bims-ginsta 2024-11-03 papers

bims-ginsta

Biomed News

on Genome instability

Issue of 2024–11–03
27 papers selected by
Jinrong Hu, National University of Singapore

EGFR-dependent actomyosin patterning coordinates morphogenetic movements between tissues in Drosophila melanogaster.
PI3K/AKT signaling controls ICM maturation and proper epiblast and primitive endoderm specification in mice.
Bone-marrow macrophage-derived GPNMB protein binds to orphan receptor GPR39 and plays a critical role in cardiac repair.
Senescence suppresses the integrated stress response and activates a stress-remodeled secretory phenotype.
Distinct H3K9me3 heterochromatin maintenance dynamics govern different gene programmes and repeats in pluripotent cells.
Human formin FHOD3-mediated actin elongation is required for sarcomere integrity in cardiomyocytes.
Temporal recording of mammalian development and precancer.
Accumulation of F-actin drives brain aging and limits healthspan in Drosophila.
Common modes of ERK induction resolve into context-specific signalling via emergent networks and cell-type-specific transcriptional repression.
TGF-β induces an atypical EMT to evade immune mechanosurveillance in lung adenocarcinoma dormant metastasis.
Transient promoter interactions modulate developmental gene activation.
Rupture strength of living cell monolayers.
Multiparameter imaging reveals clinically relevant cancer cell-stroma interaction dynamics in head and neck cancer.
COX15 deficiency causes oocyte ferroptosis.
A humanized monoclonal antibody targeting an ectonucleotidase rescues cardiac metabolism and heart function after myocardial infarction.
Structure-guided discovery of bile acid derivatives for treating liver diseases without causing itch.
Myocardial infarction augments sleep to limit cardiac inflammation and damage.
A multimodal zebrafish developmental atlas reveals the state-transition dynamics of late-vertebrate pluripotent axial progenitors.
The de novo purine synthesis enzyme Adssl1 promotes cardiomyocyte proliferation and cardiac regeneration.
A cytoplasmic osmosensing mechanism mediated by molecular crowding-sensitive DCP5.
Germ cell progression through zebrafish spermatogenesis declines with age.
Genomic landscape of adult testicular germ cell tumours in the 100,000 Genomes Project.
Exceptional longevity of mammalian ovarian and oocyte macromolecules throughout the reproductive lifespan.
Structure of the turnover-ready state of an ancestral respiratory complex I.
EGFR-mediated HSP70 phosphorylation facilitates PCNA association with chromatin and DNA replication.
Cardiomyocyte-Specific Overexpression of Activated Yes-Associated Protein Modified-RNA Promotes Cardiomyocyte Proliferation and Myocardial Regeneration.
Nuclear deformability facilitates apical nuclear migration in the developing zebrafish retina.

Dev Cell. 2024 Oct 21. pii: S1534-5807(24)00602-6. [Epub ahead of print]

EGFR-dependent actomyosin patterning coordinates morphogenetic movements between tissues in Drosophila melanogaster.

D Nathaniel Clarke, Pearson W Miller, Adam C Martin.

  The movements that give rise to the body's structure are powered by cell shape changes and rearrangements that are coordinated at supracellular scales. How such cellular coordination arises and integrates different morphogenetic programs is unclear. Using quantitative imaging, we found a complex pattern of adherens junction (AJ) levels in the ectoderm prior to gastrulation onset in Drosophila. AJ intensity exhibited a double-sided gradient, with peaks at the dorsal midline and ventral neuroectoderm. We show that this dorsal-ventral AJ pattern is regulated by epidermal growth factor (EGF) signaling and that this signal is required for ectoderm cell movement during mesoderm invagination and axis extension. We identify AJ levels and junctional actomyosin as downstream effectors of EGFR signaling. Overall, our study demonstrates an EGF-patterned mechanical feedback mechanism that coordinates tissue folding and convergent extension to facilitate embryo-wide gastrulation movements.

Keywords:  Drosophila melanogaster; EGFR signaling; actomyosin; adherens junction; cell adhesion; gastrulation; morphogenesis

DOI:  https://doi.org/10.1016/j.devcel.2024.10.002
Dev Cell. 2024 Oct 22. pii: S1534-5807(24)00601-4. [Epub ahead of print]

PI3K/AKT signaling controls ICM maturation and proper epiblast and primitive endoderm specification in mice.

Anna Geiselmann, Adèle Micouin, Sandrine Vandormael-Pournin, Vincent Laville, Almira Chervova, Sébastien Mella, Pablo Navarro, Michel Cohen-Tannoudji.

  The inner cell mass (ICM) of early mouse embryos is specified into epiblast (Epi) and primitive endoderm (PrE) lineages during blastocyst formation. The antagonistic transcription factors (TFs) NANOG and GATA-binding protein 6 (GATA6) in combination with fibroblast growth factor (FGF)/extracellular-signal-regulated kinase (ERK) signaling are central actors in ICM fate choice. However, what initiates the specification of ICM progenitors into Epi or PrE and whether other factors are involved in this process has not been fully understood yet. Here, we show that phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT) is constitutively active during preimplantation development. Using pharmacological inhibition, we demonstrate that PI3K/AKT enables the formation of a functional ICM capable of giving rise to both the Epi and the PrE: it maintains the expression of the TF NANOG, which specifies the Epi, and confers responsiveness to FGF4, which is essential for PrE specification. Our work thus identifies PI3K/AKT signaling as an upstream regulator controlling the molecular events required for both Epi and PrE specification.

Keywords:  FGF4; FOXO3; GSK3; NANOG; epiblast; inner cell mass; lineage specification; mTOR; mouse preimplantation embryo; primitive endoderm

DOI:  https://doi.org/10.1016/j.devcel.2024.10.001
Nat Cardiovasc Res. 2024 Oct 25.

Bone-marrow macrophage-derived GPNMB protein binds to orphan receptor GPR39 and plays a critical role in cardiac repair.

