bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2025–06–22
seventeen papers selected by
Ralitsa Radostinova Madsen, MRC-PPU
  1. Light microscopy reporting for reproducibility.
  2. Dynamic decoding of VEGF signaling and coordinated control of multiple phenotypes by the Src-TEM4-YAP pathway.
  3. Leveraging data as a patient-scientist: frustrations and opportunities.
  4. E-Cadherin: A conductor of cellular signaling.
  5. RIDDEN: Data-driven inference of receptor activity from transcriptomic data.
  6. Rapid generation of functional vascular organoids via simultaneous transcription factor activation of endothelial and mural lineages.
  7. Robust signalling entropy estimation for biological process characterisation.
  8. No evidence that human GIGYF2 interacts with GRB10: implications for human disease.
  9. A nucleotide-independent, pan-RAS-targeted DARPin elicits anti-tumor activity in a multimodal manner.
  10. PI3Kα inhibition blocks osteochondroprogenitor specification and the hyper-inflammatory response to prevent heterotopic ossification.
  11. Morphodynamics of human early brain organoid development.
  12. ATR promotes mTORC1 activity via de novo cholesterol synthesis.
  13. Perturb-Multimodal: A platform for pooled genetic screens with imaging and sequencing in intact mammalian tissue.
  14. Prolonged response to PIK3CA inhibition in an advanced hormone-positive breast cancer patient with 3 mutations in the alpha subunit of PI-3 kinase.
  15. Conformational dynamics and multimodal interaction of Paxillin with the focal adhesion targeting domain.
  16. TIE1 dependent lymphatic vascular remodeling is mediated by its second tyrosine kinase domain.
  17. High-resolution profiling reveals coupled transcriptional and translational regulation of transgenes.
  1. Nat Cell Biol. 2025 Jun;27(6): 877
    Light microscopy reporting for reproducibility.
      
    DOI:  https://doi.org/10.1038/s41556-025-01704-y
  2. Cell Syst. 2025 Jun 13. pii: S2405-4712(25)00154-1. [Epub ahead of print] 101321
    Dynamic decoding of VEGF signaling and coordinated control of multiple phenotypes by the Src-TEM4-YAP pathway.
    Sung Hoon Lee, Tae-Yun Kang, Xingbo Shang, Andre Levchenko.
      Responses of endothelial cells to elevated levels of vascular endothelial growth factor (VEGF), frequently accompanying local decrease in oxygen supply, include loosening of cell contacts, rearrangement of cells in vessel remodeling, and ultimately, angiogenic growth. How these complex processes, occurring on diverse time scales, are coordinated and how they are guided by a single key signaling input is still incompletely understood. Here, we show that the various phenotypic responses associated with VEGF signaling are controlled at different steps of a pathway involving sequential activation of Src, tumor endothelial marker 4 (TEM4), YAP, and components of pro-angiogenic Notch signaling. Notably, due to feedback regulation at different pathway levels, the functional outcomes are controlled by oscillations of the pathway components occurring on distinct time scales. Deeper pathway layers integrate faster upstream responses and control progressively slower phenotypic outcomes. This signal-decoding pathway organization can ensure a high degree of complexity in a vital physiological process. A record of this paper's transparent peer review process is included in the supplemental information.
    Keywords:  Dll4; Jag1; Notch ligands; RhoA guanine exchange factor; Src; TEM4; VEGF; YAP; angiogenesis; computational model; negative feedback; oscillation
    DOI:  https://doi.org/10.1016/j.cels.2025.101321
  3. Nat Rev Nephrol. 2025 Jun 19.
    Leveraging data as a patient-scientist: frustrations and opportunities.
    Julio Saez-Rodriguez.
      
    DOI:  https://doi.org/10.1038/s41581-025-00968-9
  4. Curr Opin Cell Biol. 2025 Jun 12. pii: S0955-0674(25)00097-3. [Epub ahead of print]95 102559
    E-Cadherin: A conductor of cellular signaling.
    Rachel J Kehrberg, Kris A DeMali.
