bims-pideca 2020-12-20 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2020–12–20
seven papers selected by
Ralitsa Radostinova Madsen, University College London

Farnesoid X receptor activation impairs liver progenitor cell-mediated liver regeneration via the PTEN-PI3K-AKT-mTOR axis in zebrafish.
Mechanistic Model of Signaling Dynamics Across an Epithelial Mesenchymal Transition.
NPC1-mTORC1 Signaling Couples Cholesterol Sensing to Organelle Homeostasis and Is a Targetable Pathway in Niemann-Pick Type C.
Combined PI3Kα-mTOR Targeting of Glioma Stem Cells.
A genome engineering resource to uncover principles of cellular organization and tissue architecture by lipid signalling.
Editorial: Human Disorders of PI3K Biology.
The RNA helicase DDX3 induces neural crest by promoting AKT activity.

Hepatology. 2020 Dec 13.

Farnesoid X receptor activation impairs liver progenitor cell-mediated liver regeneration via the PTEN-PI3K-AKT-mTOR axis in zebrafish.

Kyounghwa Jung, Minwook Kim, Juhoon So, Seung-Hoon Lee, Sungjin Ko, Donghun Shin.

  Upon mild liver injury, pre-existing hepatocytes replicate. However, if hepatocyte proliferation is compromised, such as in chronic liver diseases, biliary epithelial cells (BECs) contribute to hepatocytes through liver progenitor cells (LPCs), thereby restoring hepatic mass and function. Recently, augmenting innate BEC-driven liver regeneration has garnered attention as an alternative to liver transplantation, the only reliable treatment for patients with end-stage liver diseases. Despite this attention, the molecular basis of BEC-driven liver regeneration remains poorly understood. By performing a chemical screen with the zebrafish hepatocyte ablation model, in which BECs robustly contribute to hepatocytes, we identified farnesoid X receptor (FXR) agonists as inhibitors of BEC-driven liver regeneration. Here we show that FXR activation blocks the process via the FXR-PTEN-PI3K-AKT-mTOR axis. We found that FXR activation blocked LPC-to-hepatocyte differentiation, but not BEC-to-LPC dedifferentiation. FXR activation also suppressed LPC proliferation and increased its death. These defects were rescued by suppressing PTEN activity with its chemical inhibitor and ptena/b mutants, indicating PTEN as a critical downstream mediator of FXR signaling in BEC-driven liver regeneration. Consistent with the role of PTEN in inhibiting the PI3K-AKT-mTOR pathway, FXR activation reduced the expression of pS6, a marker of mTORC1 activation, in LPCs of regenerating livers. Importantly, suppressing PI3K and mTORC1 activities with their chemical inhibitors blocked BEC-driven liver regeneration, as did FXR activation. Conclusion: FXR activation impairs BEC-driven liver regeneration by enhancing PTEN activity; the PI3K-AKT-mTOR pathway controls the regeneration process. Given clinical trials and usage of FXR agonists for multiple liver diseases due to their beneficial effects on steatosis and fibrosis, the detrimental effects of FXR activation on LPCs suggest a rather personalized use of the agonists in the clinic.

Keywords:  FXR; GW4064; Nr1h4; biliary epithelial cells

DOI:  https://doi.org/10.1002/hep.31679
Front Physiol. 2020 ;11 579117

Mechanistic Model of Signaling Dynamics Across an Epithelial Mesenchymal Transition.

James D Wade, Xiao-Kang Lun, Nevena Zivanovic, Eberhard O Voit, Bernd Bodenmiller.

