bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2023‒12‒24
27 papers selected by
Ralitsa Radostinova Madsen, MRC-PPU
  1. NUAK1 coordinates growth factor-dependent activation of mTORC2 and Akt signaling.
  2. Nutrient signaling: Starvation flips a phosphoinositide switch on lysosomal catabolism.
  3. Patient derived glioma stem cell spheroid reporter assays for live cell high content analysis.
  4. High-throughput deconvolution of 3D organoid dynamics at cellular resolution for cancer pharmacology with Cellos.
  5. Akt Is Controlled by Bag5 through a Monoubiquitination to Polyubiquitination Switch.
  6. A data analysis framework for combining multiple batches increases the power of isobaric proteomics experiments.
  7. Akt may associate with insulin-responsive vesicles via interaction with sortilin.
  8. Hyperactive mTORC1 in lung mesenchyme induces endothelial cell dysfunction and pulmonary vascular remodeling.
  9. Work-Up and Treatment Strategies for Individuals with PIK3CA-Related Disorders: A Consensus of Experts from the Scientific Committee of the Italian Macrodactyly and PROS Association.
  10. JOINTLY: interpretable joint clustering of single-cell transcriptomes.
  11. Automatic cell-type harmonization and integration across Human Cell Atlas datasets.
  12. Autophagy supports PDGFRA-dependent brain tumor development by enhancing oncogenic signaling.
  13. What approaches are needed to understand human development and disease?
  14. MORG1 limits mTORC1 signaling by inhibiting Rag GTPases.
  15. Nano-CUT&Tag for multimodal chromatin profiling at single-cell resolution.
  16. High-throughput PRIME-editing screens identify functional DNA variants in the human genome.
  17. Phenotypic consequences of logarithmic signaling in MAPK stress response.
  18. An ERK5-PFKFB3 axis regulates glycolysis and represents a therapeutic vulnerability in pediatric diffuse midline glioma.
  19. Modeling elucidates context dependence in adipose regulation.
  20. A Fluorescence-Based Sensor for Calibrated Measurement of Protein Kinase Stability in Live Cells.
  21. Antigen perception in T cells by long-term Erk and NFAT signaling dynamics.
  22. Mutation of p53 increases the competitive ability of pluripotent stem cells.
  23. Subcytoplasmic location of translation controls protein output.
  24. Organoid Cultures for the Study of Mammary Biology and Breast Cancer: The Promise and Challenges.
  25. The energetic and allosteric landscape for KRAS inhibition.
  26. Proteolysis-targeting chimeras with reduced off-targets.
  27. Inferring Metabolic States from Single Cell Transcriptomic Data via Geometric Deep Learning.
  1. Cell Biosci. 2023 Dec 22. 13(1): 232
    NUAK1 coordinates growth factor-dependent activation of mTORC2 and Akt signaling.
    Mario Palma, Elizabeth Riffo, Alejandro Farias, Viviana Coliboro-Dannich, Luis Espinoza-Francine, Emilia Escalona, Roberto Amigo, José L Gutiérrez, Roxana Pincheira, Ariel F Castro.
      BACKGROUND: mTORC2 is a critical regulator of cytoskeleton organization, cell proliferation, and cancer cell survival. Activated mTORC2 induces maximal activation of Akt by phosphorylation of Ser-473, but regulation of Akt activity and signaling crosstalk upon growth factor stimulation are still unclear.RESULTS: We identified that NUAK1 regulates growth factor-dependent activation of Akt by two mechanisms. NUAK1 interacts with mTORC2 components and regulates mTORC2-dependent activation of Akt by controlling lysosome positioning and mTOR association with this organelle. A second mechanism involves NUAK1 directly phosphorylating Akt at Ser-473. The effect of NUAK1 correlated with a growth factor-dependent activation of specific Akt substrates. NUAK1 induced the Akt-dependent phosphorylation of FOXO1/3a (Thr-24/Thr-32) but not of TSC2 (Thr-1462). According to a subcellular compartmentalization that could explain NUAK1's differential effect on the Akt substrates, we found that NUAK1 is associated with early endosomes but not with plasma membrane, late endosomes, or lysosomes. NUAK1 was required for the Akt/FOXO1/3a axis, regulating p21CIP1, p27KIP1, and FoxM1 expression and cancer cell survival upon EGFR stimulation. Pharmacological inhibition of NUAK1 potentiated the cell death effect induced by Akt or mTOR pharmacological blockage. Analysis of human tissue data revealed that NUAK1 expression positively correlates with EGFR expression and Akt Ser-473 phosphorylation in several human cancers.
    CONCLUSIONS: Our results showed that NUAK1 kinase controls mTOR subcellular localization and induces Akt phosphorylation, demonstrating that NUAK1 regulates the growth factor-dependent activation of Akt signaling. Therefore, targeting NUAK1, or co-targeting it with Akt or mTOR inhibitors, may be effective in cancers with hyperactivated Akt signaling.
    Keywords:  Akt; Cancer signaling; Co-targeting; NUAK1; mTORC2
    DOI:  https://doi.org/10.1186/s13578-023-01185-2
  2. Curr Biol. 2023 Dec 18. pii: S0960-9822(23)01489-6. [Epub ahead of print]33(24): R1289-R1291
    Nutrient signaling: Starvation flips a phosphoinositide switch on lysosomal catabolism.
    Michal J Nagiec, John Blenis.
