bims-ginsta 2024-09-29 papers

bims-ginsta

Biomed News

on Genome instability

Issue of 2024–09–29
thirty-one papers selected by
Jinrong Hu, National University of Singapore

Marmoset and human trophoblast stem cells differ in signaling requirements and recapitulate divergent modes of trophoblast invasion.
Nuclei as mechanical bumpers during epithelial remodeling.
mTOR activity paces human blastocyst stage developmental progression.
CEP192 localises mitotic Aurora-A activity by priming its interaction with TPX2.
Evolution of translational control and the emergence of genes and open reading frames in human and non-human primate hearts.
Arp2/3 complex activity enables nuclear YAP for naïve pluripotency of human embryonic stem cells.
EDC-3 and EDC-4 regulate embryonic mRNA clearance and biomolecular condensate specialization.
Designed endocytosis-inducing proteins degrade targets and amplify signals.
Single cell genome and epigenome co-profiling reveals hardwiring and plasticity in breast cancer.
Mitochondrial protein heterogeneity stems from the stochastic nature of co-translational protein targeting in cell senescence.
Long-range repulsion between chromosomes in mammalian oocyte spindles.
Partial closure of the γ-tubulin ring complex by CDK5RAP2 activates microtubule nucleation.
An ILK/STAT3 pathway controls glioblastoma stem cell plasticity.
Single-cell multi-omics map of human fetal blood in Down syndrome.
Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.
Wnt target gene activation requires β-catenin separation into biomolecular condensates.
Exercise activates AMPK in mouse and human pancreatic islets to decrease senescence.
SUN2 mediates calcium-triggered nuclear actin polymerization to cluster active RNA polymerase II.
Transcriptional machinery as an architect of genome structure.
A single particle analysis method for detecting membrane remodelling and curvature sensing.
The genetic architecture of protein stability.
RNF20-mediated transcriptional pausing and VEGFA splicing orchestrate vessel growth.
Inverse bleb membrane protrusions pump fluid within the early mouse embryo.
Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes.
The human heart shows signs of ageing after just a month in space.
A transmitochondrial sodium gradient controls membrane potential in mammalian mitochondria.
A sustained calcium response mediated by IP3 receptor anchoring to the desmosome is essential for apoptotic cell elimination.
Genetic excision of the regulatory cardiac troponin I extension in high-heart rate mammal clades.
ARHGEF3 Regulates Hair Follicle Morphogenesis.
Morphogens in the evolution of size, shape and patterning.
Human induced pluripotent stem cell-derived cardiomyocytes to study inflammation-induced aberrant calcium transient.

Cell Stem Cell. 2024 Sep 20. pii: S1934-5909(24)00318-7. [Epub ahead of print]

Marmoset and human trophoblast stem cells differ in signaling requirements and recapitulate divergent modes of trophoblast invasion.

Dylan Siriwardena, Clara Munger, Christopher Penfold, Timo N Kohler, Antonia Weberling, Madeleine Linneberg-Agerholm, Erin Slatery, Anna L Ellermann, Sophie Bergmann, Stephen J Clark, Thomas M Rawlings, Joshua M Brickman, Wolf Reik, Jan J Brosens, Magdalena Zernicka-Goetz, Erika Sasaki, Rüdiger Behr, Florian Hollfelder, Thorsten E Boroviak.

  Early human trophoblast development has remained elusive due to the inaccessibility of the early conceptus. Non-human primate models recapitulate many features of human development and allow access to early postimplantation stages. Here, we tracked the pre- to postimplantation transition of the trophoblast lineage in superficially implanting marmoset embryos in vivo. We differentiated marmoset naive pluripotent stem cells into trophoblast stem cells (TSCs), which exhibited trophoblast-specific transcriptome, methylome, differentiation potential, and long-term self-renewal. Notably, human TSC culture conditions failed to support marmoset TSC derivation, instead inducing an extraembryonic mesoderm-like fate in marmoset cells. We show that combined MEK, TGF-β/NODAL, and histone deacetylase inhibition stabilizes a periimplantation trophoblast-like identity in marmoset TSCs. By contrast, these conditions differentiated human TSCs toward extravillous trophoblasts. Our work presents a paradigm to harness the evolutionary divergence in implantation strategies to elucidate human trophoblast development and invasion.

Keywords:  extraembryonic mesoderm; human development; interstitial implantation; marmoset embryo; marmoset trophoblast stem cells; non-human primate trophoblast; primate trophoblast stem cells; superficial implantation; trophoblast; trophoblast stem cells

DOI:  https://doi.org/10.1016/j.stem.2024.09.004
J Cell Biol. 2024 Dec 02. pii: e202405078. [Epub ahead of print]223(12):

Nuclei as mechanical bumpers during epithelial remodeling.

Noah F de Leeuw, Rashmi Budhathoki, Liam J Russell, Dinah Loerke, J Todd Blankenship.

The morphogenesis of developing tissues relies on extensive cellular rearrangements in shape, position, and identity. A key process in reshaping tissues is cell intercalation-driven elongation, where epithelial cells align and intercalate along a common axis. Typically, analyses focus on how peripheral cortical forces influence cell shape changes. Less attention is given to how inhomogeneities in internal structures, particularly the nucleus, impact cell shaping. Here, we examine how pulsed contractile and extension dynamics interact with the nucleus in elongating Drosophila embryos. Our data show that tightly packed nuclei in apical layers hinder tissue remodeling/oscillatory behaviors. We identify two mechanisms for resolving internuclear tensions: nuclear deformation and dispersion. Embryos with non-deformable nuclei use nuclear dispersion to maintain near-normal extensile rates, while those with non-dispersible nuclei due to microtubule inhibition exhibit disruptions in contractile behaviors. Disrupting both mechanisms leads to severe tissue extension defects and cell extrusion. These findings highlight the critical role of nuclear shape and positioning in topological remodeling of epithelia.

DOI: https://doi.org/10.1083/jcb.202405078
Cell. 2024 Sep 18. pii: S0092-8674(24)00977-2. [Epub ahead of print]

mTOR activity paces human blastocyst stage developmental progression.

