bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2020‒07‒12
seventeen papers selected by
Ralitsa Radostinova Madsen
University College London Cancer Institute

  1. Nat Commun. 2020 Jul 06. 11(1): 3377
    Kutys ML, Polacheck WJ, Welch MK, Gagnon KA, Koorman T, Kim S, Li L, McClatchey AI, Chen CS.
      The mammary gland is a highly vascularized tissue capable of expansion and regression during development and disease. To enable mechanistic insight into the coordinated morphogenic crosstalk between the epithelium and vasculature, we introduce a 3D microfluidic platform that juxtaposes a human mammary duct in proximity to a perfused endothelial vessel. Both compartments recapitulate stable architectural features of native tissue and the ability to undergo distinct forms of branching morphogenesis. Modeling HER2/ERBB2 amplification or activating PIK3CA(H1047R) mutation each produces ductal changes observed in invasive progression, yet with striking morphogenic and behavioral differences. Interestingly, PI3KαH1047R ducts also elicit increased permeability and structural disorganization of the endothelium, and we identify the distinct secretion of IL-6 as the paracrine cause of PI3KαH1047R-associated vascular dysfunction. These results demonstrate the functionality of a model system that facilitates the dissection of 3D morphogenic behaviors and bidirectional signaling between mammary epithelium and endothelium during homeostasis and pathogenesis.
  2. EMBO Rep. 2020 Jul 09. e49898
    Zhang J, Andersen JP, Sun H, Liu X, Sonenberg N, Nie J, Shi Y.
      Nutrient sensing by the mTOR complex 1 (mTORC1) requires its translocation to the lysosomal membrane. Upon amino acids removal, mTORC1 becomes cytosolic and inactive, yet its precise subcellular localization and the mechanism of inhibition remain elusive. Here, we identified Aster-C as a negative regulator of mTORC1 signaling. Aster-C earmarked a special rough ER subdomain where it sequestered mTOR together with the GATOR2 complex to prevent mTORC1 activation during nutrient starvation. Amino acids stimulated rapid disassociation of mTORC1 from Aster-C concurrently with assembly of COP I vesicles which escorted mTORC1 to the lysosomal membrane. Consequently, ablation of Aster-C led to spontaneous activation of mTORC1 and dissociation of TSC2 from lysosomes, whereas inhibition of COP I vesicle biogenesis or actin dynamics prevented mTORC1 activation. Together, these findings identified Aster-C as a missing link between lysosomal trafficking and mTORC1 activation by revealing an unexpected role of COP I vesicles in mTORC1 signaling.
    Keywords:  ARF1; COP I; GRAMD1C; lysosomes; mTORC1
  3. Science. 2020 Jul 10. 369(6500): 202-207
    Cook SA, Comrie WA, Poli MC, Similuk M, Oler AJ, Faruqi AJ, Kuhns DB, Yang S, Vargas-Hernández A, Carisey AF, Fournier B, Anderson DE, Price S, Smelkinson M, Abou Chahla W, Forbes LR, Mace EM, Cao TN, Coban-Akdemir ZH, Jhangiani SN, Muzny DM, Gibbs RA, Lupski JR, Orange JS, Cuvelier GDE, Al Hassani M, Al Kaabi N, Al Yafei Z, Jyonouchi S, Raje N, Caldwell JW, Huang Y, Burkhardt JK, Latour S, Chen B, ElGhazali G, Rao VK, Chinn IK, Lenardo MJ.
      Immunodeficiency often coincides with hyperactive immune disorders such as autoimmunity, lymphoproliferation, or atopy, but this coincidence is rarely understood on a molecular level. We describe five patients from four families with immunodeficiency coupled with atopy, lymphoproliferation, and cytokine overproduction harboring mutations in NCKAP1L, which encodes the hematopoietic-specific HEM1 protein. These mutations cause the loss of the HEM1 protein and the WAVE regulatory complex (WRC) or disrupt binding to the WRC regulator, Arf1, thereby impairing actin polymerization, synapse formation, and immune cell migration. Diminished cortical actin networks caused by WRC loss led to uncontrolled cytokine release and immune hyperresponsiveness. HEM1 loss also blocked mechanistic target of rapamycin complex 2 (mTORC2)-dependent AKT phosphorylation, T cell proliferation, and selected effector functions, leading to immunodeficiency. Thus, the evolutionarily conserved HEM1 protein simultaneously regulates filamentous actin (F-actin) and mTORC2 signaling to achieve equipoise in immune responses.