      Lysosomes are highly dynamic organelles that rapidly respond to changes in cellular nutrient status. A new study identifies a phosphoinositide switch that dictates lysosome function during nutrient starvation.
    DOI:  https://doi.org/10.1016/j.cub.2023.10.066
  3. SLAS Discov. 2023 Dec 13. pii: S2472-5552(23)00095-3. [Epub ahead of print]
    Patient derived glioma stem cell spheroid reporter assays for live cell high content analysis.
    Jayne Culley, Peter W Nagle, John C Dawson, Neil O Carragher.
      Three dimensional models of cell culture enables researchers to recreate aspects of tumour biology not replicated by traditional two dimensional techniques. Here we describe a protocol to enable automated high throughput phenotypic profiling across panels of patient derived glioma stem cell spheroid models. We demonstrate the use of both live/dead cell end-points and monitor the dynamic changes in the cell cycle using cell lines expressing the FUCCI cell cycle reporter. Together, these assays provide additional insight into the mechanism of action of compound treatments over traditional cell viability assay endpoints.
    Keywords:  3-dimensional; Glioblastoma; Spheroid; cell cycle; drug discovery
    DOI:  https://doi.org/10.1016/j.slasd.2023.12.005
  4. Nat Commun. 2023 Dec 18. 14(1): 8406
    High-throughput deconvolution of 3D organoid dynamics at cellular resolution for cancer pharmacology with Cellos.
    Patience Mukashyaka, Pooja Kumar, David J Mellert, Shadae Nicholas, Javad Noorbakhsh, Mattia Brugiolo, Elise T Courtois, Olga Anczukow, Edison T Liu, Jeffrey H Chuang.
      Three-dimensional (3D) organoid cultures are flexible systems to interrogate cellular growth, morphology, multicellular spatial architecture, and cellular interactions in response to treatment. However, computational methods for analysis of 3D organoids with sufficiently high-throughput and cellular resolution are needed. Here we report Cellos, an accurate, high-throughput pipeline for 3D organoid segmentation using classical algorithms and nuclear segmentation using a trained Stardist-3D convolutional neural network. To evaluate Cellos, we analyze ~100,000 organoids with ~2.35 million cells from multiple treatment experiments. Cellos segments dye-stained or fluorescently-labeled nuclei and accurately distinguishes distinct labeled cell populations within organoids. Cellos can recapitulate traditional luminescence-based drug response of cells with complex drug sensitivities, while also quantifying changes in organoid and nuclear morphologies caused by treatment as well as cell-cell spatial relationships that reflect ecological affinity. Cellos provides powerful tools to perform high-throughput analysis for pharmacological testing and biological investigation of organoids based on 3D imaging.
    DOI:  https://doi.org/10.1038/s41467-023-44162-6
  5. Int J Mol Sci. 2023 Dec 15. pii: 17531. [Epub ahead of print]24(24):
    Akt Is Controlled by Bag5 through a Monoubiquitination to Polyubiquitination Switch.
    Ismael Bracho-Valdés, Rodolfo Daniel Cervantes-Villagrana, Yarely Mabell Beltrán-Navarro, Adán Olguín-Olguín, Estanislao Escobar-Islas, Jorge Carretero-Ortega, J Alberto Olivares-Reyes, Guadalupe Reyes-Cruz, J Silvio Gutkind, José Vázquez-Prado.
      The serine-threonine kinase Akt plays a fundamental role in cell survival, metabolism, proliferation, and migration. To keep these essential processes under control, Akt activity and stability must be tightly regulated; otherwise, life-threatening conditions might prevail. Although it is well understood that phosphorylation regulates Akt activity, much remains to be known about how its stability is maintained. Here, we characterize BAG5, a chaperone regulator, as a novel Akt-interactor and substrate that attenuates Akt stability together with Hsp70. BAG5 switches monoubiquitination to polyubiquitination of Akt and increases its degradation caused by Hsp90 inhibition and Hsp70 overexpression. Akt interacts with BAG5 at the linker region that joins the first and second BAG domains and phosphorylates the first BAG domain. The Akt-BAG5 complex is formed in serum-starved conditions and dissociates in response to HGF, coincident with BAG5 phosphorylation. BAG5 knockdown attenuated Akt degradation and facilitated its activation, whereas the opposite effect was caused by BAG5 overexpression. Altogether, our results indicate that Akt stability and signaling are dynamically regulated by BAG5, depending on growth factor availability.
    Keywords:  Akt; BAG-5; Bcl-2 associated athanogene 5; Hsp70; ubiquitin-dependent degradation
    DOI:  https://doi.org/10.3390/ijms242417531
  6. Nat Methods. 2023 Dec 18.
    A data analysis framework for combining multiple batches increases the power of isobaric proteomics experiments.
    Jonathon J O'Brien, Anil Raj, Aleksandr Gaun, Adam Waite, Wenzhou Li, David G Hendrickson, Niclas Olsson, Fiona E McAllister.
      We present a framework for the analysis of multiplexed mass spectrometry proteomics data that reduces estimation error when combining multiple isobaric batches. Variations in the number and quality of observations have long complicated the analysis of isobaric proteomics data. Here we show that the power to detect statistical associations is substantially improved by utilizing models that directly account for known sources of variation in the number and quality of observations that occur across batches.In a multibatch benchmarking experiment, our open-source software (msTrawler) increases the power to detect changes, especially in the range of less than twofold changes, while simultaneously increasing quantitative proteome coverage by utilizing more low-signal observations. Further analyses of previously published multiplexed datasets of 4 and 23 batches highlight both increased power and the ability to navigate complex missing data patterns without relying on unverifiable imputations or discarding reliable measurements.
