bims-pideca 2019-09-22 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2019–09–22
twelve papers selected by
Ralitsa Radostinova Madsen, University College London

Predictive and Pharmacodynamic Biomarkers of Response to the Phosphatidylinositol 3-Kinase Inhibitor Taselisib in Breast Cancer Preclinical Models.
A Systems Biology Roadmap to Decode mTOR Control System in Cancer.
High-Throughput Assessment of Kinome-wide Activation States.
mTORC1 feedback to AKT modulates lysosomal biogenesis through MiT/TFE regulation.
A framework for examining how diet impacts tumour metabolism.
mTORC1 as a cell-intrinsic rheostat that shapes development, preimmune repertoire, and function of B lymphocytes.
How Sweet It Is: Small-Molecule Inhibitors of mTORC1 Glucose Sensing.
An update on PTEN modulators - A patent review.
Weak membrane interactions allow rheb to activate mTORC1 signaling without major lysosome enrichment.
Nuclear Glycogenolysis Modulates Histone Acetylation in Human Non-Small Cell Lung Cancers.
Caspase-10 inhibits ATP-citrate lyase-mediated metabolic and epigenetic reprogramming to suppress tumorigenesis.
Chromosomal instability and mTORC1 activation through PTEN loss contribute to proteotoxic stress in ovarian carcinoma.

Mol Cancer Ther. 2019 Sep 18. pii: molcanther.0284.2019. [Epub ahead of print]

Predictive and Pharmacodynamic Biomarkers of Response to the Phosphatidylinositol 3-Kinase Inhibitor Taselisib in Breast Cancer Preclinical Models.

Heather M Moore, Heidi M Savage, Carol O'Brien, Wei Zhou, Ethan S Sokol, Michael E Goldberg, Ciara Metcalfe, Lori S Friedman, Mark R Lackner, Timothy R Wilson.

The phosphatidylinositol 3-kinase (PI3K) signaling pathway serves as a central node in regulating cell survival, proliferation and metabolism. PIK3CA, the gene encoding the PI3K catalytic subunit p110-alpha, is commonly altered in breast cancer resulting in the constitutive activation of the PI3K pathway. Using an unbiased cell line screening approach, we tested the sensitivity of breast cancer cell lines to taselisib, a potent PI3K inhibitor, and correlated sensitivity with key biomarkers (PIK3CA, HER2, PTEN, ESR1). We further assessed how taselisib modulates downstream signaling in the different genomic backgrounds that occur within breast cancer. We found that sensitivity to taselisib correlated with the presence of PIK3CA mutations, but was independent of HER2 status. We further showed that HER2 amplified/PIK3CA wild-type cell lines are not as sensitive to taselisib when compared to HER2 amplified/PIK3CA mutant cell lines. In a PIK3CA mutant/PTEN null background, PI3K downstream signaling rebounded in the presence of taselisib correlating with decreased sensitivity at later time points. Finally, we observed that PIK3CA mutations co-occurred with mutations in the estrogen receptor (ESR1) in metastatic tumors from ER+ breast cancer patients. However, the co-occurrence of an ESR1 mutation with a PIK3CA mutation did not affect response to taselisib in a single agent setting or in combination with fulvestrant. In summary, these data suggest that development of taselisib in breast cancer should occur in a PIK3CA mutant setting with co-treatments determined by the specific subtypes under investigation.

DOI: https://doi.org/10.1158/1535-7163.MCT-19-0284
Interdiscip Sci. 2019 Sep 17.

A Systems Biology Roadmap to Decode mTOR Control System in Cancer.

Mohammadreza Dorvash, Mohammad Farahmandnia, Iman Tavassoly.