  4. Proc Natl Acad Sci U S A. 2020 Jul 07. pii: 201915719. [Epub ahead of print]
    Shin MG, Lee JW, Han JS, Lee B, Jeong JH, Park SH, Kim JH, Jang S, Park M, Kim SY, Kim S, Yang YR, Kim JY, Hoe KL, Park C, Lee KP, Kwon KS, Kwon ES.
      Gut microbes play diverse roles in modulating host fitness, including longevity; however, the molecular mechanisms underlying their mediation of longevity remain poorly understood. We performed genome-wide screens using 3,792 Escherichia coli mutants and identified 44 E. coli mutants that modulated Caenorhabditis elegans longevity. Three of these mutants modulated C. elegans longevity via the bacterial metabolite methylglyoxal (MG). Importantly, we found that low MG-producing E. coli mutants, Δhns E. coli, extended the lifespan of C. elegans through activation of the DAF-16/FOXO family transcription factor and the mitochondrial unfolded protein response (UPRmt). Interestingly, the lifespan modulation by Δhns did not require insulin/insulin-like growth factor 1 signaling (IIS) but did require TORC2/SGK-1 signaling. Transcriptome analysis revealed that Δhns E. coli activated novel class 3 DAF-16 target genes that were distinct from those regulated by IIS. Taken together, our data suggest that bacteria-derived MG modulates host longevity through regulation of the host signaling pathways rather than through nonspecific damage on biomolecules known as advanced glycation end products. Finally, we demonstrate that MG enhances the phosphorylation of hSGK1 and accelerates cellular senescence in human dermal fibroblasts, suggesting the conserved role of MG in controlling longevity across species. Together, our studies demonstrate that bacteria-derived MG is a novel therapeutic target for aging and aging-associated pathophysiology.
    Keywords:  DAF-16; gut microbe; longevity; methylglyoxal
  5. PLoS One. 2020 ;15(7): e0232072
    Cohen EB, Geck RC, Toker A.
      The vasculature within a tumor is highly disordered both structurally and functionally. Endothelial cells that comprise the vasculature are poorly connected causing vessel leakage and exposing the endothelium to a hypoxic microenvironment. Therefore, most anti-angiogenic therapies are generally inefficient and result in acquired resistance to increased hypoxia due to elimination of the vasculature. Recent studies have explored the efficacy of targeting metabolic pathways in tumor cells in combination with anti-angiogenic therapy. However, the metabolic alterations of endothelial cells in response to hypoxia have been relatively unexplored. Here, we measured polar metabolite levels in microvascular endothelial cells exposed to short- and long-term hypoxia with the goal of identifying metabolic vulnerabilities that can be targeted to normalize tumor vasculature and improve drug delivery. We found that many amino acid-related metabolites were altered by hypoxia exposure, especially within alanine-aspartate-glutamate, serine-threonine, and cysteine-methionine metabolism. Additionally, there were significant changes in de novo pyrimidine synthesis as well as glutathione and taurine metabolism. These results provide key insights into the metabolic alterations that occur in endothelial cells in response to hypoxia, which serve as a foundation for future studies to develop therapies that lead to vessel normalization and more efficient drug delivery.
  6. Trends Endocrinol Metab. 2020 Jul 01. pii: S1043-2760(20)30121-1. [Epub ahead of print]
    Dumas SJ, García-Caballero M, Carmeliet P.
      Angiogenesis is crucial for the development of the blood vasculature during embryogenesis, but also contributes to cancer and other diseases. While therapeutic targeting of endothelial cells (ECs) through growth factor inhibition is limited by insufficient efficacy and resistance, a new paradigm for modulating angiogenesis by targeting EC metabolism has emerged. Findings from the past decade highlight how ECs adapt their metabolism to proliferate or migrate during vessel sprouting, or to maintain the vascular barrier and protect themselves against oxidative stress in the high-oxygen environment they are exposed to in healthy conditions. We overview key endothelial metabolic pathways underlying the different EC phenotypes, as well as potential opportunities for targeting EC metabolism in therapeutic settings.
