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Jessica Thiel, Duran Sürün, Desiree C Brändle, Madeleine Teichert, Stephan R Künzel, Ulrike Friedrich, Andreas Dahl, Kristin Schubert, Ignacy Rzagalinski, Andrej Shevchenko, Sofia Traikov, Peter Mirtschink, Lisa Wagenführ, Frank Buchholz, Kristina Hölig, Torsten Tonn, Romy Kronstein-Wiedemann
Knock Out of miRNA-30a-5p and Reconstitution of the Actin Network Dynamics Partly Restores the Impaired Terminal Erythroid Differentiation during Blood Pharming.
Stem Cell Rev Rep, 21(8) 2637-2653 (2025)
Open Access PubMed Source   

In vitro red blood cell (RBC) production offers a promising complement to conventional blood donation, particularly for patients with rare blood types. Previously, we developed imBMEP-A, the first erythroid cell line derived from reticulocyte progenitors, which maintains robust hemoglobin expression and erythroid differentiation in the presence of erythropoietin (EPO) despite its immortalized state. However, clinical translation remains hindered by the inability to scale up production due to impaired in vitro enucleation of RBC progenitor cell lines. Enhancing enucleation efficiency in imBMEP-A cells involved CRISPR/Cas9-mediated knockout (K.O.) of miR-30a-5p, a key enucleation inhibitor, moderately increasing rates to 3.3 ± 0.4%- 8.9 ± 1.7%. Further investigation of enucleation inefficiencies led to transcriptome and proteome comparisons between imBMEP-miR30a-K.O. cells and hematopoietic stem cells (HSCs). These analyses revealed altered gene expression and protein abundances linked to metabolic transitions, apoptosis promotion, and cytoskeletal regulation. Notably, forced expression of the proto-oncogene c-Myc, required for cell immortalization, emerged as a key driver of these physiological changes. Counteracting these effects required optimization of imBMEP-A cells by activating BCL-XL transcription and knocking out SCIN, which encodes the actin-severing protein scinderin. While BCL-XL is upregulated in normal erythropoiesis, it is downregulated in imBMEP-A. Conversely, SCIN, typically absent in erythroid cells, is highly expressed in imBMEP-A, disrupting actin organization. These interventions improved viability, restored actin network formation, and increased terminal erythropoiesis, yielding 22.1 ± 1.7% more orthochromatic erythroblasts. These findings establish a foundation for optimizing imBMEP-A cells for therapeutic use and advancing the understanding the pathophysiology of erythroleukemia.
@article{Thiel9053,
author={Jessica Thiel, Duran Sürün, Desiree C Brändle, Madeleine Teichert, Stephan R Künzel, Ulrike Friedrich, Andreas Dahl, Kristin Schubert, Ignacy Rzagalinski, Andrej Shevchenko, Sofia Traikov, Peter Mirtschink, Lisa Wagenführ, Frank Buchholz, Kristina Hölig, Torsten Tonn, Romy Kronstein-Wiedemann},
title={Knock Out of miRNA-30a-5p and Reconstitution of the Actin Network Dynamics Partly Restores the Impaired Terminal Erythroid Differentiation during Blood Pharming.},
journal ={Stem cell reviews and reports},
volume={21},
issue ={8},
pages={2637--2653},
year=2025
}

Sophie Achilles, Jan-Niklas Tomczak, Fabiane-Samira Baumann, Bassam G Haddad, Stefan Oswald, Jan-Philipp Machtens, Eric R Geertsma, Ilka Wittig, Georg Lamprecht
N-glycans on SLC26A3 do not significantly alter plasma membrane or lipid raft trafficking, but appear to stabilize interdomain contacts to stimulate transport.
Am J Physiol Gastrointest Liver Physiol, Art. No. doi: 10.1152/ajpgi.00362.2024 (2025)
Open Access PubMed Source   

