bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2023–04–09
sixteen papers selected by
Ralitsa Radostinova Madsen, MRC-PPU
  1. Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics.
  2. Activating mutations in EGFR and PI3K promote ATF4 induction for NSCLC cell survival during amino acid deprivation.
  3. DUSP6 is a memory retention feedback regulator of ERK signaling for cellular resilience of human pluripotent stem cells in response to dissociation.
  4. Extending the sensitivity, consistency and depth of single-cell proteomics.
  5. Detection of rare mutations, copy number alterations, and methylation in the same template DNA molecules.
  6. Improving the sensitivity of in vivo CRISPR off-target detection with DISCOVER-Seq.
  7. Rate thresholds in cell signaling have functional and phenotypic consequences in non-linear time-dependent environments.
  8. A relay velocity model infers cell-dependent RNA velocity.
  9. Computational speed-up of large-scale, single-cell model simulations via a fully integrated SBML-based format.
  10. Large-scale mapping and mutagenesis of human transcriptional effector domains.
  11. A stress-induced cilium-to-PML-NB route drives senescence initiation.
  12. Light-Deactivated Fluorescent Probes (FLASH-Off) for Multiplexed Imaging.
  13. ITK degradation to block T cell receptor signaling and overcome therapeutic resistance in T cell lymphomas.
  14. Identification of cell barcodes from long-read single-cell RNA-seq with BLAZE.
  15. Starvation-induced changes in somatic insulin/IGF-1R signaling drive metabolic programming across generations.
  16. ERK1/2 inhibitors act as monovalent degraders inducing ubiquitylation and proteasome-dependent turnover of ERK2, but not ERK1.
  1. Nat Methods. 2023 Apr 03.
    Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics.
    R Gray Huffman, Andrew Leduc, Christoph Wichmann, Marco Di Gioia, Francesco Borriello, Harrison Specht, Jason Derks, Saad Khan, Luke Khoury, Edward Emmott, Aleksandra A Petelski, David H Perlman, Jürgen Cox, Ivan Zanoni, Nikolai Slavov.
      Major aims of single-cell proteomics include increasing the consistency, sensitivity and depth of protein quantification, especially for proteins and modifications of biological interest. Here, to simultaneously advance all these aims, we developed prioritized Single-Cell ProtEomics (pSCoPE). pSCoPE consistently analyzes thousands of prioritized peptides across all single cells (thus increasing data completeness) while maximizing instrument time spent analyzing identifiable peptides, thus increasing proteome depth. These strategies increased the sensitivity, data completeness and proteome coverage over twofold. The gains enabled quantifying protein variation in untreated and lipopolysaccharide-treated primary macrophages. Within each condition, proteins covaried within functional sets, including phagosome maturation and proton transport, similarly across both treatment conditions. This covariation is coupled to phenotypic variability in endocytic activity. pSCoPE also enabled quantifying proteolytic products, suggesting a gradient of cathepsin activities within a treatment condition. pSCoPE is freely available and widely applicable, especially for analyzing proteins of interest without sacrificing proteome coverage. Support for pSCoPE is available at http://scp.slavovlab.net/pSCoPE .
    DOI:  https://doi.org/10.1038/s41592-023-01830-1
  2. Heliyon. 2023 Apr;9(4): e14799
    Activating mutations in EGFR and PI3K promote ATF4 induction for NSCLC cell survival during amino acid deprivation.
    Mizuki Takahashi, Yuka Okamoto, Yu Kato, Hitomi Shirahama, Satomi Tsukahara, Yoshikazu Sugimoto, Akihiro Tomida.