    Keywords:  angiogenesis; endothelial cell; metabolism; phalanx/tip/stalk cell; therapeutic target
  7. Breast Cancer Res. 2020 Jul 08. 22(1): 74
    Emad A, Ray T, Jensen TW, Parat M, Natrajan R, Sinha S, Ray PS.
      BACKGROUND: Cancer cells are known to display varying degrees of metastatic propensity, but the molecular basis underlying such heterogeneity remains unclear. Our aims in this study were to (i) elucidate prognostic subtypes in primary tumors based on an epithelial-to-mesenchymal-to-amoeboid transition (EMAT) continuum that captures the heterogeneity of metastatic propensity and (ii) to more comprehensively define biologically informed subtypes predictive of breast cancer metastasis and survival in lymph node-negative (LNN) patients.METHODS: We constructed a novel metastasis biology-based gene signature (EMAT) derived exclusively from cancer cells induced to undergo either epithelial-to-mesenchymal transition (EMT) or mesenchymal-to-amoeboid transition (MAT) to gauge their metastatic potential. Genome-wide gene expression data obtained from 913 primary tumors of lymph node-negative breast cancer (LNNBC) patients were analyzed. EMAT gene signature-based prognostic stratification of patients was performed to identify biologically relevant subtypes associated with distinct metastatic propensity.
    RESULTS: Delineated EMAT subtypes display a biologic range from less stem-like to more stem-like cell states and from less invasive to more invasive modes of cancer progression. Consideration of EMAT subtypes in combination with standard clinical parameters significantly improved survival prediction. EMAT subtypes outperformed prognosis accuracy of receptor or PAM50-based BC intrinsic subtypes even after adjusting for treatment variables in 3 independent, LNNBC cohorts including a treatment-naïve patient cohort.
    CONCLUSIONS: EMAT classification is a biologically informed method that provides prognostic information beyond that which can be provided by traditional cancer staging or PAM50 molecular subtype status and may improve metastasis risk assessment in early stage, LNNBC patients, who may otherwise be perceived to be at low metastasis risk.
    Keywords:  Breast cancer subtypes; Epithelial-to-mesenchymal transition; Mesenchymal-to-amoeboid transition; Metastasis; Metastatic risk assessment
  8. Mol Syst Biol. 2020 Jul;16(7): e9405
    Gonçalves E, Segura-Cabrera A, Pacini C, Picco G, Behan FM, Jaaks P, Coker EA, van der Meer D, Barthorpe A, Lightfoot H, Mironenko T, Beck A, Richardson L, Yang W, Lleshi E, Hall J, Tolley C, Hall C, Mali I, Thomas F, Morris J, Leach AR, Lynch JT, Sidders B, Crafter C, Iorio F, Fawell S, Garnett MJ.
      Low success rates during drug development are due, in part, to the difficulty of defining drug mechanism-of-action and molecular markers of therapeutic activity. Here, we integrated 199,219 drug sensitivity measurements for 397 unique anti-cancer drugs with genome-wide CRISPR loss-of-function screens in 484 cell lines to systematically investigate cellular drug mechanism-of-action. We observed an enrichment for positive associations between the profile of drug sensitivity and knockout of a drug's nominal target, and by leveraging protein-protein networks, we identified pathways underpinning drug sensitivity. This revealed an unappreciated positive association between mitochondrial E3 ubiquitin-protein ligase MARCH5 dependency and sensitivity to MCL1 inhibitors in breast cancer cell lines. We also estimated drug on-target and off-target activity, informing on specificity, potency and toxicity. Linking drug and gene dependency together with genomic data sets uncovered contexts in which molecular networks when perturbed mediate cancer cell loss-of-fitness and thereby provide independent and orthogonal evidence of biomarkers for drug development. This study illustrates how integrating cell line drug sensitivity with CRISPR loss-of-function screens can elucidate mechanism-of-action to advance drug development.
