bims-ginsta Biomed News
on Genome instability
Issue of 2025–02–02
23 papers selected by
Jinrong Hu, National University of Singapore
  1. Centromeric chromatin clearings demarcate the site of kinetochore formation.
  2. Comparative proteomic landscapes elucidate human preimplantation development and failure.
  3. Extracellular volume expansion drives vertebrate axis elongation.
  4. C-terminal amides mark proteins for degradation via SCF-FBXO31.
  5. Long-lived cytokinetic bridges coordinate sister-cell elimination in mouse embryos.
  6. Dynamic map illuminates Hippo-cMyc module crosstalk driving cardiomyocyte proliferation.
  7. Multiomics reveals that triacylglycerol mobilization helps drive recovery from mitochondrial stress.
  8. Shaping epithelial tissues by stem cell mechanics in development and cancer.
  9. Quantitative chromatin protein dynamics during replication origin firing in human cells.
  10. eIF3 engages with 3'-UTR termini of highly translated mRNAs.
  11. Niche-derived Semaphorin 4A safeguards functional identity of myeloid-biased hematopoietic stem cells.
  12. A network of interacting ciliary tip proteins with opposing activities imparts slow and processive microtubule growth.
  13. Engineered heart muscle allografts for heart repair in primates and humans.
  14. PRC2 promotes canalisation during endodermal differentiation.
  15. Sphingolipid metabolism orchestrates establishment of the hair follicle stem cell compartment.
  16. High-resolution spatially resolved proteomics of complex tissues based on microfluidics and transfer learning.
  17. Multiplex generation and single-cell analysis of structural variants in mammalian genomes.
  18. Casz1 is required for both inner hair cell fate stabilization and outer hair cell survival.
  19. Proximity proteomics provides a new resource for exploring the function of Afadin and the complexity of cell-cell adherens junctions.
  20. Randomizing the human genome by engineering recombination between repeat elements.
  21. Temporal dynamics of the interstitial fluid proteome in human skeletal muscle following exhaustive exercise.
  22. Artificial cells with all-aqueous droplet-in-droplet structures for spatially separated transcription and translation.
  23. Genome-wide CRISPR activation screening in senescent cells reveals SOX5 as a driver and therapeutic target of rejuvenation.
  1. Cell. 2025 Jan 23. pii: S0092-8674(24)01467-3. [Epub ahead of print]
    Centromeric chromatin clearings demarcate the site of kinetochore formation.
    Kathryn Kixmoeller, Ekaterina V Tarasovetc, Elie Mer, Yi-Wei Chang, Ben E Black.
      The centromere is the chromosomal locus that recruits the kinetochore, directing faithful propagation of the genome during cell division. Using cryo-ET on human mitotic chromosomes, we reveal a distinctive architecture at the centromere: clustered 20- to 25-nm nucleosome-associated complexes within chromatin clearings that delineate them from surrounding chromatin. Centromere components CENP-C and CENP-N are each required for the integrity of the complexes, while CENP-C is also required to maintain the chromatin clearing. We find that CENP-C is required in mitosis, not just for kinetochore assembly, likely reflecting its role in organizing the inner kinetochore during chromosome segregation. We further visualize the scaffold of the fibrous corona, a structure amplified at unattached kinetochores, revealing crescent-shaped parallel arrays of fibrils extending >1 μm. Thus, we reveal how the organization of centromeric chromatin creates a clearing at the site of kinetochore formation as well as the nature of kinetochore amplification mediated by corona fibrils.
    Keywords:  centromere; chromatin; chromosome; cryo-ET; kinetochore; mitosis; mitotic chromosome; nucleosome
    DOI:  https://doi.org/10.1016/j.cell.2024.12.025
  2. Cell. 2025 Jan 17. pii: S0092-8674(24)01470-3. [Epub ahead of print]
    Comparative proteomic landscapes elucidate human preimplantation development and failure.
    Wencheng Zhu, Juan Meng, Yan Li, Lei Gu, Wenjun Liu, Ziyi Li, Yi Shen, Xiaoyu Shen, Zihong Wang, Yonggen Wu, Guiquan Wang, Junfeng Zhang, Huiping Zhang, Haiyan Yang, Xi Dong, Hui Wang, Xuefeng Huang, Yidi Sun, Chen Li, Liangshan Mu, Zhen Liu.