      Upon engagement of E-cadherin or when mechanical force is applied, E-cadherin recruits cytoskeletal proteins and triggers various signal transduction cascades including PI3K, Src, Rho family GTPases, kinases, YAP/TAZ, AMPK, and other metabolic enzymes. These cascades modulate E-cadherin's stability, viscosity, and its connection to the actin cytoskeleton, thereby reinforcing cell-cell adhesion.
    DOI:  https://doi.org/10.1016/j.ceb.2025.102559
  5. PLoS Comput Biol. 2025 Jun 16. 21(6): e1013188
    RIDDEN: Data-driven inference of receptor activity from transcriptomic data.
    Szilvia Barsi, Eszter Varga, Daniel Dimitrov, Julio Saez-Rodriguez, László Hunyady, Bence Szalai.
      Intracellular signaling initiated from ligand-bound receptors plays a fundamental role in both physiological regulation and development of disease states, making receptors one of the most frequent drug targets. Systems level analysis of receptor activity can help to identify cell and disease type-specific receptor activity alterations. While several computational methods have been developed to analyze ligand-receptor interactions based on transcriptomics data, none of them focuses directly on the receptor side of these interactions. Also, most of the methods use directly the expression of ligands and receptors to infer active interaction, while co-expression of genes does not necessarily indicate functional interactions or activated state. To address these problems, we developed RIDDEN (Receptor actIvity Data Driven inferENce), a computational tool, which predicts receptor activities from the receptor-regulated gene expression profiles, and not from the expressions of ligand and receptor genes. We collected 14463 perturbation gene expression profiles for 229 different receptors. Using these data, we trained the RIDDEN model, which can effectively predict receptor activity for new bulk and single-cell transcriptomics datasets. We validated RIDDEN's performance on independent in vitro and in vivo receptor perturbation data, showing that RIDDEN's model weights correspond to known regulatory interactions between receptors and transcription factors, and that predicted receptor activities correlate with receptor and ligand expressions in in vivo datasets. We also show that RIDDEN can be used to identify mechanistic biomarkers in an immune checkpoint blockade-treated cancer patient cohort. RIDDEN, the largest transcriptomics-based receptor activity inference model, can be used to identify cell populations with altered receptor activity and, in turn, foster the study of cell-cell communication using transcriptomics data.
    DOI:  https://doi.org/10.1371/journal.pcbi.1013188
  6. Cell Stem Cell. 2025 Jun 10. pii: S1934-5909(25)00221-8. [Epub ahead of print]
    Rapid generation of functional vascular organoids via simultaneous transcription factor activation of endothelial and mural lineages.
    Liyan Gong, Yadong Zhang, Yonglin Zhu, Umji Lee, Allen Chilun Luo, Xiang Li, Xi Wang, Danyang Chen, William T Pu, Ruei-Zeng Lin, Minglin Ma, Miao Cui, Kaifu Chen, Kai Wang, Juan M Melero-Martin.
      Vascular organoids (VOs) are valuable tools for studying vascular development, disease, and regenerative medicine. However, controlling endothelial and mural compartments independently remains challenging. Here, we present a streamlined method to generate VOs from induced pluripotent stem cells (iPSCs) via orthogonal activation of the transcription factors (TFs) ETV2 and NKX3.1 using Dox-inducible or modRNA systems. This approach enables efficient co-differentiation of endothelial cells (iECs) and mural cells (iMCs), producing functional 3D VOs in 5 days without ECM embedding. VOs matured further upon ECM exposure, forming larger, structured vessels. Single-cell RNA sequencing revealed vascular heterogeneity, and temporal regulation of TF expression allowed modulation of arterial and angiogenic iEC phenotypes. In vivo, VOs engrafted into immunodeficient mice, formed perfused vasculature, and promoted revascularization in models of hind limb ischemia and pancreatic islet transplantation. These findings establish a rapid and versatile VO platform with broad potential for vascular modeling, disease studies, and regenerative cell therapy.
