bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2020‒10‒25
thirteen papers selected by
Ralitsa Radostinova Madsen
University College London Cancer Institute
  1. Crosstalk of Hedgehog and mTORC1 Pathways.
  2. Enhancer Reprogramming Confers Dependence on Glycolysis and IGF Signaling in KMT2D Mutant Melanoma.
  3. Pharmacological intervention to restore connectivity deficits of neuronal networks derived from ASD patient iPSC with a TSC2 mutation.
  4. Replication Study: Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs.
  5. The Loss of Nuclear PTEN Increases Tumorigenesis in a Preclinical Mouse Model for Hepatocellular Carcinoma.
  6. Cep55 overexpression promotes genomic instability and tumorigenesis in mice.
  7. Mechanism of action biomarkers predicting response to AKT inhibition in the I-SPY 2 breast cancer trial.
  8. Automated microfluidic platform for dynamic and combinatorial drug screening of tumor organoids.
  9. Project Score database: a resource for investigating cancer cell dependencies and prioritizing therapeutic targets.
  10. Approaches to Investigating the Protein Interactome of PTEN.
  11. Oncogenic mutant RAS signaling activity is rescaled by the ERK/MAPK pathway.
  12. Adipocyte lipolysis drives acute stress-induced insulin resistance.
  13. Diverse Cell Stimulation Kinetics Identify Predictive Signal Transduction Models.
  1. Cells. 2020 Oct 18. pii: E2316. [Epub ahead of print]9(10):
    Crosstalk of Hedgehog and mTORC1 Pathways.
    Lasse Jonsgaard Larsen, Lisbeth Birk Møller.
      Hedgehog (Hh) signaling and mTOR signaling, essential for embryonic development and cellular metabolism, are both coordinated by the primary cilium. Observations from cancer cells strongly indicate crosstalk between Hh and mTOR signaling. This hypothesis is supported by several studies: Evidence points to a TGFβ-mediated crosstalk; Increased PI3K/AKT/mTOR activity leads to increased Hh signaling through regulation of the GLI transcription factors; increased Hh signaling regulates mTORC1 activity positively by upregulating NKX2.2, leading to downregulation of negative mTOR regulators; GSK3 and AMPK are, as members of both signaling pathways, potentially important links between Hh and mTORC1 signaling; The kinase DYRK2 regulates Hh positively and mTORC1 signaling negatively. In contrast, both positive and negative regulation of Hh has been observed for DYRK1A and DYRK1B, which both regulate mTORC1 signaling positively. Based on crosstalk observed between cilia, Hh, and mTORC1, we suggest that the interaction between Hh and mTORC1 is more widespread than it appears from our current knowledge. Although many studies focusing on crosstalk have been carried out, contradictory observations appear and the interplay involving multiple partners is far from solved.
    Keywords:  4E-BP1; GLI1; GLI2; GLI3; Mammalian target of rapamycin; S6K; TSC; autophagy; eIF4E; primary cilia
    DOI:  https://doi.org/10.3390/cells9102316
  2. Cell Rep. 2020 Oct 20. pii: S2211-1247(20)31282-1. [Epub ahead of print]33(3): 108293
    Enhancer Reprogramming Confers Dependence on Glycolysis and IGF Signaling in KMT2D Mutant Melanoma.
    Mayinuer Maitituoheti, Emily Z Keung, Ming Tang, Liang Yan, Hunain Alam, Guangchun Han, Anand K Singh, Ayush T Raman, Christopher Terranova, Sharmistha Sarkar, Elias Orouji, Samir B Amin, Sneha Sharma, Maura Williams, Neha S Samant, Mayura Dhamdhere, Norman Zheng, Tara Shah, Amiksha Shah, Jacob B Axelrad, Nazanin E Anvar, Yu-Hsi Lin, Shan Jiang, Edward Q Chang, Davis R Ingram, Wei-Lien Wang, Alexander Lazar, Min Gyu Lee, Florian Muller, Linghua Wang, Haoqiang Ying, Kunal Rai.