Dhanur P Iyer, Heidar Heidari Khoei, Vera A van der Weijden, Harunobu Kagawa, Saurabh J Pradhan, Maria Novatchkova, Afshan McCarthy, Teresa Rayon, Claire S Simon, Ilona Dunkel, Sissy E Wamaitha, Kay Elder, Phil Snell, Leila Christie, Edda G Schulz, Kathy K Niakan, Nicolas Rivron, Aydan Bulut-Karslioğlu.

  Many mammals can temporally uncouple conception from parturition by pacing down their development around the blastocyst stage. In mice, this dormant state is achieved by decreasing the activity of the growth-regulating mTOR signaling pathway. It is unknown whether this ability is conserved in mammals in general and in humans in particular. Here, we show that decreasing the activity of the mTOR signaling pathway induces human pluripotent stem cells (hPSCs) and blastoids to enter a dormant state with limited proliferation, developmental progression, and capacity to attach to endometrial cells. These in vitro assays show that, similar to other species, the ability to enter dormancy is active in human cells around the blastocyst stage and is reversible at both functional and molecular levels. The pacing of human blastocyst development has potential implications for reproductive therapies.

Keywords:  blastoid; development; diapause; dormancy; human; mTOR; pluripotent stem cells

DOI:  https://doi.org/10.1016/j.cell.2024.08.048
EMBO J. 2024 Sep 26.

CEP192 localises mitotic Aurora-A activity by priming its interaction with TPX2.

James Holder, Jennifer A Miles, Matthew Batchelor, Harrison Popple, Martin Walko, Wayland Yeung, Natarajan Kannan, Andrew J Wilson, Richard Bayliss, Fanni Gergely.

  Aurora-A is an essential cell-cycle kinase with critical roles in mitotic entry and spindle dynamics. These functions require binding partners such as CEP192 and TPX2, which modulate both kinase activity and localisation of Aurora-A. Here we investigate the structure and role of the centrosomal Aurora-A:CEP192 complex in the wider molecular network. We find that CEP192 wraps around Aurora-A, occupies the binding sites for mitotic spindle-associated partners, and thus competes with them. Comparison of two different Aurora-A conformations reveals how CEP192 modifies kinase activity through the site used for TPX2-mediated activation. Deleting the Aurora-A-binding interface in CEP192 prevents centrosomal accumulation of Aurora-A, curtails its activation-loop phosphorylation, and reduces spindle-bound TPX2:Aurora-A complexes, resulting in error-prone mitosis. Thus, by supplying the pool of phosphorylated Aurora-A necessary for TPX2 binding, CEP192:Aurora-A complexes regulate spindle function. We propose an evolutionarily conserved spatial hierarchy, which protects genome integrity through fine-tuning and correctly localising Aurora-A activity.

Keywords:  Aurora-A; Centrosome; Kinase; Mitosis; Mitotic Spindle

DOI:  https://doi.org/10.1038/s44318-024-00240-z
Nat Cardiovasc Res. 2024 Sep 24.

Evolution of translational control and the emergence of genes and open reading frames in human and non-human primate hearts.

Jorge Ruiz-Orera, Duncan C Miller, Johannes Greiner, Carolin Genehr, Aliki Grammatikaki, Susanne Blachut, Jeanne Mbebi, Giannino Patone, Anna Myronova, Eleonora Adami, Nikita Dewani, Ning Liang, Oliver Hummel, Michael B Muecke, Thomas B Hildebrandt, Guido Fritsch, Lisa Schrade, Wolfram H Zimmermann, Ivanela Kondova, Sebastian Diecke, Sebastiaan van Heesch, Norbert Hübner.

Evolutionary innovations can be driven by changes in the rates of RNA translation and the emergence of new genes and small open reading frames (sORFs). In this study, we characterized the transcriptional and translational landscape of the hearts of four primate and two rodent species through integrative ribosome and transcriptomic profiling, including adult left ventricle tissues and induced pluripotent stem cell-derived cardiomyocyte cell cultures. We show here that the translational efficiencies of subunits of the mitochondrial oxidative phosphorylation chain complexes IV and V evolved rapidly across mammalian evolution. Moreover, we discovered hundreds of species-specific and lineage-specific genomic innovations that emerged during primate evolution in the heart, including 551 genes, 504 sORFs and 76 evolutionarily conserved genes displaying human-specific cardiac-enriched expression. Overall, our work describes the evolutionary processes and mechanisms that have shaped cardiac transcription and translation in recent primate evolution and sheds light on how these can contribute to cardiac development and disease.

DOI: https://doi.org/10.1038/s44161-024-00544-7
Elife. 2024 Sep 25. pii: e89725. [Epub ahead of print]13

Arp2/3 complex activity enables nuclear YAP for naïve pluripotency of human embryonic stem cells.

Nathaniel Paul Meyer, Tania Singh, Matthew L Kutys, Todd G Nystul, Diane L Barber.

  Our understanding of the transitions of human embryonic stem cells between distinct stages of pluripotency relies predominantly on regulation by transcriptional and epigenetic programs with limited insight on the role of established morphological changes. We report remodeling of the actin cytoskeleton of human embryonic stem cells (hESCs) as they transition from primed to naïve pluripotency which includes assembly of a ring of contractile actin filaments encapsulating colonies of naïve hESCs. Activity of the Arp2/3 complex is required for the actin ring, to establish uniform cell mechanics within naïve colonies, promote nuclear translocation of the Hippo pathway effectors YAP and TAZ, and effective transition to naïve pluripotency. RNA-sequencing analysis confirms that Arp2/3 complex activity regulates Hippo signaling in hESCs, and impaired naïve pluripotency with inhibited Arp2/3 complex activity is rescued by expressing a constitutively active, nuclear-localized YAP-S127A. Moreover, expression of YAP-S127A partially restores the actin filament fence with Arp2/3 complex inhibition, suggesting that actin filament remodeling is both upstream and downstream of YAP activity. These new findings on the cell biology of hESCs reveal a mechanism for cytoskeletal dynamics coordinating cell mechanics to regulate gene expression and facilitate transitions between pluripotency states.