Sivakumar Ramadoss, Juan Qin, Bo Tao, Nathan E Thomas, Edward Cao, Rimao Wu, Daniel R Sandoval, Ann Piermatteo, Kaare V Grunddal, Feiyang Ma, Shen Li, Baiming Sun, Yonggang Zhou, Jijun Wan, Matteo Pellegrini, Birgitte Holst, Aldons J Lusis, Philip L S M Gordts, Arjun Deb.

Glycoprotein nonmetastatic melanoma protein B (GPNMB) is a type I transmembrane protein initially identified in nonmetastatic melanomas and has been associated with human heart failure; however, its role in cardiac injury and function remains unclear. Here we show that GPNMB expression is elevated in failing human and mouse hearts after myocardial infarction (MI). Lineage tracing and bone-marrow transplantation reveal that bone-marrow-derived macrophages are the main source of GPNMB in injured hearts. Using genetic loss-of-function models, we demonstrate that GPNMB deficiency leads to increased mortality, cardiac rupture and rapid post-MI left ventricular dysfunction. Conversely, increasing circulating GPNMB levels through viral delivery improves heart function after MI. Single-cell transcriptomics show that GPNMB enhances myocyte contraction and reduces fibroblast activation. Additionally, we identified GPR39 as a receptor for circulating GPNMB, with its absence negating the beneficial effects. These findings highlight a pivotal role of macrophage-derived GPNMBs in post-MI cardiac repair through GPR39 signaling.

DOI: https://doi.org/10.1038/s44161-024-00555-4
Mol Cell. 2024 Oct 24. pii: S1097-2765(24)00826-8. [Epub ahead of print]

Senescence suppresses the integrated stress response and activates a stress-remodeled secretory phenotype.

Matthew J Payea, Showkat A Dar, Carlos Anerillas, Jennifer L Martindale, Cedric Belair, Rachel Munk, Sulochan Malla, Jinshui Fan, Yulan Piao, Xiaoling Yang, Abid Rehman, Nirad Banskota, Kotb Abdelmohsen, Myriam Gorospe, Manolis Maragkakis.

  Senescence is a state of indefinite cell-cycle arrest associated with aging, cancer, and age-related diseases. Here, we find that translational deregulation, together with a corresponding maladaptive integrated stress response (ISR), is a hallmark of senescence that desensitizes senescent cells to stress. We present evidence that senescent cells maintain high levels of eIF2α phosphorylation, typical of ISR activation, but translationally repress production of the stress response activating transcription factor 4 (ATF4) by ineffective bypass of the inhibitory upstream open reading frames (uORFs). Surprisingly, ATF4 translation remains inhibited even after acute proteotoxic and amino acid starvation stressors, resulting in a highly diminished stress response. We also find that stress augments the senescence-associated secretory phenotype with sustained remodeling of inflammatory factors expression that is suppressed by non-uORF carrying ATF4 mRNA expression. Our results thus show that senescent cells possess a unique response to stress, which entails an increase in their inflammatory profile.

Keywords:  ATF4; ER stress; ISR; SASP; integrated stress response; nanopore direct RNA sequencing; proteomics; ribosome sequencing; senescence; senescence-associated secretory phenotype; translation

DOI:  https://doi.org/10.1016/j.molcel.2024.10.003
Nat Cell Biol. 2024 Oct 31.

Distinct H3K9me3 heterochromatin maintenance dynamics govern different gene programmes and repeats in pluripotent cells.

Jingchao Zhang, Greg Donahue, Michael B Gilbert, Tomer Lapidot, Dario Nicetto, Kenneth S Zaret.

H3K9me3 heterochromatin, established by lysine methyltransferases (KMTs) and compacted by heterochromatin protein 1 (HP1) isoforms, represses alternative lineage genes and DNA repeats. Our understanding of H3K9me3 heterochromatin stability is presently limited to individual domains and DNA repeats. Here we engineered Suv39h2-knockout mouse embryonic stem cells to degrade remaining two H3K9me3 KMTs within 1 hour and found that both passive dilution and active removal contribute to H3K9me3 decay within 12-24 hours. We discovered four different H3K9me3 decay rates across the genome and chromatin features and transcription factor binding patterns that predict the stability classes. A 'binary switch' governs heterochromatin compaction, with HP1 rapidly dissociating from heterochromatin upon KMT depletion and a particular threshold level of HP1 limiting pioneer factor binding, chromatin opening and exit from pluripotency within 12 h. Unexpectedly, receding H3K9me3 domains unearth residual HP1β peaks enriched with heterochromatin-inducing proteins. Our findings reveal distinct H3K9me3 heterochromatin maintenance dynamics governing gene networks and repeats that together safeguard pluripotency.

DOI: https://doi.org/10.1038/s41556-024-01547-z
bioRxiv. 2024 Oct 14. pii: 2024.10.13.618125. [Epub ahead of print]

Human formin FHOD3-mediated actin elongation is required for sarcomere integrity in cardiomyocytes.

Dylan A Valencia, Angela N Koeberlein, Haruko Nakano, Akos Rudas, Airi Harui, Cassandra Spencer, Atsushi Nakano, Margot E Quinlan.

  Contractility and cell motility depend on accurately controlled assembly of the actin cytoskeleton. Formins are a large group of actin assembly proteins that nucleate new actin filaments and act as elongation factors. Some formins may cap filaments, instead of elongating them, and others are known to sever or bundle filaments. The Formin HOmology Domain-containing protein (FHOD)-family of formins is critical to the formation of the fundamental contractile unit in muscle, the sarcomere. Specifically, mammalian FHOD3L plays an essential role in cardiomyocytes. Despite our knowledge of FHOD3L's importance in cardiomyocytes, its biochemical and cellular activities remain poorly understood. It has been proposed that FHOD-family formins act by capping and bundling, as opposed to assembling new filaments. Here, we demonstrate that FHOD3L nucleates actin and rapidly but briefly elongates filaments after temporarily pausing elongation, in vitro. We designed function-separating mutants that enabled us to distinguish which biochemical roles are reqùired in the cell. We found that human FHOD3L's elongation activity, but not its nucleation, capping, or bundling activity, is necessary for proper sarcomere formation and contractile function in neonatal rat ventricular myocytes. The results of this work provide new insight into the mechanisms by which formins build specific structures and will contribute to knowledge regarding how cardiomyopathies arise from defects in sarcomere formation and maintenance.