  Mechanistic target of rapamycin (mTOR) is a critical protein in the regulation of cell fate decision making, especially in cancer cells. mTOR acts as a signal integrator and is one of the main elements of interactions among the pivotal cellular processes such as cell death, autophagy, metabolic reprogramming, cell growth, and cell cycle. The temporal control of these processes is essential for the cellular homeostasis and dysregulation of mTOR signaling pathway results in different phenotypes, including aging, oncogenesis, cell survival, cell growth, senescence, quiescence, and cell death. In this paper, we have proposed a systems biology roadmap to study mTOR control system, which introduces the theoretical and experimental modalities to decode temporal and dynamical characteristics of mTOR signaling in cancer.

Keywords:  Aging; Bistability; Cancer; Cell fate; Dynamic modeling; Mathematical models; Oscillations; Signaling network; Systems biology; mTOR

DOI:  https://doi.org/10.1007/s12539-019-00347-6
Cell Syst. 2019 Sep 06. pii: S2405-4712(19)30274-1. [Epub ahead of print]

High-Throughput Assessment of Kinome-wide Activation States.

Thierry Schmidlin, Donna O Debets, Charlotte A G H van Gelder, Kelly E Stecker, Stamatia Rontogianni, Bart L van den Eshof, Kristel Kemper, Esther H Lips, Maartje van den Biggelaar, Daniel S Peeper, Albert J R Heck, Maarten Altelaar.

  Aberrant kinase activity has been linked to a variety of disorders; however, methods to probe kinase activation states in cells have been lacking. Until now, kinase activity has mainly been deduced from either protein expression or substrate phosphorylation levels. Here, we describe a strategy to directly infer kinase activation through targeted quantification of T-loop phosphorylation, which serves as a critical activation switch in a majority of protein kinases. Combining selective phosphopeptide enrichment with robust targeted mass spectrometry, we provide highly specific assays for 248 peptides, covering 221 phosphosites in the T-loop region of 178 human kinases. Using these assays, we monitored the activation of 63 kinases through 73 T-loop phosphosites across different cell types, primary cells, and patient-derived tissue material. The sensitivity of our assays is highlighted by the reproducible detection of TNF-α-induced RIPK1 activation and the detection of 46 T-loop phosphorylation sites from a breast tumor needle biopsy.

Keywords:  SRM; T-loop phosphorylation; cancer; kinase; kinase activity; phosphoproteomics; proteomics; signaling; targeted mass spectrometry

DOI:  https://doi.org/10.1016/j.cels.2019.08.005
J Clin Invest. 2019 Sep 17. pii: 128287. [Epub ahead of print]

mTORC1 feedback to AKT modulates lysosomal biogenesis through MiT/TFE regulation.

Kaushal Asrani, Sanjana Murali, Brandon Lam, Chan-Hyun Na, Pornima Phatak, Akshay Sood, Harsimar Kaur, Zoya Khan, Michaël Noë, Ravi K Anchoori, C Conover Talbot, Barbara Smith, Michael Skaro, Tamara L Lotan.

  The Microphthalmia family of transcription factors (MiT/TFE) controls lysosomal biogenesis and is negatively regulated by the nutrient sensor mTORC1. However, the mechanisms by which cells with constitutive mTORC1 signaling maintain lysosomal catabolism remain to be elucidated. Using the murine epidermis as a model system, we found that epidermal Tsc1 deletion resulted in a phenotype characterized by wavy hair and curly whiskers, and was associated with increased EGFR and HER2 degradation. Unexpectedly, constitutive mTORC1 activation with Tsc1 loss increased lysosomal content via up-regulated expression and activity of MiT/TFEs, while genetic deletion of Rheb or Rptor or prolonged pharmacologic mTORC1 inactivation had the reverse effect. This paradoxical increase in lysosomal biogenesis by mTORC1 was mediated by feedback inhibition of AKT, and a resulting suppression of AKT-induced MiT/TFE down-regulation. Thus, inhibiting hyperactive AKT signaling in the context of mTORC1 loss-of-function fully restored MiT/TFE expression and activity. These data suggest that signaling feedback loops work to restrain or maintain cellular lysosomal content during chronically inhibited or constitutively active mTORC1 signaling respectively, and reveal a mechanism by which mTORC1 regulates upstream receptor tyrosine kinase signaling.

