bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2023–09–24
sixteen papers selected by
Ralitsa Radostinova Madsen, MRC-PPU
  1. MAD2-dependent insulin receptor endocytosis regulates metabolic homeostasis.
  2. Protocol for the design, conduct, and evaluation of prime editing in human pluripotent stem cells.
  3. Neuronal mTORC1 inhibition promotes longevity without suppressing anabolic growth and reproduction in C. elegans.
  4. CRISPR-mediated reversion of oncogenic KRAS mutation results in increased proliferation and reveals independent roles of Ras and mTORC2 in the migration of A549 lung cancer cells.
  5. Regulation of ERK2 activity by dynamic S-acylation.
  6. Exploration of cell state heterogeneity using single-cell proteomics through sensitivity-tailored data-independent acquisition.
  7. Michael D. Waterfield.
  8. A cleavage rule for selection of increased-fidelity SpCas9 variants with high efficiency and no detectable off-targets.
  9. The human cell count and size distribution.
  10. Quantifying cancer cell plasticity with gene regulatory networks and single-cell dynamics.
  11. Modeling unveils sex differences of signaling networks in mouse embryonic stem cells.
  12. Greening the lab.
  13. Sustainability & molecular biology.
  14. A microwell platform for high-throughput longitudinal phenotyping and selective retrieval of organoids.
  15. SiR-DNA/SiR-Hoechst-induced chromosome entanglement generates severe anaphase bridges and DNA damage.
  16. Chemical biology tools for protein labelling: insights into cell-cell communication.
  1. Diabetes. 2023 Sep 19. pii: db230314. [Epub ahead of print]
    MAD2-dependent insulin receptor endocytosis regulates metabolic homeostasis.
    Junhee Park, Catherine Hall, Brandon Hubbard, Traci LaMoia, Rafael Gaspar, Ali Nasiri, Fang Li, Hanrui Zhang, Jiyeon Kim, Rebecca A Haeusler, Domenico Accili, Gerald I Shulman, Hongtao Yu, Eunhee Choi.
      Insulin activates insulin receptor (IR) signaling and subsequently triggers IR endocytosis to attenuate signaling. Cell division regulators MAD2, BUBR1, and p31comet promote IR endocytosis upon insulin stimulation. Here, we show that genetic ablation of the IR-MAD2 interaction in mice delays IR endocytosis, increases IR levels, and prolongs insulin action at the cell surface. This in turn causes a defect in insulin clearance and increases circulating insulin levels, unexpectedly increasing glucagon levels, which alters glucose metabolism modestly. Disruption of the IR-MAD2 interaction increases serum fatty acid concentrations and hepatic fat accumulation in fasted male mice. Furthermore, disruption of the IR-MAD2 interaction distinctly changes metabolic and transcriptomic profiles in the liver and adipose tissues. Our findings establish the function of cell division regulators in insulin signaling and provide insights into the metabolic functions of IR endocytosis.
    DOI:  https://doi.org/10.2337/db23-0314
  2. STAR Protoc. 2023 Sep 20. pii: S2666-1667(23)00550-6. [Epub ahead of print]4(4): 102583
    Protocol for the design, conduct, and evaluation of prime editing in human pluripotent stem cells.
    Youjun Wu, Mega Sidharta, Aaron Zhong, Benjamin Persily, Mu Li, Ting Zhou.
      Prime editing introduces single-nucleotide polymorphism changes, small deletions, or insertions at a specific genome site without double-stranded DNA breaks or the need for the donor template. Here, we present a protocol to design, conduct, and evaluate prime editing in human pluripotent stem cells. We describe steps for pegRNA and nicking sgRNA design and cloning, the prime editing tool electroporation, and the efficiency evaluation using Miseq. We elaborate the process of GBA (N370S) mutation induction and correction as an example. For complete details on the use and execution of this protocol, please refer to Li et al. (2022).1.
    Keywords:  CRISPR; Stem Cells
    DOI:  https://doi.org/10.1016/j.xpro.2023.102583
  3. PLoS Genet. 2023 Sep 18. 19(9): e1010938
    Neuronal mTORC1 inhibition promotes longevity without suppressing anabolic growth and reproduction in C. elegans.