      Histone methyltransferase KMT2D harbors frequent loss-of-function somatic point mutations in several tumor types, including melanoma. Here, we identify KMT2D as a potent tumor suppressor in melanoma through an in vivo epigenome-focused pooled RNAi screen and confirm the finding by using a genetically engineered mouse model (GEMM) based on conditional and melanocyte-specific deletion of KMT2D. KMT2D-deficient tumors show substantial reprogramming of key metabolic pathways, including glycolysis. KMT2D deficiency aberrantly upregulates glycolysis enzymes, intermediate metabolites, and glucose consumption rates. Mechanistically, KMT2D loss causes genome-wide reduction of H3K4me1-marked active enhancer chromatin states. Enhancer loss and subsequent repression of IGFBP5 activates IGF1R-AKT to increase glycolysis in KMT2D-deficient cells. Pharmacological inhibition of glycolysis and insulin growth factor (IGF) signaling reduce proliferation and tumorigenesis preferentially in KMT2D-deficient cells. We conclude that KMT2D loss promotes tumorigenesis by facilitating an increased use of the glycolysis pathway for enhanced biomass needs via enhancer reprogramming, thus presenting an opportunity for therapeutic intervention through glycolysis or IGF pathway inhibitors.
    Keywords:  2-DG; IGFBP5; KMT2D; Linsitinib; RNAi screen; chromatin; epigenetics; glycolysis; melanoma; mouse model
    DOI:  https://doi.org/10.1016/j.celrep.2020.108293
  3. Mol Autism. 2020 Oct 19. 11(1): 80
    Pharmacological intervention to restore connectivity deficits of neuronal networks derived from ASD patient iPSC with a TSC2 mutation.
    Mouhamed Alsaqati, Vivi M Heine, Adrian J Harwood.
      BACKGROUND: Tuberous sclerosis complex (TSC) is a rare genetic multisystemic disorder resulting from autosomal dominant mutations in the TSC1 or TSC2 genes. It is characterised by hyperactivation of the mechanistic target of rapamycin complex 1 (mTORC1) pathway and has severe neurodevelopmental and neurological components including autism, intellectual disability and epilepsy. In human and rodent models, loss of the TSC proteins causes neuronal hyperexcitability and synaptic dysfunction, although the consequences of these changes for the developing central nervous system are currently unclear.METHODS: Here we apply multi-electrode array-based assays to study the effects of TSC2 loss on neuronal network activity using autism spectrum disorder (ASD) patient-derived iPSCs. We examine both temporal synchronisation of neuronal bursting and spatial connectivity between electrodes across the network.
    RESULTS: We find that ASD patient-derived neurons with a functional loss of TSC2, in addition to possessing neuronal hyperactivity, develop a dysfunctional neuronal network with reduced synchronisation of neuronal bursting and lower spatial connectivity. These deficits of network function are associated with elevated expression of genes for inhibitory GABA signalling and glutamate signalling, indicating a potential abnormality of synaptic inhibitory-excitatory signalling. mTORC1 activity functions within a homeostatic triad of protein kinases, mTOR, AMP-dependent protein Kinase 1 (AMPK) and Unc-51 like Autophagy Activating Kinase 1 (ULK1) that orchestrate the interplay of anabolic cell growth and catabolic autophagy while balancing energy and nutrient homeostasis. The mTOR inhibitor rapamycin suppresses neuronal hyperactivity, but does not increase synchronised network activity, whereas activation of AMPK restores some aspects of network activity. In contrast, the ULK1 activator, LYN-1604, increases the network behaviour, shortens the network burst lengths and reduces the number of uncorrelated spikes.
    LIMITATIONS: Although a robust and consistent phenotype is observed across multiple independent iPSC cultures, the results are based on one patient. There may be more subtle differences between patients with different TSC2 mutations or differences of polygenic background within their genomes. This may affect the severity of the network deficit or the pharmacological response between TSC2 patients.
    CONCLUSIONS: Our observations suggest that there is a reduction in the network connectivity of the in vitro neuronal network associated with ASD patients with TSC2 mutation, which may arise via an excitatory/inhibitory imbalance due to increased GABA-signalling at inhibitory synapses. This abnormality can be effectively suppressed via activation of ULK1.