    DOI:  https://doi.org/10.1038/s41592-023-02120-6
  7. FEBS Lett. 2023 Dec 17.
    Akt may associate with insulin-responsive vesicles via interaction with sortilin.
    Nava Zaarur, Anatoli B Meriin, Maneet Singh, Raghuveera K Goel, Joseph Zaia, Konstantin V Kandror.
      Insulin-responsive vesicles (IRVs) deliver the glucose transporter Glut4 to the plasma membrane in response to activation of the insulin signaling cascade: insulin receptor-IRS-PI3 kinase-Akt-TBC1D4-Rab10. Previous studies have shown that Akt, TBC1D4, and Rab10 are compartmentalized on the IRVs. Although functionally significant, the mechanism of Akt association with the IRVs remains unknown. Using pull-down assays, immunofluorescence microscopy, and cross-linking, we have found that Akt may be recruited to the IRVs via the interaction with the juxtamembrane domain of the cytoplasmic C terminus of sortilin, a major IRV protein. Overexpression of full-length sortilin increases insulin-stimulated phosphorylation of TBC1D4 and glucose uptake in adipocytes, while overexpression of the cytoplasmic tail of sortilin has the opposite effect. Our findings demonstrate that the IRVs represent both a scaffold and a target of insulin signaling.
    Keywords:  Akt; insulin; signaling; sortilin; vesicles
    DOI:  https://doi.org/10.1002/1873-3468.14790
  8. J Clin Invest. 2023 Dec 21. pii: e172116. [Epub ahead of print]
    Hyperactive mTORC1 in lung mesenchyme induces endothelial cell dysfunction and pulmonary vascular remodeling.
    Susan M Lin, Ryan Rue, Alexander R Mukhitov, Akansha Goel, Maria C Basil, Kseniya Obraztsova, Apoorva Babu, Slaven Crnkovic, Owen Ledwell, Laura T Ferguson, Joseph D Planer, Ana N Nottingham, Kanth Swaroop Vanka, Carly J Smith, Edward Cantu Iii, Grazyna Kwapiszewska, Edward E Morrisey, Jillian F Evans, Vera P Krymskaya.
      Lymphangioleiomyomatosis (LAM) is a progressive cystic lung disease caused by tuberous sclerosis complex 1/2 (TSC1/2) gene mutations in pulmonary mesenchymal cells resulting in activation of the mechanistic target of rapamycin complex 1 (mTORC1). A subset of LAM patients develops pulmonary vascular remodeling and pulmonary hypertension. Little, however, is known regarding how LAM cells communicate with endothelial cells (ECs) to trigger vascular remodeling. In end-stage LAM lung explants, we identified endothelial cell dysfunction characterized by increased proliferation, migration, defective angiogenesis, and dysmorphic endothelial tube network formation. To model LAM disease, we utilized an mTORC1 gain-of-function mouse model with a Tsc2 knock-out (Tsc2KO) specific to lung mesenchyme (Tbx4LME-CreTsc2fl/fl), similar to the mesenchyme specific genetic alterations seen in human disease. As early as 8 weeks of age, ECs from Tbx4LME-CreTsc2fl/fl mice exhibited marked transcriptomic changes despite absence of morphological changes to the distal lung microvasculature. In contrast, 1 year old Tbx4LME-CreTsc2fl/fl mice spontaneously developed pulmonary vascular remodeling with increased medial thickness. Single cell RNA-sequencing of 1 year old mouse lung identified paracrine ligands originating from Tsc2KO mesenchyme which can signal through receptors in arterial ECs. These ECs had transcriptionally altered genes including those in pathways associated with blood vessel remodeling. The proposed pathophysiologic mesenchymal ligand/ EC receptor crosstalk highlights the importance of an altered mesenchymal-EC axis in LAM and other hyperactive mTORC1-driven diseases. Since ECs in LAM patients and in Tbx4LME-CreTsc2fl/fl mice do not harbor TSC2 mutations, our study demonstrates that constitutively active mTORC1 lung mesenchymal cells orchestrate dysfunctional EC responses which contribute to pulmonary vascular remodeling.
    Keywords:  Cell Biology; Endothelial cells; Mouse models; Vascular Biology
    DOI:  https://doi.org/10.1172/JCI172116
  9. Genes (Basel). 2023 Nov 27. pii: 2134. [Epub ahead of print]14(12):
    Work-Up and Treatment Strategies for Individuals with PIK3CA-Related Disorders: A Consensus of Experts from the Scientific Committee of the Italian Macrodactyly and PROS Association.
    Italian Macrodactyly and PROS Association
      PIK3CA-related disorders encompass many rare and ultra-rare conditions caused by somatic genetic variants that hyperactivate the PI3K-AKT-mTOR signaling pathway, which is essential for cell cycle control. PIK3CA-related disorders include PIK3CA-related overgrowth spectrum (PROS), PIK3CA-related vascular malformations and PIK3CA-related non-vascular lesions. Phenotypes are extremely heterogeneous and overlapping. Therefore, diagnosis and management frequently involve various health specialists. Given the rarity of these disorders and the limited number of centers offering optimal care, the Scientific Committee of the Italian Macrodactyly and PROS Association has proposed a revision of the most recent recommendations for the diagnosis, molecular testing, clinical management, follow-up, and treatment strategies. These recommendations give insight on molecular diagnosis, eligible samples, preferable sequencing, and validation methods and management of negative results. The purpose of this paper is to promote collaboration between health care centers and clinicians with a joint shared approach. Finally, we suggest the direction of present and future research studies, including new systemic target therapies, which are currently under evaluation in several clinical trials, such as specific inhibitors that can be employed to downregulate the signaling pathway.