DRA (SLC26A3) is a major apical intestinal Cl-/HCO3- exchanger, which is expressed in complex and hybrid N-glycosylated forms. While the importance of N-glycosylation is evident from the significantly reduced transport activity of non-N-glycosylated DRA constructs (DRA-N0), the underlying molecular mechanisms are controversial. Therefore, plasma membrane expression and lipid raft localization of glycosylation-deficient DRA-N0 were analyzed in HEK cells. The activity of DRA-N0 was reduced by 70% compared to the wildtype construct. Absolute expression of DRA-N0 was significantly reduced by approximately 57% in the cell lysate and by 34 and 45% in the plasma membrane and in plasma membrane-derived lipid rafts, respectively. These amounts are insufficient to account for the reduction in activity. Furthermore, the statistical analysis did not support a difference in the relative expression of DRA and DRA-N0 in the plasma membrane and in plasma membrane-derived lipid rafts, indicating that N-glycosylation does not affect transport activity through trafficking and localization in these cell compartments. To gain insight into potential intramolecular effects of N-glycosylation on DRA, its 3D-structure was predicted using AlphaFold3 with complex N-glycans covalently attached to N153, N161, and N164 in the transport domain. This revealed multiple inward- and outward-facing conformations of the protein. The number of interdomain contacts of the transport domain-bound glycans with the scaffold domain was higher in the inward-facing state. Because substrate release to the cytoplasm represents the rate-limiting step in many transport proteins, this suggests that in DRA glycans stabilize the inward-facing state facilitating anion transport.
@article{Achilles9069,
author={Sophie Achilles, Jan-Niklas Tomczak, Fabiane-Samira Baumann, Bassam G Haddad, Stefan Oswald, Jan-Philipp Machtens, Eric R Geertsma, Ilka Wittig, Georg Lamprecht},
title={N-glycans on SLC26A3 do not significantly alter plasma membrane or lipid raft trafficking, but appear to stabilize interdomain contacts to stimulate transport.},
journal ={American journal of physiology. Gastrointestinal and liver physiology},
volume={},
pages={1--1},
year=2025
}

Aleksandra Sljukic*, Joshua Green Jenkinson*, Armin Niksic*, Nicole Prior#, Meritxell Huch#
Advances in liver and pancreas organoids: how far we have come and where we go next.
Nat Rev Gastroenterol Hepatol, Art. No. doi: doi: 10.1038/s41575-025-01116-1 (2025)
Open Access PubMed Source   

Over the past decade, advances in organoid culturing methods have enabled the growth of three-dimensional cellular cultures in vitro with increasing fidelity with respect to the cellular composition, architecture and function of in vivo organs. The increased accessibility and ability to manipulate organoids as an in vitro system have led to a shift in the landscape of experimental biology. Whether derived from stem cells or tissue-resident cells, organoids are now routinely used in studies of development, homeostasis, regeneration and disease modelling, including viral infection and cancer. These applications of organoids are highly relevant for gastrointestinal tissues, including the liver and pancreas. In this Review, we explore the current and emerging advances in liver and pancreas organoid technologies for both discovery and clinical translation research and provide an outlook on the challenges ahead.
@article{Sljukic9068,
author={Aleksandra Sljukic, Joshua Green Jenkinson, Armin Niksic, Nicole Prior, Meritxell Huch},
title={Advances in liver and pancreas organoids: how far we have come and where we go next.},
journal ={Nature reviews. Gastroenterology & hepatology},
volume={},
pages={1--1},
year=2025
}

Basusree Ghosh*, Patrick M McCall*, Kristian Le Vay, Archishman Ghosh, Lars Hubatsch, David Thomas Gonzales, Jan Brugués, Hannes Mutschler#, T-Y Dora Tang#
RNA-peptide interactions tune the ribozyme activity within coacervate microdroplet dispersions.
Nat Commun, 16(1) Art. No. 8765 (2025)
Open Access PubMed Source Full Text   

Membrane-free complex coacervate microdroplets are compelling models for primitive compartmentalisation with the ability to form from biological molecules. However, understanding how molecular interactions can influence physicochemical properties and catalytic activity of membrane-free compartments is still in its infancy. This is important for defining the function of membrane-free compartments during the origin of life as well as in modern biology. Here, we use RNA-peptide coacervate microdroplets prepared with prebiotically relevant amino acids and a minimal hammerhead ribozyme. This is a model system to probe the relationship between coacervate composition, its properties and ribozyme activity. We show that ribozyme catalytic activity is inhibited within the coacervate compared to buffer solution, whilst variations in peptide sequence can modulate rates and yield of the ribozyme within the coacervate droplet by up to 15-fold. The apparent ribozyme rate constant is anti-correlated with its concentration and correlated to its diffusion coefficient within the coacervates. Our results provide a relationship between the physicochemical properties of the coacervate microenvironment and the catalytic activity of the ribozyme where membrane-free compartments could provide a selection pressure to drive molecular evolution on prebiotic earth.
@article{Ghosh9066,
author={Basusree Ghosh, Patrick M McCall, Kristian Le Vay, Archishman Ghosh, Lars Hubatsch, David Thomas Gonzales, Jan Brugués, Hannes Mutschler, T-Y Dora Tang},
title={RNA-peptide interactions tune the ribozyme activity within coacervate microdroplet dispersions.},
journal ={Nature communications},
volume={16},
issue ={1},
pages={null--null},
year=2025
}