    Keywords:  CRISPR-Cas9; drug mechanism-of-action; protein networks
  9. Cell. 2020 Jul 09. pii: S0092-8674(20)30756-X. [Epub ahead of print]182(1): 12-23
    Vijg J, Dong X.
      Age-related accumulation of postzygotic DNA mutations results in tissue genetic heterogeneity known as somatic mosaicism. Although implicated in aging as early as the 1950s, somatic mutations in normal tissue have been difficult to study because of their low allele fractions. With the recent emergence of cost-effective high-throughput sequencing down to the single-cell level, enormous progress has been made in our capability to quantitatively analyze somatic mutations in human tissue in relation to aging and disease. Here we first review how recent technological progress has opened up this field, providing the first broad sets of quantitative information on somatic mutations in vivo necessary to gain insight into their possible causal role in human aging and disease. We then propose three major mechanisms that can lead from accumulated de novo mutations across tissues to cell functional loss and human disease.
    Keywords:  age-related disease; aging; genome mosaicism; pathogenic effects; somatic DNA mutation; transcriptional noise
  10. J Clin Pediatr Dent. 2020 ;44(3): 190-195
    Korporowicz E, Olczak-Kowalczyk D, Lipiec M, Słowińska M, Gozdowski D, Jóźwiak S.
      Objectives: Tuberous sclerosis complex (TSC) is a multisystem genetic disorder characterized by the development of benign tumors. The aim of the study was to assess the prevalence of oral lesions in patients with TSC and healthy individuals. Study design: The study included 120 patients aged 1.1 to 42.7 years: 60 patients with TSC and 60 controls. Clinical assessment of oral hygiene (Plaque Index-PLI), gingiva (Gingival Index-GI, Gingival Overgrowth Index-GOI), oral mucosa and dentition (caries, tooth wear, enamel defects) was performed. Statistical analysis was performed. Results: 40 patients with TSC received anticonvulsants. Neglected hygiene (PLI: 1.50±0.96 vs 0.92±0.72), gingival hyperplasia (50.0% vs.1.7%), gingivitis (80.7% vs. 53.4%), oral mucosal fibromas (10.0% vs. 0.0%), mucous membrane traumatic lesions (11.7% vs. 1.7%), enamel pits and hypoplasia of incisal borders (41.7% vs. 6.7%), tooth wear (35.0% vs. 11.7%) were more common in patients with TSC compared to controls; increased gingival hyperplasia was correlated with vigabatrin and levetiracetam treatment (r = 0.266 and 0.279, respectively), gingivitis was correlated with PLI (r= 0.635). Conclusions: Although gingival fibromas in TSC are independent of patient's age, young age, anticonvulsant therapy and local factors increase their severity. Enamel defects in TSC include pits, but also enamel loss on the incisal edges and tooth wear.
    Keywords:  Dental Enamel Hypoplasia; Oral Mucosa; Tooth wear; Tuberous Sclerosis
  11. Int J Breast Cancer. 2020 ;2020 3759179
    Anderson EJ, Mollon LE, Dean JL, Warholak TL, Aizer A, Platt EA, Tang DH, Davis LE.
      PIK3CA mutation frequency varies among breast cancer (BC) subtypes. Recent evidence suggests combination therapy with the PI3K inhibitor (PI3Ki) alpelisib and endocrine therapy (ET) improves response rates and progression-free survival (PFS) in PIK3CA-mutant, hormone receptor positive (HR+) BC versus ET alone; thus, better understanding the clinical and epidemiologic elements of these mutations is warranted. This systematic review characterizes the PIK3CA mutation epidemiology, type of testing approaches (e.g., liquid or tissue tumor biopsy), and stability/concordance (e.g., consistency in results by liquid versus solid tumor sample, by the same method over time) in patients with HR+/HER2- advanced (locally unresectable) or metastatic disease (HR+/HER2- mBC) and explores performance (e.g., pairwise concordance, sensitivity, specificity, or predictive value) of respective mutation findings. A comprehensive search of PubMed/MEDLINE, EMBASE, Cochrane Central, and select conference abstracts (i.e., AACR, ASCO, SABCS, ECCO, and ESMO conferences between 2014 and 2017) identified 39 studies of patients with HR+, HER2- mBC. The median prevalence of PIK3CA mutation was 36% (range: 13.3% to 61.5%); identified testing approaches more commonly used tissue over liquid biopsies and primarily utilized next-generation sequencing (NGS), polymerase chain reaction (PCR), or Sanger sequencing. There was concordance and stability between tissues (range: 70.4% to 94%) based on limited data. Given the clinical benefit of the PI3Ki alpelisib in patients with PIK3CA mutant HR+/HER2- mBC, determination of tumor PIK3CA mutation status is of importance in managing patients with HR+/HER2- mBC. Prevalence of this mutation and utility of test methodologies likely warrants PIK3CA mutation testing in all patients with this breast cancer subtype via definitive assessment of PIK3CA mutational status.