Keywords:  cell biology; human; regenerative medicine; stem cells

DOI:  https://doi.org/10.7554/eLife.89725
Cell Rep. 2024 Sep 25. pii: S2211-1247(24)01132-X. [Epub ahead of print]43(10): 114781

EDC-3 and EDC-4 regulate embryonic mRNA clearance and biomolecular condensate specialization.

Elva Vidya, Yasaman Jami-Alahmadi, Adarsh K Mayank, Javeria Rizwan, Jia Ming Stella Xu, Tianhao Cheng, Rania Leventis, Nahum Sonenberg, James A Wohlschlegel, Maria Vera, Thomas F Duchaine.

  Animal development is dictated by the selective and timely decay of mRNAs in developmental transitions, but the impact of mRNA decapping scaffold proteins in development is unclear. This study unveils the roles and interactions of the DCAP-2 decapping scaffolds EDC-3 and EDC-4 in the embryonic development of C. elegans. EDC-3 facilitates the timely removal of specific embryonic mRNAs, including cgh-1, car-1, and ifet-1 by reducing their expression and preventing excessive accumulation of DCAP-2 condensates in somatic cells. We further uncover a role for EDC-3 in defining the boundaries between P bodies, germ granules, and stress granules. Finally, we show that EDC-4 counteracts EDC-3 and engenders the assembly of DCAP-2 with the GID (CTLH) complex, a ubiquitin ligase involved in maternal-to-zygotic transition (MZT). Our findings support a model where multiple RNA decay mechanisms temporally clear maternal and zygotic mRNAs throughout embryonic development.

Keywords:  C. elegans;; CP: Developmental biology; CP: Molecular biology; DCAP-2/Dcp2; EDC-3; EDC-4; GID/CTLH complex; IFET-1/CAR-1/CGH-1 complex; P bodies; decapping; germ granules; mRNA decay; microRNA

DOI:  https://doi.org/10.1016/j.celrep.2024.114781
Nature. 2024 Sep 25.

Designed endocytosis-inducing proteins degrade targets and amplify signals.

Buwei Huang, Mohamad Abedi, Green Ahn, Brian Coventry, Isaac Sappington, Cong Tang, Rong Wang, Thomas Schlichthaerle, Jason Z Zhang, Yujia Wang, Inna Goreshnik, Ching Wen Chiu, Adam Chazin-Gray, Sidney Chan, Stacey Gerben, Analisa Murray, Shunzhi Wang, Jason O'Neill, Li Yi, Ronald Yeh, Ayesha Misquith, Anitra Wolf, Luke M Tomasovic, Dan I Piraner, Maria J Duran Gonzalez, Nathaniel R Bennett, Preetham Venkatesh, Maggie Ahlrichs, Craig Dobbins, Wei Yang, Xinru Wang, Danny D Sahtoe, Dionne Vafeados, Rubul Mout, Shirin Shivaei, Longxing Cao, Lauren Carter, Lance Stewart, Jamie B Spangler, Kole T Roybal, Per Jr Greisen, Xiaochun Li, Gonçalo J L Bernardes, Carolyn R Bertozzi, David Baker.

Endocytosis and lysosomal trafficking of cell surface receptors can be triggered by endogenous ligands. Therapeutic approaches such as lysosome-targeting chimaeras1,2 (LYTACs) and cytokine receptor-targeting chimeras3 (KineTACs) have used this to target specific proteins for degradation by fusing modified native ligands to target binding proteins. Although powerful, these approaches can be limited by competition with native ligands and requirements for chemical modification that limit genetic encodability and can complicate manufacturing, and, more generally, there may be no native ligands that stimulate endocytosis through a given receptor. Here we describe computational design approaches for endocytosis-triggering binding proteins (EndoTags) that overcome these challenges. We present EndoTags for insulin-like growth factor 2 receptor (IGF2R) and asialoglycoprotein receptor (ASGPR), sortilin and transferrin receptors, and show that fusing these tags to soluble or transmembrane target protein binders leads to lysosomal trafficking and target degradation. As these receptors have different tissue distributions, the different EndoTags could enable targeting of degradation to different tissues. EndoTag fusion to a PD-L1 antibody considerably increases efficacy in a mouse tumour model compared to antibody alone. The modularity and genetic encodability of EndoTags enables AND gate control for higher-specificity targeted degradation, and the localized secretion of degraders from engineered cells. By promoting endocytosis, EndoTag fusion increases signalling through an engineered ligand-receptor system by nearly 100-fold. EndoTags have considerable therapeutic potential as targeted degradation inducers, signalling activators for endocytosis-dependent pathways, and cellular uptake inducers for targeted antibody-drug and antibody-RNA conjugates.

DOI: https://doi.org/10.1038/s41586-024-07948-2
bioRxiv. 2024 Sep 10. pii: 2024.09.06.611519. [Epub ahead of print]

Single cell genome and epigenome co-profiling reveals hardwiring and plasticity in breast cancer.

Kaile Wang, Yun Yan, Heba Elgamal, Jianzhuo Li, Chenling Tang, Shanshan Bai, Zhenna Xiao, Emi Sei, Yiyun Lin, Junke Wang, Jessica Montalvan, Changandeep Nagi, Alastair M Thompson, Nicholas Navin.

Understanding the impact of genetic alterations on epigenomic phenotypes during breast cancer progression is challenging with unimodal measurements. Here, we report wellDA-seq, the first high-genomic resolution, high-throughput method that can simultaneously measure the whole genome and chromatin accessibility profiles of thousands of single cells. Using wellDA-seq, we profiled 22,123 single cells from 2 normal and 9 tumors breast tissues. By directly mapping the epigenomic phenotypes to genetic lineages across cancer subclones, we found evidence of both genetic hardwiring and epigenetic plasticity. In 6 estrogen-receptor positive breast cancers, we directly identified the ancestral cancer cells, and found that their epithelial cell-of-origin was Luminal Hormone Responsive cells. We also identified cell types with copy number aberrations (CNA) in normal breast tissues and discovered non-epithelial cell types in the microenvironment with CNAs in breast cancers. These data provide insights into the complex relationship between genetic alterations and epigenomic phenotypes during breast tumor evolution.