    Keywords:  blood vessels organoids; endothelial cells; iPSCs; ischemia models; mural cells; pluripotent stem cells; therapeutic vascularization; transcription factor induction; vascular differentiation; vascular organoids
    DOI:  https://doi.org/10.1016/j.stem.2025.05.014
  7. Brief Bioinform. 2025 May 01. pii: bbaf269. [Epub ahead of print]26(3):
    Robust signalling entropy estimation for biological process characterisation.
    Ana Stolnicu, Nensi Ikonomi, Peter Eckhardt-Bellmann, Johann M Kraus, Hans A Kestler.
       MOTIVATION: Signalling entropy measures the uncertainty or randomness in the signalling pathways of a biological system. It reflects the complexity and variability of protein interactions and can indicate how information is processed within cells. Higher signalling entropy often indicates a more dynamic and adaptive state, whereas lower entropy may imply a more stable and less responsive condition. Estimating signalling entropy has become a valuable method for studying and understanding the complexity of biological processes. This measure has the potential to shed valuable insights into various phenomena, including the mechanisms behind cell fate decisions, drug resistance, and disease progression. To examine the molecular changes within a system, signalling entropy is quantified through the integration of expression measurements and protein interaction networks. Experimental and computational issues, such as false positives and additional noise, can all compromise the accuracy of protein interaction networks. Correction methods can be used to mitigate spurious results, correct for experimental bias, and integrate data from multiple sources. However, to date, the effect of such approaches on entropy calculations, together with the impact of different underlying networks, has yet to be evaluated.
    RESULTS: Here, we investigate how the topology of distinct protein interaction networks can alter the entropy calculation. We examine the entropy derived from different protein interaction networks. Additionally, we systematically evaluate different correction strategies, outlining their benefits and drawbacks along with identifying the most effective approaches for specific types of data and biological scenarios. This protocol outlines how to optimize the reliability of entropy calculations and ultimately leads to a deeper comprehension of biological processes and disease mechanisms.
    Keywords:  correction methods; false-positive interactions; protein interaction networks; signalling entropy
    DOI:  https://doi.org/10.1093/bib/bbaf269
  8. Life Sci Alliance. 2025 Sep;pii: e202503334. [Epub ahead of print]8(9):
    No evidence that human GIGYF2 interacts with GRB10: implications for human disease.
    Jung-Hyun Choi, Israel Shpilman, Niaz Mahmood, Shaghayegh Farhangmehr, Ulrich Braunschweig, Nathalia Gomide Cruz, Jun Luo, Reese Jalal Ladak, Angelos Pistofidis, Jiannis Ragoussis, T Martin Schmeing, Seyed Mehdi Jafarnejad, Benjamin J Blencowe, Nahum Sonenberg.
      GIGYF2 (growth factor receptor-bound protein 10 [GRB10]-interacting GYF [glycine-tyrosine-phenylalanine] protein 2) reduces mRNA stability and translation via microRNAs, ribosome quality control, and several RNA-binding proteins. GIGYF2 was first identified in mouse cell lines as an interacting partner with GRB10, which binds to the insulin receptor and the insulin-like growth factor receptor 1. Mutations in the human GIGYF2 gene were reported in autism. In mouse models, Gigyf2 mutations engender several diseases. It was therefore thought that the GIGYF2-associated disease in humans is caused by defective GRB10 signaling. We show here that GIGYF2 does not interact with GRB10 in human cell lines, as determined by co-immunoprecipitation and proximity ligation assays. The lack of interaction is explained by the absence of the critical GYF domain-binding PPGΦ sequence in the human GRB10 protein. These results contrast with the current understanding that a GIGYF2/GRB10 complex is associated with human disease via insulin receptor and insulin-like growth factor receptor 1 signaling and underscore alternative mechanisms responsible for the observed phenotypes associated with mutations in the human GIGYF2 gene.
    DOI:  https://doi.org/10.26508/lsa.202503334
  9. Mol Oncol. 2025 Jun 15.
    A nucleotide-independent, pan-RAS-targeted DARPin elicits anti-tumor activity in a multimodal manner.