      Understanding mammalian preimplantation development, particularly in humans, at the proteomic level remains limited. Here, we applied our comprehensive solution of ultrasensitive proteomic technology to measure the proteomic profiles of oocytes and early embryos and identified nearly 8,000 proteins in humans and over 6,300 proteins in mice. We observed distinct proteomic dynamics before and around zygotic genome activation (ZGA) between the two species. Integrative analysis with translatomic data revealed extensive divergence between translation activation and protein accumulation. Multi-omic analysis indicated that ZGA transcripts often contribute to protein accumulation in blastocysts. Using mouse embryos, we identified several transcriptional regulators critical for early development, thereby linking ZGA to the first lineage specification. Furthermore, single-embryo proteomics of poor-quality embryos from over 100 patient couples provided insights into preimplantation development failure. Our study may contribute to reshaping the framework of mammalian preimplantation development and opening avenues for addressing human infertility.
    Keywords:  ZGA; human preimplantation development; multi-omic analysis; poor-quality embryo; ultrasensitive proteomics
    DOI:  https://doi.org/10.1016/j.cell.2024.12.028
  3. Curr Biol. 2025 Jan 24. pii: S0960-9822(24)01719-6. [Epub ahead of print]
    Extracellular volume expansion drives vertebrate axis elongation.
    Arthur Michaut, Alessandro Mongera, Anupam Gupta, Oscar A Tarazona, Mattia Serra, Georgia-Maria Kefala, Pietro Rigoni, Jong Gwan Lee, Felipe Rivas, Adam R Hall, L Mahadevan, Karine Guevorkian, Olivier Pourquié.
      The vertebrate bauplan is primarily established via the formation of embryonic tissues in a head-to-tail progression. The mechanics of this elongation, which requires the presomitic mesoderm (PSM), remain poorly understood. Here, we find that avian PSM explants can elongate autonomously when physically confined in vitro, producing a pushing force promoting posterior elongation of the embryo. This tissue elongation is caused by volumetric expansion, which results from an increase in the extracellular fraction accompanied by graded cellular motility. We show that fibroblast growth factor (FGF) signaling promotes glycolysis-dependent production of hyaluronic acid (HA), which is required for expansion of the posterior PSM. Our findings link body axis elongation to tissue expansion through the metabolic control of extracellular matrix production downstream of FGF signaling.
    DOI:  https://doi.org/10.1016/j.cub.2024.12.051
  4. Nature. 2025 Jan 29.
    C-terminal amides mark proteins for degradation via SCF-FBXO31.
    Matthias F Muhar, Jakob Farnung, Martina Cernakova, Raphael Hofmann, Lukas T Henneberg, Moritz M Pfleiderer, Annina Denoth-Lippuner, Filip Kalčic, Ajse S Nievergelt, Marwa Peters Al-Bayati, Nikolaos D Sidiropoulos, Viola Beier, Matthias Mann, Sebastian Jessberger, Martin Jinek, Brenda A Schulman, Jeffrey W Bode, Jacob E Corn.
      During normal cellular homeostasis, unfolded and mislocalized proteins are recognized and removed, preventing the build-up of toxic byproducts1. When protein homeostasis is perturbed during ageing, neurodegeneration or cellular stress, proteins can accumulate several forms of chemical damage through reactive metabolites2,3. Such modifications have been proposed to trigger the selective removal of chemically marked proteins3-6; however, identifying modifications that are sufficient to induce protein degradation has remained challenging. Here, using a semi-synthetic chemical biology approach coupled to cellular assays, we found that C-terminal amide-bearing proteins (CTAPs) are rapidly cleared from human cells. A CRISPR screen identified FBXO31 as a reader of C-terminal amides. FBXO31 is a substrate receptor for the SKP1-CUL1-F-box protein (SCF) ubiquitin ligase SCF-FBXO31, which ubiquitylates CTAPs for subsequent proteasomal degradation. A conserved binding pocket enables FBXO31 to bind to almost any C-terminal peptide bearing an amide while retaining exquisite selectivity over non-modified clients. This mechanism facilitates binding and turnover of endogenous CTAPs that are formed after oxidative stress. A dominant human mutation found in neurodevelopmental disorders reverses CTAP recognition, such that non-amidated neosubstrates are now degraded and FBXO31 becomes markedly toxic. We propose that CTAPs may represent the vanguard of a largely unexplored class of modified amino acid degrons that could provide a general strategy for selective yet broad surveillance of chemically damaged proteins.
    DOI:  https://doi.org/10.1038/s41586-024-08475-w
  5. Dev Cell. 2025 Jan 18. pii: S1534-5807(25)00002-4. [Epub ahead of print]
    Long-lived cytokinetic bridges coordinate sister-cell elimination in mouse embryos.
