bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2025–03–30
nineteen papers selected by
Ralitsa Radostinova Madsen, MRC-PPU
  1. Lysosomal PIP3 revealed by genetically encoded lipid biosensors.
  2. Somatic uniparental disomy of PTEN in endothelial cells causes vascular malformations in patients with PTEN Hamartoma Tumor Syndrome.
  3. Advancing cell-cell communication analysis from single-cell genomics data.
  4. Using Prime Editing Guide Generator (PEGG) for high-throughput generation of prime editing sensor libraries.
  5. The metabolically protective energy expenditure increase of Pik3r1-related insulin resistance is not explained by Ucp1-mediated thermogenesis.
  6. An advanced toolset to manipulate and monitor subcellular phosphatidylinositol 3,5-bisphosphate.
  7. CellPhoneDB v5: inferring cell-cell communication from single-cell multiomics data.
  8. A quick guide to evaluating prime editing efficiency in mammalian cells.
  9. Orchestration of pluripotent stem cell genome reactivation during mitotic exit.
  10. High-throughput screening of human genetic variants by pooled prime editing.
  11. In vivo targeted and deterministic single-cell malignant transformation.
  12. Structural basis for cholesterol sensing of LYCHOS and its interaction with indoxyl sulfate.
  13. Somatic mosaicism and interneuron involvement in mTORopathies.
  14. Cell compression - relevance, mechanotransduction mechanisms and tools.
  15. PI3Kβ functions as a protein kinase to promote cellular protein O-GlcNAcylation and acetyl-CoA production for tumor growth.
  16. Sirolimus treatment for intractable vascular anomalies (SIVA): An open-label, single-arm, multicenter, prospective trial.
  17. Time, the final frontier.
  18. Cloning and validating systems for high throughput molecular recording.
  19. Plasticity of the mammalian integrated stress response.
  1. Proc Natl Acad Sci U S A. 2025 Apr;122(13): e2426929122
    Lysosomal PIP3 revealed by genetically encoded lipid biosensors.
    Ayse Z Sahan, Mingyuan Chen, Qi Su, Qingrong Li, Dong Wang, Jin Zhang.
      3-Phosphoinositides (3-PIs), phosphatidylinositol (3,4) bisphosphate [PI(3,4)P2] and phosphatidylinositol (3,4,5) trisphosphate (PIP3), are important lipid second messengers in the Phosphoinositide 3-Kinase (PI3K)/Akt signaling pathway, which is crucial to cell growth and frequently dysregulated in cancer. Emerging evidence suggests these lipid second messengers may be present in membranes beyond the plasma membrane, yet their spatial regulation within other membrane compartments is not well understood. To dissect the spatial regulation of specific 3-PI species, we developed genetically encodable biosensors with selectivity for PIP3 or PI(3,4)P2. Using these biosensors, we showed that PIP3 significantly accumulated at the lysosome upon growth factor stimulation, in contrast to the conventional view that PIP3 is exclusively present in the plasma membrane. Furthermore, we showed that lysosomal PIP3 originates from the plasma membrane and relies on dynamin-dependent endocytosis for lipid internalization. Thus, PIP3 can exploit dynamic trafficking pathways to access subcellular compartments and regulate signaling in a spatially selective manner.
    Keywords:  3-phosphoinositide; cellular signaling; fluorescent biosensor; lysosome; spatiotemporal regulation
    DOI:  https://doi.org/10.1073/pnas.2426929122
  2. Cancer Discov. 2025 Mar 28.
    Somatic uniparental disomy of PTEN in endothelial cells causes vascular malformations in patients with PTEN Hamartoma Tumor Syndrome.
    Sandra D Castillo, Xabier Perosanz, Andrew K Ressler, Marta Ivars, Jairo Rodriguez, Carlota Rovira, Emanuele M Nola, Judith Llena, Joaquim Grego-Bessa, Monica Roldan, Raquel Arnau, Anabel Martínez-Romero, Ignasi Barber, Miguel Bejarano, Asuncion Vicente, Veronica Celis, Héctor Salvador, Jaume Mora, Douglas A Marchuk, Eulalia Baselga, Mariona Graupera.