    DOI:  https://doi.org/10.1186/s13229-020-00391-w
  4. Elife. 2020 Oct 19. pii: e56651. [Epub ahead of print]9
    Replication Study: Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs.
    Hongyan Wang, Hanna S Radomska, Mitch A Phelps, , Elizabeth Iorns, Rachel Tsui, Alexandria Denis, Nicole Perfito, Timothy M Errington.
      As part of the Reproducibility Project: Cancer Biology, we published a Registered Report (Phelps et al., 2016) that described how we intended to replicate selected experiments from the paper 'Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs' (Tay et al., 2011). Here, we report the results. We found depletion of putative PTEN competing endogenous mRNAs (ceRNAs) in DU145 cells did not impact PTEN 3'UTR regulation using a reporter, while the original study reported decreased activity when SERINC1, VAPA, and CNOT6L were depleted (Figure 3C; Tay et al., 2011). Using the same reporter, we found decreased activity when ceRNA 3'UTRs were overexpressed, while the original study reported increased activity (Figure 3D; Tay et al., 2011). In HCT116 cells, ceRNA depletion resulted in decreased PTEN protein levels, a result similar to the findings reported in the original study (Figure 3G,H; Tay et al., 2011); however, while the original study reported an attenuated ceRNA effect in microRNA deficient (DicerEx5) HCT116 cells, we observed increased PTEN protein levels. Further, we found depletion of the ceRNAs VAPA or CNOT6L did not statistically impact DU145, wild-type HCT116, or DicerEx5 HCT116 cell proliferation. The original study reported increased DU145 and wild-type HCT116 cell proliferation when these ceRNAs were depleted, which was attenuated in the DicerEx5 HCT116 cells (Figure 5B; Tay et al., 2011). Differences between the original study and this replication attempt, such as variance between biological repeats, are factors that might have influenced the results. Finally, we report meta-analyses for each result.
    Keywords:  PTEN; cancer biology; ceRNA; human; metascience; microRNA; replication; reproducibility
    DOI:  https://doi.org/10.7554/eLife.56651
  5. iScience. 2020 Oct 23. 23(10): 101548
    The Loss of Nuclear PTEN Increases Tumorigenesis in a Preclinical Mouse Model for Hepatocellular Carcinoma.
    Takashi Kato, Tatsuya Yamada, Hideki Nakamura, Atsushi Igarashi, Robert A Anders, Hiromi Sesaki, Miho Iijima.
      The PTEN gene is highly mutated in many cancers, including hepatocellular carcinoma. The PTEN protein is located at different subcellular regions-PTEN at the plasma membrane suppresses PI3-kinase signaling in cell growth, whereas PTEN in the nucleus maintains genome integrity. Here, using nuclear PTEN-deficient mice, we analyzed the role of PTEN in the nucleus in hepatocellular carcinoma that is induced by carcinogen and oxidative stress-producing hepatotoxin. Upon oxidative stress, PTEN was accumulated in the nucleus of the liver, and this accumulation promoted repair of DNA damage in wild-type mice. In contrast, nuclear PTEN-deficient mice had increased DNA damage and accelerated hepatocellular carcinoma formation. Both basal and oxidative stress-induced localization of PTEN in the nucleus require ubiquitination of lysine 13 in PTEN. Taken together, these data suggest the critical role of nuclear PTEN in the protection from DNA damage and tumorigenesis in vivo.
    Keywords:  Cancer; Cell Biology
    DOI:  https://doi.org/10.1016/j.isci.2020.101548
  6. Commun Biol. 2020 Oct 21. 3(1): 593
    Cep55 overexpression promotes genomic instability and tumorigenesis in mice.
    Debottam Sinha, Purba Nag, Devathri Nanayakkara, Pascal H G Duijf, Andrew Burgess, Prahlad Raninga, Veronique A J Smits, Amanda L Bain, Goutham Subramanian, Meaghan Wall, John W Finnie, Murugan Kalimutho, Kum Kum Khanna.