Anna Hadarovich, David Kuster, Maria Luisa Romero Romero, Agnes Toth-Petroczy
On the Evolution of Biomolecular Condensates: From Prebiotic Origins to Subcellular Diversity.
Annu Rev Cell Dev Biol, 41(1) 403-432 (2025)
Open Access PubMed Source   

Biomolecular condensates provide a way to compartmentalize subcellular components with high temporal and spatial resolution, enabling rapid responses to signals and environmental changes. While the formation, components, and function of some condensates are well-characterized, their presence across organisms, their evolutionary history, and their origin are less well-understood. Here, we review the diversity of condensate components and highlight that not only disordered but also fully structured proteins are capable of driving condensate formation. We compare how proteomes of condensates overlap within and across species, and we present functionally analogous condensates across organisms. Additionally, we discuss the potential role of condensation in early life, suggesting that phase separation could have facilitated the selection and concentration of prebiotic molecules, promoting essential biochemical processes. We conclude that condensate-related organization principles are ubiquitously used across organisms from bacteria to mammals, and they potentially played a key role in prebiotic evolution, serving as primitive compartments for early biochemical processes.
@article{Hadarovich9033,
author={Anna Hadarovich, David Kuster, Maria Luisa Romero Romero, Agnes Toth-Petroczy},
title={On the Evolution of Biomolecular Condensates: From Prebiotic Origins to Subcellular Diversity.},
journal ={Annual review of cell and developmental biology},
volume={41},
issue ={1},
pages={403--432},
year=2025
}

Juan M Iglesias-Artola, Kristin Böhlig, Kai Schuhmann, Katelyn C Cook, H Mathilda Lennartz, Milena Schuhmacher, Pavel Barahtjan, Cristina Jiménez López, Radek Šachl, Vannuruswamy Garikapati, Karina Pombo-Garcia, Annett Lohmann, Petra Riegerová, Martin Hof, Björn Drobot, Andrej Shevchenko, Alf Honigmann#, André Nadler#
Quantitative imaging of lipid transport in mammalian cells.
Nature, 646(8084) 474-482 (2025)
Open Access PubMed Source   

Eukaryotic cells produce over 1,000 different lipid species that tune organelle membrane properties, control signalling and store energy1,2. How lipid species are selectively sorted between organelles to maintain specific membrane identities is largely unclear, owing to the difficulty of imaging lipid transport in cells3. Here we measured the retrograde transport and metabolism of individual lipid species in mammalian cells using time-resolved fluorescence imaging of bifunctional lipid probes in combination with ultra-high-resolution mass spectrometry and mathematical modelling. Quantification of lipid flux between organelles revealed that directional, non-vesicular lipid transport is responsible for fast, species-selective lipid sorting, in contrast to the slow, unspecific vesicular membrane trafficking. Using genetic perturbations, we found that coupling between energy-dependent lipid flipping and non-vesicular transport is a mechanism for directional lipid transport. Comparison of metabolic conversion and transport rates showed that non-vesicular transport dominates the organelle distribution of lipids, while species-specific phospholipid metabolism controls neutral lipid accumulation. Our results provide the first quantitative map of retrograde lipid flux in cells4. We anticipate that our pipeline for mapping of lipid flux through physical and chemical space in cells will boost our understanding of lipids in cell biology and disease.
@article{Iglesias-Artola9051,
author={Juan M Iglesias-Artola, Kristin Böhlig, Kai Schuhmann, Katelyn C Cook, H Mathilda Lennartz, Milena Schuhmacher, Pavel Barahtjan, Cristina Jiménez López, Radek Šachl, Vannuruswamy Garikapati, Karina Pombo-Garcia, Annett Lohmann, Petra Riegerová, Martin Hof, Björn Drobot, Andrej Shevchenko, Alf Honigmann, André Nadler},
title={Quantitative imaging of lipid transport in mammalian cells.},
journal ={Nature},
volume={646},
issue ={8084},
pages={474--482},
year=2025
}