      PTEN Hamartoma Tumor Syndrome (PHTS) is a rare tumor risk disorder caused by germline loss-of-function mutations in PTEN. Half of these patients develop vascular malformations, a hamartoma characterized by overgrowth of vessels. Here, we harness biopsies and patient-derived endothelial cells (ECs) to study the genetic etiology of PHTS-related vascular malformations. We discover that these lesions are generated by the somatic loss of the PTEN wild-type allele through copy-neutral loss of heterozygosity, leading to somatic uniparental disomy of the PTEN mutated allele in ECs. We established a mouse model of PHTS-related vascular malformations and identified that the mTOR inhibitor rapamycin and AKT inhibitor capivasertib block vascular lesion growth. As proof-of-concept for clinical activity, off-label treatment with rapamycin of two patients with PHTS reduced vascular overgrowth and abrogated lesion-associated pain. Overall, our results uncover the genetic cause of vascular malformations in patients with PHTS and open new avenues for therapeutic intervention.
    DOI:  https://doi.org/10.1158/2159-8290.CD-24-0807
  3. Nat Protoc. 2025 Mar 25.
    Advancing cell-cell communication analysis from single-cell genomics data.
    Iguaracy Pinheiro-de-Sousa, Evangelia Petsalaki.
      
    DOI:  https://doi.org/10.1038/s41596-025-01140-0
  4. Methods Enzymol. 2025 ;pii: S0076-6879(25)00006-0. [Epub ahead of print]712 437-451
    Using Prime Editing Guide Generator (PEGG) for high-throughput generation of prime editing sensor libraries.
    Samuel I Gould, Francisco J Sánchez-Rivera.
      Prime editing enables the generation of nearly any small genetic variant. However, the process of prime editing guide RNA (pegRNA) design is challenging and requires automated computational design tools. We developed Prime Editing Guide Generator (PEGG), a fast, flexible, and user-friendly Python package that enables the rapid generation of pegRNA and pegRNA-sensor libraries. Here, we describe the installation and use of PEGG (https://pegg.readthedocs.io) to rapidly generate custom pegRNA-sensor libraries for use in high-throughput prime editing screens.
    Keywords:  Genome editing; PegRNA; Prime editing; Python
    DOI:  https://doi.org/10.1016/bs.mie.2025.01.006
  5. Am J Physiol Endocrinol Metab. 2025 Mar 28.
    The metabolically protective energy expenditure increase of Pik3r1-related insulin resistance is not explained by Ucp1-mediated thermogenesis.
    Ineke Luijten, Ami Onishi, Eleanor J McKay, Tore Bengtsson, Robert K Semple.
      Human SHORT syndrome is caused by dominant negative human PIK3R1 mutations that impair insulin-stimulated phosphoinositide 3-kinase (PI3K) activity. This produces severe insulin resistance (IR) and often reduced adiposity, commonly described as lipodystrophy. However unlike human primary lipodystrophies, SHORT syndrome does not feature fatty liver or dyslipidaemia. Pik3r1Y657*/WT (Pik3r1Y657*) mice metabolically phenocopy humans, moreover exhibiting increased energy expenditure on high fat feeding. We have hypothesised that this increased energy expenditure explains protection from lipotoxicity, and suggested that understanding its mechanism may offer novel approaches to mitigating the metabolic syndrome. We set out to determine whether increased Ucp1-dependent thermogenesis explains the increased energy expenditure in Pik3r1-related IR. Male and female Pik3r1Y657* mice challenged with a 45% fat diet for 3 weeks at 21°C showed reduced metabolic efficiency not explained by changes in food intake or physical activity. No changes were seen in thermoregulation, assessed by thermal imaging and a modified Scholander protocol. Ucp1- dependent thermogenesis, assessed by norepinephrine-induced oxygen consumption, was also unaltered. Housing at 30°C did not alter the metabolic phenotype of male Pik3r1Y657* mice, but led to lowered physical activity in female Pik3r1Y657* mice compared to controls. Nevertheless these mice still exhibited increased energy expenditure. Ucp1-dependent thermogenic capacity at 30°C was similar in Pik3r1Y657* and WT mice. We conclude that the likely metabolically protective 'energy leak' in Pik3r1-related IR is not caused by Ucp1- mediated BAT hyperactivation, nor impaired thermal insulation. Further metabolic studies are required to seek alternative explanations such as non Ucp1-mediated futile cycling.