      High expression of centrosomal protein CEP55 has been correlated with clinico-pathological parameters across multiple human cancers. Despite significant in vitro studies and association of aberrantly overexpressed CEP55 with worse prognosis, its causal role in vivo tumorigenesis remains elusive. Here, using a ubiquitously overexpressing transgenic mouse model, we show that Cep55 overexpression causes spontaneous tumorigenesis and accelerates Trp53+/- induced tumours in vivo. At the cellular level, using mouse embryonic fibroblasts (MEFs), we demonstrate that Cep55 overexpression induces proliferation advantage by modulating multiple cellular signalling networks including the hyperactivation of the Pi3k/Akt pathway. Notably, Cep55 overexpressing MEFs have a compromised Chk1-dependent S-phase checkpoint, causing increased replication speed and DNA damage, resulting in a prolonged aberrant mitotic division. Importantly, this phenotype was rescued by pharmacological inhibition of Pi3k/Akt or expression of mutant Chk1 (S280A) protein, which is insensitive to regulation by active Akt, in Cep55 overexpressing MEFs. Moreover, we report that Cep55 overexpression causes stabilized microtubules. Collectively, our data demonstrates causative effects of deregulated Cep55 on genome stability and tumorigenesis which have potential implications for tumour initiation and therapy development.
    DOI:  https://doi.org/10.1038/s42003-020-01304-6
  7. NPJ Breast Cancer. 2020 ;6 48
    Mechanism of action biomarkers predicting response to AKT inhibition in the I-SPY 2 breast cancer trial.
    Denise M Wolf, Christina Yau, Julia Wulfkuhle, Lamorna Brown-Swigart, Rosa I Gallagher, Mark Jesus M Magbanua, Nick O'Grady, Gillian Hirst, , Smita Asare, Debu Tripathy, Don Berry, Laura Esserman, A Jo Chien, Emanuel F Petricoin, Laura van 't Veer.
      The AKT inhibitor MK2206 (M) was evaluated in I-SPY 2 and graduated in the HER2+, HR-, and HR- HER2+ signatures. We hypothesized that AKT signaling axis proteins/genes may specifically predict response to M and tested 26 phospho-proteins and 10 genes involved in AKT-mTOR-HER signaling; in addition, we tested 9 genes from a previous study in the metastatic setting. One hundred and fifty patients had gene expression data from pretreatment biopsies available for analysis (M: 94, control: 56) and 138 had protein data (M: 87, control: 51). Logistic modeling was used to assess biomarker performance in pre-specified analysis. In general, phospho-protein biomarkers of activity in the AKT-mTOR-HER pathway appeared more predictive of response to M than gene expression or total protein biomarkers in the same pathway; however, the nature of the predictive biomarkers differed in the HER2+ and TN groups. In the HER2+ subset, patients achieving a pCR in M had higher levels of multiple AKT kinase substrate phospho-proteins (e.g., pmTOR, pTSC2). In contrast, in the TN subset responding patients had lower levels of AKT pathway phospho-proteins, such as pAKT, pmTOR, and pTSC2. Pathway mutations did not appear to account for these associations. Additional exploratory whole-transcriptome analysis revealed immune signaling as strongly associated with response to M in the HER2+ subset. While our sample size is small, these results suggest that the measurement of particular AKT kinase substrate phospho-proteins could be predictive of MK2206 efficacy in both HER2+ and TN tumors and that immune signaling may play a role in response in HER2+ patients.
    Keywords:  Breast cancer; Predictive markers
    DOI:  https://doi.org/10.1038/s41523-020-00189-2
  8. Nat Commun. 2020 10 19. 11(1): 5271
    Automated microfluidic platform for dynamic and combinatorial drug screening of tumor organoids.
    Brooke Schuster, Michael Junkin, Sara Saheb Kashaf, Isabel Romero-Calvo, Kori Kirby, Jonathan Matthews, Christopher R Weber, Andrey Rzhetsky, Kevin P White, Savaş Tay.
      Three-dimensional (3D) cell culture technologies, such as organoids, are physiologically relevant models for basic and clinical applications. Automated microfluidics offers advantages in high-throughput and precision analysis of cells but is not yet compatible with organoids. Here, we present an automated, high-throughput, microfluidic 3D organoid culture and analysis system to facilitate preclinical research and personalized therapies. Our system provides combinatorial and dynamic drug treatments to hundreds of cultures and enables real-time analysis of organoids. We validate our system by performing individual, combinatorial, and sequential drug screens on human-derived pancreatic tumor organoids. We observe significant differences in the response of individual patient-based organoids to drug treatments and find that temporally-modified drug treatments can be more effective than constant-dose monotherapy or combination therapy in vitro. This integrated platform advances organoids models to screen and mirror real patient treatment courses with potential to facilitate treatment decisions for personalized therapy.