    Filip Vasilev, Aleksandar I Mihajlović, Gaudeline Rémillard-Labrosse, Greg FitzHarris.
      Apoptosis is a key feature of preimplantation development, but whether it occurs in a cell-autonomous or coordinated manner was unknown. Here, we report that plasma membrane abscission, the final step of cell division, is profoundly delayed in early mouse embryos such that a cytokinetic bridge is maintained for the vast majority of the following interphase. Early embryos thus consist of many pairs of sister cells connected by stable cytokinetic bridges that allow them to share diffusible molecules. We show that apoptotic regulators are shared through cytokinetic bridges and that these bridges ensure that if one cell enters apoptosis, its sister cell does as well. Long-lived cytokinetic bridges are thus a previously unappreciated form of cell-cell communication within the mouse embryo that coordinate the clearance of pairs of cells with similar developmental histories.
    Keywords:  abscission; apoptosis; cytokinesis; cytokinetic bridge; embryo; mitosis
    DOI:  https://doi.org/10.1016/j.devcel.2025.01.002
  6. Development. 2025 Jan 27. pii: dev.204397. [Epub ahead of print]
    Dynamic map illuminates Hippo-cMyc module crosstalk driving cardiomyocyte proliferation.
    Bryana N Harris, Laura A Woo, R Noah Perry, Alexia M Wallace, Mete Civelek, Matthew J Wolf, Jeffrey J Saucerman.
      Numerous regulators of cardiomyocyte (CM) proliferation have been identified, yet how they coordinate during cardiac development or regeneration is poorly understood. Here, we developed a computational model of the CM proliferation regulatory network to obtain key regulators and systems-level understanding. The model defines five modules (DNA replication, mitosis, cytokinesis, growth factor, Hippo pathway) and integrates them into a network of 72 nodes and 88 reactions that correctly predicts 73 of 78 (93.6%) independent experiments from the literature. The model predicts that in response to YAP activation, the Hippo module crosstalks to the growth factor module via PI3K and cMyc to drive cell cycle activity. This predicted YAP-cMyc axis is validated experimentally in rat cardiomyocytes and further supported by YAP-stimulated cMyc open chromatin and mRNA in mouse hearts. This validated computational model predicts how individual regulators and modules coordinate to control CM proliferation.
    Keywords:  Cardiomyocyte proliferation; Regeneration; Systems biology
    DOI:  https://doi.org/10.1242/dev.204397
  7. Nat Cell Biol. 2025 Jan 24.
    Multiomics reveals that triacylglycerol mobilization helps drive recovery from mitochondrial stress.
      
    DOI:  https://doi.org/10.1038/s41556-024-01603-8
  8. Nat Rev Mol Cell Biol. 2025 Jan 29.
    Shaping epithelial tissues by stem cell mechanics in development and cancer.
    Vincent F Fiore, Jorge Almagro, Elaine Fuchs.
      Adult stem cells balance self-renewal and differentiation to build, maintain and repair tissues. The role of signalling pathways and transcriptional networks in controlling stem cell function has been extensively studied, but there is increasing appreciation that mechanical forces also have a crucial regulatory role. Mechanical forces, signalling pathways and transcriptional networks must be coordinated across diverse length and timescales to maintain tissue homeostasis and function. Such coordination between stem cells and neighbouring cells dictates when cells divide, migrate and differentiate. Recent advances in measuring and manipulating the mechanical forces that act upon and are produced by stem cells are providing new insights into development and disease. In this Review, we discuss the mechanical forces involved when epithelial stem cells construct their microenvironment and what happens in cancer when stem cell niche mechanics are disrupted or dysregulated. As the skin has evolved to withstand the harsh mechanical pressures from the outside environment, we often use the stem cells of mammalian skin epithelium as a paradigm for adult stem cells shaping their surrounding tissues.
    DOI:  https://doi.org/10.1038/s41580-024-00821-0
  9. Mol Cell Proteomics. 2025 Jan 27. pii: S1535-9476(25)00013-1. [Epub ahead of print] 100915
    Quantitative chromatin protein dynamics during replication origin firing in human cells.
    Sampath Amitash Gadi, Ivo Alexander Hendriks, Christian Friberg Nielsen, Petya Popova, Ian D Hickson, Michael Lund Nielsen, Luis Toledo.