    Keywords:  Insulin resistance; PI 3-Kinase; Pik3r1; brown adipose tissue; energy expenditure
    DOI:  https://doi.org/10.1152/ajpendo.00449.2024
  6. J Cell Biol. 2025 Jun 02. pii: e202408158. [Epub ahead of print]224(6):
    An advanced toolset to manipulate and monitor subcellular phosphatidylinositol 3,5-bisphosphate.
    Joshua G Pemberton, Isobel Barlow-Busch, Meredith L Jenkins, Matthew A H Parson, Farkas Sarnyai, Seyma Nur Bektas, Yeun Ju Kim, John E Heuser, John E Burke, Tamas Balla.
      Phosphatidylinositol (PI) 3,5-bisphosphate (PI(3,5)P2) is a minor inositol-containing phospholipid that serves as an important regulator of endolysosomal functions. However, the precise sites of subcellular enrichment and molecular targets of this regulatory lipid are poorly understood. Here, we describe the generation and detailed characterization of a short engineered catalytic fragment of the human PIKfyve enzyme, which potently converts PI 3-phosphate to PI(3,5)P2. This novel tool allowed for the evaluation of reported PI(3,5)P2-sensitive biosensors and showed that the recently identified phox homology (PX) domain of the Dictyostelium discoideum (Dd) protein, SNXA, can be used to monitor the production of PI(3,5)P2 in live cells. Modification and adaptation of the DdSNXAPX-based probes into compartment-specific bioluminescence resonance energy transfer-based biosensors allows for the real-time monitoring of PI(3,5)P2 generation within the endocytic compartments of entire cell populations. Collectively, these molecular tools should allow for exciting new studies to better understand the cellular processes controlled by localized PI(3,5)P2 metabolism.
    DOI:  https://doi.org/10.1083/jcb.202408158
  7. Nat Protoc. 2025 Mar 25.
    CellPhoneDB v5: inferring cell-cell communication from single-cell multiomics data.
    Kevin Troulé, Robert Petryszak, Batuhan Cakir, James Cranley, Alicia Harasty, Martin Prete, Zewen Kelvin Tuong, Sarah A Teichmann, Luz Garcia-Alonso, Roser Vento-Tormo.
      Cell-cell communication is essential for tissue development, function and regeneration. The revolution of single-cell genomics technologies offers an unprecedented opportunity to uncover how cells communicate in vivo within their tissue niches and how disruption of these niches can lead to diseases and developmental abnormalities. CellPhoneDB is a bioinformatics toolkit designed to infer cell-cell communication by combining a curated repository of bona fide ligand-receptor interactions with methods to integrate these interactions with single-cell genomics data. Here we present a protocol for the latest version of CellPhoneDB (v5), offering several new features. First, the repository has been expanded by one-third with the addition of new interactions, including ~1,000 interactions mediated by nonpeptidic ligands such as steroidogenic hormones, neurotransmitters and small G-protein-coupled receptor (GPCR)-binding ligands. Second, we outline a new way of using the database that allows users to tailor queries to their experimental designs. Third, the update incorporates novel strategies to prioritize specific cell-cell interactions, leveraging information from other modalities such as tissue microenvironments derived from spatial transcriptomics technologies or transcription factor activities derived from a single-cell assay for transposase accessible chromatin assays. Finally, we describe the new CellPhoneDBViz module to interactively visualize and share results. Altogether, CellPhoneDB v5 enhances the precision of cell-cell communication inference, offering new insights into tissue biology in physiological microenvironments. This protocol typically takes ~15 min and requires basic knowledge of python.
    DOI:  https://doi.org/10.1038/s41596-024-01137-1
  8. Methods Enzymol. 2025 ;pii: S0076-6879(25)00016-3. [Epub ahead of print]712 419-436
    A quick guide to evaluating prime editing efficiency in mammalian cells.
    Chengfang Liu, Sifan Cheng, Junjie Zhu, Lina Zhou, Jia Chen.
      According to the Clinvar database, modeling the diseases associated with pathogenic mutations requires the installation of base substitutions, small insertions or deletions. Prime editor (PE) was recently developed to precisely install any base substitutions and/or small insertions/deletions (indels) in mammalian cells and animals without requiring DSBs or donor DNA templates. PE also offers greater editing and targeting flexibility compared to other precision CRISPR editing methods because the versatile editing information is encoded in the reverse-transcription template of its prime editing guide RNA. However, optimal PE system selection and experimental design can be complex, and there are various factors that can affect PE efficiency. This chapter serves as a rapid entry-level guideline for the application of PE, providing an experimental framework for using PE at a specific genomic locus. RUNX1 was selected as a representative target site to illustrate the detailed methodology for constructing PE plasmids and the process of transfecting these plasmids into 293FT cells. We further examined the efficiency of PE-mediated genome editing in mammalian cells by using next-generation sequencing.