    Hannah J Smith, Anne Lanjuin, Arpit Sharma, Aditi Prabhakar, Ewelina Nowak, Peter G Stine, Rohan Sehgal, Klement Stojanovski, Benjamin D Towbin, William B Mair.
      mTORC1 (mechanistic target of rapamycin complex 1) is a metabolic sensor that promotes growth when nutrients are abundant. Ubiquitous inhibition of mTORC1 extends lifespan in multiple organisms but also disrupts several anabolic processes resulting in stunted growth, slowed development, reduced fertility, and disrupted metabolism. However, it is unclear if these pleotropic effects of mTORC1 inhibition can be uncoupled from longevity. Here, we utilize the auxin-inducible degradation (AID) system to restrict mTORC1 inhibition to C. elegans neurons. We find that neuron-specific degradation of RAGA-1, an upstream activator of mTORC1, or LET-363, the ortholog of mammalian mTOR, is sufficient to extend lifespan in C. elegans. Unlike raga-1 loss of function genetic mutations or somatic AID of RAGA-1, neuronal AID of RAGA-1 robustly extends lifespan without impairing body size, developmental rate, brood size, or neuronal function. Moreover, while degradation of RAGA-1 in all somatic tissues alters the expression of thousands of genes, demonstrating the widespread effects of mTORC1 inhibition, degradation of RAGA-1 in neurons only results in around 200 differentially expressed genes with a specific enrichment in metabolism and stress response. Notably, our work demonstrates that targeting mTORC1 specifically in the nervous system in C. elegans uncouples longevity from growth and reproductive impairments, and that many canonical effects of low mTORC1 activity are not required to promote healthy aging. These data challenge previously held ideas about the mechanisms of mTORC1 lifespan extension and underscore the potential of promoting longevity by neuron-specific mTORC1 modulation.
    DOI:  https://doi.org/10.1371/journal.pgen.1010938
  4. Mol Biol Cell. 2023 Sep 20. mbcE23050152
    CRISPR-mediated reversion of oncogenic KRAS mutation results in increased proliferation and reveals independent roles of Ras and mTORC2 in the migration of A549 lung cancer cells.
    Alyssa N Werner, Avani I Kumar, Pascale G Charest.
      Although the RAS oncogene has been extensively studied, new aspects concerning its role and regulation in normal biology and cancer continue to be discovered. Recently, others and we have shown that the mechanistic Target of Rapamycin Complex 2 (mTORC2) is a Ras effector in Dictyostelium and mammalian cells. mTORC2 plays evolutionarily conserved roles in cell survival and migration and has been linked to tumorigenesis. Since RAS is often mutated in lung cancer, we investigated whether a Ras-mTORC2 pathway contributes to enhancing the migration of lung cancer cells expressing oncogenic Ras. We used A549 cells and CRISPR/Cas9 to revert the cells' KRAS G12S mutation to wild-type and establish A549 revertant (REV) cell lines, which we then used to evaluate the Ras-mediated regulation of mTORC2 and cell migration. Interestingly, our results suggest that K-Ras and mTORC2 promote A549 cell migration but as part of different pathways and independently of Ras's mutational status. Moreover, further characterization of the A549REV cells revealed that loss of mutant K-Ras expression for the wild-type protein leads to an increase in cell growth and proliferation, suggesting that the A549 cells have low KRAS mutant dependency and that recovering expression of wild-type K-Ras protein increases these cells tumorigenic potential.
    DOI:  https://doi.org/10.1091/mbc.E23-05-0152
  5. Cell Rep. 2023 Sep 15. pii: S2211-1247(23)01147-6. [Epub ahead of print]42(9): 113135
    Regulation of ERK2 activity by dynamic S-acylation.
    Saara-Anne Azizi, Tian Qiu, Noah E Brookes, Bryan C Dickinson.
      Extracellular signal-regulated kinases (ERK1/2) are key effector proteins of the mitogen-activated protein kinase pathway, choreographing essential processes of cellular physiology. Here, we discover that ERK1/2 are subject to S-acylation, a reversible lipid modification of cysteine residues, at C271/C254. The levels of ERK1/2 S-acylation are modulated by epidermal growth factor (EGF) signaling, mirroring its phosphorylation dynamics, and acylation-deficient ERK2 displays altered phosphorylation patterns. We show that ERK1/2 S-acylation is mediated by "writer" protein acyl transferases (PATs) and "eraser" acyl protein thioesterases (APTs) and that chemical inhibition of either lipid addition or removal alters ERK1/2's EGF-triggered transcriptional program. Finally, in a mouse model of metabolic syndrome, we find that ERK1/2 lipidation levels correlate with alterations in ERK1/2 lipidation writer/eraser expression, solidifying a link between ERK1/2 activity, ERK1/2 lipidation, and organismal health. This study describes how lipidation regulates ERK1/2 and offers insight into the role of dynamic S-acylation in cell signaling more broadly.