DOI: https://doi.org/10.1101/2024.09.06.611519
Nat Commun. 2024 Sep 27. 15(1): 8274

Mitochondrial protein heterogeneity stems from the stochastic nature of co-translational protein targeting in cell senescence.

Abdul Haseeb Khan, Xuefang Gu, Rutvik J Patel, Prabha Chuphal, Matheus P Viana, Aidan I Brown, Brian M Zid, Tatsuhisa Tsuboi.

A decline in mitochondrial function is a hallmark of aging and neurodegenerative diseases. It has been proposed that changes in mitochondrial morphology, including fragmentation of the tubular mitochondrial network, can lead to mitochondrial dysfunction, yet the mechanism of this loss of function is unclear. Most proteins contained within mitochondria are nuclear-encoded and must be properly targeted to the mitochondria. Here, we report that sustained mRNA localization and co-translational protein delivery leads to a heterogeneous protein distribution across fragmented mitochondria. We find that age-induced mitochondrial fragmentation drives a substantial increase in protein expression noise across fragments. Using a translational kinetic and molecular diffusion model, we find that protein expression noise is explained by the nature of stochastic compartmentalization and that co-translational protein delivery is the main contributor to increased heterogeneity. We observed that cells primarily reduce the variability in protein distribution by utilizing mitochondrial fission-fusion processes rather than relying on the mitophagy pathway. Furthermore, we are able to reduce the heterogeneity of the protein distribution by inhibiting co-translational protein targeting. This research lays the framework for a better understanding of the detrimental impact of mitochondrial fragmentation on the physiology of cells in aging and disease.

DOI: https://doi.org/10.1038/s41467-024-52183-y
Sci Adv. 2024 Sep 27. 10(39): eadq7540

Long-range repulsion between chromosomes in mammalian oocyte spindles.

Colm P Kelleher, Yash P Rana, Daniel J Needleman.

During eukaryotic cell division, a microtubule-based structure called the spindle exerts forces on chromosomes. The best-studied spindle forces, including those responsible for the separation of sister chromatids, are directed parallel to the spindle's long axis. By contrast, little is known about forces perpendicular to the spindle axis, which determine the metaphase plate configuration and thus the location of chromosomes in the subsequent nucleus. Using live-cell microscopy, we find that metaphase chromosomes are spatially anti-correlated in mouse oocyte spindles, evidence of previously unknown long-range forces acting perpendicular to the spindle axis. We explain this observation by showing that the spindle's microtubule network behaves as a nematic liquid crystal and that deformation of the nematic field around embedded chromosomes causes long-range repulsion between them.

DOI: https://doi.org/10.1126/sciadv.adq7540
Dev Cell. 2024 Sep 23. pii: S1534-5807(24)00530-6. [Epub ahead of print]

Partial closure of the γ-tubulin ring complex by CDK5RAP2 activates microtubule nucleation.

Yixin Xu, Hugo Muñoz-Hernández, Rościsław Krutyhołowa, Florina Marxer, Ferdane Cetin, Michal Wieczorek.

  Microtubule nucleation is templated by the γ-tubulin ring complex (γ-TuRC), but its structure deviates from the geometry of α-/β-tubulin in the microtubule, explaining the complex's poor nucleating activity. Several proteins may activate the γ-TuRC, but the mechanisms underlying activation are not known. Here, we determined the structure of the porcine γ-TuRC purified using CDK5RAP2's centrosomin motif 1 (CM1). We identified an unexpected conformation of the γ-TuRC bound to multiple protein modules containing MZT2, GCP2, and CDK5RAP2, resulting in a long-range constriction of the γ-tubulin ring that brings it in closer agreement with the 13-protofilament microtubule. Additional CDK5RAP2 promoted γ-TuRC decoration and stimulated the microtubule-nucleating activities of the porcine γ-TuRC and a reconstituted, CM1-free human complex in single-molecule assays. Our results provide a structural mechanism for the control of microtubule nucleation by CM1 proteins and identify conformational transitions in the γ-TuRC that prime it for microtubule nucleation.

Keywords:  CDK5RAP2; centrosomes; cryo-EM; microtubule nucleation; microtubules; γ-tubulin ring complex

DOI:  https://doi.org/10.1016/j.devcel.2024.09.002
Dev Cell. 2024 Sep 20. pii: S1534-5807(24)00531-8. [Epub ahead of print]

An ILK/STAT3 pathway controls glioblastoma stem cell plasticity.

Alexander E P Loftus, Marianna S Romano, Anh Nguyen Phuong, Ben J McKinnel, Morwenna T Muir, Muhammad Furqan, John C Dawson, Lidia Avalle, Adam T Douglas, Richard L Mort, Adam Byron, Neil O Carragher, Steven M Pollard, Valerie G Brunton, Margaret C Frame.

  Glioblastoma (GBM) is driven by malignant neural stem-like cells that display extensive heterogeneity and phenotypic plasticity, which drive tumor progression and therapeutic resistance. Here, we show that the extracellular matrix-cell adhesion protein integrin-linked kinase (ILK) stimulates phenotypic plasticity and mesenchymal-like, invasive behavior in a murine GBM stem cell model. ILK is required for the interconversion of GBM stem cells between malignancy-associated glial-like states, and its loss produces cells that are unresponsive to multiple cell state transition cues. We further show that an ILK/STAT3 signaling pathway controls the plasticity that enables transition of GBM stem cells to an astrocyte-like state in vitro and in vivo. Finally, we find that ILK expression correlates with expression of STAT3-regulated proteins and protein signatures describing astrocyte-like and mesenchymal states in patient tumors. This work identifies ILK as a pivotal regulator of multiple malignancy-associated GBM phenotypes, including phenotypic plasticity and mesenchymal state.

Keywords:  STAT3; adhesion; astrocytes; cancer; glioblastoma; integrin-linked kinase; plasticity; stem cells

DOI:  https://doi.org/10.1016/j.devcel.2024.09.003
Nature. 2024 Sep 25.