    Keywords:  PI3K/AKT/mTOR; PIK3CA; PIK3CA-related overgrowth spectrum; overgrowth; personalized medicine; repurposed drugs; target therapy
    DOI:  https://doi.org/10.3390/genes14122134
  10. Nat Commun. 2023 Dec 20. 14(1): 8473
    JOINTLY: interpretable joint clustering of single-cell transcriptomes.
    Andreas Fønss Møller, Jesper Grud Skat Madsen.
      Single-cell and single-nucleus RNA-sequencing (sxRNA-seq) is increasingly being used to characterise the transcriptomic state of cell types at homeostasis, during development and in disease. However, this is a challenging task, as biological effects can be masked by technical variation. Here, we present JOINTLY, an algorithm enabling joint clustering of sxRNA-seq datasets across batches. JOINTLY performs on par or better than state-of-the-art batch integration methods in clustering tasks and outperforms other intrinsically interpretable methods. We demonstrate that JOINTLY is robust against over-correction while retaining subtle cell state differences between biological conditions and highlight how the interpretation of JOINTLY can be used to annotate cell types and identify active signalling programs across cell types and pseudo-time. Finally, we use JOINTLY to construct a reference atlas of white adipose tissue (WATLAS), an expandable and comprehensive community resource, in which we describe four adipocyte subpopulations and map compositional changes in obesity and between depots.
    DOI:  https://doi.org/10.1038/s41467-023-44279-8
  11. Cell. 2023 Dec 21. pii: S0092-8674(23)01312-0. [Epub ahead of print]186(26): 5876-5891.e20
    Automatic cell-type harmonization and integration across Human Cell Atlas datasets.
    Chuan Xu, Martin Prete, Simone Webb, Laura Jardine, Benjamin J Stewart, Regina Hoo, Peng He, Kerstin B Meyer, Sarah A Teichmann.
      Harmonizing cell types across the single-cell community and assembling them into a common framework is central to building a standardized Human Cell Atlas. Here, we present CellHint, a predictive clustering tree-based tool to resolve cell-type differences in annotation resolution and technical biases across datasets. CellHint accurately quantifies cell-cell transcriptomic similarities and places cell types into a relationship graph that hierarchically defines shared and unique cell subtypes. Application to multiple immune datasets recapitulates expert-curated annotations. CellHint also reveals underexplored relationships between healthy and diseased lung cell states in eight diseases. Furthermore, we present a workflow for fast cross-dataset integration guided by harmonized cell types and cell hierarchy, which uncovers underappreciated cell types in adult human hippocampus. Finally, we apply CellHint to 12 tissues from 38 datasets, providing a deeply curated cross-tissue database with ∼3.7 million cells and various machine learning models for automatic cell annotation across human tissues.
    Keywords:  Human Cell Atlas; cell hierarchy; cell-type harmonization; data integration; harmonization graph; machine learning; organ atlas; predictive clustering tree; single cell
    DOI:  https://doi.org/10.1016/j.cell.2023.11.026
  12. Dev Cell. 2023 Dec 08. pii: S1534-5807(23)00621-4. [Epub ahead of print]
    Autophagy supports PDGFRA-dependent brain tumor development by enhancing oncogenic signaling.
    Joanne E Simpson, Morwenna T Muir, Martin Lee, Catherine Naughton, Nick Gilbert, Steven M Pollard, Noor Gammoh.
      Autophagy is a conserved cellular degradation process. While autophagy-related proteins were shown to influence the signaling and trafficking of some receptor tyrosine kinases, the relevance of this during cancer development is unclear. Here, we identify a role for autophagy in regulating platelet-derived growth factor receptor alpha (PDGFRA) signaling and levels. We find that PDGFRA can be targeted for autophagic degradation through the activity of the autophagy cargo receptor p62. As a result, short-term autophagy inhibition leads to elevated levels of PDGFRA but an unexpected defect in PDGFA-mediated signaling due to perturbed receptor trafficking. Defective PDGFRA signaling led to its reduced levels during prolonged autophagy inhibition, suggesting a mechanism of adaptation. Importantly, PDGFA-driven gliomagenesis in mice was disrupted when autophagy was inhibited in a manner dependent on Pten status, thus highlighting a genotype-specific role for autophagy during tumorigenesis. In summary, our data provide a mechanism by which cells require autophagy to drive tumor formation.
    Keywords:  PDGFRA; PTEN; RTK; autophagy; cancer; endocytosis; glioblastoma; signaling
    DOI:  https://doi.org/10.1016/j.devcel.2023.11.023
  13. Dev Cell. 2023 Dec 18. pii: S1534-5807(23)00647-0. [Epub ahead of print]58(24): 2822-2825
    What approaches are needed to understand human development and disease?
    Berna Sozen, Richard A Flavell, Dudley W Lamming, Debra L Silver, Simona Parrinello, Cory Abate-Shen, Franziska Michor, Vijay G Sankaran.