  12. Adv Biosyst. 2019 Oct;3(10): e1900094
    Lo LM, Raghunath M, Lee KKH.
      Suspension spheroid cultures of anchorage-dependent cell types have been widely used in cancer and stem cell research, as well as for producing organoids. It is believed that the 3-dimensional spheroid presents cells with a more physiological microenvironment to grow so that they behave more like cells in vivo, which is lacking in conventional 2-dimensional monolayer cultures. Recently, it has been reported that cancer cells grown as spheroids could express stem cell-associated genes. Hence, it is investigated whether normal mouse and human fibroblasts cultured as spheroids could also be induced to express stem cell-associated genes. The transcriptomes of human fibroblasts cultured as a monolayer and spheroids are compared and analyzed using real-time RT-qPCR, RNA-sequencing, and bioinformatics. The results reveal that the spheroid transcriptome resemble somatic cells being reprogramed into stem cells, including the induced expression of stemness-associated genes, increased expression of mesenchymal-to-epithelial transition-associated genes, and decreased expression of epithelial-to-mesenchymal transition-associated genes. In this context, it is hypothesized that during the process of spheroid formation, matrix-cell signaling is lost in favor of cell-cell contact signaling and that this subsequently increases the activity of the PI3K/Akt pathway that then upregulates Tbdx3 and stemness-associated genes.
    Keywords:  RNAseq; bioinformatics; human fibroblasts; pluripotency; spheroid culture
  13. Dev Cell. 2020 Jun 30. pii: S1534-5807(20)30497-4. [Epub ahead of print]
    Li F, Simon MC.
      Solid tumors reside in harsh tumor microenvironments (TMEs) together with various stromal cell types. During tumor progression and metastasis, both tumor and stromal cells undergo rapid metabolic adaptations. Tumor cells metabolically coordinate or compete with their "neighbors" to maintain biosynthetic and bioenergetic demands while escaping immunosurveillance or therapeutic interventions. Here, we provide an update on metabolic communication between tumor cells and heterogeneous stromal components in primary and metastatic TMEs and discuss emerging strategies to target metabolic communications for improved cancer treatments.
    Keywords:  antitumor immunity; combination therapy; immunomodulation; metabolic communication; metabolic symbiosis; metabolism; metastasis; nutrient competition; signaling molecule; stromal cells; tumor microenvironment
  14. Front Cell Dev Biol. 2020 ;8 442
    Pádua D, Figueira P, Ribeiro I, Almeida R, Mesquita P.
      Gastric and colorectal cancers have a high incidence and mortality worldwide. The presence of cancer stem cells (CSCs) within the tumor mass has been indicated as the main reason for tumor relapse, metastasis and therapy resistance, leading to poor overall survival. Thus, the elimination of CSCs became a crucial goal for cancer treatment. The identification of these cells has been performed by using cell-surface markers, a reliable approach, however it lacks specificity and usually differs among tumor type and in some cases even within the same type. In theory, the ideal CSC markers are those that are required to maintain their stemness features. The knowledge that CSCs exhibit characteristics comparable to normal stem cells that could be associated with the expression of similar transcription factors (TFs) including SOX2, OCT4, NANOG, KLF4 and c-Myc, and signaling pathways such as the Wnt/β-catenin, Hedgehog (Hh), Notch and PI3K/AKT/mTOR directed the attention to the use of these similarities to identify and target CSCs in different tumor types. Several studies have demonstrated that the abnormal expression of some TFs and the dysregulation of signaling pathways are associated with tumorigenesis and CSC phenotype. The disclosure of common and appropriate biomarkers for CSCs will provide an incredible tool for cancer prognosis and treatment. Therefore, this review aims to gather the new insights in gastric and colorectal CSC identification specially by using TFs as biomarkers and divulge promising drugs that have been found and tested for targeting these cells.