Single-cell multi-omics map of human fetal blood in Down syndrome.

Andrew R Marderstein, Marco De Zuani, Rebecca Moeller, Jon Bezney, Evin M Padhi, Shuo Wong, Tim H H Coorens, Yilin Xie, Haoliang Xue, Stephen B Montgomery, Ana Cvejic.

Down syndrome predisposes individuals to haematological abnormalities, such as increased number of erythrocytes and leukaemia in a process that is initiated before birth and is not entirely understood1-3. Here, to understand dysregulated haematopoiesis in Down syndrome, we integrated single-cell transcriptomics of over 1.1 million cells with chromatin accessibility and spatial transcriptomics datasets using human fetal liver and bone marrow samples from 3 fetuses with disomy and 15 fetuses with trisomy. We found that differences in gene expression in Down syndrome were dependent on both cell type and environment. Furthermore, we found multiple lines of evidence that haematopoietic stem cells (HSCs) in Down syndrome are 'primed' to differentiate. We subsequently established a Down syndrome-specific map linking non-coding elements to genes in disomic and trisomic HSCs using 10X multiome data. By integrating this map with genetic variants associated with blood cell counts, we discovered that trisomy restructured regulatory interactions to dysregulate enhancer activity and gene expression critical to erythroid lineage differentiation. Furthermore, as mutations in Down syndrome display a signature of oxidative stress4,5, we validated both increased mitochondrial mass and oxidative stress in Down syndrome, and observed that these mutations preferentially fell into regulatory regions of expressed genes in HSCs. Together, our single-cell, multi-omic resource provides a high-resolution molecular map of fetal haematopoiesis in Down syndrome and indicates significant regulatory restructuring giving rise to co-occurring haematological conditions.

DOI: https://doi.org/10.1038/s41586-024-07946-4
Cell Rep. 2024 Sep 19. pii: S2211-1247(24)01120-3. [Epub ahead of print]43(10): 114769

Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.

Gabriel da Silva Pescador, Danielson Baia Amaral, Joseph M Varberg, Ying Zhang, Yan Hao, Laurence Florens, Ariel A Bazzini.

  The maternal-to-zygotic transition is crucial in embryonic development, marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However, the changes occurring at the protein level during this transition remain unclear. Here, we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry, integrating transcriptomics and translatomics datasets. Our data show that, unlike RNA changes, protein changes are less dynamic. Further, increases in protein levels correlate with mRNA translation, whereas declines in protein levels do not, suggesting active protein degradation processes. Interestingly, proteins from pure zygotic genes are present at fertilization, challenging existing mRNA-based gene classifications. As a proof of concept, we utilized CRISPR-Cas13d to target znf281b mRNA, a gene whose protein significantly accumulates within the first 2 h post-fertilization, demonstrating its crucial role in development. Consequently, our protein profiling, coupled with CRISPR-Cas13d, offers a complementary approach to unraveling maternal factor function during embryonic development.

Keywords:  CP: Developmental biology; CP: Molecular biology; CRISPR-Cas13d; SLAM-seq; Zfp281; maternal-to-zygotic transition; pure zygotic; quantitative proteomics; tandem mass tag; znf281b

DOI:  https://doi.org/10.1016/j.celrep.2024.114769
PLoS Biol. 2024 Sep 24. 22(9): e3002368

Wnt target gene activation requires β-catenin separation into biomolecular condensates.

Richard A Stewart, Zhihao Ding, Ung Seop Jeon, Lauren B Goodman, Jeannine J Tran, John P Zientko, Malavika Sabu, Ken M Cadigan.

The Wnt/β-catenin signaling pathway plays numerous essential roles in animal development and tissue/stem cell maintenance. The activation of genes regulated by Wnt/β-catenin signaling requires the nuclear accumulation of β-catenin, a transcriptional co-activator. β-catenin is recruited to many Wnt-regulated enhancers through direct binding to T-cell factor/lymphoid enhancer factor (TCF/LEF) family transcription factors. β-catenin has previously been reported to form phase-separated biomolecular condensates (BMCs), which was implicated as a component of β-catenin's mechanism of action. This function required aromatic amino acid residues in the intrinsically disordered regions (IDRs) at the N- and C-termini of the protein. In this report, we further explore a role for β-catenin BMCs in Wnt target gene regulation. We find that β-catenin BMCs are miscible with LEF1 BMCs in vitro and in cultured cells. We characterized a panel of β-catenin mutants with different combinations of aromatic residue mutations in human cell culture and Drosophila melanogaster. Our data support a model in which aromatic residues across both IDRs contribute to BMC formation and signaling activity. Although different Wnt targets have different sensitivities to loss of β-catenin's aromatic residues, the activation of every target examined was compromised by aromatic substitution. These mutants are not defective in nuclear import or co-immunoprecipitation with several β-catenin binding partners. In addition, residues in the N-terminal IDR with no previously known role in signaling are clearly required for the activation of various Wnt readouts. Consistent with this, deletion of the N-terminal IDR results in a loss of signaling activity, which can be rescued by the addition of heterologous IDRs enriched in aromatic residues. Overall, our work supports a model in which the ability of β-catenin to form biomolecular condensates in the nucleus is tightly linked to its function as a transcriptional co-regulator.

DOI: https://doi.org/10.1371/journal.pbio.3002368
Nat Metab. 2024 Sep 24.

Exercise activates AMPK in mouse and human pancreatic islets to decrease senescence.

Priscila Carapeto, Kanako Iwasaki, Francesko Hela, Jiho Kahng, Ana B Alves-Wagner, Roeland J W Middelbeek, Michael F Hirshman, Guy A Rutter, Laurie J Goodyear, Cristina Aguayo-Mazzucato.