      Some oncoproteins along with stress kinase general control non-derepressible 2 (GCN2) can ensure the induction of activating transcription factor 4 (ATF4) to counteract amino acid deprivation; however, little is known regarding the role of the oncogenic EGFR-PI3K pathway. In this study, we demonstrate that both mutated EGFR and PIK3CA contribute to ATF4 induction following GCN2 activation in NSCLC cells. The inhibition of EGFR or PI3K mutant proteins, pharmacologically or through genetic knockdown, inhibited ATF4 induction without affecting GCN2 activation. A downstream analysis revealed that the oncogenic EGFR-PI3K pathway may utilize mTOR-mediated translation control mechanisms for ATF4 induction. Furthermore, in NSCLC cells harboring co-mutations in EGFR and PIK3CA, the combined inhibition of these oncoproteins markedly suppressed ATF4 induction and the subsequent gene expression program as well as cell viability during amino acid deprivation. Our findings establish a role for the oncogenic EGFR-PI3K pathway in the adaptive stress response and provide a strategy to improve EGFR-targeted NSCLC therapy.
    Keywords:  ATF4; EGFR; ISR; NSCLC; Oncogenic mutation; PI3K
    DOI:  https://doi.org/10.1016/j.heliyon.2023.e14799
  3. Sci Rep. 2023 Apr 07. 13(1): 5683
    DUSP6 is a memory retention feedback regulator of ERK signaling for cellular resilience of human pluripotent stem cells in response to dissociation.
    Dae Hoon Yoo, Young Sam Im, Ji Young Oh, Dayeon Gil, Yong-Ou Kim.
      Cultured human pluripotent stem cells (hPSCs) grow as colonies that require breakdown into small clumps for further propagation. Although cell death mechanism by single-cell dissociation of hPSCs has been well defined, how hPSCs respond to the deadly stimulus and recover the original status remains unclear. Here we show that dissociation of hPSCs immediately activates ERK, which subsequently activates RSK and induces DUSP6, an ERK-specific phosphatase. Although the activation is transient, DUSP6 expression persists days after passaging. DUSP6 depletion using the CRISPR/Cas9 system reveals that DUSP6 suppresses the ERK activity over the long term. Elevated ERK activity by DUSP6 depletion increases both viability of hPSCs after single-cell dissociation and differentiation propensity towards mesoderm and endoderm lineages. These findings provide new insights into how hPSCs respond to dissociation in order to maintain pluripotency.
    DOI:  https://doi.org/10.1038/s41598-023-32567-8
  4. Nat Methods. 2023 Apr 03.
    Extending the sensitivity, consistency and depth of single-cell proteomics.
      
    DOI:  https://doi.org/10.1038/s41592-023-01786-2
  5. Proc Natl Acad Sci U S A. 2023 Apr 11. 120(15): e2220704120
    Detection of rare mutations, copy number alterations, and methylation in the same template DNA molecules.
    Yuxuan Wang, Christopher Douville, Joshua D Cohen, Austin Mattox, Sam Curtis, Natalie Silliman, Maria Popoli, Janine Ptak, Lisa Dobbyn, Nadine Nehme, Jonathan C Dudley, Mahmoud Summers, Ming Zhang, Lan T Ho-Pham, Bich N H Tran, Thach S Tran, Tuan V Nguyen, Chetan Bettegowda, Nickolas Papadopoulos, Kenneth W Kinzler, Bert Vogelstein.
      The analysis of cell-free DNA (cfDNA) from plasma offers great promise for the earlier detection of cancer. At present, changes in DNA sequence, methylation, or copy number are the most sensitive ways to detect the presence of cancer. To further increase the sensitivity of such assays with limited amounts of sample, it would be useful to be able to evaluate the same template molecules for all these changes. Here, we report an approach, called MethylSaferSeqS, that achieves this goal, and can be applied to any standard library preparation method suitable for massively parallel sequencing. The innovative step was to copy both strands of each DNA-barcoded molecule with a primer that allows the subsequent separation of the original strands (retaining their 5-methylcytosine residues) from the copied strands (in which the 5-methylcytosine residues are replaced with unmodified cytosine residues). The epigenetic and genetic alterations present in the DNA molecules can then be obtained from the original and copied strands, respectively. We applied this approach to plasma from 265 individuals, including 198 with cancers of the pancreas, ovary, lung, and colon, and found the expected patterns of mutations, copy number alterations, and methylation. Furthermore, we could determine which original template DNA molecules were methylated and/or mutated. MethylSaferSeqS should be useful for addressing a variety of questions relating genetics and epigenetics.