      Researchers are leveraging what we have learned from model organisms to understand if the same principles arise in human physiology, development, and disease. In this collection of Voices, we asked researchers from different fields to discuss what tools and insights they are using to answer fundamental questions in human biology.
    DOI:  https://doi.org/10.1016/j.devcel.2023.11.026
  14. Mol Cell. 2023 Dec 11. pii: S1097-2765(23)00968-1. [Epub ahead of print]
    MORG1 limits mTORC1 signaling by inhibiting Rag GTPases.
    Yakubu Princely Abudu, Athanasios Kournoutis, Hanne Britt Brenne, Trond Lamark, Terje Johansen.
      Autophagy, an important quality control and recycling process vital for cellular homeostasis, is tightly regulated. The mTORC1 signaling pathway regulates autophagy under conditions of nutrient availability and scarcity. However, how mTORC1 activity is fine-tuned during nutrient availability to allow basal autophagy is unclear. Here, we report that the WD-domain repeat protein MORG1 facilitates basal constitutive autophagy by inhibiting mTORC1 signaling through Rag GTPases. Mechanistically, MORG1 interacts with active Rag GTPase complex inhibiting the Rag GTPase-mediated recruitment of mTORC1 to the lysosome. MORG1 depletion in HeLa cells increases mTORC1 activity and decreases autophagy. The autophagy receptor p62/SQSTM1 binds to MORG1, but MORG1 is not an autophagy substrate. However, p62/SQSTM1 binding to MORG1 upon re-addition of amino acids following amino acid's depletion precludes MORG1 from inhibiting the Rag GTPases, allowing mTORC1 activation. MORG1 depletion increases cell proliferation and migration. Low expression of MORG1 correlates with poor survival in several important cancers.
    Keywords:  MORG1; Rag GTPases; WD-domain repeat protein; autophagy; mTORC1; p62/SQSTM1
    DOI:  https://doi.org/10.1016/j.molcel.2023.11.023
  15. Nat Protoc. 2023 Dec 21.
    Nano-CUT&Tag for multimodal chromatin profiling at single-cell resolution.
    José Ramón Bárcenas-Walls, Federico Ansaloni, Bastien Hervé, Emilia Strandback, Tomas Nyman, Gonçalo Castelo-Branco, Marek Bartošovič.
      The ability to comprehensively analyze the chromatin state with single-cell resolution is crucial for understanding gene regulatory principles in heterogenous tissues or during development. Recently, we developed a nanobody-based single-cell CUT&Tag (nano-CT) protocol to simultaneously profile three epigenetic modalities-two histone marks and open chromatin state-from the same single cell. Nano-CT implements a new set of secondary nanobody-Tn5 fusion proteins to direct barcoded tagmentation by Tn5 transposase to genomic targets labeled by primary antibodies raised in different species. Such nanobody-Tn5 fusion proteins are currently not commercially available, and their in-house production and purification can be completed in 3-4 d by following our detailed protocol. The single-cell indexing in nano-CT is performed on a commercially available platform, making it widely accessible to the community. In comparison to other multimodal methods, nano-CT stands out in data complexity, low sample requirements and the flexibility to choose two of the three modalities. In addition, nano-CT works efficiently with fresh brain samples, generating multimodal epigenomic profiles for thousands of brain cells at single-cell resolution. The nano-CT protocol can be completed in just 3 d by users with basic skills in standard molecular biology and bioinformatics, although previous experience with single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) is beneficial for more in-depth data analysis. As a multimodal assay, nano-CT holds immense potential to reveal interactions of various chromatin modalities, to explore epigenetic heterogeneity and to increase our understanding of the role and interplay that chromatin dynamics has in cellular development.
    DOI:  https://doi.org/10.1038/s41596-023-00932-6
  16. Mol Cell. 2023 Dec 21. pii: S1097-2765(23)00966-8. [Epub ahead of print]83(24): 4633-4645.e9
    High-throughput PRIME-editing screens identify functional DNA variants in the human genome.
    Xingjie Ren, Han Yang, Jovia L Nierenberg, Yifan Sun, Jiawen Chen, Cooper Beaman, Thu Pham, Mai Nobuhara, Maya Asami Takagi, Vivek Narayan, Yun Li, Elad Ziv, Yin Shen.
      Despite tremendous progress in detecting DNA variants associated with human disease, interpreting their functional impact in a high-throughput and single-base resolution manner remains challenging. Here, we develop a pooled prime-editing screen method, PRIME, that can be applied to characterize thousands of coding and non-coding variants in a single experiment with high reproducibility. To showcase its applications, we first identified essential nucleotides for a 716 bp MYC enhancer via PRIME-mediated single-base resolution analysis. Next, we applied PRIME to functionally characterize 1,304 genome-wide association study (GWAS)-identified non-coding variants associated with breast cancer and 3,699 variants from ClinVar. We discovered that 103 non-coding variants and 156 variants of uncertain significance are functional via affecting cell fitness. Collectively, we demonstrate that PRIME is capable of characterizing genetic variants at single-base resolution and scale, advancing accurate genome annotation for disease risk prediction, diagnosis, and therapeutic target identification.
    Keywords:  disease variants; enhancer; high-throughput screens; prime editing; single-base resolution
    DOI:  https://doi.org/10.1016/j.molcel.2023.11.021
  17. bioRxiv. 2023 Dec 07. pii: 2023.12.05.570188. [Epub ahead of print]
    Phenotypic consequences of logarithmic signaling in MAPK stress response.