Beta (β)-cell senescence contributes to type 2 diabetes mellitus (T2DM). While exercise is vital for T2DM management and significantly affects cellular ageing markers, its effect on β-cell senescence remains unexplored. Here, we show that short-term endurance exercise training (treadmill running, 1 h per day for 10 days) in two male and female mouse models of insulin resistance decreases β-cell senescence. In vivo and in vitro experiments revealed that this effect is mediated, at least in part, by training-induced increases in serum glucagon, leading to activation of 5'-AMP-activated protein kinase (AMPK) signalling in β-cells. AMPK activation resulted in the nuclear translocation of NRF2 and decreased expression of senescence markers and effectors. Remarkably, human islets from male and female donors with T2DM treated with serum collected after a 10-week endurance exercise training programme showed a significant decrease in the levels of senescence markers. These findings indicate that exercise training decreases senescence in pancreatic islets, offering promising therapeutic implications for T2DM.

DOI: https://doi.org/10.1038/s42255-024-01130-8
EMBO Rep. 2024 Sep 24.

SUN2 mediates calcium-triggered nuclear actin polymerization to cluster active RNA polymerase II.

Svenja Ulferts, Robert Grosse.

  The nucleoskeleton is essential for nuclear architecture as well as genome integrity and gene expression. In addition to lamins, titin or spectrins, dynamic actin filament polymerization has emerged as a potential intranuclear structural element but its functions are less well explored. Here we found that calcium elevations trigger rapid nuclear actin assembly requiring the nuclear membrane protein SUN2 independently of its function as a component of the LINC complex. Instead, SUN2 colocalized and associated with the formin and actin nucleator INF2 in the nuclear envelope in a calcium-regulated manner. Moreover, SUN2 is required for active RNA polymerase II (RNA Pol II) clustering in response to calcium elevations. Thus, our data uncover a SUN2-formin module linking the nuclear envelope to intranuclear actin assembly to promote signal-dependent spatial reorganization of active RNA Pol II.

Keywords:  Formin; Nuclear Actin; RNA Pol II Clustering; SUN2

DOI:  https://doi.org/10.1038/s44319-024-00274-8
Curr Opin Struct Biol. 2024 Sep 21. pii: S0959-440X(24)00147-7. [Epub ahead of print]89 102920

Transcriptional machinery as an architect of genome structure.

Nadezda A Fursova, Daniel R Larson.

Chromatin organization, facilitated by compartmentalization and loop extrusion, is crucial for proper gene expression and cell viability. Transcription has long been considered important for shaping genome architecture due to its pervasive activity across the genome and impact on the local chromatin environment. Although earlier studies suggested a minimal contribution of transcription to shaping global genome structure, recent insights from high-resolution chromatin contact mapping, polymer simulations, and acute perturbations have revealed its critical role in dynamic chromatin organization at the level of active genes and enhancer-promoter interactions. In this review, we discuss these latest advances, highlighting the direct interplay between transcriptional machinery and loop extrusion. Finally, we explore how transcription of genes and non-coding regulatory elements may contribute to the specificity of gene regulation, focusing on enhancers as sites of targeted cohesin loading.

DOI: https://doi.org/10.1016/j.sbi.2024.102920
J Cell Sci. 2024 Sep 26. pii: jcs.263533. [Epub ahead of print]

A single particle analysis method for detecting membrane remodelling and curvature sensing.

Adeline Colussi, Leonardo Almeida-Souza, Harvey T McMahon.

  In biology, shape and function are related. Therefore, it is important to understand how membrane shape is generated, stabilised and sensed by proteins and how this relates to organelle function. Here we present an assay that can detect curvature preference and membrane remodelling using free-floating liposomes using protein concentrations in a physiologically relevant ranges. The assay reproduced known curvature preferences of BAR domains and allowed the discovery of high curvature preference for the PH domain of AKT and the FYVE domain of HRS. In addition, our method reproduced the membrane vesiculation activity of the ENTH domain of Epsin1 and showed similar activity for the ANTH domains of PiCALM and Hip1R. Finally, we found that the curvature sensitivity of the N-BAR domain of Endophilin inversely correlates to membrane charge and that deletion of its N-terminal amphipathic helix increased its curvature specificity. Thus, our method is a generally applicable qualitative method for assessing membrane curvature sensing and remodelling by proteins.

Keywords:  Endophilin; Membrane curvature preference; Membrane remodeling; Single particle analysis

DOI:  https://doi.org/10.1242/jcs.263533
Nature. 2024 Sep 25.

The genetic architecture of protein stability.

Andre J Faure, Aina Martí-Aranda, Cristina Hidalgo-Carcedo, Antoni Beltran, Jörn M Schmiedel, Ben Lehner.

There are more ways to synthesize a 100-amino acid (aa) protein (20100) than there are atoms in the universe. Only a very small fraction of such a vast sequence space can ever be experimentally or computationally surveyed. Deep neural networks are increasingly being used to navigate high-dimensional sequence spaces1. However, these models are extremely complicated. Here, by experimentally sampling from sequence spaces larger than 1010, we show that the genetic architecture of at least some proteins is remarkably simple, allowing accurate genetic prediction in high-dimensional sequence spaces with fully interpretable energy models. These models capture the nonlinear relationships between free energies and phenotypes but otherwise consist of additive free energy changes with a small contribution from pairwise energetic couplings. These energetic couplings are sparse and associated with structural contacts and backbone proximity. Our results indicate that protein genetics is actually both rather simple and intelligible.

DOI: https://doi.org/10.1038/s41586-024-07966-0
Nat Cardiovasc Res. 2024 Sep 25.

RNF20-mediated transcriptional pausing and VEGFA splicing orchestrate vessel growth.

Nalan Tetik-Elsherbiny, Adel Elsherbiny, Aadhyaa Setya, Johannes Gahn, Yongqin Tang, Purnima Gupta, Yanliang Dou, Heike Serke, Thomas Wieland, Alexandre Dubrac, Joerg Heineke, Michael Potente, Julio Cordero, Roxana Ola, Gergana Dobreva.