    Keywords:  biomarker; cfDNA; copy number alteration; methylation; mutation
    DOI:  https://doi.org/10.1073/pnas.2220704120
  6. Nat Methods. 2023 Apr 06.
    Improving the sensitivity of in vivo CRISPR off-target detection with DISCOVER-Seq.
    Roger S Zou, Yang Liu, Oscar E Reyes Gaido, Maximilian F Konig, Brian J Mog, Leo L Shen, Franklin Aviles-Vazquez, Alberto Marin-Gonzalez, Taekjip Ha.
      Discovery of off-target CRISPR-Cas activity in patient-derived cells and animal models is crucial for genome editing applications, but currently exhibits low sensitivity. We demonstrate that inhibition of DNA-dependent protein kinase catalytic subunit accumulates the repair protein MRE11 at CRISPR-Cas-targeted sites, enabling high-sensitivity mapping of off-target sites to positions of MRE11 binding using chromatin immunoprecipitation followed by sequencing. This technique, termed DISCOVER-Seq+, discovered up to fivefold more CRISPR off-target sites in immortalized cell lines, primary human cells and mice compared with previous methods. We demonstrate applicability to ex vivo knock-in of a cancer-directed transgenic T cell receptor in primary human T cells and in vivo adenovirus knock-out of cardiovascular risk gene PCSK9 in mice. Thus, DISCOVER-Seq+ is, to our knowledge, the most sensitive method to-date for discovering off-target genome editing in vivo.
    DOI:  https://doi.org/10.1038/s41592-023-01840-z
  7. Front Cell Dev Biol. 2023 ;11 1124874
    Rate thresholds in cell signaling have functional and phenotypic consequences in non-linear time-dependent environments.
    Alexander Thiemicke, Gregor Neuert.
      All cells employ signal transduction pathways to respond to physiologically relevant extracellular cytokines, stressors, nutrient levels, hormones, morphogens, and other stimuli that vary in concentration and rate in healthy and diseased states. A central unsolved fundamental question in cell signaling is whether and how cells sense and integrate information conveyed by changes in the rate of extracellular stimuli concentrations, in addition to the absolute difference in concentration. We propose that different environmental changes over time influence cell behavior in addition to different signaling molecules or different genetic backgrounds. However, most current biomedical research focuses on acute environmental changes and does not consider how cells respond to environments that change slowly over time. As an example of such environmental change, we review cell sensitivity to environmental rate changes, including the novel mechanism of rate threshold. A rate threshold is defined as a threshold in the rate of change in the environment in which a rate value below the threshold does not activate signaling and a rate value above the threshold leads to signal activation. We reviewed p38/Hog1 osmotic stress signaling in yeast, chemotaxis and stress response in bacteria, cyclic adenosine monophosphate signaling in Amoebae, growth factors signaling in mammalian cells, morphogen dynamics during development, temporal dynamics of glucose and insulin signaling, and spatio-temproral stressors in the kidney. These reviewed examples from the literature indicate that rate thresholds are widespread and an underappreciated fundamental property of cell signaling. Finally, by studying cells in non-linear environments, we outline future directions to understand cell physiology better in normal and pathophysiological conditions.
    Keywords:  cell signaling; dynamic environments; flow cytometry; quantitative biology; rate threshold; single cell; systems biology; time lapse microscopy
    DOI:  https://doi.org/10.3389/fcell.2023.1124874
  8. Nat Biotechnol. 2023 Apr 03.
    A relay velocity model infers cell-dependent RNA velocity.
    Shengyu Li, Pengzhi Zhang, Weiqing Chen, Lingqun Ye, Kristopher W Brannan, Nhat-Tu Le, Jun-Ichi Abe, John P Cooke, Guangyu Wang.