    Keywords:  Mammalian cells; Prime editing; Prime editor
    DOI:  https://doi.org/10.1016/bs.mie.2025.01.016
  9. Cell Rep. 2025 Mar 27. pii: S2211-1247(25)00257-8. [Epub ahead of print]44(4): 115486
    Orchestration of pluripotent stem cell genome reactivation during mitotic exit.
    Silja Placzek, Ludovica Vanzan, Cédric Deluz, David M Suter.
      Cell identity maintenance faces many challenges during mitosis, as most DNA-binding proteins are evicted from DNA and transcription is virtually abolished. How cells maintain their identity through division and faithfully re-initiate gene expression during mitotic exit is unclear. Here, we develop a novel reporter system enabling cell cycle synchronization-free separation of pluripotent stem cells in temporal bins of <30 min during mitotic exit. This allows us to quantify genome-wide reactivation of transcription, sequential changes in chromatin accessibility and transcription factor footprints, and re-binding of the pluripotency transcription factors OCT4, SOX2, and NANOG (OSN). We find that transcriptional activity progressively ramps up after mitosis and that OSN rapidly reoccupy the genome during the anaphase-telophase transition. We also demonstrate transcription factor-specific, dynamic relocation patterns and a hierarchical reorganization of the OSN binding landscape governed by OCT4 and SOX2. Our study sheds light on the dynamic orchestration of transcriptional reactivation after mitosis.
    Keywords:  ATAC-seq; CP: Cell biology; CP: Stem cell research; ChIP-seq; NANOG; OCT4; RNA-seq; SOX2; chromatin; mitosis; pluripotent stem cells; transcription factors
    DOI:  https://doi.org/10.1016/j.celrep.2025.115486
  10. Cell Genom. 2025 Mar 18. pii: S2666-979X(25)00070-9. [Epub ahead of print] 100814
    High-throughput screening of human genetic variants by pooled prime editing.
    Michael Herger, Christina M Kajba, Megan Buckley, Ana Cunha, Molly Strom, Gregory M Findlay.
      Multiplexed assays of variant effect (MAVEs) enable scalable functional assessment of human genetic variants. However, established MAVEs are limited by exogenous expression of variants or constraints of genome editing. Here, we introduce a pooled prime editing (PE) platform to scalably assay variants in their endogenous context. We first improve efficiency of PE in HAP1 cells, defining optimal prime editing guide RNA (pegRNA) designs and establishing enrichment of edited cells via co-selection. We next demonstrate negative selection screening by testing over 7,500 pegRNAs targeting SMARCB1 and observing depletion of efficiently installed loss-of-function (LoF) variants. We then screen for LoF variants in MLH1 via 6-thioguanine selection, testing 65.3% of all possible SNVs in a 200-bp region including exon 10 and 362 non-coding variants from ClinVar spanning a 60-kb region. The platform's overall accuracy for discriminating pathogenic variants indicates that it will be highly valuable for identifying new variants underlying diverse human phenotypes across large genomic regions.
    Keywords:  MAVE; MLH1; PE; SMARCB1; functional genomics; genome-editing technology; multiplexed assay of variant effect; precision medicine; prime editing; saturation mutagenesis
    DOI:  https://doi.org/10.1016/j.xgen.2025.100814
  11. Elife. 2025 Mar 25. pii: RP97650. [Epub ahead of print]13
    In vivo targeted and deterministic single-cell malignant transformation.
    Pierluigi Scerbo, Benjamin Tisserand, Marine Delagrange, Héloise Debare, David Bensimon, Bertrand Ducos.
      Why does a normal cell possibly harboring genetic mutations in oncogene or tumor suppressor genes becomes malignant and develops a tumor is a subject of intense debate. Various theories have been proposed but their experimental test has been hampered by the unpredictable and improbable malignant transformation of single cells. Here, using an optogenetic approach we permanently turn on an oncogene (KRASG12V) in a single cell of a zebrafish brain that, only in synergy with the transient co-activation of a reprogramming factor (VENTX/NANOG/OCT4), undergoes a deterministic malignant transition and robustly and reproducibly develops within 6 days into a full-blown tumor. The controlled way in which a single cell can thus be manipulated to give rise to cancer lends support to the 'ground state theory of cancer initiation' through 'short-range dispersal' of the first malignant cells preceding tumor growth.