      Accurate genome duplication requires a tightly regulated DNA replication program, which relies on the fine regulation of origin firing. While the molecular steps involved in origin firing have been determined predominantly in budding yeast, the complexity of this process in human cells has yet to be fully elucidated. Here, we describe a straightforward proteomics approach to systematically analyse protein recruitment to the chromatin during induced origin firing in human cells. Using a specific inhibitor against CHK1 kinase, we induced a synchronised wave of dormant origin firing (DOF) and assessed the S phase chromatin proteome at different time points. We provide time-resolved loading dynamics of 3,269 proteins, including the core replication machinery and origin firing factors. This dataset accurately represents known temporal dynamics of proteins on the chromatin during the activation of replication forks and the subsequent DNA damage due to the hyperactivation of excessive replication forks. Finally, we used our dataset to identify the condensin II subunit NCAPH2 as a novel factor required for efficient origin firing and replication. Overall, we provide a comprehensive resource to interrogate the protein recruitment dynamics of replication origin firing events in human cells.
    DOI:  https://doi.org/10.1016/j.mcpro.2025.100915
  10. Elife. 2025 Jan 29. pii: RP102977. [Epub ahead of print]13
    eIF3 engages with 3'-UTR termini of highly translated mRNAs.
    Santi Mestre-Fos, Lucas Ferguson, Marena I Trinidad, Nicholas T Ingolia, Jamie H D Cate.
      Stem cell differentiation involves a global increase in protein synthesis to meet the demands of specialized cell types. However, the molecular mechanisms underlying this translational burst and the involvement of initiation factors remains largely unknown. Here, we investigate the role of eukaryotic initiation factor 3 (eIF3) in early differentiation of human pluripotent stem cell (hPSC)-derived neural progenitor cells (NPCs). Using Quick-irCLIP and alternative polyadenylation (APA) Seq, we show eIF3 crosslinks predominantly with 3' untranslated region (3'-UTR) termini of multiple mRNA isoforms, adjacent to the poly(A) tail. Furthermore, we find that eIF3 engagement at 3'-UTR ends is dependent on polyadenylation. High eIF3 crosslinking at 3'-UTR termini of mRNAs correlates with high translational activity, as determined by ribosome profiling, but not with translational efficiency. The results presented here show that eIF3 engages with 3'-UTR termini of highly translated mRNAs, likely reflecting a general rather than specific regulatory function of eIF3, and supporting a role of mRNA circularization in the mechanisms governing mRNA translation.
    Keywords:  3'-UTR; biochemistry; cell biology; chemical biology; eIF3; human; protein synthesis; quick-irCLIP; ribosome profiling
    DOI:  https://doi.org/10.7554/eLife.102977
  11. Nat Aging. 2025 Jan 29.
    Niche-derived Semaphorin 4A safeguards functional identity of myeloid-biased hematopoietic stem cells.
    Dorsa Toghani, Sanika Gupte, Sharon Zeng, Elmir Mahammadov, Edie I Crosse, Negar Seyedhassantehrani, Christian Burns, David Gravano, Stefan Radtke, Hans-Peter Kiem, Sonia Rodriguez, Nadia Carlesso, Amogh Pradeep, Alexis Georgiades, Fabienne Lucas, Nicola K Wilson, Sarah J Kinston, Berthold Göttgens, Le Zong, Isabel Beerman, Bongsoo Park, Derek H Janssens, Daniel Jones, Ali Toghani, Claus Nerlov, Eric M Pietras, Marion Mesnieres, Christa Maes, Atsushi Kumanogoh, Thomas Worzfeld, Jin-Gyu Cheong, Steven Z Josefowicz, Peter Kharchenko, David T Scadden, Antonio Scialdone, Joel A Spencer, Lev Silberstein.
      Somatic stem cell pools comprise diverse, highly specialized subsets whose individual contribution is critical for the overall regenerative function. In the bone marrow, myeloid-biased hematopoietic stem cells (myHSCs) are indispensable for replenishment of myeloid cells and platelets during inflammatory response but, at the same time, become irreversibly damaged during inflammation and aging. Here we identify an extrinsic factor, semaphorin 4A (Sema4A), which non-cell-autonomously confers myHSC resilience to inflammatory stress. We show that, in the absence of Sema4A, myHSC inflammatory hyper-responsiveness in young mice drives excessive myHSC expansion, myeloid bias and profound loss of regenerative function with age. Mechanistically, Sema4A is mainly produced by neutrophils, signals via a cell surface receptor, plexin D1, and safeguards the myHSC epigenetic state. Our study shows that, by selectively protecting a distinct stem cell subset, an extrinsic factor preserves functional diversity of somatic stem cell pool throughout organismal lifespan.