Keywords:  Actin; Cardiomyocyte; Formin; Formin Homology Domain-Containing Protein 3 (FHOD3); Hypertrophic cardiomyopathy (HCM); Sarcomere

DOI:  https://doi.org/10.1101/2024.10.13.618125
Nature. 2024 Oct;634(8036): 1187-1195

Temporal recording of mammalian development and precancer.

Mirazul Islam, Yilin Yang, Alan J Simmons, Vishal M Shah, Krushna Pavan Musale, Yanwen Xu, Naila Tasneem, Zhengyi Chen, Linh T Trinh, Paola Molina, Marisol A Ramirez-Solano, Iannish D Sadien, Jinzhuang Dou, Andrea Rolong, Ken Chen, Mark A Magnuson, Jeffrey C Rathmell, Ian G Macara, Douglas J Winton, Qi Liu, Hamim Zafar, Reza Kalhor, George M Church, Martha J Shrubsole, Robert J Coffey, Ken S Lau.

Temporal ordering of cellular events offers fundamental insights into biological phenomena. Although this is traditionally achieved through continuous direct observations1,2, an alternative solution leverages irreversible genetic changes, such as naturally occurring mutations, to create indelible marks that enables retrospective temporal ordering3-5. Using a multipurpose, single-cell CRISPR platform, we developed a molecular clock approach to record the timing of cellular events and clonality in vivo, with incorporation of cell state and lineage information. Using this approach, we uncovered precise timing of tissue-specific cell expansion during mouse embryonic development, unconventional developmental relationships between cell types and new epithelial progenitor states by their unique genetic histories. Analysis of mouse adenomas, coupled to multiomic and single-cell profiling of human precancers, with clonal analysis of 418 human polyps, demonstrated the occurrence of polyclonal initiation in 15-30% of colonic precancers, showing their origins from multiple normal founders. Our study presents a multimodal framework that lays the foundation for in vivo recording, integrating synthetic or natural indelible genetic changes with single-cell analyses, to explore the origins and timing of development and tumorigenesis in mammalian systems.

DOI: https://doi.org/10.1038/s41586-024-07954-4
Nat Commun. 2024 Oct 25. 15(1): 9238

Accumulation of F-actin drives brain aging and limits healthspan in Drosophila.

Edward T Schmid, Joseph M Schinaman, Naomi Liu-Abramowicz, Kylie S Williams, David W Walker.

The actin cytoskeleton is a key determinant of cell structure and homeostasis. However, possible tissue-specific changes to actin dynamics during aging, notably brain aging, are not understood. Here, we show that there is an age-related increase in filamentous actin (F-actin) in Drosophila brains, which is counteracted by prolongevity interventions. Critically, decreasing F-actin levels in aging neurons prevents age-onset cognitive decline and extends organismal healthspan. Mechanistically, we show that autophagy, a recycling process required for neuronal homeostasis, is disabled upon actin dysregulation in the aged brain. Remarkably, disrupting actin polymerization in aged animals with cytoskeletal drugs restores brain autophagy to youthful levels and reverses cellular hallmarks of brain aging. Finally, reducing F-actin levels in aging neurons slows brain aging and promotes healthspan in an autophagy-dependent manner. Our data identify excess actin polymerization as a hallmark of brain aging, which can be targeted to reverse brain aging phenotypes and prolong healthspan.

DOI: https://doi.org/10.1038/s41467-024-53389-w
Development. 2024 Nov 01. pii: dev202842. [Epub ahead of print]151(21):

Common modes of ERK induction resolve into context-specific signalling via emergent networks and cell-type-specific transcriptional repression.

Marta Perera, Joshua M Brickman.

  Fibroblast Growth Factor signalling via ERK exerts diverse roles in development and disease. In mammalian preimplantation embryos and naïve pluripotent stem cells ERK promotes differentiation, whereas in primed pluripotent states closer to somatic differentiation ERK sustains self-renewal. How can the same pathway produce different outcomes in two related cell types? To explore context-dependent ERK signalling we generated cell and mouse lines that allow for tissue- and time-specific ERK activation. Using these tools, we find that specificity in ERK response is mostly mediated by repression of transcriptional targets that occur in tandem with reductions in chromatin accessibility at regulatory regions. Furthermore, immediate early ERK responses are largely shared by different cell types but produce cell-specific programmes as these responses interface with emergent networks in the responding cells. Induction in naïve pluripotency is accompanied by chromatin changes, whereas in later stages it is not, suggesting that chromatin context does not shape signalling response. Altogether, our data suggest that cell-type-specific responses to ERK signalling exploit the same immediate early response, but then sculpt it to specific lineages via repression of distinct cellular programmes.

Keywords:  Chromatin; ERK; FGF; Pluripotency; Signalling; Transcription

DOI:  https://doi.org/10.1242/dev.202842
bioRxiv. 2024 Oct 15. pii: 2024.10.15.618357. [Epub ahead of print]

TGF-β induces an atypical EMT to evade immune mechanosurveillance in lung adenocarcinoma dormant metastasis.

Zhenghan Wang, Yassmin Elbanna, Inês Godet, Lila Peters, George Lampe, Yanyan Chen, Joao Xavier, Morgan Huse, Joan Massagué.

The heterogeneity of epithelial-to-mesenchymal transition (EMT) programs is manifest in the diverse EMT-like phenotypes occurring during tumor progression. However, little is known about the mechanistic basis and functional role of specific forms of EMT in cancer. Here we address this question in lung adenocarcinoma (LUAD) cells that enter a dormancy period in response to TGF-β upon disseminating to distant sites. LUAD cells with the capacity to enter dormancy are characterized by expression of SOX2 and NKX2-1 primitive progenitor markers. In these cells, TGF-β induces growth inhibition accompanied by a full EMT response that subsequently transitions into an atypical mesenchymal state of round morphology and lacking actin stress fibers. TGF-β induces this transition by driving the expression of the actin-depolymerizing factor gelsolin, which changes a migratory, stress fiber-rich mesenchymal phenotype into a cortical actin-rich, spheroidal state. This transition lowers the biomechanical stiffness of metastatic progenitors, protecting them from killing by mechanosensitive cytotoxic T lymphocytes (CTLs) and natural killer (NK) cells. Inhibiting this actin depolymerization process clears tissues of dormant metastatic cells. Thus, LUAD primitive progenitors undergo an atypical EMT as part of a strategy to evade immune-mediated elimination during dormancy. Our results provide a mechanistic basis and functional role of this atypical EMT response of LUAD metastatic progenitors and further illuminate the role of TGF-β as a crucial driver of immune evasive metastatic dormancy.