    Keywords:  Danio rerio; cancer; cancer biology; optogenetics; zebrafish
    DOI:  https://doi.org/10.7554/eLife.97650
  12. Nat Commun. 2025 Mar 21. 16(1): 2815
    Structural basis for cholesterol sensing of LYCHOS and its interaction with indoxyl sulfate.
    Zhenhua Wang, Jingjing He, Yufan Yang, Yonglin He, Hongwu Qian.
      The lysosome serves as an essential nutrient-sensing hub within the cell, where the mechanistic target of rapamycin complex 1 (mTORC1) is activated. Lysosomal cholesterol signaling (LYCHOS), a lysosome membrane protein, has been identified as a cholesterol sensor that couples cholesterol concentration to mTORC1 activation. However, the molecular basis is unknown. Here, we determine the cryo-electron microscopy (cryo-EM) structure of human LYCHOS at a resolution of 3.1 Å, revealing a cholesterol-like density at the interface between the permease and G-protein coupled receptor (GPCR) domains. Advanced 3D classification reveals two distinct states of LYCHOS. Comparative structural analysis between these two states demonstrated a cholesterol-related movement of GPCR domain relative to permease domain, providing structural insights into how LYCHOS senses lysosomal cholesterol levels. Additionally, we identify indoxyl sulfate (IS) as a binding ligand to the permease domain, confirmed by the LYCHOS-IS complex structure. Overall, our study provides a foundation and indicates additional directions for further investigation of the essential role of LYCHOS in the mTORC1 signaling pathway.
    DOI:  https://doi.org/10.1038/s41467-025-58087-9
  13. Trends Neurosci. 2025 Mar 21. pii: S0166-2236(25)00040-2. [Epub ahead of print]
    Somatic mosaicism and interneuron involvement in mTORopathies.
    Lilian G Jerow, Darcy A Krueger, Christina Gross, Steve C Danzer.
      Somatic mutations in genes regulating mechanistic target of rapamycin (mTOR) pathway signaling can cause epilepsy, autism, and cognitive dysfunction. Research has predominantly focused on mTOR regulation of excitatory neurons in these conditions; however, dysregulated mTOR signaling among interneurons may also be critical. In this review, we discuss clinical evidence for interneuron involvement, and potential mechanisms, known and hypothetical, by which interneurons might come to directly harbor pathogenic mutations. To understand how mTOR hyperactive interneurons might drive dysfunction, we review studies in which mTOR signaling has been selectively disrupted among interneurons and interneuron progenitors in mouse model systems. Complex cellular mosaicism and dual roles for mTOR (hyper)activation in mediating disease pathogenesis and homeostatic responses raise challenging questions for effective treatment of these disorders.
    Keywords:  epilepsy; focal cortical dysplasia; parvalbumin; somatostatin; tuberous sclerosis complex
    DOI:  https://doi.org/10.1016/j.tins.2025.02.009
  14. J Cell Sci. 2025 Mar 15. pii: jcs263704. [Epub ahead of print]138(6):
    Cell compression - relevance, mechanotransduction mechanisms and tools.
    Laura M Faure, Valeria Venturini, Pere Roca-Cusachs.
      From border cell migration during Drosophila embryogenesis to solid stresses inside tumors, cells are often compressed during physiological and pathological processes, triggering major cell responses. Cell compression can be observed in vivo but also controlled in vitro through tools such as micro-channels or planar confinement assays. Such tools have recently become commercially available, allowing a broad research community to tackle the role of cell compression in a variety of contexts. This has led to the discovery of conserved compression-triggered migration modes, cell fate determinants and mechanosensitive pathways, among others. In this Review, we will first address the different ways in which cells can be compressed and their biological contexts. Then, we will discuss the distinct mechanosensing and mechanotransducing pathways that cells activate in response to compression. Finally, we will describe the different in vitro systems that have been engineered to compress cells.