  Intracellular signaling pathways are at the core of cellular information processing. The states of these pathways and their inputs determine signaling dynamics and drive cell function. Within a cancerous tumor, many combinations of cell states and microenvironments can lead to dramatic variations in responses to treatment. Network rewiring has been thought to underlie these context-dependent differences in signaling; however, from a biochemical standpoint, rewiring of signaling networks should not be a prerequisite for heterogeneity in responses to stimuli. Here we address this conundrum by analyzing an in vitro model of the epithelial mesenchymal transition (EMT), a biological program implicated in increased tumor invasiveness, heterogeneity, and drug resistance. We used mass cytometry to measure EGF signaling dynamics in the ERK and AKT signaling pathways before and after induction of EMT in Py2T murine breast cancer cells. Analysis of the data with standard network inference methods suggested EMT-dependent network rewiring. In contrast, use of a modeling approach that adequately accounts for single-cell variation demonstrated that a single reaction-based pathway model with constant structure and near-constant parameters is sufficient to represent differences in EGF signaling across EMT. This result indicates that rewiring of the signaling network is not necessary for heterogeneous responses to a signal and that unifying reaction-based models should be employed for characterization of signaling in heterogeneous environments, such as cancer.

Keywords:  AKT pathway; ERK pathway; computational biology; epithelial-to-mesenchymal transition (EMT); kinetic model; ordinary differential equations; single cell modeling; systems biology

DOI:  https://doi.org/10.3389/fphys.2020.579117
Dev Cell. 2020 Dec 07. pii: S1534-5807(20)30925-4. [Epub ahead of print]

NPC1-mTORC1 Signaling Couples Cholesterol Sensing to Organelle Homeostasis and Is a Targetable Pathway in Niemann-Pick Type C.

Oliver B Davis, Hijai R Shin, Chun-Yan Lim, Emma Y Wu, Matthew Kukurugya, Claire F Maher, Rushika M Perera, M Paulina Ordonez, Roberto Zoncu.

  Lysosomes promote cellular homeostasis through macromolecular hydrolysis within their lumen and metabolic signaling by the mTORC1 kinase on their limiting membranes. Both hydrolytic and signaling functions require precise regulation of lysosomal cholesterol content. In Niemann-Pick type C (NPC), loss of the cholesterol exporter, NPC1, causes cholesterol accumulation within lysosomes, leading to mTORC1 hyperactivation, disrupted mitochondrial function, and neurodegeneration. The compositional and functional alterations in NPC lysosomes and nature of aberrant cholesterol-mTORC1 signaling contribution to organelle pathogenesis are not understood. Through proteomic profiling of NPC lysosomes, we find pronounced proteolytic impairment compounded with hydrolase depletion, enhanced membrane damage, and defective mitophagy. Genetic and pharmacologic mTORC1 inhibition restores lysosomal proteolysis without correcting cholesterol storage, implicating aberrant mTORC1 as a pathogenic driver downstream of cholesterol accumulation. Consistently, mTORC1 inhibition ameliorates mitochondrial dysfunction in a neuronal model of NPC. Thus, cholesterol-mTORC1 signaling controls organelle homeostasis and is a targetable pathway in NPC.

Keywords:  ESCRT; NPC1; autophagy; cholesterol; lysosome; mTORC1; mitochondria; proteolysis; proteomics

DOI:  https://doi.org/10.1016/j.devcel.2020.11.016
Sci Rep. 2020 Dec 14. 10(1): 21873

Combined PI3Kα-mTOR Targeting of Glioma Stem Cells.

Frank D Eckerdt, Jonathan B Bell, Christopher Gonzalez, Michael S Oh, Ricardo E Perez, Candice Mazewski, Mariafausta Fischietti, Stewart Goldman, Ichiro Nakano, Leonidas C Platanias.