DOI: https://doi.org/10.1101/2024.10.15.618357
Mol Cell. 2024 Oct 23. pii: S1097-2765(24)00828-1. [Epub ahead of print]

Transient promoter interactions modulate developmental gene activation.

Sylvia Mahara, Sonja Prüssing, Valeriia Smialkovska, Samuel Krall, Susannah Holliman, Belinda Blum, Victoria Dachtler, Helena Borgers, Etienne Sollier, Christoph Plass, Angelika Feldmann.

  Transcriptional induction coincides with the formation of various chromatin topologies. Strong evidence supports that gene activation is accompanied by a general increase in promoter-enhancer interactions. However, it remains unclear how these topological changes are coordinated across time and space during transcriptional activation. Here, we combine chromatin conformation capture with transcription and chromatin profiling during an embryonic stem cell (ESC) differentiation time course to determine how 3D genome restructuring is related to transcriptional transitions. This approach allows us to identify distinct topological alterations that are associated with the magnitude of transcriptional induction. We detect transiently formed interactions and demonstrate by genetic deletions that associated distal regulatory elements (DREs), as well as appropriate formation and disruption of these interactions, can contribute to the transcriptional induction of linked genes. Together, our study links topological dynamics to the magnitude of transcriptional induction and detects an uncharacterized type of transcriptionally important DREs.

Keywords:  Capture-C; chromatin organization; distal regulatory elements; embryonic stem cell differentiation; gene expression; genome topology; histone modifications; temporal dynamics

DOI:  https://doi.org/10.1016/j.molcel.2024.10.005
Nat Mater. 2024 Nov;23(11): 1563-1574

Rupture strength of living cell monolayers.

Julia Duque, Alessandra Bonfanti, Jonathan Fouchard, Lucia Baldauf, Sara R Azenha, Emma Ferber, Andrew Harris, Elias H Barriga, Alexandre J Kabla, Guillaume Charras.

To fulfil their function, epithelial tissues need to sustain mechanical stresses and avoid rupture. Although rupture is usually undesired, it is central to some developmental processes, for example, blastocoel formation. Nonetheless, little is known about tissue rupture because it is a multiscale phenomenon that necessitates comprehension of the interplay between mechanical forces and biological processes at the molecular and cellular scales. Here we characterize rupture in epithelial monolayers using mechanical measurements, live imaging and computational modelling. We show that despite consisting of only a single layer of cells, monolayers can withstand surprisingly large deformations, often accommodating several-fold increases in their length before rupture. At large deformation, epithelia increase their stiffness multiple fold in a process controlled by a supracellular network of keratin filaments. Perturbing the keratin network organization fragilized the monolayers and prevented strain-stiffening. Although the kinetics of adhesive bond rupture ultimately control tissue strength, tissue rheology and the history of deformation set the strain and stress at the onset of fracture.

DOI: https://doi.org/10.1038/s41563-024-02027-3
Cell. 2024 Oct 22. pii: S0092-8674(24)01146-2. [Epub ahead of print]

Multiparameter imaging reveals clinically relevant cancer cell-stroma interaction dynamics in head and neck cancer.

Karolina Punovuori, Fabien Bertillot, Yekaterina A Miroshnikova, Mirjam I Binner, Satu-Marja Myllymäki, Gautier Follain, Kai Kruse, Johannes Routila, Teemu Huusko, Teijo Pellinen, Jaana Hagström, Noemi Kedei, Sami Ventelä, Antti Mäkitie, Johanna Ivaska, Sara A Wickström.

  Epithelial tumors are characterized by abundant inter- and intra-tumor heterogeneity, which complicates diagnostics and treatment. The contribution of cancer-stroma interactions to this heterogeneity is poorly understood. Here, we report a paradigm to quantify phenotypic diversity in head and neck squamous cell carcinoma (HNSCC) with single-cell resolution. By combining cell-state markers with morphological features, we identify phenotypic signatures that correlate with clinical features, including metastasis and recurrence. Integration of tumor and stromal signatures reveals that partial epithelial-mesenchymal transition (pEMT) renders disease outcome highly sensitive to stromal composition, generating a strong prognostic and predictive signature. Spatial transcriptomics and subsequent analyses of cancer spheroid dynamics identify the cancer-associated fibroblast-pEMT axis as a nexus for intercompartmental signaling that reprograms pEMT cells into an invasive phenotype. Taken together, we establish a paradigm to identify clinically relevant tumor phenotypes and discover a cell-state-dependent interplay between stromal and epithelial compartments that drives cancer aggression.

Keywords:  cancer; cancer biomarker; cancer stem cell; epithelial-to-mesenchyme-transition

DOI:  https://doi.org/10.1016/j.cell.2024.09.046
Proc Natl Acad Sci U S A. 2024 Nov 05. 121(45): e2406174121

COX15 deficiency causes oocyte ferroptosis.

Zhihua Zhang, Ran Yu, Qiuwen Shi, Zhi-Jing Wu, Qingchun Li, Jian Mu, Biaobang Chen, Juanzi Shi, Renmin Ni, Ling Wu, Qiaoli Li, Jing Fu, Rong Li, Xiaoxi Sun, Jiucun Wang, Lin He, Yanping Kuang, Qing Sang, Lei Wang.