    Hossein Jashnsaz, Gregor Neuert.
      How cells respond to dynamic environmental changes is crucial for understanding fundamental biological processes and cell physiology. In this study, we developed an experimental and quantitative analytical framework to explore how dynamic stress gradients that change over time regulate cellular volume, signaling activation, and growth phenotypes. Our findings reveal that gradual stress conditions substantially enhance cell growth compared to conventional acute stress. This growth advantage correlates with a minimal reduction in cell volume dependent on the dynamic of stress. We explain the growth phenotype with our finding of a logarithmic signal transduction mechanism in the yeast Mitogen-Activated Protein Kinase (MAPK) osmotic stress response pathway. These insights into the interplay between gradual environments, cell volume change, dynamic cell signaling, and growth, advance our understanding of fundamental cellular processes in gradual stress environments.
    DOI:  https://doi.org/10.1101/2023.12.05.570188
  18. Cell Rep. 2023 Dec 18. pii: S2211-1247(23)01569-3. [Epub ahead of print]43(1): 113557
    An ERK5-PFKFB3 axis regulates glycolysis and represents a therapeutic vulnerability in pediatric diffuse midline glioma.
    Stephanie M Casillo, Taylor A Gatesman, Akanksha Chilukuri, Srinidhi Varadharajan, Brenden J Johnson, Daniel R David Premkumar, Esther P Jane, Tritan J Plute, Robert F Koncar, Ann-Catherine J Stanton, Carlos A O Biagi-Junior, Callie S Barber, Matthew E Halbert, Brian J Golbourn, Katharine Halligan, Andrea F Cruz, Neveen M Mansi, Allison Cheney, Steven J Mullett, Clinton Van't Land, Jennifer L Perez, Max I Myers, Nishant Agrawal, Joshua J Michel, Yue-Fang Chang, Olena M Vaske, Antony MichaelRaj, Frank S Lieberman, James Felker, Sruti Shiva, Kelsey C Bertrand, Nduka Amankulor, Costas G Hadjipanayis, Kalil G Abdullah, Pascal O Zinn, Robert M Friedlander, Taylor J Abel, Javad Nazarian, Sriram Venneti, Mariella G Filbin, Stacy L Gelhaus, Stephen C Mack, Ian F Pollack, Sameer Agnihotri.
      Metabolic reprogramming in pediatric diffuse midline glioma is driven by gene expression changes induced by the hallmark histone mutation H3K27M, which results in aberrantly permissive activation of oncogenic signaling pathways. Previous studies of diffuse midline glioma with altered H3K27 (DMG-H3K27a) have shown that the RAS pathway, specifically through its downstream kinase, extracellular-signal-related kinase 5 (ERK5), is critical for tumor growth. Further downstream effectors of ERK5 and their role in DMG-H3K27a metabolic reprogramming have not been explored. We establish that ERK5 is a critical regulator of cell proliferation and glycolysis in DMG-H3K27a. We demonstrate that ERK5 mediates glycolysis through activation of transcription factor MEF2A, which subsequently modulates expression of glycolytic enzyme PFKFB3. We show that in vitro and mouse models of DMG-H3K27a are sensitive to the loss of PFKFB3. Multi-targeted drug therapy against the ERK5-PFKFB3 axis, such as with small-molecule inhibitors, may represent a promising therapeutic approach in patients with pediatric diffuse midline glioma.
    Keywords:  CP: Cancer; CP: Metabolism; ERK5; H3K27a-DMG; MEF2A; PFKFB3; glioma; glycolysis; metabolism; multi targeted; pediatric; synergy
    DOI:  https://doi.org/10.1016/j.celrep.2023.113557
  19. Cell Syst. 2023 Dec 20. pii: S2405-4712(23)00325-3. [Epub ahead of print]14(12): 1021-1023
    Modeling elucidates context dependence in adipose regulation.
    Cameron D Vasquez, John G Albeck.
      Single-cell data and computational simulations reveal the dynamics of the transcription factors HIF1α and PPARγ during adipocyte differentiation and maturation. Modeling feedback within this network predicts a HIF1α-mediated choice between lipid accumulation and incomplete differentiation. In vitro experiments support this model, with implications for adipose dynamics in metabolic disorders involving hypoxia.
    DOI:  https://doi.org/10.1016/j.cels.2023.11.002
  20. bioRxiv. 2023 Dec 08. pii: 2023.12.07.570636. [Epub ahead of print]
    A Fluorescence-Based Sensor for Calibrated Measurement of Protein Kinase Stability in Live Cells.
    Joseph W Paul, Serena Muratcioğlu, John Kuriyan.
      Oncogenic mutations can destabilize signaling proteins, resulting in increased or unregulated activity. Thus, there is considerable interest in mapping the relationship between mutations and the stability of proteins, to better understand the consequences of oncogenic mutations and potentially inform the development of new therapeutics. Here, we develop a tool to study protein-kinase stability in live mammalian cells and the effects of the HSP90 chaperone system on the stability of these kinases. We monitor the fluorescence of kinases fused to a fluorescent protein relative to that of a co-expressed reference fluorescent protein. We used this tool to study the dependence of Src- and Raf-family kinases on the HSP90 system. We demonstrate that this sensor reports on destabilization induced by oncogenic mutations in these kinases. We also show that Src-homology 2 (SH2) and Src-homology 3 (SH3) domains, which are required for autoinhibition of Src-family kinases, stabilize these kinase domains in the cell. Our expression-calibrated sensor enables the facile characterization of the effects of mutations and small-molecule drugs on protein-kinase stability.