Signal-responsive gene expression is essential for vascular development, yet the mechanisms integrating signaling inputs with transcriptional activities are largely unknown. Here we show that RNF20, the primary E3 ubiquitin ligase for histone H2B, plays a multifaceted role in sprouting angiogenesis. RNF20 mediates RNA polymerase (Pol II) promoter-proximal pausing at genes highly paused in endothelial cells, involved in VEGFA signaling, stress response, cell cycle control and mRNA splicing. It also orchestrates large-scale mRNA processing events that alter the bioavailability and function of critical pro-angiogenic factors, such as VEGFA. Mechanistically, RNF20 restricts ERG-dependent Pol II pause release at highly paused genes while binding to Notch1 to promote H2B monoubiquitination at Notch target genes and Notch-dependent gene expression. This balance is crucial, as loss of Rnf20 leads to uncontrolled tip cell specification. Our findings highlight the pivotal role of RNF20 in regulating VEGF-Notch signaling circuits during vessel growth, underscoring its potential for therapeutic modulation of angiogenesis.

DOI: https://doi.org/10.1038/s44161-024-00546-5
Nat Cell Biol. 2024 Sep 20.

Inverse bleb membrane protrusions pump fluid within the early mouse embryo.

DOI: https://doi.org/10.1038/s41556-024-01510-y
bioRxiv. 2024 Sep 09. pii: 2024.09.09.611392. [Epub ahead of print]

Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes.

Jorge Diego Martin-Rufino, Alexis Caulier, Seayoung Lee, Nicole Castano, Emily King, Samantha Joubran, Marcus Jones, Seth R Goldman, Uma P Arora, Lara Wahlster, Eric S Lander, Vijay G Sankaran.

Most phenotype-associated genetic variants map to non-coding regulatory regions of the human genome. Moreover, variants associated with blood cell phenotypes are enriched in regulatory regions active during hematopoiesis. To systematically explore the nature of these regions, we developed a highly efficient strategy, Perturb-multiome, that makes it possible to simultaneously profile both chromatin accessibility and gene expression in single cells with CRISPR-mediated perturbation of a range of master transcription factors (TFs). This approach allowed us to examine the connection between TFs, accessible regions, and gene expression across the genome throughout hematopoietic differentiation. We discovered that variants within the TF-sensitive accessible chromatin regions, while representing less than 0.3% of the genome, show a ~100-fold enrichment in heritability across certain blood cell phenotypes; this enrichment is strikingly higher than for other accessible chromatin regions. Our approach facilitates large-scale mechanistic understanding of phenotype-associated genetic variants by connecting key cis-regulatory elements and their target genes within gene regulatory networks.

DOI: https://doi.org/10.1101/2024.09.09.611392
Nature. 2024 Sep 24.

The human heart shows signs of ageing after just a month in space.

Gemma Conroy.



Keywords:  Cardiovascular biology; Cell biology; Space physics

DOI:  https://doi.org/10.1038/d41586-024-03105-x
Cell. 2024 Sep 17. pii: S0092-8674(24)00974-7. [Epub ahead of print]

A transmitochondrial sodium gradient controls membrane potential in mammalian mitochondria.

Pablo Hernansanz-Agustín, Carmen Morales-Vidal, Enrique Calvo, Paolo Natale, Yolanda Martí-Mateos, Sara Natalia Jaroszewicz, José Luis Cabrera-Alarcón, Rebeca Acín-Pérez, Iván López-Montero, Jesús Vázquez, José Antonio Enríquez.

  Eukaryotic cell function and survival rely on the use of a mitochondrial H+ electrochemical gradient (Δp), which is composed of an inner mitochondrial membrane (IMM) potential (ΔΨmt) and a pH gradient (ΔpH). So far, ΔΨmt has been assumed to be composed exclusively of H+. Here, using a rainbow of mitochondrial and nuclear genetic models, we have discovered that a Na+ gradient equates with the H+ gradient and controls half of ΔΨmt in coupled-respiring mammalian mitochondria. This parallelism is controlled by the activity of the long-sought Na+-specific Na+/H+ exchanger (mNHE), which we have identified as the P-module of complex I (CI). Deregulation of this mNHE function, without affecting the canonical enzymatic activity or the assembly of CI, occurs in Leber's hereditary optic neuropathy (LHON), which has profound consequences in ΔΨmt and mitochondrial Ca2+ homeostasis and explains the previously unknown molecular pathogenesis of this neurodegenerative disease.

Keywords:  LHON; Na(+) gradient; complex I; mitochondrial Na(+)/H(+) antiporter; ΔΨmt

DOI:  https://doi.org/10.1016/j.cell.2024.08.045
Curr Biol. 2024 Sep 17. pii: S0960-9822(24)01173-4. [Epub ahead of print]

A sustained calcium response mediated by IP3 receptor anchoring to the desmosome is essential for apoptotic cell elimination.

Yuma Cho, Ikuko Koyama-Honda, Akihiko Tanimura, Kenji Matsuzawa, Junichi Ikenouchi.

  Efficient elimination of apoptotic cells within epithelial cell sheets is crucial for preserving epithelial barrier integrity.1 It is well established that immediate neighbors of an apoptotic cell actively participate in its removal by enclosing it within a wall of actomyosin, pushing it out in a purse-string manner in a process called apical extrusion.2,3,4,5,6,7 Here, we found that sustained elevation of calcium ions in neighboring epithelial cells is necessary to generate the contractility required for apoptotic cell elimination. This phenomenon, which we call calcium response in effectors of apical extrusion (CaRE), highlights the disparate calcium dynamics within the epithelial sheet. Furthermore, we elucidate the essential role of desmosomes in CaRE. Specifically, we identify a subset of IP3 receptors within the endoplasmic reticulum that is recruited to the desmosome by K-Ras-induced actin-binding protein as the core component of this process. The interplay between these cellular structures heightens actomyosin contractility to drive apoptotic cell removal. Our findings underscore the physiological significance of integrating desmosomes with the endoplasmic reticulum in epithelial sheet homeostasis, shedding new light on cell-cell communication and tissue maintenance.

Keywords:  IP3R; apical extrusion; calcium dynamics; desmosome

DOI:  https://doi.org/10.1016/j.cub.2024.08.057
Science. 2024 Sep 27. 385(6716): 1466-1471

Genetic excision of the regulatory cardiac troponin I extension in high-heart rate mammal clades.