  Mitochondria play diverse roles in mammalian physiology. The architecture, activity, and physiological functions of mitochondria in oocytes are largely different from those in somatic cells, but the mitochondrial proteins related to oocyte quality and reproductive longevity remain largely unknown. Here, using whole-exome sequencing data from 1,024 women (characterized by oocyte maturation arrest and degenerated or morphologically abnormal oocytes) and 2,868 healthy controls, we performed a population and gene-based burden test for mitochondrial genes and identified a candidate gene, cytochrome c oxidase assembly protein 15 (COX15). We report that biallelic COX15 pathogenic variants cause human oocyte ferroptosis and female infertility in a recessive inheritance pattern. COX15 variants impaired mitochondrial respiration in Saccharomyces cerevisiae and led to reduced protein levels in HeLa cells. Oocyte-specific deletion of Cox15 led to impaired Fe2+ and reactive oxygen species homeostasis that caused mitochondrial dysfunction and ultimately sensitized oocytes to ferroptosis. In addition, ferrostatin-1 (an inhibitor of ferroptosis) could rescue the oocyte ferroptosis phenotype in vitro and ex vivo. Our findings not only provide a genetic diagnostic marker for oocyte development defects but also expand the spectrum of mitochondrial disorders to female infertility and contribute to unique insights into the role of ferroptosis in human oocyte defects.

Keywords:  COX15 deficiency; female infertility; ferroptosis; mitochondrial disorders; oocyte defects

DOI:  https://doi.org/10.1073/pnas.2406174121
Cell Rep Med. 2024 Oct 17. pii: S2666-3791(24)00542-1. [Epub ahead of print] 101795

A humanized monoclonal antibody targeting an ectonucleotidase rescues cardiac metabolism and heart function after myocardial infarction.

Shen Li, Bo Tao, Jijun Wan, Enca Montecino-Rodriguez, Ping Wang, Feiyang Ma, Baiming Sun, Yiqian Gu, Sivakumar Ramadoss, Lianjiu Su, Qihao Sun, Johanna Ten Hoeve, Linsey Stiles, Jeffrey Collins, R Michael van Dam, Mikayla Tamboline, Richard Taschereau, Orian Shirihai, Douglas B Kitchen, Matteo Pellegrini, Thomas Graeber, Kenneth Dorshkind, Shili Xu, Arjun Deb.

Myocardial infarction (MI) results in aberrant cardiac metabolism, but no therapeutics have been designed to target cardiac metabolism to enhance heart repair. We engineer a humanized monoclonal antibody against the ectonucleotidase ENPP1 (hENPP1mAb) that targets metabolic crosstalk in the infarcted heart. In mice expressing human ENPP1, systemic administration of hENPP1mAb metabolically reprograms myocytes and non-myocytes and leads to a significant rescue of post-MI heart dysfunction. Using metabolomics, single-nuclear transcriptomics, and cellular respiration studies, we show that the administration of the hENPP1mAb induces organ-wide metabolic and transcriptional reprogramming of the heart that enhances myocyte cellular respiration and decreases cell death and fibrosis in the infarcted heart. Biodistribution and safety studies showed specific organ-wide distribution with the antibody being well tolerated. In humanized animals, with drug clearance kinetics similar to humans, we demonstrate that a single "shot" of the hENPP1mAb after MI is sufficient to rescue cardiac dysfunction.

DOI: https://doi.org/10.1016/j.xcrm.2024.101795
Cell. 2024 Oct 24. pii: S0092-8674(24)01149-8. [Epub ahead of print]

Structure-guided discovery of bile acid derivatives for treating liver diseases without causing itch.

Jun Yang, Tianjun Zhao, Junping Fan, Huaibin Zou, Guangyi Lan, Fusheng Guo, Yaocheng Shi, Han Ke, Huasheng Yu, Zongwei Yue, Xin Wang, Yingjie Bai, Shuai Li, Yingjun Liu, Xiaoming Wang, Yu Chen, Yulong Li, Xiaoguang Lei.

  Chronic itch is a debilitating symptom profoundly impacting the quality of life in patients with liver diseases like cholestasis. Activation of the human G-protein coupled receptor, MRGPRX4 (hX4), by bile acids (BAs) is implicated in promoting cholestasis itch. However, the detailed underlying mechanisms remain elusive. Here, we identified 3-sulfated BAs that are elevated in cholestatic patients with itch symptoms. We solved the cryo-EM structure of hX4-Gq in a complex with 3-phosphated deoxycholic acid (DCA-3P), a mimic of the endogenous 3-sulfated deoxycholic acid (DCA-3S). This structure revealed an unprecedented ligand-binding pocket in MRGPR family proteins, highlighting the crucial role of the 3-hydroxyl (3-OH) group on BAs in activating hX4. Guided by this structural information, we designed and developed compound 7 (C7), a BA derivative lacking the 3-OH. Notably, C7 effectively alleviates hepatic injury and fibrosis in liver disease models while significantly mitigating the itch side effects.

Keywords:  3-sulfonated bile acids; MRGPRX4; OCA; bile acids; cholestatic pruritus; cryo-EM structure; deoxycholic acid; farnesoid X receptor; liver diseases; non-alcoholic steatohepatitis

DOI:  https://doi.org/10.1016/j.cell.2024.10.001
Nature. 2024 Oct 30.

Myocardial infarction augments sleep to limit cardiac inflammation and damage.

Pacific Huynh, Jan D Hoffmann, Teresa Gerhardt, Máté G Kiss, Faris M Zuraikat, Oren Cohen, Christopher Wolfram, Abi G Yates, Alexander Leunig, Merlin Heiser, Lena Gaebel, Matteo Gianeselli, Sukanya Goswami, Annie Khamhoung, Jeffrey Downey, Seonghun Yoon, Zhihong Chen, Vladimir Roudko, Travis Dawson, Joana Ferreira da Silva, Natalie J Ameral, Jarod Morgenroth-Rebin, Darwin D'Souza, Laura L Koekkoek, Walter Jacob, Jazz Munitz, Donghoon Lee, John F Fullard, Mandy M T van Leent, Panos Roussos, Seunghee Kim-Schulze, Neomi Shah, Benjamin P Kleinstiver, Filip K Swirski, David Leistner, Marie-Pierre St-Onge, Cameron S McAlpine.