    DOI:  https://doi.org/10.1038/s43587-024-00798-7
  12. Nat Struct Mol Biol. 2025 Jan 24.
    A network of interacting ciliary tip proteins with opposing activities imparts slow and processive microtubule growth.
    Harriet A J Saunders, Cyntha M van den Berg, Robin A Hoogebeen, Donna Schweizer, Kelly E Stecker, Ronald Roepman, Stuart C Howes, Anna Akhmanova.
      Cilia are motile or sensory organelles present on many eukaryotic cells. Their formation and function rely on axonemal microtubules, which exhibit very slow dynamics, but the underlying mechanisms are largely unexplored. Here we reconstituted in vitro the individual and collective activities of the ciliary tip module proteins CEP104, CSPP1, TOGARAM1, ARMC9 and CCDC66, which interact with each other and with microtubules and, when mutated in humans, cause ciliopathies such as Joubert syndrome. We show that CEP104, a protein with a tubulin-binding TOG domain, and its luminal partner CSPP1 inhibit microtubule growth and shortening. Another TOG-domain protein, TOGARAM1, overcomes growth inhibition imposed by CEP104 and CSPP1. CCDC66 and ARMC9 do not affect microtubule dynamics but act as scaffolds for their partners. Cryo-electron tomography demonstrated that, together, ciliary tip module members form plus-end-specific cork-like structures that reduce protofilament flaring. The combined effect of these proteins is very slow processive microtubule elongation, which recapitulates axonemal dynamics in cells.
    DOI:  https://doi.org/10.1038/s41594-025-01483-y
  13. Nature. 2025 Jan 29.
    Engineered heart muscle allografts for heart repair in primates and humans.
    Ahmad-Fawad Jebran, Tim Seidler, Malte Tiburcy, Maria Daskalaki, Ingo Kutschka, Buntaro Fujita, Stephan Ensminger, Felix Bremmer, Amir Moussavi, Huaxiao Yang, Xulei Qin, Sophie Mißbach, Charis Drummer, Hassina Baraki, Susann Boretius, Christopher Hasenauer, Tobias Nette, Johannes Kowallick, Christian O Ritter, Joachim Lotz, Michael Didié, Mathias Mietsch, Tim Meyer, George Kensah, Dennis Krüger, Md Sadman Sakib, Lalit Kaurani, Andre Fischer, Ralf Dressel, Ignacio Rodriguez-Polo, Michael Stauske, Sebastian Diecke, Kerstin Maetz-Rensing, Eva Gruber-Dujardin, Martina Bleyer, Beatrix Petersen, Christian Roos, Liye Zhang, Lutz Walter, Silke Kaulfuß, Gökhan Yigit, Bernd Wollnik, Elif Levent, Berit Roshani, Christiane Stahl-Henning, Philipp Ströbel, Tobias Legler, Joachim Riggert, Kristian Hellenkamp, Jens-Uwe Voigt, Gerd Hasenfuß, Rabea Hinkel, Joseph C Wu, Rüdiger Behr, Wolfram-Hubertus Zimmermann.
      Cardiomyocytes can be implanted to remuscularize the failing heart1-7. Challenges include sufficient cardiomyocyte retention for a sustainable therapeutic impact without intolerable side effects, such as arrhythmia and tumour growth. We investigated the hypothesis that epicardial engineered heart muscle (EHM) allografts from induced pluripotent stem cell-derived cardiomyocytes and stromal cells structurally and functionally remuscularize the chronically failing heart without limiting side effects in rhesus macaques. After confirmation of in vitro and in vivo (nude rat model) equivalence of the newly developed rhesus macaque EHM model with a previously established Good Manufacturing Practice-compatible human EHM formulation8, long-term retention (up to 6 months) and dose-dependent enhancement of the target heart wall by EHM grafts constructed from 40 to 200 million cardiomyocytes/stromal cells were demonstrated in macaques with and without myocardial infarction-induced heart failure. In the heart failure model, evidence for EHM allograft-enhanced target heart wall contractility and ejection fraction, which are measures for local and global heart support, was obtained. Histopathological and gadolinium-based perfusion magnetic resonance imaging analyses confirmed cell retention and functional vascularization. Arrhythmia and tumour growth were not observed. The obtained feasibility, safety and efficacy data provided the pivotal underpinnings for the approval of a first-in-human clinical trial on tissue-engineered heart repair. Our clinical data confirmed remuscularization by EHM implantation in a patient with advanced heart failure.