    Keywords:  CP: Molecular biology; chemical biology; kinase signaling; lipidation
    DOI:  https://doi.org/10.1016/j.celrep.2023.113135
  6. Nat Commun. 2023 Sep 22. 14(1): 5910
    Exploration of cell state heterogeneity using single-cell proteomics through sensitivity-tailored data-independent acquisition.
    Valdemaras Petrosius, Pedro Aragon-Fernandez, Nil Üresin, Gergo Kovacs, Teeradon Phlairaharn, Benjamin Furtwängler, Jeff Op De Beeck, Sarah L Skovbakke, Steffen Goletz, Simon Francis Thomsen, Ulrich Auf dem Keller, Kedar N Natarajan, Bo T Porse, Erwin M Schoof.
      Single-cell resolution analysis of complex biological tissues is fundamental to capture cell-state heterogeneity and distinct cellular signaling patterns that remain obscured with population-based techniques. The limited amount of material encapsulated in a single cell however, raises significant technical challenges to molecular profiling. Due to extensive optimization efforts, single-cell proteomics by Mass Spectrometry (scp-MS) has emerged as a powerful tool to facilitate proteome profiling from ultra-low amounts of input, although further development is needed to realize its full potential. To this end, we carry out comprehensive analysis of orbitrap-based data-independent acquisition (DIA) for limited material proteomics. Notably, we find a fundamental difference between optimal DIA methods for high- and low-load samples. We further improve our low-input DIA method by relying on high-resolution MS1 quantification, thus enhancing sensitivity by more efficiently utilizing available mass analyzer time. With our ultra-low input tailored DIA method, we are able to accommodate long injection times and high resolution, while keeping the scan cycle time low enough to ensure robust quantification. Finally, we demonstrate the capability of our approach by profiling mouse embryonic stem cell culture conditions, showcasing heterogeneity in global proteomes and highlighting distinct differences in key metabolic enzyme expression in distinct cell subclusters.
    DOI:  https://doi.org/10.1038/s41467-023-41602-1
  7. Biochem J. 2023 Sep 27. 480(18): 1475-1478
    Michael D. Waterfield.
    Julian Downward, Peter J Parker, Bart Vanhaesebroeck.
      
    DOI:  https://doi.org/10.1042/BCJ20230368
  8. Nat Commun. 2023 09 16. 14(1): 5746
    A cleavage rule for selection of increased-fidelity SpCas9 variants with high efficiency and no detectable off-targets.
    Péter István Kulcsár, András Tálas, Zoltán Ligeti, Eszter Tóth, Zsófia Rakvács, Zsuzsa Bartos, Sarah Laura Krausz, Ágnes Welker, Vanessza Laura Végi, Krisztina Huszár, Ervin Welker.
      Streptococcus pyogenes Cas9 (SpCas9) has been employed as a genome engineering tool with a promising potential within therapeutics. However, its off-target effects present major safety concerns for applications requiring high specificity. Approaches developed to date to mitigate this effect, including any of the increased-fidelity (i.e., high-fidelity) SpCas9 variants, only provide efficient editing on a relatively small fraction of targets without detectable off-targets. Upon addressing this problem, we reveal a rather unexpected cleavability ranking of target sequences, and a cleavage rule that governs the on-target and off-target cleavage of increased-fidelity SpCas9 variants but not that of SpCas9-NG or xCas9. According to this rule, for each target, an optimal variant with matching fidelity must be identified for efficient cleavage without detectable off-target effects. Based on this insight, we develop here an extended set of variants, the CRISPRecise set, with increased fidelity spanning across a wide range, with differences in fidelity small enough to comprise an optimal variant for each target, regardless of its cleavability ranking. We demonstrate efficient editing with maximum specificity even on those targets that have not been possible in previous studies.
    DOI:  https://doi.org/10.1038/s41467-023-41393-5
  9. Proc Natl Acad Sci U S A. 2023 Sep 26. 120(39): e2303077120
    The human cell count and size distribution.