Glioblastoma (GBM) is the most common and lethal primary intrinsic tumour of the adult brain and evidence indicates disease progression is driven by glioma stem cells (GSCs). Extensive advances in the molecular characterization of GBM allowed classification into proneural, mesenchymal and classical subtypes, and have raised expectations these insights may predict response to targeted therapies. We utilized GBM neurospheres that display GSC characteristics and found activation of the PI3K/AKT pathway in sphere-forming cells. The PI3Kα selective inhibitor alpelisib blocked PI3K/AKT activation and inhibited spheroid growth, suggesting an essential role for the PI3Kα catalytic isoform. p110α expression was highest in the proneural subtype and this was associated with increased phosphorylation of AKT. Further, employing the GBM BioDP, we found co-expression of PIK3CA with the neuronal stem/progenitor marker NES was associated with poor prognosis in PN GBM patients, indicating a unique role for PI3Kα in PN GSCs. Alpelisib inhibited GSC neurosphere growth and these effects were more pronounced in GSCs of the PN subtype. The antineoplastic effects of alpelisib were substantially enhanced when combined with pharmacologic mTOR inhibition. These findings identify the alpha catalytic PI3K isoform as a unique therapeutic target in proneural GBM and suggest that pharmacological mTOR inhibition may sensitize GSCs to selective PI3Kα inhibition.

DOI: https://doi.org/10.1038/s41598-020-78788-z
Elife. 2020 Dec 15. pii: e55793. [Epub ahead of print]9

A genome engineering resource to uncover principles of cellular organization and tissue architecture by lipid signalling.

Deepti Trivedi, Vinitha Cm, Karishma Bisht, Vishnu Janardan, Awadhesh Pandit, Bishal Basak, Shwetha H, Navyashree Ramesh, Padinjat Raghu.

  Phosphoinositides (PI) are key regulators of cellular organization in eukaryotes and genes that tune PI signalling are implicated in human disease mechanisms. Biochemical analyses and studies in cultured cells have identified a large number of proteins that can mediate PI signalling. However, the role of such proteins in regulating cellular processes in vivo and development in metazoans remains to be understood. Here we describe a set of CRISPR based genome engineering tools that allow the manipulation of each of these proteins with spatial and temporal control during metazoan development. We demonstrate the use of these reagents to deplete a set of 103 proteins individually in the Drosophila eye and identify several new molecules that control eye development. Our work demonstrates the power of this resource in uncovering the molecular basis of tissue homeostasis during normal development and in human disease biology.

Keywords:  D. melanogaster; developmental biology; genetics; genomics

DOI:  https://doi.org/10.7554/eLife.55793
Front Immunol. 2020 ;11 617464

Editorial: Human Disorders of PI3K Biology.

Carrie L Lucas, Stuart G Tangye.



Keywords:  Activated PI3Kδ Syndrome; PI3K; human genetics; immunology; primary immunodeficiencies

DOI:  https://doi.org/10.3389/fimmu.2020.617464
Development. 2020 Dec 14. pii: dev.184341. [Epub ahead of print]

The RNA helicase DDX3 induces neural crest by promoting AKT activity.

Mark Perfetto, Xiaolu Xu, Congyu Lu, Yu Shi, Natasha Yousaf, Jiejing Li, Yvette Y Yien, Shuo Wei.

  Mutations in the RNA helicase DDX3 have emerged as a frequent cause of intellectual disability in humans. Because many patients carrying DDX3 mutations have additional defects in craniofacial structures and other tissues containing neural crest (NC)-derived cells, we hypothesized that DDX3 is also important for NC development. Using Xenopus tropicalis as a model, we show that DDX3 is required for normal NC induction and craniofacial morphogenesis by regulating AKT kinase activity. Depletion of DDX3 decreases AKT activity and AKT-dependent inhibitory phosphorylation of GSK3β, leading to reduced levels of β-catenin and Snai1, two GSK3β substrates that are critical for NC induction. DDX3 function in regulating these downstream signaling events during NC induction is likely mediated by RAC1, a small GTPase whose translation depends on the RNA helicase activity of DDX3. These results suggest an evolutionarily conserved role of DDX3 in NC development by promoting AKT activity, and provide a potential mechanism for the NC-related birth defects displayed by patients harboring mutations in DDX3 and its downstream effectors in this signaling cascade.

Keywords:  AKT; DDX3; GSK3β; Neural crest (NC); Wnt signaling; Xenopus

DOI:  https://doi.org/10.1242/dev.184341