Hiroyuki Uechi, Sindhuja Sridharan, Jik Nijssen, Jessica Bilstein, Juan M Iglesias-Artola, Satoshi Kishigami, Virginia Casablancas-Antras, Ina Poser, Eduardo J Martinez, Edgar Boczek, Michael Wagner, Nadine Tomschke, Antonio Domingues, Arun Pal, Thom Doeleman, Sukhleen Kour, Eric D Anderson, Frank Stein, Hyun O. Lee, Xiaojie Zhang, Anatol Fritsch, Marcus Jahnel, Julius Fürsch, Anastasia C Murthy, Simon Alberti, Marc Bickle, Nicolas L Fawzi, André Nadler, Della C David, Udai Pandey, Andreas Hermann, Florian Stengel, Benjamin G Davis, Andrew J Baldwin, Mikhail M Savitski, Anthony Hyman#, Richard Wheeler#
Small-molecule dissolution of stress granules by redox modulation benefits ALS models.
Nat Chem Biol, 21(10) 1577-1588 (2025)
Open Access PubMed Source   

Neurodegenerative diseases, such as amyotrophic lateral sclerosis, are often associated with mutations in stress granule proteins. Aberrant stress granule condensate formation is associated with disease, making it a potential target for pharmacological intervention. Here, we identified lipoamide, a small molecule that specifically prevents cytoplasmic condensation of stress granule proteins. Thermal proteome profiling showed that lipoamide stabilizes intrinsically disordered domain-containing proteins, including SRSF1 and SFPQ, which are stress granule proteins necessary for lipoamide activity. SFPQ has redox-state-specific condensate dissolving behavior, which is modulated by the redox-active lipoamide dithiolane ring. In animals, lipoamide ameliorates aging-associated aggregation of a stress granule reporter protein, improves neuronal morphology and recovers motor defects caused by amyotrophic lateral sclerosis-associated FUS and TDP-43 mutants. Thus, lipoamide is a well-tolerated small-molecule modulator of stress granule condensation, and dissection of its molecular mechanism identified a cellular pathway for redox regulation of stress granule formation.
@article{Uechi9000,
author={Hiroyuki Uechi, Sindhuja Sridharan, Jik Nijssen, Jessica Bilstein, Juan M Iglesias-Artola, Satoshi Kishigami, Virginia Casablancas-Antras, Ina Poser, Eduardo J Martinez, Edgar Boczek, Michael Wagner, Nadine Tomschke, Antonio Domingues, Arun Pal, Thom Doeleman, Sukhleen Kour, Eric D Anderson, Frank Stein, Hyun O. Lee, Xiaojie Zhang, Anatol Fritsch, Marcus Jahnel, Julius Fürsch, Anastasia C Murthy, Simon Alberti, Marc Bickle, Nicolas L Fawzi, André Nadler, Della C David, Udai Pandey, Andreas Hermann, Florian Stengel, Benjamin G Davis, Andrew J Baldwin, Mikhail M Savitski, Anthony Hyman, Richard Wheeler},
title={Small-molecule dissolution of stress granules by redox modulation benefits ALS models.},
journal ={Nature chemical biology},
volume={21},
issue ={10},
pages={1577--1588},
year=2025
}

Tommaso Cossetto, Jonathan Rodenfels#, Pablo Sartori#
Thermodynamic dissipation constrains metabolic versatility of unicellular growth.
Nat Commun, 16(1) Art. No. 8543 (2025)
Open Access PubMed Source Full Text   

Metabolic versatility enables unicellular organisms to grow in vastly different environments. Since growth occurs far from thermodynamic equilibrium, the second law of thermodynamics has long been believed to pose key constraints to life. Yet, such constraints remain largely unknown. Here, we integrate published data spanning decades of experiments on unicellular chemotrophic growth and compute the corresponding thermodynamic dissipation. Due to its span in chemical substrates and microbial species, this dataset samples the versatility of metabolism. We find two empirical thermodynamic rules: first, the amount of energy dissipation per unit of biomass grown is largely conserved across metabolic types and domains of life; second, aerobic respiration exhibits a trade-off between dissipation and growth, reflecting in its high thermodynamic efficiency. By relating these rules to the fundamental thermodynamic forces that drive and oppose growth, our results show that dissipation imposes tight constraints on metabolic versatility.
@article{Cossetto9067,
author={Tommaso Cossetto, Jonathan Rodenfels, Pablo Sartori},
title={Thermodynamic dissipation constrains metabolic versatility of unicellular growth.},
journal ={Nature communications},
volume={16},
issue ={1},
pages={null--null},
year=2025
}