Sleep is integral to cardiovascular health1,2. Yet, the circuits that connect cardiovascular pathology and sleep are incompletely understood. It remains unclear whether cardiac injury influences sleep and whether sleep-mediated neural outputs contribute to heart healing and inflammation. Here we report that in humans and mice, monocytes are actively recruited to the brain after myocardial infarction (MI) to augment sleep, which suppresses sympathetic outflow to the heart, limiting inflammation and promoting healing. After MI, microglia rapidly recruit circulating monocytes to the brain's thalamic lateral posterior nucleus (LPN) via the choroid plexus, where they are reprogrammed to generate tumour necrosis factor (TNF). In the thalamic LPN, monocytic TNF engages Tnfrsf1a-expressing glutamatergic neurons to increase slow wave sleep pressure and abundance. Disrupting sleep after MI worsens cardiac function, decreases heart rate variability and causes spontaneous ventricular tachycardia. After MI, disrupting or curtailing sleep by manipulating glutamatergic TNF signalling in the thalamic LPN increases cardiac sympathetic input which signals through the β2-adrenergic receptor of macrophages to promote a chemotactic signature that increases monocyte influx. Poor sleep in the weeks following acute coronary syndrome increases susceptibility to secondary cardiovascular events and reduces the heart's functional recovery. In parallel, insufficient sleep in humans reprogrammes β2-adrenergic receptor-expressing monocytes towards a chemotactic phenotype, enhancing their migratory capacity. Collectively, our data uncover cardiogenic regulation of sleep after heart injury, which restricts cardiac sympathetic input, limiting inflammation and damage.

DOI: https://doi.org/10.1038/s41586-024-08100-w
Cell. 2024 Oct 23. pii: S0092-8674(24)01147-4. [Epub ahead of print]

A multimodal zebrafish developmental atlas reveals the state-transition dynamics of late-vertebrate pluripotent axial progenitors.

Merlin Lange, Alejandro Granados, Shruthi VijayKumar, Jordão Bragantini, Sarah Ancheta, Yang-Joon Kim, Sreejith Santhosh, Michael Borja, Hirofumi Kobayashi, Erin McGeever, Ahmet Can Solak, Bin Yang, Xiang Zhao, Yang Liu, Angela M Detweiler, Sheryl Paul, Ilan Theodoro, Honey Mekonen, Chris Charlton, Tiger Lao, Rachel Banks, Sheng Xiao, Adrian Jacobo, Keir Balla, Kyle Awayan, Samuel D'Souza, Robert Haase, Alexandre Dizeux, Olivier Pourquie, Rafael Gómez-Sjöberg, Greg Huber, Mattia Serra, Norma Neff, Angela Oliveira Pisco, Loïc A Royer.

  Elucidating organismal developmental processes requires a comprehensive understanding of cellular lineages in the spatial, temporal, and molecular domains. In this study, we introduce Zebrahub, a dynamic atlas of zebrafish embryonic development that integrates single-cell sequencing time course data with lineage reconstructions facilitated by light-sheet microscopy. This atlas offers high-resolution and in-depth molecular insights into zebrafish development, achieved through the sequencing of individual embryos across ten developmental stages, complemented by reconstructions of cellular trajectories. Zebrahub also incorporates an interactive tool to navigate the complex cellular flows and lineages derived from light-sheet microscopy data, enabling in silico fate-mapping experiments. To demonstrate the versatility of our multimodal resource, we utilize Zebrahub to provide fresh insights into the pluripotency of neuro-mesodermal progenitors (NMPs) and the origins of a joint kidney-hemangioblast progenitor population.

Keywords:  NMPs; RNA velocity; cell state transition; embryonic pluripotency; in silico fate mapping; light-sheet microscopy; lineage reconstruction; neuro-mesodermal progenitors; scRNA-seq; single-cell RNA sequencing; transcriptomic variability; zebrafish developmental atlas

DOI:  https://doi.org/10.1016/j.cell.2024.09.047
Sci Signal. 2024 Oct 29. 17(860): eadn3285

The de novo purine synthesis enzyme Adssl1 promotes cardiomyocyte proliferation and cardiac regeneration.

Zhigang Li, Xiaxi Dong, Lingfang Zhuang, Kangni Jia, Haomai Cheng, Hang Sun, Yuke Cui, Wenqi Ma, Keying Wei, Pupu Zhang, Hongyang Xie, Lei Yi, Zhiyong Chen, Lin Lu, Tao Li, Ruiyan Zhang, Xiaoxiang Yan.

There is a short window during which the neonatal heart has the proliferative capacity to completely repair damage, an ability that is lost in adulthood. Inducing proliferation in adult cardiomyocytes by reactivating cell cycle reentry after myocardial infarction (MI) improves cardiac function. De novo purine synthesis is a critical source of nucleotides for cell proliferation. Here, using loss- and gain-of-function genetic approaches, we explored the role of the muscle-specific de novo purine synthesis enzyme Adssl1 in cardiac regeneration. Deletion of Adssl1 in mouse neonatal hearts reduced cardiomyocyte proliferation and attenuated heart regeneration after apical resection. Conversely, cardiomyocyte-specific Adssl1 overexpression extended the postnatal regenerative window and induced robust cell cycle reentry after MI, which decreased fibrotic scar size and improved cardiac function. RNA sequencing analysis suggested that Adssl1 overexpression induced strong dedifferentiation and cell cycle entry. Moreover, LC-MS/MS analysis showed that Adssl1 overexpression was associated with increased amounts of purine metabolites, including inosine, which is in clinical use. Administration of exogenous inosine promoted cardiac repair after MI in adult mice. At a molecular level, the increase in purine metabolite production mediated by Adssl1 enhanced the activity of the proliferation-promoting mTORC1 pathway. Our study identifies a role for Adssl1 in supporting cardiomyocyte proliferation and cardiac regeneration.

DOI: https://doi.org/10.1126/scisignal.adn3285
Science. 2024 Nov;386(6721): eadk9067

A cytoplasmic osmosensing mechanism mediated by molecular crowding-sensitive DCP5.