Keywords:  Genetic diseases; Lysosomes; Metabolism; Oncology

DOI:  https://doi.org/10.1172/JCI128287
Nat Rev Cancer. 2019 Sep 17.

A framework for examining how diet impacts tumour metabolism.

Evan C Lien, Matthew G Vander Heiden.

The way cancer cells utilize nutrients to support their growth and proliferation is determined by cancer cell-intrinsic and cancer cell-extrinsic factors, including interactions with the environment. These interactions can define therapeutic vulnerabilities and impact the effectiveness of cancer therapy. Diet-mediated changes in whole-body metabolism and systemic nutrient availability can affect the environment that cancer cells are exposed to within tumours, and a better understanding of how diet modulates nutrient availability and utilization by cancer cells is needed. How diet impacts cancer outcomes is also of great interest to patients, yet clear evidence for how diet interacts with therapy and impacts tumour growth is lacking. Here we propose an experimental framework to probe the connections between diet and cancer metabolism. We examine how dietary factors may affect tumour growth by altering the access to and utilization of nutrients by cancer cells. Our growing understanding of how certain cancer types respond to various diets, how diet impacts cancer cell metabolism to mediate these responses and whether dietary interventions may constitute new therapeutic opportunities will begin to provide guidance on how best to use diet and nutrition to manage cancer in patients.

DOI: https://doi.org/10.1038/s41568-019-0198-5
FASEB J. 2019 Sep 18. fj201900069R

mTORC1 as a cell-intrinsic rheostat that shapes development, preimmune repertoire, and function of B lymphocytes.

Ariel L Raybuck, Keunwook Lee, Sung Hoon Cho, Jingxin Li, James W Thomas, Mark R Boothby.

  Ample evidence indicates that nutrient concentrations in extracellular milieux affect signaling mediated by environmental sensor proteins. For instance, the mechanistic target of rapamycin (mTOR) is reduced during protein malnutrition and is known to be modulated by concentrations of several amino acids when in a multiprotein signaling complex that contains regulatory-associated protein of mTOR. We hypothesized that a partial decrease in mTOR complex 1 (mTORC1) activity intrinsic to B-lineage cells would perturb lymphocyte development or function, or both. We show that a cell-intrinsic decrease in mTORC1 activity impacted developmental progression, antigen receptor repertoire, and function along the B lineage. Thus, preimmune repertoires of B-lineage cells were altered in the marrow and periphery in a genetic model of regulatory-associated protein of mTOR haplo-insufficiency. An additional role for mTORC1 was revealed when a B-cell antigen receptor transgene was found to circumvent the abnormal B-cell development: haplo-insufficient B cells were profoundly impaired in responses to antigen in vivo. Collectively, our findings indicate that mTORC1 serves as a rheostat that shapes differentiation along the B lineage, the preimmune repertoire, and antigen-driven selection of mature B cells. The findings also reveal a range in the impact of this nutrient sensor on activity-response relationships for distinct endpoints.-Raybuck, A. L., Lee, K., Cho, S. H., Li, J., Thomas, J. W., Boothby, M. R. mTORC1 as a cell-intrinsic rheostat that shapes development, preimmune repertoire, and function of B lymphocytes.

Keywords:  immunity; protein malnutrition; signaling

DOI:  https://doi.org/10.1096/fj.201900069R
Cell Chem Biol. 2019 Sep 19. pii: S2451-9456(19)30275-2. [Epub ahead of print]26(9): 1195-1196

How Sweet It Is: Small-Molecule Inhibitors of mTORC1 Glucose Sensing.

Junbing Zhang, Liron Bar-Peled.

In this issue of Cell Chemical Biology, Kang et al. (2019) describe the use of a high-throughput cell-based screen to identify chemical scaffolds that selectively inhibit mTORC1 nutrient sensing. Chemical proteomic-based target identification reveals class I glucose transporters as direct targets for these inhibitors, linking glucose sensing with mTORC1 regulation.