    Ian A Hatton, Eric D Galbraith, Nono S C Merleau, Teemu P Miettinen, Benjamin McDonald Smith, Jeffery A Shander.
      Cell size and cell count are adaptively regulated and intimately linked to growth and function. Yet, despite their widespread relevance, the relation between cell size and count has never been formally examined over the whole human body. Here, we compile a comprehensive dataset of cell size and count over all major cell types, with data drawn from >1,500 published sources. We consider the body of a representative male (70 kg), which allows further estimates of a female (60 kg) and 10-y-old child (32 kg). We build a hierarchical interface for the cellular organization of the body, giving easy access to data, methods, and sources (https://humancelltreemap.mis.mpg.de/). In total, we estimate total body counts of ≈36 trillion cells in the male, ≈28 trillion in the female, and ≈17 trillion in the child. These data reveal a surprising inverse relation between cell size and count, implying a trade-off between these variables, such that all cells within a given logarithmic size class contribute an equal fraction to the body's total cellular biomass. We also find that the coefficient of variation is approximately independent of mean cell size, implying the existence of cell-size regulation across cell types. Our data serve to establish a holistic quantitative framework for the cells of the human body, and highlight large-scale patterns in cell biology.
    Keywords:  cell biomass; cell count; cell size; size distribution; size homeostasis
    DOI:  https://doi.org/10.1073/pnas.2303077120
  10. Front Netw Physiol. 2023 ;3 1225736
    Quantifying cancer cell plasticity with gene regulatory networks and single-cell dynamics.
    Sarah M Groves, Vito Quaranta.
      Phenotypic plasticity of cancer cells can lead to complex cell state dynamics during tumor progression and acquired resistance. Highly plastic stem-like states may be inherently drug-resistant. Moreover, cell state dynamics in response to therapy allow a tumor to evade treatment. In both scenarios, quantifying plasticity is essential for identifying high-plasticity states or elucidating transition paths between states. Currently, methods to quantify plasticity tend to focus on 1) quantification of quasi-potential based on the underlying gene regulatory network dynamics of the system; or 2) inference of cell potency based on trajectory inference or lineage tracing in single-cell dynamics. Here, we explore both of these approaches and associated computational tools. We then discuss implications of each approach to plasticity metrics, and relevance to cancer treatment strategies.
    Keywords:  ScRNA-seq; cancer; dynamical systems; gene regulatory networks; network physiology; plasticity
    DOI:  https://doi.org/10.3389/fnetp.2023.1225736
  11. Mol Syst Biol. 2023 Sep 21. e11510
    Modeling unveils sex differences of signaling networks in mouse embryonic stem cells.
    Zeba Sultana, Mathurin Dorel, Bertram Klinger, Anja Sieber, Ilona Dunkel, Nils Blüthgen, Edda G Schulz.
      For a short period during early development of mammalian embryos, both X chromosomes in females are active, before dosage compensation is ensured through X-chromosome inactivation. In female mouse embryonic stem cells (mESCs), which carry two active X chromosomes, increased X-dosage affects cell signaling and impairs differentiation. The underlying mechanisms, however, remain poorly understood. To dissect X-dosage effects on the signaling network in mESCs, we combine systematic perturbation experiments with mathematical modeling. We quantify the response to a variety of inhibitors and growth factors for cells with one (XO) or two X chromosomes (XX). We then build models of the signaling networks in XX and XO cells through a semi-quantitative modeling approach based on modular response analysis. We identify a novel negative feedback in the PI3K/AKT pathway through GSK3. Moreover, the presence of a single active X makes mESCs more sensitive to the differentiation-promoting Activin A signal and leads to a stronger RAF1-mediated negative feedback in the FGF-triggered MAPK pathway. The differential response to these differentiation-promoting pathways can explain the impaired differentiation propensity of female mESCs.
    Keywords:  X chromosome; X-chromosome inactivation; cell signaling; mathematical modeling; pluripotency; stem cells
    DOI:  https://doi.org/10.15252/msb.202211510
  12. Nat Methods. 2023 Sep 20.
    Greening the lab.
    Caroline Seydel.
      
    DOI:  https://doi.org/10.1038/s41592-023-02024-5
  13. Mol Cell. 2023 Sep 21. pii: S1097-2765(23)00660-3. [Epub ahead of print]83(18): 3219
    Sustainability & molecular biology.