    Jonas N Kapp, Wouter P R Verdurmen, Jonas V Schaefer, Kari Kopra, Gabriela Nagy-Davidescu, Elodie Richard, Marie-Julie Nokin, Patrick Ernst, Rastislav Tamaskovic, Martin Schwill, Ralph Degen, Claudia Scholl, David Santamaria, Andreas Plückthun.
      The KRAS oncoprotein is a frequent tumor driver in lung, pancreatic, and colorectal cancers and has proven to be a challenging pharmaceutical target. The first KRAS-targeted therapeutics are now being tested in clinical trials but the consequences of preferentially targeting the GDP or GTP state of KRAS and the relevance of RAS nanoclustering have remained unclear. Here we report a Designed Ankyrin Repeat Protein (DARPin) that recognizes the RAS switch I/II region with low nm affinity, independently of the nucleotide bound (GDP- or GTP state). This DARPin, termed '784_F5', occupies the effector recognition lobe, resulting in interference with SOS-mediated activation, RAS downstream effector interactions, and KRAS nanoclustering. Consequently, this anti-RAS DARPin potently blocks downstream signaling, leading to a strong reduction in proliferation and anchorage-independent growth in RAS-dependent cell lines. We showed that the expression of '784_F5', the pan-RAS, nucleotide-independent DARPin can lead to tumor regression in a colorectal xenograft model which may hold promise for further investigation and development.
    Keywords:  Designed Ankyrin Repeat Protein; RAS; cancer; drug development; oncogene; small GTPase
    DOI:  https://doi.org/10.1002/1878-0261.70061
  10. Elife. 2025 Jun 17. pii: RP91779. [Epub ahead of print]12
    PI3Kα inhibition blocks osteochondroprogenitor specification and the hyper-inflammatory response to prevent heterotopic ossification.
    José Antonio Valer, Alexandre Deber, Marius Wits, Carolina Pimenta-Lope, Marie-José Goumans, Jose Luis Rosa, Gonzalo Sánchez-Duffhues, Francesc Ventura.
      Heterotopic ossification (HO) occurs following mechanical trauma and burns, or congenitally in patients suffering from fibrodysplasia ossificans progressiva (FOP). Recently, we demonstrated that inhibitors of phosphatidylinositol 3-kinase alpha (PI3Kα) may be a useful therapy for patients undergoing HO. In this study, using the already marketed BYL719/Alpelisib/Piqray drug, we have further confirmed these results, detailed the underlying mechanisms of action, and optimized the timing of the administration of BYL719. We found that BYL719 effectively prevents HO even when administered up to 3-7 days after injury. We demonstrate in cell cultures and in a mouse model of HO that the major actions of BYL719 are on-target effects through the inhibition of PI3Kα, without directly affecting ACVR1 or FOP-inducing ACVR1R206H kinase activities. In vivo, we found that a lack of PI3Kα in progenitors at injury sites is sufficient to prevent HO. Moreover, time course assays in HO lesions demonstrate that BYL719 not only blocks osteochondroprogenitor specification but also reduces the inflammatory response. BYL719 inhibits the migration, proliferation, and expression of pro-inflammatory cytokines in monocytes and mast cells, suggesting that BYL719 hampers the hyper-inflammatory status of HO lesions. Altogether, these results highlight the potential of PI3Kα inhibition as a safe and effective therapeutic strategy for HO.
    Keywords:  fibrodysplasia ossificans progressiva; heterotopic bone; mesenchymal progenitors; mouse; rare diseases; regenerative medicine; stem cells
    DOI:  https://doi.org/10.7554/eLife.91779
  11. Nature. 2025 Jun 18.
    Morphodynamics of human early brain organoid development.
    Akanksha Jain, Gilles Gut, Fátima Sanchis-Calleja, Reto Tschannen, Zhisong He, Nicolas Luginbühl, Fides Zenk, Antonius Chrisnandy, Simon Streib, Christoph Harmel, Ryoko Okamoto, Malgorzata Santel, Makiko Seimiya, René Holtackers, Juliane K Rohland, Sophie Martina Johanna Jansen, Matthias P Lutolf, J Gray Camp, Barbara Treutlein.