      RNA velocity provides an approach for inferring cellular state transitions from single-cell RNA sequencing (scRNA-seq) data. Conventional RNA velocity models infer universal kinetics from all cells in an scRNA-seq experiment, resulting in unpredictable performance in experiments with multi-stage and/or multi-lineage transition of cell states where the assumption of the same kinetic rates for all cells no longer holds. Here we present cellDancer, a scalable deep neural network that locally infers velocity for each cell from its neighbors and then relays a series of local velocities to provide single-cell resolution inference of velocity kinetics. In the simulation benchmark, cellDancer shows robust performance in multiple kinetic regimes, high dropout ratio datasets and sparse datasets. We show that cellDancer overcomes the limitations of existing RNA velocity models in modeling erythroid maturation and hippocampus development. Moreover, cellDancer provides cell-specific predictions of transcription, splicing and degradation rates, which we identify as potential indicators of cell fate in the mouse pancreas.
    DOI:  https://doi.org/10.1038/s41587-023-01728-5
  9. Bioinform Adv. 2023 ;3(1): vbad039
    Computational speed-up of large-scale, single-cell model simulations via a fully integrated SBML-based format.
    Arnab Mutsuddy, Cemal Erdem, Jonah R Huggins, Misha Salim, Daniel Cook, Nicole Hobbs, F Alex Feltus, Marc R Birtwistle.
       Summary: Large-scale and whole-cell modeling has multiple challenges, including scalable model building and module communication bottlenecks (e.g. between metabolism, gene expression, signaling, etc.). We previously developed an open-source, scalable format for a large-scale mechanistic model of proliferation and death signaling dynamics, but communication bottlenecks between gene expression and protein biochemistry modules remained. Here, we developed two solutions to communication bottlenecks that speed-up simulation by ∼4-fold for hybrid stochastic-deterministic simulations and by over 100-fold for fully deterministic simulations. Fully deterministic speed-up facilitates model initialization, parameter estimation and sensitivity analysis tasks.
    Availability and implementation: Source code is freely available at https://github.com/birtwistlelab/SPARCED/releases/tag/v1.3.0 implemented in python, and supported on Linux, Windows and MacOS (via Docker).
    DOI:  https://doi.org/10.1093/bioadv/vbad039
  10. Nature. 2023 Apr 05.
    Large-scale mapping and mutagenesis of human transcriptional effector domains.
    Nicole DelRosso, Josh Tycko, Peter Suzuki, Cecelia Andrews, Aradhana, Adi Mukund, Ivan Liongson, Connor Ludwig, Kaitlyn Spees, Polly Fordyce, Michael C Bassik, Lacramioara Bintu.
      Human gene expression is regulated by more than 2,000 transcription factors and chromatin regulators1,2. Effector domains within these proteins can activate or repress transcription. However, for many of these regulators we do not know what type of effector domains they contain, their location in the protein, their activation and repression strengths, and the sequences that are necessary for their functions. Here, we systematically measure the effector activity of more than 100,000 protein fragments tiling across most chromatin regulators and transcription factors in human cells (2,047 proteins). By testing the effect they have when recruited at reporter genes, we annotate 374 activation domains and 715 repression domains, roughly 80% of which are new and have not been previously annotated3-5. Rational mutagenesis and deletion scans across all the effector domains reveal aromatic and/or leucine residues interspersed with acidic, proline, serine and/or glutamine residues are necessary for activation domain activity. Furthermore, most repression domain sequences contain sites for small ubiquitin-like modifier (SUMO)ylation, short interaction motifs for recruiting corepressors or are structured binding domains for recruiting other repressive proteins. We discover bifunctional domains that can both activate and repress, some of which dynamically split a cell population into high- and low-expression subpopulations. Our systematic annotation and characterization of effector domains provide a rich resource for understanding the function of human transcription factors and chromatin regulators, engineering compact tools for controlling gene expression and refining predictive models of effector domain function.
    DOI:  https://doi.org/10.1038/s41586-023-05906-y
  11. Nat Commun. 2023 Apr 03. 14(1): 1840
    A stress-induced cilium-to-PML-NB route drives senescence initiation.
    Xiaoyu Ma, Yingyi Zhang, Yuanyuan Zhang, Xu Zhang, Yan Huang, Kai He, Chuan Chen, Jielu Hao, Debiao Zhao, Nathan K LeBrasseur, James L Kirkland, Eduardo N Chini, Qing Wei, Kun Ling, Jinghua Hu.