    DOI:  https://doi.org/10.1038/s41467-020-19058-4
  9. Nucleic Acids Res. 2020 Oct 17. pii: gkaa882. [Epub ahead of print]
    Project Score database: a resource for investigating cancer cell dependencies and prioritizing therapeutic targets.
    Lisa Dwane, Fiona M Behan, Emanuel Gonçalves, Howard Lightfoot, Wanjuan Yang, Dieudonne van der Meer, Rebecca Shepherd, Miguel Pignatelli, Francesco Iorio, Mathew J Garnett.
      CRISPR genetic screens in cancer cell models are a powerful tool to elucidate oncogenic mechanisms and to identify promising therapeutic targets. The Project Score database (https://score.depmap.sanger.ac.uk/) uses genome-wide CRISPR-Cas9 dropout screening data in hundreds of highly annotated cancer cell models to identify genes required for cell fitness and prioritize novel oncology targets. The Project Score database currently allows users to investigate the fitness effect of 18 009 genes tested across 323 cancer cell models. Through interactive interfaces, users can investigate data by selecting a specific gene, cancer cell model or tissue type, as well as browsing all gene fitness scores. Additionally, users can identify and rank candidate drug targets based on an established oncology target prioritization pipeline, incorporating genetic biomarkers and clinical datasets for each target, and including suitability for drug development based on pharmaceutical tractability. Data are freely available and downloadable. To enhance analyses, links to other key resources including Open Targets, COSMIC, the Cell Model Passports, UniProt and the Genomics of Drug Sensitivity in Cancer are provided. The Project Score database is a valuable new tool for investigating genetic dependencies in cancer cells and the identification of candidate oncology targets.
    DOI:  https://doi.org/10.1093/nar/gkaa882
  10. J Proteome Res. 2020 Oct 19.
    Approaches to Investigating the Protein Interactome of PTEN.
    Sarah L Smith, Andrew R Pitt, Corinne M Spickett.
      The tumor suppressor phosphatase and tensin homologue (PTEN) is a redox-sensitive dual specificity phosphatase with an essential role in the negative regulation of the PI3K-AKT signaling pathway, affecting metabolic and cell survival processes. PTEN is commonly mutated in cancer, and dysregulation in the metabolism of PIP3 is implicated in other diseases such as diabetes. PTEN interactors are responsible for some functional roles of PTEN beyond the negative regulation of the PI3K pathway and are thus of great importance in cell biology. Both high-data content proteomics-based approaches and low-data content PPI approaches have been used to investigate the interactome of PTEN and elucidate further functions of PTEN. While low-data content approaches rely on co-immunoprecipitation and Western blotting, and as such require previously generated hypotheses, high-data content approaches such as affinity pull-down proteomic assays or the yeast 2-hybrid system are hypothesis generating. This review provides an overview of the PTEN interactome, including redox effects, and critically appraises the methods and results of high-data content investigations into the global interactome of PTEN. The biological significance of findings from recent studies is discussed and illustrates the breadth of cellular functions of PTEN that can be discovered by these approaches.
    Keywords:  affinity pull-down; global interactome; high-data content; protein−protein interactions; redox regulation; yeast 2-hybrid
    DOI:  https://doi.org/10.1021/acs.jproteome.0c00570
  11. Mol Syst Biol. 2020 Oct;16(10): e9518
    Oncogenic mutant RAS signaling activity is rescaled by the ERK/MAPK pathway.
    Taryn E Gillies, Michael Pargett, Jillian M Silva, Carolyn K Teragawa, Frank McCormick, John G Albeck.