William Joyce, Kai He, Mengdie Zhang, Samuel Ogunsola, Xini Wu, Kelvin T Joseph, David Bogomolny, Wenhua Yu, Mark S Springer, Jiuyong Xie, Anthony V Signore, Kevin L Campbell.

Mammalian cardiac troponin I (cTnI) contains a highly conserved amino-terminal extension harboring protein kinase A targets [serine-23 and -24 (Ser23/24)] that are phosphorylated during β-adrenergic stimulation to defend diastolic filling by means of an increased cardiomyocyte relaxation rate. In this work, we show that the Ser23/24-encoding exon 3 of TNNI3 was pseudoexonized multiple times in shrews and moles to mimic Ser23/24 phosphorylation without adrenergic stimulation, facilitating the evolution of exceptionally high resting heart rates (~1000 beats per minute). We further reveal alternative exon 3 splicing in distantly related bat families and confirm that both cTnI splice variants are incorporated into cardiac myofibrils. Because exon 3 of human TNNI3 exhibits a relatively low splice strength score, our findings offer an evolutionarily informed strategy to excise this exon to improve diastolic function during heart failure.

DOI: https://doi.org/10.1126/science.adi8146
bioRxiv. 2024 Sep 15. pii: 2024.09.13.612256. [Epub ahead of print]

ARHGEF3 Regulates Hair Follicle Morphogenesis.

Krithika Kalyanakrishnan, Amy Beaudin, Alexandra Jetté, Sarah Ghezelbash, Diana Ioana Hotea, Jie Chen, Philippe Lefrançois, Mélanie Laurin.

During embryogenesis, cells arrange into precise patterns that enable tissues and organs to develop specialized functions. Despite its critical importance, the molecular choreography behind these collective cellular behaviors remains elusive, posing a major challenge in developmental biology and limiting advances in regenerative medicine. By using the mouse hair follicle as a mini-organ system to study the formation of bud-like structures during embryonic development, our work uncovers a crucial role for the Rho GTPase regulator ARHGEF3 in hair follicle morphogenesis. We demonstrate that Arhgef3 expression is upregulated at the onset of hair follicle placode formation. In Arhgef3 knockout animals, we observed defects in placode compaction, leading to impaired hair follicle downgrowth. Through cell culture models, we show that ARHGEF3 promotes F-actin accumulation at the cell cortex and P-cadherin enrichment at cell-cell junctions. Collectively, our study identifies ARHGEF3 as a new regulator of cell shape rearrangements during hair placode morphogenesis, warranting further exploration of its role in other epithelial appendages that arise from similar developmental processes.

DOI: https://doi.org/10.1101/2024.09.13.612256
Development. 2024 Sep 15. pii: dev202412. [Epub ahead of print]151(18):

Morphogens in the evolution of size, shape and patterning.

Lewis S Mosby, Amy E Bowen, Zena Hadjivasiliou.

  Much of the striking diversity of life on Earth has arisen from variations in the way that the same molecules and networks operate during development to shape and pattern tissues and organs into different morphologies. However, we still understand very little about the potential for diversification exhibited by different, highly conserved mechanisms during evolution, or, conversely, the constraints that they place on evolution. With the aim of steering the field in new directions, we focus on morphogen-mediated patterning and growth as a case study to demonstrate how conserved developmental mechanisms can adapt during evolution to drive morphological diversification and optimise functionality, and to illustrate how evolution algorithms and computational tools can be used alongside experiments to provide insights into how these conserved mechanisms can evolve. We first introduce key conserved properties of morphogen-driven patterning mechanisms, before summarising comparative studies that exemplify how changes in the spatiotemporal expression and signalling levels of morphogens impact the diversification of organ size, shape and patterning in nature. Finally, we detail how theoretical frameworks can be used in conjunction with experiments to probe the role of morphogen-driven patterning mechanisms in evolution. We conclude that morphogen-mediated patterning is an excellent model system and offers a generally applicable framework to investigate the evolution of developmental mechanisms.

Keywords:  Evolution; GRNs; Morphogens; Patterning

DOI:  https://doi.org/10.1242/dev.202412
Elife. 2024 Sep 27. pii: RP95867. [Epub ahead of print]13

Human induced pluripotent stem cell-derived cardiomyocytes to study inflammation-induced aberrant calcium transient.

Yuki Tatekoshi, Chunlei Chen, Jason Solomon Shapiro, Hsiang-Chun Chang, Malorie Blancard, Davi M Lyra-Leite, Paul W Burridge, Matthew Feinstein, Richard D'Aquila, Priscilla Hsue, Hossein Ardehali.

  Heart failure with preserved ejection fraction (HFpEF) is commonly found in persons living with HIV (PLWH) even when antiretroviral therapy suppresses HIV viremia. However, studying this condition has been challenging because an appropriate animal model is not available. In this article, we studied calcium transient in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) in culture to simulate the cardiomyocyte relaxation defect noted in PLWH and HFpEF and assess whether various drugs have an effect. We show that treatment of hiPSC-CMs with inflammatory cytokines (such as interferon-γ or TNF-α) impairs their Ca2+ uptake into sarcoplasmic reticulum and that SGLT2 inhibitors, clinically proven as effective for HFpEF, reverse this effect. Additionally, treatment with mitochondrial antioxidants (like mito-Tempo) and certain antiretrovirals resulted in the reversal of the effects of these cytokines on calcium transient. Finally, incubation of hiPSC-CMs with serum from HIV patients with and without diastolic dysfunction did not alter their Ca2+-decay time, indicating that the exposure to the serum of these patients is not sufficient to induce the decrease in Ca2+ uptake in vitro. Together, our results indicate that hiPSC-CMs can be used as a model to study molecular mechanisms of inflammation-mediated abnormal cardiomyocyte relaxation and screen for potential new interventions.

Keywords:  calcium transient; heart failure with preserved ejection fraction; human; human immunodeficiency virus; human induced pluripotent stem cell-derived cardiomyocyte; infectious disease; inflammation; microbiology

DOI:  https://doi.org/10.7554/eLife.95867