Zhenyu Wang, Qiuhua Yang, Dan Zhang, Yuanyi Lu, Yichuan Wang, Yajie Pan, Yuping Qiu, Yongfan Men, Wei Yan, Zhina Xiao, Ruixue Sun, Wenyang Li, Hongda Huang, Hongwei Guo.

Plants are frequently challenged by osmotic stresses. How plant cells sense environmental osmolarity changes is not fully understood. We report that Arabidopsis Decapping 5 (DCP5) functions as a multifunctional cytoplasmic osmosensor that senses and responds to extracellular hyperosmolarity. DCP5 harbors a plant-specific intramolecular crowding sensor (ICS) that undergoes conformational change and drives phase separation in response to osmotically intensified molecular crowding. Upon hyperosmolarity exposure, DCP5 rapidly and reversibly assembles to DCP5-enriched osmotic stress granules (DOSGs), which sequestrate plenty of mRNA and regulatory proteins, and thus adaptively reprograms both the translatome and transcriptome to facilitate plant osmotic stress adaptation. Our findings uncover a cytoplasmic osmosensing mechanism mediated by DCP5 with plant-specific molecular crowding sensitivity and suggest a stress sensory function for hyperosmotically induced stress granules.

DOI: https://doi.org/10.1126/science.adk9067
Development. 2024 Oct 29. pii: dev.204319. [Epub ahead of print]

Germ cell progression through zebrafish spermatogenesis declines with age.

Andrea L Sposato, Hailey L Hollins, Darren R Llewellyn, Jenna M Weber, Madison N Schrock, Jeffrey A Farrell, James A Gagnon.

  Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis, the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single-cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia, but we observed a progressive decline in spermatogenesis that correlates with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males are transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increase in abundance in testes that cannot complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis.

Keywords:  Aging; Immune cells; Male fertility; Single-cell RNA sequencing; Spermatogenesis; Testis

DOI:  https://doi.org/10.1242/dev.204319
Nat Commun. 2024 Oct 26. 15(1): 9247

Genomic landscape of adult testicular germ cell tumours in the 100,000 Genomes Project.

Testicular Cancer Genomics England Clinical Interpretation Partnership Consortium

Testicular germ cell tumours (TGCT), which comprise seminoma and non-seminoma subtypes, are the most common cancers in young men. In this study, we present a comprehensive whole genome sequencing analysis of adult TGCTs. Leveraging samples from participants recruited via the UK National Health Service and data from the Genomics England 100,000 Genomes Project, our results provide an extended description of genomic elements underlying TGCT pathogenesis. This catalogue offers a comprehensive, high-resolution map of copy number alterations, structural variation, and key global genome features, including mutational signatures and analysis of extrachromosomal DNA amplification. This study establishes correlations between genomic alterations and histological diversification, revealing divergent evolutionary trajectories among TGCT subtypes. By reconstructing the chronological order of driver events, we identify a subgroup of adult TGCTs undergoing relatively late whole genome duplication. Additionally, we present evidence that human leukocyte antigen loss is a more prevalent mechanism of immune disruption in seminomas. Collectively, our findings provide valuable insights into the developmental and immune modulatory processes implicated in TGCT pathogenesis and progression.

DOI: https://doi.org/10.1038/s41467-024-53193-6
Elife. 2024 Oct 31. pii: RP93172. [Epub ahead of print]13

Exceptional longevity of mammalian ovarian and oocyte macromolecules throughout the reproductive lifespan.

Ewa K Bomba-Warczak, Karen M Velez, Luhan T Zhou, Christelle Guillermier, Seby Edassery, Matthew L Steinhauser, Jeffrey N Savas, Francesca E Duncan.

  The mechanisms contributing to age-related deterioration of the female reproductive system are complex, however aberrant protein homeostasis is a major contributor. We elucidated exceptionally stable proteins, structures, and macromolecules that persist in mammalian ovaries and gametes across the reproductive lifespan. Ovaries exhibit localized structural and cell-type-specific enrichment of stable macromolecules in both the follicular and extrafollicular environments. Moreover, ovaries and oocytes both harbor a panel of exceptionally long-lived proteins, including cytoskeletal, mitochondrial, and oocyte-derived proteins. The exceptional persistence of these long-lived molecules suggest a critical role in lifelong maintenance and age-dependent deterioration of reproductive tissues.

Keywords:  cell biology; long-lived proteins; mass spectrometry imaging; mouse; oocyte; ovaries; proteomics; reproductive aging

DOI:  https://doi.org/10.7554/eLife.93172
Nat Commun. 2024 Oct 29. 15(1): 9340

Structure of the turnover-ready state of an ancestral respiratory complex I.

Bozhidar S Ivanov, Hannah R Bridges, Owen D Jarman, Judy Hirst.

Respiratory complex I is pivotal for cellular energy conversion, harnessing energy from NADH:ubiquinone oxidoreduction to drive protons across energy-transducing membranes for ATP synthesis. Despite detailed structural information on complex I, its mechanism of catalysis remains elusive due to lack of accompanying functional data for comprehensive structure-function analyses. Here, we present the 2.3-Å resolution structure of complex I from the α-proteobacterium Paracoccus denitrificans, a close relative of the mitochondrial progenitor, in phospholipid-bilayer nanodiscs. Three eukaryotic-type supernumerary subunits (NDUFS4, NDUFS6 and NDUFA12) plus a novel L-isoaspartyl-O-methyltransferase are bound to the core complex. Importantly, the enzyme is in a single, homogeneous resting state that matches the closed, turnover-ready (active) state of mammalian complex I. Our structure reveals the elements that stabilise the closed state and completes P. denitrificans complex I as a unified platform for combining structure, function and genetics in mechanistic studies.

DOI: https://doi.org/10.1038/s41467-024-53679-3
Nucleic Acids Res. 2024 Oct 29. pii: gkae938. [Epub ahead of print]

EGFR-mediated HSP70 phosphorylation facilitates PCNA association with chromatin and DNA replication.

Yingying Wang, Anthony Fernandez, Xinyu Pei, Bing Liu, Lei Shen, Yao Yan, Hitendra S Solanki, Lin Yang, Mian Zhou, Yuming Guo, Jun Wu, Karen L Reckamp, Li Zheng, Binghui Shen.