    DOI:  https://doi.org/10.1038/s41586-024-08463-0
  14. PLoS Genet. 2025 Jan 30. 21(1): e1011584
    PRC2 promotes canalisation during endodermal differentiation.
    Jurriaan Jochem Hölzenspies, Dipta Sengupta, Wendy Anne Bickmore, Joshua Mark Brickman, Robert Scott Illingworth.
      The genetic circuitry that encodes the developmental programme of mammals is regulated by transcription factors and chromatin modifiers. During early gestation, the three embryonic germ layers are established in a process termed gastrulation. The impact of deleterious mutations in chromatin modifiers such as the polycomb proteins manifests during gastrulation, leading to early developmental failure and lethality in mouse models. Embryonic stem cells have provided key insights into the molecular function of polycomb proteins, but it is impossible to fully appreciate the role of these epigenetic factors in development, or how development is perturbed due to their deficiency, in the steady-state. To address this, we have employed a tractable embryonic stem cell differentiation system to model primitive streak formation and early gastrulation. Using this approach, we find that loss of the repressive polycomb mark H3K27me3 is delayed relative to transcriptional activation, indicating a subordinate rather than instructive role in gene repression. Despite this, chemical inhibition of polycomb enhanced endodermal differentiation efficiency, but did so at the cost of lineage fidelity. These findings highlight the importance of the polycomb system in stabilising the developmental transcriptional response and, in so doing, in shoring up cellular specification.
    DOI:  https://doi.org/10.1371/journal.pgen.1011584
  15. J Cell Biol. 2025 Apr 07. pii: e202403083. [Epub ahead of print]224(4):
    Sphingolipid metabolism orchestrates establishment of the hair follicle stem cell compartment.
    Franziska Peters, Windie Höfs, Hunki Lee, Susanne Brodesser, Kai Kruse, Hannes C A Drexler, Jiali Hu, Verena K Raker, Dominika Lukas, Esther von Stebut, Martin Krönke, Carien M Niessen, Sara A Wickström.
      Sphingolipids serve as building blocks of membranes to ensure subcellular compartmentalization and facilitate intercellular communication. How cell type-specific lipid compositions are achieved and what is their functional significance in tissue morphogenesis and maintenance has remained unclear. Here, we identify a stem cell-specific role for ceramide synthase 4 (CerS4) in orchestrating fate decisions in skin epidermis. Deletion of CerS4 prevents the proper development of the adult hair follicle bulge stem cell (HFSC) compartment due to altered differentiation trajectories. Mechanistically, HFSC differentiation defects arise from an imbalance of key ceramides and their derivate sphingolipids, resulting in hyperactivation of noncanonical Wnt signaling. This impaired HFSC compartment establishment leads to disruption of hair follicle architecture and skin barrier function, ultimately triggering a T helper cell 2-dominated immune infiltration resembling human atopic dermatitis. This work uncovers a fundamental role for a cell state-specific sphingolipid profile in stem cell homeostasis and in maintaining an intact skin barrier.
    DOI:  https://doi.org/10.1083/jcb.202403083
  16. Cell. 2025 Jan 20. pii: S0092-8674(24)01436-3. [Epub ahead of print]
    High-resolution spatially resolved proteomics of complex tissues based on microfluidics and transfer learning.
    Beiyu Hu, Ruiqiao He, Kun Pang, Guibin Wang, Ning Wang, Wenzhuo Zhu, Xin Sui, Huajing Teng, Tianxin Liu, Junjie Zhu, Zewen Jiang, Jinyang Zhang, Zhenqiang Zuo, Weihu Wang, Peifeng Ji, Fangqing Zhao.
      Despite recent advances in imaging- and antibody-based methods, achieving in-depth, high-resolution protein mapping across entire tissues remains a significant challenge in spatial proteomics. Here, we present parallel-flow projection and transfer learning across omics data (PLATO), an integrated framework combining microfluidics with deep learning to enable high-resolution mapping of thousands of proteins in whole tissue sections. We validated the PLATO framework by profiling the spatial proteome of the mouse cerebellum, identifying 2,564 protein groups in a single run. We then applied PLATO to rat villus and human breast cancer samples, achieving a spatial resolution of 25 μm and uncovering proteomic dynamics associated with disease states. This approach revealed spatially distinct tumor subtypes, identified key dysregulated proteins, and provided novel insights into the complexity of the tumor microenvironment. We believe that PLATO represents a transformative platform for exploring spatial proteomic regulation and its interplay with genetic and environmental factors.