      Activating mutations in RAS are present in ~ 30% of human tumors, and the resulting aberrations in ERK/MAPK signaling play a central role in oncogenesis. However, the form of these signaling changes is uncertain, with activating RAS mutants linked to both increased and decreased ERK activation in vivo. Rationally targeting the kinase activity of this pathway requires clarification of the quantitative effects of RAS mutations. Here, we use live-cell imaging in cells expressing only one RAS isoform to quantify ERK activity with a new level of accuracy. We find that despite large differences in their biochemical activity, mutant KRAS isoforms within cells have similar ranges of ERK output. We identify roles for pathway-level effects, including variation in feedback strength and feedforward modulation of phosphatase activity, that act to rescale pathway sensitivity, ultimately resisting changes in the dynamic range of ERK activity while preserving responsiveness to growth factor stimuli. Our results reconcile seemingly inconsistent reports within the literature and imply that the signaling changes induced by RAS mutations early in oncogenesis are subtle.
    Keywords:  FRET biosensor; RAS disease; computational modeling; epidermal growth factor; single-cell kinetics
    DOI:  https://doi.org/10.15252/msb.20209518
  12. Sci Rep. 2020 Oct 23. 10(1): 18166
    Adipocyte lipolysis drives acute stress-induced insulin resistance.
    Vidisha Raje, Katelyn W Ahern, Brittany A Martinez, Nancy L Howell, Vici Oenarto, Mitchell E Granade, Jae Woo Kim, Smanla Tundup, Katharina Bottermann, Axel Gödecke, Susanna R Keller, Alexandra Kadl, Michelle L Bland, Thurl E Harris.
      Stress hyperglycemia and insulin resistance are evolutionarily conserved metabolic adaptations to severe injury including major trauma, burns, or hemorrhagic shock (HS). In response to injury, the neuroendocrine system increases secretion of counterregulatory hormones that promote rapid mobilization of nutrient stores, impair insulin action, and ultimately cause hyperglycemia, a condition known to impair recovery from injury in the clinical setting. We investigated the contributions of adipocyte lipolysis to the metabolic response to acute stress. Both surgical injury with HS and counterregulatory hormone (epinephrine) infusion profoundly stimulated adipocyte lipolysis and simultaneously triggered insulin resistance and hyperglycemia. When lipolysis was inhibited, the stress-induced insulin resistance and hyperglycemia were largely abolished demonstrating an essential requirement for adipocyte lipolysis in promoting stress-induced insulin resistance. Interestingly, circulating non-esterified fatty acid levels did not increase with lipolysis or correlate with insulin resistance during acute stress. Instead, we show that impaired insulin sensitivity correlated with circulating levels of the adipokine resistin in a lipolysis-dependent manner. Our findings demonstrate the central importance of adipocyte lipolysis in the metabolic response to injury. This insight suggests new approaches to prevent insulin resistance and stress hyperglycemia in trauma and surgery patients and thereby improve outcomes.
    DOI:  https://doi.org/10.1038/s41598-020-75321-0
  13. iScience. 2020 Oct 23. 23(10): 101565
    Diverse Cell Stimulation Kinetics Identify Predictive Signal Transduction Models.
    Hossein Jashnsaz, Zachary R Fox, Jason J Hughes, Guoliang Li, Brian Munsky, Gregor Neuert.
      Computationally understanding the molecular mechanisms that give rise to cell signaling responses upon different environmental, chemical, and genetic perturbations is a long-standing challenge that requires models that fit and predict quantitative responses for new biological conditions. Overcoming this challenge depends not only on good models and detailed experimental data but also on the rigorous integration of both. We propose a quantitative framework to perturb and model generic signaling networks using multiple and diverse changing environments (hereafter "kinetic stimulations") resulting in distinct pathway activation dynamics. We demonstrate that utilizing multiple diverse kinetic stimulations better constrains model parameters and enables predictions of signaling dynamics that would be impossible using traditional dose-response or individual kinetic stimulations. To demonstrate our approach, we use experimentally identified models to predict signaling dynamics in normal, mutated, and drug-treated conditions upon multitudes of kinetic stimulations and quantify which proteins and reaction rates are most sensitive to which extracellular stimulations.
    Keywords:  Bioinformatics; Complex System Biology; Systems Biology
    DOI:  https://doi.org/10.1016/j.isci.2020.101565
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