Efficient DNA replication requires highly coordinated programs for the timely recruitment of protein complexes to DNA replication forks. Defects in this process result in replication stress, which in turn activates cell cycle checkpoints, suppresses cell proliferation and induces apoptosis. In response to persistent cell growth signals that speed up DNA replication processes, cells accelerate the recruitment of DNA replication proteins to avoid DNA replication stress. The mechanisms by which cell growth signals induce processes to facilitate the recruitment of DNA replication proteins onto the replication sites remain unclear. Here, we report that the epidermal growth factor receptor (EGFR) phosphorylates heat shock protein 70 (HSP70) for DNA replication. Such a modification promotes nuclear localization and chromatin association of HSP70, which interacts with the DNA replication coordinator, proliferating cell nuclear antigen (PCNA). HSP70 subsequently facilitates the loading of PCNA onto chromatin. Knockdown or chemical inhibition of HSP70 suppresses PCNA association with chromatin and impairs DNA synthesis and Okazaki fragment maturation, leading to replicative DNA double-strand breaks and apoptosis. Furthermore, chemical inhibition of HSP70 potentiates EGFR-tyrosine kinase inhibitor-induced tumor reduction in vivo. This work expands our understanding of oncogenesis-induced DNA replication processes and provides a foundation for improved treatments for EGFR-mutated lung cancer by simultaneously targeting HSP70.

DOI: https://doi.org/10.1093/nar/gkae938
J Am Heart Assoc. 2024 Oct 29. e037120

Cardiomyocyte-Specific Overexpression of Activated Yes-Associated Protein Modified-RNA Promotes Cardiomyocyte Proliferation and Myocardial Regeneration.

Yongyu Wang, Yalin Wu, Yu Jiang, Huilan Tan, Bijay Guragain, Thanh Nguyen, Jianli Zhao, Yang Zhou, Yuji Nakada, Jianyi Zhang.

   BACKGROUND: The proliferative capacity of cardiomyocytes in adult mammalian hearts is far too low to replace the cells that are lost to myocardial infarction. Both cardiomyocyte proliferation and myocardial regeneration can be improved via the overexpression of a constitutively active variant of YAP5SA (Yes-associated protein, 5SA [active] mutant), but persistent overexpression of proliferation-inducing genes could lead to hypertrophy and arrhythmia, whereas off-target expression in fibroblasts and macrophages could increase fibrosis and inflammation.
METHODS AND RESULTS: Transient overexpression of YAP5SA or GFP (green fluorescent protein; control) was targeted to cardiomyocytes via our cardiomyocyte-specific modified mRNA translation system (YAP5SACM-SMRTs or GFPCM-SMRTs, respectively). YAP5SA-cardiomyocyte specificity was confirmed via in vitro experiments in cardiomyocytes and cardiac fibroblasts that had been differentiated from human induced- pluripotent stem cells and in human umbilical-vein endothelial cells, and the regenerative potency of YAP5SACM-SMRTs was evaluated in a mouse myocardial infarction model. In cultured human induced-pluripotent stem cells-cardiomyocytes, YAP was abundantly expressed for 3 days after YAP5SACM-SMRTs administration and was accompanied by increases in the expression of markers for proliferation, before declining to near-background levels after day 7, whereas GFP fluorescence remained high from days 1 to 3 after GFPCM-SMRTs treatment and then slowly declined. GFP fluorescence was also observed in human induced-pluripotent stem cells-cardiac fibroblasts and human umbilical-vein endothelial cells on day 1 after GFPCM-SMRTs administration but declined substantially by day 3. In the mouse myocardial infarction model, echocardiographic assessments of left-ventricular ejection fraction and fractional shortening were significantly greater, whereas infarct sizes were significantly smaller in YAP5SACM-SMRTs-treated mice than in vehicle-treated control animals, and YAP5SACM-SMRTs appeared to promote cardiomyocyte proliferation.
CONCLUSIONS: The CM-SMRTs can be used to transiently and specifically overexpress YAP5SA in cardiomyocytes, and this treatment strategy significantly promoted cardiomyocyte proliferation and myocardial regeneration in a mouse myocardial infarction model.

Keywords:  YAP5SA; cardiomyocyte; modified RNA; myocardial infarction

DOI:  https://doi.org/10.1161/JAHA.124.037120
Curr Biol. 2024 Oct 23. pii: S0960-9822(24)01369-1. [Epub ahead of print]

Nuclear deformability facilitates apical nuclear migration in the developing zebrafish retina.

Mariana Maia-Gil, Maria Gorjão, Roman Belousov, Jaime A Espina, João Coelho, Juliette Gouhier, Ana P Ramos, Elias H Barriga, Anna Erzberger, Caren Norden.

  Nuclear positioning is a crucial aspect of cell and developmental biology. One example is the apical movement of nuclei in neuroepithelia before mitosis, which is essential for proper tissue formation. While the cytoskeletal mechanisms that drive nuclei to the apical side have been explored, the influence of nuclear properties on apical nuclear migration is less understood. Nuclear properties, such as deformability, can be linked to lamin A/C expression levels, as shown in various in vitro studies. Interestingly, many nuclei in early development, including neuroepithelial nuclei, express only low levels of lamin A/C. Therefore, we investigated whether increased lamin A expression in the densely packed zebrafish retinal neuroepithelium affects nuclear deformability and, consequently, migration phenomena. We found that overexpressing lamin A in retinal nuclei increases nuclear stiffness, which in turn indeed impairs apical nuclear migration. Interestingly, nuclei that do not overexpress lamin A but are embedded in a stiffer lamin A-overexpressing environment also exhibit impaired apical nuclear migration, indicating that these effects can be cell non-autonomous. Additionally, in the less crowded hindbrain neuroepithelium, only minor effects on apical nuclear migration are observed. Together, this suggests that the material properties of the nucleus influence nuclear movements in a tissue-dependent manner.

Keywords:  Lamin A/C; nuclear migration; nuclear properties; pseudostratified neuroepithelia; zebrafish

DOI:  https://doi.org/10.1016/j.cub.2024.10.015