi.org/10.1038/s41467-024-53806-0
Proc Natl Acad Sci U S A. 2024 Nov 12. 121(46): e2405020121

Dilated cardiomyopathy-associated skeletal muscle actin (ACTA1) mutation R256H disrupts actin structure and function and causes cardiomyocyte hypocontractility.

Ankit Garg, Silvia Jansen, Lina Greenberg, Rui Zhang, Kory J Lavine, Michael J Greenberg.

  Skeletal muscle actin (ACTA1) mutations are a prevalent cause of skeletal myopathies consistent with ACTA1's high expression in skeletal muscle. Rare de novo mutations in ACTA1 associated with combined cardiac and skeletal myopathies have been reported, but ACTA1 represents only ~20% of the total actin pool in cardiomyocytes, making its role in cardiomyopathy controversial. Here we demonstrate how a mutation in an actin isoform expressed at low levels in cardiomyocytes can cause cardiomyopathy by focusing on a unique ACTA1 variant, R256H. We previously identified this variant in a family with dilated cardiomyopathy, who had reduced systolic function without clinical skeletal myopathy. Using a battery of multiscale biophysical tools, we show that R256H has potent effects on ACTA1 function at the molecular scale and in human cardiomyocytes. Importantly, we demonstrate that R256H acts in a dominant manner, where the incorporation of small amounts of mutant protein into thin filaments is sufficient to disrupt molecular contractility, and that this effect is dependent on the presence of troponin and tropomyosin. To understand the structural basis of this change in regulation, we resolved a structure of R256H filaments using cryoelectron microscopy, and we see alterations in actin's structure that have the potential to disrupt interactions with tropomyosin. Finally, we show that ACTA1R256H/+ human-induced pluripotent stem cell cardiomyocytes demonstrate reduced contractility and sarcomeric organization. Taken together, we demonstrate that R256H has multiple effects on ACTA1 function that are sufficient to cause reduced contractility and establish a likely causative relationship between ACTA1 R256H and clinical cardiomyopathy.

Keywords:  actin; cardiomyopathy; contractility; muscle

DOI:  https://doi.org/10.1073/pnas.2405020121
Nature. 2024 Nov 06.

A multicellular developmental program in a close animal relative.

Marine Olivetta, Chandni Bhickta, Nicolas Chiaruttini, John Burns, Omaya Dudin.

All animals develop from a single-celled zygote into a complex multicellular organism through a series of precisely orchestrated processes1,2. Despite the remarkable conservation of early embryogenesis across animals, the evolutionary origins of how and when this process first emerged remain elusive. Here, by combining time-resolved imaging and transcriptomic profiling, we show that single cells of the ichthyosporean Chromosphaera perkinsii-a close relative that diverged from animals about 1 billion years ago3,4-undergo symmetry breaking and develop through cleavage divisions to produce a prolonged multicellular colony with distinct co-existing cell types. Our findings about the autonomous and palintomic developmental program of C. perkinsii hint that such multicellular development either is much older than previously thought or evolved convergently in ichthyosporeans.

DOI: https://doi.org/10.1038/s41586-024-08115-3
Cell. 2024 Oct 30. pii: S0092-8674(24)01158-9. [Epub ahead of print]

Type III interferons induce pyroptosis in gut epithelial cells and impair mucosal repair.

Kautilya K Jena, Julien Mambu, Daniel Boehmer, Benedetta Sposito, Virginie Millet, Joshua de Sousa Casal, Hayley I Muendlein, Roberto Spreafico, Romain Fenouil, Lionel Spinelli, Sarah Wurbel, Chloé Riquier, Franck Galland, Philippe Naquet, Lionel Chasson, Megan Elkins, Vanessa Mitsialis, Natália Ketelut-Carneiro, Katlynn Bugda Gwilt, Jay R Thiagarajah, Hai-Bin Ruan, Zhaoyu Lin, Egil Lien, Feng Shao, Janet Chou, Alexander Poltorak, Jose Ordovas-Montanes, Katherine A Fitzgerald, Scott B Snapper, Achille Broggi, Ivan Zanoni.

  Tissue damage and repair are hallmarks of inflammation. Despite a wealth of information on the mechanisms that govern tissue damage, mechanistic insight into how inflammation affects repair is lacking. Here, we investigated how interferons influence tissue repair after damage to the intestinal mucosa. We found that type III, not type I or type II, interferons delay epithelial cell regeneration by inducing the upregulation of Z-DNA-binding protein 1 (ZBP1). Z-nucleic acids formed following intestinal damage are sensed by ZBP1, leading to caspase-8 activation and the cleavage of gasdermin C (GSDMC). Cleaved GSDMC drives epithelial cell death by pyroptosis and delays repair of the large or small intestine after colitis or irradiation, respectively. The type III interferon/ZBP1/caspase-8/GSDMC axis is also active in patients with inflammatory bowel disease (IBD). Our findings highlight the capacity of type III interferons to delay gut repair, which has implications for IBD patients or individuals exposed to radiation therapies.

Keywords:  Z-nucleic acid; colitis; damage; gasdermin; inflammation; inflammatory bowel disease; interferons; intestinal epithelial cell; intestinal stem cell; irradiation; pattern recognition receptors; pyroptosis; repair

DOI:  https://doi.org/10.1016/j.cell.2024.10.010
Zygote. 2024 Nov 05. 1-10

The effect of rapamycin treatment on mouse ovarian follicle development in dehydroepiandrosterone-induced polycystic ovary syndrome mouse model.

Ecem Yildirim, Tugce Onel, Sami Agus, Elif Gunalan, Bayram Yilmaz, Mehmet Serif Aydin, Aylin Yaba.

  Polycystic ovary syndrome (PCOS) is a complex reproductive and endocrine disorder affecting 5-10% of women of reproductive age, but the pathophysiology of PCOS still remains unknown. Here, the aim of our study was to analyze the effects of rapamycin treatment that may regulate impaired hormonal levels and folliculogenesis in dehydroepiandrosterone (DHEA)-treated PCOS mouse. We hypothesized that rapamycin may ameliorate the negative effects of PCOS in DHEA-induced PCOS mouse model. The target of rapamycin (TOR) gene product is a serine/threonine kinase that has been implicated in the control of cell growth, proliferation and autophagy, and rapamycin is a potent inhibitor of mTORC1 pathway. In this study, for the first time, mTORC1 and activation products are presented at protein and mRNA levels after rapamycin treatment in DHEA-induced PCOS mouse ovary. We showed that rapamycin treatment may regulate follicular development, hormonal levels and provide ovulation in DHEA-induced PCOS mouse. Additionally, we assessed decreased primordial follicle reserve, increased number of primary and secondary follicles, corpus luteum structure forms again after 10 days of rapamycin treatment. This study presented here suggests rapamycin treatment regulates hormonal phenotype and folliculogenesis in the ovary and also mTOR signalling pathway in granulosa cells of DHEA-induced PCOS mouse ovary which may have potential to attenuate understanding the mechanism of dominant follicle selection and anovulatory infertility.

Keywords:  Ovulation; dehidroepiandrostenedion; folliculogenesis; mammalian target of rapamycin; polycystic ovary syndrome; rapamycin

DOI:  https://doi.org/10.1017/S0967199424000388