    Keywords:  deep learning; mass spectrometry; microfluidics; spatial multi-omics; spatial proteomics; tomography
    DOI:  https://doi.org/10.1016/j.cell.2024.12.023
  17. Science. 2025 Jan 31. 387(6733): eado5978
    Multiplex generation and single-cell analysis of structural variants in mammalian genomes.
    Sudarshan Pinglay, Jean-Benoît Lalanne, Riza M Daza, Sanjay Kottapalli, Faaiz Quaisar, Jonas Koeppel, Riddhiman K Garge, Xiaoyi Li, David S Lee, Jay Shendure.
      Studying the functional consequences of structural variants (SVs) in mammalian genomes is challenging because (i) SVs arise much less commonly than single-nucleotide variants or small indels and (ii) methods to generate, map, and characterize SVs in model systems are underdeveloped. To address these challenges, we developed Genome-Shuffle-seq, a method that enables the multiplex generation and mapping of thousands of SVs (deletions, inversions, translocations, and extrachromosomal circles) throughout mammalian genomes. We also demonstrate the co-capture of SV identity with single-cell transcriptomes, facilitating the measurement of SV impact on gene expression. We anticipate that Genome-Shuffle-seq will be broadly useful for the systematic exploration of the functional consequences of SVs on gene expression, the chromatin landscape, and three-dimensional nuclear architecture, while also initiating a path toward a minimal mammalian genome.
    DOI:  https://doi.org/10.1126/science.ado5978
  18. Science. 2025 Jan 30. eado4930
    Casz1 is required for both inner hair cell fate stabilization and outer hair cell survival.
    Yuwei Sun, Minhui Ren, Yu Zhang, Shuting Li, Zhengnan Luo, Suhong Sun, Shunji He, Guangqin Wang, Di Zhang, Suzanne L Mansour, Lei Song, Zhiyong Liu.
      Cochlear inner hair cells (IHCs) and outer hair cells (OHCs) require different transcription factors for their cell fate stabilization and survival, suggesting separate mechanisms are involved. Here, we found that the transcription factor Casz1 was crucial for early IHC fate consolidation and for OHC survival during mouse development. Loss of Casz1 resulted in transdifferentiation of IHCs into OHCs, without affecting OHC production. However, long-term OHC survival was compromised in Casz1 mutant mice. In addition, the transcription factor Gata3 was down-regulated in Casz1-deleted IHCs and overexpressing Gata3 partially rescued IHC properties, OHC numbers, and hearing in Casz1-deleted mice. Thus, Casz1 plays critical roles in early IHC fate stabilization and OHC survival and could potentially provide a lead for therapies aimed at regenerating both IHCs and OHCs.
    DOI:  https://doi.org/10.1126/science.ado4930
  19. Biol Open. 2025 Feb 15. pii: bio061811. [Epub ahead of print]14(2):
    Proximity proteomics provides a new resource for exploring the function of Afadin and the complexity of cell-cell adherens junctions.
    Wangsun Choi, Dennis Goldfarb, Feng Yan, Michael B Major, Alan S Fanning, Mark Peifer.
      The network of proteins at the interface between cell-cell adherens junctions and the actomyosin cytoskeleton provides robust yet dynamic connections that facilitate cell shape change and motility. While this was initially thought to be a simple linear connection via classic cadherins and their associated catenins, we now have come to appreciate that many more proteins are involved, providing robustness and mechanosensitivity. Defining the full set of proteins in this network remains a key objective in our field. Proximity proteomics provides a means to define these networks. Mammalian Afadin and its Drosophila homolog Canoe are key parts of this protein network, facilitating diverse cell shape changes during gastrulation and other events of embryonic morphogenesis. Here we report results of several proximity proteomics screens, defining proteins in the neighborhood of both the N- and C-termini of mammalian Afadin in the premier epithelial model, MDCK cells. We compare our results with previous screens done in other cell types, and with proximity proteomics efforts with other junctional proteins. These reveal the value of multiple screens in defining the full network of neighbors and offer interesting insights into the overlap in protein composition between different epithelial cell junctions.
    Keywords:  Adherens junctions; Afadin; BioID; Canoe; Cell adhesion
    DOI:  https://doi.org/10.1242/bio.061811
  20. Science. 2025 Jan 31. 387(6733): eado3979
    Randomizing the human genome by engineering recombination between repeat elements.
    Jonas Koeppel, Raphael Ferreira, Thomas Vanderstichele, Lisa Maria Riedmayr, Elin Madli Peets, Gareth Girling, Juliane Weller, Pierre Murat, Fabio Giuseppe Liberante, Tom Ellis, George McDonald Church, Leopold Parts.