    DOI:  https://doi.org/10.1101/2023.12.07.570636
  21. Proc Natl Acad Sci U S A. 2023 Dec 26. 120(52): e2308366120
    Antigen perception in T cells by long-term Erk and NFAT signaling dynamics.
    Matthew J Wither, William L White, Sriram Pendyala, Paul J Leanza, Douglas M Fowler, Hao Yuan Kueh.
      Immune system threat detection hinges on T cells' ability to perceive varying peptide-major histocompatibility complex (pMHC) antigens. As the Erk and NFAT pathways link T cell receptor engagement to gene regulation, their signaling dynamics may convey information about pMHC inputs. To test this idea, we developed a dual reporter mouse strain and a quantitative imaging assay that, together, enable simultaneous monitoring of Erk and NFAT dynamics in live T cells over day-long timescales as they respond to varying pMHC inputs. Both pathways initially activate uniformly across various pMHC inputs but diverge only over longer (9+ h) timescales, enabling independent encoding of pMHC affinity and dose. These late signaling dynamics are decoded via multiple temporal and combinatorial mechanisms to generate pMHC-specific transcriptional responses. Our findings underscore the importance of long timescale signaling dynamics in antigen perception and establish a framework for understanding T cell responses under diverse contexts.
    Keywords:  T cell receptor signaling; gene regulation; live-cell imaging; signal encoding; signaling dynamics
    DOI:  https://doi.org/10.1073/pnas.2308366120
  22. Development. 2023 Dec 22. pii: dev.202503. [Epub ahead of print]
    Mutation of p53 increases the competitive ability of pluripotent stem cells.
    Salvador Perez Montero, Pranab K Paul, Aida di Gregorio, Sarah Bowling, Solomon Shepherd, Nadia Fernandes, Ana Lima, Rubén Pérez-Carrasco, Tristan A Rodriguez.
      During development, the rate of tissue growth is determined by the relative balance of cell division and cell death. Cell competition is a fitness quality control mechanism that contributes to this balance by eliminating viable cells that are less-fit than their neighbours. What mutations confer cells with a competitive advantage or the dynamics of the interactions between winner and loser cells are not well understood. Here, we show that embryonic cells lacking the tumour suppressor p53 are super-competitors that eliminate their wild-type neighbours through the direct induction of apoptosis. This elimination is context dependant, as does not occur when cells are pluripotent and is triggered by the onset of differentiation. Furthermore, by combining mathematical modelling and cell-based assays we show that the elimination of wild-type cells is not through a competition for space or nutrients, but instead is mediated by short range interactions that are dependent on the local cell neighbourhood. This highlights the importance of the local cell neighbourhood and the competitive interactions within this neighbourhood for the regulation of proliferation during early embryonic development.
    Keywords:  Cell competition; Mathematical modelling.; P53
    DOI:  https://doi.org/10.1242/dev.202503
  23. Mol Cell. 2023 Dec 21. pii: S1097-2765(23)00970-X. [Epub ahead of print]83(24): 4509-4523.e11
    Subcytoplasmic location of translation controls protein output.
    Ellen L Horste, Mervin M Fansler, Ting Cai, Xiuzhen Chen, Sibylle Mitschka, Gang Zhen, Flora C Y Lee, Jernej Ule, Christine Mayr.
      The cytoplasm is highly compartmentalized, but the extent and consequences of subcytoplasmic mRNA localization in non-polarized cells are largely unknown. We determined mRNA enrichment in TIS granules (TGs) and the rough endoplasmic reticulum (ER) through particle sorting and isolated cytosolic mRNAs by digitonin extraction. When focusing on genes that encode non-membrane proteins, we observed that 52% have transcripts enriched in specific compartments. Compartment enrichment correlates with a combinatorial code based on mRNA length, exon length, and 3' UTR-bound RNA-binding proteins. Compartment-biased mRNAs differ in the functional classes of their encoded proteins: TG-enriched mRNAs encode low-abundance proteins with strong enrichment of transcription factors, whereas ER-enriched mRNAs encode large and highly expressed proteins. Compartment localization is an important determinant of mRNA and protein abundance, which is supported by reporter experiments showing that redirecting cytosolic mRNAs to the ER increases their protein expression. In summary, the cytoplasm is functionally compartmentalized by local translation environments.
    Keywords:  3′ UTR; CDS exon length; RNA-binding proteins; TIAL1; TIS granules; TIS11B; condensates; cytoplasmic organization; endoplasmic reticulum; gene architecture; mRNA length; mRNA localization; spatial regulation of protein synthesis; translation environment
    DOI:  https://doi.org/10.1016/j.molcel.2023.11.025
  24. Cold Spring Harb Perspect Med. 2023 Dec 18. pii: a041661. [Epub ahead of print]
    Organoid Cultures for the Study of Mammary Biology and Breast Cancer: The Promise and Challenges.
    Senthil K Muthuswamy, Joan S Brugge.