    Keywords:   In vitro systems; Cytoskeleton; Mechanobiology; Mechanosensation; Mechanotransduction; Membrane
    DOI:  https://doi.org/10.1242/jcs.263704
  15. Mol Cell. 2025 Mar 19. pii: S1097-2765(25)00186-8. [Epub ahead of print]
    PI3Kβ functions as a protein kinase to promote cellular protein O-GlcNAcylation and acetyl-CoA production for tumor growth.
    Xuxiao He, Deyu Chen, Guijun Liu, Qingang Wu, Hong Zhao, Dong Guo, Xiaoming Jiang, Min Li, Ying Meng, Yucheng Yin, Xianglai Ye, Shudi Luo, Yan Xia, Tony Hunter, Zhimin Lu.
      Phosphatidylinositol 3-kinase (PI3K) phosphorylates PI(4,5)P2 to produce PI(3,4,5)P3, thereby activating AKT and other effector proteins. However, whether PI3K has non-PI(3,4,5)P3-related functions critical for tumor development remains unclear. Here, we demonstrate that high glucose induces PI3Kβ binding to O-linked β-D-N-acetylglucosamine (O-GlcNAc) transferase (OGT) in glioblastoma cells, dependent on hexokinase 1 (HK1)-mediated OGT Y889 phosphorylation and subsequent p85α recruitment. Importantly, PI3Kβ functions as a protein kinase, phosphorylating OGT at T985 and enhancing OGT activity and total cellular protein O-GlcNAcylation. Activated OGT O-GlcNAcylates ATP-citrate synthase (ACLY) at T639 and S667, leading to ACLY activation-dependent acetyl-coenzyme A (CoA) production to increase fatty acid levels and histone H3 acetylation for gene transcription. Intervention in PI3Kβ-mediated OGT phosphorylation and ACLY O-GlcNAcylation inhibits glioblastoma cell proliferation and tumor growth in xenografts. These findings underscore the critical role of PI3Kβ in governing protein O-GlcNAcylation, fatty acid metabolism, and chromatin modification through its protein kinase activity and provide instrumental insight into the roles of PI3K in tumor progression.
    Keywords:  ACLY; HK1; OGT; PI3K; acetyl-CoA; fatty acid production; histone; tumor
    DOI:  https://doi.org/10.1016/j.molcel.2025.02.024
  16. Pediatr Int. 2025 Jan-Dec;67(1):67(1): e70002
    Sirolimus treatment for intractable vascular anomalies (SIVA): An open-label, single-arm, multicenter, prospective trial.
    Michio Ozeki, Saori Endo, Shiho Yasue, Ryuta Asada, Akiko M Saito, Hiroya Hashimoto, Shigeru Ueno, Shoji Watanabe, Motoi Kato, Kyoichi Deie, Shunsuke Nosaka, Mikiko Miyasaka, Akihiro Umezawa, Kentaro Matsuoka, Mototoshi Kato, Tatsuo Kuroda, Takanobu Maekawa, Satoshi Hirakawa, Taizo Furukawa, Shigehisa Fumino, Tatsuro Tajiri, Junkichi Takemoto, Naonori Kawakubo, Akihiro Fujino.
       BACKGROUND: Intractable vascular anomalies (VAs), including vascular tumors and venous, lymphatic, and mixed malformations, often have severe symptoms and a poor prognosis, highlighting the need for new treatments. We conducted a prospective trial of sirolimus (tablet and granule forms) for the treatment of VAs.
    METHODS: In this open-label, single-arm, multicenter trial across four Japanese institutions, patients with VAs received oral sirolimus daily, targeting a trough concentration of 5-15 ng/mL. We evaluated response rates (radiological volume changes in lesions), skin lesions, performance status, respiratory function, visceral symptoms (bleeding, pain), laboratory data, quality of life, and safety at 12, 24, and 52 weeks.
    RESULTS: Thirteen patients with VAs were treated with sirolimus. Seven patients (53.8%; 95% confidence interval: 25.1%-80.8%) showed a partial radiological response at 24 weeks, with no complete responses, and 61.5% had a partial response by 12 weeks, with little subsequent change in patients who had stable disease thereafter. Improvements in skin lesions, blood coagulation, and activities of daily living were noted. Common adverse events included stomatitis, dermatitis, diarrhea, and fever.
    CONCLUSIONS: Sirolimus may reduce VA tissue volume and potentially improve symptoms and activities of daily living in patients with VAs.