DOI: https://doi.org/10.1016/j.chembiol.2019.09.001
Expert Opin Ther Pat. 2019 Sep 17.

An update on PTEN modulators - A patent review.

Chandra S Boosani, Palanikumar Gunasekar, Devendra K Agrawal.

  Introduction: A multitude of cellular and physiological functions have been attributed to the biological activity of PTEN (Phosphatase and tensin homolog) such as inhibiting angiogenesis, promoting apoptosis, preventing cell proliferation, and maintaining cellular homeostasis. Based on whether cell growth is needed to be initiated or to be inhibited, enhancing PTEN expression or seeking to inhibit it was pursued. Areas covered: Here the authors provide recent updates to their previous publication on "PTEN modulators: A patent review", and discuss on new specificities that affirm the therapeutic potential of PTEN in promoting neuro-regeneration, stem cell regeneration, autophagy, bone and cartilage regeneration. Also, targeting PTEN appears to be effective in developing new treatment strategies for Parkinson's disease, Alzheimer's disease, macular degeneration, immune disorders, asthma, arthritis, lupus, Crohn's disease, and several cancer types. Expert opinion: PTEN mainly inhibits the PI3k/Akt pathway. However, the PI3k/Akt pathway can be activated by other signaling proteins. Thus, novel treatment strategies that can regulate PTEN alone, or combinational treatment approaches that can induce PTEN and simultaneously affect downstream mediators in the PI3K/Akt pathway, are needed, which were not investigated in detail. Commercial interests associated with molecules that regulate PTEN are discussed here, along with limitations and new possibilities to improve them.

Keywords:  PTEN regulators; chemical compounds; human diseases; peptides; viral vectors

DOI:  https://doi.org/10.1080/13543776.2019.1669562
Mol Biol Cell. 2019 Sep 18. mbcE19030146

Weak membrane interactions allow rheb to activate mTORC1 signaling without major lysosome enrichment.

Brittany Angarola, Shawn M Ferguson.

Stable localization of the Rheb GTPase to lysosomes is thought to be required for activation of mTORC1 signaling. However, the lysosome targeting mechanisms for Rheb remain unclear. We therefore investigated the relationship between Rheb subcellular localization and mTORC1 activation. Surprisingly, we found that Rheb was undetectable at lysosomes. Nonetheless, functional assays in knockout human cells revealed that farnesylation of the C-terminal CaaX motif on Rheb was essential for Rheb-dependent mTORC1 activation. Although farnesylated Rheb exhibited partial endoplasmic reticulum localization, constitutively targeting Rheb to ER membranes did not support mTORC1 activation. Further systematic analysis of Rheb lipidation revealed that weak, non-selective, membrane interactions support Rheb-dependent mTORC1 activation without the need for a specific lysosome targeting motif. Collectively, these results argue against stable interactions of Rheb with lysosomes and instead that transient membrane interactions optimally allow Rheb to activate mTORC1 signaling. [Media: see text].

DOI: https://doi.org/10.1091/mbc.E19-03-0146
Cell Metab. 2019 Aug 29. pii: S1550-4131(19)30443-7. [Epub ahead of print]

Nuclear Glycogenolysis Modulates Histone Acetylation in Human Non-Small Cell Lung Cancers.

Ramon C Sun, Vikas V Dukhande, Zhengqiu Zhou, Lyndsay E A Young, Shane Emanuelle, Christine Fillmore Brainson, Matthew S Gentry.

  Nuclear glycogen was first documented in the early 1940s, but its role in cellular physiology remained elusive. In this study, we utilized pure nuclei preparations and stable isotope tracers to define the origin and metabolic fate of nuclear glycogen. Herein, we describe a key function for nuclear glycogen in epigenetic regulation through compartmentalized pyruvate production and histone acetylation. This pathway is altered in human non-small cell lung cancers, as surgical specimens accumulate glycogen in the nucleus. We demonstrate that the decreased abundance of malin, an E3 ubiquitin ligase, impaired nuclear glycogenolysis by preventing the nuclear translocation of glycogen phosphorylase and causing nuclear glycogen accumulation. Re-introduction of malin in lung cancer cells restored nuclear glycogenolysis, increased histone acetylation, and decreased growth of cancer cells transplanted into mice. This study uncovers a previously unknown role for glycogen metabolism in the nucleus and elucidates another mechanism by which cellular metabolites control epigenetic regulation.