      Cellular senescence contributes to tissue homeostasis and age-related pathologies. However, how senescence is initiated in stressed cells remains vague. Here, we discover that exposure to irradiation, oxidative or inflammatory stressors induces transient biogenesis of primary cilia, which are then used by stressed cells to communicate with the promyelocytic leukemia nuclear bodies (PML-NBs) to initiate senescence responses in human cells. Mechanistically, a ciliary ARL13B-ARL3 GTPase cascade negatively regulates the association of transition fiber protein FBF1 and SUMO-conjugating enzyme UBC9. Irreparable stresses downregulate the ciliary ARLs and release UBC9 to SUMOylate FBF1 at the ciliary base. SUMOylated FBF1 then translocates to PML-NBs to promote PML-NB biogenesis and PML-NB-dependent senescence initiation. Remarkably, Fbf1 ablation effectively subdues global senescence burden and prevents associated health decline in irradiation-treated mice. Collectively, our findings assign the primary cilium a key role in senescence induction in mammalian cells and, also, a promising target in future senotherapy strategies.
    DOI:  https://doi.org/10.1038/s41467-023-37362-7
  12. J Am Chem Soc. 2023 Apr 05.
    Light-Deactivated Fluorescent Probes (FLASH-Off) for Multiplexed Imaging.
    Elias A Halabi, Ralph Weissleder.
      Highly multiplexed, cyclic fluorescence imaging has advanced our understanding of the biology, evolution, and complexity of human diseases. Currently available cyclic methods still have considerable limitations including the need for long quenching times and extensive wash steps. Here, we report a new series of fluorochromes that can be efficiently inactivated by a single light pulse (∼405 nm) by means of a photo-immolating triazene linker. Upon UV-light irradiation, the rhodamines are cleaved off from the antibody conjugates and undergo a fast intramolecular spirocyclization that inherently switches off their fluorescence emission without the need to wash or add exogenous chemicals. We show that these switch-off probes are fast, highly controllable, biocompatible, and allow spatiotemporal quenching control of live and fixed samples.
    DOI:  https://doi.org/10.1021/jacs.3c00170
  13. Cell Chem Biol. 2023 Mar 27. pii: S2451-9456(23)00086-7. [Epub ahead of print]
    ITK degradation to block T cell receptor signaling and overcome therapeutic resistance in T cell lymphomas.
    Baishan Jiang, David M Weinstock, Katherine A Donovan, Hong-Wei Sun, Ashley Wolfe, Sam Amaka, Nicholas L Donaldson, Gongwei Wu, Yuan Jiang, Ryan A Wilcox, Eric S Fischer, Nathanael S Gray, Wenchao Wu.
      Interleukin (IL)-2-inducible T cell kinase (ITK) is essential for T cell receptor (TCR) signaling and plays an integral role in T cell proliferation and differentiation. Unlike the ITK homolog BTK, no inhibitors of ITK are currently US Food and Drug Administration (FDA) approved. In addition, recent studies have identified mutations within BTK that confer resistance to both covalent and non-covalent inhibitors. Here, as an alternative strategy, we report the development of BSJ-05-037, a potent and selective heterobifunctional degrader of ITK. BSJ-05-037 displayed enhanced anti-proliferative effects relative to its parent inhibitor BMS-509744, blocked the activation of NF-kB/GATA-3 signaling, and increased the sensitivity of T cell lymphoma cells to cytotoxic chemotherapy both in vitro and in vivo. In summary, targeted degradation of ITK is a novel approach to modulate TCR signal strength that could have broad application for the investigation and treatment of T cell-mediated diseases.
    Keywords:  GATA-3; ITK; PROTAC; T cell lymphoma; TCR signaling
    DOI:  https://doi.org/10.1016/j.chembiol.2023.03.007
  14. Genome Biol. 2023 Apr 06. 24(1): 66
    Identification of cell barcodes from long-read single-cell RNA-seq with BLAZE.
    Yupei You, Yair D J Prawer, Ricardo De Paoli-Iseppi, Cameron P J Hunt, Clare L Parish, Heejung Shim, Michael B Clark.