    Keywords:  mammalian target of rapamycin; sirolimus granule; vascular malformations; vascular tumors; venous malformations
    DOI:  https://doi.org/10.1111/ped.70002
  17. Mol Oncol. 2025 Mar 24.
    Time, the final frontier.
    Gautier Follain, Michal Dibus, Omkar Joshi, Guillaume Jacquemet.
      Cancer's notorious heterogeneity poses significant challenges, as each tumor comprises a unique ecosystem. While single-cell and spatial transcriptomics advancements have transformed our understanding of spatial diversity within tumors, the temporal dimension remains underexplored. Tumors are dynamic entities that continuously evolve and adapt, and relying solely on static snapshots obscures the intricate interplay between cancer cells and their microenvironment. Here, we advocate for integrating temporal dynamics into cancer research, emphasizing a fundamental shift from traditional endpoint experiments to data-driven, continuous approaches. This integration involves, for instance, the development of advanced live imaging techniques, innovative temporal omics methodologies, and novel computational tools.
    Keywords:  cancer heterogeneity; circadian clock; live‐cell imaging; metastasis; temporal dynamics; temporal omics
    DOI:  https://doi.org/10.1002/1878-0261.70025
  18. Methods Enzymol. 2025 ;pii: S0076-6879(25)00015-1. [Epub ahead of print]712 453-473
    Cloning and validating systems for high throughput molecular recording.
    Anqi Zhao, Michelle M Chan.
      Molecular recording technologies record and store information about cellular history. Lineage tracing is one form of molecular recording and produces information describing cellular trajectories during mammalian development, differentiation and maintenance of adult stem cell niches, and tumor evolution. Our molecular recorder technology utilizes CRISPR-Cas9 barcode editing to generate mutations in genomically integrated, engineered DNA cassettes, which are read out by single-cell RNA sequencing and used to produce high-resolution lineage trees. Here, we describe optimized cloning and validation procedures to construct the molecular recorder lineage tracing system. We include information on considerations of technology design, cloning procedures, the generation of lineage tracing cell lines, and time course experiments to assess their performance.
    Keywords:  CRISPR-Cas9; Cellular engineering; Genome editing; Lineage tracing; Molecular recorder
    DOI:  https://doi.org/10.1016/bs.mie.2025.01.015
  19. Nature. 2025 Mar 26.
    Plasticity of the mammalian integrated stress response.
    Chien-Wen Chen, David Papadopoli, Krzysztof J Szkop, Bo-Jhih Guan, Mohammed Alzahrani, Jing Wu, Raul Jobava, Mais M Asraf, Dawid Krokowski, Anastasios Vourekas, William C Merrick, Anton A Komar, Antonis E Koromilas, Myriam Gorospe, Matthew J Payea, Fangfang Wang, Benjamin L L Clayton, Paul J Tesar, Ashleigh Schaffer, Alexander Miron, Ilya Bederman, Eckhard Jankowsky, Christine Vogel, Leoš Shivaya Valášek, Jonathan D Dinman, Youwei Zhang, Boaz Tirosh, Ola Larsson, Ivan Topisirovic, Maria Hatzoglou.
      An increased level of phosphorylation of eukaryotic translation initiation factor 2 subunit-α (eIF2α, encoded by EIF2S1; eIF2α-p) coupled with decreased guanine nucleotide exchange activity of eIF2B is a hallmark of the 'canonical' integrated stress response (c-ISR)1. It is unclear whether impaired eIF2B activity in human diseases including leukodystrophies2, which occurs in the absence of eIF2α-p induction, is synonymous with the c-ISR. Here we describe a mechanism triggered by decreased eIF2B activity, distinct from the c-ISR, which we term the split ISR (s-ISR). The s-ISR is characterized by translational and transcriptional programs that are different from those observed in the c-ISR. Opposite to the c-ISR, the s-ISR requires eIF4E-dependent translation of the upstream open reading frame 1 and subsequent stabilization of ATF4 mRNA. This is followed by altered expression of a subset of metabolic genes (for example, PCK2), resulting in metabolic rewiring required to maintain cellular bioenergetics when eIF2B activity is attenuated. Overall, these data demonstrate a plasticity of the mammalian ISR, whereby the loss of eIF2B activity in the absence of eIF2α-p induction activates the eIF4E-ATF4-PCK2 axis to maintain energy homeostasis.
    DOI:  https://doi.org/10.1038/s41586-025-08794-6
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