      Brain organoids enable the mechanistic study of human brain development and provide opportunities to explore self-organization in unconstrained developmental systems1-3. Here we establish long-term, live light-sheet microscopy on unguided brain organoids generated from fluorescently labelled human induced pluripotent stem cells, which enables tracking of tissue morphology, cell behaviours and subcellular features over weeks of organoid development4. We provide a novel dual-channel, multi-mosaic and multi-protein labelling strategy combined with a computational demultiplexing approach to enable simultaneous quantification of distinct subcellular features during organoid development. We track actin, tubulin, plasma membrane, nucleus and nuclear envelope dynamics, and quantify cell morphometric and alignment changes during tissue-state transitions including neuroepithelial induction, maturation, lumenization and brain regionalization. On the basis of imaging and single-cell transcriptome modalities, we find that lumenal expansion and cell morphotype composition within the developing neuroepithelium are associated with modulation of gene expression programs involving extracellular matrix pathway regulators and mechanosensing. We show that an extrinsically provided matrix enhances lumen expansion as well as telencephalon formation, and unguided organoids grown in the absence of an extrinsic matrix have altered morphologies with increased neural crest and caudalized tissue identity. Matrix-induced regional guidance and lumen morphogenesis are linked to the WNT and Hippo (YAP1) signalling pathways, including spatially restricted induction of the WNT ligand secretion mediator (WLS) that marks the earliest emergence of non-telencephalic brain regions. Together, our work provides an inroad into studying human brain morphodynamics and supports a view that matrix-linked mechanosensing dynamics have a central role during brain regionalization.
    DOI:  https://doi.org/10.1038/s41586-025-09151-3
  12. EMBO Rep. 2025 Jun 13.
    ATR promotes mTORC1 activity via de novo cholesterol synthesis.
    Naveen Kumar Tangudu, Alexandra N Grumet, Richard Fang, Raquel Buj, Aidan R Cole, Apoorva Uboveja, Amandine Amalric, Baixue Yang, Zhentai Huang, Cassandra Happe, Mai Sun, Stacy L Gelhaus, Matthew L MacDonald, Nadine Hempel, Nathaniel W Snyder, Katarzyna M Kedziora, Alexander J Valvezan, Katherine M Aird.
      DNA damage and cellular metabolism exhibit a complex interplay characterized by bidirectional feedback. Key mediators of these pathways include ATR and mTORC1, respectively. Previous studies established ATR as a regulatory upstream factor of mTORC1 during replication stress; however, the precise mechanisms remain poorly defined. Additionally, the activity of this signaling axis in unperturbed cells has not been extensively investigated. We demonstrate that ATR promotes mTORC1 activity across various human cancer cells and both human and mouse normal cells under basal conditions. This effect is enhanced in human cancer cells (SKMEL28, RPMI-7951, HeLa) following knockdown of p16, a cell cycle inhibitor that we have previously found increases mTORC1 activity and here found increases ATR activity. Mechanistically, ATR promotes de novo cholesterol synthesis and mTORC1 activation through the phosphorylation and upregulation of lanosterol synthase (LSS), independently of both CHK1 and the TSC complex. Interestingly, this pathway is distinct from the regulation of mTORC1 by ATM and may be specific to cancer cells. Finally, ATR-mediated increased cholesterol correlates with enhanced localization of mTOR to lysosomes. Collectively, our findings demonstrate a novel connection linking ATR and mTORC1 signaling through the modulation of cholesterol metabolism.
    Keywords:  Cholesterol; Lanosterol Synthase; Lysosome; Metabolism; p16
    DOI:  https://doi.org/10.1038/s44319-025-00451-3
  13. Cell. 2025 Jun 11. pii: S0092-8674(25)00572-0. [Epub ahead of print]
    Perturb-Multimodal: A platform for pooled genetic screens with imaging and sequencing in intact mammalian tissue.
    Reuben A Saunders, William E Allen, Xingjie Pan, Jaspreet Sandhu, Jiaqi Lu, Thomas K Lau, Karina Smolyar, Zuri A Sullivan, Catherine Dulac, Jonathan S Weissman, Xiaowei Zhuang.