    Brian Plosky.
      
    DOI:  https://doi.org/10.1016/j.molcel.2023.08.024
  14. Cell Syst. 2023 Sep 20. pii: S2405-4712(23)00241-7. [Epub ahead of print]14(9): 764-776.e6
    A microwell platform for high-throughput longitudinal phenotyping and selective retrieval of organoids.
    Alexandra Sockell, Wing Wong, Scott Longwell, Thy Vu, Kasper Karlsson, Daniel Mokhtari, Julia Schaepe, Yuan-Hung Lo, Vincent Cornelius, Calvin Kuo, David Van Valen, Christina Curtis, Polly M Fordyce.
      Organoids are powerful experimental models for studying the ontogeny and progression of various diseases including cancer. Organoids are conventionally cultured in bulk using an extracellular matrix mimic. However, bulk-cultured organoids physically overlap, making it impossible to track the growth of individual organoids over time in high throughput. Moreover, local spatial variations in bulk matrix properties make it difficult to assess whether observed phenotypic heterogeneity between organoids results from intrinsic cell differences or differences in the microenvironment. Here, we developed a microwell-based method that enables high-throughput quantification of image-based parameters for organoids grown from single cells, which can further be retrieved from their microwells for molecular profiling. Coupled with a deep learning image-processing pipeline, we characterized phenotypic traits including growth rates, cellular movement, and apical-basal polarity in two CRISPR-engineered human gastric organoid models, identifying genomic changes associated with increased growth rate and changes in accessibility and expression correlated with apical-basal polarity. A record of this paper's transparent peer review process is included in the supplemental information.
    Keywords:  cell polarity; deep learning; genotype-to-phenotype; high-throughput imaging; microwell arrays; organoids; quantitative phenotyping; single-organoid sequencing; tumorigenesis
    DOI:  https://doi.org/10.1016/j.cels.2023.08.002
  15. Life Sci Alliance. 2023 Dec;pii: e202302260. [Epub ahead of print]6(12):
    SiR-DNA/SiR-Hoechst-induced chromosome entanglement generates severe anaphase bridges and DNA damage.
    Girish Rajendraprasad, Sergi Rodriguez-Calado, Marin Barisic.
      SiR-DNA/SiR-Hoechst is a far-red fluorescent DNA probe that is routinely used for live-cell imaging of cell nuclei in interphase and chromosomes during mitosis. Despite being reported to induce DNA damage, SiR-DNA has been used in more than 300 research articles, covering topics like mitosis, chromatin biology, cancer research, cytoskeletal research, and DNA damage response. Here, we used live-cell imaging to perform a comprehensive analysis of the effects of SiR-DNA on mitosis of four human cell lines (RPE-1, DLD-1, HeLa, and U2OS). We report a dose-, time-, and light-dependent effect of SiR-DNA on chromosome segregation. We found that, upon the exposure to light during imaging, nanomolar concentrations of SiR-DNA induce non-centromeric chromosome entanglement that severely impairs sister chromatid segregation and spindle elongation during anaphase. This causes DNA damage that is passed forward to the following cell cycle, thereby having a detrimental effect on genome integrity. Our findings highlight the drawbacks in using SiR-DNA for investigation of late mitotic events and DNA damage-related topics and urge the use of alternative labeling strategies to study these processes.
    DOI:  https://doi.org/10.26508/lsa.202302260
  16. Biochem J. 2023 Sep 27. 480(18): 1445-1457
    Chemical biology tools for protein labelling: insights into cell-cell communication.
    Megan H Wright.
      Multicellular organisms require carefully orchestrated communication between and within cell types and tissues, and many unicellular organisms also sense their context and environment, sometimes coordinating their responses. This review highlights contributions from chemical biology in discovering and probing mechanisms of cell-cell communication. We focus on chemical tools for labelling proteins in a cellular context and how these can be applied to decipher the target receptor of a signalling molecule, label a receptor of interest in situ to understand its biology, provide a read-out of protein activity or interactions in downstream signalling pathways, or discover protein-protein interactions across cell-cell interfaces.
    Keywords:  biochemical techniques and resources; cell–cell communication; chemical biology; proteomics; signalling
    DOI:  https://doi.org/10.1042/BCJ20220309
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