Keywords:  E3 ubiquitin ligase; EPM2B; Lafora disease; NHLRC1; glycogen; glycogen phosphorylase; histone acetylation; malin; non-small cell lung cancer; nuclear metabolism

DOI:  https://doi.org/10.1016/j.cmet.2019.08.014
Nat Commun. 2019 Sep 18. 10(1): 4255

Caspase-10 inhibits ATP-citrate lyase-mediated metabolic and epigenetic reprogramming to suppress tumorigenesis.

Rajni Kumari, Ruhi S Deshmukh, Sanjeev Das.

Caspase-10 belongs to the class of initiator caspases and is a close homolog of caspase-8. However, the lack of caspase-10 in mice and limited substrate repertoire restricts the understanding of its physiological functions. Here, we report that ATP-citrate lyase (ACLY) is a caspase-10 substrate. Caspase-10 cleaves ACLY at the conserved Asp1026 site under conditions of altered metabolic homeostasis. Cleavage of ACLY abrogates its enzymatic activity and suppresses the generation of acetyl-CoA, which is critical for lipogenesis and histone acetylation. Thus, caspase-10-mediated ACLY cleavage results in reduced intracellular lipid levels and represses GCN5-mediated histone H3 and H4 acetylation. Furthermore, decline in GCN5 activity alters the epigenetic profile, resulting in downregulation of proliferative and metastatic genes. Thus caspase-10 suppresses ACLY-promoted malignant phenotype. These findings expand the substrate repertoire of caspase-10 and highlight its pivotal role in inhibiting tumorigenesis through metabolic and epigenetic mechanisms.

DOI: https://doi.org/10.1038/s41467-019-12194-6
Cancer Res. 2019 Sep 17. pii: canres.3029.2018. [Epub ahead of print]

Chromosomal instability and mTORC1 activation through PTEN loss contribute to proteotoxic stress in ovarian carcinoma.

M Herman Chui, Sasha A Doodnauth, Natalie Erdmann, Rodger E Tiedemann, Fabrice Sircoulomb, Ronny Drapkin, Patricia Shaw, Robert Rottapel.

High-grade serous ovarian carcinoma commonly arises from fallopian tube secretory epithelium and is characterized by a high level of chromosomal instability. To model the acquisition of aneuploidy during early carcinogenesis, chromosome missegregation was induced in immortalized tubal epithelial cells, which proved acutely detrimental to cellular fitness. The phenotype was characterized by accumulation of misfolded proteins, activation of the Unfolded Protein Response (UPR), decreased protein synthesis and enhanced vulnerability to proteasome inhibition. However, chromosome missegregation also resulted in heightened transformation potential, assessed by colony formation in soft agar. Interestingly, established ovarian cancer cells retained intrinsic sensitivity to proteasome inhibitors under adherent culture conditions, but acquired resistance as spheroids (recapitulating their native configuration in ascites) by downregulating protein synthesis via mTORC1 suppression. Loss of PTEN drove constitutive mTORC1 activity, enhanced proteotoxic stress, as evidenced by UPR induction, and re-sensitized tumor spheroids to proteasome inhibition both in vitro and in vivo. In cohorts of primary ovarian carcinomas, mTORC1 and UPR signaling pathways were closely associated. These results implicate attenuation of protein synthesis as a protective mechanism in tumor spheroids, which may explain the overall poor response to bortezomib in clinical trials of patients with advanced ovarian cancer. However, patients with PTEN-deficient tumors may represent a subpopulation potentially amenable to treatment with proteasome inhibitors or other therapeutic agents that disrupt protein homeostasis.

DOI: https://doi.org/10.1158/0008-5472.CAN-18-3029