      Long-read single-cell RNA sequencing (scRNA-seq) enables the quantification of RNA isoforms in individual cells. However, long-read scRNA-seq using the Oxford Nanopore platform has largely relied upon matched short-read data to identify cell barcodes. We introduce BLAZE, which accurately and efficiently identifies 10x cell barcodes using only nanopore long-read scRNA-seq data. BLAZE outperforms the existing tools and provides an accurate representation of the cells present in long-read scRNA-seq when compared to matched short reads. BLAZE simplifies long-read scRNA-seq while improving the results, is compatible with downstream tools accepting a cell barcode file, and is available at https://github.com/shimlab/BLAZE .
    DOI:  https://doi.org/10.1186/s13059-023-02907-y
  15. Sci Adv. 2023 Apr 07. 9(14): eade1817
    Starvation-induced changes in somatic insulin/IGF-1R signaling drive metabolic programming across generations.
    Merly C Vogt, Oliver Hobert.
      Exposure to adverse nutritional and metabolic environments during critical periods of development can exert long-lasting effects on health outcomes of an individual and its descendants. Although such metabolic programming has been observed in multiple species and in response to distinct nutritional stressors, conclusive insights into signaling pathways and mechanisms responsible for initiating, mediating, and manifesting changes to metabolism and behavior across generations remain scarce. By using a starvation paradigm in Caenorhabditis elegans, we show that starvation-induced changes in dauer formation-16/forkhead box transcription factor class O (DAF-16/FoxO) activity, the main downstream target of insulin/insulin-like growth factor 1 (IGF-1) receptor signaling, are responsible for metabolic programming phenotypes. Tissue-specific depletion of DAF-16/FoxO during distinct developmental time points demonstrates that DAF-16/FoxO acts in somatic tissues, but not directly in the germline, to both initiate and manifest metabolic programming. In conclusion, our study deciphers multifaceted and critical roles of highly conserved insulin/IGF-1 receptor signaling in determining health outcomes and behavior across generations.
    DOI:  https://doi.org/10.1126/sciadv.ade1817
  16. Biochem J. 2023 Apr 05. pii: BCJ20220598. [Epub ahead of print]
    ERK1/2 inhibitors act as monovalent degraders inducing ubiquitylation and proteasome-dependent turnover of ERK2, but not ERK1.
    Kathryn Balmanno, Andrew M Kidger, Dominic P Byrne, Matthew J Sale, Nejma Nassman, Patrick A Eyers, Simon J Cook.
      Innate or acquired resistance to small molecule BRAF or MEK1/2 inhibitors (BRAFi or MEKi) typically arises through mechanisms that sustain or reinstate ERK1/2 activation. This has led to the development of a range of ERK1/2 inhibitors (ERKi) that either inhibit kinase catalytic activity (catERKi) or additionally prevent the activating pT-E-pY dual phosphorylation of ERK1/2 by MEK1/2 (dual-mechanism or dmERKi).  Here we show that eight different ERKi (both catERKi or dmERKi) drive the turnover of ERK2, the most abundant ERK isoform, with little or no effect on ERK1.  Thermal stability assays show that ERKi do not destabilise ERK2 (or ERK1) in vitro, suggesting that ERK2 turnover is a cellular consequence of ERKi binding.  ERK2 turnover is not observed upon treatment with MEKi alone, suggesting it is ERKi binding to ERK2 that drives ERK2 turnover. However, MEKi pre-treatment, which blocks ERK2 pT-E-pY phosphorylation and dissociation from MEK1/2, prevents ERK2 turnover.  ERKi treatment of cells drives the poly-ubiquitylation and proteasome-dependent turnover of ERK2 and pharmacological or genetic inhibition of Cullin-RING E3 ligases prevents this. Our results suggest that ERKi, including current clinical candidates, act as 'kinase degraders', driving the proteasome-dependent turnover of their major target, ERK2. This may be relevant to the suggestion of kinase-independent effects of ERK1/2 and the therapeutic use of ERKi.
    Keywords:  ERK inhibitors; MEK; RAF; RAS; extracellular signal-regulated kinases; ubiquitin proteasome system
    DOI:  https://doi.org/10.1042/BCJ20220598
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