      Metazoan life requires the coordinated activities of thousands of genes in spatially organized cell types. Understanding the basis of tissue function requires approaches to dissect the genetic control of diverse cellular and tissue phenotypes in vivo. Here, we present Perturb-Multimodal (Perturb-Multi), a paired imaging and sequencing method to construct large-scale, multimodal genotype-phenotype maps in tissues with pooled genetic perturbations. Using imaging, we identify perturbations in individual cells while simultaneously measuring their gene expression profiles and subcellular morphology. Using single-cell sequencing, we measure full transcriptomic responses to the same perturbations. We apply Perturb-Multi to study hundreds of genetic perturbations in the mouse liver. Our data suggest the genetic regulators and mechanisms underlying the dynamic control of hepatocyte zonation, the unfolded protein response, and steatosis. Perturb-Multi accelerates discoveries of the genetic basis of complex cell and tissue physiology and provides critical training data for emerging machine learning models of cellular function.
    Keywords:  RCA-MERFISH; hepatocyte stress response; in vivo pooled screening; lipid droplet accumulation; liver zonation; machine learning morphology; multimodal phenotyping; multiplexed RNA imaging; multiplexed protein imaging; scRNA-seq
    DOI:  https://doi.org/10.1016/j.cell.2025.05.022
  14. Oncologist. 2025 Jun 04. pii: oyaf126. [Epub ahead of print]30(6):
    Prolonged response to PIK3CA inhibition in an advanced hormone-positive breast cancer patient with 3 mutations in the alpha subunit of PI-3 kinase.
    Rotem Merose, Raya Leibowitz.
      Mutations in the oncogene PIK3CA are implicated in many types of solid tumors and are prevalent in estrogen-receptor (ER)-positive Her2-negative (ER+Her2-) breast cancer (BC). In recent years, a combination of a drug-modulating ER and a PIK3CA inhibitor was approved for PIK3CA-mutant BC. We present a case of a 69-year-old otherwise healthy woman who was diagnosed with early ER+Her2- BC at the age of 47 and was treated with lumpectomy, adjuvant chemotherapy, radiation, and adjuvant tamoxifen. Five years after the termination of chemotherapy, she was diagnosed with bone metastasis and received several lines of endocrine therapy and subsequent capecitabine for 17 years altogether. Upon disease progression in the liver and lung, a "liquid biopsy" from the blood detected 3 missense mutations in PIK3CA, one of which was known to be deleterious (H1047R). The patient started a combination of Fulvestrant and Alpelisib with a deep and prolonged clinical and radiological response for 3 years. The occurrence of multiple mutations in PIK3CA was documented in 12-15% of BCs. A retrospective analysis showed that ER+Her2- BC patients with multiple PIK3CA mutations had a significantly higher response rate to PIK3CA inhibitor. It is impossible to determine whether our patient's extremely prolonged progression-free survival on Alpelisib-Fulvestrant was a result of the multiplicity of mutations in PIK3CA, the existence of the known deleterious mutation H1047R, or other clinical/biological factors. Our case highlights the potential importance of the number of PIK3CA mutations observed in a pathological sample or liquid biopsy, despite it being still unknown how to incorporate the multiplicity or singularity of PIK3CA mutations into clinical decision-making.
    Keywords:  PIK3CA; alpelisib; breast cancer; mutation
    DOI:  https://doi.org/10.1093/oncolo/oyaf126
  15. Sci Adv. 2025 Jun 20. 11(25): eadt9936
    Conformational dynamics and multimodal interaction of Paxillin with the focal adhesion targeting domain.
    Supriyo Bhattacharya, Yanan He, Yihong Chen, Atish Mohanty, Alexander Grishaev, Prakash Kulkarni, Ravi Salgia, John Orban.