      During the last decade, biomedical research has experienced a resurgence in the use of three-dimensional culture models for studies of normal and cancer biology. This resurgence has been driven by the development of models in which primary cells are grown in tissue-mimicking media and extracellular matrices to create organoid or organotypic cultures that more faithfully replicate the complex architecture and physiology of normal tissues and tumors. In addition, patient-derived tumor organoids preserve the three-dimensional organization and characteristics of the patient tumors ex vivo, becoming excellent preclinical models to supplement studies of tumor xenografts transplanted into immunocompromised mice. In this perspective, we provide an overview of how organoids are being used to investigate normal mammary biology and as preclinical models of breast cancer and discuss improvements that would enhance their utility and relevance to the field.
    DOI:  https://doi.org/10.1101/cshperspect.a041661
  25. Nature. 2023 Dec 18.
    The energetic and allosteric landscape for KRAS inhibition.
    Chenchun Weng, Andre J Faure, Albert Escobedo, Ben Lehner.
      Thousands of proteins have now been genetically-validated as therapeutic targets in hundreds of human diseases1. However, very few have actually been successfully targeted and many are considered 'undruggable'. This is particularly true for proteins that function via protein-protein interactions: direct inhibition of binding interfaces is difficult, requiring the identification of allosteric sites. However, most proteins have no known allosteric sites and a comprehensive allosteric map does not exist for any protein. Here we address this shortcoming by charting multiple global atlases of inhibitory allosteric communication in KRAS. We quantified the impact of >26,000 mutations on the folding of KRAS and its binding to six interaction partners. Genetic interactions in double mutants allowed us to perform biophysical measurements at scale, inferring >22,000 causal free energy changes. These energy landscapes quantify how mutations tune the binding specificity of a signalling protein and map the inhibitory allosteric sites for an important therapeutic target. Allosteric propagation is particularly effective across the central beta sheet of KRAS and multiple surface pockets are genetically-validated as allosterically active, including a distal pocket in the C-terminal lobe of the protein. Allosteric mutations typically inhibit binding to all tested effectors but they can also change the binding specificity, revealing the regulatory, evolutionary and therapeutic potential to tune pathway activation. Using the approach described here it should be possible to rapidly and comprehensively identify allosteric target sites in many proteins.
    DOI:  https://doi.org/10.1038/s41586-023-06954-0
  26. Nat Chem. 2023 Dec 18.
    Proteolysis-targeting chimeras with reduced off-targets.
    Tuan M Nguyen, Vedagopuram Sreekanth, Arghya Deb, Praveen Kokkonda, Praveen K Tiwari, Katherine A Donovan, Veronika Shoba, Santosh K Chaudhary, Jaron A M Mercer, Sophia Lai, Ananthan Sadagopan, Max Jan, Eric S Fischer, David R Liu, Benjamin L Ebert, Amit Choudhary.
      Proteolysis-targeting chimeras (PROTACs) are molecules that induce proximity between target proteins and E3 ligases triggering target protein degradation. Pomalidomide, a widely used E3 ligase recruiter in PROTACs, can independently degrade other proteins, including zinc-finger (ZF) proteins, with vital roles in health and disease. This off-target degradation hampers the therapeutic applicability of pomalidomide-based PROTACs, requiring development of PROTAC design rules that minimize off-target degradation. Here we developed a high-throughput platform that interrogates off-target degradation and found that reported pomalidomide-based PROTACs induce degradation of several ZF proteins. We generated a library of pomalidomide analogues to understand how functionalizing different positions of the phthalimide ring, hydrogen bonding, and steric and hydrophobic effects impact ZF protein degradation. Modifications of appropriate size on the C5 position reduced off-target ZF degradation, which we validated through target engagement and proteomics studies. By applying these design principles, we developed anaplastic lymphoma kinase oncoprotein-targeting PROTACs with enhanced potency and minimal off-target degradation.
    DOI:  https://doi.org/10.1038/s41557-023-01379-8
  27. bioRxiv. 2023 Dec 07. pii: 2023.12.05.570153. [Epub ahead of print]
    Inferring Metabolic States from Single Cell Transcriptomic Data via Geometric Deep Learning.
    Holly Steach, Siddharth Viswanath, Yixuan He, Xitong Zhang, Natalia Ivanova, Matthew Hirn, Michael Perlmutter, Smita Krishnaswamy.
      The ability to measure gene expression at single-cell resolution has elevated our understanding of how biological features emerge from complex and interdependent networks at molecular, cellular, and tissue scales. As technologies have evolved that complement scRNAseq measurements with things like single-cell proteomic, epigenomic, and genomic information, it becomes increasingly apparent how much biology exists as a product of multimodal regulation. Biological processes such as transcription, translation, and post-translational or epigenetic modification impose both energetic and specific molecular demands on a cell and are therefore implicitly constrained by the metabolic state of the cell. While metabolomics is crucial for defining a holistic model of any biological process, the chemical heterogeneity of the metabolome makes it particularly difficult to measure, and technologies capable of doing this at single-cell resolution are far behind other multiomics modalities. To address these challenges, we present GEFMAP (Gene Expression-based Flux Mapping and Metabolic Pathway Prediction), a method based on geometric deep learning for predicting flux through reactions in a global metabolic network using transcriptomics data, which we ultimately apply to scRNAseq. GEFMAP leverages the natural graph structure of metabolic networks to learn both a biological objective for each cell and estimate a mass-balanced relative flux rate for each reaction in each cell using novel deep learning models.
    DOI:  https://doi.org/10.1101/2023.12.05.570153
This page is being maintained by Thomas Krichel. It was last updated on 2023‒12‒24 at 22:24.