      We lack tools to edit DNA sequences at scales necessary to study 99% of the human genome that is noncoding. To address this gap, we applied CRISPR prime editing to insert recombination handles into repetitive sequences, up to 1697 per cell line, which enables generating large-scale deletions, inversions, translocations, and circular DNA. Recombinase induction produced more than 100 stochastic megabase-sized rearrangements in each cell. We tracked these rearrangements over time to measure selection pressures, finding a preference for shorter variants that avoided essential genes. We characterized 29 clones with multiple rearrangements, finding an impact of deletions on expression of genes in the variant but not on nearby genes. This genome-scrambling strategy enables large deletions, sequence relocations, and the insertion of regulatory elements to explore genome dispensability and organization.
    DOI:  https://doi.org/10.1126/science.ado3979
  21. Sci Adv. 2025 Jan 31. 11(5): eadp8608
    Temporal dynamics of the interstitial fluid proteome in human skeletal muscle following exhaustive exercise.
    Ben Stocks, Julia Prats Quesada, Anthony M Mozzicato, Carolina Jacob, Simone Jensen, Kirstin A MacGregor, Jens Bangsbo, Juleen R Zierath, Morten Hostrup, Atul S Deshmukh.
      The skeletal muscle interstitial space is the extracellular region around myofibers and mediates cross-talk between resident cell types. We applied a proteomic workflow to characterize the human skeletal muscle interstitial fluid proteome at rest and in response to exercise. Following exhaustive exercise, markers of skeletal muscle damage accumulate in the interstitial space followed by the appearance of immune cell-derived proteins. Among the proteins up-regulated after exercise, we identified cathelicidin-related antimicrobial peptide (CAMP) as a bioactive molecule regulating muscle fiber development. Treatment with the bioactive peptide derivative of CAMP (LL-37) resulted in the growth of larger C2C12 skeletal muscle myotubes. Phosphoproteomics revealed that LL-37 activated pathways central to muscle growth and proliferation, including phosphatidylinositol 3-kinase, AKT serine/threonine kinase 1, mitogen-activated protein kinases, and mammalian target of rapamycin. Our findings provide a proof of concept that the interstitial fluid proteome is quantifiable via microdialysis sampling in vivo. These data highlight the importance of cellular communication in the adaptive response to exercise.
    DOI:  https://doi.org/10.1126/sciadv.adp8608
  22. Nat Commun. 2025 Jan 24. 16(1): 627
    Artificial cells with all-aqueous droplet-in-droplet structures for spatially separated transcription and translation.
    Kanji Tomohara, Yoshihiro Minagawa, Hiroyuki Noji.
      The design of functional artificial cells involves compartmentalizing biochemical processes to mimic cellular organization. To emulate the complex chemical systems in biological cells, it is necessary to incorporate an increasing number of cellular functions into single compartments. Artificial organelles that spatially segregate reactions inside artificial cells will be beneficial in this context by rectifying biochemical pathways. Here, we develop artificial cells with all-aqueous droplet-in-droplet structures that separate transcription and translation processes like the nucleus and cytosol in eukaryotic cells. This architecture uses protein-based inner droplets and aqueous two-phase outer compartments, stabilized by colloidal emulsifiers. The inner droplet is designed to enrich DNA and RNA polymerase for transcription, coupled to translation at the outer droplet via mRNA-mediated cascade reactions. We show that these processes proceed independently within each compartment, maintaining genotype-phenotype correspondence. This approach provides a practical tool for exploring complex systems of artificial organelles within large ensembles of artificial cells.
    DOI:  https://doi.org/10.1038/s41467-024-55366-9
  23. Cell Stem Cell. 2025 Jan 28. pii: S1934-5909(25)00007-4. [Epub ahead of print]
    Genome-wide CRISPR activation screening in senescent cells reveals SOX5 as a driver and therapeutic target of rejuvenation.
    Yaobin Jing, Xiaoyu Jiang, Qianzhao Ji, Zeming Wu, Wei Wang, Zunpeng Liu, Pedro Guillen-Garcia, Concepcion Rodriguez Esteban, Pradeep Reddy, Steve Horvath, Jingyi Li, Lingling Geng, Qinchao Hu, Si Wang, Juan Carlos Izpisua Belmonte, Jie Ren, Weiqi Zhang, Jing Qu, Guang-Hui Liu.
      
    DOI:  https://doi.org/10.1016/j.stem.2025.01.007
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