Daniel S Alber*, Shiheng Zhao*, Alexandre O Jacinto, Eric F Wieschaus, Stanislav Y. Shvartsman#, Pierre A. Haas#
A model for boundary-driven tissue morphogenesis.
Proc Natl Acad Sci U.S.A., 122(38) Art. No. e2505160122 (2025)
Open Access PubMed Source   

Tissue deformations during morphogenesis can be active, driven by internal processes, or passive, resulting from stresses applied at their boundaries. Here, we introduce the Drosophila hindgut primordium as a model for studying boundary-driven tissue morphogenesis. We characterize its deformations and show that its complex shape changes can be a passive consequence of the deformations of the active regions of the embryo that surround it. First, we find an intermediate characteristic "triangular keyhole" shape in the 3D deformations of the hindgut. We construct a minimal model of the hindgut primordium as an elastic ring deformed by active midgut invagination and germ band extension on an ellipsoidal surface, which robustly captures the symmetry-breaking into this triangular keyhole shape. We then quantify the 3D kinematics of the tissue by a set of contours and find that the hindgut deforms in two stages: An initial translation on the curved embryo surface followed by a rapid breaking of shape symmetry. We extend our model to show that the contour kinematics in both stages are consistent with our passive picture. Our results suggest that the role of in-plane deformations during hindgut morphogenesis is to translate the tissue to a region with anisotropic embryonic curvature and show that uniform boundary conditions are sufficient to generate the observed nonuniform shape change. Our work thus provides a possible explanation for the various characteristic shapes of blastopore-equivalents in different organisms and a framework for the mechanical emergence of global morphologies in complex developmental systems.
@article{Alber9060,
author={Daniel S Alber, Shiheng Zhao, Alexandre O Jacinto, Eric F Wieschaus, Stanislav Y. Shvartsman, Pierre A. Haas},
title={A model for boundary-driven tissue morphogenesis.},
journal ={Proceedings of the National Academy of Sciences of the United States of America},
volume={122},
issue ={38},
pages={null--null},
year=2025
}

Kristin Böhlig, Juan M Iglesias-Artola, Antonino Asaro, H Mathilda Lennartz, Anna C Link, Björn Drobot, André Nadler
Bifunctional Probes Reveal the Rules of Intracellular Ether Lipid Transport.
Angew Chem Int Ed Engl, Art. No. doi: 10.1002/anie.202513360 (2025)
Open Access PubMed Source   

Ether glycerophospholipids bear a long chain alcohol attached via an alkyl or vinyl ether bond at the sn1 position of the glycerol backbone. Ether lipids play a significant role in physiology and human health. However, their cellular functions remain largely unknown due to a lack of tools for identifying their subcellular localization and interacting proteins. Here, we address this methodological gap by synthesizing minimally modified bifunctional ether lipid probes by introducing diazirine and alkyne groups. To interrogate the subcellular kinetics of intracellular ether lipid transport in mammalian cells, we used a combination of fluorescence imaging, machine learning-assisted image analysis, and mathematical modelling. We find that alkyl-linked ether lipids are transported up to twofold faster than vinyl-linked species (plasmalogens), pointing to yet undiscovered cellular lipid transport machinery able to distinguish between linkage types differing by as little as two hydrogen atoms. We find that ether lipid transport predominantly occurs via non-vesicular pathways, with varying contributions from vesicular mechanisms between cell types. Altogether, our results suggest that differential recognition of alkyl- and vinyl ether lipids by lipid transfer proteins contributes to their distinct biological functions. In the future, the probes reported here will enable studying ether lipid biology in much greater detail through identification of interacting proteins and in-depth characterization of intracellular ether lipid dynamics.
@article{Böhlig9058,
author={Kristin Böhlig, Juan M Iglesias-Artola, Antonino Asaro, H Mathilda Lennartz, Anna C Link, Björn Drobot, André Nadler},
title={Bifunctional Probes Reveal the Rules of Intracellular Ether Lipid Transport.},
journal ={Angewandte Chemie (International ed. in English)},
volume={},
pages={1--1},
year=2025
}
* joint first authors, # joint corresponding authors