      Paxillin (PXN) and focal adhesion kinase (FAK) are two major components of the focal adhesion complex, a multiprotein structure linking the intracellular cytoskeleton to the cell exterior. The interaction between the disordered amino-terminal domain of PXN and the carboxyl-terminal targeting domain of FAK (FAT) is necessary and sufficient for localizing FAK to focal adhesions. Furthermore, PXN serves as a platform for recruiting other proteins that together control the dynamic changes needed for cell migration and survival. Here, we show that the PXN N-domain undergoes significant compaction upon FAT binding, forming a 48-kilodalton multimodal complex with four major interconverting states. Although the complex is flexible, each state has unique sets of contacts involving disordered regions that are both highly represented in ensembles and conserved. PXN being a hub protein, the results provide a structural basis for understanding how shifts in the multistate equilibrium (e.g., through ligand binding and phosphorylation) may rewire cellular networks leading to phenotypic changes.
    DOI:  https://doi.org/10.1126/sciadv.adt9936
  16. Development. 2025 Jun 13. pii: dev.204469. [Epub ahead of print]
    TIE1 dependent lymphatic vascular remodeling is mediated by its second tyrosine kinase domain.
    H Scott Baldwin, Michael J Davis, Cristina Harmelink, Xianghu Qu.
      Mutations in ANG2 and TIE1 are associated with primary lymphedema in humans, but the mechanisms of ANG/TIE signaling in the lymphatic vasculature remain incompletely understood. We document that TIE2 is not detected in lymphatic endothelial cells (LECs) before E14.5 but is expressed in collecting vessels from later embryonic stages, in contrast to robust TIE1 expression in all LECs from early stages. Accordingly, only LEC-specific deletion of Tie1 but not Tie2 resulted in defective lymphatic development and abnormal valve function. We discovered that defects of Tie1 lymphatic knockout mice were largely rescued by simultaneous loss of FoxO1. In addition, FOXC2 expression was abolished in Tie1 deficient lymphatics but restored by simultaneous loss of FoxO1, indicating that FOXO1, regulating FOXC2, might be a direct downstream effector of TIE1 signaling in lymphatic system. Further, we generated point mutations in each tyrosine kinase domain of TIE1 and found that the second, but not the first, tyrosine kinase domain of TIE1 is essential for its function in the lymphatic system. Thus, our results suggest new avenues for manipulation of TIE1 signaling to enhance therapeutic lymphangiogenesis.
    Keywords:  FOXC2; FOXO1; Lymphatic system; TIE1; TIE2; Tyrosine kinase domain
    DOI:  https://doi.org/10.1242/dev.204469
  17. Nucleic Acids Res. 2025 Jun 06. pii: gkaf528. [Epub ahead of print]53(11):
    High-resolution profiling reveals coupled transcriptional and translational regulation of transgenes.
    Emma L Peterman, Deon S Ploessl, Kasey S Love, Valeria Sanabria, Rachel F Daniels, Christopher P Johnstone, Diya R Godavarti, Sneha R Kabaria, Conrad G Oakes, Athma A Pai, Kate E Galloway.
      Concentrations of RNAs and proteins provide important determinants of cell fate. Robust gene circuit design requires an understanding of how the combined actions of individual genetic components influence both messenger RNA (mRNA) and protein levels. Here, we simultaneously measure mRNA and protein levels in single cells using hybridization chain reaction Flow-FISH (HCR Flow-FISH) for a set of commonly used synthetic promoters. We find that promoters generate differences in both the mRNA abundance and the effective translation rate of these transcripts. Stronger promoters not only transcribe more RNA but also show higher effective translation rates. While the strength of the promoter is largely preserved upon genome integration with identical elements, the choice of polyadenylation signal and coding sequence can generate large differences in the profiles of the mRNAs and proteins. We used long-read direct RNA sequencing to define the transcription start and splice sites of common synthetic promoters and independently vary the defined promoter and 5' UTR sequences in HCR Flow-FISH. Together, our high-resolution profiling of transgenic mRNAs and proteins offers insight into the impact of common synthetic genetic components on transcriptional and translational mechanisms. By developing a novel framework for quantifying expression profiles of transgenes, we have established a system for building more robust transgenic systems.
    DOI:  https://doi.org/10.1093/nar/gkaf528
This page is being maintained by Thomas Krichel. It was last updated on 2025‒06‒22 at 11:49.