    Keywords:  cancer stem cells; colorectal cancer; gastric cancer; signaling pathways; targeted therapy; transcription factors
  15. Nat Rev Mol Cell Biol. 2020 Jul 07.
    Kim J, Koo BK, Knoblich JA.
      The historical reliance of biological research on the use of animal models has sometimes made it challenging to address questions that are specific to the understanding of human biology and disease. But with the advent of human organoids - which are stem cell-derived 3D culture systems - it is now possible to re-create the architecture and physiology of human organs in remarkable detail. Human organoids provide unique opportunities for the study of human disease and complement animal models. Human organoids have been used to study infectious diseases, genetic disorders and cancers through the genetic engineering of human stem cells, as well as directly when organoids are generated from patient biopsy samples. This Review discusses the applications, advantages and disadvantages of human organoids as models of development and disease and outlines the challenges that have to be overcome for organoids to be able to substantially reduce the need for animal experiments.
  16. Curr Opin Syst Biol. 2019 Oct;17 24-34
    Harris LA, Beik S, Ozawa PMM, Jimenez L, Weaver AM.
      Cancer is a complex, dynamic disease that despite recent advances remains mostly incurable. Inter- and intratumoral heterogeneity are generally considered major drivers of therapy resistance, metastasis, and treatment failure. Recent advances in high-throughput experimentation have produced a wealth of data on tumor heterogeneity and researchers are increasingly turning to mathematical modeling to aid in the interpretation of these complex datasets. In this mini-review, we discuss three important classes of approaches for modeling cellular dynamics within heterogeneous tumors: agent-based models, population dynamics, and multiscale models. An important new focus, for which we provide an example, is the role of intratumoral cell-cell interactions.
  17. Aging (Albany NY). 2020 Jul 04. 12
    Liu Y, Ma L, Shangguan F, Zhao X, Wang W, Gao Z, Zhou H, Qu G, Huang Y, An J, Xue J, Yang S, Cao Q.
      Recently, over-expression of LAIR-1 has been found in some solid cancers, including ovarian cancer. The role of LAIR-1 in cancer progression needs further investigation. In this study, we identified the LAIR-1 cDNA sequence of the ovarian cancer cells HO8910. Using SKOV3 cells, we confirmed the finding from our previous study that LAIR-1 could suppress in vitro cell proliferation and cell migration. We also found LAIR-1 overexpression can induce apoptosis of SKOV3 cells. We revealed LAIR-1 suppressed cell growth by inhibiting the PI3K-AKT-mTOR axis. Moreover, the LAIR-1 antitumor activity and its mechanism were also identified in vivo. We used Co-IP assay and mass spectrometry to identify potential LAIR-1-binding proteins in LAIR-1 overexpressing SKOV3 cells. MS analysis identified 167 potentially interacting proteins. GO analyses indicated a possible involvement of LAIR-1 in mRNA processing through its interaction with some eukaryotic translation initiation factors (eIF4E1B, eIF2S3, eIF3D, eIF4G2, eIF5B) and eukaryotic translation elongation factors (eEF1A2 and eEF1B2). Our findings suggest that LAIR-1 may suppress the growth of ovarian cancer cells by serving as a modulator that suppresses PI3K-AKT-mTOR directly or regulating protein synthesis at the translational level. Our results indicate that a LAIR-1-based strategy may prevent or suppress the progression of ovarian cancer.
    Keywords:  LAIR-1; PI3K-AKT-mTOR pathway; cell proliferation; eEF1A2; ovarian cancer